# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Aeropyrum_pernix_K1_uid57757/NC_000854.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Aeropyrum_pernix_K1_uid57757/NC_000854.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Aeropyrum_pernix_K1_uid57757/NC_000854.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|14600380|ref|NP_146894.1|  [L=241]
Description: hypothetical protein APE_0001 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.2    6.6  11.8        6.7    6.0   0.9    2.5  2  DUF4191   Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9   0.00037       6.7      16      64 ..      44      92 ..      32     102 .. 0.82
   2 ?    4.8   4.0   0.00084        15      34      71 ..     198     236 ..     182     240 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00037
                       DUF4191 16 kltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllv 64
                                  ++t k+ k l  l+l+a l+ +vv+ ++g+ ++   l l+l++++ ++v
  gi|14600380|ref|NP_146894.1| 44 RVTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTV 92
                                  67888999999999****************9988888888888876665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.00084
                       DUF4191  34 lvvvvvfvvlgll.lgslilllilgillgllvalivltr 71 
                                   l  ++++v + l+ ++ ++++l+ g+ + ++v+++++ +
  gi|14600380|ref|NP_146894.1| 198 LSLIAIGVYMILAgFHMWWIILLAGVTTLFVVTMLIMIN 236
                                   3344444444443123599999*****999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1713.85
//
Query:       gi|14600381|ref|NP_146895.1|  [L=112]
Description: PadR family transcriptional regulator [Aeropyrum pernix K1]
Scores for 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-23   80.3   0.2    9.4e-23   80.0   0.2    1.1  1  PadR      Transcriptional regulator PadR-like family
    0.00069   19.7   0.0     0.0012   19.0   0.0    1.5  1  HTH_34    Winged helix DNA-binding domain
      0.003   17.4   0.1     0.0056   16.5   0.1    1.6  1  HxlR      HxlR-like helix-turn-helix
     0.0032   18.1   0.0     0.0043   17.7   0.0    1.3  1  RTP       Replication terminator protein
  ------ inclusion threshold ------
      0.015   15.1   0.0       0.03   14.2   0.0    1.6  1  TrmB      Sugar-specific transcriptional regulator TrmB
      0.057   11.8   0.0      0.068   11.5   0.0    1.0  1  DUF505    Protein of unknown function (DUF505)
       0.12   12.4   0.0       0.18   11.8   0.0    1.3  1  Cdc6_C    CDC6, C terminal winged helix domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.2   3.7e-26   9.4e-23       1      73 [.      20      91 ..      20      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 3.7e-26
                                  HHHHH.CCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHH CS
                          PadR  1 iLall.eeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrel 73
                                  +L++l +++ ++Gy+++k l +l+ g +++ e+slY+aLkrLek gl++++w++sg+gp rkyY++TdaGr+++
  gi|14600381|ref|NP_146895.1| 20 VLHVLvNHGALHGYWLRKILGNLM-G-WTPPETSLYDALKRLEKLGLIKGRWVRSGRGPLRKYYEITDAGRETY 91
                                  79999677***************7.7.********************************************986 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 !   19.0   0.0   4.6e-07    0.0012      29      79 ..      50     101 ..      16     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.6e-07
                        HTH_34  29 gnLsvhlkkLekagYievdkefkgkkp.rtllriTpeGreafkkyvkaLksl 79 
                                     L+  lk Lek g i+ +   +g+ p r  ++iT++Gre ++ +vk  +++
  gi|14600381|ref|NP_146895.1|  50 TSLYDALKRLEKLGLIKGRWVRSGRGPlRKYYEITDAGRETYEVVVKDFSKM 101
                                   479999*********************45689***********999988776 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   2.2e-06    0.0056      34      77 ..      50      95 ..      20     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                                  HHHHHHHHHHHHTTSEEEEEES..SSS-EEEEEE-TCGGGGHHHHH CS
                          HxlR 34 kmLaqrLreLeqdglierevyp..evPpkveYsltekGrslepvlq 77
                                    L   L++Le+ gli+ + +   + P +  Y++t++Gr+ ++v+ 
  gi|14600381|ref|NP_146895.1| 50 TSLYDALKRLEKLGLIKGRWVRsgRGPLRKYYEITDAGRETYEVVV 95
                                  568899**********9776651257**************999875 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0043      39      94 ..      43      96 ..      17     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                  TT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHHHHHHH CS
                           RTP 39 lgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkekaklykk 94
                                  +g++P+++ +y al+ l + g++k r     +  l+   +Y++td+G+e  ++  k
  gi|14600381|ref|NP_146895.1| 43 MGWTPPETSLYDALKRLEKLGLIKGRWVRSGRGPLR--KYYEITDAGRETYEVVVK 96
                                  79*********************9988888666666..48*********9987655 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   1.2e-05      0.03      35      65 ..      48      84 ..      18      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                  SCHCHHHHHHHHHHCTSEEEESST......TTEEEE- CS
                          TrmB 35 prskvYevLrsLedkGlVerekgr......pklYrav 65
                                  p+++ Y++L++Le+ Gl++ +  r      +k+Y+ +
  gi|14600381|ref|NP_146895.1| 48 PETSLYDALKRLEKLGLIKGRWVRsgrgplRKYYEIT 84
                                  899***************9877666777776677665 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.7e-05     0.068     358     407 ..      44      97 ..      36     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                        DUF505 358 kWyednfdlreaLysLesfeLieseveekg....kevyvlTeyGekvledqekk 407
                                    W   + +l  aL++Le  +Li+ +  + g    +++y++T+ G++  e   k+
  gi|14600381|ref|NP_146895.1|  44 GWTPPETSLYDALKRLEKLGLIKGRWVRSGrgplRKYYEITDAGRETYEVVVKD 97 
                                   58888889999**************97777668899*********998876555 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05      0.18      39      72 ..      49      81 ..      45      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                                  HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEE CS
                        Cdc6_C 39 qrevsdllseLemlgileleksskGrregrtrki 72
                                  +++ +d l++Le+lg+++ + ++ Gr +   +++
  gi|14600381|ref|NP_146895.1| 49 ETSLYDALKRLEKLGLIKGRWVRSGR-GPLRKYY 81
                                  57899***************998898.3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 884.79
//
Query:       gi|14600382|ref|NP_146896.1|  [L=304]
Description: hypothetical protein APE_0004 [Aeropyrum pernix K1]
Scores for complete 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-12   47.1   2.6    2.3e-12   47.1   2.6    2.7  3  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 ?    0.6   1.6     0.042   7.5e+02      21      70 ..      57     152 ..      52     158 .. 0.51
   2 !   47.1   2.6   1.3e-16   2.3e-12       7      91 ..     151     260 ..     136     261 .. 0.84
   3 ?   -1.2   0.1      0.15   2.8e+03      56      75 ..     280     300 ..     263     303 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.042
                                   HHHTTCH.............HHHHHHH.S-HHHHHHHHHHHHHCSGGG....HHHH......................... CS
                          CPBP  21 llfRgll.............lqllqergsstlailissilFglaHlpn....gpsv......................... 59 
                                   llfR +l             ++ +++  +++l+i i s+ ++++ ++     +  v                         
  gi|14600382|ref|NP_146896.1|  57 LLFRMWLpatgviaalwvegYRNMEKI-KEILRINIPSLKWTILSAVAplasY--Vmslpiakalgvsigpcgyfkevsnt 134
                                   577777744444333333332223333.4477777777777777777643330..13444444445555555555555555 PP

                                   .......HHHHHHHHHHH CS
                          CPBP  60 .......llaalaGlvlg 70 
                                          + ++l+Gl+ g
  gi|14600382|ref|NP_146896.1| 135 tllittvIILILLGLIAG 152
                                   555433344455555444 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 1.3e-16
                                   HHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.......HHHH....................H CS
                          CPBP   7 vfllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.......gpsv....................l 60 
                                     + +  l++l+EEl++Rg+l++ l ++++ +  ++i +++++++H+p        +  v                    l
  gi|14600382|ref|NP_146896.1| 151 AGVTMNALVALGEELGWRGYLFTILDKKVNDLGKVIIIGLIWSVWHAPLiyagynyN--VsmlgdcgsysqgwpaivvftL 229
                                   44557889999*****************9999****************976666552..155777777777777788888* PP

                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          CPBP  61 laalaGlvlgylylktgsllaaillHallnl 91 
                                   +++++  +l  l+++++s+++++++H+ +n 
  gi|14600382|ref|NP_146896.1| 230 YTIAFTSILLPLRRHSNSIITPAIAHGTVNG 260
                                   ****************************996 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.15
                                   HHH.HHHHHHHHHHHHHHHHH CS
                          CPBP  56 gps.vllaalaGlvlgylylk 75 
                                   g+s v+ ++++G+++ +   +
  gi|14600382|ref|NP_146896.1| 280 GISvVVSMLIVGFLIKWWVSR 300
                                   677788888888888887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2291.85
//
Query:       gi|118430836|ref|NP_146897.2|  [L=188]
Description: hypothetical protein APE_0006.1 [Aeropyrum pernix K1]
Scores for 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   17.2   1.1     0.0051   16.9   1.1    1.2  1  ECF_trnsprt  ECF transporter, substrate-specific component
  ------ inclusion threshold ------
       0.02   13.9   1.2      0.024   13.7   1.2    1.1  1  DUF808       Protein of unknown function (DUF808)
      0.031   14.5   1.6      0.043   14.1   1.6    1.2  1  DUF4293      Domain of unknown function (DUF4293)
       0.19   11.7   3.7       0.53   10.2   0.4    2.2  2  DUF3377      Domain of unknown function (DUF3377)


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 !   16.9   1.1   1.1e-06    0.0051      74     129 ..      23      76 ..       5     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC.HHHH CS
                    ECF_trnsprt  74 piaflsriligliagllykkgkkknlkeivvsfilagvlgtivatllvllii.lply 129
                                    +i +l +++i+++a+   +k +k+++++ +v++i+a+v+  +v   + + ++ l  y
  gi|118430836|ref|NP_146897.2|  23 VIGVLLSVWIVIVAV---IKLRKYSRNRQIVGLIVAAVATVVVLGTIAYIFNpLQTY 76 
                                    7889999********...67788888899***********99999997766643333 PP

>> DUF808  Protein of unknown function (DUF808)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.2   5.4e-06     0.024     146     207 ..      22      83 ..       4     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                         DUF808 146 irtDfiLSaEiivialgevaeeslltqvlvlvvvavliTvgvYGlValivk.lDdvGlalakk 207
                                    +   ++LS+ i+++a+ ++++ s   q++ l +va + Tv+v G++a i   l   G +l+++
  gi|118430836|ref|NP_146897.2|  22 LVIGVLLSVWIVIVAVIKLRKYSRNRQIVGL-IVAAVATVVVLGTIAYIFNpLQTYGAYLESR 83 
                                    555679*************998877777665.678889**********986477788888774 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.6   9.6e-06     0.043      48     125 ..      16      90 ..       1      96 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.6e-06
                        DUF4293  48 tsvnvsvwvlvilllliailaliaIflyknRklQlrlclinllllvllyvllallllvnkanaaaeslgesslkigli 125
                                    ++ + + ++ v+l++ i+i+a+i++ +y  R  Q+   ++ ++ +v++++++a+++   ++  a+ +    +l+i ++
  gi|118430836|ref|NP_146897.2|  16 HELTSKLVIGVLLSVWIVIVAVIKLRKYS-RNRQIVGLIVAAVATVVVLGTIAYIFNPLQTYGAYLES--RTLQIRFY 90 
                                    4445566777889999************5.99**********************55555555555444..55666555 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5    0.0045        20      36      62 ..      26      50 ..      20      50 .. 0.76
   2 ?   10.2   0.4   0.00012      0.53      22      57 ..      43      78 ..      37      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0045
                        DUF3377 36 lvLllciLvliyailqfrrkgtprrll 62
                                   ++L   + ++i+a++++r+++  r+++
  gi|118430836|ref|NP_146897.2| 26 VLL--SVWIVIVAVIKLRKYSRNRQIV 50
                                   444..4556889********9999885 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                        DUF3377 22 eesgtvnaiaVvvPlvLllciLvliyailq.frrkgt 57
                                   + s++ +++  +v  v  +++L++i+ i++ ++ +g+
  gi|118430836|ref|NP_146897.2| 43 Y-SRNRQIVGLIVAAVATVVVLGTIAYIFNpLQTYGA 78
                                   4.77889999*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1524.03
//
Query:       gi|118430837|ref|NP_146898.2|  [L=511]
Description: hypothetical protein APE_0007.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0016   18.3   1.8       0.42   10.6   0.1    4.0  5  PQQ       PQQ enzyme repeat
  ------ inclusion threshold ------
      0.025   14.1   0.1      0.071   12.7   0.1    1.8  1  PQQ_2     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 ?   -2.7   0.0      0.77   6.9e+03       7      17 ..     169     179 ..     164     180 .. 0.82
   2 !   10.6   0.1   4.7e-05      0.42       5      29 ..     203     227 ..     199     229 .. 0.85
   3 !    4.0   0.0     0.006        54      18      28 ..     266     276 ..     264     280 .. 0.85
   4 ?   -2.2   0.0      0.56     5e+03      20      27 ..     405     412 ..     404     418 .. 0.82
   5 ?   -1.9   0.0      0.42   3.8e+03      14      23 ..     414     423 ..     413     423 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.77
                                    ETTSEEEEEET CS
                            PQQ   7 sadGylyAlDa 17 
                                    ++  yly +D+
  gi|118430837|ref|NP_146898.2| 169 PNTPYLYVVDL 179
                                    67789***996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.7e-05
                                    EEETTSEEEEEETTTCCEEEEEESS CS
                            PQQ   5 lgsadGylyAlDadTGkvlWrfktg 29 
                                    +  +dG++ A D+  G+vlW++k+ 
  gi|118430837|ref|NP_146898.2| 203 YEYKDGTISATDVVEGRVLWSHKLT 227
                                    5578******************986 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.006
                                    TTCCEEEEEES CS
                            PQQ  18 dTGkvlWrfkt 28 
                                    +TG+++W++ +
  gi|118430837|ref|NP_146898.2| 266 ATGELVWVYSL 276
                                    6*******976 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.56
                                    CCEEEEEE CS
                            PQQ  20 GkvlWrfk 27 
                                    G+vlW  +
  gi|118430837|ref|NP_146898.2| 405 GEVLWARE 412
                                    99***865 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 0.42
                                    EEETTTCCEE CS
                            PQQ  14 AlDadTGkvl 23 
                                    A+D++ Gk+l
  gi|118430837|ref|NP_146898.2| 414 AVDIEQGKLL 423
                                    9******986 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1     8e-06     0.071       1      82 [.     206     315 ..     206     423 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8e-06
                          PQQ_2   1 degvvsaldaatGaelWrvdlar.......p.....lgggvsravlsggtlfvatgggrlvaldaatGkvlWettl.... 64 
                                    ++g++sa d   G++lW+ +l++       +     ++g +++a ++++ l+       l   d atG+++W ++l    
  gi|118430837|ref|NP_146898.2| 206 KDGTISATDVVEGRVLWSHKLTPgyvfpepQgpgraFTGVLKGAWVDDNSLILL-----LQDSDQATGELVWVYSLvvas 280
                                    589****************99886666555045555888888888777777775.....8889999*******9995554 PP

                          PQQ_2  65 egpvvga.................plvaegrvvvv 82 
                                    e+ v+++                   ++++rv+v 
  gi|118430837|ref|NP_146898.2| 281 EEGVRESyleafrvksdfasydirVGFDGERVYVL 315
                                    44444445555555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3704.18
//
Query:       gi|118430838|ref|NP_146899.2|  [L=94]
Description: mercury ion binding protein [Aeropyrum pernix K1]
Scores for complete 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   46.6   0.1    5.1e-12   46.1   0.1    1.2  1  HMA       Heavy-metal-associated domain
     0.0038   17.4   0.1       0.21   11.7   0.0    2.2  2  PMSR      Peptide methionine sulfoxide reductase


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   5.7e-16   5.1e-12       4      54 ..      25      75 ..      23      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 5.7e-16
                            HMA  4 vsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiie 54
                                   ++gmhC+gCa ++e +L++++g+ + kv++  +++ V++d++ +++++i+e
  gi|118430838|ref|NP_146899.2| 25 IEGMHCEGCAIAIETALKNVKGIIDTKVNYSRGSAIVTFDDTLVSINDILE 75
                                   89****************************************988888876 PP

>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   2.4e-05      0.21       6      33 ..      31      58 ..      27      60 .. 0.92
   2 !    3.6   0.1    0.0076        68      55      72 ..      61      78 ..      59      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                   -S-HHHHHHHHCTSTTEEEEEEEEESSS CS
                           PMSR  6 gGCFWgveklfeklkGvlstevGYagGk 33
                                    GC  ++e +++++kG+++t+v Y  G+
  gi|118430838|ref|NP_146899.2| 31 EGCAIAIETALKNVKGIIDTKVNYSRGS 58
                                   69**********************9996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0076
                                   EEEETTTS-HHHHHHHHH CS
                           PMSR 55 vvydpekvsleellelff 72
                                   v++d++ vs++++le++ 
  gi|118430838|ref|NP_146899.2| 61 VTFDDTLVSINDILEHYI 78
                                   89*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 757.18
//
Query:       gi|118430839|ref|NP_146900.2|  [L=535]
Description: amino acid transporter [Aeropyrum pernix K1]
Scores for 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  100.9  39.7    9.1e-29  100.5  39.7    1.1  1  AA_permease_2    Amino acid permease
    3.1e-23   82.1  39.3    5.3e-23   81.3  39.0    1.5  1  AA_permease      Amino acid permease
    3.9e-08   32.5  12.4    7.8e-08   31.5  12.4    1.5  1  Spore_permease   Spore germination protein
    4.2e-08   33.4   0.0    8.1e-08   32.5   0.0    1.5  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0024   18.0   0.0     0.0054   16.9   0.0    1.5  1  DNA_pol_B_palm   DNA polymerase beta palm
     0.0026   17.8   0.0     0.0076   16.3   0.0    1.8  2  Polbeta          Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.22   11.4   0.0       0.43   10.5   0.0    1.4  1  Polysacc_deac_1  Polysaccharide deacetylase


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 !  100.5  39.7   3.6e-32   9.1e-29       1     399 [.      10     389 ..      10     413 .. 0.82

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 3.6e-32
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafg.kkva 77 
                                    l+++ +f + +g +ig gif++   +++ +g+a+ l +++a  +  l+ ++ ya lss+ p++gG + +  +a+g +++ 
  gi|118430839|ref|NP_146900.2|  10 LGFWEVFSIGVGGMIGGGIFATLglSLELAGAAAPLAFLLAGSVA-LITSYSYAKLSSRYPSEGGTIEFIVRAYGdNVIS 88 
                                    79*******************99888888*******999999988.8*********999***************725555 PP

                  AA_permease_2  78 flsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpli 157
                                        ++++ +y++++++++ +++sy +++++    +   +++ ++++++++++++n +g   s+++   l+i+k+ l+li
  gi|118430839|ref|NP_146900.2|  89 GGLNIMLLASYIVMISLYAHAFGSYGASMIN--CCPRE-AYIALVVFVIAGLTVVNMLGAIMSGRVELGLVIFKL-LVLI 164
                                    788888899999999999999*******997..44544.778888******************************.5777 PP

                  AA_permease_2 158 iliilglitvdgggfsslstetdtffpngwpgv...llgllivlwsfdGfesaanvseevkk.kdvpkaifigllivlvl 233
                                    ++ ++ + +v  +++              wp++   ++g +i+++++ Gfe +an ++ v+  ++++k++  ++++v+++
  gi|118430839|ref|NP_146900.2| 165 LVAVVSMPLV--DWNR--------LGVREWPSIlsiVAGGMIIFLAYEGFELVANTAKDVRDtTTLRKGLYASVVTVIIV 234
                                    7777777777..5554........4555666541113333459******************9789*************** PP

                  AA_permease_2 234 yllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffa 313
                                    y+l++i+++g + +d++   ++  +++a+++e v gk+++++vv+++  s   ain+ ++gs+rv + +a+ g+ P  + 
  gi|118430839|ref|NP_146900.2| 235 YVLIAIVAAGTLDPDTVRIARD--YALAVLVEPVLGKIGFTLVVAAALASTSSAINATLYGSARVSYIIAKYGEAPQLLG 312
                                    *****************99898..4699*******9****************************************7775 PP

                  AA_permease_2 314 kvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgkilvaiigal 393
                                    +   +   + ++ ++ i+ l+l+    l  +a++  +++++s g++i+++++ ++a +lr+       p + lv++i  l
  gi|118430839|ref|NP_146900.2| 313 RHIWR-GAYEGLLVISILGLLLA----L--YASLEQISTAGSGGFLIIFAAVNLAAYKLRRETGAN--PLISLVGFILNL 383
                                    43333.35777888888874443....3..356899*****************9999999884442..333444444433 PP

                  AA_permease_2 394 fllfll 399
                                    ++l +l
  gi|118430839|ref|NP_146900.2| 384 TSLAIL 389
                                    333333 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3  39.0   2.1e-26   5.3e-23       2     412 ..      15     385 ..      14     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 2.1e-26
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfviGl 80 
                                    v+ i +gg+iG g+f  lg  l  aG  +a la+llag v +++ +s + +++ +p+ gg+  ++ r  g+   ++  ++
  gi|118430839|ref|NP_146900.2|  15 VFSIGVGGMIGGGIFATLGLSLELAGA-AAPLAFLLAGSVALITSYSYAKLSSRYPSEGGTIEFIVRAYGDnVISGGLNI 93 
                                    67899*********************9.999*************************999999998888887477888888 PP

                    AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvv..lliinlvgvkvygeaefilalikiiaiiafiivg. 157
                                    ++l s+i+ + l   a +++   +  +   p + ++++v++v+  l+++n++g+ ++g++e+ l ++k++ +i + +v+ 
  gi|118430839|ref|NP_146900.2|  94 MLLASYIVMISLYAHAFGSYGASM--INCCPREAYIALVVFVIagLTVVNMLGAIMSGRVELGLVIFKLLVLILVAVVSm 171
                                    888888888888877777777777..7777755555444444445899*******************************4 PP

                    AA_permease 158 iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkail 237
                                    + + ++  + ++                  p+        +++++++ +i+++a+ G+elva++a++v+d   ++ k+  
  gi|118430839|ref|NP_146900.2| 172 PLVDWNRLGVRE-----------------WPS--------ILSIVAGGMIIFLAYEGFELVANTAKDVRDT-TTLRKGLY 225
                                    444444444444.................467........899**************************95.79****** PP

                    AA_permease 238 qvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlys 317
                                      v++++i+Yvl+++++  +++ +   +  d a    + v++   +g +++ +l++a+ l+++ s++n+ ly + Rv y 
  gi|118430839|ref|NP_146900.2| 226 ASVVTVIIVYVLIAIVAAGTLDPDTVRIARDYA----LAVLVEPVLGKIGF-TLVVAAALASTSSAINATLYGSARVSYI 300
                                    ******************************988....55888888888888.57778889******************** PP

                    AA_permease 318 lakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyq 397
                                     ak g aP  l+++  rg  + ++l+ +i++ll+ l asl  +        +++    +li++ +++l+ +++R++  ++
  gi|118430839|ref|NP_146900.2| 301 IAKYGEAPQLLGRHIWRGA-YEGLLVISILGLLLALYASLEQI--------STAGSGGFLIIFAAVNLAAYKLRRETGAN 371
                                    ***********99998886.***************99999999........55555567888999999999999998877 PP

                    AA_permease 398 grsieelgfkaallp 412
                                       i+++gf++ l +
  gi|118430839|ref|NP_146900.2| 372 PL-ISLVGFILNLTS 385
                                    77.777777766655 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5  12.4   3.1e-11   7.8e-08       4     239 ..      12     251 ..       9     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.1e-11
                 Spore_permease   4 tkqlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpek.tliellkkilg.kwLGsll 81 
                                    + ++f++ v  ++G gi  +++   e a++ + ++ llag ++li  + + kl++++p++   ie++    g  +++  l
  gi|118430839|ref|NP_146900.2|  12 FWEVFSIGVGGMIGGGIFATLGLSLELAGAAAPLAFLLAGSVALITSYSYAKLSSRYPSEgGTIEFIVRAYGdNVISGGL 91 
                                    56789999999**********************************************97526899999999989****** PP

                 Spore_permease  82 silfilyFlllaafelRefseliqvflledtpl.wiiilllllvilYlvvkGieslar..eflfiivilliilllillfs 158
                                    +i++++ ++++++  +  f+     ++++  p  + i l++++++ ++vv+ +  ++   + l ++++ l++l+l+ ++s
  gi|118430839|ref|NP_146900.2|  92 NIMLLASYIVMISLYAHAFGSY-GASMINCCPReAYIALVVFVIAGLTVVNMLGAIMSgrVELGLVIFKLLVLILVAVVS 170
                                    *******************995.778888888625666777777789999999999986344444555577888888999 PP

                 Spore_permease 159 lklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkkvkkaallgvlistllyllttlivilvlsveq 238
                                    + l++++ l      +i +++ +   + l++ g+e++    + ++d  + +k +  +v++++++y+l+ +++ ++l+ + 
  gi|118430839|ref|NP_146900.2| 171 MPLVDWNRLGVREWPSILSIVAGGMIIFLAYEGFELVANTAKDVRDTTTLRKGLYASVVTVIIVYVLIAIVAAGTLDPDT 250
                                    99*******977778***********************************************************998777 PP

                 Spore_permease 239 l 239
                                    +
  gi|118430839|ref|NP_146900.2| 251 V 251
                                    6 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   3.2e-11   8.1e-08       3      82 ..     450     529 ..     448     535 .] 0.75

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.2e-11
                                    HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.HHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                   NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre.kkeegleklaeiikfleellglevdlvtrekled 81 
                                    +++e++k++  +a+v+++GS arG++ k  DiDl+v + ++ s + +++ ++e+l+++     + ++l+++ vtr+kle+
  gi|118430839|ref|NP_146900.2| 450 RAAEIIKREIMNAEVYITGSIARGEYEKSGDIDLIVSTTKPLS-PhEVKFIEERLVKELNLPPS-HPLHIHTVTRDKLEN 527
                                    56788888777******************************66.24444455555555555555.788888889999997 PP

                                    .C CS
                   NTP_transf_2  82 .p 82 
                                     +
  gi|118430839|ref|NP_146900.2| 528 fK 529
                                    43 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   2.1e-06    0.0054      19      70 ..     456     507 ..     443     515 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                                    HHH-TT-EEEE-HHHHTT-.SEESSEEEEEEBTTBSTTSS--HHHHHHHHHHH CS
                 DNA_pol_B_palm  19 keldpevevivcGSYRRga.essGDvDvlitkkdakseskklkklleklvkkl 70 
                                    k+   ++ev+++GS  Rg+ e+sGD+D++++ ++  s + + k + e+lvk+l
  gi|118430839|ref|NP_146900.2| 456 KREIMNAEVYITGSIARGEyEKSGDIDLIVSTTKPLSPH-EVKFIEERLVKEL 507
                                    33345689*******9996489********999888844.6777777888877 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.5   1.7e+04      13      25 ..     403     415 ..     400     417 .. 0.81
   2 !   16.3   0.0     3e-06    0.0076      16      54 ..     464     502 ..     451     532 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.5
                                    HHSTTEEEEEE-S CS
                        Polbeta  13 ielaylFGSrakg 25 
                                    i ++++ GS+a +
  gi|118430839|ref|NP_146900.2| 403 ILAVLIAGSMAAE 415
                                    7899999**9976 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3e-06
                                    TTEEEEEE-S------EEEEEEEESS---HHHHHHHHHH CS
                        Polbeta  16 aylFGSrakgkareeSDiDlavllkekldleeelelaae 54 
                                    +y+ GS+a+g++ ++ DiDl v + + l+  e   +++ 
  gi|118430839|ref|NP_146900.2| 464 VYITGSIARGEYEKSGDIDLIVSTTKPLSPHEVKFIEER 502
                                    89*********************9998666665555544 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.43      16      74 ..     443     528 ..     442     534 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                    SSCSCHHHHHHHHHHCT--EEEEE-HHHHCH-..........................HHHHHHHHHTT.EEEEE--SS- CS
                Polysacc_deac_1  16 gprdntteilpvLkkykvkatffvigglvedy..........................pdevremaasG.veignHtinh 68 
                                    g+r+ t ++ ++ k++ ++a ++++g+ +  +                          + +v+e+   + + ++ Ht+++
  gi|118430839|ref|NP_146900.2| 443 GWRNLTARAAEIIKREIMNAEVYITGSIARGEyeksgdidlivsttkplsphevkfieERLVKELNLPPsHPLHIHTVTR 522
                                    78999*********************9744445999******************************************** PP

                                    -EGGGS CS
                Polysacc_deac_1  69 snlkrl 74 
                                    ++l++ 
  gi|118430839|ref|NP_146900.2| 523 DKLENF 528
                                    *99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 3743.08
//
Query:       gi|118430840|ref|NP_146901.2|  [L=272]
Description: fructose-bisphosphate aldolase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-36  125.3   0.0    3.3e-36  125.1   0.0    1.0  1  DeoC           DeoC/LacD family aldolase
    2.6e-05   23.7   0.3    0.00023   20.6   0.3    2.0  2  ThiG           Thiazole biosynthesis protein ThiG
     0.0006   19.6   0.0        1.1    8.9   0.0    2.1  2  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.031   14.7   0.0       0.11   13.0   0.0    1.9  1  GDPD_2         Glycerophosphoryl diester phosphodiesterase fa
       0.07   12.8   0.0        0.2   11.3   0.0    1.7  1  DAGK_cat       Diacylglycerol kinase catalytic domain


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 !  125.1   0.0   9.1e-40   3.3e-36       2     234 ..      23     243 ..      22     244 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 9.1e-40
                                    EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEE CS
                           DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvd 81 
                                    vi+a+D+++++++++     e   d++ l++e++++g +a++++pg+++   +  a+++a+++k++ +t + ++   d++
  gi|118430840|ref|NP_146901.2|  23 VIFAFDHGIEHGPGEIP---EERLDPRLLIREVVEAGVDAIMTTPGIARLTWDIWANRVAMIIKVSGKTSIRPQD--DQF 97 
                                    89**************9...7889******************************************766666554..444 PP

                                    ...TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHH CS
                           DeoC  82 ...evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAar 158
                                          sv e++alG+d v ++vy+   gs+ e ++l+   r++ +++++glp +  +y+r+++ik+ + + d va +ar
  gi|118430840|ref|NP_146901.2|  98 lqsAISSVDEVVALGGDGVAATVYW---GSQFEDKMLERWTRIRLRAEKLGLPALQLAYPRGPHIKNRY-AVDIVAYGAR 173
                                    467999*******************...*****************************************.********** PP

                                    HHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCH.SSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESHHHHT CS
                           DeoC 159 vsaelGaDiiKvevpkevvnateedaevfkdvikaa.pvpgvvlsGGv...seedfletvedAvkeagasGvlsGRaifq 234
                                    +++e GaD+iK+ ++        ++ e+f++v++aa  vp v++sGG+   s ++fl +v   + eag+ Gv++GR+ifq
  gi|118430840|ref|NP_146901.2| 174 AAMETGADLIKTYYT--------GSTESFRRVVSAAgGVP-VLMSGGArtpSPQEFLHKVYSVM-EAGGGGVVVGRNIFQ 243
                                    ***************........9********99883588.***********************.**************9 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.072   2.6e+02     192     209 ..      51      68 ..      15      90 .. 0.77
   2 !   20.6   0.3   6.3e-08   0.00023     140     233 ..     167     267 ..     159     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.072
                                    HHHHTT-SEEEESHHHHT CS
                           ThiG 192 qamelGadavllntavae 209
                                    +++e G+da++    +a+
  gi|118430840|ref|NP_146901.2|  51 EVVEAGVDAIMTTPGIAR 68 
                                    567777777777777765 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.3e-08
                                    HHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-.SS-BEEES---SHH......HHHHHHHTT-SEEEESHHHHTSSS CS
                           ThiG 140 leevGcaavmPlaapiGsglGllnkealkiiieea.kvPvivDAGigsps......daaqamelGadavllntavaeakd 212
                                    +   G++a m  +a +       ++e ++ +++ a  vPv++  G ++ps      ++  +me G  +v++   + +a d
  gi|118430840|ref|NP_146901.2| 167 IVAYGARAAMETGADLIKTYYTGSTESFRRVVSAAgGVPVLMSGGARTPSpqeflhKVYSVMEAGGGGVVVGRNIFQAGD 246
                                    567799999999998777776777777777777777************985555545789******************** PP

                                    HHHHHHHHHHHHHHHHHHHHH CS
                           ThiG 213 pvamArafklaveaGrlayla 233
                                    + am +a+++ v+ G    +a
  gi|118430840|ref|NP_146901.2| 247 IRAMVKAIRAIVHEGFDPEKA 267
                                    ***********9999866555 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00036       1.3      47      82 ..      93     128 ..      65     141 .. 0.80
   2 !    8.9   0.0   0.00032       1.1      19      70 ..     184     235 ..     166     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00036
                  Peptidase_C26  47 edeedvkaildkldgllltGgqdvePslygeepsek 82 
                                    +d++ ++++++++d ++  Gg+ v++++y+  + e+
  gi|118430840|ref|NP_146901.2|  93 QDDQFLQSAISSVDEVVALGGDGVAATVYWGSQFED 128
                                    37999*************************986554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00032
                  Peptidase_C26  19 daeesylaasyveavekagglpvllpieedeedvkaildkldgllltGgqdv 70 
                                    ++ ++   +s+ ++v +agg+pvl+   + + + +++l+k+  ++ +Gg  v
  gi|118430840|ref|NP_146901.2| 184 KTYYTGSTESFRRVVSAAGGVPVLMSGGARTPSPQEFLHKVYSVMEAGGGGV 235
                                    444445567799********************************99999754 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.1e-05      0.11      11      26 ..      47      62 ..      40      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                         GDPD_2 11 avwrelvgaGVdgInT 26
                                    ++re v+aGVd I+T
  gi|118430840|ref|NP_146901.2| 47 LLIREVVEAGVDAIMT 62
                                   489************9 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.4e-05       0.2      43      71 ..      93     120 ..      75     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.4e-05
                                    HHHHHHHHHHHCC-SEEEEEESHHHHHHH CS
                       DAGK_cat  43 dakelakeakeegvdlivvaGGDGtvsev 71 
                                    + ++++++a + +vd +v++GGDG++  v
  gi|118430840|ref|NP_146901.2|  93 QDDQFLQSAIS-SVDEVVALGGDGVAATV 120
                                    45677777777.79**********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2041.20
//
Query:       gi|14600388|ref|NP_146902.1|  [L=310]
Description: ATP-dependent 6-phosphofructokinase [Aeropyrum pernix K1]
Scores for complete 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  205.3   0.1    1.7e-60  204.9   0.1    1.0  1  PfkB          pfkB family carbohydrate kinase
    1.5e-08   34.4   0.0    2.1e-08   33.9   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.34   11.0   0.0    1.6  1  DUF4853       Domain of unknown function (DUF4853)


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 !  204.9   0.1   2.8e-64   1.7e-60       5     297 ..       9     292 ..       7     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 204.9 bits;  conditional E-value: 2.8e-64
                                   EEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEE CS
                          PfkB   5 vviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvk 83 
                                   v++G+al+dl +++e++   +e    k+ ++s GG++aNvAv+l rlg+++  ig++G D+fG+   ++l  egvd+++++
  gi|14600388|ref|NP_146902.1|   9 VAVGHALVDLRLYVERIpgVDEEAVIKDETRSVGGSAANVAVVLRRLGVQSGIIGKIGLDDFGRIAVDNLMREGVDISGLR 89 
                                   89***************9766666999****************************************************** PP

                                   EESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE..EE CS
                          PfkB  84 idedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt..fd 162
                                   ++ + rtg  ++v d++g  ti+ + gaa++l++ e   d+d+++ ++++++++      p+++l++++ a+k + t   d
  gi|14600388|ref|NP_146902.1|  90 VSLRDRTGFSVVVRDKEGSITIYSFKGAAEKLEPGEI--DADAIGRSKHVHVAS----LRPDTTLKTVEIAKKRSITvsWD 164
                                   **********************************876..***************....66789999999999999888978 PP

                                   EEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEE CS
                          PfkB 163 pnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkv 243
                                   p  + ++    +e+l ++++++d++++n++E++ ltg +  d  +a++ l+k    g+k vv++lG+ G+++  +dge++v
  gi|14600388|ref|NP_146902.1| 165 PGRVLSKMG--AERLANIISKVDIIFVNRNEAKNLTGYH--DYRQAARHLKK---LGPKIVVIKLGASGSYILYSDGEVFV 238
                                   877777764..8***************************..77777777777...899*********************** PP

                                   EE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSST CS
                          PfkB 244 pavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaia 297
                                   pa++++ vvDttGAGDs+++gf+a+ll+g ++e+a  +a+ vA++ v++ g++a
  gi|14600388|ref|NP_146902.1| 239 PAIKPERVVDTTGAGDSYAAGFIAGLLRGYTIEKASLYATIVASIKVSRLGSNA 292
                                   *************************************************99986 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   3.5e-12   2.1e-08     103     222 ..     168     275 ..     158     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3.5e-12
                                   BSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEE CS
                  Phos_pyr_kin 103 lleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeev 183
                                   +l++   e l++ ++ ++++i  N  Ea+ L+g      +d ++aa++l klg k V+ik g          ++ly+++ev
  gi|14600388|ref|NP_146902.1| 168 VLSKMGAERLAN-IISKVDIIFVNRNEAKNLTG-----YHDYRQAARHLKKLGPKIVVIKLGAS----GS--YILYSDGEV 236
                                   556666677776.99******************.....89**********************83....33..69**88887 PP

                                   EEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHH CS
                  Phos_pyr_kin 184 eeleaerietknthGtGCtlssaiaaelakgesleeAvk 222
                                   +    +     +t G+G+++++   a l +g+++e+A  
  gi|14600388|ref|NP_146902.1| 237 FVPAIKPERVVDTTGAGDSYAAGFIAGLLRGYTIEKASL 275
                                   765555555569***********************9965 PP

>> DUF4853  Domain of unknown function (DUF4853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.7e-05      0.34      61     105 ..      64     108 ..      45     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.7e-05
                                   ---HHHHHHHHHHT.--TTEEEEEE-SS--TTS-EEEEEEET.TS CS
                       DUF4853  61 eidfddlrevveeelkplGfkysekpderdkdesrtvvwgderyG 105
                                   +i  dd  +++ ++l + G+++s+ ++  ++ + ++vv++d++ +
  gi|14600388|ref|NP_146902.1|  64 KIGLDDFGRIAVDNLMREGVDISGLRVSLRDRTGFSVVVRDKEGS 108
                                   6778999**********************************9433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2342.79
//
Query:       gi|118430841|ref|NP_146903.2|  [L=553]
Description: dihydroxy-acid dehydratase [Aeropyrum pernix K1]
Scores for complete 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-197  656.2   0.0   3.8e-197  656.0   0.0    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  656.0   0.0  2.1e-201  3.8e-197       1     517 []      34     550 ..      34     550 .. 0.98

  Alignments for each domain:
  == domain 1  score: 656.0 bits;  conditional E-value: 2.1e-201
                       ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaqll 80 
                                    kp+i+++ ++se  pc+ ++     +vkegv++aggvp+ ++ti v+Dgi mg+ gmrysL+sReliad++e+ + ++ +
  gi|118430841|ref|NP_146903.2|  34 KPLIAVVAAWSEAGPCNFNVLPGSLRVKEGVRSAGGVPLAVPTIVVNDGINMGTPGMRYSLISRELIADTIEAQVASHGF 113
                                    8******************************************************************************* PP

                       ILVD_EDD  81 DalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacpgaGs 158
                                    D+ v i+gCDK+ Pg++ma+arl++P+i+++gG+ e+g  +  +++++s+feavga+ +g i+ee+l e+e+aa+p++G+
  gi|118430841|ref|NP_146903.2| 114 DGWVGIGGCDKTQPGIMMAMARLDLPSIYIYGGTAEHGVLDgeTVTVQSAFEAVGAYLKGLIDEERLYEIEKAAMPTPGT 193
                                    *************************************874455899********************************** PP

                       ILVD_EDD 159 CsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvllalGGStNa 238
                                    C+g++TAntma+laealGls  gsas pats+er+++ ++ag+ +v lve+ l+pr+ilt eaf NAiv+l+a++GStNa
  gi|118430841|ref|NP_146903.2| 194 CQGLFTANTMAILAEALGLSPLGSASPPATSSERARELARAGALAVGLVETGLTPRRILTYEAFYNAIVTLMAISGSTNA 273
                                    ******************************************************************************** PP

                       ILVD_EDD 239 vlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltvtgktlaenle 318
                                    vlHllAiAreagv+l lddfde srkvp++a l+P+gky+m dlh++GG p++l++Ll++gll g++ tv+g ++++ l+
  gi|118430841|ref|NP_146903.2| 274 VLHLLAIAREAGVKLALDDFDEASRKVPVIAALAPAGKYTMVDLHNVGGAPVILRKLLDRGLLYGEAVTVEGVEIGKLLS 353
                                    *******************************************************************************9 PP

                       ILVD_EDD 319 e.aevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveailkgkikagdvvvi 397
                                    + +  ++ +++ +++kp+++++gl++L+G+Lap+Gav+K+ a    +lkf+g A+vfdseeea++ai++g +++gdvvv+
  gi|118430841|ref|NP_146903.2| 354 KwEPRTDYNILYDFDKPYKPHAGLRILRGSLAPRGAVMKIGASG--ILKFKGAAKVFDSEEEAFKAIERGYVEEGDVVVV 431
                                    98888************************************999..9********************99*********** PP

                       ILVD_EDD 398 ryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialvedGDiieidiekrtlel 477
                                    ry GPkG+pGmpEmlk+t+a++g+glg+kvalitDGRfSGa++g+++gh +PEAa+gGpialve+GD i id ek+tl++
  gi|118430841|ref|NP_146903.2| 432 RYVGPKGAPGMPEMLKITAAIVGAGLGEKVALITDGRFSGATRGVMVGHAAPEAAVGGPIALVENGDEIVIDGEKGTLDV 511
                                    ******************************************************************************** PP

                       ILVD_EDD 478 evseeelaaRraawkpekkvktrgllakyaklvssaseGA 517
                                    ++  +ela+Rr++w+p + + ++gll+kyaklv++a+eGA
  gi|118430841|ref|NP_146903.2| 512 LLGGDELARRRDKWSPPPLP-KQGLLRKYAKLVTQADEGA 550
                                    ***************95444.59****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 4316.71
//
Query:       gi|118430842|ref|NP_146905.2|  [L=506]
Description: carbohydrate kinase [Aeropyrum pernix K1]
Scores for complete 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-39  134.4   0.0    1.4e-38  132.9   0.0    1.7  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    6.4e-26   91.3   0.2    1.1e-25   90.5   0.2    1.3  1  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
  ------ inclusion threshold ------
      0.024   14.2   0.1        2.1    7.8   0.0    2.2  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
      0.037   13.7   0.3       0.11   12.2   0.1    1.8  2  Raco_middle  RACo middle region


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.0     3e-42   1.4e-38       2     245 .]       7     262 ..       6     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 3e-42
                                    EEEEEEESSEEEEEEEE.TTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS CS
                         FGGY_N   2 ilglDcGttstkaivld.ekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqre 80 
                                    il++D+Gtt +ka ++d ++ ++ +++++  ++s+p++gw+eqdpee+wqa+ +a  ++le    +++ ++++ +s+   
  gi|118430842|ref|NP_146905.2|   7 ILSIDIGTTRIKAGLVDcNTLEITGRGSVSTPVSYPRKGWSEQDPEELWQAIVRASSAALEGF--EASRVSGVIFSTYLA 84 
                                    799*********************************************************988..*************** PP

                                    -EEEEETTTEESSEEE-TT--TTHHHHHHHHH...TTCH.......CCHHHHHSS-SSTTS.HHHHHHHHHHHSCCHHCC CS
                         FGGY_N  81 glvllDkndkpLynailwkdrrtaeiveklke...egne.......kklyektglvlstgf.tlsklkWlkenepevfek 149
                                    g+vllD+++  L+++i+w d+r+ +  ++l     +++        + l+   g + +tg  +lsk+ Wl+en+p+ f k
  gi|118430842|ref|NP_146905.2|  85 GVVLLDRDNYELTPIITWLDERAHGLPRELFSgvlKVSGynllhlvDLLRLTGGAPSKTGKdPLSKMVWLRENKPDLFTK 164
                                    *************************99998664432222001111133444455666666449***************** PP

                                    HCEEEEHHHHHHHHHCT--EEEHHHHCTTTSEETTTTE..E-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S CS
                         FGGY_N 150 iekflliddyLiwrLtgqfvtdvtnasesmlfnikkle..wdeellailgipeelLPklvesseiigelkpelaaklGlk 227
                                    ++++++ ++++  +  ++  +   +a  + l + + +   w++ l+   gip e+LP +  ++ ++g l +++a  lGl 
  gi|118430842|ref|NP_146905.2| 165 AHTIGTLKTWVLAKTAEARLVSPDDAHLTWLADTRGGRavWSPRLARRYGIPLEKLPGIAGPTDVAGGLVSSAARDLGLP 244
                                    *********************************9866444**************************************** PP

                                    -EEEEEEEEEHHHHHHHH CS
                         FGGY_N 228 egvpvvggggDqqaaalG 245
                                    +g+pv+ g+gD +++a+G
  gi|118430842|ref|NP_146905.2| 245 QGIPVIVGAGDIASSAVG 262
                                    ****************98 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 !   90.5   0.2   2.5e-29   1.1e-25       5     197 ..     275     455 ..     272     456 .. 0.92

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2.5e-29
                         FGGY_C   5 lGTssflllvgtkpvisehglltpvagedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaaeava 84 
                                    +GTss +++ +t+ ++++    + +  + +++ey++ g + +ag+ ++w+ld  g+     d   v e++      +  +
  gi|118430842|ref|NP_146905.2| 275 VGTSSWIGVHSTRRLLDVRHYIGSLL-SAKPGEYLVIGEQEIAGGMIDWILDVTGM-----DYRAV-EDIH-----SIPP 342
                                    7********88888889998888888.679***********************999.....55556.7778.....999* PP

                         FGGY_C  85 daggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskndl 164
                                     ++g++  p++ g+r+p+ dp+a+g+++gl+ ++t+ h++rAa+e+val +++ +e +++    +++ ++ +GGg++ + 
  gi|118430842|ref|NP_146905.2| 343 GSEGLIATPWLYGERTPIDDPHAKGVLVGLTLRHTKKHLVRAAVEGVALNIAWAMEHMTRL-AGKPKLVRGVGGGFRLRT 421
                                    *************************************************************.9999************** PP

                         FGGY_C 165 lmqllAdilgvpVerpkt.aeatalGaAilAava 197
                                    l++++A++l+ ++e++ + + a++ Ga  lAa a
  gi|118430842|ref|NP_146905.2| 422 LAKVIASALNATIETVSQpEMAGVRGAGALAAAA 455
                                    **************99997888899998888876 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 ?    7.8   0.0   0.00046       2.1       3      57 ..      10      71 ..       8     182 .. 0.80
   2 ?    4.4   0.1     0.005        22     205     267 .]     395     452 ..     372     452 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00046
                                   EEE-SSEEEEEEEETTTE.EEEEEEE--......TTS-HHH.........HHHHHHHHHHT- CS
                    BcrAD_BadFG  3 iDgGsTttkavlmdekge.vlgrgitns......anlesvrfeaaekvleealtealerage 57
                                   iD+G+T +ka l+d++   + grg   +      +  ++ + e+ ++ +++a ++ale  + 
  gi|118430842|ref|NP_146905.2| 10 IDIGTTRIKAGLVDCNTLeITGRGSVSTpvsyprKGWSEQDPEELWQAIVRASSAALEGFEA 71
                                   9***************9956666654445555555555555556666666666666664443 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.005
                                    HHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHHH CS
                    BcrAD_BadFG 205 rvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAalfA 267
                                     +++++ r++g ++ v  +GG ++     ++l k + ++ +  +i++  +++++g+ GA  +A
  gi|118430842|ref|NP_146905.2| 395 WAMEHMTRLAGKPKLVRGVGGGFRL----RTLAKVIASALNA-TIETVSQPEMAGVRGAGALA 452
                                    368899999999999*********9....8888888888888.8999***********97665 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.4e-05      0.11       3      28 ..       8      33 ..       7      38 .. 0.87
   2 ?   -2.9   0.0       1.1   4.8e+03      55      75 ..     419     439 ..     418     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                    Raco_middle  3 lavDiGtTtvvaaLvdletgkelaea 28
                                   l++DiGtT++ a Lvd++t ++ ++ 
  gi|118430842|ref|NP_146905.2|  8 LSIDIGTTRIKAGLVDCNTLEITGRG 33
                                   579***************99887665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                    Raco_middle  55 leklqkavveeinelieelle 75 
                                    l++l k++ +++n  ie++ +
  gi|118430842|ref|NP_146905.2| 419 LRTLAKVIASALNATIETVSQ 439
                                    678999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3777.39
//
Query:       gi|118430843|ref|NP_146906.2|  [L=464]
Description: pyridoxal-dependent decarboxylase [Aeropyrum pernix K1]
Scores for complete 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   98.3   0.0    5.5e-28   97.8   0.0    1.1  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    4.2e-09   35.8   0.0    2.1e-08   33.5   0.0    2.0  1  Aminotran_5      Aminotransferase class-V
    3.6e-07   29.8   0.1    5.2e-07   29.3   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.3e-06   27.1   0.0    1.5e-05   24.3   0.0    1.9  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   1.2e-31   5.5e-28      62     354 ..      45     315 ..      16     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.2e-31
                                    HHHT-BTSSTTTSHHHHHHHHHHHHHHHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHH CS
                  Pyridoxal_deC  62 dainkngftweesPaltelevvvldwlaellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeae 141
                                        k +++++ +P ++ele  +l   ++l+++p    +    g+++ g++es++la+lAar+++++  k          
  gi|118430843|ref|NP_146906.2|  45 LYRDKTMLDFTVYPSIIELEKQLLGFAGHLFHAP---EG--YSGTFTYGGTESIILAVLAARERWRRAGKSGA------- 112
                                    555789****************************...22..4699********************98776544....... PP

                                    HHCCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHH CS
                  Pyridoxal_deC 142 ildklvlytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelg 221
                                      +k v+     ah +  kaa +lg+k+  +p+d    +  +a  + iee++++ +++ ++va +    +g+ d +++lg
  gi|118430843|ref|NP_146906.2| 113 --GKIVMPIT--AHPAFAKAAYLLGLKVERVPVDS---VTLQADPAIIEEKIDR-DTV-MIVASAVDYPYGSLDPVEDLG 183
                                    ..57777665..59********************7...4556666899999999.666.57788888899********** PP

                                    HHHHHCT-EEEEE-TTGGGGGGSGGGGG.....GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCC CS
                  Pyridoxal_deC 222 dicekydlwlHvDAAyaGsaficpeirh.....llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYL 296
                                    di +  d+wlHvDA  +G ++     ++     +++g+e + S++v  hK++ ++ + s l+++   + + +  ++  + 
  gi|118430843|ref|NP_146906.2| 184 DIAAARDVWLHVDACIGGMVLAFASDAGeevgkFDFGVEGVRSFSVDMHKYGYAPKGSSILLFRRARDKKPTIFVDSSWP 263
                                    ******************654322222245666************************************99999999999 PP

                                    T.TTTTTSEECCCGSSSSSG.HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Pyridoxal_deC 297 ehedsdvaadlgtkaiplsr.rvrilklwfvlralGveglqnqirksvelakyleklir 354
                                    +       + l + ai   r     +  w v r+lGveg+++     +e  + ++k ++
  gi|118430843|ref|NP_146906.2| 264 G-------YPLVNQAILSTRsAGTLAAAWAVARTLGVEGYRELAGMVLEARRRIQKGLE 315
                                    9.......78888999999934456789************9988888777777777665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   4.8e-12   2.1e-08      55     179 ..      74     200 ..      71     373 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.8e-12
                                    HHT-STGGGEEEESSHHHHHHHHHHHCCCC.....-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSC.BE CS
                    Aminotran_5  55 linaeseeeiiftsGtteainlvalslars.....lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeege.ld 128
                                    l++a++ +   ft G+te+i l++l+++++      +   +iv+  + h a      ++a   g+kv+ +p+d+  +  d
  gi|118430843|ref|NP_146906.2|  74 LFHAPEGYSGTFTYGGTESIILAVLAARERwrragKSGAGKIVMPITAHPAFA----KAAYLLGLKVERVPVDSVTLqAD 149
                                    78888888999**********99999887764442222345666666666655....6667889********98665156 PP

                                    GGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTT CS
                    Aminotran_5 129 ldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqa 179
                                    +  +e++++ +t ++  ++v    G ++pve++g++a +++++++vDa+ +
  gi|118430843|ref|NP_146906.2| 150 PAIIEEKIDRDTVMIVASAVDYPYGSLDPVEDLGDIAAARDVWLHVDACIG 200
                                    9999*******************************************9743 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 !   29.3   0.1   1.2e-10   5.2e-07      47     162 ..      89     218 ..      57     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.2e-10
                                    HHHHHHHHHHH.......TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEE.. CS
                DegT_DnrJ_EryC1  47 GtaAlhlaLra.......lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlp.. 117
                                    Gt+++ la  a        g +   ++++p +   a a+a+  lg+k+  v vd  t++ dpa ie++i + t  I++  
  gi|118430843|ref|NP_146906.2|  89 GTESIILAVLAarerwrrAGKSGAGKIVMPITAHPAFAKAAYLLGLKVERVPVDSVTLQADPAIIEEKIDRDTVMIVAsa 168
                                    6666666666544444332333445899*********************************************9999633 PP

                                    B-G.GGB---HHHHHHHHHHCT-EEEEE-TT-TT....-EETTEECCCSS CS
                DegT_DnrJ_EryC1 118 Vhl.yGqvadmdalkaiaakhglkvieDaAhAlG....atykgkkvGalg 162
                                    V++ yG    ++ l +iaa+ ++++  Da+ +      a+ +g++vG+++
  gi|118430843|ref|NP_146906.2| 169 VDYpYGSLDPVEDLGDIAAARDVWLHVDACIGGMvlafASDAGEEVGKFD 218
                                    66689************************975333444666777777765 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 !   24.3   0.0   3.4e-09   1.5e-05      21     310 ..      33     333 ..      27     373 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.4e-09
                                    HHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH......HTT CS
                  Aminotran_1_2  21 pevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk......lnp 92 
                                    +ev+ka+ +   +   +t   ++ +    ele++l  f+g +  ++ +  +   + +G+ ++i a+ ++ +      +  
  gi|118430843|ref|NP_146906.2|  33 DEVRKAASKalELYRDKTMLDFTVYPSIIELEKQLLGFAG-HLFHAPEGYSGTFTYGGTESIILAVLAARErwrragKSG 111
                                    5677777773324444444444445556778888888888.333333333377777777777777777665888877777 PP

                                    T-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHH CS
                  Aminotran_1_2  93 gdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleelek 172
                                      +i++p   ++ + +++ l g++v r+p++ + + + d   +ee++++       t +i+   +  P G++ + e+l +
  gi|118430843|ref|NP_146906.2| 112 AGKIVMPITAHPAFAKAAYLLGLKVERVPVD-SVTLQADPAIIEEKIDR------DTVMIVASAVDYPYGSLDPVEDLGD 184
                                    779**************************55.9999999999*****99......778999999**************** PP

                                    HHHHHHHTTEEEEEEETTTTCBSSSS.HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH.............. CS
                  Aminotran_1_2 173 lldlakkynlllfvDeaYagfvfgsl.davatranveeepnllivgslsKafGlaGeRvGyilgna.............. 237
                                    +   a ++ ++l vD   +g+v+    da + + +++ +++   v+s+s ++  +G    y  + +              
  gi|118430843|ref|NP_146906.2| 185 I---AAARDVWLHVDACIGGMVLAFAsDAGEEVGKFDFGVE--GVRSFSVDMHKYG----Y--APKgssillfrrardkk 253
                                    *...9999********9999999843555555666666655..7777777777777....2..22222354444455555 PP

                                    ......HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEE CS
                  Aminotran_1_2 238 ......avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmfllt 310
                                                  + +++ls+ ++  ++aa++ +  l  +   e +  + + r+++ ++L++lgl+vl+ + +g++++t
  gi|118430843|ref|NP_146906.2| 254 ptifvdSSWPGYPLVNQAILSTRSAGTLAAAWAVARTLGVEGYRELAGMVLEARRRIQKGLESLGLEVLGRPkAGILSFT 333
                                    55444433333333333333333333333333333333333455555555556666666666666666655556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 3652.90
//
Query:       gi|118430844|ref|NP_146907.2|  [L=172]
Description: hypothetical protein APE_0023.1 [Aeropyrum pernix K1]
Scores for complete 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   27.6   0.0    4.6e-06   26.6   0.0    1.5  1  Acid_PPase  Acid Phosphatase


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.5e-10   4.6e-06       5     140 ..       6     136 ..       4     158 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.5e-10
                                    EEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHTT CS
                     Acid_PPase   5 livFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLklle 84 
                                    l+ +DLD TLW+      +++p+++ s++  +vD+ g e++ly    ++  + + ++  ++ + + + p  a e+L++l 
  gi|118430844|ref|NP_146907.2|   6 LLLLDLDGTLWDHLDVSSLKPPFTRVSHN-AIVDSGGVEVRLYGYMVALALWAR-RSGAVVSSFSWNVPFKALEALRVLG 83 
                                    6789*******8877777***********.*************97765544444.4444444444566777777766666 PP

                                    -G..........GGESEEEESS.....S..-HHHHHHHHHHHH---GGGEEEEES-HHHHHHH CS
                     Acid_PPase  85 indakekekklldvfddveiyk.....g..sktkhfeklkkktgieyedmlfFDdesrnieve 140
                                                ++f++  i +        +k   + +++++  ++  ++++FDd +   ++ 
  gi|118430844|ref|NP_146907.2|  84 AS----------HIFHYHVIEPhpwkgRmlTKLLRVLRVERRLYLTPGRIVYFDDREIHLDDI 136
                                    55..........444444343311111222334444444446666777777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1309.58
//
Query:       gi|118430845|ref|NP_146908.2|  [L=132]
Description: hypothetical protein APE_0024.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 998.60
//
Query:       gi|118430846|ref|NP_146909.2|  [L=135]
Description: TrmB family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete 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-27   95.1   0.1    2.4e-27   94.6   0.1    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
    4.3e-05   23.3   0.0    7.2e-05   22.6   0.0    1.4  1  MarR_2    MarR family
    0.00024   20.8   0.0    0.00042   20.0   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.029   14.0   0.0    1.5  1  GntR      Bacterial regulatory proteins, gntR family
      0.029   14.3   0.0      0.049   13.6   0.0    1.3  1  MarR      MarR family
       0.14   12.5   0.0       0.22   11.9   0.0    1.4  1  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.1   7.9e-31   2.4e-27       1      68 []      10      77 ..      10      77 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 7.9e-31
                                   HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                           TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                   L  lG++eyEa+vY+aL+ +gp++a ei+ ++gvpr++vY+vLr L+ kG+Ver +g+p++Yravdpe
  gi|118430846|ref|NP_146909.2| 10 LTSLGFKEYEARVYAALVLYGPSKAGEISLRSGVPRPRVYDVLRDLIAKGFVERTQGSPTYYRAVDPE 77
                                   5689***************************************************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.4e-08   7.2e-05       7      56 ..      19      66 ..      13      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.4e-08
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   +arv aaL   ++    +ge+  r g+++++v  +l++L a+G+ver+ g
  gi|118430846|ref|NP_146909.2| 19 EARVYAALVLYGP--SKAGEISLRSGVPRPRVYDVLRDLIAKGFVERTQG 66
                                   6788888899998..79******************************976 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 !   20.0   0.0   1.4e-07   0.00042      19      50 ..      32      63 ..      29      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
                                   -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                    +  e++ r+g+p++ v+  L+ L+  G+ve+
  gi|118430846|ref|NP_146909.2| 32 SKAGEISLRSGVPRPRVYDVLRDLIAKGFVER 63
                                   5789***************************8 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.6e-06     0.029      30      63 ..      37      70 ..      33      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.6e-06
                                   HHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEE CS
                           GntR 30 LaaefgVsrttvReALrrLeaeglverrqgrGtf 63
                                   ++ + gV r+ v  +Lr L a+g ver qg+ t+
  gi|118430846|ref|NP_146909.2| 37 ISLRSGVPRPRVYDVLRDLIAKGFVERTQGSPTY 70
                                   55567999***********************997 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   1.6e-05     0.049      16      51 ..      30      65 ..      28      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                   TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                   gp +  e+  ++gv ++ v  vl+ L+ kG++eR++
  gi|118430846|ref|NP_146909.2| 30 GPSKAGEISLRSGVPRPRVYDVLRDLIAKGFVERTQ 65
                                   6667889999************************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.4e-05      0.22      25      61 ..      31      67 ..      17      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                                   -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                           Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                   p ++ ei+ r +++++ +  +l+ L  +g+v+ ++G 
  gi|118430846|ref|NP_146909.2| 31 PSKAGEISLRSGVPRPRVYDVLRDLIAKGFVERTQGS 67
                                   46789*****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1062.28
//
Query:       gi|14600396|ref|NP_146910.1|  [L=622]
Description: hypothetical protein APE_0026 [Aeropyrum pernix K1]
Scores for complete 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-85  287.8   0.0    3.2e-83  279.7   0.0    2.2  1  PPDK_N    Pyruvate phosphate dikinase, PEP/pyruvate binding d


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.7   0.0   1.8e-87   3.2e-83       3     314 ..      23     291 ..      21     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 1.8e-87
                        PPDK_N   3 lvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeelee 83 
                                   +vGGK+a+L+ell+  g+pvPpgf++t+ a++ f+e+ngl++ i++   +          ++++ +r+lil+ e+P+e++e
  gi|14600396|ref|NP_146910.1|  23 MVGGKAASLGELLE-HGLPVPPGFVVTTRAYDLFVEKNGLKSVIENFSGA----------NQAAILRRLILEGEVPREVVE 92 
                                   7***********66.*****************************876554..........788999*************** PP

                        PPDK_N  84 aikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgldhee 164
                                   ai+eay + g+       +vaVRSSat EDlp+a+faGq dt+Lnv+g ++v+ea+k+++aSl+++rA++Yr++ g++h++
  gi|14600396|ref|NP_146910.1|  93 AIREAYYSRGD------GRVAVRSSATVEDLPEAAFAGQHDTFLNVEGIDRVVEAVKKCWASLWSDRAVAYRESLGVSHSK 167
                                   *********97......89************************************************************** PP

                        PPDK_N 165 valavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekkigekeikivyde 245
                                    ++av+vq+mv++d  +sGV+f+++p tG ++ev++na  GlGe++V+G vtpd++v+ k +      ki ek+i    + 
  gi|14600396|ref|NP_146910.1| 168 AKMAVIVQRMVDAD--VSGVMFTANPVTGVREEVVVNAFRGLGESIVSGVVTPDHYVLVKTRFG---WKIVEKRI----SG 239
                                   **************..*******************************************98766...23333332....22 PP

                        PPDK_N 246 keegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtse 314
                                                  +k++L+d+ + +La+i+ +i++ +gtp+diE+a++  +g++y+lQ+Rp+t   e
  gi|14600396|ref|NP_146910.1| 240 ---------------DKPVLDDRTLVRLASIGARIQRLFGTPQDIEWALE--KGRIYILQSRPITSLPE 291
                                   ...............24568889999************************..************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4359.17
//
Query:       gi|14600397|ref|NP_146911.1|  [L=218]
Description: hypothetical protein APE_0028 [Aeropyrum pernix K1]
Scores for 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   86.0   0.1    1.7e-24   85.4   0.1    1.3  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
       0.16   12.1   0.0       0.31   11.2   0.0    1.5  1  PEP-utilisers_N  PEP-utilising enzyme, N-terminal


Domain annotation for each model (and alignments):
>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.1   1.8e-28   1.7e-24       2      73 .]     142     213 ..     141     213 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.8e-28
                                   --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                 PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                   l++g+ILva+ t+p++++ ++ aa++vt++GG+ SHaA+ Are+giPaVvg+g at++lk+g ++ vDg++G
  gi|14600397|ref|NP_146911.1| 142 LRHGDILVAPFTTPAWTPLFRVAAAVVTDTGGPLSHAALTAREYGIPAVVGTGLATKVLKDGMRVRVDGYRG 213
                                   6789******************************************************************99 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.5e-05      0.31       1      16 [.     117     135 ..     117     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.5e-05
                                   E-EEEE-SEEEEEEE...- CS
               PEP-utilisers_N   1 kGiaaspGiaiGkav...e 16 
                                   +Gi+aspGia+G++    +
  gi|14600397|ref|NP_146911.1| 117 TGIPASPGIAVGTVKivrD 135
                                   6************985441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1644.49
//
Query:       gi|118430847|ref|NP_146912.2|  [L=484]
Description: MFS transporter [Aeropyrum pernix K1]
Scores for 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-59  200.0  64.1    9.6e-49  166.2  40.4    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.071   12.7   0.4       0.15   11.7   0.4    1.5  1  DUF2370   Protein of unknown function (DUF2370)
       0.52    8.8  38.9     0.0088   14.6  16.9    3.2  3  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.2  40.4   1.6e-52   9.6e-49       1     353 []      18     417 ..      18     417 .. 0.92
   2 !   47.8  15.7   1.5e-16   9.1e-13       3     184 ..     276     479 ..     274     482 .. 0.82

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 1.6e-52
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l+l+afl+++  ++l++++p a++ +lgisp e+++++t y ++ +v+++++Grl+d +Grrr+l+l l++f+++lll+ 
  gi|118430847|ref|NP_146912.2|  18 LALTAFLVMYVEAVLYTSVP-AIQAELGISPVEASWIFTSYLVTGSVLIPLMGRLGDAVGRRRTLILILIIFGISLLLGG 96 
                                    6899****************.******************************************************55555 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                     + +++ lll lr+ qG+g+ +++p+++a++++ fp+++ +   g+l+a++++G +++ ++gg+++++l Wr+ f+++ +
  gi|118430847|ref|NP_146912.2|  97 -SVNSFrLLLGLRAAQGVGM-TALPLIYAIVREEFPPNRAPVIQGILAAMNGIGLLIALPAGGWVTENLDWRLNFVLISP 174
                                    .356666************8.****************8888888************************************ PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeee..................................................k 189
                                    ++ll+++l ++ll +++  +  ks    +                                                  +
  gi|118430847|ref|NP_146912.2| 175 LALLSILLNIALLKDTRDLSLDKSLSGMRvsvasvlsfaalvtsllilitihttgesgeyaqglllaifivsllafrwsE 254
                                    *******999999999998888888888899*********************************************9999 PP

                          MFS_1 190 gtgpaplvpawkallkdpvlwillialllfffgfsglltllply....lqevlglsglllaglllallalvgailallag 265
                                    ++  apl+p ++ + ++  l  +++a++++ + f+++l+ lp +        +gl+   ++g++++ll +  ai+++lag
  gi|118430847|ref|NP_146912.2| 255 RRSSAPLLP-ISTFNRSVRLG-VFCASIIA-VTFQLVLFVLPYLlqtpHPNGFGLT-PTESGVYMMLLIVSYAISSPLAG 330
                                    999999999.99999999884.44444444.4666666666665222246677777.7********************** PP

                          MFS_1 266 rlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgfvfpsllalasdlappeeagtasglfnta 344
                                    +l+ r+g +r+ + + ll ++a+l++a+ ++   ++ll + lv +Gf g++f++ sl+++++ +a +++  t ++l++++
  gi|118430847|ref|NP_146912.2| 331 YLVVRVGMKRIAYAGSLLSAAAYLAVAVKPLQ--SPLLEVTLVSLGFvGMAFINNSLINIVVYSADKSYLSTTTSLYTLL 408
                                    ****************************9999..9999999*************************************** PP

                          MFS_1 345 gslggalgp 353
                                    ++lg+algp
  gi|118430847|ref|NP_146912.2| 409 RTLGSALGP 417
                                    ********8 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 1.5e-16
                          MFS_1   3 laaflsalarsilgpalplalaed.....lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                    ++a ++a ++ +++++lp +l ++     +g++p+e g  + l  + +a++s+++G+l+ r+G +r+  +g ll+a++ +
  gi|118430847|ref|NP_146912.2| 276 FCASIIAVTFQLVLFVLP-YLLQTphpngFGLTPTESGVYMMLLIVSYAISSPLAGYLVVRVGMKRIAYAGSLLSAAA-Y 353
                                    788999999999999999.888888899999***********************************888888888888.4 PP

                          MFS_1  78 lllfa..sslwlllvlrvlqGlga.galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..... 149
                                    l++ +   +++ll v  v  G+ + ++++ + + +++  + k+  +  ++l+++   lG++lgpl+ggl+ s  +     
  gi|118430847|ref|NP_146912.2| 354 LAVAVkpLQSPLLEVTLVSLGFVGmAFINNSLINIVVYSADKSYLSTTTSLYTLLRTLGSALGPLIGGLIFSMCSyseik 433
                                    44422444455455555555554447999999999999999*****************************9999999*** PP

                          MFS_1 150 ...........Wravfyilaivsllafvlfllllpeepperkrksp 184
                                                +++  ++a+ sl+++vl+++l  +ep+  k  sp
  gi|118430847|ref|NP_146912.2| 434 ttqitsfsidpLSYSLAFAAASSLFLIVLAMVLQIDEPSLLKDLSP 479
                                    ***********66666666666666666888999998887776665 PP

>> DUF2370  Protein of unknown function (DUF2370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   2.4e-05      0.15      85     108 ..     279     302 ..     273     326 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                        DUF2370  85 llvsvsFqlvGFlltYlLHtthAa 108
                                     +++v+Fqlv F+l YlL t h  
  gi|118430847|ref|NP_146912.2| 279 SIIAVTFQLVLFVLPYLLQTPHPN 302
                                    689*****************9965 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   6.5    0.0017        10     251     327 ..      39     114 ..       7     187 .. 0.65
   2 ?   -1.4   2.7      0.11   6.6e+02     143     182 ..     205     249 ..     136     252 .. 0.60
   3 ?   14.6  16.9   1.5e-06    0.0088     256     419 ..     305     465 ..     266     468 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0017
                          MFS_2 251 ltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfg 327
                                    ++  lg +  +as++++   + + + ipl+ +l    g+++t +l +++  + l+l   +  ++  l+l l ++ g+g
  gi|118430847|ref|NP_146912.2|  39 IQAELGiSPVEASWIFTSYLVTGSVLIPLMGRLGDAVGRRRTLILILIIFGISLLLGGSV--NSFRLLLGLRAAQGVG 114
                                    455566677777888888877778888888888888887766665555555444444444..4555555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                          MFS_2 143 svlggvlaailafllvlilgg.....lkserkgylifaliialLm 182
                                    sv+  + +a+l++ l++  +       ++ ++g l++++i +lL+
  gi|118430847|ref|NP_146912.2| 205 SVASVLSFAALVTSLLILITIhttgeSGEYAQGLLLAIFIVSLLA 249
                                    222222222222222222222223345677777777777777776 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 1.5e-06
                          MFS_2 256 g.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaall 334
                                    g + ++  v+++++++s ++++pl+ +l+ r g k+++++g+ll ++ ++ v + + ++ ll ++   ++++g++++a++
  gi|118430847|ref|NP_146912.2| 305 GlTPTESGVYMMLLIVSYAISSPLAGYLVVRVGMKRIAYAGSLLSAAAYLAVAVKPLQSPLLEVT---LVSLGFVGMAFI 381
                                    44556778999999********************************9999998885555555554...455555568888 PP

                          MFS_2 335 pwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgy.rakasvqspqvvlalrll..yavlpav 411
                                      s++  vv        k+  ++++++++++  l++++g ++ gl+ s+  y + k  ++++  ++ l+++  +a++ ++
  gi|118430847|ref|NP_146912.2| 382 NNSLINIVVYSAD----KSYLSTTTSLYTLLRTLGSALGPLIGGLIFSMCSYsEIKTTQITSFSIDPLSYSlaFAAASSL 457
                                    8888877664444....677899*****************************6556666677777766655005555555 PP

                          MFS_2 412 lllvalll 419
                                    +l+v +++
  gi|118430847|ref|NP_146912.2| 458 FLIVLAMV 465
                                    55555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3211.30
//
Query:       gi|118430848|ref|NP_146913.2|  [L=489]
Description: phosphoenolpyruvate carboxykinase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-40  139.3   0.0    1.2e-39  136.3   0.0    2.1  1  PEPCK_ATP  Phosphoenolpyruvate carboxykinase
     0.0084   16.3   0.0      0.015   15.5   0.0    1.4  1  AAA_33     AAA domain


Domain annotation for each model (and alignments):
>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.0   1.3e-43   1.2e-39      66     462 ..      63     446 ..      16     449 .. 0.80

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 1.3e-43
                                    E-HHHHHHHHHHHHHHHHTS-EEEEEEEE-SSTTT-EEEEEEES-HHHHH.HHHHHSBGGS-S-TTT---SEEEEEETT- CS
                      PEPCK_ATP  66 iseekfealkekvleylkekelyvvdafagadpkyrlkvrviterawqal.fvknllirpteeeleefepdftilnapef 144
                                    +++e f++l  ++ +y+ + ++y v++ +g+ +  r+++  ++e+++ +l  +++l + p  +     + d++ +++p+ 
  gi|118430848|ref|NP_146913.2|  63 LRDEGFDRLVVDAWDYVVKASFYAVERCVGSGD-RRFRILALVEKSYPHLaLMSHLNFFPCGST---GSYDMVTIDVPS- 137
                                    567788888888888888888888888888754.355555555555544414445555554433...356888888888. PP

                                    ---HHHH--SSS-EEEEETTTTEEEEES---THHHHHHHHHHHHHHHH.HTT-EEEEEEEEE......-T.TS-EE.EEE CS
                      PEPCK_ATP 145 kadpekdglnsetvvalnlekklvlilgteYaGEikKsifsvmnyllp.kkgvlsmhcsanv......gekkgdva.lfF 216
                                              s+  ++++ +++ +l+lg++Y GE+k s++++++   + ++  +++h++++       g+ + +v+ l F
  gi|118430848|ref|NP_146913.2| 138 ---------YSDVWMLVERRSNSTLVLGSDYYGELKMSFLRLAMNEARdRHLGVGLHAASKLyrvrveGSMR-EVGvLVF 207
                                    .........7899999************************98665555377889*******87778777555.888688* PP

                                    E-TTSSHHHHH......-BTTB-EEESSEEEE-SS.-E.EES-SEEEEE-TT--TTTSHHHHHHHS.TT-EEES-EE-TT CS
                      PEPCK_ATP 217 GLSGtGKTtLs......adperkligdDehgwsde.gv.fniegGcYaKtidLskekepeiynair.fgavlENvvldee 287
                                    GLSGtGKTtL+       +pe + + +D++++ d  gv  ++e  +Y Kt ++ +   +++  a+  ++avlENvv++ +
  gi|118430848|ref|NP_146913.2| 208 GLSGTGKTTLTvedhglREPEYVRVMQDDIVILDWrGVaHGTEMNLYPKTDSVPEL--KKLEPAVLhPDAVLENVVVK-S 284
                                    ***********999988778877777777776665496379**********99854..445556555**********5.6 PP

                                    T--EETT--SS-S--EEEEEGGGSSSB-TTSEE--EEEEEEEE--TTS-S-SEEEE-.HHHHHHHHHH-EEEE------- CS
                      PEPCK_ATP 288 trevdfddtslteNtrvaypiehienakeesvaghpkniifLtadafgvlPpvskLt.keqamyhFlsGytakvaGterg 366
                                    ++++df+d slt N+r+   +e i+ a+ +      + ++fLt++    +Pp+++Lt + qa+++F++G++ +++  e+g
  gi|118430848|ref|NP_146913.2| 285 DGTPDFTDLSLTRNARALAIREAIPIASGSVDLMGTNVLVFLTRRP--EMPPLARLTsPYQAVAYFMLGESFRTS-AEAG 361
                                    7999*********************98766666888999*****98..79******8357***********9986.5888 PP

                                    ----EEEE-GGG-GGG-SS-HHHHHHHHHHHHHHH--EEEEEE-SEESSSTTTSEE--HHHHHHHHHHHHTTCCCTS-EE CS
                      PEPCK_ATP 367 vtepeatFsacfgapFlplhpteyaelLaeklekhnakvyLvNtGwtggaygvgkrislkatraiikaildgeleavefe 446
                                      +pe+     f  pF+  ++ + a  L + +++ n++vy++NtG +       ++i+ + +++++ +++++++   +++
  gi|118430848|ref|NP_146913.2| 362 --KPEPVRVPGF-DPFMLEPKWRSAYSLLDLIKSLNMNVYVMNTGHAK-----DRKIPPELSKHLLLSLVKENV---DWK 430
                                    ..6777778888.7*******************************554.....599999999999999999988...567 PP

                                    E-TTT--EEES-BTTC CS
                      PEPCK_ATP 447 kdpvfglevptevpgv 462
                                     d+ +g+e+ ++  gv
  gi|118430848|ref|NP_146913.2| 431 LDKHMGFEIAVRAGGV 446
                                    7777777777766666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-06     0.015       2      33 ..     204     237 ..     204     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                         AAA_33   2 vllvGlpGsGKstlaer.l.lkklgavllssdtl 33 
                                    vl+ Gl+G+GK+tl  + + l++  +v++ +d++
  gi|118430848|ref|NP_146913.2| 204 VLVFGLSGTGKTTLTVEdHgLREPEYVRVMQDDI 237
                                    7899*********976525577777*******94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3451.53
//
Query:       gi|118430849|ref|NP_146914.2|  [L=468]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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-32  113.3   8.1    2.9e-32  112.9   8.1    1.1  1  SBP_bac_1        Bacterial extracellular solute-binding prote
    2.2e-23   83.5   2.0      3e-23   83.0   2.0    1.2  1  SBP_bac_8        Bacterial extracellular solute-binding prote
     0.0003   20.6   0.0      0.012   15.3   0.0    2.2  2  SBP_bac_11       Bacterial extracellular solute-binding prote
  ------ inclusion threshold ------
       0.02   14.6   0.2      0.046   13.5   0.2    1.5  1  DivIC            Septum formation initiator
      0.033   13.3   0.1      0.048   12.8   0.1    1.2  1  AI-2E_transport  AI-2E family transporter
       0.08   13.3   2.1        0.2   12.1   2.1    1.6  1  FlaC_arch        Flagella accessory protein C (FlaC)
       0.15   12.1   0.9       0.33   11.0   0.9    1.5  1  Laminin_II       Laminin Domain II
       0.24   11.5   0.6       0.46   10.6   0.6    1.4  1  COG2             COG (conserved oligomeric Golgi) complex com


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 !  112.9   8.1   1.3e-35   2.9e-32       4     314 ..     102     382 ..      98     383 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.3e-35
                                    HHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTT CS
                      SBP_bac_1   4 ltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkayl 82 
                                    ++e  +++ ++ ++f++e+p++++++++    ++a  l+++++aG  paDv+++ + +wi ++a++g +++++ +++++ 
  gi|118430849|ref|NP_146914.2| 102 EQE--YFMTAL-EKFMEENPNVTIKYVPMRAEEVARTLSVQFEAGVTPADVVITpWAWWIVEMAQKGHVIEVTGLINEDE 178
                                    444..888899.99*****************************************************************6 PP

                                    ECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEE.E.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCC CS
                      SBP_bac_1  83 apgvkdaadklsssvlpkilds.kv...ly.vPly.a.argliYNkdlfekagldppwtWdelveaakklkekgkkpigg 155
                                                  ++++ild  k+   l+ vP+      g++Y k+ f+k gl++p +W+e++ ++  +k+  + +  +
  gi|118430849|ref|NP_146914.2| 179 --------------YVGGILDNvKWnnkLWgVPFTmWlKPGFWYKKSFFAKHGLSEPNSWEEFLQLLDQIKGIEGIKNPI 244
                                    ..............99*****88999*********************************************999999899 PP

                                    HCCEEHHHHHHHHHHHHHHHHTGGGEECCCT....HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHH CS
                      SBP_bac_1 156 arggsasgtayyfalalakslggkvfdkdgg....gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfe 231
                                    + g s ++ ++  +++++  +gg++   +       +++p  v+ ++ l  l+          g+ +e   +++a+  + 
  gi|118430849|ref|NP_146914.2| 245 VSGDSVGWPLSDVTEHFIIAFGGPELQYKLItgevSFTDPQVVEIFEKLAMLI--------EQGYFSEPIEWTSAVEKWW 316
                                    9999999999999*********9999998878777777777777777777777........7899*************** PP

                                    TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                      SBP_bac_1 232 aGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllsp 311
                                    a e a++++g+w               + + + +++l+++plP+ +g  +   g+++  ipk + n eaAk +l++l+++
  gi|118430849|ref|NP_146914.2| 317 AEEYALYFMGTWI--------------TGMVEDPNDLAFFPLPGARGVVG---GTDYAFIPKYTENLEAAKLLLQYLATE 379
                                    ************7..............9999999*********9999999...9*************************9 PP

                                    HHH CS
                      SBP_bac_1 312 eaq 314
                                    +++
  gi|118430849|ref|NP_146914.2| 380 GQA 382
                                    986 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 !   83.0   2.0   1.3e-26     3e-23       3     264 ..     110     394 ..     108     408 .. 0.80

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.3e-26
                                    HHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HH.HHHTT-- CS
                      SBP_bac_8   3 akefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltd.alaavgy 80 
                                     ++f +++ +v++++v++  ++++ +l+ + +ag +p+ +v+++++ ++ ++a++g + +++ l n d++    l+ v++
  gi|118430849|ref|NP_146914.2| 110 LEKFMEENpNVTIKYVPMRAEEVARTLSVQFEAGVTPADVVITPWAWWIVEMAQKGHVIEVTGLINEDEYVGgILDNVKW 189
                                    689***************99******************99************************999999886888889* PP

                                    TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-............SEGG---G.GGGGGTHH.. CS
                      SBP_bac_8  81 dgklygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkf............glpdpasg.wlqaalla.. 143
                                    + kl gvP+++    ++ y k+ + k+  + p +w+e+l++++++kg              g+p   s+ + +++  +  
  gi|118430849|ref|NP_146914.2| 190 NNKLWGVPFTMWLKPGFWYKKSFFAKHglSEPNSWEEFLQLLDQIKGIEgiknpivsgdsvGWPL--SDvTEHFIIAFgg 267
                                    **********87544**********98999***************98883334444443333332..2233344444433 PP

                                    ..ETTEE---H........HHH.HHHHHHHHHHHHTT-EE.-.S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE CS
                      SBP_bac_8 144 ..kdgksldddg......gkdglkealellkklkdngkty.d.tgadavsefanGevaftingswdiaaaqkagkklgai 213
                                       +     + +      ++++++e++e+l+ l ++g++  +  +++av+++   e+a ++ g+w+   +++   +l++ 
  gi|118430849|ref|NP_146914.2| 268 peLQ----YKLItgevsfTDPQVVEIFEKLAMLIEQGYFSePiEWTSAVEKWWAEEYALYFMGTWITGMVED-PNDLAFF 342
                                    4322....2222334478889*****************9963578999***********************9.4467888 PP

                                    .--S--EEEEEE.EEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS CS
                      SBP_bac_8 214 .vpkqgsfaggk.glavpknaknedlaAldFlkwltspenqaalaektgyipv 264
                                     +p    ++gg+ +  +pk ++n + aA+ +l++l+++ +    ++  g +p+
  gi|118430849|ref|NP_146914.2| 343 pLPGARGVVGGTdYAFIPKYTENLE-AAKLLLQYLATEGQAVHVSTPAGKVPT 394
                                    4464446666661566*********.6********998776666667777666 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 !   15.3   0.0   5.5e-06     0.012      14      70 ..     107     169 ..      99     236 .. 0.82
   2 ?    3.1   0.0      0.03        67     190     221 ..     352     381 ..     310     386 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                                    HHHHHHH.HHHH---EEEEESSHHHHHHHH....HHH...-SEEEESSH.HHHHHHHHGGGGG CS
                     SBP_bac_11  14 relaaaF.eahtgvkvevsaggsgklarqi....adga.rpDvwipassawlellaaaglvqa 70 
                                    + + ++F e++++v++++    + ++ar++    ++g  ++Dv+i   + w+ ++a++g+v +
  gi|118430849|ref|NP_146914.2| 107 MTALEKFmEENPNVTIKYVPMRAEEVARTLsvqfEAGVtPADVVITPWAWWIVEMAQKGHVIE 169
                                    55678887999*****************88888888877*******************99874 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.03
                                    ...EEEEEEEE-TT--HHHHHHHHHTTSHHHH CS
                     SBP_bac_11 190 dpldypaavlkkaakreaAraFlafLrspeaq 221
                                      +dy++ ++k + + eaA+ +l++L++ e+q
  gi|118430849|ref|NP_146914.2| 352 GGTDYAF-IPKYTENLEAAKLLLQYLAT-EGQ 381
                                    4678877.99****************95.455 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2     2e-05     0.046       1      50 [.      14      63 ..      14      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                   XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                          DivIC  1 llllfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                   l++++l++l+ + +  +++ +++q +   q+++ ++k+++   e+e+k  
  gi|118430849|ref|NP_146914.2| 14 LIVVILISLFSYLSITSRIESVEQSVSSVQEDISEVKQRISGIEQEIKGI 63
                                   678999999999999********************************966 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 ?   12.8   0.1   2.2e-05     0.048      47     105 ..       3      61 ..       1      93 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                AI-2E_transport  47 vkrvlavllvlllllvllvllvlllvplliaqltqlvkslpayidslqnilnelpslle 105
                                     +r+la+++ ll++++l+ l+ +l +++ i++++q v+s++  i+++++ ++ ++++ +
  gi|118430849|ref|NP_146914.2|   3 APRSLAITAGLLIVVILISLFSYLSITSRIESVEQSVSSVQEDISEVKQRISGIEQEIK 61 
                                    689**************************************999999998888877655 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 ?   12.1   2.1   8.7e-05       0.2       8      38 ..      31      61 ..      27      66 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.7e-05
                      FlaC_arch  8 klsklsteletvkkeneelsksveelkenVk 38
                                   ++++++ ++++v+++++e+++ +  +++++k
  gi|118430849|ref|NP_146914.2| 31 RIESVEQSVSSVQEDISEVKQRISGIEQEIK 61
                                   4555666666666666666666666666654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   0.00015      0.33       5      40 ..      32      67 ..      27      91 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II  5 aaeanetakevleqlaplsqnlentkeklseinrsv 40
                                   ++++++++++v+e++ +++q+++ +++++++i++ +
  gi|118430849|ref|NP_146914.2| 32 IESVEQSVSSVQEDISEVKQRISGIEQEIKGIKEAA 67
                                   566667777777777777777777777777666554 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 ?   10.6   0.6   0.00021      0.46      67     121 ..      28      81 ..      24      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                           COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllk 121
                                    + +++e ve++++++++++++v++ +s  e+e+++ ++ea+  e +  + +  +k
  gi|118430849|ref|NP_146914.2|  28 ITSRIESVEQSVSSVQEDISEVKQRISGIEQEIKG-IKEAAGGETTTPVTETEVK 81 
                                    5678999**************************87.5666555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      885  (0.0493614); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); 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 0.30s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 3213.79
//
Query:       gi|118430850|ref|NP_146915.2|  [L=298]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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  20.5    1.2e-20   74.0  20.5    1.8  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 ?   -0.8   0.2     0.059   1.1e+03      22      38 ..      20      36 ..      10      89 .. 0.62
   2 !   74.0  20.5   6.9e-25   1.2e-20       3     168 ..      93     283 ..      91     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.059
                   BPD_transp_1 22 pliivllslPsfvlail 38
                                   ++i ++   Ps++ + l
  gi|118430850|ref|NP_146915.2| 20 TFITIFVIAPSIATVYL 36
                                   33444444444443333 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 6.9e-25
                   BPD_transp_1   3 llGilaa.lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpviill 60 
                                    +lG+++a l +  +++ ++ +++++++ +P++v ++++ ++f                      + ++ + + l++i+ +
  gi|118430850|ref|NP_146915.2|  93 FLGLFLAyLLKYTFGSSIVKTIVFIGMVIPMVVGGLIVRFMFdeyvgvvplvfkalgvdflakTWTNYPQLSLLSLILGS 172
                                    79*****99999*********************9999999999999999999***********9**************** PP

                   BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtl 140
                                    ++ ++++ + +++aal s+p++++eaar++Ga++w+if+k+v+P++ p +i  +++++ + l+ + +++  + +++ g+ 
  gi|118430850|ref|NP_146915.2| 173 VWLWTGFSLTVYSAALGSIPSSFIEAARIDGAGHWHIFWKIVFPLVRPATIIVVVMTMLWDLKIFDIVYVATLGGPGGSS 252
                                    ***********************************************************997777776666655556666 PP

                   BPD_transp_1 141 lleailgydyseis...nggvlalviavlll 168
                                     + a+ +y+y + +    ++++++vi++ll 
  gi|118430850|ref|NP_146915.2| 253 NVLALVMYQYMARAldyQAASAVAVILTLLT 283
                                    6666666666666666655555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2317.72
//
Query:       gi|118430851|ref|NP_146916.2|  [L=286]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-21   75.0  17.5      6e-21   75.0  17.5    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 ?   -1.5   1.9       0.1   1.8e+03      26      44 ..      27      51 ..       2      99 .. 0.52
   2 !   75.0  17.5   3.3e-25     6e-21       3     181 ..      96     277 ..      94     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.1
                   BPD_transp_1 26 vllslPsfvlaillvlvf.............v 44
                                   +++ lP++ l       f              
  gi|118430851|ref|NP_146916.2| 27 LVWLLPFIGL-------FmvsvrpygevivkG 51
                                   2222222222.......223333444443331 PP

  == domain 2  score: 75.0 bits;  conditional E-value: 3.3e-25
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                     ++++aa    +++++l+  l  ++i+l++lP  +++++l+l++++l +l +++ ++i++     ++++++++++++++l
  gi|118430851|ref|NP_146916.2|  96 AAASFAAygfSRFSFPLKSYLFLVTILLMALPQQIVVVPLFLLLKNL-GLINTFPGIILVHSAWGMAWIIFFMKNFFDIL 174
                                    56788999999999*********************999999765555.5555666677777777789************* PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyseisng 156
                                    p++ +eaar++Gas+++if+k+vlP++lp i++  +l+f++++  +++ ++++ +p    +++++ +    y +++++  
  gi|118430851|ref|NP_146916.2| 175 PREVEEAARVDGASDFRIFYKIVLPMSLPGILSASVLQFTWVWSSFFFELIFLIDPSkwvITQRIANMKGTYLVDWGL-- 252
                                    ********************************************9998877776765677777777777777777777.. PP

                   BPD_transp_1 157 gvlalviavlllnlvadilqrlldp 181
                                    +++  v+a+++ ++v+++lqr+  +
  gi|118430851|ref|NP_146916.2| 253 IAAGSVFAMAVPLAVYMLLQRYYIR 277
                                    999999999999******9999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2269.02
//
Query:       gi|118430852|ref|NP_146917.2|  [L=368]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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  118.4   0.0    4.5e-34  117.9   0.0    1.3  1  ABC_tran     ABC transporter
    7.7e-14   51.7   0.0    2.5e-13   50.1   0.0    2.0  2  TOBE         TOBE domain
    7.1e-11   42.1   0.0    3.3e-10   40.0   0.0    2.2  2  TOBE_2       TOBE domain
    7.6e-07   29.9   0.0    3.8e-06   27.6   0.0    2.3  2  OB_MalK      MalK OB fold domain
    1.6e-05   24.9   0.0      0.029   14.2   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00065   19.2   0.0     0.0032   16.9   0.0    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0029   17.9   0.0     0.0065   16.7   0.0    1.7  1  AAA_22       AAA domain
      0.004   17.5   0.1     0.0071   16.7   0.1    1.5  1  AAA_16       AAA ATPase domain
     0.0046   17.0   0.0     0.0088   16.1   0.0    1.5  1  AAA_14       AAA domain
     0.0067   16.4   0.0     0.0099   15.8   0.0    1.3  1  Rad17        Rad17 P-loop domain
     0.0079   16.6   0.0      0.018   15.5   0.0    1.6  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.019   15.5   0.3      0.036   14.6   0.3    1.6  1  AAA_23       AAA domain
      0.045   14.0   0.0       0.11   12.7   0.0    1.7  1  AAA_28       AAA domain
       0.09   12.7   0.1       0.23   11.4   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
       0.17   11.6   0.0       0.34   10.7   0.0    1.5  1  AAA_29       P-loop containing region of 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 !  117.9   0.0   3.8e-37   4.5e-34       2     136 ..      20     165 ..      19     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 3.8e-37
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++v+l++k ge  +++G++G+GK+t l+l+agl+ p+eG+il+dg+d++   +   ++++++++q+  l p+++v +n  
  gi|118430852|ref|NP_146917.2|  20 DHVDLSIKDGEFFVLLGPSGCGKTTTLRLIAGLEYPDEGRILIDGEDVTF--KDPKDRNVAMVFQNYALYPHMSVFDNia 97 
                                    789***********************************************..778899********************** PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   + ++++ ++++ l++++l d++      +LSgGq+qrvalaral+++pk++l+DEp 
  gi|118430852|ref|NP_146917.2|  98 ftlhlrrkemgltkdDIRRRVIEVAKLLRIEDLLDRKP----GQLSGGQQQRVALARALVRRPKVWLMDEPL 165
                                    ********99999877778899*******999999998....*****************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.3   7.5e+03      40      62 ..     214     234 ..     208     235 .. 0.58
   2 !   50.1   0.0   2.1e-16   2.5e-13       2      64 .]     299     358 ..     298     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.3
                           TOBE  40 rsaeeLgLapGeeVfalikaakv 62 
                                     ++++  + + eeV++++k + v
  gi|118430852|ref|NP_146917.2| 214 GRVVQ--VGTPEEVYMRPKHTFV 234
                                    55555..3333678888887665 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 2.1e-16
                           TOBE   2 sarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                    ++++ + g+V+vveplgse++V+vd+g+g ++ A+v    +e+  ++pG++V++ ++++kv++
  gi|118430852|ref|NP_146917.2| 299 ETEGSIAGKVYVVEPLGSEYVVNVDIGDGIIIKAKV-LGLREK--MTPGDKVYLKLDWSKVKI 358
                                    57899*******************************.9*****..****************85 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.3   3.9e+03      56      74 ..     215     233 ..     190     234 .. 0.57
   2 !   40.0   0.0   2.8e-13   3.3e-10       1      69 [.     286     352 ..     286     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.3
                         TOBE_2  56 salapGdtVelswdpddav 74 
                                    + +++G+  e+ ++p +++
  gi|118430852|ref|NP_146917.2| 215 RVVQVGTPEEVYMRPKHTF 233
                                    3667777777777777766 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 2.8e-13
                         TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswd 69 
                                    l+iRPE+++++ ++++++++G+V  ve lGs++++ v++++g ++++++   ++   ++pGd+V l +d
  gi|118430852|ref|NP_146917.2| 286 LGIRPEFISVSRRETEGSIAGKVYVVEPLGSEYVVNVDIGDGIIIKAKVLGLRE--KMTPGDKVYLKLD 352
                                    79********6444456***********************************95..9*********998 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       7.9   9.4e+03      10      32 ..       8      30 ..       6      46 .. 0.60
   2 !   27.6   0.0   3.2e-09   3.8e-06       1      53 []     239     293 ..     239     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 7.9
                        OB_MalK 10 atveedgvlvegggvtlplpeeq 32
                                   + v++ g +v+ ++v+l +++++
  gi|118430852|ref|NP_146917.2|  8 GVVKRFGKVVAVDHVDLSIKDGE 30
                                   56666665666677777777766 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.2e-09
                        OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                    G P+MN++++ ve  g  + +   g++ ++pee++   +++  +++ lGiRPE i
  gi|118430852|ref|NP_146917.2| 239 GAPPMNLVECDVESVGedLWISCPGFSRRVPEEARSVIESKGVRKIYLGIRPEFI 293
                                    99***********888999999999********9667777788**********65 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.4e-05     0.029       1      60 [.      31      81 ..      31     100 .. 0.70
   2 !    8.6   0.0    0.0012       1.5     220     298 ..     121     197 ..      86     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60
                                   + vl Gp g+GK++ L+++ +l         + ++++++   +++  + d++d + +++f
  gi|118430852|ref|NP_146917.2| 31 FFVLLGPSGCGKTTTLRLIAGL---------EYPDEGRILIDGEDVTFKDPKDRNVAMVF 81
                                   68*****************999.........44555555555555555555555555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsr.ngaQviltTH 297
                                       +l  +d  ++ + +lS G+++  al+ al r++   ++ l DEp ++L+  llr  +   lk+l++  ++  + +TH
  gi|118430852|ref|NP_146917.2| 121 VAKLLRIEDLLDRKPGQLSGGQQQRVALARALVRRP---KVWLMDEPLSNLDA-LLRLAMrAELKKLQKdLKITTVYVTH 196
                                    444455566777888999*******9**********...9************9.55555544455555557777788888 PP

                         AAA_21 298 S 298
                                    +
  gi|118430852|ref|NP_146917.2| 197 D 197
                                    7 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 !   16.9   0.0   2.7e-06    0.0032      25     214 ..      30     211 ..       9     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE...SSSSSSCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk...lkiekeevsis 100
                                    +f +++Gp G+GK+  l  i    G +       ++ + li     + +  k  +v+++f+n       ++ ++  +++ 
  gi|118430852|ref|NP_146917.2|  30 EFFVLLGPSGCGKTTTLRLI---AGLEY-----PDEGRILIDGeDVTFKDPKDRNVAMVFQNYALYphmSVFDNIAFTLH 101
                                    57788888888888877776...55433.....34555555554445556666667777766665533255666667777 PP

                                    EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkva 180
                                     r k+ g ++  i ++ ++ +++ ++    + ++ +LSgG+++ vala       v++  ++l+De  ++LD+  + ++ 
  gi|118430852|ref|NP_146917.2| 102 LRRKEMGLTKDDIRRRVIEVAKLLRIEDLLDRKPGQLSGGQQQRVALARA----LVRRPKVWLMDEPLSNLDALLRLAMR 177
                                    77777777666666666655555555555555778********9988754....4677779******************* PP

                                    HHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 181 ellkeksknaQfivislreemlekadklvgvtkv 214
                                      lk+ +k+  +  + +++++ e ++   ++   
  gi|118430852|ref|NP_146917.2| 178 AELKKLQKDLKITTVYVTHDQAEAMSMADRIAVM 211
                                    *********9998888888888887776666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.5e-06    0.0065       4      83 ..      28     119 ..      24     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.5e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsst..sskdllrellralgle 67 
                                    +  + v+ G+sG+GKTt+lr ++       +++e              ++++ v +  ++       +++ +++  l+l+
  gi|118430852|ref|NP_146917.2|  28 DGEFFVLLGPSGCGKTTTLRLIAGLE----YPDEgrilidgedvtfkdPKDRNVAMVFQNYAlyPHMSVFDNIAFTLHLR 103
                                    567899**************998875....23333455777888888866666666666666657777788888888887 PP

                         AAA_22  68 lkaerlsseelleale 83 
                                    +k+ +l+++++++++ 
  gi|118430852|ref|NP_146917.2| 104 RKEMGLTKDDIRRRVI 119
                                    7774444444444443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1     6e-06    0.0071      22      63 ..      27      69 ..      19     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrellr.alekdggiflrgkcdql 63
                                    ++e  +l G+sG+GK++ +r ++  ++ ++g i++ g+ + +
  gi|118430852|ref|NP_146917.2| 27 KDGEFFVLLGPSGCGKTTTLRLIAGlEYPDEGRILIDGEDVTF 69
                                   4558899***************995344444566666666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.4e-06    0.0088       4      75 ..      31      98 ..      28     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.4e-06
                         AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqe 75
                                     v+ G+  +GKTt l+ ++  ++ ++e  + i+ +d ++k+ +d  ++  ++++  l+    ++ ++D i  
  gi|118430852|ref|NP_146917.2| 31 FFVLLGPSGCGKTTTLRLIAGLEY-PDEGRILIDGEDVTFKDPKDR-NVAMVFQNYaLY---PHMSVFDNIAF 98
                                   6799************99998888.99***********99987766.355555554334...46778888865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.3e-06    0.0099      46      69 ..      30      53 ..      16     133 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.3e-06
                          Rad17 46 riLLisGPsGCgkstvvkvLskel 69
                                   +  ++ GPsGCgk+t+++ ++   
  gi|118430852|ref|NP_146917.2| 30 EFFVLLGPSGCGKTTTLRLIAGLE 53
                                   467889************988644 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 !   15.5   0.0   1.5e-05     0.018       2      52 ..      33      83 ..      32     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                   EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfke 52
                                   +l Gp G+GKT++ + +a         + i+g +++  +   + ++++++f++
  gi|118430852|ref|NP_146917.2| 33 VLLGPSGCGKTTTLRLIAGLEYpdEGRILIDGEDVT--FKDPKDRNVAMVFQN 83
                                   689***************874322345777777777..667777777777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3     3e-05     0.036      15      41 ..      22      51 ..       9     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                         AAA_23 15 idF...skgltlItGpNGaGKTTildAikl 41
                                   +d+   +  ++++ Gp G+GKTT l+ i  
  gi|118430852|ref|NP_146917.2| 22 VDLsikDGEFFVLLGPSGCGKTTTLRLIAG 51
                                   4555556679***************98875 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   9.2e-05      0.11       2      24 ..      32      54 ..      31      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-05
                         AAA_28  2 ivitGgestGKTtlleaLaargy 24
                                   +v++G++++GKTt+l+ +a  +y
  gi|118430852|ref|NP_146917.2| 32 FVLLGPSGCGKTTTLRLIAGLEY 54
                                   79**************9986554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.23      91     121 ..      20      51 ..       6      61 .. 0.83
   2 ?   -2.8   0.0       4.3   5.1e+03      40      57 ..     176     193 ..     158     217 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +++   +kd ++ vl+G+SG GK+t +  +++
  gi|118430852|ref|NP_146917.2|  20 DHVDLSIKDgEFFVLLGPSGCGKTTTLRLIAG 51 
                                    666667777799*************9988765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                                    HHHHHTT-EEEEEEE-GG CS
                    RsgA_GTPase  40 vlaeekgiepvivlnKiD 57 
                                    + ae k+++  + ++ + 
  gi|118430852|ref|NP_146917.2| 176 MRAELKKLQKDLKITTVY 193
                                    333333333333333332 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 ?   10.7   0.0   0.00029      0.34      14      39 ..      21      46 ..      17      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                   + +++i+  ++++l GpsG GK+T l
  gi|118430852|ref|NP_146917.2| 21 HVDLSIKDGEFFVLLGPSGCGKTTTL 46
                                   566777755599***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.37
# Mc/sec: 2945.70
//
Query:       gi|14600404|ref|NP_146918.1|  [L=373]
Description: phosphate ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for 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-52  176.9   1.1      9e-52  176.5   1.1    1.0  1  PBP_like_2  PBP superfamily domain
    1.6e-13   51.3   8.2    2.5e-13   50.6   8.2    1.3  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    8.6e-07   28.3   0.0    5.1e-06   25.7   0.0    2.2  2  PBP_like    PBP superfamily domain


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 !  176.5   1.1   1.5e-55     9e-52       3     278 ..      39     339 ..      36     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 1.5e-55
                    PBP_like_2   3 aaeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangag 83 
                                   ++ a++v  ++g Gst+++p ++++ +  +k +p +++ny +tGSgag+ a+++g vdfagsd pl  +    +w a + g
  gi|14600404|ref|NP_146918.1|  39 SGPAQVV--LQGEGSTFIYPQIQAWSEEIKKTYPWITINYNPTGSGAGQSAFKDGVVDFAGSDTPLPRE----VWSAMQ-G 112
                                   6778899..*********************************************************888....8*****.* PP

                    PBP_like_2  84 gliqvpvaigaialvvnkd..nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgttflfstal 154
                                   + iq+pv+ig +a+v+n +   +l+l+++++a I++g+I  W+d        +++lp  + I  vhrsd+sgtt +f+  l
  gi|14600404|ref|NP_146918.1| 113 NVIQIPVVIGMLAIVYNIPglEDLKLDAKTIALIYKGEIEYWDDpriaslnpGASLP-HEKIVAVHRSDSSGTTHVFTIFL 192
                                   *****************99899******************************99999.*******************9999 PP

                    PBP_like_2 155 aeq.................gpwtasgigasgsegvasav.snngaigyvsvaywlavk.gysladvtngagkfvlptaat 216
                                   ++                   ++t +g+g +g+ gv  +v ++++ igyv++ay      g  +a v+n + +f  p++++
  gi|14600404|ref|NP_146918.1| 193 HKGapdvwtedlvgksvdwpVDATGRGVGGKGNQGVMEVVkNTPYSIGYVEYAYVVKAGeGVNVALVANRDDVFLKPSPEG 273
                                   988**999999999999966566677888888********566**********8875447999****************** PP

                    PBP_like_2 217 aasalkvakias......nplaws..lqpveeniadgayPlsrftyiivyqpyayh.gnnaalakaFldyl 278
                                   a++a++ a +++      +  +ws  ++   +++++++yP++  +++++y++y      +a+++k+F++++
  gi|14600404|ref|NP_146918.1| 274 AQAAASGA-VQNlpdspdD--DWStgYDAIIYAPGKDSYPITSWSFLLFYKQY--NdRDKAEAIKKFIEWI 339
                                   *8877762.2235778563..34322788999*******************55..53555**********8 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 !   50.6   8.2   4.3e-17   2.5e-13       7     314 ..      50     345 ..      45     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.3e-17
                                   HHHHHHHHHHHH....HHHHTTEEEEEEEECHHHHHH...HHHHHHHTTS..SSCSEEEECGGHHHHHHHT...TSBECCH CS
                     SBP_bac_1   7 gaalqalvakaf....ekehpgikVeiesvgsgslaq...kltlaiaaGd..gpaDviavdndwiarlaka...glllpld 75 
                                   g+++ ++ ++a+    +k++p i+++++++gsg+++     + +++a++d   p   +++       +  +   + +  ++
  gi|14600404|ref|NP_146918.1|  50 GSTFIYPQIQAWseeiKKTYPWITINYNPTGSGAGQSafkDGVVDFAGSDtpLP-REVWS------AMQ-GnviQIPVVIG 122
                                   7788888888855555*********************99999999999995422.33444......333.24889****** PP

                                   HHHHHTTECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGG.SHBHHHHHHHHHHHHHHCTCT.HC CS
                     SBP_bac_1  76 pyvkaylapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldp.pwtWdelveaakklkekgkkp.ig 154
                                    +++ y++pg +d ++++           k        + +liY          ++  + Wd++ +a  +++++ + + i+
  gi|14600404|ref|NP_146918.1| 123 MLAIVYNIPGLEDLKLDA-----------K--------TIALIY----------KGeIEYWDDPRIASLNPGASLPHEkIV 174
                                   **********99887774...........3........999***..........33355********************** PP

                                   CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT...............HHCSHHHHS.......HHHHHHHHHHHHHHHHHH CS
                     SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgg...............gldnpegvt.......aatylvklyavanltkel 213
                                    +++++ sgt+ +f+++l k+++  +  + +g               g+ n +  +       +++y++++y v+++ ++ 
  gi|14600404|ref|NP_146918.1| 175 AVHRSDSSGTTHVFTIFLHKGAPDVWTEDLVGksvdwpvdatgrgvgGKGNQGVMEvvkntpySIGYVEYAY-VVKAGEGV 254
                                   ***********************888888888************9996666666665555577888888888.55567777 PP

                                   HTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE.EEEEEEEEBT CS
                     SBP_bac_1 214 kgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi.lgayglaipk 293
                                     + ++n d+ ++++  e  +aa+  +g  +         + ++ +d++   + +++++ +  + gk++  + ++ + +++
  gi|14600404|ref|NP_146918.1| 255 NVALVANRDDVFLKPSPEGAQAAA--SGAVQ---------NLPDSPDDDWSTG-YDAIIYA--P-GKDSYpITSWSFLLFY 320
                                   777777777777777777666666..34444.........3333333333333.3333322..2.33333579999***** PP

                                   TCST....HHHHHHHHHHHTSHHHH CS
                     SBP_bac_1 294 gskn....peaAkkFldfllspeaq 314
                                   +  n     ea+kkF++++ ++++ 
  gi|14600404|ref|NP_146918.1| 321 KQYNdrdkAEAIKKFIEWINTEGQT 345
                                   99999986777********999885 PP

>> PBP_like  PBP superfamily domain
   #    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       2     115 ..      63     194 ..      62     242 .. 0.72
   2 ?   -2.0   0.0      0.26   1.6e+03     144     190 ..     290     337 ..     268     339 .. 0.62

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.5e-10
                                   HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH.....................HCCCCCEEEEEEEEE CS
                      PBP_like   2 eelaeknpgvrvavanvGsggGlkalrageadiagshlldketee.....................ynapalrkaldgiev 61 
                                   ee++++ p +++++  +Gsg+G +a+++g +d ags+ + +++                       yn+p l+++  +++ 
  gi|14600404|ref|NP_146918.1|  63 EEIKKTYPWITINYNPTGSGAGQSAFKDGVVDFAGSDTPLPRE-VwsamqgnviqipvvigmlaivYNIPGLEDLKLDAK- 141
                                   7899999********************************7743.223444444444444444445566666666544432. PP

                                   EEE-CC-HCHCCCCHCCHHHS--BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC- CS
                      PBP_like  62 vlvnlarreqglvvakgnpkkitnwkdladaplrlvnRetGSGtrdlfdellkk 115
                                   +++  ++ e+++   +     ++  + l+ ++++ v R  +SGt ++f+  l+k
  gi|14600404|ref|NP_146918.1| 142 TIALIYKGEIEYWDDPRIA-SLNPGASLPHEKIVAVHRSDSSGTTHVFTIFLHK 194
                                   4444444455555444422.466667899*******************999865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.26
                                   TTCCECCCGG-HCCCCCCECTTCE-EEEEEEEECTCCCS..HHHHHHHH CS
                      PBP_like 144 radvgvgieavaeelkgldfvplaeerydlvvrkealdd..pevqafle 190
                                   + d++ g +a+   + g d  p++ +++ l +++    d  +++++f+e
  gi|14600404|ref|NP_146918.1| 290 DDDWSTGYDAIIY-APGKDSYPITSWSFLLFYKQYNDRDkaEAIKKFIE 337
                                   5566666666663.45667778888888777776543332266777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3146.44
//
Query:       gi|118430853|ref|NP_146919.2|  [L=310]
Description: phosphate ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-13   48.7  15.7    7.2e-13   48.7  15.7    2.5  2  BPD_transp_1   Binding-protein-dependent transport system inn


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   3.2     0.063   1.1e+03     155     170 ..      21      36 ..       1      45 [. 0.41
   2 !   48.7  15.7     4e-17   7.2e-13      15     179 ..     105     302 ..      91     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.063
                   BPD_transp_1 155 nggvlalviavlllnl 170
                                    + +++ ++++v+ll  
  gi|118430853|ref|NP_146919.2|  21 ISASILVILFVVLLYY 36 
                                    2233333333333333 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 4e-17
                   BPD_transp_1  15 kldkllrpliivllslPsfvlaillvlvf......................vilsilghlilpviillllsaapyvrlir 72 
                                    ++++++ ++++++ +lP++v ++  v ++                      + +   g++il + +ll+l+++p+++ ++
  gi|118430853|ref|NP_146919.2| 105 RVREAFNTIVDMMTGLPTIVYGLWGVTFLapalkgtllewlytylsfiplfSCKPLTGTTILTASLLLALMIVPFIYSVV 184
                                    68999***************66666655566677788888888899999987788899********************** PP

                   BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.......lgtllleai 145
                                    r+  r++p+ ++eaa+ lG ++ + + + +l ++ p i++g+++ fg++ g++v++ ++ +++          + +++++
  gi|118430853|ref|NP_146919.2| 185 RESYRQIPRTYREAALSLGTTKYE-YTRLMLGMVRPAILAGVLIGFGRAAGETVAVALVVGNTFnmptcllAPSYTVSSL 263
                                    ************************.999********************************66635555555333333333 PP

                   BPD_transp_1 146 lgydyseis.............nggvlalviavlllnlvadilqrll 179
                                            +               +++a+++++l+l +v++il    
  gi|118430853|ref|NP_146919.2| 264 --------IanqfanaslypymTNVLVAGGLFLLALGIVTNILGLSY 302
                                    ........344445555777777999***************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2542.77
//
Query:       gi|14600406|ref|NP_146920.1|  [L=284]
Description: phosphate ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-16   58.3  12.0      8e-16   58.3  12.0    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   3.1     0.015   2.6e+02      11      60 ..       6      81 ..       1      85 [. 0.73
   2 !   58.3  12.0   4.5e-20     8e-16       1     178 [.      83     277 ..      83     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.015
                  BPD_transp_1 11 nrnkkldkllrpliivllslPsfvlaillvlvf..........................vilsilghlilpviill 60
                                  + + k   ll +li ++   P f ++ +++l                            v   ilg+l+l++ +++
  gi|14600406|ref|NP_146920.1|  6 RLKEKAFILLVTLITLVTVAPLFHIIAMVTLKGsyvivkagiefftatpgppgseilggVGPAILGSLWLAITTAI 81
                                  5666777789999999999999998888887768888999999999888888886666655555555555544444 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 4.5e-20
                  BPD_transp_1   1 gillGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                   g++l++l+a     +r ++l k+  +++  ll +P++++++l++lv  + +  gh+ l  + i+l++ ++py++  +++al
  gi|14600406|ref|NP_146920.1|  83 GVPLSVLTAifivEYRENPLAKIAKVFSGSLLEIPTVLIGMLVFLV--VVTPMGHYSLLaGSIALAIVMLPYTVSYVERAL 161
                                   78888899988889****************************9975..88999999988899999**************** PP

                  BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis... 154
                                   +++pk ++ea + lG++r q++ kvv+  a + i++g+++ +  ++ +++ l+f++++   +++l  + l ++ ++     
  gi|14600406|ref|NP_146920.1| 162 ENVPKTYREAGYSLGMTRAQVVAKVVVGIARRGIAAGVLIGLSKVVAETAPLLFTIGSARSNYPLYPSDLLQPGDALPlli 242
                                   ********************************************************8888888888888888888777888 PP

                  BPD_transp_1 155 ..............nggvlalviavlllnlvadilqrl 178
                                                 +   +  ++++ +++l+++  +rl
  gi|14600406|ref|NP_146920.1| 243 fqfaqtpyenwqelA---WGSAFILTAIVLATFSAMRL 277
                                   888888899996663...44444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2337.83
//
Query:       gi|14600407|ref|NP_146921.1|  [L=253]
Description: phosphate ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-36  123.9   0.0    8.7e-36  123.4   0.0    1.2  1  ABC_tran        ABC transporter
    2.2e-10   40.9   0.1    0.00015   21.7   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    8.4e-08   31.9   0.0     0.0011   18.4   0.0    2.1  2  SMC_N           RecF/RecN/SMC N terminal domain
    3.9e-05   23.3   0.1    7.1e-05   22.5   0.1    1.4  1  AAA_29          P-loop containing region of AAA domain
    9.4e-05   21.7   0.0    0.00011   21.4   0.0    1.1  1  NB-ARC          NB-ARC domain
    0.00021   21.2   0.1     0.0013   18.6   0.0    2.0  2  RsgA_GTPase     RsgA GTPase
    0.00057   19.9   0.0     0.0021   18.0   0.0    1.8  2  Rad17           Rad17 P-loop domain
     0.0013   18.5   0.1      0.014   15.1   0.0    2.1  2  AAA_30          AAA domain
     0.0027   18.2   0.1     0.0052   17.3   0.1    1.4  1  AAA_23          AAA domain
     0.0033   18.0   0.0     0.0071   16.9   0.0    1.5  1  AAA_18          AAA domain
     0.0037   17.5   0.2      0.011   16.0   0.1    2.0  1  AAA_22          AAA domain
     0.0043   16.8   0.0       0.36   10.5   0.0    2.1  2  AAA_15          AAA ATPase domain
     0.0074   16.7   0.1      0.024   15.0   0.0    1.8  2  AAA_16          AAA ATPase domain
  ------ inclusion threshold ------
       0.02   13.7   0.1      0.031   13.1   0.1    1.2  1  Adeno_IVa2      Adenovirus IVa2 protein
       0.02   15.1   0.0       0.03   14.5   0.0    1.6  1  AAA_33          AAA domain
      0.024   13.4   0.1       0.71    8.6   0.1    2.1  2  ABC_ATPase      Predicted ATPase of the ABC class
      0.031   14.7   0.0        0.7   10.3   0.0    2.4  1  AAA             ATPase family associated with various cellula
      0.048   13.6   0.0      0.094   12.6   0.0    1.4  1  ATPase_2        ATPase domain predominantly from Archaea
       0.07   12.9   0.0       0.12   12.1   0.0    1.4  1  PRK             Phosphoribulokinase / Uridine kinase family
      0.079   13.3   0.7        1.7    9.0   0.1    2.2  2  AAA_19          AAA domain
      0.095   12.8   0.2       0.21   11.6   0.1    1.6  2  DUF87           Helicase HerA, central domain
       0.11   12.1   0.1       0.42   10.2   0.0    1.9  2  AAA_25          AAA domain
       0.12   12.0   0.1       0.26   10.8   0.0    1.6  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
       0.13   11.2   0.0       0.22   10.4   0.0    1.3  1  AAA_PrkA        PrkA AAA domain
       0.14   11.8   0.1        0.3   10.8   0.0    1.5  2  Cytidylate_kin  Cytidylate kinase
       0.15   11.1   0.1       0.32   10.0   0.0    1.5  2  DUF3987         Protein of unknown function (DUF3987)
       0.16   12.1   0.2       0.49   10.5   0.0    1.8  2  MMR_HSR1        50S ribosome-binding GTPase
       0.16   11.7   0.1       0.44   10.2   0.0    1.7  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 !  123.4   0.0   1.4e-38   8.7e-36       1     137 []      21     177 ..      21     177 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1.4e-38
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                   lk +s+k ++g+++ai+G++G+GKStL++++ +l +       eGe+++++ ++ +++    r+  g+++qep+ fp++t+
  gi|14600407|ref|NP_146921.1|  21 LKGISFKAQPGTVTAIMGPSGSGKSTLIRVINRLIDLipgarVEGEVWINNMNVMKEDPYNIRRYTGMVFQEPNPFPHMTI 101
                                   789*******************************998889999*******9999999************************ PP

                                   HHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  77 ren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                   +en               e de +e al+   l +  ++++++ p++LSgGq+qr++laral+ kp++lllDEpta
  gi|14600407|ref|NP_146921.1| 102 YENvaigpklhglaknkkELDEIVEWALKMAHLWDEVKDRLSDYPHQLSGGQRQRLSLARALALKPRVLLLDEPTA 177
                                   *************97766666669**************************************************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 !   17.3   0.0     5e-06    0.0032       1      25 [.      33      57 ..      33      83 .. 0.84
   2 !   21.7   0.0   2.3e-07   0.00015     231     299 ..     143     209 ..     120     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                  ++++ Gp gsGKS+L++ +  l +l
  gi|14600407|ref|NP_146921.1| 33 VTAIMGPSGSGKSTLIRVINRLIDL 57
                                  699****************999665 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.3e-07
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHP....kllrrllellkelsrngaQviltTHSp 299
                                      +++lS G+++ l l+ al+  +   ++ll+DEp ++++P    k+  +++e  ke+ +    vi++TH p
  gi|14600407|ref|NP_146921.1| 143 SDYPHQLSGGQRQRLSLARALALKP---RVLLLDEPTANIDPvstvKIEQSIVEYAKEEMA---TVIIVTHTP 209
                                   4467899******999999999877...**************6666666666666666666...*******76 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   0.0    0.0002      0.13      25      44 ..      32      51 ..      19      57 .. 0.85
   2 !   18.4   0.0   1.8e-06    0.0011     135     205 ..     110     215 ..      59     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                                  SEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                   +tai+Gp GSGKs l+  i
  gi|14600407|ref|NP_146921.1| 32 TVTAIMGPSGSGKSTLIRVI 51
                                  589************99766 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-06
                                   T.....................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                   x.....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 135 e.....................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                   +                                     +LSgG+++ ++la  +A++   p+ + llDe  a++D   + k
  gi|14600407|ref|NP_146921.1| 110 KlhglaknkkeldeivewalkmahlwdevkdrlsdyphQLSGGQRQRLSLARALALK---PR-VLLLDEPTANIDPVSTVK 186
                                   055555555555555555555555555566666666669************999975...55.5699************** PP

                                   HHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                   xxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                         SMC_N 179 vaellkekskn..aQfivislreemleka 205
                                   + + + e  k+  a +i+++++ ++ ++ 
  gi|14600407|ref|NP_146921.1| 187 IEQSIVEYAKEemATVIIVTHTPQQAARI 215
                                   999998766655599******99887765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.1e-07   7.1e-05      13      39 ..      22      48 ..      12      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                  +g +++ ++  +t ++GpsGsGKSTl+
  gi|14600407|ref|NP_146921.1| 22 KGISFKAQPGTVTAIMGPSGSGKSTLI 48
                                  555667776679**************9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.8e-07   0.00011      16     111 ..      28     174 ..      17     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-07
                                   TTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE...................................... CS
                        NB-ARC  16 delqslvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv...................................... 57 
                                    +++  v a++G  G+GK+tl++ i++  d + g r ++ +w+                                      
  gi|14600407|ref|NP_146921.1|  28 AQPG-TVTAIMGPSGSGKSTLIRVINRLIDLIPGaRVEGEVWInnmnvmkedpynirrytgmvfqepnpfphmtiyenvai 107
                                   5666.7899***********************999********************************************** PP

                                   ................EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEEE CS
                        NB-ARC  58 ................vvsktdkseeiletilkeLslseddleekeeveslkrklvrlLltkrfllvlDD 111
                                                    v    k  ++++++  +Ls+  ++l+  + +      l r+L  k  +l+lD 
  gi|14600407|ref|NP_146921.1| 108 gpklhglaknkkeldeIVEWALKMAHLWDEVKDRLSDYPHQLSGGQRQ---RLSLARALALKPRVLLLDE 174
                                   ***************9999999*************9998888877744...48999****9977888884 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   2.1e-06    0.0013      87     120 ..      18      52 ..       3      63 .. 0.77
   2 ?   -0.1   0.0       1.2   7.4e+02      30      54 ..     182     206 ..     165     226 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                                   HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                   RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                   k+ l+ ++ + +   +++++G+SG GKStLi +++
  gi|14600407|ref|NP_146921.1|  18 KHILKGISFKAQPgTVTAIMGPSGSGKSTLIRVIN 52 
                                   4456666766666699***************9886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                   --HHHHHHHHHHHHHTT-EEEEEEE CS
                   RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivln 54 
                                   +s+  +++ +v++ ++++  vi+++
  gi|14600407|ref|NP_146921.1| 182 VSTVKIEQSIVEYAKEEMATVIIVT 206
                                   3444455555555555554444444 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   3.3e-06    0.0021      34     112 ..      20     105 ..      15     123 .. 0.77
   2 ?   -0.9   0.0       2.1   1.4e+03      17      37 ..     110     130 ..     106     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.3e-06
                         Rad17  34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskel....gikl..rewlnpvs.lkepdnqksdfkgltekesrflsqie 107
                                    lk  + + ++  +  i GPsG gkst ++v+ +      g ++  + w+n ++ +ke +++   + g++ +e +  + + 
  gi|14600407|ref|NP_146921.1|  20 ILKGISFKAQPGTVTAIMGPSGSGKSTLIRVINRLIdlipGARVegEVWINNMNvMKEDPYNIRRYTGMVFQEPNPFPHMT 100
                                   6777788889999999***************99854222255552246999998457888899999999988888888888 PP

                         Rad17 108 sfkel 112
                                    ++++
  gi|14600407|ref|NP_146921.1| 101 IYENV 105
                                   88766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                         Rad17  17 kaeelavhkkkieevkewlka 37 
                                   k++ la  kk ++e+ ew   
  gi|14600407|ref|NP_146921.1| 110 KLHGLAKNKKELDEIVEWALK 130
                                   67899999******9999544 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   2.2e-05     0.014      17      49 ..      30      63 ..      25      67 .. 0.82
   2 ?    1.3   0.0      0.39   2.5e+02      37      63 ..     190     216 ..     128     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                        AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.ggrv 49
                                  +  v+++ Gp G+GK+t++++++++++   g rv
  gi|14600407|ref|NP_146921.1| 30 PGTVTAIMGPSGSGKSTLIRVINRLIDLIpGARV 63
                                  56799*****************999876655555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.39
                        AAA_30  37 alreaweaaggrviglAptgkaAkvLa 63 
                                   +++e ++++  +vi++++t ++A++++
  gi|14600407|ref|NP_146921.1| 190 SIVEYAKEEMATVIIVTHTPQQAARIS 216
                                   344455555556666666666666555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   8.1e-06    0.0052      20      39 ..      32      51 ..      14      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.1e-06
                        AAA_23 20 gltlItGpNGaGKTTildAi 39
                                   +t+I Gp G+GK+T+++ i
  gi|14600407|ref|NP_146921.1| 32 TVTAIMGPSGSGKSTLIRVI 51
                                  59***************987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-05    0.0071       3      45 ..      36      81 ..      35      96 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                        AAA_18  3 ltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpea 45
                                  ++G++G+GK+tl + ++++  +    ++ ++v+ +n+ +  +dp+ 
  gi|14600407|ref|NP_146921.1| 36 IMGPSGSGKSTLIRVINRLIDLipgARVEGEVWINNMNVMKEDPYN 81
                                  89**************998766894444445555555555555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.7e-05     0.011       5      28 ..      31      54 ..      28     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                        AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                   ++++++G+sG+GK+tl+r + + 
  gi|14600407|ref|NP_146921.1| 31 GTVTAIMGPSGSGKSTLIRVINRL 54
                                  57899************9977665 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   0.00057      0.36      20      48 ..      25      56 ..      21      87 .. 0.79
   2 ?    4.5   0.0     0.038        24     295     366 ..     147     209 ..     100     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00057
                        AAA_15 20 dlsee...ltvliGkNnsGKSsilealdlFln 48
                                  +++ +   +t + G+ +sGKS+++++++ +++
  gi|14600407|ref|NP_146921.1| 25 SFKAQpgtVTAIMGPSGSGKSTLIRVINRLID 56
                                  555556679******************99987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                        AAA_15 295 nknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                   ++ + G+++ l+l+  ++ +         + +ll++EP a++ p     + +++ e a+++   vii TH+p
  gi|14600407|ref|NP_146921.1| 147 HQLSGGQRQRLSLARALALK---------PRVLLLDEPTANIDPVSTVKIEQSIVEYAKEEMATVIIVTHTP 209
                                   56666666666655544443.........3569****************************99*******98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.7e-05     0.024      25      46 ..      32      53 ..      21      70 .. 0.85
   2 ?   -1.0   0.0         3   1.9e+03     134     143 ..     165     174 ..     109     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-05
                        AAA_16 25 elvllsGesGvGKsslvrellr 46
                                   ++ + G+sG+GKs+l+r + r
  gi|14600407|ref|NP_146921.1| 32 TVTAIMGPSGSGKSTLIRVINR 53
                                  6789*************98876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                        AAA_16 134 erplvlvlDd 143
                                    +p vl+lD+
  gi|14600407|ref|NP_146921.1| 165 LKPRVLLLDE 174
                                   2345555554 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.8e-05     0.031      78     117 ..      21      59 ..      10      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                    Adeno_IVa2  78 lsslnyglqP.viGviyGPtGsGksqllrnlissklisPiP 117
                                   l  + ++ qP  +  i GP GsGks l+r +  ++li+ iP
  gi|14600407|ref|NP_146921.1|  21 LKGISFKAQPgTVTAIMGPSGSGKSTLIRVI--NRLIDLIP 59 
                                   666778888856889**************64..78888877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.6e-05      0.03       2      44 ..      34      79 ..      33     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklg...avllssdtlrrrlfgtdqqs 44
                                  + + G++GsGKstl++ + +  +   + +++  ++++++ + ++++
  gi|14600407|ref|NP_146921.1| 34 TAIMGPSGSGKSTLIRVINRLIDlipGARVEGEVWINNMNVMKEDP 79
                                  5678**********98653322255588999999888888754443 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 ?    8.6   0.1    0.0011      0.71     244     266 ..      30      53 ..      11      60 .. 0.78
   2 ?    2.7   0.0     0.068        44     324     371 ..     150     197 ..     145     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                                   SS.EEEEEE-TTSSHHHHHHHHHH CS
                    ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAlek 266
                                    G vt+I+G+   GKsTL++ +++
  gi|14600407|ref|NP_146921.1|  30 PGtVTAIMGPSGSGKSTLIRVINR 53 
                                   346*****************9987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.068
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG- CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskeke 371
                                   SG   q  ++++al ++ ++lL+DE t+    +   +  q++v+  ke
  gi|14600407|ref|NP_146921.1| 150 SGGQRQRLSLARALALKPRVLLLDEPTANIDPVSTVKIEQSIVEYAKE 197
                                   899999999****************99866655555555555555555 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 ?   10.3   0.0    0.0011       0.7       3      66 ..      36     174 ..      34     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                   EESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSS............................................. CS
                           AAA   3 lyGppGtGKTllakavakelg.vefleisgsellsk............................................. 37 
                                   ++Gp G GK++l++ + + ++ ++  +++g   +++                                             
  gi|14600407|ref|NP_146921.1|  36 IMGPSGSGKSTLIRVINRLIDlIPGARVEGEVWINNmnvmkedpynirrytgmvfqepnpfphmtiyenvaigpklhglak 116
                                   689***********9988874333233333333322232223445555555555555666666666666666666666666 PP

                                   ............................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                           AAA  38 ............................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                               y  + +   r+ ++ a++ a kp +l++DE
  gi|14600407|ref|NP_146921.1| 117 nkkeldeivewalkmahlwdevkdrlsdYPHQLSGGQRQRLSLARALAlKPRVLLLDE 174
                                   6666666666666666666666667776777777777777777777777777777777 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   0.00015     0.094      17      40 ..      28      51 ..      20      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                      ATPase_2 17 repneiyfiYGpegsGKtaLlkei 40
                                   +p ++  i Gp gsGK++L++ i
  gi|14600407|ref|NP_146921.1| 28 AQPGTVTAIMGPSGSGKSTLIRVI 51
                                  57889999*************965 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.12       2      41 ..      34      71 ..      33     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                           PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrl 41
                                   ++ g+SG+Gk+t+ r ++ ++    ++ a +eg + ++ 
  gi|14600407|ref|NP_146921.1| 34 TAIMGPSGSGKSTLIRVINRLID--LIPGARVEGEVWINN 71
                                  589****************9999..677777776665543 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0026       1.7       7      34 ..      28      55 ..      22      67 .. 0.83
   2 ?    2.5   0.0      0.27   1.7e+02      31      62 ..     188     219 ..     182     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0026
                        AAA_19  7 alkekvllvtaGpGtGKTrvlkhivall 34
                                  a + +v +++++ G+GK+++++ i +l+
  gi|14600407|ref|NP_146921.1| 28 AQPGTVTAIMGPSGSGKSTLIRVINRLI 55
                                  56778999*************9887665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.27
                        AAA_19  31 vallvelggvkpeeillvaftgrAakelrerl 62 
                                    + +ve  +++++++++v+ t + a ++++++
  gi|14600407|ref|NP_146921.1| 188 EQSIVEYAKEEMATVIIVTHTPQQAARISDQI 219
                                   4556677777789***************9987 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00033      0.21      26      45 ..      34      53 ..      32      63 .. 0.87
   2 ?   -2.1   0.0       5.1   3.3e+03     182     182 ..     177     177 ..     110     218 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                         DUF87 26 lAilgsTGsGKSntvavLle 45
                                  +Ai+g +GsGKS++++v+ +
  gi|14600407|ref|NP_146921.1| 34 TAIMGPSGSGKSTLIRVINR 53
                                  59***************965 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.1
                         DUF87 182 f 182
                                    
  gi|14600407|ref|NP_146921.1| 177 A 177
                                   2 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00066      0.42      32      50 ..      30      48 ..       2      52 .. 0.87
   2 ?   -0.9   0.0       1.6     1e+03     176     192 ..     195     211 ..     154     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                        AAA_25 32 agelallaGapgtGKttla 50
                                   g++++++G++g+GK+tl 
  gi|14600407|ref|NP_146921.1| 30 PGTVTAIMGPSGSGKSTLI 48
                                  699**************95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                        AAA_25 176 arrtgaavllvhHvgKe 192
                                   a++  a+v++v H+  +
  gi|14600407|ref|NP_146921.1| 195 AKEEMATVIIVTHTPQQ 211
                                   55566899999998765 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 ?   10.8   0.0   0.00041      0.26       2      20 ..      33      51 ..      32      91 .. 0.73
   2 ?   -2.3   0.0       4.6   2.9e+03      94     118 ..     179     202 ..     157     219 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                                  EEEEEESTTCCHHHHHHHH CS
                          cobW  2 vtvltGflGsGKTtLlnhl 20
                                  vt + G+ GsGK+tL++ +
  gi|14600407|ref|NP_146921.1| 33 VTAIMGPSGSGKSTLIRVI 51
                                  899************9765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.6
                                   TTHHHHHTTSHHHHHCCCECEEEEE CS
                          cobW  94 aePapvafteeelksdltldavvav 118
                                    +P   +  e+++ + ++++ + +v
  gi|14600407|ref|NP_146921.1| 179 IDPVSTVKIEQSIVEYAKEE-MATV 202
                                   44444433333333322222.2222 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00035      0.22      91     130 ..      34      80 ..      27      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                      AAA_PrkA  91 lyllGPvggGksslverlkklleaa.......piyalegsPvfeePl 130
                                     ++GP g+Gks+l+  + +l++          +++ ++  ++e+P+
  gi|14600407|ref|NP_146921.1|  34 TAIMGPSGSGKSTLIRVINRLIDLIpgarvegEVWINNMNVMKEDPY 80 
                                   568*******************9984444444444446666666665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046       0.3       2      20 ..      35      53 ..      34      58 .. 0.86
   2 ?   -3.1   0.0       8.3   5.3e+03      82      95 ..     184     197 ..     158     226 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                                  EEE-STTSSHHHHHHHHHH CS
                Cytidylate_kin  2 aiDGPagsGKssvaralae 20
                                  ai GP+gsGKs++ r + +
  gi|14600407|ref|NP_146921.1| 35 AIMGPSGSGKSTLIRVINR 53
                                  899**********998865 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.3
                                   SHHHHHHHHHHTTS CS
                Cytidylate_kin  82 sdevekavSavaai 95 
                                   + ++e+ + ++a+ 
  gi|14600407|ref|NP_146921.1| 184 TVKIEQSIVEYAKE 197
                                   33333333333332 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0005      0.32      34      62 ..      29      57 ..      21      62 .. 0.87
   2 ?   -3.6   0.0       6.7   4.3e+03     303     317 ..     119     133 ..     114     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0005
                       DUF3987 34 plnLytlvvapsGerKSpvdklvlrplee 62
                                  ++   t++++psG++KS++ +++ r++  
  gi|14600407|ref|NP_146921.1| 29 QPGTVTAIMGPSGSGKSTLIRVINRLIDL 57
                                  577789***************99999875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.7
                       DUF3987 303 gdledirdwasKlag 317
                                   ++l++i +wa K+a 
  gi|14600407|ref|NP_146921.1| 119 KELDEIVEWALKMAH 133
                                   455667777777764 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   0.00077      0.49       3      19 ..      35      51 ..      33      69 .. 0.86
   2 ?   -1.6   0.0       4.4   2.8e+03      95     109 ..     189     203 ..     147     224 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00077
                                  EEEESTTSSHHHHHHHH CS
                      MMR_HSR1  3 aivGrpNvGKStLinal 19
                                  ai+G + +GKStLi+ +
  gi|14600407|ref|NP_146921.1| 35 AIMGPSGSGKSTLIRVI 51
                                  89***********9876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                                   HHHHHHHHHTTSEEE CS
                      MMR_HSR1  95 eeleelleeakkpli 109
                                   +++ e+ +e++  +i
  gi|14600407|ref|NP_146921.1| 189 QSIVEYAKEEMATVI 203
                                   333333333333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00069      0.44       4      22 ..      33      51 ..      31      58 .. 0.84
   2 ?   -2.7   0.0       6.3     4e+03      34      47 ..     175     188 ..     159     218 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00069
                        AAA_24  4 kiliyGpsgiGKTtlakel 22
                                    +i+Gpsg+GK+tl++ +
  gi|14600407|ref|NP_146921.1| 33 VTAIMGPSGSGKSTLIRVI 51
                                  578************9765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.3
                        AAA_24  34 Glksldadkfpdie 47 
                                    ++++d+   ++ie
  gi|14600407|ref|NP_146921.1| 175 PTANIDPVSTVKIE 188
                                   45555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 1821.70
//
Query:       gi|14600408|ref|NP_146922.1|  [L=201]
Description: phosphate transport system protein PhoU [Aeropyrum pernix K1]
Scores for complete 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   92.9  11.4    7.8e-16   58.3   5.0    2.1  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.084   13.6   0.3       0.26   12.0   0.1    1.9  2  PMC2NT    PMC2NT (NUC016) domain


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 !   38.8   0.4   1.1e-13   9.4e-10       1      88 [.      17     102 ..      17     103 .. 0.91
   2 !   58.3   5.0   8.7e-20   7.8e-16       2      88 ..     120     199 ..     119     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.1e-13
                                   HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                   l+rm +iv +++ d+l++lee    + +++ +    +++l   +e+++ + +ak+qpl+ +l e+ sl+r ++dl+Ri+++
  gi|14600408|ref|NP_146922.1|  17 LDRMYNIVVKIVADTLRSLEEWS--INEALEDHLYLAENLSAVVEEQATFFIAKYQPLGPELLEAKSLIRTSYDLYRIARY 95 
                                   68*****************9965..446666678999999999****99999***************************** PP

                                   HHHHHHH CS
                          PhoU  82 avniaer 88 
                                   +++i + 
  gi|14600408|ref|NP_146922.1|  96 CREINRV 102
                                   ****876 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 8.7e-20
                                   HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDha 82 
                                   r+ aeiv +m+ da++a++++d el r+v e d+ id++++++ +++ +  + +q +a         l i+r+lERi+Dha
  gi|14600408|ref|NP_146922.1| 120 RKAAEIVASMVGDAYKAYRSRDNELRRKVEETDNMIDKIYDAMLERIGKVESLSQTEAV-------DLLIVRHLERIADHA 193
                                   7889**************************************98884333344444433.......3679*********** PP

                                   HHHHHH CS
                          PhoU  83 vniaer 88 
                                   v ia+ 
  gi|14600408|ref|NP_146922.1| 194 VYIARQ 199
                                   ****96 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.44     4e+03      28      53 ..      16      41 ..       7      59 .. 0.53
   2 ?   12.0   0.1   2.9e-05      0.26      10      56 ..     125     175 ..     117     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.44
                        PMC2NT 28 sldeqserllslinsllklaasksei 53
                                  +ld+  + +++++ + l+++++ s +
  gi|14600408|ref|NP_146922.1| 16 NLDRMYNIVVKIVADTLRSLEEWSIN 41
                                  45555555666666666666555444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.9e-05
                        PMC2NT  10 Lp....aeDldfyrsldpefaksldeqserllslinsllklaaskseisas 56 
                                   +     ++ ++ yrs d+e++++++e+ + + ++ +++l+ +++ ++ s++
  gi|14600408|ref|NP_146922.1| 125 IVasmvGDAYKAYRSRDNELRRKVEETDNMIDKIYDAMLERIGKVESLSQT 175
                                   33355599********************************99999888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 1623.26
//
Query:       gi|118430854|ref|NP_146923.2|  [L=171]
Description: hypothetical protein APE_0052.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.2   0.8       0.31   11.3   0.8    1.5  1  DUF4148   Domain of unknown function (DUF4148)
       0.55   10.1   3.4        1.2    9.1   3.4    1.6  1  PsbN      Photosystem II reaction centre N protein (psbN)


Domain annotation for each model (and alignments):
>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   3.4e-05      0.31       3      31 ..       3      40 ..       1      43 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.4e-05
                        DUF4148  3 stliaaalaaavaaaaala..........ahskspkTRA 31
                                   +t+ a+a+++a++++a  a          +++ +++TRA
  gi|118430854|ref|NP_146923.2|  3 RTI-AIAAVLALVFIAIGAyaiytseysdVSTLQSVTRA 40
                                   444.55555566666666679********99*******9 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.4   0.00013       1.2       4      26 ..       4      26 ..       1      27 [. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00013
                           PsbN  4 AtvlsisiaavlvaiTgfsiYta 26
                                   +++++  +a v +ai +++iYt+
  gi|118430854|ref|NP_146923.2|  4 TIAIAAVLALVFIAIGAYAIYTS 26
                                   567778889999**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1499.36
//
Query:       gi|118430855|ref|NP_146924.2|  [L=286]
Description: fumarylacetoacetate hydrolase [Aeropyrum pernix K1]
Scores for 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-58  195.9   0.0    8.6e-58  195.6   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.6   0.0   4.8e-62   8.6e-58       3     218 .]      80     280 ..      78     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 4.8e-62
                                    EEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHH CS
                  FAA_hydrolase   3 vcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAe 82 
                                    +++g++yaeh+re+g     +++     + +ff k+ +sl+g+ +p+++P  sek+dyE+E++++igk+++++ s +eA 
  gi|118430855|ref|NP_146924.2|  80 WGVGRSYAEHAREMG-----MSK-----QIAFFSKPVTSLTGHLNPVVVPPVSEKPDYEGEIVIIIGKRIKNA-STAEAG 148
                                    789**********98.....344.....3369*****************************************.99**** PP

                                    TTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGTTTSHHH CS
                  FAA_hydrolase  83 daiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdmifspae 162
                                    +aiaGyt++ D++ R lq+       w  +k+ dt  p+Gp+++  d+ +d + l + +++nge+vq++ t dmi+s+++
  gi|118430855|ref|NP_146924.2| 149 KAIAGYTAGADITDRLLQDMM----SWSMAKGLDTYGPVGPVATIIDSPDDLDGLCVHTWLNGEKVQRGCTGDMIVSIPD 224
                                    *****************9544....6****************************************************** PP

                                    HHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                  FAA_hydrolase 163 liahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                    ++++lsa+ tL+pGd+++tGTp+gvg++++++++l++gDe+ev+++gl  lrn+++
  gi|118430855|ref|NP_146924.2| 225 MVSRLSALATLRPGDIVFTGTPPGVGHARKPPRYLRHGDELEVRVSGLPPLRNQIV 280
                                    **************************99*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2150.56
//
Query:       gi|118430856|ref|NP_146925.2|  [L=176]
Description: hypothetical protein APE_0054.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1345.79
//
Query:       gi|14600412|ref|NP_146926.1|  [L=430]
Description: hypothetical protein APE_0055 [Aeropyrum pernix K1]
Scores for 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  114.2  28.5    6.4e-33  114.2  28.5    1.6  1  CitMHS    Citrate transporter
  ------ inclusion threshold ------
        5.4    5.7  29.7       0.15   10.9  11.2    2.5  2  DctM      Tripartite ATP-independent periplasmic transporter,


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 !  114.2  28.5   7.1e-37   6.4e-33       2     297 ..      14     369 ..      12     372 .. 0.72

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 7.1e-37
                                   xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS   2 vllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvll 78 
                                   +l++   ++  ++al ++++l      t+eea++ + +++i++llg+ ii+++++e G+ +  ++ + r ag+ r+ l+ +
  gi|14600412|ref|NP_146926.1|  14 MLVVSRYVDEVAAALAGVTALilltNYTPEEAFNFVEWNVIAILLGMWIIAGYMIEGGFTEATIRLVSRSAGTYRKFLLYM 94 
                                   566666677778888777777878999***********************************************998888* PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxx RF
                        CitMHS  79 vlltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraa.............arpgl 146
                                   +ll++++s+f++n+ v+l++++++++ ak+ +++p+l++++++++an +g+++++G+ +                 +r ++
  gi|14600412|ref|NP_146926.1|  95 ALLSGFISMFIDNVLVILLVGSLTIAAAKKAGGNPVLAILLVGFSANFMGTALLMGDLPPQLLhtiagaefldfiwTRGKP 175
                                   *********************************************************933333677777777777744443 PP

                                   xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                        CitMHS 147 slpnlll.lalllvgllplvllfmfgvalalpvnap............................................. 181
                                   s + ll  + ll  g+++++++          +n                                               
  gi|14600412|ref|NP_146926.1| 176 SSFPLLTaTFLLTLGVFYILFIR-------REPNSRiddaglsgestnrgglliisltfftmtviamalrpllgfplgfit 249
                                   33333223333333334444443.......111111222223322222222222222222222222222222223344455 PP

                                   .xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxx RF
                        CitMHS 182 .kvkkqkaiieaiarsllpvatillla.....ykkveWsvlllfaGvfllvgaleqtGilealadll.ga..ggplvalal 253
                                     +++q a++  + r+l   a++   +     +k+veW  ll+ a++f lvg+le  G++e +a ll g+  + p++a+++
  gi|14600412|ref|NP_146926.1| 250 mAGASQLALTVEVLRRLG-LAGM---VefenaLKHVEWRALLFYAALFSLVGGLESEGVIEEIARLLvGSvsSDPAIAYTV 326
                                   555555555555555444.4444...15679************************************777854888999** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        CitMHS 254 vlgliallsafisnvavaalmapialgmapalgllspsplalal 297
                                   +++ ++lls++i  +a+ ++++ i+  +a+ +g ++p  +++ +
  gi|14600412|ref|NP_146926.1| 327 MYWSVGLLSLVIEHDALLLTFLYIVKDAASLAG-IDPWNIYWGM 369
                                   *****************9999999999888666.5555566655 PP

>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  11.2   1.7e-05      0.15     276     364 ..      51     139 ..       2     146 .. 0.81
   2 ?    0.5  10.5     0.023   2.1e+02     243     415 ..     250     429 ..     180     430 .] 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.7e-05
                          DctM 276 aavlfilaaagifaglltltgvplklselllslsggkllfLilvnllvlvlGmfldttaaiiilvpilaPaaaklgidpih 356
                                     v++il ++ i+ag +   g+  +  +l++  +g+   fL+ ++ll+ ++ mf+d + +i++++ + ++aa+k+g +p+ 
  gi|14600412|ref|NP_146926.1|  51 WNVIAILLGMWIIAGYMIEGGFTEATIRLVSRSAGTYRKFLLYMALLSGFISMFIDNVLVILLVGSLTIAAAKKAGGNPVL 131
                                   6799*************9999999999999999999999****************************************** PP

                          DctM 357 fgvvivln 364
                                   + +++ + 
  gi|14600412|ref|NP_146926.1| 132 AILLVGFS 139
                                   **999875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.023
                          DctM 243 vavvyalviallvyrrltleevaaallstakttaavlfilaaagifaglltltgvplklselllslsggkllfLilvnllv 323
                                   +a +  l++++ v rrl l+ + ++      +    l+  aa   ++g l  +gv  ++++ll++  ++   +   v+  +
  gi|14600412|ref|NP_146926.1| 250 MAGASQLALTVEVLRRLGLAGMVEFENALKHVEWRALLFYAALFSLVGGLESEGVIEEIARLLVGSVSSDPAIAYTVMYWS 330
                                   33333344444445888888877774444444555555667888889999**************99888854444444444 PP

                          DctM 324 l.vlGmfldttaaiiilvpilaPaaaklgidpihfgvvivl.nlsiglitPPvGlalfvassia.....kvsveeivkalv 397
                                     +l ++++  a+++ +  i+  aa  +gidp+ +   +   ++  + +t   + al+va +++     +v   e +k+++
  gi|14600412|ref|NP_146926.1| 331 VgLLSLVIEHDALLLTFLYIVKDAASLAGIDPWNIYWGMAWsATLASNATTAAAPALYVAVAMSdreghRVRALEFLKYSL 411
                                   45999***************************8776654440455677888899999**99999999988999******** PP

                          DctM 398 Pflvvlvvalvlitlvpe 415
                                    f+++ +++  +itl+++
  gi|14600412|ref|NP_146926.1| 412 TFAFTSLIIHYIITLIVW 429
                                   ***999998888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3284.58
//
Query:       gi|118430857|ref|NP_146927.2|  [L=250]
Description: enoyl-CoA hydratase/isomerase [Aeropyrum pernix K1]
Scores for 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-45  153.5   0.0    6.9e-45  153.3   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    3.4e-33  115.5   0.0      4e-33  115.3   0.0    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   7.7e-49   6.9e-45       1     245 [.       9     248 ..       9     250 .] 0.91

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 7.7e-49
                                    EEETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHH CS
                          ECH_1   1 eieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.akqallkeevle 79 
                                    e+ +gva i+lnrPe++Nal+ e    l + l k+  +  ++avv+tG+++aF++G d++ m+  e  ++  ++ +++  
  gi|118430857|ref|NP_146927.2|   9 EERNGVAIIRLNRPEKLNALNLEAWMQLGEYLRKACRS-GIKAVVITGSGRAFSSGDDIRSMYSLESlEDSLSFFKTLHG 87 
                                    5789*****************************99999.9************************9887888889999999 PP

                                    HHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHH.HHHHHHHHHHHT-E CS
                          ECH_1  80 lwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkv.GkskAeeilllgkk 158
                                     ++++  +  p++aavnG a+gGG+e+ l +D+v a+++a f+ +e+ +Glip+     +l r v G++kA+ + ++g k
  gi|118430857|ref|NP_146927.2|  88 ALEAMARCRRPIVAAVNGLAVGGGAEILLLADVVLASREAWFAFPESHIGLIPPL--LSTLGRSVfGERKARMLGITGAK 165
                                    9****************************************************64..556667655************** PP

                                    EEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHH CS
                          ECH_1 159 isaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlq 238
                                    + ++ea+ +Glvd vv   +l+ +ale+ae l   + ++++ ++ a  ++++ +l++ ++  a    +++ +++ ke + 
  gi|118430857|ref|NP_146927.2| 166 LDVEEAKAMGLVDDVVEPGELEAKALEVAESLGLIPDQSVAEIRRATVEPYRVELENMVNRLA----ELVLTKEAKERMR 241
                                    *********************************999999999999999888887777665444....44445566799** PP

                                    HHHTCSH CS
                          ECH_1 239 aflEkrk 245
                                     flE+rk
  gi|118430857|ref|NP_146927.2| 242 LFLERRK 248
                                    *****99 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   4.4e-37     4e-33       2     203 ..      15     213 ..      14     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 4.4e-37
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    ++i Lnrp++lNaL+le   +l e l++    + +k+vv++g+g +af++G D+r++y+ ++ +++   +ff++ +    
  gi|118430857|ref|NP_146927.2|  15 AIIRLNRPEKLNALNLEAWMQLGEYLRKA-CRSGIKAVVITGSG-RAFSSGDDIRSMYSLESLEDSL--SFFKTLHGALE 90 
                                    789************************95.7889********88.**************99997755..7********** PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HHH CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkgad 161
                                    ++a++++p+va ++G+++GgG+ + + + +  ++ ++ fA PE  IGl+P    +   s   ++ +++l++TGa+l+ ++
  gi|118430857|ref|NP_146927.2|  91 AMARCRRPIVAAVNGLAVGGGAEILLLADVVLASREAWFAFPESHIGLIPPLLSTLGRSVFGERKARMLGITGAKLDVEE 170
                                    ***************************************************9999988889999**************** PP

                                    HHHTTS--EE--GGGHHHHHHHHHTT............-------- CS
                          ECH_2 162 alaaglathyvpseklealeeaLaelessd....eeaveevleela 203
                                    a a+gl + +v+  +lea + ++ae         +++v+e+ +++ 
  gi|118430857|ref|NP_146927.2| 171 AKAMGLVDDVVEPGELEAKALEVAES---LglipDQSVAEIRRATV 213
                                    ************99887654444442...11233445555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2121.07
//
Query:       gi|118430858|ref|NP_146928.2|  [L=1488]
Description: hypothetical protein APE_0057.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.5   2.4        4.7    7.5   0.0    3.1  2  AP3B1_C   Clathrin-adaptor complex-3 beta-1 subunit C-termina


Domain annotation for each model (and alignments):
>> AP3B1_C  Clathrin-adaptor complex-3 beta-1 subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00026       4.7      48      88 ..      69     109 ..      44     112 .. 0.80
   2 ?    2.0   1.8     0.013   2.3e+02       6      51 ..    1371    1418 ..    1368    1458 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00026
                        AP3B1_C  48 ievvspsfvpvkkkellnkvtGegLsveyrFtRqpslyspk 88 
                                    + v   + v + +++ ++ vtG gL+  y ++R+p +y  +
  gi|118430858|ref|NP_146928.2|  69 VAVAGNVNVASYSENSVELVTGDGLATVYVYAREPRVYTVS 109
                                    4566666777777788899*****************99765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.013
                        AP3B1_C    6 lLLDLdDfspsapvvtpslgsvlspslatdleglslsd..sssaievv 51  
                                      L  L D++p ++ +t+++ ++ ++ ++t++e ++ +   ++++ +++
  gi|118430858|ref|NP_146928.2| 1371 WLISLKDIEPDSVETTTVTETLTTTLATTETEYQTYTLveTETSTSII 1418
                                     58899*****66655555535656555555555554431144444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.83u 0.27s 00:00:01.10 Elapsed: 00:00:00.44
# Mc/sec: 10124.00
//
Query:       gi|118430859|ref|NP_146931.2|  [L=233]
Description: hypothetical protein APE_0060.1 [Aeropyrum pernix K1]
Scores for 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   33.9   0.1    3.4e-08   33.2   0.1    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    9.2e-06   25.9   2.7    3.2e-05   24.2   2.7    1.9  1  HTH_31        Helix-turn-helix domain
    7.2e-05   22.8   0.1    0.00014   21.8   0.1    1.5  1  HTH_3         Helix-turn-helix
     0.0098   15.9   0.0      0.019   15.0   0.0    1.4  1  HTH_19        Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.014   14.9   0.0    1.3  1  PRTase_2      Phosphoribosyl transferase
      0.032   14.7   0.0      0.064   13.7   0.0    1.5  1  HTH_26        Cro/C1-type HTH DNA-binding domain
      0.038   13.4   0.1       0.09   12.2   0.0    1.7  2  UPRTase       Uracil phosphoribosyltransferase
       0.13   12.4   0.0       0.21   11.7   0.0    1.3  1  RepB          RepB plasmid partitioning protein
       0.14   11.7   0.4       0.31   10.6   0.0    1.8  2  HTH_24        Winged helix-turn-helix DNA-binding


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 !   33.2   0.1   1.7e-11   3.4e-08      28     130 ..     107     217 ..      96     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.7e-11
                                    GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.................EE----TTSEEEEE-SEES CS
                   Pribosyltran  28 gkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.........rlledpagkkVliVDDild 98 
                                     + d ++ ++  G+ +a++l  +L+v +++ r++k +++   + a g++d+          r+  +   + +liVDDi+ 
  gi|118430859|ref|NP_146931.2| 107 ARVDRILVPEAAGIGLATALGIALGVHVVVARRTKEYTWAEYVEA-GFEDPAsgrsmifyaRKDLLSGAEWILIVDDIVQ 185
                                    56778889999****************************999997.7888889*******98888888999********* PP

                                    SSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHH CS
                   Pribosyltran  99 tGgTllaalelLkekgpeevriavlvdkpate 130
                                    tG+Tl+a+ ++++++g  +  ia+++  ++ +
  gi|118430859|ref|NP_146931.2| 186 TGRTLHAMEKIVESVGGRVAAIAAVIVVGSEW 217
                                    ******9999********99999888666655 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   2.7   1.6e-08   3.2e-05       6      50 ..      17      59 ..      13      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.6e-08
                         HTH_31  6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavleal 50
                                   Lr++R  +G++ +e+Ae++gv e+ l r+ +Gr   p  ++ e++
  gi|118430859|ref|NP_146931.2| 17 LRRAR-SRGVTYRELAEATGVDETLLARYVSGRVM-PGARQAERI 59
                                   55555.459*************************5.988888776 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   7.2e-08   0.00014       5      44 ..      18      59 ..      14      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.2e-08
                                   HH..HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                          HTH_3  5 Rk..qlglsqeeLAeklGvsrstisriEnGernPsletlkkl 44
                                   R    +g + +eLAe++Gv  + ++r+ +G+ +P  + ++++
  gi|118430859|ref|NP_146931.2| 18 RRarSRGVTYRELAEATGVDETLLARYVSGRVMPGARQAERI 59
                                   445789****************************99888776 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.7e-06     0.019       2      44 ..      15      55 ..      15      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                         HTH_19  2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsael 44
                                   e L++aR+ +g t +elae +g++ + ++ + +g+  +p+a+ 
  gi|118430859|ref|NP_146931.2| 15 EALRRARS-RGVTYRELAEATGVDETLLARYVSGRV-MPGARQ 55
                                   67899997.8************************99.999765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   7.1e-06     0.014      82     147 ..     137     200 ..      69     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.1e-06
                       PRTase_2  82 lhtTRekvagveelleFeEeHSHAtdhllyaedeellaaakelvLvDDEistGktalnliralqek 147
                                       T+e +      + Fe+  S   + +++ ++++ll++a+ +++vDD + tG+t+ ++ + +++ 
  gi|118430859|ref|NP_146931.2| 137 ARRTKEYTWAEYVEAGFEDPAS--GRSMIFYARKDLLSGAEWILIVDDIVQTGRTLHAMEKIVESV 200
                                    4445555555555566666655..3456667899*********************87665544443 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   3.2e-05     0.064       6      35 ..      20      49 ..      18      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                         HTH_26  6 madrgitkseLargtgisaatlsrlvkgkp 35
                                   ++ rg+t+ eLa++tg++++ l+r+v+g++
  gi|118430859|ref|NP_146931.2| 20 ARSRGVTYRELAEATGVDETLLARYVSGRV 49
                                   5789************************86 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   2.5e+03      27      42 ..       4      19 ..       2      37 .. 0.74
   2 ?   12.2   0.0   4.5e-05      0.09     110     163 ..     163     216 ..     127     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                        UPRTase 27 lvdriarllaeealsa 42
                                   +  ++ r++++eal++
  gi|118430859|ref|NP_146931.2|  4 YKTEVLRVVVVEALRR 19
                                   5678888999999886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.5e-05
                        UPRTase 110 eyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlase 163
                                    ++y +      ++ +l++D ++ TG+++ a+ +++ + g ++  I  + v+ se
  gi|118430859|ref|NP_146931.2| 163 IFYARKDLLSGAEWILIVDDIVQTGRTLHAMEKIVESVGGRVAAIAAVIVVGSE 216
                                    444443333356679****************99***************999886 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.21      14      55 ..      17      59 ..      13      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                           RepB 14 aarleerGvdreeiasalgldkqtvskmva.raipegicaeev 55
                                   + r++ rGv+ +e+a a+g+d++ ++++v+ r  p+ ++ae++
  gi|118430859|ref|NP_146931.2| 17 LRRARSRGVTYRELAEATGVDETLLARYVSgRVMPGARQAERI 59
                                   679***************************9999998887765 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 ?   10.6   0.0   0.00015      0.31      17      38 ..      24      45 ..      14      46 .. 0.88
   2 ?   -3.4   0.1       3.9   7.7e+03      23      32 ..     122     131 ..     122     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                         HTH_24 17 risqreLAerlglSpstvnrrl 38
                                   + ++reLAe++g+  + + r++
  gi|118430859|ref|NP_146931.2| 24 GVTYRELAEATGVDETLLARYV 45
                                   69**************999998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.9
                         HTH_24  23 LAerlglSps 32 
                                    LA +lg+ ++
  gi|118430859|ref|NP_146931.2| 122 LATALGIALG 131
                                    8999**9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1708.87
//
Query:       gi|118430860|ref|NP_146932.2|  [L=429]
Description: hypothetical protein APE_0061.1 [Aeropyrum pernix K1]
Scores for 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   67.3   0.0    1.9e-18   66.5   0.0    1.3  1  Bmp         ABC transporter substrate-binding protein PnrA-li
    6.7e-07   28.9   3.4    6.7e-07   28.9   3.4    2.1  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.091   12.1   0.3       0.19   11.1   0.3    1.5  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


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 !   66.5   0.0   3.1e-22   1.9e-18       5     219 ..      50     278 ..      47     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 3.1e-22
                                    EEECSS-TTTSCHHHHHHHHHHHHHHHC.TTEEEEEEEEC.GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHHHHH-T CS
                            Bmp   5 avlvegtidDksfnessyeGirrlkkeq.nieliskesslltdedyiadlknlkeegsdlivatgfalqdalqevssdfp 83 
                                      +++g+++D +++  +++G  +++++   +e+ + e +++ d++y     +l  eg+d ++at++ ++dal+ ++ ++p
  gi|118430860|ref|NP_146932.2|  50 LWIYVGPVEDYGWTRAHHDGHMKARSKLgWLESSYIETVSE-DKAYDVIKAQLDAEGYDAVFATSYGYMDALKRLATEYP 128
                                    56899***********************99**********5.8888888889**************************** PP

                                    TS-EEEESS--TT-S..TTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHHH........ CS
                            Bmp  84 kvkFliiDavvekey..knvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGikyv........ 153
                                    +vkF ++++  e+     nv++++   ++  +L G+aaA +++t   g++ +  ip+v + in++  G+           
  gi|118430860|ref|NP_146932.2| 129 DVKFYHCSGPWEEFRdlPNVSTYFAEFYQLYYLNGLAAAGATETCNLGYIPAFLIPEVVRHINAYVIGAVEGakvlgkcg 208
                                    **********99987789***********************************************988754311122222 PP

                                    .-TT-EEEE.EE-SSSS-HHHHHHHHHHHHH.CT--EEEEE-GGGHHHHHHHHHH...HCHCTEEEEEES-- CS
                            Bmp 154 .npdievvv.kvagtfsDakkgkslAsslyk.egvdvifpaagkagkgvieaake...lglsnyvIgvdkdq 219
                                     + +i+v v   ++++  ++k++++A+ l++   vdvi+     + ++v+e a++   +g++ y+    +d+
  gi|118430860|ref|NP_146932.2| 209 dGRNIRVLVtPPLNSWFAPDKARDAARLLVEtYDVDVIAY--TEDTTAVLETAESywdQGVKVYSFSHYTDM 278
                                    2457777551579******************99*****99..888889999888622245555776666666 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 !   28.9   3.4   1.1e-10   6.7e-07       1      25 [.       2      26 ..       2      26 .. 0.94
   2 ?   -1.4   1.2      0.41   2.5e+03      11      16 ..     164     169 ..     163     173 .. 0.54

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.1e-10
                     TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaa 25
                                   +++RRdFLK ++Aa+A++++gg+++
  gi|118430860|ref|NP_146932.2|  2 SMNRRDFLKLAGAAGAGLVVGGLGG 26
                                   59********************975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.41
                     TAT_signal  11 sAAaaA 16 
                                     AAa+A
  gi|118430860|ref|NP_146932.2| 164 LAAAGA 169
                                    344444 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 ?   11.1   0.3   3.1e-05      0.19       9      28 ..       3      22 ..       1      24 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.1e-05
                     UCR_Fe-S_N  9 ptRRDFLyiATgavgaVGaa 28
                                    +RRDFL +A +a ++ +++
  gi|118430860|ref|NP_146932.2|  3 MNRRDFLKLAGAAGAGLVVG 22
                                   58*****9997776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3238.95
//
Query:       gi|14600419|ref|NP_146933.1|  [L=492]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-40  137.9   0.0    1.4e-21   77.5   0.0    2.8  3  ABC_tran     ABC transporter
    1.2e-09   38.4   0.0    2.4e-05   24.3   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-05   24.7   0.2    8.1e-05   22.3   0.1    2.2  2  AAA_29       P-loop containing region of AAA domain
    0.00037   21.1   0.0    0.00056   20.5   0.0    1.2  1  AAA_23       AAA domain
    0.00079   18.4   0.1     0.0013   17.7   0.1    1.2  1  DLIC         Dynein light intermediate chain (DLIC)
     0.0017   18.6   0.9     0.0064   16.7   0.1    2.3  2  FeoA         FeoA domain
     0.0021   17.6   0.0      0.093   12.2   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0056   16.3   2.2       0.38   10.3   0.2    2.9  3  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.094   12.4   0.0    1.9  2  AAA_15       AAA ATPase domain
      0.021   14.7   0.3       0.06   13.3   0.3    1.8  1  NACHT        NACHT domain
      0.024   14.8   0.0      0.076   13.2   0.0    1.8  1  AAA_33       AAA domain
      0.028   14.8   0.6      0.064   13.6   0.3    1.9  1  AAA_16       AAA ATPase domain
      0.046   14.0   0.0       0.16   12.2   0.0    1.9  1  DUF3253      Protein of unknown function (DUF3253)
      0.058   13.2   0.1        0.1   12.4   0.1    1.3  1  MukB         MukB N-terminal
      0.088   12.1   0.2       0.19   11.0   0.1    1.5  2  Zeta_toxin   Zeta toxin
        0.1   12.5   0.1       0.19   11.6   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.15   12.5   0.0       0.67   10.4   0.0    2.2  2  AAA          ATPase family associated with various cellular a
       0.15   10.8   1.1       0.59    8.9   0.6    2.1  2  ABC_ATPase   Predicted ATPase of the ABC class
       0.19   11.3   0.2       0.38   10.3   0.2    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
        0.2   11.7   0.2       0.39   10.7   0.2    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.86    9.3   6.3        0.2   11.4   0.4    2.7  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 !   77.5   0.0   1.6e-24   1.4e-21       1     136 [.      21     168 ..      21     169 .. 0.95
   2 !   57.1   0.0   3.2e-18   2.7e-15       4     132 ..     273     419 ..     270     424 .. 0.91
   3 ?   -0.7   0.1       2.1   1.8e+03     112     134 ..     430     452 ..     429     454 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 1.6e-24
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                   lk v+ ++ +g ++a++GenGaGK+tLlk+++g +kp +G+il+dg +l+   +  slr+ i + +q+p + p+++++e  
  gi|14600419|ref|NP_146933.1|  21 LKGVTASFPAGVVTALLGENGAGKTTLLKAIMGVVKPRKGRILVDGYELRPkGPGDSLRSGIYMASQNPPVYPGIKAYEDl 101
                                   7899**********************************************98899*********************9999* PP

                                   ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 +++  +++a + lgl+ ++d+ +     ++   ++qr+++ +al+  ++ +llDEpt
  gi|14600419|ref|NP_146933.1| 102 avtlmvagrkaglrQARTMLAEASEALGLNIDPDRYL----GEMGFSERQRLEVIKALALGSRAVLLDEPT 168
                                   *******99998866666699****************....99***************************9 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 3.2e-18
                                   EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxxxx. RF
                      ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpeltvren. 79 
                                     l++++ge+v++ G  G G   L++++ gl kp++G+il+ g d+++  +l + r  +gv+p+e   + l p+ +++ n 
  gi|14600419|ref|NP_146933.1| 273 ARLEVRQGEVVGVAGVAGNGQEELFEVIVGLRKPAKGRILIAGVDVTRaPPLARRRLGLGVIPEErlgHALVPGESIAFNi 353
                                   5799********************************************999**************8888888888888889 PP

                                   ................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                   ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                                   ++++ +e++++ +g+k +  + +     +LSgG  qr++lar l+ kp+ll++
  gi|14600419|ref|NP_146933.1| 354 alsihtardgfivdwrYYEKLAEEMIRDMGIKAVSPRQM---VDELSGGNMQRLVLARELWLKPRLLVA 419
                                   ****99999998888777777999999999999887777...7************************97 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHHTSSEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 112 GqkqrvalarallkkpkllllDE 134
                                   Gq+   +++r+  ++  +l++DE
  gi|14600419|ref|NP_146933.1| 430 GQQAVAEMMRMSSERGGVLVIDE 452
                                   99********************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 !   24.3   0.0   2.8e-08   2.4e-05       1     126 [.      33     147 ..      33     157 .. 0.83
   2 !   12.4   0.0   0.00012       0.1     255     297 ..     157     198 ..     147     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.8e-08
                        AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                   +++l G Ng+GK++LL+a+            ++ +++++g i ++ ++l+++ p  + + +i+   ++ ++y ++   e+ 
  gi|14600419|ref|NP_146933.1|  33 VTALLGENGAGKTTLLKAI------------MGVVKPRKGRILVDGYELRPKGPGDSLRSGIYMASQNPPVYPGIKAYEDL 101
                                   699****************............45599999999999999999999999999999999999999999999999 PP

                        AAA_21  82 qv.eeklssvetllesgllldkrsleeedvfnpeargirggvsvfs 126
                                   +v  +  +++  l++ +++l + s+  + + +p+ +    g s+++
  gi|14600419|ref|NP_146933.1| 102 AVtLMVAGRKAGLRQARTMLAEASEALGLNIDPDRYLGEMGFSERQ 147
                                   9988888888888888888888888887777777766666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                        AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                   l++ + +l+DEp ++L P+  +r le   +l++ ga v+l+TH
  gi|14600419|ref|NP_146933.1| 157 LGS-RAVLLDEPTTHLTPEEAARMLEAAGRLAASGAAVLLVTH 198
                                   444.89************9999999999888888********* PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   9.5e-08   8.1e-05      13      50 ..      22      59 ..      18      63 .. 0.85
   2 ?   -2.2   0.0       4.3   3.7e+03      46      57 ..     343     354 ..     341     355 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.5e-08
                        AAA_29 13 dghtieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                  +g t+++  +g +t l G++G+GK+Tll Ai+ +  p+k
  gi|14600419|ref|NP_146933.1| 22 KGVTASFP-AGvVTALLGENGAGKTTLLKAIMGVVKPRK 59
                                  66777785.788*********************999987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                        AAA_29  46 LvpakkvrfNka 57 
                                   Lvp ++++fN a
  gi|14600419|ref|NP_146933.1| 343 LVPGESIAFNIA 354
                                   899999****76 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   6.5e-07   0.00056      21      40 ..      33      52 ..      17      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.5e-07
                        AAA_23 21 ltlItGpNGaGKTTildAik 40
                                  +t++ G+NGaGKTT+l Ai 
  gi|14600419|ref|NP_146933.1| 33 VTALLGENGAGKTTLLKAIM 52
                                  799***************95 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.5e-06    0.0013      21      57 ..      27      63 ..      22      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                          DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGrGl 57
                                   +P+g    +lGe+g+Gkttl+  + Gv +++kGr l
  gi|14600419|ref|NP_146933.1| 27 SFPAGVVTALLGENGAGKTTLLKAIMGVVKPRKGRIL 63
                                  579999999*************************976 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   7.5e-06    0.0064      26      69 ..     136     178 ..     107     180 .. 0.84
   2 ?   -1.2   0.1       2.9   2.5e+03      15      15 ..     301     301 ..     275     339 .. 0.42

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.5e-06
                                   HHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTT CS
                          FeoA  26 rrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqa 69 
                                   r+L emG+ + +r+ev+ +a   g  +v +++ +  L  eeA++
  gi|14600419|ref|NP_146933.1| 136 RYLGEMGFSERQRLEVI-KALALGSRAVLLDEPTTHLTPEEAAR 178
                                   9****************.89999********99999***99987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                                   E CS
                          FeoA  15 a 15 
                                   +
  gi|14600419|ref|NP_146933.1| 301 V 301
                                   1 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 !   12.2   0.0   0.00011     0.093      25      45 ..      32      52 ..      17      63 .. 0.79
   2 ?    3.4   0.0     0.052        44     136     196 ..     395     451 ..     120     468 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                  SEEEEEESTTSSHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                   +ta++G+NG+GK+ ll Ai+
  gi|14600419|ref|NP_146933.1| 32 VVTALLGENGAGKTTLLKAIM 52
                                  479*****************5 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.052
                                   CS-HHHHHHHHHHHHHH.HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfA.iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                   +LSgG+       L++A     kp+ l+ +   +a LD +  ++vae+++ +s++  ++vi 
  gi|14600419|ref|NP_146933.1| 395 ELSGGNM----QRLVLArELWLKPRLLVAMN-PAAGLDLEGQQAVAEMMRMSSERGGVLVID 451
                                   6666653....35555522345666666664.4789**************999999999985 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00044      0.38      30      51 ..      28      49 ..      19      67 .. 0.88
   2 ?    4.4   0.1     0.029        25     164     188 ..     175     198 ..     165     200 .. 0.91
   3 ?   -2.3   0.0       3.3   2.8e+03     113     135 ..     436     459 ..     412     465 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
                        AAA_25 30 lpagelallaGapgtGKttlal 51
                                   pag +++l G  g+GKttl+ 
  gi|14600419|ref|NP_146933.1| 28 FPAGVVTALLGENGAGKTTLLK 49
                                  59*****************985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.029
                        AAA_25 164 dvgalvealeriarrtgaavllvhH 188
                                   ++++++ea+ r+ ++ gaavllv H
  gi|14600419|ref|NP_146933.1| 175 EAARMLEAAGRL-AASGAAVLLVTH 198
                                   679*********.69*********9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.3
                        AAA_25 113 slpLfakdrggtl.ltadvdalea 135
                                   +++ ++++rgg l +++d+d l +
  gi|14600419|ref|NP_146933.1| 436 EMMRMSSERGGVLvIDEDLDFLLR 459
                                   223334455555555666555555 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   0.00011     0.094      25      43 ..      33      51 ..      20      64 .. 0.87
   2 ?    0.4   0.0      0.48   4.1e+02     327     364 ..     162     198 ..     159     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                        AAA_15 25 ltvliGkNnsGKSsileal 43
                                  +t l G+N++GK+++l+a+
  gi|14600419|ref|NP_146933.1| 33 VTALLGENGAGKTTLLKAI 51
                                  899***************9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.48
                        AAA_15 327 lliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                   +l++EP +hL p+    + ++  +la ++   v++ TH
  gi|14600419|ref|NP_146933.1| 162 VLLDEPTTHLTPEEAARMLEAAGRLAASGA-AVLLVTH 198
                                   689************************997.8999999 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3     7e-05      0.06       3      22 ..      34      53 ..      32      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7e-05
                                  EEEEC-TTTCHHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqklal 22
                                   +l Ge+G GKTtLl+ ++ 
  gi|14600419|ref|NP_146933.1| 34 TALLGENGAGKTTLLKAIMG 53
                                  6899*************985 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   8.9e-05     0.076       3     106 ..      35     197 ..      33     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                        AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt............................................... 32 
                                    l G +G+GK+tl++ ++   +     +l++  +                                               
  gi|14600419|ref|NP_146933.1|  35 ALLGENGAGKTTLLKAIMGVVKprkgRILVDGYElrpkgpgdslrsgiymasqnppvypgikayedlavtlmvagrkaglr 115
                                   67899**********985444444477888888899999999999999999999999999998888888887777777755 PP

                        AAA_33  33 .lrrrlfgtdqqskt.................dytrvldrlyqilnelarkalsag.rnvildat..nlsrrerarflkla 92 
                                    +r           t                 ++ +  ++ +q+l e++ kal+ g r+v+ld +   l+++e ar+l++a
  gi|14600419|ref|NP_146933.1| 116 qAR-----------TmlaeasealglnidpdrYLGEMGFSERQRL-EVI-KALALGsRAVLLDEPttHLTPEEAARMLEAA 183
                                   422...........022333333444444444899999******9.999.566666266778766337889********** PP

                        AAA_33  93 rrlgvpvrivvvet 106
                                    rl +  ++v + t
  gi|14600419|ref|NP_146933.1| 184 GRLAASGAAVLLVT 197
                                   *9999888887765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   7.4e-05     0.064      15     127 ..      20     187 ..      18     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-05
                        AAA_16  15 alervrsgrp..elvllsGesGvGKsslvrellralekd......................ggiflrgkcdqlesaipysa 71 
                                   al+ v ++ p   ++ l Ge G GK++l+++++  ++ +                      g++ ++++   +       +
  gi|14600419|ref|NP_146933.1|  20 ALKGVTASFPagVVTALLGENGAGKTTLLKAIMGVVKPRkgrilvdgyelrpkgpgdslrsGIYMASQNPPVY-------P 93 
                                   5666666666667889*****************8777776666665555544444444443333344444444.......3 PP

                        AAA_16  72 laqalareellrqlldeaesaeleawrekleeala........................................avpela 112
                                    ++a  + +l   l  + ++a l+++r+ l ea +                                        ++ +l+
  gi|14600419|ref|NP_146933.1|  94 GIKAY-E-DLAVTLMVAGRKAGLRQARTMLAEASEalglnidpdrylgemgfserqrlevikalalgsravlldePTTHLT 172
                                   33333.2.3333333333333444444444444444444444555555555777777777777777777777777777777 PP

                        AAA_16 113 gaeasrllellkrll 127
                                   ++ea r+le+  rl+
  gi|14600419|ref|NP_146933.1| 173 PEEAARMLEAAGRLA 187
                                   777777777766666 PP

>> DUF3253  Protein of unknown function (DUF3253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.16      16      67 ..     166     219 ..     159     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                   -TT--B-HHHHHHHH...-T..TS-GGGHHHHHHHHHHHHHTTSEEEEETTEE- CS
                       DUF3253  16 epgkticPsevAralsaeeg..eeWrelmekvRevavrlaaaGeveilqkGkvv 67 
                                   ep++ + P+e+Ar+l+a++   ++  +++    ++  ++++a +++il+kG  v
  gi|14600419|ref|NP_146933.1| 166 EPTTHLTPEEAARMLEAAGRlaASGAAVLLVTHRIGEAMEHADRLVILRKGVKV 219
                                   5667789********88887887789999999*******************988 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012       0.1      27      53 ..      32      58 ..      28      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                  HHHHHHS--SHHHHHHHHHHHHHHS-- CS
                          MukB 27 lvttlsGgnGaGksttmaafvtaliPd 53
                                  +vt+l G nGaGk+t + a++ ++ P 
  gi|14600419|ref|NP_146933.1| 32 VVTALLGENGAGKTTLLKAIMGVVKPR 58
                                  69*****************99998876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00022      0.19      19      59 ..      34      74 ..      21      81 .. 0.87
   2 ?   -3.5   0.0       5.9     5e+03      31      52 ..     433     453 ..     430     454 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                    Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRelhP 59
                                    l G  GAGK++l++++   ++++++ + +d+ +lR+  P
  gi|14600419|ref|NP_146933.1| 34 TALLGENGAGKTTLLKAIMGVVKPRKGRILVDGYELRPKGP 74
                                  567799**************************999998666 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.9
                    Zeta_toxin  31 elaellkdelerqgnvvrldpD 52 
                                   ++ae+++ +  ++g+v+++d+D
  gi|14600419|ref|NP_146933.1| 433 AVAEMMRMSS-ERGGVLVIDED 453
                                   5677777776.69999999999 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00023      0.19      99     124 ..      31      56 ..      15      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   TSEEEEECSTTSSHHHHHHHHCTT-- CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                   + +++l+G+ G+GK+tL++a+++  +
  gi|14600419|ref|NP_146933.1|  31 GVVTALLGENGAGKTTLLKAIMGVVK 56 
                                   47899***************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 ?   10.4   0.0   0.00079      0.67       3      38 ..      36      73 ..      34     167 .. 0.83
   2 ?   -1.4   0.0       3.4   2.9e+03      41      66 ..     429     452 ..     419     461 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00079
                                  EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSS CS
                           AAA  3 lyGppGtGKTllakavakelg..vefleisgsellsky 38
                                  l G  G GKT+l ka++  ++     + ++g el+ k 
  gi|14600419|ref|NP_146933.1| 36 LLGENGAGKTTLLKAIMGVVKprKGRILVDGYELRPKG 73
                                  88**************9988732224666777777664 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                                   HHHHHHHHHHHHHHHTSTSEEEEEET CS
                           AAA  41 esekkirelfkeakekakpsilfiDE 66 
                                   e+++ ++e+++  +e     +l+iDE
  gi|14600419|ref|NP_146933.1| 429 EGQQAVAEMMRMSSERG--GVLVIDE 452
                                   45667777777665555..99***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 ?    8.9   0.6    0.0007      0.59     242     266 ..      28      53 ..      17      66 .. 0.86
   2 ?   -1.1   0.0      0.74   6.3e+02     330     350 ..     148     168 ..     144     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0007
                                   E-SS.EEEEEE-TTSSHHHHHHHHHH CS
                    ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlek 266
                                    p G vt++ G +  GK+TLL+A+  
  gi|14600419|ref|NP_146933.1|  28 FPAGvVTALLGENGAGKTTLLKAIMG 53 
                                   588989*****************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.74
                                   HHHHHHHHHTT-SEEEEEGGG CS
                    ABC_ATPase 330 AanimealeagakllLiDEDt 350
                                     ++++al +g++++L+DE t
  gi|14600419|ref|NP_146933.1| 148 RLEVIKALALGSRAVLLDEPT 168
                                   567999*************77 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 ?   10.3   0.2   0.00044      0.38       2      22 ..      33      56 ..      32      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
                                  EEEEEESTTCCHHHHHHHHH...C CS
                          cobW  2 vtvltGflGsGKTtLlnhll...e 22
                                  vt l G  G+GKTtLl++++   +
  gi|14600419|ref|NP_146933.1| 33 VTALLGENGAGKTTLLKAIMgvvK 56
                                  7889999**********9985532 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00045      0.39      19      41 ..      31      53 ..      18      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                  TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                  g v +L G+ GaGKTtl ++++ 
  gi|14600419|ref|NP_146933.1| 31 GVVTALLGENGAGKTTLLKAIMG 53
                                  56789**************9975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00023       0.2      19      49 ..      32      62 ..      20      67 .. 0.85
   2 ?   -2.4   0.1       3.8   3.2e+03     103     122 ..     174     196 ..     145     212 .. 0.56
   3 ?   -1.7   0.0       2.3     2e+03      18      53 ..     280     315 ..     271     344 .. 0.77
   4 ?   -1.2   0.0       1.6   1.4e+03      57      96 ..     373     452 ..     345     453 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                   v++l G  G+GKtt+lka+  +++ ++gr+
  gi|14600419|ref|NP_146933.1| 32 VVTALLGENGAGKTTLLKAIMGVVKPRKGRI 62
                                  588999**************99998886666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.8
                        AAA_30 103 kqlaallkaaek...agakvilv 122
                                   +++a++l+aa +   +ga v+lv
  gi|14600419|ref|NP_146933.1| 174 EEAARMLEAAGRlaaSGAAVLLV 196
                                   33444444333311124444444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.3
                        AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrviglA 53 
                                     v+ + G+AG G   + ++++ + + a+gr++++ 
  gi|14600419|ref|NP_146933.1| 280 GEVVGVAGVAGNGQEELFEVIVGLRKPAKGRILIAG 315
                                   348889999999999999988888888877777665 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.6
                        AAA_30  57 kaAkvLaeelgieastiakllkrlk........................................grarlepgtllivDE 96 
                                   k A+++ +++gi+a +  +++++l                                          r++ e+g +l++DE
  gi|14600419|ref|NP_146933.1| 373 KLAEEMIRDMGIKAVSPRQMVDELSggnmqrlvlarelwlkprllvamnpaagldlegqqavaemMRMSSERGGVLVIDE 452
                                   66777777777777777777777666666666666555555555555555555555555555554334444556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3700.61
//
Query:       gi|14600420|ref|NP_146934.1|  [L=311]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-18   66.8  37.7    1.7e-18   66.8  37.7    1.8  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 ?   -1.0   0.8     0.045   8.1e+02      38      65 ..      11      37 ..       4      51 .. 0.43
   2 !   66.8  37.7   9.5e-23   1.7e-18       4     264 ..      47     302 ..      44     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.045
                  BPD_transp_2 38 alGayvaalllalllsllllallvallv 65
                                  +l+ ++a+++l + ++  ++a++ +l+ 
  gi|14600420|ref|NP_146934.1| 11 VLSTIIAGIMLSFIGP-GPAAFVEGLIK 37
                                  2333333333333333.33333333333 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 9.5e-23
                  BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkvde 84 
                                     + +aail+ aA Gl l++ +aG+i +g++++++ +a++a+++la+ +  l+ al +a +v++a+g ++++l ++l v+e
  gi|14600420|ref|NP_146934.1|  47 YSVIYAAILVAAASGLVLSY-RAGLITIGVEAQVTASAVAALYALAYAGLGLPGALTLAAIVSLAIGIVIAALRVYLDVNE 126
                                   567899**************.************************************************************ PP

                  BPD_transp_2  85 liitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.llalllvlavllllrrtrfGralravgen 164
                                   ++++l+++++++++++ l+ g+ +  +        +++++ +  f++   + l a+ ++++ ++ll rt++G  lra g  
  gi|14600420|ref|NP_146934.1| 127 ILSSLMINYIVLYMVNGLVSGPLREGA--------FTKTRSIEAFVGPLEAgLAAVSMAALSWILLERTSLGISLRASGPA 199
                                   ****************44444443333........3333333333322222388999************************ PP

                  BPD_transp_2 165 eeaaralGinvkrvklltfvisgalAglaGallalllgsipp..nigvglgfnaiaavvlGgagsllgtviGaliigvvks 243
                                   ++aa+   i   r  ll+ +  ++ A+ aG++l   ++++ +     +g+g+ a+++  ++ + s+   + ++l ++ +  
  gi|14600420|ref|NP_146934.1| 200 PRAADIYTIGRARAMLLSSLPQSLAAAAAGLILLGGIQTVFTalKQPQGYGYAAVLVSWMAEL-SPTTLIPVSLFFAWIAG 279
                                   ******************************9998888777776899999**************.************99988 PP

                  BPD_transp_2 244 llltllgi...ptelarvllgall 264
                                    ++++l++   p++l  +l+ + l
  gi|14600420|ref|NP_146934.1| 280 -AGFILQAygmPSSLVLLLQSIAL 302
                                   .77777666667777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2277.78
//
Query:       gi|118430861|ref|NP_146935.2|  [L=277]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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  40.0    1.8e-34  119.1  40.0    1.3  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 !  119.1  40.0     1e-38   1.8e-34       2     268 .]       2     255 ..       1     255 [. 0.95

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 1e-38
                   BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlk 81 
                                    i+ +lt+ ++l +aAlG a++  ++G +nlg+ g+ma+Ga v al+ +  +s ll++l+++ l+g++  l +++l+ rl+
  gi|118430861|ref|NP_146935.2|   2 ISAVLTTLIPLSLAALGEAVLE-RTGRVNLGVDGLMAVGAAVGALAGVETGS-LLAGLAAGALAGGVGSLSYIILTDRLG 79 
                                    7889******************.*****************************.*************************** PP

                   BPD_transp_2  82 vdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGralrav 161
                                    v+ ++++ll++++ +gl          g+k    + ++l++ ++ + +++        ++++a++l+l++t++G+alr+v
  gi|118430861|ref|NP_146935.2|  80 VNMIVAGLLVFFAGIGLGD------LVGSKIAGRPGPVLTSLYTTAATIG--------IAAVALHLILYNTVTGTALRVV 145
                                    *******************......8999999999999999999999998........7999****************** PP

                   BPD_transp_2 162 geneeaaralGinvkrvklltfvisgalAglaGallalllgsipp..nigvglgfnaiaavvlGgagsllgtviGaliig 239
                                    gen+ aa+  G++v+r++l + ++ g+ AglaG ++++ l  +++   +  glg+ a+ +v+lG++ +++g++i++++++
  gi|118430861|ref|NP_146935.2| 146 GENPAAAKERGVPVWRLRLSAALVQGLSAGLAGYIMVAGLSYGKWysGVTAGLGWVALGIVILGYW-TPIGVLIASTAVS 224
                                    *********************************************8888889**************.************* PP

                   BPD_transp_2 240 vvksllltllgip...telarvllgallilvl 268
                                    +v s ++t++ ++   + la+++ ++l++++l
  gi|118430861|ref|NP_146935.2| 225 TVFS-MRTQIAAAtgiPPLADAIPYILVLILL 255
                                    ****.888887744559999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2124.71
//
Query:       gi|118430862|ref|YP_874799.1|  [L=153]
Description: hypothetical protein APE_0067a [Aeropyrum pernix K1]
Scores for 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-07   29.7   0.0    2.7e-06   27.6   0.0    1.8  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.5e-10   2.7e-06       7      93 ..      20     125 ..      17     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.5e-10
                                    STCCC-SEEEEEEESSSCEEEEEEE...............E.GCCCTSS.......CSSTHHHHHHHH..TT-SEEEESS CS
                  Nitro_FeMo-Co   7 qhFGrapyFaiyeveegevkivenr...............veeaadaeg.......ggggklaqllae..egvdvvivgk 62 
                                    +hF++ap F+iy v++g  k+ e r               v       +       +g+ k + l ++  ++v+++i+g+
  gi|118430862|ref|YP_874799.1|  20 GHFAHAPIFLIYKVDNGVPKLEEIRenplaaipdedaggdVH------HhhhhkglHGPSKYKYLKDNvlSDVNLIIAGG 93 
                                    7**************999997777777799877777665422......02333456888888888888899********* PP

                                    SCHHHHHHHCTTTSEEEES.-SSBHHHHHHHH CS
                  Nitro_FeMo-Co  63 iGpralakleaagievykg.aggtveealkev 93 
                                        ++a + ++g+    + +g++ +e+lk+ 
  gi|118430862|ref|YP_874799.1|  94 ACMTSIAYFLSEGVSLSFAdPGTPADEVLKAA 125
                                    ****************9999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1157.63
//
Query:       gi|118430863|ref|NP_146937.2|  [L=159]
Description: deoxyuridine 5'-triphosphate nucleotidohydrolase [Aeropyrum pernix K1]
Scores for complete 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-10   39.6   0.0    5.3e-10   39.1   0.0    1.2  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   2.9e-14   5.3e-10      32     111 ..      70     149 ..      62     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 2.9e-14
                                    EEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBECGEEEE CS
                        dUTPase  32 vlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifariltaelee 111
                                    +++ ++  + +p g+ ++ +pRS+l + g      v+d  y+G  + +l + +    +++ g RiAqL++ar++ + +++
  gi|118430863|ref|NP_146937.2|  70 YRLRFNEVVSIPPGHVGFCFPRSSLLRMGCYLGCAVWDPGYTGRGQAMLLVANPHGLRLEMGSRIAQLVVARVEGPLTSL 149
                                    57889999*********************99999*********8888888888888***************998855554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1166.61
//
Query:       gi|118430864|ref|NP_146938.2|  [L=180]
Description: hypothetical protein APE_0070.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1343.27
//
Query:       gi|118430865|ref|NP_146939.2|  [L=219]
Description: hypothetical protein APE_0071.1 [Aeropyrum pernix K1]
Scores for complete 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  111.5   0.0    4.2e-32  111.1   0.0    1.1  1  Oxidored_molyb  Oxidoreductase molybdopterin binding domain


Domain annotation for each model (and alignments):
>> Oxidored_molyb  Oxidoreductase molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   0.0   2.3e-36   4.2e-32       5     172 .]      32     175 ..      28     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 2.3e-36
                                    --.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHH CS
                 Oxidored_molyb   5 pkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLek 84 
                                    +kvd++ wrl+++g+vekplsl ++dL +l + +   +++C++              +w   +v+   W+G++l++++ +
  gi|118430865|ref|NP_146939.2|  32 QKVDTKGWRLRIEGNVEKPLSLAYSDLLELASDRGRFDFHCVT--------------GW---SVMGRVWEGISLKHLIHM 94 
                                    467999*************************************..............8*...9***************** PP

                                    TTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEE CS
                 Oxidored_molyb  85 agvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievs 164
                                    a+++ p+ ++v + ++       +y++ iple+ l+d+ ++A+ ++g+pLp ++GyP R+++p l+g++ +Kw+++i + 
  gi|118430865|ref|NP_146939.2|  95 AKPR-PSVNWVAIVSTG------GYTTVIPLEESLRDESMVALLLDGRPLPEENGYPARIFIPSLYGWKHAKWVEKIVLL 167
                                    ***7.**********75......7***********999****************************************** PP

                                    SS---SHH CS
                 Oxidored_molyb 165 deesegyw 172
                                    de  +gyw
  gi|118430865|ref|NP_146939.2| 168 DEYVDGYW 175
                                    ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       207  (0.0115455); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1638.48
//
Query:       gi|14600426|ref|NP_146940.1|  [L=345]
Description: heme exporter protein C [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-19   69.9   4.9    2.4e-19   69.9   4.9    2.0  2  Cytochrom_C_asm  Cytochrome C assembly protein
     0.0035   16.0  15.9       0.12   11.0   4.6    2.2  2  DUF2339          Predicted membrane protein (DUF2339)
  ------ inclusion threshold ------
      0.017   15.1   7.1      0.018   15.0   0.1    3.2  2  PGF-CTERM        PGF-CTERM motif
       0.69    9.7   7.9       0.23   11.2   3.2    2.4  2  DUF1282          Protein of unknown function (DUF1282)


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   4.9   5.5e-23   2.4e-19      40     213 ..      17     173 ..       2     174 .. 0.74
   2 ?   -1.4   0.1      0.38   1.7e+03      17      42 ..     205     229 ..     192     271 .. 0.56

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 5.5e-23
               Cytochrom_C_asm  40 iaalillgfalflllaelqesadlnpalqspilmiHvplallsYatliigallsialliierqlkkkkklklsanlkllkq 120
                                   ia l + ++a+      +    +l   l ++ ++iH+p+a+++Y +++++ l+s ++l                  ++  +
  gi|14600426|ref|NP_146940.1|  17 IADLAIAVYAA--YEGPFPAVVPLGSPLAYRNIYIHPPVAFTTYIIFGLAGLASALYL-----------------WRRDVR 78 
                                   33333333333..366667777899999******************************.................555667 PP

               Cytochrom_C_asm 121 ldrlsyriiliGfvlltigiilGsvWaeeaWGsywsWDpketaslitWlvfaallhsri..ekgwrgkkaailailg.fll 198
                                   + rl+  ++++G++  + ++ +G  Wa+e WG  wsWDpk+ta+l+ +l +++++ +r    ++ r + ++ + +++ + l
  gi|14600426|ref|NP_146940.1|  79 FSRLALYAAGLGVIYGFTTLATGIAWASESWGAPWSWDPKQTAVLLMLLAYLGYFPLRSsiGDPERRELVSSVYLVAsLSL 159
                                   7788999***********************************************999987544444444444444440444 PP

               Cytochrom_C_asm 199 lllayfgvrllgegl 213
                                   ++l  +  r+  e l
  gi|14600426|ref|NP_146940.1| 160 VILSILANRV-LESL 173
                                   4454444444.4455 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.38
               Cytochrom_C_asm  17 llgllleylarklnlsllaavaliaa 42 
                                   l +++l+y++ +l+  ll  va iaa
  gi|14600426|ref|NP_146940.1| 205 LSMIVLSYMKTGLPRPLLTLVA-IAA 229
                                   4444444444443333322222.222 PP

>> DUF2339  Predicted membrane protein (DUF2339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   4.6   2.6e-05      0.12      24      76 ..      43      95 ..      41     100 .. 0.88
   2 !    9.9   5.0   5.3e-05      0.24     171     265 ..      97     239 ..      94     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.6e-05
                       DUF2339 24 aieqglLgpevRlalgalfGlaLlalGerlrrrsrrvfalaLqGgGlavlYlt 76
                                  a+ + ++ p v   + ++fGla la +++l rr  r  +laL ++Gl+v+Y+ 
  gi|14600426|ref|NP_146940.1| 43 AYRNIYIHPPVAFTTYIIFGLAGLASALYLWRRDVRFSRLALYAAGLGVIYGF 95
                                  6777788899999********************7778889***********85 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 5.3e-05
                       DUF2339 171 tfgiaalWgl.lnyapdlfastelflllfllly.....................lalalllallfvaa............. 216
                                   t++++++W+  + +ap ++  ++ ++ll+ll+y                     + l + l+l+++ +             
  gi|14600426|ref|NP_146940.1|  97 TLATGIAWASeSWGAPWSWDPKQTAVLLMLLAYlgyfplrssigdperrelvssVYLVASLSLVILSIlanrvleslhptg 177
                                   556699999988889999***************888888888888888888776333333333333334455556666665 PP

                       DUF2339 217 .........rra......vdatlvfgaplvalvlqyalladleygwalaalalaalylalaawl 265
                                              +      + + l+ g+ l + vl+y+ ++  ++ ++l+a+a a+l la a+ +
  gi|14600426|ref|NP_146940.1| 178 eavrdfasdF-QagwmfgARMILAIGTGLSMIVLSYMKTGLPRPLLTLVAIA-ALLSLASAVYM 239
                                   5554444332.04666667777777777777777766666666666666666.44444444433 PP

>> PGF-CTERM  PGF-CTERM motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1     4e-06     0.018       6      22 ..      59      75 ..      59      76 .. 0.95
   2 ?    0.7   2.8      0.12   5.5e+02       8      15 ..     225     232 ..     223     240 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                     PGF-CTERM  6 avlAlaGLLaaalLaRR 22
                                  ++++laGL++a +L+RR
  gi|14600426|ref|NP_146940.1| 59 IIFGLAGLASALYLWRR 75
                                  79**************9 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                     PGF-CTERM   8 lAlaGLLa 15 
                                   +A+a+LL+
  gi|14600426|ref|NP_146940.1| 225 VAIAALLS 232
                                   66666664 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.2   5.2e-05      0.23      87     166 ..      36     156 ..       7     166 .. 0.82
   2 ?   -0.2   0.2      0.17   7.6e+02      23      42 ..     221     240 ..     184     259 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.2e-05
                       DUF1282  87 rtydsqhsyskifafaayalvplflgglalglsllllva.......................................... 125
                                    +++s  +y +i++   +a++ ++++gla ++s+l l+                                           
  gi|14600426|ref|NP_146940.1|  36 VPLGSPLAYRNIYIHPPVAFTTYIIFGLAGLASALYLWRrdvrfsrlalyaaglgviygfttlatgiawaseswgapwswd 116
                                   5678888999*********************************************************************** PP

                       DUF1282 126 .lvslllllyvvvLlylGvptlmnirekdraiviallvlvvs 166
                                     + ++ll+ +++L+y  + ++ +  ++ r +v ++  lv+s
  gi|14600426|ref|NP_146940.1| 117 pKQTAVLLMLLAYLGYFPLRSSIGD-PERRELVSSVY-LVAS 156
                                   *99999999999****999998887.44444444443.3333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.17
                       DUF1282  23 yivlillllliglvvfiyst 42 
                                    ++l+++++l  l++++y+ 
  gi|14600426|ref|NP_146940.1| 221 LLTLVAIAALLSLASAVYMA 240
                                   33333444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); 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:                         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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2573.85
//
Query:       gi|118430866|ref|NP_146941.2|  [L=596]
Description: hypothetical protein APE_0073.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-05   25.3   0.0    7.2e-05   22.6   0.0    2.0  2  UPF0020          Putative RNA methylase family UPF0020
    1.2e-05   25.2   0.0    0.00083   19.1   0.0    2.2  2  N6_N4_Mtase      DNA methylase
     0.0019   17.9   0.0     0.0039   16.9   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0021   17.8   0.4     0.0037   17.0   0.0    1.5  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.088   12.9   0.2        0.2   11.8   0.2    1.5  1  DUF1156          Protein of unknown function (DUF1156)


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 !   22.6   0.0     2e-08   7.2e-05      25      65 ..      75     134 ..      68     156 .. 0.65
   2 ?   -0.2   0.0      0.18   6.6e+02     113     131 ..     405     422 ..     391     432 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2e-08
                                    T--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS...................H CS
                        UPF0020  25 gwkpgepllDPmCGsGtilIEaallganiapgllrefvle...................l 65 
                                     ++ g+ ++DP++G+Gti++Ea  +g +++     + ++                    l
  gi|118430866|ref|NP_146941.2|  75 SYTSGKLIVDPFSGGGTIPLEASRMGYKAIGLDSNPYAVSvakasstlldgrcrgkavcL 134
                                    578999********************9998333333332255666666666666655533 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                                    GG--STTS---EEEE---- CS
                        UPF0020 113 akLrlkegevdvivtnpPY 131
                                    + L++    + ++vt+pPY
  gi|118430866|ref|NP_146941.2| 405 RGLPEGIRPY-AVVTDPPY 422
                                    5566444445.89****** PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.3e-07   0.00083     190     230 ..      77     117 ..      72     118 .. 0.90
   2 ?    3.8   0.0     0.011        40       4      57 ..     416     479 ..     414     488 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.3e-07
                                    -TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                    N6_N4_Mtase 190 kkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                      g++++DpF G Gt+  +a ++g k+iG + ++++v  a+
  gi|118430866|ref|NP_146941.2|  77 TSGKLIVDPFSGGGTIPLEASRMGYKAIGLDSNPYAVSVAK 117
                                    4699******************************9998765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                                    EEE--SSSSSCS...............GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE- CS
                    N6_N4_Mtase   4 ivtdpPYntgkdy..........endeqyeeedsyeeyleflekvlkevrrvLkddgsifinid 57 
                                    +vtdpPY   ++y               + + +s +e  +  +++++ + r L+ +gs++ + +
  gi|118430866|ref|NP_146941.2| 416 VVTDPPYPGMQSYgqlslvyslpHVLSGLPAPHSWSEIDSMSRSYVEDLSRALSASGSLVESGG 479
                                    9***********9999999988877777888888888888888888888888888888876655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0039      26     103 ..      63     141 ..      58     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T..TTEEEEES-HHH CS
                  Cons_hypoth95  26 drvrealFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee..etaelkedalea 103
                                    d v +  F+ ++++  g+ ++D f+G G++ lEA SR   ka+ +++++ av++ k+    l+ +   ++  l e a++a
  gi|118430866|ref|NP_146941.2|  63 DAVDGRGFEKIRSYTSGKLIVDPFSGGGTIPLEA-SRMGYKAIGLDSNPYAVSVAKASSTLLDGRCrgKAVCLLEAAQRA 141
                                    5566677999***********************9.9*****************999988877633233555555555555 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 !   17.0   0.0     1e-06    0.0037      20      60 ..      78     118 ..      70     124 .. 0.90
   2 ?   -3.4   0.6       1.8   6.3e+03     183     192 ..     418     427 ..     413     432 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                                    --SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHH CS
                MethyltransfD12  20 kgktfvepFaGggaVffeakkqgkkvlinDinedlinlyka 60 
                                    +gk +v+pF+Ggg + +ea + g+k++  D n++ ++++ka
  gi|118430866|ref|NP_146941.2|  78 SGKLIVDPFSGGGTIPLEASRMGYKAIGLDSNPYAVSVAKA 118
                                    56789*******************************99995 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                                    E--S-T.S.. CS
                MethyltransfD12 183 lDPPYnprqy 192
                                     DPPY + q+
  gi|118430866|ref|NP_146941.2| 418 TDPPYPGMQS 427
                                    6****98554 PP

>> DUF1156  Protein of unknown function (DUF1156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   5.5e-05       0.2      27      54 ..      35      63 ..      15      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.5e-05
                        DUF1156 27 lWW.aRrPLaaaRAvifaqLvpdpssele 54
                                    WW +Rr    +RAv+ a  vpdp++ ++
  gi|118430866|ref|NP_146941.2| 35 FWWpGRRLVGGVRAVLAALSVPDPGVVVD 63
                                   5999999999**************98554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 4819.57
//
Query:       gi|118430867|ref|NP_146944.2|  [L=283]
Description: hypothetical protein APE_0076.1 [Aeropyrum pernix K1]
Scores for 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  113.7  36.4    1.5e-16   60.8  12.7    2.1  2  EamA             EamA-like transporter family
      0.007   15.7  11.4      0.027   13.8  11.3    2.4  1  Sugar_transport  Sugar transport protein
  ------ inclusion threshold ------
       0.14   11.5   6.3       0.43    9.9   1.3    2.3  2  TPT              Triose-phosphate Transporter family
       0.53   10.3   6.2        7.6    6.6   0.3    3.5  3  DUF5510          Family of unknown function (DUF5510)
       0.71    9.3   8.1       0.04   13.4   1.2    2.1  2  MdcE             Malonate decarboxylase gamma subunit (MdcE)
        2.7    8.1   5.8         17    5.6   0.2    3.6  3  DUF2953          Protein of unknown function (DUF2953)


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 !   59.2  15.7   1.6e-19   4.8e-16       2     136 ..       9     137 ..       8     138 .. 0.93
   2 !   60.8  12.7   4.9e-20   1.5e-16       2     135 ..     150     280 ..     149     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1.6e-19
                           EamA   2 lgillallaalfwaiyfvlskil.lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                    lg+  al+aal+w++ +v+++ +  r  ++ tl + r+l +++l l+++++ +  +   ++++    + +++lg +  ++
  gi|118430867|ref|NP_146944.2|   9 LGVAAALTAALLWSTIGVVQRLAeARGADTETLIVGRTLGGSLLALALLAIYRAVP---TRRS----FAVAVLGLAPLYY 81 
                                    79999******************88888999*******999999999988888888...6666....8899999****** PP

                           EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                     ++++++ ++a++asl+++++P+++++l+ ++lge++++++++ i+l+l+G++l++
  gi|118430867|ref|NP_146944.2|  82 TYMMSVSIVGAAVASLLLYTAPAWVALLGTVFLGETPSVRDVVTIILGLAGAALVS 137
                                    ******************************************************97 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 4.9e-20
                           EamA   2 lgillallaalfwaiyfvlskil.lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                    lgi+l +++ +f+a+y+v+++ + +r    ++++   + + g ll + + ++  ++      ++++ ++++++ +v  +l
  gi|118430867|ref|NP_146944.2| 150 LGIVLGVASGFFYALYIVMARFFqSRGAGVMEVSLAPIALTGPLLGVALKPSLPPN----SVEVAASIYFAVFTMVTPYL 225
                                    79******************999566667777777777777777766666655555....8889999************* PP

                           EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                    l +yal++++a ++s+++++eP+ +++l+vlllge lt +q lg vlil+++l  
  gi|118430867|ref|NP_146944.2| 226 LNVYALRRIEAHRVSVMSLIEPLSAVLLAVLLLGEDLTALQALGGVLILAAALGA 280
                                    ***************************************************9876 PP

>> Sugar_transport  Sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  11.3   9.1e-06     0.027       3     176 ..      14     179 ..      12     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.1e-06
                Sugar_transport   3 aliPllaWGsipli...askiggkpeqqilGttlgallfalilflvkqpeltlkillvslisGllWaigqllqfkalklv 79 
                                    al  +l+W +i+++   a+  g+++e  i+G tlg  l+al+l+++ ++  t +++ v++++ +       + + ++++v
  gi|118430867|ref|NP_146944.2|  14 ALTAALLWSTIGVVqrlAEARGADTETLIVGRTLGGSLLALALLAIYRAVPTRRSFAVAVLGLAPL---YYTYMMSVSIV 90 
                                    89999***99888722245678889999*******************************9975544...45566799999 PP

                Sugar_transport  80 gvskamPi.stglqLvgasLigvlvlgeWstsiqvilGllaliliviGivltslkekkekkseeenlkkgllllllstig 158
                                    g ++a+ +  t+   v  +L+g ++lge +++ +v+    ++il ++G++l sl  + ++ + +     g++l + s ++
  gi|118430867|ref|NP_146944.2|  91 GAAVASLLlYTAPAWV--ALLGTVFLGETPSVRDVV----TIILGLAGAALVSLGGEGKAGELR---LLGIVLGVASGFF 161
                                    *999987614555555..6999999***99988887....899999********9999888887...78999999***** PP

                Sugar_transport 159 yviyvvlaqlvkvdglea 176
                                    y++y v+a+ ++  g  +
  gi|118430867|ref|NP_146944.2| 162 YALYIVMARFFQSRGAGV 179
                                    ********9998777655 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   0.00014      0.43      83     137 ..      84     138 ..      49     168 .. 0.84
   2 ?    4.5   0.3    0.0061        18     239     282 ..     230     273 ..     181     283 .] 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                            TPT  83 vvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasv 137
                                    ++s+s v    +  +  ++P++ ++l +++lge++s+  +++++  ++G al s+
  gi|118430867|ref|NP_146944.2|  84 MMSVSIVGAAVASLLLYTAPAWVALLGTVFLGETPSVRDVVTIILGLAGAALVSL 138
                                    466666666668888899************************9999999999886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0061
                            TPT 239 vLervspvthsvantvKrvvvIvlsvlvfknpvsllnaiGtava 282
                                    +L r+ +   sv + +     + l+vl++++ ++ l+a+G ++ 
  gi|118430867|ref|NP_146944.2| 230 ALRRIEAHRVSVMSLIEPLSAVLLAVLLLGEDLTALQALGGVLI 273
                                    34455555555555555555555555555555555555554443 PP

>> DUF5510  Family of unknown function (DUF5510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0025       7.6      37      58 ..      72      93 ..      52      97 .. 0.80
   2 ?    1.3   0.1      0.11   3.3e+02      16      44 ..     107     133 ..     104     137 .. 0.68
   3 ?    3.6   0.1     0.021        64      34      52 ..     149     167 ..     145     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                        DUF5510 37 tilGlacayftykyiipifias 58
                                   ++lGla  y+ty   + i  a+
  gi|118430867|ref|NP_146944.2| 72 AVLGLAPLYYTYMMSVSIVGAA 93
                                   69**********9888876554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                        DUF5510  16 iilGivilifspakfriiviGtilGlaca 44 
                                     +lG v l  +p+     v+  ilGla a
  gi|118430867|ref|NP_146944.2| 107 ALLGTVFLGETPSVRD--VVTIILGLAGA 133
                                    5677777777776544..45669999987 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.021
                        DUF5510  34 viGtilGlacayftykyii 52 
                                    ++G +lG+a  +f   yi+
  gi|118430867|ref|NP_146944.2| 149 LLGIVLGVASGFFYALYIV 167
                                    5799*********999997 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.2   1.3e-05      0.04      80     128 ..       4      58 ..       1      80 [. 0.73
   2 ?   -0.8   0.9       0.3   8.9e+02      95     140 ..     226     274 ..     222     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                    HHHHHHTHHHHHHHH.....H.HHHHHHHHHT--EEEEEEEEEEHHHHHHTTTT- CS
                           MdcE  80 rrdEllGihealahl.....a.kalarArlaGhpvigllvGkavsGaflahglqa 128
                                    r  EllG+  al+ +     +  +  +A+++G+ + +l+vG+++ G++la +l a
  gi|118430867|ref|NP_146944.2|   4 RSSELLGVAAALTAAllwstIgVVQRLAEARGADTETLIVGRTLGGSLLALALLA 58 
                                    557999999999765222222134568************************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.3
                                    HHHHHHHHHHT--EEEEEEEEEEHHHHHHTTTT-SEEEEEE...T-EEE CS
                           MdcE  95 akalarArlaGhpvigllvGkavsGaflahglqanrlialp...gvqva 140
                                     +++a+ r++ h+v  +   + +s  +la  l  + l al+   gv + 
  gi|118430867|ref|NP_146944.2| 226 LNVYALRRIEAHRVSVMSLIEPLSAVLLAVLLLGEDLTALQalgGVLIL 274
                                    5789999999999988888899999999999999999999877677665 PP

>> DUF2953  Protein of unknown function (DUF2953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.16   4.8e+02       8      25 ..      13      27 ..      12      33 .. 0.78
   2 ?    5.6   0.2    0.0058        17      12      34 ..     151     173 ..     151     184 .. 0.91
   3 ?    1.8   0.1     0.085   2.5e+02      12      42 ..     212     241 ..     210     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.16
                        DUF2953  8 aadTgilyGliwaikgll 25
                                   aa+T+   +l+w+++g +
  gi|118430867|ref|NP_146944.2| 13 AALTA---ALLWSTIGVV 27
                                   56666...88****9975 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0058
                        DUF2953  12 gilyGliwaikgllygllsnlfn 34 
                                    gi++G+++++ + ly ++ ++f+
  gi|118430867|ref|NP_146944.2| 151 GIVLGVASGFFYALYIVMARFFQ 173
                                    8****************999986 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.085
                        DUF2953  12 gilyGliwaikgllygllsnlfnikkpeiev 42 
                                     i+++++ +++++l+++ ++l +i+ ++++v
  gi|118430867|ref|NP_146944.2| 212 SIYFAVFTMVTPYLLNV-YALRRIEAHRVSV 241
                                    5889999*******996.8999998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2090.00
//
Query:       gi|14600431|ref|NP_146945.1|  [L=171]
Description: molybdopterin biosynthesis protein MogA [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-29  103.0   0.0    1.3e-29  102.7   0.0    1.0  1  MoCF_biosynth   Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.072   13.4   0.0       0.11   12.8   0.0    1.3  1  ATP-synt_F      ATP synthase (F/14-kDa) subunit
       0.14   10.9   0.0       0.17   10.6   0.0    1.1  1  Acetate_kinase  Acetokinase 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 !  102.7   0.0   2.1e-33   1.3e-29       2     138 ..      17     156 ..      16     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 2.1e-33
                                   EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH..HHHHHTSSEEEEESS-SSSTT--HHHHHHH CS
                 MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeal..laaleeadviittGGtGptpdDvtpealak 80 
                                   +++++d++++g  eD+ +pl+++ l+++g +++++t v+   eei++++  +a+ +e d+i++tGGtGp+p+Dvt +a+++
  gi|14600431|ref|NP_146945.1|  17 MVITSDKVYAGLKEDRITPLVSSTLESRGRRLAAVTKVRNTFEEIVSTIasMASRRECDIILVTGGTGPGPRDVTADAVSR 97 
                                   799**********************************************987776777*********************** PP

                                   HHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTE.EEEE-SSHHHHHHHHHHHH CS
                 MoCF_biosynth  81 lfekelegfeeafrrvslkpgkpvgvapgailsrav.....gkt.iigLPGspkavkealeeil 138
                                   l   +l+g +e frr+s+ +     v+p   lsra+     g+t +++ PG+p+av  al++il
  gi|14600431|ref|NP_146945.1|  98 LAIYTLPGYGEEFRRLSASE-----VGPRGLLSRAEayvlpGGTpVFTTPGNPGAVSLALKIIL 156
                                   *******************9.....****************6666***************9997 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05      0.11      12      52 ..      45      84 ..      38     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                  HHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHH CS
                    ATP-synt_F 12 gfrlaGvgevevtdeeeieealkelleredigiilitekia 52
                                  g rla v++v++t  eei +++ ++++r+++ iil+t    
  gi|14600431|ref|NP_146945.1| 45 GRRLAAVTKVRNT-FEEIVSTIASMASRRECDIILVTGGTG 84
                                  5689999999877.6*********************97655 PP

>> Acetate_kinase  Acetokinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   2.8e-05      0.17     306     373 ..      60     129 ..      44     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.8e-05
                Acetate_kinase 306 rlakyigeyaavlegkvDaivFTgGigenaalvrelvlkalevlglevdkekn...k.nrsGedelisteqs 373
                                    + ++i+++a +   + D i  TgG g  + +v +++++ l+++ l  + e       ++ G ++l+s +++
  gi|14600431|ref|NP_146945.1|  60 EIVSTIASMASRR--ECDIILVTGGTGPGPRDVTADAVSRLAIYTLPGYGEEFrrlSaSEVGPRGLLSRAEA 129
                                   4667788887776..5***************************99988766542222467788888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1383.84
//
Query:       gi|118430868|ref|YP_874800.1|  [L=73]
Description: hypothetical protein APE_0077a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.4   0.0      0.096   13.3   0.0    1.1  1  DUF4646   Domain of unknown function (DUF4646)


Domain annotation for each model (and alignments):
>> DUF4646  Domain of unknown function (DUF4646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.3e-06     0.096      32      67 ..      24      60 ..       7      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.3e-06
                        DUF4646 32 gFp.elaPpskavphplvthdVseedWkrFledikaa 67
                                    F+ ++ P ++a+++ l + dV++++W  ++ +i+++
  gi|118430868|ref|YP_874800.1| 24 PFSkNVWPLVRAAEKALEEGDVEAAEWLALIAEIRTS 60
                                   476688999*************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 569.27
//
Query:       gi|14600432|ref|NP_146946.1|  [L=132]
Description: S-adenosylmethionine decarboxylase proenzyme [Aeropyrum pernix K1]
Scores for 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  111.6   0.0    2.3e-32  111.4   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.0   1.3e-36   2.3e-32       1     105 [.      12     119 ..      12     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.3e-36
                                   EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-..SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST CS
                     AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkf..epeGvsvvvliaeShlsiHtwpetgyaaiDvftcge 79 
                                   h++  lyg+ +e+ +d+e l+ ++ +aae +gatv  v+++++  e++Gvsv+vl+ eShl++Htwpe+ ya++D++tcge
  gi|14600432|ref|NP_146946.1|  12 HVYGSLYGVPREKATDEEYLRGVVVRAAESAGATVHAVNSWTIpgEKGGVSVIVLVLESHLALHTWPEYDYATFDIYTCGE 92 
                                   9999***************************************87778********************************* PP

                                   .HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                     AdoMet_dc  80 .ispekaleylieafkadrvtvdelkR 105
                                    ++p+ka+e+l +++k++++tv++++R
  gi|14600432|ref|NP_146946.1|  93 hTDPWKAFELLLSELKPRKYTVHYVDR 119
                                   *************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1059.64
//
Query:       gi|118430869|ref|NP_146947.2|  [L=673]
Description: hypothetical protein APE_0080.1 [Aeropyrum pernix K1]
Scores for 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-13   48.9   0.2    1.2e-12   47.8   0.2    1.6  1  HAS-barrel     HAS barrel domain
    8.3e-09   35.9   0.0    2.1e-08   34.6   0.0    1.6  1  DUF87          Helicase HerA, central domain
    6.1e-07   29.8   0.0     0.0074   16.6   0.0    3.0  3  AAA_22         AAA domain
      1e-06   28.3   1.3      5e-06   26.1   0.3    2.1  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
    1.3e-06   28.9   0.0     0.0029   18.0   0.0    2.4  2  AAA            ATPase family associated with various cellular
    2.5e-06   26.4   0.0      0.033   12.8   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    1.6e-05   24.0   0.0    4.3e-05   22.6   0.0    1.6  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00016   21.7   0.1       0.57   10.2   0.0    2.3  2  ResIII         Type III restriction enzyme, res subunit
     0.0009   18.9   0.1     0.0024   17.5   0.0    1.7  2  Zot            Zonular occludens toxin (Zot)
     0.0035   16.5   0.1     0.0093   15.0   0.1    1.7  1  T2SSE          Type II/IV secretion system protein
     0.0035   17.7   0.1      0.095   13.1   0.0    2.5  2  AAA_16         AAA ATPase domain
     0.0046   16.7   0.1     0.0088   15.8   0.1    1.4  1  AAA_29         P-loop containing region of AAA domain
     0.0052   17.3   0.0      0.017   15.7   0.0    1.8  1  ABC_tran       ABC transporter
     0.0078   15.2   0.1       0.97    8.3   0.0    2.2  2  AAA_10         AAA-like domain
       0.01   15.8   0.0      0.091   12.7   0.0    2.1  2  NACHT          NACHT domain
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.028   13.9   0.0    1.5  1  AAA_7          P-loop containing dynein motor region
      0.018   14.9   0.1       0.74    9.6   0.1    2.3  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
      0.019   15.3   0.1      0.095   13.0   0.1    1.9  2  AAA_19         AAA domain
      0.026   14.1   0.1      0.047   13.3   0.1    1.4  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.027   14.3   0.0        5.1    6.8   0.0    2.3  2  DEAD           DEAD/DEAH box helicase
      0.042   13.7   0.2      0.095   12.6   0.2    1.5  1  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.056   13.4   0.0       0.24   11.3   0.0    1.8  2  ATPase_2       ATPase domain predominantly from Archaea
      0.061   12.9   0.1          2    7.9   0.1    2.3  2  AAA_25         AAA domain
      0.064   13.4   0.0       0.24   11.6   0.0    1.9  2  AAA_33         AAA domain
      0.068   12.9   0.0       0.75    9.5   0.0    2.1  2  AAA_30         AAA domain
        0.1   11.8   0.1        6.9    5.8   0.0    2.1  2  DUF2075        Uncharacterized conserved protein (DUF2075)
        0.1   12.6   0.0        1.2    9.2   0.0    2.2  2  AAA_14         AAA domain
       0.13   12.8   0.1       0.23   11.9   0.1    1.3  1  AAA_23         AAA domain
       0.19   11.1   0.0       0.34   10.3   0.0    1.3  1  Pox_A32        Poxvirus A32 protein
       0.21   12.1   0.0       0.54   10.8   0.0    1.6  1  AAA_18         AAA domain


Domain annotation for each model (and alignments):
>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.2     2e-15   1.2e-12       1      91 [.      18     122 ..      18     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2e-15
                     HAS-barrel   1 iGevigestssslifrvegsk..............dvkvGeyVeielp.dgeivlGmvtdirrgnselsndlalvlslee 65 
                                    +Gev+g++t++s++++++gs+              +v++G+y++i +p + +i+lG+v++i+r                 
  gi|118430869|ref|NP_146947.2|  18 MGEVVGRVTRYSPVTTSPGSIvevevdtvkyfsrgGVRIGDYLCIVDPkTLHIILGVVSTIKR----------------- 80 
                                    8**************************************************************................. PP

                     HAS-barrel  66 leeangddevalatedt......................gvkvlGeve 91 
                                          +de+ala +d+                      gv++l+e++
  gi|118430869|ref|NP_146947.2|  81 ------ADELALAGVDVpltpnsspgptspesiltspiaGVRLLLEAD 122
                                    ......*********999999999999999999999999999998876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   3.5e-11   2.1e-08       8      82 ..     174     250 ..     168     296 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 3.5e-11
                          DUF87   8 sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkga..tililDpHGEYgkal.ekllsekvkvitps 82 
                                    +g +v v+l   k++ +H++++g+TGsGK+++ + ++++l +++g     +ilD+++++ ++  +++++++++v++  
  gi|118430869|ref|NP_146947.2| 174 KGGSVAVRLPY-KALLHHTLVIGTTGSGKTTLLKNMIASLTSEDGDfiVPIILDMNSDFIQLPiPSRGESDLEVLRSV 250
                                    67788899998.6669*************************8444434778*********998866666666666554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.2e-05    0.0074       7      32 ..     190     215 ..     189     288 .. 0.79
   2 ?   -1.1   0.0       3.4     2e+03      50      98 ..     426     471 ..     400     478 .. 0.69
   3 !    9.5   0.0    0.0018       1.1      76     105 ..     524     558 ..     485     600 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldee 32 
                                    +++v+G +G+GKTtll+++  +l+ e
  gi|118430869|ref|NP_146947.2| 190 HTLVIGTTGSGKTTLLKNMIASLTSE 215
                                    689****************9999543 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.4
                         AAA_22  50 stsskdllrellralglelkaerlsseellealeqalraravielliiD 98 
                                    ++  ++l   +l++l + + + r + e+l+++++  +++  v  + i++
  gi|118430869|ref|NP_146947.2| 426 LG-MRSLVDLVLEILSSIRPH-RSTAEALYRKIQGLMDSGVV-DVSIVE 471
                                    44.444444455555544455.55899999999988888777.776665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0018
                         AAA_22  76 eellealeqalrarav..ielliiDEaqhlr...s 105
                                    + +l++ ++ + +r+v  + l+iiDEa+ ++   +
  gi|118430869|ref|NP_146947.2| 524 QSILRMRQDEWARRRVskQLLIIIDEAHQFFpqeR 558
                                    44556666677777778999*********876541 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.3   8.3e-09     5e-06      40      64 ..     189     213 ..     172     217 .. 0.85
   2 ?    0.5   0.0      0.54   3.2e+02     209     241 ..     563     595 ..     533     597 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 8.3e-09
                                    .SEEEE--TTSSHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  40 shllvaGatgsGKStalntLilSla 64 
                                     h+lv+G+tgsGK+t l+++i+Sl 
  gi|118430869|ref|NP_146947.2| 189 HHTLVIGTTGSGKTTLLKNMIASLT 213
                                    7**********************96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.54
                                    HHH....HHHHHHHHHHHCGGGTEEEEEEES-- CS
                   FtsK_SpoIIIE 209 pkdssvlvedaivRlarkgraaglHlllatqrl 241
                                    ++++s+ v ++i+ +ar gra g+ +++ t ++
  gi|118430869|ref|NP_146947.2| 563 EQEASRQVASMISSMARLGRARGIGFVFSTHSP 595
                                    456689999***************999988766 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   0.0    0.0044       2.7       2      24 ..     192     214 ..     191     250 .. 0.77
   2 !   18.0   0.0   4.9e-06    0.0029      57     122 ..     539     606 ..     512     615 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0044
                                    EEESSTTSSHHHHHHHHHHHHTH CS
                            AAA   2 llyGppGtGKTllakavakelgv 24 
                                    l++G+ G GKT+l k ++ +l +
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTTLLKNMIASLTS 214
                                    899************99999743 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.9e-06
                                    S.TSEEEEEETGGGHHHHH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.T CS
                            AAA  57 a.kpsilfiDEidalaksr.sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.g 122
                                      k+  ++iDE++++++++  g e++e++r v+ +++ + ++ + ++ + ++  t++p++l + +l  +
  gi|118430869|ref|NP_146947.2| 539 VsKQLLIIIDEAHQFFPQErGGYEEQEASRQVASMISSMARLGRARG-IGFVFSTHSPNDLHDIILQlS 606
                                    235689*************6667999*****************9766.*************99998444 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00014     0.085      13      60 ..     180     230 ..     172     250 .. 0.74
   2 !   12.8   0.0   5.6e-05     0.033     259     313 ..     543     605 ..     539     614 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                         DUF853  13 lalalklanrhGliaGatGtGktvtLqvlaesl.seaG...vpvfladvkGd 60 
                                    ++l  k    h l+ G tG Gkt  L+ +  sl se+G   vp+ + d+  d
  gi|118430869|ref|NP_146947.2| 180 VRLPYKALLHHTLVIGTTGSGKTTLLKNMIASLtSEDGdfiVPI-ILDMNSD 230
                                    6677788889****************988776636666443333.3466555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 5.6e-05
                         DUF853 259 lvfffdeahLLf.........ndapkallekveqvvrLirskGvGvyfvtqnPldlPdtvLaqL 313
                                    l +  deah +f         ++a++ +   +  + rL r++G+G  f t +P dl d +L qL
  gi|118430869|ref|NP_146947.2| 543 LLIIIDEAHQFFpqerggyeeQEASRQVASMISSMARLGRARGIGFVFSTHSPNDLHDIIL-QL 605
                                    6677899999885555555545799999999*************************99877.55 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 !   22.6   0.0   7.2e-08   4.3e-05      10      56 ..     183     232 ..     177     236 .. 0.79
   2 ?   -2.7   0.0       3.5   2.1e+03     268     311 ..     581     616 ..     571     621 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.2e-08
                  TrwB_AAD_bind  10 pkeretqhilivGttGsGKtqalekllrairargdra...ivlDltGafv 56 
                                    p ++  +h+l++GttGsGKt+ l+++++++ +        i+lD++ +f+
  gi|118430869|ref|NP_146947.2| 183 PYKALLHHTLVIGTTGSGKTTLLKNMIASLTSEDGDFivpIILDMNSDFI 232
                                    5566678**********************998876551235788888887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                  TrwB_AAD_bind 268 gRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsd 311
                                    gR  G+ +v   +s + l+++        il+l ntk++lr++ 
  gi|118430869|ref|NP_146947.2| 581 GRARGIGFVFSTHSPNDLHDI--------ILQLSNTKIVLRTEK 616
                                    555666666666655555544........777888888888765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00095      0.57      25      54 ..     189     218 ..     179     229 .. 0.84
   2 !    9.1   0.0     0.002       1.2     122     163 ..     531     580 ..     516     582 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                                    SEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                         ResIII  25 krglikmaTGtGKTlvaaklierllkkgke 54 
                                    ++ l+  +TG+GKT ++ ++i++l+++ + 
  gi|118430869|ref|NP_146947.2| 189 HHTLVIGTTGSGKTTLLKNMIASLTSEDGD 218
                                    5789999****************9998664 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.002
                                    .....HHHTTT-SEEEEETGGGTTS.........TTTHHHHHT---SEEE CS
                         ResIII 122 eeeseellrdrfdviiiDEaHrlgak........kswreilekfkeavll 163
                                    + e  + + +++++iiiDEaH +  +        ++ r+++ ++++  +l
  gi|118430869|ref|NP_146947.2| 531 QDEWARRRVSKQLLIIIDEAHQFFPQerggyeeqEASRQVASMISSMARL 580
                                    5555566677888*********9988444444333777777777766555 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.9   3.6e+03       4      15 ..     192     203 ..     191     217 .. 0.85
   2 !   17.5   0.0   4.1e-06    0.0024      72     134 ..     531     602 ..     500     621 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.9
                            Zot   4 lvtGapGsgKts 15 
                                    lv G  GsgKt 
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTT 203
                                    6789******96 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.1e-06
                            Zot  72 fakwat..idkgallviDEcqeifpvrakegrkd.......pevinafteh.RhlgwDivlltqdiskihkev 134
                                       wa+  + k  l++iDE++++fp++++   +          +i   +++ R  g   v+ t  ++ +h+ +
  gi|118430869|ref|NP_146947.2| 531 QDEWARrrVSKQLLIIIDEAHQFFPQERGG-YEEqeasrqvASMISSMARLgRARGIGFVFSTHSPNDLHDII 602
                                    3344442267******************95.444366666545554444442556777777777777777766 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.6e-05    0.0093     132     160 ..     191     219 ..     181     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                          T2SSE 132 ilvsGgTgsGKttllyallkeinksderi 160
                                     lv G+TgsGKttll  +++ + ++d  +
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTSEDGDF 219
                                    5899***********99999998886554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00016     0.095      25      53 ..     189     217 ..     156     250 .. 0.75
   2 ?    1.8   0.0      0.46   2.8e+02     134     149 ..     540     555 ..     471     589 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                         AAA_16  25 elvllsGesGvGKsslvrellralekdgg 53 
                                    + +l++G  G+GK++l++    +l+ ++g
  gi|118430869|ref|NP_146947.2| 189 HHTLVIGTTGSGKTTLLKNMIASLTSEDG 217
                                    789**************888878887744 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.46
                         AAA_16 134 erplvlvlDdlqwade 149
                                    +++l++++D+++++ +
  gi|118430869|ref|NP_146947.2| 540 SKQLLIIIDEAHQFFP 555
                                    346*********7765 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 !   15.8   0.1   1.5e-05    0.0088      24      49 ..     190     215 ..     181     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                         AAA_29  24 atlltGpsGsGKSTllDAiqalLvpa 49 
                                     tl++G++GsGK+Tll  ++a L+++
  gi|118430869|ref|NP_146947.2| 190 HTLVIGTTGSGKTTLLKNMIASLTSE 215
                                    49**************9988888765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.8e-05     0.017      14      41 ..     191     218 ..     187     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-05
                                    EEEEESTTSSHHHHHHHHTTSS--SEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  14 vaivGenGaGKStLlkllagllkpteGe 41 
                                    + ++G +G+GK+tLlk ++  l+ + G+
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTSEDGD 218
                                    6789************999998888886 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.022        13      22      47 ..     189     214 ..     184     227 .. 0.83
   2 !    8.3   0.0    0.0016      0.97     254     288 ..     566     600 ..     514     625 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.022
                         AAA_10  22 sasliiGdlGnGKSvlakllvlyisl 47 
                                     ++l+iG +G GK  l k ++  ++ 
  gi|118430869|ref|NP_146947.2| 189 HHTLVIGTTGSGKTTLLKNMIASLTS 214
                                    589***************99877665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                         AAA_10 254 ssaeGkkllkelvRiGRsynaavylvtqsadDvlk 288
                                     s + + +++++ R GR+     ++ t+s++D+ +
  gi|118430869|ref|NP_146947.2| 566 ASRQVASMISSMARLGRARGIGFVFSTHSPNDLHD 600
                                    456667899***********************976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00015     0.091       3      28 ..     191     216 ..     189     230 .. 0.82
   2 ?    0.5   0.0      0.83     5e+02      78     111 ..     538     576 ..     522     623 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                    EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegk 28 
                                     ++ G  GsGKTtLl+ ++  + +++
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTSED 216
                                    5899************9998887765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.83
                                    CSCCCEEEEEE-STT-SS-TCH..............HHH CS
                          NACHT  78 elperlLlilDglDelvtdlgq.....kekqpvrtlLse 111
                                    ++ ++lL+i+D + ++  + +      +  ++v  ++s+
  gi|118430869|ref|NP_146947.2| 538 RVSKQLLIIIDEAHQFFPQERGgyeeqEASRQVASMISS 576
                                    5678999***99999988666575544333444444444 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   4.7e-05     0.028      34      61 ..     189     216 ..     184     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                          AAA_7  34 kpvllvGptGtGKtviikdllkkldkek 61 
                                    +++l++G+tG+GKt+++k+++ +l +e+
  gi|118430869|ref|NP_146947.2| 189 HHTLVIGTTGSGKTTLLKNMIASLTSED 216
                                    799****************999998765 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 ?    9.6   0.1    0.0012      0.74       2      63 ..     191     243 ..     191     251 .. 0.75
   2 ?    3.0   0.0      0.13        76     287     300 ..     579     596 ..     543     599 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63 
                                    +++iG  gsGK++LL+ +         + +lt+e++++  +++ +  +d+++  ip++ e +
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNM---------IASLTSEDGDFIVPIILDMNSDFIQLPIPSRGESD 243
                                    789************988.........34577777777788888888888777777766555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                         AAA_21 287 r....ngaQviltTHSpl 300
                                    r    +g+ ++++THSp 
  gi|118430869|ref|NP_146947.2| 579 RlgraRGIGFVFSTHSPN 596
                                    3444599*********96 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00016     0.095      12      39 ..     190     217 ..     184     225 .. 0.86
   2 ?   -1.0   0.0       3.4     2e+03      96     112 ..     535     551 ..     515     557 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                         AAA_19  12 vllvtaGpGtGKTrvlkhivallvelgg 39 
                                    + lv++  G+GKT++lk ++a l ++ g
  gi|118430869|ref|NP_146947.2| 190 HTLVIGTTGSGKTTLLKNMIASLTSEDG 217
                                    679******************9998775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                         AAA_19  96 eekklqeeellivDEfq 112
                                     ++ + ++ l+i+DE+ 
  gi|118430869|ref|NP_146947.2| 535 ARRRVSKQLLIIIDEAH 551
                                    4556756669*****86 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 ?   13.3   0.1   7.8e-05     0.047       3      22 ..     191     213 ..     189     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                                    EEEEESTTCCHHHHHHHHH...C CS
                           cobW   3 tvltGflGsGKTtLlnhll...e 22 
                                    t++ G  GsGKTtLl++++   +
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIaslT 213
                                    7899**************95432 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0086       5.1      15      41 ..     189     214 ..     181     295 .. 0.69
   2 ?    5.0   0.0     0.032        19     119     137 ..     539     560 ..     520     592 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0086
                                    CEEEEEESTTSSHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlaflipvlqivye 41 
                                    ++ lv + TGsGKT+  l  +++++++
  gi|118430869|ref|NP_146947.2| 189 HHTLVIGTTGSGKTTL-LKNMIASLTS 214
                                    578999********98.4555555544 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.032
                                    CTTEEEEEEETHHHHHHT...T CS
                                    xxxxxxxxxxxxxxxxxx...x RF
                           DEAD 119 lsqvrflVlDEadrlldq...g 137
                                    +s+  ++++DEa+++  q   g
  gi|118430869|ref|NP_146947.2| 539 VSKQLLIIIDEAHQFFPQergG 560
                                    667779********99884443 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   0.2   0.00016     0.095       4      26 ..     193     215 ..     191     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                           MobB   4 ivgksgsGKTtLleklipelkar 26 
                                    ++g+ gsGKTtLl+++i+ l+++
  gi|118430869|ref|NP_146947.2| 193 VIGTTGSGKTTLLKNMIASLTSE 215
                                    689****************9986 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    0.0004      0.24      24      60 ..     192     230 ..     188     242 .. 0.77
   2 ?   -1.3   0.0       2.8   1.7e+03     116     129 ..     539     552 ..     533     561 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                       ATPase_2  24 fiYGpegsGKtaLlkeiienl..edkdkyviyyialree 60 
                                    ++ G  gsGKt+Llk++i  l  ed d+ v  + +++++
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTTLLKNMIASLtsEDGDFIVPIILDMNSD 230
                                    688****************99434444466666665555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                       ATPase_2 116 kgkkiiiiiDelqk 129
                                      k++ iiiDe+ +
  gi|118430869|ref|NP_146947.2| 539 VSKQLLIIIDEAHQ 552
                                    4678*******987 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    0.0034         2      36      59 ..     191     214 ..     186     223 .. 0.86
   2 ?    2.3   0.0      0.19   1.1e+02     144     189 ..     543     594 ..     493     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0034
                         AAA_25  36 allaGapgtGKttlaldlalavat 59 
                                    +l++G +g+GKttl+ ++ +++++
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTS 214
                                    7999**************999984 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                         AAA_25 144 rlvviDplsralgg......densnsdvgalvealeriarrtgaavllvhHv 189
                                     l++iD   ++++       + +++++v+++++ ++r+ r+ g+ +++  H+
  gi|118430869|ref|NP_146947.2| 543 LLIIIDEAHQFFPQerggyeEQEASRQVASMISSMARLGRARGIGFVFSTHS 594
                                    5999999999998777777555666778999999999999999888888887 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0004      0.24       3      24 ..     192     213 ..     191     226 .. 0.87
   2 ?   -2.2   0.0       6.9   4.1e+03      27      72 ..     528     587 ..     508     592 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                         AAA_33   3 llvGlpGsGKstlaerllkklg 24 
                                    l++G  GsGK+tl++++++ l+
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTTLLKNMIASLT 213
                                    789*************998876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.9
                         AAA_33  27 llssdtlrrrlfg..............tdqqsktdytrvldrlyqilnelarkalsagrn 72 
                                    + ++d++ rr +                +++   + ++++ ++  +++ +ar  +++g++
  gi|118430869|ref|NP_146947.2| 528 RMRQDEWARRRVSkqlliiideahqffPQERGGYEEQEASRQVASMISSMARLGRARGIG 587
                                    555555444333223333333222222111222233445555555555666666666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012      0.75      21      48 ..     191     218 ..     185     226 .. 0.82
   2 ?    0.6   0.0      0.65   3.9e+02      81      97 ..     531     550 ..     487     557 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggr 48 
                                    +++ G  G+GKtt+lk + + ++++ g+
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTSEDGD 218
                                    6899*************98888887444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.65
                         AAA_30  81 k...grarlepgtllivDEa 97 
                                    +   +r r++++ l+i+DEa
  gi|118430869|ref|NP_146947.2| 531 QdewARRRVSKQLLIIIDEA 550
                                    266656788888999****9 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.011       6.9       4      27 ..     191     214 ..     189     232 .. 0.83
   2 ?    3.7   0.0     0.051        30      78     120 ..     531     574 ..     517     581 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeled 27 
                                     lV G +G+GKt +l n++a l++
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTS 214
                                    5899***************99932 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.051
                        DUF2075  78 kkaeekkeepkedvvivDEAhrlltksdq.aekqseenqlkelm 120
                                    +++ ++++  k  ++i+DEAh    +++  +e+q+   q+ +++
  gi|118430869|ref|NP_146947.2| 531 QDEWARRRVSKQLLIIIDEAHQFFPQERGgYEEQEASRQVASMI 574
                                    56667788888999********9985544244554555555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     0.002       1.2       6      34 ..     192     221 ..     189     259 .. 0.75
   2 ?    0.7   0.0      0.82   4.9e+02      62      76 ..     537     553 ..     515     613 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.002
                         AAA_14   6 vitGaRrvGKTtllkqlikell.vkkesil 34 
                                    ++ G   +GKTtllk++i +l   + + i+
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTTLLKNMIASLTsEDGDFIV 221
                                    789999************998854444444 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.82
                         AAA_14  62 e..ekktylflDEiqev 76 
                                    +  +k+ ++++DE+++ 
  gi|118430869|ref|NP_146947.2| 537 RrvSKQLLIIIDEAHQF 553
                                    14467899*****9986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00039      0.23      22      46 ..     191     215 ..     189     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                         AAA_23  22 tlItGpNGaGKTTildAiklaLyge 46 
                                    tl++G +G+GKTT+l  +   L+ e
  gi|118430869|ref|NP_146947.2| 191 TLVIGTTGSGKTTLLKNMIASLTSE 215
                                    899************8887777765 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00057      0.34      17      39 ..     192     214 ..     180     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00057
                        Pox_A32  17 alvGgsGsGktvyLlsLlrtlvk 39 
                                     ++G +GsGkt+ L++++ +l +
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTTLLKNMIASLTS 214
                                    579**************998875 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   0.00091      0.54       2      34 ..     192     226 ..     192     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00091
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf..gvnlrdvake 34 
                                    l+ Gt G+GKttl k+   +l +  g+ +  ++ +
  gi|118430869|ref|NP_146947.2| 192 LVIGTTGSGKTTLLKNMIASLTSedGDFIVPIILD 226
                                    589***********998444433445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 4602.19
//
Query:       gi|118430870|ref|NP_146948.2|  [L=394]
Description: hypothetical protein APE_0082.1 [Aeropyrum pernix K1]
Scores for 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-21   77.7   1.5    1.3e-21   77.4   1.5    1.1  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 !   77.4   1.5   7.4e-26   1.3e-21       2     241 ..      70     357 ..      69     358 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 7.4e-26
                                    EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE..................HHHHHHHHH CS
                           NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel..................errirllme 63 
                                    +v+A+D+S++ v +   +l++++a++  ++  +rle ++  ++++++s + ++                  +++ ++l+ 
  gi|118430870|ref|NP_146948.2|  70 DVYAIDSSSRTV-ETPLHLILIGAVS-LSSRLKRLEADYPSFEKPLVSLNIRPylvldrlnlagepdphlgDAYSDILRF 147
                                    79**********.9999999999999.77788888888899999999*99999*************************** PP

                                    HHHHH........HHHHHCGGCCSCEEEEECSHHCCCH.HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SC CS
                           NurA  64 tlElk........lgallleekgedllllDGsligslv.efdelheeleyeeylyslsrllea....glnlvgvaKsfrs 130
                                    +lE++        l +++++e+ ++++++DG+++   + +++   +++ + e++++++r++ +    g++++g++K+++ 
  gi|118430870|ref|NP_146948.2| 148 SLENAmlsyllerLIEDRYPEDYASAVIIDGPILNGSIlAKLSTRIGDVWSELYRERQRIIASiealGVPVIGYVKRIEA 227
                                    ********************************9988887999************************************** PP

                                    TCCHCCC.........S--HHHHCCHHCCHCH..........---STTS-HHHHTT-HCCHHHHHH-EEEEEEES..... CS
                           NurA 131 kellnll...letlligesisDiallgallrk..........pgytspllkilrekpllrealidkeiyfaYvrl..... 192
                                    ++ll ++   le l++++ ++++a  +a+++           p      +  l ++  ++   + +e+ f Y++l     
  gi|118430870|ref|NP_146948.2| 228 STLLSRAnayLELLEDCLGFAPRASDSAIIEAavgygchkwrP------GYALKSLLSRVVYGNGDEKLFEYLILpggry 301
                                    **********999999*99999999999996697774443333......334444477777777788************* PP

                                    ...STTTTEEEEEHHHHHHCCHHHHHHHHHH...........TTB-SSSBCCHHHHHHHHC CS
                           NurA 193 ...egggsilrleipaevstakdedvlslla.........sqrlsisGYprpLalAhelak 241
                                       +++++++r+e     +t +   +l+            ++ l +s+ p+ La+ +++a+
  gi|118430870|ref|NP_146948.2| 302 qlfSPKRRVYRIE-----YTRHSLRLLEGYGfrpyhivlsETLLRGSLEPVTLARSDRRAR 357
                                    *************.....99**********9***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2906.45
//
Query:       gi|118430871|ref|NP_146950.2|  [L=237]
Description: NADH dehydrogenase [Aeropyrum pernix K1]
Scores for 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   62.0   0.2    2.4e-16   60.2   0.2    1.7  1  Nitroreductase  Nitroreductase family
  ------ inclusion threshold ------
      0.064   13.7   0.1       0.12   12.8   0.1    1.4  1  SHS2_FTSA       SHS2 domain inserted in FTSA
       0.13   11.8   0.0        0.2   11.2   0.0    1.3  1  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 !   60.2   0.2     4e-20   2.4e-16       1     169 [.      11     164 ..      11     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 4e-20
                                    HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGHHH CS
                 Nitroreductase   1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkeelk 80 
                                    i + rS+R F+ ep+p+e+++kileaarr  s  n+qp++++vv+d +l+ +l +a++++ + +ea+ +++++       
  gi|118430871|ref|NP_146950.2|  11 ISRHRSVRSFSTEPIPQEDIRKILEAARRHVSPWNIQPVHVTVVTDSKLKSRLSDALWGQEQIKEAPVFFVFS------- 83 
                                    6678********************************************************************9....... PP

                                    HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..S CS
                 Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdee 160
                                      ++k l+   +l +         r ++  +    +++a+ a+   +  A++lG+ + +i ++ +   ev+++lglp+  
  gi|118430871|ref|NP_146950.2|  84 VDYAKVLESIKLLGLE-------AREPGLTELLQGYISASVALAWSIAVAEDLGYVVNIIAAYGNPC-EVADILGLPSYV 155
                                    5577777777766666.......67777777777777777777777777777777777777777555.69*******988 PP

                                    EEEEEEEEE CS
                 Nitroreductase 161 eivvliavG 169
                                     +v+ + vG
  gi|118430871|ref|NP_146950.2| 156 VPVAGLLVG 164
                                    888888888 PP

>> SHS2_FTSA  SHS2 domain inserted in FTSA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     2e-05      0.12       8      48 ..      13      52 ..      10      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                   EEEEEEE-TTS-E--HHHHHHHHHHH....CHTTEEEEEEE CS
                      SHS2_FTSA  8 nskgvvaisgedeiteedvervleaakavaipedreilhvi 48
                                   +++ v ++s+e  i +ed++++leaa+++  p + + +hv 
  gi|118430871|ref|NP_146950.2| 13 RHRSVRSFSTE-PIPQEDIRKILEAARRHVSPWNIQPVHVT 52
                                   56778889999.**************99999*****99996 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.4e-05       0.2       5      53 ..      10      61 ..       7      92 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                                   HHHH--B---B--S---HHHHHHHHH----.-S.....S-----EE.E.... CS
                 TM1586_NiRdase  5 aiekRhsvRkYkdealeeelleelkeaiee.inkes..glelqlvidenkaf 53
                                    i   +svR+++ e++++e + ++ ea+++ +++ +   +++ +v+d++ ++
  gi|118430871|ref|NP_146950.2| 10 VISRHRSVRSFSTEPIPQEDIRKILEAARRhVSPWNiqPVHVTVVTDSKLKS 61
                                   5677789*********998888877776651444443356666666664443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1754.49
//
Query:       gi|118430872|ref|NP_146951.2|  [L=219]
Description: hypothetical protein APE_0085.1 [Aeropyrum pernix K1]
Scores for complete 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-14   52.7   0.1    1.4e-13   50.4   0.1    2.3  2  PHP_C     PHP-associated
    9.8e-08   32.5   0.0    1.7e-07   31.7   0.0    1.5  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.28   2.5e+03       5      14 ..      89      98 ..      70     105 .. 0.55
   2 !   50.4   0.1   1.5e-17   1.4e-13       2      55 ..     140     193 ..     139     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.28
                          PHP_C  5 rrArrfAekl 14
                                   ++ r++A ++
  gi|118430872|ref|NP_146951.2| 89 EELREWAVER 98
                                   3334555555 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 1.5e-17
                          PHP_C   2 eaNrrArrfAeklglpgtgGSDAHrleeVGrayTefeepiatpdelleairegr 55 
                                    + N +A r+Ae l+   + GSDAH++ +VG a  ++++++++++ ++eai +gr
  gi|118430872|ref|NP_146951.2| 140 HFNFMAIRLAEDLNHTPVSGSDAHVPSMVGVAPALVDSDNESAEGVVEAIAKGR 193
                                    68***************************************************8 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.9e-11   1.7e-07       1      86 [.       4      78 ..       4     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.9e-11
                                   EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE................ CS
                                   xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP  1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGleayvaddsekerpshlt 81
                                   +lH+Ht+ s +  ++    e+vk a++ gl aia+TDh+ + g   + +aak    +g+ +i  +e       ++++   ++
  gi|118430872|ref|NP_146951.2|  4 ELHSHTTVSdGF-QTP--MEIVKIAAKAGLAAIAVTDHDTFRGSSLAKRAAKLL--GGVAVIPAAE-------VRSEWGDVV 73
                                   79*******877.455..7***********************877666666433..4777777777.......445555566 PP

                                   ..E.. CS
                                   xxxxx RF
                            PHP 82 llakn 86
                                   +l+ n
  gi|118430872|ref|NP_146951.2| 74 VLCSN 78
                                   66654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1667.04
//
Query:       gi|118430873|ref|YP_874801.1|  [L=148]
Description: hypothetical protein APE_0085a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1178.41
//
Query:       gi|14600438|ref|NP_146952.1|  [L=163]
Description: thiol peroxidase [Aeropyrum pernix K1]
Scores for complete 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-39  133.4   0.0    4.5e-39  133.2   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    1.7e-25   89.4   0.0    2.1e-25   89.2   0.0    1.0  1  Redoxin     Redoxin
    4.5e-05   23.6   0.0    5.6e-05   23.2   0.0    1.2  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
     0.0025   17.7   0.0     0.0052   16.7   0.0    1.5  1  SCO1-SenC   SCO1/SenC
     0.0091   15.6   0.0       0.01   15.3   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.033   13.8   0.0    1.2  1  GSHPx       Glutathione peroxidase


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 !  133.2   0.0   1.5e-42   4.5e-39       1     123 [.       4     128 ..       4     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 1.5e-42
                                   TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                   vg++apdfe+  + ge+++lsd++g++vvl+fyp++ +p+Ct+e  ++++l++ef+++g+ vigvs+ds+e+ +kf+ek++
  gi|14600438|ref|NP_146952.1|   4 VGEQAPDFEGIAHTGEKIRLSDFRGRIVVLYFYPRAMTPGCTREGVRFNELLDEFEKLGAVVIGVSTDSVEKNRKFAEKHG 84 
                                   79******************************************************************************* PP

                                   .SSEEEE-TTSHHHHHTT-EETT..TTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  82 lnfpllsDeegkvakaygvlkee..kglalratfvidkegkiry 123
                                   + f+l+sDe+g++  +ygv++ e  + +a r tf+id+eg+ir+
  gi|14600438|ref|NP_146952.1|  85 FRFKLVSDEKGEIGMKYGVVRGEgsNLAAERVTFIIDREGNIRA 128
                                   ********************999*******************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.2   0.0   6.9e-29   2.1e-25       2     136 ..       4     135 ..       3     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 89.2 bits;  conditional E-value: 6.9e-29
                                   TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH CS
                       Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk 82 
                                   +g++aPdf+  ++a  g+++ ls+f+g+ vv++f+p+a +P C++e + +++l +++++ g  v++v++d+ +  ++f++k
  gi|14600438|ref|NP_146952.1|   4 VGEQAPDFE--GIAHTGEKIRLSDFRGRIVVLYFYPRAMTPGCTREGVRFNELLDEFEKLGAVVIGVSTDSVEKNRKFAEK 82 
                                   699******..689**********************************999998888************************ PP

                                   TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSC CS
                       Redoxin  83 eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepep 136
                                   +g  f+++sD+++++  ++G+      +++  + + +++id++g+++++ +   p
  gi|14600438|ref|NP_146952.1|  83 HGFRFKLVSDEKGEIGMKYGVV--RGEGSNlAAERVTFIIDREGNIRAILRNIRP 135
                                   ********************66..4444555688889*********998666655 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 !   23.2   0.0   1.9e-08   5.6e-05       4      67 ..      53     117 ..      50     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.9e-08
                    AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkrglklklaplslq 67 
                                   ++++e+++ g  +++++ +++ + +kF++  gf f+l+ D+++++  + g+ rg    la ++ +
  gi|14600438|ref|NP_146952.1|  53 ELLDEFEKLGAVVIGVSTDSVeKNRKFAEKHGFRFKLVSDEKGEIGMKYGVVRGEGSNLAAERVT 117
                                   668999***************55*****************************9988887766554 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.8e-06    0.0052       2      96 ..       9      97 ..       8     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-06
                     SCO1-SenC  2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdp 84
                                   +Fe + ++ge+++ +d++g++++++f     +  C+ +  + +e+ld++++      +++i v   +D++e+ ++++e+++ 
  gi|14600438|ref|NP_146952.1|  9 PDFEGIAHTGEKIRLSDFRGRIVVLYFYPRAMTPGCTREGVRFNELLDEFEKL----GAVVIGV--STDSVEKNRKFAEKHGF 85
                                  58*************************98888888999888888888888766....6666666..57999999999999999 PP

                     SCO1-SenC 85 riigltGskeei 96
                                  r++ ++++k ei
  gi|14600438|ref|NP_146952.1| 86 RFKLVSDEKGEI 97
                                  999888887766 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 !   15.3   0.0   3.5e-06      0.01      85     171 ..      41     126 ..      21     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-06
                        DUF899  85 CpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpglsvfl 165
                                    pgC+     +++ l ++e+ +  ++ vs   +ek  ++ ++ G+++++vs+ + +  ++++v   e++ +  +  ++  +
  gi|14600438|ref|NP_146952.1|  41 TPGCTREGVRFNELLDEFEKLGAVVIGVSTDSVEKNRKFAEKHGFRFKLVSDEKGEIGMKYGVVRGEGS-NLAAERVTFII 120
                                   589999999999999***********************************************9777663.33333333333 PP

                        DUF899 166 rddgrv 171
                                    ++g++
  gi|14600438|ref|NP_146952.1| 121 DREGNI 126
                                   334555 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.1e-05     0.033       4      67 ..      11      76 ..       9     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                  BEEEBTTSSEEEGGGGTTSEEEE..EEEESSSTTHHHHHHHHHHHHHHGGGTEEEEEEEE-TTTT- CS
                         GSHPx  4 lsakdidgekvkleklrgkvvli..vnvaskCglteqykeleelqkrykdkglvilgfPCnqfgkq 67
                                  ++ ++  gek+ l+ +rg++v++     a + g t +  +++el  ++++ g v++g   +   k 
  gi|14600438|ref|NP_146952.1| 11 FEGIAHTGEKIRLSDFRGRIVVLyfYPRAMTPGCTREGVRFNELLDEFEKLGAVVIGVSTDSVEKN 76
                                  7788999************88761156799**************************9877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1219.30
//
Query:       gi|118430874|ref|NP_146953.2|  [L=104]
Description: hypothetical protein APE_0087.1 [Aeropyrum pernix K1]
Scores for complete 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  107.9   0.0    2.8e-31  107.7   0.0    1.0  1  DUF2175     Uncharacterized protein conserved in archaea (DUF
  ------ inclusion threshold ------
      0.038   14.4   0.0       0.13   12.7   0.0    1.7  2  Vps39_2     Vacuolar sorting protein 39 domain 2
      0.056   13.2   0.6       0.19   11.5   0.6    1.9  1  zf-RING_11  RING-like zinc finger


Domain annotation for each model (and alignments):
>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   4.7e-35   2.8e-31       1      97 [.       4      99 ..       4     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 4.7e-35
                        DUF2175  1 kkwkCyiCgkeivegekFTft.kkgvvHyeClvekarkklkesedaaaLleleevlneeivklkelervaedeevkkvleqk 81
                                   k+w+C+iCg++i+eg++FTf+  +g+vH+eCl+e++ kk +   da+aLl+++evl ++iv+lke++r+ae+ee+k+ ++++
  gi|118430874|ref|NP_146953.2|  4 KTWECSICGGTIIEGQRFTFIpGQGAVHFECLAESTLKKPSG--DAVALLDANEVLLYTIVRLKEAARIAESEEIKNSIDNV 83
                                   58*************************************996..9************************************* PP

                        DUF2175 82 rkelEkaaakltkkle 97
                                   r+e+E+ a+ l+kkl+
  gi|118430874|ref|NP_146953.2| 84 RIEVERLAGILSKKLV 99
                                   *************986 PP

>> Vps39_2  Vacuolar sorting protein 39 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05      0.13      80     108 ..       7      36 ..       4      37 .. 0.92
   2 ?   -0.7   0.0      0.32   1.9e+03      61      80 ..      71      90 ..      49     102 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                        Vps39_2  80 vCavCkkrlge.svfvvyPngsvvHlgCak 108
                                    +C++C  ++ e + f   P +  vH++C +
  gi|118430874|ref|NP_146953.2|   7 ECSICGGTIIEgQRFTFIPGQGAVHFECLA 36 
                                    7*******9999****************75 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.32
                        Vps39_2 61 veeellklrskkvvvteekv 80
                                   +e+e +k++  +v+++ e+ 
  gi|118430874|ref|NP_146953.2| 71 AESEEIKNSIDNVRIEVERL 90
                                   33444555555566655555 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 ?   11.5   0.6   3.2e-05      0.19       1      20 [.       7      26 ..       7      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                     zf-RING_11  1 eCsICLeefkpgqalfilpC 20
                                   eCsIC  ++ +gq+ ++ p 
  gi|118430874|ref|NP_146953.2|  7 ECSICGGTIIEGQRFTFIPG 26
                                   9************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 759.01
//
Query:       gi|118430875|ref|NP_146954.2|  [L=323]
Description: hypothetical protein APE_0088.1 [Aeropyrum pernix K1]
Scores for complete 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   33.5   0.8    6.6e-08   32.3   0.1    2.1  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   3.7e-12   6.6e-08       3      41 ..      17      55 ..      15      60 .. 0.88
   2 ?   -2.8   0.1      0.37   6.7e+03      23      31 ..     313     322 ..     309     323 .] 0.76

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.7e-12
                                   ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCC CS
                 MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrpl 41
                                   +G+s+++++Pk +  +++i++Gd ++++ +g+ + ++p 
  gi|118430875|ref|NP_146954.2| 17 GGSSLIITLPKQWINKMNINAGDVLVVVDEGEYLKIIPE 55
                                   8**************************777778888875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.37
                                    C.TCEEEEEE CS
                 MazE_antitoxin  23 e.Gdevelev 31 
                                    e Gd v ++v
  gi|118430875|ref|NP_146954.2| 313 EqGDLVGIRV 322
                                    3599999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2517.04
//
Query:       gi|118430876|ref|NP_146955.2|  [L=482]
Description: peptidase [Aeropyrum pernix K1]
Scores for complete 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-46  157.8   0.8    6.5e-46  157.4   0.8    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.4   0.8   3.6e-50   6.5e-46       1     276 [.      33     333 ..      33     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 3.6e-50
                                    EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                      PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea..... 75 
                                    +ae+r++ + + sv + n++v   ++++++g+++rvi++g+lgfast+ +s+e+l+++v+ av+ia++++    +     
  gi|118430876|ref|NP_146955.2|  33 YAEARFHARLGDSVLVVNDRVVGGGFEIEEGVAFRVIVDGALGFASTSLLSEESLDSVVDHAVSIARSSSRGFRKkvgms 112
                                    89********************************************999999**************999988888***** PP

                                    .................GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEE CS
                      PmbA_TldD  76 .................eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrt 138
                                                     ++++ e+k ++++e +k l+s++         +++  + s+s++ e kli++S+G ++e+  +
  gi|118430876|ref|NP_146955.2| 113 eerlgqaqyslkvkkdfRNLELEDKASIVLEYSKSLESKSV--------DLKAKTFSYSDVLEAKLIITSDGGNIESIIP 184
                                    ****9977777777777777777777666666666555444........45555669*********************** PP

                                    EEEEEEEEEE..STCS....ETEEEEEEEESSHHHS..SSHHHHHHHHHHCTTT.-B---SEEEEEEE-HHHHHHHHHGH CS
                      PmbA_TldD 139 rvslslsvia.ddggs....gdgmgggsgyedleeedleeiaeeaaekalasle.akplppgkypVvlspeavgsllhea 212
                                    rvs+++++ a  ++++    g+ + g +g e + e  le+++++ ++ +  +l  a+p p g ++V++spe vg+ lhe+
  gi|118430876|ref|NP_146955.2| 185 RVSIFYNIAAeHGDRRankwGH-LAGSGGLELVGELGLESMLKDDVNSLEVNLVkAEPSPKGVMDVIISPEIVGLALHES 263
                                    **********444333553333.3333333566668889999999****9999779************************ PP

                                    HHHHTBHHHHHTT--TT...TT-....TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE CS
                      PmbA_TldD 213 vghaleadavlegrSfl...kdk....lGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvL 276
                                    +gh+ ead+v  gr +      +    l  +++s+++t+ ddpt  g++g+y +DdE vp++++ lI +G L
  gi|118430876|ref|NP_146955.2| 264 IGHPSEADRVM-GREAAqagL-SyrmwLDGRIGSSKVTVADDPTVpGSYGFYLYDDEAVPARERILINKGEL 333
                                    ***********.555553331.13358*****************99************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3536.37
//
Query:       gi|14600442|ref|NP_146956.1|  [L=449]
Description: peptidase [Aeropyrum pernix K1]
Scores for complete 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-37  128.6   0.1    5.8e-37  128.0   0.1    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.1   3.2e-41   5.8e-37       5     279 .]      32     308 ..      30     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 3.2e-41
                                   EEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-...GGS-HHH CS
                     PmbA_TldD   5 rleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea...eevsaee 82 
                                    ++ s+s  v++++g+v+ ++  +d  l + + ++g+++++s++++    l++a++ a +   + ++ p +   +e+s + 
  gi|14600442|ref|NP_146956.1|  32 KIVGSKSIMVKAARGSVSVAQGFQDLLLEIYLARDGKIAVTSFKTPR---LDDAAKIAARVVDKLEKSPLYaplPEPSGSS 109
                                   67899***********************************9966555...8888888888887777777779995555555 PP

                                   HHHHHHHHHHH.CHCST..TEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE.STCSETEEEEEE CS
                     PmbA_TldD  83 kielleelekalrsadp..kienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsviaddggsgdgmgggs 161
                                    +++ e+++  +++ d+    ++++  r+ ++s++ +  ++++++  S+G++++ ++t+++ +  +  ++++     +g +
  gi|14600442|ref|NP_146956.1| 110 SQAVDEKVATMVAEGDTagLTSLLDPDRWGDISGMAELAVTTTVLTASNGAELTLEKTSFNGYTRIFGREFR-----SGQW 185
                                   5555666664444444432222222448999999999999********************988888883322.....2334 PP

                                   EE..SSHHHS..SSHHHHHHHHHHCTTT.-B-.....--SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT--TTTT.-T CS
                     PmbA_TldD 162 gy..edleeedleeiaeeaaekalasle.akp.....lppgkypVvlspeavgsllheavghaleadavlegrSflkd.kl 233
                                   ++  ++++e    ++aeea+++a+++ e  ++     ++pg y+++lsp++ g+ll+ +  ++l a +vl g S++++ k 
  gi|14600442|ref|NP_146956.1| 186 SWvsTRFDE----KLAEEAIRTAKQLAEeCSKlpeevPEPGSYRLLLSPMVGGNLLEIVA-SSLLAGSVLLGFSMFSHnKP 261
                                   445666666....55555555555555433223334678999**************8555.5776777777*****9989* PP

                                   TSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                     PmbA_TldD 234 Gekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                   G+++as+ lt+++ p++ + +g++ fDdEGv+t++   IenGvLk++
  gi|14600442|ref|NP_146956.1| 262 GDRIASDALTLSSTPLDdELPGYSMFDDEGVATRDIAAIENGVLKTF 308
                                   ****************99***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3324.74
//
Query:       gi|14602183|ref|NP_146957.1|  [L=366]
Description: hypothetical protein APE_0092.1 [Aeropyrum pernix K1]
Scores for 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-60  203.3   0.0    9.4e-60  202.7   0.0    1.3  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 !  202.7   0.0   5.2e-64   9.4e-60       1     293 [.      21     295 ..      21     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 202.7 bits;  conditional E-value: 5.2e-64
                                   SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklldddt 81 
                                   hpenp+Rl  ++  l+es g+ ++le  ++p+  +    ++vHs++Yl+++ s++++  +                ld dt
  gi|14602183|ref|NP_146957.1|  21 HPENPSRLVEAVRGLEES-GVYKHLEA-VTPPVGDVGLYTRVHSPAYLRHVLSTAESGLD---------------WLDPDT 84 
                                   9****************9.99998886.66666666666************986633211...............35789* PP

                                   HCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-.BTTB-B.....TTBSS-HHHHHHHHHHHCC-SS-EEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl  82 pvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHa.kaseas.....GFClvNnvaiaikylqakhelkrvai 156
                                   +v p+tl a ++  ga++e  + v sg   +a+ l rPpgHHa  +++a      GFC+vN +a+ ++ l +     + +i
  gi|14602183|ref|NP_146957.1|  85 YVGPGTLVALKRLGGASVEVYNIVRSG--GEALLLGRPPGHHAgIRGRALgaptaGFCIVNTAALIARMLSE---QGKTVI 160
                                   *************************99..9*************999996556667***************99...569*** PP

                                   EE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 157 lDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleef 237
                                   lD+D+HhGnGt+e+fy+dpdv+++++H+ ++++yPgtg  ed+geg++kg+++n+ l++++gd+ y+++ + +l  +le+ 
  gi|14602183|ref|NP_146957.1| 161 LDFDLHHGNGTQEIFYDDPDVYHVDVHQDPTTIYPGTGFPEDIGEGDAKGTKINIILPPNSGDDIYVSAARLAL-GILERL 240
                                   ********************************************************************998777.99**** PP

                                   --SEEEEEE-STTBTTS.TT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---H CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Hist_deacetyl 238 kPdlilvsaGfDalkgd.plgelnlsvegykeltkklaeladkvkkvvllleGGYnl 293
                                   +Pd+i+vsaGfDa++gd  +  ++  +  y+ + ++l ++a+++  v ++leGGY  
  gi|14602183|ref|NP_146957.1| 241 EPDYIVVSAGFDAYRGDnAFTVMRGGTAMYYLIGSELSRMARRG--VAAVLEGGYGV 295
                                   *****************55566699999*************976..*********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2707.00
//
Query:       gi|118430877|ref|NP_146958.2|  [L=345]
Description: hypothetical protein APE_0093.1 [Aeropyrum pernix K1]
Scores for complete 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-08   34.2   0.4    4.9e-08   32.7   0.4    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.4   2.7e-12   4.9e-08       5      40 ..      23      58 ..      20      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.7e-12
                                   TEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                 MazE_antitoxin  5 nsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                   +s++v+iPke+++ +++++Gd v l+  gd++i+ p
  gi|118430877|ref|NP_146958.2| 23 SSLIVTIPKEWAKRNNVDVGDVVSLVDIGDRLIILP 58
                                   79***********************99999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2467.74
//
Query:       gi|118430878|ref|NP_146961.2|  [L=165]
Description: hypothetical protein APE_0096.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1196.03
//
Query:       gi|118430879|ref|NP_146962.2|  [L=214]
Description: hypothetical protein APE_0097.1 [Aeropyrum pernix K1]
Scores for complete 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   31.7   0.1    4.3e-07   29.9   0.1    1.8  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 !   29.9   0.1   2.4e-11   4.3e-07       1     146 [.      16     145 ..      16     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.4e-11
                         DUF429   1 GvDlagcrtgw..aavaledgrlrlvdv.eae..eivaalaallaaaeeaavvaiDaPiglperetggRaaDraarklla 75 
                                    G+D +g r+ w  a+v + +gr+++++  e +  +++++l+ l  a+   ++v++DaP+ +   +  +R ++ +a   l+
  gi|118430879|ref|NP_146962.2|  16 GIDPSGGRSSWgfAVVSWLPGRCHIIEAwESRpsRVYSSLERL--ASIPVDAVGVDAPVNVLREAGPWRGCELEA---LK 90 
                                    8887755554421677777******999966679*********..66899**********99777789*******...35 PP

                         DUF429  76 rrgasvfpvpar.aalaagkglserafgllpklrevdelldarpelrgrvvEvhPeaafvalnggaplakkk 146
                                    + ga+ +p ++  ++  ++      ++ +++  +e++            vvE+hP  ++  l  +a +a+++
  gi|118430879|ref|NP_146962.2|  91 K-GARLLPLNTPgMVRLSR-----NGLSVFRLFEEAG----------VPVVETHPTSILSSL-DLANTAYRR 145
                                    5.********997877777.....9999999988664..........6799********999.899988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1592.93
//
Query:       gi|14600448|ref|NP_146963.1|  [L=959]
Description: DNA polymerase I [Aeropyrum pernix K1]
Scores for complete 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  165.3   0.0    4.2e-48  164.2   0.0    1.5  1  DNA_pol_B       DNA polymerase family B
    2.5e-28   99.2   0.0    4.9e-28   98.2   0.0    1.4  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    2.7e-06   27.5   0.1    7.4e-05   22.8   0.1    2.4  1  RNase_H_2       RNase_H superfamily
     0.0082   14.9   0.0      0.013   14.2   0.0    1.2  1  tRNA-synt_1g    tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.065   12.9   0.0       0.12   12.0   0.0    1.4  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
       0.17   11.8   0.0        2.1    8.3   0.0    2.3  2  GATase_7        Glutamine amidotransferase 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 !  164.2   0.0   1.4e-51   4.2e-48      17     418 ..     542     911 ..     531     934 .. 0.80

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 1.4e-51
                                   HHHHHHHHHTTBE-B-----.--SS.............-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE CS
                     DNA_pol_B  17 slLlrlakeegfilpdrtekkgkeee............gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlv 85 
                                   +l++ ++++++  +p+r e  +k ++            +Y Ga Vl+P  g++   vlvlDFaSLYPs+i + Nl+y+t+ 
  gi|14600448|ref|NP_146963.1| 542 GLMYWEHRRRRWLIPSRGEI-EKLSSagarvgaiikdkKYRGAIVLDPPVGIFF-RVLVLDFASLYPSLIKQWNLSYETVN 620
                                   56666677777777742222.222224555556666647*************96.59**********************99 PP

                                   -HCCHCC.T--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHH.HHHHHH.CS--HHHHHHHHHHHHHHHHHH CS
                     DNA_pol_B  86 aseeeak.eleaedeyleveveprlvefvkksvregllpklLkdllakRka.ikkelk.eekdefekalldkqQlalKvta 163
                                   + + ++  e+++  +           ++   ++ +g+  +++  l + R + +kk+ k ++  e+e+  +d  Q a+Kv  
  gi|14600448|ref|NP_146963.1| 621 NPNCRDTiEVPEVGH-----------RV--CREFKGISNEIVGMLRDFRVRlYKKKSKdKSLREEERLWYDVVQSAMKVYI 688
                                   888776645554332...........22..3445667667766666667552566666577788899************** PP

                                   HHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHH CS
                     DNA_pol_B 164 NsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdvee 244
                                   N+ YG+ G ++  l++l++A+svT+ GR +L  t e   +                  +l+++YGDTDS+fi    kdv  
  gi|14600448|ref|NP_146963.1| 689 NASYGVFGSEKFSLYSLPVAESVTALGRAVLRGTLEKSREL-----------------NLHIVYGDTDSLFIWDPPKDV-- 750
                                   ******************************98775544433.................9*************7666654.. PP

                                   HHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHH CS
                     DNA_pol_B 245 llkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvektskanklliKGvdlvRrdncklvkevikkvlel 324
                                        ++l  +v++   +  l+le++kv+  +l+   KK Y g++ e     + ++iKG+   + +  +++k+  +k ++ 
  gi|14600448|ref|NP_146963.1| 751 ----LNDLVDYVER---TYGLELELDKVFRAILFSGlKKNYLGITEE-----GDIVIKGMVAKKSNTPEFIKDEFSKAVKI 819
                                   ....5788899999...55689************965999****999.....99***********************9987 PP

                                   HSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEE CS
                     DNA_pol_B 325 llkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneeapevgdris 405
                                   l k  ++ +++e +l++l++ +++v+++++++   l++f +  +lsk+p++y++++  h+++a  l +r + + + gd ++
  gi|14600448|ref|NP_146963.1| 820 LSKL-EKPEDVEAILAELRDHINTVYNNVKKKVYTLDQFAIKVMLSKNPREYDKNTPQHVKAAM-LLQRLGLTLSRGDIVY 898
                                   7777.899********************************************999978887665.66777999******** PP

                                   EEEBETSS..... CS
                     DNA_pol_B 406 Yvivekkkevkkk 418
                                   Yv + +k  vk  
  gi|14600448|ref|NP_146963.1| 899 YVKTRDKLGVKPV 911
                                   **99887655444 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 !   98.2   0.0   1.7e-31   4.9e-28      11     278 ..     162     416 ..     157     431 .. 0.82

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.7e-31
                                   EEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHHHH CS
                DNA_pol_B_exo1  11 nvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirkelsp 91 
                                   + +g+kpyf+++a+    +e++ +   ++++++s       + +lv+k + ++ +  +  ++k++vs+p +++++r+++  
  gi|14600448|ref|NP_146963.1| 162 DRTGHKPYFLTDAR----PEDLRAAGVDVSHDES-----FLQYDLVEKFHPIDRKLVK--LTKIVVSDPLAVRRLREKV-- 229
                                   67899*******99....4444555555555543.....3345677777777777776..*******************.. PP

                                   CCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE.....TEEEEGCC--C-.SEEEEEETTTSCEETTTCC........S-E CS
                DNA_pol_B_exo1  92 leeivdvyeydvdylerflidnkivgfgwysvk.....kylvraegkisncdveidcdvddliakpkese........ppl 159
                                   ++ +++v+e+d++y+ +++ d+++ ++  y+v       +l   ++ ++    ei  + ++ +++++ +         p+l
  gi|14600448|ref|NP_146963.1| 230 SSAGFSVWEADIKYHHNYIFDRQLIPGILYEVGgvrivHTLPLEMDDATRIVDEIFREEPREVRERAREWlrifeappPKL 310
                                   789******************************999976666777777777778999999999988874455556668888 PP

                                   EEEEEEEEETEETTS.EETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSH CS
                DNA_pol_B_exo1 160 rvlsFDIeckskkgk.fpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsE 238
                                    +++FDIe++s     +pd++    p+i  s++  d+ g      r+++ +r  +       e+t+ +  +g++v ++dsE
  gi|14600448|ref|NP_146963.1| 311 PLIAFDIEVYSPIATrLPDPSTAPYPVI--SAATaDSSG----RSRVVLLYRDGV-------EFTEGALPEGTEVEIYDSE 378
                                   88*********98877******555555..555545555....5799********.......77777886788******** PP

                                   HHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCC CS
                DNA_pol_B_exo1 239 kelLqaflefikqydPdvitgYNidnFDlpYilnRakely 278
                                   +++L + + ++++y    ++ +N+dnFDlpYi  R++ l 
  gi|14600448|ref|NP_146963.1| 379 RAMLLDLVRILQRY--PLVVSFNGDNFDLPYIARRLEVLG 416
                                   **************..9*******************9665 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.5e-08   7.4e-05      43     114 ..     378     471 ..     356     510 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.5e-08
                     RNase_H_2  43 eekailelflellekkkalvtfngksFDvpflkrlfkkyklde..............eefrhiDLlkel..rkkkl..... 102
                                   e++ +l+ ++ +l++++ +v+fng +FD+p++ r+++   ++               ++  hiDL+k +  r  ++     
  gi|14600448|ref|NP_146963.1| 378 ERAMLLD-LVRILQRYPLVVSFNGDNFDLPYIARRLEVLGVPRefapielkqdyatfRRSLHIDLHKLFgiRALQVyafgn 457
                                   3344444.4699************************777777633334444444444455666666544221111122222 PP

                     RNase_H_2 103 ..esysLksvekel 114
                                     + +sL+s+ ++l
  gi|14600448|ref|NP_146963.1| 458 kyRELSLESISRAL 471
                                   22333444444443 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 !   14.2   0.0   4.5e-06     0.013      35      87 ..     893     945 ..     885     950 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-06
                                   TT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SE CS
                  tRNA-synt_1g  35 rgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdk 87 
                                   rg+ v++v   D+ G++  + A+ ++v+p ++ve+v++++++++  ++is+d+
  gi|14600448|ref|NP_146963.1| 893 RGDIVYYVKTRDKLGVKPVQLARLSDVDPGKYVEHVKTAFEQMLMAFGISWDD 945
                                   68889**********************************************97 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 ?   12.0   0.0     4e-05      0.12      36      71 ..     377     411 ..     348     446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                DNA_pol_B_exo2  36 sekelikkffegvekkkpqlVsfngrgfDlpvleyr 71 
                                   se++++    ++++++ p +Vsfng +fDlp +  r
  gi|14600448|ref|NP_146963.1| 377 SERAMLLDLVRILQRY-PLVVSFNGDNFDLPYIARR 411
                                   5666666666666655.89************99877 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00069       2.1      52     108 ..     111     175 ..      99     184 .. 0.72
   2 ?    0.3   0.0      0.21   6.2e+02      93     106 ..     902     915 ..     895     920 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00069
                      GATase_7  52 ksDtevllallea........ewgeealerlnGmfAfaiwdeeekrlllaRDrlGikPLyygedk 108
                                    sD  v+l+l+++          ++  ++   G   ++++d ++++l+   Dr G+kP +++ ++
  gi|14600448|ref|NP_146963.1| 111 LSDDDVILELVREpwvesvrgYLLDVRYDGSLGKAVLMLYDPSSGSLVKWADRTGHKPYFLTDAR 175
                                   588888999998855533222222222334457778999********************999876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.21
                      GATase_7  93 aRDrlGikPLyyge 106
                                    RD+lG+kP+ +++
  gi|14600448|ref|NP_146963.1| 902 TRDKLGVKPVQLAR 915
                                   7********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (959 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.44
# Mc/sec: 6509.77
//
Query:       gi|118430880|ref|NP_146964.2|  [L=672]
Description: iron-sulfur protein [Aeropyrum pernix K1]
Scores for 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-27   93.5   0.0    6.8e-13   48.6   0.0    2.5  2  CCG              Cysteine-rich domain
    3.1e-11   43.5   5.0      4e-11   43.2   2.2    2.4  2  Fer4_8           4Fe-4S dicluster domain
    8.3e-09   35.4   6.6    8.3e-09   35.4   6.6    2.5  2  Fer4_10          4Fe-4S dicluster domain
      1e-06   28.8   8.4      1e-06   28.8   8.4    2.6  3  Fer4_9           4Fe-4S dicluster domain
    0.00013   21.6   0.4    0.00024   20.7   0.4    1.3  1  Nitrate_red_gam  Nitrate reductase gamma subunit
    0.00015   21.6  17.2      0.002   18.1   2.0    3.1  3  Fer4_2           4Fe-4S binding domain
    0.00019   21.7  15.5     0.0073   16.7   2.0    2.9  2  Fer4_4           4Fe-4S binding domain
    0.00047   20.6  10.9     0.0012   19.3   8.9    2.6  2  Fer4_17          4Fe-4S dicluster domain
     0.0015   18.2  17.8     0.0085   15.9   1.0    2.7  2  Fer4             4Fe-4S binding domain
     0.0028   18.2  12.8     0.0028   18.2  12.8    2.9  2  Fer4_7           4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.01   16.0   3.2       0.82    9.9   0.2    2.7  2  Fer4_18          4Fe-4S dicluster domain
       0.02   14.6   0.4        1.8    8.4   0.1    2.7  2  zinc_ribbon_5    zinc-ribbon domain
      0.036   14.4   0.0      0.036   14.4   0.0    2.6  2  RNA_pol_N        RNA polymerases N / 8 kDa subunit
      0.054   13.6  10.4       0.32   11.2   0.4    2.8  2  Fer4_21          4Fe-4S dicluster domain
      0.061   13.6   3.9        7.7    6.8   1.8    2.3  2  DUF1772          Domain of unknown function (DUF1772)
      0.064   14.0   2.7         11    6.8   0.2    2.9  2  Fer4_15          4Fe-4S single cluster domain
      0.089   13.6  10.4        0.2   12.5   0.2    3.3  3  Fer4_22          4Fe-4S dicluster domain
       0.15   13.0  14.2        4.2    8.4  14.5    2.5  2  Fer4_16          4Fe-4S double cluster binding domain
       0.16   12.1  21.7       0.06   13.5   3.5    3.0  2  Fer4_6           4Fe-4S binding domain
          3    7.9   4.4          1    9.4   0.0    2.2  2  Eapp_C           E2F-associated phosphoprotein


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 !   42.5   0.0   6.5e-14   5.8e-11       1      85 []     419     504 ..     419     504 .. 0.95
   2 !   48.6   0.0   7.6e-16   6.8e-13       1      85 []     558     648 ..     558     648 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.5e-14
                            CCG   1 vayfdgCh.llraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                    v+y+ gC   ++++ + v++++ +ll+++gv+  ++    C G ++ r+g+e l+ +l+ + +e++ +++ +++v++cp+
  gi|118430880|ref|NP_146964.2| 419 VLYWAGCVtGYDPRIRPVGESILRLLRKAGVKAAIMPYTGCTGEPALRMGEEALFVELMIQFLEELSKYKFKKLVVNCPH 498
                                    79*****7567777****************************************************************** PP

                            CCG  80 Cllqlk 85 
                                    Cl+++k
  gi|118430880|ref|NP_146964.2| 499 CLTTIK 504
                                    **9986 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 7.6e-16
                            CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkee.laealakrnvetaeet..gadaiv 74 
                                    v+y+d+C+l+r +  y+e+r++l++  +    e++++ ek+ CCG ggg   +e  + +++ + ++e+a +t  g  +++
  gi|118430880|ref|NP_146964.2| 558 VTYHDPCYLGRWNgvYSEPREVLRRGAGLRIREMPRNmEKSFCCGGGGGQLFYEVkRGRRVSRIRAEEASQTlgGEGVVA 637
                                    89***************************************************9989999**********9876788999 PP

                            CCG  75 tacpgCllqlk 85 
                                    +acp+C ++++
  gi|118430880|ref|NP_146964.2| 638 VACPFCNTMFR 648
                                    *******9985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   2.2   4.5e-14     4e-11       1      63 [.     267     346 ..     267     348 .. 0.73
   2 ?   -0.3   0.0       1.6   1.5e+03      14      39 ..     495     519 ..     493     543 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.5e-14
                         Fer4_8   1 elekCieCgaCqsaCpvlrrtkkhlldargeaae.......dvqeeqvlee....................eealwsCtt 53 
                                    ++e+C+ C++C+++Cp++++     ld+rg + +                +                     ea+wsC+t
  gi|118430880|ref|NP_146964.2| 267 DFEACTSCMRCTNSCPAAESG--KVLDPRGVVYGlrlklreG--------DwesevldpenpgdgskagvnPEAIWSCLT 336
                                    589*************88886..4456666666544333321........1222355668888888999999******** PP

                         Fer4_8  54 cgaCtevCpv 63 
                                    cgaC+++Cpv
  gi|118430880|ref|NP_146964.2| 337 CGACVNECPV 346
                                    *********8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                         Fer4_8  14 aCpvlrrtkkhlldargeaaedvqee 39 
                                    +Cp + +t kh +  +++  e ++e+
  gi|118430880|ref|NP_146964.2| 495 NCPHCLTTIKHDYRRYKRYLE-KRED 519
                                    899999998887766666555.3333 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   6.6   9.3e-12   8.3e-09       3      56 .]     265     345 ..     263     345 .. 0.90
   2 ?   -2.2   0.0       5.1   4.6e+03      18      31 ..     639     652 ..     633     661 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 9.3e-12
                        Fer4_10   3 vidddtCirCgkCvkaCPadl...........................tsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    ++d + C+ C +C+++CPa                                ++ g  s+ +++ +++++C +cgaCv +C
  gi|118430880|ref|NP_146964.2| 265 RLDFEACTSCMRCTNSCPAAEsgkvldprgvvyglrlklregdwesevLDPENPGDGSKAGVNPEAIWSCLTCGACVNEC 344
                                    57889**************77***********************8876666677777888888889************** PP

                        Fer4_10  56 P 56 
                                    P
  gi|118430880|ref|NP_146964.2| 345 P 345
                                    9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                        Fer4_10  18 aCPadltsvgakge 31 
                                    aCP+++t+ +a++e
  gi|118430880|ref|NP_146964.2| 639 ACPFCNTMFRAEAE 652
                                    68886666655555 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   3.1   4.3e-05     0.039      33      48 ..     264     283 ..     245     286 .. 0.69
   2 !   28.8   8.4   1.1e-09     1e-06       1      48 [.     270     346 ..     270     348 .. 0.92
   3 ?   -2.7   0.0       7.9   7.1e+03      33      40 ..     628     644 ..     610     645 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                         Fer4_9  33 e....eaCigCgaCveaCpk 48 
                                    +    eaC++C++C++ Cp 
  gi|118430880|ref|NP_146964.2| 264 QrldfEACTSCMRCTNSCPA 283
                                    13444699999999999996 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.1e-09
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.............................eaCigCgaCveaCpk 48 
                                    +Ct+C +C+++Cpa    +   +r + +  + +                             ++C++CgaCv+ Cp 
  gi|118430880|ref|NP_146964.2| 270 ACTSCMRCTNSCPAAESGKVLDPRGVVYGLRLKlregdwesevldpenpgdgskagvnpeaiWSCLTCGACVNECPV 346
                                    6***********9999999999999888776668899**************************************95 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.9
                         Fer4_9  33 e.........eaCigCg 40 
                                    +          aC +C+
  gi|118430880|ref|NP_146964.2| 628 QtlggegvvaVACPFCN 644
                                    14566666666788886 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 !   20.7   0.4   2.6e-07   0.00024      91     203 ..     100     219 ..      90     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.6e-07
                Nitrate_red_gam  91 GliagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsal..dygse....retispwlrsllt 164
                                      +ag+l++vG+++  +RR+   +         ++vl+lL++ +++G+++  +     +yg+     +   + +l  l +
  gi|118430880|ref|NP_146964.2| 100 NNMAGILVIVGVTMAAYRRWRGLTPGLPRDPGYYLVLALLAAIVVTGFVVEGMVVAlyRYGEGfespLYDPVGYLVYLAL 179
                                    5789*****************999999999999**************998655444346655531234444555555555 PP

                Nitrate_red_gam 165 lqpd.aellaevplifklHvllglllfalfPFtrLvHvls 203
                                       d   l++    ++ lH+ ++ l +al+PFt L H+ +
  gi|118430880|ref|NP_146964.2| 180 EGVDrDILVEAYRGLWLLHLAMAQLGIALIPFTNLWHIPA 219
                                    5555344566778899*********************965 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.0   2.2e-06     0.002       5      22 .]     266     283 ..     262     283 .. 0.89
   2 !   12.4   2.8   0.00015      0.13       6      21 ..     327     345 ..     323     346 .. 0.81
   3 ?   -2.3   0.2       6.9   6.1e+03       6       9 ..     495     498 ..     491     501 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                         Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                     d ++C++C  C+++CPa
  gi|118430880|ref|NP_146964.2| 266 LDFEACTSCMRCTNSCPA 283
                                    799**************8 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00015
                         Fer4_2   6 dtd...rCigCgaCvsaCP 21 
                                    +++   +C+ CgaCv+ CP
  gi|118430880|ref|NP_146964.2| 327 NPEaiwSCLTCGACVNECP 345
                                    5555668************ PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.9
                         Fer4_2   6 dtdr 9  
                                    ++ +
  gi|118430880|ref|NP_146964.2| 495 NCPH 498
                                    3333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.0   8.2e-06    0.0073       2      16 ..     269     283 ..     268     291 .. 0.91
   2 !   14.3   0.6   4.8e-05     0.043       3      16 ..     333     346 ..     331     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.2e-06
                         Fer4_4   2 erCigCgsCvaaCPq 16 
                                    e C+ C++C+++CP 
  gi|118430880|ref|NP_146964.2| 269 EACTSCMRCTNSCPA 283
                                    78************4 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.8e-05
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                    +C+ Cg+Cv+ CP+
  gi|118430880|ref|NP_146964.2| 333 SCLTCGACVNECPV 346
                                    6************5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   2.6   0.00044      0.39      27      58 ..     253     283 ..     237     286 .. 0.69
   2 !   19.3   8.9   1.3e-06    0.0012       1      57 [.     270     345 ..     270     352 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                        Fer4_17  27 raaklglleeaekee.kaslCieCgeCerkCPq 58 
                                      +kl+  +++ k++  ++ C++C +C+ +CP+
  gi|118430880|ref|NP_146964.2| 253 GVVKLS--DTTWKQRlDFEACTSCMRCTNSCPA 283
                                    444443..34434433899************96 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.3e-06
                        Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraaklglleeaeke..................ekaslCieCgeCerkCP 57 
                                    +C++C  C+++Cp  e     +p+ +++ ++l+l e+  ++                  e++ +C++Cg C+ +CP
  gi|118430880|ref|NP_146964.2| 270 ACTSCMRCTNSCPAAESgKVLDPRGVVYGLRLKLREGDWESevldpenpgdgskagvnpEAIWSCLTCGACVNECP 345
                                    6************99995446899999988885555433333444444555555667778**************** PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   9.5e-06    0.0085       4      20 ..     267     283 ..     265     284 .. 0.92
   2 !   11.9   4.5   0.00017      0.15       8      20 ..     334     346 ..     333     348 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.5e-06
                                    ETTTSSS-THHHHHSTT CS
                           Fer4   4 deekCigCGaCvevCPv 20 
                                    d e C+ C++C + CP 
  gi|118430880|ref|NP_146964.2| 267 DFEACTSCMRCTNSCPA 283
                                    99**************5 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                                    SSS-THHHHHSTT CS
                           Fer4   8 CigCGaCvevCPv 20 
                                    C  CGaCv+ CPv
  gi|118430880|ref|NP_146964.2| 334 CLTCGACVNECPV 346
                                    999*********8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   3.4   0.00035      0.31      32      50 ..     265     283 ..     237     285 .. 0.76
   2 !   18.2  12.8   3.2e-06    0.0028       1      50 [.     270     346 ..     270     348 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                         Fer4_7  32 eidpekClgCgaCvavCPt 50 
                                    ++d e C++C +C + CP+
  gi|118430880|ref|NP_146964.2| 265 RLDFEACTSCMRCTNSCPA 283
                                    7889999999999999996 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.2e-06
                         Fer4_7   1 rCigCgaCvaaC.........................pvkaieldeeenek...........gtekveidpe...kClgC 41 
                                    +C+ C +C++ C                                                     k+ ++pe   +Cl+C
  gi|118430880|ref|NP_146964.2| 270 ACTSCMRCTNSCpaaesgkvldprgvvyglrlklregD------------WesevldpenpgDGSKAGVNPEaiwSCLTC 337
                                    5***********44444444442222222222222221............02222222222222555666653338**** PP

                         Fer4_7  42 gaCvavCPt 50 
                                    gaCv++CP+
  gi|118430880|ref|NP_146964.2| 338 GACVNECPV 346
                                    ********7 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.019        17      49      73 ..     259     283 ..     237     288 .. 0.73
   2 ?    9.9   0.2   0.00092      0.82      57      75 ..     330     348 ..     315     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                        Fer4_18  49 ekeerkekgagdcidcescvkvcPt 73 
                                    ++  +++ +   c++c  c + cP 
  gi|118430880|ref|NP_146964.2| 259 DTTWKQRLDFEACTSCMRCTNSCPA 283
                                    344466677889***********96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00092
                        Fer4_18  57 gagdcidcescvkvcPtgi 75 
                                    +   c++c++cv+ cP+ i
  gi|118430880|ref|NP_146964.2| 330 AIWSCLTCGACVNECPVLI 348
                                    5568************844 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.061        54       1      13 [.     492     504 ..     492     512 .. 0.84
   2 ?    8.4   0.1     0.002       1.8       3      16 ..     638     651 ..     636     659 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.061
                  zinc_ribbon_5   1 LiirCpdCdtkFk 13 
                                    L++ Cp C t+ k
  gi|118430880|ref|NP_146964.2| 492 LVVNCPHCLTTIK 504
                                    6799******987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.002
                  zinc_ribbon_5   3 irCpdCdtkFklvd 16 
                                    + Cp C+t+F+   
  gi|118430880|ref|NP_146964.2| 638 VACPFCNTMFRAEA 651
                                    67********9765 PP

>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.8       2.4   2.1e+03       7      16 ..     334     343 ..     333     353 .. 0.88
   2 ?   14.4   0.0     4e-05     0.036       5      41 ..     494     533 ..     492     536 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.4
                                    -TTT--B-ST CS
                      RNA_pol_N   7 CFtCGkvige 16 
                                    C tCG  + e
  gi|118430880|ref|NP_146964.2| 334 CLTCGACVNE 343
                                    *****99865 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4e-05
                                    SS-TTT--B-STHHHHHHHHHHTT--HH...HHHHHHT-- CS
                      RNA_pol_N   5 VrCFtCGkvigekweeylellekgeepk...daLdaLglk 41 
                                    V C  C + i++++++y++ lek+e+ k   ++Ld L+++
  gi|118430880|ref|NP_146964.2| 494 VNCPHCLTTIKHDYRRYKRYLEKREDAKhltEVLDRLEVE 533
                                    7899*****************9997766666******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 ?   11.2   0.4   0.00035      0.32      36      53 ..     266     283 ..     248     287 .. 0.72
   2 ?    7.4   1.8    0.0052       4.6      40      53 ..     333     346 ..     323     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                        Fer4_21  36 vvedeCvGCnlCssvCPv 53 
                                    +  + C+ C  C++ CP 
  gi|118430880|ref|NP_146964.2| 266 LDFEACTSCMRCTNSCPA 283
                                    345899999999999996 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0052
                        Fer4_21  40 eCvGCnlCssvCPv 53 
                                    +C  C  C++ CPv
  gi|118430880|ref|NP_146964.2| 333 SCLTCGACVNECPV 346
                                    58888888888888 PP

>> DUF1772  Domain of unknown function (DUF1772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.8    0.0085       7.7      26      85 ..      90     149 ..      62     161 .. 0.75
   2 ?    6.5   0.0     0.011       9.8      50      89 ..     173     220 ..     170     265 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0085
                        DUF1772  26 kqwrrlfkrgkavfpplallsalafayla...araasrgarllylaaaallllsivpyTllvm 85 
                                    + ++ ++k ++ + + l+++ ++++ay          ++ +++yl++a+l++   +++T +v+
  gi|118430880|ref|NP_146964.2|  90 PPFFYVYKLANNMAGILVIVGVTMAAYRRwrgLTPGLPRDPGYYLVLALLAA---IVVTGFVV 149
                                    5588899888888888888877777766688878888899999966666555...45555554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                        DUF1772  50 fa.yla........araasrgarllylaaaal.lllsivpyTllvmvPtN 89 
                                    ++ yla           a rg +ll  + a + l ++++p+T l+ +P  
  gi|118430880|ref|NP_146964.2| 173 YLvYLAlegvdrdiLVEAYRGLWLLH-L-AMAqLGIALIPFTNLWHIPAV 220
                                    55566677777776566777777777.5.44448999*********9943 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 ?    6.8   0.2     0.013        11       3      21 ..     266     284 ..     265     309 .. 0.88
   2 ?    6.4   0.2     0.017        16       7      22 ..     333     348 ..     331     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                        Fer4_15   3 vDrdaCigcglCvaeapev 21 
                                    +D +aC++c +C   +p  
  gi|118430880|ref|NP_146964.2| 266 LDFEACTSCMRCTNSCPAA 284
                                    7999***********9965 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                        Fer4_15   7 aCigcglCvaeapevf 22 
                                     C  cg+Cv e+p ++
  gi|118430880|ref|NP_146964.2| 333 SCLTCGACVNECPVLI 348
                                    7***********9776 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00023       0.2      71      94 ..     260     283 ..     241     285 .. 0.86
   2 ?    5.9   1.1     0.026        24       2      14 ..     334     346 ..     329     353 .. 0.69
   3 ?   -1.9   0.0       7.1   6.4e+03      60      86 ..     578     604 ..     555     607 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                        Fer4_22  71 sefkekfgesgCvGCgRCieacpv 94 
                                    +++k++ + ++C+ C RC+++cp+
  gi|118430880|ref|NP_146964.2| 260 TTWKQRLDFEACTSCMRCTNSCPA 283
                                    3789999***************97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.026
                        Fer4_22   2 ClsCgaCtlvCpt 14 
                                    Cl+CgaC   Cp 
  gi|118430880|ref|NP_146964.2| 334 CLTCGACVNECPV 346
                                    6666666666653 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.1
                        Fer4_22  60 erlrqrllhklsefkekfgesgCvGCg 86 
                                    e lr+    +++e+ +++++s C+G g
  gi|118430880|ref|NP_146964.2| 578 EVLRRGAGLRIREMPRNMEKSFCCGGG 604
                                    556666667788899999999999976 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  14.5    0.0047       4.2       2      66 ..     271     346 ..     270     347 .. 0.60
   2 ?    7.4   3.3    0.0091       8.2       2      14 ..     334     346 ..     333     360 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0047
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare.......cisy..........ntaekkdlaedeekckkqeaitgCdiCqdvC 64 
                                    C++C +C+++CP++   +     +++r        +               ++  d ++   + +  + +  C++C++ C
  gi|118430880|ref|NP_146964.2| 271 CTSCMRCTNSCPAAESGKV----LDPRGvvyglrlK--LregdwesevlDPENPGDGSKAGVNPEAIWSCLTCGACVNEC 344
                                    ************9764433....3333322222232..13445555563233334444555556667************* PP

                        Fer4_16  65 Pa 66 
                                    P+
  gi|118430880|ref|NP_146964.2| 345 PV 346
                                    *6 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0091
                        Fer4_16   2 CgtCgkCaevCPt 14 
                                    C tCg+C++ CP+
  gi|118430880|ref|NP_146964.2| 334 CLTCGACVNECPV 346
                                    9999999999997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.5   6.7e-05      0.06       7      21 ..     269     283 ..     269     287 .. 0.91
   2 ?   10.6   2.8   0.00055      0.49       8      21 ..     333     346 ..     333     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
                         Fer4_6   7 dkCigCgdCvrvCPe 21 
                                    ++C++C++C++ CP+
  gi|118430880|ref|NP_146964.2| 269 EACTSCMRCTNSCPA 283
                                    68************8 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00055
                         Fer4_6   8 kCigCgdCvrvCPe 21 
                                    +C+ Cg+Cv+ CP 
  gi|118430880|ref|NP_146964.2| 333 SCLTCGACVNECPV 346
                                    69***********5 PP

>> Eapp_C  E2F-associated phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011         1      26      56 ..     485     515 ..     466     522 .. 0.80
   2 ?   -0.9   0.0       1.8   1.6e+03     110     131 ..     625     646 ..     611     654 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                         Eapp_C  26 kkkkksdavLsCpaCfttvcldcqrHekykn 56 
                                    +k k    v +Cp C+tt+  d +r ++y +
  gi|118430880|ref|NP_146964.2| 485 SKYKFKKLVVNCPHCLTTIKHDYRRYKRYLE 515
                                    5556667899****************99975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                         Eapp_C 110 eeeeeeeeesyhpvkCseCste 131
                                    e++++ + e + +v C  C+t 
  gi|118430880|ref|NP_146964.2| 625 EASQTLGGEGVVAVACPFCNTM 646
                                    3445555777788888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); 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):              20  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 4683.28
//
Query:       gi|118430881|ref|NP_146965.2|  [L=155]
Description: small heat shock protein [Aeropyrum pernix K1]
Scores for complete 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   25.4   0.0    1.6e-05   25.0   0.0    1.2  1  HSP20       Hsp20/alpha crystallin family
     0.0039   16.7   0.4       0.15   11.6   0.1    2.2  2  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 !   25.0   0.0   1.8e-09   1.6e-05       7      88 ..      69     152 ..      64     155 .] 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.8e-09
                                    EEEEEEEE-TT--CCCEEEEEETTEEEEEEE--....---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEEE CS
                          HSP20   7 eefevkldvpglkkeelkvkvednrvlvkgehe..eeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtvt 84 
                                    ++ ++ +d+pg+++e l++ v ++rv +++  +    +     l+++ s r+++  ++LP  vd+ +v+  ++  +  v+
  gi|118430881|ref|NP_146965.2|  69 DRLRILIDLPGMDRESLNIVVLEDRVEISARIRehVVKRALGSLSEKFSFREYRGVYRLPAPVDPRSVRIRTRGSLIIVE 148
                                    5668899************************9953233333445566899******************988877677777 PP

                                    EEBS CS
                          HSP20  85 vpkk 88 
                                    ++kk
  gi|118430881|ref|NP_146965.2| 149 ADKK 152
                                    7776 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 !   11.6   0.1   1.7e-05      0.15       2      32 ..      69      99 ..      68     119 .. 0.86
   2 !    3.4   0.0    0.0064        57       9      32 ..     126     150 ..     119     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                     ArsA_HSP20  2 deyvlkldLPfvdkeeidlsrsgdeLtIkig 32
                                   d+ ++ +dLP++d+e++++   +d   I++ 
  gi|118430881|ref|NP_146965.2| 69 DRLRILIDLPGMDRESLNIVVLEDRVEISAR 99
                                   778899**************99998888775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0064
                     ArsA_HSP20   9 dLPf.vdkeeidlsrsgdeLtIkig 32 
                                    +LP  vd+ ++ ++ +g+ ++++++
  gi|118430881|ref|NP_146965.2| 126 RLPApVDPRSVRIRTRGSLIIVEAD 150
                                    6665269***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1198.16
//
Query:       gi|118430882|ref|NP_146966.2|  [L=259]
Description: hypothetical protein APE_0104.1 [Aeropyrum pernix K1]
Scores for complete 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  120.0   0.1    1.5e-34  119.8   0.1    1.0  1  PAC2        PAC2 family
  ------ inclusion threshold ------
       0.16   11.6   0.0       0.22   11.2   0.0    1.2  1  SBP_bac_11  Bacterial extracellular solute-binding protein


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 !  119.8   0.1   1.7e-38   1.5e-34       2     210 ..      29     233 ..      28     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 1.7e-38
                                    EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEEE-HSCHH CS
                           PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqgrepilqy 81 
                                    i+G+p++G+Vg ++  +Li+s ++ +   id  + lp     pvv++++gr l+p+r+y +    +d+++l    pil+ 
  gi|118430882|ref|NP_146966.2|  29 IVGLPDVGLVGAITGMHLIRSKDMSYTVGIDHYGALP-----PVVIMNRGRVLHPIRIYRS----GDVAALITDVPILPA 99 
                                    89***********************************.....*****************55....47***********99 PP

                                    H..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT.......-CEEEEHHHHHHH CS
                           PAC2  82 e..efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.ees.......eyggivgitglLl 151
                                       +f+ a++++ ++ g++ ++  +g+++ +r +  +++p ++++ a+d++    l  +s       e+g+ivg+ +++l
  gi|118430882|ref|NP_146966.2| 100 AipSFSAAVVEYSRRRGIEYIISATGVGNPKRLE--QEKP-SLYWLASDKKAS--LlASSlrmasepEQGIIVGPYAIIL 174
                                    999*************************998864..6777.999999777754..322113344467************* PP

                                    HHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHH CS
                           PAC2 152 saakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqle 210
                                    ++a +++++ ++lla +   +pdP+aaa+++e ++ ++gl+v++++L+++aee++ ++ 
  gi|118430882|ref|NP_146966.2| 175 KEAMKKHVHNLVLLADSFIDIPDPEAAAVIVEGINSITGLNVSVDELIKQAEEIKLRMR 233
                                    ******************************************************98775 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 ?   11.2   0.0   2.4e-05      0.22      14     115 ..     105     202 ..      96     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEESTT-TT-- CS
                     SBP_bac_11  14 relaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviavpkgnpkki 93 
                                    ++++ +++++ g+++ +sa+g g+  ++++++ +p ++++as +   lla++ ++++e+++ +   p +i+ ++ + k++
  gi|118430882|ref|NP_146966.2| 105 SAAVVEYSRRRGIEYIISATGVGNP-KRLEQE-KPSLYWLASDKKASLLASSLRMASEPEQGIIVGPYAIILKEAMKKHV 182
                                    5566667777777777777777664.444443.7***********999999999999*********************** PP

                                    -SHHHHHHSS--EEEE--T-TT CS
                     SBP_bac_11  94 kgwadLlkpglklavadPttsp 115
                                    +++  L++    + ++dP++++
  gi|118430882|ref|NP_146966.2| 183 HNLVLLADS--FIDIPDPEAAA 202
                                    *99777765..24456665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1953.31
//
Query:       gi|118430883|ref|NP_146967.2|  [L=74]
Description: ferredoxin [Aeropyrum pernix K1]
Scores for complete 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   62.4   1.0    5.5e-17   62.3   1.0    1.0  1  Fer4_15   4Fe-4S single cluster domain
    5.6e-10   39.6   0.1    7.9e-10   39.1   0.1    1.2  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.076   13.1   1.3       0.11   12.6   1.3    1.5  1  Fer4_10   4Fe-4S dicluster domain
       0.22   11.6   2.0          1    9.5   2.1    1.9  1  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   1.0   1.2e-20   5.5e-17       1      66 []       4      67 ..       4      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.2e-20
                        Fer4_15  1 VvvD.rdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                   Vv++ r+ C+ +++Cva++pevfe+++dg a+v++    ++eg+++  +e++a eAar CP + Irv
  gi|118430883|ref|NP_146967.2|  4 VVIEpRESCMPDFVCVAVCPEVFEKHGDGRARVRG---GLGEGFFDRSLEACASEAARLCPRGIIRV 67
                                   678889*************************9995...5789***********************98 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 !   39.1   0.1   1.8e-13   7.9e-10       3      58 .]       9      67 ..       6      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.8e-13
                        Fer4_13  3 rdtCiacgaCvelaPdvFeeddeggasvvaeqpts....eeekadaeeAadaCPvesIgv 58
                                   r++C+ + +Cv+++P+vFe   + g+++v  +         ++a+a eAa  CP  +I+v
  gi|118430883|ref|NP_146967.2|  9 RESCMPDFVCVAVCPEVFEKHGD-GRARVRGGLGEgffdRSLEACASEAARLCPRGIIRV 67
                                   799******************98.778887654445777999****************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.3   2.5e-05      0.11       3      30 ..       6      33 ..       3      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                        Fer4_10  3 vidddtCirCgkCvkaCPadltsvgakg 30
                                   + ++++C+    Cv++CP  ++++g   
  gi|118430883|ref|NP_146967.2|  6 IEPRESCMPDFVCVAVCPEVFEKHGDGR 33
                                   556788************9663333333 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.1   0.00023         1      11      61 ..       8      67 ..       1      70 [. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00023
                        Fer4_19 11 nrelCihsgnCvkglpevFdpkrkpwi.........kpdeasteeiievverCPSGALsy 61
                                    re C    +Cv   pevF+++ ++             d +  + + e+++ CP G +++
  gi|118430883|ref|NP_146967.2|  8 PRESCMPDFVCVAVCPEVFEKHGDGRArvrgglgegFFDRSLEACASEAARLCPRGIIRV 67
                                   4689******************99877445554444444444477777888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 531.62
//
Query:       gi|14600453|ref|NP_146968.1|  [L=263]
Description: GTP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-12   46.9   0.0    4.3e-12   46.3   0.0    1.2  1  RsgA_GTPase  RsgA GTPase
    2.5e-11   43.6   0.0    1.4e-08   34.8   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
    7.7e-07   29.3   2.0     0.0031   17.6   0.1    3.1  3  Dynamin_N    Dynamin family
     0.0011   18.6   0.1       0.42   10.1   0.0    2.2  2  FeoB_N       Ferrous iron transport protein B
     0.0019   17.8   1.1     0.0055   16.3   0.4    1.9  3  GTP_EFTU     Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.011   15.4   0.3      0.033   13.8   0.0    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   1.4e-15   4.3e-12       8     161 ..       8     160 ..       5     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.4e-15
                                   ETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHT CS
                   RsgA_GTPase   8 lvrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktke 88 
                                   l+ +++ Nvd ++ vv + +p ++ +   r+  +ae+ + +++ivlnK Dl+  +  +e+++  +e +g++v++vsa+++ 
  gi|14600453|ref|NP_146968.1|   8 LLARTIKNVDVVVEVVDIRDPMVTRS--RRAERMAEALDKRLLIVLNKSDLVPLRV-AEKWARIIEGMGFDVIYVSARHRL 85 
                                   5667899***********98876654..34445688888899*************9.*********************999 PP

                                   THHHHHHHCTT..SEEE....EECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                   RsgA_GTPase  89 gleelkellkd..ktsv....lvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                   ++++l+  +k+  ++      ++G    GKS++inal++++ + t+ +  + g     T+  +ll+++ g +++DtPG+
  gi|14600453|ref|NP_146968.1|  86 STRRLRGFIKHlaDVKPfsagVIGFPKTGKSSVINALRGRKGAPTSPIPGSPGY----TKGLQLLKIEPGFYMVDTPGV 160
                                   9999887666632222211124555557********************998654....999*****************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 !    6.9   0.1    0.0022       6.6      73     114 .]      13      53 ..       4      53 .. 0.74
   2 !   34.8   0.0   4.9e-12   1.4e-08       2      58 ..     105     162 ..     104     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                                   HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  73 leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                   ++++d+++ vvd++ + +    ++ e++ e  +k+l++vlnk
  gi|14600453|ref|NP_146968.1|  13 IKNVDVVVEVVDIR-DPMVTRSRRAERMAEALDKRLLIVLNK 53 
                                   4569********99.54444446666666667899*****98 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 4.9e-12
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSST...TSSSSEEEEEEEETTEEEEEEECGGCSS CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkp...gtTrdinegrvklkgkeielvDtpGlie 58 
                                   ++++G p +GKS++inal g+  a +s +p   g T+  +  +++   + +++vDtpG+i 
  gi|14600453|ref|NP_146968.1| 105 AGVIGFPKTGKSSVINALRGRkGAPTSPIPgspGYTKGLQLLKIE---PGFYMVDTPGVIP 162
                                   589****************9854677776655599*******998...67********874 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0014       4.1     121     167 ..       8      53 ..       3      54 .. 0.92
   2 !   17.6   0.1     1e-06    0.0031       3      31 ..     107     135 ..     106     141 .. 0.91
   3 ?    2.5   0.0     0.047   1.4e+02     100     115 ..     149     164 ..     143     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                                   HHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                     Dynamin_N 121 lvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                   l+ ++ik+ d+++ v++    +  +++++ +r+++  +kr ++vl+k
  gi|14600453|ref|NP_146968.1|   8 LLARTIKNVDVVVEVVDIRDPMV-TRSRRAERMAEALDKRLLIVLNK 53 
                                   567899*****************.89999****************98 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1e-06
                                   EEEBTTTTHHHHHHHHHTS--S---SSS- CS
                     Dynamin_N   3 vvGsqSsGKSSvlnaLlgedilprgpnpt 31 
                                   v+G  + GKSSv+naL g++  p++p+p 
  gi|14600453|ref|NP_146968.1| 107 VIGFPKTGKSSVINALRGRKGAPTSPIPG 135
                                   899999*******************9985 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.047
                                   S-SEEEEE---B-SSS CS
                     Dynamin_N 100 vkgltlvDlPGldsvn 115
                                   ++g  +vD+PG++ v+
  gi|14600453|ref|NP_146968.1| 149 EPGFYMVDTPGVIPVE 164
                                   577889*****98765 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 !    6.4   0.0    0.0019       5.8      77     152 ..      14      90 ..       6      94 .. 0.78
   2 !   10.1   0.0   0.00014      0.42       4      57 ..     106     160 ..     103     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0019
                                   TSSSEEEEEEEGGG..HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHH CS
                        FeoB_N  77 eepdvvvnvvdatn..lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieel 152
                                   +++dvvv+vvd     + r+         l+++++++ln++d +  +  e   +++ e +g++v+ +sa+++  +++l
  gi|14600453|ref|NP_146968.1|  14 KNVDVVVEVVDIRDpmVTRSRRAERMAEALDKRLLIVLNKSDLVPLRVAE-KWARIIEGMGFDVIYVSARHRLSTRRL 90 
                                   57899999999865226677666666667899**********99876555.78889999*********9998776665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                                   EEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE---- CS
                        FeoB_N   4 alvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGi 57 
                                    ++G p +Gk++++nal g k    +  pG     k  +l   +  + +vD PG+
  gi|14600453|ref|NP_146968.1| 106 GVIGFPKTGKSSVINALRGRKgAPTSPIPGSPGYTKGLQLLKIEPGFYMVDTPGV 160
                                   589***************9873445556665555555555555577777777776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   1.8e-06    0.0055      88     141 ..      10      63 ..       7      88 .. 0.87
   2 ?   -1.5   0.0      0.52   1.6e+03       6      27 ..     105     126 ..     100     134 .. 0.83
   3 ?   -2.8   0.0       1.3   3.7e+03      71      79 ..     151     159 ..     138     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                                   HHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHH CS
                      GTP_EFTU  88 irglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelke 141
                                    r+++ +D++v vvd+++ + +++++  r+a +++ ++ +++NK D +  ++ e
  gi|14600453|ref|NP_146968.1|  10 ARTIKNVDVVVEVVDIRDPMVTRSRRAERMAEALDKRLLIVLNKSDLVPLRVAE 63 
                                   578899*****************************************9555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.52
                                   EEEEESTTSSHHHHHHHHHHHT CS
                      GTP_EFTU   6 igiighvDhGKtTLtdrLlykt 27 
                                    g+ig   +GK++++ +L  ++
  gi|14600453|ref|NP_146968.1| 105 AGVIGFPKTGKSSVINALRGRK 126
                                   589999999*****99997665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.3
                                   EEEEEEESS CS
                      GTP_EFTU  71 linliDtPG 79 
                                    + ++DtPG
  gi|14600453|ref|NP_146968.1| 151 GFYMVDTPG 159
                                   57799***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 ?   13.8   0.0   1.1e-05     0.033     110     156 ..      14      60 ..       2      73 .. 0.83
   2 ?   -1.2   0.0      0.44   1.3e+03       4      20 ..     106     122 ..     104     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                   CCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                          cobW 110 ltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                    ++d+vv vvD +     +++ +e + + l +  l+vlnK Dl++ +
  gi|14600453|ref|NP_146968.1|  14 KNVDVVVEVVDIRDPMVTRSRRAERMAEALDKRLLIVLNKSDLVPLR 60 
                                   5799********999899999999999*****************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.44
                                   EEEESTTCCHHHHHHHH CS
                          cobW   4 vltGflGsGKTtLlnhl 20 
                                   ++ Gf+ +GK++++n+l
  gi|14600453|ref|NP_146968.1| 106 GVIGFPKTGKSSVINAL 122
                                   5789999*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2034.69
//
Query:       gi|118430884|ref|NP_146969.2|  [L=123]
Description: hypothetical protein APE_0106.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       503  (0.0280551); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 945.49
//
Query:       gi|14600455|ref|NP_146970.1|  [L=546]
Description: bipolar DNA helicase [Aeropyrum pernix K1]
Scores for 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-49  166.8   0.0    1.3e-48  166.1   0.0    1.3  1  DUF87          Helicase HerA, central domain
    9.6e-11   41.7   0.4    3.1e-10   40.1   0.4    1.9  1  HAS-barrel     HAS barrel domain
    3.4e-08   32.6   0.1    8.2e-06   24.7   0.0    2.3  2  DUF853         Bacterial protein of unknown function (DUF853)
  ------ inclusion threshold ------
      0.015   14.3   0.0        1.1    8.1   0.0    2.2  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
       0.17   11.2   1.0        9.9    5.4   0.0    2.7  3  FtsK_SpoIIIE   FtsK/SpoIIIE family


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 !  166.1   0.0   3.6e-52   1.3e-48       1     227 []     146     380 ..     146     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 3.6e-52
                         DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitp 81 
                                   ++iG+ll gs+v+ ++d+nkl trHlAil+ TG GKSntv+v+ ++l+ + g+t++i+D+HGEYg++   l+++++++++p
  gi|14600455|ref|NP_146970.1| 146 VRIGSLL-GSGVEYRIDVNKL-TRHLAILAVTGGGKSNTVCVITRRLVGQLGVTTVIFDRHGEYGTLG--LGAGEARLLRP 222
                                   689***6.9************.**********************************************..*********** PP

                         DUF87  82 spsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepveklleelk........... 151
                                   +        ++np+sl+++ell +++   +p+a++q++vl++++ ++ ++ +++k+ ++++++k  e l+           
  gi|14600455|ref|NP_146970.1| 223 A--------RVNPASLSYWELLYMAGF--EPQATAQKRVLRWLWGELARRYRQGKIGAADLIPKAVEVLEkasrssksskq 293
                                   8........9*****************..**************************************************** PP

                         DUF87 152 ..............kekeelrklknqaiarlldkledllrkggsf..snsstdliallleklekegkitiidlsgvdelaq 216
                                                 +e ++++  ++++i ++ldkl+dl++ +gs    n + dl++ +     ++gk ti+dls+++++++
  gi|14600455|ref|NP_146970.1| 294 dpgslarafsevlgDEPSNAPAVRQDQILGVLDKLNDLQDLYGSAldPNIPIDLTRII-----EPGKATIMDLSMMEDNVA 369
                                   *************99999***************************9999999999999.....****************** PP

                         DUF87 217 qlvvsvilrri 227
                                   ++v+s++lrr+
  gi|14600455|ref|NP_146970.1| 370 DAVASHYLRRL 380
                                   *********86 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.4   8.6e-14   3.1e-10       1      90 [.      13     104 ..      13     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 8.6e-14
                    HAS-barrel   1 iGevigestssslifrvegsk..dvkvGeyVeielpdgeivlGmvtdirrgn...selsndlalvlsleeleeangddeva 76 
                                   iG++iges++s  ++ +e++   +v vG+ V+  l+ g++vlG+v++ir+g    +++++dl+ v++++e++ a    ++ 
  gi|14600455|ref|NP_146970.1|  13 IGVIIGESSYSYSTILLERDSlgKVIVGSHVVSTLN-GRCVLGIVESIRSGLpllGDEVRDLDSVKRMLESDVASVVESTR 92 
                                   8*********777777777778**************.*************99***********************999999 PP

                    HAS-barrel  77 latedtgvkvlGev 90 
                                    +++++  +++ ++
  gi|14600455|ref|NP_146970.1|  93 YHVARV--RWVSYL 104
                                   999966..555444 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 !    5.5   0.0    0.0015       5.5      14      65 ..     159     211 ..     153     237 .. 0.78
   2 !   24.7   0.0   2.3e-09   8.2e-06     262     382 ..     405     519 ..     398     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0015
                        DUF853  14 alalklanrhGliaGatGtGktvtLqvlaesl.seaGvpvfladvkGdLsgia 65 
                                   ++ ++   rh  i   tG Gk  t+ v++  l  + Gv+ ++ d  G+   + 
  gi|14600455|ref|NP_146970.1| 159 RIDVNKLTRHLAILAVTGGGKSNTVCVITRRLvGQLGVTTVIFDRHGEYGTLG 211
                                   66778889*********************9983589********999987775 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 2.3e-09
                        DUF853 262 ffdeahLLfndapkallek.veqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfra 341
                                     +eah+L      +l ++   ++ r  r  GvG+  v+q P  l  +vL+q  n++   l+   p+d   v+aa++ + +
  gi|14600455|ref|NP_146970.1| 405 IIEEAHVLIPRDEPTLTKRwAARIAREGRKFGVGLVIVSQRPKKLDVDVLSQTNNKI--ILKMVEPQDISYVRAASEELSE 483
                                   578***99987777787772568999******************************9..59999***********998865 PP

                        DUF853 342 npefdveeaiteLgvGealvsvLdekGaPsiveralvvpPa 382
                                       d+++ + +L++Geal+   +   +P++v+     +P+
  gi|14600455|ref|NP_146970.1| 484 ----DLASLLPSLNTGEALIMG-SMARMPAVVKIDKCEAPT 519
                                   ....899************954.555688888877777775 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 ?    8.1   0.0    0.0003       1.1      11      57 ..     162     209 ..     155     233 .. 0.82
   2 ?    3.8   0.0    0.0063        22     264     306 ..     428     471 ..     423     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0003
                 TrwB_AAD_bind  11 keretqhilivGttGsGKtqalekllra.irargdraivlDltGafvs 57 
                                   +++ t+h++i+  tG GK++++  + r  + + g + +++D +G++  
  gi|14600455|ref|NP_146970.1| 162 VNKLTRHLAILAVTGGGKSNTVCVITRRlVGQLGVTTVIFDRHGEYGT 209
                                   56779******************999872456689*********9865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0063
                 TrwB_AAD_bind 264 llaegRkfGgavvlglqsiaqlr.evYGedaaqsilslvntkli 306
                                   ++ egRkfG+ +v+  q  ++l  +v ++ + + il++v+ + i
  gi|14600455|ref|NP_146970.1| 428 IAREGRKFGVGLVIVSQRPKKLDvDVLSQTNNKIILKMVEPQDI 471
                                   6789******************5489999999999999876644 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0027       9.9      27      56 ..     154     183 ..     144     190 .. 0.89
   2 ?   -2.4   0.0      0.68   2.4e+03     107     121 ..     250     264 ..     244     268 .. 0.87
   3 ?    3.5   0.0     0.011        40     165     211 ..     424     470 ..     344     486 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0027
                                   TS-EEEEEGGGS-.SEEEE--TTSSHHHHH CS
                  FtsK_SpoIIIE  27 sgnplvldlkkmashllvaGatgsGKStal 56 
                                   sg  + +d +k + hl ++  tg GKS+++
  gi|14600455|ref|NP_146970.1| 154 SGVEYRIDVNKLTRHLAILAVTGGGKSNTV 183
                                   7888999*********************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.68
                                   HHHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE 107 raleeLvkemeerya 121
                                   r+l++L  e+ +ry+
  gi|14600455|ref|NP_146970.1| 250 RVLRWLWGELARRYR 264
                                   799**********96 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.011
                                   ...........-----------B-----EEEEEEC-HHHHHHHHHHH CS
                  FtsK_SpoIIIE 165 ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkd 211
                                       ++ +g ++gv +++ ++r  +    ++++  + i L ++ p+d
  gi|14600455|ref|NP_146970.1| 424 WAARIAREGRKFGVGLVIVSQRPKKLDVDVLSQTNNKIILKMVEPQD 470
                                   23345566666666666666666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3864.47
//
Query:       gi|118430885|ref|NP_146971.2|  [L=401]
Description: 5' to 3' nuclease repair protein NurA [Aeropyrum pernix K1]
Scores for complete 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-45  155.7   0.0    1.9e-45  155.5   0.0    1.0  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 !  155.5   0.0   1.1e-49   1.9e-45       2     242 .]      50     375 ..      49     375 .. 0.98

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 1.1e-49
                                    EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCE CS
                           NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedl 81 
                                    +++AvDG+n++++++++ +y+++a+a +ggg+e l ++l + +++s+      e+ri++++e+lE  ++ ++ + +g +l
  gi|118430885|ref|NP_146971.2|  50 NIVAVDGGNRSRDYREFTIYLARAWA-GGGGREALLHSLGVVVPPSDA-----EARISIYREILEAVVAKEAVPGGGRGL 123
                                    89************************.********************9.....*************************** PP

                                    EEEECSHHCCCH.................................................................... CS
                           NurA  82 lllDGsligslv.................................................................... 93 
                                    lllDGs + +l                                                                     
  gi|118430885|ref|NP_146971.2| 124 LLLDGSPSTALKwwrpglsrwglkmsaaiseaekmlpsirgqtlipdcveggcvetllekatrrpasnraamilatltdn 203
                                    ******************************************************************************** PP

                                    .HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH---STTS-H CS
                           NurA  94 .efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnllletlligesisDiallgallrkpgytspllk 168
                                     e++++ +  e +e ly+++++le+    g+ +v+vaK++rs+e+++           i+D+a+++a +++    sp + 
  gi|118430885|ref|NP_146971.2| 204 iEQLRWIVAVEVAEKLYMYKTMLEEawarGYTPVFVAKTSRSTEICRGP---------IADAAYIEARAPQ----SPSYA 270
                                    *************************************************.........***********99....99999 PP

                                    HHHTT..........................-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHH.C......CHHHHH CS
                           NurA 169 ilrek..........................pllrealidkeiyfaYvrlegggsilrleipaevs.t......akdedv 215
                                    + re+                            lr+++++++ +++Y rl++gg+ilr+ i ++++ +       + e++
  gi|118430885|ref|NP_146971.2| 271 VAREDlmvkvglnnmlgievgegdgrfipdvAGLRKFYENLAEVSTYARLAPGGPILRVSILLPGGdKklgdhlGLLESI 350
                                    99999999999999****************************************************669999999999** PP

                                    HHHHH..TTB-SSSBCCHHHHHHHHCC CS
                           NurA 216 lsllasqrlsisGYprpLalAhelaki 242
                                    ls+la  ++s+sGYp+pL +Ahe+a++
  gi|118430885|ref|NP_146971.2| 351 LSRLA--NFSPSGYPVPLLIAHEKARV 375
                                    *****..******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2986.94
//
Query:       gi|14600457|ref|NP_146972.1|  [L=919]
Description: DNA double-strand break repair rad50 ATPase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-22   79.5   3.3    5.6e-11   42.3   0.0    2.3  2  SMC_N          RecF/RecN/SMC N terminal domain
    1.8e-16   60.8   2.1    3.5e-08   33.5   0.1    3.9  2  AAA_15         AAA ATPase domain
      6e-15   56.3  64.6    4.5e-07   30.6  41.8    5.7  2  AAA_23         AAA domain
    7.6e-12   44.7  44.9    0.00069   18.4   2.9    5.6  4  AAA_13         AAA domain
    8.7e-11   41.5   5.5    1.4e-10   40.9   0.0    4.6  2  Rad50_zn_hook  Rad50 zinc hook motif
    2.5e-10   40.6  17.3    2.9e-05   24.0   0.1    3.7  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    5.9e-08   32.8   0.0    1.2e-06   28.6   0.0    2.6  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
    4.9e-07   29.4   0.0    8.7e-07   28.6   0.0    1.3  1  AAA_29         P-loop containing region of AAA domain
    2.9e-06   27.9  12.5    0.00012   22.7   0.1    5.0  3  ABC_tran       ABC transporter
    0.00085   19.0   0.0    0.00085   19.0   0.0    5.3  5  AAA_27         AAA domain
     0.0016   18.9  16.2        1.6    9.2   0.5    7.5  7  NPV_P10        Nucleopolyhedrovirus P10 protein
     0.0027   17.8  19.8        2.3    8.3   0.2    6.3  6  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
     0.0075   16.5  43.7       0.93    9.8   6.4    7.7  7  BLOC1_2        Biogenesis of lysosome-related organelles comp
     0.0078   16.1   0.4      0.036   13.9   0.0    2.4  1  MukB           MukB N-terminal
     0.0081   15.5   4.2     0.0081   15.5   4.2    6.3  7  DUF3450        Protein of unknown function (DUF3450)
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.012   14.9   0.0    3.8  4  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.013   15.6  14.2      0.013   15.6  14.2    7.2  6  BRE1           BRE1 E3 ubiquitin ligase
      0.019   15.0  36.2      0.053   13.6   4.2    6.0  6  DUF1664        Protein of unknown function (DUF1664)
      0.022   14.7   0.0       0.17   11.8   0.0    2.6  1  RsgA_GTPase    RsgA GTPase
      0.034   14.7   1.4      0.034   14.7   1.4    8.6  8  SlyX           SlyX
      0.049   14.0   0.1      0.049   14.0   0.1    4.9  2  AAA_16         AAA ATPase domain
      0.065   13.5  14.8         15    5.9   0.3    6.5  6  DUF948         Bacterial protein of unknown function (DUF948)
        0.1   12.7   0.0       0.45   10.6   0.0    2.2  1  MMR_HSR1       50S ribosome-binding GTPase
       0.18   11.9   8.3       0.13   12.4   1.1    3.7  3  TssO           Type VI secretion system, TssO
       0.19   12.0   4.8       0.19   12.0   0.0    3.1  2  AAA_22         AAA domain
       0.25   11.8  41.2       0.95   10.0   6.3    6.1  6  DUF16          Protein of unknown function DUF16
        0.3    9.9  88.2      0.038   12.9  19.2    5.6  6  Spc7           Spc7 kinetochore protein
       0.52   10.1   6.0       0.29   11.0   1.5    2.8  2  PhageMin_Tail  Phage-related minor tail protein
        1.6    8.8   0.0        1.6    8.8   0.0    3.8  2  Dynamin_N      Dynamin family
        2.8    7.2  88.4       0.18   11.2  17.6    6.3  6  GAS            Growth-arrest specific micro-tubule binding
          4    6.9  74.1     0.0097   15.5  12.1    5.8  5  MscS_porin     Mechanosensitive ion channel porin 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 !   37.7   0.1   2.4e-12   1.4e-09       2      64 ..       4      59 ..       3     111 .. 0.84
   2 !   42.3   0.0   9.6e-14   5.6e-11     100     217 ..     685     912 ..     642     915 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.4e-12
                                  EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdl 64
                                  lkrle++n  s    +++++f ++ftaivG+NG+GKs +l+AilF +  ++a      + s++
  gi|14600457|ref|NP_146972.1|  4 LKRLELRNIMSHF--NTSIDFREGFTAIVGRNGAGKSTILEAILFSITPHQA-----PRRSSM 59
                                  89*********96..8999*************************99884333.....444444 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 9.6e-14
                                   EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                         SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske............................................. 135
                                   ++r+++ +  e k+ ++  +k+e++  l++++ +                                               
  gi|14600457|ref|NP_146972.1| 685 MKRLEELEAEEKKLRKEVSRKSEIEARLKEVQNTLAelddrisridremgelqtriremksrkasgeealklylpaaasrr 765
                                   33333333344444444444444444444444433345555555555577999999999999999999************* PP

                                   ............................................................CS-HHHHHHHHHHHHHHHHCC CS
                                   ............................................................xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 136 ............................................................lLSgGektLvalaLlfAiqkv 156
                                                                                               + SgGe+t++al++++A++k+
  gi|14600457|ref|NP_146972.1| 766 imeeigeiayrrllavledemndilsrfnldvagveirekaareievkaiggngayrpleAVSGGERTVLALSFVLALNKA 846
                                   ******************************************************************************998 PP

                                   ..S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT...SEEEEE-SSHHHCCC-SCEEEEEEEETT CS
                                   ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 157 ..kpaplyllDeidaaLDeknvkkvaellkekskn...aQfivislreemlekadklvgvtkveng 217
                                      +  +  lDe  a+LDe +++ ++e+l+  s +    Q++v++++e++   ad+++ vt +++g
  gi|14600457|ref|NP_146972.1| 847 vgGKLGFLALDEPTANLDEDRRRSLVEVLRGISVEglvRQLVVVTHHEDVRDYADTICLVTRTQQG 912
                                   3357899**********************9666554558*********************998887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   6.1e-11   3.5e-08       3      48 ..       4      47 ..       1     444 [. 0.66
   2 !   23.3   0.0   8.2e-08   4.7e-05     148     365 ..     663     893 ..     590     896 .. 0.57

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.1e-11
                        AAA_15  3 IkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFln 48
                                  +k+++++N  s+ +++id+ e +t ++G+N++GKS+ilea+  +++
  gi|14600457|ref|NP_146972.1|  4 LKRLELRNIMSHFNTSIDFREGFTAIVGRNGAGKSTILEAI--LFS 47
                                  78999999999******************************..444 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 8.2e-08
                        AAA_15 148 pkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekilee 228
                                     e+   l++e ++lk + e + k +++le   kk                                              
  gi|14600457|ref|NP_146972.1| 663 RLEEARRLKEEAAKLKWEAEQVMKRLEELEAEEKK---------------------------------------------- 697
                                   33333333333333333333333333333333322.............................................. PP

                        AAA_15 229 alqekl.............eeelteklkeiqeklkeidkklaeelk................................... 261
                                        l              +e++  l e+++ ++ id                                           
  gi|14600457|ref|NP_146972.1| 698 -----LrkevsrkseiearLKEVQNTLAELDDRISRID-------Remgelqtriremksrkasgeealklylpaaasrri 766
                                   .....122333322222222222222222222222222.......122222234444444555555566666666666666 PP

                        AAA_15 262 .....................kilkkkidkikkfnykgkkneeieik....ddeelplnknGsGvqrllllillileaekk 317
                                                        +il  +  ++  +++ +k   eie+k    ++ + pl+ ++ G +  l l++ ++ ++  
  gi|14600457|ref|NP_146972.1| 767 meeigeiayrrllavledemnDILSRFNLDVAGVEIREKAAREIEVKaiggNGAYRPLEAVSGGERTVLALSFVLALNKAV 847
                                   66666666666664444333366666666666677777777777777**************************99999999 PP

                        AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnkt.QviitTHS 365
                                        k  +l+++EP a+L  +  ++l++ l+ ++ ++   Q+++ TH 
  gi|14600457|ref|NP_146972.1| 848 ---GGKLGFLALDEPTANLDEDRRRSLVEVLRGISVEGLVrQLVVVTHH 893
                                   ...9**********************************889*******5 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6  41.8   7.8e-10   4.5e-07       1     196 [.       6     260 ..       6     621 .. 0.86
   2 ?    2.8  14.8      0.25   1.5e+02     117     199 ..     642     726 ..     621     727 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 7.8e-10
                        AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLy.getprlsrksgrgfeksdveiesegkvkayvelt.. 78 
                                   +L+++n++s+ +++idF  g+t+I+G NGaGK+Til+Ai +  + +++pr s+  ++++ ++++ ++ + +  + +el+  
  gi|14600457|ref|NP_146972.1|   6 RLELRNIMSHFNTSIDFREGFTAIVGRNGAGKSTILEAILFSITpHQAPRRSSMISENSSRGEIYLALQSSEGRLLELRnk 86 
                                   79***************************************9985777999998899********9999555555888855 PP

                        AAA_23  79 .fenkdgry..trsiererelskkkgkttkkaklelleideleqfisellgskkiil.nlilflgqerfeefelkdkke.. 153
                                    +++ +g++    +i+ e  ++ +k   +k+++ ++l+ + l +  s ++++  ii+   ++ l++   e++el d ++  
  gi|14600457|ref|NP_146972.1|  87 lIRRGGGTNteAAIITLEGRRIASKPTGYKEEIHKILGLRGLPNPAS-YIEKAIIISqGGLQTLAEILSEPKELRDLLDaa 166
                                   43333443366555666777777777777888888887765533333.222222222222222333333333444444477 PP

                        AAA_23 154 .....................................................rleelekeleeledekkllekleqekek 181
                                                                                        +++e++k leele e+++le++ +  + 
  gi|14600457|ref|NP_146972.1| 167 lgyallkqaisnigdvvlgvspdgspvklgsksitrlqsgymtlrnevlgvdrEIREASKRLEELEREREELERRAR--DL 245
                                   77777777888888899999999999999999999999999999998888888888888888888888888887743..23 PP

                        AAA_23 182 ekeleeleeeleeil 196
                                   e e ++l++e+ +++
  gi|14600457|ref|NP_146972.1| 246 ESEAKALQSEIGKLE 260
                                   334445555444433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.25
                        AAA_23 117 leqfisellgskkiil.nlilflgqerfeefelkdkkerleelekeleeledekkllekl.eqekekekeleeleeeleei 195
                                   l ++ +e l+  +++l  +   l + r  ++e ++ k + e++ k leele+e+k+l+k+  ++ e e++l+e++++l e+
  gi|14600457|ref|NP_146972.1| 642 LLEKAREALEGVDKELsAIERRLEEARRLKEEAAKLKWEAEQVMKRLEELEAEEKKLRKEvSRKSEIEARLKEVQNTLAEL 722
                                   444444444433333313334455555555555666669999********9999999999567777888**********99 PP

                        AAA_23 196 lkel 199
                                   ++ +
  gi|14600457|ref|NP_146972.1| 723 DDRI 726
                                   8876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.051        29      21      36 ..      29      44 ..      13      70 .. 0.79
   2 !   14.2  13.1   2.2e-05     0.013      92     307 ..     222     453 ..     214     459 .. 0.72
   3 !   18.4   2.9   1.2e-06   0.00069     255     362 ..     461     586 ..     452     598 .. 0.76
   4 !   16.1  11.8   5.8e-06    0.0033     286     570 ..     604     893 ..     585     904 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.051
                        AAA_13 21 iYGwNGaGKTtLSrll 36
                                  i G+NGaGK+t+ +++
  gi|14600457|ref|NP_146972.1| 29 IVGRNGAGKSTILEAI 44
                                  78*********97766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-05
                        AAA_13  92 iekqekieklkkeikkleekleaaeaqlqkaekekkklek..eledeawkkivkkknsalsealkglkyeekfkerllkel 170
                                    e+ +++e+l+ e+++le++ +  e +++++++e  kle+  e++ +++  ++++++s+l++  + l+y e + +  +++l
  gi|14600457|ref|NP_146972.1| 222 REASKRLEELEREREELERRARDLESEAKALQSEIGKLETmeEMLVNVTS-MIRSERSKLDTINTRLRYAESKIS-SIDDL 300
                                   58999***************999999999999977766651134455544.668999999988778888443322.22332 PP

                        AAA_13 171 kkk.......nrkaaellsdeelkakletv...esenlpelaplslssidldalek.aeilkkkvvgkdseieeLienldl 240
                                   +k           a e+ ++++l+++l+++    +  +  +++l++ s+ l+++e+     ++++    s i+e +++  l
  gi|14600457|ref|NP_146972.1| 301 EKRraelrakASLAHEVAELARLQSRLDKLgrdLEMIRDAVEKLEV-SRRLKEIESaRREAENRLLEARSSIKEEQRRYTL 380
                                   2221111111334445555566666666663212223344677775.6777788886778888888889999999999999 PP

                        AAA_13 241 adW.VkqGlelheas...sdtCp...FCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklk 307
                                    d+ V +G+++ ++    +++C+    Cg++ p++  ++L+a+++d  e k ++L++ ++ +e + ++l++ l 
  gi|14600457|ref|NP_146972.1| 381 LDYrVTRGRSIVTNIrrvLSECRskdLCGSEKPESVLERLDAVIND-LESKARALDQEASALEAEARRLVQALS 453
                                   9998********98656889**76669*******************.9999***************99999885 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.2e-06
                        AAA_13 255 sdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsde...............asensafe 320
                                   s  Cp Cg +lp  r++a+++h+  e e+  ++ ++++++ e++++e+  +l++   +                ++ +++ 
  gi|14600457|ref|NP_146972.1| 461 SARCPVCGAELPPGRAEAIARHYRHEAERLRKAAKEKAAEAEKARAEA-SRLQDKRRRielllsrlnqleeglRELGFQTP 540
                                   689**************************************9998765.55555444445566666666666656666677 PP

                        AAA_13 321 edkeelkaeaealeeqLkg...lqraleaKrkepfk.svelesvka 362
                                   ed ++++++++ l+e+L++   l++ le+K+ ++++ +v l ++k 
  gi|14600457|ref|NP_146972.1| 541 EDLAKAEQKLRMLRERLEElrkLENSLEEKVRNLSReEVALREAKT 586
                                   7799999999999999766333778999999999985666665555 PP

  == domain 4  score: 16.1 bits;  conditional E-value: 5.8e-06
                        AAA_13 286 erLekliekveskkselleklkavsde..asensafeedkeelkaeaealeeqLkglqralea..Krkepfk..svelesv 360
                                   e+L+ l ++ ++ ++ l+ k ++++++   ++++  ++  e++++++e ++++L +++r+le+  + ke ++  + e e+v
  gi|14600457|ref|NP_146972.1| 604 EKLKTLSSESKKLERMLVSKAEDLATRlgITAYRSLDDLLEKAREALEGVDKELSAIERRLEEarRLKEEAAklKWEAEQV 684
                                   334444444444433344444444443233445556666778888888888888888888875334444444145567888 PP

                        AAA_13 361 kakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelke..eeael 439
                                    +++e+++ + +++ + +++  e+ a+l+e ++++++    +++++++ e+ e+++ +++++    + e++lk    +a+ 
  gi|14600457|ref|NP_146972.1| 685 MKRLEELEAEEKKLRKEVSRKSEIEARLKEVQNTLAELD--DRISRIDREMGELQTRIREMKSRKASGEEALKLylPAAAS 763
                                   888888888888888888888888888888888877643..3577788888888877777777766666666641146667 PP

                        AAA_13 440 kkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfeee....kkgYrivrkggsqaaetLSeGEktaIaflYFlks 516
                                   + + eei e+  + r      +e+n++L++f l  +  ++ e+     +   i  +g + + e  S GE+t+ a+ + l++
  gi|14600457|ref|NP_146972.1| 764 RRIMEEIGEIAYR-RLLAVLEDEMNDILSRFNLDVAGVEIREKaareIEVKAIGGNGAYRPLEAVSGGERTVLALSFVLAL 843
                                   7777888887533.2233334788888888844444444444333434445555566677778999999999998866665 PP

                        AAA_13 517 lkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                    k      gk +   +D P   LD +   + +  ++     +  ++Ql + TH+
  gi|14600457|ref|NP_146972.1| 844 NK--AVG-GKLGFLALDEPTANLDEDRRRSLVEVLRGIS-VEGLVRQLVVVTHH 893
                                   55..333.5789999999999999998888888888876.57888999999997 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 ?   -2.3   0.1         7   4.1e+03      35      51 ..     421     437 ..     418     438 .. 0.81
   2 !   40.9   0.0   2.4e-13   1.4e-10       1      50 [.     441     492 ..     441     494 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7
                                   HHHHHHHHHHHHHHH.. CS
                 Rad50_zn_hook  35 seLikelqsklerlpee 51 
                                     +i++l+sk + l +e
  gi|14600457|ref|NP_146972.1| 421 DAVINDLESKARALDQE 437
                                   57899999999999876 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 2.4e-13
                                   HHHHHHHHHHHHHHHTT-SE..E-TTT--EE-HHHHHHHHHHHHHHHHHHH. CS
                 Rad50_zn_hook   1 lhqeteelnkkieelkeakg..cCPlCgReldeehrseLikelqsklerlpe 50 
                                   l++e+ +l +++++l+e++g  +CP+Cg el++ +++ ++++++++ erl++
  gi|14600457|ref|NP_146972.1| 441 LEAEARRLVQALSMLEESGGsaRCPVCGAELPPGRAEAIARHYRHEAERLRK 492
                                   68999*********************************************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 !   24.0   0.1     5e-08   2.9e-05       1      48 [.      26      66 ..      26     129 .. 0.67
   2 ?   -1.5   0.0         3   1.7e+03      72     115 ..     381     427 ..     365     438 .. 0.88
   3 ?   -1.3   0.2       2.6   1.5e+03     150     214 ..     521     589 ..     485     617 .. 0.58
   4 !   23.8   4.6   5.8e-08   3.4e-05     137     298 ..     664     893 ..     622     896 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5e-08
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsl 48
                                  +++++G+Ng+GKS++L+a+ +        +  +  ++++++i++ +s+
  gi|14600457|ref|NP_146972.1| 26 FTAIVGRNGAGKSTILEAILFS-------ITPHQAPRRSSMISENSSR 66
                                  89*****************664.......4455555555555555544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3
                        AAA_21  72 yryglrlersqv...eeklssvetllesgllldkrsleeedvfnpea 115
                                    +y+++ +rs+v   ++ ls+ +++ ++g  +++++le+ d+++++ 
  gi|14600457|ref|NP_146972.1| 381 LDYRVTRGRSIVtniRRVLSECRSKDLCGSEKPESVLERLDAVINDL 427
                                   679999999999999************************99998876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.6
                        AAA_21 150 rawsllllldglrke....rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvde 214
                                    +++l++l +glr+       +l+ + +++    ++++ l++l++sl +   +ls ++++ ++ +++++
  gi|14600457|ref|NP_146972.1| 521 LLSRLNQLEEGLRELgfqtPEDLAKAEQKLRMLRERLEELRKLENSLEEKVRNLSREEVALREAKTRAL 589
                                   333444444444444544555555555555566666666666666666666666666666655555554 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 5.8e-08
                        AAA_21 137 dlqfgkaltditsrawsllllldglrke.......rigllnifadyfgfakekrllqrlvrslklveielsdlgegeelia 210
                                    ++  ++  +  + +w++++ +  l +        r+ + + +  ++  +++++ l +l +++++++ e   l+ ++++++
  gi|14600457|ref|NP_146972.1| 664 LEEARRLKEEAAKLKWEAEQVMKRLEELeaeekklRKEVSRKSEIEARLKEVQNTLAELDDRISRIDREMGELQTRIREMK 744
                                   333333333334444444444444444455566666666666666666666666666666666666666666666666666 PP

                        AAA_21 211 svderlrer........................................................gvvflengdgqelpar 235
                                   s++    e+                                                          v    g+g  +p+ 
  gi|14600457|ref|NP_146972.1| 745 SRKASGEEAlklylpaaasrrimeeigeiayrrllavledemndilsrfnldvagveirekaareIEVKAIGGNGAYRPLE 825
                                   666666666999999999999999999999999999999999999999999999999999********************* PP

                        AAA_21 236 elSdGtkrllalltallralkkg...sllliDEpEngLHPkllrrllell..kelsrngaQviltTHS 298
                                    +S G + +lal   l+     g   ++l++DEp ++L+  + r+l+e+l   + +    Q++++TH 
  gi|14600457|ref|NP_146972.1| 826 AVSGGERTVLALSFVLALNKAVGgklGFLALDEPTANLDEDRRRSLVEVLrgISVEGLVRQLVVVTHH 893
                                   *********888888887776669**************************9955555667*******5 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.97   5.6e+02      21      49 ..     735     763 ..     722     779 .. 0.76
   2 !   28.6   0.0   2.1e-09   1.2e-06       7      89 ..     803     876 ..     799     877 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.97
                       SbcCD_C  21 gkekelsrssgtlSGGekqflaylalaaa 49 
                                   + +++++++ +++  Ge ++ +yl+ aa+
  gi|14600457|ref|NP_146972.1| 735 ELQTRIREMKSRKASGEEALKLYLPAAAS 763
                                   44566888888999999989999999887 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.1e-09
                       SbcCD_C   7 RnylsfevevrdedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                   R++   e+ev++ +g+    +r  ++ SGGe+ ++++l +++al  +++       +l++++LDE  ++lDe+++++l+e+
  gi|14600457|ref|NP_146972.1| 803 REKAAREIEVKAIGGNG--AYRPLEAVSGGER-TVLALSFVLALNKAVGG------KLGFLALDEPTANLDEDRRRSLVEV 874
                                   67777788888777775..79***********.99999999999999999......59*********************99 PP

                       SbcCD_C  88 le 89 
                                   l+
  gi|14600457|ref|NP_146972.1| 875 LR 876
                                   87 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 !   28.6   0.0   1.5e-09   8.7e-07       1      50 [.       4      52 ..       4      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.5e-09
                        AAA_29  1 LkrlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  Lkrl+l N  +  +++i+++ +g+t ++G++G+GKST+l Ai + ++p++
  gi|14600457|ref|NP_146972.1|  4 LKRLELRNIMSHFNTSIDFR-EGFTAIVGRNGAGKSTILEAILFSITPHQ 52
                                  67888888877777899998.779********************999998 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1     2e-07   0.00012      13      38 ..      26      51 ..      16     148 .. 0.81
   2 ?   -1.7   0.2       6.7   3.9e+03      79      80 ..     276     295 ..     222     384 .. 0.54
   3 ?    4.2   3.3       0.1        58      79     137 .]     743     861 ..     426     861 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2e-07
                                  EEEEEESTTSSHHHHHHHHTTSS--S CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran 13 kvaivGenGaGKStLlkllagllkpt 38
                                   +aivG+nGaGKSt+l++++   +p 
  gi|14600457|ref|NP_146972.1| 26 FTAIVGRNGAGKSTILEAILFSITPH 51
                                  589****************9888774 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.7
                                   H..................H CS
                                   x..................x RF
                      ABC_tran  79 n..................e 80 
                                   +                   
  gi|14600457|ref|NP_146972.1| 276 ErskldtintrlryaeskiS 295
                                   23333333222222222220 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.1
                                   H.....................................HHHTCHHHHHHHSTTGG.................TTCBGESTT CS
                                   x.....................................xxxxxxxxxxxxxxxxx.................xxxxxxxxx RF
                      ABC_tran  79 n.....................................esdeeiekalsklglke.................lkdtvvkss 105
                                                                           ++e++++ls+++l+                  +  + +++ 
  gi|14600457|ref|NP_146972.1| 743 MksrkasgeealklylpaaasrrimeeigeiayrrllaVLEDEMNDILSRFNLDVagveirekaareievkaIGGNGAYRP 823
                                   133455555556666666555555555566666666664444455555555554455555554444443333445554444 PP

                                   SGGS-HHHHHHHHHHHHHHHTSSE......EEEESTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx RF
                      ABC_tran 106 pssLSgGqkqrvalarallkkpkl......lllDEpta 137
                                    + +SgG++  +al  +l+ ++ +      l lDEpta
  gi|14600457|ref|NP_146972.1| 824 LEAVSGGERTVLALSFVLALNKAVggklgfLALDEPTA 861
                                   49999999998887777766654333333388888885 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.5e-06   0.00085       3      50 ..       4      45 ..       3      83 .. 0.87
   2 ?   -0.1   0.2         1   5.9e+02     148     172 ..     221     245 ..     193     273 .. 0.54
   3 ?   -1.2   0.6       2.2   1.3e+03     162     199 ..     320     359 ..     296     387 .. 0.50
   4 ?   -2.9   0.0       7.5   4.4e+03     159     180 ..     421     442 ..     406     460 .. 0.49
   5 ?    1.1   1.3      0.44   2.6e+02     156     197 ..     682     722 ..     633     744 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                        AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                  l+rL+L+   +  ++s+df+   ++++ i+G N AGKst+l+Ai   l
  gi|14600457|ref|NP_146972.1|  4 LKRLELRNIMSHFNTSIDFR---EGFTAIVGRNGAGKSTILEAI---L 45
                                  5778888877777899***8...8******************98...4 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                        AAA_27 148 LfeasaGlaslrevleaLeaeadel 172
                                   + eas  l++l++ +e+Le++a++l
  gi|14600457|ref|NP_146972.1| 221 IREASKRLEELEREREELERRARDL 245
                                   2233333333333333333333333 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.2
                        AAA_27 162 leaLeaeadelfkprkskk..rainealeeleeakkelre 199
                                   l++L+++ d+l ++ +  +   +  e  ++l+e +++ re
  gi|14600457|ref|NP_146972.1| 320 LARLQSRLDKLGRDLEMIRdaVEKLEVSRRLKEIESARRE 359
                                   4444444444443333222111111222222222222222 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 7.5
                        AAA_27 159 revleaLeaeadelfkprkskk 180
                                    +v+++Le++a++l ++ ++ +
  gi|14600457|ref|NP_146972.1| 421 DAVINDLESKARALDQEASALE 442
                                   4444444444444433333322 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.44
                        AAA_27 156 aslrevleaLeaeadelfkprkskkrainealeeleeakkel 197
                                   +++ + le+Leae ++l k+ ++k+ +i + l+e++++ +el
  gi|14600457|ref|NP_146972.1| 682 EQVMKRLEELEAEEKKLRKEVSRKS-EIEARLKEVQNTLAEL 722
                                   3556667777777777777666666.6666666655555554 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3     0.037        21      13      66 ..     221     274 ..     208     305 .. 0.60
   2 ?    3.1   0.0      0.24   1.4e+02      22      55 ..     322     354 ..     309     403 .. 0.62
   3 ?    1.1   0.1      0.97   5.6e+02       4      36 ..     415     447 ..     412     458 .. 0.73
   4 ?    1.6   0.1      0.69     4e+02      28      61 ..     541     574 ..     511     586 .. 0.74
   5 ?    0.2   0.0       1.8   1.1e+03      40      65 ..     639     664 ..     602     675 .. 0.73
   6 ?    2.2   0.1      0.44   2.6e+02       5      56 ..     642     693 ..     637     704 .. 0.72
   7 !    9.2   0.5    0.0028       1.6      15      62 ..     683     730 ..     678     737 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                       NPV_P10  13 ikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                   i++ +++++ l+ + ++++   +d++   + L++   +L+++e+ + n++++  
  gi|14600457|ref|NP_146972.1| 221 IREASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEEMLVNVTSMIR 274
                                   555566666666666666666666555555555555555555555555555543 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.24
                       NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                    lq+++d++  +l+ + +  ekL+  s  L+e+e
  gi|14600457|ref|NP_146972.1| 322 RLQSRLDKLGRDLEMIRDAVEKLE-VSRRLKEIE 354
                                   456666666666666666666665.355555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.97
                       NPV_P10   4 niLlvIradikavddkVdalqqqvddvqenlpd 36 
                                   ++L    a i+++++k  al+q+   ++++ + 
  gi|14600457|ref|NP_146972.1| 415 SVLERLDAVINDLESKARALDQEASALEAEARR 447
                                   566667777888888999998888888877665 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.69
                       NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                   +d+++  +++  l e+L+++ +  ++le+kv n 
  gi|14600457|ref|NP_146972.1| 541 EDLAKAEQKLRMLRERLEELRKLENSLEEKVRNL 574
                                   4555566666667777777777777777777664 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.8
                       NPV_P10  40 lnekLdaqsaqLaeletkvenIqdiL 65 
                                   l + L++  ++L+ +++++++I+  L
  gi|14600457|ref|NP_146972.1| 639 LDDLLEKAREALEGVDKELSAIERRL 664
                                   45555566666666666666665544 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.44
                       NPV_P10   5 iLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                    L   r++ + vd+ ++a++ ++++ +   ++  +l+ + ++  + L+ele+
  gi|14600457|ref|NP_146972.1| 642 LLEKAREALEGVDKELSAIERRLEEARRLKEEAAKLKWEAEQVMKRLEELEA 693
                                   5667789999999999999999988777666666666666666666666654 PP

  == domain 7  score: 9.2 bits;  conditional E-value: 0.0028
                       NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                   +v ++++ l+++ +++++++   +e++++L + +++Lael++ ++ I+
  gi|14600457|ref|NP_146972.1| 683 QVMKRLEELEAEEKKLRKEVSRKSEIEARLKEVQNTLAELDDRISRID 730
                                   6778889999999********************************997 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 ?    5.8   0.3     0.023        13      44     106 ..     218     285 ..     195     299 .. 0.50
   2 ?    5.6   0.0     0.025        15      33     109 ..     320     400 ..     310     402 .. 0.75
   3 ?    1.1   0.1      0.65   3.8e+02      43      78 ..     416     454 ..     410     459 .. 0.54
   4 ?    4.1   0.7     0.076        44      38      90 ..     541     592 ..     516     595 .. 0.71
   5 ?    1.6   0.2      0.47   2.7e+02      38      96 ..     597     659 ..     580     666 .. 0.60
   6 !    8.3   0.2    0.0039       2.3      33      99 ..     674     745 ..     664     755 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.023
                  Baculo_PEP_C  44 etqLnalsedlksllaeldt......rldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNins 106
                                   ++++ + s++l+       +      +l+  +  L++  +alq      +t+++ L n++s + +  s++  in+
  gi|14600457|ref|NP_146972.1| 218 DREIREASKRLE-------ElerereELERRARDLESEAKALQseigklETMEEMLVNVTSMIRSERSKLDTINT 285
                                   333333444444.......33333334444444444444444422222236666666666666555555555554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                  Baculo_PEP_C  33 laqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsiltnLlssvtNinst 107
                                   la l++ ld++ + L+ + +++++l  e+++rl++  ++  +a n+l       ++ + + t l+  +t   s vtNi   
  gi|14600457|ref|NP_146972.1| 320 LARLQSRLDKLGRDLEMIRDAVEKL--EVSRRLKEIESARREAENRLLearssiKEEQRRYTLLDYRVTRGRSIVTNIRRV 398
                                   5889999999999999999999994..678888888888888888887666444333456788888888888888888877 PP

                  Baculo_PEP_C 108 Ln 109
                                   L+
  gi|14600457|ref|NP_146972.1| 399 LS 400
                                   75 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.65
                  Baculo_PEP_C  43 ietqLnalsedlksllaeldt...rldtlltnLtdalna 78 
                                   + ++L+a+ +dl+s   +ld+   +l++ + +L +al  
  gi|14600457|ref|NP_146972.1| 416 VLERLDAVINDLESKARALDQeasALEAEARRLVQALSM 454
                                   455566666666665555555444555555555555544 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.076
                  Baculo_PEP_C  38 tlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnl 90 
                                   ++l++ e++L  l e+l++ l +l++ l++ + nL++   al ++ + +L+ l
  gi|14600457|ref|NP_146972.1| 541 EDLAKAEQKLRMLRERLEE-LRKLENSLEEKVRNLSREEVALREAKTRALEVL 592
                                   4566677788888888888.566888888888888888888887777766655 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.47
                  Baculo_PEP_C  38 tlldaietqLnalsedlksllaeldtrldtlltnLt.dalnalq...dtlrneLtnlnsiltn 96 
                                      ++  ++L++ls++ k+l   l ++ ++l+t+L  +a  +l    ++ r++L++++++l+ 
  gi|14600457|ref|NP_146972.1| 597 IKEEEAREKLKTLSSESKKLERMLVSKAEDLATRLGiTAYRSLDdllEKAREALEGVDKELSA 659
                                   555566666777776666666666666666666663233333334448888888888887765 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0039
                  Baculo_PEP_C  33 laqlatlldaietqLnalsedlksllaeldt..rldtlltnLtdalnalq...dtlrneLtnlnsiltnLls 99 
                                   +a+l+   +++ ++L++l+++ k+l +e+++  ++++ l++++++l++l      ++ e+  l++ + ++ s
  gi|14600457|ref|NP_146972.1| 674 AAKLKWEAEQVMKRLEELEAEEKKLRKEVSRksEIEARLKEVQNTLAELDdriSRIDREMGELQTRIREMKS 745
                                   478888899999999999999999999998867777777778888877774444556677777776666655 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 ?    7.2   2.3      0.01         6      30      74 ..     222     266 ..     200     287 .. 0.76
   2 ?    1.8   0.3      0.52     3e+02      39      81 ..     269     311 ..     258     313 .. 0.76
   3 ?    4.3   0.4     0.085        49      44      85 ..     311     345 ..     291     356 .. 0.55
   4 !    8.6   0.0     0.004       2.3      41      94 ..     390     444 ..     379     446 .. 0.78
   5 ?    5.2   0.5     0.045        26      41      81 ..     492     532 ..     477     541 .. 0.55
   6 ?    2.3   0.6      0.35     2e+02      37      67 ..     544     574 ..     538     583 .. 0.58
   7 !    9.8   6.4    0.0016      0.93      33      92 ..     671     730 ..     647     734 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                       BLOC1_2  30 eaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqv 74 
                                   ++as++ ++l+++ ++le+ + +l+++ ++lq+ + +++ +e+ +
  gi|14600457|ref|NP_146972.1| 222 REASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEEML 266
                                   467778888888888888888888888888888888888777755 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.52
                       BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                   +++++ s ++kl+ +n +    ++++++id++ek+ +eL + +
  gi|14600457|ref|NP_146972.1| 269 VTSMIRSERSKLDTINTRLRYAESKISSIDDLEKRRAELRAKA 311
                                   5666777778888888888888899999999999988887765 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.085
                       BLOC1_2  44 aslekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                   asl+ ++        el+ + +++d++ ++++ + +av++L+
  gi|14600457|ref|NP_146972.1| 311 ASLAHEVA-------ELARLQSRLDKLGRDLEMIRDAVEKLE 345
                                   34444445.......555555555555555555555555554 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.004
                       BLOC1_2  41 dvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                   +++ ++++ l++ ++k+    ++  + ++++++ +++Le+ + +LD+  ++LEa 
  gi|14600457|ref|NP_146972.1| 390 SIVTNIRRVLSECRSKDLcGSEKPESVLERLDAVINDLESKARALDQEASALEAE 444
                                   556666666666666666556666677999**********************985 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.045
                       BLOC1_2  41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                   ++a++ ++++ek +++   lq + ++i+ +  ++++Lee  
  gi|14600457|ref|NP_146972.1| 492 KAAKEKAAEAEKARAEASRLQDKRRRIELLLSRLNQLEEGL 532
                                   44455555555555555555555555555555555555433 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.35
                       BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqi 67 
                                   +k ++++  l++ le+l++++++l+++++++
  gi|14600457|ref|NP_146972.1| 544 AKAEQKLRMLRERLEELRKLENSLEEKVRNL 574
                                   3445555555555555555555555555554 PP

  == domain 7  score: 9.8 bits;  conditional E-value: 0.0016
                       BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                    e+ +klk +a+++ k le+l++++++l++ +++  +ie++++e +++ +eLD  ++++ 
  gi|14600457|ref|NP_146972.1| 671 KEEAAKLKWEAEQVMKRLEELEAEEKKLRKEVSRKSEIEARLKEVQNTLAELDDRISRID 730
                                   567789999**********************************************99986 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   6.2e-05     0.036       9      58 ..       7      56 ..       3      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                                  EEEEEETTEEEEEE-HHHHHHHHHS--SHHHHHHHHHHHHHHS--TTT-- CS
                          MukB  9 ltlinWnGffartfdldelvttlsGgnGaGksttmaafvtaliPdlsllh 58
                                  l l n    f    d+ e  t++ G nGaGkst++ a++ ++ P ++  +
  gi|14600457|ref|NP_146972.1|  7 LELRNIMSHFNTSIDFREGFTAIVGRNGAGKSTILEAILFSITPHQAPRR 56
                                  666777888999999999**********************9999887555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.2   1.4e-05    0.0081      36     100 ..     204     268 ..     197     282 .. 0.89
   2 ?   -1.5   3.8       2.2   1.2e+03      37     107 ..     295     369 ..     277     377 .. 0.71
   3 ?    0.8   0.4      0.42   2.4e+02      34      60 ..     426     452 ..     410     458 .. 0.42
   4 ?    5.8   7.6     0.013       7.5      15      99 ..     484     568 ..     476     574 .. 0.93
   5 ?    0.7   2.8      0.47   2.7e+02      19      86 ..     551     618 ..     548     648 .. 0.68
   6 ?    3.5  11.3     0.065        38      48     100 ..     662     714 ..     627     745 .. 0.57
   7 ?    3.2   0.5     0.082        48      22      62 ..     709     749 ..     705     758 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                       DUF3450  36 qkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvp 100
                                   q+ +  l +e   + +e+r+++++le+le ++e+ler  +++e+e + l+ +i ++e +e+ lv 
  gi|14600457|ref|NP_146972.1| 204 QSGYMTLRNEVLGVDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEEMLVN 268
                                   5666677778888899********************************************99986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                       DUF3450  37 kkidklddekqellaeyralke..eleslevyneqlerlvasqeqeiasle..eqieeieeierelvpllekmid 107
                                   + id+l++ ++el a+   ++e  el++l+   ++l r ++  +  +++le  ++++eie  +re +  l++  +
  gi|14600457|ref|NP_146972.1| 295 SSIDDLEKRRAELRAKASLAHEvaELARLQSRLDKLGRDLEMIRDAVEKLEvsRRLKEIESARREAENRLLEARS 369
                                   567888888888887777765422667777777888888888888888776447788999988888877776655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.42
                       DUF3450  34 qsqkkidklddekqellaeyralkeel 60 
                                   + ++k  +ld+e++ l+ae r+l + l
  gi|14600457|ref|NP_146972.1| 426 DLESKARALDQEASALEAEARRLVQAL 452
                                   223333333333333333333333333 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.013
                       DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                    ++++ ++k+a++  a+a+++ ++ ++l+d+++ ++  + +l++  e l+    q  + +a++eq++  l+e++ee++++e
  gi|14600457|ref|NP_146972.1| 484 RHEAERLRKAAKEKAAEAEKARAEASRLQDKRRRIELLLSRLNQLEEGLRELGFQTPEDLAKAEQKLRMLRERLEELRKLE 564
                                   6678999*************************************************************************9 PP

                       DUF3450  96 relv 99 
                                   ++l+
  gi|14600457|ref|NP_146972.1| 565 NSLE 568
                                   9886 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.47
                       DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                   + +++  e+  + + + ++k+ +l++e   l +  +++ e l++l +++e+ ++ ++++ +e ++le+
  gi|14600457|ref|NP_146972.1| 551 RMLRERLEELRKLENSLEEKVRNLSREEVALREAKTRALEVLQRLGIKEEEAREKLKTLSSESKKLER 618
                                   44555666666666667777777777777777777777777777777777777777777777666666 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.065
                       DUF3450  48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvp 100
                                     l+e r+lkee+++l+++ eq+ + ++++e+e ++l+++ ++ +eie++l+ 
  gi|14600457|ref|NP_146972.1| 662 RRLEEARRLKEEAAKLKWEAEQVMKRLEELEAEEKKLRKEVSRKSEIEARLKE 714
                                   34455555555555555555555555555555555555555555555554443 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.082
                       DUF3450  22 lkeaekavaaaaqsqkkidklddekqellaeyralkeeles 62 
                                   ++  ++ +++ a+   +i+++d+e  el+ ++r++k++++s
  gi|14600457|ref|NP_146972.1| 709 EARLKEVQNTLAELDDRISRIDREMGELQTRIREMKSRKAS 749
                                   45556666777777777777777777777777777777654 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   2.1e-05     0.012      40      74 ..      25      59 ..       5      68 .. 0.82
   2 ?   -3.3   4.4         8   4.6e+03     101     200 ..     220     319 ..     212     368 .. 0.53
   3 ?   -1.3   0.0         2   1.1e+03      98     126 ..     409     437 ..     377     446 .. 0.76
   4 ?   -2.0   0.5       3.3   1.9e+03      99     137 ..     543     583 ..     534     621 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                                  .SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEE CS
                  FtsK_SpoIIIE 40 shllvaGatgsGKStalntLilSlatthtPeeVql 74
                                  + + ++G+ g GKSt l +++ S+   ++P + ++
  gi|14600457|ref|NP_146972.1| 25 GFTAIVGRNGAGKSTILEAILFSITPHQAPRRSSM 59
                                  4589**********************999987655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8
                                   SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-T...T-......................... CS
                  FtsK_SpoIIIE 101 dperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvfl...vlDnyddlaaene..........rits 168
                                   ++ +a++ leeL+ e+ee ++  r+   +  a  ++ei++ +++ + +v++   ++ + ++l + n+          +i  
  gi|14600457|ref|NP_146972.1| 220 EIREASKRLEELEREREELERRARDLESEAKA-LQSEIGKLETMEEMLVNVtsmIRSERSKLDTINTrlryaeskisSIDD 299
                                   56677777888877777666555544433333.466666666665444444000444444444444433333333333333 PP

                                   .......-----------B-----EEEEEEC- CS
                  FtsK_SpoIIIE 169 Lsnqgpsygvhvlvtagrelekrpslvvivde 200
                                   L +++            +el+ + sl   v+e
  gi|14600457|ref|NP_146972.1| 300 LEKRR------------AELRAKASLAHEVAE 319
                                   33333............333333333333333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2
                                   -B-SHHHHHHHHHHHHHHHHHHHHHHHHT CS
                  FtsK_SpoIIIE  98 vatdperalraleeLvkemeeryalfrea 126
                                   + + pe +l+ l+++++ +e+ ++ ++++
  gi|14600457|ref|NP_146972.1| 409 GSEKPESVLERLDAVINDLESKARALDQE 437
                                   56899****************99999886 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.3
                                   B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH...HHHH CS
                  FtsK_SpoIIIE  99 atdperalraleeLvkemeeryalfreagvrsiaa...ydge 137
                                    + +e+ lr+l+e ++e+++ +++++e +vr++++   +  e
  gi|14600457|ref|NP_146972.1| 543 LAKAEQKLRMLRERLEELRKLENSLEE-KVRNLSReevALRE 583
                                   555666677777777777777777654.45555552222222 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.1     0.012       7.2      31      83 ..     212     264 ..     196     282 .. 0.59
   2 ?    3.0   7.5      0.18   1.1e+02       3      41 ..     226     264 ..     220     317 .. 0.73
   3 ?   -1.0   2.0       3.3   1.9e+03      22      38 ..     316     332 ..     293     374 .. 0.51
   4 ?   -1.4   0.1       4.4   2.6e+03       5      32 ..     350     377 ..     346     397 .. 0.73
   5 ?    2.2   0.4      0.32   1.9e+02       5      36 ..     417     448 ..     411     457 .. 0.49
   6 ?   15.6  14.2   2.2e-05     0.013       7      86 ..     641     720 ..     636     732 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                          BRE1  31 ekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelek 83 
                                   +++l ++ e+ +a +   +++r+++ le   + L +  +  ++ i +L+ +e+
  gi|14600457|ref|NP_146972.1| 212 NEVLGVDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEE 264
                                   55555555555555555555555555555555555555555555555555554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.18
                          BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaeka 41 
                                   k L++le+++eel++ ++++ +e ++l++++ +le++ +
  gi|14600457|ref|NP_146972.1| 226 KRLEELEREREELERRARDLESEAKALQSEIGKLETMEE 264
                                   568999999999999999999999999999999998755 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3.3
                          BRE1  22 kvkeltileekklrlea 38 
                                    v+el++l++++ +l  
  gi|14600457|ref|NP_146972.1| 316 EVAELARLQSRLDKLGR 332
                                   34444444444444422 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.4
                          BRE1   5 Lvklekafeelseqlskkvkeltileek 32 
                                   L+++e a++e+++ l +  ++++  + +
  gi|14600457|ref|NP_146972.1| 350 LKEIESARREAENRLLEARSSIKEEQRR 377
                                   7788888888888888877776665555 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.32
                          BRE1   5 Lvklekafeelseqlskkvkeltileekklrl 36 
                                   L++l + +++l+++++++ +e ++le +  rl
  gi|14600457|ref|NP_146972.1| 417 LERLDAVINDLESKARALDQEASALEAEARRL 448
                                   34444444444444444444444444444444 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 2.2e-05
                          BRE1   7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefv 86 
                                   +l +  +e+ e ++k ++ +++  e+  rl+ e ak + +  ++m+  + le+e kkL+k +s++se+ ++Lke+++ + 
  gi|14600457|ref|NP_146972.1| 641 DLLEKAREALEGVDKELSAIERRLEEARRLKEEAAKLKWEAEQVMKRLEELEAEEKKLRKEVSRKSEIEARLKEVQNTLA 720
                                   55555667778889999999999999************************************************777664 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.7     0.055        32      67     115 ..     213     261 ..     197     287 .. 0.53
   2 ?    8.8   1.4    0.0028       1.6      48     122 ..     278     355 ..     267     357 .. 0.67
   3 ?   -0.8   0.0       2.5   1.4e+03      47      73 ..     417     443 ..     408     458 .. 0.46
   4 ?    7.2   1.2    0.0086         5      55     121 ..     509     575 ..     490     578 .. 0.87
   5 ?   -1.9   0.1       5.5   3.2e+03      73     110 ..     597     620 ..     579     632 .. 0.55
   6 ?   13.6   4.2   9.2e-05     0.053      41     122 ..     648     731 ..     633     746 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.055
                       DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                   ++  vd+++ e ++  +e+++e +e+++  ++++++ +++++ + +le+
  gi|14600457|ref|NP_146972.1| 213 EVLGVDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLET 261
                                   4444555555555555555555555555555555555555544444443 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
                       DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeisk..eikeevtevredlseigedvesvkeavegle..skleriee 122
                                   ++l+++ + l+ +  ++s  id ++k+  e  + ++  +  +e++++++ l+++g+d+e +++ave+le   +l++ie+
  gi|14600457|ref|NP_146972.1| 278 SKLDTINTRLRYAESKIS-SIDDLEKRRAELRAKASlaHEVAELARLQSRLDKLGRDLEMIRDAVEKLEvsRRLKEIES 355
                                   567777777777777765.466666655544333220022346788999*******************93346777775 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.5
                       DUF1664  47 skqleqvseslaatkrhLssridrvdk 73 
                                    ++l+ v ++l++  r L ++   +++
  gi|14600457|ref|NP_146972.1| 417 LERLDAVINDLESKARALDQEASALEA 443
                                   344444444444444444444333333 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0086
                       DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                   + l++ +r+++  + r+++  +   e+  ++ e++++++++l+ ++e +e+++++ ++le+k+++++
  gi|14600457|ref|NP_146972.1| 509 SRLQDKRRRIELLLSRLNQLEEGLRELGFQTPEDLAKAEQKLRMLRERLEELRKLENSLEEKVRNLS 575
                                   56777888888888888888888899999**********************************9987 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 5.5
                       DUF1664  73 kkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                    k               +e+re+l+++++++++++++ 
  gi|14600457|ref|NP_146972.1| 597 IKE--------------EEAREKLKTLSSESKKLERML 620
                                   333..............455555666666655555553 PP

  == domain 6  score: 13.6 bits;  conditional E-value: 9.2e-05
                       DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls...eigedvesvkeavegleskle 118
                                   +a+e v k+l  +   l++++ +L+++ +++ ++ +++++  +e+++e +++r+++s   ei+  +++v+++  +l+ +++
  gi|14600457|ref|NP_146972.1| 648 EALEGVDKELSAIERRLEEAR-RLKEEAAKLKWEAEQVMKRLEELEAEEKKLRKEVSrksEIEARLKEVQNTLAELDDRIS 727
                                   567778888888888887775.58999999999999999999999999999999885333799999**************9 PP

                       DUF1664 119 riee 122
                                   ri+ 
  gi|14600457|ref|NP_146972.1| 728 RIDR 731
                                   9975 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    0.0003      0.17      98     137 ..      23      67 ..       9      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                                   TTSEEEEECSTTSSHHHHHHHHCTT.....-----S--------- CS
                   RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe.....lelktgevseklgrG 137
                                   ++ ++++vG  G+GKSt+++a+l +     +  + + +se+++rG
  gi|14600457|ref|NP_146972.1|  23 REGFTAIVGRNGAGKSTILEAILFSitphqAPRRSSMISENSSRG 67 
                                   667899*************99864422222567778888888888 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.7     0.082        48       5      58 ..     200     253 ..     197     258 .. 0.85
   2 ?   -0.5   0.1       3.4   1.9e+03      20      53 ..     260     293 ..     255     316 .. 0.60
   3 ?    5.1   1.0     0.062        36      25      54 ..     319     348 ..     280     363 .. 0.87
   4 ?    7.9   0.0    0.0082       4.8      14      65 ..     419     473 ..     414     473 .. 0.81
   5 ?    2.0   6.5      0.58   3.4e+02       7      55 ..     517     565 ..     511     579 .. 0.79
   6 ?   -1.6   0.1       7.8   4.5e+03       8      53 ..     567     612 ..     564     620 .. 0.58
   7 ?   -0.7   2.2       3.9   2.2e+03      29      54 ..     670     695 ..     636     707 .. 0.72
   8 ?   14.7   1.4     6e-05     0.034       6      52 ..     706     752 ..     702     756 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.082
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                          SlyX   5 leeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                   +++L++ ++ + + +   ++++ e  +++++l+r+ ++l++r ++le++++a +
  gi|14600457|ref|NP_146972.1| 200 ITRLQSGYMTLRNEVLGVDREIREASKRLEELEREREELERRARDLESEAKALQ 253
                                   78888888888888888899999999********************99987655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.4
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX  20 eeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                   e++ +++++    i   + +l+ ++ rl+ +e++
  gi|14600457|ref|NP_146972.1| 260 ETMEEMLVNVTSMIRSERSKLDTINTRLRYAESK 293
                                   4555555555555555555555555555444433 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.062
                                   HHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                          SlyX  25 vvaeqqqqidrlqrqlrllaerlkeleess 54 
                                   ++a+ q ++d+l r l+++++ +++le s 
  gi|14600457|ref|NP_146972.1| 319 ELARLQSRLDKLGRDLEMIRDAVEKLEVSR 348
                                   68999******************9998765 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0082
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX...XXXXXX CS
                          SlyX  14 fqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgasea...eeepPP 65 
                                    ++ +i++L     + +q+ ++l+++ r+l++ l+ lees g+++      e PP
  gi|14600457|ref|NP_146972.1| 419 RLDAVINDLESKARALDQEASALEAEARRLVQALSMLEESGGSARCpvcGAELPP 473
                                   578899999999999*******************999999886554666555555 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.58
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                          SlyX   7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                   ++E  l+ + ++ e L +  ++  +++++ +++lr+l+erl+el++ ++
  gi|14600457|ref|NP_146972.1| 517 RIELLLSRLNQLEEGLRELGFQTPEDLAKAEQKLRMLRERLEELRKLEN 565
                                   5677777777777778888888889999*************99987655 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 7.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX   8 LEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                   LE+k+  + +   +L ++ ++  + ++rl  + ++ +e+lk+l+++
  gi|14600457|ref|NP_146972.1| 567 LEEKVRNLSREEVALREAKTRALEVLQRLGIKEEEAREKLKTLSSE 612
                                   4555555555555555555555566666666666666666666665 PP

  == domain 7  score: -0.7 bits;  conditional E-value: 3.9
                                   HHHHHHHHHHHHHHHHHT-XXXXXXX CS
                          SlyX  29 qqqqidrlqrqlrllaerlkeleess 54 
                                     ++ ++l+ + +++++rl+ele+++
  gi|14600457|ref|NP_146972.1| 670 LKEEAAKLKWEAEQVMKRLEELEAEE 695
                                   44556666777777777777777665 PP

  == domain 8  score: 14.7 bits;  conditional E-value: 6e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                          SlyX   6 eeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                    e+E +l   ++t+ eL+d + + ++++ +lq+++r+++ r ++ ee
  gi|14600457|ref|NP_146972.1| 706 SEIEARLKEVQNTLAELDDRISRIDREMGELQTRIREMKSRKASGEE 752
                                   58999999999999999999999999999999999999998776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   8.5e-05     0.049       6      51 ..       6      51 ..       2     173 .. 0.85
   2 ?   -1.3   1.3       4.4   2.5e+03      85     145 ..     231     301 ..     216     345 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.5e-05
                        AAA_16  6 eeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                  + el+ + s +++  + r++ + ++G  G GKs++++++l +++ +
  gi|14600457|ref|NP_146972.1|  6 RLELRNIMSHFNTSIDFREGFTAIVGRNGAGKSTILEAILFSITPH 51
                                  67999999*******************************9999877 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.4
                        AAA_16  85 lldeaesaeleawrekleeala............avpelagaea............srllellkrllallsrderplvlvl 141
                                   l++e    ele+ ++ le++++            +        +            ++ l++++  l+++++     +  +
  gi|14600457|ref|NP_146972.1| 231 LERE--REELERRARDLESEAKalqseigkletmE--------EmlvnvtsmirseRSKLDTINTRLRYAES----KISSI 297
                                   3333..22344444444444443444222222230........24444444444444444444444444444....24455 PP

                        AAA_16 142 Ddlq 145
                                   Ddl+
  gi|14600457|ref|NP_146972.1| 298 DDLE 301
                                   5555 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 ?    5.9   0.3     0.026        15      25      78 ..     218     270 ..     208     308 .. 0.72
   2 ?    1.6   0.0       0.6   3.4e+02      26      61 ..     415     450 ..     405     455 .. 0.78
   3 ?   -2.1   0.0       8.3   4.8e+03      35      85 ..     487     533 ..     476     537 .. 0.60
   4 ?   -0.3   0.1       2.2   1.3e+03      22      48 ..     551     577 ..     543     619 .. 0.77
   5 ?    5.3   0.0     0.042        24      48      87 ..     638     677 ..     624     679 .. 0.86
   6 ?    4.1   0.4     0.098        57      21      47 ..     712     738 ..     681     748 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.026
                        DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteava 78 
                                    + ++ea++++eele++ +++ + ++dl +++++l++++ +kle+++++  +v 
  gi|14600457|ref|NP_146972.1| 218 DREIREASKRLEELEREREELERRARDLESEAKALQSEI-GKLETMEEMLVNVT 270
                                   566777777777777777777777777777777755555.35666665555553 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.6
                        DUF948  26 ktldeaaatieelekqvdpilkevedllakvnelle 61 
                                   ++l+++ a i++le++++++ +e+ +l a++++l++
  gi|14600457|ref|NP_146972.1| 415 SVLERLDAVINDLESKARALDQEASALEAEARRLVQ 450
                                   567778888888888888888888888888777765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 8.3
                        DUF948  35 ieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    e l+k +++   e+e++ a++ +    +++k  +++ l + +++l e ++
  gi|14600457|ref|NP_146972.1| 487 AERLRKAAKEKAAEAEKARAEASR----LQDKRRRIELLLSRLNQLEEGLR 533
                                   555555555555566666555555....66677777777777766666555 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2.2
                        DUF948  22 lklkktldeaaatieelekqvdpilke 48 
                                   + l++ l+e+++  ++le++v+++++e
  gi|14600457|ref|NP_146972.1| 551 RMLRERLEELRKLENSLEEKVRNLSRE 577
                                   556788888888888888888888877 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.042
                        DUF948  48 evedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    ++dll+k++e le+v ++l ++++  e+++ l e  ++l
  gi|14600457|ref|NP_146972.1| 638 SLDDLLEKAREALEGVDKELSAIERRLEEARRLKEEAAKL 677
                                   5789999999999999999999999999999998887776 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.098
                        DUF948  21 llklkktldeaaatieelekqvdpilk 47 
                                   l+++++tl e+ ++i  + ++++++ +
  gi|14600457|ref|NP_146972.1| 712 LKEVQNTLAELDDRISRIDREMGELQT 738
                                   333444444444444444444444433 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   0.0   0.00078      0.45       3      20 ..      28      45 ..      26      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00078
                                  EEEESTTSSHHHHHHHHH CS
                      MMR_HSR1  3 aivGrpNvGKStLinalt 20
                                  aivGr  +GKSt++ a++
  gi|14600457|ref|NP_146972.1| 28 AIVGRNGAGKSTILEAIL 45
                                  8**************997 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.52     3e+02     119     146 ..     206     233 ..     195     275 .. 0.86
   2 ?   -1.6   0.1       4.4   2.5e+03      36      75 ..     288     328 ..     281     360 .. 0.62
   3 ?   12.4   1.1   0.00022      0.13      38      79 ..     693     734 ..     683     742 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.52
                          TssO 119 mlledKkelksvseniklfkkqLeecei 146
                                    ++++++e+  v  +i ++ k Lee e 
  gi|14600457|ref|NP_146972.1| 206 GYMTLRNEVLGVDREIREASKRLEELER 233
                                   5888999999999999999999998765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.4
                          TssO  36 plqekeil.lkelerkkkfeekqkelkkkvdsiykkIdsLk 75 
                                   ++ e++i  +++le+ ++++  +  l+ +v ++ +  ++L+
  gi|14600457|ref|NP_146972.1| 288 RYAESKISsIDDLEKRRAELRAKASLAHEVAELARLQSRLD 328
                                   56677777788888888888888888877776655444442 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00022
                          TssO  38 qekeillkelerkkkfeekqkelkkkvdsiykkIdsLkpevn 79 
                                    e+++l+ke++rk+++e + ke+++++ +++ +I++++ e  
  gi|14600457|ref|NP_146972.1| 693 AEEKKLRKEVSRKSEIEARLKEVQNTLAELDDRISRIDREMG 734
                                   4566677******************************87755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00034      0.19       4      38 ..      23      62 ..      20     111 .. 0.70
   2 ?   -1.8   2.4       6.1   3.5e+03      37      84 ..     506     559 ..     478     633 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.....e 38
                                  ++g+++++G  G+GK+t l+ +l + + ++++++     e
  gi|14600457|ref|NP_146972.1| 23 REGFTAIVGRNGAGKSTILEAILFSITPHQAPRRssmisE 62
                                  689*****************99877655544444555552 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.1
                        AAA_22  37 e......erpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                           +++ ++  l+ ++ +++ lrel  ++ ++l +++++++ l+e+le+
  gi|14600457|ref|NP_146972.1| 506 AeasrlqDKRRRIELLLSRLNQLEEGLRELGFQTPEDLAKAEQKLRMLRERLEE 559
                                   133444444444455555555555555555555555555544444444455544 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.1     0.026        15      39     103 ..     217     284 ..     209     285 .. 0.77
   2 ?    3.7   0.8      0.15        84      34     103 ..     318     354 ..     279     376 .. 0.53
   3 ?    0.5   0.0       1.5   8.6e+02      57      92 ..     417     452 ..     397     458 .. 0.51
   4 ?    7.0   6.6     0.014       8.3      32      87 ..     539     594 ..     508     661 .. 0.84
   5 ?   10.0   6.3    0.0016      0.95      32     103 ..     653     730 ..     633     731 .. 0.84
   6 ?    8.1   0.6    0.0064       3.7      30      79 ..     706     755 ..     699     777 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.026
                                   HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHH...HHHHHHHHHHHHC CS
                         DUF16  39 ieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelile...tLqkinkRlDsie 103
                                   ++ +++   +++++le + e+++ + ++l+ e ka + e+ k++   e++++    + +   +lD i+
  gi|14600457|ref|NP_146972.1| 217 VDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEEMLVNvtsMIRSERSKLDTIN 284
                                   67788889999999**********************99999766666666651115556667788776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.15
                                   HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                         DUF16  34 qrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                   ++L +++ ++dklg  ++ + ++vek++                                  + Rl +ie
  gi|14600457|ref|NP_146972.1| 318 AELARLQSRLDKLGRDLEMIRDAVEKLEV---------------------------------SRRLKEIE 354
                                   34444444444455555555555544443.................................34444444 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHHH.......HHHHHHHHH CS
                         DUF16  57 vekqgekikelkveqkaqgeelnkvdetleliletL 92 
                                    e++++ i++l+ +  a ++e  +++   + ++++L
  gi|14600457|ref|NP_146972.1| 417 LERLDAVINDLESKARALDQEASALEAEARRLVQAL 452
                                   333333444444444444443333333333333333 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.014
                                   BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHH CS
                         DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlel 87 
                                   + ++L k e+k+++l e++++l +  + ++ek+++l+ e  a +e+  +  e l+ 
  gi|14600457|ref|NP_146972.1| 539 TPEDLAKAEQKLRMLRERLEELRKLENSLEEKVRNLSREEVALREAKTRALEVLQR 594
                                   8899***********************************99999966644444443 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0016
                                   BHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHHHHHHC CS
                         DUF16  32 nkqrLkkieakvd...klgeqinkleqkvekqgekikelkveqkaqgeeln...kvdetleliletLqkinkRlDsie 103
                                    +++L  ie +++    l+e+ +kl+ + e+  ++++el++e k+ ++e+    +++  l+ + +tL+++++R+ +i+
  gi|14600457|ref|NP_146972.1| 653 VDKELSAIERRLEearRLKEEAAKLKWEAEQVMKRLEELEAEEKKLRKEVSrksEIEARLKEVQNTLAELDDRISRID 730
                                   58899999999996666788888888888888888999999999999999887778899**************99886 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0064
                                   ..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                         DUF16  30 dsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln 79 
                                    + ++rLk+++++++ l+ +i+++  ++ +++ +i+e+k +    +e+l+
  gi|14600457|ref|NP_146972.1| 706 SEIEARLKEVQNTLAELDDRISRIDREMGELQTRIREMKSRKASGEEALK 755
                                   55689********************************9988776666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.6   7.1e-05     0.041     203     259 ..     209     265 ..     200     272 .. 0.92
   2 ?    5.5  12.2     0.011       6.5     138     255 ..     260     376 ..     257     382 .. 0.54
   3 ?    1.2   7.5      0.24   1.4e+02     150     241 ..     419     527 ..     410     536 .. 0.71
   4 ?    1.5  14.4      0.19   1.1e+02     146     228 ..     541     626 ..     525     636 .. 0.49
   5 ?    2.3  20.9      0.11        64     134     232 ..     557     674 ..     554     683 .. 0.80
   6 ?   12.9  19.2   6.6e-05     0.038     136     243 ..     638     754 ..     635     801 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                          Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                   +lr+e+  ++ ei+e +k+l+el++++eele +  +l+++ + l++ei + e + e+
  gi|14600457|ref|NP_146972.1| 209 TLRNEVLGVDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEEM 265
                                   6899*********************************************99988775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                          Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                   e+++e l +  + +++++++L+  +  l  +  ++++  ++le++ ++l+++a    + + +eL+ l+++l++l  ++e  
  gi|14600457|ref|NP_146972.1| 260 ETMEEMLVNVTSMIRSERSKLDTINTRLRYAESKISS-IDDLEKRRAELRAKASL--AHEVAELARLQSRLDKLGRDLEMI 337
                                   4444444444444455555555555555444444433.34555555555554432..345667777777777777777766 PP

                          Spc7 219 kkelaelq..eqleeleekieelkeqkseleeeiaeaer 255
                                   ++ +++l+  ++l+e+e++  e++++  e+++ i+e++r
  gi|14600457|ref|NP_146972.1| 338 RDAVEKLEvsRRLKEIESARREAENRLLEARSSIKEEQR 376
                                   666666542255666666666666666666666666665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.24
                          Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqe.................aaeelesidkeeLeelreelaelka 213
                                    l++  + Le++   ld+   +le+e  +l + l +l+e                 +ae ++   + e e lr++ +e  a
  gi|14600457|ref|NP_146972.1| 419 RLDAVINDLESKARALDQEASALEAEARRLVQALSMLEEsggsarcpvcgaelppgRAEAIARHYRHEAERLRKAAKEKAA 499
                                   333444455666666666666666666666666666666666666699999999999999999999999999999999999 PP

                          Spc7 214 eieekkkelaelqeqleeleekieelke 241
                                   e e+ ++e ++lq+++ ++e  ++ l++
  gi|14600457|ref|NP_146972.1| 500 EAEKARAEASRLQDKRRRIELLLSRLNQ 527
                                   9999999999999998888876666644 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.19
                          Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqe.aaeelesidkeeL..eelreelaelkaeieekkkela 223
                                   e l++ e+  ++L ++ eel +l ++lee+  +l++e   l+e + + le +++  +  ee+re+l++l++e ++++++l 
  gi|14600457|ref|NP_146972.1| 541 EDLAKAEQKLRMLRERLEELRKLENSLEEKVRNLSREEVALREaKTRALEVLQRLGIkeEEAREKLKTLSSESKKLERMLV 621
                                   333344444445555555555555666666666665555555532333333443333224455555555555555555555 PP

                          Spc7 224 elqeq 228
                                   ++ e+
  gi|14600457|ref|NP_146972.1| 622 SKAED 626
                                   55444 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.11
                          Spc7 134 mqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles................... 195
                                   ++ l +L+++lee++ +l +++  L + +  + e+l++l  +++e +e+l++l +++++le                    
  gi|14600457|ref|NP_146972.1| 557 LEELRKLENSLEEKVRNLSREEVALREAKTRALEVLQRLGIKEEEAREKLKTLSSESKKLERmlvskaedlatrlgitayr 637
                                   566889*************************************************99999987776666677777777765 PP

                          Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                   +  + Le++re+l+ +++e+++ +++l+e ++ +ee 
  gi|14600457|ref|NP_146972.1| 638 SLDDLLEKAREALEGVDKELSAIERRLEEARRLKEEA 674
                                   5577778888888888888877777777766544443 PP

  == domain 6  score: 12.9 bits;  conditional E-value: 6.6e-05
                          Spc7 136 llegLkegleenlegleedkelLekqeeeldellpelee...ekaeleeeleklqeaaeeles.....id.keeLeelree 207
                                    l++L e+++e leg++++ + +e++ ee+ +l++e  +   e ++++++le+l++++++l +     ++ +++L+e++++
  gi|14600457|ref|NP_146972.1| 638 SLDDLLEKAREALEGVDKELSAIERRLEEARRLKEEAAKlkwEAEQVMKRLEELEAEEKKLRKevsrkSEiEARLKEVQNT 718
                                   577888888888888888888888888888777766544111556777777777776665555443333335566666666 PP

                          Spc7 208 laelkaeieekkkelaelqeqleeleekieelkeqk 243
                                   lael+  i++  +e+ elq+++ e +++ ++ +e  
  gi|14600457|ref|NP_146972.1| 719 LAELDDRISRIDREMGELQTRIREMKSRKASGEEAL 754
                                   666666666666666666666666666665555544 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   9.7e+02     141     179 ..     521     562 ..     517     579 .. 0.71
   2 ?   11.0   1.5   0.00051      0.29     118     183 ..     586     659 ..     573     738 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                 PhageMin_Tail 141 llsrltkeaaealkklGis.tkdaq...gkmksldeiledlse 179
                                   llsrl ++ +e+l++lG++  +d++   +k + l e le+l++
  gi|14600457|ref|NP_146972.1| 521 LLSRL-NQLEEGLRELGFQtPEDLAkaeQKLRMLRERLEELRK 562
                                   67888.89999******98666666432444777777777765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00051
                 PhageMin_Tail 118 aaalallaaagikgseAgtalknllsrltk.......eaaealkklGistkdaq.gkmksldeiledlsealkk 183
                                   + al +l+  gik +eA   lk+l s+ +k       +a++++  lGi+++ +  +    + e+le + + l+ 
  gi|14600457|ref|NP_146972.1| 586 TRALEVLQRLGIKEEEAREKLKTLSSESKKlermlvsKAEDLATRLGITAYRSLdDLLEKAREALEGVDKELSA 659
                                   5689999*******************99224455666999999999*995433313335555555555555444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0027       1.6       2      19 ..      28      45 ..      27      55 .. 0.92
   2 ?    0.2   0.3       1.2   6.7e+02      50      96 ..     216     262 ..     194     316 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0027
                                  EEEEBTTTTHHHHHHHHH CS
                     Dynamin_N  2 avvGsqSsGKSSvlnaLl 19
                                  a+vG   +GKS++l+a+l
  gi|14600457|ref|NP_146972.1| 28 AIVGRNGAGKSTILEAIL 45
                                  79**************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                                   ...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEE CS
                     Dynamin_N  50 avkeelkekekkledfsevreeieketekiagankgiskkvillkil 96 
                                    v+ e++e +k+le++++ ree+e++ + ++++ k+ ++++ +l+  
  gi|14600457|ref|NP_146972.1| 216 GVDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLETM 262
                                   46677788888888888888888888888888877777775444443 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 ?   10.8   6.4   0.00039      0.23      35     107 ..     200     272 ..     194     293 .. 0.84
   2 ?    0.7   6.7      0.48   2.8e+02      63     137 ..     297     372 ..     280     386 .. 0.68
   3 ?    4.3   0.8     0.039        23      75     125 ..     405     455 ..     372     461 .. 0.75
   4 ?   -1.0   6.4       1.6   9.2e+02      49     105 ..     480     536 ..     474     542 .. 0.81
   5 ?   11.2  17.6    0.0003      0.18      48     168 ..     542     660 ..     537     665 .. 0.92
   6 ?    8.3  15.2    0.0022       1.3      40     121 ..     665     746 ..     659     755 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                           GAS  35 ieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwe 107
                                   i++l+      ++e+  +  e ++ ++ L+++e+e+eeL++++++ e++ ++l++   +l+++e+ l +++  
  gi|14600457|ref|NP_146972.1| 200 ITRLQSGYMTLRNEVLGVDREIREASKRLEELEREREELERRARDLESEAKALQSEIGKLETMEEMLVNVTSM 272
                                   56666667777888888999*******************************************9999887655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.48
                           GAS  63 LkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevle..qrfekvekerdelykkfeaaiqevq 137
                                   +  +e+ ++eLr+++   + + ++l++l++rl +l + l+ ++   e le   r++++e++r e +++  +a   ++
  gi|14600457|ref|NP_146972.1| 297 IDDLEKRRAELRAKASLAH-EVAELARLQSRLDKLGRDLEMIRDAVEKLEvsRRLKEIESARREAENRLLEARSSIK 372
                                   4566777777777765544.477777888888877777777776666654336788888888887777665544443 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.039
                           GAS  75 kqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdel 125
                                   k+l   ek  + l++l a +++le++ ++l +e+  le +  ++ ++   l
  gi|14600457|ref|NP_146972.1| 405 KDLCGSEKPESVLERLDAVINDLESKARALDQEASALEAEARRLVQALSML 455
                                   667777777788888888888888888888888888887777777766555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.6
                           GAS  49 lseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                     ++ +e +rl++  k+  +e e+ r+++ + + ++ +++ l +rl++le+ l++l 
  gi|14600457|ref|NP_146972.1| 480 ARHYRHEAERLRKAAKEKAAEAEKARAEASRLQDKRRRIELLLSRLNQLEEGLRELG 536
                                   566778888999999999999999999999999999999999999999999988875 PP

  == domain 5  score: 11.2 bits;  conditional E-value: 0.0003
                           GAS  48 elseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykk 128
                                   +l++++q+ + l+e L+++++  + L+++++n +++ ++l+++k+r  e+   l++l  + e  +++++++++e ++l++ 
  gi|14600457|ref|NP_146972.1| 542 DLAKAEQKLRMLRERLEELRKLENSLEEKVRNLSREEVALREAKTRALEV---LQRLGIKEEEAREKLKTLSSESKKLERM 619
                                   68899****************************************99877...667889999999**************** PP

                           GAS 129 feaaiqevqqktglknl.lLekklkalqeelEkkeaqleev 168
                                     ++ +++  + g  ++  L   l++ +e+lE  +++l+++
  gi|14600457|ref|NP_146972.1| 620 LVSKAEDLATRLGITAYrSLDDLLEKAREALEGVDKELSAI 660
                                   *************9987479*****************9986 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.0022
                           GAS  40 kkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvek 120
                                   ++++r + e ++++ e ++ ++ L+++e+e ++Lrk++ + ++  ++lk++++ l el++ ++++  e   l+ r+ ++++
  gi|14600457|ref|NP_146972.1| 665 EEARRLKEEAAKLKWEAEQVMKRLEELEAEEKKLRKEVSRKSEIEARLKEVQNTLAELDDRISRIDREMGELQTRIREMKS 745
                                   456666777777777777777777777777777777777777777777777777777777777777777777777777765 PP

                           GAS 121 e 121
                                    
  gi|14600457|ref|NP_146972.1| 746 R 746
                                   4 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 ?    5.1   2.9     0.025        15     147     207 ..     196     256 ..     172     263 .. 0.72
   2 ?    0.6  16.8      0.58   3.4e+02      50     204 ..     218     366 ..     209     366 .. 0.77
   3 ?    7.5  11.0    0.0047       2.7      21     173 ..     286     446 ..     279     457 .. 0.74
   4 ?   -0.4  15.1       1.2   6.8e+02      17     134 ..     580     690 ..     566     700 .. 0.77
   5 ?   15.5  12.1   1.7e-05    0.0097      18     121 ..     646     746 ..     644     795 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                    MscS_porin 147 sqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqell 207
                                        t lq  +  l++++   ++e   +++r e l+ +r++l+ r ++le+e +aLq+ +
  gi|14600457|ref|NP_146972.1| 196 GSKSITRLQSGYMTLRNEVLGVDREIREASKRLEELEREREELERRARDLESEAKALQSEI 256
                                   5555555555556666666666888888999999999999999999999999999999876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.58
                    MscS_porin  50 PkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlq 130
                                    +e+re++++le+l + + e+ + + +   le   + l+++  +l++ +e l +  s +++ ++ ++++ ++l  a  +++
  gi|14600457|ref|NP_146972.1| 218 DREIREASKRLEEL-EREREELERRAR--DLESEAKALQSEIGKLETMEEMLVNVTSMIRSERSKLDTINTRLRYAESKIS 295
                                   67889999999999.333333333333..3333346666666778888888888888888888888888888888888888 PP

                    MscS_porin 131 eirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLq 204
                                    i + L++   + e  ++a  +   aela l+++++ l + l+      e l+  r l++ + ++ e+e ++L+
  gi|14600457|ref|NP_146972.1| 296 SIDD-LEKR--RAELRAKASLAHEVAELARLQSRLDKLGRDLEMIRDAVEKLEVSRRLKEIESARREAENRLLE 366
                                   8888.6555..566788888888899999999999999999999999999999999999999999999998885 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0047
                    MscS_porin  21 dLeqalnlLdkidkskkkaeelqkaiddaP..kelrelqqeleal...qkkkeeaskeilaklsleeLeqrllqtssqlqe 96 
                                    L+ a + +  id+ +k+ +el+ +   a   +el+ lq +l++l    +   +a+++   +  l+e+e+   +++++l+e
  gi|14600457|ref|NP_146972.1| 286 RLRYAESKISSIDDLEKRRAELRAKASLAHevAELARLQSRLDKLgrdLEMIRDAVEKLEVSRRLKEIESARREAENRLLE 366
                                   466666667777777777777776544443226788888888888544444477777777788899*************** PP

                    MscS_porin  97 lqeqlaqlnsqlvelqtrperaqqqltearqrlqeirn.rLnstaaage..alsqaqrtalqaelaaleaqieeleqell 173
                                   +++ +++++ + + l  r +r ++  t+ r+ l+e r+ +L +++++++  +  +a  + l+ +  al+++ + le e+ 
  gi|14600457|ref|NP_146972.1| 367 ARSSIKEEQRRYTLLDYRVTRGRSIVTNIRRVLSECRSkDLCGSEKPESvlERLDAVINDLESKARALDQEASALEAEAR 446
                                   ************************************87577666666665655567777777777777777777777654 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.2
                    MscS_porin  17 allqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqel 97 
                                   al+++ ++al++L+       k ee ++++++   e+++l++ l +     +e+ +++l  +  + L   l+++ ++l+ +
  gi|14600457|ref|NP_146972.1| 580 ALREAKTRALEVLQRLG---IKEEEAREKLKTLSSESKKLERMLVSK----AEDLATRLGITAYRSLDDLLEKAREALEGV 653
                                   55555555555555444...444555679999999999999999999....9***************************** PP

                    MscS_porin  98 qeqlaqlnsqlvelqtrperaqqqltearqrlqeirn 134
                                    ++l+ ++ +l e++   e+a +   ea q ++ ++ 
  gi|14600457|ref|NP_146972.1| 654 DKELSAIERRLEEARRLKEEAAKLKWEAEQVMKRLEE 690
                                   *************999999998877777776666655 PP

  == domain 5  score: 15.5 bits;  conditional E-value: 1.7e-05
                    MscS_porin  18 llqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelq 98 
                                   ++++Le   + L +i++  ++a+ l++  ++   e +++ ++le+l   ++e+ k + +    +e+e rl+++++ l+el 
  gi|14600457|ref|NP_146972.1| 646 AREALEGVDKELSAIERRLEEARRLKEEAAKLKWEAEQVMKRLEEL---EAEEKKLRKEVSRKSEIEARLKEVQNTLAELD 723
                                   6788888888999999999999999999999999999999999999...66666666666667899999999999999999 PP

                    MscS_porin  99 eqlaqlnsqlvelqtrperaqqq 121
                                    +++ ++ +  elqtr+ +  ++
  gi|14600457|ref|NP_146972.1| 724 DRISRIDREMGELQTRIREMKSR 746
                                   99999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (919 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2307  (0.128674); expected 358.6 (0.02)
Passed bias filter:                      843  (0.0470188); expected 358.6 (0.02)
Passed Vit filter:                       248  (0.0138323); expected 17.9 (0.001)
Passed Fwd filter:                       167  (0.00931452); 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: 2.90u 0.41s 00:00:03.31 Elapsed: 00:00:00.69
# Mc/sec: 3995.68
//
Query:       gi|14600458|ref|NP_146973.1|  [L=409]
Description: double-strand break repair protein MRE11 [Aeropyrum pernix K1]
Scores for complete 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   45.0   0.0    2.8e-11   44.3   0.0    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    1.1e-07   32.2   0.0      3e-07   30.8   0.0    1.6  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 !   44.3   0.0   3.1e-15   2.8e-11       2     203 ..       3     202 ..       2     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.1e-15
                                   EEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHHTSEEEE CS
                   Metallophos   2 rilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaalvkypipvyl 69 
                                   ++l+++D+Hl        ++++  +++++ +++ +l++ +pd+vl+aGDl+d       d+ +  +el++al + +ipv +
  gi|14600458|ref|NP_146973.1|   3 KVLHVADVHLgarpygleERRDDIFRSFEFVVETALKD-RPDAVLIAGDLFDKPklplrDVKQ-AVELVRALTDAGIPVLA 81 
                                   8**********988888888888888888888888999.**************9788766666.77777888888****** PP

                                   EC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.HH CS
                   Metallophos  70 llGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg.de 149
                                   ++G H+      + +  ++++ s    s ++++  l+ ++   g  +++++ G       ++  +  ++ +le+ +     
  gi|14600458|ref|NP_146973.1|  82 AHGEHD----TPSVR--DETLLSLMEASLDGFKAPLYRSGMRPG--DFVVDLGS-----LKVAVVPFFKVPLEERRRLtLR 149
                                   ******....44444..444445555555777777777777777..88888888.....4444444444444443333799 PP

                                   HHHH..HHHHTTCSEEEEEESSESSCSSSCSCCHHHHH.HHHHHTTESEEEEESSSS CS
                   Metallophos 150 wlkd..lekrekadwvivlgHsplyrgsgylfgdeale.dllkkygvdlvisGHtHv 203
                                   +l++  +  r+   ++++l+H+ l       +  +a++ +     g+++   GH H 
  gi|14600458|ref|NP_146973.1| 150 FLREfdQISRTSSGTLVLLAHMSLD----AEMQFDAVAsPSDLPSGAKYAALGHLHA 202
                                   9999999999************999....3333333333445567788888888886 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 !   30.8   0.0   3.3e-11     3e-07       2     148 ..       3     221 ..       3     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3.3e-11
                 Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl..eeeep........evleellela....pvl 55 
                                   k+++++D+H             + ++  e v+e + + ++da++ aGDl  + + p        e +++l   +    pvl
  gi|14600458|ref|NP_146973.1|   3 KVLHVADVHlgarpygleerrdDIFRSFEFVVETALKDRPDAVLIAGDLfdKPKLPlrdvkqavELVRAL---TdagiPVL 80 
                                   799***************9998888888999***99999*********7633333355554333444444...2556**** PP

                 Metallophos_2  56 aVrGNnD...........................................eev.veedvlreaaelgtdlp.eeaelel.. 89 
                                   a +G +D                                             v + +  l+e  +l+ ++  e ++++   
  gi|14600458|ref|NP_146973.1|  81 AAHGEHDtpsvrdetllslmeasldgfkaplyrsgmrpgdfvvdlgslkvAVVpFFKVPLEERRRLTLRFLrEFDQISRts 161
                                   ************999999999998888888888888888777777776543335555555555555555533555555344 PP

                 Metallophos_2  90 agekvlliHgdpl..gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvge 148
                                    g+ vll H + l  + + +  +  ++  +g++++++GH H p+++ +  + + +PG + +
  gi|14600458|ref|NP_146973.1| 162 SGTLVLLAHMS-LdaEMQFDAVASPSDLPSGAKYAALGHLHAPRIRLDAPTPYAYPGVLDP 221
                                   66669999998.536666666666666667777***********************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2954.95
//
Query:       gi|14600459|ref|NP_146974.1|  [L=50]
Description: 50S ribosomal protein L40 [Aeropyrum pernix K1]
Scores for 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   39.8   6.8    3.4e-10   39.7   6.8    1.0  1  Ribosomal_L40e  Ribosomal L40e family
      0.001   18.7   1.0     0.0014   18.3   1.0    1.2  1  zinc_ribbon_2   zinc-ribbon domain
      0.009   16.0   1.2      0.011   15.8   1.2    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.069   12.5   4.5       0.12   11.7   4.3    1.5  2  zf-RanBP        Zn-finger in Ran binding protein and others
        6.9    6.6   8.8        5.3    7.0   0.7    2.2  2  zf-CCHC_2       Zinc knuckle


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 !   39.7   6.8   9.4e-14   3.4e-10       2      49 ..       5      49 ..       4      50 .] 0.96

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 9.4e-14
                Ribosomal_L40e  2 epsLrqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKKk 49
                                  +p L+++ +K   +K++Cr+C A  p+ At+Cr  +C +s+nlrpKKk
  gi|14600459|ref|NP_146974.1|  5 DPELVAIFEKRVLNKKVCRRCGALNPMSATKCR--RC-RSKNLRPKKK 49
                                  89*******************************..89.8********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 !   18.3   1.0   3.9e-07    0.0014       2      22 ..      22      42 ..      21      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.9e-07
                 zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                  C +CGa ++  a+ C +C+++
  gi|14600459|ref|NP_146974.1| 22 CRRCGALNPMSATKCRRCRSK 42
                                  ******************986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.2     3e-06     0.011       1      21 [.      22      42 ..      12      49 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
                           DZR  1 CpqCgeelppdarfCseCgtk 21
                                  C +Cg+ +p +a  C +C++k
  gi|14600459|ref|NP_146974.1| 22 CRRCGALNPMSATKCRRCRSK 42
                                  666666666666666666655 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 ?    6.1   0.1    0.0019       6.6      19      29 ..      20      30 ..      18      31 .. 0.86
   2 ?   11.7   4.3   3.4e-05      0.12       7      27 ..      22      42 ..      21      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0019
                                  SB-TTT--BTS CS
                      zf-RanBP 19 tkCvaCqapkp 29
                                   +C +C+a++p
  gi|14600459|ref|NP_146974.1| 20 KVCRRCGALNP 30
                                  68******987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                                  -SSS--EEESSSSB-TTT--B CS
                      zf-RanBP  7 CskClvqNfawstkCvaCqap 27
                                  C  C++ N+ ++tkC +C ++
  gi|14600459|ref|NP_146974.1| 22 CRRCGALNPMSATKCRRCRSK 42
                                  999***************987 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7    0.0015       5.3       5      10 ..      21      26 ..      21      27 .. 0.89
   2 ?    3.9   1.9     0.013        47       5      12 ..      35      42 ..      35      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                     zf-CCHC_2  5 vChiCg 10
                                  vC++Cg
  gi|14600459|ref|NP_146974.1| 21 VCRRCG 26
                                  8****9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                     zf-CCHC_2  5 vChiCgkk 12
                                  +C++C +k
  gi|14600459|ref|NP_146974.1| 35 KCRRCRSK 42
                                  7****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 378.88
//
Query:       gi|77640971|ref|NP_146975.2|  [L=350]
Description: flap endonuclease-1 [Aeropyrum pernix K1]
Scores for complete 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-27   94.1   0.0    8.2e-27   93.4   0.0    1.4  1  XPG_I       XPG I-region
    7.8e-22   77.7   0.0    1.2e-21   77.0   0.0    1.3  1  XPG_N       XPG N-terminal domain
  ------ inclusion threshold ------
      0.046   14.3   0.0       0.12   12.9   0.0    1.9  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold


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   1.4e-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: 1.4e-30
                                   HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHHT- CS
                         XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkelgl 79 
                                   +mg+p+v+Ap E+EAq+ay+++kg+++a+ s+D+D+llFG+p+++rnl  ++++k    +++++ k+e+i+le +l++lg+
  gi|77640971|ref|NP_146975.2| 144 AMGMPWVQAPAEGEAQAAYMARKGDAWATGSQDYDSLLFGSPRLVRNLAiTGRRKLPgrDQYVEIKPEIIELEPLLSKLGI 224
                                   79**********************************************96555555588999******************* PP

                                   -HHHHHHHHHHHCET CS
                         XPG_I  80 treqlidlaillgcD 94 
                                   treqli + illg+D
  gi|77640971|ref|NP_146975.2| 225 TREQLIAVGILLGTD 239
                                   **************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0     2e-25   1.2e-21       1     101 []       1     104 [.       1     104 [. 0.93

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2e-25
                                   X--TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEE CS
                         XPG_N   1 MGikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPi 76 
                                   MG++ L +l+ + a  r+v+++al+g +la Da+ +ly+fl+a+r+++g+ l       tshl glf+r++ l++ gikP+
  gi|77640971|ref|NP_146975.2|   1 MGVN-LRELIPPEA-RREVELRALSGYVLALDAYNMLYQFLTAIRQPDGTPLLDregrvTSHLSGLFYRTINLVEEGIKPV 79 
                                   5554.777777777.79*********************************9988899************************ PP

                                   EEE--S--GGGHHHHHHHHHHHHHH CS
                         XPG_N  77 fVFdgkapdlkkeelekrserrqea 101
                                   +VFdgk+p++k+ e e r  r++ea
  gi|77640971|ref|NP_146975.2|  80 YVFDGKPPEMKSREVEERLRRKAEA 104
                                   ******************9999875 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 ?   -2.8   0.0       1.7     1e+04      56      69 ..      94     107 ..      85     132 .. 0.54
   2 ?   12.9   0.0   2.1e-05      0.12      19      49 ..     241     271 ..     224     317 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                    5_3_exonuc  56 lkekLeenkeearl 69 
                                   ++e+L++++e    
  gi|77640971|ref|NP_146975.2|  94 VEERLRRKAEAEAR 107
                                   45555554443332 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.1e-05
                    5_3_exonuc  19 nipGvpgiGektAakLlkeygsleeilenld 49 
                                   n  Gv+g G+ktA +L+k  g+  ++l+++ 
  gi|77640971|ref|NP_146975.2| 241 NPGGVRGYGPKTALRLVKSLGDPMKVLASVP 271
                                   5569*****************9999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2664.26
//
Query:       gi|118430886|ref|NP_146976.2|  [L=185]
Description: hypothetical protein APE_0116.1 [Aeropyrum pernix K1]
Scores for complete 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   56.2   0.1    6.7e-15   55.6   0.1    1.3  1  ASCH      ASCH domain


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 !   55.6   0.1   3.7e-19   6.7e-15       4     105 ..       3      97 ..       1      99 [. 0.90

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 3.7e-19
                                    -TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHHH CS
                           ASCH   4 hqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleewrevh 82 
                                    +  +a+++++G+Kt++ir +  + p++  + +++  +++ gr+l+++e+++v+vk+++e+t e+a  +g+ s+ e++e +
  gi|118430886|ref|NP_146976.2|   3 KGVYADKLLEGRKTTTIRLGIVK-PRY--R-EVI--IHGHGRPLAKAEIVDVHVKKVSELTLEDARRDGFrSVRELIESL 76 
                                    5679*******************.554..4.444..479***************************************** PP

                                    HCCHHHHHCCEEEEEEEEEEEEE CS
                           ASCH  83 eefyeeeseeyedelvvveefel 105
                                    e+ y+  ++  +++ v+++++++
  gi|118430886|ref|NP_146976.2|  77 ERVYGYKLD--PEDAVTIIHLRV 97 
                                    ******999..999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        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 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1454.56
//
Query:       gi|118430887|ref|YP_874802.1|  [L=95]
Description: hypothetical protein APE_0116a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.063   13.4   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.04   13.8   0.3       0.38   10.7   0.0    2.0  2  Prok-RING_1     Prokaryotic RING finger family 1
      0.081   12.9   2.4        5.3    7.1   0.3    2.3  2  PriA_CRR        PriA DNA helicase Cys-rich region (CRR) domai
       0.19   11.8   0.6         20    5.3   0.0    2.2  2  Rubredoxin      Rubredoxin
       0.19   11.9   0.4        1.2    9.3   0.4    2.0  1  DUF2387         Probable metal-binding protein (DUF2387)


Domain annotation for each model (and alignments):
>> 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 ?   13.4   0.0   1.8e-05     0.063       1      33 [.      46      78 ..      46      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                 MqsA_antitoxin  1 mkCpvCgkaelvrdtrdvpytykgektvikavt 33
                                   mkC +Cg +e +r++  ++ +yk ++++i  v+
  gi|118430887|ref|YP_874802.1| 46 MKCDICGYSESMRGSMPLSVAYKLRHLFIPRVK 78
                                   9****************************9886 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 ?   10.7   0.0   0.00011      0.38      18      29 ..      10      21 ..       2      25 .. 0.83
   2 ?    1.3   0.1     0.096   3.4e+02       5      11 ..      46      52 ..      43      57 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                    Prok-RING_1 18 dDiVvCpeCgtp 29
                                    Di +Cp C +p
  gi|118430887|ref|YP_874802.1| 10 TDITICPRCSAP 21
                                   7*********99 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.096
                    Prok-RING_1  5 kkCpvCg 11
                                    kC +Cg
  gi|118430887|ref|YP_874802.1| 46 MKCDICG 52
                                   5888887 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 ?    7.1   0.3    0.0015       5.3       1      11 [.      15      25 ..      15      28 .. 0.79
   2 ?    5.7   0.1    0.0042        15      16      26 ..      45      55 ..      44      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                       PriA_CRR  1 CpnCdvsltyH 11
                                   Cp+C+++   +
  gi|118430887|ref|YP_874802.1| 15 CPRCSAPSAIY 25
                                   ******96665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0042
                       PriA_CRR 16 rLrCHyCgyte 26
                                   +++C  Cgy+e
  gi|118430887|ref|YP_874802.1| 45 SMKCDICGYSE 55
                                   589******86 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0057        20      29      43 ..       7      21 ..       3      25 .. 0.76
   2 ?    5.0   0.2    0.0068        24       2       9 ..      46      53 ..      45      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0057
                                   GGS-TT-BBTTTB-B CS
                     Rubredoxin 29 edlPddWvCPdCgve 43
                                   e+l d  +CP C+++
  gi|118430887|ref|YP_874802.1|  7 EQLTDITICPRCSAP 21
                                   56667779****997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0068
                                   EEETTT-B CS
                     Rubredoxin  2 yeCkvCgy 9 
                                   ++C++Cgy
  gi|118430887|ref|YP_874802.1| 46 MKCDICGY 53
                                   79*****9 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4   0.00034       1.2      10      34 ..      14      38 ..      12      71 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00034
                        DUF2387 10 vCPrCsemDkirmweedeveyrECv 34
                                   +CPrCs+   i  ++   ++  E v
  gi|118430887|ref|YP_874802.1| 14 ICPRCSAPSAIYRYSISSERSNEGV 38
                                   8********9998875544444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 737.92
//
Query:       gi|118430888|ref|NP_146977.2|  [L=421]
Description: misacylated tRNAthr hydrolase [Aeropyrum pernix K1]
Scores for complete 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-43  148.1   0.0    2.2e-43  147.6   0.0    1.3  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    3.9e-16   59.0   0.1    5.8e-16   58.4   0.1    1.3  1  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.6   0.0   2.5e-47   2.2e-43       1     136 [.       1     133 [.       1     134 [. 0.98

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 2.5e-47
                                    -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE-S CS
                    tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypya 80 
                                    mrlL++had++ey+++k+alk++ ++++ e+++ ealvvF++vE++D     ++v  a+++i+++ +++k+++v+lypya
  gi|118430888|ref|NP_146977.2|   1 MRLLYLHADRFEYKTVKPALKNP-PDPPGEASFGEALVVFTTVEDGDGP---QTVMYAASDIASHSSRLKVTTVILYPYA 76 
                                    9**********************.*************************...899************************* PP

                                    TS-SSB--HHHHHHHHHHHHHHHHTT..-EEEE--SSEEEEEEEEE--STTSEEEEE CS
                    tRNA-Thr_ED  81 HLssslaspevakeilkkleeklkekg.levkraPFGwykefeisckGhpLaelsre 136
                                    HLss+la+p +a++ l +le +l++k   +v+raPFGwyk+f+i ckGhpLaelsr+
  gi|118430888|ref|NP_146977.2|  77 HLSSRLAKPMAAHKRLIELEGALRTKFpGHVHRAPFGWYKSFSIACKGHPLAELSRS 133
                                    ************************996569*************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   6.5e-20   5.8e-16       1      93 [.     318     407 ..     318     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 6.5e-20
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET.TTCEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr.dtreq 79 
                                    q +vip+ +   e e ya+++ae+L a g+rv +  +++ +g+++rea + +  +++vvG++e e+gtv vr+r + ++q
  gi|118430888|ref|NP_146977.2| 318 QSAVIPVDS---ESEGYAQRIAEDLAASGVRVSIV-RGSGLGRRVREAGRSWASLVIVVGKREEETGTVVVRRRwEPGKQ 393
                                    679******...99****************99996.9*************************************8888** PP

                                    EEEETTHHHHHHHH CS
                 HGTP_anticodon  80 ervsldelveklke 93 
                                    e ++ldel ++ k+
  gi|118430888|ref|NP_146977.2| 394 EVLTLDELSSEAKK 407
                                    ********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3054.93
//
Query:       gi|14600463|ref|NP_146978.1|  [L=319]
Description: DNA repair and recombination protein RadA [Aeropyrum pernix K1]
Scores for 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-94  313.7   0.0    9.3e-94  313.4   0.0    1.0  1  Rad51            Rad51
    7.9e-16   58.3   0.1      1e-15   57.9   0.1    1.1  1  RecA             recA bacterial DNA recombination protein
    2.3e-13   50.5   0.2    6.2e-13   49.1   0.2    1.8  1  HHH_5            Helix-hairpin-helix domain
    5.2e-11   42.3   0.0    7.6e-11   41.8   0.0    1.3  1  ATPase           KaiC
    8.5e-09   35.3   0.0    1.3e-08   34.6   0.0    1.2  1  AAA_25           AAA domain
    1.3e-05   25.2   0.0    3.3e-05   23.9   0.0    1.7  1  HHH_2            Helix-hairpin-helix motif
    1.7e-05   24.6   0.0    4.9e-05   23.1   0.0    1.9  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
      2e-05   24.8   0.0    4.6e-05   23.6   0.0    1.6  1  Cdd1             Pathogenicity locus
    0.00014   21.6   0.3      0.001   18.8   0.0    2.4  2  HHH              Helix-hairpin-helix motif
     0.0014   19.2   1.6     0.0027   18.3   0.2    2.1  1  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
     0.0026   18.3   0.3      0.007   16.9   0.0    1.9  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.014   15.6   0.0        4.8    7.5   0.1    2.4  2  HHH_3            Helix-hairpin-helix motif
      0.015   15.6   0.0      0.069   13.5   0.0    2.1  2  IMS_HHH          IMS family HHH motif
       0.02   15.1   0.1       0.14   12.4   0.0    2.2  2  DUF4332          Domain of unknown function (DUF4332)
      0.022   14.5   0.0      0.044   13.5   0.0    1.5  1  AAA_24           AAA domain
      0.022   15.0   0.0      0.063   13.5   0.0    1.8  1  AAA_22           AAA domain
      0.027   14.9   0.0      0.069   13.6   0.0    1.7  1  BAF              Barrier to autointegration factor
      0.049   13.8   0.1        0.1   12.8   0.1    1.4  1  OCRL_clath_bd    Inositol polyphosphate 5-phosphatase clathri
       0.14   12.5   0.0       0.38   11.2   0.0    1.7  1  HHH_8            Helix-hairpin-helix 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 !  313.4   0.0   9.8e-97   9.3e-94       2     254 ..      69     317 ..      68     318 .. 0.99

  Alignments for each domain:
  == domain 1  score: 313.4 bits;  conditional E-value: 9.8e-97
                                   S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS- CS
                         Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegt 82 
                                   +f +a +l  +  ++ ++ttGs++lDelLgGGiet++ite+fGef+sGktq+ch+l+v vqlp ++gG egkavy+dtegt
  gi|14600463|ref|NP_146978.1|  69 DFKTAYDLKIESMNIKKITTGSRNLDELLGGGIETKTITELFGEFGSGKTQICHQLSVNVQLPEDKGGLEGKAVYVDTEGT 149
                                   68999**************************************************************************** PP

                                   --GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHH CS
                         Rad51  83 frperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklg 163
                                   fr er+ ++a   +ld++ev++n+   Ra ++ hq  +++++ +++++d+++l++vDsvt+++R++f gr++la Rqq l+
  gi|14600463|ref|NP_146978.1| 150 FRWERIEQMARGVGLDPDEVMKNIYWIRAINSHHQIAIVDKLFTMVKNDNIKLVVVDSVTSHFRAEFPGRENLAMRQQLLN 230
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEE CS
                         Rad51 164 kllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleav 244
                                   ++l++L +lad f+vavvitnqv+a++d     f +dp++ +gG+vl+ha  +R++l+k +g++Ri++vvd+P+lpe e+v
  gi|14600463|ref|NP_146978.1| 231 RHLHQLMRLADIFNVAVVITNQVMARPDV----FYGDPTQAVGGHVLGHAPGVRVYLKKSRGNKRIARVVDAPHLPEGETV 307
                                   ****************************9....************************************************ PP

                                   EEEETTEEE- CS
                         Rad51 245 faigeeGied 254
                                   fai+e Gi d
  gi|14600463|ref|NP_146978.1| 308 FAITEWGIRD 317
                                   ********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 !   57.9   0.1   1.1e-18     1e-15      27     225 ..      79     289 ..      57     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.1e-18
                                   .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----....HHH CS
                          RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehald....pky 97 
                                   e+++++ i++Gs  ld  lG GG+    i+e++G   sGkt ++ ++ +++q    kg   g a+++d+e ++      + 
  gi|14600463|ref|NP_146978.1|  79 ESMNIKKITTGSRNLDELLG-GGIETKTITELFGEFGSGKTQICHQLSVNVQlpeDKGgleGKAVYVDTEGTFRweriEQM 158
                                   4689****************.**********************999888888444344233679******99862232468 PP

                                   HHHTT--GGG-E....EE--SSHHHHHHHHHHH...HTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHH CS
                          RecA  98 akklGvdidell....vsqpdtGeqaleiadal...vrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrk 171
                                   a+ +G+d de++      +  +  + + i+d+l   v+   i l+vvdsv++   +ae  G    ++++++ +l+ + l +
  gi|14600463|ref|NP_146978.1| 159 ARGVGLDPDEVMkniyWIRAINSHHQIAIVDKLftmVKNDNIKLVVVDSVTSH-FRAEFPGR---ENLAMRQQLLNRHLHQ 235
                                   999999977655221156778888899999975443899***********986.59999985...67889999******** PP

                                   HHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES-- CS
                          RecA 172 ltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieei 225
                                   l    +  n++v+  nq+  +  v +g+p  + GG+ l     vr+ ++++   
  gi|14600463|ref|NP_146978.1| 236 LMRLADIFNVAVVITNQVMARPDVFYGDPTQAVGGHVLGHAPGVRVYLKKSRGN 289
                                   *********************************************999987655 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   6.6e-16   6.2e-13       2      57 .]       9      64 ..       8      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 6.6e-16
                                  HHHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                         HHH_5  2 eeLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                  +++++++G+Gp tA +l +aG++++e++aaa+++e+++++Gi   tA++i++++++
  gi|14600463|ref|NP_146978.1|  9 KDITDLPGVGPTTAQKLMEAGYTTLEAIAAATPQEVSQATGIPILTAQKIVDAARE 64
                                  789**************************************************996 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0     8e-14   7.6e-11       2     167 ..      87     264 ..      86     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 8e-14
                        ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekyge.....pgvfvtveepa..edlrenakslGwdle 75 
                                    tg   lDe+l gGi  ++++ + Ge G+GKt ++ q  ++     ++     + v+v +e +   e + + a+ +G d +
  gi|14600463|ref|NP_146978.1|  87 TTGSRNLDELLGGGIETKTITELFGEFGSGKTQICHQLSVNVQLPEDKgglegKAVYVDTEGTFrwERIEQMARGVGLDPD 167
                                   79999*********************************99976554441122266999999998889************** PP

                        ATPase  76 kleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeav....aReil.....rql 147
                                   ++ ++  ++ i a +s ++           +++++l +++k+ ++k vv+Ds+t++ + e +      +R++l     +ql
  gi|14600463|ref|NP_146978.1| 168 EVMKN--IYWIRAINSHHQ----------IAIVDKLFTMVKNDNIKLVVVDSVTSHFRAEFPGRenlaMRQQLlnrhlHQL 236
                                   *****..999999999766..........468999999*****************94443322111124554322111566 PP

                        ATPase 148 vrvlkklgvTailvsekss........s 167
                                   +r     +v  ++++++           
  gi|14600463|ref|NP_146978.1| 237 MRLADIFNVAVVITNQVMArpdvfygdP 264
                                   6666667777777777655555555443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   1.4e-11   1.3e-08       5     188 ..      76     252 ..      72     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.4e-11
                        AAA_25   5 lelsavsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsede 85 
                                   l++++  + ++ +  + ++ l++g +  ++++ l+G  g+GKt ++ +l++ v + +   g      gk +yv++E++  +
  gi|14600463|ref|NP_146978.1|  76 LKIESMNIKKITTGSRNLDELLGGGIETKTITELFGEFGSGKTQICHQLSVNVQLPEDKGG----LEGKAVYVDTEGTF-R 151
                                   6677777778888899999***********************************6554333....68***********9.4 PP

                        AAA_25  86 lrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg....densn 162
                                   + +R++++ + + +d ++         ++  + +++ ++++ a vd+l   ++   +++lvv+D++++ +++     en +
  gi|14600463|ref|NP_146978.1| 152 W-ERIEQMARGVGLDPDEVMK------NIYWIRAINSHHQI-AIVDKLFTMVKN-DNIKLVVVDSVTSHFRAefpgRENLA 223
                                   4.6788888887444444333......33444455555555.67899**99999.78***********9988665434433 PP

                        AAA_25 163 sd...v.galvealeriarrtgaavllvhH 188
                                          ++ + +l r+a+ +++av+++ +
  gi|14600463|ref|NP_146978.1| 224 -MrqqLlNRHLHQLMRLADIFNVAVVITNQ 252
                                   .12343588899999999999999998865 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.5e-08   3.3e-05       9      57 ..      15      64 ..      13      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.5e-08
                         HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivefFen 57
                                  + VG +tA++L+++ + +l+a+++a+ +e ++  +i   +Aq+iv+  ++
  gi|14600463|ref|NP_146978.1| 15 PGVGPTTAQKLMEAgYTTLEAIAAATPQEVSQATGIPILTAQKIVDAARE 64
                                  78**********976*****************************997665 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 !   23.1   0.0   5.2e-08   4.9e-05       7      31 ..      15      40 ..       9      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.2e-08
               DNA_pol_lambd_f  7 yGVGpktAkkwyakGirtledlra.k 31
                                   GVGp+tA+k++++G++tle + a  
  gi|14600463|ref|NP_146978.1| 15 PGVGPTTAQKLMEAGYTTLEAIAAaT 40
                                  5********************99943 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.8e-08   4.6e-05       2      43 ..       5      46 ..       4      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.8e-08
                          Cdd1  2 rkalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                  ++++k+++d+P++G+ +a++l+e G++++e ++  +p+e+ +
  gi|14600463|ref|NP_146978.1|  5 KREIKDITDLPGVGPTTAQKLMEAGYTTLEAIAAATPQEVSQ 46
                                  56899********************************99876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06     0.001      10      29 ..       8      27 ..       6      28 .. 0.91
   2 ?   -0.6   0.1       1.6   1.5e+03       2      19 ..      33      50 ..      32      61 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                  HHHHHTSTT-SHHHHHHHHH CS
                           HHH 10 reeLlalPGVGpktAeaIls 29
                                  ++++++lPGVGp tA++ ++
  gi|14600463|ref|NP_146978.1|  8 IKDITDLPGVGPTTAQKLME 27
                                  689*************9987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                  HHHHHTSSHHHHHTSTT- CS
                           HHH  2 leglipasreeLlalPGV 19
                                  le++ +a++ e  +  G+
  gi|14600463|ref|NP_146978.1| 33 LEAIAAATPQEVSQATGI 50
                                  788888888886666555 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 !   18.3   0.2   2.9e-06    0.0027      19      94 ..      10      86 ..       4      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                    5_3_exonuc 19 nipGvpgiGektAakLlk.eygsleeilenld.elkekklkekLeenkeearlskkLatiktdvpleleledlklkep 94
                                  +i   pg+G+ tA+kL++  y +le+i +++  e++ +++   + ++++ ++ +++  +i+ ++  +l++e++++k++
  gi|14600463|ref|NP_146978.1| 10 DITDLPGVGPTTAQKLMEaGYTTLEAIAAATPqEVS-QATGIPILTAQKIVDAAREALNIDFKTAYDLKIESMNIKKI 86
                                  68889************6269********9874555.47788888889999999999999999999999999999876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.4e-06     0.007       3      89 ..     109     215 ..     108     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.4e-06
                        AAA_18   3 ltGtpGvGKttlakeLskrlgf.......gvnlrdvakenglllevdpe.....aldeskrldedkldklldaleenss.. 69 
                                   l G  G+GKt++++ Ls   ++         +   v +e+  ++e+ ++      ld+ ++++  +  ++++ +++++   
  gi|14600463|ref|NP_146978.1| 109 LFGEFGSGKTQICHQLSVNVQLpedkgglEGKAVYVDTEGTFRWERIEQmargvGLDPDEVMKNIYWIRAINSHHQIAIvd 189
                                   67889***********76655577776556666667777777777777766666666677777777666666666666699 PP

                        AAA_18  70 ...aleegknl...vidghlaelese 89 
                                      ++ +++n+   v+d++ ++++ e
  gi|14600463|ref|NP_146978.1| 190 klfTMVKNDNIklvVVDSVTSHFRAE 215
                                   99955555555555********9876 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.021        19      15      32 ..      10      27 ..       7      30 .. 0.85
   2 ?    7.5   0.1    0.0051       4.8      10      47 ..      38      77 ..      35      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.021
                         HHH_3 15 eLqklpGlgpklAknIva 32
                                  +++ lpG+gp++A+++++
  gi|14600463|ref|NP_146978.1| 10 DITDLPGVGPTTAQKLME 27
                                  67889*********9987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                         HHH_3 10 tAsaeeLqklpGlgpklAknIv.ayReknG.pfksreeLl 47
                                   A+ +e ++  G+   +A++Iv a+Re+    fk+  +L+
  gi|14600463|ref|NP_146978.1| 38 AATPQEVSQATGIPILTAQKIVdAAREALNiDFKTAYDLK 77
                                  699999****************446999866999999997 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.3e-05     0.069      12      27 ..      10      25 ..       7      30 .. 0.85
   2 ?   -2.4   0.0       8.6   8.1e+03       8      16 ..      78      86 ..      75      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-05
                       IMS_HHH 12 pitkipGiGgklgekL 27
                                  +it++pG+G+ +++kL
  gi|14600463|ref|NP_146978.1| 10 DITDLPGVGPTTAQKL 25
                                  8**************5 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.6
                       IMS_HHH  8 Lwplpitki 16
                                  +++++i+ki
  gi|14600463|ref|NP_146978.1| 78 IESMNIKKI 86
                                  788999998 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.14      54      92 ..      10      48 ..       6      57 .. 0.89
   2 ?   -0.6   0.0       1.6   1.5e+03      31      59 ..     218     246 ..     211     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                       DUF4332 54 dLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqkl 92
                                  d    +g+g+  a+ L++aG ++ +++a  +p+++ q++
  gi|14600463|ref|NP_146978.1| 10 DITDLPGVGPTTAQKLMEAGYTTLEAIAAATPQEVSQAT 48
                                  566789***************************998875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                       DUF4332  31 grkalaeklgisernvlklanlAdLarik 59 
                                   gr +la + ++  r + +l  lAd +++ 
  gi|14600463|ref|NP_146978.1| 218 GRENLAMRQQLLNRHLHQLMRLADIFNVA 246
                                   67888999999999999999999998775 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   4.7e-05     0.044       7      77 ..     109     211 ..     103     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                        AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel.......... 59 
                                   ++G+ g+GKT ++ +l             + k++++dte+ +      +++++        +++++ +  +          
  gi|14600463|ref|NP_146978.1| 109 LFGEFGSGKTQICHQLsvnvqlpedkgglEGKAVYVDTEGTF---RWERIEQMArgvglDPDEVMKNIYWIrainshhqia 186
                                   89************************99999*******9944...444444444788884444444444445555556668 PP

                        AAA_24  60 .......aaeladyktlviDtidel 77 
                                            +++++k +v+D+++  
  gi|14600463|ref|NP_146978.1| 187 ivdklftMVKNDNIKLVVVDSVTSH 211
                                   88999998888889******99965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.7e-05     0.063       4     104 ..     103     213 ..     101     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.7e-05
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelka........... 70 
                                   t++i+ ++Ge G+GKT  + +l  + +  +   +    + + v+v+  +   ++ + ++++r +gl+ ++           
  gi|14600463|ref|NP_146978.1| 103 TKTITELFGEFGSGKTQICHQLSVNVQLPE---DkggLEGKAVYVDTEGTFRWERI-EQMARGVGLDPDEvmkniywirai 179
                                   89999*****************99875433...33468889999999999988888.999999999888877777776554 PP

                        AAA_22  71 ................erlsseellealeqalrarav..ielliiDEaqh.lr 104
                                                   +                      i+l+++D +   +r
  gi|14600463|ref|NP_146978.1| 180 nshhqiaivdklftmvK-------------------NdnIKLVVVDSVTShFR 213
                                   32222222222222220...................23335666655544343 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-05     0.069      18      41 ..       9      32 ..       3      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                           BAF 18 KevtalaGigevlgkkLeekGfdk 41
                                  K++t+l+G+g++ ++kL e+G+ +
  gi|14600463|ref|NP_146978.1|  9 KDITDLPGVGPTTAQKLMEAGYTT 32
                                  99*******************986 PP

>> OCRL_clath_bd  Inositol polyphosphate 5-phosphatase clathrin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00011       0.1      25      70 ..      34      78 ..      22      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                 OCRL_clath_bd 25 eilipkaqekesvaqlsiPinskfkivrEAeEaLLidistnsgvki 70
                                  e  i  a+ +e ++   iPi +  kiv  A EaL id+ t+  +ki
  gi|14600463|ref|NP_146978.1| 34 EA-IAAATPQEVSQATGIPILTAQKIVDAAREALNIDFKTAYDLKI 78
                                  44.34455566666788*********************99988887 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004      0.38      43      65 ..       6      27 ..       1      28 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                                  HHHTTHCTTSTT--HHHHHHHHH CS
                         HHH_8 43 tsleeeltklpgiGkkiaakiee 65
                                  +++++ +t+lpg+G+ +a+k+ e
  gi|14600463|ref|NP_146978.1|  6 REIKD-ITDLPGVGPTTAQKLME 27
                                  45555.9*************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2260.72
//
Query:       gi|14600464|ref|NP_146979.1|  [L=246]
Description: hypothetical protein APE_0121 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       493  (0.0274974); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1952.41
//
Query:       gi|118430889|ref|NP_146980.2|  [L=177]
Description: hypothetical protein APE_0122.1 [Aeropyrum pernix K1]
Scores for 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-14   52.2   0.0    1.2e-13   51.6   0.0    1.2  1  HIT       HIT domain
    3.6e-07   30.1   0.0    5.2e-07   29.5   0.0    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
    4.7e-07   30.3   0.0      7e-07   29.7   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 !   51.6   0.0     2e-17   1.2e-13       5      95 ..      45     136 ..      42     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2e-17
                                    -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-S CS
                            HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqs 84 
                                    ++ +vy+  l++++l++ p   gh+ v p +h++el+dlt++e+ ++ ++v+  +kal+++++  g+++ +n g++ag  
  gi|118430889|ref|NP_146980.2|  45 KALIVYRGSLSYVILNKYPYNSGHIMVTPYRHVAELEDLTMDEIVEMAKLVRASVKALKRVYAPHGFNIGVNIGEAAGAG 124
                                    67799*************************************************************************99 PP

                                    SS.S-EEEEEEC CS
                            HIT  85 va.hlHiHvipr 95 
                                    +a h HiH++pr
  gi|118430889|ref|NP_146980.2| 125 IAgHFHIHIVPR 136
                                    877*******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 !   29.5   0.0   8.8e-11   5.2e-07      10     108 ..      28     135 ..      20     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.8e-11
                                    HHHH-S---..-SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHH....HHHHHHHHHHHH CS
                       CwfJ_C_1  10 sldsClfCl..snpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldei....rkfrkalvkmyk 83 
                                    s + C fC   s  + +k+liv  g+  Y+ l k p +sgH++++p  H+++l  l  ++  e+    r+  kal ++y+
  gi|118430889|ref|NP_146980.2|  28 SREGCVFCEapSMGDDAKALIVYRGSLSYVILNKYPYNSGHIMVTPYRHVAELEDLTMDEIVEMaklvRASVKALKRVYA 107
                                    5678****62255678899**********************************777776666651111555677778887 PP

                                    HTT..--EEEEEE-.SSS-----EEEEE CS
                       CwfJ_C_1  84 kqd..kdavvfEis.sersvHlaiqvip 108
                                      +    + + E +      H++i+++p
  gi|118430889|ref|NP_146980.2| 108 PHGfnIGVNIGEAAgAGIAGHFHIHIVP 135
                                    5441034444455555555566666665 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 !   29.7   0.0   1.2e-10     7e-07       2     100 ..      32     134 ..      31     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-10
                                    -HHHHHHTTSS..-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EE CS
                         DcpS_C   2 wvfnilakgke..pervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevda 79 
                                    +vf++  ++ +  ++ +vy+ +   v+  ++p ++ h++v p+r++++l+dLt +++  ++++++   k++++ y    +
  gi|118430889|ref|NP_146980.2|  32 CVFCEAPSMGDdaKALIVYRGSLSYVILNKYPYNSGHIMVTPYRHVAELEDLTMDEIVEMAKLVRASVKALKRVY---AP 108
                                    566665444332245569999999***********************************************9999...46 PP

                                    EEE--SCCCT-.....-S-S--EEEE CS
                         DcpS_C  80 eelrvgvhyqP.....svyhlHlHvi 100
                                      +++gv++          h+H+H++
  gi|118430889|ref|NP_146980.2| 109 HGFNIGVNIGEaagagIAGHFHIHIV 134
                                    6677777766655557889*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1360.39
//
Query:       gi|14600466|ref|NP_146981.1|  [L=332]
Description: hypothetical protein APE_0124 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-15   57.1   0.0    7.9e-15   55.5   0.0    1.8  2  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.19   3.4e+03      40      69 ..      61      88 ..      44      95 .. 0.65
   2 !   55.5   0.0   4.4e-19   7.9e-15       3     123 ..     169     294 ..     167     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.19
                                  CEEEEEECHCCHHHHHHHHHHHHHHTHGBT CS
                         DHHA1 40 vkvlvaevgeewdagalgiaadklksklkk 69
                                  + ++++    ++++  l  aad l s   k
  gi|14600466|ref|NP_146981.1| 61 DLIIISD--LGANRESLPRAADLLASATSK 88
                                  3344444..589999999999999885555 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 4.4e-19
                                   HHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC.....TCEEEEEECHCCHHHHHHHHHHHHHHTHG.BT.TCEEEEE CS
                         DHHA1   3 slneerkelekeleelkealaklkaeellekaeevk.....gvkvlvaevgeewdagalgiaadklkskl.kk.pvivfva 76 
                                   + n++ ++ +k l  +k a+  ++ eel++++e +      g+++++++   +++ ++l+ia ++ + +  ++  +i +++
  gi|14600466|ref|NP_146981.1| 169 ERNQDMEWKHKVL--AKFAAGVMWDEELEKRLEGYVneelrGYTTAIKNA-VTIKIHDLRIASTYKNFRGpPSsSMIGALL 246
                                   789**********..********************9**************.*******************96669999999 PP

                                   EEECT.EEEEEEEESSH......SS-HHHHHHHHHHHTTCCEEEETCEEEEEEE CS
                         DHHA1  77 keegd.kvkvsarskkd......gvdagelakeaaaklgggGGGHdlAaGagip 123
                                    ++ +  +++++rs ++      +v+++ +a+e      +gGGGH+ AaGa+i+
  gi|14600466|ref|NP_146981.1| 247 LHRYNaDIAIIVRSDGGlslrsrRVNVQPIARE------LGGGGHPKAAGAKIE 294
                                   999999*********99****************......**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2453.07
//
Query:       gi|118430890|ref|NP_146982.2|  [L=483]
Description: hypothetical protein APE_0125.1 [Aeropyrum pernix K1]
Scores for 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   54.5   1.9    4.1e-14   52.6   1.9    2.1  1  DUF4129   Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
       0.29   10.7   0.4       0.49   10.0   0.4    1.2  1  Snf7      Snf7


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 !   52.6   1.9   4.5e-18   4.1e-14       1      68 [.     402     471 ..     402     475 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 4.5e-18
                        DUF4129   1 ayrallraLaergldrrpgeTprEyarrv..riapspaa..alaalaelfeearYGgrpasaeeyrrlveal 68 
                                    +yra+l+ L+ +gl+r p+eTprE++ r+       +++  a++ ++ l+e  rYGg  +s++e++++++ +
  gi|118430890|ref|NP_146982.2| 402 CYRAALEVLETQGLRRMPWETPREFLVRAekS--LVDEQvyAMRYITWLYELHRYGGLKPSPGEAEECMRMV 471
                                    8****************************432..3333366*****************99999999998865 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   5.4e-05      0.49     115     159 ..      61     108 ..      59     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.4e-05
                                    HHHHHHTCHHHHHHHHHTT-...GGTTHHHHHHHHHHHHHHHHHCSH. CS
                           Snf7 115 dqmekaeeisEalsrsldda...deedEeeleaeLdaLeqelgdeell 159
                                    d  + a+++sE++s+++  a   + +++ +l+a++ +L + ++ + ++
  gi|118430890|ref|NP_146982.2|  61 DYAMLAKQLSEVMSNAIAEAlqgSLVSDNDLDAVVAMLGASEALSRMP 108
                                    78899************99999999**************999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3338.26
//
Query:       gi|118430891|ref|NP_146983.2|  [L=333]
Description: hypothetical protein APE_0126.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   15.4   0.5      0.085   13.3   0.1    2.3  2  DUF4350   Domain of unknown function (DUF4350)
       0.13   11.7   0.0       0.38   10.1   0.0    1.7  2  DUF4392   Domain of unknown function (DUF4392)


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.4e-06     0.085       2      63 ..      38     105 ..      37     114 .. 0.72
   2 ?   -1.1   0.0       0.3   2.7e+03      38      63 ..     273     296 ..     242     300 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.4e-06
                        DUF4350   2 kspnGtralaelLeaqGvevrrvrkpfd..al.egedg...tllvvapdlrlteeela.allewvarGn 63 
                                      p G + la+ Le+ G++v++   ++d  +  +g++g   +++v++ d +l  + la  l  ++++G+
  gi|118430891|ref|NP_146983.2|  38 DGPLGVSDLASSLENMGYSVTVLPEVDDvaRIlAGPGGerlVFIVIGAD-SLRGDVLAkMLTVLADNGD 105
                                    679*****************98888888764426655566699999999.5555455515555555664 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                        DUF4350  38 llvvapdlrlteeelaallewvarGn 63 
                                     + +ap ++lt   +a+l   +++G 
  gi|118430891|ref|NP_146983.2| 273 AVMLAPSVLLTA--AADLYSTLESGV 296
                                    455666666665..355555555555 PP

>> DUF4392  Domain of unknown function (DUF4392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   4.3e-05      0.38      50      78 ..      32      60 ..      20      73 .. 0.85
   2 ?   -2.1   0.0      0.23   2.1e+03      27      44 ..     148     166 ..     136     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.3e-05
                        DUF4392 50 sppeEtDGplGAialaraLqalgkkvviv 78
                                    p + +DGplG   la  L+ +g++v+++
  gi|118430891|ref|NP_146983.2| 32 APLPYNDGPLGVSDLASSLENMGYSVTVL 60
                                   477789********************987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.23
                        DUF4392  27 aeslshak.ksvlItTGFp 44 
                                     + + +++ +s+ ++TGF 
  gi|118430891|ref|NP_146983.2| 148 ESLIVSTSdGSISVLTGFA 166
                                    44444444599*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2454.65
//
Query:       gi|14600469|ref|NP_146984.1|  [L=314]
Description: hypothetical protein APE_0127 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-58  196.3   0.0    2.2e-58  195.8   0.0    1.2  1  AAA_3            ATPase family associated with various cellul
    6.4e-18   64.4   0.5    1.8e-17   63.0   0.3    1.9  2  AAA_lid_2        AAA lid domain
    1.1e-14   54.7   0.0    2.2e-14   53.6   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    1.6e-05   25.3   0.0    4.2e-05   24.0   0.0    1.7  1  AAA              ATPase family associated with various cellul
    0.00025   20.2   0.0     0.0016   17.6   0.0    2.0  1  MCM              MCM P-loop domain
    0.00054   19.4   1.4       0.17   11.3   0.6    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0013   18.5   0.1      0.041   13.6   0.0    2.4  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0018   18.0   0.1      0.058   13.1   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
     0.0053   17.1   0.4      0.011   16.1   0.4    1.6  1  MCM_lid          MCM AAA-lid domain
  ------ inclusion threshold ------
      0.028   14.8   0.1      0.096   13.1   0.1    1.8  2  AAA_16           AAA ATPase 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 !  195.8   0.0   1.2e-61   2.2e-58       1     130 [.      46     173 ..      46     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 1.2e-61
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsa 81 
                                   h+l+egvPG+akt+l+kala a++l+f+riqftpd lPsd++Gt+v+    + f f++Gpvfan++lade+nra+p+tqsa
  gi|14600469|ref|NP_146984.1|  46 HLLVEGVPGVAKTTLAKALAGAFGLRFSRIQFTPDTLPSDVIGTHVYVG--NGFVFRRGPVFANVVLADEVNRANPRTQSA 124
                                   9**********************************************86..579*************************** PP

                         AAA_3  82 lleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                   +leam+e qvtv geth+lp+pf+vlat nPie eG+yplpeaqldrf+
  gi|14600469|ref|NP_146984.1| 125 FLEAMQEGQVTVWGETHRLPSPFIVLATMNPIELEGVYPLPEAQLDRFM 173
                                   ************************************************9 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       6.7   1.2e+04      38      46 ..     205     213 ..     202     214 .. 0.79
   2 !   63.0   0.3   9.8e-21   1.8e-17       2      65 ..     236     299 ..     235     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.7
                     AAA_lid_2  38 VtpeDvkea 46 
                                    +peD+k++
  gi|14600469|ref|NP_146984.1| 205 ASPEDLKRL 213
                                   689999975 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 9.8e-21
                     AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr.repeaeget 65 
                                   +tr  + +e+g+s+r a +++l+ +rAlA++ grd+ tp+Dvkeaa+ +L+HRl+ r+   ++++
  gi|14600469|ref|NP_146984.1| 236 ETRRIEEVEIGASPR-AGIHILKLSRALALMSGRDFATPDDVKEAARAALPHRLKlRKVYISKHS 299
                                   6888899********.**************************************98766555555 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 !   53.6   0.0   1.2e-17   2.2e-14       1     138 []      46     172 ..      46     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.2e-17
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHH CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesev 81 
                                   ++l+ G pG++K++la+ la a++ ++  +q+t dt ++d++g   + + + +++ +p+      + +++ DEv+ra++ +
  gi|14600469|ref|NP_146984.1|  46 HLLVEGVPGVAKTTLAKALAGAFGLRFSRIQFTPDTLPSDVIGTHVYVGNGFVFRRGPVF-----ANVVLADEVNRANPRT 121
                                   68999*******************************************************.....9*************** PP

                                   HHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                         AAA_5  82 lnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                   ++++l  + e ++   +g +    ++      f v+at+np +  ++ +l +a ++Rf
  gi|14600469|ref|NP_146984.1| 122 QSAFLEAMQEGQVT-VWGETHRLPSP------FIVLATMNPIElEGVYPLPEAQLDRF 172
                                   *************9.67777776777......***********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 !   24.0   0.0   2.3e-08   4.2e-05       1     129 [.      47     177 ..      47     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.3e-08
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHH.HHHHHHHTSTSEEEEEETGGGHHHHHTTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkire.lfkeakekakpsilfiDEidalaksrsgse 78 
                                   +l+ G pG+ KT+laka+a  +g +f +i+  ++ l s+++g      ++ +f++    a   +++ DE+ + +++     
  gi|14600469|ref|NP_146984.1|  47 LLVEGVPGVAKTTLAKALAGAFGLRFSRIQFtPDTLpSDVIGTHVYVGNGfVFRRGPVFA--NVVLADEVNRANPRT---- 121
                                   5899**********************9998625566566666555544441344444443..9**********9999.... PP

                                   CHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEE CS
                           AAA  79 seeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkie 129
                                          ++++l+++++ +           s++iv+++ n      +  l++a l +Rf  +i+
  gi|14600469|ref|NP_146984.1| 122 -------QSAFLEAMQEGQVTvwgethrlPSPFIVLATMNPielegVYPLPEAQL-DRFMARIR 177
                                   .......666666666666666666666688899999988744444445666666.77766666 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   9.1e-07    0.0016      31     174 ..      18     156 ..       9     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.1e-07
                                   HHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEES..SSSS CS
                           MCM  31 dvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaavvrde..etge 109
                                    vk+ ++  ++g  ++ +   ++++++ ++l+ g pg+aK++l k+++     +   s  + +   L   v   +    + 
  gi|14600469|ref|NP_146984.1|  18 RVKREVARFVIGKEREVKLALATMIAKGHLLVEGVPGVAKTTLAKALAGA--FGLRFSRIQFTPDTLPSDVIGTHvyVGNG 96 
                                   68888888888888888888889999*****************9999843..34444455555556655554333114566 PP

                                   EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                           MCM 110 fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                   fv+  G +      v++ De+++ + +++sa +Eam + ++++   G +  L++   vla +np+
  gi|14600469|ref|NP_146984.1|  97 FVFRRGPVFA---NVVLADEVNRANPRTQSAFLEAMQEGQVTVW--GETHRLPSPFIVLATMNPI 156
                                   8888888764...49**************************997..66799************98 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   9.3e-05      0.17       5      44 ..      27      66 ..      24      73 .. 0.77
   2 !    6.7   0.0    0.0023       4.1      90     159 ..      92     156 ..      73     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-05
                  Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                  v+G+e+  +    + + + +ll+ G pG  Kt lak+l++
  gi|14600469|ref|NP_146984.1| 27 VIGKEREVKLALATMIAKGHLLVEGVPGVAKTTLAKALAG 66
                                  7787765554444555566799**************9976 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0023
                  Mg_chelatase  90 lvGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                    vG g   + G +      v++ DE+   + ++  ++ e +++g+vt+   ++  + p+ f ++a+mNp 
  gi|14600469|ref|NP_146984.1|  92 YVGNGFVFRRGPVF---ANVVLADEVNRANPRTQSAFLEAMQEGQVTVWGETH--RLPSPFIVLATMNPI 156
                                   56666666666653...358889*************************87665..67999********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 !   13.6   0.0   2.3e-05     0.041      31      60 ..      42      71 ..      28      91 .. 0.84
   2 ?    2.0   0.0     0.086   1.5e+02      87     115 ..     108     136 ..     102     150 .. 0.68
   3 ?   -3.1   0.0       3.2   5.8e+03      83     103 ..     223     243 ..     204     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                        RuvB_N 31 ealdhvllyGpPGlGkttlakiiakelgvk 60
                                   a  h+l+ G PG+ kttlak +a  +g +
  gi|14600469|ref|NP_146984.1| 42 IAKGHLLVEGVPGVAKTTLAKALAGAFGLR 71
                                  5678******************99887765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.086
                        RuvB_N  87 vlfideihrlsraveevlysamedfrldi 115
                                   v++ de+ r ++ ++  +  am++ ++ +
  gi|14600469|ref|NP_146984.1| 108 VVLADEVNRANPRTQSAFLEAMQEGQVTV 136
                                   66667777777777777777776655543 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.2
                        RuvB_N  83 eekdvlfideihrlsraveev 103
                                   ++k v +i +i r +r +eev
  gi|14600469|ref|NP_146984.1| 223 DRKLVEYIADIVRETRRIEEV 243
                                   455567888888888888887 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.058     1e+02      17      42 ..      39      64 ..      28      76 .. 0.81
   2 !   13.1   0.0   3.3e-05     0.058      97     141 ..     109     153 ..     105     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.058
                                  HHCTSSS-EEEECSTTSSHHHHHHHH CS
               Sigma54_activat 17 kvaktdlsvlitGesGtGKellarai 42
                                  +++  + ++l++G  G+ K++la+a+
  gi|14600469|ref|NP_146984.1| 39 ATMIAKGHLLVEGVPGVAKTTLAKAL 64
                                  445556799**************997 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.3e-05
                                   EEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEE CS
               Sigma54_activat  97 lfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaat 141
                                   ++ De+++ ++++Q+ +l+++qeg+v+  G+++  +  + ++a+ 
  gi|14600469|ref|NP_146984.1| 109 VLADEVNRANPRTQSAFLEAMQEGQVTVWGETHRLPSPFIVLATM 153
                                   567*****************************9999877555443 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   6.4e-06     0.011      22      81 ..     226     281 ..     208     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.4e-06
                                   HHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                       MCM_lid  22 akeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                     e+++++  e+R+ e    + +i +++R+   +++Ls+AlA ++ ++++t++dv+ea+r
  gi|14600469|ref|NP_146984.1| 226 LVEYIADIVRETRRIE----EVEIGASPRAGIHILKLSRALALMSGRDFATPDDVKEAAR 281
                                   4555566656666655....4578999999999*************************87 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.3e-05     0.096       4      51 ..      29      71 ..      27     131 .. 0.75
   2 ?   -1.9   0.0       2.2   3.9e+03     138     160 ..     108     131 ..     100     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
                        AAA_16  4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                  G+e+e+   + al +  +   + +l+ G +Gv K++l+++l+ a+  +
  gi|14600469|ref|NP_146984.1| 29 GKEREV---KLALATMIAK--GHLLVEGVPGVAKTTLAKALAGAFGLR 71
                                  666666...5556655555..68****************999766655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                        AAA_16 138 vlvlDdlqwadeaslql.laaLlr 160
                                   v++ D++ +a + ++++ l+a+ +
  gi|14600469|ref|NP_146984.1| 108 VVLADEVNRANPRTQSAfLEAMQE 131
                                   677788889999888885555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2262.55
//
Query:       gi|118430892|ref|NP_146985.2|  [L=371]
Description: hypothetical protein APE_0129.1 [Aeropyrum pernix K1]
Scores for complete 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   0.0    4.7e-18   65.2   0.0    1.6  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 !   65.2   0.0   2.6e-22   4.7e-18       1      85 [.     210     295 ..     210     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.6e-22
                          DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaera.rtvllvldlspemslgstgdekletavsaaaslarqlld 79 
                                    gld++++ReY+pgD++r+I+Wk t R+g ++vre e++++ ++v lvl ++p+++++    +++ +a++ + +++++l++
  gi|118430892|ref|NP_146985.2| 210 GLDYRSFREYQPGDDPRSIEWKLTGRRGAPVVREVEGAESsKPVRLVLAIRPQHYRKPLYNSPYGAAARRLYTISMMLAE 289
                                    689********************************998887**************977778888888888888*****99 PP

                          DUF58  80 egdrvg 85 
                                    eg r++
  gi|118430892|ref|NP_146985.2| 290 EGVRHS 295
                                    999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 00:00:00.40
# Mc/sec: 2786.00
//
Query:       gi|118430893|ref|NP_146986.2|  [L=367]
Description: hypothetical protein APE_0130.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2863.19
//
Query:       gi|118430894|ref|NP_146987.2|  [L=181]
Description: hypothetical protein APE_0131.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.057   13.2   0.0        0.4   10.5   0.0    2.2  2  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 


Domain annotation for each model (and alignments):
>> 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 ?   -0.3   0.0     0.053   9.5e+02      42      62 ..      44      64 ..      25      73 .. 0.76
   2 ?   10.5   0.0   2.2e-05       0.4      14      52 ..     102     138 ..     100     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.053
                                   HHHHHHHHH.HHHHHCSHHHH CS
                PhdYeFM_antitox 42 leeyerlqeltekllslplna 62
                                   l+e e l++++++ll++ +++
  gi|118430894|ref|NP_146987.2| 44 LDEVEGLLKAILRLLKSSEKR 64
                                   467777777777777776665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 2.2e-05
                                    HHHHHHHHHHT-EEEEEETTEEEEEEEEHHHHHHHHH.H CS
                PhdYeFM_antitox  14 selldeveegeepviItrrGkpvaVlvsleeyerlqelt 52 
                                    ++l+  +++++  +iI + G++vaVl +++ ++ +  l+
  gi|118430894|ref|NP_146987.2| 102 AALISLARSTG--LIILDAGGDVAVLTPESYTRFRGMLR 138
                                    67788899999..***************97776655553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.35
# Mc/sec: 1530.35
//
Query:       gi|118430895|ref|NP_146988.2|  [L=104]
Description: hypothetical protein APE_0132.1 [Aeropyrum pernix K1]
Scores for 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-23   80.5   0.2    8.7e-23   80.4   0.2    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 !   80.4   0.2   4.9e-27   8.7e-23       2      91 ..      10     101 ..       9     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 4.9e-27
                                    EETTE.EEEEEEEGGGTT-EEEETT..EEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-E CS
                         DUF424   2 rtddllklvavcdkellgktfkege..lllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVl 79 
                                    +t++ l++v v d++++++ + ++e  +++ vs++fygg+l +e++aik++eka+i+ ++ge++v++ v++Glv+pdsVl
  gi|118430895|ref|NP_146988.2|  10 ETPEGLVMVLVTDEDVMERAVYDEErgVRIIVSRSFYGGSLGTEADAIKTIEKADIIVLTGEKSVSIGVRMGLVNPDSVL 89 
                                    577889****************99999***************************************************** PP

                                    EETTEEEEEEEE CS
                         DUF424  80 vidgvphaqigk 91 
                                    +++g++++q++k
  gi|118430895|ref|NP_146988.2|  90 EVKGIKQVQVFK 101
                                    **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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 0.19s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 920.56
//
Query:       gi|118430896|ref|NP_146989.2|  [L=266]
Description: electron transfer flavoprotein beta-subunit [Aeropyrum pernix K1]
Scores for complete 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-40  138.3   1.7    3.6e-40  137.8   1.7    1.2  1  ETF         Electron transfer flavoprotein domain
  ------ inclusion threshold ------
       0.15   11.3   0.1       0.39    9.9   0.0    1.7  2  RE_HindIII  HindIII restriction endonuclease
       0.15   12.1   0.1       0.48   10.5   0.1    1.9  2  DUF218      DUF218 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 !  137.8   1.7   6.1e-44   3.6e-40       9     181 ..      30     216 ..      24     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 6.1e-44
                                    .CCCE-HHHHHHHHHHHHHHHH..HT.--EEEEEEES....S-.....CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHH CS
                            ETF   9 vdgklnpvdlealeaArrlkek..ag.gevtavvvGppeaeea.....lrealaamGadkvilvddpalagydaeataka 80 
                                     + k++++d++a+e+A++lkek  ++   v+++++Gp +  +      ++eala +G+d++i+v d++l   d  +taka
  gi|118430896|ref|NP_146989.2|  30 IPLKISDIDRNAVEEAVKLKEKlgGKlYAVSVLTWGPVKLRNKdlrlaVQEALA-KGVDEAIVVADDELTPGDQTTTAKA 108
                                    57799*****************6533466********65555566777899***.************************* PP

                                    HHHHHHHC..--SEEEEESSCCH...HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEE CS
                            ETF  81 laalikke..dpdlvlagataig...kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavlt 155
                                    ++a+++k   +p+l+lag+ +i+    qv++rlA+lLg+ +++ v +l+v++g+++++R++e+   + evvea+lpav++
  gi|118430896|ref|NP_146989.2| 109 IKAALEKHgvKPELILAGEATIDevtSQVPGRLASLLGYKYLSFVRKLDVDNGRIIAERDLED--YI-EVVEASLPAVVS 185
                                    ********889***********55***************************999*********..99.************ PP

                                    E-TTSS--.....--S-TT---EEEE--HHH CS
                            ETF 156 vrpgafep.....aaimaakkkeveevevad 181
                                    v+ +++ep     ++i++a++k+v+e+++++
  gi|118430896|ref|NP_146989.2| 186 VTQEINEPrpptlLQIRRAARKPVKEYSASE 216
                                    ********9999999************9986 PP

>> RE_HindIII  HindIII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.24   1.4e+03     230     271 ..      74     115 ..      67     125 .. 0.76
   2 ?    9.9   0.0   6.6e-05      0.39     161     240 ..     143     222 ..     132     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.24
                     RE_HindIII 230 eklaasellkeakqeelarleaekerirglsdeealkelive 271
                                      la +e+l++ ++e++ + + e     + + ++a+k+ + +
  gi|118430896|ref|NP_146989.2|  74 LRLAVQEALAKGVDEAIVVADDELTPGDQTTTAKAIKAALEK 115
                                    567888999999999999988888888888888888887765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.6e-05
                     RE_HindIII 161 vllsykhLslLvktaskespteaerlLkeyakivaaldpaklkeakaYWskinqtilklaettkellreeklaasellke 240
                                     ll yk+Ls++ k    ++   aer L +y ++v+a  pa +  +++  +    t+l++    ++  +e+ +   e + +
  gi|118430896|ref|NP_146989.2| 143 SLLGYKYLSFVRKLDVDNGRIIAERDLEDYIEVVEASLPAVVSVTQEINEPRPPTLLQIRRAARKPVKEYSASELENVGK 222
                                    589************************************99877777766666777777777777776666666665555 PP

>> DUF218  DUF218 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1     8e-05      0.48      20      63 ..      77     125 ..      52     135 .. 0.72
   2 ?   -1.7   0.0      0.47   2.8e+03      53      96 ..     156     194 ..     149     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8e-05
                         DUF218  20 aaelyrag....kiivsGg..gadedvseaeamaeylrelgvpeeaille 63 
                                    a++ + a+     i+v  +  +++++++ a+a+++ l+++gv++e il  
  gi|118430896|ref|NP_146989.2|  77 AVQEALAKgvdeAIVVADDelTPGDQTTTAKAIKAALEKHGVKPELIL-A 125
                                    4433333335534999988997789******************84554.3 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.47
                         DUF218  53 lgvpeeailledrsrnTeenarfskellkersillVTsafHmpR 96 
                                    l v++ +i+ e+   +  e +++s        ++ VT+ +  pR
  gi|118430896|ref|NP_146989.2| 156 LDVDNGRIIAERDLEDYIEVVEASLP-----AVVSVTQEINEPR 194
                                    55555555554443333333333322.....2344555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); 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: 0.48u 0.19s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 2266.35
//
Query:       gi|14600475|ref|NP_146990.1|  [L=308]
Description: electron transfer flavoprotein alpha-subunit [Aeropyrum pernix K1]
Scores for complete 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  105.5   0.0    2.2e-30  104.5   0.0    1.5  1  ETF_alpha     Electron transfer flavoprotein FAD-binding doma
    1.6e-13   51.0   0.0    2.7e-13   50.2   0.0    1.4  1  ETF           Electron transfer flavoprotein domain
     0.0031   17.2   0.2       0.26   11.0   0.0    2.9  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central 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 !  104.5   0.0   3.7e-34   2.2e-30       2      84 .]     182     265 ..     181     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 3.7e-34
                                   -TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTT.TSS-CCCB-SSSS-----S-EEEES----HHHHGGG CS
                     ETF_alpha   2 dLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvda.gwipeerqvGqtGktvaPklyiavGisGaiqhlaGm 81 
                                   +Leea+++v++GrG+kske+l+l+ elae l+a++g++R+++ + +w++e++ +G +Gk vaPkly+a+GisG+ qh+ G+
  gi|14600475|ref|NP_146990.1| 182 NLEEAEIIVGVGRGFKSKEDLKLAFELAELLNAQIGCTRPIAADlKWLSEDHWIGISGKRVAPKLYLAIGISGSPQHMSGV 262
                                   79**************************************98777************************************ PP

                                   TT- CS
                     ETF_alpha  82 kes 84 
                                   +++
  gi|14600475|ref|NP_146990.1| 263 QNA 265
                                   985 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   4.5e-17   2.7e-13      71     180 ..      56     164 ..      17     165 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 4.5e-17
                                   S--CCHHHHHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSS CS
                           ETF  71 gydaeatakalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlp 151
                                   ++ +e +a +l +li +e+pd+++  a    ++ + r+A +L++p++tdv+++ ve+gk+++++   +++++    e ++p
  gi|14600475|ref|NP_146990.1|  56 TSSPESIALLLEKLISEEKPDIIVGEAYKNLRDALSRVAGKLDLPMATDVSSFSVENGKVKFRKGFLSEKAV-MEAEIPKP 135
                                   56799******************99999999*************************9***************.556778** PP

                                   EEEEE-TTSS----S-TT---EEEE--HH CS
                           ETF 152 avltvrpgafepaaimaakkkeveeveva 180
                                   av+   ++  +p++i+++ ++ ++e+e++
  gi|14600475|ref|NP_146990.1| 136 AVILFLTRFTKPKEISPESQARIVELEPP 164
                                   ************************99875 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 !   11.0   0.0   4.4e-05      0.26       3      55 ..      64     114 ..      62     178 .. 0.75
   2 ?    3.1   0.1     0.012        70     101     134 ..     262     295 ..     183     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.4e-05
                                   HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TT CS
                  TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgviped 55 
                                    ++e l + ++p i+vG   +  + +++l ++a kl++P++t +   +v + +
  gi|14600475|ref|NP_146990.1|  64 LLLEKLISEEKPDIIVGEAYK--NLRDALSRVAGKLDLPMATDVSSFSVENGK 114
                                   578899999**********99..******************988766655555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.012
                                   TTT-EEEEEESSCCCCTTCC--SEEEECTHHHHH CS
                  TPP_enzyme_M 101 apeakiihididpaeigknyqvdlaivgdvketl 134
                                    ++akii    + +++   +q+d+++v+d+ +++
  gi|14600475|ref|NP_146990.1| 262 VQNAKIIVAVNKDKNAPIFKQADYGVVADLYQFI 295
                                   3445665555566666667778888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2368.70
//
Query:       gi|118430897|ref|NP_146991.2|  [L=376]
Description: hypothetical protein APE_0136.1 [Aeropyrum pernix K1]
Scores for 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-160  532.2  32.0   7.6e-160  532.0  32.0    1.0  1  DUF1646   Protein of unknown function (DUF1646)


Domain annotation for each model (and alignments):
>> DUF1646  Protein of unknown function (DUF1646)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.0  32.0  4.3e-164  7.6e-160       2     347 .]      16     368 ..      15     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 532.0 bits;  conditional E-value: 4.3e-164
                        DUF1646   2 aallvilvlvlilPlvvrkveenlelfllim...gvaavtvsgl.....fslelliealktplailevgaipigitqavl 73 
                                    a+l++il+lvl+lP++vr+veenle+f++im   gva+++++g+       + l+i+a+ktplai++vg+ipigi+qav+
  gi|118430897|ref|NP_146991.2|  16 AVLSAILILVLVLPFKVRIVEENLEAFFFIMgllGVATIYYYGIlptpdSLIGLFIKAFKTPLAIAHVGPIPIGIVQAVV 95 
                                    7899***************************88889********888865579*************************** PP

                        DUF1646  74 laGlvfellkkklksllaevldklalkvfvfllivilGlassvisaivaavilaeivallplerkekvklvviasfaiGl 153
                                    ++Glvf++++k+++s+la++++k++++vf+f+l+++lGl+ssvis+iv+avilaei+a+l+++r++kvk+vv+asfa+G+
  gi|118430897|ref|NP_146991.2|  96 FFGLVFYFFHKHIYSILASTMEKVGIPVFAFILTFLLGLISSVISVIVTAVILAEIAAALNISRERKVKYVVYASFAVGI 175
                                    ******************************************************************************** PP

                        DUF1646 154 GaaltPvGePlstiavsklnedflylidvlgeyiiiavlvlallaalslkrlskreelvevveyeeelkevliravkvfv 233
                                    GaaltP+GePlstia+skln++f+ylid+lg+yi+++++v+a++aa+sl+++++re lv++v yee+++e+l+r+++vf+
  gi|118430897|ref|NP_146991.2| 176 GAALTPLGEPLSTIAISKLNAHFTYLIDILGVYIVPGIAVSAVAAAYSLRGEVYREGLVKFV-YEESINEILLRGFRVFL 254
                                    **************************************************************.***************** PP

                        DUF1646 234 filalellGegfkPlikayiaklkseilywvnlisavvdnatlaaaeisPelteeqirailmsllisGGlliPGniPniv 313
                                    f++alellG++f+P++k+y+a+l+s++lyw+n+isavvdnatl+aae++P+lteeqir++lmsllisGG+liPGniPniv
  gi|118430897|ref|NP_146991.2| 255 FVAALELLGASFTPMVKWYFAQLPSWALYWINTISAVVDNATLTAAEMGPFLTEEQIRSALMSLLISGGMLIPGNIPNIV 334
                                    ******************************************************************************** PP

                        DUF1646 314 saGklkikskeWarvgvPlgiilliiyfivllvl 347
                                    +aG+l+i+++eWarvgvP+gi+ll++yfiv++vl
  gi|118430897|ref|NP_146991.2| 335 AAGRLRITMNEWARVGVPFGIALLLAYFIVIEVL 368
                                    *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2734.73
//
Query:       gi|14600477|ref|NP_146992.1|  [L=499]
Description: gamma-glutamyltranspeptidase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-86  290.0   0.0    4.6e-86  289.6   0.0    1.1  1  G_glu_transpept  Gamma-glutamyltranspeptidase
  ------ inclusion threshold ------
       0.43    9.9   2.7       0.68    9.3   2.7    1.2  1  EII-Sor          PTS system sorbose-specific iic component


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.6   0.0   5.1e-90   4.6e-86       3     465 ..      27     458 ..      25     476 .. 0.92

  Alignments for each domain:
  == domain 1  score: 289.6 bits;  conditional E-value: 5.1e-90
                                   HHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSGGG-BB CS
               G_glu_transpept   3 vLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktgalavgV 83 
                                   +L +GGnAvDAavA++l+l+v+ p+  G+GG++f+l+++ +++   ++++++ AP+ +t++ + ++g +++++ g+l+ ++
  gi|14600477|ref|NP_146992.1|  27 ILSSGGNAVDAAVATSLALTVLIPHLGGVGGDFFMLYRSPEGRVF-FVNGSGFAPRRLTREEVLGRGLQEIPESGPLSPTT 106
                                   9****************************************9987.9****************9***************** PP

                                   --HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTSEE--HHHHH CS
               G_glu_transpept  84 PGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkagellkqpalAk 164
                                   PG +agl++ ++ +G+++wa l++pa  la++Gfp+ + +ar l+ ++e l++dp++++  l+ + + ++g+  + p lA+
  gi|14600477|ref|NP_146992.1| 107 PGYLAGLYHSWRSFGTMEWASLVKPARLLASRGFPLPPSTARSLKLRRECLEADPGSREAVLK-TLPREEGSPARLPGLAA 186
                                   ***********************************************************9998.567899*********** PP

                                   HHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHHHHHHHHHHHHCTT CS
               G_glu_transpept 165 tLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssggivllqiLnilegf 245
                                    L+ + e  +  +Y+Ge Ae+l + l+  gG++ aeDLa  +    epl  +y +g +v+e+pp+++g+++l+ L +le+ 
  gi|14600477|ref|NP_146992.1| 187 LLSGVEE-DPLYLYQGEPAEALEEYLASIGGVMGAEDLAGTRGFTAEPLYSEY-RGWKVWEMPPNTQGVTTLHLLMLLEEE 265
                                   ****965.57789****************************************.899************************ PP

                                   TGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTTB..SGGGCSCGGCSCG.T CS
               G_glu_transpept 246 dlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdkaatpsseyykaaeaaees 326
                                   +l +    s+e++  l+   ++ay+ R+ry+gDp++++         +++  +++ ++l+k   +++s       +  +  
  gi|14600477|ref|NP_146992.1| 266 ELPEPF--SPERVDILAGLARMAYSIRDRYVGDPRYMP---------IDPHELARKETLLKLLGQEES-------NGSKAT 328
                                   966544..49***************************9.........455555555555555555542.......345679 PP

                                   TEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B----EEEEE CS
               G_glu_transpept 327 ggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpspanaiePgkRplssmaPtivlk 407
                                   g+Tt+++v+Dreg +V+ ++++ +++Gs+v+ p+  ++Lnn+   f+        l++  ++ ++Pg  pl++++ +i+++
  gi|14600477|ref|NP_146992.1| 329 GDTTFFAVADREGGIVAGIQSLFYPWGSCVTEPRFQVTLNNRARGFT--------LKEGLPSTLRPGAFPLHTLSSVIMEQ 401
                                   ***********************************************........********************988777 PP

                                   TTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEESSSSTEEEESTTS CS
               G_glu_transpept 408 dgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihhqllpdkvevEegf 465
                                     + v++lGa+GG   ++ ++  ++n++d+g+++ +a++apr +++    ++  Eegf
  gi|14600477|ref|NP_146992.1| 402 -RERVIALGASGGHLRPQQHALFVTNIVDYGMNVLDAINAPRAVWDPGRGEILCEEGF 458
                                   .88899***************************************7333377777766 PP

>> EII-Sor  PTS system sorbose-specific iic component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.7   7.6e-05      0.68      61     102 ..       8      49 ..       3      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.6e-05
                       EII-Sor  61 tiGgavppdaalagiigtalailsgasaeaavalavpvallg 102
                                   ++Gg+v+++  +a++ig+ +  + g++++aava ++++ +l+
  gi|14600477|ref|NP_146992.1|   8 SLGGTVASEESIASYIGAGILSSGGNAVDAAVATSLALTVLI 49 
                                   58*******************************999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3865.83
//
Query:       gi|118430898|ref|NP_146993.2|  [L=288]
Description: ATP-dependent universal stress protein [Aeropyrum pernix K1]
Scores for complete 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  129.3   5.5    6.6e-19   68.8   0.9    2.5  2  Usp             Universal stress protein family
     0.0018   18.3   0.2        1.3    9.0   0.0    2.7  2  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.9   7.4e-23   6.6e-19       3     138 ..       6     143 ..       5     146 .. 0.96
   2 !   62.2   0.3   8.3e-21   7.4e-17       2     141 .]     163     287 ..     162     287 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 7.4e-23
                                    SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHHCTTC CS
                            Usp   3 krIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada..akaaaeaggv 80 
                                    ++Il+++D se sk ++   +ela +++++++llhvi++    +v+++ + +   ++ ++ a++++d+  + ++++++ v
  gi|118430898|ref|NP_146993.2|   6 EHILLPLDLSEVSKPLAISVAELASRHKSRVTLLHVIEEAMVIHVAAGYDVSSLIRSIEKNAREKLDKikKLMMEKGANV 85 
                                    58************9999******************************9999999999999999999999********** PP

                                    EEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEE CS
                            Usp  81 kvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVl 138
                                    +v  ++ +g+p+++i evaee +a  iV+Gs+g++ ++ l lGS+ +  ++ + +pV+
  gi|118430898|ref|NP_146993.2|  86 VVYEDIPVGNPGTVISEVAEEVGATEIVMGSKGLGIFRILPLGSTVRETVKISRKPVI 143
                                    *********************************98888899****************8 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 8.3e-21
                                    -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCE CS
                            Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvk 81 
                                    +++IlV+  + ++sk  +++A++ a ++++++il+h+i+p+  +++ + +   ++ e++ ee+              gv+
  gi|118430898|ref|NP_146993.2| 163 FRKILVGA-DRNTSKSMIDYAVNAASTDDGKVILAHIIEPPLEEPSYEVKNVFKYGEKAGEER--------------GVE 227
                                    79******.8899*************************************9999999999996..............9** PP

                                    EEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  82 vevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    ve+vv  g p+ +++ +a + da+ ++vG++ +++ls+l+lGS+ ++++  ++ p++v++
  gi|118430898|ref|NP_146993.2| 228 VEIVVARGRPDKMLTAIASQMDASSVLVGRTVERRLSELILGSTLDRLMTLCELPLIVYP 287
                                    *********************************************************975 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0012        11      52      94 ..      68     114 ..      27     117 .. 0.64
   2 !    9.0   0.0   0.00014       1.3      67     100 ..     228     261 ..     218     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHHHTT--EEEEESS....HHHHHHHHHHHCTECEEEE CS
                 DNA_photolyase  52 lesLadLdeeLrelgirLvvrrgd....padvlpelakelgasavva 94 
                                     e L ++++ + e+g + vv++      p +v+ e+a+e+ga+++v+
  gi|118430898|ref|NP_146993.2|  68 REKLDKIKKLMMEKGANVVVYEDIpvgnPGTVISEVAEEVGATEIVM 114
                                    45566666666666666666664344448888888888888887775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00014
                                    --EEEEESSHHHHHHHHHHHCTECEEEEE---SH CS
                 DNA_photolyase  67 irLvvrrgdpadvlpelakelgasavvanreyep 100
                                    ++ vv rg+p + l ++a++++as+v++ r +e+
  gi|118430898|ref|NP_146993.2| 228 VEIVVARGRPDKMLTAIASQMDASSVLVGRTVER 261
                                    6889*************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2036.57
//
Query:       gi|118430899|ref|NP_146994.2|  [L=400]
Description: hypothetical protein APE_0141.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-16   60.8   0.0    1.7e-16   60.2   0.0    1.2  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
    5.1e-14   52.3   0.0    8.4e-14   51.6   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    2.9e-09   37.0   0.0    4.5e-09   36.3   0.0    1.2  1  Met_10           Met-10+ like-protein
    4.3e-07   29.6   0.6    2.1e-06   27.4   0.2    2.2  2  PUA_3            PUA-like domain
    0.00083   18.8   0.0     0.0014   18.1   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0013   18.3   0.0     0.0022   17.6   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0071   16.3   0.1      0.023   14.6   0.1    1.8  1  PUA              PUA domain
  ------ inclusion threshold ------
       0.07   12.7   0.0       0.11   12.0   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   7.6e-20   1.7e-16      76     207 ..     172     303 ..     153     319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 7.6e-20
                Methyltrans_SAM  76 evlvgeldespvvvesglkyqldigrnqnfglfldmrlgrdwv.qenakdknvlnlfaytcgfsvaaiaggaskvvnvdm 154
                                     +l+g+ +e  v++e   ++ +d+ r q++g+fld r  r  + +    +  vl++f+yt gf + a+  gask v ++ 
  gi|118430899|ref|NP_146994.2| 172 RWLMGRRKE-VVIEEGQARFIVDVERGQKTGFFLDQRVNRLELaRVAGPGDSVLDVFSYTGGFGIHALLSGASKAVFIEE 250
                                    578887654.57888889*********************965515566799***************************** PP

                Methyltrans_SAM 155 argslnkgrdnhrlnghdlrrvsflgydifkswgkikksgpydlviidppsfq 207
                                       +++  r+n rlng + ++  +l   i+k+         +d+v +dpp+f 
  gi|118430899|ref|NP_146994.2| 251 DAHAVKLLRKNLRLNGIQENKALILNTSIWKAIQAGEPRESFDIVTVDPPAFI 303
                                    ********************************99999999***********94 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   3.8e-17   8.4e-14      40     122 ..     218     300 ..     207     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.8e-17
                                    HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE CS
                  Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivfl 119
                                    + g +vLD+f+ +G+ g+ Al  ga+kav++e+d++avk+l++nl+  +++e+ a + +++  ++ + ++  e+fdiv +
  gi|118430899|ref|NP_146994.2| 218 GPGDSVLDVFSYTGGFGIHALLSGASKAVFIEEDAHAVKLLRKNLRLNGIQENKALILNTSIWKAIQAGEPRESFDIVTV 297
                                    67889***********************************************99999999999999999*********** PP

                                    --S CS
                  Cons_hypoth95 120 DPP 122
                                    DPP
  gi|118430899|ref|NP_146994.2| 298 DPP 300
                                    *** PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0     2e-12   4.5e-09       8     151 ..     122     269 ..     118     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2e-12
                                    TEEEEEB-T.TSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTT...B--EEEEEES-.SEEEEEETTEEEEEETT...T CS
                         Met_10   8 dvvilnlre.elkeykkvigevildktkvktvlrkvsevegefR...tfelevlaGsdstetihkEngcrfklDvs...k 80 
                                    dv++++ ++  ++ + + i+++i ++t v  v++k  + ++++    +++ + l G    e++ +E   rf +Dv    k
  gi|118430899|ref|NP_146994.2| 122 DVAVVQSSSpAIDRHISYISQAIRKFTGVTHVYEKSVQ-RSRLDiglEPRRRWLMGRR-KEVVIEEGQARFIVDVErgqK 199
                                    777777765145569999***************99877.5554322268999****99.899999*********963336 PP

                                    S---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                         Met_10  81 vyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                      f       r  la+++ +g+ V+dvf   G f i +   s a++ + i+ + ++vk+l++n++lN +++
  gi|118430899|ref|NP_146994.2| 200 TGFFLDQRVNRLELARVAGPGDSVLDVFSYTGGFGIHALL-SGASKAVFIEEDAHAVKLLRKNLRLNGIQE 269
                                    8899999999**************************9986.667777789*****************9876 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.2   9.5e-10   2.1e-06       8      64 .]      12      67 ..       8      67 .. 0.93
   2 ?   -0.7   0.0      0.58   1.3e+03      22      53 ..     212     241 ..     207     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.5e-10
                          PUA_3  8 ekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtGyynpqskiavRilsr 64
                                   +++  +G   ++++ +  + g l +Gd+V+v +++g  +++G++ ++ + avRi+ +
  gi|118430899|ref|NP_146994.2| 12 AAKAARGSSIIYRKWVRGTGG-LISGDLVEVIDRNGSEIACGLWEENTPVAVRIIHW 67
                                   6778899999******99996.89******************************987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.58
                          PUA_3  22 eiasvegeledGdvVdvfsekgkflGtGyynp 53 
                                    e+a+v+g  +  +v dvfs  g f  +++++ 
  gi|118430899|ref|NP_146994.2| 212 ELARVAG--PGDSVLDVFSYTGGFGIHALLSG 241
                                    5666664..567899****9999966666555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.1e-07    0.0014     156     230 ..     214     295 ..     208     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.1e-07
                           PrmA 156 eklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk.......eekad 228
                                     ++  +g++vlDv   +G   i a++ ga+k+v +  D  Avk  ++N++lN+++++  ++l+ ++ k       +e++d
  gi|118430899|ref|NP_146994.2| 214 ARVAGPGDSVLDVFSYTGGFGIHALLSGASKAVFIEEDAHAVKLLRKNLRLNGIQENKALILNTSIWKaiqagepRESFD 293
                                    56677899************************************************877766555553233444556666 PP

                           PrmA 229 vi 230
                                    ++
  gi|118430899|ref|NP_146994.2| 294 IV 295
                                    65 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   9.8e-07    0.0022      32     107 ..     220     301 ..     208     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.8e-07
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.......EEEEE-STTTTSTTS-EEEEEE- CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.......vevvasdvleeveekkfdlivsN 104
                                     ++vlD+ + +G  g++++    + + +++++da+A+++ ++nl+ n+++        + +++ + +  + ++fd++   
  gi|118430899|ref|NP_146994.2| 220 GDSVLDVFSYTGGFGIHALLSGAS-KAVFIEEDAHAVKLLRKNLRLNGIQenkalilNTSIWKAIQAGEPRESFDIVTVD 298
                                    567999999999999998876555.899*********************99997765566777777777899******** PP

                                    --S CS
                            MTS 105 PPf 107
                                    PP 
  gi|118430899|ref|NP_146994.2| 299 PPA 301
                                    **5 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     1e-05     0.023       8      52 ..      11      54 ..       9      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                                   HHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEE CS
                            PUA  8 gAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGla 52
                                   gA+ka ++g+s+     v+  g +  gd V+++d++g ++a+Gl 
  gi|118430899|ref|NP_146994.2| 11 GAAKA-ARGSSIIYRKWVRGTGGLISGDLVEVIDRNGSEIACGLW 54
                                   67777.66777777777777788********************86 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 ?   12.0   0.0   5.1e-05      0.11       3      80 ..     222     300 ..     220     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgv.sdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                     +lD+fs +GG  i+  l+  +k + ie + + +++  +N ++ g+ ++k  +   ++ ++++  + ++  +d+v + pP
  gi|118430899|ref|NP_146994.2| 222 SVLDVFSYTGGFGIHALLSgASKAVFIEEDAHAVKLLRKNLRLNGIqENKALILNTSIWKAIQAGEPRES-FDIVTVDPP 300
                                    58************988884567899********************555666666777777777666666.899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2884.89
//
Query:       gi|14600480|ref|NP_146995.1|  [L=180]
Description: DtxR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-10   39.2   0.0    9.5e-10   38.4   0.0    1.4  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    1.5e-09   37.9   0.0    2.8e-09   37.1   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    3.4e-05   23.6   0.0    0.00022   21.0   0.0    2.2  2  MarR_2          MarR family
      8e-05   22.5   0.0    0.00013   21.8   0.0    1.4  1  MarR            MarR family
     0.0021   17.7   0.5        1.4    8.6   0.2    2.4  2  DUF3096         Protein of unknown function (DUF3096)
     0.0056   16.4   0.0      0.011   15.5   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0062   16.1   0.1      0.025   14.2   0.0    2.1  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.051   13.6   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.029   14.1   0.1       0.07   12.9   0.1    1.6  1  HTH_38          Helix-turn-helix domain
      0.033   14.0   0.1       0.14   12.0   0.0    2.0  2  HTH_23          Homeodomain-like domain
      0.073   12.6   0.0       0.18   11.3   0.0    1.6  1  GerE            Bacterial regulatory proteins, luxR family
       0.12   12.2   0.1       0.71    9.8   0.1    2.2  1  HTH_5           Bacterial regulatory protein, arsR family
       0.13   12.2   0.0       0.32   10.9   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB


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 !   38.4   0.0   6.9e-13   9.5e-10       1      69 [.      80     147 ..      80     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.9e-13
                                   -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B-- CS
                 Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpip 69 
                                   Te+G ++  + + +  +le++L++  gvd ++      r+   ls+e +  l++ lg p++cPh +pi+
  gi|14600480|ref|NP_146995.1|  80 TEQGLKILSNYLWKSAILEVLLAR-AGVDIDNCRGMGLRMAEGLSDEDAWILYKVLGEPKYCPHKKPII 147
                                   9*********************99.******************************************95 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 !   37.1   0.0     2e-12   2.8e-09       8      59 ..      23      76 ..      19      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 2e-12
                                  HHHHHHHHHHH..HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                Fe_dep_repress  8 dYLetIYtlse..ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                   YL +IY l++  ++++++  ++a+ L+vsps+Vs m ++L+ +G+ve  +  g
  gi|14600480|ref|NP_146995.1| 23 HYLMAIYLLNGlpGGEYARFIKIARLLDVSPSTVSIMTRRLQMKGLVELIPNMG 76
                                  7***********99*********************************9888776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-07   0.00022      23      56 ..      41      74 ..      19      76 .. 0.83
   2 ?   -0.2   0.0       0.7   9.6e+02      10      34 ..     129     167 ..     120     168 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-07
                                  EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                        MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                  +   +ar l++s+s+vs + +rL+ +GLve  p+
  gi|14600480|ref|NP_146995.1| 41 RFIKIARLLDVSPSTVSIMTRRLQMKGLVELIPN 74
                                  56679*************************8775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.7
                                   HHHHHHCTTTS...............EEEHHHHHHHHTSS CS
                        MarR_2  10 vLaaLgrrpgr...............dltvgelarrlgls 34 
                                   +L+ +  +p +               + +++++a  +g+s
  gi|14600480|ref|NP_146995.1| 129 ILYKVLGEPKYcphkkpiippdeinaE-NARQIALCCGIS 167
                                   555555555555555555555555333.789999999997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   9.8e-08   0.00013      19      48 ..      41      70 ..      22      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.8e-08
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGlie 48
                                  + +++a+ l vs+stv+ +++rL  kGl+e
  gi|14600480|ref|NP_146995.1| 41 RFIKIARLLDVSPSTVSIMTRRLQMKGLVE 70
                                  5679************************98 PP

>> DUF3096  Protein of unknown function (DUF3096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2     0.001       1.4      16      27 ..      20      31 ..      19      36 .. 0.88
   2 !    6.9   0.0    0.0036         5       3      15 ..     160     172 ..     159     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                       DUF3096 16 RLLNyiVAiYLI 27
                                  R+L y++AiYL+
  gi|14600480|ref|NP_146995.1| 20 RILHYLMAIYLL 31
                                  89********96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0036
                       DUF3096   3 vALiaGiLILimP 15 
                                   +AL +Gi IL +P
  gi|14600480|ref|NP_146995.1| 160 IALCCGISILQIP 172
                                   8*********999 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   7.8e-06     0.011      20      50 ..      41      71 ..      22      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.8e-06
                                  BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyveq 50
                                  ++  +Ar +++++Stv+ +++ L+  G+ve 
  gi|14600480|ref|NP_146995.1| 41 RFIKIARLLDVSPSTVSIMTRRLQMKGLVEL 71
                                  6678*************************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 !   14.2   0.0   1.8e-05     0.025      23      48 .]      45      70 ..      42      70 .. 0.95
   2 ?   -3.8   0.0       7.3     1e+04       8      14 ..      96     102 ..      95     105 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                        HTH_24 23 LAerlglSpstvnrrlkrLeeeGlIk 48
                                  +A+ l++Spstv+   +rL+ +Gl++
  gi|14600480|ref|NP_146995.1| 45 IARLLDVSPSTVSIMTRRLQMKGLVE 70
                                  9***********************96 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.3
                        HTH_24   8 ILelLqk 14 
                                   ILe+L +
  gi|14600480|ref|NP_146995.1|  96 ILEVLLA 102
                                   9999876 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 ?   13.6   0.0   3.7e-05     0.051      27      54 ..      45      74 ..      19      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
                                  HHHHTTSSHHHHHHHHHHHHHTTSEE.E.T CS
                     HTH_Crp_2 27 lAsmlGltretvsrilseLkreglis.r.g 54
                                  +A++l ++++tvs + ++L+ +gl++   +
  gi|14600480|ref|NP_146995.1| 45 IARLLDVSPSTVSIMTRRLQMKGLVElIpN 74
                                  9************************95324 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.1e-05      0.07      25      38 ..      44      57 ..      39      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                        HTH_38 25 eIArrLgrspsTIs 38
                                  +IAr+L++spsT+s
  gi|14600480|ref|NP_146995.1| 44 KIARLLDVSPSTVS 57
                                  8************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.14      22      45 ..      44      67 ..      41      72 .. 0.82
   2 ?   -1.8   0.1       2.1   2.9e+03      21      30 ..     158     167 ..     155     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                        HTH_23 22 eIAreLgvsrrTvyrwlkryre.eG 45
                                  +IAr+L+vs++Tv+   +r  + +G
  gi|14600480|ref|NP_146995.1| 44 KIARLLDVSPSTVSIMTRRL-QmKG 67
                                  6************9887775.4455 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.1
                        HTH_23  21 reIAreLgvs 30 
                                   r+IA  +g+s
  gi|14600480|ref|NP_146995.1| 158 RQIALCCGIS 167
                                   8999999998 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.18      22      44 ..      44      66 ..      41      71 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                  HHHHHHTS-HHHHHHHHHHHHHH CS
                          GerE 22 eIAeelniSekTVkvhksnimkK 44
                                  +IA+ l++S+ TV++  +++++K
  gi|14600480|ref|NP_146995.1| 44 KIARLLDVSPSTVSIMTRRLQMK 66
                                  6******************9998 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 ?    9.8   0.1   0.00051      0.71      13      43 ..      33      67 ..      15      70 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00051
                                  T...SS.EEHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                         HTH_5 13 e...ge.lcvcelaeelglsqstvShHLkkLreaG 43
                                      ge + +  +a+ l++s+stvS   ++L   G
  gi|14600480|ref|NP_146995.1| 33 GlpgGEyARFIKIARLLDVSPSTVSIMTRRLQMKG 67
                                  355566667778************96555555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.32      27      55 ..      44      72 ..      38      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                  HHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 27 eiaeelgvprskvYevLrsLedkGlVere 55
                                  +ia+ l+v+ s+v  + r+L  kGlVe +
  gi|14600480|ref|NP_146995.1| 44 KIARLLDVSPSTVSIMTRRLQMKGLVELI 72
                                  699***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1333.66
//
Query:       gi|118430900|ref|NP_146996.2|  [L=223]
Description: hypothetical protein APE_0143.1 [Aeropyrum pernix K1]
Scores for 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-07   29.0   1.7    9.1e-07   28.6   1.7    1.1  1  Snf7             Snf7
     0.0072   16.4   0.0        1.1    9.4   0.0    2.2  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
  ------ inclusion threshold ------
      0.099   11.4   0.1       0.14   11.0   0.1    1.2  1  RHSP             Retrotransposon hot spot protein
       0.12   13.1   0.2       0.27   12.0   0.2    1.5  1  Phage_int_SAM_2  Phage integrase, N-terminal


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 !   28.6   1.7     2e-10   9.1e-07      13     170 ..      38     206 ..      34     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHCTT-..............HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Snf7  13 ldkkqeslekkikkleaelkklakkgn..............kdralllLKqkkryekqldqldnqlanleqvslaienlk 78 
                                    + +   +++ +i+kl+ +l+kl+   +              k +a  +++++ + +k+ + + ++++ le v+l +e+++
  gi|118430900|ref|NP_146996.2|  38 IIQAVYRIQGQISKLDYSLAKLQSYDKmlfekvvnslvegdKSKATMYANELAEVRKMAKVIITVRYALERVRLRLETAM 117
                                    55555566666666666666666665555555555566666*************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHCTCCHHHHHHHHH.HHHHHHHHTCHHHHHHHHHTT-.GGTTHHHHHHHHHHHHHHHHHC CS
                           Snf7  79 snkevlnamkqgakamkamnkkvdidkidklmde.iedqmekaeeisEalsrsldda.deedEeeleaeLdaLeqelgde 156
                                    +  +v +++  +  a+k++   ++      +m + +++ me+ e ++ a+ +    +  + d + + +e ++++++  + 
  gi|118430900|ref|NP_146996.2| 118 VFGDVNATLAPAIVALKQVAGHLK-----GMMPDvFTELMEVDESLQAAMMQMTAHVpIALDNAYVSEEASKILKDASIV 192
                                    *********************999.....666552799999999999988777777779***************998888 PP

                                    SH.HHHHHHHTXXX CS
                           Snf7 157 elldesvklpevPs 170
                                     ++  +++ p++Ps
  gi|118430900|ref|NP_146996.2| 193 AEQRLKEHFPDLPS 206
                                    87789999999998 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 !    4.9   0.0    0.0055        25      32      72 ..      34      74 ..      31      95 .. 0.78
   2 !    9.4   0.0   0.00023       1.1      25      89 ..     111     175 ..     104     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0055
                   Baculo_PEP_C 32 ilaqlatlldaietqLnalsedlksllaeldtrldtlltnL 72
                                   i +q+ +++  i++q+++l+ +l +l +  +  ++++++ L
  gi|118430900|ref|NP_146996.2| 34 IRNQIIQAVYRIQGQISKLDYSLAKLQSYDKMLFEKVVNSL 74
                                   67899999999*******99999996554444555566555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00023
                   Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtn 89 
                                    +rl ++ + ++++++l+     L++++ +lk +++++ t+l ++ + L++a+ +++  +  +L+n
  gi|118430900|ref|NP_146996.2| 111 LRLETAMVFGDVNATLAPAIVALKQVAGHLKGMMPDVFTELMEVDESLQAAMMQMTAHVPIALDN 175
                                    57778889999999999999999999999999999999999999999999999999888888877 PP

>> RHSP  Retrotransposon hot spot protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   3.1e-05      0.14     275     362 ..       8      94 ..       3     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                           RHSP 275 eeskpseakikveseWqeikgrikkvGPllrqile.eesykrrvakieeavdeissvdkesyakvlqtaaeWetdkvser 353
                                    ++++p e+    e+  q++++ i    P+  qi++   + +++++k++  ++++ s+dk  + kv+++ +e ++ k++ +
  gi|118430900|ref|NP_146996.2|   8 KKWNPPEST--TETVGQKLRNFISPPPPIRNQIIQaVYRIQGQISKLDYSLAKLQSYDKMLFEKVVNSLVEGDKSKATMY 85 
                                    567777776..788999*****************9778999*************************************99 PP

                           RHSP 354 larvvrvkk 362
                                       +  v+k
  gi|118430900|ref|NP_146996.2|  86 ANELAEVRK 94 
                                    888887776 PP

>> Phage_int_SAM_2  Phage integrase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     6e-05      0.27      23      85 ..      36      99 ..      34     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                Phage_int_SAM_2 23 ndrerilqrlareLlalniqvrdvkslKarHieayieerlaeeiskrtl.qNemaalRsvlrka 85
                                   n+ ++ + r+  ++ +l++ + + +s      e+ +++  + ++sk+t+  Ne+a +R +++ +
  gi|118430900|ref|NP_146996.2| 36 NQIIQAVYRIQGQISKLDYSLAKLQSYDKMLFEKVVNSLVEGDKSKATMyANELAEVRKMAKVI 99
                                   777888999999************************************956*******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1754.53
//
Query:       gi|14600482|ref|NP_146997.1|  [L=246]
Description: hypothetical protein APE_0145 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-32  109.6   8.8    9.6e-32  109.4   8.0    1.5  2  CdvA             CdvA-like coiled-coil domain
     0.0039   17.2   4.3     0.0081   16.2   0.5    2.4  3  DUF1664          Protein of unknown function (DUF1664)
  ------ inclusion threshold ------
      0.026   14.8   7.3        4.1    7.7   5.9    3.0  3  DUF5082          Domain of unknown function (DUF5082)
      0.051   13.3   1.1      0.071   12.8   1.1    1.3  1  DUF2228          Uncharacterised conserved protein (DUF2228)
      0.073   12.9   2.1       0.11   12.3   1.1    1.8  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.076   11.9   1.2       0.11   11.4   1.2    1.2  1  LMBR1            LMBR1-like membrane protein
       0.12   11.9   3.4        1.8    8.1   0.4    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.16   12.4   6.3       0.47   10.8   1.2    2.2  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.19   12.2   3.7       0.34   11.3   3.7    1.4  1  DUF1690          Protein of Unknown function (DUF1690)
       0.19   12.1   6.4        2.2    8.6   0.2    2.2  2  OmpH             Outer membrane protein (OmpH-like)
       0.24   11.4   5.9        1.1    9.1   3.1    2.1  2  Ax_dynein_light  Axonemal dynein light chain
       0.49   11.0   3.6       0.56   10.9   0.5    2.1  2  YabA             Initiation control protein YabA
       0.58   10.8   5.3        4.4    8.0   2.7    2.2  2  KfrA_N           Plasmid replication region DNA-binding N-ter
       0.77    9.3   3.5       0.59    9.7   1.3    1.8  2  Fzo_mitofusin    fzo-like conserved region
          1    9.4   6.8       0.76    9.9   1.1    2.5  3  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
        1.5    9.4   4.3        8.8    6.9   0.5    2.6  2  YtxH             YtxH-like protein


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 ?   -2.6   0.0       4.2   4.7e+03      36      62 ..      18      44 ..      14      53 .. 0.52
   2 !  109.4   8.0   8.6e-35   9.6e-32       1     116 [.      87     202 ..      87     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.2
                          CdvA 36 ekakelkeklkkrlkeledqiksleka 62
                                  ++ + +  +l +  + ++ +i+s+e  
  gi|14600482|ref|NP_146997.1| 18 DEYERVVGTLVSFSSNVDGEIQSIELK 44
                                  444444444444445555555555554 PP

  == domain 2  score: 109.4 bits;  conditional E-value: 8.6e-35
                          CdvA   1 krkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYk 81 
                                   kr++A e++ ++  ip+s +e++k++l+e++k+lk ka+e k ++k+r++e++d++ +++ a+anl++ y+sGEi++++Y+
  gi|14600482|ref|NP_146997.1|  87 KRRRAVENIAKQSSIPSSIVENMKRQLTEEIKRLKIKAEEAKTRIKERIAEIDDEMLHIAGATANLQMLYFSGEISDRSYT 167
                                   8******************************************************************************** PP

                          CdvA  82 saieairellesaleekeeikklleklskleleee 116
                                   s ++++r+l +s+++ek+++k++l+kl+k  ++ +
  gi|14600482|ref|NP_146997.1| 168 SGMNHLRKLNDSLEREKSDAKRVLDKLEKTYEAAT 202
                                   ***************************76655444 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.2   8.1e+03      95     120 ..      30      41 ..      14      46 .. 0.44
   2 !   16.2   0.5   7.2e-06    0.0081      41     106 ..      90     152 ..      86     158 .. 0.81
   3 ?    1.9   0.0      0.19   2.1e+02      48      81 ..     171     204 ..     163     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.2
                       DUF1664  95 dlseigedvesvkeavegleskleri 120
                                     s+++ +++s              i
  gi|14600482|ref|NP_146997.1|  30 FSSNVDGEIQS--------------I 41 
                                   33333333333..............3 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.2e-06
                       DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                    ave+++kq    s+ +++ kr+L+++i+r+  k +e k   + ike ++e+ +++ +i     ++
  gi|14600482|ref|NP_146997.1|  90 RAVENIAKQSSIPSSIVENMKRQLTEEIKRLKIKAEEAK---TRIKERIAEIDDEMLHIAGATANL 152
                                   6999*****9999********************999865...566677777777777666655554 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.19
                       DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkei 81 
                                   ++l ++ +sl++ k + ++ +d+++k+ ++ +++
  gi|14600482|ref|NP_146997.1| 171 NHLRKLNDSLEREKSDAKRVLDKLEKTYEAATNV 204
                                   7899999999999999999999999999988776 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.027        30      73     105 ..      14      46 ..       4      50 .. 0.84
   2 ?   -2.1   0.0         4   4.4e+03      26      46 ..      79      99 ..      77     103 .. 0.80
   3 ?    7.7   5.9    0.0037       4.1      16      56 ..     107     151 ..      86     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.027
                       DUF5082  73 snlessyqtyvdkldelidaieeEIerLenqis 105
                                   s++ ++y+++v  l +  ++++ EI+ +e +i 
  gi|14600482|ref|NP_146997.1|  14 SEVRDEYERVVGTLVSFSSNVDGEIQSIELKIV 46 
                                   38999************************9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                       DUF5082 26 IerLkeaktklsdekeslkqk 46
                                  Ie L++a+++  ++++ +kq+
  gi|14600482|ref|NP_146997.1| 79 IEALERAYKRRRAVENIAKQS 99
                                  889999998888888877765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0037
                       DUF5082  16 rseiaaleekIerLk....eaktklsdekeslkqkkkklekplns 56 
                                   ++  ++l e I+rLk    eakt++++  ++++++   +++  ++
  gi|14600482|ref|NP_146997.1| 107 ENMKRQLTEEIKRLKikaeEAKTRIKERIAEIDDEMLHIAGATAN 151
                                   455667777777777777777777777777777776666655544 PP

>> DUF2228  Uncharacterised conserved protein (DUF2228)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.1   6.3e-05     0.071      80     196 ..      74     196 ..      58     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                       DUF2228  80 vgdnlfaavkkflekklkkkdk.....kkkkelkklkkklekfakekeisleqkteklkkRkkkvvaktfhgaGivvpvdk 155
                                    +  +++a++   +++ + ++        +++++++k +l++  k+ +i+ e++++ +k+R +++  + +h aG   +++ 
  gi|14600482|ref|NP_146997.1|  74 EATRVIEALERAYKRRRAVENIakqssIPSSIVENMKRQLTEEIKRLKIKAEEAKTRIKERIAEIDDEMLHIAGATANLQM 154
                                   556666666665555544444343333778899****************************************98877543 PP

                       DUF2228 156 ...ktdvGYReLsesdaelkkllkkieeakneeerekaleklqe 196
                                       +++  R+ +   ++l+kl +++e+ k  ++ +++l+kl++
  gi|14600482|ref|NP_146997.1| 155 lyfSGEISDRSYTSGMNHLRKLNDSLEREK--SDAKRVLDKLEK 196
                                   111455667777777777777777777776..444555555555 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 ?   12.3   1.1   9.8e-05      0.11      85     154 ..      82     152 ..      61     163 .. 0.82
   2 ?   -2.3   0.0         3   3.3e+03      88     109 ..     184     205 ..     168     223 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-05
                                   HHHHHHHHHHH..............HHHHHHHHHHHHHHH.HHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  85 aqaakeiealiieiqkeindsvesleetrqrveegselve.etgealkeiveavaevadlvqeiaaaseeq 154
                                    ++a + ++++++i k++    +++e+ +++  e  +  + +++ea  +i e++ae++d++  ia a++++
  gi|14600482|ref|NP_146997.1|  82 LERAYKRRRAVENIAKQSSIPSSIVENMKRQLTEEIKRLKiKAEEAKTRIKERIAEIDDEMLHIAGATANL 152
                                   456777788999***************999988887776548899999*****************999875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3
                                   HHHHHHHH.............. CS
                     MCPsignal  88 akeiealiieiqkeindsvesl 109
                                     + ++++ +++k  + ++++l
  gi|14600482|ref|NP_146997.1| 184 KSDAKRVLDKLEKTYEAATNVL 205
                                   3333344444444444444444 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   9.8e-05      0.11     185     300 ..     100     200 ..      98     230 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.8e-05
                         LMBR1 185 elPrslwreiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklksn 265
                                   ++P s++ ++k++l ee+k+l+++a++ +t+ +e   e++d + +++ ++ +++               +  ei+++  + 
  gi|14600482|ref|NP_146997.1| 100 SIPSSIVENMKRQLTEEIKRLKIKAEEAKTRIKERIAEIDDEMLHIAGATANLQMLY------------FSGEISDRSYT- 167
                                   58999*******************************999999999998888775544............23333333222. PP

                         LMBR1 266 enkteeslaklekqlikalqkrertekqwkrllek 300
                                     + +++l kl+ +l ++ ++ +r  +++++  e 
  gi|14600482|ref|NP_146997.1| 168 --SGMNHLRKLNDSLEREKSDAKRVLDKLEKTYEA 200
                                   ..223344444444444444444444444444444 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 ?    8.1   0.4    0.0016       1.8     111     161 ..     106     156 ..      79     168 .. 0.84
   2 ?    4.9   0.2     0.015        17     127     161 ..     171     205 ..     162     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                  HAUS-augmin3 111 lqqelrkleeeekeakkklkeaqeelraenaetnavLqqlteeakqlaeyf 161
                                    ++ +r+l+ee k  k k +ea+  +++++ae++ ++  ++ ++ +l   +
  gi|14600482|ref|NP_146997.1| 106 VENMKRQLTEEIKRLKIKAEEAKTRIKERIAEIDDEMLHIAGATANLQMLY 156
                                   67899******************************9999999888876544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.015
                  HAUS-augmin3 127 kklkeaqeelraenaetnavLqqlteeakqlaeyf 161
                                   ++l++++++l++e +++++vL++l ++ +  ++ +
  gi|14600482|ref|NP_146997.1| 171 NHLRKLNDSLEREKSDAKRVLDKLEKTYEAATNVL 205
                                   68999999999999999999999988665555554 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 ?   10.8   1.2   0.00042      0.47      39      87 ..      95     143 ..      71     154 .. 0.76
   2 ?    4.2   0.3     0.046        52       8      35 ..     175     202 ..     163     228 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                   Uso1_p115_C  39 akkaaesqakeleaenkklekeleklraelkeekekekekqkEldDLLl 87 
                                     k+++  ++ +e+++ +l++e++ l+ +++e+k + ke  +E+dD +l
  gi|14600482|ref|NP_146997.1|  95 IAKQSSIPSSIVENMKRQLTEEIKRLKIKAEEAKTRIKERIAEIDDEML 143
                                   3445566677899999*****************************9777 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.046
                   Uso1_p115_C   8 seaaslkdeneklkaelqslskalesle 35 
                                   + + sl++e++++k  l++l+k +e + 
  gi|14600482|ref|NP_146997.1| 175 KLNDSLEREKSDAKRVLDKLEKTYEAAT 202
                                   3444455555555555555555554443 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.7    0.0003      0.34       6     113 ..      98     200 ..      93     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                       DUF1690   6 piqfSqslvsqLessketdasraqalekliqerVaeeLkkLraeeeetlkkfeeklekellkdeadakdelsskalnekie 86 
                                   + ++ +s+v++++++  ++ +r +   +  + r++e+++++   + e l+ + ++ + ++l  +  + +  s ++ ++ ++
  gi|14600482|ref|NP_146997.1|  98 QSSIPSSIVENMKRQLTEEIKRLKIKAEEAKTRIKERIAEI---DDEMLHIAGATANLQMLYFS-GEISDRSYTSGMNHLR 174
                                   566778999999999999999*99999999***********...77777777777777777776.46889999999***** PP

                       DUF1690  87 eLrkkleefkkkeeeklpeeveearee 113
                                   +L++ le+ +k++ ++  +++e++ e+
  gi|14600482|ref|NP_146997.1| 175 KLNDSLER-EKSDAKRVLDKLEKTYEA 200
                                   ********.555555777777765554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.9     0.016        18      11      66 ..      82     139 ..      76     156 .. 0.70
   2 ?    8.6   0.2     0.002       2.2      14      70 ..     170     224 ..     165     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                                   HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...-HHHHHHHH CS
                          OmpH  11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e.keekeqelq 66 
                                   le   ++++a e+++k+++     +e+++++l++++++l+ ka+++ +  +e+  e++
  gi|14600482|ref|NP_146997.1|  82 LERAYKRRRAVENIAKQSSIPSSIVENMKRQLTEEIKRLKIKAEEAkTrIKERIAEID 139
                                   6666777888999999998888899999999999999998666664224344433343 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHH CS
                          OmpH  14 spegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeq 70 
                                   ++  ++ ++ le+++++ +  l+++ek ++++ + l++ a++  k+e e+ +q+k +
  gi|14600482|ref|NP_146997.1| 170 MNHLRKLNDSLEREKSDAKRVLDKLEKTYEAATNVLEAPAPS--KPEGEKSIQAKGE 224
                                   6777889999999999999***********999999988887..8999999999876 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.1     0.001       1.1     108     162 ..      85     137 ..      73     145 .. 0.87
   2 ?    2.7   0.0     0.095   1.1e+02     128     159 ..     170     201 ..     157     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
               Ax_dynein_light 108 aFgmrkalqaeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqe 162
                                   a++ r+a+++  ++s + + i  +e+ k++l+++++ lk k+e+++ r ker +e
  gi|14600482|ref|NP_146997.1|  85 AYKRRRAVENIAKQSSIPSSI--VENMKRQLTEEIKRLKIKAEEAKTRIKERIAE 137
                                   788899999999999999997..99**************************9876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.095
               Ax_dynein_light 128 ikeLeeekeelekqvaelkaklealekreker 159
                                   +++L++ +++le++ ++ k+ l++lek  +  
  gi|14600482|ref|NP_146997.1| 170 MNHLRKLNDSLEREKSDAKRVLDKLEKTYEAA 201
                                   55666667777777777777777777666554 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5    0.0005      0.56      21      80 ..     103     159 ..      85     171 .. 0.80
   2 ?    0.6   0.1      0.77   8.6e+02      33      58 ..     172     197 ..     164     209 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA  21 leeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlYeeG 80 
                                   ++ +e++k+   +l+ee ++L++  e+ ++r++e+ ++ +++  ++  +  nL++lY  G
  gi|14600482|ref|NP_146997.1| 103 SSIVENMKR---QLTEEIKRLKIKAEEAKTRIKERIAEIDDEMLHIAGATANLQMLYFSG 159
                                   444444444...5678999**************************************887 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.77
                                   HHHHHHHHHHHHHHHHHHHHXXXXXX CS
                          YabA  33 elleenaeLeleneklrerleeeekk 58 
                                   +l + n++Le e++  ++ l++ ek+
  gi|14600482|ref|NP_146997.1| 172 HLRKLNDSLEREKSDAKRVLDKLEKT 197
                                   34444555555555555554333322 PP

>> KfrA_N  Plasmid replication region DNA-binding N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.7    0.0039       4.4      38     111 ..      77     152 ..      74     155 .. 0.67
   2 ?    3.2   0.0      0.12   1.4e+02      80     107 ..     177     204 ..     161     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                        KfrA_N  38 rvlkeweaelaaalaaraa...pelPealaeallaalwqaaleeaeeelaaaraelqaaraaleaeraeaearveel 111
                                   rv++++e++ ++++a++     +++P  ++e + ++l ++ +++   + ++a++++++++a+++ e   ++ ++++l
  gi|14600482|ref|NP_146997.1|  77 RVIEALERAYKRRRAVENIakqSSIPSSIVENMKRQLTEEIKRLK-IKAEEAKTRIKERIAEIDDEMLHIAGATANL 152
                                   55666666555555544334578**********555555555554.4588999999999999998886665555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                        KfrA_N  80 eeelaaaraelqaaraaleaeraeaear 107
                                   +++l+++++++++  ++le++ ++a++ 
  gi|14600482|ref|NP_146997.1| 177 NDSLEREKSDAKRVLDKLEKTYEAATNV 204
                                   5678888888888888888887777665 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.3   0.00053      0.59      87     141 ..     102     155 ..      72     165 .. 0.76
   2 ?   -1.4   0.0       1.3   1.5e+03     112     136 ..     175     199 ..     161     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                 Fzo_mitofusin  87 tsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakll 141
                                    s ++ + ++++l++ ++rl+ + +e+++ ++e+i+e++ e+ +++ ++ ++++l
  gi|14600482|ref|NP_146997.1| 102 PS-SIVENMKRQLTEEIKRLKIKAEEAKTRIKERIAEIDDEMLHIAGATANLQML 155
                                   33.334567888899999************************9999998888776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                 Fzo_mitofusin 112 etekeleeeikelekeiekleevqk 136
                                   + +++le+e ++ ++ ++kle++ +
  gi|14600482|ref|NP_146997.1| 175 KLNDSLEREKSDAKRVLDKLEKTYE 199
                                   4455666666666666677766655 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 ?   -2.5   0.0       4.4     5e+03      27      50 ..      16      39 ..      13      45 .. 0.65
   2 ?    9.9   1.1   0.00068      0.76      24      88 ..      68     134 ..      64     153 .. 0.61
   3 ?    2.1   0.3      0.17   1.9e+02      44      87 ..     175     221 ..     167     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.4
                     ApoLp-III 27 iKensenlvdqlkqvikslqeelk 50
                                  ++++ e +v  l +++++++ e++
  gi|14600482|ref|NP_146997.1| 16 VRDEYERVVGTLVSFSSNVDGEIQ 39
                                  555566667777777777776664 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00068
                     ApoLp-III  24 vetiKensenlvdqlkqviks..lqeelkkksdeleealkevkkkieetadklseenPevkkkaqel 88 
                                   v ++K +++ +++ l+   k   + e+++k+s++  ++++++k +++e  + l+ +  e+k  ++e 
  gi|14600482|ref|NP_146997.1|  68 VPEWKYEATRVIEALERAYKRrrAVENIAKQSSIPSSIVENMKRQLTEEIKRLKIKAEEAKTRIKER 134
                                   5566666666666666665541144667777777777777777777777777766555555555543 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.17
                     ApoLp-III  44 slqeelkkksdeleealkevkkkieetadklse...enPevkkkaqe 87 
                                   +l+++l ++ + ++++l+ + k  e +++ l++   ++Pe +k++q+
  gi|14600482|ref|NP_146997.1| 175 KLNDSLEREKSDAKRVLDKLEKTYEAATNVLEApapSKPEGEKSIQA 221
                                   56777888888888888888888888777777777778888877775 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0079       8.8      35      72 ..     107     140 ..      70     148 .. 0.62
   2 ?    3.4   0.2       0.1   1.2e+02      28      53 ..     174     202 ..     167     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0079
                          YtxH  35 ddlkekakelleeakekakekaedlkekvkekadelke 72 
                                   +++k +++e ++++    k kae++k+ +ke++ e+ +
  gi|14600482|ref|NP_146997.1| 107 ENMKRQLTEEIKRL----KIKAEEAKTRIKERIAEIDD 140
                                   33333333333333....55566666666666555544 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                          YtxH  28 kdlkekaddlkekakelleeakeka...k 53 
                                   ++l+++++  k +ak++l++++++    +
  gi|14600482|ref|NP_146997.1| 174 RKLNDSLEREKSDAKRVLDKLEKTYeaaT 202
                                   78999999999999999888866654430 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1788  (0.0997267); expected 358.6 (0.02)
Passed bias filter:                      925  (0.0515924); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 1777.46
//
Query:       gi|118430901|ref|NP_146998.2|  [L=279]
Description: pyrroline-5-carboxylate reductase [Aeropyrum pernix K1]
Scores for 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  103.7   0.4    9.8e-30  102.9   0.4    1.5  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
    1.1e-17   64.4   0.5    2.4e-17   63.3   0.5    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.2e-07   31.5   0.9      5e-07   29.5   0.9    1.9  1  ApbA             Ketopantoate reductase PanE/ApbA
    0.00011   21.7   0.1    0.00017   21.0   0.1    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00035   20.8   0.1    0.00055   20.1   0.1    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0037   17.1   2.1     0.0073   16.2   2.1    1.5  1  Rossmann-like    Rossmann-like domain
     0.0041   16.4   1.4     0.0064   15.8   1.4    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0058   15.7   0.0      0.024   13.6   0.0    1.8  2  PDH              Prephenate dehydrogenase
     0.0074   16.3   1.0       0.93    9.5   1.0    2.2  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
  ------ inclusion threshold ------
       0.02   14.9   0.1      0.063   13.3   0.1    1.9  1  ADH_zinc_N       Zinc-binding dehydrogenase
      0.094   12.6   0.7       0.31   10.9   0.7    1.8  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
        1.3    9.5   4.6        5.7    7.4   0.0    3.1  3  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9   0.4   6.5e-33   9.8e-30       1     101 [.     160     262 ..     160     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 6.5e-33
                                    CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHHHHH CS
                     P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTiaglk 78 
                                    E+ +d++tal Gs+pAyv+++i++l+ +gv +Gl+re+A + ++ t+  +a+ l +++  p++lrd+vt+p+GtTi+glk
  gi|118430901|ref|NP_146998.2| 160 EEWMDVWTALVGSMPAYVAVMIDSLTLGGVSAGLPREVAFKAVIDTLGATAEHLGKRDihPSVLRDEVTTPAGTTIEGLK 239
                                    788*************************************************98766689******************** PP

                                    HHHHTTHHHHHHHHHHHHHHHHH CS
                     P5CR_dimer  79 eleegglraavieaveaaakrsk 101
                                    ++e +g++aa+i++veaaa+r++
  gi|118430901|ref|NP_146998.2| 240 VIEGEGVDAALIRTVEAAARRAA 262
                                    *********************86 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.5   1.6e-20   2.4e-17       1      97 []      11     100 ..      11     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.6e-20
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80 
                                    +++++G G++g a+++ ll++g     +v ++ r  e++e + ++lg+++t  dn  aa+ +dvv+l+vkp++++ +l+e
  gi|118430901|ref|NP_146998.2|  11 RVAVLGVGKIGGAIVKSLLSCG----AVVTGTGRRRETLERI-SRLGAEATV-DNRLAAKVSDVVILSVKPYQLPRLLEE 84 
                                    69********************....6666*********999.66799***9.*************************** PP

                                    CGHHHHTTSEEEEESSS CS
                  F420_oxidored  81 lakdalkgklvisvlag 97 
                                    + +d  +gk+v+sv+ag
  gi|118430901|ref|NP_146998.2|  85 I-RDVMEGKIVVSVVAG 100
                                    *.9***********997 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.9   3.3e-10     5e-07       1     123 [.      12     118 ..      12     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.3e-10
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGG CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKay 79 
                                    +a+lG G iG+ +  +L   ga vt  +r+r  le++++ G + t ++       + a+           d+vi++vK y
  gi|118430901|ref|NP_146998.2|  12 VAVLGVGKIGGAIVKSLLSCGAVVTGTGRRReTLERISRLGAEATVDN-------RLAAK--------VSDVVILSVKPY 76 
                                    69***************************************9988888.......33333........4599******** PP

                                    GHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEE CS
                           ApbA  80 qteealeeikplldpntvvlllqNGlgheeelrealpkprvlgg 123
                                    q+   leei+++++ + +v+++  G++   +l  al  ++v+ +
  gi|118430901|ref|NP_146998.2|  77 QLPRLLEEIRDVMEGK-IVVSVVAGVRL-STLSRALEGSHVYRA 118
                                    ***************9.99999999875.345555555555555 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 !   21.0   0.1   1.1e-07   0.00017      35      99 ..       8      73 ..       2      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                   TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S CS
                   2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhl 99
                                   +g +v+++G+G+IG a+ k l + g+ v+++ r++++ e+ ++lg+e + +   + + sD+v+l +
  gi|118430901|ref|NP_146998.2|  8 KGLRVAVLGVGKIGGAIVKSLLSCGAVVTGTGRRRETLERISRLGAEATvDNRLAAKVSDVVILSV 73
                                   7899*******************************999999999*9555377778889****9987 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   3.7e-07   0.00055       2      75 ..      12      84 ..      11     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.7e-07
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
                  NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg 75
                                   ++++G+G++G  +++ ll+ g  v++  r++e +e++   ga+a+ + + +++  dvvi+ vk   +   ++e+
  gi|118430901|ref|NP_146998.2| 12 VAVLGVGKIGGAIVKSLLSCGAVVTGTGRRRETLERISRLGAEATVDNRLAAKVSDVVILSVKP-YQLPRLLEE 84
                                   89****************************************9999999888888******985.344445555 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.1   4.9e-06    0.0073      10     106 ..       9     100 ..       2     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
                  Rossmann-like  10 rlsvGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkgla 89 
                                     l v +++ G++G a+ ++l   g vv+g     ++ ++    rl   + ++ +  a+ +++++l+v   +lp l++++ 
  gi|118430901|ref|NP_146998.2|   9 GLRVAVLGVGKIGGAIVKSLLSCGAVVTGTGRRRETLERI--SRLGAEATVDNRLAAKVSDVVILSVKPYQLPRLLEEIR 86 
                                    5899*************************98877765543..46788888888889999*******************97 PP

                  Rossmann-like  90 atgavraGtivahtsga 106
                                          +G+iv+ + + 
  gi|118430901|ref|NP_146998.2|  87 DV---MEGKIVVSVVAG 100
                                    65...89***9987664 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.4   4.3e-06    0.0064      21      85 ..       4      65 ..       1     102 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.3e-06
                                   CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHH CS
                    AlaDh_PNT_C 21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeell 85
                                   G vp  +  +v v+G+G  G + ++   + ga+Vt +  r ++le+++ lga+  +v ++ ++++
  gi|118430901|ref|NP_146998.2|  4 GAVP--KGLRVAVLGVGKIGGAIVKSLLSCGAVVTGTGRRRETLERISRLGAE-ATVDNRLAAKV 65
                                   6677..7779******************************************9.55544333333 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.6e-05     0.024      12      83 ..      33     103 ..      25     118 .. 0.86
   2 ?   -1.0   0.0      0.46   6.9e+02     133     179 ..     136     181 ..     133     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                    SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--C CS
                            PDH  12 vtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKe 83 
                                      v+g+ +  e+ e+  +lg++ ++++   a+k  d+v+l+v + ++ + l+e+   ++ + ++  v++v+ 
  gi|118430901|ref|NP_146998.2|  33 AVVTGTGRRRETLERISRLGAEATVDN-RLAAKVSDVVILSVKPYQLPRLLEEIRDVMEGKIVVSVVAGVRL 103
                                    67999**********************.5888999*********************7777777777788875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.46
                                    TS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHHHH CS
                            PDH 133 ktdkealekvkelleevgarvilmspeeHDrvvavvshlphvvaial 179
                                    +t+ ++   v ++l  + + v+ ++ e  D  +a+v  +p  va+ +
  gi|118430901|ref|NP_146998.2| 136 YTGDKRASFVESILS-CMGSVYWIPEEWMDVWTALVGSMPAYVAVMI 181
                                    566666666666665.5567888999999***********9999866 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 !    9.5   1.0   0.00062      0.93       2     107 ..      12     102 ..      11     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00062
                                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHH CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqa 81 
                                    +avlG G+ G a+ k+l + g  v+  +r++e++e+i++                 +at d + a+k +d+++l v    
  gi|118430901|ref|NP_146998.2|  12 VAVLGVGKIGGAIVKSLLSCGAVVTGTGRRRETLERISRLGA--------------EATVDNRLAAKVSDVVILSVKPYQ 77 
                                    899999999999999999999999999999999988875432..............345555556666666666666666 PP

                                    HHHHHHHHCCC--TT-EEEE---SEE CS
                 NAD_Gly3P_dh_N  82 lrevlkklkgllkkkailvsliKGie 107
                                    l + l+++ +++ + +i+vs++ G+ 
  gi|118430901|ref|NP_146998.2|  78 LPRLLEEIRDVM-EGKIVVSVVAGVR 102
                                    666666666644.5556666666665 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.2e-05     0.063       2      54 ..      20      89 ..      16     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.2e-05
                                   HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEET................TTC.HHHHHHHHHT CS
                     ADH_zinc_N  2 vGlaavqlAkalGaeviavdsseeklelakklGadeviny................kea.dlverikelt 54
                                   +G a v+ +  +Ga v+++ + +e le   +lGa++++++                 +  +l e+i++  
  gi|118430901|ref|NP_146998.2| 20 IGGAIVKSLLSCGAVVTGTGRRRETLERISRLGAEATVDNrlaakvsdvvilsvkpYQLpRLLEEIRDVM 89
                                   57777888888999**************************666555555555554444444555555555 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 ?   10.9   0.7   0.00021      0.31       2      40 ..      12      50 ..      11      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                   vav+G G +G  i + ++s g  V+ + +++e+le+  +
  gi|118430901|ref|NP_146998.2| 12 VAVLGVGKIGGAIVKSLLSCGAVVTGTGRRRETLERISR 50
                                   9*******************************9998654 PP

>> 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 ?   -0.1   0.4      0.82   1.2e+03      35      62 ..       9      36 ..       1      39 [. 0.74
   2 ?    7.4   0.0    0.0038       5.7      38      81 ..      94     137 ..      87     148 .. 0.88
   3 ?    1.8   0.1      0.21   3.1e+02      29      56 ..     156     183 ..     142     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.82
                Phage_holin_5_1 35 wlptvsilvgailgalatsldgsgslat 62
                                    l    + vg i ga+  sl   g++ t
  gi|118430901|ref|NP_146998.2|  9 GLRVAVLGVGKIGGAIVKSLLSCGAVVT 36
                                   4555556699999999999999988766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0038
                Phage_holin_5_1  38 tvsilvgailgalatsldgsgslatmiwagalagaggtglfeqf 81 
                                     vs++ g  l +l+ +l+gs    +m    al g   t + e  
  gi|118430901|ref|NP_146998.2|  94 VVSVVAGVRLSTLSRALEGSHVYRAMPNINALIGRSTTAVAEYT 137
                                    599*******************************9999988755 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.21
                Phage_holin_5_1  29 elvpskwlptvsilvgailgalatsldg 56 
                                      +p  w+   + lvg++   +a ++d 
  gi|118430901|ref|NP_146998.2| 156 YWIPEEWMDVWTALVGSMPAYVAVMIDS 183
                                    5699************999988888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2073.88
//
Query:       gi|118430902|ref|NP_146999.2|  [L=183]
Description: hypothetical protein APE_0147.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-32  111.2   0.0    6.9e-32  111.0   0.0    1.0  1  Peptidase_M54  Peptidase family M54
    0.00028   20.8   0.0    0.00029   20.7   0.0    1.2  1  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
      0.024   13.6   0.0      0.029   13.3   0.0    1.1  1  Peptidase_M66  Peptidase M66
      0.026   13.7   0.4      0.034   13.3   0.4    1.2  1  CoiA           Competence protein CoiA-like family
      0.039   13.6   0.0      0.054   13.1   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
      0.042   12.5   0.1      0.058   12.0   0.1    1.1  1  Metallopep     Putative peptidase family
      0.046   14.2   0.0      0.056   14.0   0.0    1.2  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
       0.11   12.6   0.0       0.14   12.3   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12
       0.17   11.8   0.0       0.25   11.2   0.0    1.3  1  Peptidase_M43  Pregnancy-associated plasma protein-A


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 !  111.0   0.0   3.5e-35   6.9e-32      57     192 ..      46     174 ..      18     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 3.5e-35
                                    .GGGEETTTTEEEHHHHHHHHHT--S--..SEE........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T--..... CS
                  Peptidase_M54  57 eegavkmyrleavveallgkLkemkddvndDsitkifgittlplgsrdqyidiykkvlGievsiGnyavlalsikefyte 136
                                     ++a++++r+++++e++ ++++++      D +    gi  +++ + d yi+++++v+G++ +     v ++    + t 
  gi|118430902|ref|NP_146999.2|  46 PIEAYSWERMQFDAEKVNEHIHSVLY----DYV--REGIRIIGVVDADGYIPGFNFVFGLAST--ALGVATVYTRRLKTG 117
                                    5689**************99988874....556..55889999*****************988..556666666666799 PP

                                    SHHHHHHHHHHHHHHHHHHHTT----S-.TSTTS--SSHHHHHHS-SS--HHHHHHH CS
                  Peptidase_M54 137 dkeLflervvkevlhelGhlyGLshCke.dCvmnfsndlkdvDrkapkyCksClekl 192
                                     + L+ er +kevlhe Ghl+GL hC++ +Cvm+fs+++++vDrkap +C sC  kl
  gi|118430902|ref|NP_146999.2| 118 GNGLYTERLLKEVLHEAGHLLGLDHCSNrECVMSFSRSVEEVDRKAPLFCSSCKAKL 174
                                    *****************************************************9987 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-07   0.00029     113     134 ..     130     151 ..      53     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                                    HHHHHHHHTTBESXSSTTSTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M10 113 aaHEiGHalGLeHssdkdalmy 134
                                    ++HE GH+lGL+H s+++ +m 
  gi|118430902|ref|NP_146999.2| 130 VLHEAGHLLGLDHCSNRECVMS 151
                                    68******************96 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.029     181     210 ..     117     144 ..      74     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                  Peptidase_M66 181 gssGivtgdatltgefiHEqGHalGLpHyl 210
                                    g++G     ++l +e +HE+GH lGL H  
  gi|118430902|ref|NP_146999.2| 117 GGNG--LYTERLLKEVLHEAGHLLGLDHCS 144
                                    4467..4446999***************43 PP

>> CoiA  Competence protein CoiA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   1.7e-05     0.034      20      48 ..     157     181 ..     143     183 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                           CoiA  20 keilqslqkkerfyCpaCksklvikiGsq 48 
                                    +e      +k  ++C +Ck klv+k Gs+
  gi|118430902|ref|NP_146999.2| 157 EE----VDRKAPLFCSSCKAKLVLKYGSR 181
                                    33....455999***************97 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 ?   13.1   0.0   2.7e-05     0.054     137     165 ..     128     157 ..      97     164 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                   Reprolysin_4 137 difAHEiGHtfGaaHdlsdegegl.sskte 165
                                    + + HE GH +G++H  + e+    s ++e
  gi|118430902|ref|NP_146999.2| 128 KEVLHEAGHLLGLDHCSNRECVMSfSRSVE 157
                                    4478***********999999744455555 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.9e-05     0.058     318     336 ..     130     150 ..     127     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                     Metallopep 318 flHEiGHllglpHqed..Gvm 336
                                    +lHE GHllgl H+++   vm
  gi|118430902|ref|NP_146999.2| 130 VLHEAGHLLGLDHCSNreCVM 150
                                    79************9866777 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 ?   14.0   0.0   2.8e-05     0.056      80     123 ..      98     142 ..      51     143 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                   Reprolysin_3  80 GlAyv.gsvcnsskkagvnsgssvlgkvgadtvaHEiGHnfganH 123
                                    GlA    +v +++ +   + g++ +++   + v HE GH +g++H
  gi|118430902|ref|NP_146999.2|  98 GLASTaLGVATVYTRRLKTGGNGLYTERLLKEVLHEAGHLLGLDH 142
                                    444443222223333233444444555556899************ PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.2e-05      0.14     133     170 ..     118     149 ..      92     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                   Reprolysin_5 133 nsvvvstatevqvvaHElGHnfGavHDcdsssesqsCs 170
                                     ++++ t   ++ v HE+GH +G  H  +     ++C 
  gi|118430902|ref|NP_146999.2| 118 GNGLY-TERLLKEVLHEAGHLLGLDHCSN-----RECV 149
                                    44555.667788899**********9666.....4454 PP

>> Peptidase_M43  Pregnancy-associated plasma protein-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.25      70      94 ..     128     152 ..     103     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                  Peptidase_M43  70 stLthelGhfLgLihtfeggCerGe 94 
                                      + he Gh+LgL h  + +C    
  gi|118430902|ref|NP_146999.2| 128 KEVLHEAGHLLGLDHCSNRECVMSF 152
                                    4567*****************7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1399.33
//
Query:       gi|118430903|ref|NP_147000.2|  [L=144]
Description: hypothetical protein APE_0148.1 [Aeropyrum pernix K1]
Scores for 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-41  139.5   0.1    9.2e-41  139.3   0.1    1.0  1  Archease  Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.22   11.8   0.0    1.4  1  DUF1257   Protein of unknown function (DUF1257)


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 !  139.3   0.1     1e-44   9.2e-41       3     138 .]       8     144 .]       6     144 .] 0.95

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 1e-44
                                    E---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----EE CS
                       Archease   3 yldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevkv 82 
                                    + +htADv + a+G++leeafe+aa++++e++td+s+vep+++++ ++e+ dle+lL++f+++l+++ d+e +vf  ++v
  gi|118430903|ref|NP_147000.2|   8 HEEHTADVLVIAYGRTLEEAFENAARGVYEVVTDTSRVEPRRRVDASIEGIDLENLLYRFIENLIAYTDSEGLVFGLFRV 87 
                                    679***********************************************************************999999 PP

                                    .EE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                       Archease  83 .deeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                     + e + e++++ a+a+ge+fd+++he +t vKA+Ty +++i+ee++ w++++vvDi
  gi|118430903|ref|NP_147000.2|  88 cKIECNGESCSIVASAWGEEFDPSRHEHRTIVKAMTYADMEIKEENGCWRVQFVVDI 144
                                    633566789******************99***************************9 PP

>> DUF1257  Protein of unknown function (DUF1257)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.4e-05      0.22      17      67 ..       4      55 ..       1      62 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                        DUF1257 17 rgyrgqtrsaevvirqk.ngydigFrwngegeYelvaDlqfwkqslsveefl 67
                                    g++ ++++a+v++    +  + +F+  + g Ye+v+D++ ++ +  v+  +
  gi|118430903|ref|NP_147000.2|  4 GGWMHEEHTADVLVIAYgRTLEEAFENAARGVYEVVTDTSRVEPRRRVDASI 55
                                   588899999998766654888999**************99999777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1098.01
//
Query:       gi|118430904|ref|NP_147001.2|  [L=229]
Description: endonuclease III [Aeropyrum pernix K1]
Scores for 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-21   77.4   0.0    1.3e-21   77.1   0.0    1.1  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
    2.7e-05   23.8   0.1    0.00059   19.6   0.0    2.7  2  HHH             Helix-hairpin-helix motif
     0.0036   17.9   0.1       0.13   12.9   0.0    2.6  2  HHH_5           Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.022   15.1   9.2      0.035   14.5   9.2    1.3  1  EndIII_4Fe-2S   Iron-sulfur binding domain of endonuclease II
      0.042   14.2   0.1        1.2    9.6   0.0    2.7  2  HHH_8           Helix-hairpin-helix domain
      0.054   13.8   0.0       0.23   11.8   0.0    2.0  2  Transposase_20  Transposase IS116/IS110/IS902 family
       0.11   12.7   0.0       0.19   12.0   0.0    1.3  1  P5CR_dimer      Pyrroline-5-carboxylate reductase dimerisatio


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 !   77.1   0.0   5.1e-25   1.3e-21       2     105 ..      48     188 ..      47     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 5.1e-25
                                    HHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                        HhH-GPD   2 sailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv............... 66 
                                    +++lsq+t+d++  r++ +l++++g +tpe++++a+ ++L+e+ire+G++r+Ka+ +k+lA+++v               
  gi|118430904|ref|NP_147001.2|  48 AVVLSQNTNDKNSIRAYLKLRQTIG-VTPEAILEASYDDLVEAIREAGLPRQKASALKALAEAVVrwggenyllkappee 126
                                    689*********************7.****************************************************** PP

                                    ........................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                    ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ........................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                            + p+ +++vD+h +r+++r++++ ek  ++++ k+l ++
  gi|118430904|ref|NP_147001.2| 127 lreklmsirgigpktadvflslvrKAPG-VFAVDTHAARVARRWGLVGEKAGYDEISKALYNY 188
                                    **********************964455.999***********************99998655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.17   4.4e+02       3      14 ..      76      87 ..      74      89 .. 0.84
   2 !   19.6   0.0   2.3e-07   0.00059      10      29 ..     128     147 ..     125     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.17
                                   HHHHTSSHHHHH CS
                            HHH  3 eglipasreeLl 14
                                   e++ +as+++L+
  gi|118430904|ref|NP_147001.2| 76 EAILEASYDDLV 87
                                   78999*****97 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.3e-07
                                    HHHHHTSTT-SHHHHHHHHH CS
                            HHH  10 reeLlalPGVGpktAeaIls 29 
                                    re L+++ G+GpktA+++ls
  gi|118430904|ref|NP_147001.2| 128 REKLMSIRGIGPKTADVFLS 147
                                    799**************997 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.11   2.8e+02      19      40 ..      68      89 ..      62     111 .. 0.74
   2 !   12.9   0.0     5e-05      0.13       2      19 ..     129     146 ..     128     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                                   HTTT--.SHHHHHHS-HHHHHTS CS
                          HHH_5 19 lsaGie.svedlaaadveeLaki 40
                                     + i+ ++e++++a+ ++L ++
  gi|118430904|ref|NP_147001.2| 68 RQT-IGvTPEAILEASYDDLVEA 89
                                   555.6658899999988888764 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5e-05
                                    HHHHTSTT--HHHHHHHH CS
                          HHH_5   2 eeLlsvsGiGpktAlall 19 
                                    e+L+s+ GiGpktA   l
  gi|118430904|ref|NP_147001.2| 129 EKLMSIRGIGPKTADVFL 146
                                    689999999999996655 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 ?   14.5   9.2   1.4e-05     0.035       1      17 []     209     225 ..     209     225 .. 0.99

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                    C+AR+P+C +CPL+  C
  gi|118430904|ref|NP_147001.2| 209 CKARRPRCRECPLRSVC 225
                                    ***************99 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.13   3.4e+02      16      45 ..      52      81 ..      45     110 .. 0.71
   2 ?    9.6   0.0   0.00046       1.2      38      63 ..     123     145 ..     119     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
                                   HHCT--CCCHHHHHHHHCCCCC-SS-HHHH CS
                          HHH_8 16 elkgedpfrvraYrrAaraiealpeeitsl 45
                                    ++ +d++ +raY +  ++i   pe+i ++
  gi|118430904|ref|NP_147001.2| 52 SQNTNDKNSIRAYLKLRQTIGVTPEAILEA 81
                                   445589999999999888888888877665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00046
                                    -SS-HHHHTTHCTTSTT--HHHHHHH CS
                          HHH_8  38 lpeeitsleeeltklpgiGkkiaaki 63 
                                     pee+++   +l +++giG+k+a++ 
  gi|118430904|ref|NP_147001.2| 123 PPEELRE---KLMSIRGIGPKTADVF 145
                                    4556666...7************975 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   3.9e+03      14      42 ..      46      75 ..      44      78 .. 0.66
   2 ?   11.8   0.0     9e-05      0.23       2      29 ..     129     157 ..     128     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                 Transposase_20 14 taaallaei.gdlrrfksakqlaayaGlap 42
                                   +aa++l++  +d + ++   +l   +G++p
  gi|118430904|ref|NP_147001.2| 46 LAAVVLSQNtNDKNSIRAYLKLRQTIGVTP 75
                                   555555554367677777778888888887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9e-05
                 Transposase_20   2 elLesipGiGpvtaaallaei.gdlrrfk 29 
                                    e L+si GiGp ta ++l+ +   +  f 
  gi|118430904|ref|NP_147001.2| 129 EKLMSIRGIGPKTADVFLSLVrKAPGVFA 157
                                    68****************99833335555 PP

>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-05      0.19      22      72 ..      83     137 ..      71     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                                    HHHHHHHHHHTT--HHHHHHH...HHHHH.HHHHHHHHCHSHHHHHHHH--TTSH CS
                     P5CR_dimer  22 iealadagvklGlsreeArel...aaqtv.aGaaklllesepaelrdkvtspgGt 72 
                                     + l++a  ++Gl+r++A +l   a+ +v  G  + ll+  p+elr+k +s +G+
  gi|118430904|ref|NP_147001.2|  83 YDDLVEAIREAGLPRQKASALkalAEAVVrWGGENYLLKAPPEELREKLMSIRGI 137
                                    678999**********9976521133444223333444444**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1732.09
//
Query:       gi|118430905|ref|NP_147002.2|  [L=185]
Description: hypothetical protein APE_0151.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.2   0.0      0.049   13.6   0.0    1.2  1  DUF1445   Protein of unknown function (DUF1445)


Domain annotation for each model (and alignments):
>> DUF1445  Protein of unknown function (DUF1445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.7e-06     0.049      20      94 ..      84     157 ..      69     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-06
                        DUF1445  20 lpvrhveqgrnvpmYktniplapagvfsgklvvsmrpikkekvervveitrrfkkvhgePvhigdpealgikdls 94 
                                    +  r  e+++  +m++t++++ pagv +  ++ s+r  +k+ v+ v ++++ ++++  +Pv+ g +e + ++ ++
  gi|118430905|ref|NP_147002.2|  84 ICGRIRESREAYSMFETALKILPAGVGKVLFISSLRGSSKDMVD-VARLSEILARAGLKPVKRGAQEVVDVEGVD 157
                                    556677888999*****************9******99988876.7789999999999********999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1479.64
//
Query:       gi|118430906|ref|NP_147003.2|  [L=410]
Description: origin recognition complex subunit 2 Orc2 [Aeropyrum pernix K1]
Scores for 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-08   32.6   0.0    2.3e-07   31.2   0.0    1.7  1  AAA_22    AAA domain
    1.3e-07   31.4   0.0    4.5e-07   29.8   0.0    1.8  2  Cdc6_C    CDC6, C terminal winged helix domain
    0.00025   20.5   0.0     0.0004   19.9   0.0    1.2  1  TniB      Bacterial TniB protein
     0.0028   16.5   0.2      0.021   13.6   0.1    2.4  4  AAA_35    AAA-like domain
  ------ inclusion threshold ------
      0.041   13.1   0.1        2.1    7.5   0.0    2.2  2  NB-ARC    NB-ARC domain
      0.074   13.4   1.7        1.9    8.9   1.1    2.6  2  AAA_16    AAA ATPase domain


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 !   31.2   0.0   7.6e-11   2.3e-07      11     119 ..      56     171 ..      52     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 7.6e-11
                         AAA_22  11 tGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrara 90 
                                    +G +G+GKTtl++  +++  e+a+ e   +++++v++ +  ++ ++l+ ++r++g +   +++   ++l+al ++l    
  gi|118430906|ref|NP_147003.2|  56 IGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVEN 135
                                    79****************988777777****************************9999978888888877777666666 PP

                         AAA_22  91 vielliiDEaqh.lrs.....eealeeLrsllnl..s 119
                                       l+i+DE+q  l s     +e l +L + ++   s
  gi|118430906|ref|NP_147003.2| 136 HYLLVILDEFQSmL-SspriaAEDLYTLLRVHEEipS 171
                                    679*********66.3354555555555444332453 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 ?   -4.0   0.0       5.2   1.6e+04      36      54 ..     212     230 ..     208     232 .. 0.71
   2 !   29.8   0.0   1.5e-10   4.5e-07      11      75 ..     321     385 ..     312     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 5.2
                                    ---HHHHHHHHHHHHHTTS CS
                         Cdc6_C  36 pltqrevsdllseLemlgi 54 
                                    + ++re + +l + + lg+
  gi|118430906|ref|NP_147003.2| 212 AYKSRELYTILEQRAELGL 230
                                    5677888888877777765 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.5e-10
                                    CSSS-EEHHHHHHHHHHHHHHT.T-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
                         Cdc6_C  11 sgkeevttgevyevYkslCese.gvdpltqrevsdllseLemlgileleksskGrregrtrkisLn 75 
                                    +g e++  g + ++Y++    + +v+p+  ++++ +l+ L +lg+++++ s++G+r grt++++L 
  gi|118430906|ref|NP_147003.2| 321 GGMEWINAGLLRQRYEDASLTMyNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMR-GRTTLFRLA 385
                                    67788889999999999999988********************************7.******995 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.3e-07    0.0004      41     147 ..      56     164 ..      31     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                           TniB  41 vGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkararvs..kleqqvlrllrel 118
                                    +G+  +GKt++++   ++ +++  ++  +v+  +v+a + p+   + + i+++ g+p++ r   +   l++ v +l  e 
  gi|118430906|ref|NP_147003.2|  56 IGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPAldILKALVDNLYVEN 135
                                    79999*****9876667777777888889*****************************9998554327888888888999 PP

                           TniB 119 kvrvLiiDEihnllagsarkqreflnalk 147
                                    +  ++i+DE++++l+  + + + +  +l+
  gi|118430906|ref|NP_147003.2| 136 HYLLVILDEFQSMLSSPRIAAEDLYTLLR 164
                                    9999999*******999888888777776 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.18   5.5e+02     195     223 ..      63      91 ..      52     108 .. 0.82
   2 !   13.6   0.1   7.2e-06     0.021     126     215 ..     135     228 ..     122     244 .. 0.81
   3 ?   -3.4   0.0       1.1   3.2e+03      39      61 ..     271     293 ..     267     308 .. 0.73
   4 ?   -3.4   0.0       1.1   3.4e+03     302     314 ..     357     369 ..     349     383 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                         AAA_35 195 pieLpeFtkeqvqeLaqryglelsekqle 223
                                    + +L++Ft + v+e a + gl+++++ ++
  gi|118430906|ref|NP_147003.2|  63 KTTLAKFTVKRVSEAAAKEGLTVKQAYVN 91 
                                    36799999999999999999998887665 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.2e-06
                         AAA_35 126 dkplvLaldevdrlfeypeia.kdflslLRswheeaknkeiwqkLrLvvvhs...tevyipldinqSpfnvGlpieLpeF 201
                                    ++ l+++lde++++++ p+ia +d+ +lLR+ hee  +++  +++ +++v s      y++ +i q    +G +++Lp +
  gi|118430906|ref|NP_147003.2| 135 NHYLLVILDEFQSMLSSPRIAaEDLYTLLRV-HEEIPSRDGVNRIGFLLVASdvrALSYMREKIPQVESQIGFKLHLPAY 213
                                    5679999************972677788875.8999999999********994433579999****************** PP

                         AAA_35 202 tkeqvqe.Laqrygl 215
                                    ++++  + L qr +l
  gi|118430906|ref|NP_147003.2| 214 KSRELYTiLEQRAEL 228
                                    *99986525566555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                         AAA_35  39 pkkmGKtSLlarilakakqqgyk 61 
                                    ++ mG+ SL + +++ka +++  
  gi|118430906|ref|NP_147003.2| 271 AEAMGRDSLSEDLVRKAVSENEA 293
                                    56799999999999888877643 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.1
                         AAA_35 302 aykLeslGLvkle 314
                                      +L+slGLv+ +
  gi|118430906|ref|NP_147003.2| 357 LKHLTSLGLVDAK 369
                                    4678888888765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0007       2.1      21      45 ..      51      75 ..      36      81 .. 0.78
   2 ?    3.3   0.0     0.013        38      92     128 ..     214     250 ..     185     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0007
                                   EEEEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnksd 45
                                   ++ +  G+ G+GKttlak  ++  +
  gi|118430906|ref|NP_147003.2| 51 MIYGSIGRVGIGKTTLAKFTVKRVS 75
                                   4566789**********98877765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.013
                                    HHHHHHHHCCCTTEEEEEEEE-SHHHH.....HHHHC CS
                         NB-ARC  92 lkrklvrlLltkrfllvlDDVweeedwdkigvvlpar 128
                                    + r+l+ +L+++  l + D Vwe   ++ i+ v+ + 
  gi|118430906|ref|NP_147003.2| 214 KSRELYTILEQRAELGLRDTVWEPRHLELISDVYGED 250
                                    7899**************************9998743 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1   0.00063       1.9       5     152 ..      25     153 ..      21     171 .. 0.54
   2 ?   -2.4   0.0       1.9   5.6e+03     103     103 ..     302     302 ..     260     399 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00063
                         AAA_16   5 ReeeleqL.lsalervrsgrp..elvlls...GesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalar 78 
                                    R+ e e+L + +l+r+ sg +   + +++   G  G+GK++l++   ++++++    ++ +    +     +a+++a+ +
  gi|118430906|ref|NP_147003.2|  25 RRGEAEALaRIYLNRLLSGAGlsDVNMIYgsiGRVGIGKTTLAKFTVKRVSEA----AAKEGLTVK-----QAYVNAFNA 95 
                                    66666666555556777777776333344011566899999998888888877....222222221.....225555544 PP

                         AAA_16  79 eellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeasl 152
                                      l++ l        +  ++ + ++                l+ lk+l++ l  + + l+++lD++q   ++++
  gi|118430906|ref|NP_147003.2|  96 PNLYTILSLI---VRQTGYPIQVRG-------------APALDILKALVDNLYVENHYLLVILDEFQSMLSSPR 153
                                    3333333322...112222222222.............245778888884444447778888888886666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                         AAA_16 103 e 103
                                    e
  gi|118430906|ref|NP_147003.2| 302 E 302
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.36
# Mc/sec: 3382.40
//
Query:       gi|118430907|ref|YP_874803.1|  [L=88]
Description: hypothetical protein APE_0152a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0027   17.6   0.2     0.0027   17.6   0.2    1.9  3  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.012   15.2   0.2      0.023   14.2   0.2    1.4  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.015   15.3   0.0      0.024   14.6   0.0    1.4  1  HTH_45    Winged helix-turn-helix
      0.047   13.6   0.2       0.09   12.7   0.2    1.4  2  MarR_2    MarR family
      0.061   13.4   0.4       0.14   12.3   0.2    1.7  2  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d


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 !   17.6   0.2   7.4e-07    0.0027       3      45 ..      12      55 ..      10      56 .. 0.96
   2 ?   -1.7   0.1      0.76   2.7e+03       3       9 ..      61      67 ..      61      68 .. 0.83
   3 ?   -2.7   0.0       1.6   5.8e+03      20      28 ..      80      88 .]      76      88 .] 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.4e-07
                                   HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   ++lkILk L + g++ ++ +++e+gl    vS H   L+ a++V
  gi|118430907|ref|YP_874803.1| 12 GKLKILKVLFRrGQANITLIVRETGLHHRLVSKHIEELKTANIV 55
                                   68****************************************99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.76
                                   HHHHHHH CS
                          HTH_5  3 tRlkILk 9 
                                   +Rl+I++
  gi|118430907|ref|YP_874803.1| 61 GRLRIIY 67
                                   59***98 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.6
                                   HHHHHHTS- CS
                          HTH_5 20 elaeelgls 28
                                   ++++ l++s
  gi|118430907|ref|YP_874803.1| 80 DIVKTLDIS 88
                                   677777665 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 ?   14.2   0.2   6.4e-06     0.023       6      47 ..      14      55 ..      13      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.4e-06
                         HTH_24  6 rkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +kIL++L + +  +++ + +++gl    v++++++L+ + ++
  gi|118430907|ref|YP_874803.1| 14 LKILKVLFRRGQANITLIVRETGLHHRLVSKHIEELKTANIV 55
                                   8***********************************998876 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   6.7e-06     0.024      10      51 ..      15      57 ..      10      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.7e-06
                         HTH_45 10 dILeais.egeakkTkimykanLsykllnkYLdmLvekglikk 51
                                    IL+++  +g+a+ T i+ +  L  +l++k ++ L   +++ +
  gi|118430907|ref|YP_874803.1| 15 KILKVLFrRGQANITLIVRETGLHHRLVSKHIEELKTANIVGE 57
                                   577766449*****************************99965 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.5e-05      0.09       9      54 ..      15      58 ..      10      64 .. 0.88
   2 ?   -2.4   0.0       1.3   4.5e+03      24      33 ..      78      87 ..      69      88 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                    +L +L rr+    +++ ++r++gl +  vs+++++L  a  v +r
  gi|118430907|ref|YP_874803.1| 15 KILKVLFRRGQ--ANITLIVRETGLHHRLVSKHIEELKTANIVGER 58
                                   57889999998..8**************************999665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                   HHHHHHHHTS CS
                         MarR_2 24 vgelarrlgl 33
                                    ++++++l++
  gi|118430907|ref|YP_874803.1| 78 LRDIVKTLDI 87
                                   4566666665 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   0.2   3.9e-05      0.14      17      46 ..      15      44 ..      14      55 .. 0.92
   2 ?   -1.7   0.0      0.92   3.3e+03      30      39 ..      78      87 ..      73      88 .] 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                                   HHHHHHHHHSSBEHHHHHHHHSSTHHHHHH CS
                          HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkk 46
                                   k+ ++L+r+g   ++ +v++t+L +++V k
  gi|118430907|ref|YP_874803.1| 15 KILKVLFRRGQANITLIVRETGLHHRLVSK 44
                                   7999**********************9976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.92
                                   HHHHHHHHSS CS
                          HTH_9 30 lrelvkktkL 39
                                   lr++vk++++
  gi|118430907|ref|YP_874803.1| 78 LRDIVKTLDI 87
                                   6777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 691.13
//
Query:       gi|118430908|ref|NP_147005.2|  [L=248]
Description: TrmB family transcriptional regulator [Aeropyrum pernix K1]
Scores for 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   54.7   2.1    1.2e-11   44.4   0.1    3.4  3  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0025   17.7   2.0       0.65    9.9   0.7    3.1  3  MarR_2       MarR family
  ------ inclusion threshold ------
      0.014   15.4   0.1        3.2    7.9   0.2    2.6  3  HTH_20       Helix-turn-helix domain
      0.042   14.0   0.6        1.5    9.0   0.0    3.2  4  HTH_28       Helix-turn-helix domain
      0.052   13.7   0.1       0.15   12.2   0.1    1.8  1  Gas_vesicle  Gas vesicle protein
      0.079   13.0   0.0       0.62   10.1   0.0    2.5  3  HTH_29       Winged helix-turn helix


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1   3.9e-15   1.2e-11       1      64 [.      13      76 ..      13      79 .. 0.90
   2 !    5.2   0.3    0.0065        20      25      56 ..      79     110 ..      75     122 .. 0.68
   3 ?    4.5   0.0     0.011        32      32      56 ..     122     146 ..     103     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 3.9e-15
                                   HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                           TrmB  1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                   Lq  + L+ yEak+YlaLl +g ++ +e + ++gvp ++vY+v+r Le+kGl   + +  ++Y++
  gi|118430908|ref|NP_147005.2| 13 LQrSFRLTAYEAKIYLALL-KGASSPKEASAMSGVPLPRVYDVIRVLESKGLAVPSSEGWYRYVP 76
                                   677889*************.9*******************************9988777776665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0065
                                    HCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB  25 adeiaeelgvprskvYevLrsLedkGlVerek 56 
                                    a  +ae++ +++ +  ++L+ Le + l ere 
  gi|118430908|ref|NP_147005.2|  79 AAAVAEIARIEEESRSRALKVLEAAELLEREI 110
                                    66777777777777777777777777777764 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.011
                                    TTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB  32 lgvprskvYevLrsLedkGlVerek 56 
                                    l+ p++ +  ++  L d G+V++  
  gi|118430908|ref|NP_147005.2| 122 LDSPYQAISLAVDALRDSGFVYITV 146
                                    67899****************9875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0075        22      23      52 ..      36      65 ..      20      70 .. 0.85
   2 !    9.9   0.7   0.00022      0.65      23      56 ..      78     111 ..      72     115 .. 0.83
   3 ?   -0.5   0.0      0.38   1.1e+03      36      52 ..     127     143 ..     121     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0075
                                   EHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLve 52
                                   +++e  +  g++ ++v  +++ L+++GL +
  gi|118430908|ref|NP_147005.2| 36 SPKEASAMSGVPLPRVYDVIRVLESKGLAV 65
                                   899999**********************86 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                    EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2  23 tvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                    +++++a+  +++  + sr+lk L+aa L+er+ +
  gi|118430908|ref|NP_147005.2|  78 RAAAVAEIARIEEESRSRALKVLEAAELLEREIA 111
                                    7888888899999999***************944 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.38
                                    HHHHHHHHHHHHTTSEE CS
                         MarR_2  36 savsrilkrLvaaGLve 52 
                                    +a+s +++ L + G+v 
  gi|118430908|ref|NP_147005.2| 127 QAISLAVDALRDSGFVY 143
                                    78888899999988883 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.012        36      14      55 ..      25      65 ..      22      71 .. 0.81
   2 ?    7.9   0.2    0.0011       3.2      27      57 ..      79     109 ..      73     113 .. 0.84
   3 ?   -3.3   0.0       3.4     1e+04      41      54 ..     129     142 ..     122     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   +i+ aL  +++ +++e  +  +++   +++ +rvLe+ gL  
  gi|118430908|ref|NP_147005.2| 25 KIYLAL-LKGASSPKEASAMSGVPLPRVYDVIRVLESKGLAV 65
                                   677888.788888888888779***************99955 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                                    HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20  27 aselaerldlskntlsyHLrvLeeagLvevv 57 
                                    a+++ae  ++   + s+ L+vLe a+L+e++
  gi|118430908|ref|NP_147005.2|  79 AAAVAEIARIEEESRSRALKVLEAAELLERE 109
                                    456667777899999**************86 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHCTTE CS
                         HTH_20  41 lsyHLrvLeeagLv 54 
                                    +s  +++L++ g+v
  gi|118430908|ref|NP_147005.2| 129 ISLAVDALRDSGFV 142
                                    55567788888886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00051       1.5       7      42 ..      28      64 ..      24      65 .. 0.91
   2 ?   -1.7   0.3       1.1   3.4e+03       5      21 ..      81      88 ..      78     106 .. 0.50
   3 ?   -2.4   0.0       1.8   5.5e+03      28      38 ..     145     155 ..     140     156 .. 0.84
   4 ?    1.2   0.0      0.14   4.2e+02      27      38 ..     236     247 ..     235     248 .] 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00051
                         HTH_28  7 kllaaGh.svreaArelgisrrtvyrWikryeegGia 42
                                   ++l++G  s +ea++  g+   +vy+ i+ +e+ G+a
  gi|118430908|ref|NP_147005.2| 28 LALLKGAsSPKEASAMSGVPLPRVYDVIRVLESKGLA 64
                                   67899*99**********************9999975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                         HTH_28  5 iikllaaGhsvreaAre 21
                                   ++ ++a         r+
  gi|118430908|ref|NP_147005.2| 81 AVAEIA---------RI 88
                                   444444.........33 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.8
                         HTH_28  28 tvyrWikryee 38 
                                    tv   ++rye+
  gi|118430908|ref|NP_147005.2| 145 TVLNVLHRYES 155
                                    788899***96 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.14
                         HTH_28  27 rtvyrWikryee 38 
                                    +t+++ +k+y++
  gi|118430908|ref|NP_147005.2| 236 DTIRKAVKKYRA 247
                                    69********97 PP

>> Gas_vesicle  Gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.1e-05      0.15      18      34 ..     181     197 ..     180     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.1e-05
                    Gas_vesicle  18 gditisvagieLltikL 34 
                                    +d++isv g+eL++++L
  gi|118430908|ref|NP_147005.2| 181 ADLKISVEGVELVRLEL 197
                                    8*************998 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00021      0.62       2      42 ..      24      64 ..      24      74 .. 0.92
   2 ?   -3.7   0.0       4.3   1.3e+04      28      37 ..     145     154 ..     139     155 .. 0.83
   3 ?   -1.2   0.0      0.71   2.1e+03      27      38 ..     236     247 ..     234     248 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                         HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGla 42
                                   a++ l+l +G s+++++ ++ g+  + vy++++  e +Gla
  gi|118430908|ref|NP_147005.2| 24 AKIYLALLKGASSPKEASAMSGVPLPRVYDVIRVLESKGLA 64
                                   689999********************************997 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.3
                         HTH_29  28 tvyrwlkrfe 37 
                                    tv ++l+r+e
  gi|118430908|ref|NP_147005.2| 145 TVLNVLHRYE 154
                                    7889999998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.71
                         HTH_29  27 rtvyrwlkrfee 38 
                                    +t+++++k +++
  gi|118430908|ref|NP_147005.2| 236 DTIRKAVKKYRA 247
                                    899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1885.74
//
Query:       gi|14600490|ref|NP_147006.1|  [L=452]
Description: hypothetical protein APE_0154 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 3175.85
//
Query:       gi|118430909|ref|NP_147007.2|  [L=176]
Description: hypothetical protein APE_0155.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1264.12
//
Query:       gi|118430910|ref|NP_147008.2|  [L=386]
Description: hypothetical protein APE_0156.1 [Aeropyrum pernix K1]
Scores for complete 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   46.7  36.6    7.4e-11   42.5  12.1    3.5  4  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.61   1.1e+04      68      80 ..      37      49 ..      22      58 .. 0.57
   2 !   17.9  16.5   1.7e-07    0.0031       4     121 ..      62     176 ..      59     179 .. 0.70
   3 ?   -0.2   5.8      0.07   1.2e+03      47      83 ..     173     209 ..     171     248 .. 0.82
   4 !   42.5  12.1   4.1e-15   7.4e-11       2     122 ..     253     376 ..     252     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.61
                                   HHHHHHHHHHHHH CS
                           MgtE 68 alvvglalvlvll 80
                                   + +v ++++ ++l
  gi|118430910|ref|NP_147008.2| 37 INMVVISMFSNYL 49
                                   3334444444444 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.7e-07
                                    HHHHHHHHHHHHHHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHH CS
                           MgtE   4 ilglgGnlgaqlasristalhlgelekklkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvllaaa 83 
                                    +++l G l   l+sr ++   lg       +v+l+ l+v    g++l ++ +  + +  + l  +++v +al+++l + +
  gi|118430910|ref|NP_147008.2|  62 LSALTGGLLLSLSSRAISNHVLGGA---GPEVYLTGLAVSAASGIFLTTVFSTATSIALG-LEPVMMVPAALITLLGVLL 137
                                    5666666666666666666666655...45688888888888888888888877655444.4455555555555544444 PP

                                    HH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHH CS
                           MgtE  84 ll.ilgvllplllwklglDPdnaaiPlltalgDllgtll 121
                                    +l +l+++++++l +lg+ Pdn++  +lt++ D+  ++l
  gi|118430910|ref|NP_147008.2| 138 VLtLLTWIIIVMLLRLGVSPDNVMPAILTSIIDMAVLIL 176
                                    44566****************************987766 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.07
                                    HHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHH CS
                           MgtE  47 gvilgllifllalllgwslllalvvglalvlvllaaa 83 
                                     +il++++f+++  + + ++l++vv+++l+l++ aaa
  gi|118430910|ref|NP_147008.2| 173 VLILAIVAFSMVSRMDEGIYLVAVVTFSLALAFSAAA 209
                                    4677777777777778899999999999998888776 PP

  == domain 4  score: 42.5 bits;  conditional E-value: 4.1e-15
                                    HHHHHHHHHHHHHHHHHHHHHHHT.T.SS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHH CS
                           MgtE   2 PvilglgGnlgaqlasristalhl.g.elekk.lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlv 78 
                                    P ++ l+G+++  +as  +t+ +l g  l+   + + l+k ++ ++  ++ +g++ ++la +  +s+    +v ++l++ 
  gi|118430910|ref|NP_147008.2| 253 PPLNKLAGSVAGSMASAATTSVSLyGhYLDLPsMISTLFKITVGAIPSALYIGVIGYVLASVGEGSVGPQ-IVLASLLVS 331
                                    99********************994443344455666666666666666666666666654433322222.333333333 PP

                                    HHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHH CS
                           MgtE  79 llaaall.ilgvllplllwklglDPdnaaiPlltalgDllgtlll 122
                                    +++++l  ++++ll++++ + glDPd +a Pl t+l+Dllg++ l
  gi|118430910|ref|NP_147008.2| 332 IVLSILGsLIAWLLVVVSIRAGLDPDAIAMPLATSLVDLLGVVSL 376
                                    33333335669*******************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.53u 0.20s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2974.86
//
Query:       gi|14600493|ref|NP_147009.1|  [L=246]
Description: hypothetical protein APE_0157 [Aeropyrum pernix K1]
Scores for complete 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-44  151.0   0.0    3.9e-44  150.7   0.0    1.0  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 !  150.7   0.0   2.2e-48   3.9e-44       1     187 []       7     205 ..       7     205 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 2.2e-48
                                   HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEEEEEE CS
                5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegkevllP 72 
                                   Kq++R++   ++r+l+e++v+ ++ a ++ri+++++++ea  r+        + +++v++++++++++ ++leegk +l+P
  gi|14600493|ref|NP_147009.1|   7 KQAIRER---VWRLLEEKGVTLPPGA-WGRIPNFRGAREAaLRLfslrewqnSSTIKVNPDSPQRWVRLRALEEGKLLLMP 83 
                                   8999999...**************88.*************99*************************************** PP

                                   EECSSCTEECEEEEEECCCCCCCCC...HCTSSCE--TTECCBCGGG.G-SEEEE--SEEETTS-EE-SSTTHHHHHHHHH CS
                5-FTHF_cyc-lig  73 rvrlesgslkvvrlttlkeedsles...gkyglkePeeeeerelale.kldlvlvPgvAfdkeGaRlGkGkGyyDrflarl 149
                                   ++rl+sg+l ++ +t++++ +++ s   g++ l  P ++++   ++  k+d+v++++vA++++G+RlGkG+Gy+D ++a l
  gi|14600493|ref|NP_147009.1|  84 TPRLRSGFLLLDPSTIPRNLYRVGStikGAFRLARPLASIQDLVQHVeKIDFVVEGSVAVNRWGERLGKGEGYGDLEFAIL 164
                                   ****************99998877511145557777777765444337********************************* PP

                                   TS.T-SS--EEEEE--GGGEES..-----ST----SEEE-S CS
                5-FTHF_cyc-lig 150 kg.gagdkpltvglaldeqlve..rlPleehDvpvdevvte 187
                                    + g +d+++++++++++ +v   rlP+eehDv+vd++ t+
  gi|14600493|ref|NP_147009.1| 165 VEaGILDREVAIATTVHDLQVLphRLPQEEHDVSVDIISTP 205
                                   ******************999999**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1863.39
//
Query:       gi|118430911|ref|NP_147010.2|  [L=236]
Description: hypothetical protein APE_0158.1 [Aeropyrum pernix K1]
Scores for 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   21.2   0.0    0.00016   21.1   0.0    1.2  1  MTHFR     Methylenetetrahydrofolate reductase


Domain annotation for each model (and alignments):
>> MTHFR  Methylenetetrahydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.7e-09   0.00016      60     116 ..      44     101 ..       9     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.7e-09
                                    HHHHHHHHHH-S-.EEEEEESTTS-HHHHHHHHHHHHHCT--EEEEE--S--TT-GGC CS
                          MTHFR  60 siakviqqelgle.ailhlTctdaskeeldkalekakelGirnilALrGDppkdedkw 116
                                    ++a+ +  ++g e  ++h+  +d+s+ +l++++++  +lG+ ni+ LrGDp+  e  +
  gi|118430911|ref|NP_147010.2|  44 IAASYLSCRVGGErIVAHIRTVDYSVHSLKAIVKTLSSLGVSNIVLLRGDPLGREVGL 101
                                    55555555555541468*********************************87664333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1769.95
//
Query:       gi|14600495|ref|NP_147011.1|  [L=282]
Description: (S)-2,3-di-O-farnesylgeranylglyceryl synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-36  124.8  19.2    4.8e-36  124.3  19.2    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 !  124.3  19.2   2.7e-40   4.8e-36      13     240 ..      31     254 ..      16     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 2.7e-40
                          UbiA  13 aggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnplta 93 
                                   + + +++  l +++++++++++ a++ Nd++D eiD++  + p+RPl++G++s+ ea i++i+l++lg+l + + + + t 
  gi|14600495|ref|NP_147011.1|  31 SFQGFTPIDLMAVVVAGYCLSSVAMITNDIIDLEIDRI--NAPHRPLPAGKVSTVEATILSIFLAALGFLAA-ISVDLITT 108
                                   33445557899999999*********************..********************************.******** PP

                          UbiA  94 llgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrka 174
                                   ++ l +l+l ++Y+   lKr++l g++v+++    p++ +   ++g    ++ +++ +vfl +++  +a+ ++d+egD++a
  gi|14600495|ref|NP_147011.1| 109 AFYLGGLALSLLYN-TLLKRTGLPGNIVVAALVSAPFMYASLEAGGL-GGPMSVFSTMVFLAVLGREVAKGVPDVEGDKAA 187
                                   **************.5**********************999999995.88889999999********************** PP

                          UbiA 175 giktlpvvlGrkaarillalllavllla..llllllalllllylllalllaalallraarlvrrrdak 240
                                   g++t +vv+G+k+a+ + a++l+++++a  ++ l ++++ +l++  ++ll++l++lr+a l+ +r  +
  gi|14600495|ref|NP_147011.1| 188 GVRTVAVVFGKKTAAAV-ASALYLASAAlgYIPLIYGYVDPLIYTPFILLLTLLVLREALLIVKRPTR 254
                                   ***************96.33344444444799*************************99998887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2162.52
//
Query:       gi|118430912|ref|NP_147012.2|  [L=545]
Description: lysyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for 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-109  365.9   0.0   2.5e-109  365.5   0.0    1.1  1  tRNA-synt_1f   tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.052   13.5   1.1       0.12   12.4   1.1    1.6  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.27   11.9   2.7       0.63   10.7   0.7    2.6  2  HTH_32         Homeodomain-like domain
        0.3   11.0   2.4        1.3    9.0   2.4    2.1  1  Nudix_N_2      Nudix N-terminal


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 !  365.5   0.0  5.7e-113  2.5e-109       2     359 ..       4     369 ..       3     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: 365.5 bits;  conditional E-value: 5.7e-113
                   tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlr.evltadlvaralrkrgeevrlilisDdmDglRkvpe. 79 
                                    +W+dkl+++l ++ +++  +kde++++ G+s+SGl+HiG+lr evl +++v+r+l+krg +v+++l+ +++D+++  +e 
  gi|118430912|ref|NP_147012.2|   4 HWVDKLVAELEAKLQNR--GKDEYIFNGGLSVSGLQHIGRLRgEVLLGEAVRRELEKRGFRVKQLLTLYTVDPWKGKDEq 81 
                                    9**********999777..89********************99********************************99988 PP

                   tRNA-synt_1f  80 ..nlpek.llekylgkpltsiPdpkgkhesyaehfnaelvesLdelgi.evefisatelYksglydeaikealenrekik 155
                                      ++p+  ++e+y+g+pl+++Pdpkg+h+s+++hf++++  ++  ++  ++e+++++elYk +l +  ++++l +r++i+
  gi|118430912|ref|NP_147012.2|  82 rrEFPDPkAAERYVGWPLDRVPDPKGCHASWVDHFWSDFGPYIGVFTDgKIEVVTTRELYKGRLKEFITTMVLPRRDEIR 161
                                    88999999**************************************999******************************* PP

                   tRNA-synt_1f 156 eilekyrgee.reetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalg 234
                                    ++++kyrg++ ++e ++p++p c +cgr+d+te+ e+   +e+++Y+c+ cG+++e++i++  +KL+W+++wa  W++lg
  gi|118430912|ref|NP_147012.2| 162 RVINKYRGRKpYQEGWIPLEPRCARCGRIDSTEALEIL-GGERVRYRCSYCGYQGESSIED--SKLNWRIEWAGVWWSLG 238
                                    ********999**************************9.*********************9..8**************** PP

                   tRNA-synt_1f 235 VdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkgge...kmssSkGnvltledwlevaepevlrflilrr 311
                                    VdfEp+GkDha++GgS d ++++a++lg+e+Pe+v+Ye+++l+ g+   +mssS ++++t+++wl++a+p++lrf+++ +
  gi|118430912|ref|NP_147012.2| 239 VDFEPYGKDHATPGGSRDSAAELARLLGFEPPEGVWYEWVSLRAGGreaDMSSSGFTGITPREWLDIAHPQILRFIYFLH 318
                                    ******************************************99887889****************************** PP

                   tRNA-synt_1f 312 kPkkakkldldleilrlvdeYdklerkyf....aeqeeeeekekrvyelsav 359
                                     P++++ +dl+ ei++++ +Y+++er+yf    a++ ee++  +r+yels++
  gi|118430912|ref|NP_147012.2| 319 PPTRRVVVDLS-EIPSYYSQYYRAERIYFgieeASTVEETRYLARTYELSHP 369
                                    ***********.*******************998999999*********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 ?   12.4   1.1   2.7e-05      0.12      18      46 .]     181     214 ..     173     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                  Zn_Tnp_IS1595  18 gfvCPhCgsr...kayrikt..rglfqCkeCrkq 46 
                                     ++C +Cg     +a +i +  r +++C+ C++q
  gi|118430912|ref|NP_147012.2| 181 EPRCARCGRIdstEALEILGgeRVRYRCSYCGYQ 214
                                    489*****777667777777************98 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.68   3.1e+03       9      47 ..     359     398 ..     356     419 .. 0.62
   2 ?   10.7   0.7   0.00014      0.63       3      70 ..     429     497 ..     428     501 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.68
                         HTH_32   9 yneeGlegLkdrprrgrpr.klsdevrariiallre.eprW 47 
                                    y ++ +e  ++   + +p+ +++  + a + +++   e+ W
  gi|118430912|ref|NP_147012.2| 359 YLARTYELSHPSNPPAKPPsQIPYSHAAIVAQVV-GpERLW 398
                                    5555444334444444777678888888887777.323366 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                         HTH_32   3 srwlkRyneeGle.gLkdrprrgrpr.klsdevrariiallreeprWsprqlaarlaeregvkvShstvy 70 
                                    ++w +Ry+   l   + d p   + r    +++ +++ ++l++  +Ws +++ ++l  ++g+ +S s  +
  gi|118430912|ref|NP_147012.2| 429 YKWARRYAPKHLKfEIPDSPPEDALRrIEKPDLLEKLAEVLESVEEWSEERIKQAL-VEFGEGMSSSERR 497
                                    89*****988777666677655544425899**********7656***********.8888888766544 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.4   0.00029       1.3       3      30 ..     184     213 ..     184     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                                    -TTT--B..-E.EE--TT-SS-EEEETTTTE CS
                      Nudix_N_2   3 CsqCGtp..ve.lripdgDnreRlvCpaCgt 30 
                                    C  CG    +e l+i  g++r R++C+ Cg+
  gi|118430912|ref|NP_147012.2| 184 CARCGRIdsTEaLEI-LGGERVRYRCSYCGY 213
                                    888887542443445.6************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3793.55
//
Query:       gi|14600497|ref|NP_147013.1|  [L=263]
Description: DNA polymerase sliding clamp A [Aeropyrum pernix K1]
Scores for complete 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   40.6   0.0    1.2e-09   38.0   0.0    2.0  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    1.7e-06   28.2   0.0    7.5e-05   22.9   0.0    2.6  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
  ------ inclusion threshold ------
      0.063   12.7   0.0       0.17   11.3   0.0    1.7  2  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.9e-13   1.2e-09       8     104 ..      21     118 ..      15     133 .. 0.85
   2 ?    0.2   0.0     0.096   5.7e+02      59     111 ..     203     254 ..     146     258 .. 0.58

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.9e-13
                                   SHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEE..S.S-EEEEEEHHHHHHHHTTSTTT CS
                        PCNA_N   8 qasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrC..D.rnlalgvnlnslskilkcanne 85 
                                   +a ++k l++++  +++e  f +  +G++l+ +D ++vaLv +e+ s++f ++    D   + lgvn+++l  ++  a++ 
  gi|14600497|ref|NP_147013.1|  21 EAKVFKELVDSVSKILDEGLFIITGEGLRLRGMDPARVALVDIEIPSSSFFDFYMagDvERVELGVNMETLKGVVARAKKG 101
                                   689******************************************999987665412523578****************** PP

                                   SEEEEEEETTSSEEEEEEE CS
                        PCNA_N  86 dsvtlkaedeadtlalvfe 104
                                   d++ ++  +  d++ +++e
  gi|14600497|ref|NP_147013.1| 102 DQLEVRVRE--DKVLFIVE 118
                                   *99988764..55656655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.096
                                   EEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEETTSSEEEEEEEECTSSEE CS
                        PCNA_N  59 kyrCDrnlalgvnlnslskilkcannedsvtlkaedeadtlalvfesekkdki 111
                                   +     + +   +++ l ++l +a+  +s+ l+   ++  l++vf+s++  ++
  gi|14600497|ref|NP_147013.1| 203 DLEVKEPATSRYDVGYLKRMLGVAKIAESIELSFS-TDKPLKMVFKSPDGSRV 254
                                   44444555555667777788888888888877654.33456677777776666 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 ?    3.0   0.0     0.019   1.1e+02       5      44 ..      12      51 ..       9     129 .. 0.90
   2 !   22.9   0.0   1.3e-08   7.5e-05      63     127 ..     196     260 ..     139     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.019
                                  SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEE CS
                        PCNA_C  5 seydavvklpssefaricrdlsqlsdsvvisvtkegvkfs 44
                                  ++y+a+ +  +  f+ ++  +s++ d+    +t eg++ +
  gi|14600497|ref|NP_147013.1| 12 TDYKAMFRYEAKVFKELVDSVSKILDEGLFIITGEGLRLR 51
                                  6999999****************99999999999999876 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.3e-08
                                   SSGGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                        PCNA_C  63 dkeeeavklelkepvtltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                    ++   + le+kep t  + + Yl ++   + ++e ++ls+s + Pl++ +k  d+  ++ylla+
  gi|14600497|ref|NP_147013.1| 196 RESPALIDLEVKEPATSRYDVGYLKRMLGVAKIAESIELSFSTDKPLKMVFKSPDGSRVTYLLAP 260
                                   45556789*******************************************************98 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.17       3      86 ..      27     107 ..      25     162 .. 0.72
   2 ?   -1.6   0.0      0.25   1.5e+03       8      29 ..     162     183 ..     155     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                          Rad9   3 ralqclsrigdelyleisedglelrtvnssrSayalvtl.kksfFdkyekevseqirckilvKsvlsvfrslsakektvek 82 
                                    ++ ++s+i de  + i+ +gl+lr ++ +r a + +++ ++sfFd y     e +++ +++ ++  v     a+ k+ ++
  gi|14600497|ref|NP_147013.1|  27 ELVDSVSKILDEGLFIITGEGLRLRGMDPARVALVDIEIpSSSFFDFYMAGDVERVELGVNMETLKGVV----ARAKKGDQ 103
                                   5799********999**********************99457899999443334444444443333332....33334444 PP

                          Rad9  83 vkis 86 
                                   ++++
  gi|14600497|ref|NP_147013.1| 104 LEVR 107
                                   4444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.25
                          Rad9   8 lsrigdelyleisedglelrtv 29 
                                   +  +gd + ++++ed+l++r+v
  gi|14600497|ref|NP_147013.1| 162 VELVGDIVEFDAGEDYLSIRSV 183
                                   55699999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2014.60
//
Query:       gi|118430913|ref|NP_147014.2|  [L=442]
Description: hypothetical protein APE_0163.1 [Aeropyrum pernix K1]
Scores for complete 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   91.9   0.1    1.2e-24   86.7   0.1    2.3  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 !   86.7   0.1   6.5e-29   1.2e-24      57     390 ..      63     361 ..      60     367 .. 0.92

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 6.5e-29
                                    HHHHHHHHHHTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-S CS
                         Aldedh  57 LrkaadlleerkeelaeletletGkplaearaeveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPW 136
                                    L+++ + l +  e l+e+++l+tGk+  ear eve +++ lr  a+l e+                     Gv +a   +
  gi|118430913|ref|NP_147014.2|  63 LEALEAELSDMDEILVETLVLDTGKTRVEARLEVEASLRLLRSSAGLGEERF------------------RGVLVAMPDY 124
                                    67778889999999********************************998833..................3999999*** PP

                                    SSCCHHHHHHHHHHHHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HH CS
                         Aldedh 137 NfPlllaawklapalaaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGste 216
                                     +Pl  ++ +l  a   G  v+lKP  ++pl  +l+a ++ + g+ +  ln+v ++g+++   l +  + + ++ft  ++
  gi|118430913|ref|NP_147014.2| 125 TMPLYNTVYSLFYAAGRGMGVLLKPPRKAPLAPALVAAAASRLGMEDS-LNLVFTTGASL-LGLSRVFRSESIAFTCPSK 202
                                    ********************************************9765.78888878754.468999999******9877 PP

                                    HHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT- CS
                         Aldedh 217 vgrkiakaaaknlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakkl 296
                                     +   a  +a+          G +++iv +    d  ++ i+ g  ++aGQ C ++  ++    +    v++lv+aa++l
  gi|118430913|ref|NP_147014.2| 203 AAVARAGISAS---------RGRSAAIVSAGSVDDVIAKFIMYGRSLHAGQACGSIGWVIAIGRLSRGEVDALVDAAESL 273
                                    76555555554.........49******998866999******************************************* PP

                                    -BS-TTSTT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEE CS
                         Aldedh 297 kvgdpldedtdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVls 376
                                    +vgdp d++t +GPli++  +e  e+yv+  +  g  + +G       +++g +v P v+++v +d  ++  +   PVl+
  gi|118430913|ref|NP_147014.2| 274 RVGDPTDPSTAMGPLIKPGLAEASERYVNYIEGMGGVVPTGY------KRNGRYVWPSVVEGVVKDPIVLSRDPRFPVLP 347
                                    ****************************************99......78****************************** PP

                                    EEEESSHHHHHHHH CS
                         Aldedh 377 vikfkdeeeaieia 390
                                    ++ +++ eea +ia
  gi|118430913|ref|NP_147014.2| 348 IVYVSSPEEAASIA 361
                                    **********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 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:                        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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3697.49
//
Query:       gi|118430914|ref|NP_147015.2|  [L=180]
Description: ATP:cobalamin adenosyltransferase [Aeropyrum pernix K1]
Scores for complete 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-42  143.9   0.0    5.3e-42  143.7   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 !  143.7   0.0     3e-46   5.3e-42       2     162 ..       5     168 ..       4     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 3e-46
                                    XXXXXXXXXXXXX.XX......XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTT..THHHHHHHHHHHHHHHHHHHHHHT CS
                Cob_adeno_trans   2 yTrtGDkGtTslv.gge.....rvsKddprveayGtvDelnsaiglarallaee..eeelkeaLeeiqneLfdlgaelat 73 
                                    yTrtGD+G+T ++  ge     rv+Kd+p +e++Gt+De+ns+iglar++l+ e  e +++++L+++q+ Lf++g ++++
  gi|118430914|ref|NP_147015.2|   5 YTRTGDSGETWCFaLGEgrkpvRVPKDHPLIEFLGTLDEANSLIGLARSFLSGEglEGSIDNDLKWMQRLLFNIGFTFSS 84 
                                    9*********9864333347889***************************988899999*******************73 PP

                                    .-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS...HHHHHHHHH CS
                Cob_adeno_trans  74 pekkkekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee..veeevlkylN 151
                                         ++ ++ ee++++le+  d++    +pl++f+lp gs  +aa+h aR+ +RraER++v+++++   v++ +l+++N
  gi|118430914|ref|NP_147015.2|  85 -----TEPRVGEEDLKKLESMADSYYG--EPLRRFVLPAGSSKVAAIHAARAAVRRAERRLVTAMRSGvsVDPLILRIVN 157
                                    .....567899999***********97..79*********************************99888889******** PP

                                    HHHHHHHHHHH CS
                Cob_adeno_trans 152 RLSDlLfvlar 162
                                    R SD Lf++a 
  gi|118430914|ref|NP_147015.2| 158 RASDALFAMAV 168
                                    *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1347.39
//
Query:       gi|14600500|ref|NP_147016.1|  [L=128]
Description: hypothetical protein APE_0167 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1015.92
//
Query:       gi|118430915|ref|NP_147017.2|  [L=127]
Description: hypothetical protein APE_0168.1 [Aeropyrum pernix K1]
Scores for 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-07   28.8   1.0    1.7e-06   28.0   0.1    1.9  3  HTH_3           Helix-turn-helix
    0.00038   20.4   0.3     0.0043   17.0   0.1    2.4  2  HTH_11          HTH domain
     0.0032   17.0   0.3      0.014   14.9   0.3    2.1  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0036   16.9   0.6       0.43   10.2   0.2    2.9  3  HTH_50          Helix-turn-helix domain
     0.0048   16.9   0.3      0.024   14.6   0.0    2.2  3  HTH_19          Helix-turn-helix domain
     0.0073   16.6   0.1     0.0073   16.6   0.1    1.7  2  HTH_31          Helix-turn-helix domain
     0.0081   15.8   0.1      0.024   14.3   0.1    1.8  1  Sigma70_r4_2    Sigma-70, region 4
     0.0096   16.0   0.2      0.028   14.6   0.2    1.8  1  HTH_28          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   14.5   0.2      0.024   14.5   0.2    2.3  3  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      0.064   13.1   0.0       0.19   11.7   0.0    1.8  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.075   13.2   0.3       0.18   12.0   0.1    1.7  2  Trp_repressor   Trp repressor protein
       0.08   13.3   0.5        1.5    9.2   0.3    2.4  3  ATP-synt_F      ATP synthase (F/14-kDa) subunit
       0.08   12.8   0.6       0.32   10.8   0.0    2.1  2  HTH_10          HTH DNA binding domain
      0.098   12.5   1.0       0.26   11.1   0.2    2.1  2  HTH_23          Homeodomain-like domain
        0.1   12.9   0.0       0.19   12.0   0.0    1.6  1  KORA            TrfB plasmid transcriptional repressor
       0.32   10.8   1.8        1.6    8.6   0.0    2.8  4  LacI            Bacterial regulatory proteins, lacI family


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 !   28.0   0.1   1.5e-09   1.7e-06      10      45 ..      27      62 ..      21      64 .. 0.91
   2 ?   -2.9   0.0       6.6   7.4e+03      41      50 ..      74      83 ..      71      87 .. 0.55
   3 ?   -3.2   0.0       8.4   9.4e+03      44      51 ..     102     109 ..     100     111 .. 0.61

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                                   HHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHH CS
                          HTH_3 10 lsqeeLAeklGvsrstisriEnGernPsletlkkla 45
                                    + +eLA +lGv++++i+++++G ++Ps +t+ k +
  gi|118430915|ref|NP_147017.2| 27 RTYRELASELGVTPAAIAKYISGATHPSDKTVAKAL 62
                                   5889***************************99965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                                   HHHHHHHHTS CS
                          HTH_3 41 lkklakaLgv 50
                                   ++++++ L  
  gi|118430915|ref|NP_147017.2| 74 AIAISEDLAE 83
                                   5555555544 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8.4
                                    HHHHHTSE CS
                          HTH_3  44 lakaLgvs 51 
                                    la+aL  s
  gi|118430915|ref|NP_147017.2| 102 LAEALEES 109
                                    67777554 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.9e-06    0.0043       2      36 ..      16      47 ..      15      49 .. 0.92
   2 ?    0.8   0.0      0.43   4.8e+02       6      26 ..      89     107 ..      85     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdI 36
                                   +++i+ +Ll++r   +  eLA eL+v+ +++ ++I
  gi|118430915|ref|NP_147017.2| 16 RRKIIAILLSTR---TYRELASELGVTPAAIAKYI 47
                                   799*****9999...78*****************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.43
                         HTH_11   6 lelLleargpisgeeLAeeLn 26 
                                    + +++e+r  ++g  LAe L+
  gi|118430915|ref|NP_147017.2|  89 VNWIIEER--LPGRLLAEALE 107
                                    55666666..99******997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   1.2e-05     0.014       3      38 ..      14      47 ..      13      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                         HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrl 38
                                   et+rkI+ +L      ++reLA +lg++p+++ +++
  gi|118430915|ref|NP_147017.2| 14 ETRRKIIAILLS--TRTYRELASELGVTPAAIAKYI 47
                                   789999999999..89****************9998 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2   0.00038      0.43      13      42 ..      17      45 ..      11      48 .. 0.78
   2 ?    3.4   0.0     0.054        60      22      35 ..      51      64 ..      49      66 .. 0.88
   3 ?   -0.7   0.0         1   1.2e+03      27      33 ..     100     106 ..      78     111 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00038
                         HTH_50 13 relikkayekYpStRklAkrLGvShtaian 42
                                   r++i+ ++++    R lA  LGv+ +aia+
  gi|118430915|ref|NP_147017.2| 17 RKIIAILLST-RTYRELASELGVTPAAIAK 45
                                   6666666655.558**************96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.054
                         HTH_50 22 kYpStRklAkrLGv 35
                                   ++pS  ++Ak+L +
  gi|118430915|ref|NP_147017.2| 51 THPSDKTVAKALEI 64
                                   89*********976 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1
                         HTH_50  27 RklAkrL 33 
                                    R+lA++L
  gi|118430915|ref|NP_147017.2| 100 RLLAEAL 106
                                    8888887 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.2   5.9e+03      24      32 ..      13      22 ..       8      25 .. 0.67
   2 !   14.6   0.0   2.2e-05     0.024      14      51 ..      28      64 ..      26      65 .. 0.92
   3 ?   -0.8   0.1       1.4   1.6e+03      20      40 ..      79      98 ..      67     112 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.2
                         HTH_19 24 is.rskisai 32
                                      r+ki+ai
  gi|118430915|ref|NP_147017.2| 13 KEtRRKIIAI 22
                                   4448888887 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.2e-05
                         HTH_19 14 tqeelaerlgisrskisaiEngkkdvpsaelllkiaea 51
                                   t +ela++lg++++ i+++++g +  ps +++ k++e+
  gi|118430915|ref|NP_147017.2| 28 TYRELASELGVTPAAIAKYISGAT-HPSDKTVAKALEI 64
                                   789*******************99.9999999998875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.4
                         HTH_19 20 erlgisrskisaiEngkkdvp 40
                                   e+l  s++++ +++ +++  p
  gi|118430915|ref|NP_147017.2| 79 EDLAESIRSLVNWIIEER-LP 98
                                   455555555555554433.33 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.5e-06    0.0073      16      52 ..      28      63 ..      24      72 .. 0.92
   2 ?   -2.4   0.3       5.7   6.4e+03      15      15 ..     113     113 ..      99     124 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.5e-06
                         HTH_31 16 sqeevAerlgvsestlsrlEqGrrgrpspavlealar 52
                                   + +e+A  lgv+++ + ++ +G+   ps  +++++++
  gi|118430915|ref|NP_147017.2| 28 TYRELASELGVTPAAIAKYISGAT-HPSDKTVAKALE 63
                                   789*********************.7******99987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.7
                         HTH_31  15 L 15 
                                    +
  gi|118430915|ref|NP_147017.2| 113 M 113
                                    1 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 !   14.3   0.1   2.2e-05     0.024      11      48 ..      11      48 ..       7      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                   S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVksrls 48
                                   L ++ r+ ++ + l   +y+E A++lg++++++ +++s
  gi|118430915|ref|NP_147017.2| 11 LGKETRRKIIAILLSTRTYRELASELGVTPAAIAKYIS 48
                                   55677888888899999*****************9997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   2.5e-05     0.028       2      33 ..      16      47 ..      15      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                         HTH_28  2 RleiikllaaGhsvreaArelgisrrtvyrWi 33
                                   R++ii  l++ +++re+A elg+++  + + i
  gi|118430915|ref|NP_147017.2| 16 RRKIIAILLSTRTYRELASELGVTPAAIAKYI 47
                                   889999999****************9998765 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 ?   14.5   0.2   2.1e-05     0.024       6      35 ..      17      44 ..      14      45 .. 0.86
   2 ?   -2.9   0.0       5.8   6.5e+03      11      18 ..      61      68 ..      55      74 .. 0.56
   3 ?   -2.1   0.1       3.3   3.7e+03      21      28 ..     100     107 ..      95     114 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                  HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlSestvl 35
                                   rkI+++L   + ++y+eLA ++G+++++++
  gi|118430915|ref|NP_147017.2| 17 RKIIAILL--STRTYRELASELGVTPAAIA 44
                                   67777777..789**************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                  HTH_AsnC-type 11 aLqedaRi 18
                                   aL+  +R 
  gi|118430915|ref|NP_147017.2| 61 ALEIASRE 68
                                   45555555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.3
                  HTH_AsnC-type  21 aeLAervG 28 
                                    + LAe++ 
  gi|118430915|ref|NP_147017.2| 100 RLLAEALE 107
                                    55666664 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.19      11      33 ..      29      51 ..      20      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                 YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkk 33
                                    ++LA +lgv+++a+ + ++g +
  gi|118430915|ref|NP_147017.2| 29 YRELASELGVTPAAIAKYISGAT 51
                                   579**************998865 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00016      0.18      37      67 ..      15      44 ..      12      63 .. 0.90
   2 ?   -1.8   0.0       3.1   3.4e+03      42      64 ..      89     111 ..      76     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                  Trp_repressor 37 qRlqvvkeLLkeelsqreIaeelgvSiAtIt 67
                                   +R +++  +L   +++re+a+elgv  A I 
  gi|118430915|ref|NP_147017.2| 15 TRRKIIA-ILLSTRTYRELASELGVTPAAIA 44
                                   69999*9.888999***********999996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.1
                  Trp_repressor  42 vkeLLkeelsqreIaeelgvSiA 64 
                                    v+ +++e l+ r +ae l+ S+A
  gi|118430915|ref|NP_147017.2|  89 VNWIIEERLPGRLLAEALEESVA 111
                                    44467777777777777777777 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.6     4e+03      37      51 ..      15      29 ..       8      41 .. 0.59
   2 ?    9.2   0.3    0.0014       1.5      25      68 ..      54      98 ..      34      99 .. 0.73
   3 ?    1.4   0.0      0.37   4.1e+02       7      20 ..     107     120 ..     105     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.6
                                   HHHTTEEEEEEEHHH CS
                     ATP-synt_F 37 leredigiiliteki 51
                                   ++r+ i+i+l t ++
  gi|118430915|ref|NP_147017.2| 15 TRRKIIAILLSTRTY 29
                                   445555555544443 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                                   SHHHHHHHHHHHHH..HTTEEEEEEEHHHHCCCHHHHHHCTCSSSS CS
                     ATP-synt_F 25 deeeieealkelle..redigiilitekiaeeirelideykeealP 68
                                   +++++++al+ + +  +e+i+ i+i+e++ae ir+l++ + ee lP
  gi|118430915|ref|NP_147017.2| 54 SDKTVAKALEIASReeKEEIA-IAISEDLAESIRSLVNWIIEERLP 98
                                   567788888888863134444.79************9988777666 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.37
                                    HHHHHHHHHTTCEE CS
                     ATP-synt_F   7 edtvtgfrlaGvge 20 
                                    e++v  +rlaGv+ 
  gi|118430915|ref|NP_147017.2| 107 EESVARMRLAGVRR 120
                                    68999******986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00028      0.32      25      47 ..      28      50 ..      26      52 .. 0.89
   2 ?   -0.9   0.1       1.3   1.4e+03      28      38 ..      57      67 ..      54      83 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                         HTH_10 25 tlkeLAkelGIskstlsehLrka 47
                                   t +eLA elG++++++ ++++ a
  gi|118430915|ref|NP_147017.2| 28 TYRELASELGVTPAAIAKYISGA 50
                                   779***************99877 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                         HTH_10 28 eLAkelGIsks 38
                                    +Ak+l I+  
  gi|118430915|ref|NP_147017.2| 57 TVAKALEIASR 67
                                   46777777655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00023      0.26       4      39 ..      15      48 ..      13      51 .. 0.80
   2 ?   -1.4   0.0       2.1   2.3e+03      22      29 ..      57      64 ..      54      76 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                         HTH_23  4 ereRlrillllaeGlsvreIAreLgvsrrTvyrwlk 39
                                    r+++ ++ll     ++re A eLgv++  + ++++
  gi|118430915|ref|NP_147017.2| 15 TRRKIIAILLST--RTYRELASELGVTPAAIAKYIS 48
                                   566666777777..5**************9998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                         HTH_23 22 eIAreLgv 29
                                   ++A++L +
  gi|118430915|ref|NP_147017.2| 57 TVAKALEI 64
                                   55555544 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.19      16      53 ..      11      48 ..       5      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                           KORA 16 laeqtveiargvLVegkkqadvatelgltkqavsqavk 53
                                   l+++t+  +  +L   ++  ++a elg+t  a+ + + 
  gi|118430915|ref|NP_147017.2| 11 LGKETRRKIIAILLSTRTYRELASELGVTPAAIAKYIS 48
                                   8999***9*************************98765 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.82   9.1e+02      28      38 ..      13      23 ..      11      25 .. 0.87
   2 ?    8.6   0.0    0.0014       1.6       3      38 ..      30      65 ..      28      69 .. 0.90
   3 ?   -1.4   0.1       1.9   2.1e+03      26      40 ..      81      95 ..      70      96 .. 0.69
   4 ?   -3.4   0.0       8.1   9.1e+03       7      11 ..     114     118 ..     114     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.82
                                   HHHHHHHHHHH CS
                           LacI 28 eetrerVeaam 38
                                   +etr ++ a++
  gi|118430915|ref|NP_147017.2| 13 KETRRKIIAIL 23
                                   69*****9985 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0014
                                   HHHHHHCTS-HHHHHHHCTTSSSSTHHHHHHHHHHH CS
                           LacI  3 kDVArlAGVSkaTVSrvLnnkerVseetrerVeaam 38
                                   +++A + GV+ a++ ++++++ + s++t  + ++++
  gi|118430915|ref|NP_147017.2| 30 RELASELGVTPAAIAKYISGATHPSDKTVAKALEIA 65
                                   6889999*********************99988887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.9
                                   STHHHHHHHHHHHHH CS
                           LacI 26 VseetrerVeaamee 40
                                    +e++r  V+ ++ee
  gi|118430915|ref|NP_147017.2| 81 LAESIRSLVNWIIEE 95
                                   456667777777776 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 8.1
                                    HHCTS CS
                           LacI   7 rlAGV 11 
                                    rlAGV
  gi|118430915|ref|NP_147017.2| 114 RLAGV 118
                                    799*9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 955.76
//
Query:       gi|118430916|ref|NP_147018.2|  [L=403]
Description: alanine glyoxylate transaminase [Aeropyrum pernix K1]
Scores for complete 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-37  128.6   0.0    3.7e-37  128.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    8.8e-11   41.2   0.0    1.7e-10   40.3   0.0    1.3  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
    0.00012   21.2   0.0    0.00019   20.5   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.036   13.4   0.0    1.7  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.052   12.9   0.0       0.16   11.3   0.0    1.7  2  ECH_1            Enoyl-CoA hydratase/isomerase
      0.093   12.0   0.0       0.13   11.6   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  128.3   0.0   1.3e-40   3.7e-37      32     357 ..      60     388 ..      35     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 1.3e-40
                                    HHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                  Aminotran_1_2  32 laggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                    + g ++ +y+p+ g   ++e+  +fl r   ++ +r+  ++v++G+++++ + +  + l pgd++++ +p y   +n+++
  gi|118430916|ref|NP_147018.2|  60 ELGDKALQYSPTPGVSIFRERALSFLERMGLKTSDRQ--LLVTTGSQEALFLTALST-LSPGDVVIMEEPGYLAAINVFK 136
                                    6678999********************7777777777..*********999999888.9********************* PP

                                    HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEE.SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETT CS
                  Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilve.sphNPtGtvatleeleklldlakkynlllfvDeaY 190
                                    + g+ +v++p++   d +l+   l e l+++ ++ +k+k+++++ +++NP Gt ++l+  ++ll+la  y +l++ D+ Y
  gi|118430916|ref|NP_147018.2| 137 ALGARIVPVPVD---DKGLNTGVLAETLDRLDAEGVKPKLVYTNpTCNNPNGTTMPLDRRRELLQLASNYDMLVIEDDPY 213
                                    **********66...999*************************979********************************** PP

                                    TTCBSSSS.HTHHH.HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHH CS
                  Aminotran_1_2 191 agfvfgsl.davat.ranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaaalsd 266
                                    ++ +f+++ +   + +  ++ e  ++ v+++sK + ++G+R+G +l+ ++v   ++ l++ +    s+l q+++a+al+ 
  gi|118430916|ref|NP_147018.2| 214 SHIAFEKTgEE--VpLQALDSEGRVVYVTTFSKIL-APGLRLGLTLAPSEVTARIELLKQIVDLhtSTLDQYIAAEALER 290
                                    ******76433..247777777779********98.6************999999999999888889999********99 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCS.CSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGGGGTS.. CS
                  Aminotran_1_2 267 allkqseleemrqrlqkrrkelrdeLael..glkvlasq.sgmflltdlsae.takelskkLleevgvyvtpgtsftv.. 340
                                       +++ ++ +++ + ++r+ + ++L+e   g++ ++++ +g+f + +++   ++ +l  k +e+ gv+ +pg  f+v  
  gi|118430916|ref|NP_147018.2| 291 GI-VDKVISRAVSIYRRKRDIMIESLEENmsGVATWTKPiGGFFIFLRINGPvDMRALMPKAVER-GVAYVPGDAFHVtp 368
                                    88.7789*******************999**888888887*********9998999*********.*************7 PP

                                    ...TTEEEEECTTS-HHHHH CS
                  Aminotran_1_2 341 ...pgrlRitvAglteeele 357
                                       ++  R++++  teee+ 
  gi|118430916|ref|NP_147018.2| 369 gagRNTARLSYSFNTEEEIP 388
                                    77766777777666666665 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   5.6e-14   1.7e-10     127     376 ..     121     366 ..     116     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 5.6e-14
                                    EEEEES--HHHHHHHHHHT-EEEEEEEETTEE-H....HHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT-- CS
                 Aminotran_MocR 127 llvtvpGydrhfllleelGielltvdlqddGpdv....daveklvaedasvkGilavpkysnptGetiseevarrlaalk 202
                                    +++  pGy     + + lG +++ v+++d G +     +++++l ae    k +++ p+  np G+t+  ++ r+l  l 
  gi|118430916|ref|NP_147018.2| 121 VIMEEPGYLAAINVFKALGARIVPVPVDDKGLNTgvlaETLDRLDAEGVKPKLVYTNPTCNNPNGTTMPLDRRRELLQLA 200
                                    57889************************99886222256789999999999************************9995 PP

                                    -SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S CS
                 Aminotran_MocR 203 aaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkylGlqsi 282
                                     +  d+ +  dd y+  ++     k+ + v+l +      r + +++ ski   G  +++  + ++  a ++    +  +
  gi|118430916|ref|NP_147018.2| 201 -SNYDMLVIEDDPYSHIAF-E---KTGEEVPLQAL-DSEGRVVYVTTFSKILAPGLRLGLTLAPSEVTARIELLKQIVDL 274
                                    .5789*********85555.3...33333444222.223466666778********999988888888888888888888 PP

                                    ---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EEEEESSS-HHHHH.HHH CS
                 Aminotran_MocR 283 GpdkveqlrhvkflkdyeGlealmrdhaeliapkfeavlevleaelggaevatwteprGGyfisldtldgvakrvv.kla 361
                                        ++q      l+    +   + +   + + k + + e le++++  +vatwt+p GG+fi l +  +v  r +   a
  gi|118430916|ref|NP_147018.2| 275 HTSTLDQYIAAEALER-GIVDKVISRAVSIYRRKRDIMIESLEENMS--GVATWTKPIGGFFIFLRINGPVDMRALmPKA 351
                                    8899999888777753.3456677888899999999999***99987..59*******************9988751578 PP

                                    HHCTEE---TTTTSS CS
                 Aminotran_MocR 362 eeaGvsltaaGatyp 376
                                     e Gv+  +  a + 
  gi|118430916|ref|NP_147018.2| 352 VERGVAYVPGDAFHV 366
                                    899999888766544 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.3e-08   0.00019      60     173 ..      93     208 ..      85     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.3e-08
                                    TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBE..GGGHHHH-- CS
                    Aminotran_5  60 seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeld..ldeleklln 137
                                    s+ ++++t G+ ea+ l als    l+pgd +++ e ++ a++    ++ k+ ga+++ +p+d++g+ +  l e  + l+
  gi|118430916|ref|NP_147018.2|  93 SDRQLLVTTGSQEALFLTALST---LSPGDVVIMEEPGYLAAI----NVFKALGARIVPVPVDDKGLNTgvLAETLDRLD 165
                                    458999****************...******************....7777889*************9988888888885 PP

                                    ...TTEEEEEEESB.ETTTTEB--HH...HHHHHHHHTT-EEE CS
                    Aminotran_5 138 ...ektklvaithv.snvtGtiqpve...eigklakkkgalvl 173
                                        k+klv+ + + +n  Gt  p++   e+ +la ++++lv+
  gi|118430916|ref|NP_147018.2| 166 aegVKPKLVYTNPTcNNPNGTTMPLDrrrELLQLASNYDMLVI 208
                                    3236899999987538899999999633357777777777776 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 ?   13.4   0.0   1.2e-05     0.036      52      98 ..     106     153 ..      86     160 .. 0.82
   2 ?   -2.1   0.0       0.6   1.8e+03     129     146 ..     195     212 ..     192     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                    HHHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSS CS
                DegT_DnrJ_EryC1  52 hlaLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtyn 98 
                                    +l L+a   ++pgd VI+   +++a +n+   lga+ v+v vd + +n
  gi|118430916|ref|NP_147018.2| 106 ALFLTAlSTLSPGDVVIMEEPGYLAAINVFKALGARIVPVPVDDKGLN 153
                                    35566746778*************************999999987665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.6
                                    HHHHHHHHCT-EEEEE-T CS
                DegT_DnrJ_EryC1 129 alkaiaakhglkvieDaA 146
                                    +l ++a+++++ vieD  
  gi|118430916|ref|NP_147018.2| 195 ELLQLASNYDMLVIEDDP 212
                                    6899************65 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.54   1.6e+03     172     194 ..      43      65 ..      37      69 .. 0.84
   2 ?   11.3   0.0   5.3e-05      0.16     146     189 ..     269     313 ..     236     328 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.54
                                    EEESGGGHHHHHHHHHHHHHHSC CS
                          ECH_1 172 kvvpeeqlleealelaeklaeks 194
                                    +v+p+e+l + a++++ +l +k+
  gi|118430916|ref|NP_147018.2|  43 RVFPAEELADIARNVVSELGDKA 65 
                                    799************99998765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.3e-05
                                    HHHHHHHHHHT-EEEHHHHHHCTSSSEEESG.GGHHHHHHHHHHH CS
                          ECH_1 146 kskAeeilllgkkisaqealkvGlvdkvvpe.eqlleealelaek 189
                                    k+++   + + +++ a+eal++G+vdkv+++   + +  + ++ +
  gi|118430916|ref|NP_147018.2| 269 KQIVDLHTSTLDQYIAAEALERGIVDKVISRaVSIYRRKRDIMIE 313
                                    5555666677889*****************955666666666554 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.13      95     166 ..     139     209 ..      62     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                    --EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEE CS
                Beta_elim_lyase  95 gvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhl 166
                                    g++ ++++ ++   ++   l++ +++ +a   k+kl+++  T+n   G+ ++l+  re+ ++a +y++ ++ 
  gi|118430916|ref|NP_147018.2| 139 GARIVPVPVDD-KGLNTGVLAETLDRLDAEGVKPKLVYTNPTCNNPNGTTMPLDRRRELLQLASNYDMLVIE 209
                                    33444444444.23555555555555555557**********************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2867.69
//
Query:       gi|118430917|ref|NP_147019.2|  [L=343]
Description: glyceraldehyde-3-phosphate dehydrogenase [Aeropyrum pernix K1]
Scores for 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-19   68.4   0.1    8.6e-19   67.7   0.1    1.4  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
    3.9e-11   43.1   0.1    9.9e-11   41.8   0.1    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    7.3e-06   26.3   1.1    3.3e-05   24.1   0.6    2.4  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
    0.00061   19.2   0.7        0.2   11.0   0.2    2.8  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00065   20.5   0.2     0.0019   19.0   0.0    1.9  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
      0.053   13.8   0.0        0.1   12.8   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.061   14.0   0.1       0.21   12.2   0.1    1.9  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.1   3.4e-22   8.6e-19       1     157 [.     147     300 ..     147     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3.4e-22
                                    HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEEEEE CS
                        Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldglAvr 78 
                                    L +l+  ln +fg++++++++v++ +++         k+++++++ +   n+ + ++++a +v +Vlp    ++++ Av 
  gi|118430917|ref|NP_147019.2| 147 LLRLICTLNREFGVESVRAVLVRRGADP---------KEVKKGPIDSivLNPPTLPSHHAVDVRTVLPW--LDIKTAAVA 215
                                    5689999*********************.........9*******99999******************6..57889**** PP

                                    ESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH.....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEETTTE CS
                        Gp_dh_C  79 VPtpnvsvvdlvvelekevtveevnaalkeaae.....galkgilsyteeelvssDlvgdph..ssifdaketivveenl 151
                                    VPt+ ++++ ++++l+k+v++ ev ++l  a++     +  +gi s+++    +  l ++ +   ++++ +e+ +v++++
  gi|118430917|ref|NP_147019.2| 216 VPTTFMHMHHVTLKLAKPVEKREVLETLASAPRimlvsSGDTGIKSTSQLVD-AARLSRMGYdiPELVVFEESVAVDGRE 294
                                    *********************************9988655556655555443.444555544467888888888888888 PP

                                    EEEEEE CS
                        Gp_dh_C 152 vkvvaw 157
                                    v ++++
  gi|118430917|ref|NP_147019.2| 295 VMLFQA 300
                                    888877 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.1   3.9e-14   9.9e-11       1      95 [.       4     108 ..       4     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 3.9e-14
                                    EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHH.........HHSSSS--S-BEBSSHHHHHHH-S CS
                         DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdag.........ellglgklgvavtddleevlekad 69 
                                    +kv+v+G+ G++G++v+ a++ ++d++lv++v+r++   +l + + g         e+ +++k g++v  +l e+l+ +d
  gi|118430917|ref|NP_147019.2|   4 VKVGVNGF-GTIGRRVALAITLQKDMKLVGVVKRTPdyAALYAASRGipiytptakEAEEFEKRGIKVGGTLRELLARVD 82 
                                    69******.**************************94444444455599*****98888889****************** PP

                                    EEEE-S-HHHHHHHHHHHHHT.T-EEE CS
                         DapB_N  70 vliDFTtpeavlenlklalek.gvklV 95 
                                    v++D T pe+  ++ k ++++ gvk V
  gi|118430917|ref|NP_147019.2|  83 VVVDAT-PEGQGAKNKPLYREaGVKQV 108
                                    ******.77666666666554488877 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.6   1.3e-08   3.3e-05       1      37 [.       4      41 ..       4      93 .. 0.82
   2 ?   -2.9   0.0       3.4   8.6e+03      60      77 ..     285     302 ..     272     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                                   CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HH CS
                        Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaind.ltdle 37
                                   vkv++nGfG IGr v+ a+  +k++++v + + + d +
  gi|118430917|ref|NP_147019.2|  4 VKVGVNGFGTIGRRVALAITLQKDMKLVGVVKrTPDYA 41
                                   69****************************99444443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.4
                                    TTEEEETTEEEEEE--SS CS
                        Gp_dh_N  60 eealvvngkkikvlaekd 77 
                                    ee++ v+g+++ ++++ +
  gi|118430917|ref|NP_147019.2| 285 EESVAVDGREVMLFQAVH 302
                                    677788888888877655 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 !   11.0   0.2   7.8e-05       0.2      38      69 ..       5      37 ..       1     108 [. 0.71
   2 ?   -1.2   0.0      0.44   1.1e+03     101     117 ..     258     274 ..     220     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.8e-05
                                   EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSH CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrsk 69
                                   +vG+ G+G IG++va  ++ + +mk++++ ++ 
  gi|118430917|ref|NP_147019.2|  5 KVGVNGFGTIGRRVALAITlQKDMKLVGVVKRT 37
                                   799**********99888778899887764443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.44
                                    -STTTTTSBSHHHHHCS CS
                   2-Hacid_dh_C 101 ltpetrhlinaeelakm 117
                                      ++t +l++a++l++m
  gi|118430917|ref|NP_147019.2| 258 GIKSTSQLVDAARLSRM 274
                                    45789999999999998 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 !   19.0   0.0   7.4e-07    0.0019       2      77 ..       5      95 ..       4     123 .. 0.89
   2 ?   -2.4   0.1       3.2   8.2e+03      61      79 ..     207     226 ..     189     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.4e-07
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..................HHHHHTCTTESE CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..................leelladpeida 65
                                   +v++ G+G ig++ + ++  + ++ ++v+++++ +  a   a+s g++ y+                   l+ella  ++d+
  gi|118430917|ref|NP_147019.2|  5 KVGVNGFGTIGRRVALAITLQ-KDMKLVGVVKRTPDYAALYAASRGIPIYTPtakeaeefekrgikvggtLRELLA--RVDV 83
                                   89*************777777.**************************88888899999999**************..9*** PP

                                   EEE-S-GGGHHH CS
                   GFO_IDH_MocA 66 vivatpngthee 77
                                   v+ atp g++++
  gi|118430917|ref|NP_147019.2| 84 VVDATPEGQGAK 95
                                   *****9988765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.2
                                    TTESEEEE-S-GGG.HHHHH CS
                   GFO_IDH_MocA  61 peidavivatpngt.heela 79 
                                     +i+ + va+p++  h+ ++
  gi|118430917|ref|NP_147019.2| 207 LDIKTAAVAVPTTFmHMHHV 226
                                    47888899999944355554 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 ?   12.8   0.0     4e-05       0.1       3      81 ..       8      92 ..       6     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4e-05
                                   EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......TTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                Sacchrp_dh_NADP  3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......lgvrfeaialdaenyeavLaallkegdlvvnls 77
                                   + G+G +G+ va  +  ++d++  + v+ r+ + ++  aa+        + +++e  +    ++  +L +ll+  d+vv+++
  gi|118430917|ref|NP_147019.2|  8 VNGFGTIGRRVALAITLQKDMK-LVGVVKRTPDYAALYAASRgipiytpTAKEAEEFEKRGIKVGGTLRELLARVDVVVDAT 88
                                   66*******************6.999********88888887999998855555555555556677899************9 PP

                                   SGGG CS
                Sacchrp_dh_NADP 78 ppis 81
                                   p  +
  gi|118430917|ref|NP_147019.2| 89 PEGQ 92
                                   9765 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 ?   12.2   0.1   8.2e-05      0.21       1      69 [.      10      90 ..      10      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                                   --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT.................HHHHHT--CB---HHHHHHHHS-EEEEE CS
                  NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrdsllskd.................rkallasealtldlddliahldpdvvVE 65
                                   G+G+iG++v+ +++ q++   ++lv+v++r +  ++                   + + +  ++   l +l+a  ++dvvV+
  gi|118430917|ref|NP_147019.2| 10 GFGTIGRRVALAITLQKD---MKLVGVVKRTPDYAALyaasrgipiytptakeaEEFEKRGIKVGGTLRELLA--RVDVVVD 86
                                   99***************6...8********9333333788999999988876533333444566677788888..9****** PP

                                   -S-- CS
                  NAD_binding_3 66 cass 69
                                   +++ 
  gi|118430917|ref|NP_147019.2| 87 ATPE 90
                                   *986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); 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:                         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 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2616.72
//
Query:       gi|118430918|ref|NP_147020.2|  [L=415]
Description: phosphoglycerate kinase [Aeropyrum pernix K1]
Scores for complete 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-92  310.2   0.0    2.1e-92  310.0   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 !  310.0   0.0   1.2e-96   2.1e-92       1     377 [.      13     396 ..      13     397 .. 0.90

  Alignments for each domain:
  == domain 1  score: 310.0 bits;  conditional E-value: 1.2e-96
                                    GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHHHT CS
                            PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLsellg 80 
                                    ++d+d++gk+v+vR D+N+p+ + g+i dd+ri +a+ T+++l+++ga+vv lsH+grp  e++ +sl+ +a+ Ls++ g
  gi|118430918|ref|NP_147020.2|  13 LDDVDVRGKKVIVRFDLNSPVGNGGEILDDSRIAEAAGTLRELCDRGAAVVALSHQGRP-LESDFVSLERHASLLSRYSG 91 
                                    589********************************************************.599***************** PP

                                    T-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTT..TTT-H....H...HHHHHHHT-SEEEE--GGGTTS--TTT CS
                            PGK  81 keVkfvedvvgeeveeaiaelkegevllLeNvrfykeE..eknde....e...lakklasladvyVnDAFgtahrahaSt 151
                                     eV+fv dv+g+e+ +++a+l++ge +lL+N+r+ +e+  e   e    +   ++++l++la++yVn+AF+++hr++aS+
  gi|118430918|ref|NP_147020.2|  92 VEVRFVMDVIGPEALRTVASLRPGEAVLLDNTRIISEDfiE--AEgtvhArgiMVTRLSKLANMYVNEAFSASHRSQASI 169
                                    ***********************************999543..3333542566*************************** PP

                                    THHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT-B-T CS
                            PGK 152 vgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlkaqgleig 229
                                    vg++ vl++a G+++ekE++ l++++++ erp v++lGGak +d +++++ L ++   d+++++G++   Fl a+g+++ 
  gi|118430918|ref|NP_147020.2| 170 VGFPYVLPSAGGRVLEKEIRSLNRAVSSGERPKVVVLGGAKLKDAVRIVDYLSSSGvaDEVLTTGLVGLLFLYARGYRLP 249
                                    *******98*******************************************998777********************99 PP

                                    TSS-...-G....GGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHHHC CS
                            PGK 230 kslv...ee....dklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaeaik 302
                                    ++++   e+    + +  a++++e+      ++ +p+D+vv+     ++  +++++++ e+    Digp+t+e f++ ++
  gi|118430918|ref|NP_147020.2| 250 RDVTkllEKkggeEAIAKARRIVEEG----RRVRTPIDFVVEV---GDKIYIKPADELTEG-VPKDIGPSTVEYFRAKMR 321
                                    66663335523223466666666665....69**********7...333567788888665.578*************** PP

                                    C-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT..-GGGSSEEESSSHHHHHHHCT CS
                            PGK 303 eaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklg..ladkvshvStGGgAsLelLeg 377
                                     a+++v+ Gp+Gv+e ++f++GT +++ka+ ++  ga++++GGg+  a ++ l   l++kv h+StGGgA+L +L+g
  gi|118430918|ref|NP_147020.2| 322 GARVIVMRGPAGVIEDPRFRRGTVELVKAALSS--GAYTVFGGGHFRAILRDLPehLSSKVGHLSTGGGALLYYLSG 396
                                    ******************************998..68***************9644789****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3064.49
//
Query:       gi|118430919|ref|NP_147021.2|  [L=219]
Description: hypothetical protein APE_0176.1 [Aeropyrum pernix K1]
Scores for 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-34  119.8   0.1    1.3e-34  119.4   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.2e-11   44.5   2.9    5.1e-08   32.7   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.1   1.5e-38   1.3e-34       2     163 .]       5     167 ..       4     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 1.5e-38
                  Lactamase_B_3   2 ltwlghnsflletagarilvDPfka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee.geslevggleir 79 
                                    ++w  h+ +ll+ +++ +++DP ++ +lg+   +++aD +l+++++ dH+++e  ++ ++  +vl++  +s ++g + ++
  gi|118430919|ref|NP_147021.2|   5 VEWCYHAYILLKAGDVLMAIDPHDGgSLGLPTCRVDADYILVTHDHFDHNAVEVARG-KRTKEVLKRfYGSKNLGPFTVT 83 
                                    89*********************999*******************************.999999999679999******* PP

                  Lactamase_B_3  80 avatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklv 159
                                    +v+ +hd+ gg+ rge  ++++e++gl+++hlG+++h ++s+++ el r+Dv+++Pvgg++t++++ea ++++ L+p++ 
  gi|118430919|ref|NP_147021.2|  84 GVKVYHDKAGGTLRGEVAAYRVEVEGLSLVHLGDIGHVITSSSHPELSRPDVLFVPVGGTFTVNAAEAWKIVENLRPRIA 163
                                    ******************************************************************************** PP

                  Lactamase_B_3 160 lPmh 163
                                    +P+h
  gi|118430919|ref|NP_147021.2| 164 VPIH 167
                                    ***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 !   12.4   0.7   9.4e-06     0.084      30      63 ..      40      74 ..      33      79 .. 0.68
   2 !   32.7   0.0   5.7e-12   5.1e-08      99     201 .]      78     168 ..      73     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.4e-06
                                   SEEEEE-SS--HHHHGGGGCCCCC--EE..EEEEEE CS
                  Lactamase_B_2 30 pidaVllthaHyDHlaglltlrelrpkk..lplyap 63
                                   + d +l+th+H+DH a +   r  r k+   ++y++
  gi|118430919|ref|NP_147021.2| 40 DADYILVTHDHFDHNA-VEVARGKRTKEvlKRFYGS 74
                                   5799**********84.5554444444453335555 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 5.7e-12
                                    CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT CS
                  Lactamase_B_2  99 gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlggadllllditayeddemirhmg 177
                                    g   +++t + + h+++   ++ +g+++++r+e +g +++++gD g++   +   +l  +d+l+++++         + +
  gi|118430919|ref|NP_147021.2|  78 G--PFTVTGVKVYHDKAG--GTLRGEVAAYRVEVEGLSLVHLGDIGHVItSSSHPELSRPDVLFVPVG---------GTF 144
                                    4..478999999999999..999***********************987688999*************.........889 PP

                                    ---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 178 HltpeeaveaaadlgakrlvliHi 201
                                    +++  ea+++++ l+++++v+iH+
  gi|118430919|ref|NP_147021.2| 145 TVNAAEAWKIVENLRPRIAVPIHY 168
                                    9999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1600.77
//
Query:       gi|14600506|ref|NP_147022.1|  [L=386]
Description: molybdopterin biosynthesis protein MoeA [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-29  102.7   0.1    2.4e-29  102.1   0.1    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    4.1e-11   42.7   0.0    1.2e-10   41.2   0.0    1.8  2  MoCF_biosynth  Probable molybdopterin binding domain


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 !  102.1   0.1   2.7e-33   2.4e-29       3     157 .]       9     160 ..       7     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 2.7e-33
                                   HHHHHHHHHHH-HH...-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...........-S--- CS
                        MoeA_N   3 veealaiilaalel...eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeepsaageeperll 79 
                                   veea+++i+ +  l    ++e +p  ++++gr+laed+ +p d+P+   +amDGYAv++++ +   +       ++++++ 
  gi|14600506|ref|NP_147022.1|   9 VEEARKRIEFLK-LdyrLHTEiIPS-SQSVGRILAEDLESPNDTPEEPLAAMDGYAVDSTSAKPGARL----RLKDRGPVA 83 
                                   788888765443.345745555999.99*****************************88877777443....345555566 PP

                                   TT-EEEE-TTSB--TT--EEEEGGGE..E......EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHC CS
                        MoeA_N  80 pggavrimTGaplPegadaVvpvEdte.eee..aketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasv 156
                                   +g+av + TG+plP+gadaVv+ E ++ e+         v + v+++env r Ge +++G+ l+++g++++p   +l+ ++
  gi|14600506|ref|NP_147022.1|  84 SGEAVPVDTGDPLPPGADAVVRREAARvEDGyiY-----VsAGVSKWENVFRPGEFVARGSRLASRGDVISPYLAALIMQA 159
                                   666**********************964432331.....14799*****************************99999888 PP

                                   T CS
                        MoeA_N 157 G 157
                                   G
  gi|14600506|ref|NP_147022.1| 160 G 160
                                   7 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.4   3.6e+03      15      35 ..     145     165 ..     137     169 .. 0.77
   2 !   41.2   0.0   1.4e-14   1.2e-10       3     139 ..     174     302 ..     172     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.4
                                   GBHHHHHHHHHHHTTSEEEEE CS
                 MoCF_biosynth  15 eDtngpllaellkelgvevsk 35 
                                    D  +p+la+l+ ++gv+  k
  gi|14600506|ref|NP_147022.1| 145 GDVISPYLAALIMQAGVKSVK 165
                                   578899999999999996554 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 1.4e-14
                                   EEE-HHHH.....TTSS...GBHHHHHHHHHHHTTSE.EEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--H CS
                 MoCF_biosynth   3 itvGdell.....sgki...eDtngpllaellkelgv.evskytvvpDdeeeikeallaaleeadviittGGtGptpdDvt 74 
                                   + vG+ell     +       D  gp++  ll+  g+ e + +  vpD  ee++ea+ +al+ead+++t+GG +++++D  
  gi|14600506|ref|NP_147022.1| 174 MPVGSELLhpetmT--GdgsLDYIGPMVTGLLR--GWsEPRLVPPVPDGREELEEAINRALDEADILVTIGGSSVGRRDSL 250
                                   66788888554441..03336777777777777..8857777779************9999******************** PP

                                   HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHH CS
                 MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeill 139
                                   ++ +a +++  ++gf++ + + +         a +   +++    + +LPG  ++++  l+e l 
  gi|14600506|ref|NP_147022.1| 251 KALVASMGQLVVPGFGASVVKRGGL-------AVV---RNR---IVTMLPGGCVSAAISLHETLF 302
                                   *********9999999998887776.......222...222...355999888877777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3018.46
//
Query:       gi|118430920|ref|NP_147023.2|  [L=140]
Description: molybdopterin-guanine dinucleotide biosynthesis protein MobB [Aeropyrum pernix K1]
Scores for complete 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   92.6   0.1      2e-26   92.4   0.1    1.1  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
    6.3e-05   22.9   0.2    0.00056   19.8   0.2    1.9  1  AAA_26       AAA domain
    6.9e-05   23.3   0.2    0.00012   22.5   0.2    1.6  1  AAA_16       AAA ATPase domain
    0.00059   19.5   0.1     0.0011   18.6   0.1    1.5  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
     0.0017   18.8   0.0     0.0019   18.7   0.0    1.2  1  ABC_tran     ABC transporter
     0.0023   18.0   0.4     0.0033   17.5   0.4    1.7  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0036   17.6   0.0     0.0043   17.3   0.0    1.2  1  AAA_22       AAA domain
     0.0083   16.0   0.3      0.021   14.8   0.1    1.7  2  NTPase_1     NTPase
     0.0089   16.0   0.0      0.011   15.7   0.0    1.2  1  ATPase_2     ATPase domain predominantly from Archaea
      0.009   15.8   0.0      0.017   14.9   0.0    1.4  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0097   16.1   0.1      0.013   15.7   0.1    1.4  1  AAA_33       AAA domain
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.013   15.9   0.0    1.4  1  AAA          ATPase family associated with various cellular a
       0.01   15.6   0.2      0.063   13.0   0.5    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.011   15.6   0.1      0.024   14.5   0.0    1.5  2  APS_kinase   Adenylylsulphate kinase
      0.012   14.7   1.2      0.022   13.9   1.2    1.6  1  LpxK         Tetraacyldisaccharide-1-P 4'-kinase
      0.023   14.4   0.2      0.079   12.7   0.1    1.8  2  PRK          Phosphoribulokinase / Uridine kinase family
      0.033   13.9   0.2       0.04   13.6   0.2    1.3  1  AAA_30       AAA domain
      0.044   13.4   0.1       0.16   11.6   0.0    1.7  2  SRP54        SRP54-type protein, GTPase domain
      0.048   13.2   0.0      0.071   12.6   0.0    1.2  1  AAA_7        P-loop containing dynein motor region
      0.052   13.0   0.0        0.1   12.0   0.0    1.5  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.056   13.2   0.0      0.074   12.8   0.0    1.2  1  AAA_11       AAA domain
      0.058   13.3   0.1       0.11   12.4   0.1    1.5  1  NACHT        NACHT domain
      0.061   12.5   0.1       0.19   10.9   0.1    1.7  2  NB-ARC       NB-ARC domain
      0.065   13.0   0.1        0.1   12.3   0.1    1.3  1  AAA_29       P-loop containing region of AAA domain
      0.073   12.5   0.0       0.12   11.9   0.0    1.3  1  RecA         recA bacterial DNA recombination protein
      0.082   12.2   0.7       0.89    8.8   0.6    2.1  1  MipZ         ATPase MipZ
      0.093   12.6   0.0       0.11   12.3   0.0    1.3  1  TK           Thymidine kinase
      0.094   11.5   0.0       0.12   11.2   0.0    1.1  1  AAA_35       AAA-like domain
      0.097   12.4   0.1       0.17   11.6   0.1    1.3  1  IstB_IS21    IstB-like ATP binding protein
      0.097   11.6   1.7       0.12   11.3   0.3    1.7  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.097   13.2   0.0       0.14   12.7   0.0    1.4  1  AAA_18       AAA domain
        0.1   11.9   0.2       0.17   11.2   0.2    1.4  1  Zeta_toxin   Zeta toxin
       0.11   12.6   0.6       0.51   10.4   0.6    1.9  1  MMR_HSR1     50S ribosome-binding GTPase
       0.17   11.6   0.1       0.37   10.5   0.1    1.6  1  AAA_24       AAA domain
       0.17   12.2   0.0       0.24   11.7   0.0    1.3  1  AAA_19       AAA domain
       0.23   11.3   1.2       0.37   10.7   0.6    1.6  1  RsgA_GTPase  RsgA GTPase


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 !   92.4   0.1   4.1e-29     2e-26       1     105 [.       4     106 ..       4     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 4.1e-29
                           MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrh.rkAGAkevlvask..erlalikeleea 77 
                                    +++ivg sgsGKT+L+  ++++l+ rg++v+++Kh+hh+  +d+pgkDs+r+ ++AGA+  +v+    er+a++++    
  gi|118430920|ref|NP_147023.2|   4 IVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHTHHD--IDTPGKDSWRFlEEAGASYAAVVKGrgERVAVFTR---- 77 
                                    799**********************************95..799*******6389****98888651256777776.... PP

                           MobB  78 elsleellarl.sevDlvlvEGfkkealp 105
                                    ++ l+ +l+ l ++vD+++vEGfk+ +l 
  gi|118430920|ref|NP_147023.2|  78 DTGLHAVLEDLaRKVDIIVVEGFKNLRLG 106
                                    357889999885569*********98764 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   1.1e-06   0.00056      11     111 ..      12     104 ..       7     114 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                         AAA_26  11 gvGKTvvslgLvralkrkgvkvgyfKPiqtgiee.dedselikellgldqtyelpeplalsaplspelaarqegedidle 89 
                                    g+GKT+++  +vr l+ +g+kv+++K    +i + ++ds +  e +g++ +     + + ++     +  r++g    l 
  gi|118430920|ref|NP_147023.2|  12 GSGKTSLIVSVVRQLSGRGIKVAVVKHTHHDIDTpGKDSWRFLEEAGASYAAV--VKGRGERV---AVFTRDTG----LH 82 
                                    89******************************998999998888887665544..33333332...33444455....44 PP

                         AAA_26  90 kivkelekdadivvVEGagglg 111
                                     + ++l+ + di+vVEG++ l+
  gi|118430920|ref|NP_147023.2|  83 AVLEDLARKVDIIVVEGFKNLR 104
                                    4445668888999999998876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   2.4e-07   0.00012      24      68 ..       2      46 ..       1     124 [. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.4e-07
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaip 68
                                   p++v ++G+sG+GK+sl+ ++ r+l+++g+ ++  k ++++ ++p
  gi|118430920|ref|NP_147023.2|  2 PCIVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHTHHDIDTP 46
                                   57899***********************98887777777755555 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 !   18.6   0.1   2.1e-06    0.0011       3      37 ..       5      41 ..       3     100 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                                   EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-S CS
                           cobW  3 tvltGflGsGKTtLlnhll..enraglklavivNefg 37
                                   + ++G+ GsGKT+L+ +++     +g k+av+     
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVrqLSGRGIKVAVVKHTHH 41
                                   679****************443445566677654333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.8e-06    0.0019      13      51 ..       4      42 ..       3     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.8e-06
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                   +v+ivG++G+GK++L+  + ++l+    ++ + ++  ++
  gi|118430920|ref|NP_147023.2|  4 IVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHTHHD 42
                                   689*************99999998766666555444444 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   6.7e-06    0.0033       6      34 ..       9      37 ..       4     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-06
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  6 tkGGvGKTtlaanLaralarrglrVllvD 34
                                   + +G+GKT+l ++  r l+ rg +V++v+
  gi|118430920|ref|NP_147023.2|  9 GPSGSGKTSLIVSVVRQLSGRGIKVAVVK 37
                                   569************************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.7e-06    0.0043       9     103 ..       6     103 ..       3     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.7e-06
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka.........erlssee 77 
                                     ++G+sG+GKT l+  +++ql  +      + +v+ v+ ++    ++ +   ++l++ g +  a         +  +++ 
  gi|118430920|ref|NP_147023.2|   6 QIVGPSGSGKTSLIVSVVRQLSGR------GIKVAVVKHTHHDidTPGKDSWRFLEEAGASYAAvvkgrgervAVFTRDT 79 
                                    59*******************654......66666666666666666666666666666655556666666665555555 PP

                         AAA_22  78 llealeqalraravielliiDEaqhl 103
                                     l+a+ + l ++ +  +++++ + +l
  gi|118430920|ref|NP_147023.2|  80 GLHAVLEDLARKVD--IIVVEGFKNL 103
                                    55666666665555..6666666666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   4.1e-05     0.021       2      31 ..       5      34 ..       4      46 .. 0.91
   2 ?   -1.6   0.0       4.3   2.1e+03     133     148 ..      76      92 ..      54     102 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.1e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   v i Gp+G+GKt l+  v+++l+ +g+kv+
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVRQLSGRGIKVA 34
                                   5689***********************996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                                    -SS-.-SHHHHHHHT-T CS
                       NTPase_1 133 hrrk.dlalveeirerk 148
                                     r +  +a++e++ ++ 
  gi|118430920|ref|NP_147023.2|  76 TRDTgLHAVLEDLARKV 92 
                                    33333344444444432 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 !   15.7   0.0   2.2e-05     0.011      22      60 ..       4      42 ..       2     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.2e-05
                       ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdkyviyyialree 60
                                   i+ i Gp gsGKt+L+  ++ +l+  + +v  +   + +
  gi|118430920|ref|NP_147023.2|  4 IVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHTHHD 42
                                   67799******************9999888777666554 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.3e-05     0.017       4      46 ..       5      48 ..       3      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-05
                      PduV-EutP  4 illiGkvgsGKttLtqa.lkgeelkYkktqaiefsdeviDtPGe 46
                                   + ++G++gsGKt+L  + +++ + +  k   ++++++ iDtPG+
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSvVRQLSGRGIKVAVVKHTHHDIDTPGK 48
                                   5689*********9755156666777799999***********6 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.5e-05     0.013       2      33 ..       5      36 ..       4     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtl 33
                                   v +vG++GsGK+ l+ +++++l +  +   ++
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   668******************98555554444 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 ?   15.9   0.0   2.7e-05     0.013       3      34 ..       7      38 ..       5      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-05
                                   EESSTTSSHHHHHHHHHHHHTHEEEEEETTTC CS
                            AAA  3 lyGppGtGKTllakavakelgvefleisgsel 34
                                   ++Gp G GKT+l+ +v+++l+ + +++ + + 
  gi|118430920|ref|NP_147023.2|  7 IVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKH 38
                                   79*****************9755555444443 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 ?   13.0   0.5   0.00013     0.063       1      30 [.       7      36 ..       7      38 .. 0.95
   2 ?    0.1   0.0       1.1   5.5e+02      96     132 ..      43      79 ..      37      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavv 30
                                   +vGp GsGKt+++ +++  l+ rg +vavv
  gi|118430920|ref|NP_147023.2|  7 IVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   79**********************999998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                     ATP_bind_1  96 fDtPGQielfthseslakiveeLesefalvvvyLvDs 132
                                    +DtPG +   ++ e++a      + +++ v+v+  D+
  gi|118430920|ref|NP_147023.2|  43 IDTPGKDSWRFLEEAGASYAAVVKGRGERVAVFTRDT 79 
                                    7999999999999999988888888999898888777 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.9e-05     0.024       2      36 ..       2      36 ..       1      40 [. 0.92
   2 ?   -2.5   0.0       8.2   4.1e+03      33      58 ..      94     121 ..      81     130 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.9e-05
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                     APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylL 36
                                   +++v + G sgsGK+++ + + ++L  +gi+v ++
  gi|118430920|ref|NP_147023.2|  2 PCIVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   799**************************999875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.2
                                    EEEEEH.HHHTT.TTTTT--SSHHHHHH CS
                     APS_kinase  33 vylLdG.dnvRh.gLnkdLgfseedRke 58 
                                    +++++G  n+R  gL+ dL+ ++  R e
  gi|118430920|ref|NP_147023.2|  94 IIVVEGfKNLRLgGLKIDLSTKRPGRIE 121
                                    4555554567752477777777777766 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.2   4.5e-05     0.022      47      71 ..      12      36 ..       2     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.5e-05
                                   -HSHHHHHHHHHHHTTTS..-EEEE CS
                           LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                   G+GKT+l++ +v++l+ rg+kv+v+
  gi|118430920|ref|NP_147023.2| 12 GSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   9***********************9 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00016     0.079       1      40 [.       4      42 ..       4      69 .. 0.78
   2 ?    0.5   0.0      0.89   4.4e+02      88     118 ..      71     100 ..      37     104 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                            PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflr 40
                                   ++ + g+SG+Gkt++   ++  + + ++k a+++++  + 
  gi|118430920|ref|NP_147023.2|  4 IVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHT-HHD 42
                                   67899*******************999996666554.344 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.89
                            PRK  88 dkpiYsheteeaapdkeeliegadvlviEGl 118
                                    ++ ++  +t++ a   e+l  + d++v+EG 
  gi|118430920|ref|NP_147023.2|  71 RVAVFTRDTGLHAV-LEDLARKVDIIVVEGF 100
                                    44455555666665.7889999999999996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   8.1e-05      0.04      22      55 ..       6      39 ..       3      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.1e-05
                         AAA_30 22 vltGpAGtGKttalkalreaweaaggrviglApt 55
                                    ++Gp G+GKt ++ ++++ +  +g +v+++ +t
  gi|118430920|ref|NP_147023.2|  6 QIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHT 39
                                   689*******************999999988666 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   0.0   0.00032      0.16       2      35 ..       3      36 ..       2      41 .. 0.91
   2 ?   -0.7   0.0       1.8   9.2e+02      20      52 ..      60      92 ..      57     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                          SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllv 35
                                    ++ +vG+ G+GKT+ +  + ++l+ +g kv++v
  gi|118430920|ref|NP_147023.2|  3 CIVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   57889************************99987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                                   HHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHH CS
                          SRP54 20 KLaallkkegkkvllvaaDtfRaaAveQLktla 52
                                     aa++k +g++v++ + Dt   a +e L+   
  gi|118430920|ref|NP_147023.2| 60 SYAAVVKGRGERVAVFTRDTGLHAVLEDLARKV 92
                                   567888888999999999987777777665544 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 ?   12.6   0.0   0.00014     0.071      37      67 ..       6      36 ..       3      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                          AAA_7 37 llvGptGtGKtviikdllkkldkekylslti 67
                                    +vGp+G+GKt++i +++++l+ + ++++++
  gi|118430920|ref|NP_147023.2|  6 QIVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   68******************99877776665 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    0.0002       0.1      26      49 ..       4      27 ..       1      50 [. 0.82
   2 ?   -2.3   0.0       4.8   2.4e+03       4      14 ..      94     104 ..      91     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                   EEEEEESTTSSHHHHHHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAilFvLG 49
                                   +  ivGp GSGK++l+ ++   L+
  gi|118430920|ref|NP_147023.2|  4 IVQIVGPSGSGKTSLIVSVVRQLS 27
                                   678************999866555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.8
                                    EEEEESETTEE CS
                                    xxxxxxxxxxx RF
                          SMC_N   4 rleienFksya 14 
                                     +++e+Fk+++
  gi|118430920|ref|NP_147023.2|  94 IIVVEGFKNLR 104
                                    6899****986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015     0.074      21      42 ..       6      27 ..       2      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                         AAA_11 21 liqGPPGtgKTktivellsqll 42
                                    i GP G+gKT+ iv++++ql 
  gi|118430920|ref|NP_147023.2|  6 QIVGPSGSGKTSLIVSVVRQLS 27
                                   689******************4 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00023      0.11       3      27 ..       5      29 ..       3      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00023
                                   EEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaeg 27
                                   v + G++GsGKT L+ ++++++  +
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVRQLSGR 29
                                   6799**************9998766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00038      0.19      22      44 ..       4      26 ..       2      36 .. 0.90
   2 ?   -0.7   0.0       1.3   6.6e+02     130     143 ..      68      81 ..      47     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                   EEEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC 22 vvalvGmgGvGKttlakqilnks 44
                                   +v +vG  G+GKt l+ ++++++
  gi|118430920|ref|NP_147023.2|  4 IVQIVGPSGSGKTSLIVSVVRQL 26
                                   899**************999874 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                    TTSEEEEEESBCCC CS
                         NB-ARC 130 nrlrvllTTRdeev 143
                                    ++ rv++ TRd  +
  gi|118430920|ref|NP_147023.2|  68 RGERVAVFTRDTGL 81 
                                    44556666666554 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   0.1   0.00021       0.1      27      39 ..       7      19 ..       3      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                         AAA_29 27 ltGpsGsGKSTll 39
                                   ++GpsGsGK++l+
  gi|118430920|ref|NP_147023.2|  7 IVGPSGSGKTSLI 19
                                   99**********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 ?   11.9   0.0   0.00023      0.12      55      94 ..       4      44 ..       1      49 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                   EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE.SS---- CS
                           RecA 55 iieiyGpessGkttlalhaiaeaqkkggvaafid.aehald 94
                                   i++i Gp  sGkt+l ++++ +   +g  +a +  + h +d
  gi|118430920|ref|NP_147023.2|  4 IVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKhTHHDID 44
                                   99**********************99988888861455566 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6    0.0018      0.89      10      51 ..      11      57 ..       3     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                   TTSSHHHHHHHHHHHHHTTT--EEEE.....E--TTT-HHHHHHHHH CS
                           MipZ 10 GGsGksttavhvavaLlkkGarvaai.....dldlrqrtlarylenr 51
                                    GsGk+   v v+  L+ +G +va++     d+d+  + + r+le  
  gi|118430920|ref|NP_147023.2| 11 SGSGKTSLIVSVVRQLSGRGIKVAVVkhthhDIDTPGKDSWRFLEEA 57
                                   69**********************98666668888888888888765 PP

>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022      0.11       5      41 ..       6      42 ..       3      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                             TK  5 lilgpmfaGKsteLlrrvkryqlaekkvvvikaakdn 41
                                    i+gp  +GK++ ++  v++++ +  kv v+k++  +
  gi|118430920|ref|NP_147023.2|  6 QIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHTHHD 42
                                   589*****************************99766 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.12      32      69 ..       3      40 ..       2      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                         AAA_35 32 alirikapkkmGKtSLlarilakakqqgyktvsldlql 69
                                   ++++i +p+  GKtSL+  ++++ + +g k+++++  +
  gi|118430920|ref|NP_147023.2|  3 CIVQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVVKHTH 40
                                   6899*******************999999988876655 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   0.1   0.00034      0.17      51      81 ..       6      36 ..       3      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                      IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfv 81
                                    ++GpsG GK+ l +++ ++   +g++v  v
  gi|118430920|ref|NP_147023.2|  6 QIVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   599******************9999999766 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 ?   11.3   0.3   0.00024      0.12      32      63 ..       5      36 ..       2      41 .. 0.93
   2 ?   -1.3   0.0       1.7   8.6e+02      53      66 ..      65      78 ..      55      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                   EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                           MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavl 63
                                   v + G  G+Gk  l+  ++ +l  rG +vav+
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVRQLSGRGIKVAVV 36
                                   6789999************************8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                   HHCTT--EEEEEE- CS
                           MeaB 53 lrrrGkrvavlavD 66
                                   ++ rG+rvav   D
  gi|118430920|ref|NP_147023.2| 65 VKGRGERVAVFTRD 78
                                   56689999998766 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   0.00027      0.14       3      34 ..       7      42 ..       5     105 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00027
                         AAA_18  3 ltGtpGvGKttlakeLskrl.gf...gvnlrdvake 34
                                   + G++G+GKt+l   + + l g    + ++++++ +
  gi|118430920|ref|NP_147023.2|  7 IVGPSGSGKTSLIVSVVRQLsGRgikVAVVKHTHHD 42
                                   89*************999985555554444444333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00034      0.17      16      42 ..       2      29 ..       1      42 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                     Zeta_toxin 16 PklillgGqpGAGKselaellkdele.r 42
                                   P +++++G +G+GK++l+  + ++l  r
  gi|118430920|ref|NP_147023.2|  2 PCIVQIVGPSGSGKTSLIVSVVRQLSgR 29
                                   899***************9999999633 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   0.6     0.001      0.51       2      23 ..       5      29 ..       4     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                                   EEEEESTTSSHHHHHHHHHTS...T CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge...k 23
                                   v ivG + +GK++Li + +++   +
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVRQlsgR 29
                                   679************9999863232 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00074      0.37       5      21 ..       5      21 ..       1      37 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00074
                         AAA_24  5 iliyGpsgiGKTtlake 21
                                   ++i+Gpsg+GKT+l+ +
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVS 21
                                   89***********9865 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00048      0.24      13      38 ..       5      30 ..       2      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                         AAA_19 13 llvtaGpGtGKTrvlkhivallvelg 38
                                   + ++++ G+GKT +++ +v+ l  +g
  gi|118430920|ref|NP_147023.2|  5 VQIVGPSGSGKTSLIVSVVRQLSGRG 30
                                   67999**************9998766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00075      0.37     102     123 ..       5      26 ..       2      42 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                                    EEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                    + +vG+SG GK++Li +++ +l
  gi|118430920|ref|NP_147023.2|   5 VQIVGPSGSGKTSLIVSVVRQL 26 
                                    679************8887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 991.41
//
Query:       gi|14600508|ref|NP_147024.1|  [L=281]
Description: molybdopterin-guanine dinucleotide biosynthesis protein MobA [Aeropyrum pernix K1]
Scores for complete 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   74.7   1.4    1.7e-20   74.0   1.4    1.3  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0086   15.8   0.1      0.013   15.2   0.1    1.3  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr


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 !   74.0   1.4   1.9e-24   1.7e-20       1     157 [.      10     174 ..      10     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.9e-24
                                   EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCT..S-EEE-TTSS-SHHHHH CS
                  NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd...eevlaalarlg..vrvvededpgkgplasl 76 
                                   av+LAGG ++R+g++Kal+ ++g +l+er+++al++   ++v+v++ +   ++v++ + +++  v++ve+  p +gpl ++
  gi|14600508|ref|NP_147024.1|  10 AVVLAGGVGRRFGRPKALAMMDGISLVERAVEALSSG-PADVYVSVSPaleRPVARLVGSRRviVDLVEQ-APCEGPLRAF 88 
                                   79*********************************97.79*****9885544566666666633455555.589******* PP

                                   HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHH......CTHTTHH CS
                  NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaal......lgdqgar 151
                                   ++a++ + + + ++++++D P+ +   +e + +a +a g+ + +++ eg   hpl++ ar  s l a+      +++++a 
  gi|14600508|ref|NP_147024.1|  89 LTAASTLVSYSNLVFMPVDAPWASWRDLEPIYNASKAIGSGASYFSGEGIV-HPLFLAARRKSLLTAAwtacwgRAEKRAS 168
                                   ******88***************************9999999888877766.***77555544444333233555566677 PP

                                   HCHHHH CS
                  NTP_transf_3 152 rllrrl 157
                                   ++lr+l
  gi|14600508|ref|NP_147024.1| 169 AILRSL 174
                                   777765 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.5e-06     0.013       1      65 [.       8      68 ..       8      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
                                  EEEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG CS
                          IspD  1 vvvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld 65
                                  v++v+ A G+G+R   g+pK++  ++g +l+e++v+al + +    + v vs+     ++ l ++
  gi|14600508|ref|NP_147024.1|  8 VAAVVLAGGVGRRF--GRPKALAMMDGISLVERAVEALSSGP--ADVYVSVSPALERPVARLVGS 68
                                  689**********7..79*******************99854..356666666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2011.40
//
Query:       gi|14600510|ref|NP_147026.1|  [L=67]
Description: 50S ribosomal protein L38 [Aeropyrum pernix K1]
Scores for complete 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-08   34.7   2.0    1.6e-08   34.5   2.0    1.2  1  Ribosomal_L38e  Ribosomal L38e protein family


Domain annotation for each model (and alignments):
>> Ribosomal_L38e  Ribosomal L38e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   2.0     9e-13   1.6e-08       3      58 ..       4      56 ..       2      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 9e-13
                Ribosomal_L38e  3 eikdiKeFLeiarrkDaksvkikknkkdntKfKvRcsryLYTLvvkdkekaeklkq 58
                                  e k   eF+++++r  a + ++k+ k d +K+K R++ryLYTL+v  ++ ae l+q
  gi|14600510|ref|NP_147026.1|  4 ELKSFDEFVKVVER--AVECRVKRGK-DVVKIKARTKRYLYTLKVPPEKEAEVLEQ 56
                                  45555566666665..7899******.*************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 498.33
//
Query:       gi|14600511|ref|NP_147027.1|  [L=420]
Description: exonuclease [Aeropyrum pernix K1]
Scores for 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-17   61.6   0.0    1.3e-16   60.8   0.0    1.3  1  Beta-Casp      Beta-Casp domain
    5.2e-14   51.9   0.0      1e-13   51.0   0.0    1.5  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    6.9e-11   42.5   2.1    2.7e-10   40.6   2.1    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
      4e-09   36.3   0.0    3.2e-08   33.3   0.0    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain
    3.2e-06   26.7   0.0    1.5e-05   24.5   0.0    2.0  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
     0.0015   18.5   0.0       0.01   15.8   0.0    2.1  1  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 !   60.8   0.0   4.4e-20   1.3e-16      19     110 .]     240     339 ..     230     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.4e-20
                                   S-S-EEEEE-HHHHHHHHHGGGGGG..............E-SHH.....HHHH..HHHS-SSEEEEES-TTSSSSHHHHHH CS
                     Beta-Casp  19 dlklpiyldsplaskatevYkeyae..............veaks.lewmeskkeelnsskgpkvilassgmlegGrsrell 84 
                                     ++p+ ld+ +++++ e+Y ++++                 +    w ++++      k+p vi+as gml+gG+s ++ 
  gi|14600511|ref|NP_147027.1| 240 GFEYPVWLDG-MIRQVAEIYAANPRfilnpgllmkvmseF--RIvSGWQDRRR----AFKKPGVIIASAGMLKGGPSLYYA 313
                                   3568******.****************9999998776331..22224444444....4579******************** PP

                                   HHHTTSTTSEEEESS---TTSHHHHH CS
                     Beta-Casp  85 kklledprntvilvgyqaegTlgrkl 110
                                   +k++++++n +++v+yqa+gT+gr +
  gi|14600511|ref|NP_147027.1| 314 RKMATNKKNGIFMVSYQAPGTPGRMI 339
                                   ***********************976 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 !   51.0   0.0   3.4e-17     1e-13       2      58 ..     350     407 ..     349     412 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3.4e-17
                         RMMBL   2 ipvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegid 58 
                                   ipv ar+e++dfS H d++++++l+r+++    v+lvHG+++a++al+ +++ee gi+
  gi|14600511|ref|NP_147027.1| 350 IPVLARVEWFDFSSHIDQSGIIKLLRSVNGVEkVVLVHGDPKAQEALKTRIREELGIR 407
                                   89***************************9888******************9999974 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   2.1   9.2e-14   2.7e-10       6     155 ..      15     167 ..      10     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.2e-14
                                   SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                   Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                     ++l+e +g+ +L D G+  ++++     +  ++ p+d+d ++lTH+HlDHiG++++l    + +v+  + ++++ +   
  gi|14600511|ref|NP_147027.1|  15 RAAILVESGGRGLLLDYGVNFDENDRP--VFPGDVRPRDLDGLVLTHSHLDHIGAAPYLYVSQGPKVFGTRVTLHVSRLLL 93 
                                   56899**************99999988..8999************************************************ PP

                                   HHHHHHHCCHH.....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                   Lactamase_B  87 addaasrkgll.....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                    d     +  l       ++     +  + +++ +ag   +  ++ g+ +g++ + ve +g+++l+t D+  ++
  gi|14600511|ref|NP_147027.1|  94 YDMIKLNGAYLpyderSVEDMLGTAEYIDYGREYEAGRFAFKTFYSGHIPGSTAVLVEVDGRRILYTSDVNVIE 167
                                   *988888765566663333333333333333344444444556899*********************9986655 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 !   33.3   0.0   1.1e-11   3.2e-08       3     173 ..      27     197 ..      25     219 .. 0.68
   2 ?   -0.3   0.0      0.21   6.2e+02     176     200 ..     362     387 ..     350     388 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.1e-11
                                   EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT. CS
                 Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee. 82 
                                   +L+D g ++ ++ ++   P+  r   +++d+++lth+H DH+  ++ l   ++ k  ++++ +v  ++++ + y++ + + 
  gi|14600511|ref|NP_147027.1|  27 LLLDYGVNFDENDRPV-FPGDVRP--RDLDGLVLTHSHLDHIGAAPYLYVSQGPK--VFGT-RVTLHVSRLLLYDMIKLNg 101
                                   5777777777774444.5877554..49**************8888888866654..4433.3444444444444444444 PP

                                   ............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH CS
                 Lactamase_B_2  83 ............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig 151
                                                  +++ +d g + e g   + ++++   +++ +          ++++e +g+r++y+ D++ i+ ++ 
  gi|14600511|ref|NP_147027.1| 102 aylpydersvedMLGTAEYIDYGREYEAG--RFAFKTF--YSGHIP-------GSTAVLVEVDGRRILYTSDVNVIETKLV 171
                                   44443222444544455566677777776..4445555..566666.......458999999***************6544 PP

                                   ..HHHCT..-SEEEEE-S-SSTTHHH CS
                 Lactamase_B_2 152 ..erlgg..adllllditayeddemi 173
                                     +rl+g  ad+++++ t+ ++d + 
  gi|14600511|ref|NP_147027.1| 172 gpARLEGakADVVIVESTYGDSDHPP 197
                                   4788988889********98888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                                   HT---STSHHHHCTTSS.SSEEEEES CS
                 Lactamase_B_2 176 mgHltpeeaveaaadlg.akrlvliH 200
                                    +H+++++ +++++ ++ ++++vl+H
  gi|14600511|ref|NP_147027.1| 362 SSHIDQSGIIKLLRSVNgVEKVVLVH 387
                                   68*************99899999999 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 !   24.5   0.0     5e-09   1.5e-05       9     170 ..      27     171 ..      17     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5e-09
                 Lactamase_B_6   9 iLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyas 89 
                                   +LlD G++  +   ++ + + +    ++d  +L+h+ l+h+Ga ++ly++         +v++t  + +  r++l+d ++ 
  gi|14600511|ref|NP_147027.1|  27 LLLDYGVNFDEN--DRPVFPGDVRPRDLDGLVLTHSHLDHIGAAPYLYVSQ------GPKVFGTRVTLHVSRLLLYDMIKL 99 
                                   677777774322..2344444445578999***************999864......579********************* PP

                 Lactamase_B_6  90 kgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshL 170
                                   +g+  p+d++++     + +    + + Y  + e      + ++  + +Gh +G t   ++    +i+Y  d+n    +++
  gi|14600511|ref|NP_147027.1| 100 NGAYLPYDERSV-----EDMLGTAEYIDYGREYEAG----RFAFKTFYSGHIPGSTAVLVEVDGRRILYTSDVNVIETKLV 171
                                   *******98844.....5666777778898887655....6999****************************998766655 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 !   15.8   0.0   3.3e-06      0.01       6     114 ..      14     163 ..      12     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-06
                 Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa........eeaDlvlisqaledHahletlkql.................... 58 
                                   g +++l+e++g  +l+D++  n + +  +        ++ D +++++++ dH  +++   +                    
  gi|14600511|ref|NP_147027.1|  14 GRAAILVESGGRGLLLDYGV-NFDENDRPvfpgdvrpRDLDGLVLTHSHLDHIGAAPYLYVsqgpkvfgtrvtlhvsrlll 93 
                                   8899**************95.3333333346677777***************99998888855555555555555555555 PP

                 Lactamase_B_3  59 .....................aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhl 114
                                                           +++++ g ++e+g + ++++ + h   +g      ++ l+e+dg +i++  ++
  gi|14600511|ref|NP_147027.1|  94 ydmiklngaylpydersvedmLGTAEYIDYGREYEAGRFAFKTFYSGHI--PG-----STAVLVEVDGRRILYTSDV 163
                                   5555444444444444444443344444445666666666665555552..22.....2333555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2962.19
//
Query:       gi|118430921|ref|NP_147028.2|  [L=108]
Description: hypothetical protein APE_0182.1 [Aeropyrum pernix K1]
Scores for 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   67.8   0.1    8.9e-19   67.4   0.1    1.2  1  DUF167    Uncharacterised ACR, YggU family COG1872
  ------ inclusion threshold ------
      0.094   12.5   0.0      0.094   12.5   0.0    1.0  1  Tub       Tub family


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.1     1e-22   8.9e-19       2      76 ..      19      88 ..      18      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1e-22
                                   EEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                         DUF167  2 vilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                   v+++v+vkP+ ++ ++       ++++l +   +pp +G+AN+ li+fLa+ l+v+ +++eiv+G++sr+Kvv+i
  gi|118430921|ref|NP_147028.2| 19 VRIRVYVKPEGRERRLR-----LEEGELVFYTDEPPLEGRANASLINFLARGLKVSVKNIEIVHGARSRSKVVEI 88
                                   89***************.....44567***********************************************9 PP

>> Tub  Tub family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05     0.094     160     203 ..      38      81 ..       5      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                            Tub 160 sdllvlknksprwneqlqayvLnFrgRvtvaSvKNfqLvaaede 203
                                    +  lv+ + +p  + + +a ++nF  R  + SvKN+ +v+   +
  gi|118430921|ref|NP_147028.2|  38 EGELVFYTDEPPLEGRANASLINFLARGLKVSVKNIEIVHGARS 81 
                                    45688899999999999**********************97544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 868.66
//
Query:       gi|118430922|ref|NP_147029.2|  [L=266]
Description: hypothetical protein APE_0183.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-48  165.8  39.7    1.4e-48  165.6  39.7    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 !  165.6  39.7   7.8e-53   1.4e-48       2     236 .]      17     264 ..      15     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 7.8e-53
                           TauE   2 llagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGall 79 
                                    +l+g++a ++a+l G+Ggg+++vP++l+ + lpp +av++s ++v++ s+++ l+++r+g+ +++++ +l++++++Ga l
  gi|118430922|ref|NP_147029.2|  17 ILMGVAAAALASLSGVGGGVFFVPIFLFiVgLPPNIAVGSSKVVVAIVSIVSGLTYLRQGTTRLSRAAPLMVSMIPGAAL 96 
                                    689*************************6678************************************************ PP

                           TauE  80 Gallllllpsellkllfgvlllllallmll..rkkr..........srak..grerrptaillvligglvGllsGllGiG 145
                                    Ga+l+++++++ll++++g+++++++l++ll    ++          +  +  + +r+ ++ l++++g+++Gl++Gl+G G
  gi|118430922|ref|NP_147029.2|  97 GAYLVAYIDPRLLEVILGLFITYYSLRLLLvtA-RKalareakpveE--EgsRGPRPGGRYLMLATGVAAGLFAGLTGTG 173
                                    ****************************87643.3357877766652..04244566666666666666*********** PP

                           TauE 146 gGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlf 225
                                    gG++lvp+l+ll+   lk+ava s+l i + ++++a++++++g vd+  ++++++gal+G++lG  +a+rls+ +lr ++
  gi|118430922|ref|NP_147029.2| 174 GGAILVPMLTLLRIAKLKEAVAISMLSISLGAVVSAAIHVWTGVVDFGGAAPFALGALIGSILGPMAASRLSTDALRPIV 253
                                    ******************************************************************************** PP

                           TauE 226 allllvlgvkl 236
                                    al+ll+++++l
  gi|118430922|ref|NP_147029.2| 254 ALVLLLVALRL 264
                                    ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1914.72
//
Query:       gi|118430923|ref|NP_147030.2|  [L=418]
Description: MFS transporter [Aeropyrum pernix K1]
Scores for complete 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   89.8  44.2    7.7e-15   54.7  28.9    2.0  2  MFS_1          Major Facilitator Superfamily
    2.6e-11   43.0  21.9    1.4e-07   30.8  11.8    2.1  2  MFS_1_like     MFS_1 like family
    6.5e-05   22.1  17.0    0.00011   21.4  17.0    1.3  1  Nuc_H_symport  Nucleoside H+ symporter
    7.4e-05   21.7   9.6    0.00011   21.1   9.6    1.3  1  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 !   54.7  28.9   1.7e-18   7.7e-15       2     222 ..      12     227 ..      11     235 .. 0.80
   2 !   39.9  11.4   5.4e-14   2.4e-10       3     180 ..     223     401 ..     221     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 1.7e-18
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                    l++a+l++l+++++ ++l +++  + g+s++e gll+++ ++++++++l+ G+lsd +G+rrv+ +g+++ a++++ll++
  gi|118430923|ref|NP_147030.2|  12 LVLAALNGLSFGVIVTVLAPYM-YSAGFSGTEWGLLTSTATVTSIIFTLLSGPLSDALGARRVVAAGYIVKAASFTLLAV 90 
                                    78899*************9766.666************************************************777774 PP

                          MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg...llasslg......Wra 152
                                     +s  +++++  l+G+ +g++++a  al+a+   +e   r + +++a++ +G +lg l g    ll+s  +      +ra
  gi|118430923|ref|NP_147030.2|  91 -PSTVFMAAGFTLSGVSMGISWSATTALVARSGRDEMLHRSFTFFMASNMVGGALGSLMGVippLLSSITSltlleaYRA 169
                                    .55447999999************************9999999999999999999965554444677666699******* PP

                          MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffg 222
                                    + +++a++sll +   ++l ++e+++ +  +++         +l+ ++++ ++d+ +      l+lf ++
  gi|118430923|ref|NP_147030.2| 170 TILLVAPLSLLQAG--IALAVREEVSAEGRASIGP------GELLRGFREAVSDRRF----RLLILFNMV 227
                                    ***********944..3666666666666655554......3444458889999966....222222222 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 5.4e-14
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllf 81 
                                    l  ++++l++s+ + ++  + a  +g++ +eig + +l  + +a+ ++ ++r+++r+G+   v+++   l++  l+++++
  gi|118430923|ref|NP_147030.2| 223 LFNMVIGLGASMSIHNIAYYFAAKYGVTSAEIGVVNALEQVSMALVAVGASRIAERVGSTLkVYIALTSLSVPLLVAMTL 302
                                    566778888888888888899*************************************8888***999999999555556 PP

                          MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    + s+ + ++  v+  + + a++p+  al+ +++p+e+rg+a ++ls++f l a  g ++gg+l+  ++ +++  + a+++
  gi|118430923|ref|NP_147030.2| 303 VDSYVVAAAIYVVRTVLMNAANPLLEALTMRVVPRERRGSASSILSLSFTLPATAGRAIGGALL-DINLELPLRLTAAIY 381
                                    566669999999999*************************************************.7799*********** PP

                          MFS_1 162 llafv.lfllllpeepperk 180
                                     la+  l +   + e+ + +
  gi|118430923|ref|NP_147030.2| 382 TLALAhLYMRRRFLEEGRAW 401
                                    *9966333333355555554 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 !   30.8  11.8     3e-11   1.4e-07     230     370 ..      11     149 ..       7     158 .. 0.91
   2 !   17.8   2.6   2.7e-07    0.0012     175     376 ..     162     368 ..     154     372 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 3e-11
                     MFS_1_like 230 fllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyai 309
                                    +l+ a++ g s+g+i + l  Y+ + g+s+t +G l+   +v +i++ +++  l + lG+++++ ++ ++ ++ f l+a+
  gi|118430923|ref|NP_147030.2|  11 LLVLAALNGLSFGVIVTVLAPYMYSAGFSGTEWGLLTSTATVTSIIFTLLSGPLSDALGARRVVAAGYIVKAASFTLLAV 90 
                                    678899*************************************************************************9 PP

                     MFS_1_like 310 ienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliG 370
                                     + + +     +L+g+s+g+ w+a +  v++   +++  +   ++ +++  +G+alGsl+G
  gi|118430923|ref|NP_147030.2|  91 PSTVFM-AAGFTLSGVSMGISWSATTALVARSGRDEMLHRSFTFF-MASNMVGGALGSLMG 149
                                    766555.55559******************999999988888876.556779999999998 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.7e-07
                     MFS_1_like 175 nllp.ysallyvlaallvisllvvlilnetekes...klkvtkslqvllnilknpeviifllvalilgmswgiienFlfl 250
                                    +ll+ y+a ++++a l ++   ++l++ e   ++   +++  + l+ + + +++++  +++l+ +++g   ++    +  
  gi|118430923|ref|NP_147030.2| 162 TLLEaYRATILLVAPLSLLQAGIALAVREEVSAEgraSIGPGELLRGFREAVSDRRFRLLILFNMVIGLGASMSIHNIAY 241
                                    44456777777777777777777666655433320013344455588999999999999999999999998887777777 PP

                     MFS_1_like 251 YL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievLhgisfg 328
                                    Y+  ++g ++  +G++ al+ v+   + + a+++ e++G +  + ial++  + +l+  ++ ++ +++  i v   + + 
  gi|118430923|ref|NP_147030.2| 242 YFaAKYGVTSAEIGVVNALEQVSMALVAVGASRIAERVGSTLKVYIALTSLSVPLLVAMTLvDSYVVAAAIYVVRTVLMN 321
                                    7779***********************************************99887766666999999999999999999 PP

                     MFS_1_like 329 llwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdl 376
                                    +    +     +++p++ ++   ++ls l+f l    G  iGG+l d+
  gi|118430923|ref|NP_147030.2| 322 AANPLLEALTMRVVPRERRGSASSILS-LSFTLPATAGRAIGGALLDI 368
                                    999999999999*************97.679************99875 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4  17.0   2.4e-08   0.00011       5     271 ..       9     280 ..       6     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-08
                  Nuc_H_symport   5 lrLkvlsflqyfiWGaWlvklfsylsktlfaaaeiglvysslgiaailspilvgiiaDkflsaervlavlhligavvl.f 83 
                                    + L vl+ l+ + +G  ++ l +y+  ++f+++e gl  s+ ++ +i+   l+g ++D  l a+rv+a  +++ a  + +
  gi|118430923|ref|NP_147030.2|   9 APLLVLAALNGLSFGVIVTVLAPYMYSAGFSGTEWGLLTSTATVTSIIFTLLSGPLSDA-LGARRVVAAGYIVKAASFtL 87 
                                    56788889999999********************************************5.99******999997765515 PP

                  Nuc_H_symport  84 laaqvtefeal.flvl.LvyslaymPtlaltnsiafa.nlrDvvtdfpri.rvlGtvGfilasla.flllvvsladlels 158
                                    la  +t f a  f++  +   + +  t al+        l+   t f     v G++G ++  ++ +l  + sl+ le  
  gi|118430923|ref|NP_147030.2|  88 LAVPSTVFMAAgFTLSgVSMGISWSATTALVARSGRDeMLHRSFTFFMASnMVGGALGSLMGVIPpLLSSITSLTLLEAY 167
                                    56667776543154441456789999999887665550555666666555156789*****99987999*********** PP

                  Nuc_H_symport 159 rlqlliaagvslllavyaltLPkiP.akkkakqslkkllgldafv.Llknkrllvfflvslllav.....vlqiyyvfan 231
                                    r ++l+ a +sll a+ al + +   a+ +a  s+     l+ f   + ++r+ ++ l+ +++++     +++i y fa 
  gi|118430923|ref|NP_147030.2| 168 RATILLVAPLSLLQAGIALAVREEVsAEGRA--SIGPGELLRGFReAVSDRRFRLLILFNMVIGLgasmsIHNIAYYFAA 245
                                    ********************98876355555..55544444555314566666666666666543222235666777777 PP

                  Nuc_H_symport 232 afLtevakivvklasillslsqvaeilfiLtlpfflkrfG 271
                                     +    a+       ++ +l qv+  l+ +  +++ +r G
  gi|118430923|ref|NP_147030.2| 246 KYGVTSAE-----IGVVNALEQVSMALVAVGASRIAERVG 280
                                    77555554.....333444444444444444444444444 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   9.6   2.4e-08   0.00011      38     313 ..      36     306 ..      21     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.4e-08
                      LacY_symp  38 lglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfepllqlnilvGalvGgvflGlv 117
                                     g+s+te G++ s  +++si+f  l G +sd lG ++ +    +  +v  a f +        + + +G  + gv +G+ 
  gi|118430923|ref|NP_147030.2|  36 AGFSGTEWGLLTSTATVTSIIFTLLSGPLSDALGARRVV---AAGYIVKAASFTLLAVPS--TVFMAAGFTLSGVSMGIS 110
                                    5899********************************964...566777888887765543..567899************ PP

                      LacY_symp 118 ysagagaie..ayiekvsraskfeyGkarvfGclGyalcaslaGilfsidp.......slvfwlasgfalilllllllsk 188
                                    +sa ++++      e + r+++f      v G+lG  +  ++  +l si +       + +  l++  +l+ + + l ++
  gi|118430923|ref|NP_147030.2| 111 WSATTALVArsGRDEMLHRSFTFFMASNMVGGALGSLM-GVIPPLLSSITSltlleayRATILLVAPLSLLQAGIALAVR 189
                                    ****9999621456888999999988888888888654.45666666665410000003333344444444444444444 PP

                      LacY_symp 189 pdksssakvadalGankeafslrlalelfkdrklwvfvly..vvGvasvydvfdqqfavffkslfespeaGtrvfGyvtt 266
                                     ++s +     ++G  +    lr   e   dr++ +++l+  v+G  +   +   + a +f++ +  + a     G v++
  gi|118430923|ref|NP_147030.2| 190 EEVSAEGR--ASIGPGEL---LRGFREAVSDRRFRLLILFnmVIGLGASMSIH--NIAYYFAAKYGVTSAE---IGVVNA 259
                                    33333333..33333322...45555666688888888875578888888876..5788888887766554...599*** PP

                      LacY_symp 267 agellnalimfiaplivnriGaknalliagvimsvrilgsafattal 313
                                     +++  al+ + a  i +r+G+   + ia + +sv +l +   + ++
  gi|118430923|ref|NP_147030.2| 260 LEQVSMALVAVGASRIAERVGSTLKVYIALTSLSVPLLVAMTLVDSY 306
                                    ******************************99999887754443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); 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:                         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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3020.77
//
Query:       gi|14600516|ref|NP_147032.1|  [L=188]
Description: hypothetical protein APE_0187 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-08   35.2   0.2    1.8e-08   34.8   0.2    1.2  1  Sld5      GINS complex protein


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 !   34.8   0.2     1e-12   1.8e-08       1     104 [.      47     159 ..      47     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1e-12
                                   EEEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS....SSSTTTTTTHHHHHHHHHHHHT.............HC CS
                          Sld5   1 veLPlWlaelLkrqrrveieppewlspesleailedetks....sdlpslpphflelavkllelard............ld 65 
                                   veLP W+a++L+++++ve ++ +++ +++++ ++ +e k+    s l+ +++++l++ + + +l r              +
  gi|14600516|ref|NP_147032.1|  47 VELPRWQARMLREKGYVEYKE-KIVDIDYVNLVHYHEVKKsaanSLLGVPSDFYLRVKELVEDLDRRirenpgymlfqdRE 126
                                   69*****************96.5789**************9**99********************9666678888888899 PP

                                   HHHHHHHHHHHHHHHHHHHTHCHHHHHHHTS-TCCHCCS CS
                          Sld5  66 elkrllrdllevRlakirkfaenledaagggggellsgl 104
                                   ++ r ++++ e Rl k+  ++ + ++++       +++l
  gi|14600516|ref|NP_147032.1| 127 NVERAIMQISERRLVKMMRLVLSGGGEE------VRERL 159
                                   9********************9999888......33344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 1369.10
//
Query:       gi|118430924|ref|NP_147033.2|  [L=697]
Description: minichromosome maintenance protein [Aeropyrum pernix K1]
Scores for 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-97  325.7   0.0    1.4e-97  325.2   0.0    1.2  1  MCM           MCM P-loop domain
    5.5e-35  120.0   0.0    9.7e-35  119.2   0.0    1.4  1  MCM_OB        MCM OB domain
    3.1e-29  101.2   1.3    7.2e-29  100.0   1.3    1.7  1  MCM_lid       MCM AAA-lid domain
    7.4e-20   71.5   0.1    1.7e-19   70.3   0.1    1.6  1  MCM_N         MCM N-terminal domain
    1.1e-07   31.4   0.0    2.4e-05   23.8   0.0    2.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    5.4e-07   29.7   0.0    1.3e-06   28.5   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
     0.0019   18.8   0.0     0.0042   17.7   0.0    1.5  1  RPA_C         Replication protein A C terminal
     0.0027   17.5   0.0     0.0058   16.5   0.0    1.5  1  AAA_3         ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.036   13.8   0.1        0.4   10.4   0.1    2.5  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.18   11.5   0.9       0.41   10.3   0.9    1.5  1  AAA_30        AAA domain
       0.51   11.0   2.7         14    6.4   0.1    3.8  4  HTH_32        Homeodomain-like 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 !  325.2   0.0  8.5e-101   1.4e-97       1     224 []     278     501 ..     278     501 .. 0.99

  Alignments for each domain:
  == domain 1  score: 325.2 bits;  conditional E-value: 8.5e-101
                                    HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHH CS
                            MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekl 80 
                                    ++e+i +l++++ i ek+++siap+iygh d k+ai+l+lfggv k+++d+t++rgdi+vl+vgdpg+aKsqlL++++++
  gi|118430924|ref|NP_147033.2| 278 DEEKILQLSRDPWIKEKIIASIAPTIYGHWDLKEAIALLLFGGVPKQRPDGTRTRGDIHVLFVGDPGVAKSQLLQSTAQV 357
                                    5799**************************************************************************** PP

                                    SSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEE CS
                            MCM  81 apravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivat 160
                                    apr vyt+gkgs+aagLtaav rd++tge++leaGalvlad+G+++iDefdkm++edr ++hEamEqqt+siaKaGi+at
  gi|118430924|ref|NP_147033.2| 358 APRVVYTTGKGSTAAGLTAAVLRDPRTGEYFLEAGALVLADGGIAVIDEFDKMSKEDRGVIHEAMEQQTVSIAKAGIKAT 437
                                    ******************************************************************************** PP

                                    EE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 161 LnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    L+ar+s+laA npk+g yd+++s+++n++l+a+++srFDlifv++D +++++De+la++++++h
  gi|118430924|ref|NP_147033.2| 438 LSARASLLAAGNPKFGYYDPSRSFVDNVDLPAPIISRFDLIFVVRDVIERSRDEMLASYVLETH 501
                                    *************************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0     6e-38   9.7e-35       2     122 ..     112     241 ..     111     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 6e-38
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE..........S----SB-..TTT-HHH.-EEE-GG CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev..........eleePrkCeekeCeskd.pfklete 70 
                                    +Rd+ s+h+gklv+++Givtr++   +++++a f++++cg++  +          ++e+P+ C  + C++ + +f+l+ +
  gi|118430924|ref|NP_147033.2| 112 IRDIGSDHVGKLVQINGIVTRMHPRATRMVRARFRHDRCGAEFWWpanedevlgeRIERPSIC--PVCGEGGgKFTLVRD 189
                                    8***************************************9777766666666655666****..99**6557******* PP

                                    GSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEE CS
                         MCM_OB  71 kskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiy 122
                                    ks ++d+qk+ +QE+pe+vp G++Prs+ev+l++dlv+kv+PGdrv+++G++
  gi|118430924|ref|NP_147033.2| 190 KSLYIDWQKIMVQERPEDVPGGQIPRSIEVHLSRDLVEKVRPGDRVKIVGVV 241
                                    **************************************************97 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   1.3   4.4e-32   7.2e-29       1      86 [.     514     603 ..     514     604 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 4.4e-32
                                    HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHH....TSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHH CS
                        MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkee....edskrksipitvRqLesliRLseAlAklrlsevvteedv 76 
                                    +llrkYia+ar+++kP+l+++ak+ l+++Yve+R+++    +++ +k +pit+RqLe+liRL+eA+A+++l++++teed+
  gi|118430924|ref|NP_147033.2| 514 DLLRKYIAFARKHVKPRLTPQAKKLLKDFYVEMRSSAlhhsSQEGAKPVPITTRQLEALIRLTEAHARMSLKQEATEEDA 593
                                    58*********************************999875444899********************************* PP

                                    HHHHHHHHHH CS
                        MCM_lid  77 eeairllkes 86 
                                      air+++++
  gi|118430924|ref|NP_147033.2| 594 IAAIRIMTSV 603
                                    *******875 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.1     1e-22   1.7e-19       2      86 ..      16      96 ..      15     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1e-22
                          MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklepsy 83
                                   e+F++FLe+f    ++e+g+ kY++ +++m+++e+t+Lev+++dL+ +d+ L+e +le+p+e+l+  +ealke+v++  p+y
  gi|118430924|ref|NP_147033.2| 16 ERFKTFLENF----RTEEGKLKYVEAIRRMINYEETSLEVEFKDLYRYDPLLSEILLEKPREFLKEASEALKEIVAQESPEY 93
                                   79********....7999**************************************************************99 PP

                          MCM_N 84 kdd 86
                                   ++ 
  gi|118430924|ref|NP_147033.2| 94 AQG 96
                                   886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.01        17      21      49 ..     333     361 ..     330     372 .. 0.88
   2 !   23.8   0.0   1.4e-08   2.4e-05      97     159 ..     389     451 ..     384     486 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.01
                   Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllppl 49 
                                    G  ++l+vG pG  K+ l +  +++ p++
  gi|118430924|ref|NP_147033.2| 333 GDIHVLFVGDPGVAKSQLLQSTAQVAPRV 361
                                    7789***************9999998876 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.4e-08
                   Mg_chelatase  97 pkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                     + G++ la  G+ ++DE+ +++++   v+ e +e+++v+i++a  k++  ar  l+aa Np 
  gi|118430924|ref|NP_147033.2| 389 LEAGALVLADGGIAVIDEFDKMSKEDRGVIHEAMEQQTVSIAKAGIKATLSARASLLAAGNPK 451
                                    6789*********************************************************94 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   7.8e-10   1.3e-06       1     122 [.     336     450 ..     336     475 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 7.8e-10
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEverae 78 
                                    +vl vG+pG++Ks+l ++ a++  r v +    ++ t++ l+  +  +   g++ l+ ++lv     g i+v+DE+++++
  gi|118430924|ref|NP_147033.2| 336 HVLFVGDPGVAKSQLLQSTAQVAPRVVYT--TGKGSTAAGLTAAVLRDprTGEYFLEAGALV--LADGGIAVIDEFDKMS 411
                                    79*******************98655444..445555666655544333369**********..99************** PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanp 122
                                    +e  ++ +  +e++++++++ g     ++       +++a++np
  gi|118430924|ref|NP_147033.2| 412 KEDRGVIHEAMEQQTVSIAKAGIKATLSAR-----ASLLAAGNP 450
                                    ****************99888766666554.....677777776 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 !   17.7   0.0   2.6e-06    0.0042      50      97 ..     632     686 ..     621     688 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                                    HHHHHHHHHHH.SXSTTT....EEHHHHHHHS...TSXHHHHHHHHHHHHHTTSE CS
                          RPA_C  50 laqqvlnlikqspeseeG....vhvdeiaqkl...rlsvndvkqavdeLsneGii 97 
                                      ++vl+lik+ +e+e G    v ++ei ++l   ++++++v+ a+d+L  +G+i
  gi|118430924|ref|NP_147033.2| 632 IMSEVLDLIKSIVEEERGgqgcVRASEIVRRLgekNIPEEKVRDAIDKLYRQGLI 686
                                    55789999999555444444469*********9999*****************98 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 !   16.5   0.0   3.6e-06    0.0058       1     112 [.     336     450 ..     336     462 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpd..llPsdilGtevfeekekefefkkGpvf.an..llladeinrap 75 
                                    hvl+ g PG+ak +l ++ a++      r+ +t+      + ++ + + + ++ e+ +++G+++ a+  + + de ++ +
  gi|118430924|ref|NP_147033.2| 336 HVLFVGDPGVAKSQLLQSTAQVA----PRVVYTTGkgSTAAGLTAAVLRDPRTGEYFLEAGALVlADggIAVIDEFDKMS 411
                                    9**************99999875....577776541257788999999999**********976243449999******* PP

                          AAA_3  76 pktqsalleameerqvtvege..thklpepflvlatqnP 112
                                       +  + eame+++v+++++  + +l+    +la+ nP
  gi|118430924|ref|NP_147033.2| 412 KEDRGVIHEAMEQQTVSIAKAgiKATLSARASLLAAGNP 450
                                    ****************99875115678899999999998 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 ?   10.4   0.1   0.00024       0.4      33     116 ..     334     430 ..     325     447 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                         RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltn..............leekdvlfideihrlsr 98 
                                      hvl++G PG+ k+ l +  a+    ++  t+g     ag  aa+l +              l ++ +  ide  ++s+
  gi|118430924|ref|NP_147033.2| 334 DIHVLFVGDPGVAKSQLLQSTAQVA-PRVVYTTGKGSTAAGLTAAVLRDprtgeyfleagalvLADGGIAVIDEFDKMSK 412
                                    459***********99977666533.333334444334444444444321111111111222278888999********* PP

                         RuvB_N  99 aveevlysamedfrldiv 116
                                    +   v++ ame  ++ i 
  gi|118430924|ref|NP_147033.2| 413 EDRGVIHEAMEQQTVSIA 430
                                    ***********9999885 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00025      0.41      15     123 ..     331     433 ..     325     440 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                         AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlliv 94 
                                    t gd  ++ +G +G  K+ +l++ ++++     rv+  + +g  A+ L++++  + +t + +l++  g+  l++g + ++
  gi|118430924|ref|NP_147033.2| 331 TRGDIHVLFVGDPGVAKSQLLQSTAQVAP----RVVYTTGKGSTAAGLTAAVLRDPRTGEYFLEA--GALVLADGGIAVI 404
                                    667778899***************99987....89**************99999*********44..44568899***** PP

                         AAA_30  95 DEagmvdtkqlaallkaaekagakvilvG 123
                                    DE   ++ ++   + +a+e++ +++  +G
  gi|118430924|ref|NP_147033.2| 405 DEFDKMSKEDRGVIHEAMEQQTVSIAKAG 433
                                    **********9999999999888776555 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.54   8.8e+02      29      51 ..     274     311 ..     270     325 .. 0.77
   2 ?   -1.6   0.0       2.7   4.3e+03      29      50 ..     511     534 ..     500     554 .. 0.69
   3 ?    6.4   0.1    0.0085        14      15      51 ..     549     586 ..     535     595 .. 0.82
   4 ?    0.5   0.0       0.6   9.7e+02      25      69 ..     628     673 ..     623     677 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.54
                         HTH_32  29 lsdevrariiallreep................rWsprq 51 
                                    ++ e +++i++l  ++p                +W +++
  gi|118430924|ref|NP_147033.2| 274 ITREDEEKILQLS-RDPwikekiiasiaptiygHWDLKE 311
                                    89999*******9.8987777777777777777777766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                         HTH_32  29 lsdevrariiallree..prWspr 50 
                                    +++++ ++ ia +r++  pr++p+
  gi|118430924|ref|NP_147033.2| 511 IDPDLLRKYIAFARKHvkPRLTPQ 534
                                    677777777777755444577773 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0085
                         HTH_32  15 egLkdrprrgrpr.klsdevrariiallreeprWsprq 51 
                                    ++L++ ++ g+++  ++ ++ +++i+l++ + r+s++q
  gi|118430924|ref|NP_147033.2| 549 SALHHSSQEGAKPvPITTRQLEALIRLTEAHARMSLKQ 586
                                    489999999966647*************7788999988 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.6
                         HTH_32  25 rprklsdevrariiallreep....rWsprqlaarlaeregvkvShstv 69 
                                    r rk+  ev + i+ +++ee+       ++++++rl e+    + ++ v
  gi|118430924|ref|NP_147033.2| 628 RSRKIMSEVLDLIKSIVEEERggqgCVRASEIVRRLGEKN---IPEEKV 673
                                    6678999999999999966668888888999999994444...555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 4614.99
//
Query:       gi|118430925|ref|NP_147034.2|  [L=735]
Description: holliday junction migration helicase [Aeropyrum pernix K1]
Scores for 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   70.0   0.0    3.7e-19   69.2   0.0    1.4  1  DEAD             DEAD/DEAH box helicase
      1e-11   45.1   0.0    8.5e-11   42.2   0.0    2.2  1  Helicase_C       Helicase conserved C-terminal domain
    4.5e-11   43.2   0.1    2.2e-10   41.0   0.1    2.3  1  HHH_5            Helix-hairpin-helix domain
    2.8e-10   40.4   0.0    4.3e-10   39.9   0.0    1.2  1  ResIII           Type III restriction enzyme, res subunit
    9.5e-10   37.9   0.0    8.8e-06   25.3   0.0    3.1  2  HHH              Helix-hairpin-helix motif
    5.3e-08   32.8   0.0    5.4e-07   29.6   0.0    2.4  2  HHH_2            Helix-hairpin-helix motif
    2.2e-05   24.2   0.0    0.00011   21.9   0.0    2.2  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0002   21.5   0.0     0.0099   16.1   0.0    3.0  3  HHH_3            Helix-hairpin-helix motif
    0.00047   20.1   0.0     0.0033   17.4   0.0    2.2  2  Flavi_DEAD       Flavivirus DEAD domain
    0.00085   19.5   0.0      0.027   14.7   0.0    2.5  2  Cdd1             Pathogenicity locus
    0.00089   19.5   0.0     0.0039   17.4   0.0    2.1  1  DUF4332          Domain of unknown function (DUF4332)
     0.0038   17.6   0.2       0.39   11.1   0.1    3.2  2  AAA_19           AAA domain
     0.0052   16.5   0.1      0.022   14.5   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.058   13.1   0.0    2.2  2  AAA_30           AAA domain
      0.016   15.5   0.4       0.61   10.4   0.1    3.1  2  AAA_22           AAA domain
      0.025   13.7   0.0      0.041   12.9   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.049   13.5   0.2        0.9    9.5   0.0    3.1  2  MarR_2           MarR family
      0.058   13.8   0.0       0.13   12.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
      0.062   13.5   0.0       0.19   12.0   0.0    1.9  1  DUF1611_N        Domain of unknown function (DUF1611_N) Rossm
      0.072   13.5   0.0       0.44   10.9   0.0    2.3  2  HHH_8            Helix-hairpin-helix domain
      0.075   12.6   0.2       0.38   10.3   0.1    2.3  2  AAA_25           AAA domain
      0.082   12.3   0.0       0.16   11.4   0.0    1.4  1  PhoH             PhoH-like protein
       0.23   10.9   0.8       0.62    9.5   0.1    1.8  2  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 !   69.2   0.0   4.7e-22   3.7e-19       4     170 ..      32     184 ..      29     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 4.7e-22
                                    HHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 Qaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                    Q  a+++ + +g++++vaa+TGsGKT ++l+++++++     + g +a++++P+++ a + ++ ++ +   ++l+++  +
  gi|118430925|ref|NP_147034.2|  32 QYMALQAGVeKGENLVVAAPTGSGKTFIALVAIVNSL----ARAGGRAFYLVPLKSVAYEKYTSFSILSR-MGLKLKISV 106
                                    5566666665788************************....57999*******************87777.677776444 PP

                                    TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                    g+   r+       ++ +v++t +++d+ll+      ++v++l++DE++ ++d ++++ +++i++++    + g+   q+
  gi|118430925|ref|NP_147034.2| 107 GD--FREGP----PEAPVVIATYEKFDSLLRVSPSLARNVSVLIVDEIHSVSDPKRGPILESIVSRM--LASAGE--AQL 176
                                    42..32222....4479*************6556569******************************..455555..45* PP

                                    EEEESSBS CS
                                    xxxxxxxx RF
                           DEAD 163 ivlSATlp 170
                                    + lSAT+p
  gi|118430925|ref|NP_147034.2| 177 VGLSATVP 184
                                    ******98 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 !   42.2   0.0   1.1e-13   8.5e-11      34     111 .]     299     384 ..     232     384 .. 0.66

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.1e-13
                                    HHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH........HHHH CS
                     Helicase_C  34 lllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv........tsyi 101
                                              +  +a++h+ lp + r+ + e+f++g ++v+ +t  ++ G+++p  ++Vi+  + ++         ++y+
  gi|118430925|ref|NP_147034.2| 299 E----LasliAAGIAYHHAGLPPSLRKTVEEAFRAGAVKVVYSTPTLAAGVNLPARRVVIDSYYRYEAgfrepirvAEYK 374
                                    2....13445788999********************************************8888844333333444**** PP

                                    HHHTTSSSTT CS
                     Helicase_C 102 qriGRtgRag 111
                                    q++GR+gR g
  gi|118430925|ref|NP_147034.2| 375 QMAGRAGRPG 384
                                    ********75 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.1   2.8e-13   2.2e-10       3      56 ..     648     701 ..     645     702 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.8e-13
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                    +L +++G+G+++A+ l +aG++s+edla a +e+L ++p iG+ tA++i++ l 
  gi|118430925|ref|NP_147034.2| 648 QLVEIPGVGRVRARILFEAGYRSIEDLATARAEDLMRLPLIGPSTARQILEFLG 701
                                    5779**********************************************9986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   5.5e-13   4.3e-10      22     170 ..      41     184 ..      14     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 5.5e-13
                                    .TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.... CS
                         ResIII  22 krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekd 100
                                    ++ ++++++++TG+GKT++a ++++ +l+++g+  +++ lvp ks+    ++ f+ ++      + k+  gd ++     
  gi|118430925|ref|NP_147034.2|  41 EKGENLVVAAPTGSGKTFIAlVAIVNSLARAGG--RAFYLVPLKSVAYEKYTSFSILSRMGL--KLKISVGDFREG---- 112
                                    6778999*************8888899999888..9******99998888888877777665..455555666555.... PP

                                    ...-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS-S CS
                         ResIII 101 stnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATpe 170
                                      ++ ++++t++++d+ +          l  +  v+i+DE H +++ k        + + l +  ea l+gl+AT +
  gi|118430925|ref|NP_147034.2| 113 PPEAPVVIATYEKFDSLL-----RVSPSLARNVSVLIVDEIHSVSDPKrgpilesIVSRMLASAGEAQLVGLSATVP 184
                                    77999*************.....67777888888************74555333344445666677*********75 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0014       1.1      12      25 ..     648     661 ..     648     666 .. 0.87
   2 !   25.3   0.0   1.1e-08   8.8e-06       1      30 []     670     699 ..     670     699 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                                    HHHTSTT-SHHHHH CS
                            HHH  12 eLlalPGVGpktAe 25 
                                    +L+++PGVG+ +A+
  gi|118430925|ref|NP_147034.2| 648 QLVEIPGVGRVRAR 661
                                    699**********8 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 1.1e-08
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                    s+e l +a  e+L+ lP +Gp+tA++Il++
  gi|118430925|ref|NP_147034.2| 670 SIEDLATARAEDLMRLPLIGPSTARQILEF 699
                                    6899************************97 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   1.1e+03      26      46 ..     546     566 ..     544     574 .. 0.85
   2 !   29.6   0.0   6.9e-10   5.4e-07       8      55 ..     652     700 ..     646     708 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                          HHH_2  26 ldaLkkasleeLlevddiGee 46 
                                    l+a+ +as   L++vd  G+e
  gi|118430925|ref|NP_147034.2| 546 LEAILDASPRMLSSVDWLGPE 566
                                    799*************99986 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 6.9e-10
                          HHH_2   8 IrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsivefF 55 
                                    I+ VG   A++L ++ ++s++ L++a +e+L  ++ iG+ +A++i ef+
  gi|118430925|ref|NP_147034.2| 652 IPGVGRVRARILFEAgYRSIEDLATARAEDLMRLPLIGPSTARQILEFL 700
                                    9***********9866********************************8 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 !   21.9   0.0   1.5e-07   0.00011       2      30 ..     648     676 ..     648     689 .. 0.87
   2 ?   -1.7   0.0       3.4   2.7e+03       9      16 ..     688     695 ..     680     698 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.5e-07
                DNA_pol_lambd_f   2 lFtkvyGVGpktAkkwyakGirtledlra 30 
                                    ++ ++ GVG+++A+ ++++G+r++edl +
  gi|118430925|ref|NP_147034.2| 648 QLVEIPGVGRVRARILFEAGYRSIEDLAT 676
                                    5789***********************88 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                DNA_pol_lambd_f   9 VGpktAkk 16 
                                    +Gp+tA++
  gi|118430925|ref|NP_147034.2| 688 IGPSTARQ 695
                                    8*****98 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.4     5e+03      11      30 ..     121     140 ..     121     141 .. 0.87
   2 ?    1.3   0.0      0.55   4.3e+02      21      54 ..     622     657 ..     610     662 .. 0.76
   3 !   16.1   0.0   1.3e-05    0.0099       7      33 ..     673     699 ..     671     704 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.4
                          HHH_3  11 AsaeeLqklpGlgpklAknI 30 
                                    A++e  + l  ++p+lA+n+
  gi|118430925|ref|NP_147034.2| 121 ATYEKFDSLLRVSPSLARNV 140
                                    788899999999*****985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                          HHH_3  21 GlgpklAk..nIvayReknGpfksreeLlkvkglgp 54 
                                    Gl++k+++   ++a R k+G    + +L++++g+g 
  gi|118430925|ref|NP_147034.2| 622 GLNSKVSHilSVIARRIKHGVKPELLQLVEIPGVGR 657
                                    666666663356899999999999999999999986 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.3e-05
                          HHH_3   7 diNtAsaeeLqklpGlgpklAknIvay 33 
                                    d+ tA ae+L++lp +gp++A++I+++
  gi|118430925|ref|NP_147034.2| 673 DLATARAEDLMRLPLIGPSTARQILEF 699
                                    788*********************986 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.3e-06    0.0033       2     138 ..      41     185 ..      40     191 .. 0.74
   2 ?   -0.7   0.0       1.6   1.2e+03     104     138 ..     496     531 ..     494     537 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.3e-06
                                    XX--EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHH...TTTS-EEE------.-------SEEE CS
                     Flavi_DEAD   2 rkkkltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeea...lkglevryktsavk.eektgrelvdv 77 
                                    +k++  v+ +  G+Gkt   l+ +v++ ++   r+  L+P + v+ e + +   l+ + ++ k s+   +e   ++ v +
  gi|118430925|ref|NP_147034.2|  41 EKGENLVVAAPTGSGKTFIALVAIVNSLARAGGRAFYLVPLKSVAYEKYTSfsiLSRMGLKLKISVGDfREGPPEAPVVI 120
                                    678888999999***********************************987622256666776666553134445556667 PP

                                    EEHHHHHHH.HHHT------SEEEEETTT--.SHHH..HHHHHHHHHHHHTTS-EEEEEESS-TT CS
                     Flavi_DEAD  78 mchatftkr.llspvrkknyeliimDeahfl.DPas..iaarGyletkaeegeaalilltatPPG 138
                                    + +  f +  ++sp    n+ ++i+De h + DP+   i      + +a++gea+l+ l+at P 
  gi|118430925|ref|NP_147034.2| 121 ATYEKFDSLlRVSPSLARNVSVLIVDEIHSVsDPKRgpILESIVSRMLASAGEAQLVGLSATVPN 185
                                    67777755425779***************754997521333333345678899999999999885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                    TT--SHHHHHH.HHHHHHHHHTTS-EEEEEESS-TT CS
                     Flavi_DEAD 104 ahflDPasiaa.rGyletkaeegeaalilltatPPG 138
                                    a +lDP+s+ + r  +++++  +e  +++l +t P 
  gi|118430925|ref|NP_147034.2| 496 AVYLDPESVPVfREEVKHLSFDNEFDILYLISTMPD 531
                                    6699*****755999**************9999885 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.4e-05     0.027       5      42 ..     646     683 ..     643     684 .. 0.92
   2 ?    5.6   0.0     0.024        19       3      41 ..     677     714 ..     675     722 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                           Cdd1   5 lkelqdiPniGkalaedlvelGirsveelkgedpeely 42 
                                    l +l +iP++G+  a+ l e G+rs+e+l+   +e+l+
  gi|118430925|ref|NP_147034.2| 646 LLQLVEIPGVGRVRARILFEAGYRSIEDLATARAEDLM 683
                                    67899**************************9999986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.024
                           Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpeel 41 
                                    +++++l ++P iG+++a+++ e  + +v+e ++ ++ e+
  gi|118430925|ref|NP_147034.2| 677 ARAEDLMRLPLIGPSTARQILEF-LGRVDEAREAEAREM 714
                                    67899************998753.335666666666666 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     5e-06    0.0039      54      89 ..     648     683 ..     643     685 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
                        DUF4332  54 dLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLh 89 
                                    +L+ i+g+g+  a +L +aG +s+++La+ ++++L+
  gi|118430925|ref|NP_147034.2| 648 QLVEIPGVGRVRARILFEAGYRSIEDLATARAEDLM 683
                                    799*******************************98 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   0.00049      0.39       9     126 ..      42     164 ..      32     177 .. 0.59
   2 ?    2.7   0.0      0.19   1.5e+02      46      68 ..     258     280 ..     241     588 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                         AAA_19   9 kekvllvtaGpGtGKTrv.lkhivallvelggvkpeeillvaftgrAakelre.....rlaalgae.............. 68 
                                    k ++l+v a+ G+GKT + l++iv+ l ++gg+    ++lv + + A ++ +      r+ +l  +              
  gi|118430925|ref|NP_147034.2|  42 KGENLVVAAPTGSGKTFIaLVAIVNSLARAGGR---AFYLVPLKSVAYEKYTSfsilsRM-GL--Klkisvgdfregppe 115
                                    56789999999*****97588999999999976...455555555555555442211133.22..233556666666666 PP

                         AAA_19  69 ....atTiHrlalldfddlltealelleeaeeekklqeee.llivDEfqdvd.elqyrLlkall 126
                                        + T+ ++     d+ll            +  l ++  +livDE+  v+ +    +l+ ++
  gi|118430925|ref|NP_147034.2| 116 apvvIATYEKF-----DSLLRV----------SPSLARNVsVLIVDEIHSVSdPKRGPILESIV 164
                                    54444444433.....444411..........12233333477888877777666666666665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                         AAA_19  46 llvaftgrAakelrerlaalgae 68 
                                     +v++++rAak+l  rl++ +a+
  gi|118430925|ref|NP_147034.2| 258 RAVTLAKRAAKRLGRRLSSREAR 280
                                    5799999****999999554444 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 !   14.5   0.0   2.8e-05     0.022      43      81 ..      39      78 ..      17      84 .. 0.86
   2 ?   -3.1   0.0       6.9   5.4e+03     108     117 ..     139     148 ..     124     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-05
                      IstB_IS21 43 fiekkenivllGpsGvGKshla.ialgveavraglsvlfv 81
                                    +ek en+v+  p+G GK+++a +a+  + +rag + +++
  gi|118430925|ref|NP_147034.2| 39 GVEKGENLVVAAPTGSGKTFIAlVAIVNSLARAGGRAFYL 78
                                   4899******************569999999999888875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.9
                      IstB_IS21 108 kvdllilDdl 117
                                    +v++li+D++
  gi|118430925|ref|NP_147034.2| 139 NVSVLIVDEI 148
                                    4699****98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.5e-05     0.058       5     111 ..      31     162 ..      27     178 .. 0.70
   2 ?   -2.7   0.1       5.1     4e+03      50      68 ..     258     276 ..     236     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                         AAA_30   5 eQaaavealltsgdrvavltGpAGtGKtta.lkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.. 81 
                                     Q  a++a +++g+   v+ +p G+GKt++ l a+++ +++aggr + l p + +A +  +++ i ++   kl  + +  
  gi|118430925|ref|NP_147034.2|  31 PQYMALQAGVEKGE-NLVVAAPTGSGKTFIaLVAIVNSLARAGGRAFYLVPLKSVAYEKYTSFSILSRMGLKLKISVGdf 109
                                    58888888888887.78999********9637777999999998888888888888776655555554444444444455 PP

                         AAA_30  82 ......................grarlepg.tllivDEagmvdtkqlaallka 111
                                                             +l+++ ++livDE+  v+  +   +l++
  gi|118430925|ref|NP_147034.2| 110 regppeapvviatyekfdsllrVSPSLARNvSVLIVDEIHSVSDPKRGPILES 162
                                    55555555555555555566665567888889******999987776666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                         AAA_30  50 iglAptgkaAkvLaeelgi 68 
                                     +++  ++aAk+L++ l  
  gi|118430925|ref|NP_147034.2| 258 RAVTLAKRAAKRLGRRLSS 276
                                    3455566777777766554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00078      0.61       6     115 ..      44     166 ..      40     179 .. 0.57
   2 ?   -0.6   0.0       1.9   1.5e+03      23      87 ..     268     328 ..     253     336 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00078
                         AAA_22   6 gilvvtGesGtGKTtllr.rlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka............ 70 
                                      lvv +++G+GKT+ +   ++++l ++      ++ +++v l+s    + +++   +l+ +gl+lk             
  gi|118430925|ref|NP_147034.2|  44 ENLVVAAPTGSGKTFIALvAIVNSLARA-----GGRAFYLVPLKSVAyeKYTSF--SILSRMGLKLKIsvgdfregppea 116
                                    5689999999999987651555555322.....133333444444443333333..555555555555555676544433 PP

                         AAA_22  71 ....erlsseellealeqalrarav........ielliiDEaqhlr...seealeeLrsl 115
                                        +           ++ +++  +        +++li+DE++ ++   +  +le ++s+
  gi|118430925|ref|NP_147034.2| 117 pvviA----------TYEKFDSLLRvspslarnVSVLIVDEIHSVSdpkRGPILESIVSR 166
                                    33333..........44444444444445565677*********9655338888888554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                         AAA_22  23 rrlleqldeeakaee.....erpevvfvtlpsst.sskdllrellralglelka.erlsseellealeqalr 87 
                                    +rl                 ++++v++ +++  +  ++++++el++ +  +  +   +    l++++e+a+r
  gi|118430925|ref|NP_147034.2| 268 KRL-----------GrrlssREARVYSAEASRAEgAPRSVAEELASLIAAGIAYhHAGLPPSLRKTVEEAFR 328
                                    222...........1344456899999999988889999999999999877666433333344455555555 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 ?   12.9   0.0   5.3e-05     0.041     104     153 ..      18      68 ..      12      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                          T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttll.yallkei 153
                                    tl++l+  e+l e +  +l++ v++  +++v+ +TgsGKt ++  a+++ +
  gi|118430925|ref|NP_147034.2|  18 TLAKLAGVERLFEPQYMALQAGVEKGENLVVAAPTGSGKTFIAlVAIVNSL 68 
                                    567777777777888889**********************76426666665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012       0.9      32      53 ..     459     480 ..     430     484 .. 0.94
   2 ?   -0.6   0.0       1.6   1.3e+03       6      20 ..     692     706 ..     688     721 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                                    TSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  32 glsksavsrilkrLvaaGLver 53 
                                    gl++ ++ r++++L+a GLve 
  gi|118430925|ref|NP_147034.2| 459 GLPRETIARAVEDLSAWGLVEV 480
                                    8999****************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHCTTTS CS
                         MarR_2   6 aqarvLaaLgrrpgr 20 
                                    + +++L +Lgr ++ 
  gi|118430925|ref|NP_147034.2| 692 TARQILEFLGRVDEA 706
                                    77999*****99974 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.13       3      73 ..      48     154 ..      46     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                    EESSTTSSHHHHHH.HHHHHH....THEEEEEETTTCS.SS.............................STTHHHHHHH CS
                            AAA   3 lyGppGtGKTllak.avakel....gvefleisgsell.sk.............................yvgesekkir 47 
                                    +  p G GKT +a  a++++l    g+ f+ + ++++  +k                             +v ++ +k+ 
  gi|118430925|ref|NP_147034.2|  48 VAAPTGSGKTFIALvAIVNSLaragGRAFYLVPLKSVAyEKytsfsilsrmglklkisvgdfregppeapVVIATYEKFD 127
                                    67899******9963677776555434444444444443335555555556666667777777789****9999999999 PP

                                    HHHHHHHHTS.TSEEEEEETGGGHHHH CS
                            AAA  48 elfkeakeka.kpsilfiDEidalaks 73 
                                     l++   + a + s+l++DEi+++   
  gi|118430925|ref|NP_147034.2| 128 SLLRVSPSLArNVSVLIVDEIHSVSDP 154
                                    9999888888667**********9654 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 ?   12.0   0.0   0.00025      0.19      27      61 ..     297     331 ..     264     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                      DUF1611_N  27 laagaevlviGiapeggklpeswreavkeAleaGl 61 
                                    +++ a  +  Gia ++  lp+s+r++v+eA +aG 
  gi|118430925|ref|NP_147034.2| 297 AEELASLIAAGIAYHHAGLPPSLRKTVEEAFRAGA 331
                                    5677888999***********************95 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.9   4.6e+03      47      57 ..     648     657 ..     635     666 .. 0.75
   2 ?   10.9   0.0   0.00057      0.44      34      67 ..     670     700 ..     664     701 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.9
                                    THCTTSTT--H CS
                          HHH_8  47 eeltklpgiGk 57 
                                    + l ++pg+G 
  gi|118430925|ref|NP_147034.2| 648 Q-LVEIPGVGR 657
                                    4.889****96 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00057
                                    CCCC-SS-HHHHTTHCTTSTT--HHHHHHHHHHH CS
                          HHH_8  34 aiealpeeitsleeeltklpgiGkkiaakieeil 67 
                                    +ie+l ++ ++   +l +lp iG+++a++i e+l
  gi|118430925|ref|NP_147034.2| 670 SIEDLATARAE---DLMRLPLIGPSTARQILEFL 700
                                    55555555555...7*****************98 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00048      0.38      29      55 ..      40      65 ..      20      85 .. 0.79
   2 ?   -2.5   0.0       4.1   3.2e+03       3      37 ..     396     431 ..     395     438 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                         AAA_25 29 llpagelallaGapgtGKttlaldlal 55
                                   +  +ge  ++a+++g+GKt++al   +
  gi|118430925|ref|NP_147034.2| 40 V-EKGENLVVAAPTGSGKTFIALVAIV 65
                                   4.789999*************997755 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                         AAA_25   3 eplelsavsvad.laapppprrwlvkgllpagelal 37 
                                    e+l++++  +++ ++app++++  + gl+ + +++l
  gi|118430925|ref|NP_147034.2| 396 ERLDRPEDLISGyIRAPPERVESRLAGLRGLRHFIL 431
                                    566666666777689999999999999988777765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.16      18      46 ..      42      70 ..      29      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                   H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                           PhoH 18 kndivfaiGpaGtGKtylavalavealkk 46
                                   k + +++++p+G+GKt++a+++ v+ l +
  gi|118430925|ref|NP_147034.2| 42 KGENLVVAAPTGSGKTFIALVAIVNSLAR 70
                                   555677899************99988765 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 ?    9.5   0.1   0.00079      0.62      10      41 ..      40      71 ..      33      78 .. 0.80
   2 ?   -1.2   0.1       1.4   1.1e+03      49      85 ..     250     284 ..     240     308 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00079
                                   HS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTS CS
                  UvrD-helicase 10 aslggpilveAsAGsGKTfvlaerilrlikee 41
                                   +  g++++v+A  GsGKTf+    i++ ++ +
  gi|118430925|ref|NP_147034.2| 40 VEKGENLVVAAPTGSGKTFIALVAIVNSLARA 71
                                   4567889999999*******999999888765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                    EEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHH CS
                  UvrD-helicase  49 lvvTFTnkAaeElkeRieealkkaeqessdderlrla 85 
                                    lv+T+ ++ a  l +R +++l+ ++  ss++ r++ a
  gi|118430925|ref|NP_147034.2| 250 LVFTYSRRRAVTLAKRAAKRLGRRL--SSREARVYSA 284
                                    5666666666666666666666543..3333344433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (735 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4717.17
//
Query:       gi|14602185|ref|NP_147035.1|  [L=367]
Description: L-lysine 6-dehydrogenase [Aeropyrum pernix K1]
Scores for 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-10   39.2   0.0    1.1e-09   38.8   0.0    1.2  1  Sacchrp_dh_C    Saccharopine dehydrogenase C-terminal domain
    2.3e-05   24.1   0.0    3.8e-05   23.3   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00018   21.5   0.0    0.00042   20.3   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    0.00073   19.7   0.1      0.002   18.3   0.0    1.9  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.003   17.8   0.0      0.005   17.1   0.0    1.4  1  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.015   14.9   0.1      0.026   14.1   0.1    1.4  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.032   13.8   0.0      0.054   13.1   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.039   13.3   0.0      0.067   12.5   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.042   14.1   1.0       0.81   10.0   0.3    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.066   12.5   0.1        0.1   11.9   0.1    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.13   11.5   0.1        0.2   10.8   0.1    1.2  1  FAD_binding_3   FAD binding domain


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 !   38.8   0.0     7e-13   1.1e-09       1     265 []     116     362 ..     103     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 7e-13
                                   BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCCESTTCEEESS-HHHHHHHCCSEEEEEETTE.EEECT.CCC CS
                  Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeasdnplgYkfsWspegvlreltnpakvlengq.vkevp.gse 79 
                                   G+ PG+++++  ++  e    gg   s   y+g   a e     l    +W +e +l+++  pak++++g   +  p + +
  gi|14602185|ref|NP_147035.1| 116 GVSPGLSNVILYSMAAET---GG-GVSARVYVGSFGAREDG--LLSHASTWRVEEMLEQYVTPAKLIQDGSeAVADPlDPS 190
                                   788999999998888854...33.34666677777655554..6777779*********************5444454444 PP

                                   SGCC.TCEEECCCCCEECTTECEEECTHCHHHH.HHC.SCSEEEEEEEEEHHHHHHHHHHHTTT--SCECCCCCCHHSTT. CS
                  Sacchrp_dh_C  80 llkgakkpiyilpglslegypnrdslpyeelyg.lpeaktlfrgtlrypgfsellkslkelGllseepkeealkawlseg. 158
                                   l     +  + ++g  le++p++    + +  g l   k+l+  +lr  g+ +++ +++ lGll+++p    lk+   +g 
  gi|14602185|ref|NP_147035.1| 191 LWM---EYSDPEHG-VLECFPSQGLAGFISRRGsLF--KELMECSLRRRGHLKVVLTMRGLGLLDSTP----LKV---SGc 258
                                   432...22223345.799999998888877776566..9****************************9....666...555 PP

                                   C.EHHHHHHHHCCHHCCCCTTEEEEEEEEEEEEEETTSEE.EEEEEEEEEEEEHH.SSSHHHHHHHHHHHHHHHHHHT.T. CS
                  Sacchrp_dh_C 159 e.spldvlaalLekklalepgerDlvvlqhefgiesdgkk.kekktstlvgydee.gssamaktvGvpaaiaaklild.g. 234
                                     +p+d+  +l e++  + p+  D +v+++e      g + ++ ++ +l   +   g sa +k vG  ++  a+ +++ g 
  gi|14602185|ref|NP_147035.1| 259 IvRPFDMAVKLVETR--YPPDVGDVAVFTVEA---RRGGRwETLARASLR--H-GgGWSASSKMVGGASSAFAEVFAAeGl 331
                                   458***999999766..567777778888887...445543333334444..2.25********************99456 PP

                                   SCTSSEEEEGGGS.CHHHHHHHHHHHHHCT- CS
                  Sacchrp_dh_C 235 kikkrGvvtpeelvdpeiyeplleeLekeGi 265
                                   + +++G++ pe+l++  ++e+ll  L ++G+
  gi|14602185|ref|NP_147035.1| 332 SEEEPGIIYPEDLYELGLAEKLLSLLPSHGV 362
                                   4456*********99999*******999985 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 !   23.3   0.0   2.3e-08   3.8e-05       2      40 ..       3      41 ..       2      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.3e-08
                                  EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHC CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdkln 40
                                  ki+v+GlG vGl  a  la++g++v+g+D ++ +v+  +
  gi|14602185|ref|NP_147035.1|  3 KIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRAR 41
                                  8*******************************9998766 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 !   20.3   0.0   2.6e-07   0.00042       1      40 [.       3      42 ..       3      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.6e-07
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHH CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekale 40
                                  k+av+G G +G   a+ +as+g++V  +d s++a+ +a++
  gi|14602185|ref|NP_147035.1|  3 KIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARS 42
                                  69**********************************9986 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 !   18.3   0.0   1.3e-06     0.002       1      42 [.       3      44 ..       3      99 .. 0.83
   2 ?   -2.1   0.1       2.3   3.7e+03     129     142 ..     312     325 ..     306     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                                  EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                 NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42
                                  ki+++GlG  G   a nl+++g++v + + ++++v ++ + g
  gi|14602185|ref|NP_147035.1|  3 KIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG 44
                                  79********************************99988877 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.3
                                   EEEEEE-HHHHHHH CS
                 NAD_binding_2 129 simvGGseeaferv 142
                                   s mvGG ++af++v
  gi|14602185|ref|NP_147035.1| 312 SKMVGGASSAFAEV 325
                                   67*******99876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.1e-06     0.005       1      49 [.       4      52 ..       4      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.1e-06
                                  EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-T CS
                        TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgda 49
                                  i+++GlGrvG + a +L ++g dv++ d + ++v ++r  gle+   d+
  gi|14602185|ref|NP_147035.1|  4 IAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLGLEARLYDV 52
                                  79*****************7768****************9998876665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    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      47 [.       4      51 ..       4      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47
                                  ia+lG+G +G   a++La  g dv  ++ s+  + + ++ Gl+ + ++
  gi|14602185|ref|NP_147035.1|  4 IAVLGLGRVGLRAAYNLASRGFDVLGLDASNdAVSRARSLGLEARLYD 51
                                  89*****************************99999999999887665 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 ?   13.1   0.0   3.3e-05     0.054       6      52 ..       3      48 ..       1      58 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                                  -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE CS
                          IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl 52
                                  kiav+G G  G   a nl   g+dv +gl +++  v++A++ g+e  
  gi|14602185|ref|NP_147035.1|  3 KIAVLGLGRVGLRAAYNLASRGFDV-LGLDASNDAVSRARSLGLEAR 48
                                  8***********************8.69*99999******9999865 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 ?   12.5   0.0   4.1e-05     0.067      38      79 ..       3      44 ..       2      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.1e-05
                                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelg 79
                                  +++++GlGr+G ++a  l++ g++v++ d s+++ +++++lg
  gi|14602185|ref|NP_147035.1|  3 KIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG 44
                                  689***************************988776665555 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 ?   10.0   0.3   0.00049      0.81       2      37 ..       7      42 ..       6      59 .. 0.82
   2 ?    1.8   0.0      0.18   2.9e+02      21      54 ..     280     313 ..     265     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                                  E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                 NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                  +G G  Gl aAy La +gfdvl l+++++   ra+s
  gi|14602185|ref|NP_147035.1|  7 LGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARS 42
                                  666888********************9997666665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                   EEEEE-SSSSSSGGG-EECETTCEECTS---EEE CS
                 NAD_binding_8  21 dvlllekrdrlGGraasyevpgvrvdygahifhg 54 
                                   dv ++    r GGr+ +  +   r+  g+++  +
  gi|14602185|ref|NP_147035.1| 280 DVAVFTVEARRGGRWETLARASLRHGGGWSASSK 313
                                   7888888999999999999999999999887655 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 ?   11.9   0.1   6.2e-05       0.1      30      82 ..       3      54 ..       1      88 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.2e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqe 82
                                  k+ v+G G +Gl A+ + ++ g +V  lD + ++  + +slg +  +++  + 
  gi|14602185|ref|NP_147035.1|  3 KIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLGLE-ARLYDVEG 54
                                  899***********************************997766.55544444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00013       0.2       2      48 ..       2      48 ..       1      53 [. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHH CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqr 48
                                  +++++ G G +Gl +a  L+++G +v+ ++  +++v   r+ gl+ r
  gi|14602185|ref|NP_147035.1|  2 VKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLGLEAR 48
                                  578899**************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2846.90
//
Query:       gi|118430926|ref|YP_874804.1|  [L=87]
Description: hypothetical protein APE_0193a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   0.3      0.051   13.4   0.3    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.076   12.9   0.0       0.12   12.2   0.0    1.3  1  RuvB_C         RuvB C-terminal winged 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 ?   13.4   0.3   5.7e-06     0.051       4      30 ..      18      46 ..      17      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-06
                  HTH_AsnC-type  4 iDrkILeaLqed..aRisyaeLAervGlS 30
                                   iD kILe+L++     +s  +LA+++Gl+
  gi|118430926|ref|YP_874804.1| 18 IDEKILEILRRYrtTEMSLDQLAAALGLD 46
                                   8**************************96 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 ?   12.2   0.0   1.4e-05      0.12       7      37 ..      18      47 ..      17      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHHHT.TT--B-HHHHHHHTT--H CS
                         RuvB_C  7 ldikyLkllkekfkggpvglktlaailgeek 37
                                   +d k+L++l  +++ ++++l+ laa+lg+++
  gi|118430926|ref|YP_874804.1| 18 IDEKILEILR-RYRTTEMSLDQLAAALGLDS 47
                                   699******7.7***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 660.93
//
Query:       gi|118430927|ref|NP_147038.2|  [L=255]
Description: HTH-type transcriptional regulator [Aeropyrum pernix K1]
Scores for complete 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   30.1   0.3      1e-06   29.0   0.0    1.7  2  HTH_31      Helix-turn-helix domain
    5.7e-06   26.3   0.0    2.1e-05   24.5   0.0    2.0  2  HTH_3       Helix-turn-helix
    7.4e-05   22.7   0.0    0.00016   21.6   0.0    1.5  1  HTH_19      Helix-turn-helix domain
     0.0087   16.0   0.0      0.018   15.0   0.0    1.4  1  YAcAr       YspA, cpYpsA-related SLOG family
  ------ inclusion threshold ------
      0.075   12.9   0.0       0.45   10.4   0.0    2.4  3  MarR_2      MarR family
      0.082   12.7   0.0       0.18   11.6   0.0    1.5  1  HTH_38      Helix-turn-helix domain
      0.093   12.3   0.1       0.29   10.7   0.0    1.8  2  Sigma70_r4  Sigma-70, region 4
       0.12   11.3   0.0       0.17   10.8   0.0    1.1  1  DUF1207     Protein of unknown function (DUF1207)


Domain annotation for each model (and alignments):
>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.5e-10     1e-06       1      51 [.      35      84 ..      35      87 .. 0.91
   2 ?   -3.8   0.2       7.6   1.7e+04       1       9 [.     237     245 ..     237     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.5e-10
                         HTH_31  1 aLGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51
                                   ++G+ Lr +Re   +sq e A+  gv++s +s++E  rr+ p   ++ +++
  gi|118430927|ref|NP_147038.2| 35 DFGEALRKWREYFEVSQSEIAREMGVTASVISDYEKSRRT-PGAVFIKRFV 84
                                   69*************************************5.9887777766 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.6
                         HTH_31   1 aLGalLral 9  
                                    +L+ +Lr l
  gi|118430927|ref|NP_147038.2| 237 ELASRLRSL 245
                                    588888876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   9.2e-09   2.1e-05       1      38 [.      40      77 ..      40      87 .. 0.87
   2 ?   -3.2   0.0       4.2   9.4e+03       8      20 ..      94     107 ..      93     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.2e-09
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsl 38
                                   l+++R+    sq e+A+++Gv+ s is++E+ +r P  
  gi|118430927|ref|NP_147038.2| 40 LRKWREYFEVSQSEIAREMGVTASVISDYEKSRRTPGA 77
                                   6788888889************************9976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                                    TTHHH.HHHHHHHT CS
                          HTH_3   8 lglsq.eeLAeklG 20 
                                    +g+ + ++LA ++G
  gi|118430927|ref|NP_147038.2|  94 RGWKKtKDLAMLAG 107
                                    78888899998887 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   7.1e-08   0.00016       1      48 [.      37      83 ..      37      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.1e-08
                         HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48
                                   Ge L++ Re +  +q e+a++ g++ s is +E+ ++ +p+a  ++++
  gi|118430927|ref|NP_147038.2| 37 GEALRKWREYFEVSQSEIAREMGVTASVISDYEKSRR-TPGAVFIKRF 83
                                   99*********************************99.**99888775 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.9e-06     0.018      29      64 ..     200     234 ..     193     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.9e-06
                          YAcAr  29 pidmvlvhGgakGaDrlAarWAaergvelvrfpaDw 64 
                                    p  +v+vhG  + +DrlA + A++  v+lv+ ++D 
  gi|118430927|ref|NP_147038.2| 200 P-AVVIVHGPGRNVDRLAIEIAKADRVPLVVSQLDS 234
                                    6.59**************************999996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002      0.45      21      39 ..      48      66 ..      29      68 .. 0.84
   2 ?   -3.0   0.0       3.2   7.2e+03      19      28 ..     122     129 ..     116     130 .. 0.75
   3 ?   -3.7   0.0       5.4   1.2e+04       3      14 ..     161     172 ..     160     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                   EEEHHHHHHHHTSSHHHHH CS
                         MarR_2 21 dltvgelarrlglsksavs 39
                                   +++++e+ar++g++ s +s
  gi|118430927|ref|NP_147038.2| 48 EVSQSEIAREMGVTASVIS 66
                                   589*************998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                                    TSEEEHHHHH CS
                         MarR_2  19 grdltvgela 28 
                                    +  ltvgel 
  gi|118430927|ref|NP_147038.2| 122 P--LTVGELS 129
                                    3..9***995 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 5.4
                                    --HHHHHHHHHH CS
                         MarR_2   3 ltpaqarvLaaL 14 
                                    l++ q+ vL+ L
  gi|118430927|ref|NP_147038.2| 161 LSGLQFTVLFGL 172
                                    677899999865 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.2e-05      0.18      22      38 ..      50      66 ..      40      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.2e-05
                         HTH_38 22 slreIArrLgrspsTIs 38
                                   s++eIAr++g+  s Is
  gi|118430927|ref|NP_147038.2| 50 SQSEIAREMGVTASVIS 66
                                   99**************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 ?   10.7   0.0   0.00013      0.29      18      39 ..      46      67 ..      30      71 .. 0.81
   2 ?   -2.7   0.0         2   4.4e+03      12      26 ..     113     128 ..     112     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                   TTT--HHHHHHHHTS-HHHHHH CS
                     Sigma70_r4 18 geglTleEIgerlgiSrerVrq 39
                                   + + +++EI++++g++ + ++ 
  gi|118430927|ref|NP_147038.2| 46 YFEVSQSEIAREMGVTASVISD 67
                                   7788************998875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                    HHHHHH.TTT--HHHH CS
                     Sigma70_r4  12 vlelrf.geglTleEI 26 
                                    ++ +r  +++lT  E+
  gi|118430927|ref|NP_147038.2| 113 IVDMREfEKPLTVGEL 128
                                    6667766899998887 PP

>> DUF1207  Protein of unknown function (DUF1207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.4e-05      0.17     116     163 ..      23      72 ..      13      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.4e-05
                        DUF1207 116 ndnvdGknvgsvsfGetipfyra..nigqsivqweiGlqaavfsdfnlga 163
                                       + G+ + s  fGe +  +r   +++qs    e+G+ a+v sd++   
  gi|118430927|ref|NP_147038.2|  23 AIRIAGDIIYSRDFGEALRKWREyfEVSQSEIAREMGVTASVISDYEKSR 72 
                                    5568899999************87899******************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1984.48
//
Query:       gi|118430928|ref|NP_147039.2|  [L=117]
Description: nascent polypeptide-associated complex protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00026   20.9   0.0     0.0005   20.0   0.0    1.5  1  NAC       NAC domain
     0.0058   16.7   0.1      0.015   15.3   0.1    1.7  2  HOIP-UBA  HOIP UBA domain pair
  ------ inclusion threshold ------
      0.032   14.1   0.0      0.047   13.5   0.0    1.3  1  UBA_4     UBA-like 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 !   20.0   0.0   8.3e-08    0.0005       1      53 [.       6      62 ..       6      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.3e-08
                            NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsn.tyvvfGe 53
                                   +++l k++++lg+  +++  ++e+ i    g+ +vf  P V   +++g+  + + +G+
  gi|118430928|ref|NP_147039.2|  6 PRDLEKMMRRLGIkvEQL-SADEARIVLGSGETMVFRSPTVIvmRAKGQPpMVYLVGD 62
                                   689***********8888.7*********************98888888655555565 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.32   1.9e+03      69      82 ..      19      32 ..      10      40 .. 0.79
   2 !   15.3   0.1   2.4e-06     0.015      68      93 ..      85     110 ..      46     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.32
                       HOIP-UBA 69 evgklsraEakeal 82
                                   +v +ls+ Ea+ +l
  gi|118430928|ref|NP_147039.2| 19 KVEQLSADEARIVL 32
                                   56789999999776 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-06
                       HOIP-UBA  68 nevgklsraEakealleagGdvekAv 93 
                                    +e   +s +Ea++al e+gGd+ +A+
  gi|118430928|ref|NP_147039.2|  85 AEQAGVSMEEARKALEESGGDIAEAI 110
                                    6667799****************997 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.9e-06     0.047      11      33 ..      88     110 ..      78     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-06
                          UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                    +G++ e+Ar+ Le +++d+  Ai
  gi|118430928|ref|NP_147039.2|  88 AGVSMEEARKALEESGGDIAEAI 110
                                    6999***************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 963.86
//
Query:       gi|118430929|ref|NP_147040.2|  [L=406]
Description: hypothetical protein APE_0199.1 [Aeropyrum pernix K1]
Scores for 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-07   29.5  11.8    7.4e-07   29.5  11.8    2.5  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
  ------ inclusion threshold ------
        3.8    7.0  17.6        3.3    7.2  10.5    3.6  2  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 !   29.5  11.8   8.3e-11   7.4e-07       2     148 ..      87     232 ..      86     247 .. 0.78
   2 ?    2.0   3.4     0.024   2.1e+02      71     131 ..     299     359 ..     285     380 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8.3e-11
                          PMT_2   2 hPPliawllalftklfgfselairlvsalagvltillly....llarrlfgkraallaalllavvplfvalsalftpdap 77 
                                    hPPl  +++al++ l g+  l  rl+s++ + l  ++l+    l  r ++g++a+++aal +a  p++ +++    +d+ 
  gi|118430929|ref|NP_147040.2|  87 HPPLGKYIIALSMLLCGDRPLCWRLPSVVEAGLIPVILWaglaLAYRGVLGPVAGAAAALAAASDPVLRVMGSVAMLDIH 166
                                    9***************************9999888888833324568899****************99999999999*** PP

                          PMT_2  78 lvllwalalylllraleknklkywllagvlfGlgflsKytaalllia.allyllisarrilkekkpyl.alll 148
                                    + +++ala+     al  n+   ++ a  ++Gl+  +K+  + +++a a++++ + +++i++   ++  +ll+
  gi|118430929|ref|NP_147040.2| 167 QAFFTALAI-----ALAANR--RFIPAISAAGLAASVKMSGGAIVLAtATVAASWAQGSIWRRLAVFTaGLLI 232
                                    *****9987.....555565..6899**************999999845557777733344443333323332 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.024
                          PMT_2  71 lftpdaplvllwalalylllraleknklkywllagvlfGlgflsKytaallliaallylli 131
                                      ++ +  ++l  +a+ ll+++le++    w  ++ +  l +l+ yta++l+   +ly ++
  gi|118430929|ref|NP_147040.2| 299 VTNTVVHATALGFAAIALLAELLERRGRPSWPGVAHVYMLFILILYTAVYLAGNRTLYSFY 359
                                    3444566777888888888899996665699999999999999999999999877776555 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.5   0.00037       3.3      38     190 ..      80     205 ..      60     256 .. 0.77
   2 ?   -3.0   0.3       0.5   4.4e+03     184     208 ..     330     354 ..     329     366 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00037
                            PMT  38 hsffmdvhpplgkmllalggyLagkdgnftfesigaeyypenvpyvslRlfsallgslivplvyltllelgfskltalla 117
                                    + ++  +hpplgk+ +al++ L+g  +  +   +          +v + l + +l+++++ l+y ++l        ++ a
  gi|118430929|ref|NP_147040.2|  80 EDYYNAEHPPLGKYIIALSMLLCGDRPLCWRLPS----------VVEAGLIPVILWAGLA-LAYRGVLGPVA----GAAA 144
                                    568999******************9999887666..........4556799******975.67777766554....6667 PP

                            PMT 118 allvllenslitlsryilldspLlfftllsmyclvkferkapfsrswwlwllltgvalglavsvKwvglftvl 190
                                    al  ++++ l +++  ++ld+  +fft+l++++                 ++ +  a gla svK+ g+ +vl
  gi|118430929|ref|NP_147040.2| 145 ALAAASDPVLRVMGSVAMLDIHQAFFTALAIALAANRR------------FIPAISAAGLAASVKMSGGAIVL 205
                                    777789************************99866553............55566666777777766665553 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.5
                            PMT 184 vglftvllvgllliwelwqllgdks 208
                                    +g+  v ++++l+++ +++l g+++
  gi|118430929|ref|NP_147040.2| 330 PGVAHVYMLFILILYTAVYLAGNRT 354
                                    5565566666666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3153.04
//
Query:       gi|14600524|ref|NP_147041.1|  [L=196]
Description: hypothetical protein APE_0200 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.7   0.4       0.45   10.7   0.1    2.2  2  DUF2795   Protein of unknown function (DUF2795)
       0.14   12.0   0.0       0.56   10.1   0.0    2.0  3  TusA      Sulfurtransferase TusA
       0.15   12.3   0.1       0.28   11.5   0.1    1.4  1  AbiEi_1   AbiEi antitoxin C-terminal domain


Domain annotation for each model (and alignments):
>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1     6e+03      15      32 ..      26      41 ..      23      42 .. 0.63
   2 ?   10.7   0.1   7.6e-05      0.45      12      33 ..      73      94 ..      72     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                       DUF2795 15 eyArrngApdevleaLea 32
                                  +yA   + p  v+e +++
  gi|14600524|ref|NP_147041.1| 26 RYAA--KLPASVVEDIRD 41
                                  5555..457778887776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.6e-05
                       DUF2795 12 eLveyArrngApdevleaLeaL 33
                                  +LveyA ++gA   ++e+L+aL
  gi|14600524|ref|NP_147041.1| 73 DLVEYAANTGALSMLVEILDAL 94
                                  9*******************99 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         1   6.3e+03      43      66 ..      39      52 ..      23      54 .. 0.49
   2 ?   -3.0   0.0       1.1   6.5e+03      41      51 ..      72      82 ..      60      89 .. 0.48
   3 ?   10.1   0.0   9.4e-05      0.56       9      68 ..     101     163 ..      99     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                                  HHHHHHHHTEEEEEEE-....GCC-EEE CS
                          TusA 43 iprfakklghelvevee....edgeyri 66
                                  i+              +     +++yr+
  gi|14600524|ref|NP_147041.1| 39 IR--------------DmlgrGEDKYRF 52
                                  22..............133334455555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                                  HHHHHHHHHHT CS
                          TusA 41 ediprfakklg 51
                                  +d+ ++a ++g
  gi|14600524|ref|NP_147041.1| 72 RDLVEYAANTG 82
                                  34444444444 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 9.4e-05
                                   STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-.....GCC-EEEEE CS
                          TusA   9 vCPePllklkkalekleegevlevladdpaatediprfakklghelvevee.....edgeyrivi 68 
                                    CPe    + +++e+l++ge+  +    + + e i r++   g+++++  +     ++g ++++i
  gi|14600524|ref|NP_147041.1| 101 ECPEVAEAAEREVERLKAGEEK-LGRREELSLERIYRMLSLAGYRVESK-DgslevDEGLIKLII 163
                                   6******************998.778888899*************6655.447776667777776 PP

>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.7e-05      0.28      92     120 ..      73     101 ..      71     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                       AbiEi_1  92 dlatrpsavggldnvlevLdelaeevkpe 120
                                   dl++++++ g l+ ++e+Ld+la+e ++e
  gi|14600524|ref|NP_147041.1|  73 DLVEYAANTGALSMLVEILDALAAEYRRE 101
                                   8************************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1463.58
//
Query:       gi|118430930|ref|NP_147042.2|  [L=368]
Description: hypothetical protein APE_0201.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00059   20.0   0.1     0.0015   18.7   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.085   13.0   0.0       0.13   12.4   0.0    1.3  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
       0.18   11.6   0.1       0.27   11.1   0.1    1.2  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.5e-07    0.0015       2      28 ..      11      38 ..      11      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.5e-07
                                   E--.SHHHHHHHHHHHCCTEEEEEE-SS CS
                  NAD_binding_8  2 vGa.GlsGlvaAylLakagfdvlllekr 28
                                   +G+ G+sG+++AylLa++gf+v+ ++ +
  gi|118430930|ref|NP_147042.2| 11 IGGlGVSGATLAYLLAREGFRVEAFDVA 38
                                   5666*********************976 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 ?   12.4   0.0   2.2e-05      0.13       5      64 ..      12      70 ..       8      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                                   E--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SS CS
                  NAD_binding_2  5 iGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvk 64
                                    GlGv G+ +a  l+++g++v ++++ +   +++  + +++    ee++++ + v+t+v+
  gi|118430930|ref|NP_147042.2| 12 GGLGVSGATLAYLLAREGFRVEAFDVARG-YRKACGDALTLKPFTEEIARATRSVVTLVT 70
                                   59***********************9865.555556667777777888888888888886 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 ?   11.1   0.1   4.6e-05      0.27       2      41 ..       9      48 ..       8      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalek 41
                                   v + G G+ Ga +a+++a++g++V  +d+++   +++ ++
  gi|118430930|ref|NP_147042.2|  9 VSIGGLGVSGATLAYLLAREGFRVEAFDVARGYRKACGDA 48
                                   677899***********************88776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2855.52
//
Query:       gi|118430931|ref|NP_147043.2|  [L=142]
Description: hypothetical protein APE_0202.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1087.22
//
Query:       gi|118430932|ref|NP_147044.2|  [L=264]
Description: hypothetical protein APE_0203.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0092   15.2   3.4     0.0092   15.2   3.4    2.8  3  Zip             ZIP Zinc transporter
  ------ inclusion threshold ------
        4.1    6.7  13.6       0.15   11.4   0.8    3.5  4  Form_Nir_trans  Formate/nitrite transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   1.2   0.00061       5.5     247     295 ..       9      53 ..       2      55 .. 0.76
   2 !   15.2   3.4     1e-06    0.0092     184     243 ..     111     173 ..     104     194 .. 0.79
   3 ?   -1.7   0.2      0.15   1.3e+03      76      96 ..     238     258 ..     180     261 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00061
                            Zip 247 llnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYval 295
                                    ll l+ ++t   G+l  i+     + +     +g+l+al++G++ Y al
  gi|118430932|ref|NP_147044.2|   9 LLGLVAGITVTFGALTYIV----VGRRLGRRGQGVLNALAGGVLAYLAL 53 
                                    5556666666666666666....677889999***************98 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1e-06
                            Zip 184 vraiilllglilHsfidGLAlG...vssssstgislfiAvllHelpeelglgaiLlkaglsrk 243
                                    ++++++  +l+lH++ +GLA++   +  ++s +i   +   +H+  e++ + a+L+ ++ +  
  gi|118430932|ref|NP_147044.2| 111 MVSLTVASALGLHNLGEGLAIAaslIEGKVSLAILFAVGFAIHNYTEGFPIAAPLAGEKKRTG 173
                                    5789999***************98555556666666667789*************98877654 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.15
                            Zip  76 plagllvllGflllllvekll 96 
                                    p+    ++lG+ l +++e+++
  gi|118430932|ref|NP_147044.2| 238 PSFWSSLFLGIALAYVTESII 258
                                    455555667777777777665 PP

>> Form_Nir_trans  Formate/nitrite transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8   1.6e-05      0.15      22      60 ..       8      46 ..       2      53 .. 0.82
   2 ?    0.1   0.1     0.048   4.3e+02      15      40 ..      64      89 ..      50     115 .. 0.69
   3 ?   -1.0   0.1       0.1   9.2e+02      49      67 ..     128     151 ..      93     156 .. 0.60
   4 ?    2.0   0.6     0.013   1.1e+02      18      69 ..     174     217 ..     161     254 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHHHHHHHHHHHCCCHCCTTCHHHHHHHHH CS
                 Form_Nir_trans 22 fllgilAGafigfgvllalvvaaalaesnpglakllggl 60
                                   +llg++AG+ ++fg+l ++vv+  l +  +g+ + l+g 
  gi|118430932|ref|NP_147044.2|  8 ILLGLVAGITVTFGALTYIVVGRRLGRRGQGVLNALAGG 46
                                   89**********************988866776666664 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.048
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Form_Nir_trans 15 klsldklfllgilAGafigfgvllal 40
                                   ++ +++  l ++lAG++++  +ll +
  gi|118430932|ref|NP_147044.2| 64 EQFATRETLDSFLAGLMVTSIALLGT 89
                                   44555667889999998876666654 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.1
                                    T.....TCHHHHHHHHHCCCHHHH CS
                 Form_Nir_trans  49 s.....npglakllgglvFpvGli 67 
                                          +   +k+ ++++F+vG+ 
  gi|118430932|ref|NP_147044.2| 128 GlaiaaSLIEGKVSLAILFAVGFA 151
                                    133433334456677777777775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCTTCHHHHHHHHHCCCHHHHHH CS
                 Form_Nir_trans  18 ldklfllgilAGafigfgvllalvvaaalaesnpglakllgglvFpvGlilv 69 
                                    l++++ l++lAG+ +  g++++ + ++      pg   l+++ +++v+   +
  gi|118430932|ref|NP_147044.2| 174 LRTIIGLSLLAGLPVVPGAMVYYLGSNL-----PG---LAIATLYTVAAASI 217
                                    5555566666666666666555544442.....11...22222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2004.72
//
Query:       gi|118430933|ref|NP_147045.2|  [L=220]
Description: RNA 2'-phosphotransferase-like protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.1e-24   84.8   0.0    9.1e-24   84.5   0.0    1.1  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family


Domain annotation for each model (and alignments):
>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.0   5.1e-28   9.1e-24       3     176 ..      36     197 ..      35     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 5.1e-28
                      PTS_2-RNA   3 evqlskaLsyiLRhgaekegLkiredGyvkvedlLelpklkslk...vtleeikevVesndKqRFelveleelliranqg 79 
                                    +v+lsk+L+ iLRh++ + g++++++G+++v++++e   l++     v++ +i  v  +++K R+el + e   ira  g
  gi|118430933|ref|NP_147045.2|  36 RVRLSKTLAGILRHHPGRYGVRLTREGWARVSEVVE--GLRKAGwswVEEWHIVGVALHDPKGRYELRNGE---IRARYG 110
                                    589*********************************..55555533577888999999********66555...****** PP

                      PTS_2-RNA  80 hsi.kkvesselllepiesaeelpevvvHgTylkawesilasggLkrmsrnhihlatglpgekevisgmrksae.vliyi 157
                                    hsi ++       +ep+    e p +++HgT+ +a++ i+ ++g+ r +r ++hl+++l+  ++v +g r+ +   ++ +
  gi|118430933|ref|NP_147045.2| 111 HSIpVN-------VEPLPG--EPPPILYHGTTEEALPLIM-ERGIMRGRRLKVHLTSSLE--DAVSTGRRHGNLvAVLLV 178
                                    **8332.......688844..44899**************.99**************986..679999999665166789 PP

                      PTS_2-RNA 158 dvekaladgikfyvsengv 176
                                    dve   + g+k+ + +  v
  gi|118430933|ref|NP_147045.2| 179 DVECLRRRGLKVERMSKTV 197
                                    ***9999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1623.45
//
Query:       gi|14600529|ref|NP_147046.1|  [L=129]
Description: hypothetical protein APE_0207 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-13   49.0   0.6    6.9e-13   48.5   0.6    1.2  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (


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 !   48.5   0.6   3.8e-17   6.9e-13       1      40 []      13      51 ..      13      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 3.8e-17
                 Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                  kkm++l+++G+ ML++tCp  g PL++ + +g+v+C++++
  gi|14600529|ref|NP_147046.1| 13 KKMAQLMMQGAVMLDKTCPADGLPLFKLK-TGDVVCPVHG 51
                                  89**************************7.79*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1018.80
//
Query:       gi|14600530|ref|NP_147047.1|  [L=295]
Description: hypothetical protein APE_0208 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2213.44
//
Query:       gi|118430934|ref|NP_147048.2|  [L=380]
Description: peptidase [Aeropyrum pernix K1]
Scores for 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-11   41.6  10.5    2.9e-10   39.9  10.5    1.8  1  Peptidase_M50  Peptidase family M50
    2.6e-09   36.8   0.1    5.2e-09   35.8   0.1    1.5  1  PDZ_6          PDZ domain
    3.1e-09   37.0   1.4    1.2e-08   35.1   0.0    2.2  2  PDZ_2          PDZ domain
    5.2e-05   23.5   0.0    0.00014   22.1   0.0    1.7  2  PDZ            PDZ domain
  ------ inclusion threshold ------
       0.03   14.3   0.5      0.069   13.1   0.1    1.8  2  Tricorn_PDZ    Tricorn protease PDZ domain
       0.04   13.9   0.0      0.082   12.9   0.0    1.4  1  PDZ_1          PDZ-like domain
       0.12   12.7   0.0       0.22   11.8   0.0    1.4  1  GRASP55_65     GRASP55/65 PDZ-like 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 !   39.9  10.5   1.1e-13   2.9e-10       2     220 ..     120     341 ..     119     366 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.1e-13
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflk 81 
                                    ++++lg+ vv HElGH++vA ++g++v++ +i                 + ++p  ++V++++e+            + k
  gi|118430934|ref|NP_147048.2| 120 VAVALGVGVVAHELGHAVVAVAEGIRVKNAGIAI---------------LLFIP-AAFVELDEEQ------------LMK 171
                                    689*****************************99...............99999.8*********............999 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX-EEECECTTTSCEE-SEEEC-........................XXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................xxxxxxxx RF
                  Peptidase_M50  82 kspwqrllivlAGplanfilailvfvvpkkskeseeekrgviGvspkp........................vkkeglle 137
                                    +++++rl ++ AG  an+++a+l +++  +    e ++ +++Gv+  +                        +     l+
  gi|118430934|ref|NP_147048.2| 172 ARLVSRLKVFSAGVTANILIALLTLLIAMTAPVAEPSGVKILGVEEGSpadaaglgpgmvivevngepvkslE----DLR 247
                                    ***********************99995333346777777777777776776666666666666666643331....222 PP

                                    XXXX..XXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                    xxxx..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx RF
                  Peptidase_M50 138 alke..gvektlkvvvltvkalgklitg.klslktlggpisiaqlaseaaeaglssflqllalisvnLgilN....LlPi 210
                                     + e  gv++  + v +tv++ ++     +l++ +  g  +i+  ++e  ++ l ++++ l+l+++ ++++N    LlP+
  gi|118430934|ref|NP_147048.2| 248 RIFEkiGVTDPASNVEFTVRVKKEGGELlDLKVVKEAGRSTIGVRVAEFYDSPLATIMNALFLLNLGVALVNaaplLLPL 327
                                    22110133444444444444333333333445556666666666667788888889999999999999999933333343 PP

                                    X....XXXXXXXXX CS
                                    x....xxxxxxxxx RF
                  Peptidase_M50 211 p....vLDGghllf 220
                                    p    + DGgh++ 
  gi|118430934|ref|NP_147048.2| 328 PgaaiMSDGGHVAV 341
                                    33322446666655 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1     2e-12   5.2e-09       4      43 ..     214     251 ..     211     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2e-12
                          PDZ_6   4 aVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr 43 
                                     V++gsPAd AGl +G +i++vNG+pv  +sl+d++++ +
  gi|118430934|ref|NP_147048.2| 214 GVEEGSPADAAGLGPGMVIVEVNGEPV--KSLEDLRRIFE 251
                                    799************************..*******9875 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4      0.39     1e+03       2      32 ..     123     151 ..     122     153 .. 0.83
   2 !   35.1   0.0   4.9e-12   1.2e-08      14      70 ..     208     267 ..     196     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.39
                                    ...XX------..-EEEEEE-TTSGGGGT.- CS
                          PDZ_2   2 ylGvsvsdeedtggvlvvsVkeggPaakagl 32 
                                    +lGv v+ +e   g  vv V eg   ++ag+
  gi|118430934|ref|NP_147048.2| 123 ALGVGVVAHEL--GHAVVAVAEGIRVKNAGI 151
                                    69********9..999999999877766666 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 4.9e-12
                                    .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHH...HHHHTS-TT-EEEEEEE CS
                          PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledli...slllkkkpGdtVkltvl 70 
                                    +gv +  V+eg+Pa++agl +g vi++v+g +vksledl+   +++  ++p ++V++tv 
  gi|118430934|ref|NP_147048.2| 208 SGVKILGVEEGSPADAAGLGPGMVIVEVNGEPVKSLEDLRrifEKIGVTDPASNVEFTVR 267
                                    79**************************************88888889999999999885 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.6e-08   0.00014      26      65 ..     208     247 ..     198     267 .. 0.88
   2 ?   -3.0   0.0       3.8   9.8e+03       4      18 ..     280     295 ..     277     301 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.6e-08
                                    SSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHH CS
                            PDZ  26 kgifvsevlpggaaeadglkvGDkIlsvNgvdvenvshee 65 
                                     g+ +  v++g++a+a+gl +G +I++vNg++v+++++++
  gi|118430934|ref|NP_147048.2| 208 SGVKILGVEEGSPADAAGLGPGMVIVEVNGEPVKSLEDLR 247
                                    5889999**************************9998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                                    EETS.TTSESSEEEEE CS
                            PDZ   4 leke.grgglGfslkg 18 
                                    + ke gr+ +G+++++
  gi|118430934|ref|NP_147048.2| 280 VVKEaGRSTIGVRVAE 295
                                    5556699999999987 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1         4     1e+04      42      60 ..     133     151 ..     126     158 .. 0.58
   2 ?   13.1   0.1   2.7e-05     0.069      28      67 ..     216     253 ..     212     277 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4
                                    TT-EEEEET.TEE-BTTB-H CS
                    Tricorn_PDZ  42 eGdlilavd.gepvskekgi 60 
                                     G++++av  g +v+ ++gi
  gi|118430934|ref|NP_147048.2| 133 LGHAVVAVAeGIRVK-NAGI 151
                                    577777775144443.4555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.7e-05
                                    S-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTT CS
                    Tricorn_PDZ  28 earSPLaepGvnvreGdlilavdgepvskekgiaelLvgk 67 
                                    e+ SP  + G+    G +i++v+gepv++ +++ ++++  
  gi|118430934|ref|NP_147048.2| 216 EEGSPADAAGLG--PGMVIVEVNGEPVKSLEDLRRIFEKI 253
                                    678999999999..8*****************99998653 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.082      27      75 ..     205     253 ..     199     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                          PDZ_1  27 aipvkgvyvseasgsfklsskekkgviitsinnqptpnLdefievvkki 75 
                                    a+p+++ ++   +gs++ + +   g++i ++n++p+++L+++ ++++ki
  gi|118430934|ref|NP_147048.2| 205 AEPSGVKILGVEEGSPADAAGLGPGMVIVEVNGEPVKSLEDLRRIFEKI 253
                                    56777778888899999999999**********************9998 PP

>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.6e-05      0.22      27      87 ..     193     251 ..     167     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.6e-05
                                    SSSEEEEEEE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHT CS
                     GRASP55_65  27 llGlslrlaslekaaeevwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselve 87 
                                    ll l + ++    a  + +++l v+egsPa+ agL p    i+ ++ + +k+ edl+++ e
  gi|118430934|ref|NP_147048.2| 193 LLTLLIAMTAPV-AEPSGVKILGVEEGSPADAAGLGPGM-VIVEVNGEPVKSLEDLRRIFE 251
                                    556666666666.778899****************9976.677888888887777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2900.94
//
Query:       gi|118430935|ref|NP_147049.2|  [L=278]
Description: hypothetical protein APE_0211.1 [Aeropyrum pernix K1]
Scores for 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   31.6   0.0    0.00011   21.7   0.0    2.1  2  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 !    7.8   0.0   9.6e-05       1.7      24      63 ..      15      55 ..       3      64 .. 0.86
   2 !   21.7   0.0   5.9e-09   0.00011     220     274 ..     186     239 ..     176     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 9.6e-05
                                   SEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSH CS
                           PfkB 24 elv.evktveksaGGagaNvAvalarlgadvafigavGdDn 63
                                   ++v  ++++++++GG ++    a+ +lg++++++g vG  +
  gi|118430935|ref|NP_147049.2| 15 DVVeIGGSIVRRPGGPALYAGYAAGKLGCRAYAVGPVGYTT 55
                                   455578999*****************************765 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 5.9e-09
                                    SSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHH CS
                           PfkB 220 aktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegks 274
                                    a+ +v t+G+ G  v + +g+l +p+ p++ v D+tGAGD f+  f+  l +g++
  gi|118430935|ref|NP_147049.2| 186 ANIIVYTRGEAGGEVLSPSGSLTIPP-PPKLVEDPTGAGDIFTMVFAIMLFRGAP 239
                                    6789**********************.99*************9999988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2144.59
//
Query:       gi|118430936|ref|NP_147050.2|  [L=402]
Description: peptidase [Aeropyrum pernix K1]
Scores for complete 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-20   73.8   0.0    2.3e-20   73.1   0.0    1.2  1  Peptidase_M16    Insulinase (Peptidase family M16)
    6.4e-20   71.9   0.0      1e-19   71.3   0.0    1.3  1  Peptidase_M16_C  Peptidase M16 inactive domain


Domain annotation for each model (and alignments):
>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   2.6e-24   2.3e-20      10     146 ..      22     158 ..      19     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 2.6e-24
                                    SSEEEEEEEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEEEEEEEGGGHHHHHH CS
                  Peptidase_M16  10 aktsavglvvdaGSryepkdlnGlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvYyvevlskdlekald 89 
                                    ++++a+ +    GS  ep+   G+AHl ehm+f g +  ++ +l++ +e  Gg+ nA+t+re +   +e+ s++l+ + +
  gi|118430936|ref|NP_147050.2|  22 SESAAICIAARGGSSFEPPGKYGIAHLTEHMIFRGNEYLQDGELDRAVELSGGEANAYTTRELILLCAEFVSDSLARVAE 101
                                    567889999999***********************888888*************************************** PP

                                    HHHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHTTTSGGGSHSS CS
                  Peptidase_M16  90 vladvfkaplleesevererkvvekeveavdaepekvveenlhaaayrekalgrsll 146
                                     l   + a +l e e+erer vve+ev+ + + pe ++ +  ha a+ + +lgr+++
  gi|118430936|ref|NP_147050.2| 102 KLFLAVSARRLVEGEFERERAVVEAEVKGLISSPESRIYRLAHASAWGDSHLGRPIE 158
                                    ******************************************************986 PP

>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   1.1e-23     1e-19       1     182 [.     166     341 ..     166     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.1e-23
                                    CH-HHHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSHCSGSCTSSSSSGGGSSEEEEEEEESSS.SSE CS
                Peptidase_M16_C   1 sltredlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaskappakptgepltpatlkkppvvlkklde.eqa 79 
                                    ++++ d+ e+  + ++pe+m laivG ++  e++++  k+f++l+        p g+ ++p+t+ +++ +l+++   e a
  gi|118430936|ref|NP_147050.2| 166 NISKADVEEYKASVFSPERMSLAIVGRISRLEALRV-VKLFSQLE--------PGGKVREPETPEPRTTFLREERGiEAA 236
                                    68999******************************9.9*******........456666777789999999999877999 PP

                                    EEEEEEEEECTCTHTTHHHHHHHHHHHHSS......TTSHHHHHHHTTTTSESEEEEEEEEES.SCEEEEEEEEEECTTH CS
                Peptidase_M16_C  80 hlslafegpskendeddlalavlntlLggg......mesrLytnlrekeglaysvsafndsyr.dsglfgisatadpenv 152
                                    +++l++++p++     +   +vl++l g        ++s L++++re++glay+++ ++++++ +s++  i + ++ ++v
  gi|118430936|ref|NP_147050.2| 237 YAALTLPLPPR-----SGLANVLARLRGVVfnleagATSILFKEVREERGLAYGFNVDVHITSwGSSMSLIVLEGNRDRV 311
                                    99999999999.....88888888888887888888******************************************** PP

                                    HHHHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
                Peptidase_M16_C 153 eevvevilkelrklkkeglteeeleraknq 182
                                     e+ +++ + l++  + g +e+e+ + ++ 
  gi|118430936|ref|NP_147050.2| 312 GELFDAMTRSLERALRGGYPESEWREGRRR 341
                                    ***********************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2941.20
//
Query:       gi|118430937|ref|NP_147051.2|  [L=230]
Description: hypothetical protein APE_0213.1 [Aeropyrum pernix K1]
Scores for complete 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   36.8   0.0    5.8e-09   36.1   0.0    1.4  1  NTP_transf_2  Nucleotidyltransferase domain
      2e-05   24.6   0.0    3.2e-05   23.9   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.024   14.4   0.0       0.31   10.8   0.0    2.4  2  HTH_8         Bacterial regulatory protein, Fis family
       0.08   12.5   4.0       0.14   11.7   0.6    2.6  2  Sigma70_r4    Sigma-70, region 4
       0.09   12.3   1.1       0.13   11.9   0.2    1.7  2  HTH_24        Winged helix-turn-helix DNA-binding


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 !   36.1   0.0   1.6e-12   5.8e-09       2      45 ..      18      64 ..      17     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.6e-12
                                   HHHHHHHHHHTT...TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCH CS
                   NTP_transf_2  2 kklleelkelep...vakvvlfGSyarGtalkgSDiDllvvlpeevs 45
                                   +k+le+++ l+    +  +v++GS+arG+ ++gSD+D+++v p +  
  gi|118430937|ref|NP_147051.2| 18 RKALEIVRALSRtvhPGLAVVHGSVARGDVHPGSDVDVAIVEPVPPG 64
                                   789999999999999****************************9965 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     9e-09   3.2e-05       5      38 ..      25      58 ..      22      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9e-09
                                   TTHHHHHHHHSTTEEEEEE-S------EEEEEEE CS
                        Polbeta  5 eilekekeielaylFGSrakgkareeSDiDlavl 38
                                     l++  +  la+++GS+a+g+ ++ SD+D+a++
  gi|118430937|ref|NP_147051.2| 25 RALSRTVHPGLAVVHGSVARGDVHPGSDVDVAIV 58
                                   55666667889*********************97 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 ?    0.5   0.0      0.15   5.4e+02       9      20 ..      65      76 ..      64      79 .. 0.83
   2 ?   10.8   0.0   8.7e-05      0.31      19      39 ..     161     181 ..     160     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.15
                                   HHHHHHHHTTT- CS
                          HTH_8  9 lIeaALertgGn 20
                                   l e+ALe++g+ 
  gi|118430937|ref|NP_147051.2| 65 LVEEALEASGFT 76
                                   5699*****986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.7e-05
                                    T-HHHHHHHHTS-HHHHHHHH CS
                          HTH_8  19 GnkskAArlLGisRrtLyrKL 39 
                                    Gn  ++A+ LGis  t++ + 
  gi|118430937|ref|NP_147051.2| 161 GNEGRVAEVLGISLETVRERV 181
                                    78889************9985 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2     0.098   3.5e+02       2      11 ..     109     118 ..     109     119 .. 0.92
   2 ?   11.7   0.6   3.9e-05      0.14      26      42 ..     166     182 ..     164     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.098
                                    HHHS-HHHHH CS
                     Sigma70_r4   2 LasLperere 11 
                                    La+L +rere
  gi|118430937|ref|NP_147051.2| 109 LARLQPRERE 118
                                    899******7 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.9e-05
                                    HHHHHTS-HHHHHHHHH CS
                     Sigma70_r4  26 IgerlgiSrerVrqiek 42 
                                    ++e+lgiS+e+Vr + +
  gi|118430937|ref|NP_147051.2| 166 VAEVLGISLETVRERVR 182
                                    8************9875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.5   5.3e+03       3      13 ..      15      25 ..      13      30 .. 0.66
   2 ?   11.9   0.2   3.5e-05      0.13      23      43 ..     166     186 ..     164     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                         HTH_24  3 etdrkILelLq 13
                                   e++rk Le+++
  gi|118430937|ref|NP_147051.2| 15 EKRRKALEIVR 25
                                   66777777765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.5e-05
                         HTH_24  23 LAerlglSpstvnrrlkrLee 43 
                                    +Ae lg+S+ tv++r++ L++
  gi|118430937|ref|NP_147051.2| 166 VAEVLGISLETVRERVRVLTR 186
                                    79***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1709.24
//
Query:       gi|118430938|ref|NP_147052.2|  [L=196]
Description: hypothetical protein APE_0214.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1462.77
//
Query:       gi|118430939|ref|NP_147054.2|  [L=189]
Description: methyltransferase [Aeropyrum pernix K1]
Scores for complete 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   54.7   0.0    2.7e-14   53.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      2e-13   50.9   0.0    3.7e-13   50.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.2e-09   38.2   0.0    1.5e-09   37.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.3e-07   30.7   0.0    3.2e-07   30.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    3.6e-07   30.9   0.0    5.9e-07   30.2   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.9e-05   24.1   0.0    2.4e-05   23.8   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0011   18.6   0.0      0.002   17.8   0.0    1.6  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
       0.15   11.0   0.0       0.18   10.7   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.19   11.3   0.0       0.32   10.5   0.0    1.4  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 !   53.6   0.0   1.4e-17   2.7e-14       1      88 [.      50     144 ..      50     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.4e-17
                                    EEET-TTSHHHHHHHHTT.....SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.....arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                    Ld+GcGtG+l+e++a++g        +++D+s+ ml +a+ ++       ++  +++++eklpf ++ fD v+s+ vl+ 
  gi|118430939|ref|NP_147054.2|  50 LDAGCGTGLLLEYMASYGsldavDLFTCLDYSPCMLSIARFRIGVLCGngSCIALEGNVEKLPFGSGVFDTVYSFTVLDL 129
                                    8**************88888888999*************988876544576666************************** PP

                                    -CCHHHHHHHHHHHE CS
                Methyltransf_11  74 vedpekalkeiaRvL 88 
                                    v+d+ +a+ke+ Rv 
  gi|118430939|ref|NP_147054.2| 130 VDDLWRAVKELIRVS 144
                                    *************95 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.9e-16   3.7e-13       1      93 [.      49     144 ..      49     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.9e-16
                                    EEEET-TTSHHHHHHHCTS..T.SSEEEEEESSHHHHHHHHHHHHHTTT.....TEEEEESBCCGBSSSTTTEEEEEEES CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl..g.kakvtgvDiseemleaareraeeegl.....nvefvqgdaedlpfedgsfDlvvssg 72 
                                    vLd+GcGtG l++++a  +       +t++D+s+ ml +ar r+    +     ++  ++g++e+lpf +g fD v+s+ 
  gi|118430939|ref|NP_147054.2|  49 VLDAGCGTGLLLEYMASYGslDaVDLFTCLDYSPCMLSIARFRIG---VlcgngSCIALEGNVEKLPFGSGVFDTVYSFT 125
                                    9***************99755247888****************95...4445569999********************87 PP

                                    TGGGSSHHHHHHHHHHHHHHE CS
                Methyltransf_25  73 alhhlsdedlekalkeiarvL 93 
                                    +l +++  dl +a+ke+ rv 
  gi|118430939|ref|NP_147054.2| 126 VLDLVD--DLWRAVKELIRVS 144
                                    7**987..8999*****9985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   7.5e-13   1.5e-09       7     108 ..      31     143 ..      24     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.5e-13
                Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengf.....svtgvDlspeaveiae........kakkaqkdqfde 73 
                                    e++ ++   +l++ r++grvLd GcGtG lle+++ +g       +t  D sp + +ia+        + ++   +    
  gi|118430939|ref|NP_147054.2|  31 EQYEKFFV-ALKRVRPQGRVLDAGCGTGLLLEYMASYGSldavdLFTCLDYSPCMLSIARfrigvlcgNGSCIALEGN-V 108
                                    44444444.3356799******************99996665644779***************999995566555555.6 PP

                Methyltransf_23  74 qeaaepqgkfdlIvlrevlehvpdppellrqiatl 108
                                    ++ ++ +g fd+++++ vl  v+d+ ++++ + + 
  gi|118430939|ref|NP_147054.2| 109 EKLPFGSGVFDTVYSFTVLDLVDDLWRAVKELIRV 143
                                    78889*******************99998888774 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.6e-10   3.2e-07       5     102 ..      47     145 ..      44     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.6e-10
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgp.kae..vvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80 
                                     rvlD+GCGtG l+  +a+  g+ +a   ++ +D+s+ +++ Ar +   l  +  +   +g++e+l+  +    fD + s
  gi|118430939|ref|NP_147054.2|  47 GRVLDAGCGTGLLLEYMASY-GSlDAVdlFTCLDYSPCMLSIARFRIGVLCGNgSCIALEGNVEKLP--FGSGVFDTVYS 123
                                    58****************73.33355468****************988876655899999*******..*********** PP

                Methyltransf_31  81 nevlnaladpdkileeiervlk 102
                                    + vl+++ d+  + +e++rv +
  gi|118430939|ref|NP_147054.2| 124 FTVLDLVDDLWRAVKELIRVSR 145
                                    ****************999977 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.9e-10   5.9e-07       1      91 [.      50     142 ..      50     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.9e-10
                Methyltransf_12   1 LeiGcGtGsllrallekl...pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                    L+ GcGtG ll++++ +        +t++D+sp ++  a+ ++   ++ n +++ le +     +g++ fD+v+++ vl 
  gi|118430939|ref|NP_147054.2|  50 LDAGCGTGLLLEYMASYGsldAVDLFTCLDYSPCMLSIARFRIGVLCG-NGSCIALEGNVEKLPFGSGVFDTVYSFTVLD 128
                                    89***************9995555577********************7.6688888876655555559************ PP

                Methyltransf_12  78 hlkdirevldnirk 91 
                                     ++d+ ++++++ +
  gi|118430939|ref|NP_147054.2| 129 LVDDLWRAVKELIR 142
                                    ****9999987755 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.2e-08   2.4e-05      35     144 ..      33     145 ..      15     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                                    HHHHHHHH--S--TTEEEEES-TT-HHHHHHHH..HHHHHHEEEEEES-HHHHHHHHHHHHHH.TSSTEEEEE--TTT-T CS
                Ubie_methyltran  35 WkkfveklvavkrgakvlDvagGtgDlafklsd..svgekgkvvvlDinenmLkvgekklkee.gkinieflqanaeeLp 111
                                    + kf   l+ v++  +vlD  +Gtg l   +++  s+++    + lD+++ mL++++ ++    g  +   l +n e+Lp
  gi|118430939|ref|NP_147054.2|  33 YEKFFVALKRVRPQGRVLDAGCGTGLLLEYMASygSLDAVDLFTCLDYSPCMLSIARFRIGVLcGNGSCIALEGNVEKLP 112
                                    567778888899999**********775555431133444466789*************986515558999********* PP

                                    TS-T-EEEEEEES-GGG.-S-HHHHHHHHHHHEE CS
                Ubie_methyltran 112 feddsfDvvtvsfGlrn.vtDklkaLkeayrvlk 144
                                    f  + fD+v  sf + + v D  +a+ke+ rv +
  gi|118430939|ref|NP_147054.2| 113 FGSGVFDTVY-SFTVLDlVDDLWRAVKELIRVSR 145
                                    *******985.7776651667889*******965 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.8e-07     0.002       5      39 ..      37      71 ..      33     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.8e-07
                           MetW  5 eliaelikpgsrvldlGcGdGellellkeekqvdg 39
                                    + ++ ++p+ rvld GcG G lle+++    +d+
  gi|118430939|ref|NP_147054.2| 37 FVALKRVRPQGRVLDAGCGTGLLLEYMASYGSLDA 71
                                   5567889******************9987666665 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 ?   10.7   0.0   9.1e-05      0.18     118     192 ..      48     127 ..      29     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.1e-05
                                    EEEEET-TTSHHHHHHHHCT-SEEEEE......---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES CS
                 Methyltransf_9 118 tildvGcgnGyhlwrmvgegaklvvGi......dPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmG 190
                                    ++ld Gcg+G  l  m++ g+  +v +       P  l +  f+ +  l   +   + l   +e+lp     fdtv+s  
  gi|118430939|ref|NP_147054.2|  48 RVLDAGCGTGLLLEYMASYGSLDAVDLftcldySPCMLSIARFR-IGVLC-GNGSCIALEGNVEKLPFgSGVFDTVYSFT 125
                                    69***********9999988876665411111145556666665.34445.5567788999******97889*******9 PP

                                    -G CS
                 Methyltransf_9 191 vl 192
                                    vl
  gi|118430939|ref|NP_147054.2| 126 VL 127
                                    98 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.32      30      52 ..      44      66 ..      34      92 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                                   CTCSEEEEET-TTSHHHHHHHHH CS
                            MTS 30 elsgkvlDlGcGaGvlgaalake 52
                                   + +g+vlD GcG+G+l   +a+ 
  gi|118430939|ref|NP_147054.2| 44 RPQGRVLDAGCGTGLLLEYMASY 66
                                   37899**********98777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1473.43
//
Query:       gi|14600538|ref|NP_147055.1|  [L=238]
Description: 50S ribosomal protein L2 [Aeropyrum pernix K1]
Scores for complete 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  150.5   0.6    3.6e-44  150.0   0.6    1.2  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    4.7e-17   61.7   0.0    9.9e-17   60.7   0.0    1.6  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 !  150.0   0.6   4.1e-48   3.6e-44       2     121 ..      90     214 ..      89     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 4.1e-48
                                   SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT---- CS
                Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekklg 82 
                                    Gn+lpl++ipeGt v+n+el+pg+ggklar aG+ya vv++ g k++++lpSg+ ++v++++rAtiG+ +++++ ek+++
  gi|14600538|ref|NP_147055.1|  90 AGNILPLGKIPEGTEVFNVELRPGDGGKLARQAGSYALVVGRAGAKTILRLPSGKDKEVPNDSRATIGIPAGAGRIEKPIM 170
                                   6*****************************************9************************************** PP

                                   STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--SSSST CS
                Ribosomal_L2_C  83 kAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktksrkap 121
                                   kAg ++++     +++p+vrGvamn+vdHp+GGG+ ++k+r + 
  gi|14600538|ref|NP_147055.1| 171 KAGFAYHKwkvkaRKWPRVRGVAMNAVDHPFGGGRHQHKGRPST 214
                                   *******999*************************555555332 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 !   60.7   0.0   1.1e-20   9.9e-17       1      76 [.      11      81 ..      11      82 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.1e-20
                                  TB-TT.--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                  Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                  Gr+++ +r++++ + g   +ky+ ++     ++++gkVve+++DpgR  p+A+v+ edg ++++ a+eg+ vG++++
  gi|14600538|ref|NP_147055.1| 11 GRGTPtYRSRAHIHPG--PAKYPPLSG----DTLRGKVVELIHDPGRYVPLARVVREDGVEFLMPAAEGMYVGQIIE 81
                                  9***************..*********....89******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1855.33
//
Query:       gi|14600539|ref|NP_147056.1|  [L=461]
Description: hypothetical protein APE_0219 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-06   26.3   0.0      0.041   12.8   0.0    2.1  2  AAA_10           AAA-like domain
    7.2e-06   24.9   0.0     0.0077   14.9   0.0    2.4  2  DUF853           Bacterial protein of unknown function (DUF85
    8.5e-06   26.1   0.0    1.8e-05   25.0   0.0    1.5  1  AAA_22           AAA domain
    2.4e-05   23.8   0.0     0.0014   18.1   0.0    2.2  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
    2.4e-05   24.5   0.0    3.7e-05   23.9   0.0    1.3  1  DUF87            Helicase HerA, central domain
    0.00032   19.8   0.0     0.0045   16.0   0.0    2.0  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0026   17.4   0.2      0.037   13.6   0.0    2.3  2  AAA_25           AAA domain
     0.0057   16.7   0.0      0.034   14.1   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.011   16.2   1.1      0.059   13.8   0.2    2.3  2  AAA_16           AAA ATPase domain
      0.049   13.5   0.1        0.1   12.5   0.1    1.5  1  NACHT            NACHT domain
      0.059   13.4   0.0      0.099   12.6   0.0    1.4  1  TraG-D_C         TraM recognition site of TraD and TraG
      0.069   11.9   0.0      0.098   11.4   0.0    1.1  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
       0.18   11.6   0.1       0.53   10.0   0.1    1.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.19   10.8   0.0        0.3   10.1   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
       0.25   10.8   0.0       0.43   10.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.4e-05     0.041      21      64 ..     230     279 ..     222     291 .. 0.84
   2 !   11.2   0.0    0.0001      0.12     243     302 ..     347     402 ..     329     416 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                        AAA_10  21 asasliiGdlGnGKSvlakllvlyisllg......gkaliiDpkkerekf 64 
                                     ++l++G++G GK vl   l ++++ll         ++++Dpk +  + 
  gi|14600539|ref|NP_147056.1| 230 EAHMLVVGPTGRGKTVLLAGLAVQLALLSevegdpLGVVVVDPKGDLAEL 279
                                   6799**************99999999999888888789******986655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0001
                        AAA_10 243 vvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglklaFr 302
                                   v i+DEaw +  s       + + R GRs     +++tqs+ D+ +e ++ n g++ aF 
  gi|14600539|ref|NP_147056.1| 347 VLIVDEAWRLSRST---SFFEGIAREGRSRGLYGVFATQSPGDL-PEAIEFNAGVVAAFG 402
                                   6899******9985...799***********************7.677888888888875 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 !   14.9   0.0   6.4e-06    0.0077      20      66 ..     229     281 ..     213     291 .. 0.77
   2 !    7.5   0.0    0.0011       1.4     259     309 ..     346     391 ..     341     434 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.4e-06
                        DUF853  20 anrhGliaGatGtGktvtLqvlaesl...se.aG..vpvfladvkGdLsgiak 66 
                                      h l+ G tG Gktv L  la +l   se  G    v+++d kGdL+ + +
  gi|14600539|ref|NP_147056.1| 229 LEAHMLVVGPTGRGKTVLLAGLAVQLallSEvEGdpLGVVVVDPKGDLAELLE 281
                                   5679*******************99722244234225699********98865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0011
                        DUF853 259 lvfffdeahLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtv 309
                                   lv+  dea  L   ++  +    e + r  rs+G    f tq+P dlP+++
  gi|14600539|ref|NP_147056.1| 346 LVLIVDEAWRLSRSTS--F---FEGIAREGRSRGLYGVFATQSPGDLPEAI 391
                                   6666677766655443..3...47788999****98789*********987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.5e-08   1.8e-05       6     105 ..     231     359 ..     227     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-08
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka............... 70 
                                    +++v+G++G GKT+ll+ l+ ql   +   e e++++  v +  ++++++ll+ l  +l +++++               
  gi|14600539|ref|NP_147056.1| 231 AHMLVVGPTGRGKTVLLAGLAVQLALLS---EvEGDPLGVVVVDPKGDLAELLEPLTTFLLEPRDTgqlpvpgatippvsp 308
                                   689*********************5444...455666666666667778******************************** PP

                        AAA_22  71 .........erlsseellealeqalrarav......ielliiDEaqhlr.s 105
                                            e+ ++ +  +a++  l ++a       + +li+DEa +l+ s
  gi|14600539|ref|NP_147056.1| 309 ltvyslrrlEGSDRNAAAQAVASSLVEYALspggrgRLVLIVDEAWRLSrS 359
                                   ****9999855555555566666666666677778**********999543 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0014      38      68 ..     229     259 ..     205     287 .. 0.73
   2 ?    3.5   0.0     0.033        39     220     242 ..     363     385 ..     348     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                   S-.SEEEE--TTSSHHHHHHHHHHHHHTT-- CS
                  FtsK_SpoIIIE  38 mashllvaGatgsGKStalntLilSlattht 68 
                                    ++h+lv+G tg+GK++ l  L + la+ ++
  gi|14600539|ref|NP_147056.1| 229 LEAHMLVVGPTGRGKTVLLAGLAVQLALLSE 259
                                   348*******************998887654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.033
                                   HHHHHHHCGGGTEEEEEEES--- CS
                  FtsK_SpoIIIE 220 ivRlarkgraaglHlllatqrls 242
                                   +  +ar gr+ gl+ ++atq+++
  gi|14600539|ref|NP_147056.1| 363 FEGIAREGRSRGLYGVFATQSPG 385
                                   5568999*************997 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   3.1e-08   3.7e-05       9      68 ..     216     280 ..     207     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.1e-08
                         DUF87   9 gsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.....kkgatililDpHGEYgkal 68 
                                   +++ pv l+  + ++ H++++g TG GK+ + a L  +l+       + + ++++Dp G+ + +l
  gi|14600539|ref|NP_147056.1| 216 ETGGPVALRWPRDLEAHMLVVGPTGRGKTVLLAGLAVQLALlseveGDPLGVVVVDPKGDLAELL 280
                                   56779******************************999998887777777*********988777 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   3.7e-06    0.0045      13      72 ..     228     292 ..     217     294 .. 0.73
   2 ?    1.4   0.0       0.1   1.2e+02     237     285 ..     338     387 ..     320     390 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                 TrwB_AAD_bind  13 retqhilivGttGsGKtqalek......llrairargdraivlDltGafvsrfydegkdillnPlD 72 
                                   + ++h+l+vG tG GKt+ l +      ll +++     ++v+D++G++ +   ++ +  ll+P D
  gi|14600539|ref|NP_147056.1| 228 DLEAHMLVVGPTGRGKTVLLAGlavqlaLLSEVEGDPLGVVVVDPKGDLAE-LLEPLTTFLLEPRD 292
                                   3478**************997611111267777777799*********976.55666688888877 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                 TrwB_AAD_bind 237 lpesrerrlWfflDElpaLgrleel.ksllaegRkfGgavvlglqsiaql 285
                                   l++  + rl +++DE   L r  ++ + ++ egR+ G   v + qs   l
  gi|14600539|ref|NP_147056.1| 338 LSPGGRGRLVLIVDEAWRLSRSTSFfEGIAREGRSRGLYGVFATQSPGDL 387
                                   77778889************987651566779*********999997665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.18   2.2e+02      56      95 ..     132     166 ..     120     196 .. 0.77
   2 !   13.6   0.0   3.1e-05     0.037      35      86 ..     232     279 ..     224     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                        AAA_25  56 avatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravge 95 
                                   avatG+p lg    + g+V+++  E++ d  +  ++ ++e
  gi|14600539|ref|NP_147056.1| 132 AVATGSPRLG----RLGAVVWIE-EGADDSKAIQFKSMLE 166
                                   799*******....78*****98.8877777777776664 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.1e-05
                        AAA_25  35 lallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedel 86 
                                     l++G++g GKt+l+  la+ +a+ +++ g     +  V++v+  ++ +el
  gi|14600539|ref|NP_147056.1| 232 HMLVVGPTGRGKTVLLAGLAVQLALLSEVEG----DPLGVVVVDPKGDLAEL 279
                                   5789********************7665655....78899999877776665 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 !   14.1   0.0   2.8e-05     0.034      24     147 ..     230     359 ..     208     373 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                                   TSEEEEEESTTSTHHHHHHHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG....GEEE.ESSS-B--... CS
                        ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkee....kflflvprkslleqtleefkkflseaykeigkk.vsgdkkkakek 99 
                                   + ++l++ +TG GKT+++a l+ +l+   + e     ++++ p+ +l e +le ++ fl e+++ +g+  v g +  +   
  gi|14600539|ref|NP_147056.1| 230 EAHMLVVGPTGRGKTVLLAGLAVQLALLSEVEgdplGVVVVDPKGDLAE-LLEPLTTFLLEPRD-TGQLpVPGATIPP--- 305
                                   67999****************9999998777788977777777777766.66667777777664.3333144444444... PP

                                   ....-SEEEEEHHHHHHTH.................HHHTTT-SEEEEETGGGTTS. CS
                        ResIII 100 dstnkkilvttiqsldadseee.........eeeseellrdrfdviiiDEaHrlgak 147
                                       + ++v +  +l  + +++          e+  + +    +v+i+DEa rl+++
  gi|14600539|ref|NP_147056.1| 306 ---VSPLTVYSLRRLEGSDRNAaaqavasslVEYALSPGGRGRLVLIVDEAWRLSRS 359
                                   ...666777777777766666566666665555566666666668888888777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.69   8.2e+02      37      66 ..      92     121 ..      91     198 .. 0.63
   2 ?   13.8   0.2   4.9e-05     0.059      26     161 ..     232     369 ..     222     378 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.69
                        AAA_16  37 Ksslvrellralekdggiflrgkcdqlesa 66 
                                   Ks+lv++l +++++ ++ + +++  +++sa
  gi|14600539|ref|NP_147056.1|  92 KSRLVETLEEEIKRVEFKYSTTRLGRYRSA 121
                                   788888888777776555555555555333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.9e-05
                        AAA_16  26 lvllsGesGvGKsslvrellr..alekd......ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                    +l++G+ G GK+ l+  l+   al  +      g++++  k d            ++l +  l + ll++ ++ +l+   
  gi|14600539|ref|NP_147056.1| 232 HMLVVGPTGRGKTVLLAGLAVqlALLSEvegdplGVVVVDPKGDLA----------ELL-E-PLTTFLLEPRDTGQLPVPG 300
                                   79**************766651233333444344444444444444..........556.3.5556666665555566666 PP

                        AAA_16  99 ekleeala....avpelagaeasrllellkrll.allsrderp..lvlvlDdlqwadeaslqllaaLlrl 161
                                   ++++ +      + + l+g+++++ ++++++ l +++ +++    lvl++D++ ++   s ++++ ++r+
  gi|14600539|ref|NP_147056.1| 301 ATIPPVSPltvySLRRLEGSDRNAAAQAVASSLvEYALSPGGRgrLVLIVDEAWRLS-RSTSFFEGIARE 369
                                   655555559999999999999988888888888755544444336******984443.466666665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.6e-05       0.1       3      25 ..     233     255 ..     231     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.6e-05
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                   +++ G+ G GKT+Ll++la+++a
  gi|14600539|ref|NP_147056.1| 233 MLVVGPTGRGKTVLLAGLAVQLA 255
                                   789****************9987 PP

>> TraG-D_C  TraM recognition site of TraD and TraG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.3e-05     0.099       1      44 [.     345     389 ..     345     415 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                      TraG-D_C   1 pvlfllDEfanlgki.pdleellstgrsrgislvlilQsiaqlee 44 
                                   ++++++DE+ +l +    +e +  +grsrg+  v+++Qs  +l e
  gi|14600539|ref|NP_147056.1| 345 RLVLIVDEAWRLSRStSFFEGIAREGRSRGLYGVFATQSPGDLPE 389
                                   6899**********9788999999***************999876 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-05     0.098      45      85 ..     231     279 ..     184     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
               T4SS-DNA_transf  45 ehvlvvAptrsgKgv...gvviPnll.kwkq....siVvlDpkgElael 85 
                                   +h+lvv+pt+ gK+v   g+ +  +l ++ +     +Vv+Dpkg+lael
  gi|14600539|ref|NP_147056.1| 231 AHMLVVGPTGRGKTVllaGLAVQLALlSEVEgdplGVVVVDPKGDLAEL 279
                                   8*************7666777775552432223568**********997 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00044      0.53      34      83 ..     231     284 ..     222     288 .. 0.82
   2 ?   -2.6   0.0       3.3     4e+03      87      99 ..     347     359 ..     343     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgP....vlekagdlaalltnle 83 
                                    h+l++Gp G Gkt l + +a +l    ++   P    v++ +gdla ll  l+
  gi|14600539|ref|NP_147056.1| 231 AHMLVVGPTGRGKTVLLAGLAVQLALLSEVEGDPlgvvVVDPKGDLAELLEPLT 284
                                   6**************999999999887777777644446899999999998775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.3
                        RuvB_N  87 vlfideihrlsra 99 
                                   vl +de  rlsr+
  gi|14600539|ref|NP_147056.1| 347 VLIVDEAWRLSRS 359
                                   899*******986 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 ?   10.1   0.0   0.00025       0.3     129     148 ..     230     249 ..     219     270 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                         T2SSE 129 rglilvsGgTgsGKttllya 148
                                   +  +lv G+Tg GKt+ll  
  gi|14600539|ref|NP_147056.1| 230 EAHMLVVGPTGRGKTVLLAG 249
                                   5679*************954 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00036      0.43      33      54 ..     230     251 ..     227     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00036
                         AAA_7  33 kkpvllvGptGtGKtviikdll 54 
                                   + ++l+vGptG GKtv++  l 
  gi|14600539|ref|NP_147056.1| 230 EAHMLVVGPTGRGKTVLLAGLA 251
                                   5799************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3251.82
//
Query:       gi|14600540|ref|NP_147057.1|  [L=452]
Description: hypothetical protein APE_0220 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.4    8.0   5.4        0.5   10.1   0.2    2.2  2  SPC25     Microsomal signal peptidase 25 kDa subunit (SPC25)


Domain annotation for each model (and alignments):
>> 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 ?   -0.9   1.0     0.069   1.2e+03      32      65 ..      51      86 ..      46     100 .. 0.79
   2 ?   10.1   0.2   2.8e-05       0.5      28      81 ..     135     186 ..     129     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.069
                         SPC25 32 lGylavaiaavaflydykv..eFeeskpvlaiavvl 65
                                  l ++a a+ ava +++ +   ++++   +l+ avv+
  gi|14600540|ref|NP_147057.1| 51 LALTAAALIAVAGYLQLLIggSWPQLDAWLFDAVVF 86
                                  7788889999999999988999***99999988886 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 2.8e-05
                         SPC25  28 vrLalGylavaiaavaflydykveFeeskpvlaiavvlYfilsgiltlystfve 81 
                                   ++ +lGy+ ++++++++ly    +F   kp+ a+++++ ++++++l +   fve
  gi|14600540|ref|NP_147057.1| 135 LKYLLGYSQILLSLGVLLYAV--PFRVAKPAGAWLIAFVIVFNAALPALPLFVE 186
                                   6889**************997..***********************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.20s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3494.62
//
Query:       gi|118430940|ref|YP_874805.1|  [L=87]
Description: hypothetical protein APE_0220a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       442  (0.0246528); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.35
# Mc/sec: 747.80
//
Query:       gi|118430941|ref|NP_147059.2|  [L=308]
Description: carboxyvinyl-carboxyphosphonate phosphorylmutase [Aeropyrum pernix K1]
Scores for complete 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-53  182.0   1.8    1.5e-53  181.7   1.8    1.1  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
    3.4e-12   45.6   1.0    9.4e-12   44.2   1.0    1.5  1  ICL         Isocitrate lyase family


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   1.8   1.7e-57   1.5e-53       1     238 [.      16     256 ..      16     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 1.7e-57
                     PEP_mutase   1 lraLhakgeplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDledGy 80 
                                    lr+L +k +++v+p +++++ a ++e++gf+al +s++a++ sl++pD   ++l+el   ++ i++vv++P+ivD+++G+
  gi|118430941|ref|NP_147059.2|  16 LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAMFTSYITRVVRVPVIVDADTGF 95 
                                    68988999************************************************************************ PP

                     PEP_mutase  81 gespeevaetvrrliaaGvvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdalllsagagl 155
                                    ge + +v++tvr+l++aG++++ iED+    k++  +++ l+++e++++ki aa+ a ++   +i+ARtda      +g+
  gi|118430941|ref|NP_147059.2|  96 GE-AINVERTVRELERAGAAAIQIEDQvmpkKCGHlQGKALISPEDMVKKIIAAVGARRD--ALIVARTDAR---GVEGF 169
                                    *9.88**********************998655566888999************999877..8********4...5788* PP

                     PEP_mutase 156 eeaieRaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvp.l.kgt..lsvaelaelGvarislgnhllraalaal 231
                                    e+a+eRa++Y+eAGAd +f   l++ +e +e++++v++pl + + + ++t  ++v++++e+G +++++   ++ra l+a 
  gi|118430941|ref|NP_147059.2| 170 EKAVERAQLYVEAGADIIFPEALTSLEEFREFARRVKAPLLANMtEfGKTpyITVDQFREAGYKIVIFPVTTFRASLKAS 249
                                    ***************************************9999944544467**************************** PP

                     PEP_mutase 232 reaaeei 238
                                    + +++ei
  gi|118430941|ref|NP_147059.2| 250 ETVLREI 256
                                    9999988 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   1.0     1e-15   9.4e-12     150     237 ..      85     167 ..      76     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1e-15
                                    --EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEE CS
                            ICL 150 rpiiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvva 229
                                     p+i dadtG+G    v + ++ +   Gaa i iedq    kkcGh+ Gk l++ ++ + +++a+         d l+va
  gi|118430941|ref|NP_147059.2|  85 VPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQV-MPKKCGHLQGKALISPEDMVKKIIAAVG----ARRDALIVA 159
                                    49***************9999999899**********7.579*******************998654....357999*** PP

                                    E--GGGEE CS
                            ICL 230 rtdseaat 237
                                    rtd+    
  gi|118430941|ref|NP_147059.2| 160 RTDARGVE 167
                                    ***98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2300.09
//
Query:       gi|118430942|ref|NP_147061.2|  [L=270]
Description: hypothetical protein APE_0226.1 [Aeropyrum pernix K1]
Scores for complete 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-42  144.5   0.0    6.3e-42  144.0   0.0    1.2  1  Methyltrn_RNA_3  Putative RNA methyltransferase
  ------ inclusion threshold ------
      0.098   12.8   0.0       0.47   10.6   0.0    1.9  2  SpoU_methylase   SpoU rRNA Methylase family


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 !  144.0   0.0     7e-46   6.3e-42       5     285 ..       2     256 ..       1     257 [. 0.84

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 7e-46
                Methyltrn_RNA_3   5 aiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFplhkelk 84 
                                    a+Pssi++   +l +kt +agqI R aai++Vdei vf+d++s+ +     s +l+ lL+Y +tPp+L+k++Fpl++elk
  gi|118430942|ref|NP_147061.2|   2 ALPSSILRVEPTLLLKTLKAGQIGRVAAIYRVDEIAVFEDPDSSPR----LSRLLQLLLNYQATPPHLKKRVFPLRRELK 77 
                                    8*****************************************9885....679*************************** PP

                Methyltrn_RNA_3  85 yaglLppldaphhlrsse..egeyreGvvvekskekkskkklVniG.lkkevklelkqevpegtRVtVklsseesveakv 161
                                    ya+l+ppl++p h    e   g +  G v + s   ks   +V  G +   v l    + ++g  VtV++   e   +++
  gi|118430942|ref|NP_147061.2|  78 YASLMPPLKIPSHTVPAEpkVGAILDGYVESCSG--KS--CRVFLGsMGYGV-LRG--RARPGDVVTVRI--GEISGGRI 148
                                    *************953332366666676655543..22..389999334444.666..99**********..77899999 PP

                Methyltrn_RNA_3 162 VspsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkkefkhllivfGg.vrgleaa 240
                                    V +++     +ly+G+sV + k l++++t      gy  +++t ++g    e+ + l ++++ ++ l+vfGg ++g+ + 
  gi|118430942|ref|NP_147061.2| 149 VLEKAS--WGELYYGFSVSRFKRLEEAVTSFRR-RGYR-VVATDKNGLCPPESWKIL-AEIPSAKTLVVFGGpYKGVLEY 223
                                    999988..59*******************8742.3444.355888886444444444.45589*********99999888 PP

                Methyltrn_RNA_3 241 leadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLal 285
                                     +              l+d+++n++p+qg++t+rtEEa+l++L +
  gi|118430942|ref|NP_147061.2| 224 TN------------PYLYDGVVNVIPRQGTETVRTEEALLATLEA 256
                                    83............469*************************975 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.8e+03      16      35 ..      22      41 ..      21      55 .. 0.81
   2 ?   10.6   0.0   5.2e-05      0.47      57     107 ..     163     219 ..     145     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                                   HHHHHHHHHTT-SEEEEESG CS
                 SpoU_methylase 16 GaiaRtakafgaselvlvkp 35
                                   G i R+a+++ ++e+ + ++
  gi|118430942|ref|NP_147061.2| 22 GQIGRVAAIYRVDEIAVFED 41
                                   999**********9998764 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.2e-05
                                    HEEEESSHHHHHHHHCCCTEEEEEESTT-SEGC...CS..HHH.TTEEEEEEBTTTB CS
                 SpoU_methylase  57 elkvvdsleealkelkeegfalvatslkgksls...ei..dlk.ekvalvfGnEdkG 107
                                     + +++ leea++ ++++g+++vat+++g       +i  +++  k+++vfG   kG
  gi|118430942|ref|NP_147061.2| 163 SVSRFKRLEEAVTSFRRRGYRVVATDKNGLCPPeswKIlaEIPsAKTLVVFGGPYKG 219
                                    48899********************99776444233333344488999999965555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2220.97
//
Query:       gi|14600545|ref|NP_147062.1|  [L=344]
Description: 50S ribosomal protein L3 [Aeropyrum pernix K1]
Scores for complete 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-80  269.4   0.0      8e-80  268.6   0.0    1.4  1  Ribosomal_L3  Ribosomal protein L3


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 !  268.6   0.0   4.4e-84     8e-80       1     369 []       1     343 [.       1     343 [. 0.88

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 4.4e-84
                                   XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC CS
                  Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvet 81 
                                   m  rk  apr+gslGf+prkRa+r +++vk +P+ d  kpv l aflGy+aGmth+  ++d+pg ++ +ke+ ++vt+vet
  gi|14600545|ref|NP_147062.1|   1 MGARKKRAPRRGSLGFSPRKRASRLVPRVKRWPEVDIGKPVPL-AFLGYRAGMTHVFMVDDRPGRPTSGKEIFVPVTIVET 80 
                                   7789999**********************************99.8************************************ PP

                                   --EEEEEEEEE.EEETTEEEEEEEEESSS.SH.HHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCE CS
                  Ribosomal_L3  82 ppmvivgvvgy.vetprGlrslktvwaehlse.evkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvv 160
                                   ppm +++v++y  + +rG  sl + wa+   e e++rr+                  +++++  k++e  l++ ++    v
  gi|14600545|ref|NP_147062.1|  81 PPMFVAAVRLYgYDPNRGRYSLGEAWAQPPPElELQRRI-------------STLGSFDTDKMLKSLEERLDKAED----V 144
                                   ********999457789***********87666999*99.............223445566666666666666555....* PP

                                   EEEEEEECCCSS-SCCSSHHEEEEECHCS.CHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT--- CS
                  Ribosomal_L3 161 rviahtvirktkslaqKkahllEiqvngG.tiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkk 240
                                   r+ia ++ +   +l +Kk++llEi+v+g   +++ +d+a++ l + +av++vF++g+l+Dvi+vtkGkGf+Gv+kRWgvk+
  gi|14600545|ref|NP_147062.1| 145 RLIAASQPKLAGGLSKKKPDLLEIKVGGVsDVTKLFDYAKDVLGNLIAVNDVFEEGQLVDVIAVTKGKGFQGVIKRWGVKE 225
                                   **************************9975788999********************************************* PP

                                   -ST..TTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB. CS
                  Ribosomal_L3 241 lpr..kthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGe 319
                                   lpr  k+ +g R+++a + +      + +++aGq+G+h+Rte+nk+i  i++              + ++tP GGf +yG+
  gi|14600545|ref|NP_147062.1| 226 LPRwhKHRKGSRRIGARSHG--RSTFWETPQAGQTGFHRRTEYNKRILMIDD-------------DGYKVTPAGGFLRYGV 291
                                   **944556669999876544..456799**********************99.............4678************ PP

                                   .TSCEEEEES--SSSTTEEEEEEE-SSGGGS....CCCSS-EEEEEE-TTCTSS CS
                  Ribosomal_L3 320 vkndfilvkGsvpGpkkrlvklrkslltqts....rkaeeevslkfidtaskfg 369
                                   v+  f+++ Gs+pG+ kr + +r ++++ +        ++e+   +i+ ask+g
  gi|14600545|ref|NP_147062.1| 292 VRSTFVMLSGSIPGTPKRPIVMRWAIRPPEWylklGVRKPEI--TYISLASKQG 343
                                   **************************9987644333334444..7888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2708.16
//
Query:       gi|118430943|ref|NP_147063.2|  [L=272]
Description: 50S ribosomal protein L4 [Aeropyrum pernix K1]
Scores for complete 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  139.0   0.2    1.7e-40  138.8   0.2    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 !  138.8   0.2   9.3e-45   1.7e-40       3     190 ..      31     264 ..      29     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 9.3e-45
                                    E-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT---SS CS
                   Ribosomal_L4   3 LspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGgvah 74 
                                    L p++F  p+r+dli+ra++++ ++r q++++++ a++++s+   +l+   G+G ARv++i+       +++argG+ ah
  gi|118430943|ref|NP_147063.2|  31 L-PQIFRFPVRKDLIRRAFLSEFTARLQPKGRDPmAGKRTSA--VSLGV--GRGVARVPRIKgslraalVNMARGGRAAH 105
                                    5.99**************************************..5****..***************************** PP

                                    ---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES...---..-S..........S--HHHHHHHHHHTT-...... CS
                   Ribosomal_L4  75 gpkperdystklnkKvrrlAlrsaLsakakqglllvvd...nle.ple..........esktkelvellkklgl...... 134
                                    +p++e+  ++ +nkK++rlA  sa+sa+ +++l++ ++   +   +l+          +s ++e+++ll+++g+      
  gi|118430943|ref|NP_147063.2| 106 PPRVEKVLKEYINKKEKRLATISAISATSREDLVRQRGhrfS-AeTLPivldssvlakISTAREARSLLESVGVyedvlr 184
                                    **************************************8442.224447788888887888**********888888888 PP

                                    ....................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHH CS
                   Ribosomal_L4 135 ....................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksavekle 190
                                                         +ksvL+v+++ ++ l+la++ +pgv+v++ + l+v++l+++ +    +++t +a++ l 
  gi|118430943|ref|NP_147063.2| 185 akegkrynagkgkmrgrrykVPKSVLFVLEDPRSPLALAVKGMPGVDVVTPTLLSVLHLAPGGHpgrlTIYTTEALKLLS 264
                                    88888888898888888888899*****************************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 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:                        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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 2013.79
//
Query:       gi|118430944|ref|NP_147064.2|  [L=86]
Description: 50S ribosomal protein L23 [Aeropyrum pernix K1]
Scores for complete 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-19   68.5   5.7    6.4e-18   64.9   5.7    1.9  1  Ribosomal_L23   Ribosomal protein L23
  ------ inclusion threshold ------
      0.024   14.3   0.1      0.027   14.1   0.1    1.1  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
      0.038   13.8   0.1       0.05   13.4   0.1    1.3  1  TusA            Sulfurtransferase TusA


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 !   64.9   5.7   1.1e-21   6.4e-18       1      83 [.       5      75 ..       5      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1.1e-21
                                   SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEESSS CS
                  Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtLkeg 81
                                   +vi++ ++tEk+t++ e+ n+++F V+++a+K ++k+ave+lFgVkVekV+tl+ ++              yKka+V+L+++
  gi|118430944|ref|NP_147064.2|  5 EVIIRVYVTEKTTRMLEEeNTLTFIVRREATKNDVKRAVEQLFGVKVEKVRTLITPR-------------GYKKAYVKLAPE 73
                                   599**********99998789*********************************998.............789999999877 PP

                                   -S CS
                  Ribosomal_L23 82 ek 83
                                   +k
  gi|118430944|ref|NP_147064.2| 74 YK 75
                                   65 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.6e-06     0.027      21      89 ..       4      79 ..       1      81 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                                   TTEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHH.......CCSSSSSB-EEEEEEEESSGGEE- CS
                 DNA_mis_repair 21 eqlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYk.......ellpkgrypvvvLnleidpeevDv 89
                                   e++ i+ +++++++   ++++ ++f+ +R  +++++k+a+++ +        +l+  + y  ++++l  + +++Dv
  gi|118430944|ref|NP_147064.2|  4 EEVIIRVYVTEKTTRMLEEENTLTFIVRREATKNDVKRAVEQLFGvkvekvrTLITPRGYKKAYVKLAPEYKALDV 79
                                   5688999*************************************96666665556666666666666666666665 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.3e-06      0.05      16      57 ..      12      54 ..      10      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.3e-06
                                   HHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHH.TEEEEEE CS
                           TusA 16 klkkalekleegevlevladdpaatediprfakkl.ghelvev 57
                                    + k+ + lee+++l +++  +a+++d++r +++l g ++++v
  gi|118430944|ref|NP_147064.2| 12 VTEKTTRMLEEENTLTFIVRREATKNDVKRAVEQLfGVKVEKV 54
                                   58899999**********************9987525565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 657.85
//
Query:       gi|118430945|ref|NP_147065.2|  [L=309]
Description: MRP/NBP35 family protein [Aeropyrum pernix K1]
Scores for 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-87  290.5   0.0    1.3e-86  290.1   0.0    1.1  1  ParA         NUBPL iron-transfer P-loop NTPase
    4.6e-16   59.0   0.0    2.5e-15   56.7   0.0    2.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    2.5e-10   40.3   0.1    0.00019   21.0   0.0    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    5.7e-08   32.9   0.6    3.9e-06   26.9   0.1    2.2  2  AAA_31       AAA domain
    5.2e-06   26.4   0.1     0.0016   18.3   0.1    2.2  2  AAA_26       AAA domain
    7.6e-05   22.1   0.1    0.00015   21.1   0.1    1.5  2  MipZ         ATPase MipZ
    8.1e-05   22.0   0.0    0.00014   21.3   0.0    1.3  1  VirC1        VirC1 protein
    0.00026   20.3   0.5     0.0028   16.9   0.3    2.2  2  ArsA_ATPase  Anion-transporting ATPase
     0.0025   17.5   0.2     0.0039   16.9   0.2    1.3  1  AAA_30       AAA domain
      0.006   16.2   0.0      0.013   15.1   0.0    1.6  2  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.016   14.2   0.3      0.055   12.4   0.1    1.8  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.019   14.4   0.1       0.09   12.2   0.1    1.9  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      0.074   12.5   0.1       0.13   11.6   0.1    1.4  1  PhoH         PhoH-like protein
       0.27    9.8   0.1       0.37    9.3   0.1    1.1  1  DUF3138      Protein of unknown function (DUF3138)


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 !  290.1   0.0   9.9e-90   1.3e-86       2     245 ..      44     290 ..      43     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 290.1 bits;  conditional E-value: 9.9e-90
                           ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee..ekpeqsekkliPvea.kgikvmSi 78 
                                    ++ +iav+S+KGGVGKS v+++lA+aLa++g +vg++DaDi Gps+ ++lg+++    p+q + ++ Pve+  gikv Si
  gi|118430945|ref|NP_147065.2|  44 IRYKIAVISTKGGVGKSFVTASLAAALAAEGRRVGVFDADISGPSVHKMLGLQTgmGMPSQLDGTVKPVEVpPGIKVASI 123
                                    7899***********************************************9994434555588899****99******* PP

                           ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkai 157
                                    g+ll+ ++ +++wrG++k++ai++ll+ v+wgelDyL+iDlPPGtgDe lt++q + +++g ++Vt p e+a ++vkka+
  gi|118430945|ref|NP_147065.2| 124 GLLLPMDEVPLIWRGAIKTSAIRELLAYVDWGELDYLLIDLPPGTGDEVLTITQIIpNITGFLVVTIPSEIAKSVVKKAV 203
                                    ********************************************************889********************* PP

                           ParA 158 emfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaaka 237
                                    +++k+++++v+G+veNms+f c++ g+ ++ifg+g +e++a+++g++llg+ip+dp+ire++d+gk ++l++pesea+++
  gi|118430945|ref|NP_147065.2| 204 SFAKRIEAPVIGIVENMSYFRCSD-GSIHYIFGRGAAEEIASQYGIELLGKIPIDPAIRESNDKGKIFFLENPESEASRE 282
                                    **********************97.9999*************************************************** PP

                           ParA 238 leeiaekv 245
                                    + +ia+++
  gi|118430945|ref|NP_147065.2| 283 FLKIARRI 290
                                    *****998 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 !   56.7   0.0   1.9e-18   2.5e-15       1     126 [.      48     268 ..      48     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.9e-18
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    ia++stkGGvGK++++a+La+ala +g+rV ++DaD  +++ +   gl+                               
  gi|118430945|ref|NP_147065.2|  48 IAVISTKGGVGKSFVTASLAAALAAEGRRVGVFDADISGPSVHKMLGLQTGMGMpsqldgtvkpvevppgikvasiglll 127
                                    89*****************************************744443333336667888888888************* PP

                                    ......................................................................CCHCCCHHHH CS
                                    ......................................................................xxxxxxxxxx RF
                           CbiA  55 ......................................................................dlkrllelle 64 
                                                                                                           +k+ + +++
  gi|118430945|ref|NP_147065.2| 128 pmdevpliwrgaiktsairellayvdwgeldyllidlppgtgdevltitqiipnitgflvvtipseiaksVVKKAVSFAK 207
                                    *******************************************************9999987777655555555555555 PP

                                    HHCHCHHHH..EEEEEEEEE.....SS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                    xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  65 algkkkalllkiagvvlnrv.....dgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                    ++         ++g+v n+      dg+ ++   + a ee+  +yg+++lg+ip d a+ e+  +g+
  gi|118430945|ref|NP_147065.2| 208 RIE------APVIGIVENMSyfrcsDGSIHYIFGRGAAEEIASQYGIELLGKIPIDPAIRESNDKGK 268
                                    555......569****99953333377788888899999999999**************99988775 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 !   17.1   0.1   2.3e-06    0.0029       4      38 ..      50      84 ..      46     102 .. 0.82
   2 !   21.0   0.0   1.4e-07   0.00019     189     255 ..     235     301 ..     182     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                      Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCDP 38
                                    i  kGG+Gks+ ++ l+aala+ g++v +   D 
  gi|118430945|ref|NP_147065.2| 50 VISTKGGVGKSFVTASLAAALAAEGRRVGVFDADI 84
                                   4668************************8887775 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.4e-07
                      Fer4_NifH 189 ereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilenkklviPkp 255
                                    +r+ +e++a++ g+++l ++P d  +r+++ + k+ +  +pese + e+ ++ar+i+e  + + Pkp
  gi|118430945|ref|NP_147065.2| 235 GRGAAEEIASQYGIELLGKIPIDPAIRESNDKGKIFFLENPESEASREFLKIARRIIEIVEKLGPKP 301
                                    456789999*************************************************999999998 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.1     3e-09   3.9e-06       3      40 ..      47      84 ..      45     101 .. 0.92
   2 ?    4.2   0.0     0.028        36     116     166 ..     155     208 ..     122     218 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3e-09
                         AAA_31  3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                    Ia++  KGGvGK+  +  laaala +g +v + D+D 
  gi|118430945|ref|NP_147065.2| 47 KIAVISTKGGVGKSFVTASLAAALAAEGRRVGVFDADI 84
                                   59**********************************96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.028
                         AAA_31 116 deYDyiiiDcpPsLg..lltenaLv.asdsviipvqaeayaleGleqllktiee 166
                                     e Dy +iD pP  g  +lt++ ++     +++++ +++ a + +++ +++ ++
  gi|118430945|ref|NP_147065.2| 155 GELDYLLIDLPPGTGdeVLTITQIIpNITGFLVVTIPSEIAKSVVKKAVSFAKR 208
                                    468*********886445555544413445666666667776666666666555 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.2e-06    0.0016       3      35 ..      48      80 ..      46      91 .. 0.94
   2 !    6.1   0.0    0.0068       8.7     148     195 ..     202     261 ..     183     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                         AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyf 35
                                   i v++t  gvGK++v++ L++al ++g +vg+f
  gi|118430945|ref|NP_147065.2| 48 IAVISTKGGVGKSFVTASLAAALAAEGRRVGVF 80
                                   78*****************************98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0068
                         AAA_26 148 tiealrqknvrvlGvilNkvrnp...e..........nvetlekksgipvlGvvPylpdle 195
                                    +++++++ + +v+G++ N        +          + e++ ++ gi++lG +P +p ++
  gi|118430945|ref|NP_147065.2| 202 AVSFAKRIEAPVIGIVENM-SYFrcsDgsihyifgrgAAEEIASQYGIELLGKIPIDPAIR 261
                                    4566677788999999997.22233315566666667999***************999876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.2e-07   0.00015       3      49 ..      48      94 ..      46     114 .. 0.89
   2 ?   -4.0   0.0       5.4     7e+03      98     108 ..     155     165 ..     138     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHH CS
                           MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryle 49
                                   i +   kGG Gks ++  +a aL+++G rv++ d d+   ++++ l+
  gi|118430945|ref|NP_147065.2| 48 IAVISTKGGVGKSFVTASLAAALAAEGRRVGVFDADISGPSVHKMLG 94
                                   667778*******************************9999998876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.4
                                    HH-SEEEEE-- CS
                           MipZ  98 aeldfividtP 108
                                     eld+++id P
  gi|118430945|ref|NP_147065.2| 155 GELDYLLIDLP 165
                                    46899999976 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.1e-07   0.00014       4      43 ..      48      87 ..      46      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                          VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                   i++ s kGG Gk+    +l +ala++g+rv++f+ad   P
  gi|118430945|ref|NP_147065.2| 48 IAVISTKGGVGKSFVTASLAAALAAEGRRVGVFDADISGP 87
                                   6789********************************7655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   2.2e-06    0.0028       2      35 ..      47      80 ..      46      92 .. 0.89
   2 ?    1.0   0.0      0.15   1.9e+02     112     137 ..     144     170 ..     136     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                    ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvlli 35
                                   k+ +++ KGGVGK+ v a++a+ l+ +g++v + 
  gi|118430945|ref|NP_147065.2| 47 KIAVISTKGGVGKSFVTASLAAALAAEGRRVGVF 80
                                   677899**********************998665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHCSSSSEEEEESBS.CCH CS
                    ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaP.TGh 137
                                    +  ell yv+  e d++++D +P TG+
  gi|118430945|ref|NP_147065.2| 144 AIRELLAYVDWGELDYLLIDLPPgTGD 170
                                    5678899999999*******9996775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.1e-06    0.0039       2      51 ..      30      79 ..      29     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                         AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                   ++++Q ++v+++   + ++av+    G GK+++ ++l++a++a+g+rv +
  gi|118430945|ref|NP_147065.2| 30 IQEQQMKIVRNMRRIRYKIAVISTKGGVGKSFVTASLAAALAAEGRRVGV 79
                                   5799*****************************************99965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     1e-05     0.013      16      62 ..      28      76 ..      14      90 .. 0.76
   2 ?   -3.3   0.0       4.5   5.7e+03     166     186 ..     196     216 ..     192     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                         AAA_25 16 aapppprrwlvkg.llpagelallaGapgtGKttlaldlalava.tGkp 62
                                   ++ ++++ ++v++  +++ ++a++   +g+GK++++ +la+a+a +G+ 
  gi|118430945|ref|NP_147065.2| 28 KTIQEQQMKIVRNmRRIRYKIAVISTKGGVGKSFVTASLAAALAaEGRR 76
                                   555556666666524457788999999*****************88875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.5
                         AAA_25 166 galvealeriarrtgaavllv 186
                                    +++v+++ ++a+r  a v+++
  gi|118430945|ref|NP_147065.2| 196 KSVVKKAVSFAKRIEAPVIGI 216
                                    789999999999999999876 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 ?   12.4   0.1   4.3e-05     0.055      36      70 ..      53      87 ..      23     105 .. 0.82
   2 ?   -1.0   0.0      0.54     7e+02     150     180 ..     164     194 ..     156     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                   E-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                           MeaB 36 GvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      G+Gks ++  l++ l+++G+rv+v   D s p
  gi|118430945|ref|NP_147065.2| 53 TKGGVGKSFVTASLAAALAAEGRRVGVFDADISGP 87
                                   4569************************9998766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.54
                                    EESSTTTTTTT--CCCHHH-SEEEEE---HH CS
                           MeaB 150 llpeaGDelqgikkGileiaDiivvnkaDkk 180
                                    l p++GDe+ +i + i +i+  +vv    + 
  gi|118430945|ref|NP_147065.2| 164 LPPGTGDEVLTITQIIPNITGFLVVTIPSEI 194
                                    55899***99999999999999988765544 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     7e-05      0.09       4      38 ..      48      82 ..      46     104 .. 0.85
   2 ?   -0.6   0.0      0.59   7.6e+02     108     131 ..     148     172 ..     130     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-05
                       CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                   +a+   +GGvG++ ++a+La al + g +v v D+
  gi|118430945|ref|NP_147065.2| 48 IAVISTKGGVGKSFVTASLAAALAAEGRRVGVFDA 82
                                   5666679***********************99997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.59
                       CBP_BcsQ 108 alkelk.eqyrwillDlpagasalt 131
                                     l+ +  ++ +++l+Dlp g+ + +
  gi|118430945|ref|NP_147065.2| 148 LLAYVDwGELDYLLIDLPPGTGDEV 172
                                    445555678899******9877654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0001      0.13       3      47 ..      28      74 ..      26      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   ---SHHHHHHHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                           PhoH  3 kpktkeQkeylealk..kndivfaiGpaGtGKtylavalavealkkk 47
                                   k+ +++Q +++++++  +++i ++  + G GK++++ +la+++  ++
  gi|118430945|ref|NP_147065.2| 28 KTIQEQQMKIVRNMRriRYKIAVISTKGGVGKSFVTASLAAALAAEG 74
                                   5678899999**99999999*****************9999887765 PP

>> DUF3138  Protein of unknown function (DUF3138)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00029      0.37      21      78 ..      21      80 ..      10      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00029
                        DUF3138 21 aatadrikalkaqltalqrqvkelra..alaaakaaaGgkissqkaaaaaaaaaeaaaal 78
                                   +a a+r+k+++ q  ++ r+++ +r   a+ ++k+  G    + + aaa aa ++   ++
  gi|118430945|ref|NP_147065.2| 21 KAIAERMKTIQEQQMKIVRNMRRIRYkiAVISTKGGVGKSFVTASLAAALAAEGRRVGVF 80
                                   5669******************99861255666666666666666666666556655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 2332.30
//
Query:       gi|14600549|ref|NP_147066.1|  [L=287]
Description: hypothetical protein APE_0231 [Aeropyrum pernix K1]
Scores for complete 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-50  168.0  15.0    3.8e-14   52.9   0.7    4.1  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.7   2.1e-18   3.8e-14       3      56 ..       7      59 ..       2      60 .. 0.90
   2 !   49.5   0.2   2.3e-17   4.2e-13       1      55 [.      72     126 ..      72     128 .. 0.95
   3 !   24.2   0.0   1.9e-09   3.4e-05       1      52 [.     136     186 ..     136     189 .. 0.89
   4 !   49.9   0.8   1.8e-17   3.1e-13       1      56 [.     224     278 ..     224     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.1e-18
                                  HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS  3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                  ++mtrdv tv+pd+tl+ a +lm  +++srlPVV+   kl Gi+t +D+++al+
  gi|14600549|ref|NP_147066.1|  7 SYMTRDVYTVSPDDTLAHARKLMLTHDISRLPVVE-GSKLRGIITITDIADALV 59
                                  46*********************9999*******5.446************996 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 2.3e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                   V+++m rdvvt+  + +++ a+ lm +++++++PVV  dg l Gi+t++Dl r+ 
  gi|14600549|ref|NP_147066.1|  72 VREVMARDVVTIEGTKSVKTAASLMLKHNIGGVPVVAPDGTLEGIITRTDLTRYY 126
                                   89**********************************77999***********996 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 1.9e-09
                                   HHHHSBSSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTBEEEEEEHHHHH CS
                           CBS   1 Vgdimtrdvvtvppdttleealelmr.ekgvsrlPVVdedgklvGivtlrDll 52 
                                   V+++m++ +  ++ + ++  +l+lm+ ++  + ++++ + gklvG++t+rD++
  gi|14600549|ref|NP_147066.1| 136 VKEFMREIYAKARREHSIFYVLKLMEiDA-TGKVLIL-DGGKLVGVITKRDIA 186
                                   899****9*****************5433.6999999.6999**********8 PP

  == domain 4  score: 49.9 bits;  conditional E-value: 1.8e-17
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   ++d+mt++++tv p+++l++a+++m+++gv+ lPVVd+d+ ++G+vt+  +l+a++
  gi|14600549|ref|NP_147066.1| 224 AEDVMTPNPITVEPEEDLAKAADIMVKEGVGILPVVDGDN-VLGVVTKVEVLQAIV 278
                                   579***************************888***9999.***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2179.26
//
Query:       gi|14600550|ref|NP_147067.1|  [L=340]
Description: hypothetical protein APE_0233 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-41  139.8  11.7    5.6e-10   39.5   0.8    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.069   13.2   0.0       0.11   12.5   0.0    1.3  1  DUF2300   Predicted secreted protein (DUF2300)
       0.19   11.5   0.9       0.29   11.0   0.2    1.7  2  S4_2      S4 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 !   29.5   0.0   1.3e-10   7.5e-07       2      55 ..      60     115 ..      59     117 .. 0.87
   2 !   37.7   0.8   3.3e-13     2e-09       1      56 [.     141     196 ..     140     197 .. 0.92
   3 !   38.0   0.0   2.9e-13   1.7e-09       1      54 [.     204     258 ..     204     261 .. 0.94
   4 !   39.5   0.8   9.3e-14   5.6e-10       4      54 ..     284     333 ..     273     335 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.3e-10
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT..BEEEEEEHHHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedg..klvGivtlrDllral 55 
                                   +++ +r+ v+v+ ++++  a+e++++++v++l V+ ++g   l Gi+  +Dl+++l
  gi|14600550|ref|NP_147067.1|  60 KELASRPAVSVHKSAPILSAAEKIASHRVRGLVVIKGSGdaVLEGILLATDLVNYL 115
                                   78999***************************666666642588*********998 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 3.3e-13
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                   V+ im+r ++ v+ +++l  +l++m+ +g++ lPV+ +dg l+G++t+r +l  ++
  gi|14600550|ref|NP_147067.1| 141 VATIMNRHPIAVSVSDDLDTILRIMVGEGIGFLPVLYDDGTLHGVITERNILGRIA 196
                                   6779**************************999**735999***********9886 PP

  == domain 3  score: 38.0 bits;  conditional E-value: 2.9e-13
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                                   Vgd+mt  +v v+p+++l+ea++ m+ +g++rl+V+  + g++ G++t +D++ +
  gi|14600550|ref|NP_147067.1| 204 VGDYMTATIVGVDPEAPLKEAMRSMVTYGFRRLLVIsSSTGEIKGVITAKDIVAY 258
                                   89*******************************99988888***********987 PP

  == domain 4  score: 39.5 bits;  conditional E-value: 9.3e-14
                                   HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                           CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                   +m+++v t+++ +++++a+++m+e gv++l VV + g+  Gi+t+rD+l a
  gi|14600550|ref|NP_147067.1| 284 VMSPEVYTIDEKASVADAARRMVELGVDSLIVV-DGGEAKGIITERDVLVA 333
                                   6*****************************999.5889**********965 PP

>> DUF2300  Predicted secreted protein (DUF2300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.11      34      86 ..      22      76 ..      16      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                       DUF2300 34 yfepqrlalqalawaeaWlar.qapaWlrelralqgee.rvsvkalltllaglPa 86
                                  + +p+r+  ++ ++  +Wl++ ++p+W +++r+l+g   +  + + + ++++ P+
  gi|14600550|ref|NP_147067.1| 22 APKPSRVVTRSRPEGVRWLRAdGTPNWSQRVRRLPGDAkELASRPAVSVHKSAPI 76
                                  568889889999999***97539***********986515556777788888887 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   1.3e+04      23      35 ..     243     255 ..     239     257 .. 0.72
   2 ?   11.0   0.2   4.9e-05      0.29      19      45 ..     314     340 .]     312     340 .] 0.88

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                          S4_2  23 GgeaKafiaegeV 35 
                                    ge K +i+ +++
  gi|14600550|ref|NP_147067.1| 243 TGEIKGVITAKDI 255
                                   5888998887765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.9e-05
                          S4_2  19 lvesGgeaKafiaegeVkvNGevetrR 45 
                                   +v +GgeaK +i+e +V+v   ve +R
  gi|14600550|ref|NP_147067.1| 314 IVVDGGEAKGIITERDVLVASVVEGER 340
                                   6889***************88888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2436.85
//
Query:       gi|14600551|ref|NP_147068.1|  [L=278]
Description: hypothetical protein APE_0234 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-39  133.2  14.4      2e-12   47.4   1.6    4.1  4  CBS             CBS domain
  ------ inclusion threshold ------
       0.15   10.8   0.0       0.22   10.2   0.0    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !   29.7   0.4   7.3e-11   6.6e-07       8      52 ..      22      66 ..      13      69 .. 0.90
   2 !   24.5   0.0   3.1e-09   2.8e-05       3      50 ..      79     126 ..      77     133 .. 0.84
   3 !   38.8   0.2   1.1e-13   9.4e-10       2      53 ..     143     194 ..     142     196 .. 0.91
   4 !   47.4   1.6   2.2e-16     2e-12       1      54 [.     213     268 ..     213     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.3e-11
                                  SCEEEETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHH CS
                           CBS  8 dvvtvppdttleealelmrekgvsrl.PVVdedgklvGivtlrDll 52
                                  ++vtv  +++++e+ +++r++g sr+ +VV+++g+l G++ ++ ++
  gi|14600551|ref|NP_147068.1| 22 KPVTVEKEAPIGEIRRILRDTG-SRIvLVVNGEGRLEGVIYRSSVI 66
                                  789*******************.6886799***********99887 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.1e-09
                                   HHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHH CS
                           CBS   3 dimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrD 50 
                                   dim ++ v+++p+ +leea+  m + +     PVV++ ++lvG++ l+ 
  gi|14600551|ref|NP_147068.1|  79 DIMEEPAVVLKPSYSLEEAVFSMLKFDeW-YAPVVNDANRLVGVLGLET 126
                                   89********************9885534.66************97765 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 1.1e-13
                                   HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEE.EEEEHHHHHH CS
                           CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklv.GivtlrDllr 53 
                                   +d mtrdv +v + ++l  + e+m+e+++ ++PVVd    +v Givt+ Dl+r
  gi|14600551|ref|NP_147068.1| 143 SDAMTRDVEYVLEGDSLTRVWEIMVERRYAGVPVVDQRM-VVrGIVTQYDLIR 194
                                   799********************************7666.666*********9 PP

  == domain 4  score: 47.4 bits;  conditional E-value: 2.2e-16
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTT.BEE.EEEEHHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedg.klv.GivtlrDllra 54 
                                   V+++mtr v++v ++++le+++++m ++gv+r+PVV    + +++ Gi+ ++Dl+r+
  gi|14600551|ref|NP_147068.1| 213 VESVMTRSVIYVAESDNLEDVARIMLDRGVGRVPVVkS-RDsRVLtGIIDREDLVRL 268
                                   789*********************************63.4436666********997 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 ?   10.2   0.0   2.5e-05      0.22     147     214 ..      17      83 ..       2      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.5e-05
                                   EEEEEEETTCGH.GHHHHHHHHHHHHTEEEEEEECTSB-HHHHGGGGG-SEEEEESHHCHHHHHHHHHH CS
                Oxidored_nitro 147 kvnilgeynlgp.gdlrelkelleklGlevnavftggtsleelraagraklnlvlcprsanyaaellee 214
                                    vn+l ++ +++ + + e++++l++ G +++ v+ g+ +le +  + r+++ lv +++s ++a +++ee
  gi|14600551|ref|NP_147068.1|  17 EVNLLKPVTVEKeAPIGEIRRILRDTGSRIVLVVNGEGRLEGV--IYRSSVILVTSRKSEAKALDIMEE 83 
                                   79***99999988****************************98..56999999*****99999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1992.47
//
Query:       gi|118430946|ref|NP_147069.2|  [L=309]
Description: thiamine-monophosphate kinase [Aeropyrum pernix K1]
Scores for complete 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-09   37.1   0.3    9.8e-09   35.8   0.2    1.7  2  AIRS      AIR synthase related protein, N-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 !   35.8   0.2   5.4e-13   9.8e-09      23      93 ..      44     129 ..      26     130 .. 0.84
   2 ?   -2.9   0.0      0.63   1.1e+04      69      80 ..     253     264 ..     248     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 5.4e-13
                                    C............HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC...HHHHHHHHHHHHHHHTT-EEEEEEEEEESSEEEE CS
                           AIRS  23 f............iGakavavnlsDlaamGArPlalllslalp...wleevvrglaeaaeelgvplvgGdtsfsneptis 87 
                                    +             G+k+v +++sD+aa G+ P  +++sl l     + +v+rg++eaa  +g+ +   d + s++p i 
  gi|118430946|ref|NP_147069.2|  44 MdssrlpwmslgdWGWKSVVAAASDVAASGGAPFHVMYSLGLDsveRAVDVARGVGEAAVWMGATVGKSDFNTSKSPWID 123
                                    23333345667778*****************************9999999**********************9999**** PP

                                    EEEEEE CS
                           AIRS  88 vtavGl 93 
                                    v+++G 
  gi|118430946|ref|NP_147069.2| 124 VAVLGK 129
                                    ****97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.63
                                    TT-EEEEEEEEE CS
                           AIRS  69 lgvplvgGdtsf 80 
                                    +++  vgGd s 
  gi|118430946|ref|NP_147069.2| 253 YNIVAVGGDGSI 264
                                    667777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2404.34
//
Query:       gi|118430947|ref|NP_147070.2|  [L=249]
Description: uroporphyrin-III C-methyltransferase [Aeropyrum pernix K1]
Scores for 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-43  147.0   0.4    8.4e-43  146.8   0.4    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.8   0.4   4.7e-47   8.4e-43       1     210 [.       7     216 ..       7     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 146.8 bits;  conditional E-value: 4.7e-47
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel.eleapmgkekepleeayeeiaealaealrag 79 
                                    k+++VG GpGdp l+Tv++++al++ad++l+d+ +a++ l ++l+  + +++  +   k  ++  +eei++ +  ++ +g
  gi|118430947|ref|NP_147070.2|   7 KVVIVGGGPGDPGLITVKGMKALEEADAILYDR-LAPKGLVEKLQTPAlKIYVGK---KPGEGMSQEEINRLMEILACRG 82 
                                    799******************************.999999998866433333333...3346667*************** PP

                   TP_methylase  80 kdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl......lpglakeeere 153
                                    ++V++l++GDP+ yg+g e++  l++  +g+e+ viPGv+s  aa a +giplt +g ++s+        pg+ + ++ +
  gi|118430947|ref|NP_147070.2|  83 MTVARLKGGDPYTYGRGEEECMYLME--KGVECIVIPGVPSYIAASALHGIPLTSRGISSSFAvitgkeAPGKPAGKRVK 160
                                    **************************..9****************************************88888999999 PP

                   TP_methylase 154 leallangdtlvllkaprklaelaelLkealyddttpvavveragtedervvrgtle 210
                                    le+++   dtlv+l++ ++ aelae+L++ l+++t pva+++ ++t++ ++ ++ l+
  gi|118430947|ref|NP_147070.2| 161 LEDIARSVDTLVILMGASTSAELAERLIKVLPPET-PVAIASSVSTPEAETLVTDLR 216
                                    ***9999***********************88866.***********8666667765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.41
# Mc/sec: 1826.88
//
Query:       gi|118430948|ref|NP_147071.2|  [L=211]
Description: hypothetical protein APE_0237.1 [Aeropyrum pernix K1]
Scores for 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-35  120.2   0.1    9.5e-35  119.9   0.1    1.0  1  Chlor_dismutase  Chlorite dismutase


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.1   5.3e-39   9.5e-35       4     193 ..      24     210 ..      22     211 .] 0.84

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 5.3e-39
                                    HHHHHHHHHHHTTSC...EEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSS CS
                Chlor_dismutase   4 aveelealleeaeeg...vlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYke 80 
                                    a+e+ +++++ea+e+   ++++  ++l +   ++l l+ + +++  l +++ el+r   ++++e+a+++ +++++s Y  
  gi|118430948|ref|NP_147071.2|  24 AAEAWRSVVSEAAESsdaTVSR--AYLNISGPGHLSLVAAFTEAGGLGRLRLELSR---WGCVEEAVWWPAYYKESPY-- 96 
                                    6777788888866665443333..344444458***********************...9******************.. PP

                                    S-GGGHHHCHHHHS----SSS..EEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTT...EEEEEEE-TTTSSSSEE CS
                Chlor_dismutase  81 edeenkshvearlapelpkkk..yvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgk...VrqiitgsfGldDyEwg 155
                                        ++s++ +++++ l+++k  ++++YPm+ks +WYl pee Rr+ m eH++i+++ ++   V +++t++fG++DyE++
  gi|118430948|ref|NP_147071.2|  97 ----ARSKTAEEVVEALKNSKfrFLVAYPMKKSPTWYLEPEEVRRRAMGEHIRIAMERTRenpVLSVTTYAFGIADYEFL 172
                                    ....45555455554444444339********************************9944489***************** PP

                                    EEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEEE CS
                Chlor_dismutase 156 valeaddleefkdlvyelRfdeasakvaeegpfyvGrr 193
                                    v +e d++ ++ + v++lR++ea++++ +e+p+++G r
  gi|118430948|ref|NP_147071.2| 173 VLYEVDSIPAWIETVEALRAAEARKWIIREEPVLLGLR 210
                                    ***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 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:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1551.96
//
Query:       gi|14600555|ref|NP_147072.1|  [L=141]
Description: hypothetical protein APE_0238 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1054.05
//
Query:       gi|14600556|ref|NP_147073.1|  [L=108]
Description: hypothetical protein APE_0239 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 794.93
//
Query:       gi|14600557|ref|NP_147074.1|  [L=176]
Description: hypothetical protein APE_0240 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       386  (0.0215294); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1242.33
//
Query:       gi|118430949|ref|YP_874806.1|  [L=96]
Description: hypothetical protein APE_0240a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 711.32
//
Query:       gi|118430950|ref|NP_147076.2|  [L=103]
Description: hypothetical protein APE_0242.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0029   17.9   0.9     0.0029   17.9   0.9    3.0  2  C6_DPF       Cysteine-rich domain
     0.0063   16.6   6.8     0.0063   16.6   6.8    3.8  4  zf-B_box     B-box zinc finger
  ------ inclusion threshold ------
      0.055   13.5  22.5       0.86    9.7   0.4    3.2  3  DZR          Double zinc ribbon
        4.7    7.5  21.2         14    6.0   4.1    3.2  2  IBR          IBR domain, a half RING-finger domain


Domain annotation for each model (and alignments):
>> C6_DPF  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4  10.2         3   1.3e+04      52      80 ..      14      45 ..       7      50 .. 0.65
   2 !   17.9   0.9   6.5e-07    0.0029      51      91 ..      50      90 ..      45      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3
                         C6_DPF 52 kCslCekavCvdee...CslfytkrfClkCvk 80
                                   +C lC++ vC  +      +   ++ C+ C +
  gi|118430950|ref|NP_147076.2| 14 SCRLCGRPVCDTHGgggVCVACREAICAVCGR 45
                                   68889999997654111334455667777765 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 6.5e-07
                         C6_DPF 51 akCslCekavCvdeeCslfy..tkrfClkCvkeelkefPkeiq 91
                                   + Cs C++  Cvd  C + y   +rfC  C  + ++ef  e+ 
  gi|118430950|ref|NP_147076.2| 50 SYCSGCGRLGCVD--CLVQYdpVRRFCRDCLARGASEFKPEAL 90
                                   68**********9..999985569************9977655 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   3.1   0.00071       3.2       5      27 ..       3      24 ..       1      25 [. 0.90
   2 !    8.5   1.6   0.00051       2.3      18      29 ..      32      43 ..      30      48 .. 0.86
   3 !   16.6   6.8   1.4e-06    0.0063       3      31 ..      37      65 ..      35      68 .. 0.91
   4 ?    2.1   0.3     0.048   2.1e+02      14      21 ..      70      77 ..      66      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00071
                       zf-B_box  5 kCpeHknkpatlfCedCqqplCe 27
                                    C  +  ++a+  C+ C+ p+C+
  gi|118430950|ref|NP_147076.2|  3 ECYFCL-SKASHSCRLCGRPVCD 24
                                   699999.9**************7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00051
                       zf-B_box 18 CedCqqplCeeC 29
                                   C  C++ +C+ C
  gi|118430950|ref|NP_147076.2| 32 CVACREAICAVC 43
                                   ************ PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.4e-06
                       zf-B_box  3 etkCpeHknkpatlfCedCqqplCeeCst 31
                                   e +C  ++++ a  +C  C+ + C +C++
  gi|118430950|ref|NP_147076.2| 37 EAICAVCGRELAVSYCSGCGRLGCVDCLV 65
                                   789************************55 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.048
                       zf-B_box 14 atlfCedC 21
                                    + fC+dC
  gi|118430950|ref|NP_147076.2| 70 VRRFCRDC 77
                                   66789998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  16.7      0.05   2.2e+02       4      49 .]       4      56 ..       2      56 .. 0.82
   2 ?    9.5   7.5   0.00022      0.99      13      48 ..      38      77 ..      36      78 .. 0.81
   3 ?    9.7   0.4   0.00019      0.86       1      20 [.      60      79 ..      60      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.05
                            DZR  4 CgeelppdarfCseCgtklkavaa.........edrCpsCgekvdpearfCpeCG 49
                                   C   l++ ++ C  Cg ++  +           e  C  Cg+++     +C  CG
  gi|118430950|ref|NP_147076.2|  4 CYFCLSKASHSCRLCGRPVCDTHGgggvcvacrEAICAVCGRELAVS--YCSGCG 56
                                   6777788999*********9666699999999899999999987765..888887 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00022
                            DZR 13 rfCseCgtklkavaa.....edrCpsCgekvdpearfCpeC 48
                                     C  Cg +l  v+         C+ C  + dp  rfC  C
  gi|118430950|ref|NP_147076.2| 38 AICAVCGRELA-VSYcsgcgRLGCVDCLVQYDPVRRFCRDC 77
                                   57888888885.33357888888****************99 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00019
                            DZR  1 CpqCgeelppdarfCseCgt 20
                                   C  C  + +p  rfC +C +
  gi|118430950|ref|NP_147076.2| 60 CVDCLVQYDPVRRFCRDCLA 79
                                   77788888888888888865 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.7    0.0043        19      19      55 ..      13      46 ..       3      48 .. 0.72
   2 ?    6.0   4.1    0.0031        14      40      57 ..      51      68 ..      45      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0043
                            IBR 19 kwCprpdCeaiieksegcksvtCskCgfefCfnCkke 55
                                     C    C++++ +++g +   C  C++++C  C++e
  gi|118430950|ref|NP_147076.2| 13 HSCR--LCGRPVCDTHGGGG-VCVACREAICAVCGRE 46
                                   4565..67766666777444.5999*********976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0031
                            IBR 40 tCskCgfefCfnCkkewH 57
                                    Cs Cg   C++C++++ 
  gi|118430950|ref|NP_147076.2| 51 YCSGCGRLGCVDCLVQYD 68
                                   4*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 694.08
//
Query:       gi|14600560|ref|NP_147077.1|  [L=148]
Description: hypothetical protein APE_0243 [Aeropyrum pernix K1]
Scores for 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   18.3   0.2     0.0057   16.4   0.1    1.7  2  Redoxin        Redoxin
     0.0029   17.6   0.1     0.0072   16.3   0.1    1.6  1  Thioredoxin    Thioredoxin
  ------ inclusion threshold ------
      0.013   15.8   0.1        1.6    9.1   0.2    2.3  2  Thioredoxin_8  Thioredoxin-like
      0.033   14.4   0.4      0.064   13.4   0.2    1.4  1  Thioredoxin_4  Thioredoxin
      0.035   14.6   0.0      0.047   14.1   0.0    1.2  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.6e-06    0.0057      16      93 ..      29     108 ..      19     114 .. 0.72
   2 ?    1.4   0.0     0.067   2.4e+02     114     136 ..     106     129 ..      86     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                   TCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHH..HHHHHHHTT-TSEEEE-T CS
                       Redoxin  16 tdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndaf..vkefwgkeglkfpvlsDg 93 
                                    dg +++ +e+ +++ vv+ +  a cP C+ + +  le +++  +++ v++v+v +d  ++   ++++++  +++++ +++
  gi|14600560|ref|NP_147077.1|  29 VDGGALDPKELGDGV-VVVYFDNALCPACRLQDRyWLEVVSKYSGDSRVKFVVVLCDWFSQncSSKAAAESFNHYRIGASP 108
                                   678888888886666.66666666**********55555599999*******99888655566666666655566666555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.067
                                   EE-EEEEE.EETTEEEEEEESSSC CS
                       Redoxin 114 rtpryavi.dedgkvvylevepep 136
                                   ++p+ av+ +++g vvy+e+ +  
  gi|14600560|ref|NP_147077.1| 106 ASPTIAVFaVKNGEVVYKEYLEGV 129
                                   6777777648999****9987655 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     2e-06    0.0072      19      98 ..      42     136 ..      37     141 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2e-06
                                   SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT..TSEEEEEETT.........TSHHHHHHTT-SSSSEEEEE..ETTE..E CS
                   Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkd..kvklakvdvd.........enedlakkyevegiPtlklf..kngk..e 84 
                                     v+v F    C+ C+     + ++ +++++  +vk++ v +d         + ++  ++y + + Pt+ +f  kng+  +
  gi|14600560|ref|NP_147077.1|  42 GVVVVYFDNALCPACRLQDRYWLEVVSKYSGdsRVKFVVVLCDwfsqncsskAAAESFNHYRIGASPTIAVFavKNGEvvY 122
                                   6799***************************99677766655511111111133445567899999**9987447888755 PP

                                   EEEEESS-HHHHHH CS
                   Thioredoxin  85 vkkyegarekekla 98 
                                    + +eg r+ + ++
  gi|14600560|ref|NP_147077.1| 123 KEYLEGVRPSNIIQ 136
                                   55567777755555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2   0.00044       1.6       3      44 ..      43      84 ..      41      92 .. 0.90
   2 ?    5.1   0.0    0.0079        28      61      95 .]      85     120 ..      83     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                                  EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S CS
                 Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsld 44
                                  vv++yf +  cp c+   +   e+ +k++ + +v++v v +d
  gi|14600560|ref|NP_147077.1| 43 VVVVYFDNALCPACRLQDRYWLEVVSKYSGDSRVKFVVVLCD 84
                                  89**************************98999999999877 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0079
                                   SEE.EE-TT-HHHHTT-S--TT-SEEEEE-.TT-BE CS
                 Thioredoxin_8  61 wlsvpfddkkrnklkkkynvkaiPtlvvld.kngev 95 
                                   w s   ++k   +  ++y++ a Pt+ v   kngev
  gi|14600560|ref|NP_147077.1|  85 WFSQNCSSKAAAESFNHYRIGASPTIAVFAvKNGEV 120
                                   777777888889999***************999997 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.8e-05     0.064      15      55 ..      43      83 ..      40     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                  EEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTT..SEEEEEEE- CS
                 Thioredoxin_4 15 vtvieyedlrCphCakfeeeveklleeyidtG..kvkfiirdf 55
                                  v+v+ + +  Cp C+  ++  ++++++y  +G  +vkf++   
  gi|14600560|ref|NP_147077.1| 43 VVVVYFDNALCPACRLQDRYWLEVVSKY--SGdsRVKFVVVLC 83
                                  78999999********************..5545999998666 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.047       7      92 ..      43     120 ..      37     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                 Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv.f 86 
                                    v+v+f+   Cp C++  +   e+  v +      ++ ++  k+v + c+   + +    ++  e  + y++ + Pti  f
  gi|14600560|ref|NP_147077.1|  43 VVVVYFDNALCPACRLQDRYWLEV--VSK------YSGDSRVKFVVVLCDWFSQ-NCSS-KAAAESFNHYRIGASPTIAvF 113
                                   578999999*******88877777..544......59999**********9995.5655.7888888899*******7725 PP

                 Thioredoxin_2  87 ldgk.ei 92 
                                     ++ e+
  gi|14600560|ref|NP_147077.1| 114 AVKNgEV 120
                                   4444533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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:                         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: 1069.68
//
Query:       gi|118430951|ref|NP_147078.2|  [L=203]
Description: glutamine amidotransferase subunit PdxT [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-50  170.0   0.0    5.4e-50  169.9   0.0    1.0  1  SNO            SNO glutamine amidotransferase family
    9.7e-09   35.3   0.0    1.4e-08   34.7   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    3.9e-08   33.1   0.0    4.7e-08   32.9   0.0    1.1  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    2.4e-06   27.3   0.0    3.3e-06   26.9   0.0    1.1  1  Peptidase_S51  Peptidase family S51
  ------ inclusion threshold ------
      0.083   12.7   0.2       0.13   12.1   0.2    1.3  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.0   1.5e-53   5.4e-50       1     186 [.       5     201 ..       5     203 .] 0.90

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 1.5e-53
                                    EESSSSSHHHHHHHHHHTTSEE......EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEE CS
                            SNO   1 vlalqGaveehveaikkclaen......ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlGt 74 
                                    vl+ qG v ehv  ++++           +vk++edl+++d++iiPGGest+++ l++r g++e+l+e v n+ ++ +Gt
  gi|118430951|ref|NP_147078.2|   5 VLGYQGGVYEHVYMLRRTFDRLgvhgeaVVVKKPEDLKGLDGVIIPGGESTTIGILAKRLGVLEPLREQVLNG-LPAMGT 83 
                                    89**********99998764434444559********************************************.****** PP

                                    THHHHHHCCEETTB.....SS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEE CS
                            SNO  75 CaGlillskelene.....lvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlye 149
                                    CaG i+l+ ++  +       + l+++ v+v rn fGrq +sfe++l++++l+  f +vfir+P i  + ++  + +  +
  gi|118430951|ref|NP_147078.2|  84 CAGAIILAGKVRDKvvgekSQPLLGVMRVEVVRNFFGRQRESFEADLEIEGLDGRFRGVFIRSPAITAAESPARIISWLD 163
                                    ********888766555456778********************************************************* PP

                                    CTT.EEEEEE.ETTEEEESS-GGGSTTHCHHHHHHHHHH CS
                            SNO 150 ldg.eivvak.qkkilatsfhPelaeddirvhdyfveev 186
                                     +g ++ va+ q+ +latsfhPel+ d +r+h+++++ v
  gi|118430951|ref|NP_147078.2| 164 YNGqRVGVAAvQGPLLATSFHPELTGD-TRLHELWLRLV 201
                                    ***65655557**************99.*****999865 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.9e-12   1.4e-08      11     178 ..      17     192 ..      12     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.9e-12
                                    HHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCT...STS-EEEETHHHHHHH CS
                         GATase  11 enlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikeare...nkiPiLGICLGmQlla 85 
                                    ++l + + +lgv  e v ++++  e    lk+ dg++++gG  +      + + +++ +re   n++P +G C G  +la
  gi|118430951|ref|NP_147078.2|  17 YMLRRTFDRLGVHGEAVVVKKP--ED---LKGLDGVIIPGGESTTIgiLAKRLGVLEPLREqvlNGLPAMGTCAGAIILA 91 
                                    5666666666666666666642..33...689*********988878966666666666666669*************** PP

                                    HHTTTEEEEEECEEEEEEEEEEEETTT............CGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEE CS
                         GATase  86 iefgrkvvkekekehhggtmrlgddet............allyglknevierhrHryevnpkelepaglevtakseddee 153
                                     ++  kvv ek  + + g mr++  ++             +++gl+ +++  +  + +++     ++  +++ + + +++
  gi|118430951|ref|NP_147078.2|  92 GKVRDKVVGEK-SQPLLGVMRVEVVRNffgrqresfeadLEIEGLDGRFRGVFIRSPAITA---AESPARIISWLDYNGQ 167
                                    ********999.6677778999997789999999988887888888888888888888887...5555666666666679 PP

                                    EEEEEEETTTEEEESSBTTSTTSTT CS
                         GATase 154 lmeiiekknpfvgvQFHPEststpe 178
                                    ++++   + p+ ++ FHPE t  ++
  gi|118430951|ref|NP_147078.2| 168 RVGVAAVQGPLLATSFHPELTGDTR 192
                                    ********************98776 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 !   32.9   0.0   1.3e-11   4.7e-08      29     147 ..      34     147 ..      13     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.3e-11
                       GATase_3  29 fvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeagevegl 108
                                    +v+ k e+l+  +d vi+pGg++t+  + ++r  g+ e ++e + +g p +g C+G ++L  +++d+      +++ + l
  gi|118430951|ref|NP_147078.2|  34 VVK-KPEDLKG-LDGVIIPGGESTTIGILAKRL-GVLEPLREQVLNGLPAMGTCAGAIILAGKVRDKVV---GEKSQPLL 107
                                    445.7799965.*************99999998.******************************99764...45689999 PP

                       GATase_3 109 glLdietefek.ekltgqvegevelaaegeevkGyEiHsG 147
                                    g++ +e++ +   ++ ++ e+++e +  + +++G  i+s 
  gi|118430951|ref|NP_147078.2| 108 GVMRVEVVRNFfGRQRESFEADLEIEGLDGRFRGVFIRSP 147
                                    **99999866544555555555444433455666555555 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   9.1e-10   3.3e-06      74     134 ..      39      95 ..      12     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 9.1e-10
                                    HHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-G CS
                  Peptidase_S51  74 eeieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesie 134
                                    e+++      d++++ GG+   +  l k+ g+ ++lre+v +gl+ +G+ AGai+ + +++
  gi|118430951|ref|NP_147078.2|  39 EDLK----GLDGVIIPGGESTTIGILAKRLGVLEPLREQVLNGLPAMGTCAGAIILAGKVR 95 
                                    4444....49********************************************9887665 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   3.5e-05      0.13      61     108 ..      43      91 ..      26     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                                    G-SEEEE--BHHHH.HHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHH CS
                      DJ-1_PfpI  61 eyDalvlpGGragp.erlrenekvvelvkefaekgklvaaICagpqlLa 108
                                      D +++pGG++     l++   v+e ++e++ +g +    Cag+++La
  gi|118430951|ref|NP_147078.2|  43 GLDGVIIPGGESTTiGILAKRLGVLEPLREQVLNGLPAMGTCAGAIILA 91 
                                    579*******9965245777779************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1492.91
//
Query:       gi|118430952|ref|NP_147079.2|  [L=353]
Description: pyridoxal biosynthesis lyase PdxS [Aeropyrum pernix K1]
Scores for complete 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-96  322.4   3.2    1.9e-96  321.8   3.2    1.3  1  SOR_SNZ         SOR/SNZ family
      3e-05   23.4   0.5      3e-05   23.4   0.5    2.5  2  ThiG            Thiazole biosynthesis protein ThiG
     0.0011   18.5   0.8       0.34   10.3   0.1    3.2  2  His_biosynth    Histidine biosynthesis protein
     0.0029   16.7   0.7        0.4    9.7   0.1    2.5  2  Dus             Dihydrouridine synthase (Dus)
     0.0086   15.5   0.1     0.0086   15.5   0.1    2.2  2  NMO             Nitronate monooxygenase
     0.0092   15.2   0.3        0.5    9.5   0.0    2.4  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
  ------ inclusion threshold ------
      0.023   13.9   0.0        1.1    8.4   0.0    2.3  2  IGPS            Indole-3-glycerol phosphate synthase
      0.037   14.6   0.0      0.083   13.4   0.0    1.5  1  Peptidase_S66C  LD-carboxypeptidase C-terminal domain
      0.042   13.9   0.0      0.091   12.8   0.0    1.5  1  TetR_C_27       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.8   3.2  9.8e-100   1.9e-96       2     207 .]      62     267 ..      61     267 .. 0.99

  Alignments for each domain:
  == domain 1  score: 321.8 bits;  conditional E-value: 9.8e-100
                                    THHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEETT- CS
                        SOR_SNZ   2 lkvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvriGh 81 
                                    ++vk g+   +kgGv+mdv+n+eqa iae+aGavavm+l+++p d+rk+ggvarm+d+k+i++++++++ipvmakvriGh
  gi|118430952|ref|NP_147079.2|  62 VAVKLGFPIYQKGGVVMDVTNVEQAGIAEDAGAVAVMVLDKLPYDVRKAGGVARMADVKVIEQVMSSITIPVMAKVRIGH 141
                                    57999*************************************************************************** PP

                                    HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHHHHHHH CS
                        SOR_SNZ  82 fveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveavrhvrk 161
                                    + ea ile++gvd+iDesevltp+de++hi+k+ fkvpfv+Gar+l+ealrriaeGa+mirtkGeagtG+v+eavrh++ 
  gi|118430952|ref|NP_147079.2| 142 YYEAMILESIGVDMIDESEVLTPVDEKHHINKWLFKVPFVNGARSLAEALRRIAEGASMIRTKGEAGTGNVAEAVRHMKL 221
                                    ******************************************************************************** PP

                                    HHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHHHHHTTS-S---T. CS
                        SOR_SNZ 162 ikeeirklkslseeelvalakelkaplelvkevaelgrlpvvnfaa 207
                                    i+ +i +l+ ls ee  ++a+e+ +p +lv  +a+lgrlpvvnfaa
  gi|118430952|ref|NP_147079.2| 222 IMGDIWRLRGLSAEERLRVAREYGVPHQLVDLTARLGRLPVVNFAA 267
                                    ********************************************98 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   1.3     0.066   1.3e+02     141     200 ..      90     155 ..      70     165 .. 0.72
   2 !   23.4   0.5   1.5e-08     3e-05     171     225 ..     254     311 ..     244     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.066
                                    HHTT-SEBEEBSS...STTS----S...-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SE CS
                           ThiG 141 eevGcaavmPlaa...piGsglGll...nkealkiiieeakvPvivDAGigspsdaaqamelGada 200
                                    e++G+ avm l      +  + G++   + ++++ +++++++Pv+    ig+  +a+    +G+d 
  gi|118430952|ref|NP_147079.2|  90 EDAGAVAVMVLDKlpyDVRKAGGVArmaDVKVIEQVMSSITIPVMAKVRIGHYYEAMILESIGVDM 155
                                    78888888866432113444555550004556666778889******9***999999988888885 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.5e-08
                                    HHH-.SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                           ThiG 171 ieea.kvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                    ++++ ++Pv+  A  Gi +p daa  m lGad+v++ + + +++dp + A+a+ la++
  gi|118430952|ref|NP_147079.2| 254 TARLgRLPVVNFAagGIATPADAALMMWLGADGVFVGSGIFKSSDPSERAAAIVLATS 311
                                    5555578888544349*************************************99975 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.11   2.1e+02     186     210 ..      99     123 ..      62     145 .. 0.75
   2 !   10.3   0.1   0.00017      0.34      77     132 ..     288     339 ..     248     353 .] 0.66

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                                    HHHHHSSEEEEESS--SHHHHHHHH CS
                   His_biosynth 186 laeavkipviasGGvgsledlkelk 210
                                    + +++   v  +GGv++++d+k ++
  gi|118430952|ref|NP_147079.2|  99 VLDKLPYDVRKAGGVARMADVKVIE 123
                                    5556666677788888888887665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                                    EEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE CS
                   His_biosynth  77 qvGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr 132
                                     vG+GI + +d     +  a  ++++t++ ++pe + e+ + + + k +++iD+r+
  gi|118430952|ref|NP_147079.2| 288 FVGSGIFKSSDP----SERAAAIVLATSMWDDPEAVAEAQRMVSEAKSMMGIDIRK 339
                                    344444444322....2234567888888888888888888888888888888776 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0    0.0054        11     141     189 ..      83     136 ..      49     202 .. 0.77
   2 !    9.7   0.1    0.0002       0.4     182     219 ..     260     296 ..     252     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0054
                                    HHHHHHHHHCT-SEEEEESS....ECCCTT-C.G--CHHHHHHHHH-SS-EEEE CS
                            Dus 141 lelakiveaaGaqaltvHgR....traqnyeg.tadweaIkevkqavsipviaN 189
                                    +e a i+e+aGa a++v       +r+ +  +  ad + I++v  +++ipv+a 
  gi|118430952|ref|NP_147079.2|  83 VEQAGIAEDAGAVAVMVLDKlpydVRKAGGVArMADVKVIEQVMSSITIPVMAK 136
                                    566667777777777777776666555555555677777777777777777764 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0002
                                    -SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCS CS
                            Dus 182 vsipviaNGdIkdaedaqaileetGadgvmigrgalgn 219
                                    ++++ +a G+I ++ da  +++  Gadgv +g g  + 
  gi|118430952|ref|NP_147079.2| 260 LPVVNFAAGGIATPADAALMMWL-GADGVFVGSGIFKS 296
                                    56777899**************9.********997654 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.9     0.074   1.5e+02     142     198 ..      79     135 ..      72     139 .. 0.68
   2 !   15.5   0.1   4.3e-06    0.0086     182     230 ..     248     298 ..     237     316 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.074
                            NMO 142 tissvkearkvearGaDaliv......qGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                     ++ v++a ++e +Ga a+ v      +  +aGG            +++++qv++ + iPv+A
  gi|118430952|ref|NP_147079.2|  79 DVTNVEQAGIAEDAGAVAVMVldklpyDVRKAGGVAR------MADVKVIEQVMSSITIPVMA 135
                                    5677888888888885554441111114455666555......34689**************9 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.3e-06
                            NMO 182 faLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                    ++Lv+  +    +Pv+  AaGGi +  + a ++ lGA gv +g+     ++
  gi|118430952|ref|NP_147079.2| 248 HQLVDLTARLGRLPVVnfAAGGIATPADAALMMWLGADGVFVGSGIFKSSD 298
                                    677777777778999777*************************98776665 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.018        37      98     177 ..      79     163 ..      68     178 .. 0.62
   2 !    9.5   0.0   0.00025       0.5     147     179 ..     264     296 ..     248     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.018
                                    E-SSHHHHHHHHHTT-SEEE.-TTTTSSTTS-....SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE CS
                           NanE  98 DistleeglvakklGvdivG.ttlsGytkeeek...aepDfalvkalsea.glkviaeGrintPekakkaieiGvdavvv 172
                                    D+ ++e++ +a+++G+  v       y  ++        D++++++++++  + v+a  ri    +a     iGvd++  
  gi|118430952|ref|NP_147079.2|  79 DVTNVEQAGIAEDAGAVAVMvLDKLPYDVRKAGgvaRMADVKVIEQVMSSiTIPVMAKVRIGHYYEAMILESIGVDMIDE 158
                                    66666666666666643332022223333222234467888888886654267799999999999999888899888765 PP

                                    -HHHH CS
                           NanE 173 Gsait 177
                                       +t
  gi|118430952|ref|NP_147079.2| 159 SEVLT 163
                                    55555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00025
                                    EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                           NanE 147 viaeGrintPekakkaieiGvdavvvGsaitrl 179
                                      a G i tP+ a+ ++ +G+d v vGs i + 
  gi|118430952|ref|NP_147079.2| 264 NFAAGGIATPADAALMMWLGADGVFVGSGIFKS 296
                                    568999**********************99765 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.02        41      61      89 ..      73     101 ..      50     138 .. 0.89
   2 ?    8.4   0.0   0.00055       1.1     210     250 ..     262     302 ..     248     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.02
                                    TEESBSS--HHHHHHHHTTT.-SEEEEE- CS
                           IGPS  61 kgliredfdpaeiAkkyeeagAsaiSVLt 89 
                                    kg + +d+  +e+A   e+agA a+ VL 
  gi|118430952|ref|NP_147079.2|  73 KGGVVMDVTNVEQAGIAEDAGAVAVMVLD 101
                                    89999*********************996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00055
                                    SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHH CS
                           IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedveka 250
                                    v+  a  Gi+t++d+  +   g++++ vG+ + +++d ++ 
  gi|118430952|ref|NP_147079.2| 262 VVNFAAGGIATPADAALMMWLGADGVFVGSGIFKSSDPSER 302
                                    6777999***************************9998765 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.2e-05     0.083      47     116 ..      80     148 ..      75     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.2e-05
                                    HHHHCTSTTGGG--EEEEEE--..G......CC...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS---E CS
                 Peptidase_S66C  47 LtqlkeagvldkvkGivlGrftkpeek...eeeeekeeykealeevlaeiledlkiPvlynldiGHtspnltl 116
                                    +t+ ++ag+ +++ ++++   +k +++   +  +++    +++e+v+    +  +iPv++++ iGH ++ ++l
  gi|118430952|ref|NP_147079.2|  80 VTNVEQAGIAEDAGAVAVMVLDKLPYDvrkAGGVARMADVKVIEQVM----SSITIPVMAKVRIGHYYEAMIL 148
                                    57889999999999999998887744433344445555556666665....7999***********9988776 PP

>> TetR_C_27  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.5e-05     0.091      61     100 ..     290     329 ..     285     332 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                                    HCT-STT--HHHHHHHHHHHSGGGTSHHHHHHHGGG--HH CS
                      TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaaewsdpeiea 100
                                     +G Fk++dp++ a a++ at++  +P  +ae ++  +ea
  gi|118430952|ref|NP_147079.2| 290 GSGIFKSSDPSERAAAIVLATSMWDDPEAVAEAQRMVSEA 329
                                    689*****************************99877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2598.23
//
Query:       gi|118430953|ref|NP_147080.2|  [L=284]
Description: hypothetical protein APE_0248.1 [Aeropyrum pernix K1]
Scores for 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-86  288.1   0.1    7.7e-86  287.9   0.1    1.0  1  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.9   0.1   4.3e-90   7.7e-86       1     266 []       7     268 ..       7     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 287.9 bits;  conditional E-value: 4.3e-90
                                    EEEEEESSHHHHHHHHHHHTTSS..SGCC.EEEEEE-HHHHHHHHHTT..S-SEEEEEHHHHTTCTTTEEEESEESCEEE CS
                 VitK2_biosynth   1 lrlGhspylNdlflfyaLvegkvdsegle.veivledpetlnralleg..elDvakiSsaayariaddyalLpdlsisal 77 
                                    l+++h+p+++d+f+fy++v+g+v+ +g++ v++v+ed+etlnr+l+e+  ++D +++S++aya+i d+y+lL+  +++++
  gi|118430953|ref|NP_147080.2|   7 LTIAHTPDADDAFMFYGIVAGAVEIRGFRgVRHVIEDIETLNRWLVEEgrDVDASAVSAHAYAYIVDRYFLLR--TGASM 84 
                                    689***********************9988****************97224666*******************..***** PP

                                    ESSSSEEEEESS-CCC-SSS.T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEECCHHH CS
                 VitK2_biosynth  78 GrvygvllvskvpleelegelgkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIgesal 156
                                    G++yg+++vsk++ ++leg+   r+a+pg++tT+ l+l ++l++r+    + v+++fdei+a+v +g+ dagLlI+e+++
  gi|118430953|ref|NP_147080.2|  85 GEGYGPVVVSKSESVRLEGS---RIAVPGRYTTAGLILTIALRGRF----TPVYARFDEIPAMVEDGRvDAGLLIHEEQI 157
                                    **********9977777766...**********************9....****************************** PP

                                    TGGGGTTEEEEEHHHHHHHHH.SS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHH CS
                 VitK2_biosynth 157 tyaeeglkkvlDLgelWeelt.glPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqemddevle 235
                                    +y+++gl++vlDL+++W + t glP++lg+ v +r+l++ aa+++ +alr S+eya++h+de+++ya+++++++d+e ++
  gi|118430953|ref|NP_147080.2| 158 AYSRRGLTVVLDLWDWWARVTgGLPMPLGVDVFSRRLGRGAAEAFRDALRLSIEYAYQHFDEALDYAMRYSRVKDRELVA 237
                                    *********************77********************************************************* PP

                                    HHHHHHCSHHHHS-CHHHHHHHHHHHHHHHC CS
                 VitK2_biosynth 236 khlelYvnelsydlgeegragleeflelaae 266
                                    +++++Yvne ++d+g++g ++ +++++la+e
  gi|118430953|ref|NP_147080.2| 238 RFIKMYVNERTMDMGDDGVEAHRTLYRLARE 268
                                    ****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2022.30
//
Query:       gi|118430954|ref|NP_147081.2|  [L=382]
Description: hypothetical protein APE_0249.1 [Aeropyrum pernix K1]
Scores for 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   65.0   0.0    1.5e-17   64.4   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.21   11.7   0.0       0.47   10.6   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   1.7e-21   1.5e-17       2     164 ..      78     250 ..      77     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.7e-21
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEESSTGGGSTTHHHHHHHHHHTC..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg..vkevilgggepllypdfvellerlakla..... 74 
                                    + t+ C  +C+fC+++++  +++ ++ l  +e +++v e+ ++k     ++++gg +p    +++e+++r++k +     
  gi|118430954|ref|NP_147081.2|  78 NYTNICVVGCTFCSFYRK-PKHPEAYKLEAREAAAQVVEA-WRKYriRQVLFQGGVDPAIPIEYYEEAFRAIKSEtggev 155
                                    6799************96.888888899999999999888.888885667777899***********************9 PP

                                    ....CCTEEEEEEECSSCHG.HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEE CS
                                    ....xxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 ....vpgiritvetngtlpd.eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvd 147
                                         + ++i   +   + +  e++erl+++g   +   g+e+++d+ v++++   + + + +++++e++ e+g++ ++ 
  gi|118430954|ref|NP_147081.2| 156 aihgLSVVEIEWLSKVSRMSvGEVVERLRDAGmDSVPGAGAEILSDR-VRRIISpLKSSADTWIRTMETIMEKGLP-ISA 233
                                    999988888888888888889***********7777799*******9.*******99*******************.*** PP

                                    EEEEBTTTSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                    Radical_SAM 148 rivglpGendeeleell 164
                                    ++v ++ e+ ee+ e+l
  gi|118430954|ref|NP_147081.2| 234 TMVYGHVETLEERAEHL 250
                                    ************99876 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 ?   10.6   0.0   5.2e-05      0.47       5      72 ..      80     138 ..      76     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.2e-05
                        Fer4_14   5 lsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGG.ePLhyenkkellklvk 72 
                                    ++ C + C++C   ++ ++ e+ k +++e   q+++   k++i  +++ + GG +P ++         ++
  gi|118430954|ref|NP_147081.2|  80 TNICVVGCTFCSfYRKPKHPEAYKLEAREAAAQVVEAWRKYRI--RQVLFQGGvDPAIP---------IE 138
                                    688********855556778999999999999***77777777..56999998677766.........44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 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:                        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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2765.50
//
Query:       gi|14600565|ref|NP_147082.1|  [L=392]
Description: hypothetical protein APE_0252 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-15   56.2   0.1    1.1e-14   55.2   0.1    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1     6e-19   1.1e-14       4     155 ..      74     236 ..      72     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 6e-19
                                   ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTC......... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                   Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakla......... 74 
                                   t+ C  rC+fC+++   +r+  g++ ++e + + +  ++++ g  ++ ++gg +p l  +++e++ r++k+          
  gi|14600565|ref|NP_147082.1|  74 TNVCVTRCTFCDFYVPPERRSSGYTHPPEHLGRVAGLARKRLGvREVHMVGGNDPELPLEYYEEAIREIKRVapgvvlkaf 154
                                   789************99**************************77777778889999999999999999999********9 PP

                                   .CCTEEEEEEECSSCHGHHHHHHHHHTT-SEE.EEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                   .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  75 .vpgiritvetngtlpdeeklerllelgvdrv.slgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivgl 152
                                     ++i +   + g +p +e+l+r++e+g+d +   g+e +++e v+k++   + + +e+le  +++++ gi+++++ ++ +
  gi|14600565|ref|NP_147082.1| 155 tAEEIGFIAKATGNTP-KEVLARFREAGLDALpGGGAEVLSEE-VRKRIApLKISSDEYLEIHRLAHSMGIRSNITLLYAH 233
                                   9999999999999999.***********666516677777777.*******99*******************655555554 PP

                                   TTT CS
                                   xxx RF
                   Radical_SAM 153 pGe 155
                                     e
  gi|14600565|ref|NP_147082.1| 234 IEE 236
                                   433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3042.34
//
Query:       gi|14600566|ref|NP_147083.1|  [L=235]
Description: hypothetical protein APE_0254 [Aeropyrum pernix K1]
Scores for complete 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-07   31.4   0.0    1.8e-07   31.0   0.0    1.1  1  VitK2_biosynth  Menaquinone biosynthesis
  ------ inclusion threshold ------
      0.092   12.5   0.3       0.23   11.2   0.0    1.8  3  IL13            Interleukin-13


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0     2e-11   1.8e-07      25     192 ..      19     179 ..      10     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2e-11
                                   .S.GCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC-SSS.T.EEEE CS
                VitK2_biosynth  25 se.gleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvpleelegelgkrval 104
                                   ++ + + ++v  +p +  +al+eg++  a+i+ a+         + p+  + +l   ++v + s  ++ +l++   + va+
  gi|14600566|ref|NP_147083.1|  19 EAlSRGLTVVELQPPEAYDALVEGRVRAALIPLALARG----AKICPGPMVWSLSATMSVAIYS-FSVRRLDDC--AAVAV 92 
                                   44445688889999999999999999999999876544....5677777**************9.335666655..8**** PP

                                   STTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEECCHHHTGGGGTTEEEEEHHHHHHHHHSS-EEEE CS
                VitK2_biosynth 105 pgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIgesaltyaeeglkkvlDLgelWeeltglPlvlg 184
                                   +ges+Ts + lr + ++  +++ ++v+++   +  + l ++ d +Ll g++al+ + + l+ + DLg+l ++  g   v++
  gi|14600566|ref|NP_147083.1|  93 SGESRTSLVYLREVREKL-QAPWSIVQAERGCVTLECLLSRaDCALLLGDEALRARTR-LPPIEDLGRLVKRVLGISPVYA 171
                                   ************966666.7888****995556666555555***********97765.****************9999*9 PP

                                   EEEEECCC CS
                VitK2_biosynth 185 lwvvrrdl 192
                                   + +  +d 
  gi|14600566|ref|NP_147083.1| 172 VTASIEDC 179
                                   99876665 PP

>> IL13  Interleukin-13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.6e-05      0.23      38      78 ..      51      90 ..      38     111 .. 0.81
   2 ?   -3.2   0.1      0.75   6.7e+03      58      76 ..     118     136 ..     113     138 .. 0.73
   3 ?   -3.2   0.0      0.73   6.5e+03      11      32 ..     178     199 ..     172     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.6e-05
                                  HHHSTSS-CGTC-EEE---SSSSHHHHHHHHHTTSTS-GGG CS
                          IL13 38 itqnqkasLCngsmvWsvnltaevycaaleslinvsdCsai 78
                                  ++  + a++C g mvWs+  t++v   +  s+  + dC a+
  gi|14600566|ref|NP_147083.1| 51 LALARGAKICPGPMVWSLSATMSVAIYSF-SVRRLDDCAAV 90
                                  55667789************999876665.45567888776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.75
                                   SSSHHHHHHHHHTTSTS-G CS
                          IL13  58 taevycaaleslinvsdCs 76 
                                   +ae  c+ le l + +dC 
  gi|14600566|ref|NP_147083.1| 118 QAERGCVTLECLLSRADCA 136
                                   5677788888888888885 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.73
                                   XXXXXXXXXXSS-CHHHHHHHH CS
                          IL13  11 tClgglaspgpvprskalkeLi 32 
                                   +C +gl   +p  r ++++eL 
  gi|14600566|ref|NP_147083.1| 178 DCPSGLPRGEPAVRRRHIEELC 199
                                   5778888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1747.93
//
Query:       gi|118430955|ref|NP_147084.2|  [L=250]
Description: sugar-phosphate nucleotidyl transferase [Aeropyrum pernix K1]
Scores for complete 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-28   98.5   0.0    4.9e-28   98.4   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
      1e-14   55.2   0.0    1.3e-14   54.9   0.0    1.2  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 !   98.4   0.0   5.5e-32   4.9e-28       2     245 ..       7     237 ..       6     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 5.5e-32
                                    EEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEE CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevliale 80 
                                    a+ILaGG+G R++P t  ++k+++p + +e +l++++++ la +g+e+ iv l  ++   + +++++g+k+gv++ +++ 
  gi|118430955|ref|NP_147084.2|   7 ALILAGGKGRRFRPYTDLIPKPMIPLGRSEkPLLEYVVKMLALQGVEN-IVLLVGYKWRYIYNYFGRGEKLGVKIDYSID 85 
                                    79**********************************************.77777788888999***************** PP

                                    SS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBE CS
                NTP_transferase  81 pegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrv 159
                                    +e+  gt ++v++a+e  + ++  e +lv  gD++ +  +  +   +++++a    ++++v ++ +   Gv++a+ eg +
  gi|118430955|ref|NP_147084.2|  86 DERYsGTGGSVLKALEEGRVSD--EDFLVWYGDIIAEVGLASMYSLHRQHDA---SATLAVAERYQVPVGVVKAGREGVI 160
                                    99988*********99988777..59**************************...45556667777889*********** PP

                                    EEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHH CS
                NTP_transferase 160 erfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsll 239
                                    e+ +EKP        +  G+ +f +e++ ++a   e l ++ d ++d++p +++++ +a+a++ ++   W DvG+l+ + 
  gi|118430955|ref|NP_147084.2| 161 EDVEEKPWIGV---NVFIGVAIFRKEAFREAA---EGLGTSFDIMGDMMPILVRKS-KAVAYIYDG--PWFDVGSLERYE 231
                                    ********988...4677888**********6...59****************997.556779999..5********998 PP

                                    HHHHHH CS
                NTP_transferase 240 eanekl 245
                                    +  e++
  gi|118430955|ref|NP_147084.2| 232 KLREDV 237
                                    887765 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 !   54.9   0.0   1.4e-18   1.3e-14       1     133 [.       7     151 ..       7     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.4e-18
                                    EEEEEESS-TTTTT.....THHHHCC..CCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCT..S-EEE-T CS
                   NTP_transf_3   1 aviLAGGrSsRmgg.....dKallpl..ggkpllervldalraagvdevvvvggd..eevlaal...arlg..vrvvede 66 
                                    a+iLAGG+++R+       +K+++pl   +kplle+v+++l+ +gv+++v+ +g+  + +++++   ++lg  +++  d+
  gi|118430955|ref|NP_147084.2|   7 ALILAGGKGRRFRPytdliPKPMIPLgrSEKPLLEYVVKMLALQGVENIVLLVGYkwRYIYNYFgrgEKLGvkIDYSIDD 86 
                                    79**********9445689*******88899**********************995557777663334555226678888 PP

                                    TSS-SHHHHHHHHHHH..H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEE CS
                   NTP_transf_3  67 dpgkgplaslaaalra..aadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllf 133
                                    + + g+++s++ al++  + +++ +lv  +D++   +  ++ +   +++++a+++ +++e +++ p+  
  gi|118430955|ref|NP_147084.2|  87 ERYSGTGGSVLKALEEgrV-SDEDFLVWYGDIIA--EVGLASMYSLHRQHDASATLAVAE-RYQVPVGV 151
                                    899************9533.99*********955..667888888888888877777654.55556633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 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:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1971.73
//
Query:       gi|14600568|ref|NP_147085.1|  [L=185]
Description: hypothetical protein APE_0256 [Aeropyrum pernix K1]
Scores for 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-23   80.2   0.0    1.3e-22   79.8   0.0    1.1  1  DUF359    Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.044   13.5   0.0    1.2  1  IspD      2-C-methyl-D-erythritol 4-phosphate cytidylyltransf


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 !   79.8   0.0   1.5e-26   1.3e-22       4     110 ..      59     158 ..      57     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 1.5e-26
                        DUF359   4 nllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEEDLavl 84 
                                   +l +a++ P + +vDgkt+Re      + ++++ +++++v++v+ p+G ++ e++++i++ +e+  +++++V+GEEDL++l
  gi|14600568|ref|NP_147085.1|  59 TLSTAWTGPLILVVDGKTRRE------SWRDMVVPQGFRVHRVRSPPGSLSLEAYTTICKLMEEYGRHVVFVEGEEDLIAL 133
                                   57789999*************......334457899********************************************* PP

                        DUF359  85 paillapegsvvvYGqpdeGvvlvkv 110
                                   +a+ +  + + vvYG p+ G v+v+ 
  gi|14600568|ref|NP_147085.1| 134 AALDCGIDWT-VVYGLPGVGGVVVHR 158
                                   **99998875.9**********9986 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 ?   13.5   0.0   4.9e-06     0.044     142     205 ..      71     132 ..      47     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-06
                                   BEEEEETGTTEEEEEEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT--EEEEE--TTG-- CS
                          IspD 142 lvaetedRegLwaaqtPqgFrvdlllaahakgeqegaeitDdaslvekiGlsvkvVeGeednlK 205
                                   +v + + Re+ +    PqgFrv+ +++     + e   +t   +l+e+ G +v  VeGeed + 
  gi|14600568|ref|NP_147085.1|  71 VVDGKTRRESWRDMVVPQGFRVHRVRSPPGSLSLE--AYTTICKLMEEYGRHVVFVEGEEDLIA 132
                                   5555666777788899*********9988887777..788899****************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1408.44
//
Query:       gi|118430956|ref|NP_147086.2|  [L=72]
Description: DNA-directed RNA polymerase subunit E [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-11   43.5   0.1    3.2e-11   43.2   0.1    1.1  1  Spt4            Spt4/RpoE2 zinc finger
    4.2e-05   23.5   0.7    5.6e-05   23.1   0.7    1.2  1  DZR             Double zinc ribbon
    4.6e-05   22.7   2.5    6.3e-05   22.2   2.5    1.3  1  zf-ribbon_3     zinc-ribbon domain
      7e-05   22.6   1.9    9.7e-05   22.2   1.9    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00013   21.5   3.7     0.0002   21.0   3.7    1.3  1  zinc_ribbon_2   zinc-ribbon domain
     0.0002   20.8   2.0      0.018   14.5   0.2    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
    0.00054   19.6   1.5       0.01   15.5   0.1    2.1  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
     0.0034   17.4   0.2     0.0041   17.1   0.2    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0045   17.0   2.7     0.0073   16.4   2.7    1.3  1  UPF0547         Uncharacterised protein family UPF0547
     0.0049   16.5   0.8       0.38   10.5   0.1    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0062   17.3   0.8     0.0082   16.9   0.8    1.2  1  zinc_ribbon_15  zinc-ribbon family
  ------ inclusion threshold ------
      0.016   14.9   0.3       0.02   14.6   0.3    1.1  1  TackOD1         Thaumarchaeal output domain 1
      0.029   14.8   0.6        1.3    9.4   0.0    2.2  2  zf-IS66         zinc-finger binding domain of transposase IS6
      0.055   13.4   2.8        2.2    8.3   3.0    2.1  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.06   13.3   1.3       0.52   10.3   0.2    2.2  2  YhfH            YhfH-like protein
      0.066   12.9   1.0       0.64    9.7   0.1    2.1  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.078   11.8   0.4      0.091   11.5   0.4    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.08   13.1   4.9        1.6    8.9   5.3    2.1  2  Zn-ribbon_8     Zinc ribbon domain
        0.1   12.4   3.0       0.24   11.2   3.0    1.6  1  Rubredoxin_2    Rubredoxin metal binding domain
       0.13   12.6   2.0       0.24   11.7   2.0    1.4  1  Ribosomal_L32p  Ribosomal L32p protein family
       0.24   11.1   2.0        3.1    7.6   0.1    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.25   11.2   1.7        4.6    7.1   0.1    2.2  2  zf-HYPF         HypF finger
       0.34   10.5   2.4        6.7    6.4   0.4    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.38   11.1   3.4        4.8    7.5   3.4    2.1  1  zinc_ribbon_9   zinc-ribbon
       0.54   10.2   4.0        1.8    8.6   0.4    2.3  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.6    8.4   7.6       0.64    9.7   0.5    2.3  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        1.9    8.5   5.5        2.6    8.0   0.4    2.3  2  zinc_ribbon_4   zinc-ribbon 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 !   43.2   0.1   4.8e-14   3.2e-11       3      68 ..       9      60 ..       7      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4.8e-14
                           Spt4  3 ACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkv 68
                                   AC++C+++++  +   + Cp C           +s++++e+++G+++i+dpe+S +A+ + ++k v
  gi|118430956|ref|NP_147086.2|  9 ACKNCGTLVPRGS---KVCPEC-----------GSTQFTENWSGMLVIIDPENSAIARELGIEKPV 60
                                   9**********99...******...........**************************8777765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.7   8.4e-08   5.6e-05       1      21 [.      10      30 ..       5      39 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8.4e-08
                            DZR  1 CpqCgeelppdarfCseCgtk 21
                                   C++Cg+ +p ++++C+eCg++
  gi|118430956|ref|NP_147086.2| 10 CKNCGTLVPRGSKVCPECGST 30
                                   888888888888888888875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   2.5   9.5e-08   6.3e-05       3      24 ..       8      29 ..       6      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.5e-08
                    zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGt 24
                                   v C nCG+++  + +vCp CG+
  gi|118430956|ref|NP_147086.2|  8 VACKNCGTLVPRGSKVCPECGS 29
                                   78******99***********6 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 !   22.2   1.9   1.5e-07   9.7e-05      14      36 ..      10      32 ..       4      33 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                        DUF35_N 14 CpdCGtvqfPPr.avCphCgsddl 36
                                   C++CGt+ +P+   vCp Cgs+++
  gi|118430956|ref|NP_147086.2| 10 CKNCGTL-VPRGsKVCPECGSTQF 32
                                   *******.7************998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   3.7     3e-07    0.0002       2      21 ..      10      29 ..       9      30 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                  zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                   C+nCG+ ++ ++k Cp+CG+
  gi|118430956|ref|NP_147086.2| 10 CKNCGTLVPRGSKVCPECGS 29
                                   *******************6 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.011       7.6      22      29 ..      10      17 ..       3      21 .. 0.73
   2 !   14.5   0.2   2.8e-05     0.018       2      14 ..      23      35 ..      22      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                                   ESSSSBEE CS
                   TF_Zn_Ribbon 22 CtdCGlVl 29
                                   C++CG+++
  gi|118430956|ref|NP_147086.2| 10 CKNCGTLV 17
                                   77777655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.8e-05
                                   EETTTTCEECHEE CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                   +CP+Cgst+++e+
  gi|118430956|ref|NP_147086.2| 23 VCPECGSTQFTEN 35
                                   7*******98765 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 ?    3.5   0.2     0.087        58      24      29 ..      10      15 ..       9      17 .. 0.86
   2 !   15.5   0.1   1.6e-05      0.01       5      17 ..      22      34 ..      19      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.087
                        zf-RRN7 24 CrrCht 29
                                   C++C+t
  gi|118430956|ref|NP_147086.2| 10 CKNCGT 15
                                   999999 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.6e-05
                        zf-RRN7  5 ppCgvCgcrsftl 17
                                   ++C++Cg++ ft+
  gi|118430956|ref|NP_147086.2| 22 KVCPECGSTQFTE 34
                                   89**********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 !   17.1   0.2   6.2e-06    0.0041      69      98 ..       6      33 ..       1      44 [. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-06
                                   -EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA 69 vkvrCreCgkefeleekalrCpkCgsadve 98
                                     v C++Cg+ +   +k   Cp+Cgs++++
  gi|118430956|ref|NP_147086.2|  6 SLVACKNCGTLVPRGSK--VCPECGSTQFT 33
                                   5689*****99997644..8******9875 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.7   1.1e-05    0.0073       3      21 ..      10      28 ..       9      32 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                        UPF0547  3 CPeCeakvPvaaqfCphCG 21
                                   C+ C + vP   ++Cp+CG
  gi|118430956|ref|NP_147086.2| 10 CKNCGTLVPRGSKVCPECG 28
                                   ******************9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.036        24      24      29 ..      10      15 ..       5      18 .. 0.62
   2 !   10.5   0.1   0.00057      0.38      22      31 ..      22      31 ..      19      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.036
                  A2L_zn_ribbon 24 CieCga 29
                                   C++Cg+
  gi|118430956|ref|NP_147086.2| 10 CKNCGT 15
                                   666654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00057
                  A2L_zn_ribbon 22 lvCieCgasf 31
                                    vC+eCg+++
  gi|118430956|ref|NP_147086.2| 22 KVCPECGSTQ 31
                                   59******98 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   1.2e-05    0.0082      67      86 .]       9      28 ..       2      28 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                 zinc_ribbon_15 67 eCknCgkeveeefkyCpkCg 86
                                    CknCg+ v   +k Cp+Cg
  gi|118430956|ref|NP_147086.2|  9 ACKNCGTLVPRGSKVCPECG 28
                                   7******************9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.3   2.9e-05      0.02      72     101 ..       6      35 ..       2      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-05
                        TackOD1  72 rirlCpsCksghlnvrevCpkCkSidieeq 101
                                    ++++C++C +      +vCp+C+S++++e+
  gi|118430956|ref|NP_147086.2|   6 SLVACKNCGTLVPRGSKVCPECGSTQFTEN 35 
                                    5789**********************9876 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2      0.13        83       3      10 ..       9      16 ..       8      20 .. 0.73
   2 ?    9.4   0.0     0.002       1.3       2      21 ..      22      38 ..      21      48 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                        zf-IS66  3 tCpcCGgl 10
                                   +C++CG+l
  gi|118430956|ref|NP_147086.2|  9 ACKNCGTL 16
                                   58888875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.002
                        zf-IS66  2 rtCpcCGgllkpigedrvre 21
                                   ++Cp+CG++     e  ++ 
  gi|118430956|ref|NP_147086.2| 22 KVCPECGST--QFTEN-WSG 38
                                   79*****94..45555.555 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 ?    5.7   0.2     0.022        14      20      28 ..       7      15 ..       1      21 [. 0.84
   2 ?    8.3   3.0    0.0033       2.2       7      35 ..      10      36 ..       9      39 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                    Prok-RING_1 20 iVvCpeCgt 28
                                   +V C +Cgt
  gi|118430956|ref|NP_147086.2|  7 LVACKNCGT 15
                                   79******9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0033
                    Prok-RING_1  7 CpvCgkelkeedDiVvCpeCgtpyHraCy 35
                                   C+ Cg  +  ++   vCpeCg+ +  + +
  gi|118430956|ref|NP_147086.2| 10 CKNCGTLVPRGS--KVCPECGSTQFTENW 36
                                   888888888874..58*****99877766 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.32   2.1e+02      16      20 ..      10      14 ..       3      17 .. 0.83
   2 ?   10.3   0.2   0.00079      0.52      13      21 ..      21      29 ..      19      35 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.32
                           YhfH 16 CteCG 20
                                   C +CG
  gi|118430956|ref|NP_147086.2| 10 CKNCG 14
                                   99999 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00079
                           YhfH 13 kKkCteCGk 21
                                   +K+C+eCG+
  gi|118430956|ref|NP_147086.2| 21 SKVCPECGS 29
                                   7*******8 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 ?    1.9   0.1      0.27   1.8e+02      24      30 ..      10      16 ..       8      17 .. 0.84
   2 ?    9.7   0.1   0.00096      0.64      21      32 .]      21      32 ..      21      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.27
                  zf-NADH-PPase 24 CpaCgle 30
                                   C +Cg+ 
  gi|118430956|ref|NP_147086.2| 10 CKNCGTL 16
                                   999*986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00096
                  zf-NADH-PPase 21 arvCpaCglehY 32
                                   ++vCp Cg  ++
  gi|118430956|ref|NP_147086.2| 21 SKVCPECGSTQF 32
                                   58******9887 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00014     0.091     509     534 ..       9      36 ..       3      40 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                    EETT.--...EESSSB-TTT--BE.EEEE CS
                           NRDD 509 vCnecgy...kgeiekCpkCgseeevevi 534
                                     C++cg+   +g  + Cp+Cgs++ +e +
  gi|118430956|ref|NP_147086.2|   9 ACKNCGTlvpRGS-KVCPECGSTQFTENW 36 
                                    7******985555.55*****87756665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.017        11      25      37 ..       6      18 ..       1      20 [. 0.67
   2 ?    8.9   5.3    0.0024       1.6       8      35 ..      10      31 ..       8      34 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                    Zn-ribbon_8 25 pltaCPeCgsevr 37
                                   +l+aC++Cg  v 
  gi|118430956|ref|NP_147086.2|  6 SLVACKNCGTLVP 18
                                   5677999987665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0024
                    Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.e 35
                                   C++Cg     l++      ++CPeCgs +
  gi|118430956|ref|NP_147086.2| 10 CKNCG----TLVPRG---SKVCPECGStQ 31
                                   99999....455444...678*****955 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.0   0.00036      0.24       3      22 ..      10      29 ..       9      30 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                   Rubredoxin_2  3 CsqCGfesakwfGrCpsCgs 22
                                   C++CG   ++    Cp+Cgs
  gi|118430956|ref|NP_147086.2| 10 CKNCGTLVPRGSKVCPECGS 29
                                   ******************97 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.0   0.00036      0.24      24      46 ..       5      28 ..       2      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                   --EEEETTTCCEE.CTTC-BTTTT CS
                 Ribosomal_L32p 24 pnlvecpncgelk.lpHrvcpscG 46
                                    +lv c+ncg l  +   vcp+cG
  gi|118430956|ref|NP_147086.2|  5 TSLVACKNCGTLVpRGSKVCPECG 28
                                   589*******76537788*****9 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 ?    7.6   0.1    0.0046       3.1      15      25 ..       5      15 ..       2      17 .. 0.80
   2 ?    3.0   0.3      0.13        83      20      25 ..      24      29 ..      19      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0046
                                   SS----SSS-- CS
                 DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                   +  + Ck+CG 
  gi|118430956|ref|NP_147086.2|  5 TSLVACKNCGT 15
                                   56789*****5 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                                   -SSS-- CS
                 DNA_RNApol_7kD 20 CkeCGh 25
                                   C eCG+
  gi|118430956|ref|NP_147086.2| 24 CPECGS 29
                                   888885 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    0.0069       4.6      22      28 ..       8      14 ..       4      17 .. 0.87
   2 ?    3.3   0.2       0.1        69      24      28 ..      24      28 ..      23      32 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0069
                                   ---TTTS CS
                        zf-HYPF 22 isCtnCG 28
                                   ++C+nCG
  gi|118430956|ref|NP_147086.2|  8 VACKNCG 14
                                   89****9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                   -TTTS CS
                        zf-HYPF 24 CtnCG 28
                                   C++CG
  gi|118430956|ref|NP_147086.2| 24 CPECG 28
                                   88888 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.04        27       3      13 ..       8      18 ..       6      22 .. 0.83
   2 ?    6.4   0.4      0.01       6.7       2      10 ..      21      29 ..      20      31 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.04
                         zf_UBZ  3 ylCerCgkeip 13
                                   + C+ Cg+ +p
  gi|118430956|ref|NP_147086.2|  8 VACKNCGTLVP 18
                                   67*****9998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                         zf_UBZ  2 tylCerCgk 10
                                   + +C++Cg+
  gi|118430956|ref|NP_147086.2| 21 SKVCPECGS 29
                                   579****97 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.4    0.0072       4.8      20      33 ..      21      34 ..       2      35 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0072
                  zinc_ribbon_9 20 sdvlCPhCgg.gFVE 33
                                   s v CP+Cg+ +F E
  gi|118430956|ref|NP_147086.2| 21 SKV-CPECGStQFTE 34
                                   556.****9868877 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 ?    3.1   0.2      0.14        90      45      54 ..       6      15 ..       2      20 .. 0.67
   2 ?    8.6   0.4    0.0027       1.8      28      38 ..      21      31 ..      18      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
                 OrfB_Zn_ribbon 45 rtfkCpnCgf 54
                                    ++ C+nCg+
  gi|118430956|ref|NP_147086.2|  6 SLVACKNCGT 15
                                   5667777775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0027
                 OrfB_Zn_ribbon 28 SktCseCgskn 38
                                   Sk C+eCgs++
  gi|118430956|ref|NP_147086.2| 21 SKVCPECGSTQ 31
                                   9*******987 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 ?    2.8   1.3      0.14        92      12      19 ..       9      16 ..       3      19 .. 0.82
   2 ?    9.7   0.5   0.00096      0.64       8      18 ..      19      29 ..      16      31 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                        zf-tcix 12 kCpkCGty 19
                                   +C +CGt 
  gi|118430956|ref|NP_147086.2|  9 ACKNCGTL 16
                                   79999995 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00096
                        zf-tcix  8 RGvrkCpkCGt 18
                                   RG + Cp+CG 
  gi|118430956|ref|NP_147086.2| 19 RGSKVCPECGS 29
                                   999*******5 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0039       2.6      22      34 ..       4      16 ..       1      18 [. 0.79
   2 ?    2.9   0.6      0.16     1e+02       5      10 ..      24      29 ..      21      33 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0039
                  zinc_ribbon_4 22 kgvkvrCskCghv 34
                                   +++ v C++Cg++
  gi|118430956|ref|NP_147086.2|  4 RTSLVACKNCGTL 16
                                   6678999999985 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                  zinc_ribbon_4  5 CpsCka 10
                                   Cp+C++
  gi|118430956|ref|NP_147086.2| 24 CPECGS 29
                                   888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 522.88
//
Query:       gi|14600570|ref|NP_147087.1|  [L=186]
Description: DNA-directed RNA polymerase subunit E' [Aeropyrum pernix K1]
Scores for 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   48.6   0.0    1.3e-12   47.9   0.0    1.4  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    3.3e-09   36.9   0.7    7.7e-09   35.8   0.7    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 !   47.9   0.0   1.4e-16   1.3e-12      10      70 .]      19      80 ..       8      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.4e-16
                                  GTTS.THHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE..-TTTSSEEEEEEEEEEEE CS
                   SHS2_Rpb7-N 10 ylgs.tledallerllekyegkvvpslGvivavldiaeysegkv..lggsGsvyvrVtfralvF 70
                                  y +s +l++a+le l +++eg++++++Gvivavld + +++g++  + g++s+y+ V++r+l F
  gi|14600570|ref|NP_147087.1| 19 Y-SSeDLDKAALEHL-RRLEGRIDEEMGVIVAVLDAKIVGDGIIppVSGDPSIYYPVRYRVLAF 80
                                  3.4449999998877.8***************************88899*************99 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.7   8.6e-13   7.7e-09       6      65 ..      86     154 ..      82     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 8.6e-13
                                   CEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..............CEESCHHHCEETTEEEEEEEEEEET CS
                            S1   6 evveGeVtsvtkgGafVelgngvegfvpaselsrd..............arvedpdevlkvGdevkvkvlkvdk 65 
                                   e+v G+Vt+ +++G+ V+lg + +g v++++++++              a    ++++++vGd v+++v  v +
  gi|14600570|ref|NP_147087.1|  86 EIVRGVVTRADDFGLVVNLG-PLDGKVHRNQIMDEgvellpdrsgfvglA----SKREIRVGDVVRARVVHVSR 154
                                   79******************.*********************99965544....9**************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1320.32
//
Query:       gi|14600571|ref|NP_147088.1|  [L=56]
Description: hypothetical protein APE_0257a, partial [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-05   24.3   0.2    3.9e-05   24.0   0.2    1.2  1  Fer4_8     4Fe-4S dicluster domain
    0.00011   22.2   0.2    0.00012   22.1   0.2    1.1  1  Fer4_10    4Fe-4S dicluster domain
    0.00012   21.7   3.6    0.00018   21.2   3.6    1.2  1  Fer4       4Fe-4S binding domain
    0.00023   21.9   0.7    0.00029   21.6   0.7    1.2  1  Fer4_22    4Fe-4S dicluster domain
    0.00031   20.8   0.4    0.00037   20.6   0.4    1.2  1  Fer4_21    4Fe-4S dicluster domain
    0.00056   20.4   0.2    0.00065   20.2   0.2    1.2  1  Fer4_17    4Fe-4S dicluster domain
    0.00074   20.1   0.4     0.0009   19.8   0.4    1.2  1  Fer4_7     4Fe-4S dicluster domain
     0.0013   18.9   0.1     0.0013   18.9   0.1    1.2  1  Fer4_9     4Fe-4S dicluster domain
     0.0023   18.8   0.1     0.0023   18.8   0.1    1.2  1  Fer4_16    4Fe-4S double cluster binding domain
     0.0025   17.8   2.1     0.0033   17.4   2.1    1.2  1  Fer4_2     4Fe-4S binding domain
      0.009   16.1   2.7      0.013   15.5   2.7    1.2  1  Fer4_6     4Fe-4S binding domain
  ------ inclusion threshold ------
       0.01   15.6   0.1       0.01   15.6   0.1    1.1  1  Fer4_20    Dihydroprymidine dehydrogenase domain II, 4Fe-4S c
      0.012   16.5   4.0      0.016   16.1   4.0    1.2  1  Fer4_3     4Fe-4S binding domain
      0.026   14.4   0.0      0.028   14.3   0.0    1.0  1  SCO1-SenC  SCO1/SenC
      0.032   14.8   1.4      0.044   14.3   1.4    1.2  1  Fer4_4     4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   3.2e-08   3.9e-05      45      65 .]      16      36 ..       3      36 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.2e-08
                        Fer4_8 45 eealwsCttcgaCtevCpvgi 65
                                   e+ + C++cg+C+evCpv+i
  gi|14600571|ref|NP_147088.1| 16 GEISYLCLGCGRCDEVCPVEI 36
                                  57889*************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2     1e-07   0.00012       8      24 ..      21      43 ..      16      56 .] 0.71

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1e-07
                       Fer4_10  8 tCirCgkCvkaCPadl......t 24
                                   C++Cg+C ++CP+ +      +
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPVEIplssiiS 43
                                  5*************776654431 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.6   1.5e-07   0.00018       7      21 ..      21      35 ..      18      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.5e-07
                                  TSSS-THHHHHSTTT CS
                          Fer4  7 kCigCGaCvevCPvg 21
                                  +C gCG+C evCPv+
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPVE 35
                                  7************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.7   2.5e-07   0.00029      80      96 .]      20      36 ..       8      36 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-07
                       Fer4_22 80 sgCvGCgRCieacpvki 96
                                  + C GCgRC+e+cpv+i
  gi|14600571|ref|NP_147088.1| 20 YLCLGCGRCDEVCPVEI 36
                                  68************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   3.1e-07   0.00037      37      54 ..      18      35 ..       3      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.1e-07
                       Fer4_21 37 vedeCvGCnlCssvCPve 54
                                  ++  C GC  C +vCPve
  gi|14600571|ref|NP_147088.1| 18 ISYLCLGCGRCDEVCPVE 35
                                  5678************95 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.2   5.4e-07   0.00065      40      60 ..      16      36 ..       3      37 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-07
                       Fer4_17 40 eekaslCieCgeCerkCPqgl 60
                                   e   lC++Cg+C+++CP ++
  gi|14600571|ref|NP_147088.1| 16 GEISYLCLGCGRCDEVCPVEI 36
                                  466789************887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4   7.5e-07    0.0009      37      51 ..      21      35 ..       7      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.5e-07
                        Fer4_7 37 kClgCgaCvavCPtg 51
                                   ClgCg+C +vCP++
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPVE 35
                                  588888888888876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.1e-06    0.0013      35      49 ..      21      35 ..       5      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                        Fer4_9 35 aCigCgaCveaCpkg 49
                                   C+gCg+C e+Cp +
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPVE 35
                                  577777777777755 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.9e-06    0.0023      53      66 ..      21      34 ..      10      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                       Fer4_16 53 aitgCdiCqdvCPa 66
                                   + gC++C +vCP+
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPV 34
                                  46677777777775 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   2.1   2.8e-06    0.0033       9      21 ..      21      33 ..      15      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
                        Fer4_2  9 rCigCgaCvsaCP 21
                                   C+gCg C  +CP
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCP 33
                                  5************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.7   1.1e-05     0.013       8      22 ..      21      35 ..      19      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                        Fer4_6  8 kCigCgdCvrvCPeg 22
                                  +C+gCg+C  vCP  
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPVE 35
                                  7************76 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 ?   15.6   0.1   8.6e-06      0.01      21      54 ..      19      50 ..       6      56 .] 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.6e-06
                                  HTT----TT-HHHHCSTT---HHHHHHHHHTT-H CS
                       Fer4_20 21 AsRClqCkkapcvkgCPveidipefikkiaegnl 54
                                  +  Cl C    c + CPvei   + i+k++++  
  gi|14600571|ref|NP_147088.1| 19 SYLCLGC--GRCDEVCPVEIPLSSIISKLKARAA 50
                                  556****..78*****************998765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   4.0   1.3e-05     0.016       1      13 [.      22      34 ..      22      36 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                        Fer4_3  1 CtgCgaCvevCPv 13
                                  C+gCg+C evCPv
  gi|14600571|ref|NP_147088.1| 22 CLGCGRCDEVCPV 34
                                  ************8 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.028      17      54 ..      12      48 ..       7      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                     SCO1-SenC 17 edlegkpslvffgFthCpdvCpttlanmaevldalgee 54
                                  edl+g++s + +g  +C +vCp++++ +++++++l+++
  gi|14600571|ref|NP_147088.1| 12 EDLAGEISYLCLGCGRCDEVCPVEIP-LSSIISKLKAR 48
                                  799********************998.45555555554 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   1.4   3.7e-05     0.044       3      16 ..      21      34 ..      19      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                        Fer4_4  3 rCigCgsCvaaCPq 16
                                   C+gCg+C  +CP+
  gi|14600571|ref|NP_147088.1| 21 LCLGCGRCDEVCPV 34
                                  5************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 453.34
//
Query:       gi|118430957|ref|NP_147089.2|  [L=310]
Description: hypothetical protein APE_0258.1, partial [Aeropyrum pernix K1]
Scores for complete 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-55  187.0   1.2    1.3e-54  184.9   1.2    1.8  1  LUD_dom   LUD domain
  ------ inclusion threshold ------
       0.13   12.3   0.3        9.4    6.3   0.0    2.5  2  DUF1931   Domain of unknown function (DUF1931)


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 !  184.9   1.2   1.4e-58   1.3e-54       1     189 []      68     298 ..      68     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 1.4e-58
                        LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.....................vseggstdlgeigl........ 51 
                                    +e+++e+l+++ga+ yya+tae+a+e++ +++ ++s+                     + e+++tdlg++ +        
  gi|118430957|ref|NP_147089.2|  68 VERAVESLRRVGANPYYAETAEDAREIVGKIVGSGSIvvmsksmaaeeiglrehlesmGNEVWETDLGQLLVmlegvkpm 147
                                    589**********************************99999999999999999999999999999999999******** PP

                        LUD_dom  52 ...apalhsgreevldlfeekl............treareelrekfltadvgitganfaiAetGtlvlvdnegnrraltf 116
                                       apa+h++re  +++ +ekl            +++ re lrekf++a vgitgan + A+tGt+vlv+negn r++++
  gi|118430957|ref|NP_147089.2| 148 hnvAPAVHMTRERAARIIREKLgievderdvegmVAAVREFLREKFFKARVGITGANSMSADTGTIVLVENEGNIRLVSS 227
                                    ******************************************************************************** PP

                        LUD_dom 117 lpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielvlvygvhgpkrihvilv 189
                                    lp+vh+++v+i+kivp++ dav+++    + a     ++ y+s+i+gps t+die+++v g+hgp+++hv+l+
  gi|118430957|ref|NP_147089.2| 228 LPPVHVALVPIDKIVPSVWDAVNVALV--QAAFAGFWMPVYISLITGPSATGDIEQIKVLGAHGPREVHVVLL 298
                                    *************************99..7777789***********************************96 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0074        66      12      38 ..      55      81 ..      45      98 .. 0.80
   2 ?    6.3   0.0    0.0011       9.4       3      37 ..     163     197 ..     161     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0074
                                   ---HHHHHHHHHHHHHHHHHCCCCHHH CS
                        DUF1931 12 dvdkedlkrisdfVekklydLllvaee 38
                                   +v++e +kr+ ++Ve++++ L +v+ +
  gi|118430957|ref|NP_147089.2| 55 EVKRESVKRLGELVERAVESLRRVGAN 81
                                   6999*****************999865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0011
                                    HHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHH CS
                        DUF1931   3 rlfreaagLdvdkedlkrisdfVekklydLllvae 37 
                                    r++re+ g++vd+ d++ +   V++ l + + +a+
  gi|118430957|ref|NP_147089.2| 163 RIIREKLGIEVDERDVEGMVAAVREFLREKFFKAR 197
                                    899********************999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2264.54
//
Query:       gi|118430958|ref|NP_147090.2|  [L=306]
Description: dihydroorotate dehydrogenase 1B [Aeropyrum pernix K1]
Scores for complete 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-50  171.3   0.0    2.9e-50  171.2   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    8.6e-08   31.6   0.0    5.6e-07   28.9   0.0    1.9  1  Dus           Dihydrouridine synthase (Dus)
     0.0022   17.5   1.9        1.2    8.5   0.1    3.1  3  PEP_mutase    Phosphoenolpyruvate phosphomutase
     0.0023   17.4   0.7      0.043   13.3   0.0    2.7  3  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.047   12.7   0.9       0.52    9.2   0.0    2.3  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.072   12.6   0.0       0.15   11.6   0.0    1.5  2  HMGL-like     HMGL-like
       0.36    9.8   4.6        0.3   10.0   0.2    2.6  4  FMN_dh        FMN-dependent dehydrogenase
        0.4   10.0  13.7       0.14   11.5   0.6    3.0  3  NMO           Nitronate monooxygenase
       0.91    8.2   3.6        4.6    5.9   0.1    2.3  3  DHDPS         Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0   1.4e-53   2.9e-50       2     294 ..       7     287 ..       6     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 1.4e-53
                                    G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTT.SSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHH CS
                         DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklg.fgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldav 80 
                                    l+ +++gl+++ p+g+A+G+ +     ++l++ g  g++  +svt +p++G p+P +  ++ +  ++N++Gl n+G+ + 
  gi|118430958|ref|NP_147090.2|   7 LSISIAGLRLQRPVGNASGILGWEPREARLVEEGgGGFFVAKSVTYQPRKGYPQPHLYPVAGG--IVNAVGLANPGFREA 84 
                                    67899**************************9999****************************..*************** PP

                                    HHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHG.GGESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHH CS
                         DHO_dh  81 lekllkrrkeqeekkelginlskakktenavddyvevvrkig.pfadilelNvSsPntp.glrdlqekeelkaillkvvk 158
                                     + l+++++e      +++++s+a+       ++ve++ +++   ++++elN+S+P+ + g+ +l+++++  a ++++v+
  gi|118430958|ref|NP_147090.2|  85 SKMLAQTVEE----ASIPVIASIAGGA---PGEWVEMASTLEeAGVSAVELNLSCPHFAgGGLELGQDPAAVASVVSAVA 157
                                    9999999977....369*********8...9***********7789*************999****************** PP

                                    HHHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHH CS
                         DHO_dh 159 evskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirely 238
                                     + ++pv++Kl          d a+++le +  g+  +N+ ++ ++id+ ++k+v  n+ GGlsGk++ +ia++ ++e+y
  gi|118430958|ref|NP_147090.2| 158 STLRIPVIAKLGY---SDRLVDAASKALEAGARGLTLINS-MRAMKIDVYAKKPVLGNRVGGLSGKPIHPIAVRAVYEVY 233
                                    ***********97...344555555555665555555555.56666********************************** PP

                                    HHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHH CS
                         DHO_dh 239 krlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleel 294
                                     +++    i + GG+es eDa+e + aGA +vqv++a++  gp + + i +++ + 
  gi|118430958|ref|NP_147090.2| 234 GETR--ADIFAAGGVESWEDAVEFYLAGAKAVQVGAAFITIGPHVLRSIVEGVRRY 287
                                    ****..8899***************************************9998765 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.8e-10   5.6e-07      41     213 ..      84     266 ..      77     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.8e-10
                                    HHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCC CS
                            Dus  41 kvrirmlseeeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvka 120
                                    +++++  + ee + p++  ++g  p + +e A   ++ g+++++lN+ CP       g+G  L ++p+ va++v+av + 
  gi|118430958|ref|NP_147090.2|  84 ASKMLAQTVEEASIPVIASIAGGAPGEWVEMASTLEEAGVSAVELNLSCPHF----AGGGLELGQDPAAVASVVSAVAST 159
                                    455566666777789***********************************74....69999******************* PP

                                    SSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEEEESS................ECCCTT-C....G--CHHHHHHHH CS
                            Dus 121 veiPvtvkirigiddeeenalelakiveaaGaqaltvHgR................traqnyeg....tadweaIkevkq 180
                                    + iPv +k           ++++a ++ +aGa  lt+                    r  + +g    ++  +a++ev  
  gi|118430958|ref|NP_147090.2| 160 LRIPVIAKLGYSD-----RLVDAASKALEAGARGLTLINSmramkidvyakkpvlgNRVGGLSGkpihPIAVRAVYEVYG 234
                                    *****99865544.....48999999999999999874332366666666666666444444444345566666666666 PP

                                    H-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                            Dus 181 avsipviaNGdIkdaedaqaileetGadgvmig 213
                                    + +  ++a G+++++eda +     Ga++v +g
  gi|118430958|ref|NP_147090.2| 235 ETRADIFAAGGVESWEDAVEFYLA-GAKAVQVG 266
                                    666666666666666666666555.66666655 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1   0.00061       1.2      55     104 ..      82     128 ..      29     131 .. 0.89
   2 !    4.6   0.1    0.0097        19      55     104 ..     147     191 ..     137     207 .. 0.83
   3 ?    2.3   0.0     0.048        96     208     233 ..     261     286 ..     240     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00061
                     PEP_mutase  55 eellaavraiaevvslPlivDledGygespeevaetvrrliaaGvvgvni 104
                                     e+ +++++ +e  s+P+i+ +  G   +p e  e   +l++aGv++v +
  gi|118430958|ref|NP_147090.2|  82 REASKMLAQTVEEASIPVIASIAGG---APGEWVEMASTLEEAGVSAVEL 128
                                    6778899999**************9...599****************976 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0097
                     PEP_mutase  55 eellaavraiaevvslPlivDledGygespeevaetvrrliaaGvvgvni 104
                                    + + ++v+a+a+++++P+i+ l  Gy++   ++ ++  ++++aG+ g+++
  gi|118430958|ref|NP_147090.2| 147 AAVASVVSAVASTLRIPVIAKL--GYSD---RLVDAASKALEAGARGLTL 191
                                    567889999999999****876..9966...6788889999999999887 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.048
                     PEP_mutase 208 elaelGvarislgnhllraalaalre 233
                                    +  ++G+a i++g+h+lr+ ++ +r+
  gi|118430958|ref|NP_147090.2| 261 KAVQVGAAFITIGPHVLRSIVEGVRR 286
                                    55689***************999887 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.4   7.9e+02     181     200 ..      86     107 ..      79     128 .. 0.69
   2 ?    0.6   0.0      0.17   3.3e+02      62     104 ..     150     195 ..     139     205 .. 0.70
   3 !   13.3   0.0   2.1e-05     0.043      62     107 ..     226     271 ..     216     287 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHSSEEEEE..SS- CS
                   His_biosynth 181 eltkelaeavkipvias..GGv 200
                                    +++ +  e+ +ipvias  GG+
  gi|118430958|ref|NP_147090.2|  86 KMLAQTVEEASIPVIASiaGGA 107
                                    5677777888899988744554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                                    HHHHHHHHHH-SSEEEEESSSSS..HHHHHHHHHCT-S.EEEESHH CS
                   His_biosynth  62 ldlveeiaeevfipvqvGGGIrs..ledveelleagad.kviigta 104
                                     ++v+++a++++ipv    G ++  ++++ ++leaga+    i+++
  gi|118430958|ref|NP_147090.2| 150 ASVVSAVASTLRIPVIAKLGYSDrlVDAASKALEAGARgLTLINSM 195
                                    5788888888888888888854422788888899888733445665 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                   His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                      +v e+  e+++++   GG+ s ed+ e   aga+ v +g a ++
  gi|118430958|ref|NP_147090.2| 226 VRAVYEVYGETRADIFAAGGVESWEDAVEFYLAGAKAVQVGAAFIT 271
                                    5667777777777777777777777777777777777777777664 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2     0.064   1.3e+02     194     232 ..     147     188 ..     135     198 .. 0.77
   2 ?    9.2   0.0   0.00026      0.52     195     239 ..     225     269 ..     216     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.064
                                    HHHHHHHH.HHCTCT-EEEEES--..-SHHHHHHHHHTT-SE CS
                                    xxxxxxxx.xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                          IMPDH 194 tAvaevae.aakkagvpviaDGGi..kysgdivkAlaaGada 232
                                     Ava+v++ +a++  +pvia  G   +      kAl aGa  
  gi|118430958|ref|NP_147090.2| 147 AAVASVVSaVASTLRIPVIAKLGYsdRLVDAASKALEAGARG 188
                                    578887763677779******9982234677889*****975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                    Av +v+e+  ++   + a GG+++ +d v    aGa+av +G  +
  gi|118430958|ref|NP_147090.2| 225 AVRAVYEVYGETRADIFAAGGVESWEDAVEFYLAGAKAVQVGAAF 269
                                    8999999999999***************************99987 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.6e-05      0.15      26     105 ..     112     201 ..     107     208 .. 0.76
   2 ?   -3.0   0.0       2.1   4.3e+03     157     175 ..     257     275 ..     226     287 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.6e-05
                                    HHHHHHHHHHT-SEE--.........TSGGGT.THHHHHHHS---TT-B....--EE-SSHHHHHHHHH....TT-SEEE CS
                      HMGL-like  26 laiakaLdeagvdeiEv.........gfpaaseddfevvraiakavkkar..ilalvrarekdikaavealkgagakrvh 94 
                                    +++a  L+eagv+++E+         g   +++d+ +v   + +++ + r  ++a + + +++++aa + + +aga+ + 
  gi|118430958|ref|NP_147090.2| 112 VEMASTLEEAGVSAVELnlscphfagGGLELGQDPAAVASVVSAVASTLRipVIAKLGYSDRLVDAASK-ALEAGARGLT 190
                                    789*****************9999986667776655544444444444445588888899999**9999.6679999999 PP

                                    EEEES-HHHHH CS
                      HMGL-like  95 vfiatselhlk 105
                                    +++++  + + 
  gi|118430958|ref|NP_147090.2| 191 LINSMRAMKID 201
                                    99999887765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                                    HHT-SEEEEEETTS---HH CS
                      HMGL-like 157 eaGatriniaDtvGvltPn 175
                                     aGa+ +++ +    + P+
  gi|118430958|ref|NP_147090.2| 257 LAGAKAVQVGAAFITIGPH 275
                                    3344444444444444444 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5   3.1e+03      44      64 ..       3      23 ..       2      24 .. 0.88
   2 ?    0.5   0.1      0.12   2.4e+02      64     105 ..      72     113 ..      61     128 .. 0.82
   3 ?   -2.1   0.0      0.74   1.5e+03     227     243 ..     175     191 ..     141     205 .. 0.70
   4 ?   10.0   0.2   0.00015       0.3     267     304 ..     232     270 ..     207     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                                   SS-B--EEETTEEESSSEEE- CS
                         FMN_dh 44 skvdlsttllGqklslPvlia 64
                                   s+++ls+++ G +l+ Pv+ a
  gi|118430958|ref|NP_147090.2|  3 SQPELSISIAGLRLQRPVGNA 23
                                   68899************9876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                                    --BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HHHHH CS
                         FMN_dh  64 aPvglaklahpdgelalaraaakagipfvlstvastsleeva 105
                                     +vgla+   +++  +la++ ++a ip++ s +  ++ e v 
  gi|118430958|ref|NP_147090.2|  72 NAVGLANPGFREASKMLAQTVEEASIPVIASIAGGAPGEWVE 113
                                    4677777788889999**************999888777665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.74
                                    HHHHHHHHHTTESEEEE CS
                         FMN_dh 227 aedakraveaGvdgivv 243
                                    ++ a +a+eaG+ g+ +
  gi|118430958|ref|NP_147090.2| 175 VDAASKALEAGARGLTL 191
                                    56788888888888765 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00015
                                    HH...SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                         FMN_dh 267 avgg.rievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                      g+ r+++++ gG+ + +D++     GA+av +G +f+
  gi|118430958|ref|NP_147090.2| 232 VYGEtRADIFAAGGVESWEDAVEFYLAGAKAVQVGAAFI 270
                                    3333489****************************9986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.6      0.14   2.7e+02     178     201 ..      81     106 ..      65     128 .. 0.75
   2 ?    5.7   0.8    0.0041       8.2     180     219 ..     148     189 ..     134     195 .. 0.71
   3 ?   11.5   0.6   7.1e-05      0.14     194     227 ..     238     271 ..     208     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.14
                            NMO 178 dkglfaLvpqvldavdiPviA..aGG 201
                                     ++  ++++q ++  +iPviA  aGG
  gi|118430958|ref|NP_147090.2|  81 FREASKMLAQTVEEASIPVIAsiAGG 106
                                    3677788888888899****966677 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0041
                            NMO 180 glfaLvpqvldavdiPviAaGGiidrrgvaa...aLalGAsgv 219
                                       ++v  v++ + iPviA  G  dr  v+a   aL +GA g 
  gi|118430958|ref|NP_147090.2| 148 AVASVVSAVASTLRIPVIAKLGYSDRL-VDAaskALEAGARGL 189
                                    45566777777777********99975.444234799999986 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 7.1e-05
                            NMO 194 iPviAaGGiidrrgvaaaLalGAsgvqigtrfLl 227
                                      + AaGG+   ++      +GA++vq+g++f+ 
  gi|118430958|ref|NP_147090.2| 238 ADIFAAGGVESWEDAVEFYLAGAKAVQVGAAFIT 271
                                    5699**********99999*************95 PP

>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0023       4.6      55     100 ..      83     126 ..      80     130 .. 0.88
   2 ?    3.0   0.1     0.018        35      65     104 ..     155     193 ..     142     195 .. 0.78
   3 ?   -3.4   0.0       1.5     3e+03      69     114 ..     236     283 ..     228     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHHTTSSEEEEE---SSHHHHHHHHHCCCCCT-SEE CS
                          DHDPS  55 ekeqlveiaveaakgripviagvGsnstseaiklakkaeeaGadgv 100
                                    e  +++ ++ve+a  +ipvia + + +  e +++a   eeaG+ +v
  gi|118430958|ref|NP_147090.2|  83 EASKMLAQTVEEA--SIPVIASIAGGAPGEWVEMASTLEEAGVSAV 126
                                    6677888888876..7******9999*****************987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.018
                                    HHHTT.SSEEEEE---SSHHHHHHHHHCCCCCT-SEEEEE- CS
                          DHDPS  65 eaakg.ripviagvGsnstseaiklakkaeeaGadgvlavt 104
                                     +a + ripvia+ G    +  +++a ka eaGa g+ +++
  gi|118430958|ref|NP_147090.2| 155 AVASTlRIPVIAKLGY--SDRLVDAASKALEAGARGLTLIN 193
                                    3333349********8..6888999**********998876 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.5
                                    TSSEEEEE---SSHHHHHH...HHHCCCCCT-SEEEEE---SS---HHH CS
                          DHDPS  69 gripviagvGsnstseaik...lakkaeeaGadgvlavtPYYnkpsqeg 114
                                    +r  ++a  G  s ++a++   +++ka ++Ga + +++ P+  +   eg
  gi|118430958|ref|NP_147090.2| 236 TRADIFAAGGVESWEDAVEfylAGAKAVQVGA-AFITIGPHVLRSIVEG 283
                                    56777777888888888873333566666665.4556666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2176.37
//
Query:       gi|118430959|ref|NP_147091.2|  [L=425]
Description: dihydroorotase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-07   29.7   0.0    8.3e-07   28.6   0.0    1.8  1  Amidohydro_1  Amidohydrolase family
    0.00012   21.7   0.0       0.41   10.0   0.0    2.4  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
       0.25   11.5   1.1       0.46   10.7   1.1    1.4  1  RINGv         RING-variant 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 !   28.6   0.0   1.4e-10   8.3e-07       2     155 ..      53     179 ..      52     404 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.4e-10
                                    EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH..HHHHHHHHHHTSSSEEEE CS
                   Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst..giealleaaeelplglri 79 
                                     lPG ID+HvHl++              +  ++e   sg+++a ++ +t vadm++t+++    eal+e + +l    ++
  gi|118430959|ref|NP_147091.2|  53 ALPGVIDMHVHLRG-------------LKLSYKEDEVSGTAAAASGCVTLVADMPNTQPPlrTPEALREKLASL--EAGA 117
                                    69**********83.............345699999*********************98888777777766664..4444 PP

                                    EEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETSS CS
                   Amidohydro_1  80 lggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHalet 155
                                     + +++++ g++ +  + +e    g+             ++++ ++   +  + +k++l++a+++++ v+ H  ++
  gi|118430959|ref|NP_147091.2| 118 KVDYTVYA-GVPRSYGEAVEMASMGI-------------AGFKIYPEDLVNLDSIKNVLEAAEEAGILVVLHPESH 179
                                    45555555.66665555555555555.............56666666666668*******************7444 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0001       0.6       4      30 ..      45      73 ..      44     126 .. 0.74
   2 !   10.0   0.0   6.9e-05      0.41     300     473 .]     211     405 ..     155     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                   Amidohydro_3  4 DakGr..lvlPGFvDsHtHlagggvnlrl 30
                                   D++Gr  l lPG +D+H Hl g ++ + +
  gi|118430959|ref|NP_147091.2| 45 DLRGRssLALPGVIDMHVHLRGLKLSYKE 73
                                   6777644689*********8888855532 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.9e-05
                   Amidohydro_3 300 aekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnf.....edelldsrlg.perargs..........tpvkel 363
                                    a++ g++ r+ ++ha+   ++++ + ++ + + +v p + f              g ++ +  +          + +  l
  gi|118430959|ref|NP_147091.2| 211 ARECGCKPRVHITHASC--PATVVESKKRGFTVDVTPHHLFlseeeV-------AGpTHSWGKVnpplrgvgerSLLTQL 281
                                    56667777888888888..9999999999999999999999985441.......3333333333444455589999999* PP

                   Amidohydro_3 364 lnagvkvalgsD.apvgpfdpwprigaavmrktrrgg....evlrpdeelsleealalyTrgpAkalgledrkGtLevGa 438
                                    +  g+  a +sD ap ++  +w +   a ++ ++ +     + +r ++ + le    +++++p ++lg  dr   L  G+
  gi|118430959|ref|NP_147091.2| 282 TIEGLVDAIASDhAPHSTWEKWMHPAIAPPGFPWLEWwpgfTAARLMRAVGLERFYSMVSQTPSTILGVGDR--CLWDGC 359
                                    **********************************777**********************************9..****** PP

                   Amidohydro_3 439 dADlvvldadpldvdppelaear...........vrltvvdGrvvy 473
                                    +A + vl  ++ +v ++   +a+           + +tv++G++ y
  gi|118430959|ref|NP_147091.2| 360 PATISVLQLERTRVYHKGYTKALytpvlgmesfdCAATVIRGKIAY 405
                                    *******8777777776544444999****************9987 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.1   7.7e-05      0.46       4      32 ..     197     228 ..     194     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.7e-05
                                    TTEE-SSSS...--B-SS--STCCCSB-HHHH CS
                          RINGv   4 Cleeeeese...plispCkCrGslklvHesCl 32 
                                    C+ e+++ e   +  ++C C+  +++ H sC 
  gi|118430959|ref|NP_147091.2| 197 CHAEAASVEllhDAARECGCKPRVHITHASCP 228
                                    9999999997777889***************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 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:                        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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3061.10
//
Query:       gi|14600575|ref|NP_147092.1|  [L=230]
Description: hypothetical protein APE_0262 [Aeropyrum pernix K1]
Scores for 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-17   62.8   0.0    6.8e-15   55.5   0.0    2.0  1  GDPD        Glycerophosphoryl diester phosphodiesterase famil
    0.00016   22.0   0.4     0.0007   20.0   0.2    2.2  2  GDPD_2      Glycerophosphoryl diester phosphodiesterase famil
     0.0077   16.2   0.0      0.017   15.1   0.0    1.5  1  ADH_zinc_N  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.017   14.7   0.1      0.024   14.1   0.1    1.2  1  EAL         EAL domain
      0.092   12.1   0.1       0.14   11.5   0.1    1.4  1  TMP-TENI    Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   1.9e-18   6.8e-15     105     259 .]      85     220 ..      15     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.9e-18
                                   CCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC- CS
                          GDPD 105 vglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdilkllrekqpklpllflteggteaea 185
                                    +l+  + ++ ++ +++ +++ i+  +l+s  e++       ++ +vi++s n++ l++lre+++++ ++ ++  +    +
  gi|14600575|ref|NP_147092.1|  85 NWLERLWSMGFTKVVIDVKSGGIDPTLLASEVERG-------WPGQVIYTSENHRYLRRLREEASAVVYTTYSILPVDVAD 158
                                   55666667777777777777777777777777777.......***********************8888888887888887 PP

                                   E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC-SEEEES-HHH CS
                          GDPD 186 dssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnedeeemkrlleagvdgvitDfpdt 259
                                   +      a +a+a+++  +++++ e      ++++++++gl+v+v+tvn+e  ++ k+++++gvd+++ D+pd+
  gi|14600575|ref|NP_147092.1| 159 P------ALKAGAEGVSIRFDLAIED----NVIRALRQSGLKVVVWTVNTE--DQAKTVEKLGVDAIVSDRPDK 220
                                   7......9999********9999999....6********************..*******************96 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.84     3e+03      10      18 ..     178     186 ..     143     189 .. 0.61
   2 !   20.0   0.2   1.9e-07    0.0007       1      30 []     190     219 ..     190     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.84
                        GDPD_2  10 eavwrelvg 18 
                                   ++v+r l++
  gi|14600575|ref|NP_147092.1| 178 DNVIRALRQ 186
                                   677777765 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.9e-07
                        GDPD_2   1 kvrfWttddeavwrelvgaGVdgInTDdld 30 
                                   kv  Wt+++e++ ++  ++GVd I  D++d
  gi|14600575|ref|NP_147092.1| 190 KVVVWTVNTEDQAKTVEKLGVDAIVSDRPD 219
                                   6899************************98 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.9e-06     0.017       6      53 ..     180     225 ..     178     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-06
                                   HHHHHHHTT-EEEE.EESSHHHHHHHHHTTESEEEETTTCHHHHHHHHH CS
                    ADH_zinc_N   6 avqlAkalGaevia.vdsseeklelakklGadevinykeadlverikel 53 
                                   ++ +++ +G +v++ ++ +e++++ ++klG+d+++     ++++ +++l
  gi|14600575|ref|NP_147092.1| 180 VIRALRQSGLKVVVwTVNTEDQAKTVEKLGVDAIVSD---RPDKVLRAL 225
                                   6788999***99999********************99...566666655 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.8e-06     0.024     195     229 ..     178     212 ..     172     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-06
                                   HHCHHHHCCCT-EEEE-S--SHHHHHHHHHHT-SE CS
                           EAL 195 kalialakelgikvvaegVeteeqlealrelgcdl 229
                                   + +i++ ++ g+kvv+  V te+q++++++lg+d 
  gi|14600575|ref|NP_147092.1| 178 DNVIRALRQSGLKVVVWTVNTEDQAKTVEKLGVDA 212
                                   678999***************************97 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.9e-05      0.14      64     121 ..     155     214 ..      79     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                      TMP-TENI  64 drvdlalavgadgvHlgqd.dlpvaearellgpdl.iiGlSvhsleeaeeaealgadYig 121
                                   d +d al++ga+gv +  d  ++ + +r+l +++l ++ ++v+++++a+++e+lg+d i+
  gi|14600575|ref|NP_147092.1| 155 DVADPALKAGAEGVSIRFDlAIEDNVIRALRQSGLkVVVWTVNTEDQAKTVEKLGVDAIV 214
                                   6678899999999999885255788889999888615678*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 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:                        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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1709.92
//
Query:       gi|118430960|ref|NP_147093.2|  [L=430]
Description: pernisine [Aeropyrum pernix K1]
Scores for complete 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-45  154.2   4.0    7.9e-45  153.4   4.0    1.4  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
        2.3    7.8   5.3         19    4.9   0.7    3.6  3  EF-hand_5     EF hand


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 !  153.4   4.0   8.8e-49   7.9e-45       4     298 .]     143     416 ..     140     416 .. 0.87

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 8.8e-49
                                    -EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   4 vlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeegekn 83 
                                    + vav+DtGvd++hpdl  +      +v+ i+     +ng+ s      +++d ng    HGthv G++aa  +++ ++ 
  gi|118430960|ref|NP_147093.2| 143 IEVAVIDTGVDKDHPDLAGN------IVWGISV----LNGRISS-----NYQDRNG----HGTHVTGTVAAI-DNDIGVI 202
                                    679***************55......5543333....5555554.....4556677....************.9999*** PP

                                    -SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-S.....................EEEE-EESCETTCHHCHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8  84 gvapgakilsvkvldtsggsmetgteliraieeaaedkvd.....................vinmslgestslpktgrsi 142
                                    gva +++i++vk+l++ g  +   ++li ai+ a++ ++d                     vi+mslg+s+  p+  +  
  gi|118430960|ref|NP_147093.2| 203 GVAHSVEIYAVKALGNGGYGS--WSDLIIAIDLAVK-GPDgvidadgdgvvagdpdddapeVISMSLGGSSPPPELHD-- 277
                                    **************6655444..39***99999998.777888999**********************8888888887.. PP

                                    HHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 143 ealainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGg 222
                                       +i++a  + g+ +v++aGN+g          + ++p+ + +vi+vga++++g++ ++S+r p+        ++apG+
  gi|118430960|ref|NP_147093.2| 278 ---VIKAAY-NLGITIVAAAGNDG--------ADSPSYPAAYPEVIAVGAIDENGNVPSWSNRNPE--------VAAPGV 337
                                    ...677787.89************........444577999***********************96........57**** PP

                                    -CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT.............--HHHHHHHHHCCS-EE..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 223 nivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk.............ltpetvraallntAqdlgkadn 289
                                    ni+st++ ++        y+  sGTSmA+P+++g +Al++ a  +              tp+tvr +l +tA+d g++  
  gi|118430960|ref|NP_147093.2| 338 NILSTYPDDT--------YEELSGTSMATPHVSGTVALIQAARLAaglpllppgsesdTTPDTVRGVLHTTATDAGDP-- 407
                                    **********........***********************55555**************************998777.. PP

                                    .SSSSSSTT CS
                                    xxxxxxxxx RF
                   Peptidase_S8 290 iesfaqGaG 298
                                    + +  +G+G
  gi|118430960|ref|NP_147093.2| 408 GYDSLYGYG 416
                                    999999999 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.2   1.8e+03      15      21 ..      36      42 ..      36      45 .. 0.91
   2 ?    2.7   0.3     0.011     1e+02       9      14 ..     134     139 ..     133     145 .. 0.78
   3 ?    4.9   0.7    0.0022        19       8      16 ..     242     250 ..     240     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.2
                                   CE-HHHH CS
                      EF-hand_5 15 kIskeEL 21
                                   kI++eE+
  gi|118430960|ref|NP_147093.2| 36 KINPEEF 42
                                   8*****9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.011
                                    -SS-SS CS
                      EF-hand_5   9 DlNgDG 14 
                                    D+NgDG
  gi|118430960|ref|NP_147093.2| 134 DVNGDG 139
                                    888888 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0022
                                    H-SS-SSCE CS
                      EF-hand_5   8 iDlNgDGkI 16 
                                    iD++gDG +
  gi|118430960|ref|NP_147093.2| 242 IDADGDGVV 250
                                    9******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3349.88
//
Query:       gi|118430961|ref|NP_147094.2|  [L=210]
Description: hypothetical protein APE_0264.1 [Aeropyrum pernix K1]
Scores for complete 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-05   23.9   0.1    7.6e-05   22.8   0.1    1.6  1  DUF4145        Domain of unknown function (DUF4145)
     0.0085   16.2   0.1        1.7    8.8   0.0    2.6  3  NGP1NT         NGP1NT (NUC091) domain
  ------ inclusion threshold ------
      0.017   15.2   0.1       0.03   14.4   0.1    1.5  1  HEPN_Cthe2314  Cthe_2314-like HEPN
      0.023   14.0   0.0      0.031   13.5   0.0    1.3  1  PsiA           PsiA protein
       0.11   12.4   2.4       0.14   12.0   1.8    1.5  2  DUF4294        Domain of unknown function (DUF4294)


Domain annotation for each model (and alignments):
>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   2.1e-08   7.6e-05       2      83 ..      52     156 ..      51     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.1e-08
                        DUF4145   2 eaekllnas.pkasavliRraLEkllkdkgiakgk......................dLknkiealvekgvipeklkell 58 
                                    ea ++ ++  + a++ ++  aLE+l+ d+ +a                         +L  ++++l + g+i++ l    
  gi|118430961|ref|NP_147094.2|  52 EALSAYQNGaYMAAILMSGVALEALVYDLVAALRGyvkcyegniyeaeldsnvykwvRLDSALQELKNSGIINKPLERRF 131
                                    788888888799******************6643358899998999988877777777********************** PP

                        DUF4145  59 dairviGNdgaHelkditkedaedl 83 
                                     + r+++N  aH++++ +k   e +
  gi|118430961|ref|NP_147094.2| 132 YRAREMRNLVAHYAQKRQKRLRESI 156
                                    ************8676666544444 PP

>> NGP1NT  NGP1NT (NUC091) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0023       8.3      44      73 ..       5      34 ..       2      35 .. 0.92
   2 !    8.8   0.0   0.00046       1.7      35      66 ..      32      63 ..      30      76 .. 0.88
   3 ?   -2.1   0.1       1.1     4e+03       4     123 ..     148     163 ..     139     169 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                         NGP1NT 44 visqeaLekfreeleekvkdpysvllkrnk 73
                                   vi+ ++ +++re+ ++k++d +++l++ ++
  gi|118430961|ref|NP_147094.2|  5 VIGPTECDEYREQRNSKINDEWNLLIEDKN 34
                                   99***********************99886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00046
                         NGP1NT 35 drrWFgntrvisqeaLekfreeleekvkdpys 66
                                   d++ F+nt +i  +a + +re+l++ ++ +y 
  gi|118430961|ref|NP_147094.2| 32 DKNVFANTYIIVSTAVDLYREALSAYQNGAYM 63
                                   8899*******************999998885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.1
                         NGP1NT   4 egkakrdkkGkiikaaalqskeasksariepdrrWFgntrvisqeaLekfreeleekvkdpysvllkrnklPmsLledka 83 
                                    ++k  r++  +iika                                                                 
  gi|118430961|ref|NP_147094.2| 148 RQKRLRESIAEIIKA----------------------------------------------------------------- 162
                                    233333444444443................................................................. PP

                         NGP1NT  84 kkkkvklletesfeetFgpkaqrkrpklevsdleelakka 123
                                                                            
  gi|118430961|ref|NP_147094.2| 163 ---------------------------------------R 163
                                    .......................................3 PP

>> HEPN_Cthe2314  Cthe_2314-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   8.4e-06      0.03      96     140 ..     109     158 ..      88     207 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.4e-06
                  HEPN_Cthe2314  96 elakkLkeikes........esfkelrkeRNketHr.qinseliqddllqshqg 140
                                    +l+++L+e+k+s          f ++r++RN ++H+ q +    q  l++s+  
  gi|118430961|ref|NP_147094.2| 109 RLDSALQELKNSgiinkpleRRFYRAREMRNLVAHYaQKR----QKRLRESIAE 158
                                    5899999***999999999999**************5222....3333333322 PP

>> PsiA  PsiA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.8e-06     0.031     167     228 ..      88     149 ..      51     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-06
                           PsiA 167 ysrWsdeldadelasafyrWqtrftslkeldwlrisgeklyevmyeisfivrelaedirlae 228
                                     + ++ +++++el+s++y+W +  ++l+el+   i +++l +  y  + + +  a++ ++++
  gi|118430961|ref|NP_147094.2|  88 VKCYEGNIYEAELDSNVYKWVRLDSALQELKNSGIINKPLERRFYRAREMRNLVAHYAQKRQ 149
                                    55577899********************************9999876666555555444433 PP

>> DUF4294  Domain of unknown function (DUF4294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.2   7.9e+03     107     119 ..      77      89 ..      73      94 .. 0.76
   2 ?   12.0   1.8     4e-05      0.14      19     108 ..     122     210 .]     103     210 .] 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.2
                        DUF4294 107 sYelikelrggfk 119
                                     Y+l+ +lrg +k
  gi|118430961|ref|NP_147094.2|  77 VYDLVAALRGYVK 89 
                                    6888888888776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4e-05
                        DUF4294  19 fknkkerkrylrlrrkvkkvyPyaklaaerlieleeeletlkdkkerkkyikevekelkkefekeLkkLtrsqGkiLikL 98 
                                      nk  ++r++r r+  + v  ya+  ++rl+e   e+ +  ++++  ++ik +ek l  + e+ L +L  + + iL  L
  gi|118430961|ref|NP_147094.2| 122 IINKPLERRFYRAREMRNLVAHYAQKRQKRLRESIAEIIKAREDRKTYAIIKGLEKGLWATEEEALNTLK-ETAWILKAL 200
                                    556667899999999999***************9999999999999999******************995.56899999* PP

                        DUF4294  99 idRetgqtsY 108
                                    i+R  ++ +Y
  gi|118430961|ref|NP_147094.2| 201 IERAYKEFCY 210
                                    ***9887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1563.54
//
Query:       gi|14600578|ref|NP_147095.1|  [L=121]
Description: hypothetical protein APE_0265 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.8   0.0       0.29   10.8   0.0    1.5  1  Fis1_TPR_N  Fis1 N-terminal tetratricopeptide repeat
        1.1    9.4   4.7       0.29   11.2   1.2    1.8  2  SPC12       Microsomal signal peptidase 12 kDa subunit (SPC12


Domain annotation for each model (and alignments):
>> Fis1_TPR_N  Fis1 N-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.3e-05      0.29       1      13 [.      81      93 ..      81      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.3e-05
                    Fis1_TPR_N  1 qtkFnYAWgLvkS 13
                                  +t Fn+A gL+ S
  gi|14600578|ref|NP_147095.1| 81 DTIFNLAIGLILS 93
                                  599********98 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.16   1.5e+03      34      41 ..      34      41 ..      18      54 .. 0.47
   2 ?   11.2   1.2   3.3e-05      0.29       9      62 ..      55     107 ..      48     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.16
                         SPC12 34 lkltlyil 41
                                  ++l++y++
  gi|14600578|ref|NP_147095.1| 34 ITLVFYFY 41
                                  22222222 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.3e-05
                         SPC12   9 aekllqvilvlsaviafivGyitqdlkltlyillagvvltllvvvPpWpfYnrn 62 
                                   +e+l+ v+++++   a  vG +++++++  + l++g++l+ll  vPp  +  r+
  gi|14600578|ref|NP_147095.1|  55 SEQLIIVTMITVRNYAATVGLWAESFDTI-FNLAIGLILSLLSLVPPLAILIRH 107
                                   68899999999999************965.56788999********98776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 902.80
//
Query:       gi|14600580|ref|NP_147097.1|  [L=143]
Description: hypothetical protein APE_0267 [Aeropyrum pernix K1]
Scores for complete 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  107.8   7.5    3.2e-16   59.5   3.4    2.1  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.011   15.5   0.2        3.8    7.3   0.1    2.2  2  Robl_LC7  Roadblock/LC7 domain
      0.048   13.9   0.7       0.28   11.5   0.0    2.3  3  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 !   50.5   0.1   3.4e-17     2e-13       2      56 ..      16      70 ..      15      71 .. 0.93
   2 !   59.5   3.4   5.3e-20   3.2e-16       1      53 [.      80     132 ..      80     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.4e-17
                                  HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEE.EEEEHHHHHHHHH CS
                           CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklv.GivtlrDllrall 56
                                  +++m++++vt+    +++ea++lm+e+gv++l VVd++g lv Gi+t+rD+++ l+
  gi|14600580|ref|NP_147097.1| 16 KHVMSTPPVTIEVGRSIAEAARLMAERGVGSLIVVDKQG-LVkGILTERDIINSLA 70
                                  789*********************9999****999****.777*********9875 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 5.3e-20
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                           CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                   V+dim+r++++++pd++le ++e+mr+ +++++PV+dedg+++G+++ rD+++
  gi|14600580|ref|NP_147097.1|  80 VEDIMSRNPIVASPDDDLEIIIEKMRDMNIRHIPVIDEDGRPLGMISVRDIID 132
                                   89************************999**********************97 PP

>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1   0.00064       3.8       8      30 ..      37      59 ..      35      80 .. 0.81
   2 ?    6.3   0.0    0.0014       8.2      11      30 ..     105     124 ..      96     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00064
                                  HCCHHCTECEEEEEETTS-EEEE CS
                      Robl_LC7  8 elqsvpgvrgalvvskdGlviat 30
                                  +l  ++gv   +vv+k Glv+  
  gi|14600580|ref|NP_147097.1| 37 RLMAERGVGSLIVVDKQGLVKGI 59
                                  788899**************876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0014
                                   HHCTECEEEEEETTS-EEEE CS
                      Robl_LC7  11 svpgvrgalvvskdGlviat 30 
                                   +  ++r++ v++ dG ++ +
  gi|14600580|ref|NP_147097.1| 105 RDMNIRHIPVIDEDGRPLGM 124
                                   5569*************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 ?   -2.0   0.0      0.77   4.6e+03      24      37 ..      31      44 ..      30      57 .. 0.67
   2 ?   -0.3   0.0      0.23   1.4e+03      11      30 ..      48      67 ..      43      73 .. 0.82
   3 ?   11.5   0.0   4.7e-05      0.28       6      30 ..     108     132 ..     102     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.77
                                  EHHHHHHHHHHHTS CS
                         IF3_N 24 streAlrlaeekgl 37
                                  s++eA rl+ e+g+
  gi|14600580|ref|NP_147097.1| 31 SIAEAARLMAERGV 44
                                  56778887777765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.23
                                  EEE-SSS-EEEEEEHHHHHH CS
                         IF3_N 11 rlvdedGeqlGvistreAlr 30
                                   +vd++G   G+++ r++++
  gi|14600580|ref|NP_147097.1| 48 IVVDKQGLVKGILTERDIIN 67
                                  58999999889999999886 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 4.7e-05
                                   -SSEEEEE-SSS-EEEEEEHHHHHH CS
                         IF3_N   6 rarevrlvdedGeqlGvistreAlr 30 
                                   + r++ ++dedG  lG+is+r++++
  gi|14600580|ref|NP_147097.1| 108 NIRHIPVIDEDGRPLGMISVRDIID 132
                                   5699******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1085.23
//
Query:       gi|118430962|ref|NP_147096.2|  [L=609]
Description: tungsten-containing aldehyde ferredoxin oxidoreductase [Aeropyrum pernix K1]
Scores for complete 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-69  233.6   0.0    5.1e-69  233.1   0.0    1.1  1  AFOR_C           Aldehyde ferredoxin oxidoreductase, domains 
    2.7e-57  193.8   0.0    4.2e-57  193.2   0.0    1.3  1  AFOR_N           Aldehyde ferredoxin oxidoreductase, N-termin
  ------ inclusion threshold ------
       0.11   13.1   0.0       0.22   12.1   0.0    1.4  1  Caskin-Pro-rich  Proline rich region of Caskin proteins


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 !  233.1   0.0   8.6e-73   5.1e-69      17     379 ..     238     598 ..     220     599 .. 0.91

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 8.6e-73
                                    HHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE......ET..EE-- CS
                         AFOR_C  17 taelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkveegkkvk..vegp 94 
                                    ++ l+ yGT++ ++++  ++a+p+ n+++ + e++e +sg  +++++l ++  C sCp+aC+r++   +       +egp
  gi|118430962|ref|NP_147096.2| 238 KGLLAVYGTPVAMEALGPAEAVPHLNYRNPVLERWEALSGRIMSKTILAGRLTCSSCPVACRRDTVGVSL---SfrTEGP 314
                                    347999***********************999*******************99************95444...24599** PP

                                    -HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THHHHHHHHHHHT CS
                         AFOR_C  95 eyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaeallellekiAk 174
                                    +y  + +lGsn+g  +le + +l  l  +lGlD i+aGn++a++ e++e + l +       l +gd ea+++ll  +A+
  gi|118430962|ref|NP_147096.2| 315 DYAQISSLGSNTGLISLEGVGYLTSLSYRLGLDPIEAGNILAMYAEITELEDLGR-----EGLVWGDLEAMEKLLVSTAY 389
                                    **************************************************66665.....456***************** PP

                                    T-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TT.SS-SGG.G-THHHH.......S---T CS
                         AFOR_C 175 regigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnr.GacHlr.ayliale.......ekvdp 245
                                    r+g+gdllA G++ +aekl+ +e+   vkG+ ++  dpr  k++++   ++   Ga H+     i +         +vd 
  gi|118430962|ref|NP_147096.2| 390 RRGVGDLLAGGARVVAEKLKRPEVRTDVKGVTIQNADPRVEKAWGVINSVEAFgGAAHIWvYGGIVASfktlgvnVAVDW 469
                                    *************************************************9999778899853344444789999955554 PP

                                    T.--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHT-- CS
                         AFOR_C 246 l.etegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleRlfnlreGlt 324
                                      ++e  a++v  +q l a+ d l++C f+    +   + +ya++lsavtG++++ e+l+ a+e    leRl+n ++G++
  gi|118430962|ref|NP_147096.2| 470 SfNPETTAKAVYEHQLLVAAADTLQVCAFSQ---YAAGWRDYARALSAVTGVKWSVEKLRGAAETLLDLERLLNQQLGIE 546
                                    41669**************************...9999****************************************** PP

                                    HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHH CS
                         AFOR_C 325 rkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkr 379
                                    + +d+lp++++e+p ++g++kg+++  ++   ++eyY lr  + +G++  e++++
  gi|118430962|ref|NP_147096.2| 547 PTEDVLPPKFTENPVPKGKHKGETA--DVSSHIEEYYSLRNLK-NGKIGSERMRE 598
                                    ************************8..7**************9.99999888875 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 !  193.2   0.0   7.1e-61   4.2e-57       2     196 ..      11     201 ..      10     203 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 7.1e-61
                                    EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTT CS
                         AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPlt 81 
                                    +++ v+L++ +ie  +l++e++e + Ggr+l+++ll++ +         + plv+at+pl+g+++++++rl++v+ksPlt
  gi|118430962|ref|NP_147096.2|  11 RVALVNLNKLRIEAVDLDPEALEYFPGGRALGVALLYNLL------GRYDSPLVLATSPLVGSGFVMANRLTIVFKSPLT 84 
                                    6889**********************************76......45789***************************** PP

                                    SSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS.EEEEE-HHHH CS
                         AFOR_N  82 gtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd.kvaviGpaGe 160
                                    gt++ +n Gg+++++lk+aG+da+vi G++++p yl ied++v++ +aedlwgld+ e++ +l++++gd +v++iGpaGe
  gi|118430962|ref|NP_147096.2|  85 GTIAWANTGGYVSPALKKAGFDALVIVGRSREPHYLLIEDGSVDLLPAEDLWGLDAVEVALMLRRRHGDvRVLSIGPAGE 164
                                    *********************************************************************9999******* PP

                                    TT-TTB-E.EETTEEE.-SSSHHHHHHHTTEEEEEEE CS
                         AFOR_N 161 nlvrfAsisvddgraa.grgGlGavmgsKnlkaivvr 196
                                    ++v++A+++ d+gr+   r G Gavmg K+lkai+++
  gi|118430962|ref|NP_147096.2| 165 RGVSYATVINDTGRSSgVRHGAGAVMGLKRLKAIALK 201
                                    ********6669996648****************987 PP

>> Caskin-Pro-rich  Proline rich region of Caskin proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05      0.22      30      80 ..     165     215 ..     152     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                Caskin-Pro-rich  30 elgsYatltrrpgRsqlvraqaaaeknvnRsqsfavRarkkGPPPPPPkRl 80 
                                    +  sYat+   +gRs  vr+ a+a  + +R ++ a++a+  G    P  R+
  gi|118430962|ref|NP_147096.2| 165 RGVSYATVINDTGRSSGVRHGAGAVMGLKRLKAIALKAKGVGSKAKPSDRS 215
                                    5679***********************************999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4447.21
//
Query:       gi|118430963|ref|NP_147099.2|  [L=84]
Description: hypothetical protein APE_0266a.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   50.2  10.7    1.4e-13   50.2  10.7    1.8  2  DUF131           Protein of unknown function DUF131
  ------ inclusion threshold ------
      0.051   13.4  10.7       0.12   12.2   2.2    2.3  2  DUF3955          Protein of unknown function (DUF3955)
        2.5    8.3  10.2        1.6    8.9   6.4    1.9  2  DUF872           Eukaryotic protein of unknown function (DUF8
        3.4    6.3  10.0        3.9    6.1  10.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
        9.8    6.3   7.8         20    5.3   1.1    2.0  2  DUF2614          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4       0.2   7.3e+02      47      58 ..      14      25 ..       9      29 .. 0.77
   2 !   50.2  10.7     4e-17   1.4e-13      15      61 ..      30      76 ..      20      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                         DUF131 47 aiiLaIilmill 58
                                   +i+L++ l+++ 
  gi|118430963|ref|NP_147099.2| 14 LIFLGVFLVFIG 25
                                   788888888876 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 4e-17
                         DUF131 15 aekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                   a ++ +rv+gGGVv++GPIPI+FGs++r+  ++ i+++++mil+++l
  gi|118430963|ref|NP_147099.2| 30 AVQGGGRVEGGGVVVVGPIPIVFGSSERMFLLSAIIGLVFMILAIAL 76
                                   667889**************************************997 PP

>> DUF3955  Protein of unknown function (DUF3955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.2   3.4e-05      0.12      32      52 ..       7      28 ..       2      32 .. 0.75
   2 ?    6.1   1.5    0.0028       9.9       3      18 ..      64      79 ..      62      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                        DUF3955 32 LhEP.FfLipiGylllligiis 52
                                   L+   F Li +G++l++ig+++
  gi|118430963|ref|NP_147099.2|  7 LVAAgFLLIFLGVFLVFIGVFA 28
                                   5555688999999999998876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0028
                        DUF3955  3 iigllllllgiillii 18
                                   iigl++++l+i+l+++
  gi|118430963|ref|NP_147099.2| 64 IIGLVFMILAIALVLL 79
                                   89**********9876 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.4   0.00044       1.6      46      96 ..       8      59 ..       3      67 .. 0.73
   2 ?    1.9   1.4     0.067   2.4e+02      73     103 ..      53      83 ..      37      84 .] 0.62

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00044
                         DUF872 46 vlaallLlllGlvLlllgvvilvepseGvss.avflvlGlllfiPGvYhvvy 96
                                   v+a +lL++lG+ L+++gv+  + +  G  +    +v+G + ++ G  + ++
  gi|118430963|ref|NP_147099.2|  8 VAAGFLLIFLGVFLVFIGVFASAVQGGGRVEgGGVVVVGPIPIVFGSSERMF 59
                                   8899****************99988877544034466666666666655555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.067
                         DUF872  73 GvssavflvlGlllfiPGvYhvvyiylavrG 103
                                    G+s+ +fl+  ++ ++  +  + ++ la +G
  gi|118430963|ref|NP_147099.2|  53 GSSERMFLLSAIIGLVFMILAIALVLLARKG 83 
                                    6666666666666666555556655555555 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.0    0.0011       3.9     380     430 ..       4      80 ..       2      84 .] 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                        DUF2207 380 lkklsalglgliilglilillallllvll..........................lvfllilllillliaiivlllf 430
                                      +l a+g++li+lg++l+++++++ ++                           + + +i++l+++++ai+++ll+
  gi|118430963|ref|NP_147099.2|   4 WGWLVAAGFLLIFLGVFLVFIGVFASAVQgggrvegggvvvvgpipivfgssermFLLSAIIGLVFMILAIALVLLA 80 
                                    568889999999999999988888888779*********************88877777777777777776666665 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.8    0.0066        24      14      32 ..      12      30 ..       7      33 .. 0.84
   2 ?    5.3   1.1    0.0055        20      23      55 ..      45      77 ..      39      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0066
                        DUF2614 14 lllvfiglivmyigllfke 32
                                   +ll+f g+ +++ig++ ++
  gi|118430963|ref|NP_147099.2| 12 FLLIFLGVFLVFIGVFASA 30
                                   789************9875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0055
                        DUF2614 23 vmyigllfkeselllvlflllGlllvlastvvy 55
                                   v  i ++f +se ++ l  ++Gl+++++++++ 
  gi|118430963|ref|NP_147099.2| 45 VGPIPIVFGSSERMFLLSAIIGLVFMILAIALV 77
                                   445678999999999999999999999887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 660.83
//
Query:       gi|14600583|ref|NP_147100.1|  [L=60]
Description: hypothetical protein APE_0266b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1150  (0.0641419); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 490.52
//
Query:       gi|118430964|ref|NP_147101.2|  [L=261]
Description: molybdate ABC transporter permease ModB [Aeropyrum pernix K1]
Scores for 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-19   68.1  13.5    8.2e-19   68.1  13.5    1.6  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 !   68.1  13.5   4.6e-23   8.2e-19       7     183 ..      72     256 ..      58     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 4.6e-23
                   BPD_transp_1   7 laalnrnkkldkllrpliivllslPsfvlaillvlvf.......vilsilghlilp..viillllsaapyvrlirraalr 77 
                                     +a ++ ++l++l++ l  +lls+P++ l+   + +f       +i+  lg  + p  vi++ ll ++p+++ +  ++++
  gi|118430964|ref|NP_147101.2|  72 AMA-RQEGRLTRLISQLHLLLLSIPPVGLGTAALILFtrypplnSISETLGLFFSPkaVILAQLLVTTPIAVSMLTGVFS 150
                                    456.999*********************9999998899******88888887777764788999**************** PP

                   BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailgydyse 152
                                     +p++l+eaa+a+Ga+r qi+ ++vlP++lp i++ l+++f ++lg++ +++ l+++ +     l + l +ai+  d+  
  gi|118430964|ref|NP_147101.2| 151 MVPRELEEAAEAYGAGRLQILIRIVLPLSLPGILSALAVTFFRALGEFGATLVLAGNIPgrtetLPLALYNAISLADV-- 228
                                    ***************************************************999988773555555555555555555.. PP

                   BPD_transp_1 153 isnggvlalviavlllnlvadilqrlldprv 183
                                        ++ a+  +vl++ lv+  +++ll+ r+
  gi|118430964|ref|NP_147101.2| 229 ---ETASAIYTLVLAVGLVTLGVHTLLYTRL 256
                                    ...5555666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1971.56
//
Query:       gi|118430965|ref|NP_147102.2|  [L=264]
Description: molybdate ABC transporter molybdate-binding protein ModA precursor [Aeropyrum pernix K1]
Scores for 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   78.4   0.1    7.8e-22   78.2   0.1    1.1  1  SBP_bac_11      Bacterial extracellular solute-binding protei
     0.0024   17.5   0.2     0.0042   16.7   0.2    1.5  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
  ------ inclusion threshold ------
      0.013   14.6   0.1      0.019   14.1   0.1    1.3  1  PBP_like        PBP superfamily domain


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 !   78.2   0.1   1.3e-25   7.8e-22       3     166 ..      37     202 ..      35     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.3e-25
                                    EEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEE CS
                     SBP_bac_11   3 vaaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplv 82 
                                    v+a  +l+a+l+e+   F+++ gv+v + +g+sg +++q++     D+++++  +   + +++gl+++e  +++   +l+
  gi|118430965|ref|NP_147102.2|  37 VFADRTLQAPLEEVLSSFSRERGVNVSYVYGSSGFVLAQLELRGNGDLYVSDGWEFAVKGVEEGLLDKEYFTVVGCIRLA 116
                                    89999***********************************9999***********************999999999**** PP

                                    EEESTT-TT---SHHH.HHHSS--EEEE--T-TTTTHH.HHHHGGG--.HHHHHHHHHTEEEEESSHHHHHHHHHTTT-S CS
                     SBP_bac_11  83 iavpkgnpkkikgwad.LlkpglklavadPttspsGlaalalleaaga.qellkalekkvvklgessrqlltaveagead 160
                                    ++v kgnpk+++++ d L ++++++a+ +P++ ++G  a+ lle +g  ++ +k + ++ v+l++s++q++ +v++g ad
  gi|118430965|ref|NP_147102.2| 117 LIVEKGNPKGVSSLRDaLERDDVTVALGNPEHVTAGVLAWRLLEELGLeEAAVKGIGDGRVVLVDSASQAAYYVATGLAD 196
                                    *************98857779**************************9999********999****************** PP

                                    EEEEEH CS
                     SBP_bac_11 161 agivye 166
                                    a+++  
  gi|118430965|ref|NP_147102.2| 197 AAVTFN 202
                                    **9875 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 !   16.7   0.2     7e-07    0.0042      84     174 ..     112     211 ..      38     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7e-07
                                    EEEEEEEEETTSS..--SHHHH...GG-EEEE--TT-TTTTHHHHHHTCCCCT--HH.....HHSSEEEE--HHHHHHHH CS
                 Phosphonate-bd  84 syrsviivradsd..iqsledL...kgktiafvspsStsGylvpaalLvkeagldpe.....ddfsevfsgshdaavlav 153
                                     +r ++iv ++++  + sl d    ++ t+a++ p+ + + ++   lL +e gl+        d + v ++s ++a+  v
  gi|118430965|ref|NP_147102.2| 112 CIRLALIVEKGNPkgVSSLRDAlerDDVTVALGNPEHVTAGVLAWRLL-EELGLEEAavkgiGDGRVVLVDSASQAAYYV 190
                                    67888999999865699**9999*9**********9988888888879.99999888443323555559*********** PP

                                    HTTSSSEEEEEHHHHHHHHHH CS
                 Phosphonate-bd 154 lsgdadaaavsadaledlvae 174
                                    + g adaa++++  +  + ++
  gi|118430965|ref|NP_147102.2| 191 ATGLADAAVTFNVYTVLMGDK 211
                                    *********988665555544 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.2e-06     0.019      39     152 ..      84     202 ..      52     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-06
                                    S---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC.-S-B-EEEEE-TTSHHHHHHHH.HHC-C CS
                       PBP_like  39 lldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdl.adaplrlvnRetGSGtrdlfde.llkke 116
                                    l+ ++  e  ++ +++ l ++e+  v +++r + l+v+kgnpk++++++d   + +++++  +    t  ++   ll++ 
  gi|118430965|ref|NP_147102.2|  84 LYVSDGWEFAVKGVEEGLLDKEYFTVVGCIRLA-LIVEKGNPKGVSSLRDAlERDDVTVALGNPEHVTAGVLAWrLLEEL 162
                                    555566677788888888888999999999976.899***********99768888888877777777766665155666 PP

                                    EECTE-SSTTSEE....ESSHHHHHCCHCCETTCCECCCG CS
                       PBP_like 117 giskssikgyaqe....arshlavaaaVaagradvgvgie 152
                                    g++++++kg +      ++s +++a +Va+g ad++v++ 
  gi|118430965|ref|NP_147102.2| 163 GLEEAAVKGIGDGrvvlVDSASQAAYYVATGLADAAVTFN 202
                                    999988888876433348999***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2082.12
//
Query:       gi|14600586|ref|NP_147103.1|  [L=144]
Description: hypothetical protein APE_0273 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   77.2   0.1    1.8e-21   76.9   0.1    1.1  1  PIN       PIN domain
    0.00021   22.0   0.2    0.00041   21.1   0.2    1.5  1  PIN_3     PIN domain
     0.0021   18.6   0.0     0.0033   18.0   0.0    1.3  1  PIN_12    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 !   76.9   0.1   2.9e-25   1.8e-21       1     121 [.       3     139 ..       3     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2.9e-25
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS...............SCHCHHHHHHHHHHH CS
                           PIN   1 ivlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlar...............rkskrekaaelvell 62 
                                   i++DTs+++a+l g++++  a++l+ ++     + ++++lv+ E+++++ r               r+++r+ +    e++
  gi|14600586|ref|NP_147103.1|   3 IFVDTSIILAFLAGQDDR--AKDLMRKVerheITGYINPLVIDEVIHGYLRlatglsarrirkllaRRDERLIKMIKGEVW 81 
                                   79**********555544..344444444458************************************************* PP

                                   HHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                           PIN  63 lllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                     l+ +  lp+ ae  e++ e++++ygl+p+Dalia t+k+h ++ iat Dedf+r+ +
  gi|14600586|ref|NP_147103.1|  82 PVLKLFTTLPLMAEPGEII-EFIEEYGLMPADALIALTCKQHELDTIATLDEDFKRIPW 139
                                   ****************999.99999*******************************975 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   6.8e-08   0.00041       1     114 [.       2     131 ..       2     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.8e-08
                         PIN_3   1 rvvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakva.ler..... 75 
                                   r+++Dt+++l+ l  ++  a+ +++ +e+++it ++ p ++dE+     r        +r+  k++++ +   ++      
  gi|14600586|ref|NP_147103.1|   2 RIFVDTSIILAFLAGQDDRAKDLMRKVERHEITGYINPLVIDEVIHGYLRL--ATGLSARRIRKLLARRDERlIKMikgev 80 
                                   799*****************************************9877666..5555566665544444433222266776 PP

                         PIN_3  76 .................kavapdaelrpllkcrDpdDqkvlelAlaaradvlVTkd 114
                                                    + ++  +e+        p+D+ ++ ++ +++ d + T d
  gi|14600586|ref|NP_147103.1|  81 wpvlklfttlplmaepgEIIEFIEEYGLM-----PADALIALTCKQHELDTIATLD 131
                                   66666666666555555444444444443.....5777777777777777777776 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.5e-07    0.0033       1      55 [.       3      55 ..       3      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.5e-07
                        PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkiee 55
                                  if+DT+i+l   f  ++++  k l + +e ++i+ +++ +v+dE+++ + +    
  gi|14600586|ref|NP_147103.1|  3 IFVDTSIILA--FLAGQDDRAKDLMRKVERHEITGYINPLVIDEVIHGYLRLATG 55
                                  9********5..55566669*************************9988766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 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:                        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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1168.11
//
Query:       gi|118430966|ref|YP_874807.1|  [L=73]
Description: hypothetical protein APE_0273a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-22   80.3   3.2    1.3e-22   80.0   3.2    1.1  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   3.2   7.4e-27   1.3e-22       1      59 []       1      63 [.       1      63 [. 0.98

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 7.4e-27
                         DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilk....eadeeeleelle 59
                                   MskvI+++YE+GvLKPLe++dL+EGeev+++I+  + i++k++gi +    ++d++e+ e+le
  gi|118430966|ref|YP_874807.1|  1 MSKVIRVKYEKGVLKPLEPLDLQEGEEVQVIIQPGEPIAEKYYGIARkhrpNLDKKEFLEVLE 63
                                   9**********************************************9**********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 615.62
//
Query:       gi|14600587|ref|NP_147104.1|  [L=116]
Description: hypothetical protein APE_0274 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 961.40
//
Query:       gi|118430967|ref|YP_874808.1|  [L=71]
Description: hypothetical protein APE_0274a [Aeropyrum pernix K1]
Scores for 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   19.4   0.2    0.00051   19.3   0.2    1.3  1  N2227            N2227-like protein
  ------ inclusion threshold ------
       0.03   15.0   0.1       0.26   12.0   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
      0.037   13.9   0.0       0.04   13.8   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      0.062   14.0   0.1       0.25   12.1   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
       0.11   11.8   0.0       0.11   11.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
       0.16   11.4   0.0       0.16   11.4   0.0    1.1  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   1.7e-07   0.00051      44      82 ..      33      70 ..       1      71 [] 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                                   HHHHHS-T......T-EEEEET-TT-HHHHHHHHTT-EE CS
                          N2227 44 elkelvpseskerekvkilvPGaGlGrlavelatkgyqv 82
                                    l ++++++  +r   +il PG+G+Gr+a+ la++gy+v
  gi|118430967|ref|YP_874808.1| 33 DLARVLEKHGIPR-GSTILEPGCGIGRVAIPLAKLGYRV 70
                                   4445555444444.468********************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.18   5.3e+02      78      93 ..      28      43 ..       8      44 .. 0.76
   2 ?   12.0   0.0   8.7e-05      0.26       1      22 [.      50      71 .]      50      71 .] 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHEEEEEE CS
                Methyltransf_11 78 ekalkeiaRvLkpgGl 93
                                   ++  + +aRvL++ G+
  gi|118430967|ref|YP_874808.1| 28 RREAEDLARVLEKHGI 43
                                   5556788999999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.7e-05
                                   EEET-TTSHHHHHHHHTTSEEE CS
                Methyltransf_11  1 LdvGcGtGrlaealakrgarvv 22
                                   L+ GcG Gr+a +lak g+rv+
  gi|118430967|ref|YP_874808.1| 50 LEPGCGIGRVAIPLAKLGYRVT 71
                                   799***************9997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05      0.04      11      48 ..      32      71 .]      16      71 .] 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                Methyltransf_23 11 dklerllpk..lraggrvLdiGcGtGillevlrengfsvt 48
                                   + l+r+l+k   ++g+ +L+ GcG G+++  l++ g+ vt
  gi|118430967|ref|YP_874808.1| 32 EDLARVLEKhgIPRGSTILEPGCGIGRVAIPLAKLGYRVT 71
                                   4455666555578999****************99998775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       0.5   1.5e+03      76      97 .]      22      42 ..      10      42 .. 0.61
   2 ?   12.1   0.0   8.4e-05      0.25       1      24 [.      49      70 ..      49      71 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.5
                                   GSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25 76 hlsdedlekalkeiarvLkpgG 97
                                    ++d+  ++  + +arvL++ G
  gi|118430967|ref|YP_874808.1| 22 RVWDRG-RREAEDLARVLEKHG 42
                                   444443.344677788887766 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.4e-05
                                   EEEET-TTSHHHHHHHCTSTSSEE CS
                Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakv 24
                                   +L+ GcG Gr+++ lak +  ++v
  gi|118430967|ref|YP_874808.1| 49 ILEPGCGIGRVAIPLAKLG--YRV 70
                                   89**************994..666 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.7e-05      0.11      51      81 ..      34      64 ..      14      71 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                                   HHHHHTTTT--TT-EEEEES-TTSHHHHHHH CS
                           CMAS 51 ldlileklelkpGmtlLdiGcGWGslvrrav 81
                                   l ++lek ++  G+t+L+ GcG G +++  +
  gi|118430967|ref|YP_874808.1| 34 LARVLEKHGIPRGSTILEPGCGIGRVAIPLA 64
                                   66899*******************9987655 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   5.3e-05      0.16      22      56 ..      37      71 .]      20      71 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                                   HHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-EEE CS
                           TehB 22 vveavkivkpgkvldlgcgqgrnslylsllgydvt 56
                                   v+e   i + + +l+ gcg gr ++ l+ lgy vt
  gi|118430967|ref|YP_874808.1| 37 VLEKHGIPRGSTILEPGCGIGRVAIPLAKLGYRVT 71
                                   55566666778899******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 592.21
//
Query:       gi|118430968|ref|NP_147105.2|  [L=133]
Description: hypothetical protein APE_0275.1, partial [Aeropyrum pernix K1]
Scores for complete 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   25.6   0.0    1.6e-05   25.3   0.0    1.2  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    0.00016   22.2   0.1      0.041   14.5   0.0    2.4  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.015   15.6   0.1        1.3    9.3   0.0    2.2  2  HHH_3     Helix-hairpin-helix motif
      0.076   12.9   1.5       0.18   11.8   0.1    2.3  3  HHH       Helix-hairpin-helix motif


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 !   25.3   0.0   3.5e-09   1.6e-05      11      88 ..       1     128 [.       1     133 [] 0.88

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.5e-09
                                    HHHHHHHHHHHHHHHS............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH............ CS
                                    xxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                        HhH-GPD  11 deranriierlferfg............fptpedladadeekLrelirelGfyrrKakyikelArilv............ 66 
                                    +++a ri  rl   +g            fp+pe+l +++ + Lr +    G+ r Ka+ ik++A                
  gi|118430968|ref|NP_147105.2|   1 MKAALRIQSRLITSYGehvsigrevfysFPDPERLISLSLDRLRRI----GLTRMKAQAIKNIAMTEYegrlpsveeieq 76 
                                    68899999999999999999**************************....**************9999999999999999 PP

                                    ...............................S-SSS--TTSHHHHHHHHHHTT CS
                                    ...............................xxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ...............................gkpdvlivvDvhvrrilkrlrs 88 
                                                                    +p  ++  D+ vrr++k + +
  gi|118430968|ref|NP_147105.2|  77 aeelssivkeltrlkgvgpwtaelaiaqvhpLFP-LGPRTDLAVRRGFKNYWG 128
                                    9999999999999999999999999988766544.366699999999988765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0     0.005        22      24      52 ..      30      57 ..      23      62 .. 0.88
   2 !   14.5   0.0   9.1e-06     0.041      23      49 ..      68      99 ..      57     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.005
                                   -SHHHHHHS-HHHHHTSTTS-HHHHHHHH CS
                          HHH_5 24 esvedlaaadveeLakipGiGkktAerii 52
                                     +e l++++ ++L +i G+   +A+ i+
  gi|118430968|ref|NP_147105.2| 30 PDPERLISLSLDRLRRI-GLTRMKAQAIK 57
                                   57899************.*9999999996 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 9.1e-06
                                   --SHHHHHHS.....-HHHHHTSTTS-HHHHH CS
                          HHH_5 23 iesvedlaaa.....dveeLakipGiGkktAe 49
                                     sve++ +a      v+eL++++G+G+ tAe
  gi|118430968|ref|NP_147105.2| 68 LPSVEEIEQAeelssIVKELTRLKGVGPWTAE 99
                                   67999998874454359***********9998 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0095        43      12      52 ..      39      80 ..      37      83 .. 0.79
   2 ?    9.3   0.0   0.00029       1.3      12      35 ..      83     106 ..      81     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0095
                          HHH_3 12 saeeLqklpGlgpklAknI..vayReknGpfksreeLlkvkgl 52
                                   s++ L+++ Gl+ ++A++I  +a+ e  G++ s+ee  + ++l
  gi|118430968|ref|NP_147105.2| 39 SLDRLRRI-GLTRMKAQAIknIAMTEYEGRLPSVEEIEQAEEL 80
                                   67788888.9*******99777788888888888887776665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00029
                          HHH_3  12 saeeLqklpGlgpklAknIvayRe 35 
                                     ++eL++l+G+gp +A+  +a  +
  gi|118430968|ref|NP_147105.2|  83 IVKELTRLKGVGPWTAELAIAQVH 106
                                    579*************98888665 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   5.7e+03      23      29 ..      52      58 ..      48      59 .. 0.81
   2 ?   -1.8   0.0      0.78   3.5e+03       9      15 ..      70      76 ..      66      82 .. 0.77
   3 ?   11.8   0.1   3.9e-05      0.18      10      25 ..      84      99 ..      84     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                                   HHHHHHH CS
                            HHH 23 tAeaIls 29
                                   +A+aI +
  gi|118430968|ref|NP_147105.2| 52 KAQAIKN 58
                                   7999976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.78
                                   SHHHHHT CS
                            HHH  9 sreeLla 15
                                   s+ee+++
  gi|118430968|ref|NP_147105.2| 70 SVEEIEQ 76
                                   7888875 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 3.9e-05
                                   HHHHHTSTT-SHHHHH CS
                            HHH 10 reeLlalPGVGpktAe 25
                                   ++eL+ l+GVGp tAe
  gi|118430968|ref|NP_147105.2| 84 VKELTRLKGVGPWTAE 99
                                   68**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1069.21
//
Query:       gi|118430969|ref|YP_874809.1|  [L=75]
Description: hypothetical protein APE_0275a [Aeropyrum pernix K1]
Scores for complete 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   72.7   1.4    2.6e-20   72.4   1.4    1.1  1  DUF2283          Protein of unknown function (DUF2283)
  ------ inclusion threshold ------
      0.054   12.4   0.1      0.062   12.2   0.1    1.0  1  Transposase_mut  Transposase, Mutator family


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 !   72.4   1.4   2.9e-24   2.6e-20       2      49 .]       7      54 ..       6      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 2.9e-24
                        DUF2283  2 itYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                    +YD+  DalYI+ +e+++++see++++ii+D+De+G++vGIEiL++S
  gi|118430969|ref|YP_874809.1|  7 LKYDRSSDALYIRVKESRIVDSEEIAPGIIVDYDEHGEIVGIEILGFS 54
                                   69*******************************************997 PP

>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.9e-06     0.062     168     205 ..      14      51 ..      11      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.9e-06
                Transposase_mut 168 DalylkvReegrvvskavliaigvdadGsreiLgleva 205
                                    Daly++v+e   v s+ +  +i vd d + ei+g+e+ 
  gi|118430969|ref|YP_874809.1|  14 DALYIRVKESRIVDSEEIAPGIIVDYDEHGEIVGIEIL 51 
                                    9**********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 575.32
//
Query:       gi|118430970|ref|NP_147106.2|  [L=108]
Description: hypothetical protein APE_0275b.1 [Aeropyrum pernix K1]
Scores for 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-08   32.3   0.0    6.6e-08   32.1   0.0    1.1  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.089   12.6   0.0       0.13   12.1   0.0    1.3  1  DUF724     Protein of unknown function (DUF724)


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 !   32.1   0.0   7.4e-12   6.6e-08     170     209 ..      47      86 ..      29     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7.4e-12
                                    -CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTC CS
                      PNP_UDP_1 170 adaveMEtaavaqlArelgipfaairvvsdlaaggadaea 209
                                    a  ++MEta v++lA+ ++ip++ai +vsd+ a+   +  
  gi|118430970|ref|NP_147106.2|  47 AESIDMETAIVYHLANKFHIPAIAILGVSDYKAKNKVEFV 86 
                                    679***************************6666322222 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.4e-05      0.13      73     100 ..      12      39 ..       7      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                         DUF724  73 lkeslaeLekhGFdVkalqsrlnkLlsl 100
                                    +k  l+  ekhGF+V  + ++l+kL   
  gi|118430970|ref|NP_147106.2|  12 KKAALNIAEKHGFNVILPDNHLTKLSLT 39 
                                    66777788****************8544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 871.41
//
Query:       gi|118430971|ref|NP_147107.2|  [L=172]
Description: hypothetical protein APE_0276.1 [Aeropyrum pernix K1]
Scores for complete 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-17   61.9   0.3      1e-16   60.4   0.2    1.9  2  DUF3368   Domain of unknown function (DUF3368)


Domain annotation for each model (and alignments):
>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.3   5.5e+03      21      25 ..      69      73 ..      60      85 .. 0.57
   2 !   60.4   0.2   5.8e-21     1e-16       1      45 [.     121     165 ..     121     166 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.3
                        DUF3368 21 kplld 25
                                    +++d
  gi|118430971|ref|NP_147107.2| 69 EEVVD 73
                                   44444 PP

  == domain 2  score: 60.4 bits;  conditional E-value: 5.8e-21
                        DUF3368   1 vtGTLGiLllAKqrGlIpsvkplldaLiqaGfrispklyaevLrl 45 
                                    v+GTLG++ lAK +Gl +++kp++d+Li++Gf+is+++++e+Lr+
  gi|118430971|ref|NP_147107.2| 121 VMGTLGVIALAKYKGLTSKAKPIIDKLIESGFWISRRTLEEFLRK 165
                                    8*******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1336.99
//
Query:       gi|118430972|ref|YP_874810.1|  [L=89]
Description: hypothetical protein APE_0276a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-26   90.2   0.1    5.8e-26   90.0   0.1    1.1  1  UPF0175   Uncharacterised protein family (UPF0175)


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 !   90.0   0.1   3.2e-30   5.8e-26       4      74 ..      12      81 ..       9      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 3.2e-30
                        UPF0175  4 ellqalklteeelerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeeleeDle 74
                                   e+++ l+ ++ ele++lri+lA+ lYe+g+ Slg+A+++agls+++flelLar+gip ++y+eeel+eDle
  gi|118430972|ref|YP_874810.1| 12 EVPEGLRVPPGELEKRLRIELALRLYEKGIASLGQARKIAGLSKWDFLELLAREGIP-LHYSEEELKEDLE 81
                                   78999****************************************************.7**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 713.18
//
Query:       gi|14600592|ref|NP_147109.1|  [L=158]
Description: hypothetical protein APE_0278 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-15   55.4   0.8    9.1e-15   55.1   0.8    1.1  1  PIN_2           PIN domain
    2.3e-08   34.8   0.2    2.8e-08   34.5   0.2    1.1  1  PIN_3           PIN domain
     0.0069   16.9   2.6     0.0094   16.4   2.6    1.2  1  PIN             PIN domain
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.019   14.6   0.1    1.1  1  DUF1367         Protein of unknown function (DUF1367)
      0.018   15.3   1.0      0.034   14.4   1.0    1.5  1  PIN_4           PIN domain
      0.025   15.1   1.1      0.077   13.5   1.1    1.7  1  PIN_12          PIN domain
      0.027   14.0   0.2      0.066   12.7   0.1    1.6  2  LuxQ-periplasm  LuxQ, periplasmic
      0.073   13.3   0.0       0.11   12.7   0.0    1.3  1  NAF             NAF domain
        0.1   12.4   0.3       0.13   12.1   0.3    1.2  1  PIN_8           PIN like domain


Domain annotation for each model (and alignments):
>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.8   4.6e-18   9.1e-15       1     104 [.      13     118 ..      13     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4.6e-18
                         PIN_2   1 VvdaNivvsallk..srikkrli..lvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslye 77 
                                   V+d+Ni+++++l+  s +++ +i  +    ++ ++ e+a++ei +h e+l+k++k+s eel +++++l  ++++ve+ +y+
  gi|14600592|ref|NP_147109.1|  13 VLDTNIILASVLRhgSYTRQVVIylIDVLGIKAFTSEKALHEIDEHLEELAKRKKVSVEELRAAIRILLLNVNMVEKGTYN 93 
                                   89***********65333333330033456789************************************************ PP

                         PIN_2  78 skikeAkeriarvDpdDtpfvAlaLll 104
                                    ++++A e +++    D+ f AlaL l
  gi|14600592|ref|NP_147109.1|  94 AYMEKAGECVKD--LADADFAALALHL 118
                                   **********97..7777778888776 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.2   1.4e-11   2.8e-08       2     115 ..      12     132 ..      11     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.4e-11
                         PIN_3   2 vvlDtnvlldallfdsp.aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvaler.....k 76 
                                    vlDtn++l+ +l++++  ++ +++++    i +++s+++l E+ + l  ela+ ++k + +++ a++    l+       
  gi|14600592|ref|NP_147109.1|  12 LVLDTNIILASVLRHGSyTRQVVIYLIDVLGIKAFTSEKALHEIDEHL-EELAK-RKKVSVEELRAAIRILLLNVnmvekG 90 
                                   69*******999999997888888999*********************.44444.44555555544444443333445558 PP

                         PIN_3  77 avapdaelrpllkcrDpdDqkvlelAla....aradvlVTkdr 115
                                   + +++ e++ ++ ++D +D+ +++lAl      +  +l+T+++
  gi|14600592|ref|NP_147109.1|  91 TYNAYMEKAGEC-VKDLADADFAALALHlsekYKNVILLTWNK 132
                                   888888888888.99************9665447889999996 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.6   4.7e-06    0.0094       2     107 ..      13     121 ..      12     136 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-06
                                   EE-HHHHHHHH.TTSHHHHHHHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                           PIN   2 vlDTsvliall.rgeekaeaarklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79 
                                   vlDT++++a + r    +++++  l ++   + +ts+ +l E+   l+      +++++ v +++l++a++il ++ + +e
  gi|14600592|ref|NP_147109.1|  13 VLDTNIILASVlRHGSYTRQVVIYLIDVlgIKAFTSEKALHEIDEHLEE-----LAKRKKVSVEELRAAIRILLLNVNMVE 88 
                                   89*********63333333333333333689999999999988888888.....555555555555555555554444444 PP

                                   H..HHHHHHHHH...SBHHHHHHHHHHHHHT-E CS
                           PIN  80 e..aaeialkyg...llpnDaliaAtAkehgik 107
                                   +  + ++++k+g   ++++Da  aA+A++   k
  gi|14600592|ref|NP_147109.1|  89 KgtYNAYMEKAGecvKDLADADFAALALHLSEK 121
                                   322445555555555************665544 PP

>> DUF1367  Protein of unknown function (DUF1367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.8e-06     0.019      73     174 ..      31     132 ..      26     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                       DUF1367  73 rklvrglakflaavagsesvlkeaadeylakvakkRaeklisidksldafr.ewvtveaGfydivelpdGslkkeaksisf 152
                                   r++v  l++ l + a   +   + +de l+++ak+++  + ++  ++   + +  +ve G y+++  ++G  +k+     f
  gi|14600592|ref|NP_147109.1|  31 RQVVIYLIDVLGIKAFTSEKALHEIDEHLEELAKRKKVSVEELRAAIRILLlNVNMVEKGTYNAYMEKAGECVKDLADADF 111
                                   6677777888877776665556667999******9988888888888876515569************************* PP

                       DUF1367 153 anmdeeeFqelYkavlnvlWnl 174
                                   a +   +  e Yk+v+   Wn 
  gi|14600592|ref|NP_147109.1| 112 AALA-LHLSEKYKNVILLTWNK 132
                                   *996.678999****9999995 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   1.7e-05     0.034       1     115 [.      12     133 ..      12     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                         PIN_4   1 fVlDTnvlLhdpealksfkeehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeelpee. 80 
                                   +VlDTn++L ++ + +      +vvi ++ +  + ++ +++ ++e++++ ++  +  + ++e+    +++  ++ ++ e+ 
  gi|14600592|ref|NP_147109.1|  12 LVLDTNIILASV-LRHGS-YTRQVVIYLIDVLGIKAFTSEKALHEIDEHLEELAKRKKVSVEELRAAIRILLLNVNMVEKg 90 
                                   59********99.55555.8999**99998888988888888844444444444433333333333333333322222221 PP

                         PIN_4  81 e........se..seknDnrIlavalelkeekpdrkvvLvskDin 115
                                             e  ++ +D    a al+l+e++  ++v+L++  +n
  gi|14600592|ref|NP_147109.1|  91 TynaymekaGEcvKDLADADFAALALHLSEKY--KNVILLTWNKN 133
                                   1223333331144679***************9..89****97666 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   3.8e-05     0.077       1      80 [.      12      95 ..      12     143 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                        PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkiees....kklekalks.lsklksakkklne 78
                                  +++DTni+l + +r +     +    li+  +ik ++++  l+E+ +++e+  +++    ++l+ a++  l +++  +k +++
  gi|14600592|ref|NP_147109.1| 12 LVLDTNIILASVLRHGSY-TRQVVIYLIDVLGIKAFTSEKALHEIDEHLEELAKRKkvsvEELRAAIRIlLLNVNMVEKGTYN 93
                                  68*******866666555.7777799****************************99444444444444353333333333333 PP

                        PIN_12 79 kk 80
                                  + 
  gi|14600592|ref|NP_147109.1| 94 AY 95
                                  33 PP

>> LuxQ-periplasm  LuxQ, periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.3e-05     0.066     149     207 ..      11      70 ..       9      92 .. 0.81
   2 ?   -1.0   0.0      0.51     1e+03      14      45 ..      97     128 ..      83     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                                   EEE-TT-HHHHHHHHHHTT-SEEEEECTTCEEEE---S-SS.S-H.HHHHT--TT----- CS
                LuxQ-periplasm 149 avvLnnNlsLleklkkgsnsenvvlivdekvvastlsgdes.yklvdvleskerdklldk 207
                                   a vL+ N+ L+  l++gs + +vv+   +    +++++++   ++++ le+ ++ k+++ 
  gi|14600592|ref|NP_147109.1|  11 ALVLDTNIILASVLRHGSYTRQVVIYLIDVLGIKAFTSEKAlHEIDEHLEELAKRKKVSV 70 
                                   89**************************99999*******98889999999887777654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                                   HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHH CS
                LuxQ-periplasm  14 qqtssliqnlfdsrLsiLqihqdssakneala 45 
                                   +++   ++ l d  +++L  h + + kn  l 
  gi|14600592|ref|NP_147109.1|  97 EKAGECVKDLADADFAALALHLSEKYKNVILL 128
                                   55666788888999999999988888776665 PP

>> NAF  NAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.6e-05      0.11      26      53 ..      44      71 ..      25      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                           NAF 26 arFtskkpaeeiiskleevakklgfkVk 53
                                  + Fts+k   ei + lee+ak+ + +V+
  gi|14600592|ref|NP_147109.1| 44 KAFTSEKALHEIDEHLEELAKRKKVSVE 71
                                  57********************999986 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   6.4e-05      0.13       2      75 ..      12      86 ..      11     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                         PIN_8  2 vvlDtNvLL.nlYryseetrkdllkvlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaek 75
                                   vlDtN++L ++ r+   tr+ ++ +++ l+ + + +  +++E  +  e++ +++k ++e+l+++++ l  ++++
  gi|14600592|ref|NP_147109.1| 12 LVLDTNIILaSVLRHGSYTRQVVIYLIDVLGIKAFTSEKALHEIDEHLEELAKRKKVSVEELRAAIRILLLNVNM 86
                                  69****9884699*************************************************9988776666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      866  (0.0483016); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 1292.08
//
Query:       gi|118430973|ref|YP_874811.1|  [L=66]
Description: hypothetical protein APE_0278a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         0  (0); expected 0.2 (1e-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: 506.96
//
Query:       gi|118430974|ref|NP_147110.2|  [L=152]
Description: hypothetical protein APE_0279.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.8   0.8    1.7e-06   28.5   0.8    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.19   12.0   0.0       0.33   11.2   0.0    1.4  1  Clr5      Clr5 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 !   28.5   0.8   1.9e-10   1.7e-06       2     120 ..       7     126 ..       6     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.9e-10
                                    EE-HHHHHHHH..TTSHHHHHHHHHHHTS.....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEB CS
                            PIN   2 vlDTsvliall..rgeekaeaarklleel.....eelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpi 73 
                                    v+D+s   +l+  +++ +a  a+k +e         ++ + l l E++ vl r     ++a  +ve+ l+  s+  il  
  gi|118430974|ref|NP_147110.2|   7 VVDASLAADLFaaKDKARAQIAEKVVE-CierhsISVYAPRLFLVEVAGVLVR-----YLAPSIVERVLDaFSSKVILVG 80 
                                    899999999998544444444444444.34777********************.....8888888888884666666667 PP

                                    CHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  74 daeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                    d++ +++a eial  g + +D + + +Ak  ++++  t D+  ++ a
  gi|118430974|ref|NP_147110.2|  81 DEAYFRIAVEIALATGSRGADSYYLGLAKTLNLPVA-TSDKVQAQNA 126
                                    8888999***************************99.***9877655 PP

>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.7e-05      0.33       7      30 ..     126     149 ..     123     152 .] 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                           Clr5   7 ahkatIrrLYleenrsLkdvmeiM 30 
                                    a ka I++ Y+  n  L+++m++M
  gi|118430974|ref|NP_147110.2| 126 ARKAGIKSFYILSNNELEELMKYM 149
                                    67999******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1159.33
//
Query:       gi|118430975|ref|NP_147111.2|  [L=66]
Description: hypothetical protein APE_0279a.1 [Aeropyrum pernix K1]
Scores for complete 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   2.6    2.8e-20   72.5   2.6    1.1  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   2.6   1.5e-24   2.8e-20       1      58 [.       1      58 [.       1      59 [. 0.93

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.5e-24
                         DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIee.akeilkklkgilkeadeeeleell 58
                                   MskvI+++YE+GvLKPLe+v+L++Geev i+I+e   e++++++  l  +++ee  e+l
  gi|118430975|ref|NP_147111.2|  1 MSKVIRVRYEKGVLKPLEPVNLEDGEEVDIIIREnLAELARRIRRRLS-QEREEPSEIL 58
                                   9*********************************99999999999888.8999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 528.95
//
Query:       gi|118430976|ref|NP_147114.2|  [L=660]
Description: hypothetical protein APE_0283.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.8   8.0       0.23   11.8   0.1    4.2  5  DUF1376       Protein of unknown function (DUF1376)
        2.2    7.9   7.7        5.2    6.7   0.8    3.1  3  GrpE          GrpE
        3.8    6.3   7.6    1.3e+02    1.2   7.6    2.2  1  LMBR1         LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> DUF1376  Protein of unknown function (DUF1376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.58   3.5e+03      15      30 ..      55      70 ..      40      77 .. 0.80
   2 ?   -2.1   0.0      0.86   5.1e+03      22      39 ..     123     140 ..     119     147 .. 0.83
   3 ?    2.6   0.1     0.029   1.7e+02      25      68 ..     188     228 ..     184     246 .. 0.67
   4 ?   -3.0   0.0       1.6   9.5e+03      59      74 ..     311     326 ..     285     331 .. 0.72
   5 ?   11.8   0.1   3.9e-05      0.23      23      74 ..     481     531 ..     477     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.58
                        DUF1376 15 ahLsaeehgaYllLld 30
                                   ++L+ae  +aY+ Ll+
  gi|118430976|ref|NP_147114.2| 55 EQLQAEYDRAYRELLK 70
                                   6789999999999987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.86
                        DUF1376  22 hgaYllLldlyyategpi 39 
                                     ++Y  +l++ +  ++ i
  gi|118430976|ref|NP_147114.2| 123 DKIYQYILKASWEYAKEI 140
                                    689999999*99998776 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.029
                        DUF1376  25 YllLldlyyategpipdDdkklarlagasteewraaveevleef 68 
                                    Y+++ dly+++   ipdD    a+     + +  + +ee l e 
  gi|118430976|ref|NP_147114.2| 188 YTQMFDLYWNK---IPDDIYNRADSQHHEVTKYLQLLEEALREA 228
                                    99********7...**9986666666555555555555555555 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.6
                        DUF1376  59 aaveevleeffelsdg 74 
                                    + + ++l+e+fe  ++
  gi|118430976|ref|NP_147114.2| 311 NHWYPFLAEWFENLEK 326
                                    5566788888876665 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 3.9e-05
                        DUF1376  23 gaYllLldlyyategpipdDdkklarlagasteewraaveevleeffelsdg 74 
                                     aY ++l +y +t g ip D ++l r++    +e +++++ +  e  +ls+g
  gi|118430976|ref|NP_147114.2| 481 EAYKRILEHYQRTHGEIPRDLRYLERVVEEE-RELEEKLKGLERENRKLSEG 531
                                    79**************************999.56556666666665566666 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.8   0.00086       5.2      30      71 ..      49      90 ..      19     109 .. 0.82
   2 ?    4.2   0.1     0.005        30      24      83 ..     367     429 ..     342     453 .. 0.71
   3 ?   -1.7   0.1      0.32   1.9e+03      12      32 ..     509     529 ..     479     538 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00086
                                   SCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           GrpE 30 elkekllrllaefenlrkrtekekeeakkfaiekfakdLLpv 71
                                    + e++++l+ae++ + + + k+ +ea++  i+k+++++ ++
  gi|118430976|ref|NP_147114.2| 49 TIDEAYEQLQAEYDRAYRELLKREKEAEDPHIKKLIQNIKEY 90
                                   458999********9999999999999*******99998665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.005
                                    HHHCTTSCCCCCCTTTTTTTTHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.. CS
                           GrpE  24 lekevkelkekllrllaefenlrkrt...ekekeeakkfaiekfakdLLpvlDnleralksak 83 
                                     e+e k++ e ++rl++e+     r+    +e+  a    i++ ak L+ vlD++ +  +  k
  gi|118430976|ref|NP_147114.2| 367 PEEERKAFREVIERLKNEIWRNPDRFvpiVEELTYATGMNIKDAAKTLIGVLDDFAKIYSGEK 429
                                    5668888888888888888844444435567888889999***************99887665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.32
                                    HHHCCCCCCTTCHHHCTTSCC CS
                           GrpE  12 deeeeleeeleelekevkelk 32 
                                    +ee elee+l+ le+e ++l+
  gi|118430976|ref|NP_147114.2| 509 EEERELEEKLKGLERENRKLS 529
                                    455666666666666666654 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   7.6     0.022   1.3e+02     197     281 ..      49     226 ..      33     548 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.022
                          LMBR1 197 dldeelkklyfeaaklntekeeaereledllkevkklrksisesd................................... 241
                                    ++de +++l++e ++ + e+ + e+e e    ++kkl ++i+e +                                   
  gi|118430976|ref|NP_147114.2|  49 TIDEAYEQLQAEYDRAYRELLKREKEAE--DPHIKKLIQNIKEYHelfrkdnemrppwmltaillnealkhgvkdrdkiy 126
                                    5666666666666666666666665555..55666666666666655555556666666666666655555555555555 PP

                          LMBR1 242 .....plrkyleeilk.......................................................kvPeeiaek 261
                                           ++y +ei +                                                       k+P +i ++
  gi|118430976|ref|NP_147114.2| 127 qyilkASWEYAKEIAQalpakkyqgrytrayadqmrnpfisiieieamireanrddpkwkkytqmfdlywnKIPDDIYNR 206
                                    55553244555555553333333332222222222223333333333333333333333333333333333333333333 PP

                          LMBR1 262 lksnenkteeslaklekqli 281
                                    + s+ ++ +++l+ le++l 
  gi|118430976|ref|NP_147114.2| 207 ADSQHHEVTKYLQLLEEALR 226
                                    33333333333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1433  (0.0799264); expected 358.6 (0.02)
Passed bias filter:                      845  (0.0471303); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.77u 0.27s 00:00:01.04 Elapsed: 00:00:00.44
# Mc/sec: 4552.38
//
Query:       gi|118430977|ref|YP_874812.1|  [L=40]
Description: hypothetical protein APE_0283a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-15   57.4   1.0    1.5e-15   57.4   1.0    1.0  1  DUF104    Protein of unknown function DUF104
  ------ inclusion threshold ------
      0.031   14.7   0.0      0.035   14.5   0.0    1.0  1  Cadherin  Cadherin domain


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   1.0   1.7e-19   1.5e-15       2      33 ..       6      37 ..       5      40 .] 0.95

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.7e-19
                         DUF104  2 skvIeavYEnGvLKPLekvdLkEGeevkikIe 33
                                   sk+I+++YE+GvLKPLe++dL+EGeev++++ 
  gi|118430977|ref|YP_874812.1|  6 SKAIRVKYEKGVLKPLEPLDLEEGEEVVVTVN 37
                                   8****************************997 PP

>> Cadherin  Cadherin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.9e-06     0.035      45      74 ..      10      39 ..       3      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                                   EEETTTTEEEESSTC-TTTSSEEEEEEEEE CS
                       Cadherin 45 ridtetgdlsttkpLdrEsqgeYeLtveat 74
                                   r+  e+g+l+  +pLd E+ +e+++tv at
  gi|118430977|ref|YP_874812.1| 10 RVKYEKGVLKPLEPLDLEEGEEVVVTVNAT 39
                                   8999***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); 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: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 314.20
//
Query:       gi|14600601|ref|NP_147118.1|  [L=195]
Description: protogloblin ApPgb [Aeropyrum pernix K1]
Scores for complete 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-35  122.2   0.0    1.9e-35  122.1   0.0    1.0  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 !  122.1   0.0   1.1e-39   1.9e-35       4     157 ..      23     194 ..      20     195 .] 0.98

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 1.1e-39
                                   HHHHHHHHTT-SHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSHHHHHHHCH.......HCHHHHHHHHHHHHHHHCCCS CS
                   Protoglobin   4 rlayllsflglteedlaaLralapliealipavvdafYekllsfpetarifet.......ssqierlkdflksyllklfsg 77 
                                   +++ l+++++l e+d+ +L+++++++++++++++d +Y +++s +++ ++f++       ++++er+++++ +++l+++ +
  gi|14600601|ref|NP_147118.1|  23 EFDLLKKTVMLGEKDVMYLKKACDVLKDQVDEILDLWYGWVASNEHLIYYFSNpdtgepiKEYLERVRARFGAWILDTTCR 103
                                   8999***************************************************************************** PP

                                   SCCHHHHHHHHHHHHHHC............HCT--HHHHHHCHHHHHHHHHHHHCCCS.-SHHHHHHHHHHHHHHHHHHHH CS
                   Protoglobin  78 pfdsayveyldkvGkmht............rlgleprwyiaalglvqevlleallekeklsaaektalvkalnKliwldnd 146
                                   ++++++++y+ +vG +h+              ++++r++ia+++++++++ ++l++k+  s+++++ +++a++K ++l+++
  gi|14600601|ref|NP_147118.1| 104 DYNREWLDYQYEVGLRHHrskkgvtdgvrtVPHIPLRYLIAFIYPITATIKPFLAKKG-GSPEDIEGMYNAWFKSVVLQVA 183
                                   **********************************************************.********************** PP

                                   HHCGGGBXTTX CS
                   Protoglobin 147 laleaYvrege 157
                                   +++++Y++e++
  gi|14600601|ref|NP_147118.1| 184 IWSHPYTKEND 194
                                   ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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 0.20s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1535.27
//
Query:       gi|14600602|ref|NP_147119.1|  [L=196]
Description: MarR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete 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-14   52.0   0.0    1.1e-13   50.9   0.0    1.6  1  MarR_2          MarR family
    1.3e-09   38.4   0.0    2.4e-09   37.6   0.0    1.4  1  HTH_27          Winged helix DNA-binding domain
    3.6e-09   36.4   0.0    6.8e-09   35.5   0.0    1.5  1  MarR            MarR family
    5.7e-06   26.1   0.2    3.1e-05   23.8   0.0    2.3  2  TrmB            Sugar-specific transcriptional regulator TrmB
    1.3e-05   24.9   0.3    6.8e-05   22.7   0.0    2.2  2  HTH_5           Bacterial regulatory protein, arsR family
    1.5e-05   24.7   0.0    0.00097   18.9   0.0    2.5  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
    0.00023   21.3   0.0    0.00048   20.3   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0056   16.7   0.0       0.02   14.9   0.0    2.0  2  HTH_20          Helix-turn-helix domain
     0.0059   16.2   0.1      0.022   14.4   0.0    1.9  2  GntR            Bacterial regulatory proteins, gntR family
     0.0064   16.0   0.1      0.035   13.7   0.0    2.4  2  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.041   14.1   0.0      0.068   13.4   0.0    1.3  1  HTH_34          Winged helix DNA-binding domain
      0.054   13.3   0.0       0.22   11.3   0.0    2.1  1  LexA_DNA_bind   LexA DNA binding domain
       0.13   12.5   0.0       0.19   12.0   0.0    1.4  1  DUF2513         Hypothetical protein (DUF2513)


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 !   50.9   0.0   7.8e-17   1.1e-13       1      61 [.      32      92 ..      32      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 7.8e-17
                                  TT--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  1 lgltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                  +gltp qa +L++++++p++  t++ l+r+lg++++++s  ++ L ++GLv+++p   D+R
  gi|14600602|ref|NP_147119.1| 32 HGLTPLQASILLYIYNSPPNHRTISSLVRELGVKQPTISDSVRALISKGLVTYEPHRSDRR 92
                                  79*****************966**********************************99**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 !   37.6   0.0   1.7e-12   2.4e-09       1      68 []      34     102 ..      34     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.7e-12
                        HTH_27   1 ltrqqalvLhlir.hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                   lt++qa +L  i+  + +  +++ l++ l v + +is s+++L+ kGLv+ ++ + drr k ++lT+kG
  gi|14600602|ref|NP_147119.1|  34 LTPLQASILLYIYnSPPNHRTISSLVRELGVKQPTISDSVRALISKGLVTYEPHRSDRRVKILKLTPKG 102
                                   7999****99999777777788**********************************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   4.9e-12   6.8e-09       1      58 [.      34      93 ..      34      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.9e-12
                                  --HHHHHHHHHHHHSTT..EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                          MarR  1 ltltqfviLrilyeqgp..lsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                  lt+ q +iL  +y+++p   ++s L + lgv+++t++  +++L+ kGl++ +++ +DrR+
  gi|14600602|ref|NP_147119.1| 34 LTPLQASILLYIYNSPPnhRTISSLVRELGVKQPTISDSVRALISKGLVTYEPHRSDRRV 93
                                  8999*************944566************************************7 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.2e-08   3.1e-05       3      58 ..      31      88 ..      29     101 .. 0.84
   2 ?   -2.2   0.0       2.9     4e+03      42      54 ..     137     149 ..     133     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.2e-08
                                  HCHHHHHCCCHCHHHHHHCC..CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  3 klGLseyEakvYlaLlklgp..atadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                  k+GL+   a++ l++ ++ p   t++ + +elgv ++++ +++r L++kGlV+ e+ r
  gi|14600602|ref|NP_147119.1| 31 KHGLTPLQASILLYIYNSPPnhRTISSLVRELGVKQPTISDSVRALISKGLVTYEPHR 88
                                  789999999999999977663369999*************************999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                                   HHHHHHHCTSEEE CS
                          TrmB  42 vLrsLedkGlVer 54 
                                   ++ sL + G++e+
  gi|14600602|ref|NP_147119.1| 137 YMASLYRYGVIEV 149
                                   6789999999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   4.9e-08   6.8e-05       8      47 .]      42      84 ..      35      84 .. 0.83
   2 ?   -0.7   0.1      0.97   1.3e+03       2      10 ..      90      98 ..      89      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.9e-08
                                  HHHHTT...SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  8 LklLae...gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                  L +  +   + ++++ l++elg+ q+t+S   ++L   GLV++
  gi|14600602|ref|NP_147119.1| 42 LLYIYNsppNHRTISSLVRELGVKQPTISDSVRALISKGLVTY 84
                                  555555455669*****************************86 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.97
                                  HHHHHHHHH CS
                         HTH_5  2 ptRlkILkl 10
                                    R+kILkl
  gi|14600602|ref|NP_147119.1| 90 DRRVKILKL 98
                                  57*****96 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 !   18.9   0.0     7e-07   0.00097      13      90 .]      40     109 ..      35     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7e-07
                       DUF1495  13 kvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeee..seglklYklteeGieivevl 90 
                                   ++lly+y+  p++++++ + r+ + k+  +           +s ++Li++GLv++e +  ++ +k+ klt++G ei+e l
  gi|14600602|ref|NP_147119.1|  40 SILLYIYNSPPNHRTISSLVRELGVKQPTIS----------DSVRALISKGLVTYEPHrsDRRVKILKLTPKGVEIAESL 109
                                   5777777777777777777777777776665..........55689*******998654488899************975 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.5e-07   0.00048      27      58 ..      57      88 ..      50      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-07
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                Fe_dep_repress 27 dlaerLnvspssVsemlkkLekdGyveyekyk 58
                                   l ++L+v+ +++s +++ L ++G+v ye+ +
  gi|14600602|ref|NP_147119.1| 57 SLVRELGVKQPTISDSVRALISKGLVTYEPHR 88
                                  6779*************************987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05      0.02      10      60 ..      36      88 ..      34      89 .. 0.90
   2 ?   -2.5   0.0       3.9   5.4e+03      45      58 ..     138     151 ..     132     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20 10 PvRrrilraL..araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                  P ++ il ++  +++  +t s l ++l++++ t+s+ +r+L + gLv+ + ++
  gi|14600602|ref|NP_147119.1| 36 PLQASILLYIynSPPNHRTISSLVRELGVKQPTISDSVRALISKGLVTYEPHR 88
                                  778888888888888899******************************98876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.9
                                   HHHHHHCTTEEEEC CS
                        HTH_20  45 LrvLeeagLvevvr 58 
                                   ++ L + g +ev r
  gi|14600602|ref|NP_147119.1| 138 MASLYRYGVIEVAR 151
                                   55677777777766 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       5.3   7.4e+03       4      20 ..      16      32 ..      14      33 .. 0.60
   2 !   14.4   0.0   1.6e-05     0.022      27      60 ..      55      88 ..      54      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.3
                                  HHHHHHHHHHHTTSS-T CS
                          GntR  4 qvyerLredIlsgelrp 20
                                  +++++ r +I +  +++
  gi|14600602|ref|NP_147119.1| 16 RIARAYRILIARESYKH 32
                                  56666666666666666 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.6e-05
                                  HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                          GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                   ++L+ e+gV+ +t+  + r L ++glv+ ++ r
  gi|14600602|ref|NP_147119.1| 55 ISSLVRELGVKQPTISDSVRALISKGLVTYEPHR 88
                                  5789************************988765 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   2.6e-05     0.035      19      48 .]      54      83 ..      41      83 .. 0.93
   2 ?   -2.1   0.0       2.1   2.9e+03      24      32 ..     117     125 ..     113     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                        HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +++ L ++lg+ ++t++  ++ L+++Gl++
  gi|14600602|ref|NP_147119.1| 54 TISSLVRELGVKQPTISDSVRALISKGLVT 83
                                  788999**********************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                        HTH_24  24 AerlglSps 32 
                                   Ae+++lS++
  gi|14600602|ref|NP_147119.1| 117 AEAVDLSRG 125
                                   99****986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     5e-05     0.068      17      74 ..      55     111 ..      39     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5e-05
                        HTH_34  17 fvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvk 74 
                                    ++l  +l++ +  +s  +++L ++g ++++   +++ +  +l++Tp+G e +++ ++
  gi|14600602|ref|NP_147119.1|  55 ISSLVRELGVKQPTISDSVRALISKGLVTYEPHRSDR-RVKILKLTPKGVEIAESLKS 111
                                   56677788999999*****************999999.99**********99887665 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 ?   11.3   0.0   0.00016      0.22       3      63 ..      33      89 ..      31      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                  ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG-C CS
                 LexA_DNA_bind  3 kLTerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpgkp 63
                                  +LT+ Q+ +l +i +s  ++    +i  + r+lg+k   ++    +aL  KG++  +p+++
  gi|14600602|ref|NP_147119.1| 33 GLTPLQASILLYIYNSPPNHR---TISSLVRELGVK-QPTISDSVRALISKGLVTYEPHRS 89
                                  688888888888877644333...5666679*****.668******************997 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.19      36      87 ..      63     111 ..      21     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                       DUF2513  36 gyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiRd 87 
                                   g+++ +i+  ++ l+ +gL+  e ++++ +   +++ +Lt +G +  +s+++
  gi|14600602|ref|NP_147119.1|  63 GVKQPTISDSVRALISKGLVTYEPHRSDRR---VKILKLTPKGVEIAESLKS 111
                                   5677799999******************99...************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 1713.16
//
Query:       gi|118430978|ref|NP_147120.2|  [L=181]
Description: ArsR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-12   46.5   0.6    4.7e-12   45.8   0.6    1.4  1  HTH_20           Helix-turn-helix domain
    6.9e-08   32.2   1.1    4.5e-07   29.6   1.1    2.2  1  HTH_5            Bacterial regulatory protein, arsR family
    2.6e-07   30.5   2.2    3.7e-07   30.0   0.6    2.1  2  HTH_12           Ribonuclease R winged-helix domain
    4.1e-06   27.1   0.7    1.3e-05   25.5   0.2    1.9  2  Penicillinase_R  Penicillinase repressor
     0.0038   17.0   1.1        1.8    8.5   0.0    2.7  2  IF2_N            Translation initiation factor IF-2, N-termin
  ------ inclusion threshold ------
      0.018   15.2   0.1       0.03   14.5   0.1    1.3  1  FUR              Ferric uptake regulator family
      0.024   14.6   0.1       0.77    9.8   0.1    2.1  2  DUF1870          Domain of unknown function (DUF1870)
      0.036   14.0   0.1       0.13   12.2   0.0    2.0  2  TBPIP            TBPIP/Hop2 winged helix domain
      0.039   13.9   3.3       0.13   12.2   0.2    2.3  2  Type2_restr_D3   Type-2 restriction enzyme D3 domain
      0.064   13.9   0.7       0.19   12.3   0.2    2.0  2  HTH_32           Homeodomain-like domain
      0.075   13.6   0.1        0.2   12.2   0.0    1.7  2  Peptidase_S66C   LD-carboxypeptidase C-terminal domain
      0.079   13.4   0.5        7.9    7.0   0.0    2.2  2  Sld5             GINS complex protein
      0.091   13.1   0.0       0.32   11.3   0.0    1.9  1  DUF2513          Hypothetical protein (DUF2513)
       0.16   11.7   0.9       0.45   10.3   0.1    2.1  3  EKR              Domain of unknown function


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 !   45.8   0.6   3.7e-15   4.7e-12       4      61 .]      23      84 ..      20      84 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 3.7e-15
                                   HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHT.....S-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  4 aeALahPvRrrilraLaraegltaselaerld.....lskntlsyHLrvLeeagLvevvregr 61
                                   a+AL+++ R +il +L  +++++++e+ + l+      + nt++yHL +L + gLv+++r+gr
  gi|118430978|ref|NP_147120.2| 23 AKALSDELRIMILEML-HERPMSVEEIVRSLRergimKTANTIRYHLSILKDSGLVDLTRVGR 84
                                   79**************.**************778899************************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   1.1   3.5e-10   4.5e-07       1      46 [.      28      78 ..      28      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.5e-10
                                   SHHHHHHHHHHTTSSEEHHHHHHHHT.....S-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelg.....lsqstvShHLkkLreaGLVe 46
                                   d+ R+ IL +L e++++v e+++ l+     ++  t+++HL++L+++GLV+
  gi|118430978|ref|NP_147120.2| 28 DELRIMILEMLHERPMSVEEIVRSLRergimKTANTIRYHLSILKDSGLVD 78
                                   789********************9977777799****************95 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 !   30.0   0.6   2.9e-10   3.7e-07       1      49 [.      32      78 ..      32      89 .. 0.88
   2 ?   -1.9   0.0       2.6   3.3e+03      18      29 ..     121     132 ..     107     143 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.9e-10
                         HTH_12  1 veILkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltr 49
                                   ++IL++l+e  +p++ +ei  +L++rg    + ++Ry+L +l + gl+ 
  gi|118430978|ref|NP_147120.2| 32 IMILEMLHE--RPMSVEEIVRSLRERGIMKTANTIRYHLSILKDSGLVD 78
                                   699999987..6****************999***************875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                         HTH_12  18 eiaeeLkkrgyd 29 
                                    ++++ +  rg +
  gi|118430978|ref|NP_147120.2| 121 IVEKLIATRGDE 132
                                    444444444444 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2     1e-08   1.3e-05       7     113 ..      31     140 ..      27     142 .. 0.80
   2 ?   -0.2   0.0      0.97   1.2e+03      72      98 ..     148     174 ..     146     181 .] 0.75

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1e-08
                                    HHHHHHHHHS-.EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXX.XXXXXXXXX CS
                Penicillinase_R   7 evmeilwekge.atvkevveeleee.kelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavas.avkqlldkl 83 
                                     +m +   +++ ++v+e+v  l e+    + +T++  l+ L + gl++  + gr++ Y +  +   ++   ++++l++++
  gi|118430978|ref|NP_147120.2|  31 RIMILEMLHERpMSVEEIVRSLRERgIMKTANTIRYHLSILKDSGLVDLTRVGRTYKYVAKSRYYAYTGDpEADKLIEEM 110
                                    555544444444*************78889*******************************9999998762666677766 PP

                                    XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                Penicillinase_R  84 fegsvkelvaafveee.klseddleeLrell 113
                                      ++vk+ v ++ve+      d+l +++e l
  gi|118430978|ref|NP_147120.2| 111 A-EEVKDDVKRIVEKLiATRGDELVAIAEKL 140
                                    6.59999999999998666677777777766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.97
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Penicillinase_R  72 vasavkqlldklfegsvkelvaafvee 98 
                                    ++++v+q++ +++++s+ +++a+ +  
  gi|118430978|ref|NP_147120.2| 148 TKHFVEQVIFEIIKKSLGSVLAETTLA 174
                                    577889999999999999999876655 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 !    8.5   0.0    0.0014       1.8      15      37 ..      43      63 ..      23      64 .. 0.84
   2 !    6.5   0.7    0.0058       7.4       6      26 ..     107     127 ..     102     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                          IF2_N 15 vkskevikkLfkelGievkshss 37
                                   ++++e+++ L +  Gi+ k+++ 
  gi|118430978|ref|NP_147120.2| 43 MSVEEIVRSLRE-RGIM-KTANT 63
                                   899*******55.****.**996 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0058
                          IF2_N   6 VyeLAkeLgvkskevikkLfk 26 
                                    + e A+e + ++k++++kL +
  gi|118430978|ref|NP_147120.2| 107 IEEMAEEVKDDVKRIVEKLIA 127
                                    7899***************65 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.3e-05      0.03      10     100 ..      31     125 ..      27     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHHHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETT.....SEEEEEESS.SSSEEEEEE CS
                            FUR  10 RekilevlekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefed.....gesryelak.kehhdhlic 83 
                                    R  ile+l++ +  +s+ee++++l+e++      T+   L +l+++glv+ + +       ++sry+  + + + d li+
  gi|118430978|ref|NP_147120.2|  31 RIMILEMLHERP--MSVEEIVRSLRERGIMKTANTIRYHLSILKDSGLVDLTRVGRtykyvAKSRYYAYTgDPEADKLIE 108
                                    555666666555..8**********************************9877763111224566666665778888888 PP

                                    TTT--EEEE--HHHHHH CS
                            FUR  84 ekCgkviefkddeieki 100
                                    e   +v++  +  +ek+
  gi|118430978|ref|NP_147120.2| 109 EMAEEVKDDVKRIVEKL 125
                                    88777777666666665 PP

>> DUF1870  Domain of unknown function (DUF1870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0006      0.77      40      82 ..      23      68 ..      20      74 .. 0.85
   2 ?    2.9   0.0     0.081     1e+02      22      70 ..      93     141 ..      79     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                                   SS---HHHHHHHHHHHHHHHHHHHHHHHHHCCS...-S--EEE--S CS
                        DUF1870 40 alpipdeivaelkelkklrkkkieeiveklndr...ignstlryys 82
                                   a +++de+   + e+ + r   +eeiv +l +r     ++t+ry+ 
  gi|118430978|ref|NP_147120.2| 23 AKALSDELRIMILEMLHERPMSVEEIVRSLRERgimKTANTIRYHL 68
                                   56899***************************94433567999986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.081
                                    HHTSSS--HHHHHHHHTTSS---HHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        DUF1870  22 eyigkavdsatWknWesgalpipdeivaelkelkklrkkkieeivekln 70 
                                     y + ++d ++ k  e+ a  + d ++  +++l ++r +++ +i ekl+
  gi|118430978|ref|NP_147120.2|  93 RYYAYTGDPEADKLIEEMAEEVKDDVKRIVEKLIATRGDELVAIAEKLK 141
                                    5666667777777778888889999999999999999999988888775 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.13       6      61 ..      34      90 ..      29      91 .. 0.81
   2 ?   -1.7   0.1       2.2   2.8e+03      32      42 ..     115     125 ..     103     129 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                          TBPIP  6 vleylqeqnrPfsvqdvvanlqk.klgKt..avqkaLdeLvdegkiieKeyGKqkiYla 61
                                   +le+l+e  rP+sv+++v  l++ ++ Kt  ++   L  L+d+g++  +  G +  Y+a
  gi|118430978|ref|NP_147120.2| 34 ILEMLHE--RPMSVEEIVRSLRErGIMKTanTIRYHLSILKDSGLVDLTRVGRTYKYVA 90
                                   6677765..9************9988886225888999999999999999998877765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.2
                          TBPIP  32 KtavqkaLdeL 42 
                                    K  v +++++L
  gi|118430978|ref|NP_147120.2| 115 KDDVKRIVEKL 125
                                    44555566655 PP

>> Type2_restr_D3  Type-2 restriction enzyme D3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2    0.0001      0.13      15      62 ..      31      76 ..      29      82 .. 0.87
   2 ?    1.9   0.3      0.16   2.1e+02      43      57 ..     107     121 ..     102     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                 Type2_restr_D3 15 RtiilkylleskkrrsleeikayLklagleEdveTIkDDiqgliniGl 62
                                   R +il++l e    +s+eei   L+  g+  + +TI+  +  l + Gl
  gi|118430978|ref|NP_147120.2| 31 RIMILEMLHERP--MSVEEIVRSLRERGIMKTANTIRYHLSILKDSGL 76
                                   778999996655..***********************88887777776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                 Type2_restr_D3  43 leEdveTIkDDiqgl 57 
                                    +eE  e +kDD++ +
  gi|118430978|ref|NP_147120.2| 107 IEEMAEEVKDDVKRI 121
                                    899999*****9865 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   0.00015      0.19      16      62 ..      14      57 ..       6      68 .. 0.69
   2 ?   -0.5   0.0       1.6     2e+03      31      56 ..     101     125 ..      73     140 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         HTH_32 16 gLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregv 62
                                    L + +     + lsde+r  i+++l +e+ +s +++++ l+er+ +
  gi|118430978|ref|NP_147120.2| 14 RLIPVRLE-EAKALSDELRIMILEML-HERPMSVEEIVRSLRERG-I 57
                                   55555333.3345*************.55579*********5444.4 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.6
                         HTH_32  31 devrariiallreeprWsprqlaarl 56 
                                    +e  + i +++ ee +   ++++++l
  gi|118430978|ref|NP_147120.2| 101 PEADKLIEEMA-EEVKDDVKRIVEKL 125
                                    45555555555.33222344444444 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016       0.2      27      62 ..      29      64 ..       7      67 .. 0.81
   2 ?   -2.0   0.0       3.8   4.8e+03      87      94 ..     108     115 ..      83     131 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                   ..EEEEEE--TTHHHHHHHHHHHHCTSTTGGG--EE CS
                 Peptidase_S66C 27 kgkILflEdvsespyridrmLtqlkeagvldkvkGi 62
                                   + +I++lE ++e p ++++++++l+e+g+++ ++ i
  gi|118430978|ref|NP_147120.2| 29 ELRIMILEMLHERPMSVEEIVRSLRERGIMKTANTI 64
                                   449***************************998765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                                    HHHHHT-G CS
                 Peptidase_S66C  87 eevlaeil 94 
                                    ee+ +e+ 
  gi|118430978|ref|NP_147120.2| 108 EEMAEEVK 115
                                    22222221 PP

>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.029        38      52      91 ..      29      69 ..      15      85 .. 0.65
   2 ?    7.0   0.0    0.0061       7.9      56      89 ..     106     140 ..      90     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.029
                                   HHHHHHHHHHT..HCHHHHHHHHHHHHHHHHHHHTHCHHHH CS
                           Sld5 52 elavkllelard.ldelkrllrdllevRlakirkfaenled 91
                                   el +++le+  + +  + +++r+l+e  + k  +  ++  +
  gi|118430978|ref|NP_147120.2| 29 ELRIMILEMLHErPMSVEEIVRSLRERGIMKTANTIRYHLS 69
                                   66777788877777777777777777666665555555555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0061
                                    HHHHHHT..HCHHHHHHHHHHHHHHHHHHHTHCHH CS
                           Sld5  56 kllelard.ldelkrllrdllevRlakirkfaenl 89 
                                     + e+a++  d++kr++++l+ +R +++  +ae+l
  gi|118430978|ref|NP_147120.2| 106 LIEEMAEEvKDDVKRIVEKLIATRGDELVAIAEKL 140
                                    577899988999***************99999987 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.32      37      65 ..      59      87 ..      32     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                        DUF2513 37 yskeeiiyhlkllaeagLieaekkkakss 65
                                    ++++i yhl++l + gL++ + + ++ +
  gi|118430978|ref|NP_147120.2| 59 KTANTIRYHLSILKDSGLVDLTRVGRTYK 87
                                   45679***************999888777 PP

>> EKR  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.3   5.4e+03      10      21 ..      39      50 ..      36      54 .. 0.76
   2 ?   10.3   0.1   0.00035      0.45       6      31 ..     108     133 ..     103     135 .. 0.87
   3 ?   -2.2   0.0         3   3.8e+03      14      25 ..     150     161 ..     141     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                                   ----HHHHHTHH CS
                            EKR 10 edapefVkevla 21
                                   +++p  V+e+++
  gi|118430978|ref|NP_147120.2| 39 HERPMSVEEIVR 50
                                   678888999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                                    --..----HHHHHTHHHHHTT-GGGS CS
                            EKR   6 pkvpedapefVkevlapinaqeGDeL 31 
                                    +++ e+  + Vk+++++ +a +GDeL
  gi|118430978|ref|NP_147120.2| 108 EEMAEEVKDDVKRIVEKLIATRGDEL 133
                                    6677889999**************99 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3
                                    HHHHHTHHHHHT CS
                            EKR  14 efVkevlapina 25 
                                     fV++v+ +i++
  gi|118430978|ref|NP_147120.2| 150 HFVEQVIFEIIK 161
                                    699999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1395.67
//
Query:       gi|118430979|ref|YP_874813.1|  [L=71]
Description: hypothetical protein APE_0290a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.1   0.0       0.18   11.7   0.0    1.3  1  AhpC-TSA  AhpC/TSA family
       0.15   11.8   0.0       0.16   11.7   0.0    1.2  1  Redoxin   Redoxin


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 ?   11.7   0.0     2e-05      0.18      96     123 ..       8      37 ..       2      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                                    HHTT-EETT..TTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  96 kaygvlkee..kglalratfvidkegkiry 123
                                      +gvlk      +a ratfvid+eg i++
  gi|118430979|ref|YP_874813.1|   8 SLFGVLKGLgpIRFADRATFVIDSEGRIAK 37 
                                    5677886667788999***********986 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.7e-05      0.16     113     142 ..      21      49 ..       5      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                                    EEE-EEEEEEETTEEEEEEESSSCHTSTTS CS
                        Redoxin 113 lrtpryavidedgkvvylevepepeteesn 142
                                    ++ ++++vid +g++ +++++ ++ + ++ 
  gi|118430979|ref|YP_874813.1|  21 FADRATFVIDSEGRIAKVIRGFMNAE-RHV 49 
                                    56689****************99965.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.19s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 583.35
//
Query:       gi|14600604|ref|NP_147121.1|  [L=110]
Description: thiol peroxidase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-29  102.8   0.0    1.3e-29  102.7   0.0    1.0  1  AhpC-TSA       AhpC/TSA family
    1.4e-20   73.5   0.0    1.7e-20   73.3   0.0    1.0  1  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.029   13.9   0.0      0.098   12.2   0.0    1.8  1  GSHPx          Glutathione peroxidase
      0.081   13.3   0.0      0.095   13.0   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
       0.15   12.2   0.0       0.19   11.9   0.0    1.1  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.0   3.5e-33   1.3e-29       1      98 [.       4     101 ..       4     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 3.5e-33
                                   TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes 81 
                                   vgd+apd+e +  dg t++ls+++g+ vvl+fypk+++p+Ct+e+  ++ lyeefk++g+evigvs+d+p + ++f++ ++
  gi|14600604|ref|NP_147121.1|   4 VGDPAPDIEIQLIDGSTIRLSQLRGRSVVLYFYPKAFTPGCTREAIGFNGLYEEFKKLGAEVIGVSMDPPGRNRRFAQNYG 84 
                                   89******************************************************************************* PP

                                   .SSEEEE-TTSHHHHHT CS
                      AhpC-TSA  82 lnfpllsDeegkvakay 98 
                                   + f+l+sD eg+++k++
  gi|14600604|ref|NP_147121.1|  85 VRFRLASDVEGEAFKSF 101
                                   **************998 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   4.7e-24   1.7e-20       2     103 ..       4     104 ..       3     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 4.7e-24
                                   TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH CS
                       Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk 82 
                                   +gd+aPd++ +l   dg+++ ls+++g++vv++f+p af+P C++e++ ++ l+e++k+ g +v++v++d     ++f+ +
  gi|14600604|ref|NP_147121.1|   4 VGDPAPDIEIQL--IDGSTIRLSQLRGRSVVLYFYPKAFTPGCTREAIGFNGLYEEFKKLGAEVIGVSMDPPGRNRRFAQN 82 
                                   7********999..******************************************************************* PP

                                   TT-TSEEEE-.TTSHHHHHTT- CS
                       Redoxin  83 eglkfpvlsD.gsaaftkalGl 103
                                   +g+ f+++sD ++ af + +G+
  gi|14600604|ref|NP_147121.1|  83 YGVRFRLASDvEGEAFKSFWGA 104
                                   **********666666666665 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.7e-05     0.098       5      60 ..      12      69 ..       9     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.7e-05
                                  EEEBTTSSEEEGGGGTTSEEEE..EEEESSSTTHHHHHHHHHHHHHHGGGTEEEEEEE CS
                         GSHPx  5 sakdidgekvkleklrgkvvli..vnvaskCglteqykeleelqkrykdkglvilgfP 60
                                  + + idg+++ l++lrg+ v++     a + g t +   ++ l++++k+ g  ++g  
  gi|14600604|ref|NP_147121.1| 12 EIQLIDGSTIRLSQLRGRSVVLyfYPKAFTPGCTREAIGFNGLYEEFKKLGAEVIGVS 69
                                  566799***********98775115679999***********************9975 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.095       2      45 ..      29      72 ..      28     100 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                  SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
                 Thioredoxin_8  2 kvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsldk 45
                                  + v+Lyf+ + + p c++     + lye++k k + e++ vs+d 
  gi|14600604|ref|NP_147121.1| 29 RSVVLYFYPKaFTPGCTREAIGFNGLYEEFK-KLGAEVIGVSMDP 72
                                  678888886538888***************9.7**********95 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.2e-05      0.19       6      51 ..      55     101 ..      51     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-05
                    AhpC-TSA_2   6 kpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqal 51 
                                    +e+++ g ++++++ + p+  ++F++  g+ f l  D ++++++++
  gi|14600604|ref|NP_147121.1|  55 YEEFKKLGAEVIGVSMDPPGrNRRFAQNYGVRFRLASDVEGEAFKSF 101
                                   6899***************55******************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 851.77
//
Query:       gi|118430980|ref|YP_874814.1|  [L=92]
Description: hypothetical protein APE_0291a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.84    9.8   5.1        1.9    8.6   5.1    1.7  1  DUF4079   Protein of unknown function (DUF4079)
       0.88    9.9  10.2       0.47   10.8   8.5    1.5  1  DUF3995   Protein of unknown function (DUF3995)
          2    8.3   5.7        1.3    8.9   4.1    1.5  2  DUF3487   Protein of unknown function (DUF3487)
        2.2    8.3  10.5        0.8    9.7   0.6    2.8  3  DUF485    Protein of unknown function, DUF485


Domain annotation for each model (and alignments):
>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.1   0.00043       1.9      47      89 ..      28      72 ..       3      91 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00043
                        DUF4079 47 rdeHvklgslllllvvlgaigglvll..ylrrgklfpssHlyaGl 89
                                   r  H  +g+ +++l++l+++ g++++  y+r  ++ ++  l a l
  gi|118430980|ref|YP_874814.1| 28 RISHTPVGKAMVVLAALFLVQGVIATatYYRLASEGYGMELAAPL 72
                                   345666666666666666666666431146666666666555555 PP

>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   8.5   0.00011      0.47      41      97 ..       4      60 ..       1      73 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                        DUF3995 41 tlavallllaaAllvlalarllgaplssrllrlaawvvaavlllRgilgdfkyvgvf 97
                                   ++a+al+ + a l++++l  +  ++ s++ +  a++v+aa++l+ g++++++y+++ 
  gi|118430980|ref|YP_874814.1|  4 LWAIALVAAIAQLVLAILLAANYGRISHTPVGKAMVVLAALFLVQGVIATATYYRLA 60
                                   45555555555555555555555888999999*****************99999876 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.1    0.0003       1.3      25      74 ..       4      53 ..       1      58 [. 0.89
   2 ?   -1.8   0.0      0.62   2.8e+03      43      44 ..      77      78 ..      59      91 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0003
                        DUF3487 25 llvlaglglvvglvlglllallvgslaliptialllvllvvlvggkllar 74
                                   l+++a++++++ lvl++lla+  g +   p +  ++vl+ ++++ +++a+
  gi|118430980|ref|YP_874814.1|  4 LWAIALVAAIAQLVLAILLAANYGRISHTPVGKAMVVLAALFLVQGVIAT 53
                                   99****************************99999998888888887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.62
                        DUF3487 43 la 44
                                   +a
  gi|118430980|ref|YP_874814.1| 77 VA 78
                                   11 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   0.00018       0.8      52      78 ..       6      32 ..       2      38 .. 0.88
   2 ?    4.0   0.7     0.011        48      54      78 ..      38      62 ..      31      67 .. 0.79
   3 ?    0.8   0.1      0.11   4.9e+02      42      63 ..      68      87 ..      63      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00018
                         DUF485 52 tvglllgllqivltflltglYvrrAnr 78
                                    ++l+++++q+vl++ll++ Y r++ +
  gi|118430980|ref|YP_874814.1|  6 AIALVAAIAQLVLAILLAANYGRISHT 32
                                   5899*****************999876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.011
                         DUF485 54 glllgllqivltflltglYvrrAnr 78
                                    ++l++l +v  +++t+ Y r A +
  gi|118430980|ref|YP_874814.1| 38 MVVLAALFLVQGVIATATYYRLASE 62
                                   567788888888999999*999976 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.11
                         DUF485 42 latkvgegnitvglllgllqiv 63
                                   la++++  +itv+ l+gl+++ 
  gi|118430980|ref|YP_874814.1| 68 LAAPLA--AITVASLAGLSILY 87
                                   556666..57777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 695.24
//
Query:       gi|14600606|ref|NP_147123.1|  [L=101]
Description: ArsR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-10   39.3   0.6    5.6e-10   38.9   0.6    1.2  1  HTH_5          Bacterial regulatory protein, arsR family
    5.5e-08   32.8   1.5    8.8e-08   32.1   1.5    1.3  1  HTH_20         Helix-turn-helix domain
     0.0004   20.2   0.7    0.00069   19.5   0.7    1.3  1  MarR_2         MarR family
    0.00067   19.7   0.5      0.001   19.1   0.5    1.3  1  DprA_WH        DprA winged helix domain
     0.0019   18.0   0.0     0.0026   17.6   0.0    1.2  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0077   16.0   0.1      0.015   15.0   0.1    1.5  1  LexA_DNA_bind  LexA DNA binding domain
  ------ inclusion threshold ------
      0.012   15.7   0.4      0.018   15.1   0.4    1.4  1  HTH_29         Winged helix-turn helix
       0.02   14.5   0.1      0.025   14.2   0.1    1.3  1  RP-C           Replication protein C N-terminal domain
      0.031   13.9   0.1      0.057   13.0   0.1    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.033   14.1   0.1      0.057   13.4   0.1    1.4  1  HTH_11         HTH domain
      0.039   14.0   0.0      0.047   13.7   0.0    1.1  1  HTH_45         Winged helix-turn-helix
      0.045   14.1   0.4      0.073   13.4   0.4    1.4  1  Rrf2           Transcriptional regulator
      0.049   13.4   0.3       0.11   12.4   0.3    1.7  1  HTH_23         Homeodomain-like domain
       0.05   13.4   3.9      0.054   13.3   3.1    1.5  2  HTH_IclR       IclR helix-turn-helix domain
      0.061   12.5   0.0       0.07   12.4   0.0    1.1  1  DDE_Tnp_2      Archaeal putative transposase ISC1217
      0.078   13.1   0.1       0.11   12.7   0.1    1.2  1  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
      0.082   13.0   0.6        0.1   12.7   0.6    1.1  1  Replic_Relax   Replication-relaxation
       0.18   11.8   0.0       0.24   11.4   0.0    1.1  1  Dimerisation2  Dimerisation 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 !   38.9   0.6   5.6e-13   5.6e-10       3      45 ..      24      66 ..      22      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.6e-13
                                  HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  3 tRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                  tR +IL+lL+e+++ +++l+ elgl+  tv hHL +L   GL+
  gi|14600606|ref|NP_147123.1| 24 TRARILMLLRERPRNAHQLSQELGLNYRTVLHHLEVLARHGLI 66
                                  9****************************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   1.5   8.8e-11   8.8e-08      11      56 ..      24      68 ..      23      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 8.8e-11
                                  HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  +R+ril +L r++++ a +l ++l+l   t+ +HL+vL+++gL+ +
  gi|14600606|ref|NP_147123.1| 24 TRARILMLL-RERPRNAHQLSQELGLNYRTVLHHLEVLARHGLIAR 68
                                  8********.**********************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.7   6.9e-07   0.00069       6      53 ..      24      68 ..      22      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 6.9e-07
                                  HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  + ar+L+ L+ rp+   ++ +l ++lgl   +v  +l+ L ++GL+ r
  gi|14600606|ref|NP_147123.1| 24 TRARILMLLRERPR---NAHQLSQELGLNYRTVLHHLEVLARHGLIAR 68
                                  789**********6...*****************************87 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.5     1e-06     0.001      14      58 ..      25      69 ..      23      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                       DprA_WH 14 errvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58
                                  ++r+L +L   P+   qL++++gl  ++v+++L  L   Gl++rl
  gi|14600606|ref|NP_147123.1| 25 RARILMLLRERPRNAHQLSQELGLNYRTVLHHLEVLARHGLIARL 69
                                  89*******************************999999998887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.6e-06    0.0026      16      58 ..      30      72 ..      28      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                  HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   Ll++ p +a ++++elg+ + +v   L+ L + Gl+ r  + 
  gi|14600606|ref|NP_147123.1| 30 MLLRERPRNAHQLSQELGLNYRTVLHHLEVLARHGLIARLYEG 72
                                  699**********************************997765 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 !   15.0   0.1   1.5e-05     0.015      29      58 ..      40      68 ..      27      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                 LexA_DNA_bind 29 reiaralglkSpsaveehLkaLerKGyier 58
                                   +++++lgl+  ++v +hL+ L+r G+i r
  gi|14600606|ref|NP_147123.1| 40 HQLSQELGLN-YRTVLHHLEVLARHGLIAR 68
                                  6899******.9***************986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.4   1.8e-05     0.018       1      55 [.      25      78 ..      25      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                        HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegG.laalldrrrsgrprn 55
                                  Ra++l+ll+e   +  q+ + lgl +rtv ++l+    +G +a l +++  g+p+ 
  gi|14600606|ref|NP_147123.1| 25 RARILMLLRERPRNAHQLSQELGLNYRTVLHHLEVLARHGlIARLYEGY--GAPYA 78
                                  89999*9999755***************************666698888..66665 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 ?   14.2   0.1   2.5e-05     0.025      74     103 ..      39      68 ..      22      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                          RP-C  74 NaqLsralglsestlrrhlaaLveaGliir 103
                                   ++qLs++lgl  +t+ +hl  L+  Gli+r
  gi|14600606|ref|NP_147123.1|  39 AHQLSQELGLNYRTVLHHLEVLARHGLIAR 68 
                                   45788***********************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.7e-05     0.057      21      47 ..      40      66 ..      24      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.7e-05
                        HTH_24 21 reLAerlglSpstvnrrlkrLeeeGlI 47
                                   +L+++lgl   tv+ +l+ L + GlI
  gi|14600606|ref|NP_147123.1| 40 HQLSQELGLNYRTVLHHLEVLARHGLI 66
                                  58**********************999 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.7e-05     0.057       4      43 ..      27      64 ..      24      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-05
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                   il lL ++r+  ++ +L++eL++  rtv  +++ L   g
  gi|14600606|ref|NP_147123.1| 27 RILMLL-RERP-RNAHQLSQELGLNYRTVLHHLEVLARHG 64
                                  566666.6665.79****************9999986655 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.7e-05     0.047      10      60 ..      27      81 ..      24      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                        HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTe 60
                                   IL  ++e   +  ++  +  L+y+++   L+ L   gli    +  +  Y lT+
  gi|14600606|ref|NP_147123.1| 27 RILMLLRERPRNAHQLSQELGLNYRTVLHHLEVLARHGLIarlyEGYGAPYALTN 81
                                  68999999999999**************************776655667777776 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   7.3e-05     0.073      12      69 ..      27      81 ..      17      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                                  HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE.EETTT-TCEEESS CS
                          Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk.svrGkgGGyrLak 69
                                  ++l+ L ++++    ++++++++ +++ + + + l+ L+++gl+    +G g  y+L+ 
  gi|14600606|ref|NP_147123.1| 27 RILMLLRERPR----NAHQLSQELGLNYRTVLHHLEVLARHGLIArLYEGYGAPYALTN 81
                                  56666666666....56**************************9614567777776665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00011      0.11       6      39 ..      24      58 ..      22      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                        HTH_23  6 eRlrillllae.GlsvreIAreLgvsrrTvyrwlk 39
                                   R+ril ll+e   + ++ ++eLg ++rTv + l+
  gi|14600606|ref|NP_147123.1| 24 TRARILMLLRErPRNAHQLSQELGLNYRTVLHHLE 58
                                  7*********9966****************76655 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 ?   13.3   3.1   5.4e-05     0.054       6      50 ..      26      68 ..      23      69 .. 0.94
   2 ?   -3.2   0.0       7.8   7.8e+03      20      27 ..      78      85 ..      74      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                                  HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                  ++iL +l+e+p+     +l++++gl+  tv ++L  L ++G++ +
  gi|14600606|ref|NP_147123.1| 26 ARILMLLRERPRN--AHQLSQELGLNYRTVLHHLEVLARHGLIAR 68
                                  58999*******7..9**************************976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.8
                                  BHHHHHHH CS
                      HTH_IclR 20 tlselArr 27
                                   l+ lA+r
  gi|14600606|ref|NP_147123.1| 78 ALTNLAER 85
                                  68888875 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     7e-05      0.07      31      74 ..      22      67 ..       9      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7e-05
                     DDE_Tnp_2 31 dvavrlvlgav..iGgrateiaqeveldyetvlknldklanidlle 74
                                   v    +l+ +    ++a +++qe+ l+y tvl+ l+ la+  l+ 
  gi|14600606|ref|NP_147123.1| 22 GVTRARILMLLreRPRNAHQLSQELGLNYRTVLHHLEVLARHGLIA 67
                                  5555444554411457999********************9988875 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 ?   12.7   0.1   0.00011      0.11       6      57 ..      15      66 ..      10      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                  HHHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                         HTH_9  6 iieehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                  +ie   G v ++ + +Llr+  + + +l+++++L+ + V + L vL +h+l+
  gi|14600606|ref|NP_147123.1| 15 LIEGSRGGVTRARILMLLRERPRNAHQLSQELGLNYRTVLHHLEVLARHGLI 66
                                  5555556666666889*********************************997 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6    0.0001       0.1       4      69 ..      31      87 ..      29     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                  Replic_Relax  4 LaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarll 69
                                  L + r+ +++q+ + l  + r+ +   L  L+++gl++rl++      +   ++ YaLt++++r+ 
  gi|14600606|ref|NP_147123.1| 31 LLRERPRNAHQLSQELGLNYRT-VLHHLEVLARHGLIARLYEG-----Y---GAPYALTNLAERHW 87
                                  5567899999****99999999.****************8887.....3...56899****99997 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.24      26      83 ..      31      86 ..      24      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                 Dimerisation2 26 lLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelasty 83
                                  lL+e +p +a+++++elg++ + +   l++++  gL  r   e+ +a Y  t+la+++
  gi|14600606|ref|NP_147123.1| 31 LLRE-RPRNAHQLSQELGLNYRTVLHHLEVLARHGLIARL-YEGYGAPYALTNLAERH 86
                                  5666.9********************************66.4555799******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 809.85
//
Query:       gi|118430981|ref|NP_147124.2|  [L=146]
Description: hypothetical protein APE_0294.1 [Aeropyrum pernix K1]
Scores for complete 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-11   42.9   0.0    4.6e-11   42.7   0.0    1.1  1  Cupredoxin_1  Cupredoxin-like domain
    3.9e-05   24.0   0.1    9.1e-05   22.8   0.1    1.6  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
      0.015   14.8   0.0       0.25   10.8   0.0    2.1  2  SoxE          Sulfocyanin (SoxE) domain
      0.073   12.8   0.0       0.15   11.8   0.0    1.5  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 !   42.7   0.0     1e-14   4.6e-11      17      96 ..      48     132 ..      16     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1e-14
                   Cupredoxin_1  17 aaaektveitvkdggfePskievkagekvklkiknkdktpeefesed....lgee.kvlapgktttitiaplkpGeYeft 91 
                                    a ++++v++++ + g++ +k   kagekv ++++nk++ ++ fe+e+    +++e k+lapg++t++++   +pGeYe +
  gi|118430981|ref|NP_147124.2|  48 AGGSTVVKVELYEWGIKIDKTMFKAGEKVVFEVVNKGSYTHAFEIENddigFEVEtKNLAPGESTKLEVVFPQPGEYEVY 127
                                    6778899***************************************9999977666************************ PP

                   Cupredoxin_1  92 cdmhm 96 
                                    c ++ 
  gi|118430981|ref|NP_147124.2| 128 CPIDG 132
                                    *9765 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 !   22.8   0.1     2e-08   9.1e-05      22      98 ..      71     144 ..      63     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2e-08
                                    ETTEEEEE..EEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEET.T.TTTTTSEEEEE CS
                    Copper-bind  22 kkgekvtf..vnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCs.P.HaaagMkgkvt 97 
                                    k+gekv+f  vn+ ++ H  ++++d +  +v+++++ ++++t       k +v f ++g+Y+++C    H+  gM++ +t
  gi|118430981|ref|NP_147124.2|  71 KAGEKVVFevVNKGSYTHAFEIENDDIGFEVETKNLAPGEST-------KLEVVFPQPGEYEVYCPiDgHRDFGMEALIT 143
                                    567776662244466777777777777666666666665444.......5677788*********9857**********9 PP

                                    E CS
                    Copper-bind  98 v 98 
                                    v
  gi|118430981|ref|NP_147124.2| 144 V 144
                                    9 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.028   1.3e+02      44      65 ..      71      92 ..      65     105 .. 0.85
   2 ?   10.8   0.0   5.6e-05      0.25     115     139 ..     121     145 ..     100     146 .] 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.028
                           SoxE 44 Pagwsvlvklvneeslphnlvl 65
                                    ag +v++++vn+ s +h+  +
  gi|118430981|ref|NP_147124.2| 71 KAGEKVVFEVVNKGSYTHAFEI 92
                                   68999*************9877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 5.6e-05
                           SoxE 115 aGtywlacgilGhaesGmWvdlivs 139
                                    +G+y + c+i Gh + Gm + + vs
  gi|118430981|ref|NP_147124.2| 121 PGEYEVYCPIDGHRDFGMEALITVS 145
                                    79****************9999887 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.4e-05      0.15      89     132 ..     100     143 ..      71     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                                    CBSEEEE-TTEEEEEEEES.S-EEEEEEESSHHHHHTT-EEEEE CS
                   Cu-oxidase_2  89 rrdtvqvppggwvairfkadnpGvwllHCHilwHldqGmalqfv 132
                                    +  t ++ pg+ + +++   +pG + + C i+ H d Gm + ++
  gi|118430981|ref|NP_147124.2| 100 EVETKNLAPGESTKLEVVFPQPGEYEVYCPIDGHRDFGMEALIT 143
                                    45788999*******************************87665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1069.82
//
Query:       gi|14600608|ref|NP_147125.1|  [L=243]
Description: hypothetical protein APE_0295 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1783.01
//
Query:       gi|118430982|ref|YP_874815.1|  [L=105]
Description: hypothetical protein APE_0295a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 750.13
//
Query:       gi|14600610|ref|NP_147127.1|  [L=139]
Description: hypothetical protein APE_0297 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.001   19.1   5.1      0.001   19.1   5.1    2.4  2  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   14.7   0.7       0.03   14.0   0.1    1.7  2  Ribosomal_S19e  Ribosomal protein S19e
      0.044   13.5   2.4        1.6    8.5   0.2    2.9  3  HTH_41          Helix-turn-helix domain
      0.057   12.6   0.3      0.075   12.2   0.3    1.2  1  CobD_Cbib       CobD/Cbib protein
       0.21   11.5   1.4       0.41   10.5   0.2    1.9  2  HxlR            HxlR-like helix-turn-helix
        0.9    9.4   5.4        0.2   11.5   0.4    2.4  3  LexA_DNA_bind   LexA DNA binding domain
        1.4    8.8   9.7        1.6    8.6   0.1    3.3  3  HTH_30          PucR C-terminal 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 ?    0.9   0.1      0.19   4.7e+02      23      23 ..      34      34 ..       8      76 .. 0.58
   2 !   19.1   5.1     4e-07     0.001      12      61 .]      76     130 ..      49     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                                  T CS
                        HTH_20 23 e 23
                                  e
  gi|14600610|ref|NP_147127.1| 34 E 34
                                  3 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 4e-07
                                   HHHHHHHHSTCTTB-HHHHHHHHT.....S-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20  12 RrrilraLaraegltaselaerld.....lskntlsyHLrvLeeagLvevvregr 61 
                                     +i  aLa +++lt+  l ++++      s+  ++ +Lr+Le+ g+vev+r gr
  gi|14600610|ref|NP_147127.1|  76 AKAIVEALAVNGPLTLRGLEREVRrlrgtASRRVIRERLRALERLGIVEVERRGR 130
                                   568999*****************55666799999******************997 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   3.5e+03      98     112 ..      16      31 ..       8      44 .. 0.55
   2 ?   14.0   0.1   1.2e-05      0.03      90     119 ..     104     132 ..      75     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                                   SS--SSS---SS.-HH CS
                Ribosomal_S19e  98 kilqqLeklglv.kke 112
                                   ++lq L +++ + ++ 
  gi|14600610|ref|NP_147127.1|  16 EVLQRLRRIEEMaEAG 31 
                                   4555555554443333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   HHHHHTTSSS--SSS---SS-HHHHHTHHH CS
                Ribosomal_S19e  90 kasgsvirkilqqLeklglvkkekkkgrrl 119
                                   +as++vir+ l++Le+lg+v+ e ++grrl
  gi|14600610|ref|NP_147127.1| 104 TASRRVIRERLRALERLGIVEVE-RRGRRL 132
                                   79******************777.559987 PP

>> HTH_41  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      0.45   1.1e+03       4      15 ..       5      16 ..       5      18 .. 0.83
   2 ?    3.2   0.0     0.028        72       5      14 ..      20      29 ..      19      32 .. 0.87
   3 ?    8.5   0.2   0.00064       1.6      23      43 ..     110     130 ..     105     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.45
                        HTH_41  4 dRlktIeelake 15
                                  +Rl++Ie l  e
  gi|14600610|ref|NP_147127.1|  5 ERLERIERLLAE 16
                                  79****999766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.028
                        HTH_41  5 RlktIeelak 14
                                  Rl++Iee+a+
  gi|14600610|ref|NP_147127.1| 20 RLRRIEEMAE 29
                                  9*******97 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00064
                        HTH_41  23 vQkALklLeddkaislerrGr 43 
                                   +   L  Le  +++++errGr
  gi|14600610|ref|NP_147127.1| 110 IRERLRALERLGIVEVERRGR 130
                                   5566899*************9 PP

>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   2.9e-05     0.075      88     139 ..      36      86 ..      19      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                     CobD_Cbib  88 rsLleevrkvakalkgdleaaReavsmiVgRdtseldeeeiarAavEsvaEN 139
                                   r+ +e +++   ++++ l++aR +v++ V+R  + l +++ia+A vE++a N
  gi|14600610|ref|NP_147127.1|  36 RMAAEMAMAFTLPIHEALSTAR-RVARAVSRLDKGLGDDGIAKAIVEALAVN 86 
                                   5556666666667777888998.899***********************977 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.52   1.3e+03      35      43 ..      13      21 ..       3      36 .. 0.57
   2 ?   10.5   0.2   0.00016      0.41      23      51 ..      97     125 ..      84     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.52
                                  HHHHHHHHH CS
                          HxlR 35 mLaqrLreL 43
                                  +La+ L++L
  gi|14600610|ref|NP_147127.1| 13 LLAEVLQRL 21
                                  333333333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00016
                                   HHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
                          HxlR  23 elkralpkisqkmLaqrLreLeqdglier 51 
                                   e++r  ++ s++++ +rLr+Le+ g++e 
  gi|14600610|ref|NP_147127.1|  97 EVRRLRGTASRRVIRERLRALERLGIVEV 125
                                   788999999*****************985 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 ?   -3.4   0.0       3.3   8.6e+03      44      52 ..       4      12 ..       2      12 .. 0.77
   2 ?   -0.4   0.2      0.39     1e+03      29      49 ..      35      55 ..      15      59 .. 0.69
   3 ?   11.5   0.4   7.7e-05       0.2      29      59 ..      96     126 ..      88     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.3
                                  HHHHHHHHH CS
                 LexA_DNA_bind 44 eehLkaLer 52
                                  ee+L++ er
  gi|14600610|ref|NP_147127.1|  4 EERLERIER 12
                                  789999886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.39
                                  HHHHHHHTS-.HHHHHHHHHH CS
                 LexA_DNA_bind 29 reiaralglkSpsaveehLka 49
                                  + +a ++ ++ + +++e L +
  gi|14600610|ref|NP_147127.1| 35 ARMAAEMAMAFTLPIHEALST 55
                                  456777777777777777765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind  29 reiaralglkSpsaveehLkaLerKGyierd 59 
                                   re+ r  g +S + + e+L+aLer G++e++
  gi|14600610|ref|NP_147127.1|  96 REVRRLRGTASRRVIRERLRALERLGIVEVE 126
                                   6777777889999***************986 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 ?    3.7   0.2      0.02        52      31      40 ..       5      14 ..       2      15 .. 0.86
   2 ?    8.6   0.1   0.00063       1.6      29      57 ..      17      43 ..      17      47 .. 0.66
   3 ?    0.9   0.9      0.15     4e+02      26      56 ..     107     137 ..     104     139 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.02
                                  HHHHHHHHHH CS
                        HTH_30 31 yRLrrieell 40
                                   RL+rie+ll
  gi|14600610|ref|NP_147127.1|  5 ERLERIERLL 14
                                  7*******98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00063
                                  HHHHHHHHHHHHS--TTSHHHHHHHHHHH CS
                        HTH_30 29 lryRLrrieellgldlddpddrlaLylAl 57
                                  + +RLrriee+     +  ++r+a ++A+
  gi|14600610|ref|NP_147127.1| 17 VLQRLRRIEEMAEAGEQ--EARMAAEMAM 43
                                  679********765544..5555555444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.15
                                   HHHHHHHHHHHHHHHS--TTSHHHHHHHHHH CS
                        HTH_30  26 rnTlryRLrrieellgldlddpddrlaLylA 56 
                                   r  +r RLr +e+l  + +++  +rl + lA
  gi|14600610|ref|NP_147127.1| 107 RRVIRERLRALERLGIVEVERRGRRLVIKLA 137
                                   556899******9988888888888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1001.66
//
Query:       gi|118430983|ref|NP_147129.2|  [L=134]
Description: hypothetical protein APE_0299.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.5   0.3      0.046   13.7   0.3    1.5  1  T2SSF           Type II secretion system (T2SS), protein F
       0.13   12.4   3.1        3.1    8.0   0.3    2.3  2  JIP_LZII        JNK-interacting protein  leucine zipper II
       0.15   10.5   2.7       0.14   10.5   2.7    1.2  1  Adeno_terminal  Adenoviral DNA terminal protein


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 ?   13.7   0.3   7.6e-06     0.046      30     100 ..      43     118 ..      30     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.6e-06
                                    HHHHHHHHHHHHHHTTS.....SHHHHHCT-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHH CS
                          T2SSF  30 plaeelkriarrlraGg.....slsealertpssefpelvvqlirageeggnLaevLerlaeyleeerelrrklla 100
                                    +l+e+l +i + +++ +      l++al+ +  s++ e v+++ r  + +g  +e+ e l +++ ++r+   +++ 
  gi|118430983|ref|NP_147129.2|  43 ELREVLTAISEFIKNLEeplgnILKTALSVMDGSKLGEEVAAFYRNLRDSGMPDEMVEELTREYFRMRMESLNIAR 118
                                    688888888888888886555566799998888999******************************9998877665 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 ?    8.0   0.3   0.00052       3.1      37      70 ..      29      62 ..      26      63 .. 0.93
   2 ?    4.8   0.2    0.0053        32      35      56 ..      99     120 ..      97     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00052
                       JIP_LZII 37 eLtsereiLreEleslqkakerlesrikelEeel 70
                                   e + e+e  r+++e+l+++++++ + ik+lEe l
  gi|118430983|ref|NP_147129.2| 29 EVSHEHEDSRSDVEELREVLTAISEFIKNLEEPL 62
                                   6799***************************965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0053
                       JIP_LZII  35 vdeLtsereiLreEleslqkak 56 
                                    v+eLt e+  +r+E  ++  + 
  gi|118430983|ref|NP_147129.2|  99 VEELTREYFRMRMESLNIARII 120
                                    9************987766655 PP

>> Adeno_terminal  Adenoviral DNA terminal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.7   2.3e-05      0.14     310     365 ..       6      64 ..       3     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.3e-05
                 Adeno_terminal 310 RRrRreesPlppPeeeeeGiaaeeee.eeeeeeeele..devissvaelirlLeeeLse 365
                                    RR+ re    + P  ee G  + e++ e+e+++ ++e  +ev++++ e i++Lee L +
  gi|118430983|ref|NP_147129.2|   6 RREAREAVKEAFPVSEEAGGVEVEVShEHEDSRSDVEelREVLTAISEFIKNLEEPLGN 64 
                                    6666666666677788888888887756666655554227**************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1056.20
//
Query:       gi|118430984|ref|NP_147130.2|  [L=419]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-33  114.1   0.0    1.5e-32  113.0   0.0    1.6  1  ABC_tran         ABC transporter
    1.3e-16   60.9   0.2    3.1e-16   59.6   0.2    1.7  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    1.9e-10   41.0   0.0    6.3e-07   29.5   0.0    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    3.1e-06   26.8   0.0    1.9e-05   24.2   0.0    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
    3.1e-06   27.5   0.2      0.003   17.8   0.2    2.3  1  AAA_22           AAA domain
     0.0028   17.4   0.0     0.0045   16.7   0.0    1.4  1  AAA_24           AAA domain
     0.0045   17.4   0.0       0.38   11.2   0.0    2.5  2  AAA              ATPase family associated with various cellul
     0.0056   15.9   0.1      0.012   14.9   0.1    1.5  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.018   14.7   0.1       0.41   10.3   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.022   15.2   0.2      0.056   13.8   0.0    1.7  2  AAA_16           AAA ATPase domain
      0.025   13.9   2.1       0.82    9.0   0.0    3.0  3  ATPase           KaiC
      0.025   13.2   0.0        1.7    7.2   0.0    2.2  2  AAA_13           AAA domain
      0.033   14.3   0.0      0.069   13.3   0.0    1.6  1  AAA_33           AAA domain
      0.036   13.6   0.5        7.6    6.0   0.0    2.4  2  AAA_25           AAA domain
      0.038   13.9   0.3      0.083   12.8   0.3    1.5  1  NACHT            NACHT domain
      0.039   13.8   0.1      0.083   12.8   0.1    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.041   13.3   0.1        2.7    7.3   0.0    2.3  2  TniB             Bacterial TniB protein
      0.064   13.2   0.1       0.13   12.1   0.1    1.5  1  RsgA_GTPase      RsgA GTPase
      0.073   12.8   0.3       0.14   11.9   0.3    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.084   12.6   0.0       0.19   11.5   0.0    1.7  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.087   12.2   0.0       0.15   11.4   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.11   12.6   0.0       0.21   11.7   0.0    1.4  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
       0.74    8.5   6.8          3    6.5   0.0    3.0  3  ABC_ATPase       Predicted ATPase of the ABC class
        1.2    9.2   5.9       0.91    9.6   2.3    2.4  3  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0     2e-35   1.5e-32       2     137 .]      31     218 ..      30     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 2e-35
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...................................EETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................xxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei...................................lldg 46 
                                    + vsl+lk+ge++++vGe+G+GK+tL+k+++gl++p  G++                                       
  gi|118430984|ref|NP_147130.2|  31 DGVSLSLKKGEILGVVGESGSGKTTLAKTIIGLHRPFTGHVfididkgeleeavsiyealkrgenvqredikryrkI--- 107
                                    78********************************************************9999996666655555552... PP

                                    CEGGG..........B-HHHCCHCEEEE-SS..--S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTC CS
                                    xxxxx..........xxxxxxxxxxxxxxxx..xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  47 kdlke..........qeleslrkeigvlpqe..pqlfpeltvren...............esdeeiekalsklglkelkd 99 
                                                    + +++r+++++++q+  ++l+p+++v+e                  ++++ ++l+ +gl +   
  gi|118430984|ref|NP_147130.2| 108 ----IkthdpyymdrSNYKKFRRKVQMVQQDpySSLNPRMKVGEIigepvrvhgieksseGVKRRVIEVLEAVGLGK--- 180
                                    ....0455555577799**************999*********************7655444555777777777655... PP

                                    BGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 100 tvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    + +++ p++LSgGq+qrva+aral+ +pk+l+lDEpt+
  gi|118430984|ref|NP_147130.2| 181 EFADRYPYELSGGQRQRVAIARALALNPKILVLDEPTS 218
                                    8888889*****************************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 !   59.6   0.2   4.2e-19   3.1e-16       1      65 []     269     336 ..     269     336 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4.2e-19
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekik..geapslerldeGCpFapRCpfalee.C 65 
                                    +E +p+  lf++plHPYTk+Ll++vp +d++ ++++++k  ge+p++ + + GC+F +RCp a+ e C
  gi|118430984|ref|NP_147130.2| 269 MESAPKHILFTNPLHPYTKLLLSAVPIPDPRSRRIKEFKdiGEPPNPAKPPVGCRFVTRCPIASREiC 336
                                    799******************************666665338999*****************988766 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 !    9.6   0.0   0.00097      0.72       3      25 ..      44      66 ..      42     134 .. 0.81
   2 !   29.5   0.0   8.5e-10   6.3e-07     232     302 ..     185     253 ..     148     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00097
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                   +++G  gsGK++L +++ +l+r 
  gi|118430984|ref|NP_147130.2| 44 GVVGESGSGKTTLAKTIIGLHRP 66
                                   79***************999763 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 8.5e-10
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                    + ++elS G+++  a++ al+  +   ++l++DEp + L+ ++++ +l+ll+el +  g   +l TH+ +++
  gi|118430984|ref|NP_147130.2| 185 RYPYELSGGQRQRVAIARALALNP---KILVLDEPTSALDVSIQAQILRLLRELWKkYGLTYLLITHDISVV 253
                                    5789*********88888888888...9****************************9**********97765 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 !   24.2   0.0   2.6e-08   1.9e-05      26     213 ..      42     264 ..      24     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.6e-08
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                    +  +vG+ GSGK+ l   i   +G    + +     +  i    +k ++++a v+i ++  ++ +++++e+++  r++++
  gi|118430984|ref|NP_147130.2|  42 ILGVVGESGSGKTTLAKTI---IGL--HRPFTG---HVFIDI--DKGELEEA-VSI-YEALKRGENVQREDIKRYRKIIK 109
                                    5679999999999999999...884..323433...334443..33344443.666.45556666789999999999999 PP

                                    TSEEEEEETTEEE-HHHHHHHHHCTT-STT.................................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                          SMC_N 106 kgeseykingkevtkkevsellesagiske.................................................. 135
                                    + +  y++++++ +k   + ++ +++ +++                                                  
  gi|118430984|ref|NP_147130.2| 110 THD-PYYMDRSNYKKFRRKVQMVQQDPYSSlnprmkvgeiigepvrvhgiekssegvkrrvievleavglgkefadrypy 188
                                    998.999999999886666555555555556888********************************************** PP

                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                    +LSgG+++ va+a  +A++      + +lDe  +aLD +  +++ +ll+e  k+    ++ i+++  +++ +++ v v+ 
  gi|118430984|ref|NP_147130.2| 189 ELSGGQRQRVAIARALALNP----KILVLDEPTSALDVSIQAQILRLLRELWKKygLTYLLITHDISVVRYMSSSVVVMY 264
                                    ***************99864....3889**********************998866789999999999999977766654 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     4e-06     0.003       5      66 ..      40      96 ..      36     256 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsst..sskdllrellralgl 66
                                     il v+GesG+GKTtl++++   +         rp +   f+++ +++  +  +++++l r  ++
  gi|118430984|ref|NP_147130.2| 40 GEILGVVGESGSGKTTLAKTIIGLH---------RPFTGhvFIDIDKGEleEAVSIYEALKRGENV 96
                                   567889**************99987.........33332234444444433444444444443333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     6e-06    0.0045       5      35 ..      43      79 ..      39     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                         AAA_24  5 iliyGpsgiGKTtlakel......gpkplfidtekGl 35
                                   + ++G+sg+GKTtlak++          +fid++kG 
  gi|118430984|ref|NP_147130.2| 43 LGVVGESGSGKTTLAKTIiglhrpFTGHVFIDIDKGE 79
                                   5699****************77665666899**9996 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   0.0   0.00051      0.38       3      37 ..      45      83 ..      43     115 .. 0.70
   2 ?    3.7   0.0       0.1        76      33      93 ..     181     232 ..     158     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00051
                                   EESSTTSSHHHHHHHHHHH....HTHEEEEEETTTCSSS CS
                            AAA  3 lyGppGtGKTllakavake....lgvefleisgsellsk 37
                                   ++G  G GKT+lak ++      +g  f+ i+  el + 
  gi|118430984|ref|NP_147130.2| 45 VVGESGSGKTTLAKTIIGLhrpfTGHVFIDIDKGELEEA 83
                                   68**************99844433566888888887743 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                                    TCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                            AAA  33 ellskyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                    e+ + y  e +   r+ ++ a++ a +p+il++DE  +    +          +++q+l+ l
  gi|118430984|ref|NP_147130.2| 181 EFADRYPYELSGGQRQRVAIARALAlNPKILVLDEPTSALDVS----------IQAQILRLL 232
                                    555667777777888888888888889********77766555..........455555444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.6e-05     0.012      21      54 ..      41      70 ..      28     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                   EEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEE CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnksdevegrFdsv 54
                                    ++++vG  G+GKttlak i+      ++ F ++
  gi|118430984|ref|NP_147130.2| 41 EILGVVGESGSGKTTLAKTIIGL----HRPFTGH 70
                                   489****************9865....3444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00055      0.41      27      63 ..      45      82 ..      23      89 .. 0.79
   2 ?    1.9   0.0      0.21   1.6e+02      96     119 ..     210     234 ..     175     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                                   EECSTTSSHHHHHHHHHH.HSTTTTS-EEEEETTTS-T CS
                Sigma54_activat 27 itGesGtGKellaraihe.askrkekpfvavncaaipe 63
                                   ++GesG+GK++la++i   +++ + + f+ ++ ++++e
  gi|118430984|ref|NP_147130.2| 45 VVGESGSGKTTLAKTIIGlHRPFTGHVFIDIDKGELEE 82
                                   89*************98834455778899888887766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.21
                                    EEEEET.GGGS-HHHHHHHHHHHHH CS
                Sigma54_activat  96 tlfLDe.igelplelQekLlrvlqe 119
                                    +l LDe  + l++++Q+++lr+l e
  gi|118430984|ref|NP_147130.2| 210 ILVLDEpTSALDVSIQAQILRLLRE 234
                                    789999456799*********9976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.5e-05     0.056      24      45 ..      40      61 ..      29     107 .. 0.78
   2 ?   -2.3   0.0       6.6     5e+03     124     160 ..     201     233 ..     166     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-05
                         AAA_16 24 pelvllsGesGvGKsslvrell 45
                                   +e++ ++GesG+GK++l++++ 
  gi|118430984|ref|NP_147130.2| 40 GEILGVVGESGSGKTTLAKTII 61
                                   47899*************9886 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.6
                         AAA_16 124 krllallsrderplvlvlDdlqwadeaslql.laaLlr 160
                                    +r+lal      p +lvlD+   a + s q+ +  Llr
  gi|118430984|ref|NP_147130.2| 201 ARALALN-----PKILVLDEPTSALDVSIQAqILRLLR 233
                                    3333222.....23666666555555555554444444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0011      0.82      16      38 ..      37      59 ..      26     110 .. 0.89
   2 ?    2.7   0.0     0.091        68     138     164 ..     222     249 ..     200     272 .. 0.73
   3 ?   -0.3   0.1      0.75   5.6e+02      75     118 ..     341     382 ..     332     397 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                         ATPase 16 ipegrvvlitGepGtGKtifalq 38
                                   + +g++  ++Ge+G+GKt++a++
  gi|118430984|ref|NP_147130.2| 37 LKKGEILGVVGESGSGKTTLAKT 59
                                   67899999************986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.091
                         ATPase 138 avaReilrqlvrvl.kklgvTailvsek 164
                                      + +++ +l+r+l kk+g+T +l++  
  gi|118430984|ref|NP_147130.2| 222 VSIQAQILRLLRELwKKYGLTYLLITHD 249
                                    456678888888888********99874 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.75
                         ATPase  75 ekleeegklaiidasesaeesaeekdkedleelieelaeaikei 118
                                    e+  ++  + iid+++ ++++   + ++++e+l+++l+e  ++i
  gi|118430984|ref|NP_147130.2| 341 EDHADS-DVEIIDVTKIGDTIRI-RVSKNAENLAKKLRETNSTI 382
                                    555555.6788888888776443.88888888888888765554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.025        18      23      48 ..      47      67 ..      43     111 .. 0.71
   2 ?    7.2   0.0    0.0023       1.7     526     578 ..     207     257 ..     198     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.025
                         AAA_13 23 GwNGaGKTtLSrllrslelgetepkf 48
                                   G  G+GKTtL++ +  l +      f
  gi|118430984|ref|NP_147130.2| 47 GESGSGKTTLAKTIIGLHR-----PF 67
                                   788**********999854.....33 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0023
                         AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                    + ki v+D P S LD  ++  +  l+++   kk     l + TH ++  ++++
  gi|118430984|ref|NP_147130.2| 207 NPKILVLDEPTSALDVSIQAQILRLLRELW-KKYGLTYL-LITHDISVVRYMS 257
                                    789**************************9.44444444.459**99999886 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   9.3e-05     0.069       4      50 ..      45     106 ..      42     171 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-05
                         AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdt...........lrrrlfgtdqqsktdytr 50 
                                    +vG +GsGK+tla+ ++  +      v+++ d+           +++r ++ +++++++y +
  gi|118430984|ref|NP_147130.2|  45 VVGESGSGKTTLAKTIIGLHRpftgHVFIDIDKgeleeavsiyeALKRGENVQREDIKRYRK 106
                                    79************985433344477777777777777777666555555555555555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.021        15      31      50 ..      38      57 ..      32      64 .. 0.89
   2 ?    6.0   0.0      0.01       7.6      76     188 ..     155     248 ..     146     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                         AAA_25 31 pagelallaGapgtGKttla 50
                                    +ge+  ++G +g+GKttla
  gi|118430984|ref|NP_147130.2| 38 KKGEILGVVGESGSGKTTLA 57
                                   67888899**********98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
                         AAA_25  76 yvsaEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                    +   E s ++++rR+ +v+ea+   +++++  ++ +         +gg++ ++   a+++a+    +++ +v+D  ++al
  gi|118430984|ref|NP_147130.2| 155 VHGIEKSSEGVKRRVIEVLEAVG-LGKEFADRYPYE--------LSGGQR-QR--VAIARALAL--NPKILVLDEPTSAL 220
                                    55678999999999999999993.344444443332........233433.23..347777766..499*****999999 PP

                         AAA_25 156 ggdensnsdvgalvealeriarrtgaavllvhH 188
                                    + + +     ++++  l+++ +++g + ll+ H
  gi|118430984|ref|NP_147130.2| 221 DVSIQ-----AQILRLLRELWKKYGLTYLLITH 248
                                    99988.....8999999*************999 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00011     0.083       5      21 ..      45      61 ..      41      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                   EEC-TTTCHHHHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlqkla 21
                                   + Ge+GsGKTtL++ ++
  gi|118430984|ref|NP_147130.2| 45 VVGESGSGKTTLAKTII 61
                                   89************997 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 ?   12.8   0.1   0.00011     0.083       1      21 [.      42      62 ..      42      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                           MobB  1 vlgivgksgsGKTtLleklip 21
                                   +lg+vg sgsGKTtL + +i 
  gi|118430984|ref|NP_147130.2| 42 ILGVVGESGSGKTTLAKTIIG 62
                                   799*************99986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.052        39      38      60 ..      43      65 ..      36      74 .. 0.83
   2 ?    7.3   0.0    0.0036       2.7     109     156 ..     197     242 ..     153     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.052
                           TniB 38 lllvGdsnnGKtmivekFarlhp 60
                                   l +vG+s  GKt++++    lh+
  gi|118430984|ref|NP_147130.2| 43 LGVVGESGSGKTTLAKTIIGLHR 65
                                   569***********998776665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0036
                           TniB 109 qqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                    + +++   +l++++L++DE  ++l   ++ q ++l +l+ L  ++ ++
  gi|118430984|ref|NP_147130.2| 197 RVAIARALALNPKILVLDEPTSAL--DVSIQAQILRLLRELWKKYGLT 242
                                    44455555789*************..67778889999*9999887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00018      0.13      96     137 ..      36      78 ..      20      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                    HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--------- CS
                    RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrG 137
                                     lk+ ++  +vG+SG GK+tL +++++ ++  tg+v  + ++G
  gi|118430984|ref|NP_147130.2|  36 SLKKgEILGVVGESGSGKTTLAKTIIGLHRPFTGHVFIDIDKG 78 
                                    5665589999***************998888888877777766 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 ?   11.9   0.3   0.00019      0.14      13      38 ..      31      56 ..      28      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                   dg +++++  ++  ++G+sGsGK+Tl
  gi|118430984|ref|NP_147130.2| 31 DGVSLSLKKGEILGVVGESGSGKTTL 56
                                   667777875558889**********9 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025      0.19       1      21 [.      42      62 ..      42     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                            PRK  1 vIgvagsSGaGkttvarklek 21
                                   ++gv g+SG+Gktt+a+++  
  gi|118430984|ref|NP_147130.2| 42 ILGVVGESGSGKTTLAKTIIG 62
                                   689**************9865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.15       2      55 ..      20      73 ..      19     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                   Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                   lk+v+G  +a   + ++   g  l +vG +GsGKt lak + +l  p + +  +
  gi|118430984|ref|NP_147130.2| 20 LKKVIGYVKAVDGVSLSLKKGEILGVVGESGSGKTTLAKTIIGLHRPFTGHVFI 73
                                   67888888999999999998999999****************998887766555 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 ?   11.7   0.0   0.00028      0.21      11      43 ..      93     125 ..      87     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                MaoC_dehydrat_N  11 kaevereavrefakavgetnpayldeeaaraag 43 
                                       v+re+++++ k ++  +p+y+d+++ ++ +
  gi|118430984|ref|NP_147130.2|  93 GENVQREDIKRYRKIIKTHDPYYMDRSNYKKFR 125
                                    5789***********************987655 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   1.5     0.046        34     236     264 ..      29      60 ..      22      65 .. 0.83
   2 ?   -0.9   0.1      0.72   5.4e+02      25      45 ..     118     138 ..      89     146 .. 0.62
   3 ?    6.5   0.0     0.004         3     324     370 ..     191     237 ..     179     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.046
                                    EEEE..EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 236 kvsG..mgipkG.vtlIvGggfhGKsTLLeAl 264
                                    +v G  + ++kG +  +vG    GK+TL + +
  gi|118430984|ref|NP_147130.2|  29 AVDGvsLSLKKGeILGVVGESGSGKTTLAKTI 60 
                                    5666225689**9***************9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.72
                                    -EESSSEEEEES---SSTTSS CS
                     ABC_ATPase  25 eydlsdltllidrvqsdpfap 45 
                                    + ++++++  ++ vq+dp+ +
  gi|118430984|ref|NP_147130.2| 118 RSNYKKFRRKVQMVQQDPYSS 138
                                    2234469999999*****975 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.004
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskek 370
                                    SG   q ++i++al ++ k+l++DE tsA    i+ + ++ l + +k
  gi|118430984|ref|NP_147130.2| 191 SGGQRQRVAIARALALNPKILVLDEPTSALDVSIQAQILRLLRELWK 237
                                    899999***********************988887666655554444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.3    0.0012      0.91       3      44 ..      24      61 ..      22      64 .. 0.74
   2 ?   -0.4   0.0       1.3     1e+03      90     172 ..      71     173 ..      67     214 .. 0.62
   3 ?   -1.7   0.0       3.5   2.6e+03      86     130 ..     200     238 ..     179     259 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                          DUF87  3 iGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLl 44
                                   iG++   ++v ++l+  ++    l+++g++GsGK+++++ ++
  gi|118430984|ref|NP_147130.2| 24 IGYVKAVDGVSLSLKKGEI----LGVVGESGSGKTTLAKTII 61
                                   5555555555555555444....8***************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                          DUF87  90 lkinpwsldpeelldllee.ddkpaaav.qrsvleealdqaka..........keekeklssdepveklleelk...... 151
                                    + i++++ + ee ++++e  +  ++ ++   + +++++++++            ++k ++  ++p  +l+  +k      
  gi|118430984|ref|NP_147130.2|  71 VFIDIDKGELEEAVSIYEAlKRGENVQReDIKRYRKIIKTHDPyymdrsnykkFRRKVQMVQQDPYSSLNPRMKvgeiig 150
                                    55666666777777777776555555554445555555555545555555444444445555555555555555666666 PP

                          DUF87 152 ..kekeelrklknqaiarlldkl 172
                                       ++ +++k+++  ++r+++ l
  gi|118430984|ref|NP_147130.2| 151 epVRVHGIEKSSEGVKRRVIEVL 173
                                    55555555555555555555555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.5
                          DUF87  86 kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka 130
                                    +++ l +np+ l  +e  + l++      ++q ++l+ + + +k+
  gi|118430984|ref|NP_147130.2| 200 IARALALNPKILVLDEPTSALDV------SIQAQILRLLRELWKK 238
                                    55667777777777777777777......3444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      774  (0.0431703); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); 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: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 2908.49
//
Query:       gi|118430985|ref|NP_147131.2|  [L=322]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-28   97.4   0.0    1.6e-27   96.7   0.0    1.3  1  ABC_tran      ABC transporter
    6.1e-20   71.5   0.2    1.3e-19   70.4   0.2    1.6  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    3.2e-07   30.7   0.1    4.5e-06   27.0   0.1    2.0  1  AAA_22        AAA domain
      6e-07   29.6   2.5    0.00012   22.0   0.3    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.4e-05   24.6   0.2    3.3e-05   23.4   0.2    1.5  1  SMC_N         RecF/RecN/SMC N terminal domain
    1.9e-05   25.1   0.0    4.8e-05   23.8   0.0    1.7  1  AAA_16        AAA ATPase domain
     0.0001   22.8   1.6     0.0055   17.1   1.6    2.3  1  AAA           ATPase family associated with various cellular 
    0.00029   20.3   0.4       0.12   11.8   0.3    2.3  2  TniB          Bacterial TniB protein
     0.0011   18.9   0.1     0.0068   16.3   0.0    2.1  2  Rad17         Rad17 P-loop domain
     0.0013   18.7   0.1     0.0029   17.5   0.0    1.6  1  NACHT         NACHT domain
     0.0021   18.1   0.1     0.0067   16.4   0.0    1.8  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0021   17.3   1.0     0.0053   16.0   1.0    1.8  1  NB-ARC        NB-ARC domain
     0.0035   17.1   0.0     0.0066   16.2   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0044   16.4   0.2      0.034   13.5   0.0    2.4  3  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.005   16.7   0.0       0.01   15.8   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0057   17.0   0.0      0.016   15.5   0.0    1.8  1  RNA_helicase  RNA helicase
     0.0058   16.4   0.1       0.01   15.6   0.1    1.4  1  PRK           Phosphoribulokinase / Uridine kinase family
     0.0059   16.3   0.1     0.0087   15.7   0.1    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
     0.0065   16.2   0.3        0.3   10.8   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
     0.0073   15.9   0.0       0.46   10.0   0.0    2.3  2  AAA_25        AAA domain
     0.0083   16.6   0.0      0.014   15.9   0.0    1.4  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.017   15.3   0.1       0.04   14.1   0.1    1.8  1  AAA_33        AAA domain
      0.022   14.7   0.4       0.19   11.6   0.4    2.0  1  ATPase_2      ATPase domain predominantly from Archaea
      0.033   13.9   0.6       0.63    9.7   0.0    2.1  2  AAA_15        AAA ATPase domain
      0.048   13.1   0.2        2.2    7.7   0.0    2.2  2  PhoH          PhoH-like protein
      0.056   13.1   0.3       0.19   11.4   0.0    1.8  2  AAA_24        AAA domain
      0.059   12.5   0.2        2.2    7.3   0.0    2.6  3  MCM           MCM P-loop domain
       0.07   13.2   0.6       0.16   12.1   0.2    1.8  2  DUF87         Helicase HerA, central domain
        0.1   13.2   0.1       0.16   12.5   0.1    1.6  1  AAA_18        AAA domain
       0.13   12.4   0.8       0.29   11.2   0.2    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
       0.15   10.7   0.0        2.2    6.8   0.0    2.1  2  AAA_13        AAA domain
       0.22   10.7   0.0       0.22   10.6   0.0    1.1  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 !   96.7   0.0   2.8e-30   1.6e-27       1     136 [.      25     184 ..      25     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 2.8e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEE........EETTCEGGG......B-HHHCCHCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx........xxxxxxxxx......xxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp....teGei........lldgkdlke......qeleslrkeig 62 
                                    l+ v+l++++ge++aivGe+G+GKStL++ +a+ l      ++G+i        ++d            +  ++  k ++
  gi|118430985|ref|NP_147131.2|  25 LDGVELDVYQGEILAIVGESGCGKSTLARSIARILPSnaviEKGSIilnlgsgnTVD-----LvrlsedELVKIRGKIVS 99 
                                    789*******************************98889999999955555554444.....155555455566667789 PP

                                    EE-SS..--S-TTSBHHHH..........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS CS
                                    xxxxx..xxxxxxxxxxxx..........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  63 vlpqe..pqlfpeltvren..........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp 127
                                    +++q+  + l p ++v+++                  ++++l+kl ++  ++ ++++ p++LSgG+kqr+++a++l+++p
  gi|118430985|ref|NP_147131.2| 100 MIFQDpsAALSPVHKVKKQvtdhvsgekrR---VekiAQEILKKLMMPA-PHMILEKYPHELSGGMKQRIVIAASLITRP 175
                                    *****9889999999999999999865333...14669999****9999.99**************************** PP

                                    SEEEEESTT CS
                                    xxxxxxxxx RF
                       ABC_tran 128 kllllDEpt 136
                                    +++++DEpt
  gi|118430985|ref|NP_147131.2| 176 RIIIADEPT 184
                                    ********9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.2   2.3e-22   1.3e-19       1      65 []     236     299 ..     236     299 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 2.3e-22
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE +++  lf++plHPYTk+Ll+s+p+++   + +e i+ge+psl + + GC+F+pRCp++++ C
  gi|118430985|ref|NP_147131.2| 236 VEVADVFSLFERPLHPYTKGLLKSIPKPHVDEE-IEPIRGEPPSLADPPPGCRFHPRCPYVMDVC 299
                                    899999**********************99999.*****************************99 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   8.1e-09   4.5e-06       5     128 ..      35     213 ..      31     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.1e-09
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..............................................e 38 
                                      il+++GesG+GK+tl+r +++ l+  a +e+                                              +
  gi|118430985|ref|NP_147131.2|  35 GEILAIVGESGCGKSTLARSIARILPSNAVIEKgsiilnlgsgntvdlvrlsedelvkirgkivsmifqdpsaalspvhK 114
                                    679***********************99999999****998776666666666666666666666666555555532222 PP

                         AAA_22  39 rpevv..fvtlpsst...sskdllrellralglelka..erlsseell.ealeqalrarav...ielliiDEaqh.lr.. 104
                                        v   vt  +s+     +++++e+l++l  ++ +   ++  +el   + ++ + a++    ++++i DE    l+  
  gi|118430985|ref|NP_147131.2| 115 ----VkkQVTDHVSGekrRVEKIAQEILKKLMMPAPHmiLEKYPHELSgGMKQRIVIAASLitrPRIIIADEPTTaLDvt 190
                                    ....2333333333333455566666666666666668855555555523333333333335567888888888877775 PP

                         AAA_22 105 .seealeeLrsllnlsrkgvqliLv 128
                                     ++++l+ L++l +  +  +++iL+
  gi|118430985|ref|NP_147131.2| 191 vQAQILKMLSRLRE--ELETTIILI 213
                                    55777777777777..777777776 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 !    7.3   0.1    0.0066       3.7       2      23 ..      38      59 ..      37      92 .. 0.78
   2 !   22.0   0.3   2.2e-07   0.00012     234     301 ..     154     219 ..     149     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0066
                         AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                    +++G  g+GKS+L + +  + 
  gi|118430985|ref|NP_147131.2| 38 LAIVGESGCGKSTLARSIARIL 59
                                   58*************9997774 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.2e-07
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                    ++elS G+k+ + ++++l+ ++   ++++ DEp + L+  +++ +l++l++l++   + +il TH+  +
  gi|118430985|ref|NP_147131.2| 154 PHELSGGMKQRIVIAASLITRP---RIIIADEPTTALDVTVQAQILKMLSRLREeLETTIILITHNLAV 219
                                    6899*******77777777777...************************666555668*******9765 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 !   23.4   0.2   5.9e-08   3.3e-05      25     207 ..      36     225 ..      27     236 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.9e-08
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTT.......TTTCHCCCCCC--BTTCSSTTEEE.EEEEEEETTEE.SSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersak.......klrseklsdlihkskekasvkkae.veitfdnedkk.lkieke 95 
                                    ++ aivG+ G+GKs l  +i  +L  ++         +l s ++ dl+  s+++    +++ v+++f++++++ ++++k 
  gi|118430985|ref|NP_147131.2|  36 EILAIVGESGCGKSTLARSIARILPSNAVIekgsiilNLGSGNTVDLVRLSEDELVKIRGKiVSMIFQDPSAAlSPVHKV 115
                                    6789********************87653211222237889999999998555544444442889998888875667777 PP

                                    CEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  96 evsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                    + +++ +v+ +++   ki ++  +k  +       + ++++LSgG k+     +++A   + +  + + De   aLD + 
  gi|118430985|ref|NP_147131.2| 116 KKQVTDHVSGEKRRVEKIAQEILKKLMMPAPHMILEKYPHELSGGMKQR----IVIAASLITRPRIIIADEPTTALDVTV 191
                                    7777777777777777777777776655555555556778*****8874....4444445566668999*********** PP

                                    HHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                          SMC_N 176 vkkvaellkekskn..aQfivislreemlekadk 207
                                     +++ ++l + +++  + +i i+++  + ++   
  gi|118430985|ref|NP_147131.2| 192 QAQILKMLSRLREEleTTIILITHNLAVAAEIAD 225
                                    *********9999843556666666555544433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.5e-08   4.8e-05      23      63 ..      34      73 ..      18     213 .. 0.54

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.5e-08
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekd.....ggiflrgkcdql 63
                                   ++e++ ++GesG+GKs+l+r+++r l  +     g          +
  gi|118430985|ref|NP_147131.2| 34 QGEILAIVGESGCGKSTLARSIARILPSNaviekG------SIILN 73
                                   4489*******************877666444442......32222 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   1.6   9.8e-06    0.0055       3      52 ..      40      89 ..      38     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.8e-06
                                   EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfke 52
                                   ++G  G+GK++la+++a+ l ++ +  +gs +l+   g++ + +r   +e
  gi|118430985|ref|NP_147131.2| 40 IVGESGCGKSTLARSIARILPSNAVIEKGSIILNLGSGNTVDLVRLSEDE 89
                                   79*****************9777666666666655444444444333332 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0097       5.4      38      59 ..      38      59 ..      10      71 .. 0.85
   2 !   11.8   0.3   0.00022      0.12      83     167 ..     130     220 ..     104     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0097
                           TniB 38 lllvGdsnnGKtmivekFarlh 59
                                   l +vG+s +GK++++++ ar  
  gi|118430985|ref|NP_147131.2| 38 LAIVGESGCGKSTLARSIARIL 59
                                   78************99887755 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                           TniB  83 ekrlyaaiLealgaplkara........rvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelk 154
                                     +++ ++iL++l++p+            +   +++ v++    +++r++i DE   +l   ++ q ++l +l +L +el+
  gi|118430985|ref|NP_147131.2| 130 VEKIAQEILKKLMMPAPHMIlekyphelSGGMKQRIVIAASLITRPRIIIADEPTTAL--DVTVQAQILKMLSRLREELE 207
                                    5667777888887775332222333322334555666666667899**********99..6677889************* PP

                           TniB 155 ipivlvGteealr 167
                                     +i+l+  + a++
  gi|118430985|ref|NP_147131.2| 208 TTIILITHNLAVA 220
                                    ****997777766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0068      29      70 ..      19      60 ..       7      73 .. 0.84
   2 ?   -0.5   0.1       1.8     1e+03      10      48 ..     112     150 ..     106     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                          Rad17 29 eevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                   + v ++l+   L+  + +iL i G sGCgkst  + ++++l 
  gi|118430985|ref|NP_147131.2| 19 QGVVNALDGVELDVYQGEILAIVGESGCGKSTLARSIARILP 60
                                   567788999999999999*****************9999875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                          Rad17  10 fekykPekaeelavhkkkieevkewlkadvLesrkkriL 48 
                                    + k k + +++++  k+++e++ + +  + +  +++ iL
  gi|118430985|ref|NP_147131.2| 112 VHKVKKQVTDHVSGEKRRVEKIAQEILKKLMMPAPHMIL 150
                                    568888999999999*******99988888888888876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   5.2e-06    0.0029       2      26 ..      37      61 ..      36      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.2e-06
                                   CEEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                   ++++ Ge+G+GK+tL++++a+ + +
  gi|118430985|ref|NP_147131.2| 37 ILAIVGESGCGKSTLARSIARILPS 61
                                   5789****************98765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0067       4      28 ..      40      64 ..      37      69 .. 0.85
   2 ?   -1.9   0.0       5.5   3.1e+03     107     107 ..     161     161 ..     130     209 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                   EE--SSSSHHHHHHHGGGGBS--EE CS
                          AAA_5  4 LvGppGtgKselaerlaaalnreve 28
                                   +vG++G+gKs+la+++a+ l ++ +
  gi|118430985|ref|NP_147131.2| 40 IVGESGCGKSTLARSIARILPSNAV 64
                                   89******************77665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.5
                                    - CS
                          AAA_5 107 n 107
                                     
  gi|118430985|ref|NP_147131.2| 161 M 161
                                    1 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.0   9.5e-06    0.0053      19      43 ..      34      58 ..      18     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.5e-06
                                   CSEEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 19 qslvvalvGmgGvGKttlakqilnk 43
                                   q  ++a+vG  G+GK+tla++i + 
  gi|118430985|ref|NP_147131.2| 34 QGEILAIVGESGCGKSTLARSIARI 58
                                   5569****************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 !   16.2   0.0   1.2e-05    0.0066      13      46 ..      26      59 ..      21      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   dg ++++ + ++  ++G+sG GKSTl  +i+ +L
  gi|118430985|ref|NP_147131.2| 26 DGVELDVYQGEILAIVGESGCGKSTLARSIARIL 59
                                   6667777755599*************88887777 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.1e-05     0.034      24      50 ..      37      63 ..      19      73 .. 0.83
   2 ?   -1.2   0.0         2   1.1e+03     178     197 ..     150     169 ..     139     177 .. 0.83
   3 ?   -1.2   0.0         2   1.1e+03     121     140 ..     197     216 ..     186     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                   Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppls 50
                                    l +vG +G+GK+ la+ ++ +lp+  
  gi|118430985|ref|NP_147131.2| 37 ILAIVGESGCGKSTLARSIARILPSNA 63
                                   57899*******************865 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                   Mg_chelatase 178 ierYlsklsgplldRidlqv 197
                                     e+Y + lsg +  Ri +  
  gi|118430985|ref|NP_147131.2| 150 LEKYPHELSGGMKQRIVIAA 169
                                    57999**********98875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                   Mg_chelatase 121 kvlevLRePledgevtisra 140
                                    k+l  LRe le++ + i+ +
  gi|118430985|ref|NP_147131.2| 197 KMLSRLREELETTIILITHN 216
                                    57888999999999998765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.8e-05      0.01      96     121 ..      32      57 ..      10      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                                    HCTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                    + ++++ ++vG+SG GKStL  +++ 
  gi|118430985|ref|NP_147131.2|  32 VYQGEILAIVGESGCGKSTLARSIAR 57 
                                    457799**************887653 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.9e-05     0.016       2      34 ..      39      70 ..      38      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.9e-05
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                    ++G+sg+GKStla+++a+ l ++   ++k+s+
  gi|118430985|ref|NP_147131.2| 39 AIVGESGCGKSTLARSIARILPSNA-VIEKGSI 70
                                   589*************888776555.4444555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.8e-05      0.01       1      29 [.      37      65 ..      37      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                            PRK  1 vIgvagsSGaGkttvarklekifgrekvk 29
                                   ++++ g+SG+Gk+t+ar +  i+  ++v 
  gi|118430985|ref|NP_147131.2| 37 ILAIVGESGCGKSTLARSIARILPSNAVI 65
                                   689*******************9866654 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   0.1   1.6e-05    0.0087      10      49 ..      31     123 ..      22     242 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                                    -EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                    ATP-synt_ab  10 pivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg......................................... 48 
                                     + qG+ ++i+g++g+Gk+++++s+++   s+ a+i  g                                         
  gi|118430985|ref|NP_147131.2|  31 DVYQGEILAIVGESGCGKSTLARSIARILPSN-AVIEKGsiilnlgsgntvdlvrlsedelvkirgkivsmifqdpsaal 109
                                    5789***********************98887.66655555555566666666666666666666666666666666666 PP

                                    .............E CS
                                    .............x RF
                    ATP-synt_ab  49 .............i 49 
                                                 +
  gi|118430985|ref|NP_147131.2| 110 spvhkvkkqvtdhV 123
                                    66666666666662 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 !   10.8   0.0   0.00054       0.3      44      69 ..      32      57 ..      10      85 .. 0.85
   2 ?    3.5   0.1     0.096        54     102     152 ..     168     220 ..     155     228 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialgv 69
                                   + + e ++++G sG GKs la ++++
  gi|118430985|ref|NP_147131.2| 32 VYQGEILAIVGESGCGKSTLARSIAR 57
                                   5577899**************99985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.096
                      IstB_IS21 102 alkrllkvdllilDdlgl..lpldqaeaellfeviekryerrsiiitsnlpfa 152
                                    a++ +++++++i D+  +      qa+  +++  + +  e++ i+it nl +a
  gi|118430985|ref|NP_147131.2| 168 AASLITRPRIIIADEPTTalDVTVQAQILKMLSRLREELETTIILITHNLAVA 220
                                    556678899999999543103334444555555566778899999***99886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00082      0.46      32      54 ..      34      56 ..      28      60 .. 0.88
   2 ?    3.3   0.0     0.093        52     165     188 ..     191     215 ..     176     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00082
                         AAA_25 32 agelallaGapgtGKttlaldla 54
                                    ge+ +++G +g+GK+tla ++a
  gi|118430985|ref|NP_147131.2| 34 QGEILAIVGESGCGKSTLARSIA 56
                                   68999**************8887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.093
                         AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                    v ++++++l r+++++  +++l+ H
  gi|118430985|ref|NP_147131.2| 191 VqAQILKMLSRLREELETTIILITH 215
                                    35899*******************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-05     0.014      12      43 ..      27      59 ..      22     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-05
                         AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAiklaL 43
                                   ++e+d     + +I+G+ G+GK+T+ + i  +L
  gi|118430985|ref|NP_147131.2| 27 GVELDVyQGEILAIVGESGCGKSTLARSIARIL 59
                                   5666664446889**************999877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.1e-05      0.04       3      28 ..      39      65 ..      37     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.1e-05
                         AAA_33  3 llvGlpGsGKstlaerllkklg.avll 28
                                    +vG +G+GKstla+++++ l+   ++
  gi|118430985|ref|NP_147131.2| 39 AIVGESGCGKSTLARSIARILPsNAVI 65
                                   689**************9988863333 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   0.4   0.00034      0.19      20      83 ..      35     127 ..      29     222 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                       ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldefieeeeekkklekal............... 82 
                                     ei+ i G  g+GK++L + i+  l +     +   + +l + ++  l +    e+e  k++ ++               
  gi|118430985|ref|NP_147131.2|  35 GEILAIVGESGCGKSTLARSIARILPSNAVieKGSIILNLGSGNTVDLVRL--SEDELVKIRGKIvsmifqdpsaalspv 112
                                    57999***************9998844333335566667776666666666..333333344444445566666665553 PP

                       ATPase_2  83 ..............g 83 
                                                  +
  gi|118430985|ref|NP_147131.2| 113 hkvkkqvtdhvsgeK 127
                                    333333333333331 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011      0.63      24      50 ..      35      62 ..      24     141 .. 0.77
   2 ?    2.7   0.3      0.15        83     322     368 ..     173     219 ..     153     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                         AAA_15 24 e.ltvliGkNnsGKSsilealdlFlnnk 50
                                     +  ++G+ ++GKS++++ +  +l  +
  gi|118430985|ref|NP_147131.2| 35 GeILAIVGESGCGKSTLARSIARILPSN 62
                                   24899**************998777644 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    +++ i++ +EP + L    q ++ k l +l ++ +t +i+ TH+  +
  gi|118430985|ref|NP_147131.2| 173 TRPRIIIADEPTTALDVTVQAQILKMLSRLREELETTIILITHNLAV 219
                                    567899*************************************9765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0039       2.2      18      41 ..      34      57 ..      17      73 .. 0.80
   2 ?    3.4   0.1     0.082        46      53     110 ..     171     241 ..     158     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0039
                                   H-SEEEEE--TTSSTTHHHHHHHH CS
                           PhoH 18 kndivfaiGpaGtGKtylavalav 41
                                   + +i+ ++G++G+GK+ la ++a 
  gi|118430985|ref|NP_147131.2| 34 QGEILAIVGESGCGKSTLARSIAR 57
                                   567999*************99885 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.082
                                    EEEE-S-.-TT----SS---------TTTHHHHHHHTTTS............-TTCHHHHHHTTSEEEEEG CS
                           PhoH  53 iltrpav.eageelGflpgdleekvdpylrplydaLkdll............gaekvekllekgkievapl 110
                                    ++trp +  a+e  ++l+ +++ ++  +l+ l ++L++++             a++++ ++  +++eva++
  gi|118430985|ref|NP_147131.2| 171 LITRPRIiIADEPTTALDVTVQAQILKMLSRLREELETTIilithnlavaaeIADRIAVMYAGHVVEVADV 241
                                    57999884669999**********************99998999888888877788888888888888876 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   0.00035      0.19       5      23 ..      38      59 ..      35      85 .. 0.83
   2 ?   -1.4   0.1       2.9   1.6e+03     113     130 ..     194     215 ..     190     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                         AAA_24  5 iliyGpsgiGKTtlakel...g 23
                                   ++i+G+sg GK+tla+++    
  gi|118430985|ref|NP_147131.2| 38 LAIVGESGCGKSTLARSIariL 59
                                   689*************995553 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.9
                         AAA_24 113 rllkklqelrk....nvifiah 130
                                    ++lk+l+ lr+    ++i+i h
  gi|118430985|ref|NP_147131.2| 194 QILKMLSRLREeletTIILITH 215
                                    5666677777766689**9999 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.004       2.2      61      87 ..      39      65 ..      24      72 .. 0.85
   2 ?    1.9   0.0      0.18     1e+02      48      78 ..      87     117 ..      67     128 .. 0.77
   3 ?   -2.2   0.0       3.1   1.7e+03     184     222 ..     161     197 ..     147     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.004
                                   EEEESSTSTHHHHHHHHHHHSSSEEEE CS
                            MCM 61 llvgdpgtaKsqlLkyveklapravyt 87
                                    +vg++g++Ks+l +++++++p +  +
  gi|118430985|ref|NP_147131.2| 39 AIVGESGCGKSTLARSIARILPSNAVI 65
                                   58*******************988765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.18
                                    BSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                            MCM  48 ledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                    +++ +k+rg+i  ++  dp+ a s + k  +
  gi|118430985|ref|NP_147131.2|  87 EDELVKIRGKIVSMIFQDPSAALSPVHKVKK 117
                                    455689**************99987766555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
                                    HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHH CS
                            MCM 184 vaeninlsaalLsrFDlifvllDkvdeekDeelaehivs 222
                                    +++ i + a+l++r  +  ++ D++ +  D ++  +i++
  gi|118430985|ref|NP_147131.2| 161 MKQRIVIAASLITRPRI--IIADEPTTALDVTVQAQILK 197
                                    56666777777777654..46788888877777777776 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00028      0.16      26      48 ..      38      60 ..      28      74 .. 0.82
   2 ?   -1.3   0.0       3.4   1.9e+03     144     148 ..     131     135 ..      73     213 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00028
                          DUF87 26 lAilgsTGsGKSntvavLleell 48
                                   lAi+g++G GKS++++++ + l 
  gi|118430985|ref|NP_147131.2| 38 LAIVGESGCGKSTLARSIARILP 60
                                   7****************988665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.4
                          DUF87 144 eklle 148
                                    ek+++
  gi|118430985|ref|NP_147131.2| 131 EKIAQ 135
                                    22222 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00028      0.16       3      34 ..      40      73 ..      38     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00028
                         AAA_18  3 ltGtpGvGKttlakeLskrl.gf.gvnlrdvake 34
                                   + G +G+GK+tla+ +++ l  + +++ ++++ +
  gi|118430985|ref|NP_147131.2| 40 IVGESGCGKSTLARSIARILpSNaVIEKGSIILN 73
                                   8899************999855574443333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00051      0.29       3      21 ..      39      57 ..      37      82 .. 0.85
   2 ?   -1.9   0.0       5.9   3.3e+03      23      38 ..     176     191 ..     167     230 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00051
                                   EEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                   aivG +  GKStL +++ +
  gi|118430985|ref|NP_147131.2| 39 AIVGESGCGKSTLARSIAR 57
                                   8**************9976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.9
                                    TEEESSSTTSSSSEEE CS
                       MMR_HSR1  23 kaivsdkpgtTrdine 38 
                                    + i++d+p t +d++ 
  gi|118430985|ref|NP_147131.2| 176 RIIIADEPTTALDVTV 191
                                    5566666666666543 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.17        93      21      40 ..      40      59 ..      35      93 .. 0.77
   2 ?    6.8   0.0    0.0039       2.2     524     580 ..     172     226 ..     164     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                         AAA_13 21 iYGwNGaGKTtLSrllrsle 40
                                   i G  G GK+tL+r ++ + 
  gi|118430985|ref|NP_147131.2| 40 IVGESGCGKSTLARSIARIL 59
                                   66999***********9873 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0039
                         AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                    i+  +i++ D P   LD +++  +  ++      ++    +++ THnl    e+ ++
  gi|118430985|ref|NP_147131.2| 172 ITRPRIIIADEPTTALDVTVQAQILKMLSRLR--EELETTIILITHNLAVAAEIADR 226
                                    6789*********************9988775..6777788999****988887765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0004      0.22      26     114 ..      38     125 ..      30     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                                    EEEEESTTSSHHHHHHHHHHHCS----HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.......HHHC-SS-SCCCS-HC CS
                        G-alpha  26 llllGqseSGKsTilkqlkllykkgfseeelatwraviqlnivrsiktilealesleselsesfelqelkerldplkkve 105
                                    l ++G+s++GKsT+ +++ ++   +   e+  ++ ++   n+v+ +++  ++l +   ++ ++   q+ +++l+p+ kv+
  gi|118430985|ref|NP_147131.2|  38 LAIVGESGCGKSTLARSIARILPSNAVIEKGSIILNLGSGNTVDLVRLSEDELVKIRGKIVSM-IFQDPSAALSPVHKVK 116
                                    6789**************977755433343455777888888887777777777776666544.4677777777777777 PP

                                    HHHH..... CS
                        G-alpha 106 asliaklss 114
                                    ++  ++ s+
  gi|118430985|ref|NP_147131.2| 117 KQVTDHVSG 125
                                    776665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 2297.23
//
Query:       gi|118430986|ref|NP_147132.2|  [L=301]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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  106.3  12.2    1.5e-30  106.3  12.2    1.6  2  BPD_transp_1  Binding-protein-dependent transport system inne
    1.6e-05   24.8   1.1    1.6e-05   24.8   1.1    3.2  3  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
       0.45    9.6   0.9       0.58    9.2   0.9    1.1  1  DUF945        Bacterial protein of unknown function (DUF945)


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 ?   -3.1   0.3      0.94   5.6e+03     159     166 ..      32      39 ..      16      47 .. 0.50
   2 !  106.3  12.2   2.5e-34   1.5e-30       1     185 []     111     296 ..     111     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.94
                   BPD_transp_1 159 lalviavl 166
                                    ++++++++
  gi|118430986|ref|NP_147132.2|  32 IITGFILI 39 
                                    22222221 PP

  == domain 2  score: 106.3 bits;  conditional E-value: 2.5e-34
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrsl 79 
                                    g+++G+++a ++++++d++l+++++v+lslP ++la+ +       s    +    +++l+++ +++y+r++r+++lr+ 
  gi|118430986|ref|NP_147132.2| 111 GVVVGSISA-YFGGIIDNILMRITEVFLSLPGLILAMAIA------SMMERSLQNmILALIAVWWPAYARIVRAEVLRVK 183
                                    89*******.******************************......8888777777************************ PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..... 154
                                    ++ +veaa++lG+++ +i+ +++lPn++ +++  + + +g+++  a+ l flg    lg +  +a++g ++se+      
  gi|118430986|ref|NP_147132.2| 184 NEPYVEAAKILGLNTYRIIARHILPNSIYTVLVIASMDLGLVVLVASGLGFLG----LGAQPGTAEWGIMISEGRnwllq 259
                                    *****************************************************....*********************** PP

                   BPD_transp_1 155 ......nggvlalviavlllnlvadilqrlldprvrk 185
                                          +++ +a+ + vl  +l+ d l ++ldpr+rk
  gi|118430986|ref|NP_147132.2| 260 gawwpvFFPGIAIFLWVLGWSLLGDGLRDVLDPRTRK 296
                                    **999999999999999999**************996 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 !   24.8   1.1   2.6e-09   1.6e-05      10      42 ..      20      56 ..      16      68 .. 0.79
   2 ?   -2.0   1.6      0.63   3.8e+03      18      36 ..      99     117 ..      98     130 .. 0.66
   3 ?   -1.7   0.0      0.49   2.9e+03      25      36 ..     160     171 ..     159     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.6e-09
                         OppC_N 10 FkrNklAvvglvilllllliaifaPliaPydp....q 42
                                   + +N+l   gl+i+  ++lia+ aPl+aP+++     
  gi|118430986|ref|NP_147132.2| 20 LYSNPLSRMGLIIITGFILIAVAAPLLAPPNYpdpyK 56
                                   678*************************998854441 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.63
                         OppC_N  18 vglvilllllliaifaPli 36 
                                    ++l+++ + ++i ++   i
  gi|118430986|ref|NP_147132.2|  99 ISLIVVGVAVAIGVVVGSI 117
                                    6788888777776554444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.49
                         OppC_N  25 lllliaifaPli 36 
                                    +l+lia++ P  
  gi|118430986|ref|NP_147132.2| 160 ILALIAVWWPAY 171
                                    678888876654 PP

>> DUF945  Bacterial protein of unknown function (DUF945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.9   9.7e-05      0.58       4      45 ..     100     141 ..      98     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 9.7e-05
                         DUF945   4 slvavgvvvalgaawtGaswytGkqaeerldeqvaqlnkqlg 45 
                                    sl++vgv+va+g++++  s y+G  + + l  +++ + + +g
  gi|118430986|ref|NP_147132.2| 100 SLIVVGVAVAIGVVVGSISAYFGGIIDNILMRITEVFLSLPG 141
                                    579***********************9998888777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); 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:                         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: 2258.56
//
Query:       gi|14600616|ref|NP_147133.1|  [L=342]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for 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  126.8   9.1    1.5e-36  125.9   5.4    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 !    2.7   0.1    0.0052        94      22      44 ..       6      63 ..       2      99 .. 0.67
   2 !  125.9   5.4   8.4e-41   1.5e-36       1     185 []     113     341 ..     109     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0052
                  BPD_transp_1 22 pliivllslPsfvlaillvlvf...................................v 44
                                  +++ +l+++P++  + +lv+++                                   v
  gi|14600616|ref|NP_147133.1|  6 IIYRFLSAIPTLFGLSILVFILtrlvgdpaaiyihpdmtpedvqrvrelyhfddplyV 63
                                  67889999***99777777666666677766666666666666666666666555551 PP

  == domain 2  score: 125.9 bits;  conditional E-value: 8.4e-41
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf...................................... 43 
                                   g+ lG  aa n+ k +d+l r l   ++s+P+f+la++l+++f                                      
  gi|14600616|ref|NP_147133.1| 113 GVYLGTKAAANKDKLIDHLTRLLALSGYSMPVFWLALMLLYLFynvldfvgpgrlslevrfkymppygdfkfytglltida 193
                                   455666666************************************************************************ PP

                  BPD_transp_1  44 .......vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglila 117
                                          v++++++hli pv++ + +++a+++r++r++++++++k++v +a+ +G++r  +++ +v +n+ ++++  ++l+
  gi|14600616|ref|NP_147133.1| 194 llnrnieVFIDAVKHLIPPVLTQTYIHIAIFIRVLRSSMIEEMNKEYVDFALSKGLRREVVLKDYVRRNSYISLVNVAGLQ 274
                                   ********************************************************************************* PP

                  BPD_transp_1 118 fggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                   f+gl+ g vl+e++++wpGlg++  +a ++ d ++   g +l+++ +++++nl++dil ++ldpr+r+
  gi|14600616|ref|NP_147133.1| 275 FVGLMSGVVLTETVFNWPGLGRFAANAAIQLDPAAVV-GFTLFVGTLFIVVNLAVDILLAYLDPRIRY 341
                                   *************************************.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2691.06
//
Query:       gi|118430987|ref|NP_147134.2|  [L=799]
Description: ABC transporter substrate-binding protein precursor [Aeropyrum pernix K1]
Scores for 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-94  315.2   4.0    5.5e-94  315.2   4.0    1.8  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
    1.6e-28   98.3   1.4    1.7e-14   53.4   0.0    2.5  2  PKD        PKD domain
  ------ inclusion threshold ------
      0.059   13.1   0.2       0.42   10.4   0.0    2.5  2  PKD_3      PKD-like domain
       0.12   12.5   1.7       0.62   10.3   0.1    2.3  2  DUF4330    Domain of unknown function (DUF4330)


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 ?   -1.4   0.0       0.2   8.9e+02     252     296 ..      48      93 ..      33     107 .. 0.68
   2 !  315.2   4.0   1.2e-97   5.5e-94       1     369 [.     315     710 ..     315     716 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.2
                                    STTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC.E CS
                      SBP_bac_5 252 lppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrek.k 296
                                     p+  p+    ++ ++++y ++ A  l+++ G    ++g l+++  
  gi|118430987|ref|NP_147134.2|  48 SPTEAPKETIAPEVNNPPYAIARASSLFAKVGEVIEFDGTLSKDpD 93 
                                    44444444444444445599************99999998887752 PP

  == domain 2  score: 315.2 bits;  conditional E-value: 1.2e-97
                                    SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC........TCTEEEEEE CS
                      SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee........dqdikkvea 72 
                                    e++p+LAe+ we+ d+g+ty+f++RkgvkF++G++ltA Dv++sf+rll  d ++g    +++        dq ++++ a
  gi|118430987|ref|NP_147134.2| 315 EIKPWLAER-WEIKDNGTTYIFYIRKGVKFHNGEELTAYDVEYSFKRLLVLDLPQGHVRQIKPflidewdpDQIDQAIRA 393
                                    689******.7**************************************************99***************** PP

                                    EETTEEEEEESSETTTTTTHCHHHHHHHGC..................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT CS
                      SBP_bac_5  73 vddytvrftlkkpnalfltllaavpasiak..................kaaekeddkdkdtnekpvgtGPYklkefkpgq 134
                                    +d+ytv+f+lkkp+a+fl++la   a +                    ++ +  ++ +++ +++p+gtGPYk++e++pgq
  gi|118430987|ref|NP_147134.2| 394 IDKYTVVFKLKKPFAPFLRILASDYAFVIInkkwaiehgdwdpslpksEWSKFRGKINDYIMRNPMGTGPYKMVEWVPGQ 473
                                    ********************99988888889****************977778888899********************* PP

                                    EEEEEE-TTSTTTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT CS
                      SBP_bac_5 135 kivlernpdYwgggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkvlyespgggvtylafNtk 214
                                    +ivler++dYw +g++  +r+++ ++p+ ++r+++l++G++ d+a++p s+  q+++ +g++++  ++++ v++++fN++
  gi|118430987|ref|NP_147134.2| 474 RIVLERFEDYW-QGPAPTKRVVIMFVPELSTRLLMLKNGDV-DIADIPVSYKSQVENVPGITIFTGAATNVVEFIQFNFN 551
                                    ***********.*****************************.999******************99999************ PP

                                    ...........STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT CS
                      SBP_bac_5 215 ...........kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaG 283
                                                ++f d++vR+A++yA+++ee+++++++g+a++a +++pp++pg+ e y++   +ydpekA +++k+a+
  gi|118430987|ref|NP_147134.2| 552 iskipegdtiwPDFFTDVNVRKAFAYAFPYEEFIEKAYQGLAIRARACVPPGWPGYVEAYNY---EYDPEKAAEYFKKAW 628
                                    **********988************************************************9...78************* PP

                                    -BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTT..EEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTST CS
                      SBP_bac_5 284 ykdgdggglrekklkltlllasgspaekaiaeliqqqlkkiG..ikvevktvdwaatylervkdgdfdmillgwgadypd 361
                                       ++++g+     ++t ++++g++ ++ ++el++++l+ki+  +k++v+++dw  +yle++++ +++++  g + +y d
  gi|118430987|ref|NP_147134.2| 629 GGRVWEEGF-----VITAFYNAGNEQRRIALELLAESLQKINpkFKLRVQALDW-PVYLEKMENFELPLFAIGDWINYLD 702
                                    *******99.....89999999999999**************8899999999**.************************* PP

                                    THHHHHHH CS
                      SBP_bac_5 362 pdnflnpf 369
                                    p+  +++ 
  gi|118430987|ref|NP_147134.2| 703 PHIAVEQQ 710
                                    *9877665 PP

>> PKD  PKD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   3.8e-18   1.7e-14       2      70 ..      70     138 ..      69     139 .. 0.95
   2 !   43.6   0.3   4.4e-15     2e-11      10      67 ..     175     246 ..     166     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 3.8e-18
                                    E---S--BSSEEEEEEEES....-SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS-EEE CS
                            PKD   2 sasptvlvpgatvaftaav...pdganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavgsat 70 
                                    +as+ ++ +g+ ++f +++   pdg++v y Wdfgd   +++  + +v+h Y+ pG+Y V +t++++ g+++
  gi|118430987|ref|NP_147134.2|  70 RASSLFAKVGEVIEFDGTLskdPDGKIVEYVWDFGD---GTTAFGAKVSHAYELPGSYIVVLTVKDDKGAVD 138
                                    5889999*****************************...*****************************9986 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 4.4e-15
                                    SSEEEEEEEES..-................SS-SEEEEE--SS--EEEEETTEEEEEE-SSEEEEEEEEEE-SS- CS
                            PKD  10 pgatvaftaav.pd................ganvtysWdfgdgsvvqvlseptvthtYlspGeYeVtvtasnavg 67 
                                    pg++v f +++ +                  a++ y Wdfgd   +++ ++++vtht+++pG+Y V++t++   g
  gi|118430987|ref|NP_147134.2| 175 PGEEVSFDGSSsWAwvekkeddkvsivksvEAITEYVWDFGD---GTTATGKSVTHTFEKPGSYPVKLTVKAVNG 246
                                    6666666666642244445555666666667899********...*************************97655 PP

>> PKD_3  PKD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   9.4e-05      0.42      29      67 ..     203     242 ..     200     243 .. 0.88
   2 ?   -1.7   0.0      0.56   2.5e+03       2      27 ..     264     289 ..     263     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.4e-05
                          PKD_3  29 naenaa.faWtieGkivsteptytfteeelgsyevtleve 67 
                                    ++e  + + W   +    t ++ t t+e+ gsy v+l+v+
  gi|118430987|ref|NP_147134.2| 203 SVEAITeYVWDFGDGTTATGKSVTHTFEKPGSYPVKLTVK 242
                                    55665569*****99**********************996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                          PKD_3   2 PvIsLdletegykvkvgreltiaPtv 27 
                                    P I+L+ ++ +   ++g++  + P +
  gi|118430987|ref|NP_147134.2| 264 PAIQLKHPDTIIVARIGEPQGLDPAF 289
                                    99*********999999999998876 PP

>> DUF4330  Domain of unknown function (DUF4330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00014      0.62      17     113 ..      13      99 ..       2     152 .. 0.72
   2 ?    0.9   0.2       0.1   4.5e+02      91     153 ..     201     269 ..     186     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                        DUF4330  17 lDllailvilavivgiflkpgtsgsvaqaeaaatkpvevdvvvrglevpeelakvkegektniiirnqPagdv..eikdv 94 
                                    + +l+i+ i+++++ +f+ pg +        ++++p++ + v    e+p+e+++ ++++  ++i+r    +++  ++ +v
  gi|118430987|ref|NP_147134.2|  13 IAALIIVFIIVAAWQLFTTPGGG--------ETASPTTTETVASPTEAPKETIAPEVNNPPYAIARA---SSLfaKVGEV 81 
                                    44567777777777777777777........234555566677777778999988888888888877...5555588888 PP

                        DUF4330  95 kvlprkvvvpqpdGkvkal 113
                                       + ++  ++pdGk+++ 
  gi|118430987|ref|NP_147134.2|  82 IEFDGTLS-KDPDGKIVEY 99 
                                    77777776.7888887765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.1
                        DUF4330  91 ikdvkvlprkv....vvpqpdGkvkalede.pylkdllvtleg.kakitedglvlggqkvkvGkevele 153
                                    +k+v++    v    + ++++Gk ++++ e p+++ + +t+++ ++k+ ++  ++   + k G  ++l+
  gi|118430987|ref|NP_147134.2| 201 VKSVEAITEYVwdfgDGTTATGKSVTHTFEkPGSYPVKLTVKAvNGKTASAIKTIRVVEEKKGPAIQLK 269
                                    5677777777755444588888888888877*********99734444444445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (799 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); 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: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.42
# Mc/sec: 5648.91
//
Query:       gi|118430988|ref|NP_147135.2|  [L=475]
Description: carbohydrate kinase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-14   53.9   0.1      3e-14   53.2   0.1    1.4  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
    5.5e-10   39.2   0.0    7.5e-10   38.8   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom


Domain annotation for each model (and alignments):
>> 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 !   53.2   0.1   3.3e-18     3e-14       2     197 ..     235     416 ..     234     417 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.3e-18
                         FGGY_C   2 kvslGTssflll..vgtkpv...isehglltpvagedgkpeyalegsiavagslva.wlldnlglreeirdageveesla 75 
                                    k++lGT+ fl +  +g+ p+     +++++  ++   g+ +y+leg+ a +g +++ + +   g+           + l+
  gi|118430988|ref|NP_147135.2| 235 KATLGTGLFLDApvEGKPPLftgDLIPVVNLALP---GRVYYGLEGFAAGVGMVFDaFARVLGGF-----------SVLE 300
                                    7899999999999566666666555566666666...779**************88666666566...........5566 PP

                         FGGY_C  76 elaaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlav 155
                                    e     a ++a    +vp + glr+py +p +rg+++g+s ++t+a++a  ++ ++ l +  i+++l++     + +l++
  gi|118430988|ref|NP_147135.2| 301 E----KALEPADPAPVVPVLAGLRTPY-RPLLRGAVLGVSPGFTAASLAKGLIIGTLLTVLSIYRELARR-MGGFGELRI 374
                                    3....33444445568899*******7.***************************************888.888****** PP

                         FGGY_C 156 dGGgskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                     GG+s+  ll+  +A+++gv+V+r  + +  a GaA++A++a
  gi|118430988|ref|NP_147135.2| 375 GGGLSRLGLLASSIASAVGVKVYRSVDYNDSARGAALVAGYA 416
                                    ****************************************98 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   8.4e-14   7.5e-10       3     211 ..       7     202 ..       5     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 8.4e-14
                                    EEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS-E CS
                         FGGY_N   3 lglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqregl 82 
                                     ++D+Gt++++  ++ e+  +va+ ++el+l++   +++eqd+  + + + + + k+ +      +++++++i   r ++
  gi|118430988|ref|NP_147135.2|   7 CSVDVGTSGIRLSLYGEDLGLVARYTEELTLYYS-GNRVEQDALILAANVRDMLGKAARSG----CNVVGLSI--YRGSV 79 
                                    689****************************998.77899999887777777776666555....77777766..66667 PP

                                    EEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEEHHHHHHH CS
                         FGGY_N  83 vllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekflliddyLiw 162
                                    v++ +n+kpL  +i+w d r  e+  kl    +  +  +  g  l++g ++  ++ l  n+p+++     +  id +L  
  gi|118430988|ref|NP_147135.2|  80 VAW-RNGKPLSDVITWMDSRGLEEYSKLPLGARLVSKSPVLGKALKPGSPALVMRRLWLNHPGAR-----IWSIDGFLSD 153
                                    777.89************************999999999***********************975.....889******* PP

                                    HHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCC CS
                         FGGY_N 163 rLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesse 211
                                     Ltg+f++d ++a+ ++l+  ++l+    ++ +lg+    LP+l+  +e
  gi|118430988|ref|NP_147135.2| 154 MLTGEFTSDPGQAALTGLVSPYSLKPLSLVIRLLGLRGLELPRLRLHNE 202
                                    *************************999999999999999999986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3626.97
//
Query:       gi|118430989|ref|NP_147137.2|  [L=476]
Description: alkyldihydroxyacetonephosphate synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-31  108.6   0.4    4.4e-31  107.5   0.4    1.6  1  FAD_binding_4  FAD binding domain
    7.8e-21   74.8   0.0      1e-20   74.4   0.0    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.4   4.9e-35   4.4e-31       2     135 ..      63     198 ..      61     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 4.9e-35
                                    EEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                  FAD_binding_4   2 aavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                    a+v++p+s   v++++++a+eag+++++rGgGs+++g++     +++ldl+ l++il+++ e+ +++veaG+++++++e+
  gi|118430989|ref|NP_147137.2|  63 AYVAKPRSRGAVERIVEAAAEAGACLVPRGGGSNVVGASPpLGCCLILDLRMLDKILWFSGEDLVVHVEAGAVVSKVEEW 142
                                    689*********************************999856667*****66**************************** PP

                                    HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEE.TTSEE CS
                  FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvl.adGev 135
                                    l+++g++lg +p+s++ +tvGG ia+ ++G  +   G+i+d+vl+le v  + G+v
  gi|118430989|ref|NP_147137.2| 143 LNRRGYTLGYHPQSQSLATVGGSIAMLGSGALAPGLGNIEDMVLWLETVIpGLGTV 198
                                    *************************************************9777766 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   1.1e-24     1e-20      60     247 ..     286     465 ..     239     468 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.1e-24
                                    T-EEEEEEEEE-HHHHHHHHHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEH CS
                  FAD-oxidase_C  60 eealllvefegddeeeaeeelealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPv 139
                                     +a+l+ve+e++d   + e++e  ve+ ++a g++        + + + w+  ++++    + l+ ag +v++ Dt+ P+
  gi|118430989|ref|NP_147137.2| 286 DGAVLMVEVEAPD-RGLLEAMEGYVEKVASASGGSR------VEGVYEKWARARYMYDEHVRQLWSAGLWVDTIDTAAPW 358
                                    456999******9.4555555536666666655555......3333466666666666677788**************** PP

                                    HHHHHHHHHHHHHHHHHH...EEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT------------- CS
                  FAD-oxidase_C 140 srladlvrdikalldkyg...levvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldk 216
                                    sr+ dl r++ + l+      +++++ gH++ g++ ly ++ ++     +++ +++ +v++++ +lg si+++HG Gl +
  gi|118430989|ref|NP_147137.2| 359 SRVEDLNRRLLEDLAGIPgvvAVMSHAGHFYSGGASLYHTVVME--RRLDTYWRVWSRVAEAVRQLGASITHQHGWGLLR 436
                                    ********99999998878999999****************996..9999999*************************** PP

                                    ----------THHHHHHHHHHHH-TT--BST CS
                  FAD-oxidase_C 217 kaylerekgeeglalmrriKaalDPkgiLNP 247
                                    k+yl    g   + ++ r+K++lDP ++LNP
  gi|118430989|ref|NP_147137.2| 437 KPYLGFLGGN--YRVFCRVKNTLDPGNVLNP 465
                                    ****998877..******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3931.32
//
Query:       gi|118430990|ref|NP_147138.2|  [L=367]
Description: oxidoreductase [Aeropyrum pernix K1]
Scores for 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-40  137.5   0.8    8.9e-40  137.3   0.8    1.0  1  DAO             FAD dependent oxidoreductase
    1.8e-05   24.0   1.1      2e-05   23.9   0.3    1.4  2  FAD_binding_2   FAD binding domain
      4e-05   23.0   0.3      0.013   14.7   0.3    2.1  2  FAD_binding_3   FAD binding domain
    4.1e-05   23.7   0.1    8.5e-05   22.7   0.1    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00016   21.0   0.4    0.00031   20.1   0.4    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00019   20.6   0.3      0.062   12.3   0.0    2.3  2  Lycopene_cycl   Lycopene cyclase protein
    0.00059   18.6   0.4     0.0012   17.7   0.3    1.5  2  HI0933_like     HI0933-like protein
     0.0012   19.3   0.6     0.0026   18.3   0.6    1.6  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0045   16.4   1.0     0.0064   15.9   1.0    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.043   13.4   0.1      0.072   12.7   0.1    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.074   12.3   0.2       0.27   10.5   0.0    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.097   12.6   1.2       0.13   12.2   0.3    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.12   11.6   0.2       0.12   11.6   0.2    2.2  3  Thi4            Thi4 family
       0.13   12.2   0.2        2.1    8.3   0.1    2.1  2  NAD_binding_9   FAD-NAD(P)-binding
       0.14   11.2   0.5        0.2   10.7   0.5    1.2  1  GIDA            Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   0.8   7.4e-43   8.9e-40       1     351 [.       5     358 ..       5     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 7.4e-43
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    d v++G+G++Gl+tA +La rg  V+++e  d++  g S+r++ ++h     +p  s + rl+ e++++   l++elg  
  gi|118430990|ref|NP_147138.2|   5 DTVVVGAGVVGLFTAIQLAWRGysVAVVEELDRVMGGVSSRSANVIHVLQ--TPFSSLKSRLCVEGNRLHFVLSRELGY- 81 
                                    89*****************999********988888************55..55556788****************994. PP

                                    TSEEEEEEEEEESSHHHHHHHHHHHHHH..........HHTTTTE..EEEEHHHHHHHSTT.STTTSEEEEETTEEEEEH CS
                            DAO  79 idyrrtGllslaadeeelealdkllall..........leaglda..elldaeevrelepa.lpgllgalfypdtgqvdp 145
                                        +  l+   ++ee ++ l++ + +l           +ag++   e l++ ++r+lep+ +++++g++++++ g+vd+
  gi|118430990|ref|NP_147138.2|  82 -SIVEAPLILA-YSEEYKAPLAATVSRLlprlvpkpsaDDAGPEIrfEHLRGPRLRDLEPGlSDRVKGGVVVYGYGVVDY 159
                                    .5555555555.567778888877777778889999986677755337799989*******777**************** PP

                                    HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEEE CS
                            DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdll.gll.keldlpispvrg 222
                                    + l+ +l r++++l +e+++ ++ +++ee+   ++ +    +ge   aa+avVnaaG+ s  + +l+  ++ +  +p++g
  gi|118430990|ref|NP_147138.2| 160 RSLASSLERRVKRL-GELFLSSPLRRVEER---GGYIL-LHAGEAtLAAKAVVNAAGLMSHVVaRLFaDKV-PSQTPLKG 233
                                    **************.6888888*****886...44442.3334443578***********97756666555.444***** PP

                                    EEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG.GCG CS
                            DAO 223 qvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPq.lgd 301
                                     +   + + +    +  ++p+  ++ + +g  ++p  dg++l+G++   + + +d + + ed+d l+++ + l+ + +g+
  gi|118430990|ref|NP_147138.2| 234 VMSIHRGPRL----RSIVAPLELRRGETKGGGAIPQSDGSLLLGPNNAGPTKLGDESYTKEDLDGLRSRFQPLLAEpVGE 309
                                    **99966555....446677766999999999*************9863333334689999*************775699 PP

                                    EEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                            DAO 302 vlrkwaGlrpl.pdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                      r  +Glrp  p +++ + ++     +++  G++++Glt ap  + ++a 
  gi|118430990|ref|NP_147138.2| 310 PYRVVVGLRPVaPGRDFKVARG--KGSVVHMVGIESPGLTAAPSLAAVAAS 358
                                    999*******54899****996..569*****************9998886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.3   1.7e-08     2e-05       1      36 [.       5      40 ..       5      61 .. 0.82
   2 ?   -3.9   0.0       4.4   5.3e+03     187     204 ..     198     215 ..     190     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.7e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   D +V+G+G+ GL  A+++a++G +vavve  +++ g
  gi|118430990|ref|NP_147138.2|  5 DTVVVGAGVVGLFTAIQLAWRGYSVAVVEELDRVMG 40
                                   89***************************9877655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.4
                                    EEEEEESEEEE-----GG CS
                  FAD_binding_2 187 evrirakavvlatgGfgr 204
                                    e +++akavv a+g +++
  gi|118430990|ref|NP_147138.2| 198 EATLAAKAVVNAAGLMSH 215
                                    566778888888887776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   1.1e-05     0.013       2      35 ..       4      37 ..       3      51 .. 0.89
   2 !    6.2   0.0    0.0044       5.3     147     220 ..     196     266 ..     183     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.1e-05
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                    d+++VGaG +Gl +a  L+ +G +v +ve  ++
  gi|118430990|ref|NP_147138.2|  4 FDTVVVGAGVVGLFTAIQLAWRGYSVAVVEELDR 37
                                   5899**************************8765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                                    TTEEEEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEEEEEECC CS
                  FAD_binding_3 147 tgeeetvrakYlvGaDGgrStvrktlgie.fegeetvyeagvldvlfdadlsdiveplvlilsaesrgvmviPle 220
                                    +ge  t+ ak +v a G  S v ++l  + ++++  +   gv++++   +l++iv+pl+l + + ++g   iP++
  gi|118430990|ref|NP_147138.2| 196 AGEA-TLAAKAVVNAAGLMSHVVARLFADkVPSQTPL--KGVMSIHRGPRLRSIVAPLELRRGETKGG-GAIPQS 266
                                    5666.*********************99977777777..******************66666555555.666665 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 !   22.7   0.1   7.1e-08   8.5e-05       1      39 [.       8      46 ..       8      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.1e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EEC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasye 39
                                   +vGaG+ Gl +A  La +g++v ++e  dr+ G ++s++
  gi|118430990|ref|NP_147138.2|  8 VVGAGVVGLFTAIQLAWRGYSVAVVEELDRVMGGVSSRS 46
                                   8*****************************666666654 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   0.4   2.6e-07   0.00031     145     184 ..       6      45 ..       2      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                                    EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllraldke 184
                                    +vvvG+G++G+ +A++la  g+ v +ve +dr++ ++ ++
  gi|118430990|ref|NP_147138.2|   6 TVVVGAGVVGLFTAIQLAWRGYSVAVVEELDRVMGGVSSR 45 
                                    79*******************************9666555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1    0.0032       3.9       1      36 [.       5      38 ..       5      70 .. 0.91
   2 !   12.3   0.0   5.2e-05     0.062      79     145 ..     152     216 ..     141     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0032
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   D vv+GaG  gl  A +l  a  g +v ++e  + +
  gi|118430990|ref|NP_147138.2|  5 DTVVVGAGVVGLFTAIQL--AWRGYSVAVVEELDRV 38
                                   88****************..9999999999876655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                  Lycopene_cycl  79 raYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggr.kirarlvvdarglaslk 145
                                    + Yg v  + l++ l++r+   g  +l++   +vee      ++ l++g+ ++ a++vv a gl s  
  gi|118430990|ref|NP_147138.2| 152 YGYGVVDYRSLASSLERRVKRLGELFLSSPLRRVEERGG---YILLHAGEaTLAAKAVVNAAGLMSHV 216
                                    57**********************************999...888888887************98876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   9.8e-07    0.0012       2      34 ..       5      37 ..       4      42 .. 0.92
   2 ?   -2.8   0.0       1.6   1.9e+03     125     166 ..     175     214 ..     162     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.8e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                   d++v+G+G  Gl++Ai++a rg +V+++e+ ++
  gi|118430990|ref|NP_147138.2|  5 DTVVVGAGVVGLFTAIQLAWRGYSVAVVEELDR 37
                                   89**************************98765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                    EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                    HI0933_like 125 klrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                    +l l++ +++ve+ ++g + +++ +e +l+a+++v A G +S
  gi|118430990|ref|NP_147138.2| 175 ELFLSSPLRRVEE-RGGYILLHA-GEATLAAKAVVNAAGLMS 214
                                    5566667777744.555577777.999999999999988666 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   0.6   2.2e-06    0.0026       2      36 ..       6      40 ..       5      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSST CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllr 36
                                    vvvG+G++gl  A  la  g +V vve  d+++ 
  gi|118430990|ref|NP_147138.2|  6 TVVVGAGVVGLFTAIQLAWRGYSVAVVEELDRVMG 40
                                   69*******************************94 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.0   5.4e-06    0.0064       1      41 [.       5      46 ..       5      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.4e-06
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee.rgvlGGlltsg 41
                                   D vVvG+g+ G+  Ai+ a +G +v++vee ++v+GG +++ 
  gi|118430990|ref|NP_147138.2|  5 DTVVVGAGVVGLFTAIQLAWRGYSVAVVEElDRVMGGVSSRS 46
                                   789**************************8356779988765 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   0.1     6e-05     0.072       4      31 ..       7      34 ..       5      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6e-05
                                   EEE--STTHHHHHHHHHHCTSEEEEE-S CS
                 UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDi 31
                                   +v+G+G vGl ta+ la +g  v +v  
  gi|118430990|ref|NP_147138.2|  7 VVVGAGVVGLFTAIQLAWRGYSVAVVEE 34
                                   69*********************99964 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 ?   10.5   0.0   0.00023      0.27      31      80 ..       6      55 ..       2      82 .. 0.82
   2 ?   -1.8   0.0       1.3   1.5e+03      28      46 ..     146     164 ..     140     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                                   EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCH CS
                    AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlks 80
                                   ++v+G+Gv+Gl  +   +  g +V v++   +++  ++s  a++++vl+ 
  gi|118430990|ref|NP_147138.2|  6 TVVVGAGVVGLFTAIQLAWRGYSVAVVEELDRVMGGVSSRSANVIHVLQT 55
                                   79********9766666666999999999999999999988888888654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                    --EEEEESTSHHHHHHHHH CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiat 46 
                                    ++ v+v G Gv+   ++a 
  gi|118430990|ref|NP_147138.2| 146 KGGVVVYGYGVVDYRSLAS 164
                                    4679999999998877654 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 ?   12.2   0.3   0.00011      0.13       3      31 ..       7      35 ..       5      56 .. 0.86
   2 ?   -2.8   0.0       4.2     5e+03       7      20 ..     210     223 ..     205     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                        3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdis 31
                                    v+GaG++G   a ++a +g++V +v+  
  gi|118430990|ref|NP_147138.2|  7 VVVGAGVVGLFTAIQLAWRGYSVAVVEEL 35
                                   59***********************9865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.2
                                    -SCCHHHHHHHHHH CS
                        3HCDH_N   7 aGtmGagiaavfas 20 
                                    aG+m + +a +fa 
  gi|118430990|ref|NP_147138.2| 210 AGLMSHVVARLFAD 223
                                    7*********9996 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0001      0.12      18      56 ..       4      41 ..       1      52 [. 0.87
   2 ?   -2.3   0.0       1.7     2e+03     156     174 ..     200     218 ..     196     237 .. 0.65
   3 ?   -1.4   0.1      0.97   1.2e+03      20      38 ..     336     354 ..     332     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                    D v+vGaG  GL +a  la + +  va++e+   + GG
  gi|118430990|ref|NP_147138.2|  4 FDTVVVGAGVVGLFTAIQLAWR-GYSVAVVEELDRVMGG 41
                                   599*******************.*******986555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                    EEEEEEEEE--GSSSTTTT CS
                           Thi4 156 virakvvvdatGhdgeiva 174
                                    ++ ak+vv+a+G  +++va
  gi|118430990|ref|NP_147138.2| 200 TLAAKAVVNAAGLMSHVVA 218
                                    5677788888877666655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.97
                                    EEEE--SHHHHHHHHHHHH CS
                           Thi4  20 vvivGaGssGLtaayylak 38 
                                    v +vG  s GLtaa  la 
  gi|118430990|ref|NP_147138.2| 336 VHMVGIESPGLTAAPSLAA 354
                                    668999********99885 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 ?    8.3   0.1    0.0017       2.1       1      57 [.       7      58 ..       7      63 .. 0.83
   2 ?    1.7   0.0      0.18   2.2e+02     130     154 ..     187     211 ..     162     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpas 57
                                   ++vGaG+ Gl ++ +L+ r       ++ ++++ +  + g+v +++ +  + l +p s
  gi|118430990|ref|NP_147138.2|  7 VVVGAGVVGLFTAIQLAWR-----GYSVAVVEElDRVM-GGVSSRSANVIHVLQTPFS 58
                                   69**************988.....699******54555.9999998888888888765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                  NAD_binding_9 130 radgqavlladgaslaadaVvLAlG 154
                                    +++g+ +l a++a+laa+aVv A G
  gi|118430990|ref|NP_147138.2| 187 ERGGYILLHAGEATLAAKAVVNAAG 211
                                    34556677788899*******9988 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00017       0.2       1      36 [.       5      39 ..       5      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtia 36
                                   d +V+G+G  G+  A+++a +G++v+ + ++ld+++
  gi|118430990|ref|NP_147138.2|  5 DTVVVGAGVVGLFTAIQLAWRGYSVAVV-EELDRVM 39
                                   569***********************99.6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2729.47
//
Query:       gi|14600622|ref|NP_147139.1|  [L=276]
Description: malyl-CoA lyase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-35  121.9   0.0    2.6e-34  118.3   0.0    2.1  1  HpcH_HpaI       HpcH/HpaI aldolase/citrate lyase family
    1.8e-18   66.8   0.0    3.3e-13   49.5   0.0    2.1  2  C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold


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 !  118.3   0.0     3e-38   2.6e-34       1     221 []       3     209 ..       3     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 3e-38
                                   EEEEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGG.H CS
                     HpcH_HpaI   1 riglflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdle.v 80 
                                   r++l++pg +++ ++k +  +aD+v++DlEd+v   +Kd+AR  v+ +l++l+        v+VRvn+  s+ +++dl  v
  gi|14600622|ref|NP_147139.1|   3 RSMLYVPGVDERKIRKSTRVEADAVILDLEDSVPQGRKDEARSIVERLLRELEWSG----DVCVRVNTPASRDGIRDLDaV 79 
                                   89****************************************************55....67*****************75 PP

                                   HH.TTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHHHTT- CS
                     HpcH_HpaI  81 ld.lgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsadlgt 160
                                    +   ++ +lvPk e +  + +v++a+ +             ++a +E+a+g++ +ee+a++egl ++  G++Dl+a+lg+
  gi|14600622|ref|NP_147139.1|  80 SRwDRVSCLLVPKAEAR--LDTVYKATGR------------SVVAIVETARGLLRVEEVASSEGLVALNWGPADLAASLGA 146
                                   55257999****98865..5566666554............479************************************* PP

                                   TTSTTSHHHH..HHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHHHHHH CS
                     HpcH_HpaI 161 krspegtevl..dareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgkllinp 221
                                   + +p    v+    r  i+ aar  g++ +d v++ +++ eg+++e  +++a+Gf+gk++i+p
  gi|14600622|ref|NP_147139.1| 147 SVEPLDSGVYtpILRLLIASAARSYGLEPVDKVYFRVRELEGLRRECLEAKAIGFSGKTVIHP 209
                                   **********76677778899*****************************************8 PP

>> C-C_Bond_Lyase  C-C_Bond_Lyase of the TIM-Barrel fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.2e-07    0.0074      10      64 ..       5      56 ..       4     115 .. 0.84
   2 !   49.5   0.0   3.6e-17   3.3e-13     247     333 ..     183     272 ..     154     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-07
                C-C_Bond_Lyase 10 tLYmPatrediaekilkqklegltslvlclEDavseeeveaAeenlkellkelae 64
                                   LY+P+  e   +ki+k++  ++ +++l+lED+v + + ++A + +++ll+el+ 
  gi|14600622|ref|NP_147139.1|  5 MLYVPGVDE---RKIRKSTRVEADAVILDLEDSVPQGRKDEARSIVERLLRELEW 56
                                  69****995...6888999999*****************************9986 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 3.6e-17
                C-C_Bond_Lyase 247 ekdldglirEvalDkanGlvGKtvIhPsqialvqallvVskeeyedAldilesakggvfk....seyankmnEvkphraWA 323
                                    ++l+gl rE    ka G+ GKtvIhPs++++v+++++ s+ee e A++++e+ +++v k    + ++++++  + h++ A
  gi|14600622|ref|NP_147139.1| 183 VRELEGLRRECLEAKAIGFSGKTVIHPSHVPIVNEAFTPSREEVERARRVVEAYEEAVRKglgaVAVEDELV-DAVHYRLA 262
                                   5789************************************************96667766111144556665.46788888 PP

                C-C_Bond_Lyase 324 ekilkrakvy 333
                                    ++l+ra+ y
  gi|14600622|ref|NP_147139.1| 263 LNLLRRASRY 272
                                   8888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2131.25
//
Query:       gi|118430991|ref|NP_147140.2|  [L=164]
Description: hypothetical protein APE_0313.1 [Aeropyrum pernix K1]
Scores for 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-29  100.3   0.0    1.1e-28   99.8   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 !   99.8   0.0   6.2e-33   1.1e-28      12     116 ..      27     134 ..      17     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 6.2e-33
                                    -EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.....SS--E.-TT-.SS-E.EGGGS--S-SSS-EEEEEEE CS
                           TrmO  12 aeaeielepeynseealegleefshlwllfvfhenaekkl....kakvr.pprlggnervGvfatRsphRpnpiglsvvk 86 
                                    +e+ ie+ pey  + +l+gl +fsh++++ ++h+++ ++l    + ++r   rl++  +vGvfat sp Rpnp++l++++
  gi|118430991|ref|NP_147140.2|  27 VEGFIEVLPEY--APGLDGLAGFSHIIVIAYLHKSKGRALrvrpRGLLRlGFRLEDLPEVGVFATDSPSRPNPLALTIAR 104
                                    6899*******..9*******************9954443222244444566889999********************** PP

                                    EEEEETTEEEEES----TT-EEEEEEE--H CS
                           TrmO  87 lekvegnvlevsgvDlldgtpvlDiKPYvp 116
                                    l ++eg++l+vsg+Dl dgtpvlDiKPY+p
  gi|118430991|ref|NP_147140.2| 105 LLDIEGRRLRVSGLDLYDGTPVLDIKPYTP 134
                                    ****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1308.52
//
Query:       gi|118430992|ref|NP_147141.2|  [L=276]
Description: D-aminopeptidase DppA [Aeropyrum pernix K1]
Scores for 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-74  249.7   0.0    3.5e-74  249.5   0.0    1.0  1  Peptidase_M55  D-aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M55  D-aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.5   0.0   1.9e-78   3.5e-74       2     262 ..       4     264 ..       3     266 .. 0.96

  Alignments for each domain:
  == domain 1  score: 249.5 bits;  conditional E-value: 1.9e-78
                  Peptidase_M55   2 kvyISaDiEGvagvvsweqvepgeaeyerarrlmteevnaaiegalaagatevlVnDsHgsmrNllpeeLdervrlisGk 81 
                                    + ++S+D EG+    s+ ++ p+++ y + rr+mt+  n+++e+++a+ga+ v+V+DsHgsm Nl+p e+d+rv+l++G 
  gi|118430992|ref|NP_147141.2|   4 RFFVSVDAEGMPYSPSRVMMMPRDPLYGELRRIMTRVTNIVVEEVFASGAEGVVVADSHGSMVNLDPFEIDDRVELVRGF 83 
                                    68****************************************************************************** PP

                  Peptidase_M55  82 pkplsmmegldesfdavlfvGyHaragtekgvlaHTysgsaieevrlngkevg.EfglnaalagelgVPvvlvsGDdalc 160
                                    p+pl m+ g  ++++a+lf+GyH + ++  gvl HTy+g+ +++vr+ g e+  E+ ln+++ ge+gVPvvlv+GD++l+
  gi|118430992|ref|NP_147141.2|  84 PRPLAMVYGA-RGCAAALFIGYHGSPQSG-GVLGHTYAGRIVQRVRVHGSEAAtEYLLNTYALGEMGVPVVLVAGDSVLE 161
                                    *********5.9*****************.*******************98655************************** PP

                  Peptidase_M55 161 eeakellpevetvavkeglgrfaakslspeeaeeaireavkeavekake..akplkleepvelevefkstalAdaaslvp 238
                                    +e+++++p++++v++k+  ++ a ++ +++++e+ +r+av+eav++++   a+plk++ep+ +eve+k++ +Ad+a+l+p
  gi|118430992|ref|NP_147141.2| 162 DEVRRHTPWAVFVPLKKPASSLADVTPPWQRVEKSLRSAVREAVAARSLerAEPLKPAEPW-IEVELKRPWHADVAELFP 240
                                    *******************************************998764559999987777.9***************** PP

                  Peptidase_M55 239 gveridartvefeaedveellral 262
                                     ver+d++tv+++++++++ +++l
  gi|118430992|ref|NP_147141.2| 241 CVERLDGVTVRLSCSSFVDNYKLL 264
                                    *******************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.18s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2335.30
//
Query:       gi|118430993|ref|NP_147142.2|  [L=218]
Description: hypothetical protein APE_0316.1 [Aeropyrum pernix K1]
Scores for 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-55  189.2   0.0    1.3e-55  188.9   0.0    1.1  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 !  188.9   0.0   7.2e-60   1.3e-55      56     277 ..       2     206 ..       1     208 [. 0.91

  Alignments for each domain:
  == domain 1  score: 188.9 bits;  conditional E-value: 7.2e-60
                                    EEEE--SSCHHHHHHHHHHHHHHHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTT CS
                       Arginase  56 gdvavtpvdneevleqieeavaeilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshG 135
                                    gdv+    + +ev+ ++ee+va+ l+ g+l i+lGGDHsi++++lral+  y ++lg++ +DAH Dl +++ eg+++sh+
  gi|118430993|ref|NP_147142.2|   2 GDVTAR--SYREVVSAVEEKVAS-LRGGRLFIFLGGDHSITYATLRALRSFYRGRLGLVYLDAHPDLYDEY-EGDRYSHA 77 
                                    555544..566678888888876.6789************************99*****************.9******* PP

                                    SHHHHHHHHTSECGCEEEEEEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBT CS
                       Arginase 136 tpfrraaeegllkpkklvqiGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDp 215
                                    + +rr++eeg+++p++++ +G+r+ ++++ ++a++ gi+v+  +e ++         + ++++ e  p y+S+D+DvlDp
  gi|118430993|ref|NP_147142.2|  78 CTLRRIVEEGFVDPRDVILAGVRAATPSQLDFAEKAGITVLGVEEAED---------LAAYLK-EGMPYYISYDLDVLDP 147
                                    *********************************************976.........445674.557************* PP

                                    TTSTSSSS-BSS-B-HHHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                       Arginase 216 avaPGtGtpepgGltlrellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                    a+aPG+G pepgGl++re+ ++++ l e  ++ ++DvvE +P+ d+++  t  +aa+++re 
  gi|118430993|ref|NP_147142.2| 148 AYAPGVGNPEPGGLSTREMVRIIKSLPE--DVLAFDVVEASPPHDPSG-LTLFTAAKIIRET 206
                                    **************************77..8***************66.***********94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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 0.20s 00:00:00.58 Elapsed: 00:00:00.34
# Mc/sec: 1902.07
//
Query:       gi|118430994|ref|NP_147143.2|  [L=464]
Description: phospho-sugar mutase [Aeropyrum pernix K1]
Scores for complete 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-44  149.8   0.0    7.1e-44  148.9   0.0    1.5  1  PGM_PMM_I      Phosphoglucomutase/phosphomannomutase, alpha/b
    1.2e-22   80.5   0.0    4.2e-22   78.7   0.0    2.0  2  PGM_PMM_II     Phosphoglucomutase/phosphomannomutase, alpha/b
    1.1e-17   64.2   0.0    1.9e-17   63.5   0.0    1.4  1  PGM_PMM_III    Phosphoglucomutase/phosphomannomutase, alpha/b
    1.7e-13   50.5   1.0    6.4e-13   48.7   0.5    2.2  2  PGM_PMM_IV     Phosphoglucomutase/phosphomannomutase, C-termi
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.084   13.0   0.0    1.6  1  Tautomerase_2  Tautomerase enzyme
      0.057   13.4   0.2       0.35   10.8   0.1    2.2  2  ADH_zinc_N     Zinc-binding dehydrogenase


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 !  148.9   0.0   2.4e-47   7.1e-44       1     135 [.       4     134 ..       4     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 2.4e-47
                                    CGGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HH CS
                      PGM_PMM_I   1 rqkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptP 80 
                                    r++fgt+G+Rg++g  eltpe+v++l++ai+ y+ +   +++++vGrDtR  ++ ++  +aagla +Gvev+l+g lptP
  gi|118430994|ref|NP_147143.2|   4 RRLFGTDGVRGVIG-SELTPEFVLRLARAIGAYFGR---GSRILVGRDTRSGGELFEGLVAAGLAFEGVEVHLAGTLPTP 79 
                                    579***********.66******************9...8**************************************** PP

                                    HHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                      PGM_PMM_I  81 avsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                    a++ ++r +++dag+m+taSHnppeyngiKv+  +G++++++vee Iea + + +
  gi|118430994|ref|NP_147143.2|  80 ALQLYVRDHGYDAGVMVTASHNPPEYNGIKVVGGDGVEVPRDVEEGIEALFWEGK 134
                                    *************************************************998766 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 ?   -2.4   0.0       2.5   7.4e+03      74      88 ..      81      95 ..      78      96 .. 0.83
   2 !   78.7   0.0   1.4e-25   4.2e-22       2     103 .]     156     256 ..     155     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                                   HHHHGGGGG-SEEEE CS
                     PGM_PMM_II 74 lielvkkegadlgla 88
                                   l+ +v+++g+d+g++
  gi|118430994|ref|NP_147143.2| 81 LQLYVRDHGYDAGVM 95
                                   5679********996 PP

  == domain 2  score: 78.7 bits;  conditional E-value: 1.4e-25
                                    HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGG CS
                     PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkke 81 
                                     Y+++++e+v+  + ++ g +vv+d+++Ga++ ++ e+lk+lg+++++l ++pdp f+++ p+p++ ++l  ++ lv+++
  gi|118430994|ref|NP_147143.2| 156 YYVNRVVENVSAFTQRGGGERVVVDCGGGATSFTTVEILKRLGARPIPLSCKPDPLFSSRDPEPTP-DTLGPAASLVRSS 234
                                    59*********777788899**********************************************.************* PP

                                    G-SEEEEE-TTS-BEEEEETTE CS
                     PGM_PMM_II  82 gadlglafDgDaDRlgvvderG 103
                                    ga +g+ +D D+DR +v+d+rG
  gi|118430994|ref|NP_147143.2| 235 GAVFGVGHDADGDRAIVIDDRG 256
                                    *******************998 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 !   63.5   0.0   6.4e-21   1.9e-17       2     111 ..     261     371 ..     260     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 6.4e-21
                                    HHHHHHHHHHHHHCHCSTTTC.EEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTB CS
                    PGM_PMM_III   2 gdqllallakylleeklkpga.gvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldea 80 
                                    gd+ +alla  ++e  l++g  +v + v++s ++e++++ +gi++v t+vG   +++++  +g   ++Ee+g+++ + ++
  gi|118430994|ref|NP_147143.2| 261 GDRSGALLAGFVAEVGLAKGPlKVYTGVSSSIVVEDYLRPRGIEVVWTPVGAPIIARAILTQGGIAAFEENGGYMHPPHQ 340
                                    8999******9977777777669********************************************************* PP

                                    SS--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                    PGM_PMM_III  81 ttkDGilaallvleilaetgkslselleell 111
                                    + +DG + a+l+l++l+ tg+sls+ll++l+
  gi|118430994|ref|NP_147143.2| 341 YVRDGGMKAALLLAMLRATGESLSSLLDRLP 371
                                    ***************************6654 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 ?   -2.0   0.0       1.5   4.3e+03      23      36 ..     115     133 ..      91     137 .. 0.57
   2 !   48.7   0.5   2.1e-16   6.4e-13       7      73 ..     392     452 ..     381     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
                                    H.....HCCCCCCCCGCCE CS
                     PGM_PMM_IV  23 a.....sikeglkilledG 36 
                                    +     +  eg++ l+++G
  gi|118430994|ref|NP_147143.2| 115 GvevprDVEEGIEALFWEG 133
                                    0333334556666666665 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 2.1e-16
                                    CC-TT..EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHHH CS
                     PGM_PMM_IV   7 eekakvvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevaell 73 
                                    e    v +++++   v  +++g+k+ +e  ++l vRpSGTep++r+++Ea+s+ee+  l e+v++++
  gi|118430994|ref|NP_147143.2| 392 EA---VKQEFQGERMV--TIDGVKVIGEGYWVL-VRPSGTEPVVRIMLEARSEEEARALFERVLRAV 452
                                    33...46789999899..9********999999.**************************9998876 PP

>> Tautomerase_2  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.8e-05     0.084      30      63 ..     427     459 ..     404     461 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                    EEEEEEEES---HHHHHHHHHHHHHHHHHHH--- CS
                  Tautomerase_2  30 vvieitlsegRseeqKkaLyralaerlaaklgir 63 
                                     v++i l   Rsee+ +aL++++ + +++k+gi+
  gi|118430994|ref|NP_147143.2| 427 PVVRIMLE-ARSEEEARALFERVLRAVKEKCGIP 459
                                    57888888.***********************97 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00012      0.35      35      83 ..     154     198 ..     149     200 .. 0.87
   2 ?   -1.1   0.0       0.6   1.8e+03      69      90 ..     221     242 ..     219     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                                    ESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHHHCEEEEE CS
                     ADH_zinc_N  35 adevinykeadlverikeltg.gegvdvvfecvGsgatleaalkllkpgG 83 
                                    +d+++n+    +ve + ++t+ g+g  vv++c G gat  + +++lk+ G
  gi|118430994|ref|NP_147143.2| 154 VDYYVNR----VVENVSAFTQrGGGERVVVDCGG-GATSFTTVEILKRLG 198
                                    4566666....9********8899**********.***********9987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                                    HHHHHHHHHCEEEEEEEEECSC CS
                     ADH_zinc_N  69 gatleaalkllkpgGrlvvvGg 90 
                                    ++tl  a +l++  G ++ vG 
  gi|118430994|ref|NP_147143.2| 221 PDTLGPAASLVRSSGAVFGVGH 242
                                    778889999***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3482.98
//
Query:       gi|14600627|ref|NP_147144.1|  [L=180]
Description: protease I [Aeropyrum pernix K1]
Scores for complete 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-59  199.7   0.0      3e-59  199.5   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
    0.00059   19.7   0.0    0.00074   19.3   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.14   11.9   0.0    2.2  2  ThiJ_like      ThiJ/PfpI family-like
      0.059   13.1   0.0      0.089   12.5   0.0    1.3  1  Peptidase_C26  Peptidase C26
      0.068   12.3   0.0       0.11   11.6   0.0    1.4  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      0.083   12.5   0.0       0.11   12.0   0.0    1.1  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


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 !  199.5   0.0     1e-62     3e-59       2     164 ..       3     164 ..       2     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 199.5 bits;  conditional E-value: 1e-62
                                   EEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHHHTSHH CS
                     DJ-1_PfpI   2 kvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperlrenek 82 
                                   ++l++ adg+edvEl +p+ +l +ag+++ v+ ++++e+kg+ G+kv +  s+++vk++e+D+lv+pGGra per+r +e+
  gi|14600627|ref|NP_147144.1|   3 RALIISADGFEDVELLYPYYRLVEAGFETLVAAPSRGEIKGKMGYKVEAKLSFEEVKPEEFDVLVIPGGRA-PERVRLHEA 82 
                                   799********************************************************************.********* PP

                                   HHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGGHHHHHHHHH CS
                     DJ-1_PfpI  83 vvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpgaaiefalell 163
                                   ++++v++f+ek+k+va+IC+gpq+L++agv+kgrr+Tsy++vkd++ +ag ++vd++vvvdgnlv+sr p++++ +++e++
  gi|14600627|ref|NP_147144.1|  83 ALNIVRHFFEKNKPVATICHGPQVLISAGVVKGRRLTSYWGVKDDVIAAGGNWVDEPVVVDGNLVSSRYPPDIPYWMREFM 163
                                   ******************************************************************************998 PP

                                   H CS
                     DJ-1_PfpI 164 e 164
                                   +
  gi|14600627|ref|NP_147144.1| 164 R 164
                                   5 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.5e-07   0.00074      33      87 ..      55     110 ..      41     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                                   HHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                        GATase  33 aeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaie 87 
                                   +ee   + +++d ++++gG         e +++++++++e+++P+  IC G Q+l+ +
  gi|14600627|ref|NP_147144.1|  55 FEEV--KPEEFDVLVIPGGRAPERvrlHEAALNIVRHFFEKNKPVATICHGPQVLISA 110
                                   3334..35789999***9955554559999************************9865 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.15   4.4e+02       2      27 ..       8      33 ..       7      42 .. 0.83
   2 ?   11.9   0.0   4.6e-05      0.14      77     141 ..      55     110 ..      40     120 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.15
                     ThiJ_like  2 adeGydvtevaipwkvlkdagfsveF 27
                                  +  G++  e+  p+  l +agf+   
  gi|14600627|ref|NP_147144.1|  8 SADGFEDVELLYPYYRLVEAGFETLV 33
                                  67899999*************98655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.6e-05
                     ThiJ_like  77 sesFsleeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafa 141
                                    e+ + ee+d++ +pGG+ +         rlh+   + +   ++  e++k +++ic+g  +l  a
  gi|14600627|ref|NP_147144.1|  55 FEEVKPEEFDVLVIPGGRAPER------VRLHEAALNIV---RHFFEKNKPVATICHGPQVLISA 110
                                   55556689**********9854......45555544433...2223789*********9888766 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05     0.089      91     119 ..      80     108 ..      56     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                 Peptidase_C26  91 dalelaLiraalergvPilgiCrGlqlln 119
                                   ++  l ++r+  e+++P+  iC G q+l 
  gi|14600627|ref|NP_147144.1|  80 HEAALNIVRHFFEKNKPVATICHGPQVLI 108
                                   778899********************994 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 ?   11.6   0.0   3.6e-05      0.11      70     111 ..      75     115 ..      51     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                      GATase_5  70 kslllneklrealekflnredtlaLGiCnGfqlLvklglvpg 111
                                   ++++l+e++ + +++f+++ ++ +  iC G q+L+  g+v g
  gi|14600627|ref|NP_147144.1|  75 ERVRLHEAALNIVRHFFEK-NKPVATICHGPQVLISAGVVKG 115
                                   678999*************.99999**************988 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 ?   12.0   0.0   3.8e-05      0.11      35      88 ..      58     107 ..      43     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                      GATase_3  35 eslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88 
                                    +  e+ d++++pGg+  ++   ++++    + ++++ e+++pv  iC G q+L
  gi|14600627|ref|NP_147144.1|  58 VKP-EEFDVLVIPGGRAPERVRLHEAA---LNIVRHFFEKNKPVATICHGPQVL 107
                                   333.679********987766655555...7889999***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.39
# Mc/sec: 1377.65
//
Query:       gi|118430995|ref|NP_147145.2|  [L=110]
Description: ferredoxin [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   45.2  19.7    2.1e-07   31.4   9.4    2.0  3  Fer4_7    4Fe-4S dicluster domain
    1.1e-10   40.9  16.9    2.6e-09   36.5   4.7    2.5  2  Fer4      4Fe-4S binding domain
    1.7e-09   37.6   6.3    3.1e-09   36.8   6.3    1.4  1  Fer4_10   4Fe-4S dicluster domain
    4.3e-09   36.4  10.0    5.6e-09   36.0  10.0    1.2  1  Fer4_21   4Fe-4S dicluster domain
    1.9e-08   35.1   9.1    2.5e-05   25.1   1.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    8.5e-08   32.0   4.2    8.5e-08   32.0   4.2    2.4  2  Fer4_6    4Fe-4S binding domain
    4.9e-07   29.8  20.9    0.00017   21.7   1.8    2.1  3  Fer4_9    4Fe-4S dicluster domain
    2.9e-06   27.1   3.4    2.9e-06   27.1   3.4    2.5  2  Fer4_2    4Fe-4S binding domain
     0.0001   23.0  13.4    0.00069   20.4   3.7    2.3  2  Fer4_3    4Fe-4S binding domain
    0.00091   19.9  13.4      0.058   14.1  13.4    2.8  1  Fer4_15   4Fe-4S single cluster domain
     0.0019   18.3   4.2      0.034   14.2   3.6    2.1  2  Fer4_11   4Fe-4S dicluster domain
     0.0019   18.7  17.2     0.0047   17.4  14.7    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0023   18.3   3.3     0.0023   18.3   3.3    2.5  2  Fer4_4    4Fe-4S binding domain
     0.0034   17.9  11.4      0.026   15.1   1.7    2.3  4  Fer4_17   4Fe-4S dicluster domain
     0.0081   16.6  11.6          2    9.0  11.1    2.4  2  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
        0.1   13.5   0.5        0.1   13.5   0.5    2.3  2  Fer4_22   4Fe-4S dicluster domain
          2    8.7  11.1        8.7    6.6  10.5    2.1  1  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   2.6   1.4e-08   1.5e-05      30      52 .]       9      31 ..       5      31 .. 0.91
   2 !   31.4   9.4     2e-10   2.1e-07       1      51 [.      16      60 ..      16      61 .. 0.94
   3 !    7.5   2.8     0.006       6.3       7      23 ..      52      68 ..      45     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.4e-08
                         Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                   +v+id+++C++CgaC++vCP++a
  gi|118430995|ref|NP_147145.2|  9 RVAIDQDTCISCGACIEVCPYDA 31
                                   7899****************997 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 2e-10
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                   +Ci CgaC ++Cp++a+e+de       +k+++  ekC++  +C++ CP++
  gi|118430995|ref|NP_147145.2| 16 TCISCGACIEVCPYDALEFDEN------MKARLIWEKCQDDFSCIESCPVN 60
                                   6******************985......7899*****************98 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.006
                         Fer4_7  7 aCvaaCpvkaieldeee 23
                                    C + Cpv++i+  ee+
  gi|118430995|ref|NP_147145.2| 52 SCIESCPVNCIYKVEEA 68
                                   68888888888877654 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   4.7   2.4e-12   2.6e-09       2      24 .]      11      33 ..      10      33 .. 0.93
   2 !   10.0   4.3   0.00058      0.62       5      24 .]      44      63 ..      40      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.4e-12
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                    id++ Ci CGaC+evCP++A++
  gi|118430995|ref|NP_147145.2| 11 AIDQDTCISCGACIEVCPYDALE 33
                                   69*******************85 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                                   TTTSSS-THHHHHSTTTEEE CS
                           Fer4  5 eekCigCGaCvevCPvgAIt 24
                                   +ekC     C+e CPv++I+
  gi|118430995|ref|NP_147145.2| 44 WEKCQDDFSCIESCPVNCIY 63
                                   566666668*********96 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   6.3   2.9e-12   3.1e-09       2      56 .]      10      58 ..       9      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.9e-12
                        Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   v id+dtCi Cg+C ++CP+         e +e+ + r   ekC++ ++C+e+CP
  gi|118430995|ref|NP_147145.2| 10 VAIDQDTCISCGACIEVCPY------DALEFDENMKARLIWEKCQDDFSCIESCP 58
                                   689*****************......555555555666679*************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 !   36.0  10.0   5.3e-12   5.6e-09       2      57 ..      11      62 ..      10      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.3e-12
                        Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                    id+d+Ci+Cg C+ +C+   ++a+e+d++ +++++ ++C     C++ CPv +ci
  gi|118430995|ref|NP_147145.2| 11 AIDQDTCISCGACIEVCP---YDALEFDENMKARLIWEKCQDDFSCIESCPV-NCI 62
                                   59****************...9*****************************9.9*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 !   25.1   1.6   2.3e-08   2.5e-05       1      28 [.      16      41 ..      16      51 .. 0.81
   2 !   14.1   2.0   6.4e-05     0.068       2      43 ..      47      96 ..      46     105 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.3e-08
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiear 28
                                   +C++Cg+C+evCP +a++ +  ++++ar
  gi|118430995|ref|NP_147145.2| 16 TCISCGACIEVCPYDALEFD--ENMKAR 41
                                   5*****************99..455544 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.4e-05
                        Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy........ntaekkdlae 43
                                   C++   C+e+CP+n+i + +e+  e +++++         n++ekk ++e
  gi|118430995|ref|NP_147145.2| 47 CQDDFSCIESCPVNCIYKVEEAPEELKTEKAGwyrlgrelNEEEKKAFEE 96
                                   555557***********995544444444443445555433333333333 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   4.2     8e-11   8.5e-08       2      24 .]      10      32 ..       9      32 .. 0.95
   2 ?    4.1   3.0     0.053        56       7      24 .]      45      62 ..      45      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 8e-11
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   v+id+d Ci+Cg+C+ vCP++a+
  gi|118430995|ref|NP_147145.2| 10 VAIDQDTCISCGACIEVCPYDAL 32
                                   89******************997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.053
                         Fer4_6  7 dkCigCgdCvrvCPegai 24
                                   +kC +   C+  CP + i
  gi|118430995|ref|NP_147145.2| 45 EKCQDDFSCIESCPVNCI 62
                                   58888889******9876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.8   1.6e-07   0.00017      26      50 ..       8      31 ..       2      32 .. 0.76
   2 !   19.6  11.5   7.2e-07   0.00075       2      51 .]      17      62 ..      16      62 .. 0.89
   3 ?    6.3   2.2      0.01        11       5      24 ..      47      70 ..      45      91 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                         Fer4_9 26 arlraaseeaCigCgaCveaCpkga 50
                                   +r+ ++++  Ci+CgaC+e+Cp +a
  gi|118430995|ref|NP_147145.2|  8 VRVAIDQD-TCISCGACIEVCPYDA 31
                                   55555555.8************987 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 7.2e-07
                         Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   C++CgaC+e+Cp+++ + d++ + + +  +  e+C +  +C+e Cp ++i
  gi|118430995|ref|NP_147145.2| 17 CISCGACIEVCPYDALEFDENMKARLI--W--EKCQDDFSCIESCPVNCI 62
                                   ****************99999998887..3..47999999******9976 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.01
                         Fer4_9  5 Cga...CveaCpagvv.vedaaer 24
                                   C+    C+e+Cp + + + ++a++
  gi|118430995|ref|NP_147145.2| 47 CQDdfsCIESCPVNCIyKVEEAPE 70
                                   443334888888777634444444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   3.4   2.7e-09   2.9e-06       2      22 .]       9      29 ..       8      29 .. 0.93
   2 ?    3.2   0.5       0.1   1.1e+02      15      21 ..      52      58 ..      45      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.7e-09
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                   +v++d d+Ci+CgaC+ +CP+
  gi|118430995|ref|NP_147145.2|  9 RVAIDQDTCISCGACIEVCPY 29
                                   589*****************5 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                         Fer4_2 15 aCvsaCP 21
                                   +C+ +CP
  gi|118430995|ref|NP_147145.2| 52 SCIESCP 58
                                   8*****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 !   20.4   3.7   6.5e-07   0.00069       1      15 []      17      31 ..      17      31 .. 0.97
   2 !    8.0   2.1    0.0059       6.3       4      14 ..      47      60 ..      45      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.5e-07
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+ CgaC evCP++A
  gi|118430995|ref|NP_147145.2| 17 CISCGACIEVCPYDA 31
                                   *************98 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0059
                         Fer4_3  4 Cg...aCvevCPvg 14
                                   C+    C e+CPv+
  gi|118430995|ref|NP_147145.2| 47 CQddfSCIESCPVN 60
                                   765557******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 !   14.1  13.4   5.5e-05     0.058       1      34 [.      10      50 ..      10      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-05
                        Fer4_15  1 VvvDrdaCigcglCvaeap.evfeldedglasvl......l 34
                                   V +D+d+Ci+cg+C++++p +  e+de+ +a+++       
  gi|118430995|ref|NP_147145.2| 10 VAIDQDTCISCGACIEVCPyDALEFDENMKARLIwekcqdD 50
                                   89****************65899999999998874444330 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.6   3.3e-05     0.034      36      77 ..      10      53 ..       7      63 .. 0.73
   2 ?    5.2   0.6     0.021        22      43      64 ..      47      67 ..      42      76 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                        Fer4_11 36 VlldektkkeevrevveacPykivrkneetgk...vekCdmcldr 77
                                   V +d++t+  ++ +++e+cPy++   +e+ ++   +ekC+  ++ 
  gi|118430995|ref|NP_147145.2| 10 VAIDQDTCI-SCGACIEVCPYDALEFDENMKArliWEKCQDDFSC 53
                                   789999997.9*************999988752226777654443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                        Fer4_11 43 kkeevrevveacPykivrknee 64
                                   ++ +  +++e+cP ++++k ee
  gi|118430995|ref|NP_147145.2| 47 CQ-DDFSCIESCPVNCIYKVEE 67
                                   43.3345667777776666554 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 !   17.4  14.7   4.5e-06    0.0047       1      56 [.      12      62 ..      12      64 .. 0.86
   2 ?   -2.4   0.0       6.9   7.3e+03      37      37 ..      87      87 ..      65      96 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.5e-06
                        Fer4_13  1 VDrdtCiacgaCvelaP.dvFeeddeggasvvaeqptseeekadaeeAadaCPvesI 56
                                   +D+dtCi+cgaC e++P d  e d++ +a  + e+ +++       + +++CPv++I
  gi|118430995|ref|NP_147145.2| 12 IDQDTCISCGACIEVCPyDALEFDENMKARLIWEKCQDD------FSCIESCPVNCI 62
                                   8****************999****998888887766654......35789******9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                        Fer4_13 37 s 37
                                   +
  gi|118430995|ref|NP_147145.2| 87 N 87
                                   2 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.3   2.1e-06    0.0023       1      16 [.      14      29 ..      14      31 .. 0.93
   2 ?    3.1   2.6      0.16   1.7e+02       9      17 .]      52      60 ..      44      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                         Fer4_4  1 qerCigCgsCvaaCPq 16
                                   q++Ci Cg+C+ +CP+
  gi|118430995|ref|NP_147145.2| 14 QDTCISCGACIEVCPY 29
                                   79*************8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.16
                         Fer4_4  9 sCvaaCPqg 17
                                   sC+ +CP++
  gi|118430995|ref|NP_147145.2| 52 SCIESCPVN 60
                                   8*****975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   2.5   5.3e-05     0.056      45      59 ..      16      30 ..      10      33 .. 0.73
   2 !   15.1   1.7   2.5e-05     0.026       2      16 ..      17      31 ..      16      44 .. 0.67
   3 ?    5.9   1.0     0.017        18      37      59 ..      38      60 ..      31      65 .. 0.76
   4 ?    4.5   2.1      0.05        52       4      23 ..      49      68 ..      45      99 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                        Fer4_17 45 lCieCgeCerkCPqg 59
                                   +Ci+Cg C ++CP++
  gi|118430995|ref|NP_147145.2| 16 TCISCGACIEVCPYD 30
                                   677777777777765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.5e-05
                        Fer4_17  2 CiqCgyClpeCpsye 16
                                   Ci+Cg+C+++Cp+ +
  gi|118430995|ref|NP_147145.2| 17 CISCGACIEVCPYDA 31
                                   888888888888754 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.017
                        Fer4_17 37 aekeekaslCieCgeCerkCPqg 59
                                   ++++  +++C     C ++CP +
  gi|118430995|ref|NP_147145.2| 38 MKARLIWEKCQDDFSCIESCPVN 60
                                   44445789999999999999965 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.05
                        Fer4_17  4 qCgyClpeCpsyeaydnepk 23
                                       C+++Cp + +y+ e++
  gi|118430995|ref|NP_147145.2| 49 DDFSCIESCPVNCIYKVEEA 68
                                   33349999999888776543 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0  11.1    0.0019         2       3      64 ..      15      60 ..      13      61 .. 0.59
   2 ?    5.7   2.2     0.019        20      50      64 ..      46      60 ..      44     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                   + Ci CgaC + Cp + +  ++     +e+++    +        +++C+   +C e Cpv+
  gi|118430995|ref|NP_147145.2| 15 DTCISCGACIEVCP-YDAL-EF-----DENMK---ARLI------WEKCQDDFSCIESCPVN 60
                                   68999999999999.3333.22.....12222...1222......45677777777777775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                         Fer4_8 50 sCttcgaCtevCpvg 64
                                   +C+   +C e Cpv+
  gi|118430995|ref|NP_147145.2| 46 KCQDDFSCIESCPVN 60
                                   566667777777765 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   9.7e-05       0.1      76      94 ..      11      29 ..       2      31 .. 0.75
   2 ?    2.4   1.0      0.27   2.9e+02       2      26 ..      47      71 ..      46     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-05
                        Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                    +++ +C+ Cg Cie+cp 
  gi|118430995|ref|NP_147145.2| 11 AIDQDTCISCGACIEVCPY 29
                                   5578888888888888875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                        Fer4_22  2 ClsCgaCtlvCptCsCfdvedetke 26
                                   C +  +C   Cp    ++ve+  +e
  gi|118430995|ref|NP_147145.2| 47 CQDDFSCIESCPVNCIYKVEEAPEE 71
                                   6666789999998777788777632 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  10.5    0.0083       8.7      57      95 ..      13      57 ..       5      72 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0083
                        Fer4_18 57 gagdcidcescvkvcPtg.idirkGlql.....eciscllcidac 95
                                   ++  ci+c++c++vcP + ++  + ++      +c     ci++c
  gi|118430995|ref|NP_147145.2| 13 DQDTCISCGACIEVCPYDaLEFDENMKArliweKCQDDFSCIESC 57
                                   5678************75245555555411112344445677777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 782.03
//
Query:       gi|118430996|ref|NP_147146.2|  [L=126]
Description: hypothetical protein APE_0321.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   15.0   0.1      0.012   14.7   0.1    1.1  1  Plant_NMP1  Plant nuclear matrix protein 1 (NMP1)
      0.012   15.7   1.2      0.035   14.2   0.1    2.0  2  DUF3782     Protein of unknown function (DUF3782)
      0.045   13.8   0.0      0.075   13.1   0.0    1.3  1  DUF1664     Protein of unknown function (DUF1664)
      0.052   13.9   0.0      0.072   13.4   0.0    1.3  1  Mis14       Kinetochore protein Mis14 like
      0.069   13.4   2.8       0.23   11.7   0.1    2.8  3  Halo_GVPC   Halobacterial gas vesicle protein C (GVPC) repeat
      0.074   13.4   0.7        1.1    9.6   0.4    2.2  2  PqqD        Coenzyme PQQ synthesis protein D (PqqD)


Domain annotation for each model (and alignments):
>> Plant_NMP1  Plant nuclear matrix protein 1 (NMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.1e-06     0.012     165     219 ..      71     125 ..      59     126 .] 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.1e-06
                     Plant_NMP1 165 iaelekklseyskklsslqqvvdelaskkdynpdeeyaeaelklraqlesfleta 219
                                    + el +k+ e  +++ sl ++v  la k  +n +  y  + l++r  le ++et+
  gi|118430996|ref|NP_147146.2|  71 VEELRNKVEELLDEVESLGDLVSGLARKFGFNVEARYRRSLLDFRDALEDYIETM 125
                                    789**************************************************95 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.33   9.9e+02      39      51 ..       5      17 ..       4      25 .. 0.82
   2 ?   14.2   0.1   1.2e-05     0.035       6      51 ..      67     112 ..      60     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.33
                        DUF3782 39 GlvsEeafReglk 51
                                   G + Ee++Re+ +
  gi|118430996|ref|NP_147146.2|  5 GEFLEEVVREASR 17
                                   7789999999865 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                        DUF3782   6 leeeeeetkedleelekeieklertigaLGaRWGlvsEeafReglk 51 
                                     e+  ee+++++eel  e+e+l + ++ L++ +G   E+  R +l 
  gi|118430996|ref|NP_147146.2|  67 YEDSVEELRNKVEELLDEVESLGDLVSGLARKFGFNVEARYRRSLL 112
                                    455689999*********************************9873 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.5e-05     0.075      75     117 ..      57      99 ..      51     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                        DUF1664  75 ldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                    l ++++i ++ ++ v+e+r++++e+ ++ves+ ++v+gl+ k 
  gi|118430996|ref|NP_147146.2|  57 LGDVEDIFEDYEDSVEELRNKVEELLDEVESLGDLVSGLARKF 99 
                                    56778899999****************************9985 PP

>> Mis14  Kinetochore protein Mis14 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05     0.072       3      84 ..      46     120 ..      44     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                                    HHCTEECTTBXSTT.SHHHHHHHHHHTT.XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH CS
                          Mis14   3 asesvvinGldsssksikdllsesqkeevEpfdlelnekvrslyqelEdltvevAqlRreaPrkiaeayakelkaeleel 82 
                                    a  s+vi++      ++ d+      e  E+  +el+ kv++l++e+E+l   v+ l r++  ++++ y ++l + +  l
  gi|118430996|ref|NP_147146.2|  46 AGGSIVIDAVS--LGDVEDIF-----EDYEDSVEELRNKVEELLDEVESLGDLVSGLARKFGFNVEARYRRSLLDFRDAL 118
                                    67799999965..35677777.....77899999****************999999999999999999988887777777 PP

                                    HC CS
                          Mis14  83 de 84 
                                    + 
  gi|118430996|ref|NP_147146.2| 119 ED 120
                                    76 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 ?   11.7   0.1   7.7e-05      0.23      15      30 ..      57      72 ..      56      73 .. 0.87
   2 ?   -1.1   0.0      0.78   2.3e+03       1      10 [.      78      87 ..      78      88 .. 0.80
   3 ?    0.2   0.0      0.33   9.8e+02      17      25 ..     113     121 ..     106     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                      Halo_GVPC 15 fdatqdaFeaYadeFa 30
                                    ++++d Fe+Y+d+++
  gi|118430996|ref|NP_147146.2| 57 LGDVEDIFEDYEDSVE 72
                                   579**********976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.78
                      Halo_GVPC  1 VsaLlaaIaa 10
                                   V  Ll++++ 
  gi|118430996|ref|NP_147146.2| 78 VEELLDEVES 87
                                   7789999985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.33
                      Halo_GVPC  17 atqdaFeaY 25 
                                    +++da e+Y
  gi|118430996|ref|NP_147146.2| 113 DFRDALEDY 121
                                    677777777 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00038       1.1      36      63 ..      60      87 ..      60      89 .. 0.88
   2 ?    6.5   0.0    0.0034        10      24      62 ..      80     119 ..      80     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                                   HHHHHHHCT--HHHHHHHHHHHHHHHHC CS
                           PqqD 36 vaalaeeydvdeeeaeadvlafldqLre 63
                                   v++++e y+++ ee+++ v+++ld+ ++
  gi|118430996|ref|NP_147146.2| 60 VEDIFEDYEDSVEELRNKVEELLDEVES 87
                                   68899***9999***********99765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0034
                                    HH-SSSS-HHHHHHHHHHHC..T--HHHHHHHHHHHHHHHH CS
                           PqqD  24 klldgersveeivaalaeey..dvdeeeaeadvlafldqLr 62 
                                    +lld+  s+ ++v  la+++  +v e++ ++ +l+f d L+
  gi|118430996|ref|NP_147146.2|  80 ELLDEVESLGDLVSGLARKFgfNV-EARYRRSLLDFRDALE 119
                                    68999999************5444.4789999999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1274  (0.0710581); expected 358.6 (0.02)
Passed bias filter:                     1162  (0.0648112); expected 358.6 (0.02)
Passed Vit filter:                       151  (0.00842211); 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: 927.02
//
Query:       gi|118430997|ref|NP_147147.2|  [L=621]
Description: DNA repair helicase Rad3 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-22   80.2   0.0    3.6e-22   79.3   0.0    1.3  1  Helicase_C_2  Helicase C-terminal domain
    7.9e-13   48.4   0.0    1.2e-12   47.9   0.0    1.3  1  DEAD_2        DEAD_2
      1e-05   25.3   0.0    2.4e-05   24.1   0.0    1.5  1  HBB           Helical and beta-bridge domain
     0.0017   18.1   0.0       0.02   14.6   0.0    2.3  2  DEAD          DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.036   14.0   0.0       0.58   10.1   0.0    2.4  3  ResIII        Type III restriction enzyme, res subunit
       0.15   12.0   0.1         16    5.4   0.0    3.0  3  Cas_APE2256   CRISPR-associated protein (Cas_APE2256)


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   0.0   1.2e-25   3.6e-22       9     162 ..     438     591 ..     432     596 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.2e-25
                   Helicase_C_2   9 pggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykek.kkkgaillavcrGklsEGidfsd....d 83 
                                    pg  l++ pSy+++ +vverl +       e +ve+   s ++v +++ ++  +++ i+ av++Gkl EG++f d    +
  gi|118430997|ref|NP_147147.2| 438 PGLKLAVYPSYEVMYRVVERLPADV-----ETIVETRGISLDEVEAKILARdPGEKIIINAVAGGKLVEGVEFVDyegrN 512
                                    56668999*************9976.....567775555777777777764489999*****************833334 PP

                   Helicase_C_2  84 llraviivglPfpnpkdpeveakreyldekgk.knsgkewylpealravnQaiGRliRhkdDygaivllDeRfakeeire 162
                                    ll+ vi+vg+Pfp+p+d + +   e+++++ + +n+ k +yl + + +v+Qa+GR iR  +D++  +l+D R+ +++++e
  gi|118430997|ref|NP_147147.2| 513 LLSTVIVVGVPFPQPDDYT-RKHLEVMASRIGvSNARKLVYLVNPMIKVRQALGRGIRGPEDRALYILMDYRYLRRDLKE 591
                                    56689**********8887.5556666666555888999***********************************998876 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.9e-16   1.2e-12       1     175 [.      62     227 ..      62     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.9e-16
                                    EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHC.CCCHHHHHHHHHCCHHCCHTTTTTT-SC CS
                         DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekk.ekavneaCkelkkkkaeekeekCsffen 79 
                                    y +RT+++++ vv+elk+           + + L S +++C    ++ +   +++    C+  ++k        Cs++e+
  gi|118430997|ref|NP_147147.2|  62 YLVRTVNEIDPVVRELKRFG--------ARFTFLFSARRMCPLMTAEGSLPsVEDFWGNCRIARAKG------VCSYYEE 127
                                    899***************94........57899********77555543322555556677666666......6****** PP

                                    CCCHHHH...HHHHHHC---CHHHHH.HHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH.T..GCGCEEEEC CS
                         DEAD_2  80 leelkkl...kkllleevvdiedlve.lgeklklCPYylsrelledadiiilpYqyLldekireslk.gislknsivilD 154
                                    l++l++    +    + v++   l   + + +++CP+++ + l+ed + i++ Y yL++e i +s+    +  + + ++D
  gi|118430997|ref|NP_147147.2| 128 LSRLDEAevaQYVRSRPVISAYRLAWdIAKFKGACPFFALKGLVEDSQFIVATYPYLFKEDIFRSFLePYDYGDFVAVVD 207
                                    *8887765545555667788888875599999****************************99666654889********* PP

                                    TCCCHHHHHHHCC-EEEECHH CS
                         DEAD_2 155 EAhNiedvceeaasveisees 175
                                    EAh + ++ ++++ +++s+++
  gi|118430997|ref|NP_147147.2| 208 EAHSLLNI-HSLHEYRVSQRD 227
                                    ****9985.678888887776 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   8.1e-09   2.4e-05      64     165 ..     280     387 ..     277     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.1e-09
                                    HHHHHHHHHHHHCCHHCCCTCC-SHHH...HHHHHHHHHHHHT..S.TTTEEEEEE.STT..EECCCCS-TCCHH.HHHH CS
                            HBB  64 sllkrlveygkarreekieksesPrsf...lsrlaefllawls..sdeedYvrlvskeeg.esLeavcldPskal.rflk 136
                                    s+++++ve ++ar + +++ s s  s    ++++a++++ wls    +++Y++  + e g + L a+ ldPs+++ ++l+
  gi|118430997|ref|NP_147147.2| 280 SVVEDVVETIRAR-KAEEALSLSGPSGigrVKTMASRIYSWLSvlVRDDSYLFAEKDEGGvLWLIATPLDPSRVVkEPLE 358
                                    5677788888888.44555555544540115566789******988999*****999999999*********987469** PP

                                    HCHCCCCCCTS-SSHHHHHHHHT....EE CS
                            HBB 137 erlssllmsgtltpleeysdiiGleaklk 165
                                    ++  ++l sgt+   + y +++G+   +k
  gi|118430997|ref|NP_147147.2| 359 KVKAAVLLSGTMPSTKLYMEVLGVSRSFK 387
                                    ***********************986665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-06      0.02       6      72 ..      23      82 ..      16     101 .. 0.77
   2 ?    0.3   0.0      0.17   5.1e+02     125     136 ..     204     215 ..     176     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-06
                                   HHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  6 eaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72
                                   e+   + +g+ +l++a+TG GKT+a +  +l       +  + ++l+++ t   +  ++++lk+f+ 
  gi|118430997|ref|NP_147147.2| 23 EVRRSVSEGELLLASAPTGFGKTAAVIYGLL-------SAGAERVLYLVRTVNEIDPVVRELKRFGA 82
                                   555667799999*************999888.......45566777777777777777777777765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                    EEEETHHHHHHT CS
                                    xxxxxxxxxxxx RF
                           DEAD 125 lVlDEadrlldq 136
                                     V+DEa+ ll+ 
  gi|118430997|ref|NP_147147.2| 204 AVVDEAHSLLNI 215
                                    59******9975 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00019      0.58       4      66 ..      13      69 ..      11     100 .. 0.82
   2 ?    0.9   0.0      0.14     4e+02     106     145 ..     176     213 ..     148     241 .. 0.71
   3 ?   -3.9   0.0       4.1   1.2e+04      13      46 ..     283     317 ..     280     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHH CS
                         ResIII  4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprksl 66
                                   +r+ Q e  e+++ +++  + + +l  ++TG GKT   a++i+ ll++g  e++l lv + + 
  gi|118430997|ref|NP_147147.2| 13 WRKGQRELAEEVRRSVS--EGELLLASAPTGFGKT---AAVIYGLLSAGA-ERVLYLVRTVNE 69
                                   7999********99995..77888999********...678888888755.699999988765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.14
                                    EEEEEHHHHHHTH........HHHTTT-S.EEEEETGGGTT CS
                         ResIII 106 ilvttiqsldadseeeeeeseellrdrfd.viiiDEaHrlg 145
                                    ++v+t+  l ++    ++  e ++ +  d v ++DEaH l 
  gi|118430997|ref|NP_147147.2| 176 FIVATYPYLFKEDIF-RSFLEPYDYG--DfVAVVDEAHSLL 213
                                    555555555555511.2222222222..148899****875 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 4.1
                                    HHHT......TTSEEE.EEESTTSTHHHHHHHHHH CS
                         ResIII  13 enlleklkskrdkrgl.ikmaTGtGKTlvaaklie 46 
                                    e+++e++ +++ +++l +  + G G   ++a+ i+
  gi|118430997|ref|NP_147147.2| 283 EDVVETIRARKAEEALsLSGPSGIGRVKTMASRIY 317
                                    56666666645554444999999999888888776 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 ?    5.4   0.0    0.0053        16      74     129 ..      18      69 ..      10      71 .. 0.81
   2 ?   -0.6   0.0      0.38   1.1e+03      53      86 ..     259     291 ..     234     302 .. 0.67
   3 ?    2.3   0.0     0.047   1.4e+02      79     107 ..     475     502 ..     464     506 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0053
                    Cas_APE2256  74 rnLveklarevknkkregekvlinaTgGfKpeiavltlvallladevyYihEsfse 129
                                    r+L    a+ev++ + ege +l  a  Gf   +av++ + +++a +v Y+  + +e
  gi|118430997|ref|NP_147147.2|  18 REL----AEEVRRSVSEGELLLASAPTGFGKTAAVIYGLLSAGAERVLYLVRTVNE 69 
                                    555....5555555669********************9999********9888777 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                    Cas_APE2256  53 vevveieklsdlgreeFreglrnL..veklarevkn 86 
                                    ++v    +++ l+++ F egl++L  ve + + +++
  gi|118430997|ref|NP_147147.2| 259 LKV---SRITLLDKQPFLEGLDDLsvVEDVVETIRA 291
                                    444...4588888999*****998545666666663 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.047
                    Cas_APE2256  79 klarevknkkregekvlinaTgGfKpeia 107
                                    +++ ++  +++ gek++ina++G K + +
  gi|118430997|ref|NP_147147.2| 475 EVEAKIL-ARDPGEKIIINAVAGGKLVEG 502
                                    5566666.6899***********997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); 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:                         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 0.25s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4340.83
//
Query:       gi|14600632|ref|NP_147149.1|  [L=111]
Description: hypothetical protein APE_0325 [Aeropyrum pernix K1]
Scores for complete 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-07   30.7  39.3    3.4e-07   30.4  39.3    1.0  1  DUF5518   Family of unknown function (DUF5518)
  ------ inclusion threshold ------
        8.1    6.6  22.2         22    5.2  21.1    1.8  2  EI24      Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4  39.3   3.7e-11   3.4e-07       3     118 .]       4     106 ..       2     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.7e-11
                       DUF5518   3 aaliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlllglvaaiggla 83 
                                   a+++Ga++ ++l ++l         ++g +++G+vaG +agg  ++ga+aG+ +G+i+++ + +l+++++l       +++
  gi|14600632|ref|NP_147149.1|   4 AVVVGAILHLILLFILP--------VIGNILAGAVAGVIAGG-LSRGAIAGLASGAIASLAASALFFLGAL--ALSWIPPL 73 
                                   78888888888888888........************99977.89*****************888888884..44456667 PP

                       DUF5518  84 gfvallvalllvvllllvvllvilgaiGGaiGgll 118
                                    f+a+l+++l++  ++l++ll++ g+iGG iGg+l
  gi|14600632|ref|NP_147149.1|  74 AFIAGLAGVLVM--IVLLILLGLTGLIGGLIGGAL 106
                                   777777777777..8889999999********986 PP

>> EI24  Etoposide-induced protein 2.4 (EI24)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  21.1    0.0025        22      41     120 ..       2      80 ..       1      94 [. 0.78
   2 ?    2.9  11.3     0.013   1.2e+02      20      68 ..      51     101 ..      38     110 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0025
                                   THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHCCTTSHH.HHHHHHHHHHHHHHHHHHH.HHTTHHH.... CS
                          EI24  41 llasllvllllllplwlfplvalllaapfygllaekvekrhlglvksla.eslkslllllllllvllpl.liPvvglilsp 119
                                   lla++++ +l l++l+++p++ ++la+ + g++a  + +   g +++la  ++ sl++  l++l +l+l  iP++ +i+ +
  gi|14600632|ref|NP_147149.1|   2 LLAVVVGAILHLILLFILPVIGNILAGAVAGVIAGGLSR---GAIAGLAsGAIASLAASALFFLGALALsWIPPLAFIAGL 79 
                                   678889999999999**********************98...778888887888888888888888888855666544433 PP

                                   H CS
                          EI24 120 l 120
                                   +
  gi|14600632|ref|NP_147149.1|  80 A 80 
                                   3 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHH-....TTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EI24  20 llplllnlllfllllvlllw....vllasllvllllllplwlfplvalllaap 68 
                                   + +l+ ++l+fl ++++l+w    +++a l+++l+++++l+l+ +++ l++++
  gi|14600632|ref|NP_147149.1|  51 IASLAASALFFL-GALALSWipplAFIAGLAGVLVMIVLLILL-GLTGLIGGL 101
                                   445555555555.777777777766555555555555554444.444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); 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:                        23  (0.00128284); expected 0.2 (1e-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: 808.53
//
Query:       gi|118430998|ref|NP_147150.2|  [L=449]
Description: TATA box-binding protein-interacting protein TIP49 [Aeropyrum pernix K1]
Scores for complete 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-141  471.4   0.1   2.6e-141  470.9   0.1    1.2  1  TIP49            TIP49 P-loop domain
    4.2e-27   94.1   1.7    9.9e-27   92.9   1.2    1.9  2  TIP49_C          TIP49 AAA-lid domain
    1.4e-10   41.7   0.7    4.1e-08   33.7   0.0    2.7  2  AAA              ATPase family associated with various cellul
    3.6e-09   37.2   3.1    1.3e-06   28.9   0.1    3.0  3  AAA_16           AAA ATPase domain
    3.2e-08   34.0   0.2      0.014   15.7   0.0    3.0  2  AAA_22           AAA domain
    2.9e-07   30.3   2.9    9.8e-06   25.4   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00024   21.5   0.1      0.001   19.5   0.0    2.2  1  AAA_17           AAA domain
    0.00087   19.1   0.1     0.0019   17.9   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0016   19.0   0.1     0.0088   16.6   0.0    2.4  2  AAA_18           AAA domain
     0.0021   17.8   0.1     0.0075   16.0   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
     0.0023   17.9   0.1      0.011   15.8   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0049   17.0   0.1       0.02   15.1   0.0    2.0  2  AAA_33           AAA domain
     0.0051   16.4   0.2      0.017   14.7   0.0    1.9  1  AAA_25           AAA domain
     0.0059   16.0   0.6      0.013   14.9   0.2    1.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0083   16.1   0.0      0.029   14.3   0.0    1.9  2  NACHT            NACHT domain
     0.0087   16.3   1.5      0.016   15.4   0.0    2.1  2  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.022   13.5   0.2          4    6.1   0.0    2.2  2  AAA_32           AAA domain
      0.025   13.9   0.0      0.055   12.7   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.027   13.8   0.1      0.065   12.6   0.1    1.6  1  ATPase           KaiC
      0.028   13.7   0.1      0.093   12.0   0.0    1.8  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.034   13.5   0.0      0.086   12.2   0.0    1.6  1  IPT              Isopentenyl transferase
      0.036   13.5   0.0      0.073   12.5   0.0    1.4  1  PhoH             PhoH-like protein
      0.055   13.5   0.0        0.6   10.1   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
       0.06   13.7   0.4       0.26   11.6   0.4    2.0  1  AAA_19           AAA domain
      0.064   12.8   0.1       0.21   11.1   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
      0.075   12.8   0.0       0.16   11.7   0.0    1.5  1  AAA_11           AAA domain
      0.092   12.5   0.1       0.42   10.3   0.0    2.1  3  AAA_24           AAA domain
       0.12   12.5   0.1       0.25   11.4   0.1    1.5  1  SUKH-4           SUKH-4 immunity protein
       0.12   11.9   0.0       0.27   10.9   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
       0.15   12.5   0.0       0.28   11.6   0.0    1.4  1  RNA_helicase     RNA helicase
       0.16   12.5   0.0       0.36   11.4   0.0    1.6  1  ABC_tran         ABC transporter
        0.3   10.8   2.4       0.42   10.3   0.4    2.3  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.9   0.1  4.6e-144  2.6e-141       3     350 ..      16     362 ..      14     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 470.9 bits;  conditional E-value: 4.6e-144
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49   3 slhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfva 82 
                                    s hshi+gLGld+dg+a+k  +glvGq++areaagvive+++e++l+Gr++L++Gp+gtGktalaiai++elged+pfva
  gi|118430998|ref|NP_147150.2|  16 SRHSHITGLGLDADGRARKIGGGLVGQEEAREAAGVIVEMVREGRLGGRGILIVGPPGTGKTALAIAIARELGEDTPFVA 95 
                                    78****************************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHH CS
                          TIP49  83 lsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenplskekkikevkitlktakeekklklgski 162
                                    l+++e+++ +  k e+l+qa+rk+igvr++e++ev+eG v++++v+++++p+s    i+ ++itl+t++e++++++g+++
  gi|118430998|ref|NP_147150.2|  96 LNAGELFRGDSGKLEMLLQAFRKAIGVRVRERREVVEGVVTSISVSKRRTPFSPYPVIAGARITLETKDESRTFTVGPEV 175
                                    ******************************************************************************** PP

                                    HHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXXXXX.XXXXX...XX CS
                          TIP49 163 aeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhdlDv.anarp...qd 238
                                    ae+l    v++gDvivi+ e+G v+ +Gr++ r ++fDi+  + velP+G v+k ke+v+++tLhd+D+ ++a++   ++
  gi|118430998|ref|NP_147150.2| 176 AEQLVALGVRRGDVIVIDLETGVVRVVGRGKGRGQSFDIDVVREVELPEGPVRKVKEFVRTLTLHDIDAsIAAQRvafTG 255
                                    ********************************************************************944555555556 PP

                                    XXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 239 llslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnraleselaPivilatnrgi 318
                                    lls++    +++++ +t++ r+++++ v+k+v egkaeiv+Gv+fiD++h+lD+e+fs+l++a+es+laPi++latnrg+
  gi|118430998|ref|NP_147150.2| 256 LLSMF----EAERG-VTSEDRKKTDELVKKWVGEGKAEIVAGVIFIDDAHLLDMESFSFLSKAMESDLAPIIVLATNRGV 330
                                    66666....88887.***************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 319 akirGtdiisphGipvDlldrlliiktekytk 350
                                    akirGtdi+sphGip+Dlldrllii+t++yt+
  gi|118430998|ref|NP_147150.2| 331 AKIRGTDIESPHGIPRDLLDRLLIITTRPYTR 362
                                    ******************************97 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       7.9   4.4e+03      37      59 ..     318     340 ..     318     342 .. 0.84
   2 !   92.9   1.2   1.8e-29   9.9e-27       1      66 []     368     433 ..     368     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.9
                        TIP49_C  37 ltpasilakkrkkkevevedvee 59 
                                    l+p  +la+ r+  ++   d+e+
  gi|118430998|ref|NP_147150.2| 318 LAPIIVLATNRGVAKIRGTDIES 340
                                    57778899999999999999985 PP

  == domain 2  score: 92.9 bits;  conditional E-value: 1.8e-29
                        TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                    I++iRa+eE+v l+e+Al++La+ig+e+SLRYaiqLl+pa+i+ak+r++++ve e+vee+e+LF+D
  gi|118430998|ref|NP_147150.2| 368 IIRIRADEEEVLLSENALERLADIGSEKSLRYAIQLLEPAMIVAKRRGSRRVEAEHVEEAERLFAD 433
                                    9***************************************************************99 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   7.3e-11   4.1e-08       1      53 [.      66     116 ..      66     137 .. 0.80
   2 ?    5.7   0.2     0.033        19      41     111 ..     269     328 ..     244     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 7.3e-11
                                    EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfkea 53 
                                    +l++GppGtGKT+la a+a+elg  ++f+ +++ el+       + k+++l+++ 
  gi|118430998|ref|NP_147150.2|  66 ILIVGPPGTGKTALAIAIARELGedTPFVALNAGELF----RGDSGKLEMLLQAF 116
                                    699*******************77799**********....33444555555443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.033
                                    HHHHHHHHHHHH.HHHTS...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                            AAA  41 esekkirelfke.akeka...kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                    e  kk+ el+k+ + e +      ++fiD+++ l  ++            + L ++++         i+++atnr
  gi|118430998|ref|NP_147150.2| 269 EDRKKTDELVKKwVGEGKaeiVAGVIFIDDAHLLDMES-----------FSFLSKAMESDLA----PIIVLATNR 328
                                    455555555555222222344459********998877...........7777777776666....266666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   2.3e-09   1.3e-06       2      76 ..      39     116 ..      38     181 .. 0.82
   2 ?    7.2   0.0     0.011       6.2      88     161 ..     240     316 ..     217     324 .. 0.68
   3 ?    0.3   0.1       1.4     8e+02     106     131 ..     389     442 ..     326     447 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.3e-09
                         AAA_16   2 lvGReeeleqLlsalervrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdql.esaipysalaqal 76 
                                    lvG ee +e+   ++e+vr+gr   + +l++G++G+GK++l+ +++r+l +d  +++    + + + +  + +l+qa+
  gi|118430998|ref|NP_147150.2|  39 LVGQEEAREAAGVIVEMVREGRLggRGILIVGPPGTGKTALAIAIARELGEDTPFVALNAGELFrGDSGKLEMLLQAF 116
                                    78999999999999**************************************65553333333322222334455555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                         AAA_16  88 eaesaeleawrekleeala...avpelagaeasrllellkrll..allsrderplvlvlDdlqwadeaslqllaaLlrl 161
                                    ++ +a+ +a r ++++ l+   a + +++++++   el+k+ +   +++      v+++Dd++ +d +s ++l+  +++
  gi|118430998|ref|NP_147150.2| 240 HDIDASIAAQRVAFTGLLSmfeAERGVTSEDRKKTDELVKKWVgeGKAEI--VAGVIFIDDAHLLDMESFSFLSKAMES 316
                                    54555555555555555555556666777777777777777774333333..345**************9999988776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.4
                         AAA_16 106 a............................avpelagaeasrllellkrllalls 131
                                    a                             v + + +ea+rl++ +kr ++l +
  gi|118430998|ref|NP_147150.2| 389 AdigsekslryaiqllepamivakrrgsrRVEAEHVEEAERLFADIKRSIQLVE 442
                                    012234444444444444555555555554445555555999998888887665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.4e-05     0.014       7      48 ..      65      99 ..      60     193 .. 0.74
   2 !   15.3   0.0   3.2e-05     0.018      70     134 ..     259     331 ..     194     333 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48
                                    ++++G++GtGKT l+  ++++l e       + ++v  ++ 
  gi|118430998|ref|NP_147150.2| 65 GILIVGPPGTGKTALAIAIARELGE-------DTPFVALNAG 99
                                   589****************999954.......4444443333 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.2e-05
                         AAA_22  70 a..........erlsseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp.elr 134
                                                r++++el+++     +a  v +++ iD+a+ l  +e +++L++ ++  +++ ++i+  t+ +++
  gi|118430998|ref|NP_147150.2| 259 MfeaergvtseDRKKTDELVKKWVGEGKAEIVAGVIFIDDAHLL-DMESFSFLSKAME--SDLAPIIVLATNrGVA 331
                                    033333344445778888886666666666667***********.9********9999..*******999986665 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 !   25.4   0.0   1.7e-08   9.8e-06       9      60 ..      39      90 ..      33     113 .. 0.93
   2 ?    4.7   0.0     0.041        23      86     117 ..     292     323 ..     287     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-08
                         RuvB_N  9 yigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                    +gqe+ +e   +++e  ++ +     +l++GpPG Gkt+la  ia+elg +
  gi|118430998|ref|NP_147150.2| 39 LVGQEEAREAAGVIVEMVREGRLGGRGILIVGPPGTGKTALAIAIARELGED 90
                                   58******************99999************************976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.041
                         RuvB_N  86 dvlfideihrlsraveevlysamedfrldivi 117
                                     v+fid+ h l+ +   +l +ame     i++
  gi|118430998|ref|NP_147150.2| 292 GVIFIDDAHLLDMESFSFLSKAMESDLAPIIV 323
                                    59**********************76666655 PP

>> AAA_17  AAA 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     0.001       1      67 [.      69     140 ..      69     181 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-06
                                    EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTSHSSHHHHCT...SHHHHHHHHHHHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrgglakardemrk...lpleekkelqkeaaekiae 67 
                                    +G+PG GK+ ++  +++++     f  l+aG+l+r    +g+l++  +++rk   +  +e++e+ + +  +i  
  gi|118430998|ref|NP_147150.2|  69 VGPPGTGKTALAIAIARELgedtPFVALNAGELFRGD--SGKLEMLLQAFRKaigVRVRERREVVEGVVTSISV 140
                                    7***************98855557***********76..45555555666652116777777777766666655 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 !   17.9   0.1   3.4e-06    0.0019      49      71 ..      65      87 ..      61      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-06
                      IstB_IS21 49 nivllGpsGvGKshlaialgvea 71
                                   +i+++Gp+G+GK+ laia+++e 
  gi|118430998|ref|NP_147150.2| 65 GILIVGPPGTGKTALAIAIAREL 87
                                   699****************9986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-05    0.0088       1      36 [.      66      99 ..      66     165 .. 0.82
   2 ?   -1.5   0.0       6.2   3.5e+03      41      97 ..     260     322 ..     240     334 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakeng 36
                                   Il+ G+pG+GKt la +++++l  g+   +va + g
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIAREL--GEDTPFVALNAG 99
                                   99******************99..766666666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.2
                         AAA_18  41 vdpealdeskrldedkldklldaleenssaleegknlvi.dghlaeleseaakdikk.......v 97 
                                    +++e  +    +d++k+d+l++++ +  +a+  ++++ i d hl ++es ++  + +       +
  gi|118430998|ref|NP_147150.2| 260 FEAE--RGVTSEDRKKTDELVKKWVGEGKAEIVAGVIFIdDAHLLDMESFSFLSKAMesdlapiI 322
                                    4444..44444555555555555555444344444444414566666666555555455555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05    0.0075      21      61 ..      62     101 ..      39     109 .. 0.79
   2 ?   -2.0   0.0       4.4   2.5e+03      94     117 ..     291     314 ..     284     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                    SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                        +li+G  GtGK+ la ai ++   +++pfva+n +++
  gi|118430998|ref|NP_147150.2|  62 GGRGILIVGPPGTGKTALAIAIARELG-EDTPFVALNAGEL 101
                                    44679*****************98776.799******9875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.4
                                    TSEEEEETGGGS-HHHHHHHHHHH CS
                Sigma54_activat  94 gGtlfLDeigelplelQekLlrvl 117
                                     G++f+D+ + l++e  + L +++
  gi|118430998|ref|NP_147150.2| 291 AGVIFIDDAHLLDMESFSFLSKAM 314
                                    699******999998776666655 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 !   15.8   0.0   1.9e-05     0.011       2      33 ..      66      97 ..      65     100 .. 0.84
   2 ?   -2.7   0.0       9.5   5.3e+03      31      53 ..     355     377 ..     351     385 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE-- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqlt 33
                                   +l+vGppGtgK+ la  +a+ l+  +  v+l+
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIARELGEDTPFVALN 97
                                   79******************997766666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.5
                                    E--TT--HHHHH--B--...... CS
                          AAA_5  31 qltrdtteedlkgrreikngtts 53 
                                      tr +t++++k  ++i+ ++++
  gi|118430998|ref|NP_147150.2| 355 ITTRPYTRDEIKEIIRIRADEEE 377
                                    56788999999999999855544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.5e-05      0.02       2      30 ..      66      98 ..      66     144 .. 0.85
   2 ?   -1.0   0.0       3.1   1.7e+03      79     121 ..     379     421 ..     308     439 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg....avllss 30
                                   +l+vG+pG+GK+ la  ++++lg    +v l+ 
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIARELGedtpFVALNA 98
                                   689*******************98877666665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                         AAA_33  79 nlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                    +ls+++ +r+  + ++ + + +i  +e+   ++k+R  +R ++
  gi|118430998|ref|NP_147150.2| 379 LLSENALERLADIGSEKSLRYAIQLLEPAMIVAKRRGSRRVEA 421
                                    4455555566666666666666666666666666665555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     3e-05     0.017      33      63 ..      63      93 ..      52     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                         AAA_25 33 gelallaGapgtGKttlaldlalavatGkpw 63
                                   g  +l++G+pgtGKt+la+ +a ++ ++ p+
  gi|118430998|ref|NP_147150.2| 63 GRGILIVGPPGTGKTALAIAIARELGEDTPF 93
                                   666899****************998887777 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   2.3e-05     0.013       6      44 ..      40      85 ..      38     100 .. 0.73
   2 ?   -2.3   0.0       4.3   2.4e+03     107     133 ..     291     317 ..     287     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                   Mg_chelatase  6 kGqeeakraleiaa.......aGgHnlllvGppGsGKtmlakrlps 44
                                   +Gqeea++a  + +        Gg  +l+vGppG+GKt la +++ 
  gi|118430998|ref|NP_147150.2| 40 VGQEEAREAAGVIVemvregrLGGRGILIVGPPGTGKTALAIAIAR 85
                                   57777777765543222222259999***************88865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                   Mg_chelatase 107 nGvLfLDElpefkrkvlevLRePledg 133
                                     Gv+f+D++  ++ + +  L + +e+ 
  gi|118430998|ref|NP_147150.2| 291 AGVIFIDDAHLLDMESFSFLSKAMESD 317
                                    69******9999999999998888875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.2e-05     0.029       3      29 ..      66      92 ..      64      97 .. 0.90
   2 ?   -2.2   0.0       6.1   3.4e+03     122     139 ..     352     369 ..     345     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                   +++ G++G GKT+L+  +a+++ e+++
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIARELGEDTP 92
                                   89********************99886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.1
                                    EEEEEEECCCHHHHCTTS CS
                          NACHT 122 sllltvrpralrdleeql 139
                                     l++t+rp ++ +++e +
  gi|118430998|ref|NP_147150.2| 352 LLIITTRPYTRDEIKEII 369
                                    589999999999988765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.9e-05     0.016       2      48 ..      66     115 ..      65     133 .. 0.77
   2 ?   -1.6   0.1       5.2   2.9e+03     105     144 ..     395     434 ..     372     440 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpw 48 
                                    i i+G+++tGKT l+ a+a++   ++p v+  a e+++  + k e  l++
  gi|118430998|ref|NP_147150.2|  66 ILIVGPPGTGKTALAIAIARElgeDTPFVALNAGELFRGDSGKLEMLLQA 115
                                    78*****************8887789999888888887777666655554 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.2
                         AAA_28 105 rekrydlvfllppapeidddgeRredleereaiderlrea 144
                                    ++ ry+  +l p +  +++ g Rr + e  e+ ++++ ++
  gi|118430998|ref|NP_147150.2| 395 KSLRYAIQLLEPAMIVAKRRGSRRVEAEHVEEAERLFADI 434
                                    4555666665556666678888877777777777766655 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    0.0072         4       9      56 ..      38      89 ..      33      94 .. 0.82
   2 ?    5.3   0.0     0.013         7     480     507 ..     400     427 ..     387     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0072
                         AAA_32  9 eiigqeRAvealefglkikkkg....YNifvlGesgtGrttlvkrlleeiak 56
                                   +++gqe A ea  + +++ ++g      i ++G++gtG+t l+  + +e  +
  gi|118430998|ref|NP_147150.2| 38 GLVGQEEAREAAGVIVEMVREGrlggRGILIVGPPGTGKTALAIAIARELGE 89
                                   6799********9999999886222268**************9998887655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.013
                         AAA_32 480 iadllrEAdywakkegaevveaehVekA 507
                                     ++ll+ A ++ak++g++ veaehVe+A
  gi|118430998|ref|NP_147150.2| 400 AIQLLEPAMIVAKRRGSRRVEAEHVEEA 427
                                    67999*********************99 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.8e-05     0.055      19      52 ..      66      99 ..      64     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                     Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpD 52
                                   il++G pG GK++la ++++el+++  +v l++ 
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIARELGEDTPFVALNAG 99
                                   899**********************999999875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00012     0.065      13      57 ..      57      97 ..      51     142 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                         ATPase 13 kgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtve 57
                                    +G   gr +li+G pGtGKt +a       a++ ge + fv+++
  gi|118430998|ref|NP_147150.2| 57 REGRLGGRGILIVGPPGTGKTALAIA----IARELGEDTPFVALN 97
                                   567778999************99854....455667777777775 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017     0.093       4      25 ..      66      87 ..      64     136 .. 0.86
   2 ?   -1.5   0.0         2   1.1e+03      82     104 ..     284     306 ..     261     324 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                        DUF2075  4 vlVtGvaGtGKtvvllnllael 25
                                   +l+ G +GtGKt ++++++ el
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIAREL 87
                                   7899***************999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                        DUF2075  82 ekkeepkedvvivDEAhrlltks 104
                                    e k+e  + v+ +D Ah+l  +s
  gi|118430998|ref|NP_147150.2| 284 EGKAEIVAGVIFIDDAHLLDMES 306
                                    45566667899999999997644 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015     0.086       5      26 ..      67      88 ..      64      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            IPT  5 lifGatttGKtaeaiklaketg 26
                                   li+G+ +tGKta ai++a+e g
  gi|118430998|ref|NP_147150.2| 67 LIVGPPGTGKTALAIAIARELG 88
                                   8******************987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013     0.073      23      43 ..      67      87 ..      53      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                   EEE--TTSSTTHHHHHHHHHH CS
                           PhoH 23 faiGpaGtGKtylavalavea 43
                                    ++Gp GtGKt la+a+a e+
  gi|118430998|ref|NP_147150.2| 67 LIVGPPGTGKTALAIAIAREL 87
                                   689*************99765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011       0.6      25      50 ..      64      89 ..      41      99 .. 0.82
   2 ?    0.8   0.0      0.78   4.4e+02     134     145 ..     279     303 ..     229     323 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                   SEEEEEESTTSTHHHHHHHHHHHH-S CS
                         ResIII 25 krglikmaTGtGKTlvaaklierllk 50
                                   + +li+ + GtGKT +a++++++l +
  gi|118430998|ref|NP_147150.2| 64 RGILIVGPPGTGKTALAIAIARELGE 89
                                   5688****************999865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.78
                                    S.............EEEEETGGGTT CS
                         ResIII 134 d.............viiiDEaHrlg 145
                                    +             vi+iD aH l 
  gi|118430998|ref|NP_147150.2| 279 KkwvgegkaeivagVIFIDDAHLLD 303
                                    1333455556777799999999765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00046      0.26      10      38 ..      63      91 ..      54     324 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                    + +l++++pGtGKT +  +i ++l e +
  gi|118430998|ref|NP_147150.2| 63 GRGILIVGPPGTGKTALAIAIARELGEDT 91
                                   56789**********99888877776654 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   0.00038      0.21      34      60 ..      64      90 ..      56      99 .. 0.85
   2 ?   -1.8   0.1       3.4   1.9e+03     103     117 ..     293     307 ..     290     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldke 60
                                   + +l+vGp GtGKt+++  + ++l ++
  gi|118430998|ref|NP_147150.2| 64 RGILIVGPPGTGKTALAIAIARELGED 90
                                   679*************99999988744 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.4
                          AAA_7 103 vvFvDDlnmpakeky 117
                                    v+F+DD ++  +e +
  gi|118430998|ref|NP_147150.2| 293 VIFIDDAHLLDMESF 307
                                    89****998877765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00028      0.16      20      41 ..      66      87 ..      52     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                         AAA_11 20 tliqGPPGtgKTktivellsql 41
                                    li GPPGtgKT   +++ ++l
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIAREL 87
                                   59**********9999998887 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   0.00074      0.42       5      30 ..      66      95 ..      63     121 .. 0.80
   2 ?   -3.1   0.0       9.8   5.5e+03      25      38 ..     188     201 ..     180     208 .. 0.72
   3 ?   -2.6   0.0         7   3.9e+03      26      48 ..     321     343 ..     311     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00074
                         AAA_24  5 iliyGpsgiGKTtlakel....gpkplfid 30
                                   ili+Gp+g+GKT la  +    g+++ f+ 
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIarelGEDTPFVA 95
                                   89***********99777566555555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.8
                         AAA_24  25 kplfidtekGlksl 38 
                                    ++++id+e G+ ++
  gi|118430998|ref|NP_147150.2| 188 DVIVIDLETGVVRV 201
                                    56777777776555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7
                         AAA_24  26 plfidtekGlksldadkfpdies 48 
                                    ++++ t++G++++ +++++++++
  gi|118430998|ref|NP_147150.2| 321 IIVLATNRGVAKIRGTDIESPHG 343
                                    67889999999999999988873 PP

>> SUKH-4  SUKH-4 immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00044      0.25      63     105 ..     166     208 ..     153     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                         SUKH-4  63 aerseelpaeaggllvLGalesaslvldpgtGaVlavdleeee 105
                                    + +++  p+ a++l+ LG   ++++v+d +tG V +v +++++
  gi|118430998|ref|NP_147150.2| 166 SRTFTVGPEVAEQLVALGVRRGDVIVIDLETGVVRVVGRGKGR 208
                                    56778899******************************99885 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00048      0.27       4      42 ..      66     104 ..      64     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                                    EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa 42 
                                    il+vG+ G+GKT  +  +a+ l ++   v+l a   fR 
  gi|118430998|ref|NP_147150.2|  66 ILIVGPPGTGKTALAIAIARELGEDTPFVALNAGELFRG 104
                                    89************************************4 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    0.0005      0.28       1      25 [.      66      90 ..      66     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0005
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                   i+++Gp+g+GK+ la  +a++l ++
  gi|118430998|ref|NP_147150.2| 66 ILIVGPPGTGKTALAIAIARELGED 90
                                   689*****************99865 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   0.00064      0.36      13      45 ..      65      97 ..      62     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00064
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilld 45
                                    + ivG+ G+GK+ L+ ++a++l  +   + l+
  gi|118430998|ref|NP_147150.2| 65 GILIVGPPGTGKTALAIAIARELGEDTPFVALN 97
                                   578*****************9987765555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00076      0.42      20      41 ..      65      87 ..      53     200 .. 0.83
   2 ?   -1.0   0.1       2.1   1.2e+03      75     121 ..     276     323 ..     243     330 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00076
                         AAA_30 20 vavltGpAGtGKttalkal.rea 41
                                     +++Gp+GtGKt +  a+ re+
  gi|118430998|ref|NP_147150.2| 65 GILIVGPPGTGKTALAIAIaREL 87
                                   5689*********9877762444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                         AAA_30  75 kllkrlk..grarlepg.tllivDEagmvdtkqlaallkaaekagakvil 121
                                    +l+k++   g  + e    ++ +D a ++d++++  l ka+e++ a +i+
  gi|118430998|ref|NP_147150.2| 276 ELVKKWVgeG--KAEIVaGVIFIDDAHLLDMESFSFLSKAMESDLAPIIV 323
                                    4444444432..22222268999999999999999999998886666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 3405.88
//
Query:       gi|118430999|ref|NP_147152.2|  [L=165]
Description: hypothetical protein APE_0329.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   13.8   3.2      0.064   12.7   0.3    2.1  2  DUF4349   Domain of unknown function (DUF4349)
       0.12   13.0   0.2       0.38   11.3   0.0    1.8  2  Sec16     Vesicle coat trafficking protein Sec16 mid-region
        2.7    8.1   6.5        7.2    6.8   0.1    3.4  4  DUF1192   Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.1e-05     0.064     122     166 ..       4      48 ..       1      81 [. 0.83
   2 ?    1.8   0.2     0.023   1.4e+02     120     142 ..      85     107 ..      84     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                        DUF4349 122 ereLsevqaeieslegqlryLdnqvaystvtvtlrepeaeteaee 166
                                    er+L ++++ ie +++++r L+++++y +  + + e+ +++++ +
  gi|118430999|ref|NP_147152.2|   4 ERQLMRREEVIEWIKTRIRDLEEEISYYKTILAIVEKGSTASSLP 48 
                                    9**************************999899988887776544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.023
                        DUF4349 120 eiereLsevqaeieslegqlryL 142
                                    eie  L +v++e+ s +++   +
  gi|118430999|ref|NP_147152.2|  85 EIEAYLRSVEEELRSVQARTGDI 107
                                    68889999999999999987655 PP

>> Sec16  Vesicle coat trafficking protein Sec16 mid-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.4e-05      0.38      66      88 ..       9      39 ..       5      63 .. 0.77
   2 ?   -1.2   0.0      0.48   2.9e+03      56      56 ..     130     130 ..      80     163 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.4e-05
                          Sec16 66 kkkevlkwLserieeleaevay........a 88
                                   +++ev++w+++ri +le+e++y        +
  gi|118430999|ref|NP_147152.2|  9 RREEVIEWIKTRIRDLEEEISYyktilaivE 39
                                   5789*****************9655555542 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.48
                          Sec16  56 f 56 
                                    f
  gi|118430999|ref|NP_147152.2| 130 F 130
                                    3 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0012       7.2      25      43 ..      17      35 ..      14      46 .. 0.79
   2 ?   -0.7   0.3      0.25   1.5e+03      23      41 ..      84     102 ..      83     113 .. 0.76
   3 ?    0.3   0.1      0.12   7.3e+02      10      23 ..     105     118 ..      94     122 .. 0.73
   4 ?    2.1   0.1     0.034   2.1e+02      41      56 ..     138     153 ..     136     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                        DUF1192 25 LeerIalLeaEIaRleaai 43
                                   +++rI +Le+EI   ++ +
  gi|118430999|ref|NP_147152.2| 17 IKTRIRDLEEEISYYKTIL 35
                                   789*********8777665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.25
                        DUF1192  23 eELeerIalLeaEIaRlea 41 
                                    eE+e++    e+E   ++a
  gi|118430999|ref|NP_147152.2|  84 EEIEAYLRSVEEELRSVQA 102
                                    6888998888888765554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.12
                        DUF1192  10 theigqDLslLSve 23 
                                    +  +g+DL +L + 
  gi|118430999|ref|NP_147152.2| 105 GDIAGEDLATLDIR 118
                                    55789****99876 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.034
                        DUF1192  41 aaiakkkasraAAeal 56 
                                    +++++k+a + AAe++
  gi|118430999|ref|NP_147152.2| 138 EHLKAKSALKYAAESM 153
                                    5799**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1272.82
//
Query:       gi|118431000|ref|NP_147153.2|  [L=334]
Description: hypothetical protein APE_0330.1 [Aeropyrum pernix K1]
Scores for 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-29  101.5   2.5      9e-29  100.9   2.5    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.3e-06   28.0   0.1    3.4e-06   26.7   0.1    1.8  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   2.5     1e-32     9e-29       4     197 .]      21     239 ..      18     239 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1e-32
                                    CSSEEEEEE.ETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                    Lactamase_B   4 dpvnsylie.gdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                    ++vn+++   + g+v L+D+G+ ++++   l   +  +++ k++dvd +++TH+H+DH++g++ l+e +   v++   e+
  gi|118431000|ref|NP_147153.2|  21 GSVNVTVFKkDAGEVDLVDAGMYSARSVHDLlakIKSRIRGKIRDVDKIVITHFHVDHMSGAAILREVFEPTVFIGIGEL 100
                                    789******5559999*************999*9********************************************** PP

                                    HCCHCHHHHHHHHHCCHH..........................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSC CS
                    Lactamase_B  80 palfmeeaddaasrkgll..........................lagvsadkpdvdeeeldgnaggrralyvtggpghgh 133
                                    + +++ +  d ++   l                           ++++    +  ++ ++d+ ++g  ++ + + pgh++
  gi|118431000|ref|NP_147153.2| 101 ELPLRSGSPDVFVDNILTlyrehgvpepvlesirrshpvfrtvlAYRAFSSLDLKPIYPGDILRLGEASYRALPAPGHTP 180
                                    ********9999998888************************************************************** PP

                                    CEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 134 ghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                    gh+v+e+ +g+ +++GD+ll++ t+++ l     ++  +++ ++yl++l++la+ k+ v +pgH
  gi|118431000|ref|NP_147153.2| 181 GHIVLESLDGTHAIVGDTLLERITPSVIL-----YDEEHDPLGSYLRTLEMLAQKKYLVAYPGH 239
                                    *****************************.....****************************** 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 !   26.7   0.1   3.8e-10   3.4e-06      21      56 ..      56      92 ..      37     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.8e-10
                                   --S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C--E CS
                  Lactamase_B_2 21 Pve.lrdelppidaVllthaHyDHlaglltlre.lrpk 56
                                   + +  r +++++d +++th H+DH+ g+  lre ++p+
  gi|118431000|ref|NP_147153.2| 56 K-SrIRGKIRDVDKIVITHFHVDHMSGAAILREvFEPT 92
                                   2.2368999************************88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2374.34
//
Query:       gi|118431001|ref|NP_147155.2|  [L=178]
Description: deoxycytidine triphosphate deaminase [Aeropyrum pernix K1]
Scores for 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-16   58.1   0.0    9.6e-16   57.6   0.0    1.2  1  dUTPase   dUTPase
    2.9e-06   26.3   0.0    0.00012   21.0   0.0    2.9  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)
  ------ inclusion threshold ------
      0.044   13.4   0.2       0.52    9.9   0.1    2.0  2  AOC_like  Allene oxide cyclase barrel like domain


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 !   57.6   0.0   1.6e-19   9.6e-16      16     121 ..      62     166 ..      47     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.6e-19
                                    EEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-E CS
                        dUTPase  16 yDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdR 95 
                                    y+    ++++v pge+ l+ t+ +i lp  +a+l++ RS  a+ g+ ++ +v+d+ ++G++ + ++ ++  +vk+  gdR
  gi|118431001|ref|NP_147155.2|  62 YECGEGDEIIVGPGEHMLLHTQEYIRLPGYVAGLVNLRSTWARTGIYIPATVVDAGFEGQLTIEVVGSGF-PVKLYPGDR 140
                                    67777899***************************************************77766666666.********* PP

                                    EEEEEEEEBECGEEEEESSTTTESSB CS
                        dUTPase  96 iAqLifariltaeleevetlkaterg 121
                                    +++L++++++ + +++++   + +rg
  gi|118431001|ref|NP_147155.2| 141 FLHLVLVKLQSPAMNPYRGRYQGQRG 166
                                    *******9999999999965444444 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 !   21.0   0.0     2e-08   0.00012       4     162 ..       2     148 ..       1     165 [. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2e-08
                            DCD   4 ilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekl..eelklheldLtegavlekg 81 
                                    il+d++i+al++ g +   epl+ + +  + lDLrLg+   r + s      + ++ +   +  +++e    ++ ++  g
  gi|118431001|ref|NP_147155.2|   2 ILSDRDIRALLAIGDL-VVEPLSGDTVRENGLDLRLGRGFCRFKRSD-----RVLDPRApgSPGEFYECGEGDEIIVGPG 75 
                                    899************9.6789****************9999988763.....333333322445677777788999999* PP

                            DCD  82 cvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLsqirfr 161
                                       +++ +e ++Lp  +++ +n +s+  R  +++            v+ag++G+l +e++   F++++ +G+r   + + 
  gi|118431001|ref|NP_147155.2|  76 EHMLLHTQEYIRLPGYVAGLVNLRSTWARTGIYIPA--------TVVDAGFEGQLTIEVVGSGFPVKLYPGDRFLHLVLV 147
                                    ******************************999753........35899***********************98877765 PP

                            DCD 162 r 162
                                    +
  gi|118431001|ref|NP_147155.2| 148 K 148
                                    5 PP

>> AOC_like  Allene oxide cyclase barrel like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   8.6e-05      0.52      71     102 ..      91     122 ..      64     128 .. 0.78
   2 ?    1.4   0.0     0.037   2.2e+02      95     106 ..     158     169 ..     149     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.6e-05
                                    EEEEEEEHHHHHTT-EEEEEEEE-SGGGTT-E CS
                       AOC_like  71 rvaGlvdltaltagewatlpavGvgGryaGlv 102
                                     vaGlv+l + +a    ++pa++v+  ++G++
  gi|118431001|ref|NP_147155.2|  91 YVAGLVNLRSTWARTGIYIPATVVDAGFEGQL 122
                                    479*************************9986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.037
                                    SGGGTT-EEEEE CS
                       AOC_like  95 gGryaGlvGfrq 106
                                     Gry+G+ G+r 
  gi|118431001|ref|NP_147155.2| 158 RGRYQGQRGVRL 169
                                    59********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       118  (0.00658152); expected 358.6 (0.02)
Passed bias filter:                      115  (0.00641419); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1288.26
//
Query:       gi|14600639|ref|NP_147156.1|  [L=114]
Description: hypothetical protein APE_0334 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.9   1.9      0.042   14.0   1.7    1.6  1  DUF2545   Protein of unknown function (DUF2545)


Domain annotation for each model (and alignments):
>> DUF2545  Protein of unknown function (DUF2545)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.7   2.4e-06     0.042      10      63 ..      35      90 ..      28     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-06
                       DUF2545 10 lailavslyigsvlgavaaissllgmviLaaliy..fftlwltdGnelvsGifllL 63
                                  la   vsl+    +  v+a ssl+g v++aa+    + +++l+ G +  +G++ +L
  gi|14600639|ref|NP_147156.1| 35 LASAIVSLFSTRLRPLVSACSSLIGYVLVAAASAplLDAMRLQVGIAGLAGLLPFL 90
                                  555679*********************999876422669******99999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 897.00
//
Query:       gi|118431002|ref|NP_147157.2|  [L=851]
Description: penicillin acylase II precursor [Aeropyrum pernix K1]
Scores for 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-154  514.6   0.0   7.7e-154  514.2   0.0    1.0  1  Penicil_amidase  Penicillin amidase


Domain annotation for each model (and alignments):
>> Penicil_amidase  Penicillin amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.2   0.0  4.3e-158  7.7e-154       2     664 ..      63     833 ..      62     838 .. 0.87

  Alignments for each domain:
  == domain 1  score: 514.2 bits;  conditional E-value: 4.3e-158
                                    EEEEEEGGGEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-TBHHHHHHHHHHHT-HHHHHHHHHTS. CS
                Penicil_amidase   2 VeirrDewgvphIyAkneedlffaqGyvhAqdrlwqmellrrtarGrlaelfGpealesDrllrtlglrraaeaelaal. 80 
                                    +++++D+ gvp I+A+++e +f+a+G+vhA+ rl+qm+++rr++ G+l+ l+G++ le Dr +  lglr +++ae++   
  gi|118431002|ref|NP_147157.2|  63 AKVYFDDEGVPYIHASSDEAAFYAAGWVHASLRLFQMDVFRRVGLGELSGLVGEAGLEADRRAAILGLRSVVDAEWRHIq 142
                                    79**************************************************************************7776 PP

                                    ........HHHHHHHHHHHHHHHHH-..-S.T-HH.HHHH---....S.........SS-.XXXXXX.....XXX.XXXX CS
                Penicil_amidase  81 ldp...etralleaYaaGvNaylaelkaka.lPlefallgykpepWtpvdslavakvmaldlagnleeelararalaakl 156
                                     +p   e  +++eaY+aGvN y++ + + + lP+e+++lg+kp pW p d+la+akv+al l++  e++l + r l +k 
  gi|118431002|ref|NP_147157.2| 143 NNPefgEIVRIVEAYTAGVNGYISYALKTGrLPVEYRVLGVKPSPWLPQDTLAMAKVLALMLSY-SEDDLILDR-LVRKW 220
                                    44545344***************988855569****************************9965.556777777.88999 PP

                                    XXXX............................................................................ CS
                Penicil_amidase 157 gdekvaelfpp..................................................................... 167
                                    g+e +a++  +                                                                     
  gi|118431002|ref|NP_147157.2| 221 GPEVIADF--Divgrslnmphascdmavdwgdvtglegpynpllsveerreplhesepldlgynpdpeiiaavvdrvlym 298
                                    *****999..2233444455677777788888888888888899999999999999999999999999999999999999 PP

                                    .....X-EEEEE-TTTBTTSS-EEEEE-EEESSGGG--EEEEEEETTEEEEEEE-TT-S.SSEEEESSEEEEEEE-SS-S CS
                Penicil_amidase 168 .....gSNnwvvsgerTasGkpllanDPHlglsapslwyqahlqapgldviGaslpGlPgvliGhnediAWglTnagadv 242
                                         +SNnwvvsg+ T sG+pllanDPHl+l+ap++w  + +++p+++++G+++pG+P v+iG+n ++AWg+Tn+g+d 
  gi|118431002|ref|NP_147157.2| 299 lswnaASNNWVVSGSLTVSGNPLLANDPHLSLTAPGIWLPIVISSPSYSLAGVTIPGVPLVVIGRNSHVAWGFTNVGSDF 378
                                    999999************************************************************************** PP

                                    EEEEEEEEETTEEEEEEETTEEEE-EEEEEEEEEE-TT.......EEEEEEEEETTEEEE-......TB--EEEEG-TTH CS
                Penicil_amidase 243 qdlyaeklnpddptrylydgkwepmetrtetikvkggdd......svtltvreTrhGPvvsd.gkavalrwtalepgdrs 315
                                    +d+y+++  +++  ry+y+g+   +e+ + +  v +  +      ++++ v +T hGPv++  g+++a+++t + p+  +
  gi|118431002|ref|NP_147157.2| 379 TDFYRYQWVDEN--RYFYKGRIFGVEKSSIEAYVWD--PlarsyrVQEISVARTIHGPVIEWqGEKFAVSYTSARPT-FE 453
                                    *******99766..8889*98888888888888844..3447777899************975445*****999987.88 PP

                                    HHHHHHHHT--SHHHHHHHHHHH---SEEEEEEETT--EEEE--S--B---...............TT--EEETT-GGGS CS
                Penicil_amidase 316 ldallalnrarnvaefraalkdlaapaqnvvyADreGnigyqaagrvPvrp............aaddgllpvpGsdsaye 383
                                    +  l+ ln+a +v ++ +a +++ +p+qn+v+AD++Gni+y   g++P r+             + +g lp++Gs ++ e
  gi|118431002|ref|NP_147157.2| 454 MIFLWLLNKASSVRDALSAQRYFYGPPQNMVVADSAGNIAYSPVGAYPERAtlptietgygpiVN-TGFLPFDGSAGEGE 532
                                    889999****************************************************9887633.5************* PP

                                    --TB--GGGS-EEEE..SSEEEESSS----S.........--T-HHHHHHHHHH..SS...-B-HHHHHHHHHT-BBTHH CS
                Penicil_amidase 384 WtgyipfeelPqvvnPargyivtaNnrvlpddypaalgsdwappyRarrirelLeekaagkkvtledmaalqtdtrslla 463
                                    W+g+ p++ lP ++nP++g+++taN ++++d+   +lg+d+a+ +R++ri++lL+e++a++ +++ dm+++q+d+ +l  
  gi|118431002|ref|NP_147157.2| 533 WRGFKPYSSLPVLFNPPQGFVATANSKPFEDGCWDGLGWDYADRFRTERIYTLLQERSAEEPLDAGDMRDIQLDVEDLGL 612
                                    *******************************9777*******************99977778****************** PP

                                    HHHHHHH..........-..GGGHHHHHHHHH-...SB-STT-THHHH..HHHHHHHHTT.................... CS
                Penicil_amidase 464 erllpll.al......eaaeaeaaaaldlLraW..dgrmdadsaaaal..faawlaalvralfedelg...........r 521
                                    ++l+ l+ ++      +     +++ +d+L++W  + +m+ d  +++l   a w+  ++r ++e   g            
  gi|118431002|ref|NP_147157.2| 613 KTLVSLMvRVasgdggH----VLERYMDMLAEWaeNPQMNVDDYKPTLalLASWY--FARDFWESLYGseehwrfikleY 686
                                    *****888334443322....334479******9889999998775551155554..44555545455555588987775 PP

                                    ............---TTSTTT-SESHH.HHHHHHHHHHHHHHHST-T-B.....HHHHEEEE.E...........EE--- CS
                Penicil_amidase 522 laealeklledasfwwddptttpktrdelllaalaealaeleaaglgadpakwrwgklhrlelrhplg..fnrg.lpvgG 598
                                      +al++ l+ ++ w+  +  ++ t + ++++++++a+++ e+ + +++p++w +g++h ++++h l   +  g  p++G
  gi|118431002|ref|NP_147157.2| 687 AEKALKAYLRGED-WVF-NYFPEGTLEGMVNRSVERAVKTSETFFASPNPEAWVYGEMHYYNPEHLLSeaLGFGeCPAPG 764
                                    5677777777532.222.23333488999**********8888766999****************999**88899***** PP

                                    B-GGG.............EEEEEEE-EEEEEE--T.S.EEEEETT-S-S-TTSTTSSHHHHHHHTT--EE CS
                Penicil_amidase 599 geetvnatsysara....frvtrgpsyrmvvdladrdkaravlpgGqsgnpgsphyaDqlelwaegeylp 664
                                    g  tvn++ +s  +      v  gps r ++dl+     ++ lpgG sg p s +y+++   + +gey+ 
  gi|118431002|ref|NP_147157.2| 765 GPFTVNVAPPSSVSetrgAPVEAGPSVRLIADLST-TMLYMSLPGGSSGVPLSSFYDNLYWGYCRGEYHI 833
                                    ******998877669999****************6.459****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 5800.66
//
Query:       gi|118431003|ref|NP_147158.2|  [L=332]
Description: dipeptidase [Aeropyrum pernix K1]
Scores for 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-69  232.6   0.0    6.9e-69  232.4   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
    0.00021   21.2   0.1    0.00031   20.6   0.1    1.3  1  Amidohydro_2   Amidohydrolase
  ------ inclusion threshold ------
       0.15   10.5   0.1       0.21   10.1   0.1    1.1  1  Tic110         Chloroplast envelope transporter


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 !  232.4   0.0   1.2e-72   6.9e-69       7     319 .]       5     327 ..       1     327 [. 0.93

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 1.2e-72
                                    .EEEEEE-HHHHHHHCTTTTT...-TTTHCTSSS-HHHHHHHTEEEEEEEEE--C........CCCCCCHHHHHHHHHHH CS
                  Peptidase_M19   7 iviDghndlplklrqekkesl...llekdselqtdlerlraggvsavlfaifvpe........dasyeeavkatleqidl 75 
                                    +v+D h d++++  + +  +    + e+ +  q dl+++ ++ v +v++a+f+++          + + ++   l+q++ 
  gi|118431003|ref|NP_147158.2|   5 PVVDLHEDISFYYASMGAGQPlggYAEDLEGRQADLPKYSRANVRIVFAAVFPESnvyqggegYPTPSSSRLLLLDQVKT 84 
                                    89**********9999988889*999**************************888*****98866777888889999999 PP

                                    HHHHHHHGTTTEEE-SSHHHHHHHHHTT..-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEEES-SSS-BSSB-BCCGTT CS
                  Peptidase_M19  76 irrlvrknpeqlklvrtaddierakkeg..kiavllgiegaealgddlallrafyalGvrvlgltynrnnkfAdgaleek 153
                                    ++ l + +   ++++++++ +++  ++   ++++ll++ega+al  d+  l+ +++lG r+lglt+n++n +A ++  + 
  gi|118431003|ref|NP_147158.2|  85 YYALSSIHG--VEIIESWRSAQEVLEAPrwRLGLLLHLEGADAL-ADILDLELLHRLGFRSLGLTWNHDNRWAASCKTR- 160
                                    999888666..8999999999999996522799***********.99*******************************9. PP

                                    .SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--TTSB-HHHHHHHHHTT-EEEE- CS
                  Peptidase_M19 154 dedgGLsefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhpRNltDeqlkaiaesgGvvgvt 233
                                     +d GL++ G++lV+++ +lg++iDl+h+s+kt+ d+++ S +Pv++SH+n r  +d+pRN+  e ++a++ +gGv+g  
  gi|118431003|ref|NP_147158.2| 161 -RDYGLTQSGEDLVKKAAELGVIIDLAHASDKTVADAASASPKPVIVSHANFRWKVDSPRNVGEEAVEAVVSKGGVIGYS 239
                                    .******************************************************************************* PP

                                    SSHHHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---T...TTTSS-BBTBSSGGGHHHHHHHHHHTTS-HHHHHHHHT CS
                  Peptidase_M19 234 fvpaflkekaeatledvvdhidyivelaGidhVGlGsDf...dgggelpegledvsklpnltaeLlrrgyseadiekilg 310
                                    ++++ +++ + +tl dv+ ++  +ve++G +h ++G+D+    ++   p gle++++lp+l+++L+++g s+++ie+i++
  gi|118431003|ref|NP_147158.2| 240 LISTLITRGRHPTLHDVASQMAEFVEVYGHRHLAIGTDYhglLDIR-PPTGLESIDRLPRLLEALADAGLSDRQIEAIAY 318
                                    ***************************************5543333.4******************************** PP

                                    HHHHHHHHH CS
                  Peptidase_M19 311 gNflrvlee 319
                                    gN+ rv++e
  gi|118431003|ref|NP_147158.2| 319 GNIARVIRE 327
                                    ******986 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   5.2e-08   0.00031     131     289 ..     163     325 ..     101     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.2e-08
                                    H......HHHHHHHHHHT-EEE.EE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTT..........T CS
                   Amidohydro_2 131 d......rpifealeelglpvd.ihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgp..........s 193
                                    +        ++++++elg+ +d  h                    +  ++++a   P+ +++++H+ +            
  gi|118431003|ref|NP_147158.2| 163 YgltqsgEDLVKKAAELGVIIDlAH------------------ASDKTVADAASASPK-PVIVSHANFRwkvdsprnvgE 223
                                    2466666678999*********555..................679999********9.**********88888877777 PP

                                    TCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.. CS
                   Amidohydro_2 194 erlraalellarrpnvyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval.. 271
                                    e+++a++         y  +s l t+     ++ + +  +a+ +e++g  ++  G+Dy      ++p+ l  +d++ +  
  gi|118431003|ref|NP_147158.2| 224 EAVEAVVSKGGVIG--YSLISTLITR-GRHPTLHDVASQMAEFVEVYGHRHLAIGTDYHGLLDIRPPTGLESIDRLPRll 300
                                    77777777777777..6556666665.777777777788***********************************99999* PP

                                    .......SSHHHHHHHHTHHHHHHC CS
                   Amidohydro_2 272 .......lsdeerekilggNAarly 289
                                           lsd + e+i++gN ar+ 
  gi|118431003|ref|NP_147158.2| 301 ealadagLSDRQIEAIAYGNIARVI 325
                                    **********************986 PP

>> Tic110  Chloroplast envelope transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   3.5e-05      0.21      41     102 ..     174     235 ..     155     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.5e-05
                         Tic110  41 sraaalagavvlgaagaaaayalnsaaPevaavelhnlvvelddptkltkeeveaiaskyGv 102
                                     +aa+l+  + l+ a+  ++   +sa P+ ++v+  n+  ++d p+++ +e vea+ sk Gv
  gi|118431003|ref|NP_147158.2| 174 KKAAELGVIIDLAHASDKTVADAASASPKPVIVSHANFRWKVDSPRNVGEEAVEAVVSKGGV 235
                                    355678888889999999999999***********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2545.47
//
Query:       gi|118431004|ref|NP_147159.2|  [L=456]
Description: hypothetical protein APE_0338.1 [Aeropyrum pernix K1]
Scores for 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-60  203.2   0.7    8.7e-60  202.7   0.7    1.3  1  Beta-lactamase  Beta-lactamase
      1e-05   25.5   0.0    2.4e-05   24.3   0.0    1.6  1  Pab87_oct       Pab87 octamerisation domain


Domain annotation for each model (and alignments):
>> Beta-lactamase  Beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.7   0.7   9.8e-64   8.7e-60       5     314 ..      12     327 ..       8     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 202.7 bits;  conditional E-value: 9.8e-64
                                    HHHHHHHTTESEEEEEEEETTEEEEEEEEEEEETTTTEEESTTSBEEEGGGHHHHHHHHHHHHHHTTSSCTTSBGGGTST CS
                 Beta-lactamase   5 vrelmaqggipGvavavvrdgkvvldkggGvadleggrpvtadtlfriaSvtKtftaaavlqlveeGkldLddpVskylP 84 
                                    + e m ++++p++ +   ++g v   +++G++++e+g p++ dt + i+S+tK+fta+avl+l eeGkl+LddpV  +l 
  gi|118431004|ref|NP_147159.2|  12 ILEKMSRYRMPSLTLSAFKGGDVF-QASYGYSSIEKGSPASVDTAYGIGSITKSFTALAVLALEEEGKLSLDDPVGNHLG 90 
                                    5567888****************6.7777*************************************************** PP

                                    TCTTGGGTTEBHHHHHTTHSSCSSSSTSTTCTSHHHTH..............HHHHHHHHHSBSSSSTTSCEE-SHHHHH CS
                 Beta-lactamase  85 efagpgkgkiTlrdLltHtsGlpdlfasdlleeaaada..............aellralatlppkyapGtkwgYsntgyg 150
                                     +    +++iTl++LltHtsG+p+  + ++l ++                    l ra+ + + +++pG ++ Y n gy 
  gi|118431004|ref|NP_147159.2|  91 IDLEVEGQPITLEHLLTHTSGVPATAYAEALLRGFLGVggywkpysrpwdavLYLKRAIDKGWAVSKPGRRFFYLNEGYV 170
                                    99********************9997666666666666**********9999999999999999999************* PP

                                    HHHHHHHHHHTSHHHHHHHHHTTTTTTSTTEESSTTGGGGGGBEEEEEEETCEEECSCETTHHHHCTTTBEEEEHHHHHH CS
                 Beta-lactamase 151 llgellekvtgrsleqllreeilrpLgmkdtelgppesgdprdaagytgngpearappanlpaeaegagglistardlar 230
                                     lg ++e+ +g s+e+++r+ +++ Lgm++ ++   + +     +++t+ +p+ r++p++lpa+ +++gg++stard++r
  gi|118431004|ref|NP_147159.2| 171 ALGIVVERSSGYSYEEYIRRLVFEKLGMTSSGFIGERLE-----HAATPYKPGDRLEPVPLPAGITADGGIMSTARDMLR 245
                                    *********************************995555.....5555678899************************** PP

                                    HHHHHHHCCSSSSHHHHHHHHHHHTSEEEECTTEEEECECSSEEEEECCHTEEEEEEE..STEEEEEEEECGGTEEEEEE CS
                 Beta-lactamase 231 flglalegglllsaetlaqltaklssgttrpagiraglglGwvladktgapgtfghtG..ggygtyvfvdpeanlvvavl 308
                                    ++   l++g+  + +++++   k + +  ++a++++++g+G+ +++   ++++ +h+G  + y++++++    + +v++l
  gi|118431004|ref|NP_147159.2| 246 YV-ESLARGEFRGYAERME---KPRVRVPWQALGGEAYGYGLIIYPDFMGGRLASHGGslLAYTAWMGYSTRLDSGVVLL 321
                                    **.5566666666666655...589999999999********************************************** PP

                                    ESBCSS CS
                 Beta-lactamase 309 tnrdpp 314
                                    +n+++ 
  gi|118431004|ref|NP_147159.2| 322 SNTTGY 327
                                    **9985 PP

>> Pab87_oct  Pab87 octamerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   2.6e-09   2.4e-05      12      97 .]     356     446 ..     349     446 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.6e-09
                      Pab87_oct  12 kleeLeGeYesYrGiveasverkggtLalkvggkieeeeslpLvPedl......e..gdyaeFytltangerlpvefeik 83 
                                     +e+LeG Ye++  +   +++r g+ L ++  g +  ++ + L P ++      e  ++ + F  +   g  l+vef+ +
  gi|118431004|ref|NP_147159.2| 356 IVERLEGYYEGFDSSIAFNIRRVGTGLLVEPVGGV--GSPMALSPREIpgpgelEagEGSVVFVSPY-MGGVLEVEFNWS 432
                                    579***************************98888..777888877642222224114567888888.5669******** PP

                      Pab87_oct  84 gddvsllleRyrlh 97 
                                    g++v+ lleRyrl+
  gi|118431004|ref|NP_147159.2| 433 GERVEALLERYRLV 446
                                    ************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3307.35
//
Query:       gi|118431005|ref|NP_147160.2|  [L=363]
Description: hypothetical protein APE_0339.1 [Aeropyrum pernix K1]
Scores for 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-119  397.0   0.0   6.1e-119  396.7   0.0    1.0  1  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.7   0.0  3.4e-123  6.1e-119       2     320 ..      24     352 ..      23     356 .. 0.98

  Alignments for each domain:
  == domain 1  score: 396.7 bits;  conditional E-value: 3.4e-123
                                    S---TT-------TT--SSEEE-TTS-STTEEEEEEEEEEEETTE......EEEEEEEEETTS-E.EEEEEEESSS.... CS
                Glyco_hydro_130   2 lrkietidileRvsyitgedvrisnnpvrkpvavFNpavvlvekeLevyaRvvllYrkyvsdiaslrigledlkdG.... 77 
                                    +r+++t+di++R++yi++e+v+++++++r++v++FN++++l++++Levy+Rvv++Y+kyvs +aslrigled+++G    
  gi|118431005|ref|NP_147160.2|  24 YRRRHTVDIARRIGYIRPENVELERGSTRRVVSFFNSTLRLAREGLEVYGRVVVGYYKYVSLVASLRIGLEDISSGrcsr 103
                                    89*********************99******************************************************* PP

                                    ..SS-EE-SS---EE-TTS-B--EEEEEEEEETTEEEEEEE.EESSSEEEEEEEESSSSSEEEE-....-SSSSSE.... CS
                Glyco_hydro_130  78 ..ikktlepeevvlpedkqellgveDPRvvkinskyyltYtgrdlkgvrievattkdlltvkrle....ekialielkkd 151
                                      +k+t++pe  vlp+d+++++g+eDPR++++ns+++ltYtgr+l++++++v++t+++++v+r++    +k+a+i+l++d
  gi|118431005|ref|NP_147160.2| 104 ceEKHTARPE--VLPGDWIDFWGAEDPRYTSVNSHDVLTYTGRTLAYYSSSVGQTFPVVAVRRAPngewVKEAYITLEPD 181
                                    **********..*****************************************************99999********** PP

                                    ......EEEEE-SS-BTTBEEEEEESS-S---EEEEEE.SSSS-BEEEEEEE-..--SS-GGGS...SEEEE-S--EEET CS
                Glyco_hydro_130 152 eislatkdgalfpkkikgkylmfsrvhtvsekifLavs.ddlvlweneleela..ssreimfenpfelkigwgtppvetk 228
                                    e++lat+++++f+ +++g++l+f+rvh+vs++++L+++ +d ++ e+++++la  s+++im+++pfe+kigw+tp++++k
  gi|118431005|ref|NP_147160.2| 182 EAPLATSIKNAFILSHRGILLAFYRVHDVSGRFHLLAGiSDGLP-EGPISPLApkSVWRIMDPAPFEEKIGWATPVNGYK 260
                                    ********************************************.*******999************************* PP

                                    TE.EEEEEEEEETTEEEEEEEEEEE-SS-S...EEEEBSS-SB-S-SHHHHSSSSSSBEEEEEE.EE-TTEEEEEEEETT CS
                Glyco_hydro_130 229 eg.lLvlihgvdteklvYrvgaalldlegk...vlartkeyilePeeeyEeyGdrpnvvFpcga.lveeekvlvyyGaaD 303
                                    +g lLvl+hgvdte++vYrv+aa+ldleg+   ++a+t+eyi+eP++ +E++Gdrp+++Fpcga lv++e ++v+yGaaD
  gi|118431005|ref|NP_147160.2| 261 GGsLLVLLHGVDTEQQVYRVLAAELDLEGRelvLKAVTPEYIMEPSTLEERFGDRPYTIFPCGAwLVDGE-IIVSYGAAD 339
                                    **99*************************667699*****************************999999.********* PP

                                    TEEEEEEEEHHHHHHHH CS
                Glyco_hydro_130 304 taiglaeisveeildll 320
                                    ta+gla+i+    ld+l
  gi|118431005|ref|NP_147160.2| 340 TATGLASIP----LDVL 352
                                    *********....4544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2510.88
//
Query:       gi|118431006|ref|NP_147161.2|  [L=739]
Description: hypothetical protein APE_0340.1 [Aeropyrum pernix K1]
Scores for 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-45  153.3   0.0    1.5e-44  151.5   0.0    2.0  2  GHL6             Hypothetical glycosyl hydrolase 6
     0.0003   20.3   0.1     0.0021   17.6   0.0    2.2  2  Glyco_hydro_42M  Beta-galactosidase trimerisation domain
     0.0017   18.6   0.0     0.0057   16.9   0.0    1.9  1  ThuA             Trehalose utilisation
  ------ inclusion threshold ------
       0.03   13.4   0.0      0.047   12.7   0.0    1.2  1  DUF4015          Putative glycosyl hydrolase domain
      0.078   12.4   0.0       0.14   11.6   0.0    1.3  1  ABC_transp_aux   ABC-type uncharacterized transport system
       0.14   12.5   0.0        1.3    9.3   0.0    2.2  2  PHP              PHP domain


Domain annotation for each model (and alignments):
>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.0   4.9e-48   1.5e-44       1     137 []      30     168 ..      30     168 .. 0.97
   2 ?   -2.8   0.0       2.1   6.4e+03      45      64 ..     527     546 ..     516     548 .. 0.74

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 4.9e-48
                           GHL6   1 daeelveelkeagadtlvifardaggvvyYrtkldfvtehpklkrdllkelvkachregikvvvrvdfskaderiyeqhp 80 
                                    +ae+lv+ +k+a+a+tlv+farda+g+v+Yr+++  +++h++++ d+ +elvka++reg++vv+++d++ a+++iy++hp
  gi|118431006|ref|NP_147161.2|  30 SAEDLVSLAKKARANTLVVFARDAWGRVFYRGSR-LYPRHRRARLDV-AELVKAAKREGLRVVIMTDHT-ANRYIYRRHP 106
                                    5899*****************************7.7**********9.*********************.********** PP

                           GHL6  81 eWaavkenGevi....iiegervgepgwptlCinsgyqe.klaeeleealkrldlDGifldi 137
                                    +Wa+++++Gevi    ++++e+v++p+wp++Cins+++e ++++e+eealk++d+DG++ld+
  gi|118431006|ref|NP_147161.2| 107 GWAQRTRSGEVIvlehYPVKEKVRDPQWPQICINSPAMEsYFIPEAEEALKATDADGVLLDS 168
                                    ************999999********************659******************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                           GHL6  45 rdllkelvkachregikvvv 64 
                                    +  l+elv+a   eg +v++
  gi|118431006|ref|NP_147161.2| 527 EPRLGELVRARPVEGARVLA 546
                                    55689999999999999986 PP

>> Glyco_hydro_42M  Beta-galactosidase trimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0     7e-07    0.0021      44      96 ..     410     464 ..     379     480 .. 0.83
   2 ?   -0.6   0.0      0.27     8e+02     165     192 ..     571     598 ..     561     608 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7e-07
                Glyco_hydro_42M  44 vpvDvvseea..dlsgYklvvaPtlylvseelvkkleafvenGGtlvltylsGvv 96 
                                    +p ++ s+++  +  +Yk++va    ++s+e   +le++ve+GG lv+t   G  
  gi|118431006|ref|NP_147161.2| 410 LPYEFLSMKDihKAGRYKVLVAAETDVLSDEEEAALEDYVERGGFLVVTHSLGRM 464
                                    5556666655445679*********************************877765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                Glyco_hydro_42M 165 yagtpAvtrnnygkGkaiYvgsrleddl 192
                                    + +++A+t    g Gk  Y ++rl++++
  gi|118431006|ref|NP_147161.2| 571 KLNMAAITLGGRGSGKTLYYSVRLGAHY 598
                                    567899**9999**********999876 PP

>> ThuA  Trehalose utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.9e-06    0.0057      50      88 ..     425     461 ..     415     478 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.9e-06
                                    T-SEEEEE-G..GS-HHHHHH.HHHHHHTT-EEEEEGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThuA  50 qydvvvflstegevldaaqeaalqryveaGgGfvglhsA 88 
                                    +y+v+v   t  +vl++++eaal++yve Gg +v+ hs 
  gi|118431006|ref|NP_147161.2| 425 RYKVLVAAET--DVLSDEEEAALEDYVERGGFLVVTHSL 461
                                    7999999999..9*********************99985 PP

>> DUF4015  Putative glycosyl hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.047      14     105 ..      30     117 ..      24     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHHHSS--EEEEEEE-TTS-BSS----HHHHHCT-B--S.--HHHHHHHHHHTT-EEEEEEE-S--TTHHHHS CS
                        DUF4015  14 rleellelidetelnavviDvKddeGnvtyesklelaeelgaskkyisdleellkklkergiyviaRivvfkDkvlaear 93 
                                    + e+l++l+++++ n++v+  +d  G+v y    + ++ +   +++  d++el+k +k++g+ v+        +++++++
  gi|118431006|ref|NP_147161.2|  30 SAEDLVSLAKKARANTLVVFARDAWGRVFY----RGSRLYPRHRRARLDVAELVKAAKREGLRVVIMTDHTANRYIYRRH 105
                                    56899*************************....55556666666669*************955555555555566777* PP

                                    GGGB-EETTSSB CS
                        DUF4015  94 pelavkkkdgev 105
                                    p +a ++++gev
  gi|118431006|ref|NP_147161.2| 106 PGWAQRTRSGEV 117
                                    *****9999997 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 ?   11.6   0.0   4.6e-05      0.14     192     233 ..     424     464 ..     405     482 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                 ABC_transp_aux 192 edidvlviakptkdlseeelykldqflmnGgkllvfldpvae 233
                                     +++vlv a  t+ ls+ee  +l++++++Gg l+v  +  ++
  gi|118431006|ref|NP_147161.2| 424 GRYKVLVAA-ETDVLSDEEEAALEDYVERGGFLVVTHSLGRM 464
                                    468999999.*********************99998766665 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00044       1.3      15      38 ..      73      96 ..      69     161 .. 0.86
   2 ?    0.3   0.0      0.25   7.3e+02      28      74 ..     400     466 ..     395     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00044
                                   H..HHHHHHHHHCT-SEEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP 15 lsieelvkkakelglkaiaiTDhg 38
                                   l + elvk+ak+ gl  + +TDh 
  gi|118431006|ref|NP_147161.2| 73 LDVAELVKAAKREGLRVVIMTDHT 96
                                   5678*******************6 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                                    T-SEEEEEEEEBTT.HHHHHHHHHHHHTTTTSEEEEEEE................................. CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................x RF
                            PHP  28 glkaiaiTDhgnlf.gyvefykaakkkykagikpiiGleayvaddse........................k 74 
                                    g+  ia+  h ++    ++++++a     ++ k+++ +e +v +d+e                         
  gi|118431006|ref|NP_147161.2| 400 GMAMIAFHRHLPYEfLSMKDIHKA-----GRYKVLVAAETDVLSDEEeaaledyverggflvvthslgrmyP 466
                                    666677777776654234444444.....3579999999999999885555555555555555555555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5306.50
//
Query:       gi|118431007|ref|NP_147163.2|  [L=349]
Description: acyl coenzyme A thioester hydrolase [Aeropyrum pernix K1]
Scores for 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-13   48.5   4.0    2.2e-08   34.3   1.1    2.4  2  4HBT      Thioesterase superfamily


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 !   14.6   0.1   1.8e-06     0.032       2      71 ..      31      99 ..      30     104 .. 0.87
   2 !   34.3   1.1   1.2e-12   2.2e-08       3      68 ..     202     266 ..     200     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-06
                                   SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEE CS
                           4HBT  2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevr 71
                                   G++hgG++ ++l  a+++a+++   + + + +  + i   +pv +g+++ v a+  ++gr+s++v    +
  gi|118431007|ref|NP_147163.2| 31 GILHGGNMIRWLVDAGTLAASKVVVG-YPLLAGIDFIYLGKPVGVGETIAVFAWSPYAGRSSVEVGLAAY 99
                                   9************************7.666666666666689*********************9987665 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.2e-12
                                    SB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEE CS
                           4HBT   3 vvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvev 68 
                                    v+h G++l ++De +++a+ +   + i+v++    +df++p+r+g++l++ ar +++gr+s++v +
  gi|118431007|ref|NP_147163.2| 202 VMHAGAMLYIVDELGAVAALRSSAG-IVVTGFVGPADFVAPMRVGEVLRMWARTSYVGRSSVEVLI 266
                                    89*********************97.************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2677.42
//
Query:       gi|14600647|ref|NP_147164.1|  [L=158]
Description: 50S ribosomal protein L15 [Aeropyrum pernix K1]
Scores for 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-18   65.3   0.2    1.1e-17   64.9   0.2    1.1  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 !   64.9   0.2     6e-22   1.1e-17       2     127 ..      31     146 ..      30     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 6e-22
                                   GGGTSSTTTTTTTTT-..S--........S--.........---..GGG..---EEEEHHHHHHTTTTGTTS.--...--- CS
                Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfk..nskfkkeykvvnlkdLdelideerle.la...dea 72 
                                   G++gG G +G  k+++  + k +p  +  G+          Gf+  + +   e +++n+++Lde+++ ++ + +a   d++
  gi|14600647|ref|NP_147164.1|  31 GSKGGYGAAGLGKHEWtwTIKyAPTwY--GKK---------GFNppRIRAGLEVTTINVGQLDEIAALLEAQgKAekeDGK 100
                                   99**************98555566558..999.........**96433344667***********999998876688889* PP

                                   -EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  73 eeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                    +++le+l          g+ K+lg+g++ ++lkv    +S+ A++kIe+aGG+v+
  gi|14600647|ref|NP_147164.1| 101 IVVNLEKL----------GIhKLLGEGRVARPLKVITPLASELAIKKIEEAGGEVI 146
                                   ********..........************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1261.17
//
Query:       gi|118431008|ref|NP_147166.2|  [L=159]
Description: 50S ribosomal protein L30 [Aeropyrum pernix K1]
Scores for complete 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   47.6   0.0    2.3e-12   46.6   0.0    1.5  1  Ribosomal_L30  Ribosomal protein L30p/L7e


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 !   46.6   0.0   1.3e-16   2.3e-12       1      48 [.       4      52 ..       4      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.3e-16
                                   EEEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCC CS
                  Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVk 48
                                   ++V+rir++++vpp++ ktL lL+Lr++  ++ ++   p +r mL+ V+
  gi|118431008|ref|NP_147166.2|  4 YAVIRIRGTVDVPPDIDKTLYLLRLRRRYtASIYHDSLPGLRDMLRTVE 52
                                   58**********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1110.07
//
Query:       gi|14600650|ref|NP_147167.1|  [L=218]
Description: 30S ribosomal protein S5 [Aeropyrum pernix K1]
Scores for complete 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-26   90.5   1.1    4.9e-26   90.5   1.1    1.7  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    9.7e-24   82.6   0.0    1.8e-23   81.7   0.0    1.4  1  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 ?   -3.3   0.1       1.1   9.6e+03      10      22 ..      19      31 ..      18      32 .. 0.77
   2 !   90.5   1.1   5.4e-30   4.9e-26       1      65 []      55     119 ..      55     119 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.1
                                  EEEEEETTEEEEE CS
                  Ribosomal_S5 10 rvqkvtkgGrrts 22
                                  rv + +k G++ s
  gi|14600650|ref|NP_147167.1| 19 RVGRLVKEGKIKS 31
                                  7778899999876 PP

  == domain 2  score: 90.5 bits;  conditional E-value: 5.4e-30
                                   XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                  Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                   l+++v++++ vqk+t++Gr+t+f+a+vvvG+++G+vGlG gka++ + Ai+kAi++Ak+n++pv+
  gi|14600650|ref|NP_147167.1|  55 LDHEVIDVSIVQKMTDAGRITRFRAVVVVGNKDGYVGLGKGKARQFRFAIEKAIRNAKLNIIPVR 119
                                   6799***********************************************************96 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   2.1e-27   1.8e-23       2      68 ..     141     207 ..     140     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 2.1e-27
                                   EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT-.- CS
                Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspeev 68 
                                   gk g+v+v+lkpap+GtG++ag++++ vl+laGi+Dv++ ++g +r+ +n+++At+ AL++++ +  +
  gi|14600650|ref|NP_147167.1| 141 GKSGSVEVILKPAPKGTGLVAGDVAKVVLRLAGISDVWTFTKGeTRTSYNFARATYLALRNTYRFV-T 207
                                   9*************************************************************9987.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1671.44
//
Query:       gi|14600651|ref|NP_147168.1|  [L=214]
Description: 50S ribosomal protein L18 [Aeropyrum pernix K1]
Scores for 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-34  116.8   1.3    1.9e-21   76.7   0.3    2.8  3  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    1.3e-09   38.8   0.4    2.1e-09   38.2   0.4    1.3  1  Ribosomal_L18_c  Ribosomal L18 C-terminal region
    4.7e-05   23.7   0.6    7.5e-05   23.1   0.0    1.6  2  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 
  ------ inclusion threshold ------
      0.057   13.1   0.0      0.085   12.5   0.0    1.2  1  DUF1390          Protein of unknown function (DUF1390)


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 !   76.7   0.3   4.2e-25   1.9e-21       2      99 ..       6      97 ..       5     100 .. 0.95
   2 !   38.4   0.0   2.6e-13   1.1e-09     129     163 .]     100     134 ..      96     134 .. 0.93
   3 ?   -0.9   0.0      0.31   1.4e+03     117     138 ..     156     177 ..     141     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 4.2e-25
                 Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelp.kygvkvgltnya 83
                                  r++v +rrrregkt+Yy+r rl+        + k R+ Vr++n+ + +q+ +a+iegd+v+aaa+s+el  k+g k   +n  
  gi|14600651|ref|NP_147168.1|  6 RYRVPLRRRREGKTNYYRRFRLVK-------SGKPRMAVRISNEYLWVQFLEARIEGDRVIAAAHSRELIkKFGWKGDGNNTC 81
                                  9*********************96.......5578*********************************8549*********** PP

                 Ribosomal_L5e 84 aaYatglllarrllkk 99
                                  aaY+tg+l + r+l+k
  gi|14600651|ref|NP_147168.1| 82 AAYLTGYLAGLRALEK 97
                                  ************9987 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 2.6e-13
                 Ribosomal_L5e 129 fkaiLdvGLartttgakvfgalkgavdgglsiphs 163
                                    +a+LdvGL++  +g++vf+alkga+d+g++iphs
  gi|14600651|ref|NP_147168.1| 100 REAVLDVGLHKPVKGSRVFAALKGALDAGVEIPHS 134
                                   579*******************************7 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.31
                 Ribosomal_L5e 117 ynveeideekrafkaiLdvGLa 138
                                    + e+++  +r f  +Ld GL+
  gi|14600651|ref|NP_147168.1| 156 LKEENAELYQRQFSRYLDRGLN 177
                                   4445556678999999999997 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.4   4.7e-13   2.1e-09       6      64 ..     142     200 ..     140     214 .] 0.84

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.7e-13
               Ribosomal_L18_c   6 krIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIredpvkke 64 
                                   +r+ ++h+a++ e Lkee+ e y++qFs+y+++g+++++l    +++ +aI e  ++ +
  gi|14600651|ref|NP_147168.1| 142 ERVRCEHIAQWAEALKEENAELYQRQFSRYLDRGLNPEELPGHVEEVKKAIEEAYKHVA 200
                                   577899*********************************************99876532 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 !   23.1   0.0   1.7e-08   7.5e-05      21      97 ..      29     110 ..       9     131 .. 0.74
   2 ?   -2.4   0.3       1.4   6.2e+03      66      86 ..     192     212 ..     183     214 .] 0.60

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.7e-08
                                   TSSS-EEEEEE-SS-EEEEEE-TT..T--EEEEECS-SCCCT...S-SSSCHHHHHHHHHHHHHHHCHHCHTC-EE--TTS CS
                Ribosomal_L18p  21 taerprlvvfrsnrhiyaQviddv..kgktlasastlekelk...lkstknkeaakkvgeliAerakekgiekvvfDrggy 96 
                                   ++ +pr++v  sn+++++Q ++     ++++a+a + e   k   +  ++n+ aa   g l   ra+ekg++++v D g +
  gi|14600651|ref|NP_147168.1|  29 KSGKPRMAVRISNEYLWVQFLEARieGDRVIAAAHSRELIKKfgwKGDGNNTCAAYLTGYLAGLRALEKGVREAVLDVGLH 109
                                   5669****************99752256899999998865555555666667777777777778*************9866 PP

                                   S CS
                Ribosomal_L18p  97 k 97 
                                   k
  gi|14600651|ref|NP_147168.1| 110 K 110
                                   5 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                   CHHHHHHHHHHHHHHHCHHCH CS
                Ribosomal_L18p  66 nkeaakkvgeliAerakekgi 86 
                                    +ea k+v+e+ A +  e ++
  gi|14600651|ref|NP_147168.1| 192 IEEAYKHVAEETAAEGEEVEV 212
                                   345556777777777666665 PP

>> DUF1390  Protein of unknown function (DUF1390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05     0.085     171     216 ..     157     202 ..     142     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                       DUF1390 171 leknadviqvkfakelvddlktenlpGkkkdekisaaealkayasg 216
                                    e+na+++q +f++ l   l+ e+lpG+ ++ k ++ ea k  a+ 
  gi|14600651|ref|NP_147168.1| 157 KEENAELYQRQFSRYLDRGLNPEELPGHVEEVKKAIEEAYKHVAEE 202
                                   378**************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1624.28
//
Query:       gi|14600652|ref|NP_147169.1|  [L=155]
Description: 50S ribosomal protein L19 [Aeropyrum pernix K1]
Scores for complete 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-50  170.7   7.2    2.1e-50  170.5   7.2    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.5   7.2   1.2e-54   2.1e-50       2     142 ..       3     145 ..       2     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.5 bits;  conditional E-value: 1.2e-54
                                   THHHHHHHHHHTTS-GGGEEE..-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG-- CS
                Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwl..dpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrk 80 
                                   ++ q+rlaa++l+vG++r+w+  dpe  eei+ A+t++d+r+lik+g+I++ p+kgn+ +  + r+ ++rkgrrrg G+rk
  gi|14600652|ref|NP_147169.1|   3 YRFQRRLAAEILGVGESRIWIspDPELREEIEGAVTKADVRALIKRGVIKVLPEKGNAGHASKVRHLQRRKGRRRGMGRRK 83 
                                   688******************88999******************************************************* PP

                                   S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
                Ribosomal_L19e  81 GtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                                   G ++aRl+ ke+W++riR++Rr+L+ lr+k+ id+ktYr+lY+ akGg+f++ a+Lk+y+ +
  gi|14600652|ref|NP_147169.1|  84 GVATARLDPKERWMHRIRKIRRYLRYLRDKQVIDRKTYRRLYMLAKGGTFRDLASLKRYMAD 145
                                   ***********************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1179.18
//
Query:       gi|14600653|ref|NP_147170.1|  [L=145]
Description: 50S ribosomal protein L32 [Aeropyrum pernix K1]
Scores for 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-34  116.9   0.1    7.2e-34  116.5   0.1    1.2  1  Ribosomal_L32e  Ribosomal protein L32
  ------ inclusion threshold ------
      0.023   14.8   1.7       0.04   14.1   1.7    1.5  1  MTES_1575       REase_MTES_1575


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 !  116.5   0.1   8.1e-38   7.2e-34       2     108 .]      39     145 .]      38     145 .] 0.98

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 8.1e-38
                                   -----TTTTT-TTS-S..S------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..E CS
                Ribosomal_L32e   2 kkFirhqsdryvklke..swrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksya 80 
                                   ++F r+ s+r+ k+++   wrkp+G dn++r ++kg+++++k+GY++pk++rg++psG++ v+V+++k+Le l +e++  +
  gi|14600653|ref|NP_147170.1|  39 HRFLRYLSWRFWKFERrdYWRKPKGNDNKMRLQLKGYPPIVKVGYRTPKAIRGMHPSGLEPVIVSSAKDLERLSPERH--I 117
                                   68*************7779*********************************************************99..* PP

                                   EEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                Ribosomal_L32e  81 aeiahsVsskkrkeiverAaelgikVtN 108
                                   ++ia+ V+ +k++ei + A e g++V+N
  gi|14600653|ref|NP_147170.1| 118 VYIASGVGLRKKQEIRRAALERGFRVAN 145
                                   **************************99 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.7   4.5e-06      0.04      59      92 ..      36      69 ..      19      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-06
                     MTES_1575 59 ierqevLerlGWkilRiwssdwyrnpeeeleklv 92
                                   +r+++L+ l W+++++  +d++r+p+ + +k++
  gi|14600653|ref|NP_147170.1| 36 KSRHRFLRYLSWRFWKFERRDYWRKPKGNDNKMR 69
                                  5799**********************99877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1143.13
//
Query:       gi|14600654|ref|NP_147171.1|  [L=182]
Description: 50S ribosomal protein L6 [Aeropyrum pernix K1]
Scores for 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  113.9   7.6      1e-17   64.6   0.5    2.1  2  Ribosomal_L6  Ribosomal protein L6


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 !   64.6   0.5   5.6e-22     1e-17       1      76 []      13      86 ..      13      86 .. 0.98
   2 !   53.2   1.5     2e-18   3.5e-14       1      76 []      98     172 ..      98     172 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 5.6e-22
                                  CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                  +P+gv+vsi+g   v+v Gpkge++r+++++  v +  e+n+v+v++ + + ++++ l+g +  +i+nmikGV+ g
  gi|14600654|ref|NP_147171.1| 13 VPEGVTVSIDG-MRVKVSGPKGEVERDFSHARGVLIRLEDNSVVVESFFAKARQRA-LVGAIAGHIRNMIKGVQGG 86
                                  7*********8.************************9*******************.****************976 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 2e-18
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHHHTC CS
                  Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGVteg 76 
                                   +P++v+v++++  + ++lG+kg + ++i +gv+v+vk     + +++v+gid ekv    A+i++++++++++ +++++g
  gi|14600654|ref|NP_147171.1|  98 FPINVKVEGDKFIISNFLGEKGLRIARIMPGVKVQVK-----GSDVIVEGIDVEKVaqtaANIELATKVKDKDRRKFMDG 172
                                   8**********************************99.....9***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1494.99
//
Query:       gi|118431009|ref|NP_147172.2|  [L=133]
Description: 30S ribosomal protein S8 [Aeropyrum pernix K1]
Scores for 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-28   96.6   0.0    1.2e-27   96.4   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   6.7e-32   1.2e-27       1     127 []       5     133 .]       5     133 .] 0.85

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 6.7e-32
                                    -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCC..CCCEEEEE-BSSS-SBSSSEEEE-S CS
                   Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eek..kkkikielkynkkkksvikklkrvs 76 
                                    D++a+++++i+Nae+++k e+ + p+skl++++l++L++eGyi +fe+  + +  k  +k+ +++n+   +v+k  + vs
  gi|118431009|ref|NP_147172.2|   5 DTLANAMAAIKNAEMRGKGEAIImPSSKLIANVLRILEKEGYIGGFEYIdDGRwgKFRVKLLGRIND--IGVVKPRTPVS 82 
                                    89****************998888************************8444444444889999999..89999888888 PP

                                    BTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                   Ribosomal_S8  77 kpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       +    ++ +     + +G++i+sT++Gvmt++eA k+k+GG v+ayv+
  gi|118431009|ref|NP_147172.2|  83 YRELAKMPEHLRKYLASRDVGLLILSTPQGVMTHREALKRKIGGIVIAYVY 133
                                    86666444444444456789******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 00:00:00.39
# Mc/sec: 1013.13
//
Query:       gi|118431010|ref|YP_874816.1|  [L=54]
Description: 30S ribosomal protein S14 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-12   44.8   5.3    8.7e-12   44.6   5.3    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
     0.0021   17.9   2.7      0.003   17.4   2.7    1.3  1  zf-FPG_IleRS   Zinc finger found in FPG and IleRS
     0.0034   17.4   0.3     0.0043   17.1   0.3    1.2  1  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.033   14.2   0.4      0.034   14.2   0.4    1.1  1  Zn_Tnp_IS91    Transposase zinc-binding domain
       0.15   11.7   0.9        9.9    5.9   0.2    2.1  2  zf_UBZ         Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   5.3   2.4e-15   8.7e-12       5      52 ..       6      52 ..       4      54 .] 0.93

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.4e-15
                                   ---SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE CS
                  Ribosomal_S14  5 lprnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkK 52
                                    p+ ++++r+ +rC+ +G + +vi+k+gL  +R+cfRe A      G++K
  gi|118431010|ref|YP_874816.1|  6 PPKPKRMGRGAQRCQRCGTRDAVIQKYGLylCRQCFREIAPT---LGFRK 52
                                   6899999*********************************99...88888 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 !   17.4   2.7   8.5e-07     0.003       2      27 ..      17      40 ..      16      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.5e-07
                                   SB-TTT--BBEEEECTTEEEEE-TTT CS
                   zf-FPG_IleRS  2 epCpRCwryiervgqagrstyfCprC 27
                                   ++C RC++ ++ + +  ++ y+C +C
  gi|118431010|ref|YP_874816.1| 17 QRCQRCGTRDAVIQK--YGLYLCRQC 40
                                   79*************..********* PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   1.2e-06    0.0043      10      41 ..      14      47 ..       9      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                            DZR 10 pdarfCseCgtk..lkavaaedrCpsCgekvdpe 41
                                    +a+ C++Cgt+  + +    + C +C +++ p+
  gi|118431010|ref|YP_874816.1| 14 RGAQRCQRCGTRdaVIQKYGLYLCRQCFREIAPT 47
                                   68999*******66555555*******9987765 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 ?   14.2   0.4   9.4e-06     0.034      31      64 ..       8      41 ..       1      47 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.4e-06
                    Zn_Tnp_IS91 31 rtaalGfaryeCeeCghekivyfsCksrhCpsCq 64
                                   + +++G    +C+ Cg +  v ++ +   C +C 
  gi|118431010|ref|YP_874816.1|  8 KPKRMGRGAQRCQRCGTRDAVIQKYGLYLCRQCF 41
                                   56789****************************5 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0028       9.9       4      10 ..      18      24 ..      15      28 .. 0.85
   2 ?    4.8   0.0    0.0059        21       3      14 ..      35      46 ..      33      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0028
                         zf_UBZ  4 lCerCgk 10
                                    C+rCg+
  gi|118431010|ref|YP_874816.1| 18 RCQRCGT 24
                                   7****97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0059
                         zf_UBZ  3 ylCerCgkeipe 14
                                   ylC +C +ei +
  gi|118431010|ref|YP_874816.1| 35 YLCRQCFREIAP 46
                                   9*****999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 405.39
//
Query:       gi|118431011|ref|NP_147174.2|  [L=192]
Description: 50S ribosomal protein L5 [Aeropyrum pernix K1]
Scores for complete 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-23   82.6   0.0      3e-23   81.8   0.0    1.4  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
      3e-21   75.5   0.3    5.6e-21   74.6   0.3    1.5  1  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
      0.032   14.5   0.0      0.065   13.5   0.0    1.5  1  V-SNARE_C       Snare region anchored in the vesicle membrane
      0.042   14.3   0.1        0.1   13.0   0.1    1.6  1  GP68            Phage protein Gp68


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 !   81.8   0.0   6.7e-27     3e-23       2      92 ..      83     180 ..      82     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 6.7e-27
                 Ribosomal_L5_C   2 iGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak... 78 
                                    i+v+vtLrgek+ +fl+++l++v  r++      +ss+d++GnvsfGi+e+i +p+++yd+  gi Gmd++i+++++   
  gi|118431011|ref|NP_147174.2|  83 IAVMVTLRGEKALNFLKRALDAVGHRIK------TSSIDEHGNVSFGIEEHILIPGVKYDPRVGILGMDVAITIQRPghr 156
                                    99**************************......*******************************************665 PP

                 Ribosomal_L5_C  79 .tde...........earallkelgi 92 
                                     + e           ++r +++e+++
  gi|118431011|ref|NP_147174.2| 157 iV-ErrrqrrghiprRHR-VTREETM 180
                                    52.146677777776666.7777766 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.3   1.3e-24   5.6e-21       1      57 []      25      78 ..      25      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                                   SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                   Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                   ++M+ Pr+ K+++n+ +G++ge+   l++aa++L+e+tGQkPv++kak++i++F++R
  gi|118431011|ref|NP_147174.2| 25 SPMRRPRIVKVTVNISIGQSGER---LQRAAEVLEELTGQKPVFRKAKRTIRAFGVR 78
                                   59*********************...******************************9 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 ?   13.5   0.0   1.5e-05     0.065      19      47 ..      46      74 ..      36      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                      V-SNARE_C 19 etisiGaailedLhsQretLkrarsklhn 47
                                   e ++++a++le+L+ Q+ +++ a+++++ 
  gi|118431011|ref|NP_147174.2| 46 ERLQRAAEVLEELTGQKPVFRKAKRTIRA 74
                                   7799********************99875 PP

>> GP68  Phage protein Gp68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.3e-05       0.1      31      59 ..      79     107 ..      67     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                           GP68  31 kGaailkllklrGtrlvnqmqraldaeta 59 
                                    kG +i  ++ lrG + +n ++ralda  +
  gi|118431011|ref|NP_147174.2|  79 KGENIAVMVTLRGEKALNFLKRALDAVGH 107
                                    8999999******************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1519.54
//
Query:       gi|118431012|ref|NP_147175.2|  [L=253]
Description: 30S ribosomal protein S4 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-24   84.6   0.0    5.1e-24   84.0   0.0    1.3  1  Ribosomal_S4e  Ribosomal family S4e
      2e-15   56.6   3.4    3.1e-15   56.0   3.4    1.3  1  RS4NT          RS4NT (NUC023) domain
    2.5e-15   55.9   0.3    2.3e-14   52.8   0.0    2.4  2  S4             S4 domain
    9.7e-06   25.1   0.0    1.9e-05   24.2   0.0    1.5  1  40S_S4_C       40S ribosomal protein S4 C-terminus
     0.0025   17.7   2.3     0.0075   16.2   2.3    1.9  1  KOW            KOW motif


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 !   84.0   0.0   1.4e-27   5.1e-24       1      75 []      96     178 ..      96     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 1.4e-27
                                    TTEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES.........STT-STTEEEEEETT CS
                  Ribosomal_S4e   1 tgenyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp.........dpdikvnDtvkidle 71 
                                    tge++r+l+ + + f+lh+I +ee ++K ++i++kttvk+g++ql++hdGr+i+++         d  +++ Dt++i+++
  gi|118431012|ref|NP_147175.2|  96 TGEKFRMLPYPVKFFKLHPIPEEEGDLKPVRIENKTTVKGGHVQLNLHDGRNILVRvkdprnpveD-VYRTMDTLLITVP 174
                                    89***************************************************9999999999955.5************ PP

                                    TTEE CS
                  Ribosomal_S4e  72 enkI 75 
                                     ++I
  gi|118431012|ref|NP_147175.2| 175 GQEI 178
                                    **98 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   3.4   8.7e-19   3.1e-15       1      36 [.       4      39 ..       4      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 8.7e-19
                                   -S----EETTTS-TTS---SSSSSEE----SSSS-T CS
                          RS4NT  1 rGpkkHLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                   +G+ + LK laAP++Wp+ +ke+++avkP+pGPH++
  gi|118431012|ref|NP_147175.2|  4 MGGQRRLKALAAPRFWPILRKEYKWAVKPRPGPHPA 39
                                   8*********************************97 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   6.4e-18   2.3e-14       8      48 .]      51      91 ..      43      91 .. 0.91
   2 ?    0.1   0.0      0.18   6.6e+02      23      31 ..     133     141 ..     130     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 6.4e-18
                                   HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                             S4  8 arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                     lg+a + reAr+lI++G+++V+G v+kd++++V+++Dvi
  gi|118431012|ref|NP_147175.2| 51 NVLGYAQTAREARKLISEGHFRVDGVVRKDYKFPVGFMDVI 91
                                   559************************************98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                                    HHTTTEEET CS
                             S4  23 IehGrVlVN 31 
                                    +++G+V++N
  gi|118431012|ref|NP_147175.2| 133 VKGGHVQLN 141
                                    899***998 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.2e-09   1.9e-05       1      30 [.     222     250 ..     222     251 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.2e-09
                                    -SSS-EEEEEGGGEEE--STTS-SS---SS CS
                       40S_S4_C   1 DaaGntFATRlsNvFvIGkgnkpwvsLPkg 30 
                                    Da+Gn F T l +vFvIG  ++p++sLP+g
  gi|118431012|ref|NP_147175.2| 222 DASGNLFQTSLDYVFVIGL-DRPVISLPEG 250
                                    9*****************5.89******98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.3   2.1e-06    0.0075       2      24 ..     187     209 ..     186     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                                    TSEEEESSSTTTTCEEEEEEEET CS
                            KOW   2 GdhVkVvsGphkGktGkVvkvdq 24 
                                    G + ++v+G++ G++G+V++v +
  gi|118431012|ref|NP_147175.2| 187 GAIAIIVGGRNVGRVGVVKSVQK 209
                                    8899****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1900.05
//
Query:       gi|14600658|ref|NP_147176.1|  [L=132]
Description: 50S ribosomal protein L24 [Aeropyrum pernix K1]
Scores for complete 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-34  118.1   0.4    2.2e-34  117.7   0.4    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    2.7e-09   36.6   3.5    2.7e-09   36.6   3.5    1.8  2  KOW            KOW motif
  ------ inclusion threshold ------
       0.12   12.8   0.5        2.7    8.5   0.0    2.6  2  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L


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 !  117.7   0.4   3.7e-38   2.2e-34       1      82 []       7     121 ..       7     121 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.7 bits;  conditional E-value: 3.7e-38
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxx RF
                 Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gvtrek 49 
                                   s ++rkqr+a++ ap+h r+kl+sa Ls eLrekygvrslp+r                                gvt++k
  gi|14600658|ref|NP_147176.1|   7 SRQPRKQRRALYRAPLHARQKLVSATLSPELREKYGVRSLPVRkgdkvrvmrgdfkghegkvvkvdlrrlriyidGVTVTK 87 
                                   789****************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                 Ribosomal_L26  50 angttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                   a+gt+v ++ihpS+v+I++l+l D+ rkk++er+
  gi|14600658|ref|NP_147176.1|  88 ADGTPVFRPIHPSNVMIVELDLsDEYRKKMIERR 121
                                   ********************************98 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   3.5   4.5e-13   2.7e-09       1      32 []      50      81 ..      50      81 .. 0.97
   2 ?   -2.4   0.0      0.89   5.3e+03      18      23 ..     103     108 ..     101     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.5e-13
                                  TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                           KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                  +Gd V+V++G +kG +GkVvkvd  + r+++d
  gi|14600658|ref|NP_147176.1| 50 KGDKVRVMRGDFKGHEGKVVKVDLRRLRIYID 81
                                  7****************************998 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.89
                                   EEEEEE CS
                           KOW  18 kVvkvd 23 
                                   ++v+ d
  gi|14600658|ref|NP_147176.1| 103 MIVELD 108
                                   888877 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 ?    2.0   0.6     0.046   2.8e+02      50      59 ..      49      58 ..      19      90 .. 0.80
   2 ?    8.5   0.0   0.00045       2.7      25      35 ..      96     106 ..      93     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.046
                 ribosomal_L24 50 edgkkvRvsk 59
                                  ++g kvRv +
  gi|14600658|ref|NP_147176.1| 49 RKGDKVRVMR 58
                                  5788999986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00045
                 ribosomal_L24  25 pIhvSnVmlvd 35 
                                   pIh SnVm+v 
  gi|14600658|ref|NP_147176.1|  96 PIHPSNVMIVE 106
                                   9********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1047.30
//
Query:       gi|14600659|ref|NP_147177.1|  [L=140]
Description: 50S ribosomal protein L14 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-38  131.8   0.2    1.5e-38  131.6   0.2    1.1  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
      0.076   13.3   0.0       0.13   12.5   0.0    1.4  1  PAS_3          PAS fold


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.6   0.2   1.7e-42   1.5e-38       2     122 .]      20     140 .]      19     140 .] 0.95

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 1.7e-42
                                   .CSS-EEE--SSSSBSEEEEEEETT-.--....-EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEE CS
                 Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggkkr....kaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvir 78 
                                   +q+++++ vaDNsgakev++i+v + k+r    ++a vGd +vvsvkk++p   +++++vv+avvvr+++++rr+dG++++
  gi|14600659|ref|NP_147177.1|  20 LQVGSYVPVADNSGAKEVMIISVPQVKTRlrrlPSAGVGDLVVVSVKKGTP---QMRRQVVYAVVVRQRRPFRRPDGTWVS 97 
                                   68999*******************9994445569*****************...899************************ PP

                                   ESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                 Ribosomal_L14  79 fddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                   f+dna+V++n +g+p+G+++ gp+are++e+ +++++++A++++
  gi|14600659|ref|NP_147177.1|  98 FEDNAVVIVNPDGTPRGSEVRGPIAREAAER-WPRVAKIATMIV 140
                                   ******************************9.********9986 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.5e-05      0.13      58      83 ..      88     113 ..      75     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                         PAS_3  58 irrkdGeyrwveararvirdengkpv 83 
                                   +rr+dG+++ +e+ a+vi + +g p 
  gi|14600659|ref|NP_147177.1|  88 FRRPDGTWVSFEDNAVVIVNPDGTPR 113
                                   79********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1068.28
//
Query:       gi|118431013|ref|NP_147178.2|  [L=114]
Description: 30S ribosomal protein S17 [Aeropyrum pernix K1]
Scores for 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   80.6   2.8    8.6e-23   80.2   2.8    1.2  1  Ribosomal_S17  Ribosomal protein S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2   2.8   4.8e-27   8.6e-23       1      67 [.      42     109 ..      42     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 4.8e-27
                                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEE CS
                  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvv 67 
                                    GvV +++  + vvV++ +l++++ky++y++r+kk++ah ++++ vk+GD+V i+e+ P+Skt++f+v+
  gi|118431013|ref|NP_147178.2|  42 GVVAKARARRMVVVQHVYLYYDKKYNRYERRSKKIHAHLPDCIsVKEGDVVVIGETMPISKTVKFTVL 109
                                    89****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 926.06
//
Query:       gi|14600661|ref|NP_147179.1|  [L=110]
Description: ribonuclease P protein component 1 [Aeropyrum pernix K1]
Scores for 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-13   48.7   0.0    6.5e-13   48.4   0.0    1.1  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 !   48.4   0.0   3.6e-17   6.5e-13       8      83 ..      17      92 ..      10      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 3.6e-17
                                  XSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHHC CS
                       UPF0086  8 lhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRae 83
                                  l+G++v+V+++++psl g++G Vv E    l+i t + rv tv K+ +v+e+e  +  +++++G+ l+  p dR++
  gi|14600661|ref|NP_147179.1| 17 LTGLRVKVLAHSDPSLEGLEGWVVVEEARSLRILTLEGRVSTVLKDLAVIEVEAPGGEYIRISGRVLIGNPLDRVK 92
                                  89****************************************************9999****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 860.96
//
Query:       gi|118431014|ref|YP_874817.1|  [L=71]
Description: 50S ribosomal protein L29 [Aeropyrum pernix K1]
Scores for 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-21   74.0   2.6    7.8e-21   73.8   2.6    1.1  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
      0.035   13.9   0.0      0.051   13.4   0.0    1.2  1  PASTA          PASTA domain
       0.18   11.9   1.9        0.2   11.7   0.0    1.8  2  DUF1192        Protein of unknown function (DUF1192)


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 !   73.8   2.6   1.3e-24   7.8e-21       1      57 []       9      65 ..       9      65 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.3e-24
                                   HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHHH CS
                  Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlrer 57
                                   k+lr++s+eeL++ l el+ +L+ Lr ++++g lenp+++r++R+++ARi+Tvlre+
  gi|118431014|ref|YP_874817.1|  9 KDLRGMSVEELEKTLRELRIKLMGLRYKAKVGLLENPGELREARRNVARILTVLREK 65
                                   79******************************************************8 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.5e-06     0.051       5      24 ..      10      29 ..       7      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                                   TTTTSBHHHHHHHHHHTT-- CS
                          PASTA  5 dvtGmsvdeAkatLkalGlk 24
                                   d++Gmsv+e ++tL++l +k
  gi|118431014|ref|YP_874817.1| 10 DLRGMSVEELEKTLRELRIK 29
                                   9***************8773 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    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      13      33 ..       7      27 ..       3      28 .. 0.87
   2 ?   -0.9   0.5      0.29   1.7e+03      36      52 ..      55      71 .]      48      71 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                        DUF1192 13 igqDLslLSveELeerIalLe 33
                                    ++DL  +SveELe+   +L+
  gi|118431014|ref|YP_874817.1|  7 RSKDLRGMSVEELEKTLRELR 27
                                   579************998885 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                        DUF1192 36 IaRleaaiakkkasraA 52
                                   +aR+ + +++k+++++A
  gi|118431014|ref|YP_874817.1| 55 VARILTVLREKREGEKA 71
                                   67888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 573.38
//
Query:       gi|14600662|ref|NP_147181.1|  [L=246]
Description: 30S ribosomal protein S3 [Aeropyrum pernix K1]
Scores for complete 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-25   88.3   1.0    9.8e-25   86.9   0.9    1.8  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    1.6e-11   43.9   0.2    9.2e-11   41.4   0.0    2.3  3  KH_2            KH domain
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.049   13.5   0.0    2.0  2  KH_4            KH domain
      0.026   14.4   6.6      0.033   14.0   0.2    3.2  4  KH_1            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.5   6.9e+03      59      81 ..      15      37 ..      10      38 .. 0.82
   2 !   86.9   0.9   2.2e-28   9.8e-25       1      83 []     101     184 ..     101     184 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.5
                                  HHHH-EEEEEEEEETTEEEEEEE CS
                Ribosomal_S3_C 59 lradidyavaeaktkyGiiGvkV 81
                                  lr +id+ +a+   + G   vkV
  gi|14600662|ref|NP_147181.1| 15 LRTKIDEWLAQNFYEAGYSRVKV 37
                                  78899999999988888888887 PP

  == domain 2  score: 86.9 bits;  conditional E-value: 2.2e-28
                                   HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEEE CS
                Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiGv 79 
                                   ia+++e++++fRr++  ai+r+m++ga G++i++sG+L+ +e+ar ek+k+G+v++  h++++ +d+a a a++  G+iGv
  gi|14600662|ref|NP_147181.1| 101 IARSIERGIHFRRVAFAAINRIMSNGALGVEITISGKLT-SERARFEKFKAGKVYKsgHKVDELVDRASAYARLPKGVIGV 180
                                   89*************************************.***************************************** PP

                                   EEEE CS
                Ribosomal_S3_C  80 kVwI 83 
                                    V I
  gi|14600662|ref|NP_147181.1| 181 DVII 184
                                   **88 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   2.1e-14   9.2e-11       1      68 [.      18      84 ..      18      89 .. 0.93
   2 ?   -1.9   0.0      0.66   2.9e+03      55      74 ..     142     161 ..     139     163 .. 0.81
   3 ?   -1.8   0.1      0.64   2.9e+03      66      74 ..     194     203 ..     180     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.1e-14
                                  HHHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                          KH_2  1 eipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68
                                  +i+e+la+++++ag+s+v++ +t  +++i+i +++p+++IG++G++i+++++ ++  ++ l + ++++
  gi|14600662|ref|NP_147181.1| 18 KIDEWLAQNFYEAGYSRVKVVQTSLGTNITIWAERPALIIGRRGATIRRLQEVFQTVFG-LPNPRIRV 84
                                  799**************************************************999997.88877776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                                   HHHHHHHHTTCEEEEEEEET CS
                          KH_2  55 rkdieklegkkVklnivkVk 74 
                                   r ++ek++ +kV+   +kV 
  gi|14600662|ref|NP_147181.1| 142 RARFEKFKAGKVYKSGHKVD 161
                                   67899999999998777776 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.64
                                   EEEEEE.EET CS
                          KH_2  66 Vklniv.kVk 74 
                                   V+++++ +Vk
  gi|14600662|ref|NP_147181.1| 194 VRIKSEeEVK 203
                                   4444443333 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.049      32      63 ..      45      76 ..      23      85 .. 0.80
   2 ?   -2.1   0.0      0.84   3.8e+03       4      12 ..     202     210 ..     190     242 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                          KH_4 32 elnvegedlGrvIGkrGrtldAlqylvsaaan 63
                                  ++++  e  +++IG+rG t++ lq + + +  
  gi|14600662|ref|NP_147181.1| 45 NITIWAERPALIIGRRGATIRRLQEVFQTVFG 76
                                  6777788999**************99988765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.84
                          KH_4   4 vedilkalv 12 
                                   v+d+++a+ 
  gi|14600662|ref|NP_147181.1| 202 VKDVVDAIR 210
                                   333333333 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.83   3.7e+03      21      35 ..      34      48 ..      31      54 .. 0.74
   2 ?   14.0   0.2   7.4e-06     0.033      13      30 ..      55      72 ..      50      89 .. 0.88
   3 ?   -1.1   0.0       0.4   1.8e+03      30      52 ..     129     136 ..     117     145 .. 0.54
   4 ?    2.1   0.4     0.037   1.7e+02      30      65 ..     179     210 ..     176     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.83
                                  HHHHHHHHH.T-EEEE CS
                          KH_1 21 nIkeIreet.gakIkv 35
                                  ++k  +  + g++I++
  gi|14600662|ref|NP_147181.1| 34 RVKVVQT-SlGTNITI 48
                                  5666777.77999996 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.4e-06
                                  HHHTGGGHHHHHHHHHHT CS
                          KH_1 13 riIGkgGsnIkeIreetg 30
                                  +iIG++G++I++++e  +
  gi|14600662|ref|NP_147181.1| 55 LIIGRRGATIRRLQEVFQ 72
                                  69************9665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.4
                                   T-EEEEESSTT...T.-EEEEEE CS
                          KH_1  30 gakIkvpksedegsderevtisG 52 
                                   g+ I+               isG
  gi|14600662|ref|NP_147181.1| 129 GVEIT---------------ISG 136
                                   44444...............444 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.037
                                   T-EEEEES.STT...T.-EEEEEESHHHHHHHHHHHH CS
                          KH_1  30 gakIkvpk.sedegsderevtisGspeavekAkelie 65 
                                   g+ + ++k +++     + v+i+ ++e v++ +++i+
  gi|14600662|ref|NP_147181.1| 179 GVDVIIVKpGKP----GDHVRIKSEEE-VKDVVDAIR 210
                                   666666654544....599***99999.999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1840.50
//
Query:       gi|14600663|ref|NP_147182.1|  [L=156]
Description: 50S ribosomal protein L22 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-29  102.3   0.9    1.7e-29  102.1   0.9    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
       0.14   12.7   1.0       0.67   10.5   0.1    2.1  3  DinB_2         DinB superfamily


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 !  102.1   0.9   1.9e-33   1.7e-29       2     102 ..      20     153 ..      19     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.9e-33
                                   EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT.-SST................................THHHHHHHHHH CS
                 Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf.skkk................................aakfvlklLkn 49 
                                     +n++v++k + evar+I gm v+eA +yL+   +k+                                aa+++lklL n
  gi|14600663|ref|NP_147182.1|  20 VLRNVPVHPKIMAEVARAISGMRVDEARRYLRAvIEKReavpfrrahgkqahrrgladkwgwpvgrypvkAARYMLKLLDN 100
                                   679******************************955556****************************************** PP

                                   HHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                 Ribosomal_L22  50 aeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                   +eana +k+ldv++l I ++ ++kg +lkr+++rA Gr++p ++ ++hie+++
  gi|14600663|ref|NP_147182.1| 101 VEANAANKNLDVERLKIIHVAAHKGITLKRWMPRAWGRATPRNRVHSHIEIMV 153
                                   ***************************************************98 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.093   8.3e+02      67      80 ..      42      55 ..      15      81 .. 0.70
   2 ?    0.0   0.1      0.13   1.1e+03      48      63 ..      63      78 ..      43     105 .. 0.56
   3 ?   10.5   0.1   7.4e-05      0.67       8      58 ..      93     143 ..      88     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.093
                        DinB_2 67 saaealaylaevra 80
                                   ++ea++yl++v +
  gi|14600663|ref|NP_147182.1| 42 RVDEARRYLRAVIE 55
                                  45666666666644 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.13
                        DinB_2 48 erlrgeeaprpgldpl 63
                                  +r+ g++a+r+gl ++
  gi|14600663|ref|NP_147182.1| 63 RRAHGKQAHRRGLADK 78
                                  3444555555444444 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 7.4e-05
                        DinB_2   8 rllalledlteeelnrqpspgkwsiawllaHlgnveelllerlrgeeaprp 58 
                                    +l+ll+++ +  +n   +  +  i+++ aH g++ + + +r++g+++pr 
  gi|14600663|ref|NP_147182.1|  93 YMLKLLDNVEANAANKNLDVERLKIIHVAAHKGITLKRWMPRAWGRATPRN 143
                                   57999999999999***9***************************999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 00:00:00.40
# Mc/sec: 1174.58
//
Query:       gi|118431015|ref|NP_147183.2|  [L=144]
Description: 30S ribosomal protein S19 [Aeropyrum pernix K1]
Scores for 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  112.5   0.0    8.5e-33  112.1   0.0    1.2  1  Ribosomal_S19  Ribosomal protein S19
  ------ inclusion threshold ------
      0.015   15.4   1.8      0.032   14.3   0.1    2.1  2  FA             FERM adjacent (FA)


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 !  112.1   0.0   9.5e-37   8.5e-33       1      81 []      40     127 ..      40     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 9.5e-37
                                    .HHHSS.TTCCCHHHHHHHHHH...TS-...----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT CS
                  Ribosomal_S19   1 rslkkg.pfvqesllkkvrkak...aek...kkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFs 73 
                                    rsl +g +  q++ll kvrk +   +e+   ++ vi+th+Rd++IlPemvglt++VynGk+f+pv+i +em+Gh+LgEFs
  gi|118431015|ref|NP_147183.2|  40 RSLLRGlTPAQQKLLLKVRKIRrrlEEGrlkRPPVIRTHVRDMVILPEMVGLTIAVYNGKEFIPVKIVPEMIGHYLGEFS 119
                                    67888888899999999*99998773336779************************************************ PP

                                    -SS----S CS
                  Ribosomal_S19  74 pTrkpvkh 81 
                                    pT  +v+h
  gi|118431015|ref|NP_147183.2| 120 PTTRIVQH 127
                                    ******99 PP

>> FA  FERM adjacent (FA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   3.6e-06     0.032       8      36 ..      11      40 ..      11      46 .. 0.75
   2 ?   -0.2   0.3      0.12   1.1e+03      26      37 ..      67      78 ..      59      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.6e-06
                             FA  8 kFRYSGRTekQtvedskeil.rpqpsfeRs 36
                                   kFRY GRT  ++++   e l r  p  +R+
  gi|118431015|ref|NP_147183.2| 11 KFRYRGRTLEELLKMDIEELaRLFPARQRR 40
                                   9********999987777666655555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                             FA 26 ilrpqpsfeRsp 37
                                   +  ++p++ R++
  gi|118431015|ref|NP_147183.2| 67 GRLKRPPVIRTH 78
                                   457899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1069.85
//
Query:       gi|14600666|ref|NP_147185.1|  [L=659]
Description: hypothetical protein APE_0370 [Aeropyrum pernix K1]
Scores for complete 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   57.6   2.5    2.8e-15   56.3   2.5    1.5  1  VWA_CoxE   VWA domain containing CoxE-like protein
    0.00011   22.0   0.4    0.00053   19.8   0.4    2.2  1  AAA_lid_2  AAA lid 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 !   56.3   2.5   3.1e-19   2.8e-15      20     203 ..     470     635 ..     456     649 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 3.1e-19
                      VWA_CoxE  20 krrrrgrriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflallhAllqqlprtevfaFdtrl 100
                                    ++rr  r+D+rr++ +++r+g++  ++v+r+ r r   +l l +DvS Sm +ys + +a++   l +++  +++ F+ + 
  gi|14600666|ref|NP_147185.1| 470 LSQRRSPRVDVRRSIYQSIRSGRP--SIVYRE-RLRAG-RLSLALDVSSSMIDYSSWAIAVASLFLSNIS--RLVIFSHAS 544
                                   5789999***************97..569999.98999.9*****************9988877777775..688899999 PP

                      VWA_CoxE 101 vdlTralrerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvlvsDglergdreellaelarlvrrar 181
                                   + l   l+ r+ a++L +v+       G T+i++al++++     +       +v vsD+ ++ d++ l+  +++l+r++ 
  gi|14600666|ref|NP_147185.1| 545 TILEGPLSRREVARSLLSVE-----FRGYTDISTALEKAAHPGV-KK------IVAVSDLQQTVDSQPLQLVVRSLHRSGY 613
                                   9999****************.....************9876555.44......89************************** PP

                      VWA_CoxE 182 rlvwlnplsdagtpgydpe.ara 203
                                   r++ ++p s +  + ++++  ++
  gi|14600666|ref|NP_147185.1| 614 RIAFITPPSAR-PEDVEAArEAG 635
                                   *******9433.33333332333 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4   5.9e-08   0.00053      22      59 ..      36      73 ..      26      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.9e-08
                     AAA_lid_2 22 llraArAlAalegrdyVtpeDvkeaaplVLaHRlrrep 59
                                  ++r Ar +A legrd+ +++ ++ ++  V  HR    +
  gi|14600666|ref|NP_147185.1| 36 IIRLARSYADLEGRDFLAEDELEMVVDAVVKHRRLSHA 73
                                  79*******************************87554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4637.39
//
Query:       gi|118431016|ref|NP_147187.2|  [L=291]
Description: hypothetical protein APE_0372.1 [Aeropyrum pernix K1]
Scores for complete 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-19   69.1   0.0    6.4e-19   68.3   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
    3.8e-08   33.1   1.9      1e-07   31.7   1.9    1.6  1  AAA_lid_2        AAA lid domain
    0.00018   21.4   0.0     0.0023   17.8   0.0    2.3  1  AAA_3            ATPase family associated with various cellul
     0.0002   21.9   0.0    0.00036   21.1   0.0    1.5  1  AAA_18           AAA domain
     0.0002   21.8   0.1     0.0013   19.2   0.1    2.1  1  AAA              ATPase family associated with various cellul
    0.00084   19.1   0.0       0.94    9.2   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
     0.0049   16.6   0.0      0.015   15.0   0.0    1.9  1  AAA_30           AAA domain
     0.0063   15.9   0.0       0.53    9.6   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.009   16.0   0.0      0.015   15.3   0.0    1.4  1  Baculo_RING      Baculovirus U-box/Ring-like domain
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.064   12.8   0.0    2.0  2  AAA_7            P-loop containing dynein motor region
      0.022   15.1   0.0      0.043   14.2   0.0    1.8  1  AAA_16           AAA ATPase domain
      0.029   13.6   0.0      0.084   12.1   0.0    1.7  2  TIP49            TIP49 P-loop domain
      0.037   14.1   0.0      0.082   13.0   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.047   14.0   0.1        0.7   10.2   0.0    2.3  2  AAA_19           AAA domain
      0.073   12.8   0.0       0.19   11.5   0.0    1.7  2  AAA_11           AAA domain
       0.14   11.8   0.0       0.23   11.2   0.0    1.4  1  AAA_24           AAA domain
       0.16   11.8   0.0        0.4   10.6   0.0    1.8  1  NACHT            NACHT domain
       0.17   12.3   0.6       0.43   11.0   0.6    1.6  1  MCM_lid          MCM AAA-lid 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 !   68.3   0.0   6.4e-22   6.4e-19       1     137 [.      43     182 ..      43     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 6.4e-22
                                    EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--...............--------G-SEEEEES CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik......ngttslvdsplvraaregeilvlDE 73 
                                    +vl  GppGtgK+e+ e l+++  +r+ ++  +++++ e +++g  +++        ++s+v+ pl  a      +++DE
  gi|118431016|ref|NP_147187.2|  43 PVLFEGPPGTGKTEIGEALLELWaGRKPFILPCSEGYDEYKVIGDFHPQmamkhgFNEESFVPRPLLAALILDTGVLVDE 122
                                    5899*******************************************99999888789*********9999999999*** PP

                                    GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                          AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                    + r + e +n Ll ++++rr+ ++e +++ ka+ ++    f++i+t+np d  +nels a+++R
  gi|118431016|ref|NP_147187.2| 123 IRRSSEEFQNMLLDIIDKRRIVVPEIRRVFKARGTG----FQLIMTSNPEDIAQNELSDAFLRR 182
                                    *********************************998....***********************9 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   1.9     1e-10     1e-07      20      56 ..     240     276 ..     239     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1e-10
                      AAA_lid_2  20 lallraArAlAalegrdyVtpeDvkeaaplVLaHRlr 56 
                                    +a++r+A+ +Aal+grd+V+ eD+ eaa+ VL  R+ 
  gi|118431016|ref|NP_147187.2| 240 VAWARMAQSIAALKGRDRVSLEDLAEAAEAVLVKRVD 276
                                    89******************************99986 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 !   17.8   0.0   2.4e-06    0.0023       2     124 ..      44     178 ..      43     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpd.llPsdilG....tevfeekekefefkkGpvfanl.....lladei 71 
                                    vl+eg PG++kt + +al +    +   i   ++      ++G    ++ +++  +e +f + p++a l     +l+dei
  gi|118431016|ref|NP_147187.2|  44 VLFEGPPGTGKTEIGEALLELWAGRKPFILPCSEgYDEYKVIGdfhpQMAMKHGFNEESFVPRPLLAALildtgVLVDEI 123
                                    57777777777777777776666555555433331222334441110344444446667777777777622222579*** PP

                          AAA_3  72 nrappktqsalleameerqvtvegethklp...epflvlatqnPieqeGtyplpea 124
                                     r++   q  ll++++ r++ v + ++ ++   + f ++ t nP +     +l +a
  gi|118431016|ref|NP_147187.2| 124 RRSSEEFQNMLLDIIDKRRIVVPEIRRVFKargTGFQLIMTSNPEDIA-QNELSDA 178
                                    ********************99887766651125799*******6643.4455555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.6e-07   0.00036       1      90 [.      44     174 ..      44     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.6e-07
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe.............aldes 49 
                                    +l  G+pG+GKt+++++L ++  g                  g+ + ++a ++g  +e + +              +de 
  gi|118431016|ref|NP_147187.2|  44 VLFEGPPGTGKTEIGEALLELWaGRkpfilpcsegydeykviGDFHPQMAMKHGFNEESFVPrpllaalildtgvLVDEI 123
                                    6789**************77743335667777888899788888888888888888888888888888888888888888 PP

                         AAA_18  50 krldedkldklldaleenss..........aleegknlvidghlaelesea 90 
                                    +r  e++++ lld++++ +           a++ g  l++ + +++  + +
  gi|118431016|ref|NP_147187.2| 124 RRSSEEFQNMLLDIIDKRRIvvpeirrvfkARGTGFQLIMTSNPEDIAQNE 174
                                    888888888888888886557777777777667677777766665555554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.3e-06    0.0013       1     124 [.      44     179 ..      44     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                                    EEEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TS..EEEEEET...GGGH CS
                            AAA   1 vllyGppGtGKTllakavakel.gvefleisgsellskyvgesekkirelfkeakeka....kp..silfiDE...idal 70 
                                    vl+ GppGtGKT + +a+ + + g++ + + +se  ++y   +  + ++ +k+  +++    +p    l++D    +d++
  gi|118431016|ref|NP_147187.2|  44 VLFEGPPGTGKTEIGEALLELWaGRKPFILPCSEGYDEYKVIGDFHPQMAMKHGFNEEsfvpRPllAALILDTgvlVDEI 123
                                    799*****************964799999999999977544444444444444322223566333344555542223333 PP

                                    HHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESSGGGSTHHHHSTTS CS
                            AAA  71 aksrsgseseeeervvnqLlteldgvkkk...........eskvivigatnrpdkldpallrgRf 124
                                     +        ++e+ +n Ll  +d+ +                + +i+++n +d  +++l  + f
  gi|118431016|ref|NP_147187.2| 124 RR--------SSEEFQNMLLDIIDKRRIVvpeirrvfkarGTGFQLIMTSNPEDIAQNELS-DAF 179
                                    22........346678888888888888888888888888555888888888655555554.444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0026       2.5      10      46 ..      29      65 ..      24      78 .. 0.79
   2 !    9.2   0.0   0.00094      0.94      97     122 ..     118     143 ..     112     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0026
                                   HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat 10 elleqikkvaktdlsvlitGesGtGKellaraiheas 46
                                   ++++ + ++  +  +vl +G  GtGK+ + +a+ e  
  gi|118431016|ref|NP_147187.2| 29 RVVTLVYAAFLNGRPVLFEGPPGTGKTEIGEALLELW 65
                                   566667777788899**************99987754 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00094
                                    EEEETGGGS-HHHHHHHHHHHHHSEE CS
                Sigma54_activat  97 lfLDeigelplelQekLlrvlqegev 122
                                    +++Dei + + e+Q++Ll +++++++
  gi|118431016|ref|NP_147187.2| 118 VLVDEIRRSSEEFQNMLLDIIDKRRI 143
                                    458********************986 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   1.5e-05     0.015      20      48 ..      43      71 ..      32     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggr 48
                                    ++ +Gp+GtGKt + +al e+w+ ++  
  gi|118431016|ref|NP_147187.2| 43 PVLFEGPPGTGKTEIGEALLELWAGRKPF 71
                                   6789*******************988633 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00053      0.53      22      45 ..      41      64 ..      26      70 .. 0.81
   2 ?    4.0   0.0     0.028        28     108     163 ..     117     172 ..     108     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00053
                   Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsl 45
                                   g  +l+ GppG+GKt + ++l +l
  gi|118431016|ref|NP_147187.2| 41 GRPVLFEGPPGTGKTEIGEALLEL 64
                                   55699***********99998776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.028
                   Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevtisrakakvef.parfqlvaamNpcpcgk 163
                                    GvL +DE+   +++  ++L + ++++++++   ++ ++   + fql+++ Np   ++
  gi|118431016|ref|NP_147187.2| 117 GVL-VDEIRRSSEEFQNMLLDIIDKRRIVVPEIRRVFKArGTGFQLIMTSNPEDIAQ 172
                                    666.6*************************9988887651567********977665 PP

>> Baculo_RING  Baculovirus U-box/Ring-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05     0.015      68     119 ..     173     225 ..     119     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                    Baculo_RING  68 eekrdpy.krvikyrfeypfktleeakvllee.sktfvGdeeiievykkvlkrv 119
                                    +e  d + +rv++ rf+yp++  ee  v l+   k ++G  e+ ev  +v+ r 
  gi|118431016|ref|NP_147187.2| 173 NELSDAFlRRVVRVRFDYPPRHVEERIVRLRTeEKPLLG-AEVMEVIMRVVSRL 225
                                    555676637899****************99861566666.57888888887765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.4e-05     0.064      24      54 ..      32      62 ..      25      72 .. 0.82
   2 ?   -1.2   0.0       1.3   1.3e+03      73      90 ..     125     142 ..     122     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                          AAA_7 24 yllelllknkkpvllvGptGtGKtviikdll 54
                                   +l+   + n++pvl+ Gp GtGKt i + ll
  gi|118431016|ref|NP_147187.2| 32 TLVYAAFLNGRPVLFEGPPGTGKTEIGEALL 62
                                   5666777899**************9877766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                          AAA_7  73 tsanqlqdiiesklekrr 90 
                                     s++++q+++ + ++krr
  gi|118431016|ref|NP_147187.2| 125 RSSEEFQNMLLDIIDKRR 142
                                    68999**********998 PP

>> AAA_16  AAA ATPase 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     0.043      22      56 ..      41      75 ..      28     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekdg.gif.l 56
                                   g  + vl+ G++G+GK+ + ++ll+ + +++ +i+  
  gi|118431016|ref|NP_147187.2| 41 G--RPVLFEGPPGTGKTEIGEALLELWAGRKpFILpC 75
                                   4..56*******************9999885222233 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.4e-05     0.084      39      72 ..      30      63 ..      24      81 .. 0.82
   2 ?   -1.9   0.0       1.5   1.5e+03      94     135 ..     171     210 ..     159     251 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.4e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 39 ivelikekklaGravLlaGpsgtGktalaiaisk 72
                                   +v l+ +  l Gr vL+ Gp+gtGkt +  a+ +
  gi|118431016|ref|NP_147187.2| 30 VVTLVYAAFLNGRPVLFEGPPGTGKTEIGEALLE 63
                                   688999999*****************99877765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                                    XXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS- CS
                          TIP49  94 kktevltqalrksigvrikeekevleGevveleveeaenpls 135
                                     + e+    lr+ + vr       +e  +v l++ee  +pl 
  gi|118431016|ref|NP_147187.2| 171 AQNELSDAFLRRVVRVRFDYPPRHVEERIVRLRTEE--KPLL 210
                                    555655666788888888888888888888888753..3332 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.3e-05     0.082       6     128 ..      44     166 ..      42     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.3e-05
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..............E CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..............i 71 
                                    +l+ gp g+Gkte+ +al el     +k++i      + e     +++  +  +  +  g++e+                
  gi|118431016|ref|NP_147187.2|  44 VLFEGPPGTGKTEIGEALLELWA--GRKPFILPCSEGYDE----YKVIGDFHPQMAMKHGFNEESfvprpllaalildtG 117
                                    6899******************7..689999988888999....9*******************99*******9988888 PP

                                    EEEETGGG-------------HHHHHHHHHHHH--EE-----.--EE-TT-EE..EEEE- CS
                          AAA_2  72 vllDEidKihpkessgadvSregVqrdLLqileggtltdkqg.rkvdtknilf..Imtga 128
                                    vl+DEi + ++           + q++LL i+++ ++   +  r  + + + f  Imt++
  gi|118431016|ref|NP_147187.2| 118 VLVDEIRRSSE-----------EFQNMLLDIIDKRRIVVPEIrRVFKARGTGFqlIMTSN 166
                                    99999876655...........***********999874444355555555333377776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00071       0.7       8      34 ..      39      65 ..      34      72 .. 0.82
   2 ?    1.0   0.0      0.48   4.8e+02     105     126 ..     117     139 ..      92     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                         AAA_19  8 lkekvllvtaGpGtGKTrvlkhivall 34
                                   l+ +++l  ++pGtGKT++ ++ ++l+
  gi|118431016|ref|NP_147187.2| 39 LNGRPVLFEGPPGTGKTEIGEALLELW 65
                                   78899************9977777665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.48
                         AAA_19 105 llivDEfqdvd.elqyrLlkall 126
                                     ++vDE+   + e q+ Ll+ + 
  gi|118431016|ref|NP_147187.2| 117 GVLVDEIRRSSeEFQNMLLDIID 139
                                    589*******9667777776665 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   0.00019      0.19      13      36 ..      38      63 ..      29     111 .. 0.80
   2 ?   -1.6   0.0       1.9   1.9e+03      18      29 ..     226     237 ..     171     278 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                         AAA_11 13 alseseitliqGPPGtgKT...ktive 36
                                   +l+ +  +l++GPPGtgKT    +++e
  gi|118431016|ref|NP_147187.2| 38 FLNGRP-VLFEGPPGTGKTeigEALLE 63
                                   556666.89**********44444444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                         AAA_11  18 eitliqGPPGtg 29 
                                      + i+ +PGt 
  gi|118431016|ref|NP_147187.2| 226 RTSNISHKPGTS 237
                                    222222233333 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   0.00023      0.23       7      86 ..      46     149 ..      40     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                         AAA_24   7 iyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdieswedfldevvel...................... 59 
                                      Gp+g+GKT +   l     g kp+++ + +G+++ +++     +   ++++ ++e                       
  gi|118431016|ref|NP_147187.2|  46 FEGPPGTGKTEIGEALlelwaGRKPFILPCSEGYDEYKVIGDF--HPQMAMKHGFNEEsfvprpllaalildtgvlvdei 123
                                    56***********999999***************998887633..32333333333334555555555555555555555 PP

                         AAA_24  60 aaeladyktlviDtideleelclaevi 86 
                                    ++  ++++   +D id+  ++++ e++
  gi|118431016|ref|NP_147187.2| 124 RRSSEEFQNMLLDIIDKR-RIVVPEIR 149
                                    677777777777777765.66666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0004       0.4       1      30 [.      42      71 ..      42     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0004
                                   SCEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                          NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklp 30
                                   r+v+ +G++G GKT   + l ++wa +k++
  gi|118431016|ref|NP_147187.2| 42 RPVLFEGPPGTGKTEIGEALLELWAGRKPF 71
                                   6899*********************99864 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   0.00043      0.43      11      81 ..     203     268 ..     195     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                                    HHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                        MCM_lid  11 rekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                    r++ kP l  e++e + ++  +lR ++  s   + p t     +  R+++++A l+ ++ v+ ed  ea++
  gi|118431016|ref|NP_147187.2| 203 RTEEKPLLGAEVMEVIMRVVSRLRTSNI-S---HKPGTSE-SVAWARMAQSIAALKGRDRVSLEDLAEAAE 268
                                    6788999999999999999999999774.3...3344444.45889**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2080.79
//
Query:       gi|14600669|ref|NP_147188.1|  [L=236]
Description: hypothetical protein APE_0373 [Aeropyrum pernix K1]
Scores for complete 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-14   53.1   0.1    5.8e-07   29.7   0.0    2.2  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
    1.9e-05   24.8   0.0    2.5e-05   24.4   0.0    1.1  1  Cas_Cas4  Domain of unknown function DUF83


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   7.6e-09   6.8e-05       2      49 ..      20      68 ..      19      81 .. 0.77
   2 !   29.7   0.0   6.4e-11   5.8e-07     114     254 ..      73     198 ..      65     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.6e-09
                      PDDEXK_1  2 lSvsrletfleCplrfflryllgl.re.eeeleapdlGtlvHaaleefye 49
                                  + +srl+tf  Cp+ +f++ ++   r  +e+++ + lGt++Haa++ + +
  gi|14600669|ref|NP_147188.1| 20 IAPSRLRTFVYCPRLYFFETHMPAeRGlTERVR-MILGTVYHAAAALLDR 68
                                  789****************99999444455555.4**********88776 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 6.4e-11
                      PDDEXK_1 114 frpvalelefggekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagaly 194
                                   + ++ +e+++gg  + + Gr D    ++ge+ +++ K+g+ p k     +l++ lQ  +Y+ al + +++ ++  +++++y
  gi|14600669|ref|NP_147188.1|  73 RAEEPVEASIGG--YLIAGRPDSWRMDDGEVLVVERKSGRGP-KVGV--WLSDLLQAVAYAIALSRRSNARAA--RVKIVY 146
                                   556667777776..78*********99999**********55.5555..99999*************665544..888888 PP

                      PDDEXK_1 195 lrleepkvkdeevvkkmalteeel.eallqeleelaeeilagefparpskkCeyCpyksvC 254
                                   lr        +++++   ++      ++ ++++  ae il   +p r  +kC+ Cpy++ C
  gi|14600669|ref|NP_147188.1| 147 LRG------GSGEYSVG-EDLVYTaMRAMEDMRLAAEGIL--PYPHRSPRKCAICPYREEC 198
                                   887......44444433.2222222445555555689999..899888889*******999 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.8e-09   2.5e-05       5     161 ..      25     199 ..      22     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.8e-09
                      Cas_Cas4   5 iqyyliCkrklwlisheitleensetvel..Gkllhe.........esyerekkevelse.....sikiDvvekekeklvv 69 
                                   ++ +++C+r  ++  h    +   e+v++  G + h             +r ++ ve s       ++ D  + +++++ v
  gi|14600669|ref|NP_147188.1|  25 LRTFVYCPRLYFFETHMPAERGLTERVRMilGTVYHAaaalldrirG--SRAEEPVEASIggyliAGRPDSWRMDDGEVLV 103
                                   6789*****8777776444333344444333******8877765321..2323444442235799**************** PP

                      Cas_Cas4  70 vEvKkskkk...eeaa.klQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkv 145
                                   vE K+++      + +  lQ  +Y++ L  +++ ++ + ++ y+      e ++ e+l   + +a+++++   +   p + 
  gi|14600669|ref|NP_147188.1| 104 VERKSGRGPkvgVWLSdLLQAVAYAIALSrRSNARAARVKIVYLRGGS-GEYSVGEDLVYTAMRAMEDMRLAAEGILPYPH 183
                                   ******9884443434499**********8888888888888887665.5678999*************999988777777 PP

                      Cas_Cas4 146 kkkkiCkkCayaelCl 161
                                    + ++C  C y+e C+
  gi|14600669|ref|NP_147188.1| 184 RSPRKCAICPYREECY 199
                                   8888***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1698.16
//
Query:       gi|14600670|ref|NP_147189.1|  [L=1064]
Description: isoleucyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-178  593.5   0.0   5.1e-178  593.1   0.0    1.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.5e-29  101.7   1.0    7.2e-29  100.7   1.0    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
      1e-22   80.4   0.1      6e-08   31.8   0.0    4.1  3  tRNA-synt_1g   tRNA synthetases class I (M)
    9.2e-05   21.9   0.0      0.079   12.3   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.012   14.5   0.0      0.052   12.5   0.0    2.0  2  tRNA-synt_1f   tRNA synthetases class I (K)
      0.015   14.6   0.8        9.9    5.6   0.0    3.3  3  zf-TFIIB       Transcription factor zinc-finger
      0.044   13.3   0.0       0.17   11.4   0.0    1.9  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
       0.13   11.7   1.2       0.95    9.0   0.1    2.7  2  Mu-like_Com    Mu-like prophage protein Com
       0.63   10.5   3.5         10    6.6   0.2    3.8  3  zf-IS66        zinc-finger binding domain of transposase IS66
       0.93    9.7   5.3        1.1    9.4   1.9    2.7  2  Zn-ribbon_8    Zinc ribbon domain
        3.9    7.4  11.9        4.7    7.2   0.2    3.6  4  zf-FPG_IleRS   Zinc finger found in FPG and IleRS


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 !  593.1   0.0  3.2e-181  5.1e-178       4     602 .]      24     642 ..      22     642 .. 0.94

  Alignments for each domain:
  == domain 1  score: 593.1 bits;  conditional E-value: 3.2e-181
                   tRNA-synt_1   4 ekWeeedvfkkelekeke.kkefilvdgPPyvtG.slHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvek 82 
                                   + Wee+ +++k +ek+ +  ++f + dgPPy+   s+HiG a++k++kd+v r++rm+G++v  +pG+D++Gl+ie k+e+
  gi|14600670|ref|NP_147189.1|  24 SYWEENSIYRKVKEKSSRaPRKFYFLDGPPYASAkSIHIGTAWNKVVKDVVLRFYRMTGYNVWDKPGYDTHGLPIEVKIEQ 104
                                   57**********9999995667**********87369******************************************** PP

                   tRNA-synt_1  83 klgakek.kerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkkl 162
                                    lg + k +  +k+g+e+f++ ++ +++e +e +++q+k++Gv +D++++y+T  +e+ e+ ++  ++  +kgl+y+g ++
  gi|14600670|ref|NP_147189.1| 105 SLGVRVKrEIEEKVGVENFIAACKRFVDENMEAMTRQFKEIGVFMDWENPYVTYRDEYIESGWWLVKKAWEKGLLYKGYRV 185
                                   ***8865156789******************************************************************** PP

                   tRNA-synt_1 163 vnwstklktalselEv.eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...itkeklilaeal 239
                                   ++w+++++t+l++ Ev ey++ +d++i+v+fp+++ e  +l ++TTtP+Tl+++  v  +p+++yv   +  ++lila+a+
  gi|14600670|ref|NP_147189.1| 186 LHWCPRCETTLADYEVsEYRELEDPSIYVKFPVEGREGEYLLVWTTTPWTLPANAFVMAHPDMEYVkvrVGRDTLILAKAR 266
                                   ******************************************************************9988899******** PP

                   tRNA-synt_1 240 lkslvkke..sekkiledergkeLegkevelpl..........vnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                   l+ ++++   se+++le  +g++Leg+++++pl           + + +++a + v+  +G+G+V+ aP+h++ Dye++++
  gi|14600670|ref|NP_147189.1| 267 LDHVMREAgvSEYEVLEVLKGSQLEGLRYRHPLedvvdaqrelSKWHKVVMAPEAVTPHEGSGLVHSAPGHGTIDYEIAQR 347
                                   *****99886667***********************99888755555566777**************************** PP

                   tRNA-synt_1 309 ynlevinildedgtlteeaaefeglk.vfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkela 388
                                    + +v++ +de g +te a++++gl+ + +a+k++ve+l+++g+l++a +i h +p+c+r k+p++ rat+qWfv v++l+
  gi|14600670|ref|NP_147189.1| 348 IGAPVVSLVDERGFMTEAAGKYSGLYfRGEANKAIVEDLRARGALFHAATIVHRYPVCWRCKTPLLLRATTQWFVAVTRLK 428
                                   ************************984679*************************************************** PP

                   tRNA-synt_1 389 daalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekea 469
                                   ++++++ ekv++ p ++++r++++l++ +dW+iSRqr+WG ++p+++ ++ + ++v+ +++el+    +  ++ ++l++  
  gi|14600670|ref|NP_147189.1| 429 NQLMREAEKVEWQPGWAKTRFMNMLRELRDWVISRQRYWGIPLPVWRCSSCGYEHVVGSVEELES---MGGRRPENLHRPW 506
                                   ****************************************************9999776666655...7777777777777 PP

                   tRNA-synt_1 470 kdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgseP 546
                                   +d++     +  g++++++dvlDvWF+Sg  ++++lgyp   +e  ++  p d+++eG D+irgW+ +l+  ++  +g++P
  gi|14600670|ref|NP_147189.1| 507 VDRVelkcPRCGGSMKRVPDVLDVWFDSGIAFYASLGYPRD-RETWERLKPVDFIVEGHDQIRGWFFSLLRSGVIGFGETP 586
                                   7777664445569**************************99.9999*********************************** PP

                   tRNA-synt_1 547 fkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdinls 602
                                   +++vlvhg+ +de+Gr m KslgN++d +++i k+  d++R+++++++v +d+++s
  gi|14600670|ref|NP_147189.1| 587 YRRVLVHGFALDEQGREMHKSLGNYVDFEELIAKVPRDVVRFWVLQNTVWEDLRFS 642
                                   *************************************************9999885 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 !  100.7   1.0   4.4e-32   7.2e-29       1     151 [.     690     843 ..     690     844 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 4.4e-32
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPf 80 
                                   drwils+l++l +++  a+e++r+++aa+al +f+++d++ wyl+++++r + e ++++++ a+++l++vl ++l + aP 
  gi|14600670|ref|NP_147189.1| 690 DRWILSRLASLKRRYLTAMEDLRIHDAARALRSFIIEDVSHWYLRIIRRRVWEEVDTPSKRaAYATLYKVLWEWLLMAAPL 770
                                   9*****************************************************99999555******************* PP

                   Anticodon_1  81 mPfitEelwqr...eeeelgkkesimlaewpekaeel..ekeleeeevellkeivkairklrselkikpsselkvv 151
                                   +P+++E+l+ +   e  e   +esi++ ++pe +e++  + +l ee++e ++ +++ai ++r+e ++k + +++ v
  gi|14600670|ref|NP_147189.1| 771 IPYTAEYLYIKvfrE-AEERPEESIHMLDMPE-PEDHliDSTL-EEDMEKARMVLEAILSARNEAGLKLRRPVRRV 843
                                   *********777853.344678*********7.4344467777.99**********************99998876 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 !   31.8   0.0   3.7e-11     6e-08       8     135 ..      53     201 ..      51     204 .. 0.75
   2 !   19.3   0.0   2.4e-07   0.00039     167     238 ..     403     472 ..     378     484 .. 0.84
   3 !   23.0   0.0   1.8e-08   2.9e-05     244     370 ..     527     645 ..     511     656 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.7e-11
                                   B--SS.---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH...........HTTS-H.......HHHHHH CS
                  tRNA-synt_1g   8 pYang.klHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe...........kegvtp.......eelvek 69 
                                   pYa++ ++H+G + + +  D++ R+ r++g++v+   g D+hG pie+k e           +e+v +       + +v++
  gi|14600670|ref|NP_147189.1|  53 PYASAkSIHIGTAWNKVVKDVVLRFYRMTGYNVWDKPGYDTHGLPIEVKIEqslgvrvkreiEEKVGVenfiaacKRFVDE 133
                                   67765269***************************************9986222222222223344441111111456677 PP

                                   HHHHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                  tRNA-synt_1g  70 vheeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                   + e+++++fk++++  d  + + t  +e  e    ++kk  ekgl+y++     +cp++e++l+d +v
  gi|14600670|ref|NP_147189.1| 134 NMEAMTRQFKEIGVFMDweNPYVTYRDEYIESGWWLVKKAWEKGLLYKGYRVLHWCPRCETTLADYEV 201
                                   77888888999888655325667888888889999999999999999999999999999999999877 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.4e-07
                                   ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                  tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                   p++  +++   ++ t+++f  + +++++l +   e+ + ++  +k+   ++l+e L+d+ isr+  wGip+P
  gi|14600670|ref|NP_147189.1| 403 PVCWRCKTPLLLRATTQWFVAVTRLKNQLMREA-EKVEWQPGWAKTRFMNMLRE-LRDWVISRQRYWGIPLP 472
                                   89999*9999*******************9987.44433555677778899998.***************99 PP

  == domain 3  score: 23.0 bits;  conditional E-value: 1.8e-08
                                   EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEE..EGGGHHHHHTHHHHHHHH...TT----S-EEEE- CS
                  tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfi..gkdiikFHtifwPaillg...aelklpkkvvahe 319
                                   vl VW+d  i + +++++      + e+w++          v fi  g d i+    f+  +  g    + +  ++v +h+
  gi|14600670|ref|NP_147189.1| 527 VLDVWFDSGIAFYASLGYPR----DRETWERLK-------PVDFIveGHDQIR--GWFFSLLRSGvigFGETPYRRVLVHG 594
                                   67799999999999999986....456676554.......4666633666665..55555554444438888999****** PP

                                   -.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHH CS
                  tRNA-synt_1g 320 y.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswed 370
                                   + l  +g+ + kS g+ v+ +e++ +++ d++R+++++++   +Dl fsw+ 
  gi|14600670|ref|NP_147189.1| 595 FaLDEQGREMHKSLGNYVDFEELIAKVPRDVVRFWVLQNTV-WEDLRFSWKG 645
                                   *5567899***************************998765.689****985 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 !    6.9   0.0    0.0021       3.5      22      48 ..      59      85 ..      48      88 .. 0.93
   2 !   12.3   0.0   4.8e-05     0.079     236     293 ..     586     643 ..     579     650 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0021
                                  --BHHHHHHHHHHHHHHHHHHHTT-EE CS
                  tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdv 48
                                   +h+G a + v+ D++ r+ +++gY+v
  gi|14600670|ref|NP_147189.1| 59 SIHIGTAWNKVVKDVVLRFYRMTGYNV 85
                                  68***********************98 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.8e-05
                                   --EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-H CS
                  tRNA-synt_1e 236 qlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfke 293
                                   ++ +  +h   l  +g+ m ksL+n++  ++++ k+   ++R+ +l++   + l f+ 
  gi|14600670|ref|NP_147189.1| 586 PYRRVLVHGFALDEQGREMHKSLGNYVDFEELIAKVPRDVVRFWVLQNTVWEDLRFSW 643
                                   56667788888899999*****************************999888888875 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 ?   -2.2   0.0       0.9   1.5e+03     104     138 ..     127     161 ..     122     167 .. 0.88
   2 ?   12.5   0.0   3.2e-05     0.052     271     322 ..     593     644 ..     557     663 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.9
                  tRNA-synt_1f 104 hesyaehfnaelvesLdelgievefisatelYksg 138
                                   ++ +++ + +++ ++ +e+g+ +++ +   +Y++ 
  gi|14600670|ref|NP_147189.1| 127 CKRFVDENMEAMTRQFKEIGVFMDWENPYVTYRDE 161
                                   789**********************9999999886 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.2e-05
                  tRNA-synt_1f 271 YelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                     + l+++g++m++S Gn++  e+++  ++++v+rf +l++   + ++++ +
  gi|14600670|ref|NP_147189.1| 593 HGFALDEQGREMHKSLGNYVDFEELIAKVPRDVVRFWVLQNTVWEDLRFSWK 644
                                   5577899999******************************888777777765 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0061       9.9       2      16 ..     189     203 ..     188     206 .. 0.91
   2 ?   -0.9   0.1      0.66   1.1e+03      18      26 ..     472     480 ..     470     480 .. 0.87
   3 ?    5.3   0.0    0.0073        12       1      10 [.     513     522 ..     513     536 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0061
                      zf-TFIIB   2 CPkCqdeleesergg 16 
                                   CP+C ++l ++e+++
  gi|14600670|ref|NP_147189.1| 189 CPRCETTLADYEVSE 203
                                   **********99986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.66
                      zf-TFIIB  18 eidyCpqCr 26 
                                   ++++C +C+
  gi|14600670|ref|NP_147189.1| 472 PVWRCSSCG 480
                                   899*****7 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0073
                      zf-TFIIB   1 kCPkCqdele 10 
                                   kCP+C+ +++
  gi|14600670|ref|NP_147189.1| 513 KCPRCGGSMK 522
                                   7999999987 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 ?   -2.3   0.0       1.7   2.7e+03      52      85 ..     114     149 ..     106     153 .. 0.67
   2 ?   11.4   0.0    0.0001      0.17      11     144 ..     213     360 ..     209     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                 tRNA-synt_1_2  52 aekkkelaafieevkk..ksesereletkekeGvft 85 
                                    e+k  +++fi+ +k+  ++++e+++++ +  Gvf 
  gi|14600670|ref|NP_147189.1| 114 IEEKVGVENFIAACKRfvDENMEAMTRQFKEIGVFM 149
                                   567778999**9999832344455555555667765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0001
                 tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplveklaekkkel..aafieev.kkksesereletkekeGvftgl 87 
                                    ++f+ve++  e l v+tt p tl    fv+  p+ + v+    ++  +  +a +++v ++   se e+ +  k    +gl
  gi|14600670|ref|NP_147189.1| 213 YVKFPVEGReGEYLLVWTTTPWTLPANAFVMAHPDMEYVKVRVGRDTLIlaKARLDHVmREAGVSEYEVLEVLKGSQLEGL 293
                                   689****996689*************************99885555444224445555045555666666666666699** PP

                 tRNA-synt_1_2  88 kaihPitgek..........ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikped 144
                                      hP+++              +   + v  + g+g v + P+h + D+e a++ + p+   + +++
  gi|14600670|ref|NP_147189.1| 294 RYRHPLEDVVdaqrelskwhKVVMAPEAVTPHEGSGLVHSAPGHGTIDYEIAQRIGAPVVSLVDERG 360
                                   *****98544455676666444667799******************************999998654 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 ?   -0.3   0.1      0.46   7.5e+02      27      32 ..     189     194 ..     185     197 .. 0.86
   2 ?    9.0   0.1   0.00058      0.95      21      31 ..     508     518 ..     506     522 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.46
                   Mu-like_Com  27 CPRCGt 32 
                                   CPRC t
  gi|14600670|ref|NP_147189.1| 189 CPRCET 194
                                   ****87 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00058
                   Mu-like_Com  21 DeltiKCPRCG 31 
                                   D +++KCPRCG
  gi|14600670|ref|NP_147189.1| 508 DRVELKCPRCG 518
                                   8899******9 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 ?    1.1   0.0      0.34   5.5e+02       4      22 ..     189     204 ..     183     215 .. 0.57
   2 ?    0.1   0.1      0.66   1.1e+03      38      46 .]     472     480 ..     471     492 .. 0.71
   3 ?    6.6   0.2    0.0061        10       3      16 ..     513     526 ..     511     528 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                       zf-IS66   4 CpcCGgllkpigedrvree 22 
                                   Cp C ++l  +  + v+e 
  gi|14600670|ref|NP_147189.1| 189 CPRCETTL--ADYE-VSEY 204
                                   77777643..3333.5554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.66
                       zf-IS66  38 pkyaCpcCe 46 
                                   p+++C++C+
  gi|14600670|ref|NP_147189.1| 472 PVWRCSSCG 480
                                   567777775 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0061
                       zf-IS66   3 tCpcCGgllkpige 16 
                                   +Cp CGg +k++++
  gi|14600670|ref|NP_147189.1| 513 KCPRCGGSMKRVPD 526
                                   7*******999976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.1   1.8e+03      29      35 ..     189     195 ..     184     197 .. 0.74
   2 ?    9.4   1.9   0.00067       1.1       7      39 ..     475     524 ..     473     525 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                   Zn-ribbon_8  29 CPeCgse 35 
                                   CP+C  +
  gi|14600670|ref|NP_147189.1| 189 CPRCETT 195
                                   ****865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00067
                   Zn-ribbon_8   7 rCeeCghefe.....vlqsis.dap...........ltaCPeCgsevrrv 39 
                                   rC +Cg e+      +l s+  ++p           + +CP+Cg+ ++rv
  gi|14600670|ref|NP_147189.1| 475 RCSSCGYEHVvgsveELESMGgRRPenlhrpwvdrvELKCPRCGGSMKRV 524
                                   788888766677777677776655567777777776888********997 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 ?    7.2   0.2    0.0029       4.7      19      28 ..     184     193 ..     182     197 .. 0.86
   2 ?   -0.7   0.0      0.83   1.4e+03       8      20 ..     296     308 ..     296     309 .. 0.89
   3 ?   -3.3   1.3       5.4   8.9e+03       6       9 ..     404     407 ..     403     412 .. 0.55
   4 ?    6.5   0.3    0.0045       7.4       3      13 ..     513     523 ..     511     524 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0029
                                   EEEEE-TTTT CS
                  zf-FPG_IleRS  19 rstyfCprCq 28 
                                   r  ++CprC 
  gi|14600670|ref|NP_147189.1| 184 RVLHWCPRCE 193
                                   6689*****6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.83
                                   --BBEEEECTTEE CS
                  zf-FPG_IleRS   8 wryiervgqagrs 20 
                                   ++++e+v+ a+r 
  gi|14600670|ref|NP_147189.1| 296 RHPLEDVVDAQRE 308
                                   689********96 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 5.4
                                   TT-- CS
                  zf-FPG_IleRS   6 RCwr 9  
                                   +Cwr
  gi|14600670|ref|NP_147189.1| 404 VCWR 407
                                   5554 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0045
                                   B-TTT--BBEE CS
                  zf-FPG_IleRS   3 pCpRCwryier 13 
                                   +CpRC++  +r
  gi|14600670|ref|NP_147189.1| 513 KCPRCGGSMKR 523
                                   9*****87666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1064 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); 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):              11  [number of targets reported over threshold]
# CPU time: 0.84u 0.29s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 6784.72
//
Query:       gi|118431017|ref|YP_874818.1|  [L=85]
Description: hypothetical protein APE_0374a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 634.81
//
Query:       gi|14602188|ref|NP_147191.1|  [L=142]
Description: hypothetical protein APE_0381.1 [Aeropyrum pernix K1]
Scores for complete 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   34.4   0.1    2.5e-08   33.5   0.1    1.5  1  ACT             ACT domain
    2.7e-05   24.1   0.0    4.9e-05   23.2   0.0    1.4  1  MraZ            MraZ protein, putative antitoxin-like
    4.3e-05   23.3   0.2    7.5e-05   22.6   0.2    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    6.8e-05   22.8   0.1    0.00014   21.8   0.1    1.6  1  ACT_6           ACT domain
     0.0023   18.5   0.0     0.0043   17.6   0.0    1.5  1  ACT_4           ACT domain
  ------ inclusion threshold ------
      0.015   15.5   0.2       0.14   12.4   0.0    2.1  2  CDC48_N         Cell division protein 48 (CDC48), N-terminal 
      0.048   13.5   0.1       0.11   12.3   0.0    1.6  2  ACT_7           ACT domain
       0.06   13.8   0.0       0.11   13.0   0.0    1.5  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin


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 !   33.5   0.1   1.1e-11   2.5e-08       2      63 ..      59     125 ..      58     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.1e-11
                                   EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT.....ECEEEEEEEEEEHHHHHHHHHHHH CS
                           ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedk.....vagivfvvivvdeedleevlealk 63 
                                   v+   ++DrPG+La+v+ +la++ i i+    +s  ++          f+   +d+edl+  le+l 
  gi|14602188|ref|NP_147191.1|  59 VIDATLRDRPGALAAVTEVLARHKIDIVASKCASIVRGeeggcTIIADFSRADIDPEDLKRELERLD 125
                                   677789********************************99888888888888888888888888875 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.2e-08   4.9e-05       8      39 ..       8      41 ..       4      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.2e-08
                                  EEB-TTSEEE--CHHHHHTTSC..SEEEEEECCS CS
                          MraZ  8 velDakGRlllPaklreeakle..kevvviGvsn 39
                                  v++D+kGR+++P++ r +++ e  ++v++iG  n
  gi|14602188|ref|NP_147191.1|  8 VKVDSKGRVTIPQSIRSALGIEpgMVVLLIGDVN 41
                                  899*******************999999999766 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 !   22.6   0.2   3.3e-08   7.5e-05       1      30 [.       8      37 ..       8      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.3e-08
                                  EEETTEEEEEE-CCCHHHCCEECTCEEEEE CS
                MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevele 30
                                  +kv+++g+v+iP  +r +lgi++G  v l+
  gi|14602188|ref|NP_147191.1|  8 VKVDSKGRVTIPQSIRSALGIEPGMVVLLI 37
                                  69*********************9888776 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   6.1e-08   0.00014       4      64 ..      59     123 ..      56     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 6.1e-08
                         ACT_6   4 litvtGpdrpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgp....edalarlekaLlf 64 
                                   +i +t  drpG +a++t+vla+++++i+ ++ a i +    g  + ++    + + + l+++L++
  gi|14602188|ref|NP_147191.1|  59 VIDATLRDRPGALAAVTEVLARHKIDIVASKCASIVRGEEGGCTIIADfsraDIDPEDLKRELER 123
                                   8999999************************9999543333333333333325566666666666 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0043       9      39 ..      60      90 ..      56     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                         ACT_4  9 leveaedrkglLaditqviseekanivsvna 39
                                  ++ + +dr+g+La +t+v++ +k++iv+ + 
  gi|14602188|ref|NP_147191.1| 60 IDATLRDRPGALAAVTEVLARHKIDIVASKC 90
                                  78899*********************98775 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 ?   12.4   0.0   6.1e-05      0.14      13      66 ..      12      64 ..       5      70 .. 0.77
   2 ?    0.9   0.0      0.23   5.1e+02      15      35 ..     108     127 ..     104     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                                  STTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHH CS
                       CDC48_N 13 grgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvt 66
                                   +g+v i ++  ++lg+epg+vv + g  +k   i+ p+      + i  +d+ +
  gi|14602188|ref|NP_147191.1| 12 SKGRVTIPQSIRSALGIEPGMVVLLIGdVNKRELIATPITSRS--ESIYVIDATL 64
                                  5899***********************6555777777776553..4555555555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.23
                                   TEEEE-HHHHHHHTS-TTSEE CS
                       CDC48_N  15 givridpedmeelglepgdvv 35 
                                   +++ idped+++ +le+ dvv
  gi|14602188|ref|NP_147191.1| 108 SRADIDPEDLKR-ELERLDVV 127
                                   67889******9.99999998 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.8   6.3e+03       7      24 ..      18      33 ..      15      37 .. 0.72
   2 ?   12.3   0.0     5e-05      0.11      19      41 ..      66      88 ..      55      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                                  EEEEE-S-.---SS--HH CS
                         ACT_7  7 iklsvvgsglpfdvtGiv 24
                                  i+ s+ ++ l +  +G+v
  gi|14602188|ref|NP_147191.1| 18 IPQSIRSA-LGI-EPGMV 33
                                  56677777.777.78876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5e-05
                                  SS--HHHHHHHHHHTTT---EEE CS
                         ACT_7 19 dvtGivaklaspLaeagIsifqi 41
                                  d +G +a+++++La+++I i ++
  gi|14602188|ref|NP_147191.1| 66 DRPGALAAVTEVLARHKIDIVAS 88
                                  59*****************9876 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 ?   13.0   0.0   4.8e-05      0.11       3      26 ..       9      32 ..       8      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.8e-05
                PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgr 26
                                  ++ ++g  tiP+s+R aL++++g 
  gi|14602188|ref|NP_147191.1|  9 KVDSKGRVTIPQSIRSALGIEPGM 32
                                  577899**************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1083.73
//
Query:       gi|14600672|ref|NP_147192.1|  [L=229]
Description: hypothetical protein APE_0382 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-18   66.8   0.1    3.1e-18   66.5   0.1    1.1  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   1.7e-22   3.1e-18       8     195 ..      17     194 ..      10     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.7e-22
                                   EEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                   Lactamase_B   8 syliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                   + l + +g  +L+DtG++++ +  al  +la++g+kp  +   i++H+H+   Gg+++l + + v ++a + + ++ ++  
  gi|14600672|ref|NP_147192.1|  17 VLLARVGGCSVLYDTGSGEPGSIVALaaNLASAGVKPWSINVAIVSHAHVPSSGGARWLHDNHRVTIAARRPDSRWIEEGD 97 
                                   5566789999*********************************************************************** PP

                                   HHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCE CS
                   Lactamase_B  87 addaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrga 167
                                   + + a  + +l+  +++++ +  +e++  ++ +++++ +t+g+++g+++++++ g+++vl + Dal + ++ +++      
  gi|14600672|ref|NP_147192.1|  98 PVKTAAVDYGLPTKPVPIGLELEREGRMPGECEGVEVLFTPGHTPGSVSVSLDTGDATVLAVSDALGRLKRDWGSS----- 173
                                   *9999999999********************************************************888888888..... PP

                                   EE-SHCHHHHHHHHHHHHHHHCHSEEEE CS
                   Lactamase_B 168 evrdpsdaekyldsllklaglkaevlvp 195
                                           +++++sl+k+   ++++l++
  gi|14600672|ref|NP_147192.1| 174 -------EREWMESLDKISSRDPDYLCT 194
                                   .......999999999999****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1683.55
//
Query:       gi|118431018|ref|NP_147193.2|  [L=158]
Description: hypothetical protein APE_0383.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-32  110.9   3.4      3e-15   56.4   0.1    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 !   55.3   0.7   3.6e-19   6.4e-15       1      55 [.      12      66 ..      12      68 .. 0.96
   2 !   56.4   0.1   1.7e-19     3e-15       1      54 [.      78     132 ..      78     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 3.6e-19
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   V+dim+++++t  p t+++ea+++m e++v++l VV+e + l+Gi+t++D++r +
  gi|118431018|ref|NP_147193.2| 12 VRDIMSSPPITTLPMTSVKEAAKIMLENRVGSLIVVNERNTLLGILTKTDIIREV 66
                                   89*******************************999****************987 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 1.7e-19
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                                    Vgdimtr++ +v+ d+++e a+ lm e+++++lPV+ +e +k+vGivt++D++++
  gi|118431018|ref|NP_147193.2|  78 VGDIMTRNPYYVYTDDSVERAASLMGEHNIGHLPVLdPETEKPVGIVTKTDIVKL 132
                                    89**********************************766669**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1271.88
//
Query:       gi|14600674|ref|NP_147194.1|  [L=369]
Description: hypothetical protein APE_0384 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2454.28
//
Query:       gi|118431019|ref|NP_147195.2|  [L=543]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-40  137.5   1.7    6.7e-40  136.7   1.7    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    2.3e-17   63.0   0.1    5.1e-17   61.9   0.0    1.6  2  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.7e-08   34.9   2.0    3.5e-08   33.8   0.2    2.2  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    4.8e-08   33.1   0.1    2.7e-07   30.6   0.0    2.1  2  AidB_N         Adaptive response protein AidB N-terminal doma
  ------ inclusion threshold ------
      0.026   14.8   0.3      0.051   13.8   0.3    1.4  1  DUF4142        Domain of unknown function (DUF4142)
      0.057   14.0   0.3       0.59   10.8   0.1    2.3  2  PrmC_N         PrmC N-terminal domain
       0.13   12.5   0.1        1.6    9.0   0.0    2.3  2  DUF4798        Domain of unknown function (DUF4798)


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 !  136.7   1.7   2.6e-43   6.7e-40       1     149 [.     272     431 ..     272     432 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 2.6e-43
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    +kG+++++e l+ +R+a+ a+a+g+ar+a+ ea++ya++r+afgk++i+h+lvr+ l em++ +e + +l+ +a+ ++++
  gi|118431019|ref|NP_147195.2| 272 DKGIYYTLEDLMISRIANSAGAVGIARKAYLEAYNYAKHRRAFGKRIIEHPLVRRDLLEMEVLIEESLALTHKAVDLFEK 351
                                    58*****************************************************************************9 PP

                                    ----...........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd...........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                     + d           r  +++aK++++++a +v+ lam+l+Gg G+l+ey+ver++r+a++++i+eGts+iq +++ +++
  gi|118431019|ref|NP_147195.2| 352 STGDrppysmtyhyaRLMTHIAKNMTAQAAARVTMLAMELFGGIGFLREYAVERWHREALITPIWEGTSNIQALDMLEAM 431
                                    999999*******************************************************************9998876 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 !   61.9   0.0     2e-20   5.1e-17       1      96 [.     162     262 ..     162     263 .. 0.89
   2 ?   -3.7   0.0       5.5   1.4e+04      42      66 ..     365     389 ..     362     396 .. 0.65

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2e-20
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS-------EEEEEEE..GG....GEEE CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpdrarglslflvprdap....gvsv 75 
                                    a+++TE q+Gsd+ +++t a +  +g + l+G K + ++a+ a++alv ar ++ p++a+glslf+vpr +     + sv
  gi|118431019|ref|NP_147195.2| 162 ATWFTEIQGGSDLGANETVARKAGDGVWLLTGYKYFASGAGLADIALVTARpEGAPAGAKGLSLFAVPRYRRggglNYSV 241
                                    5789**************887777779************************7555559**********666666788899 PP

                                    -----BSS-TTS-EEEEEEE. CS
                  Acyl-CoA_dh_M  76 rrieeklGlrglptgelvfed 96 
                                    rr+++k G+  +ptge++++d
  gi|118431019|ref|NP_147195.2| 242 RRLKDKSGTIAVPTGEVELQD 262
                                    *****************9987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.5
                                    T-SEEEEEEETS---.----EEEEEE CS
                  Acyl-CoA_dh_M  42 iatlalvlartekpd.rarglslflv 66 
                                    +a l++ +a+ ++++ +a ++++++ 
  gi|118431019|ref|NP_147195.2| 365 YARLMTHIAK-NMTAqAAARVTMLAM 389
                                    5778888888.333334677777765 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.2   1.4e-11   3.5e-08       4     131 ..     290     418 ..     287     421 .. 0.83
   2 ?   -0.1   0.1      0.42   1.1e+03      47      65 ..     457     475 ..     429     497 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.4e-11
                                    HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHH CS
                  Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraea 83 
                                    +a a+G+Ar a+ e+  +a++r    +g+++ ++p +   l e++  ++   al+++a++  e+   ++ +++  +   a
  gi|118431019|ref|NP_147195.2| 290 SAGAVGIARKAYLEAYNYAKHRRA--FGKRIIEHPLVRRDLLEMEVLIEESLALTHKAVDLFEKSTGDRPPYS-MTYHYA 366
                                    6889*******************9..***********************************887655555553.344444 PP

                                    HHH....HHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGG CS
                  Acyl-CoA_dh_2  84 rra....aalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaa 131
                                    r+     + ++++ a++++  ++e++Gg + + e+ ++R  R+a ++ ++++
  gi|118431019|ref|NP_147195.2| 367 RLMthiaKNMTAQAAARVTMLAMELFGGIGFLREYAVERWHREALITPIWEG 418
                                    4442222777777788888889*********************988766665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.42
                                    HHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2  47 aaarldAAralleraaara 65 
                                    a+ +++AA+++++r a+  
  gi|118431019|ref|NP_147195.2| 457 ASKAVEAAEETVRRLASMS 475
                                    4556666666666665543 PP

>> AidB_N  Adaptive response protein AidB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   1.1e-10   2.7e-07       8     136 ..      15     138 ..      10     154 .. 0.83
   2 ?   -1.5   0.1      0.82   2.1e+03     120     149 ..     354     384 ..     348     388 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.1e-10
                         AidB_N   8 dvnlfasdpaLqeavaregaaeaaeelaalGellgsaevlelarlanrnp.PrlrthDrfGrRiDevefhpayhalmaaa 86 
                                      n +  d++L++ ++   ++  + +la lGe++g+ e++e a +++r + P+   +  +G+R D+v  +pa ++ +++ 
  gi|118431019|ref|NP_147195.2|  15 GLNHYLVDKPLRDTLRYFTSK--EPDLAGLGEYVGT-ELYEVAYRVDRLSwPVHVMWSVRGERSDTVLVDPALRRAVDRL 91 
                                    5799************88765..78***********.999999999886449**********************999765 PP

                         AidB_N  87 v.eaglhasaweearegahvaraallyllaqveaGhlCPltmThAavpaL.k 136
                                    + e+g++ +++     g++ +++a + l+ +  +G+ C lt T   + aL k
  gi|118431019|ref|NP_147195.2|  92 MyEYGVNRHPYV---GGSWHEHFAGINLVGD--PGVGCILTITMQTAYALwK 138
                                    4399********...799**********986..8888888888766666645 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.82
                         AidB_N 120 GhlCPltmThAavpaL.kaepalaeewlpkl 149
                                    G   P +mT+  ++++ + +++++++ + ++
  gi|118431019|ref|NP_147195.2| 354 GDRPPYSMTYHYARLMtHIAKNMTAQAAARV 384
                                    6666899999988888666777777776665 PP

>> DUF4142  Domain of unknown function (DUF4142)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     2e-05     0.051      71     120 ..     436     485 ..     423     493 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                        DUF4142  71 eaqakldkLkalsgaaFDkaYleaqvaahqkavellekaaasgkdaelka 120
                                    +++  l++L+al+g+a+Dk  ++++v+a +++v+ l ++++s+++   k 
  gi|118431019|ref|NP_147195.2| 436 AHKPLLEDLRALAGDAYDKGLASKAVEAAEETVRRLASMSPSQAEFNAKY 485
                                    677889******************************99998887766655 PP

>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.35   9.1e+02      19      56 ..     328     387 ..     315     395 .. 0.71
   2 ?   10.8   0.1   0.00023      0.59       1      60 [.     462     526 ..     462     531 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.35
                         PrmC_N  19 eldAelLlahvlglsrs......................dlllrgerelteeqlerfeel 56 
                                     l+ e+L++++l l+                        +l+++  + +t+++++r++ l
  gi|118431019|ref|NP_147195.2| 328 LLEMEVLIEESLALTHKavdlfekstgdrppysmtyhyaRLMTHIAKNMTAQAAARVTML 387
                                    567788888888776666666666666666666666666778888888888888877665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                         PrmC_N   1 eaLreaearLkaagieeaeldAelLlahvlglsrsdlllrgerelteeqler.....feelierR 60 
                                    ea +e  +rL++   ++ae++A++ l+++ + s++ +l ++   l ee ++      +++l++rR
  gi|118431019|ref|NP_147195.2| 462 EAAEETVRRLASMSPSQAEFNAKYALEDLGHASSTVILENMAAVLGEERYHYvaeivYNSLLQRR 526
                                    57788999*****************************************9972233366666665 PP

>> DUF4798  Domain of unknown function (DUF4798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00063       1.6      38      74 ..      22      58 ..      18      61 .. 0.92
   2 ?    0.4   0.0      0.29   7.4e+02      30      50 ..     297     317 ..     293     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00063
                        DUF4798 38 ekyyrHrrRYyqlmEKrlkaLgravskllkqlAtrld 74
                                   +k  r   RY+  +E  l +Lg+ v+  l ++A r+d
  gi|118431019|ref|NP_147195.2| 22 DKPLRDTLRYFTSKEPDLAGLGEYVGTELYEVAYRVD 58
                                   57778899*************************9987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.29
                        DUF4798  30 arkelsekekyyrHrrRYyql 50 
                                    ark  +e   y +Hrr + ++
  gi|118431019|ref|NP_147195.2| 297 ARKAYLEAYNYAKHRRAFGKR 317
                                    688899999999999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3932.70
//
Query:       gi|14600676|ref|NP_147196.1|  [L=160]
Description: acetyltransferase [Aeropyrum pernix K1]
Scores for 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   55.3   0.1    8.8e-15   55.0   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.3e-10   41.6   0.1    2.1e-10   40.9   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.5e-10   39.6   0.1    5.5e-10   39.3   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.2e-07   31.8   0.1    1.6e-07   31.5   0.1    1.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      3e-07   30.3   0.1    4.7e-07   29.7   0.1    1.4  1  FR47             FR47-like protein
    0.00045   20.4   0.2    0.00054   20.1   0.2    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00058   19.9   0.0    0.00093   19.3   0.0    1.5  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.018   14.7   0.1      0.032   14.0   0.1    1.4  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
      0.025   15.3   0.0      0.029   15.1   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.043   14.0   0.3      0.071   13.3   0.3    1.5  1  Acetyltransf_6   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.1   4.9e-18   8.8e-15      15     117 .]      42     148 ..      18     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 4.9e-18
                                   HHHHHHHHH.HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHH CS
                Acetyltransf_1  15 pnedaseee.feesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerare 91 
                                   ++ +a+ e+ f+e +s++ ++++va++++ l+Gfi++  ++      + +a+i +++V+p yr++ +G++L ++++e+ar+
  gi|14600676|ref|NP_147196.1|  42 EDIRAEAERyFRETLSDDKSFIIVAQHGEGLAGFIRVELVDRrfyKPRIKAVITDIYVKPRYRRRAIGQLLTQKAAEEARR 122
                                   333444444677779999999999*********************7899******************************** PP

                                   TTESEE.EEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  92 egikki.vlaveedndaairlYeklGF 117
                                   +g+  +  l+   +n  a r+Y +lGF
  gi|14600676|ref|NP_147196.1| 123 RGAGMMsALYP-ITNYVAKRFYSQLGF 148
                                   *9977646666.669*******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 !   40.9   0.1   1.2e-13   2.1e-10       3      76 .]      61     150 ..      58     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.2e-13
                                   EEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.H.TT.....SEEEEE.EEEE.THHHH CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.a.ae.....kgiile.qlel.naeka 65 
                                   + ++Va+++++  Gfi+++l+d         a it ++V+p yr++ iG+ L + a +e      g+     l+  ++  a
  gi|14600676|ref|NP_147196.1|  61 SFIIVAQHGEGLAGFIRVELVDrrfykprikAVITDIYVKPRYRRRAIGQLLTQkAaEEarrrgAGM--MsALYPiTNYVA 139
                                   557899999***************999888777777*****************94342245533332..222222333379 PP

                                   HHHHHHTTEEE CS
                Acetyltransf_7  66 ikfYeklGFee 76 
                                    +fY +lGF+e
  gi|14600676|ref|NP_147196.1| 140 KRFYSQLGFRE 150
                                   99*******96 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.1   3.1e-13   5.5e-10      20     110 ..      50     152 ..      19     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 3.1e-13
               Acetyltransf_10  20 ealrerieegealllvaeeggkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekdgikl..e 88 
                                     +re +++ + +++va  g+ ++G+i++   ++          i+ ++V+p yr++ ig+ L +++ eea+++g +   +
  gi|14600676|ref|NP_147196.1|  50 RYFRETLSDDKSFIIVAQHGEGLAGFIRVeLVDRrfykprikaVITDIYVKPRYRRRAIGQLLTQKAAEEARRRGAGMmsA 130
                                   346777789999***************6643333479**99999******************************9999955 PP

               Acetyltransf_10  89 ltvnaspyavpfYeklGFkavg 110
                                   l    +  a++fY +lGF++ +
  gi|14600676|ref|NP_147196.1| 131 LYPITNYVAKRFYSQLGFREFQ 152
                                   55566669**********9875 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   8.8e-11   1.6e-07       7     126 ..      14     149 ..       9     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 8.8e-11
                                   GGGHHHHHHH..HHHHTT----H..........HHHHHHHHHHTTS..EEEEEEETTEEEEEEEEEEEEEEETTEEEEEEE CS
                Acetyltransf_9   7 eedldevlel..lkyaFqdeespl.......e.eireyfrkllees..rvlgaedngelvgqlallplelnvpGktlkaag 75 
                                   e+d  e++++   ++ F++e +pl       + e+++yfr++l+++   +++a  ++ l+g +++  ++ +++  ++ka  
  gi|14600676|ref|NP_147196.1|  14 ESDEAEIVDMivRQKIFNEELNPLfktvediRaEAERYFRETLSDDksFIIVAQHGEGLAGFIRVELVDRRFYKPRIKA-V 93 
                                   5555555553114678888888888888888678999******975337888888999******999999999999985.8 PP

                                   EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--.EEEE--....SSHHHHHTTT-E CS
                Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqp.lsllfP....ssipiYrrfGye 126
                                   +t++ v+p +r+r + + L+++a ee+r +g+  +s l+P     + ++Y ++G++
  gi|14600676|ref|NP_147196.1|  94 ITDIYVKPRYRRRAIGQLLTQKAAEEARRRGAGmMSALYPitnyVAKRFYSQLGFR 149
                                   ******************************9862699***8665556*******97 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   2.6e-10   4.7e-07      11      81 ..      79     152 ..      71     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.6e-10
                                   -EEEEEEE-TT..SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EEEE CS
                          FR47  11 elaawilrkdg..gelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfekie 81 
                                   el++ ++ k+     +  ++v+p  rrr  g++l+++ a+e ++rg  ++ ++  ++N  + r+y++lGf++ +
  gi|14600676|ref|NP_147196.1|  79 ELVDRRFYKPRikAVITDIYVKPRYRRRAIGQLLTQKAAEEARRRGAGMMsALYPITNYVAKRFYSQLGFREFQ 152
                                   566666666655688999***************************98754389999***************874 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2     3e-07   0.00054       4     139 ..      12     153 ..       9     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                Acetyltransf_4   4 ateeDakeilaiy.aeyvvntait..feyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkr.akd..wk 77 
                                   a e+D +ei ++   ++  n++++  f+ +++   e+e+   ++   +k+++  ++  + ++G  +++ ++ r +k   ++
  gi|14600676|ref|NP_147196.1|  12 AVESDEAEIVDMIvRQKIFNEELNplFKTVEDIRAEAERYFRETlSDDKSFIIVAQHGEGLAGFIRVELVDRRfYKPriKA 92 
                                   5566666666555233345556666666667888899999999934455555555559*************9976433389 PP

                Acetyltransf_4  78 aelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgi 139
                                   +++ +y++    + + +g+ l +   + +++ +   + a    +n  ++ f+++lGF+  +i
  gi|14600676|ref|NP_147196.1|  93 VITDIYVK-PRYRRRAIGQLLTQKAAEEARRRGAGMMSALYPITNYVAKRFYSQLGFREFQI 153
                                   *******9.569****************************999**************97776 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 !   19.3   0.0   5.2e-07   0.00093      24      58 ..      91     125 ..      61     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
               Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaalddareegl 58 
                                   + ++t ++V++++r++ i++ L+++a ++ar++g 
  gi|14600676|ref|NP_147196.1|  91 KAVITDIYVKPRYRRRAIGQLLTQKAAEEARRRGA 125
                                   67899***************************996 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.8e-05     0.032      27     121 ..      49     149 ..      16     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.8e-05
                          PanZ  27 aealeaalteega.lfaarFNdRlLgAvkveledk.......eaelsdlcVRevTRrRGVgsyLleearrqaPevkswvla 99 
                                   ++ ++++l ++++ +++a+  + l g ++vel d+       +a ++d+ V+   RrR +g+ L ++a ++a   ++   +
  gi|14600676|ref|NP_147196.1|  49 ERYFRETLSDDKSfIIVAQHGEGLAGFIRVELVDRrfykpriKAVITDIYVKPRYRRRAIGQLLTQKAAEEA--RRRGAGM 127
                                   4455555555554157899999999999999887766666667899*******************9999888..3344445 PP

                          PanZ 100 eedvkeldlavlqaflealgfa 121
                                   +++  ++ + v+++f ++lgf 
  gi|14600676|ref|NP_147196.1| 128 MSALYPITNYVAKRFYSQLGFR 149
                                   5566778889999999999994 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.6e-05     0.029       2     138 .]       7     149 ..       6     149 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                Acetyltransf_3   2 LlLrplteeDlealfelrsdpe.vmry.lpepltleeaeewlerawaeeseeegygwaivlkdtg.viGsvglrdleeede 79 
                                   ++Lr++ e+D ++++ +  +++ +++   p  +t+e+ ++  er+++e   +++  ++iv ++++   G++++  ++++  
  gi|14600676|ref|NP_147196.1|   7 VVLRHAVESDEAEIVDMIVRQKiFNEElNPLFKTVEDIRAEAERYFRETLSDDK-SFIIVAQHGEgLAGFIRVELVDRRFY 86 
                                   578888888888888755544535542233344555555555544443333333.58887766642799999999999988 PP

                Acetyltransf_3  80 e.....aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                   +     +  +++++p ++++ +++  ++ + e a ++ g+ ++ a +  +N    r +  lGf+
  gi|14600676|ref|NP_147196.1|  87 KprikaVITDIYVKPRYRRRAIGQLLTQKAAEEA-RRRGAGMMSALYPITNYVAKRFYSQLGFR 149
                                   8556544445777777777777777777777777.55578899999999999999999999996 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3     4e-05     0.071      46     134 ..      36     131 ..       3     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                Acetyltransf_6  46 pdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgdrly.....ywlggy..dpelaklspgllllwel 119
                                   p  ++ +  ra  ++++++  ++++  + v+ +++ +++++ +   ++r+y     + ++ +   p++++  +g+ll +++
  gi|14600676|ref|NP_147196.1|  36 PLFKTVEDIRAEAERYFRETLSDDKSFIIVAQHGEGLAGFIRVELVDRRFYkprikAVITDIyvKPRYRRRAIGQLLTQKA 116
                                   4555556777777777777777777777788888888777766666666665544433333334999************** PP

                Acetyltransf_6 120 iedaaeeGlrrfdlg 134
                                   +e+a+++G   ++ +
  gi|14600676|ref|NP_147196.1| 117 AEEARRRGAGMMSAL 131
                                   ********8776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1187.70
//
Query:       gi|14600677|ref|NP_147197.1|  [L=159]
Description: acetyltransferase [Aeropyrum pernix K1]
Scores for complete 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   60.5   0.4    2.4e-16   60.0   0.4    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.8e-12   47.5   0.2    2.9e-12   46.8   0.2    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.1e-10   41.6   0.1    1.5e-10   41.1   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    9.6e-08   31.9   0.3    3.7e-07   30.0   0.0    1.8  2  FR47             FR47-like protein
     0.0001   22.3   0.0    0.00012   22.1   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00019   21.6   0.0    0.00022   21.4   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
     0.0087   15.8   0.0      0.014   15.1   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.047   13.8   0.0      0.096   12.8   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.08   11.1   0.0      0.095   10.8   0.0    1.0  1  Rota_VP2         Rotavirus VP2 protein
       0.13   12.0   0.1       0.36   10.5   0.1    1.8  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.4   1.3e-19   2.4e-16      33     117 .]      60     148 ..      20     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.3e-19
                                   CEEEE.EEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE.EEETTEHHH CS
                Acetyltransf_1  33 egllv.aeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl.aveedndaa 108
                                   +++++ a+  +e++G+i+++++      +g+ a++ +++V+p++r+ GlGs+Lle   e+ar+ g+++ v+ +  + n  a
  gi|14600677|ref|NP_147197.1|  60 GEIVLvAQVAEEVVGYIRGYIREMpllANGRMAVVKEIYVKPQARRLGLGSLLLERFSEEARRLGARA-VAgEFPAQNAIA 139
                                   2333359999*****************99*************************************99.66355555**** PP

                                   HHHHHHTTE CS
                Acetyltransf_1 109 irlYeklGF 117
                                   +r+Ye+lGF
  gi|14600677|ref|NP_147197.1| 140 HRFYERLGF 148
                                   ********9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.2   1.6e-15   2.9e-12       3      75 ..      61     149 ..      58     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.6e-15
                                   EEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHH.H..TT..SEEEEEEEEE.....THHH CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLle.a..ae..kgiileqlel.....naek 64 
                                   + v+Va+  +++vG+i+ ++++         a  ++++V+p++r+ G+G+ Lle +  ++   g + +         ++  
  gi|14600677|ref|NP_147197.1|  61 EIVLVAQVAEEVVGYIRGYIREmpllangrmAVVKEIYVKPQARRLGLGSLLLErFseEArrLGARAV---AgefpaQNAI 138
                                   568999999**********99999987766555555*****************966541134332211...1112222238 PP

                                   HHHHHHHTTEE CS
                Acetyltransf_7  65 aikfYeklGFe 75 
                                   a++fYe+lGF+
  gi|14600677|ref|NP_147197.1| 139 AHRFYERLGFR 149
                                   899*******8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   8.4e-14   1.5e-10      28     108 ..      58     150 ..      38     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 8.4e-14
               Acetyltransf_10  28 egealllvaeeggkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.y 96 
                                    g  ++lva + +++vG+i+   ++           +  ++V+p++r+ G+g+ Lle+  eea++ g +  + +  a++  
  gi|14600677|ref|NP_147197.1|  58 GGGEIVLVAQVAEEVVGYIRGyIREMpllangrmaVVKEIYVKPQARRLGLGSLLLERFSEEARRLGARAvAGEFPAQNaI 138
                                   6778899************65344446888888999*********************************9*********9* PP

               Acetyltransf_10  97 avpfYeklGFka 108
                                   a +fYe+lGF+ 
  gi|14600677|ref|NP_147197.1| 139 AHRFYERLGFRS 150
                                   **********86 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.61   1.1e+03      38      51 ..      60      73 ..      37      84 .. 0.69
   2 !   30.0   0.0   2.1e-10   3.7e-07      25      80 ..      95     151 ..      85     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.61
                                  HHHHHHHHHHHHHH CS
                          FR47 38 lgsrlvkalakeia 51
                                    ++lv+++a+e++
  gi|14600677|ref|NP_147197.1| 60 GEIVLVAQVAEEVV 73
                                  44577778877775 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 2.1e-10
                                   EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEE.EETT-HHHHHHHHHHT-EEE CS
                          FR47  25 galqvlpehrrrGlgsrlvkalakeiaergktvllv.vvasNtpsirlyeklGfeki 80 
                                     ++v+p++rr Glgs+l +  ++e ++ g  +++    a+N  + r+ye+lGf+  
  gi|14600677|ref|NP_147197.1|  95 KEIYVKPQARRLGLGSLLLERFSEEARRLGARAVAGeFPAQNAIAHRFYERLGFRSF 151
                                   5799**************************9999852778999***********975 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   6.8e-08   0.00012      41     126 ..      60     149 ..       8     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.8e-08
                                   TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE.--....SS CS
                Acetyltransf_9  41 esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemreegqplsll.fP....ss 116
                                    + vl+a   +e+vg ++ + +e+ +   + ++a v  + v+p+ r+ g+ s Ll+r+ ee+r  g++ + + fP    ++
  gi|14600677|ref|NP_147197.1|  60 GEIVLVAQVAEEVVGYIRGYIREMPLLA-NGRMAVVKEIYVKPQARRLGLGSLLLERFSEEARRLGARAVAGeFPaqnaIA 139
                                   357888888***************9963.4479********************************9998887588887788 PP

                                   HHHHHTTT-E CS
                Acetyltransf_9 117 ipiYrrfGye 126
                                    ++Y+r+G++
  gi|14600677|ref|NP_147197.1| 140 HRFYERLGFR 149
                                   8*******96 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.2e-07   0.00022      14     135 ..      22     149 ..       8     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                Acetyltransf_4  14 aiyaeyvvntait......feyevssveefekflealdsekeyvflvaesdrivGya..ylgqfkkr.akdwkaelsvyla 85 
                                    iy +y +n++++       ++++ ++ e+ek+ +    ++e+v+ ++ ++++vGy   y++++      + ++  ++y++
  gi|14600677|ref|NP_147197.1|  22 LIYRFYMLNEEFDplwtlkDDAKEAAAAEAEKIVAGG--GGEIVLVAQVAEEVVGYIrgYIREMPLLaNGRMAVVKEIYVK 100
                                   467999999999999888888999999********97..99***99999*******722556888875667788889***8 PP

                Acetyltransf_4  86 erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                     +++  glg+ l++  ++ +++ + +    e  ++n+++  f+++lGF+
  gi|14600677|ref|NP_147197.1| 101 -PQARRLGLGSLLLERFSEEARRLGARAVAGEFPAQNAIAHRFYERLGFR 149
                                   .78******************************99**************8 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.7e-06     0.014      58     121 ..      88     149 ..      83     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.7e-06
                          PanZ  58 edkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqaflealgfa 121
                                   ++++a ++++ V+   Rr G gs Lle+  ++a ++ +  +a e   ++++a++++f e+lgf 
  gi|14600677|ref|NP_147197.1|  88 NGRMAVVKEIYVKPQARRLGLGSLLLERFSEEARRLGARAVAGEF--PAQNAIAHRFYERLGFR 149
                                   5678999**************************999998888777..56899999**9999995 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 ?   12.8   0.0   5.4e-05     0.096      23      61 ..      90     128 ..      65     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-05
               Acetyltransf_CG  23 gvldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                    + ++  ++V+++ r+ G+++ L ++  ++ar+ g + v
  gi|14600677|ref|NP_147197.1|  90 RMAVVKEIYVKPQARRLGLGSLLLERFSEEARRLGARAV 128
                                   4567889*************************9988765 PP

>> Rota_VP2  Rotavirus VP2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.3e-05     0.095     178     243 ..      30      94 ..      12     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                      Rota_VP2 178 leempdylllkdmavenkysaeagkvvdskskeilielyqdeetegavrryiaelrqkvsaernvv 243
                                    ee+     lkd a e   +aea k+v +   ei+      ee  g++r yi e+    ++   vv
  gi|14600677|ref|NP_147197.1|  30 NEEFDPLWTLKDDAKEA-AAAEAEKIVAGGGGEIVLVAQVAEEVVGYIRGYIREMPLLANGRMAVV 94 
                                   44555556789988765.689**************99999**************977666666665 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0002      0.36      90     138 ..     102     149 ..      27     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                   HHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-E CS
                Acetyltransf_8  90 eargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfe 138
                                   +ar+ gl++ ll+++ + +  + ++r v +E  ++N+ a+r++e++Gf+
  gi|14600677|ref|NP_147197.1| 102 QARRLGLGSLLLERFSEEAR-RLGARAVAGEFPAQNAIAHRFYERLGFR 149
                                   55566677777777766654.4499***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1249.50
//
Query:       gi|14600678|ref|NP_147198.1|  [L=446]
Description: malate dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-27   95.8   0.0    1.1e-25   90.4   0.0    2.2  1  Malic_M   Malic enzyme, NAD binding domain
      6e-20   71.8   0.0    2.5e-14   53.5   0.0    2.6  2  malic     Malic enzyme, N-terminal domain


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 !   90.4   0.0   1.2e-29   1.1e-25       2     256 ..     169     402 ..     168     404 .. 0.81

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 1.2e-29
                                   HHHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S---T.. CS
                       Malic_M   2 qgTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedreklee.. 80 
                                   qgTaa +lagl++a ki gk+l+e++iv+lGaG+a i +       l++ G++     ++i +vD+kG+l+ +re+++   
  gi|14600678|ref|NP_147198.1| 169 QGTAAASLAGLINAFKIVGKNLRESRIVLLGAGAANIALYRF----LKAYGVN----PRNIVVVDSKGVLHPEREDMDRll 241
                                   9**********************************9976555....5555655....478**************9996422 PP

                                   TTGGGSBS--SS--S........SHHHHHHHH--SEEEE-SS.SSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHH CS
                       Malic_M  81 ekkpfakkkeelkeak....dkltLeevvkkvkptvliGlsg.vagafteeivremaksterPiilplSNPtskaEataed 156
                                   +++++  + +  +e         +Lee+++ +  ++l+ +s   +g+ ++e +r m++    Pi+++l NPt   E  + +
  gi|14600678|ref|NP_147198.1| 242 FSNRYKYEIALETE-GgglaPGSSLEEALRGA--DALVAASRpGPGVVKKEWIRGMSR---DPIVFALANPTP--EIWPWE 314
                                   44555444322221.12455999******986..678888752589**********86...7**********7..556666 PP

                                   HHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HH.HHHTT-SS CS
                       Malic_M 157 vlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvsee.elkegsll 236
                                   + +   g+ +va+G          +   ++Q NNa++fPg+  g++ +r++ itd m  aaae++a++++ee  ++e+++l
  gi|14600678|ref|NP_147198.1| 315 ARD--AGARVVATG----------RSDLPNQVNNALVFPGVFRGALDVRSRAITDGMAIAAAEEIARYTEEEiGIEEDRIL 383
                                   654..477777876..........67789****************************************98835889**** PP

                                   --GGGHHHHHHHHHHHHHHH CS
                       Malic_M 237 Pelseirevslkvavavaka 256
                                   P++++  +v ++va+ava a
  gi|14600678|ref|NP_147198.1| 384 PPITDW-QVHYRVAAAVAWA 402
                                   ****97.5889999999865 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   2.8e-18   2.5e-14       2     114 ..      24     115 ..      23     119 .. 0.94
   2 !   15.8   0.0     1e-06    0.0092     149     180 ..     123     154 ..     116     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.8e-18
                                   TTECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTTB CS
                         malic   2 eknetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGlG 82 
                                   +k+e++++ +++    e+++i+YtP+v+ea  ++++++++   +++s+ ++                v++vtd++r+LGlG
  gi|14600678|ref|NP_147198.1|  24 GKIEVMPKVPVSGV--EDFAIWYTPGVAEASIRINKDPDESF-ELTSRWNM----------------VAIVTDATRVLGLG 85 
                                   57888888888888..9************************9.9*******................************** PP

                                   S-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEE CS
                         malic  83 dlG.vagvgimvGKlaLytalagidPekvlpvv 114
                                    l   a+ ++m+GK+ +++ ++g+d   ++p+v
  gi|14600678|ref|NP_147198.1|  86 KLLpEAAYPVMEGKALIFKLFGGVD---AVPIV 115
                                   *999*********************...88876 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1e-06
                                   HHHHHHHHHHGCTSEEEE-S--CCHHHHHHHH CS
                         malic 149 efveavkelfppkaliqfEDfkaknafeiler 180
                                   +f + vk+l+p+++++++ED++++++f++l+ 
  gi|14600678|ref|NP_147198.1| 123 AFASLVKDLEPSFGGVNLEDIESPKCFYLLDF 154
                                   57789************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3180.11
//
Query:       gi|118431020|ref|NP_147199.2|  [L=555]
Description: medium-chain-fatty-acid--CoA ligase [Aeropyrum pernix K1]
Scores for 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-100  334.3   0.1    1.1e-99  334.0   0.1    1.0  1  AMP-binding    AMP-binding enzyme
    1.6e-22   80.2   0.5    3.8e-22   79.0   0.0    1.9  2  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 !  334.0   0.1  1.2e-103   1.1e-99      17     422 ..      38     443 ..      24     444 .. 0.88

  Alignments for each domain:
  == domain 1  score: 334.0 bits;  conditional E-value: 1.2e-103
                                    CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTES CS
                    AMP-binding  17 sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseak 96 
                                    +++ +++T+++  +r+++lA++Lr+lGv   drVa + +n++ ++ +++a+ ++Gav+ pln +l + e+ayi++++e k
  gi|118431020|ref|NP_147199.2|  38 TKGLERYTFSDAARRIESLANALRALGVSGLDRVATMDWNTHWHYETYFAAPMMGAVLHPLNVRLAPNEIAYIMNHAEDK 117
                                    556799************************************************************************** PP

                                    EEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-TSCCCS-BTTSEEEEEEE--S CS
                    AMP-binding  97 vliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae......kpeeeeelkpddlayiiYTSGT 170
                                    vli  v+s+ l+ ++++ +  ++v++v+++da++ ++     ++   + ++       +  e +el+++ +a + YTSGT
  gi|118431020|ref|NP_147199.2| 118 VLI--VHSDFLKLAEAILPHAPSVEHVVIVDAESHPDR--IAGRRLHNYEDLikehggRF-EWPELDENRPAAMGYTSGT 192
                                    ***..888888888999999999********9887766..33333333333134667544.6669*************** PP

                                    SSS-EEEEEEHHHHHHHHHHHH..HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHH CS
                    AMP-binding 171 TGkPKGVmlshrnlvanvaslk..letr..fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklll 246
                                    TG PKGV +shr +v  + s +  l tr  ++++ dd++l+i+p++h++++    ++a l G++ v++    +ldpk+ll
  gi|118431020|ref|NP_147199.2| 193 TGLPKGVYHSHRMIVVHALSGAlaLATRgrRRVTGDDTLLHIVPMFHVLAW-GLPYMATLTGMKQVFPG---RLDPKVLL 268
                                    ***********999777777666755555455778****************.***************66...6789**** PP

                                    HHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE CS
                    AMP-binding 247 elieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtv 326
                                    +li  +kvtv+agvP++l +ll++++      ++dls+l + + gg++l++ l++++r++++e v+ gYG+TEt++++t 
  gi|118431020|ref|NP_147199.2| 269 DLIVGEKVTVTAGVPTILYMLLSHPESG----KYDLSGLLF-VNGGQALPKGLADAARKRGIE-VIVGYGMTETAPILTL 342
                                    ***********************98777....569***988.58****************997.**************88 PP

                                    .......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEE.TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEE CS
                    AMP-binding 327 .......lpleedkkklgsvGkplpgvevkivDeetgepvp.dgee.GellvrgpgvmkgYlkkpeataeafdsegrwlr 397
                                           +  +++++   ++G+p+p ve++++D+et+epvp dg++ Ge++vr p+v++ Y+k+pe+t++a+   g+w++
  gi|118431020|ref|NP_147199.2| 343 anvpqkyM--DRSEELSLTTGWPVPLVELMVADPETLEPVPkDGKTmGEIVVRTPWVTPEYYKDPEKTEKAWR--GGWFH 418
                                    88999543..555567789*********************9566669*************************8..57*** PP

                                    EEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 398 TGDlgrldedGyleivgRkkdlikl 422
                                    TGD+++++++Gy++iv+R kd+ik+
  gi|118431020|ref|NP_147199.2| 419 TGDIAVWTPEGYIQIVDRDKDIIKS 443
                                    ***********************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   1.7e+04       3      20 ..     130     148 ..     129     158 .. 0.62
   2 !   79.0   0.0   4.3e-26   3.8e-22       2      76 .]     453     535 ..     452     535 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                                    HHHHHSSTTEEEEEEE.-- CS
                  AMP-binding_C   3 EsalvshpaVaeaaVv.Gv 20 
                                    E++l   p V+ +++v + 
  gi|118431020|ref|NP_147199.2| 130 EAILPHAPSVEHVVIVdAE 148
                                    5666666777777755344 PP

  == domain 2  score: 79.0 bits;  conditional E-value: 4.3e-26
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.-.--HHHHHHHHHHH......HT-TTTS-SEEEE-S---B-T CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.s.ealeeeLkahvrk......elgpyavpkkvvfvdelpktr 73 
                                    +Es +++hp+Va++aV+G +++++Ge++va++v+k+g + +++ ee++++++k      e+++++ p+k+v+vd+lpkt 
  gi|118431020|ref|NP_147199.2| 453 LESLISQHPGVAQVAVIGARHPKWGERPVAIIVPKPGwQdKLTTEEVREWLAKnfvekgEIPKWWLPDKIVLVDDLPKTS 532
                                    79*********************************99753559********77777777********************* PP

                                    TS- CS
                  AMP-binding_C  74 sGK 76 
                                     GK
  gi|118431020|ref|NP_147199.2| 533 VGK 535
                                    **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.58u 0.20s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4120.15
//
Query:       gi|118431021|ref|NP_147200.2|  [L=135]
Description: hypothetical protein APE_0399.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1063.85
//
Query:       gi|118431022|ref|NP_147201.2|  [L=225]
Description: uridylate kinase [Aeropyrum pernix K1]
Scores for complete 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   76.1   0.0    7.1e-21   74.9   0.0    1.5  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 !   74.9   0.0     4e-25   7.1e-21       3     240 ..       4     203 ..       2     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 4e-25
                                    EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHH CS
                      AA_kinase   3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeagevatrd 80 
                                    vVvK+ Gs++ ++  ++l rl + +  l+  g +++vV+Ggg+ ++ +++   ++g+s+  l                 d
  gi|118431022|ref|NP_147201.2|   4 VVVKISGSLVHPPRLDYLTRLRDVLWGLVDGGFRVAVVVGGGGLARSYIDVlrRAGVSEALL-----------------D 66 
                                    8**********88779*********************************9987788888877.................8 PP

                                    HHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-H CS
                      AA_kinase  81 alaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgss 160
                                    ++++  +rl+a+lla++l  ++ +                        +++ e +  g +pv +gf+    +g+    s+
  gi|118431022|ref|NP_147201.2|  67 EMGIESSRLNASLLAKLLYPRSQPYPLAS------------------LREVLEVFMTGLIPVSGGFQ----PGQ----ST 120
                                    ******************99999877776..................4567789999*********9....999....9* PP

                                    HHHHHHHHHHCTSSEEEE.EESSSSCESSTTTTCCTTCECCEEEHHHCHH...CSSS.TTTHHHHCHHHHHHHHHCTT-E CS
                      AA_kinase 161 DtiaallAealgAdklii.ltdVdGVydadpkkvpdarllpeisvdeaee...saselatgGmkvkhpaalaaarrggip 236
                                      +aa +AealgA++l++ l+ V+GVy+++p+ +  arll++++++++e+   + s    g+    +  al +arr+g +
  gi|118431022|ref|NP_147201.2| 121 NAVAAVIAEALGARTLLNcLKGVEGVYSDEPSTP-GARLLRRLTYRQLEDilvKVSSQRAGSYTLWDMVALSVARRSGLR 199
                                    *************77765389************7.*****************87777788888889**********9999 PP

                                    EEEE CS
                      AA_kinase 237 vvIt 240
                                    +v +
  gi|118431022|ref|NP_147201.2| 200 IVFF 203
                                    9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1647.23
//
Query:       gi|118431023|ref|YP_874819.1|  [L=82]
Description: hypothetical protein APE_0401a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.93    9.4   8.3        4.1    7.3   8.3    1.8  1  DUF2721   Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.3   0.00023       4.1      68     115 ..      34      81 ..      27      82 .] 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00023
                        DUF2721  68 lllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslll 115
                                    +ll + +++++ +v   +l+a++++d++ l++i+f+la +ll+v++ll
  gi|118431023|ref|YP_874819.1|  34 ALLSVVGAFTLGLVGYRLLNAAVNTDTAGLLKITFILASVLLVVGVLL 81 
                                    44444445555555566668999**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 626.39
//
Query:       gi|118431024|ref|NP_147203.2|  [L=211]
Description: V-type ATP synthase subunit D [Aeropyrum pernix K1]
Scores for 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  135.4   4.5    2.3e-39  135.3   4.5    1.0  1  ATP-synt_D  ATP synthase subunit D
  ------ inclusion threshold ------
      0.063   13.2   0.2        3.6    7.5   0.1    2.2  2  AAA_31      AAA domain
       0.08   12.2   3.6          1    8.6   0.6    2.1  2  CorA        CorA-like Mg2+ transporter protein
       0.89    9.6   4.4        1.1    9.3   0.6    2.8  3  GPAT_N      Glycerol-3-phosphate acyltransferase N-terminal


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 !  135.3   4.5   5.2e-43   2.3e-39       1     195 [.      14     203 ..      14     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 5.2e-43
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TS CS
                     ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakv 80 
                                    +Lirl+++l++ +r+++++++Kr++++  + ++++e+ ++++e+  el+++y+ + +  aa+g e+ +++ + +++   +
  gi|118431024|ref|NP_147203.2|  14 NLIRLRRELAMLRRIRRVMEEKREVILHYITSMAAEYVRYQREVYSELERIYQNYYLGVAAEGIERARAFTA-PAE--GS 90 
                                    79******************************************************9999998888886666.333..56 PP

                                    S-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_D  81 vkvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNa 160
                                    ++v+++t+ ++ Vk+pvf+l+e  ++  +l   +++ ++l + +  +r++l++l++la++e++l++L  e+k t+r +Na
  gi|118431024|ref|NP_147203.2|  91 LEVDVSTRTLFAVKTPVFSLRE--ETVPPLPLPAGSDPKLVQSILDMRSILDKLLKLAEYEETLQRLISELKDTQRLINA 168
                                    ********************66..44556677799999****************************************** PP

                                    HHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_D 161 LekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                    L++v++P ++++ik+Ik  L+++ re+f+rlk++k
  gi|118431024|ref|NP_147203.2| 169 LDYVILPSYQNAIKFIKLVLEDRMREDFVRLKIIK 203
                                    **********************************9 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.011        49      82     110 ..       7      35 ..       2      50 .. 0.80
   2 ?    7.5   0.1   0.00081       3.6      80     123 ..     125     174 ..     107     183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                         AAA_31  82 dlipssidLaeaeielvelekkeeilkel 110
                                    +++p++i+L+++  el+ l++ +++++e+
  gi|118431024|ref|NP_147203.2|   7 KVLPTKINLIRLRRELAMLRRIRRVMEEK 35 
                                    79**************9999887776554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00081
                         AAA_31  80 nldlipssidLaeaeielvelekkeeilkellekvkde......YDyiii 123
                                    +++l+ s +d+ ++ ++l++l + ee+l++l++++kd+       Dy+i+
  gi|118431024|ref|NP_147203.2| 125 DPKLVQSILDMRSILDKLLKLAEYEETLQRLISELKDTqrlinaLDYVIL 174
                                    568999**************************999875334434677765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6   0.00023         1     153     207 ..      15      67 ..       7      80 .. 0.83
   2 ?    4.5   0.1    0.0041        19     192     222 ..     133     163 ..     120     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00023
                           CorA 153 laqlrrrlvkl...rralapnrevlkrllakaddkllddedkeylrdlldelerllem 207
                                    l++lrr+l+ l   rr++ ++rev+  +++      + +e  +y r++++eler+++ 
  gi|118431024|ref|NP_147203.2|  15 LIRLRRELAMLrriRRVMEEKREVILHYIT-----SMAAEYVRYQREVYSELERIYQN 67 
                                    789999988777779**********99999.....55566666679********9874 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0041
                           CorA 192 eylrdlldelerllemlealrerleslqdty 222
                                    + +r +ld+l +l+e+ e+l+++++ l+dt 
  gi|118431024|ref|NP_147203.2| 133 LDMRSILDKLLKLAEYEETLQRLISELKDTQ 163
                                    4588899999999999999999999999875 PP

>> GPAT_N  Glycerol-3-phosphate acyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2       0.2     9e+02       5      25 ..      16      36 ..      14      58 .. 0.69
   2 ?    9.3   0.6   0.00025       1.1      22      54 ..      49      81 ..      33      84 .. 0.84
   3 ?   -0.6   0.1       0.3   1.3e+03       7      39 ..     146     178 ..     137     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.2
                         GPAT_N  5 ldarseeellsvirkeveagk 25
                                    + r e  +l +ir+ +e+ +
  gi|118431024|ref|NP_147203.2| 16 IRLRRELAMLRRIRRVMEEKR 36
                                   567889999999999988765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00025
                         GPAT_N 22 eagkLpanvaagmeelYqNYknAVlqsGipkAd 54
                                   e  +   +v +++e +YqNY   V   Gi++A+
  gi|118431024|ref|NP_147203.2| 49 EYVRYQREVYSELERIYQNYYLGVAAEGIERAR 81
                                   55667789999*******************996 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.3
                         GPAT_N   7 arseeellsvirkeveagkLpanvaagmeelYq 39 
                                    a+ ee l   i + ++ ++L + ++  +   Yq
  gi|118431024|ref|NP_147203.2| 146 AEYEETLQRLISELKDTQRLINALDYVILPSYQ 178
                                    556777888888888888887766655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1684.05
//
Query:       gi|118431025|ref|NP_147204.2|  [L=463]
Description: V-type ATP synthase subunit B [Aeropyrum pernix K1]
Scores for complete 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-68  230.1   0.0      3e-68  229.7   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    1.5e-12   47.9   4.7    4.1e-12   46.4   4.7    1.8  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.7   0.0   3.4e-72     3e-68       1     213 []     134     352 ..     134     352 .. 0.98

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 3.4e-72
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlv 75 
                                    G++++D + ++v+Gq++ i++++g++++ +++++++q++ +    + a+++ +iG + ++   + + f+e++++ r+ ++
  gi|118431025|ref|NP_147204.2| 134 GVSAIDGMNTLVRGQKLPIFSGAGLPHNRLAAQIARQATVRgeeeEfAVVFSAIGIKYDDFLFFKKFFEETGALGRVAMF 213
                                    899**********************************9887999768********************************* PP

                                    EEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  76 antsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagk 154
                                    +n ++ep++ r++++++++tlAEy+++ ++++vl+i+++++++aeAlreis++ +e+p++qgyp+yl+++las+yERag+
  gi|118431025|ref|NP_147204.2| 214 VNLADEPAMIRLITPRAALTLAEYLAYeRDMHVLVIITDMTNYAEALREISAAREEVPGRQGYPGYLYSDLASIYERAGR 293
                                    **************************999*************************************************** PP

                                    ETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 155 apdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++ ++Gs+t++++++++++D+++p+++ t +it+g+ivL+++l++r+++P+invl+S+S
  gi|118431025|ref|NP_147204.2| 294 VKGKKGSITQMPILTMPNDDITHPIPDLTGYITEGQIVLSRELHNRGIYPPINVLMSLS 352
                                    *********************************************************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 !   46.4   4.7   4.6e-16   4.1e-12       1      69 []      11      77 ..      11      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4.6e-16
                                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                   i+++ Gp++ ve+++ +++ +++ +e+     g++++g +l++g + ++v+v+++t+G+s+ Gt V++ G
  gi|118431025|ref|NP_147204.2| 11 ISEIKGPLLVVEGVSRVAYDEIVEVETA--A-GEKRRGRVLEVGMGYAVVQVFEGTTGISPtGTVVRFMG 77
                                   799*************666666666666..7.***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3516.98
//
Query:       gi|118431026|ref|NP_147205.2|  [L=597]
Description: V-type ATP synthase subunit A [Aeropyrum pernix K1]
Scores for complete 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-92  307.6   0.0    5.6e-92  307.2   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    2.4e-41  140.4   0.0    4.9e-41  139.4   0.0    1.5  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.7e-15   57.3   1.1    4.6e-15   55.9   1.1    1.8  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.079   13.2   0.5       0.31   11.3   0.1    2.1  2  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 !  307.2   0.0   1.3e-95   5.6e-92       1     213 []     221     444 ..     221     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 307.2 bits;  conditional E-value: 1.3e-95
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtv 73 
                                    G+r++D++fp+++G++ ++pg+fg+Gktv ++sl+++s+++ ++iy+g+Gergne++evle+fp+      g+ +m+rtv
  gi|118431026|ref|NP_147205.2| 221 GVRIIDTFFPMAKGGTGAVPGGFGTGKTVTLHSLAQWSEAR-VVIYIGCGERGNEMTEVLERFPQykdpwtGKpLMDRTV 299
                                    89***********************************9888.***********************877776337****** PP

                                    EEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  74 lvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERag 153
                                    l+antsn+pvaareasiy+git+AEy+rd+g++vll+ads+srwaeAlrei++rl+empa++gyp+yl+++la++yERag
  gi|118431026|ref|NP_147205.2| 300 LIANTSNMPVAAREASIYVGITIAEYYRDMGYDVLLVADSTSRWAEALREIAGRLEEMPAEEGYPSYLASRLAEFYERAG 379
                                    ******************************************************************************** PP

                                    EE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 154 ka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++     p+r+Gsvt+v avsp+ggDfs+pvt++t +++ +f+ Ld+kla ++h+Pain+l+S+S
  gi|118431026|ref|NP_147205.2| 380 RVkalgsPERSGSVTVVGAVSPPGGDFSEPVTSHTTRFIRVFWALDTKLAYSRHYPAINWLMSYS 444
                                    *******99*******************************************************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 !  139.4   0.0   1.1e-44   4.9e-41       1     121 []      85     212 ..      85     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 1.1e-44
                                    EETTS-BHHHHHHHH......TS.BE-TT----SS-SSS-EEEEE.SS-TT-EEETT-EEEEEECTTCEEEEEE--TT-E CS
                ATP-synt_ab_Xtn   1 yDGiqrpLekiaeks......gs.fierGvkvpaldrekkwefkp.kvkvgdkvsggdilGtvqeteliehkimvppkve 72 
                                    yDG+qrpL  iaek        + f+erG+++p+l r++k++fkp  +k+gdkv+ggd lG v+et+lieh +mvpp+++
  gi|118431026|ref|NP_147205.2|  85 YDGVQRPLPIIAEKVaevdprRRmFVERGIQAPPLPRDRKFHFKPePLKEGDKVEGGDALGRVPETSLIEHVVMVPPGIR 164
                                    9**********9998555554227*********************88********************************* PP

                                    EEEEEE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                ATP-synt_ab_Xtn  73 gkvkeiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                    g++k++a+eg+y+vedtia+ve ++ +++e++++q+wPvr prp+kekl
  gi|118431026|ref|NP_147205.2| 165 GRLKWLASEGDYSVEDTIAVVERDG-RDVEIRMHQRWPVRIPRPFKEKL 212
                                    **********************877.7********************97 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   1.1     1e-18   4.6e-15       1      69 []       7      69 ..       7      69 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1e-18
                                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                   iv+++Gp+v +e+++g   ++y+++ v+  e  + l+g++ ++++d++ ++v++st+Gl++G++V+ TG
  gi|118431026|ref|NP_147205.2|  7 IVRISGPLVVAEGMSG--AQMYEMVYVG--E--DRLIGEITRIRGDRAFIQVYESTSGLKPGEPVVGTG 69
                                   89**************..**********..8..9**********************************8 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     7e-05      0.31       5      51 ..     234     272 ..     231     285 .. 0.77
   2 ?   -1.2   0.1       0.5   2.3e+03      75     126 ..     494     545 ..     475     553 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst 51 
                                     g ++v G  GtGKT++l  l+++          +++vv ++ + + +
  gi|118431026|ref|NP_147205.2| 234 GGTGAVPGGFGTGKTVTLHSLAQWS---------EARVViYIGCGERG 272
                                    577999******************9.........55555477776666 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.5
                         AAA_22  75 seellealeqalraravielliiDEaqhlr.seealeeLrsllnlsrkgvqli 126
                                    ++ ++   ++ +++ +  +    D ++ +  ++++++ L+++++++rk++ li
  gi|118431026|ref|NP_147205.2| 494 KDKMVLETARLIKDGFL-KQNAFDPIDAFAtPQKQFRLLKMIMDIHRKSLELI 545
                                    44455555555555555.55556777777655999999999999888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 4616.18
//
Query:       gi|118431027|ref|NP_147206.2|  [L=200]
Description: V-type ATP synthase subunit E [Aeropyrum pernix K1]
Scores for complete 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-07   30.5   7.5    8.4e-07   28.6   7.4    1.9  1  vATP-synt_E  ATP synthase (E/31 kDa) subunit
    0.00045   19.9   0.1    0.00052   19.6   0.1    1.1  1  ERAP1_C      ERAP1-like C-terminal domain
  ------ inclusion threshold ------
       0.03   13.1   2.7       0.04   12.7   2.7    1.1  1  AAA_32       AAA domain
      0.042   13.8   5.0      0.072   13.0   5.0    1.5  1  GvpL_GvpF    Gas vesicle synthesis protein GvpL/GvpF
      0.046   14.2   0.6      0.063   13.8   0.6    1.2  1  T3SSipB      Type III cell invasion protein SipB
      0.067   13.5   0.4          7    7.0   0.1    2.4  2  DUF3135      Protein of unknown function (DUF3135)
       0.18   11.9   1.0       0.37   10.9   1.0    1.5  1  Caudo_TAP    Caudovirales tail fibre assembly protein, lambda
       0.19   12.3   8.1       0.36   11.5   6.7    2.0  2  DUF883       Bacterial protein of unknown function (DUF883)
       0.71    8.1   3.4        3.1    6.0   1.0    2.0  2  DUF2309      Uncharacterized protein conserved in bacteria (D
        8.6    6.5  14.1          3    7.9  10.9    1.8  2  ATP-synt_B   ATP synthase B/B' CF(0)


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 !   28.6   7.4   4.7e-10   8.4e-07      12     199 .]      29     198 ..      20     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 4.7e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS CS
                    vATP-synt_E  12 eIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeeaekkLaeveed 91 
                                    e    a e   + ++++ + +  + ++++e+   +a  + +  +S+a ++ r +  ++++e++++++eea  + +  +  
  gi|118431027|ref|NP_147206.2|  29 E----AREAGLKLVEEAYKSALSAARKRLESRVEEARERLQGLKSKADLEVRTEAERVKDELVSRLIEEALAEFRRRKAG 104
                                    3....334444556666666777777777777777777778889************************************ PP

                                    HHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTSSSEEEECCSSS CS
                    vATP-synt_E  92 kdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfledvlGGvvleaadg 171
                                     + Y++ l+  +  a+ + ++  + v +  eD+e+v+e+l k    +      + v v +      e + GGvv+e a+g
  gi|118431027|ref|NP_147206.2| 105 MESYRQYLERVLGSAAGESGGSVAKVLCAPEDEEIVREVLGK----LGL----DGVSVEA-----VEGIYGGVVVELAEG 171
                                    **************************************7544....344....2222333.....34799*****99998 PP

                                    CEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                    vATP-synt_E 172 kikvnnTlearLelvleqllpeirkaLF 199
                                      +++ T + ++      l+ ++++aLF
  gi|118431027|ref|NP_147206.2| 172 A-RLDYTVNNIIAAEEPRLRRAVKRALF 198
                                    5.89999999999999999999999998 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   2.9e-07   0.00052     100     239 ..       9     164 ..       2     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.9e-07
                                    HHHHHHHHHHHHHHHHH...T.TTS-....HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT.......-.S-HH CS
                        ERAP1_C 100 kaflrklleplaeklgw...epgesh....ldaqlrslllsaacaagdpevveearklfkawlegdd.......l.ippd 164
                                    ++f++++le+ +++  +   e+   +    l  +  +++lsaa +   ++ veear+++++  ++ d       + +  +
  gi|118431027|ref|NP_147206.2|   9 RRFADTVLEKPFKEALArveEAR--EaglkLVEEAYKSALSAA-RKRLESRVEEARERLQGLKSKADlevrteaErVKDE 85 
                                    56777777777776643232111..112336666667888777.888999************775446677776469999 PP

                                    HHHHHHHHHHHH.S....-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHC.TTT..S-GGGHHHHHHH CS
                        ERAP1_C 165 lrwavycalaan.g....geaewdallerykdtsapsekeaalralaatpdpellerllnfv.lesdevrnqdlrallag 238
                                    l ++++  ++a       g + + + ler+  + a++    +++ l+a +d+e+++++l  + l  d v+ + ++ + +g
  gi|118431027|ref|NP_147206.2|  86 LVSRLIEEALAEfRrrkaGMESYRQYLERVLGSAAGESGGSVAKVLCAPEDEEIVREVLGKLgL--DGVSVEAVEGIYGG 163
                                    9999999999553344569999*******97777778889********************9966..67888888888887 PP

                                    H CS
                        ERAP1_C 239 l 239
                                    +
  gi|118431027|ref|NP_147206.2| 164 V 164
                                    7 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.7   2.2e-05      0.04     170     245 ..      36     115 ..      17     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                         AAA_32 170 ealpeeerkeleekseeleeeleeilrelrelek....eakeklkelerevakeaveplleelkekykdlekvleyLeav 245
                                    + ++e+ + +l ++ ++le+++ee+ ++l+ l++    e++ + +++++e++++++e++l+e++++ + +e+  +yLe+v
  gi|118431027|ref|NP_147206.2|  36 KLVEEAYKSALSAARKRLESRVEEARERLQGLKSkadlEVRTEAERVKDELVSRLIEEALAEFRRRKAGMESYRQYLERV 115
                                    33455556666666666666666666666655541111667777889999999999999999999999999999**9987 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   5.0     4e-05     0.072      99     185 ..      18      93 ..      15     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-05
                      GvpL_GvpF  99 delreaLerlagkvEygvkvlwde..ealleelleedpelrelreeieaasesgtayllrkrlgqrleealeerreelae 176
                                    + ++eaL+r+++ +E g+k++++   +al ++  + + +++e+re++++ ++             +++ ++++++e++ +
  gi|118431027|ref|NP_147206.2|  18 KPFKEALARVEEAREAGLKLVEEAykSALSAARKRLESRVEEARERLQGLKS-------------KADLEVRTEAERVKD 84 
                                    5699******************993322222222223333333333333333.............222222222222222 PP

                      GvpL_GvpF 177 eleeaLapl 185
                                    el ++L + 
  gi|118431027|ref|NP_147206.2|  85 ELVSRLIEE 93 
                                    222222221 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 ?   13.8   0.6   3.5e-05     0.063      44     104 ..      16      74 ..       4     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                                    --STHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH.HHHHHHHHHHHHHHTT---------CHH CS
                        T3SSipB  44 lSdelqtalseakgatddlea.aiekadqaksaa.daatkkvdeaqkrlkeLaPdePekakle 104
                                    l + +++al   ++a ++  +   e++++a saa + ++ +v+ea +rl++L      ka+le
  gi|118431027|ref|NP_147206.2|  16 LEKPFKEALARVEEAREAGLKlVEEAYKSALSAArKRLESRVEEARERLQGL----KSKADLE 74 
                                    56789**********9996550556788887766388***************....3344443 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0039         7      31      54 ..      53      76 ..      40      80 .. 0.86
   2 ?    4.6   0.0     0.021        38      20      45 ..      80     105 ..      77     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0039
                        DUF3135 31 IesapeemqrrLrglqfqiDmqls 54
                                   +es+ ee ++rL+gl+++ D++++
  gi|118431027|ref|NP_147206.2| 53 LESRVEEARERLQGLKSKADLEVR 76
                                   688899**************9987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                        DUF3135  20 ealrqelieelIesapeemqrrLrgl 45 
                                    e++++el+ +lIe+a +e++rr  g+
  gi|118431027|ref|NP_147206.2|  80 ERVKDELVSRLIEEALAEFRRRKAGM 105
                                    7899*****************97776 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 ?   10.9   1.0   0.00021      0.37      56     100 ..      38      82 ..      19      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                      Caudo_TAP  56 vedkkeeqiqqAeqekqqllaqAseqiaplqdavdlgiatdeEka 100
                                    ve++ ++  ++A ++ ++++++A+e+ + l+ ++dl+  t++E+ 
  gi|118431027|ref|NP_147206.2|  38 VEEAYKSALSAARKRLESRVEEARERLQGLKSKADLEVRTEAERV 82 
                                    4445677889999*****************************975 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 ?   11.5   6.7    0.0002      0.36      10      67 ..      27      84 ..      17      90 .. 0.77
   2 ?   -1.4   0.0         2   3.7e+03       6      30 ..     104     128 ..      99     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                         DUF883 10 lladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67
                                   + +  e+ lk  ++  ++ ++++R+rle+r+e+arerl+ ++ ++  +++  ae+++d
  gi|118431027|ref|NP_147206.2| 27 VEEAREAGLKLVEEAYKSALSAARKRLESRVEEARERLQGLKSKADLEVRTEAERVKD 84
                                   444445556666677788999***********************99998887776654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                         DUF883   6 eleslladleellkeaadeageeae 30 
                                     +es ++ le +l +aa e+g +++
  gi|118431027|ref|NP_147206.2| 104 GMESYRQYLERVLGSAAGESGGSVA 128
                                    5677777888888888888877665 PP

>> DUF2309  Uncharacterized protein conserved in bacteria (DUF2309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.0    0.0017       3.1      28     105 ..      17      95 ..      12     110 .. 0.69
   2 ?    2.4   0.0     0.022        39     489     521 ..     117     149 ..     116     151 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0017
                        DUF2309  28 dlpfeeavaelaklfgarlylseeeyrealaegrid.eedLeaaeeeleeeetlaelldaltgedldelvdeqliklla 105
                                    ++pf+ea+a++++  +a l l ee y++al++ r + e+ +e+a+e+l+  ++ a+l  +++ e++++++ ++li+ + 
  gi|118431027|ref|NP_147206.2|  17 EKPFKEALARVEEAREAGLKLVEEAYKSALSAARKRlESRVEEARERLQGLKSKADLEVRTEAERVKDELVSRLIEEAL 95 
                                    78**************************998765441445666655666666666666666666655555555444333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.022
                        DUF2309 489 GACgGrsGgvnARvlAallNdpeVRegLaergi 521
                                    G ++G+sGg  A+vl+a  +++ VRe L + g+
  gi|118431027|ref|NP_147206.2| 117 GSAAGESGGSVAKVLCAPEDEEIVREVLGKLGL 149
                                    7889***********************998876 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.9    0.0017         3      58     120 ..      25      91 ..      15     101 .. 0.46
   2 ?   -2.9   0.0       3.7   6.6e+03     103     116 ..     181     194 ..     169     198 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                     ATP-synt_B  58 qqlkeAraeAaeiiknAkk....eaeklkeeieaeaeaeaerlkesAaaeIeqekdralaeLreqvv 120
                                    ++ +eAr    +++++A+k    +a+k  e +++ea++ ++ lk++A  e+ +e +r+++eL  +  
  gi|118431027|ref|NP_147206.2|  25 ARVEEAREAGLKLVEEAYKsalsAARKRLESRVEEARERLQGLKSKADLEVRTEAERVKDELVSRLI 91 
                                    3333333333333333333111033444455555555555555555555555555555555544444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                     ATP-synt_B 103 eIeqekdralaeLr 116
                                     I++e+ r++++++
  gi|118431027|ref|NP_147206.2| 181 IIAAEEPRLRRAVK 194
                                    34444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1395  (0.0778069); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 1571.09
//
Query:       gi|118431028|ref|NP_147207.2|  [L=102]
Description: V-type ATP synthase subunit F [Aeropyrum pernix K1]
Scores for 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-09   35.6   0.2      1e-08   35.4   0.2    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.15   12.3   0.1    1.3  1  DUF1611_N   Domain of unknown function (DUF1611_N) Rossmann-l


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 !   35.4   0.2   1.2e-12     1e-08       1      81 [.       8      87 ..       8      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-12
                                   EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCSCCGGS CS
                     ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykeealPaileIPskegpyd 81
                                   i +I d++t+  f  +G ++vev+  ee+ +a+++ + ++++ i+l+ ++++e+ ++l +e ++    ++l IPs +++ +
  gi|118431028|ref|NP_147207.2|  8 ILAIVDRETAPLFMGVGASVVEVAGSEEVLDAFRRSVVENGVRIVLVLKHLVEDEESLRREADR-LGVTLLIIPSMGEKAE 87
                                   6789**************************************************8888777777.999*******998543 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 ?   12.3   0.1   1.7e-05      0.15      38      88 ..      30      76 ..       2      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                      DUF1611_N 38 iapeggklpeswreavkeAleaGldvvsGlHerLsddpelaalakkkgvki 88
                                   +a ++++l ++ r++v   +e+G+ +v  l+  ++d+++l++ a++ gv++
  gi|118431028|ref|NP_147207.2| 30 VAGSEEVL-DAFRRSV---VENGVRIVLVLKHLVEDEESLRREADRLGVTL 76
                                   44455555.4444444...579***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 802.58
//
Query:       gi|14600688|ref|NP_147208.1|  [L=362]
Description: hypothetical protein APE_0412 [Aeropyrum pernix K1]
Scores for 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-16   58.0   0.0    2.7e-15   56.0   0.0    1.8  1  Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved do
      3e-06   26.5   0.0    4.2e-06   26.0   0.0    1.1  1  Aminotran_5    Aminotransferase class-V
  ------ inclusion threshold ------
        0.1   11.3   0.0       0.22   10.2   0.0    1.5  2  OKR_DC_1       Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   4.6e-19   2.7e-15     149     295 ..      85     222 ..      43     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 4.6e-19
                                   EEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT- CS
                 Pyridoxal_deC 149 ytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydl 229
                                   ++ d +h+s++k al l ++l ++p++  g+ r + le+ i  d        +vvat+Gtt  g  d ++e++ + e  + 
  gi|14600688|ref|NP_147208.1|  85 VAFDTSHYSIKKSALTLSMELDLLPTHG-GRPRLDLLERRITPDS-------VVVATVGTTQEGLVDPVEEIAGVAESVGA 157
                                   455778*********************8.99**********9874.......589************************** PP

                                   EEEEE-TTGGGGGGSGGGGG.GGTTGG.GESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECC CS
                 Pyridoxal_deC 230 wlHvDAAyaGsaficpeirh.llkgie.radSitvnphKlllvlldcsalivkdkealqqalqleaeY 295
                                    +HvDAAy+G  +i+++  +   +++e  +  + v  hK+  ++  +++++  ++ +l + l +e  Y
  gi|14600688|ref|NP_147208.1| 158 AVHVDAAYGG--YIARFLTGkARFRLEpPVMTVVVDAHKIPEAPPPAGVILASKQ-KLLDNLWFESPY 222
                                   **********..*******987778863699999999999999888876665544.444445566666 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     7e-10   4.2e-06      67     177 ..      62     164 ..      37     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7e-10
                                   ESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEES CS
                   Aminotran_5  67 tsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaith 147
                                   tsG++e++ l++++l++  +  +++v  ++ h +    +  l+    ++++ +p  ++g+ +ld le  ++++  +va t 
  gi|14600688|ref|NP_147208.1|  62 TSGASEGNLLALYTLRE--EGYRRVVAFDTSHYSIKKSALTLS----MELDLLPT-HGGRPRLDLLERRITPDSVVVA-TV 134
                                   99999999999999954..677889999999999995555555....88988887.9****************87776.67 PP

                                   BETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                   Aminotran_5 148 vsnvtGtiqpveeigklakkkgalvlvDaa 177
                                     +  G ++pveei+ +a  +ga v+vDaa
  gi|14600688|ref|NP_147208.1| 135 GTTQEGLVDPVEEIAGVAESVGAAVHVDAA 164
                                   88999************************8 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.27   1.6e+03      78     125 ..      52     101 ..      49     103 .. 0.76
   2 ?   10.2   0.0   3.7e-05      0.22     176     244 ..     135     198 ..     119     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.27
                                   HCT-SEEEEESSHHHHHHHHHHHHH--TTEE.EEEESS--HHHHH.HHHH CS
                      OKR_DC_1  78 vfgadksyfvvnGTsssnkvvlnavltpgdl.vlvdRNcHKSieh.alvl 125
                                   vfg +k   ++ G s +n   l ++ ++g   v+     H Si++ al l
  gi|14600688|ref|NP_147208.1|  52 VFGVEKPGWITSGASEGNLLALYTLREEGYRrVVAFDTSHYSIKKsALTL 101
                                   78899988999999999999999999999641443445788888767665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 3.7e-05
                                   SS-TTSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS-BTTBEEEEEEEHCCCCS- CS
                      OKR_DC_1 176 nsTYdGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllaenendpgilvtqSvHKllaa 244
                                    +T  G++  ++ei   +e+++  +++D A++gy+    + +++ + ++e    p++ v+  +HK+  a
  gi|14600688|ref|NP_147208.1| 135 GTTQEGLVDPVEEIAGVAESVGAAVHVDAAYGGYIA--RFLTGKARFRLE---PPVMTVVVDAHKIPEA 198
                                   357889****************************74..788899999988...8888888888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2858.50
//
Query:       gi|14600689|ref|NP_147209.1|  [L=1039]
Description: hypothetical protein APE_0413 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-17   63.2   1.0    5.3e-17   61.7   1.0    1.9  1  DUF3883         Domain of unknown function (DUF3883)
    4.2e-14   52.8   0.0    1.9e-13   50.7   0.0    2.2  2  Helicase_C      Helicase conserved C-terminal domain
    8.8e-12   45.4   0.0    1.9e-11   44.3   0.0    1.6  1  ResIII          Type III restriction enzyme, res subunit
    1.1e-11   44.0   0.1    4.2e-11   42.2   0.1    1.9  1  SNF2_N          SNF2 family N-terminal domain
    5.9e-05   22.9   0.0    0.00027   20.7   0.0    2.1  2  DEAD            DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.025   13.8   0.0       0.11   11.7   0.0    2.0  2  DUF2075         Uncharacterized conserved protein (DUF2075)
      0.084   12.7   1.5        1.8    8.4   0.2    2.4  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
       0.13   11.4   0.0       0.29   10.3   0.0    1.5  1  ERCC3_RAD25_C   ERCC3/RAD25/XPB C-terminal helicase
       0.99    9.8   3.5         15    6.0   0.5    3.0  2  DUF2573         Protein of unknown function (DUF2573)


Domain annotation for each model (and alignments):
>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   1.0   2.6e-20   5.3e-17       2      88 ..     917    1005 ..     916    1010 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.6e-20
                       DUF3883    2 EklvlealkekekeegvewvnedvedglgYDiesvd.kedge...erfIEVKttakgkkdfelsrnElefaqekgdkYw 76  
                                    E+ ++  + ++ek+e   ++++ v+ + +YD++sv+  edg+   erfIEVKt++k+  +f l ++E+++a++kgd+Yw
  gi|14600689|ref|NP_147209.1|  917 EDEAISTVLDYEKQED--REPTRVSGHEHYDVRSVKrGEDGSikeERFIEVKTKIKRSLNFGLKSEEFKVAEKKGDNYW 993 
                                    7778999999999997..******999********9633444666********************************** PP

                       DUF3883   77 lyrVfnagkepk 88  
                                    ly+V+++ +e+ 
  gi|14600689|ref|NP_147209.1|  994 LYIVYGVRTEKP 1005
                                    *******66653 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.1   8.2e+03      13      32 ..     228     251 ..     217     270 .. 0.72
   2 !   50.7   0.0   9.5e-17   1.9e-13      14     111 .]     450     553 ..     439     553 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                                   TTTTSEEEEEESSHHHHHH....H CS
                    Helicase_C  13 eeeggkilifvntidrlek....v 32 
                                    ++++++++f +++d+++k    +
  gi|14600689|ref|NP_147209.1| 228 YQRTHNVILFRRNKDDVNKiyerA 251
                                   567889999999999886443333 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 9.5e-17
                                   TTTSEEEEEESSHHHHHH.HHHHHHHT.........TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                    Helicase_C  14 eeggkilifvntidrlek.vklllekk.........gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                      +k+++f++++d++    +               +  ++++  + +  e e+i +   ++ ++vL++tdva++G++++ 
  gi|14600689|ref|NP_147209.1| 450 LASQKAIVFTEFKDTATYlYEK----LrkwaedefgDPGIVRVFTSENRGEIEDIKRWLSEDGRRVLVTTDVAGEGLNLQY 526
                                   467899********77333222....222233434534444444433444444444444466667**************** PP

                                   ESEEEESSSSSSHHHHHHHHTTSSSTT CS
                    Helicase_C  85 vnlVinfdlprnvtsyiqriGRtgRag 111
                                   +n++in+++ +++ ++ qriGR++R+g
  gi|14600689|ref|NP_147209.1| 527 ANVIINYEITWSPIRLEQRIGRVWRYG 553
                                   *************************86 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 !   44.3   0.0   9.4e-15   1.9e-11       6     170 ..      31     191 ..      26     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 9.4e-15
                                   HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                        ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflseayke 84 
                                    +Q+e++ + l      + +r+li+   G GKT++a+++ + + + ++++  ++l+ vp   l+eq+++e++++  ++   
  gi|14600689|ref|NP_147209.1|  31 LHQTEVVAKSL-F---IKPTRILIADVIGLGKTVTALRILKTIEHYKNQKlgRVLIAVPA-VLVEQWKDEMRSMGINPILI 106
                                   56666666655.2...4689****************999888887666667688877775.699**************876 PP

                                   GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...T...TTHHH...HHT- CS
                        ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..k...swrei...lekf 157
                                   + k+++ + k++    +  +  ++ +i++l++++     +   l+r++ d i++DEaH+lg    +    wr++   +  +
  gi|14600689|ref|NP_147209.1| 107 ERKSLDFRAKQP----ELPSGWYIGSIDTLKRPE-----YMAFLQRNKWDAIVVDEAHKLGVVggEpnmRWRNLgklIMEN 178
                                   666666666666....9999**************.....899999***************997551567999985554445 PP

                                   --SEEEEEESS-S CS
                        ResIII 158 keavllglTATpe 170
                                   ++a++l l+ATp 
  gi|14600689|ref|NP_147209.1| 179 RDAIVLLLSATPH 191
                                   77**********7 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 !   42.2   0.1   2.1e-14   4.2e-11      59     250 ..      49     227 ..      31     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 2.1e-14
                                   EE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH----- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  59 iLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkmkkkn 139
                                   ++aD  GLGKTv++l +++   ++e+ +++k      +g +Li vPa l++qW++e+++   ++ l     + +     + 
  gi|14600689|ref|NP_147209.1|  49 LIADVIGLGKTVTALRILK---TIEHYKNQK------LGRVLIAVPAVLVEQWKDEMRSMGINPIL----IERK-----SL 111
                                   789****************...666666654......899****************9887666633....4442.....33 PP

                                   ------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T....TSHHHHHHHH---S-E....EEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx....xxxx RF
                        SNF2_N 140 tkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns....tskaaeavskLstsnr....wilt 212
                                   ++ a++     +  i + d+l+r       +  l++ +w+ +v+DE+h+l+      +      + kL  +nr    ++l+
  gi|14600689|ref|NP_147209.1| 112 DFRAKQPELPSGWYIGSIDTLKRPE----YMAFLQRNKWDAIVVDEAHKLGVVggepN-MRWRNLGKLIMENRdaivLLLS 187
                                   444555555677789999****777....799******************98866533.33333444666666555599** PP

                                   S--SSS-HHHHHHHHHHH-TTTT--HH..HHHHHTHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                        SNF2_N 213 GTPiqnsledlygLlkfLreepfgekq..tfdkllqrpie 250
                                   +TP   + +d+ + l+++ +  ++     t +k +++p  
  gi|14600689|ref|NP_147209.1| 188 ATPHRGKANDYLSRLALVDPTLLDVTSvsTLEKVFDKPEF 227
                                   *******************999987444478888888765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.4e-07   0.00027      12     171 ..      41     192 ..      31     197 .. 0.69
   2 ?   -3.2   0.0       3.1   6.2e+03      66     110 ..     404     445 ..     396     463 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.4e-07
                                   H..TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHH CS
                                   x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  12 l..gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardq 90 
                                   l  +   +l+a   G GKT   ++ +l+++ + k+++  ++li +P   L+eq  +++++++ +    +l   ++ + r +
  gi|14600689|ref|NP_147209.1|  41 LfiKPTRILIADVIGLGKTVT-ALRILKTIEHYKNQKLGRVLIAVPA-VLVEQWKDEMRSMGIN---PILIERKSLDFRAK 116
                                   43366789999999*****98.56777788666999999******96.7************996...22322233334445 PP

                                   HHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  91 lskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpk 171
                                   + +l      ++g  + l +      l+ ++   +V+DEa++l   g ++ ++   ++l +   +   +  v++lSAT+++
  gi|14600689|ref|NP_147209.1| 117 QPEL--PSGWYIGSIDTLKRPEYMAFLQRNKWDAIVVDEAHKLGVVGGEPNMRW--RNLGKLIMEN-RDAIVLLLSATPHR 192
                                   5555..3445555555555533344566788999************99999887..4443333332.3456********94 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.1
                                   HHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEH.HHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          DEAD  66 nlkkfkkyidlrvlliiggvaardqlskldngvdivvgtp.grldd 110
                                   +lkk  ky++     i+ g+a ++++++l++ + +v+ tp + l d
  gi|14600689|ref|NP_147209.1| 404 ELKKAQKYAE----DILVGKAVDSKVETLKKILGLVLYTPpEELPD 445
                                   4455555432....45556777778888854455555554244544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.11      10     129 ..      54     185 ..      46     188 .. 0.70
   2 ?   -1.5   0.0      0.58   1.2e+03     289     306 ..     521     538 ..     369     550 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                       DUF2075  10 aGtGKtvvllnllael.eddeeertavylsvNhplvlvlrealakke..........ekkkkkeafeklssfinnlsef.. 77 
                                    G GKtv +l++l ++ + ++++  +v++ v   lv+  + ++++             + + k+    +  +i ++++   
  gi|14600689|ref|NP_147209.1|  54 IGLGKTVTALRILKTIeHYKNQKLGRVLIAVPAVLVEQWKDEMRSMGinpilierksLDFRAKQPELPSGWYIGSIDTLkr 134
                                   588*************54556667788888999999999999988879888774422222222333334458888887776 PP

                       DUF2075  78 kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvval 129
                                    +  +  +++k d ++vDEAh+l   +    +++ +n  k +m++ + +v+l
  gi|14600689|ref|NP_147209.1| 135 PEYMAFLQRNKWDAIVVDEAHKLGVVGGE-PNMRWRNLGKLIMENRDAIVLL 185
                                   66677789**************9884443.4555666666677766666665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.58
                       DUF2075 289 GleldyvgviiGpdlvyr 306
                                   Gl l y+ vii  +++++
  gi|14600689|ref|NP_147209.1| 521 GLNLQYANVIINYEITWS 538
                                   778888888888877776 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0009       1.8      58     173 ..     350     464 ..     348     480 .. 0.59
   2 ?    2.8   0.1     0.046        92      31      70 ..     675     719 ..     646     724 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0009
                                   HHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHH.....HHHHHHHHHHHHHHHHCHHHHHHH..HHHH CS
                Apolipoprotein  58 devqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaee.....lrerlerhvealkarlapyveelr..qkla 131
                                   de+q+++++++e++ ++l+++++     ++++++e  e+la y ++     +re+l+++        + y+e++   + ++
  gi|14600689|ref|NP_147209.1| 350 DEAQKKIAEEIEDYARKLDEILSGDIGEIDEELDEEFERLAIYFDKllddmFREELKKA--------QKYAEDILvgKAVD 422
                                   78899999999999999888888888888888888888888888884333322222222........22333322223355 PP

                                   HHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHHHS CS
                Apolipoprotein 132 erleelkeslaphaeeveerlssrveelrekleeqaeelrer 173
                                   +++e lk+ l   +   +e+l ++ ++l  + +    e ++ 
  gi|14600689|ref|NP_147209.1| 423 SKVETLKKILGLVLYTPPEELPDEFKDLASQKAIVFTEFKDT 464
                                   666666666666655555555555555555555555555555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.046
                                   HHHHHHHHHHHH.....HHHHHHHHHHCCCCHHHHHHCCCHHHHH CS
                Apolipoprotein  31 lskeleelrarl.....raeleevrarlepyrdevqeqlgqnlee 70 
                                   + +++e++r++l      +++e+v++ l++  +++ + l  + ee
  gi|14600689|ref|NP_147209.1| 675 VRADAEKVREELlhltgFRDMEDVVETLKNAGEAFSKILDLSFEE 719
                                   567999999999999999************999998877766666 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 ?   10.3   0.0   0.00014      0.29      98     178 ..     500     579 ..     454     582 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                 ERCC3_RAD25_C  98 lqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemays 178
                                   ++++ +++  ++++   v+ + ++l  anv+i  +   +  r e qr+Gr+ r  +++++  fn f    + k+  e +++
  gi|14600689|ref|NP_147209.1| 500 IKRWLSEDGRRVLVTTDVAGEGLNLQYANVIINYEITWSPIRLE-QRIGRVWRYGQDKTTYVFNLFLADGLEKEVAETVFA 579
                                   56666777788899999***********************9999.*********999999999999988888888888887 PP

>> DUF2573  Protein of unknown function (DUF2573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.5    0.0073        15       2      36 ..     355     392 ..     354     396 .. 0.87
   2 ?    3.2   0.1     0.057   1.1e+02      11      33 ..     408     431 ..     399     479 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0073
                       DUF2573   2 klkeelegLveKytELL...lGesseelkekvkvwilY 36 
                                   k+ ee+e+  +K  E+L   +Ge +eel e+    ++Y
  gi|14600689|ref|NP_147209.1| 355 KIAEEIEDYARKLDEILsgdIGEIDEELDEEFERLAIY 392
                                   789**************666678899999999999999 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.057
                       DUF2573  11 veKytE.LLlGesseelkekvkvw 33 
                                    +Ky+E +L+G + + ++e +k+ 
  gi|14600689|ref|NP_147209.1| 408 AQKYAEdILVGKAVDSKVETLKKI 431
                                   57999879*****99999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); 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: 0.84u 0.30s 00:00:01.13 Elapsed: 00:00:00.45
# Mc/sec: 6945.38
//
Query:       gi|118431029|ref|NP_147210.2|  [L=182]
Description: hypothetical protein APE_0414.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1409.31
//
Query:       gi|14600691|ref|NP_147211.1|  [L=1188]
Description: hypothetical protein APE_0415 [Aeropyrum pernix K1]
Scores for 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 1195.6  21.7          0 1195.1  21.7    1.1  1  DUF499    Protein of unknown function (DUF499)


Domain annotation for each model (and alignments):
>> DUF499  Protein of unknown function (DUF499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1195.1  21.7         0         0       1    1024 []     118    1184 ..     118    1184 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1195.1 bits;  conditional E-value: 0
                        DUF499    1 eelreldeeladrvk...kLirnvkvkvvvvdgkssklvpsPvkPleaggrkikTlWGylayeLgrYeiveksDrneta 76  
                                    ++lr+ld+++ad+v+   +Li+n+++++vv+d+k+s+l+psPv+P+e+ggr++kTlWGyl+yeLgrY+iv++sD++eta
  gi|14600691|ref|NP_147211.1|  118 SKLRILDNDIADFVDgnwDLIKNMSLNLVVIDCKYSDLAPSPVRPIEIGGRRVKTLWGYLGYELGRYDIVKISDERETA 196 
                                    589**************************************************************************** PP

                        DUF499   77 PdieelrkllqgekvliLiDEIadyvdnllrSgledkkdYaeevsaFldnLakAle...vsevalvitipaekr.eG.e 150 
                                    P++++++kll+g+++l+LiDEI++y+d   +Sgle++k     +saFl+nLa+Al+   vseva+vi+ip+e+r +G e
  gi|14600691|ref|NP_147211.1|  197 PYADDVSKLLNGSRALVLIDEIGRYYD---QSGLEPTK-----ISAFLMNLAEALSkynVSEVAVVISIPYEVRgGGaE 267 
                                    ***************************...********.....***************9***************6669* PP

                        DUF499  151 akaeeeYkr..evvrailealrrvageiykPvrrneelvevlkkRiFsevdedekkkelkkl..........ret.aev 216 
                                    aka++eY++  e++rai+e+l+r+++ei+kPv ++++l+e+l+kRiF++     kk+elkk+          re+ a+v
  gi|14600691|ref|NP_147211.1|  268 AKAGMEYVHrpELIRAINEVLSRPSVEIIKPV-GRRDLAEILRKRIFAH-----KKNELKKFfnelvsrefnREYpAQV 340 
                                    ********************************.****************.....999999999999************* PP

                        DUF499  217 reifgdesdlekeleetYPFHPeylevLreiierl.dlqrTRdlirItrivv....rklldalEdepelImPwHIdlvd 290 
                                    r+i++d+s +++e+eetYPFHP++l+vL+++++rl +lqrTRd+i+I++++v    ++l+dalEde++lImP+HI+l++
  gi|14600691|ref|NP_147211.1|  341 RRILDDRS-FWREAEETYPFHPMFLNVLEKLAYRLpYLQRTRDAIKIAVQTVlalkEGLFDALEDEINLIMPHHIPLFV 418 
                                    ********.********************************************************************** PP

                        DUF499  291 eevrglllleka..eykdykkileaeivaeeklgklkalskpe...................LakkilkvifLktypyd 348 
                                    +ev ++++l++a  ey++++ il++++v++e+lg+lk+lsk+e                   L++k++++i+L++++++
  gi|14600691|ref|NP_147211.1|  419 SEVLDETILRNApdEYRVFYLILRSNVVVPENLGNLKKLSKEEfyervmsralkslkedeakLGLKLASNIWLHSLVGL 497 
                                    ******************************************************************************* PP

                        DUF499  349 slktplkeFPtlkdiarmvYepetfekndlkPaDikdtvee.ikklpklvfla..esdsrfWffr.iasveelverkak 423 
                                    +l+++++eFPt++d+   +Y+++++e+      D+k+++++ +++lp+l++++  esds++Wff+ i+sveel+     
  gi|14600691|ref|NP_147211.1|  498 GLPMNMGEFPTTADL---IYSVSPTEQ------DAKGVLGIlRSVLPQLIVHGdpESDSAKWFFTiIPSVEELI----- 562 
                                    ***************...*********......********9***********************9********..... PP

                        DUF499  424 ellkknvtdverkLvnkvdkllksgrsiergrgressgekevevFdkkavivlkyaaeipkEllDnkeykLvvlvkkdv 502 
                                    e+lkknvtd+++k  nk+++ll+sg++++rgrgr+++g+ke++vF+++av+  k+aa+ipkE+lD+++++L+v+++k +
  gi|14600691|ref|NP_147211.1|  563 EILKKNVTDEMAK--NKLAELLESGLIGRRGRGRPPKGYKEESVFAGYAVV--KNAATIPKEILDSRDPALIVFADK-I 636 
                                    *************..************************************..***********************9.* PP

                        DUF499  503 skeeleklifkegggeRtyaNtvvvvapvkekl..........................esllellarlvAaeeikee. 554 
                                    sk+el+k+++++        N++vv+ap++e++                          +slle+l+++vA+e+i+ee 
  gi|14600691|ref|NP_147211.1|  637 SKDELFKVLKGR--------NNIVVLAPHVEGMgeeeklapediagirelaglrgktvwDSLLEILKYYVATESIREEn 707 
                                    ***********9........*********************************************************99 PP

                        DUF499  555 lrelyg........eYakevlkiqknkveskkekaledllnqilslfrkVaYpvlgkereeveeveateSdksivekVe 625 
                                    lr+++g        eY+ke+l+++k+kveskk++++++++n+i++++rkV+Y++lg++r  +ee+ ++eSdk+i+++Ve
  gi|14600691|ref|NP_147211.1|  708 LRAFLGekvvkgdeEYLKELLNLLKTKVESKKDYYYIHSWNMINRCYRKVYYYRLGQIR--FEEGLSLESDKPILPLVE 784 
                                    ***********************************************************..****************** PP

                        DUF499  626 saLkekekiveeldfeelkdilkdnlgidilpg.rkikvgelinviltnpka..PmirekalieaikeavkkLdiaier 701 
                                    ++L+eke+i++e+++e++++i+kd+lg++  p+ ++ikvgel+n+il+++ka  P+ir++++i+a++++vk+Ld+ai++
  gi|14600691|ref|NP_147211.1|  785 EFLREKELIPYEFKGENIISIVKDYLGKN--PKeEPIKVGELWNFILSTDKAnvPIIRYRDFIGAVEDLVKSLDYAIRV 861 
                                    *****************************..776********************************************* PP

                        DUF499  702 kgkllfKriyseissekekgeepksieeadiileakkalekvleell..keekdevrkekvilklvYevyipeeklplk 778 
                                    kgkll+K+i++             s+eead+++e++k+lekv+e+l+  k+++d+v       +lvY            
  gi|14600691|ref|NP_147211.1|  862 KGKLLWKPIFK-------------SKEEADALDEGNKLLEKVREHLTriKASWDDV-------ELVY------------ 908 
                                    ***********.............9*******************************.......9***............ PP

                        DUF499  779 dlvkveewekvlrelliekrEeilksefelkVkrrs..............................velkpg......e 821 
                                           wekv++e+li+++E+i +s++++kVk+rs                              vel+++      e
  gi|14600691|ref|NP_147211.1|  909 -------WEKVFDEWLIRETESI-PSDKIIKVKDRSgqvfdirdikfdvknviksgklfyeekkylVELNYElpddilE 979 
                                    .......****************.******************************************************* PP

                        DUF499  822 kveveveiepi.kdyeee..iklssdeGelsveevelkgkeplkvkwrlkasrvkrvrikikaksnegklkekiivvv. 896 
                                    ++e+ev++e+i k+ye+e  +kl++deG lsve++e+kgk+pl++k+rlka+r++++rik+++++n+++l+++ii+v+ 
  gi|14600691|ref|NP_147211.1|  980 DKEYEVAGEVIvKNYENEflVKLQPDEG-LSVEPSEFKGKSPLPIKFRLKAGRAGNYRIKVEVYGNGSILDSRIISVSv 1057
                                    ***********9****************.************************************************99 PP

                        DUF499  897 ..pkiEedviiveeidevekgeiLvsiksindldsLksiteeakvlegkikgsleve.eagsvrvefeevdpkifellv 972 
                                      ++iEe+++i+ee+++ve++++Lvsi+ +nd+++L+sit++akv++gki+gsl+v+ +a+sv+++++++dpk+fell+
  gi|14600691|ref|NP_147211.1| 1058 kgEWIEEEITIGEEGEAVEEDAKLVSIR-VNDVVGLPSITRVAKVYPGKIRGSLSVSgKAVSVSFNVDTTDPKVFELLW 1135
                                    9***************************.9************************************************* PP

                        DUF499  973 seleeilrskkalneakalvdielseevvlndrkiakLkrllgkvkFklkkk 1024
                                    s++++ilr++k   ea+alvdie+s+e++l++r++akL ++++++kFk+kkk
  gi|14600691|ref|NP_147211.1| 1136 SPINSILRNMK---EASALVDIEYSPEGELELRDVAKLLVSTKGLKFKVKKK 1184
                                    *********99...8***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.46
# Mc/sec: 7822.56
//
Query:       gi|118431030|ref|NP_147212.2|  [L=1004]
Description: hypothetical protein APE_0416.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-10   39.6   0.0    1.1e-09   38.3   0.0    1.7  1  DUF1156        Protein of unknown function (DUF1156)
    1.4e-07   31.3   0.0     0.0013   18.4   0.0    2.3  2  Cons_hypoth95  Conserved hypothetical protein 95
    0.00073   19.3   0.0        1.6    8.4   0.0    2.5  2  UPF0020        Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
       0.13   11.9   0.0        1.7    8.3   0.0    2.4  2  N6_N4_Mtase    DNA methylase
       0.21   11.3   0.4        1.4    8.7   0.0    2.4  3  MBD            Methyl-CpG binding domain


Domain annotation for each model (and alignments):
>> DUF1156  Protein of unknown function (DUF1156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0     3e-13   1.1e-09       2      48 ..      15      62 ..      14      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3e-13
                        DUF1156  2 lPldkinaesakEksirhg.hlstLhlWWaRrPLaaaRAvifaqLvpd 48
                                   +P++ in+ sa+Ek+ +       +  WW R+PLa aRAvi ++L+p 
  gi|118431030|ref|NP_147212.2| 15 FPISLINEVSAREKQGGGRpPYWEMVFWWTRKPLAGARAVIAGALLPG 62
                                   9**************997767789**********************96 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.7e-07    0.0013      38      91 ..      94     147 ..      88     167 .. 0.85
   2 !   10.3   0.0   0.00011      0.39      93     128 ..     553     585 ..     528     602 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.7e-07
                                    CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T CS
                  Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee 91 
                                    +++++a++LD faG G++ lEA+  g+ ++v+ve  ++a+  lk+ le  k  +
  gi|118431030|ref|NP_147212.2|  94 ERFKQAKLLDPFAGFGSIPLEAIRLGVGEVVAVEFLPTAYIFLKAMLEYPKEYS 147
                                    568999*****************************9999999998887766554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                                    TEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH CS
                  Cons_hypoth95  93 taelkedaleallklakkkeefdivflDPPyakell 128
                                    +++l +da   l+kl  ++e+fd++  DPPy+++  
  gi|118431030|ref|NP_147212.2| 553 VRVLLDDA-TVLSKL--EGERFDVIVTDPPYRDDVP 585
                                    44444444.445555..6889**********99865 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00055         2      30      50 ..      99     119 ..      94     166 .. 0.79
   2 !    8.4   0.0   0.00044       1.6     109     133 ..     557     582 ..     545     608 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00055
                                    S-EEETT-TTSHHHHHHHHHH CS
                        UPF0020  30 epllDPmCGsGtilIEaallg 50 
                                     +llDP+ G G+i++Ea  lg
  gi|118431030|ref|NP_147212.2|  99 AKLLDPFAGFGSIPLEAIRLG 119
                                    689*************97665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00044
                                    E--GGG--STTS.---EEEE------ CS
                        UPF0020 109 qadaakLrlkeg.evdvivtnpPYGe 133
                                      da+ L + eg  +dvivt+pPY +
  gi|118431030|ref|NP_147212.2| 557 LDDATVLSKLEGeRFDVIVTDPPYRD 582
                                    55778888444438**********65 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.11     4e+02     196     213 ..     102     119 ..      97     133 .. 0.89
   2 ?    8.3   0.0   0.00047       1.7       2      57 ..     572     674 ..     571     711 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                                    EETT-TTTHHHHHHHHTT CS
                    N6_N4_Mtase 196 lDpFaGSGtTavaakelg 213
                                    lDpFaG G++  +a++lg
  gi|118431030|ref|NP_147212.2| 102 LDPFAGFGSIPLEAIRLG 119
                                    9********999999887 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00047
                                    EEEEE--SSSSSCS...................................................GCCGCCH.HHHHHHH CS
                    N6_N4_Mtase   2 dlivtdpPYntgkdy..............................................endeqyeeeds.yeeylef 34 
                                    d+ivtdpPY     y                                              e +  y +  +  ++y ++
  gi|118431030|ref|NP_147212.2| 572 DVIVTDPPYRDDVPYaelsdfyyvwlkrslsgdglalrfhsdalvsntqwegfalneisynEGRLRYFGVREaEDYYERL 651
                                    79********99999********************************999999988888774444444444415555556 PP

                                    HHHHHHHHHHHEEEEEEEEEEE- CS
                    N6_N4_Mtase  35 lekvlkevrrvLkddgsifinid 57 
                                    +   +k + ++Lkddg i+  + 
  gi|118431030|ref|NP_147212.2| 652 MGMAFKRLSELLKDDGLIVTYFA 674
                                    777899************97665 PP

>> MBD  Methyl-CpG binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00038       1.4      33      73 ..     295     336 ..     281     339 .. 0.85
   2 ?   -1.1   0.0      0.45   1.6e+03       7      20 ..     448     461 ..     443     468 .. 0.77
   3 ?   -4.0   0.1       3.6   1.3e+04      11      17 ..     685     691 ..     684     693 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00038
                                    EEEE-T.TS-EE-SHHHHHHHHHHCT-.SSS-CCCS---TTX CS
                            MBD  33 vfYysP.tGkkfsskkevaayLenakqstsaklknFsfekrl 73 
                                    + Y+ P tG++ ++k+eva+ L + + + ++k    +++k+l
  gi|118431030|ref|NP_147212.2| 295 ITYIDPrTGRTYRTKNEVANTLIRSRLEFYPKHALKDWNKKL 336
                                    78*****************99988877777777777777665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.45
                                    HHCHCHCT-EEEEE CS
                            MBD   7 dcsvLpkGWrreer 20 
                                     +  L  GW ree 
  gi|118431030|ref|NP_147212.2| 448 EEEKLREGWSREEA 461
                                    5677999*****98 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 3.6
                                    CHCT-EE CS
                            MBD  11 LpkGWrr 17 
                                    ++ GWrr
  gi|118431030|ref|NP_147212.2| 685 VEAGWRR 691
                                    579***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1004 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 6770.08
//
Query:       gi|118431031|ref|YP_874820.1|  [L=58]
Description: hypothetical protein APE_0416a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      118  (0.00658152); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 469.72
//
Query:       gi|118431032|ref|NP_147214.2|  [L=57]
Description: hypothetical protein APE_0416b.1 [Aeropyrum pernix K1]
Scores for complete 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-11   42.2   0.5    5.9e-11   41.9   0.5    1.2  1  RHH_1            Ribbon-helix-helix protein, copG family
    0.00046   20.7   0.1    0.00053   20.5   0.1    1.1  1  CopG_antitoxin   CopG antitoxin of type II toxin-antitoxin sy
     0.0047   17.0   0.1     0.0049   17.0   0.1    1.1  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
  ------ inclusion threshold ------
      0.048   13.6   0.1      0.052   13.5   0.1    1.1  1  RepB-RCR_reg     Replication regulatory protein RepB


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 !   41.9   0.5   1.3e-14   5.9e-11       2      37 ..      19      54 ..      18      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.3e-14
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   v+++++++lle++d++a++ g +rSe+IReA++  l
  gi|118431032|ref|NP_147214.2| 19 VTFKIEADLLEEIDRRAEKKGLTRSEFIREAILKQL 54
                                   9*******************************9877 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.2e-07   0.00053      40      76 ..      14      50 ..      10      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                 CopG_antitoxin 40 kktksislrlpedlLealkekAnkrdvpyqslikell 76
                                   k+ k +++++++dlLe++  +A+k+++  +++i+e++
  gi|118431032|ref|NP_147214.2| 14 KRIKVVTFKIEADLLEEIDRRAEKKGLTRSEFIREAI 50
                                   677899****************************987 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.1e-06    0.0049      87     121 ..      14      48 ..       2      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                HicB_lk_antitox  87 gkaeriNitlpervlkriDaavkaagesRSgflak 121
                                    ++ + +   + +++l++iD++++++g +RS f+ +
  gi|118431032|ref|NP_147214.2|  14 KRIKVVTFKIEADLLEEIDRRAEKKGLTRSEFIRE 48 
                                    3334444567899*******************986 PP

>> RepB-RCR_reg  Replication regulatory protein RepB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.052      39      78 ..      13      55 ..       4      57 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                   RepB-RCR_reg 39 hkeikvf...iknelkdslvqlCeeeGitqaqlieklikkela 78
                                    k ikv    i+  l +++ +  e++G+t+ ++i + i k+l 
  gi|118431032|ref|NP_147214.2| 13 EKRIKVVtfkIEADLLEEIDRRAEKKGLTRSEFIREAILKQLH 55
                                   45566541126777777778889***********999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 451.00
//
Query:       gi|14600695|ref|NP_147215.1|  [L=261]
Description: hypothetical protein APE_0419 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       395  (0.0220313); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2021.75
//
Query:       gi|118431033|ref|YP_874821.1|  [L=88]
Description: hypothetical protein APE_0419a [Aeropyrum pernix K1]
Scores for 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   23.0   1.9       0.17   11.9   0.1    2.1  2  DZR              Double zinc ribbon
    0.00012   21.8   0.8    0.00012   21.8   0.8    1.9  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
    0.00054   19.9   5.5       0.13   12.3   2.3    2.5  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
     0.0016   18.0   1.5       0.37   10.4   0.0    2.9  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
     0.0018   18.3   0.2        1.2    9.3   0.0    2.3  2  zf-BED           BED zinc finger
     0.0031   17.5   1.4       0.14   12.2   1.4    2.1  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0053   16.7   1.2      0.065   13.2   1.2    2.4  1  zinc-ribbons_6   zinc-ribbons
     0.0077   15.6   4.8       0.26   10.8   0.1    3.2  3  zf-ribbon_3      zinc-ribbon domain
     0.0094   16.0   3.8        3.2    7.9   0.1    3.0  3  Elf1             Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
      0.011   15.7   1.7      0.039   13.9   0.6    2.1  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
       0.02   14.8  10.7       0.64   10.0   6.5    3.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.02   15.3   3.2        6.9    7.3   0.3    3.1  3  zf-H2C2_2        Zinc-finger double domain
      0.035   13.6   7.0       0.18   11.3   3.2    2.6  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.035   14.1   1.9        1.4    9.0   0.0    2.7  2  Nop10p           Nucleolar RNA-binding protein, Nop10p family
       0.04   14.0   7.9       0.25   11.5   4.2    2.5  3  Zn-ribbon_8      Zinc ribbon domain
      0.043   13.5   5.9       0.44   10.3   0.3    2.7  3  Ribosomal_S27e   Ribosomal protein S27
      0.044   14.2   4.0         11    6.5   0.0    3.2  3  zf-IS66          zinc-finger binding domain of transposase IS
      0.094   12.8   4.9        2.2    8.4   4.9    2.6  1  DUF1272          Protein of unknown function (DUF1272)
        0.1   12.9   4.3        1.4    9.3   0.1    2.9  3  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.13   12.3  11.1        1.8    8.6   0.2    3.0  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   12.4   5.3        3.4    8.0   1.6    2.8  3  C1_4             TFIIH C1-like domain
       0.16   11.9  14.1        4.5    7.2   1.8    3.2  3  zf-HIT           HIT zinc finger
       0.27   11.6   0.1       0.27   11.6   0.1    2.9  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.28   11.5   5.4         65    4.0   5.4    2.6  1  C1_2             C1 domain
        0.3   11.3   6.3         12    6.1   0.4    3.0  3  zf-AN1           AN1-like Zinc finger
       0.48   10.4   8.3          9    6.3   0.1    3.0  2  zinc_ribbon_4    zinc-ribbon domain
       0.48   10.5   0.2       0.48   10.5   0.2    3.1  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.48   10.4   3.5        1.5    8.8   0.4    2.4  2  PyrI_C           Aspartate carbamoyltransferase regulatory ch
       0.68   10.2   4.6         13    6.1   0.0    3.0  3  DUF2757          Protein of unknown function (DUF2757)
       0.84   10.4   7.3         11    6.7   0.1    3.3  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.95    9.3   9.7        2.3    8.1   0.2    3.5  3  zinc_ribbon_2    zinc-ribbon domain
        1.9    8.7   4.7        5.5    7.2   2.6    2.3  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        2.6    9.1   7.7         28    5.9   0.2    3.3  3  zf-C2H2_4        C2H2-type zinc finger
        3.4    7.3   4.7         22    4.8   0.2    3.0  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
        5.3    7.0   8.8    1.7e+02    2.2   8.8    2.7  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        5.5    6.8  12.3        8.5    6.2   0.4    3.3  3  Zn_Tnp_IS1       InsA N-terminal 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 !   11.9   0.1   0.00035      0.17      15      36 ..      22      52 ..      17      55 .. 0.90
   2 !   11.5   4.0   0.00045      0.22       1      37 [.      47      76 ..      47      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                            DZR 15 CseCgtklkavaa.........edrCpsCge 36
                                   C  Cgt l+ + +          ++Cp+C +
  gi|118431033|ref|YP_874821.1| 22 CRVCGTYLDITGQppggrsitlVYACPRCAK 52
                                   ********9777799**************86 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00045
                            DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgek 37
                                   Cp+C ++   +a fC +   +lk     +rCp Cg++
  gi|118431033|ref|YP_874821.1| 47 CPRCAKD--YGAYFCRADARSLK-----YRCPFCGSE 76
                                   9999887..89***********8.....*******87 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 ?    0.1   0.1       1.4   6.9e+02      46      52 ..      21      27 ..      14      29 .. 0.80
   2 !   21.8   0.8   2.4e-07   0.00012      25      52 ..      47      75 ..      34      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.4
                 zinc_ribbon_10 46 rCpkCga 52
                                   rC  Cg+
  gi|118431033|ref|YP_874821.1| 21 RCRVCGT 27
                                   8999997 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.4e-07
                 zinc_ribbon_10 25 CskChshnGlap.keeleevkyrCpkCga 52
                                   C+ C +  G +  + +++ +kyrCp+Cg+
  gi|118431033|ref|YP_874821.1| 47 CPRCAKDYGAYFcRADARSLKYRCPFCGS 75
                                   ************999999*********97 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 !    8.5   0.1    0.0041       2.1       2      11 ..      20      29 ..      20      41 .. 0.93
   2 !   12.3   2.3   0.00026      0.13       4      31 ..      47      75 ..      44      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0041
                 zf-Sec23_Sec24  2 irCrrCrayl 11
                                   +rCr C++yl
  gi|118431033|ref|YP_874821.1| 20 VRCRVCGTYL 29
                                   7********8 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
                 zf-Sec23_Sec24  4 CrrC.raylNpfckidfggkrwiCnfCnh 31
                                   C rC + y   fc+ d ++ +++C+fC++
  gi|118431033|ref|YP_874821.1| 47 CPRCaKDYGAYFCRADARSLKYRCPFCGS 75
                                   666534577789***************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 ?    5.4   0.1     0.028        14       8      18 ..      21      31 ..      18      38 .. 0.81
   2 ?   -0.5   0.1       1.9   9.7e+02       6      12 ..      44      50 ..      40      52 .. 0.82
   3 !   10.4   0.0   0.00075      0.37       6      20 ..      67      81 ..      63      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.028
                                   E-TTT--EEEE CS
                Desulfoferrod_N  8 kCevCGniVeV 18
                                   +C vCG    +
  gi|118431033|ref|YP_874821.1| 21 RCRVCGTYLDI 31
                                   9*****76665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                                   EEE-TTT CS
                Desulfoferrod_N  6 vYkCevC 12
                                   vY C  C
  gi|118431033|ref|YP_874821.1| 44 VYACPRC 50
                                   9999988 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00075
                                   EEE-TTT--EEEECC CS
                Desulfoferrod_N  6 vYkCevCGniVeVle 20
                                   +Y+C  CG + +V+ 
  gi|118431033|ref|YP_874821.1| 67 KYRCPFCGSELVVIS 81
                                   7*******9999875 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0023       1.2      13      27 ..      16      30 ..       7      42 .. 0.84
   2 !    7.3   0.1    0.0092       4.6       6      26 ..      57      77 ..      53      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0023
                                   GSS--EETTTTEE-- CS
                         zf-BED 13 keqkavCryCgkils 27
                                    +++++Cr Cg  l+
  gi|118431033|ref|YP_874821.1| 16 GWTRVRCRVCGTYLD 30
                                   79********97665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0092
                                   SS----GGSS--EETTTTEE- CS
                         zf-BED  6 yftpvslkeqkavCryCgkil 26
                                   yf ++++++ k +C +Cg +l
  gi|118431033|ref|YP_874821.1| 57 YFCRADARSLKYRCPFCGSEL 77
                                   99999*************876 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 !   12.2   1.4   0.00027      0.14      71      97 ..      20      78 ..      14      88 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                   EEETTTS-EEECHHHHH.................................S-TTTSSS-E CS
                           HypA 71 vrCreCgkefeleekal.................................rCpkCgsadv 97
                                   vrCr+Cg+  +++ +                                   rCp Cgs+ v
  gi|118431033|ref|YP_874821.1| 20 VRCRVCGTYLDITGQ-PpggrsitlvyacprcakdygayfcradarslkyRCPFCGSELV 78
                                   667777766665543.12344556666444444444444555555666668888888765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.2   0.00013     0.065       2      42 ..      21      80 ..       8      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                   --SSS-S--EE-S.........SEEE-TTT--..........EEEEEEE-SSS-S---EE CS
                 zinc-ribbons_6  2 kCpeCqqelekrg.........eqyhCeaCqe..........dlkkealCpeCeqelevl 42
                                    C+ C + l+ +g           y C  C +            + +  Cp C++el v+
  gi|118431033|ref|YP_874821.1| 21 RCRVCGTYLDITGqppggrsitLVYACPRCAKdygayfcradARSLKYRCPFCGSELVVI 80
                                   588899888855558888888877888888887777777775556778899999999876 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.26   1.3e+02       3      11 ..      20      29 ..      19      34 .. 0.72
   2 ?    3.2   0.6      0.12        61       4       9 ..      46      51 ..      44      60 .. 0.83
   3 !   10.8   0.1   0.00052      0.26       2      11 ..      67      77 ..      66      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.26
                    zf-ribbon_3  3 vrCPnCGa.p 11
                                   vrC  CG+ +
  gi|118431033|ref|YP_874821.1| 20 VRCRVCGTyL 29
                                   6788888744 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                    zf-ribbon_3  4 rCPnCG 9 
                                    CP+C 
  gi|118431033|ref|YP_874821.1| 46 ACPRCA 51
                                   799996 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00052
                    zf-ribbon_3  2 tvrCPnCGa.p 11
                                   ++rCP CG+ +
  gi|118431033|ref|YP_874821.1| 67 KYRCPFCGSeL 77
                                   58999999866 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.017       8.6      42      57 ..      16      31 ..       9      38 .. 0.82
   2 ?    2.0   0.1      0.45   2.2e+02      20      29 ..      43      52 ..      36      56 .. 0.79
   3 !    7.9   0.1    0.0064       3.2      21      35 ..      67      80 ..      59      88 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                           Elf1 42 kiaevsCkvCgesfet 57
                                   +  +v+C+vCg+++++
  gi|118431033|ref|YP_874821.1| 16 GWTRVRCRVCGTYLDI 31
                                   56789******98875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.45
                           Elf1 20 tkFdCpfCnh 29
                                    ++ Cp+C +
  gi|118431033|ref|YP_874821.1| 43 LVYACPRCAK 52
                                   5789****87 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0064
                           Elf1 21 kFdCpfCnheksvev 35
                                   k++CpfC++e  v +
  gi|118431033|ref|YP_874821.1| 67 KYRCPFCGSE-LVVI 80
                                   799******9.5544 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 ?    0.2   0.0       1.5   7.5e+02      36      42 ..      21      27 ..      14      34 .. 0.71
   2 ?   13.9   0.6   7.9e-05     0.039      14      46 ..      44      79 ..      38      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.5
                       zf-C2HC5 36 pCsfCgs 42
                                   +C  Cg+
  gi|118431033|ref|YP_874821.1| 21 RCRVCGT 27
                                   5666665 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.9e-05
                       zf-C2HC5 14 leaapnCln.CGkiiCakegls..kpCsfCgsplls 46
                                   + a p C +  G   C +++ s   +C+fCgs+l+ 
  gi|118431033|ref|YP_874821.1| 44 VYACPRCAKdYGAYFCRADARSlkYRCPFCGSELVV 79
                                   4455666532488899999877779********975 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 ?    5.1   0.1     0.042        21      25      34 ..      20      29 ..       7      33 .. 0.77
   2 ?   10.0   6.5    0.0013      0.64       4      36 ..      44      79 ..      43      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.042
                 Zn_ribbon_SprT 25 YrCrrCkgtL 34
                                    rCr C+  L
  gi|118431033|ref|YP_874821.1| 20 VRCRVCGTYL 29
                                   69****8766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                 Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhn...YrCrrCkgtLrg 36
                                   vY C++C + y++ +    ++   YrC+ C+++L+ 
  gi|118431033|ref|YP_874821.1| 44 VYACPRCAKDYGAYFCRADARslkYRCPFCGSELVV 79
                                   79*********999988555569*********9986 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0         1   5.1e+02       9      21 ..      14      26 ..      12      28 .. 0.79
   2 ?    5.6   0.0     0.046        23      15      24 ..      45      54 ..      38      56 .. 0.85
   3 ?    7.3   0.3     0.014       6.9      14      21 ..      67      74 ..      64      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1
                      zf-H2C2_2  9 HtgekpyeCplCd 21
                                   H g +++ C +C+
  gi|118431033|ref|YP_874821.1| 14 HEGWTRVRCRVCG 26
                                   55667899****7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.046
                      zf-H2C2_2 15 yeCplCdkaF 24
                                   y Cp C+k +
  gi|118431033|ref|YP_874821.1| 45 YACPRCAKDY 54
                                   99*****987 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.014
                      zf-H2C2_2 14 pyeCplCd 21
                                   +y Cp+C+
  gi|118431033|ref|YP_874821.1| 67 KYRCPFCG 74
                                   49*****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.13        67       2       9 ..      21      28 ..      19      33 .. 0.62
   2 ?   11.3   3.2   0.00036      0.18       1      28 [.      45      76 ..      45      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                                   EETTTTCE CS
                   TF_Zn_Ribbon  2 kCPnCgst 9 
                                   +C +Cg++
  gi|118431033|ref|YP_874821.1| 21 RCRVCGTY 28
                                   46666653 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00036
                                   EEETTTTCEE.C...HEETSTTCEEESSSSBE CS
                   TF_Zn_Ribbon  1 ykCPnCgstn.l...veDpergelvCtdCGlV 28
                                   y CP C  ++       D+ +  ++C++CG+ 
  gi|118431033|ref|YP_874821.1| 45 YACPRCAKDYgAyfcRADARSLKYRCPFCGSE 76
                                   6799999887557788899999*******986 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 ?    3.5   1.1      0.15        76      15      26 ..      42      53 ..      17      64 .. 0.83
   2 ?    9.0   0.0    0.0029       1.4      15      32 ..      65      82 ..      57      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                                   ESSSB-TTT-SB CS
                         Nop10p 15 TLkkvcpecggp 26
                                   TL + cp+c ++
  gi|118431033|ref|YP_874821.1| 42 TLVYACPRCAKD 53
                                   999999999875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0029
                                   ESSSB-TTT-SB-B-SS- CS
                         Nop10p 15 TLkkvcpecggptksahP 32
                                    Lk++cp cg+++++  P
  gi|118431033|ref|YP_874821.1| 65 SLKYRCPFCGSELVVISP 82
                                   69**********999888 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.0     0.015       7.6       7      34 ..      21      52 ..      19      55 .. 0.68
   2 ?   11.5   4.2   0.00051      0.25       6      36 ..      45      77 ..      42      80 .. 0.86
   3 ?    8.9   0.1    0.0033       1.6       6      18 ..      68      80 ..      65      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.015
                    Zn-ribbon_8  7 rCeeCghefevlqsisdap......lta.CPeCgs 34
                                   rC+ Cg+  ++     ++p      l+  CP+C +
  gi|118431033|ref|YP_874821.1| 21 RCRVCGTYLDITG---QPPggrsitLVYaCPRCAK 52
                                   8999999988333...3344444567788****75 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00051
                    Zn-ribbon_8  6 YrCeeCghefe.vlqsisdaplta.CPeCgsev 36
                                   Y C +C +++   +++++ ++l+  CP Cgse+
  gi|118431033|ref|YP_874821.1| 45 YACPRCAKDYGaYFCRADARSLKYrCPFCGSEL 77
                                   9*********977787778889999*****965 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0033
                    Zn-ribbon_8  6 YrCeeCghefevl 18
                                   YrC  Cg+e  v+
  gi|118431033|ref|YP_874821.1| 68 YRCPFCGSELVVI 80
                                   8888888776665 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00087      0.44      25      44 ..      18      40 ..      13      43 .. 0.86
   2 ?   -0.4   0.1         2   9.9e+02      10      15 ..      47      52 ..      40      60 .. 0.78
   3 ?    5.5   0.0     0.028        14       6      22 ..      66      82 ..      61      88 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00087
                                   S-EEESSSTCEE...EEECSSSE CS
                 Ribosomal_S27e 25 tvvkCisCgkvL...vePtGGka 44
                                   t v C  Cg+ L   ++P GG++
  gi|118431033|ref|YP_874821.1| 18 TRVRCRVCGTYLditGQPPGGRS 40
                                   78*******9876668*****96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                                   -TTTS- CS
                 Ribosomal_S27e 10 CpdCen 15
                                   Cp C +
  gi|118431033|ref|YP_874821.1| 47 CPRCAK 52
                                   888865 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.028
                                   EEEE-TTTS-EEEEESS CS
                 Ribosomal_S27e  6 ldvkCpdCenetvvFsh 22
                                   l+ +Cp C+ e vv s 
  gi|118431033|ref|YP_874821.1| 66 LKYRCPFCGSELVVISP 82
                                   7889*******999875 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 ?    1.9   0.1       0.6     3e+02       4       9 ..      22      27 ..      18      34 .. 0.65
   2 ?    5.9   0.3     0.035        17      37      45 ..      42      50 ..      39      51 .. 0.83
   3 ?    6.5   0.0     0.022        11       4      17 ..      70      83 ..      64      88 .] 0.65

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.6
                        zf-IS66  4 CpcCGg 9 
                                   C  CG+
  gi|118431033|ref|YP_874821.1| 22 CRVCGT 27
                                   666666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.035
                        zf-IS66 37 rpkyaCpcC 45
                                     +yaCp+C
  gi|118431033|ref|YP_874821.1| 42 TLVYACPRC 50
                                   568****** PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.022
                        zf-IS66  4 CpcCGgllkpiged 17
                                   Cp CG++l+ i  +
  gi|118431033|ref|YP_874821.1| 70 CPFCGSELVVISPV 83
                                   77777766666655 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.9    0.0044       2.2      27      52 ..      54      78 ..      18      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0044
                        DUF1272 27 yEctFCaeCaeevlenvCPncgGelv 52
                                   y   FC++ a ++ + +CP cg elv
  gi|118431033|ref|YP_874821.1| 54 YGAYFCRADARSL-KYRCPFCGSELV 78
                                   5556888877765.99******9998 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 ?    0.2   0.0       1.9   9.4e+02      31      40 ..      19      28 ..      13      33 .. 0.71
   2 ?    3.2   0.6      0.22   1.1e+02       3      12 ..      45      54 ..      42      61 .. 0.71
   3 ?    9.3   0.1    0.0028       1.4       2      12 ..      67      77 ..      66      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.9
                        zf-Di19 31 evvCPvCaek 40
                                    v C vC ++
  gi|118431033|ref|YP_874821.1| 19 RVRCRVCGTY 28
                                   5778888654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.22
                        zf-Di19  3 ftCPyCgkel 12
                                   ++CP C k++
  gi|118431033|ref|YP_874821.1| 45 YACPRCAKDY 54
                                   5677777654 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0028
                        zf-Di19  2 sftCPyCgkel 12
                                   ++ CP+Cg el
  gi|118431033|ref|YP_874821.1| 67 KYRCPFCGSEL 77
                                   589****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 ?    2.7   0.5      0.25   1.3e+02      18      32 ..      19      31 ..      13      42 .. 0.75
   2 ?    7.4   1.0    0.0083       4.1      20      34 ..      46      61 ..      36      67 .. 0.83
   3 ?    8.6   0.2    0.0035       1.8      20      28 ..      69      78 ..      64      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.25
                  Zn_Tnp_IS1595 18 gfvCPhCgsrkayri 32
                                   +++C  Cg  ++  i
  gi|118431033|ref|YP_874821.1| 19 RVRCRVCG--TYLDI 31
                                   46799999..55555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0083
                  Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt 34
                                    CP+C+++  ay+ ++
  gi|118431033|ref|YP_874821.1| 46 ACPRCAKDyGAYFCRA 61
                                   5******999999876 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0035
                  Zn_Tnp_IS1595 20 vCPhCgsr.k 28
                                   +CP+Cgs+  
  gi|118431033|ref|YP_874821.1| 69 RCPFCGSElV 78
                                   7*****9863 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.5   7.6e+02      24      33 ..      18      27 ..       7      31 .. 0.80
   2 ?    8.0   1.6    0.0068       3.4      19      35 ..      38      54 ..      21      60 .. 0.69
   3 ?    4.6   0.4     0.076        38      21      33 ..      63      75 ..      57      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                           C1_4 24 sryrCekCkn 33
                                   +r+rC+ C +
  gi|118431033|ref|YP_874821.1| 18 TRVRCRVCGT 27
                                   5899999965 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0068
                           C1_4 19 eeltssryrCekCkndF 35
                                    ++ +++y+C++C +d+
  gi|118431033|ref|YP_874821.1| 38 GRSITLVYACPRCAKDY 54
                                   467899*******9987 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.076
                           C1_4 21 ltssryrCekCkn 33
                                   + s+ yrC+ C +
  gi|118431033|ref|YP_874821.1| 63 ARSLKYRCPFCGS 75
                                   56899******76 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.088        44       2      10 ..      19      27 ..      15      29 .. 0.70
   2 ?    6.1   3.4      0.02        10      14      23 ..      45      54 ..      44      60 .. 0.87
   3 ?    7.2   1.8     0.009       4.5      12      21 ..      66      75 ..      55      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.088
                                   --B-TTT-S CS
                         zf-HIT  2 rklCgvCgf 10
                                   r  C vCg 
  gi|118431033|ref|YP_874821.1| 19 RVRCRVCGT 27
                                   556777764 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                                   EE-TTT--EE CS
                         zf-HIT 14 YkCpkCntry 23
                                   Y Cp+C+  y
  gi|118431033|ref|YP_874821.1| 45 YACPRCAKDY 54
                                   9*****9986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.009
                                   -SEE-TTT-- CS
                         zf-HIT 12 akYkCpkCnt 21
                                    kY+Cp C+ 
  gi|118431033|ref|YP_874821.1| 66 LKYRCPFCGS 75
                                   59******86 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 ?   -0.2   3.3       2.8   1.4e+03       4       9 ..      45      50 ..       5      62 .. 0.73
   2 ?   11.6   0.1   0.00055      0.27       4      16 ..      68      80 ..      67      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.8
                Lar_restr_allev  4 kpCPfC 9 
                                   + CP C
  gi|118431033|ref|YP_874821.1| 45 YACPRC 50
                                   556666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00055
                Lar_restr_allev  4 kpCPfCggravle 16
                                   + CPfCg++ v++
  gi|118431033|ref|YP_874821.1| 68 YRCPFCGSELVVI 80
                                   68******98876 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   5.4      0.13        65      20      38 ..      21      50 ..       3      79 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
                           C1_2 20 nCsaCgrk.......idgff.......YsCseC 38
                                   +C++Cg+                    Y C++C
  gi|118431033|ref|YP_874821.1| 21 RCRVCGTYlditgqpP---GgrsitlvYACPRC 50
                                   6666666655433330...02334455666666 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.63   3.1e+02      14      20 ..      20      26 ..      13      28 .. 0.81
   2 ?    5.5   0.4     0.038        19       9      23 ..      40      54 ..      37      59 .. 0.85
   3 ?    6.1   0.4     0.025        12       6      21 ..      59      75 ..      56      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.63
                         zf-AN1 14 fkCryCg 20
                                   ++Cr Cg
  gi|118431033|ref|YP_874821.1| 20 VRCRVCG 26
                                   89****8 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.038
                         zf-AN1  9 kdflpfkCryCgkvF 23
                                   +++l++ C++C k++
  gi|118431033|ref|YP_874821.1| 40 SITLVYACPRCAKDY 54
                                   567789*****9998 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.025
                         zf-AN1  6 Ckkkdflp.fkCryCgk 21
                                   C+       ++C++Cg 
  gi|118431033|ref|YP_874821.1| 59 CRADARSLkYRCPFCGS 75
                                   777774444******96 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.018         9      24      33 ..      18      27 ..      12      29 .. 0.86
   2 ?    3.5   4.6      0.13        67       5      32 ..      47      74 ..      45      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.018
                  zinc_ribbon_4 24 vkvrCskCgh 33
                                   ++vrC  Cg+
  gi|118431033|ref|YP_874821.1| 18 TRVRCRVCGT 27
                                   589*****97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                  zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCg 32
                                   Cp+C + y     +  a+  k rC+ Cg
  gi|118431033|ref|YP_874821.1| 47 CPRCAKDYGAYFCRADARSLKYRCPFCG 74
                                   ******9987777777777777777776 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 ?   -0.2   0.1       2.1   1.1e+03       2       7 ..      22      27 ..      20      29 .. 0.76
   2 ?   -0.0   0.4       1.9   9.5e+02       2       5 ..      47      50 ..      46      52 .. 0.85
   3 ?   10.5   0.2   0.00096      0.48       1      10 [.      69      78 ..      69      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.1
                 DNA_ligase_ZBD  2 CPvCGs 7 
                                   C vCG+
  gi|118431033|ref|YP_874821.1| 22 CRVCGT 27
                                   559997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.9
                 DNA_ligase_ZBD  2 CPvC 5 
                                   CP C
  gi|118431033|ref|YP_874821.1| 47 CPRC 50
                                   9999 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00096
                 DNA_ligase_ZBD  1 hCPvCGsavv 10
                                   +CP CGs++v
  gi|118431033|ref|YP_874821.1| 69 RCPFCGSELV 78
                                   5*******98 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 ?    2.0   0.0      0.41     2e+02      32      43 ..      18      29 ..      11      32 .. 0.80
   2 ?    8.8   0.4     0.003       1.5      23      42 ..      57      76 ..      54      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.41
                                   TEEEETTT--EE CS
                         PyrI_C 32 vklkCkYCekei 43
                                   ++++C+ C++ +
  gi|118431033|ref|YP_874821.1| 18 TRVRCRVCGTYL 29
                                   789*****9876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.003
                                   EEEEEETTTTEEEETTT--E CS
                         PyrI_C 23 kFkvedkekvklkCkYCeke 42
                                    F + d   +k++C +C+ e
  gi|118431033|ref|YP_874821.1| 57 YFCRADARSLKYRCPFCGSE 76
                                   57789999*********986 PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.5   7.7e+02       6      14 ..      21      29 ..      18      34 .. 0.81
   2 ?    4.0   0.3      0.12        58       2      15 ..      42      55 ..      41      63 .. 0.84
   3 ?    6.1   0.0     0.026        13       3      19 ..      66      82 ..      64      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                                   EETTT--BT CS
                        DUF2757  6 rCrhCgkki 14
                                   rCr Cg+ +
  gi|118431033|ref|YP_874821.1| 21 RCRVCGTYL 29
                                   7****9876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                                   --EEEETTT--BTT CS
                        DUF2757  2 aihYrCrhCgkkig 15
                                   +++Y C++C k  g
  gi|118431033|ref|YP_874821.1| 42 TLVYACPRCAKDYG 55
                                   589******98766 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.026
                                   -EEEETTT--BTT-SST CS
                        DUF2757  3 ihYrCrhCgkkigtlek 19
                                   ++YrC+ Cg ++  ++ 
  gi|118431033|ref|YP_874821.1| 66 LKYRCPFCGSELVVISP 82
                                   89*******99887765 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 ?    3.8   0.2      0.19        95       2      10 ..      19      27 ..      18      35 .. 0.78
   2 ?    3.0   0.5      0.34   1.7e+02       4      10 ..      46      52 ..      44      61 .. 0.85
   3 ?    6.7   0.1     0.023        11       4      16 ..      69      81 ..      67      88 .] 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.19
                        zf-ISL3  2 phrCPnCgs 10
                                   + rC+ Cg 
  gi|118431033|ref|YP_874821.1| 19 RVRCRVCGT 27
                                   467888886 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.34
                        zf-ISL3  4 rCPnCgs 10
                                   +CP+C++
  gi|118431033|ref|YP_874821.1| 46 ACPRCAK 52
                                   6****86 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.023
                        zf-ISL3  4 rCPnCgsktvvkh 16
                                   rCP Cgs  vv+ 
  gi|118431033|ref|YP_874821.1| 69 RCPFCGSELVVIS 81
                                   8******976665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.13        63      16      21 ..      22      27 ..      20      32 .. 0.61
   2 ?    0.8   1.9      0.87   4.3e+02       2       5 ..      47      50 ..      46      61 .. 0.73
   3 ?    8.1   0.2    0.0046       2.3      16      23 .]      70      77 ..      67      78 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                  zinc_ribbon_2 16 CpyCGt 21
                                   C  CGt
  gi|118431033|ref|YP_874821.1| 22 CRVCGT 27
                                   555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.87
                  zinc_ribbon_2  2 CpnC 5 
                                   Cp+C
  gi|118431033|ref|YP_874821.1| 47 CPRC 50
                                   6666 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0046
                  zinc_ribbon_2 16 CpyCGtpl 23
                                   Cp CG++l
  gi|118431033|ref|YP_874821.1| 70 CPFCGSEL 77
                                   66666554 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 ?    0.6   0.0       1.2   6.2e+02      15      24 ..      18      27 ..       9      32 .. 0.81
   2 ?    2.3   0.3      0.38   1.9e+02      17      23 ..      45      51 ..      40      63 .. 0.82
   3 ?    7.2   2.6     0.011       5.5       2      23 ..      47      74 ..      46      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.2
                       zf-Mss51 15 vdfeCpdCGi 24
                                    ++ C  CG 
  gi|118431033|ref|YP_874821.1| 18 TRVRCRVCGT 27
                                   5678****95 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.38
                       zf-Mss51 17 feCpdCG 23
                                   + Cp+C+
  gi|118431033|ref|YP_874821.1| 45 YACPRCA 51
                                   8999996 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.011
                       zf-Mss51  2 CPvpkhkqt......apkhvdfeCpdCG 23
                                   CP ++++ +      + ++ ++ Cp CG
  gi|118431033|ref|YP_874821.1| 47 CPRCAKDYGayfcraDARSLKYRCPFCG 74
                                   9999988889999999999********9 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 ?    2.7   0.1      0.62   3.1e+02       2       8 ..      21      27 ..      20      32 .. 0.80
   2 ?    3.8   0.5      0.27   1.3e+02       1      10 [.      45      54 ..      45      63 .. 0.83
   3 ?    5.9   0.2     0.056        28       1       7 [.      68      74 ..      68      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.62
                      zf-C2H2_4  2 kCpiCgk 8 
                                   +C++Cg+
  gi|118431033|ref|YP_874821.1| 21 RCRVCGT 27
                                   7****76 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.27
                      zf-C2H2_4  1 fkCpiCgksF 10
                                   + Cp C k +
  gi|118431033|ref|YP_874821.1| 45 YACPRCAKDY 54
                                   89****7776 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.056
                      zf-C2H2_4  1 fkCpiCg 7 
                                   ++Cp+Cg
  gi|118431033|ref|YP_874821.1| 68 YRCPFCG 74
                                   89****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 ?    0.0   0.0       1.3   6.5e+02       3      14 ..      20      31 ..      18      35 .. 0.76
   2 ?    4.8   0.2     0.044        22       3      10 ..      45      52 ..      44      54 .. 0.86
   3 ?    2.8   0.1      0.18        89       3      12 ..      68      77 ..      67      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
                         zf_UBZ  3 ylCerCgkeipe 14
                                   + C  Cg+++ +
  gi|118431033|ref|YP_874821.1| 20 VRCRVCGTYLDI 31
                                   57999*998876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.044
                         zf_UBZ  3 ylCerCgk 10
                                   y C+rC k
  gi|118431033|ref|YP_874821.1| 45 YACPRCAK 52
                                   89****76 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.18
                         zf_UBZ  3 ylCerCgkei 12
                                   y C+ Cg+e+
  gi|118431033|ref|YP_874821.1| 68 YRCPFCGSEL 77
                                   99*****875 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 ?    2.2   8.8      0.34   1.7e+02      25      46 ..      46      76 ..      18      78 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.34
                                   E-HHHHHHHHH.........TT-B-TTT--B CS
                     zf-C3HC4_3 25 lCeeCaekllk.........rkkkCpiCrrp 46
                                   +C +Ca+++ +          k +Cp+C ++
  gi|118431033|ref|YP_874821.1| 46 ACPRCAKDYGAyfcradarsLKYRCPFCGSE 76
                                   4555555554444445554459******876 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4     0.017       8.5      20      34 ..       8      25 ..       6      26 .. 0.81
   2 ?    1.8   5.6       0.4     2e+02       7      34 ..      46      73 ..      40      74 .. 0.75
   3 ?    3.5   0.1      0.12        61       7      17 ..      69      79 ..      63      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                     Zn_Tnp_IS1 20 GkstagHe...RfrCrdC 34
                                   G ++ gHe   R rCr C
  gi|118431033|ref|YP_874821.1|  8 GTNAMGHEgwtRVRCRVC 25
                                   7888889766699***99 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.4
                     Zn_Tnp_IS1  7 hCPrCsstdVyRhGkstagHeRfrCrdC 34
                                    CPrC  +      +  a+  ++rC  C
  gi|118431033|ref|YP_874821.1| 46 ACPRCAKDYGAYFCRADARSLKYRCPFC 73
                                   6****98875556777777778888666 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                     Zn_Tnp_IS1  7 hCPrCsstdVy 17
                                    CP C s+ V+
  gi|118431033|ref|YP_874821.1| 69 RCPFCGSELVV 79
                                   69999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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):              36  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 601.43
//
Query:       gi|118431034|ref|YP_874822.1|  [L=112]
Description: hypothetical protein APE_0420.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 846.42
//
Query:       gi|14600696|ref|NP_147216.1|  [L=238]
Description: hypothetical protein APE_0421 [Aeropyrum pernix K1]
Scores for complete 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-47  161.3   0.0    2.8e-47  161.0   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
      0.002   17.8   0.0      0.003   17.2   0.0    1.4  1  ThiI             Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.039   14.5   0.1      0.064   13.8   0.1    1.4  1  Usp              Universal stress protein family
      0.075   12.5   0.0       0.12   11.8   0.0    1.4  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.0   6.3e-51   2.8e-47       2     198 ..       3     206 ..       2     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 6.3e-51
               Diphthami_syn_2   2 kvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGipli..kletaGeeekevedLkg 79 
                                   +v +l sGGkDs++aLy  l +  ev  + +v +  ++s+mfh+  ++   l+ae++G+     +  ++G++e eve+Lk 
  gi|14600696|ref|NP_147216.1|   3 RVCALLSGGKDSNYALYLSLARgDEVVCILAVKPRRRDSWMFHTAALEAPRLQAEAMGLSHAyrEAVVSGVREREVEELKA 83 
                                   799***************998879***********************************8651166789************ PP

               Diphthami_syn_2  80 tlkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrri 156
                                    l +l+     +++v G+i+s yq +r   + r++     aP+W+ dpee+l++ v ++f+ ++   + +gl+ +++Gr +
  gi|14600696|ref|NP_147216.1|  84 VLTRLRsetgFDTIVLGGIASRYQLERARMLARHVAAGVYAPIWGVDPEEHLLNLVRNGFKFVISRASTMGLGAEYVGRVF 164
                                   *****97777789******************************************************************** PP

               Diphthami_syn_2 157 dkklidelkklsekygidkagegGeaetlvlDaPlfkkrlev 198
                                   d +l  e+  ls +yg ++a+egGeaetlvlDaP ++  l v
  gi|14600696|ref|NP_147216.1| 165 DEDLAREVIALSRRYGFNPAFEGGEAETLVLDAPHYRMGLCV 206
                                   ************************************988766 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.6e-07     0.003       5      34 ..       3      32 ..       1      89 [. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.6e-07
                          ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvh 34
                                  +v aLlSgG DS  a yl l RG +vv++ 
  gi|14600696|ref|NP_147216.1|  3 RVCALLSGGKDSNYALYLSLARGDEVVCIL 32
                                  689************************986 PP

>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.4e-05     0.064      21     111 ..      16     101 ..      13     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEEESSHHHHHHHHHHH CS
                           Usp  21 wAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvveegdpaeeilevaee 101
                                   +Al l  arg+e++++ +++pr+ +++     + e  +l+ e++ l       a ++++v+ + ++e+ + + +++++  e
  gi|14600696|ref|NP_147216.1|  16 YALYLSLARGDEVVCILAVKPRRRDSWMFHTAALEAPRLQAEAMGLS-----HAYREAVVSGVREREVEELKAVLTRLRSE 91 
                                   68889999999999999999998888877766666666666666665.....456************************** PP

                                   TTSSEEEEES CS
                           Usp 102 edadliVvGs 111
                                    + d iV+G 
  gi|14600696|ref|NP_147216.1|  92 TGFDTIVLGG 101
                                   ********96 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.8e-05      0.12       3      29 ..       5      31 ..       3      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                                  EEE--SSHHHHHHHHHHHHH-SEEEEE CS
                          QueC  3 vvllSGGlDSttvlalakkegkeveal 29
                                    llSGG DS  +l+l +++g+ev ++
  gi|14600696|ref|NP_147216.1|  5 CALLSGGKDSNYALYLSLARGDEVVCI 31
                                  579********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1749.84
//
Query:       gi|118431035|ref|NP_147217.2|  [L=246]
Description: deoxyribonuclease [Aeropyrum pernix K1]
Scores for complete 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-45  154.8   0.0    2.9e-45  154.6   0.0    1.0  1  TatD_DNase    TatD related DNase
  ------ inclusion threshold ------
       0.11   11.8   0.0       0.73    9.1   0.0    2.0  2  Amidohydro_1  Amidohydrolase family


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 !  154.6   0.0   3.3e-49   2.9e-45       2     254 ..       5     243 ..       4     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 3.3e-49
                                    EEEE-TTSCCCTTTHHHHH.HHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHH CS
                     TatD_DNase   2 DaHcHldskefeedreeil.eraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkel 80 
                                    D+H+Hl++  +    ++++ e  ++ +   vv v+ ++++  ++l+l +++ ++v+++lG+HP++v+e +    +e+ +l
  gi|118431035|ref|NP_147217.2|   5 DMHVHLHE--Y---SDREVeEILDADKSLVVVAVSDDLESAWRTLDLWHTFGGRVVPCLGFHPWNVREGRVWEAWEVLRL 79 
                                    9*******..6...44444233333344455667777787889************************9988888999999 PP

                                    HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S- CS
                     TatD_DNase  81 anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgs 160
                                      + ++ v ++Ge+GLD   ++e+t+++q+evF+++++lA++++ +l iH+ +a++++ + +  +    a+++ H+++g 
  gi|118431035|ref|NP_147217.2|  80 --AYRYGVPCLGEVGLDRRFVDEYTWRVQNEVFDAFVQLAEDMGVMLNIHAPDAWKHVAHRIGWTSR--ARFMYHWYTGP 155
                                    ..**************************************************************964..47********* PP

                                    HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HH CS
                     TatD_DNase 161 aeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltle 240
                                    a+  +++ ++++++s++ +++   +++  ++++++pl++l++E+D Py       g r  p +v+++v+ +ae++++++ 
  gi|118431035|ref|NP_147217.2| 156 ATLPRALPEGRVWFSINSAIRV--QEKSVRVAREIPLRSLVVESDGPYNYR----GLRLSPLMVRETVKLVAEARGEDPG 229
                                    ********************99..7899********************888....9************************ PP

                                    HHHHHHHHHHHHHH CS
                     TatD_DNase 241 elaeitaeNakrlf 254
                                     l e+++ N++rl+
  gi|118431035|ref|NP_147217.2| 230 RLMEAISLNSERLL 243
                                    ***********997 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.035   3.1e+02       8      27 ..       5      22 ..       3      47 .. 0.62
   2 ?    9.1   0.0   8.2e-05      0.73     126     173 ..     102     148 ..      91     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.035
                                   EEEEECETTECSSSGHHHHH CS
                   Amidohydro_1  8 DaHvHleqsllrgatledwl 27
                                   D+HvHl  +   ++ +e++l
  gi|118431035|ref|NP_147217.2|  5 DMHVHLHEYS--DREVEEIL 22
                                   99***97663..33455555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 8.2e-05
                                    TCCSHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEE CS
                   Amidohydro_1 126 apafsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehg 173
                                     + +++e  ++ +++a+++++++ iHa +  ++v++++ +   ++ ++
  gi|118431035|ref|NP_147217.2| 102 TWRVQNEVFDAFVQLAEDMGVMLNIHAPDAWKHVAHRIGWTS-RARFM 148
                                    5778899999*****************999999988887776.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1850.77
//
Query:       gi|118431036|ref|NP_147218.2|  [L=116]
Description: hypothetical protein APE_0424.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      143  (0.0079759); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 867.70
//
Query:       gi|118431037|ref|YP_874823.1|  [L=68]
Description: hypothetical protein APE_0424a [Aeropyrum pernix K1]
Scores for complete 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  107.6   0.5    2.7e-31  107.5   0.5    1.0  1  DUF5622   Domain of unknown function (DUF5622)


Domain annotation for each model (and alignments):
>> DUF5622  Domain of unknown function (DUF5622)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.5   1.5e-35   2.7e-31       1      65 [.       3      66 ..       3      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.5e-35
                        DUF5622  1 lKHgKYvYVeredgwYvKvRvLksreevndpekYivlgkkvkkpprkakvlkeddlPeevreklk 65
                                   +KHgKYvYV+r+dgwYvKvRv+k+r + ++pe+Y+++g+k++++p++++vl+ed+lPeevr++l+
  gi|118431037|ref|YP_874823.1|  3 GKHGKYVYVKRGDGWYVKVRVFKNRPQ-DSPERYLIVGPKRREAPITFQVLEEDELPEEVRRALY 66
                                   7**************************.**********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 505.48
//
Query:       gi|118431038|ref|NP_147219.2|  [L=361]
Description: dolichol-phosphate mannosyltransferase [Aeropyrum pernix K1]
Scores for complete 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  105.1   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.5e-20   73.6   5.5    2.4e-20   72.9   5.5    1.4  1  GtrA             GtrA-like protein
    1.2e-10   41.7   0.0    1.9e-10   41.1   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00038   20.9   0.1     0.0078   16.6   0.0    2.5  2  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.16   11.4   0.0       0.35   10.3   0.0    1.6  1  Glyco_transf_21  Glycosyl transferase family 21


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 !  105.1   0.0   9.3e-34   3.3e-30       1     132 [.      12     146 ..      12     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 9.3e-34
                                    EEEEEESS-TTTHHHHHHHHHHH...GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                Glycos_transf_2   1 svviptyNeektlletlesllaq...dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                    sv++pt Ne ++++ ++  l++       + fei++vDD+StD+t e +e+l+++dprvr+i r   +G+++a+ +glr+
  gi|118431038|ref|NP_147219.2|  12 SVIVPTLNERDNIRPLYVGLKKSlegAGLECFEIVFVDDSSTDGTIEEVERLSRSDPRVRLIVRRGEKGLSRAVLEGLRR 91 
                                    8************************99999************************************************** PP

                                    --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
                Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                    a+g++ +++DaD++++p++++ lve+   ++ad+++++r++ +g    ++  +r+
  gi|118431038|ref|NP_147219.2|  92 ARGRVAVVMDADLQHPPETVPLLVEKVAGGEADLAVASRYAPGGRVEGWSLVRRI 146
                                    *****************************************99998888877665 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   5.5   6.8e-24   2.4e-20       1     117 []     242     360 ..     242     360 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 6.8e-24
                           GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakl...lkqflkFvlvsllglll 77 
                                    rF++vG+lg lv+la+++l +++ +  + l+++++f+++++ n il++r+tF++r+  +    l++++k+++ s++g+++
  gi|118431038|ref|NP_147219.2| 242 RFIAVGALGSLVNLAVYTLAFSA-TGVHPLSSILGFEAGLIHNAILHDRITFRNRSMWRShsfLRRLAKYHATSAAGIAV 320
                                    8********************88.55566899***********************98877899***************** PP

                           GtrA  78 nllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                     ++ +++l++ +gl++ll++++gi++++++n++l +++++
  gi|118431038|ref|NP_147219.2| 321 GVAASTILYSLAGLHPLLSQALGIGAGFIVNFTLASRYIW 360
                                    **************************************98 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 !   41.1   0.0   5.2e-14   1.9e-10       1     109 [.       9     115 ..       8     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 5.2e-14
                Glyco_tranf_2_3   1 prdlavlVptfneedvlge...vlesllaqey.prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                    p  ++v+Vpt+ne d ++     l   l  +    +e+v+v+d s+++t+e++e l +  p+  vr++v+ r  g +g s
  gi|118431038|ref|NP_147219.2|   9 PE-VSVIVPTLNERDNIRPlyvGLKKSLEGAGlECFEIVFVDDSSTDGTIEEVERLSRSDPR--VRLIVR-R--GEKGLS 82 
                                    45.9***********88884444667776664255******************998666655..688866.4..56799* PP

                Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrll 109
                                    ra+ e+lr++++++ +++D+D    P+t++ l+
  gi|118431038|ref|NP_147219.2|  83 RAVLEGLRRARGRVAVVMDADLQHPPETVPLLV 115
                                    ****************************98877 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 !   16.6   0.0   2.2e-06    0.0078      50     123 ..      59     130 ..      22     199 .. 0.77
   2 ?    1.9   0.1     0.073   2.6e+02      19      52 ..     220     253 ..     212     343 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                                    HHHHHH.TTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEES CS
                   NTP_transf_3  50 evlaal.arlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvpty 123
                                    ev++    +++vr+++ +  +kg + +++ +lr+a +   ++v+ +D+ + +pe+v  l+++ a  +ad +v+++
  gi|118431038|ref|NP_147219.2|  59 EVERLSrSDPRVRLIVRR-GEKGLSRAVLEGLRRA-RGRVAVVMDADLQH-PPETVPLLVEKVAGGEADLAVASR 130
                                    444332123358888877.48*************9.9***********88.9************99999988865 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.073
                                    HCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHH CS
                   NTP_transf_3  19 lplggkpllervldalraagvdevvvvggdeevl 52 
                                     +lg  ++l+++l+ l+ +++++ + vg   ++ 
  gi|118431038|ref|NP_147219.2| 220 SKLGPSTILDYLLQVLQLSSIPRFIAVGALGSLV 253
                                    6778888999999999988888888877654433 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 ?   10.3   0.0   9.8e-05      0.35       1      68 [.      68     131 ..      68     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.8e-05
                Glyco_transf_21   1 PsvrrllvsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpv 68 
                                    P+vr l+v + ++g+++ v   l +l++a+ ++ v+ D+d   +p+++  l+++++  ++ l ++  +
  gi|118431038|ref|NP_147219.2|  68 PRVR-LIVRRGEKGLSRAV---LEGLRRARGRVAVVMDADLQHPPETVPLLVEKVAGGEADLAVASRY 131
                                    5566.77777777777766...99********************************999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2645.16
//
Query:       gi|118431039|ref|NP_147220.2|  [L=227]
Description: uracil-DNA glycosylase [Aeropyrum pernix K1]
Scores for 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-42  144.3   0.0    3.8e-42  143.9   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 !  143.9   0.0   2.1e-46   3.8e-42       1     140 [.      30     173 ..      30     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 2.1e-46
                                    HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCC CS
                            UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikac 80 
                                    pgegp +a v++vGeaPg+ ed+ g+pF+g+ag+ll++ll+ agl+r      +vyitnvvkcrppgnr +p+++ei+ac
  gi|118431039|ref|NP_147220.2|  30 PGEGPGEAGVMVVGEAPGRMEDRLGRPFVGPAGKLLDSLLELAGLSR-----GEVYITNVVKCRPPGNR-DPREEEIEAC 103
                                    799********************************************.....*****************.********** PP

                                    HHHHHHHHHHHHSSEEEEESHHHHHH........HHHHSCESCCCSCT......SEEEEES-SSTTTTTTT CS
                            UDG  81 aplleeeiellkprlivllGktaakall......geklgklrgklleak.....irvlplphPsplnrnff 140
                                     p+l e+i+l++prl++++G++a ++l+         l ++rg++ + +       + +++hP+++++n  
  gi|118431039|ref|NP_147220.2| 104 LPYLVEQISLIRPRLVIAVGRHAGRTLFrlaglrWPGLARARGRVWRGRiggveLLIAVTYHPAAALYN-P 173
                                    **************************96667665224558888888886777889**************.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1694.00
//
Query:       gi|118431040|ref|NP_147221.2|  [L=600]
Description: hypothetical protein APE_0428.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.2   0.3      0.023   14.3   0.3    1.8  2  Lon_C     Lon protease (S16) C-terminal proteolytic domain
  ------ inclusion threshold ------
      0.043   14.4   0.0      0.089   13.4   0.0    1.5  1  DUF4296   Domain of unknown function (DUF4296)
      0.068   13.2   0.0         13    6.1   0.0    3.2  2  TPR_7     Tetratricopeptide repeat
       0.11   12.6   0.1       0.44   10.6   0.1    2.0  2  MIT       MIT (microtubule interacting and transport) domain
        1.8    9.6   9.3         24    6.1   0.1    4.3  4  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   6.3e-06     0.023     106     175 ..      97     170 ..      85     174 .. 0.79
   2 ?   -1.8   0.0      0.52   1.9e+03      45      91 ..     357     403 ..     350     419 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-06
                                    GGGGGGGHHHHHHHHHHHHTS...--B-TT..BEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGG CS
                          Lon_C 106 PkdGPsaGvtlatalvslltg...kkvrkd..vamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekd 175
                                    P  GPs  ++ a+a+v + +g   ++v+ +    +tG it  G    +GG+  k+ aa+r g   + +P +n+ d
  gi|118431040|ref|NP_147221.2|  97 PVAGPSGSLATAVAVVMAAAGyddVSVHGNygYVITGAITPGGLAAKVGGIPAKCAAANREGY-VLAIPLSNKAD 170
                                    67799999999999988876522245666511569*************************996.46678888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.52
                                    EEEEEESS-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-T CS
                          Lon_C  45 ieavllpgkgklkltGklgdvmkesaqaalsyvrsraeelgidkevf 91 
                                    i a l + +g lk++G ++d+ +e  +  l ++ s  +e+g  +  +
  gi|118431040|ref|NP_147221.2| 357 IKARLESVEGWLKTAGAVKDIGRELRSEDLRIIYSVFREYGYTSADY 403
                                    66777778899999999999999988888888888888887766655 PP

>> DUF4296  Domain of unknown function (DUF4296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.5e-05     0.089      41      68 ..     388     415 ..     368     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                        DUF4296  41 yyeavlkkygitsaefdsSlvyYsrnpe 68 
                                    +  +v+++yg+tsa++ +Slv Y+ n+ 
  gi|118431040|ref|NP_147221.2| 388 IIYSVFREYGYTSADYGRSLVEYMINAY 415
                                    5579********************8875 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.03   1.1e+02       5      24 ..     322     341 ..     319     352 .. 0.91
   2 ?    6.1   0.0    0.0036        13       6      27 ..     436     455 ..     436     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.03
                          TPR_7   5 LarlysrlGdyeeAielyeq 24 
                                    La++y rl d e  ie +++
  gi|118431040|ref|NP_147221.2| 322 LAVAYTRLADAEASIESLKA 341
                                    9**************99886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                          TPR_7   6 arlysrlGdyeeAielyeqsLa 27 
                                    ar+y+++G+y  Ai++++   a
  gi|118431040|ref|NP_147221.2| 436 ARMYEERGNYVAAIGFLRD--A 455
                                    899*************997..3 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8   9.9e+03      33      44 ..      22      34 ..      20      40 .. 0.68
   2 ?   10.6   0.1   0.00012      0.44       6      56 ..     431     486 ..     427     497 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                            MIT 33 lLlqalk.eknee 44
                                   +Ll+a+  e++++
  gi|118431040|ref|NP_147221.2| 22 YLLPAVEgESDSR 34
                                   8999999666643 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                            MIT   6 elvkkAveeDnagnyeeAlelYkealelLlqalk.ekne....errellrekieeY 56 
                                    +lv++A  ++++gny +A+   ++a+   lq+++   +e    e+ el+r+++e  
  gi|118431040|ref|NP_147221.2| 431 KLVSEARMYEERGNYVAAIGFLRDAVSMTLQVVSaAPEEapqpEDLELYRREMEAI 486
                                    699******************************95433345666666666666544 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         5   1.8e+04      20      30 ..     222     232 ..     217     237 .. 0.71
   2 ?    5.7   0.1    0.0091        33       6      43 ..     321     358 ..     318     359 .. 0.91
   3 ?    6.1   0.1    0.0067        24       8      29 ..     436     457 ..     428     481 .. 0.87
   4 ?    0.6   0.4      0.39   1.4e+03       2      29 ..     505     531 ..     504     542 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5
                         TPR_14  20 Aiallrralal 30 
                                    A+++l++a  +
  gi|118431040|ref|NP_147221.2| 222 ALKALEDARGR 232
                                    88888888655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0091
                         TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    +la a+ +l d +++i+ l++     P++a+a+l + +
  gi|118431040|ref|NP_147221.2| 321 MLAVAYTRLADAEASIESLKASPPGEPSSAAAQLGYIK 358
                                    7999******************9999999999998875 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0067
                         TPR_14   8 aeallalGdpdeAiallrrala 29 
                                    a+ ++++G++ +Ai  lr+a++
  gi|118431040|ref|NP_147221.2| 436 ARMYEERGNYVAAIGFLRDAVS 457
                                    7889****************97 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.39
                         TPR_14   2 eallalaeallalGdpdeAiallrrala 29 
                                    ea+ ++ae+l+  +dp+ Aia+ ++a a
  gi|118431040|ref|NP_147221.2| 505 EAYIQYAEVLA-GDDPQLAIAMMEEATA 531
                                    56677777775.7889999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4172.91
//
Query:       gi|118431041|ref|NP_147222.2|  [L=176]
Description: hypothetical protein APE_0429.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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       0.16   12.0   0.0    1.2  1  THP2      Tho complex subunit THP2


Domain annotation for each model (and alignments):
>> THP2  Tho complex subunit THP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.9e-06      0.16      24      70 ..     115     162 ..     103     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.9e-06
                           THP2  24 evseivvddekppkelqeilekyeeesedaeelra.klekYldeiKme 70 
                                    ++ + +++++ +pk ++e+lek+ ee +++++l++ k++++l  iK  
  gi|118431041|ref|NP_147222.2| 115 NDGKEALEKHGAPKGVVEVLEKHYEEIRNIASLEDwKVDEHLKTIKQL 162
                                    44456899***********************998659********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1288.47
//
Query:       gi|14600703|ref|NP_147223.1|  [L=187]
Description: hypothetical protein APE_0431 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00014   21.6   0.0    0.00022   21.0   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.001   18.8   0.0     0.0026   17.5   0.0    1.6  1  AAA_24           AAA domain
     0.0064   16.1   0.0      0.032   13.8   0.0    1.9  2  AAA_25           AAA domain
     0.0067   16.8   0.0     0.0079   16.6   0.0    1.2  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.015   15.6   0.0    1.3  1  AAA_22           AAA domain
      0.037   14.1   0.0      0.057   13.5   0.0    1.3  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.038   14.4   0.0      0.053   13.9   0.0    1.3  1  RNA_helicase     RNA helicase
      0.042   13.4   0.0      0.057   12.9   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.063   12.6   0.0      0.098   12.0   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.12   12.7   0.0       0.18   12.2   0.0    1.3  1  AAA              ATPase family associated with various cellul
       0.13   12.1   0.0       0.21   11.5   0.0    1.3  1  NTPase_1         NTPase
       0.17   11.6   0.0       0.24   11.1   0.0    1.2  1  Sigma54_activat  Sigma-54 interaction domain
       0.26   10.6   0.0        6.7    6.0   0.0    2.0  2  ATPase           KaiC


Domain annotation for each model (and alignments):
>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.6e-07   0.00022      44      82 ..      14      52 ..       9      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-07
                     IstB_IS21 44 iekkenivllGpsGvGKshlaialgveavraglsvlfvr 82
                                  ++++ ++ l G +G GKs +a  +g +av+agl+v ++ 
  gi|14600703|ref|NP_147223.1| 14 VQHRLSLFLYGAPGSGKSLIAHYMGSRAVEAGLRVCHFY 52
                                  67777899***************************8764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.9e-06    0.0026       3      80 ..      18     102 ..      16     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                        AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..........swedfldevvel.......aaelady 66 
                                   l++++yG +g+GK+ +a  +g +++    e+Gl+   +   p+ +           + d+              +a l ++
  gi|14600703|ref|NP_147223.1|  18 LSLFLYGAPGSGKSLIAHYMGSRAV----EAGLRVCHFYTPPNKPrnvvegvmyrEVLDM------SglassllSASLGRC 88 
                                   5789****************77765....8888777666655544676655544444444......14445559999**** PP

                        AAA_24  67 ktlviDtideleel 80 
                                   + lv+Dti+el++l
  gi|14600703|ref|NP_147223.1|  89 SFLVVDTINELYRL 102
                                   ***********986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.3e-05     0.032      22      75 ..       6      62 ..       3      66 .. 0.78
   2 ?   -0.3   0.0      0.48   6.6e+02     143     161 ..      88     106 ..      76     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                        AAA_25 22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlg...pvapeqgkVl 75
                                  + w+++ ++       l+Gapg+GK+ +a  ++   +  G  + +   p ++++++V+
  gi|14600703|ref|NP_147223.1|  6 VPWVLRSVVQHRLSLFLYGAPGSGKSLIAHYMGSRAVeAGLRVCHfytP-PNKPRNVV 62
                                  6799999998888889*************99998888777776666432.33777665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                        AAA_25 143 vrlvviDplsralggdens 161
                                     ++v+D+++++++ +++ 
  gi|14600703|ref|NP_147223.1|  88 CSFLVVDTINELYRLEPTI 106
                                   5689999999999887663 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.7e-06    0.0079      16      55 ..      10      48 ..       8     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                        AAA_16 16 lervrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                  l++v ++r  +++l+G++G+GKs ++     ++ ++g  +
  gi|14600703|ref|NP_147223.1| 10 LRSVVQHR-LSLFLYGAPGSGKSLIAHYMGSRAVEAGLRV 48
                                  77888888.8***************999888888885443 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   1.1e-05     0.015       4      49 ..      16      56 ..      11     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlps 49
                                  ++ +l+++G +G+GK++ +  + ++++e+      + +v  f+t+p+
  gi|14600703|ref|NP_147223.1| 16 HRLSLFLYGAPGSGKSLIAHYMGSRAVEA------GLRVChFYTPPN 56
                                  7899******************9999865......555554555554 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   4.1e-05     0.057      14      43 ..      10      39 ..       7      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                  HHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
               Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhk 43
                                  L +++q  l +fl G++Gsgk+l+A ++ +
  gi|14600703|ref|NP_147223.1| 10 LRSVVQHRLSLFLYGAPGSGKSLIAHYMGS 39
                                  67899*********************9865 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.8e-05     0.053       1      39 [.      20      57 ..      20      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.8e-05
                  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnp 39
                                  ++lyG++g GKS++a+++ ++  ++    +  ++y+  n+
  gi|14600703|ref|NP_147223.1| 20 LFLYGAPGSGKSLIAHYMGSRAVEAG--LRVCHFYTpPNK 57
                                  589**************988877555..344666665554 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 ?   12.9   0.0   4.1e-05     0.057      21      53 ..       5      37 ..       1      66 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                         AAA_7 21 rysyllelllknkkpvllvGptGtGKtviikdl 53
                                  r+ ++l+ +++++ +++l+G  G+GK++i++ +
  gi|14600703|ref|NP_147223.1|  5 RVPWVLRSVVQHRLSLFLYGAPGSGKSLIAHYM 37
                                  7789************************98765 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   7.1e-05     0.098      24      42 ..      19      37 ..       9      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                  Mg_chelatase 24 nlllvGppGsGKtmlakrl 42
                                  +l+l+G+pGsGK+++a+ +
  gi|14600703|ref|NP_147223.1| 19 SLFLYGAPGSGKSLIAHYM 37
                                  6899************876 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   0.0   0.00013      0.18       2      21 ..      21      40 ..      20     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                  EEESSTTSSHHHHHHHHHHH CS
                           AAA  2 llyGppGtGKTllakavake 21
                                   lyG pG GK+l+a+ + + 
  gi|14600703|ref|NP_147223.1| 21 FLYGAPGSGKSLIAHYMGSR 40
                                  79************988766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.21       2      39 ..      20      57 ..      19      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                  EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39
                                  +f+ G pG+GK+ + + + +   + g++v+ fyt+  +
  gi|14600703|ref|NP_147223.1| 20 LFLYGAPGSGKSLIAHYMGSRAVEAGLRVCHFYTPPNK 57
                                  7899******************************9655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.24      15      44 ..      10      39 ..       5      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                  HHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
               Sigma54_activat 15 ikkvaktdlsvlitGesGtGKellaraihe 44
                                  +++v++++ls+++ G  G+GK+l+a+ + +
  gi|14600703|ref|NP_147223.1| 10 LRSVVQHRLSLFLYGAPGSGKSLIAHYMGS 39
                                  57889999*****************99865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0049       6.7      21      46 ..      19      43 ..      13      65 .. 0.77
   2 ?    2.7   0.0     0.049        67     122     178 ..      90     146 ..      79     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0049
                        ATPase 21 vvlitGepGtGKtifalqFlikgaek 46
                                  +  ++G pG+GK+++a +++ + a++
  gi|14600703|ref|NP_147223.1| 19 SLFLYGAPGSGKSLIA-HYMGSRAVE 43
                                  56789*********98.455555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.049
                        ATPase 122 rvviDsitglayeekeavaReilrqlvrvl.kklgvTailvsekssseeaaggygvee 178
                                    +v+D+i+ l y+ ++      +  ++    + +g +a+ v+  +++ee++ gy v e
  gi|14600703|ref|NP_147223.1|  90 FLVVDTINEL-YRLEPTIESVSMLAMAASAvRSTGGVALGVASLRDGEESTPGYSVLE 146
                                   589*******.88888887776666655444****************9*999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1375.28
//
Query:       gi|14600705|ref|NP_147225.1|  [L=174]
Description: hypothetical protein APE_0433 [Aeropyrum pernix K1]
Scores for complete 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-42  144.3   2.1    1.1e-41  142.8   2.1    1.6  1  CarS-like     CDP-archaeol synthase
    9.4e-05   22.3   0.8    9.4e-05   22.3   0.8    1.8  2  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
        6.6    6.8   8.9        1.4    9.1   3.6    2.1  2  Shadoo        Shadow of prion protein, neuroprotective


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 !  142.8   2.1   1.8e-45   1.1e-41       3     175 .]      12     174 .]      10     174 .] 0.86

  Alignments for each domain:
  == domain 1  score: 142.8 bits;  conditional E-value: 1.8e-45
                     CarS-like   3 dlilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilaldssgs 83 
                                   d il++i l+lpa +ana+ v+ GG +pvd+G  l dGrrl+GdG+t  G++aG ++G   g++  l           sg+
  gi|14600705|ref|NP_147225.1|  12 DNILEAIILMLPAMIANATPVVAGGRRPVDMGVVLPDGRRLLGDGKTIEGLLAGFAAGSAAGVLAALA----------SGN 82 
                                   6699******************************************************9999887666..........555 PP

                     CarS-like  84 vlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllaypvk.llpieliilivlitlvlhlsani 163
                                   +l  v  +  +a+Gal Gd++Gsf+krrl+ierG+pa++ldqldf lgal+++  +    +  + + +    l+lhl+ani
  gi|14600705|ref|NP_147225.1|  83 MLLAVH-SPAIALGALAGDMAGSFVKRRLGIERGRPAPLLDQLDFYLGALAVSIALGyTWTPRVAVEAAAAVLLLHLAANI 162
                                   554443.446799*************************************9986543034444455566667789****** PP

                     CarS-like 164 iayklglkdvwy 175
                                    ay lglk+v++
  gi|14600705|ref|NP_147225.1| 163 TAYLLGLKKVPW 174
                                   ***********9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.8   1.6e-08   9.4e-05     170     232 ..      56     112 ..      54     115 .. 0.92
   2 ?   -1.0   0.1       0.2   1.2e+03     129     155 ..     142     168 ..     120     170 .. 0.53

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-08
                                   --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                  CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafgi 232
                                   +KT+eG+++G++a  ++g+l al+ ++      + l++ s  ++l a  GD+  S +KR++gi
  gi|14600705|ref|NP_147225.1|  56 GKTIEGLLAGFAAGSAAGVLAALASGN------MLLAVHSPAIALGALAGDMAGSFVKRRLGI 112
                                   6**********************9999......46777788889999**************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  CTP_transf_1 129 nikeglllvllllalvvaaDigaYffG 155
                                   +++ ++ ++ ++l+l  aa i+aY+ G
  gi|14600705|ref|NP_147225.1| 142 TPRVAVEAAAAVLLLHLAANITAYLLG 168
                                   333344444445555556666666665 PP

>> Shadoo  Shadow of prion protein, neuroprotective
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.6   0.00023       1.4      24      72 ..      36      85 ..      27      93 .. 0.74
   2 ?    1.3   0.3     0.059   3.5e+02      57      77 ..      92     112 ..      82     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
                        Shadoo 24 gargasrvrvrpap.rysaagsslrvaaagaaagaaagaaaglaagsgwr 72
                                  g r      v p   r  + g ++    ag aag+aag+ a la+g+   
  gi|14600705|ref|NP_147225.1| 36 GRRPVDMGVVLPDGrRLLGDGKTIEGLLAGFAAGSAAGVLAALASGNMLL 85
                                  5555555455554415678899999999*****************98665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.059
                        Shadoo  57 aaagaaaglaagsgwrraagp 77 
                                    a ga ag  ags  +r  g 
  gi|14600705|ref|NP_147225.1|  92 IALGALAGDMAGSFVKRRLGI 112
                                   456777777777777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1384.99
//
Query:       gi|118431042|ref|YP_874824.1|  [L=58]
Description: small nucleolar RNP protein Nop10p [Aeropyrum pernix K1]
Scores for complete 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   78.9   1.3    2.3e-22   78.7   1.3    1.0  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
     0.0014   18.5   5.6     0.0014   18.5   5.6    1.6  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.011   15.3   0.4      0.016   14.8   0.4    1.2  1  RecR            RecR protein
      0.017   14.9   6.8       0.66    9.9   3.1    2.2  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.028   14.7   1.0      0.041   14.2   1.0    1.3  1  Ribosomal_L32p  Ribosomal L32p protein family
      0.071   12.6   0.1      0.091   12.2   0.1    1.1  1  DUF1258         Protein of unknown function (DUF1258)
       0.22   11.5   0.4       0.29   11.2   0.4    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.45   10.7   5.9        3.6    7.8   6.0    2.1  1  Zn-ribbon_8     Zinc ribbon domain
       0.99    9.0   4.1         25    4.5   4.2    2.1  1  TF_Zn_Ribbon    TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   1.3   1.2e-25   2.3e-22       1      51 [.       1      52 [.       1      53 [. 0.98

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.2e-25
                                   .----EE-TTT--EESS.SB-TTT-SB-B-SS--S--TT-TTCHHHHHCHHH CS
                         Nop10p  1 mksylrkcgkcrvYTLk.kvcpecggptksahPaRFSPdDkyskyRralKkr 51
                                   m++ lrkc++c++YTL+ + cp cggp+ ++hP+RFSPd ++ kyR++l+k+
  gi|118431042|ref|YP_874824.1|  1 MQWLLRKCRRCGRYTLRrDACPVCGGPVAVPHPPRFSPDNRFIKYRYELQKK 52
                                   99***********************************************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 !   18.5   5.6   6.9e-07    0.0014      10      33 ..       4      26 ..       2      30 .. 0.90
   2 ?   -2.8   0.3       3.2   6.5e+03      22      25 ..      32      35 ..      32      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.9e-07
                        DUF35_N 10 vgqrCpdCGtvqfPPravCphCgs 33
                                   ++++C+ CG++   +r +Cp Cg+
  gi|118431042|ref|YP_874824.1|  4 LLRKCRRCGRYTL-RRDACPVCGG 26
                                   789********96.********98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.2
                        DUF35_N 22 fPPr 25
                                   +PPr
  gi|118431042|ref|YP_874824.1| 32 HPPR 35
                                   8998 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.4     8e-06     0.016      16      34 ..       5      24 ..       4      27 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8e-06
                                   -EE-TTT--EESS.SS-CCC CS
                           RecR 16 vrhCsrCgnltee.dlCaIC 34
                                   +r C+rCg +t + d C++C
  gi|118431042|ref|YP_874824.1|  5 LRKCRRCGRYTLRrDACPVC 24
                                   589*******988689**** 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 ?    9.9   3.1   0.00033      0.66       3      11 ..       7      15 ..       7      18 .. 0.87
   2 ?    6.7   0.1    0.0032       6.4       4      11 ..      21      28 ..      19      29 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                                   B-TTT--BB CS
                   zf-FPG_IleRS  3 pCpRCwryi 11
                                   +C+RC+ry+
  gi|118431042|ref|YP_874824.1|  7 KCRRCGRYT 15
                                   8*******7 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0032
                                   -TTT--BB CS
                   zf-FPG_IleRS  4 CpRCwryi 11
                                   Cp+C++++
  gi|118431042|ref|YP_874824.1| 21 CPVCGGPV 28
                                   *****986 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0     2e-05     0.041      26      46 ..       5      25 ..       3      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                   EEEETTTCCEECTTC-BTTTT CS
                 Ribosomal_L32p 26 lvecpncgelklpHrvcpscG 46
                                   l +c  cg ++l++ +cp cG
  gi|118431042|ref|YP_874824.1|  5 LRKCRRCGRYTLRRDACPVCG 25
                                   569*****************7 PP

>> DUF1258  Protein of unknown function (DUF1258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.5e-05     0.091      18      40 ..       7      29 ..       3      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                        DUF1258 18 fcnkcGkvvaksekcelcggkva 40
                                    c +cG+ + +++ c +cgg+va
  gi|118431042|ref|YP_874824.1|  7 KCRRCGRYTLRRDACPVCGGPVA 29
                                   6*******************997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00015      0.29      72      95 ..       7      27 ..       3      31 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                   EETTTS-EEECHHHHHS-TTTSSS CS
                           HypA 72 rCreCgkefeleekalrCpkCgsa 95
                                   +Cr+Cg +++l+++   Cp Cg+ 
  gi|118431042|ref|YP_874824.1|  7 KCRRCG-RYTLRRD--ACPVCGGP 27
                                   7*****.7777756..7****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 ?    7.8   6.0    0.0018       3.6       7      36 ..       7      28 ..       6      30 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0018
                    Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsev 36
                                   +C++Cg +++ ++        aCP Cg++v
  gi|118431042|ref|YP_874824.1|  7 KCRRCG-RYTLRR-------DACPVCGGPV 28
                                   7*****.888654.......35*****977 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   4.2     0.013        25       2      26 ..       7      26 ..       6      28 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.013
                                   EETTTTCEECHEETSTTCEEESSS.S CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdC.G 26
                                   kC  Cg ++l +D       C+ C G
  gi|118431042|ref|YP_874824.1|  7 KCRRCGRYTLRRD------ACPVCgG 26
                                   7888887665555......3777744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 518.15
//
Query:       gi|118431043|ref|NP_147227.2|  [L=277]
Description: translation initiation factor IF-2 [Aeropyrum pernix K1]
Scores for complete 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   83.3   0.0    2.9e-23   82.2   0.0    1.6  1  EIF_2_alpha    Eukaryotic translation initiation factor 2 alp
    2.6e-13   50.1   0.6      6e-13   48.9   0.6    1.7  1  S1             S1 RNA binding domain
     0.0065   16.6   0.0      0.015   15.4   0.0    1.6  1  Lsr2           Lsr2
  ------ inclusion threshold ------
      0.016   15.5   1.3       0.26   11.6   0.0    2.5  2  Ribosomal_S10  Ribosomal protein S10p/S20e
       0.12   12.7   0.3        1.7    9.0   0.0    2.6  3  DUF2524        Protein of unknown function (DUF2524)
       0.13   12.5   0.2        4.8    7.4   0.0    3.3  4  cwf21          cwf21 domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   9.7e-27   2.9e-23       1     113 [.     131     243 ..     131     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 9.7e-27
                                    HHHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHH CS
                    EIF_2_alpha   1 lyeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaL 79 
                                    +y+ev wkl++ yg+ ++++  ++++++e+l+k+++pee++e L+e++k+++++++vki+ +++l++++ dGve+++++L
  gi|118431043|ref|NP_147227.2| 131 AYREVLWKLEDAYGDPMKGLeAAVLQGREALEKAGVPEEWIEPLLETAKTHVRVKTVKITFYLTLRSMAGDGVERVRKVL 210
                                    599*****************99999******************************************************* PP

                                    HHHST.S..TTSSSEEEEEEEESSSSEEEEEEEE CS
                    EIF_2_alpha  80 kageeasneeeveeeeevkikliapPeYvltvet 113
                                    + +++ + e+ +++++  +i+++++P+Y+++++ 
  gi|118431043|ref|NP_147227.2| 211 E-AAKSQIESFKDSKVVARIYTVGAPKYRVELQG 243
                                    *.5555889889999***************9986 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.6     2e-16     6e-13       2      75 .]      19      93 ..      18      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2e-16
                                   STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                   p +ge+v G+V++v ++Ga+  l+  +gv++f+p se++++  v++++ vlk+ ++v vkv++v k+r+ +++s+k
  gi|118431043|ref|NP_147227.2| 19 PDVGEIVVGTVQEVHDYGAYLILDeyGGVRAFLPWSEIASR-AVRNIHAVLKPRQKVVVKVIRVYKKRGQVDVSLK 93
                                   679*********************999**************.******************************9986 PP

>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     5e-06     0.015      26      59 ..     232     265 ..     212     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5e-06
                           Lsr2  26 ldgveYeiDLseenaeklrdaLapyieaarrvgg 59 
                                    +   +Y ++L+  n+++l++aL++++eaar++ +
  gi|118431043|ref|NP_147227.2| 232 VGAPKYRVELQGYNYKTLEKALEKMVEAARKTAS 265
                                    55568**************************875 PP

>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4     0.083   2.5e+02      14      71 ..      59     114 ..      54     133 .. 0.75
   2 ?   11.6   0.0   8.6e-05      0.26       1      29 [.     238     266 ..     238     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.083
                                    HHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--S--EEEEEEEEEEEEEEEE CS
                  Ribosomal_S10  14 kavkkivraakelgikvkgpvplPtkrkrvtvlksphvdkksreqfeirthkRlidis 71 
                                    +av++i+ ++k  +  v ++++  +kr +v v  +     +s+++ ++  +kR ++  
  gi|118431043|ref|NP_147227.2|  59 RAVRNIHAVLKPRQKVVVKVIRVYKKRGQVDVSLKRVM--DSEKKRKMMFYKRYLKAA 114
                                    68889999999888888889999999999998877777..666777788888888874 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.6e-05
                                    EEEEEESSHHHHHHHHHHHHHHTTSSS-E CS
                  Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgik 29 
                                    r++l++y++k Leka +k+v+aa+++  k
  gi|118431043|ref|NP_147227.2| 238 RVELQGYNYKTLEKALEKMVEAARKTASK 266
                                    789*********************98776 PP

>> DUF2524  Protein of unknown function (DUF2524)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00056       1.7      28      71 ..     121     164 ..     107     166 .. 0.89
   2 ?    0.1   0.0      0.33   9.9e+02       6      26 ..     198     218 ..     193     228 .. 0.72
   3 ?   -1.7   0.0       1.2   3.6e+03      39      48 ..     249     258 ..     239     267 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00056
                        DUF2524  28 akrqehyndeeYteAqlkLEeavneLeklaksandqQreqLeRa 71 
                                    a++ ++  de+Y e + kLE+a+ +  k +++a  q re+Le+a
  gi|118431043|ref|NP_147227.2| 121 AEKLGKSVDEAYREVLWKLEDAYGDPMKGLEAAVLQGREALEKA 164
                                    6677788899***************999999*********9875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.33
                        DUF2524   6 sveellqkceqaieeaeeqfe 26 
                                       + ++++ +++e a++q e
  gi|118431043|ref|NP_147227.2| 198 MAGDGVERVRKVLEAAKSQIE 218
                                    555667888888888888865 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.2
                        DUF2524  39 YteAqlkLEe 48 
                                      +A++k+ e
  gi|118431043|ref|NP_147227.2| 249 LEKALEKMVE 258
                                    3333322221 PP

>> cwf21  cwf21 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.57   1.7e+03       9      20 ..       7      18 ..       6      48 .. 0.86
   2 ?   -1.5   0.0         1     3e+03      35      43 ..     130     138 ..     122     138 .. 0.87
   3 ?    7.4   0.0    0.0016       4.8      10      35 ..     151     176 ..     148     181 .. 0.87
   4 ?   -1.0   0.0      0.67     2e+03      26      39 ..     249     262 ..     234     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.57
                          cwf21  9 IEvkvlelrdeL 20
                                   +Evk+l+ r  L
  gi|118431043|ref|NP_147227.2|  7 VEVKLLKPRKPL 18
                                   89**99988766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1
                          cwf21  35 delRekLlk 43 
                                    +++Re L+k
  gi|118431043|ref|NP_147227.2| 130 EAYREVLWK 138
                                    589*99997 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0016
                          cwf21  10 EvkvlelrdeLEeeglseeeIeervd 35 
                                    E  vl+ r+ LE  g++ee Ie  ++
  gi|118431043|ref|NP_147227.2| 151 EAAVLQGREALEKAGVPEEWIEPLLE 176
                                    889******************98776 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.67
                          cwf21  26 seeeIeervdelRe 39 
                                     e+  e+ v++ R+
  gi|118431043|ref|NP_147227.2| 249 LEKALEKMVEAARK 262
                                    47778999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2009.97
//
Query:       gi|14600707|ref|NP_147228.1|  [L=73]
Description: 30S ribosomal protein S27 [Aeropyrum pernix K1]
Scores for 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-21   74.1   0.4    5.8e-21   73.9   0.4    1.1  1  Ribosomal_S27e   Ribosomal protein S27
    2.1e-05   23.9   1.7    2.8e-05   23.5   1.7    1.1  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00084   18.7   0.9       0.18   11.3   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
    0.00092   19.0   0.4        1.4    8.9   0.0    2.3  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.002   18.0   1.8     0.0028   17.6   1.8    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0023   18.3   0.3     0.0029   17.9   0.3    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.003   17.4   2.9       0.13   12.2   2.9    2.1  1  TFIIS_C          Transcription factor S-II (TFIIS)
     0.0031   17.2   0.6       0.69    9.7   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
     0.0056   16.5   2.2        0.1   12.5   0.7    2.1  2  DUF3797          Domain of unknown function (DUF3797)
     0.0061   16.6   0.2     0.0081   16.2   0.2    1.2  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.011   15.6   0.9        1.6    8.7   0.0    2.3  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.012   15.5   2.3        1.2    9.1   0.1    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.015   15.3   0.1      0.019   15.0   0.1    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.018   15.2   0.3        1.8    8.8   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.039   13.7   1.4       0.13   12.0   1.7    1.7  2  PADR1            PADR1 (NUC008) domain
      0.071   13.0   1.3        0.1   12.5   1.3    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.074   13.1   1.8        1.9    8.6   0.2    2.1  2  CpXC             CpXC protein
       0.21   11.5   2.6        1.4    8.9   2.6    2.1  1  Nudix_N_2        Nudix N-terminal
       0.26   10.7   0.2       0.29   10.5   0.2    1.0  1  Mcm10            Mcm10 replication factor
        6.8    6.8   9.4        6.7    6.8   3.0    2.6  2  DUF1610          Domain of unknown function (DUF1610)
        6.9    7.4   9.2        1.1   10.0   0.7    2.4  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10


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 !   73.9   0.4   6.8e-24   5.8e-21       1      51 [.      19      69 ..      19      73 .] 0.95

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 6.8e-24
                                  -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEE CS
                Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqil 51
                                  prs+Fl v Cp+C+n +vvFsh+     C+ Cg+vLvePtGGka++  +i 
  gi|14600707|ref|NP_147228.1| 19 PRSRFLLVTCPKCGNRQVVFSHSTFRARCLNCGEVLVEPTGGKARILGKIE 69
                                  89********************************************88875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   1.7   3.3e-08   2.8e-05       2      29 ..      27      54 ..      26      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.3e-08
                                  EETTTTCEECHEETSTTCEEESSSSBEE CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                  +CP+Cg++++v+ +++   +C +CG+Vl
  gi|14600707|ref|NP_147228.1| 27 TCPKCGNRQVVFSHSTFRARCLNCGEVL 54
                                  7**************************8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00021      0.18       3      11 ..      26      35 ..      25      38 .. 0.75
   2 !    6.1   0.1    0.0088       7.5       4      14 ..      46      57 ..      44      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                   zf-ribbon_3  3 vrCPnCGa.p 11
                                  v+CP+CG+ +
  gi|14600707|ref|NP_147228.1| 26 VTCPKCGNrQ 35
                                  6788888755 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0088
                   zf-ribbon_3  4 rCPnCGa.plss 14
                                  rC nCG+ ++++
  gi|14600707|ref|NP_147228.1| 46 RCLNCGEvLVEP 57
                                  788999966765 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 !    8.4   0.2    0.0024         2       7      21 ..      21      35 ..      17      37 .. 0.74
   2 !    8.9   0.0    0.0016       1.4      13      25 ..      46      58 ..      45      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0024
                       DUF35_N  7 grLvgqrCpdCGtvq 21
                                   r+++  Cp+CG  q
  gi|14600707|ref|NP_147228.1| 21 SRFLLVTCPKCGNRQ 35
                                  578888888888766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                       DUF35_N 13 rCpdCGtvqfPPr 25
                                  rC +CG v + P+
  gi|14600707|ref|NP_147228.1| 46 RCLNCGEVLVEPT 58
                                  9*******99997 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 !   17.6   1.8   3.3e-06    0.0028      19      44 ..      26      51 ..      18      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                 Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCr 44
                                  ++CP+Cg+r++ +  + ++ +C  C+
  gi|14600707|ref|NP_147228.1| 26 VTCPKCGNRQVVFSHSTFRARCLNCG 51
                                  68*******66666666999**9998 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 !   17.9   0.3   3.4e-06    0.0029       4      36 ..      26      52 ..      24      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-06
               Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga 36
                                    CP Cg+r+v++ +   +a       C +Cg 
  gi|14600707|ref|NP_147228.1| 26 VTCPKCGNRQVVFSHSTFRA------RCLNCGE 52
                                  68*************99987......6777775 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 !   12.2   2.9   0.00015      0.13       2      15 ..      27      40 ..      26      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                       TFIIS_C  2 kCpkCgsreayffq 15
                                  +CpkCg+r+++f  
  gi|14600707|ref|NP_147228.1| 27 TCPKCGNRQVVFSH 40
                                  8**********984 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0008      0.69       2       7 ..      28      33 ..      18      35 .. 0.71
   2 ?    6.0   0.0     0.012        10       2       7 ..      47      52 ..      40      56 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0008
                 zinc_ribbon_2  2 CpnCGa 7 
                                  Cp+CG+
  gi|14600707|ref|NP_147228.1| 28 CPKCGN 33
                                  555554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                 zinc_ribbon_2  2 CpnCGa 7 
                                  C nCG+
  gi|14600707|ref|NP_147228.1| 47 CLNCGE 52
                                  666665 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.7   0.00012       0.1      14      30 ..      26      42 ..      20      47 .. 0.83
   2 ?    4.0   0.1     0.053        45      14      33 ..      45      64 ..      41      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                       DUF3797 14 vqCPeCgNnkvlNsegk 30
                                  v CP+CgN +v  s ++
  gi|14600707|ref|NP_147228.1| 26 VTCPKCGNRQVVFSHST 42
                                  79********9877655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.053
                       DUF3797 14 vqCPeCgNnkvlNsegkvii 33
                                  + C +Cg   v   +gk +i
  gi|14600707|ref|NP_147228.1| 45 ARCLNCGEVLVEPTGGKARI 64
                                  5799***9999999999876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   9.5e-06    0.0081      14      38 ..      27      55 ..      17      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.5e-06
                           DZR 14 fCseCgtklkavaa...edrCpsCgek.v 38
                                  +C++Cg++    ++     rC +Cge  v
  gi|14600707|ref|NP_147228.1| 27 TCPKCGNRQVVFSHstfRARCLNCGEVlV 55
                                  7*******8777778899*******9855 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 ?    5.3   0.3     0.022        19       6      17 ..      27      35 ..      27      39 .. 0.75
   2 ?    8.7   0.0    0.0019       1.6       2      11 ..      42      51 ..      41      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                Zn_ribbon_SprT  6 rCtgCgreythh 17
                                  +C+ Cg   +++
  gi|14600707|ref|NP_147228.1| 27 TCPKCG---NRQ 35
                                  599999...555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0019
                Zn_ribbon_SprT  2 kyvYrCtgCg 11
                                  ++ +rC +Cg
  gi|14600707|ref|NP_147228.1| 42 TFRARCLNCG 51
                                  89******** PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0014       1.2      25      33 ..      25      33 ..      18      34 .. 0.78
   2 ?    6.2   0.2     0.011       9.8      22      34 ..      41      53 ..      37      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                 zinc_ribbon_4 25 kvrCskCgh 33
                                   v+C+kCg+
  gi|14600707|ref|NP_147228.1| 25 LVTCPKCGN 33
                                  588888887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                 zinc_ribbon_4 22 kgvkvrCskCghv 34
                                  ++ ++rC +Cg+v
  gi|14600707|ref|NP_147228.1| 41 STFRARCLNCGEV 53
                                  56789*****987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.2e-05     0.019      70     110 ..      25      68 ..      18      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                   EEEETTTS-EEECHH.H..HHS-TTTSSS-EEEEESSSEEEEEE CS
                          HypA  70 kvrCreCgkefelee.k..alrCpkCgsadveivsGeellvksi 110
                                    v+C +Cg++  + + +  ++rC +Cg+  ve ++G+   + +i
  gi|14600707|ref|NP_147228.1|  25 LVTCPKCGNRQVVFShStfRARCLNCGEVLVEPTGGKARILGKI 68 
                                   589*****9887444223677************99998766665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0021       1.8      26      35 ..      25      35 ..      16      37 .. 0.76
   2 ?    4.7   0.0     0.039        33       7      14 ..      46      53 ..      41      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0021
                   Zn-ribbon_8 26 ltaCPeCgs.e 35
                                  l++CP+Cg  +
  gi|14600707|ref|NP_147228.1| 25 LVTCPKCGNrQ 35
                                  467*****855 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.039
                   Zn-ribbon_8  7 rCeeCghe 14
                                  rC +Cg++
  gi|14600707|ref|NP_147228.1| 46 RCLNCGEV 53
                                  79999964 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.7   0.00016      0.13      14      32 ..      26      44 ..      24      50 .. 0.86
   2 ?   -0.7   0.1       1.5   1.3e+03      15      21 ..      46      52 ..      44      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         PADR1 14 ekCpeCkegqlvfdssgYk 32
                                    Cp+C++ q+vf++s+++
  gi|14600707|ref|NP_147228.1| 26 VTCPKCGNRQVVFSHSTFR 44
                                  57************99764 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                         PADR1 15 kCpeCke 21
                                  +C +C+e
  gi|14600707|ref|NP_147228.1| 46 RCLNCGE 52
                                  7999986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   0.00012       0.1      30      55 ..      27      53 ..      26      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfe 55
                                  tC++Cg ++   + s+ + +C nCg +
  gi|14600707|ref|NP_147228.1| 27 TCPKCGNRQVVfSHSTFRARCLNCGEV 53
                                  8**********999999999****986 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0022       1.9      34      47 ..      22      35 ..      19      39 .. 0.79
   2 ?    5.6   0.1     0.018        16      28      46 ..      35      53 ..      33      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0022
                          CpXC 34 slfeatCpkCgata 47
                                  +++ +tCpkCg++ 
  gi|14600707|ref|NP_147228.1| 22 RFLLVTCPKCGNRQ 35
                                  67889999999865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                          CpXC 28 eklldgslfeatCpkCgat 46
                                  + +++ s f+a+C +Cg+ 
  gi|14600707|ref|NP_147228.1| 35 QVVFSHSTFRARCLNCGEV 53
                                  668999***********85 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.6    0.0017       1.4       3      31 ..      28      53 ..      27      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                                  -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                     Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                  C++CG++   ++    +  R++C +Cg +
  gi|14600707|ref|NP_147228.1| 28 CPKCGNR---QVVFSHSTFRARCLNCGEV 53
                                  9****99...444455899*******987 PP

>> Mcm10  Mcm10 replication factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00034      0.29     294     323 ..      27      57 ..      21      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                         Mcm10 294 kCakCgkRtvsldrlP.skhCsnCgeskwer 323
                                    C+kCg+R v +++      C nCge   e 
  gi|14600707|ref|NP_147228.1|  27 TCPKCGNRQVVFSHSTfRARCLNCGEVLVEP 57 
                                   5***********98762678*****987665 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.0    0.0079       6.7      19      24 .]      28      33 ..      13      33 .. 0.76
   2 ?    3.4   0.5     0.091        78       3       7 ..      49      53 ..      47      59 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0079
                       DUF1610 19 CPNCGE 24
                                  CP+CG+
  gi|14600707|ref|NP_147228.1| 28 CPKCGN 33
                                  *****7 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.091
                       DUF1610  3 SCGae 7 
                                   CG +
  gi|14600707|ref|NP_147228.1| 49 NCGEV 53
                                  45555 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 ?   -2.4   0.2       9.4     8e+03      33      33 ..      14      14 ..       7      23 .. 0.51
   2 ?   10.0   0.7    0.0013       1.1       3      14 ..      26      37 ..      25      45 .. 0.77
   3 ?    3.5   0.1      0.13   1.1e+02       3      13 ..      45      55 ..      43      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.4
                       zf-ISL3 33 v 33
                                  v
  gi|14600707|ref|NP_147228.1| 14 V 14
                                  2 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                       zf-ISL3  3 hrCPnCgsktvv 14
                                   +CP+Cg++ vv
  gi|14600707|ref|NP_147228.1| 26 VTCPKCGNRQVV 37
                                  59*******653 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.13
                       zf-ISL3  3 hrCPnCgsktv 13
                                   rC nCg++ v
  gi|14600707|ref|NP_147228.1| 45 ARCLNCGEVLV 55
                                  68999*99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 556.40
//
Query:       gi|118431044|ref|NP_147229.2|  [L=95]
Description: 50S ribosomal protein L44 [Aeropyrum pernix K1]
Scores for complete 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   93.1   6.5    1.6e-26   92.6   6.5    1.2  1  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.024   15.1   0.9      0.024   15.1   0.9    3.0  3  Ribosomal_L33  Ribosomal protein L33
       0.14   12.1   2.8        7.3    6.6   0.1    2.3  2  zinc_ribbon_4  zinc-ribbon domain
       0.21   11.9   3.3        0.5   10.7   3.3    1.7  1  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.28   11.2   2.0        6.3    6.9   0.1    2.1  2  CpXC           CpXC protein
       0.63   10.1   3.3       0.54   10.3   2.5    1.5  1  NST1           Salt tolerance down-regulator
          6    6.7   7.6         10    5.9   1.1    2.6  3  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB


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 !   92.6   6.5   6.1e-30   1.6e-26       1      76 []      16      91 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 6.1e-30
                                   EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                  Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                   +Hteh+v qy++gk++ +a g+Rry+rkq+gyg+q++p +k++aK+tKK vl ++Ct C++kr   ++R+k++elv
  gi|118431044|ref|NP_147229.2| 16 THTEHRVAQYRAGKRRAMALGERRYRRKQEGYGSQRRPEQKRFAKVTKKQVLVITCTVCGRKRPFLGIRLKRLELV 91
                                   6*************************************************************************96 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.9   9.5e-06     0.024      31      44 ..       8      21 ..       5      22 .. 0.90
   2 ?    1.8   0.4      0.13   3.3e+02      13      42 ..      38      67 ..      29      69 .. 0.81
   3 ?    0.7   0.1      0.29   7.4e+02       6      13 ..      70      77 ..      66      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.5e-06
                                   EEEETTTTEEEEEE CS
                  Ribosomal_L33 31 kKYcprcrkhtlhk 44
                                   + Ycprc+ ht h+
  gi|118431044|ref|NP_147229.2|  8 RTYCPRCNTHTEHR 21
                                   67***********7 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                                   ..EEEEETT..--S--EEEEEETTTTEEEE CS
                  Ribosomal_L33 13 rnYtttknkkntperLelkKYcprcrkhtl 42
                                   r+Y  ++     + r e k++ ++ +k +l
  gi|118431044|ref|NP_147229.2| 38 RRYRRKQEGYGSQRRPEQKRFAKVTKKQVL 67
                                   557777777778888899999999999987 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.29
                                   EET..... CS
                  Ribosomal_L33  6 eCtecksr 13
                                    Ct c+++
  gi|118431044|ref|NP_147229.2| 70 TCTVCGRK 77
                                   69999985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0028       7.3       3      10 ..       9      16 ..       8      33 .. 0.84
   2 ?    5.6   0.5    0.0059        15      18      33 ..      60      76 ..      58      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0028
                  zinc_ribbon_4  3 itCpsCka 10
                                   + Cp+C++
  gi|118431044|ref|NP_147229.2|  9 TYCPRCNT 16
                                   67****98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0059
                  zinc_ribbon_4 18 klpakgv.kvrCskCgh 33
                                   k+++k v  ++C+ Cg 
  gi|118431044|ref|NP_147229.2| 60 KVTKKQVlVITCTVCGR 76
                                   6665555599*****96 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.3    0.0002       0.5      44      90 .]       7      75 ..       1      75 [. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                   CCTB-TTT--B--CTTTEEEEE.......................E-SSS-E.....................EEEEETTTT CS
                           Rpr2 44 krtvCkkCgsvlipgvtcsvrv.......................enkskkkkkkkkka............dvlvvtClaCg 90
                                    rt+C +C++   +   ++ r                        +            +            +vlv+tC+ Cg
  gi|118431044|ref|NP_147229.2|  7 IRTYCPRCNTHT-EHRVAQYRAgkrramalgerryrrkqegygsqR------------RpeqkrfakvtkkQVLVITCTVCG 75
                                   4899****9986.444455555566666667666655444444332............0344555566666999*******7 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.017        44       3      16 ..      11      24 ..       9      37 .. 0.79
   2 ?    6.9   0.1    0.0025       6.3      28      47 ..      59      78 ..      45      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.017
                           CpXC  3 CpaCgkefeaeiwt 16
                                   Cp+C++++e ++ +
  gi|118431044|ref|NP_147229.2| 11 CPRCNTHTEHRVAQ 24
                                   99999998887765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                           CpXC 28 eklldgslfeatCpkCgata 47
                                   +k+ +++++ +tC  Cg+++
  gi|118431044|ref|NP_147229.2| 59 AKVTKKQVLVITCTVCGRKR 78
                                   68999************987 PP

>> NST1  Salt tolerance down-regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.5   0.00021      0.54     136     154 ..      60      78 ..      33      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                           NST1 136 KmKeqqKhsCsCsvCGRkR 154
                                    K+  +q    +C+vCGRkR
  gi|118431044|ref|NP_147229.2|  60 KVTKKQVLVITCTVCGRKR 78 
                                    5666778889********9 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 ?    5.9   1.1     0.004        10      21      29 ..       8      16 ..       8      19 .. 0.89
   2 ?   -1.8   0.0         1   2.6e+03      11      20 ..      36      46 ..      36      47 .. 0.79
   3 ?    4.2   0.1     0.013        34       5      13 ..      69      77 ..      67      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.004
                        zf-RRN7 21 fyyCrrCht 29
                                   ++yC rC t
  gi|118431044|ref|NP_147229.2|  8 RTYCPRCNT 16
                                   69*****98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                        zf-RRN7 11 gcrsftl.ddG 20
                                   g r+++   +G
  gi|118431044|ref|NP_147229.2| 36 GERRYRRkQEG 46
                                   56899999998 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.013
                        zf-RRN7  5 ppCgvCgcr 13
                                   + C vCg +
  gi|118431044|ref|NP_147229.2| 69 ITCTVCGRK 77
                                   68*****75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 706.57
//
Query:       gi|118431045|ref|NP_147230.2|  [L=159]
Description: hypothetical protein APE_0437.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1257.66
//
Query:       gi|118431046|ref|NP_147231.2|  [L=342]
Description: DNA primase small subunit [Aeropyrum pernix K1]
Scores for complete 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   86.0   0.0    5.3e-24   85.2   0.0    1.4  1  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
      0.071   13.6   0.0       0.14   12.6   0.0    1.4  1  Phage_TAC_13   Phage tail assembly chaperone, TAC


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 !   85.2   0.0   5.9e-28   5.3e-24       1     173 [.      96     262 ..      96     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 5.9e-28
                                    EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH... CS
                  DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnl 80 
                                    FDiD+d++++c e ++  ++++  ++av++++ l+  dfg + + ++f+g+rGfH++  + ++r+l++eer++i++y++l
  gi|118431046|ref|NP_147231.2|  96 FDIDVDSLEGCGEVLGDSCLSRGYKQAVRLVEALY-RDFGVP-STLYFTGNRGFHVLADCGWCRRLGREERREIARYFTL 173
                                    9******************************9999.*****9.************************************* PP

                                    ................................HCHHHHCT--------..................-------------- CS
                  DNA_primase_S  81 yrplhpflsrs.mlkivkpvveeiileeqdpfeikkllrllpdkslrekkkweakedivlvllyprldeqvtkgikhllk 159
                                     + + + +  +  ++ v+p   + ++ + + +  +  l++  d s  +     +++++ l+  ++ +d++vt++i++l++
  gi|118431046|ref|NP_147231.2| 174 EGLRLELIIPRpGRRGVRPAPPSPDDPGLRGWIARAALERGVDLSAVH-----EAIEDLLDDVRVAIDVKVTQDISRLAR 248
                                    ********************************99999******99999.....9************************** PP

                                    ---....------- CS
                  DNA_primase_S 160 apfcihgktgnvcv 173
                                    + ++++gk g +++
  gi|118431046|ref|NP_147231.2| 249 IVGSLNGKAGLLVA 262
                                    **********6665 PP

>> Phage_TAC_13  Phage tail assembly chaperone, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05      0.14      16      59 ..      28      71 ..      13      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                   Phage_TAC_13 16 keikwkqgegeeltatvyvrklsfktaeadlkalkkkedkvAar 59
                                   ++i +++   + ++++vyvr ++f+++e++l+ ++ +  k+A++
  gi|118431046|ref|NP_147231.2| 28 RDIAYREFAFQLFDGDVYVRHIGFDSMEELLSYMAREAPKNAYY 71
                                   567777777788999*******************9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2484.35
//
Query:       gi|118431047|ref|NP_147232.2|  [L=249]
Description: DNA polymerase sliding clamp B2 [Aeropyrum pernix K1]
Scores for complete 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-12   46.6   0.0    2.7e-11   43.2   0.0    2.1  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    1.4e-05   25.3   0.0    2.8e-05   24.3   0.0    1.5  1  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    0.00024   20.3   0.2    0.00091   18.4   0.1    1.7  2  Rad1      Repair protein Rad1/Rec1/Rad17
     0.0055   16.2   0.0     0.0093   15.4   0.0    1.4  1  Rad9      Rad9


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   6.1e-15   2.7e-11       6      99 ..       8     102 ..       1     121 [. 0.87
   2 ?    1.2   0.0      0.06   2.7e+02      42      94 ..     170     224 ..     142     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.1e-15
                                    ESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEES.S-EEEEEEHHHHHHHHTTSTT CS
                         PCNA_N   6 leqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCD.rnlalgvnlnslskilkcann 84 
                                    +++a   + ++ +i  +++e  f +  +G+sl+alD+shva+v l   + +f +y      + +gv++  lsk+l+ a +
  gi|118431047|ref|NP_147232.2|   8 FSDARTWRYMVASIEKIIEEGVFVATGEGLSLRALDTSHVAMVDLYYPNTAFIEYDIGgESVEFGVSFDLLSKVLRRARK 87 
                                    467777888999*******************************************97626799***************** PP

                                    TSEEEEEEETTSSEE CS
                         PCNA_N  85 edsvtlkaedeadtl 99 
                                    ed ++l+ e +  ++
  gi|118431047|ref|NP_147232.2|  88 EDELVLEVEGSRLAV 102
                                    ******988766555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.06
                                    TTSSEEEEEEEEGG..GSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEEEEET CS
                         PCNA_N  42 sshvaLvslelrse..gfekyrCDrnlalgvnlnslskilkcannedsvtlkaed 94 
                                    ss +a v++el ++  +  +y  + +   + +++ +s +l  a++ d v+++  +
  gi|118431047|ref|NP_147232.2| 170 SSEMATVEIELSQSrgSLLDYEAESQDRASYSIEYFSEMLSAAQAADAVVVSFSE 224
                                    5556666666654322455666766667777888888999999999988887444 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 !   24.3   0.0   6.3e-09   2.8e-05       6     128 .]     130     247 ..     123     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.3e-09
                                    S-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEEHHH CS
                         PCNA_C   6 eydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfalkY 85 
                                     +    ++  s f   +rdl   s+++++ +  +++  + s ++ + +i l+q +      +    e++      ++++Y
  gi|118431047|ref|NP_147232.2| 130 SFTVRARMLGSTFREAVRDLEPHSETLTLRALEDALLLVGSSEMATVEIELSQSRG-----SLLDYEAESQDRASYSIEY 204
                                    45555689999***************************999999999888887654.....45566677777889***** PP

                                    HHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-BS CS
                         PCNA_C  86 laeftkatsLservtlslssevPlvveykikdvgllayllakk 128
                                    + e+  a+  ++ v +s+s+++P+ v+ +   +g l++++++k
  gi|118431047|ref|NP_147232.2| 205 FSEMLSAAQAADAVVVSFSEDAPVRVDMEYLGGGRLTFYVSPK 247
                                    ***************************************9986 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.13     6e+02      27      90 ..      30      82 ..      17     112 .. 0.69
   2 !   18.4   0.1     2e-07   0.00091     168     261 ..     134     220 ..     120     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.13
                           Rad1 27 vqissdGlkfiv.ednrvlqaqafldkalFtsYtfenaqddedeedeeedsvsfevsLsallecL 90
                                     ++ +Gl++ + + ++v    ++ +++ F +Y +              +sv+f vs + l + L
  gi|118431047|ref|NP_147232.2| 30 FVATGEGLSLRAlDTSHVAMVDLYYPNTAFIEYDI------------GGESVEFGVSFDLLSKVL 82
                                   55677777775426778888889999999999988............344555555555555444 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2e-07
                           Rad1 168 kvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkfallk 247
                                       + ++ +++a+++L+  s++l++ a +      + l +++e+  +e+e+++++  l  +e+   s+ + s Y +++++
  gi|118431047|ref|NP_147232.2| 134 RARMLGSTFREAVRDLEPHSETLTLRALED----ALLLVGSSEMATVEIELSQSRGSLLDYEAE--SQDRAS-YSIEYFS 206
                                    45688999*******************994....8****************************9..555555.99***** PP

                           Rad1 248 kaakalalssKvsl 261
                                    ++ +a +++  v +
  gi|118431047|ref|NP_147232.2| 207 EMLSAAQAADAVVV 220
                                    *****999987765 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.1e-06    0.0093       5     185 ..      18     184 ..      15     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                           Rad9   5 lqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvekvk 84 
                                    + ++ +i +e ++ ++ +gl+lr+++ s+ a + + + ++ F +y     e +++ ++   + +v+r + +++      +
  gi|118431047|ref|NP_147232.2|  18 VASIEKIIEEGVFVATGEGLSLRALDTSHVAMVDLYYPNTAFIEY-DIGGESVEFGVSFDLLSKVLRRARKED------E 90 
                                    67888999999999999****************************.788999**************9666433......3 PP

                           Rad9  85 isidekksrlivqllCkhgvkkthkisledseslkavfdkettpsklriksrvLsdllehfsssleeitielakervllk 164
                                    + ++ + srl v+l  +    +t++i        k+   k ++    r+   ++++++  ++ + e++t+++ ++++ll 
  gi|118431047|ref|NP_147232.2|  91 LVLEVEGSRLAVKLKSRG--ERTFRIPQVVMTYEKLPEPKVSFTVRARMLGSTFREAVRDLEPHSETLTLRALEDALLLV 168
                                    445556777777776554..355555555555555555555556666666667777777777777777777666666665 PP

                           Rad9 165 syeeeekdnkkalstelside 185
                                     ++e ++ +      els ++
  gi|118431047|ref|NP_147232.2| 169 GSSEMATVE-----IELSQSR 184
                                    554433322.....3333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1932.91
//
Query:       gi|118431048|ref|NP_147233.2|  [L=76]
Description: hypothetical protein APE_0441a.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 650.64
//
Query:       gi|118431049|ref|NP_147234.2|  [L=118]
Description: transcription factor S [Aeropyrum pernix K1]
Scores for 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-22   76.8  14.4    2.7e-21   75.1   6.5    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
      2e-10   40.4   9.3    9.2e-10   38.2   0.6    2.9  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    1.6e-08   34.4   9.5      6e-06   26.1   1.5    2.5  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    1.2e-07   31.2   4.6     0.0012   18.3   0.3    2.6  2  TF_Zn_Ribbon     TFIIB zinc-binding
    2.4e-06   27.4   5.7      0.017   15.0   0.7    2.3  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
    3.3e-06   26.6  10.9     0.0056   16.4   0.1    4.0  4  zinc_ribbon_2    zinc-ribbon domain
    3.2e-05   24.2   5.5      0.027   14.8   0.3    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
    5.1e-05   23.4   3.6      0.042   14.1   0.3    3.1  3  IBR              IBR domain, a half RING-finger domain
    0.00016   21.6   6.1      0.032   14.3   0.3    2.6  2  DZR              Double zinc ribbon
    0.00055   19.8   9.5       0.29   11.1   0.1    4.1  4  zinc_ribbon_4    zinc-ribbon domain
    0.00071   19.7   4.3      0.052   13.7   0.1    2.4  2  DUF2387          Probable metal-binding protein (DUF2387)
      0.003   17.2   7.6        1.1    9.1   0.1    3.7  4  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0056   16.8  12.3        3.3    7.9   0.1    4.3  4  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.011   16.2  14.5        0.5   10.9   1.8    3.0  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.012   15.7  12.0       0.86    9.8   0.0    3.9  4  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
      0.014   15.1   0.2      0.014   15.1   0.2    2.5  3  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
      0.015   14.9   2.5      0.015   14.9   2.5    3.5  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.016   15.9   7.3       0.98   10.2   2.5    3.2  2  zinc_ribbon_15   zinc-ribbon family
      0.021   14.2   2.4       0.16   11.4   0.3    3.5  3  zf-ribbon_3      zinc-ribbon domain
      0.032   14.2   5.3        2.1    8.4   0.2    3.1  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.034   14.1   4.7       0.15   12.1   0.1    2.9  3  HypA             Hydrogenase/urease nickel incorporation, met
      0.055   13.4   3.6      0.055   13.4   3.6    3.4  2  Nudix_N_2        Nudix N-terminal
      0.079   12.8   5.2       0.45   10.4   0.3    2.2  2  FdhE             Protein involved in formate dehydrogenase fo
       0.17   11.8   3.6          3    7.8   0.4    2.3  2  eIF-5_eIF-2B     Domain found in IF2B/IF5
       0.42   10.8   7.9        6.8    6.9   0.1    3.6  3  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.48   10.3  11.4        1.3    9.0   0.2    4.0  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.49   10.2   0.1       0.49   10.2   0.1    2.4  2  Cys_rich_CPCC    Cysteine-rich CPCC
        0.6    9.9  10.9        5.6    6.8   3.5    3.3  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.61   10.1   5.2        6.3    6.8   0.1    2.8  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.79    9.1   6.1        3.4    7.0   0.0    2.5  4  NMD3             NMD3 family
       0.91    9.7  14.5        7.5    6.7   0.4    4.1  4  UPF0547          Uncharacterised protein family UPF0547
        1.2    8.8  11.8        6.2    6.5   0.0    3.8  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.2    9.5   9.0        2.6    8.4   0.8    3.4  3  GFA              Glutathione-dependent formaldehyde-activatin
        1.4    8.6   5.3        2.4    7.9   0.0    2.8  2  Ribosomal_S27e   Ribosomal protein S27
        1.7    8.9   8.3        4.8    7.5   0.2    3.3  3  zf-RING_7        C4-type zinc ribbon domain
        2.1    8.3   8.3        6.5    6.7   0.2    2.8  3  PHD              PHD-finger
        2.4    8.4  16.0       0.13   12.4   5.0    2.8  2  zf-Dof           Dof domain, zinc finger
        2.4    8.0   8.1       0.62    9.9   0.4    2.4  2  zf-ZPR1          ZPR1 zinc-finger domain
        2.5    7.8  10.9        3.5    7.3   2.3    3.7  4  RecR             RecR protein
        2.6    8.2  10.2         13    5.9   1.3    3.4  4  zf-MYND          MYND finger
        2.9    8.1  14.8          1    9.5   2.5    3.6  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        2.9    7.9  14.3        1.3    8.9   0.7    3.6  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        3.6    7.4  10.9        4.8    7.0   0.0    3.7  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
        4.4    8.0  11.4         13    6.5   0.1    3.8  4  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        5.4    7.4   9.3      1e+02    3.3   9.3    2.9  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
        5.5    6.5   7.7        4.6    6.8   0.2    3.1  3  Mu-like_Com      Mu-like prophage protein Com
        8.3    6.5  10.8        1.3    9.1   0.1    3.5  3  CpXC             CpXC protein
        9.2    6.8  11.9         14    6.1   0.0    4.1  4  zf-IS66          zinc-finger binding domain of transposase IS
        9.8    6.4  13.3         26    5.0   3.4    3.5  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre


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 ?    2.8   0.2       0.3   1.1e+02       2       8 ..       7      13 ..       6      15 .. 0.85
   2 ?    3.2   0.0      0.23        83      29      36 ..      26      33 ..      20      36 .. 0.76
   3 !   75.1   6.5   7.5e-24   2.7e-21       2      39 .]      78     115 ..      77     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.3
                        TFIIS_C  2 kCpkCgs 8 
                                    Cp+Cgs
  gi|118431049|ref|NP_147234.2|  7 FCPRCGS 13
                                   5****96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                        TFIIS_C 29 ykCtkCgh 36
                                    +C++Cg+
  gi|118431049|ref|NP_147234.2| 26 LVCKSCGY 33
                                   57888886 PP

  == domain 3  score: 75.1 bits;  conditional E-value: 7.5e-24
                        TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                    +CpkCg++e+yf+++QtRsaDEpmt+fy+C+ C ++Wr
  gi|118431049|ref|NP_147234.2|  78 TCPKCGHDEVYFWMMQTRSADEPMTRFYRCKRCRYTWR 115
                                    8************************************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 !   38.2   0.6   2.5e-12   9.2e-10       1      35 [.       5      39 ..       5      40 .. 0.92
   2 ?    4.7   2.6     0.076        28       4      29 ..      79     112 ..      78     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.5e-12
                                   EEBESTTTSBEEEEECSCCCE.EEESSSS-EEESSC CS
                 RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegkn.feCrqCgYeepadq 35
                                   +kFCp Cg+ ++pk+d    + + C +CgY e+a+ 
  gi|118431049|ref|NP_147234.2|  5 IKFCPRCGSIMYPKRDGAR-YlLVCKSCGYSEEASR 39
                                   69**************999.56***********986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.076
                                    ESTTTS......BEEEEECSCCCE..EEESSSS- CS
                 RNA_POL_M_15KD   4 CpkCgN......lLlpkedkegkn..feCrqCgY 29 
                                    CpkCg       ++  ++++e     + C  C Y
  gi|118431049|ref|NP_147234.2|  79 CPKCGHdevyfwMMQTRSADEPMTrfYRCKRCRY 112
                                    8888876777779999999887667999****99 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 !   12.6   1.3   0.00027       0.1      21      45 ..       8      33 ..       2      47 .. 0.82
   2 !   26.1   1.5   1.6e-08     6e-06      17      46 .]      75     113 ..      69     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00027
                  Zn_Tnp_IS1595 21 CPhCgsrkayrikt.rglfqCkeCrk 45
                                   CP+Cgs  + +  + r l+ Ck+C++
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYPKRDGaRYLLVCKSCGY 33
                                   *****874444444699*******98 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.6e-08
                  Zn_Tnp_IS1595  17 ngfvCPhCgsrkayrikt.........rglfqCkeCrkq 46 
                                    + ++CP+Cg++++y+             + ++Ck+Cr++
  gi|118431049|ref|NP_147234.2|  75 GSVTCPKCGHDEVYFWMMqtrsadepmTRFYRCKRCRYT 113
                                    5689*******8888666669****************95 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.3   3.2e-06    0.0012       3      30 ..       8      36 ..       7      43 .. 0.85
   2 !   14.0   0.5   7.1e-05     0.026       2      25 ..      78     110 ..      77     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.2e-06
                                   ETTTTCEE.CHEETSTTCEEESSSSBEEE CS
                   TF_Zn_Ribbon  3 CPnCgstn.lveDpergelvCtdCGlVle 30
                                   CP Cgs +   +D +r  lvC++CG+  e
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMyPKRDGARYLLVCKSCGYSEE 36
                                   ******6636***************9776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.1e-05
                                    EETTTTCEEC.........HEETSTTCEEESSS CS
                   TF_Zn_Ribbon   2 kCPnCgstnl.........veDpergelvCtdC 25 
                                    +CP+Cg++++           +p++  ++C++C
  gi|118431049|ref|NP_147234.2|  78 TCPKCGHDEVyfwmmqtrsADEPMTRFYRCKRC 110
                                    7*******9669****997777*********** 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 !   15.0   0.7   4.6e-05     0.017      30      57 ..       7      36 ..       6      44 .. 0.85
   2 !   14.7   0.4     6e-05     0.022      28      56 ..      76     114 ..      70     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.6e-05
                 OrfB_Zn_ribbon 30 tCseCgsknke..alsgrtfkCpnCgfead 57
                                    C++Cgs++++  + ++ +++C++Cg++  
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSIMYPkrDGARYLLVCKSCGYSEE 36
                                   5**********777777889******9865 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6e-05
                 OrfB_Zn_ribbon  28 SktCseCgsknke..........alsgrtfkCpnCgfea 56 
                                    S tC++Cg+   +          ++ +r ++C++C +++
  gi|118431049|ref|NP_147234.2|  76 SVTCPKCGHDEVYfwmmqtrsadEPMTRFYRCKRCRYTW 114
                                    99**********99***99999999999*******9986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1    0.0009      0.33      14      21 ..       6      13 ..       4      15 .. 0.85
   2 ?    4.4   0.1     0.087        32       2       7 ..      28      33 ..      19      34 .. 0.65
   3 !   16.4   0.1   1.5e-05    0.0056       6      21 ..      69      84 ..      69      85 .. 0.94
   4 ?   -0.2   0.5       2.5   9.3e+02       1       5 [.     106     110 ..     105     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0009
                  zinc_ribbon_2 14 kFCpyCGt 21
                                   kFCp+CG+
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGS 13
                                   79999995 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.087
                  zinc_ribbon_2  2 CpnCGa 7 
                                   C++CG+
  gi|118431049|ref|NP_147234.2| 28 CKSCGY 33
                                   666664 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.5e-05
                  zinc_ribbon_2  6 GaelqdnakFCpyCGt 21
                                   Ga++ ++++ Cp+CG+
  gi|118431049|ref|NP_147234.2| 69 GAQVLKGSVTCPKCGH 84
                                   999************9 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.5
                  zinc_ribbon_2   1 fCpnC 5  
                                    +C++C
  gi|118431049|ref|NP_147234.2| 106 RCKRC 110
                                    58888 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.3   7.4e-05     0.027       3      48 ..       5      44 ..       4      53 .. 0.71
   2 !   11.8   0.8   0.00066      0.24       5      39 ..      78     113 ..      74     118 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.4e-05
                Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedea 48
                                   +k CP Cg+    +r++  ++       C+ Cg+ + ++++++++a
  gi|118431049|ref|NP_147234.2|  5 IKFCPRCGSIMYPKRDGA-RY----LLVCKSCGY-SEEASREDHQA 44
                                   678******988777755.55....9********.44444444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00066
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigq...cvyCadCgastp 39 
                                     CP Cg+++v++ + ++++  ++   +  C+ C +  +
  gi|118431049|ref|NP_147234.2|  78 TCPKCGHDEVYFWMMQTRSADEPmtrFYRCKRCRY--T 113
                                    6*********9988888877777889999****99..4 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3   0.00012     0.042      18      47 ..       5      34 ..       1      35 [. 0.81
   2 ?    6.9   0.0      0.02       7.3      36      46 ..      74      84 ..      38      86 .. 0.74
   3 ?    2.5   0.1      0.47   1.7e+02      48      56 ..     106     114 ..      90     118 .] 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00012
                            IBR 18 lkwCprpdCeaiiekseg.cks..vtCskCgfe 47
                                   +k Cp   C++i+ ++ +   +  + C++Cg++
  gi|118431049|ref|NP_147234.2|  5 IKFCP--RCGSIMYPKRDgA-RylLVCKSCGYS 34
                                   799**..9*****9999953.43577****985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.02
                            IBR 36 cksvtCskCgf 46
                                   ++svtC+kCg+
  gi|118431049|ref|NP_147234.2| 74 KGSVTCPKCGH 84
                                   4459*****98 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.47
                            IBR  48 fCfnCkkew 56 
                                     C +C+  w
  gi|118431049|ref|NP_147234.2| 106 RCKRCRYTW 114
                                    366666666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   8.7e-05     0.032      13      37 ..       6      34 ..       2      42 .. 0.81
   2 !    9.2   1.1    0.0032       1.2       9      37 ..      73     113 ..      69     118 .] 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-05
                            DZR 13 rfCseCgtklkavaa....edrCpsCgek 37
                                   +fC++Cg+ + +  +      +C sCg++
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSIMYPKRDgaryLLVCKSCGYS 34
                                   8*******9875555889999*****997 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0032
                            DZR   9 ppdarfCseCgtk......lkavaa.........edrCpsCgek 37 
                                     +++ +C++Cg++      ++   +          +rC +C + 
  gi|118431049|ref|NP_147234.2|  73 LKGSVTCPKCGHDevyfwmMQ---TrsadepmtrFYRCKRCRYT 113
                                    567889999999987765433...24458888889999999875 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2       0.4   1.5e+02       5      32 ..       8      12 ..       6      15 .. 0.62
   2 ?    1.4   0.0      0.86   3.1e+02      28      32 ..      28      32 ..      21      34 .. 0.66
   3 !   11.1   0.1    0.0008      0.29      24      33 ..      75      84 ..      61      85 .. 0.81
   4 !    8.4   0.4    0.0054         2      27      36 .]     106     115 ..      99     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.4
                  zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCg 32
                                   Cp+C                       g
  gi|118431049|ref|NP_147234.2|  8 CPRC-----------------------G 12
                                   5555.......................5 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.86
                  zinc_ribbon_4 28 CskCg 32
                                   C+ Cg
  gi|118431049|ref|NP_147234.2| 28 CKSCG 32
                                   55555 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0008
                  zinc_ribbon_4 24 vkvrCskCgh 33
                                   ++v+C+kCgh
  gi|118431049|ref|NP_147234.2| 75 GSVTCPKCGH 84
                                   68*******9 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0054
                  zinc_ribbon_4  27 rCskCghvFr 36 
                                    rC++C+ ++r
  gi|118431049|ref|NP_147234.2| 106 RCKRCRYTWR 115
                                    9********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 !   13.7   0.1   0.00014     0.052      11      50 ..       8      44 ..       5      63 .. 0.72
   2 ?    7.3   0.7     0.014       5.3       9      39 ..      77     113 ..      70     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00014
                        DUF2387 11 CPrCsemDkirmweedevey.rECvsCgftdelsekgqsva 50
                                   CPrC +   i+  + d+ +y   C sCg+++e s +++ +a
  gi|118431049|ref|NP_147234.2|  8 CPRCGS---IMYPKRDGARYlLVCKSCGYSEEASREDH-QA 44
                                   9***85...88889999665278*********998832.22 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.014
                        DUF2387   9 avCPrCsemDkirmweede.......veyrECvsCgft 39 
                                    + CP+C + D++  w  +        +++  C  C +t
  gi|118431049|ref|NP_147234.2|  77 VTCPKCGH-DEVYFWMMQTrsadepmTRFYRCKRCRYT 113
                                    56****86.77777754431111123555667777776 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 ?    5.0   0.1     0.057        21      22      30 ..       6      14 ..       4      15 .. 0.86
   2 !    9.1   0.1     0.003       1.1      21      32 ..      25      36 ..      22      37 .. 0.87
   3 ?    5.9   0.0     0.029        11       4      15 ..      77      88 ..      75      97 .. 0.79
   4 ?   -1.7   0.2       6.9   2.5e+03       6       9 ..     107     110 ..     105     113 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.057
                  A2L_zn_ribbon 22 lvCieCgas 30
                                    +C+ Cg++
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSI 14
                                   59*****97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.003
                  A2L_zn_ribbon 21 ylvCieCgasfp 32
                                    lvC+ Cg+s++
  gi|118431049|ref|NP_147234.2| 25 LLVCKSCGYSEE 36
                                   58*******985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.029
                  A2L_zn_ribbon  4 kvCsvCggngil 15
                                   ++C +Cg++ ++
  gi|118431049|ref|NP_147234.2| 77 VTCPKCGHDEVY 88
                                   589999999876 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 6.9
                  A2L_zn_ribbon   6 CsvC 9  
                                    C+ C
  gi|118431049|ref|NP_147234.2| 107 CKRC 110
                                    5555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.025         9      27      34 ..       5      13 ..       1      19 [. 0.76
   2 ?    5.2   0.3     0.062        23       4      17 ..      24      37 ..      22      45 .. 0.71
   3 !    7.9   0.1    0.0091       3.3      27      35 ..      77      86 ..      61      88 .. 0.82
   4 ?    2.9   1.0      0.33   1.2e+02       6      13 ..     105     112 ..     104     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.025
                    Zn-ribbon_8 27 ta.CPeCgs 34
                                   ++ CP+Cgs
  gi|118431049|ref|NP_147234.2|  5 IKfCPRCGS 13
                                   566*****9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.062
                    Zn-ribbon_8  4 YeYrCeeCghefev 17
                                   Y   C++Cg   e+
  gi|118431049|ref|NP_147234.2| 24 YLLVCKSCGYSEEA 37
                                   66789999966554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0091
                    Zn-ribbon_8 27 taCPeCgs.e 35
                                   ++CP+Cg+ e
  gi|118431049|ref|NP_147234.2| 77 VTCPKCGHdE 86
                                   56****9855 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.33
                    Zn-ribbon_8   6 YrCeeCgh 13 
                                    YrC++C  
  gi|118431049|ref|NP_147234.2| 105 YRCKRCRY 112
                                    9*****75 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 ?    9.3   5.2    0.0044       1.6       7      32 ..       7      31 ..       2      58 .. 0.80
   2 ?   10.9   1.8    0.0014       0.5       2      33 ..      73     111 ..      72     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0044
                Zn_ribbon_recom  7 rCgeCGspmtrrkrkgkrhyYrCsty 32
                                   +C +CGs m+ ++  g r+  +C+++
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSIMYPKRD-GARYLLVCKSC 31
                                   8***********98.55666777754 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0014
                Zn_ribbon_recom   2 LsGllrCgeCGsp.....mtrrkrkgkr...hyYrCstyr 33 
                                    L+G + C +CG+      m ++++       + YrC+++r
  gi|118431049|ref|NP_147234.2|  73 LKGSVTCPKCGHDevyfwMMQTRSAD-EpmtRFYRCKRCR 111
                                    99***********8876644433322.2465889999875 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 ?    0.8   0.1       1.5   5.6e+02       2       9 ..       8      15 ..       7      24 .. 0.80
   2 ?    7.9   0.4     0.009       3.3      34      45 ..      25      35 ..      20      45 .. 0.82
   3 ?    9.8   0.0    0.0023      0.86      36      47 ..      77      88 ..      75      99 .. 0.79
   4 ?    2.9   0.5      0.34   1.2e+02      37      44 ..     106     113 ..     101     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.5
                 zinc_ribbon_13  2 CpKCgnte 9 
                                   Cp+Cg+  
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIM 15
                                   99999865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.009
                 zinc_ribbon_13 34 itvsCknCgYte 45
                                   +   Ck+CgY+e
  gi|118431049|ref|NP_147234.2| 25 L-LVCKSCGYSE 35
                                   3.46******98 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0023
                 zinc_ribbon_13 36 vsCknCgYtelY 47
                                   v+C +Cg+ e+Y
  gi|118431049|ref|NP_147234.2| 77 VTCPKCGHDEVY 88
                                   888888888888 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.34
                 zinc_ribbon_13  37 sCknCgYt 44 
                                     Ck+C Yt
  gi|118431049|ref|NP_147234.2| 106 RCKRCRYT 113
                                    6******8 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 ?   -0.8   0.2       3.4   1.2e+03      34      41 ..       5      12 ..       2      13 .. 0.86
   2 ?   -2.0   0.3       8.3     3e+03      36      41 ..      27      32 ..      23      33 .. 0.81
   3 ?   15.1   0.2   3.7e-05     0.014       8      40 ..      77     110 ..      73     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.4
                  Baculo_LEF5_C 34 vryCskCg 41
                                   ++ C +Cg
  gi|118431049|ref|NP_147234.2|  5 IKFCPRCG 12
                                   678****9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.3
                  Baculo_LEF5_C 36 yCskCg 41
                                   +C+ Cg
  gi|118431049|ref|NP_147234.2| 27 VCKSCG 32
                                   699998 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.7e-05
                  Baculo_LEF5_C   8 ltikqClHdfv.tiEiQnRagDE.ivsfvryCskC 40 
                                     t  +C Hd v     Q+R+ DE +  f+r C++C
  gi|118431049|ref|NP_147234.2|  77 VTCPKCGHDEVyFWMMQTRSADEpMTRFYR-CKRC 110
                                    56678******98999*******7777887.9988 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 ?   14.9   2.5   4.1e-05     0.015       4      29 ..       6      33 ..       4      35 .. 0.89
   2 ?    4.7   0.3     0.064        23       6      29 ..      79      84 ..      77      86 .. 0.65
   3 ?   -1.9   0.2       7.8   2.8e+03      23      28 ..     106     111 ..     105     112 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.1e-05
                  zf-NADH-PPase  4 rFCgrCGaptepaegg..warvCpaCgl 29
                                   +FC+rCG+ + p+++g  + +vC +Cg+
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSIMYPKRDGarYLLVCKSCGY 33
                                   6**************8668899999997 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.064
                  zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCgl 29
                                   C++CG                  +
  gi|118431049|ref|NP_147234.2| 79 CPKCG------------------H 84
                                   55555..................4 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.8
                  zf-NADH-PPase  23 vCpaCg 28 
                                    +C  C+
  gi|118431049|ref|NP_147234.2| 106 RCKRCR 111
                                    688887 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2      0.12        45      78      86 .]       4      12 ..       1      12 [. 0.83
   2 ?   10.2   2.5    0.0027      0.98      33      73 ..      21      84 ..      13     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.12
                 zinc_ribbon_15 78 efkyCpkCg 86
                                   ++k+Cp+Cg
  gi|118431049|ref|NP_147234.2|  4 RIKFCPRCG 12
                                   689*****9 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0027
                 zinc_ribbon_15 33 kkkpylacskCkslleaskelgkeiekkesse.......................kkeCknCgk 73
                                    ++++l+c++C++  eas+e +++ + + ++e                       + +C++Cg+
  gi|118431049|ref|NP_147234.2| 21 GARYLLVCKSCGYSEEASREDHQAYRMRVTVEkgprdkivviddetpvgaqvlkgSVTCPKCGH 84
                                   56899*************999999998888889999*****99999999999999677777765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0029       1.1       3      11 ..       6      14 ..       5      20 .. 0.82
   2 ?    4.5   0.2     0.067        25      18      24 ..      27      33 ..      26      34 .. 0.89
   3 ?   11.4   0.3   0.00044      0.16      12      24 ..      72      84 ..      69      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0029
                    zf-ribbon_3  3 vrCPnCGap 11
                                   ++CP+CG++
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSI 14
                                   589999984 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.067
                    zf-ribbon_3 18 vCpyCGt 24
                                   vC++CG+
  gi|118431049|ref|NP_147234.2| 27 VCKSCGY 33
                                   7*****7 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00044
                    zf-ribbon_3 12 lssddnvCpyCGt 24
                                   + ++ ++Cp+CG+
  gi|118431049|ref|NP_147234.2| 72 VLKGSVTCPKCGH 84
                                   5567788888887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.2     0.046        17       5      27 ..       8      33 ..       7      34 .. 0.69
   2 ?    8.4   0.2    0.0058       2.1       5      29 ..      79     114 ..      76     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.046
                 PhnA_Zn_Ribbon  5 CplCaSeytY....edgallvCpeCah 27
                                   Cp C+S+  Y      + llvC  C++
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIM-YpkrdGARYLLVCKSCGY 33
                                   88888874.556444445899999986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0058
                 PhnA_Zn_Ribbon   5 CplCaSeytY...........edgallvCpeCahEw 29 
                                    Cp+C+ +++Y             +  + C  C + w
  gi|118431049|ref|NP_147234.2|  79 CPKCGHDEVYfwmmqtrsadePMTRFYRCKRCRYTW 114
                                    999999999988888888777777777777777655 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 ?    1.7   0.1      0.69   2.5e+02      88      97 ..       7      16 ..       2      27 .. 0.72
   2 ?   12.1   0.1   0.00042      0.15      71      98 ..      26      88 ..      18      96 .. 0.86
   3 ?    1.5   0.2      0.82     3e+02      71      81 ..     105     115 ..      95     118 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.69
                                   S-TTTSSS-E CS
                           HypA 88 rCpkCgsadv 97
                                    Cp+Cgs   
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSIMY 16
                                   4999999765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00042
                                   EEETTTS-EEECHH.HHH..................................S-TTTSSS-EE CS
                           HypA 71 vrCreCgkefelee.kal..................................rCpkCgsadve 98
                                   + C++Cg++ e ++ ++                                   +CpkCg+ +v 
  gi|118431049|ref|NP_147234.2| 26 LVCKSCGYSEEASReDHQayrmrvtvekgprdkivviddetpvgaqvlkgsvTCPKCGHDEVY 88
                                   68*****998865533225799************************************98875 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.82
                                    EEETTTS-EEE CS
                           HypA  71 vrCreCgkefe 81 
                                    +rC++C+++++
  gi|118431049|ref|NP_147234.2| 105 YRCKRCRYTWR 115
                                    68999999886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.6   0.00015     0.055       1      30 [.       6      33 ..       6      34 .. 0.94
   2 ?    2.2   4.3      0.47   1.7e+02       3      29 ..      79     111 ..      78     114 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00015
                                   -B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                      Nudix_N_2  1 kFCsqCGtpvelripdgDnreRlvCpaCgt 30
                                   kFC+ CG+ +  +   ++ r  lvC++Cg+
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSIMYPKR--DGARYLLVCKSCGY 33
                                   9********99999..899999******97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.47
                                    -TTT--B.-E....EE--TT-SS-E.EEETTTT CS
                      Nudix_N_2   3 CsqCGtp.ve....lripdgDnreR.lvCpaCg 29 
                                    C++CG+  v     +   +++  +R ++C++C 
  gi|118431049|ref|NP_147234.2|  79 CPKCGHDeVYfwmmQTRSADEPMTRfYRCKRCR 111
                                    899998733354423333444445534566665 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.7     0.056        21     169     202 ..       6      33 ..       1      41 [. 0.75
   2 ?   10.4   0.3    0.0012      0.45     164     205 ..      72     115 ..      62     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.056
                                    SS-TTT---EEEEEEE-------EEEE.EETTT-- CS
                           FdhE 169 glCPvCgsaPvasvvriggeaeglRyl.hCslCet 202
                                    ++CP Cgs        +  +++g+Ryl  C  C  
  gi|118431049|ref|NP_147234.2|   6 KFCPRCGSI-------MYPKRDGARYLlVCKSCGY 33 
                                    79****984.......3455899999637999975 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                                    .-TT-SS-TTT---EEEEEE.E--.-----EEEEEETTT--EEE CS
                           FdhE 164 laeekglCPvCgsaPvasvv.rig.geaeglRylhCslCeteWh 205
                                    + + + +CP Cg   v   + +++ +++  +R+  C  C   W+
  gi|118431049|ref|NP_147234.2|  72 VLKGSVTCPKCGHDEVYFWMmQTRsADEPMTRFYRCKRCRYTWR 115
                                    5566789*******99865414431345679************7 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 ?    4.9   0.2     0.063        23      90     116 ..       8      33 ..       6      34 .. 0.74
   2 ?    7.8   0.4    0.0081         3      88     115 ..      77     111 ..      71     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.063
                                    TSSSTSTCEEECCSSSCEEEEESSSTC CS
                   eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCga 116
                                    C+ C+s     ++++  ++l Ck+Cg 
  gi|118431049|ref|NP_147234.2|   8 CPRCGSIMYP-KRDGARYLLVCKSCGY 33 
                                    8999987654.45666667******96 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0081
                                    TSTSSSTSTCEEECC.......SSSCEEEEESSST CS
                   eIF-5_eIF-2B  88 VlCkeCkspetelek.......eerllvlkCkaCg 115
                                    V+C++C++ e+ +         e ++ + +Ck C 
  gi|118431049|ref|NP_147234.2|  77 VTCPKCGHDEVYFWMmqtrsadEPMTRFYRCKRCR 111
                                    99*******99877666677766788899*****6 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 ?    6.9   0.1     0.019       6.8      24      31 ..       6      13 ..       2      18 .. 0.86
   2 ?    1.9   0.0      0.67   2.4e+02       6      15 ..      23      32 ..      19      58 .. 0.81
   3 ?    3.4   2.1      0.23        85      26      41 ..      79      94 ..      74     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.019
                   NOB1_Zn_bind 24 kFCpkCGn 31
                                   kFCp+CG+
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGS 13
                                   8******7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.67
                   NOB1_Zn_bind  6 swvlrChaCf 15
                                   +++l C +C 
  gi|118431049|ref|NP_147234.2| 23 RYLLVCKSCG 32
                                   5777777774 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.23
                   NOB1_Zn_bind 26 CpkCGnktLkrvavsv 41
                                   CpkCG++ +    +++
  gi|118431049|ref|NP_147234.2| 79 CPKCGHDEVYFWMMQT 94
                                   *****99876555555 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0034       1.3      14      26 ..       8      20 ..       5      23 .. 0.87
   2 ?    1.4   0.1      0.81   2.9e+02      13      18 ..      27      32 ..      24      34 .. 0.83
   3 ?    3.9   0.2      0.14        50      28      32 ..      79      83 ..      76      87 .. 0.63
   4 ?    1.1   0.2         1   3.7e+02      11      18 ..     104     111 ..      99     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0034
                        DUF35_N 14 CpdCGtvqfPPra 26
                                   Cp CG+  +P+r 
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYPKRD 20
                                   9999999999985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.81
                        DUF35_N 13 rCpdCG 18
                                    C++CG
  gi|118431049|ref|NP_147234.2| 27 VCKSCG 32
                                   699999 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.14
                        DUF35_N 28 CphCg 32
                                   Cp+Cg
  gi|118431049|ref|NP_147234.2| 79 CPKCG 83
                                   66665 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1
                        DUF35_N  11 gqrCpdCG 18 
                                    + rC+ C 
  gi|118431049|ref|NP_147234.2| 104 FYRCKRCR 111
                                    56999995 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0013      0.49       3      38 ..       8      45 ..       6      51 .. 0.81
   2 ?   -0.9   2.9       3.9   1.4e+03       2       9 ..      78      85 ..      77     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                  Cys_rich_CPCC  3 CpcCgyltleeee.gsy.diCpvCfWedDlvqlkapdl 38
                                   Cp Cg +++++++ + y  +C+ C + +++   +++++
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYPKRDgARYlLVCKSCGYSEEASREDHQAY 45
                                   *********99997666579*****9999887666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.9
                  Cys_rich_CPCC  2 qCpcCgyl 9 
                                   +Cp Cg+ 
  gi|118431049|ref|NP_147234.2| 78 TCPKCGHD 85
                                   79999985 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 ?    6.3   0.1     0.023       8.4       4      15 ..       8      19 ..       5      25 .. 0.84
   2 ?   -1.4   0.1       5.6   2.1e+03       4       9 ..      28      34 ..      26      39 .. 0.79
   3 ?    6.8   3.5     0.015       5.6       2      33 ..      77     113 ..      76     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                                   -SSS--EEEEEE CS
                 zf-C4_Topoisom  4 CPkCggdLvlkr 15
                                   CP Cg+ +  kr
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYPKR 19
                                   ******998775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.6
                                   -SSS-.- CS
                 zf-C4_Topoisom  4 CPkCg.g 9 
                                   C +Cg +
  gi|118431049|ref|NP_147234.2| 28 CKSCGyS 34
                                   8899854 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.015
                                    EE-SSS--E.....EEEEE-SSS...EEEEESST.T---- CS
                 zf-C4_Topoisom   2 ekCPkCggd.....LvlkrgkkG...kFvGCsnYPeCkft 33 
                                    ++CPkCg d     +++ r+      +F+ C++   C++t
  gi|118431049|ref|NP_147234.2|  77 VTCPKCGHDevyfwMMQTRSADEpmtRFYRCKR---CRYT 113
                                    69*****54355554455555555777777777...7776 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 ?    6.8   0.1     0.017       6.3       6      27 ..       7      32 ..       4      36 .. 0.81
   2 ?    5.0   0.2     0.062        23      21      27 ..      77      83 ..      64      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                    Prok-RING_1  6 kCpvCgkelkeedD....iVvCpeCg 27
                                    Cp Cg  + ++ D    + vC  Cg
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSIMYPKRDgaryLLVCKSCG 32
                                   59999999999977666689999999 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.062
                    Prok-RING_1 21 VvCpeCg 27
                                   V+Cp+Cg
  gi|118431049|ref|NP_147234.2| 77 VTCPKCG 83
                                   99****9 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.12        44      35      46 ..       5      17 ..       3      26 .. 0.79
   2 ?    4.8   1.4     0.046        17       1      25 [.       8      37 ..       8      49 .. 0.76
   3 ?    7.0   0.0    0.0094       3.4      94     144 ..      39      89 ..      33     106 .. 0.72
   4 ?    3.4   0.2      0.12        43      16      42 ..      79     111 ..      65     117 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                           NMD3 35 vevCkeCgryl.p 46
                                   +++C++Cg+++ p
  gi|118431049|ref|NP_147234.2|  5 IKFCPRCGSIMyP 17
                                   7999999999843 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.046
                           NMD3  1 CcrCGkeieeling.....lCedCllkevd 25
                                   C+rCG+ + +  +g     +C++C  +e  
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYPKRDGaryllVCKSCGYSEEA 37
                                   ********65555588999*****877655 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0094
                           NMD3  94 tephskrikvkvtvqgevrgenetilqqevevevkvkr..qqCprCsriaggy 144
                                     e+ ++ ++++vtv++  r+ + ++++ e  v  +v +   +Cp+C   +   
  gi|118431049|ref|NP_147234.2|  39 RED-HQAYRMRVTVEKGPRD-KIVVIDDETPVGAQVLKgsVTCPKCGHDEVYF 89 
                                    556.67899********988.555677777776666543389****9766555 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.12
                           NMD3  16 CedCllkevditegiek.ie.....vevCkeCg 42 
                                    C++C  +ev +   +++ ++     +  Ck+C 
  gi|118431049|ref|NP_147234.2|  79 CPKCGHDEVYFWMMQTRsADepmtrFYRCKRCR 111
                                    555555554444333222222322355555554 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3      0.04        15      15      21 ..       6      12 ..       5      14 .. 0.71
   2 ?    3.9   0.2      0.16        59      16      23 ..      27      34 ..      26      35 .. 0.84
   3 ?    6.7   0.4      0.02       7.5      16      22 ..      78      84 ..      76      85 .. 0.79
   4 ?    1.0   0.2       1.3   4.7e+02       3       7 ..     107     111 ..     106     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.04
                        UPF0547 15 qfCphCG 21
                                   +fCp CG
  gi|118431049|ref|NP_147234.2|  6 KFCPRCG 12
                                   5777776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.16
                        UPF0547 16 fCphCGyv 23
                                   +C  CGy+
  gi|118431049|ref|NP_147234.2| 27 VCKSCGYS 34
                                   6988**96 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.02
                        UPF0547 16 fCphCGy 22
                                    Cp CG+
  gi|118431049|ref|NP_147234.2| 78 TCPKCGH 84
                                   5999999 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1.3
                        UPF0547   3 CPeCe 7  
                                    C++C+
  gi|118431049|ref|NP_147234.2| 107 CKRCR 111
                                    78886 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.017       6.2       4      12 ..       7      15 ..       5      19 .. 0.84
   2 ?   -0.5   0.1       2.6   9.4e+02       4       9 ..      27      32 ..      25      43 .. 0.80
   3 ?    6.5   0.0     0.017       6.2       2      10 ..      76      84 ..      75      93 .. 0.89
   4 ?    1.6   0.8      0.59   2.2e+02       3       9 ..     105     111 ..     103     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                         zf_UBZ  4 lCerCgkei 12
                                   +C+rCg+ +
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSIM 15
                                   8*****866 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.6
                         zf_UBZ  4 lCerCg 9 
                                   +C+ Cg
  gi|118431049|ref|NP_147234.2| 27 VCKSCG 32
                                   799998 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.017
                         zf_UBZ  2 tylCerCgk 10
                                   +++C++Cg+
  gi|118431049|ref|NP_147234.2| 76 SVTCPKCGH 84
                                   689****96 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.59
                         zf_UBZ   3 ylCerCg 9  
                                    y C+rC 
  gi|118431049|ref|NP_147234.2| 105 YRCKRCR 111
                                    89****5 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8    0.0072       2.6      50      67 ..       6      23 ..       2      45 .. 0.77
   2 ?    3.4   0.6      0.27     1e+02       5      57 ..      28      84 ..      24      97 .. 0.59
   3 ?    2.1   0.3      0.68   2.5e+02      42      56 ..      96     111 ..      85     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0072
                            GFA 50 sfCpeCgsplyseesaap 67
                                   +fCp+Cgs +y +++ a 
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSIMYPKRDGAR 23
                                   7**********7655444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.27
                            GFA  5 CsdCrkasgsaftanavvkaealelleg...elkeykktadsgnkvtr..sfCpeCgs 57
                                   C++C  ++ ++   + +++  ++++ +g   ++ ++++++  g +v +    Cp+Cg 
  gi|118431049|ref|NP_147234.2| 28 CKSCGYSEEASREDHQAYR-MRVTVEKGprdKIVVIDDETPVGAQVLKgsVTCPKCGH 84
                                   5555444444444444433.44555566666666666666666666554567888875 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.68
                            GFA  42 dsgnkvtr.sfCpeCg 56 
                                       +++tr + C++C 
  gi|118431049|ref|NP_147234.2|  96 SADEPMTRfYRCKRCR 111
                                    4456777779999997 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.6      0.43   1.6e+02      10      33 ..       8      32 ..       4      34 .. 0.60
   2 ?    7.9   0.0    0.0066       2.4       8      24 ..      77      93 ..      75      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.43
                                   -TTTS-EEEEE.SS-SS-EEESSST CS
                 Ribosomal_S27e 10 CpdCenetvvF.shaatvvkCisCg 33
                                   Cp C+ +     + a     C sCg
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYPKrDGARYLLVCKSCG 32
                                   7777766543314455556788887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0066
                                   EE-TTTS-EEEEESS-S CS
                 Ribosomal_S27e  8 vkCpdCenetvvFshaa 24
                                   v Cp+C++  v F   +
  gi|118431049|ref|NP_147234.2| 77 VTCPKCGHDEVYFWMMQ 93
                                   89********9996655 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 ?    7.5   0.2     0.013       4.8      22      33 .]       4      15 ..       1      15 [. 0.83
   2 ?   -0.8   0.1       5.1   1.9e+03      25      30 ..      27      32 ..      21      32 .. 0.82
   3 ?    5.3   0.1     0.061        22      23      30 ..      76      83 ..      68      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                                   B-EE-TTT--EE CS
                      zf-RING_7 22 evvtCpeCGRIL 33
                                    + +Cp CG I+
  gi|118431049|ref|NP_147234.2|  4 RIKFCPRCGSIM 15
                                   6789*****995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 5.1
                                   E-TTT- CS
                      zf-RING_7 25 tCpeCG 30
                                    C +CG
  gi|118431049|ref|NP_147234.2| 27 VCKSCG 32
                                   599998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.061
                                   -EE-TTT- CS
                      zf-RING_7 23 vvtCpeCG 30
                                    vtCp CG
  gi|118431049|ref|NP_147234.2| 76 SVTCPKCG 83
                                   49*****9 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.018       6.5       1      22 [.       7      32 ..       7      35 .. 0.89
   2 ?    0.7   0.3       1.4     5e+02      44      49 ..      77      82 ..      67      85 .. 0.63
   3 ?    3.2   3.1      0.22        80      21      50 ..      79     111 ..      73     113 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                                   SBTTTTS....TTSTTSCEEEETTTS CS
                            PHD  1 rCavCkk....ksdeeeelvqCdgCk 22
                                   +C  C++    k d  + l++C++C+
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSimypKRDGARYLLVCKSCG 32
                                   69999999998888899********7 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.4
                                   BSSTTT CS
                            PHD 44 wlCekC 49
                                    +C+kC
  gi|118431049|ref|NP_147234.2| 77 VTCPKC 82
                                   456666 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.22
                                    TSCEEETTTSS..STHSHHSHHSS.TBSSTTTH CS
                            PHD  21 CkrwfHqkClk..ppleseekpeg.ewlCekCk 50 
                                    C ++ H + +   ++ +s+++p++  + C++C+
  gi|118431049|ref|NP_147234.2|  79 CPKCGHDEVYFwmMQTRSADEPMTrFYRCKRCR 111
                                    4444554443300233333444445899****7 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   3.2       1.7   6.2e+02       5      12 ..       7      14 ..       4      34 .. 0.81
   2 ?   12.4   5.0   0.00037      0.13       4      39 ..      77     115 ..      74     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.7
                         zf-Dof  5 kCprCest 12
                                    CprC s 
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSI 14
                                   59999985 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00037
                         zf-Dof   4 lkCprCestntkFcYyNNyslsqP..R.yfCkaCrryWt 39 
                                    ++Cp+C   +  F      s + P  R y Ck Cr  W 
  gi|118431049|ref|NP_147234.2|  77 VTCPKCGHDEVYFWMMQTRSADEPmtRfYRCKRCRYTWR 115
                                    78********************99664578********5 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.15        56      31      59 ..      26      50 ..      19      78 .. 0.65
   2 ?    9.9   0.4    0.0017      0.62       2      42 ..      78     116 ..      77     118 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.15
                        zf-ZPR1 31 feCehCgyknnevksageieekGkritlk 59
                                   ++C++Cgy+++  +   +      r+ ++
  gi|118431049|ref|NP_147234.2| 26 LVCKSCGYSEEASREDHQA----YRMRVT 50
                                   58******87655433332....333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0017
                        zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42 
                                    +Cp+Cg++  e ++++++     e +   ++C++C+y+ +e
  gi|118431049|ref|NP_147234.2|  78 TCPKCGHD--EVYFWMMQTRSADEPMTRFYRCKRCRYTWRE 116
                                    7****855..777788888889***************8776 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.3    0.0095       3.5      15      25 ..       4      14 ..       1      32 [. 0.80
   2 ?   -0.5   0.2       2.6   9.4e+02      19      24 ..      28      33 ..      25      38 .. 0.79
   3 ?    2.1   0.1      0.41   1.5e+02      16      24 ..      76      84 ..      70      84 .. 0.74
   4 ?    1.6   0.2      0.56   2.1e+02      17      23 ..     105     111 ..      99     113 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0095
                                   H-EE-TTT--E CS
                           RecR 15 kvrhCsrCgnl 25
                                   ++++C+rCg +
  gi|118431049|ref|NP_147234.2|  4 RIKFCPRCGSI 14
                                   79*******98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.6
                                   -TTT-- CS
                           RecR 19 CsrCgn 24
                                   C+ Cg 
  gi|118431049|ref|NP_147234.2| 28 CKSCGY 33
                                   999985 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.41
                                   -EE-TTT-- CS
                           RecR 16 vrhCsrCgn 24
                                      C++Cg+
  gi|118431049|ref|NP_147234.2| 76 SVTCPKCGH 84
                                   568****97 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.56
                                    EE-TTT- CS
                           RecR  17 rhCsrCg 23 
                                     +C+rC+
  gi|118431049|ref|NP_147234.2| 105 YRCKRCR 111
                                    58****7 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.038        14      11      21 ..       6      16 ..       2      23 .. 0.87
   2 ?   -0.1   0.4       2.7   9.9e+02       1       8 [.      28      35 ..      28      44 .. 0.65
   3 ?    1.4   0.0      0.93   3.4e+02      12      17 ..      78      83 ..      69     105 .. 0.73
   4 ?    5.9   1.3     0.036        13       1      19 [.      79     113 ..      79     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.038
                                   CE-TTTS-SEE CS
                        zf-MYND 11 kkCagCksvfY 21
                                   k C++C s++Y
  gi|118431049|ref|NP_147234.2|  6 KFCPRCGSIMY 16
                                   68********9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.7
                                   -TTT--.B CS
                        zf-MYND  1 CavCgkae 8 
                                   C++Cg +e
  gi|118431049|ref|NP_147234.2| 28 CKSCGYSE 35
                                   77787633 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.93
                                   E-TTTS CS
                        zf-MYND 12 kCagCk 17
                                    C++C 
  gi|118431049|ref|NP_147234.2| 78 TCPKCG 83
                                   788883 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.036
                                    -TTT--...............B-SC..E-TTTS-S CS
                        zf-MYND   1 CavCgk..............aealk..kCagCksv 19 
                                    C +Cg               ++ ++  +C++C+ +
  gi|118431049|ref|NP_147234.2|  79 CPKCGHdevyfwmmqtrsadEPMTRfyRCKRCRYT 113
                                    88898899999999988874444448899999866 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 ?    9.5   2.5    0.0029         1       4      26 .]       8      31 ..       7      31 .. 0.80
   2 ?    4.6   0.7     0.092        34       3       8 ..      78      83 ..      77      84 .. 0.70
   3 ?   -0.7   0.2       4.5   1.6e+03       3       7 ..     106     110 ..     104     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0029
                         zf-ACC  4 CpsCgemly.kkeLernlyVCPkC 26
                                   Cp+Cg+++y k++ +r l VC +C
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYpKRDGARYLLVCKSC 31
                                   *********666777777777777 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.092
                         zf-ACC  3 KCpsCg 8 
                                    Cp+Cg
  gi|118431049|ref|NP_147234.2| 78 TCPKCG 83
                                   588887 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 4.5
                         zf-ACC   3 KCpsC 7  
                                    +C +C
  gi|118431049|ref|NP_147234.2| 106 RCKRC 110
                                    79999 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 ?    3.0   3.0      0.27     1e+02       7      31 ..       8      32 ..       7      36 .. 0.79
   2 ?    1.9   0.1      0.58   2.1e+02       7      11 ..      79      83 ..      78      90 .. 0.77
   3 ?    8.9   0.7    0.0037       1.3      25      31 ..     105     111 ..      92     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.27
                 Zn_ribbon_SprT  7 CtgCgreythhlsirrhn..YrCrrCk 31
                                   C++Cg  +    + + ++    C+ C+
  gi|118431049|ref|NP_147234.2|  8 CPRCG--SIMYPKRDGARylLVCKSCG 32
                                   99999..67777778888888888886 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.58
                 Zn_ribbon_SprT  7 CtgCg 11
                                   C+ Cg
  gi|118431049|ref|NP_147234.2| 79 CPKCG 83
                                   78887 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0037
                 Zn_ribbon_SprT  25 YrCrrCk 31 
                                    YrC+rC+
  gi|118431049|ref|NP_147234.2| 105 YRCKRCR 111
                                    ******8 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 ?    0.3   0.2       1.6   5.7e+02      47      53 ..       8      14 ..       5      15 .. 0.82
   2 ?    7.0   0.0     0.013       4.8      18      29 ..      21      32 ..      16      45 .. 0.82
   3 ?    0.3   4.7       1.6   5.8e+02      25      52 ..      79     112 ..      74     114 .. 0.50

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.6
                 zinc_ribbon_10 47 CpkCgal 53
                                   Cp Cg++
  gi|118431049|ref|NP_147234.2|  8 CPRCGSI 14
                                   9999975 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                 zinc_ribbon_10 18 knryalICskCh 29
                                     ry l+C+ C 
  gi|118431049|ref|NP_147234.2| 21 GARYLLVCKSCG 32
                                   579********6 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.6
                 zinc_ribbon_10  25 CskChshnGlap....keeleev..kyrCpkCga 52 
                                    C+kC +   +      +++ e++   yrC  C+ 
  gi|118431049|ref|NP_147234.2|  79 CPKCGHDEVYFWmmqtRSADEPMtrFYRCKRCRY 112
                                    6666554332222224333333322588888875 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 ?    6.0   0.1     0.051        19       4      11 ..       7      14 ..       5      24 .. 0.75
   2 ?   -0.2   0.0       4.6   1.7e+03       4      11 ..      27      34 ..      26      52 .. 0.61
   3 ?    6.5   0.1     0.036        13       3      13 ..      77      87 ..      75      94 .. 0.85
   4 ?   -0.4   1.5       5.2   1.9e+03      42      47 .]     105     110 ..     103     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.051
                        zf-ISL3  4 rCPnCgsk 11
                                    CP+Cgs 
  gi|118431049|ref|NP_147234.2|  7 FCPRCGSI 14
                                   6*****96 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 4.6
                        zf-ISL3  4 rCPnCgsk 11
                                   +C  Cg  
  gi|118431049|ref|NP_147234.2| 27 VCKSCGYS 34
                                   58888866 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.036
                        zf-ISL3  3 hrCPnCgsktv 13
                                    +CP+Cg   v
  gi|118431049|ref|NP_147234.2| 77 VTCPKCGHDEV 87
                                   69*****8766 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 5.2
                        zf-ISL3  42 yrCkeC 47 
                                    yrCk+C
  gi|118431049|ref|NP_147234.2| 105 YRCKRC 110
                                    788888 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 ?    3.3   9.3      0.28     1e+02      46      89 ..       6     110 ..       2     111 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.28
                                    TB-TTT--B--CTTTEEEEE.........E-SSS-E............................................ CS
                           Rpr2  46 tvCkkCgsvlipgvtcsvrv.........enkskkkkkkkkka..................................... 79 
                                    ++C +Cgs++ p       +         e++s++++     +                                     
  gi|118431049|ref|NP_147234.2|   6 KFCPRCGSIMYPKRDGARYLlvckscgysEEASREDH-----Qayrmrvtvekgprdkivviddetpvgaqvlkgsvtcp 80 
                                    79**********9988777767766666533444433.....13445688888999888888888888888877666666 PP

                                    ......................EEEEETTT CS
                           Rpr2  80 ....................dvlvvtClaC 89 
                                                         +  ++C++C
  gi|118431049|ref|NP_147234.2|  81 kcghdevyfwmmqtrsadepMTRFYRCKRC 110
                                    666666666666666666664445777777 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 ?    6.8   0.2     0.012       4.6      26      33 ..       6      14 ..       4      23 .. 0.80
   2 ?    3.3   0.1      0.15        56      25      31 ..      77      83 ..      71      86 .. 0.87
   3 ?   -1.9   0.5       6.5   2.4e+03       5      10 ..     105     110 ..     101     112 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                    Mu-like_Com 26 K.CPRCGtL 33
                                   K CPRCG +
  gi|118431049|ref|NP_147234.2|  6 KfCPRCGSI 14
                                   55*****86 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                    Mu-like_Com 25 iKCPRCG 31
                                   + CP+CG
  gi|118431049|ref|NP_147234.2| 77 VTCPKCG 83
                                   67****9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 6.5
                    Mu-like_Com   5 lRCGeC 10 
                                     RC  C
  gi|118431049|ref|NP_147234.2| 105 YRCKRC 110
                                    466655 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   2.6      0.95   3.5e+02      38      46 ..      26      34 ..       5      66 .. 0.58
   2 ?    9.1   0.1    0.0035       1.3      17      47 ..      59      86 ..      50     102 .. 0.78
   3 ?   -1.6   0.1       7.4   2.7e+03      38      46 ..     105     113 ..      93     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.95
                           CpXC 38 atCpkCgat 46
                                    +C +Cg++
  gi|118431049|ref|NP_147234.2| 26 LVCKSCGYS 34
                                   334444433 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                           CpXC 17 sidadedpelkeklldgslfeatCpkCgata 47
                                   ++ +d++  + +++l+gs   +tCpkCg++ 
  gi|118431049|ref|NP_147234.2| 59 IVVIDDETPVGAQVLKGS---VTCPKCGHDE 86
                                   566667777777788875...6999999875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 7.4
                           CpXC  38 atCpkCgat 46 
                                    ++C +C +t
  gi|118431049|ref|NP_147234.2| 105 YRCKRCRYT 113
                                    688888765 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.25        92       3       9 ..       7      13 ..       6      20 .. 0.79
   2 ?    1.6   0.1         1   3.7e+02      40      46 .]      26      32 ..      22      44 .. 0.72
   3 ?    6.1   0.0      0.04        14       3      10 ..      78      86 ..      77      92 .. 0.83
   4 ?   -0.4   1.9       4.4   1.6e+03      40      45 ..     105     110 ..     103     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.25
                        zf-IS66  3 tCpcCGg 9 
                                    Cp CG+
  gi|118431049|ref|NP_147234.2|  7 FCPRCGS 13
                                   6999997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 1
                        zf-IS66 40 yaCpcCe 46
                                   + C++C+
  gi|118431049|ref|NP_147234.2| 26 LVCKSCG 32
                                   5666664 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.04
                        zf-IS66  3 tCpcCGg.l 10
                                   tCp+CG+ +
  gi|118431049|ref|NP_147234.2| 78 TCPKCGHdE 86
                                   7*****944 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 4.4
                        zf-IS66  40 yaCpcC 45 
                                    y+C++C
  gi|118431049|ref|NP_147234.2| 105 YRCKRC 110
                                    99***9 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3      0.44   1.6e+02      19      27 ..       8      16 ..       3      20 .. 0.83
   2 ?    5.0   3.4     0.071        26       2      33 ..       8      42 ..       7      48 .. 0.72
   3 ?    3.5   2.4      0.21        76       2      22 ..      79     110 ..      67     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.44
                       zf-Mss51 19 CpdCGipty 27
                                   Cp+CG  +y
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMY 16
                                   *****8776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.071
                       zf-Mss51  2 CPvpkhkqt...apkhvdfeCpdCGiptycseehw 33
                                   CP + + +    + ++  + C+ CG++   s+e +
  gi|118431049|ref|NP_147234.2|  8 CPRCGSIMYpkrDGARYLLVCKSCGYSEEASREDH 42
                                   66665544454467778889*****9999988865 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.21
                       zf-Mss51   2 CPvpkhkqt...........apkhvdfeCpdC 22 
                                    CP + h++            +p    + C++C
  gi|118431049|ref|NP_147234.2|  79 CPKCGHDEVyfwmmqtrsadEPMTRFYRCKRC 110
                                    66666666666666666666666666677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        75  (0.00418317); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 810.59
//
Query:       gi|118431050|ref|YP_874825.1|  [L=105]
Description: hypothetical protein APE_0442a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); 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 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 839.23
//
Query:       gi|118431051|ref|NP_147236.2|  [L=99]
Description: DNA-directed RNA polymerase subunit L [Aeropyrum pernix K1]
Scores for complete 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   53.2   0.0    2.3e-14   52.9   0.0    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.3e-18   2.3e-14       3      74 ..      15      86 ..      13      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.3e-18
                                   EEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHHH CS
                    RNA_pol_L_2  3 tfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdelee 74
                                    ++++gEDhTLg lL +++ +  + + a Y+  HP+e+ +++ ++ +++ + +e+L+ka + ll+++ ++++
  gi|118431051|ref|NP_147236.2| 15 VIQVYGEDHTLGTLLVEAIKRVSNPKLAYYEAVHPMEDIIQVYVKYEDDVDIKEVLRKASDYLLEVIGDFRR 86
                                   699**************************************************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 883.23
//
Query:       gi|118431052|ref|NP_147237.2|  [L=210]
Description: hypothetical protein APE_0444.1 [Aeropyrum pernix K1]
Scores for complete 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-55  186.4   0.0    4.2e-55  186.2   0.0    1.0  1  DUF2067        Uncharacterized protein conserved in archaea (
  ------ inclusion threshold ------
       0.02   15.1   1.0      0.034   14.4   0.2    1.8  2  CbbQ_C         CbbQ/NirQ/NorQ C-terminal
      0.031   14.3   0.0      0.066   13.3   0.0    1.5  1  DUF1266        Protein of unknown function (DUF1266)
        2.3    9.0   7.1       0.36   11.6   0.4    2.8  3  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.2   0.0   9.5e-59   4.2e-55       2     186 .]      15     201 ..      14     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 9.5e-59
                        DUF2067   2 klndeeeleeflekisekiksaeevkievegnrllievyGtekeikdiirrikellre.klkkekrglfkyslsdllrea 80 
                                    +l d +++e+fle++s+++ ++++++++ eg++llie++G e++i+++i r+k llre + ++++ glf+ysl++++rea
  gi|118431052|ref|NP_147237.2|  15 RLLDVDDFERFLERLSRAV-KVDYSSWRREGDKLLIEMVGGESSIRESIVRVKALLREyRRRARGGGLFSYSLRRVSREA 93 
                                    67899**************.**************************************99999999************** PP

                        DUF2067  81 gapvppdvLvdaLkllGykaelre.envlktnapleevvelaerlseiykelrfknlskaakrvvavvsvltgldpdevi 159
                                    g++vppdvL+++L+ +Gy++e r+ e+vl+t+ap++ vve+a+++ e ++e++ ++l+++ +++v+++s+l g ++d+++
  gi|118431052|ref|NP_147237.2|  94 GVAVPPDVLSTVLSGMGYRVEARSgEGVLDTDAPWSLVVEVAREVGERLREAAAQPLTTSSRKLVVAASILAGSTLDDAV 173
                                    ******************************************************************************** PP

                        DUF2067 160 eellekGlLe.eeegkivlrkewkkalk 186
                                    + ++e+GlLe +e+g++++r  w+++lk
  gi|118431052|ref|NP_147237.2| 174 RAAVEEGLLEeDEKGRLLVRGGWRESLK 201
                                    ************************9986 PP

>> CbbQ_C  CbbQ/NirQ/NorQ C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   5.4e+03      12      29 ..      55      72 ..      47      81 .. 0.67
   2 ?   14.4   0.2   7.6e-06     0.034      22      73 ..     138     186 ..     119     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                                   -HHHHHHHHHHHHHHHTT CS
                         CbbQ_C 12 deevakkLVklAneiRnl 29
                                   ++++++++V++ + +R++
  gi|118431052|ref|NP_147237.2| 55 ESSIRESIVRVKALLREY 72
                                   456677777777666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.6e-06
                                    HHHHHHTTBTTTBSS---HHHHHHHHHHHTTT--HHHHHHHHTTCCC---HH CS
                         CbbQ_C  22 lAneiRnlkeggLeegvSTRlLvyaAkLiasglpareacraalvepltddpe 73 
                                    +++++R+   +    ++S R Lv aA++  +g  + +a+raa+ e l ++ e
  gi|118431052|ref|NP_147237.2| 138 VGERLREAAAQP--LTTSSRKLVVAASI-LAGSTLDDAVRAAVEEGLLEEDE 186
                                    555666666655..589*********95.6799************9986554 PP

>> DUF1266  Protein of unknown function (DUF1266)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.066      98     129 ..      11      42 ..       9      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                        DUF1266  98 aydagylseeeaeelldkagraaqssyssWee 129
                                    a+++++l+ +++e +l +++ra++  yssW+ 
  gi|118431052|ref|NP_147237.2|  11 AVNLRLLDVDDFERFLERLSRAVKVDYSSWRR 42 
                                    7899**************************86 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 ?   -0.2   0.2      0.38   1.7e+03      50      61 ..      63      74 ..      19      93 .. 0.73
   2 ?   -0.3   0.1      0.43   1.9e+03      14      29 ..     131     146 ..     128     158 .. 0.60
   3 ?   11.6   0.4   7.9e-05      0.36      13      54 ..     157     206 ..     151     210 .] 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHHT CS
                  PSK_trans_fac 50 erllallrraaa 61
                                    r++allr++++
  gi|118431052|ref|NP_147237.2| 63 VRVKALLREYRR 74
                                   355555555554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.43
                                    XXXXXXXXXXXXXXXX CS
                  PSK_trans_fac  14 areLarltgeskteAv 29 
                                    + e+ar  ge + eA 
  gi|118431052|ref|NP_147237.2| 131 VVEVAREVGERLREAA 146
                                    5566666666555554 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 7.9e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XX--HHHHHHH CS
                  PSK_trans_fac  13 lareLarltgeskteAvrrAleerlerlrre........raepllerlla 54 
                                    l+   + l+g ++ +Avr+A+ee l +++++         +e+l+  l+a
  gi|118431052|ref|NP_147237.2| 157 LVVAASILAGSTLDDAVRAAVEEGLLEEDEKgrllvrggWRESLKTLLKA 206
                                    566667789****************9998767777544444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 1831.61
//
Query:       gi|14600717|ref|NP_147238.1|  [L=215]
Description: exosome complex RNA-binding protein Cs14 homologue [Aeropyrum pernix K1]
Scores for 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   32.5   1.4    6.5e-07   29.0   0.1    2.4  2  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
      4e-05   23.2   1.2    6.3e-05   22.5   1.2    1.3  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
    0.00018   21.4   0.5     0.0003   20.6   0.5    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    0.00051   20.3   0.0      0.022   15.1   0.0    2.9  2  S1              S1 RNA binding domain
     0.0019   18.2   0.0     0.0025   17.8   0.0    1.2  1  Zn_Tnp_IS91     Transposase zinc-binding domain
     0.0027   17.2   2.8        0.4   10.2   0.1    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0048   16.9   0.1     0.0073   16.3   0.1    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.007   16.5   1.1      0.012   15.7   1.1    1.3  1  Zn-ribbon_8     Zinc ribbon domain
     0.0071   16.0   1.2      0.013   15.2   1.2    1.3  1  A2L_zn_ribbon   A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.015   14.7   3.1      0.099   12.1   3.1    2.0  1  zf-ribbon_3     zinc-ribbon domain
      0.024   14.3   0.9        1.9    8.3   0.2    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.026   14.6   0.1      0.039   14.1   0.1    1.2  1  DUF2318         Predicted membrane protein (DUF2318)
      0.031   14.4   0.6      0.055   13.6   0.6    1.3  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.032   13.9   2.1      0.064   13.0   2.1    1.4  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.057   13.3   0.3        0.1   12.5   0.3    1.3  1  MCM_OB          MCM OB domain
      0.068   13.1   2.9       0.68    9.9   2.8    2.2  1  zinc_ribbon_4   zinc-ribbon domain
      0.096   13.4   1.2       0.65   10.7   0.3    2.3  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.11   12.6   0.1       0.17   12.0   0.1    1.2  1  TerY_C          TerY-C metal binding domain
       0.15   12.1   0.3       0.25   11.3   0.3    1.3  1  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh
       0.18   11.8   0.5        0.3   11.1   0.5    1.2  1  DUF1451         Zinc-ribbon containing domain
       0.18   11.8   1.1       0.31   11.1   1.1    1.2  1  DZR             Double zinc ribbon
        0.7    9.8   2.5         31    4.6   0.7    2.1  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        1.2    8.6   3.7        5.6    6.5   3.7    1.9  1  Mu-like_Com     Mu-like prophage protein Com
        3.2    7.4   3.6        8.6    6.0   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
        6.2    7.0   5.6        3.2    7.9   0.8    2.3  2  zf-ACC          Acetyl-coA carboxylase zinc finger 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 !   29.0   0.1   9.1e-10   6.5e-07       2      33 ..      14      47 ..      14      49 .. 0.89
   2 ?    2.0   0.2      0.26   1.9e+02      22      36 ..      82      96 ..      68      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 9.1e-10
                                  E-TT-EEEETTTSEE-TTEEE..ETTEEEESSSE CS
                        ECR1_N  2 VtPGevlttdeefmrGhGTYv..rggtiyAsvaG 33
                                  V+PG+vl+t eef++G+G+Yv   +g i+A+  G
  gi|14600717|ref|NP_147238.1| 14 VMPGDVLATIEEFLPGEGVYVdpVKGFIRAAAPG 47
                                  99******************97778888998666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                                  EETTEEEESSSEEEE CS
                        ECR1_N 22 vrggtiyAsvaGtve 36
                                  vrg  ++A v G+v+
  gi|14600717|ref|NP_147238.1| 82 VRGDLVVAEVYGVVR 96
                                  588889999999996 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 !   22.5   1.2   8.8e-08   6.3e-05       6      30 ..     165     188 ..     162     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.8e-08
                 zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCgle 30 
                                   C+rCGa +e ++  +++ Cp Cg+ 
  gi|14600717|ref|NP_147238.1| 165 CSRCGAVMEFQSE-RSMKCPKCGNV 188
                                   **********876.*********86 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.5   4.2e-07    0.0003      30      58 ..     164     191 ..     151     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.2e-07
                OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                    Cs+Cg++++  +s+r +kCp+Cg +  r
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEF-QSERSMKCPKCGNVEKR 191
                                   6**********.************99877 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.35   2.5e+02      22      35 ..      32      44 ..       8      86 .. 0.51
   2 !   15.1   0.0     3e-05     0.022      26      61 ..     109     143 ..      84     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.35
                                  EEETTTEEEEEEGG CS
                            S1 22 Velgngvegfvpas 35
                                  V+++ +v+gf+ a+
  gi|14600717|ref|NP_147238.1| 32 VYVD-PVKGFIRAA 44
                                  4445.666666654 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3e-05
                                   TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEE CS
                            S1  26 ngvegfvpaselsrdarvedpdevlkvGdevkvkvl 61 
                                    + ++ +p+s+++++  ++++++ +++Gd + +k+ 
  gi|14600717|ref|NP_147238.1| 109 SPYSAAIPISQIADE-YIKNIEDYYRMGDWILAKIV 143
                                   678999*********.9************9999985 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 !   17.8   0.0   3.5e-06    0.0025      33      83 ..     156     205 ..     124     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                   Zn_Tnp_IS91  33 aalGfaryeCeeCghekivyfsCksrhCpsCqkkateewlekqqeellpvp 83 
                                   +++G+    C+ Cg   + ++s +s  Cp+C++ +++++  + +++ l+++
  gi|14600717|ref|NP_147238.1| 156 PRYGVVYAICSRCGA-VMEFQSERSMKCPKCGNVEKRKVSIHAKSRHLRIR 205
                                   678999999*****6.56667778888***********9999999888754 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00055       0.4      21      32 ..     164     175 ..     157     176 .. 0.88
   2 !    6.5   0.7    0.0084         6       1       9 [.     180     188 ..     180     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                                   EESSSSBEEEEC CS
                  TF_Zn_Ribbon  21 vCtdCGlVledn 32 
                                   +C++CG+V+e +
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEFQ 175
                                   9*********86 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0084
                                   EEETTTTCE CS
                  TF_Zn_Ribbon   1 ykCPnCgst 9  
                                   +kCP+Cg+ 
  gi|14600717|ref|NP_147238.1| 180 MKCPKCGNV 188
                                   688888874 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   0.1     1e-05    0.0073      69      96 ..     161     189 ..     138     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                                   -EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                          HypA  69 vkvrCreCgkefeleek.alrCpkCgsad 96 
                                   v + C++Cg+ +e +++ +++CpkCg+ +
  gi|14600717|ref|NP_147238.1| 161 VYAICSRCGAVMEFQSErSMKCPKCGNVE 189
                                   6689*********7775599******865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.1   1.6e-05     0.012       8      38 ..     165     192 ..     156     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                   Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evrr 38 
                                   C +Cg + e +qs  +    +CP+Cg  e r+
  gi|14600717|ref|NP_147238.1| 165 CSRCGAVME-FQS--E-RSMKCPKCGNvEKRK 192
                                   *****9999.774..3.3566****9866555 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 !   15.2   1.2   1.7e-05     0.013       5      31 ..     164     189 ..     162     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                 A2L_zn_ribbon   5 vCsvCggngilnseqgylvCieCgasf 31 
                                   +Cs Cg  ++++se++ + C++Cg+++
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEFQSERS-MKCPKCGNVE 189
                                   8**********88887.99*****986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.1   0.00014     0.099       4      24 ..     164     187 ..     162     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                   zf-ribbon_3   4 rCPnCGa.p..lssddnvCpyCGt 24 
                                    C++CGa     s++ ++Cp+CG 
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAvMefQSERSMKCPKCGN 187
                                   6*****94343478899******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 ?    4.5   0.0     0.043        31       2       7 ..     165     170 ..     160     173 .. 0.68
   2 ?    8.3   0.2    0.0026       1.9       1       7 [.     181     187 ..     176     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.043
                 zinc_ribbon_2   2 CpnCGa 7  
                                   C++CGa
  gi|14600717|ref|NP_147238.1| 165 CSRCGA 170
                                   555554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0026
                 zinc_ribbon_2   1 fCpnCGa 7  
                                   +Cp+CG+
  gi|14600717|ref|NP_147238.1| 181 KCPKCGN 187
                                   6888876 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.5e-05     0.039      21      60 ..     149     188 ..     140     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-05
                       DUF2318  21 lvvkksdgklrvaldaCevCekkgYvqegeelvCknCgvr 60 
                                   + + + + ++ v+  +C+ C+    +q++ ++ C +Cg++
  gi|14600717|ref|NP_147238.1| 149 FTLSTVEPRYGVVYAICSRCGAVMEFQSERSMKCPKCGNV 188
                                   55667778999*********999999***********986 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 ?   13.6   0.6   7.6e-05     0.055      10      52 ..     164     207 ..     160     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-05
                  NOB1_Zn_bind  10 rChaCfkvt..kdmtkkFCpkCGnktLkrvavsvdengelklhlk 52 
                                    C  C  v+  +  + + CpkCGn   ++v+++ +++ +l++ l 
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMefQSERSMKCPKCGNVEKRKVSIHAKSR-HLRIRLV 207
                                   577777777444456667******9999999887776.5555555 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 ?   13.0   2.1   8.9e-05     0.064       2      24 ..     164     186 ..     163     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                                   B-SSS--B----SSS----SSS- CS
                DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCG 24 
                                   iC +Cga ++ +++ + +C +CG
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEFQSERSMKCPKCG 186
                                   8*********************9 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   0.00014       0.1      23      73 ..     151     200 ..     143     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                   E---EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH-EEE-GG.GSE CS
                        MCM_OB  23 asevkpklkkavfeckkcgktveveleePrkCeekeCeskdpfklete.ksk 73 
                                    s+v+p+   ++  c++cg+++e++ e+ +kC  ++C++ ++ k++++ ks+
  gi|14600717|ref|NP_147238.1| 151 LSTVEPRYGVVYAICSRCGAVMEFQSERSMKC--PKCGNVEKRKVSIHaKSR 200
                                   68999***************9999999999**..99**87766665443665 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.8   0.00094      0.68       4      34 ..     164     188 ..     162     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00094
                 zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCghv 34 
                                    C +C+a+ e+++e      ++++C+kCg+v
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEFQSE------RSMKCPKCGNV 188
                                   59999999999886......9********97 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 ?    0.9   0.0         1   7.4e+02       4      11 ..     164     171 ..     162     176 .. 0.83
   2 ?   10.7   0.3    0.0009      0.65       3      28 ..     180     204 ..     178     212 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1
                       zf-ISL3   4 rCPnCgsk 11 
                                    C +Cg++
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAV 171
                                   6*****87 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0009
                       zf-ISL3   3 hrCPnCgsktvvkhgkkerrvrhlpi 28 
                                   ++CP+Cg++ ++k +  + + rhl+i
  gi|14600717|ref|NP_147238.1| 180 MKCPKCGNVEKRKVS-IHAKSRHLRI 204
                                   78*******643332.3455555554 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00023      0.17      86     112 ..     162     189 ..     154     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                        TerY_C  86 favC.eCgkllCidgeeeatCpwCgkev 112
                                    a+C +Cg ++ ++ e ++ Cp+Cg+  
  gi|14600717|ref|NP_147238.1| 162 YAICsRCGAVMEFQSERSMKCPKCGNVE 189
                                   578846******************9865 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 ?   11.3   0.3   0.00035      0.25      16      38 ..     165     187 ..     160     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                                   TTTTSEETTE......E-TTTTT CS
                     Anti-TRAP  16 CngsGkiepeeprasleCPkCsG 38 
                                   C + G +   +   s++CPkC+ 
  gi|14600717|ref|NP_147238.1| 165 CSRCGAVMEFQSERSMKCPKCGN 187
                                   77777777777779*******85 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   0.5   0.00042       0.3     115     141 ..     163     188 ..     158     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                       DUF1451 115 lvCekCgkelalkkteeippCpkCgat 141
                                    +C +Cg+ +++++ +   +CpkCg+ 
  gi|14600717|ref|NP_147238.1| 163 AICSRCGAVMEFQSERS-MKCPKCGNV 188
                                   58**********98776.58****985 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00043      0.31      14      37 ..     164     188 ..     161     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                           DZR  14 fCseCgtklkavaa.edrCpsCgek 37 
                                    Cs+Cg+ ++ +++ + +Cp+Cg  
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEFQSErSMKCPKCGNV 188
                                   7999999998666689999999975 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 ?    4.0   0.0     0.066        48      24      35 ..     165     176 ..     157     177 .. 0.77
   2 ?    4.6   0.7     0.043        31       4       9 ..     182     187 ..     181     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.066
                                   ESSSS-EEESSC CS
                RNA_POL_M_15KD  24 CrqCgYeepadq 35 
                                   C+ Cg++ ++ +
  gi|14600717|ref|NP_147238.1| 165 CSRCGAVMEFQS 176
                                   999999988876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                                   ESTTTS CS
                RNA_POL_M_15KD   4 CpkCgN 9  
                                   CpkCgN
  gi|14600717|ref|NP_147238.1| 182 CPKCGN 187
                                   *****9 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 ?    6.5   3.7    0.0079       5.6      20      49 ..     175     203 ..     163     206 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0079
                   Mu-like_Com  20 lDeltiKCPRCGtLnHlkaesldaegrRer 49 
                                     e  +KCP+CG +   +  s  a  r  r
  gi|14600717|ref|NP_147238.1| 175 QSERSMKCPKCGNVEK-RKVSIHAKSRHLR 203
                                   456679******9876.4466666656555 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.012       8.6       4      14 ..     164     174 ..     162     179 .. 0.82
   2 ?    2.0   0.6      0.22   1.6e+02       4      10 ..     181     187 ..     178     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                        zf_UBZ   4 lCerCgkeipe 14 
                                   +C+rCg+ ++ 
  gi|14600717|ref|NP_147238.1| 164 ICSRCGAVMEF 174
                                   6*****99975 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.22
                        zf_UBZ   4 lCerCgk 10 
                                    C++Cg 
  gi|14600717|ref|NP_147238.1| 181 KCPKCGN 187
                                   7****95 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 ?    0.8   0.3      0.75   5.4e+02       4      11 ..     165     172 ..     165     172 .. 0.88
   2 ?    7.9   0.8    0.0044       3.2       3      10 ..     181     188 ..     180     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.75
                        zf-ACC   4 CpsCgeml 11 
                                   C +Cg+++
  gi|14600717|ref|NP_147238.1| 165 CSRCGAVM 172
                                   99***985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0044
                        zf-ACC   3 KCpsCgem 10 
                                   KCp+Cg++
  gi|14600717|ref|NP_147238.1| 181 KCPKCGNV 188
                                   9*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1838.86
//
Query:       gi|14600718|ref|NP_147239.1|  [L=219]
Description: hypothetical protein APE_0446 [Aeropyrum pernix K1]
Scores for complete 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-05   23.4   0.0    4.8e-05   23.1   0.0    1.1  1  Cons_hypoth95  Conserved hypothetical protein 95
     0.0066   16.1   0.0     0.0094   15.6   0.0    1.2  1  UPF0020        Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.016   14.8   0.0      0.025   14.1   0.0    1.5  1  MTS            Methyltransferase small domain


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 !   23.1   0.0     8e-09   4.8e-05      23     145 ..      40     159 ..      32     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8e-09
                                   SSSHHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHH CS
                 Cons_hypoth95  23 PttdrvrealFnilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedalea 103
                                   P    vr a+  +l+  +ega   Dl aG++ lgl  l  ga+++ +ve d + + ++    e+l+l +++  +      +
  gi|14600718|ref|NP_147239.1|  40 PADIAVRIAVDALLRGLLEGALAADLAAGTCRLGLALLLYGASRVAAVEADGRLAGLCLGAAEKLGLGGRIFFVAS--RVS 118
                                   666778889999999999**************************************************94433333..333 PP

                                   HCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT-EEEE CS
                 Cons_hypoth95 104 llklakkkeefdivflDPPyakellieevlelleekkllken 145
                                    ++ + +++++d+v  +PP+       +  e le    lk++
  gi|14600718|ref|NP_147239.1| 119 RRRGPLAAGSVDLVATNPPFGVWRR-GADWEVLEYALRLKPR 159
                                   34444678899*********87654.5555555555555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-06    0.0094      79     133 ..      84     140 ..      56     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-06
                                   EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--..STTS---EEEE------ CS
                       UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLr..lkegevdvivtnpPYGe 133
                                   +++++ d r+   +   aek g+g++i f++  +   r  l+ g+vd+++tnpP+G 
  gi|14600718|ref|NP_147239.1|  84 VAAVEADGRLAGLCLGAAEKLGLGGRIFFVASRVSRRRgpLAAGSVDLVATNPPFGV 140
                                   77888899999999999****************99988999999***********95 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.2e-06     0.025      23     123 ..      48     151 ..      38     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-06
                                   HHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT...STTS CS
                           MTS  23 Lletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvlee...veek 96 
                                    +++l     +   ++Dl++G+  lg+al+    + +v +v++d r   ++   +e+ +l   + +vas v      ++ +
  gi|14600718|ref|NP_147239.1|  48 AVDALLRGllEGALAADLAAGTCRLGLALLLYGAS-RVAAVEADGRLAGLCLGAAEKLGLGgrIFFVASRVSRRrgpLAAG 127
                                   4555444443344589************9986655.899999999999999999999988866556666665541115689 PP

                                   -EEEEEE---STTTCHCHHHHHHHHHH CS
                           MTS  97 kfdlivsNPPfhagkatelavaeelia 123
                                   ++dl+ +NPPf   +     + +e+++
  gi|14600718|ref|NP_147239.1| 128 SVDLVATNPPFGVWRR---GADWEVLE 151
                                   ***********66554...34444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1788.20
//
Query:       gi|118431053|ref|NP_147240.2|  [L=354]
Description: hypothetical protein APE_0447.1 [Aeropyrum pernix K1]
Scores for complete 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-61  207.7   0.0    3.4e-61  207.3   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


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 !  207.3   0.0   1.9e-65   3.4e-61       1     294 [.      37     344 ..      37     352 .. 0.91

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 1.9e-65
                Diphthamide_syn   1 fPegllpdsaeiadileef...gaevvilgDttYGaCcvdevaaeh.lgadllvHyGhsclspvd.......rlpvlYv. 68 
                                    +Peg+l++   ia+++ee+    a+v++ +D+t+GaC+++  +++  +  dl+vH Ghs+++          r +v+Yv 
  gi|118431053|ref|NP_147240.2|  37 LPEGMLQYGLYIAKCFEEMlggAAQVYLHADPTFGACDLHYGELDTtVRPDLIVHVGHSPYPAELaheglepRGRVVYVr 116
                                    6***************888898899****************99986478************95335889999*******8 PP

                Diphthamide_syn  69 .fveieldvehlvetlkknf..kekkkivlvstiqyahaleevkeeleeegyevvkvpqsekp.lspgevlgctspklke 144
                                     + +++l +++l e++         +++++++t+q++h +e+++e l+ eg ev  vp   +p   + +vlgc+++ ++ 
  gi|118431053|ref|NP_147240.2| 117 aLSKSQLPLDALREAAGLLAsrYGVRRVGIATTAQHTHLAEKAAEVLRGEGLEVA-VPPGLRPyFGAAQVLGCDYRLARG 195
                                    877777776655555444444335788************************9999.666667747899**********96 PP

                Diphthamide_syn 145 eeeevdailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrl 224
                                       ++d ++y+g+g fh+l+l+l++ k pv+++dpy++  ++ + + +kl+r R ++++++  a+++Giivg +++q+r+
  gi|118431053|ref|NP_147240.2| 196 V--RADGFVYVGGGVFHPLGLYLATLK-PVVQVDPYRGVSEDLTREGEKLYRSRLYRVSQSIGARRWGIIVGLKSGQYRP 272
                                    5..9*********************77.**************************************************** PP

                Diphthamide_syn 225 elverlkkllkeagkksylvlvgelnpakLanfae..idafVlvaCprlsiddgkeFekPvltpyElevalg 294
                                    +lve+l + +++ag ++ lv+ +  + ++L  +++  ++af +++Cprl++dd   +ekPvltp E+++al+
  gi|118431053|ref|NP_147240.2| 273 WLVEKLARAIESAGGEYLLVASEVTTLSQLVAIDNpwFEAFTVTSCPRLPTDDFWSYEKPVLTPGEAMMALE 344
                                    *********************************7689**********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2744.35
//
Query:       gi|14600720|ref|NP_147241.1|  [L=174]
Description: 50S ribosomal protein L10 [Aeropyrum pernix K1]
Scores for complete 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-40  136.7   0.1    5.1e-40  136.5   0.1    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e
  ------ inclusion threshold ------
       0.46   10.6   1.6        9.5    6.4   0.5    2.2  2  FeoC           FeoC like transcriptional regulator


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 !  136.5   0.1   5.7e-44   5.1e-40       3     132 .]      14     165 ..      12     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 5.7e-44
                                   SSXXBSSSXXSSTSXX.XSXXXXXESX..........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXX CS
                 Ribosomal_L16   3 rkkyrKsrkryirgvs.tkgtklefgd..........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfp 69 
                                    ++y++++  yi+gv+ +k+t++e+g+           +Lv+le+gq++++aleaaria+n+yl ++ g+    ++irv+p
  gi|14600720|ref|NP_147241.1|  14 GPPYTRRE--YIHGVPpPKITRFEMGNremmekweikGELVMLEAGQIRHNALEAARIAVNKYLATTIGDknfYFRIRVYP 92 
                                   579*****..***********************998777**************************998888899******* PP

                                   XEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                 Ribosomal_L16  70 hhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpiktkiv 132
                                   hh+++++     ag+dR+++G+    Gkp g++arv++g++++e+   k+  +ee++kealrr asK+p++ +iv
  gi|14600720|ref|NP_147241.1|  93 HHVIRENkmmafAGADRLQDGMrqafGKPVGTAARVYPGTVVLEVwarKG--DEENVKEALRRGASKFPLPSRIV 165
                                   *********************************************86444..9*******************997 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.5    0.0011       9.5      32      50 ..      39      57 ..      35      63 .. 0.85
   2 ?    3.1   0.0     0.011     1e+02      34      49 ..     134     149 ..     132     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0011
                          FeoC 32 eamLeqwvrkGrvekvaat 50
                                  + m+e w+ kG +  ++a+
  gi|14600720|ref|NP_147241.1| 39 REMMEKWEIKGELVMLEAG 57
                                  68**********9888775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                          FeoC  34 mLeqwvrkGrvekvaa 49 
                                    Le+w rkG  e+v++
  gi|14600720|ref|NP_147241.1| 134 VLEVWARKGDEENVKE 149
                                   59*******8776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1314.13
//
Query:       gi|14600721|ref|NP_147242.1|  [L=577]
Description: molybdopterin biosynthesis protein MoeA [Aeropyrum pernix K1]
Scores for 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-25   87.3   2.4    1.2e-24   86.9   0.5    2.1  2  MoeA_N         MoeA N-terminal region (domain I and II)
    1.1e-13   51.1   0.2    5.4e-12   45.7   0.1    3.0  2  MoeA_C         MoeA C-terminal region (domain IV)
    2.2e-09   37.1   0.0    8.2e-09   35.3   0.0    2.0  1  MoCF_biosynth  Probable molybdopterin binding domain


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 !   86.9   0.5     2e-28   1.2e-24       2     157 .]      16     182 ..      15     182 .. 0.85
   2 ?   -0.5   0.1      0.15     9e+02      27      56 ..     365     399 ..     341     501 .. 0.65

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 2e-28
                                   -HHHHHHHHHHH-HH......-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............ CS
                        MoeA_N   2 sveealaiilaalel......eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep....saa 71 
                                   ++eea+a+ + +le+      e+ e + l  +a+gr la++ vA+  +Pp+ +   DG Av+++  s+ s  +     +++
  gi|14600721|ref|NP_147242.1|  16 TLEEAIARAAGRLEVlrgsllEKREsLGL-PAAIGRPLARKAVARGCYPPYPRVNLDGCAVDSSRVSRGSVLRVtarlRPG 95 
                                   57888888777774458888866666999.889****************************99999998777778998777 PP

                                   ...-S---TT-.EEEE-TTSB--TT--EEEEGGGE...E....EETTES--STTTTEE-TTSSB-TTSEEE-TTBB--CCC CS
                        MoeA_N  72 geeperllpgg.avrimTGaplPegadaVvpvEdte..eeeaketvevkavkpgenvrraGedikaGevllragtrltpae 149
                                    e+ e + ++g +v++ TGaplP gadaVvp+E+ +  +e + +   +++++++  v    +d   G+v+l +g+++tp  
  gi|14600721|ref|NP_147242.1|  96 MEPVELVDREGgCVWVDTGAPLPVGADAVVPLEELDmlGEGVVR--LEAEPRRWMGVADPCSDAMDGSVVLGEGEVVTPEA 174
                                   777777777778**********************9654322222..337899999************************** PP

                                   HHHHHHCT CS
                        MoeA_N 150 igllasvG 157
                                   ++ las+G
  gi|14600721|ref|NP_147242.1| 175 VASLASAG 182
                                   ******98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.15
                                   -TT-BBSS-EE-SS-BSSS-EESSSEE.EE....E CS
                        MoeA_N  27 algrvlaedvvApedvPpfdnSamDGY.Av....r 56 
                                     g +l +  v++e++  +  +a DGY Av     
  gi|14600721|ref|NP_147242.1| 365 YCGGRLYAVPVSTESYMTVSWAAADGYiAVepgkA 399
                                   44555555556677777777888888833433330 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   0.0      0.04   2.4e+02       4      23 ..      17      36 ..      15      47 .. 0.85
   2 !   45.7   0.1     9e-16   5.4e-12       2      70 ..     344     409 ..     343     411 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.04
                                  ESS-EE--SSS-EEEEEEEE CS
                        MoeA_C  4 laedlksdpgrreflRvilt 23
                                  l e+++ ++gr e lR++l 
  gi|14600721|ref|NP_147242.1| 17 LEEAIARAAGRLEVLRGSLL 36
                                  778999***********996 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 9e-16
                                   EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEE CS
                        MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevi 70 
                                   a+l + +k  + r ++++v    ++g+++a p+ +++S+++ s+a A+g+i +++g++ le+Gee +v 
  gi|14600721|ref|NP_147242.1| 344 AVLLAGVKPGR-RLSYIPVAAVYCGGRLYAVPV-STESYMTVSWAAADGYIAVEPGKA-LEPGEEASVT 409
                                   67777777777.*********************.***********************9.******9997 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.4e-12   8.2e-09       2     143 ..     196     329 ..     195     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.4e-12
                                   EEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS..SEEEEESS-SSSTT-- CS
                 MoCF_biosynth   2 vitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea..dviittGGtGptpdDv 73 
                                   v +vGdel         g +  tn  l  ++l+++ vev ++++ pD +e +++  +aa +++   +++t+GG +++  D+
  gi|14600721|ref|NP_147242.1| 196 VASVGDELRsleecreGGGVCETNRLLARSRLEAAEVEVVDLGIHPDRPETLSSLAAAA-RGSgcHILVTSGGSSVGLSDY 275
                                   6689999998888888777899******************************9988555.66668***************9 PP

                                   HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                 MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                     +  ++          +++r+++ +pg+p+++  +   ++    +++ LPG+p+++  a++++llp l 
  gi|14600721|ref|NP_147242.1| 276 ALAGPED----------IVVRGLAIRPGRPTTLSIV---DG---IPVYSLPGNPRSAGSAIDLFLLPSLA 329
                                   6655544..........6789********8887777...54...37*******************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4447.20
//
Query:       gi|14600722|ref|NP_147243.1|  [L=64]
Description: hypothetical protein APE_0450a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-30  104.9   3.7    1.6e-30  104.8   3.7    1.0  1  Cren7     Chromatin protein Cren7


Domain annotation for each model (and alignments):
>> Cren7  Chromatin protein Cren7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   3.7   9.1e-35   1.6e-30       6      58 .]       8      61 ..       3      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 9.1e-35
                                  -EEEE-T.TS-EEEE--SEEEEESSTTS--EEEEEEE-TTT--EEEEEE-TTS- CS
                         Cren7  6 pvkVktp.eGkeleLvPvKvWqLaPkgkkGvkvgLFkdPetgkyfRakvpddyP 58
                                  pvkV++p +Gke+eL P+KvW+L+P+g++Gvk+gLFk+PetgkyfRakvpddyP
  gi|14600722|ref|NP_147243.1|  8 PVKVRDPtTGKEVELTPIKVWKLSPRGRRGVKIGLFKSPETGKYFRAKVPDDYP 61
                                  8******9*********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 540.15
//
Query:       gi|118431054|ref|NP_147244.2|  [L=175]
Description: hypothetical protein APE_0452.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       472  (0.0263261); 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:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1451.31
//
Query:       gi|14600724|ref|NP_147245.1|  [L=240]
Description: hypothetical protein APE_0454 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-28   97.2   0.0    1.4e-27   96.3   0.0    1.4  2  SfsA      Sugar fermentation stimulation protein RE domain
    3.6e-13   49.5   0.4    6.9e-13   48.5   0.4    1.5  1  SfsA_N    SfsA N-terminal OB domain
  ------ inclusion threshold ------
      0.014   15.9   0.0       0.62   10.6   0.0    2.4  2  NERD      Nuclease-related 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 ?   -3.1   0.0       1.1   6.8e+03      46      53 ..      19      26 ..      13      49 .. 0.70
   2 !   96.3   0.0   2.3e-31   1.4e-27       2     135 ..      85     215 ..      84     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                  EEEEEEEE CS
                          SfsA 46 kcyvEVKs 53
                                  ++ vEVKs
  gi|14600724|ref|NP_147245.1| 19 RFVVEVKS 26
                                  45667766 PP

  == domain 2  score: 96.3 bits;  conditional E-value: 2.3e-31
                                   HHHHHHHHHHEE..........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHH CS
                          SfsA   2 lpnklveealesglielagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLael 82 
                                   +pn+l++ea       + g ++i++e ++  sr+Dfl+++  +  + vEVK+v+l+ +g++lfP ap++R +khle La+l
  gi|14600724|ref|NP_147245.1|  85 VPNRLFAEAAPM---VVGGDASIEAEREVFGSRLDFLISTG-RGLWAVEVKGVNLSLDGVGLFPNAPSARAVKHLEVLARL 161
                                   79*******976...2457789*****************98.**************999********************** PP

                                   HHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT.-EEEEEEEEE- CS
                          SfsA  83 vkegyravvlfvvqredarefkpnkeidpefaealreaaeaG.Vevlaydckvt 135
                                   ++eg ++++ fv+ r+d+r f+pn  +d++fa +  +  ++G V ++ ++++++
  gi|14600724|ref|NP_147245.1| 162 AREGVKPLMAFVALRPDIRVFAPNYRVDRRFASLACTLLRRGlVGMVGIRVSID 215
                                   *************************************99999666777777666 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 !   48.5   0.4   1.2e-16   6.9e-13       1      62 [.      14      79 ..      14      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.2e-16
                                  EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....E.SSS-SEEEEEEEETTEEEE CS
                        SfsA_N  1 lrRpnRFladveld.g..tvHvpntGrlkelllpGarvllsksdnp.krKtkytleavekegtwvg 62
                                  lrR+nRF+++v+ + g  ++H+ +tGr+ +l+ pG+r +l    n  + Kt ++ +a+++ g++v 
  gi|14600724|ref|NP_147245.1| 14 LRRVNRFVVEVKSSrGvvRCHLMDTGRIDHLASPGRRGVLIAWLNRlGGKTVCRAQAFKTAGGVVA 79
                                  89**********8844656******************999999996699***********999886 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.023   1.4e+02      47      61 ..      20      34 ..      11      53 .. 0.82
   2 ?   10.6   0.0    0.0001      0.62      34      58 ..     112     137 ..      87     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.023
                          NERD 47 fviEvKnwsGwifgd 61
                                  fv+EvK+ +G+++ +
  gi|14600724|ref|NP_147245.1| 20 FVVEVKSSRGVVRCH 34
                                  99*****99988776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0001
                          NERD  34 g.eiDhlvispkgifviEvKnwsGwi 58 
                                   g  +D+l+ + +g++ +EvK  + ++
  gi|14600724|ref|NP_147245.1| 112 GsRLDFLISTGRGLWAVEVKGVNLSL 137
                                   1489****************987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1964.21
//
Query:       gi|14600726|ref|NP_147247.1|  [L=452]
Description: 4-aminobutyrate aminotransferase [Aeropyrum pernix K1]
Scores for complete 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-122  408.6   0.0   2.7e-122  408.3   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
     0.0094   15.2   0.0      0.014   14.6   0.0    1.2  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 !  408.3   0.0    3e-126  2.7e-122      10     406 .]      37     442 ..      29     442 .. 0.94

  Alignments for each domain:
  == domain 1  score: 408.3 bits;  conditional E-value: 3e-126
                                   CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S.E CS
                   Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld.k 89 
                                   +lv++++ G++++dvdg+ry+D+ ++iav+n+Gh+hP+vv+avk q++ + h s+  + +e+a+ +ae l++ +p +   k
  gi|14600726|ref|NP_147247.1|  37 PLVVKRGYGAVVEDVDGNRYIDFNAGIAVLNVGHNHPRVVEAVKRQLERFLHYSLTDFYYEEAVSAAERLARSVPISGGaK 117
                                   489*******************************************************************9999974436* PP

                                   EEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB- CS
                   Aminotran_3  90 vflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlke 170
                                   +f+ nsG+e++e+++K+ r++     +  +++ii+f g+fHGrt+ga+s+++sk+ +++ f p++p++++++ypd++++++
  gi|14600726|ref|NP_147247.1| 118 TFFTNSGAESIEASIKVVRAFF----RGTRPYIISFLGGFHGRTYGAMSASASKPVHRARFYPLVPGFIHAPYPDPYRCPF 194
                                   *******************955....567**************************************************** PP

                                   HHHHHHHHHHHHHHHH.......CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSS CS
                   Aminotran_3 171 neeeeaalleeleale.......kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGkl 244
                                    + e +a+ e++ +++        +   evaA+++EpiqgegG+vv++++fl  l++l++kh++lli+DEvqtGf+rTG +
  gi|14600726|ref|NP_147247.1| 195 PGLEGEACGEAAVSYIedyifskLVDPGEVAAFLFEPIQGEGGYVVPPDSFLPSLQKLARKHGILLIADEVQTGFARTGRM 275
                                   9966555554433333355598777889***************************************************** PP

                                   SGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH CS
                   Aminotran_3 245 fAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaalk 325
                                   fA+eh+gv+pD+m+laKa++gGlpl a++++ evm+    gsh++TfgGnp+a a+++av+++ie e l e+ q+lg++  
  gi|14600726|ref|NP_147247.1| 276 FAVEHWGVEPDVMALAKAMGGGLPLGAAVGRSEVMSLP-RGSHANTFGGNPVALAAFNAVMDVIEGERLWERSQRLGEKAL 355
                                   ***********************************998.9***************************************** PP

                                   HHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHHHH CS
                   Aminotran_3 326 egLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGdnvirllppliitdeeidelle 400
                                   + L e++++   +++vRgkGlmi++el+ +++++e      + +l++  + G+l+++aG +++r++ppl+i++e  d +le
  gi|14600726|ref|NP_147247.1| 356 KILGEAAEELSIVGHVRGKGLMIGVELVRDENTREphkealAWVLDRSFKRGLLVIGAGVSAVRIAPPLTIEEELFDRGLE 436
                                   *******999********************998889999996699************************************ PP

                                   HHHHHH CS
                   Aminotran_3 401 ilkkal 406
                                   il+++l
  gi|14600726|ref|NP_147247.1| 437 ILVEVL 442
                                   *99876 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 !   14.6   0.0   1.6e-06     0.014     168     284 ..     247     353 ..     239     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHH CS
                 Aminotran_1_2 168 eeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsr 248
                                   + l+kl   a+k+++ll+ De+  gf+ +   ++  + +ve+++       l+Ka+G  G+ +G+++g ++v s  r  ++
  gi|14600726|ref|NP_147247.1| 247 PSLQKL---ARKHGILLIADEVQTGFARTGRMFAVEHWGVEPDVM-----ALAKAMG-GGLPLGAAVGRSEVMSLPRGSHA 318
                                   456677...********************8877666999999865.....9*****8.47788***********9999999 PP

                                   HHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 249 pflsssllqaavaaalsdallkqseleemrqrlqkr 284
                                   +    ++++ a+ +a+ d+ +  ++l e+ qrl ++
  gi|14600726|ref|NP_147247.1| 319 NTFGGNPVALAAFNAVMDVIE-GERLWERSQRLGEK 353
                                   988899999999999999996.46888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3552.14
//
Query:       gi|14600727|ref|NP_147248.1|  [L=112]
Description: hypothetical protein APE_0459 [Aeropyrum pernix K1]
Scores for complete 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   25.0   0.1    1.8e-05   24.6   0.1    1.2  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00073   19.4   1.2     0.0011   18.8   1.2    1.3  1  MarR_2          MarR family
      0.002   17.7   0.3     0.0032   17.1   0.3    1.3  1  Crp             Bacterial regulatory proteins, crp family
     0.0054   16.6   0.0      0.007   16.3   0.0    1.2  1  MarR            MarR family
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.021   14.5   0.0    1.2  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.015   15.0   1.6      0.021   14.5   1.6    1.3  1  GntR            Bacterial regulatory proteins, gntR family
      0.015   15.1   1.1      0.015   15.1   1.1    1.7  2  HTH_23          Homeodomain-like domain
      0.017   15.3   0.0      0.028   14.6   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.018   14.9   0.1      0.026   14.4   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.053   13.7   3.0      0.072   13.2   3.0    1.2  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.053   13.3   0.0      0.098   12.4   0.0    1.3  1  LexA_DNA_bind   LexA DNA binding domain
      0.067   13.3   2.4       0.11   12.7   2.4    1.4  1  HTH_28          Helix-turn-helix domain
      0.072   12.9   0.2       0.12   12.2   0.2    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.086   13.3   0.2       0.13   12.8   0.2    1.2  1  HTH_27          Winged helix DNA-binding domain
      0.094   13.1   0.0       0.15   12.4   0.0    1.3  1  Rrf2            Transcriptional regulator
      0.096   12.1   1.4      0.098   12.1   0.1    1.7  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
        0.1   12.2   0.1       0.15   11.6   0.1    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding


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 !   24.6   0.1   1.7e-08   1.8e-05      22      63 ..      27      70 ..      12      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                                  HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEE.EEES-HH CS
                     HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglisr.grr.irildle 63
                                  ++ +e +++lG+t  t  ril++L+reg++sr +rr  r+l ++
  gi|14600727|ref|NP_147248.1| 27 VSVREVGELLGVTSWTAGRILARLEREGVVSRySRRtYRVLHPK 70
                                  68899**************************6345669999876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.2     1e-06    0.0011       9      53 ..      13      58 ..      10      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                                  HHHHHHHCTTTS.EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2  9 rvLaaLgrrpgr.dltvgelarrlglsksavsrilkrLvaaGLver 53
                                   v aa+ r+ gr  ++v+e+ + lg++  ++ ril+rL++ G v r
  gi|14600727|ref|NP_147248.1| 13 AVVAAILRGSGRrYVSVREVGELLGVTSWTAGRILARLEREGVVSR 58
                                  577888888887456****************************976 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3     3e-06    0.0032       6      31 ..      30      55 ..      27      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3e-06
                                  HHHHHHHTS-HHHHHHHHHHHHHTTS CS
                           Crp  6 qdIAdylGlTrETVSRlLtrLrekGL 31
                                   + +++lG T  T++R L rL+++G+
  gi|14600727|ref|NP_147248.1| 30 REVGELLGVTSWTAGRILARLEREGV 55
                                  6899*********************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   6.7e-06     0.007      19      51 ..      28      60 ..      17      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.7e-06
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGlieRsk 51
                                  sv e ++ lgv++ t+ r+l rLe++G ++R+ 
  gi|14600727|ref|NP_147248.1| 28 SVREVGELLGVTSWTAGRILARLEREGVVSRYS 60
                                  56688999***********************86 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     2e-05     0.021      12      46 ..      24      58 ..      17      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                      HTH_DeoR 12 qgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                  ++++sv e+ ellgv+  T+ R L+ Le +g++ R
  gi|14600727|ref|NP_147248.1| 24 RRYVSVREVGELLGVTSWTAGRILARLEREGVVSR 58
                                  689*****************************998 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.6     2e-05     0.021      26      64 .]      28      66 ..      10      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-05
                                  -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCEEEE CS
                          GntR 26 sereLaaefgVsrttvReALrrLeaeglverrqgrGtfV 64
                                  s+re+ + +gV+  t  + L rLe+eg+v r ++r  +V
  gi|14600727|ref|NP_147248.1| 28 SVREVGELLGVTSWTAGRILARLEREGVVSRYSRRTYRV 66
                                  89*****************************99987665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.1   1.4e-05     0.015       3      46 ..       7      55 ..       5      59 .. 0.90
   2 ?   -2.3   0.0       4.2   4.5e+03      30      35 ..      60      65 ..      58      68 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                        HTH_23  3 sereRlrillllae.....GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  +++ Rl ++ + ++       svre+ ++Lgv+  T  r+l r ++eG+
  gi|14600727|ref|NP_147248.1|  7 KVKVRLAVVAAILRgsgrrYVSVREVGELLGVTSWTAGRILARLEREGV 55
                                  678999999999977788899**********************988996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                        HTH_23 30 srrTvy 35
                                  srrT++
  gi|14600727|ref|NP_147248.1| 60 SRRTYR 65
                                  788875 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.7e-05     0.028      14      53 ..      19      57 ..      13      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                  HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                Fe_dep_repress 14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                  ++ s ++ +v++ ++ e L+v   ++   l +Le++G v 
  gi|14600727|ref|NP_147248.1| 19 LRGS-GRRYVSVREVGELLGVTSWTAGRILARLEREGVVS 57
                                  4444.789*****************************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 ?   14.4   0.1   2.5e-05     0.026      24      65 ..      28      67 ..      17      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-05
                                  HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                          TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                  +++e+ e lgv   ++ ++L +Le+ G+V r  +r   Yr++
  gi|14600727|ref|NP_147248.1| 28 SVREVGELLGVTSWTAGRILARLEREGVVSRYSRR--TYRVL 67
                                  699***************************99554..44444 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.0   6.9e-05     0.072      10      46 ..      23      64 ..      14      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.9e-05
                       AbiEi_4 10 qvGlfttrelea.aGisp.sa...lrrLvrkGwLvrlrrGvY 46
                                  ++ ++++re+ + +G++  +a   l+rL r+G + r  r +Y
  gi|14600727|ref|NP_147248.1| 23 GRRYVSVREVGElLGVTSwTAgriLARLEREGVVSRYSRRTY 64
                                  4489******999***********************998666 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 ?   12.4   0.0   9.3e-05     0.098      27      60 ..      28      60 ..      25      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                                  -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GG CS
                 LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyierdp 60
                                  s+re+++ lg++ + ++   L++Ler G++ r +
  gi|14600727|ref|NP_147248.1| 28 SVREVGELLGVT-SWTAGRILARLEREGVVSRYS 60
                                  89**********.5788999**********9876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.4    0.0001      0.11       2      41 ..      11      55 ..      10      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                        HTH_28  2 RleiikllaaG..h...svreaArelgisrrtvyrWikryeegGi 41
                                  Rl ++ ++++G  +   svre+ ++lg+++ t  r + r+e +G+
  gi|14600727|ref|NP_147248.1| 11 RLAVVAAILRGsgRryvSVREVGELLGVTSWTAGRILARLEREGV 55
                                  999******75444467*************************998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00011      0.12      13      50 ..      19      58 ..      10      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                  CTTBSS..-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR 13 aeapqe..ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   ++ ++  ++++e+ + +g++  t+ R+L+ L+++G v +
  gi|14600727|ref|NP_147248.1| 19 LRGSGRryVSVREVGELLGVTSWTAGRILARLEREGVVSR 58
                                  444444457***************************9975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00012      0.13      15      61 ..      23      65 ..      10      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                        HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekr 61
                                   rr ++ +++ + l v++ ++  +l +L++ G+v    ++ +rr+ r
  gi|14600727|ref|NP_147248.1| 23 GRRYVSVREVGELLGVTSWTAGRILARLEREGVV----SRYSRRTYR 65
                                  2555666***************************....445566666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.15       7      56 ..       8      57 ..       5      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                  HHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2  7 teyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  +++ l +++ + + ++++ vs++e+ e  ++    + +ila+L+++g+v 
  gi|14600727|ref|NP_147248.1|  8 VKVRLAVVAAILRGSGRRYVSVREVGELLGVTSWTAGRILARLEREGVVS 57
                                  5556667777778888888****************************996 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   0.1   9.3e-05     0.098      18      51 ..      16      50 ..      12      51 .. 0.86
   2 ?   -2.1   0.1       2.4   2.6e+03       7      14 ..      57      64 ..      55      66 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.3e-05
                  HTH_Tnp_ISL3 18 ayilellles.rsvkavArqlgvSwtTVwrildry 51
                                  a+il+ + ++  sv++v ++lgv+ +T  ril r+
  gi|14600727|ref|NP_147248.1| 16 AAILRGSGRRyVSVREVGELLGVTSWTAGRILARL 50
                                  566666778889********************985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                  HTH_Tnp_ISL3  7 rrrsriTl 14
                                   r+sr T 
  gi|14600727|ref|NP_147248.1| 57 SRYSRRTY 64
                                  56777665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.15      18      47 ..      27      56 ..      17      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                        HTH_24 18 isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   s re+ e lg+++ t  r l rLe+eG++
  gi|14600727|ref|NP_147248.1| 27 VSVREVGELLGVTSWTAGRILARLEREGVV 56
                                  699*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 870.41
//
Query:       gi|118431055|ref|NP_147249.2|  [L=95]
Description: hypothetical protein APE_0460.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.5   0.0       0.19   11.3   0.0    1.0  1  NIF3      NIF3 (NGG1p interacting factor 3)


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.1e-05      0.19     107     166 ..      11      80 ..       5      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.1e-05
                           NIF3 107 dwlakalglekieplepskeek..........keeeeglgrigeleepvsleelakklkkklglekvrva 166
                                    ++l++ lgl+++ +++  +e k          ++ ++ l  +g+  e+++l+e+a+kl k+lg +++ v+
  gi|118431055|ref|NP_147249.2|  11 KMLVESLGLKQLDVYRVVHEGKpvdviriqdpASGKTALVDLGTTRESLTLQEFAEKLLKALGESGITVS 80 
                                    578999999999999998888899999999998888999***********************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 689.18
//
Query:       gi|14600729|ref|NP_147250.1|  [L=143]
Description: holliday junction resolvase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-31  107.9   0.0    2.5e-31  107.5   0.0    1.1  1  Hjc        Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.057   13.9   0.0      0.065   13.7   0.0    1.3  1  NERD       Nuclease-related domain
        0.3   10.6   0.1       0.52    9.9   0.0    1.5  2  AHJR-like  REase_AHJR-like


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0   4.2e-35   2.5e-31       2      92 ..      10     102 ..       9     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 4.2e-35
                                   HHHHHHHHHHHTT-EEEEBSCSSSSSS..SS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEEE CS
                           Hjc   2 yERelvkiLrergfavvRsagSggatk..plpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllavk 80 
                                   yERel+kiL+erg+av+R+++Sgg+++  ++pD++A+rg+vvlv+E+K++++e++yl+  qv +lle+ar+agg++++a++
  gi|14600729|ref|NP_147250.1|  10 YERELAKILWERGWAVIRGPASGGGSRsrVQPDLVAVRGGVVLVFEIKKARGETVYLDPGQVLGLLEWARRAGGDAWIALR 90 
                                   8***********************999889*************************************************** PP

                                   ETTTEEEEEEGG CS
                           Hjc  81 lqgkewkllvve 92 
                                   l gk w++++++
  gi|14600729|ref|NP_147250.1|  91 LVGKGWRFHRAD 102
                                   ********9875 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.065       4      61 ..       9      67 ..       6     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                          NERD  4 egEravakeLkelkedeylvlhdvrlrpg.tg..eiDhlvispkgifviEvKnwsG.wifgd 61
                                    Er++ak L    e+++ v+++    +g ++  + D++++  + ++v+E+K  +G +++ d
  gi|14600729|ref|NP_147250.1|  9 GYERELAKILW---ERGWAVIRGPASGGGsRSrvQPDLVAVRGGVVLVFEIKKARGeTVYLD 67
                                  56888888888...45799999988866652268********************99766655 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   8.7e-05      0.52      43      64 ..      39      60 ..      12      67 .. 0.86
   2 ?   -4.2   0.2         2   1.2e+04      83      87 ..      94      98 ..      94      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.7e-05
                     AHJR-like 43 YrpDliarkdeeaviiEvksrr 64
                                   +pDl+a ++   +++E+k+ r
  gi|14600729|ref|NP_147250.1| 39 VQPDLVAVRGGVVLVFEIKKAR 60
                                  59*****************976 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 2
                     AHJR-like 83 pgWrf 87
                                  +gWrf
  gi|14600729|ref|NP_147250.1| 94 KGWRF 98
                                  69**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 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:                        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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1153.39
//
Query:       gi|14600730|ref|NP_147251.1|  [L=513]
Description: ATPase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-11   41.8   0.0    2.2e-10   40.1   0.0    1.8  2  T2SSE         Type II/IV secretion system protein
    2.7e-05   23.8   0.0    9.1e-05   22.1   0.0    1.8  1  AAA_25        AAA domain
    0.00034   21.0   0.0      0.001   19.5   0.0    2.0  1  AAA_16        AAA ATPase domain
    0.00083   19.9   0.1      0.003   18.1   0.0    2.0  1  AAA_18        AAA domain
    0.00084   19.1   0.0     0.0018   18.1   0.0    1.5  1  IstB_IS21     IstB-like ATP binding protein
      0.002   17.5   0.0     0.0049   16.2   0.0    1.6  1  DnaB_C        DnaB-like helicase C terminal domain
      0.004   17.1   0.1      0.014   15.3   0.1    1.9  1  NACHT         NACHT domain
     0.0096   15.7   0.0       0.05   13.4   0.0    2.0  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
  ------ inclusion threshold ------
      0.015   14.3   0.0      0.035   13.1   0.0    1.6  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.016   15.5   0.1      0.052   13.8   0.0    1.9  2  AAA_28        AAA domain
      0.021   14.2   0.0      0.054   12.8   0.0    1.7  1  ATPase        KaiC
      0.021   15.3   0.0      0.042   14.3   0.0    1.5  1  AAA           ATPase family associated with various cellular 
      0.025   15.1   0.0      0.055   14.0   0.0    1.6  1  ABC_tran      ABC transporter
      0.028   14.4   0.0       0.08   12.9   0.0    1.8  1  AAA_5         AAA domain (dynein-related subfamily)
      0.037   14.3   0.0      0.086   13.1   0.0    1.6  1  AAA_22        AAA domain
      0.044   13.0   0.0      0.082   12.2   0.0    1.3  1  Zeta_toxin    Zeta toxin
      0.048   13.8   0.1       0.14   12.3   0.0    1.8  1  AAA_33        AAA domain
      0.056   13.1   0.2      0.092   12.4   0.2    1.3  1  SRP54         SRP54-type protein, GTPase domain
      0.059   13.1   0.1       0.22   11.2   0.1    1.9  1  AAA_30        AAA domain
      0.065   13.1   0.0       0.26   11.2   0.0    2.0  1  NTPase_1      NTPase
      0.072   13.1   0.0       0.13   12.2   0.0    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.072   12.8   0.2       0.16   11.7   0.1    1.7  1  AAA_24        AAA domain
      0.086   12.3   0.0       0.21   11.0   0.0    1.6  1  KTI12         Chromatin associated protein KTI12
       0.11   12.4   0.0       0.31   10.9   0.0    1.7  1  NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half 
       0.13   12.0   0.1       0.23   11.2   0.1    1.4  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.17   11.1   0.0       0.28   10.3   0.0    1.2  1  DUF815        Protein of unknown function (DUF815)
       0.17   12.3   0.0       0.35   11.3   0.0    1.6  1  RNA_helicase  RNA helicase
       0.18   11.7   0.0       0.87    9.5   0.0    1.9  2  Rad17         Rad17 P-loop domain
       0.19   11.2   0.2        1.1    8.6   0.2    2.1  2  PhoH          PhoH-like protein


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.8   1.1e+03     157     177 ..      73      93 ..      60     110 .. 0.73
   2 !   40.1   0.0   3.5e-13   2.2e-10      75     245 ..     214     373 ..     176     392 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                         T2SSE 157 derivtvEDpvEiqleganqv 177
                                   d +iv+vED + +q++++  +
  gi|14600730|ref|NP_147251.1|  73 DVEIVVVEDDARVQPRDEGEL 93 
                                   678999999999888776554 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 3.5e-13
                         T2SSE  75 ekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                    k +r+ +  +P++ g e  ++    +++l+l+d++  e+    ++++l++a      il++G+ g GKtt++ al ++ +
  gi|14600730|ref|NP_147251.1| 214 LKDYRIVITRPPLSDGwEVTAVK--PVAKLRLEDYSLPEK---LYNRLLERA----EGILIAGAPGMGKTTFAQALATFYA 285
                                   56788888999999996666665..566789999998875...577889999....889********************** PP

                         T2SSE 155 ksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHan 234
                                   ++ + + t+E p+ ++l  +n++q  ++    ++ +l   +L  rPD  +  E+R  e +++ +     G    ++ +Ha 
  gi|14600730|ref|NP_147251.1| 286 EQGKVVKTIESPRDMRLP-PNVTQYSKN--YADLGELHDILLLSRPDYTVYDELRSDEDFQLyVDLRLAGIGM-IGVVHAT 362
                                   **99999*********96.677777776..778899999999********************99999999777.******* PP

                         T2SSE 235 saagalerLeq 245
                                   ++++a++r   
  gi|14600730|ref|NP_147251.1| 363 TPIDAVQRFLR 373
                                   *******9764 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.5e-07   9.1e-05      22      61 ..     249     289 ..     242     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.5e-07
                        AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGk 61 
                                   +++l+ +ll + e +l+aGapg GKtt+a  la  +a +Gk
  gi|14600730|ref|NP_147251.1| 249 PEKLYNRLLERAEGILIAGAPGMGKTTFAQALATFYAeQGK 289
                                   5789999******************************7776 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   1.6e-06     0.001      17      55 ..     254     291 ..     247     480 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                        AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                   +r+ +   e +l+ G++G+GK++ +++l++ + ++g ++
  gi|14600730|ref|NP_147251.1| 254 NRLLERA-EGILIAGAPGMGKTTFAQALATFYAEQGKVV 291
                                   4444443.89*******************9999985333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.8e-06     0.003       1      61 [.     263     347 ..     263     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.8e-06
                        AAA_18   1 IlltGtpGvGKttlakeL....skrlgf...................gvnlrdvakenglllevdpe.aldeskrldedkl 57 
                                   Il++G+pG GKtt+a++L    ++ +++                   + n+ d+   +++ll   p+  + +++r ded++
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALatfyAEQGKVvktiesprdmrlppnvtqySKNYADLGELHDILLLSRPDyTVYDELRSDEDFQ 343
                                   99****************666644433366666677777777788888888888888888888888877777777777777 PP

                        AAA_18  58 dkll 61 
                                    ++ 
  gi|14600730|ref|NP_147251.1| 344 LYVD 347
                                   7765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.9e-06    0.0018      43      79 ..     256     292 ..     245     322 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-06
                     IstB_IS21  43 fiekkenivllGpsGvGKshlaialgveavraglsvl 79 
                                    +e++e+i++ G +G+GK+ +a al++  +++g+ v 
  gi|14600730|ref|NP_147251.1| 256 LLERAEGILIAGAPGMGKTTFAQALATFYAEQGKVVK 292
                                   5799***********************9999998875 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 !   16.2   0.0   7.9e-06    0.0049      17      48 ..     258     289 ..     252     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-06
                                   XTTXEEEEEEXTTSSHHHHHHHHHHHHHHCST CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DnaB_C  17 qkgdliiiAarpsmGktalalniaenaavkek 48 
                                   ++++ i+iA+ p+mGkt++a  +a+  a++ k
  gi|14600730|ref|NP_147251.1| 258 ERAEGILIAGAPGMGKTTFAQALATFYAEQGK 289
                                   5667799*****************99997554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.2e-05     0.014       3      26 ..     263     286 ..     261     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCT CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                   +++ G++G+GKTt++q la+  ae
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYAE 286
                                   789***************987766 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 !   13.4   0.0     8e-05      0.05      33      57 ..     260     284 ..     253     303 .. 0.77
   2 ?   -0.9   0.0         2   1.3e+03      90     131 ..     365     404 ..     359     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8e-05
                        RuvB_N  33 ldhvllyGpPGlGkttlakiiakel 57 
                                    + +l++G+PG+Gktt+a+ +a+  
  gi|14600730|ref|NP_147251.1| 260 AEGILIAGAPGMGKTTFAQALATFY 284
                                   5679***************999644 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                        RuvB_N  90 ideihrlsraveevlysamedfrldivigkGpsarsikldlp 131
                                   id + r+ r ve  + +++ d    i i++G+ ++  +l+++
  gi|14600730|ref|NP_147251.1| 365 IDAVQRFLRRVELGMIPSIIDTV--IFIDSGEVSKVYELSIT 404
                                   89999999999999999999876..57888888888777664 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 ?   13.1   0.0   5.7e-05     0.035      28      61 ..     259     292 ..     241     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                   -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                          MeaB  28 raqvvGltGvPGaGkstlvealglelrrrGkrva 61 
                                   ra+ + + G PG Gk t+ +al++ ++++Gk v 
  gi|14600730|ref|NP_147251.1| 259 RAEGILIAGAPGMGKTTFAQALATFYAEQGKVVK 292
                                   788899************************9886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.1   4.4e+03      27      42 ..     183     198 ..     173     216 .. 0.67
   2 ?   13.8   0.0   8.5e-05     0.052       2      21 ..     263     285 ..     262     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.1
                        AAA_28  27 vpEaareileeklakg 42 
                                   ++E+arei+e  + ++
  gi|14600730|ref|NP_147251.1| 183 IEEIAREIIEASALEE 198
                                   5677777776655333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.5e-05
                        AAA_28   2 ivitGgestGKTtlleaLa...a 21 
                                   i i G+++ GKTt ++aLa   a
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALAtfyA 285
                                   789***************95542 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.8e-05     0.054      17      46 ..     258     287 ..     248     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                        ATPase  17 pegrvvlitGepGtGKtifalqFlikgaek 46 
                                    +++ +li+G pG GKt+fa+  +   ae+
  gi|14600730|ref|NP_147251.1| 258 ERAEGILIAGAPGMGKTTFAQALATFYAEQ 287
                                   567889**************9876665555 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 ?   14.3   0.0   6.9e-05     0.042       1      20 [.     263     282 ..     263     301 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-05
                                   EEEESSTTSSHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavak 20 
                                   +l+ G pG+GKT++a+a+a+
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALAT 282
                                   6899**************97 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.8e-05     0.055       9      45 ..     258     292 ..     253     370 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-05
                                   ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilld 45 
                                   ++ e + i G  G GK+t++++la  +  ++G++ ++
  gi|14600730|ref|NP_147251.1| 258 ERAEGILIAGAPGMGKTTFAQALATFYA-EQGKV-VK 292
                                   6778899*******************97.79998.32 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   0.00013      0.08       2      36 ..     263     300 ..     262     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                                   EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdt 36 
                                   +l+ G+pG gK+++a+ la ++   ++ v ++  +rd+
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYaeqGKVVKTIESPRDM 300
                                   7999*****************99877777777777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.086       6      33 ..     261     288 ..     255     324 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeea 33 
                                     +++ G +G+GKTt ++ l+  + e+ 
  gi|14600730|ref|NP_147251.1| 261 EGILIAGAPGMGKTTFAQALATFYAEQG 288
                                   5689*****************9996654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013     0.082      17      48 ..     261     292 ..     249     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                    Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvr 48 
                                     il++G+pG GK++ a++l++  ++qg+vv+
  gi|14600730|ref|NP_147251.1| 261 EGILIAGAPGMGKTTFAQALATFYAEQGKVVK 292
                                   569*******************9999999996 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.14       2      20 ..     263     281 ..     263     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                        AAA_33   2 vllvGlpGsGKstlaerll 20 
                                   +l+ G+pG+GK+t+a+ l+
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALA 281
                                   5789************996 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   0.00015     0.092       4      32 ..     263     291 ..     260     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                         SRP54   4 illvGlqGaGKTttlaKLaallkkegkkv 32 
                                   il++G  G+GKTt +  La  + ++gk v
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYAEQGKVV 291
                                   89**********************99866 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00035      0.22      21      49 ..     263     291 ..     251     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                        AAA_30  21 avltGpAGtGKttalkalreaweaaggrv 49 
                                    ++ G++G GKtt  +al+  ++++g+ v
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYAEQGKVV 291
                                   6799*******************999655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00042      0.26       2      31 ..     263     292 ..     262     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                   ++i G pG+GKtT+ + ++   +++g  v+
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYAEQGKVVK 292
                                   789**************9999988887765 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   0.00022      0.13      16      51 ..     254     297 ..     243     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                   HCH...TEEEEEEESTTSSHHHHHHHHHHHTT--.....----T CS
                          TsaE  16 kal...gdvilLeGdLGaGKTtlvrglakalgve.....evkSP 51 
                                   + l   ++ il+ G  G+GKTt++++la  +  +     +++SP
  gi|14600730|ref|NP_147251.1| 254 NRLlerAEGILIAGAPGMGKTTFAQALATFYAEQgkvvkTIESP 297
                                   3333334559*****************98764333222356665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00026      0.16       5      22 ..     263     280 ..     259     296 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   ili G +g+GKTt+a  l
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQAL 280
                                   89*************987 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00034      0.21       4      36 ..     263     295 ..     262     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                         KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvid 36 
                                   +++ G P  GK+t+a+ La+  +e+++ v  i+
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYAEQGKVVKTIE 295
                                   799*****************9999999887775 PP

>> NIR_SIR_ferr  Nitrite/Sulfite reductase ferredoxin-like half domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0005      0.31       5      43 ..     475     510 ..     472     510 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                  NIR_SIR_ferr   5 dgkgyymvrlrvpnGritaeqlraladiaekygsgeirl 43 
                                   d +++  vrl + + r+ta  l++  ++aek+g  +ir+
  gi|14600730|ref|NP_147251.1| 475 D-ETL-IVRLPPRSSRVTARRLKRAKKLAEKHG-YDIRF 510
                                   5.445.9**************************.99996 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 ?   11.2   0.1   0.00038      0.23       1      30 [.     265     294 ..     265     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                    ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavv 30 
                                   ++G +G GKttf +al+ ++ ++g+ v+++
  gi|14600730|ref|NP_147251.1| 265 IAGAPGMGKTTFAQALATFYAEQGKVVKTI 294
                                   68********************99988876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00045      0.28      52      89 ..     259     298 ..     254     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00045
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                   +a+ +L+ Ga G+GK +  +al + yae+g  ++ ie  +
  gi|14600730|ref|NP_147251.1| 259 RAEGILIAGAPGMGKTTFAQALATFYAEQGkvVKTIESPR 298
                                   6899************************997788887555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00057      0.35       1      26 [.     263     288 ..     263     351 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00057
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                   i++ G++g GK+t+a+ La+  +++ 
  gi|14600730|ref|NP_147251.1| 263 ILIAGAPGMGKTTFAQALATFYAEQG 288
                                   6899*************998777554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.9   1.2e+03     122     161 ..      63     102 ..      57     110 .. 0.81
   2 ?    9.5   0.0    0.0014      0.87      33      87 ..     250     305 ..     236     342 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                         Rad17 122 lqklGddlrtdkklilvedlPnkfyrdsdalrevirkylr 161
                                   l++l d   +d ++++ved   +  rd   l+ v+r+y  
  gi|14600730|ref|NP_147251.1|  63 LSRLMDAGVGDVEIVVVEDDARVQPRDEGELKSVLRRYAL 102
                                   5666677789999********9*************99854 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0014
                         Rad17  33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk...elgiklrewlnpvslkepdn 87 
                                   e l    Le++  + +Li+G +G gk+t  + L+    e g  ++    p  ++ p+n
  gi|14600730|ref|NP_147251.1| 250 EKLYNRLLERA--EGILIAGAPGMGKTTFAQALATfyaEQGKVVKTIESPRDMRLPPN 305
                                   55666778877..5679****************9722244555666667777777777 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.94   5.8e+02      50      75 ..     217     242 ..     209     256 .. 0.75
   2 ?    8.6   0.2    0.0018       1.1      11      53 ..     252     294 ..     243     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.94
                                   SEEEEEE-S--TT----SS------- CS
                          PhoH  50 kriiltrpaveageelGflpgdleek 75 
                                    ri++trp ++ g e+++++   + +
  gi|14600730|ref|NP_147251.1| 217 YRIVITRPPLSDGWEVTAVKPVAKLR 242
                                   59********9999999877655555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                                   HHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEE CS
                          PhoH  11 eylealkkndivfaiGpaGtGKtylavalavealkkkkvkrii 53 
                                    y + l++ + + ++G  G GKt +a ala  + +++kv + i
  gi|14600730|ref|NP_147251.1| 252 LYNRLLERAEGILIAGAPGMGKTTFAQALATFYAEQGKVVKTI 294
                                   56777888889999******************99999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 3870.16
//
Query:       gi|118431056|ref|NP_147252.2|  [L=279]
Description: hypothetical protein APE_0464.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2150.19
//
Query:       gi|118431057|ref|NP_147253.2|  [L=396]
Description: thiamine biosynthesis protein ThiI [Aeropyrum pernix K1]
Scores for complete 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-45  153.7   0.0    6.3e-45  153.2   0.0    1.2  1  ThiI      Thiamine biosynthesis protein (ThiI)
    3.4e-25   88.8   0.2    4.9e-25   88.3   0.2    1.2  1  THUMP     THUMP domain
     0.0012   18.4   0.0       0.31   10.5   0.0    2.3  2  QueC      Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.2   0.0   1.1e-48   6.3e-45       1     186 [.     176     358 ..     176     368 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.2 bits;  conditional E-value: 1.1e-48
                           ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                    g+++  laL SgG+DS+Vaa+++++RG  v+l + +   g +e+ +  ve + +l  e+  + + +l+vv+f+     + 
  gi|118431057|ref|NP_147253.2| 176 GSEEPSLALYSGGFDSGVAAWMIMRRGSPVHLAFYD--FGVPEALEVAVEGAKTLAGEWAWGYRPRLYVVNFRGAALIVN 253
                                    577889*************************99995..555555566677777788899999*************99999 PP

                           ThiI  81 ekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAkeig 160
                                      vk+ +++++l+r ml  A+ +a +eg +alvtGes+gqVaSqt+ Nlr+is+  +l++lrPL g+dK+ei++  +eig
  gi|118431057|ref|NP_147253.2| 254 GLVKPSYRTLVLRRLMLLHAQDLAAREGFEALVTGESVGQVASQTVRNLRLISSGLELPVLRPLAGMDKDEIVEKSREIG 333
                                    999***************************************************************************** PP

                           ThiI 161 tyeisiekedkCsvlakhPttkakle 186
                                     y+i++++ + C+v  + P+ +a ++
  gi|118431057|ref|NP_147253.2| 334 LYDIARRQVEVCGV-DQPPNPRASPQ 358
                                    ************97.45555555554 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.2   8.2e-29   4.9e-25       3     140 ..      32     162 ..      30     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 8.2e-29
                                    HHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHC CS
                          THUMP   3 ieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeee 82 
                                    +ee l   +v++e+++  +gr++v+l ++   +d++++ +a  +++g+++v+p++ev + ++ed+ e+a e++ ++ ++ 
  gi|118431057|ref|NP_147253.2|  32 LEESLAAAGVEAEVERL-QGRVLVRLRSP---GDAAAAARASARVFGVKSVSPAVEVEYSGIEDLAEKAAEFFGERVRGR 107
                                    78888889999997777.6********99...7**********************************************9 PP

                                    T-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEE CS
                          THUMP  83 ketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayi 140
                                       F+Vr++r g +  fts++++r +Gk++ e++   Vdle+P+++  ve+++++ay 
  gi|118431057|ref|NP_147253.2| 108 --VFRVRARRSGVE-GFTSKDVERLLGKLLLERGAGGVDLEKPEYTAYVEVRGRRAYF 162
                                    ..9***********.****************************************996 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   5.2e-05      0.31       3      43 ..     182     222 ..     180     237 .. 0.85
   2 !    5.7   0.0    0.0016       9.4     149     175 ..     308     334 ..     267     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.2e-05
                                    EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHH CS
                           QueC   3 vvllSGGlDSttvlalakkegkevealtfdYgqrhkkelea 43 
                                    + l SGG DS +++++ +++g  v++   d+g  ++ e+ +
  gi|118431057|ref|NP_147253.2| 182 LALYSGGFDSGVAAWMIMRRGSPVHLAFYDFGVPEALEVAV 222
                                    6799*********************9999999887777654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0016
                                    TS--EEE-TTTT--HHHHHHHHHHTTH CS
                           QueC 149 dkkieieaPlidlsKaeivklgkelgv 175
                                    + ++ +  Pl  ++K eiv+ + e+g+
  gi|118431057|ref|NP_147253.2| 308 GLELPVLRPLAGMDKDEIVEKSREIGL 334
                                    45788999****************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3131.92
//
Query:       gi|118431058|ref|NP_147254.2|  [L=150]
Description: hypothetical protein APE_0468.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1283.71
//
Query:       gi|118431059|ref|NP_147255.2|  [L=136]
Description: hypothetical protein APE_0469.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   27.7   0.1    3.6e-06   26.6   0.1    1.6  1  HTH_38           Helix-turn-helix domain
    2.6e-05   23.7   1.0    0.00055   19.4   0.0    2.4  2  GerE             Bacterial regulatory proteins, luxR family
    4.5e-05   23.0   0.5    0.00052   19.6   0.0    2.3  2  Sigma70_r4_2     Sigma-70, region 4
    5.3e-05   22.9   0.1    0.00012   21.8   0.1    1.6  1  HTH_23           Homeodomain-like domain
    9.3e-05   22.8   0.9    0.00021   21.7   0.9    1.7  1  HTH_40           Helix-turn-helix domain
    0.00039   20.3   0.3    0.00083   19.2   0.0    1.7  2  HTH_11           HTH domain
    0.00095   19.0   0.0     0.0018   18.1   0.0    1.4  1  Terminase_5      Putative ATPase subunit of terminase (gpP-li
    0.00099   19.1   0.4     0.0064   16.5   0.4    2.1  1  HTH_19           Helix-turn-helix domain
     0.0018   18.3   0.0     0.0032   17.4   0.0    1.4  1  HTH_29           Winged helix-turn helix
      0.003   17.9   0.4     0.0052   17.1   0.4    1.5  1  HTH_31           Helix-turn-helix domain
     0.0035   17.5   0.1      0.096   12.9   0.1    2.4  1  HTH_17           Helix-turn-helix domain
     0.0045   16.5   0.8      0.039   13.5   0.1    2.2  2  Sigma70_r4       Sigma-70, region 4
     0.0073   15.8   0.6      0.027   14.0   0.0    2.0  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0073   16.0   0.0      0.014   15.1   0.0    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.6   0.3      0.028   14.5   0.3    1.6  1  DUF3489          Protein of unknown function (DUF3489)
      0.019   15.1   0.1      0.033   14.3   0.1    1.4  1  HTH_28           Helix-turn-helix domain
      0.025   14.4   0.0      0.065   13.1   0.0    1.7  2  HTH_5            Bacterial regulatory protein, arsR family
      0.039   13.9   1.1        1.2    9.2   0.0    2.3  2  HTH_36           Helix-turn-helix domain
      0.045   14.0   0.2       0.17   12.2   0.2    1.9  1  PaaX             PaaX-like protein
      0.061   13.4   0.1       0.16   12.1   0.0    1.8  1  HTH_20           Helix-turn-helix domain
      0.073   12.9   0.1       0.12   12.1   0.1    1.4  1  HTH_IclR         IclR helix-turn-helix domain
      0.079   12.6   0.0       0.18   11.5   0.0    1.7  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
       0.11   12.5   0.0       0.23   11.5   0.0    1.5  1  KorB             KorB domain
       0.11   12.6   0.0       0.15   12.2   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.13   12.1   0.5       0.37   10.6   0.1    2.0  2  HTH_10           HTH DNA binding domain
        0.2   11.8   0.2        0.2   11.8   0.2    1.9  2  HTH_3            Helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   5.2e-09   3.6e-06      18      41 ..      61      84 ..      56      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.2e-09
                         HTH_38 18 aeGlslreIArrLgrspsTIsREl 41
                                   ++G+++++IA +Lgrs +TI ++l
  gi|118431059|ref|NP_147255.2| 61 KAGYTVAKIAEELGRSETTIRNHL 84
                                   69*******************998 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     8e-07   0.00055      16      38 ..      62      84 ..      57      86 .. 0.93
   2 ?    2.4   0.3      0.17   1.2e+02      32      45 ..     123     136 .]     117     136 .] 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8e-07
                                   TTS-HHHHHHHHTS-HHHHHHHH CS
                           GerE 16 eGksnkeIAeelniSekTVkvhk 38
                                   +G+++ +IAeel+ Se+T+++h+
  gi|118431059|ref|NP_147255.2| 62 AGYTVAKIAEELGRSETTIRNHL 84
                                   79********************8 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHHH CS
                           GerE  32 kTVkvhksnimkKL 45 
                                    +TVk+ ++++++KL
  gi|118431059|ref|NP_147255.2| 123 ETVKTTLKELLEKL 136
                                    6************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 !   19.6   0.0   7.5e-07   0.00052      26      48 ..      63      85 ..      57      85 .. 0.94
   2 ?    1.3   0.1       0.4   2.8e+02      34      54 .]     116     136 .]     115     136 .] 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.5e-07
                                   ---HHHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2 26 glsykEIAellgisegtVksrls 48
                                   g++ + IAe+lg se+t++++l+
  gi|118431059|ref|NP_147255.2| 63 GYTVAKIAEELGRSETTIRNHLQ 85
                                   99*******************97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.4
                                    HHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  34 ellgisegtVksrlsRArkkL 54 
                                    e+++ +  tVk+ l+  ++kL
  gi|118431059|ref|NP_147255.2| 116 EETKKKLETVKTTLKELLEKL 136
                                    77888999****999887776 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.7e-07   0.00012      13      38 ..      57      84 ..      51      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-07
                         HTH_23 13 llae..GlsvreIAreLgvsrrTvyrwl 38
                                   l++e  G++v++IA+eLg+s+ T+++ l
  gi|118431059|ref|NP_147255.2| 57 LAREkaGYTVAKIAEELGRSETTIRNHL 84
                                   334468******************9855 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.9   3.1e-07   0.00021      10      43 ..      61      94 ..      56     136 .] 0.62

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.1e-07
                         HTH_40 10 eeglsieeIAkerglkesTIegHLaelieegeei 43
                                   + g+++++IA+e g +e+TI +HL    ++g+ +
  gi|118431059|ref|NP_147255.2| 61 KAGYTVAKIAEELGRSETTIRNHLQGKTKAGQLV 94
                                   689*********************9999998622 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06   0.00083      16      37 ..      64      85 ..      56      91 .. 0.86
   2 ?   -2.7   0.1       8.5   5.8e+03      34      40 ..     127     133 ..     123     136 .] 0.45

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                         HTH_11 16 isgeeLAeeLnvSrrtvrrdIk 37
                                    + +++AeeL++S++t+r++++
  gi|118431059|ref|NP_147255.2| 64 YTVAKIAEELGRSETTIRNHLQ 85
                                   6999****************96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.5
                         HTH_11  34 rdIkaLe 40 
                                      +k+L 
  gi|118431059|ref|NP_147255.2| 127 TTLKELL 133
                                    4444443 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.6e-06    0.0018      13      35 ..      63      85 ..      62     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.6e-06
                    Terminase_5 13 GyrvaeIAeelglkeatVysWkk 35
                                   Gy+va+IAeelg++e t+ +  +
  gi|118431059|ref|NP_147255.2| 63 GYTVAKIAEELGRSETTIRNHLQ 85
                                   9*****************98766 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   9.3e-06    0.0064       7      60 ..      58     133 ..      56     136 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.3e-06
                         HTH_19   7 aReelgltqeelaerlgisrskisaiEngkkdvps......aell.................lkiaealgidleyll 60 
                                    aRe++g+t +++ae+lg s + i++   gk+ +++      ++++                 +k +e+++ +l++ll
  gi|118431059|ref|NP_147255.2|  58 AREKAGYTVAKIAEELGRSETTIRNHLQGKT-KAGqlvretYDMIktgklkitiptpeceetKKKLETVKTTLKELL 133
                                    8*************99999777777777755.554444333333344444555555555666888888888888887 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.7e-06    0.0032       5      33 ..      57      84 ..      52      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-06
                         HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwl 33
                                   l+  + G  tv+ iA+ lg s++t++++l
  gi|118431059|ref|NP_147255.2| 57 LAREKAGY-TVAKIAEELGRSETTIRNHL 84
                                   33344444.*****************987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   7.5e-06    0.0052       9      39 ..      58      88 ..      46      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.5e-06
                         HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrr 39
                                   +Re+aG + +  Ae lg se+t++   qG+ 
  gi|118431059|ref|NP_147255.2| 58 AREKAGYTVAKIAEELGRSETTIRNHLQGKT 88
                                   7***********************9999976 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00014     0.096       2      23 ..      64      85 ..      64     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                         HTH_17  2 ltveEaAelLgvsrstvyrlir 23
                                   +tv+ +Ae Lg s++t+++ ++
  gi|118431059|ref|NP_147255.2| 64 YTVAKIAEELGRSETTIRNHLQ 85
                                   8*****************9884 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   5.7e-05     0.039      19      40 ..      62      83 ..      57      85 .. 0.89
   2 ?    1.2   0.1       0.4   2.7e+02      34      48 ..     122     136 .]     116     136 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                                   TT--HHHHHHHHTS-HHHHHHH CS
                     Sigma70_r4 19 eglTleEIgerlgiSrerVrqi 40
                                    g+T + I+e+lg S+ ++r +
  gi|118431059|ref|NP_147255.2| 62 AGYTVAKIAEELGRSETTIRNH 83
                                   689*****************86 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHHHHH CS
                     Sigma70_r4  34 rerVrqiekrAlrkL 48 
                                    +e+V+  +k+ l+kL
  gi|118431059|ref|NP_147255.2| 122 LETVKTTLKELLEKL 136
                                    79********99998 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 !   14.0   0.0     4e-05     0.027      13      39 ..      59      85 ..      56      94 .. 0.85
   2 ?   -0.2   0.1       1.1   7.5e+02      25      44 ..     116     135 ..     115     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                         HTH_24 13 qknprisqreLAerlglSpstvnrrlk 39
                                   +++++ + + +Ae+lg S +t++ +l+
  gi|118431059|ref|NP_147255.2| 59 REKAGYTVAKIAEELGRSETTIRNHLQ 85
                                   68999********************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                         HTH_24  25 erlglSpstvnrrlkrLeee 44 
                                    e++   + tv++ lk+L e+
  gi|118431059|ref|NP_147255.2| 116 EETKKKLETVKTTLKELLEK 135
                                    55666677999999999875 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.014      16      46 ..      65      95 ..      57      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                       HTH_DeoR 16 sveelvellgvSeaTiRRDLneLeeqglltR 46
                                   +v +++e+lg Se+TiR+ L+  +++g l+R
  gi|118431059|ref|NP_147255.2| 65 TVAKIAEELGRSETTIRNHLQGKTKAGQLVR 95
                                   899******************9999999887 PP

>> DUF3489  Protein of unknown function (DUF3489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   4.1e-05     0.028      15      50 ..      57      92 ..      53     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.1e-05
                        DUF3489 15 lLrrpeGatiaeimeatgWqahtvRgalagalkkkl 50
                                   l r+++G t+a+i+e++g  + t+R  l g  k++ 
  gi|118431059|ref|NP_147255.2| 57 LAREKAGYTVAKIAEELGRSETTIRNHLQGKTKAGQ 92
                                   66899*************************999875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   4.8e-05     0.033      11      34 ..      62      85 ..      51      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-05
                         HTH_28 11 aGhsvreaArelgisrrtvyrWik 34
                                   aG +v+ +A+elg s++t++  ++
  gi|118431059|ref|NP_147255.2| 62 AGYTVAKIAEELGRSETTIRNHLQ 85
                                   589*****************8876 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 ?   13.1   0.0   9.4e-05     0.065      14      36 ..      62      84 ..      56      91 .. 0.86
   2 ?   -2.4   0.0       6.6   4.5e+03      14      25 ..      86      97 ..      85      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                                   SSEEHHHHHHHHTS-HHHHHHHH CS
                          HTH_5 14 gelcvcelaeelglsqstvShHL 36
                                     ++v  +aeelg s+ t++ HL
  gi|118431059|ref|NP_147255.2| 62 AGYTVAKIAEELGRSETTIRNHL 84
                                   4499******************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.6
                                   SSEEHHHHHHHH CS
                          HTH_5 14 gelcvcelaeel 25
                                   g++++++l++e+
  gi|118431059|ref|NP_147255.2| 86 GKTKAGQLVRET 97
                                   788999999985 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0017       1.2      20      47 ..      61      85 ..      49      86 .. 0.86
   2 ?    3.0   0.5      0.14        98      32      49 ..     115     132 ..     115     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
                         HTH_36 20 knggcfpsqetlakrlglsknTvsraik 47
                                   k g+   +++ +a+ lg s+ T++++++
  gi|118431059|ref|NP_147255.2| 61 KAGY---TVAKIAEELGRSETTIRNHLQ 85
                                   5555...899**************9985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                         HTH_36  32 akrlglsknTvsraikeL 49 
                                    ++ ++++ +Tv + +keL
  gi|118431059|ref|NP_147255.2| 115 CEETKKKLETVKTTLKEL 132
                                    78899999*********9 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00024      0.17      27      57 ..      67      97 ..      43     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                           PaaX 27 irllaelGiseslvRaalsRlakaGwlvrek 57
                                    ++ +elG se+++R  l   +kaG+lvre 
  gi|118431059|ref|NP_147255.2| 67 AKIAEELGRSETTIRNHLQGKTKAGQLVRET 97
                                   6799************************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 ?   12.1   0.0   0.00023      0.16      19      46 ..      57      85 ..      30      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                                   H.STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                         HTH_20 19 L.araegltaselaerldlskntlsyHLr 46
                                   L ++++g t++ +ae+l+ s +t+++HL+
  gi|118431059|ref|NP_147255.2| 57 LaREKAGYTVAKIAEELGRSETTIRNHLQ 85
                                   36788999*******************95 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 ?   12.1   0.1   0.00018      0.12      11      40 ..      56      85 ..      55      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                   T-CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                       HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLq 40
                                   ala++  + t++ +A+++g + +t +++Lq
  gi|118431059|ref|NP_147255.2| 56 ALAREKAGYTVAKIAEELGRSETTIRNHLQ 85
                                   89*************************998 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 ?   11.5   0.0   0.00026      0.18      27      53 ..      67      94 ..      56     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                   HrcA_DNA-bdg 27 eeiAevlkrneGtvRNqlq.sLkalgLv 53
                                    +iAe l+r e t+RN lq   ka +Lv
  gi|118431059|ref|NP_147255.2| 67 AKIAEELGRSETTIRNHLQgKTKAGQLV 94
                                   68***************99335666666 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.23       2      38 ..      62      99 ..      61     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                           KorB  2 kgvkqadIAkaLGksksfvslylkl.ldvpdylrelyd 38
                                   +g ++a IA++LG+s++ +  +l+   ++ + +re yd
  gi|118431059|ref|NP_147255.2| 62 AGYTVAKIAEELGRSETTIRNHLQGkTKAGQLVRETYD 99
                                   68999***************999852567777888887 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 ?   12.2   0.0   0.00022      0.15      29      61 ..      77     109 ..      46     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                Acetyltransf_CG  29 hTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                     T +  +l+Gk  A++Lv++  d ++  +lk+ 
  gi|118431059|ref|NP_147255.2|  77 ETTIRNHLQGKTKAGQLVRETYDMIKTGKLKIT 109
                                    7999***************************96 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00053      0.37      24      45 ..      64      85 ..      51      89 .. 0.91
   2 ?   -1.4   0.1       3.1   2.1e+03      33      46 ..     122     135 ..     118     136 .] 0.67

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00053
                         HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                                    t++++A+elG s++t+ +hL+
  gi|118431059|ref|NP_147255.2| 64 YTVAKIAEELGRSETTIRNHLQ 85
                                   5889****************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.1
                         HTH_10  33 lGIskstlsehLrk 46 
                                    l   k+tl+e L+k
  gi|118431059|ref|NP_147255.2| 122 LETVKTTLKELLEK 135
                                    55567788777765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00028       0.2       4      34 ..      58      88 ..      56      94 .. 0.86
   2 ?   -2.6   0.2       8.9   6.1e+03       9      15 ..     126     132 ..     119     136 .] 0.51

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                   HHHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                          HTH_3  4 lRkqlglsqeeLAeklGvsrstisriEnGer 34
                                   +R+++g++ +++Ae+lG s +ti++   G++
  gi|118431059|ref|NP_147255.2| 58 AREKAGYTVAKIAEELGRSETTIRNHLQGKT 88
                                   8*********************987666655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.9
                                    THHHHHH CS
                          HTH_3   9 glsqeeL 15 
                                    + +++eL
  gi|118431059|ref|NP_147255.2| 126 KTTLKEL 132
                                    5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1013.55
//
Query:       gi|118431060|ref|NP_147256.2|  [L=254]
Description: hypothetical protein APE_0470.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-10   40.6  21.0    6.5e-10   38.8  21.0    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
    7.2e-05   22.8   6.2    7.2e-05   22.8   6.2    1.9  2  ABC2_membrane_4  ABC-2 family transporter protein
     0.0033   17.0   3.2     0.0082   15.7   2.1    2.2  2  ABC2_membrane_5  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.034   13.2   0.3       0.17   10.9   0.1    1.9  2  7TM_GPCR_Srh     Serpentine type 7TM GPCR chemoreceptor Srh
       0.12   12.1   0.5        0.2   11.4   0.5    1.4  1  CUE              CUE domain
        0.6    9.2  13.1      0.025   13.7   7.5    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
        6.1    6.2  19.6      0.035   13.5  11.1    1.7  2  ABC2_membrane    ABC-2 type transporter


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 !   38.8  21.0   2.6e-13   6.5e-10      63     286 ..      54     250 ..       2     252 .. 0.65

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.6e-13
                ABC2_membrane_2  63 asdeaedtdqdlkvvstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatv 142
                                    ++   + +++++  +  ++avl++ ia+  +a+ai+gE   +T  +lLs+P+ R+ +ll+K +  +a+    ava   t 
  gi|118431060|ref|NP_147256.2|  54 YTLNFDTYYIMNFHGFFYTAVLGGYIAY-SSANAISGEVQGKTFWILLSSPHRRGLVLLSKYLVAVAV---AAVASAST- 128
                                    3344444444444477788888887776.69*************************************...99999998. PP

                ABC2_membrane_2 143 llalaii.lalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaella 221
                                    l+ala++  ++g +++l+ +l l  a +++l+ v  ++lg+ll +va  s +a  +a g++++ +++ ++ l +   l+ 
  gi|118431060|ref|NP_147256.2| 129 LAALALSaGVYGFEVDLARYLALYTAGTVYLASV--ASLGILLGAVAL-SPRAPWAAAGVVIAMYFVDTLTLDT--RLER 203
                                    555666515799****************999955..************.6666666777777776666665544..2222 PP

                ABC2_membrane_2 222 gpavpqeindflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrk 286
                                               lsl  +++a  ++l+    g            l++l l ++++l  +  +F+r+
  gi|118431060|ref|NP_147256.2| 204 L--------GALSLTRYHDALGIVLEGGVPGH----------DLAVLALSALAMLLTAVAIFERR 250
                                    1........12344444444444444444444..........34444444444445555555555 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   6.2   2.8e-08   7.2e-05      35     173 ..      50     187 ..       3     193 .. 0.68
   2 ?   -3.5   0.9       3.3   8.5e+03     102     116 ..     231     245 ..     229     248 .. 0.50

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.8e-08
                ABC2_membrane_4  35 llgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtf 114
                                    + g  +l+ +++y ++ +gf ++ +l   ++  ++  i+ E q++t+  Ll  P  r  +ll+K++v + ++++ +  t+
  gi|118431060|ref|NP_147256.2|  50 KGGVYTLNFDTYYIMNFHGFFYTAVLGGYIAYSSANAISGEVQGKTFWILLSSPHRRGLVLLSKYLVAVAVAAVASASTL 129
                                    223334555666666666777777777778888899*******************************9887777775444 PP

                ABC2_membrane_4 115 litvlfallsgfvgfsvklvlellkkclelgllvffavlpii..alvllkksyvlpliltl 173
                                    +   ++al +g  gf+v+l  +l   +  ++ l  +a+l i+  a++l  +  +++ ++ +
  gi|118431060|ref|NP_147256.2| 130 A---ALALSAGVYGFEVDLARYLALYTAGTVYLASVASLGILlgAVALSPRAPWAAAGVVI 187
                                    3...345677888899999888888888888888888888863457778887777655443 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
                ABC2_membrane_4 102 llllsvllmlvtfli 116
                                    +l ls+l ml+t+++
  gi|118431060|ref|NP_147256.2| 231 VLALSALAMLLTAVA 245
                                    444555555555543 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 ?   -1.1   0.0      0.47   1.2e+03     182     196 ..       7      21 ..       3      35 .. 0.59
   2 !   15.7   2.1   3.2e-06    0.0082      31     126 ..      64     158 ..      45     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.47
                ABC2_membrane_5 182 lliillviillliiv 196
                                    +l ++++++++l++ 
  gi|118431060|ref|NP_147256.2|   7 ILSMAIAVLVVLTVW 21 
                                    223333344444444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 3.2e-06
                ABC2_membrane_5  31 flndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgn 110
                                    + n ++ +  ++l   i+++   +++s + + k+ ++ll+ P +r  +  sKYl+++ + ++a+  tl++l+++  ++g 
  gi|118431060|ref|NP_147256.2|  64 M-NFHGFFYTAVLGGYIAYS-SANAISGEVQGKTFWILLSSPHRRGLVLLSKYLVAVAVAAVASASTLAALALSAGVYGF 141
                                    2.333333333333334443.4589999*******************************************998888888 PP

                ABC2_membrane_5 111 .vtisevllsiliglvi 126
                                     v++   l  +++g v+
  gi|118431060|ref|NP_147256.2| 142 eVDLARYLALYTAGTVY 158
                                    77766666555555543 PP

>> 7TM_GPCR_Srh  Serpentine type 7TM GPCR chemoreceptor Srh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.8e-05      0.17     131     202 ..       6      79 ..       3      89 .. 0.70
   2 ?   -0.5   0.0      0.19   4.8e+02      75     110 ..     216     250 ..     215     252 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.8e-05
                   7TM_GPCR_Srh 131 lilnyilallflipifl..nipdqeeaklkvlkklPclpeeffdeepvfvlaldstlllivivllllllliqil 202
                                    +il + +a+l++++++    +++  e  +++l ++P+   +ff +  v+ l++d+++++ +  ++ + +l   +
  gi|118431060|ref|NP_147256.2|   6 IILSMAIAVLVVLTVWSwkPLEEDLETLQELLAQFPEEFIKFFAKGGVYTLNFDTYYIMNFHGFFYTAVLGGYI 79 
                                    3444445544444544421566889999*********999****************887555555555544444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.19
                   7TM_GPCR_Srh  75 lGllselgvpteiqlyllvtllalvgvsiillFenR 110
                                    lG++ e gvp   +++ l ++  +++++ +++Fe R
  gi|118431060|ref|NP_147256.2| 216 LGIVLEGGVPGHDLAV-LALSALAMLLTAVAIFERR 250
                                    5666666666655544.4555668888999999998 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   7.9e-05       0.2       2      22 ..      27      47 ..      26      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                                   HHHHHHHHHHSTTS-HHHHHH CS
                            CUE  2 eqmletLkemFPdldeevIra 22
                                   e++letL+e+  +++ee+I++
  gi|118431060|ref|NP_147256.2| 27 EEDLETLQELLAQFPEEFIKF 47
                                   689****************86 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 ?   13.7   7.5   9.9e-06     0.025     165     269 ..      64     179 ..      29     196 .. 0.73
   2 ?   -3.9   0.2       2.3   5.8e+03     332     342 ..     232     242 ..     223     247 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.9e-06
                ABC2_membrane_3 165 g....liliilifit.asfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.l.....afglgi 233
                                         +++  ++  + a++ a++i  E + ++  ++l+s+ ++   +lsk+l  ++v+++ ++ +l+ l     ++g  +
  gi|118431060|ref|NP_147256.2|  64 MnfhgFFYTAVLGGYiAYSSANAISGEVQGKTFWILLSSPHRRGLVLLSKYLVAVAVAAVASASTLAaLalsagVYG--F 141
                                    2233233322222221444556788999999*******************************988876433566666..4 PP

                ABC2_membrane_3 234 pfg..nlglllllfllfglayialgyllsslfknseta 269
                                    +++   +++l     +++ ++++lg ll+++  ++++ 
  gi|118431060|ref|NP_147256.2| 142 EVDlaRYLALYTAGTVYLASVASLGILLGAVALSPRAP 179
                                    44454999999******************997777553 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.3
                ABC2_membrane_3 332 lalfavvylll 342
                                    lal+a+++ll 
  gi|118431060|ref|NP_147256.2| 232 LALSALAMLLT 242
                                    22322222222 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  11.1   1.3e-05     0.035      43     169 ..      56     187 ..       5     192 .. 0.79
   2 ?   -4.8   1.3       5.5   1.4e+04     142     154 ..     232     244 ..     229     247 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                  ABC2_membrane  43 lg.nsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyf 121
                                    l+ ++  ++n+ g+++++vl   ++  ++ a++ e++ +++  +l+sp  ++  ++l+k+lv ++v++++++  l+   +
  gi|118431060|ref|NP_147256.2|  56 LNfDTYYIMNFHGFFYTAVLGGYIAYSSANAISGEVQGKTFWILLSSPH-RRGLVLLSKYLVAVAVAAVASASTLAALAL 134
                                    33335556688************9*************************.*****************9998877774443 PP

                  ABC2_membrane 122 ...lvgldls..rfflflllllltalaasslgllisalapsfedasqlaslvl 169
                                       + g++++  r + ++ +  +++  + slg+l++a+a s +     a++v+
  gi|118431060|ref|NP_147256.2| 135 sagVYGFEVDlaRYLALYTAGTVYLASVASLGILLGAVALSPRAPWAAAGVVI 187
                                    13367999999888777777777777777888888888877766555555555 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 5.5
                  ABC2_membrane 142 laasslgllisal 154
                                    la+s+l++l+ a+
  gi|118431060|ref|NP_147256.2| 232 LALSALAMLLTAV 244
                                    4444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1914.80
//
Query:       gi|118431061|ref|YP_874826.1|  [L=83]
Description: hypothetical protein APE_0470a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 684.11
//
Query:       gi|118431062|ref|NP_147257.2|  [L=303]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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   70.7   0.0    3.1e-19   69.9   0.0    1.4  1  ABC_tran  ABC transporter
    4.5e-14   53.0   0.1    4.9e-10   39.7   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0021   18.8   0.0     0.0034   18.1   0.0    1.4  1  DUF4162   Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
      0.042   13.3   0.0        1.7    8.0   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
       0.25   11.8   0.0       0.37   11.3   0.0    1.2  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 !   69.9   0.0   8.6e-23   3.1e-19       1     136 [.      20     159 ..      20     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 8.6e-23
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs+++  ge+ + +G+nGaGK+t +++l+g ++pt+G+ ++ g +l +   + +r+++g++p e ++  +++ ++  
  gi|118431062|ref|NP_147257.2|  20 LRGVSFSVLSGEVFGYLGPNGAGKTTTIRVLMGFSRPTSGSARVFGVELYNPGASGVRRRVGYVPGEFEFYGGVSGGRMl 99 
                                    678****************************************************************9999999755558 PP

                                    .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              s+  + ++l+ + l+   ++ v     ++S G+kq++al++a+  +p+l+++DEpt
  gi|118431062|ref|NP_147257.2| 100 dywcrlvggCSRGVVRELLEAFPLPL--ERAV----GTYSRGMKQMLALVMAFSHEPDLVVMDEPT 159
                                    888877776666669********999..8888....*****************************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   6.4e-05      0.23       6      24 ..      37      55 ..      36      97 .. 0.73
   2 !   39.7   0.0   1.4e-13   4.9e-10     234     297 ..     129     189 ..     113     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                         AAA_21  6 GpNgsGKSnLLdaldllar 24
                                   GpNg+GK++ ++ l +++r
  gi|118431062|ref|NP_147257.2| 37 GPNGAGKTTTIRVLMGFSR 55
                                   **************55544 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.4e-13
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    +   S G+k++lal+ a+   +   +l++ DEp +gL+P +  r+l+++++++r+g+ v++++H
  gi|118431062|ref|NP_147257.2| 129 VGTYSRGMKQMLALVMAFSHEP---DLVVMDEPTTGLDPLARGRVLDFVRSKAREGVTVFFSSH 189
                                    45569**************999...9************************************** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   9.5e-07    0.0034      21      79 ..     235     291 ..     212     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.5e-07
                                    -----..---EEEE-TTS-EEEEE-----------------EEEEEEEE---HHHHHHH CS
                        DUF4162  21 aeelleepgveeveeeggelelkledeeaanellkaltsgveirsFeeeePsLndIFie 79 
                                      + l+++gv++++ +g elel +++++a +++l+ l  ++ ++ +e++ ++L+++F++
  gi|118431062|ref|NP_147257.2| 235 SPDRLAVDGVRVIRSNG-ELELVVTSGKALESVLRML-LDAGLEDLEVRDATLEEVFMH 291
                                    45556778899998775.8******************.778899*************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 ?    3.1   0.0     0.016        56      30      41 ..      36      47 ..      25      58 .. 0.81
   2 ?    8.0   0.0   0.00048       1.7     138     198 ..     133     190 ..     112     206 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.016
                                   EESTTSSHHHHH CS
                                   xxxxxxxxxxxx RF
                          SMC_N 30 vGpNGSGKsnll 41
                                   +GpNG+GK+  +
  gi|118431062|ref|NP_147257.2| 36 LGPNGAGKTTTI 47
                                   7*******9866 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00048
                                    -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                                    S+G k+++al  ++A  +     l+++De    LD   + +v +++++k  + + ++  s+ 
  gi|118431062|ref|NP_147257.2| 133 SRGMKQMLAL--VMAFSH--EPDLVVMDEPTTGLDPLARGRVLDFVRSKAREgVTVFFSSHV 190
                                    8888887655..555433..3359**********************9776543666655554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.37      24      37 ..      35      48 ..      12      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                         AAA_23 24 ItGpNGaGKTTild 37
                                     GpNGaGKTT ++
  gi|118431062|ref|NP_147257.2| 35 YLGPNGAGKTTTIR 48
                                   57*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2268.06
//
Query:       gi|118431063|ref|YP_874827.1|  [L=106]
Description: hypothetical protein APE_0471a [Aeropyrum pernix K1]
Scores for complete 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   0.1    2.6e-09   37.6   0.1    1.1  1  PIN           PIN domain
  ------ inclusion threshold ------
      0.096   12.0   0.0       0.12   11.7   0.0    1.1  1  Arena_ncap_C  Arenavirus nucleocapsid C-terminal 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 !   37.6   0.1   2.9e-13   2.6e-09       3      88 ..       4      86 ..       3      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.9e-13
                                   E-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHH CS
                            PIN  3 lDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaei 84
                                    DT ++i+++rg+ek + +++ll++    +t+++vlaE++++++r  ++ ++++ l++ll +   ++i+ id +i  +a+++
  gi|118431063|ref|YP_874827.1|  4 YDTYAWIEYFRGSEKGAVVKQLLDS-QGGYTPSIVLAEIARKYRR--EGFDENDILKRLLFIVGKTEIITIDVDISMKASKV 82
                                   59*********************99.*******************..999999999999999*******************9 PP

                                   HHHH CS
                            PIN 85 alky 88
                                   +l++
  gi|118431063|ref|YP_874827.1| 83 YLEL 86
                                   9875 PP

>> Arena_ncap_C  Arenavirus nucleocapsid C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.3e-05      0.12      69     133 ..      18      84 ..      10      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                                    T-B-GGGGTTB-TTHH.HHHHHHS-TT-EEEESSHHHH.HHHHHHTT-TTSEEEE-B--HHHHTTTH CS
                   Arena_ncap_C  69 hgidlkdlfdaqpgll.savigalprnmvitcqgsddi.rklldsqgrkdiklidvkltkedsrkye 133
                                    +g  +k+l d+q g + s v+  + r+        +di ++ll + g+ +i  idv+++ ++s+ y 
  gi|118431063|ref|YP_874827.1|  18 KGAVVKQLLDSQGGYTpSIVLAEIARKYRREGFDENDIlKRLLFIVGKTEIITIDVDISMKASKVYL 84 
                                    5888999999999998456677788888777766666637799********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 822.64
//
Query:       gi|118431064|ref|YP_874828.1|  [L=79]
Description: hypothetical protein APE_0471b [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.8   0.1       0.23   11.7   0.0    1.6  2  DUF2508   Protein of unknown function (DUF2508)


Domain annotation for each model (and alignments):
>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.3e-05      0.23      43      70 ..      11      38 ..       3      39 .. 0.85
   2 ?   -1.8   0.0      0.21   3.7e+03       7      15 ..      63      71 ..      58      75 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                        DUF2508 43 sdeliyqlklaeakYeFLlreAkkrkik 70
                                   + el   +k+ ++ Y+ L+r Ak+r+i+
  gi|118431064|ref|YP_874828.1| 11 DAELSETIKVKKSIYDILIRIAKERGIS 38
                                   567778899****************996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.21
                        DUF2508  7 kgklkkeed 15
                                   kgk+k + +
  gi|118431064|ref|YP_874828.1| 63 KGKIKPYTE 71
                                   455555422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 601.70
//
Query:       gi|14600737|ref|NP_147258.1|  [L=56]
Description: hypothetical protein APE_0471c [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.0   0.0      0.064   13.0   0.0    1.0  1  Vesiculo_matrix  Vesiculovirus matrix protein


Domain annotation for each model (and alignments):
>> Vesiculo_matrix  Vesiculovirus matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.6e-06     0.064     158     197 ..      12      52 ..       5      56 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-06
               Vesiculo_matrix 158 yrkylnislyketvel.sytisddkskeaaknilDaynssk 197
                                   +  y+nis +k  ++l s t     s  +++ ilDa+   +
  gi|14600737|ref|NP_147258.1|  12 FMDYMNISDMKPCISLrSHTAEVRGSNPRGPTILDAFHVLQ 52 
                                   778*************45566678899**********7555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 447.56
//
Query:       gi|14600738|ref|NP_147259.1|  [L=172]
Description: hypothetical protein APE_0472 [Aeropyrum pernix K1]
Scores for complete 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    1.5e-26   93.2   0.0    1.1  1  PIN_2     PIN domain
    9.5e-06   26.4   0.1    1.8e-05   25.5   0.0    1.5  2  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.2   0.0   1.7e-30   1.5e-26       1     122 [.      18     138 ..      18     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 1.7e-30
                         PIN_2   1 VvdaNivvsallk..srikkrlilvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslyesk 79 
                                   Vvd+Ni++s ++     ++ r+i+ ++ lel+apee++ e ++h ++l    k   +e+ + + l+++ ++i ++++ye+k
  gi|14600738|ref|NP_147259.1|  18 VVDSNIIFSIVVAgkRAKAYRVIAGHQDLELYAPEEVLLEFREHLKKLE---KSARVEFWSKALLAFSLVRITPKEIYEDK 95 
                                   9***********9744445677888999******************776...666677777777999************** PP

                         PIN_2  80 ikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdligaGlkt 122
                                   ++eA+ +++ +Dp+Dtpf+Al+L+leap+WTeDk l+ a  k+
  gi|14600738|ref|NP_147259.1|  96 LREAYSIARLFDPKDTPFIALSLKLEAPLWTEDKALLRASFKS 138
                                   ************************************9887776 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0     2e-09   1.8e-05       2     106 ..      17     121 ..      16     132 .. 0.73
   2 ?   -1.8   0.0      0.59   5.3e+03      24      53 ..     141     170 ..     124     172 .] 0.59

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2e-09
                         PIN_3   2 vvlDtnvlldallfdspaarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakvalerkavapda 82 
                                    v+D+n+++++++  ++ a++ +  +++++++l++ +++l E+++ l++   +   ++  ++ +alla        ++p++
  gi|14600738|ref|NP_147259.1|  17 LVVDSNIIFSIVV-AGKRAKAYRVIAGHQDLELYAPEEVLLEFREHLKKL-EK--SARVEFWSKALLAFSL---VRITPKE 90 
                                   699**********.677999999999******************999555.33..2444455555555554...4445555 PP

                         PIN_3  83 elrpllkcr.......DpdDqkvlelAlaar 106
                                    ++  l+ +       Dp+D  +++l l+ +
  gi|14600738|ref|NP_147259.1|  91 IYEDKLREAysiarlfDPKDTPFIALSLKLE 121
                                   5555444445566788*********998864 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.59
                         PIN_3  24 ldaletgaitlvvsprlldElervlarela 53 
                                     al t+ ++ ++  + l+ +++ l+++l+
  gi|14600738|ref|NP_147259.1| 141 YVALDTESVENLLHGEPLESIREKLYKKLF 170
                                   445566666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1299.45
//
Query:       gi|118431065|ref|YP_874829.1|  [L=75]
Description: hypothetical protein APE_0472a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00085   19.2   0.0     0.0011   18.9   0.0    1.1  1  DUF3437   Domain of unknown function (DUF3437)
  ------ inclusion threshold ------
      0.052   13.4   0.3      0.059   13.3   0.3    1.1  1  DUF3395   Domain of unknown function (DUF3395)


Domain annotation for each model (and alignments):
>> DUF3437  Domain of unknown function (DUF3437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-07    0.0011      21      72 ..      17      72 ..      12      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-07
                        DUF3437 21 dvPkwlpevlee.Lar...aardpapirktvkktlseFkrthqDtWeedkkkFtee 72
                                   dv +w+ e l++ L r    ++ ++ i  + +k+l+eF +t+ + W++ +k++ e+
  gi|118431065|ref|YP_874829.1| 17 DVAQWVAEGLSKrLLRklvVESLSEGIDVNLEKALEEFEKTRDEVWRKVEKEYREK 72
                                   67889988888775554633333336********************9988888775 PP

>> DUF3395  Domain of unknown function (DUF3395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.6e-06     0.059      16      54 ..      37      75 .]      24      75 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.6e-06
                        DUF3395 16 eelaeliaekrkeaeeaqellkeqaerkrekEerknGLv 54
                                   e l+e i+ + ++a+e+ e  ++ + rk ekE r++GL+
  gi|118431065|ref|YP_874829.1| 37 ESLSEGIDVNLEKALEEFEKTRDEVWRKVEKEYREKGLI 75
                                   677888999*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      683  (0.0380947); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 590.95
//
Query:       gi|118431066|ref|NP_147260.2|  [L=61]
Description: hypothetical protein APE_0472b.1 [Aeropyrum pernix K1]
Scores for 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-06   26.5   1.0    8.1e-06   26.2   1.0    1.2  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   1.0   4.5e-10   8.1e-06       1      47 [.       1      47 [.       1      59 [. 0.81

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.5e-10
                         DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIee.akeilkklkgilk 47
                                   Ms+ Ie +  +Gv++PL++++  EG+++kikI +  +  ++kl+++l+
  gi|118431066|ref|NP_147260.2|  1 MSE-IEGIVKSGVIIPLKPLTELEGKKIKIKIVDaESVDAEKLYSYLR 47
                                   677.999999************************54444568888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 469.98
//
Query:       gi|118431067|ref|YP_874830.1|  [L=45]
Description: hypothetical protein APE_0472c [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.011   16.1   0.1    1.0  1  DUF5546   Family of unknown function (DUF5546)


Domain annotation for each model (and alignments):
>> DUF5546  Family of unknown function (DUF5546)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.1     6e-07     0.011      37      67 ..       4      36 ..       2      45 .] 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6e-07
                        DUF5546 37 rcwmsrrdltslphpsepavldhl..gpslfpa 67
                                    cw +r dl + p p e +vl  l  gp + p 
  gi|118431067|ref|YP_874830.1|  4 NCWWARGDLNPGPPPCEGGVLTRLddGPLRAPY 36
                                   6*********************99445555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       121  (0.00674884); expected 358.6 (0.02)
Passed bias filter:                       96  (0.00535445); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 365.89
//
Query:       gi|118431068|ref|NP_147261.2|  [L=324]
Description: hypothetical protein APE_0473.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-10   38.7   0.1    6.5e-10   38.7   0.1    2.1  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.059   13.7   0.0       0.24   11.7   0.0    2.1  1  TOBE            TOBE domain
        7.5    7.2   9.4       0.58   10.8   1.2    2.4  2  ABATE           Putative stress-induced transcription regulat


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 !   38.7   0.1   1.1e-13   6.5e-10       3      40 ..      15      52 ..      13      57 .. 0.93
   2 ?   -3.4   0.0       1.7     1e+04      19      26 ..      66      74 ..      63      76 .. 0.72
   3 ?   -3.3   0.2       1.6   9.8e+03      29      35 ..     114     123 ..     112     134 .. 0.49

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.1e-13
                                   ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                 MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                   +++s+ v++Pke+++e+g+++Gd v ++v+g+++ ++p
  gi|118431068|ref|NP_147261.2| 15 GSSSLVVTLPKEWVREMGLKQGDPVYVVVEGGSLRIVP 52
                                   689*****************************999988 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                                   C.CEECTCE CS
                 MazE_antitoxin 19 l.gireGde 26
                                   l g+++Gd 
  gi|118431068|ref|NP_147261.2| 66 LsGLDPGDA 74
                                   559999996 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.6
                                    EEECTT...C CS
                 MazE_antitoxin  29 levdgd...k 35 
                                    +++d+d   +
  gi|118431068|ref|NP_147261.2| 114 VVRDDDsvsI 123
                                    5556655331 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.24      30      62 ..      17      48 ..      11      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                           TOBE 30 gatLtArvtrrsaeeLgLapGeeVfalikaakv 62
                                     +L+++++++ ++e+gL+ G++V++++  +++
  gi|118431068|ref|NP_147261.2| 17 S-SLVVTLPKEWVREMGLKQGDPVYVVVEGGSL 48
                                   3.499**********************998877 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.7      0.24   1.4e+03      55     109 ..     143     201 ..     126     219 .. 0.46
   2 ?   10.8   1.2   9.6e-05      0.58       4      87 ..     216     299 ..     213     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHHTHHHH............HHHHHH..HHHS----EEEE-TTS-E...... CS
                          ABATE  55 raLRealrallaaaaag...dpppaaalaalnal..laaappaprLvrhddgpvdrardw 109
                                     +LR+    l +aa+ g   ++ ++ a  +l +   la+      +  h++++ +ra+++
  gi|118431068|ref|NP_147261.2| 143 SDLRDIAELLTEAAR-GssvEGEAERARIRLQRSitLAERYLMGVIGSHTGQQDARATAS 201
                                    334444444443333.33444444444444444433466666666666665554444433 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.6e-05
                                    HHHHHHH.----HHHHHHHTTT-HHHHHH--TTHHHHHH..........HHHHHHHHHHHHHHTHHHH.........HHH CS
                          ABATE   4 aldlvNT.rargggrraDlLttpadLaaWleaagllpagtaaagadaelararaLRealrallaaaaagdpppaaalaal 82 
                                     ld v T ++ gg    D L+   +L + +++a l  a + + ++ ++la    LR+++ +l+ + ++    +a ala++
  gi|118431068|ref|NP_147261.2| 216 LLDTVKTlSRGGGNASKDTLDVLTALSTVASEAALNVASESLKRSSEVLANIAKLRSRVEELIYSDKT-SKTEAVALARV 294
                                    5899999977888899********************99999999998****************96555.46667777777 PP

                                    HHHHH CS
                          ABATE  83 nalla 87 
                                     + l+
  gi|118431068|ref|NP_147261.2| 295 LESLR 299
                                    66554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2718.12
//
Query:       gi|118431069|ref|NP_147262.2|  [L=395]
Description: origin recognition complex subunit 1 Orc1 [Aeropyrum pernix K1]
Scores for 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-22   77.1   0.2    2.2e-21   75.6   0.2    1.8  1  Cdc6_C           CDC6, C terminal winged helix domain
    2.3e-12   47.6   0.2    7.5e-11   42.7   0.2    2.5  2  AAA_16           AAA ATPase domain
    3.9e-11   43.4   0.0    9.3e-11   42.2   0.0    1.6  1  AAA_22           AAA domain
      5e-06   27.0   0.0    1.1e-05   25.8   0.0    1.6  1  AAA              ATPase family associated with various cellul
    2.9e-05   23.6   0.0    4.7e-05   22.9   0.0    1.3  1  TniB             Bacterial TniB protein
     0.0044   17.0   0.0     0.0092   15.9   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0088   15.2   0.0      0.017   14.3   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.024   14.4   0.0        0.5   10.1   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.033   14.2   0.0      0.071   13.1   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.038   14.3   0.1       0.11   12.9   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
      0.053   13.2   0.0       0.14   11.9   0.0    1.6  2  Sigma54_activat  Sigma-54 interaction domain
      0.062   13.1   0.0         15    5.3   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
      0.068   13.2   0.1       0.26   11.3   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
      0.069   12.7   0.0       0.11   12.0   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.071   12.4   0.0       0.14   11.5   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.086   12.6   0.0        8.8    6.0   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
      0.088   12.0   0.1          5    6.2   0.0    2.2  2  TIP49            TIP49 P-loop domain
       0.14   10.8   0.0       0.21   10.2   0.0    1.1  1  PEPCK_ATP        Phosphoenolpyruvate carboxykinase


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 !   75.6   0.2   2.2e-24   2.2e-21       1      84 []     304     384 ..     304     384 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.2e-24
                                    HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHH CS
                         Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpdd 80 
                                    L++++ l++  g ++++tge+ye+Yk+l++ +g++ +t r+vs ++seL+mlgi++++++s+Gr +g+tr++sL+ d   
  gi|118431069|ref|NP_147262.2| 304 LLSIMMLED--GGRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVSRGR-YGKTREVSLDADRLA 380
                                    778887766..99**************************************************9.************999 PP

                                    HHHH CS
                         Cdc6_C  81 vlea 84 
                                    v++a
  gi|118431069|ref|NP_147262.2| 381 VENA 384
                                    9875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.2   7.5e-14   7.5e-11       2      75 ..      29     110 ..      28     120 .. 0.83
   2 ?    2.1   0.0      0.23   2.2e+02     123     163 ..     126     168 ..     119     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 7.5e-14
                         AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd....ggif..lrgkcdqlesaipy...sa 71 
                                    l+ Re+el++L+++l ++ +g+  ++ ll+G  G+GK++++r +lr+le++    g+++  ++ +++  ++++py   sa
  gi|118431069|ref|NP_147262.2|  29 LPHREAELRRLAEVLAPALRGEKpSNALLYGLTGTGKTAVARLVLRRLEARasslGVLVkpIYVNAR--HRETPYrvaSA 106
                                    678*************99999999***************************9988777744444444..44889966555 PP

                         AAA_16  72 laqa 75 
                                    +a+a
  gi|118431069|ref|NP_147262.2| 107 IAEA 110
                                    6655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                         AAA_16 123 lkrllallsrderplvlvlDdlq..wadeaslqllaaLlrlle 163
                                      rl+++lsr +   ++vlD+++    +++ ++ll+ + r  +
  gi|118431069|ref|NP_147262.2| 126 YERLVKRLSRLRGIYIIVLDEIDflPKRPGGQDLLYRITRINQ 168
                                    567888888867779********65556688888888777655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   9.3e-14   9.3e-11       6     129 ..      53     180 ..      48     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 9.3e-14
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                    +  +++G +GtGKT ++r +l++l+++a+     ++ ++v++ + +++  +++++++a+g++    +ls  e++e+l + 
  gi|118431069|ref|NP_147262.2|  53 SNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKR 132
                                    6689********************88766555444445***************************9********888888 PP

                         AAA_22  86 lraravielliiDEaqhlrs.....eealeeLrsllnl.srkgvqliLvG 129
                                    l++ + i ++++DE+++l +     +++l  + ++ n    + v + LvG
  gi|118431069|ref|NP_147262.2| 133 LSRLRGIYIIVLDEIDFL-PkrpggQDLLYRITRI-NQeLGDRVWVSLVG 180
                                    8888888***********.5445556666666333.22345555555555 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 !   25.8   0.0   1.1e-08   1.1e-05       2      74 ..      56     154 ..      55     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-08
                                    EEESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS..........................STTHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakelgve.........fleisgsellsk..........................yvgesekki 46 
                                    llyG  GtGKT++a+ v + l+++          + ++                                  vge  +++
  gi|118431069|ref|NP_147262.2|  56 LLYGLTGTGKTAVARLVLRRLEARasslgvlvkPIYVN------ArhretpyrvasaiaeavgvrvpftglSVGEVYERL 129
                                    9*******************965433444444422222......122233456666677777778887777899999999 PP

                                    HHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA  47 relfkeakekakpsilfiDEidalaksr 74 
                                     + +++++      i+++DEid l k+ 
  gi|118431069|ref|NP_147262.2| 130 VKRLSRLRG---IYIIVLDEIDFLPKRP 154
                                    999988765...57********995444 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.8e-08   4.7e-05      18     131 ..      34     150 ..      26     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-08
                           TniB  18 eilerLeeLley.pkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealga 96 
                                    + l+rL+e+l+   + ++++n+ll+G + +GKt++++   r+ +++ ++    v+ ++v+a+++ +  r  +ai ea+g+
  gi|118431069|ref|NP_147262.2|  34 AELRRLAEVLAPaLRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGV 113
                                    5578887766642778999***************************9999999999**********************99 PP

                           TniB  97 plkara.rvskleqqvlrllrel.kvrvLiiDEihnl 131
                                    ++  +  +v + +++ ++ l++l ++ ++++DEi+ l
  gi|118431069|ref|NP_147262.2| 114 RVPFTGlSVGEVYERLVKRLSRLrGIYIIVLDEIDFL 150
                                    998776478898888888887763699******9865 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 !   15.9   0.0   9.2e-06    0.0092       4      70 ..      32     108 ..      30     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.2e-06
                       ATPase_2   4 Rekelkeleeil....erepneiyfiYGpegsGKtaLlkeiienledkdk......yviyyialreesiskldefie 70 
                                    Re+el++l e+l    + e+ +  ++YG  g GKta+ + ++ +le          + iy++a ++e   ++ + i+
  gi|118431069|ref|NP_147262.2|  32 REAELRRLAEVLapalRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASslgvlvKPIYVNARHRETPYRVASAIA 108
                                    999999999985222267888999*******************9977666677777778888888888777777655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.7e-05     0.017      38      80 ..      37      79 ..      26      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                         DUF815 38 ealventeqfleglpannvLLwGarGtGKSslvkallneyaee 80
                                   ++l e  +  l+g++ +n+LL+G  GtGK ++ + +l++++++
  gi|118431069|ref|NP_147262.2| 37 RRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEAR 79
                                   566666677799***********************99988765 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 ?   10.1   0.0    0.0005       0.5      25      60 ..      44      79 ..      24      93 .. 0.86
   2 ?    1.7   0.0       0.2     2e+02      49      98 ..     103     152 ..     100     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                         RuvB_N 25 aakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                   a   r+e+    llyG  G Gkt++a+++ + l+++
  gi|118431069|ref|NP_147262.2| 44 APALRGEKPSNALLYGLTGTGKTAVARLVLRRLEAR 79
                                   5667999999******************99998875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.2
                         RuvB_N  49 lakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsr 98 
                                    +a+ ia+ +gv++  t   v e    l+  l++l+   ++ +dei  l +
  gi|118431069|ref|NP_147262.2| 103 VASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPK 152
                                    6888999*********999999999********************98876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.1e-05     0.071       3      45 ..      32      78 ..      30      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.1e-05
                                   SHHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  3 seeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalgv 45
                                   +e+e+++l++ la al     +  lL+G  G+GKT+ +r +++ l+ 
  gi|118431069|ref|NP_147262.2| 32 REAELRRLAEVLAPALrgekPSNALLYGLTGTGKTAVARLVLRRLEA 78
                                   67899999****99888654456*******************99976 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00011      0.11      13      44 ..     240     282 ..     231     297 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX............XXXX CS
                    AAA_assoc_2  13 ealaeladGDaRkaLnlLElaaeaaeak...........egki 44 
                                    +ala+  +GDaR+aL lL +a e ae++           + ++
  gi|118431069|ref|NP_147262.2| 240 AALAAREHGDARRALDLLRVAGEIAERRreervrrehvySARA 282
                                    57888889***********999999874444444444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.14      20      48 ..      50      78 ..      30      88 .. 0.71
   2 ?   -3.1   0.0       5.6   5.6e+03      97     108 ..     142     153 ..     141     168 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                   TSSS-EEEECSTTSSHHHHHHHHHHHSTT CS
                Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskr 48
                                   +++++ l+ G +GtGK+ +ar++ ++ + 
  gi|118431069|ref|NP_147262.2| 50 EKPSNALLYGLTGTGKTAVARLVLRRLEA 78
                                   455999***************99875544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.6
                                    EEEETGGGS-HH CS
                Sigma54_activat  97 lfLDeigelple 108
                                    + LDei  lp +
  gi|118431069|ref|NP_147262.2| 142 IVLDEIDFLPKR 153
                                    566777666643 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.015        15      15      35 ..      53      73 ..      39      92 .. 0.73
   2 ?    5.2   0.0     0.016        16     117     151 ..     134     168 ..     120     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                                   CEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 15 gdvlvaaeTGsGKTlaflipv 35
                                    + l+ + TG+GKT+++ + +
  gi|118431069|ref|NP_147262.2| 53 SNALLYGLTGTGKTAVARLVL 73
                                   58899999*******987754 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                                    SHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHH CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                           DEAD 117 lnlsqvrflVlDEadrlldq.gfsdfinrilnqlpq 151
                                     +l+ + ++VlDE+d l +  g +d + r +++++q
  gi|118431069|ref|NP_147262.2| 134 SRLRGIYIIVLDEIDFLPKRpGGQDLLYR-ITRINQ 168
                                    24889999*********999777777777.555654 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 ?   11.3   0.0   0.00026      0.26       2      24 ..      55      79 ..      54     102 .. 0.86
   2 ?   -1.7   0.0       2.6   2.6e+03      67      75 ..     140     148 ..     124     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                   EEEE--SSSSHHHHHHHGGGGB..S CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal..n 24
                                    lL G +GtgK+ +a+ ++++l  +
  gi|118431069|ref|NP_147262.2| 55 ALLYGLTGTGKTAVARLVLRRLeaR 79
                                   59*******************9543 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                                    SEEEEESGG CS
                          AAA_5  67 eilvlDEve 75 
                                     i+vlDE++
  gi|118431069|ref|NP_147262.2| 140 YIIVLDEID 148
                                    699****98 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.11      34      60 ..      53      79 ..      39     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldke 60
                                    + ll+G tGtGKt++++ +l++l+ +
  gi|118431069|ref|NP_147262.2| 53 SNALLYGLTGTGKTAVARLVLRRLEAR 79
                                   678******************999854 PP

>> Zeta_toxin  Zeta toxin
   #    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      10      43 ..      46      79 ..      37      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                     Zeta_toxin 10 ypsqerPklillgGqpGAGKselaellkdelerq 43
                                     ++e+P   ll G +G GK+++a+l+ ++le++
  gi|118431069|ref|NP_147262.2| 46 ALRGEKPSNALLYGLTGTGKTAVARLVLRRLEAR 79
                                   56789************************99844 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 ?    4.2   0.0     0.032        32      46      64 ..      51      69 ..      31      83 .. 0.83
   2 ?    6.0   0.0    0.0089       8.8      93     134 ..     123     164 ..     113     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.032
                      IstB_IS21 46 kkenivllGpsGvGKshla 64
                                   k  n +l G +G+GK+ +a
  gi|118431069|ref|NP_147262.2| 51 KPSNALLYGLTGTGKTAVA 69
                                   66899***********887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0089
                      IstB_IS21  93 arrdgklaralkrllkvdllilDdlgllpldqaeaellfevi 134
                                     +  ++l ++l+rl  + +++lD++ +lp     + ll+++ 
  gi|118431069|ref|NP_147262.2| 123 GEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRIT 164
                                    556678999999999***********************9985 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.035        35      52      74 ..      54      76 ..      33      93 .. 0.75
   2 ?    6.2   0.0    0.0051         5      66      96 ..     103     133 ..      98     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.035
                                   XXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 52 avLlaGpsgtGktalaiaiskel 74
                                     Ll G +gtGkta+a  + + l
  gi|118431069|ref|NP_147262.2| 54 NALLYGLTGTGKTAVARLVLRRL 76
                                   56899**********97776666 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0051
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  66 laiaiskelgedvpfvalsgsevyslevkkt 96 
                                    +a ai++++g  vpf+ ls +evy   vk+ 
  gi|118431069|ref|NP_147262.2| 103 VASAIAEAVGVRVPFTGLSVGEVYERLVKRL 133
                                    6889********************9888775 PP

>> PEPCK_ATP  Phosphoenolpyruvate carboxykinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00021      0.21     204     227 ..      47      69 ..      35      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                                    EE-T.TS-EEEEEE-TTSSHHHHH CS
                      PEPCK_ATP 204 nvgekkgdvalfFGLSGtGKTtLs 227
                                      ge k   al++GL+GtGKT+++
  gi|118431069|ref|NP_147262.2|  47 LRGE-KPSNALLYGLTGTGKTAVA 69 
                                    5564.44889***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2948.28
//
Query:       gi|118431070|ref|NP_147263.2|  [L=185]
Description: hypothetical protein APE_0476.1 [Aeropyrum pernix K1]
Scores for complete 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-39  135.1   0.0      2e-39  134.9   0.0    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9   0.0   1.1e-43     2e-39       6     182 ..       1     178 [.       1     179 [. 0.94

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 1.1e-43
                                    EEEEEEE.......-SS-EEEEEEEEETT..EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE- CS
                          DUF99   6 lGiddsffe..rkkkdgksvlvGvvmradr.vvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNvv 82 
                                    +G+dd+ +e     ++g ++++++ ++++  ++    +g v+vdG Dat++++ lv rl  +  r vlld++ti+gFN+v
  gi|118431070|ref|NP_147263.2|   1 MGCDDGRVEklG-PQAGFTAVACISWDNRLrLPLAGSLGLVRVDGVDATSVLAGLVLRL-GAAGRPVLLDSLTIGGFNIV 78 
                                    59*****99532.379**********998846678899*********************.8899**************** PP

                                    -HHHHHHHH---EEEEESS---HHHHHHCCT..TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHHHHHHHH CS
                          DUF99  83 DlerlheetglPviavtreepdlgklekaLr.khfpdeeeRlelieklgerieevektgeelyvravGieleeaaklvrk 161
                                     ++ + + tg Pv+av++++p+l++le+ Lr +++p +  R ++++ + e+++e +++++++y+ a+G+e++ea++lv +
  gi|118431070|ref|NP_147263.2|  79 SPPGVERLTGSPVLAVYNYRPSLERLESGLRsSRLPLAGVRARVLSLV-EEAAEASTPHGPVYLVAWGLEASEARRLVLE 157
                                    *******************************7799999********99.999999999********************** PP

                                    C-SSSSS-HHHHHHHHHHHHH CS
                          DUF99 162 ltlegriPEPlRvAhliAsal 182
                                    ++++gr PEP+R+Ah+ As++
  gi|118431070|ref|NP_147263.2| 158 TQVYGRKPEPVRIAHYTASEA 178
                                    ******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1495.58
//
Query:       gi|118431071|ref|YP_874831.1|  [L=100]
Description: hypothetical protein APE_0477.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 858.07
//
Query:       gi|118431072|ref|NP_147264.2|  [L=367]
Description: molybdenum cofactor biosynthesis protein MoaA [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-23   84.5   0.0    3.4e-23   82.8   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    2.4e-21   76.0   0.0    3.6e-21   75.4   0.0    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    0.00077   19.6   0.0     0.0024   18.0   0.0    1.8  2  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.036   14.3   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   7.7e-27   3.4e-23       3     166 ..      29     189 ..      27     190 .. 0.91
   2 ?   -1.4   0.0      0.59   2.7e+03     112     141 ..     287     316 ..     282     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 7.7e-27
                                    EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                    vt+ Cnl+C fC+          r++  + +lsve+   + +++  + gv+ + l+ggepl + d  ++++ la+     
  gi|118431072|ref|NP_147264.2|  29 VTPECNLDCFFCHMEGAtesgpMRPGSWSPVLSVEDYDIIGEAA-SRLGVDSFKLTGGEPLIRGDVDKIVAVLAR----Y 103
                                    8999***********999*9997777777778888776666666.5888***************99999999999....7 PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGend 157
                                     +++++tng+l+ + k+  l+++g+ rv+++l+++++e++ k++ r+  ++  l+++e++ +ag++ v++++v+l+G n+
  gi|118431072|ref|NP_147264.2| 104 GEVSMTTNGILL-PLKASSLKRAGLARVNVSLHSISEEVYEKIT-RRRAVKLALKGVEAALKAGLR-VKVNMVLLRGLNE 180
                                    9***********.*************************777777.99*******************.************* PP

                                    HHHHHHHHH CS
                                    xxxxxxxxx RF
                    Radical_SAM 158 eeleellel 166
                                     e++ ll+l
  gi|118431072|ref|NP_147264.2| 181 GEFWRLLRL 189
                                    ******987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.59
                                    SSHHHHHHHHT.CTSHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 112 addekvlklmn.rghtfeevlealeklreag 141
                                    + +  v + ++ +g   e+v++++++l ea+
  gi|118431072|ref|NP_147264.2| 287 PYPS-VAEALKrGGSREEKVWRVMKILLEAN 316
                                    5666.78888855555578888888888775 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.0   8.1e-25   3.6e-21       2     126 ..     196     323 ..     195     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 8.1e-25
                                    EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SS..T-SSEEEEETTT--EEEEE-TTTS-.-GGG--EE CS
                    Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakket..kgpakrykikdgkgeiglIapvsep.FCasCnRl 78 
                                    +l++IE++p g+g+    k + s ++ ++ +eerl++++++ et   +++++y++++g  ++ l++pv++p FC +C R+
  gi|118431072|ref|NP_147264.2| 196 DLQVIEVHPAGRGR----KVLSSFRRPIDVVEERLSSMAVAVETgrLHNRRVYRLPSGV-RVYLVDPVENPvFCMGCYRV 270
                                    89*********997....67999******************888889********9999.8******************* PP

                                    EE-TTSEEESSSS-SS-.EEHHHHHHTT--HHH....HHHHHHHHHHT----H CS
                    Mob_synth_C  79 RltadGklktCLfaeee.idlrdllregaseee....Lkelikealarkkekh 126
                                    Rlt+dG+l +C++++    +++++l++g s+ee    +++++ ea a +++++
  gi|118431072|ref|NP_147264.2| 271 RLTWDGRLLPCIYWKGPyPSVAEALKRGGSREEkvwrVMKILLEANALRRPTY 323
                                    *****************99*********9555558888888888888888776 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 !   18.0   0.0   5.3e-07    0.0024       6      88 ..      31     111 ..      27     130 .. 0.75
   2 ?   -3.2   0.1         2   9.1e+03      11      17 ..     263     269 ..     261     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.3e-07
                        Fer4_14   6 sgCnlsCkgCdnketwks......elgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                      Cnl C +C  + + +s      ++ ++ + e+  +i+    +s+   +   ltGGePL+  + ++++ ++ r+   + 
  gi|118431072|ref|NP_147264.2|  31 PECNLDCFFCHMEGATESgpmrpgSWSPVLSVEDY-DII-GEAASRLGVDSFKLTGGEPLIRGDVDKIVAVLARY---G- 104
                                    68*********777666677788899999999999.555.46777777899*********885555555554443...3. PP

                        Fer4_14  80 ekkiwletn 88 
                                      ++ + tn
  gi|118431072|ref|NP_147264.2| 105 --EVSMTTN 111
                                    ..4555555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2
                        Fer4_14  11 sCkgCdn 17 
                                     C gC++
  gi|118431072|ref|NP_147264.2| 263 FCMGCYR 269
                                    5****95 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 ?   14.3   0.0   8.1e-06     0.036      14      79 ..      32     103 ..      25     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                        Fer4_12  14 gCnlsCkgCfnketwsfk.....sgkef.tkelleeiiedlkkesiegltllGGEPllpenaeallelvkev 79 
                                     Cnl C +C+ + + +       s  ++ + e  + i e ++   ++ + l+GGEPl +  +++++ ++ + 
  gi|118431072|ref|NP_147264.2|  32 ECNLDCFFCHMEGATESGpmrpgSWSPVlSVEDYDIIGEAASRLGVDSFKLTGGEPLIRGDVDKIVAVLARY 103
                                    7*********998886554443233333357777888888888889************77776666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.44u 0.18s 00:00:00.62 Elapsed: 00:00:00.33
# Mc/sec: 3297.26
//
Query:       gi|118431073|ref|NP_147267.2|  [L=98]
Description: hypothetical protein APE_0481.1 [Aeropyrum pernix K1]
Scores for complete 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-12   46.9   1.7    3.6e-12   46.5   1.7    1.2  1  Fer4_8         4Fe-4S dicluster domain
    4.5e-11   42.1  13.2    1.8e-06   27.5   2.9    2.2  2  Fer4           4Fe-4S binding domain
    7.1e-10   38.8  18.0    2.9e-06   27.3  10.1    2.0  2  Fer4_10        4Fe-4S dicluster domain
    1.1e-09   38.7   1.6    1.5e-09   38.2   1.6    1.2  1  Fer4_17        4Fe-4S dicluster domain
    2.1e-08   34.6  19.7      4e-07   30.5   8.7    1.8  2  Fer4_7         4Fe-4S dicluster domain
    4.3e-08   32.8   9.7     0.0009   19.2   1.8    2.2  2  Fer4_2         4Fe-4S binding domain
    1.1e-07   31.6  10.9     0.0013   18.7   3.3    2.2  2  Fer4_6         4Fe-4S binding domain
    4.9e-07   29.8   6.4    2.9e-06   27.3   6.7    1.9  2  Fer4_9         4Fe-4S dicluster domain
      1e-05   25.6   6.2      0.015   15.4   1.3    2.1  2  Fer4_21        4Fe-4S dicluster domain
    1.3e-05   25.3   8.8      0.017   15.6   0.9    2.2  2  Fer4_4         4Fe-4S binding domain
    1.4e-05   25.2   7.1     0.0011   19.2   0.3    2.1  2  Fer4_18        4Fe-4S dicluster domain
    0.00037   21.4  11.4      0.005   17.8  11.6    2.0  2  Fer4_16        4Fe-4S double cluster binding domain
    0.00067   20.4  17.4     0.0061   17.4   4.7    2.2  2  Fer4_3         4Fe-4S binding domain
     0.0056   17.5   7.5       0.54   11.1   0.5    2.1  2  Fer4_22        4Fe-4S dicluster domain
     0.0063   16.3   3.2       0.19   11.5   0.1    2.1  2  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
  ------ inclusion threshold ------
      0.021   15.3   7.9       0.43   11.2   0.5    2.2  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
       0.13   13.1   6.6        2.8    8.7   0.6    2.3  2  Fer4_15        4Fe-4S single cluster domain
        1.4    8.7   7.3        6.3    6.6   1.2    2.4  2  zf-C2H2_11     zinc-finger C2H2-type
        7.5    6.4  11.1        5.2    6.9   1.8    2.3  2  A2L_zn_ribbon  A2L zinc ribbon domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   1.7   3.8e-15   3.6e-12       2      65 .]      12      79 ..      11      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 3.8e-15
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae........dvqeeqvlee...eealwsCttcgaCtevCpvgi 65
                                    +kCi Cg+C+  Cp+l   +++ + +rg++          +        +    e+l+sC+ cgaC evCp  i
  gi|118431073|ref|NP_147267.2| 12 TSKCIYCGFCEPVCPTLPFGRHRGYGPRGRVFSarlvaldgK-------ATegdLESLYSCLLCGACMEVCPARI 79
                                   589*************99999999999999998755543321.......22455799***************876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   2.9   1.9e-09   1.8e-06       2      20 ..       9      27 ..       8      29 .. 0.92
   2 !   20.2   2.7   3.9e-07   0.00037       8      20 ..      65      77 ..      62      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.9e-09
                                   EEETTTSSS-THHHHHSTT CS
                           Fer4  2 videekCigCGaCvevCPv 20
                                   ++ ++kCi+CG C+ vCP+
  gi|118431073|ref|NP_147267.2|  9 KVETSKCIYCGFCEPVCPT 27
                                   5789**************8 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.9e-07
                                   SSS-THHHHHSTT CS
                           Fer4  8 CigCGaCvevCPv 20
                                   C  CGaC+evCP 
  gi|118431073|ref|NP_147267.2| 65 CLLCGACMEVCPA 77
                                   9***********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 !   27.3  10.1     3e-09   2.9e-06       4      56 .]      10      76 ..       7      76 .. 0.91
   2 !   22.3   1.0   1.1e-07    0.0001       8      28 ..      64      84 ..      57      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3e-09
                        Fer4_10  4 idddtCirCgkCvkaCPadl...............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +++++Ci Cg C  +CP+ l               ++  +    +  e + + +++C  cgaC+e+CP
  gi|118431073|ref|NP_147267.2| 10 VETSKCIYCGFCEPVCPT-LpfgrhrgygprgrvfSARLVALDGKATEGDLESLYSCLLCGACMEVCP 76
                                   6789**************.77***********9998888888888888888999*************9 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 1.1e-07
                        Fer4_10  8 tCirCgkCvkaCPadltsvga 28
                                   +C+ Cg+C+++CPa ++ v++
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPARIDIVSV 84
                                   7*************7744444 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   1.6   1.6e-12   1.5e-09       1      61 []      14      80 ..      14      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.6e-12
                        Fer4_17  1 rCiqCgyClpeCpsyeaydnepkkllraakl....glleeaeke...ekaslCieCgeCerkCPqgld 61
                                   +Ci Cg+C+p+Cp++   + +   ++ ++ +    +l ++a  e   e   +C+ Cg C ++CP+ +d
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCPTLPFGRHRGYGPRGRVFSarlvALDGKAT-EgdlESLYSCLLCGACMEVCPARID 80
                                   6************97775555444444443323333223322.23568****************9987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.2   1.7e-05     0.016      35      50 ..      12      27 ..       3      29 .. 0.70
   2 !   30.5   8.7   4.3e-10     4e-07       1      51 [.      14      78 ..      14      79 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                         Fer4_7 35 pekClgCgaCvavCPt 50
                                    +kC++Cg C+ vCPt
  gi|118431073|ref|NP_147267.2| 12 TSKCIYCGFCEPVCPT 27
                                   5667777777777775 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 4.3e-10
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgt...........ekveidpe...kClgCgaCvavCPtg 51
                                   +Ci Cg+C+++Cp+  +  +    ++g+           + +e+d e   +Cl CgaC++vCP+ 
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCPTLPFGRHRGYGPRGRvfsarlvaldgKATEGDLEslySCLLCGACMEVCPAR 78
                                   7***********966555554434443333333333343445666552337************85 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.8   9.5e-07    0.0009       4      22 .]       9      27 ..       6      27 .. 0.91
   2 !   18.5   1.2   1.6e-06    0.0015       9      22 .]      64      77 ..      58      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.5e-07
                         Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                   +v+t +Ci Cg C  +CP+
  gi|118431073|ref|NP_147267.2|  9 KVETSKCIYCGFCEPVCPT 27
                                   6899**************7 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.6e-06
                         Fer4_2  9 rCigCgaCvsaCPa 22
                                   +C+ CgaC  +CPa
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPA 77
                                   6************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 !   17.8   0.9   2.6e-06    0.0025       4      21 ..      10      27 ..       7      32 .. 0.89
   2 !   18.7   3.3   1.4e-06    0.0013       8      21 ..      64      77 ..      63      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                         Fer4_6  4 idpdkCigCgdCvrvCPe 21
                                   +  +kCi Cg C+ vCP+
  gi|118431073|ref|NP_147267.2| 10 VETSKCIYCGFCEPVCPT 27
                                   6779*************7 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.4e-06
                         Fer4_6  8 kCigCgdCvrvCPe 21
                                   +C+ Cg+C+ vCP+
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPA 77
                                   6************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 !   12.7   1.8   0.00012      0.11      35      48 ..      14      27 ..       3      30 .. 0.72
   2 !   27.3   6.7   3.1e-09   2.9e-06       1      49 [.      14      78 ..      14      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                         Fer4_9 35 aCigCgaCveaCpk 48
                                   +Ci Cg C+ +Cp+
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCPT 27
                                   67777777777775 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 3.1e-09
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpkg 49
                                   kC+ Cg C+++Cp+  + ++++ + +  r +s+                  +C+ CgaC+e+Cp  
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCPTLPFGRHRGYGPRG-RVFSArlvaldgkategdleslYSCLLCGACMEVCPAR 78
                                   7***********777776665555433.344444677899999999999989************76 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.3   1.6e-05     0.015      33      53 ..       7      27 ..       2      29 .. 0.83
   2 !   13.0   0.3   8.9e-05     0.084      40      53 ..      64      77 ..      45      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                        Fer4_21 33 vlkvvedeCvGCnlCssvCPv 53
                                    lkv +++C+ C  C  vCP+
  gi|118431073|ref|NP_147267.2|  7 FLKVETSKCIYCGFCEPVCPT 27
                                   567889999999999999996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.9e-05
                        Fer4_21 40 eCvGCnlCssvCPv 53
                                   +C  C  C++vCP 
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPA 77
                                   57888888888885 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.6   5.3e-05      0.05       2      16 ..      13      27 ..      12      39 .. 0.91
   2 !   15.6   0.9   1.9e-05     0.017       3      16 ..      64      77 ..      62      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-05
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   ++Ci Cg C+ +CP+
  gi|118431073|ref|NP_147267.2| 13 SKCIYCGFCEPVCPT 27
                                   58************5 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.9e-05
                         Fer4_4  3 rCigCgsCvaaCPq 16
                                   +C+ Cg+C+ +CP 
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPA 77
                                   7************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 !   10.2   1.4   0.00071      0.67      55      73 ..       9      27 ..       1      33 [. 0.85
   2 !   19.2   0.3   1.1e-06    0.0011      55      78 ..      59      82 ..      28      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                        Fer4_18 55 ekgagdcidcescvkvcPt 73
                                   + ++++ci c++c  vcPt
  gi|118431073|ref|NP_147267.2|  9 KVETSKCIYCGFCEPVCPT 27
                                   457899************8 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.1e-06
                        Fer4_18 55 ekgagdcidcescvkvcPtgidir 78
                                    ++   c+ c++c++vcP  idi 
  gi|118431073|ref|NP_147267.2| 59 LESLYSCLLCGACMEVCPARIDIV 82
                                   456678****************95 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   3.9    0.0017       1.6       1      13 [.      14      26 ..       5      27 .. 0.60
   2 !   17.8  11.6   5.3e-06     0.005       1      66 [.      14      77 ..      14      78 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                        Fer4_16  1 rCgtCgkCaevCP 13
                                   +C+ Cg C  vCP
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCP 26
                                   3555555555555 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5.3e-06
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisy.ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                   +C+ Cg C  vCPt  +    +      + +s+  +a + +++e   +  + + +  C++C++vCPa
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCPTLPFGRH-RGYGPRGRVFSArLVALDGKATEGDLE--SLYSCLLCGACMEVCPA 77
                                   6**************99999.333333444444333333333333333..3479************7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   4.8    0.0034       3.2       1      13 [.      15      27 ..      15      28 .. 0.95
   2 !   17.4   4.7   6.4e-06    0.0061       1      12 [.      65      76 ..      65      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0034
                         Fer4_3  1 CtgCgaCvevCPv 13
                                   C+ Cg C+ vCP+
  gi|118431073|ref|NP_147267.2| 15 CIYCGFCEPVCPT 27
                                   9***********6 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 6.4e-06
                         Fer4_3  1 CtgCgaCvevCP 12
                                   C+ CgaC+evCP
  gi|118431073|ref|NP_147267.2| 65 CLLCGACMEVCP 76
                                   9*********** PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   1.6    0.0013       1.2       1      14 [.      14      27 ..       9      30 .. 0.87
   2 !   11.1   0.5   0.00058      0.54       2      14 ..      65      77 ..      53      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                        Fer4_22  1 rClsCgaCtlvCpt 14
                                   +C+ Cg C  vCpt
  gi|118431073|ref|NP_147267.2| 14 KCIYCGFCEPVCPT 27
                                   69999999999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00058
                        Fer4_22  2 ClsCgaCtlvCpt 14
                                   Cl CgaC  vCp+
  gi|118431073|ref|NP_147267.2| 65 CLLCGACMEVCPA 77
                                   6777777777764 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   0.5     0.015        14      18      38 ..       9      27 ..       2      29 .. 0.84
   2 !   11.5   0.1    0.0002      0.19      23      48 ..      64      87 ..      50      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                                   HHHHTT----TT-HHHHCSTT CS
                        Fer4_20 18 leeAsRClqCkkapcvkgCPv 38
                                   + e s+C++C    c+  CP+
  gi|118431073|ref|NP_147267.2|  9 KVETSKCIYC--GFCEPVCPT 27
                                   57999*****..799999997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                                   T----TT-HHHHCSTT---HHHHHHH CS
                        Fer4_20 23 RClqCkkapcvkgCPveidipefikk 48
                                    Cl C    c++ CP++idi + +++
  gi|118431073|ref|NP_147267.2| 64 SCLLC--GACMEVCPARIDIVSVVRE 87
                                   599**..78***********998876 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 ?   11.2   0.5   0.00046      0.43       1      18 [.      10      27 ..      10      33 .. 0.93
   2 ?    7.9   1.7    0.0046       4.4       5      18 ..      64      77 ..      62      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   V+ ++Ci cg C  ++P 
  gi|118431073|ref|NP_147267.2| 10 VETSKCIYCGFCEPVCPT 27
                                   7889*************6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0046
                        Fer4_13  5 tCiacgaCvelaPd 18
                                   +C  cgaC e++P 
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPA 77
                                   6999*********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 ?    8.7   0.6     0.003       2.8       2      21 ..       9      28 ..       8      60 .. 0.88
   2 ?    7.9   0.8    0.0056       5.3       7      23 ..      64      80 ..      63      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                        Fer4_15  2 vvDrdaCigcglCvaeapev 21
                                   +v+ ++Ci cg C  ++p++
  gi|118431073|ref|NP_147267.2|  9 KVETSKCIYCGFCEPVCPTL 28
                                   58999************986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                        Fer4_15  7 aCigcglCvaeapevfe 23
                                    C  cg+C++++p ++ 
  gi|118431073|ref|NP_147267.2| 64 SCLLCGACMEVCPARID 80
                                   599**********9886 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 ?    5.3   0.6     0.018        17       4      13 ..      12      21 ..      10      21 .. 0.91
   2 ?    6.6   1.2    0.0067       6.3       6      13 ..      64      71 ..      60      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.018
                     zf-C2H2_11  4 tcqCleCGlc 13
                                   t +C  CG c
  gi|118431073|ref|NP_147267.2| 12 TSKCIYCGFC 21
                                   789*****99 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0067
                     zf-C2H2_11  6 qCleCGlc 13
                                    Cl+CG c
  gi|118431073|ref|NP_147267.2| 64 SCLLCGAC 71
                                   6******9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.1      0.03        28      24      33 .]      15      24 ..      13      24 .. 0.85
   2 ?    6.9   1.8    0.0055       5.2      20      31 ..      61      72 ..      55      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
                  A2L_zn_ribbon 24 CieCgasfpy 33
                                   Ci Cg+++p+
  gi|118431073|ref|NP_147267.2| 15 CIYCGFCEPV 24
                                   9999999985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0055
                  A2L_zn_ribbon 20 gylvCieCgasf 31
                                   + ++C  Cga+ 
  gi|118431073|ref|NP_147267.2| 61 SLYSCLLCGACM 72
                                   78********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 769.25
//
Query:       gi|14600747|ref|NP_147268.1|  [L=425]
Description: hypothetical protein APE_0482 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 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:                        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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3198.94
//
Query:       gi|118431074|ref|NP_147270.2|  [L=501]
Description: hypothetical protein APE_0485.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 3350.23
//
Query:       gi|14600751|ref|NP_147272.1|  [L=473]
Description: D-lactate dehydrogenase [Aeropyrum pernix K1]
Scores for 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-69  233.4   0.4      4e-69  233.0   0.4    1.2  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    4.3e-37  126.9   0.1      8e-37  126.1   0.1    1.5  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
       0.14   11.1   0.0       0.22   10.5   0.0    1.3  1  HDC            Histidine carboxylase PI chain


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 !  233.0   0.4   6.7e-73     4e-69       2     250 .]     216     469 ..     215     469 .. 0.98

  Alignments for each domain:
  == domain 1  score: 233.0 bits;  conditional E-value: 6.7e-73
                                   -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHH CS
                 FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeelea 82 
                                   pe+++v+l++fp++++ v+av e+++++i+ + +e+md ++ +l+++t+ga     ++ + +llv+++ ++ e+ ++ le 
  gi|14600751|ref|NP_147272.1| 216 PENVVVVLAFFPTLRQLVDAVIEVKSRAIDTLLMEFMDVDSARLAAETLGA---AIRPDGHMLLVGVPVNR-EASTRVLE- 291
                                   99*************************************************...9999*************.999*****. PP

                                   HHHHTTT-EEEEE..........E..TGGGGGGGGHH....HHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                 FAD-oxidase_C  83 lveaileatgaadvlvaqdeaeae..alwkaRkaalp....ylrdallkagvavlseDtsvPvsrladlvrdikalldkyg 157
                                   ++ +i++a+gaa+v++a++ +eae  +l+++R+++++    ++++ +++++v++l+eD++vP+s+l+d+v+++k+l +kyg
  gi|14600751|ref|NP_147272.1| 292 EMVSIAKAAGAASVYTAKSMEEAEekKLLEIRRSLFAtqalLTQKQFKGRKVMMLMEDIAVPPSKLLDAVERLKELEAKYG 372
                                   ******************99999999**************9999999********************************** PP

                                   EEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT---------------....--------THHHHHHH CS
                 FAD-oxidase_C 158 levvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkka....ylerekgeeglalmrr 234
                                   +++vl gH+gdgnlh++i ++++de+++e+a k++++v+++a+elgG++s+EHG+G+ kk+    +ler+ + ++l++m  
  gi|14600751|ref|NP_147272.1| 373 FKTVLGGHIGDGNLHPTISYPVDDEKAKEAALKWYYDVMRMAIELGGTVSAEHGIGVLKKEalrlELERMGSVKALEIMAG 453
                                   *************************************************************999999************** PP

                                   HHHHH-TT--BSTT-- CS
                 FAD-oxidase_C 235 iKaalDPkgiLNPgkv 250
                                   iK+++DPkgiLNPgkv
  gi|14600751|ref|NP_147272.1| 454 IKRVFDPKGILNPGKV 469
                                   ***************8 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.1   1.3e-40     8e-37       2     138 ..      39     178 ..      38     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 1.3e-40
                                   EEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHHH CS
                 FAD_binding_4   2 aavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgdlveal 81 
                                   +avv+pes+++v++++r+a ++++ + ++G+ ++l+g+a  ++ gvv++++r++r++e++  + +a+ve+Gv+l dl+ +l
  gi|14600751|ref|NP_147272.1|  39 EAVVFPESAQDVSRLVRYAYSREVYIYPQGSSTDLAGGAFpERPGVVVSMERMRRVREVSVLDSVAVVEPGVRLWDLNVEL 119
                                   79**********************************99999**************************************** PP

                                   HHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETT..SEEEEE CS
                 FAD_binding_4  82 aakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvlad..Gevvrl 138
                                   +++ ++++++pgs++ +tvGGai t+agG++  +yG++rd+vlgle+vl+d  G+++r+
  gi|14600751|ref|NP_147272.1| 120 SKYRYMFPIDPGSVKVATVGGAINTGAGGMRGARYGTMRDWVLGLEIVLPDeeGTILRV 178
                                   *************************************************6622666665 PP

>> HDC  Histidine carboxylase PI chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.7e-05      0.22     103     183 ..     330     416 ..     304     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.7e-05
                           HDC 103 kPlytqkqvdGkelpvy..dvk..P..lldatvelfGkeknrrftplPGafvvcankkvvaerPledrdlkegegygvWsv 177
                                   + l tqkq++G+++ +   d++  P  llda ++l   e +  f+++ G ++  +n + +   P++d++ ke    + + v
  gi|14600751|ref|NP_147272.1| 330 QALLTQKQFKGRKVMMLmeDIAvpPskLLDAVERLKELEAKYGFKTVLGGHIGDGNLHPTISYPVDDEKAKEAALKWYYDV 410
                                   468899*****99876422543323559**********************************************9999999 PP

                           HDC 178 ialsls 183
                                   + +++ 
  gi|14600751|ref|NP_147272.1| 411 MRMAIE 416
                                   988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3532.63
//
Query:       gi|118431075|ref|NP_147273.2|  [L=185]
Description: hypothetical protein APE_0488.1 [Aeropyrum pernix K1]
Scores for complete 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-64  216.2   0.0      3e-64  216.0   0.0    1.0  1  DUF2204   Nucleotidyl transferase of unknown function (DUF220


Domain annotation for each model (and alignments):
>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.0   0.0   1.7e-68     3e-64       3     181 .]       5     181 ..       3     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 216.0 bits;  conditional E-value: 1.7e-68
                        DUF2204   3 ealaevlkvLeekgvkfvviGgtvvelalgrkrlekDvDlFiteksqlleedfyreiaeeedwdvgstelgtvkliakve 82 
                                    + +a+ l+vL ++g++f++iGgtvve+alg+++l +DvDlF  e+ +llee++y ++a+e +w++g+t+lgt++lia+++
  gi|118431075|ref|NP_147273.2|   5 RGVASSLRVLLDRGFRFTIIGGTVVEYALGSRDLGDDVDLFGEEPPPLLEEEYY-GVAHELGWSSGQTWLGTPRLIARAG 83 
                                    678999************************************************.************************* PP

                        DUF2204  83 keevevdlleNildlyvpeeiLerakeveiggvevkvislEdyivlKaraareeaeeeldeiarlikelklkldvrlvke 162
                                    +eev +++++N++d+yvpe +Lera++v ++gv+vk++ lEd+ivlKa+a+r +++e+l+ei r++k+++l+++++lv+e
  gi|118431075|ref|NP_147273.2|  84 GEEVPLEFFDNVHDFYVPEPMLERAERVVMDGVRVKMVLLEDHIVLKAHAGRGSDIERLKEIGRYVKRGRLRVSRDLVRE 163
                                    ******************************************************************************** PP

                        DUF2204 163 hveafpeeeaelilkrLre 181
                                    +ve+f + ea+++l+rLre
  gi|118431075|ref|NP_147273.2| 164 AVEFFGD-EAPVLLRRLRE 181
                                    *******.*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1464.06
//
Query:       gi|14600753|ref|NP_147274.1|  [L=458]
Description: pyruvate kinase [Aeropyrum pernix K1]
Scores for 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-87  293.4   0.0    2.7e-87  292.9   0.0    1.1  1  PK         Pyruvate kinase, barrel domain
    3.9e-05   22.9   0.0    0.00011   21.4   0.0    1.7  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
    0.00057   20.1   0.0     0.0019   18.4   0.0    1.8  2  PK_C       Pyruvate kinase, alpha/beta domain


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 !  292.9   0.0   4.6e-91   2.7e-87       4     344 ..       5     333 ..       3     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 292.9 bits;  conditional E-value: 4.6e-91
                                   SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCSSSE CS
                            PK   4 tkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgkkdi 84 
                                   +kiv+t+GP+s+s+  l+++++ G++v+r+n shG  e+ ++ +e++r+ae+++gk+v++++D++Gp++rtg+ +     +
  gi|14600753|ref|NP_147274.1|   5 VKIVATVGPSSSSASILAQMLSLGVDVARINASHGGVEQWNSMLESLRRAEEAVGKRVGVAVDLEGPRVRTGNSEP----V 81 
                                   69**********************************************************************9877....8 PP

                                   EE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-BEE-T CS
                            PK  85 elkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkgvnlp 165
                                   +l++gd +++      +    e  + +d ++ ++ ++ G+++l+dDG++ l+v++v+  + ++ +v  +gvlg +kgv + 
  gi|14600753|ref|NP_147274.1|  82 KLEKGDLVTLGF----M----EGDVPVDARQFFETIDEGDIVLLDDGKIILQVESVEGFR-VKARVLEGGVLGPRKGVVVR 153
                                   9*****988554....3....34689*****************************99887.******************** PP

                                   TS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCC.TTSEEEEEE-SCHHHHTHHHHHHHSSEEEE CS
                            PK 166 gtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeeg.keikiiakienqegvenldeileasDgimv 245
                                   g + dlp ls kD++ l+f +++gv  +++sf r+a+ v++vr+v+   g ++++i+akie   gv+++ ei easDg+++
  gi|14600753|ref|NP_147274.1| 154 GKEPDLPPLSAKDRRALEFFADKGVSHVYVSFARSAEHVEKVRTVVRRLGlRQARIFAKIEGPSGVSRIGEIAEASDGVII 234
                                   **************************************************99***************************** PP

                                   EHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHTSS-HHH CS
                            PK 246 arGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetakGkyPve 326
                                   arGDlG+    e+++ +q  ++  +++  k+v+ at+ l smi++P ptr+ev D+  avl  +Da+mL geta GkyPv+
  gi|14600753|ref|NP_147274.1| 235 ARGDLGMHYSLEELPEIQELIVWEARKRYKTVVLATEFLSSMIEKPVPTRSEVVDIYQAVLQTADALMLTGETAIGKYPVK 315
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHHHHTS-H CS
                            PK 327 avkamaevaleaekalke 344
                                   +v+ ma+++ +a k+l++
  gi|14600753|ref|NP_147274.1| 316 SVQWMAKISSRAYKKLAT 333
                                   ************998875 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 !   21.4   0.0   1.9e-08   0.00011      78     176 ..     170     263 ..     146     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-08
                                   GG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH.TSTTEEEEEE-HHHHHH CS
                     HpcH_HpaI  78 le.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa.avegldgvflGaeDlsa 156
                                   le  +d+g++ v v +  +ae +++v +++r+          + r+ a iE   gv+ + eIa a+   dgv+++  Dl +
  gi|14600753|ref|NP_147274.1| 170 LEfFADKGVSHVYVSFARSAEHVEKVRTVVRRLG------LRQARIFAKIEGPSGVSRIGEIAeAS---DGVIIARGDLGM 241
                                   337899*************************999......7899*******************444...6889999***** PP

                                   HTT-TTSTTSHHHH..HHHHHH CS
                     HpcH_HpaI 157 dlgtkrspegtevl..dareri 176
                                      +++ pe +e+   +ar+r 
  gi|14600753|ref|NP_147274.1| 242 HYSLEELPEIQELIvwEARKRY 263
                                   *********9999988888774 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 ?   -2.8   0.0       1.2     7e+03      59      81 ..     177     198 ..     165     238 .. 0.56
   2 !   18.4   0.0   3.2e-07    0.0019       5     104 ..     350     443 ..     347     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                   TEEHHH.HHHHH...TTSHHHHH CS
                          PK_C  59 Gvypvlvekaktaestdellrea 81 
                                   Gv+ v+v  a++ae++++ +r++
  gi|14600753|ref|NP_147274.1| 177 GVSHVYVSFARSAEHVEK-VRTV 198
                                   566666555555444444.2222 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 3.2e-07
                                   HHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHHHHHHHH CS
                          PK_C   5 kaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellreavkva 85 
                                      ve+ae l+    vv++++G+ A +++ ++p    ++  p+++++r +  ++G  p+ v         ++ l++  + +
  gi|14600753|ref|NP_147274.1| 350 LGLVELAESLDSP-LVVYSKTGRFAERLASFKPLKTFYVGVPSREVERVVRHLWGAEPIVVG----DYPYEAGLAKTYEKL 425
                                   5668888888877.789******************************************875....344667788888888 PP

                                   HHTTSS-STSEEEEEE-SS CS
                          PK_C  86 keaglvkkgdevvvtaGtp 104
                                    ++++++ gde vv a ++
  gi|14600753|ref|NP_147274.1| 426 RRENIIH-GDETVVEAAWS 443
                                   8888877.66666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3438.24
//
Query:       gi|118431076|ref|NP_147275.2|  [L=229]
Description: purine phosphoribosyltransferase [Aeropyrum pernix K1]
Scores for 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-15   54.5   0.0    1.5e-14   53.9   0.0    1.3  1  Pribosyltran    Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.045   13.8   0.0      0.094   12.8   0.0    1.6  1  HemN_C          HemN C-terminal domain
       0.15   12.1   0.0       0.36   10.9   0.0    1.7  1  NRho            Rhomboid N-terminal domain
        0.2   12.0   0.0       0.35   11.3   0.0    1.4  1  Linker_histone  linker histone H1 and H5 family


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 !   53.9   0.0   3.3e-18   1.5e-14      20     150 ..      22     149 ..      19     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.3e-18
                                    EEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-..EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEE CS
                   Pribosyltran  20 aeileeyngkpdvvvgiargGvpfakiladeLevp..layvrkvkyrpdgseeaargssdesrlledpagkkVliVDDil 97 
                                    ++ ++e +++pdvv+++ rgG+++a  l d L+v   l + +  ++++ ++ e a+ ++ +     d+ g k l+VDDi+
  gi|118431076|ref|NP_147275.2|  22 SNMIRESGYEPDVVIAVSRGGFVPARLLCDFLDVTnlLSIQSQHWVEAARMAEKAI-LKFP--YRVDLSGLKALLVDDIV 98 
                                    5667778*************************988745666677888888888876.4454..799************** PP

                                    SSSHHHHHHHHHHHCC.-BSEEEEEEEE.E-HHHHHHHHHH-TTS.....EEEEE CS
                   Pribosyltran  98 dtGgTllaalelLkek.gpeevriavlv.dkpateeevdknakrvfslspdnfva 150
                                    dtG Tll a e+++++ +p e+r+a+l    +  ++++d+++ +v     ++ ++
  gi|118431076|ref|NP_147275.2|  99 DTGDTLLLAKEFIEKEwKPGELRVAALQwISSVAKFKPDYYYMEVR----EWAWF 149
                                    ***********665544999*****997688888888888888887....56555 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.094      24      63 ..     185     227 ..     183     229 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                         HemN_C  24 aafeqrfgld...leellaaaleklqeqGLLeldggrlrltpr 63 
                                    +af++ +g++   l  +++ ale+l e+G Le  +g++rl++r
  gi|118431076|ref|NP_147275.2| 185 EAFKEFYGIEpgsLGFYWKLALERLVEKGVLERVDGGYRLSDR 227
                                    578888888888777788999********************98 PP

>> NRho  Rhomboid N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     8e-05      0.36       2      23 ..      73      94 ..      72      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                                   ---EEEEE-TTTTGGGHHHHHH CS
                           NRho  2 savevlrlPlaeDLsglvqlLq 23
                                      ++l++P  +DLsgl +lL 
  gi|118431076|ref|NP_147275.2| 73 AEKAILKFPYRVDLSGLKALLV 94
                                   55689**************996 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.9e-05      0.35      34      64 ..     191     220 ..     160     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.9e-05
                 Linker_histone  34 ykvvdvskfksllkkalkkgvekgelvqpkg 64 
                                    y + ++  +  + k al+++vekg+l+++ g
  gi|118431076|ref|NP_147275.2| 191 YGI-EPGSLGFYWKLALERLVEKGVLERVDG 220
                                    555.6666778899***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 1732.93
//
Query:       gi|118431077|ref|NP_147276.2|  [L=201]
Description: hypothetical protein APE_0492.1 [Aeropyrum pernix K1]
Scores for complete 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-23   82.4   0.0    4.4e-23   82.2   0.0    1.0  1  Nitroreductase  Nitroreductase family
    3.4e-05   23.5   0.2       0.12   11.9   0.1    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 !   82.2   0.0   4.9e-27   4.4e-23       1     169 [.      18     198 ..      18     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 4.9e-27
                                    HHH--B---B-S----HHHHHHHHHHH.............HTS--GGG---EEEEEE..-CCCH......HHHHHHHHHH CS
                 Nitroreductase   1 irkRrSiRkFddepvpkeelekileaa.............rraPsagnlqpwrfvvv.qdkelr......yklaeaalel 60 
                                    ir+RrS R F+ +p++++e+++il                r +Psag lqp++ ++v ++ e +      y+   ++le 
  gi|118431077|ref|NP_147276.2|  18 IRRRRSRRSFSRRPLTLTEVSTILFHVagitglawwggpkRPYPSAGALQPVEAYLVvERVEGLkpglyhYNPSGHCLEM 97 
                                    89**********************98889****988888777***************9999988****888888888888 PP

                                    HHHHHTT-SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                 Nitroreductase  61 llkaeaqaelaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpi 140
                                    l++++   +la +        + q+++a+a++ +v++a + +   k++ r+yry + d+g a +n++L ++alGl+++ +
  gi|118431077|ref|NP_147276.2|  98 LREGKLLGRLADV-------SLGQDHVAEAAAALVLTAVYTRTGSKYGHRSYRYVHWDTGFAGENVYLVCEALGLATVAV 170
                                    8888766666665.......89********************************************************** PP

                                    -GGGGGHHHHHHHHT-S...SEEEEEEEEE CS
                 Nitroreductase 141 ggfdeaaeevrkllglp.deeeivvliavG 169
                                    g+f++++  ++ +l+++ + e ++++++vG
  gi|118431077|ref|NP_147276.2| 171 GAFYDDE--MCGFLEIDcPWEMPMLVFPVG 198
                                    *******..*********999999****99 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   5.6e-05       0.5       2      32 ..      14      44 ..      13      51 .. 0.82
   2 !   11.9   0.1   1.4e-05      0.12      82     114 ..     147     179 ..     136     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 5.6e-05
                                   HHHHHHH--B---B--S---HHHHHHHHH-- CS
                 TM1586_NiRdase  2 lyeaiekRhsvRkYkdealeeelleelkeai 32
                                   ++eai+ R+s+R+++ ++l+ + ++++   +
  gi|118431077|ref|NP_147276.2| 14 VLEAIRRRRSRRSFSRRPLTLTEVSTILFHV 44
                                   78****************9988777776655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHHHHHHHHTT-EEEEES--SST... CS
                 TM1586_NiRdase  82 ekaGYygeqlvLkltalGlgtcWvggtykkkka 114
                                      +G+ ge++ L + alGl+t  vg+ y+ + +
  gi|118431077|ref|NP_147276.2| 147 WDTGFAGENVYLVCEALGLATVAVGAFYDDEMC 179
                                    578**********************99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1609.44
//
Query:       gi|118431078|ref|NP_147277.2|  [L=316]
Description: hypothetical protein APE_0493.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-06   27.3   0.0    2.5e-06   26.9   0.0    1.1  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 !   26.9   0.0   1.4e-10   2.5e-06      74     216 ..      90     229 ..      50     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.4e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHH CS
                          IF-2B  74 eakksliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltake 153
                                    ea+ ++    +++++ +++++   ++ a e + + d+il ++ s+ + +++ +    +  ++V+v+E  P   Grl++  
  gi|118431078|ref|NP_147277.2|  90 EANVDVPGVFEKFVELDRRSRLEAAAKAVEEVRNADRILIVGFSSILEDFITKTLTIG-GVEVYVLEASPAKRGRLLVRA 168
                                    555556666778888899999999*****************************77766.8******************** PP

                                    HHHTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEE CS
                          IF-2B 154 LvqagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvv 216
                                     ++    + +++dsav ++ +     ++    + +++G i+  +G++    lA+e +++ lv 
  gi|118431078|ref|NP_147277.2| 169 ARRRRLKSYYAPDSAVYWLVED-SHSIVTSLYGFAREG-IVVDAGSAAALALARELSVKTLVL 229
                                    *******************999.666666667777777.666777777777788877777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2657.95
//
Query:       gi|118431079|ref|NP_147280.2|  [L=225]
Description: ribonuclease HII [Aeropyrum pernix K1]
Scores for complete 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  145.5   0.0      2e-42  145.3   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 !  145.3   0.0   1.1e-46     2e-42       1     198 []       5     201 ..       5     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 1.1e-46
                                    EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH.HHTTTS-HHHH CS
                      RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeikyaseneinlnei 80 
                                    +G+DEaGrG+++G lvva++ave++r  el+ lgv DSK+Ls+ +r eL ++i   +   +++a    + + ++in+  +
  gi|118431079|ref|NP_147280.2|   5 VGVDEAGRGSLVGDLVVAGFAVEEARLGELQSLGVRDSKQLSPAARVELYREIS-GVGFFTVEAIRPWEIDGENINIL-V 82 
                                    6*****************************************************.44444444443333445666653.5 PP

                                    HHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHH.HHC.CEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHHH CS
                      RNase_HII  81 kaaltlaviklleklgvkvdeilvdgvttpeslkkkleq.iik.ikvtvekkadekyllvaaASiiAkverdeelellkr 158
                                     +a+ + v + +  lgv+++ ++vd  + ++ l  +l    i+ + + ve+kad++y++v+aASi+Akv rd  l+ l+r
  gi|118431079|ref|NP_147280.2|  83 TKAVEEIVSRIVSYLGVHPSLVVVDKYGDVQGLRLALTRlGIEpRSILVEEKADSRYPVVSAASIVAKVVRDARLQVLRR 162
                                    56666667779999***************9999999988534469*********************************** PP

                                    HCSH.--TTSSTTSHHHHHHHHHHHHH.S--TTB-TTSHHH CS
                      RNase_HII 159 kpgtldkgsGyasdektrallkkgats.klpdivrlsfktv 198
                                     +g   +gsGy+sd++tr+++++ ++  + p + r+ + tv
  gi|118431079|ref|NP_147280.2| 163 MYG--VRGSGYPSDPETREWVREVFARgEAPRVIRYTWSTV 201
                                    *98..9*********************99*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.33
# Mc/sec: 2032.92
//
Query:       gi|14600760|ref|NP_147281.1|  [L=357]
Description: hypothetical protein APE_0498 [Aeropyrum pernix K1]
Scores for complete 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   23.2   0.0    7.5e-05   22.4   0.0    1.4  1  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.2e-09   7.5e-05      29     109 ..     158     233 ..     132     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.2e-09
                  RNA_Me_trans  29 enliltslskasleslpeelkslaklelekesveellkelkevkkekvclLDpkaekelspedaeefdvflfGGIlGddpp 109
                                    +l+lt++  ++   ++e l   +k+++ +++ +e+l +   ++ ++v++L p+a++ ls ++  ++d+fl+GGI+    p
  gi|14600760|ref|NP_147281.1| 158 PHLVLTNMDPQTSGWISEVLG-DNKVTISQSKPSEILWS---MDADRVVILRPDAPQPLSGSEVLAADAFLIGGIVDRI-P 233
                                   368999999965554655555.57788888888888866...579******************************9444.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2734.94
//
Query:       gi|118431080|ref|NP_147282.2|  [L=294]
Description: hypothetical protein APE_0500.1 [Aeropyrum pernix K1]
Scores for 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-05   22.6   0.0    8.8e-05   22.1   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0031   17.5   0.7      0.022   14.8   0.7    2.1  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 !   22.1   0.0   9.8e-09   8.8e-05      20     155 ..      54     190 ..      38     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.8e-09
                                    S--S.SS--..SEEEEE-SS--HHHH.GGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT.......TTEEEEEE CS
                  Lactamase_B_2  20 qPve.lrdelppidaVllthaHyDHl.aglltlrelrpkklplyapkgvlavleanfvylaleee.......pavnvhel 90 
                                    q    +r++l++ +  ++th HyDH+  + + l ++r     l+  k++ + ++++  +              +  ++e 
  gi|118431080|ref|NP_147282.2|  54 QALDrARRRLEESNIAIITHYHYDHYlRDEPELYAGR-----LLLAKDINRSINRSQRFRGY--RflvksglVERGRVEY 126
                                    3333467778889999**********77777777743.....55555555555554333222..1234466667778888 PP

                                    -TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---..HHHHHHHC CS
                  Lactamase_B_2  91 dwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip..eeigerlg 155
                                    +    f+l+ ggl+i++   + ++g+ ++++ g++l +ri+ +g +++++ D++     e+++e+l+
  gi|118431080|ref|NP_147282.2| 127 ADSRVFRLE-GGLTIEF-SKPVWHGE-EGTKLGKVLMVRITCEGVSIVFASDVQGPGnnEALEELLK 190
                                    889999997.7999998.58999999.99***********************996555544555554 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.7   2.4e-06     0.022      33      59 ..      48      80 ..      13     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                                   H......HHHHHTSGGGGEEEEE-SBSSHHHHT CS
                    Lactamase_B 33 l......elaalglkpkdvdavilTHlHlDHiG 59
                                   +      +l ++++ +++    i+TH+H+DH+ 
  gi|118431080|ref|NP_147282.2| 48 ElrrleqALDRARRRLEESNIAIITHYHYDHYL 80
                                   0445556889999999999999*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2274.53
//
Query:       gi|14600762|ref|NP_147283.1|  [L=224]
Description: ribosome biogenesis protein [Aeropyrum pernix K1]
Scores for 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-41  140.1   0.0    7.5e-41  139.9   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 !  139.9   0.0   4.2e-45   7.5e-41       1     194 []       3     217 ..       3     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 4.2e-45
                                   EEEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EEE CS
                          EMG1   1 ivLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllqv 65 
                                   iv+ e+s+elv+++                ++   LL+++ h++++++l  ++k++RpDI+H +Ll++ dspL ++gll++
  gi|14600762|ref|NP_147283.1|   3 IVFLECSVELVPRSlwshpqvlksarrygiEPGDLLLDKSLHYNAMAELPAKWKRGRPDILHVALLTTTDSPLYNEGLLRI 83 
                                   78999********999***************************************************************** PP

                                   EEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC.SEEEEE-TTSEE-...... CS
                          EMG1  66 yihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlppgskiillsesaekklvdlee 146
                                   y + ++++l+ev   +R+P++++rF gL++qLLk+ ++++ ege  L+++ +++++++++++ + il+ e++++++   + 
  gi|14600762|ref|NP_147283.1|  84 YFQVYDGRLFEVGTGVRVPKNYERFRGLVAQLLKTERVPPGEGE-ALIRLHSRSLAEFVEREGRFILMWEKGSPTT---TT 160
                                   *******************************************9.****************************775...45 PP

                                   ............EEEE-SSSS.......---HHEEESS.SS---HHHHHHHHHHHCH CS
                          EMG1 147 fv.....vkpvvfvigamskgsvki...dykeeeisis.nypLsaavvcskiltafE 194
                                   +v     ++ + + +g++++g+ k       +e +si+   pL++++v+s+i+ a+E
  gi|14600762|ref|NP_147283.1| 161 YVaaralSTGLPIGVGCFPRGEFKRstlRKASEAYSIMgGAPLKTWGVASRIVYALE 217
                                   555566677899*********55552223333589988689************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1801.88
//
Query:       gi|118431081|ref|NP_147284.2|  [L=143]
Description: hypothetical protein APE_0503.1 [Aeropyrum pernix K1]
Scores for complete 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-50  169.8   3.4    2.2e-50  169.6   3.4    1.0  1  DUF2153   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2153  Uncharacterized protein conserved in archaea (DUF2153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.6   3.4   1.2e-54   2.2e-50       2     123 .]      14     135 ..      13     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 1.2e-54
                        DUF2153   2 LeeWvkeqkelletlkkvekkveeaDRLdlilasraafqhmmrtlkaFdqWLqdPviishmpremLldvketlreilekl 81 
                                    Le+Wv+ qk++le++k+++++v+++DRLdli+++r+af+hm++tlkaFd+WLqdP+i s++pr++Lldv++t+++++e l
  gi|118431081|ref|NP_147284.2|  14 LERWVMLQKAVLENFKNIDSQVRSSDRLDLIIHTRLAFNHMIKTLKAFDDWLQDPFISSNIPRDLLLDVWDTTLKMMELL 93 
                                    9******************************************************************************* PP

                        DUF2153  82 lelDieHtsevrelleklskegklnpllalekeaeeekeerr 123
                                    +elDi+Hts+v++l+e+ s+eg+lnp+l++ k++++++e+rr
  gi|118431081|ref|NP_147284.2|  94 IELDIRHTSQVKNLIEEASREGRLNPILSQLKDIGGWREDRR 135
                                    ************************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1099.59
//
Query:       gi|14600764|ref|NP_147285.1|  [L=136]
Description: hypothetical protein APE_0505 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-17   64.2   0.5    1.6e-17   63.8   0.5    1.2  1  Trm112p         Trm112p-like protein
     0.0004   19.8   2.7      0.068   12.7   1.2    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.059   13.8   0.1       0.19   12.2   0.0    1.7  2  Ribosomal_L33   Ribosomal protein L33
      0.087   13.0   0.5       0.32   11.1   0.1    1.9  2  zf-UDP          Zinc-binding RING-finger
       0.11   12.8   0.1        0.2   12.0   0.1    1.6  1  Mac             Maltose acetyltransferase
       0.13   12.0   0.2       0.13   12.0   0.2    2.7  3  zf-HYPF         HypF finger
        0.3   10.5   3.8        1.6    8.3   0.3    2.5  2  zf-ribbon_3     zinc-ribbon domain
       0.47   10.5   5.0         15    5.7   1.7    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
          1    9.4   5.4        9.5    6.3   1.0    2.4  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        4.4    7.7   9.2         18    5.7   0.1    3.3  2  zinc_ribbon_9   zinc-ribbon


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 !   63.8   0.5   8.8e-21   1.6e-17       2      68 .]       4      88 ..       3      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 8.8e-21
                                  TGGCCC-B-TTTHHC--HHHHHHHHH.TT---.S-SS----S...................CHHTTEECCCCEEEETTTTEEE CS
                       Trm112p  2 llllniLaCpackgpLdwealvevaa.lglne.lpkekpedy...................ellleldieegeLvCpncgraY 63
                                  + ++++LaCp c++p     +++v++ ++ ++ +++e+ +++                   + ++e dieeg+LvCp+cgr+Y
  gi|14600764|ref|NP_147285.1|  4 YYHIEMLACPECRNPR---LILYVVReKRGAMpPQPERLKCRrwcylfdrpastvplstcvSSCVERDIEEGVLVCPACGRWY 83
                                  6789**********88...799999988899989999999999******************99******************** PP

                                  EEETT CS
                       Trm112p 64 pIkdG 68
                                  pI +G
  gi|14600764|ref|NP_147285.1| 84 PIVEG 88
                                  ***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 !    6.3   0.0    0.0039       6.9       2      18 ..      11      30 ..      10      32 .. 0.75
   2 !   12.7   1.2   3.8e-05     0.068       6      26 ..      60      80 ..      59      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0039
                                  EETTTTCEE.C..HEETSTT CS
                  TF_Zn_Ribbon  2 kCPnCgstn.l..veDperg 18
                                   CP+C +++ +  v+ ++rg
  gi|14600764|ref|NP_147285.1| 11 ACPECRNPRlIlyVVREKRG 30
                                  5******9944777767666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.8e-05
                                  TTCEECHEETSTTCEEESSSS CS
                  TF_Zn_Ribbon  6 CgstnlveDpergelvCtdCG 26
                                  C s+ +++D e+g lvC++CG
  gi|14600764|ref|NP_147285.1| 60 CVSSCVERDIEEGVLVCPACG 80
                                  778889**************9 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.19       4      34 ..       9      45 ..       7      48 .. 0.89
   2 ?   -2.1   0.0       3.1   5.6e+03       5      12 ..      74      81 ..      73      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                  EEEET.........EEEEETT.....--S--EEEEEE CS
                 Ribosomal_L33  4 tLeCtecksrn...Ytttknkkn...tperLelkKYc 34
                                  +L+C ec++ +   Y+++ ++ +   +perL+ ++ c
  gi|14600764|ref|NP_147285.1|  9 MLACPECRNPRlilYVVREKRGAmppQPERLKCRRWC 45
                                  69*******77788***999977788********999 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                  EEET.... CS
                 Ribosomal_L33  5 LeCtecks 12
                                  L+C  c++
  gi|14600764|ref|NP_147285.1| 74 LVCPACGR 81
                                  77777765 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.77   1.4e+03      52      57 ..      11      16 ..       7      30 .. 0.84
   2 ?   11.1   0.1   0.00018      0.32      35      73 ..      58      96 ..      51     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.77
                        zf-UDP 52 sCPqCk 57
                                  +CP+C+
  gi|14600764|ref|NP_147285.1| 11 ACPECR 16
                                  689887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00018
                        zf-UDP 35 fpvcrpcyeyerkdgnqsCPqCktrykrlkgsprvegde 73
                                  + ++ +c e +  +g  +CP C   y   +g p +  d+
  gi|14600764|ref|NP_147285.1| 58 STCVSSCVERDIEEGVLVCPACGRWYPIVEGIPVMMDDK 96
                                  57999******************9999999998766664 PP

>> Mac  Maltose acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00011       0.2      19      36 ..      37      52 ..      35     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHHHHTSTTT CS
                           Mac 19 eRlrarelcrryNqtrps 36
                                  eRl++r++c+ +    p+
  gi|14600764|ref|NP_147285.1| 37 ERLKCRRWCYLFDR--PA 52
                                  8***********93..44 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   7.4e-05      0.13      15      27 ..       3      15 ..       1      23 [. 0.83
   2 ?    1.7   0.1      0.13   2.3e+02      24      28 ..      76      80 ..      74      85 .. 0.70
   3 ?   -2.9   0.4       3.4   6.2e+03       8      14 ..      96     102 ..      95     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.4e-05
                                  TTTT-TT---TTT CS
                       zf-HYPF 15 RRfhaqfisCtnC 27
                                  R++h++  +C++C
  gi|14600764|ref|NP_147285.1|  3 RYYHIEMLACPEC 15
                                  9************ PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                  -TTTS CS
                       zf-HYPF 24 CtnCG 28
                                  C+ CG
  gi|14600764|ref|NP_147285.1| 76 CPACG 80
                                  66666 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.4
                                   HHC-TTS CS
                       zf-HYPF   8 Eykdpld 14 
                                   +y+dp+ 
  gi|14600764|ref|NP_147285.1|  96 KYRDPER 102
                                   6999985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.044        79       2       8 ..       9      15 ..       8      18 .. 0.69
   2 ?    8.3   0.3   0.00089       1.6      12      23 ..      69      80 ..      62      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                   zf-ribbon_3  2 tvrCPnC 8 
                                  +  CP+C
  gi|14600764|ref|NP_147285.1|  9 MLACPEC 15
                                  5567777 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00089
                   zf-ribbon_3 12 lssddnvCpyCG 23
                                  +++++ vCp CG
  gi|14600764|ref|NP_147285.1| 69 IEEGVLVCPACG 80
                                  578999999999 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.7    0.0081        15      20      43 ..      11      45 ..       6      46 .. 0.86
   2 ?    5.6   0.1    0.0085        15      19      25 ..      74      80 ..      70      87 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0081
                 Zn_Tnp_IS1595 20 vCPhCgsr..kayrikt........rglfqCke.C 43
                                   CP C +    +y ++         +++++C++ C
  gi|14600764|ref|NP_147285.1| 11 ACPECRNPrlILYVVREkrgamppqPERLKCRRwC 45
                                  6******9777788888999999999999999977 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0085
                 Zn_Tnp_IS1595 19 fvCPhCg 25
                                   vCP+Cg
  gi|14600764|ref|NP_147285.1| 74 LVCPACG 80
                                  58****9 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.015        26      18      26 ..       8      16 ..       4      17 .. 0.81
   2 ?    6.3   1.0    0.0053       9.5      18      26 ..      72      80 ..      56      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                PhnA_Zn_Ribbon 18 allvCpeCa 26
                                  ++l CpeC 
  gi|14600764|ref|NP_147285.1|  8 EMLACPECR 16
                                  578899995 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0053
                PhnA_Zn_Ribbon 18 allvCpeCa 26
                                   +lvCp C+
  gi|14600764|ref|NP_147285.1| 72 GVLVCPACG 80
                                  69******7 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.01        18      22      29 ..      10      17 ..       3      20 .. 0.79
   2 ?    0.3   5.9      0.48   8.6e+02       4      28 ..      44      80 ..      42      89 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
                 zinc_ribbon_9 22 vlCPhCgg 29
                                   +CP+C++
  gi|14600764|ref|NP_147285.1| 10 LACPECRN 17
                                  47****97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                 zinc_ribbon_9  4 WChqCdrfVsvspdedsd............vlCPhCg 28
                                  WC+  dr  s  p ++               +CP Cg
  gi|14600764|ref|NP_147285.1| 44 WCYLFDRPASTVPLSTCVsscverdieegvLVCPACG 80
                                  5665555555555544444444444556642599997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1019.90
//
Query:       gi|14600765|ref|NP_147286.1|  [L=218]
Description: endonuclease V [Aeropyrum pernix K1]
Scores for complete 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  173.2   0.1    5.8e-51  173.0   0.1    1.1  1  Endonuclease_5  Endonuclease V
  ------ inclusion threshold ------
      0.014   14.8   0.1      0.024   14.1   0.0    1.5  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 !  173.0   0.1   6.4e-55   5.8e-51      22     196 ..       3     171 ..       1     172 [. 0.92

  Alignments for each domain:
  == domain 1  score: 173.0 bits;  conditional E-value: 6.4e-55
                                   EEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEEEEC-SSSSTTS CS
                Endonuclease_5  22 GvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkpdvllvDGnGiaHprr 102
                                   G+D+s++ ++    v+a+v+++l++le v+++v ++++ +pYipg+LaFREl v+  a ++l+++ dv++vDG+GiaHprr
  gi|14600765|ref|NP_147286.1|   3 GLDASYSAKDG-VGVGAAVLISLETLEPVDCRVYISRVCIPYIPGLLAFRELAVMAPAAAALSAEADVVMVDGHGIAHPRR 82 
                                   99****54444.56******************************************************************* PP

                                   --HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEECSS-HHHHHHHHHHCS CS
                Endonuclease_5 103 lGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGhrisletalelvlall 183
                                   +G+Ash+Gv+l+ p+iGvaK++lvg++ e     g +  +v++ge ++++l t+ +   +yvS+Ghri+le+a ++++a++
  gi|14600765|ref|NP_147286.1|  83 FGIASHVGVILERPSIGVAKKKLVGTLVEG---PGGM-YVVQDGERLAIVLGTRPR--EVYVSPGHRITLEEAASIARATI 157
                                   *************************77754...3444.45668*********9986..9********************** PP

                                   -.T-SS-HHHHHHH CS
                Endonuclease_5 184 k.kyrlPepirqAd 196
                                   + +  +Pep+r+Ad
  gi|14600765|ref|NP_147286.1| 158 RpGGWMPEPTRLAD 171
                                   96779********9 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0      0.95   8.5e+03      66      77 ..      67      78 ..      62      79 .. 0.74
   2 ?   14.1   0.0   2.6e-06     0.024     139     182 ..     132     177 ..      87     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.95
                                  EEEEEESSSEET CS
                         DUF99 66 irvvlldGitia 77
                                   +vv++dG  ia
  gi|14600765|ref|NP_147286.1| 67 ADVVMVDGHGIA 78
                                  678999997766 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.6e-06
                                   ....EEEEE.ESS-HHHHHHHHHHC-SSS.SS-HHHHHHHHHHHHH CS
                         DUF99 139 tgeelyvra.vGieleeaaklvrkltleg.riPEPlRvAhliAsal 182
                                   + +e+yv   + i+leeaa++ r++++ g  +PEP R+A++i++al
  gi|14600765|ref|NP_147286.1| 132 RPREVYVSPgHRITLEEAASIARATIRPGgWMPEPTRLADVISKAL 177
                                   4566777653789***********99887369**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1725.87
//
Query:       gi|118431082|ref|NP_147287.2|  [L=203]
Description: proteasome beta subunit precursor [Aeropyrum pernix K1]
Scores for 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-52  176.9   0.0    3.4e-52  176.7   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 !  176.7   0.0   1.9e-56   3.4e-52       3     189 ..       4     184 ..       2     185 .. 0.98

  Alignments for each domain:
  == domain 1  score: 176.7 bits;  conditional E-value: 1.9e-56
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                     G t++Gi+ +dgvvlaadkr+++g  +ls++ ++Kif i+d+ig+afaGl++D+  lvr+++ +++l +l++g+p +v+
  gi|118431082|ref|NP_147287.2|   4 AGATALGIRVEDGVVLAADKRMSYGGFILSRN-FKKIFVINDRIGIAFAGLYGDMGGLVRIVEGQMRLASLETGKPATVR 82 
                                    599*************************9999.9********************************************** PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                        +va+ l++ ++++++ pf v+++++g+d  g+p+Ly +dp Gs+iee+ +va+G+g++ a ++le  yk  ++lee
  gi|118431082|ref|NP_147287.2|  83 ----NVAKFLSSLLYSYKFFPFNVEAIVGGIDPGGEPKLYVLDPLGSIIEED-YVAAGTGATTAFGLLEHVYKRGMSLEE 157
                                    ....***********************************************6.*************************** PP

                                    HHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                     Proteasome 163 avelavkalkealerdklsgknievav 189
                                    a++ av+al++++ rd+ +g++i+v v
  gi|118431082|ref|NP_147287.2| 158 AKKAAVEALRASMARDAGTGDGIDVLV 184
                                    ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1673.57
//
Query:       gi|118431083|ref|NP_147288.2|  [L=183]
Description: hypothetical protein APE_0508.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-08   33.5   1.1    3.4e-08   32.9   1.1    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0043   16.7   0.8     0.0067   16.1   0.8    1.2  1  A2L_zn_ribbon    A2L zinc ribbon domain
  ------ inclusion threshold ------
      0.017   14.5   3.1       0.23   10.9   3.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.024   14.3   1.8       0.04   13.6   1.8    1.3  1  Ribosomal_S27e   Ribosomal protein S27
      0.034   14.2   0.2      0.056   13.5   0.2    1.3  1  DZR              Double zinc ribbon
      0.097   12.4   0.7       0.24   11.1   0.7    1.6  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.42   11.2   4.9        4.4    7.9   0.1    2.7  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        2.4    7.9   4.7       0.89    9.3   1.3    1.9  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   1.1   1.5e-11   3.4e-08       3      36 ..       8      41 ..       6      42 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.5e-11
                                   ETTTTCEECHEETSTTCEEESSSSBEEEECCCCC CS
                   TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednside 36
                                   C +Cgst++v+ + +ge+vC++CG+Vl ++ id 
  gi|118431083|ref|NP_147288.2|  8 CSYCGSTMVVTLHTEGEIVCGSCGAVLAEQLIDD 41
                                   ********9999********************95 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 !   16.1   0.8     3e-06    0.0067       6      30 ..       8      33 ..       7      35 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3e-06
                  A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                   Cs+Cg+ +++   + g+ vC  Cga+
  gi|118431083|ref|NP_147288.2|  8 CSYCGSTMVVTlHTEGEIVCGSCGAV 33
                                   **********999***********97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5    0.0089        20       5      10 ..       8      13 ..       3      15 .. 0.68
   2 ?   10.9   3.2    0.0001      0.23       4      26 .]       7      34 ..       6      34 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0089
                    zf-ribbon_3  5 CPnCGa 10
                                   C++CG+
  gi|118431083|ref|NP_147288.2|  8 CSYCGS 13
                                   666664 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                    zf-ribbon_3  4 rCPnCGa.pl....ssddnvCpyCGtkl 26
                                   +C++CG+  +    +++ +vC +CG++l
  gi|118431083|ref|NP_147288.2|  7 SCSYCGStMVvtlhTEGEIVCGSCGAVL 34
                                   699999987557778**********997 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   1.8e-05      0.04      10      38 ..       8      36 ..       7      37 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                   -TTTS-EEEEESS-SS-EEESSSTCEEEE CS
                 Ribosomal_S27e 10 CpdCenetvvFshaatvvkCisCgkvLve 38
                                   C  C+ + vv  h +  + C sCg vL+e
  gi|118431083|ref|NP_147288.2|  8 CSYCGSTMVVTLHTEGEIVCGSCGAVLAE 36
                                   999************************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   2.5e-05     0.056      11      38 ..       4      34 ..       1      38 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                            DZR 11 darfCseCgtklkavaa...edrCpsCgekv 38
                                   +a  Cs+Cg+++  + +   e++C sCg+ +
  gi|118431083|ref|NP_147288.2|  4 RAGSCSYCGSTMVVTLHtegEIVCGSCGAVL 34
                                   5667999999987666688899999999875 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7   0.00011      0.24       6      29 ..       8      32 ..       8      34 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                  zf-NADH-PPase  6 CgrCGaptepaeg.gwarvCpaCgl 29
                                   C+ CG+ +++  + +   vC +Cg+
  gi|118431083|ref|NP_147288.2|  8 CSYCGSTMVVTLHtEGEIVCGSCGA 32
                                   **********9888*********97 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 ?    7.9   0.1     0.002       4.4       8      18 ..       8      18 ..       7      24 .. 0.80
   2 ?    4.9   0.4     0.017        37       6      15 ..      25      34 ..      22      52 .. 0.87
   3 ?   -3.0   0.0       4.9   1.1e+04      25      35 ..     131     141 ..     118     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                Zn_ribbon_recom  8 CgeCGspmtrr 18
                                   C +CGs+m+++
  gi|118431083|ref|NP_147288.2|  8 CSYCGSTMVVT 18
                                   ********995 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.017
                Zn_ribbon_recom  6 lrCgeCGspm 15
                                   ++Cg CG+ +
  gi|118431083|ref|NP_147288.2| 25 IVCGSCGAVL 34
                                   89*****976 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.9
                Zn_ribbon_recom  25 hyYrCstyrrk 35 
                                    + Yr ++y ++
  gi|118431083|ref|NP_147288.2| 131 ISYRLRGYSKS 141
                                    45666666554 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 ?    9.3   1.3    0.0004      0.89       6      30 ..       7      33 ..       2      34 .. 0.87
   2 ?   -0.7   0.1      0.55   1.2e+03      25      32 .]      76      83 ..      76      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0004
                        zf-RRN7  6 pCgvCgcr.sftl.ddGfyyCrrChtq 30
                                    C  Cg++  +tl  +G  +C +C+ +
  gi|118431083|ref|NP_147288.2|  7 SCSYCGSTmVVTLhTEGEIVCGSCGAV 33
                                   6******55****************87 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.55
                        zf-RRN7 25 rrChtqeg 32
                                   rr+h+++g
  gi|118431083|ref|NP_147288.2| 76 RRGHVVVG 83
                                   7****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1474.69
//
Query:       gi|118431084|ref|NP_147290.2|  [L=341]
Description: GTP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-16   59.9   1.7    1.5e-15   57.6   1.7    2.0  1  NOG1_N     NOG1 N-terminal helical domain
    4.8e-16   58.9   0.0    8.4e-16   58.1   0.0    1.4  1  MMR_HSR1   50S ribosome-binding GTPase
    1.3e-12   47.3   0.0    2.9e-12   46.2   0.0    1.6  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    1.8e-08   34.0   0.0    3.2e-08   33.2   0.0    1.5  1  FeoB_N     Ferrous iron transport protein B
    0.00026   21.4   0.7    0.00098   19.5   0.1    2.4  2  AAA_16     AAA ATPase domain
    0.00054   20.2   0.4     0.0025   18.1   0.0    2.4  2  AAA_28     AAA domain
     0.0012   19.4   0.9     0.0077   16.8   0.0    2.5  2  AAA_18     AAA domain
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.016   14.5   0.0    1.3  1  AIG1       AIG1 family
      0.013   15.5   0.4        2.4    8.2   0.2    2.4  2  Dynamin_N  Dynamin family
      0.014   14.8   0.0       0.52    9.7   0.0    2.3  2  TniB       Bacterial TniB protein
      0.019   15.1   0.7      0.078   13.1   0.0    2.3  2  AAA_33     AAA domain
      0.043   13.3   0.0       0.14   11.6   0.0    1.8  2  KTI12      Chromatin associated protein KTI12
      0.049   14.0   0.7       0.15   12.5   0.0    2.3  2  AAA_17     AAA domain
      0.072   13.1   0.0        1.7    8.7   0.0    2.5  2  AAA_14     AAA domain
      0.085   12.4   0.0          1    8.9   0.0    2.3  2  cobW       CobW/HypB/UreG, nucleotide-binding domain
      0.089   11.8   0.0       0.19   10.8   0.0    1.5  1  T2SSE      Type II/IV secretion system protein
      0.091   12.7   0.0       0.21   11.5   0.0    1.6  1  NTPase_1   NTPase
      0.095   12.5   0.0       0.19   11.5   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain
       0.11   12.8   0.1       0.45   10.8   0.0    2.0  2  AAA_22     AAA domain


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   1.7   1.6e-18   1.5e-15       7     160 .]      13     158 ..       9     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.6e-18
                         NOG1_N   7 vptseelidkalrrakraakttkkkknei...krlrnlearkvrtasntlsdkLeeivkkfPn.ldelhpFyrelldvlv 82 
                                    vpt +e+++++ rr  r a++    ++ei   +r+r++ +++            +++v++  + ld lhpF+rel+++  
  gi|118431084|ref|NP_147290.2|  13 VPTYDEILERIGRRPRRRARRRAAYEEEIellARVRDIVISR------------TDFVREVARlLDGLHPFHRELVEIEF 80 
                                    788888888888888888877777777763334444444444............4455554441799************* PP

                         NOG1_N  83 dkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpaiD 160
                                    d+  ++++ + ++ ark+++ + ++y  +l +++++kea++l rea gr+ s++k+ +  l+ L+ +   + +LpaiD
  gi|118431084|ref|NP_147290.2|  81 DRRDVSSAVSCISRARKMTDRLMEKYKVLLLASESPKEARALAREARGRILSLYKRCSRGLEVLRSLMVFMHRLPAID 158
                                    *****************************************************************************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 !   58.1   0.0   8.9e-19   8.4e-16       2     114 .]     164     284 ..     163     284 .. 0.72

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 8.9e-19
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH.HHHHHHHHHHC.T.SE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek.glgkaflalee.a.dl 78 
                                    +++ G p +GKStL++  +++k +v+d+p+tT++i  g+++ ++ ++++vDtpGl++++ ee   ++++ +a  +    +
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSRAKPKVADYPFTTKQIHIGHFEAGEGRVQVVDTPGLLDRSLEEMnPVERRAAAALRlLdGA 243
                                    7899*************************************8889*********99744444455555555555545356 PP

                                    EEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                       MMR_HSR1  79 illvvdaseeklkpldeeleellee......akkplilvlnk 114
                                    +l+++d + + +  ld++   l  +      +++++ +v+nk
  gi|118431084|ref|NP_147290.2| 244 VLFLFDPRPDAYMGLDRQASLLE-NtvaklvTGRRIYVVVNK 284
                                    999**977444444444332221.113335567888888887 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 !   46.2   0.0     3e-15   2.9e-12       2      58 .]     229     286 ..     228     286 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3e-15
                           NOG1   2 IEkqAiaALkhladavlFllDpseecgysleeQlsLlee.ikelfankpvivvlnKiD 58 
                                    +E++A aAL+ l++avlFl+Dp +++++ l+ Q sLle+ + +l+  ++++vv+nK D
  gi|118431084|ref|NP_147290.2| 229 VERRAAAALRLLDGAVLFLFDPRPDAYMGLDRQASLLENtVAKLVTGRRIYVVVNKED 286
                                    7************************************8737778888*********88 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 !   33.2   0.0   3.4e-11   3.2e-08       2      68 ..     163     231 ..     162     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 3.4e-11
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----..SSSSSSSHHHH CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi..Yslsayseeek 68 
                                    t+++ G p +Gk+tl+ +++ ak kv+ +p +t + + g+++  + +v++vD PG    sl++++  e+
  gi|118431084|ref|NP_147290.2| 163 TIIVSGPPSSGKSTLVKNVSRAKPKVADYPFTTKQIHIGHFEAGEGRVQVVDTPGLldRSLEEMNPVER 231
                                    68899*************************************999**********83335666665555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       1.1   1.1e+03     141     141 ..      80      80 ..      13     154 .. 0.50
   2 !   19.5   0.1     1e-06   0.00098      19      52 ..     156     199 ..     139     331 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                         AAA_16 141 l 141
                                    +
  gi|118431084|ref|NP_147290.2|  80 F 80 
                                    1 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1e-06
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd...........g 52 
                                    + +++++ +++sG++ +GKs+lv+ +  +++ +           +
  gi|118431084|ref|NP_147290.2| 156 AIDPGSPTIIVSGPPSSGKSTLVKNVS-RAKPKvadypfttkqiH 199
                                    34445599*****************99.56666444444433332 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       2.8   2.7e+03     122     147 ..      21      46 ..       8      82 .. 0.57
   2 !   18.1   0.0   2.6e-06    0.0025       2      79 ..     164     241 ..     163     318 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                         AAA_28 122 dddgeRredleereaiderlrealre 147
                                    ++ g R+ + ++r+a +e  +e+l +
  gi|118431084|ref|NP_147290.2|  21 ERIGRRPRRRARRRAAYEEEIELLAR 46 
                                    44444444333333333333333332 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.6e-06
                         AAA_28   2 ivitGgestGKTtlleaLaargypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcD 79 
                                    i+++G++s+GK+tl+++ ++ + +v   p +  +i   + + ge+  + v d   + +r lee    e++ aa  + ++D
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSRAKPKVAdyPFTTKQIHIGHFEAGEGRVQVV-DTPGLLDRSLEEMNPVERR-AAAALRLLD 241
                                    89*****************9977766546666667667777777777776.4444444445443322222.233333444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.3       2.3   2.2e+03     103     127 ..      16      42 ..      10      45 .. 0.76
   2 !   16.8   0.0   8.2e-06    0.0077       1      53 [.     164     226 ..     164     308 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                         AAA_18 103 peelleRlekRgyeeakik..eneeae 127
                                    ++e leR+ +R ++ a+++   +ee+e
  gi|118431084|ref|NP_147290.2|  16 YDEILERIGRRPRRRARRRaaYEEEIE 42 
                                    38999*******999998766555555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.2e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........gvnlrdvakenglllevdpe.aldeskrld 53 
                                    I+++G+p +GK+tl k++s+   ++         +++++  + +g +  vd +  ld+s+++ 
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSRAKpKVadypfttkQIHIGHFEAGEGRVQVVDTPgLLDRSLEEM 226
                                    9*****************999655566666666444444333333333333333333333333 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.7e-05     0.016       2     139 ..     163     298 ..     162     322 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                    EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCC.HHCHHHHHHHHHHHC CS
                           AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvs.adkiskeivrcllls 80 
                                    ti++ G   +GkS+ + ++ + k           tk+ +  + +  + +++V+DTPgl+d s +  + +++     l l 
  gi|118431084|ref|NP_147290.2| 163 TIIVSGPPSSGKSTLVKNVSRAKPKVAD--YPFTTKQIHIGHFEAGEGRVQVVDTPGLLDRSLEeMNPVERRAAAALRLL 240
                                    5677777777777776666555443222..3445666677777888899***********99751556666555555554 PP

                                    TT-ESEEEEEEETTB-SHHHHHHHHHHHHHHCGGGGGGEEEEEEEGGGGTTCC.HHHHHH CS
                           AIG1  81 eegihalllvlslgrfteedekalktlkelFGekilkylivvftrkddledds.ledyls 139
                                     +g   +l++ + + +   d++a + l++   + ++   i v  +k+d+ d++ le+ ++
  gi|118431084|ref|NP_147290.2| 241 -DGAVLFLFDPRPDAYMGLDRQA-SLLENTVAKLVTGRRIYVVVNKEDAVDRGrLEEAVA 298
                                    .4455555555555777777775.678888888888888888888888777776777766 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0025       2.4       1      22 [.     164     185 ..     164     202 .. 0.75
   2 ?    5.5   0.0     0.017        16      90     122 ..     197     229 ..     187     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0025
                                    EEEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlged 22 
                                    i+v G  SsGKS+++ ++ +++
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSRAK 185
                                    7899************998877 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                                    -EEEEEEETTS-SEEEEE---B-SSSGTTSHHH CS
                      Dynamin_N  90 villkilsllvkgltlvDlPGldsvnkrdqelv 122
                                     i++  ++  + ++ +vD+PGl ++  ++++ v
  gi|118431084|ref|NP_147290.2| 197 QIHIGHFEAGEGRVQVVDTPGLLDRSLEEMNPV 229
                                    5666667778899*********98877776655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.072        68      87     119 ..      16      48 ..      11      73 .. 0.92
   2 ?    9.7   0.0   0.00055      0.52      19      64 ..     143     190 ..     126     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.072
                           TniB  87 yaaiLealgaplkararvskleqqvlrllrelk 119
                                    y++iLe++g + + rar  +++++ ++ll +++
  gi|118431084|ref|NP_147290.2|  16 YDEILERIGRRPRRRARRRAAYEEEIELLARVR 48 
                                    99**************************99875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00055
                           TniB  19 ilerLeeLleypkrkrm..pnlllvGdsnnGKtmivekFarlhppekd 64 
                                    +l++L   +++ ++ ++  p +++ G++  GK+++v++ +r +p+  d
  gi|118431084|ref|NP_147290.2| 143 VLRSLMVFMHRLPAIDPgsPTIIVSGPPSSGKSTLVKNVSRAKPKVAD 190
                                    33444333333333333339999*******************998766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       3.6   3.4e+03     109     134 ..      17      42 ..       9      51 .. 0.64
   2 ?   13.1   0.0   8.3e-05     0.078       2      24 ..     164     186 ..     164     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.6
                         AAA_33 109 etlkeRlakRaangddrsevpeeald 134
                                    +++ eR+ +R +++ +r  + ee ++
  gi|118431084|ref|NP_147290.2|  17 DEILERIGRRPRRRARRRAAYEEEIE 42 
                                    56667777777766555555555554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.3e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg 24 
                                    +++ G+p sGKstl++++ ++ +
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSRAKP 186
                                    6899*************998876 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.14       2      24 ..     162     184 ..     161     214 .. 0.87
   2 ?   -1.4   0.0       1.4   1.3e+03     234     263 ..     266     293 ..     250     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                    .EEEEE--TTSSHHHHHHHHHHH CS
                          KTI12   2 pLvvltGlPssGKstrakeLaka 24 
                                    p ++++G PssGKst++k++++a
  gi|118431084|ref|NP_147290.2| 162 PTIIVSGPPSSGKSTLVKNVSRA 184
                                    679**************998765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                    ...HHHHHHHHHHHHHHHT.TSSS--HHHH CS
                          KTI12 234 kltlaeLsrlrrqFvklnkaklenvdeeki 263
                                    + t+a+L   rr +v +nk  +  vd  ++
  gi|118431084|ref|NP_147290.2| 266 ENTVAKLVTGRRIYVVVNK--EDAVDRGRL 293
                                    4589999999****99999..666776665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.4       5.4   5.1e+03     113     132 ..      17      38 ..      11      42 .. 0.52
   2 ?   12.5   0.0   0.00016      0.15       2      66 ..     168     238 ..     167     307 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.4
                                    HHHHHHHHHH.TTST-.TS-SH CS
                         AAA_17 113 eeilerrlkd.rtrgr.dddne 132
                                    +eiler  ++ r r r     e
  gi|118431084|ref|NP_147290.2|  17 DEILERIGRRpRRRARrRAAYE 38 
                                    4666666555544444233333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                                    E-TTSSHHHHHHHHHH.............HHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHH CS
                         AAA_17   2 GgPGsGKgtqceklve.............kygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekia 66 
                                    G+P sGK+t+++++ +             ++++ h++aG+   +++   gl +++ +em+         + ++aa++++
  gi|118431084|ref|NP_147290.2| 168 GPPSSGKSTLVKNVSRakpkvadypfttkQIHIGHFEAGEGRVQVVDTPGLlDRSLEEMNP--------VERRAAAALR 238
                                    9*************86666666666666578**********99999999985555565543........3334444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.28   2.6e+02      81     119 ..      97     132 ..      83     135 .. 0.76
   2 ?    8.7   0.0    0.0018       1.7       3      27 ..     162     186 ..     160     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.28
                         AAA_14  81 kalkslvdegknldvivtGSnskllskeiatslagrvae 119
                                    k+  +l+   ++++v++  S s    + +a + +gr+ +
  gi|118431084|ref|NP_147290.2|  97 KMTDRLM---EKYKVLLLASESPKEARALAREARGRILS 132
                                    3333444...4679*********************9875 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0018
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell 27 
                                    + ++++G+  +GK+tl+k++ + + 
  gi|118431084|ref|NP_147290.2| 162 PTIIVSGPPSSGKSTLVKNVSRAKP 186
                                    5789**************9987655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011         1       1      23 [.     162     184 ..     162     190 .. 0.85
   2 ?    0.6   0.0      0.39   3.7e+02      17      48 ..     265     295 ..     261     310 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                    EEEEEEESTTCCHHHHHHHHHCT CS
                           cobW   1 pvtvltGflGsGKTtLlnhllen 23 
                                    p+++++G++ sGK+tL++++ + 
  gi|118431084|ref|NP_147290.2| 162 PTIIVSGPPSSGKSTLVKNVSRA 184
                                    6899**************99754 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.39
                                    HHHHH.CT--SS-EEEEESS-SSCHCCCCCCHC CS
                           cobW  17 lnhll.enraglklavivNefgevsiDaellre 48 
                                    l++++ +   g+++ v+vN     ++D+ +l+e
  gi|118431084|ref|NP_147290.2| 265 LENTVaKLVTGRRIYVVVNKED--AVDRGRLEE 295
                                    5555545555566666666444..444444433 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 ?   10.8   0.0    0.0002      0.19     131     149 ..     163     181 ..     156     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                          T2SSE 131 lilvsGgTgsGKttllyal 149
                                    +i+vsG+ +sGK+tl+  +
  gi|118431084|ref|NP_147290.2| 163 TIIVSGPPSSGKSTLVKNV 181
                                    79************98655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.21       2      21 ..     164     183 ..     163     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                    EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                    ++++Gpp +GK+Tlvk+v++
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSR 183
                                    89***************987 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   0.00021      0.19      19      39 ..     157     178 ..     149     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                         AAA_29  19 idlkg.atlltGpsGsGKSTll 39 
                                    id+ + +++++Gp  sGKSTl+
  gi|118431084|ref|NP_147290.2| 157 IDPGSpTIIVSGPPSSGKSTLV 178
                                    6666778999***********8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.4   2.2e+03      54      66 ..      55      67 ..      16     141 .. 0.64
   2 ?   10.8   0.0   0.00047      0.45       8      33 ..     164     189 ..     160     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.4
                         AAA_22 54 kdllrellralgl 66
                                   +d+ re++r l+ 
  gi|118431084|ref|NP_147290.2| 55 TDFVREVARLLDG 67
                                   4444444444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00047
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeea 33 
                                    ++v G++ +GK+tl++++ + ++++a
  gi|118431084|ref|NP_147290.2| 164 IIVSGPPSSGKSTLVKNVSRAKPKVA 189
                                    89****************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):              19  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2411.95
//
Query:       gi|118431085|ref|NP_147291.2|  [L=361]
Description: RNA 3'-terminal-phosphate cyclase [Aeropyrum pernix K1]
Scores for complete 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-76  255.0   0.0    5.5e-76  254.6   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    2.5e-19   69.7   0.1    5.8e-19   68.5   0.1    1.6  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d
  ------ inclusion threshold ------
       0.13   12.2   0.0        0.2   11.5   0.0    1.2  1  DMAP1       DNA methyltransferase 1-associated protein 1 (DMA


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 !  254.6   0.0   9.2e-80   5.5e-76       1     216 [.      13     333 ..      13     337 .. 0.97

  Alignments for each domain:
  == domain 1  score: 254.6 bits;  conditional E-value: 9.2e-80
                                    STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikageyev 80 
                                    +gegGgqiLRta+aL+a++g+p+rI nIRa+R+ PGLr+qhltavr++a+i++++++gae+gst+leF+Pg++++g+y++
  gi|118431085|ref|NP_147291.2|  13 MGEGGGQILRTAVALAAVLGRPLRIVNIRAKRRPPGLRPQHLTAVRAVAAISGGRLRGAEVGSTSLEFTPGRVRGGRYRF 92 
                                    58****************************************************************************** PP

                                    EEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC  81 digtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGevel 160
                                    d+gtAGs++l++q+l pll+++++p+e++l+GgT+v++ap++dy+++v++++l+ +g +e+e+++ +rG+yp+GgG+v++
  gi|118431085|ref|NP_147291.2|  93 DVGTAGSVALIIQALAPLLAYSDSPVEVELTGGTDVPMAPTIDYMREVFASILAMLG-YEIEIRVLRRGHYPRGGGRVVV 171
                                    *********************************************************.8********************* PP

                                    EEE-.-S.---EB................................................................... CS
                                    xxxxxxx.xxxxx................................................................... RF
                            RTC 161 evepskk.lkpie................................................................... 172
                                    +v+ ++  +++ +                                                                   
  gi|118431085|ref|NP_147291.2| 172 RVPDPPGgFRARSfvergplkgvyvrshavklpgsiaerqarsaaslvrerlgvdpiveieaykphrdphlgpgtgvlvw 251
                                    **6655446666688***************************************************************** PP

                                    ......................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHH CS
                                    ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC 173 ......................................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieq 214
                                                                          a++D+h+ d++ +++aLa g s++  a+lt h+ t +++++ 
  gi|118431085|ref|NP_147291.2| 252 avfgetvmggdsigkkgkpaevvgreaaeslledmatgAALDRHMSDMAPVYLALAGGVSTVFGARLTGHASTILELLRI 331
                                    ****************************************************************************9987 PP

                                    HS CS
                                    xx RF
                            RTC 215 fl 216
                                    ++
  gi|118431085|ref|NP_147291.2| 332 MV 333
                                    76 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 !   68.5   0.1   9.7e-23   5.8e-19       1     102 [.     186     286 ..     186     287 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 9.7e-23
                                    -S----SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSS.EEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEE CS
                     RTC_insert   1 vdrGrvkrirGvafaarvspsvanrmveaargvLnkllp.dvyiytdvvkegkesgkspGfgisLvaetttegvllgaea 79 
                                    v+rG +k + + ++a++++ s+a+r++++a ++ ++ l  d  ++++++k +++ + +pG+g++++a +  +++++g+++
  gi|118431085|ref|NP_147291.2| 186 VERGPLKGVYVRSHAVKLPGSIAERQARSAASLVRERLGvDPIVEIEAYKPHRDPHLGPGTGVLVWAVF--GETVMGGDS 263
                                    69*********************************9988755567999999******************..679****** PP

                                    EE-TT--HHHHHHHHHHHHHHHH CS
                     RTC_insert  80 lgekgvppedvGeeaaeeLleei 102
                                    +g+kg+p+e vG+eaae Lle++
  gi|118431085|ref|NP_147291.2| 264 IGKKGKPAEVVGREAAESLLEDM 286
                                    ********************987 PP

>> DMAP1  DNA methyltransferase 1-associated protein 1 (DMAP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.4e-05       0.2      79     108 ..     192     221 ..     187     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.4e-05
                          DMAP1  79 sGvslRsqrmklPasvgqkKlKaieqllee 108
                                     Gv++Rs+ +klP s++++++++  +l++e
  gi|118431085|ref|NP_147291.2| 192 KGVYVRSHAVKLPGSIAERQARSAASLVRE 221
                                    59******************9988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2795.01
//
Query:       gi|118431086|ref|NP_147292.2|  [L=172]
Description: nicotinamide-nucleotide adenylyltransferase [Aeropyrum pernix K1]
Scores for 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-13   49.3   0.0    1.3e-12   48.1   0.0    1.6  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   7.5e-17   1.3e-12       1     142 [.       5     135 ..       5     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 7.5e-17
                                    EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHHHHH CS
                CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvdpweltrevlkk 79 
                                    l++G+F+p+HlGHl+ +++a+   ee +iv v s++++    +++++a eR++ l+l+ +e d++ +   + +++++  +
  gi|118431086|ref|NP_147292.2|   5 LVVGRFQPPHLGHLHTIKWALGRAEE-VIVVVGSAQESYTL-ENPMTAGERVHALRLMlEELDDWCRRLMIAPVPDIAMN 82 
                                    579***********************.************99.****************9999999988888888755554 PP

                                    TTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                CTP_transf_like  80 lkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                    +     ++v    +l        ++ +++ ++lv + +++     l +++ r+ ++S+t+ir+
  gi|118431086|ref|NP_147292.2|  83 K-----VWVQYLKMLLP-----PFDGVVSGNELVLMLFEDMGLAALRPPMFRRGECSGTRIRR 135
                                    4.....77777777777.....57777777777777777777777788888888888888876 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:                      242  (0.0134977); 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 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1385.07
//
Query:       gi|14600772|ref|NP_147293.1|  [L=352]
Description: RNA (cytosine-C(5)-)-methyltransferase [Aeropyrum pernix K1]
Scores for complete 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-47  161.0   0.0    3.7e-47  160.6   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    5.7e-14   52.4   0.0      1e-13   51.6   0.0    1.4  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
     0.0031   17.3   0.0     0.0049   16.6   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0037   16.9   0.0     0.0064   16.1   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
       0.02   15.0   0.0      0.035   14.2   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
      0.025   15.3   0.0       0.14   12.9   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
      0.041   13.5   1.9        5.2    6.8   0.1    2.6  2  PSRT             PSRT
      0.043   12.9   0.0      0.073   12.2   0.0    1.3  1  Fibrillarin      Fibrillarin


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 !  160.6   0.0   1.6e-50   3.7e-47       2     198 ..     143     347 ..     142     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 1.6e-50
                                   HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
               Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                   +lL  +++et+lD++aaPGgK thi +l +++  +vAvd++++R++++ + ++r+g ++   ++aD r  +++ g    Dr
  gi|14600772|ref|NP_147293.1| 143 YLLGVEPGETVLDMAAAPGGKSTHIQQLSRDSTILVAVDISRRRMRALRSHMQRMGFRSYVAVRADSRLLPRIAGTGWADR 223
                                   6889999************************************************************************** PP

                                   EEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEEE CS
               Methyltr_RsmB-F  83 iLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelv 163
                                   ++lDaP +g g+ir+dp+ + +r+++d+ +++ lq ell +a+dl ++g  ++Y+ Cs  +eE e v+ ++L+ r dve++
  gi|14600772|ref|NP_147293.1| 224 VMLDAPSTGEGIIRKDPERRRSRSQADVLRIHYLQLELLYTAVDLARPGAPILYAACSTSPEEGELVVSRLLELRSDVEVE 304
                                   *******************************************************************************99 PP

                                   SSBSTTSTTSSECEEC...........TSEEE-TTTTSS-SEEEEE CS
               Methyltr_RsmB-F 164 etelsepkglklgeea...........gtlrllPhtenkdgffiak 198
                                    +e    +g + g+++             lrl+P+++ ++gffi +
  gi|14600772|ref|NP_147293.1| 305 RLESP--VG-SPGVDSylgvdisgearRCLRLWPQRHGTEGFFICR 347
                                   88533..22.22333334445566667899*************987 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 !   51.6   0.0   4.5e-17     1e-13       6      90 .]      51     139 ..      48     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 4.5e-17
                                   HHHHHHHHGG.GHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES--.-...TTSHHHHTTS- CS
               Methyltr_RsmF_N   6 iekmkellge.eaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfylee.eerpgkhplheaGly 82 
                                   +ek+ ++lge ea++++a  ++p ++ +R+N + i ++ele++ +  +f ++++pw ++G+ + e   r g + ++++Gly
  gi|14600772|ref|NP_147293.1|  51 VEKYIQILGEeEARELIAWNDKPLPETIRCNDFLIPCSELESMLSqkGFLVSRIPWLPHGIEVLEqPIRVGATHEYMQGLY 131
                                   68899999998999***999*********************9877789************9665515699*********** PP

                                   EE--TTTH CS
               Methyltr_RsmF_N  83 YiQEpSam 90 
                                   YiQ+p +m
  gi|14600772|ref|NP_147293.1| 132 YIQDPGSM 139
                                   *******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 !   16.6   0.0   2.2e-06    0.0049      98     181 ..     147     233 ..     140     255 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                                   --TT-EEEETT-TTTCCHHHCCHHTTSSEE.EEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---...TT-EEEEEE CS
                        Met_10  98 veegevVvdvfAGiGpfaipiakyskakrv.laidlnPesvkylkeniklNkvekvvkpileDgrevir...eqladrvvm 174
                                   ve+ge+V+d+ A  G  +  i ++s+++++ +a+d+  + ++ l++ +++    ++v ++ +D+r + r   +  adrv++
  gi|14600772|ref|NP_147293.1| 147 VEPGETVLDMAAAPGGKSTHIQQLSRDSTIlVAVDISRRRMRALRSHMQRMGFRSYV-AVRADSRLLPRiagTGWADRVML 226
                                   89***********************9987637*************************.9******9988888999****** PP

                                   --TTTGG CS
                        Met_10 175 nlpksai 181
                                   ++p++ +
  gi|14600772|ref|NP_147293.1| 227 DAPSTGE 233
                                   9998765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.9e-06    0.0064      42     127 ..     150     234 ..     139     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                                   C-EEEETT-..TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  42 garvLDlfa..GsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                   g++vLD+ a  G  +  +  lSR+    v+v+ +++ +++l+ +++++++++   + ++ +++ l++ a+++   d v lD
  gi|14600772|ref|NP_147293.1| 150 GETVLDMAAapGGKSTHIQQLSRDSTILVAVDISRRRMRALRSHMQRMGFRS--YVAVRADSRLLPRIAGTG-WADRVMLD 227
                                   57789998834445778999*****************************997..677777788899997665.66****** PP

                                   -SSSTTC CS
                 Cons_hypoth95 121 PPyakel 127
                                    P   e 
  gi|14600772|ref|NP_147293.1| 228 APSTGEG 234
                                   9966555 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.6e-05     0.035      20      60 ..     148     188 ..     139     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                                   -TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH CS
                          FtsJ  20 kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl 60 
                                   +pg+tv+D +aaPGg s  + q    ++ +vavD+   +++
  gi|14600772|ref|NP_147293.1| 148 EPGETVLDMAAAPGGKSTHIQQLSRDSTILVAVDISRRRMR 188
                                   699*****************9998779********665332 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.1e-05      0.14       1      59 [.     153     213 ..     153     228 .. 0.82
   2 ?   -0.8   0.0       1.2   2.7e+03      22      38 ..     316     332 ..     308     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                                   EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlp 59 
                                   vLd+++ +G  + ++++    +  +++vDis + ++a r+++++ g+ +   v++d + lp
  gi|14600772|ref|NP_147293.1| 153 VLDMAAAPGGKSTHIQQLSRdSTILVAVDISRRRMRALRSHMQRMGFrSYVAVRADSRLLP 213
                                   8********9999999887447888*****************9999865556777776666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                   SEEEEEESSHHHHHHHH CS
               Methyltransf_25  22 akvtgvDiseemleaar 38 
                                    +++gvDis e+ +  r
  gi|14600772|ref|NP_147293.1| 316 DSYLGVDISGEARRCLR 332
                                   6789*****99877666 PP

>> PSRT  PSRT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0023       5.2      13      19 ..      33      39 ..      31      40 .. 0.94
   2 ?    5.3   0.3    0.0072        16      17      24 ..     240     247 ..     238     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                          PSRT 13 PSRTPER 19
                                  PSRT+ER
  gi|14600772|ref|NP_147293.1| 33 PSRTAER 39
                                  ******9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0072
                          PSRT  17 PERrRSts 24 
                                   PERrRS s
  gi|14600772|ref|NP_147293.1| 240 PERRRSRS 247
                                   9*****76 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.2e-05     0.073      68     114 ..     147     193 ..     138     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                   --TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHH CS
                   Fibrillarin  68 ikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreliev 114
                                   +++g+ vL + aa G    H+  +  ++ ++ av+ s r +r l + 
  gi|14600772|ref|NP_147293.1| 147 VEPGETVLDMAAAPGGKSTHIQQLSRDSTILVAVDISRRRMRALRSH 193
                                   789***************************************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); 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):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 3065.32
//
Query:       gi|118431087|ref|NP_147294.2|  [L=174]
Description: hypothetical protein APE_0516.1 [Aeropyrum pernix K1]
Scores for complete 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   59.8   0.0    3.1e-16   59.4   0.0    1.2  1  UPF0113    UPF0113 PUA domain
    2.3e-05   24.9   0.0    3.5e-05   24.3   0.0    1.3  1  UPF0113_N  UPF0113 Pre-PUA domain


Domain annotation for each model (and alignments):
>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   3.5e-20   3.1e-16       1      76 []     106     172 ..     106     172 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 3.5e-20
                        UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkaspgkivvknlaDiGeYlRr 76 
                                    ++ +++++eklFLY+rdv++++i ++t+++      +V+  ng+plG+G+       ++g ++vk+l D+G+YlRr
  gi|118431087|ref|NP_147294.2| 106 CIRLSPRGEKLFLYSRDVYGDNIASHTSGAA-----LVVGSNGQPLGWGVGLS----RDGLLIVKPLRDLGWYLRR 172
                                    57899**********************8888.....888************66....99****************7 PP

>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     4e-09   3.5e-05       1      82 []      14      90 ..      14      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4e-09
                      UPF0113_N  1 RklseeetrivfekLtkyigdnvkelld.....rkdgtycfrlkkkrVyyvseellklaetikpenlisaGtclGkftktkk 77
                                   R+++ +e+r+v+  L+++ g +v+ + +      +        k k+V+y+++ l +++e+++ +  +saG++lG++  ++ 
  gi|118431087|ref|NP_147294.2| 14 RPPTPREERLVEGFLRAI-GFKVNPYAEgmtvlDPG------GKFKEVFYLPWGLRRAVERLPLH--YSAGLNLGSIG-ERG 85
                                   88999************9.*********66666333......36******************997..9*********9.999 PP

                      UPF0113_N 78 Frlsi 82
                                   Fr+s+
  gi|118431087|ref|NP_147294.2| 86 FRPSL 90
                                   **986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1344.75
//
Query:       gi|14600774|ref|NP_147295.1|  [L=268]
Description: FKBP-type peptidyl-prolyl cis-trans isomerase [Aeropyrum pernix K1]
Scores for complete 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   36.9   0.0    7.5e-09   35.8   0.0    1.6  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   4.2e-13   7.5e-09       6      74 ..       5     100 ..       3     152 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.2e-13
                                   -TTCEEEEEEEEEET.T..SSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGT CS
                        FKBP_C   6 kegdtVtvhykgkle.d..gkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippela 70 
                                   k+gd+V ++y+ k+  d  ++v+d++              + +k++ + vG++ ++  +e+ l+++ vGe+r++++ppe+a
  gi|14600774|ref|NP_147295.1|   5 KDGDFVLINYTVKVVeDgsERVIDTTleevakksgiydpKRVYKEFPVIVGKTSLLGPLEKVLKELDVGERREVEVPPEEA 85 
                                   79************5455678899998888988888555449*************************************** PP

                                   TTT...........T CS
                        FKBP_C  71 Yge...........k 74 
                                   +ge           k
  gi|14600774|ref|NP_147295.1|  86 FGEykkelvvrvpvK 100
                                   **9554444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1950.56
//
Query:       gi|118431088|ref|NP_147296.2|  [L=352]
Description: glycerol-1-phosphate dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-63  214.7   0.2      2e-63  214.4   0.2    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    7.5e-25   87.5   2.6    2.5e-23   82.5   2.6    2.1  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.1e-10   41.1   6.2    1.4e-05   24.4   0.1    3.9  3  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 !  214.4   0.2   3.3e-67     2e-63       2     250 .]      16     274 ..      15     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 3.3e-67
                       Fe-ADH_2   2 igegaleklgellkele..lkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlv 79 
                                    +g g+l+k g +++  +  ++ vl+v++ ++++ + e+++ sl+ +g++v  + +   +a++e++e++++++ e+++++v
  gi|118431088|ref|NP_147296.2|  16 VGGGVLDKAGGYVSGVAqrGSYVLVVSGPTVSSKYFERLRASLEAEGLTVG-L-KIIRDATVETAEEVAREALESRIEVV 93 
                                    678999999999987751157**************************9997.3.36789********************* PP

                       Fe-ADH_2  80 vavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvG 159
                                     ++GgG+ iD+aky+s +++  +vs+pT aS+DG++sp++sl+   k ++  +a+aP a+i+D+dv+aeAPrr   +G+G
  gi|118431088|ref|NP_147296.2|  94 AGLGGGKSIDVAKYASKRAGSVFVSIPTVASHDGITSPFSSLKGFDKPISR-PAKAPEAIIIDVDVIAEAPRRYNIAGFG 172
                                    *********************************************999996.**************************** PP

                       Fe-ADH_2 160 Dllgkytaladwklan........evseplaklsaamvqeaaeklvedkke..tealeellea.lalsgigisrpaSGsE 228
                                    Dl+gkyta+ dw+la+        e++++la+lsa++v++ ae+++   +e  + +le+l+++ + ++++g++rpaSGsE
  gi|118431088|ref|NP_147296.2| 173 DLIGKYTAVLDWRLAHklrleyygEYAASLALLSAKHVSQYAEEIALGTREgyRVLLEALVSSgVSMCIAGSTRPASGSE 252
                                    ****************9999999999*******************874333225555666555269999999******** PP

                       Fe-ADH_2 229 HliSHaldmlalkqalHGeqVG 250
                                    Hl++Hal  +a ++ lHGe VG
  gi|118431088|ref|NP_147296.2| 253 HLFAHALHIVARNKPLHGEAVG 274
                                    *********************9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   2.6   4.2e-27   2.5e-23       1     340 [.      11     316 ..      11     341 .. 0.74

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 4.2e-27
                                    -SEEEEETTGGGGHHHHHTTT...-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS CS
                         Fe-ADH   1 Ptrivfgkgaleelgellkkl...gakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaala 77 
                                    P++iv g g+l++ g +++     g + +l+v ++ ++  s++++++++sle++g++v    ++  + t+e+ ee+a+ a
  gi|118431088|ref|NP_147296.2|  11 PRTIVVGGGVLDKAGGYVSGVaqrG-SYVLVVSGPTVS--SKYFERLRASLEAEGLTVG--LKIIRDATVETAEEVAREA 85 
                                    899**************98883324.589999999966..89**************999..59***************** PP

                                    -TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE- CS
                         Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsif 157
                                     e++++vv ++GGG++iD+AK+++  ++                    ++ iPT+a+ +  ++p++ +     g  ++i+
  gi|118431088|ref|NP_147296.2|  86 LESRIEVVAGLGGGKSIDVAKYASKRAG------------------SVFVSIPTVASHDGITSPFSSLK----GFDKPIS 143
                                    ****************************..................469********************....7889*** PP

                                    ..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH........T---TTSSB--HHHHHHHHHHHHHHHHHHH CS
                         Fe-ADH 158 dpellPdlaivDpeltltlPkrvtaatglDalahalEayvsk........kanplsdalaleairliaknleravadged 229
                                     p   P+++i+D ++++ +P+r+ +a+ +D + ++   +  +           ++   lal +++ + ++ e++     +
  gi|118431088|ref|NP_147296.2| 144 RPAKAPEAIIIDVDVIAEAPRRYNIAGFGDLIGKYTAVLDWRlahklrleYYGEYAASLALLSAKHVSQYAEEIALG--T 221
                                    *******************************9888777666622223333333333334444444444444443332..4 PP

                                    HHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.C.GGG.GGS-HHHHHHHHH..........HHHHHHT... CS
                         Fe-ADH 230 leareqmllastlaglafsnaglg.....avHalahalgalf.gip.hglanaillpavlrfnaeaaperlaqlaralgg 302
                                     e  + +l+a + +g+++  ag +       H +ahal     + p hg+a+++    ++             +a     
  gi|118431088|ref|NP_147296.2| 222 REGYRVLLEALVSSGVSMCIAGSTrpasgSEHLFAHALHIVArNKPlHGEAVGV----GT-----------IMMAYL--- 283
                                    455555666666666655555544444558888888888744344455555554....44...........112222... PP

                                    ....T--HHHHHHHHHHHHHTT---SHHHHT-TT-HH.H CS
                         Fe-ADH 303 esdeeaaeeliealrellkelglptsLselgvdeedl.d 340
                                            +  +++r llk++g+pt+ +elgv+++++ +
  gi|118431088|ref|NP_147296.2| 284 ------HGKNWRRIRGLLKTVGAPTNAKELGVEDDEVvE 316
                                    ......334578888888888888888888888864422 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.6   6.1e-05      0.36      35      62 ..      14      41 ..       4      48 .. 0.83
   2 !    5.8   0.1    0.0011       6.5      17      64 ..      76     121 ..      69     127 .. 0.75
   3 !   24.4   0.1   2.3e-09   1.4e-05      94     255 ..     148     318 ..     145     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 6.1e-05
                                   EEEESHHHHHHHHHHHHHBTT--EEEEE CS
                   DHQ_synthase 35 ialGGGvvgDlaGfvAatylRGvrfvqv 62
                                   i++GGGv+    G+v+++ +RG  ++ v
  gi|118431088|ref|NP_147296.2| 14 IVVGGGVLDKAGGYVSGVAQRGSYVLVV 41
                                   89********************665544 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0011
                                    HHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE- CS
                   DHQ_synthase  17 ekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPt 64 
                                    e+  +++ ea  +R +++  lGGG   D+a +++   + G  fv +Pt
  gi|118431088|ref|NP_147296.2|  76 ETAEEVAREALESRIEVVAGLGGGKSIDVAKYASK--RAGSVFVSIPT 121
                                    44444444555578899***************864..55888888888 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 2.3e-09
                                    --SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC.......TTTHHHHHHHHHHHHHHHHHH CS
                   DHQ_synthase  94 qPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk.......eeeeealeeliarsievkaev 165
                                     P+a++id++v++  p+r  +aG++++i Ky+++ d +l ++l+ +     +       +++ ++ +e ia  ++   +v
  gi|118431088|ref|NP_147296.2| 148 APEAIIIDVDVIAEAPRRYNIAGFGDLIgKYTAVLDWRLAHKLRLEYYGEYAaslallsAKHVSQYAEEIALGTREGYRV 227
                                    699***********************9889*******9999998766555445677777445555666666666666666 PP

                                    HHHCCTTTTGGGG........GGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT CS
                   DHQ_synthase 166 veeDekekglral........LnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklg 237
                                    + e    +g+ ++            H ++Ha+  +++  k lHGeaV +G ++ a+l         ++ +r++ llk++g
  gi|118431088|ref|NP_147296.2| 228 LLEALVSSGVSMCiagstrpaSGSEHLFAHALHIVARN-KPLHGEAVGVGTIMMAYLH-------GKNWRRIRGLLKTVG 299
                                    6666665555554222222216677********99999.9*************99988.......345789********* PP

                                    ---STTTT..-HHHHHHHH CS
                   DHQ_synthase 238 lpvslkel.leveelleal 255
                                     p++ kel +e +e++eal
  gi|118431088|ref|NP_147296.2| 300 APTNAKELgVEDDEVVEAL 318
                                    ***9999866666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2717.98
//
Query:       gi|118431089|ref|NP_147297.2|  [L=219]
Description: proteasome beta subunit precursor [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-55  187.5   0.4    1.9e-55  187.3   0.4    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 !  187.3   0.4   1.1e-59   1.9e-55       1     190 []      22     203 ..      22     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 1.1e-59
                                    HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC CS
                     Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpip 80 
                                    v+ Gtt+vG+ ++d+v+laadkratag  ++s++ v+Ki  ++++++++++Gl+aDa++l + +r+e++ly+++++ +++
  gi|118431089|ref|NP_147297.2|  22 VRSGTTTVGLIASDHVILAADKRATAGFLIASRR-VKKIVMLSNYVAMTVSGLVADAQILSDVLREEIRLYEMTNKVKPS 100
                                    578**********************999997777.9******************************************** PP

                                    HHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSH CS
                     Proteasome  81 verlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltl 160
                                    v+     va++l++ +++s++ p++v+l+++g+d ++ p+Ly++d  Gs++e+k ++a+Gsgs  a+++le++y+edl++
  gi|118431089|ref|NP_147297.2| 101 VR----FVASLLSNILFSSKFFPYIVQLIVGGYD-TQ-PRLYTLDLFGSITEDK-YTATGSGSPIAYGVLEERYREDLSV 173
                                    **....****************************.55.***************8.************************* PP

                                    HHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 161 eeavelavkalkealerdklsgknievavi 190
                                    eea+++a  a+++a+ rd++sg++++v+vi
  gi|118431089|ref|NP_147297.2| 174 EEAIKVATTAIRSAVLRDAASGDGADVVVI 203
                                    ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1610.42
//
Query:       gi|118431090|ref|NP_147298.2|  [L=671]
Description: exonuclease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-26   93.2   0.0    2.6e-26   92.1   0.0    1.6  1  Beta-Casp      Beta-Casp domain
    2.2e-18   66.0  10.3    3.8e-18   65.2   1.3    3.7  4  KH_7           KH domain
    1.4e-14   53.9   0.0    1.2e-13   50.9   0.0    2.1  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    4.1e-14   52.2   0.0    1.3e-13   50.7   0.0    1.8  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    6.3e-10   39.4   0.8    5.9e-09   36.2   0.4    2.5  2  Lactamase_B    Metallo-beta-lactamase superfamily
    5.6e-09   35.8   0.0    2.2e-08   33.8   0.0    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0033   17.3   0.0      0.015   15.2   0.0    1.9  2  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.079   11.4   0.0       0.12   10.7   0.0    1.2  1  Gag_spuma      Spumavirus gag protein


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 !   92.1   0.0   1.1e-29   2.6e-26       2     110 .]     437     561 ..     436     561 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.1e-29
                                    HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.......................E-SHH....HHHH.. CS
                      Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.......................veakslewmeskke. 57 
                                    qe+l++L+e+ +++k  ++++piy+d+ +++++t+vY++y+e                       v       +++ k+ 
  gi|118431090|ref|NP_147298.2| 437 QEILVVLNEALRSGK--IPEIPIYVDG-MVYEVTAVYTNYPEllvkpirdrilkqgenpfegpttV-----YVTDHYKRd 508
                                    9**********9955..7889******.******************************97776542.....444555555 PP

                                    .HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                      Beta-Casp  58 elnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                    e+  s++p++il++sgm++gG+++e++k l++dprn++ +v+yqa+gTlgr+l
  gi|118431090|ref|NP_147298.2| 509 EAMYSDKPAIILSTSGMMNGGPIVEYFKYLADDPRNALAFVSYQAPGTLGRRL 561
                                    778899*********************************************97 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   1.3   1.7e-21   3.8e-18       5      67 ..      20      81 ..      15      82 .. 0.87
   2 ?    4.5   0.1     0.015        35       5      50 ..      86     133 ..      82     137 .. 0.69
   3 ?   -2.0   0.1       1.6   3.7e+03      40      59 ..     466     485 ..     453     487 .. 0.53
   4 ?   -0.3   0.0      0.46     1e+03      26      38 ..     493     504 ..     490     520 .. 0.71

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.7e-21
                           KH_7  5 eelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsv 67
                                   ++l  +i ++l   + i+++eFEGPe+++Y +npk+++en+++++ lA++lrkRiv+R+ p+ 
  gi|118431090|ref|NP_147298.2| 20 KQLIMEIYNSLR-SADIASIEFEGPEIAVYIRNPKFIVENENVVKDLARKLRKRIVVRTHPKS 81
                                   455556666665.569*******************************************9986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                           KH_7   5 eelkekieeklPkevkitdveFEG..PelViYtknpklfaengdlirk 50 
                                    e + + i e++P++v i d++F     e+ + ++ p +++ +g++ r+
  gi|118431090|ref|NP_147298.2|  86 EYTIKFIRENVPPDVGIVDIQFDDvlGEVRVIAEKPGKLMGRGKVFRN 133
                                    66678899**************74223555555555555555555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.6
                           KH_7  40 lfaengdlirklAkelrkRi 59 
                                      a  +++ + l+k +r Ri
  gi|118431090|ref|NP_147298.2| 466 VTAVYTNYPELLVKPIRDRI 485
                                    44455566666666666666 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.46
                           KH_7  26 FEGPelViYtknp 38 
                                    FEGP+ V Y+++ 
  gi|118431090|ref|NP_147298.2| 493 FEGPTTV-YVTDH 504
                                    9***976.55443 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 !   50.9   0.0   5.5e-17   1.2e-13       3     162 ..     211     364 ..     208     373 .. 0.84
   2 ?    0.2   0.0      0.19   4.3e+02      24      61 ..     599     636 ..     586     645 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 5.5e-17
                  Lactamase_B_6   3 eldnvkiLlDvGwdeskvslesalkelek..viptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGr 80 
                                       + k+LlD G + s +  +s   +++    ++++d++++sha l+h+G ++ll++     ++ + pvyat p+  +  
  gi|118431090|ref|NP_147298.2| 211 DTGESKVLLDAGLSPSGYGPDSYPYYWSPefRVDELDAVVISHAHLDHVGTLPLLFK-----YGFRGPVYATPPTRDIMI 285
                                    455789********9988888887888763359******************998774.....5789*************9 PP

                  Lactamase_B_6  81 vslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki..skesekivY 158
                                    ++l dl++  +    + +  +e  d+++a ++++++ Y+  +++     ++ +t  naGh lG ++ ++   +++ +i+Y
  gi|118431090|ref|NP_147298.2| 286 IVLRDLINLMRKA--QGEPPFEPRDVEKALTRLIPVNYNTVTDVAP---DIKMTFINAGHILGSSMVHLhiGQGLYNILY 360
                                    9999998755443..44457999****************9998885...89999***********98762267888**** PP

                  Lactamase_B_6 159 avdw 162
                                      d+
  gi|118431090|ref|NP_147298.2| 361 TADF 364
                                    9987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                  Lactamase_B_6  24 salkelekviptvdliLLshatlehlGayallyakfks 61 
                                    + l++l++  p+   i+L h +++ ++a+a+ +++  s
  gi|118431090|ref|NP_147298.2| 599 ELLSFLRRLNPKPRNIVLNHGEPSAIAALAHTVKTGWS 636
                                    567888889999999**************999876555 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 !   50.7   0.0   5.6e-17   1.3e-13       2      52 ..     579     632 ..     578     642 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 5.6e-17
                          RMMBL   2 ipvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllk 52 
                                    i+v+++i  i+ f gH+ + ell ++r+l+p++  ++l+HGe+ a++ala + k
  gi|118431090|ref|NP_147298.2| 579 IKVNMEIVSIEgFTGHSTRGELLSFLRRLNPKPrnIVLNHGEPSAIAALAHTVK 632
                                    89************************************************9984 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.6   5.9e+03      80     133 ..      83     127 ..      64     130 .. 0.59
   2 !   36.2   0.4   2.6e-12   5.9e-09       2     153 ..     201     366 ..     200     395 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.6
                                    HCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSC CS
                    Lactamase_B  80 palfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghgh 133
                                    +++++  +          +++ +++++++++   d+ +g++r     +g + g 
  gi|118431090|ref|NP_147298.2|  83 KSMEYTIKF---------IRENVPPDVGIVDIQFDDVLGEVRVIAEKPGKLMGR 127
                                    222222222.........356777788888888888888888777777776665 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 2.6e-12
                                    CCCSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH.HCCEETCCEHH CS
                    Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglvea.tdvpvgavaee 78 
                                    g+++ +++l++++++ +L D+G+s++     +   + + ++  +++dav+++H+HlDH+G l+ l +  +  pv+a + +
  gi|118431090|ref|NP_147298.2| 201 GEVGRSAILVDTGESKVLLDAGLSPSGYGPDSypYYWSPEFRVDELDAVVISHAHLDHVGTLPLLFKYgFRGPVYATPPT 280
                                    5678899********************9999988888899***********************98665144455555555 PP

                                    HHCCHCHHHHHHHHHCCHH...........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEE CS
                    Lactamase_B  79 apalfmeeaddaasrkgll...........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlf 147
                                       ++   +d    + ++            +a  + +++   +  +   +  + +  + ++ g++ +h++++ g  ++l+
  gi|118431090|ref|NP_147298.2| 281 RDIMIIVLRDLINLMRKAQgeppfeprdveKALTRLIPVNYNTVTDVAPDIKMTFINAGHILGSSMVHLHIGQGLYNILY 360
                                    55555555555555555556666666766666666666666666666666666666666666666666666666677777 PP

                                    ECTTTS CS
                    Lactamase_B 148 tGDall 153
                                    t D+ +
  gi|118431090|ref|NP_147298.2| 361 TADFKF 366
                                    777665 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 !   33.8   0.0   9.9e-12   2.2e-08       3     148 ..     217     372 ..     215     407 .. 0.73
   2 ?   -1.9   0.0      0.89     2e+03      50      89 ..     447     485 ..     445     501 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 9.9e-12
                                    EEES--TT..HHHH.HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEEHHHHH........ CS
                  Lactamase_B_2   3 iLiDagpd..lrqq.alral.qPvelrdelppidaVllthaHyDHlaglltlre..lrpkklplyapkgvla........ 68 
                                    +L+Dag++    ++   ++  +P     +++++daV+++haH DH+  l+ l +  +r    p+ya++ +++        
  gi|118431090|ref|NP_147298.2| 217 VLLDAGLSpsGYGPdSYPYYwSP---EFRVDELDAVVISHAHLDHVGTLPLLFKygFR---GPVYATPPTRDimiivlrd 290
                                    78889888554444555555444...446779**************999999996555...49*******9999997776 PP

                                    ......HCCTTCGHHHCHTT.TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEES CS
                  Lactamase_B_2  69 ......vleanfvylaleee.pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyig 141
                                          + + + +++ +++e + +++ +++ ++ ++++ +++++t++ a h  g         ++ l i++g  +++y++
  gi|118431090|ref|NP_147298.2| 291 linlmrKAQGEPPFEPRDVEkALTRLIPVNYNTVTDVA-PDIKMTFINAGHILGS-------SMVHLHIGQGLYNILYTA 362
                                    66664444444444444444888999999999999998.5899999999998888.......888888888888999999 PP

                                    S-S---...H CS
                  Lactamase_B_2 142 Dtgyip...e 148
                                    D +++    +
  gi|118431090|ref|NP_147298.2| 363 DFKFYRiknD 372
                                    9987665443 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.89
                                    CCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEE CS
                  Lactamase_B_2  50 lrelrpkklplyapkgvlavleanfvylaleeepavnvhe 89 
                                    lr ++  ++p+y++ +v++v +  + y  l ++ +++ + 
  gi|118431090|ref|NP_147298.2| 447 LRSGKIPEIPIYVDGMVYEVTAVYTNYPELLVK-PIRDRI 485
                                    566555679***********9999999999888.555444 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 ?   -1.4   0.0      0.82   1.8e+03     140     163 .]      55      78 ..      28      78 .. 0.78
   2 !   15.2   0.0   6.7e-06     0.015       6      50 ..     204     259 ..     202     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.82
                  Lactamase_B_3 140 ltlgqeealelakrLkpklvlPmh 163
                                    ++ + + +++la++L+ ++v+ +h
  gi|118431090|ref|NP_147298.2|  55 IVENENVVKDLARKLRKRIVVRTH 78 
                                    444555677899999999999988 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6.7e-06
                  Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa...........eeaDlvlisqaledHa 50 
                                    g +++l++t++ ++l+D +    gy+p+            +e D+v+is+a+ dH 
  gi|118431090|ref|NP_147298.2| 204 GRSAILVDTGESKVLLDAGLSPSGYGPDSypyywspefrvDELDAVVISHAHLDHV 259
                                    8899*************9977777777777788899*******************7 PP

>> Gag_spuma  Spumavirus gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.5e-05      0.12     291     353 ..     273     343 ..     230     355 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.5e-05
                      Gag_spuma 291 pvpppppvgavip......iqhirsvtgepprnpreipiwlgrnapaidgvfptttpdlrcriina..llg 353
                                    pv   pp   ++       i+ +r   gepp +pr++   l r  p     +   +pd++   ina  +lg
  gi|118431090|ref|NP_147298.2| 273 PVYATPPTRDIMIivlrdlINLMRKAQGEPPFEPRDVEKALTRLIPVNYNTVTDVAPDIKMTFINAghILG 343
                                    4544444433322011222667899***********************9999*************833344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.30s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4397.06
//
Query:       gi|118431091|ref|NP_147299.2|  [L=178]
Description: hypothetical protein APE_0525.1 [Aeropyrum pernix K1]
Scores for 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-18   64.7   1.3    8.1e-18   64.2   1.3    1.3  1  PUA       PUA domain
    9.4e-09   35.5   0.0    2.3e-08   34.2   0.0    1.6  1  DUF1947   Domain of unknown function (DUF1947)
    2.9e-05   24.7   0.0    5.5e-05   23.8   0.0    1.4  1  Pre-PUA   Pre-PUA-like 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 !   64.2   1.3   1.4e-21   8.1e-18       1      67 [.      84     151 ..      84     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.4e-21
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEE CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggks 67 
                                    g v vd+gA+ al++ga+L++pGvv+veg+f +gdvVa + ++ +++v vG+a+++s+ l+k  + k+
  gi|118431091|ref|NP_147299.2|  84 GVVLVDKGAAIALAKGAHLMIPGVVGVEGSFTRGDVVAALYHEtRTPVMVGVAEVDSSALEKLYREKA 151
                                    6799**************************************989*****************997765 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   3.8e-12   2.3e-08       5      65 ..       9      76 ..       8      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.8e-12
                                   --HHHHHHHHHHHHTTT---TT--...-EEEE-S....S-EEEEETTEEEEEE..SSSEEE-HHHHHH CS
                        DUF1947  5 LSkKeakeileklkekyisislesdk.iEieeek....keklYlingvpilfe..eekliPtLklLlk 65
                                   LSkKe++ +le+lk +y  i+++++  + + +      +  ++ ++gvp+lfe  +++++PtL++L +
  gi|118431091|ref|NP_147299.2|  9 LSKKERRSLLERLKPYYTRIPFSEKAdLRLVKARtdsgEYEIITVDGVPCLFEwsDGRIYPTLQCLKA 76
                                   9*********************997678777655333345699***********888********975 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   9.1e-09   5.5e-05      12      83 ..       8      74 ..       5      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 9.1e-09
                        Pre-PUA 12 qlksSdrrkLraklleqfpslseeqleellpkkeevkvvklq..gehvelyvvdgeplffqdregellPtlytl 83
                                    l++++rr L ++l+  + ++        + +k+++ +vk +    + e+++vdg p +f+ ++g ++Ptl  l
  gi|118431091|ref|NP_147299.2|  8 ALSKKERRSLLERLKPYYTRI-------PFSEKADLRLVKARtdSGEYEIITVDGVPCLFEWSDGRIYPTLQCL 74
                                   578889999999999999999.......78899********9888999***********************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1426.03
//
Query:       gi|14600779|ref|NP_147300.1|  [L=77]
Description: small nucleolar RNP protein Sm [Aeropyrum pernix K1]
Scores for complete 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   68.0   0.2    4.6e-19   67.9   0.2    1.0  1  LSM       LSM domain
    0.00036   20.6   0.0    0.00039   20.5   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain
     0.0032   17.1   0.1     0.0037   16.9   0.1    1.3  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 !   67.9   0.2   7.6e-23   4.6e-19       4      67 .]      14      75 ..      11      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 7.6e-23
                                  HHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                           LSM  4 kklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                   ++++  v+v+lk+g +++G+Lk +Dq++N++L d+ee+ ++  ++r+lgl+l+RG+++v+i++
  gi|14600779|ref|NP_147300.1| 14 LDYVDTPVLVKLKSGLRIKGVLKTYDQHLNIILGDAEEIGET--SIRRLGLTLVRGDSVVVITP 75
                                  5799**********************************9977..8****************976 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   6.6e-08   0.00039      14      51 ..      19      54 ..       9      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.6e-08
                                  SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                        SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                  ++v v++k+G +++G+++t++    ++++L  a ++ +
  gi|14600779|ref|NP_147300.1| 19 TPVLVKLKSGLRIKGVLKTYDQ--HLNIILGDAEEIGE 54
                                  7899******************..******99999987 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   6.2e-07    0.0037      14      40 ..      19      45 ..      12      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.2e-07
                                  -EEEEEETTS-EEEEEEEEE-SSEEEE CS
                           Hfq 14 ipvtifLvnGiklkGviksfDnftvlL 40
                                  +pv + L +G ++kGv+k +D++  ++
  gi|14600779|ref|NP_147300.1| 19 TPVLVKLKSGLRIKGVLKTYDQHLNII 45
                                  89********************86433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 679.83
//
Query:       gi|14600780|ref|NP_147301.1|  [L=62]
Description: 50S ribosomal protein L37 [Aeropyrum pernix K1]
Scores for 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-25   86.9  13.2      8e-25   86.8  13.2    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
  ------ inclusion threshold ------
      0.043   13.9   1.1      0.046   13.9   1.1    1.1  1  zf-RING_10      zinc RING finger of MSL2
       0.24   11.0   1.3       0.41   10.3   1.3    1.4  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
        3.2    6.4   6.1        3.4    6.3   6.1    1.0  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta


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 !   86.8  13.2   1.8e-28     8e-25       2      53 ..       3      55 ..       2      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 1.8e-28
                Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                  kGt+s+Gk+ ++ktHi+CrrCg+rsy+v k +Ca+cG+ +s+++r+y+W++K+
  gi|14600780|ref|NP_147301.1|  3 KGTPSMGKHGRSKTHIVCRRCGRRSYNVAKGYCAACGFgRSRRMRRYSWQNKK 55
                                  9**************************************************97 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 ?   13.9   1.1     1e-05     0.046      19      44 ..      13      39 ..       5      58 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                    zf-RING_10 19 keCqHyvCrlCvgkkkkl.kpsCsqCk 44
                                  ++  H vCr+C +++ ++ k  C+ C 
  gi|14600780|ref|NP_147301.1| 13 RSKTHIVCRRCGRRSYNVaKGYCAACG 39
                                  5668*******99998873678*9997 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 ?   10.3   1.3   9.3e-05      0.41       2       8 ..       3       9 ..       3       9 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.3e-05
                     MraY_sig1 2 kGTPTMG 8
                                 kGTP+MG
  gi|14600780|ref|NP_147301.1| 3 KGTPSMG 9
                                 8*****9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.1   0.00077       3.4     507     551 ..      17      60 ..      10      62 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00077
                                   EEEETT.--EESS...SB-TTT--BE.EEEEEESSSSEEEHHHHHHHH CS
                          NRDD 507 idvCnecgykgei...ekCpkCgseeevevirRitGYlrpvsswnkgk 551
                                     vC++cg++ +      C  Cg    + + rR+  Y  + ++wn+ +
  gi|14600780|ref|NP_147301.1|  17 HIVCRRCGRRSYNvakGYCAACG----FGRSRRMRRYSWQNKKWNRVR 60 
                                   568******666556756*****....999***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 483.73
//
Query:       gi|118431092|ref|NP_147302.2|  [L=373]
Description: Xaa-Pro dipeptidase [Aeropyrum pernix K1]
Scores for 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-61  205.9   0.0    7.3e-61  205.5   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
    7.5e-10   39.6   0.0    1.6e-09   38.5   0.0    1.6  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.5   0.0   8.2e-65   7.3e-61       3     209 .]     159     360 ..     157     360 .. 0.97

  Alignments for each domain:
  == domain 1  score: 205.5 bits;  conditional E-value: 8.2e-65
                                    HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEE CS
                  Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlidag 82 
                                    i +aaria+aal++ +e++++gv+ere+a ++ +  + + g+ g++fp+iva+g n+a++h++ +d +l    +vl+d+g
  gi|118431092|ref|NP_147302.2| 159 IAEAARIAEAALRRGIEELREGVSEREVAGAVVDV-IMKSGGWGPSFPVIVAFGGNTALPHHHTGDARLPHASPVLFDLG 237
                                    789******************************99.777799************************************** PP

                                    EEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSSSS CS
                  Peptidase_M24  83 aeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGlevh 162
                                     +y+gy+sD+tr ++ G+  +e+r+l e+v eaq +ai+ v pGv+++e+d+aar  l ++g+ k+f hg+GHgvG e+h
  gi|118431092|ref|NP_147302.2| 238 SVYKGYMSDMTRSLWRGPGGAEYRRLEELVAEAQAEAIDSVAPGVEAWEVDKAARLRLSKEGFSKYFIHGTGHGVGVEIH 317
                                    ***************997788*********************************************************** PP

                                    EEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEES CS
                  Peptidase_M24 163 degpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvte 209
                                    ++ p++   ++++++l++Gmv+tiEpg+y  pg +gvried+vlvt+
  gi|118431092|ref|NP_147302.2| 318 EN-PYLR--PGSSEELKPGMVVTIEPGVY-LPGMYGVRIEDMVLVTK 360
                                    99.*998..799*****************.99*************96 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.8e-13   1.6e-09       2     132 .]       9     150 ..       8     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.8e-13
                                    HHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST.... CS
                   Creatinase_N   2 lerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd.... 76 
                                    +++l a+ ee+g d+l++  ++nl Y  G+    g+   +lv++++   +l+v+ l+y++a ++  t+ ev  + +    
  gi|118431092|ref|NP_147302.2|   9 RRKLLAAAEEAGFDSLVIAGEANLVYALGY----GNPAGVLVLSGKCGsTLVVPLLDYERALRSVDTDVEVKAFYRgges 84 
                                    57999*************************....666666657776666****************888888666666999 PP

                                    ............HSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHSC CS
                   Creatinase_N  77 ............pvealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRvv 132
                                                  e++a++ k  le+ ++ +v+ ++l ++++ al +al+  +  d s+li ++R v
  gi|118431092|ref|NP_147302.2|  85 giepdipksdliSSENMAEAAKRVLEGCSSPAVDFKWLRWETATALSNALD--NPGDGSQLISQVRSV 150
                                    99999999889888888888888877778889******************7..9************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2765.82
//
Query:       gi|14600782|ref|NP_147303.1|  [L=377]
Description: acetamidase/formamidase [Aeropyrum pernix K1]
Scores for 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-123  410.1   0.0   8.5e-123  409.9   0.0    1.0  1  FmdA_AmdA  Acetamidase/Formamidase family


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.9   0.0  4.8e-127  8.5e-123       3     371 ..       8     365 ..       6     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 409.9 bits;  conditional E-value: 4.8e-127
                     FmdA_AmdA   3 dlskpaaeqeeklhNRwHpdipavaevkpgetvkvecldwtdgqiknndsaddvrtvdlkkvHeltgPvevegAepGDllv 83 
                                   ++ k++ ++++++hNRwHpdi+++aev+pg+ v++e++d+ dgqi+ n   ddv+++dl+ vH+ltgPv+v+gA+pGDllv
  gi|14600782|ref|NP_147303.1|   8 NRGKRCVDEADRCHNRWHPDIEPAAEVDPGDIVVIETRDALDGQITANPGVDDVASADLNVVHPLTGPVYVRGAKPGDLLV 88 
                                   66788889999********************************************************************** PP

                     FmdA_AmdA  84 veildievleeaewGytgifdkenggGflkdafpeaakaiwdlegiyassrqipgvrfrglphpGllGtapskelldswna 164
                                   ve+ldi++ +   +G+t       g+Gfl+d f++++k  w++eg ya s+++p+vr++g p++G++G+apskell+++++
  gi|14600782|ref|NP_147303.1|  89 VEVLDIKAEP---FGFT---VAIPGFGFLRDLFDKPYKIRWRIEGGYAFSEDLPNVRIPGDPFLGVMGVAPSKELLKEIKE 163
                                   ******9986...****...6678********************************************************* PP

                     FmdA_AmdA 165 reeeliekralallpepkeallgkleeeaekvaaegartvpprengGnmDiknlsrGskvylPVkveGaklsvGDlHfsqG 245
                                   re++l+++ +++l+p+p++a++      +e va+eg+rt+pprengGn+D++++s Gsk+y+PV+veGa +svGD H++qG
  gi|14600782|ref|NP_147303.1| 164 REDRLLKRGGFVLPPTPEGAVPP-----REPVASEGLRTIPPRENGGNLDVRHFSPGSKIYFPVFVEGALFSVGDAHYAQG 239
                                   **********************9.....9**************************************************** PP

                     FmdA_AmdA 246 DGEisfcg.aiemsgvvtlkvevikggmeklgiknpiflpeevep.ry..seylsfeGisvdesgkqhyldltvAyrnall 322
                                   DGE+  cg aiem ++ tl++ vi +g++k+gi+ pif+p+e++  r+  s++++++G+ v  +  ++++++t+++++all
  gi|14600782|ref|NP_147303.1| 240 DGEV--CGtAIEMGATATLRFGVISEGAKKYGIRFPIFKPSESSVrRFthSKHVAVTGVGVI-DSLNESENATLSAKHALL 317
                                   ****..**********************************999987777799*********9.55669************* PP

                     FmdA_AmdA 323 raieyLkkfGytkeqaylllsvapvegrisgivdiPnvvatlalPldiF 371
                                   ++i++L+k Gyt+eqayll sva  + r+s++vd+Pn+ +t++lPldiF
  gi|14600782|ref|NP_147303.1| 318 NLINLLEKAGYTREQAYLLASVA-ADLRLSQLVDVPNFTVTAFLPLDIF 365
                                   ***********************.9************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2701.90
//
Query:       gi|118431093|ref|NP_147304.2|  [L=300]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-10   40.3   0.0    3.1e-10   39.9   0.0    1.2  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 !   39.9   0.0   1.7e-14   3.1e-10       1     206 [.      47     248 ..      47     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.7e-14
                                    EEESSHHHHHHHHHHH..GGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEEE CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA   1 Vvattsplgdlvrqva..GdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvevi 78 
                                    Vv+t++ l++ v+ +a  Gd  +v  +++pg+dpH+ ++ pr +r +aeAd++v+ g      l+ +  ++++ t+v+v+
  gi|118431093|ref|NP_147304.2|  47 VVVTFPGLKSDVELIAcsGD--RVIEIYNPGVDPHEAQLDPRAARMVAEADIVVTGGHTPA-DLKAA--ELASGTVVDVT 121
                                    89**************6667..699*****************************9985444.33322..22222333444 PP

                                    ETTTTC...CSEBCSSESTG.GGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEG CS
                                    xxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA  79 dlsegv...eeeeeeeDpHi.WlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeipeekr 154
                                        g+   e+ + + + H   + p+n++ +   +a+a+ e+ p  + +y  n++   +kLe+l+ +++  l+    ++ 
  gi|118431093|ref|NP_147304.2| 122 RIP-GIeilETPDGSPNLHYpIYHPENYRLFLSRLAEAMQEKRP--ECDYIGNLRVALKKLEDLE-RLQGLLK---GSE- 193
                                    333.54222334444499954789********************..578***************5.6888888...333. PP

                                    EEEESSSTTHHHHHHTT-EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA 155 klvtthdafgylarayglevagiagiste....aaqiaalieeikeagvkaifvep 206
                                      v +h+a +y a+  g ev+ i+g  +e     +++++  + + +  v  i v+ 
  gi|118431093|ref|NP_147304.2| 194 -AVADHPAAQYPAHWLGAEVVLIIGGGEEwaptVQELEKAERLLASGSVAFITVDD 248
                                    .8*******************99988888888888888888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2362.04
//
Query:       gi|118431094|ref|NP_147305.2|  [L=247]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-24   86.3   0.0    3.6e-24   85.8   0.0    1.2  1  ABC_tran  ABC transporter
    6.6e-12   45.9   0.8    3.4e-05   23.8   0.2    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.6e-06   28.8   0.2    2.3e-06   28.3   0.2    1.1  1  AAA_23    AAA domain
      4e-05   23.2   0.1      0.013   14.9   0.1    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00019   21.1   0.0    0.00037   20.2   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
    0.00027   20.7   0.0     0.0054   16.5   0.0    2.0  2  AAA_15    AAA ATPase domain
    0.00076   19.1   0.0     0.0013   18.3   0.0    1.3  1  AAA_27    AAA domain
     0.0011   18.7   0.2      0.009   15.8   0.2    2.0  1  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.023   15.1   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.024   13.7   0.0      0.035   13.2   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
      0.032   14.0   0.0       0.04   13.6   0.0    1.3  1  AAA_24    AAA domain
      0.069   13.4   0.0       0.14   12.4   0.0    1.7  1  AAA_22    AAA domain
      0.071   13.0   0.1       0.14   12.1   0.1    1.5  1  NACHT     NACHT domain
      0.074   13.2   0.0       0.18   12.0   0.0    1.7  2  AAA_33    AAA domain
        0.1   13.1   0.1       0.22   11.9   0.1    1.8  1  AAA       ATPase family associated with various cellular acti
       0.27    8.7   0.0       0.37    8.3   0.0    1.0  1  DUF3584   Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   3.2e-27   3.6e-24       1     136 [.      18     162 ..      18     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 3.2e-27
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS...--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe...pqlfpeltvr 77 
                                    l+ v+l+++   +v+i+G+nGaGK+t+lk+++gl kp+ G++ ldg + +  + e + +  g++pq+   p+l p + vr
  gi|118431094|ref|NP_147305.2|  18 LSGVNLEFRGPGLVQIIGPNGAGKTTFLKAILGLIKPARGRVFLDGFEATG-RPEMVGRYAGYVPQNpsaPKLSPMT-VR 95 
                                    567999999999**********************************99999.8899999********8877788877.99 PP

                                    HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    e             ++e++ ++l++lg+ +   +v++s+  +LS G+ qrv +ara++ +pk+l++DEp 
  gi|118431094|ref|NP_147305.2|  96 EFvetslrlrgvtRARERAVEVLHTLGIRG---EVLESRLWELSMGMLQRVFIARAIAPDPKMLVMDEPL 162
                                    99*999*99988888888888999999777...88888889****************************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 !   23.8   0.2     3e-08   3.4e-05       4      23 ..      33      52 ..      30      85 .. 0.80
   2 !   21.2   0.0     2e-07   0.00022     226     302 ..     124     196 ..      61     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3e-08
                         AAA_21  4 liGpNgsGKSnLLdaldlla 23
                                   +iGpNg+GK+++L+a+ +l 
  gi|118431094|ref|NP_147305.2| 33 IIGPNGAGKTTFLKAILGLI 52
                                   8***************9994 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2e-07
                         AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                    +g   e  ++elS+G+++  +++ a++ ++   + l+ DEp ++ +P+   ++++++  l+r    v++t+H+p+ll
  gi|118431094|ref|NP_147305.2| 124 RGEVLESRLWELSMGMLQRVFIARAIAPDP---KMLVMDEPLASVDPAGRMEIARIIAGLAR-ERLVLMTSHDPSLL 196
                                    5555556789********966666666666...9***********************55555.3668********97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.2   2.1e-09   2.3e-06      12      39 ..      20      48 ..      16      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.1e-09
                         AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAi 39
                                   +++++F ++gl+ I+GpNGaGKTT+l Ai
  gi|118431094|ref|NP_147305.2| 20 GVNLEFrGPGLVQIIGPNGAGKTTFLKAI 48
                                   67899*99********************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 !   14.9   0.1   1.2e-05     0.013      24      45 ..      28      49 ..      20      57 .. 0.86
   2 !    6.3   0.0     0.005       5.7     141     209 ..     134     203 ..      92     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                   SSEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnlldAil 45
                                   +++  i+GpNG+GK+ +l Ail
  gi|118431094|ref|NP_147305.2| 28 PGLVQIIGPNGAGKTTFLKAIL 49
                                   67789***************94 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.005
                                    HHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 141 ektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                                    e ++ +l  +f  +++ p p + ++De  a  D + + ++a+++     +  ++++s++  +l     ++
  gi|118431094|ref|NP_147305.2| 134 ELSMGMLQRVFIARAIAPDPkMLVMDEPLASVDPAGRMEIARIIAGLARERLVLMTSHDPSLLLGHTDII 203
                                    667777888888889999987899************************9999****99988776665555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.3e-07   0.00037      16      50 ..      22      56 ..      16      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.3e-07
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                    +e++  g + ++Gp+G+GK+T+l Ai  l+ pa+
  gi|118431094|ref|NP_147305.2| 22 NLEFRGPGLVQIIGPNGAGKTTFLKAILGLIKPAR 56
                                   56666566899*******************99987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.8e-06    0.0054      25      48 ..      30      53 ..      18      67 .. 0.82
   2 ?    2.3   0.0     0.097   1.1e+02     319     368 ..     148     195 ..     135     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
                         AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                   l  +iG+N++GK+++l+a+  +++
  gi|118431094|ref|NP_147305.2| 30 LVQIIGPNGAGKTTFLKAILGLIK 53
                                   6779***************87766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.097
                         AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                     +  +++ l+++EP a+  p   +++++ ++ la++    v++t+H p +
  gi|118431094|ref|NP_147305.2| 148 AIAPDPKMLVMDEPLASVDPAGRMEIARIIAGLARER--LVLMTSHDPSL 195
                                    3677999******************************..5******9975 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0013      15      49 ..      19      51 ..       3      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                         AAA_27 15 tdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   ++ +l+f+   ++l  i+GpN AGK+t l+Ai  l
  gi|118431094|ref|NP_147305.2| 19 SGVNLEFR--GPGLVQIIGPNGAGKTTFLKAILGL 51
                                   45567777..9********************9877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2     8e-06     0.009      20      96 ..      30     160 ..      24     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-06
                         AAA_30  20 vavltGpAGtGKttalkalreaweaa.g............................................grviglAp 54 
                                    ++ + Gp G+GKtt lka+  +++ a g                                             r+ g++ 
  gi|118431094|ref|NP_147305.2|  30 LVQIIGPNGAGKTTFLKAILGLIKPArGrvfldgfeatgrpemvgryagyvpqnpsapklspmtvrefvetsLRLRGVTR 109
                                    56789***************999999567777777777777777444444444444444444444444444444444444 PP

                         AAA_30  55 tgkaAkvLaeelgieastiakllkrlk.........grarlepg.tllivDE 96 
                                      + A ++ + lgi+++ +++ l +l          +  +++p+ ++l+ DE
  gi|118431094|ref|NP_147305.2| 110 ARERAVEVLHTLGIRGEVLESRLWELSmgmlqrvfiA-RAIAPDpKMLVMDE 160
                                    4444444445777777777777766667777777753.45666667777777 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     2e-05     0.023      23      63 ..      27      67 ..      21     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +p+lv ++G+ G GK++ ++++l  ++ ++g ++   ++  
  gi|118431094|ref|NP_147305.2| 27 GPGLVQIIGPNGAGKTTFLKAILGLIKPARGRVFLDGFEAT 67
                                   468999*****************999999877755555554 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 ?   13.2   0.0   3.1e-05     0.035     131     162 ..      30      61 ..      14     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                          T2SSE 131 lilvsGgTgsGKttllyallkeinksderivt 162
                                    l+ + G+ g GKtt+l a+l  i+    r+ +
  gi|118431094|ref|NP_147305.2|  30 LVQIIGPNGAGKTTFLKAILGLIKPARGRVFL 61 
                                    56678******************999888765 PP

>> AAA_24  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      0.04       5      23 ..      31      56 ..      30     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                         AAA_24  5 iliyGpsgiGKTtlakel.......g 23
                                   ++i+Gp+g+GKTt++k +        
  gi|118431094|ref|NP_147305.2| 31 VQIIGPNGAGKTTFLKAIlglikpaR 56
                                   689************99877666533 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.14       5      28 ..      28      51 ..      24     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                         AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                    g++ ++G+ G+GKTt l+ +l  
  gi|118431094|ref|NP_147305.2| 28 PGLVQIIGPNGAGKTTFLKAILGL 51
                                   67888*************998766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012      0.14       3      24 ..      31      52 ..      29      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                   v + G++G GKTt+l+ +  ++
  gi|118431094|ref|NP_147305.2| 31 VQIIGPNGAGKTTFLKAILGLI 52
                                   7799************998665 PP

>> AAA_33  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      0.18       1      20 [.      30      49 ..      30      83 .. 0.92
   2 ?   -3.4   0.0       8.8   9.8e+03      76      96 ..     159     181 ..     138     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         AAA_33  1 lvllvGlpGsGKstlaerll 20
                                   lv ++G++G+GK+t+++ +l
  gi|118431094|ref|NP_147305.2| 30 LVQIIGPNGAGKTTFLKAIL 49
                                   6789***********99865 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.8
                         AAA_33  76 datnls..rrerarflklarrlg 96 
                                    d +++s  ++ r+++ ++   l 
  gi|118431094|ref|NP_147305.2| 159 DEPLASvdPAGRMEIARIIAGLA 181
                                    55544422344555544444333 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 ?   11.9   0.1    0.0002      0.22       3      23 ..      33      53 ..      31     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                   EESSTTSSHHHHHHHHHHHHT CS
                            AAA  3 lyGppGtGKTllakavakelg 23
                                   ++Gp G GKT++ ka+   ++
  gi|118431094|ref|NP_147305.2| 33 IIGPNGAGKTTFLKAILGLIK 53
                                   79**************98775 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00033      0.37       9      36 ..      20      47 ..      15      48 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00033
                        DUF3584  9 GrvaeldldghtnieGtNaaGKTtLlrL 36
                                   G+  e +  g ++i G N+aGKTt l+ 
  gi|118431094|ref|NP_147305.2| 20 GVNLEFRGPGLVQIIGPNGAGKTTFLKA 47
                                   55567777789*************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1803.90
//
Query:       gi|118431095|ref|NP_147306.2|  [L=270]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-14   53.9  22.7    2.1e-14   53.6  22.7    1.0  1  ABC-3      ABC 3 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 !   53.6  22.7   1.2e-18   2.1e-14      15     256 ..      18     262 ..       9     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.2e-18
                          ABC-3  15 vslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellk..rktk.lkedtaigivls 91 
                                     +la + l+  +  rr  +l++a  H+al+   l+ + +    +g + ++l++ ++l + +  + ++ ++ dta ++++ 
  gi|118431095|ref|NP_147306.2|  18 AGLAYGSLSPTLYSRRLLFLAGAAPHSALAAASLGAVAAALTGVGGAWISLALGLTLIYAAgySIYRgVDPDTAAALLAG 97 
                                    57788889999999********************9999998888877777777777766651145554688********* PP

                          ABC-3  92 vflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkll 171
                                    ++ +lg++ + l+ ++ ++++  + G+ l  s+++ + ++++ ++ l++lll+   +  i +d+e A+ +g +v +++ll
  gi|118431095|ref|NP_147306.2|  98 FTASLGIAGLYLAGRTGASISTLVIGDPLLASRTEALAVLALGVLFLATLLLLGDRIAYIGVDREDAMLSGTRVWAYDLL 177
                                    ******************************************************************************** PP

                          ABC-3 172 llalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatGavivlvatllf 251
                                    l ++ial+ v  + +vG iL   ll iP+a+ + ltr  ++ ++   l g  + v Gl+l     +++ a   l+++l +
  gi|118431095|ref|NP_147306.2| 178 LYTMIALSTVGLITVVGFILEHVLLLIPGALILPLTRGSRTAALAGGLAGSAAGVGGLILGGLTGIPPAAASGLILMLTY 257
                                    ****************************************************************9999999888888888 PP

                          ABC-3 252 llall 256
                                    l++ll
  gi|118431095|ref|NP_147306.2| 258 LVVLL 262
                                    88775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2026.63
//
Query:       gi|14600786|ref|NP_147307.1|  [L=128]
Description: hypothetical protein APE_0535 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   63.0   0.1    2.6e-17   62.5   0.1    1.3  1  RHH_3          Ribbon-helix-helix domain
    6.6e-06   25.9   1.4    1.2e-05   25.1   1.4    1.5  1  RHH_1          Ribbon-helix-helix protein, copG family
    2.5e-05   24.3   0.6    5.6e-05   23.2   0.3    1.7  1  NikR_C         NikR C terminal nickel binding domain
  ------ inclusion threshold ------
       0.03   14.4   0.9       0.33   11.0   0.0    2.1  2  baeRF_family2  Bacterial archaeo-eukaryotic release factor fa
      0.082   13.0   0.0       0.22   11.6   0.0    1.7  1  DUF2120        Uncharacterized protein conserved in archaea (


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 !   62.5   0.1   7.3e-21   2.6e-17       2      44 .]       3      45 ..       2      45 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 7.3e-21
                         RHH_3  2 ktrttvsidpelaekLkaLSekTrIprSklldeAiellLekYe 44
                                  k+r++vsi+++la++L++ S++++++rS+l+++A+e lLe+Y+
  gi|14600786|ref|NP_147307.1|  3 KRRFGVSIPEDLAQRLDEASRRLGVERSRLVEKAVEALLEDYR 45
                                  9*****************************************6 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 !   25.1   1.4   3.3e-09   1.2e-05       1      38 [.       5      42 ..       5      43 .. 0.97

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.3e-09
                                  EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                         RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                  r+ ++++e+l+ rLde  rr+g+ rS l++ A++++le
  gi|14600786|ref|NP_147307.1|  5 RFGVSIPEDLAQRLDEASRRLGVERSRLVEKAVEALLE 42
                                  789*********************************98 PP

>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.3   1.6e-08   5.6e-05      19      65 ..      69     114 ..      64     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.6e-08
                                   HHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHT CS
                        NikR_C  19 ltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklra 65 
                                   +++   +++d++ + lh h + + c+e+i+++G++ +i  l  +l +
  gi|14600786|ref|NP_147307.1|  69 IATAVEKFRDIVAARLHSHTTGR-CIEAIIVEGDSMRIAMLHRQLES 114
                                   66677899***********6665.****************9998865 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 ?    2.1   0.2     0.052   1.9e+02     101     132 ..      13      45 ..       9      52 .. 0.66
   2 ?   11.0   0.0   9.2e-05      0.33      55      96 ..      72     113 ..      63     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.052
                 baeRF_family2 101 elvvevegggraagadreal.aeevaealaerr 132
                                   +l+  +++ +r  g++r  l +++v+++l+++r
  gi|14600786|ref|NP_147307.1|  13 DLAQRLDEASRRLGVERSRLvEKAVEALLEDYR 45 
                                   556677777888888777651455666666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.2e-05
                 baeRF_family2  55 swerNaeavAeevdrlvresgaelVvlaGDvrarsllrdeLp 96 
                                   ++e+  + vA+++ +  + +  e++++ GD    ++l+++L+
  gi|14600786|ref|NP_147307.1|  72 AVEKFRDIVAARLHSHTTGRCIEAIIVEGDSMRIAMLHRQLE 113
                                   55666678*******************************996 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     6e-05      0.22      45     107 ..      18     122 ..       5     126 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6e-05
                       DUF2120  45 leellekldaeevdleseeakklieklde..........................................sireveeiee 83 
                                   l+e   +l +e+  l+++ +++l+e   +                                          + r  e i  
  gi|14600786|ref|NP_147307.1|  18 LDEASRRLGVERSRLVEKAVEALLEDYRHlltrhscsgiiivscpprgeaeiatavekfrdivaarlhshtTGRCIEAIIV 98 
                                   555555555555555555555555555555555555555555555555555555555555566666666655556677888 PP

                       DUF2120  84 evdafglerlkeslEalgleveYk 107
                                   e d++ + +l+++lE++g+ + Y 
  gi|14600786|ref|NP_147307.1|  99 EGDSMRIAMLHRQLESVGCGARYI 122
                                   99*******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1014.40
//
Query:       gi|118431096|ref|NP_147308.2|  [L=327]
Description: hypothetical protein APE_0536.1 [Aeropyrum pernix K1]
Scores for complete 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   31.1   0.0    5.4e-05   22.5   0.0    2.3  2  Glyco_hydro_99   Glycosyl hydrolase family 99
    0.00027   20.5   0.0       0.49    9.8   0.1    2.6  3  Glyco_tran_WbsX  Glycosyltransferase WbsX
  ------ inclusion threshold ------
      0.043   12.6   0.3      0.081   11.7   0.3    1.5  1  Glyco_hydro_71   Glycosyl hydrolase family 71


Domain annotation for each model (and alignments):
>> Glyco_hydro_99  Glycosyl hydrolase family 99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     9e-09   5.4e-05      60     127 ..      28      94 ..      24     133 .. 0.92
   2 !    6.3   0.0   0.00077       4.6     287     313 ..     240     266 ..     226     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9e-09
                                    ETT-S--TT-HHHHHHHHHHHHHHTEEEEEEEE-GGGCCCHHHHHHHHHHHHHHTT-EEEEEE---TT CS
                 Glyco_hydro_99  60 pelGsyssrdpeiiekhlemmrkasiGvlalswydeddeaedksvdllldkaakkklkvtfhiepyss 127
                                    p lG y srdp +++  l ++  a +  l +sw++   + + +   l++++  +++lk +  +epy  
  gi|118431096|ref|NP_147308.2|  28 PLLGYYDSRDPVVVDWQLGLISDAGVDCLFVSWWGPGSFED-EASRLVFQRLGEHGLKAAILVEPYLG 94 
                                    88********************************9887766.778999*****************976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00077
                                    T-S-EEES-SS-CCCT---S-EE-EBE CS
                 Glyco_hydro_99 287 kaslisitsfnewheGtqiekavpkkt 313
                                    ++ l+++ s+ne+he + ie+    ++
  gi|118431096|ref|NP_147308.2| 240 RVRLVAVYSWNEYHERSMIEPHRDATA 266
                                    67899***************9765554 PP

>> Glyco_tran_WbsX  Glycosyltransferase WbsX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00041       2.4      48      74 ..      30      56 ..      20      66 .. 0.84
   2 ?   -2.0   0.0      0.31   1.9e+03     136     166 ..     105     138 ..     100     143 .. 0.72
   3 !    9.8   0.1   8.3e-05      0.49     311     339 ..     235     263 ..     219     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00041
                Glyco_tran_WbsX 48 lgyYdlrekevleeqaelakeygiegf 74
                                   lgyYd r++ v+ +q  l  ++g++  
  gi|118431096|ref|NP_147308.2| 30 LGYYDSRDPVVVDWQLGLISDAGVDCL 56
                                   89**********************963 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.31
                Glyco_tran_WbsX 136 dkehfeyllpafkd...erYikvdgkpllliyrp 166
                                    ++e ++y+ + f +   e Y+  +g+pl+l ++p
  gi|118431096|ref|NP_147308.2| 105 WEETLDYVYENFVEkysESYLSWEGRPLVLAFNP 138
                                    677777777766552225799******9999987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 8.3e-05
                Glyco_tran_WbsX 311 kkkkeeeklvfinaWNEWaEgayLEPdek 339
                                     ++ ++ +lv + +WNE+ E +++EP + 
  gi|118431096|ref|NP_147308.2| 235 LRNMDRVRLVAVYSWNEYHERSMIEPHRD 263
                                    55666789******************865 PP

>> Glyco_hydro_71  Glycosyl hydrolase family 71
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   1.4e-05     0.081     206     244 ..     225     267 ..     156     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                 Glyco_hydro_71 206 dlwakRweqvlelqp..dfveiitWNDygEShYigplkek..k 244
                                    + +a  we vl++ +  ++v + +WN y E + i p +++   
  gi|118431096|ref|NP_147308.2| 225 NAYAIQWEWVLRNMDrvRLVAVYSWNEYHERSMIEPHRDAtaV 267
                                    467789*****9987789******************8887441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 2897.52
//
Query:       gi|118431097|ref|NP_147309.2|  [L=338]
Description: hypothetical protein APE_0537.1 [Aeropyrum pernix K1]
Scores for 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   35.5   0.0    1.3e-08   34.8   0.0    1.3  1  ATP_bind_3      PP-loop family
     0.0015   17.7   0.0     0.0021   17.2   0.0    1.2  1  NAD_synthase    NAD synthase
     0.0018   18.3   6.7      0.014   15.4   0.2    3.2  3  DZR             Double zinc ribbon
     0.0063   16.0   0.9     0.0063   16.0   0.9    2.5  3  zn-ribbon_14    Zinc-ribbon
  ------ inclusion threshold ------
      0.018   15.0  12.1      0.052   13.5   1.6    3.6  3  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
        2.9    7.4   9.3        2.7    7.5   0.5    3.3  3  zf-ribbon_3     zinc-ribbon domain


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 !   34.8   0.0   4.3e-12   1.3e-08       2     128 ..      54     193 ..      53     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.3e-12
                                    EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE--H..........HH CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr.eeskeeaelvkelckklnikleiekvdv..........ak 70 
                                    vl+++SgG DS +Ll +l +      ++lva+ +  g+   + + + e ++++++  ++++++++++           ++
  gi|118431097|ref|NP_147309.2|  54 VLLGLSGGKDSYVLLDALSEI--VGPSRLVAVSIVEGIPgYNREGDIEKIRRVAAARGVDVIVTSIREyvgaslyeiySR 131
                                    799****************99..55889******99*997899************************9999999999966 PP

                                    CTTSTCCCHHHH....HHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH- CS
                     ATP_bind_3  71 kkgknleeaARe....lRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglag 128
                                     +g++  +aA +     R ++l+ +++ +g++ +++Ah+ dD a t+++++ rg  + +l  
  gi|118431097|ref|NP_147309.2| 132 ARGRGAGHAACTycgiSRRRILALYARLYGAHKVATAHNLDDEAQTAIVNFLRGDWVGMLKT 193
                                    66777776665422227************************************998866655 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     7e-07    0.0021      19      92 ..      52     128 ..      31     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7e-07
                                    SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--...SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHH CS
                   NAD_synthase  19 kgvvlGlSGGvDSslvaalavkalgkenvlalllP...ssvsseedvedalalaenlgievktidikpivrafeqel 92 
                                    + v+lGlSGG DS +      +++g+ + +a+ +      ++ e d+e+ + +a   g++v + +i+++v a+  e+
  gi|118431097|ref|NP_147309.2|  52 ETVLLGLSGGKDSYVLLDALSEIVGPSRLVAVSIVegiPGYNREGDIEKIRRVAAARGVDVIVTSIREYVGASLYEI 128
                                    789************999999***********987323357999************************998876544 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.021        62      14      34 ..       5      29 ..       2      35 .. 0.69
   2 ?    1.0   0.1      0.15   4.4e+02      42      49 .]     139     146 ..     129     151 .. 0.73
   3 !   15.4   0.2   4.6e-06     0.014      27      49 .]     282     307 ..     261     307 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.021
                            DZR 14 fCseCgtk....lkavaaedrCpsC 34
                                   +C+ Cg +    l++ +  + C +C
  gi|118431097|ref|NP_147309.2|  5 VCDVCGVRravvLQRHTGRRLCREC 29
                                   6888888855555544448888888 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                            DZR  42 arfCpeCG 49 
                                    ++ C +CG
  gi|118431097|ref|NP_147309.2| 139 HAACTYCG 146
                                    45555555 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 4.6e-06
                            DZR  27 a...edrCpsCgekvdpearfCpeCG 49 
                                    +     rC +Cge+++p+ r C+ C+
  gi|118431097|ref|NP_147309.2| 282 KpssLGRCERCGEPTSPKRRLCKLCE 307
                                    1444789****************995 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.4       2.3   6.8e+03       3       7 ..       6      10 ..       6      11 .. 0.86
   2 ?   -1.5   0.3       0.6   1.8e+03       2       7 ..     141     146 ..     140     150 .. 0.84
   3 !   16.0   0.9   2.1e-06    0.0063       1      22 [.     287     310 ..     287     311 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                   zn-ribbon_14  3 CerCG 7 
                                   C  CG
  gi|118431097|ref|NP_147309.2|  6 CDVCG 10
                                   999*9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.6
                   zn-ribbon_14   2 kCerCG 7  
                                     C+ CG
  gi|118431097|ref|NP_147309.2| 141 ACTYCG 146
                                    5999*9 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.1e-06
                   zn-ribbon_14   1 gkCerCGylSS..qkiCkACvLLe 22 
                                    g+CerCG  +S   ++Ck C LLe
  gi|118431097|ref|NP_147309.2| 287 GRCERCGEPTSpkRRLCKLCELLE 310
                                    79*********6668********9 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 ?   -0.9   0.2      0.53   1.6e+03       6      10 ..       6      10 ..       3      11 .. 0.87
   2 ?    6.8   0.3    0.0021       6.4      23      33 ..      22      32 ..      13      33 .. 0.89
   3 ?   13.5   1.6   1.7e-05     0.052       2      18 ..     285     301 ..     284     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.53
                   zf-dskA_traR  6 CeeCG 10
                                   C++CG
  gi|118431097|ref|NP_147309.2|  6 CDVCG 10
                                   ****9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0021
                   zf-dskA_traR 23 garlCveCqek 33
                                   g+rlC+eC+++
  gi|118431097|ref|NP_147309.2| 22 GRRLCRECFRE 32
                                   89******985 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.7e-05
                   zf-dskA_traR   2 iygsCeeCGEpIpeaRl 18 
                                    ++g+Ce+CGEp  ++R+
  gi|118431097|ref|NP_147309.2| 285 SLGRCERCGEPTSPKRR 301
                                    6799**********997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.38   1.1e+03       4       9 ..       5      10 ..       4      12 .. 0.56
   2 ?    3.8   0.4     0.014        41      18      24 ..     141     147 ..     137     148 .. 0.82
   3 ?    7.5   0.5    0.0009       2.7       4      23 ..     288     307 ..     287     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.38
                    zf-ribbon_3  4 rCPnCG 9 
                                    C  CG
  gi|118431097|ref|NP_147309.2|  5 VCDVCG 10
                                   355555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                    zf-ribbon_3  18 vCpyCGt 24 
                                    +C+yCG 
  gi|118431097|ref|NP_147309.2| 141 ACTYCGI 147
                                    7*****5 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0009
                    zf-ribbon_3   4 rCPnCGaplssddnvCpyCG 23 
                                    rC +CG+p s+  + C+ C 
  gi|118431097|ref|NP_147309.2| 288 RCERCGEPTSPKRRLCKLCE 307
                                    799*************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 2883.97
//
Query:       gi|14600790|ref|NP_147311.1|  [L=91]
Description: 50S ribosomal protein L13 [Aeropyrum pernix K1]
Scores for 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   46.4   0.0    4.2e-12   46.3   0.0    1.1  1  Ribosomal_L13e  Ribosomal protein L13e


Domain annotation for each model (and alignments):
>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.0   2.3e-16   4.2e-12      62     116 ..      34      84 ..       3      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.3e-16
                Ribosomal_L13e  62 vraGrGFtleElkaagiskklArtiGIavDhRrknkseeslkaNveRLkeYkskL 116
                                   vr GrGF+l El +ag+++k Ar++G+ vD+Rr+         Nve Lk+Y ++L
  gi|14600790|ref|NP_147311.1|  34 VRRGRGFSLGELAEAGLDAKKARKLGLHVDTRRRTVH----PWNVEALKKYIERL 84 
                                   8********************************9864....36666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 695.95
//
Query:       gi|118431098|ref|NP_147312.2|  [L=389]
Description: hypothetical protein APE_0540.1 [Aeropyrum pernix K1]
Scores for complete 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   66.3   0.0    4.1e-18   65.9   0.0    1.2  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.026   14.3   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.023   15.2   0.0      0.043   14.3   0.0    1.4  1  ABC_tran  ABC transporter
      0.087   12.9   0.0        0.3   11.2   0.0    1.8  2  MMR_HSR1  50S ribosome-binding GTPase
       0.12   12.6   0.0       0.24   11.5   0.0    1.7  1  AAA_33    AAA domain


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 !   65.9   0.0   1.1e-21   4.1e-18       1     181 [.      89     253 ..      89     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.1e-21
                         CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpi..dveegfsldaplvyffGdtspsdnps 78 
                                    Gp+dsGKSTla++++N+    g    ++ +D+Gq+e+  Pg+++la  +  +    +++fs+ +p  +f+G  +p+++ s
  gi|118431098|ref|NP_147312.2|  89 GPSDSGKSTLAAWIVNRG---GGGYRLLSADIGQNEVFAPGFMALASPQGVAvpGLDDSFSSVEP--CFVGGFTPRGSES 163
                                    99**************94...666679********************999886644566777777..5************ PP

                         CLP1_P  79 lylalvkelareveekleenkkakasgliIntpGwvkg.lgaellleliealepdvvvvldq.eellnelkrdlplskvk 156
                                    +yla+ ++la+ ++             ++++t+Gw++  +g+e + +l+ a ++ +vv+++  ++    l+r   l++++
  gi|118431098|ref|NP_147312.2| 164 RYLACASRLASLAS------------QVVVDTDGWISLwEGLESKAALAIASRARLVVAVGIaSRRARLLERVWGLDTLS 231
                                    **********8666............7**********736*********************9899999999999988888 PP

                         CLP1_P 157 vvklpkspgvvqrsreerrelreer 181
                                    v++l+   g    sr er+  re+ 
  gi|118431098|ref|NP_147312.2| 232 VERLAGEAGK---SRGERALHRERL 253
                                    8888887775...888888888765 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   0.0   7.3e-06     0.026      18      38 ..      78      98 ..      69     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.3e-06
                         AAA_29 18 eidlkgatlltGpsGsGKSTl 38
                                   e +++g + ++Gps sGKSTl
  gi|118431098|ref|NP_147312.2| 78 EASQRGRVAIVGPSDSGKSTL 98
                                   55667899************9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.043       8      32 ..      79     103 ..      72     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                    EETTSEEEEEESTTSSHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlklla 32 
                                     ++  +vaivG++ +GKStL++ + 
  gi|118431098|ref|NP_147312.2|  79 ASQRGRVAIVGPSDSGKSTLAAWIV 103
                                    566779**************99886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.4e-05       0.3       1      21 [.      84     104 ..      84     119 .. 0.88
   2 ?   -1.9   0.0      0.95   3.4e+03      49      72 ..     179     199 ..     168     224 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.4e-05
                                    EEEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg 21 
                                    +vaivG + +GKStL   +++
  gi|118431098|ref|NP_147312.2|  84 RVAIVGPSDSGKSTLAAWIVN 104
                                    69*************988877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.95
                                    EEEECGGCSSHHHHHH.HHHHHHHH CS
                       MMR_HSR1  49 elvDtpGliegaseek.glgkafla 72 
                                    ++vDt G i+     + gl+ + + 
  gi|118431098|ref|NP_147312.2| 179 VVVDTDGWIS----LWeGLESKAAL 199
                                    6899999875....33333332222 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.7e-05      0.24       3      39 ..      86     124 ..      85     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.7e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                     +vG++ sGKstla  ++++ g  + lls d+  + +f+
  gi|118431098|ref|NP_147312.2|  86 AIVGPSDSGKSTLAAWIVNRGGggYRLLSADIGQNEVFA 124
                                    689**************9888899999999996666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3066.58
//
Query:       gi|118431099|ref|NP_147314.2|  [L=124]
Description: hypothetical protein APE_0542.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.9   1.8       0.44   11.1   0.1    2.5  3  HTH_27    Winged helix DNA-binding domain


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 ?   -1.8   0.0      0.26   4.6e+03      37      45 ..       6      14 ..       3      28 .. 0.70
   2 ?    0.3   0.1     0.056     1e+03       8      24 ..      29      45 ..      20      49 .. 0.62
   3 ?   11.1   0.1   2.4e-05      0.44      35      64 ..      74     101 ..      68     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.26
                         HTH_27 37 yslkkLtek 45
                                   +++k+L e+
  gi|118431099|ref|NP_147314.2|  6 EAVKRLLER 14
                                   777887775 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.056
                         HTH_27  8 vLhlirhrrrrkkladl 24
                                    L+ +++r+++++ +++
  gi|118431099|ref|NP_147314.2| 29 ALRRLEERGEEATVERV 45
                                   45555566666665655 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 2.4e-05
                         HTH_27  35 isyslkkLtekGLvertgdeadrrekrvrl 64 
                                    +s++l++L e GLve+      r  +r+r+
  gi|118431099|ref|NP_147314.2|  74 VSSVLRELAESGLVEMVDGG--RSIVRYRI 101
                                    569***********998554..44488775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1040.01
//
Query:       gi|118431100|ref|YP_874832.1|  [L=385]
Description: hypothetical protein APE_0543 [Aeropyrum pernix K1]
Scores for complete 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   50.2  76.5    6.4e-11   41.8  48.3    2.0  2  MFS_1      Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.01   14.6   5.4      0.014   14.2   5.4    1.2  1  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 !   41.8  48.3   7.2e-15   6.4e-11       5     351 ..      14     333 ..      11     335 .. 0.76
   2 !   22.1  20.2   6.6e-09   5.9e-05       3     171 ..     202     364 ..     197     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 7.2e-15
                          MFS_1   5 aflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                     +l ++a++ ++ +++  a+ e lg     +g l+++   + ++as++lG+l+dr+G r  l lgl+  +l  ++++f +
  gi|118431100|ref|YP_874832.1|  14 SLLLFWASYSIYYTITRrAVEEGLGEGSYLLGVLMSGAEEAPLAASIVLGYLADRLGYRLPLALGLFEAGLV-AAMAF-T 91 
                                    4566677777777777779999999888889999999999********************************.66666.6 PP

                          MFS_1  84 slwlllvlrvlqGlg...agalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                    +   l    +l+G++   ++++++a + l+   +     g+ +++++a+ slG +lg l+gg+ +s lg  ++ +++a++
  gi|118431100|ref|YP_874832.1|  92 P---LETYPILAGAAslvYALSYSALMGLVLGESG--GSGFRYSVIAAFGSLGWALGGLAGGAAYSRLGSLGLLVAAALM 166
                                    6...5555555555500044444444444444444..599****************************976666666666 PP

                          MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgl 240
                                    ++    l  + l ++pp+ +  +++ e            ++al+   +   l+++l + ++++ +++    + l e l  
  gi|118431100|ref|YP_874832.1| 167 AASY--L--VALSASPPRGGAAPSVGE-----------TITALKGVLP---LFASLSTSWAALGFFFGAASIRLSEALES 228
                                    6666..4..889999999999999999...........3555555552...45555555555555555555546888888 PP

                          MFS_1 241 sglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl.iGf.glgfvf 318
                                    +   ++++l  ++al+g+ +++ agrl+d+ g+   l l+ ++ +l+al + l   +       ++l+l +++  + f  
  gi|118431100|ref|YP_874832.1| 229 P-IAYGLVLTTVPALLGFLARPAAGRLVDKAGAVAVLALSNAAYSLLALVFGLPTSP-------ALLALaWSLpLYPFRD 300
                                    8.788888899999999999**********999777777777777777777777777.......3333348999999999 PP

                          MFS_1 319 psllalasdlappeeagtasglfntagslggal 351
                                    ++++ ++s+ + ++ ++ta+gl +   s+gga 
  gi|118431100|ref|YP_874832.1| 301 AAAAIAVSSRLERRLQATAAGLLSASESVGGAA 333
                                    99****************************985 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 6.6e-09
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                     ++  s +a ++++ a+++ l+e+l  sp ++gl l+t+ al+ ++a + +Grl+d+ G+  vl l+ ++++l +l++ +
  gi|118431100|ref|YP_874832.1| 202 ASLSTSWAALGFFFGAASIRLSEALE-SPIAYGLvLTTVPALLGFLARPAAGRLVDKAGAVAVLALSNAAYSLLALVFGL 280
                                    4455566666777777777899****.*******5555599999******************************666666 PP

                          MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                     +++++ll+l     l   +  +a+a++++    ++ ++ a gllsa+ s+G + + +l+ ll   +g+r ++ +  +++
  gi|118431100|ref|YP_874832.1| 281 -PTSPALLALAWSLPLY-PFRDAAAAIAVSSRLERRLQATAAGLLSASESVGGAATLALALLLD--GGFREMMTASIALM 356
                                    .9999888888888886.79************************************99999998..99****99999999 PP

                          MFS_1 162 llafvlflll 171
                                    ll+ +l  l 
  gi|118431100|ref|YP_874832.1| 357 LLSTLL--LA 364
                                    999884..22 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.4   1.6e-06     0.014      17     175 ..      16     164 ..       7     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-06
                      LacY_symp  17 ffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfe 96 
                                     +++  +s+y+++    ++e lg     +G++ s  +   +    ++G + d+lG + +l   +       +      f+
  gi|118431100|ref|YP_874832.1|  16 LLFWASYSIYYTITRRAVEEGLGEGSYLLGVLMSGAEEAPLAASIVLGYLADRLGYRLPLALGLFEA----GLVAAMAFT 91 
                                    33333366777777777777777777789****************************9996554333....33344689* PP

                      LacY_symp  97 pllqlnilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilfsidpslvfwlasg 175
                                    pl    il+Ga   ++   l ysa  g++       s  s f y  + +fG+lG+al+    G  +s   sl + +a+ 
  gi|118431100|ref|YP_874832.1|  92 PLETYPILAGAA--SLVYALSYSALMGLVL----GESGGSGFRYSVIAAFGSLGWALGGLAGGAAYSRLGSLGLLVAAA 164
                                    **********84..6777888888888774....46899*******************999999888777776666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3112.68
//
Query:       gi|118431101|ref|NP_147316.2|  [L=214]
Description: uracil phosphoribosyltransferase [Aeropyrum pernix K1]
Scores for complete 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-41  141.4   0.0    3.2e-41  141.1   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    4.1e-09   36.1   0.0    5.8e-09   35.6   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain


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 !  141.1   0.0   3.6e-45   3.2e-41       3     204 ..      11     209 ..       9     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 3.6e-45
                        UPRTase   3 shpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGegme 82 
                                    ++pl++  l +lRd++t  ++fr++v+  + +la+ + ++ l+  e++v+tplg++ ++       + lV il a ++m+
  gi|118431101|ref|NP_147316.2|  11 ETPLARYVLKVLRDRTTGFPEFRRYVRIAGSILAVYIAGE-LGWVEEEVETPLGAKAKELAPA-GPVYLVGILGASLPMV 88 
                                    57999999********************************.**************99876655.5*************** PP

                        UPRTase  83 ealrellpearvghlglqr..eeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                    e++ +++pear+  +   r  e+  l+ + yy++LP+ + +  +++lDp++aTG+++a+a++l ++rg+  +k+++ s++
  gi|118431101|ref|NP_147316.2|  89 EGFASMMPEARIALVAARRveEPGRLKIEVYYSRLPRMF-DGPAVVLDPMLATGKTVAEAVRLARDRGA--SKVVIGSII 165
                                    ************99999883344568999*******976.889999********************876..8******** PP

                        UPRTase 161 aseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRl 204
                                    as++gv+ +++ + ++ ++t a+D+elde+ +ivpGlGD+GDR 
  gi|118431101|ref|NP_147316.2| 166 ASRQGVEYISSLYGDTPIYTLALDPELDENYFIVPGLGDAGDRA 209
                                    *******************************************6 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   6.5e-13   5.8e-09      26     131 ..      70     172 ..      55     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 6.5e-13
                                    --GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHH CS
                   Pribosyltran  26 yngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTll 104
                                    ++  p+++vgi+  ++p++   a+ + e+++a v +++++++g  ++    s   rl+++++g  V + D +l+tG+T+ 
  gi|118431101|ref|NP_147316.2|  70 APAGPVYLVGILGASLPMVEGFASMMpEARIALVAARRVEEPGRLKIEVYYS---RLPRMFDGPAV-VLDPMLATGKTVA 145
                                    566899*****************************************97665...68888888766.56*********** PP

                                    HHHHHHHCC-BSEEEEEEEEE-HHHHH CS
                   Pribosyltran 105 aalelLkekgpeevriavlvdkpatee 131
                                    +a++l +++g+ +v i  +++ ++++e
  gi|118431101|ref|NP_147316.2| 146 EAVRLARDRGASKVVIGSIIASRQGVE 172
                                    **************9999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1647.48
//
Query:       gi|118431102|ref|NP_147317.2|  [L=437]
Description: pseudouridylate synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-30  106.2   0.2    5.3e-30  104.4   0.0    1.9  2  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0     3e-34   5.3e-30       1     144 []      24     198 ..      24     198 .. 0.99
   2 ?   -1.0   0.0     0.092   1.7e+03      16      45 ..     316     344 ..     289     364 .. 0.58

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 3e-34
                                    HHHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST........TECEEEEE.......EEEEESSHH CS
                          THUMP   1 geieellkegkvnverveagkgrivvelkgekpeedeellkealekar........giqrvipv.......cevceadle 65 
                                    g+++++l++g+ n+er+ea+k+++v+el+++++e+de++lk++++ a+        ++++++p+       c+vc+ +le
  gi|118431102|ref|NP_147317.2|  24 GRLFARLGRGWSNRERGEAVKRVLVMELHRRVLEGDEAALKTLVSAAPnigevardVVEHLSPGsyreggpCAVCGGRLE 103
                                    689***************************************************************************** PP

                                    HHHHHHHHHHHHHHHHCT-.EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEE CS
                          THUMP  66 dileaakeivkkkfeeeke.tFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPdivv 129
                                    +++++a+e  ++ +++++  +F V+v++++  +               e ++ ei+revGk++v+++g +Vd+++P+ ++
  gi|118431102|ref|NP_147317.2| 104 SVIASAVEEGYRLLRAYDIeRFVVGVRLERGVAmaeeevklaagagygESIKAEIRREVGKLLVSRGGVTVDFDSPEATL 183
                                    *******************************99*********************************************** PP

                                    EEEEETTEEEEEEEC CS
                          THUMP 130 rveiikdkayisidr 144
                                    +ve+ +  + i++++
  gi|118431102|ref|NP_147317.2| 184 MVEFPGGGVDIQVNS 198
                                    ************985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.092
                                    EEEEETTEEEEECTEEEEEETHHHHHHHHH CS
                          THUMP  16 rveagkgrivvelkgekpeedeellkeale 45 
                                    rv+++++  +v + g + e+d e l +ale
  gi|118431102|ref|NP_147317.2| 316 RVRKVYRA-LVAVEGGVSEVDVEGLRRALE 344
                                    33333222.333333334555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3549.87
//
Query:       gi|118431103|ref|YP_874833.1|  [L=107]
Description: 50S ribosomal protein L21 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-32  111.7   0.0    1.4e-32  111.5   0.0    1.0  1  Ribosomal_L21e  Ribosomal protein L21e
  ------ inclusion threshold ------
       0.24   11.5   0.5       0.93    9.6   0.5    2.0  1  SH3_12          Xrn1 SH3-like domain


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 !  111.5   0.0   1.6e-36   1.4e-32       2      99 ..       3      98 ..       2     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.6e-36
                                   --S-STTTT-TTTTS--GGG-S.S--SHHHH----TT-EEEE---TT--S.S---GGGTT-EEEE..EEEETTEEEEEEEET CS
                 Ribosomal_L21e  2 knskglrrgtrklfskkfrkkg.vpplstylreykkGdkVdikidpsvqk.gmphkryhGktgrvynvtkravgvivnkkvg 81
                                   k+++g+r++tr+l++k++r+kg +p+lstylrey++GdkV+i i+ps+ + gmph+r+hG tg+v  v+kr++++ v++ +g
  gi|118431103|ref|YP_874833.1|  3 KAPRGYRNRTRRLLRKPVREKGsIPRLSTYLREYRVGDKVAIIINPSFPDwGMPHRRFHGLTGTV--VGKRGEAYEVEVYLG 82
                                   6799******************8889**********************999**************..*************** PP

                                   TE..EEEEEE-GGGEEE- CS
                 Ribosomal_L21e 82 gkileKriivriehlkks 99
                                    k  +K+++v + hlk++
  gi|118431103|ref|YP_874833.1| 83 RK--RKTLFVPPVHLKPL 98
                                   **..************97 PP

>> SH3_12  Xrn1 SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5    0.0001      0.93       4      37 ..      37      77 ..      34      95 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0001
                         SH3_12  4 rLgdrV.vyvrdngk..sVP....lGlrGtVVg..rsdtlleV 37
                                   r+gd V ++++ +     +P     Gl+GtVVg  +  + +eV
  gi|118431103|ref|YP_874833.1| 37 RVGDKVaIIINPSFPdwGMPhrrfHGLTGTVVGkrG--EAYEV 77
                                   5666665555554433445533335********552..44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 851.43
//
Query:       gi|118431104|ref|NP_147319.2|  [L=113]
Description: DNA-directed RNA polymerase subunit F [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.5   0.0      0.039   14.2   0.0    1.2  1  Neural_ProG_Cyt  Neural chondroitin sulphate proteoglycan cyt
      0.034   14.5   0.0      0.036   14.4   0.0    1.1  1  RNA_pol_Rpb4     RNA polymerase Rpb4


Domain annotation for each model (and alignments):
>> Neural_ProG_Cyt  Neural chondroitin sulphate proteoglycan cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-06     0.039      56     103 ..      35      82 ..      20      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-06
                Neural_ProG_Cyt  56 ralayydnivcqddpsas.hkieeplksplkeeeslniqnslspklend 103
                                    ++  y+ ++v  ddp+a+ + +ee +k  +  e + ni  s++pk e++
  gi|118431104|ref|NP_147319.2|  35 STWEYFRKVVFWDDPEAAsELVEEIVKEGVSREAAANI-ASICPKTEGE 82 
                                    566799*********87515679999999999999988.69******97 PP

>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-06     0.036      43     105 ..      31      92 ..       7     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-06
                                    HHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTT CS
                   RNA_pol_Rpb4  43 kilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieelee 105
                                     i++ t ey ++     +++e+++elve++ + +  +  ++++ +++P++  el+++ e +++
  gi|118431104|ref|NP_147319.2|  31 SIQESTWEYFRK-VVFWDDPEAASELVEEIVKEGVSREAAANIASICPKTEGELRSILEMDRS 92 
                                    677788888888.8888899*************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 816.75
//
Query:       gi|14600798|ref|NP_147320.1|  [L=326]
Description: hypothetical protein APE_0550 [Aeropyrum pernix K1]
Scores for 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-85  284.0   0.2      6e-85  283.8   0.2    1.1  1  DUF655    Protein of unknown function (DUF655)
    0.00085   19.5   1.7      0.001   19.2   0.2    2.0  2  HHH_3     Helix-hairpin-helix motif
     0.0026   18.0   0.4      0.012   15.9   0.2    2.1  2  HHH_6     Helix-hairpin-helix motif
     0.0081   16.0   0.6      0.031   14.1   0.0    2.2  2  HHH       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 !  283.8   0.2   1.3e-88     6e-85       1     181 []      25     290 ..      25     290 .. 0.99

  Alignments for each domain:
  == domain 1  score: 283.8 bits;  conditional E-value: 1.3e-88
                                   X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----.............................. CS
                        DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdil.............................. 51 
                                   le+eaivLDy+peGyp+d+hrehr+kpvvq+lg+r+l+L+++vpl+evdil                              
  gi|14600798|ref|NP_147320.1|  25 LEVEAIVLDYIPEGYPRDPHREHRSKPVVQGLGVRRLHLVDGVPLHEVDILervtlarevvysvpivarlpggverrvksv 105
                                   699****************************************************************************** PP

                                   .......................................................TT-EEE-SSS--SSEEEEEE.E--GG CS
                        DUF655  52 .......................................................kldevaigkgksdkivkikr.eisye 76 
                                                                                          kl+eva+g+g+s+kiv+++r +isy+
  gi|14600798|ref|NP_147320.1| 106 tvavtclpgqareggvreiycyplsyadqatlealqqllgegderhryilvdspdKLSEVARGHGLSGKIVSTPRdPISYQ 186
                                   ********************************************************************************* PP

                                   GS-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---H CS
                        DUF655  77 dLtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdp 157
                                   dLtdvara+Lpd+v+k+v+e+Ed+fveffn+aepi+iR+HaLe+L+gvgkk+ar++l+eRerrrF+sFe+vkk++k  +dp
  gi|14600798|ref|NP_147320.1| 187 DLTDVARATLPDAVRKLVREREDFFVEFFNVAEPINIRIHALEALKGVGKKMARHLLLERERRRFTSFEEVKKILK--IDP 265
                                   ****************************************************************************..*** PP

                                   HHHHHHHHHHHHH-T.TSS--SS-- CS
                        DUF655 158 aeilverileEiedk.tekYylFve 181
                                   ae+l+e+i+eEie++ t+kYy+Fve
  gi|14600798|ref|NP_147320.1| 266 AEALAEKIMEEIECRdTVKYYFFVE 290
                                   ***************9*******96 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.9   1.3e+04      11      20 ..     135     144 ..     134     145 .. 0.75
   2 !   19.2   0.2   2.3e-07     0.001      14      55 ..     226     266 ..     222     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.9
                         HHH_3  11 AsaeeLqklp 20 
                                   A++e Lq+l 
  gi|14600798|ref|NP_147320.1| 135 ATLEALQQLL 144
                                   8889999875 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.3e-07
                         HHH_3  14 eeLqklpGlgpklAknIvayReknGpfksreeLlkvkglgpk 55 
                                     L+ l+G+g+k+A+ ++  R ++ +f+s+ee +k+ +++p+
  gi|14600798|ref|NP_147320.1| 226 HALEALKGVGKKMARHLLLER-ERRRFTSFEEVKKILKIDPA 266
                                   6799*****************.777**************997 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.073   3.3e+02      38      74 ..     198     231 ..     188     231 .. 0.88
   2 !   15.9   0.2   2.6e-06     0.012      27      64 ..     226     262 ..     208     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.073
                         HHH_6  38 aaaerivaeRekegpfksledlarrvdslnkrqleaL 74 
                                   +a++++v+eRe    f +++++a+ ++ +  ++leaL
  gi|14600798|ref|NP_147320.1| 198 DAVRKLVRERE--DFFVEFFNVAEPIN-IRIHALEAL 231
                                   689999**997..79999999999999.999999987 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.6e-06
                         HHH_6  27 lGLaaikglgeaaaerivaeRekegpfksledlarrvd 64 
                                    +L+a+kg+g++ a++++ eRe ++ f+s+e++ + ++
  gi|14600798|ref|NP_147320.1| 226 HALEALKGVGKKMARHLLLERE-RRRFTSFEEVKKILK 262
                                   38*******************9.8******99876555 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.8   8.3e+03       8      16 ..     135     143 ..     134     143 .. 0.84
   2 !   14.1   0.0     7e-06     0.031      13      28 ..     228     243 ..     225     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                                   SSHHHHHTS CS
                           HHH   8 asreeLlal 16 
                                   a++e L++l
  gi|14600798|ref|NP_147320.1| 135 ATLEALQQL 143
                                   899999986 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7e-06
                                   HHTSTT-SHHHHHHHH CS
                           HHH  13 LlalPGVGpktAeaIl 28 
                                   L+al+GVG+k+A++ l
  gi|14600798|ref|NP_147320.1| 228 LEALKGVGKKMARHLL 243
                                   89***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2414.53
//
Query:       gi|14600800|ref|NP_147322.1|  [L=277]
Description: S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dimethyltransferase [Aeropyrum pernix K1]
Scores for complete 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   93.3   0.0    1.6e-26   92.9   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
       0.05   13.1   0.0      0.077   12.5   0.0    1.2  1  MTS              Methyltransferase small domain
       0.06   14.0   0.0       0.11   13.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
       0.13   11.4   0.0       0.21   10.7   0.0    1.4  1  DREV             DREV methyltransferase


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 !   92.9   0.0   3.7e-30   1.6e-26       7     229 ..      31     241 ..      26     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 3.7e-30
                                   GCG--EE--HHHHHHHHHHH-GG...TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S- CS
                        RrnaAD   7 sygqnflknkkvineIldklnle...ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqD 84 
                                   ++gq+fl++   + e l+ l+        + leigpG G  T + a+ ++  v++Eld+rLa  l+       ++ v+  D
  gi|14600800|ref|NP_147322.1|  31 RLGQHFLIDDRAVGEFLKPLEKAaaeGIREALEIGPGAGSITLPAAEVLDRIVAVELDNRLASALSR--LAPARVAVITGD 109
                                   78************99987776644356678************************************..6689******** PP

                                   CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHE CS
                        RrnaAD  85 flkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaft 165
                                   +   +  +         q  lv++n+P ++s ++v  l   +r     ++l +q e+arr++arpgs+++srlsvl+ +++
  gi|14600800|ref|NP_147322.1| 110 GVSHAAAS---------QAPLVFSNTPFNLSPAIVEALAVNNRV--AAAVLGVQYEVARRMTARPGSRDYSRLSVLVSLVF 179
                                   *******9.........7789*****************998888..89********************************* PP

                                   EEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTS CS
                        RrnaAD 166 dvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksll 229
                                    ++l   v ++++ P p+v  a+v l+r+        +++   +  +++++++k+ s++l + l
  gi|14600800|ref|NP_147322.1| 180 HAELAGVVRPQAYYPRPQVLTAVVTLRRRRRW--RSLYARALELAGCAFTQRNKKASKVLRRCL 241
                                   *****************************995..456666677999999999999999988765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05     0.077      32     113 ..      58     134 ..      40     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                                   CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCH CS
                           MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagka 112
                                    +++l +G GaG +++ +a+  ++  +++v+ d r l+sa   l+  +  v v++ d++++++  +  l+ sN Pf  + a
  gi|14600800|ref|NP_147322.1|  58 IREALEIGPGAGSITLPAAEVLDR--IVAVELDNR-LASALSRLAPAR--VAVITGDGVSHAAASQAPLVFSNTPFNLSPA 133
                                   3569****************9999..788888766.555555555444..6899**********************87766 PP

                                   C CS
                           MTS 113 t 113
                                   +
  gi|14600800|ref|NP_147322.1| 134 I 134
                                   4 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05      0.11       2      85 ..      62     137 ..      61     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGSSHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhlsded 81 
                                   L++G G G +tl +a+ l   ++++v+++ ++  a  + a    ++v +++gd  +   + ++  lv+s+ + +++ s + 
  gi|14600800|ref|NP_147322.1|  62 LEIGPGAGSITLPAAEVL--DRIVAVELDNRLASALSRLA---PARVAVITGDGVSHAAA-SQAPLVFSN-TpFNL-S-PA 133
                                   9***************99..9********99988887777...45999999999776644.488888885.43665.3.34 PP

                                   HHHH CS
               Methyltransf_25  82 leka 85 
                                   + +a
  gi|14600800|ref|NP_147322.1| 134 IVEA 137
                                   4444 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.6e-05      0.21      68     135 ..      33      98 ..      22     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.6e-05
                          DREV  68 GsmfvlseeqfrkllaiekespasdqedkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                   G+ f++ +     +l+  ++  a     ++ l++G G G it   a+ ++++ a el +++   l+++
  gi|14600800|ref|NP_147322.1|  33 GQHFLIDDRAVGEFLKPLEKAAA--EGIREALEIGPGAGSITLPAAEVLDRIVAVELDNRLASALSRL 98 
                                   66677777777777776533333..456778****************************999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2167.86
//
Query:       gi|118431105|ref|NP_147323.2|  [L=196]
Description: methyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0001   21.8   0.1    0.00014   21.3   0.1    1.1  1  PrmA      Ribosomal protein L11 methyltransferase (PrmA)
    0.00014   21.4   0.0    0.00022   20.8   0.0    1.2  1  MTS       Methyltransferase small domain


Domain annotation for each model (and alignments):
>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   1.6e-08   0.00014     148     196 ..      23      75 ..      21      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.6e-08
                           PrmA 148 Tklclealeklvkege...evlDvGtGSGiLaiaaa.kLgakkvvavDiDevA 196
                                    T l lea+e+l +eg+   + lD+GtG G La++a+  Lg ++v avD  +  
  gi|118431105|ref|NP_147323.2|  23 TILLLEAMEALRREGRvygSALDLGTGNGALALGAVeVLGVRRVAAVDAYPCP 75 
                                    678899*****999988889*************886269*********87765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-08   0.00022      21     107 ..      24     111 ..      21     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-08
                                    HHHHHHCHCC.....TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTT CS
                            MTS  21 klLletlpke.....lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleevee 95 
                                     lLle++++        g++lDlG+G+G+l++ + +     +v +vd+      +a+++l  ++l + +      + ++ 
  gi|118431105|ref|NP_147323.2|  24 ILLLEAMEALrregrVYGSALDLGTGNGALALGAVEVLGVRRVAAVDAYPCPALAARATLPPQALVAVCPYA---SCLK- 99 
                                    68888888876445555669****************************999999999999999884444443...3444. PP

                                    S-EEEEEE---S CS
                            MTS  96 kkfdlivsNPPf 107
                                    + fd+ + NPP+
  gi|118431105|ref|NP_147323.2| 100 GGFDIALVNPPY 111
                                    889********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1517.26
//
Query:       gi|118431106|ref|NP_147324.2|  [L=243]
Description: hypothetical protein APE_0555.1 [Aeropyrum pernix K1]
Scores for 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-29  100.5   0.0    1.4e-28   99.9   0.0    1.3  1  SpoU_methylase  SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.017   15.7   1.1      0.024   15.2   0.1    1.8  2  Deltaretro_Tax  Deltaretrovirus Tax protein


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0   1.5e-32   1.4e-28       2     142 .]       4     152 ..       3     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.5e-32
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalva 80 
                                    l++vlve+e + NlG +aR+a++f+a+e++lv+pr+     +eakr aa a+  l+ ++vv++leeal+ +  +    ++
  gi|118431106|ref|NP_147324.2|   4 LRIVLVETEGAVNLGFVARLAENFEADEIYLVSPRAS---LEEAKRYAARAAWRLDaARVVSNLEEALRGVSAS----LC 76 
                                    89********************************997...7789999999999999899*************99....34 PP

                                    EST..T-SEGCCS...HHH.........TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                 SpoU_methylase  81 tsl..kgkslsei...dlk.........ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                    ts+  ++++  ++    ++         + va+vfG+E+ Gl++ +++l++ + +Ip s++++SLN+++A+ai ly
  gi|118431106|ref|NP_147324.2|  77 TSShmSDRDALRAplaPWEaaevlaatpGTVAIVFGRESVGLTRGEIALCSLYSSIPASPRYPSLNLSNAAAIYLY 152
                                    4332433333322233222334445556**********************************************98 PP

>> Deltaretro_Tax  Deltaretrovirus Tax protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.6e-06     0.024       9      57 ..      38      86 ..      32     105 .. 0.84
   2 ?   -3.1   0.1       1.3   1.2e+04      42      53 ..     133     144 ..     124     148 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                 Deltaretro_Tax  9 rvrtesslripslrvwrlcsrrlvsrlrgalfgppasarpsrhlsrasd 57
                                   r   e + r  +   wrl + r+vs+l  al g  as + s h+s   +
  gi|118431106|ref|NP_147324.2| 38 RASLEEAKRYAARAAWRLDAARVVSNLEEALRGVSASLCTSSHMSDRDA 86
                                   666677778888889*****************************97665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
                 Deltaretro_Tax  42 ppasarpsrhls 53 
                                    p ++  ps  ls
  gi|118431106|ref|NP_147324.2| 133 PASPRYPSLNLS 144
                                    333444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1877.95
//
Query:       gi|14600803|ref|NP_147325.1|  [L=354]
Description: methyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-55  188.2   0.0    3.8e-55  186.6   0.0    1.7  1  UPF0020          Putative RNA methylase family UPF0020
    7.4e-21   74.8   0.0      1e-20   74.3   0.0    1.2  1  THUMP            THUMP domain
    4.7e-11   42.5   0.0    9.3e-11   41.6   0.0    1.4  1  MTS              Methyltransferase small domain
    1.3e-08   35.4   0.0    3.3e-08   34.1   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    3.5e-06   26.9   0.0    5.6e-06   26.3   0.0    1.2  1  Met_10           Met-10+ like-protein
    4.3e-06   26.6   0.0      7e-06   25.9   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    4.4e-06   27.3   0.0    2.7e-05   24.7   0.0    2.2  1  Methyltransf_11  Methyltransferase domain
    6.1e-05   22.6   0.0    8.3e-05   22.1   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    6.3e-05   22.6   0.0    9.4e-05   22.0   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00016   21.4   0.0    0.00023   20.9   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0003   20.5   0.0    0.00051   19.7   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.001   18.5   0.0     0.0015   17.9   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0038   17.0   0.0     0.0064   16.2   0.0    1.5  2  N6_N4_Mtase      DNA methylase
     0.0052   16.1   0.0      0.012   14.9   0.0    1.6  1  N6_Mtase         N-6 DNA Methylase
  ------ inclusion threshold ------
      0.052   14.3   0.0       0.14   12.9   0.0    1.7  1  Methyltransf_12  Methyltransferase domain


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 !  186.6   0.0   3.2e-58   3.8e-55       1     196 [.     173     346 ..     173     347 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.6 bits;  conditional E-value: 3.2e-58
                                   -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEE CS
                       UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklyg 81 
                                   R+yR++++pa+Lk++LA++++rlag+++g+++lDPmCG+Gt+++Eaall ++                          +y+
  gi|14600803|ref|NP_147325.1| 173 RRYRVYDHPAALKASLAYVMLRLAGARDGDTILDPMCGGGTVAVEAALLFETSR------------------------VYC 229
                                   89****************************************************........................9** PP

                                   EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--..STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT.. CS
                       UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLr..lkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrggg 160
                                   +Dl++r+++gar Nae+a+vg+++e++++da++L+  l e++vd iv+npPYG+rlg+  +++ LY+ef+ +++rvlr+gg
  gi|14600803|ref|NP_147325.1| 230 VDLNPRHTRGARLNAESARVGGRVEVYTWDARMLHelLGEDSVDRIVSNPPYGIRLGDPVDVRILYREFMPSAARVLRSGG 310
                                   ***********************************988899**************************************** PP

                                   -EEEEEESSHHHHHCC---ESEEEEEEETTEEEEEE CS
                       UPF0020 161 rlvlltsenkalekaleeralrkvkeknvklglllk 196
                                   r++++t+e+kal +a++++ lr++ +++v++g l++
  gi|14600803|ref|NP_147325.1| 311 RAAIITAETKALVAAARSSGLRMAGARRVRHGDLWV 346
                                   *******************************99875 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   8.7e-24     1e-20      10     142 ..      24     162 ..      17     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 8.7e-24
                                   TT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEE CS
                         THUMP  10 gkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrv 90 
                                      +ve+v + +griv++++ge++ ++e+++  +  +++ +     +++  +++le++++aa++   + ++++++tFaVr 
  gi|14600803|ref|NP_147325.1|  24 DSAKVEEVGEYRGRIVFRSSGEPWLVAEQIYGLRSIHSASLLLAEAEVSPGREGLEEVWRAAYKSGAHLHIPYGATFAVRG 104
                                   455788899999********************9999999776666669999****************************** PP

                                   EESSSTSSSHHHHHHHHHHHHHHCCTT......-EE-SSS-SEEEEEEEETTEEEEEE CS
                         THUMP  91 krrgkhfeftsreinrevGkaivektg......lkVdlenPdivvrveiikdkayisi 142
                                   +r g+ +++ts+ei+++vG+a+ ++ +      + V+l++P++v+++e++ +++ +++
  gi|14600803|ref|NP_147325.1| 105 ERIGEGHSYTSVEIASTVGDAVQRAAEeslgwrPMVRLNSPQVVLHAEVDIFTFRLGV 162
                                   ******************************************************9998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   7.8e-14   9.3e-11      30     141 ..     199     318 ..     187     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 7.8e-14
                                   CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-ST..T.TTSTTS-EEEEEE-- CS
                           MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdv..l.eeveekkfdlivsNP 105
                                   +  +++lD  cG G +++++a   ++ +v +vd + r  + a+ n+e+ ++   vev++ d+  l e + e+++d ivsNP
  gi|14600803|ref|NP_147325.1| 199 RDGDTILDPMCGGGTVAVEAALLFETSRVYCVDLNPRHTRGARLNAESARVGgrVEVYTWDArmLhELLGEDSVDRIVSNP 279
                                   46678********************************************9998888888775113144559********** PP

                                   -..STTTCHCHHHH.HHHHHHHHHHHEEEEEEEEEEEET CS
                           MTS 106 P..fhagkatelav.aeeliaeAkeaLkegGeLliVanr 141
                                   P  ++ g  ++ ++  +e++ +A+++L++gG+  i++ +
  gi|14600803|ref|NP_147325.1| 280 PygIRLGDPVDVRIlYREFMPSAARVLRSGGRAAIITAE 318
                                   *55567777776652689**************9999866 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   2.8e-11   3.3e-08       1      97 []     204     310 ..     204     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.8e-11
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS..SSTTTEEEEEEEST.GGG CS
               Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp..fedgsfDlvvssga.lhh 76 
                                   +Ld  cG G+++ ++a  ++ ++v++vD++++  + ar +ae++++  +ve+++ da+ l+  + ++s+D +vs+   + +
  gi|14600803|ref|NP_147325.1| 204 ILDPMCGGGTVAVEAALLFETSRVYCVDLNPRHTRGARLNAESARVggRVEVYTWDARMLHelLGEDSVDRIVSN-PpYGI 283
                                   89**************99999**********************99999*********9998445888*******5.43555 PP

                                   .SSHH.HH....HHHHHHHHHHEEEEE CS
               Methyltransf_25  77 .lsde.dl....ekalkeiarvLkpgG 97 
                                    l d+ d+    ++++  +arvL+ gG
  gi|14600803|ref|NP_147325.1| 284 rLGDPvDVrilyREFMPSAARVLRSGG 310
                                   444441333334678888999999998 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   4.6e-09   5.6e-06      98     177 ..     198     280 ..     191     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 4.6e-09
                                   --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---...TT-EEEEEE- CS
                        Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir...eqladrvvmn 175
                                   +++g++++d + G G  a+ +a + + +rv+ +dlnP+  +  + n +  +v  +v++++ D+r + +   e+ +dr+v n
  gi|14600803|ref|NP_147325.1| 198 ARDGDTILDPMCGGGTVAVEAALLFETSRVYCVDLNPRHTRGARLNAESARVGGRVEVYTWDARMLHEllgEDSVDRIVSN 278
                                   579*************************************************************988778899*****998 PP

                                   -T CS
                        Met_10 176 lp 177
                                    p
  gi|14600803|ref|NP_147325.1| 279 PP 280
                                   76 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   5.9e-09     7e-06       3     113 ..     200     318 ..     198     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.9e-09
               Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsne 82 
                                   +g ++lD+ CG G+ + e+a +l++ ++v+ +D +++  + Ar na++  +  +ve+   d+  l +ll ++++D i+sn 
  gi|14600803|ref|NP_147325.1| 200 DGDTILDPMCGGGTVAVEAA-LLFETSRVYCVDLNPRHTRGARLNAESARVGgRVEVYTWDARMLHELLGEDSVDRIVSNP 279
                                   6789****************.******************************99*********9999887779********7 PP

               Methyltransf_31  83 vl.naladpdkile.......eiervlkpggilliedpr 113
                                   +    l dp ++         ++ rvl++gg+ +i ++ 
  gi|14600803|ref|NP_147325.1| 280 PYgIRLGDPVDVRIlyrefmpSAARVLRSGGRAAIITAE 318
                                   777555555554334456666**********99998887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.3e-08   2.7e-05       1      95 [.     205     313 ..     205     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.3e-08
                                   EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTS..S-TT-EEEEEEES.....- CS
               Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklp..fednsfDlvvsse.....v 70 
                                   Ld  cG+G +a + a  +  +rv++vDl+++ ++ a+ +a+ +++  +ve+   da+ l   + ++s+D +vs+       
  gi|14600803|ref|NP_147325.1| 205 LDPMCGGGTVAVEAALLFetSRVYCVDLNPRHTRGARLNAESARVggRVEVYTWDARMLHelLGEDSVDRIVSNPpygirL 285
                                   6788***********888899************************************99557999********98554442 PP

                                   CCC-C......CHHHHHHHHHHHEEEEEEEE CS
               Methyltransf_11  71 lhhve......dpekalkeiaRvLkpgGllv 95 
                                       +        ++++  +aRvL+ gG+ +
  gi|14600803|ref|NP_147325.1| 286 G---DpvdvriLYREFMPSAARVLRSGGRAA 313
                                   2...122233367888888999999999876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     7e-08   8.3e-05     160     233 ..     199     278 ..     186     353 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7e-08
                          PrmA 160 kegeevlDvGtGSGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkveakleval.....seellkeekadvivaN 233
                                   + g+++lD  +G G  a+ aa+++++++v+ vD+++   + a+ Nae  +v  ++ev++      +ell e ++d iv+N
  gi|14600803|ref|NP_147325.1| 199 RDGDTILDPMCGGGTVAVeAALLFETSRVYCVDLNPRHTRGARLNAESARVGGRVEVYTwdarmLHELLGEDSVDRIVSN 278
                                   6789**************55667799*******************************7522222444444899*****99 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 !   22.0   0.0   7.9e-08   9.4e-05       3      82 ..     203     282 ..     201     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.9e-08
               Methyltransf_15   3 vilDlfsGaGGnviqfalvfe..kviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPw 81 
                                   +ilD+++G+G  +++ al fe  +v++++ n+++   a  Nae+  v  ++ + + d   l + l ++++  d ++  pP 
  gi|14600803|ref|NP_147325.1| 203 TILDPMCGGGTVAVEAALLFEtsRVYCVDLNPRHTRGARLNAESARVGGRVEVYTWDARMLHELLGEDSV--DRIVSNPPY 281
                                   79****************975338******************************9998877666666665..999999999 PP

               Methyltransf_15  82 G 82 
                                   G
  gi|14600803|ref|NP_147325.1| 282 G 282
                                   8 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.9e-07   0.00023      41     126 ..     200     284 ..     190     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                   CC-EEEETT-TTSHHHHHH.HHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                 Cons_hypoth95  41 egarvLDlfaGsGalglEA.lSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                   +g ++LD  +G G++++EA l  + +++++v+ +++  +  + n e+ ++ ++++++  da    + l   + ++d +  +
  gi|14600803|ref|NP_147325.1| 200 DGDTILDPMCGGGTVAVEAaLLFETSRVYCVDLNPRHTRGARLNAESARVGGRVEVYTWDARMLHELL--GEDSVDRIVSN 278
                                   56789*************7357899**************************99999999988877777..45578****** PP

                                   -SSSTT CS
                 Cons_hypoth95 121 PPyake 126
                                   PPy   
  gi|14600803|ref|NP_147325.1| 279 PPYGIR 284
                                   ***865 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 !   19.7   0.0   4.3e-07   0.00051       7      85 ..     199     277 ..     193     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.3e-07
                                   -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSC..CCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEE CS
               Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdank..eRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLl 85 
                                   ++++tilD  ++ Gg  +  a+l+ ++++v+ vd n   +R  r+++   r+g + + v + Dar  ++ lg++ +Dri  
  gi|14600803|ref|NP_147325.1| 199 RDGDTILDPMCG-GGTVAVEAALLFETSRVYCVDLNPrhTRGARLNAESARVGGR-VEVYTWDARMLHELLGEDSVDRIVS 277
                                   789*****8776.66677788999*********98852268899**********9.**********************975 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.2e-06    0.0015      55     166 ..     193     316 ..     180     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                                   HTTTT--TT-EEEEES-TTSHHHHHHHHHH--.EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.....--S CS
                          CMAS  55 leklelkpGmtlLdiGcGWGslvrraverydv.kvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.....kvd 129
                                   l+ ++ ++G+t+Ld  cG G+++++a+  ++  +v  + l   +++ a+ + +++ +  +vev+  d + l+e      vd
  gi|14600803|ref|NP_147325.1| 193 LRLAGARDGDTILDPMCGGGTVAVEAALLFETsRVYCVDLNPRHTRGARLNAESARVGGRVEVYTWDARMLHEllgedSVD 273
                                   44445679**********************863799********************************99999998999** PP

                                   EEEE.....ES-GGGTSGG.GHHHHHHHHHHHS-TT-EEEEEE CS
                          CMAS 130 rvvs.....vgafehvgke.nydtffkklkkllkedGllllht 166
                                   r+vs     + + + v ++  y +f+  + ++l+++G+ ++ t
  gi|14600803|ref|NP_147325.1| 274 RIVSnppygIRLGDPVDVRiLYREFMPSAARVLRSGGRAAIIT 316
                                   ***9666666777888776358889999999999999877654 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.3e-06    0.0064     171     213 ..     179     222 ..      51     241 .. 0.73
   2 ?   -3.3   0.0       4.9   5.8e+03       1      12 [.     272     283 ..     272     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                                   --SS---HHHHHHHH.HHHS-TT-EEEETT-TTTHHHHHHHHTT CS
                   N6_N4_Mtase 171 kHpaqkPvallerlI.klstkkgdivlDpFaGSGtTavaakelg 213
                                    Hpa   + l+  ++ ++  ++gd++lDp +G Gt av+a+ l 
  gi|14600803|ref|NP_147325.1| 179 DHPAALKASLAYVMLrLAGARDGDTILDPMCGGGTVAVEAALLF 222
                                   4899999999999995577899*****************99874 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.9
                                   EEEEEE--SSSS CS
                   N6_N4_Mtase   1 vdlivtdpPYnt 12 
                                   vd iv  pPY++
  gi|14600803|ref|NP_147325.1| 272 VDRIVSNPPYGI 283
                                   6789******97 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-05     0.012      35     138 ..     189     284 ..     185     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                      N6_Mtase  35 sklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtl 115
                                     ++ +l+  ++g +++Dp cG g + v+a+  +       +   +y +++n+  +r a++N     +       +++  +
  gi|14600803|ref|NP_147325.1| 189 AYVMLRLAGARDGDTILDPMCGGGTVAVEAALLF-------ETSRVYCVDLNPRHTRGARLNAESARVGGRVEVYTWDARM 262
                                   5678899999999*****************9987.......47789*****************999999994445566666 PP

                      N6_Mtase 116 ekpkfekdkkfdvvvaNppfnqk 138
                                    ++    + ++d +v+Npp++++
  gi|14600803|ref|NP_147325.1| 263 LHELLG-EDSVDRIVSNPPYGIR 284
                                   666666.9************976 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012      0.14       5      72 ..     209     277 ..     205     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
               Methyltransf_12   5 cGtGsllralleklpdieytgvDispsai.edakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                   cG G+++ + +  ++++++++vD++p+    ++ +  ++r + ++++++++a+ l++l g++s+D +v+
  gi|14600803|ref|NP_147325.1| 209 CGGGTVAVEAALLFETSRVYCVDLNPRHTrGARLNAESARVGGRVEVYTWDARMLHELLGEDSVDRIVS 277
                                   99999999999999***************7677777888899999************9999****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2674.08
//
Query:       gi|118431107|ref|NP_147326.2|  [L=431]
Description: hypothetical protein APE_0558.1 [Aeropyrum pernix K1]
Scores for complete 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-37  128.6   3.9    5.4e-37  128.2   3.9    1.1  1  Peripla_BP_6    Periplasmic binding protein
    0.00015   20.9   0.0      0.055   12.5   0.0    2.2  2  Peripla_BP_5    Periplasmic binding protein domain
    0.00017   20.8   0.0    0.00026   20.2   0.0    1.2  1  ANF_receptor    Receptor family ligand binding region
     0.0012   18.5   0.1       0.01   15.4   0.0    2.3  2  Peripla_BP_4    Periplasmic binding protein domain
     0.0013   17.7   0.0     0.0033   16.3   0.0    1.6  1  Fe-ADH          Iron-containing alcohol dehydrogenase
     0.0043   16.8   0.0     0.0077   16.0   0.0    1.3  1  Fe-ADH_2        Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
       0.14   11.7   0.0       0.22   11.0   0.0    1.3  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase


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 !  128.2   3.9   2.1e-40   5.4e-37       3     341 ..      44     407 ..      42     408 .. 0.83

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 2.1e-40
                                    EEEEEE-SSSTTH.HHHHHHHHHHHHHHHHHHHTTEET....TEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                   Peripla_BP_6   3 kiGlltplsGpya.ssgksllagaqaafeeiNaaGGin....GrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                     iG + +ls+ ++ ++ +++laga aa+e++N +GG+n     ++++l+ +Dd++dp+ a++  + + +q+gv + ++p 
  gi|118431107|ref|NP_147326.2|  44 VIGGVFSLSSGTSvEACRQALAGAMAAVEWVNSNGGVNiggsKVPVRLLQEDDKGDPANAVRLIEYMARQRGVGVMLAPC 123
                                    578888887777769************************844459*********************************** PP

                                    SHHHHHHHHHHHHHHT-EEEESS-HHC..CTTSTTEEESS--HHHHHHHHHHHHHHHTT..SCEEEEEEESSHHHHHHHH CS
                   Peripla_BP_6  78 ssavaaavaevlakdgvpvigpagltg..ekcspyvfslgpsysaqasalveylakelg..gkkvalvyadyafgregia 153
                                      +v   ++e+++  gv+ i  ++      +  + +  +g+ +  + + ++e +++ l+   +++a+vy+d+ f +++++
  gi|118431107|ref|NP_147326.2| 124 DPGVLVDAVEAARGYGVVSIVYGDAPAsvADPGGKTLLVGAPAEEYFTPVLE-MVSILDiqSRNLAIVYQDTGFAAAVAE 202
                                    ********************96654431245666678888888888888888.6775554489***************** PP

                                    HHHHHHHCCTEEEEEEEEE-TTH..HHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHH CS
                   Peripla_BP_6 154 alkaaakaaGgevvgeepvplgt..tdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsgseed 231
                                    a++  a ++G+ vv +  +p+++  +++ +++l+++a+++d+++++g++ d + l++a+ + G+ ak+i+++     +e 
  gi|118431107|ref|NP_147326.2| 203 ATRNRAVEQGFVVVLYSAYPPQAgeEELGTLALRLQASNPDVIIAIGGFRDGVELVRAMSSYGVEAKFIAMAVAPSVPEF 282
                                    ************999*****87777******************************************9999966666666 PP

                                    HHHHHH.HHHT............TEEEEES.CSTCCCSHHHHHHHHHHHHHH.....TTGGC--HHHHHHHHHHHHHHHH CS
                   Peripla_BP_6 232 lkalgg.eaae............gvlavtp.yfpdldnpavrafvaayeaay.....ggapppsqfaaggyiaadlllea 292
                                       lg+    +            + ++++  y +   +p  ++f   +++a      +    p ++aa + +a++++++a
  gi|118431107|ref|NP_147326.2| 283 YSELGAlS--QailyptlwelasKPYTTAEgYEW--FGPSREEFYSLFREAIeslghPV-SEPGYHAAMAALAVLAVAKA 357
                                    66666631..223455555555544555552444..35666666666666643333344.4799**************** PP

                                    HHCCTHCCHHHHHHHHHHS-BECCCTCCBEECTTSB.EE--EEEEEE-TS CS
                   Peripla_BP_6 293 lkaagsltreavraaleslgfdgllgplkftaedhq.asrpvyvvqvdgg 341
                                    +++agsl+++a+ + l+++++ ++ gp++  +e++   +r v v q+ +g
  gi|118431107|ref|NP_147326.2| 358 AEEAGSLDPDAIYESLKNIKIMTFAGPFDLNPETGLqNEREVLVGQWING 407
                                    *******************************8888658999*****9876 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 !    6.4   0.0    0.0015       3.8       3      70 ..      45     117 ..      43     122 .. 0.72
   2 !   12.5   0.0   2.1e-05     0.055     174     345 ..     226     412 ..     171     427 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0015
                   Peripla_BP_5   3 vGvLhSls.GtmaisekslkdaallaieeinaagGvl..grk..ieavvvdpasdwelfaekaeklieedkve 70 
                                    +G ++Sls Gt     ++++ +a+ a+e +n++gGv+  g k  +    +d ++d++   +  e + ++ +v 
  gi|118431107|ref|NP_147326.2|  45 IGGVFSLSsGTSVEACRQALAGAMAAVEWVNSNGGVNigGSKvpVRLLQEDDKGDPANAVRLIEYMARQRGVG 117
                                    7888998626666677888999999**********98655551155667788888877777766666666665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
                   Peripla_BP_5 174 gssdvqkivakikkakpdvvlstinG.dsnvafykelkeagikaekipv.vslsvae..eelaaidaealvG...hlaaw 246
                                    g++++ ++  ++++ +pdv++  i G    v++ +++++ g++a+ i + v+ sv e  +el a+ ++ l     +la+ 
  gi|118431107|ref|NP_147326.2| 226 GEEELGTLALRLQASNPDVIIA-IGGfRDGVELVRAMSSYGVEAKFIAMaVAPSVPEfySELGALSQAILYPtlwELASK 304
                                    5566666666666666666664.333245566666666666666655431455665544466666655443311155666 PP

                   Peripla_BP_5 247 nYfqsvd....tpenkafvakfkarvge..drvtndpmea..ayiqvklwaqAvekagstdvekvreallgqelkapeGe 318
                                    +Y  +       p+ ++f + f++ +++  + v +    a  a ++v  +a+A e+ags d++++ e+l + ++ +  G+
  gi|118431107|ref|NP_147326.2| 305 PYTTAEGyewfGPSREEFYSLFREAIESlgHPVSEPGYHAamAALAVLAVAKAAEEAGSLDPDAIYESLKNIKIMTFAGP 384
                                    6655432112257778888888888876423344444444114456667899**************************** PP

                   Peripla_BP_5 319 vkidpenh.hlsktvrigkikadGqfei 345
                                      ++pe+     + v +g++ +  +f++
  gi|118431107|ref|NP_147326.2| 385 FDLNPETGlQNEREVLVGQWINGRRFTV 412
                                    *****98624567889999876666654 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 !   20.2   0.0     1e-07   0.00026       6     332 ..      67     384 ..      62     403 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1e-07
                                    HHHHHHHHHT-TTSSTTE.EEEEEE..EE-TT-HHHHHHHHHHHCCCC.EEEEEE-SSHHHHHHHHHHHCCTT-EEEESS CS
                   ANF_receptor   6 mklAveeinsdpnllpgi.klgyei..idtccdfslaleaaldflkgk.vvaviGpssssvsdavaslanlfkiPvisyg 81 
                                    +  Ave +ns++++  g  k+ ++   +d++ d+++a++    + ++  v +++ p  ++v+  + + a+ + +  i yg
  gi|118431107|ref|NP_147326.2|  67 AMAAVEWVNSNGGVNIGGsKVPVRLlqEDDKGDPANAVRLIEYMARQRgVGVMLAPCDPGVLVDAVEAARGYGVVSIVYG 146
                                    5579999999999976655999999999999***************9549999999999******************999 PP

                                    ---GGGG-TTTTTTEEESS--CHHHHHHHHHHHH..HTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEESTC CS
                   ANF_receptor  82 stspelsdknryptflrtvpsdtsqaqAivdilk..hfgWkkvaliysdddygesglqaleeeleergicvalkekipes 159
                                      ++++ d    +t+l  +p  + + + +++++     + +  a++y+d      +++a ++++ e g+ v+l   +p++
  gi|118431107|ref|NP_147326.2| 147 DAPASVADPGG-KTLLVGAPA-EEYFTPVLEMVSilDIQSRNLAIVYQDTGFAAAVAEATRNRAVEQGFVVVLYSAYPPQ 224
                                    87777999999.666655555.666666666666446778899*************************888888888864 PP

                                    HHHCHHHHHHHHHHTTT--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC....HHHH....... CS
                   ANF_receptor 160 snddevvrkllkeikskarvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpe..ltglea....... 230
                                      ++e+ +  l+ ++s+++vi+      d  el++a+ + g+      +ia    ++  +++  e  + +l a       
  gi|118431107|ref|NP_147326.2| 225 AGEEELGTLALRLQASNPDVIIAIGGFRDGVELVRAMSSYGVEA---KFIA----MAVAPSVP-EfyS-ELGAlsqaily 295
                                    4445555555677799***************************9...5883....22222222.2331.22224444455 PP

                                    ..........HTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSS CS
                   ANF_receptor 231 ..........aegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpg 300
                                              +  + g + + p++++f++ +  re +++   ++++e ++  +++a     aV ++a+A++++++     
  gi|118431107|ref|NP_147326.2| 296 ptlwelaskpYTTAEGYEWFGPSREEFYSLF--REAIESL-GHPVSEPGYH-AAMA---ALAVLAVAKAAEEAGS----- 363
                                    6666666666777778888************..7777664.4566666655.4444...46************93..... PP

                                    HCCB-HHHHCCHHHHHHHHHHHT-EEEETTSC CS
                   ANF_receptor 301 ralscntlkpweggqkllrylrnvnfeGltGd 332
                                                + +++ + l+n+++  ++G 
  gi|118431107|ref|NP_147326.2| 364 -----------LDPDAIYESLKNIKIMTFAGP 384
                                    ...........344444555555555555555 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 !   15.4   0.0     4e-06      0.01      35      90 ..      94     152 ..      49     169 .. 0.79
   2 ?    0.3   0.0      0.16   4.1e+02      11      36 ..     195     222 ..     172     258 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4e-06
                                    ECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEESTT...G CS
                   Peripla_BP_4  35 gdaendaaeQvaqiedaiakgvdgiivapvdstalapalkkakaaGIpVvafdsd...d 90 
                                     d+++d a  v  ie +  +   g+++ap+d+  l +a+++a+  G++ +++  +   +
  gi|118431107|ref|NP_147326.2|  94 EDDKGDPANAVRLIEYMARQRGVGVMLAPCDPGVLVDAVEAARGYGVVSIVYGDApasV 152
                                    78999****************9*************************988887764444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.16
                                    CHHHHHHHHHHHHHHHTTCEEEEE..EC CS
                   Peripla_BP_4  11 pffsaaregleeaakelgaevtvv..gd 36 
                                    +f  a+ e+ ++ a e g+ v++   ++
  gi|118431107|ref|NP_147326.2| 195 GFAAAVAEATRNRAVEQGFVVVLYsaYP 222
                                    3333333333333333333333333333 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-06    0.0033      24      90 ..     185     250 ..     174     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                                    .EEEEEE.EHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEES CS
                         Fe-ADH  24 kralivt.dkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGG 90 
                                    ++  iv+ d g++  + +++  ++   e+g+ v++++  +p   +ee+  +a +++++++dv+ia+GG
  gi|118431107|ref|NP_147326.2| 185 RNLAIVYqDTGFA--AAVAEATRNRAVEQGFVVVLYSAYPPQAGEEELGTLALRLQASNPDVIIAIGG 250
                                    5666777355544..557777777778****************************************9 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     3e-06    0.0077      19     119 ..     184     287 ..     173     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-06
                       Fe-ADH_2  19 lkkvllv.adentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGt.iiDiakyv.s 95 
                                     +++++v +d++  +a++e+ ++   e+g  v +++   ++a +ee   l+ +l++++ d+++a+Gg +  + +++ + s
  gi|118431107|ref|NP_147326.2| 184 SRNLAIVyQDTGFAAAVAEATRNRAVEQGFVVVLYSAYPPQAGEEELGTLALRLQASNPDVIIAIGGFRdGVELVRAMsS 263
                                    455555526888899999999999999**99999**9******************************7535778887625 PP

                       Fe-ADH_2  96 aklnvpyvsvpTaaSvDGfaspga 119
                                    +  + ++++++ a+Sv  f s   
  gi|118431107|ref|NP_147326.2| 264 YGVEAKFIAMAVAPSVPEFYSELG 287
                                    789************998888655 PP

>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.7e-05      0.22     117     145 ..     391     421 ..     342     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.7e-05
                 PS_Dcarbxylase 117 lftlneRvvlview.kG.kvavvpvGatnvg 145
                                       +neR vlv++w +G ++ v pvG +++ 
  gi|118431107|ref|NP_147326.2| 391 TGLQNEREVLVGQWiNGrRFTVWPVGQAYAT 421
                                    55689********999*77*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3543.14
//
Query:       gi|14600805|ref|NP_147327.1|  [L=483]
Description: hypothetical protein APE_0560 [Aeropyrum pernix K1]
Scores for 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-146  485.9   0.0   7.6e-146  485.6   0.0    1.1  1  DUF2139   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2139  Uncharacterized protein conserved in archaea (DUF2139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.6   0.0  4.2e-150  7.6e-146       1     340 []      28     367 ..      28     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 485.6 bits;  conditional E-value: 4.2e-150
                       DUF2139   1 lyytlafeaeahfikddsek.iYrfelvGkaPtsGGDtYnaveavDdkiyfGGWvhaPavykg.reekkaeisfknkYshv 79 
                                   l+ytlafea++++++ d+++ +Y+++lvG++P+sGGDtYnaveavD+kiyfGGW+haPav+++  +++ ae+ f+nkYs++
  gi|14600805|ref|NP_147327.1|  28 LFYTLAFEARSTLLRGDCSWsSYDYSLVGPPPRSGGDTYNAVEAVDGKIYFGGWAHAPAVLERkGKGRLAEVVFTNKYSIL 108
                                   8*****************998****************************************99678899************ PP

                       DUF2139  80 heydieekevkLlWkesihdeeeWagevseiiYdpledkLLlaraDGhanlGvyeidrktgearklsdkpalkGalvldla 160
                                   he+d+++ ev+LlWke+++d++ Wa+evse++Y+pl+d+LLlar+DGh+n+G++e  r++g +rkls++p+lkG++++d+a
  gi|14600805|ref|NP_147327.1| 109 HEMDVDTGEVRLLWKEGARDRRLWACEVSEVLYNPLRDTLLLARGDGHINCGIFEAGRRGG-VRKLSSTPVLKGEVFMDMA 188
                                   ***********************************************************77.******************* PP

                       DUF2139 161 cfdikedfkkgvegiecldliekkvvyeeledvekasvDgedvekresGavasaytrvfafvrGGilvgnPveeeelrfvr 241
                                   cf+i++++ +g++g+ec+dl+++++vy+  ++ e+a++Dg++++++++Gav++++trv+++++GG++v++P  ++e rf+r
  gi|14600805|ref|NP_147327.1| 189 CFSIHHGW-GGNPGLECVDLESGETVYTGEAVPEEAGLDGGGLDHYREGAVFQLHTRVYVAHKGGFTVFDPEGGGEPRFYR 268
                                   ********.************************************************************************ PP

                       DUF2139 242 llDfaetqyaplrsnalplgGGvlvafnaysealvrktneeeevvkkatntivgPsvLvYiaPpvakivgalGaritslek 322
                                   +lDf++++y+p+r+nal+lgGGvl++fn+ ++a+vr+t+e +++v+++++++++P++LvY++P+ ++ivg+lGar+ts+e+
  gi|14600805|ref|NP_147327.1| 269 VLDFGDNPYSPTRTNALYLGGGVLIPFNTPTAATVRGTDELPNNVQRSSRRSPAPTLLVYVTPTDMRIVGSLGARVTSMEA 349
                                   ********************************************************************************* PP

                       DUF2139 323 vgdkvllatnttpnlery 340
                                   +gdkvlla++t+pn+ery
  gi|14600805|ref|NP_147327.1| 350 LGDKVLLAWSTQPNFERY 367
                                   ***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 4146.46
//
Query:       gi|118431108|ref|NP_147329.2|  [L=268]
Description: prephenate dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-11   44.0   0.1    5.2e-11   43.0   0.1    1.5  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
    1.1e-07   31.1   0.0    1.4e-07   30.8   0.0    1.2  1  PDH            Prephenate dehydrogenase
    3.4e-07   30.6   0.0    4.5e-07   30.2   0.0    1.2  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    4.7e-07   29.3   0.1      1e-06   28.3   0.0    1.6  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    2.6e-05   24.1   1.0    5.1e-05   23.1   1.0    1.4  1  Rossmann-like  Rossmann-like domain
    0.00018   22.3   0.1    0.00031   21.5   0.1    1.4  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.019   14.9   0.1    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
      0.012   16.1   0.1       0.02   15.4   0.1    1.5  1  XdhC_C         XdhC Rossmann domain
      0.067   13.3   0.0      0.099   12.7   0.0    1.2  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase


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 !   43.0   0.1   2.6e-14   5.2e-11       1      95 [.       4      93 ..       4      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 2.6e-14
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsela 82
                                   ++g++GaG++++ala+ ++a+g     +++  + + e+a e+a+++g   ++ + + +a+e++ +v+av+  ++  v+ e+a
  gi|118431108|ref|NP_147329.2|  4 RVGFVGAGSVARALARAASARG---WPVCFY-DIDRERAGEAASQYGGLSFS-SLQGLAAESEAIVVAVPGPAAGGVMVEAA 80
                                   69********************...****66.***************77666.9999999********************** PP

                                   HHHHTTSEEEEES CS
                  F420_oxidored 83 kdalkgklvisvl 95
                                   +++ +g+lv++++
  gi|118431108|ref|NP_147329.2| 81 RSSRSGTLVVDTA 93
                                   ***********97 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   7.2e-11   1.4e-07       2     204 ..      18     206 ..      13     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 7.2e-11
                                    HHHHHHTT--SEEEEE-SSHHHHHHH..HHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE-- CS
                            PDH   2 aralrrkgfkvtvigydideekaeaa..lelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitDvg 79 
                                    ara  ++g    v  ydid e+a +a  +  gl +   +    + e + +v+avP  +   v+ e a   + + l++D++
  gi|118431108|ref|NP_147329.2|  18 ARAASARGW--PVCFYDIDRERAGEAasQYGGLSFSSLQ--GLAAESEAIVVAVPGPAAGGVMVEAARSSRSGTLVVDTA 93 
                                    555555564..4555666666655440055678888887..58889999******************************* PP

                                    S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--H. CS
                            PDH  80 svKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvilmsp. 158
                                      K  vv +++ + + ++    +hP++G+        r++  e++ v+  P    + e +  + +l++e+g   i + + 
  gi|118431108|ref|NP_147329.2|  94 TFKRGVVAAARGMPP-RVLAALTHPLFGG--------RASRPEKHYVAVMPFP--GREGVVEAERLYREMGFNTIRLRSw 162
                                    **********99999.7777779******........78888999******98..8899************998877655 PP

                                    HHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHH CS
                            PDH 159 eeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdv 204
                                    eeHDr  ++  +l  ++a al a+l+  + d      l+s  +r +
  gi|118431108|ref|NP_147329.2| 163 EEHDRLAGYSIGLVYALAEALYAALESGGLDLD--SPLPSTTYRVL 206
                                    9********************997765544444..56677777655 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 !   30.2   0.0   2.3e-10   4.5e-07       1      94 [.       4      97 ..       4     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.3e-10
                                   EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC-- CS
                  NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdeviegllealk 81
                                   ++gf+G G   + +a+   ++g+ v++y+ ++e++ e++++ g   ++s++ l+a+ +++++ v+  +a   v+ + +++ +
  gi|118431108|ref|NP_147329.2|  4 RVGFVGAGSVARALARAASARGWPVCFYDIDRERAGEAASQyGGLSFSSLQGLAAESEAIVVAVPG-PAAGGVMVEAARSSR 84
                                   58******************************99999988846899******************96.6678888889***** PP

                                   TT-EEEE-S---H CS
                  NAD_binding_2 82 kgdilidgstssp 94
                                   +g++++d++t + 
  gi|118431108|ref|NP_147329.2| 85 SGTLVVDTATFKR 97
                                   ********99764 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 !   28.3   0.0     5e-10     1e-06      37     112 ..       3      80 ..       1      95 [. 0.83
   2 ?   -3.5   0.0       2.8   5.6e+03     135     145 ..     181     191 ..     180     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 5e-10
                                    SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTC.EECSHHHHHHH-SEEEE-S--STTTTTSBSHH CS
                   2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgv.elvsleellaesDivslhlpltpetrhlinae 112
                                     +vG +G+G++++a+a+ ++a g  v +yd  +++   +++++g  ++ sl+ l aes+ +++++p  ++   +++a+
  gi|118431108|ref|NP_147329.2|   3 CRVGFVGAGSVARALARAASARGWPVCFYDIDRERAGeAASQYGGlSFSSLQGLAAESEAIVVAVPGPAAGGVMVEAA 80 
                                    589***************************9988665544455444999*****************887777776665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.8
                                    HHHHHHHHTTS CS
                   2-Hacid_dh_C 135 eaLleaLksgk 145
                                    eaL++aL+sg 
  gi|118431108|ref|NP_147329.2| 181 EALYAALESGG 191
                                    79******996 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   1.0   2.6e-08   5.1e-05      12     105 ..       4      94 ..       2     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.6e-08
                  Rossmann-like  12 svGiisaGrvGtalgaaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkglaat 91 
                                     vG ++aG v  al+ a    g  v   + i       a  +  + +  +++ +aa++e +++avP +   g++ + a +
  gi|118431108|ref|NP_147329.2|   4 RVGFVGAGSVARALARAASARGWPVC-FYDIDRERAGEAASQYGGLSFSSLQGLAAESEAIVVAVPGPAAGGVMVEAARS 82 
                                    69***************988888875.5566665566667778999999************************9998876 PP

                  Rossmann-like  92 gavraGtivahtsg 105
                                       r+Gt+v+ t++
  gi|118431108|ref|NP_147329.2|  83 --SRSGTLVVDTAT 94 
                                    ..9*******9975 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 !   21.5   0.1   1.6e-07   0.00031       2      75 ..       4      73 ..       3      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G.GGH CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpn.gth 75
                                   rv+++GaG +++  +r+  ++      v+++d+d era ++a ++g  ++s+l+ l+a  e +a++va+p    +
  gi|118431108|ref|NP_147329.2|  4 RVGFVGAGSVARALARAASAR---GWPVCFYDIDRERAGEAASQYGGLSFSSLQGLAA--ESEAIVVAVPGpAAG 73
                                   89**********999666555...56789*****************************..88*******974334 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 ?   14.9   0.1   9.3e-06     0.019       2      42 ..       5      45 ..       4      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.3e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                   v+ +GaG + + +a ++ ++g +V  +di++e++ +a+++ 
  gi|118431108|ref|NP_147329.2|  5 VGFVGAGSVARALARAASARGWPVCFYDIDRERAGEAASQY 45
                                   899*****************************999988765 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1     1e-05      0.02       4      65 ..       8      81 ..       5     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                   E--STTHHHHHHHHHHHTEEEEEEES-GGGG.......-GGG-TT-SE.............-EEEE--S-HHHHHHHHHHHS CS
                         XdhC_C  4 fGaghvaqalarlaaalgfrvtvvdpreefa.......tkerfpeade.............tavvvlthdhklDaealeaal 65
                                   +Gag va+alar a+a g+ v+ +d ++e a                              +a+vv+  +++    ++eaa 
  gi|118431108|ref|NP_147329.2|  8 VGAGSVARALARAASARGWPVCFYDIDRERAgeaasqyG--------GlsfsslqglaaesEAIVVAVPGPAAGGVMVEAAR 81
                                   8************************99975544333330........14445555555566777777777777666666665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     5e-05     0.099      13     111 ..       3      92 ..       1      97 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                    -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-H CS
                   Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilek 92 
                                    ++v  +GaG +a+ +a++ +a+g   v+    ++era e a++++g      ++++l+ l ae++ +++a+    p    
  gi|118431108|ref|NP_147329.2|   3 CRVGFVGAGSVARALARAASARGWP-VCFYDIDRERAGEAASQYGGL-----SFSSLQGLAAESEAIVVAVPG--PAAGG 74 
                                    7899********************9.******************777.....9999************99854..45566 PP

                                    HHHHCCHHH.S..EEEEE- CS
                   Shikimate_DH  93 eeveealkkrkkplllvDi 111
                                     +ve+a ++r + +l+vD 
  gi|118431108|ref|NP_147329.2|  75 VMVEAARSSR-SGTLVVDT 92 
                                    6666665443.66677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2032.47
//
Query:       gi|118431109|ref|YP_874834.1|  [L=83]
Description: chorismate mutase [Aeropyrum pernix K1]
Scores for complete 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   54.2   1.5    1.8e-14   53.8   1.5    1.2  1  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   1.5     1e-18   1.8e-14       1      74 [.       7      74 ..       7      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1e-18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHH CS
                           CM_2  1 RkeIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleegaldeeaierifreiisasralq 74
                                   R+ Ide+D++i++LL+eR+el+++vge K++ g  ++d++Reaevl r+ +        + ++r +i+++++ q
  gi|118431109|ref|YP_874834.1|  7 RRLIDELDAKIVALLEERLELCRRVGEEKRRLGRGLRDEDREAEVLGRVPS------RWRPLYRLVIEECLREQ 74
                                   888**********************************************99......56888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 646.75
//
Query:       gi|14600808|ref|NP_147331.1|  [L=380]
Description: chorismate synthase [Aeropyrum pernix K1]
Scores for 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-123  409.1   0.0   1.1e-122  408.9   0.0    1.0  1  Chorismate_synt  Chorismate synthase


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.9   0.0    6e-127  1.1e-122       1     327 []      11     356 ..      11     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 408.9 bits;  conditional E-value: 6e-127
                                   SEEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE-TTS CS
               Chorismate_synt   1 lrvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieNkdq 81 
                                   +rv++fGeShg+++ga++ gvp+gle+de+ i++eL+rRrpg+  ++++r+E+D+veilsGvf+g+t+G+pi l+i+N d+
  gi|14600808|ref|NP_147331.1|  11 FRVSIFGESHGPGVGALVTGVPPGLEVDEAYINRELERRRPGG-PYASPRREADRVEILSGVFRGRTTGAPILLFIRNVDV 90 
                                   89****************************************8.89*********************************** PP

                                   -..SSSSSTSBE-TTSTCHHHHHHC.-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE........ CS
               Chorismate_synt  82 rskdyeeikevpRpgHADltyalkY.girdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei........ 153
                                   ++  yee++ +pRpgHAD+++ ++Y g++d+rggg +S+R Taa vaaGa+ak +L+++g+++ ayv+sig++        
  gi|14600808|ref|NP_147331.1|  91 KPGFYEEFRYKPRPGHADYVAYERYlGHQDYRGGGIFSGRRTAALVAAGAIAKLVLARYGVRVYAYVKSIGGVearveprd 171
                                   ***********************************************************************8888888888 PP

                                   .....CHH.HHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTSTTEEEEEE CS
               Chorismate_synt 154 .....eke.aenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsipAvkgvei 228
                                        + +  ++p++cpd+ea+e+m++++eea++egdslG+vve v+ +vp+GlG+p    +da La+a+m+ipA+k+ve+
  gi|14600808|ref|NP_147331.1| 172 seefrR-AiDRDPLKCPDPEASERMRRLVEEARREGDSLGSVVEAVAFNVPPGLGDPPLGGVDALLARAVMAIPAAKAVEF 251
                                   877643.33566********************************************************************* PP

                                   TTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E-EEEE--S-S- CS
               Chorismate_synt 229 GsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletkeevelevkgrhD 303
                                   G+Gf+ a ++Gsea+D+        +++tn++GGi GG++nG+piv+rva+Kp +si k+++tvdl++  e+ ++ kgrhD
  gi|14600808|ref|NP_147331.1| 252 GEGFALAFMRGSEAHDSPRavggriVHETNRSGGIVGGLTNGMPIVFRVAFKPPSSIPKPRRTVDLRSLGEAWVSGKGRHD 332
                                   *****************9977776655*******************************************9********** PP

                                   S-THHHHHHHHHHHHHHHHHHHHH CS
               Chorismate_synt 304 pcvvpravvvveamvalvladall 327
                                   p++ pra++vvea++a+vlad+ll
  gi|14600808|ref|NP_147331.1| 333 PVIGPRAAPVVEAVTAIVLADLLL 356
                                   *********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3026.72
//
Query:       gi|14600809|ref|NP_147332.1|  [L=427]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Aeropyrum pernix K1]
Scores for 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-89  298.1   0.0      1e-88  297.9   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.9   0.0   5.6e-93     1e-88       4     417 .]      14     412 ..      11     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: 297.9 bits;  conditional E-value: 5.6e-93
                                   SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHH CS
                 EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeel 84 
                                   ++ +eg+v++p+sks+++r+l lA La+g+s ++ +L s+D++++l+a+  Lg++  +l     v  veg  g++  +  +
  gi|14600809|ref|NP_147332.1|  14 PSTVEGRVEAPPSKSYTHRMLFLALLARGRSVVRRPLVSNDTLATLNAVALLGGKP-RL--GRGVAEVEG--GEVRGG--A 87 
                                   789**************************************************644.67..578899999..888887..8 PP

                                   HTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEEEEETSST CS
                 EPSP_synthase  85 vldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgveikaevs 164
                                   v+++  sgt++r+ ++++a+    + L Gdes++ RP+ +l +aLr++Ga++      +++p+kv+g l+  +ve++a +s
  gi|14600809|ref|NP_147332.1|  88 VVYAAGSGTTIRIAMGVAAHSAEATLLYGDESLNRRPVHPLSEALRSMGARVC--DTGGNPPVKVSGpLRRASVEVDAAIS 166
                                   ********************99******************************8..4448********************** PP

                                   THHHHHHHHHHHTTSBSEEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHHHHHHH CS
                 EPSP_synthase 165 SqqvtsllllaallaegtteleelasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAayflva 245
                                   Sq++tsll++ + l e ++    l s+ ++d+tl+ l  fg+ +e +g    ++ +G +k  +    v+gD+ssA++ l+a
  gi|14600809|ref|NP_147332.1| 167 SQFATSLLIAGSRLGEFELSAARLSSRGYVDITLESLSMFGVRVEREGYRL-FRLRGTPKPVD--AAVPGDYSSASFMLAA 244
                                   ********999977555666666***********************77777.*****998666..89************** PP

                                   HHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBHGGGHHHHHHHHHTS CS
                 EPSP_synthase 246 AaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeaptlavlaafaegttvi 326
                                   +ai+g +v ve++++   q d+++++  l+ mga+++ e   + v+++ +l+++dvd+   pd+ap++avlaa a g +++
  gi|14600809|ref|NP_147332.1| 245 GAIAG-RVEVEGLRPVDPQPDRRIVE-LLRSMGARVRVEGGVVAVESTGPLEPVDVDLDGSPDLAPVAAVLAAYARGVSRL 323
                                   ****9.***************99999.*************778888777******************************** PP

                                   BSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEEEETTHHHH CS
                 EPSP_synthase 327 egiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegeveiddiectd 407
                                   +g ++l++ke+drl a+a +L++lG+e++++   l+i+++   ++g+  +s +DhRiama+a+agl a+ +v ++ ++ + 
  gi|14600809|ref|NP_147332.1| 324 RGLERLKYKESDRLSAIAWNLARLGVEARVRGGILEIRGGG--VEGGVARSWGDHRIAMAMAVAGLGARRPVAVEGFSRVP 402
                                   *******************************9999999997..5************************************* PP

                                   HHSSSHHHHH CS
                 EPSP_synthase 408 ksfpefeekL 417
                                    s+p+f e+L
  gi|14600809|ref|NP_147332.1| 403 DSYPGFLEDL 412
                                   ******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3135.52
//
Query:       gi|14600810|ref|NP_147333.1|  [L=280]
Description: shikimate kinase [Aeropyrum pernix K1]
Scores for complete 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   27.6   1.3    2.6e-06   27.6   1.3    2.8  3  GHMP_kinases_N  GHMP kinases N terminal domain
    7.6e-06   26.2   0.9    7.6e-06   26.2   0.9    1.9  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.5   1.4e+04       3      14 ..      30      41 ..      29      41 .. 0.86
   2 !   27.6   1.3   2.9e-10   2.6e-06       3      63 ..      80     144 ..      78     146 .. 0.83
   3 ?   -0.1   0.8      0.12   1.1e+03      19      36 ..     212     229 ..     212     249 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                                  EEEESSHTTSSS CS
                GHMP_kinases_N  3 vikseiPvgaGL 14
                                   ++s++  ++GL
  gi|14600810|ref|NP_147333.1| 30 WVESRVREARGL 41
                                  689999999998 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.9e-10
                                   EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH...HHHHHHHHHHHHHHHHHHHHSHHH.HHHH CS
                GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallgls...leeaklaleaerlaqggngsggDv.aasv 63 
                                   ++++ +P+g GL +SAAl ++lv A+l+l g++   ++ a  a++  r a++ +++  D+ aas+
  gi|14600810|ref|NP_147333.1|  80 EVHTGFPPGVGLKGSAALLASLVEAVLRLKGVRappWRAALAAARVSRGAGLSVTGALDDhAASL 144
                                   78999**************************9943334466788888889999999999956665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHTTEH.H CS
                GHMP_kinases_N  19 AlavalvaAllallgls.l 36 
                                   A+av++va +lal  ++ l
  gi|14600810|ref|NP_147333.1| 212 AMAVSGVAGALALG-VEgL 229
                                   79999999999987.4434 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.3   1.1e+04      37      56 ..     117     134 ..     113     136 .. 0.51
   2 !   26.2   0.9   8.4e-10   7.6e-06      13      77 ..     206     265 ..     196     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                GHMP_kinases_C  37 eelleal.selGalgaklsGa 56 
                                   +++l a+  + G   a+ls +
  gi|14600810|ref|NP_147333.1| 117 RAALAAArVSRG---AGLSVT 134
                                   566666644555...444444 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 8.4e-10
                GHMP_kinases_C  13 lgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                    ge l  ++ s    v+g l   +e l + l+e+Ga +a+++G   Gp+vfal++ + +a++v++
  gi|14600810|ref|NP_147333.1| 206 AGEWLPAMAVS-G--VAGALALGVEGLASRLYEAGAAAAGVTGK--GPAVFALTERPRGAAEVLE 265
                                   55556666663.3..7888888999999****************..*************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2099.22
//
Query:       gi|118431110|ref|NP_147334.2|  [L=273]
Description: shikimate dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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   59.9   0.0    3.9e-16   59.1   0.0    1.4  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    7.5e-06   26.1   0.0    1.2e-05   25.4   0.0    1.2  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00057   20.2   0.0     0.0014   18.9   0.0    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0043   16.8   0.1      0.016   15.0   0.2    1.9  2  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
     0.0085   15.5   0.3      0.066   12.6   0.2    2.2  3  ThiF             ThiF family
  ------ inclusion threshold ------
      0.016   15.2   0.3      0.025   14.5   0.3    1.2  1  KR               KR domain
      0.023   15.3   0.2      0.047   14.3   0.2    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.046   12.8   6.6      0.076   12.1   6.6    1.3  1  FAD_binding_2    FAD binding domain
      0.063   12.6   0.0      0.093   12.1   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.088   12.3   0.3       0.13   11.7   0.3    1.2  1  adh_short        short chain dehydrogenase
       0.16   11.0   5.4       0.22   10.6   5.4    1.1  1  GIDA             Glucose inhibited division protein A
       0.19   12.1   1.8       0.36   11.2   0.2    2.1  2  PE               PE family
       0.55    9.4   3.7       0.22   10.7   0.8    1.7  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas


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 !   59.1   0.0   2.8e-19   3.9e-16       1      82 [.       6      85 ..       6      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2.8e-19
                                   EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SE CS
                 Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNt 82
                                   ++G+ ++ SlSPai++ +++++gl+ +y+  e  +  l  a++ +   +l G+nvT P+K+++++l+ +l+++A+aigAvNt
  gi|118431110|ref|NP_147334.2|  6 LFGSGVSSSLSPAIYRGFAAKRGLRLEYRVYEAGPGGLAPALRMAG--ELHGFNVTKPLKREALSLASTLDSHARAIGAVNT 85
                                   69***********************************999999887..69*******************************9 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   8.4e-09   1.2e-05      14      83 ..     117     188 ..     108     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.4e-09
                                    EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                   Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkellaeadvvisat 83 
                                    ++l+iGaG  ++ +a +L++ g+ +v++a Rt   a++ a++l   g+e+e ++   l+++ a++dvv+ at
  gi|118431110|ref|NP_147334.2| 117 TALVIGAGGAGRAAAYALATWGAGRVLIASRTGLTARRAAQDLagLGAEVEPVPPGGLEDAAAASDVVVNAT 188
                                    79******************************9999999999943356677778889************998 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 !   18.9   0.0     1e-06    0.0014       2      78 ..     119     189 ..     118     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                                    EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78 
                                    l+iGaG+ G+a+a  la  +    ++ +a+r+   ++++a++++g  +e + + +   e+    + +  d+vvn++p
  gi|118431110|ref|NP_147334.2| 119 LVIGAGGAGRAAAYALATWGAG--RVLIASRTGLTARRAAQDLAGLGAEVEPVPPGGLED----AAAASDVVVNATP 189
                                    89****************9987..*******************99999999999988888....4456899999987 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 ?   -3.2   0.0       5.7   7.9e+03      13      26 ..     107     120 ..     106     121 .. 0.76
   2 !   15.0   0.2   1.1e-05     0.016       1      24 [.     235     259 ..     235     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.7
                                    HHHHHS----HHHH CS
                          SDH_C  13 FelWTGrepPvevM 26 
                                     +l T  +p+++ +
  gi|118431110|ref|NP_147334.2| 107 LKLYTASPPDTALV 120
                                    67888889999865 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHHHHHHHS---.-HH CS
                          SDH_C   1 GLgMLveQgaeqFelWTGrep.Pve 24 
                                    GL+ML  Q+ae    W G e+ Pve
  gi|118431110|ref|NP_147334.2| 235 GLWMLAIQAAENIAVWLGLEAsPVE 259
                                    9*******************98887 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.4     6e+03     186     198 ..      77      89 ..      61      91 .. 0.76
   2 !   12.6   0.2   4.8e-05     0.066      21      47 ..     118     144 ..     107     146 .. 0.92
   3 ?    0.1   0.0       0.3   4.1e+02     136     180 ..     183     231 ..     174     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.4
                                    E-B-HHHHHHHHH CS
                                    xxxxxxxxxxxxx RF
                           ThiF 186 ipaiatttavvag 198
                                     +ai++++++vag
  gi|118431110|ref|NP_147334.2|  77 ARAIGAVNTMVAG 89 
                                    5689999999998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.8e-05
                                    EEEE--SHHHHHHHHHHHHHTTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  21 vllvGaGglGsellknLalsGvgkltl 47 
                                     l++GaGg G  ++ +La +G g++ +
  gi|118431110|ref|NP_147334.2| 118 ALVIGAGGAGRAAAYALATWGAGRVLI 144
                                    69********************98765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.3
                                    EEEEEEEETTEEEEEEEEE.CCS-ECTSS-T...GGS.EECCCCEEHHH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                           ThiF 136 plieagtlgfegqvvviip.gktgcyeCldp...sstedptekkvplct 180
                                     +++a++lg++g  +++++  ++gc+   ++    +t   +++ ++ ct
  gi|118431110|ref|NP_147334.2| 183 VVVNATPLGWDGVSTPVERgFREGCIAVDMVyrpLATPFLRRAAASGCT 231
                                    4889999999999999966678889888874444555555666666664 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   1.8e-05     0.025       4      58 ..     119     169 ..     117     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevv 58 
                                    l++G +Gg G++ a  la  ga ++++ sR++    ++++  + l+ lgaeve v
  gi|118431110|ref|NP_147334.2| 119 LVIG-AGGAGRAAAYALATWGAGRVLIASRTGL---TARRAAQDLAGLGAEVEPV 169
                                    6666.7999**********************54...3334568888999999865 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 ?   14.3   0.2   3.4e-05     0.047       4      70 ..     120     189 ..     118     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.4e-05
                                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S- CS
                  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlavk 70 
                                    +iGaG  g+a a  l++ g  +  +++a sr+  +a+ +a++l         v ++  e+aa+ +dvvv a +
  gi|118431110|ref|NP_147334.2| 120 VIGAGGAGRAAAYALATWG--AGRVLIA-SRTGLTARRAAQDLAglgaevEPVPPGGLEDAAAASDVVVNATP 189
                                    79*****************..9999988.999999999998888888665334445689*********98877 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.6   5.5e-05     0.076       2      32 ..     118     149 ..     117     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-05
                                    EEEE--SHHHHHHHHHHHHTTT.-EEEEESSS CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGl.kvavvekeq 32 
                                    ++ViG+G+AG aAA+++a  G+ +v++ + ++
  gi|118431110|ref|NP_147334.2| 118 ALVIGAGGAGRAAAYALATWGAgRVLIASRTG 149
                                    69*******************99***999876 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 ?   12.1   0.0   6.8e-05     0.093      37     101 ..     116     190 ..      75     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                                    SEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH.........CHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                   2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee.........eeeelgvelvsleellaesDivslhlpl 101
                                     t  +iG+G  G+a+a  l+ +g+ +v++ +r+  + +          +e + v    le++ a sD+v++++pl
  gi|118431110|ref|NP_147334.2| 116 DTALVIGAGGAGRAAAYALATWGAgRVLIASRTGLTARraaqdlaglGAEVEPVPPGGLEDAAAASDVVVNATPL 190
                                    5889********************99*****998755544453444444444455558999********999998 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   9.3e-05      0.13       2      55 ..     117     170 ..     116     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-05
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiq 55 
                                    ++lv+Ga+ G Gra a++la+ Ga  v+ ++r+  +++++a+ l  +ga++ +++
  gi|118431110|ref|NP_147334.2| 117 TALVIGAG-GAGRAAAYALATWGAGRVLiASRTGLTARRAAQDLAGLGAEVEPVP 170
                                    799***98.**************97666499999999999999999888887764 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.4   0.00016      0.22       3      34 ..     119     150 ..     117     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                    EEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkldt 34 
                                     ViG+G AG +AA+a+a  Ga  +Li+ +++ 
  gi|118431110|ref|NP_147334.2| 119 LVIGAGGAGRAAAYALATWGAGRVLIASRTGL 150
                                    6********************99999877665 PP

>> PE  PE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       1.5   2.1e+03      52      70 ..      70      88 ..      65      91 .. 0.57
   2 ?   11.2   0.2   0.00026      0.36      12      57 ..     153     205 ..     144     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHH CS
                             PE 52 Aalfsahaqeyqalsaqaa 70
                                   A+++ +ha++  a+++ +a
  gi|118431110|ref|NP_147334.2| 70 ASTLDSHARAIGAVNTMVA 88
                                   5555566666555555444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHHHHHHHH.......HHHHHHHHHH----SSSSHHHHHHHHHHHH CS
                             PE  12 aaaaadlagigsalsa.......anaaaaapttavlaaaaDeVSaaiAalfsa 57 
                                    ++aa+dlag+g++++         +aaa+ ++ +  + + D VS+ + + f +
  gi|118431110|ref|NP_147334.2| 153 RRAAQDLAGLGAEVEPvppggleDAAAASDVVVNATPLGWDGVSTPVERGFRE 205
                                    68*************999999977888888899999*********99988876 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 ?   -1.3   0.1      0.71   9.8e+02       8      27 ..      38      59 ..      38      84 .. 0.84
   2 ?   10.7   0.8   0.00016      0.22       4      34 ..     119     148 ..     116     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.71
                                   -SHHHHHHHHHHHH..HTS-EE CS
                                   xxxxxxxxxxxxxx..xxxxxx RF
                    Pyr_redox_2  8 gGpAGlaaaltlaq..agakvt 27
                                   +Gp+Gla al++a   +g++vt
  gi|118431110|ref|NP_147334.2| 38 AGPGGLAPALRMAGelHGFNVT 59
                                   79*******9999877788876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                    EEE--SHHHHHHHHHHHHHTS-EEEEETTHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlvelegt 34 
                                    +viG+G AG aaa  la+ ga  +l+ + +t
  gi|118431110|ref|NP_147334.2| 119 LVIGAGGAGRAAAYALATWGAGRVLI-ASRT 148
                                    7*****************87766666.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1994.26
//
Query:       gi|14600813|ref|NP_147336.1|  [L=222]
Description: 3-dehydroquinate dehydratase [Aeropyrum pernix K1]
Scores for complete 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   38.5   0.0    1.8e-09   38.2   0.0    1.1  1  DHquinase_I  Type I 3-dehydroquinase


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   9.8e-14   1.8e-09      22     229 .]      27     214 ..       8     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 9.8e-14
                                   S-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-..SEEEEEGG-. CS
                   DHquinase_I  22 kaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielga..dyvDvEltea 100
                                       vElRlD+++ + + e+++  + +l   s+  +++tlr++  gg  +r++  e+  +l ++ +l++   +vD E+   
  gi|14600813|ref|NP_147336.1|  27 PTGCVELRLDFYPGD-PGEALELLATRLH--SPARVVVTLRSAGHGGL-DRRARGERRAVLARLEDLAPegWLVDYEV--- 100
                                   4678********866.5344444444443..4999************9.89***********99999997789*****... PP

                                   HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHHHHT-SS-E CS
                   DHquinase_I 101 peeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltseakeekdeapl 181
                                        ++l+++   g +  I+S+h ++   + ++l++  + +++lga  +K++ +  +  + ++  +l     e  +    
  gi|14600813|ref|NP_147336.1| 101 -----EDLHASS--GCSGCIASSHPTTPPTPRRALEE-AAVAERLGASAYKLVYPGVEPWEQAAAARLVA---E--AGGFA 168
                                   .....4788887..77888*****7766555556665.566999************************84...3..34667 PP

                                   EEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHHH CS
                   DHquinase_I 182 IamamGelGkiSRilgevfGspvtfasleeakasapGqltarelreil 229
                                     +  G+  + SR+ ++++G+p+ f+s   ++a   G ++ +e+ e++
  gi|14600813|ref|NP_147336.1| 169 TSFTLGPGTLASRLTALALGAPLVFGS--HPRAPLDGVPQSSEIMELY 214
                                   889999999******************..7777888999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1808.89
//
Query:       gi|14600814|ref|NP_147337.1|  [L=358]
Description: 3-dehydroquinate synthase [Aeropyrum pernix K1]
Scores for complete 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-70  236.9   0.0    2.8e-70  236.5   0.0    1.1  1  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
      0.062   13.0   3.0       0.32   10.6   0.1    2.3  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.5   0.0   3.2e-74   2.8e-70       5     261 ..      71     321 ..      68     322 .. 0.94

  Alignments for each domain:
  == domain 1  score: 236.5 bits;  conditional E-value: 3.2e-74
                                   -SSGGGCCHHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTE CS
                  DHQ_synthase   5 pdgeksKsletlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplg 85 
                                     ge++Ksl+ +++++d +l+a++eR++++  +GGG+++D aGf+A+t++RG+++v++P+t+la  D++ GgKt++nl +g
  gi|14600814|ref|NP_147337.1|  71 GGGERVKSLDWVTRLWDLMLQAGVERSTTVYIIGGGALLDAAGFAASTLMRGLSTVNIPSTTLAAFDAAAGGKTGVNL-RG 150
                                   579**************************************************************************9.89 PP

                                   EEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHHHHHHHHH.T-HHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHH CS
                  DHQ_synthase  86 KNliGafaqPkavlidlevLktLperelraGlaEviKyali.kdeelfelleenaeallkeeeeealeeliarsievkaev 165
                                   KN++G+f++P++vl+++ +++  p++ +r+G+aE++K+ ++  d+e  ++l  +a a    ++++ l++l   s+ +k++v
  gi|14600814|ref|NP_147337.1| 151 KNMVGTFHNPRMVLVEPGIVAGQPDEGYRDGFAELVKHVALsGDREPAASLLPQALA----RRPAPLARLAFWSLGYKMQV 227
                                   *************************************98773577776666666533....3799**************** PP

                                   HHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT. CS
                  DHQ_synthase 166 veeDekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkell 246
                                   v+ D +e+glr++LnlGHtigHa+Ea+++y +l+HG++V+iG++ ++els++l  l++ e+e++l++l+++glp++ +   
  gi|14600814|ref|NP_147337.1| 228 VAGDPRERGLRRILNLGHTIGHALEAASSY-TLSHGRSVSIGLAGELELSRRLAGLPRGEAEDVLDMLSTAGLPLEPPPG- 306
                                   ******************************.**********************************************999. PP

                                   -HHHHHHHHTTCTTX CS
                  DHQ_synthase 247 eveellealkkDkkv 261
                                    + e++ ++  Dkk 
  gi|14600814|ref|NP_147337.1| 307 LAGEAAGLVGLDKKR 321
                                   788888888899986 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   3.6e-05      0.32      36     164 ..      52     188 ..      29     218 .. 0.72
   2 ?    2.4   0.3     0.012     1e+02     229     249 ..     245     265 ..     244     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.6e-05
                      Fe-ADH_2  36 ekveeslkeagikve..vveeveeeadleeveklveal...reketdlvvavGgGtiiDiakyvsakl..nvpyvsvp..T 107
                                    ++++ l+ +g++v   v    e  ++l+ v +l + +     ++ + v  +GgG ++D+a +++++l  +++ v +p  T
  gi|14600814|ref|NP_147337.1|  52 ARLARILEARGVEVLgaVAGGGERVKSLDWVTRLWDLMlqaGVERSTTVYIIGGGALLDAAGFAASTLmrGLSTVNIPstT 132
                                   4566677777766643233333333444444444333322144566677779*************9862256778887556 PP

                      Fe-ADH_2 108 aaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDllgk 164
                                    a+ D  a     + ++gk   v + + P  v++   ++a  P++  + G+++l+  
  gi|14600814|ref|NP_147337.1| 133 LAAFDAAAGGKTGVNLRGKNM-VGTFHNPRMVLVEPGIVAGQPDEGYRDGFAELVKH 188
                                   7999*****999999999555.56899*************************99854 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
                      Fe-ADH_2 229 HliSHaldmlalkqalHGeqV 249
                                   H i Hal+++++    HG +V
  gi|14600814|ref|NP_147337.1| 245 HTIGHALEAASSYTLSHGRSV 265
                                   9**********999****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.19s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3021.57
//
Query:       gi|118431111|ref|NP_147338.2|  [L=270]
Description: 3-deoxy-7-phosphoheptulonate synthase [Aeropyrum pernix K1]
Scores for 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-82  274.8   0.0      7e-82  274.4   0.0    1.0  1  DAHP_synth_1  DAHP synthetase I family
    4.2e-06   26.4   0.0    7.2e-06   25.6   0.0    1.4  1  NeuB          NeuB family
  ------ inclusion threshold ------
      0.025   14.6   0.0       0.24   11.5   0.0    2.3  2  Nsp1          Non structural protein Nsp1
        0.1   13.2   0.0       0.23   12.1   0.0    1.5  1  PGM_PMM_II    Phosphoglucomutase/phosphomannomutase, alpha/be


Domain annotation for each model (and alignments):
>> DAHP_synth_1  DAHP synthetase I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.4   0.0   1.6e-85     7e-82       5     262 ..      22     260 ..      11     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 274.4 bits;  conditional E-value: 1.6e-85
                                    ECHHHHCCCTTTCSEEEEEEESC-S-HHHHHHHHHHHHHHHHHHTTTEEEEEESSSC-S.SSTTS-SHTTHHHTHHHHHH CS
                   DAHP_synth_1   5 sakaadiliGkddrllviaGPCsiedpeaaleyAerlkklgeklkddleiimrayfeKpRrstvgfkGlindpdlkilsr 84 
                                    +   ++++iG++++ +viaGPCs+e++e++ e A ++k++g++     +++++a+  KpR+s+++f+Gl++++ lk l+r
  gi|118431111|ref|NP_147338.2|  22 EV--EGVRIGGGSK-AVIAGPCSVESWEQVREAALAVKEAGAH-----MLRGGAF--KPRTSPYSFQGLGLEG-LKLLRR 90 
                                    33..589*******.****************************.....*******..****************.****** PP

                                    HHHHHT-EEEEEESSCCTHHHHHHHESEEEE-CTCTTBHHHHHHHHTTSSEEEEEE-TTHHHHHHHHHHHHHHHTTEEE- CS
                   DAHP_synth_1  85 ikkelglpiatevldpisvqyladvvdiiqiGArttesqdllelasglskpvglKngtdvaidemkaaaekilflgvetk 164
                                    + +e glp++tevldp++v++++ ++d++qiGAr+++++ ll++++++ kpv+lK+g+ ++++e+ aaae+il +g  ++
  gi|118431111|ref|NP_147338.2|  91 AGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEG--NW 168
                                    ****************************************************************************..7* PP

                                    -EEEEEEEEEESTSSSSSCHCHHHHHHHHHHCTSS-EEEESCHHHTTCGGGGHHHHHHHHHHHHHTTESEEEEEBBSSCC CS
                   DAHP_synth_1 165 giilcerglrggkktnrdvedvaavkilkeetgklpvmvDvsHansrkdykrqkkvlklakaaiaaGiaGvmiEshlnpg 244
                                    ++ l erg+r+++ ++r ++dvaav++lke+t +lpv+vD+sH ++r+       v++laka++aaG++G+++E+h+np+
  gi|118431111|ref|NP_147338.2| 169 QVVLVERGIRTFEPSTRFTLDVAAVAVLKEAT-HLPVIVDPSHPAGRRS-----LVPALAKAGLAAGADGLIVEVHPNPE 242
                                    ********************************.9***************.....************************** PP

                                    C-SSTGGGGBBCTCBHHH CS
                   DAHP_synth_1 245 kalsdgkqalkygksetd 262
                                    +alsd+kq+l++g++ ++
  gi|118431111|ref|NP_147338.2| 243 EALSDAKQQLTPGEFARL 260
                                    ************776553 PP

>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.6e-09   7.2e-06      54     147 ..      81     174 ..      70     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-09
                                    -HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT-.-HHHHHHHH CS
                           NeuB  54 seeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSgeltnlpllekiaktgkpvilStGma.tleeieeav 132
                                      e  k l +  +e+g+ +++   d + v+ ++++  +++ i++ +++n+pll+++ + gkpv+l  G   t+ee+ +a 
  gi|118431111|ref|NP_147338.2|  81 GLEGLKLLRRAGDEAGLPVVTEVLDPRHVETVSRY-ADMLQIGARNMQNFPLLREVGRSGKPVLLKRGFGnTVEELLAAA 159
                                    556678889999********************666.9*******************************9626899999** PP

                                    HHH.HHHT--EEEEE CS
                           NeuB 133 evlreagaeklvllh 147
                                    e++  +g+ ++vl++
  gi|118431111|ref|NP_147338.2| 160 EYILLEGNWQVVLVE 174
                                    *99999999999875 PP

>> Nsp1  Non structural protein Nsp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.3e-05      0.24      14      48 ..     143     177 ..     137     192 .. 0.91
   2 ?    0.0   0.0      0.19   8.4e+02      22      37 ..     240     255 ..     228     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                                    -S---S-SSHHHHHHHHHHHHHHT-EEEE---TTS CS
                           Nsp1  14 vlvrgfgdsveealsearehlkngtcglvelekgv 48 
                                    +l rgfg++vee l+ a   l +g   +v +e+g+
  gi|118431111|ref|NP_147338.2| 143 LLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGI 177
                                    4679****************************997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.19
                                    SHHHHHHHHHHHHHHT CS
                           Nsp1  22 sveealsearehlkng 37 
                                      eeals+a+++l  g
  gi|118431111|ref|NP_147338.2| 240 NPEEALSDAKQQLTPG 255
                                    569*******999877 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 ?   12.1   0.0   5.2e-05      0.23      16      75 ..     197     249 ..     186     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                                    HHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHH CS
                     PGM_PMM_II  16 ikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealklli 75 
                                    ++ ++l v++dp h ag+  l  +l ++g+      a  d+  ++ +pnpee  al+++ 
  gi|118431111|ref|NP_147338.2| 197 KEATHLPVIVDPSHPAGRRSLVPALAKAGL-----AAGADGLIVEVHPNPEE--ALSDAK 249
                                    4566899********************998.....77899999999999999..777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2308.49
//
Query:       gi|14600816|ref|NP_147339.1|  [L=322]
Description: transketolase [Aeropyrum pernix K1]
Scores for 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  114.6   0.1    7.4e-33  113.7   0.0    1.4  2  Transket_pyr     Transketolase, pyrimidine binding domain
    8.9e-27   93.4   0.0    2.5e-26   92.0   0.0    1.8  2  Transketolase_C  Transketolase, C-terminal domain
    2.1e-06   28.0   0.1    5.8e-06   26.5   0.1    1.8  2  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 !  113.7   0.0   1.2e-36   7.4e-33       3     174 ..      10     172 ..       8     175 .. 0.97
   2 ?   -3.5   0.0       1.2   7.2e+03      47      61 ..     263     277 ..     240     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.2e-36
                                   EEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHH CS
                  Transket_pyr   3 iawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgd 83 
                                    ++rka++  la+l+ e +++v+++aD+ ++t+  +     ++   rv+++gisEq ++g+a+G+alag  l++v++ Fg 
  gi|14600816|ref|NP_147339.1|  10 ASYRKALGRLLARLASELEDLVVLDADTLRSTGAIEVYRSAPR---RVLNMGISEQDLIGTAAGIALAG--LRPVVTGFGA 85 
                                   689****************************************...***********************..********** PP

                                   HHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS. CS
                  Transket_pyr  84 FangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredr 163
                                   F++    + +++ir+ + + +l+v+ v t+++++ + dG +hq +e++a++r+++   v+ P+d + t + ++  +rr +r
  gi|14600816|ref|NP_147339.1|  86 FLM----RGWEQIRNTVDRDGLNVKiVATHTGLSPHVDGSSHQVLEDLALMRSLARTAVFSPADDVATVETVEWLVRR-YR 161
                                   ***....**********************************************************************5.69 PP

                                   SEEEEEE-SSE CS
                  Transket_pyr 164 kPvvlrlpksl 174
                                   +P ++rl + +
  gi|14600816|ref|NP_147339.1| 162 GPAYVRLGRDN 172
                                   *******9987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                                   TEGEEE--S-HHHHH CS
                  Transket_pyr  47 egrvidsgisEqavl 61 
                                    g v+ s ++E++++
  gi|14600816|ref|NP_147339.1| 263 LGDVVSSILAEEGAC 277
                                   567888888888876 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.8   4.8e+03      89     110 ..      30      52 ..      15      58 .. 0.58
   2 !   92.0   0.0   4.2e-30   2.5e-26       3     124 .]     189     311 ..     187     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.8
                                   CTTCSSEEEEEEE-SS.SSSSGH CS
               Transketolase_C  89 fdgldapvkrvggpdv.iepgsa 110
                                   +  lda  +r +g  + ++++++
  gi|14600816|ref|NP_147339.1|  30 LVVLDADTLRSTGAIEvYRSAPR 52 
                                   55566666666666444666665 PP

  == domain 2  score: 92.0 bits;  conditional E-value: 4.2e-30
                                   EEEEET.TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHH CS
               Transketolase_C   3 aeilre.gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaa 82 
                                   +e+l e g+ vtl+a+G mv ++l+Aa+ L++eg+++ Vvd++++kp  ++++le++++ + lv+vee+++ gG+g+ v++
  gi|14600816|ref|NP_147339.1| 189 GEVLVEpGEAVTLLATGPMVGVSLAAAALLRSEGLRVGVVDVYSIKPAPRRLVLEAAERSRLLVTVEEHRTVGGLGDVVSS 269
                                   5666666************************************************************************** PP

                                   HHHHCCCTTCSSEEEEEEE-SS.SSSSGHH..HHHHHTT-SHHHH CS
               Transketolase_C  83 alaeeafdgldapvkrvggpdv.iepgsae..elekafgldaeki 124
                                   +lae   +g  a++ r+g+p   + + s++  +l++++ ld+e++
  gi|14600816|ref|NP_147339.1| 270 ILAE---EGACARQARIGVPPGvYGSSSRDymSLLRHLRLDPESV 311
                                   ****...9************999999999999999***9999986 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6   9.5e+03      47      65 ..      22      39 ..      19      57 .. 0.69
   2 !   26.5   0.1   9.7e-10   5.8e-06       4      75 ..     200     271 ..     198     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                                  HHSTT-SEEEEEE-S--TT CS
                       PFOR_II 47 ellkkvkkvvvldrnisfg 65
                                  +l+++++ +vvld ++ + 
  gi|14600816|ref|NP_147339.1| 22 RLASELEDLVVLDADT-LR 39
                                  6677788888888887.33 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 9.7e-10
                                   EEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHH CS
                       PFOR_II   4 vivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevk 75 
                                    ++a+G ++g+  +a+  lR eg++vG++ + ++ P P++ + e++++ + +v+++   ++g  G +v+ + 
  gi|14600816|ref|NP_147339.1| 200 TLLATGPMVGVSLAAAALLRSEGLRVGVVDVYSIKPAPRRLVLEAAERSRLLVTVEEHRTVGGLGDVVSSIL 271
                                   6789999****************************************************9999988887774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2516.40
//
Query:       gi|118431112|ref|NP_147340.2|  [L=236]
Description: transketolase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-20   72.4   0.0    7.1e-20   71.2   0.0    1.5  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    1.3e-05   24.5   0.0    1.8e-05   24.1   0.0    1.1  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    0.00025   20.1   0.0    0.00034   19.7   0.0    1.1  1  E1_dh            Dehydrogenase E1 component
     0.0046   15.8   0.0     0.0058   15.5   0.0    1.1  1  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   1.6e-23   7.1e-20      57     244 ..      60     234 ..      34     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.6e-23
                                    EEEESSGGGHHHHHHHHHHTTSS--HHHHTTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH- CS
                Transketolase_N  57 RfvLsnGhaslllYsllhLtGydlsledlksfrqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatyn 136
                                    R +Ls Ghasl  Y+ll  +G+    +  + f   gs    hPe g t+   v  G LGq ++ + gl +  +    + +
  gi|118431112|ref|NP_147340.2|  60 RVILSKGHASLGFYALLEEMGLLERGSVERLFARPGSPLQAHPEAGRTPLTLVSNGSLGQALSVSNGLVIGSRLKGRRVE 139
                                    899******************954444456699*************************************9998777665 PP

                                    BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGGT-.-S-HHHHHHHTT-EEEEETT CS
                Transketolase_N 137 kpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGeteisf.tedvakrfeaygWhvieved 215
                                              + v+lgDg l eG   ea+  a+ ++L +++++ D n++   Gete    +e  ++r++++gW+ ++ve+
  gi|118431112|ref|NP_147340.2| 140 ----------VAVVLGDGELDEGQVWEAAATAAAMRLWEVVAIVDRNRVQHTGETEAIKpKEPLEDRWRSFGWEAVTVEG 209
                                    ..........789******************************************9765278899*********999765 PP

                                    TT-HHHHHHHHHHHHH-TTS-EEEEEE-- CS
                Transketolase_N 216 gedveaikaaieeakaekdkPsliklrtv 244
                                       ve+i++a+++ +a  d+P+ i ++ v
  gi|118431112|ref|NP_147340.2| 210 --RVEEIARALDS-RA-GDRPTAIIVEAV 234
                                    ..699*****986.44.48***9998765 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 !   24.1   0.0     4e-09   1.8e-05     107     175 ..     111     180 ..      91     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4e-09
                 DXP_synthase_N 107 afeagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelk.kkllvilNdNemsi 175
                                     +++g  + ++s++ Gl++ ++lkg++ +v  v+GDg l  G  +ea  ++++++  +++ i+  N+   
  gi|118431112|ref|NP_147340.2| 111 LVSNGSLGQALSVSNGLVIGSRLKGRRVEVAVVLGDGELDEGQVWEAAATAAAMRlWEVVAIVDRNRVQH 180
                                    567788889***************************************9998886257777887777655 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.5e-08   0.00034      99     194 ..     113     209 ..     101     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.5e-08
                                    E-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT-.-EEEEEEEESEETTEEHHHH-S--- CS
                          E1_dh  99 gngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwkl.pvifvveNNkygisTeaekasaske 177
                                     ng +g   ++ +G+++ ++ +g  + ++++ GDg   +G+v+ea+  aa+++l  v+ +v  N+   + e+e+ +  + 
  gi|118431112|ref|NP_147340.2| 113 SNGSLGQALSVSNGLVIGSRLKGRRVEVAVVLGDGELDEGQVWEAAATAAAMRLwEVVAIVDRNRVQHTGETEAIKPKEP 192
                                    6888999999999********************************999999887478********999999999999999 PP

                                    GGG..TTTTS-EEEEET CS
                          E1_dh 178 ladrargvgipglrVdg 194
                                    l dr r +g   ++V+g
  gi|118431112|ref|NP_147340.2| 193 LEDRWRSFGWEAVTVEG 209
                                    99999999999999988 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-06    0.0058     118     235 ..      91     210 ..      77     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-06
                          XFP_N 118 fsfPGG.ipshv.aaetPGsiheGGelGyalshayGavldn....PdlivacvvGdGeaetGPlatswhsnkflnPaedG 191
                                    f+ PG  + +h  a  tP ++   G lG als++ G v+        + va v+GdGe + G +   w++      ++  
  gi|118431112|ref|NP_147340.2|  91 FARPGSpLQAHPeAGRTPLTLVSNGSLGQALSVSNGLVIGSrlkgRRVEVAVVLGDGELDEGQV---WEAAATAAAMRLW 167
                                    66676546777514579*****************99997641211455678889*******975...9999999999999 PP

                          XFP_N 192 avlPilelnGykisnptilarisdeelkklfeGlGyepafvede 235
                                     v+ i++ n  + +  t  a  ++e l++ ++ +G+e+++ve++
  gi|118431112|ref|NP_147340.2| 168 EVVAIVDRNRVQHTGET-EAIKPKEPLEDRWRSFGWEAVTVEGR 210
                                    9*******998887776.56778999***********9999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1785.82
//
Query:       gi|118431113|ref|NP_147341.2|  [L=901]
Description: hypothetical protein APE_0588.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (901 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 6261.29
//
Query:       gi|118431114|ref|NP_147343.2|  [L=266]
Description: enoyl-CoA hydratase/isomerase [Aeropyrum pernix K1]
Scores for complete 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-40  139.3   0.0    1.6e-40  139.1   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.2e-27   96.5   0.0    2.8e-27   96.1   0.0    1.1  1  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
       0.15   12.1   0.1       0.38   10.8   0.0    1.7  2  GvpO      Gas vesicle synthesis protein GvpO


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 !  139.1   0.0   2.6e-44   1.6e-40      11     248 ..      21     257 ..      16     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 2.6e-44
                                    E--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHHHHHHHHHSSS CS
                          ECH_1  11 lnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeek.akqallkeevlelwtklytvpk 89 
                                    + rPe +Na++  ++ E+++al +le d+ vr v +tG +kaF+aG dl e+ae +  ++++ l +++    ++++ + k
  gi|118431114|ref|NP_147343.2|  21 FSRPERLNAFNTSMMREVLAALDELEGDEGVRFVAITGEGKAFSAGIDLGELAEAGSpEEAERLFSTLAMVVERILGLRK 100
                                    89***************************************************9988688888888999999******** PP

                                    EEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHHHHHHCTS CS
                          ECH_1  90 pviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaqealkvGl 169
                                    pvi avnG+aigGG+el  a Div+a ++a+++ +e++  l p++  t   +  +G ++A +++l++++i+a+ea ++Gl
  gi|118431114|ref|NP_147343.2| 101 PVIMAVNGHAIGGGAELLWAGDIVVAVRSARISWPESLWNLAPPFLPT-LGPFVLGPARAAYLALTAEPITAEEAYRMGL 179
                                    *******************************************87655.56889************************** PP

                                    SSEEESG.GGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHCTSHHHHHHHHHHHTCSH-- CS
                          ECH_1 170 vdkvvpe.eqlleealelaeklaekspaalrqlkealnakledalaeqleaea.klfestfskddikeGlqaflEkrkpe 247
                                    v+  v e  ql++    +aek++ ++paa++ + + l+a  +   ++   ae  +l ++t++  +  ++ +    kr+p+
  gi|118431114|ref|NP_147343.2| 180 VSLLVDEpGQLEDAVNRVAEKIMASPPAAVESIVSMLRAGKRGWHTQLGVAELkRLSKDTTAL-QAAKSFKD--TKRPPD 256
                                    ******999****************************99998544444444440444444444.33344433..355555 PP

                                    - CS
                          ECH_1 248 f 248
                                    +
  gi|118431114|ref|NP_147343.2| 257 Y 257
                                    5 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   4.7e-31   2.8e-27       2     203 ..      17     217 ..      16     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 4.7e-31
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    g++ + rp+ lNa +++m+r++ +al+e e d+ v++v ++g+g kaf+AG D+ +l+ea + +++e  ++f++   +  
  gi|118431114|ref|NP_147343.2|  17 GWLVFSRPERLNAFNTSMMREVLAALDELEGDEGVRFVAITGEG-KAFSAGIDLGELAEAGSPEEAE--RLFSTLAMVVE 93 
                                    678899************************************88.****************997755..7********** PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH---B-HHH CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGarlkgad 161
                                    +i  ++kpv+  ++G ++GgG+ l   g + v+  +++++ PE    l P    +     l  + + ylalT++ +++++
  gi|118431114|ref|NP_147343.2|  94 RILGLRKPVIMAVNGHAIGGGAELLWAGDIVVAVRSARISWPESLWNLAPPFLPTLGPFVLGPARAAYLALTAEPITAEE 173
                                    ***********************************************9998655555555555779************** PP

                                    HHHTTS--EE--GG.GHHHHHHHHHTT.........-------- CS
                          ECH_2 162 alaaglathyvpse.klealeeaLaelessd.eeaveevleela 203
                                    a+ +gl + +v++  +le+  +++ae   ++  +ave++++ l+
  gi|118431114|ref|NP_147343.2| 174 AYRMGLVSLLVDEPgQLEDAVNRVAEKIMASpPAAVESIVSMLR 217
                                    ***********875155555555555433334555555555444 PP

>> GvpO  Gas vesicle synthesis protein GvpO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.89   5.3e+03      18      52 ..      34      68 ..      25      74 .. 0.63
   2 ?   10.8   0.0   6.4e-05      0.38      17      65 ..     192     242 ..     184     249 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.89
                           GvpO 18 aarkareqlaeLlgrelegvssvertedgWrveve 52
                                    +r+  ++l eL g e    ++++ +    ++ ++
  gi|118431114|ref|NP_147343.2| 34 MMREVLAALDELEGDEGVRFVAITGEGKAFSAGID 68
                                   56777777777777665555555555555556555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.4e-05
                           GvpO  17 eaarkareqlaeLlgrelegvssverted.gWrvevevlElervP.dttdi 65 
                                    +a ++ +e++      ++e+++s+ r+   gW++++ v El+r+  dtt +
  gi|118431114|ref|NP_147343.2| 192 DAVNRVAEKIMASPPAAVESIVSMLRAGKrGWHTQLGVAELKRLSkDTTAL 242
                                    455555555555555678898887766555************985366655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1900.11
//
Query:       gi|118431115|ref|NP_147344.2|  [L=185]
Description: hypothetical protein APE_0593.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1452.06
//
Query:       gi|118431116|ref|NP_147345.2|  [L=187]
Description: hypothetical protein APE_0594.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); 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:                         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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1576.33
//
Query:       gi|118431117|ref|NP_147346.2|  [L=92]
Description: hypothetical protein APE_0594a.1 [Aeropyrum pernix K1]
Scores for 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-15   55.1   0.0    6.3e-15   54.9   0.0    1.0  1  HTH_45           Winged helix-turn-helix
    1.5e-06   28.0   0.0    2.2e-06   27.4   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.4e-05   24.9   0.1    2.3e-05   24.2   0.1    1.5  1  MarR_2           MarR family
     0.0008   18.9   0.2     0.0026   17.3   0.0    1.9  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.001   19.5   0.1     0.0016   18.9   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
     0.0026   17.6   0.0     0.0035   17.2   0.0    1.2  1  RuvB_C           RuvB C-terminal winged helix domain
     0.0054   17.0   0.0       0.01   16.1   0.0    1.5  1  Rrf2             Transcriptional regulator
     0.0081   15.9   0.0      0.011   15.5   0.0    1.1  1  DUF4364          Domain of unknown function (DUF4364)
  ------ inclusion threshold ------
      0.015   15.4   0.0       0.02   14.9   0.0    1.3  1  FeoC             FeoC like transcriptional regulator
      0.015   15.2   0.1      0.027   14.4   0.1    1.4  1  HTH_15           Helix-turn-helix domain of alkylmercury lyas
       0.02   15.0   0.0      0.038   14.0   0.0    1.5  1  HTH_20           Helix-turn-helix domain
      0.022   14.3   0.3      0.027   14.0   0.3    1.2  1  HTH_42           Winged helix DNA-binding domain
      0.041   14.2   0.0      0.051   13.9   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
      0.099   12.6   0.0       0.11   12.4   0.0    1.3  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_
       0.19   12.0   0.0       0.26   11.5   0.0    1.2  1  dbPDZ_assoc      Unstructured region between two PDZ domains 


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 !   54.9   0.0   5.2e-18   6.3e-15       1      76 [.       6      86 ..       6      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 5.2e-18
                         HTH_45  1 rRskleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkeleela 76
                                   rRs++eIi+d+Lea++ eg  ++T++   an+ y++l+  L+ Lv kgl+      ++++ ++T +G + l++lk++++l 
  gi|118431117|ref|NP_147346.2|  6 RRSRVEIIIDVLEALQdEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVrvrdMGRSKQVEITREGVRALHDLKRVRRLL 86
                                   8**************98999*****************************98875558999*****************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 !   27.4   0.0   1.9e-09   2.2e-06      12      57 ..      15      60 ..       8      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.9e-09
                                   CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                           TrmB 12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                   +v  aL  +gp+t + +a  ++ p+ + + vL+ L+ kGlV++++ 
  gi|118431117|ref|NP_147346.2| 15 DVLEALQDEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVRVRDM 60
                                   78899999**********************************9975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1     2e-08   2.3e-05       8      55 ..      14      59 ..      12      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2e-08
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                    +vL aL ++++  +t++ la   +++  +++ +l+ Lva+GLv+ r+
  gi|118431117|ref|NP_147346.2| 14 IDVLEALQDEGP--MTPTRLATVANMPYDRLQTVLEPLVAKGLVRVRD 59
                                   79**********..******************************9873 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   0.0   2.1e-06    0.0026       3      48 .]      11      56 ..       9      56 .. 0.95
   2 ?   -1.4   0.1       1.5   1.7e+03      36      43 ..      80      87 ..      79      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-06
                         HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   e+ +++Le+Lq+++ ++ + LA   +++   + + l+ L+ +Gl++
  gi|118431117|ref|NP_147346.2| 11 EIIIDVLEALQDEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVR 56
                                   57899**************************************996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                         HTH_24 36 rrlkrLee 43
                                   +r++rL +
  gi|118431117|ref|NP_147346.2| 80 KRVRRLLS 87
                                   79999976 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.3e-06    0.0016       8      68 .]      16      72 ..       8      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                         HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   vL+ ++  +++++ ++l+ + n+ +     +l+ L++kGLv r +d   +r+k+v++T +G
  gi|118431117|ref|NP_147346.2| 16 VLEALQ-DEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLV-RVRDM--GRSKQVEITREG 72
                                   477777.8999999***************************.99999..*********887 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 !   17.2   0.0   2.9e-06    0.0035       9      71 ..      14      76 ..      11      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEE....EE-HHHHHHH CS
                         RuvB_C  9 ikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGR....ilTkkglkyl 71
                                   i++L++l+   ++gp+  + la++++++ + +++v EP L+ +gl++  + GR    ++T++g++ l
  gi|118431117|ref|NP_147346.2| 14 IDVLEALQ---DEGPMTPTRLATVANMPYDRLQTVLEP-LVAKGLVRVRDMGRskqvEITREGVRAL 76
                                   56788888...68999999*******************.89************55555899998877 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.6e-06      0.01      16      58 ..      16      58 ..       5      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.6e-06
                                   HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   +L++ ++e+p++ + +a+  n++   l+ +l+ L  +glv+++
  gi|118431117|ref|NP_147346.2| 16 VLEALQDEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVRVR 58
                                   4677888899******************************986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     9e-06     0.011      31      73 ..      37      79 ..      29      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9e-06
                        DUF4364 31 tnYfdlqqalseLvesglieeeekenktlykiTekGketlelf 73
                                   + Y  lq +l+ Lv +gl+++++   +++ +iT +G ++l+ +
  gi|118431117|ref|NP_147346.2| 37 MPYDRLQTVLEPLVAKGLVRVRDMGRSKQVEITREGVRALHDL 79
                                   77999********************************999866 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-05      0.02       3      50 ..      14      61 ..      12      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                           FeoC  3 telkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                    ++ e+l+ +g      L++  ++  + l+  Le +v+kG v+ ++++
  gi|118431117|ref|NP_147346.2| 14 IDVLEALQDEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVRVRDMG 61
                                   5778999***********************************998875 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 ?   14.4   0.1   2.2e-05     0.027      19      57 ..       9      47 ..       4      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                         HTH_15 19 saellrpLlrlLakGepVtveeLAaatgrsveevrqaLa 57
                                     e+++ +l+ L +  p t ++LA+ ++ + ++ + +L+
  gi|118431117|ref|NP_147346.2|  9 RVEIIIDVLEALQDEGPMTPTRLATVANMPYDRLQTVLE 47
                                   5689999******************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.2e-05     0.038      14      61 .]      15      62 ..      13      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                   ++l aL +++++t++ la    ++   l   L+ L+  gLv+v++ gr
  gi|118431117|ref|NP_147346.2| 15 DVLEALQDEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVRVRDMGR 62
                                   89******************************************9886 PP

>> HTH_42  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.3e-05     0.027     174     246 ..      17      88 ..       5      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                         HTH_42 174 rrylrayGpatvadlaawsgltkarlraalaelvaegelvevrvergre.rlfdlpedlaelpgadtpvrlLpp 246
                                     ++l+  Gp t+  la+   ++  rl+ +l+ lva+  lv+vr+  gr+ ++   +e  ++l + ++ +rlL++
  gi|118431117|ref|NP_147346.2|  17 LEALQDEGPMTPTRLATVANMPYDRLQTVLEPLVAK-GLVRVRDM-GRSkQVEITREGVRALHDLKRVRRLLSD 88 
                                    456777799999999999999999999999999977.99999999.6665666666655666666666688876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.3e-05     0.051       8      60 ..      16      64 ..      12      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                Penicillinase_R  8 vmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegraf 60
                                   v+e+l ++g++t + + +  + +    y   +t+l+ Lv+Kgl++ +  gr+ 
  gi|118431117|ref|NP_147346.2| 16 VLEALQDEGPMTPTRLATVANMP----YDRLQTVLEPLVAKGLVRVRDMGRSK 64
                                   88999999999999988888888....9999*******************986 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.5e-05      0.11      48      91 ..      20      63 ..       9      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.5e-05
                Phage_rep_org_N 48 lsenipytaemlalifnreletvrlaLkvlkdlelieisedkvi 91
                                   l++++p t   la++ n + ++++ +L+ l +++l+ + + +  
  gi|118431117|ref|NP_147346.2| 20 LQDEGPMTPTRLATVANMPYDRLQTVLEPLVAKGLVRVRDMGRS 63
                                   78999*******************************99886655 PP

>> dbPDZ_assoc  Unstructured region between two PDZ domains on Dlg5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.26      40      62 ..      13      35 ..       7      49 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                    dbPDZ_assoc 40 iidtlse.qDeGtmtPpskqttPa 62
                                   iid l   qDeG+mtP+   +t a
  gi|118431117|ref|NP_147346.2| 13 IIDVLEAlQDEGPMTPTRL-ATVA 35
                                   67877534********754.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 726.60
//
Query:       gi|118431118|ref|NP_147347.2|  [L=383]
Description: dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-18   66.9   0.0    7.1e-18   64.9   0.0    1.8  1  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
     0.0017   18.9   0.0       0.23   12.0   0.0    2.5  2  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   7.9e-22   7.1e-18       2     278 ..       4     288 ..       3     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 7.9e-22
                                    SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCTC CS
                                    xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgeev 75 
                                    ++v++Gg ++Gl+aa++       +a++t+v  e     +++ l++ ++g+++ ae++    +  +k+ +   +l  + v
  gi|118431118|ref|NP_147347.2|   4 RIVILGGSFGGLQAARYTLDllgDKADITVV-NESDRIVFKPALTYLAAGMRSSAEELYiplR--EKFANTSARLEVSRV 80 
                                    79**************99998878*******.888899999**************98889652..45666655555556* PP

                                    EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.... RF
                    Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGg.... 150
                                     +i+p++ kv+l     +++  i+yd+lv+A G+ p    +pG+ e++  +  tl+ a +++++l + +r vvvG+    
  gi|118431118|ref|NP_147347.2|  81 SGIYPEENKVEL-----SSGSAIEYDYLVIALGAVPDEKALPGL-EEANANPWTLEGALKVRRALENgARKVVVGSfkpp 154
                                    ************.....66789**********************.555566699999*9999999999999****85554 PP

                                    ...SHHHHHHHHH......HHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEET CS
                                    ...xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 151 ...GyiGvElAaa......laklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvle 221
                                        +  +ElA+       + + g+evtl   ++r+l++l++e+s  le+ +e   ++ +   ++ e+d+  +   v   
  gi|118431118|ref|NP_147347.2| 155 ypcPPAPIELAGLvaktplAGNGGVEVTLGFPGPRPLPPLGEEVSSKLEALIESTPIRYVRDFKPIEVDPGRK---VLRH 231
                                    4445678999999444443344467**********************************98888888888887...99** PP

                                    TSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEE..E--TTSBES.STTEEE-GGGC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx.xxxxxxxxxxx RF
                    Pyr_redox_2 222 dgeeidadlvvvavGvrpstelleeklglelderggi..vvdeflrtn.vpgiyaiGDva 278
                                    +g e+  d + +   ++ ++ +   ++gl+  e+g+   +  +  r    ++iy+iGD  
  gi|118431118|ref|NP_147347.2| 232 EGGEESFDVLALVPPYKVNPLI--VEAGLAS-EGGWPrvLFEKGFRHGsYDNIYVIGDSS 288
                                    *******************977..5889998.88876435566667755*********76 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   2.6e-05      0.23       1      38 [.       4      45 ..       4      83 .. 0.78
   2 !    4.4   0.0    0.0062        56      22      68 ..     178     224 ..     162     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                                   EEEEECSSHHHHHHHHHHHH.TT..SEEEEEESSSSSS.TTS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalae.lg..kkVtvversdkll.rll 38
                                   ++v++Gg++ gl +A +  + lg  +++tvv  sd++  +  
  gi|118431118|ref|NP_147347.2|  4 RIVILGGSFGGLQAARYTLDlLGdkADITVVNESDRIVfKPA 45
                                   79***************99967766699********986444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0062
                                    TSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                      Pyr_redox  22 gkkVtvversdkllrllDeeaskilqeklekngievllntkveeieg 68 
                                    g +Vt+   ++++l+ l+ee+s+ l+  +e   i+ + + k+ e++ 
  gi|118431118|ref|NP_147347.2| 178 GVEVTLGFPGPRPLPPLGEEVSSKLEALIESTPIRYVRDFKPIEVDP 224
                                    6899***************************9999999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2785.90
//
Query:       gi|14600825|ref|NP_147348.1|  [L=210]
Description: hypothetical protein APE_0596 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.3   0.1        6.7    7.3   0.0    2.7  3  DUF4179    Domain of unknown function (DUF4179)
       0.24   10.4   0.0       0.32   10.0   0.0    1.1  1  Filo_VP35  Filoviridae VP35


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 ?    7.3   0.0   0.00074       6.7       7      39 ..       6      38 ..       4      68 .. 0.70
   2 ?   -0.4   0.0      0.19   1.7e+03      51      71 ..     149     176 ..     109     180 .. 0.66
   3 ?    1.5   0.1     0.045   4.1e+02       9      34 ..     184     209 ..     177     210 .] 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00074
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXX.--SS CS
                       DUF4179  7 kkvaaaaaalvllllssrllspalAsalnpvig 39
                                  k  a+a a+ ++l++++ ++ +alA    +++g
  gi|14600825|ref|NP_147348.1|  6 KMLAVALALSAILVGGGLYAASALAHGGGQGVG 38
                                  55678888888889***********66523444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                                   HHHHSEE.......EEEEEEETTEEEEE CS
                       DUF4179  51 eqeyvkp.......vnksaednGitvtv 71 
                                   e++y+ +       + k +ed G +v v
  gi|14600825|ref|NP_147348.1| 149 ENGYMVSgawifenIEKAVEDRGEEVSV 176
                                   4444444444444478888888877776 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.045
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       DUF4179   9 vaaaaaalvllllssrllspalAsal 34 
                                    a +aa+++ + +++++++pal  al
  gi|14600825|ref|NP_147348.1| 184 GAWTAAVAIEIDGVGTFVFPALYDAL 209
                                   56678888888899*******99877 PP

>> Filo_VP35  Filoviridae VP35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   3.6e-05      0.32     113     181 ..     107     174 ..     102     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.6e-05
                                   HHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Filo_VP35 113 maktlealskvlaemlakydllvistGratataaateayla.ehGvpppqpalykelavaqkieskdetv 181
                                   m  +l  ++ v+ + l +y+ +v+ tG  t  a  + ay++ e G    +  ++++  + + +e ++e v
  gi|14600825|ref|NP_147348.1| 107 MEEALAEVEGVVVNALDRYNAIVVDTGDGTVRAKILPAYIDvENGYMVSGAWIFEN--IEKAVEDRGEEV 174
                                   7778888999999**************************96599999999999997..556666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1536.99
//
Query:       gi|118431119|ref|NP_147349.2|  [L=83]
Description: hypothetical protein APE_0597.1 [Aeropyrum pernix K1]
Scores for 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   21.3   0.5    0.00061   20.8   0.5    1.3  1  DUF5320          Family of unknown function (DUF5320)
     0.0092   15.4   0.0       0.01   15.2   0.0    1.0  1  Glucos_trans_II  Glucosyl transferase GtrII
     0.0093   15.9   0.0      0.013   15.5   0.0    1.2  1  DUF4083          Domain of unknown function (DUF4083)
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.012   15.7   0.1    1.0  1  DUF4446          Protein of unknown function (DUF4446)
      0.013   15.0   0.0      0.016   14.8   0.0    1.1  1  DUF2140          Uncharacterized protein conserved in bacteri
      0.014   15.4   0.4       0.02   14.9   0.4    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
      0.016   15.0   1.2       0.03   14.1   1.2    1.5  1  DivIC            Septum formation initiator
      0.018   15.3   0.0      0.021   15.1   0.0    1.1  1  MscL             Large-conductance mechanosensitive channel, 
      0.024   14.3   0.1      0.027   14.1   0.1    1.1  1  DUF4131          Domain of unknown function (DUF4131)
      0.043   13.6   0.2      0.048   13.4   0.2    1.1  1  TMEM208_SND2     SRP-independent targeting protein 2/TMEM208
      0.045   13.5   0.0      0.048   13.4   0.0    1.1  1  EMC3_TMCO1       Integral membrane protein EMC3/TMCO1-like
      0.045   13.0   0.0      0.054   12.7   0.0    1.0  1  STE3             Pheromone A receptor
      0.052   13.6   1.7      0.065   13.3   1.7    1.1  1  DUF1192          Protein of unknown function (DUF1192)
       0.12   12.2   6.8       0.24   11.2   6.8    1.6  1  LapA_dom         Lipopolysaccharide assembly protein A domain
       0.12   12.4   0.0       0.13   12.3   0.0    1.2  1  DUF2973          Protein of unknown function (DUF2973)


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.5   5.1e-07   0.00061      36      98 ..       3      77 ..       1      78 [. 0.71

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.1e-07
                        DUF5320 36 gfGrgrggrglgrgfgrrrraggarla.....................aaetaeaskeeekelLeeqaeaLeeeleaikkrl 96
                                   g+G+  g +g   g  ++                               ++t+++ ++ +++ Le+++++L++e+e+ik+ l
  gi|118431119|ref|NP_147349.2|  3 GWGW--GFFGGLWGLFWML-------IfililgaviyaiivlirglatGQQTQQPVQQPSEKHLEQEIRSLKSEIEEIKRLL 75
                                   3333..3344444444433.......223333447788889999999889999999999********************999 PP

                        DUF5320 97 ke 98
                                   +e
  gi|118431119|ref|NP_147349.2| 76 SE 77
                                   87 PP

>> Glucos_trans_II  Glucosyl transferase GtrII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.6e-06      0.01     168     209 ..       9      66 ..       4      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                Glucos_trans_II 168 lkeilkkllllllvliisfvlylllykiilklfglelsy................ise 209
                                    +  ++ +++ l+++li++ v+y +++ i   ++g+++++                ++ 
  gi|118431119|ref|NP_147349.2|   9 FGGLWGLFWMLIFILILGAVIYAIIVLIRGLATGQQTQQpvqqpsekhleqeirsLKS 66 
                                    5668999*********************999999999889999999887776444222 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.1e-05     0.013       6      52 ..      15      62 ..      11      67 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                        DUF4083  6 iyliivivLil.llvfsftlfiRrvvsrsaakkkkskeleqKLDkiIe 52
                                   ++ +++++Lil +++ +++ +iR +     +++  +++ e+ L + I+
  gi|118431119|ref|NP_147349.2| 15 LFWMLIFILILgAVIYAIIVLIRGLATGQQTQQPVQQPSEKHLEQEIR 62
                                   4555666666515667********999999999988888888877665 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.1   9.6e-06     0.012       3      65 ..      17      79 ..      15      83 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.6e-06
                        DUF4446  3 ilvlavlvvillillivllvklkklkkkykklmkgkdgksleellkekleeveelkeeseele 65
                                   ++++++l++ ++i++i++l++   + ++ ++ +++ ++k+le+ +++  +e+ee+k+  +e +
  gi|118431119|ref|NP_147349.2| 17 WMLIFILILGAVIYAIIVLIRGLATGQQTQQPVQQPSEKHLEQEIRSLKSEIEEIKRLLSERK 79
                                   56778888889999999999999999***************************9998776654 PP

>> DUF2140  Uncharacterized protein conserved in bacteria (DUF2140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.016       2      66 ..      16      77 ..      15      83 .] 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                        DUF2140  2 kWkwaFliLlalllllvavvlvrvfapseestekssekekkseaeftitttkkqlnalinkylkk 66
                                   +W + F++ l+ ++ +++v++  + + ++++  ++ ++ ++++ e +i++ k++++++  + l++
  gi|118431119|ref|NP_147349.2| 16 FWMLIFILILGAVIYAIIVLIRGLATGQQTQ--QPVQQPSEKHLEQEIRSLKSEIEEIK-RLLSE 77
                                   5888888888888888888777777777765..45566666667777888887777643.34444 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 ?   14.9   0.4   1.7e-05      0.02      49     112 ..      10      71 ..       1      72 [. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                Phage_holin_3_6  49 lalllllvalalalaalwlaalivaavllvlagvlalvglkklkkakp.lpertieelkedvaal 112
                                     +l  l+++l+++l    l+a+i a+++l+ +++ +  + + +++ +   +e+ i++lk  ++ +
  gi|118431119|ref|NP_147349.2|  10 GGLWGLFWMLIFIL---ILGAVIYAIIVLIRGLATGQQTQQPVQQPSEkHLEQEIRSLKSEIEEI 71 
                                    22333333333333...456777888888888888888888888877679999999999888765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.2   2.5e-05      0.03       1      51 [.      24      72 ..      24      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                                   XXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  1 llllfllllifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                   +l+++++++i + +gl + +q++q +++     + l +e+++L++e+++ k
  gi|118431119|ref|NP_147349.2| 24 ILGAVIYAIIVLIRGLATGQQTQQPVQQ--PSEKHLEQEIRSLKSEIEEIK 72
                                   6899****************99999865..556678888888888888764 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.8e-05     0.021      75     119 ..      19      64 ..      12      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                           MscL  75 vinFliiafviFlivkaink.kkkeeeeeeeaeekeeellteirdl 119
                                    +i  li+++vi+ i+ +i+  ++ ++++++ ++++e++l +eir+l
  gi|118431119|ref|NP_147349.2|  19 LIFILILGAVIYAIIVLIRGlATGQQTQQPVQQPSEKHLEQEIRSL 64 
                                    5778999***********9975555666667778999999999975 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.2e-05     0.027       3      87 ..      10      80 ..       3      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                        DUF4131  3 lplalvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqllesgqeviveGvvaslpeltgs 84
                                   ++l+ ++++l+++l+l ++++         ++++l+  l+ + + +++++qp++++l+q ++s     ++ +++++ +l  +
  gi|118431119|ref|NP_147349.2| 10 GGLWGLFWMLIFILILGAVIY---------AIIVLIRGLATGQQTQQPVQQPSEKHLEQEIRS-----LKSEIEEIKRLLSE 77
                                   566777777777777777776.........899999999999999999999999999999996.....77788888777776 PP

                        DUF4131 85 gtr 87
                                   ++r
  gi|118431119|ref|NP_147349.2| 78 RKR 80
                                   665 PP

>> TMEM208_SND2  SRP-independent targeting protein 2/TMEM208
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2     4e-05     0.048     102     157 ..       4      60 ..       1      69 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                   TMEM208_SND2 102 wivqvlsilfgnkfWll.ylviPayalYklwglilgpaffkgagsa...eeaaeeeeaks 157
                                    w+  +   l+g  fW+l +++i + ++Y + +li g a    ++++   ++ +e+  +++
  gi|118431119|ref|NP_147349.2|   4 WGWGFFGGLWG-LFWMLiFILILGAVIYAIIVLIRGLATG--QQTQqpvQQPSEKHLEQE 60 
                                    66666777899.99*998999**************55433..333222444444444444 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     4e-05     0.048      10      77 ..      12      80 ..       6      83 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                     EMC3_TMCO1 10 dwvllPivivillvgiltgllsellqkllidkkkmeke.qkrekelqkrarelqkngdklklkklekrq 77
                                    w l+ ++i+il++g++   ++ l++ l + +++++ + q +ek l+++ r l+++ +++k    e+++
  gi|118431119|ref|NP_147349.2| 12 LWGLFWMLIFILILGAVIYAIIVLIRGLATGQQTQQPVqQPSEKHLEQEIRSLKSEIEEIKRLLSERKR 80
                                   58888899*********************9988766664779999999999999977766655555544 PP

>> STE3  Pheromone A receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.5e-05     0.054     150     192 ..      15      58 ..      12      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                           STE3 150 lvliwpliislvaavyavltlrafikrrkqfkellss.snsgln 192
                                    l+++  +i+ l a++ya+++l++ +   +q+++ +++ s+++l+
  gi|118431119|ref|NP_147349.2|  15 LFWMLIFILILGAVIYAIIVLIRGLATGQQTQQPVQQpSEKHLE 58 
                                    899999***************************88884456655 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.7   5.4e-05     0.065      11      48 ..      43      80 ..      38      83 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.4e-05
                        DUF1192 11 heigqDLslLSveELeerIalLeaEIaRleaaiakkka 48
                                   ++ +q+ ++ S + Le+ I  L++EI+ +++ ++++k 
  gi|118431119|ref|NP_147349.2| 43 QQTQQPVQQPSEKHLEQEIRSLKSEIEEIKRLLSERKR 80
                                   567888999999*****************999987765 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 ?   11.2   6.8    0.0002      0.24      17      58 ..      13      70 ..       6      83 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                       LapA_dom 17 lpLsllllvafgiGallgwllslwsyl...r.............lrrelrrlkkkikk 58
                                   + L  +l++ +++Ga++  ++ l++ l   +             l  e+r+lk +i++
  gi|118431119|ref|NP_147349.2| 13 WGLFWMLIFILILGAVIYAIIVLIRGLatgQqtqqpvqqpsekhLEQEIRSLKSEIEE 70
                                   77999*******************9996651566777555555566666666666665 PP

>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.13       6      39 ..      17      53 ..      12      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                        DUF2973  6 Yilaftvla...flAvanLirslitlsadsqr...kkksk 39
                                   ++l+f++++   + A+ +Lir+l t ++++q    +   +
  gi|118431119|ref|NP_147349.2| 17 WMLIFILILgavIYAIIVLIRGLATGQQTQQPvqqP---S 53
                                   45555554322268**********999988875321...2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2042  (0.113894); expected 358.6 (0.02)
Passed bias filter:                     1102  (0.0614647); expected 358.6 (0.02)
Passed Vit filter:                       161  (0.00897987); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 651.16
//
Query:       gi|14600827|ref|NP_147350.1|  [L=150]
Description: hypothetical protein APE_0598 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00088   19.0   0.0     0.0016   18.1   0.0    1.4  1  HTH_23     Homeodomain-like domain
     0.0053   16.8   0.1      0.036   14.1   0.0    2.3  3  HTH_7      Helix-turn-helix domain of resolvase
  ------ inclusion threshold ------
      0.023   14.8   0.1      0.068   13.3   0.0    1.8  2  HTH_28     Helix-turn-helix domain
        0.1   12.9   0.0       0.17   12.2   0.0    1.4  1  HTH_Tnp_1  Transposase


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.7e-07    0.0016       6      40 ..      95     131 ..      92     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.7e-07
                        HTH_23   6 eRlrillllae..GlsvreIAreLgvsrrTvyrwlkr 40 
                                   +R +illl+a+  G ++ ++Ar++g+ + ++yr  + 
  gi|14600827|ref|NP_147350.1|  95 IRSLILLLYARgrGEPPYKVARRYGIAPEQLYRMERG 131
                                   6889******999********************8765 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 ?   -1.1   0.0      0.46   2.1e+03      13      27 ..      22      36 ..      21      38 .. 0.81
   2 ?   -1.7   0.0       0.7   3.1e+03       1       8 [.      51      58 ..      51      78 .. 0.50
   3 !   14.1   0.0   8.1e-06     0.036      21      40 ..     106     127 ..      87     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                                  GGGSSTTTT--STTT CS
                         HTH_7 13 rvvkLleeGisiskI 27
                                  +vv+Ll  G  i+ I
  gi|14600827|ref|NP_147350.1| 22 EVVRLLGRGNFITRI 36
                                  799***999777765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.7
                                  S---SS-H CS
                         HTH_7  1 GRpsklsk 8 
                                  GRp+ +  
  gi|14600827|ref|NP_147350.1| 51 GRPKEIRL 58
                                  77776654 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 8.1e-06
                                   T..--STTTSSSS---SSSS-- CS
                         HTH_7  21 G..isiskIAkevnisRsTvYR 40 
                                   G  ++  k+A++++i+++++YR
  gi|14600827|ref|NP_147350.1| 106 GrgEPPYKVARRYGIAPEQLYR 127
                                   4448888*************** PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.9     4e+03       5      19 ..      62      76 ..      60      88 .. 0.54
   2 ?   13.3   0.0   1.5e-05     0.068       5      33 ..      99     129 ..      96     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.9
                        HTH_28  5 iikllaaGhsvreaA 19
                                  +i+++ +  +++ + 
  gi|14600827|ref|NP_147350.1| 62 VIEWMVDSYPITRIL 76
                                  555555555544443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.5e-05
                        HTH_28   5 iikllaaGh..svreaArelgisrrtvyrWi 33 
                                   i++l+a+G+  +   +Ar++gi ++++yr  
  gi|14600827|ref|NP_147350.1|  99 ILLLYARGRgePPYKVARRYGIAPEQLYRME 129
                                   789999877657777*************965 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.8e-05      0.17      28      47 ..     113     132 ..     104     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                     HTH_Tnp_1  28 evArrhgvspnqLykWrrqy 47 
                                    vArr+g+ p+qLy+  r  
  gi|14600827|ref|NP_147350.1| 113 KVARRYGIAPEQLYRMERGL 132
                                   7*************966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1126.88
//
Query:       gi|14600828|ref|NP_147351.1|  [L=175]
Description: hypothetical protein APE_0600 [Aeropyrum pernix K1]
Scores for complete 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-17   62.7   0.5    5.2e-17   62.1   0.3    1.4  2  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 !   62.1   0.3   2.9e-21   5.2e-17       4     119 ..       9     126 ..       6     138 .. 0.77
   2 ?   -2.1   0.0      0.21   3.8e+03      28      42 ..     136     150 ..     127     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.9e-21
                                   EEEEEEEEETTSEEEEEEESSSSTTTE....ESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                         NUDIX   4 ravgvvllnekgevLlvrrskkpfpgW....elPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                    +v ++l  + ++vLlvr +++p + W    +lPgG+v+ gE+p eAA+RE++EE+ +++  ++ l+++ ++++ ++    
  gi|14600828|ref|NP_147351.1|   9 SSVLALLWGSPTRVLLVRKRCAPGSPWacdlALPGGGVKRGEAPLEAAAREAWEEAWIPPAAVRPLASYCCEKTLTA---- 85 
                                   689999************88555555765446***********************************7776666543.... PP

                                   EEEEEEEEEEEECSGCSST.STTTEEEEEEEEHHHH..HHHH CS
                         NUDIX  81 eheilyvfleevegelepn.denevsevrwvpleel..lkek 119
                                       ++v+ ++++g  ep+ +e+ev+++ w pl+ +  ++ +
  gi|14600828|ref|NP_147351.1|  86 -GRRIHVVIAALQGPAEPRpAEEEVDAAIWAPLHIAsaKPGP 126
                                   .3335566667777777776799999999****988544444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.21
                                   TTEESSEEECBTTSH CS
                         NUDIX  28 pgWelPgGkvepgEt 42 
                                    g +lPgG + +g t
  gi|14600828|ref|NP_147351.1| 136 EGLSLPGGLILWGAT 150
                                   34679***9988866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1433.49
//
Query:       gi|14600829|ref|NP_147352.1|  [L=184]
Description: hypothetical protein APE_0601 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1512.33
//
Query:       gi|118431120|ref|YP_874835.1|  [L=76]
Description: hypothetical protein APE_0601a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 637.94
//
Query:       gi|14600831|ref|NP_147354.1|  [L=249]
Description: molybdopterin converting factor [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-20   72.8   0.2    3.6e-20   72.3   0.2    1.2  1  MoaE      MoaE protein
  ------ inclusion threshold ------
      0.097   13.3   0.0       0.31   11.7   0.0    2.0  1  ThiS      ThiS family


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 !   72.3   0.2     4e-24   3.6e-20       4     113 .]     103     214 ..     101     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 4e-24
                                   S---HHHHHHHH-..-TT--EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEET CS
                          MoaE   4 epldvaeiealva..spkaGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelev 82 
                                   ep+d+a+++a  a  sp+ GAv++FvGtv+    g +v++L yea  ++ae+++e+i++e + + +l+++ v+H +Ge ++
  gi|14600831|ref|NP_147354.1| 103 EPVDIASLVARAAsaSPANGAVAVFVGTVKSVVGGVRVEKLFYEAAWGVAERVIESILREEAGANGLSAAIVYHYTGERRP 183
                                   67788884443334699*************8878*********************************************** PP

                                   TSEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                          MoaE  83 geasvvvavssahRkeafeaceylidelKkr 113
                                   ge+++v++v++a R + +   ++++d++K++
  gi|14600831|ref|NP_147354.1| 184 GETTIVAVVAGASRGNVYPGLQRVVDRVKRE 214
                                   *****************************85 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.4e-05      0.31       3      77 .]      10      90 ..       8      90 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                                  ETTCCHHHHT...CEEEEESSTSBHHHHHHHHHHHTCHHG.TTTTEEEEETTEEEGC.C.TTTSB--TTCEEEEEESTTC- CS
                          ThiS  3 lfaelrelag...eeelelaegstvaelleaLgerypela.lerrvavavNgeivpr.l.wldtelkdgDevailppVaGG 77
                                  l++ l+++ag    ++  ++ g t++e+l++ +   ++l+ + + v  +v g + +  +  l+ +++ g +v ++pp +GG
  gi|14600831|ref|NP_147354.1| 10 LYTILKDAAGaetVRVPCPPGGVTLGEALREAARTSGGLErALDAVSWEVYGLLDDGsRlALEDRVACGSRVHVIPPPSGG 90
                                  55666666666333344467899*********999999999445555555555554444455******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2032.85
//
Query:       gi|118431121|ref|YP_874836.1|  [L=152]
Description: hypothetical protein APE_0604 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1168.93
//
Query:       gi|118431122|ref|NP_147355.2|  [L=195]
Description: hypothetical protein APE_0605.1 [Aeropyrum pernix K1]
Scores for 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-09   37.5   0.0    4.8e-09   36.8   0.0    1.3  1  VWA_2     von Willebrand factor type A domain
    8.8e-09   35.8   0.0    1.1e-08   35.6   0.0    1.1  1  VWA       von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   5.3e-13   4.8e-09       1     106 [.      12     120 ..      12     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 5.3e-13
                          VWA_2   1 lvfvlDtSgSmrngdy..gptrleaakdaveallksl....pgdrvglvtfsdgpevlipltkdkakilnalrnleakgg 74 
                                    +v  +D S+Sm++++   g ++l     ++   ++ +    pg+rvg+v f d++  ++p t++++++l+ l  l+a g 
  gi|118431122|ref|NP_147355.2|  12 VVWAIDLSKSMARTAGglGASKLKVSSGIIAMASS-RilsrPGSRVGIVGFHDRAFPILPSTDNYRRVLDSLTLLRAVGE 90 
                                    5778*******888553356666655555555555.336659************************************** PP

                          VWA_2  75 gtnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                    g+  ++++    k+l+    g++r +v+++Dg
  gi|118431122|ref|NP_147355.2|  91 GSAGGDGIVESVKMLRGS--GRERHVVMVSDG 120
                                    ***************966..79*********8 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 !   35.6   0.0   1.2e-12   1.1e-08       1     164 [.      11     174 ..      11     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.2e-12
                                    EEEEEEE-STTS..CHHHHH....HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGG CS
                            VWA   1 DivfvlDgSgsm..geenfe....kvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkys 74 
                                    D+v ++D S+sm  +++ +     kv + i+ ++++ +++++g rvg+v f + + ++ + +d  +   +l++l  l+  
  gi|118431122|ref|NP_147355.2|  11 DVVWAIDLSKSMarTAGGLGasklKVSSGIIAMASSRILSRPGSRVGIVGFHDRAFPILPSTD--NYRRVLDSLTLLRAV 88 
                                    99**********995555555456777777777777778************************..5589*********** PP

                                    GGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGC.TEEEEEEEE....SSSHHHHHHH CS
                            VWA  75 gggttntgkalkyaleklfkssagaRenakkviilltdGksndgdpkeaaneakeq.gikvfavGv....gnadekelLn 149
                                    g g++  g+++ + ++ l  s +      ++++++++dG  n g p + a+    + g++++ + v    g++++++ ++
  gi|118431122|ref|NP_147355.2|  89 GEGSA-GGDGIVESVKMLRGSGR------ERHVVMVSDGGFNTGIPIPLATIYALNmGVRLHFIIVggqpGDVVKRS-VE 160
                                    *****.********995544444......599*******99999999999999888899999999999999*****9.** PP

                                    HHSSSSCHHCEEEES CS
                            VWA 150 kiasepgeghvftvt 164
                                    + as +g g+v++v+
  gi|118431122|ref|NP_147355.2| 161 EAASRTG-GRVYIVA 174
                                    *******.8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1539.39
//
Query:       gi|118431123|ref|NP_147356.2|  [L=155]
Description: hypothetical protein APE_0606.1 [Aeropyrum pernix K1]
Scores for 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   16.3   0.0      0.012   15.9   0.0    1.2  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.6e-07     0.012     104     129 ..      86     111 ..      63     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.6e-07
                          PIN_4 104 drkvvLvskDinlrikAkalgieaed 129
                                    ++ vvL+s+D  lr++A+  g+ea +
  gi|118431123|ref|NP_147356.2|  86 REGVVLLSDDYRLRVRAREMGVEARS 111
                                    578********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1309.39
//
Query:       gi|14600834|ref|NP_147357.1|  [L=1331]
Description: surface layer-associated protease precursor [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-31  109.9   0.0    5.8e-31  107.9   0.0    1.8  1  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
       0.12   12.4   1.1       0.46   10.5   1.1    2.1  1  Rib           Rib/alpha-like repeat
        3.7    7.2   4.2        1.1    8.8   0.1    2.2  2  EF-hand_5     EF hand


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 !  107.9   0.0   9.7e-35   5.8e-31       1     298 []     195     718 ..     195     718 .. 0.77

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 9.7e-35
                                   -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.......................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                  Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag......................................... 40 
                                   g+gv+vav+DtGvd++h dl v+         +i +   g                                         
  gi|14600834|ref|NP_147357.1| 195 GEGVKVAVVDTGVDYGHSDLGVE---------SIARAEDGtplifdadqlgfaltlseavkdeegyvnvstpvpfidlffm 266
                                   79*****************9943.........4444444456677777777888888888888888888888888888888 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                  Peptidase_S8  41 ................................................................................. 40 
                                                                                                                    
  gi|14600834|ref|NP_147357.1| 267 gygeaeagwllyispdgtvayyefpidrffvgdiesaggvfkfglavqtvfilygslgilnyslpvlladgdgdgsyetvy 347
                                   888888888888888888888888888888888888888888888888888888888888888888777777777777777 PP

                                   ............................GGEETT-SS-TT-SC-S.................................... CS
                                   ............................xxxxxxxxxxxxxxxxx.................................... RF
                  Peptidase_S8  41 ............................fngadsettstnwardd.................................... 57 
                                                               +               d                                    
  gi|14600834|ref|NP_147357.1| 348 adlstayylflkalsdtgmisgepdpslL---------------Dlsfadetpasygsevlardftgdgvndfsagalagw 413
                                   77777777666665555555555555540...............1555555555555556666678888888888899999 PP

                                   ........................................SS........HHHHHHHHHH-B.........SSSSSB-SST CS
                                   ........................................xxxxxx....xxxxxxxxxxxx.......xxxxxxxxxxxx RF
                  Peptidase_S8  58 ........................................ngnsie....HGthvAGiaaan.......apeegekngvap 87 
                                                                                     HGt vA ++a            e +  gvap
  gi|14600834|ref|NP_147357.1| 414 tydwvglltgesvnlgwrlgfdyaglvlpgldpqgrwvsiL----YdtlaHGTSVATVIASRgnvefnlGYIETSLRGVAP 490
                                   99999999999999999999999999998888866555541....04455**********9988998887889999***** PP

                                   TSEEE.....EEE-SSTTSB-HH...HHHHHHHHHHHHCT-SEEEE-EESCE.TTCHHCHHHHHH..HHHHHH.CCT-EEE CS
                                   xxxxx.....xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                  Peptidase_S8  88 gakil.....svkvldtsggsmetg.teliraieeaaedkvdvinmslgest.slpktgrsieal..ainravnkkgvlvv 159
                                   gaki+      ++v+ +++  +  + ++   +  +  e++vdvin+s+g+s+  l  + ++  +   + ++ v  +g+++v
  gi|14600834|ref|NP_147357.1| 491 GAKIAaggsfLINVFVAQLFLSGFEpQDSPLNWVYTGEHQVDVINNSWGNSYiALRGFLTGADDYatIEDYIVSASGTVIV 571
                                   *****9999977777777776654446666666666679**********443144444444444465668888888***** PP

                                   EE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEES.............TTSSB-TT--B-TT.......-EEEE-S-...C CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                  Peptidase_S8 160 iSaGNngktgsslqagspvgtpstsknvitvgayt.............tegkiapfSsrGpssdgklkpdivapGgn...i 224
                                    + GN g      +   +  tp+    +i+vga t             + g++ ++S rGps+ g +kpd+v  G+    +
  gi|14600834|ref|NP_147357.1| 572 HAMGNGG------PGYGTATTPGAGSLIISVGASTlfdyrpfygylpsPGGDVISWSDRGPSQIGVAKPDVVNIGSFawaG 646
                                   *******......9999999999999**************************************************96666 PP

                                   CCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT.....--HHH..HHHHHHCCS-EE......SSSSSSTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_S8 225 vstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpk.....ltpet..vraallntAqdlgkadniesfaqGaG 298
                                   v+  +  +n    +  ++ + GTS A+P+ +g++Al++sa+++      +     v+a+l  tA+d+g    +  f qG G
  gi|14600834|ref|NP_147357.1| 647 VPVLTGLGNG---SLAFDIFGGTSEATPMTSGSVALVISAYQQafgakPS--PglVKAILKSTARDTG----ADAFTQGSG 718
                                   6666666633...3449**************************8774444..366*********9983....457777776 PP

>> Rib  Rib/alpha-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   7.6e-05      0.46      29      64 ..    1018    1061 ..    1012    1062 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.6e-05
                           Rib   29 Wke........tpdttksGekeavvvVtYPDGskdevpvtVkVt 64  
                                    ++          p+   +G ++  ++++Y DG k  vpv V V 
  gi|14600834|ref|NP_147357.1| 1018 PEGveaevaiqVPEDAAPGVYQYYIEIAYSDGGKTLVPVSVPVA 1061
                                    4444444444489999*************************996 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.2       0.4   2.4e+03       8      14 ..     335     341 ..     334     342 .. 0.83
   2 ?    8.8   0.1   0.00019       1.1       8      21 ..     911     924 ..     911     928 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                                   H-SS-SS CS
                     EF-hand_5   8 iDlNgDG 14 
                                   +D +gDG
  gi|14600834|ref|NP_147357.1| 335 ADGDGDG 341
                                   6999999 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00019
                                   H-SS-SSCE-HHHH CS
                     EF-hand_5   8 iDlNgDGkIskeEL 21 
                                   +Dl+gDG I+  E 
  gi|14600834|ref|NP_147357.1| 911 FDLDGDGVITLGET 924
                                   8********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); 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:                         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: 0.79u 0.24s 00:00:01.03 Elapsed: 00:00:00.39
# Mc/sec: 10282.38
//
Query:       gi|118431124|ref|NP_147358.2|  [L=1550]
Description: surface layer protein [Aeropyrum pernix K1]
Scores for complete 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-08   33.4  47.3     0.0025   18.2   0.6    7.2  6  NPV_P10          Nucleopolyhedrovirus P10 protein
      1e-07   31.1   9.9     0.0012   17.8   0.3    2.6  3  Spc7             Spc7 kinetochore protein
    1.2e-06   28.6  32.0     0.0022   18.0   1.5    5.6  6  Laminin_II       Laminin Domain II
      2e-06   27.9  48.0    0.00097   19.2   9.8    3.9  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    1.8e-05   22.9  10.9     0.0065   14.5   3.9    2.1  2  Prominin         Prominin
    0.00013   20.3   9.3      0.002   16.4   9.3    2.2  1  EzrA             Septation ring formation regulator, EzrA
    0.00031   21.1  11.2        1.2    9.6   0.3    4.3  5  Snapin_Pallidin  Snapin/Pallidin
     0.0017   17.1  13.0      0.027   13.1   2.3    2.6  2  AAA_13           AAA domain
     0.0017   17.9  17.7        1.3    8.6   7.3    3.4  3  MscS_porin       Mechanosensitive ion channel porin domain
     0.0017   18.4  32.7        0.2   11.7   2.1    5.6  6  DUF1664          Protein of unknown function (DUF1664)
     0.0023   17.9   1.1      0.018   15.0   0.0    2.7  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
     0.0036   16.3   8.2       0.27   10.1   0.3    3.0  4  IFT57            Intra-flagellar transport protein 57
     0.0041   17.3  18.5     0.0041   17.3   0.6    5.1  5  XhlA             Haemolysin XhlA
     0.0056   16.9  14.4       0.59   10.3   3.7    3.4  3  ATG16            Autophagy protein 16 (ATG16)
     0.0076   16.1   2.8      0.025   14.4   0.7    2.2  2  DUF724           Protein of unknown function (DUF724)
  ------ inclusion threshold ------
      0.012   15.7   9.2        6.7    6.8   2.3    4.2  3  DivIVA           DivIVA protein
      0.013   15.8  16.3         39    4.7   0.2    7.7  7  FlaC_arch        Flagella accessory protein C (FlaC)
      0.014   15.6   4.9        2.5    8.3   0.3    3.4  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.022   15.0   3.0        7.8    6.9   0.6    3.8  4  KxDL             Uncharacterized conserved protein
      0.039   13.2  10.4       0.37   10.1   0.4    2.3  2  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
      0.045   13.2   7.5        0.7    9.3   1.4    2.3  2  HMMR_N           Hyaluronan mediated motility receptor N-term
      0.059   13.0   7.6        3.3    7.2   0.2    2.4  2  Filament         Intermediate filament protein
      0.059   13.5   2.9          7    6.7   0.1    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.071   12.9  36.8       0.29   10.9   3.4    4.8  5  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.16   12.2   3.8        3.5    7.9   0.1    3.2  2  FG-GAP           FG-GAP repeat
       0.16   12.5  13.2        1.5    9.4   0.8    3.5  3  DUF16            Protein of unknown function DUF16
       0.22   10.7   4.9        1.7    7.8   0.7    2.7  2  ISG65-75         Invariant surface glycoprotein
       0.35   10.8  16.2        6.4    6.6   0.1    4.6  6  Sec34            Sec34-like family
       0.36   10.2   4.3        2.9    7.2   0.2    2.4  2  Tropomyosin      Tropomyosin
       0.39    9.9   0.8        3.3    6.9   0.0    2.6  3  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.43    9.6  10.5      0.039   13.1   1.9    2.5  3  DHC_N2           Dynein heavy chain, N-terminal region 2
       0.47   10.6   4.4         11    6.2   0.3    3.1  3  TolA_bind_tri    TolA binding protein trimerisation
       0.47   10.5   1.9          2    8.5   0.3    2.5  2  Nup54            Nucleoporin complex subunit 54
       0.48   10.4   7.0        7.8    6.5   0.1    3.1  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.52    9.7  24.6       0.99    8.8   4.1    3.5  3  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.56    8.0  10.2        1.2    6.9   2.9    2.2  2  Myosin_tail_1    Myosin tail
       0.75    9.6   6.7       0.63    9.9   0.1    3.4  4  SKA2             Spindle and kinetochore-associated protein 2
       0.83   10.2   7.5        2.8    8.5   0.6    3.0  2  Spectrin         Spectrin repeat
       0.94    9.6   6.5         22    5.1   0.0    2.8  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.97    8.2  11.8       0.99    8.2   4.7    2.7  3  DUF812           Protein of unknown function (DUF812)
       0.99   10.1  15.4        1.1   10.0   2.3    4.4  4  SlyX             SlyX
        1.2    9.5  10.3        3.2    8.1   4.1    2.9  3  HrpB7            Bacterial type III secretion protein (HrpB7)
        1.3    8.5   5.6        1.2    8.5   1.6    2.2  2  Leu_zip          Leucine zipper
        1.4    8.1   2.3         25    4.0   0.4    2.7  3  TMPIT            TMPIT-like protein
        1.4    9.0  10.6        1.4    9.1   1.9    3.1  4  Cob_adeno_trans  Cobalamin adenosyltransferase
        1.6    7.7  16.3        5.4    6.0   1.6    2.9  2  APG17            Autophagy protein Apg17
        1.7    8.8  10.5        5.2    7.2   1.6    3.4  3  COG5             Golgi transport complex subunit 5
        8.2    6.3  14.1         89    3.0   0.0    5.5  5  DASH_Duo1        DASH complex subunit Duo1


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   2.4    0.0047       1.8       3      33 ..    1180    1210 ..    1176    1218 .. 0.87
   2 !   18.2   0.6   6.7e-06    0.0025       8      62 ..    1206    1261 ..    1205    1262 .. 0.91
   3 ?    6.9   0.3     0.023       8.8      36      63 ..    1263    1290 ..    1261    1298 .. 0.90
   4 !    8.1   3.3    0.0098       3.7       8      59 ..    1330    1378 ..    1328    1407 .. 0.77
   5 ?    5.1   6.9     0.085        32      24      66 ..    1410    1459 ..    1393    1465 .. 0.65
   6 !   11.2   4.6     0.001      0.39       9      64 ..    1454    1499 ..    1442    1515 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0047
                        NPV_P10    3 qniLlvIradikavddkVdalqqqvddvqen 33  
                                     ++i l I +d + +d+k+d++++ v++++e 
  gi|118431124|ref|NP_147358.2| 1180 KSIVLAIQDDLTVIDTKLDSIEATVTEINEG 1210
                                     589999*******************999875 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 6.7e-06
                        NPV_P10    8 vIradikavddkVdalqqqvddvqenlpdv.telnekLdaqsaqLaeletkvenIq 62  
                                      I + ++ +++ +  lq++vd+++e l+++ +e++ kLd++s  Lae+++ v +Iq
  gi|118431124|ref|NP_147358.2| 1206 EINEGVAILQTDLGNLQASVDELTELLQQTgEEITMKLDEISGDLAEISNGVATIQ 1261
                                     678889999999*************99987479********************998 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.023
                        NPV_P10   36 dvtelnekLdaqsaqLaeletkvenIqd 63  
                                     dv  + e Lda++a+L++++  v +I+ 
  gi|118431124|ref|NP_147358.2| 1263 DVATILELLDAMNATLTTIQGDVAEIKT 1290
                                     78889999*****************985 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0098
                        NPV_P10    8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59  
                                     +I++    +d k++a+++ v++vq+ l dv+     L+++ ++ a++e+ v 
  gi|118431124|ref|NP_147358.2| 1330 LILESLDTLDAKITAVSDGVAEVQTILGDVSV---SLEDLVEANATIEEVVV 1378
                                     69999999*****************9999874...55555555555555444 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.085
                        NPV_P10   24 qqqvddvqenlpdvtelnekL....daqsaqLaelet...kvenIqdiLn 66  
                                     + ++d+v e+l ++++ n++L    +a++++La++++   k+++Iq++L 
  gi|118431124|ref|NP_147358.2| 1410 NVKLDQVLEDLSTISDQNAQLaaqaEAIAQTLAAVQDdtaKITDIQSTLA 1459
                                     44556666666666666665511115556677777778888888888886 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.001
                        NPV_P10    9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64  
                                     I +  + v   V +++q          d++ +++kLd+ + +L+++++kv+++++ 
  gi|118431124|ref|NP_147358.2| 1454 IQSTLASVAGDVASVKQ----------DTSTISSKLDDANGKLDSISSKVDSVSSA 1499
                                     22222233333333333..........33335555555555555555544444432 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   3.3e-06    0.0012     143     254 ..    1178    1289 ..    1170    1295 .. 0.93
   2 ?   -2.1   0.0       3.7   1.4e+03     206     255 ..    1333    1382 ..    1331    1386 .. 0.78
   3 !   16.8   3.1   6.5e-06    0.0024     145     255 ..    1388    1505 ..    1380    1519 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                           Spc7  143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220 
                                     ++++++ ++++d ++++ + + +++ + e++e  a l+  l +lq+ ++el+++ ++  ee+  +l+e++ +++e ++
  gi|118431124|ref|NP_147358.2| 1178 EVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEISN 1255
                                     566778889********************************************************************* PP

                           Spc7  221 elaelqeqleeleekieelkeqkseleeeiaeae 254 
                                      +a+ q +++++ e ++++++  ++++ ++ae +
  gi|118431124|ref|NP_147358.2| 1256 GVATIQGDVATILELLDAMNATLTTIQGDVAEIK 1289
                                     **********************999999988765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                           Spc7  206 eelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255 
                                     e+l++l+a+i + ++ +ae+q+ l +++ ++e+l e  +++ee + e ++
  gi|118431124|ref|NP_147358.2| 1333 ESLDTLDAKITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQ 1382
                                     56888899999999999999999999999998888877777776666665 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 6.5e-06
                           Spc7  145 eenlegleedkelLekqeeel.dellpeleeekaeleeeleklqeaaeeles......idkeeLeelreelaelkaei 215 
                                     +  + +l++d ++L++  e   +  l+++ e  ++++++ ++l ++ae +++       d +++  ++++la++  ++
  gi|118431124|ref|NP_147358.2| 1388 TTSMGTLTADMSTLKDLIESGvNVKLDQVLEDLSTISDQNAQLAAQAEAIAQtlaavqDDTAKITDIQSTLASVAGDV 1465
                                     444444555555555544433133334444444444444444444444444444445456888888888888888888 PP

                           Spc7  216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaer 255 
                                     ++ k+++++  ++l++ + k+++++++ +++ +++a  ++
  gi|118431124|ref|NP_147358.2| 1466 ASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQE 1505
                                     8888888888888888888888888888888888776554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.9   1.5e+03     112     136 ..    1043    1067 ..    1043    1069 .. 0.89
   2 !   14.3   1.8   8.2e-05     0.031       6      72 ..    1170    1236 ..    1167    1261 .. 0.80
   3 !    8.4   0.8    0.0055       2.1      14      80 ..    1238    1304 ..    1233    1326 .. 0.71
   4 ?    3.2   5.1      0.22        81       8      76 ..    1338    1406 ..    1331    1438 .. 0.71
   5 ?    1.3   0.7      0.83   3.1e+02       9      46 ..    1410    1447 ..    1402    1452 .. 0.69
   6 !   18.0   1.5   5.9e-06    0.0022       3      68 ..    1449    1514 ..    1447    1518 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.9
                                     EEEEES--EEEE----SSTTEEEEE CS
                     Laminin_II  112 svsfdgdsivelrppekvtdlaalt 136 
                                     s+ f  d+iv++ ++ +v+ la+ t
  gi|118431124|ref|NP_147358.2| 1043 SATFADDTIVAVTVQVSVKTLAGAT 1067
                                     578999***************9987 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.2e-05
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTG CS
                     Laminin_II    6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLl 72  
                                     ++++e ++ev++++ +++ +l  +  kl +i+++v e+ne v  +++ +   + sv +L++l++q  
  gi|118431124|ref|NP_147358.2| 1170 SSVEEGISEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTG 1236
                                     67889999***********************************999999999999999999987633 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0055
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                     Laminin_II   14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80  
                                     e+  +l ++s +l ++++ + +i+++v+ + e+++++n ++   +  v +++ +a  +l  ++ l++
  gi|118431124|ref|NP_147358.2| 1238 EITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQT 1304
                                     5666777888888888888888888888888888888888888888888888888777766666654 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.22
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                     Laminin_II    8 anetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk 76  
                                      + ++++v + +a++++ l  ++ +l+ + +  + ++e+v + n+ ++   +s+ +L+  +  L d ++
  gi|118431124|ref|NP_147358.2| 1338 LDAKITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGTLTADMSTLKDLIE 1406
                                     566778888888888888888888888887777778888888888888888888888877777666554 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.83
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II    9 netakevleqlaplsqnlentkeklseinrsveetnek 46  
                                     n ++ +vle+l  +s +  ++ ++++ i+++++ ++++
  gi|118431124|ref|NP_147358.2| 1410 NVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDD 1447
                                     55677777777777777777777777777777666655 PP

  == domain 6  score: 18.0 bits;  conditional E-value: 5.9e-06
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                     Laminin_II    3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68  
                                     ++++++++t+++v  ++a ++q+++ +++kl  +n++++ +  kv++ + a++d +++  ++  +a
  gi|118431124|ref|NP_147358.2| 1449 AKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGDTA 1514
                                     578999**********************************************99999887776666 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 !   19.2   9.8   2.6e-06   0.00097      15     119 ..    1166    1275 ..    1153    1277 .. 0.81
   2 ?    4.0  14.0      0.13        47      21     131 ..    1267    1384 ..    1262    1393 .. 0.56
   3 !   16.5  10.6   1.8e-05    0.0066      11     109 ..    1406    1508 ..    1395    1532 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.6e-06
                   Baculo_PEP_C   15 fldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalqdtlrne 86  
                                      +dL+ v + i +   +i+ +++ +l+ i+t+L+++++ +++  + ++       +l++++++Lt+ l++  ++++ +
  gi|118431124|ref|NP_147358.2| 1166 IVDLSSVEEGI-SEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAIlqtdlgNLQASVDELTELLQQTGEEITMK 1242
                                     58999999999.555566699*************99998888666655555688889999999999999999****** PP

                   Baculo_PEP_C   87 LtnlnsiltnLlssvtNinstLnnllqalnnld 119 
                                     L+ +  +l+++ + v+ i+  ++ +l+ l++++
  gi|118431124|ref|NP_147358.2| 1243 LDEISGDLAEISNGVATIQGDVATILELLDAMN 1275
                                     ******************987777766666554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                   Baculo_PEP_C   21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..........dtlrneLt 88  
                                     +L+ + + n+++ + ++ ++++i+t+ +++  ++++l + +++  d+++++++d ++ +           dtl+ ++t
  gi|118431124|ref|NP_147358.2| 1267 ILELLDAMNATL-TTIQGDVAEIKTTAGTILVSVQDLQTIVADSTDAVIKAVEDNVALVLdgqqlileslDTLDAKIT 1343
                                     444444445555.55555555555555666666666666666666666666666666554455344566667777777 PP

                   Baculo_PEP_C   89 nlnsiltnLlssvtNinstLnnllqalnnldlgalsqeledal 131 
                                     ++   +++ ++ ++ +  +L+ l++a + +  +++  e +++l
  gi|118431124|ref|NP_147358.2| 1344 AVSDGVAEVQTILGDVSVSLEDLVEANATI--EEVVVENNQLL 1384
                                     777777777777777777777777664444..33333344444 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.8e-05
                   Baculo_PEP_C   11 ggnqfldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnL...tdalnalq...dt 82  
                                     +++ ++ L +vL+++ + + q  aqla++ +ai+++L a+++d  + ++++++ l++++  +   ++   +++   d+
  gi|118431124|ref|NP_147358.2| 1406 ESGVNVKLDQVLEDLSTISDQN-AQLAAQAEAIAQTLAAVQDDTAK-ITDIQSTLASVAGDVasvKQDTSTISsklDD 1481
                                     57778999*******8888887.*****************999888.8888887777665550004444444455566 PP

                   Baculo_PEP_C   83 lrneLtnlnsiltnLlssvtNinstLn 109 
                                      + +L+++ s++ +  s v+ i++ L 
  gi|118431124|ref|NP_147358.2| 1482 ANGKLDSISSKVDSVSSAVADIQEQLG 1508
                                     666777777777777777777666554 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.7   5.5e-05     0.021     605     726 ..    1197    1324 ..    1168    1330 .. 0.75
   2 !   14.5   3.9   1.7e-05    0.0065     234     435 ..    1345    1544 ..    1325    1547 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-05
                       Prominin  605 lskihsslyleqlckkltkvnletlaekleelanelsngk.......knlkqslkneaqdlraiqqelvlplessvkk 675 
                                     l++i+ +    +    + +++l +l+++++el + l++         ++++  l +  + + +iq + v ++ ++++ 
  gi|118431124|ref|NP_147358.2| 1197 LDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGeeitmklDEISGDLAEISNGVATIQGD-VATILELLDA 1273
                                     5555555444444456678888888888888888887777444555566666666666666666555.45577899** PP

                       Prominin  676 lkksvkkldeensdlqesikkllaaveraenflkkngseiinneskklldr 726 
                                     ++ ++++++ +  +++++   +l +v++++ ++ ++++ +i+++ ++++ +
  gi|118431124|ref|NP_147358.2| 1274 MNATLTTIQGDVAEIKTTAGTILVSVQDLQTIVADSTDAVIKAVEDNVALV 1324
                                     *******************************************99998755 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.7e-05
                       Prominin  234 vlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldts 311 
                                     v   +ae++++l +++ + e L + n++ +e+  + +qL + ++     l+  +s   +    + i+s +++ kld+ 
  gi|118431124|ref|NP_147358.2| 1345 VSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGTLTADMST-LK----DLIESGVNV-KLDQV 1416
                                     34458999999999999999999999999999999999999999998888888777.33....233333433.44443 PP

                       Prominin  312 .kcldqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkip..rea 386 
                                      ++l+++++ + +l a  e++++ l  +v+++ a++ +i+++++  +a+ v+++k++ +++++++++   k+   +++
  gi|118431124|ref|NP_147358.2| 1417 lEDLSTISDQNAQLAAQAEAIAQTL-AAVQDDTAKITDIQSTLAS-VAGDVASVKQDTSTISSKLDDANGKLDsiSSK 1492
                                     0444777777777777777766665.57899999*****999975.67778899999999999999999888767899 PP

                       Prominin  387 ldavisdlenterssktfddvvekye...kyrwliglivcsllllivvilil 435 
                                     +d+v+s++ ++++++ +  d+ e ++   +++ +i+ ++++++l +   l+l
  gi|118431124|ref|NP_147358.2| 1493 VDSVSSAVADIQEQLGQVGDTAESASgraQTWGIINAVLSLAVLGVAGYLVL 1544
                                     99*******************9999733356777777777777777666555 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   9.3   5.4e-06     0.002     107     405 ..    1180    1510 ..    1164    1526 .. 0.43

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.4e-06
                                     HHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH---------.. CS
                           EzrA  107 eeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefee.. 182 
                                     ++ +  ++ ++  i ++l+ +    ++  e +  l+++  +l+ ++ +  + ++++ ee+  +l++i  +++e+++  
  gi|118431124|ref|NP_147358.2| 1180 KSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEISNgv 1257
                                     333334444444444444444444444444444444444444444444444444444444444444444444443322 PP

                                     -------HHHHHHHHHHHHHHHHHHHHHHHHHH................................HHTTTTTTSHHHH CS
                           EzrA  183 ltengdyveakeilkkleeeideleevieeiPe................................lleelkkelpkql 228 
                                     +t +gd  +  e+l++++  ++ ++ ++ ei++                                l+++ ++++ + l
  gi|118431124|ref|NP_147358.2| 1258 ATIQGDVATILELLDAMNATLTTIQGDVAEIKTtagtilvsvqdlqtivadstdavikavednvaLVLDGQQLILESL 1335
                                     333344444444444444444444444443332000000000000000000000000000000003333333333333 PP

                                     HHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHHHHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                           EzrA  229 eelkegykemkeegYaleelniekeieelekkieeilerlkel..eledveeelktieeeidsLyddlekEveAkke. 303 
                                     + l + ++   +            e++++  +++ +le+l e    +e+v  e++++   i +   +l++ +   k+ 
  gi|118431124|ref|NP_147358.2| 1336 DTLDAKITAVSDG---------VAEVQTILGDVSVSLEDLVEAnaTIEEVVVENNQLLATITTSMGTLTADMSTLKDl 1404
                                     3333333332221.........22233333333333333322211344444444444444444444444444433321 PP

                                     ....HTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STT CS
                           EzrA  304 ....veknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSel 377 
                                         v+ +l+++ e l+ + +qn +l ++ + + q+    ++++ k+ ++++ l ++  d+ ++++++++ +    + 
  gi|118431124|ref|NP_147358.2| 1405 iesgVNVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDA 1482
                                     111256667777777777777777777777777777777777777777777777777777777777776666666666 PP

                                     GGGTHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA  378 qeeleeleekleeieekqeeileslksl 405 
                                     + +l+++++k++ +++ + +i+e+l++ 
  gi|118431124|ref|NP_147358.2| 1483 NGKLDSISSKVDSVSSAVADIQEQLGQV 1510
                                     6666666666666666666666666665 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.2    0.0059       2.2      10      83 ..    1192    1261 ..    1189    1282 .. 0.69
   2 ?    7.4   0.2     0.016         6      11      48 ..    1310    1347 ..    1300    1377 .. 0.81
   3 ?   -0.8   0.2       5.8   2.2e+03      14      44 ..    1365    1395 ..    1358    1438 .. 0.59
   4 ?    5.7   0.3     0.053        20      14      86 ..    1412    1479 ..    1399    1490 .. 0.70
   5 !    9.6   0.3    0.0031       1.2      15      86 ..    1437    1507 ..    1427    1510 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0059
                Snapin_Pallidin   10 llepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklk 83  
                                     ++  kld +++++ e+ +    L+ +l +l+++++el e+ +    ++ +e   KL +i  ++ ++++ + +++
  gi|118431124|ref|NP_147358.2| 1192 VIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQ----QTGEEITMKLDEISGDLAEISNGVATIQ 1261
                                     556677777777777777777777777777777777777766....5555666677777777777766666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.016
                Snapin_Pallidin   11 lepkldeldeklkelrqsQeeLleqldrlnekLkelee 48  
                                        ++++++++++ + + Q+  le+ld+l +k++ +++
  gi|118431124|ref|NP_147358.2| 1310 TDAVIKAVEDNVALVLDGQQLILESLDTLDAKITAVSD 1347
                                     66799***************************998876 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 5.8
                Snapin_Pallidin   14 kldeldeklkelrqsQeeLleqldrlnekLk 44  
                                     +l e +++++e+  + ++Ll+++++    L+
  gi|118431124|ref|NP_147358.2| 1365 DLVEANATIEEVVVENNQLLATITTSMGTLT 1395
                                     5777888888888888888888887666664 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.053
                Snapin_Pallidin   14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86  
                                     kld++ e l+ + ++  +L++q +  ++ L+ +++++      ++   +  L+++  ++ s+++ ++++  ++
  gi|118431124|ref|NP_147358.2| 1412 KLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTA-----KITDIQSTLASVAGDVASVKQDTSTISSKL 1479
                                     78888899999999999999999999999999988887.....444444555555555555555555554444 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0031
                Snapin_Pallidin   15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86  
                                     + ++ + +++ +++ ++ +++l + + ++++++++++  + ++l+    KL +i  ++ s+++ +  +++ +
  gi|118431124|ref|NP_147358.2| 1437 IAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTS-TISSKLDDANGKLDSISSKVDSVSSAVADIQEQL 1507
                                     5556666666666777788899999999999999999.8999***************************977 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   2.3   7.3e-05     0.027     288     478 ..    1186    1364 ..    1171    1396 .. 0.76
   2 !    7.8   3.6    0.0029       1.1     284     380 ..    1397    1502 ..    1381    1526 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                         AAA_13  288 LekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakie 365 
                                     ++++++ +++k +++ + ++++ +      + + d  +l+a  ++l+e L++  ++++ K +e++   +l ++++ + 
  gi|118431124|ref|NP_147358.2| 1186 IQDDLTVIDTKLDSIEATVTEINE---GVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEISG--DLAEISNGVA 1258
                                     445555555554444333333333...33457889999999***********************99..99999999*9 PP

                         AAA_13  366 sikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkle 443 
                                      i+ +va+i el  + N++ + ++ +++e+k+     lv+   ++l++     +++++ i+ +e++++   + ++ + 
  gi|118431124|ref|NP_147358.2| 1259 TIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTILVS--VQDLQTIV--ADSTDAVIKAVEDNVALVLDGQQLIL 1332
                                     *******************************999997776..35555444..55666778888888888888889999 PP

                         AAA_13  444 eeikeLekqlrdekpaaeeinkeLkafGlgeleLk 478 
                                     e    L ++++ +  +++e+ ++L ++   + +L+
  gi|118431124|ref|NP_147358.2| 1333 ESLDTLDAKITAVSDGVAEVQTILGDV---SVSLE 1364
                                     999999999999999999999999887...44444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                         AAA_13  284 kqerLekliekv.eskkselleklkavsdeasensafeed.......keelkaeaealeeqLkglqraleaKrkepfk 353 
                                     ++++L++lie+  + k +++le l ++sd++ +  a +e+       +++ +a++  ++++L ++   +   +++ ++
  gi|118431124|ref|NP_147358.2| 1397 DMSTLKDLIESGvNVKLDQVLEDLSTISDQNAQLAAQAEAiaqtlaaVQDDTAKITDIQSTLASVAGDVASVKQDTST 1474
                                     455555555543255555555555555554433333333311111112222223333333344443333333333333 PP

                         AAA_13  354 .svelesvkakiesikklvaeineliak 380 
                                      s +l+++++k++si+++v+++   +a+
  gi|118431124|ref|NP_147358.2| 1475 iSSKLDDANGKLDSISSKVDSVSSAVAD 1502
                                     3444444444444444444444444444 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 !    7.3   0.5    0.0083       3.1      44     134 ..    1202    1290 ..    1184    1301 .. 0.80
   2 !    7.5   0.0     0.007       2.6      79     138 ..    1334    1393 ..    1326    1410 .. 0.88
   3 !    8.6   7.3    0.0034       1.3      49     149 ..    1420    1518 ..    1409    1525 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0083
                     MscS_porin   44 kaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqq 121 
                                      ++++  + ++ lq +l +l  +++ +  ++l +++ ee+  +l++ s +l+e ++  a+++ +++++   ++   ++
  gi|118431124|ref|NP_147358.2| 1202 ATVTEINEGVAILQTDLGNL--QASVDELTELLQQTGEEITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNAT 1277
                                     44444455555577777777..88888889999999999999999999999999999999999999999999999999 PP

                     MscS_porin  122 ltearqrlqeirn 134 
                                     lt+ +   +ei +
  gi|118431124|ref|NP_147358.2| 1278 LTTIQGDVAEIKT 1290
                                     9999999888876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.007
                     MscS_porin   79 sleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLns 138 
                                     sl++L  +++++s+ ++e+q+ l +   +l  l  + +++ +   e++q l++i++    
  gi|118431124|ref|NP_147358.2| 1334 SLDTLDAKITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGT 1393
                                     899***************************************************997733 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0034
                     MscS_porin   49 aPkelrelqqeleal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltea 125 
                                         +++ +++l+a  ++ +++  + ++++ +++++++ l+++  ++++++++ +++ s+l  ++  ++ + ++  + 
  gi|118431124|ref|NP_147358.2| 1420 LSTISDQ-NAQLAAQaEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSV 1496
                                     3222222.2222222233344455556666777777777777777777777777777777777777777777777777 PP

                     MscS_porin  126 rqrlqeirnrLnstaaagealsqa 149 
                                     + + ++i+ +L +   +++a s++
  gi|118431124|ref|NP_147358.2| 1497 SSAVADIQEQLGQV--GDTAESAS 1518
                                     77777777777444..33333333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.5     0.002      0.74      68     121 ..    1169    1222 ..    1166    1224 .. 0.87
   2 !   11.7   2.1   0.00054       0.2      52     121 ..    1220    1289 ..    1214    1321 .. 0.53
   3 ?    2.4   1.5      0.41   1.5e+02      43     117 ..    1310    1384 ..    1305    1391 .. 0.71
   4 ?    3.0   1.1      0.25        95      50     117 ..    1342    1405 ..    1324    1412 .. 0.68
   5 !   10.1   4.3    0.0017      0.64      46     123 ..    1409    1492 ..    1381    1493 .. 0.77
   6 !   11.1   3.1   0.00081       0.3      39     120 ..    1430    1510 ..    1421    1514 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.002
                        DUF1664   68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121 
                                     + +v++ + e+k i  +i++++t +  +l++i+  v++++e v  l++ l +++
  gi|118431124|ref|NP_147358.2| 1169 LSSVEEGISEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQ 1222
                                     567888899999999999999999999999999999999999999999988876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00054
                        DUF1664   52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121 
                                     ++++s+ +  + L++  +++  klde +   +ei++ v+++++d+++i e +++++++ +++++ +++i+
  gi|118431124|ref|NP_147358.2| 1220 NLQASVDELTELLQQTGEEITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIK 1289
                                     4444444444444444444444444444444444444444444444444444444444444444444443 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.41
                        DUF1664   43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117 
                                      + v k +e+  + + + ++ + + +d++d+k+ ++++  +e++  + +v+  l+++ e   +++e+v + ++ l
  gi|118431124|ref|NP_147358.2| 1310 TDAVIKAVEDNVALVLDGQQLILESLDTLDAKITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLL 1384
                                     556666666666666677777777888888888888888888888888888888888888888888877655555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.25
                        DUF1664   50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117 
                                     +    +++++   + +  +  v  +l++  e+ + i+e v e ++ l++i + + ++ + +++l+  +
  gi|118431124|ref|NP_147358.2| 1342 I----TAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGTLTADMSTLKDLI 1405
                                     2....233333345556667788888888888888888888888888888888888888887777655 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0017
                        DUF1664   46 vskqleqvs...eslaatkrhLssridrvdkkldeqk...eiskeikeevtevredlseigedvesvkeavegleskl 117 
                                     v  +l+qv    ++++++  +L+++ + + ++l +++   + +++i++ +++v +d++++++d +++++   + ++kl
  gi|118431124|ref|NP_147358.2| 1409 VNVKLDQVLedlSTISDQNAQLAAQAEAIAQTLAAVQddtAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKL 1486
                                     667788887333467788899999888888887665511145667888999999999999999999999999999999 PP

                        DUF1664  118 erieek 123 
                                     ++i++k
  gi|118431124|ref|NP_147358.2| 1487 DSISSK 1492
                                     999876 PP

  == domain 6  score: 11.1 bits;  conditional E-value: 0.00081
                        DUF1664   39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116 
                                     l+   e +++ l  v+++ a+   +++s +++v   + ++k+ ++ i++++++++++l++i+++v+sv++av +++++
  gi|118431124|ref|NP_147358.2| 1430 LAAQAEAIAQTLAAVQDDTAKI-TDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQ 1506
                                     4455556666666666665544.5678888888888889999999999999999999999999999999999999888 PP

                        DUF1664  117 leri 120 
                                     l ++
  gi|118431124|ref|NP_147358.2| 1507 LGQV 1510
                                     8776 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 ?   -0.2   0.1       2.3   8.5e+02     110     153 ..    1194    1237 ..    1168    1241 .. 0.70
   2 !   15.0   0.0   4.8e-05     0.018     103     171 ..    1468    1537 ..    1443    1548 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
                    EMP24_GP25L  110 kekletleselkkleekldsikreqkylrereerlrdtnestns 153 
                                     ++kl+++e ++ +++e +  +++++  l+++ ++l +++++t +
  gi|118431124|ref|NP_147358.2| 1194 DTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGE 1237
                                     56778888888888888888887777777777777777777765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.8e-05
                    EMP24_GP25L  103 dykdsak.kekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvav 171 
                                      ++d+ + ++kl++ + +l+ +++k+ds+ + +  ++e+  +  dt+es+  r   w i++ ++ ++v +
  gi|118431124|ref|NP_147358.2| 1468 VKQDTSTiSSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGDTAESASGRAQTWGIINAVLSLAVLG 1537
                                     2444444699***************************************************998776654 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.4     0.002      0.75     257     322 ..    1196    1258 ..    1169    1315 .. 0.42
   2 ?    0.2   0.2       0.8     3e+02     284     351 ..    1333    1401 ..    1280    1410 .. 0.78
   3 ?    5.5   1.5     0.019         7     226     323 ..    1363    1467 ..    1338    1479 .. 0.68
   4 !   10.1   0.3   0.00073      0.27     229     317 ..    1430    1517 ..    1418    1524 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                          IFT57  257 tlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322 
                                      l+ ie+  + +n+ +  l +++ ++q++++e++e ++q  e+++    +l+eis +l ++++ + 
  gi|118431124|ref|NP_147358.2| 1196 KLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITM---KLDEISGDLAEISNGVA 1258
                                     2333333333334444444444444444444444444333333222...22233333333322222 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.8
                          IFT57  284 eelsevkekykqlsegvseltrelaeiseelekvkq.emeergssmtDgsplvkikkaltklkkEikqm 351 
                                     e+l+++  k+  +s+gv e ++ l ++s  le++ + +    +  + +++ l +i++++ +l  +++++
  gi|118431124|ref|NP_147358.2| 1333 ESLDTLDAKITAVSDGVAEVQTILGDVSVSLEDLVEaNATIEEVVVENNQLLATITTSMGTLTADMSTL 1401
                                     567888889999999999999999999999987554044445555666666788999999998888876 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.019
                          IFT57  226 leqmkkhkksieeslpetksqlkklhedisktlekiesrEkyl....nsqleellqeyre...aqeelsevkekykql 296 
                                     le + + + +iee + e ++ l+ + + +      +++    +    n +l++ l+++++   ++++l+++ e + q 
  gi|118431124|ref|NP_147358.2| 1363 LEDLVEANATIEEVVVENNQLLATITTSMGTLTADMSTLKDLIesgvNVKLDQVLEDLSTisdQNAQLAAQAEAIAQT 1440
                                     666666777777777777777777777777777777776555522225556666666554111556666677777777 PP

                          IFT57  297 segvseltrelaeiseelekvkqemee 323 
                                      + v++ t + ++i+  l +v  ++ +
  gi|118431124|ref|NP_147358.2| 1441 LAAVQDDTAKITDIQSTLASVAGDVAS 1467
                                     777888888888888888877776654 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.00073
                          IFT57  229 mkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltre 306 
                                     +    ++i+++l  ++   +k+ +di+ tl  +      + +  ++  +++ +a+ +l++++ k++ +s+ v + +++
  gi|118431124|ref|NP_147358.2| 1430 LAAQAEAIAQTLAAVQDDTAKI-TDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQ 1506
                                     3344445555555555555555.4666677777777777777777777777777777777777777777777777777 PP

                          IFT57  307 laeiseelekv 317 
                                     l ++ +  e++
  gi|118431124|ref|NP_147358.2| 1507 LGQVGDTAESA 1517
                                     77776666655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.6   1.1e-05    0.0041       2      47 ..    1186    1231 ..    1185    1233 .. 0.96
   2 ?    2.7   0.6       0.4   1.5e+02       1      62 [.    1238    1299 ..    1238    1300 .. 0.91
   3 ?    2.5   0.1      0.46   1.7e+02       2      56 ..    1331    1388 ..    1330    1393 .. 0.78
   4 ?   -1.0   0.1       5.5     2e+03      10      47 ..    1410    1447 ..    1408    1449 .. 0.86
   5 ?    3.8   0.1      0.18        69       5      46 ..    1450    1491 ..    1448    1494 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-05
                           XhlA    2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesn 47  
                                     i+++l+ i+tkld++e +v++++e  a  ++ + nl+  +++l++ 
  gi|118431124|ref|NP_147358.2| 1186 IQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTEL 1231
                                     99*****************************************985 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.4
                           XhlA    1 eikerlerietkldnleervdkleekaaeaeekiknleedlkklesnqkWlirtiiGalisa 62  
                                     ei  +l +i ++l ++++ v +++ + a+ +e ++ ++ +l  ++  +  +++t  ++l+s+
  gi|118431124|ref|NP_147358.2| 1238 EITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTILVSV 1299
                                     5778999**************************************99999999988888875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.46
                           XhlA    2 ikerlerietkldnlee...rvdkleekaaeaeekiknleedlkklesnqkWlirtii 56  
                                     i+e l ++++k+   ++   +v+++  + +  +e + +++ ++++    ++ l+ ti+
  gi|118431124|ref|NP_147358.2| 1331 ILESLDTLDAKITAVSDgvaEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATIT 1388
                                     7888899999999999988888888888888888888888888887766666666665 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 5.5
                           XhlA   10 etkldnleervdkleekaaeaeekiknleedlkklesn 47  
                                     + kld   e+++++ + +a   ++++ +  +l+  ++ 
  gi|118431124|ref|NP_147358.2| 1410 NVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDD 1447
                                     56899999999999999999999999999999988775 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.18
                           XhlA    5 rlerietkldnleervdkleekaaeaeekiknleedlkkles 46  
                                     +++ i++ l +   +v  ++++ ++  +k++ ++ +l+++ s
  gi|118431124|ref|NP_147358.2| 1450 KITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISS 1491
                                     78888888999999999*********************9987 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.5    0.0091       3.4      98     160 ..    1177    1239 ..    1167    1246 .. 0.84
   2 ?    3.8   0.0      0.16        58      74     146 ..    1333    1405 ..    1326    1411 .. 0.92
   3 !   10.3   3.7    0.0016      0.59      27     135 ..    1416    1510 ..    1406    1520 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0091
                          ATG16   98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEl 160 
                                     +e ++ +l+ ++ l + ++kl + e+++ e+++ +a l+t l ++++ + e+++l+q+  +E+
  gi|118431124|ref|NP_147358.2| 1177 SEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEI 1239
                                     567777899999999999999999999999999999999999999999999999999887776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.16
                          ATG16   74 akiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeel 146 
                                     +++ +l++k++++ + +ae++   g+ + +l +l e+ ++ ee   e+++ la ++++  +l+  ++ +++ +
  gi|118431124|ref|NP_147358.2| 1333 ESLDTLDAKITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGTLTADMSTLKDLI 1405
                                     577899********************************************************99999888766 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0016
                          ATG16   27 Lldrtsaleaenaklekaaasakssksskksakekeasasq..snskqsakiqsleqklaqlreelaelyksrgelaq 102 
                                      l+  s+ +++na+l ++               e  a+  +    ++++aki++ +++la++  ++a + +  ++ ++
  gi|118431124|ref|NP_147358.2| 1416 VLEDLSTISDQNAQLAAQ--------------AEAIAQ--TlaAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISS 1477
                                     455556666666666222..............111122..122455689999999999******************** PP

                          ATG16  103 rllelneelqkleeklkedeerlaeleaeraal 135 
                                     +l ++n +l+   +k  + ++++a+++++  ++
  gi|118431124|ref|NP_147358.2| 1478 KLDDANGKLDSISSKVDSVSSAVADIQEQLGQV 1510
                                     ********9999999999999999999988775 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.84   3.1e+02      97     160 ..    1183    1246 ..    1168    1275 .. 0.76
   2 !   14.4   0.7   6.6e-05     0.025      62     181 ..    1386    1507 ..    1377    1513 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.84
                         DUF724   97 Llslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkei 160 
                                     +l+++d+ t + +++  +e  ++e ++  + l++++ +l+  + el + l+++ e+   +  ei
  gi|118431124|ref|NP_147358.2| 1183 VLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEI 1246
                                     6788888888888888888888888888888888888888888888887776666555555555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.6e-05
                         DUF724   62 siddsrseleslkeslaeLekhGFdVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrk...leeeidele 136 
                                     +i++s+ +l   + +l++L + G +Vk l + l++L  + d+ ++l+ + +++ + ++  +++ +k   +++ ++ + 
  gi|118431124|ref|NP_147358.2| 1386 TITTSMGTLTADMSTLKDLIESGVNVK-LDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKitdIQSTLASVA 1462
                                     58899*********************8.7899****************999999988877777665111567777888 PP

                         DUF724  137 kkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181 
                                       ++ +++   ++ +k ++a+ ++ +++s++++++ ++ d++++ 
  gi|118431124|ref|NP_147358.2| 1463 GDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQL 1507
                                     888888888888888888888899999998888888888888775 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       2.2   8.1e+02      30      83 ..    1239    1292 ..    1224    1317 .. 0.81
   2 ?    6.2   0.0     0.027        10      21      62 ..    1350    1391 ..    1348    1401 .. 0.88
   3 ?    6.8   2.3     0.018       6.7      23      86 ..    1409    1472 ..    1404    1506 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.2
                                     HHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA   30 vakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkana 83  
                                     ++ ++ ++  + +e+ + v++ + +++   el ++++ tl + q    e+k++a
  gi|118431124|ref|NP_147358.2| 1239 ITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTA 1292
                                     555556666667788888889999999999999999999999999999999887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.027
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXX CS
                         DivIVA   21 deVdeFLdqvakdyeallkeneelkekvkeleeklkeykele 62  
                                     +eV+ +L +v+ ++e+l++ n++++e v e+++ l+  ++  
  gi|118431124|ref|NP_147358.2| 1350 AEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSM 1391
                                     69****************************999998776655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.018
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA   23 VdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakke 86  
                                     V+  Ldqv +d+ ++ ++n++l ++ ++  ++l+  ++   ++ +   +  + a +v +  ++ 
  gi|118431124|ref|NP_147358.2| 1409 VNVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDT 1472
                                     77779**************************999999988776554444444444444444443 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   0.2      0.11        39       1      35 [.    1196    1230 ..    1196    1235 .. 0.91
   2 ?    3.9   0.1       0.2        73      11      43 ..    1238    1270 ..    1229    1281 .. 0.72
   3 ?   -0.5   0.0       4.5   1.7e+03      10      40 ..    1272    1302 ..    1268    1305 .. 0.82
   4 ?    0.4   0.1       2.4   8.9e+02       3      34 ..    1336    1367 ..    1334    1378 .. 0.78
   5 ?    1.8   0.2      0.89   3.3e+02       8      37 ..    1412    1441 ..    1377    1446 .. 0.76
   6 ?    3.5   0.0      0.26        98       1      32 [.    1450    1481 ..    1450    1485 .. 0.93
   7 ?    4.6   0.0      0.12        44       1      31 [.    1485    1515 ..    1485    1518 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                      FlaC_arch    1 ridelEnklsklsteletvkkeneelsksveelke 35  
                                     ++d++E  + ++   ++ +++++ +l+ sv+el e
  gi|118431124|ref|NP_147358.2| 1196 KLDSIEATVTEINEGVAILQTDLGNLQASVDELTE 1230
                                     7899***************************9987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.2
                      FlaC_arch   11 klsteletvkkeneelsksveelkenVkdllsL 43  
                                     ++ ++l+ +  ++ e+s+ v +++ +V  +l+L
  gi|118431124|ref|NP_147358.2| 1238 EITMKLDEISGDLAEISNGVATIQGDVATILEL 1270
                                     666777777777777777777777777777766 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4.5
                      FlaC_arch   10 sklsteletvkkeneelsksveelkenVkdl 40  
                                     + +  +l+t++ +  e++++  ++  +V+dl
  gi|118431124|ref|NP_147358.2| 1272 DAMNATLTTIQGDVAEIKTTAGTILVSVQDL 1302
                                     5677899999999999999999888888887 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.4
                      FlaC_arch    3 delEnklsklsteletvkkeneelsksveelk 34  
                                     d+l+ k+  +s  ++ v++ + ++s s+e+l 
  gi|118431124|ref|NP_147358.2| 1336 DTLDAKITAVSDGVAEVQTILGDVSVSLEDLV 1367
                                     78888899999999999999999998888874 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.89
                      FlaC_arch    8 klsklsteletvkkeneelsksveelkenV 37  
                                     kl+++   l+t+ ++n +l  + e + ++ 
  gi|118431124|ref|NP_147358.2| 1412 KLDQVLEDLSTISDQNAQLAAQAEAIAQTL 1441
                                     444555577888888888888888888776 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.26
                      FlaC_arch    1 ridelEnklsklsteletvkkeneelsksvee 32  
                                     +i ++++ l ++   +++vk++ + +s+++++
  gi|118431124|ref|NP_147358.2| 1450 KITDIQSTLASVAGDVASVKQDTSTISSKLDD 1481
                                     899*************************9986 PP

  == domain 7  score: 4.6 bits;  conditional E-value: 0.12
                      FlaC_arch    1 ridelEnklsklsteletvkkeneelsksve 31  
                                     ++d++ +k++++s+ ++ +++++ ++ ++ e
  gi|118431124|ref|NP_147358.2| 1485 KLDSISSKVDSVSSAVADIQEQLGQVGDTAE 1515
                                     7899999999999999999999999998766 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 ?    8.3   0.3    0.0067       2.5      16     106 ..    1199    1290 ..    1165    1295 .. 0.87
   2 ?    1.8   0.3      0.73   2.7e+02      10      79 ..    1380    1450 ..    1376    1458 .. 0.74
   3 ?    6.6   0.0     0.024       8.8       9      75 ..    1446    1512 ..    1438    1520 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0067
                    TMF_TATA_bd   16 rlsseirrlEgElaslkeelerleaerdeareeivklmke.neelkelkkeleelekeleelqeryetlLellGeksE 92  
                                     ++++++ +    +a l+++l +l+a+ de++e + +  +e + +l+e +++l+e+++ ++ +q    t+Lell   + 
  gi|118431124|ref|NP_147358.2| 1199 SIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEiTMKLDEISGDLAEISNGVATIQGDVATILELLDAMNA 1276
                                     5667777788888999999999999999998666665555245789999***************************** PP

                    TMF_TATA_bd   93 eveELraDvaDlKe 106 
                                          + Dva++K+
  gi|118431124|ref|NP_147358.2| 1277 TLTTIQGDVAEIKT 1290
                                     *********99997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.73
                    TMF_TATA_bd   10 svqlverlsseirrlEgElaslkeelerlea.erdeareeivklmkeneelkelkkeleelekeleelqer 79  
                                     + ql+  + ++   l +++++lk+ +e+  + + d++ e++ +++ +n +l+++++ ++++ + +++ + +
  gi|118431124|ref|NP_147358.2| 1380 NNQLLATITTSMGTLTADMSTLKDLIESGVNvKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAK 1450
                                     56777777778888888888888888875541558888888888888888888888888877777765555 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.024
                    TMF_TATA_bd    9 psvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekelee 75  
                                      ++  ++ ++s++ +  g++as+k++ ++++++ d+a+  + ++++++++++++ ++++e+  ++ +
  gi|118431124|ref|NP_147358.2| 1446 DDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGD 1512
                                     566778899******************************************9999999988777655 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       1.3   4.8e+02      44      79 ..    1170    1205 ..    1164    1208 .. 0.81
   2 ?    3.2   0.0      0.29   1.1e+02      28      74 ..    1214    1260 ..    1194    1267 .. 0.51
   3 ?    3.0   0.0      0.32   1.2e+02      25      76 ..    1239    1290 ..    1222    1294 .. 0.52
   4 ?    6.9   0.6     0.021       7.8      10      77 ..    1419    1492 ..    1412    1496 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.3
                           KxDL   44 aklrarfkqgtkllkevkkdLesifkkirslkakla 79  
                                     +++++ + + +  +  +++dL  i  k++s++a+++
  gi|118431124|ref|NP_147358.2| 1170 SSVEEGISEVKSIVLAIQDDLTVIDTKLDSIEATVT 1205
                                     55666666777888999**************99876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.29
                           KxDL   28 knreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74  
                                      +  L +l+a ++e  + l++  ++ t  l e+  dL  i   + ++
  gi|118431124|ref|NP_147358.2| 1214 LQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEISNGVATI 1260
                                     34455555555555555555555555555555555555555555555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.32
                           KxDL   25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslka 76  
                                     +  k  e++   a+ ++ +a ++ +++   +ll  +++ L +i+  +  +k+
  gi|118431124|ref|NP_147358.2| 1239 ITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKT 1290
                                     3333333333344445555555666666666666666666666666666665 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.021
                           KxDL   10 dldeilalQaqtsgrlnkknreLlelnals......qerlaklrarfkqgtkllkevkkdLesifkkirslkak 77  
                                     dl++i ++ aq+ ++ ++  ++L ++++ +      q+ la++  ++++ +++ + + + L+  + k++s+ +k
  gi|118431124|ref|NP_147358.2| 1419 DLSTISDQNAQLAAQAEAIAQTLAAVQDDTakitdiQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSK 1492
                                     55555555555555555555555555543211111155666666666666666666666666666666666665 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4   0.00098      0.37      96     250 ..    1230    1387 ..    1193    1393 .. 0.62
   2 ?    8.4   6.0    0.0031       1.2      88     236 ..    1363    1518 ..    1362    1530 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00098
                 ALIX_LYPXL_bnd   96 kivrqklqenkedlelLsgpeeeleaalp..ssssa..aasesveeqirklrsllekldelkaereqllkdlke.kae 168 
                                     + ++q+ +e+  +l+++sg+ +e+ + +   +      ++ e  ++  ++l ++  ++ e+k +  ++l ++++ +  
  gi|118431124|ref|NP_147358.2| 1230 ELLQQTGEEITMKLDEISGDLAEISNGVAtiQ--GDvaTILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDlQTI 1305
                                     23344444444444444444444444444211..11112234444444477777777777777777766555543233 PP

                 ALIX_LYPXL_bnd  169 ndDitpklltekkr..diaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskksdseqsqrqre 244 
                                       D t++++++ ++  ++  +  ++l  e l+++d  ++++++ +a+ +++l ++    e++ ++  + +e    +++
  gi|118431124|ref|NP_147358.2| 1306 VADSTDAVIKAVEDnvALVLDG-QQLILESLDTLDAKITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEV-VVENN 1381
                                     3345666666666655455555.99*******************************9999999998888765.56677 PP

                 ALIX_LYPXL_bnd  245 evlqkl 250 
                                     + l ++
  gi|118431124|ref|NP_147358.2| 1382 QLLATI 1387
                                     776665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0031
                 ALIX_LYPXL_bnd   88 leeAsesDkivrqklqenkedlelLsgpeeeleaalpssssaaa.....sesveeqirklrsllekldelkaereqll 160 
                                     le  +e+++++++ + en++ l+ +++++  l a +++ +         + + ++++++l+++ ++  +l a+ e + 
  gi|118431124|ref|NP_147358.2| 1363 LEDLVEANATIEEVVVENNQLLATITTSMGTLTADMSTLKD--LiesgvNVKLDQVLEDLSTISDQNAQLAAQAEAIA 1438
                                     56677888888888999999999998888888888773221..11222355777777777777777777777777777 PP

                 ALIX_LYPXL_bnd  161 kdl....kekaendDitpklltekkrdiaanefealfeeelekydplqeqleqslakqeellkeiqeaneefeqskks 234 
                                     + l     ++a+  Di+++l + + +  ++++  +   ++l+  +   + +++++++ ++ +++iqe   +  ++ +s
  gi|118431124|ref|NP_147358.2| 1439 QTLaavqDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGDTAES 1516
                                     777777666788889999999999997778888888999999999999999999999999999999888777776666 PP

                 ALIX_LYPXL_bnd  235 ds 236 
                                      s
  gi|118431124|ref|NP_147358.2| 1517 AS 1518
                                     55 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 ?    7.0   0.3    0.0096       3.6     187     278 ..    1207    1292 ..    1191    1354 .. 0.76
   2 ?    9.3   1.4    0.0019       0.7     186     297 ..    1408    1515 ..    1381    1523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0096
                         HMMR_N  187 meaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndei 264 
                                     ++  +  +q++L + +a v +L e l+++ +e       t kl e    l ++s+ +   + d+a + ell++ n  +
  gi|118431124|ref|NP_147358.2| 1207 INEGVAILQTDLGNLQASVDELTELLQQTGEE------ITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATL 1278
                                     55556789999999999999999988665555......3455666666666677777777****************** PP

                         HMMR_N  265 esLkssLeekeqel 278 
                                      +++ ++ e +++ 
  gi|118431124|ref|NP_147358.2| 1279 TTIQGDVAEIKTTA 1292
                                     ****9999877744 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0019
                         HMMR_N  186 dmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkeknde 263 
                                     ++++kl ++ ++L +   + aqL  +  ++ +  +  + +t k ++  + l +v+  +   k+d   + + l+ +n +
  gi|118431124|ref|NP_147358.2| 1408 GVNVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGK 1485
                                     678999999********************************************************************* PP

                         HMMR_N  264 iesLkssLeekeqelskqvkdlnekckllekeke 297 
                                     + s+ s    k + +s  v d +e++ ++    e
  gi|118431124|ref|NP_147358.2| 1486 LDSISS----KVDSVSSAVADIQEQLGQVGDTAE 1515
                                     *96655....555666788888888777665555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0088       3.3     204     280 ..    1190    1266 ..    1173    1273 .. 0.84
   2 ?    7.0   3.0      0.01       3.9     142     254 ..    1396    1508 ..    1271    1522 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0088
                                     XXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament  204 aeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemar 280 
                                      +  + +l s +  +te++  +  l+++l +l+++ + l + l+ + e++ ++l+++   l+e+ + +a+i+ ++a 
  gi|118431124|ref|NP_147358.2| 1190 LTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEISNGVATIQGDVAT 1266
                                     55556778888999999999999999999999999999999999999999999999999999999999998888776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.01
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX-HHH CS
                       Filament  142 eEvkelqkqvseqvlvevdaarkldLteilkeiraqyeelaeknreeaeewy..kskleelqeaaeknsealrsakee 217 
                                     + +++l+  +++ v+v +d++   dL++ +++  aq  ++ae   + + ++    +k++++q++ ++   ++ s+k++
  gi|118431124|ref|NP_147358.2| 1396 ADMSTLKDLIESGVNVKLDQV-LEDLST-ISDQNAQLAAQAEAIAQTLAAVQddTAKITDIQSTLASVAGDVASVKQD 1471
                                     456666777777777777743.345543.4555555555555555544433311578888888888888888888888 PP

                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament  218 itelrrqiqsleieleslkkqkasleaqlaeleerle 254 
                                      + +  +++  + +l+s+ ++ +s+ +++a+++e+l 
  gi|118431124|ref|NP_147358.2| 1472 TSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLG 1508
                                     8888888888888888888888888888888877764 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 ?    6.7   0.1     0.019         7      68     114 ..    1195    1241 ..    1170    1309 .. 0.78
   2 ?    6.6   0.6      0.02       7.6      99     182 ..    1381    1447 ..    1314    1507 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.019
                        UPF0242   68 skleekeaklteldeglktkeealeelqeeeeeLkeeldakeeeler 114 
                                      kl++ ea +te +eg+++ +  l +lq+  +eL e l++  ee+  
  gi|118431124|ref|NP_147358.2| 1195 TKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITM 1241
                                     45677788889999999999999999999999999998888888764 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.02
                        UPF0242   99 eeLkee.......ldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvlekrq 169 
                                     ++L          l                         +d++ lk  +e+ ++ k  ++ e   ti++q + l  + 
  gi|118431124|ref|NP_147358.2| 1381 NQLLATittsmgtL------------------------TADMSTLKDLIESGVNVKLDQVLEDLSTISDQNAQLAAQA 1434
                                     22222222222220........................2255555555555555555555555555555555555555 PP

                        UPF0242  170 dqieqLeskVrDl 182 
                                     + i+q  + V+D 
  gi|118431124|ref|NP_147358.2| 1435 EAIAQTLAAVQDD 1447
                                     5555555555543 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.4   0.00078      0.29      89     169 ..    1177    1261 ..    1170    1267 .. 0.83
   2 ?    2.5   0.9       0.3   1.1e+02      95     145 ..    1267    1318 ..    1261    1337 .. 0.77
   3 ?    4.1   4.8     0.096        36      81     170 ..    1292    1382 ..    1284    1384 .. 0.70
   4 ?    6.0   4.1     0.026       9.8      92     168 ..    1381    1461 ..    1376    1464 .. 0.82
   5 ?    9.7   5.5    0.0019      0.69      86     161 ..    1442    1517 ..    1437    1524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00078
                                     HHHHHHH.................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal   89 keiealiieiqke...indsvesleetrqrveegselveetgealkeiveavaev.adlvqeiaaaseeqsasieevn 162 
                                      e+++++ +iq +   i++ ++s+e t+++++eg+ + ++   +l+  v++ +e+ +++ +ei+   +e+s  + e++
  gi|118431124|ref|NP_147358.2| 1177 SEVKSIVLAIQDDltvIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELlQQTGEEITMKLDEISGDLAEIS 1254
                                     699999999998844458899*******************99999999998887614555789999999999999999 PP

                                     HHHHHHH CS
                      MCPsignal  163 qaveeva 169 
                                     ++v+ ++
  gi|118431124|ref|NP_147358.2| 1255 NGVATIQ 1261
                                     9998876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                                     H..............HHHHHHHHHHHHHHHHHCCHHHHHHH.HHHHHHHHHH CS
                      MCPsignal   95 iieiqkeindsvesleetrqrveegselveetgealkeive.avaevadlvq 145 
                                     i e+   +n ++++++  + ++++++ ++  + ++l++iv+ +++ v + v+
  gi|118431124|ref|NP_147358.2| 1267 ILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTIVAdSTDAVIKAVE 1318
                                     5578888999999999999999999999999999999997514555555554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.096
                                     HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHH....HHHHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal   81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselveetgeal....keiveavaevadlvqeiaaaseeq 154 
                                     A     + +++++++      ++ +++++e+ +  v  g +l+ e+ ++l      +++ vaev++++ +++++ e++
  gi|118431124|ref|NP_147358.2| 1292 AGTILVSVQDLQTIV---ADSTDAVIKAVEDNVALVLDGQQLILESLDTLdakiTAVSDGVAEVQTILGDVSVSLEDL 1366
                                     555555555555555...667777888999999999999888877666551111567888999999999999999999 PP

                                     HHHHHHHHHHHHHHHH CS
                      MCPsignal  155 sasieevnqaveevak 170 
                                      ++   + + v e+++
  gi|118431124|ref|NP_147358.2| 1367 VEANATIEEVVVENNQ 1382
                                     8888888887777766 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.026
                                     HHHH..............HHHHHHHHHHHH.HHHHHCCHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                      MCPsignal   92 ealiieiqkeindsvesleetrqrveegse.lveetgealkeiveavaevadlvqeia...aaseeqsasieevnqav 165 
                                     ++l++ i+  + + ++ ++  +  +e+g++ + ++  e+l++i+++ a++a++ + ia   aa+++ +a i+++++++
  gi|118431124|ref|NP_147358.2| 1381 NQLLATITTSMGTLTADMSTLKDLIESGVNvKLDQVLEDLSTISDQNAQLAAQAEAIAqtlAAVQDDTAKITDIQSTL 1458
                                     789999**********************9845899**************99998888822245677777777777766 PP

                                     HHH CS
                      MCPsignal  166 eev 168 
                                     + v
  gi|118431124|ref|NP_147358.2| 1459 ASV 1461
                                     665 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.0019
                                     HHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal   86 qaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieev 161 
                                      a ++ +a i++iq    +++  + +++q +++ s++ ++++ +l +i+++v++v++ v +i+    +   ++e+ 
  gi|118431124|ref|NP_147358.2| 1442 AAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGDTAESA 1517
                                     455555667889***************************************************9988888887765 PP

>> FG-GAP  FG-GAP repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.16        61       4      14 ..     326     337 ..     324     341 .. 0.84
   2 ?    7.9   0.1    0.0093       3.5       8      21 ..     894     907 ..     890     921 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                                    SEEEE.STSSSS CS
                         FG-GAP   4 slavg.DvNGDG 14 
                                    s  vg D++GDG
  gi|118431124|ref|NP_147358.2| 326 STQVGnDIDGDG 337
                                    678999*****9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0093
                                    ESTSSSSS-EEEEE CS
                         FG-GAP   8 gDvNGDGyaDLavG 21 
                                    +D++GDG+ ++a  
  gi|118431124|ref|NP_147358.2| 894 TDIDGDGVSEVAAS 907
                                    6***********98 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.1    0.0092       3.4      33      99 ..    1194    1278 ..    1178    1283 .. 0.60
   2 ?    1.5   0.2       1.1   4.1e+02      21      67 ..    1298    1345 ..    1280    1396 .. 0.62
   3 ?    9.4   0.8     0.004       1.5      37     103 ..    1424    1490 ..    1400    1491 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0092
                                     HHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........................HHHHHHHHH CS
                          DUF16   33 kqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln..................kvdetleliletL 92  
                                     +++L  iea+v+  +e ++ l+    ++++ ++el++  ++ gee+                   +++  +  ile L
  gi|118431124|ref|NP_147358.2| 1194 DTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITmkldeisgdlaeisngvaTIQGDVATILELL 1271
                                     566777777777666666666666666666666666666666666555555555555555555555555555666666 PP

                                     HHHHHHH CS
                          DUF16   93 qkinkRl 99  
                                     +++n  l
  gi|118431124|ref|NP_147358.2| 1272 DAMNATL 1278
                                     6666555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.1
                                     BHHHHHH.B-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                          DUF16   21 Trkqlne.fkdsnkqrLkkieakvdklgeqinkleqkvekqgekikel 67  
                                       ++l+    ds+++ +k +e++v+     ++ + +  +++++ki+  
  gi|118431124|ref|NP_147358.2| 1298 SVQDLQTiVADSTDAVIKAVEDNVALVLDGQQLILESLDTLDAKITAV 1345
                                     444444433455666666666666655555555555555555555444 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.004
                                     HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                          DUF16   37 kkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103 
                                      + +a+++++ e i++   +v+  ++ki++++ +      ++ +v++    i   L++ n +lDsi 
  gi|118431124|ref|NP_147358.2| 1424 SDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSIS 1490
                                     456778899********************************************************96 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.096        36      54     129 ..    1181    1256 ..    1176    1268 .. 0.85
   2 ?    7.8   0.7    0.0045       1.7      54     126 ..    1449    1521 ..    1435    1525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.096
                       ISG65-75   54 yllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaeka 129 
                                      ++  ++d+l+ i++++++++++v+++++ ++  +++    ++ +++l+++++++ ++++ + ++    l+++ + 
  gi|118431124|ref|NP_147358.2| 1181 SIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEISNG 1256
                                     5777899**********************99999998888888889999999999999999998888777777665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0045
                       ISG65-75   54 yllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkaleka 126 
                                       + +++ +la+++ ++++v++ ++ + s l+ a++k ++ +s+++ + +a+++ +++  +  ++a+ a   a
  gi|118431124|ref|NP_147358.2| 1449 AKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGDTAESASGRA 1521
                                     3467899999999999999999999999999999999999999999999999999999999999998887665 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.15        56       7      81 ..    1171    1243 ..    1167    1259 .. 0.67
   2 ?    5.6   0.2     0.035        13       4      65 ..    1220    1282 ..    1217    1289 .. 0.89
   3 ?    0.2   0.0       1.7   6.2e+02       9      60 ..    1254    1305 ..    1247    1308 .. 0.83
   4 ?    0.6   0.1       1.2   4.6e+02       8      37 ..    1348    1377 ..    1314    1411 .. 0.49
   5 ?    6.3   0.8     0.022       8.2      11      65 ..    1412    1466 ..    1406    1468 .. 0.89
   6 ?    6.6   0.1     0.017       6.4       8      52 ..    1468    1512 ..    1463    1523 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.15
                          Sec34    7 skeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkL 81  
                                     s ee + e+ + + +++++L+ + +k +s+++  ++++e    l ++  +l+  ++e++e L+  +  ++it kL
  gi|118431124|ref|NP_147358.2| 1171 SVEEGISEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQ--QTGEEITMKL 1243
                                     556666666666777777777777777777777777777777777777777777777777766..3444444444 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.035
                          Sec34    4 qLeskeeecdelleqt.dealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65  
                                     +L+++ +e++ell+qt +e+  +L+e++ +  ++s+   +++ +  ++le  + ++ +  +i+
  gi|118431124|ref|NP_147358.2| 1220 NLQASVDELTELLQQTgEEITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQ 1282
                                     79999*********99568999*************************9999999888888876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.7
                          Sec34    9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleel 60  
                                     ++ + ++  ++ ++le+L+ ++   ++++ +  ++++++ ++l + ++l+++
  gi|118431124|ref|NP_147358.2| 1254 SNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTI 1305
                                     5667788889999999999999999999999999999999999888888876 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.2
                          Sec34    8 keeecdelleqtdealeqLeeleekfksvs 37  
                                       +e++++l +++  le+L e +   ++v 
  gi|118431124|ref|NP_147358.2| 1348 GVAEVQTILGDVSVSLEDLVEANATIEEVV 1377
                                     223333333333333333333333333333 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.022
                          Sec34   11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65  
                                     ++d++le+++++ +q ++l  + +++++   ++++++ ++++ q+ l ++a ++ 
  gi|118431124|ref|NP_147358.2| 1412 KLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVA 1466
                                     6899999999999999999999999999999999999999999999999988775 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.017
                          Sec34    8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlle 52  
                                      ++ + ++ +++d+a+ +L+++++k++svs+   +++e+  q+ +
  gi|118431124|ref|NP_147358.2| 1468 VKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGD 1512
                                     566777888889999999999999999999999888888766655 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0079       2.9     115     178 ..    1176    1239 ..    1170    1290 .. 0.82
   2 ?    3.9   0.7      0.08        30      21      72 ..    1448    1499 ..    1411    1523 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0079
                    Tropomyosin  115 yeEvarklvvvesdLeraeeraeaaeskiveLeeeLkvvgnnlksLevseekaseredeyeeei 178 
                                     + Ev+  +  +++dL  +  + ++ e+ ++e+ e + + ++ l +L++s ++ +e  ++  eei
  gi|118431124|ref|NP_147358.2| 1176 ISEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEI 1239
                                     67899999999**************************************999988777766665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.08
                    Tropomyosin   21 kkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaeka 72  
                                     ++k+   + + ++   +va++++  +++ ++l+ ++ +l++  +k + ++ a
  gi|118431124|ref|NP_147358.2| 1448 TAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSA 1499
                                     4455555566666666666666666666666666666666666666555433 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.2   4.6e+02     112     148 ..    1198    1234 ..    1171    1288 .. 0.60
   2 ?   -2.0   0.0       4.6   1.7e+03     130     154 ..    1333    1357 ..    1311    1450 .. 0.60
   3 ?    6.9   0.0    0.0088       3.3     112     156 ..    1466    1510 ..    1459    1523 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
                     FmiP_Thoc5  112 keleekkkkleqeieekkkfLssLppkLkslkkatkp 148 
                                     +++e+ ++++++ ++  +  L +L+  +++l + +++
  gi|118431124|ref|NP_147358.2| 1198 DSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQ 1234
                                     3333333333333333333333333333333333333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.6
                     FmiP_Thoc5  130 kfLssLppkLkslkkatkplqealg 154 
                                     + L+ L  k++++++ ++++q  lg
  gi|118431124|ref|NP_147358.2| 1333 ESLDTLDAKITAVSDGVAEVQTILG 1357
                                     4444444444444444444444442 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0088
                     FmiP_Thoc5  112 keleekkkkleqeieekkkfLssLppkLkslkkatkplqealglp 156 
                                      +++++ ++++++    + +L+s+++k++s+++a++ +qe+lg  
  gi|118431124|ref|NP_147358.2| 1466 ASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQV 1510
                                     678999999*********************************853 PP

>> DHC_N2  Dynein heavy chain, N-terminal region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       1.4   5.2e+02     142     225 ..    1186    1232 ..    1172    1277 .. 0.51
   2 ?    0.6   0.2      0.65   2.4e+02     142     185 ..    1267    1310 ..    1240    1377 .. 0.71
   3 ?   13.1   1.9    0.0001     0.039     109     232 ..    1395    1528 ..    1380    1534 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
                                     HHHHHHHHHHHHTS---EEEE-SSS.TEEE..THHHHHHHHHHHHHHHHTCSSSTT..THHHHHHHHHHHHHHHHHHH CS
                         DHC_N2  142 lekalkkieeewkelefelteykdsgvfilkgvdeiielledhivklqsmksspyvkpfeeeveewekklsrlqeild 219 
                                     +++ l  i+++ +++e ++te                                     + e v  +++ l +lq  +d
  gi|118431124|ref|NP_147358.2| 1186 IQDDLTVIDTKLDSIEATVTE-------------------------------------INEGVAILQTDLGNLQASVD 1226
                                     333333333333333333333.....................................44444444444444444444 PP

                                     HHHHHH CS
                         DHC_N2  220 ewlkvQ 225 
                                     e+++  
  gi|118431124|ref|NP_147358.2| 1227 ELTELL 1232
                                     444332 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.65
                                     HHHHHHHHHHHHTS---EEEE-SSS.TEEE..THHHHHHHHHHH CS
                         DHC_N2  142 lekalkkieeewkelefelteykdsgvfilkgvdeiielledhi 185 
                                     + + l++++++ ++++ ++ e k++   il +v+++++ + d+ 
  gi|118431124|ref|NP_147358.2| 1267 ILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTIVADST 1310
                                     56678888888888888888888776666667777777775554 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.0001
                                     XXXX.XXXXXXXXXXX...XXXXXXXXXXXXXX-HHHHHHHHHHHHHHTS---EEEE-SSS..........TEEE... CS
                         DHC_N2  109 dseesltlgdllelgl...leeeieeisekAtkEaslekalkkieeewkelefelteykdsg.........vfilkg. 173 
                                     +++   tl+dl+e+g+   l + +e++s+   + a+l  + ++i ++ ++++ ++ + +d +         v  +k+ 
  gi|118431124|ref|NP_147358.2| 1395 TAD-MSTLKDLIESGVnvkLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQstlasvagdVASVKQd 1471
                                     333.47**********85438889************************999988888777744455566687777777 PP

                                     THHHHHHHHHHHHHHHHTCSSSTT..THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DHC_N2  174 vdeiielledhivklqsmksspyvkpfeeeveewekklsrlqeildewlkvQrkWlyLe 232 
                                     +  i ++l+d   kl s++s   v+++ + v +++++l ++ ++ +      ++W  ++
  gi|118431124|ref|NP_147358.2| 1472 TSTISSKLDDANGKLDSISSK--VDSVSSAVADIQEQLGQVGDTAESASGRAQTWGIIN 1528
                                     ******************988..54589***********99999988777777776555 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 ?    6.2   0.3     0.029        11       3      53 ..    1187    1237 ..    1185    1258 .. 0.81
   2 ?    4.4   0.4      0.11        41       8      56 ..    1372    1421 ..    1362    1440 .. 0.78
   3 ?   -0.8   0.2       4.6   1.7e+03      51      51 ..    1444    1444 ..    1412    1505 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
                  TolA_bind_tri    3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqlee 53  
                                     +d ++ ++ +l++ + + +e+ + +  lq++l  L+ +++el+  l+q+ e
  gi|118431124|ref|NP_147358.2| 1187 QDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGE 1237
                                     567777888888888888888899999999999999999999988888765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                  TolA_bind_tri    8 rLErilearsqlllelqqqlealqqelreLRGqiEe.lqyqleqleerQr 56  
                                     ++E+ +  ++qll  + + + +l +++++L+  iE   + +l+q++e   
  gi|118431124|ref|NP_147358.2| 1372 TIEEVVVENNQLLATITTSMGTLTADMSTLKDLIESgVNVKLDQVLEDLS 1421
                                     5777777789*************************746778888887665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 4.6
                  TolA_bind_tri   51 l 51  
                                     +
  gi|118431124|ref|NP_147358.2| 1444 V 1444
                                     2 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.6   9.9e+02      47      86 ..    1216    1255 ..    1187    1304 .. 0.66
   2 ?    8.5   0.3    0.0053         2      51     125 ..    1412    1495 ..    1407    1509 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.6
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Nup54   47 qhrerlkeisdrleeleqkhqletsvrlekakkrhvelsh 86  
                                          l++  d+l+el q+   e++ +l+++    +e+s+
  gi|118431124|ref|NP_147358.2| 1216 TDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEISN 1255
                                     4444555555566666666666666666666555555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0053
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........TT-SS---SSHHHHHHHHHH CS
                          Nup54   51 rlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleil..........rsrgyaldaeEeelrarlet 118 
                                     +l+++ ++l+ ++  ++++++++ e ++++ ++ +  + +++  ++ l          ++  + ++ + + + ++l++
  gi|118431124|ref|NP_147358.2| 1412 KLDQVLEDLSTIS-DQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLasvagdvasvKQDTSTISSKLDDANGKLDS 1488
                                     5555666666666.5566666666666666666655555555555544111000000044455555555555555555 PP

                                     HHHHHS- CS
                          Nup54  119 leaqlnd 125 
                                     +++++++
  gi|118431124|ref|NP_147358.2| 1489 ISSKVDS 1495
                                     5555553 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 ?    5.7   0.4     0.039        14      55      97 ..    1198    1240 ..    1193    1253 .. 0.84
   2 ?   -1.3   0.1       5.6   2.1e+03      18      79 ..    1341    1402 ..    1325    1418 .. 0.63
   3 ?    6.5   0.1     0.021       7.8      10     111 ..    1418    1501 ..    1409    1520 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                 CENP-F_leu_zip   55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervs 97  
                                      ++++ + e++e    l++dL +l+   +eL++ lq+  e++ 
  gi|118431124|ref|NP_147358.2| 1198 DSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEIT 1240
                                     56889999999**************************999985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.6
                 CENP-F_leu_zip   18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79  
                                     k   + d v + +  l ++  ++e+++    t  + v + ++ + ++++++  l++d+++l+
  gi|118431124|ref|NP_147358.2| 1341 KITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGTLTADMSTLK 1402
                                     44445555555555555555666666666666666666666677777777777777777766 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.021
                 CENP-F_leu_zip   10 ekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlk...eeieelaeelreleldLvalrsekee 84  
                                     e                     +l ++  ++ ++  +aE   +++ +++   ++i  ++++l     d+++++++  +
  gi|118431124|ref|NP_147358.2| 1418 E---------------------DLSTISDQNAQLAAQAEAIAQTLAAVQddtAKITDIQSTLASVAGDVASVKQDTST 1474
                                     4.....................44444445555555555444443333311145555556666666666666666666 PP

                 CENP-F_leu_zip   85 LekelqkkqervseLeslnsslenlle 111 
                                     +  +l + + + ++  s   s+++ + 
  gi|118431124|ref|NP_147358.2| 1475 ISSKLDDANGKLDSISSKVDSVSSAVA 1501
                                     666666666666555555444444443 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 ?    8.8   4.1    0.0026      0.99      42     129 ..    1234    1321 ..    1192    1326 .. 0.87
   2 ?    3.9   3.2     0.081        30      35     103 ..    1375    1444 ..    1355    1446 .. 0.84
   3 ?    7.4   5.8     0.007       2.6      42     115 ..    1432    1505 ..    1421    1511 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0026
                      Mce4_CUP1   42 evLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadllerngd 119 
                                     +  +e+  +l++++ d+ e+ +  ++ +     +l+ Ld++  t +Ti+   ae+++   ++    ++++++++++ d
  gi|118431124|ref|NP_147358.2| 1234 QTGEEITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTIVADSTD 1311
                                     444678899999*****9998877777777778********************************************* PP

                      Mce4_CUP1  120 nLirlaadlr 129 
                                      +i++++d +
  gi|118431124|ref|NP_147358.2| 1312 AVIKAVEDNV 1321
                                     ****999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.081
                      Mce4_CUP1   35 esltdlnevLdelNprlpqlredireladladv.YadaapdlldaLdnavttsrTiveqqaeLdalllaa 103 
                                     e +++ n++L+++ +++ +l++d+++l+dl +   +   +++l+ L+ ++  ++ +++q++++++ l+a+
  gi|118431124|ref|NP_147358.2| 1375 EVVVENNQLLATITTSMGTLTADMSTLKDLIESgVNVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAV 1444
                                     568899***********************98862445567788888888888888999999999888876 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.007
                      Mce4_CUP1   42 evLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadlle 115 
                                     +  +++ + l  +++d  +++d++ + a +a d+ ++ ++++t s+ + + + +Ld++ +++ ++s+ +ad+ e
  gi|118431124|ref|NP_147358.2| 1432 AQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQE 1505
                                     445678889999******************************************************99999865 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.9    0.0032       1.2     364     600 ..    1189    1435 ..    1177    1442 .. 0.67
   2 ?    5.2   0.9      0.01       3.7     414     477 ..    1444    1507 ..    1436    1520 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                  Myosin_tail_1  364 qleqakrskaslekakqaLesenkelqaelkslqqakqdseqkrkkleaqlqelqvklseserqreelaekvsklqae 441 
                                     +l     +  s+e +   +++ ++ lq++l +lq++  +  +    l++  +e+ +kl+e     +e+++ v+ +q +
  gi|118431124|ref|NP_147358.2| 1189 DLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTE---LLQQTGEEITMKLDEISGDLAEISNGVATIQGD 1263
                                     555555555566666666666666677777777666555332...233333455555555555555555555555555 PP

                  Myosin_tail_1  442 .......lesvsslleeaegksiklskdvsslesqlqDtqellqeetrqkLa.lssrlrqleeeknalkeqleeeeea 511 
                                            l+ ++++l+  +g    ++  + ++   +qD q ++ + t + ++ +   +  + + ++ + e l+    +
  gi|118431124|ref|NP_147358.2| 1264 vatilelLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTIVADSTDAVIKaVEDNVALVLDGQQLILESLDTLDAK 1341
                                     000000056666666666666666666666666789************99972567899999999999******9999 PP

                  Myosin_tail_1  512 kknvekqlstlqaqlsdlkkkleeeasavealeeakkrlqrelealtqrleekaaa....ydklek.tkkRlqqeldD 584 
                                       +v+  ++ +q+ l d+   le+ ++a  ++ee     ++ l ++t+ +   +a     +d +e   + +l q l+D
  gi|118431124|ref|NP_147358.2| 1342 ITAVSDGVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLATITTSMGTLTADmstlKDLIESgVNVKLDQVLED 1419
                                     9**********************9999999999877776666666666655554440001555665246799999999 PP

                  Myosin_tail_1  585 llvdldkqrqlvsnle 600 
                                     l    d++ ql ++ e
  gi|118431124|ref|NP_147358.2| 1420 LSTISDQNAQLAAQAE 1435
                                     9999999999887665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                  Myosin_tail_1  414 lqelqvklseserqreelaekvsklqaelesvsslleeaegksiklskdvsslesqlqDtqell 477 
                                     +q+  +k+++ + + + +a  v+ ++++  ++ss l++a+gk   +s  v s++s + D+qe+l
  gi|118431124|ref|NP_147358.2| 1444 VQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQL 1507
                                     777788888888889999999999999999******************************9987 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 ?    9.9   0.1    0.0017      0.63       4      90 ..    1176    1261 ..    1173    1275 .. 0.87
   2 ?   -1.3   0.0         5   1.9e+03      42      65 ..    1266    1289 ..    1253    1316 .. 0.66
   3 ?   -0.6   0.1         3   1.1e+03      51      89 ..    1363    1404 ..    1331    1422 .. 0.57
   4 ?    0.6   0.5       1.2   4.6e+02      43      69 ..    1416    1442 ..    1402    1511 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                           SKA2    4 vdklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlva 81  
                                     +++++++    + dL++++ +L++   + ++ n e ++ L ++l ++++ + +L e +++  +e  +  d+i+  l++
  gi|118431124|ref|NP_147358.2| 1176 ISEVKSIVLAIQDDLTVIDTKLDSIEATVTEIN-EGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAE 1252
                                     6777778888899**********9999999999.5**************************99999999999999988 PP

                           SKA2   82 nrellqqLq 90  
                                       + +  +q
  gi|118431124|ref|NP_147358.2| 1253 ISNGVATIQ 1261
                                     888777776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5
                           SKA2   42 kLlerlkkvkeelqaLkeqceell 65  
                                     ++le l ++++ l++++ ++ e+ 
  gi|118431124|ref|NP_147358.2| 1266 TILELLDAMNATLTTIQGDVAEIK 1289
                                     455555555555555555555544 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3
                           SKA2   51 keelqaLkeqceellaekkelidkirtt...lvanrellqqL 89  
                                      e+l + ++ +ee+  e  +l  +i t+   l a +++l++L
  gi|118431124|ref|NP_147358.2| 1363 LEDLVEANATIEEVVVENNQLLATITTSmgtLTADMSTLKDL 1404
                                     455555666666666666666666665411133444444444 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.2
                           SKA2   43 LlerlkkvkeelqaLkeqceellaekk 69  
                                     +le+l+ + ++ ++L +q+e+++++  
  gi|118431124|ref|NP_147358.2| 1416 VLEDLSTISDQNAQLAAQAEAIAQTLA 1442
                                     455555555555555555555544322 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3      0.11        40      30      86 ..    1187    1247 ..    1168    1262 .. 0.68
   2 ?    8.5   0.6    0.0075       2.8      17     103 ..    1423    1507 ..    1395    1509 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                                     SSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHH CS
                       Spectrin   30 gkdleevqallk....khkaleaelaaqqervkalnelaeklldeghsaseeieerleeln 86  
                                       dl+ + ++l+    + +++ + +a  q+ + +l++  ++l++  +++ eei+ +l+e+ 
  gi|118431124|ref|NP_147358.2| 1187 QDDLTVIDTKLDsieaTVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEIS 1247
                                     4455556666664444566666666778888888888888888888888888888888886 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0075
                                     HHHHHHHH..CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHH CS
                       Spectrin   17 ieekeell..ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeL 92  
                                     i+++ ++l  + e ++++l++vq+   k ++++ +la+  + v ++++  + + ++     ++ + +l+ + ++ +++
  gi|118431124|ref|NP_147358.2| 1423 ISDQNAQLaaQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKL----DDANGKLDSISSKVDSV 1496
                                     444444443344555999***************************998888885554....55555666666666666 PP

                                     HHHHHHHHHHH CS
                       Spectrin   93 kelaaerkqkL 103 
                                     ++++a+ +++L
  gi|118431124|ref|NP_147358.2| 1497 SSAVADIQEQL 1507
                                     66666655555 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 ?    5.1   0.0     0.059        22      59     115 ..    1190    1246 ..    1186    1262 .. 0.83
   2 ?    4.5   3.0     0.089        33      27      95 ..    1420    1487 ..    1389    1510 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.059
                     TPR_MLP1_2   59 lqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedl 115 
                                     l+ + ++l++++a+++e+++ +  ++++l + ++s +e  e l++  +e++ +++++
  gi|118431124|ref|NP_147358.2| 1190 LTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEEITMKLDEI 1246
                                     556667888889999999999999999999999999999999999999988888886 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.089
                     TPR_MLP1_2   27 lqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswe 95  
                                     l +   + a++a++a+   ++ l    +d+ +++++ + l+++  ++a++k++  + +++l+ +  +++
  gi|118431124|ref|NP_147358.2| 1420 LSTISDQNAQLAAQAEA-IAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLD 1487
                                     33333445555555555.777888888888888888888888888888888888888888877765543 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.4      0.15        58     319     413 ..    1223    1314 ..    1183    1320 .. 0.60
   2 ?    8.2   4.7    0.0026      0.99     316     415 ..    1368    1468 ..    1329    1505 .. 0.88
   3 ?   -0.0   0.0      0.82   3.1e+02     330     373 ..    1470    1513 ..    1466    1523 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.15
                         DUF812  319 eteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaee 396 
                                      + +el++  ++  ee+  +++e++ +++e+++ +++++ ++  + e l++++++ ++ + +v+  k t+  +     
  gi|118431124|ref|NP_147358.2| 1223 ASVDELTELLQQTGEEITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTI---LV 1297
                                     3333444444444456777777777777777777777777777777777777777777776665444444333...25 PP

                         DUF812  397 niekLqalveasaqrlv 413 
                                     +++ Lq +v +s++ ++
  gi|118431124|ref|NP_147358.2| 1298 SVQDLQTIVADSTDAVI 1314
                                     66667777666666665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                         DUF812  316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikk.lessikqveeeleeekeeneelekevklkkktlellp 392 
                                     ++  t ee+  ++++ l+++ + + +l +++++l++ i++ ++ ++ qv e l +   +n++l+++ +   +tl+ ++
  gi|118431124|ref|NP_147358.2| 1368 EANATIEEVVVENNQLLATITTSMGTLTADMSTLKDLIESgVNVKLDQVLEDLSTISDQNAQLAAQAEAIAQTLAAVQ 1445
                                     567899********************************97699*********************************** PP

                         DUF812  393 daeeniekLqalveasaqrlvel 415 
                                     d+ + i   q+ + + a ++ ++
  gi|118431124|ref|NP_147358.2| 1446 DDTAKITDIQSTLASVAGDVASV 1468
                                     **********9998888777665 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.82
                         DUF812  330 eeleelqeqieeleskieeleeeikklessikqveeeleeekee 373 
                                     ++ +++++++++++ k++++++++++++s +  ++e+l +   +
  gi|118431124|ref|NP_147358.2| 1470 QDTSTISSKLDDANGKLDSISSKVDSVSSAVADIQEQLGQVGDT 1513
                                     45567777777777777777777777777777777777665544 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.3    0.0028       1.1       2      53 ..    1187    1238 ..    1186    1245 .. 0.91
   2 ?    1.7   0.1       1.1   4.1e+02      11      54 ..    1263    1306 ..    1255    1315 .. 0.80
   3 ?    0.4   0.0       2.8     1e+03      14      51 ..    1372    1402 ..    1335    1411 .. 0.69
   4 ?    3.5   0.7      0.29   1.1e+02      18      54 ..    1422    1458 ..    1416    1474 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0028
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                           SlyX    2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53  
                                     ++ l+ + +kl   e t+ e n+ va  q ++  lq+ +++l+e l++  e+
  gi|118431124|ref|NP_147358.2| 1187 QDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQTGEE 1238
                                     67899999*************************************9877655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.1
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX   11 klafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54  
                                      +a   ++++++n++++  q +++++++    +   +++l++  
  gi|118431124|ref|NP_147358.2| 1263 DVATILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTIV 1306
                                     566677899***************99998888888888887765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.8
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                           SlyX   14 fqedtieeLndvvaeqqqqidrlqrqlrllaerlkele 51  
                                               +vv+e +q ++ +++ +  l+  +++l+
  gi|118431124|ref|NP_147358.2| 1372 T-------IEEVVVENNQLLATITTSMGTLTADMSTLK 1402
                                     3.......445666666666666666666665555444 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.29
                                     HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX   18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54  
                                     ti + n+++a+q++ i++  + ++  + ++ +++++ 
  gi|118431124|ref|NP_147358.2| 1422 TISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTL 1458
                                     7888999999999999998888888888887777665 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 ?    4.0   0.0      0.16        60      83     133 ..    1185    1235 ..    1174    1252 .. 0.81
   2 ?    0.7   4.3       1.6     6e+02      38     134 ..    1363    1455 ..    1328    1460 .. 0.69
   3 ?    8.1   4.1    0.0087       3.2      45     155 ..    1423    1532 ..    1407    1534 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                          HrpB7   83 vlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierl 133 
                                     ++++ +++ + +l   ++++ + ++ va+ ++ ++ ++a++d   e +++ 
  gi|118431124|ref|NP_147358.2| 1185 AIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQQT 1235
                                     678899999999999999999999999999999999999999988877775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                          HrpB7   38 laaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvraaeaelaaarqaldaaedavaatark 115 
                                     l++  ++ +  +++v ++++ l+++tt    ++++       + d +e  v++   ++     ++ ++++++aa+a++
  gi|118431124|ref|NP_147358.2| 1363 LEDLVEANATIEEVVVENNQLLATITTSMGTLTADM----STLKDLIESGVNVKLDQVLEDLSTISDQNAQLAAQAEA 1436
                                     555555555566666677777777777776665543....33445666666666666666666788888888888888 PP

                          HrpB7  116 iaRndaqidacrerierlr 134 
                                     ia  +a+++   ++i  ++
  gi|118431124|ref|NP_147358.2| 1437 IAQTLAAVQDDTAKITDIQ 1455
                                     8888888888888887665 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0087
                          HrpB7   45 veaardavraheerlddlttgsspfsiadylacrayrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaq 122 
                                     ++ + ++++a +e++++++++      a+++  +  ++ + g v+ +++ +     +ld+a+ ++     k+ +  ++
  gi|118431124|ref|NP_147358.2| 1423 ISDQNAQLAAQAEAIAQTLAAVQ-DDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSSA 1499
                                     55566778888888888888886.567789999999999999999999999999999999999999999999999999 PP

                          HrpB7  123 idacrerierlrraaeraredaadEEaeEavLA 155 
                                     +  ++e++ ++ + ae a   a+   +++avL 
  gi|118431124|ref|NP_147358.2| 1500 VADIQEQLGQVGDTAESASGRAQTWGIINAVLS 1532
                                     999999999999999999999998888888886 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.54     2e+02     166     226 ..    1193    1254 ..    1170    1295 .. 0.56
   2 ?    8.5   1.6    0.0033       1.2     105     216 ..    1387    1505 ..    1356    1516 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.54
                        Leu_zip  166 lekalkelqkelgekkdeke.nskeiskleeklaelkldlektleektasaksleedlastk 226 
                                     ++++l++++++++e ++  +  ++++ +l++++ el+  l++t ee t++ ++++ dla+  
  gi|118431124|ref|NP_147358.2| 1193 IDTKLDSIEATVTEINEGVAiLQTDLGNLQASVDELTELLQQTGEEITMKLDEISGDLAEIS 1254
                                     34444444444443333322234445555555555555555555555555555555554444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0033
                        Leu_zip  105 ssnkkeseelkkkkLePlnegGgaeLLkk...eierLkeenekLkerlkelEkqatsaleeksklekalkelqkelge 179 
                                      +++  + +   + L+ l e+G+   L++   +++ + ++n +L ++ + + + +  + ++  k++   + l + +g+
  gi|118431124|ref|NP_147358.2| 1387 ITTSMGTLTADMSTLKDLIESGVNVKLDQvleDLSTISDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGD 1464
                                     224444666777889999999988777761114455679999999999999988888888887776655555555555 PP

                        Leu_zip  180 kkdeke....nskeiskleeklaelkldlektleektasak 216 
                                       ++k+     s+++ + + kl ++ +++++ +++ ++ ++
  gi|118431124|ref|NP_147358.2| 1465 VASVKQdtstISSKLDDANGKLDSISSKVDSVSSAVADIQE 1505
                                     55444411112233333344444444444444444443333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.33   1.2e+02       5      78 ..    1177    1253 ..    1168    1282 .. 0.52
   2 ?    0.8   0.0      0.63   2.4e+02       4      77 ..    1250    1323 ..    1247    1376 .. 0.72
   3 ?    4.0   0.4     0.067        25      23      79 ..    1449    1504 ..    1390    1521 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.33
                          TMPIT    5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelker 78  
                                     +e+++ + ++++  + + +kl+++++  +++ + ++  + +l +l++s+++l++ ++   ee   +++e++ +l+e+
  gi|118431124|ref|NP_147358.2| 1177 SEVKSIVLAIQDDLTVIDTKLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQqtgEEITMKLDEISGDLAEI 1253
                                     34444444555555555555555555555555555555555555555555554443311122222333333333333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.63
                          TMPIT    4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77  
                                     ++e+++ + +++    ++ + l+ +++  ++++ ++++ k  +  +  s+++l++ v ++++  ++ ++++++ 
  gi|118431124|ref|NP_147358.2| 1250 LAEISNGVATIQGDVATILELLDAMNATLTTIQGDVAEIKTTAGTILVSVQDLQTIVADSTDAVIKAVEDNVAL 1323
                                     67889999999999999*************************************99998888888888887653 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.067
                          TMPIT   23 qkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79  
                                     +k+ ++++   +++ ++++ k++ + ++s+l++ + +++ + +++v+++++ +++++
  gi|118431124|ref|NP_147358.2| 1449 AKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLD-SISSKVDSVSSAVADIQ 1504
                                     222222222222333333333333333333333333322.22223333333333333 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.21        78      50     117 ..    1176    1240 ..    1154    1247 .. 0.67
   2 ?    3.0   0.6      0.27     1e+02      35     106 ..    1221    1282 ..    1187    1318 .. 0.56
   3 ?   -0.6   0.1       3.6   1.3e+03      96      96 ..    1322    1322 ..    1245    1410 .. 0.56
   4 ?    9.1   1.9    0.0037       1.4      20     109 ..    1411    1500 ..    1393    1521 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.21
                                     THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHH CS
                Cob_adeno_trans   50 eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplksfilpggspaa 117 
                                      +e+k+ +  iq++L  + ++l +   + + ++i+e  v+ l++ + +l+a++++l++ + ++g++  
  gi|118431124|ref|NP_147358.2| 1176 ISEVKSIVLAIQDDLTVIDTKLDS--IEATVTEINEG-VAILQTDLGNLQASVDELTELLQQTGEEIT 1240
                                     567888889999999999999953..34445555555.666777766666666666666665555554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.27
                                     HHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EE CS
                Cob_adeno_trans   35 lnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplk 106 
                                     l++ +  + +ll+++ ee++ +L ei  +L ++ + +a         +i+ + v+++ + +d+++a+l++++
  gi|118431124|ref|NP_147358.2| 1221 LQASVDELTELLQQTGEEITMKLDEISGDLAEISNGVA---------TIQGD-VATILELLDAMNATLTTIQ 1282
                                     33333333333333333333333333333333333333.........23333.5555555566665555443 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.6
                                     H CS
                Cob_adeno_trans   96 d 96  
                                      
  gi|118431124|ref|NP_147358.2| 1322 A 1322
                                     1 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0037
                                     XTTHHHHHHHHHHHHHHHHHHHHHHHCTTT...THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHH CS
                Cob_adeno_trans   20 sKddprveayGtvDelnsaiglarallaee...eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveeleke 94  
                                      K d+++e + t+   n+++   ++ +a++    ++ ++++++iq+ L ++  ++a+   k+++++i+++ +++ + +
  gi|118431124|ref|NP_147358.2| 1411 VKLDQVLEDLSTISDQNAQLAAQAEAIAQTlaaVQDDTAKITDIQSTLASVAGDVASV--KQDTSTISSK-LDDANGK 1485
                                     5888999999999999999998887777778887888999***************955..4444445544.7777777 PP

                                     HHHHHHHS--EESEE CS
                Cob_adeno_trans   95 ideleaelpplksfi 109 
                                     +d+++++++ ++s +
  gi|118431124|ref|NP_147358.2| 1486 LDSISSKVDSVSSAV 1500
                                     777776666555444 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.5      0.02       7.5     223     300 ..    1204    1282 ..    1167    1307 .. 0.52
   2 ?    6.0   1.6     0.014       5.4     252     320 ..    1418    1489 ..    1406    1518 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.02
                                     CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHH CS
                          APG17  223 eeereelleVlekDaaeledVvkelqerleem.ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkae 299 
                                       e +e +++l+ D   l++ v+el+e l++  e+++  l+e   ++ ++++ +  +  ++ ++ + l+++ a+++++
  gi|118431124|ref|NP_147358.2| 1204 VTEINEGVAILQTDLGNLQASVDELTELLQQTgEEITMKLDEISGDLAEISNGVATIQGDVATILELLDAMNATLTTI 1281
                                     333334445555555555555555555555555555555555555555555555555555544444444444444455 PP

                                     H CS
                          APG17  300 e 300 
                                     +
  gi|118431124|ref|NP_147358.2| 1282 Q 1282
                                     5 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                                     HHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHH CS
                          APG17  252 eem...ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleel 320 
                                     e++   ++++++l +++e+i ++l+a+++  +++++++++l+++   +++ ++ +++ +++ ++ + kl+ +
  gi|118431124|ref|NP_147358.2| 1418 EDLstiSDQNAQLAAQAEAIAQTLAAVQDDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSI 1489
                                     333333666666666666666666666666666666666666666655555555555555555444444443 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3      0.08        30      31     113 ..    1200    1282 ..    1176    1300 .. 0.81
   2 ?    0.6   0.2       1.5   5.7e+02      69      94 ..    1379    1404 ..    1333    1424 .. 0.55
   3 ?    7.2   1.6     0.014       5.2      23     117 ..    1422    1515 ..    1414    1526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.08
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHH CS
                           COG5   31 lstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqs 107 
                                     +++++  +n+++  l++ l + ++++ +eL+e l++  ++    l+e+ + l+++s+ +  ++ +v +  e ++  ++
  gi|118431124|ref|NP_147358.2| 1200 IEATVTEINEGVAILQTDLGN-LQASVDELTELLQQTGEEITmKLDEISGDLAEISNGVATIQGDVATILELLDAMNA 1276
                                     566666677777777777754.56778888888888877777799*********************999999999999 PP

                                     HHHHHH CS
                           COG5  108 alkrlh 113 
                                     +l +++
  gi|118431124|ref|NP_147358.2| 1277 TLTTIQ 1282
                                     988876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                                     XXXXXXXXXXXXXXXXXXXXXXXX-T CS
                           COG5   69 slssvlselksslesLsasyerlksk 94  
                                     + +++l ++++s+  L+a ++ lk  
  gi|118431124|ref|NP_147358.2| 1379 ENNQLLATITTSMGTLTADMSTLKDL 1404
                                     22335555555555555555555544 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.014
                                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHH CS
                           COG5   23 nnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepye 100 
                                       +d+++ l+++++ + + +  +++  + +it+ +++L + + + +s ++ +s++ s+l++ +  ++ ++skv     
  gi|118431124|ref|NP_147358.2| 1422 TISDQNAQLAAQAEAIAQTLAAVQDD-TAKITDIQSTLASVAGDVASVKQDTSTISSKLDDANGKLDSISSKVDSVSS 1498
                                     55788888899999999999999887.56789999******************************************* PP

                                     HHHHHHHHHHHHHHHHH CS
                           COG5  101 eaeklqsalkrlhqtld 117 
                                      +   q++l ++ +t++
  gi|118431124|ref|NP_147358.2| 1499 AVADIQEQLGQVGDTAE 1515
                                     *********99999987 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4      0.28   1.1e+02       8      45 ..    1196    1233 ..    1192    1234 .. 0.95
   2 ?    1.4   0.1      0.73   2.7e+02       6      32 ..    1268    1294 ..    1262    1308 .. 0.56
   3 ?    1.5   0.3      0.68   2.5e+02       8      46 ..    1348    1386 ..    1341    1390 .. 0.89
   4 ?    3.0   0.0      0.24        89       4      41 ..    1446    1483 ..    1441    1484 .. 0.86
   5 ?    2.7   0.0      0.28   1.1e+02       7      48 ..    1484    1525 ..    1478    1529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.28
                      DASH_Duo1    8 qLrkinevienviesLkkaksniervketvestntLLd 45  
                                     +L++i +++  ++e     ++++ +++ +v++  +LL+
  gi|118431124|ref|NP_147358.2| 1196 KLDSIEATVTEINEGVAILQTDLGNLQASVDELTELLQ 1233
                                     79**********************************97 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.73
                      DASH_Duo1    6 leqLrkinevienviesLkkaksnier 32  
                                     le L+ +n+++ +++++  ++k+   +
  gi|118431124|ref|NP_147358.2| 1268 LELLDAMNATLTTIQGDVAEIKTTAGT 1294
                                     344555555555555555555555555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.68
                      DASH_Duo1    8 qLrkinevienviesLkkaksniervketvestntLLdk 46  
                                      + ++ +++ +v  sL++  + + +++e v + n+LL +
  gi|118431124|ref|NP_147358.2| 1348 GVAEVQTILGDVSVSLEDLVEANATIEEVVVENNQLLAT 1386
                                     67788899999*************************976 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.24
                      DASH_Duo1    4 kEleqLrkinevienviesLkkaksniervketvestn 41  
                                      +  ++++i +++ +v ++  ++k+++++++++++++n
  gi|118431124|ref|NP_147358.2| 1446 DDTAKITDIQSTLASVAGDVASVKQDTSTISSKLDDAN 1483
                                     56778899999999999999999999999999988877 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.28
                      DASH_Duo1    7 eqLrkinevienviesLkkaksniervketvestntLLdkWi 48  
                                      +L++i + +++v ++  ++++++ +v  t es++   ++W 
  gi|118431124|ref|NP_147358.2| 1484 GKLDSISSKVDSVSSAVADIQEQLGQVGDTAESASGRAQTWG 1525
                                     579999999999999999999999999999999987777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); expected 17.9 (0.001)
Passed Fwd filter:                        79  (0.00440627); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 1.80u 0.33s 00:00:02.13 Elapsed: 00:00:00.52
# Mc/sec: 8960.70
//
Query:       gi|118431125|ref|NP_147363.2|  [L=541]
Description: hypothetical protein APE_0614.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3990.84
//
Query:       gi|118431126|ref|NP_147367.2|  [L=420]
Description: hypothetical protein APE_0618.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3105.30
//
Query:       gi|118431127|ref|NP_147369.2|  [L=1950]
Description: hypothetical protein APE_0620.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-31  107.3  25.2    2.9e-10   40.3   0.5   12.0 12  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.6e-13   49.2   6.3       0.02   14.8   0.0    9.4 11  PEGA             PEGA domain
    3.1e-12   46.3   0.0     0.0072   16.3   0.0    7.7  9  CarbopepD_reg_2  CarboxypepD_reg-like domain
      9e-05   22.4   0.0    0.00039   20.4   0.0    2.0  2  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    0.00016   21.7   0.2        8.7    6.5   0.0    5.9  6  DUF2012          Protein of unknown function (DUF2012)
     0.0003   20.7  14.2      0.047   13.7   0.1    6.1  8  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.044   13.7   0.0       0.38   10.7   0.0    2.5  2  DUF1416          Protein of unknown function (DUF1416)
      0.056   13.4   0.8         27    4.8   0.0    4.9  6  Y_Y_Y            Y_Y_Y domain
      0.057   13.5   0.7       0.31   11.2   0.7    2.3  1  DUF1206          Domain of Unknown Function (DUF1206)
      0.089   13.3   0.2      0.089   13.3   0.2    5.9  6  PQQ_3            PQQ-like domain
        2.3    8.4   4.1    1.8e+02    2.3   0.1    5.3  7  bMG6             Bacterial macroglobulin domain 6


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 ?    2.3   0.0      0.13   2.1e+02      38      69 ..     691     720 ..     677     734 .. 0.80
   2 ?   -3.7   0.0       9.6   1.6e+04      28      40 ..     786     798 ..     759     808 .. 0.56
   3 !   13.2   0.0     5e-05     0.082      27      76 ..     871     917 ..     857     924 .. 0.72
   4 !    9.1   0.0   0.00096       1.6      11      67 ..     944    1001 ..     931    1012 .. 0.77
   5 ?    5.3   0.0     0.015        24      16      81 ..    1036    1100 ..    1025    1101 .. 0.87
   6 !   12.8   0.5   6.6e-05      0.11      14      81 ..    1124    1192 ..    1113    1193 .. 0.75
   7 !    9.1   0.0   0.00092       1.5       8      80 ..    1207    1279 ..    1201    1281 .. 0.72
   8 ?    0.2   0.1      0.58   9.4e+02      29      59 ..    1333    1362 ..    1310    1385 .. 0.68
   9 !    7.7   0.0    0.0026       4.3      45      68 ..    1433    1455 ..    1425    1472 .. 0.81
  10 !    6.7   0.0    0.0052       8.5      40      76 ..    1604    1636 ..    1599    1642 .. 0.72
  11 ?    5.4   0.0     0.014        22      19      72 ..    1757    1813 ..    1742    1823 .. 0.69
  12 !   40.3   0.5   1.8e-13   2.9e-10       6      82 .]    1833    1905 ..    1829    1905 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                CarboxypepD_reg  38 GafrlrglppgtysvtvsapGyatatreevtl 69 
                                    G+ +l  +p g+y+++v+ pG     re v++
  gi|118431127|ref|NP_147369.2| 691 GSITL-YVPRGDYTIEVELPGLGKLYRE-VEV 720
                                    55565.3899***********9999975.655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.6
                CarboxypepD_reg  28 tvastttdadGaf 40 
                                        t+t++dG+ 
  gi|118431127|ref|NP_147369.2| 786 LPVATVTGDDGRA 798
                                    4566777777765 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 5e-05
                CarboxypepD_reg  27 gtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqttt 76 
                                     t +s++ ++ G+     lppg+y ++v+apGy +a+ +    ++g+++ 
  gi|118431127|ref|NP_147369.2| 871 PTGRSARVAEPGDSVRIPLPPGSYIIRVEAPGYSPAEAQ---AEVGRAAS 917
                                    566666666666655556*******************75...55555555 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00096
                CarboxypepD_reg   11 gapiagatVtvtnadt..gtvastttdadGafrlrglppgtysvtvsapGyatatreev 67  
                                     g  i+ga++++t ++   g + ++ t+++G+ +++ l  g y+v+v+++    + +++v
  gi|118431127|ref|NP_147369.2|  944 GGSIKGARIAFTLEEPslGYRVEVDTGEEGEAQVT-LRSGVYRVEVEHHILGKTVYSGV 1001
                                     57899****9887654226789999*********8.**********9886666666655 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.015
                CarboxypepD_reg   16 gatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatreevtltagqtttlditL 81  
                                     g tVt+t   tg+++s +t ++ +f+l+  p g y++ v s +Gy + t  +++l+ g  + +++ L
  gi|118431127|ref|NP_147369.2| 1036 GFTVTLTYLLTGESRSFVTRSS-SFSLE-APEGLYRILVsSLEGYYEDTEASLSLERGAGESVTLSL 1100
                                     6788888888888888888877.99997.899*****997889***************999999887 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 6.6e-05
                CarboxypepD_reg   14 iagatVtvtnadtgt...vastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81  
                                     +  a V++t  +t +   +   ttd++G+  +  l pg y++tv++p  + a+  e++l +   + ++++L
  gi|118431127|ref|NP_147369.2| 1124 VGDALVVATPLETPVevaSEVQTTDSQGRAVFL-LRPGVYEITVTHPYTEGARL-EIDLFKASRSGVQVKL 1192
                                     567888888877764221344589********7.*************8888887.4888777777777666 PP

  == domain 7  score: 9.1 bits;  conditional E-value: 0.00092
                CarboxypepD_reg    8 da.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldit 80  
                                     d+  g  ++ a +++t  + +++++ t   +G  +l  lp g+y+++++ pGy   +  ++tl+ ++ +  +it
  gi|118431127|ref|NP_147369.2| 1207 DSdLGVELPSALLRITWHGYSQSSQKTLQVEGGTALVRLPFGSYTLEAELPGYYRPSLYSLTLAQDR-VFATIT 1279
                                     55248888999999998777777777777777777778***************98776556666433.334555 PP

  == domain 8  score: 0.2 bits;  conditional E-value: 0.58
                CarboxypepD_reg   29 vastttdadGafrlrglppgtysvtvsapGy 59  
                                       s++ d++G+   + + +g+y +++ a   
  gi|118431127|ref|NP_147369.2| 1333 PVSVVADETGSAVAS-VRAGSYIIEAAAGSS 1362
                                     578899999999965.999999999966554 PP

  == domain 9  score: 7.7 bits;  conditional E-value: 0.0026
                CarboxypepD_reg   45 lppgtysvtvsapGyatatreevt 68  
                                     lp g y+++vsa+Gy  +t+e   
  gi|118431127|ref|NP_147369.2| 1433 LPEGVYTLEVSAEGYPGSTVE-AA 1455
                                     788*************99986.44 PP

  == domain 10  score: 6.7 bits;  conditional E-value: 0.0052
                CarboxypepD_reg   40 frlrglppgtysvtvsapGyatatreevtltagqttt 76  
                                       l +lppg  +++v+a G+++a+ +   l+  +++ 
  gi|118431127|ref|NP_147369.2| 1604 AVL-QLPPGLATLEVRALGFKPASTT---LEIWGDAS 1636
                                     555.5******************964...44444444 PP

  == domain 11  score: 5.4 bits;  conditional E-value: 0.014
                CarboxypepD_reg   19 Vtvtna..dtgtvastttdadGafrlrglppgtysvtvsapGyatatr..eevtltag 72  
                                     V+++++  ++g+ +s+ t   G+  l+ lppgty+ + + +  +++ r  +++t t++
  gi|118431127|ref|NP_147369.2| 1757 VELERQapEGGFGYSVETVVRGKALLS-LPPGTYQARLTPEAGQSFYRvdTTFTFTVD 1813
                                     5555542267899***********996.********9998888888875534444444 PP

  == domain 12  score: 40.3 bits;  conditional E-value: 1.8e-13
                CarboxypepD_reg    6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditLe 82  
                                     V+d  g+p  ga V+v ++++ +vas  tda+G f+++  p g y +++++pGy+++t +   ++  q+ttl+itL+
  gi|118431127|ref|NP_147369.2| 1833 VVDDRGTPQQGALVRVLSEEGVEVASGLTDASGVFTFQ-APYGLYILEAEKPGYRESTGT---IQIPQSTTLTITLQ 1905
                                     9****************999999**************7.999****************85...66668899999985 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0009       1.5      27      54 ..     693     720 ..     676     724 .. 0.90
   2 !   14.8   0.0   1.2e-05      0.02      27      56 ..     885     914 ..     884     924 .. 0.88
   3 ?   -2.7   0.1       3.5   5.7e+03      22      40 ..     972     988 ..     962     991 .. 0.45
   4 ?    0.2   0.0      0.42   6.9e+02      29      68 ..    1061    1102 ..    1056    1104 .. 0.74
   5 ?   -1.9   0.0         2   3.3e+03      31      61 ..    1157    1187 ..    1154    1194 .. 0.77
   6 ?    0.1   0.0      0.46   7.4e+02      30      45 ..    1243    1259 ..    1240    1280 .. 0.83
   7 ?   -0.3   0.0       0.6   9.9e+02       8      40 ..    1361    1390 ..    1358    1393 .. 0.76
   8 ?    5.4   0.1      0.01        17      28      45 ..    1430    1447 ..    1426    1463 .. 0.85
   9 ?    0.1   0.0      0.46   7.4e+02      30      62 ..    1607    1639 ..    1603    1643 .. 0.82
  10 ?   -1.9   0.0         2   3.3e+03      29      43 ..    1782    1796 ..    1780    1823 .. 0.73
  11 !    8.3   0.0    0.0013         2      32      67 ..    1872    1905 ..    1867    1908 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0009
                           PEGA  27 vtlsleaGnyslrvekeGYedlektvtv 54 
                                    +tl+++ G+y+++ve++G   l+++v+v
  gi|118431127|ref|NP_147369.2| 693 ITLYVPRGDYTIEVELPGLGKLYREVEV 720
                                    7999*********************998 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.2e-05
                           PEGA  27 vtlsleaGnyslrvekeGYedlektvtvta 56 
                                    v++ l++G+y +rve++GY+++e++ +v +
  gi|118431127|ref|NP_147369.2| 885 VRIPLPPGSYIIRVEAPGYSPAEAQAEVGR 914
                                    67889********************99974 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.5
                           PEGA  22 lGkTPvtlsleaGnyslrv 40 
                                     G++  +++l +G y+++v
  gi|118431127|ref|NP_147369.2| 972 EGEA--QVTLRSGVYRVEV 988
                                    2222..3334445555555 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.42
                           PEGA   29 lsleaGnyslrvek..eGYedlektvtvtagetvklnltLek 68  
                                     l+ ++G y++ v+    +Yed e+  ++++g   +++l L++
  gi|118431127|ref|NP_147369.2| 1061 LEAPEGLYRILVSSleGYYEDTEASLSLERGAGESVTLSLKP 1102
                                     567899999999743255799999999997777777776665 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2
                           PEGA   31 leaGnyslrvekeGYedlektvtvtagetvk 61  
                                     l +G y+++v  ++ e ++ ++++ +     
  gi|118431127|ref|NP_147369.2| 1157 LRPGVYEITVTHPYTEGARLEIDLFKASRSG 1187
                                     67999******99988888888887665555 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 0.46
                           PEGA   30 s.leaGnyslrvekeGY 45  
                                     + l+ G+y+l+ e++GY
  gi|118431127|ref|NP_147369.2| 1243 VrLPFGSYTLEAELPGY 1259
                                     44899***********9 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.6
                           PEGA    8 SnpeGatVyidGkylGkTPvtlsleaGnyslrv 40  
                                     S+ +G++  i++ +   T v++s++++ y++++
  gi|118431127|ref|NP_147369.2| 1361 SSVSGSRAFIGE-E--TTAVSISIKPKAYTVDL 1390
                                     566666666633.2..699***********998 PP

  == domain 8  score: 5.4 bits;  conditional E-value: 0.01
                           PEGA   28 tlsleaGnyslrvekeGY 45  
                                     + +l++G y+l+v++eGY
  gi|118431127|ref|NP_147369.2| 1430 RAVLPEGVYTLEVSAEGY 1447
                                     5569************** PP

  == domain 9  score: 0.1 bits;  conditional E-value: 0.46
                           PEGA   30 sleaGnyslrvekeGYedlektvtvtagetvkl 62  
                                      l++G  +l+v + G++++++t ++  +  +++
  gi|118431127|ref|NP_147369.2| 1607 QLPPGLATLEVRALGFKPASTTLEIWGDASLEV 1639
                                     499*******************99876666655 PP

  == domain 10  score: -1.9 bits;  conditional E-value: 2
                           PEGA   29 lsleaGnyslrveke 43  
                                     lsl++G+y+ r+  e
  gi|118431127|ref|NP_147369.2| 1782 LSLPPGTYQARLTPE 1796
                                     6799****9998765 PP

  == domain 11  score: 8.3 bits;  conditional E-value: 0.0013
                           PEGA   32 eaGnyslrvekeGYedlektvtvtagetvklnltLe 67  
                                     + G y l+ ek+GY++ + t+++ + +t+++  tL+
  gi|118431127|ref|NP_147369.2| 1872 PYGLYILEAEKPGYRESTGTIQIPQSTTLTI--TLQ 1905
                                     779999******************6666666..555 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.12     2e+02      34      87 ..     691     737 ..     689     742 .. 0.73
   2 ?    5.3   0.0     0.012        20      41      86 ..     889     930 ..     886     932 .. 0.77
   3 ?   -0.6   0.0      0.82   1.3e+03      35      77 ..    1058    1101 ..    1045    1107 .. 0.73
   4 ?   -2.8   0.0       4.1   6.6e+03      39      56 ..    1243    1260 ..    1237    1280 .. 0.82
   5 ?   -1.9   0.0         2   3.3e+03      17      66 ..    1334    1383 ..    1328    1397 .. 0.75
   6 ?    4.4   0.0     0.023        38      41      69 ..    1433    1461 ..    1424    1471 .. 0.81
   7 !    5.7   0.0     0.009        15      40      74 ..    1607    1641 ..    1601    1644 .. 0.87
   8 ?   -1.7   0.0       1.9   3.1e+03      36      57 ..    1808    1829 ..    1807    1852 .. 0.82
   9 !   16.3   0.0   4.4e-06    0.0072       6      74 ..    1834    1904 ..    1832    1911 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.12
                CarbopepD_reg_2  34 GnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealeleevv 87 
                                    G+ +l ++p+g+yt+ v+  G  +  ++v+v +   ld      + ++ l evv
  gi|118431127|ref|NP_147369.2| 691 GSITL-YVPRGDYTIEVELPGLGKLYREVEVLQPLILD------SIEVALREVV 737
                                    56677.69*******************99996665444......3344455555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                CarbopepD_reg_2  41 lpagkytLvvsyvGyktqekkvtvskektldvnillkeealeleev 86 
                                    lp+g y ++v++ Gy ++e + +v +  +l  ++l++++    +ev
  gi|118431127|ref|NP_147369.2| 889 LPPGSYIIRVEAPGYSPAEAQAEVGRAASLV-TVLMEPAY---NEV 930
                                    799*********************9887764.45555443...455 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.82
                CarbopepD_reg_2   35 nFelknlpagkytLvvsyv.G.yktqekkvtvskektldvnillk 77  
                                     +F+l+  p+g y++ vs++ G y+  e +++++++   +v+++lk
  gi|118431127|ref|NP_147369.2| 1058 SFSLE-APEGLYRILVSSLeGyYEDTEASLSLERGAGESVTLSLK 1101
                                     59996.899999988887635456677777777776666666555 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 4.1
                CarbopepD_reg_2   39 knlpagkytLvvsyvGyk 56  
                                      +lp g ytL ++  Gy 
  gi|118431127|ref|NP_147369.2| 1243 VRLPFGSYTLEAELPGYY 1260
                                     568999*****9999985 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2
                CarbopepD_reg_2   17 atVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvsk 66  
                                     ++V+  +t+  +++   G++ +++     +     ++G +t  ++++++ 
  gi|118431127|ref|NP_147369.2| 1334 VSVVADETGSAVASVRAGSYIIEAAAGSSVSGSRAFIGEETTAVSISIKP 1383
                                     78889999999999999999998766666666667788888777777764 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.023
                CarbopepD_reg_2   41 lpagkytLvvsyvGyktqekkvtvskekt 69  
                                     lp+g ytL vs+ Gy   +++  +s+  t
  gi|118431127|ref|NP_147369.2| 1433 LPEGVYTLEVSAEGYPGSTVEAAISSPGT 1461
                                     799************99988888776655 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.009
                CarbopepD_reg_2   40 nlpagkytLvvsyvGyktqekkvtvskektldvni 74  
                                     +lp+g  tL v+++G+k+++ ++++ ++ +l+v++
  gi|118431127|ref|NP_147369.2| 1607 QLPPGLATLEVRALGFKPASTTLEIWGDASLEVEM 1641
                                     58999*******************99998888765 PP

  == domain 8  score: -1.7 bits;  conditional E-value: 1.9
                CarbopepD_reg_2   36 FelknlpagkytLvvsyvGykt 57  
                                     F+++  ++gk++L++s + y  
  gi|118431127|ref|NP_147369.2| 1808 FTFTVDEPGKVELRISPIMYSA 1829
                                     88888899********999876 PP

  == domain 9  score: 16.3 bits;  conditional E-value: 4.4e-06
                CarbopepD_reg_2    6 vdketkeplpgatVyvkgtk....kgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvni 74  
                                     vd+  ++p  ga V v + +    +   Td++G F+++  p+g y L ++  Gy++ + ++++ + +tl++++
  gi|118431127|ref|NP_147369.2| 1834 VDDR-GTPQQGALVRVLSEEgvevASGLTDASGVFTFQ-APYGLYILEAEKPGYRESTGTIQIPQSTTLTITL 1904
                                     5544.46777777777443322225566*********7.9***********************9999888654 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 ?   -2.7   0.0       3.7   6.1e+03      46      56 ..    1145    1155 ..    1143    1158 .. 0.86
   2 !   20.4   0.0   2.4e-07   0.00039      24      59 ..    1837    1872 ..    1830    1886 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.7
                           bMG3   46 gtTDaqGvarf 56  
                                     +tTD+qG+a f
  gi|118431127|ref|NP_147369.2| 1145 QTTDSQGRAVF 1155
                                     69******988 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.4e-07
                           bMG3   24 sgkPvagaeVrlldkkgevlaegtTDaqGvarfaal 59  
                                      g P +ga Vr+l+++g ++a+g TDa+Gv +f+a+
  gi|118431127|ref|NP_147369.2| 1837 RGTPQQGALVRVLSEEGVEVASGLTDASGVFTFQAP 1872
                                     699*******************************98 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.4   1.2e+04      37      51 ..     697     711 ..     696     723 .. 0.83
   2 ?    0.7   0.0      0.34   5.5e+02      36      59 ..     888     911 ..     864     932 .. 0.78
   3 ?    1.0   0.0      0.26   4.3e+02      11      54 ..    1038    1080 ..    1032    1100 .. 0.80
   4 ?    3.3   0.0     0.051        84      17      51 ..    1225    1259 ..    1201    1270 .. 0.83
   5 ?    0.1   0.0      0.49     8e+02      37      65 ..    1433    1461 ..    1424    1479 .. 0.83
   6 !    6.5   0.0    0.0053       8.7      15      60 ..    1851    1894 ..    1827    1905 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.4
                        DUF2012  37 lpegsYlLevespey 51 
                                    +p g Y++eve p++
  gi|118431127|ref|NP_147369.2| 697 VPRGDYTIEVELPGL 711
                                    899*******99875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.34
                        DUF2012  36 dlpegsYlLevespeyvFepyrVd 59 
                                     lp+gsY+++ve+p+y  ++ + +
  gi|118431127|ref|NP_147369.2| 888 PLPPGSYIIRVEAPGYSPAEAQAE 911
                                    59************9976665555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.26
                        DUF2012   11 rvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFe 54  
                                     +v+L    + + + +v+r+ sF+++  peg Y + v s e  +e
  gi|118431127|ref|NP_147369.2| 1038 TVTLTYLLTGESRSFVTRSSSFSLE-APEGLYRILVSSLEGYYE 1080
                                     56664444555589*********96.7******99999887776 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.051
                        DUF2012   17 gqqrkfkalvrrDGsFifrdlpegsYlLevespey 51  
                                     g++++ +  ++++G  ++  lp gsY+Le+e p+y
  gi|118431127|ref|NP_147369.2| 1225 GYSQSSQKTLQVEGGTALVRLPFGSYTLEAELPGY 1259
                                     5555778889999999999************9998 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.49
                        DUF2012   37 lpegsYlLevespeyvFepyrVdvkdkgk 65  
                                     lpeg Y+Lev + +y  +++   ++++g+
  gi|118431127|ref|NP_147369.2| 1433 LPEGVYTLEVSAEGYPGSTVEAAISSPGT 1461
                                     89*********999987777777776655 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.0053
                        DUF2012   15 dsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdv 60  
                                     ++g +   ++l+ ++G F+f+  p+g Y+Le+e+p+y  ++  +++
  gi|118431127|ref|NP_147369.2| 1851 EEGVE-VASGLTDASGVFTFQ-APYGLYILEAEKPGYRESTGTIQI 1894
                                     44444.6788999*******7.6*************9866666666 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 ?   -3.4   0.1       6.3     1e+04      20      38 ..     110     129 ..     109     136 .. 0.66
   2 ?    1.7   0.0      0.16   2.6e+02      15      55 ..     756     805 ..     753     811 .. 0.78
   3 !    8.0   0.0    0.0017       2.8      17      55 ..     943     982 ..     928     986 .. 0.80
   4 ?   -3.6   0.0       7.4   1.2e+04      43      55 ..    1032    1044 ..    1032    1049 .. 0.77
   5 ?    2.0   0.0      0.13   2.1e+02      37      53 ..    1142    1158 ..    1123    1166 .. 0.80
   6 ?   -1.7   0.0       1.9     3e+03      37      62 ..    1333    1355 ..    1315    1357 .. 0.66
   7 ?   -3.8   0.0       8.4   1.4e+04      11      22 ..    1650    1661 ..    1648    1662 .. 0.81
   8 !   13.7   0.1   2.9e-05     0.047       9      51 ..    1829    1870 ..    1827    1871 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.3
                          Big_1  20 pvagatVtfsvsggals.as 38 
                                    ++ g +V + v+g++ s a+
  gi|118431127|ref|NP_147369.2| 110 ALVGDPVELAVDGSTGSwAA 129
                                    67899999999996655433 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.16
                          Big_1  15 DangnpvagatVtfsvsggals.........assgtTdanGkatvtltst 55 
                                    D +  pv g++ t+  s++a+          +  ++T+++G+at+ l s 
  gi|118431127|ref|NP_147369.2| 756 DLYSGPVGGVELTLAPSQAATEdlgytpdplPVATVTGDDGRATAILWSG 805
                                    5566688888888888887777788888888999**********987665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0017
                          Big_1  17 ngnpvagatVtfsvsggals.assgtTdanGkatvtltst 55 
                                    +g  ++ga + f+    +l    ++ T+++G+a+vtl s 
  gi|118431127|ref|NP_147369.2| 943 FGGSIKGARIAFTLEEPSLGyRVEVDTGEEGEAQVTLRSG 982
                                    466899**********66666****************985 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 7.4
                          Big_1   43 danGkatvtltst 55  
                                     da G +tvtlt  
  gi|118431127|ref|NP_147369.2| 1032 DAPGGFTVTLTYL 1044
                                     7889999999965 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.13
                          Big_1   37 assgtTdanGkatvtlt 53  
                                     +  +tTd++G+a++ l 
  gi|118431127|ref|NP_147369.2| 1142 SEVQTTDSQGRAVFLLR 1158
                                     6678********99875 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 1.9
                          Big_1   37 assgtTdanGkatvtltstkagtvtv 62  
                                     + s++ d+ G a++++    ag++ +
  gi|118431127|ref|NP_147369.2| 1333 PVSVVADETGSAVASVR---AGSYII 1355
                                     78899999999988775...666655 PP

  == domain 7  score: -3.8 bits;  conditional E-value: 8.4
                          Big_1   11 atvkDangnpva 22  
                                     +++ D +gnpv+
  gi|118431127|ref|NP_147369.2| 1650 IRLADPDGNPVE 1661
                                     67889*****96 PP

  == domain 8  score: 13.7 bits;  conditional E-value: 2.9e-05
                          Big_1    9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvt 51  
                                     +t+ v+D  g+p +ga V + +  g+   +sg Tda+G++t++
  gi|118431127|ref|NP_147369.2| 1829 ATILVVDDRGTPQQGALVRVLSEEGVE-VASGLTDASGVFTFQ 1870
                                     6899********************999.56***********96 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   1.9e+03      42      78 ..    1135    1172 ..    1122    1190 .. 0.79
   2 ?   10.7   0.0   0.00023      0.38      26      72 ..    1834    1880 ..    1826    1903 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                        DUF1416   42 dssgeFtaevvts.aeGefrFfaapGeWtvRalarkgn 78  
                                     ++  e ++ev+t+ ++G+  F  +pG + + + ++ ++
  gi|118431127|ref|NP_147369.2| 1135 ETPVEVASEVQTTdSQGRAVFLLRPGVYEITVTHPYTE 1172
                                     556688999987625899*********99998887665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                        DUF1416   26 vtrdgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRa 72  
                                     v + g+p +ga vR+L ++g  +a   t a+G f F a  G + + a
  gi|118431127|ref|NP_147369.2| 1834 VDDRGTPQQGALVRVLSEEGVEVASGLTDASGVFTFQAPYGLYILEA 1880
                                     55689********************************9999876655 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 ?   -0.2   0.0      0.63     1e+03      37      46 ..     698     707 ..     696     708 .. 0.86
   2 ?    4.8   0.0     0.017        27      35      47 ..     888     900 ..     886     906 .. 0.92
   3 ?   -3.0   0.0       4.6   7.6e+03      35      45 ..    1156    1166 ..    1144    1168 .. 0.78
   4 ?   -3.0   0.0       4.5   7.3e+03      36      45 ..    1245    1254 ..    1244    1255 .. 0.86
   5 ?    1.1   0.0      0.23   3.8e+02      36      47 ..    1433    1444 ..    1431    1455 .. 0.88
   6 ?   -2.0   0.0       2.2   3.6e+03      36      42 ..    1784    1790 ..    1783    1812 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.63
                                    -SEEEEEEEE CS
                          Y_Y_Y  37 ppGdYtlkVk 46 
                                    p GdYt++V+
  gi|118431127|ref|NP_147369.2| 698 PRGDYTIEVE 707
                                    89******96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                                    S--SEEEEEEEEE CS
                          Y_Y_Y  35 nlppGdYtlkVka 47 
                                    +lppG+Y ++V+a
  gi|118431127|ref|NP_147369.2| 888 PLPPGSYIIRVEA 900
                                    8**********98 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.6
                                     S--SEEEEEEE CS
                          Y_Y_Y   35 nlppGdYtlkV 45  
                                      l pG Y+++V
  gi|118431127|ref|NP_147369.2| 1156 LLRPGVYEITV 1166
                                     589******98 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 4.5
                                     --SEEEEEEE CS
                          Y_Y_Y   36 lppGdYtlkV 45  
                                     lp G+Ytl++
  gi|118431127|ref|NP_147369.2| 1245 LPFGSYTLEA 1254
                                     899****986 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.23
                                     --SEEEEEEEEE CS
                          Y_Y_Y   36 lppGdYtlkVka 47  
                                     lp+G Ytl+V+a
  gi|118431127|ref|NP_147369.2| 1433 LPEGVYTLEVSA 1444
                                     8*********98 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 2.2
                                     --SEEEE CS
                          Y_Y_Y   36 lppGdYt 42  
                                     lppG+Y+
  gi|118431127|ref|NP_147369.2| 1784 LPPGTYQ 1790
                                     9*****7 PP

>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00019      0.31      40      64 ..    1911    1935 ..    1909    1940 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                        DUF1206   40 leqpfGrvllglvglgllgyglwql 64  
                                     l q++G++ +g  gl+ll++gl+++
  gi|118431127|ref|NP_147369.2| 1911 LLQRYGPIAVGFTGLALLAVGLYRV 1935
                                     6699*******************98 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.5       4.6   7.5e+03       5      36 ..     107     140 ..     104     144 .. 0.69
   2 ?   -1.5   0.4       2.5   4.1e+03      18      35 ..     164     184 ..     155     188 .. 0.60
   3 ?   13.3   0.2   5.5e-05     0.089      17      36 ..     515     539 ..     497     542 .. 0.80
   4 ?   -2.2   0.0         4   6.5e+03      21      38 ..     568     585 ..     555     586 .. 0.79
   5 ?   -1.4   0.1       2.4   3.9e+03      28      37 ..     675     684 ..     659     686 .. 0.75
   6 ?   -2.0   0.2       3.4   5.6e+03      11      36 ..     755     801 ..     750     801 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.6
                          PQQ_3   5 Wsvql.pgpvnsspavdggl...vyvgtgdGtlyAl 36 
                                    Ws+ l ++pv   +avdg +     vgt+ G +  +
  gi|118431127|ref|NP_147369.2| 107 WSQALvGDPVE--LAVDGSTgswAAVGTSTGEVAVV 140
                                    77766355775..89998766668888888877665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                          PQQ_3  18 avdgg...lvyvgtgdGtlyA 35 
                                    + +gg   +++v++g G  y 
  gi|118431127|ref|NP_147369.2| 164 VWSGGdspRLVVVDGGGAAYF 184
                                    445554446777777776664 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 5.5e-05
                          PQQ_3  17 p.....avdgglvyvgtgdGtlyAl 36 
                                    p     a +gg++yvgt+ G++y+l
  gi|118431127|ref|NP_147369.2| 515 PteveiASGGGVIYVGTSSGHVYML 539
                                    134444899**************98 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 4
                          PQQ_3  21 gglvyvgtgdGtlyAlDa 38 
                                    + ++ v++ +G l A+D 
  gi|118431127|ref|NP_147369.2| 568 ETHIIVASQQGLLQAVDV 585
                                    56899***********95 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 2.4
                          PQQ_3  28 tgdGtlyAlD 37 
                                    ++ G +yA+D
  gi|118431127|ref|NP_147369.2| 675 GPGGEVYAVD 684
                                    5689999999 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 3.4
                          PQQ_3  11 gpvnssp............avdggl.........vyvgtgdGtlyAl 36 
                                    ++++s+p            a+ ++l           v+++dG+ +A+
  gi|118431127|ref|NP_147369.2| 755 YDLYSGPvggveltlapsqAATEDLgytpdplpvATVTGDDGRATAI 801
                                    55555555555555555554444442222222323344449998886 PP

>> bMG6  Bacterial macroglobulin domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.5e+03      80      99 ..     690     709 ..     683     713 .. 0.83
   2 ?    0.4   0.0      0.44   7.2e+02      59     101 ..     861     903 ..     852     913 .. 0.70
   3 ?    2.3   0.1      0.11   1.8e+02      72      98 ..     964     990 ..     956    1000 .. 0.82
   4 ?   -1.1   0.0       1.3   2.1e+03      72     101 ..    1143    1171 ..    1135    1178 .. 0.73
   5 ?   -2.4   0.0       3.3   5.3e+03      70      98 ..    1231    1256 ..    1226    1261 .. 0.66
   6 ?   -1.2   0.0       1.3   2.2e+03      73     101 ..    1334    1362 ..    1331    1370 .. 0.81
   7 ?   -1.2   0.0       1.4   2.3e+03      79     105 ..    1863    1889 ..    1847    1892 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                           bMG6  80 kaklslpvdwGrYrleVede 99 
                                    +++++l v  G+Y +eVe +
  gi|118431127|ref|NP_147369.2| 690 RGSITLYVPRGDYTIEVELP 709
                                    5678889999*******866 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                           bMG6  59 yestekdkpvasgtvdlsaegkaklslpvdwGrYrleVedees 101
                                     ++++ + +  +g+    ae   ++++p+  G+Y ++Ve+++ 
  gi|118431127|ref|NP_147369.2| 861 VKPSSVEITAPTGRSARVAEPGDSVRIPLPPGSYIIRVEAPGY 903
                                    55555555555666666666778899999**********9975 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.11
                           bMG6  72 tvdlsaegkaklslpvdwGrYrleVed 98 
                                    +v+++++++++ ++++  G Yr+eVe+
  gi|118431127|ref|NP_147369.2| 964 RVEVDTGEEGEAQVTLRSGVYRVEVEH 990
                                    567777778888888999*******97 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.3
                           bMG6   72 tvdlsaegkaklslpvdwGrYrleVedees 101 
                                     +v++++ ++++  + +  G Y+++V+++ +
  gi|118431127|ref|NP_147369.2| 1143 EVQTTD-SQGRAVFLLRPGVYEITVTHPYT 1171
                                     444544.56777778889********9977 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 3.3
                           bMG6   70 sgtvdlsaegkaklslpvdwGrYrleVed 98  
                                     ++t++++  g+a   +++ +G+Y le+e 
  gi|118431127|ref|NP_147369.2| 1231 QKTLQVEG-GTAL--VRLPFGSYTLEAEL 1256
                                     55555555.4444..45569*****9875 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 1.3
                           bMG6   73 vdlsaegkaklslpvdwGrYrleVedees 101 
                                     v++ a+++++  ++v  G+Y +e+++ +s
  gi|118431127|ref|NP_147369.2| 1334 VSVVADETGSAVASVRAGSYIIEAAAGSS 1362
                                     77888999999999*********988766 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 1.4
                           bMG6   79 gkaklslpvdwGrYrleVedeesgaat 105 
                                     +++ ++++  +G Y le+e+++   +t
  gi|118431127|ref|NP_147369.2| 1863 ASGVFTFQAPYGLYILEAEKPGYREST 1889
                                     5667889999*********99876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1950 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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):              11  [number of targets reported over threshold]
# CPU time: 1.02u 0.26s 00:00:01.28 Elapsed: 00:00:00.48
# Mc/sec: 12316.65
//
Query:       gi|118431128|ref|YP_874837.1|  [L=88]
Description: hypothetical protein APE_0620a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-11   43.2   0.1    4.8e-11   42.7   0.1    1.2  1  MazG       MazG nucleotide pyrophosphohydrolase domain
    6.7e-07   29.5   0.0    8.8e-07   29.1   0.0    1.1  1  MazG-like  MazG-like family
    5.6e-05   23.5   0.1    6.1e-05   23.4   0.1    1.1  1  PRA-PH     Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
       0.19   12.1   0.0        0.3   11.5   0.0    1.3  1  HHH_7      Helix-hairpin-helix motif


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 !   42.7   0.1   1.1e-14   4.8e-11       6      60 ..      26      76 ..      22      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.1e-14
                                   HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH CS
                           MazG  6 llaylleEvgEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvae 60
                                   +  +l+eEvgE+ ea++k+d+ +++eE++Dv+ + +++an+     g+d+e++++
  gi|118431128|ref|YP_874837.1| 26 TFSWLVEEVGELSEALRKGDKGSMAEEIADVIAWTISIANL----VGVDVEEALR 76
                                   5689************************************9....9999999986 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     2e-10   8.8e-07      15      62 ..      30      78 ..      27      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2e-10
                      MazG-like 15 llksveelfkallkgseeeildeLAdviiylylLAdrlGidfee.idek 62
                                   l+++v+el +al kg++ ++++e+Advi+ ++  A+ +G+d+ee ++ k
  gi|118431128|ref|YP_874837.1| 30 LVEEVGELSEALRKGDKGSMAEEIADVIAWTISIANLVGVDVEEaLRSK 78
                                   68899***************************************99877 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.4e-08   6.1e-05      28      76 ..      27      75 ..       7      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-08
                                   HHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHHHH CS
                         PRA-PH 28 aaligEEavElleaasegdlaeladelaDllYvtygllvllGidldavf 76
                                     +++EE+ El ea  +gd+  +a+e+aD++  t+  + l G+d ++ +
  gi|118431128|ref|YP_874837.1| 27 FSWLVEEVGELSEALRKGDKGSMAEEIADVIAWTISIANLVGVDVEEAL 75
                                   5789****************************************99866 PP

>> HHH_7  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.6e-05       0.3      28      48 ..      60      80 ..      48      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                                   HHHHHHHH-EEHHHHCT-HHH CS
                          HHH_7 28 lvdivnlvgvdvnkavankye 48
                                    + i+nlvgvdv++a+  ky 
  gi|118431128|ref|YP_874837.1| 60 TISIANLVGVDVEEALRSKYG 80
                                   5899***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 661.42
//
Query:       gi|118431129|ref|NP_147371.2|  [L=254]
Description: geranylgeranylglyceryl phosphate synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-52  176.1   0.0    9.1e-52  175.7   0.0    1.0  1  PcrB            PcrB family
    5.6e-06   26.0   0.1    1.4e-05   24.7   0.0    1.6  2  His_biosynth    Histidine biosynthesis protein
    0.00069   19.7   1.2       0.36   10.9   0.0    2.4  2  B12-binding     B12 binding domain
     0.0024   18.1   0.1        0.4   11.0   0.0    2.7  2  PucR            Purine catabolism regulatory protein-like fam
     0.0039   16.8   0.0     0.0079   15.8   0.0    1.4  1  DAGK_cat        Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.032   13.6   0.3      0.058   12.8   0.0    1.5  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.035   14.2   0.0      0.061   13.4   0.0    1.4  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
       0.11   11.7   1.3        5.3    6.2   0.1    2.2  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
       0.23   10.6   3.6       0.98    8.5   0.1    2.1  2  Glu_synthase    Conserved region in glutamate synthase


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 !  175.7   0.0   4.6e-55   9.1e-52       7     223 ..      20     248 ..      11     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 4.6e-55
                                    S.EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TTSSEEEEEE CS
                           PcrB   7 r.hltklDPeeenpdEiveiv...iesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvryaDalFvms 82 
                                    r h t++DP+++ p E+ ei+   +e g+Da+++gGs++vt ++t  ++k  +r +lP++l+p+  ++ +r+aDa+ + +
  gi|118431129|ref|NP_147371.2|  20 RlHFTLIDPDKTGPGEAGEIAaraAEAGSDAILVGGSIGVTFEETDGVVKAAKRSGLPVILFPGGHTNASRHADAVLFLT 99 
                                    37************9999998777899***************************************************** PP

                                    ETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT-SEEEEE- CS
                           PcrB  83 llnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllglrliYlEa 161
                                    ++ns n+++iv a+ lg+    kl   +e+++ +Y++v  +++++ v+ a+ ++ +k+++aa  +la  ++g r+iYlEa
  gi|118431129|ref|NP_147371.2| 100 VMNSDNPYYIVQAQILGAPLALKLG--LEAIPTSYIIVGYGGAAGFVARARpIPYEKPELAALHALAGAMMGGRIIYLEA 177
                                    *************************..***************************************************** PP

                                    .TTSSS-H..HHHHHHHHHHSSS......EEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHH CS
                           PcrB 162 .sGaledv..eevialkkkleka......rlivGGGirsaEkAkevvea.ADvivvGnvveekderkidail 223
                                     sGa+++v  e+v+a +k ++ a       l vGGG+r +E A+  +ea ADv+v+G++ ee++  k+  ++
  gi|118431129|ref|NP_147371.2| 178 gSGAPKPVppEAVAASRKLVDAAgyggevLLTVGGGVRTPEAARMLAEAgADVLVTGTLAEESP-GKLADVV 248
                                    ******99978888888888754333322689*******************************9.4444444 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.89   1.8e+03      45      81 ..      20      56 ..       8      64 .. 0.72
   2 !   24.7   0.0   7.1e-09   1.4e-05      74     121 ..     206     253 ..     188     254 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.89
                                   EEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS CS
                   His_biosynth 45 elhvvDldaakegreanldlveeiaeevfipvqvGGG 81
                                   +lh+  +d  k+g ++  ++ ++ ae+ +  + vGG 
  gi|118431129|ref|NP_147371.2| 20 RLHFTLIDPDKTGPGEAGEIAARAAEAGSDAILVGGS 56
                                   6777777777777777777777777777777777774 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 7.1e-09
                                    SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCG CS
                   His_biosynth  74 ipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfgs 121
                                    + ++vGGG+r+ e+++ l eagad ++ gt a ++p  + +++e+f s
  gi|118431129|ref|NP_147371.2| 206 VLLTVGGGVRTPEAARMLAEAGADVLVTGTLAEESPGKLADVVEAFKS 253
                                    679***************************************999986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00018      0.36      41      90 ..      37      86 ..      18     101 .. 0.86
   2 !    7.3   0.2    0.0023       4.6      70     112 ..     195     235 ..     187     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                    B12-binding 41 edivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGah 90
                                    +i+a++++   d++++   ++ ++e++  +v+++kr +  v+++ GG+ 
  gi|118431129|ref|NP_147371.2| 37 GEIAARAAEAGSDAILVGGSIGVTFEETDGVVKAAKRSGLPVILFPGGHT 86
                                   5899**********9999999***************************53 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0023
                    B12-binding  70 elvellkrirprvkvvvGGahpsldpeetleaklgiddvvvge 112
                                    +lv+ +++++ +v + vGG + +  ++++l++  g+d+ v g+
  gi|118431129|ref|NP_147371.2| 195 KLVD-AAGYGGEVLLTVGGGVRTPEAARMLAE-AGADVLVTGT 235
                                    3444.558888999999999999999999988.9988866664 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 !   11.0   0.0    0.0002       0.4      56     102 ..      33      83 ..      18      95 .. 0.81
   2 ?    4.2   0.1     0.025        50      41      83 ..     203     241 ..     195     254 .] 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                           PucR  56 pealaelvrelaeagvaaLviklg..r..eipeelieaadelglPlielpe 102
                                    p +  e+ ++ aeag  a+ ++       e  + +++aa++ glP+i +p 
  gi|118431129|ref|NP_147371.2|  33 PGEAGEIAARAAEAGSDAILVGGSigVtfEETDGVVKAAKRSGLPVILFPG 83 
                                    55666778899999999999998643245778****************997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                           PucR  41 ggeLllttglalkddpealaelvrelaeagvaaLviklg.reip 83 
                                    gge+llt g +++ +pea     r laeag+  Lv ++  +e p
  gi|118431129|ref|NP_147371.2| 203 GGEVLLTVGGGVR-TPEAA----RMLAEAGADVLVTGTLaEESP 241
                                    7888888888887.66544....445555555555544212333 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     4e-06    0.0079      17      95 ..       7      88 ..       3      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                                   HHHHHCHHHHHHCTCEEEEEE--..STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCT.HHCTTSEEEEEE-SS--H CS
                       DAGK_cat 17 kllrkvrelleeagveleliete..epgdakelakeakeegvdlivvaGGDGtvsevlnglle.elatkpplgiiPlGtgNd 95
                                   +ll+k+ e  +   ++++li+ +  +pg+a e+a++a+e+g d+i+v G  G+  e  +g+++ ++++ +p+ ++P+G +N+
  gi|118431129|ref|NP_147371.2|  7 RLLEKLLERRSRGRLHFTLIDPDktGPGEAGEIAARAAEAGSDAILVGGSIGVTFEETDGVVKaAKRSGLPVILFPGGHTNA 88
                                   45555555555556678888776568999**********************************999999*********9997 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 ?   -3.6   0.1       2.9   5.8e+03     181     195 ..      41      55 ..      38      57 .. 0.75
   2 ?   12.8   0.0   2.9e-05     0.058     153     195 ..     190     235 ..     184     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.9
                                    HHHHHHT--EEEESH CS
                 Ribul_P_3_epim 181 eqiaeagadvlVags 195
                                    +++aeag d++ +g 
  gi|118431129|ref|NP_147371.2|  41 ARAAEAGSDAILVGG 55 
                                    678899999988875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.9e-05
                                    HHHHHHHHHHHT..---EEEEESS--T.TTCHHHHHHT--EEEESH CS
                 Ribul_P_3_epim 153 ikkvrklideke..ldlkievDGGvkl.dnieqiaeagadvlVags 195
                                    + + rkl+d+ +   ++ + v GGv++ ++++ +aeagadvlV+g+
  gi|118431129|ref|NP_147371.2| 190 VAASRKLVDAAGygGEVLLTVGGGVRTpEAARMLAEAGADVLVTGT 235
                                    5566777777664468999******752778889**********97 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 ?   13.4   0.0   3.1e-05     0.061       3      33 ..     208     239 ..     206     254 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
                                    EEESB-HHHHHHHHHHHHTT-EEEEES-.TSS CS
                         DpaA_N   3 aviGGDaRqlylarkLaekgakvslygl.ele 33 
                                    + +GG  R  + ar+Lae ga+v + g   +e
  gi|118431129|ref|NP_147371.2| 208 LTVGGGVRTPEAARMLAEAGADVLVTGTlAEE 239
                                    679***********************994222 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 ?    4.5   0.2    0.0085        17     155     181 ..      36      62 ..      30      73 .. 0.79
   2 ?    6.2   0.1    0.0026       5.3     147     174 ..     208     235 ..     192     254 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0085
                                    SHHHHHHHHTT--SEEEE-HHHH-HHH CS
                           NanE 155 tPekakkaieiGvdavvvGsaitrlee 181
                                    + e a++a e G da+ vG++i    e
  gi|118431129|ref|NP_147371.2|  36 AGEIAARAAEAGSDAILVGGSIGVTFE 62 
                                    567899**************9976655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0026
                                    EEEES---SHHHHHHHHTT--SEEEE-H CS
                           NanE 147 viaeGrintPekakkaieiGvdavvvGs 174
                                    + + G + tPe a+   e G+d++v G+
  gi|118431129|ref|NP_147371.2| 208 LTVGGGVRTPEAARMLAEAGADVLVTGT 235
                                    5678999***************999986 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 ?    2.8   0.7     0.027        53     216     256 ..      36      79 ..      31      90 .. 0.78
   2 ?    8.5   0.1   0.00049      0.98     258     306 ..     189     237 ..     177     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.027
                                    HHHHHHHHHHTT-SEEEEE-TT---SSEEHHH...HHHB---HH CS
                   Glu_synthase 216 vetiaagvakanadiilidGleGGTGAspkss...ikhaGlPle 256
                                    ++ iaa +a+a+ d+il+ G+ G T    + +   +k +GlP++
  gi|118431129|ref|NP_147371.2|  36 AGEIAARAAEAGSDAILVGGSIGVTFEETDGVvkaAKRSGLPVI 79 
                                    5789999****************997655544011556788876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00049
                                    HHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHH CS
                   Glu_synthase 258 alaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaa 306
                                    a+a+  + + + g   +v l++ Gg++t++   + +  GAd + +gt a
  gi|118431129|ref|NP_147371.2| 189 AVAASRKLVDAAGYGGEVLLTVGGGVRTPEAARMLAEAGADVLVTGTLA 237
                                    788888999999*******************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 00:00:00.43
# Mc/sec: 1780.88
//
Query:       gi|118431130|ref|NP_147373.2|  [L=112]
Description: hypothetical protein APE_0623.1 [Aeropyrum pernix K1]
Scores for complete 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   63.8   0.3    1.4e-17   63.5   0.3    1.1  1  Elf1             Transcription elongation factor Elf1 like
     0.0088   15.4   2.8       0.82    9.2   0.0    2.5  3  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.057   13.4   0.5      0.057   13.4   0.5    2.2  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
      0.057   13.9   0.1      0.081   13.4   0.1    1.3  1  zf-CHY           CHY zinc finger
      0.094   13.1   1.1       0.19   12.1   1.1    1.9  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.53   10.3   4.5        2.1    8.4   3.4    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.2    8.7   9.7        1.8    8.1   0.0    2.6  3  TF_Zn_Ribbon     TFIIB zinc-binding
        1.3    8.6   0.0        1.3    8.6   0.0    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.8    8.9   7.7        1.5    9.2   2.3    2.3  2  Ribosomal_L32p   Ribosomal L32p protein family


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 !   63.5   0.3   6.9e-21   1.4e-17       1      77 [.       2      88 ..       2      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 6.9e-21
                           Elf1  1 gkRkkkakkrkkkkkkk.lptkFdCpfCnheksvevkldkkek..........iaevsCkvCgesfetkvnalsepvDvYsk 71
                                   g+R++k+++r+ +++++ ++++F+Cp+C++  +++++l++ ++          +a++ C++Cg+++e++v++  e+vDvY+ 
  gi|118431130|ref|NP_147373.2|  2 GRRRRKRMRRQVRTVPQvYKRYFTCPRCGSL-TLSITLTQAKDeegnvkagvkRAVAVCGNCGLRCEMEVPEGLEKVDVYNL 82
                                   899999999******999*************.99**999998889************************************* PP

                           Elf1 72 wiDace 77
                                   + Da+ 
  gi|118431130|ref|NP_147373.2| 83 VSDAYF 88
                                   ***986 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   0.0   0.00041      0.82       3      11 ..      24      32 ..      22      37 .. 0.78
   2 !    6.4   0.1     0.003       5.9      16      24 ..      56      64 ..      49      65 .. 0.78
   3 ?   -3.3   0.1       3.4   6.8e+03       8      10 ..      93      95 ..      93      96 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00041
                    zf-ribbon_3  3 vrCPnCGap 11
                                    +CP+CG++
  gi|118431130|ref|NP_147373.2| 24 FTCPRCGSL 32
                                   58*****95 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.003
                    zf-ribbon_3 16 dnvCpyCGt 24
                                   + vC +CG 
  gi|118431130|ref|NP_147373.2| 56 VAVCGNCGL 64
                                   679*****7 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.4
                    zf-ribbon_3  8 CGa 10
                                   CG+
  gi|118431130|ref|NP_147373.2| 93 CGE 95
                                   554 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.46   9.2e+02       7      13 ..      25      31 ..      24      32 .. 0.88
   2 ?   13.4   0.5   2.8e-05     0.057       3      24 ..      54      75 ..      52      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.46
                                   E-SSBTT CS
                 Molybdop_Fe4S4  7 aCpyCgv 13
                                   +Cp Cg+
  gi|118431130|ref|NP_147373.2| 25 TCPRCGS 31
                                   7****96 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.8e-05
                                   EEEEE-SSBTT--EEEEEEETT CS
                 Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhvkdg 24
                                    +  +C +Cg +C +ev +  +
  gi|118431130|ref|NP_147373.2| 54 RAVAVCGNCGLRCEMEVPEGLE 75
                                   56789***********977555 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.1e-05     0.081       8      62 ..      12      64 ..       7      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                         zf-CHY  8 vvairapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkk 62
                                   +v+   +  k++++C +C + + + +l++++ +e  ++    +++++ +C++C+ 
  gi|118431130|ref|NP_147373.2| 12 QVRTVPQVYKRYFTCPRCGSLTLSITLTQAKDEEGNVKA--GVKRAVAVCGNCGL 64
                                   4777778889*********86667777777666654433..34468999***976 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 ?   12.1   1.1   9.4e-05      0.19       5      36 ..      25      64 ..       5     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigq........cvyCadCga 36
                                    CP Cg+    ++ ++ + e g         +  C +Cg 
  gi|118431130|ref|NP_147373.2| 25 TCPRCGSLTLSITLTQAKDEEGNvkagvkraVAVCGNCGL 64
                                   5******9999999999988888999****9889999887 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 ?    8.4   3.4    0.0011       2.1      18      33 ..      23      39 ..      17      63 .. 0.70
   2 ?    0.3   0.9      0.36   7.1e+02      19      27 ..      57      65 ..      49      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                  Zn_Tnp_IS1595 18 gfvCPhCgsr.kayrik 33
                                    f+CP+Cgs   +++++
  gi|118431130|ref|NP_147373.2| 23 YFTCPRCGSLtLSITLT 39
                                   59******986555554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                  Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                    vC +Cg r
  gi|118431130|ref|NP_147373.2| 57 AVCGNCGLR 65
                                   689999965 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   0.0   0.00092       1.8       1       8 [.      24      31 ..      23      47 .. 0.73
   2 ?    6.7   0.8    0.0025       5.1      20      31 ..      57      68 ..      52      78 .. 0.75
   3 ?   -3.1   0.7         3   5.9e+03      25      28 ..      93      96 ..      92     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00092
                                   EEETTTTC CS
                   TF_Zn_Ribbon  1 ykCPnCgs 8 
                                   ++CP Cgs
  gi|118431130|ref|NP_147373.2| 24 FTCPRCGS 31
                                   46666666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0025
                                   EEESSSSBEEEE CS
                   TF_Zn_Ribbon 20 lvCtdCGlVled 31
                                    vC++CGl  e 
  gi|118431130|ref|NP_147373.2| 57 AVCGNCGLRCEM 68
                                   69*****97764 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3
                                   SSBE CS
                   TF_Zn_Ribbon 25 CGlV 28
                                   CG+V
  gi|118431130|ref|NP_147373.2| 93 CGEV 96
                                   9998 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   0.0   0.00067       1.3       2      10 ..      23      31 ..      22      38 .. 0.87
   2 ?   -0.9   1.4      0.63   1.3e+03       7      13 ..      65      71 ..      57      76 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00067
                         zf_UBZ  2 tylCerCgk 10
                                   +++C+rCg+
  gi|118431130|ref|NP_147373.2| 23 YFTCPRCGS 31
                                   69*****97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.63
                         zf_UBZ  7 rCgkeip 13
                                   rC  e+p
  gi|118431130|ref|NP_147373.2| 65 RCEMEVP 71
                                   4555555 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.3   0.00073       1.5       9      38 ..       4      35 ..       3      42 .. 0.73
   2 ?    2.6   0.3      0.08   1.6e+02      24      33 ..      53      63 ..      40      71 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00073
                                   HHHHHHHGGGT-----..-EEEETTTCCEECT CS
                 Ribosomal_L32p  9 ksrrrkRrahwklkap..nlvecpncgelklp 38
                                   + r+r+Rr+   +        +cp cg+l+l+
  gi|118431130|ref|NP_147373.2|  4 RRRKRMRRQVRTVPQVykRYFTCPRCGSLTLS 35
                                   5799999999643333334479*******997 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.08
                                   -.-EEEETTTC CS
                 Ribosomal_L32p 24 p.nlvecpncg 33
                                   + ++++c ncg
  gi|118431130|ref|NP_147373.2| 53 KrAVAVCGNCG 63
                                   33667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 771.78
//
Query:       gi|118431131|ref|NP_147374.2|  [L=416]
Description: S-adenosyl-L-homocysteine hydrolase [Aeropyrum pernix K1]
Scores for complete 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-72  243.1   0.0    2.2e-42  145.2   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    6.8e-59  198.5   0.8    1.3e-58  197.6   0.8    1.5  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.9e-12   45.9   0.4    7.7e-12   44.9   0.4    1.5  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      4e-09   36.3   0.4    6.8e-09   35.5   0.4    1.3  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    0.00056   20.2   0.1     0.0041   17.4   0.1    2.4  2  TrkA_N         TrkA-N domain
     0.0034   17.3   1.6      0.009   15.9   0.4    2.1  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.024   14.7   1.1       0.14   12.2   0.4    2.2  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.065   13.8   0.2       0.16   12.6   0.2    1.7  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.071   13.6   0.3       0.19   12.2   0.3    1.7  1  NAD_binding_7  Putative NAD(P)-binding
       0.36   10.1   5.0        1.2    8.4   5.0    1.8  1  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 !  145.2   0.0   1.2e-45   2.2e-42       2     141 ..       5     139 ..       4     146 .. 0.95
   2 !   97.1   0.0   5.8e-31     1e-27     176     285 ..     141     412 ..     137     414 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 1.2e-45
                                    -B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT--H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase   2 ykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstqd 81 
                                    +kv+d+sla  Gr +ie ae+ mp lm lr+ ++ +kpl g+r+a +lh+t +tavL+etL + Gaev  a  n  stqd
  gi|118431131|ref|NP_147374.2|   5 FKVRDLSLAGEGRMQIEWAERHMPVLMRLRSSMGGDKPLSGVRVAACLHVTKETAVLVETLRKWGAEVYLAPSNPLSTQD 84 
                                    89****************************************************************************** PP

                                    HHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase  82 eaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgvk 141
                                    e+aaa+aeag+ vfaw+g+t eey+w ++++      ++ep++++DdG Dl  l+h+ ++
  gi|118431131|ref|NP_147374.2|  85 EVAAALAEAGIGVFAWRGMTPEEYKWALSTVA-----GREPDIVIDDGADLHVLLHEEMR 139
                                    **************************998877.....458****************9665 PP

  == domain 2  score: 97.1 bits;  conditional E-value: 5.8e-31
                                    CHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                      AdoHcyase 176 llkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD................................... 220
                                    + +k+ G +eetttGv rL  l+++g+Ll p i vnd++tk  fD                                   
  gi|118431131|ref|NP_147374.2| 141 VGEKVWGGTEETTTGVIRLRALEREGRLLYPVIAVNDALTKFMFDnrygtgqstvdgvlratniliagktvvvagygwvg 220
                                    56789999************************************************************************ PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                      AdoHcyase 221 ................................................................................ 220
                                                                                                                    
  gi|118431131|ref|NP_147374.2| 221 rgiaarfrgmgakvvvtevdpvraleaamdgftvttmdeaaslgdvfitatgninvidarhmekmkdgailanaghfnve 300
                                    ******************************************************************************** PP

                                    ...............................................S-HHHHHHHHHHHHHHHHHHHHTTSSS-SSEEE CS
                                    ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 221 ...............................................hpsfvmsasftnqvlaqielfkkekkyekkvyv 253
                                                                                   hps vm++sf+nq+la +++  ++ + ek+v++
  gi|118431131|ref|NP_147374.2| 301 invaaleemsvskrrvrryldeyrlpdgrrlyligegrlvnlvaaegHPSEVMDMSFSNQALAVLKIAGERGRLEKRVHR 380
                                    **********************************************************************999******* PP

                                    --CHHHHHHHHHCCCCCT-------HHHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 254 lpkklDekvarlhleklgaklteltkeqaeyi 285
                                    + +  De varl+le++g+++++lt+eq  y+
  gi|118431131|ref|NP_147374.2| 381 VERIQDEMVARLKLETMGVRIDSLTEEQKLYL 412
                                    ****************************9998 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 !  197.6   0.8   7.4e-62   1.3e-58       1     161 [.     186     346 ..     186     347 .. 0.99

  Alignments for each domain:
  == domain 1  score: 197.6 bits;  conditional E-value: 7.4e-62
                                    HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-S CS
                  AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkad 80 
                                    n yg+ +s vdg+ rat++l+aGk++vvaGyG vG+G aa ++g+Ga+v+vtevdP+ al aam+Gf v+t++e+++ +d
  gi|118431131|ref|NP_147374.2| 186 NRYGTGQSTVDGVLRATNILIAGKTVVVAGYGWVGRGIAARFRGMGAKVVVTEVDPVRALEAAMDGFTVTTMDEAASLGD 265
                                    78****************************************************************************** PP

                                    EEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS CS
                  AdoHcyase_NAD  81 ivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgca 160
                                    +++t+tGn ++i + h++kmkd ai++n Ghf+ ei+vaale+++++k +v+  +d+++l+dg+++ l+ eGrl+nl +a
  gi|118431131|ref|NP_147374.2| 266 VFITATGNINVIDARHMEKMKDGAILANAGHFNVEINVAALEEMSVSKRRVRRYLDEYRLPDGRRLYLIGEGRLVNLVAA 345
                                    *****************************************************************************988 PP

                                    - CS
                  AdoHcyase_NAD 161 t 161
                                     
  gi|118431131|ref|NP_147374.2| 346 E 346
                                    6 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 !   44.9   0.4   4.3e-15   7.7e-12      33     129 ..     205     297 ..     183     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.3e-15
                                    -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHH CS
                   2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinae 112
                                     ++gktv + G+G +G+ +a r++++g+kv+++++ + +  e++  g+++++++e+ +  D+ + ++     + ++i+a+
  gi|118431131|ref|NP_147374.2| 205 LIAGKTVVVAGYGWVGRGIAARFRGMGAKVVVTEVDPVRALEAAMDGFTVTTMDEAASLGDVFITATG----NINVIDAR 280
                                    589*********************************9988899999***************9988765....99****** PP

                                    HHHCSTTTEEEEESS-G CS
                   2-Hacid_dh_C 113 elakmkkgailiNtaRG 129
                                    +++kmk+gail N++  
  gi|118431131|ref|NP_147374.2| 281 HMEKMKDGAILANAGHF 297
                                    *************9975 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 !   35.5   0.4   3.8e-12   6.8e-09       2     103 ..     206     303 ..     205     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.8e-12
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeei 81 
                                    + gk+++v GyG  G+  a  +r  g +vvv+  +  +   +A  +gf+v+t++ea++  dv ++ +    + +v++++ 
  gi|118431131|ref|NP_147374.2| 206 IAGKTVVVAGYGWVGRGIAARFRGMGAKVVVTEVDPVRA-LEAAMDGFTVTTMDEAASLGDVFITAT---GNINVIDARH 281
                                    789****************************99998855.567789***************987766...46789999** PP

                                    GGG--TT-EEEESSSHHHHTTS CS
                           IlvN  82 epnlkegkalafahGfnihfgl 103
                                    ++++k+g++la a  fn+  + 
  gi|118431131|ref|NP_147374.2| 282 MEKMKDGAILANAGHFNVEINV 303
                                    ******************9875 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   2.2e+03      36      62 ..     114     140 ..     109     174 .. 0.84
   2 !   17.4   0.1   2.3e-06    0.0041       1      48 [.     211     258 ..     211     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                    HHHHTTSEEEES-TTSHHHHHHTTGGG CS
                         TrkA_N  36 elreeglevvvgdatdeevLeeagiek 62 
                                    +++ ++ ++v+ d++d +vL + ++ +
  gi|118431131|ref|NP_147374.2| 114 TVAGREPDIVIDDGADLHVLLHEEMRS 140
                                    566777889999999999999988766 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.3e-06
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES- CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgd 48 
                                    ++++G+G vGr +a +++  g  +vvv + d+ r+ e++ +g++v   d
  gi|118431131|ref|NP_147374.2| 211 VVVAGYGWVGRGIAARFRGmGA-KVVVTEVDPVRALEAAMDGFTVTTMD 258
                                    79*****************666.6**************99999876655 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 !   15.9   0.4     5e-06     0.009       1      50 [.     210     261 ..     210     323 .. 0.82
   2 ?   -0.2   0.0      0.46   8.2e+02      15      71 ..     340     396 ..     333     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                                    EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-H.HHHHHHHHHHHH.HHHCCT CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdise.ealekalekiek.sleklv 50 
                                    +v v G G +G+giaa f   g +Vv++++++ +ale+a++  +  ++++++
  gi|118431131|ref|NP_147374.2| 210 TVVVAGYGWVGRGIAARFRGMGAKVVVTEVDPvRALEAAMDGFTVtTMDEAA 261
                                    5899**************************8735677777766653445555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.46
                                    HHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES CS
                        3HCDH_N  15 aavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisftt 71 
                                     +++a++g++  ++d+s +  + a  ki+ +  +l+++ +  e   ++++ar++ +t
  gi|118431131|ref|NP_147374.2| 340 VNLVAAEGHPSEVMDMSFSNQALAVLKIAGERGRLEKRVHRVERIQDEMVARLKLET 396
                                    567888899999999987777777777777777777776666777777777777655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   7.9e-05      0.14      10      99 ..     206     286 ..     199     312 .. 0.78
   2 ?    0.4   0.0      0.34   6.1e+02      12      44 ..     328     360 ..     322     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                                    .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-S CS
                   Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepi 89 
                                    +++k+v++ G G +++ +a  +   g+k vvv+   ++ +++l   ++g      +++ ++e+ +  dv i+at+  ++ 
  gi|118431131|ref|NP_147374.2| 206 IAGKTVVVAGYGWVGRGIAARFRGMGAK-VVVTE--VDPVRALEAAMDGF-----TVTTMDEAASLGDVFITATGNINV- 276
                                    5789***********************9.77776..55555666666555.....77888888899********98765. PP

                                    B-HHHHHCCH CS
                   Shikimate_DH  90 lekeeveeal 99 
                                    ++++++e+++
  gi|118431131|ref|NP_147374.2| 277 IDARHMEKMK 286
                                    5666666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                                    T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEES CS
                   Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNR 44 
                                    +++  liG G++ +lva   + ++v ++   N 
  gi|118431131|ref|NP_147374.2| 328 GRRLYLIGEGRLVNLVAAEGHPSEVMDMSFSNQ 360
                                    568899**********98877777777766665 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     9e-05      0.16       3      69 ..     212     271 ..     209     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                                    EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S CS
                  F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav 69 
                                     + G+G +g+++a ++   g    ++vv+ + +p +a e+a + g +vt+    eaa+  dv + a 
  gi|118431131|ref|NP_147374.2| 212 VVAGYGWVGRGIAARFRGMG---AKVVVT-EVDPVRALEAAMD-GFTVTT--MDEAASLGDVFITAT 271
                                    445*****************...****66.8888888777665.456666..788999999988775 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 ?   12.2   0.3    0.0001      0.19       5      90 ..     206     293 ..     203     322 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeelekdlegadlviaatdd.relneriaeaa 82 
                                    + gk+v+v+G G v+   + ++   gakv+v   +  ++le  ++ ++ +++++  +  d+ i+at + + + +r +e++
  gi|118431131|ref|NP_147374.2| 206 IAGKTVVVAGYGWVGRGIAARFRGMGAKVVVTEVDPVRALEAAMDgFTVTTMDEAASLGDVFITATGNiNVIDARHMEKM 285
                                    679****************************6666434444333322333333333334455666665233344455555 PP

                  NAD_binding_7  83 karrilvn 90 
                                    k+  il n
  gi|118431131|ref|NP_147374.2| 286 KDGAILAN 293
                                    65555555 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   5.0   0.00068       1.2      26      70 ..     206     250 ..     183     294 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00068
                                    B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT CS
                    AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqlesl 70 
                                    ++  +v+v G G +G   +a  +g+gakV+v++v+p r+ +    
  gi|118431131|ref|NP_147374.2| 206 IAGKTVVVAGYGWVGRGIAARFRGMGAKVVVTEVDPVRALEAAMD 250
                                    445579999**************************9876554432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3104.64
//
Query:       gi|118431132|ref|NP_147376.2|  [L=96]
Description: hypothetical protein APE_0628.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0047   16.9   2.0      0.012   15.6   2.0    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.022   13.9   0.1      0.029   13.6   0.1    1.1  1  NAD_kinase       ATP-NAD kinase
      0.037   13.5   0.4        2.5    7.7   0.0    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.042   14.4   1.2      0.072   13.6   1.2    1.3  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.091   13.2   1.5        0.4   11.1   1.5    1.9  1  Vps39_2          Vacuolar sorting protein 39 domain 2
        0.1   12.6   0.2         12    6.0   0.0    2.2  2  Gin              Inhibitor of sigma-G Gin
       0.12   12.2   5.4        1.4    8.9   0.3    3.3  3  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
       0.13   12.2   0.6         16    5.5   0.1    2.2  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.14   11.8   0.8        6.3    6.5   0.1    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.14   12.3   1.9       0.26   11.4   0.1    2.0  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        0.2   11.5   1.9        1.2    9.1   0.3    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.75    9.9   5.5        2.5    8.2   0.6    2.6  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain


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 !   15.6   2.0   7.8e-06     0.012      10      44 ..       6      49 ..       2      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.8e-06
                  Zn_Tnp_IS1595 10 LealrWpngfvCPhCgsrkayrikt.........rglfqCkeCr 44
                                   +e+lr ++ +vCP+C +  +y  +t          + + C +C+
  gi|118431132|ref|NP_147376.2|  6 FEDLRVNGSVVCPRCRIPMYYASETvkeggrhriTRFYVCPSCK 49
                                   6777888889**************9********99********8 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.9e-05     0.029     222     260 ..      37      77 ..      36      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                    TT---EEEEEESESSS-.---EEE-TT-EEEEEE-.SS--E CS
                     NAD_kinase 222 PgvlailivpicPhsls.srpiVvssssklrirva.srsea 260
                                    +++ ++ + p c ++l  +r++V++sss+++++va +r+++
  gi|118431132|ref|NP_147376.2|  37 HRITRFYVCPSCKLKLVdERIVVIPSSSTVEVEVAgDRKTI 77 
                                    7999*********99862689999**********9655544 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.022        33      17      25 ..      12      20 ..       6      24 .. 0.85
   2 ?    7.7   0.0    0.0016       2.5      20      37 ..      43      60 ..      40      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                                   TTCEEESSS CS
                   TF_Zn_Ribbon 17 rgelvCtdC 25
                                   +g +vC++C
  gi|118431132|ref|NP_147376.2| 12 NGSVVCPRC 20
                                   678888888 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                                   EEESSSSBEEEECCCCCC CS
                   TF_Zn_Ribbon 20 lvCtdCGlVlednsideg 37
                                   +vC++C l l d+ i+  
  gi|118431132|ref|NP_147376.2| 43 YVCPSCKLKLVDERIVVI 60
                                   899999999999988865 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 ?   13.6   1.2   4.8e-05     0.072       4      33 ..      13      49 ..      12      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                Zn_ribbon_recom  4 GllrCgeCGspmtrrkrk...gkr....hyYrCstyr 33
                                   G ++C +C  pm++ + +   g+r    + Y+C +++
  gi|118431132|ref|NP_147376.2| 13 GSVVCPRCRIPMYYASETvkeGGRhritRFYVCPSCK 49
                                   779***********6544446666678777***8875 PP

>> Vps39_2  Vacuolar sorting protein 39 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   0.00027       0.4      71     102 ..      35      66 ..       1      71 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                        Vps39_2  71 kkvvvteekvCavCkkrlgesvfvvyPngsvv 102
                                     + ++t+  vC+ Ck +l ++ +vv P +s v
  gi|118431132|ref|NP_147376.2|  35 GRHRITRFYVCPSCKLKLVDERIVVIPSSSTV 66 
                                    566899999******************99887 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.008        12      12      24 ..       9      21 ..       3      30 .. 0.85
   2 ?    5.0   0.1     0.016        23      13      29 ..      38      54 ..      28      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.008
                                   E-SSS--EEHHHH CS
                            Gin 12 iiilgkfICeeCe 24
                                   ++++g+ +C +C 
  gi|118431132|ref|NP_147376.2|  9 LRVNGSVVCPRCR 21
                                   789*********6 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.016
                                   -SSS--EEHHHHHHHHH CS
                            Gin 13 iilgkfICeeCekkivn 29
                                   +i   ++C +C  k+v 
  gi|118431132|ref|NP_147376.2| 38 RITRFYVCPSCKLKLVD 54
                                   577789******99985 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 ?    8.9   0.3   0.00093       1.4      13      27 ..       8      20 ..       5      22 .. 0.74
   2 ?    0.9   0.1      0.28   4.2e+02      11      20 ..      28      37 ..      27      38 .. 0.89
   3 ?    3.1   0.1      0.06        89      23      27 ..      44      48 ..      42      59 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00093
                                   EEECTTEEEEE-TTT CS
                   zf-FPG_IleRS 13 rvgqagrstyfCprC 27
                                   + ++  +++++CprC
  gi|118431132|ref|NP_147376.2|  8 DLRV--NGSVVCPRC 20
                                   5555..788999999 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.28
                                   BEEEECTTEE CS
                   zf-FPG_IleRS 11 iervgqagrs 20
                                    e+v+ +gr+
  gi|118431132|ref|NP_147376.2| 28 SETVKEGGRH 37
                                   589******8 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.06
                                   E-TTT CS
                   zf-FPG_IleRS 23 fCprC 27
                                   +Cp C
  gi|118431132|ref|NP_147376.2| 44 VCPSC 48
                                   56666 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 ?    5.5   0.1     0.011        16      21      29 ..      15      23 ..       8      28 .. 0.86
   2 ?    5.2   0.1     0.013        20       6      25 ..      44      62 ..      41      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                    Prok-RING_1 21 VvCpeCgtp 29
                                   VvCp C  p
  gi|118431132|ref|NP_147376.2| 15 VVCPRCRIP 23
                                   9*****876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                    Prok-RING_1  6 kCpvCgkelkeedDiVvCpe 25
                                    Cp C+ +l +e  iVv p 
  gi|118431132|ref|NP_147376.2| 44 VCPSCKLKLVDE-RIVVIPS 62
                                   599999999988.5777665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0042       6.3       2      12 ..      14      24 ..      13      28 .. 0.83
   2 ?    3.9   0.1     0.028        41       3      11 ..      43      51 ..      41      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0042
                         zf_UBZ  2 tylCerCgkei 12
                                   +++C+rC  ++
  gi|118431132|ref|NP_147376.2| 14 SVVCPRCRIPM 24
                                   689****8765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.028
                         zf_UBZ  3 ylCerCgke 11
                                   y+C+ C+ +
  gi|118431132|ref|NP_147376.2| 43 YVCPSCKLK 51
                                   9*****965 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 ?   11.4   0.1   0.00018      0.26      16      38 ..      14      36 ..       7      44 .. 0.84
   2 ?    0.1   0.4      0.57   8.6e+02      17      22 ..      43      48 ..      36      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                       zf-Mss51 16 dfeCpdCGiptycseehwedDye 38
                                   ++ Cp+C ip+y+  e  ++   
  gi|118431132|ref|NP_147376.2| 14 SVVCPRCRIPMYYASETVKEGGR 36
                                   568**********9999888766 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.57
                       zf-Mss51 17 feCpdC 22
                                   + Cp C
  gi|118431132|ref|NP_147376.2| 43 YVCPSC 48
                                   778888 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.17   2.5e+02       2       7 ..      16      21 ..      15      29 .. 0.77
   2 ?    9.1   0.3   0.00078       1.2      26      35 ..      40      49 ..      38      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.17
                        TFIIS_C  2 kCpkCg 7 
                                    Cp+C+
  gi|118431132|ref|NP_147376.2| 16 VCPRCR 21
                                   699997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00078
                        TFIIS_C 26 tvfykCtkCg 35
                                   t+fy+C +C+
  gi|118431132|ref|NP_147376.2| 40 TRFYVCPSCK 49
                                   9********8 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 ?    3.9   0.2      0.04        59      22      26 .]      16      20 ..      12      27 .. 0.80
   2 ?    8.2   0.6    0.0017       2.5      20      26 .]      42      48 ..      40      48 .. 0.92
   3 ?   -2.7   0.0       4.3   6.5e+03      10      17 ..      76      83 ..      75      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                         zf-ACC 22 VCPkC 26
                                   VCP C
  gi|118431132|ref|NP_147376.2| 16 VCPRC 20
                                   77777 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                         zf-ACC 20 lyVCPkC 26
                                   +yVCP+C
  gi|118431132|ref|NP_147376.2| 42 FYVCPSC 48
                                   8****** PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.3
                         zf-ACC 10 mlykkeLe 17
                                   ++y++ ++
  gi|118431132|ref|NP_147376.2| 76 TIYRQHVD 83
                                   69998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 759.12
//
Query:       gi|14600854|ref|NP_147378.1|  [L=206]
Description: hypothetical protein APE_0630 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0027   17.6  20.8     0.0088   15.9   9.4    2.0  2  VIT1           VIT family
  ------ inclusion threshold ------
      0.013   14.8   2.1      0.017   14.5   2.1    1.2  1  WBS28          Williams-Beuren syndrome chromosomal region 28
      0.034   14.0   0.1      0.071   13.0   0.1    1.5  1  COX14          Cytochrome oxidase c assembly
      0.071   12.9   0.7       0.22   11.3   0.0    2.0  2  Synaptobrevin  Synaptobrevin
        1.7    8.5   6.9        1.1    9.1   2.4    2.2  2  DUF2182        Predicted metal-binding integral membrane prot
          5    6.9   6.3        0.6    9.9   0.9    1.9  2  FA_desaturase  Fatty acid desaturase


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 !    8.8   3.0   0.00044       1.3       3      69 ..      28      94 ..      26     104 .. 0.69
   2 !   15.9   9.4   2.9e-06    0.0088     131     209 ..     110     192 ..      89     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00044
                          VIT1  3 davlGanDGLvspfalvaGlsaaslgssktvllaGlaellA.GaiSMgiGeYlsvkserdlekaerkr 69
                                   +v    DGL+  +++ +G  ++++ ++ +++l+ + + l+ G +S  +G Yls ++er  e +++++
  gi|14600854|ref|NP_147378.1| 28 MFVTNGFDGLLAAIGVNIGGFSGGA-DPVVMVLSIMGGSLSmGVLSGVVGVYLSERAERLKELSRLEK 94
                                  5777888*********999885554.55555555444333336666668*********9776665555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.9e-06
                          VIT1 131 lasplkaAlssalsfliGgliPllpylfve....svglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAa 207
                                   ++ pl  Al+s+++ + + li++lpy+ ++       +a+++s+a++l+    +G+  ++++g skl+s lr l++ ++A 
  gi|14600854|ref|NP_147378.1| 110 NIIPLYIALWSGVGVIAFPLISVLPYIAAAygmlAIEEAFAASLAIALALAGGLGLYLGVVSGESKLYSTLRGLMLAVGAI 190
                                   3568999********************99978777999999996666666666677777777**********999999998 PP

                          VIT1 208 aa 209
                                   ++
  gi|14600854|ref|NP_147378.1| 191 IL 192
                                   75 PP

>> WBS28  Williams-Beuren syndrome chromosomal region 28 protein homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.1   5.6e-06     0.017      68     149 ..     109     193 ..      86     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.6e-06
                         WBS28  68 vaacplgralraglaLlevPvwLvlrgprLvlaavlg..caralglalklgaweqlGLsvatw..tdlllsclhsLmLvaL 144
                                   +   pl  al++g+ ++  P++ vl     ++ ++l    a a +la+ l+    lGL+ +++  +  l+s+l++LmL++ 
  gi|14600854|ref|NP_147378.1| 109 ANIIPLYIALWSGVGVIAFPLISVLPYIAAAY-GMLAieEAFAASLAIALALAGGLGLYLGVVsgESKLYSTLRGLMLAVG 188
                                   46789***************988886544433.455512455566777788888889888776225789*********987 PP

                         WBS28 145 Lllll 149
                                    ++l+
  gi|14600854|ref|NP_147378.1| 189 AIILV 193
                                   66665 PP

>> COX14  Cytochrome oxidase c assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.4e-05     0.071      16      48 ..      56      88 ..      56      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                         COX14 16 ltVltLiGvTlyaggllvytvysygkynrkqka 48
                                  ++Vl+++G++l +g+l ++  + +  + ++ k+
  gi|14600854|ref|NP_147378.1| 56 VMVLSIMGGSLSMGVLSGVVGVYLSERAERLKE 88
                                  69****************988888888888777 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.3e-05      0.22      36      76 ..      79     119 ..      77     135 .. 0.76
   2 ?   -1.1   0.5      0.55   1.6e+03      71      86 ..     183     198 ..     178     201 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                   HCCCCHHHHHHHHHHHHHHHHHHHHHHHHTXXXXXXXXXXX CS
                 Synaptobrevin  36 LvdktenLqssaqqFkkqarklkrkmwwknmkliiililvv 76 
                                   L++++e+L++ ++  kk +r l+r  +wk   +i + i++ 
  gi|14600854|ref|NP_147378.1|  79 LSERAERLKELSRLEKKVSRSLRRSIYWKAANIIPLYIALW 119
                                   889**************************997665554433 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.55
                                   XXXXXXXXXXXXXXXX CS
                 Synaptobrevin  71 ililvvlililiiiiv 86 
                                   ++ +v +i+++ i+ +
  gi|14600854|ref|NP_147378.1| 183 LMLAVGAIILVHIFKF 198
                                   4455555555555544 PP

>> DUF2182  Predicted metal-binding integral membrane protein (DUF2182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.067     2e+02     123     168 ..      40      85 ..      23      97 .. 0.83
   2 ?    9.1   2.4   0.00037       1.1      36      88 ..     107     161 ..      88     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.067
                       DUF2182 123 rlGlrhGlyClgcCwalmlllfvvGvmnllwmallalvvllEkllp 168
                                    +G++ G +  g+   +m+l +++G  ++ ++  +  v l E++ +
  gi|14600854|ref|NP_147378.1|  40 AIGVNIGGFSGGADPVVMVLSIMGGSLSMGVLSGVVGVYLSERAER 85 
                                   5788888888888889999******999999999999999998755 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00037
                       DUF2182  36 alvlfvagYllvWlafglvatllqlllealallspllasasslla..glvlllag 88 
                                   + + ++  Y++ W  +g++a+ l  +l  +a++  +la +++++a  +++l+lag
  gi|14600854|ref|NP_147378.1| 107 KAANIIPLYIALWSGVGVIAFPLISVLPYIAAAYGMLAIEEAFAAslAIALALAG 161
                                   56667778************************99999966666550145555555 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.9    0.0002       0.6     109     177 ..      77     143 ..      55     154 .. 0.73
   2 ?   -0.5   0.8       0.3     9e+02     138     179 ..     150     195 ..     143     201 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0002
                 FA_desaturase 109 llalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllflla 177
                                   ++    +++l+ l r ++++ ++ r+ +++ ++ +++ +++lw ++++ ++++  + ++p+++++  + 
  gi|14600854|ref|NP_147378.1|  77 VYLSERAERLKELSRLEKKVSRSLRRSIYWKAANIIPLYIALWSGVGVIAFPL--ISVLPYIAAAYGML 143
                                   33444455888888888889999999999999999999*********999999..66666666655444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                 FA_desaturase 138 lawlllllawlglwlalllllglall....lwlvplllllfllalv 179
                                    a l+++la++g+++++l++ +        l +++l++++++l+ +
  gi|14600854|ref|NP_147378.1| 150 AASLAIALALAGGLGLYLGVVSGESKlystLRGLMLAVGAIILVHI 195
                                   4444444444444444444333322244465555566666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 1732.84
//
Query:       gi|118431133|ref|NP_147379.2|  [L=419]
Description: succinyl-diaminopimelate desuccinylase [Aeropyrum pernix K1]
Scores for complete 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-38  131.3   0.2    6.1e-38  130.6   0.2    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.6e-19   69.1   0.0    5.2e-19   68.2   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.2   6.8e-42   6.1e-38       2     204 ..      92     407 ..      91     409 .. 0.90

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 6.8e-42
                                    EEEES-BSSTTCGGGSSS..TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SS.EEEEEEESTTSSTT.TH CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xx RF
                  Peptidase_M20   2 lgsHlDvVpeeetdgwtt..pfslteedGklyGrGaddmkggvlaalealralkdegikpkg.tivllfqpdEEggr.gG 77 
                                    +++H+DvVp +   gw+   pf++ ++dGklyGrGa dmkgg++aal a++al+ +g  p+g  ++ +f+pdEE+g+  G
  gi|118431133|ref|NP_147379.2|  92 FNGHYDVVP-GGP-GWSVtePFKPVVKDGKLYGRGAIDMKGGIAAALGAFKALHLSGAWPQGlRVEAAFVPDEEIGGeCG 169
                                    89*******.666.7*999*******************************************************8777** PP

                                    HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE.......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                  Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv.......................................... 115
                                    +++l++g+  +  +++   +++ ep++le+       +                                          
  gi|118431133|ref|NP_147379.2| 170 TGYLVNGM--GVTPEY---VVLPEPSGLEKPW----HGhrgilwmkvrvkgrtahastpwhgrnafllasaialdlqqal 240
                                    ******54..344566...55899****9555....22455578888888****************************** PP

                                    ..............................................................................EE CS
                                    ..............................................................................xx RF
                  Peptidase_M20 116 ..............................................................................kv 117
                                                                                                                  +v
  gi|118431133|ref|NP_147379.2| 241 asmyagrrsrhriepeesakptvslggeagvtgggktnqvpgefyftvdrrlipeetvsqardellgvltwlsvkhgaEV 320
                                    ***************************************************************************87557 PP

                                    EEEEEEEESHEEECCHHHHHHHHHHHHHHHTSC.EEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 118 evelleggapvtlndsplvkalaeaaeelfgek.velivsgpggtdarff..agiptvmifgpgsglaHspnEyvdledl 194
                                    e e++ +++p+  + ++l++al+eaa++  g++  e++v++ gg d+ ++  +g   ++ +gp ++laH+p+E++dl +l
  gi|118431133|ref|NP_147379.2| 321 EAEEVISAEPAINEPGELYEALREAASQS-GRSiGEPVVCP-GGLDMWYYtvKGS-KALAYGPRGELAHAPDEHIDLGEL 397
                                    777556666555559*************7.*9977777***.********76666.6678**888*************** PP

                                    HHHHHHHHHH CS
                                    xxxxxxxxxx RF
                  Peptidase_M20 195 ekgikvlarl 204
                                    +  ++++arl
  gi|118431133|ref|NP_147379.2| 398 RFLVETFARL 407
                                    ******9997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   5.8e-23   5.2e-19       2     101 ..     198     309 ..     197     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 5.8e-23
                                    EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC..............TCCTCCCCCEECCE-C...CC CS
                      M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.........eerslprttlnvtgiegGs...ak 69 
                                    gh+G++++k++vkg+ +H++ p +g+NA+ +++ +  +l++   +           e++ ++++t++++g  g +   ++
  gi|118431133|ref|NP_147379.2| 198 GHRGILWMKVRVKGRTAHASTPWHGRNAFLLASAIALDLQQALASMYagrrsrhriEPEESAKPTVSLGGEAGVTgggKT 277
                                    9*****************************************99999*******999999999**9998743333666** PP

                                    CEESSEEEEEEEEEHHHHHHHHHHHHHHHHHH CS
                      M20_dimer  70 nvipdeaeakidiRllpgedpeevleeieeil 101
                                    n +p+e+++++d+Rl p+e++ ++++e+  +l
  gi|118431133|ref|NP_147379.2| 278 NQVPGEFYFTVDRRLIPEETVSQARDELLGVL 309
                                    *************************9997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.34
# Mc/sec: 3644.77
//
Query:       gi|14600857|ref|NP_147381.1|  [L=250]
Description: metal dependent hydrolase [Aeropyrum pernix K1]
Scores for complete 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   51.5   0.4    1.4e-13   51.3   0.4    1.2  1  Lactamase_B     Metallo-beta-lactamase superfamily
    1.2e-13   51.0   0.0    1.8e-13   50.4   0.0    1.2  1  Lactamase_B_2   Beta-lactamase superfamily domain
     0.0036   17.2   0.0     0.0049   16.8   0.0    1.4  1  Lactamase_B_3   Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.07   13.4   0.3       0.16   12.2   0.2    1.6  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
      0.081   13.4   0.1       0.37   11.3   0.1    2.2  1  RuvA_C          RuvA, C-terminal 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 !   51.3   0.4     4e-17   1.4e-13       4     162 ..      19     176 ..      16     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 4e-17
                                   CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                   Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                   ++++s l++  g ++L+D+ +++++a++a     lg++p+ + av++TH+H+DH+ glg l     +  g   + +  +  
  gi|14600857|ref|NP_147381.1|  19 RMQSSLLLDYMGVTVLVDASCGAANALEA-----LGYPPESIGAVVVTHGHYDHVCGLGLLSFIKSFRGGPPLKLHSPPAA 94 
                                   6788999999999***************9.....7********************************************** PP

                                   HHHHHHHHHCCHH...TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE.TTCCEEEECTTTSSHHCCCCC CS
                   Lactamase_B  85 eeaddaasrkgll...lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey.gggkvlftGDallagetgrid 161
                                   e++ ++ +  gl+   + gv        + +++g++g +r  +    ++  ++++ +++ g g +l++GD+ +++e +   
  gi|14600857|ref|NP_147381.1|  95 EGVVRSVVEAGLRssaRGGVGYSILPLRPGGEAGFGGVVRVRGLRADHTVEALSLEIGLaGLGFILVSGDTRPTEELEARA 175
                                   ***9999999999*98666666666677777778888888888888888888888888879999*******9999887766 PP

                                   C CS
                   Lactamase_B 162 l 162
                                   +
  gi|14600857|ref|NP_147381.1| 176 P 176
                                   6 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 !   50.4   0.0   5.1e-17   1.8e-13       3     197 ..      33     219 ..      32     222 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.1e-17
                                   EEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHH..GGGGCCCC.C--EE.EEEEEEHHHHH....HCCTTC CS
                 Lactamase_B_2   3 iLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHl..aglltlre.lrpkk.lplyapkgvla....vleanf 74 
                                   +L+Da+ + +   l al  P      +++i aV++th+HyDH+   gll++ + +r+   l+l+ p+        v+ea++
  gi|14600857|ref|NP_147381.1|  33 VLVDASCGAANA-LEALgYP------PESIGAVVVTHGHYDHVcgLGLLSFIKsFRGGPpLKLHSPPAAEGvvrsVVEAGL 106
                                   8*******7666.8887566......669**************44445555557655547888777555551111555555 PP

                                   GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTEEEEEESS-S---HHHHHHH CS
                 Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrie.gggkrvyyigDtgyipeeigerl 154
                                      a++   + ++ +l +g++  +g+  ++++   a h+ +          l+l i+  g   ++ +gDt  ++ e+++r 
  gi|14600857|ref|NP_147381.1| 107 RSSARGGV-GYSILPLRPGGEAGFGG-VVRVRGLRADHTVEA---------LSLEIGlAGLGFILVSGDTRPTE-ELEARA 175
                                   55555555.9**************94.578888887777777.........******55556688999**9888.455566 PP

                                   CT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEE CS
                 Lactamase_B_2 155 ggadllllditayeddemir.hmgHltpeeaveaaadlgakrlv 197
                                     a  +++++t+ +    ++   gH+t++eav +a + g++ l+
  gi|14600857|ref|NP_147381.1| 176 PRALATVHEATLPSGMAEKAaATGHSTVGEAVGVASKSGIGLLY 219
                                   6666666666654443322359***********99998887665 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 !   16.8   0.0   1.4e-06    0.0049       8      51 ..      22      69 ..      20     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                 Lactamase_B_3  8 nsflletagarilvDPf....kanlgyeppaeeaDlvlisqaledHah 51
                                  +s+ll+  g+++lvD      +a   +++p+e++ +v++++++ dH  
  gi|14600857|ref|NP_147381.1| 22 SSLLLDYMGVTVLVDAScgaaNALEALGYPPESIGAVVVTHGHYDHVC 69
                                  899************9877653356788999***************75 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 ?   12.2   0.2   4.6e-05      0.16      85     128 ..     152     194 ..     139     205 .. 0.74
   2 ?   -1.5   0.0      0.77   2.8e+03      73     109 ..     199     235 ..     192     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                baeRF_family10  85 eergverlvlgGdeeetaalldrlpkalrarvvgtlplpvdasa 128
                                      g+  ++++Gd++ t++l++r p+al+ +  +tlp ++ a++
  gi|14600857|ref|NP_147381.1| 152 GLAGLGFILVSGDTRPTEELEARAPRALATVHEATLPSGM-AEK 194
                                   5567899**********************77766666666.333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.77
                baeRF_family10  73 lkevAellaklleergverlvlgGdeeetaalldrlp 109
                                    + ++  ++ +++++g+  l    +e e++al++ + 
  gi|14600857|ref|NP_147381.1| 199 GHSTVGEAVGVASKSGIGLLYHLTPESEEEALRASRG 235
                                   5667888899999999999999999999999988765 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.37       6      24 ..      41      59 ..      41      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                                  HHHHHHHCTS-HHHHHHHH CS
                        RuvA_C  6 aveALlaLGYkekeaekAv 24
                                  a +AL+aLGY+++ +  +v
  gi|14600857|ref|NP_147381.1| 41 AANALEALGYPPESIGAVV 59
                                  679*********9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2233.57
//
Query:       gi|118431134|ref|NP_147382.2|  [L=130]
Description: S-adenosylmethionine decarboxylase proenzyme [Aeropyrum pernix K1]
Scores for 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-33  113.4   0.0    6.3e-33  113.2   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.0   3.5e-37   6.3e-33       1     105 [.      22     127 ..      22     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 3.5e-37
                                    EEEEEEES-.-HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST CS
                      AdoMet_dc   1 hllvdlygc.dpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftcge 79 
                                    h++ ++y+c + ell+++e+le+++ eaa++ g+tvl+++++k+  eGvsvv++i eSh+++Htwpe+++a++Dv++cg 
  gi|118431134|ref|NP_147382.2|  22 HVYGNFYECaNTELLKSPEELEKVVLEAAREGGMTVLDIKSWKIG-EGVSVVAIILESHITVHTWPEYRFATVDVYSCGG 100
                                    999******89999******************************9.9********************************* PP

                                    .HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                      AdoMet_dc  80 .ispekaleylieafkadrvtvdelkR 105
                                     ++p++a+e+l+ea+k+ rv+  +++R
  gi|118431134|ref|NP_147382.2| 101 hTNPHRAFEVLAEALKPARVEKGVAER 127
                                    ********************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 00:00:00.39
# Mc/sec: 996.90
//
Query:       gi|14600859|ref|NP_147383.1|  [L=257]
Description: hypothetical protein APE_0640 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 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:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2117.55
//
Query:       gi|14600860|ref|NP_147384.1|  [L=349]
Description: thioredoxin [Aeropyrum pernix K1]
Scores for complete 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    2.4e-06   27.5   0.0    1.5  1  Thioredoxin    Thioredoxin
     0.0033   17.8   0.5      0.031   14.7   0.5    2.3  1  Thioredoxin_2  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   2.6e-10   2.4e-06       4      93 ..     242     335 ..     239     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.6e-10
                                   ESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.......TSEEEEEETTTSHHHHHHTT-SSSSEEE CS
                   Thioredoxin   4 vltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkd.......kvklakvdvdenedlakkyevegiPtlk 77 
                                    +t e+F++ ++    + ++  y++ C+hC +  P+l ++++e+            + + +  + +   +k +veg Ptl+
  gi|14600860|ref|NP_147384.1| 242 YITPEEFRQLLQG---DAILAVYSKTCPHCHRDWPQLIQASKEVDVpivmfiwGSLIGERELSAARLEMNKAGVEGTPTLV 319
                                   6788999998887...889999**********************99655544444566788889999999*********** PP

                                   EEETTEEEEEEESS-H CS
                   Thioredoxin  78 lfkngkevkkyegare 93 
                                   ++k+g+ v+k++ga +
  gi|14600860|ref|NP_147384.1| 320 FYKEGRIVDKLVGATP 335
                                   *************976 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5   3.5e-06     0.031      12     101 ..     260     335 ..     252     337 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-06
                 Thioredoxin_2  12 ftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldgke 91 
                                   +++ +Cp C++   +l +  ++v v      +   ++++  ++ +++e +       + +  ++k gv+gtPt+vf+ + +
  gi|14600860|ref|NP_147384.1| 260 VYSKTCPHCHRDWPQLIQAsKEVDVP-----I---VMFIWGSLIGERELS-------AARLEMNKAGVEGTPTLVFYKEGR 325
                                   55666666666333333332333222.....3...444444444444443.......223346778*******99887777 PP

                 Thioredoxin_2  92 ivarlpGyvp 101
                                   iv++l+G++p
  gi|14600860|ref|NP_147384.1| 326 IVDKLVGATP 335
                                   *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2480.48
//
Query:       gi|118431135|ref|NP_147386.2|  [L=327]
Description: hypothetical protein APE_0644.1 [Aeropyrum pernix K1]
Scores for complete 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   49.9   0.0    1.4e-12   48.3   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
      6e-05   23.1   0.0    0.00011   22.3   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
     0.0008   19.7   0.0     0.0016   18.7   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.3e-16   1.4e-12       3     108 ..      18     125 ..      16     179 .. 0.94
   2 ?   -1.7   0.0      0.57   3.4e+03     123     141 ..     205     223 ..     192     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.3e-16
                                    EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCTEE CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpgir 79 
                                    vt  C   C +C++++   +r+  ++ +++v +++e v e+  + g+ +  l+gg+pl+  + + +++r+ k +  +g++
  gi|118431135|ref|NP_147386.2|  18 VTGLCDDSCFYCPVSRAklGRDVFYVNEVPVASVEEAVAEV-LRTGASGASLTGGDPLVALHRTLDVARALKSElGRGFH 96 
                                    6788*************************************.8************************************* PP

                                    EEEEECSSCHGHHHHHHHHHTT-SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslg 108
                                    i++ t+g + ++e++++l e+gvd v ++
  gi|118431135|ref|NP_147386.2|  97 IHLYTSGRRMTPEVARALWEAGVDEVRIH 125
                                    ************************99875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.57
                                    CTSHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 123 rghtfeevlealeklreag 141
                                     ++ +e+vl++le ++e+ 
  gi|118431135|ref|NP_147386.2| 205 VRGALEAVLRVLEWAAENS 223
                                    5678899999999999974 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 !   22.3   0.0   1.9e-08   0.00011       2      92 ..      17     106 ..      16     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.9e-08
                        Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilk..dlkkseikiqglvltGGePLhyenkkellklvkrlkeey. 78 
                                    fv ++ C  sC  C  +   k      +++e+ ++ ++   ++  +  ++g +ltGG+PL     +  l++ + lk e  
  gi|118431135|ref|NP_147386.2|  17 FV-TGLCDDSCFYCPVSR-AKLGRDVFYVNEVPVASVEeaVAEVLRTGASGASLTGGDPL--VALHRTLDVARALKSELg 92 
                                    77.899999999999544.233333333333333333322234456667899********..77**************98 PP

                        Fer4_14  79 pekkiwletngtle 92 
                                    + ++i+l+t+g  +
  gi|118431135|ref|NP_147386.2|  93 RGFHIHLYTSGRRM 106
                                    89********9866 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 !   18.7   0.0   2.7e-07    0.0016       4      84 ..      10      92 ..       8     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                        Fer4_12  4 eGvrlslfvsg.CnlsCkgCfnketw...sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevke 81
                                   +G  +++fv+g C+ sC +C    ++   ++ + +e++ +  ee+++++  +  +g +l+GG+Pl+       l++++ +k+
  gi|118431135|ref|NP_147386.2| 10 PGRKAVVFVTGlCDDSCFYCPVSRAKlgrDVFYVNEVPVASVEEAVAEVLRTGASGASLTGGDPLV--ALHRTLDVARALKS 89
                                   566789998877********988888666888999999999999999999****************..77888888888888 PP

                        Fer4_12 82 ekp 84
                                   e  
  gi|118431135|ref|NP_147386.2| 90 ELG 92
                                   776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2360.50
//
Query:       gi|118431136|ref|NP_147388.2|  [L=145]
Description: hypothetical protein APE_0648.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.22   11.1   0.0    1.4  1  DAGK_cat  Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic 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      0.22      51      77 ..     103     129 ..      92     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                                    HHHCC-SEEEEEESHHHHHHHHHHHCT CS
                       DAGK_cat  51 akeegvdlivvaGGDGtvsevlnglle 77 
                                    a ++g+d++vv GG G v+evl+ l +
  gi|118431136|ref|NP_147388.2| 103 AHRHGFDVVVVNGGPGEVREVLEMLSK 129
                                    456789******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.39
# Mc/sec: 1110.48
//
Query:       gi|118431137|ref|NP_147390.2|  [L=820]
Description: phosphoenolpyruvate synthase [Aeropyrum pernix K1]
Scores for complete 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-109  366.7   0.0   1.6e-109  366.2   0.0    1.2  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    6.5e-85  284.8   0.0    9.8e-85  284.2   0.0    1.3  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.6e-29  101.4   0.9    4.8e-29   99.9   0.9    1.9  2  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.2   0.0  2.6e-113  1.6e-109       2     326 ..      18     366 ..      17     368 .. 0.95

  Alignments for each domain:
  == domain 1  score: 366.2 bits;  conditional E-value: 2.6e-113
                         PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelke.ldvddvdelrkaskeirelilsaelPee 80 
                                    +lvGGK+a+L+e+++ agipvPpgf++t++a+r+f+ e+g++  i+++l+e +     +e++kas+ ir+ ++++++P+ 
  gi|118431137|ref|NP_147390.2|  18 PLVGGKAAGLGEMIK-AGIPVPPGFVVTSEAYRRFVFETGIAGFIKHILEEtIVSGRPEEYEKASELIRSKFVRTPMPPY 96 
                                    69***********55.**********************************94455689********************** PP

                         PPDK_N  81 leeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgl 160
                                    l++ai +ay++lg+ +g ee +vaVRSSat EDlp+asfaGqq+tyLnv+geeev+e++k  +aSl+++rA++Yr + ++
  gi|118431137|ref|NP_147390.2|  97 LRRAIVDAYRKLGTLVGVEEPRVAVRSSATVEDLPEASFAGQQETYLNVKGEEEVVEKVKTAWASLWTARALSYRDSLNI 176
                                    ******************************************************************************** PP

                         PPDK_N 161 dheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekkigekeik 240
                                    dhe   +avvvqkmv+s+  +sGV+f+++p tG++d+++i++ +GlGe +V+G+vtpd+fvv+ks+ +ile +i++k+++
  gi|118431137|ref|NP_147390.2| 177 DHETALMAVVVQKMVSSR--SSGVMFTIHPVTGEEDKIVIESIWGLGEYIVGGKVTPDRFVVSKSDLEILEVRISRKDKA 254
                                    ******************..************************************************************ PP

                         PPDK_N 241 ivydekeegtkevevpeeerekl.......................aLsdeeveeLaeiakkiekhygtpmdiEfaid.. 295
                                    + yd++ ++++e+++pe+ +e                         +Ls++ev+eLa++a k+e+h+ +pmdiE+aid  
  gi|118431137|ref|NP_147390.2| 255 LFYDPDLNENVEIKIPESGEELEdlrrkhpavaevvekygirpdapSLSEKEVKELARLAIKVENHFARPMDIEWAIDfe 334
                                    *******999999999955554477888899999999999999999*********************************9 PP

                         PPDK_N 296 .eeegklyllQaRpetrtsekkekkaaetlee 326
                                     +  ++++llQaRpet++s+kke+++a+  ee
  gi|118431137|ref|NP_147390.2| 335 lSPPENILLLQARPETVWSRKKEEAEAKPPEE 366
                                    999******************99988876655 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.2   0.0   1.6e-88   9.8e-85       6     293 ..     498     802 ..     493     803 .. 0.94

  Alignments for each domain:
  == domain 1  score: 284.2 bits;  conditional E-value: 1.6e-88
                                    SCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTS.CC.HHHHHH..........HHHHHHHHHH CS
                PEP-utilizers_C   6 klktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmar.ee.lpteee..........qaeaykkvle 73 
                                    ++ ++l+ +++++++k+++N+++pe+++++++ ++eGiGL+R+Ef++ ++  + + +++e          +ae  +kv++
  gi|118431137|ref|NP_147390.2| 498 AVAEVLSEVYPVTATKIYMNLGHPEEIDRYKHLPFEGIGLMRIEFIISSWiGYhPMYLIEqgrgvyfidkLAEGVAKVAS 577
                                    5667888999****************************************85557788888******************* PP

                                    HTTTSEEEEEXXXSSCC..GGSGGC..HHHH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCC...CCEEEEEESS CS
                PEP-utilizers_C  74 amngrpvvvRtlDiggd..kelpel..keepeevNPmlGfRgirlglse..pelfetqlrAllrasa...agkleimlPm 144
                                    a+++rpvvvR+ D++++  + l+ +   e++ e+NPm+G+Rg++++++   +  f+ ++rA++++++     ++++m+P+
  gi|118431137|ref|NP_147390.2| 578 AIYPRPVVVRFSDFKTNeyRRLKGGekYETLDERNPMIGWRGVSRYIHPnyEPAFRLEVRAIKKVREewgLKNVWVMFPF 657
                                    ****************98899*9984446788***************97679***************65555******** PP

                                    XXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHCHHH CS
                PEP-utilizers_C 145 vasveeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdneevak 224
                                    v++++ele+a ki+ee+       g+++ +++kv+iM+Evps ++lad++ak vd+fSiG+NDLtQ++l+vdRd+  +ak
  gi|118431137|ref|NP_147390.2| 658 VRTTWELERALKIMEEE-------GLSRGRDFKVWIMVEVPSTVFLADEFAKMVDGFSIGSNDLTQLVLGVDRDSGFLAK 730
                                    ***************99.......89999*************************************************** PP

                                    H..SXTTTCHHCCCHHHHHHHHHHCCXEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                PEP-utilizers_C 225 l..ydplepavlrlikevikaaeekglkvgiCGelag.dpsavellvglGldelSmsaasvpaaraalaqve 293
                                    +  +d+ +pavlr i+ +i++a+++g++v+iCG+ ++ +p+ ve+lv+ G+d++S+++++v ++r+++a++e
  gi|118431137|ref|NP_147390.2| 731 MgyFDERDPAVLRSIEILIEKAHSQGATVSICGQGPSvYPELVEFLVRRGIDSISVNPDAVVRVRRQVASIE 802
                                    **9*********************************99******************************9986 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 ?   -3.8   0.0       1.9   1.1e+04       7      26 ..       6      26 ..       3      27 .. 0.84
   2 !   99.9   0.9     8e-33   4.8e-29       2      73 .]     403     474 ..     402     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.9
                                   EEEES---HHHHTTS-.GEEE CS
                  PEP-utilizers  7 ILvaeetspsdiagld.kaaG 26
                                   IL  +e+s++ ++ +  kaaG
  gi|118431137|ref|NP_147390.2|  6 ILWLDEISKDLLPLVGgKAAG 26
                                   999999**9999988888887 PP

  == domain 2  score: 99.9 bits;  conditional E-value: 8e-33
                                    --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                  PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                    +e+g++Lv+++t+p++++ ++ a++ivt++GGmt HaAivArelgiPaVvg+g+at++lk+g l+tvDgs+G
  gi|118431137|ref|NP_147390.2| 403 MEKGDVLVTKMTDPDWVPYMKMASAIVTDEGGMTAHAAIVARELGIPAVVGTGDATKKLKDGMLVTVDGSRG 474
                                    789*******************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (820 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 5977.72
//
Query:       gi|118431138|ref|NP_147391.2|  [L=59]
Description: preprotein translocase subunit SecG [Aeropyrum pernix K1]
Scores for complete 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   50.3   1.0    1.9e-13   50.2   1.0    1.1  1  Sec61_beta     Sec61beta family
  ------ inclusion threshold ------
      0.047   13.0   0.0      0.053   12.8   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 !   50.2   1.0   2.2e-17   1.9e-13       1      40 [.      15      54 ..      15      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 2.2e-17
                                   XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                     Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                   ++aGLl +yee + +iki+P++V+++++++ a+V ++hi+
  gi|118431138|ref|NP_147391.2| 15 TAAGLLSFYEEYEGKIKISPTIVVGAAILVSAVVAAAHIF 54
                                   69*************************************8 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 ?   12.8   0.0   5.9e-06     0.053      12      53 ..       8      49 ..       2      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.9e-06
                                   --SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHH CS
                  THF_DHG_CYH_C 12 eeallpctpkgvvellketgielegkkvvvvGrsnivgkpla 53
                                   e+  +p t++g +++ +e++ +++    +vvG+  +v   +a
  gi|118431138|ref|NP_147391.2|  8 ERRATPVTAAGLLSFYEEYEGKIKISPTIVVGAAILVSAVVA 49
                                   67889******************************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 506.59
//
Query:       gi|118431139|ref|NP_147392.2|  [L=348]
Description: hypothetical protein APE_0654.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2629.70
//
Query:       gi|118431140|ref|NP_147394.2|  [L=456]
Description: hypothetical protein APE_0656.1 [Aeropyrum pernix K1]
Scores for complete 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-31  108.6   0.0      3e-31  107.9   0.0    1.4  1  DUF1743          Domain of unknown function (DUF1743)
    0.00014   21.4   7.9    0.00026   20.6   7.9    1.5  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
    0.00023   21.0   0.7    0.00041   20.2   0.7    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0043   17.0   0.8     0.0087   16.1   0.8    1.4  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.051   13.6   0.0    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.084   12.9   0.0       0.16   12.0   0.0    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.095   12.0   2.7       0.18   11.2   2.7    1.5  1  zf-TFIIB         Transcription factor zinc-finger
       0.17   11.5   1.3        5.7    6.6   0.0    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.32   10.8   3.0        8.9    6.2   0.1    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.59    9.6   2.8         18    4.9   0.3    2.4  2  zf-ribbon_3      zinc-ribbon domain
        0.7    9.8   4.5        2.8    7.9   0.2    2.4  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
        0.7    9.9   6.7        3.2    7.8   0.8    2.4  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.2    8.9   4.8        8.4    6.2   0.3    2.4  2  zf-CCHC_5        GAG-polyprotein viral zinc-finger
        2.3    8.2   5.6        5.3    7.0   5.6    1.6  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        4.8    7.4   5.8         17    5.7   0.4    2.2  2  Zn-ribbon_8      Zinc ribbon domain
        8.1    6.4   6.5        7.6    6.5   1.1    2.3  2  zf-HIT           HIT zinc finger


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 !  107.9   0.0   2.7e-34     3e-31       1     115 [.     141     253 ..     141     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 2.7e-34
                                    TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEE CS
                        DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGi 79 
                                    grgiiGA+a+l+a  + ed+t+El+aYr+pe+wg  r+vd e  +++++   p tf+n+D+++++v+ +P +pdpvl G+
  gi|118431140|ref|NP_147394.2| 141 GRGIIGAAASLAALGPAEDYTWELVAYRRPEAWGaARCVDWEAAVKVESTLPPCTFNNIDMAEGRVAAAPAGPDPVLAGF 220
                                    89**************99************************************************************** PP

                                    EES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-T CS
                        DUF1743  80 rgedpeallkaakeilskeeeseemavfrtnqgtda 115
                                    rg+ p+ l ++ +++++   e + ++++r+nq+tda
  gi|118431140|ref|NP_147394.2| 221 RGDCPHLLPRYSEALCE---EPHFWVLYRSNQHTDA 253
                                    **************999...4466**********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 !   20.6   7.9   2.3e-07   0.00026       2      29 ..     354     381 ..     353     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.3e-07
                  zf-NADH-PPase   2 thrFCgrCGaptepaeggwarvCpaCgl 29 
                                     ++ C+rCGa++e a  g++ +Cp Cg+
  gi|118431140|ref|NP_147394.2| 354 HSPLCPRCGARMESAGRGRGYRCPRCGY 381
                                    5678***********************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 !   20.2   0.7   3.6e-07   0.00041      28      54 ..     355     381 ..     344     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.6e-07
                 OrfB_Zn_ribbon  28 SktCseCgsknkealsgrtfkCpnCgf 54 
                                    S  C++Cg++++ a  gr ++Cp+Cg+
  gi|118431140|ref|NP_147394.2| 355 SPLCPRCGARMESAGRGRGYRCPRCGY 381
                                    778***********************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.8   7.8e-06    0.0087      11      38 ..     354     383 ..     350     387 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.8e-06
                            DZR  11 darfCseCgtklkavaa..edrCpsCgekv 38 
                                    ++  C++Cg++++++ +   +rCp+Cg++ 
  gi|118431140|ref|NP_147394.2| 354 HSPLCPRCGARMESAGRgrGYRCPRCGYAS 383
                                    5668********9877799********975 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 ?   13.6   0.0   4.6e-05     0.051       1      71 [.     267     340 ..     267     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEEC.TTSSEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrr.pggelelkve 71 
                                    Vtv+++v  + ++  g+++ +    g+g+  +v+ r  +   ++a  l +Gd v++ G v+ + p+g  ++ v+
  gi|118431140|ref|NP_147394.2| 267 VTVEAEVLGTPQTLPGGHVVVRASTGEGEADLVFYReaSPLNRVARLLAPGDSVEAMGSVRPYrPRGLWTVAVD 340
                                    899999999998999**********************************************9976665555555 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   0.00014      0.16      66      96 ..     351     383 ..     323     388 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                    EE--EEEETTTS-EEECHHH..HHS-TTTSSS- CS
                           HypA  66 evpvkvrCreCgkefeleek..alrCpkCgsad 96 
                                     ++ +  C +Cg+++e++ +   +rCp+Cg a+
  gi|118431140|ref|NP_147394.2| 351 YERHSPLCPRCGARMESAGRgrGYRCPRCGYAS 383
                                    5566678*********88855689*****9775 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.7   0.00016      0.18       2      26 ..     358     380 ..     357     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                       zf-TFIIB   2 CPkCqdeleeserggveidyCpqCr 26 
                                    CP+C++ +e + rg    ++Cp+C+
  gi|118431140|ref|NP_147394.2| 358 CPRCGARMESAGRGR--GYRCPRCG 380
                                    *************76..7******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 ?    6.6   0.0    0.0051       5.7       4      15 ..     357     368 ..     355     371 .. 0.86
   2 ?    3.5   0.2     0.048        54       3       9 ..     374     380 ..     372     383 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0051
                         zf_UBZ   4 lCerCgkeipes 15 
                                    lC+rCg++++++
  gi|118431140|ref|NP_147394.2| 357 LCPRCGARMESA 368
                                    6*******9875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.048
                         zf_UBZ   3 ylCerCg 9  
                                    y C+rCg
  gi|118431140|ref|NP_147394.2| 374 YRCPRCG 380
                                    99****8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0079       8.9      14      21 ..     356     363 ..     352     365 .. 0.74
   2 ?    4.3   0.5     0.031        34       2       7 ..     376     381 ..     375     383 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0079
                  zinc_ribbon_2  14 kFCpyCGt 21 
                                    + Cp+CG+
  gi|118431140|ref|NP_147394.2| 356 PLCPRCGA 363
                                    56888887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.031
                  zinc_ribbon_2   2 CpnCGa 7  
                                    Cp+CG+
  gi|118431140|ref|NP_147394.2| 376 CPRCGY 381
                                    666764 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.023        26      19      24 ..     358     363 ..     355     366 .. 0.62
   2 ?    4.9   0.3     0.016        18       3       9 ..     374     380 ..     372     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.023
                    zf-ribbon_3  19 CpyCGt 24 
                                    Cp CG+
  gi|118431140|ref|NP_147394.2| 358 CPRCGA 363
                                    555554 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.016
                    zf-ribbon_3   3 vrCPnCG 9  
                                    +rCP+CG
  gi|118431140|ref|NP_147394.2| 374 YRCPRCG 380
                                    79****9 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 ?    7.9   0.2    0.0025       2.8      18      27 ..     352     361 ..     350     370 .. 0.85
   2 ?    3.0   0.5     0.083        93       3       8 ..     375     380 ..     373     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0025
                                    TEEEEE-TTT CS
                   zf-FPG_IleRS  18 grstyfCprC 27 
                                    +r++ +CprC
  gi|118431140|ref|NP_147394.2| 352 ERHSPLCPRC 361
                                    6888999999 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.083
                                    B-TTT- CS
                   zf-FPG_IleRS   3 pCpRCw 8  
                                    +CpRC+
  gi|118431140|ref|NP_147394.2| 375 RCPRCG 380
                                    699997 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   6.3    0.0056       6.3      19      45 ..     356     381 ..     350     382 .. 0.74
   2 ?    7.8   0.8    0.0028       3.2      18      34 ..     373     391 ..     366     403 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0056
                  Zn_Tnp_IS1595  19 fvCPhCgsr..kayriktrglfqCkeCrk 45 
                                    + CP+Cg r  +a r    + ++C +C++
  gi|118431140|ref|NP_147394.2| 356 PLCPRCGARmeSAGRG---RGYRCPRCGY 381
                                    78*****885444444...55******97 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0028
                  Zn_Tnp_IS1595  18 gfvCPhCgsr..kayrikt 34 
                                    g +CP+Cg++  +a+ ++t
  gi|118431140|ref|NP_147394.2| 373 GYRCPRCGYAsrEARPLET 391
                                    678*****99888887777 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 ?    6.2   0.3    0.0075       8.4       4      11 ..     357     364 ..     354     367 .. 0.84
   2 ?    4.1   0.6     0.034        38       4       9 ..     375     380 ..     372     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0075
                                    B-TTT-SS CS
                      zf-CCHC_5   4 lCpRCkkg 11 
                                    lCpRC+ +
  gi|118431140|ref|NP_147394.2| 357 LCPRCGAR 364
                                    9****966 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.034
                                    B-TTT- CS
                      zf-CCHC_5   4 lCpRCk 9  
                                    +CpRC+
  gi|118431140|ref|NP_147394.2| 375 RCPRCG 380
                                    8****8 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 ?    7.0   5.6    0.0047       5.3       7      31 ..     358     380 ..     357     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0047
                 Zn_ribbon_SprT   7 CtgCgreythhlsirrhn.YrCrrCk 31 
                                    C++Cg    +  s  r + YrC+rC+
  gi|118431140|ref|NP_147394.2| 358 CPRCG---ARMESAGRGRgYRCPRCG 380
                                    *****...99999999999******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 ?    5.7   0.4     0.015        17      24      36 ..     353     365 ..     344     368 .. 0.72
   2 ?    3.1   0.8      0.09     1e+02       6      13 ..     374     381 ..     373     391 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                    Zn-ribbon_8  24 apltaCPeCgsev 36 
                                    +  + CP+Cg+++
  gi|118431140|ref|NP_147394.2| 353 RHSPLCPRCGARM 365
                                    44566****9976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.09
                    Zn-ribbon_8   6 YrCeeCgh 13 
                                    YrC +Cg 
  gi|118431140|ref|NP_147394.2| 374 YRCPRCGY 381
                                    78888885 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.13   1.4e+02      16      22 ..     358     364 ..     357     365 .. 0.91
   2 ?    6.5   1.1    0.0068       7.6      14      20 ..     374     380 ..     371     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                                    -TTT--E CS
                         zf-HIT  16 CpkCntr 22 
                                    Cp+C++r
  gi|118431140|ref|NP_147394.2| 358 CPRCGAR 364
                                    *****98 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0068
                                    EE-TTT- CS
                         zf-HIT  14 YkCpkCn 20 
                                    Y+Cp+C+
  gi|118431140|ref|NP_147394.2| 374 YRCPRCG 380
                                    ******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3522.06
//
Query:       gi|118431141|ref|YP_874838.1|  [L=83]
Description: hypothetical protein APE_0656a [Aeropyrum pernix K1]
Scores for 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-13   48.3   0.4    8.4e-13   48.1   0.4    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.013   15.6   0.5      0.019   15.0   0.5    1.2  1  NapD            NapD protein
      0.058   13.5   0.0      0.073   13.2   0.0    1.1  1  DUF1896         Domain of unknown function (DUF1896)


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 !   48.1   0.4   1.4e-16   8.4e-13       1      73 [.       6      75 ..       6      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.4e-16
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                 AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                   v ++++ g+    +e+  +l e+peV+e+++v G y +++ v ++ +++l++ +  k+++++gv+ t t+++ 
  gi|118431141|ref|YP_874838.1|  6 VAINVNVGK---EDEVFNKLLEMPEVKEVFMVYGIYEIIALVEAPTMDQLRETITGKIRKVDGVKMTLTMVIV 75
                                   567888888...99********************************************************986 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   3.1e-06     0.019       8      65 ..       8      67 ..       6      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-06
                           NapD  8 Vqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtiea.iealpgVl 65
                                   ++++ ++ ++v ++l ++p+v Ev  + +   ++  +Ea++ d+l +ti+  i++++gV 
  gi|118431141|ref|YP_874838.1|  8 INVNVGKEDEVFNKLLEMPEVkEVFMVYGIYEIIALVEAPTMDQLRETITGkIRKVDGVK 67
                                   67888999************9899999999*******************965******94 PP

>> DUF1896  Domain of unknown function (DUF1896)
   #    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      91     134 ..      14      61 ..       6      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHT-..HHHHHTTS---TT..GGGSTHHHHHHHHHHHHHH CS
                        DUF1896  91 kreelalkllpe..vkevFkkydlsdd..FaespeydkLyteltgtiv 134
                                    k+ e+  kll+   vkevF  y + +     e p  d+L++++tg+i+
  gi|118431141|ref|YP_874838.1|  14 KEDEVFNKLLEMpeVKEVFMVYGIYEIiaLVEAPTMDQLRETITGKIR 61 
                                    56667777876555************8557899*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 705.02
//
Query:       gi|118431142|ref|NP_147397.2|  [L=113]
Description: hypothetical protein APE_0661.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 983.71
//
Query:       gi|118431143|ref|NP_147398.2|  [L=435]
Description: histidyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for 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-51  173.8   0.0    6.3e-51  173.5   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    4.8e-14   52.3   0.0    1.1e-13   51.1   0.0    1.7  1  HGTP_anticodon  Anticodon binding domain
      1e-06   28.8   0.0    1.4e-05   25.1   0.0    2.4  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
        0.1   11.6   0.2       0.34   10.0   0.0    1.9  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
       0.13   11.7   0.0       0.39   10.2   0.0    1.7  1  tRNA-synt_2d    tRNA synthetases class II core domain (F)
       0.19   12.1   0.1       0.49   10.8   0.1    1.7  1  PPR             PPR repeat
       0.26   10.4   0.0       0.35   10.0   0.0    1.1  1  Nuc_sug_transp  Nucleotide-sugar transporter


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 !  173.5   0.0   2.5e-54   6.3e-51       1     310 []      11     323 ..      11     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 2.5e-54
                                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH..HS-EEE-T.TSSEEEE-SSSHHHHHH CS
                  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld..qtfklvDq.sgrllglRaDiTpqvaR 77 
                                    g+rd+ pe +  +++l +rl ++fes+G+++  +P +Ey ++l  + ge+++   ++++ D  sgr  +lR D+T+  aR
  gi|118431143|ref|NP_147398.2|  11 GFRDFPPEVMILRKRLLSRLERVFESYGFDPLDTPAVEYWETLSGKYGEEAEsrLIWRFQDPwSGRWYALRYDLTVPLAR 90 
                                    89*********************************************98876547******77***************** PP

                                    HHHHHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHH CS
                  tRNA-synt_His  78 iaahrlnrerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglv 157
                                    ++a +   + p + + +G+v+r ++ + gr re++Q+ a ++G+  +ead+E++sl++++++ a+g++++r+ +++ +l+
  gi|118431143|ref|NP_147398.2|  91 FVASNPGLPMPFKRYHIGKVWRHEEPQKGRYREFVQCDADIVGSPYPEADAEIVSLAVDSID-ALGLPGFRVRVNDRRLL 169
                                    *************************************************************7.***************** PP

                                    HHHHH.HTT--HHH.HHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC.....HCCHCCCHHHHCHCCHCTHHHHHHHHH CS
                  tRNA-synt_His 158 ralle.aaglsesl.eeallaalarkdlaelkelaaeaglkealrellkal..elygdaevleealealaaapalqaald 233
                                      ++e ++g+++ l   +  + l++  ++++++ +++ gl+ +++e +  +   ++ + evle  ++ + +++++++ald
  gi|118431143|ref|NP_147398.2| 170 AGVFEeELGFDNPLpIYRAIDKLDKIGVEGVRRELERLGLPGSTVERIMEIisWRGRPGEVLESVRRGYGSNEKVREALD 249
                                    ****868888776424555556666667777777778899999999998888555556688888999999999******* PP

                                    HHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-S.S-SEEEEEECTTTGGG.T---EEEEEEEEHHHH CS
                  tRNA-synt_His 234 eleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvg.qaiarGGrYdelgaaf.grarpAtGfsldleal 310
                                    +lee+ +l+++      rv lD++++rg++YytG + +++ ++ +   +a+GGrYd+l+++f gr  pAtG s+ +e++
  gi|118431143|ref|NP_147398.2| 250 HLEEMLSLADD-----KRVELDMSLVRGLDYYTGPILEVVLDEPRiGSVAGGGRYDGLVGMFaGRDIPATGVSIGIERI 323
                                    **********8.....49***********************986647****************************9986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   4.5e-17   1.1e-13       1      92 [.     342     430 ..     342     432 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 4.5e-17
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    qv+v++l +   ++  ya + a+ Lr+ g++v +d s  s + + r+a +lgip+  +vG+ke+e g +t+ + +++e++
  gi|118431143|ref|NP_147398.2| 342 QVAVVVLDR---RYYRYAWEAARILRRGGLNVRIDLSRASGQVQRRKASRLGIPVLAFVGAKEAEGGFLTLYSAAKGERV 418
                                    8********...9***************************************************99************** PP

                                    EEETTHHHHHHH CS
                 HGTP_anticodon  81 rvsldelveklk 92 
                                     v+l e+v++++
  gi|118431143|ref|NP_147398.2| 419 AVPLGEAVKAVE 430
                                    *********997 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 !   25.1   0.0   5.6e-09   1.4e-05      35     101 ..     100     161 ..      76     182 .. 0.87
   2 ?    1.2   0.0      0.13   3.2e+02      88     125 ..     201     238 ..     186     385 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.6e-09
                                    SSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  35 LPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglefrai 101
                                    +P+k y+i+ ++R+E++ ++G  R+reF q d+ +++++   ++ +++++ ++ +   +lgl+ + +
  gi|118431143|ref|NP_147398.2| 100 MPFKRYHIGKVWRHEEP-QKG--RYREFVQCDADIVGSPY--PEADAEIVSLAVDSIDALGLPGFRV 161
                                    79***************.***..**************998..8899999999888888888876655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.13
                                    HHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  88 sriferlglefraiielmsaksadykdkkefeavsesl 125
                                     r +erlgl+   ++++m+++s  + + +++e v    
  gi|118431143|ref|NP_147398.2| 201 RRELERLGLPGSTVERIMEIISWRGRPGEVLESVRRGY 238
                                    56678888888888888888886666666666665542 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 ?   10.0   0.0   0.00013      0.34      93     122 ..     103     131 ..      14     151 .. 0.66
   2 ?   -3.0   0.1       1.2     3e+03     282     295 ..     311     324 ..     299     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                                    EEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                                    + + i++++R E+ ++ r   EF+q++a +
  gi|118431143|ref|NP_147398.2| 103 KRYHIGKVWRHEEPQKGRYR-EFVQCDADI 131
                                    679****************9.******976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                    -SEEEEEEEHHHHH CS
                                    xxxxxxxxxxxxxx RF
                    tRNA-synt_2 282 pphgGlglGldRlv 295
                                     p  G+ +G++R++
  gi|118431143|ref|NP_147398.2| 311 IPATGVSIGIERII 324
                                    6899********86 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 ?   10.2   0.0   0.00015      0.39      23     133 ..      27     133 ..      20     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHHTTS-... CS
                   tRNA-synt_2d  23 leeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtlekkk... 99 
                                    l++++++f ++gf  ++ p v  e++     +  ++   R ++    +++p +   + + LR   t   +r ++++    
  gi|118431143|ref|NP_147398.2|  27 LSRLERVFESYGFDPLDTPAV--EYWETLSGKYGEEAESRLIW---RFQDPWS--GRWYALRYDLTVPLARFVASNPglp 99 
                                    566666666666666666666..45544444444444444443...2344445..6678899999999999994443344 PP

                                    SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEE CS
                   tRNA-synt_2d 100 ppikiisigrvfRrdavDathlaeFhqveglvvd 133
                                    +p+k   ig+v+R+++  + +  eF q++  +v+
  gi|118431143|ref|NP_147398.2| 100 MPFKRYHIGKVWRHEEPQKGRYREFVQCDADIVG 133
                                    99**************************987776 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00019      0.49       8      28 ..     236     256 ..     236     257 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                            PPR   8 sgycknGkleeAlelfkeMke 28 
                                    +gy++n k++eAl+ ++eM++
  gi|118431143|ref|NP_147398.2| 236 RGYGSNEKVREALDHLEEMLS 256
                                    69*****************86 PP

>> Nuc_sug_transp  Nucleotide-sugar transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00014      0.35     115     170 ..     332     387 ..     318     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00014
                 Nuc_sug_transp 115 tyqlkilttalfsvllLkrklskkqWlslllLvaGvalvqlkqkeseesekaaaaa 170
                                     y l + t a ++v++L+r+  ++ W +  +L  G   v ++ ++++ + ++++a+
  gi|118431143|ref|NP_147398.2| 332 VYSLDVKTVAQVAVVVLDRRYYRYAWEAARILRRGGLNVRIDLSRASGQVQRRKAS 387
                                    699*******************************9999999888887776665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3283.20
//
Query:       gi|14600874|ref|NP_147399.1|  [L=116]
Description: hypothetical protein APE_0663 [Aeropyrum pernix K1]
Scores for complete 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   24.3   0.1    3.4e-05   23.4   0.1    1.5  1  SWIM      SWIM zinc finger
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.056   13.5   0.0    1.8  2  Fn3-like  Fibronectin type III-like domain


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 !   23.4   0.1   3.8e-09   3.4e-05       1      38 [.      34      77 ..      34      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.8e-09
                          SWIM  1 yrVtldder..vrlnkatCsCpefqk....ngipCkHalAvlla 38
                                  ++V+l+++r    ++  +CsCp++      +g+ CkH+ +++ a
  gi|14600874|ref|NP_147399.1| 34 VWVYLGESRdyILVEGLYCSCPSMAGslvkGGWGCKHLRGLKAA 77
                                  578889888*99*************************9988765 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.28   2.5e+03      27      38 ..      24      35 ..      13      43 .. 0.73
   2 ?   13.5   0.0   6.3e-06     0.056      24      50 ..      83     109 ..      81     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.28
                                  EEE-TT-EEEEE CS
                      Fn3-like 27 veLapGesktvt 38
                                  v+L+pG  + v 
  gi|14600874|ref|NP_147399.1| 24 VRLEPGGGQGVW 35
                                  568888777664 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.3e-06
                                   EEEEEE-TT-EEEEEEEEECGGG-EEE CS
                      Fn3-like  24 FekveLapGesktvtftldrkdlsvwd 50 
                                   F++v+++pGe ++v +++ ++ l+v  
  gi|14600874|ref|NP_147399.1|  83 FRRVSVEPGEVRQVVLEVYSTGLAVTV 109
                                   ******************999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 00:00:00.40
# Mc/sec: 860.34
//
Query:       gi|14600875|ref|NP_147400.1|  [L=237]
Description: ribose 5-phosphate isomerase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-44  150.1   0.0    5.5e-44  149.8   0.0    1.0  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois


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 !  149.8   0.0   3.1e-48   5.5e-44       2     169 ..      53     220 ..      52     223 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 3.1e-48
                                   EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEET.TS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTT. CS
                Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevde.dlnliKGgGgallrEKivaaaakkfiviadesKlveklg. 80 
                                   +vp+S++t+ +++ lg ++ +   +  +++++DGaDe ++ +  ++KGgGgall EKi+ + +k  i+i+ e +lv +lg 
  gi|14600875|ref|NP_147400.1|  53 AVPSSFETAVELAGLGWSVGDPRVYRGVNVYVDGADEAEPgRGYMVKGGGGALLGEKILSSRSKLNIFIVGEDRLVGRLGe 133
                                   8***************************************999*************************************7 PP

                                   SS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE-S CS
                Rib_5-P_isom_A  81 kfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlFlg 161
                                   k pvPveV p  ++ v+ +le+l g++p++R++ gk gpvv+d g +i+D+   +++edp+ le+ l+++pGV etGlFlg
  gi|14600875|ref|NP_147400.1| 134 KTPVPVEVEPGFVSMVLASLEEL-GLNPRVRTSPGKRGPVVSDWGGVIVDLLT-GPLEDPRGLESMLRNVPGVRETGLFLG 212
                                   7********************75.***************************99.6788*********************** PP

                                   --SEEEEE CS
                Rib_5-P_isom_A 162 ladkvlvg 169
                                   lad ++vg
  gi|14600875|ref|NP_147400.1| 213 LADYIVVG 220
                                   ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1801.91
//
Query:       gi|14600877|ref|NP_147402.1|  [L=395]
Description: DNA primase large subunit [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3106.15
//
Query:       gi|118431144|ref|NP_147403.2|  [L=224]
Description: transcriptional activator TenA-like protein [Aeropyrum pernix K1]
Scores for 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-63  211.8   0.4    1.1e-62  211.6   0.4    1.0  1  TENA_THI-4  TENA/THI-4/PQQC family


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.6   0.4   5.9e-67   1.1e-62       4     209 ..      15     218 ..      12     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 5.9e-67
                                    CHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHHHHH CS
                     TENA_THI-4   4 lrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhlrla 83 
                                    ++++   + +HpFvkal++G+lp ++f++y++qdy+yl+  vr+l+i++sks+++ev r+  s++   +++e+++++rl 
  gi|118431144|ref|NP_147403.2|  15 MDLWSL-LPSHPFVKALYSGSLPLDKFRFYAVQDYNYLVGLVRSLSIAASKSWSFEVARLALSHASFLASTEMANYERLL 93 
                                    555555.999********************************************************************** PP

                                    HHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHHHCSHHH CS
                     TENA_THI-4  84 ealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvkeyaseef 163
                                     +lGls++e+++++p p+++ayv+++++++++g+ +e++++llpc+++y+eia     +lr+++ + y++w++ y+s+e+
  gi|118431144|ref|NP_147403.2|  94 GELGLSLSEVLREEPAPTNEAYVNFMIATCSTGTALECMVSLLPCYWSYREIAIANERLLRENSVDLYRRWASVYLSSEY 173
                                    *****************************************************555559********************* PP

                                    HHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                     TENA_THI-4 164 raaveeakrllerllakvsdeqleelqeiflkalefetsfltmald 209
                                    ++avee++r+++rl+a+ ++ ++++l++if ka+++e++f++ma++
  gi|118431144|ref|NP_147403.2| 174 GEAVEEYRRAVDRLWAE-EGGVYSRLKRIFRKATRYEYMFWDMAWR 218
                                    *****************.9999**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1815.15
//
Query:       gi|14600879|ref|NP_147404.1|  [L=383]
Description: MFS transporter [Aeropyrum pernix K1]
Scores for 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-26   92.2  57.2    1.8e-19   69.9  32.7    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.26   11.8   3.4         12    6.5   0.0    3.1  3  RuvA_C    RuvA, C-terminal domain
       0.95    9.8   2.3        2.4    8.5   0.4    2.5  2  DUF3930   Protein of unknown function (DUF3930)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9  32.7     3e-23   1.8e-19       9     267 ..      20     259 ..      12     263 .. 0.85
   2 !   30.5  25.1   2.9e-11   1.7e-07       9     173 ..     214     376 ..     205     383 .] 0.83

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3e-23
                         MFS_1   9 alarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa..sslwl 87 
                                   +++ + +g++lp +  ++lg+  + i l++t y+++  +a++++G lsd   rr+ ++l+  + +++++  +++   + +l
  gi|14600879|ref|NP_147404.1|  20 FYNVGSIGFWLP-LHVRELGWPYTYITLIATWYFVAVTLATPLVGLLSDLT-RRPGYILAGGMAVVAATSVAIPhvENPPL 98 
                                   67778899****.777*********************************97.9997777777777775666643446666* PP

                         MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                   l++lr+lqGlg ++++p+++  ++ +    +rg a  ++++g   G+  g+ l+gl++++lg++a+fy++a+ ++l+ ++ 
  gi|14600879|ref|NP_147404.1|  99 LMALRALQGLGLAVGLPIALGSLSLIQGV-RRGVASTVIASGL--GMSGGAFLSGLMVEYLGFPALFYAAAVPAALSTLV- 175
                                   ************************99888.******9999965..5555999*************************998. PP

                         MFS_1 169 llllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw...illialllfffgfsglltllplylqevlglsgllla 246
                                    +l +++pp+++ +++              ++ al++ p  w   ++++++++  ++ sg+++ + +++++  g+s +  +
  gi|14600879|ref|NP_147404.1| 176 -ALGWRPPPPPSGSPG--------------LLAALRSMP--WevlVVMAGIAVRNTFASGVFSVVSIIFNKIVGIS-YTAT 238
                                   .888888888888866..............366899999..9876777777777888888999999988*******.9*** PP

                         MFS_1 247 glllallalvgailallagrl 267
                                   g++la+  +v a +  ++ r+
  gi|14600879|ref|NP_147404.1| 239 GVVLAINPAVQASVTTVFERI 259
                                   *****9999987776666555 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 2.9e-11
                         MFS_1   9 alarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfasslw.l 87 
                                   ++a++ ++++++++ ++  gis ++ g +l++  +++a  + ++ r++   Gr   ++ +gl ++al+ ++l +++++   
  gi|14600879|ref|NP_147404.1| 214 TFASG-VFSVVSIIFNKIVGISYTATGVVLAINPAVQASVTTVFERIMR--GRALlLYSTGLSGTALA-FYLYLTAGSAlD 290
                                   44444.555555599*****************************99966..99999************.444445777745 PP

                         MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                   l+++ +  G+++ga + +g+++i +++p e r  a +l++ +f++G ilg  ++g +++++g  a   ++ + +l+++++ 
  gi|14600879|ref|NP_147404.1| 291 LAAAQIALGAFYGATVVSGNTMIIALAPSEIRYTASSLYTFAFNIGWILGTSIAGKVMDAAGVDAWIKLAIAGTLVSGLIP 371
                                   **************************************************************8877777777777777754 PP

                         MFS_1 169 llllp 173
                                   l ll 
  gi|14600879|ref|NP_147404.1| 372 LTLLA 376
                                   44443 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.7         1   6.2e+03       6      14 ..     101     109 ..     101     111 .. 0.81
   2 ?    6.5   0.0    0.0019        12       6      17 ..     170     181 ..     167     182 .. 0.91
   3 ?    4.7   0.0    0.0069        41      31      44 ..     349     362 ..     341     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1
                                   HHHHHHHCT CS
                        RuvA_C   6 aveALlaLG 14 
                                   a+ AL +LG
  gi|14600879|ref|NP_147404.1| 101 ALRALQGLG 109
                                   677999999 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0019
                                   HHHHHHHCTS-H CS
                        RuvA_C   6 aveALlaLGYke 17 
                                   a+++L+aLG+ +
  gi|14600879|ref|NP_147404.1| 170 ALSTLVALGWRP 181
                                   89********75 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0069
                                   TTS-HHHHHHHHHC CS
                        RuvA_C  31 pgasveelIraALk 44 
                                   ++a v+++I++A++
  gi|14600879|ref|NP_147404.1| 349 DAAGVDAWIKLAIA 362
                                   5677********97 PP

>> DUF3930  Protein of unknown function (DUF3930)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4    0.0004       2.4      29      41 ..     225     237 ..     214     242 .. 0.88
   2 ?   -0.9   0.1      0.34     2e+03      28      50 ..     312     334 ..     304     335 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0004
                       DUF3930  29 iifltivGiPyta 41 
                                   iif  ivGi yta
  gi|14600879|ref|NP_147404.1| 225 IIFNKIVGISYTA 237
                                   9***********9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                       DUF3930  28 liifltivGiPytayifiqflln 50 
                                   +ii l+   i yta  +  f +n
  gi|14600879|ref|NP_147404.1| 312 MIIALAPSEIRYTASSLYTFAFN 334
                                   799999999****9777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
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 0.19s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3177.92
//
Query:       gi|118431145|ref|NP_147405.2|  [L=308]
Description: malate dehydrogenase [Aeropyrum pernix K1]
Scores for 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-39  133.5   0.2      8e-39  133.0   0.2    1.2  1  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
      1e-21   77.6   0.0    2.2e-21   76.5   0.0    1.5  1  Ldh_1_C         lactate/malate dehydrogenase, alpha/beta C-te
    0.00026   20.6   1.7     0.0027   17.3   0.1    2.8  3  Glyco_hydro_4   Family 4 glycosyl hydrolase
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.053   13.6   0.0    1.7  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.057   13.3   0.1       0.14   12.0   0.1    1.6  2  KR              KR domain
      0.099   12.2   2.0        2.4    7.7   2.0    2.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.15   12.7   0.6        1.3    9.7   0.5    2.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


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 !  133.0   0.2   3.1e-42     8e-39       3     141 .]       2     139 ..       1     139 [. 0.98

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 3.1e-42
                                    EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE--S-SS CS
                        Ldh_1_N   3 vavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvitagvpr 81 
                                    ++++Ga G++G+++a++l+++++ d l L+  ++ k +G+aldl h+++ l v++++s+ + +e+++++d+v++tag+ r
  gi|118431145|ref|NP_147405.2|   2 ITILGA-GKVGMATAVMLMMRGYDD-LLLIARTPGKPQGEALDLAHAAAELGVDIRISGsNSYEDMRGSDIVLVTAGIGR 79 
                                    89****.****************98.999999999**********************999******************** PP

                                    -TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                        Ldh_1_N  82 kpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                    kpG+tR++Ll++Na+ +++++e+i+++a++aiv++ +NPvd +t+v++k++g+p++rvig
  gi|118431145|ref|NP_147405.2|  80 KPGMTREQLLEANANTMADLAEKIKAYAKDAIVVITTNPVDAMTYVMYKKTGFPRERVIG 139
                                    **********************************************************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 !   76.5   0.0   8.7e-25   2.2e-21       3     161 ..     144     300 ..     143     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 8.7e-25
                                    HHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHH CS
                        Ldh_1_C   3 LDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdevvkak 72 
                                    LD++R+ + +++k gv+ +sv+++V+G H++          v+++pl      +  +s++++ee + ++ n+g+++ + +
  gi|118431145|ref|NP_147405.2| 144 LDSARMAYYISQKLGVSFKSVNAIVLGMHGQkmfpvprlssVGGVPL------EHLMSKEEIEEVVSETVNAGAKITELR 217
                                    9*******************************999888877777777......5678889******************** PP

                                    TTSSSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHH CS
                        Ldh_1_C  73 kGagsatlsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleks 152
                                        s+ ++ A+ ++  vea+ rd k+i + + yl+ge+g +d   ++  vP+v+gk G+e+++e l+l++ e+ k++++
  gi|118431145|ref|NP_147405.2| 218 G--YSSNYGPAAGLVLTVEAIKRDSKRIYPYSLYLQGEYGYND---IVAEVPAVIGKSGIERIIE-LPLTEDEKRKFDEA 291
                                    6..9***************************************...9999***************.************** PP

                                    HHHHHHHHH CS
                        Ldh_1_C 153 vkeLkkeie 161
                                    v+  kk +e
  gi|118431145|ref|NP_147405.2| 292 VQAVKKLVE 300
                                    **9999766 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 ?    1.3   0.1     0.084   2.1e+02       2      87 ..       2      81 ..       1      93 [. 0.62
   2 !   17.3   0.1     1e-06    0.0027     123     166 ..      95     140 ..      89     149 .. 0.87
   3 ?   -1.6   0.0      0.68   1.7e+03      30      57 ..     277     304 ..     273     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.084
                                   EEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSHHHHHHHHHHHHHHHHHCTTTCEEEEESSHHHHHTT-SEEEE---T CS
                  Glyco_hydro_4  2 iviiGgGStifaklllgdlkkteelsvselaLvDideerldaiqtlakklveeagadlkieattdrkealkdadfVitairv 83
                                   i+i G+G   +a  ++ ++  +++l      +   + + + ++ +la+    e g+d++i+   +  e ++  d+V++++ +
  gi|118431145|ref|NP_147405.2|  2 ITILGAGKVGMATAVMLMMRGYDDLLL----IARTPGKPQGEALDLAH-AAAELGVDIRISGS-NSYEDMRGSDIVLVTAGI 77
                                   778888888888888877777776644....22333333444444433.34566777777654.445557778888888888 PP

                                   THHH CS
                  Glyco_hydro_4 84 Glek 87
                                   G ++
  gi|118431145|ref|NP_147405.2| 78 GRKP 81
                                   8666 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1e-06
                                    HHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHS..TTSEEEEE CS
                  Glyco_hydro_4 123 vlleIakdieelcPdawvlnytNPaavvteallrlv..pnikavgl 166
                                    +++++a++i+ ++ da v+  tNP+  +t ++++++  p  +++g+
  gi|118431145|ref|NP_147405.2|  95 TMADLAEKIKAYAKDAIVVITTNPVDAMTYVMYKKTgfPRERVIGF 140
                                    689******************************9862266778876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.68
                                    EEEEE-SSHHHHHHHHHHHHHHHHHCTT CS
                  Glyco_hydro_4  30 elaLvDideerldaiqtlakklveeaga 57 
                                    el L   ++++ d++ +++kklve   +
  gi|118431145|ref|NP_147405.2| 277 ELPLTEDEKRKFDEAVQAVKKLVETLPP 304
                                    677888888999*******999997655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.053      15      56 ..       2      47 ..       1     101 [. 0.61

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                                   EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHH....HHHHHHHH CS
                   Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtler....akelaeel 56
                                   ++++GaG+++  +a +L+ +g+++++ + Rt  +    a +la+  
  gi|118431145|ref|NP_147405.2|  2 ITILGAGKVGMATAVMLMMRGYDDLLLIARTPGKpqgeALDLAHAA 47
                                   78*****************************987222233444433 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.5e-05      0.14       8      56 ..       6      55 ..       2      63 .. 0.82
   2 ?   -3.2   0.0       2.7   6.9e+03     152     157 ..      93      98 ..      70     124 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.5e-05
                                   TTSHHHHHHHHHHHHHHS-EEEEE-SS...--HHHHHHHHHHHHTT-EEE CS
                             KR  8 GlGgLGlelarwlaekgarhlvllsRsa.aadedskaliaelealgaeve 56
                                   G+G++G+++a +l+ +g   l+l++R++ +++ ++ +l ++ ++lg++++
  gi|118431145|ref|NP_147405.2|  6 GAGKVGMATAVMLMMRGYDDLLLIARTPgKPQGEALDLAHAAAELGVDIR 55
                                   79*************************53455555567777777788876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.7
                                    HHHHHH CS
                             KR 152 aNaflD 157
                                    aN++ D
  gi|118431145|ref|NP_147405.2|  93 ANTMAD 98 
                                    222222 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 ?    7.7   2.0   0.00093       2.4       3     127 ..       2     121 ..       1     131 [. 0.57

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00093
                                    EEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEE CS
                 UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvif 81 
                                    i+++G+G vG+ ta++l  +g  +++++            gk + +  +L++  ++   + r+s+++++e  ++ +d+++
  gi|118431145|ref|NP_147405.2|   2 ITILGAGKVGMATAVMLMMRGyDDLLLIAR--------TPGKPQGEALDLAHAAAELGVDIRISGSNSYED-MRGSDIVL 72 
                                    89***************9999334444432........234444455566666666655666777777766.77777777 PP

                                    E-----B-T.TTTCB-THHHHHHHHHHHHHHHC..EEEEEE-S---TTH CS
                 UDPG_MGDP_dh_N  82 iaVgTPskk.kgkaaDlkyvesaarsiaealkk..gkvvvvkSTvpvgt 127
                                    ++ g   k    ++  l++  +++ ++ae +k   ++ +vv  T pv +
  gi|118431145|ref|NP_147405.2|  73 VTAGIGRKPgMTREQLLEANANTMADLAEKIKAyaKDAIVVITTNPVDA 121
                                    7776655553222222344444444444444433334444445556555 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 ?    9.7   0.5   0.00051       1.3       2      68 ..       2      74 ..       1     118 [. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00051
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE- CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvla 68
                                   i i+GaG++g a a  l+ +g    +++++  r+p k +  a +l          +++++++  e ++ +d+v+++
  gi|118431145|ref|NP_147405.2|  2 ITILGAGKVGMATAVMLMMRG--YDDLLLI-ARTPGKPQGEALDLAhaaaelgvdIRISGSNSYEDMRGSDIVLVT 74
                                   89*******************..4555544.666665433333333334456688899999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); 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: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2436.24
//
Query:       gi|118431146|ref|NP_147406.2|  [L=685]
Description: V-type ATP synthase subunit I [Aeropyrum pernix K1]
Scores for 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-33  113.9   4.3    3.4e-15   55.1   0.0    3.3  2  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.053   13.8   0.1        4.6    7.6   0.0    2.5  2  AlkA_N      AlkA N-terminal 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 !   55.1   0.0   3.8e-19   3.4e-15     274     560 ..     247     507 ..     220     515 .. 0.82
   2 !   53.1   3.9   1.5e-18   1.3e-14     707     812 ..     574     672 ..     569     673 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.8e-19
                     V_ATPase_I 274 eeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketp.P 352
                                    +e   el+e+ ++v+   +i++ L      ++ ++ i +g+v +++  +++++++++t  ++s v   l + +  e p P
  gi|118431146|ref|NP_147406.2| 247 SERLGELAEFYTVVTAFENIFKFLVST--LRRGETRIVRGFVDVRDSGRLRSIVDRMT--RGSYVLLSLGVRRGGEAPiP 322
                                    444667788888888999999998776..567899999******************99..5566666666666656666* PP

                     V_ATPase_I 353 TyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeileml 432
                                    + +   +f + f ++v+ YG ++ +E+ p++f  it P  Fa+MF D+G Gll+llf+l+ + +   +++          
  gi|118431146|ref|NP_147406.2| 323 SKVDLPQFLKPFSRVVELYGYPEPNEIVPTVFLAITLPLTFALMFPDAGQGLLVLLFSLFYLRR---VSR---------- 389
                                    **********************************************************997643...333.......... PP

                     V_ATPase_I 433 fsgRYiillmGlfsiYtGliYNdifskslnlfgSswevkekaveeeelkkekkeekvYpfGlDpaWklaenellflnSlK 512
                                     +  Y+i +mG  s+  Gl+  ++f+  ++ +      +e ++          e+ +Y++    + ++ e+ + +l    
  gi|118431146|ref|NP_147406.2| 390 -DWAYVIAVMGGASVVSGLLAGEVFGPLVSKMLG---LPELWY------RLGLETPPYAMPTYAIDHGEEELVPVLVYRA 459
                                    .467*******************99865543322...222223......2345678999998888899998888888888 PP

                     V_ATPase_I 513 mKlsvilGviqMlfgvllslvNalyfkkkldiilefiPqllfllsifg 560
                                    + +s  +G + ++fg +l +vN + +++++ ++ + +P++l++ si g
  gi|118431146|ref|NP_147406.2| 460 LNVSLFMGAFMLSFGTFLGVVNGVIKRDWVGLVESRLPRFLLFASITG 507
                                    9****************************************9999876 PP

  == domain 2  score: 53.1 bits;  conditional E-value: 1.5e-18
                     V_ATPase_I 707 IhtIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafL 786
                                    +++ E  L  + n  S+LR+ AL LAH+ L  V++  ++   + +     g+++ v++ ++++   +av   megl af 
  gi|118431146|ref|NP_147406.2| 574 LEAYESLLMLVGNIPSFLRIMALALAHSSLMFVIYYLTVMI-M-Q----GGILADVVGALLYVGGNLAV-AAMEGLLAFA 646
                                    67779999***************************999988.4.3....35667778999999999988.69******** PP

                     V_ATPase_I 787 HaLRLhWVEfqsKFykgdGykFepfs 812
                                    Ha RLh  E  sKFy+g+G++++p +
  gi|118431146|ref|NP_147406.2| 647 HASRLHFYEWFSKFYSGTGVPYTPIK 672
                                    ***********************975 PP

>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00051       4.6      32      85 ..      16      70 ..       5      77 .. 0.85
   2 ?    3.4   0.0    0.0099        89      66      93 ..     107     134 ..     101     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00051
                         AlkA_N 32 edsygRtlrldgakGvvevrhepeksalkvrlsl.sdlraleaviarvrrllDLd 85
                                   +  y R ++  +++G+++v   p+    +v  s  ++l++ ++  +r+r+ +DL 
  gi|118431146|ref|NP_147406.2| 16 ARDYDRVVAGLAVEGIFHVDSPPQGVKGEVDRSYrALLTQASERSSRIRQYFDLA 70
                                   457********************88777777666689999999**********95 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0099
                         AlkA_N  66 sdlraleaviarvrrllDLdadpeaiea 93 
                                     +l++ +++ ar+++llD++a ++ +++
  gi|118431146|ref|NP_147406.2| 107 GLLEEYSEAEARLKELLDIEARIAPVAH 134
                                    5677888999*************99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 4886.75
//
Query:       gi|118431147|ref|NP_147407.2|  [L=401]
Description: aspartate aminotransferase [Aeropyrum pernix K1]
Scores for 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  170.5   0.0    6.6e-50  170.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.3e-05   23.9   0.0    1.8e-05   23.5   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.098   11.9   0.0       0.14   11.4   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  170.3   0.0   1.1e-53   6.6e-50       2     363 .]      33     393 ..      32     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 170.3 bits;  conditional E-value: 1.1e-53
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                    dvi L+++++ ++    +++  +++ ++    + ++ l +y+p+ g+++++ea+a+ l    +   ++++ +v+ +G  a
  gi|118431147|ref|NP_147407.2|  33 DVILLSTGQPGFL----PPTFLRERLAQalLDEGFKRLYSYTPTPGYADVREAIAEDLAALGGPRMEPDDILVTAGGQEA 108
                                    89***********....88888888887544466788889***************8888556666778844555555555 PP

                                    HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-T CS
                  Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphN 159
                                    + ++l ++l  +pgd++++ dpty  y +i+++ gg v  ++  ++ +f+ d e l+ea ++       +k +++ sp N
  gi|118431147|ref|NP_147407.2| 109 MFATLSTIL--EPGDKVILMDPTYFGYRPIVEYLGGRVEWVRAPPSLGFQPDEERLKEAFTR------DVKAVVLVSPDN 180
                                    555566655..5*************************999998899***************9......88********** PP

                                    TT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHH CS
                  Aminotran_1_2 160 PtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaav 239
                                    PtG +++ e  + ++dla   +++++ DeaY ++vf+ + ++  + +++++ n++  +++sK+ G +G+R+Gy++g  ++
  gi|118431147|ref|NP_147407.2| 181 PTGRLLSTESAKLVADLAVDTGAWIVYDEAYKTLVFEGEHVY--LYKLAPD-NTISINTFSKDPGFPGWRLGYLYGPGWI 257
                                    *************************************76422..6888885.67************************** PP

                                    HHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH CS
                  Aminotran_1_2 240 vsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsae 315
                                    v  +r +s  + +  +s++q a+   l+d + + ++le +r+ l++r + +  +L+e   +  +  + + mf  +dls +
  gi|118431147|ref|NP_147407.2| 258 VGKIRLVSEELVYcpPSIAQVAAKIYLEDREGRLRHLEYAREFLKTRMEAMAGALEEMlpEAVFARPGGSMFITVDLSSY 337
                                    **********999999999*999********************************999*6666666669*********** PP

                                    ......CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 316 ......takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelveal 363
                                          t ++ls kLl+e+ v+ +pg++f+    + lR+++A+ t+e ++e + +l
  gi|118431147|ref|NP_147407.2| 338 lskasiTSEDLSVKLLDEESVATVPGRYFGPsgDTMLRLSFATETPERIREGIGRL 393
                                    99999999999999*****************99889*************9988775 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 !   23.5   0.0     3e-09   1.8e-05      54     177 ..      79     212 ..      38     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3e-09
                                    HHHHHHHHHHHHT-....SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TS CS
                Cys_Met_Meta_PP  54 rsvleeriaaLegg....eaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sd 126
                                    r+++ e +aaL g     +  l+++ G+ A++a++ ++l+ Gd+++++d  Y g + +++++  +++            d
  gi|118431147|ref|NP_147407.2|  79 REAIAEDLAALGGPrmepDDILVTAGGQEAMFATLSTILEPGDKVILMDPTYFGYRPIVEYLGGRVEWVRAPPSLgfqPD 158
                                    5666666777765544447899**********************************999999988765544433333379 PP

                                    HHHHHHHCCTTEEEEEEESS-TTTT----HHH...HHHHHHHTT-EEEEEGTTT CS
                Cys_Met_Meta_PP 127 leelekaikentklvylEtptnpllkvvDiek...iaklakkagvlvvvDntfa 177
                                    +e+l++a++  +k+v l +p np+ +++  e+   +a+la + g+ +v D ++ 
  gi|118431147|ref|NP_147407.2| 159 EERLKEAFTRDVKAVVLVSPDNPTGRLLSTESaklVADLAVDTGAWIVYDEAYK 212
                                    99*********************9776654431227777778888888887765 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 ?   11.4   0.0   2.4e-05      0.14      44     119 ..     102     177 ..      84     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                                    ESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TT.TSSB-GGGCGGG--TTEEEEEEB- CS
                DegT_DnrJ_EryC1  44 vssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpd.tynidpaaieaaitertkaIlpVh 119
                                    ++ G +A+  +L+ + ++pgd+VI    t+++    v +lg ++  v   p   +++d +++++a t+  ka+++V 
  gi|118431147|ref|NP_147407.2| 102 TAGGQEAMFATLSTI-LEPGDKVILMDPTYFGYRPIVEYLGGRVEWVRAPPSlGFQPDEERLKEAFTRDVKAVVLVS 177
                                    556667777777654.679****************************99887369*******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2975.36
//
Query:       gi|118431148|ref|NP_147408.2|  [L=116]
Description: tRNA-binding protein [Aeropyrum pernix K1]
Scores for complete 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  107.9   0.1    2.4e-31  107.7   0.1    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.1   1.4e-35   2.4e-31       1      95 [.      20     113 ..      20     114 .. 0.99

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 1.4e-35
                                    EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESS CS
                      tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldek 80 
                                    lrvG+v++ae++p+++kLl+l+vd+G+ee rq+ +g++++y+peelv++ v+vvanl+pk++ G+ S+GM+l+a ++d++
  gi|118431148|ref|NP_147408.2|  20 LRVGRVVKAERLPHSKKLLKLIVDIGGEE-RQVLAGIAKWYSPEELVGRLVIVVANLQPKRMAGEVSQGMVLAAPCGDSE 98 
                                    79***************************.************************************************** PP

                                    CEEEEEESST--TTC CS
                      tRNA_bind  81 evgilelpadveaGe 95 
                                    +  +l++ + ve+G+
  gi|118431148|ref|NP_147408.2|  99 KPVLLTVSEPVEPGS 113
                                    **************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 941.05
//
Query:       gi|14600884|ref|NP_147409.1|  [L=274]
Description: 3-methyl-2-oxobutanoate hydroxymethyltransferase [Aeropyrum pernix K1]
Scores for 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-104  347.0   0.1   6.9e-104  346.8   0.1    1.0  1  Pantoate_transf  Ketopantoate hydroxymethyltransferase
    6.9e-09   35.5   0.6    6.9e-09   35.5   0.6    1.6  2  PEP_mutase       Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> Pantoate_transf  Ketopantoate hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.8   0.1  7.7e-108  6.9e-104       1     258 [.       5     259 ..       5     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 346.8 bits;  conditional E-value: 7.7e-108
               Pantoate_transf   1 kvtvkdlrkmkeegekiamlTaydattAklvdeagvdviLVGDslgmvvlgyestlpvtleemiyhtkaVargakralvva 81 
                                   kvt +++ kmk + ++i+++Tayd++tA ++deagvdviLVGDslgmvvlgy+stl+vtl++m++ht+aVar+akr l+va
  gi|14600884|ref|NP_147409.1|   5 KVTARRILKMKGS-RPIVAVTAYDYPTAWIADEAGVDVILVGDSLGMVVLGYPSTLQVTLDDMVRHTAAVARAAKRPLIVA 84 
                                   68999******88.9****************************************************************** PP

               Pantoate_transf  82 dlPfgsyeaskeqalenAarllkeggadavKleggaevaetvkalveagipVmgHiGltPqsvnalggykvqgkteeeaek 162
                                   d+Pfgsye s+++a+e+A+ l +  ga+avKlegg+e a+ vka+v+agipVmgH+GltPq++ ++ggy+ +++ ++ea++
  gi|14600884|ref|NP_147409.1|  85 DMPFGSYEPSSSAAVESAVALARV-GAEAVKLEGGSEYADRVKAIVDAGIPVMGHLGLTPQRAMRIGGYRPRARGRDEARR 164
                                   ***********************9.******************************************************** PP

               Pantoate_transf 163 lledakaleeaGafalvlEavpaelakeiteklsiptIGIGAGaacdGqvlvlhDllgltekfkpkfvkkyaelaesieea 243
                                   ll da++l eaG+f++vlE v +e a+ +t+++ +ptI+IG+G++cdGq++v+hD++gl+ +++p f+kky++ ++++ ea
  gi|14600884|ref|NP_147409.1| 165 LLLDAESLVEAGVFSIVLEFVSEEAAEMVTRRVPVPTICIGSGRRCDGQIIVFHDIVGLS-RHTPPFAKKYVDARRIMVEA 244
                                   ***********************************************************9.889***************** PP

               Pantoate_transf 244 vkaYaeevkegsFPa 258
                                   v++Yae+v++g+FP 
  gi|14600884|ref|NP_147409.1| 245 VTRYAEDVRNGRFPG 259
                                   **************7 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.6   7.7e-13   6.9e-09       7     107 ..      15     118 ..       9     136 .. 0.83
   2 ?   -2.5   0.0      0.32   2.9e+03      91     105 ..     169     183 ..     158     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 7.7e-13
                    PEP_mutase   7 kg.eplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPl.ivDledG.ygesp 84 
                                   kg +p+v++ a+D  +a i+ eag++ + ++      +lG+p + +++l+ ++++++a+a++ + Pl  +D+  G y+ s 
  gi|14600884|ref|NP_147409.1|  15 KGsRPIVAVTAYDYPTAWIADEAGVDVILVGDSLGMVVLGYPSTLQVTLDDMVRHTAAVARAAKRPLiVADMPFGsYEPSS 95 
                                   4327***************************999999******************************44699987466566 PP

                    PEP_mutase  85 eevaetvrrliaaGvvgvniEDk 107
                                   +   e    l+++G+ +v +E  
  gi|14600884|ref|NP_147409.1|  96 SAAVESAVALARVGAEAVKLEGG 118
                                   666677788999********987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.32
                    PEP_mutase  91 vrrliaaGvvgvniE 105
                                    ++l++aGv  +++E
  gi|14600884|ref|NP_147409.1| 169 AESLVEAGVFSIVLE 183
                                   677888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2247.96
//
Query:       gi|118431149|ref|NP_147410.2|  [L=309]
Description: 2-dehydropantoate 2-reductase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-26   93.2   0.0    2.1e-26   92.6   0.0    1.3  1  ApbA_C    Ketopantoate reductase PanE/ApbA C terminal
    1.6e-14   53.8   0.0    2.7e-14   53.1   0.0    1.4  1  ApbA      Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.0   2.3e-30   2.1e-26       1     123 [.     170     291 ..     170     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 2.3e-30
                         ApbA_C   1 dirlarweKllinaainpltalldckngellespelralvrallkEalavaeaegvelseerleeaveavlektaanrsS 80 
                                    di+++rw K + n+ain +t++l+++ng ++es+e+ +l+ +++ E+  va  +g++l+e+   e+ + v+ +t +n sS
  gi|118431149|ref|NP_147410.2| 170 DIEAWRWLKAAANSAINLVTTILGSRNGFVVESREAWRLASRAASEVGLVASMLGYSLPED-PVEYTRLVALQTYDNESS 248
                                    799**********************************************************.****************** PP

                         ApbA_C  81 MlqDveagrktEidyinGavvklAeklgvetPvnellyellka 123
                                    +lqD+++ r++E  yi G vv+ A +lgv +P++e+ly+ll+a
  gi|118431149|ref|NP_147410.2| 249 TLQDLRRCRRSEAPYIAGRVVEEASRLGVGAPTVEALYSLLQA 291
                                    ****************************************987 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0     3e-18   2.7e-14       2     149 ..       5     143 ..       4     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3e-18
                                    EEES-SHHHHHHHHHHHH.HTHCEEEE-SCHHHHH.HHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGG CS
                           ApbA   2 ailGaGaiGsllaakLak.agadvtlilrsrrlea.lkknGlrltseggeeilrppealsaeekselepidlvivtvKay 79 
                                    +i+G+G++Gslla++ ++ +g +++ ++r+r  +a   ++Glrl+++  + +++ +  + ++     + + l +++vKay
  gi|118431149|ref|NP_147410.2|   5 CIVGLGGVGSLLAYYVYRgTGDTPIAVVRRR-SQAmRLQAGLRLYGVV-DAYVPLEPYVGTP----PRGCRLSFISVKAY 78 
                                    8******************************.5555899*********.9999999999999....89************ PP

                                    GHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EEEEEETTEEEECS--EEEEEE CS
                           ApbA  80 qteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthgatregpgevhhagkgeikige 149
                                    ++++a+e+++++ +    v +  NG+g +e+  +        + v++ g+++++pg  + ag g++ +g+
  gi|118431149|ref|NP_147410.2|  79 DAAAAVEAAAEFSEM---VAVAGNGWGGYEKALDLG--VDAAAIVVESGVASLEPGLARVAGLGRLIVGS 143
                                    ********9999988...9**********9888887..468889999*******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2293.72
//
Query:       gi|118431150|ref|NP_147412.2|  [L=148]
Description: hypothetical protein APE_0680.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00027   21.2   0.1    0.00039   20.7   0.1    1.3  1  4HBT      Thioesterase superfamily


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 !   20.7   0.1   2.2e-08   0.00039       3      75 ..      22     103 ..      20     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.2e-08
                                    SB-HHHHHHHHHHHHHHHHHHTTST.........TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEET CS
                           4HBT   3 vvhgGvylallDeaagaalrslggr.........gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrde 73 
                                    + h  +++++++ a  +++r+  g+         + +++ v+ +++++ p +++d+++v+   + +g +s++++ +v++e
  gi|118431150|ref|NP_147412.2|  22 IAHFSTFFKICEWAEEDFFRRALGDeafhgvlesNVMFPRVRAECTYHYPLHVHDDFRVDIVDVVIGVKSITYTFKVWNE 101
                                    6788889999999999999999999999999999*********************************************9 PP

                                    TS CS
                           4HBT  74 dg 75 
                                    + 
  gi|118431150|ref|NP_147412.2| 102 TH 103
                                    86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1183.12
//
Query:       gi|118431151|ref|NP_147413.2|  [L=98]
Description: hypothetical protein APE_0680a.1 [Aeropyrum pernix K1]
Scores for 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  119.0   2.7    8.2e-35  118.8   2.7    1.0  1  DUF211    Uncharacterized ArCR, COG1888
  ------ inclusion threshold ------
      0.082   13.4   1.6        0.2   12.1   1.5    1.8  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 !  118.8   2.7   9.1e-39   8.2e-35       2      88 ..       5      92 ..       4      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 9.1e-39
                                   EEEEEEEEEEE.SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEEES CS
                         DUF211  2 irrlvLDvlkp.hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevvaGk 82
                                   +r++vLDvlkp ++psi+++++++a+l g++gvnitvke+D+et +l++tieG++idy ++e+++eelg+++hSiD+ vaGk
  gi|118431151|ref|NP_147413.2|  5 LRKVVLDVLKPiRGPSIIDVSREVAALPGIEGVNITVKEIDVETVTLTMTIEGSDIDYGSVEKKLEELGCIVHSIDQAVAGK 86
                                   8********************************************************************************* PP

                                   S----- CS
                         DUF211 83 kiveev 88
                                   kive++
  gi|118431151|ref|NP_147413.2| 87 KIVEQE 92
                                   ****86 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.5   2.3e-05       0.2      15      59 ..      23      72 ..      20      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                            HMA 15 kvekvLselpgV.......esvkvdlatktvtVeg.daestklrkiieaieka 59
                                   +v + +++lpg+       ++++v  +t t+t+eg d++      + +++e++
  gi|118431151|ref|NP_147413.2| 23 DVSREVAALPGIegvnitvKEIDVETVTLTMTIEGsDIDY---GSVEKKLEEL 72
                                   79999*******999999999999**********974444...5555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 809.53
//
Query:       gi|118431152|ref|NP_147414.2|  [L=128]
Description: hypothetical protein APE_0681.1 [Aeropyrum pernix K1]
Scores for complete 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   56.8   0.0      2e-15   56.6   0.0    1.0  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    4.8e-05   23.3   0.0    6.1e-05   23.0   0.0    1.1  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 !   56.6   0.0   2.2e-19     2e-15      14     117 ..      16     116 ..       8     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.2e-19
                       Prok-JAB  14 rahpeEtcGlllgkeseseevivvplvnewsn......rfeipdpedslarlkfearerglevvgiwHSHpggsarPSet 87 
                                    + + +E +Gl++g ++ + +++++    +++n      +fe  dp +  ++ + +a++ glevvg++H+H+++++ PS +
  gi|118431152|ref|NP_147414.2|  16 ALAHNEEAGLVIGARRGDTVYAYILY--RTDNlkqspeEFES-DPWQVVQAHR-AAEKLGLEVVGVYHTHTTCPPSPSGK 91 
                                    55789*********954555444442..44556677999999.9999999999.************************** PP

                       Prok-JAB  88 Drrdaaalarvkalliivgdkaeelrawrl 117
                                    D + +++    +++li ++    e++aw+l
  gi|118431152|ref|NP_147414.2|  92 DVEGMKRWP--GVWLIACPG---EVKAWTL 116
                                    *******63..556666655...8889976 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 !   23.0   0.0   6.8e-09   6.1e-05      29     108 ..      21      95 ..       8      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.8e-09
                                    --EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTTSEEEEEEEESSSS-SS--HHHHHH CS
                            JAB  29 evmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrgrervvGWYhshpditvwlsevdvrt 108
                                    e +Gl+iG  ++d    + +++  + ++ +++ ++ + d   + ++++ ++kl   ++vvG Yh+h +    +s  dv+ 
  gi|118431152|ref|NP_147414.2|  21 EEAGLVIGARRGD---TVYAYILYRTDNLKQSPEEFESDPWQVVQAHRAAEKL--GLEVVGVYHTHTTCPPSPSGKDVEG 95 
                                    458**********...4577777777777777777777777778889999998..8*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 958.32
//
Query:       gi|118431153|ref|NP_147415.2|  [L=173]
Description: hypothetical protein APE_0682.1 [Aeropyrum pernix K1]
Scores for complete 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-29  102.6   0.0    2.8e-29  102.4   0.0    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.1e-07   31.7   0.3    3.5e-05   24.4   0.0    2.1  2  Metallophos    Calcineurin-like phosphoesterase
     0.0057   16.0   0.0      0.014   14.7   0.0    1.6  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


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 !  102.4   0.0   4.7e-33   2.8e-29       1     164 [.       1     163 [.       1     164 [. 0.90

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 4.7e-33
                  Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellela....pvlaVrGNnDeevveedvlreaae 76 
                                    M +++iSD+H+nl++ +++ e++++++v+a+ih+GD+  ++p +l+ell +      ++ V+GNnD   ++  ++r a +
  gi|118431153|ref|NP_147415.2|   1 MLVGVISDTHDNLALARRAGEIFARERVEAVIHLGDY--VAPFTLAELLGVVggkaVFYGVFGNND--GERLGLSRVAGG 76 
                                    99**********************************9..************9**999*********..667788899999 PP

                  Metallophos_2  77 lgtdlp.eeaelelagekvlliHgdplgvkdalaellkeaeegsd..vvvcGHtHvpevekeggvlvvnPGsvgeprdgd 153
                                    +g +l    a+++++g+++ll+Hg   g +++  el+++ ++  +   v++GHtH+++ve+ gg lv+nPG  g+     
  gi|118431153|ref|NP_147415.2|  77 FGASLLdPPATVSIGGRRLLLLHGF--GSPENTVELVDALASSGRwdAVLYGHTHKARVERVGGSLVLNPGDGGGSLE-- 152
                                    999998799***************9..88888888888855555557************************9998833.. PP

                  Metallophos_2 154 petyaildtde 164
                                    ++++aild+++
  gi|118431153|ref|NP_147415.2| 153 KPSAAILDLES 163
                                    33899999876 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.9e-09   3.5e-05       3     123 ..       3     101 ..       1     113 [. 0.73
   2 !    6.6   0.1    0.0017        10     183     203 ..     110     130 ..      91     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.9e-09
                                    EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.HH CS
                    Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee.el 81 
                                    + vi+D+H      +l+ ++++ + ++re ++ +v+++GD+v    l + ll  +  +      +y + GN +g e  +l
  gi|118431153|ref|NP_147415.2|   3 VGVISDTH-----DNLALARRAGEIFARE-RVEAVIHLGDYVAPFTLAE-LLGVVGGKAV----FYGVFGNNDG-ERlGL 70 
                                    78******.....**********999999.***************8888.7777555555....4********4.33344 PP

                                    HHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE CS
                    Metallophos  82 lnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg 123
                                    ++  g +g         a+ ++ +  +s+g+   ++lllhG 
  gi|118431153|ref|NP_147415.2|  71 SRVAGGFG---------ASLLDPPATVSIGGR--RLLLLHGF 101
                                    44433333.........445566666667777..88888876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                                    HHHHHHHHTTESEEEEESSSS CS
                    Metallophos 183 aledllkkygvdlvisGHtHv 203
                                     ++ l   ++ d+v++GHtH+
  gi|118431153|ref|NP_147415.2| 110 LVDALASSGRWDAVLYGHTHK 130
                                    34456777889*********7 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.24   1.4e+03      11      45 ..       6      40 ..       3      45 .. 0.75
   2 !   14.7   0.0   2.3e-06     0.014     200     251 ..     109     165 ..      96     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.24
                                   EE--TT-GGGHHHHHHHHHHH--SEEEEES----- CS
                  Metallophos_3 11 isdlkgevellerlveviedkdpDllvlvGdlvka 45
                                   isd +++  l  r  e+ +   +++++ +Gd v +
  gi|118431153|ref|NP_147415.2|  6 ISDTHDNLALARRAGEIFARERVEAVIHLGDYVAP 40
                                   67777777777777777777799999999998765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.3e-06
                                    HHHHHHHHHH--SEEEE-SS--EE.EEETTEEEEE--....BGGGTEEEEEETTTTE CS
                  Metallophos_3 200 evvaelvktlnPevvvvghavkeh.eelgktlvvnPG....aleeGdfavvdleekk 251
                                    e v  l  + + + v+ gh++k++ e +g +lv nPG    +le+   a++dle  +
  gi|118431153|ref|NP_147415.2| 109 ELVDALASSGRWDAVLYGHTHKARvERVGGSLVLNPGdgggSLEKPSAAILDLESME 165
                                    55666666667778999*******************733336888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1369.02
//
Query:       gi|118431154|ref|NP_147416.2|  [L=68]
Description: hypothetical protein APE_0682a.1 [Aeropyrum pernix K1]
Scores for complete 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-12   46.7   0.8    3.3e-12   46.4   0.8    1.1  1  DUF2283   Protein of unknown function (DUF2283)
  ------ inclusion threshold ------
       0.21   11.5   0.0       0.29   11.0   0.0    1.2  1  KTSC      KTSC domain


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 !   46.4   0.8   3.7e-16   3.3e-12       1      49 []      16      63 ..      16      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.7e-16
                        DUF2283  1 kitYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                   +i+YD+ +D+lYI++ eg+  es  ++d++i  + ++Grl++I + ++S
  gi|118431154|ref|NP_147416.2| 16 WIEYDRNTDTLYINFGEGEPDESVLIGDNVIANI-REGRLISIIVTDFS 63
                                   8*********************************.*********99987 PP

>> KTSC  KTSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.2e-05      0.29       8      25 ..      17      34 ..      15      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.2e-05
                                   EEEETTTTEEEEEETTTE CS
                           KTSC  8 igYdpetqtLeieFkngs 25
                                   i+Yd++t tL+i F  g+
  gi|118431154|ref|NP_147416.2| 17 IEYDRNTDTLYINFGEGE 34
                                   79************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 580.15
//
Query:       gi|14600892|ref|NP_147417.1|  [L=222]
Description: phosphoserine phosphatase [Aeropyrum pernix K1]
Scores for 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   52.3   0.1    1.2e-13   51.9   0.1    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    1.7e-13   51.3   0.0    1.4e-12   48.4   0.0    1.9  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.9e-06   27.1   0.0      0.016   15.3   0.0    2.3  2  HAD_2            Haloacid dehalogenase-like hydrolase
    0.00036   20.4   0.0    0.00082   19.2   0.0    1.5  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0031   16.9   0.0      0.039   13.4   0.0    2.0  2  Put_Phosphatase  Putative Phosphatase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1   3.2e-17   1.2e-13       1     187 [.       8     180 ..       8     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 3.2e-17
                           HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralrek.lllalfrellrldraglaelleallagls.eelaaelerfvae 79 
                                   ++fD+Dg L+   s + +++++l++ ++    a+++k  ++    ++ +++r++++  ++a  ++l   +l + ++++   
  gi|14600892|ref|NP_147417.1|   8 VIFDVDGVLVEVKSSWGYIHRRLGVEEE----AMKVKeMFERGSIDYIEWMRLDTELWIRASGGRLHrSRLMEIVGEIP-- 82 
                                   79**********9999666657777443....33333233333457777777777777777777777666777777777.. PP

                           HAD  80 virpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkvaalr 159
                                          + +a e+++  r+ G r+ +vS+g++ lv++++ae gad+  +++l +d+      l + g+p  g +k  a+ 
  gi|14600892|ref|NP_147417.1|  83 ------VRKEAFEAVRMLRRMGLRIGLVSSGIDLLVRRVAAEIGADAWASNRLLFDKnG---FLQPGGSPLVGVDKRGAVT 154
                                   ......5678888888888*****************************9**99987653...3445789999999999999 PP

                           HAD 160 ewlaaegegidleevvayGDspsDlpll 187
                                   +++++ g+  +leev ++GDs++D  ++
  gi|14600892|ref|NP_147417.1| 155 RMAYELGA--SLEEVAYVGDSRWDASAM 180
                                   96666665..55669999******9887 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   3.9e-16   1.4e-12       1     206 [.       5     180 ..       5     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 3.9e-16
                                   SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltald 81 
                                   ik+v+fD+dG+L++    v+  + ++                     +   +++++  ++ +      + +g+ ++++++ 
  gi|14600892|ref|NP_147417.1|   5 IKLVIFDVDGVLVE----VKSSWGYI---------------------HRRLGVEEEAMKVKE-----MFERGSIDYIEWM- 54 
                                   89***********4....55666666.....................666677777778888.....8889999999999. PP

                                   CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                     Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfd 161
                                        + +++ + ++           l ++  + p  v++ea eav+ L+++g++++l++++    ++r+a ++G d   +
  gi|14600892|ref|NP_147417.1|  55 -----RLDTELWIRASGGRLHR--SRLMEIVGEIP--VRKEAFEAVRMLRRMGLRIGLVSSGIDLLVRRVAAEIGaDAWAS 126
                                   .....33344444444444444..55777777777..**************************************555559 PP

                                   EEEEHHCESSTTT.........SHHHHHHHHHHHTSTGGGEEEEESSHHHHHHH CS
                                   xxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 162 aviasdietvakp.........spegkvaaireLqgkpeevamVGDgvnDaaal 206
                                   + +  d +++  p         +  ++ + + eL+++ eeva VGD+ +Da+a+
  gi|14600892|ref|NP_147417.1| 127 NRLLFDKNGFLQPggsplvgvdKRGAVTRMAYELGASLEEVAYVGDSRWDASAM 180
                                   999999999555555556666688899999**********************97 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.6e-06     0.016       1     118 [.       8     121 ..       8     132 .. 0.75
   2 !    9.6   0.0   0.00025      0.91     142     173 ..     154     185 ..     145     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.6e-06
                         HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkk..kevk 79 
                                   +iFD+Dg+l+  +  +  + ++l  e+  + ++ +e+ +   +++ e +r  +e  +      +  r +++++ +   e+ 
  gi|14600892|ref|NP_147417.1|   8 VIFDVDGVLVEVKSSWGYIHRRLGVEE--EAMKVKEMFERGSIDYIEWMRLDTE-LWIRA---SGGRLHRSRLMEivGEIP 82 
                                   7**************999999999888..4466666666666666666554444.45333...333334444444444688 PP

                         HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlgi 118
                                   + +++ e++  L+++g+++g+v+s+ +  v++  +++g 
  gi|14600892|ref|NP_147417.1|  83 VRKEAFEAVRMLRRMGLRIGLVSSGIDLLVRRVAAEIGA 121
                                   8899*********************99999988888776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00025
                         HAD_2 142 ekaleklklkkeeviyvGDsptDieaakkagi 173
                                    ++  +l+++ eev yvGDs  D  a   +g+
  gi|14600892|ref|NP_147417.1| 154 TRMAYELGASLEEVAYVGDSRWDASAMSIVGL 185
                                   56778999***************999877765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2   4.3e+03       1      11 [.       8      18 ..       8      31 .. 0.83
   2 !   19.2   0.0   2.3e-07   0.00082     185     231 ..     146     192 ..     145     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                  EEEEIIIIIS- CS
                   Hydrolase_3  1 ialDlDGTLln 11
                                  +++D+DG L+ 
  gi|14600892|ref|NP_147417.1|  8 VIFDVDGVLVE 18
                                  689****9976 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.3e-07
                                   T-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS CS
                   Hydrolase_3 185 gvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgna 231
                                   gv+K  a++++a el+ sleev+ +GD+  D + ++ +gl +A +++
  gi|14600892|ref|NP_147417.1| 146 GVDKRGAVTRMAYELGASLEEVAYVGDSRWDASAMSIVGLPIAYNDG 192
                                   79****************************************98766 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.1e-05     0.039       2      97 ..       7     106 ..       6     138 .. 0.74
   2 ?    1.6   0.0     0.042   1.5e+02     166     185 ..     161     180 ..     148     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
               Put_Phosphatase   2 lvvfDFDktiidedsd.nwvvdelpatelfeelretlrkgl..wnelm...drvlkelheqgvseadikkvlrsiplspgl 76 
                                   lv+fD D  +++++s    + + l+ +e+  +++e +++g   + e+m    ++  +      + +++ +++ +ip+  + 
  gi|14600892|ref|NP_147417.1|   7 LVIFDVDGVLVEVKSSwGYIHRRLGVEEEAMKVKEMFERGSidYIEWMrldTELWIRASGGRLHRSRLMEIVGEIPVRKEA 87 
                                   89**********8765279******************98754455555111455555555557788999************ PP

               Put_Phosphatase  77 velikslakkkleldliiiSD 97 
                                    e++++l++   +l + ++S 
  gi|14600892|ref|NP_147417.1|  88 FEAVRMLRR--MGLRIGLVSS 106
                                   *******66..5566666764 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.042
               Put_Phosphatase 166 gveyerliYvGDganDlCpv 185
                                   g++ e + YvGD++ D  ++
  gi|14600892|ref|NP_147417.1| 161 GASLEEVAYVGDSRWDASAM 180
                                   678899*******9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 1882.60
//
Query:       gi|14600893|ref|NP_147418.1|  [L=170]
Description: hypothetical protein APE_0685 [Aeropyrum pernix K1]
Scores for 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-05   22.7   0.0    0.00012   22.0   0.0    1.3  1  tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal


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 !   22.0   0.0   6.8e-09   0.00012       6      85 .]      87     160 ..      83     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.8e-09
                                   HHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTTSCEEE CS
                 tRNA_int_endo   6 avyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdaegdvty 85 
                                    vy dLr+kG  +  G++ G+  +vY    +++   y V+v+se+ +l++ +l++++r a   +   i+aivd++g +ty
  gi|14600893|ref|NP_147418.1|  87 LVYFDLRRKGRKPLVGVRRGT--LVY----EHGGRVYEVLVLSEGYPLKIGSLVEWSRGASMDNHSPIVAIVDRTGLITY 160
                                   79****************998..9**....6666678888899*********************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1282.13
//
Query:       gi|14600894|ref|NP_147419.1|  [L=370]
Description: methylthioribose-1-phosphate isomerase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-80  270.9   0.0    1.2e-80  270.7   0.0    1.0  1  IF-2B     Initiation factor 2 subunit family
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.35   10.7   0.0    1.6  2  LpxI_N    LpxI N-terminal domain


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 !  270.7   0.0   1.4e-84   1.2e-80       1     282 []      64     358 ..      64     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 270.7 bits;  conditional E-value: 1.4e-84
                                   SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHH CS
                         IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakkslie 81 
                                   ++rG+pai++aa+++l+ ++ +a    ++ ++e l++a ++++++rPta +l++a  r+  ++se   +s v++a  + +e
  gi|14600894|ref|NP_147419.1|  64 EIRGAPAIGVAAAYALALAAAEAASRGGEGFIEALSEARREIESTRPTAYNLFWATARVYGAVSEAFRRSGVDAAVRAGLE 144
                                   58******************************************************************************* PP

                                   HHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHHHH CS
                         IF-2B  82 kikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rltake 153
                                   ++++++ e+++ +  ig+++a l+++gdt+lT+cn+++        +l+v+r a+ e+k+++Vi +E+rP lqG rl ++e
  gi|14600894|ref|NP_147419.1| 145 EATRIYVEDVRGNVEIGRVGARLLESGDTVLTHCNTGAlatagfgtALGVIRYAWMEGKDIRVITTETRPVLQGaRLNVWE 225
                                   ********************************************************************************* PP

                                   HHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSS CS
                         IF-2B 154 Lvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedif 233
                                   L+++gip++l++dsav+ +ms+ +v+k+ivGAdri++ G +ankiGT+++A++A ++ +p++v+a+ ++f++  +  e i+
  gi|14600894|ref|NP_147419.1| 226 LRKEGIPFKLVVDSAVGLIMSRgMVSKAIVGADRIVSTGHTANKIGTYMVAMAASRHGVPFYVAAPASTFQPD-AGPEAIV 305
                                   *************************************************************************.6667799 PP

                                   XXBEXTHHHHEE....TTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                         IF-2B 234 ieerdpeellni....tgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                   ieer p+e+  +     ++ri+  +++ +np fDvtPpelIt++IT+ Gv++p
  gi|14600894|ref|NP_147419.1| 306 IEERSPDEVRGViseaGYVRITLGDVEAYNPSFDVTPPELITAFITDRGVIEP 358
                                   9*******9765111156677777**************************997 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     4e-05      0.35      12     104 ..      80     175 ..      76     190 .. 0.74
   2 ?   -2.7   0.0      0.59   5.3e+03      14      36 ..     274     296 ..     273     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4e-05
                        LpxI_N  12 Pllvaeaakaagrevvvvalegeadeelekivd...evaevsvgqlgklikaLkregvtevvmaGkvekpkll..dlrpDl 87 
                                   +l++aeaa ++g e ++ al++ a +e+e++     +  +      g + +a++r+gv+ +v aG  e ++++  d+r  +
  gi|14600894|ref|NP_147419.1|  80 ALAAAEAA-SRGGEGFIEALSE-ARREIESTRPtayNLFWATARVYGAVSEAFRRSGVDAAVRAGLEEATRIYveDVRGNV 158
                                   45555555.5666777777765.4444444333335999**************************9999999998888899 PP

                        LpxI_N  88 ralkllaklkdrgddal 104
                                   ++ ++ a+l + gd  l
  gi|14600894|ref|NP_147419.1| 159 EIGRVGARLLESGDTVL 175
                                   99999999885555444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.59
                        LpxI_N  14 lvaeaakaagrevvvvalegead 36 
                                   +va aa ++g +++v+a     +
  gi|14600894|ref|NP_147419.1| 274 MVAMAASRHGVPFYVAAPASTFQ 296
                                   57889999999999988666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2892.80
//
Query:       gi|14600895|ref|NP_147420.1|  [L=324]
Description: hypothetical protein APE_0688 [Aeropyrum pernix K1]
Scores for 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   91.3   0.1    5.2e-14   52.5   0.0    2.2  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    0.00035   20.8   0.0     0.0045   17.2   0.0    2.3  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.011   16.6   0.0        3.9    8.3   0.0    2.6  3  Glyoxalase_6  Glyoxalase-like domain


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   5.4e-13   3.2e-09       1      40 [.       6      48 ..       6     124 .. 0.73
   2 !   52.5   0.0   8.8e-18   5.2e-14       5     128 .]     159     271 ..     155     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5.4e-13
                                  EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE......EESTEEE CS
                    Glyoxalase  1 gidhvallvgdleksldFYtkvLGfklvkktdn......teetegl 40
                                  g++h+++l +d+++++ FYtkvLG++lvk+++n           + 
  gi|14600895|ref|NP_147420.1|  6 GLHHITALSADPQANIYFYTKVLGLRLVKVSVNqdepnvY---HFF 48
                                  79******************************74332220...222 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 8.8e-18
                                   EEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEEHC CS
                    Glyoxalase   5 vallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafialdve 85 
                                   v++ v+d   s  F +++LGf+  ++ +    +  +  + +   g+++el+  + + +++ +     +tvhhvaf ++d  
  gi|14600895|ref|NP_147420.1| 159 VVIMVRDCHTSGYFLEDILGFEKADEGE----EYAVYTIGGGGPGRVVELLCPREAAPGRLGA----GTVHHVAFAVKDLR 231
                                   7899******************999999....8999999999999**********99999999....99************ PP

                                   HHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                    Glyoxalase  86 dvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                   +++   ++l ++g++v+++++r  f+++y   fr+p+G+l ei
  gi|14600895|ref|NP_147420.1| 232 ELAVHREKLVKRGYNVTPVIDRKWFTSIY---FREPGGVLYEI 271
                                   *****************************...********997 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 ?    0.8   0.0     0.097   5.8e+02       1      24 [.       8      31 ..       5      56 .. 0.63
   2 !   17.2   0.0   7.6e-07    0.0045       3      95 ..     159     249 ..     158     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.097
                                  EEEEEE-S-HHHHHHHHHH.TT-E CS
                  Glyoxalase_4  1 dQigivVeDleaavarfsallGvg 24
                                  ++i     D +a + +++++lG++
  gi|14600895|ref|NP_147420.1|  8 HHITALSADPQANIYFYTKVLGLR 31
                                  566666677777777777777765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 7.6e-07
                                   EEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETT.EEEEEEEESSTT-THHHTS-EEEEEEEEES-HHH. CS
                  Glyoxalase_4   3 igivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgs.vqieLieplegpeflaehgeglhhlaywvddlda. 81 
                                   + i+V+D +    +++++lG+++ ++   e++ v  +    g+ +   +eL  p+e   + + + + +hh+a++v+dl + 
  gi|14600895|ref|NP_147420.1| 159 VVIMVRDCHTSGYFLEDILGFEKADEG--EEYAV--YTIGGGG-PgRVVELLCPREA-APGRLGAGTVHHVAFAVKDLREl 233
                                   6799****************9887775..44444..3333333.2368*******99.55577999**********97652 PP

                                   ..HHHHHCTTTEEEEE CS
                  Glyoxalase_4  82 ..avarleeqGfevvq 95 
                                       ++l ++G+ v++
  gi|14600895|ref|NP_147420.1| 234 avHREKLVKRGYNVTP 249
                                   1156888889988876 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0048        29       6      33 ..      14      41 ..       9      57 .. 0.80
   2 ?   -2.8   0.0       1.9   1.1e+04      18      53 ..     103     132 ..      95     141 .. 0.61
   3 ?    8.3   0.0   0.00065       3.9       2     101 ..     159     266 ..     158     272 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0048
                  Glyoxalase_6  6 aadpaalaaFwaaalgwevereeaaled 33
                                   adp+a + F+ ++lg+++++ ++ +++
  gi|14600895|ref|NP_147420.1| 14 SADPQANIYFYTKVLGLRLVKVSVNQDE 41
                                  68***************99887744444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                  Glyoxalase_6  18 aalgwevereeaaledpegvgpaaedaatllfqrvp 53 
                                   ++lg+e  +e + +   +      +d+  l++q  +
  gi|14600895|ref|NP_147420.1| 103 TLLGLEENSEGVRINFVD------WDGLGLSLQASD 132
                                   677777777774333333......344466666655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00065
                  Glyoxalase_6   2 vvldaadpaalaaFwaaalgweveree..aaledpegvgpaaedaatllfqrvpe.....paknrvHldlavedld...ae 72 
                                   vv+ ++d ++   F +++lg+e+++e   +a+    g+gp  ++ + ll  r        +  +  H+ +av+dl+    +
  gi|14600895|ref|NP_147420.1| 159 VVIMVRDCHTSGYFLEDILGFEKADEGeeYAVYTIGGGGP--GRVVELLCPREAApgrlgA-GTVHHVAFAVKDLRelaVH 236
                                   7888999999****************96644444445555..3344444444444677641.33479*****998744467 PP

                  Glyoxalase_6  73 varlvalGArvlreprdgthgr..vlaDPeG 101
                                    ++lv+ G  v    + + + +   ++ P G
  gi|14600895|ref|NP_147420.1| 237 REKLVKRGYNVTPVIDRK-WFTsiYFREPGG 266
                                   778888876666444433.333466666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2319.81
//
Query:       gi|118431155|ref|NP_147421.2|  [L=432]
Description: isocitrate dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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  327.4   0.0    1.3e-97  327.1   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 !  327.1   0.0    7e-102   1.3e-97       2     347 ..      35     413 ..      34     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: 327.1 bits;  conditional E-value: 7e-102
                                    EEEEEESTTHHHHHHHHHHHHHHHHHHHT...-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSS CS
                         Iso_dh   2 iallegdgiGpevveaalkvlkaakekag...lelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkeke 78 
                                    +a++ gdg+Gpevve+alkv++aa++k +   +++ + e  +G  a+++ ge lp++tle i+ a+v+l+g+++tp++++
  gi|118431155|ref|NP_147421.2|  35 VAFIRGDGVGPEVVESALKVVDAAVKKVYggsRRIVWWELLAGHLAREKCGELLPKATLEGIRLARVALKGPLETPVGTG 114
                                    89**************************99999*********************************************** PP

                                    SSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET............... CS
                         Iso_dh  79 vrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg............... 143
                                     r+ n  +a+r+ ldl+an+rpv+++   +++ p k  +++ vd+vi+Re+t+++Y+g+e  +++               
  gi|118431155|ref|NP_147421.2| 115 YRSLN--VAIRQALDLYANIRPVRYY---GQPAPHK--YADRVDMVIFRENTEDVYAGIEWPHDSpeaarirrflaeefg 187
                                    *****..*******************...7888888..4899******************999999************96 PP

                                    .TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC............... CS
                         Iso_dh 144 .sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee............... 206
                                     s   e+ ++++k++s+ +++r+++ a+e Al++g+  vt+++K+n++k +e ++ ++++eva e               
  gi|118431155|ref|NP_147421.2| 188 iS-IREDAGIGVKPISRFATRRLMERALEWALRNGNTVVTIMHKGNIMKYTEgAFMRWAYEVALEkfrehvvteqevqek 266
                                    54.6999*******************************************************9999*************9 PP

                                    .....TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CC CS
                         Iso_dh 207 .....eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapd 281
                                           ++i ++++++D++++q++++p  ++Viv++Nl+GD++SD+a+alvG++G++++ ++g +++a++E+vHG+ap+
  gi|118431155|ref|NP_147421.2| 267 yggvrPEGKILVNDRIADNMLQQIITRPWDYQVIVAPNLNGDYISDAASALVGGIGMAAGMNMG-DGIAVAEPVHGTAPK 345
                                    999998889*******************************************************.79************* PP

                                    CTTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS..TCCCHHHHHHHH CS
                         Iso_dh 282 iagkdkaNpiavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea..akevstsefgda 347
                                    +agkd +Np+a ilSa+l++   +g+ e  + +e A++k++++++vT+Dla+ +   + + tse+++ 
  gi|118431155|ref|NP_147421.2| 346 YAGKDLINPSAEILSASLLIGEFMGWREVKSIVEYAIRKAVQSKKVTQDLARHMpgVQPLRTSEYTET 413
                                    ********************999*******************************9999999**99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.19s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3595.86
//
Query:       gi|14600897|ref|NP_147422.1|  [L=478]
Description: hypothetical protein APE_0691 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00021   21.3  11.8    0.00039   20.4   0.8    2.7  2  T2SSF           Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.036   14.4   0.0       0.14   12.6   0.0    2.1  1  Arm-DNA-bind_3  Arm DNA-binding domain


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 !   20.4   0.8   4.4e-08   0.00039      27     120 ..     125     222 ..     108     227 .. 0.90
   2 !    4.6   4.2    0.0033        29       9     116 ..     292     404 ..     289     409 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.4e-08
                                   SSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         T2SSF  27 engplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeggnLaevLerlaeyleeerelrrkllaall 103
                                   + ++ ++e++r++  +++G ++++a +     tps+ +  +++ +i+a + g + +     + +y ++  ++++++ ++l+
  gi|14600897|ref|NP_147422.1| 125 SLRWARREVERLRLMVKSGLDPEAAARllarTTPSKTLGAMLREYIAAERLGLSRSRLTLYIIDYTMKAIKTQWDSYTRLA 205
                                   3899**************************88887777******************************************* PP

                                   TTXXXXXXXXXXXXXXX CS
                         T2SSF 104 epllllvvallvllill 120
                                   + l ++ ++l+  ++ll
  gi|14600897|ref|NP_147422.1| 206 QSLGEINLTLVSTALLL 222
                                   ******99999988887 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0033
                                   HHTT--HHHHHHHHHHHHS..SHHHHHHHHHHHHHHHTTSSHHHHHC...T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHH CS
                         T2SSF   9 lsaGvplveaLellaeeae..ngplaeelkriarrlraGgslseale...rtpssefpelvvqlirageeggnLaevLerl 84 
                                   l+aG+ l+ a+e+  + ++  +++  e l +++++ raG ++se l+   +   ++ + ++++ ++ag++g  ++++ e++
  gi|14600897|ref|NP_147422.1| 292 LAAGAALAVAVEAGYRLQSirERRALESLGAAVAKARAGLDFSEDLAnarQAAGPVVDVVISASTTAGRTG--VSKAVEAV 370
                                   778888888888777777777778888889999999***********664333334454444445445444..77777777 PP

                                   HHHHHHHHHHH..HHHHHHHHTTXXXXXXXXXXX CS
                         T2SSF  85 aeyleeerelr..rkllaallepllllvvallvl 116
                                     ++ e r l+  +k  a +l+ + ++v a+++l
  gi|14600897|ref|NP_147422.1| 371 YNTILESRLLArrAKTVAVILGAASVAVPAIAIL 404
                                   7777777666522333333333333333333333 PP

>> Arm-DNA-bind_3  Arm DNA-binding 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      0.14      41      71 ..     121     150 ..      85     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                Arm-DNA-bind_3  41 rypavslaeARkkarelraliaqGiDPaeek 71 
                                   +y   sl+ AR++ ++lr ++++G DP ++ 
  gi|14600897|ref|NP_147422.1| 121 SYH-PSLRWARREVERLRLMVKSGLDPEAAA 150
                                   554.599********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); 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:                         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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3704.30
//
Query:       gi|118431156|ref|NP_147426.2|  [L=471]
Description: hypothetical protein APE_0695.1 [Aeropyrum pernix K1]
Scores for 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  136.5   0.0    1.2e-39  136.0   0.0    1.1  1  T2SSE         Type II/IV secretion system protein
    0.00099   19.6   0.0     0.0017   18.8   0.0    1.3  1  ABC_tran      ABC transporter
     0.0015   19.1   0.0     0.0069   16.9   0.0    2.0  2  AAA_18        AAA domain
     0.0018   18.5   0.0     0.0036   17.6   0.0    1.5  1  AAA_22        AAA domain
     0.0022   17.7   0.0     0.0064   16.2   0.0    1.7  2  AAA_30        AAA domain
     0.0023   18.3   0.0     0.0087   16.5   0.0    2.0  2  AAA_16        AAA ATPase domain
     0.0043   15.8   0.0     0.0062   15.3   0.0    1.1  1  RNA12         RNA12 protein
     0.0045   16.7   0.0     0.0092   15.7   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0062   16.8   0.0      0.013   15.8   0.0    1.5  1  AAA_28        AAA domain
     0.0072   15.9   0.1      0.011   15.3   0.1    1.2  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.021   14.8   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.011   16.2   0.0       0.02   15.4   0.0    1.3  1  AAA_23        AAA domain
      0.025   14.5   0.2      0.058   13.3   0.2    1.6  1  NACHT         NACHT domain
      0.027   13.9   0.0      0.048   13.0   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.031   14.1   0.0      0.047   13.5   0.0    1.2  1  dNK           Deoxynucleoside kinase
      0.032   14.0   0.0      0.052   13.4   0.0    1.3  1  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.052   13.5   0.0      0.084   12.8   0.0    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
      0.062   13.5   0.0        0.1   12.7   0.0    1.4  1  AAA_33        AAA domain
       0.12   12.3   0.0       0.19   11.6   0.0    1.2  1  Rad17         Rad17 P-loop domain
       0.12   12.1   0.0       0.19   11.5   0.0    1.2  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.12   12.7   0.0        0.2   12.1   0.0    1.4  1  AAA           ATPase family associated with various cellular 
       0.16   11.2   0.0       0.27   10.5   0.0    1.3  1  Zeta_toxin    Zeta toxin
       0.25   10.8   0.0       0.42   10.0   0.0    1.2  1  PhoH          PhoH-like protein
       0.27   10.7   0.0       0.44   10.0   0.0    1.2  1  AAA_7         P-loop containing dynein motor region


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 !  136.0   0.0   1.6e-42   1.2e-39      11     245 ..     106     348 ..      99     369 .. 0.93

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.6e-42
                          T2SSE  11 dekvsdihvekper..vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvv 88 
                                    d ++ +i +e p+r   +++  v g  ++   +l +++++ l+ ++a  a++++s  +pl ++  +++g+r+ v +   v
  gi|118431156|ref|NP_147426.2| 106 DGHIEEIAFEGPGRgvSVIHSLVPGRWIDVDLKLGEDEANSLALQLARKAGRSLSLAQPLAEGL-TGEGHRVAVTFSREV 184
                                    67899*********94456777777678888999***************************995.559****99999888 PP

                          T2SSE  89 ag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDp 166
                                         ++viRk  +k +t++dl+a++ l++ +a+ l   v++++ i+vsG+ gsGKttll al   i+    r++t+ED+
  gi|118431156|ref|NP_147426.2| 185 SRfgSSFVIRKYPEKPVTMADLVASRVLTPLQAAYLWLLVESQQFIVVSGPMGSGKTTLLQALAGLIPPF-YRVITIEDT 263
                                    877799****************************************************************.********* PP

                          T2SSE 167 vEiqleganqvqlnak.......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaaga 239
                                     Ei+l + +  +l+++        ++v++++llr aLR+r   i+vGE+R++e+  + +A+ +GH   ++T+H +++ g+
  gi|118431156|ref|NP_147426.2| 264 PEIRLYNRHWDSLVTRpplpgesMVEVDLEALLRFALRRRAEYIIVGEVRGREARLLAQAAASGHGS-MTTMHGDTPEGV 342
                                    **********************99*****************************************77.************ PP

                          T2SSE 240 lerLeq 245
                                    + rL+ 
  gi|118431156|ref|NP_147426.2| 343 ILRLQL 348
                                    ***985 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   2.3e-06    0.0017       8      45 ..     224     261 ..     220     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-06
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilld 45 
                                    ++  + +++ G+ G+GK+tLl++lagl  p    i+++
  gi|118431156|ref|NP_147426.2| 224 VESQQFIVVSGPMGSGKTTLLQALAGLIPPFYRVITIE 261
                                    67789999*******************99866666555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.2   2.4e+03      76      90 ..     102     116 ..      43     135 .. 0.68
   2 !   16.9   0.0   9.3e-06    0.0069       1      20 [.     230     249 ..     230     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.2
                         AAA_18  76 nlvidghlaelesea 90 
                                    +l+idgh++e  +e 
  gi|118431156|ref|NP_147426.2| 102 PLIIDGHIEEIAFEG 116
                                    569999999887765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 9.3e-06
                         AAA_18   1 IlltGtpGvGKttlakeLsk 20 
                                    I+++G++G+GKttl ++L+ 
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAG 249
                                    89****************75 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.8e-06    0.0036       4      28 ..     226     250 ..     224     313 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.8e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleq 28 
                                    +++++vv G+ G+GKTtll+ l+  
  gi|118431156|ref|NP_147426.2| 226 SQQFIVVSGPMGSGKTTLLQALAGL 250
                                    89******************99866 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.6e-06    0.0064       3      41 ..     213     250 ..     211     258 .. 0.84
   2 ?   -2.1   0.0       3.6   2.7e+03     104     124 ..     291     311 ..     286     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.6e-06
                         AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKttalkalrea 41 
                                    ++ Qaa +  l++s++ + v+ Gp G+GKtt+l+al+ +
  gi|118431156|ref|NP_147426.2| 213 TPLQAAYLWLLVESQQ-FIVVSGPMGSGKTTLLQALAGL 250
                                    5668888877777775.******************9865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                         AAA_30 104 qlaallkaaekagakvilvGD 124
                                    +l+all+ a ++ a+ i+vG 
  gi|118431156|ref|NP_147426.2| 291 DLEALLRFALRRRAEYIIVGE 311
                                    689999999999999999997 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   0.0   1.2e-05    0.0087      25      48 ..     228     251 ..     213     333 .. 0.81
   2 ?   -2.4   0.0       7.4   5.6e+03      81     124 ..     426     461 ..     407     467 .. 0.48

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                         AAA_16  25 elvllsGesGvGKsslvrellral 48 
                                    + +++sG+ G+GK++l+++l+  +
  gi|118431156|ref|NP_147426.2| 228 QFIVVSGPMGSGKTTLLQALAGLI 251
                                    689***************998544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.4
                         AAA_16  81 llrqlldeaesaeleawrekleealaavpelagaeasrllellk 124
                                     + +l +++e+ el++ +  le+       lag+ ++ ++ +l+
  gi|118431156|ref|NP_147426.2| 426 RIPDLITDLEA-ELSERAGLLEK-------LAGSPPEVFHKALA 461
                                    34444444333.22222222332.......22333344444444 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.3e-06    0.0062      10      34 ..     220     244 ..     214     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.3e-06
                          RNA12  10 ewleEnvntFivvkGPrGSGkkeLv 34 
                                     wl  + + Fivv+GP GSGk+ L+
  gi|118431156|ref|NP_147426.2| 220 LWLLVESQQFIVVSGPMGSGKTTLL 244
                                    6999999***************997 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0092      23      48 ..     228     253 ..     221     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                         AAA_29  23 gatlltGpsGsGKSTllDAiqalLvp 48 
                                    ++++++Gp GsGK+Tll A++ l+ p
  gi|118431156|ref|NP_147426.2| 228 QFIVVSGPMGSGKTTLLQALAGLIPP 253
                                    47889**************9987655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05     0.013       2      22 ..     230     250 ..     229     275 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar 22 
                                    iv++G+ ++GKTtll+aLa  
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAGL 250
                                    9*****************954 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 !   15.3   0.1   1.5e-05     0.011       3      20 ..     230     247 ..     228     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                    EEEEESTTCCHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhl 20 
                                    +v++G++GsGKTtLl++l
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQAL 247
                                    79*************987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.8e-05     0.021      19      40 ..     227     248 ..     207     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                                    TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrgla 40 
                                    +++i+ +G++G+GKTtl ++la
  gi|118431156|ref|NP_147426.2| 227 QQFIVVSGPMGSGKTTLLQALA 248
                                    678****************997 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   2.7e-05      0.02      19      40 ..     227     248 ..     219     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-05
                         AAA_23  19 kgltlItGpNGaGKTTildAik 40 
                                    + + +++Gp G+GKTT+l+A+ 
  gi|118431156|ref|NP_147426.2| 227 QQFIVVSGPMGSGKTTLLQALA 248
                                    678899**************95 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   7.8e-05     0.058       3      21 ..     230     248 ..     228     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                                    EEEEC-TTTCHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                    +++ G+ GsGKTtLlq la
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALA 248
                                    89**************998 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.4e-05     0.048      25      57 ..     230     262 ..     220     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealev 57 
                                    +++ Gp GsGKt l ++l++l+pp  +  ++e 
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAGLIPPFYRVITIED 262
                                    7889********************987666665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.3e-05     0.047       1      20 [.     230     249 ..     230     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                                    EEEEESTTSSHHHHHHHHHC CS
                            dNK   1 ivveGnIgaGKstlvklLsk 20 
                                    ivv+G++g+GK+tl++ L+ 
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAG 249
                                    89**************9985 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   0.0   6.9e-05     0.052       2      22 ..     230     250 ..     229     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.9e-05
                         AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                     v+ Gp gsGK++LL+al +l
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAGL 250
                                    5777999***********999 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   0.00011     0.084      14      40 ..     221     247 ..     215     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                       ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkei 40 
                                    +l  e+++++++ Gp gsGKt+Ll+ +
  gi|118431156|ref|NP_147426.2| 221 WLLVESQQFIVVSGPMGSGKTTLLQAL 247
                                    56668899***************9865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014       0.1       2      96 ..     230     329 ..     229     345 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt.....lrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvi 74 
                                    +++ G+ GsGK+tl++ l+   +  + +++  +     l++r+  + ++++      ++ +   l++l+r al++++ +i
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAGLIPpfYRVITIEDtpeirLYNRHWDSLVTRPPL--PGESMVEVDLEALLRFALRRRAEYI 307
                                    6789**************97777876666655523333333333333333322..2223344445666666677777777 PP

                         AAA_33  75 ldatnlsrrerarflklarrlg 96 
                                    +    + r++r    ++a+ +g
  gi|118431156|ref|NP_147426.2| 308 IVGEVRGREARLLAQAAASGHG 329
                                    7666666666665555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00025      0.19      36      67 ..     220     249 ..     193     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                          Rad17  36 kadvLesrkkriLLisGPsGCgkstvvkvLsk 67 
                                        +es+  + +++sGP G gk+t ++ L+ 
  gi|118431156|ref|NP_147426.2| 220 LWLLVESQ--QFIVVSGPMGSGKTTLLQALAG 249
                                    44445555..99*****************985 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.19       4      24 ..     230     250 ..     227     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                      PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                    i++ G++gsGKttL qal g 
  gi|118431156|ref|NP_147426.2| 230 IVVSGPMGSGKTTLLQALAGL 250
                                    7889**************983 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   0.0   0.00027       0.2       2      22 ..     231     251 ..     230     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                                    EEESSTTSSHHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakel 22 
                                    +++Gp G GKT+l +a+a  +
  gi|118431156|ref|NP_147426.2| 231 VVSGPMGSGKTTLLQALAGLI 251
                                    789**************9865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00037      0.27      17      70 ..     228     282 ..     224     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                     Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrl.dpDdlRelhPeyeeilkadpk 70 
                                      i+++G  G+GK++l+++l+  + +  +v+++ d+ ++R + ++ +++    p 
  gi|118431156|ref|NP_147426.2| 228 QFIVVSGPMGSGKTTLLQALAGLIPPFYRVITIeDTPEIRLYNRHWDSLVTRPPL 282
                                    5799******************999999999994456899999999988876665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00056      0.42       6      40 ..     213     248 ..     210     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                                    SHHHHHHHHHHH.H-SEEEEE--TTSSTTHHHHHHH CS
                           PhoH   6 tkeQkeylealk.kndivfaiGpaGtGKtylavala 40 
                                    t  Q++yl  l  +++++++ Gp G+GKt l  ala
  gi|118431156|ref|NP_147426.2| 213 TPLQAAYLWLLVeSQQFIVVSGPMGSGKTTLLQALA 248
                                    6779999999886889*************9866655 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 ?   10.0   0.0   0.00059      0.44      24      54 ..     218     248 ..     197     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                          AAA_7  24 yllelllknkkpvllvGptGtGKtviikdll 54 
                                      l ll+++++ +++ Gp G+GKt++++ l 
  gi|118431156|ref|NP_147426.2| 218 AYLWLLVESQQFIVVSGPMGSGKTTLLQALA 248
                                    5677899*******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3428.24
//
Query:       gi|14600902|ref|NP_147427.1|  [L=142]
Description: hypothetical protein APE_0697 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1149.78
//
Query:       gi|118431157|ref|NP_147428.2|  [L=310]
Description: deoxyhypusine synthase [Aeropyrum pernix K1]
Scores for complete 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-87  292.2   0.0    4.3e-87  292.0   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 !  292.0   0.0   2.4e-91   4.3e-87       2     286 ..      18     303 ..      17     305 .. 0.95

  Alignments for each domain:
  == domain 1  score: 292.0 bits;  conditional E-value: 2.4e-91
                             DS   2 llesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgk 80 
                                    l+e y++i gf+a +l+ea+++l++  ++ +   +l++t+nl+++Glr+++a+l++ +l++v+ tTag +++D+++ +g 
  gi|118431157|ref|NP_147428.2|  18 LVECYRDIhGFMAGHLAEAVEVLREGLEA-SSVRVLTFTGNLVATGLRGVLAQLIDGGLFNVVFTTAGALDHDIARFMGG 96 
                                    8999**********************765.56889********************************************* PP

                             DS  81 ktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkein.deeSilywAyk 158
                                    k+ +g+fe+dd+eL+++g++R+gn+++p e+y   +e++vr+++++    + +w++ el++  G+ ++ d++Sil++A++
  gi|118431157|ref|NP_147428.2|  97 KYLKGRFEADDTELHRRGVHRLGNVFIPVESYgPLVERFVRTLAEQAAGVRGEWGVYELLRLAGSLMEgDRDSILAAAAR 176
                                    ********************************99**************9999****************999********* PP

                             DS 159 ndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndial.kakktgaiilGGGvpKhhilnanlmrngadya 237
                                    ++++vf+p++ Dg++G++l++ +  ++ +++++d ++D+ +l+di + ++ +++a+i+GGG++Khh++++ ++r g+dya
  gi|118431157|ref|NP_147428.2| 177 RGVDVFVPGWPDGAFGTSLFMER--QRGTSITVDYFRDMARLADIFFpQEGEAAALIVGGGISKHHAIWWSQFRGGLDYA 254
                                    *****************555555..57777*****************555799*************************** PP

                             DS 238 vyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                    vy+tta e+dGslsga+++EavSwgkik++++ v vy+DaTi+lP+++ 
  gi|118431157|ref|NP_147428.2| 255 VYVTTAVEYDGSLSGAHPREAVSWGKIKESSRRVVVYGDATITLPVIAY 303
                                    **********************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2305.58
//
Query:       gi|14600904|ref|NP_147429.1|  [L=166]
Description: hypothetical protein APE_0700 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1300.80
//
Query:       gi|118431158|ref|NP_147431.2|  [L=137]
Description: hypothetical protein APE_0702.1 [Aeropyrum pernix K1]
Scores for complete 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-08   33.2   0.0    6.5e-08   32.8   0.0    1.2  1  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 !   32.8   0.0   3.6e-12   6.5e-08      12      77 ..       6      70 ..       1      76 [. 0.86

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.6e-12
                          ParBc 12 plqprkd.spekieelvasIkkkGll.qPiivrktrqgryeiiaGerRlrAakrlglkevpvivleid 77
                                   +l+p+ + +++++e l + I+ + l  +Pi+v+ +      i++G++R+ A+k+lg+++ p+++ + d
  gi|118431158|ref|NP_147431.2|  6 SLKPHEEvEDDRLELLLDDIRRRRLVvKPILVDAKT---LVILDGHHRFNALKILGARYAPAVLVDYD 70
                                   4455555578************88777********9...***********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1082.84
//
Query:       gi|118431159|ref|NP_147432.2|  [L=389]
Description: DNA topoisomerase VI subunit A [Aeropyrum pernix K1]
Scores for 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   74.5   0.5    8.6e-21   73.7   0.5    1.4  1  TP6A_N    Type IIB DNA topoisomerase
  ------ inclusion threshold ------
      0.032   14.2   0.0      0.049   13.6   0.0    1.3  1  TrbM      TrbM


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 !   73.7   0.5   9.6e-25   8.6e-21       1      62 []      78     154 ..      78     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 9.6e-25
                                    HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH...............GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                         TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr...............dvelFksQaesdrliddievllgvsReeLnv 62 
                                    r+f+q+l+++++i++ l e++++T+Rd+YY+               +++++++Q+esd++i+diev++g+ Re++ +
  gi|118431159|ref|NP_147432.2|  78 RRFMQTLLMASIIYQSLIENEYPTIRDLYYKgkhtivyrdysgrkrEENTWDEQKESDSVIQDIEVYTGLFREDMLI 154
                                    79******************************************999***************************986 PP

>> TrbM  TrbM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.5e-06     0.049     100     154 ..      86     140 ..      31     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-06
                           TrbM 100 iraveietviedklPayCvayeahaytdikvryvgepeeggeWvkakdkekilae 154
                                    + ++ ++ +ie++ P++   y + ++t +   y g++ e+++W++ k+ + + ++
  gi|118431159|ref|NP_147432.2|  86 MASIIYQSLIENEYPTIRDLYYKGKHTIVYRDYSGRKREENTWDEQKESDSVIQD 140
                                    445677899***************************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3106.47
//
Query:       gi|118431160|ref|NP_147433.2|  [L=568]
Description: DNA topoisomerase VI subunit B [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-63  213.6   0.0    2.1e-63  212.9   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    3.5e-10   40.4   0.0    5.6e-10   39.7   0.0    1.4  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    4.6e-09   36.2   0.0    9.5e-09   35.2   0.0    1.5  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00073   18.4   0.0     0.0013   17.6   0.0    1.3  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp


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 !  212.9   0.0   4.8e-67   2.1e-63       1     157 [.     337     492 ..     337     494 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.9 bits;  conditional E-value: 4.8e-67
                 Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvi 80 
                                    P++d lspig+++ie gl+++++pe+v av+r+pk+y+ghpfivEvgiayGG +e ++++ +lR+aN++PLly+e++dv 
  gi|118431160|ref|NP_147433.2| 337 PKSDYLSPIGSDIIEIGLRRMFNPEWVGAVSRSPKAYRGHPFIVEVGIAYGGGIEARSEPLLLRYANKIPLLYEEREDVS 416
                                    99****************************************************************************** PP

                 Topo-VIb_trans  81 tkavksinwkrYkleqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekekeek 157
                                    +k+v+sinw++Y+++ p+ p+vvlvh+astkvP+k++gKe+++dv+eie+ei++a+qevar+L+ yls+k++e+e+ 
  gi|118431160|ref|NP_147433.2| 417 YKVVSSINWRQYNVDFPA-PLVVLVHIASTKVPYKGVGKESVSDVPEIEAEIRNAVQEVARRLRLYLSRKAREEEAI 492
                                    ***************999.*****************************************************99875 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 !   39.7   0.0   1.3e-13   5.6e-10       4      89 ..      51     169 ..      48     205 .. 0.58

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.3e-13
                                    HHHHHHHHHHHHHHHHHHSTTTEE....EEEEEE...EE.....TEEEEEEEESSSSSTTHHHTGTCS..TTCHHCSTCH CS
                      HATPase_c   4 krLrqiisnlvdNavkfatkagei....eveika...se.....ddlvisveDnGiGipkedlkklfe..kfsqddstkr 69 
                                    + L+q i++lv+N++++ t+a+ i    +++i++   se      +++++veDnGiG+p+  + + f+   fs+  ++ +
  gi|118431160|ref|NP_147433.2|  51 RALYQTIRELVENSLDA-TDAKGIlpwiHISIRQiegSEgrggrPRYTVTVEDNGIGVPVTSMAMAFGkvLFSS--KYVI 127
                                    689*************9.644433342244444355622556667*******************9999866777..3333 PP

                                    TS..TSSSHHHHHH....................HHHHHHTT CS
                      HATPase_c  70 gg..ggtGlGlsiv....................kklvelmg 89 
                                    ++  g  GlG++ +                     ++v +m+
  gi|118431160|ref|NP_147433.2| 128 RQtrGMYGLGVKAAilygqmtagtpvevysatkgSQYVYMMK 169
                                    321244555554443344444444444444443333333333 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 !   35.2   0.0   2.1e-12   9.5e-09       6     105 ..      56     170 ..      51     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.1e-12
                    HATPase_c_3   6 AlaelvdNsldAdaen.....vkievnknrgkt.......geivieDdGkGmseeelknal.rlatsskeakrkstslGk 72 
                                     + elv+NsldA   +     ++i++ + +g++        ++++eD+G G++   +  a+ ++  ssk+    ++++G 
  gi|118431160|ref|NP_147433.2|  56 TIRELVENSLDATDAKgilpwIHISIRQIEGSEgrggrprYTVTVEDNGIGVPVTSMAMAFgKVLFSSKYV--IRQTRGM 133
                                    678********988888****9999998887777788888899*************9997768*******5..89***** PP

                    HATPase_c_3  73 kGiGlklAsl....slgkkltvitkkegesstltldv 105
                                    +G+G+k A+l      g  ++v++ ++g+++++ +++
  gi|118431160|ref|NP_147433.2| 134 YGLGVKAAILygqmTAGTPVEVYSATKGSQYVYMMKL 170
                                    ********86333378999*********999554443 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 !   17.6   0.0     3e-07    0.0013     161     239 ..     251     329 ..     243     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-07
                                    SXXXSXBXTTSXXH.HHHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHH CS
                           FbpA 161 PpsqdklnPleaeeleefkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqell 239
                                    Pp  +k+ P  ++  e++k+ l+   + +l+++Lvk+fq ++  +a++ le+ gld++ + +el ++  ++l  +l + l
  gi|118431160|ref|NP_147433.2| 251 PPRESKPHPHGVDI-EQLKSMLRStRASTLREFLVKEFQSIGDKTAQDFLEKYGLDPDLKPRELLKKGRDKLLRRLADAL 329
                                    999999***97777.7777777777889******************************9999999999999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4187.14
//
Query:       gi|118431161|ref|NP_147434.2|  [L=764]
Description: aldehyde dehydrogenase, large subunit [Aeropyrum pernix K1]
Scores for complete 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-163  545.4   0.0   1.6e-163  545.2   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.1e-30  106.3   0.0    2.3e-30  105.2   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 !  545.2   0.0  1.7e-167  1.6e-163       1     550 []     151     694 ..     151     694 .. 0.97

  Alignments for each domain:
  == domain 1  score: 545.2 bits;  conditional E-value: 1.7e-167
                                    STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHH CS
                  Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaev 78 
                                    vh+ea++n+++  +++ Gdve+af+ea++vve+++ + r + + lE++++ a +  ++ +ltv++stq+ph +r+ + e 
  gi|118431161|ref|NP_147434.2| 151 VHDEAERNIAYsrRLSCGDVEKAFREAAVVVEDTLWVARKYAASLEPRGVAASY--DGSTLTVWVSTQTPHDHRDELLEK 228
                                    6999999*999888889*************************************..689********************* PP

                                    HT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEE CS
                  Ald_Xan_dh_C2  79 lglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitald 158
                                    +  p+++vrvi+p+vGG+FG K++++p+ev++ ++A+++grpVk++ +R+edm+at++++++++++ ++a++dG+i++++
  gi|118431161|ref|NP_147434.2| 229 IVPPPSDVRVIQPDVGGAFGAKIEVYPEEVVVPYLAMRLGRPVKWYPSRREDMVATTHGRDIRAELALAASRDGRILGVR 308
                                    ******************************************************************************** PP

                                    EEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHH CS
                  Ald_Xan_dh_C2 159 vdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldple 238
                                     +++ d+Gay +l+ +++  a   l gpY+i++ +ve+ +vytN++p  a+RG+G+p+++f++Er++d lA+elg+dp+e
  gi|118431161|ref|NP_147434.2| 309 GRIIGDVGAY-PLGIFLPLIAGRILPGPYDIRSGDVEVLAVYTNKTPLAAYRGAGRPEGIFFMERMVDLLADELGMDPAE 387
                                    **********.9******************************************************************** PP

                                    HHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEE CS
                  Ald_Xan_dh_C2 239 lRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnq 315
                                    lR rN++kp+++ py++     ydsgd+p +l+++++ ++++e++  ++e +++++  G+g+a++ve ++ g+       
  gi|118431161|ref|NP_147434.2| 388 LRLRNMVKPEAM-PYRNCfgwQYDSGDYPGTLKRGLKLLRLRELESWVEEERRKGRLLGLGYAFYVEITSGGPF------ 460
                                    ************.**9977888******************************88899************66653...... PP

                                    EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHH CS
                  Ald_Xan_dh_C2 316 egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaek 395
                                    e+a+v+++  G+v++ +g+t+ GqG  t +aqiaa+ Lgv +e+vrv++gdt  + +g+gt++Sr+ +++g+Av +A  +
  gi|118431161|ref|NP_147434.2| 461 ETAKVSLERGGTVSIVVGSTPTGQGDATGFAQIAADILGVGVERVRVRWGDTGLIGEGVGTFGSRTITVGGGAVIEAVSE 540
                                    69****************************************************************************** PP

                                    HHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH.....TTSSEEEEEEE...EEEETHCHCSBBE CS
                  Ald_Xan_dh_C2 396 lrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl.....ervslsatgfyktldeetgkgppfayf 467
                                    l erl++ aae+l+v+p  +e++ g+++v    e  v l +++++ y+     +++ lsa ++y         +p++ ++
  gi|118431161|ref|NP_147434.2| 541 LVERLRPKAAEMLGVDPGRVEYRPGEFYVVdspEDFVGLWDVVEQLYRelgekAGEVLSAYAKY---------DPKKPVY 611
                                    ******************************8877778999999999998887777789999999.........78888** PP

                                    EEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GG CS
                  Ald_Xan_dh_C2 468 aygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaa 547
                                    +yg ++a+Ve+D+etg  +v ++ +++DvG+++Np++ egQ+ GG+vqGiG +l+Ee+vy  dG + t sl+dY +Pta 
  gi|118431161|ref|NP_147434.2| 612 PYGLHAAVVEIDPETGVPRVVEYRALDDVGRIVNPMLLEGQLVGGIVQGIGDTLYEEMVYTGDGYPATLSLSDYGVPTAL 691
                                    *******************************************************************************9 PP

                                    GS- CS
                  Ald_Xan_dh_C2 548 diP 550
                                    + P
  gi|118431161|ref|NP_147434.2| 692 EYP 694
                                    987 PP

>> Ald_Xan_dh_C  Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   2.6e-34   2.3e-30       1     109 [.      26     134 ..      26     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 2.6e-34
                                    TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEESST CS
                   Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvrsv 80 
                                    tG+++YvdD+ ++g+ly+af rS ++hA + ++d s+al++pGVva ++++dl+++ k +   + +++ + la+d+vr++
  gi|118431161|ref|NP_147434.2|  26 TGRGRYVDDVRLEGMLYAAFARSEYPHAVVRKVDLSDALKAPGVVAAFSYSDLEGSLKPWTFDAPSSPMYPLARDRVRYY 105
                                    8***********************************************************9555666789********** PP

                                    T-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                   Ald_Xan_dh_C  81 gqavaavvAedeetArkAaklvkveYeel 109
                                    g++va+vvA d ++A++A++lv+v+Ye+l
  gi|118431161|ref|NP_147434.2| 106 GEPVAVVVASDPYQAADAVELVSVDYEPL 134
                                    ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (764 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5537.43
//
Query:       gi|118431162|ref|YP_874839.1|  [L=69]
Description: hypothetical protein APE_0708a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.054   13.5   8.8      0.066   13.2   8.8    1.0  1  Colicin_V  Colicin V production protein
        1.2    9.7   5.7        1.6    9.3   5.7    1.2  1  DUF4231    Protein of unknown function (DUF4231)
        2.4    8.6   6.5        2.6    8.5   6.5    1.1  1  DUF805     Protein of unknown function (DUF805)


Domain annotation for each model (and alignments):
>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   8.8   1.1e-05     0.066      18      78 ..       7      65 ..       6      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                      Colicin_V 18 rrGfvrevlsllgwvvafvvasllypslaellae.lilspalaaiiaflllfllvllivsll 78
                                   rrGf+r++ +l+  +++fv+a++l+  la+ + +  i  + l++i+a ++++++v+++   l
  gi|118431162|ref|YP_874839.1|  7 RRGFLRRLKTLVLAALVFVIAYRLALALAASILKgAIAAAMLVSILAAAAVVIAVVML---L 65
                                   8***************************999998544555555555554444444443...3 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.7   0.00026       1.6      10      66 ..       3      65 ..       1      68 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                        DUF4231 10 asrakrrfrllrlitivlgallpilvs.......sklgagvsvlkiltallsalvailaaleef 66
                                   a++++r f   rl t+vl+al+ +++             g+ ++++l+++l+a+++++a ++ +
  gi|118431162|ref|YP_874839.1|  3 ARQSRRGFL-RRLKTLVLAALVFVIAYrlalalaASILKGAIAAAMLVSILAAAAVVIAVVMLL 65
                                   677788887.9999******99999999888777444556666666666666666666666655 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.5   0.00044       2.6       5      62 ..       2      67 ..       1      69 [] 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00044
                         DUF805  5 kGRasRsefw....wfvlfllllviv....lallaavlaaaavasalsvvlallllvpslavtvRR 62
                                   + R sR+ f       vl+ l++vi+    lal a++l++a++a++l ++la +++v+++ ++ RR
  gi|118431162|ref|YP_874839.1|  2 QARQSRRGFLrrlkTLVLAALVFVIAyrlaLALAASILKGAIAAAMLVSILAAAAVVIAVVMLLRR 67
                                   578999999888773333333333331111444444444477778888888888888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1319  (0.073568); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 544.89
//
Query:       gi|118431163|ref|NP_147435.2|  [L=288]
Description: N-glycosylase/DNA lyase [Aeropyrum pernix K1]
Scores for 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-69  232.4   0.0    6.3e-69  232.1   0.0    1.0  1  AGOG      N-glycosylase/DNA lyase


Domain annotation for each model (and alignments):
>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.1   0.0   3.5e-73   6.3e-69       2     244 ..      15     259 ..      14     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 232.1 bits;  conditional E-value: 3.5e-73
                                    HHHCCCHHHHHHHHHCCTSHHHHHHHHHHCCC-H...HHHHHHHHHHHHT-SS-TT-HHHHHHHHHHHH.....CTS--S CS
                           AGOG   2 ellkelgieevlkleekvDpQykaveelveklged..elfvklvilNaLvSYqLsgrGEewWkefskyf.....sekeik 74 
                                    e++++l+i evl +ee+vDpQyk+v++l+ ++g++  +l ++lv   +L SY+L++rGEewW +f++++     + + ++
  gi|118431163|ref|NP_147435.2|  15 EAFSRLSIGEVLGFEEQVDPQYKLVSRLAGEIGAGkaALSALLV---GLASYRLAMRGEEWWLCFYRHMrsslpRAEGLR 91 
                                    789*****************************998667777777...**********************88777677788 PP

                                    SHHHHHHHHHHH-TTS-TTHHHHHHHHHHHCCHHHTTTHHHHHHHHHT...HHHHHHHHHHHHTS-TTSHHHHHHHHHHH CS
                           AGOG  75 nileefikflekskgnrrlreakikRiekivefledleleelksylen...leelleelakilgskkesKTvvFavKmly 151
                                     +l+++  fl++++g++++reak++R++++++++e +  e l+++l+    ++e+le+l+ +lg+k  +KT vF+vK++y
  gi|118431163|ref|NP_147435.2|  92 GVLRAVEGFLTSCSGAAIGREAKLRRVRRAASAAE-VLGEVLDNPLVLverPSEVLEALRVALGEKGFRKTTVFSVKIAY 170
                                    8*****************************77766.7889*****944468***************************** PP

                                    HHHHHHHTS-----TTS-----HHHHHHHHHTTS-SS-HHHHHHTHCCHC..S.HHHHHHHHHHHHT--HHHHHHHHHHH CS
                           AGOG 152 YalrialgeeiplpfeipiPvDvRiakltktsglielknekklarkelvq..eevieaWkevsreseiPplhlDsllWvl 229
                                    Ya+r  l+ ++pl++++piPvDvR+a+++++s+++e+++  +     +v+  e++++aW +v+r+s+iP+lh+Ds+lWv+
  gi|118431163|ref|NP_147435.2| 171 YAVR-PLAGRKPLTLDVPIPVDVRVACASISSEMVEAPSYRE-----VVArpEAAQRAWGRVARSSGIPVLHIDSILWVT 244
                                    ****.99999***************************85444.....44447999************************* PP

                                    CCHHHCCS-HCCCCC CS
                           AGOG 230 gksaleledaevkel 244
                                    g++ +el + e++e+
  gi|118431163|ref|NP_147435.2| 245 GWAPRELPPGEAREA 259
                                    *****9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2216.36
//
Query:       gi|118431164|ref|NP_147436.2|  [L=375]
Description: O-succinylbenzoate synthase [Aeropyrum pernix K1]
Scores for complete 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  119.0   0.0    2.9e-34  118.6   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    5.1e-11   42.8   0.0    8.9e-11   42.0   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   0.0   3.2e-38   2.9e-34       2     217 ..     145     354 ..     144     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 3.2e-38
                                    HHHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESSS CS
                       MR_MLE_C   2 laeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEPv 81 
                                    l++ + ++++e g+ ++K+k+    + +d+e v+a+r+++ p+  v l vDan+a++  +A r+ r l++++ll++E+P+
  gi|118431164|ref|NP_147436.2| 145 LVRTVSRYLEE-GYGRIKIKIE---PGWDLEPVEALRREF-PD--VPLQVDANAAYTFLDAPRLSR-LDDYGLLMIEQPF 216
                                    67888777776.********55...47*************.74..5***************87665.659********** PP

                                    STTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHH.HTT-EEEEBSCS. CS
                       MR_MLE_C  82 ppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalae.afgvpvapHsgs. 158
                                    ++ ddl ++a+ ++   ++p++++Es++s+ d+ ++l+ g + +++++++rvgGi  ++++ +  + ++++pv+++++  
  gi|118431164|ref|NP_147436.2| 217 HH-DDLLEHAHFQS-MvRTPVCLDESVKSVRDAVAALKLGSARVINIKPGRVGGIASSLEIHDFWSlKAHLPVWIGGMLe 294
                                    *9.78********6.3479********************************************98747*********955 PP

                                    SHHHHHHHHHHHHTTTTBEEEEEEGGGGH.TSGCSBSSSSEEETT.EEECTSSSBTSSEB- CS
                       MR_MLE_C 159 gglglaaslhlaaaipnllileyfldael.leeelleeplevedG.rvtvpdgpGlGveld 217
                                    +g+g+  +l  + ++p++++ ++   + +   e++++ep e e G  +++ ++pG+Gve+d
  gi|118431164|ref|NP_147436.2| 295 TGVGR-GHLVALGTLPGVRYPSDISASRRyYMEDIVDEPWELERGsVIRARSRPGIGVEVD 354
                                    89999.577778899999999999988888999************7888999********9 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0     1e-14   8.9e-11       6     117 .]       8     124 ..       3     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1e-14
                                    EEEEEEEEC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STT...GHHHHHHHHHHHHHHHHTTSBTTHHHHHHHH CS
                       MR_MLE_N   6 vveeavklr.PvqlavttvqkqslvlvkietseGvvGigeatsvgg...raetikaelddhlapllvgkdaanisdlaql 81 
                                    v+e+ ++l   +++++++ +  +  lv+   ++G +G+ge ++  g   + et+  + +  + +++    ++ i++ +++
  gi|118431164|ref|NP_147436.2|   8 VFEVWMPLVsEFRTSFGSTRLRPALLVRAVEKGGEEGWGEVVAGEGpwySSETVWTAWHV-IEDYIARLLPSTIEHPREV 86 
                                    555555665678999*999999999999777**********9987779977777665554.5555555567777777777 PP

                                    HHHHCSS..CHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                       MR_MLE_N  82 lkravlg..nmsAkaaidmAlwDlkakalnlpladLlG 117
                                      r        +Aka+++mAlwDlka+    pl+ L+G
  gi|118431164|ref|NP_147436.2|  87 GGRLSRIrgHNMAKAGVEMALWDLKARMESKPLWSLIG 124
                                    76665444499**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2797.36
//
Query:       gi|118431165|ref|NP_147437.2|  [L=503]
Description: Trk system potassium uptake protein TrkH [Aeropyrum pernix K1]
Scores for 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-47  159.6  12.2    4.1e-25   88.2   1.9    2.2  2  TrkH            Cation transport protein
  ------ inclusion threshold ------
      0.024   14.4   1.4      0.024   14.4   1.4    3.2  2  Form-deh_trans  Formate dehydrogenase N, transmembrane


Domain annotation for each model (and alignments):
>> TrkH  Cation transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   2.9   1.6e-25   1.4e-21      37     249 ..      82     285 ..      60     298 .. 0.85
   2 !   88.2   1.9   4.5e-29   4.1e-25     314     496 ..     318     498 ..     309     501 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.6e-25
                           TrkH  37 qivkaaeialsvdgtlklllesaslafldalfeavsgltttglsvivveesl...........prsgltlraqlqqiGgl 105
                                     i++a+++++   ++   ++e   +++ dal e+v g+tttgls  + +es+           p s + +r++lq++Gg+
  gi|118431165|ref|NP_147437.2|  82 FITVATWLSVPLFSAAL-MSEILDIPYVDALLETVAGWTTTGLSILTGAESSsggyvpsvdeiPESVKLWRSMLQWVGGV 160
                                    56666777776665554.567788889*******************9999877777777778899*************** PP

                           TrkH 106 gvvvlaylslptlgrgsaflylseaqkeelggkelrslselikilvvyyvgleilafvllvvliytakaysevvdstgvs 185
                                    g+vv++++ l+++g+  a+ly +e       +    sl+  +  ++++y+++++l+++++         y +++      
  gi|118431165|ref|NP_147437.2| 161 GIVVFTVAFLARPGISAAALYIAEGRF----ERLEASLKASAIRMTLVYMVYTLLGALII---------YLSGM------ 221
                                    ************************944....444456677777778889999********.........*****...... PP

                           TrkH 186 plwwaffhsmSafnnlGfsltpnSlasfnknivillvaiifiilGnigFpillrviiaikkkil 249
                                    +l +a+ hsm+a++++Gfs++++S + ++  + +++ ++++++lG+ +F+ l++++  +  ++l
  gi|118431165|ref|NP_147437.2| 222 SLSDAIQHSMTAISTAGFSTHADSVGFYKGDYAVYASTLLVSFLGALSFVDLDNIMRLRLGRVL 285
                                    *************************************************877766655555555 PP

  == domain 2  score: 88.2 bits;  conditional E-value: 4.5e-29
                           TrkH 314 srvlkalFqsvstrta.GFsvvdlsnlhpaikvllvlmmyigglpgStaggIrrtnvyeefslgkyeieqekepk.avsk 391
                                    +   + ++ svs   + GFs+++l   +++ k+l+     igg++ StaggI+ ++++++ ++++ e+ +  +p+  v k
  gi|118431165|ref|NP_147437.2| 318 YTLADTIYNSVSGYITvGFSTASLEGASDSYKLLIAALGLIGGSAFSTAGGIKVLRLAIALKTLDVETTRILKPSsYVPK 397
                                    56667889999988777**********************************************************89999 PP

                           TrkH 392 ksidgkhlerqllvdlwslflvlliilileglklsdvqepdfsffdiLfevvSaygtvGLSlGaknaslsaqlttisklv 471
                                      i+g++l+++++    ++++ +  + il gl         + ++di+f v+Sa++++GLS+G     +s++ +t  k++
  gi|118431165|ref|NP_147437.2| 398 NLIGGRRLTEDMVKRSLAVIIAFATVEILLGLTAVALYSDIYPTVDIIFDVTSALANIGLSTG----VTSPEAPTGLKVI 473
                                    99***********999997777776666666655555555799********************....9************ PP

                           TrkH 472 lialmirGrlrglpvlldraillps 496
                                    lia m++Grl++lp+++++  l++s
  gi|118431165|ref|NP_147437.2| 474 LIAGMLLGRLEILPYIVAAKYLVES 498
                                    *****************99877665 PP

>> Form-deh_trans  Formate dehydrogenase N, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.4   2.6e-06     0.024       1      27 [.     143     169 ..     143     171 .. 0.91
   2 ?   -1.0   0.9      0.18   1.6e+03      14      32 ..     292     310 ..     290     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-06
                                    --HHHHHHHTTHHHHHHHHHHHHHHHH CS
                 Form-deh_trans   1 ISplVelWKGvlKplgalgmaatalag 27 
                                    I+ +V+lW+ +l ++g +g+++  +a 
  gi|118431165|ref|NP_147437.2| 143 IPESVKLWRSMLQWVGGVGIVVFTVAF 169
                                    899*****************9988875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHHHHHHHHHH CS
                 Form-deh_trans  14 plgalgmaatalagffHYi 32 
                                    +++ l+  ++a+a+++ Yi
  gi|118431165|ref|NP_147437.2| 292 VIAGLTALSAAAAAAVWYI 310
                                    5677777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 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:                        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 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3949.76
//
Query:       gi|118431166|ref|NP_147438.2|  [L=315]
Description: hypothetical protein APE_0716.1 [Aeropyrum pernix K1]
Scores for 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-55  186.1   0.0    5.8e-55  185.6   0.0    1.2  1  Phage_integr_3  Archaeal phage integrase
  ------ inclusion threshold ------
        0.2   12.1   0.0       0.43   11.1   0.0    1.6  1  CBS             CBS domain


Domain annotation for each model (and alignments):
>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.6   0.0   6.4e-59   5.8e-55       2     158 ..     138     298 ..     137     300 .. 0.97

  Alignments for each domain:
  == domain 1  score: 185.6 bits;  conditional E-value: 6.4e-59
                                    T---HHHHHHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHHHHS...GGG-..EEETTEEEEEEEE-SSS-EEEEEEES CS
                 Phage_integr_3   2 viptdeevrealeelkekseevelvykllvfsGiRLkevlklLre.yDpekl..iveddiarYpialekgeKkafyiylp 78 
                                    ++p+d+++ ea+++l+ +  +v++v++llv sG+RL++v++lLr+ +D+++l  +++++++rY++++ kgeK ++++y+p
  gi|118431166|ref|NP_147438.2| 138 YVPPDSSILEAARRLEGT--RVYHVFLLLVGSGARLSTVHWLLRQgLDSSRLvcLEDRGFCRYHVDYVKGEKLQWALYSP 215
                                    89**************98..********************************8778999********************* PP

                                    S---.......--B--HHHHHHHHHT-T--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHHHHHHHHHHH CS
                 Phage_integr_3  79 tela.kele..rlelseeavkefeakkkvkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnllvlAdeaYk 155
                                    +e++ + le  rl+ls+++v+e+ a ++vkak+iR+wv++k+++lg+pe+v++Fi+G+k+ss++++hY+n++v+Ad++Y+
  gi|118431166|ref|NP_147438.2| 216 REFWeRVLEepRLTLSYNRVQEQIAGAGVKAKHIRNWVYNKMLSLGMPEGVVEFIVGHKASSIGRRHYMNMIVQADMWYT 295
                                    ****8889899********************************************************************* PP

                                    HHH CS
                 Phage_integr_3 156 kvv 158
                                    +++
  gi|118431166|ref|NP_147438.2| 296 TYL 298
                                    *97 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.8e-05      0.43      11      34 ..     138     162 ..     130     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                                    EEETTSBHHHHHHHHHHHT.SSEEE CS
                            CBS  11 tvppdttleealelmrekg.vsrlP 34 
                                    +vppd+++ ea+++++ ++ ++ ++
  gi|118431166|ref|NP_147438.2| 138 YVPPDSSILEAARRLEGTRvYHVFL 162
                                    79*************7777665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        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 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2689.82
//
Query:       gi|14600914|ref|NP_147439.1|  [L=128]
Description: hypothetical protein APE_0718 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.015   15.6   0.0    1.2  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 ?   15.6   0.0   8.6e-07     0.015      21      64 ..      39      82 ..      34     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.6e-07
                                  HHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE- CS
               Penicillinase_R 21 kevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsp 64
                                  ++++ +l++   ++  TV   +rrL + ++++r + gr+ i++p
  gi|14600914|ref|NP_147439.1| 39 SWIHYALPKHERPEWHTVERAIRRLAELEVVRRLRRGRKVIFCP 82
                                  589999****9*******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1001.29
//
Query:       gi|118431167|ref|YP_874840.1|  [L=89]
Description: hypothetical protein APE_0718a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.7   0.0       0.16   11.9   0.0    1.4  1  RelB      RelB antitoxin


Domain annotation for each model (and alignments):
>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.1e-06      0.16      21      34 ..      15      28 ..       9      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.1e-06
                                   HCCT--HHHHHHHH CS
                           RelB 21 ekmGltiSqairlf 34
                                   e+mGltiS+a++++
  gi|118431167|ref|YP_874840.1| 15 ERMGLTISEAVEIM 28
                                   89*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 679.79
//
Query:       gi|14600916|ref|NP_147441.1|  [L=113]
Description: hypothetical protein APE_0720 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.7   0.1      0.076   12.5   0.1    1.1  1  ROK       ROK family


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 ?   12.5   0.1   4.2e-06     0.076     168     229 ..      28      94 ..      16      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-06
                                   TTS-BS.BHHHCCSHHHHHHCHTC..CGTTS-HHHHHHHHCTT..-HHHHHHHHHHHHHHHHHHHHH CS
                           ROK 168 gCGnqg.ClEtlasgralekraqq..kgekleakeiiklaekg..devaeevverlaeylakaiadl 229
                                    C+  + C+ ++as +a+ +  +   +++  ea++i++ a+ g   e + +v+++lae  a+ + d+
  gi|14600916|ref|NP_147441.1|  28 LCPGSDaCYSGYASIMAVDREKRSeaAERLREARKILEDARLGleRELTRAVLKELAEEKARELLDA 94 
                                   5777766***********7654444399999********9987335678899999999888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 873.22
//
Query:       gi|118431168|ref|YP_874841.1|  [L=81]
Description: hypothetical protein APE_0720a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-11   43.2   0.0    3.3e-11   42.8   0.0    1.2  1  HTH_IclR        IclR helix-turn-helix domain
    1.7e-06   27.8   0.0    2.3e-06   27.4   0.0    1.1  1  MarR_2          MarR family
     0.0001   21.8   0.0    0.00016   21.2   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00023   21.5   0.0    0.00025   21.3   0.0    1.1  1  Rrf2            Transcriptional regulator
     0.0006   19.6   0.0    0.00068   19.4   0.0    1.1  1  DUF4423         Domain of unknown function (DUF4423)
    0.00074   19.2   0.0     0.0023   17.6   0.0    1.8  2  HTH_23          Homeodomain-like domain
    0.00091   19.2   0.0     0.0011   18.9   0.0    1.2  1  HTH_45          Winged helix-turn-helix
      0.002   17.6   0.1     0.0039   16.7   0.0    1.6  2  Sigma70_r4      Sigma-70, region 4
     0.0027   17.5   0.0     0.0036   17.2   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0069   16.3   0.0     0.0077   16.2   0.0    1.1  1  Dimerisation2   Dimerisation domain
  ------ inclusion threshold ------
      0.031   13.8   0.1        0.1   12.2   0.1    1.9  1  GerE            Bacterial regulatory proteins, luxR family
      0.039   14.1   0.1       0.17   12.1   0.0    1.8  2  Mrr_N           Mrr N-terminal domain
      0.041   13.7   0.0       0.11   12.3   0.0    1.7  2  HTH_10          HTH DNA binding domain
      0.046   13.7   0.0       0.07   13.1   0.0    1.3  1  MarR            MarR family
       0.05   13.7   0.0      0.076   13.1   0.0    1.3  1  HTH_20          Helix-turn-helix domain
      0.084   13.1   0.0       0.19   12.0   0.0    1.6  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.096   11.0   0.0      0.096   11.0   0.0    1.1  1  DUF505          Protein of unknown function (DUF505)
       0.14   11.9   0.1       0.29   10.8   0.0    1.4  1  Ribosomal_S19e  Ribosomal protein S19e


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 !   42.8   0.0   3.3e-14   3.3e-11       6      52 .]      12      58 ..       9      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.3e-14
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                   l+ L++l+e pq+ +l+e+++ +g+p+S++h+l+q L  l +v ++g
  gi|118431168|ref|YP_874841.1| 12 LRALRFLREKPQGASLKEISDSLGIPPSSAHGLMQKLLALNLVDKNG 58
                                   788****************************************9986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   2.3e-09   2.3e-06       3      53 ..       7      56 ..       6      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.3e-09
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   l++ ++r+L +L+  p +  + +e+ + lg+++s+++ + ++L a  Lv +
  gi|118431168|ref|YP_874841.1|  7 LSVRELRALRFLREKPQG-ASLKEISDSLGIPPSSAHGLMQKLLALNLVDK 56
                                   6889************98.7*****************************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 !   21.2   0.0   1.6e-07   0.00016       5      47 ..      11      54 ..       7      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                         HTH_24  5 drkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +++ L+ L+++p   s +e+++ lg++ps  +  +++L    l+
  gi|118431168|ref|YP_874841.1| 11 ELRALRFLREKPQgASLKEISDSLGIPPSSAHGLMQKLLALNLV 54
                                   6899*********************************9887765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.5e-07   0.00025      11      74 ..      12      71 ..       3      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.5e-07
                                   HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCS CS
                           Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeI 74
                                   l+al +L +++++  +s++ei+++ +i+ps +  +++kL   +lv  + G+ G y L+k+ e++
  gi|118431168|ref|YP_874841.1| 12 LRALRFLREKPQG--ASLKEISDSLGIPPSSAHGLMQKLLALNLVD-KNGQ-GKYYLTKAGEQV 71
                                   7899999999997..5*****************************8.5788.999999998886 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.8e-07   0.00068      32      82 ..      21      68 ..       9      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.8e-07
                        DUF4423 32 lkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteks 82
                                    +++ a+ +e+++ l+  i+ + ++  ++ Ll l+l++k+++gky  t++ 
  gi|118431168|ref|YP_874841.1| 21 KPQG-ASLKEISDSLG--IPPSSAHGLMQKLLALNLVDKNGQGKYYLTKAG 68
                                   3444.99*********..***************************999875 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.4e-06    0.0023       6      33 ..      10      40 ..       5      50 .. 0.85
   2 ?   -0.7   0.0       1.4   1.4e+03       5      18 ..      45      59 ..      42      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                         HTH_23  6 eRlrillllae...GlsvreIAreLgvsrrT 33
                                   + lr+l+ l+e   G+s +eI++ Lg++++ 
  gi|118431168|ref|YP_874841.1| 10 RELRALRFLREkpqGASLKEISDSLGIPPSS 40
                                   55788888887777**************997 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                         HTH_23  5 reRlrillllae.Gl 18
                                   +++l++l l+++ G+
  gi|118431168|ref|YP_874841.1| 45 MQKLLALNLVDKnGQ 59
                                   579999999997654 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-06    0.0011      39      72 ..      44      78 ..      21      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                         HTH_45 39 YLdmLvekgli.kkskekYvlTekGlelleklkel 72
                                    +++L+  +l+ k+ ++kY+lT+ G+++lek+  +
  gi|118431168|ref|YP_874841.1| 44 LMQKLLALNLVdKNGQGKYYLTKAGEQVLEKIGAI 78
                                   57899999***77799***************9765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.9e-06    0.0039       1      42 [.       3      46 ..       3      50 .. 0.86
   2 ?   -3.0   0.0       5.6   5.6e+03      22      28 ..      71      77 ..      64      78 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-06
                                   HHHHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHHHHHHH CS
                     Sigma70_r4  1 aLasLpererevlelrf..geglTleEIgerlgiSrerVrqiek 42
                                   +L++L+ re + l+  +   +g +l+EI++ lgi+ + ++ ++ 
  gi|118431168|ref|YP_874841.1|  3 WLDRLSVRELRALRFLRekPQGASLKEISDSLGIPPSSAHGLMQ 46
                                   799999999999998888999**************887766655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                                   -HHHHHH CS
                     Sigma70_r4 22 TleEIge 28
                                    le Ig+
  gi|118431168|ref|YP_874841.1| 71 VLEKIGA 77
                                   4666765 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   3.6e-06    0.0036      10      60 ..      11      63 ..       7      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.6e-06
                                   CCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TT CS
                           TrmB 10 EakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pk 60
                                   E ++   L  k + a+ +ei+  lg+p s++   +++L+   lV+++ +  ++
  gi|118431168|ref|YP_874841.1| 11 ELRALRFLReKPQGASLKEISDSLGIPPSSAHGLMQKLLALNLVDKNGQGkYY 63
                                   555555555455678899***************************99644144 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.7e-06    0.0077      20      85 ..      11      73 ..       7      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                  Dimerisation2 20 eLgvFdlLke.eeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelastyLv 85
                                   eL+   +L+e  +  s++e++++lg+ +++ + L++ + aL+L  ++   + ++ Y  t++ ++ L 
  gi|118431168|ref|YP_874841.1| 11 ELRALRFLREkPQGASLKEISDSLGIPPSSAHGLMQKLLALNLVDKN---G-QGKYYLTKAGEQVLE 73
                                   566666889988999******************************44...3.368999999998886 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   0.1    0.0001       0.1       2      32 ..       6      39 ..       5      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                   SS-HHHHHHHHHHC...TTS-HHHHHHHHTS-HH CS
                           GerE  2 sLskRErevLrlla...eGksnkeIAeelniSek 32
                                    Ls RE+  Lr l    +G s keI+++l+i + 
  gi|118431168|ref|YP_874841.1|  6 RLSVRELRALRFLRekpQGASLKEISDSLGIPPS 39
                                   689999988877753338************9765 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1   1.1e+03       8      27 ..      14      34 ..      11      37 .. 0.78
   2 ?   12.1   0.0   0.00017      0.17      59      86 ..      46      73 ..      41      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                          Mrr_N  8 lLealad.gsehrlkeirerv 27
                                   +L++l++  ++ +lkei + +
  gi|118431168|ref|YP_874841.1| 14 ALRFLREkPQGASLKEISDSL 34
                                   789999987788888888765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00017
                          Mrr_N 59 tyLkkagllespkrgvwkiTekGrevlk 86
                                   ++L   +l++++ +g++ +T++G +vl+
  gi|118431168|ref|YP_874841.1| 46 QKLLALNLVDKNGQGKYYLTKAGEQVLE 73
                                   5677789*******************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.11      19      44 ..      20      45 ..      20      50 .. 0.87
   2 ?   -2.4   0.0       4.4   4.3e+03      42      52 ..      62      72 ..      61      73 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                         HTH_10 19 dyPRrvtlkeLAkelGIskstlsehL 44
                                   + P  ++lke+++ lGI +s+++  +
  gi|118431168|ref|YP_874841.1| 20 EKPQGASLKEISDSLGIPPSSAHGLM 45
                                   57999***************998665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                         HTH_10 42 ehLrkaeskli 52
                                   ++L ka ++++
  gi|118431168|ref|YP_874841.1| 62 YYLTKAGEQVL 72
                                   68888877776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     7e-05      0.07       1      48 [.       7      55 ..       7      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-05
                                   --HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  1 ltltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                   l+  ++++Lr l+e+++ +s++e+ + lg+ +s++  +  +L   +l++
  gi|118431168|ref|YP_874841.1|  7 LSVRELRALRFLREKPQgASLKEISDSLGIPPSSAHGLMQKLLALNLVD 55
                                   67899***********99************************9999987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.6e-05     0.076      19      60 ..      15      60 ..       6      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.6e-05
                                   H....STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20 19 L....araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   L      ++g++++e+ + l++++++++  +++L    Lv+  ++g
  gi|118431168|ref|YP_874841.1| 15 LrflrEKPQGASLKEISDSLGIPPSSAHGLMQKLLALNLVDKNGQG 60
                                   45556679**************************999999988776 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 ?   12.0   0.0   0.00019      0.19      16      53 ..      18      55 ..      11      61 .. 0.81
   2 ?   -2.0   0.0       4.3   4.2e+03       2      13 ..      64      75 ..      63      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                   HHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress 16 lseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                   l e+ + ++ k+++  L++ pss+   ++kL    +v+
  gi|118431168|ref|YP_874841.1| 18 LREKPQGASLKEISDSLGIPPSSAHGLMQKLLALNLVD 55
                                   5666777899*******************998777776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                   --HHHHHHHHHH CS
                 Fe_dep_repress  2 LvestEdYLetI 13
                                   L++  E++Le I
  gi|118431168|ref|YP_874841.1| 64 LTKAGEQVLEKI 75
                                   677789999987 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.7e-05     0.096     376     403 ..      51      74 ..      15      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                         DUF505 376 feLieseveekgkevyvlTeyGekvled 403
                                     +L    v+++g+  y+lT+ Ge+vle+
  gi|118431168|ref|YP_874841.1|  51 LNL----VDKNGQGKYYLTKAGEQVLEK 74 
                                    223....366799999999999999986 PP

>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.29      97     131 ..      42      76 ..      35      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                                    SSS--SSS---SS-HHHHHTHHHHH--SS--S--X CS
                 Ribosomal_S19e  97 rkilqqLeklglvkkekkkgrrltkkGqrlldria 131
                                    + ++q+L +l+lv k+ +++  ltk+G++ l++i 
  gi|118431168|ref|YP_874841.1|  42 HGLMQKLLALNLVDKNGQGKYYLTKAGEQVLEKIG 76 
                                    6689*********777666889**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 606.64
//
Query:       gi|14600918|ref|NP_147443.1|  [L=219]
Description: hypothetical protein APE_0722 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00081   19.2   0.1      0.015   15.1   0.0    2.3  2  MarR_2      MarR family
     0.0014   18.6   0.0     0.0026   17.7   0.0    1.4  1  HTH_45      Winged helix-turn-helix
     0.0015   18.4   0.4       0.72    9.8   0.1    2.3  2  TrmB        Sugar-specific transcriptional regulator TrmB
     0.0033   17.0   0.0      0.012   15.2   0.0    1.9  2  HTH_24      Winged helix-turn-helix DNA-binding
     0.0068   16.4   0.1       0.95    9.5   0.0    2.7  3  HTH_Crp_2   Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.6   0.1        5.4    7.4   0.0    2.3  2  Rrf2        Transcriptional regulator
      0.037   13.9   0.0      0.067   13.1   0.0    1.5  1  HTH_5       Bacterial regulatory protein, arsR family
      0.046   13.5   0.0       0.11   12.4   0.0    1.6  1  HTH_23      Homeodomain-like domain
      0.089   13.2   0.2       0.31   11.4   0.1    1.9  2  FaeA        FaeA-like protein
       0.12   12.5   0.0       0.23   11.6   0.0    1.5  1  MotA_activ  Transcription factor MotA, activation 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 !   15.1   0.0   8.6e-06     0.015       4      54 ..       9      57 ..       7      62 .. 0.94
   2 ?    1.6   0.0      0.14   2.5e+02      33      51 ..     159     177 ..     146     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                                  -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                  +p+ a +L  L  r     +  ela +lg+ +s v+  l    ++G ve++
  gi|14600918|ref|NP_147443.1|  9 SPTTASILILLLQRAQ--ASSVELAVELGVYPSQVNAYLHYYRKQGIVEKS 57
                                  7999***********9..9******************************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                                   SSHHHHHHHHHHHHHTTSE CS
                        MarR_2  33 lsksavsrilkrLvaaGLv 51 
                                   +s+ +v+  l++L+++G v
  gi|14600918|ref|NP_147443.1| 159 VSPFRVQECLAELSQRGVV 177
                                   6777899999999999998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.4e-06    0.0026      25      69 ..      30      74 ..      12      82 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                        HTH_45 25 imykanLsykllnkYLdmLvekglikkskekYvlTekGlellekl 69
                                  +  +     +++n YL++  ++g+++ks++ ++lTe Gl+++++ 
  gi|14600918|ref|NP_147443.1| 30 LAVELGVYPSQVNAYLHYYRKQGIVEKSGDVWRLTEDGLKYVQER 74
                                  444444455789****************************99875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0004      0.72      11      55 ..      13      57 ..       9      71 .. 0.93
   2 !    6.6   0.0     0.004       7.1      38      59 ..     163     184 ..     147     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                                  CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                          TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                  a++ + Ll++ +a+  e+a elgv  s+v+ +L    + G+Ve++
  gi|14600918|ref|NP_147443.1| 13 ASILILLLQRAQASSVELAVELGVYPSQVNAYLHYYRKQGIVEKS 57
                                  6788999***********************************986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.004
                                   CHHHHHHHHHHCTSEEEESSTT CS
                          TrmB  38 kvYevLrsLedkGlVerekgrp 59 
                                   +v+e L +L+++G+V++ +gr+
  gi|14600918|ref|NP_147443.1| 163 RVQECLAELSQRGVVYIWRGRK 184
                                   8***************999884 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.4e-06     0.012       7      38 ..      14      45 ..       9      55 .. 0.86
   2 ?   -2.4   0.0         2   3.6e+03      34      47 ..     164     177 ..     160     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.4e-06
                        HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrl 38
                                   IL lL + +  s  eLA +lg+ ps vn++l
  gi|14600918|ref|NP_147443.1| 14 SILILLLQRAQASSVELAVELGVYPSQVNAYL 45
                                  69****************************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                        HTH_24  34 vnrrlkrLeeeGlI 47 
                                   v ++l +L + G++
  gi|14600918|ref|NP_147443.1| 164 VQECLAELSQRGVV 177
                                   67788888888886 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 !    9.5   0.0   0.00053      0.95      24      55 ..      27      58 ..      13      69 .. 0.82
   2 ?    3.7   0.0     0.033        60      34      59 ..     160     187 ..     157     191 .. 0.78
   3 ?   -0.1   0.0      0.52   9.3e+02       2      14 ..     186     198 ..     185     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00053
                                  HHHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                     HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglisrgr 55
                                    elA  lG+ +++v+  l+  +++g++++++
  gi|14600918|ref|NP_147443.1| 27 SVELAVELGVYPSQVNAYLHYYRKQGIVEKSG 58
                                  569**************************643 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.033
                                   SHHHHHHHHHHHHHTTSEE..ETEEEEE CS
                     HTH_Crp_2  34 tretvsrilseLkreglis..rgrriri 59 
                                   ++  v   l+eL+++g++   rgr++r+
  gi|14600918|ref|NP_147443.1| 160 SPFRVQECLAELSQRGVVYiwRGRKVRL 187
                                   56678899**********9766654765 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.52
                                   HHHHHHHHHHCTT CS
                     HTH_Crp_2   2 RlArfLlrlaera 14 
                                   RlA+ L++ a+r+
  gi|14600918|ref|NP_147443.1| 186 RLAKQLIEAARRQ 198
                                   9******987774 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.003       5.4      15      56 ..      17      55 ..       9      58 .. 0.81
   2 ?    5.9   0.0    0.0089        16      37      69 ..     159     189 ..     148     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.003
                                  HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                  + L ++++   +ss e+a + ++ ps +   l+  rk+g+v+
  gi|14600918|ref|NP_147443.1| 17 ILLLQRAQ---ASSVELAVELGVYPSQVNAYLHYYRKQGIVE 55
                                  33333333...79****************************8 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0089
                                   S-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS CS
                          Rrf2  37 ispsylekilakLrkaglvksvrGkgGGyrLak 69 
                                   +sp  ++  la+L++ g+v   rG+   +rLak
  gi|14600918|ref|NP_147443.1| 159 VSPFRVQECLAELSQRGVVYIWRGR--KVRLAK 189
                                   677778999***************9..466666 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 ?   13.1   0.0   3.7e-05     0.067       6      47 .]      15      56 ..       9      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                  HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5  6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   ++ lL++ ++++ ela elg+ +s v  +L   r++G+Vek
  gi|14600918|ref|NP_147443.1| 15 ILILLLQRAQASSVELAVELGVYPSQVNAYLHYYRKQGIVEK 56
                                  4566677799******************************97 PP

>> HTH_23  Homeodomain-like 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      0.11      10      46 ..      15      53 ..      13      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                        HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                  il ll++   +s  e A eLgv +++v  +l+ yr+ G+
  gi|14600918|ref|NP_147443.1| 15 ILILLLQraQASSVELAVELGVYPSQVNAYLHYYRKQGI 53
                                  6666666699************************99995 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.31       5      48 ..      15      57 ..      12      60 .. 0.89
   2 ?   -2.6   0.0       4.1   7.3e+03      19      27 ..      79      87 ..      67      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                  HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE CS
                          FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrs 48
                                  Il  l + +a +   e+A  lg+   Q+  YL   +k+g +++s
  gi|14600918|ref|NP_147443.1| 15 ILILLLQ-RAQASSVELAVELGVYPSQVNAYLHYYRKQGIVEKS 57
                                  6666666.8888999***************************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                                  HHHHHHHTS CS
                          FaeA 19 reiAdalgl 27
                                  +++A a+g+
  gi|14600918|ref|NP_147443.1| 79 TNVASAFGI 87
                                  457777776 PP

>> MotA_activ  Transcription factor MotA, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.23      16      73 ..      10      66 ..       4      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                  HHHHHHHHHHHHSTTB-HHHHHHT-TTS-HHHHHHHHHHHHHTTSEEEETTEEEE-HH CS
                    MotA_activ 16 ektatilitiakkdfitaaevrevhpdlgnavvnsnigvlikkglveksgdgliitge 73
                                    ta+ili + ++   ++ e+  v   +  + vn+ +    k+g+veksgd   +t +
  gi|14600918|ref|NP_147443.1| 10 PTTASILILLLQRAQASSVEL-AVELGVYPSQVNAYLHYYRKQGIVEKSGDVWRLTED 66
                                  568889998888876666554.344445568899999*************96655543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1534.22
//
Query:       gi|118431169|ref|YP_874842.1|  [L=91]
Description: hypothetical protein APE_0722a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0026   18.2   0.2     0.0061   17.0   0.0    1.9  2  HTH_27    Winged helix DNA-binding domain
     0.0031   17.4   0.0     0.0039   17.1   0.0    1.2  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.068   13.0   0.0      0.077   12.8   0.0    1.2  1  DUF1495   Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-06    0.0061      35      68 .]      36      72 ..       6      72 .. 0.80
   2 ?   -1.7   0.0      0.71   4.2e+03      34      44 ..      74      84 ..      73      86 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                         HTH_27 35 isyslkkLtekGLvert...gdeadrrekrvrlTdkG 68
                                   +  ++++L + GL+e+t     e+  r k+vrlTdkG
  gi|118431169|ref|YP_874842.1| 36 FYQNVEHLKRLGLIEETvcfSEEKGVRVKCVRLTDKG 72
                                   55789*********77622255667777********9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.71
                         HTH_27 34 hisyslkkLte 44
                                   ++++ l++L e
  gi|118431169|ref|YP_874842.1| 74 QVVERLRELRE 84
                                   56677777765 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.5e-07    0.0039      30      74 ..      32      77 ..      19      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.5e-07
                                   THHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEESHCCCHHHH CS
                           PadR 30 seGslYpaLkrLekeglvesewees.gegpprkyYrlTdaGrrela 74
                                     Gs Y++ + L++ gl+e++   s ++g + k+ rlTd+G + ++
  gi|118431169|ref|YP_874842.1| 32 GSGSFYQNVEHLKRLGLIEETVCFSeEKGVRVKCVRLTDKGVQVVE 77
                                   48*******************99887889999*********88765 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 ?   12.8   0.0   1.3e-05     0.077      46      90 .]      30      79 ..       7      79 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                        DUF1495 46 leGmgkrynsessLielGLveee...eeseglk..lYklteeGieivevl 90
                                    +G g  y++ + L  lGL+ee+   +e++g++  + +lt++G ++ve+l
  gi|118431169|ref|YP_874842.1| 30 FAGSGSFYQNVEHLKRLGLIEETvcfSEEKGVRvkCVRLTDKGVQVVERL 79
                                   67999999999*********976222457887644899*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 724.70
//
Query:       gi|118431170|ref|YP_874843.1|  [L=57]
Description: hypothetical protein APE_0722b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.17s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 493.33
//
Query:       gi|118431171|ref|YP_874844.1|  [L=107]
Description: hypothetical protein APE_0722c [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); 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:                         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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 863.58
//
Query:       gi|118431172|ref|NP_147446.2|  [L=678]
Description: hypothetical protein APE_0725.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.28   11.2   0.0    1.5  1  Wzt_C     Wzt C-terminal domain


Domain annotation for each model (and alignments):
>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.6e-05      0.28      48     108 ..     589     649 ..     574     659 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.6e-05
                          Wzt_C  48 dpvfgfaikdrngqevfgt.ntelekksfeleelkagervevefef.klpLapGeYlltvale 108
                                     ++  + ++d  g+ +    +t  +  +  + +    ++ + +fe+ +l+L++G+Y++ v+l+
  gi|118431172|ref|NP_147446.2| 589 YVIAVVKLYDPSGNLIKHVeDTVVTIEK--DLPPGMEGVKTLSFELnNLQLGAGDYYVEVGLK 649
                                    6777888899999988333355443322..3334555566667777989************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 5565.63
//
Query:       gi|14600923|ref|NP_147448.1|  [L=284]
Description: hypothetical protein APE_0727 [Aeropyrum pernix K1]
Scores for complete 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   57.2   0.1      1e-08   34.7   0.0    2.1  2  Glyco_hydro_99   Glycosyl hydrolase family 99
    8.4e-06   25.5   0.0      0.034   13.6   0.1    3.1  3  Glyco_tran_WbsX  Glycosyltransferase WbsX
     0.0073   15.2   0.6      0.015   14.1   0.6    1.5  1  Glyco_hydro_71   Glycosyl hydrolase family 71


Domain annotation for each model (and alignments):
>> Glyco_hydro_99  Glycosyl hydrolase family 99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   1.7e-12     1e-08      60     161 ..       2     109 ..       1     116 [. 0.81
   2 !   20.2   0.5   4.3e-08   0.00026     252     322 ..     169     239 ..     164     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.7e-12
                                   ETT-S--TT-HHHHHHHHHHHHHHTEEEEEEEE-GGGCCCHHHHHHHHHHHHHHTT-EEEEEE---....TT--HHHH.HH CS
                Glyco_hydro_99  60 pelGsyssrdpeiiekhlemmrkasiGvlalswydeddeaedksvdllldkaakkklkvtfhiepy....ssrdaqnl.re 135
                                   p +G y srd  +i+  l+ mr+a i  l +sw++  ++ + +    ++ +a+ ++lk +  +epy    +sr ++ + ++
  gi|14600923|ref|NP_147448.1|   2 PVIGLYDSRDVRVIDWQLQRMREAGIDCLFISWWGPGGFED-EAARRVFWRAQLYGLKAAIFVEPYlgndPSRYDRAFwEQ 81 
                                   889*******************************9999877.77788899****************444434555555245 PP

                                   HHHHHHHHHTT.ST.TB--BTTB-EEEE CS
                Glyco_hydro_99 136 nikklidkyGn.hp.afyrkkgkplfyi 161
                                    ++++ +++ + +p a+ r +gkpl   
  gi|14600923|ref|NP_147448.1|  82 TLAYIKQNFIDrYPgAYLRLDGKPLVLA 109
                                   677777777652453788******9765 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 4.3e-08
                                   S-B--TTT-TT-GGG-B--GGGHHHHHHHHHHHHC..T-S-EEES-SS-CCCT---S-EE-EBESSEBEB--T CS
                Glyco_hydro_99 252 pGyidtrirpwngsntrnrenGkyydamlsaalet..kaslisitsfnewheGtqiekavpkktsefeyldyk 322
                                   p y d++ r    s   +  +G +y++ ++  l+   ++ li+its+ne+he t ie+a    +++  yl y+
  gi|14600923|ref|NP_147448.1| 169 PRYRDDHFRSPGLSIDYDLSQG-WYERQWEWVLRNldRVRLIAITSWNEYHENTFIEPANDPAIKDPYYL-YN 239
                                   6677777776655555555555.67888888887533899*******************99999998888.33 PP

>> Glyco_tran_WbsX  Glycosyltransferase WbsX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0048        28      49      75 ..       5      31 ..       1      39 [. 0.84
   2 !    4.1   0.0    0.0045        27     129     166 ..      73     112 ..      70     118 .. 0.85
   3 !   13.6   0.1   5.6e-06     0.034     301     338 ..     190     227 ..     169     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0048
               Glyco_tran_WbsX 49 gyYdlrekevleeqaelakeygiegfc 75
                                  g Yd r+ +v+ +q + ++e+gi+   
  gi|14600923|ref|NP_147448.1|  5 GLYDSRDVRVIDWQLQRMREAGIDCLF 31
                                  78*********************9643 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0045
               Glyco_tran_WbsX 129 eygseeddkehfeyllpafkde...rYikvdgkpllliyrp 166
                                   +y +++ +++ ++y+ + f d+    Y+++dgkpl+l ++p
  gi|14600923|ref|NP_147448.1|  73 RY-DRAFWEQTLAYIKQNFIDRypgAYLRLDGKPLVLAFNP 112
                                   57.8889999*********9974446***********9997 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 5.6e-06
               Glyco_tran_WbsX 301 kllekalekakkkkeeeklvfinaWNEWaEgayLEPde 338
                                    + e++ e + ++ ++ +l+ i++WNE+ E +++EP +
  gi|14600923|ref|NP_147448.1| 190 GWYERQWEWVLRNLDRVRLIAITSWNEYHENTFIEPAN 227
                                   57788888888888899*******************86 PP

>> Glyco_hydro_71  Glycosyl hydrolase family 71
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.6   2.6e-06     0.015     207     247 ..     191     233 ..     174     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-06
                Glyco_hydro_71 207 lwakRweqvlelqp..dfveiitWNDygEShYigplkekkaqd 247
                                    +++ we vl++ +  +++ i +WN y E  +i p ++ + +d
  gi|14600923|ref|NP_147448.1| 191 WYERQWEWVLRNLDrvRLIAITSWNEYHENTFIEPANDPAIKD 233
                                   46667*****8866579******************99874444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2038.53
//
Query:       gi|14600924|ref|NP_147449.1|  [L=222]
Description: hypothetical protein APE_0728 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1719.96
//
Query:       gi|118431173|ref|YP_874845.1|  [L=85]
Description: hypothetical protein APE_0728a [Aeropyrum pernix K1]
Scores for 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   16.2   0.1      0.011   15.9   0.1    1.1  1  DUF2104   Predicted membrane protein (DUF2104)


Domain annotation for each model (and alignments):
>> DUF2104  Predicted membrane protein (DUF2104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   6.3e-07     0.011      15      73 ..       9      67 ..       2      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.3e-07
                        DUF2104 15 ilGLlysYkkysepyvekkidklalvlaviGwllllnvsllvlvpsyilitigllligl 73
                                   + GL  s k+ ++ + ++ +  +al lav+G +   +++ + +    i +++ +lli l
  gi|118431173|ref|YP_874845.1|  9 LAGLRESIKHAATGFKARALAGVALALAVLGQTTTTDMTSIINQMLPIIMSLFALLIPL 67
                                   789*******************************6666665555444444444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 628.44
//
Query:       gi|118431174|ref|YP_874846.1|  [L=94]
Description: hypothetical protein APE_0728b [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.3   0.6      0.048   13.7   0.6    1.2  1  NADH_Oxid_Nqo15  NADH-quinone oxidoreductase chain 15


Domain annotation for each model (and alignments):
>> NADH_Oxid_Nqo15  NADH-quinone oxidoreductase chain 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   2.7e-06     0.048       3      47 ..      34      80 ..      32      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-06
                                   HHHHHHHHHHHHHHHHHHHHH..TT-EEEEEEE-HHHHT--SS---- CS
                NADH_Oxid_Nqo15  3 dealyeaWvellgWlkeyaae..kglsfekeadfPdyiyrmerPydL 47
                                   ++al + W  +l++++ey  +  + + + +e  +P++i r  r +++
  gi|118431174|ref|YP_874846.1| 34 HRALIKMWAWVLSYMEEYPPKsyRLVAYIHEGPYPEFIARKLREWNI 80
                                   67999*************75522689**************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 748.34
//
Query:       gi|14600926|ref|NP_147451.1|  [L=121]
Description: hypothetical protein APE_0730 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1000.99
//
Query:       gi|118431175|ref|YP_874847.1|  [L=259]
Description: hypothetical protein APE_0730a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.046   14.2   0.7      0.046   14.2   0.7    2.1  2  GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain


Domain annotation for each model (and alignments):
>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   2.6e-06     0.046      15      80 ..      65     128 ..      63     145 .. 0.88
   2 ?   -0.7   0.1      0.11     2e+03      28      45 ..     206     223 ..     198     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHHHHHHHHHHHHHSS CS
                    GlutR_dimer  15 awlkslevvptIkalrekaeeireeeleralkklaldgedreelekltrslvnkllheptarLkea 80 
                                    aw++++++++t+++l++ +++ + +  +r+ +k +l+ +d++  ++l+r++  k l + ++r ++ 
  gi|118431175|ref|YP_874847.1|  65 AWRHTHDLAKTVRRLKNGVKQGAVKGAARLARKSGLKSRDAR--RALARAIAAKTLAQAVKRARRT 128
                                    7********************************996666666..9****************99987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHH CS
                    GlutR_dimer  28 alrekaeeireeeleral 45 
                                    al + +eei++e ++r  
  gi|118431175|ref|YP_874847.1| 206 ALGKTLEEIAREDMARWE 223
                                    344455555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1949.20
//
Query:       gi|14600928|ref|NP_147453.1|  [L=391]
Description: hypothetical protein APE_0731 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.13   12.3   0.8         65    3.8   0.1    3.4  3  EF-hand_6  EF-hand domain
       0.34   10.6   2.3         15    5.4   0.1    3.2  3  EF-hand_1  EF hand
        1.7    8.3   7.3       0.53    9.9   0.3    3.1  3  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.042   2.5e+02       5      13 ..      61      69 ..      57      69 .. 0.86
   2 ?    2.9   0.0     0.022   1.3e+02       7      19 ..     159     171 ..     155     173 .. 0.81
   3 ?    3.8   0.1     0.011        65      10      19 ..     231     240 ..     228     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.042
                     EF-hand_6  5 aFklfDkdg 13
                                  +Fk++D dg
  gi|14600928|ref|NP_147453.1| 61 VFKAYDDDG 69
                                  8******97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.022
                     EF-hand_6   7 klfDkdgdGkida 19 
                                   +++D +gdG++ +
  gi|14600928|ref|NP_147453.1| 159 RIWDSNGDGSWEP 171
                                   789******9876 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.011
                     EF-hand_6  10 DkdgdGkida 19 
                                   D++gdG +d+
  gi|14600928|ref|NP_147453.1| 231 DTNGDGVLDK 240
                                   9*******96 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.13   7.7e+02       5      13 ..      61      69 ..      58      69 .. 0.85
   2 ?    2.7   0.0     0.019   1.1e+02       4      15 ..     156     167 ..     155     168 .. 0.89
   3 ?    5.4   0.1    0.0025        15       9      19 ..     230     240 ..     229     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                  HHHHHTTTS CS
                     EF-hand_1  5 iFrefDkDg 13
                                  +F+ +D Dg
  gi|14600928|ref|NP_147453.1| 61 VFKAYDDDG 69
                                  8******98 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.019
                                   HHHHHHTTTSSS CS
                     EF-hand_1   4 eiFrefDkDgdG 15 
                                   ++ r+ D +gdG
  gi|14600928|ref|NP_147453.1| 156 KMVRIWDSNGDG 167
                                   68899******9 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0025
                                   HTTTSSSEEEH CS
                     EF-hand_1   9 fDkDgdGkIdf 19 
                                   +D++gdG +d+
  gi|14600928|ref|NP_147453.1| 230 ADTNGDGVLDK 240
                                   7*******995 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.12   7.4e+02       4      12 ..      61      69 ..      58      69 .. 0.84
   2 ?    0.5   0.3     0.082   4.9e+02       9      14 ..     162     167 ..     161     168 .. 0.91
   3 ?    9.9   0.3   8.9e-05      0.53       7      18 ..     229     240 ..     228     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                                  HHHHH-SS- CS
                     EF-hand_5  4 tFqaiDlNg 12
                                  +F+a D +g
  gi|14600928|ref|NP_147453.1| 61 VFKAYDDDG 69
                                  8*****998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.082
                                   -SS-SS CS
                     EF-hand_5   9 DlNgDG 14 
                                   D NgDG
  gi|14600928|ref|NP_147453.1| 162 DSNGDG 167
                                   99**** PP

  == domain 3  score: 9.9 bits;  conditional E-value: 8.9e-05
                                   HH-SS-SSCE-H CS
                     EF-hand_5   7 aiDlNgDGkIsk 18 
                                   a+D+NgDG ++k
  gi|14600928|ref|NP_147453.1| 229 AADTNGDGVLDK 240
                                   79*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 3262.80
//
Query:       gi|14600931|ref|NP_147456.1|  [L=201]
Description: hypothetical protein APE_0734 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1692.91
//
Query:       gi|118431176|ref|NP_147457.2|  [L=132]
Description: hypothetical protein APE_0735.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.19s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 1187.18
//
Query:       gi|14600933|ref|NP_147458.1|  [L=247]
Description: hypothetical protein APE_0736 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1933.13
//
Query:       gi|14600934|ref|NP_147459.1|  [L=100]
Description: hypothetical protein APE_0737 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 809.14
//
Query:       gi|14600935|ref|NP_147460.1|  [L=345]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for 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-31  109.2   5.2      4e-31  108.3   5.2    1.5  1  Acyl-CoA_dh_1   Acyl-CoA dehydrogenase, C-terminal domain
    7.3e-12   45.7   2.7    7.3e-12   45.7   2.7    1.8  2  Acyl-CoA_dh_2   Acyl-CoA dehydrogenase, C-terminal domain
    5.8e-11   42.5   0.0    9.8e-11   41.7   0.0    1.4  1  Acyl-CoA_dh_M   Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
      0.049   14.3   0.0       0.21   12.3   0.0    2.0  1  Acyl-CoA_dh_N   Acyl-CoA dehydrogenase, N-terminal domain
        0.2   10.9   0.0        0.3   10.3   0.0    1.1  1  ATPgrasp_YheCD  YheC/D like ATP-grasp


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 !  108.3   5.2   1.1e-34     4e-31       2     148 ..     191     335 ..     190     337 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.1e-34
                                   BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH------ CS
                 Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagk 82 
                                   +G+r+a+  +n++Rl+ a  alg+a ra+e ++e a + + fgk+l+d+q v++++a++aa+ +a+ +lv  a  +  + +
  gi|14600935|ref|NP_147460.1| 191 DGVRAALGYINVGRLGYASLALGIADRAIEVIVEAASSKRVFGKRLLDYQGVQWRIASIAARRAALESLVVSALDGGGRVD 271
                                   799******************************************************************998887655555 PP

                                   --HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                 Acyl-CoA_dh_1  83 pdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                     + +a+maK+++ ela e+a +a+q+lGg+G++  ++ er+yrda+v  igeG+ e++++ ia r
  gi|14600935|ref|NP_147460.1| 272 --PEKAAMAKVLGGELALEAAWSAVQILGGRGLAMWGEAERMYRDAKVIDIGEGAKEVLMDYIAGR 335
                                   ..55******************************9999***********************99966 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 ?   -2.2   0.1       1.3   4.7e+03      53      86 ..      10      43 ..       9      69 .. 0.55
   2 !   45.7   2.7     2e-15   7.3e-12       2     127 ..     206     319 ..     205     325 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                                  HHHHHHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                 Acyl-CoA_dh_2 53 AAralleraaaraealaaagkevtvedraearra 86
                                  AA +ll +  a+    ++++++v+ ++  +a+++
  gi|14600935|ref|NP_147460.1| 10 AASRLLDEELAALAGDIDRENRVPDSLIEKAAAE 43
                                  6666666666666666666666654444444444 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 2e-15
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   g a  alG+A +a++ +ve a  +    +g++l d + +q ++a +aar  A++ l+ +a +        g +v+     +
  gi|14600935|ref|NP_147460.1| 206 GYASLALGIADRAIEVIVEAASSKRV--FGKRLLDYQGVQWRIASIAARRAALESLVVSALDG-------GGRVD---PEK 274
                                   67999*****************8888..8********************99999999888776.......77874...457 PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                   a++a++l  ela +a+ +++++ Gg++l++  + +R++RDa+++ 
  gi|14600935|ref|NP_147460.1| 275 AAMAKVLGGELALEAAWSAVQILGGRGLAMWGEAERMYRDAKVID 319
                                   8899*************************************9975 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 !   41.7   0.0   2.7e-14   9.8e-11       1      96 [.      90     179 ..      90     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.7e-14
                                   EEE---SS-SS-GG.G---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE----- CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdva.svkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrriee 80 
                                   a+++TE ++G+dv+ +++t+a e  gg+y+l+G K + +na +a++++vla  +     ++  lfl + ++p ++v+++ +
  gi|14600935|ref|NP_147460.1|  90 ALGITEAGGGTDVRaNIATRAEELGGGSYRLEGMKYFTSNALYASHFVVLAL-A----GEEPALFLCE-KQPRIRVEPL-D 163
                                   789*********9725778779999999************************.2....3345689999.6888*****9.5 PP

                                   BSS-TTS-EEEEEEE. CS
                 Acyl-CoA_dh_M  81 klGlrglptgelvfed 96 
                                     G rg   g++vf+ 
  gi|14600935|ref|NP_147460.1| 164 LSGFRGSGVGKVVFDG 179
                                   89************85 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 ?   12.3   0.0   5.7e-05      0.21      11      48 ..      11      48 ..       4      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                                  HHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTST CS
                 Acyl-CoA_dh_N 11 vrefaeeelaphaaewdeegefprelwkklaelGllgi 48
                                  + ++++eela  a ++d+e+++p++l++k+a+ Gl+ i
  gi|14600935|ref|NP_147460.1| 11 ASRLLDEELAALAGDIDRENRVPDSLIEKAAAEGLFDI 48
                                  67899******************************977 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   8.4e-05       0.3     137     176 ..     243     284 ..     237     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.4e-05
                ATPgrasp_YheCD 137 kWevtgiaaRiagkgs.ittnlsrGGtalpleellkkafg.e 176
                                   +W++++iaaR a+ +s +++ l +GG++ p + +++k++g e
  gi|14600935|ref|NP_147460.1| 243 QWRIASIAARRAALESlVVSALDGGGRVDPEKAAMAKVLGgE 284
                                   8**********9988835789*******99999999998854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      172  (0.0095934); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); 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 0.20s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2822.89
//
Query:       gi|14600936|ref|NP_147461.1|  [L=214]
Description: superoxide dismutase [Aeropyrum pernix K1]
Scores for complete 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-36  123.0   0.1    8.2e-36  122.3   0.1    1.4  1  Sod_Fe_C       Iron/manganese superoxide dismutases, C-termin
    8.3e-29   99.9   3.0    8.3e-29   99.9   3.0    1.9  2  Sod_Fe_N       Iron/manganese superoxide dismutases, alpha-ha
  ------ inclusion threshold ------
       0.17   12.3   0.4        9.2    6.7   0.0    2.3  2  DNTTIP1_dimer  DNTTIP1 dimerisation domain


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 !  122.3   0.1   1.4e-39   8.2e-36       1     102 []      96     198 ..      96     198 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 1.4e-39
                                   --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHHT CS
                      Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldyq 80 
                                   p g++a+ ie++fg +ekfk+ f+aaa +v+g Gw++L++d+  ++L+i+++++++  ++++ +p+L++DvwehAYyl+y+
  gi|14600936|ref|NP_147461.1|  96 PGGRVADLIEKQFGGFEKFKALFSAAAKTVEGVGWGVLAFDPLtEELRILQVEKHNVLMTAGLVPILVIDVWEHAYYLQYK 176
                                   6799*************************************97589***********9999******************** PP

                                   T-HHHHHHHHGGGBBHHHHHHH CS
                      Sod_Fe_C  81 nkradYieafwnvvnWkeveer 102
                                   n+r +Y+e++wnvvnW++ve+r
  gi|14600936|ref|NP_147461.1| 177 NDRGSYVENWWNVVNWDDVEKR 198
                                   *******************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 !   99.9   3.0   1.4e-32   8.3e-29       1      82 []       6      87 ..       6      87 .. 0.98
   2 ?   -0.5   0.1      0.31   1.8e+03      27      47 ..     175     195 ..     164     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1.4e-32
                                  S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTB- CS
                      Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwknls 82
                                  +yeLp+LpY+y+aLeP+i +e+++lHh+kHh+tYv+++N+alek+e++ k   ++++++  ++ ++n +gh+ H++fw n++
  gi|14600936|ref|NP_147461.1|  6 RYELPPLPYNYNALEPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKHLKGEIQIDVRAVMRDFSFNYAGHIMHTIFWPNMA 87
                                  59*****************************************************************************995 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.31
                                   HHTHHHHHHHHHHHHHHCHHH CS
                      Sod_Fe_N  27 hdkHhktYvnnlNkaleklee 47 
                                   ++    +Yv+n+ ++++  + 
  gi|14600936|ref|NP_147461.1| 175 YKNDRGSYVENWWNVVNWDDV 195
                                   666677899888777765444 PP

>> DNTTIP1_dimer  DNTTIP1 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.017     1e+02      11      44 ..      20      53 ..      17      73 .. 0.71
   2 ?    6.7   0.0    0.0015       9.2      44      66 ..     188     210 ..     176     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                 DNTTIP1_dimer 11 QpainkevdevikkylrkvfkpAveNireNlgee 44
                                   p i +e++++ ++  ++++ ++++ + e ++++
  gi|14600936|ref|NP_147461.1| 20 EPYIIEEIMKLHHQKHHNTYVKGANAALEKIEKH 53
                                  577889*****99999999999998777766666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                 DNTTIP1_dimer  44 evvteadvqklcrsiLeeakklf 66 
                                   +vv+ +dv+k   ++L++ak l+
  gi|14600936|ref|NP_147461.1| 188 NVVNWDDVEKRLEQALNNAKPLY 210
                                   69******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1605.80
//
Query:       gi|14600937|ref|NP_147462.1|  [L=103]
Description: hypothetical protein APE_0743 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 797.89
//
Query:       gi|118431177|ref|NP_147464.2|  [L=723]
Description: hypothetical protein APE_0745.1 [Aeropyrum pernix K1]
Scores for complete 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-48  165.6   0.0    2.9e-37  128.2   0.0    2.2  2  ATPase           KaiC
    6.4e-14   52.0   0.0    1.8e-13   50.6   0.0    2.0  1  Intein_splicing  Intein splicing domain
    8.5e-07   28.7   0.1    1.5e-06   27.9   0.1    1.4  1  AAA_25           AAA domain
    2.4e-05   24.1   0.0    3.9e-05   23.4   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
    0.00012   22.3   0.9     0.0004   20.7   0.1    2.3  2  LAGLIDADG_3      LAGLIDADG-like domain
    0.00021   20.1   0.1      0.004   15.8   0.0    2.1  2  GvpD             GvpD gas vesicle protein
    0.00043   20.1   0.1    0.00087   19.2   0.1    1.4  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
    0.00069   18.9   0.0     0.0011   18.3   0.0    1.3  1  Rad51            Rad51
     0.0039   16.6   0.0     0.0062   15.9   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
     0.0092   15.5   0.0      0.015   14.8   0.0    1.3  1  RecA             recA bacterial DNA recombination protein
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.029   14.6   0.0    1.6  1  AAA_22           AAA domain
      0.028   13.6   0.0      0.046   13.0   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.059   13.1   0.0      0.097   12.4   0.0    1.3  1  AAA_24           AAA domain
      0.071   12.8   0.0       0.12   12.0   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.0   2.3e-40   2.9e-37       2     165 ..       5     168 ..       4     175 .. 0.95
   2 !   35.1   0.1   6.5e-12   8.4e-09     170     228 ..     641     699 ..     636     702 .. 0.92

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 2.3e-40
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                    +tg+eg+D ++ gGip+g  v ++GepGtGKt+f+ +F+++g+++ g+++++vt+ee+ e++ ++a+++G+dl +  +eg
  gi|118431177|ref|NP_147464.2|   5 RTGVEGFDPLVAGGIPRGFFVAVVGEPGTGKTVFSIHFAYQGVRE-GDKVIYVTTEESRESVLKQAAMFGMDLGRAVDEG 83 
                                    7*****************************************999.********************************** PP

                         ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkklgvTai 159
                                    + ++ida  +++ ++ + +  ++e+l++++ ea ++++    r+v+Ds +++   +k+a+aR++   ++rvl  ++ T++
  gi|118431177|ref|NP_147464.2|  84 RAIVIDALLKSRSDEWSLEDVSVESLVNKVLEAKRALGYgrARLVVDSMSAF-WLDKPAMARKYSYMVKRVLYRWDFTTL 162
                                    ********9998877779999************999887769**********.*************************** PP

                         ATPase 160 lvseks 165
                                    lvs+  
  gi|118431177|ref|NP_147464.2| 163 LVSQYA 168
                                    ***965 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.5e-12
                         ATPase 170 aaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvle 228
                                    +a g g+e+ ++dg+i+ +++ + + l+R++ + kmR+t+h+ ++h  eI++ +g ++  
  gi|118431177|ref|NP_147464.2| 641 SAFGWGLEH-VADGIIRFRRRIVGGALRRYVVVEKMRQTPHDLRVHRVEIEDgRGMRIAG 699
                                    566889***.******************************************99999975 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.4e-16   1.8e-13       9     134 .]     189     640 ..     181     640 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.4e-16
                                    E.EEHHHHCC............ECTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCT. CS
                                    x.xxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                Intein_splicing   9 k.vkieelve............kegeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrd. 73 
                                    + ++i+e+v+              g+  lsl+  +lk  + ++  +ik++++  l+++k ++gr+i +T+ H++  ++  
  gi|118431177|ref|NP_147464.2| 189 RvTSIGEFVDsflegeggldigGLGYYTLSLDTRTLKPVWRRIRGVIKHRIRgRLLRVKASKGRSIDLTGSHSIYRISRg 268
                                    4467888888888888888887889999*************************************************996 PP

                                    TEEEEEECCC--TT-EEEEE............................................................ CS
                                    xxxxxxxxxxxxxxxxxxxx............................................................ RF
                Intein_splicing  74 egivEkradeLkegdliavp............................................................ 93 
                                    +g+  +  ++L++gd +++p                                                            
  gi|118431177|ref|NP_147464.2| 269 GGLEVVGSSDLRPGDSLVTPasvelpesapssinaarelwsrgvegifvvglpgeaagyrgversrgydgghaipletlv 348
                                    666446789*********************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|118431177|ref|NP_147464.2| 349 erygdsvwslvsgaklavsrgaagdhpvpatipldtgfylllgfivsagsvdvegghvtvtlgpgregyvgdvveavnst 428
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|118431177|ref|NP_147464.2| 429 apgagvrissgargmevtirsrvlsellarvfgagpgpnrdipsivfrapkpmkrvflkglyagggvfdrssgsliyatd 508
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                Intein_splicing  94 ................................................................................ 93 
                                                                                                                    
  gi|118431177|ref|NP_147464.2| 509 srsllnglallllnvgaggyridsgdsgralalivenagrldaigevlehlgfhggreavqgvgalerataglagqatva 588
                                    ******************************************************************************** PP

                                    ..........HSCEEEEEEEEEEEEEC.EEEEEEEEETTT-EEEE.CTTE.EE- CS
                                    ..........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxx.xxx RF
                Intein_splicing  94 ..........dadvvwdkvksievede.eeyVYdltvednhNFva.ngii.vHN 134
                                                 v    v   e+ +  +e VYdl+ve+ +NF+a  g i vHN
  gi|118431177|ref|NP_147464.2| 589 vqrpatrggpG--VDVAGVTGLEHLEAsTEFVYDLSVEGDENFFAgLGWIlVHN 640
                                    ******98443..557788888886655899**************977777**9 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   1.2e-09   1.5e-06      24     163 ..      13     144 ..       2     166 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.2e-09
                         AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal..rdda 101
                                     lv g +p+g +++++G pgtGKt++ ++ a+  ++          e  kV+yv +E+s++ + + ++  g +l  + d+
  gi|118431177|ref|NP_147464.2|  13 PLVAGGIPRGFFVAVVGEPGTGKTVFSIHFAYQGVR----------EGDKVIYVTTEESRESVLKQAAMFGMDLgrAVDE 82 
                                    689999**************************9994..........4459**********99988888877777763333 PP

                         AAA_25 102 rllvl.d.lagv.eslpLfakdrggtlltadvdaleaaieev.egvrlvviDplsralggdensns 163
                                    + +++ d l ++  +   +++ +    +++ v+++ +a ++  +g + +v+D++s+++   +  ++
  gi|118431177|ref|NP_147464.2|  83 GRAIViDaLLKSrSDEWSLEDVS----VESLVNKVLEAKRALgYGRARLVVDSMSAFWLDKPAMAR 144
                                    33333031111111111112222....344444444433332123555667888888766555555 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 !   23.4   0.0   3.1e-08   3.9e-05      50      89 ..      25      64 ..      19     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.1e-08
                      IstB_IS21 50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLvee 89
                                   ++++G +G+GK+ ++i +++++vr+g +v++v++e+  e+
  gi|118431177|ref|NP_147464.2| 25 VAVVGEPGTGKTVFSIHFAYQGVREGDKVIYVTTEESRES 64
                                   789******************************9976554 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.1   2.7e+03       6      29 ..     388     408 ..     384     423 .. 0.83
   2 !   20.7   0.1   3.1e-07    0.0004       3      51 ..     482     527 ..     480     557 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                                    HHHHHHHHCCECCECSTTTTSEEE CS
                    LAGLIDADG_3   6 fLrGlfdaDGsvskskkkgvsisl 29 
                                    +L G++ + Gsv++++++   +++
  gi|118431177|ref|NP_147464.2| 388 LLLGFIVSAGSVDVEGGH---VTV 408
                                    689999********9988...443 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.1e-07
                                    HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HS CS
                    LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIes 51 
                                    k+ fL+Gl+++ G ++ s++    + +++ s++ll++++ lLl+ G   
  gi|118431177|ref|NP_147464.2| 482 KRVFLKGLYAGGGVFDRSSGS---LIYATDSRSLLNGLALLLLNVGAGG 527
                                    788****************99...********************99655 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.1e-06     0.004      14      54 ..      26      67 ..      20     133 .. 0.80
   2 ?    2.0   0.0      0.05        64     150     208 ..     635     692 ..     625     699 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.1e-06
                           GvpD 14 likGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvse 54
                                    + G+PGtGkt+f +++  + +r+ ++v+yv+t    e+v  
  gi|118431177|ref|NP_147464.2| 26 AVVGEPGTGKTVFSIHFAyQGVREGDKVIYVTTEESRESVLK 67
                                   578*************96267888899******988888754 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.05
                           GvpD 150 lvlvletaansrleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladG 208
                                     +lv ++a    le+++dG++ ++ +    g lrr + +ek+r    + r++   + dG
  gi|118431177|ref|NP_147464.2| 635 WILVHNSAFGWGLEHVADGIIRFRRRIV-GGALRRYVVVEKMRQTPHDLRVHRVEIEDG 692
                                    577888888889**********966555.68************8777766666666665 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 !   19.2   0.1   6.8e-07   0.00087      20     130 ..      42     152 ..      37     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.8e-07
                           MEDS  20 fikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralakal.adg 98 
                                    f  +g+++g+kv+yv+++++++ ++++ +  g+d+ +a+++g+  ++da     ++  +  +  +e l +++ +a  a g
  gi|118431177|ref|NP_147464.2|  42 FAYQGVREGDKVIYVTTEESRESVLKQAAMFGMDLGRAVDEGRAIVIDALLKSRSDEWSLEDVSVESLVNKVLEAKrALG 121
                                    7779****************************************99997755555555555888999999999999677* PP

                           MEDS  99 yaglrvigemt.walrspaereelleyEallne 130
                                    y + r++++     + +  +++ + +y   + +
  gi|118431177|ref|NP_147464.2| 122 YGRARLVVDSMsAFWLD--KPAMARKYSYMVKR 152
                                    *****999865244444..45666666666666 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.5e-07    0.0011      18      98 ..       3      75 ..       1     120 [. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.5e-07
                                   EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT-- CS
                          Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykld 98
                                   +l tG + +D l+ GGi+ g    ++Ge ++Gkt ++  ++             +k++y+ te +   e +++ a  +++d
  gi|118431177|ref|NP_147464.2|  3 RLRTGVEGFDPLVAGGIPRGFFVAVVGEPGTGKTVFSIHFAYQG------VREGDKVIYVTTEESR--ESVLKQAAMFGMD 75
                                   689********************************998876432......2223577888887653..3345555556665 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 !   15.9   0.0   4.8e-06    0.0062       3      66 ..       5      68 ..       4      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.8e-06
                                   XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHH CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqR 66
                                   +tg + +D l+ +G+ +g ++ + + p++Gkt++ +++a + +  e  +v+++  e s+e+++++
  gi|118431177|ref|NP_147464.2|  5 RTGVEGFDPLVaGGIPRGFFVAVVGEPGTGKTVFSIHFAYQGVR-EGDKVIYVTTEESRESVLKQ 68
                                   6788888866516799999999*****************99886.55689999999999998765 PP

>> RecA  recA bacterial DNA recombination protein
   #    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      36     104 ..       6      75 ..       1      96 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                    -S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHH..HHHTT-- CS
                           RecA  36 sGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpky..akklGvd 104
                                    +G  ++d  l  GG+p+G  + + G   +Gkt +++h   +  ++g  + ++ +e + +++   a+ +G+d
  gi|118431177|ref|NP_147464.2|   6 TGVEGFDP-LVAGGIPRGFFVAVVGEPGTGKTVFSIHFAYQGVREGDKVIYVTTEESRESVLkqAAMFGMD 75 
                                    55556664.456******************************************99887653114455555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.3e-05     0.029       7      68 ..      24      80 ..      21     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglel 68
                                   +++v+Ge+GtGKT+    +++q ++e      +++v++vt  +s  s  + + ++  +lg+  
  gi|118431177|ref|NP_147464.2| 24 FVAVVGEPGTGKTVFSIHFAYQGVRE------GDKVIYVTTEESReSVLKQAAMFGMDLGRAV 80
                                   679*******************9877......*******999988655555555555555544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.6e-05     0.046       5      50 ..      26      69 ..      23      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                        DUF2075  5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrea 50
                                    V G++GtGKtv  ++++++    +e+ +++y++  ++   vl++a
  gi|118431177|ref|NP_147464.2| 26 AVVGEPGTGKTVFSIHFAYQG--VREGDKVIYVTTEESRESVLKQA 69
                                   689*****************9..99999999999888888888775 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   7.6e-05     0.097       5      38 ..      25      65 ..      22     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.6e-05
                         AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksl 38
                                   ++++G++g+GKT +  ++       g+k++++ te++  s+
  gi|118431177|ref|NP_147464.2| 25 VAVVGEPGTGKTVFSIHFayqgvreGDKVIYVTTEESRESV 65
                                   689*******************************9987665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.7e-05      0.12      25      76 ..      25      77 ..      17      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.7e-05
                                   EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCH.HHHHHEBSSS CS
                Sigma54_activat 25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeell.eseLFGhekG 76
                                   v ++Ge GtGK++++ +   +  r+  +++ v   +  e++l ++ +FG+  G
  gi|118431177|ref|NP_147464.2| 25 VAVVGEPGTGKTVFSIHFAYQGVREGDKVIYVTTEESRESVLkQAAMFGMDLG 77
                                   7799***********99999999************999997725789*98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (723 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4960.74
//
Query:       gi|118431178|ref|NP_147465.2|  [L=362]
Description: hypothetical protein APE_0748.1 [Aeropyrum pernix K1]
Scores for complete 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-43  147.9   0.0    3.9e-43  147.7   0.0    1.0  1  NMD3             NMD3 family
  ------ inclusion threshold ------
      0.038   14.0   1.0       0.33   11.0   0.2    2.2  2  zinc-ribbons_6   zinc-ribbons
      0.045   13.5   5.9       0.65    9.8   0.7    3.3  3  zinc_ribbon_2    zinc-ribbon domain
       0.77    9.8   7.7         24    5.0   5.7    2.9  2  DZR              Double zinc ribbon
        2.2    8.7   6.3         12    6.4   4.7    2.7  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.7   0.0   1.1e-46   3.9e-43       1     243 []       5     241 ..       5     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 147.7 bits;  conditional E-value: 1.1e-46
                           NMD3   1 CcrCGkeieeling...lCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                    C+ CG++ e +  g   lC+dC+++++ +++++e +++ +C++Cg+y+++g W +  ++ e++l+e+l+ +++  +k +e
  gi|118431178|ref|NP_147465.2|   5 CPSCGRTLEGS--GvrrLCPDCYVERYGVARIPEAVKFVYCRDCGAYRYQGGWNEGLESVEDTLREYLHMVLTVRMKPTE 82 
                                    *******9522..2345************************************887678899999******9999**999 PP

                           NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriagg.yyeaivQvRqk.r 155
                                    +vee  ve ++  +    p    + + vtv g++ g   + l +++ ++v+ ++  CprC+++++g  +ea v+vR++  
  gi|118431178|ref|NP_147465.2|  83 AVEEAWVESIELVQAFAGP--GVYTALVTVAGRAGG---QSLVERKIITVEASQALCPRCTARSTGrGFEAEVKVRSTaG 157
                                    9**9999988777555555..777889******966...6799***********************9***********66 PP

                           NMD3 156 elteeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkevy 235
                                    +l ++ +  + ++l++     +   f++k++e++eGlD+y+++++aAr l+ +l+se+ ++vkes+klv+++ + g+++ 
  gi|118431178|ref|NP_147465.2| 158 SLGRDVKTGIARVLRRSR---SIAGFVVKVDENREGLDIYLTDQTAARMLAGKLRSEFSAEVKESYKLVGRQPS-GRRKG 233
                                    666666666666666555...79************************************************666.***** PP

                           NMD3 236 rltysvrl 243
                                    rlt+svr+
  gi|118431178|ref|NP_147465.2| 234 RLTISVRI 241
                                    *******8 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   0.2   9.2e-05      0.33       3      51 ..       5      52 ..       3      64 .. 0.78
   2 ?    1.3   0.0     0.096   3.4e+02      28      37 ..     130     139 ..     123     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
                                   -SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S---EEEETTEEEE- CS
                 zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedlkkealCpeCeqelevlkaCgavdyf 51
                                   Cp+C + le +g +  C  C  +   +a  pe   +   ++ Cga  y 
  gi|118431178|ref|NP_147465.2|  5 CPSCGRTLEGSGVRRLCPDCYVERYGVARIPEAV-KFVYCRDCGAYRYQ 52
                                   *********************9888888888865.45577888887775 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.096
                                    EEEE-SSS-S CS
                 zinc-ribbons_6  28 kealCpeCeq 37 
                                     +alCp+C  
  gi|118431178|ref|NP_147465.2| 130 SQALCPRCTA 139
                                    5788999975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7   0.00018      0.65       2      19 ..       5      24 ..       4      27 .. 0.86
   2 ?    3.1   0.1     0.023        81       1      21 [.      42      48 ..      32      49 .. 0.64
   3 ?    1.4   0.0     0.079   2.8e+02      13      19 ..     131     137 ..     126     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                  zinc_ribbon_2  2 CpnCGaelq.dnakF.CpyC 19
                                   Cp+CG++l+  +++  Cp C
  gi|118431178|ref|NP_147465.2|  5 CPSCGRTLEgSGVRRlCPDC 24
                                   ********868887779988 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.023
                  zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                   +              C  CG+
  gi|118431178|ref|NP_147465.2| 42 Y--------------CRDCGA 48
                                   3..............666665 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.079
                  zinc_ribbon_2  13 akFCpyC 19 
                                    +  Cp+C
  gi|118431178|ref|NP_147465.2| 131 QALCPRC 137
                                    5678888 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.7    0.0067        24      14      35 ..       4      25 ..       1      48 [. 0.72
   2 ?    2.2   0.0     0.053   1.9e+02      28      36 ..     131     139 ..     109     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0067
                            DZR 14 fCseCgtklkavaaedrCpsCg 35
                                   +C+ Cg +l+     + Cp C 
  gi|118431178|ref|NP_147465.2|  4 VCPSCGRTLEGSGVRRLCPDCY 25
                                   7999999998777799999994 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.053
                            DZR  28 edrCpsCge 36 
                                    +  Cp+C++
  gi|118431178|ref|NP_147465.2| 131 QALCPRCTA 139
                                    455666655 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 ?    6.4   4.7    0.0034        12       6      37 ..      21      52 ..       4      71 .. 0.61
   2 ?   -0.0   0.0      0.33   1.2e+03       6      13 ..     134     141 ..     115     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                Lar_restr_allev  6 CPfCggravlersqrvvaeigq..........cvyCadCga...s 37
                                   CP C+ +              +          +vyC dCga    
  gi|118431178|ref|NP_147465.2| 21 CPDCYVER-------------YgvaripeavkFVYCRDCGAyryQ 52
                                   55554333.............03333333444*********5543 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.33
                Lar_restr_allev   6 CPfCggra 13 
                                    CP C  r 
  gi|118431178|ref|NP_147465.2| 134 CPRCTARS 141
                                    66666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2715.70
//
Query:       gi|118431179|ref|YP_874848.1|  [L=111]
Description: translation initiation factor 1A [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-18   66.4   0.2      2e-18   65.9   0.2    1.2  1  eIF-1a    Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
      0.052   13.3   0.8       0.11   12.3   0.1    1.8  2  RsgA_N    RsgA N-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 !   65.9   0.2   2.2e-22     2e-18       2      64 .]      23      84 ..      22      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.2e-22
                                   EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                         eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                   ++ ++V ++ g +  +V ++d g+ ++a+ipgk+R+++w+++Gd+Vl  ++  +++kG++vyr
  gi|118431179|ref|YP_874848.1| 23 TMLCIVQRVVGAGFLEVLCTD-GEVYMARIPGKMRRRVWMREGDVVLFLPWGTADKKGEVVYR 84
                                   689****************96.****************************************8 PP

>> RsgA_N  RsgA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.19   1.7e+03      23      37 ..       2      16 ..       1      17 [. 0.72
   2 ?   12.3   0.1   1.2e-05      0.11       9      44 ..      34      69 ..      27      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.19
                         RsgA_N 23 cRaRGkFRkkkispl 37
                                   +R RG+  +++  pl
  gi|118431179|ref|YP_874848.1|  2 ARGRGRHERRGEMPL 16
                                   788998777776665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.2e-05
                         RsgA_N  9 sgfYyVk.eegeiyecRaRGkFRkkkisplVGDrVef 44
                                   +gf +V+ ++ge+y +R+ Gk R++ + +  GD V f
  gi|118431179|ref|YP_874848.1| 34 AGFLEVLcTDGEVYMARIPGKMRRR-VWMREGDVVLF 69
                                   6999**97888************77.44557777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 852.50
//
Query:       gi|14600941|ref|NP_147467.1|  [L=266]
Description: hypothetical protein APE_0751 [Aeropyrum pernix K1]
Scores for complete 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-62  210.4   0.0    2.3e-62  210.0   0.0    1.2  1  RIO1      RIO1 family
    1.4e-06   27.8   0.2    1.3e-05   24.7   0.2    2.1  1  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family
    6.9e-06   26.1   0.9     0.0052   16.7   0.0    2.4  2  APH       Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.068   12.5   0.0    2.0  1  Pkinase   Protein kinase domain


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 !  210.0   0.0   5.1e-66   2.3e-62       1     186 [.      62     250 ..      62     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 5.1e-66
                                   EEEEEEETTTEEEEEEEE-S---SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEET CS
                          RIO1   1 nVyhavsedgkevaiKiyktstteFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkr 80 
                                   +Vy++v++d+++va+Kiy   t++F+k ++ky+ g++rf+d     n r+l+  wa+kE+rnL+r++e+gv+vP+p++++ 
  gi|14600941|ref|NP_147467.1|  62 KVYWGVAWDRSDVAVKIYLSFTSDFRKsIRKYIVGDPRFEDI-PAGNIRRLIYEWARKEYRNLRRMRESGVRVPRPVAVEA 141
                                   69************************99************99.69************************************ PP

                                   TEEEEE--EETTEEGGBHHHCG.-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTST CS
                          RIO1  81 hvlvmefigedgvaapklkdve.e..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhp 158
                                   +++vmef+ge+g++ap+l ++  e  + eae +++evl++ ++++ +a+lvHaDLSeyN+lv++++++iIDvsQav+++hp
  gi|14600941|ref|NP_147467.1| 142 NIIVMEFLGEKGYRAPTLAEAVeEldRGEAEAIAAEVLRQAEAIVCRARLVHADLSEYNILVWRGEPWIIDVSQAVPHSHP 222
                                   *******************998558899***************************************************** PP

                                   THHHHHHHHHHHHHHHHHTTC-----HH CS
                          RIO1 159 nalefLerDveniikfFrrkgvekvdee 186
                                   na+efLerDven+++f++ k+  ++d++
  gi|14600941|ref|NP_147467.1| 223 NAEEFLERDVENLHRFLTGKMGFEFDFD 250
                                   *****************99998888876 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.2   2.9e-09   1.3e-05      58     190 ..     116     239 ..     105     254 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.9e-09
                           Kdo  58 avrEfrllkrLeeagvavpkpvaagavkvgle......yrAlllterlegaqdLedllakwaelaeelkrallkavgrlia 132
                                   a++E+r+l+r++e gv+vp+pva +a+ + +e      yrA  l e++e+   L+   a      e+  ++ l++  +++ 
  gi|14600941|ref|NP_147467.1| 116 ARKEYRNLRRMRESGVRVPRPVAVEANIIVMEflgekgYRAPTLAEAVEE---LDRGEA------EAIAAEVLRQAEAIV- 186
                                   789********************998754433001123555555554443...333333......455555555544443. PP

                           Kdo 133 klhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLkrsf 190
                                      ra + Hadl   nil+  +e      w+iD  +a + +   a+   e+d ++L+r +
  gi|14600941|ref|NP_147467.1| 187 --CRARLVHADLSEYNILVWRGE-----PWIIDVSQAVPHSHpnAEEFLERDVENLHRFL 239
                                   ..58999************9997.....9*********9998556777899*****9964 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1   0.00057       2.6      34      61 ..     113     140 ..      54     151 .. 0.61
   2 !   16.7   0.0   1.2e-06    0.0052     135     192 ..     153     212 ..     146     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00057
                                   HHHHHHHHHHHHHHHHTT-B--B-CTTB CS
                           APH  34 aeeirrevallrlLakagvpvPevlagd 61 
                                   +e +r+e++ lr ++++gv+vP+++a +
  gi|14600941|ref|NP_147467.1| 113 YEWARKEYRNLRRMRESGVRVPRPVAVE 140
                                   556789*******************953 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.2e-06
                                   CCCGCCTCCHHHHHHHHHHHHHHHH--S.....SS-EEEE-SS-SGGGEEEC..TTEEEEE-- CS
                           APH 135 rllaselldlleeleeqvlaalaallpg.....elptvllHgDlhpgNllvdpddgrvtGviD 192
                                   +++a+ l + +eel++  ++a+aa++++       +++l+H Dl+  N+lv  ++ +   +iD
  gi|14600941|ref|NP_147467.1| 153 GYRAPTLAEAVEELDRGEAEAIAAEVLRqaeaiVCRARLVHADLSEYNILVW-RGEPW--IID 212
                                   56666666666666666666666666666666889***************98.66777..888 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.5e-05     0.068       8     141 ..      56     212 ..      49     228 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                   EEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEE.................. CS
                       Pkinase   8 GeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfee.................. 69 
                                    +G+ +kVy +v ++++  vAvK+      + +k  +k++     ++ +   ni rl++ + +                  
  gi|14600941|ref|NP_147467.1|  56 SSGKESKVYWGV-AWDRSDVAVKIYLSFTSDFRKSiRKYIVGDPRFEDIPAGNIRRLIYEWARkeyrnlrrmresgvrvpr 135
                                   566666666666.56666666665544333333322333333334444445566665555555556666666666666666 PP

                                   ...SSEEEEEEE--TTEB.....HHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-S CS
                       Pkinase  70 ...kdelylvleyvegge.....ladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitD 141
                                       +  ++v+e++ ++      la+++     l+  ea+ ia+++l+  e +  +++++H Dl   NiL+  +ge  i+D
  gi|14600941|ref|NP_147467.1| 136 pvaVEANIIVMEFLGEKGyraptLAEAV---EELDRGEAEAIAAEVLRQAEAIVcRARLVHADLSEYNILVW-RGEPWIID 212
                                   6654555689999876654433333333...359**************9999985677************99.88888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1949.59
//
Query:       gi|118431180|ref|NP_147468.2|  [L=195]
Description: RNA-processing protein [Aeropyrum pernix K1]
Scores for complete 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   47.4   5.8    2.9e-06   27.0   0.2    2.4  2  KH_1      KH domain
  ------ inclusion threshold ------
      0.013   15.3   1.0       0.79    9.6   0.0    2.6  2  KH_4      KH domain
      0.027   14.5   0.0      0.062   13.4   0.0    1.5  1  KH_8      Krr1 KH1 domain
      0.042   13.7   6.7       0.79    9.6   0.8    2.8  2  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   6.5e-10   2.9e-06       3      48 ..      11      50 ..       9      73 .. 0.80
   2 !   22.5   1.3   1.6e-08   7.3e-05      10      65 ..     112     159 ..     106     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.5e-10
                                   EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EE CS
                           KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderev 48
                                    ++v+ +  g++IG++G++  eI+++tg+ I+v+  e+     ++v
  gi|118431180|ref|NP_147468.2| 11 YVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVD-TEN-----SMV 50
                                   57899999************************98.443.....233 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.6e-08
                                    HHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                           KH_1  10 lvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                      griIG gG+  + I+e t ++I+v         e ev i+G+ e+  +Ak++ie
  gi|118431180|ref|NP_147468.2| 112 IKGRIIGEGGRARRTIEEMTDTYINVG--------EYEVAIIGDYERAMAAKQAIE 159
                                    569**********************74........578********9999999986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00018      0.79      29      50 ..       8      29 ..       2      31 .. 0.88
   2 ?    3.8   0.2     0.012        54      40      63 ..     113     136 ..     109     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                           KH_4 29 veielnvegedlGrvIGkrGrt 50
                                    +i ++v++e lG vIG rG++
  gi|118431180|ref|NP_147468.2|  8 PRIYVKVKPERLGAVIGPRGEV 29
                                   5799****************85 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.012
                           KH_4  40 lGrvIGkrGrtldAlqylvsaaan 63 
                                    +Gr+IG  Gr  + +  ++  ++n
  gi|118431180|ref|NP_147468.2| 113 KGRIIGEGGRARRTIEEMTDTYIN 136
                                    6********987777666666655 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.062      27      80 ..      35      88 ..      26      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                           KH_8 27 eekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvle 80
                                   ++    ++vd ++ +++v+   +   P  ++ka +++k is g p e+a ++le
  gi|118431180|ref|NP_147468.2| 35 RRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPEKAFRLLE 88
                                   55666789*******************************************998 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00018      0.79      24      56 ..       7      39 ..       3      72 .. 0.84
   2 ?    6.4   0.7    0.0017       7.8      36      59 ..     113     136 ..     110     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00018
                                   SCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHH CS
                           KH_2 24 anrviiviresqpgivIGkgGsnikkigkelrk 56
                                   + r+ + ++ ++ g vIG +G+   +i    + 
  gi|118431180|ref|NP_147468.2|  7 KPRIYVKVKPERLGAVIGPRGEVKAEIMRRTGT 39
                                   468999****************99888766655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0017
                                    HHHHHTGGGHHHHHHHHHHHHHHH CS
                           KH_2  36 pgivIGkgGsnikkigkelrkdie 59 
                                    +g++IG gG+  ++i++     i 
  gi|118431180|ref|NP_147468.2| 113 KGRIIGEGGRARRTIEEMTDTYIN 136
                                    8**********9999998877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1523.49
//
Query:       gi|118431181|ref|NP_147470.2|  [L=291]
Description: dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-23   82.1   0.1      7e-23   81.5   0.1    1.2  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    3.2e-13   50.0   0.2    6.9e-13   48.9   0.0    1.6  1  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
      5e-09   36.6   0.3    1.3e-08   35.3   0.1    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    1.7e-08   34.6   0.1    4.1e-08   33.4   0.1    1.6  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.1e-07   32.0   0.1    1.6e-07   31.4   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    9.2e-07   29.2   0.1    1.7e-06   28.3   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      5e-05   22.7   0.0    7.4e-05   22.2   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    9.8e-05   22.6   0.1    0.00073   19.8   0.1    2.2  1  TrkA_N           TrkA-N domain
    0.00036   20.9   0.2    0.00069   20.0   0.2    1.4  1  NAD_binding_7    Putative NAD(P)-binding
    0.00049   19.8   0.1     0.0008   19.1   0.1    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
    0.00061   20.6   0.1     0.0012   19.6   0.1    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00093   19.2   0.0     0.0017   18.4   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    0.00097   19.3   1.5     0.0026   18.0   0.1    2.4  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
     0.0018   17.8   0.2     0.0048   16.4   0.2    1.7  1  adh_short        short chain dehydrogenase
      0.002   17.8   5.9      0.014   15.0   1.2    2.1  2  DAO              FAD dependent oxidoreductase
      0.002   17.7   0.1      0.004   16.7   0.1    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
  ------ inclusion threshold ------
      0.013   15.3   0.7      0.031   14.2   0.5    1.7  2  NAD_binding_10   NAD(P)H-binding
      0.037   13.1   0.2       0.05   12.7   0.2    1.2  1  GIDA             Glucose inhibited division protein A
      0.045   13.0   0.1      0.075   12.3   0.1    1.3  1  FAD_binding_3    FAD binding domain
      0.053   12.7   0.4       0.17   11.0   0.2    1.6  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.072   12.6   0.2       0.14   11.7   0.2    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.079   12.4   0.0       0.12   11.8   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.11   12.8   0.1       0.61   10.4   0.0    2.1  2  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor
       0.13   12.3   0.1       0.23   11.6   0.1    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.23   11.5   0.9        1.3    9.1   0.4    2.4  2  DUF2647          Protein of unknown function (DUF2647)


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 !   81.5   0.1   9.7e-26     7e-23       2     154 ..       5     156 ..       4     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 9.7e-26
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT.TEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvae.gakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                    ++++G G MGs  a++l+++gy+v+v+ r+ ek+e+l+ e g++aa s+ +++a+ ++ i +v++++a  +v++++ +  
  gi|118431181|ref|NP_147470.2|   5 VAVVGAGRMGSGAARRLASRGYRVVVWSRSWEKAERLAREaGLEAARSLVDALAESEAAIAFVSDDDALLNVVSQVRR-- 82 
                                    89***********************************99845*********************************876.. PP

                                    -TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEE CS
                  NAD_binding_2  81 kkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvt 154
                                    + g i+++++t+ p+++   a++l+  g+++++aPV GG    e+G+  ++++++++a++ + p+l+++g+ v 
  gi|118431181|ref|NP_147470.2|  83 SDGLIFVNSATTTPRASVSAARYLEGLGVQYVEAPVIGGPGALERGEAIVLAAAPRSALAPAVPLLSELGELVK 156
                                    89*********************************************99999*****************99554 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 !   48.9   0.0   9.6e-16   6.9e-13       1     122 []     162     280 ..     162     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 9.6e-16
                 NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlmlKDlgl 80 
                                    G ++a+Kl+ n ll ++l+ ++E l++++++G+d   +  ++++    s    ++++++    + +p+F+++l  KD + 
  gi|118431181|ref|NP_147470.2| 162 GMAAAMKLAFNNLLLTTLVGLGESLLILDAYGVDKTLFSSILERTV-FSGLAGKYFERA--VSKPKPTFTVSLAEKDARY 238
                                    7899******************************999988888776.888888899864..45799************** PP

                 NAD_binding_11  81 alelareagaplpllalaeqlyaaaaaegggdaDhsaivrll 122
                                    a ++  + g+p  + ++++++ya++++ g gd+D+  ++rll
  gi|118431181|ref|NP_147470.2| 239 AFQALADRGYPRLVSQAVSNVYAMLSHMGFGDEDYVGVYRLL 280
                                    ***************************************986 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 !   35.3   0.1   1.9e-11   1.3e-08       1      70 [.       4      68 ..       4      93 .. 0.85
   2 ?   -2.2   0.0       9.1   6.6e+03      58      72 ..     124     138 ..     118     150 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.9e-11
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S- CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavk 70
                                   +++++GaG+mg++ a++l+++g   + +vv  sr+ ekae la+e+g ++   +  +a++e++  +  v 
  gi|118431181|ref|NP_147470.2|  4 RVAVVGAGRMGSGAARRLASRG---YRVVVW-SRSWEKAERLAREAGLEAAR-SLVDALAESEAAIAFVS 68
                                   69********************...****66.***************99999.99999998887776554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.1
                                    HHHH-SEEEE-S-HH CS
                  F420_oxidored  58 aaeeadvvvlavkpe 72 
                                    a+e+ + +vla  p+
  gi|118431181|ref|NP_147470.2| 124 ALERGEAIVLAAAPR 138
                                    567777777776665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   5.7e-11   4.1e-08      13      83 ..       3      67 ..       1      90 [. 0.80
   2 ?   -2.5   0.0       6.8   4.9e+03     104     124 ..     239     259 ..     219     262 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 5.7e-11
                                   -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                   Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83
                                   ++v ++GaG+m++ +a+ L+++g++ vvv  R+ e+a++la+e + e     +  +l ++lae++  i+ +
  gi|118431181|ref|NP_147470.2|  3 ERVAVVGAGRMGSGAARRLASRGYR-VVVWSRSWEKAERLAREAGLE-----AARSLVDALAESEAAIAFV 67
                                   689**********************.*****************9655.....4455555556665555544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.8
                                    ..EEEEE--SS-SB-TTGGGS CS
                   Shikimate_DH 104 kplllvDiavPRdvepevael 124
                                      + l D + PR v+++v+++
  gi|118431181|ref|NP_147470.2| 239 AFQALADRGYPRLVSQAVSNV 259
                                    445678888999999888775 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 !   31.4   0.1   2.3e-10   1.6e-07       2      49 ..       5      52 ..       4      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.3e-10
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCC CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiekslekl 49
                                   vav+GaG mG+g a  +as+g++Vv+  +s e++e+ ++++  + ++ 
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRGYRVVVWSRSWEKAERLAREAGLEAARS 52
                                   9*****************************999999888776654444 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 !   28.3   0.1   2.3e-09   1.7e-06       1      80 [.       5      80 ..       5      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.3e-09
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80
                                   v ++GaG++G+++a+ la ++ +  +++v++rs ek+e+la + +g ++    +da  +++   a +++ d+++n++ ++
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRG-Y--RVVVWSRSWEKAERLARE-AGLEAARSLVDALAESEAAIAFVSDDDALLNVVSQV 80
                                   679****************98.6..9**************987.8999********9999989999*********99877 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 !   22.2   0.0     1e-07   7.4e-05      38      95 ..       4      63 ..       2      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                                   EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEE CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelv.sleellaesDiv 95
                                   +v+++G+Gr+G+ +a+rl++ g +v++++rs +k e  ++e g+e + sl ++laes+  
  gi|118431181|ref|NP_147470.2|  4 RVAVVGAGRMGSGAARRLASRGYRVVVWSRSWEKAErLAREAGLEAArSLVDALAESEAA 63
                                   799****************************99888666677776655999999998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1     1e-06   0.00073       1      44 [.       5      49 ..       5     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEE CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.lev 44
                                   ++++G+Gr+G+  a++L + g+ +vvv  ++ e++e+l++e  le+
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASrGY-RVVVWSRSWEKAERLAREAgLEA 49
                                   68*****************667.6*************987652443 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 !   20.0   0.2   9.6e-07   0.00069       8      99 ..       3      99 ..       2     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.6e-07
                  NAD_binding_7  8 kkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk...l.aeeelekdlegadlviaatddrelneriaeaa.ka 84
                                   ++v vvG+G+++   +r+l++ g +v+v +    e++e+l +   l a + l + l++ + +ia ++d++   +++ +  ++
  gi|118431181|ref|NP_147470.2|  3 ERVAVVGAGRMGSGAARRLASRGYRVVVWSRS-WEKAERLAReagLeAARSLVDALAESEAAIAFVSDDDALLNVVSQVrRS 83
                                   589*****************************.4444544443332124445566777777777766666666666655255 PP

                  NAD_binding_7 85 rr.ilvnvadkpelcd 99
                                    + i+vn a++ +  +
  gi|118431181|ref|NP_147470.2| 84 DGlIFVNSATTTPRAS 99
                                   4426899999887665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.1e-06    0.0008       1      61 [.       5      67 ..       5      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHH.HHHHCEEEEETTCEEEEEECEEECCH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlea.lkknGlrltseggeeilrppealsae 61
                                   +a++GaG +Gs  a +La  g+ v+++ rs  ++e+  +++Gl+  ++  +  ++ ++a++++
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRGYRVVVWSRSWeKAERlAREAGLEAARSLVDALAESEAAIAFV 67
                                   69****************************99****889999998877766666666666555 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 !   19.6   0.1   1.7e-06    0.0012       2      68 ..       4      67 ..       3      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-06
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidaviv 68
                                   rva++GaG++gs  +r l    r+++vv +++++ e+ae++a++ g+ea  +l + la++e+ +++v
  gi|118431181|ref|NP_147470.2|  4 RVAVVGAGRMGSGAARRLAS--RGYRVV-VWSRSWEKAERLAREAGLEAARSLVDALAESEAAIAFV 67
                                   89**********99955544..589988.*******************9999777666565555554 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 !   18.4   0.0   2.3e-06    0.0017       2      41 ..       5      44 ..       4      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHH CS
                 NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeinee 41
                                   +av+GaG  G+  A+ la++g +v++w+r+ e +e++ +e
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRGYRVVVWSRSWEKAERLARE 44
                                   9*****************************9999998765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   3.6e-06    0.0026       1      29 [.       7      35 ..       7      44 .. 0.94
   2 ?   -1.1   0.0       3.2   2.3e+03       4      32 ..     209     239 ..     209     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrd 29
                                   +vGaG  G+ aA++La +g++v+++ +++
  gi|118431181|ref|NP_147470.2|  7 VVGAGRMGSGAARRLASRGYRVVVWSRSW 35
                                   8***********************98876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.2
                                    -SHHHHHHHHHHHCC..TEEEEEE-SSSSSS CS
                  NAD_binding_8   4 aGlsGlvaAylLaka..gfdvlllekrdrlG 32 
                                    +Gl+G ++ ++ +k    f v l ek  r  
  gi|118431181|ref|NP_147470.2| 209 SGLAGKYFERAVSKPkpTFTVSLAEKDARYA 239
                                    6999999999999855688999999987755 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   6.7e-06    0.0048       3      48 ..       5      49 ..       3     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.7e-06
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTT CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeeg 48
                                   v v+Ga++ +G   a++la++G++vvv +rs ek+e++a e + e+
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGR-MGSGAARRLASRGYRVVVWSRSWEKAERLAREAGLEA 49
                                   77888885.9******************************988652 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.2     2e-05     0.014       1      29 [.       4      34 ..       4      50 .. 0.88
   2 ?    5.5   0.3     0.015        11      96     227 ..      47     157 ..      34     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                   +v+++G+G +G+++A+ La rg  V++  ++
  gi|118431181|ref|NP_147470.2|  4 RVAVVGAGRMGSGAARRLASRGyrVVVWSRS 34
                                   59***********************999886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                                    HHHHHHHHHHHHHTTTTEEEEEH.HHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEE CS
                            DAO  96 lealdkllallleagldaellda.eevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtglee 174
                                    lea + l+++l+e  +   +++  + ++ + +++++  g +f+ + ++  p++ + a ar +e lGv+ +e  +v g   
  gi|118431181|ref|NP_147470.2|  47 LEAARSLVDALAESEAAIAFVSDdDALLNVVSQVRRSDGLIFVNS-ATTTPRASVSA-ARYLEGLGVQYVEA-PVIGG-- 121
                                    344444444443333333444443444455554434445455555.88888888877.999**********8.**996.. PP

                                    EETCEEEEEEECTEEEEEEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEE CS
                            DAO 175 edgkvwgverttpgendaadavVnaaGawsdllgllkeldlpispvrgqvlvl 227
                                         + +     ++    +a+V+aa + s l+   + +  p+    g+ + +
  gi|118431181|ref|NP_147470.2| 122 ----PGAL-----ER---GEAIVLAAAPRSALA---PAV--PLLSELGELVKV 157
                                    ....4566.....33...479*******99877...555..666666666666 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.6e-06     0.004       6      71 ..       4      70 ..       2      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.6e-06
                                   -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEE.EHHHHHHT-SEEEE-S-HH CS
                           IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevl.tvaeavkkadvvmiliPDe 71
                                   ++av+G G  G   a+ l   g  vvv  r+ +k  + A+e+g+e + ++ +a ++++  +  + D 
  gi|118431181|ref|NP_147470.2|  4 RVAVVGAGRMGSGAARRLASRGYRVVVWSRSWEKAERLAREAGLEAArSLVDALAESEAAIAFVSDD 70
                                   79******************************************98625678888888777666654 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 ?   14.2   0.5   4.3e-05     0.031       3      69 ..      10      78 ..       9     112 .. 0.73
   2 ?   -2.0   0.0         4   2.9e+03      54      70 ..     252     268 ..     207     285 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                                   TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHT...T-SEEEES-- CS
                 NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealk...gadaVvsalg 69
                                    G+ G+ ++++l++r g++v++  R+ ek+++l++e+gle+    v   ++ ++a++   + da +  ++
  gi|118431181|ref|NP_147470.2| 10 AGRMGSGAARRLASR-GYRVVVWSRSWEKAERLAREAGLEAARSLVDALAESEAAIAfvsDDDALLNVVS 78
                                   79*************.5*****************99***9988666655555555543336667655554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                    HHHHHTT-SEEEES--- CS
                 NAD_binding_10  54 laealkgadaVvsalgg 70 
                                    + +a++++ a +s +g 
  gi|118431181|ref|NP_147470.2| 252 VSQAVSNVYAMLSHMGF 268
                                    34444444444444444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   6.9e-05      0.05       2      34 ..       5      37 ..       4      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE...ES-GGG CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLi...thkldt 34
                                   v V+G+G  G+ AA  +a +G++v+         ++
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRGYRVVVWsrsW---EK 37
                                   89***********************994442...33 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1    0.0001     0.075       4      36 ..       5      37 ..       3      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                   V++VGaG  G  +a+ L+++G rvv+  +  ++
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRGYRVVVWSRSWEK 37
                                   99**********************998876544 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 ?   11.0   0.2   0.00024      0.17       2      29 ..       4      31 ..       3      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlv 29
                                   +v+v+G+G  G  aa++la  g++v++ 
  gi|118431181|ref|NP_147470.2|  4 RVAVVGAGRMGSGAARRLASRGYRVVVW 31
                                   6899999999999999999999999876 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 ?   11.7   0.2   0.00019      0.14       6      61 ..      13      65 ..       9     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHH CS
                   adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealve 61
                                   +G ++A++la++G++vv++ ++ e+   +e+la+e g e+ +  V   ++ ea+++
  gi|118431181|ref|NP_147470.2| 13 MGSGAARRLASRGYRVVVWSRSWEK---AERLAREAGLEAARSLVDALAESEAAIA 65
                                   799*****************99998...6666666665543333333333333333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.12       3      50 ..       7      67 ..       5     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                   EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..............EEEE--T CS
                      Epimerase  3 VtGatGfiGsalvkallekgyevigldrlssasntarledl..............elveldl 50
                                   V+Ga G +Gs  +++l+++gy+v++++r  ++ ++ ++e                e   + +
  gi|118431181|ref|NP_147470.2|  7 VVGA-GRMGSGAARRLASRGYRVVVWSRSWEKAERLAREAGleaarslvdalaesEAAIAFV 67
                                   6665.99*********************9554443333222566554444333333333333 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00085      0.61      55      80 ..       5      30 ..       2      45 .. 0.84
   2 ?   -1.0   0.0       3.2   2.3e+03      41      66 ..      97     122 ..      77     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00085
                                   -SEEEESSSCHHHHHHHCTTTSEEEE CS
                  Nitro_FeMo-Co 55 vdvvivgkiGpralakleaagievyk 80
                                   v vv +g++G +a+++l+++g +v++
  gi|118431181|ref|NP_147470.2|  5 VAVVGAGRMGSGAARRLASRGYRVVV 30
                                   88999*******************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.2
                                    CSSTHHHHHHHHTT-SEEEESSSCHH CS
                  Nitro_FeMo-Co  41 ggggklaqllaeegvdvvivgkiGpr 66 
                                    ++  ++a+ l+  gv+ v +  iG++
  gi|118431181|ref|NP_147470.2|  97 RASVSAARYLEGLGVQYVEAPVIGGP 122
                                    55667778888899999999888654 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00031      0.23       2      66 ..       4      58 ..       3     124 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                                   EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC.STTTTTBHHHHSSSS--S-BEBSSHHHHHH CS
                         DapB_N  2 kvavvGasGrmGkevvkaveeaedlelvaavdrke.selegkdagellglgklgvavtddleevle 66
                                   +vavvGa GrmG+  ++ + + +++++v    + e  e  +++ag  + ++         l ++l+
  gi|118431181|ref|NP_147470.2|  4 RVAVVGA-GRMGSGAARRLAS-RGYRVVVWSRSWEkAERLAREAGLEAARS---------LVDALA 58
                                   79****9.********99998.66666655444431333444444333333.........333333 PP

>> DUF2647  Protein of unknown function (DUF2647)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4    0.0019       1.3      36      55 ..       6      25 ..       3      35 .. 0.86
   2 ?   -1.4   0.0       3.6   2.6e+03      17      28 ..      80      91 ..      77      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                        DUF2647 36 slvGsGrsGGGttallssri 55
                                   ++vG+Gr G G+++ l sr 
  gi|118431181|ref|NP_147470.2|  6 AVVGAGRMGSGAARRLASRG 25
                                   58****************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                        DUF2647 17 lrridGaiqvrs 28
                                   +rr dG i v s
  gi|118431181|ref|NP_147470.2| 80 VRRSDGLIFVNS 91
                                   699****99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2034.96
//
Query:       gi|118431182|ref|NP_147471.2|  [L=356]
Description: hypothetical protein APE_0759.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.03   14.5   0.1      0.076   13.3   0.1    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.062   12.0   0.4      0.091   11.4   0.4    1.2  1  HI0933_like    HI0933-like protein
      0.069   12.2   0.4       0.11   11.6   0.4    1.2  1  GIDA           Glucose inhibited division protein A
       0.28   10.5   1.0       0.41    9.9   1.0    1.2  1  FAD_oxidored   FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.7e-05     0.076       1      33 [.       6      38 ..       6      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                   +vG G +G+ aA+++++ g++ +++e+ +++G 
  gi|118431182|ref|NP_147471.2|  6 VVGLGPAGAGAAAAASRLGVKPVIYEAMEKPGL 38
                                   899************************999994 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4     2e-05     0.091       4      38 ..       5      39 ..       2      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2e-05
                                   EEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                    HI0933_like  4 iviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                    v+G G+AG  aA++a++ g + +++e+++k+g K
  gi|118431182|ref|NP_147471.2|  5 SVVGLGPAGAGAAAAASRLGVKPVIYEAMEKPGLK 39
                                   69******************************987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   2.4e-05      0.11       3      28 ..       5      30 ..       3      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                                   EEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  3 iViGgGhAGceAAlaaarlGakvlLi 28
                                    V+G G AG  AA+aa+rlG+k +++
  gi|118431182|ref|NP_147471.2|  5 SVVGLGPAGAGAAAAASRLGVKPVIY 30
                                   69*******************98887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   9.2e-05      0.41       4      31 ..       6      33 ..       4      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.2e-05
                   FAD_oxidored  4 VvGGgpaGvaAAiaAaraGakvlLveer 31
                                   VvG gpaG  AA aA r G k ++ e  
  gi|118431182|ref|NP_147471.2|  6 VVGLGPAGAGAAAAASRLGVKPVIYEAM 33
                                   9*******************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2706.68
//
Query:       gi|118431183|ref|NP_147472.2|  [L=135]
Description: hypothetical protein APE_0760.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-31  107.5   0.5    5.4e-31  107.2   0.5    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 !  107.2   0.5     3e-35   5.4e-31       3     117 ..       7     126 ..       5     128 .. 0.97

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 3e-35
                                    HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHHHC CS
                           HEPN   3 ewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeLek 82 
                                     wlr A++dl  Ae++l+ gd ++a f++qqaaekalK+lll+ +g++pkth++r+Lle l   l+ se   e++ eL++
  gi|118431183|ref|NP_147472.2|   7 LWLRAARRDLGRAEYSLKVGDRAAATFWSQQAAEKALKGLLLAFKGDYPKTHSIRRLLEDLGLDLGLSEGELEDAFELTQ 86 
                                    7**********************************************************99999999************* PP

                                    CCHHCCCTSS--S.....--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  83 ayiesrYpdakee.....yteedaeealkdaeevlelvee 117
                                    +y  srYpd  ee     + ++ ae+a++ a++++e++e+
  gi|118431183|ref|NP_147472.2|  87 YYYLSRYPDVVEElpdevIGRRSAERAVNAARRIVEAAER 126
                                    ************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1076.35
//
Query:       gi|118431184|ref|NP_147473.2|  [L=91]
Description: hypothetical protein APE_0761.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-10   40.0   0.0    4.1e-10   39.8   0.0    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
      1e-06   28.8   0.0    1.1e-06   28.6   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   4.6e-14   4.1e-10      16      80 ..       3      61 ..       2      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 4.6e-14
                                   EEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                   NTP_transf_2 16 kvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80
                                   +v lfGS+arG++ +gSD+Dl+vv++++       ++ e+l+   k +++  +l + +++ ++ e
  gi|118431184|ref|NP_147473.2|  3 EVKLFGSFARGDYAEGSDLDLVVVSRDWEG----VNYVERLSLLYKLWDK--PLDANFIPLTPEE 61
                                   6889************************54....3555555555555555..5555555444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.3e-10   1.1e-06      17      58 ..       5      48 ..       2      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-10
                                   TEEEEEE-S------EEEEEEEESS-..--HHHHHHHHHHHHHH CS
                        Polbeta 17 ylFGSrakgkareeSDiDlavllkek..ldleeelelaaeledi 58
                                    lFGS+a+g++ e SD+Dl v+ ++    ++ e+l+l  +l d 
  gi|118431184|ref|NP_147473.2|  5 KLFGSFARGDYAEGSDLDLVVVSRDWegVNYVERLSLLYKLWDK 48
                                   59***********************9665666666666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 696.06
//
Query:       gi|118431185|ref|NP_147474.2|  [L=83]
Description: hypothetical protein APE_0762.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); 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 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 664.43
//
Query:       gi|118431186|ref|YP_874849.1|  [L=322]
Description: hypothetical protein APE_0763.1 [Aeropyrum pernix K1]
Scores for complete 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   43.6   0.0    3.3e-11   43.1   0.0    1.2  1  Epimerase      NAD dependent epimerase/dehydratase family
    0.00027   20.2   0.0    0.00037   19.7   0.0    1.3  1  NAD_binding_4  Male sterility protein
     0.0051   15.9   0.0      0.013   14.5   0.0    1.5  1  3Beta_HSD      3-beta hydroxysteroid dehydrogenase/isomerase 
  ------ inclusion threshold ------
       0.54   10.9   1.7        1.2    9.7   1.7    1.6  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


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 !   43.1   0.0   7.4e-15   3.3e-11       1     181 [.       4     186 ..       4     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 7.4e-15
                                    EEEETTTSHHHHHHHHHHHHCT.....SE.EEEEES-STTTTCHHCHHC......EEEE--T.T-HHHHHHHHHHHT-SE CS
                      Epimerase   1 ilVtGatGfiGsalvkallekg.....ye.vigldrlssasntarledl......elveldl.tdrsalerlfkeeqpda 67 
                                    i+V+G+ G++G +++ al++ g     y+ v+g  r+  as              +lv++d  + +++lerl    + d+
  gi|118431186|ref|YP_874849.1|   4 IVVVGGLGYVGVNIAPALADLGelvvvYRgVVGGFRRVIAS-------RleslgaRLVRIDApMTADELERL----GGDV 72 
                                    89********************5544444444444443333.......345556688888862344466666....669* PP

                                    EEE--S.---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSS......BSTCSTTS----SS CS
                      Epimerase  68 vihlAa.vggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqp......keettltgplkpns 140
                                     ihlA+ ++g  +        +e+++ +   ++eaa + g  r+++ sS+  YG+ ++ p      +e++ l+g    +s
  gi|118431186|ref|YP_874849.1|  73 YIHLAGkISGGYR------VQWESHVGLLEAIVEAAGRIGS-RVVYTSSVLAYGRLEDLPpgslvyEEDEHLSGRRWWRS 145
                                    ****997655544......34778999999***********.****************8559888655555566668999 PP

                                    HHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTS CS
                      Epimerase 141 pYaaaKlageklveayaaqyglnaiilrlfnlyGprngege 181
                                      a++K+ ge+l+ +  +  g ++ i+r+  ++G + +++e
  gi|118431186|ref|YP_874849.1| 146 YHARTKAEGERLLVSSSRRLGGRFSIVRPGLVVGSHAYHRE 186
                                    9**********************************977766 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.3e-08   0.00037     108     209 ..      88     193 ..      43     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.3e-08
                                    HHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--EEEETTTCCCHH.HHHHHHHHHH CS
                  NAD_binding_4 108 lrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldederaklkglpntY.eqsKalaEkl 186
                                    ++  v   + ++e a ++ +   +++ S+  ++g  e+            +   +ede+ +++ + + Y  ++Ka++E+l
  gi|118431186|ref|YP_874849.1|  88 WESHVGLLEAIVEAAGRIGSR--VVYTSSVLAYGRLEDLPP--------GSLVYEEDEHLSGRRWWRSYhARTKAEGERL 157
                                    555555555555555555444..677777444443333221........23345677777788888877368******** PP

                                    HHHHHHHH---EEEEEE-EEE-.............- CS
                  NAD_binding_4 187 vrearrrsglpvvivRpsiitg.............e 209
                                    + + +rr g +++ivRp+ ++g              
  gi|118431186|ref|YP_874849.1| 158 LVSSSRRLGGRFSIVRPGLVVGshayhrewsmlfrL 193
                                    *******9*************965555544444444 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 !   14.5   0.0   2.9e-06     0.013       1     162 [.       5     163 ..       5     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-06
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkev.rvlDlrespelleelskvnvkkviegDvtdk.dkleealegvdvvihlaslvd 78 
                                    vv+Gg G++G ++  +L +l+el  v r +   ++  + ++l++++ + ++  D   + d+le+   g dv ihla+  +
  gi|118431186|ref|YP_874849.1|   5 VVVGGLGYVGVNIAPALADLGELVVVyRGVVGGFRRVIASRLESLGAR-LVRIDAPMTaDELERL--GGDVYIHLAG--K 79 
                                    79*******************955552555567788888899999999.8888886550555554..6789999966..5 PP

                      3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnsl...geeilngdEeleyeslhqdaypesKalaEk 155
                                    + g ++ +   +  v   + ++ea+ + g  ++vYtSs+ + g       g  + + dE+l     + +  +++Ka  E+
  gi|118431186|ref|YP_874849.1|  80 ISGGYRVQ--WESHVGLLEAIVEAAGRIGS-RVVYTSSVLAYGRLEDlppGSLVYEEDEHLSGRRWWRSYHARTKAEGER 156
                                    56666666..34445556889999999995.689*****9998633222388899************************* PP

                      3Beta_HSD 156 lvlkaNg 162
                                    l++++  
  gi|118431186|ref|YP_874849.1| 157 LLVSSSR 163
                                    9998876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.7   0.00027       1.2       1      27 [.       3      30 ..       3      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                                   EEEEECS.SHHHHHHHHHHHHTTSEEEE CS
                      Pyr_redox  1 kvvvvGg.GyiglElAgalaelgkkVtv 27
                                   ++vvvGg Gy+g+  A ala+lg  V v
  gi|118431186|ref|YP_874849.1|  3 RIVVVGGlGYVGVNIAPALADLGELVVV 30
                                   68999988***************66544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2294.34
//
Query:       gi|14600951|ref|NP_147477.1|  [L=239]
Description: phosphoglycolate phosphatase [Aeropyrum pernix K1]
Scores for complete 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   73.9   0.0    1.9e-12   47.5   0.0    3.0  3  Hydrolase_3  haloacid dehalogenase-like hydrolase
    4.3e-08   33.7   0.4    0.00097   19.5   0.1    3.2  3  Hydrolase    haloacid dehalogenase-like hydrolase
    0.00026   21.5   1.5       0.17   12.3   0.0    3.4  3  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.061   12.8   0.0       0.13   11.7   0.0    1.6  2  S6PP         Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.2e-08   0.00037       2      66 ..      12      78 ..      11      86 .. 0.85
   2 ?    3.3   0.0     0.013        57      33      55 ..      84     106 ..      79     112 .. 0.86
   3 !   47.5   0.0   4.2e-16   1.9e-12     174     247 ..     146     219 ..     128     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.2e-08
                                  EEEIIIIIS-TTS-..--HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE CS
                   Hydrolase_3  2 alDlDGTLlnsdkk..isektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali 66
                                  alD+DGTL    +   ++  ++++ + l + g++ ++ TG+sl  ++ v+  lgl+ pv+a NG++ 
  gi|14600951|ref|NP_147477.1| 12 ALDIDGTLTERRGAarLDGCSIAVARLLNDLGVTSILMTGNSLPVARGVAVYLGLEGPVVAENGCVA 78
                                  79*******988874355666666666778***********************************97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.013
                                   EEEEE-SS-HHHHHHHHHHCCCC CS
                   Hydrolase_3  33 kvviATGRslravlpvleelgld 55 
                                    v i++GR+++++ + + elg++
  gi|14600951|ref|NP_147477.1|  84 RVHICSGRPPEGLVKRIMELGFK 106
                                   789*********99999999976 PP

  == domain 3  score: 47.5 bits;  conditional E-value: 4.2e-16
                                   ESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                   Hydrolase_3 174 sskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                   +s++ l i p+g  K+ ++ +++ +++   +ev+a+GDgeND+e L +ag++ A g+a e++k aA+ v  s  
  gi|14600951|ref|NP_147477.1| 146 WSGYALHIQPPGGGKARGVGEVLARIGAGWSEVLAIGDGENDVEVLARAGYSGAPGDAAEQAKRAAKIVARSPG 219
                                   578999***************************************************************98865 PP

>> Hydrolase  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    0.0069        31       2      16 ..       9      23 ..       8      35 .. 0.83
   2 !    6.4   0.0    0.0022        10     128     190 ..      37     107 ..      28     109 .. 0.74
   3 !   19.5   0.1   2.2e-07   0.00097     148     210 .]     133     195 ..     128     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0069
                                  SEEEEESBTTTBCHH CS
                                  xxxxxxxxxxxxxxx RF
                     Hydrolase  2 ktvvfDkdGTLttge 16
                                  ++ ++D+dGTLt+ +
  gi|14600951|ref|NP_147477.1|  9 RVAALDIDGTLTERR 23
                                  67899*******765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0022
                                   HHHHHTTEEEEEEESSEHHHHHHHHHHTT........GGGESEEEEHHCES......STTTSHHHHHHHHHHHTSTG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 128 asLkaagievvlltgdnpetaeraanqlG........ddyfdaviasdiet......vakpspegkvaaireLqgkp 190
                                   + L++ g+  +l+tg++   a+ +a  lG        + +  av+     +      +++  peg+v+ i eL+ kp
  gi|14600951|ref|NP_147477.1|  37 RLLNDLGVTSILMTGNSLPVARGVAVYLGlegpvvaeNGC-VAVV-----GgervhiCSGRPPEGLVKRIMELGFKP 107
                                   4478889999999*99999999*******98666542222.3333.....333334688888***********9998 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 2.2e-07
                                   HHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hydrolase 148 aeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                   a ++a++ G ++++  +a  i   ++ + +g+ +++ ++++  +ev+++GDg nD++ la+Ag
  gi|14600951|ref|NP_147477.1| 133 ASAIAEEEGYRAIWSGYALHIQPPGGGKARGVGEVLARIGAGWSEVLAIGDGENDVEVLARAG 195
                                   556677777445556666667778999999*******************************98 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.045     2e+02       1      12 [.      11      22 ..      11      35 .. 0.82
   2 ?    4.3   0.0     0.011        47      94     141 ..      39      82 ..      33     115 .. 0.67
   3 !   12.3   0.0   3.7e-05      0.17     137     187 ..     145     191 ..     120     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.045
                           HAD  1 alfDfDgTLldg 12
                                  a +D+DgTL+  
  gi|14600951|ref|NP_147477.1| 11 AALDIDGTLTER 22
                                  568******976 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                           HAD  94 laahraaGdrvvvvSgglrplvepllaelgadevlatelevdd...rltge 141
                                   l+   + G++ ++ +g+  p+++ ++  lg    l   +  ++    + g+
  gi|14600951|ref|NP_147477.1|  39 LN---DLGVTSILMTGNSLPVARGVAVYLG----LEGPVVAENgcvAVVGG 82 
                                   33...889999***************9999....66643333445533333 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.7e-05
                           HAD 137 rltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                    ++g + ++++p  g  k++ + e    +  g+ ++ev a+GD+++D++ l
  gi|14600951|ref|NP_147477.1| 145 IWSGYALHIQPPGGG--KARGVGE--VLARIGAGWSEVLAIGDGENDVEVL 191
                                   667777777777777..9999999..55566666677**********9876 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.55   2.5e+03       6      24 ..      12      28 ..       9      64 .. 0.71
   2 ?   11.7   0.0     3e-05      0.13     153     240 ..     147     225 ..     109     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.55
                                  EE-TBTTTB.S-HHHHHHH CS
                          S6PP  6 vsdLDntlvdgdnealarl 24
                                  + d+D+tl+  +++  arl
  gi|14600951|ref|NP_147477.1| 12 ALDIDGTLT--ERRGAARL 28
                                  679999999..44444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3e-05
                                   TTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH--TTE..EE-SS- CS
                          S6PP 153 sgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllenakeneriylaeer 233
                                   sg +l + P +++k++ +   + + ++  +++l  Gd +nD e+l    ++   g+a e+       + +  +  ++a+++
  gi|14600951|ref|NP_147477.1| 147 SGYALHIQPPGGGKARGVGEVLARIGAGWSEVLAIGDGENDVEVLARAGYSGAPGDAAEQ-------AKRAAK--IVARSP 218
                                   578999***************************************555444455555554.......222222..456666 PP

                                   THHHHHH CS
                          S6PP 234 caaGile 240
                                    a+G le
  gi|14600951|ref|NP_147477.1| 219 GARGTLE 225
                                   6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1902.27
//
Query:       gi|118431187|ref|NP_147478.2|  [L=314]
Description: spermidine synthase [Aeropyrum pernix K1]
Scores for 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-48  162.5   0.0      1e-47  162.0   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    2.8e-09   36.7   0.0    5.7e-09   35.7   0.0    1.5  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    1.1e-06   29.3   0.0    2.1e-06   28.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.5e-05   24.9   0.0    7.6e-05   23.4   0.0    1.9  1  Methyltransf_12  Methyltransferase domain
      3e-05   23.9   0.0    4.4e-05   23.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
     0.0084   16.7   0.0      0.021   15.5   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.019   14.3   0.0      0.049   12.9   0.0    1.6  2  Methyltransf_2   O-methyltransferase domain
      0.022   14.3   0.0      0.032   13.8   0.0    1.2  1  MTS              Methyltransferase small domain
      0.027   14.1   0.0      0.039   13.6   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.0   5.2e-51     1e-47       1     181 [.      69     250 ..      69     255 .. 0.95

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 5.2e-51
                                    THHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEES CS
                 Spermine_synth   1 efaykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlg 80 
                                    ef+y+e+++h ++ lh +p++vLi+GGg G +lrev+kh +vek+++vdiD+ v+++ ++ l++ + +af+d+r ++v++
  gi|118431187|ref|NP_147478.2|  69 EFMYHEALVHPAMILHGSPRKVLILGGGEGATLREVLKHRSVEKAVMVDIDETVVNVAREHLREWHRGAFDDPRAEVVID 148
                                    799***************************************************************************** PP

                                    TCHHHHCTCSS.-EEEEEEECCS..TTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCE CS
                 Spermine_synth  81 dgfkflkayek.kfdvvivdsld..pvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalq 157
                                    d+ ++++  ++  fdvvi+d++d  + gpa  l+s+e+++ +k+v++++Gv+++qa ++    e+   +++++  vf+  
  gi|118431187|ref|NP_147478.2| 149 DAWNYVASKAEtGFDVVIADLVDplEAGPATRLYSEEYYRMVKDVMNPGGVFVTQAVSISHLTEYHAIIRNTVARVFK-H 227
                                    ******9988889**********777899999************************999999999999********99.* PP

                                    EEEEEEETTTSCSCEEEEEEEESS CS
                 Spermine_synth 158 vepsavlvPtylsgminfvveskk 181
                                    ve + v+vP++ s m++fvv+s++
  gi|118431187|ref|NP_147478.2| 228 VESYGVYVPSFDS-MWGFVVASDD 250
                                    **********975.8899998876 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 !   35.7   0.0   2.8e-12   5.7e-09       2      53 .]      15      66 ..      14      66 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.8e-12
                                   EEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                Spermine_synt_N  2 WfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                   Wf e  +p +a    +e+v+++++S++Q+i +++ +  GkvLvLDg+ q +E
  gi|118431187|ref|NP_147478.2| 15 WFLEWLTPDRATLKHIEDVIFQGRSRFQEIAVVRVSGEGKVLVLDGKTQSSE 66
                                   ***********************************************99877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     1e-09   2.1e-06       1      97 []      90     198 ..      90     198 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1e-09
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH..TTT....TEEEEESBCCG..BSSSTTTEEEEEEES CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee..egl....nvefvqgdaed..lpfedgsfDlvvssg 72 
                                    vL lG G+G ++++++k+ + +k ++vDi+e+ ++ are+++e  +g+    ++e+v  da +   + ++  fD+v++  
  gi|118431187|ref|NP_147478.2|  90 VLILGGGEGATLREVLKHRSVEKAVMVDIDETVVNVAREHLREwhRGAfddpRAEVVIDDAWNyvASKAETGFDVVIADL 169
                                    7889*************9768********************99873335566*********7732357888*******43 PP

                                    T..GGGSSHHHH..HHHHHHHHHHEEEEE CS
                Methyltransf_25  73 a..lhhlsdedl..ekalkeiarvLkpgG 97 
                                    +  l+  +  +l  e++++ +++v++pgG
  gi|118431187|ref|NP_147478.2| 170 VdpLEAGPATRLysEEYYRMVKDVMNPGG 198
                                    32344433222222555666666666665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.8e-08   7.6e-05       2      97 ..      92     198 ..      91     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.8e-08
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.......ssfDlvvas. 73 
                                     +G+G G++lr++l++ +  + + vDi++ +++ a+e+l+++++  ++  + e+  +  ++ +         fD+v+a  
  gi|118431187|ref|NP_147478.2|  92 ILGGGEGATLREVLKHRSVEKAVMVDIDETVVNVAREHLREWHRGAFDDPRAEVVID--DAWNyvaskaeTGFDVVIADl 169
                                    68**************99999***********************9999888887664..444468999999999999641 PP

                Methyltransf_12  74 .nvlhhl....kdirevldnirklLkpgG 97 
                                     + l++        +e+ + ++++++pgG
  gi|118431187|ref|NP_147478.2| 170 vDPLEAGpatrLYSEEYYRMVKDVMNPGG 198
                                    24455555444444555556666666666 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   4.4e-05       6     127 ..      89     222 ..      84     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.2e-08
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaq...klgld..nveFeqgdiee.leklledekfDlil 79 
                                    +vl lG G+G+ + e   + ++  + v +Di+e+++++Are+++   +  +d  ++e+ + d+ +   ++ ++  fD+++
  gi|118431187|ref|NP_147478.2|  89 KVLILGGGEGATLREVL-KHRSVEKAVMVDIDETVVNVAREHLRewhRGAFDdpRAEVVIDDAWNyVASK-AETGFDVVI 166
                                    67779************.77888899***************66511145677999999999999965543.4489***** PP

                Methyltransf_31  80 sn..evl....naladpdkileeiervlkpggilliedpr..llaelpakveeesk 127
                                    ++  ++l    ++   ++++++ +++v++pgg+++++ ++  +l+e+ a+++++  
  gi|118431187|ref|NP_147478.2| 167 ADlvDPLeagpATRLYSEEYYRMVKDVMNPGGVFVTQAVSisHLTEYHAIIRNTVA 222
                                    *955444666666666778888**************99987777777666666544 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     1e-05     0.021       3      95 ..      93     201 ..      91     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                    ET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-......EEEETTEECCC.T.SS-TT-EEEEEEES-CC CS
                Methyltransf_11   3 vGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl......kvefvvadaek.l.pfednsfDlvvssevlh 72 
                                    +G G G+ ++++ k+   ++ v vD++++++++a+e+ +e +       + e+v  da + +   ++  fD+v++  v  
  gi|118431187|ref|NP_147478.2|  93 LGGGEGATLREVLKHRsvEKAVMVDIDETVVNVAREHLREWHRgafddpRAEVVIDDAWNyVaSKAETGFDVVIADLVDP 172
                                    799*********966668*********************999999999988999999998433566679***99988644 PP

                                    C-..C....CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  73 hv..e....dpekalkeiaRvLkpgGllv 95 
                                        +      e++ + ++ v+ pgG++v
  gi|118431187|ref|NP_147478.2| 173 LEagPatrlYSEEYYRMVKDVMNPGGVFV 201
                                    44332444477777788888888888886 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.4e-05     0.049      66     107 ..      90     132 ..      62     142 .. 0.86
   2 ?   -2.6   0.0       1.4   2.7e+03      96     123 ..     145     171 ..     134     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.4e-05
                                    EEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-- CS
                 Methyltransf_2  66 lvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsa 107
                                    ++ +GGG Ga+++++ ++    k+++ D+ e Vv+ A+ehl  
  gi|118431187|ref|NP_147478.2|  90 VLILGGGEGATLREVLKHRSVEKAVMVDIDEtVVNVAREHLRE 132
                                    5569*************************754999*****854 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                    HHHHHHHHHS-----TTEEEEES-TTTS CS
                 Methyltransf_2  96 eVveaAkehlsageeervefvgGdffkd 123
                                     V+ +A +++ +++e+++++v  d+  d
  gi|118431187|ref|NP_147478.2| 145 VVIDDAWNYVASKAETGFDVVIADLV-D 171
                                    58899999999999999999988887.5 PP

>> MTS  Methyltransferase small 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     0.032      33     156 ..      88     224 ..      76     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                    SEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTTTST...TS-EEEEEE CS
                            MTS  33 gkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdvleeve...ekkfdlivs 103
                                    +kvl lG G G+   +++k+ +  + ++vd+d   +++a+e l++ +        +evv  d+ + v+   e  fd+++ 
  gi|118431187|ref|NP_147478.2|  88 RKVLILGGGEGATLREVLKHRSVEKAVMVDIDETVVNVAREHLREWHRGafddprAEVVIDDAWNYVAskaETGFDVVIA 167
                                    68999*******9999999999999****************9987554345588889988887665542235889***98 PP

                                    -..--STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE..EEETTS.CHHHHHHHHHS-- CS
                            MTS 104 N..PPfhagkatelavaeeliaeAkeaLkegGeLli..Vanrkl.gyeslleelfgnv 156
                                        P+ ag a +    ee  +  k+++++gG ++   V  ++l +y++++++++ +v
  gi|118431187|ref|NP_147478.2| 168 DlvDPLEAGPA-TRLYSEEYYRMVKDVMNPGGVFVTqaVSISHLtEYHAIIRNTVARV 224
                                    64479999999.6667888899999999999988642255555525677766655543 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     2e-05     0.039      44     120 ..      89     168 ..      77     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                                    EEEETT-TTSHHHHHHH.HTT-SEEEEEES-HHHHHHHHHHHCCCT--T....TTEEEEES-HHHHCTS--SS-EEEEEE CS
                  Cons_hypoth95  44 rvLDlfaGsGalglEAl.SRgakkavlvekdkeavkilkenleelklee....etaelkedaleallklakkkeefdivf 118
                                    +vL l +G Ga   E l  R ++kav+v+ d+++v++ +e+l+e +  +    +++++++da + + ++a++   fd+v 
  gi|118431187|ref|NP_147478.2|  89 KVLILGGGEGATLREVLkHRSVEKAVMVDIDETVVNVAREHLREWHRGAfddpRAEVVIDDAWNYVASKAET--GFDVVI 166
                                    56667788888888988459************************9976688899999999999999888655..69*998 PP

                                    E- CS
                  Cons_hypoth95 119 lD 120
                                     D
  gi|118431187|ref|NP_147478.2| 167 AD 168
                                    76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2294.71
//
Query:       gi|118431188|ref|NP_147479.2|  [L=333]
Description: bifunctional phosphoglucose/phosphomannose isomerase [Aeropyrum pernix K1]
Scores for complete 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   0.0    4.6e-32  111.2   0.0    1.2  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI


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 !  111.2   0.0   2.6e-36   4.6e-32       3     152 .]     175     325 ..     173     325 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 2.6e-36
                                    -HHHHHHHHHTT.SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH. CS
                     bact-PGI_C   3 npakqlAlelag.klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeee 81 
                                     +a++lA +++  +++ +++ +++  ++A+R+kn+l+enAK+p+  +++pe++hn+iv+le + e+     ++++++e  
  gi|118431188|ref|NP_147479.2| 175 GEAERLAGFISRyRIASLVT-CGPGIPLAVRLKNELAENAKMPSRLEIYPESSHNDIVALE-AAEGLYGAVFIWIEHEG- 251
                                    68**********88999988.***************************************5.78889999999999777. PP

                                    .......HHHHHHHHTTTSSEEEEE---...SSSH.HHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH.. CS
                     bact-PGI_C  82 hprvkkraeivkelaeergvrvtevkae...gesp.lerlaslillgDfvSvylAllrgvDPtpvpaIdelKeel 152
                                     + + +++++v+ +++e+gv++++++++   g ++ +++++s +l+++++Sv+lAl+rg++P+++p+Id++K++l
  gi|118431188|ref|NP_147479.2| 252 -SLCPAVLDVVEGIYREYGVDTISIESSargGPNAtVAEYLSRTLVFGLASVRLALMRGFNPEETPPIDKYKRRL 325
                                    .8*********************9998866655556************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2592.91
//
Query:       gi|118431189|ref|NP_147481.2|  [L=384]
Description: hypothetical protein APE_0771.1 [Aeropyrum pernix K1]
Scores for 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-71  242.2  13.2    1.4e-71  241.7  13.0    1.3  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
       0.63    9.4   3.7        1.1    8.5   0.0    2.6  3  DUF4191   Domain of unknown function (DUF4191)


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 !  241.7  13.0   1.5e-75   1.4e-71       2     320 ..      22     351 ..      21     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 241.7 bits;  conditional E-value: 1.5e-75
                         DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvgvea 81 
                                     Lv++vD+DdD+g+++g ++ +vG+++vleaav++a+++P+D+D+N++f+++++y++Lk e  dve+avv+G+++ gvea
  gi|118431189|ref|NP_147481.2|  22 ALVIVVDLDDDVGETLG-ESVIVGYDRVLEAAVRFAIERPDDADANTMFAGLRLYRKLKGEYGDVEIAVVGGSRRLGVEA 100
                                    79***************.************************************************************** PP

                         DUF373  82 drkiaeqldevlsklead.saivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpelrkt 156
                                    +r+++e++ +++s++ +d ++++V DG e++ + +i++   +v++++ V+V+q+ +iEs y+l+    +ka++dp+++++
  gi|118431189|ref|NP_147481.2| 101 QRNLRERVASIVSEMGPDvDIYIVGDGGEEALASHILRGVGRVAGIESVIVSQHLGIESNYMLIakylRKAVTDPHYSTL 180
                                    ******************9************************************************************* PP

                         DUF373 157 iLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelle.klkesleegritfvtyvvallllligi 235
                                    +L+++Gl++ + all+l+g+ +lal+i ll++Gl+++++Gf+ld++++++l+  ++e  e+ +i++    v++llll+g+
  gi|118431189|ref|NP_147481.2| 181 VLGVPGLVISVAALLMLAGFFSLALKISLLIVGLAMVVYGFKLDDTVRTSLQsFVEELREAPHIRLGGLAVMTLLLLLGV 260
                                    **************************************************99455666677899999999********** PP

                         DUF373 236 isgyislesvssasvssglltlilafiygave.wlalailtaslgkiideylkre...ekdiarllllpflvlaiglvly 311
                                      +yis   +    vs+g + +i++++ ++++  +a +++++++++ii  +++++   +k+ia l +l f++la++ +  
  gi|118431189|ref|NP_147481.2| 261 SLTYIS---Y----VSEGATSAIVSLLTYTIPlSMAGVMMYIIISRIIVGATEGRvdlSKNIAMLSMLGFTALAFYDLGA 333
                                    ***999...2....23455556666555555505666777889999******9998888888888899999999998887 PP

                         DUF373 312 gasaylls.........l 320
                                    ++   l s          
  gi|118431189|ref|NP_147481.2| 334 SLRLVLESgqpvianviD 351
                                    777666445554444440 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.45   4.1e+03     144     163 ..     107     128 ..      75     142 .. 0.58
   2 ?    0.5   0.8     0.035   3.1e+02      25      61 ..     180     217 ..     159     229 .. 0.61
   3 ?    8.5   0.0   0.00013       1.1     123     170 ..     265     313 ..     255     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.45
                        DUF4191 144 rikrvva..dvpvyeivvGnge 163
                                    r++ +v+  + +v  ++vG+g 
  gi|118431189|ref|NP_147481.2| 107 RVASIVSemGPDVDIYIVGDGG 128
                                    3444443222233333444443 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.035
                        DUF4191  25 llwlllaaflvvvvvfvvlglllgs.lilllilgillg 61 
                                    l+  + ++++ v+++++++g++     i lli+g+++ 
  gi|118431189|ref|NP_147481.2| 180 LVLGVPGLVISVAALLMLAGFFSLAlKISLLIVGLAMV 217
                                    33334445566666666666665444777777776654 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00013
                        DUF4191 123 vvLvgEGnkkrvkkllaqe.kkrikrvvadvpvyeivvGngegqvplkk 170
                                    +  v+EG+++++ +ll+      ++ v+  + + +i+vG  eg+v l+k
  gi|118431189|ref|NP_147481.2| 265 ISYVSEGATSAIVSLLTYTiPLSMAGVMMYIIISRIIVGATEGRVDLSK 313
                                    67799*****99999997625799***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2740.12
//
Query:       gi|14600956|ref|NP_147482.1|  [L=112]
Description: signal recognition particle 19 kDa protein [Aeropyrum pernix K1]
Scores for 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-17   62.4   0.0    8.4e-17   61.9   0.0    1.2  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 !   61.9   0.0   4.7e-21   8.4e-17       1      93 [.      19     103 ..      19     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 4.7e-21
                                   EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS-C CS
                         SRP19   1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekiknk 80 
                                   +++P+Y+ds+  r+ GRrvp++ +v +P+ +++aea+++ g+e+vve e syPr w++   r+ v          ++  +k
  gi|14600956|ref|NP_147482.1|  19 ILWPAYFDSTLPRRLGRRVPRDMGVPSPKPEDVAEAARRAGFEAVVE-ESSYPRLWWRVrRRIVVLA--------PEDVSK 90 
                                   69*********************************************.9******886526666665........667899 PP

                                   HHHHHHHHHHHHH CS
                         SRP19  81 kellkkiaellke 93 
                                   ++++k++a++l++
  gi|14600956|ref|NP_147482.1|  91 TDIIKAVATELRK 103
                                   9999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 898.71
//
Query:       gi|118431190|ref|NP_147483.2|  [L=119]
Description: hypothetical protein APE_0773.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.19   11.1   0.0        5.2    6.4   0.0    2.0  2  AnfO_nitrog  Iron only nitrogenase protein AnfO (AnfO_nitrog)


Domain annotation for each model (and alignments):
>> AnfO_nitrog  Iron only nitrogenase protein AnfO (AnfO_nitrog)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0    0.0032        57      70      95 ..       7      32 ..       5      58 .. 0.82
   2 ?    6.4   0.0   0.00029       5.2      60      94 ..      65      99 ..      62     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0032
                    AnfO_nitrog 70 kevsGilyslLekagfsiweiegkpe 95
                                    e+ G+++s+Le++gf++  + ++ +
  gi|118431190|ref|NP_147483.2|  7 GEACGAVMSMLESMGFTVSVSRESYA 32
                                   57889***********9987777655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00029
                    AnfO_nitrog 60 eLgdckifvakevsGilyslLekagfsiweiegkp 94
                                   ++g++ ifv  ++ G   ++Le+ag s+ e++g++
  gi|118431190|ref|NP_147483.2| 65 SIGKVHIFVRGSLGGSRLEALEEAGASVDEVDGDT 99
                                   57899*************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 881.29
//
Query:       gi|118431191|ref|NP_147484.2|  [L=394]
Description: hypothetical protein APE_0774.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2919.70
//
Query:       gi|14600959|ref|NP_147485.1|  [L=243]
Description: protein-disulfide oxidoreductase [Aeropyrum pernix K1]
Scores for complete 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  114.1   0.0    3.5e-16   59.0   0.0    2.3  2  Thioredoxin_3   Thioredoxin domain
    0.00032   20.9   5.1      0.043   14.0   0.1    4.3  3  Glutaredoxin    Glutaredoxin
     0.0058   16.6   0.0       0.19   11.7   0.0    2.2  2  Thioredoxin     Thioredoxin
  ------ inclusion threshold ------
      0.034   14.0   0.0        5.1    6.9   0.0    2.6  2  TraF            F plasmid transfer operon protein
      0.039   14.1   0.1        1.8    8.7   0.0    2.7  3  Thioredoxin_4   Thioredoxin
      0.052   13.0   0.0        2.3    7.6   0.0    2.4  2  ABC_transp_aux  ABC-type uncharacterized transport system
      0.074   12.7   0.2       0.16   11.6   0.2    1.5  1  DUF2312         Uncharacterized protein conserved in bacteria
      0.078   13.4   0.0       0.69   10.4   0.0    2.2  2  DUF836          Glutaredoxin-like domain (DUF836)
      0.085   12.9   0.1          7    6.7   0.0    2.5  2  TrbC_Ftype      Type-F conjugative transfer system pilin asse


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 !   53.1   0.0   1.2e-17   2.4e-14       1      76 []      28     113 ..      28     113 .. 0.91
   2 !   59.0   0.0   1.8e-19   3.5e-16       3      73 ..     142     219 ..     126     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.2e-17
                                   EEEEE.E.SSSSTTCH...HHHHHHHHHCHCC.TCEC....EEECCTTHHHHHHCT-SSSSEE.ECTTCEEEESS---CCH CS
                 Thioredoxin_3   1 meikv.l.gpgCakCp...klekavkeaaaek.gika....evekvtdfeeiekygVmsvPal.vidgkvvvsGkvpseee 70 
                                   +e++v l ++gC++C+   +l+k+++e+ +++ g k+     +++ +d++++++++V++vP++ ++ g+v+++G +p +ee
  gi|14600959|ref|NP_147485.1|  28 VEVHVfLsKSGCETCEdtlRLMKLFEEESPTRnGGKLlklnVYYRESDSDKFSEFKVERVPTVaFLGGEVRWTG-IPAGEE 107
                                   58999656778*******************9955888999777888****************************.****** PP

                                   HHHHHH CS
                 Thioredoxin_3  71 irklle 76 
                                   ir+l+e
  gi|14600959|ref|NP_147485.1| 108 IRALVE 113
                                   ***986 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 1.8e-19
                                   EEE.ESSSSTTCH...HHHHHHHHHCHCCTCEC...EEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHH CS
                 Thioredoxin_3   3 ikv.lgpgCakCp...klekavkeaaaekgika...evekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirk 73 
                                   i+  ++p+C++Cp    l+ +++ +a+++g  +   e ++++++++i +kygVmsvP+++i+g++v++G vp ee++  
  gi|14600959|ref|NP_147485.1| 142 IETiITPSCPYCPyavLLAHMFAYEAWKQGNPVilsEAVEAYENPDIaDKYGVMSVPSIAINGYLVFVG-VPYEEDFLD 219
                                   55449*********9988999999999997555457999******************************.****98765 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.27   5.4e+02      26      44 ..       4      20 ..       2      30 .. 0.61
   2 ?    4.7   0.2     0.017        34       4      21 ..      34      51 ..      30      97 .. 0.70
   3 !   14.0   0.1   2.2e-05     0.043       5      59 ..     146     206 ..     140     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.27
                                  EEEEEGCCSHHHHHHHHHH CS
                  Glutaredoxin 26 feeidvdkdeeireelkel 44
                                  + + d+++d  +r el+e 
  gi|14600959|ref|NP_147485.1|  4 YYVLDLSED--FRRELRET 20
                                  666777776..66666554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                                  EESTSSHHHHHHHHHHHH CS
                  Glutaredoxin  4 ftkptCpyCkkakrlLke 21
                                   +k++C+ C  + rl+k 
  gi|14600959|ref|NP_147485.1| 34 LSKSGCETCEDTLRLMKL 51
                                  5789******99999953 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 2.2e-05
                                   ESTSSHHHHHHHHHHHHTT.........GG.EEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEE CS
                  Glutaredoxin   5 tkptCpyCkkakrlLkelg.........vk.feeidvdkdeeireelkelsgvrtvPqvfidgkh 59 
                                    +p CpyC+ a+ l++ +          v   e ++  ++++i ++     gv++vP + i+g +
  gi|14600959|ref|NP_147485.1| 146 ITPSCPYCPYAVLLAHMFAyeawkqgnpVIlSEAVEAYENPDIADKY----GVMSVPSIAINGYL 206
                                   579************76664444444554436999999999999999....***********965 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.056   1.1e+02      60      82 ..      74      96 ..      19     116 .. 0.76
   2 !   11.7   0.0   9.7e-05      0.19      22      78 ..     145     202 ..     127     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.056
                                  TSHHHHHHTT-SSSSEEEEEETT CS
                   Thioredoxin 60 enedlakkyevegiPtlklfkng 82
                                  + +d  ++++ve +Pt+ ++  +
  gi|14600959|ref|NP_147485.1| 74 SDSDKFSEFKVERVPTVAFLGGE 96
                                  345678999*******9987654 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.7e-05
                                   EEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                   Thioredoxin  22 lveFyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlkl 78 
                                   ++    p+C+    la +++  a +  +  +    v++ en+d+a+ky+v ++P + +
  gi|14600959|ref|NP_147485.1| 145 IITPSCPYCPYAVLLAHMFAYEAWKQGNpVILSEAVEAYENPDIADKYGVMSVPSIAI 202
                                   55556788888889999987555555552666668*******************9976 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.017        34     134     196 ..      32      90 ..       9     100 .. 0.65
   2 ?    6.9   0.0    0.0025       5.1     118     196 ..     127     200 ..     119     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                          TraF 134 lfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpe.lpnarvdkgqaarlgvkrtPal 196
                                   +f+ +++c+ ce  +  ++ f+++           g+ l+  +   + d+++  +++v+r+P++
  gi|14600959|ref|NP_147485.1|  32 VFLSKSGCETCEDTLRLMKLFEEESPT-----RNGGKLLKLnVYYRESDSDKFSEFKVERVPTV 90 
                                   466779999999999999999987532.....22222222111112335555666666666666 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                          TraF 118 eekeaalkklakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPal 196
                                   + +++alk+l++++ +  +  ++cpyc  ++    +fa +   +  +V + + +   ++n     + a ++gv ++P +
  gi|14600959|ref|NP_147485.1| 127 DATKEALKSLKGRVHIETIITPSCPYCPYAVLLAHMFAYEAWKQGNPVILSEAVEA-YEN----PDIADKYGVMSVPSI 200
                                   567899**********************9999999999888777777777777662.344....566667777777766 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.096   1.9e+02     129     164 ..      75     112 ..      70     114 .. 0.71
   2 ?   -2.0   0.2       1.8   3.6e+03      19      28 ..     144     153 ..     137     157 .. 0.74
   3 ?    8.7   0.0   0.00089       1.8     130     157 ..     186     213 ..     176     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.096
                                   HHHHHHHHT--SS-EE.EETTEEE-TT-.-HHHHHHHH CS
                 Thioredoxin_4 129 eskeakkagiestPtf.iingekveepq.tyeelkali 164
                                   +s ++ + ++e +Pt+ +++ge+ ++ +   ee++al+
  gi|14600959|ref|NP_147485.1|  75 DSDKFSEFKVERVPTVaFLGGEVRWTGIpAGEEIRALV 112
                                   67788999*******94569998655440446666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                   EEE-TT-HHH CS
                 Thioredoxin_4  19 eyedlrCphC 28 
                                   +    +Cp+C
  gi|14600959|ref|NP_147485.1| 144 TIITPSCPYC 153
                                   556679**** PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00089
                                   HHHHHHHT--SS-EEEETTEEE-TT--H CS
                 Thioredoxin_4 130 skeakkagiestPtfiingekveepqty 157
                                      a+k g+ s+P++ ing  v    +y
  gi|14600959|ref|NP_147485.1| 186 PDIADKYGVMSVPSIAINGYLVFVGVPY 213
                                   56789**************986544444 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 ?    3.1   0.0     0.027        53      17      37 ..      18      38 ..       7      88 .. 0.70
   2 ?    7.6   0.0    0.0012       2.3      12      37 ..     125     150 ..     120     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                ABC_transp_aux 17 kellknleepvtikvylsenl 37
                                  +e+l+++ +pv++ v+ls++ 
  gi|14600959|ref|NP_147485.1| 18 RETLAEMVNPVEVHVFLSKSG 38
                                  568999999*********984 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                ABC_transp_aux  12 Lsdatkellknleepvtikvylsenl 37 
                                   L datke+lk+l+  v+i+++++++ 
  gi|14600959|ref|NP_147485.1| 125 LEDATKEALKSLKGRVHIETIITPSC 150
                                   89********************9984 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 ?   11.6   0.2   8.1e-05      0.16       2      36 ..     105     139 ..     104     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                       DUF2312   2 adqLrqfieRiErleeEkkaiaedikdvyaeaKse 36 
                                    +++r+++e i rl e+ +++++  k+  +  K++
  gi|14600959|ref|NP_147485.1| 105 GEEIRALVEVIMRLSEDESGLEDATKEALKSLKGR 139
                                   689************************99999985 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00035      0.69       4      55 ..      33      92 ..      31     115 .. 0.79
   2 ?    0.3   0.0      0.47   9.3e+02      29      57 ..     175     204 ..     141     210 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                                  EEE-TT-HHHHHHHHHHHHHCCCTT....EEEEEEETT...T-CCCHCCCCTT.TTEEEE CS
                        DUF836  4 LyskpgChlCeqakekLkelkleeg....leleviDIa...kdeeleakYgle.ipvlal 55
                                  ++sk gC  Ce+   ++k +++e+      +l++ +++   +d + ++++++e +p +a+
  gi|14600959|ref|NP_147485.1| 33 FLSKSGCETCEDTLRLMKLFEEESPtrngGKLLKLNVYyreSDSDKFSEFKVErVPTVAF 92
                                  79**********999999666555577778899999987655555788887643777776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.47
                                   EEEEEEETTT-CCCHCCCCTT.TTEEEECT CS
                        DUF836  29 leleviDIakdeeleakYgle.ipvlaleg 57 
                                   +  e +  +++++  +kYg++ +p +a++g
  gi|14600959|ref|NP_147485.1| 175 ILSEAVEAYENPDIADKYGVMsVPSIAING 204
                                   444555666778888888864367777765 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 ?    6.7   0.0    0.0035         7      63      78 ..      78      93 ..      72     107 .. 0.87
   2 ?    3.7   0.0     0.032        63      59      77 ..     184     202 ..     161     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0035
                    TrbC_Ftype 63 lFrqfkitaVPalvla 78
                                   F++fk+++VP++++ 
  gi|14600959|ref|NP_147485.1| 78 KFSEFKVERVPTVAFL 93
                                  6***********9875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.032
                    TrbC_Ftype  59 idPllFrqfkitaVPalvl 77 
                                    +P++ +++++ +VP++++
  gi|14600959|ref|NP_147485.1| 184 ENPDIADKYGVMSVPSIAI 202
                                   599999**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1830.77
//
Query:       gi|14600960|ref|NP_147486.1|  [L=129]
Description: hypothetical protein APE_0776 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0034   17.4   0.1     0.0078   16.2   0.0    1.8  2  HTH_3     Helix-turn-helix
  ------ inclusion threshold ------
      0.082   12.1   0.0      0.085   12.1   0.0    1.0  1  DUF2813   Protein of unknown function (DUF2813)
      0.098   13.1   0.5       0.28   11.6   0.0    1.9  2  NTS_2     N-terminal segments of P. falciparum erythrocyte me
       0.11   12.2   0.0        1.5    8.5   0.0    2.5  2  CENP-B_N  CENP-B N-terminal 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 !   16.2   0.0   1.7e-06    0.0078       5      34 ..      29      58 ..      24      78 .. 0.89
   2 ?   -2.7   0.0       1.5   6.7e+03      44      50 ..     116     122 ..     112     124 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                                  HHHTTHHHHHHHHHHTSSHHHHHHHHTTSS CS
                         HTH_3  5 RkqlglsqeeLAeklGvsrstisriEnGer 34
                                   ++ ++s+  +A++lG +++++s +++G+r
  gi|14600960|ref|NP_147486.1| 29 VEEYKMSKYSVAKMLGATPTAVSYYISGKR 58
                                  3599************************86 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                                   HHHHHTS CS
                         HTH_3  44 lakaLgv 50 
                                   la+ +g+
  gi|14600960|ref|NP_147486.1| 116 LAQKYGC 122
                                   5555555 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.9e-05     0.085     183     274 ..      20     109 ..       3     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.9e-05
                       DUF2813 183 lenllrrllskpqklsedelkselqalssllehYfleksasrkkkrkeressskeqllweklkslnqllkqeeekslrlll 263
                                   +   + ++l ++ k+s+ ++ + l a  + +++Y++ k+ ++  +r  r+++ ++ + +    sl    +++eeks+ + l
  gi|14600960|ref|NP_147486.1|  20 IRASIAKILVEEYKMSKYSVAKMLGATPTAVSYYISGKRGEKFVDRIIRDEEIYSIVREA--ASLLVEAHEREEKSDEKEL 98 
                                   5556778899999***********************999999999999998888655444..589899999********** PP

                       DUF2813 264 lgllatllqak 274
                                   +g l+ l+ + 
  gi|14600960|ref|NP_147486.1|  99 MGKLQVLMCKA 109
                                   ****9988654 PP

>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.28      11      45 ..      29      60 ..      20      66 .. 0.79
   2 ?   -1.1   0.1      0.56   2.5e+03      16      23 ..      90      97 ..      84     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                         NTS_2 11 iEaYLekksDdSkieqsLKADPSevqYYrsGGDGd 45
                                  +E+Y   k     + + L A P  v YY sG  G+
  gi|14600960|ref|NP_147486.1| 29 VEEY---KMSKYSVAKMLGATPTAVSYYISGKRGE 60
                                  6888...555566899***************7775 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.56
                         NTS_2 16 ekksDdSk 23
                                  e ksD+ +
  gi|14600960|ref|NP_147486.1| 90 EEKSDEKE 97
                                  78999976 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 ?    8.5   0.0   0.00034       1.5      19      40 ..      29      51 ..      21      59 .. 0.84
   2 ?    0.8   0.0     0.089     4e+02      26      36 ..     114     124 ..     108     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00034
                                  HHCTT.-HHHHHHHHT--CCHHH CS
                      CENP-B_N 19 leege.Skaelarrfnvpestls 40
                                  +ee + Sk ++a++++  ++ +s
  gi|14600960|ref|NP_147486.1| 29 VEEYKmSKYSVAKMLGATPTAVS 51
                                  677777**********9999887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.089
                                   HHHHHHHT--C CS
                      CENP-B_N  26 aelarrfnvpe 36 
                                   + la+++++p+
  gi|14600960|ref|NP_147486.1| 114 NMLAQKYGCPA 124
                                   569******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 905.91
//
Query:       gi|14600961|ref|NP_147487.1|  [L=266]
Description: serine/threonine protein phosphatase [Aeropyrum pernix K1]
Scores for complete 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-18   66.5   0.0    5.6e-18   66.2   0.0    1.2  1  Metallophos  Calcineurin-like phosphoesterase


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 !   66.2   0.0   3.1e-22   5.6e-18       6     202 ..       1     198 [.       1     200 [. 0.70

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.1e-22
                                   EESBTBTTCCTHHHHHHHHHHHHHHH..TTESEEEEESTSSSSSHHHHHHHHH..HHHHHHH.TSEEEEEC-TTS...... CS
                   Metallophos   6 igDlHlalgggqlddllkllddllre..ekpdlvllaGDlvdrgdlekellel..laalvky.pipvylllGNHe...... 75 
                                   +gD+H     g++ ++ +++++ l+    + +++l +GD++drg +e  +l    l++l k+ p +v++l+GNHe      
  gi|14600961|ref|NP_147487.1|   1 MGDIH-----GDYTTFSTIVERSLQTleGGGYMFL-LGDYIDRGTPEGQVLTIyrLCRLTKEyPGRVVMLRGNHEppegle 75 
                                   59***.....**********888555533445555.7*******66665555523566666689***********666554 PP

                                   ....CHHHHHHHHHHHHHHHHHHHEHH........HCEEETSEEEEEETTEEEEEEEESECEEE.THHHHHHHHHHHSCHH CS
                   Metallophos  76 ....gfeeellnkygylgifsepwrsd........aevfnnlplaslgsgslkvlllhGgspel.lvsldklgslnlelea 143
                                             l +++ +g        d         + f+ lp a l++g   +l lhGg+p + l++ +    l l  + 
  gi|14600961|ref|NP_147487.1|  76 pmphD---YPLALQTVYGS-------DgrrlyslsRKLFDSLPHAILVEG--ALLMLHGGPPTInLETASRDPALYLGSDG 144
                                   43211...22222222222.......23444445699*************..********888842222222222222222 PP

                                   HHCC.....HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                   Metallophos 144 pepg.....dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtH 202
                                      +     +++++d     +a+ +i+ +  p++rg g l+g+ ++    +  +++ +++GH+ 
  gi|14600961|ref|NP_147487.1| 145 ---DpeviaEILWND-----PAELDIIRA--PNPRGVGSLWGPGVTVHMARSLNIKRIVRGHEP 198
                                   ...255688******.....666666666..88899**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2083.03
//
Query:       gi|14600962|ref|NP_147488.1|  [L=329]
Description: HTH-type transcriptional regulator [Aeropyrum pernix K1]
Scores for 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-09   35.6   1.3    3.3e-08   33.5   0.4    2.3  2  HTH_3     Helix-turn-helix
      2e-07   30.9   0.5    7.3e-07   29.1   0.3    1.9  2  HTH_19    Helix-turn-helix domain
    0.00011   22.4   0.1    0.00038   20.7   0.0    1.9  2  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 ?    0.2   0.0      0.14   8.1e+02      37      52 ..      68      83 ..      64      86 .. 0.82
   2 !   33.5   0.4   5.5e-12   3.3e-08       1      52 [.     142     193 ..     142     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
                                  BHHHHHHHHHHHTSEH CS
                         HTH_3 37 sletlkklakaLgvsl 52
                                   +e l ++a+ Lgvs 
  gi|14600962|ref|NP_147488.1| 68 EVEELSAVANSLGVSA 83
                                  5799999999999996 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 5.5e-12
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                         HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                   l+e+R+++gls+  LA +l  sr +i+ +E+G  +Ps+e+++kl + Lg ++
  gi|14600962|ref|NP_147488.1| 142 LREKRLEKGLSLGHLAYMLKTSRKSIYEYERGVMSPSVEKAEKLVDILGEEI 193
                                   89**********************************************9776 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3   7.6e+03      43      55 ..      70      82 ..      65      85 .. 0.74
   2 !   29.1   0.3   1.2e-10   7.3e-07       2      55 ..     140     192 ..     140     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                        HTH_19 43 elllkiaealgid 55
                                  e+l ++a+ lg++
  gi|14600962|ref|NP_147488.1| 70 EELSAVANSLGVS 82
                                  5677788888877 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1.2e-10
                        HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55 
                                   e+L+e R e+gl++  la++l++sr++i+++E g +  ps e+  k++ +lg +
  gi|14600962|ref|NP_147488.1| 140 EKLREKRLEKGLSLGHLAYMLKTSRKSIYEYERGVM-SPSVEKAEKLVDILGEE 192
                                   789*********************************.***99999999999976 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   7.7e+03      18      28 ..      73      83 ..      70      85 .. 0.75
   2 !   20.7   0.0   6.3e-08   0.00038       6      55 ..     142     190 ..     139     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                        HTH_31 18 eevAerlgvse 28
                                   +vA  lgvs+
  gi|14600962|ref|NP_147488.1| 73 SAVANSLGVSA 83
                                  57888888885 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 6.3e-08
                        HTH_31   6 LralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                   Lr+ R + GLs+ ++A  l  s+  +  +E+G    ps +  e+l+++lg
  gi|14600962|ref|NP_147488.1| 142 LREKRLEKGLSLGHLAYMLKTSRKSIYEYERGVM-SPSVEKAEKLVDILG 190
                                   78888889**************************.6************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2573.42
//
Query:       gi|118431192|ref|NP_147489.2|  [L=206]
Description: hypothetical protein APE_0781.1 [Aeropyrum pernix K1]
Scores for complete 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-53  179.5   0.0    5.4e-53  179.3   0.0    1.1  1  NTPase_1         NTPase
    1.7e-07   31.0   0.0    2.5e-06   27.2   0.0    2.1  1  DUF2478          Protein of unknown function (DUF2478)
    5.5e-06   25.6   0.3    1.6e-05   24.1   0.3    1.8  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.4e-05   24.9   0.2    8.2e-05   22.4   0.2    2.1  1  AAA_30           AAA domain
    1.9e-05   24.9   0.0    5.7e-05   23.4   0.0    1.9  1  AAA_22           AAA domain
    4.9e-05   23.8   0.0    6.4e-05   23.4   0.0    1.3  1  AAA_17           AAA domain
      8e-05   23.1   0.1    0.00014   22.3   0.1    1.7  1  AAA_16           AAA ATPase domain
    9.2e-05   22.9   0.0     0.0005   20.5   0.0    2.1  2  AAA              ATPase family associated with various cellul
     0.0001   22.8   0.0    0.00018   22.0   0.0    1.4  1  AAA_18           AAA domain
    0.00016   21.7   0.5      0.012   15.6   0.1    3.0  3  AAA_5            AAA domain (dynein-related subfamily)
    0.00029   21.0   0.1    0.00047   20.3   0.1    1.6  1  AAA_33           AAA domain
     0.0014   18.5   0.1      0.002   18.0   0.1    1.2  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0019   18.0   0.0       0.11   12.2   0.0    2.2  2  IstB_IS21        IstB-like ATP binding protein
     0.0026   17.7   0.0       0.08   12.9   0.0    2.2  2  Rad17            Rad17 P-loop domain
     0.0033   17.3   0.0     0.0061   16.5   0.0    1.4  1  NACHT            NACHT domain
     0.0045   16.8   0.0      0.041   13.7   0.0    2.1  2  AAA_11           AAA domain
     0.0078   15.3   0.0      0.012   14.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0085   16.1   0.0       0.37   10.8   0.0    2.4  1  AAA_14           AAA domain
  ------ inclusion threshold ------
       0.01   15.6   0.1       0.18   11.5   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.012   15.2   0.4      0.028   14.0   0.4    1.7  1  AAA_25           AAA domain
      0.012   15.3   0.0      0.028   14.1   0.0    1.8  1  AAA_24           AAA domain
      0.013   15.4   0.0        0.3   11.0   0.0    2.4  2  APS_kinase       Adenylylsulphate kinase
      0.013   15.8   0.2       0.32   11.3   0.0    2.4  2  AAA_19           AAA domain
      0.018   15.4   0.0      0.043   14.2   0.0    1.6  1  RNA_helicase     RNA helicase
      0.019   14.7   0.0      0.035   13.9   0.0    1.3  1  AAA_29           P-loop containing region of AAA domain
      0.022   14.1   0.0      0.063   12.6   0.0    1.9  1  ATPase           KaiC
      0.023   14.9   0.1      0.037   14.3   0.0    1.5  1  AAA_28           AAA domain
      0.043   13.3   0.0      0.087   12.3   0.0    1.5  2  KTI12            Chromatin associated protein KTI12
      0.056   13.6   0.0        0.1   12.8   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.09   10.7   0.0        5.4    4.8   0.0    2.0  2  Herpes_Helicase  Helicase
      0.091   12.3   0.0       0.14   11.7   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.097   12.0   0.0       0.16   11.3   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
        0.1   12.6   0.0       0.17   11.9   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.11   12.1   0.1       0.31   10.6   0.0    1.7  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.9   0.1        0.3   11.6   0.0    1.7  1  ABC_tran         ABC transporter
       0.15   12.2   0.0       0.23   11.5   0.0    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
       0.19   11.6   0.0       0.36   10.7   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
       0.19   11.3   0.0        1.8    8.1   0.0    2.0  2  SRP54            SRP54-type protein, GTPase domain
       0.22   11.4   0.1         65    3.5   0.0    3.1  3  Op_neuropeptide  Opioids neuropeptide
       0.23   10.7   0.0       0.47    9.6   0.0    1.6  1  DUF2075          Uncharacterized conserved protein (DUF2075)


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 !  179.3   0.0   1.2e-55   5.4e-53       2     164 ..      20     188 ..      19     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 1.2e-55
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT......---SSEETTEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarve......akreprvgkyv 75 
                                    +++TGppG+GK+T+v++++e+l+ +g+++gGf+++evr+ggrr++Fkivd+asgeeg+La  +      + r++r+g+y 
  gi|118431192|ref|NP_147489.2|  20 LHVTGPPGSGKSTFVSRLAEALRVKGCRLGGFMAPEVRRGGRRVAFKIVDIASGEEGYLAVADeslaapGGRRARHGRYL 99 
                                    68************************************************************99****99********** PP

                                    E-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-...-SHHHHHHHT-TT-EE CS
                       NTPase_1  76 vdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrk...dlalveeirerkdvkv 152
                                    v v+++++++++a+r+a+++ad+i++DEiG+mEl ++ f+ea++e+L+s+kp+++v+hrr    d+ l++ +++   +++
  gi|118431192|ref|NP_147489.2| 100 VLVDEAWRVMSHAIRNAFEHADIIIVDEIGPMELAVPGFREALTEILDSGKPLVTVFHRRLrtlDPGLYKLLER---GCI 176
                                    ************************************************************98877777777776...8** PP

                                    EE--TTTTTTHH CS
                       NTPase_1 153 fevteenrdall 164
                                    ++++e+nr  l 
  gi|118431192|ref|NP_147489.2| 177 VWLDERNRGPLI 188
                                    ********8654 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   5.6e-09   2.5e-06       4     134 ..      22     160 ..      20     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.6e-09
                        DUF2478   4 vvyadgeavdalLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsqdl.......gsgsqgCr... 73 
                                    v + +g+   ++++++ae+lr +G+r++G+   + +++ g++ + +++d+a+ge+  +           g++++  r   
  gi|118431192|ref|NP_147489.2|  22 VTGPPGSGKSTFVSRLAEALRVKGCRLGGFMAPEVRRG-GRRVAFKIVDIASGEEGYLAVADeslaapgGRRARHGRylv 100
                                    5667778888999******************8888865.7888**********986554332001111144443332222 PP

                        DUF2478  74 LdpeaLaeaaaaveralaegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsekl 134
                                    L  ea    + a+++a  e+ad++iv   G  E +  G+re++ ++l +g P++t+ +++l
  gi|118431192|ref|NP_147489.2| 101 LVDEAWRVMSHAIRNAF-EHADIIIVDEIGPMELAVPGFREALTEILDSGKPLVTVFHRRL 160
                                    55566666666666666.899**********************************998875 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 !   24.1   0.3   3.5e-08   1.6e-05      15      61 ..       3      49 ..       1      83 [. 0.91

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.5e-08
                                   HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                           MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrva 61
                                   ++el e+ll      + + +tG PG+Gkst+v++l++ lr +G r +
  gi|118431192|ref|NP_147489.2|  3 SRELREQLLGCVKSRKSLHVTGPPGSGKSTFVSRLAEALRVKGCRLG 49
                                   7788888888888888999************************9975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   1.8e-07   8.2e-05      18      98 ..      17     129 ..       7     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.8e-07
                         AAA_30  18 drvavltGpAGtGKttalkalreaweaaggrvig.lAptgkaAkv.Laeelgieastiakllkrlk.............. 81 
                                    ++   +tGp+G+GK+t ++ l+ea++ +g r+ g +Ap+ +   + +a ++   as  + +l   +              
  gi|118431192|ref|NP_147489.2|  17 RKSLHVTGPPGSGKSTFVSRLAEALRVKGCRLGGfMAPEVRRGGRrVAFKIVDIASGEEGYLAVADeslaapggrrarhg 96 
                                    446789***********************666542455554433325533332222222222222233334432222222 PP

                         AAA_30  82 ................grarlepgtllivDEag 98 
                                                     r+++e+++++ivDE+g
  gi|118431192|ref|NP_147489.2|  97 rylvlvdeawrvmshaIRNAFEHADIIIVDEIG 129
                                    222244445555555422344455555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.3e-07   5.7e-05       4     112 ..      16     145 ..      13     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-07
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...............erpevvfvtlpsst.sskdllrellralgle 67 
                                    ++++l vtG++G+GK+t + rl+e l  ++                   +r+ +  v+++s++ +   ++ e l a g +
  gi|118431192|ref|NP_147489.2|  16 SRKSLHVTGPPGSGKSTFVSRLAEALR-VK---GcrlggfmapevrrggRRVAFKIVDIASGEeGYLAVADESLAAPGGR 91 
                                    78999********************94.33...23347898888887555555558888888866666666666666655 PP

                         AAA_22  68 lkaerlsseell.ealeqalrarav....ielliiDEaqhlrs......eealeeL 112
                                    + +  ++   l+ ea +  ++a +       ++i+DE+  + +       eal+e+
  gi|118431192|ref|NP_147489.2|  92 RAR-HGRYLVLVdEAWRVMSHAIRNafehADIIIVDEIGPM-ElavpgfREALTEI 145
                                    555.6666666633333333333337778889999999887.33344555555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.4e-07   6.4e-05       1      64 [.      23      84 ..      23     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-07
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHH.HHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekke.lqkeaaek 64
                                   +G+PGsGK+t +++l+e + ++    G  +  e++rgg    r +++ +++   +e +++ a e+
  gi|118431192|ref|NP_147489.2| 23 TGPPGSGKSTFVSRLAEALRVKGCRLGGFMAPEVRRGGR---RVAFKIVDIASGEEgYLAVADES 84
                                   7*********************************99998...55566555555433134444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   3.1e-07   0.00014      11      53 ..       9      46 ..       2     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.1e-07
                         AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrellralekdgg 53
                                   qLl +++    +r  ++ ++G++G+GKs+ v +l++al+ +g+
  gi|118431192|ref|NP_147489.2|  9 QLLGCVK----SR-KSLHVTGPPGSGKSTFVSRLAEALRVKGC 46
                                   4444444....33.799*******************9998843 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 !   20.5   0.0   1.1e-06    0.0005       3      68 ..      22     129 ..      20     135 .. 0.75
   2 ?   -1.4   0.0       6.5   2.9e+03      58      66 ..     173     181 ..     138     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                                    EESSTTSSHHHHHHHHHHHHTHE...EEEEETTTCSSS.......................................... CS
                            AAA   3 lyGppGtGKTllakavakelgve...fleisgsellsk.......................................... 37 
                                    ++GppG GK+++++ +a+ l v+   +  + ++e++                                            
  gi|118431192|ref|NP_147489.2|  22 VTGPPGSGKSTFVSRLAEALRVKgcrLGGFMAPEVR-Rggrrvafkivdiasgeegylavadeslaapggrrarhgrylv 100
                                    78*****************96553332222333333.13455555555555567788889999999999999999**999 PP

                                    STTHHHHHHHHHHHHHHHTSTSEEEEEETGG CS
                            AAA  38 yvgesekkirelfkeakekakpsilfiDEid 68 
                                    +v e+ + +++ +++a e+a   i+++DEi 
  gi|118431192|ref|NP_147489.2| 101 LVDEAWRVMSHAIRNAFEHA--DIIIVDEIG 129
                                    88888888888888888888..9******96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.5
                                    TSEEEEEET CS
                            AAA  58 kpsilfiDE 66 
                                    + +i+++DE
  gi|118431192|ref|NP_147489.2| 173 RGCIVWLDE 181
                                    349999999 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.1e-07   0.00018       3      80 ..      22     126 ..      21     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.1e-07
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf....................gvnlrdvakenglllevdpe..........aldeskrl 52 
                                    +tG+pG+GK+t+  +L++ l +                     +++ d+a+ ++ +l v +e           + ++++l
  gi|118431192|ref|NP_147489.2|  22 VTGPPGSGKSTFVSRLAEALRVkgcrlggfmapevrrggrrvAFKIVDIASGEEGYLAVADEslaapggrraRHGRYLVL 101
                                    8*****************97667778888899999999999999999999999999999999553333333333333333 PP

                         AAA_18  53 dedkldklldaleenss.....aleegknlvid 80 
                                    +++   +         s     a e+++ +++d
  gi|118431192|ref|NP_147489.2| 102 VDEAWRVM--------ShairnAFEHADIIIVD 126
                                    33332222........13333344566666666 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 !   15.6   0.1   2.8e-05     0.012       4      24 ..      22      42 ..      19      49 .. 0.86
   2 ?    2.2   0.0      0.37   1.7e+02      57      75 ..     111     129 ..      91     150 .. 0.74
   3 ?   -0.1   0.0       1.9   8.4e+02      59      78 ..     167     186 ..     154     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-05
                                   EE--SSSSHHHHHHHGGGGBS CS
                          AAA_5  4 LvGppGtgKselaerlaaaln 24
                                   + GppG+gKs+++ rla+al+
  gi|118431192|ref|NP_147489.2| 22 VTGPPGSGKSTFVSRLAEALR 42
                                   68*****************94 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                                    --------G-SEEEEESGG CS
                          AAA_5  57 splvraaregeilvlDEve 75 
                                     ++ +a+++++i+++DE+ 
  gi|118431192|ref|NP_147489.2| 111 HAIRNAFEHADIIIVDEIG 129
                                    3455677799999999996 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.9
                                    ------G-SEEEEESGGG-- CS
                          AAA_5  59 lvraaregeilvlDEverae 78 
                                    l++  ++g+i+ lDE +r +
  gi|118431192|ref|NP_147489.2| 167 LYKLLERGCIVWLDERNRGP 186
                                    566677999999*9988876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.1e-06   0.00047       4      28 ..      22      48 ..      20     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-06
                         AAA_33  4 lvGlpGsGKstlaerllkklg..avll 28
                                   + G+pGsGKst++ rl+++l   +++l
  gi|118431192|ref|NP_147489.2| 22 VTGPPGSGKSTFVSRLAEALRvkGCRL 48
                                   67****************998877777 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 !   18.0   0.1   4.4e-06     0.002       1      24 [.      22      45 ..      22      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.4e-06
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrg 24
                                   v+Gp+GsGK+tfv++l+e l+ +g
  gi|118431192|ref|NP_147489.2| 22 VTGPPGSGKSTFVSRLAEALRVKG 45
                                   89****************998776 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   0.00024      0.11      44      75 ..      14      49 ..       2      53 .. 0.78
   2 ?    3.6   0.0      0.11        48     104     123 ..     115     134 ..     100     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                      IstB_IS21 44 iekkenivllGpsGvGKs....hlaialgveavrag 75
                                   +++++++ ++Gp+G GKs     la al v+++r g
  gi|118431192|ref|NP_147489.2| 14 VKSRKSLHVTGPPGSGKStfvsRLAEALRVKGCRLG 49
                                   788999***********7322257888888888865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.11
                      IstB_IS21 104 krllkvdllilDdlgllpld 123
                                    +++ ++d++i+D++g  +l 
  gi|118431192|ref|NP_147489.2| 115 NAFEHADIIIVDEIGPMELA 134
                                    467889*********87765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00018      0.08      45      70 ..      17      42 ..       3      54 .. 0.80
   2 ?    2.5   0.0      0.27   1.2e+02     113     169 ..     100     155 ..      95     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                          Rad17 45 kriLLisGPsGCgkstvvkvLskelg 70
                                   ++ L ++GP+G gkst v  L+  l 
  gi|118431192|ref|NP_147489.2| 17 RKSLHVTGPPGSGKSTFVSRLAEALR 42
                                   45899****************98775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.27
                          Rad17 113 eLkdakylklqklGddlrtdkklilvedlPnkfyrdsdalrevirkylrssealpli 169
                                     L d  + ++++   ++  +  +i+v+++    +  +  +re + + l s+++l  +
  gi|118431192|ref|NP_147489.2| 100 VLVDEAWRVMSHAIRNAFEHADIIIVDEIGP-MELAVPGFREALTEILDSGKPLVTV 155
                                    56777788999999999999********953.4667788999999999999986544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-05    0.0061       4      30 ..      21      47 ..      18      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                          NACHT  4 ilqGeaGsGKTtLlqklalawaegklp 30
                                    ++G++GsGK+t++ +la+a++ + + 
  gi|118431192|ref|NP_147489.2| 21 HVTGPPGSGKSTFVSRLAEALRVKGCR 47
                                   689*****************9988775 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   9.1e-05     0.041       7      42 ..       7      42 ..       2      87 .. 0.81
   2 ?    0.9   0.0      0.73   3.3e+02     208     225 ..     110     127 ..     106     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-05
                         AAA_11  7 reaiksalseseitliqGPPGtgKTktivellsqll 42
                                   re +  ++++++   + GPPG+gK++++  l ++l 
  gi|118431192|ref|NP_147489.2|  7 REQLLGCVKSRKSLHVTGPPGSGKSTFVSRLAEALR 42
                                   677778889999899***************999984 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.73
                         AAA_11 208 sklleklakkfdvviIDE 225
                                    s++++++ +  d++i+DE
  gi|118431192|ref|NP_147489.2| 110 SHAIRNAFEHADIIIVDE 127
                                    67788888899******* 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   2.6e-05     0.012     116     152 ..       4      40 ..       1      48 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                          T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                     +++e l   v++r+++ v+G+ gsGK+t++  l + 
  gi|118431192|ref|NP_147489.2|   4 RELREQLLGCVKSRKSLHVTGPPGSGKSTFVSRLAEA 40 
                                    56677788889*******************9877665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00083      0.37       2      90 ..      17     149 ..      16     157 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00083
                         AAA_14   2 rkilvitGaRrvGKTtllkqlikell..............vkkesilyinldderd.........kkladpe..klleli 56 
                                    rk l +tG+  +GK+t++ +l++ l                                              +  + +e +
  gi|118431192|ref|NP_147489.2|  17 RKSLHVTGPPGSGKSTFVSRLAEALRvkgcrlggfmapevR--------------RggrrvafkiV-----DiaSGEEGY 77 
                                    677889*************9998777333333333222220..............22211111110.....011111111 PP

                         AAA_14  57 leklke.............ekktylflDEiqev...........................pewekalkslvdeg 90 
                                    l+   +             +++++++ DE+ +v                           p++++al +++d+g
  gi|118431192|ref|NP_147489.2|  78 LAV--AdeslaapggrrarHGRYLVLVDEAWRVmshairnafehadiiivdeigpmelavPGFREALTEILDSG 149
                                    111..011222233444445555566666655555555555555555555555555666666666666666666 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 ?   11.5   0.0    0.0004      0.18       2      21 ..      21      40 ..      20      90 .. 0.87
   2 ?    2.0   0.0      0.32   1.4e+02      48      74 ..     106     131 ..      92     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                   +v G pG+GKSt + +l++ 
  gi|118431192|ref|NP_147489.2| 21 HVTGPPGSGKSTFVSRLAEA 40
                                   89***********9999977 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                Viral_helicase1  48 rtvdsflmalvkstkgkililDEylll 74 
                                    ++v+s    +  + +++i+i+DE++ +
  gi|118431192|ref|NP_147489.2| 106 WRVMSHAIRNAFE-HADIIIVDEIGPM 131
                                    4444444433333.59*******9755 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   6.3e-05     0.028      28      66 ..      12      55 ..       2     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-05
                         AAA_25 28 gllpagelallaGapgtGKttlaldlalava.tGkpwlg....p 66
                                   g++   +   ++G+pg+GK+t+++ la a+  +G+ + g    +
  gi|118431192|ref|NP_147489.2| 12 GCVKSRKSLHVTGPPGSGKSTFVSRLAEALRvKGCRLGGfmapE 55
                                   555666677799**************998877888776665533 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.2e-05     0.028       3      28 ..      18      42 ..      16     166 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakelgpkplf 28
                                   +++ ++Gp+g+GK+t++++l  ++l 
  gi|118431192|ref|NP_147489.2| 18 KSLHVTGPPGSGKSTFVSRL-AEALR 42
                                   56789**************9.66664 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00067       0.3       5      42 ..      20      57 ..      16      66 .. 0.84
   2 ?    1.8   0.0      0.45     2e+02      58     108 ..     104     158 ..     102     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00067
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHT CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvR 42
                                   +++tG  gsGKst   +l+++L+ kg +       +vR
  gi|118431192|ref|NP_147489.2| 20 LHVTGPPGSGKSTFVSRLAEALRVKGCRLGGFMAPEVR 57
                                   789********************999887666666666 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.45
                                    HHHHHHHHHHHHHHHTT-EEEEE----SHHH....HHHHHHHHHCHTEEEEEEEE CS
                     APS_kinase  58 enirrvaevaklladaglivlvafisPyree....Reaarelleealkfievfvd 108
                                    e +r +++  ++  +++ i++v  i P++ +    Rea  e+l++++ +++vf +
  gi|118431192|ref|NP_147489.2| 104 EAWRVMSHAIRNAFEHADIIIVDEIGPMELAvpgfREALTEILDSGKPLVTVFHR 158
                                    5677788888888899999999999999865333377777777777888888854 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00072      0.32      10      35 ..      17      42 ..      10      57 .. 0.83
   2 ?    2.2   0.0      0.47   2.1e+02      94     112 ..     111     129 ..      78     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00072
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallv 35
                                   +k l vt++pG+GK++ +    + l 
  gi|118431192|ref|NP_147489.2| 17 RKSLHVTGPPGSGKSTFVSRLAEALR 42
                                   67789**********99988777665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.47
                         AAA_19  94 aeeekklqeeellivDEfq 112
                                    ++ ++ +++++++ivDE+ 
  gi|118431192|ref|NP_147489.2| 111 HAIRNAFEHADIIIVDEIG 129
                                    4556677667799999975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.5e-05     0.043       2      23 ..      21      42 ..      20      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.5e-05
                   RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                                    ++Gp+g GKSt++ +La+al 
  gi|118431192|ref|NP_147489.2| 21 HVTGPPGSGKSTFVSRLAEALR 42
                                   589***************9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.7e-05     0.035      24      39 ..      19      34 ..      10      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-05
                         AAA_29 24 atlltGpsGsGKSTll 39
                                   +  +tGp GsGKST++
  gi|118431192|ref|NP_147489.2| 19 SLHVTGPPGSGKSTFV 34
                                   5779**********97 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014     0.063      14      38 ..      12      36 ..       4     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         ATPase 14 gGipegrvvlitGepGtGKtifalq 38
                                   g + ++++ ++tG pG+GK++f+ +
  gi|118431192|ref|NP_147489.2| 12 GCVKSRKSLHVTGPPGSGKSTFVSR 36
                                   7778899***************876 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   8.3e-05     0.037       4      23 ..      22      45 ..      20     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.3e-05
                         AAA_28  4 itGgestGKTtlleaLaar....g 23
                                   +tG++++GK+t +++La+     g
  gi|118431192|ref|NP_147489.2| 22 VTGPPGSGKSTFVSRLAEAlrvkG 45
                                   79***************8654553 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002     0.087       6      28 ..      22      44 ..      20      69 .. 0.91
   2 ?   -3.0   0.0         9     4e+03      62      78 ..     111     127 ..     106     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                   EE--TTSSHHHHHHHHHHHHHHT CS
                          KTI12  6 ltGlPssGKstrakeLakaleee 28
                                   +tG P sGKst++++La+al+ +
  gi|118431192|ref|NP_147489.2| 22 VTGPPGSGKSTFVSRLAEALRVK 44
                                   89****************99865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9
                                    HHHHHHHTT.SEEEE-S CS
                          KTI12  62 savkrdLskekvVIvDs 78 
                                     a++ + ++ +++IvD+
  gi|118431192|ref|NP_147489.2| 111 HAIRNAFEHADIIIVDE 127
                                    56788889999999997 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 ?   12.8   0.0   0.00022       0.1       7      41 ..       3      37 ..       1      51 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHHHHT-SS-EEEEEETT--HHHHHHCC CS
                Sigma54_activ_2  7 iqelkerLeqaaqsklpvfltGekGsgkelvArlL 41
                                   + el+e+L   ++s   +++tG++Gsgk+++   L
  gi|118431192|ref|NP_147489.2|  3 SRELREQLLGCVKSRKSLHVTGPPGSGKSTFVSRL 37
                                   67999**********************98654433 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.012       5.4      61      83 ..      19      41 ..      16      46 .. 0.90
   2 ?    3.9   0.0     0.023        10     167     205 ..      93     131 ..      77     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
                Herpes_Helicase 61 aylitGtAGaGkstsiqalaenl 83
                                    + +tG  G+Gkst ++ lae+l
  gi|118431192|ref|NP_147489.2| 19 SLHVTGPPGSGKSTFVSRLAEAL 41
                                   5779****************998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                Herpes_Helicase 167 kergkaaslsaaalavlakelspeltesnviviDEaGll 205
                                     ++g++  l  +a +v+++   +++ ++++i++DE G +
  gi|118431192|ref|NP_147489.2|  93 ARHGRYLVLVDEAWRVMSHAIRNAFEHADIIIVDEIGPM 131
                                    5677888888999***********************977 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 ?   11.7   0.0   0.00031      0.14      29      58 ..      13      42 ..       3      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                          AAA_7 29 llknkkpvllvGptGtGKtviikdllkkld 58
                                   ++k++k++ ++Gp G+GK++ +++l ++l 
  gi|118431192|ref|NP_147489.2| 13 CVKSRKSLHVTGPPGSGKSTFVSRLAEALR 42
                                   7899*******************9988876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00037      0.16      22      46 ..      17      41 ..       3      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                   Mg_chelatase 22 gHnlllvGppGsGKtmlakrlpsll 46
                                   + +l ++GppGsGK+   +rl++ l
  gi|118431192|ref|NP_147489.2| 17 RKSLHVTGPPGSGKSTFVSRLAEAL 41
                                   567889**************98755 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00037      0.17      11      46 ..       7      44 ..       1      50 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                                   HHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE 11 gkklakal..gdvilLeGdLGaGKTtlvrglakalgve 46
                                    ++l   +  ++ ++ +G+ G+GK+t+v  la+al v+
  gi|118431192|ref|NP_147489.2|  7 REQLLGCVksRKSLHVTGPPGSGKSTFVSRLAEALRVK 44
                                   444444334456699*******************9886 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0007      0.31       4      22 ..      21      39 ..      18      48 .. 0.85
   2 ?   -1.7   0.0       4.1   1.9e+03     134     148 ..     112     126 ..      98     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                                   EEEESTTCCHHHHHHHHHC CS
                           cobW  4 vltGflGsGKTtLlnhlle 22
                                    +tG++GsGK+t++++l e
  gi|118431192|ref|NP_147489.2| 21 HVTGPPGSGKSTFVSRLAE 39
                                   69************99874 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.1
                                    HHHHHHHTSSEEEEE CS
                           cobW 134 kaedqlaaadllvln 148
                                     +++ ++ ad++++ 
  gi|118431192|ref|NP_147489.2| 112 AIRNAFEHADIIIVD 126
                                    445556666666654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00066       0.3       8      34 ..      14      40 ..       8      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00066
                                   EETTSEEEEEESTTSSHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  8 lkegekvaivGenGaGKStLlkllagl 34
                                   +k  + + ++G+ G+GKSt+++ la+ 
  gi|118431192|ref|NP_147489.2| 14 VKSRKSLHVTGPPGSGKSTFVSRLAEA 40
                                   677788999***********9988765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00052      0.23       4      23 ..      22      42 ..      19     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00052
                                   EEESTTSSHHHHHHHHHTS.T CS
                       MMR_HSR1  4 ivGrpNvGKStLinaltge.k 23
                                   + G p +GKSt++++l ++ +
  gi|118431192|ref|NP_147489.2| 22 VTGPPGSGKSTFVSRLAEAlR 42
                                   78**************98743 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 ?   10.7   0.0   0.00081      0.36      20      49 ..      17      46 ..       3     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00081
                       ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdk 49
                                   ++ + ++Gp gsGK++++ +++e l+ k+ 
  gi|118431192|ref|NP_147489.2| 17 RKSLHVTGPPGSGKSTFVSRLAEALRVKGC 46
                                   566789*****************9987665 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0041       1.8       5      30 ..      21      46 ..      17      60 .. 0.85
   2 ?    1.2   0.0      0.56   2.5e+02      70      97 ..     107     133 ..      99     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                                   EEEESTTSSHHHHHHHHHHHHHHTTS CS
                          SRP54  5 llvGlqGaGKTttlaKLaallkkegk 30
                                    + G+ G+GK t +++La+ l+ +g 
  gi|118431192|ref|NP_147489.2| 21 HVTGPPGSGKSTFVSRLAEALRVKGC 46
                                   578****************9988765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.56
                                    HHHHHHHHHHHHTTSSEEEEEE--SSTT CS
                          SRP54  70 avakeavekakeekidvvlvDTaGrlqn 97 
                                     v+++a+++a e ++d+++vD  G ++ 
  gi|118431192|ref|NP_147489.2| 107 RVMSHAIRNAFE-HADIIIVDEIGPMEL 133
                                    677788888877.67******9887765 PP

>> Op_neuropeptide  Opioids neuropeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.2        91       2      10 ..      49      55 ..      48      58 .. 0.85
   2 ?    3.5   0.0      0.14        65      12      20 ..     148     156 ..     147     157 .. 0.86
   3 ?    0.3   0.0       1.5   6.6e+02       9      19 ..     180     190 ..     178     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                Op_neuropeptide  2 GGFMksWdE 10
                                   GGFM +  E
  gi|118431192|ref|NP_147489.2| 49 GGFMAP--E 55
                                   9***99..5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                Op_neuropeptide  12 sqkPLiTLf 20 
                                    s kPL+T f
  gi|118431192|ref|NP_147489.2| 148 SGKPLVTVF 156
                                    78*****98 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.5
                Op_neuropeptide   9 dErsqkPLiTL 19 
                                    dEr + PLi L
  gi|118431192|ref|NP_147489.2| 180 DERNRGPLIRL 190
                                    799999**965 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0011      0.47       4      96 ..      20     127 ..      17     129 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                        DUF2075   4 vlVtGvaGtGKtvvllnllael.............eddeeertavylsvNhplvlvlrealakke..ekkkkkeafekls 68 
                                    + VtG +G+GK+   ++l+ +l             e  + +r++++ +v  +  +  + a+a ++   +  ++++  ++ 
  gi|118431192|ref|NP_147489.2|  20 LHVTGPPGSGKSTFVSRLAEALrvkgcrlggfmapEVRRGGRRVAFKIVDIASGEEGYLAVADESlaAPGGRRARHGRYL 99 
                                    569***************99997777777777776555566666666666666666666666665443333333333333 PP

                        DUF2075  69 sfinnlsefkkaeekkeepkedvvivDE 96 
                                     ++ ++ +  +++ +++ +++d++ivDE
  gi|118431192|ref|NP_147489.2| 100 VLVDEAWRVMSHAIRNAFEHADIIIVDE 127
                                    3334333345555667778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 1654.78
//
Query:       gi|118431193|ref|NP_147490.2|  [L=407]
Description: N(2),N(2)-dimethylguanosine tRNA methyltransferase [Aeropyrum pernix K1]
Scores for complete 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-80  271.4   0.0    1.6e-80  271.1   0.0    1.0  1  TRM       N2,N2-dimethylguanosine tRNA methyltransferase
     0.0066   16.0   0.0      0.011   15.3   0.0    1.3  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.039   13.5   0.0    1.3  1  MTS       Methyltransferase small domain
      0.028   14.2   0.0      0.042   13.6   0.0    1.3  1  Met_10    Met-10+ like-protein


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 !  271.1   0.0   3.6e-84   1.6e-80      19     374 ..      39     399 ..      25     401 .. 0.88

  Alignments for each domain:
  == domain 1  score: 271.1 bits;  conditional E-value: 3.6e-84
                                    -SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT CS
                            TRM  19 eVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklne 98 
                                    eVFYNP++efnRD+sv++   l  ++  l++    +da ++ G+R++R+a+E +g  +v++NDi++kA  l   N++ n 
  gi|118431193|ref|NP_147490.2|  39 EVFYNPAMEFNRDVSVVAASALRRTGL-LTRSGVAFDAHAGVGVRGVRYAVE-AGYVKVIMNDINPKASMLAALNARANG 116
                                    8****************9444433333.34555679****************.88889999******************* PP

                                    --..GGEEEE-S-HHHHHC....--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHS CS
                            TRM  99 ve..eivvineddAnvlla....ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYg 172
                                     e    + i +++ n l+     e+ +    iD+DP+Gspapf+d+a++   ++ ++++TaTD+avL G + ++ +r+Y+
  gi|118431193|ref|NP_147490.2| 117 LEpgS-YMIFNKESNSLMFhlsrERPTPVSLIDIDPYGSPAPFVDAALALSGKGTVVAMTATDLAVLEGGKARAAVRRYM 195
                                    **644.5555559999998676666677999******************99999************************** PP

                                    SB--.-STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHT.TEEEEEEETTT--EEE CS
                            TRM 173 aval.kselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvle.klglvlhCsgClseek 250
                                     +++ k+ +  E++lR+ll++var aa  +kav+pll+++ad+Y+rv+v v++ga++++ +le +lg +++   C ++++
  gi|118431193|ref|NP_147490.2| 196 LRSVsKTPVSKETGLRVLLGYVARVAAAHDKAVKPLLAYYADHYYRVYVAVERGARRSDSMLEeNLGRLVY---CPETGV 272
                                    8777256799*************************************************988626788888...666667 PP

                                    E--GGG--SB-TTT-SBEEE.EEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHH..S--SS-EEHHHH CS
                            TRM 251 vkglakfkaecehcgaklhl.aGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeEl..ldaplyydlsql 327
                                       l   +   + cg ++ + a P w+g l d++f+e +l++a +     ++ rv+klL++++ E+  +   +y +l  +
  gi|118431193|ref|NP_147490.2| 273 ALALSYAEDPASACGGSYVVaADPAWIGSLGDQAFLEAMLNIAVEAVWLGTRPRVEKLLNTLHGEAplSPRSIYVSLTSV 352
                                    77777777889999988776268**********************888888**************953334467799*** PP

                                    HHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHH CS
                            TRM 328 asvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavvev 374
                                    as+ ++++p+++kvv+ l+++g++++ tH+++++++T+ap+ +v+e+
  gi|118431193|ref|NP_147490.2| 353 ASKARVNTPKKSKVVELLRSMGYRAVATHFSGEGVRTDAPWGEVLEA 399
                                    ******************************************99886 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 !   15.3   0.0   2.4e-06     0.011      54     124 ..     328     403 ..     323     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-06
                        DUF2067  54 kellre..klkkekrglfkyslsdllreagapvppdv.LvdaLkllGykaelre..envlktnapleevvelaerl 124
                                    ++ll++   + + + +   +sl  + ++a+++ p+   +v++L+ +Gy+a      ++ ++t+ap+ ev+e + +l
  gi|118431193|ref|NP_147490.2| 328 EKLLNTlhGEAPLSPRSIYVSLTSVASKARVNTPKKSkVVELLRSMGYRAVATHfsGEGVRTDAPWGEVLEAVVKL 403
                                    55555555456666677789999*******888876549***********9998889**************99887 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.7e-06     0.039      31      85 ..      68     123 ..      52     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.7e-06
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEE CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevv 85 
                                    +sg + D  +G+Gv g+  a e   ++v + d++ +A  +a  n++an+le ++++
  gi|118431193|ref|NP_147490.2|  68 RSGVAFDAHAGVGVRGVRYAVEAGYVKVIMNDINPKASMLAALNARANGLEpGSYM 123
                                    567789999****************************************9975554 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.3e-06     0.042     102     150 ..      70     118 ..      58     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-06
                                    -EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-T CS
                         Met_10 102 evVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkve 150
                                     v  d  AG+G   +  a+ +  ++v+ +d+nP++  +   n + N +e
  gi|118431193|ref|NP_147490.2|  70 GVAFDAHAGVGVRGVRYAVEAGYVKVIMNDINPKASMLAALNARANGLE 118
                                    5778999******************************999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 3491.42
//
Query:       gi|118431194|ref|NP_147491.2|  [L=121]
Description: hypothetical protein APE_0784.1 [Aeropyrum pernix K1]
Scores for 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-06   25.9   0.6    1.1e-05   25.3   0.6    1.3  1  MarR            MarR family
    0.00049   20.2   0.0    0.00063   19.9   0.0    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0007   19.1   0.1     0.0033   16.8   0.0    1.7  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
  ------ inclusion threshold ------
       0.01   15.7   0.3      0.014   15.3   0.3    1.2  1  MarR_2          MarR family
      0.056   13.0   1.1      0.097   12.2   1.1    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.064   13.7   0.4      0.083   13.3   0.4    1.2  1  BAG             BAG domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.6   3.6e-09   1.1e-05       7      58 ..      11      62 ..       9      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.6e-09
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                   ++L+++++ +++ +seL+k lg+++   +r++ rL +kG i+R++   + R+
  gi|118431194|ref|NP_147491.2| 11 RALELIKQTEGILQSELWKLLGLDSREGSRIVLRLARKGIIRREQVVINGRK 62
                                   579*****************************************97777775 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.1e-07   0.00063      14      67 ..      17      66 ..       8      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.1e-07
                 B-block_TFIIIC 14 sRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsll 67
                                   + ++Gi+qs+L+k+++ d+r    ++  L +kg I + ++     +++ +t+ l
  gi|118431194|ref|NP_147491.2| 17 KQTEGILQSELWKLLGLDSREGSRIVLRLARKGIIRREQV----VINGRKTYRL 66
                                   5689************************************....5555555555 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 ?    1.3   0.0     0.061   1.8e+02     101     155 ..      20      73 ..      12      76 .. 0.82
   2 !   16.8   0.0   1.1e-06    0.0033     286     335 ..      69     118 ..      55     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.061
                                    SXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEESSSTXXXX CS
                  RNA_pol_Rpc34 101 eGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYllanLePse 155
                                    eGI + ++ + l+L   +  +++  L  k+ i+    v    +k Y l+  eP +
  gi|118431194|ref|NP_147491.2|  20 EGILQSELWKLLGLDSREGSRIVLRLARKGIIRRE-QVVINGRKTYRLFPAEPTD 73 
                                    79999999999999999999999999999988765.5556678999999888876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.1e-06
                                    TTTS.XXXXXXXSSSSSTTXXSSXSSSSSXXTSSSSSSSSSSTTSSSSXX CS
                  RNA_pol_Rpc34 286 krrkeakvvqpealasglveapcgecpvfdlceeggavspkncvYlkeWl 335
                                    +++++ k  +  +    ++  pc  cp +d c egg  sp++c  ++eW+
  gi|118431194|ref|NP_147491.2|  69 AEPTDRKKLNIIVDIGSILDIPCVVCPYIDECGEGGFYSPESCRLIDEWV 118
                                    555555555555666667889****************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   4.7e-06     0.014       9      54 ..      11      54 ..       5      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.7e-06
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   r+L  +   +g  + ++el + lgl+    sri+ rL ++G ++r+
  gi|118431194|ref|NP_147491.2| 11 RALELIKQTEG--ILQSELWKLLGLDSREGSRIVLRLARKGIIRRE 54
                                   88999999999..*******************************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 ?   12.2   1.1   3.2e-05     0.097       5      48 .]       9      52 ..       7      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                         HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +++ Lel+++  +i q+eL + lgl +   +r + rL ++G+I+
  gi|118431194|ref|NP_147491.2|  9 EKRALELIKQTEGILQSELWKLLGLDSREGSRIVLRLARKGIIR 52
                                   6788***************************************7 PP

>> BAG  BAG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   2.8e-05     0.083      20      69 ..       9      58 ..       1      60 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                                   HHHH..HHH..HHHHHHHHH.HHHHHTCEE.STH.HHHHHHHHHHHHHHHHHH CS
                            BAG 20 ektvkkekeylylsElLlkl.LlkLDsiei.egd.eeaRekRKeavkevqkll 69
                                   ek      e  + +E +l++ L kL + +  eg    +R +RK ++++ q ++
  gi|118431194|ref|NP_147491.2|  9 EKR---ALELIKQTEGILQSeLWKLLGLDSrEGSrIVLRLARKGIIRREQVVI 58
                                   444...333235678888888*********877799************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 948.45
//
Query:       gi|118431195|ref|NP_147492.2|  [L=630]
Description: hypothetical protein APE_0785.1 [Aeropyrum pernix K1]
Scores for 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-59  195.7  31.2    3.7e-13   49.7   2.2    7.6  7  CBS             CBS domain
      0.005   17.3   0.1         13    6.4   0.0    3.6  3  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
  ------ inclusion threshold ------
       0.33   11.3   5.1         20    5.5   0.0    4.2  6  IF3_N           Translation initiation factor IF-3, N-termina
        1.1    9.2   4.6         63    3.6   0.0    4.0  4  PELOTA_1        PELOTA RNA binding 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 !   17.6   0.1     9e-07     0.004       4      53 ..       6      58 ..       3      62 .. 0.83
   2 !   30.6   0.3   7.8e-11   3.5e-07       8      55 ..      74     123 ..      68     125 .. 0.83
   3 !   38.8   1.2   2.1e-13   9.5e-10       1      55 [.     212     267 ..     212     269 .. 0.93
   4 !   31.9   0.0   3.1e-11   1.4e-07       2      55 ..     322     375 ..     321     377 .. 0.93
   5 !   33.2   0.2   1.2e-11   5.3e-08       4      55 ..     395     446 ..     392     448 .. 0.87
   6 !   10.7   0.1   0.00012      0.55       1      48 [.     456     503 ..     456     506 .. 0.82
   7 !   49.7   2.2   8.3e-17   3.7e-13      10      56 ..     556     602 ..     545     603 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9e-07
                                   HSBSSCEEEETTSBHHHHHHHHHHHT..SSEEEEE..ETTTBEEEEEEHHHHHH CS
                            CBS  4 imtrdvvtvppdttleealelmrekg..vsrlPVV..dedgklvGivtlrDllr 53
                                   i +++ v+v+p ++l  +  +mr+++  + ++ VV  ++++k+vG++t   +++
  gi|118431195|ref|NP_147492.2|  6 IARKPRVVVYPGDPLTYVRAMMRREEepI-AVVVVesEKSEKVVGYITWNEVIQ 58
                                   6678889***************977779*.996787766779******888776 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 7.8e-11
                                    SCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTT..BEEEEEEHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmrekgvsrlPVV..dedg..klvGivtlrDllral 55 
                                    d++++  d++++++ ++m+e++v ++PV+     +  +lvG+vt  D++ral
  gi|118431195|ref|NP_147492.2|  74 DYPVAFKDDDIGDVYKRMVEEKVYAIPVLesR--DnpNLVGVVTVADIVRAL 123
                                    4568999***************77*****653..4247************98 PP

  == domain 3  score: 38.8 bits;  conditional E-value: 2.1e-13
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55 
                                    V+ im r v++++p+t++e +++ m+e++++ lPV+ +++g++vG+vt  D++ra 
  gi|118431195|ref|NP_147492.2| 212 VRRIMLRGVPVATPETPIEYVADVMAEHDYTVLPVIdEKEGRVVGVVTIFDVARAY 267
                                    789***************************999***77777************985 PP

  == domain 4  score: 31.9 bits;  conditional E-value: 3.1e-11
                                    HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    ++i +++++ ++ ++++e a + m +++ + ++VVdedg++ G+v++   l+a+
  gi|118431195|ref|NP_147492.2| 322 SEIARSELPAITVNDSIEHARRVMLRYRSNYVLVVDEDGNIKGVVSKWSMLKAI 375
                                    7899999*****************9*9988999*****************9997 PP

  == domain 5  score: 33.2 bits;  conditional E-value: 1.2e-11
                                    HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                            CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55 
                                    +m +++  ++pd+++ee++ +m++++ s + +V  +dgk++G +t+ Dl++a 
  gi|118431195|ref|NP_147492.2| 395 VMDTNIERIKPDASIEEVALKMASSR-SEVVIVeGDDGKPIGFITKDDLVEAY 446
                                    599*******************8766.78855798899***********9985 PP

  == domain 6  score: 10.7 bits;  conditional E-value: 0.00012
                                    HHHHSBS.SCEEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEH CS
                            CBS   1 Vgdimtr.dvvtvppdttleealelmrekg..vsrlPVVdedgklvGivtl 48 
                                    V+ imt+ ++  v+p  +l  a+++m  ++  +++l V d+ + ++G+v+ 
  gi|118431195|ref|NP_147492.2| 456 VENIMTPgRIGIVHPHHSLYHAVNKM--HNfyLDALTVYDGRE-VIGVVSA 503
                                    567888855559**************..9*8778999997555.*****96 PP

  == domain 7  score: 49.7 bits;  conditional E-value: 8.3e-17
                                    EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    v+v+pd+++ +a+elm++++v+++PVVd+dg+++G+vt++D++r l+
  gi|118431195|ref|NP_147492.2| 556 VYVSPDDDVVKAIELMEKYNVDGIPVVDKDGRVLGVVTKTDVVRELA 602
                                    79******************************************986 PP

>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.042   1.9e+02      24      48 ..     106     129 ..      89     136 .. 0.83
   2 ?    3.6   0.0     0.021        93       4      43 ..     410     448 ..     407     466 .. 0.77
   3 !    6.4   0.0    0.0029        13      22      51 ..     582     611 ..     564     612 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.042
                                    TT-BBSS---HHHHHHHHHHHT--- CS
                 Ribosomal_L9_C  24 edgklFGsVtakdIaealkkklgie 48 
                                    ++ +l G Vt +dI+ al+ + g++
  gi|118431195|ref|NP_147492.2| 106 DNPNLVGVVTVADIVRALRRA-GFK 129
                                    567788************998.875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                                    HHHHHHHSS..-EEEE--B-TT-BBSS---HHHHHHHHHH CS
                 Ribosomal_L9_C   4 ealaekLeakvkvtikakagedgklFGsVtakdIaealkk 43 
                                    e++a k++ + + ++    g+dgk  G +t+ d++ea k 
  gi|118431195|ref|NP_147492.2| 410 EEVALKMA-SSRSEVVIVEGDDGKPIGFITKDDLVEAYKR 448
                                    56666776.34445566669****************9986 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0029
                                    B-TT-BBSS---HHHHHHHHHHHT-----G CS
                 Ribosomal_L9_C  22 agedgklFGsVtakdIaealkkklgieidk 51 
                                    + +dg++ G Vt+ d++ +l+    i i++
  gi|118431195|ref|NP_147492.2| 582 VDKDGRVLGVVTKTDVVRELARTARIRIER 611
                                    5689*****************998998876 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 ?   -3.4   0.0       2.8   1.2e+04      27      45 ..      24      42 ..       7      59 .. 0.52
   2 ?   -3.7   0.0       3.4   1.5e+04      20      35 ..     111     126 ..     102     128 .. 0.74
   3 ?   -3.7   0.0       3.4   1.5e+04      12      28 ..     246     263 ..     245     266 .. 0.75
   4 ?    5.5   0.0    0.0045        20       6      31 ..     349     374 ..     334     379 .. 0.82
   5 ?   -0.1   0.0      0.26   1.2e+03       9      31 ..     422     445 ..     418     450 .. 0.77
   6 ?    4.6   0.1    0.0089        40       8      30 ..     577     599 ..     572     609 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.8
                                   HHHHHHHHHTSEEEEEESS CS
                          IF3_N 27 eAlrlaeekgldLVevspn 45
                                    A+ + ee+ +  V v+ +
  gi|118431195|ref|NP_147492.2| 24 RAMMRREEEPIAVVVVESE 42
                                   4555555555555544433 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.4
                                    EEEEEHHHHHHHHHHH CS
                          IF3_N  20 lGvistreAlrlaeek 35 
                                    +Gv+++++++r  +++
  gi|118431195|ref|NP_147492.2| 111 VGVVTVADIVRALRRA 126
                                    6899999988877765 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.4
                                    EE-SS.S-EEEEEEHHHH CS
                          IF3_N  12 lvded.GeqlGvistreA 28 
                                    ++de+ G  +Gv+++ ++
  gi|118431195|ref|NP_147492.2| 246 VIDEKeGRVVGVVTIFDV 263
                                    688777888899887665 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0045
                                    -SSEEEEE-SSS-EEEEEEHHHHHHH CS
                          IF3_N   6 rarevrlvdedGeqlGvistreAlrl 31 
                                    r + v +vdedG+  Gv+s++  l+ 
  gi|118431195|ref|NP_147492.2| 349 RSNYVLVVDEDGNIKGVVSKWSMLKA 374
                                    567799*******99*****999876 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.26
                                    EEEEE-SS.S-EEEEEEHHHHHHH CS
                          IF3_N   9 evrlvded.GeqlGvistreAlrl 31 
                                    ev +v+ d G+ +G i++++ ++ 
  gi|118431195|ref|NP_147492.2| 422 EVVIVEGDdGKPIGFITKDDLVEA 445
                                    677777555********9997765 PP

  == domain 6  score: 4.6 bits;  conditional E-value: 0.0089
                                    SEEEEE-SSS-EEEEEEHHHHHH CS
                          IF3_N   8 revrlvdedGeqlGvistreAlr 30 
                                    + + +vd+dG  lGv+++ +++r
  gi|118431195|ref|NP_147492.2| 577 DGIPVVDKDGRVLGVVTKTDVVR 599
                                    5688**********888777665 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.14   6.5e+02      31      52 ..      24      45 ..      21      64 .. 0.64
   2 ?    3.5   0.1     0.014        64      34      49 ..     164     179 ..     161     184 .. 0.88
   3 ?   -3.2   0.3       1.8     8e+03      26      38 ..     209     221 ..     208     223 .. 0.80
   4 ?    3.6   0.0     0.014        63      25      47 ..     337     359 ..     331     369 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.14
                       PELOTA_1 31 RvlLRRvPekvlvrdeeepdla 52
                                   R+++RR  e + v   e+++ +
  gi|118431195|ref|NP_147492.2| 24 RAMMRREEEPIAVVVVESEKSE 45
                                   99****8666555444333333 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                       PELOTA_1  34 LRRvPekvlvrdeeep 49 
                                     RR+P k++vr++eep
  gi|118431195|ref|NP_147492.2| 164 YRRMPGKIVVRSREEP 179
                                    6**********99876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.8
                       PELOTA_1  26 igEaTRvlLRRvP 38 
                                    ++   R++LR vP
  gi|118431195|ref|NP_147492.2| 209 VAKVRRIMLRGVP 221
                                    677789****999 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.014
                       PELOTA_1  25 gigEaTRvlLRRvPekvlvrdee 47 
                                    +i  a Rv+LR   + vlv de+
  gi|118431195|ref|NP_147492.2| 337 SIEHARRVMLRYRSNYVLVVDED 359
                                    678899***********998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 4725.73
//
Query:       gi|118431196|ref|NP_147493.2|  [L=133]
Description: small nucleolar RNP protein Gar1p [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-06   28.1   0.0    1.8e-06   27.8   0.0    1.1  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0     1e-10   1.8e-06      21      97 ..      25     100 ..      14     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1e-10
                                    EEEEEEEEEETT.EEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTSEE CS
                           Gar1  21 leiGtvssiven.evviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgdkv 97 
                                    +++G+++ iv++  vv++ +++ + + +     + l+   ++G V +++Gp+n+p+ +V++   e+   ++++ g ++
  gi|118431196|ref|NP_147493.2|  25 VPLGFIKAIVKTgHVVVEPSEKVRRNPPRGRFQVLLAGDGEVGYVSDVIGPINSPFIVVRVR--ERGVIEKLSPGAEL 100
                                    799*******98789999998888888999999999**************************..44444467777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       191  (0.0106531); expected 358.6 (0.02)
Passed bias filter:                      145  (0.00808746); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 947.46
//
Query:       gi|118431197|ref|NP_147494.2|  [L=303]
Description: transcription initiation factor IIB [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-12   47.4   2.0    4.6e-09   36.2   0.2    2.5  2  TFIIB           Transcription factor TFIIB repeat
    0.00057   20.0   0.4     0.0048   17.0   0.1    2.3  2  Cyclin_C        Cyclin, C-terminal domain
      0.002   18.1   0.1       0.05   13.6   0.0    2.6  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0033   17.0   0.6       0.26   11.0   0.1    3.2  3  GntR            Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.016   14.8   0.4       0.28   10.9   0.0    2.8  2  Sigma70_r4_2    Sigma-70, region 4
      0.018   15.0   0.1      0.041   13.8   0.1    1.6  1  HTH_15          Helix-turn-helix domain of alkylmercury lyase
      0.044   13.8   0.7        5.1    7.2   0.1    2.8  2  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.069   13.5   1.8        1.8    9.0   0.2    2.4  2  Rrf2            Transcriptional regulator
       0.15   12.1   0.8       0.79    9.8   0.1    2.2  2  TFIIB_C_1       Transcription factor IIB C-terminal module 1


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 !   10.5   0.1   0.00024      0.47       2      71 .]     101     170 ..     100     170 .. 0.91
   2 !   36.2   0.2   2.3e-12   4.6e-09       1      71 []     210     286 ..     210     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                                    HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    k++++ l++p  V + A  +++  l+       + + ++AA++  A    +   +  ei++ + V+++++
  gi|118431197|ref|NP_147494.2| 101 KEMVEILKIPTSVHETAALILRSYLDSVSRRPGRVEQYVAASIAKAVEIHGIPISSGEIAKAAGVEVESV 170
                                    7899*********************99877766788899**************************99875 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 2.3e-12
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTS......TTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklalee......kvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    i+r++ +l+L  +V++ A e +k +l+       k+  G+++a++aAA++y+A+r+ +   +qk i+s+l+ +e  i
  gi|118431197|ref|NP_147494.2| 210 INRLVTNLGLDPEVKRIALEFVKVSLKAgsgasiKTFHGKKSAALAAAAVYLAARLLNYDVSQKKIASILELKESNI 286
                                    899*******************998765333333799*********************************9998765 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.3     6e+02      49     106 ..     140     200 ..     136     211 .. 0.62
   2 !   17.0   0.1   2.4e-06    0.0048      39      89 ..     246     296 ..     206     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.3
                                    HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH...HHHHGSS--HHCCCCT CS
                       Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcvelilell...ssapssklqavrrkys 106
                                    aa+++ a  + + p  + ++ +  g+++e +++ + ++ +     s  ++s  +a +r ys
  gi|118431197|ref|NP_147494.2| 140 AASIAKAVEIHGIPISSGEIAKAAGVEVESVQKAILQMSQTDvvkSLVRKSIAKARFRGYS 200
                                    5666666666677777777778888888888888877777664432233333355555555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.4e-06
                                    HCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                       Cyclin_C  39 flsyppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                    f + +   +Aaaa++la + ln+   ++++ ++++++++++++ ++ + ++
  gi|118431197|ref|NP_147494.2| 246 FHGKKSAALAAAAVYLAARLLNYDVSQKKIASILELKESNIRKHYRFLIDN 296
                                    555677789**********************************99988765 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 !   13.6   0.0   2.5e-05      0.05      19      53 ..     151     186 ..     117     193 .. 0.78
   2 ?    1.4   0.0      0.16   3.2e+02      17      34 ..     265     282 ..     252     295 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                                    EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                      HTH_Crp_2  19 elpltqeelAsmlGltretvsrilseLkreglis.r 53 
                                     +p++  e+A   G+  e+v +++ ++++  +++  
  gi|118431197|ref|NP_147494.2| 151 GIPISSGEIAKAAGVEVESVQKAILQMSQTDVVKsL 186
                                    38***************************9999853 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                                    EEEEEHHHHHHHHHTTSS CS
                      HTH_Crp_2  17 eielpltqeelAsmlGlt 34 
                                     ++ +++q+ +As+l l 
  gi|118431197|ref|NP_147494.2| 265 LLNYDVSQKKIASILELK 282
                                    467899*******99876 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.072   1.4e+02      19      39 ..      20      39 ..      18      40 .. 0.90
   2 ?   -0.9   0.0      0.65   1.3e+03      34      46 ..      65      77 ..      62      79 .. 0.81
   3 !   11.0   0.1   0.00013      0.26       4      61 ..     134     190 ..     132     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.072
                                   -TTSB---HHHHHHHHTS-HH CS
                           GntR 19 rpGdkLPsereLaaefgVsrt 39
                                     G+ L +e++ a+ ++Vsr+
  gi|118431197|ref|NP_147494.2| 20 DTGEVL-RESSFAEYIAVSRH 39
                                   679***.************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.65
                                   HTS-HHHHHHHHH CS
                           GntR 34 fgVsrttvReALr 46
                                   f   r+++R++Lr
  gi|118431197|ref|NP_147494.2| 65 FSSARNPLRRSLR 77
                                   66679******98 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                           GntR   4 qvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61 
                                    +v++++ + I + +  +G ++ s  e+a++ gV   +v++A+ + ++ ++v +  +++
  gi|118431197|ref|NP_147494.2| 134 RVEQYVAASIAKAVEIHGIPI-SSGEIAKAAGVEVESVQKAILQMSQTDVVKSLVRKS 190
                                    688888888888888899999.99***************************9988876 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 ?    0.8   0.1      0.21   4.1e+02      28      47 ..     155     174 ..     154     176 .. 0.87
   2 ?   10.9   0.0   0.00014      0.28      26      48 ..     269     291 ..     259     292 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                                    -HHHHHHHHT--HHHHHHHH CS
                   Sigma70_r4_2  28 sykEIAellgisegtVksrl 47 
                                    s  EIA+  g+ + +V++++
  gi|118431197|ref|NP_147494.2| 155 SSGEIAKAAGVEVESVQKAI 174
                                    567*************9987 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00014
                                    ---HHHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2  26 glsykEIAellgisegtVksrls 48 
                                    + s+k IA++l+++e++++++++
  gi|118431197|ref|NP_147494.2| 269 DVSQKKIASILELKESNIRKHYR 291
                                    679******************95 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 ?   13.8   0.1   2.1e-05     0.041      31      63 ..     149     181 ..     129     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                         HTH_15  31 akGepVtveeLAaatgrsveevrqaLaalpstE 63 
                                    ++G p++  e+A+a+g  ve v++a+ +++ t 
  gi|118431197|ref|NP_147494.2| 149 IHGIPISSGEIAKAAGVEVESVQKAILQMSQTD 181
                                    69****************************985 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0026       5.1      28      46 ..     154     172 ..     138     172 .. 0.88
   2 ?    4.1   0.1     0.024        47      28      46 ..     270     288 ..     267     288 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0026
                                    E-HHHHHHHCTS-HHHHHH CS
                 Put_DNA-bind_N  28 iSSteLaealgvtaaqvRK 46 
                                    iSS e+a+a+gv+   v K
  gi|118431197|ref|NP_147494.2| 154 ISSGEIAKAAGVEVESVQK 172
                                    9***********9888766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.024
                                    E-HHHHHHHCTS-HHHHHH CS
                 Put_DNA-bind_N  28 iSSteLaealgvtaaqvRK 46 
                                    +S +++a  l+++++ +RK
  gi|118431197|ref|NP_147494.2| 270 VSQKKIASILELKESNIRK 288
                                    67899*************9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2   0.00088       1.8      23      57 ..     151     185 ..     134     187 .. 0.88
   2 ?    3.4   0.1     0.051     1e+02      13      49 ..     257     293 ..     248     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00088
                                    CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           Rrf2  23 eepvsseeiaerqnispsylekilakLrkaglvks 57 
                                    + p+ss eia+  +++ + ++k + ++++ ++vks
  gi|118431197|ref|NP_147494.2| 151 GIPISSGEIAKAAGVEVESVQKAILQMSQTDVVKS 185
                                    5679*****************************98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.051
                                    HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHH CS
                           Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakL 49 
                                    a +yLa++  +  vs ++ia+  ++++s ++k  + L
  gi|118431197|ref|NP_147494.2| 257 AAVYLAARLLNYDVSQKKIASILELKESNIRKHYRFL 293
                                    5689999999999******************998776 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0004      0.79       6      75 ..      97     163 ..      93     184 .. 0.83
   2 ?    0.2   0.0      0.39   7.7e+02      45      61 ..     249     265 ..     202     284 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0004
                      TFIIB_C_1   6 rnalevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLaelrvld 75 
                                    +++l+ +++  + + +v+e a  +++ +  +   r  rve+    +aa++  a e ++ P+   e+ + +
  gi|118431197|ref|NP_147494.2|  97 LQKLKEMVEILKIPTSVHETAALILRSYLDSVSRRPGRVEQ---YVAASIAKAVEIHGIPISSGEIAKAA 163
                                    6789999999999*************************997...58999*9*******999999986544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                      TFIIB_C_1  45 ekqeevaaaclmlaaer 61 
                                     k    aaa++ laa  
  gi|118431197|ref|NP_147494.2| 249 KKSAALAAAAVYLAARL 265
                                    34455678888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2429.92
//
Query:       gi|118431198|ref|NP_147495.2|  [L=197]
Description: hypothetical protein APE_0788.1 [Aeropyrum pernix K1]
Scores for 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-41  139.6   0.2    9.4e-41  139.3   0.2    1.1  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.3   0.2   5.2e-45   9.4e-41       1     162 [.       8     168 ..       8     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 5.2e-45
                                    S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET......T CS
                     NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek..l 78 
                                    g++Np+K +Av +af+++++ v+v+ vsv+sgv +qP g ++++ GA+ Ra +a e+a+   +gvG+E+G  e+  +  +
  gi|118431198|ref|NP_147495.2|   8 GTSNPIKYRAVLRAFSRYYD-VRVVMVSVDSGVGPQPSGVADVVGGALARAVRAVEKAD-SYFGVGVEAGPIEFPASggY 85 
                                    89****************98.9***********************************77.88*********99988888* PP

                                    EEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHHHHHHH CS
                     NTPase_I-T  79 ldvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlyeqavilA 158
                                    +++++aa+vd++ r ++g+s+sfe+ ++v+ ++++g+e+++++  + ++ +++++ G++g+ T+g+vtR+dl+e+avi+A
  gi|118431198|ref|NP_147495.2|  86 VETQVAAIVDRDCRATIGMSPSFEVDRRVLALMLDGVEMEKAVG-VERHGGLGESVGFVGVATSGAVTRQDLTEHAVIMA 164
                                    ******************************************98.699999***************************** PP

                                    THHH CS
                     NTPase_I-T 159 lipf 162
                                    lip+
  gi|118431198|ref|NP_147495.2| 165 LIPR 168
                                    **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1616.13
//
Query:       gi|14600970|ref|NP_147496.1|  [L=136]
Description: 30S ribosomal protein S8 [Aeropyrum pernix K1]
Scores for 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-31  107.7   0.8    5.9e-31  107.5   0.8    1.1  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 !  107.5   0.8   3.3e-35   5.9e-31       5     137 .]       4     129 ..       1     129 [. 0.95

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 3.3e-35
                                   XXCCCSEESSTEEXXXSSX.XXCCSBXXXXXXXEES...SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEE CS
                 Ribosomal_S8e   5 rdskhkrkltGgkakllrk.krkielgrkekatklg...aervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgV 81 
                                    + ++k+k +Ggk++ + k krk+  gr+++ t l+   +e  k vr+rgG +k +a ++  a v++p+++ ++k++Il++
  gi|14600970|ref|NP_147496.1|   4 YQWRDKKKPSGGKRRYYYKvKRKYAAGRPPTYTTLSaaeEEERKPVRARGGSYKIKAKKVAFAVVSNPKTGEARKARILRI 84 
                                   577999*******9999988***************545699**************************************** PP

                                   ECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                 Ribosomal_S8e  82 kknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                   +++p+++ey+r+g+++Kga+i + +++           A+vtsrPgq+G+vnavlL
  gi|14600970|ref|NP_147496.1|  85 VETPAHREYARRGIIVKGAVIDTTLGR-----------AVVTSRPGQEGVVNAVLL 129
                                   ***************************...........*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1212.24
//
Query:       gi|14600971|ref|NP_147497.1|  [L=297]
Description: hypothetical protein APE_0790 [Aeropyrum pernix K1]
Scores for complete 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-06   27.5  12.3    8.3e-05   22.8   0.5    4.0  3  DUF948           Bacterial protein of unknown function (DUF94
    7.4e-05   23.3   0.9    7.4e-05   23.3   0.9    3.0  3  T3SSipB          Type III cell invasion protein SipB
    0.00083   18.8  22.2    0.00083   18.8  22.2    3.6  3  GAS              Growth-arrest specific micro-tubule binding
    0.00093   19.3  51.5        0.1   12.7  20.7    3.7  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0015   17.5  53.2     0.0037   16.2  21.7    3.0  3  Spc7             Spc7 kinetochore protein
     0.0022   18.1   5.4     0.0022   18.1   5.4    6.2  5  JIP_LZII         JNK-interacting protein  leucine zipper II
     0.0025   17.5  59.6      0.074   12.8  17.6    3.9  2  DUF4201          Domain of unknown function (DUF4201)
      0.003   17.8  12.0      0.003   17.8  12.0    3.7  3  FliJ             Flagellar FliJ protein
     0.0032   18.2   4.0     0.0032   18.2   4.0    3.6  4  DUF2203          Uncharacterized conserved protein (DUF2203)
     0.0033   15.7  52.9     0.0053   15.0  40.9    2.1  2  HOOK             HOOK protein
     0.0035   17.7  12.3         13    6.3   0.1    5.4  5  LPP              Lipoprotein leucine-zipper
     0.0048   16.8   0.8     0.0048   16.8   0.8    4.0  3  Dynactin_p22     Dynactin subunit p22
     0.0048   16.7  17.3      0.065   13.1   3.0    3.1  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.007   15.7   2.9      0.007   15.7   2.9    3.2  3  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0074   13.9  40.1     0.0098   13.5  40.1    1.0  1  DUF3584          Protein of unknown function (DUF3584)
     0.0079   16.4  54.4       0.32   11.2  19.4    5.0  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.009   16.4  14.6      0.009   16.4  14.6    3.9  3  CENP-H           Centromere protein H (CENP-H)
     0.0098   16.1   5.8     0.0098   16.1   5.8    3.7  3  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
  ------ inclusion threshold ------
       0.01   15.8   3.7       0.01   15.8   3.7    6.3  4  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.012   16.1   6.4       0.42   11.1   2.6    3.6  1  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.012   16.1  11.2      0.012   16.1  11.2    5.7  5  ZapB             Cell division protein ZapB
      0.012   15.6   9.0      0.023   14.7   2.5    3.2  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.013   15.7   4.7      0.013   15.7   4.7    5.7  5  XhlA             Haemolysin XhlA
      0.017   15.7   5.2      0.017   15.7   5.2    5.0  5  YabA             Initiation control protein YabA
      0.018   15.3  52.7       0.11   12.8  19.2    4.2  2  ATG16            Autophagy protein 16 (ATG16)
      0.018   15.1  35.9      0.027   14.5   5.7    3.9  4  Laminin_II       Laminin Domain II
      0.019   13.2  44.0      0.018   13.2  21.1    3.0  3  EzrA             Septation ring formation regulator, EzrA
       0.02   15.1   4.8       0.02   15.1   4.8    6.0  3  ABC_tran_CTD     ABC transporter C-terminal domain
      0.028   14.9   4.8      0.028   14.9   4.8    4.4  2  DUF16            Protein of unknown function DUF16
      0.028   13.8  27.6       0.07   12.5   9.2    2.4  2  DUF4407          Domain of unknown function (DUF4407)
      0.032   13.3  48.5      0.055   12.5  18.0    2.3  2  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.04   14.3   2.7          3    8.3   0.1    3.7  4  MtrB             Tetrahydromethanopterin S-methyltransferase 
      0.042   13.2  38.1      0.039   13.2  11.1    3.1  3  DUF3450          Protein of unknown function (DUF3450)
       0.06   11.3  24.8      0.082   10.8  24.8    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
      0.069   11.8  36.9       0.16   10.6  25.4    2.2  2  AAA_13           AAA domain
       0.07   13.0  21.7      0.091   12.6   4.3    3.8  3  Sec34            Sec34-like family
      0.074   13.4  13.6       0.36   11.2   2.2    3.1  3  DUF2935          Domain of unknown function (DUF2935)
      0.081   12.6  42.3      0.022   14.4  18.7    2.6  2  Syntaxin         Syntaxin
      0.089   12.6  13.1      0.022   14.6   4.1    2.6  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.14   11.6  37.3      0.045   13.3  13.4    3.3  3  MscS_porin       Mechanosensitive ion channel porin domain
       0.32   11.0  65.4      0.082   12.9  22.7    3.3  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.34   11.4  35.9       0.71   10.4  10.7    3.7  3  Spectrin         Spectrin repeat
       0.41   11.3  24.9        2.9    8.6   9.8    3.3  2  AATF-Che1        Apoptosis antagonizing transcription factor
       0.42   10.4  59.1       0.13   12.1  29.7    2.9  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.47   10.6  49.8          1    9.5  15.8    4.0  3  BRE1             BRE1 E3 ubiquitin ligase
       0.49   10.0  47.4       0.18   11.4  16.6    2.7  2  YkyA             Putative cell-wall binding lipoprotein
        0.6    9.2  49.6       0.15   11.2  16.8    2.7  2  HAP1_N           HAP1 N-terminal conserved region
       0.62    8.2  24.1       0.16   10.2   2.7    3.1  3  COG6             Conserved oligomeric complex COG6
       0.69    8.4  16.9       0.51    8.8   5.8    2.1  2  FUSC             Fusaric acid resistance protein family
        0.7    8.4  49.8       0.39    9.3  16.5    3.1  3  FapA             Flagellar Assembly Protein A
       0.76   10.0   3.4         14    6.0   0.2    3.0  3  PI_PP_I          Phosphoinositide phosphatase insertion domai
       0.88   10.0  38.5       0.58   10.6   4.4    6.5  5  FlaC_arch        Flagella accessory protein C (FlaC)
       0.92    9.6  42.8        1.3    9.1  14.2    3.3  3  ADIP             Afadin- and alpha -actinin-Binding
        1.1    8.5  31.4      0.098   11.9   6.0    2.9  3  TMPIT            TMPIT-like protein
        1.2    8.5  20.3      0.012   15.2   9.0    2.5  2  DUF3829          Protein of unknown function (DUF3829)
        1.2    8.7  12.9        3.6    7.2   0.7    3.6  4  DUF4988          Domain of unknown function
        1.3    9.7  33.5        0.1   13.2   1.0    5.7  3  SlyX             SlyX
        1.5    8.2  45.1        2.3    7.6   9.5    3.3  2  DUF4618          Domain of unknown function (DUF4618)
        1.8    9.0  50.0       0.37   11.2  12.4    3.1  3  Fez1             Fez1
        2.1    7.3  36.6      0.087   11.9  14.2    3.0  1  TelA             Toxic anion resistance protein (TelA)
        2.2    8.4  43.9      1e+02    3.0  20.4    4.3  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
        2.4    8.2  28.8       0.19   11.8   8.2    3.9  4  DUF1664          Protein of unknown function (DUF1664)
        2.4    8.3  34.2        1.8    8.7  12.7    3.7  3  Fib_alpha        Fibrinogen alpha/beta chain family
        2.7    7.8  63.3       0.28   11.0  24.7    3.0  2  ERM              Ezrin/radixin/moesin family
        3.1    6.7  38.6       0.15   11.0  17.7    2.3  2  IFT57            Intra-flagellar transport protein 57
        3.6    8.1  68.0        1.5    9.3  26.8    4.8  4  APG6_N           Apg6 coiled-coil region
        3.8    6.5  30.8       0.18   10.9   4.6    3.2  3  APG17            Autophagy protein Apg17
        4.3    7.2  33.1       0.02   14.8   5.3    3.4  1  STAT_alpha       STAT protein, all-alpha domain
        4.6    7.1  35.5       0.95    9.3   4.7    4.6  3  SKA2             Spindle and kinetochore-associated protein 2
        4.8    7.0  51.6        1.9    8.3   8.3    6.4  4  DivIC            Septum formation initiator
        5.2    6.6  40.0       0.17   11.4  12.1    3.1  4  HAUS-augmin3     HAUS augmin-like complex subunit 3
          6    7.1  12.1       0.86    9.8   0.9    4.3  4  MbeD_MobD        MbeD/MobD like
        6.2    5.6  29.0      0.017   14.1   3.7    2.8  3  5_nucleotid      5' nucleotidase family
        6.4    7.1  42.6       0.59   10.4   8.9    4.8  4  DUF5082          Domain of unknown function (DUF5082)
          7    4.9  54.0        1.3    7.3  42.7    2.0  2  MAD              Mitotic checkpoint protein
          7    7.0   7.9       0.79   10.1   1.0    2.7  2  PRANC            PRANC domain
        7.1    6.1  35.4       0.39   10.3  10.4    3.1  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
        8.3    6.4  23.1         12    5.9   8.4    3.1  2  GldM_N           GldM N-terminal domain
        8.7    7.0  21.7       0.16   12.6   4.1    3.7  3  DUF4665          Domain of unknown function (DUF4665)


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4     0.018       4.1      25      61 ..      10      46 ..       3      54 .. 0.81
   2 ?    3.2   0.2      0.47   1.1e+02      29      70 ..      56      97 ..      48     115 .. 0.82
   3 !   22.8   0.5   3.7e-07   8.3e-05      16      83 ..     176     243 ..     170     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.018
                        DUF948 25 kktldeaaatieelekqvdpilkevedllakvnelle 61
                                  kk  +e+ +tieel++++  + +e ++l+++v++l e
  gi|14600971|ref|NP_147497.1| 10 KKEEEELLKTIEELKEEIVRLKEERRKLINEVKALRE 46
                                  5666788999999999999999999999999998655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.47
                        DUF948 29 deaaatieelekqvdpilkevedllakvnelledvneklekv 70
                                  +e  + +++l+++ ++il+e+++l ++ +++ +++  k +++
  gi|14600971|ref|NP_147497.1| 56 REYVEKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQL 97
                                  56667899999*************999999888887776665 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 3.7e-07
                        DUF948  16 flivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                    l++ l+ l++ +de++++  ++++++  ++ ++e+  + +++l e++++++ ++d+l +++ +l ++
  gi|14600971|ref|NP_147497.1| 176 ALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAK 243
                                   688999****************************************************9999988665 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 ?    3.0   1.5      0.56   1.3e+02      40     112 ..      12      81 ..       5     100 .. 0.75
   2 ?    6.3   0.6     0.056        13      16      93 ..     112     191 ..     110     191 .. 0.78
   3 !   23.3   0.9   3.3e-07   7.4e-05      20      93 ..     181     254 ..     178     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.56
                                   TT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH. CS
                       T3SSipB  40 aasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQaga 112
                                   + ++l + ++++ +e   ++++  + i++++ +  +  +a +   e  ++l +L     e++k+  +  Q+++
  gi|14600971|ref|NP_147497.1|  12 EEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSL---REERKKILDELAQLKE 81 
                                   556777788888888888999999999999999999999999999999999999...5566666666666654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.056
                                   HHHCHHHHHHHHHHHHHHHHHTT...TTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                       T3SSipB  16 gnkSLsqLenrlaawkamskaqq...eaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                   ++ SL+ L+ rl+  + m+  ++   e+ ++l +e+ ++ +  + + ++ e+a   + +++++++a+  k+++  +r++eL
  gi|14600971|ref|NP_147497.1| 112 AKISLKRLQRRLQELEMMQMTRVlrpEEEKRLVEEISRLEELIERVRKAKEQAL-STMELQAEVKALVIKLKDLNQRIDEL 191
                                   567999999999999998888753337788999999987766666666655555.56679999999999999999999998 PP

  == domain 3  score: 23.3 bits;  conditional E-value: 3.3e-07
                                   HHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                       T3SSipB  20 LsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                   L++L++r++  +++  + +e++  lS ++++  +  k++ +++e+   ++d++ +++d++ +k  e+ +rlk++
  gi|14600971|ref|NP_147497.1| 181 LKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDI 254
                                   899********************************************************************998 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 ?    4.9  22.5     0.064        14      35     111 ..       6      86 ..       4      99 .. 0.67
   2 ?    0.2   9.9       1.7   3.9e+02      33      99 ..      60     128 ..      56     143 .. 0.82
   3 !   18.8  22.2   3.7e-06   0.00083      26     136 ..     145     251 ..     140     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.064
                           GAS  35 ieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdk....qslknlkarlkelekelkdlkwehevl 111
                                   i+e kk+ee+  k ++e+++e  rlke+ +k+ +ev+ Lr++ ++ +++k    ++l++l+++ k+  +el +lk+e +  
  gi|14600971|ref|NP_147497.1|   6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKreyvEKLRSLREERKKILDELAQLKEERKKT 86 
                                   788888888888888888888888888888888888888888777777772222345566666666666666666555433 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                           GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlkny..ekdkqslknlkarlkelek 99 
                                   e++  l+++ ++   el+++++e k+ +++L   + ++  Lr  l++   +  k slk+l++rl+ele+
  gi|14600971|ref|NP_147497.1|  60 EKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQLRVLRGLLEKEggRLAKISLKRLQRRLQELEM 128
                                   566778888888888999999999999999999999999999988876224579999999999999986 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 3.7e-06
                           GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                   e I +l e ie+ +k +e++   + e+++e k l+ +Lk +++ ++eLr+q+      k++l+ l ++++e ++ +k+l++
  gi|14600971|ref|NP_147497.1| 145 EEISRLEELIERVRKAKEQALSTM-ELQAEVKALVIKLKDLNQRIDELRQQAGS---VKEELATLSSKIEEYNERIKKLSE 221
                                   679999999999999999998887.79**********************99765...5679******************** PP

                           GAS 107 ehevleqrfekvekerdelykkfeaaiqev 136
                                   e e  + r+++++ke+d+ly+k+++++  +
  gi|14600971|ref|NP_147497.1| 222 EIEKRSTRIDELSKEIDNLYAKYREVMTRL 251
                                   ***********************9986554 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 !   12.7  20.7   0.00044       0.1       3     104 ..       6     107 ..       4     128 .. 0.86
   2 ?    4.8   8.0      0.12        28      66     118 ..     140     194 ..     123     196 .. 0.78
   3 !   11.7   9.3   0.00087       0.2       2      89 ..     194     280 ..     193     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00044
                    TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesa 83 
                                   ++++++e ++l++ +ee+++++  l+e+ +k  +++k+  +   +   ++ e v++l++lree +++ +e+a+lk+e++++
  gi|14600971|ref|NP_147497.1|   6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKT 86 
                                   6778888888888888888888888888888888888888888888889******************************** PP

                    TPR_MLP1_2  84 kaeleeseesweeqkeeleke 104
                                   + el  ++ ++   +  leke
  gi|14600971|ref|NP_147497.1|  87 RDELVIKRDQLRVLRGLLEKE 107
                                   *****************9998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.12
                    TPR_MLP1_2  66 lnelkaeiaelkaeaesakaeleeseeswe..eqkeelekelselekriedlneq 118
                                    ++l +ei+ l++  e+++++ e++ + +e   + ++l  +l++l++ri++l +q
  gi|14600971|ref|NP_147497.1| 140 EKRLVEEISRLEELIERVRKAKEQALSTMElqAEVKALVIKLKDLNQRIDELRQQ 194
                                   4667788899999999998888887766551166789***************999 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00087
                    TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaes 82 
                                   +  s++ee+++l++++ee++++++kl e++ek + +  e  +   +   k  e ++ l+++r  +++   e++e+++++e+
  gi|14600971|ref|NP_147497.1| 194 QAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIAMAR-GMELSEVEKRREE 273
                                   5678999*************************************************99999998855.4566666666666 PP

                    TPR_MLP1_2  83 akaelee 89 
                                    k+++e+
  gi|14600971|ref|NP_147497.1| 274 IKKKMEK 280
                                   6666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  23.2     0.084        19     148     239 ..       6      97 ..       2     132 .. 0.70
   2 ?    1.7  22.7      0.43        98     147     274 ..      40     171 ..      39     177 .. 0.83
   3 !   16.2  21.7   1.6e-05    0.0037     145     277 ..     144     276 ..     140     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.084
                          Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                   ++++++++e+L k  eel+e   +l+ee+ +l +e++ l+e++++ +  ++e++e+lr+  +e k+ ++e+ +  +e+++ 
  gi|14600971|ref|NP_147497.1|   6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKT 86 
                                   677888888888999999999999999999999999999998888777777777777666666666666555555555555 PP

                          Spc7 229 leeleekieel 239
                                   ++el  k ++l
  gi|14600971|ref|NP_147497.1|  87 RDELVIKRDQL 97 
                                   55555544444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.43
                          Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelae 224
                                   ++++l+e++++ ++++ e  e l +l+ee++++ +el++l+e++++  +   i++++L+ lr  l++    ++  k  l++
  gi|14600971|ref|NP_147497.1|  40 EVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDelvIKRDQLRVLRGLLEKEGGRLA--KISLKR 118
                                   57789999999999999999999*******************999988889999*******************..677777 PP

                          Spc7 225 lqeqleele...ekieelkeqkseleeeiaeaervleeckgwsesevsrlkee 274
                                   lq++l+ele    +     e+ ++l eei++ e+++e+ ++ +e+ +s+++ +
  gi|14600971|ref|NP_147497.1| 119 LQRRLQELEmmqMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALSTMELQ 171
                                   777777776211344456788999********************999865433 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 1.6e-05
                          Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkel 222
                                    e+++ lee  e++ k +e++ + + el++e ++l  +l++l+++ +el +   + keeL++l ++++e ++ i+++++e+
  gi|14600971|ref|NP_147497.1| 144 VEEISRLEELIERVRKAKEQALSTM-ELQAEVKALVIKLKDLNQRIDELRQqagSVKEELATLSSKIEEYNERIKKLSEEI 223
                                   4555555555555555555555443.5677777777777777777777666554679999999999999999999999999 PP

                          Spc7 223 aelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevka 277
                                   +++ ++++el+++i++l ++++e++++++  +  + + +g++ sev++ +ee k+
  gi|14600971|ref|NP_147497.1| 224 EKRSTRIDELSKEIDNLYAKYREVMTRLK--DIRIAMARGMELSEVEKRREEIKK 276
                                   99999999999999999999999999999..445566899999999999988764 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 ?    4.1   8.6      0.24        54      30      65 ..      15      50 ..      10      56 .. 0.81
   2 ?    4.1   8.3      0.23        52       6      68 ..      68     128 ..      64     130 .. 0.83
   3 ?    0.3   0.7       3.5   7.9e+02      41      61 ..     139     159 ..     135     169 .. 0.72
   4 !   18.1   5.4   9.6e-06    0.0022      16      70 ..     169     223 ..     165     224 .. 0.93
   5 ?    2.3   0.1      0.84   1.9e+02      34      55 ..     229     250 ..     228     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.24
                      JIP_LZII 30 dLIarvdeLtsereiLreEleslqkakerlesrike 65
                                  +L++ ++eL++e   L+eE ++l ++ ++l+++ ++
  gi|14600971|ref|NP_147497.1| 15 ELLKTIEELKEEIVRLKEERRKLINEVKALREERRK 50
                                  789999999999999999999999988888876655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.23
                      JIP_LZII   6 evenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqk.akerlesrikelEe 68 
                                   e  +++ E ++L+e + +    +d+L+ + d+L   r  L++E  +l k +++rl+ r++elE 
  gi|14600971|ref|NP_147497.1|  68 ERKKILDELAQLKEERKKT---RDELVIKRDQLRVLRGLLEKEGGRLAKiSLKRLQRRLQELEM 128
                                   5566777777777777776...*********************9998773689*********96 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 3.5
                      JIP_LZII  41 ereiLreEleslqkakerles 61 
                                   e++ L eE+++l++  er+++
  gi|14600971|ref|NP_147497.1| 139 EEKRLVEEISRLEELIERVRK 159
                                   666777888888877777764 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 9.6e-06
                      JIP_LZII  16 eLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                   eL++   aL +  +dL +r+deL ++  +++eEl +l +  e+ ++rik+l ee+
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEI 223
                                   7888888998999**************************************9996 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.84
                      JIP_LZII  34 rvdeLtsereiLreEleslqka 55 
                                   r+deL++e + L    +++++ 
  gi|14600971|ref|NP_147497.1| 229 RIDELSKEIDNLYAKYREVMTR 250
                                   8999999988877666666555 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4  28.5    0.0017      0.39      48     138 ..      10     100 ..       7     132 .. 0.85
   2 !   12.8  17.6   0.00033     0.074      47     132 ..     170     255 ..     165     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0017
                       DUF4201  48 qienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqn 128
                                   + e ++l k+Iee ++e++rlk+   k + +++ l+e +   ++e +e  ++l+++ e+++k+ +el ++k+er+k r++ 
  gi|14600971|ref|NP_147497.1|  10 KKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDEL 90 
                                   778999************************************************************************998 PP

                       DUF4201 129 eklkqqggll 138
                                      ++q+  l
  gi|14600971|ref|NP_147497.1|  91 VIKRDQLRVL 100
                                   7777776654 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00033
                       DUF4201  47 lqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkq 127
                                   lq+e++al+ k+ + n+ + +l++++++   +l++l  k  ++++  ++l +e++++ +r+++l ke+ ++ ++   + ++
  gi|14600971|ref|NP_147497.1| 170 LQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTR 250
                                   677777777777777777777777777777777777777777777777777777777777777777777777776666666 PP

                       DUF4201 128 neklk 132
                                    ++++
  gi|14600971|ref|NP_147497.1| 251 LKDIR 255
                                   66655 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  21.7       1.6   3.7e+02      13     122 ..      19     130 ..       4     131 .. 0.80
   2 ?    2.8   4.3      0.56   1.3e+02      20      77 ..     115     170 ..     110     173 .. 0.75
   3 !   17.8  12.0   1.3e-05     0.003       4     112 ..     164     274 ..     161     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.6
                          FliJ  13 elqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkk 91 
                                    +++ +e++ +l+++r+++ ++ ++   +   +  e r y + +++l+e+ +++  elaq++++++k r+e+  +r +++ 
  gi|14600971|ref|NP_147497.1|  19 TIEELKEEIVRLKEERRKLINEVKALReErRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQLRV 99 
                                   4455555555555555555555555554444445999******************************************** PP

                          FliJ  92 lekLkerekkeeqkeenrrEqkqlDElalrr 122
                                   l+ L e+e  + +k   +r q++l El +++
  gi|14600971|ref|NP_147497.1| 100 LRGLLEKEGGRLAKISLKRLQRRLQELEMMQ 130
                                   ********99999999999999998888776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.56
                          FliJ  20 kleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvek 77 
                                    l +l++ +qe++  ++ +   l ++e + + + is+l+e i++ +++ +qa   +e 
  gi|14600971|ref|NP_147497.1| 115 SLKRLQRRLQELEMMQMTR--VLRPEEEKRLVEEISRLEELIERVRKAKEQALSTMEL 170
                                   5677777777774444444..5999999999999999999999999999998887775 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1.3e-05
                          FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82 
                                   a    e q+e+++   kl  l+q ++e+++q+ +   + +   +++  y++ i++l e+i++    ++ + k++++  +++
  gi|14600971|ref|NP_147497.1| 164 ALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKeElATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKY 244
                                   556678999***********************9999999999*************************************** PP

                          FliJ  83 qearqerkklekLkerekkeeqkeenrrEq 112
                                    e + ++k +++  +r  +    e +r+E 
  gi|14600971|ref|NP_147497.1| 245 REVMTRLKDIRIAMARGMELSEVEKRREEI 274
                                   ***********9999988888887777775 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  10.4     0.015       3.4       7      83 ..      12      90 ..       9      92 .. 0.85
   2 ?    3.3   3.9      0.56   1.3e+02      22      68 ..     143     187 ..     105     190 .. 0.36
   3 !   18.2   4.0   1.4e-05    0.0032       6      85 ..     172     253 ..     169     262 .. 0.89
   4 ?    1.5   0.1         2   4.6e+02      20      57 ..     238     276 ..     233     288 .. 0.35

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.015
                       DUF2203  7 eAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdleagl 83
                                  e ++lL +++el ee+++l++e ++l +e+++ ++e++k +  ++e  ++l++l++e +++++e+ +l+ e k  +  l
  gi|14600971|ref|NP_147497.1| 12 EEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASreKREYVEKLRSLREERKKILDELAQLKEERKKTRDEL 90
                                  557999**********************9999999877666667777899999999*********99998888776655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.56
                       DUF2203  22 lralrkeleeleeeleeakaeaekse.aaeleaeleeleaeieelvee 68 
                                   l++  ++leel e++++ak++a      +el+ae+++l  ++++l ++
  gi|14600971|ref|NP_147497.1| 143 LVEEISRLEELIERVRKAKEQA---LsTMELQAEVKALVIKLKDLNQR 187
                                   1111111222222222222221...12444444444444444444444 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.4e-05
                       DUF2203   6 eeAnalLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdleaglv 84 
                                   +e +al+ +lk+l +++ +lr+++ +++eel++ +++ e+ +   ++l +e+e+ +++i+el +ei++l ++++++   l 
  gi|14600971|ref|NP_147497.1| 172 AEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNerIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLK 252
                                   57899999************************99999887777799999********************999998876665 PP

                       DUF2203  85 D 85 
                                   D
  gi|14600971|ref|NP_147497.1| 253 D 253
                                   5 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 2
                       DUF2203  20 eelralrkeleeleeeleeakaeaekse.aaeleaelee 57 
                                   ++l+a+ +e+ ++ ++++ a a+  + +  +++++e+++
  gi|14600971|ref|NP_147497.1| 238 DNLYAKYREVMTRLKDIRIAMARGMELSeVEKRREEIKK 276
                                   333333333333333222222222211112222222222 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.3     0.022         5     175     219 ..       7      51 ..       2      59 .. 0.87
   2 !   15.0  40.9   2.3e-05    0.0053     382     583 ..      50     253 ..      46     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                          HOOK 175 keaqeekdelaQrcheldkqlsllqeEknaLlaenkklqerlsel 219
                                    e ++e++el   ++el +++  l eE+ +L++e k l+e+  + 
  gi|14600971|ref|NP_147497.1|   7 AEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKA 51 
                                   5778899*******************************9987655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-05
                          HOOK 382 klefelkkleeklealqkekerllaerdaLke....tneELkcaqlqqkelsqad..alaskssssgenlaaellpaevre 456
                                   k++ e ++  ekl +l  e+ ++l e  +Lke    t +EL + + q + l+     +  +  + s + l++ l+  e+ +
  gi|14600971|ref|NP_147497.1|  50 KASREKREYVEKLRSLREERKKILDELAQLKEerkkTRDELVIKRDQLRVLRGLLekEGGRLAKISLKRLQRRLQELEMMQ 130
                                   6677999999********************986666899*99977666664432211222223345789999999999998 PP

                          HOOK 457 klirLq.hENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllk 536
                                   +   L+ +E K+L ++  +  ee ++++ + +e+a  +  eL+ e ++   ++++L+++++el+   q+ gs +e+ ++l 
  gi|14600971|ref|NP_147497.1| 131 MTRVLRpEEEKRLVEEISRL-EELIERVRKAKEQALST-MELQAEVKALVIKLKDLNQRIDELR---QQAGSVKEELATLS 206
                                   88888735789995555554.88888888888877655.57*******************9996...5679999999**** PP

                          HOOK 537 kkleehleklkevqeelqkkkeqleelepklssnkqkieeleeaLkk 583
                                   +k+ee  e++k++ ee++k++  ++el++++++   k +e+++ Lk 
  gi|14600971|ref|NP_147497.1| 207 SKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKD 253
                                   *******************************************9974 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.077        17       2      33 ..      20      51 ..      14      55 .. 0.52
   2 ?   -0.3   0.1       6.3   1.4e+03      18      36 ..      64      82 ..      59      90 .. 0.48
   3 ?    5.9   0.6     0.075        17       4      36 ..     169     201 ..     166     204 .. 0.87
   4 ?    5.2   0.1      0.12        28       3      28 ..     203     228 ..     201     232 .. 0.78
   5 ?    6.3   0.1     0.057        13       4      28 ..     218     242 ..     216     261 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.077
                           LPP  2 ldeLssqVsqLkskvdqlssdvnsakaaaqaa 33
                                  ++eL +++ +Lk++  +l ++v++++++  +a
  gi|14600971|ref|NP_147497.1| 20 IEELKEEIVRLKEERRKLINEVKALREERRKA 51
                                  34555555555555555555555555554444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 6.3
                           LPP 18 qlssdvnsakaaaqaakeE 36
                                  +l ++ +++ +++++ keE
  gi|14600971|ref|NP_147497.1| 64 SLREERKKILDELAQLKEE 82
                                  4444444444444444444 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.075
                           LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                   eL ++V++L  k + l++ +++++++a ++keE
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEE 201
                                   788999999999999999999999999999998 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.12
                           LPP   3 deLssqVsqLkskvdqlssdvnsaka 28 
                                     Lss +++ ++ +++ls+++++ ++
  gi|14600971|ref|NP_147497.1| 203 ATLSSKIEEYNERIKKLSEEIEKRST 228
                                   56899999999999999999887655 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.057
                           LPP   4 eLssqVsqLkskvdqlssdvnsaka 28 
                                   +Ls+++++ ++ +d+ls++++++ a
  gi|14600971|ref|NP_147497.1| 218 KLSEEIEKRSTRIDELSKEIDNLYA 242
                                   5555555555555555555554433 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.7      0.55   1.2e+02     111     146 ..      15      50 ..       8      63 .. 0.69
   2 ?    6.6   8.6     0.028       6.4       2      68 ..     116     191 ..     115     208 .. 0.77
   3 !   16.8   0.8   2.1e-05    0.0048     114     160 ..     207     253 ..     203     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.55
                  Dynactin_p22 111 eeikdvpelkekLekLsqihlkqqeeveelseevkk 146
                                   e +k ++elke++ +L++   k  +ev++l ee +k
  gi|14600971|ref|NP_147497.1|  15 ELLKTIEELKEEIVRLKEERRKLINEVKALREERRK 50 
                                   446677777777777777777777777777766555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.028
                  Dynactin_p22   2 ldaLEeriaeLEkrvl.....Geekekeked....esiidsLakvqkklssavskrekikellkkleelekyLdpe 68 
                                   l++L++r++eLE   +     +ee+++  e+    e++i+++ k++++  s+++ + ++k+l+ kl++l++ +d  
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLQELEMMQMtrvlrPEEEKRLVEEisrlEELIERVRKAKEQALSTMELQAEVKALVIKLKDLNQRIDEL 191
                                   899*********865511112455555555599999999999999999999999999*************999963 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.1e-05
                  Dynactin_p22 114 kdvpelkekLekLsqihlkqqeeveelseevkkllekYnklvltlsk 160
                                   ++++e++e+++kLs+   k + +++els+e+ +l  kY +++++l+ 
  gi|14600971|ref|NP_147497.1| 207 SKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKD 253
                                   5799***************************************9986 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   3.0   0.00029     0.065      97     163 ..      10      76 ..       5      93 .. 0.79
   2 !    9.1   5.0    0.0046         1     114     173 ..     167     229 ..     128     237 .. 0.71
   3 ?   -0.1   0.0       3.1     7e+02     104     136 ..     227     259 ..     220     272 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00029
                  Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisql 163
                                   kk+ +ell+ +e+L+eei+  ++e ++li+e+k+l+++  k s++  + v++l s  +  ++ +++l
  gi|14600971|ref|NP_147497.1|  10 KKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDEL 76 
                                   67899********************************999999988888888887766666544333 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0046
                  Bacillus_HBL 114 iqqnqkevkqlikeLkklklkla...kdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                    ++ q+evk+l+ +Lk+l+++++   +   + k+++++l s ++  +  i++l +eie+    
  gi|14600971|ref|NP_147497.1| 167 TMELQAEVKALVIKLKDLNQRIDelrQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTR 229
                                   467889999999999999876552216777788888888888888888888888888876655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3.1
                  Bacillus_HBL 104 lellekLqeeiqqnqkevkqlikeLkklklkla 136
                                   + ++ +L++ei +  ++ ++++  Lk+ + ++a
  gi|14600971|ref|NP_147497.1| 227 STRIDELSKEIDNLYAKYREVMTRLKDIRIAMA 259
                                   567888888888888888888888888887776 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 ?    1.7   5.6      0.55   1.2e+02      38     101 ..      11      74 ..       2     106 .. 0.70
   2 ?    1.9   2.4      0.49   1.1e+02      37      98 ..     116     176 ..     104     182 .. 0.77
   3 !   15.7   2.9   3.1e-05     0.007      35     102 ..     179     243 ..     167     267 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.55
                          HemX  38 aelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsg 101
                                   +e ++ l+++e+ ++++  +ke+  +l++++++l e+  ++++e+ ++ ++l +l+++ +k+  
  gi|14600971|ref|NP_147497.1|  11 KEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILD 74 
                                   4445556666666666666777777777777777777777777777777777777776666554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.49
                          HemX  37 vaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlsk 98 
                                    ++lq +l++le  + +     e++++l e++  l+e +e+ +k++eq   +  elq+++++
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLQELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQAL-STMELQAEVKA 176
                                   47899999999999988666678888999999999999998888776654.44567777765 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.1e-05
                          HemX  35 aevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                    + ++l+q++ +l qq+++    ke+ ++l++++++ +e++++l++e+e+ + +++el++++ ++ ++
  gi|14600971|ref|NP_147497.1| 179 IKLKDLNQRIDELRQQAGS---VKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAK 243
                                   3447888888888888888...5555555566666666666666666666666666666666555554 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5  40.1   4.3e-05    0.0098     637     911 ..       7     279 ..       3     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                       DUF3584 637 eeakravaeaatalknardtlerlqnekesekdklekaiaerkqqae......eqlqkldaqlkqleeqqkaaleelkedl 711
                                    e k++++e  +++++ ++++ rl++e++++ +++++ ++er+++ +      e+l++l ++ k ++ + ++++ee k++ 
  gi|14600971|ref|NP_147497.1|   7 AEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASRekreyvEKLRSLREERKKILDELAQLKEERKKTR 87 
                                   566788888888999999999999999999998888877777665441111116788889999999999999888888877 PP

                       DUF3584 712 seerlekkakwqevvgeldeqlaelkkaieaartqakarlkeleeaykreLkskdvDpetvkelkrkieeLekkieriekr 792
                                   +e    k+++++++ g l+++  +l k   ++ + + ++l+ ++  ++r L      pe  k+l ++i  Le+ ier++k 
  gi|14600971|ref|NP_147497.1|  88 DELV-IKRDQLRVLRGLLEKEGGRLAKISLKRLQRRLQELEMMQ--MTRVL-----RPEEEKRLVEEISRLEELIERVRKA 160
                                   7766.667789999999999999999888887776666666664..44444.....3677788999*************99 PP

                       DUF3584 793 reevreYraflqe...twlkvdslaeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenl 870
                                   +e++++  + + e      k ++l ++ ++l +q  +++++++ l  + ++ +e  k+  +++ek + +++++ +++d++ 
  gi|14600971|ref|NP_147497.1| 161 KEQALSTMELQAEvkaLVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLY 241
                                   999987655544300034444555555555555555555555555555555555555555555555555555555555555 PP

                       DUF3584 871 rklrdllsklaelkldadaeqaegelaerlaaleelkrkre 911
                                    k r ++ +l +++++        el+e  ++ ee+k+k e
  gi|14600971|ref|NP_147497.1| 242 AKYREVMTRLKDIRIAMAR---GMELSEVEKRREEIKKKME 279
                                   5555555555555544332...2344555555555555544 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 !   11.2  19.4    0.0014      0.32      23      90 ..      19      90 ..       4     100 .. 0.71
   2 ?    7.1   9.9     0.027         6      21      94 ..      53     127 ..      49     136 .. 0.77
   3 !   11.2  16.0    0.0015      0.33      14     101 ..     150     241 ..     133     258 .. 0.68
   4 ?    1.9   1.1       1.1   2.5e+02      57      88 ..     252     283 ..     249     290 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0014
                                  CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N 23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleael 90
                                    +++ +e++ l e+rr+l++e+ +l++er ++s+e  +  +k     e+++++++e ++lkee k++ +el
  gi|14600971|ref|NP_147497.1| 19 TIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLrslrEERKKILDELAQLKEERKKTRDEL 90
                                  4678889****************************9777775544444555555555555555555555555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.027
                                   CTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHH.HHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  21 RgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkel.keelkaleaelkele 94 
                                   R e  + v++l +l e+r+++  el +l++er++   e   + ++    +  l +e+  l k  lk+l+ +l+ele
  gi|14600971|ref|NP_147497.1|  53 R-EKREYVEKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQLrVLRGLLEKEGGRLaKISLKRLQRRLQELE 127
                                   4.56788***************************999998888887555555555555552567788888777776 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0015
                                   HHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  14 vkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleael 90 
                                   ++e +++ +++k++  + +el+++ ++l ++l +l+++  el ++ g+ k++      ++ee  +++k+l+ee+++ +++ 
  gi|14600971|ref|NP_147497.1| 150 LEELIERVRKAKEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELatlsSKIEEYNERIKKLSEEIEKRSTRI 230
                                   455555545666666777777777777777777777777777777777776666666666666666666666666666666 PP

                                   HHHHHHHHHHH CS
                  Seryl_tRNA_N  91 keleaelekll 101
                                   +el++e+++l 
  gi|14600971|ref|NP_147497.1| 231 DELSKEIDNLY 241
                                   66666666654 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 1.1
                                   HHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHH CS
                  Seryl_tRNA_N  57 keIgkakkkkedaeeliaevkelkeelkalea 88 
                                   k I  a++++ + +e+ ++ +e+k+++++ e 
  gi|14600971|ref|NP_147497.1| 252 KDIRIAMARGMELSEVEKRREEIKKKMEKGEP 283
                                   67888888888888888888888888887765 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 !   16.4  14.6     4e-05     0.009       3      89 ..      15     104 ..       5     106 .. 0.90
   2 !   12.5   7.4   0.00067      0.15       7      81 ..     173     250 ..     165     255 .. 0.81
   3 !    8.8   5.0    0.0089         2       3      70 ..     211     280 ..     202     285 .. 0.47

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-05
                        CENP-H   3 plieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrq 80 
                                   +l++ ++el +e+ +l++e r+l +e+  +++e+++++r++re +++l+ l++e ++      +lkee +k + el  +r+
  gi|14600971|ref|NP_147497.1|  15 ELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILdelAQLKEERKKTRDELVIKRD 95 
                                   6899999*****************************************777777666666788899999************ PP

                        CENP-H  81 rwrvvknva 89 
                                   + rv+++ +
  gi|14600971|ref|NP_147497.1|  96 QLRVLRGLL 104
                                   ****99876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00067
                        CENP-H   7 qrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrqr 81 
                                   +  +l+ +l++l+q + el+++  +v++e   l+ k +e  +++ +l++e e+++   ++l++e+++l a++++   r
  gi|14600971|ref|NP_147497.1| 173 EVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRStriDELSKEIDNLYAKYREVMTR 250
                                   567788889999999999999999999999999999999999998888888888888888999999999988876665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0089
                        CENP-H   3 plieqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.l.elakekesekeklkeelek 70 
                                   ++ e++ +ls+e++k s+ + el +e++++ ++ +++ ++ + +   + + ++ +e e+++e+ k+++ek
  gi|14600971|ref|NP_147497.1| 211 EYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIAMaRgMELSEVEKRREEIKKKMEK 280
                                   3334455555555555555555555555555555555555555544443222222222222344444444 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 ?    4.5  22.0      0.16        36      39     109 ..      14      87 ..       7     106 .. 0.68
   2 !   10.2  21.2    0.0028      0.64      52     153 ..     116     225 ..      88     228 .. 0.82
   3 !   16.1   5.8   4.3e-05    0.0098      80     149 ..     184     253 ..     181     255 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.16
                 Jnk-SapK_ap_N  39 eslasrneeeeaeleelreeleqLeteyerekelrkrae...eeleeiedqweeerkelqekveqleeenrele 109
                                   e+l++  ee ++e+ +l+ee+ +L +e +  +e+r++a    +e+ e+  +++eerk++ ++++ql+ee+++  
  gi|14600971|ref|NP_147497.1|  14 EELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASrekREYVEKLRSLREERKKILDELAQLKEERKKTR 87 
                                   45666667777777777777777777777666666665544466777777777777777777777777777765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0028
                 Jnk-SapK_ap_N  52 leelreeleqLeteyer...ekelrkraeeeleeiedqweeerkelqekve..qleeenrelelkaknaadqlsrleekea 127
                                   l++l++ l++Le  ++    + e++kr  ee+ ++e+ +e+ rk+ +++++  +l+ e++ l +k+k++++++ +l ++  
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLQELEMMQMTrvlRPEEEKRLVEEISRLEELIERVRKAKEQALStmELQAEVKALVIKLKDLNQRIDELRQQAG 196
                                   555555555555554440005555666669999**********99999998335679************************ PP

                 Jnk-SapK_ap_N 128 elkkeysklhe...retellkklkelver 153
                                   ++k+e ++l++   +++e +kkl e +e+
  gi|14600971|ref|NP_147497.1| 197 SVKEELATLSSkieEYNERIKKLSEEIEK 225
                                   ********999888999999999999988 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 4.3e-05
                 Jnk-SapK_ap_N  80 leeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretellkklke 149
                                   l +  d++++++  ++e+++ l ++++e++ ++k++++++++ + + +el+ke ++l  +++e++ +lk+
  gi|14600971|ref|NP_147497.1| 184 LNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKD 253
                                   5555667777777777777777777777777777777888888888888888888888888888888887 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6  20.1       1.3   2.9e+02      13      66 ..      19      72 ..       4      80 .. 0.69
   2 ?   14.0   6.5   0.00017     0.039      16      61 ..     169     214 ..     158     215 .. 0.94
   3 ?   15.8   3.7   4.6e-05      0.01       6      50 ..     208     252 ..     208     260 .. 0.83
   4 ?    5.5   3.8     0.076        17       6      31 ..     266     291 ..     261     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.3
                    TMF_DNA_bd 13 qIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleel 66
                                  +I++L+eE  +L+ + +kl n +k Lr++ +++  e +e+ +kl++l +e +++
  gi|14600971|ref|NP_147497.1| 19 TIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKI 72
                                  677777777777777777777777777777777777777777777777766555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00017
                    TMF_DNA_bd  16 qLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklek 61 
                                   +L++E ++L  k  +ln+ i++Lr+++    +e+++l++k+e++++
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNE 214
                                   89****************************************9875 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 4.6e-05
                    TMF_DNA_bd   6 klkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeik 50 
                                   k++e +e+I++L eE ek s   ++l++ i++L +k +e  + +k
  gi|14600971|ref|NP_147497.1| 208 KIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLK 252
                                   578889999999999999999999999999999999988665555 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.076
                    TMF_DNA_bd   6 klkeKDeqIaqLmeEGekLskkelkl 31 
                                    ++++ e+I+++me Ge L  +elkl
  gi|14600971|ref|NP_147497.1| 266 EVEKRREEIKKKMEKGEPLTLEELKL 291
                                   578899*****************996 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.6    0.0018      0.42      14      59 ..     182     224 ..     142     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0018
                       NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                   k++++++d l qq  +v+e+l +   l++k+++ ++ +++l++++e
  gi|14600971|ref|NP_147497.1| 182 KDLNQRIDELRQQAGSVKEELAT---LSSKIEEYNERIKKLSEEIE 224
                                   55666666666666666665555...55666666666666666554 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1  11.2   5.2e-05     0.012      15      65 ..      15      65 ..      11      65 .. 0.94
   2 ?    7.3  13.2     0.029       6.5      15      61 ..      36      89 ..      35     106 .. 0.86
   3 ?    2.0   8.4       1.3   2.8e+02      15      65 ..     142     191 ..     138     191 .. 0.87
   4 ?   13.1   9.1   0.00044       0.1       8      62 ..     169     230 ..     167     232 .. 0.81
   5 ?    5.6   7.7     0.096        22       9      62 ..     205     278 ..     202     281 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-05
                          ZapB 15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65
                                  +++ ti++L++ei +Lkee ++l +e ++l+ee  +   e+ +  e+l++L
  gi|14600971|ref|NP_147497.1| 15 ELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSL 65
                                  6899**********************************9999999999987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.029
                          ZapB 15 kaidtitlLqmeieeLkeeneelkeenrele.......eeneqlkeereawqer 61
                                  k+i+++++L++e ++  +e++e+ e+ r l+        e+ qlkeer+++++ 
  gi|14600971|ref|NP_147497.1| 36 KLINEVKALREERRKASREKREYVEKLRSLReerkkilDELAQLKEERKKTRDE 89
                                  789999999999999999999988888888888888888999999999887765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1.3
                          ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    ++++i++L + ie++++ +e+  +   el++e+++l    + +++r++ L
  gi|14600971|ref|NP_147497.1| 142 RLVEEISRLEELIERVRKAKEQALS-TMELQAEVKALVIKLKDLNQRIDEL 191
                                   68999****9999999988887777.78999******99999999999876 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 0.00044
                          ZapB   8 qLEskiqkaidtitlLqmeieeLkeeneelkeenrele.......eeneqlkeereawqerl 62 
                                   +L++ +++++ +++ L ++i+eL+++  + kee + l+       e +++l ee e+   r+
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSskieeynERIKKLSEEIEKRSTRI 230
                                   7999999999999**********999999999999998777766677777777777666666 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.096
                          ZapB   9 LEskiqkaidtitlLqmeieeLkeeneelkeenrele....................eeneqlkeereawqerl 62 
                                   L ski++  ++i++L++eie+   +  el++e+++l                      e+++ ++ re++++++
  gi|14600971|ref|NP_147497.1| 205 LSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYakyrevmtrlkdiriamargMELSEVEKRREEIKKKM 278
                                   55666666666666666666666666666666666665555444555555566666644455555555555555 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 ?    2.4   0.3      0.67   1.5e+02      21      79 ..      16      79 ..       5      91 .. 0.53
   2 ?    3.5   0.7      0.29        67      60     106 ..     138     186 ..      97     191 .. 0.54
   3 ?   14.7   2.5    0.0001     0.023      44     117 ..     148     225 ..     124     250 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.67
                  Baculo_PEP_C 21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnal 79
                                  +L++i  ++ +i   l++   ++ ++++al e+ ++++ e ++       l +  +++ d l++l
  gi|14600971|ref|NP_147497.1| 16 LLKTIEELKEEI-VRLKEERRKLINEVKALREERRKASREKREyveklrSLREERKKILDELAQL 79
                                  344444444444.4444444455555555555444444444445554545555555555555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.29
                  Baculo_PEP_C  60 eldtrldtlltnLtdalnalqdtlrneLtn..lnsiltnLlssvtNins 106
                                   e ++rl + +++L++ + ++ ++ +++L +  l++++  L+ ++  +n+
  gi|14600971|ref|NP_147497.1| 138 EEEKRLVEEISRLEELIERVRKAKEQALSTmeLQAEVKALVIKLKDLNQ 186
                                   4444666666666666666664444444431134444444444444444 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 0.0001
                  Baculo_PEP_C  44 etqLnalsedlksllaeldt....rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstLnnllqalnn 117
                                     +L++l e+++++ ++  +    +l++ +++L  +l+ l+   d+lr++  +++ +l++L s++   n+ ++ l + ++ 
  gi|14600971|ref|NP_147497.1| 148 S-RLEELIERVRKAKEQ--AlstmELQAEVKALVIKLKDLNqriDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEK 225
                                   3.355555555554433..03356888888888888888888888999999999999999999999999998888887765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   1.6       2.1   4.9e+02      21      46 ..       7      32 ..       3      38 .. 0.81
   2 ?   -0.1   0.1       4.8   1.1e+03      32      48 ..     114     130 ..     106     132 .. 0.66
   3 ?    7.8   1.9     0.017       3.9       4      42 ..     172     210 ..     169     211 .. 0.81
   4 ?   15.7   4.7   5.6e-05     0.013       2      44 ..     198     240 ..     197     245 .. 0.95
   5 ?    8.8   2.8    0.0079       1.8       3      44 ..     213     254 ..     211     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.1
                          XhlA 21 dkleekaaeaeekiknleedlkkles 46
                                   + ++ ++e ++ i++l e++ +l++
  gi|14600971|ref|NP_147497.1|  7 AEFKKEEEELLKTIEELKEEIVRLKE 32
                                  56678888999999999999988887 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 4.8
                          XhlA  32 ekiknleedlkklesnq 48 
                                    ++k l+ +l +le +q
  gi|14600971|ref|NP_147497.1| 114 ISLKRLQRRLQELEMMQ 130
                                   45677777777776655 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.017
                          XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlk 42 
                                    +++ +  kl++l++r+d+l + a  ++e++  l  +++
  gi|14600971|ref|NP_147497.1| 172 AEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIE 210
                                   556666679999999999999999999999999998887 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 5.6e-05
                          XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                   +ke+l+++ +k+++++er++kl e  ++  ++i++l +++++l
  gi|14600971|ref|NP_147497.1| 198 VKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNL 240
                                   89***************************************98 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.0079
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                    er++++ +++++ ++r+d+l +  ++ ++k  ++  +lk++
  gi|14600971|ref|NP_147497.1| 213 NERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDI 254
                                   589999999999999999999999999999999999999998 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.8   0.00099      0.23       9      60 ..       5      56 ..       3      60 .. 0.87
   2 ?    6.4   3.0      0.06        14       3      52 ..      55      90 ..      51     108 .. 0.55
   3 ?    1.0   4.9       2.9   6.6e+02      15      62 ..     117     164 ..     106     171 .. 0.74
   4 ?   15.7   5.2   7.7e-05     0.017       4      78 ..     168     242 ..     165     246 .. 0.90
   5 ?    1.3   0.6       2.4   5.5e+02       5      47 ..     246     290 ..     242     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00099
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXX CS
                          YabA  9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkek 60
                                  +++e++++ eell+++eelkee+++l ee ++L  e + lre+ ++++++++
  gi|14600971|ref|NP_147497.1|  5 SIAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKR 56
                                  67899999**********************************9866555544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.06
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA  3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52
                                  k+e ++kl++l e+ +++l+el++lkee               +k r++l
  gi|14600971|ref|NP_147497.1| 55 KREYVEKLRSLREERKKILDELAQLKEE--------------RKKTRDEL 90
                                  4555555555555555555555555555..............55555444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 2.9
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                          YabA  15 eqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62 
                                   ++l++ l+ele ++++ +   ee+++L  e ++l e++e+ +k++++ 
  gi|14600971|ref|NP_147497.1| 117 KRLQRRLQELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQA 164
                                   45666677777777777777899***********99996655555544 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 7.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlYe 78 
                                    el +++++l  +l++l+++++el+++  ++ ee a+L+   e+  er+++ +++ ++++++++e  +++ +lY 
  gi|14600971|ref|NP_147497.1| 168 MELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYA 242
                                   5889999**********************************9999999999999999999999999999988886 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   5 elfdkleeleeqlee..lleeleelkeelaelleenaeLelenek 47 
                                   e++++l+++   +++   l+e+e+ +ee+++ +e+ + L+le  k
  gi|14600971|ref|NP_147497.1| 246 EVMTRLKDIRIAMARgmELSEVEKRREEIKKKMEKGEPLTLEELK 290
                                   666666666655544114578888899999999999999998766 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0  24.1       1.9   4.4e+02      22     140 ..      18     124 ..      15     148 .. 0.65
   2 ?   12.8  19.2   0.00047      0.11      26     143 ..     142     255 ..     141     280 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.9
                         ATG16  22 qaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaq 102
                                   ++  +L + +  l++e++kl ++ ++ ++       + + ++    ++ +  +k+ sl ++++++ +ela+l  +r ++ +
  gi|14600971|ref|NP_147497.1|  18 KTIEELKEEIVRLKEERRKLINEVKALRE------ERRKASR----EKREYVEKLRSLREERKKILDELAQLKEERKKTRD 88 
                                   44445555555666666666444332222......1112222....23457788999999999999999999999999999 PP

                         ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklk 140
                                    l+ + ++l++l+  l+++  rla+++   ++l+++l+
  gi|14600971|ref|NP_147497.1|  89 ELVIKRDQLRVLRGLLEKEGGRLAKISL--KRLQRRLQ 124
                                   9999999999999999999888877543..33444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00047
                         ATG16  26 rLldrtsaleaenaklekaaasakssksskksakekeasasq....snskqsakiqsleqklaqlreelaelyksrgelaq 102
                                   rL + +s le+  ++ +ka ++a s        + +++ + +    + ++ +++i +l q+  +++eela+l  + +e ++
  gi|14600971|ref|NP_147497.1| 142 RLVEEISRLEELIERVRKAKEQALS--------TMELQAEVKalviKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNE 214
                                   6777777777777777666555554........111111111233444556667777777777777777777777777777 PP

                         ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdre 143
                                   r+++l+ee++k+ +++ e ++++++l a+ +++ t+lkd +
  gi|14600971|ref|NP_147497.1| 215 RIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIR 255
                                   77777777777777777777777777777777777777754 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.5      0.06        14       5      86 ..       6      87 ..       4     106 .. 0.87
   2 ?    6.3   4.1      0.04         9      55     105 ..     110     160 ..     103     168 .. 0.81
   3 ?    2.7   0.5      0.53   1.2e+02      62      84 ..     168     190 ..     160     194 .. 0.74
   4 ?   14.5   5.7   0.00012     0.027      13      83 ..     182     252 ..     174     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.06
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH.. CS
                    Laminin_II  5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeass 86
                                  +ae ++  +e l+ +++l++++ ++ke+  ++ ++v+   e+ ++a++  r+  ++ + L ++  ++ld l +lk+ +++  
  gi|14600971|ref|NP_147497.1|  6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTR 87
                                  56667778899999*************************************************************9998755 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.04
                                   XXXXXXXXXX--TTTTTG.GGHHHHHHHHHH...HHHHHHHHHHHHHHHHHH CS
                    Laminin_II  55 rdArrsvkkLeklapqLl.dklkelkqleeassslsdniseikelIaqARka 105
                                   r+A+ s k L++ +++L+  ++ ++   ee++  l ++is++ elI++ Rka
  gi|14600971|ref|NP_147497.1| 110 RLAKISLKRLQRRLQELEmMQMTRVLRPEEEKR-LVEEISRLEELIERVRKA 160
                                   788889999999999995257777777666644.****************97 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.53
                                   XXX--TTTTTGGGHHHHHHHHHH CS
                    Laminin_II  62 kkLeklapqLldklkelkqleea 84 
                                    +L+ ++  L+ klk l+q+ ++
  gi|14600971|ref|NP_147497.1| 168 MELQAEVKALVIKLKDLNQRIDE 190
                                   46777778899999999987654 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 0.00012
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                    Laminin_II  13 kevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                   k   + + +l q+   +ke+l ++ +++ee ne +k++++ i+  ++ + +L k++++L +k +e+ ++ +
  gi|14600971|ref|NP_147497.1| 182 KDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLK 252
                                   55667788888899999999999999999999999999999999999999999999999999888876654 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   8.1      0.04       9.1     376     427 ..      15      66 ..       6      68 .. 0.79
   2 ?   -2.6  20.2       5.1   1.2e+03      97     238 ..      49     191 ..      37     194 .. 0.66
   3 ?   13.2  21.1   7.9e-05     0.018      21     194 ..     117     288 ..     110     291 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.04
                                   TTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 376 elqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeik 427
                                   el + +eel+e++ +++e+  ++ +++k+lr++ ++A ++  e+ ++l++++
  gi|14600971|ref|NP_147497.1|  15 ELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLR 66 
                                   5677788888888888888888888888888888888888888888887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.1
                                   HHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHH.HHHHHHHHHHH--- CS
                          EzrA  97 kkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygea.leelekqlenieke 176
                                   +ka ++ +e  e+l +++e+ kkil+el++l+e  +k r+e    +++ r lr  l+++   + ++ l+ l+ +l+++e +
  gi|14600971|ref|NP_147497.1|  49 RKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQLRVLRGLLEKEGGRLAKIsLKRLQRRLQELEMM 129
                                   5788888899999**********************************************9999886368999999999853 PP

                                   -------------HHHHHHHHHHHHHHHHHH...HHHHHHHHHHTTTTTTSHHHHHHHHHHHHHS CS
                          EzrA 177 fsefeeltengdyveakeilkkleeeidele...evieeiPelleelkkelpkqleelkegykem 238
                                     +++ +   ++ +   e +++lee i++++   e+     el +e+k  l  +l++l++ ++e+
  gi|14600971|ref|NP_147497.1| 130 --QMTRVLRPEEEKRLVEEISRLEELIERVRkakEQALSTMELQAEVK-ALVIKLKDLNQRIDEL 191
                                   ..3333333333333333333333333333300033333333333333.3444566666666665 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 7.9e-05
                                   X-THHHHHHHHHHHHHHHHHHHHHTTTSSS-S---TTTHHHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-SHHHHHTTH CS
                          EzrA  21 kkikkeideLeerkneiknlpvqeelskvkklnltgeseekfeewkkkwdeiktkklpeieellfeaeelldkykfkkakk 101
                                   k+++++++eLe  +++ + +p +ee   v++++  +e+ e++++ k++     +   +e++ l++++++l++  ++ ++++
  gi|14600971|ref|NP_147497.1| 117 KRLQRRLQELEMMQMTRVLRP-EEEKRLVEEISRLEELIERVRKAKEQALSTME-LQAEVKALVIKLKDLNQ--RIDELRQ 193
                                   444444444444433333333.33334566666666666666666655544444.44678888888888876..4678899 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHH..HHHHHH------- CS
                          EzrA 102 klaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeele..kqleniekefsef 180
                                   +  +++eel+++ +ki++ +e +k+l e  ek +++i++l ++ ++l  k+++    ++++  ++    +l+++ek+ +e+
  gi|14600971|ref|NP_147497.1| 194 QAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIAMArgMELSEVEKRREEI 274
                                   999999999999999999999999999999999999999999999999999999999998877776226899********* PP

                                   ---------HHHHH CS
                          EzrA 181 eeltengdyveake 194
                                   ++ +e+g++++ +e
  gi|14600971|ref|NP_147497.1| 275 KKKMEKGEPLTLEE 288
                                   ********988766 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 ?   -0.3   0.1       5.7   1.3e+03      43      54 ..     116     127 ..     105     138 .. 0.73
   2 ?   15.1   4.8     9e-05      0.02       7      63 ..     199     250 ..     196     254 .. 0.88
   3 ?    1.4   0.5       1.7   3.8e+02      17      34 ..     264     281 ..     261     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 5.7
                  ABC_tran_CTD  43 laelsaeleele 54 
                                   l++l+++l+ele
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLQELE 127
                                   445555555555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9e-05
                  ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                   + el++l ++Ie+  e+i++l +e+++ +     +++ els+e+++l a+  e + r
  gi|14600971|ref|NP_147497.1| 199 KEELATLSSKIEEYNERIKKLSEEIEKRS-----TRIDELSKEIDNLYAKYREVMTR 250
                                   67999999*************99999666.....99999999999999998888877 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.7
                  ABC_tran_CTD  17 IeaLEeeiaeleaeladp 34 
                                   + + E++ +e+ +++++ 
  gi|14600971|ref|NP_147497.1| 264 LSEVEKRREEIKKKMEKG 281
                                   556777777777777665 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.8      0.14        31      38     102 ..     128     191 ..     112     193 .. 0.66
   2 ?   14.9   4.8   0.00012     0.028      31      86 ..     197     252 ..     190     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.14
                                   HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                         DUF16  38 kieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                    ++ +   + e+ ++l +++++++e i++ ++  ++    ++ ++  ++ ++  L+++n+R+D++
  gi|14600971|ref|NP_147497.1| 128 MMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALSTME-LQAEVKALVIKLKDLNQRIDEL 191
                                   333333356778889999999999999666554444444444.45556667778*********87 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 0.00012
                                   .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHH CS
                         DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetle 86 
                                   s k++L  +  k++  +e+i+kl +++ek   +i+el++e++   ++  +v   l+
  gi|14600971|ref|NP_147497.1| 197 SVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLK 252
                                   67899999********************************9998887776655555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  14.3      0.14        33     131     229 ..       9     133 ..       2     164 .. 0.69
   2 ?   12.5   9.2   0.00031      0.07     122     227 ..     152     279 ..     132     288 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                       DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.... 207
                                   +++e +el + i++l++ei  +++++++l +e+++  +  +++    ++ + +  ++ +++ +++  ela+lk++++    
  gi|14600971|ref|NP_147497.1|   9 FKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKAS-REKREYVEKLRSLREERKKILDELAQLKEERKktrd 88 
                                   67788888888889999999999999998888887777655444.447888888999999999999999999999667666 PP

                       DUF4407 208 .......................atarlaalraelaeleaerake 229
                                                          a+  l++l+++l+ele  + ++
  gi|14600971|ref|NP_147497.1|  89 elvikrdqlrvlrgllekeggrlAKISLKRLQRRLQELEMMQMTR 133
                                   666766666677777777777665555555555555555555444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00031
                       DUF4407 122 elkeqlaaa..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaela 200
                                   el e++++a      + el+a+++al  +++ +++r+d+lr++a +  + +  t  ++++ + ++ k+  +++++++++++
  gi|14600971|ref|NP_147497.1| 152 ELIERVRKAkeQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKE-ELATLSSKIEEYNERIKKLSEEIEKRSTRID 231
                                   4445555553333445577888888888888888888888888864433.3444555578899999999999999999999 PP

                       DUF4407 201 elkakld.....................atarlaalraelaeleaera 227
                                   el++++d                     ++ +l++ +++++e++++++
  gi|14600971|ref|NP_147497.1| 232 ELSKEIDnlyakyrevmtrlkdiriamaRGMELSEVEKRREEIKKKME 279
                                   999998888888888888888888888866677777777776666655 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 ?    5.7  23.2      0.03       6.8      23     137 ..      19     135 ..      10     141 .. 0.86
   2 ?   12.5  18.0   0.00024     0.055      23     157 ..     149     254 ..     138     291 .. 0.45

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.03
                         Atg14  23 rlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkk 103
                                    ++el+e++ +lk+e+  l ++++++ e+++   +++++ +   +kl++l+ ++ ++ ++l++lk+ +++ ++e+ +k+ +
  gi|14600971|ref|NP_147497.1|  19 TIEELKEEIVRLKEERRKLINEVKALREERR---KASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQ 96 
                                   699*********************9999999...778888888899999999999************************** PP

                         Atg14 104 laklsdklk.....kRrsdleslqneleerrkkqiaklq 137
                                   l+ l+  l        + +l+ lq +l+e +  q+++++
  gi|14600971|ref|NP_147497.1|  97 LRVLRGLLEkeggrLAKISLKRLQRRLQELEMMQMTRVL 135
                                   *******99677654456667777777777777777776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00024
                         Atg14  23 rlyelrerlaklkse...keslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                   rl+el er++k k++     +l+ ++++++ + +   +l+++i+ +++++ + k + a l+++++e ++++++l +eie++
  gi|14600971|ref|NP_147497.1| 149 RLEELIERVRKAKEQalsTMELQAEVKALVIKLK---DLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKR 226
                                   3333333333333321112234444444444333...55555555555555555555555555555555555555555555 PP

                         Atg14 101 kkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktles 157
                                   + ++ +ls+++                              +   k+ ++ + + + 
  gi|14600971|ref|NP_147497.1| 227 STRIDELSKEID-----------------------------NLYAKYREVMTRLKDI 254
                                   555555555555.............................3333333333333332 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       6.7   1.5e+03      25      54 ..      14      43 ..       6      64 .. 0.74
   2 ?    3.0   0.0       0.6   1.4e+02      15      55 ..     100     138 ..      96     144 .. 0.83
   3 ?    8.3   0.1     0.013         3      25      67 ..     175     217 ..     164     223 .. 0.87
   4 ?   -0.4   0.1       6.8   1.5e+03      36      46 ..     228     238 ..     198     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 6.7
                          MtrB 25 dvvllsldpvleeidkLekiaddlvnsLdp 54
                                  + +l ++++++eei +L++    l+n ++ 
  gi|14600971|ref|NP_147497.1| 14 EELLKTIEELKEEIVRLKEERRKLINEVKA 43
                                  446678899999999999988888887664 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.6
                          MtrB  15 etgvvaearedvvllsldpvleeidkLekiaddlvnsLdpe 55 
                                     g+++++++ +  +sl+ ++ ++++Le +  ++ + L pe
  gi|14600971|ref|NP_147497.1| 100 LRGLLEKEGGRLAKISLKRLQRRLQELEMM--QMTRVLRPE 138
                                   67999***999****************987..466666666 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.013
                          MtrB  25 dvvllsldpvleeidkLekiaddlvnsLdpetallesypgRek 67 
                                     ++++l++++++id+L + a  + + L+  ++ +e y++R k
  gi|14600971|ref|NP_147497.1| 175 KALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIK 217
                                   468999**************************99999999966 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 6.8
                          MtrB  36 eeidkLekiad 46 
                                   ++id+L k  d
  gi|14600971|ref|NP_147497.1| 228 TRIDELSKEID 238
                                   23333333333 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  18.3     0.069        16      18      97 ..       6      85 ..       2     151 .. 0.80
   2 ?   -1.4   2.4       5.1   1.2e+03      73      95 ..     139     161 ..      93     169 .. 0.49
   3 ?   13.2  11.1   0.00017     0.039      19     103 ..     168     252 ..     157     296 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.069
                       DUF3450 18 ldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeiere 97
                                  +++ +ke+e+  ++ ++  ++i +l++e+++l +e++al+ee  +++ +++++ + ++s+++e++++  ++++++e +++
  gi|14600971|ref|NP_147497.1|  6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKK 85
                                  5678899***************************************9999999999999999988887777777665444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.1
                       DUF3450  73 lvasqeqeiasleeqieeieeie 95 
                                     + + +ei++lee ie++++ +
  gi|14600971|ref|NP_147497.1| 139 EEKRLVEEISRLEELIERVRKAK 161
                                   22222233333333333333333 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00017
                       DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelv 99 
                                    ++++e ++ v + ++ +++id+l +++ ++++e+ +l++++e+ +   ++l++ +++  ++i++l ++i+++ +  re+ 
  gi|14600971|ref|NP_147497.1| 168 MELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVM 248
                                   567888899999999999999999999999999999999999999999999999999999999999999999877777766 PP

                       DUF3450 100 plle 103
                                     l+
  gi|14600971|ref|NP_147497.1| 249 TRLK 252
                                   5554 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 ?   10.8  24.8   0.00036     0.082      21     265 ..       9     261 ..       3     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                    V_ATPase_I  21 fqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelne 101
                                   f+++  + ++ ++e+++++  l+ee +kl ++v   +e+ ++ ++++++++++l +  e+ ++ l el + +e+ kk++ e
  gi|14600971|ref|NP_147497.1|   9 FKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDE 89 
                                   555555667888888888888888888876666666666677777777777777777777777777777777777888888 PP

                    V_ATPase_I 102 lvelkavlekakefleee.eeeeeeeeseeeeee...keeeeeeeseeeeeeelleeeeelsfvaGvikrekveaferilw 178
                                   lv ++  l+  + +le+e  + ++ + ++ +++    + +++++  + eee++l ee ++l+ ++  ++++k +a++ +  
  gi|14600971|ref|NP_147497.1|  90 LVIKRDQLRVLRGLLEKEgGRLAKISLKRLQRRLqelEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALSTMEL 170
                                   8888888888888888775443333333222222334666667777788888888888889******************** PP

                    V_ATPase_I 179 ralrgnlflrqaeieepledpet.gekveksvfiiffqgeqlkekikkicesfgaklyelpeseeeree...klkeveeri 255
                                   +a  + l+++ +++++++ + ++   +v+ ++  +  + e+ +e+ikk+ e ++ +  +++e ++e ++   k++ev++r+
  gi|14600971|ref|NP_147497.1| 171 QAEVKALVIKLKDLNQRIDELRQqAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNlyaKYREVMTRL 251
                                   ****************99998763667888888888999**************9999888877766665111666777777 PP

                    V_ATPase_I 256 edlekvleqt 265
                                   +d++ ++ + 
  gi|14600971|ref|NP_147497.1| 252 KDIRIAMARG 261
                                   7776555433 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0  13.2      0.14        31     396     470 ..      17      86 ..       3     102 .. 0.66
   2 ?   10.6  25.4   0.00071      0.16     297     469 ..      53     239 ..      50     283 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                        AAA_13 396 kkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                           +eel++e+ ++k++ +kl ++++ l +e +++++e++++ e+ + L+++ +++    +++ +e k+ 
  gi|14600971|ref|NP_147497.1|  17 L-----KTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKT 86 
                                   2.....235667788888888888888888888888888888888888888888877777777666666655544 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00071
                        AAA_13 297 skkselleklkavsde....asensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakie........ 365
                                   ++k+e++ekl ++ +e     +e  + +e++++ ++e+   ++qL+ l+  le+   +++k ++l++++ +++        
  gi|14600971|ref|NP_147497.1|  53 REKREYVEKLRSLREErkkiLDELAQLKEERKKTRDELVIKRDQLRVLRGLLEKEGGRLAK-ISLKRLQRRLQelemmqmt 132
                                   5667777888777776443433445677779999999999999999999998888877776.9999999999656677555 PP

                        AAA_13 366 ..sikklvaeineliakhNekvanleeekeeakkklelhl.veeleseldeykkkykklekaieklekelkeeeaelkkle 443
                                        ++ +++ e i++  e ++++ ++ke+a + +el+  v+ l  +l+ +++ +++l +++ ++++el+  ++++++++
  gi|14600971|ref|NP_147497.1| 133 rvLRPEEEKRLVEEISRLEELIERVRKAKEQALSTMELQAeVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYN 213
                                   552234456777788888888888888888888887776447777778888888888888888888888888888888888 PP

                        AAA_13 444 eeikeLekqlrdekpaaeeinkeLka 469
                                   e+ik L +++++    ++e+ ke+ +
  gi|14600971|ref|NP_147497.1| 214 ERIKKLSEEIEKRSTRIDELSKEIDN 239
                                   88888888888888888888877654 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.6     0.053        12       8      66 ..       9      67 ..       4     100 .. 0.72
   2 ?    2.2   1.3      0.66   1.5e+02      13      66 ..     141     193 ..     136     195 .. 0.61
   3 ?   12.6   4.3    0.0004     0.091       6      65 ..     196     255 ..     171     280 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.053
                         Sec34  8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66
                                   ++e +ell+ ++e++e++  l+e+ ++  ++ ++l+e+  +  +e++++ e  ++++e
  gi|14600971|ref|NP_147497.1|  9 FKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLRE 67
                                  56667788888888888888888888888888888888888888888877777666655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.66
                         Sec34  13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                   ++l+e++++++e++e +++   + + +t +l+++ + l+ + k+l++  +e+++
  gi|14600971|ref|NP_147497.1| 141 KRLVEEISRLEELIERVRKAK-EQALSTMELQAEVKALVIKLKDLNQRIDELRQ 193
                                   456666666666666655443.33455677777777777777777776666655 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.0004
                         Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                    s +ee+ +l ++++e +e +++l+e+ ++ s++  +l+++ ++l+++ +++++  ++i+
  gi|14600971|ref|NP_147497.1| 196 GSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIR 255
                                   344556666666666666666666666666666666666666666666666665555554 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.2    0.0016      0.36      38      91 ..       8      85 ..       4      95 .. 0.68
   2 ?    0.7   0.2       2.7   6.1e+02      56      91 ..     132     166 ..     110     181 .. 0.53
   3 ?    6.3   3.3      0.05        11      58      92 ..     175     226 ..     129     262 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0016
                       DUF2935 38 efkkeFekllaeavelseglv........................rasseleeavakLneealkltreliqFkkelle 91
                                  efkke e+ll+  +el+e +v                        r + e +e++++L ee  k ++el q+k+e ++
  gi|14600971|ref|NP_147497.1|  8 EFKKEEEELLKTIEELKEEIVrlkeerrklinevkalreerrkasREKREYVEKLRSLREERKKILDELAQLKEERKK 85
                                  677777777777777777777666544444455557777777777777777777777777777777777777776655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 2.7
                       DUF2935  56 glvrasseleeavakLneealkltreliqFkkelle 91 
                                   +   +++e+e+++ + +++  +l++++++ k++ l+
  gi|14600971|ref|NP_147497.1| 132 TR-VLRPEEEKRLVEEISRLEELIERVRKAKEQALS 166
                                   33.444444444444444444444444444444443 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.05
                       DUF2935  58 v.................rasseleeavakLneealkltreliqFkkellek 92 
                                                     +++++ +e++a+L +++ ++ +++ ++ +e++++
  gi|14600971|ref|NP_147497.1| 175 KalviklkdlnqridelrQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKR 226
                                   0333333333333333333333333333333333333333333333333333 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  12.5     0.028       6.3       2      79 ..      14      90 ..       8     106 .. 0.83
   2 ?   14.4  18.7   9.6e-05     0.022      10     147 ..     142     283 ..     131     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.028
                      Syntaxin  2 eeffkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekks 79
                                  ee++k++ee+k+ei  l+ee +kl ++ + + +  r+ s   k++  ++ ++ +++ +++  +L +L+++ k+++ + 
  gi|14600971|ref|NP_147497.1| 14 EELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASR-EKREYVEKLRSLREERKKILDELAQLKEERKKTRDEL 90
                                  5788999999999999999999999988877666555555.999999999999**************99999998664 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.6e-05
                      Syntaxin  10 eikkeiekleeevkklkkqneesktstraks.vk...lk.krmesdikeikkraesvkarLeaLdksnkenekksgegsav 85 
                                   ++ +ei+ lee++++++k++e+ +++++ ++ vk   +k k++++ i+e +++a svk++L +L+ +++e +++ ++ s +
  gi|14600971|ref|NP_147497.1| 142 RLVEEISRLEELIERVRKAKEQALSTMELQAeVKalvIKlKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEE 222
                                   56789999*************9999997543122222444788****************************9999999999 PP

                      Syntaxin  86 dRirksqtaaLrkklkevmteynelrekireeykerieRrlevtGkevseeeieelietges 147
                                      r++  + L+k++ ++  +y+e+ ++ ++  +    R +e    e  +eei + +e+ge 
  gi|14600971|ref|NP_147497.1| 223 IEKRSTRIDELSKEIDNLYAKYREVMTRLKD-IRIAMARGMELSEVEKRREEIKKKMEKGEP 283
                                   999*********************9888765.99*************************985 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 ?    2.9   1.4      0.37        84      91     155 ..      20      84 ..       4      97 .. 0.53
   2 ?   14.6   4.1   9.6e-05     0.022      88     167 ..     160     239 ..     143     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.37
                                   HHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  91 iealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqs 155
                                   ie+l +ei++  ++  + ++e++   ee  +  +e +e ++++ +  +e +++++e+a+  ee  
  gi|14600971|ref|NP_147497.1|  20 IEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERK 84 
                                   44444444444444445555554444444444444444444444444444555555555554444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.6e-05
                                   HHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  88 akeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqavee 167
                                   ake +   +e+q+e++  v  l++ +qr++e  +++ + +e+l++++++++e ++ ++ ++   e+ s+ i+e ++ +++
  gi|14600971|ref|NP_147497.1| 160 AKEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDN 239
                                   34433334455666666666666666666666666666666666666666666666666666666666666665555543 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 ?   -0.4  19.5         3   6.9e+02      30     164 ..      11     153 ..       6     160 .. 0.79
   2 ?    1.0   4.9       1.1   2.5e+02      75     129 ..     111     164 ..     105     177 .. 0.74
   3 ?   13.3  13.4    0.0002     0.045      43     139 ..     144     240 ..     136     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3
                    MscS_porin  30 dkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilak.lsleeLeqrllqtssqlqelqeqlaqlnsqlv 109
                                   ++ ++  k +eel++ i +  +e r+l +e +al+++  +as+e+ +   +l+ L  + ++ +++l++l+e++++  ++lv
  gi|14600971|ref|NP_147497.1|  11 KEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYvEKLRSLREERKKILDELAQLKEERKKTRDELV 91 
                                   566788899999999999999*************6666666655555516799**************************** PP

                    MscS_porin 110 elqtrperaqqqltearqrlqei.....rnrLnstaaage..alsqaqrtalqaelaaleaq 164
                                     ++++  ++  l +   rl++i     ++rL++++  +    l++++   l  e + le  
  gi|14600971|ref|NP_147497.1|  92 IKRDQLRVLRGLLEKEGGRLAKIslkrlQRRLQELEMMQMtrVLRPEEEKRLVEEISRLEEL 153
                                   ******************99999877777778777554445566666666666665555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 1.1
                    MscS_porin  75 laklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrl 129
                                   lak+sl+ L++rl q+++ +q ++  + +++++lve  +r+e++ ++  +a+++ 
  gi|14600971|ref|NP_147497.1| 111 LAKISLKRLQRRL-QELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQA 164
                                   6788888888887.55677777888888888888888888888877777777664 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.0002
                    MscS_porin  43 qkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqlt 123
                                    + i +  ++++ +++  e+   + e + + +   ++l++L+qr+++  +q  +++e+la+l s++ e++ r+ ++ +++ 
  gi|14600971|ref|NP_147497.1| 144 VEEISRLEELIERVRKAKEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIE 224
                                   555555566666666666555444444555555556788888888888888888888888888888888888888888888 PP

                    MscS_porin 124 earqrlqeirnrLnst 139
                                   + ++r++e++++++++
  gi|14600971|ref|NP_147497.1| 225 KRSTRIDELSKEIDNL 240
                                   8888888888777665 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 ?    7.6  23.8     0.016       3.5      40     127 ..       6      93 ..       1     105 [. 0.72
   2 ?   -0.6  14.6       5.4   1.2e+03      27      99 ..     117     191 ..     105     193 .. 0.75
   3 ?   12.9  22.7   0.00036     0.082      11     125 ..     159     277 ..     151     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.016
                CENP-F_leu_zip  40 qekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleek...Eqek 117
                                     + + e E+  +++e+lkeei +l+ee+r+l  +++alr+e+ +     ++k+e v+ L sl+++ +++l e+    +e+
  gi|14600971|ref|NP_147497.1|   6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKA---SREKREYVEKLRSLREERKKILDELaqlKEER 83 
                                   55677899999********************************876...66677777777777777777776540003344 PP

                CENP-F_leu_zip 118 vqmkeeskaa 127
                                   ++ ++e   +
  gi|14600971|ref|NP_147497.1|  84 KKTRDELVIK 93 
                                   4444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 5.4
                CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLva..lrsekeeLekelqkkqervseL 99 
                                   ++L+r l+++e  q   +l  E++k  ve++    e +++ ++  e+ L++  l+ e + L  +l++ ++r++eL
  gi|14600971|ref|NP_147497.1| 117 KRLQRRLQELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALSTmeLQAEVKALVIKLKDLNQRIDEL 191
                                   689999999999999999999999988887554444444444445555554115689999999999999999999 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00036
                CENP-F_leu_zip  11 kLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq. 90 
                                   k Ke   +   L+  v++L   l+++++  +++  +a + k+e+ tl ++iee +e+ ++l+ ++++ +   +eL ke+  
  gi|14600971|ref|NP_147497.1| 159 KAKEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDn 239
                                   55666777788******************************************************************9863 PP

                CENP-F_leu_zip  91 ...kkqervseLeslnsslenlleekEqekvqmkeesk 125
                                      k +e +  L+ ++  + + +e +E ek++++ + k
  gi|14600971|ref|NP_147497.1| 240 lyaKYREVMTRLKDIRIAMARGMELSEVEKRREEIKKK 277
                                   33257888899******************887665544 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  10.7    0.0031      0.71       4      94 ..       7      99 ..       4     101 .. 0.92
   2 ?    6.3   7.9      0.06        14      42     103 ..     139     202 ..     112     204 .. 0.82
   3 ?    5.9   2.8     0.078        18      20      81 ..     208     277 ..     197     282 .. 0.35

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0031
                                  HHHHHHHHHHHHHHHHH.HHHH.CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHH CS
                      Spectrin  4 qqfaqdadeleeWieek.eell.ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerlee 84
                                   +f+++ +el++ iee  ee++  +e+  k ++ev+al ++ +   +e +++ e++++l e  +k+lde  + +ee +++ +e
  gi|14600971|ref|NP_147497.1|  7 AEFKKEEEELLKTIEELkEEIVrLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDE 89
                                  5899************835555888888******************************************************* PP

                                  HHHHHHHHHH CS
                      Spectrin 85 lnerWeeLke 94
                                  l  + ++L+ 
  gi|14600971|ref|NP_147497.1| 90 LVIKRDQLRV 99
                                  ******9985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.06
                                   HHHHHHHHHHHHHHHHHHHH.HHHHHH.HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  42 khkaleaelaaqqervkaln.elaekl.ldeghsaseeieerleelnerWeeLkelaaerkqkL 103
                                   + k+l +e++  +e ++++  + +++l + e + + +++  +l++ln+r +eL+++a + k++L
  gi|14600971|ref|NP_147497.1| 139 EEKRLVEEISRLEELIERVRkAKEQALsTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEEL 202
                                   668999*************97777888555558888********************99888887 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.078
                                   HHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHH.HHTTHTTHHHHHHH CS
                      Spectrin  20 keellssedlgkdleevqallkkhkaleaelaaqqervkaln........elaekl.ldeghsaseeieer 81 
                                   k e+  +e++ k  ee+++  ++ ++l +e+++   + ++++        ++a+ + l+e ++  eei+++
  gi|14600971|ref|NP_147497.1| 208 KIEEY-NERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMtrlkdiriAMARGMeLSEVEKRREEIKKK 277
                                   22222.22223333333333333333333333333333333222222224444444444444444444444 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   7.1     0.042       9.6      56     133 ..       7      91 ..       2     107 .. 0.56
   2 ?    8.6   9.8     0.013       2.9      36     128 ..     130     247 ..     112     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.042
                     AATF-Che1  56 eeaekalkklleslleLreelleqne.ikkla...eskeeeekkkskrkrkkkkkeetslee....lwkeleklekalkpf 128
                                   +e++k+ ++ll+++ eL+ee+++ +e  +kl    + +  ee+ k++r++++  ++ +sl e    + +el++l+++ k+ 
  gi|14600971|ref|NP_147497.1|   7 AEFKKEEEELLKTIEELKEEIVRLKEeRRKLInevK-ALREERRKASREKREYVEKLRSLREerkkILDELAQLKEERKKT 86 
                                   556666666666666666666554444333333321.22233333333333333333333333344888888888888888 PP

                     AATF-Che1 129 rnatl 133
                                   r++ +
  gi|14600971|ref|NP_147497.1|  87 RDELV 91 
                                   88765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.013
                     AATF-Che1  36 p.....qpetlkefles....................seefeealeeaekalkklleslleLreelleqne.ikklaeske 90 
                                         +pe+ k+++e+                    + e++++++++  +lk+l + + eLr++    +e +++l+ sk 
  gi|14600971|ref|NP_147497.1| 130 QmtrvlRPEEEKRLVEEisrleeliervrkakeqalsTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEeLATLS-SKI 209
                                   44455555555555555433333333344444444445566666677777777777777777777755555555443.333 PP

                     AATF-Che1  91 eeekkkskrkrkkkkkeetsleelwkeleklekalkpf 128
                                   ee +++ k+  ++ +k++t ++el+ke+++l++++++ 
  gi|14600971|ref|NP_147497.1| 210 EEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREV 247
                                   34445555555556888999999******999999875 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 ?   -1.2  26.0       6.6   1.5e+03       3     110 ..      13     122 ..       4     131 .. 0.60
   2 ?   12.1  29.7   0.00058      0.13      27     168 ..     129     279 ..     113     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6.6
                      KASH_CCD   3 tsdlistvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleE.. 81 
                                    ++l++t+++L+    +L+ee +kL + v +  e+  k + e  e  +kl+s+       k + +El++lk+  k++ +  
  gi|14600971|ref|NP_147497.1|  13 EEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREE---RKKILDELAQLKEERKKTRDel 90 
                                   46777777777777777777777777777777777777777777777777776543...3334444554444444433312 PP

                      KASH_CCD  82 ..krarlkaqnkqlekenqsLi.akiesLqee 110
                                     kr +l   +  leke   L  + ++ Lq +
  gi|14600971|ref|NP_147497.1|  91 viKRDQLRVLRGLLEKEGGRLAkISLKRLQRR 122
                                   22566777777777777666641455555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00058
                      KASH_CCD  27 LkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrar...lkaqnkqlekenqsLiaki 104
                                   ++ +     e+ ++L+eei+ L + +  + +a ++a +  e  +e+kalv +l++ ++r   l +q+  ++ e   L++ki
  gi|14600971|ref|NP_147497.1| 129 MQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALSTMELQAEVKALVIKLKDLNQRideLRQQAGSVKEELATLSSKI 209
                                   3444444567789*******9999888888888888777777777777766666666551115667777899999****** PP

                      KASH_CCD 105 esLqeenikllaekdelkkklkeLlkekaeLkkqlhelee......llaekealleektkqieeLkltie 168
                                   e+ +e+++kl  e+++  +++ eL+ke+++L  +  e+ +      ++  +  +l+e +k+ ee+k  +e
  gi|14600971|ref|NP_147497.1| 210 EEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTrlkdirIAMARGMELSEVEKRREEIKKKME 279
                                   *******************************999866543111122445556666666666666665554 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  15.8    0.0044         1       7      90 ..       8      91 ..       4     108 .. 0.93
   2 ?    2.4   8.7      0.73   1.7e+02       3      68 ..     124     188 ..     122     195 .. 0.85
   3 ?    8.8   9.8    0.0075       1.7       3      79 ..     200     279 ..     198     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0044
                          BRE1  7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefvrkl 89
                                  + +k+ eel ++++++++e+ +l+e+  +l +e +  +++   a r+k+    +l+ L++  +K  +  +qLke  k+++ +l
  gi|14600971|ref|NP_147497.1|  8 EFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDEL 90
                                  6788999*******************************************************************999999887 PP

                          BRE1 90 k 90
                                   
  gi|14600971|ref|NP_147497.1| 91 V 91
                                  5 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.73
                          BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkll 68 
                                   +EL+ ++  +    e+ + +v+e+++lee + r+ + k++a    ++++ + +al ++lk Ln+ +
  gi|14600971|ref|NP_147497.1| 124 QELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALS-TMELQAEVKALVIKLKDLNQRI 188
                                   79999999999999999*****************999999976.5688888888888888888765 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0075
                          BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkk...LnkllsKsselieqLk 79 
                                    EL  l+  +ee +e ++k+ +e++    ++  l++e++    ky ++m   +++++ + +   L++  ++  e+ ++++
  gi|14600971|ref|NP_147497.1| 200 EELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIAMARgmeLSEVEKRREEIKKKME 279
                                   7999*********************************************8888888777642225555555555555555 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  16.6   0.00081      0.18      45     121 ..      12      91 ..       6      94 .. 0.90
   2 ?    3.8  22.6      0.18        40      15     159 ..     138     278 ..     136     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00081
                          YkyA  45 gmde.fdkikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryeaydkly 121
                                   + +e +++i++l +e + + eeR++l+++ k+  ee +++  + +e++e++    ee kk ++el++  eer+++ d+l+
  gi|14600971|ref|NP_147497.1|  12 EEEElLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLrsLREERKKILDELAQLKEERKKTRDELV 91 
                                   45566899*******************************************7647789****************999986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.18
                          YkyA  15 elEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei. 94 
                                   e+Ek ++e+ + L+el +   +  e+ ++ +m+ + ++k+l+ ++ + +++R ++l ++     + kee+ +++++iee+ 
  gi|14600971|ref|NP_147497.1| 138 EEEKRLVEEISRLEELIERVRKAKEQALS-TMELQAEVKALVIKLKD-LNQRIDELRQQ---AGSVKEELATLSSKIEEYn 213
                                   67899999999999999999999999987.77777888888877655.56777777774...4455556666666666662 PP

                          YkyA  95 .edeelkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNesy 159
                                      ++l +e+e+  + ++e  + +d+ly++Y e+++  k++   +    ++l e+e++ e+i ++ 
  gi|14600971|ref|NP_147497.1| 214 eRIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIAMAR-GMELSEVEKRREEIKKKM 278
                                   22247889999999999999999999999999998887777666666.666666666666666655 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 ?   11.2  16.8   0.00067      0.15     212     306 ..       7     101 ..       3     102 .. 0.92
   2 ?    3.2  24.8      0.19        43     165     299 ..     116     255 ..     105     282 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00067
                        HAP1_N 212 seanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaeve 292
                                   +e +++ +el + +++ +ee+ r +ee  +L  ++  l++  ++ + e+ e  ++L++ +e ++++ +EL +l+e  + + 
  gi|14600971|ref|NP_147497.1|   7 AEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTR 87 
                                   555666778888888899*************************************************************** PP

                        HAP1_N 293 gmLheaqeevkelr 306
                                   + L  ++++++ lr
  gi|14600971|ref|NP_147497.1|  88 DELVIKRDQLRVLR 101
                                   *********99988 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                        HAP1_N 165 ldlLqeklreLe..........eeNekLreeasqLktetdtl.EekEqqL.vldcveqlseanqqiaelseelarkleele 233
                                   l  Lq++l+eLe          ee ++L ee s+L++  +++  +kEq L  +++ ++++    ++++l++ +++ ++++ 
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLQELEmmqmtrvlrpEEEKRLVEEISRLEELIERVrKAKEQALsTMELQAEVKALVIKLKDLNQRIDELRQQAG 196
                                   555566666555321111111245555555555554444443134666663355666666666666666666666666666 PP

                        HAP1_N 234 rqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLheaq 299
                                     +ee ++L ++i + ++++k+l++e e+ ++++        +L +E+ +l  ky+ev++ L++ +
  gi|14600971|ref|NP_147497.1| 197 SVKEELATLSSKIEEYNERIKKLSEEIEKRSTRI-------DELSKEIDNLYAKYREVMTRLKDIR 255
                                   6666666666666666666666666666655544.......5788888888888888888887754 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.3    0.0026      0.59      30      91 ..      11      72 ..       4      92 .. 0.85
   2 ?   -0.4   1.6       1.1   2.6e+02      47      94 ..     141     187 ..     109     193 .. 0.63
   3 ?   10.2   2.7    0.0007      0.16      37      96 ..     193     252 ..     183     270 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                          COG6 30 kineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkl 91
                                  k+ ee l+  ++++e++ r++++  kl + ++ ++++ ++a++e ++++e+  +L+ee+kk+
  gi|14600971|ref|NP_147497.1| 11 KEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKI 72
                                  56788899999999999999999999999999999999999999999999999999999887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                          COG6  47 kriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelk 94 
                                   kr+ ++++ l+el+++++k+ ++a  +t +l  e+++L  ++k+l+++
  gi|14600971|ref|NP_147497.1| 141 KRLVEEISRLEELIERVRKAKEQA-LSTMELQAEVKALVIKLKDLNQR 187
                                   455566666666666666554444.44556666666666666666555 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0007
                          COG6  37 eefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqk 96 
                                   ++ + v+e+L +++s++e+ ne ++++++++++ +++ ++l +e+++L ++ +++ ++ k
  gi|14600971|ref|NP_147497.1| 193 QQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLK 252
                                   67899**********************************************999988854 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.4     0.028       6.3     256     347 ..      13     100 ..       3     105 .. 0.77
   2 ?    8.8   5.8    0.0022      0.51     237     331 ..     128     227 ..     101     274 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.028
                          FUSC 256 laallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaaarraer 336
                                    ++ll+++++l  ++   +l+++++ l  +++alr+++ +++  +++ ++ l++l +e   +l++l++l++++++   +  
  gi|14600971|ref|NP_147497.1|  13 EEELLKTIEEL--KEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKK--TRDE 89 
                                   45666666664..34688899999999999999999999999999999999999999999999999999999885..5566 PP

                          FUSC 337 larhrdhlaal 347
                                   l+ +rd l +l
  gi|14600971|ref|NP_147497.1|  90 LVIKRDQLRVL 100
                                   77777766655 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                          FUSC 237 slarllarlr.aeeaaavpe...laallaelaal.eaaaaaealeaalaalrarlralrraleadadtaalllarlaella 312
                                    ++ + + lr +ee++ v+e   l++l+++++++ e+a ++ +l+a+++al  +l++l+++ ++ +++a+ + ++la+l +
  gi|14600971|ref|NP_147497.1| 128 MMQ-MTRVLRpEEEKRLVEEisrLEELIERVRKAkEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSS 207
                                   222.22222202222222234557777777777777778888888888888888888888888888888888888888888 PP

                          FUSC 313 elaqllaslraleaaiaa.a 331
                                   +  + ++ +++l+++i++  
  gi|14600971|ref|NP_147497.1| 208 KIEEYNERIKKLSEEIEKrS 227
                                   88888888888888877631 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  16.5    0.0017      0.39     332     420 ..       6      87 ..       1     101 [. 0.70
   2 ?    7.5   9.8     0.006       1.4     331     412 ..     124     206 ..      96     211 .. 0.83
   3 ?    5.5  10.5     0.025       5.6     335     426 ..     198     281 ..     197     294 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                          FapA 332 epelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskk 412
                                     e+k++ +el + +eel+ee+ +lk++ +kl + +      +  +e+  k+ ++k +++e+l++l+ee+k++ +el++  
  gi|14600971|ref|NP_147497.1|   6 IAEFKKEEEELLKTIEELKEEIVRLKEERRKLIN-E-----VKALREERRKASREKREYVEKLRSLREERKKILDELAQL- 79 
                                   5678888899999999999999999999555554.1.....223567777777777888888888888888777777777. PP

                          FapA 413 eeakikvn 420
                                   +e++ k++
  gi|14600971|ref|NP_147497.1|  80 KEERKKTR 87 
                                   44444433 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.006
                          FapA 331 depelkeklkele.eeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                   +e+e++++++ l+ ee ++l ee+ +l++ i++++k k++   ++e + ++k l  +++ l++++ el+++  ++keel++
  gi|14600971|ref|NP_147497.1| 124 QELEMMQMTRVLRpEEEKRLVEEISRLEELIERVRKAKEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELAT 204
                                   555666666666623445569***************999999*************************************99 PP

                          FapA 411 kk 412
                                    +
  gi|14600971|ref|NP_147497.1| 205 LS 206
                                   83 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.025
                          FapA 335 lkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkeea 415
                                   +ke+l+ l  ++ee++e+++kl ++i+k +  ++ ++l++e+ + ++k++e        ++ l++++ ++   +e ++ e+
  gi|14600971|ref|NP_147497.1| 198 VKEELATLSSKIEEYNERIKKLSEEIEKRST-RI-DELSKEIDNLYAKYREV-------MTRLKDIRIAMARGMELSEVEK 269
                                   5677777777777777777777777666666.33.33344444444444444.......4444444443333333333333 PP

                          FapA 416 .kikvnkeiypg 426
                                    + +++k++ +g
  gi|14600971|ref|NP_147497.1| 270 rREEIKKKMEKG 281
                                   333444444443 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.39        89      25      86 ..      19      80 ..       4      91 .. 0.68
   2 ?    6.0   0.2      0.06        14      23      74 ..     171     222 ..     155     237 .. 0.84
   3 ?   -0.9   0.0       8.7     2e+03      19      46 ..     223     250 ..     219     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.39
                                  SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHHHHHHHT.T. CS
                       PI_PP_I 25 slkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelskaqqellrvlaeak 86
                                  ++++lk ++ ++  + +++ ++   L e+ +k + +k  + + +++l ++++++l  la+ k
  gi|14600971|ref|NP_147497.1| 19 TIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLK 80
                                  45666666666666666666777777777777777788888888888888888877777554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.06
                                   --SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HH CS
                       PI_PP_I  23 easlkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelska 74 
                                   +a++k l  +l ++ ++ +e+++++ s++e+L +++++ + + +  ++ls++
  gi|14600971|ref|NP_147497.1| 171 QAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEE 222
                                   4678889999999*********************999999998888888765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 8.7
                                   --TT--SHHHHHHHHHHHHHHHHHHHHH CS
                       PI_PP_I  19 leskeaslkklkqdlnqfllkWeeikkt 46 
                                   +e++++ + +l +++ ++  k++e+ ++
  gi|14600971|ref|NP_147497.1| 223 IEKRSTRIDELSKEIDNLYAKYREVMTR 250
                                   5666677777777777777777776544 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.3    0.0081       1.8      15      40 ..       5      30 ..       2      47 .. 0.89
   2 ?    1.0   0.4       2.6   5.8e+02      15      36 ..      61      82 ..      49      87 .. 0.86
   3 ?   -0.5   3.0       7.3   1.7e+03       7      25 ..     145     163 ..     104     179 .. 0.67
   4 ?   10.6   4.4    0.0025      0.58       1      38 [.     187     224 ..     187     255 .. 0.82
   5 ?    3.4   0.8      0.44     1e+02      13      32 ..     261     280 ..     250     282 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0081
                     FlaC_arch 15 eletvkkeneelsksveelkenVkdl 40
                                  +++  kke eel k++eelke++ +l
  gi|14600971|ref|NP_147497.1|  5 SIAEFKKEEEELLKTIEELKEEIVRL 30
                                  68899****************99654 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.6
                     FlaC_arch 15 eletvkkeneelsksveelken 36
                                  +l ++++e +++ +++ +lke+
  gi|14600971|ref|NP_147497.1| 61 KLRSLREERKKILDELAQLKEE 82
                                  6889999999999999999986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 7.3
                     FlaC_arch   7 nklsklsteletvkkenee 25 
                                   +++s+l+  +e v+k  e+
  gi|14600971|ref|NP_147497.1| 145 EEISRLEELIERVRKAKEQ 163
                                   4556666666666655555 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.0025
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                   ridel ++ ++++ el+t+ +++ee ++ +++l e+++
  gi|14600971|ref|NP_147497.1| 187 RIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIE 224
                                   78888888888888888888888888888888888874 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.44
                     FlaC_arch  13 steletvkkeneelsksvee 32 
                                    +el+ v+k  ee++k+ e+
  gi|14600971|ref|NP_147497.1| 261 GMELSEVEKRREEIKKKMEK 280
                                   47999999999999999886 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  14.2    0.0057       1.3      63     130 ..      14      81 ..       7      99 .. 0.83
   2 ?    2.6   9.7      0.58   1.3e+02      46     131 ..     117     201 ..     115     203 .. 0.76
   3 ?    8.8  14.6    0.0071       1.6      49     147 ..     155     252 ..     136     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0057
                          ADIP  63 rkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqikt 130
                                   ++l  +ie l+ +i rlk++  +l +e++++ ++ r++ ++ ++  +kl++++ee ++    l+q+k 
  gi|14600971|ref|NP_147497.1|  14 EELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKE 81 
                                   56677899999999999999999999999999999999999999999999999999998888888875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.58
                          ADIP  46 qardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalq 126
                                   ++++r l++ e ++ t+     e +rl  +i+rl++  e+ ++  +++ + + +l++++k+l  klk + + +  l++++ 
  gi|14600971|ref|NP_147497.1| 117 KRLQRRLQELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALS-TMELQAEVKALVIKLKDLNQRIDELRQQAG 196
                                   66677777777777777777778889999999999888887666665554.568999999999999999999999999988 PP

                          ADIP 127 qiktq 131
                                   ++k  
  gi|14600971|ref|NP_147497.1| 197 SVKEE 201
                                   88865 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0071
                          ADIP  49 drdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqik 129
                                   +r ++++e+   t+ +l+ae + l  k + l ++  +l++++ +v++++++l  k+++ ++ +k+++ee+++  + +++++
  gi|14600971|ref|NP_147497.1| 155 ERVRKAKEQALSTM-ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELS 234
                                   55555555555554.588999999999999999999999999999999999999999999999999999999999999999 PP

                          ADIP 130 tqyahelkkkdreiekLk 147
                                   +   +   k    +++Lk
  gi|14600971|ref|NP_147497.1| 235 KEIDNLYAKYREVMTRLK 252
                                   999887777777777777 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  10.3     0.067        15      26      88 ..      14      79 ..       4     120 .. 0.44
   2 ?   10.3  10.6    0.0014      0.31       6      89 ..     169     237 ..     115     255 .. 0.61
   3 ?   11.9   6.0   0.00043     0.098       3      74 ..     187     277 ..     185     288 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.067
                         TMPIT 26 eelsklqskcskeikkqkkrlkelksslkklkks...vkeeeeeeveelkeelkerkkvlkevesl 88
                                  eel k ++++++ei + k++ ++l +++k l+++   +++e++e ve+l++  +erkk+l+e+++l
  gi|14600971|ref|NP_147497.1| 14 EELLKTIEELKEEIVRLKEERRKLINEVKALREErrkASREKREYVEKLRSLREERKKILDELAQL 79
                                  333333333333333333333333333333332211122334444444444444444444433332 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0014
                         TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeve 86 
                                   el+ e+k               l    +++ ++i++ ++++ ++k++l +l++++ ee++e++++l+ee+++r++ ++e++
  gi|14600971|ref|NP_147497.1| 169 ELQAEVK--------------ALVIKLKDLNQRIDELRQQAGSVKEELATLSSKI-EEYNERIKKLSEEIEKRSTRIDELS 234
                                   2333333..............3333344455555555555555555555555554.5666666666666666666666555 PP

                         TMPIT  87 sll 89 
                                   + +
  gi|14600971|ref|NP_147497.1| 235 KEI 237
                                   443 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00043
                         TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...................eee 64 
                                   +++el++++ +++e+  ++ +k+ee+++ ++k+s+ei+k + r+ el++++++l ++ +                   +e 
  gi|14600971|ref|NP_147497.1| 187 RIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYRevmtrlkdiriamargmelSEV 267
                                   567777777777777777777777777777777777777777777777777777776443444444454444444444344 PP

                         TMPIT  65 eeeveelkee 74 
                                   e++ ee+k++
  gi|14600971|ref|NP_147497.1| 268 EKRREEIKKK 277
                                   4444444444 PP

>> DUF3829  Protein of unknown function (DUF3829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   3.5       5.5   1.3e+03     201     237 ..      19      52 ..       4      96 .. 0.39
   2 ?   15.2   9.0   5.1e-05     0.012     135     254 ..     150     265 ..     141     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.5
                       DUF3829 201 aleklekaskeekrkkpalesfkssakeflaaarkii 237
                                   ++e+l++ +   k+   + +++++++k++ ++ rk  
  gi|14600971|ref|NP_147497.1|  19 TIEELKEEIVRLKE---ERRKLINEVKALREERRKAS 52 
                                   33333333222222...11222222222222222222 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.1e-05
                       DUF3829 135 lekvsderekeelekikkdermikyytlklmieakqlidlidrdkitakne.ldlaklkkklddlekaleklekaskeekr 214
                                   le++ ++ +k++ +++   e   +  + +l+i+ k+l++ id+  ++a++  ++la l++k+++++++++kl++ +++   
  gi|14600971|ref|NP_147497.1| 150 LEELIERVRKAKEQALSTME--LQAEVKALVIKLKDLNQRIDELRQQAGSVkEELATLSSKIEEYNERIKKLSEEIEKR-- 226
                                   66666777777777777777..8899999**********************************************7777.. PP

                       DUF3829 215 kkpalesfkssakeflaaarkiirrirdkepysdsdkell 254
                                    ++ ++++ +++ ++ a+ r+ ++r++d  ++  +  el+
  gi|14600971|ref|NP_147497.1| 227 -STRIDELSKEIDNLYAKYREVMTRLKDIRIAMARGMELS 265
                                   .457789999999999999999999998666554444444 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.6      0.62   1.4e+02       3      31 ..      18      46 ..      13      78 .. 0.87
   2 ?    0.8   0.1       1.5   3.3e+02       7      30 ..     169     192 ..     162     194 .. 0.86
   3 ?    7.2   0.7     0.016       3.6       5      44 ..     181     221 ..     177     228 .. 0.67
   4 ?    6.3   0.2     0.031         7       4      64 ..     229     288 ..     227     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.62
                       DUF4988  3 ddvndlkdrvaaleeqvkelndniealkk 31
                                  + +++lk+++  l+e+ ++l ++++al++
  gi|14600971|ref|NP_147497.1| 18 KTIEELKEEIVRLKEERRKLINEVKALRE 46
                                  57999999999999999999999999865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                       DUF4988   7 dlkdrvaaleeqvkelndniealk 30 
                                   +l+ +v+al  ++k+ln+ i+ l+
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELR 192
                                   588899999999999999999886 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.016
                       DUF4988   5 vndlkdrvaaleeqvkelndniealkkll.eegkvitevee 44 
                                   + dl++r+  l +q+ ++++++++l+  + e ++ i +++e
  gi|14600971|ref|NP_147497.1| 181 LKDLNQRIDELRQQAGSVKEELATLSSKIeEYNERIKKLSE 221
                                   67788888888888888888888876544255666655554 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.031
                       DUF4988   4 dvndlkdrvaaleeqvkelndniealkklleegkviteveensdgsyvltlsdgktitltq 64 
                                   ++++l +++  l ++++e+ + ++ ++  +  g  ++eve++ +   + +++ g+ +tl +
  gi|14600971|ref|NP_147497.1| 229 RIDELSKEIDNLYAKYREVMTRLKDIRIAMARGMELSEVEKRREE-IKKKMEKGEPLTLEE 288
                                   89************************9999***********9888.777788888777765 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.5     0.088        20      17      53 ..      18      54 ..      11     105 .. 0.85
   2 ?    0.7   0.6       3.7   8.4e+02       2      10 ..     120     128 ..     112     142 .. 0.63
   3 ?   13.2   1.0   0.00046       0.1       3      53 ..     200     250 ..     198     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.088
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX 17 dtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                  +tieeL +++++  ++  +l  ++++l+e+ ++++ +
  gi|14600971|ref|NP_147497.1| 18 KTIEELKEEIVRLKEERRKLINEVKALREERRKASRE 54
                                  5888888888888888888888888888877665554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 3.7
                                   HHHHHHHHH CS
                          SlyX   2 eerleeLEi 10 
                                   + rl+eLE+
  gi|14600971|ref|NP_147497.1| 120 QRRLQELEM 128
                                   344444444 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00046
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                   e l  L +k+    + i++L++++ +   +id+l ++++ l+ + +e+ ++
  gi|14600971|ref|NP_147497.1| 200 EELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTR 250
                                   678889999999999*****************************9998776 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  36.8     0.044        10       6     227 ..       4     220 ..       2     224 .. 0.73
   2 ?    7.6   9.5    0.0099       2.3      64     166 ..     183     274 ..     179     289 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.044
                       DUF4618   6 ksleelkkheaeLtklnkeLvkeIqdtedstakkvrklLqqyeklktvisileksskkqleqakaeLqeweekeekklekL 86 
                                   +s++e+kk e+eL k+ +eL++eI        ++ rkl++  + l++   + ++++++ +e++++ L e  +k+  +l++L
  gi|14600971|ref|NP_147497.1|   4 RSIAEFKKEEEELLKTIEELKEEIVRLK----EERRKLINEVKALREERRKASREKREYVEKLRS-LREERKKILDELAQL 79 
                                   699*********************9875....5679**************************986.999999********* PP

                       DUF4618  87 eqqleqlnakvqklqeelnvLstYkDkeYp.vkavqIanlvrqlqqlkdsqqdel...deleelikev..leklskkiqkk 161
                                   +++ ++  +++  ++++l vL+   +ke   + ++ ++ l+r lq+l+ +q   +   +e ++l++e+  le+l ++++k 
  gi|14600971|ref|NP_147497.1|  80 KEERKKTRDELVIKRDQLRVLRGLLEKEGGrLAKISLKRLQRRLQELEMMQMTRVlrpEEEKRLVEEIsrLEELIERVRKA 160
                                   ****************************7526779999***********99887622234444443322244454555555 PP

                       DUF4618 162 kekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepr 227
                                   ke+ l+++        q  +++ +++ ++l++ i++ r++    +ee+ +L +++e+ ++++++  
  gi|14600971|ref|NP_147497.1| 161 KEQALSTM---E---LQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLS 220
                                   55555444...3...333444555555555555555555555555555555555555555444333 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0099
                       DUF4618  64 qleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqdeldele 144
                                   +l+q  +eL + +  ++++l+ L  ++e+ n++++kl+ee++            ++ +I +l++++++l ++ ++ +  l+
  gi|14600971|ref|NP_147497.1| 183 DLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIE-----------KRSTRIDELSKEIDNLYAKYREVMTRLK 252
                                   455555555555555555555555555555555555555554...........5677777777777777777777777777 PP

                       DUF4618 145 elikevleklskkiqkkkekll 166
                                   +++ ++   ++ + ++k+++ +
  gi|14600971|ref|NP_147497.1| 253 DIRIAMARGMELSEVEKRREEI 274
                                   7776666666655444443332 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3  16.8      0.44        99      80     164 ..      11      85 ..       2      89 .. 0.43
   2 ?    4.7  11.7      0.16        36      19     109 ..      79     166 ..      76     176 .. 0.77
   3 ?   11.2  12.4    0.0016      0.37      32     141 ..     173     275 ..     163     291 .. 0.46

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.44
                          Fez1  80 seaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeq 160
                                   +e+e l +++e+l+ee+ +l+ee ++        ++e ++ +++r++  +++e ++ ve+lr +L+eer+k  ++ ++ ++
  gi|14600971|ref|NP_147497.1|  11 KEEEELLKTIEELKEEIVRLKEERRK-------LINEVKALREERRK--ASREKREYVEKLR-SLREERKKILDELAQLKE 81 
                                   22222222344444444444443333.......33333333333322..3444444455554.466666666666666666 PP

                          Fez1 161 ERrt 164
                                   ER++
  gi|14600971|ref|NP_147497.1|  82 ERKK 85 
                                   6655 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.16
                          Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikele.esleektlelevcenelqrkkseaellrekvekleeelke 98 
                                   L   + e  +  +e+v  + qlr lr  le++  ++ +++ ++l+ + +ele ++     + +e++ l e++++lee +++
  gi|14600971|ref|NP_147497.1|  79 L---KEERKKTRDELVIKRDQLRVLRGLLEKEGGRLAKISlKRLQRRLQELEMMQMTRVLRPEEEKRLVEEISRLEELIER 156
                                   3...446667779**********************99998356788899***9998766666677777777********** PP

                          Fez1  99 lreelselsle 109
                                   +r++ +++  +
  gi|14600971|ref|NP_147497.1| 157 VRKAKEQAL-S 166
                                   *99766643.3 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0016
                          Fez1  32 eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeee 112
                                   e+ al  +l++l+++++e  +++ +++e+l + + ++e++++++++ ++e e  + ++++l++e+ +l  +++e+ ++ ++
  gi|14600971|ref|NP_147497.1| 173 EVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKD 253
                                   344444455555555555555555555555555555555555555555555555555555555555555555554433333 PP

                          Fez1 113 aa......lesdeakaqrqeaeeleelkreverlr 141
                                    +      +e +e++++r+e             ++
  gi|14600971|ref|NP_147497.1| 254 IRiamargMELSEVEKRREE-------------IK 275
                                   33333333222222222222.............22 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  14.2   0.00039     0.087      42     171 ..     166     289 ..     144     293 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                          TelA  42 dlgevgklLseLvkelkeldpdelkeekklgllplfkkaknkieklfakYekaeeqidkIvkeLekgqdellkdnaaLdql 122
                                   ++ e  + ++ Lv +lk+l+ + ++e++++      +++k++++ l +k e+ +e i k+++e+ek  +++ +  +++d+l
  gi|14600971|ref|NP_147497.1| 166 STMELQAEVKALVIKLKDLNQR-IDELRQQ-----AGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNL 240
                                   3456667788889999999985.7677663.....2358899999999999999999999999999999999999999999 PP

                          TelA 123 yeknleyfkeLeky.iaaGe.kkleeldekllpeleakaeasgdpedaqal 171
                                   y+k +e +++L+   ia+++ ++l e++++  +e+++k e +g+p + ++l
  gi|14600971|ref|NP_147497.1| 241 YAKYREVMTRLKDIrIAMARgMELSEVEKR-REEIKKKME-KGEPLTLEEL 289
                                   999999999998651333331347777755.566666666.5887776666 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 ?    0.8  19.6       2.1   4.8e+02       9      84 ..       7      90 ..       2     131 .. 0.66
   2 ?    3.0  20.4      0.45     1e+02      12      93 ..     178     246 ..     111     289 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.1
                         Mod_r  9 qelledeeklealvktl.pevkqlkeekeellaeneslaeknlsl.ep......eleelrselqekleelkelekefeekeqe 83
                                   e+ ++ee l + +++l +e+ +lkee+ +l++e ++l e+  +  ++      +l+ lr+e ++ l+el++l++e ++   e
  gi|14600971|ref|NP_147497.1|  7 AEFKKEEEELLKTIEELkEEIVRLKEERRKLINEVKALREERRKAsREkreyveKLRSLREERKKILDELAQLKEERKKTRDE 89
                                  56667777777777888777888888888888888888766555533357777788888888888888888888887777666 PP

                         Mod_r 84 l 84
                                  l
  gi|14600971|ref|NP_147497.1| 90 L 90
                                  6 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.45
                         Mod_r  12 ledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfs 92 
                                   +              ++k+l+++ +el+++  s+ e+   l  ++ee  +++++  ee+++ +++ +e+ +e d+l+ k+ 
  gi|14600971|ref|NP_147497.1| 178 V-------------IKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYR 245
                                   2.............2334444444444444444444444444444444444444444444444444444444444444444 PP

                         Mod_r  93 p 93 
                                   +
  gi|14600971|ref|NP_147497.1| 246 E 246
                                   3 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   6.7      0.34        76      45     107 ..      15      80 ..       4      90 .. 0.58
   2 ?    1.5   0.3       1.3   2.9e+02      37      65 ..      63      91 ..      58      99 .. 0.75
   3 ?   11.8   8.2   0.00082      0.19      55     121 ..     168     234 ..     127     243 .. 0.71
   4 ?    5.7   1.3     0.062        14      68     108 ..     216     256 ..     212     282 .. 0.40

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.34
                       DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeis...keikeevtevredlseigedvesvk 107
                                   ++ k +e+++e++ + k++  + i++v +  +e  ++s   +e  e++ ++re+ ++i +++ ++k
  gi|14600971|ref|NP_147497.1|  15 ELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASrekREYVEKLRSLREERKKILDELAQLK 80 
                                   556777777777665555555555555554444444440004455555556666666666666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.3
                       DUF1664 37 rslsdavesvskqleqvseslaatkrhLs 65
                                  rsl++  +++  +l q++e+ ++t+++L 
  gi|14600971|ref|NP_147497.1| 63 RSLREERKKILDELAQLKEERKKTRDELV 91
                                  77888888888888888888888888876 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00082
                       DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    +l+a  + L  +++ +++++de  + + ++kee+++++++++e +e +++++e +e+  +++++++
  gi|14600971|ref|NP_147497.1| 168 MELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELS 234
                                   3456666777777777777777777777777777777777777777777777777777777777765 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.062
                       DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                   i+++ +++++ +  + e+++e++++  + +e+ + ++ ++ 
  gi|14600971|ref|NP_147497.1| 216 IKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRI 256
                                   44444444444444444444444444433333333333332 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   9.8     0.072        16      26     121 ..       9     114 ..       6     124 .. 0.73
   2 ?    8.7  12.7    0.0079       1.8      30     131 ..     140     243 ..     130     249 .. 0.72
   3 ?    7.9   3.8     0.015       3.4      26     108 ..     205     290 ..     203     294 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.072
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHCCCHHHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkd..........ndnvikksskeleeeilrlket 96 
                                   ++k e+++ k++e+l++e+ +++++ ++  + vk++++  r++ ++k++          + + i +   +l+ee  + +++
  gi|14600971|ref|NP_147497.1|   9 FKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREyveklrslreERKKILDELAQLKEERKKTRDE 89 
                                   57899999******************9999999999999999999998855555544432233333333445566666666 PP

                                   HHCCHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  97 idaqesnirvLqnvlesneqkiqkL 121
                                   ++ +  ++rvL+++le+   +++k+
  gi|14600971|ref|NP_147497.1|  90 LVIKRDQLRVLRGLLEKEGGRLAKI 114
                                   7777788888888888887777766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0079
                                   CCCCCHHHCCCCCCCCCCCCHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                     Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvk...eikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                   ek + +++++le+ +e++++ +++a ++++   e+k  + + +  ++     +++ + +++ee ++l  +i +  ++i++L
  gi|14600971|ref|NP_147497.1| 140 EKRLVEEISRLEELIERVRKAKEQALSTMElqaEVKALVIKLKDLNQ-RIDELRQQAGSVKEELATLSSKIEEYNERIKKL 219
                                   56667777888887777777776665554300044444433333333.33344455556788******************* PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 108 qnvlesneqkiqkLeqdidqkerk 131
                                    + +e+ + +i +L ++id++ +k
  gi|14600971|ref|NP_147497.1| 220 SEEIEKRSTRIDELSKEIDNLYAK 243
                                   *******************98765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.015
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCH.HH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn..dnvikksskeleeeilrlketidaqe.sn 103
                                   l+++ ++++++++kl +e+e+ s +  e ++ + +++ ++re  +  kd     +     +e+e++ +++k+++ + e  +
  gi|14600971|ref|NP_147497.1| 205 LSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIriAMARGMELSEVEKRREEIKKKMEKGEpLT 285
                                   455556677777777777777777766666666677777776666666653333334445678888888888887777677 PP

                                   HHHHH CS
                     Fib_alpha 104 irvLq 108
                                   +++L+
  gi|14600971|ref|NP_147497.1| 286 LEELK 290
                                   77776 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4  29.8       7.3   1.7e+03       5     113 ..      11      91 ..       4     127 .. 0.37
   2 ?   11.0  24.7    0.0012      0.28      26     147 ..     151     273 ..     138     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.3
                           ERM   5 rekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklr 85 
                                   +e++el + +++l+ee+ + +e+ r+  ++++ L e++r+a +e+++  +k + ++ee                       
  gi|14600971|ref|NP_147497.1|  11 KEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREE----------------------- 68 
                                   3344444444444444444444444444444444444444444433222222222222....................... PP

                           ERM  86 eaeleaarleeeserkeeeaerLkeele 113
                                         +++ +e  + +ee ++ ++el 
  gi|14600971|ref|NP_147497.1|  69 -----RKKILDELAQLKEERKKTRDELV 91 
                                   .....22222222222222222222222 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0012
                           ERM  26 eaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeae 106
                                   e+L e  ++a++ a +  +++ e + L  k +++++ i++l+++a   +ee + l  k++e+++++++l ee e++    +
  gi|14600971|ref|NP_147497.1| 151 EELIERVRKAKEQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRID 231
                                   4555556666666666667777777777777788*********************************************** PP

                           ERM 107 rLkeeleeareaeeeakekllealstpskses.eenveeset 147
                                   +L +e+ + +++ +e  ++l+++  + ++  + +e +++ e+
  gi|14600971|ref|NP_147497.1| 232 ELSKEIDNLYAKYREVMTRLKDIRIAMARGMElSEVEKRREE 273
                                   ********************9998887554332222222222 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4  12.8      0.54   1.2e+02     240     321 ..       9      90 ..       4      99 .. 0.69
   2 ?   11.0  17.7   0.00068      0.15     182     322 ..     145     279 ..     114     285 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.54
                         IFT57 240 lpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqe 320
                                   +++ +++l k  e++++++ ++++  + l ++++ l +e r+a++e  e  ek++ l e+ ++  +ela+++ee +k+  e
  gi|14600971|ref|NP_147497.1|   9 FKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDE 89 
                                   444566666777777777777776666666677777777777777777777777777777777777777777777777766 PP

                         IFT57 321 m 321
                                   +
  gi|14600971|ref|NP_147497.1|  90 L 90 
                                   5 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00068
                         IFT57 182 kekekeeeiieskvdaaeWklEleRvlpqLkvtikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekie 262
                                   +e+++ ee+ie    a+e  l ++  + + k+ +  + kd  ++++++++   s++e+l +++s++++  e i+k  e+ie
  gi|14600971|ref|NP_147497.1| 145 EEISRLEELIERVRKAKEQALSTMELQAEVKALV-IKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIE 224
                                   5555555555555555555555544444544422.3467888999999999999999999999999999999999999999 PP

                         IFT57 263 srEkyl...nsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322
                                   +r +++    +++++l ++yre+ ++l++++  +    e        l+e++++ e++k++me
  gi|14600971|ref|NP_147497.1| 225 KRSTRIdelSKEIDNLYAKYREVMTRLKDIRIAMARGME--------LSEVEKRREEIKKKME 279
                                   999888333457777888888888888888776655443........3334444444444444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  26.8    0.0067       1.5      48     132 ..       5      89 ..       2      90 .. 0.77
   2 ?    1.8  16.6       1.4   3.1e+02      47     100 ..      53     106 ..      46     133 .. 0.62
   3 ?    2.7  24.2      0.77   1.7e+02      21     128 ..     143     246 ..     113     251 .. 0.91
   4 ?    5.2  11.4      0.13        30      14      80 ..     198     261 ..     196     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0067
                        APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyeh 128
                                   +++e ++e e+l k+ eel ee+ +l++er++l +e++al+ee ++  +e+++++++ ++l+ e ++  +el++l+ + + 
  gi|14600971|ref|NP_147497.1|   5 SIAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKK 85 
                                   567778888888888888888888888888888888888888888888888888888888888888888888888877776 PP

                        APG6_N 129 aqnq 132
                                   ++++
  gi|14600971|ref|NP_147497.1|  86 TRDE 89 
                                   6665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.4
                        APG6_N  47 eeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                    e +e  e+l+ l++e+++ l eL++l++er++ ++el   + +l+ l    e+
  gi|14600971|ref|NP_147497.1|  53 REKREYVEKLRSLREERKKILDELAQLKEERKKTRDELVIKRDQLRVLRGLLEK 106
                                   344555666777888888888888888888888887777777777766655554 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.77
                        APG6_N  21 aekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                   + +e+  +ee  ++++k k+++     ++ el+ e+++l  + ++l + ++el ++  ++++ela+l+++ e+ +e  ++ 
  gi|14600971|ref|NP_147497.1| 143 LVEEISRLEELIERVRKAKEQAL----STMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKL 219
                                   66788999999999999977766....8899************************************************99 PP

                        APG6_N 102 wreynelqlelleleeeldsleaqyeh 128
                                    +e  + ++   el +e d l a+y+ 
  gi|14600971|ref|NP_147497.1| 220 SEEIEKRSTRIDELSKEIDNLYAKYRE 246
                                   999999**************9999975 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.13
                        APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereel 80 
                                   ++++l+++ +++++Y+e  kkl +e ++ +   + ++el +e+++l ++ +e ++ Lk++  + ++ 
  gi|14600971|ref|NP_147497.1| 198 VKEELATLSSKIEEYNERIKKLSEEIEKRS---TRIDELSKEIDNLYAKYREVMTRLKDIRIAMARG 261
                                   578999999999999999999999977765...7889999998888888888888888776554432 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   6.7      0.38        87     238     305 ..      14      85 ..       5     106 .. 0.45
   2 ?    5.1   6.8     0.046        10      84     175 ..     116     207 ..     110     220 .. 0.53
   3 ?   10.9   4.6    0.0008      0.18     245     319 ..     214     280 ..     198     297 .] 0.46

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH CS
                         APG17 238 aeledVvkelqerleem....ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeefler 305
                                   +el + ++el+e++  +     k  +++++ +ee +k++++ ++ +e+l++++++ +++l  +++ +e +++
  gi|14600971|ref|NP_147497.1|  14 EELLKTIEELKEEIVRLkeerRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKK 85 
                                   344444444444444444333333333333334444444444444444444444444444433333333333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.046
                                   HHHHHHHHHHHHTSS-TTS.......STGGGCS--TTTTHHHHHHHHH......HHHHHHHHHHHHTTHH..HHHHHHHHH CS
                         APG17  84 nerLektlekLrktkvepsfrpegeektLlDFvdedsveelkealkes......idelqaaqkkldssllefdtdlrelkk 158
                                    +rL++ l++L+ ++   ++rpe+ ek L + +++   eel e++++       + elqa  k l  +l+ ++++++el++
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLQELEMMQMTRVLRPEE-EKRLVEEISR--LEELIERVRKAkeqalsTMELQAEVKALVIKLKDLNQRIDELRQ 193
                                   689******************999.9999998873..45555555444222245333333333333333333333333333 PP

                                   HH.-------STCCHHHH CS
                         APG17 159 el.sksksksessslipe 175
                                   +  s     +e+ +++++
  gi|14600971|ref|NP_147497.1| 194 QAgS----VKEELATLSS 207
                                   3321....1122222222 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0008
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHH CS
                         APG17 245 kelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieeklee 319
                                   + +++  ee+ek + +++e  +ei++l+++ ++++++l++++ ++++ ++     +e+    e+ +e+i++k+e+
  gi|14600971|ref|NP_147497.1| 214 ERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIAMARGME----LSEV----EKRREEIKKKMEK 280
                                   23333344445555555555555555555555555555555555555444....3333....4444444444443 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 ?   14.8   5.3     9e-05      0.02       2      79 ..     182     262 ..     181     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9e-05
                    STAT_alpha   2 qeieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlna....LdqkRkelvdk 78 
                                   ++++qr++elr++   +++++ +L ++ ee++ ++++l+++  e++++   el+k+ ++l +  ++    L++ R +++  
  gi|14600971|ref|NP_147497.1| 182 KDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEI-EKRSTRIDELSKEIDNLYAKYREvmtrLKDIRIAMARG 261
                                   5899**********************************9993.33344444477777777774444333366666665554 PP

                    STAT_alpha  79 l 79 
                                   +
  gi|14600971|ref|NP_147497.1| 262 M 262
                                   4 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 ?    6.8   9.2     0.025       5.7      29     101 ..      16      88 ..       6      96 .. 0.79
   2 ?   -1.5  10.8       9.4   2.1e+03      18      93 ..     116     195 ..     110     211 .. 0.51
   3 ?    9.3   4.7    0.0042      0.95      19      91 ..     182     253 ..     178     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.025
                          SKA2  29 fqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasaelpplsee 101
                                   + +  ++ +e+ v+L e+ +k+ +e++aL+e+ ++ + ek+e ++k+r+   + +++l +L +  e   ++++
  gi|14600971|ref|NP_147497.1|  16 LLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRD 88 
                                   4445555558899999999999999999999999999999999999999999999999998876666555544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 9.4
                          SKA2  18 LdyvqhrL.ekefqqsypdna....eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa 93 
                                   L+ +q+rL e e++q ++       + +v+ ++rl+++ e++ + keq+    + + e+ +++  +l +  + + +L+++a
  gi|14600971|ref|NP_147497.1| 116 LKRLQRRLqELEMMQMTRVLRpeeeKRLVEEISRLEELIERVRKAKEQALSTMELQAEV-KALVIKLKDLNQRIDELRQQA 195
                                   66677777334666665544441123344444444444555555555555554444443.334444555555555555555 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0042
                          SKA2  19 dyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqa 91 
                                   + +++r ++  qq+ + + e++++L +++++ +e++++L+e++e+ +++  el ++i +  ++ re++++L+ 
  gi|14600971|ref|NP_147497.1| 182 KDLNQRIDELRQQAGSVK-EELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKD 253
                                   555666665556666665.7************************************************99985 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.3    0.0083       1.9      24      54 ..      18      47 ..       3      62 .. 0.56
   2 ?    3.2   4.2      0.34        77      18      47 ..      61      90 ..      56      99 .. 0.84
   3 ?    0.7   1.1       1.9   4.4e+02      32      52 ..     139     159 ..     115     164 .. 0.75
   4 ?    3.1  13.2      0.36        81      18      60 ..     187     226 ..     160     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0083
                                  HHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                         DivIC 24 qeiaalqaelaklkaeneeLeaevkdLksde 54
                                  + i++l++e+++lk+e+++L  evk L+ +e
  gi|14600971|ref|NP_147497.1| 18 KTIEELKEEIVRLKEERRKLINEVKALR-EE 47
                                  4455555555555555555555555554.22 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.34
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         DivIC 18 aykqlkqeiaalqaelaklkaeneeLeaev 47
                                  ++++l++e++++ +ela+lk+e+++  +e+
  gi|14600971|ref|NP_147497.1| 61 KLRSLREERKKILDELAQLKEERKKTRDEL 90
                                  578899999999999999999999988775 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHHHHCC-XX CS
                         DivIC  32 elaklkaeneeLeaevkdLks 52 
                                   e ++l +e+ +Le+ +++ ++
  gi|14600971|ref|NP_147497.1| 139 EEKRLVEEISRLEELIERVRK 159
                                   566777777777777777765 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.36
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                         DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                   ++ +l+q+    ++ela+l+ ++ee ++++k+L+   + ie+r
  gi|14600971|ref|NP_147497.1| 187 RIDELRQQAGSVKEELATLSSKIEEYNERIKKLS---EEIEKR 226
                                   5667777777777777777777777777777775...555555 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 ?    3.7  14.7      0.18        40      70     145 ..      10      85 ..       2     107 .. 0.83
   2 ?   -0.7   1.3       3.9   8.8e+02      95     112 ..     117     134 ..     102     163 .. 0.49
   3 ?   11.4  12.1   0.00075      0.17      52     148 ..     153     235 ..     138     253 .. 0.51
   4 ?    8.4   3.3    0.0061       1.4      52     131 ..     201     280 ..     200     285 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                  HAUS-augmin3  70 evileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetna 145
                                   +++ ee+ +++e+L++e+  L++e++ ++++ + L     ++++e+r+  e+  + +++ k++ +el++   e ++
  gi|14600971|ref|NP_147497.1|  10 KKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKK 85 
                                   5667788889999999999999999999999999999999999999999999999999999999988887666554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.9
                  HAUS-augmin3  95 alklkrlnkLqvqaaslq 112
                                   +++++rl++L+++ +++ 
  gi|14600971|ref|NP_147497.1| 117 KRLQRRLQELEMMQMTRV 134
                                   344555555555544432 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00075
                  HAUS-augmin3  52 aLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkea 132
                                     +++ + +              e+  s+ +L++e+++L    + +++r ++L  qa s ++el +l+++ +e ++++k++
  gi|14600971|ref|NP_147497.1| 153 LIERVRKAK--------------EQALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKL 219
                                   333333333..............3344555556666666555555556666666666666666666666666666666666 PP

                  HAUS-augmin3 133 qeelraenaetnavLq 148
                                    ee+++++ +++++ +
  gi|14600971|ref|NP_147497.1| 220 SEEIEKRSTRIDELSK 235
                                   6666555555543322 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0061
                  HAUS-augmin3  52 aLktiepsdlkq.edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklke 131
                                    L t++++ +++ e  ++l++++e+  + + +L +e+++L    +    rl+ + ++ +++  el+++e++ +e kkk+++
  gi|14600971|ref|NP_147497.1| 201 ELATLSSKIEEYnERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVMTRLKDIRIA-MARGMELSEVEKRREEIKKKMEK 280
                                   5778887777777999**************************************875.56778899999999999999987 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       2.3   5.2e+02       5      22 ..      13      30 ..       4      64 .. 0.64
   2 ?   -0.5   0.8       5.9   1.4e+03       7      61 ..      71     126 ..      65     159 .. 0.64
   3 ?    2.4   3.6      0.78   1.8e+02      32      69 ..     169     206 ..     119     207 .. 0.72
   4 ?    9.8   0.9    0.0038      0.86      22      68 ..     180     226 ..     159     249 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.3
                     MbeD_MobD  5 ekqLLsAlEqLQqdYeqr 22
                                  e++LL  +E+L ++  + 
  gi|14600971|ref|NP_147497.1| 13 EEELLKTIEELKEEIVRL 30
                                  455555555555544333 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 5.9
                     MbeD_MobD   7 qLLsAlEqLQqdYeqrlqeWesafaelqrmfeltqrenaaLse.qvtgLsqQVesL 61 
                                   ++L  l qL ++ ++ ++e      +l+ + +l ++e + L +   ++L +  ++L
  gi|14600971|ref|NP_147497.1|  71 KILDELAQLKEERKKTRDELVIKRDQLRVLRGLLEKEGGRLAKiSLKRLQRRLQEL 126
                                   56666666666666666666666666666666666666655431445555555555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.78
                     MbeD_MobD  32 elqrmfeltqrenaaLseqvtgLsqQVesLseqvrRls 69 
                                   elq+ ++    ++  L++++++L qQ  s  e+++ ls
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLS 206
                                   44444444444445899999999999999888888777 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0038
                     MbeD_MobD  22 rlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                   +l++ ++   el++  +  + e+a Ls ++++    +++Lse++++ 
  gi|14600971|ref|NP_147497.1| 180 KLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKR 226
                                   55666666778999999999999999999999999999999888765 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1  10.8      0.32        72     330     397 ..      20      89 ..      15      96 .. 0.72
   2 ?   -0.7   0.5       2.2   5.1e+02     357     399 ..     124     162 ..     104     168 .. 0.44
   3 ?   14.1   3.7   7.5e-05     0.017     331     411 ..     168     250 ..     164     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.32
                                   -TTHHHHHHHHHHTHHH..HHHHHHHHHHHHHHHHHHHHHHHT.TTHHHHHHHHHHHHHHHHHHHHHHHH CS
                   5_nucleotid 330 vpELeeElevleekkek..eeleelekleelledelkklksseeeskekleeleedleelkkeirelree 397
                                   ++EL+eE+  l+e+++k  +e++ l++++++ ++e +++  + ++ +e+ +++ ++l +lk+e++++r+e
  gi|14600971|ref|NP_147497.1|  20 IEELKEEIVRLKEERRKliNEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDE 89 
                                   89*******9999996666666666666666666555555554446667777888888888888888776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                                   HHHHHHHHHHHHHT.T..THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   5_nucleotid 357 elledelkklksseee..skekleeleedleelkkeirelreelk 399
                                   ++le     ++++  +    e+ ++l e++++l++ i+++r++ +
  gi|14600971|ref|NP_147497.1| 124 QELEM----MQMT--RvlRPEEEKRLVEEISRLEELIERVRKAKE 162
                                   22222....2222..122233334444444444444444444433 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 7.5e-05
                                   TTHHHHHHHHHHTHHH..HHHHHHHHHHHHHHHHHHHHHHHT.TTHHHHHHHHHHHHHHHHHHHHHHHHHHCCS-TTT--S CS
                   5_nucleotid 331 pELeeElevleekkek..eeleelekleelledelkklksseeeskekleeleedleelkkeirelreelkelfnkqfGsl 409
                                    EL++E+++l  k +   ++++el+++  ++++el +l+s+ ee +e+ ++l+e++e+  ++i+el++e+++l+ k+   +
  gi|14600971|ref|NP_147497.1| 168 MELQAEVKALVIKLKDlnQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAKYREVM 248
                                   599****99877766667***********************9999*****************************8877666 PP

                                   SE CS
                   5_nucleotid 410 fr 411
                                    r
  gi|14600971|ref|NP_147497.1| 249 TR 250
                                   65 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.8    0.0099       2.3       4      49 ..       5      50 ..       3      53 .. 0.91
   2 ?    2.0   5.2         1   2.4e+02       9      54 ..      45      90 ..      41      98 .. 0.86
   3 ?    4.3   0.9       0.2        45      15      35 ..     143     163 ..     136     169 .. 0.81
   4 ?   10.4   8.9    0.0026      0.59       7      95 ..     169     260 ..     166     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0099
                       DUF5082  4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkk 49
                                  +i++ +++ +el ++i+ l e I rLke ++kl  e ++l ++++k
  gi|14600971|ref|NP_147497.1|  5 SIAEFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRK 50
                                  799999****************************999999988876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1
                       DUF5082  9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekpl 54
                                  +++  +++ e + + ek++ L+e ++k+ de ++lk+++kk ++ l
  gi|14600971|ref|NP_147497.1| 45 REERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRDEL 90
                                  556667788999999************************9998765 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.2
                       DUF5082  15 lrseiaaleekIerLkeaktk 35 
                                   l +ei+ lee Ier ++ak++
  gi|14600971|ref|NP_147497.1| 143 LVEEISRLEELIERVRKAKEQ 163
                                   678999999999999999976 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0026
                       DUF5082   7 klqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse.sWkGk.eennydgirs.nlessyqtyvd 84 
                                   +lqa++  l  ++++l++ I +L++   ++++e ++l++k+++ ++ + + + +  ++ ++ ++ +++  nl+ +y+++ +
  gi|14600971|ref|NP_147497.1| 169 ELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSeEIEKRsTRIDELSKEIdNLYAKYREVMT 249
                                   58999999****************9999999999999999988887665544355555577777777779*********** PP

                       DUF5082  85 kldelidaiee 95 
                                   +l+++  a+ +
  gi|14600971|ref|NP_147497.1| 250 RLKDIRIAMAR 260
                                   ****9999874 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  42.7    0.0057       1.3      45     242 ..       8     214 ..       2     219 .. 0.90
   2 ?    6.3  11.7     0.011       2.6     126     215 ..     180     276 ..     179     290 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0057
                           MAD  45 eesdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekqel 125
                                   e ++ ++el+k i++l+++    +e+ r+ i ++++++    +++++++e  +kl ++re  +++ +ela+lk++ +k+  
  gi|14600971|ref|NP_147497.1|   8 EFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQLKEERKKTRD 88 
                                   45567899************999999******************************************************* PP

                           MAD 126 elsekeseleelqerldllkkklseleqli.....qqlekkqkelaeaeqrikeLefeiqsqeddslivknskselaripe 201
                                   el  k+ +l+ l+  l+ +  +l++++ ++     q+le+ q ++  + +  k L  ei+  e+  + v+++k++ ++  e
  gi|14600971|ref|NP_147497.1|  89 ELVIKRDQLRVLRGLLEKEGGRLAKISLKRlqrrlQELEMMQMTRVLRPEEEKRLVEEISRLEELIERVRKAKEQALSTME 169
                                   *****************999999999888778888********************************************** PP

                           MAD 202 lekele....rlreenkklnelkenkelLkEevedlkkkLereEk 242
                                   l++e++    +l+  n+++ el+++ + +kEe++ l +k+e + +
  gi|14600971|ref|NP_147497.1| 170 LQAEVKalviKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNE 214
                                   ****99222235666777778889999************998754 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.011
                           MAD 126 elsekeseleelqerldllkkklseleqliqqlekkqkelaea....eqrikeLefeiqs....qeddslivknskselar 198
                                   +l+  ++ + el+++    k++l+ l+ +i++++++ k+l+e+      ri eL+ ei +    + +    +k+++  +ar
  gi|14600971|ref|NP_147497.1| 180 KLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEiekrSTRIDELSKEIDNlyakYREVMTRLKDIRIAMAR 260
                                   566777777777777777777777777777777766666554411114578888888877744455555555666666666 PP

                           MAD 199 ipelekelerlreenkk 215
                                     el +e+e+ ree+kk
  gi|14600971|ref|NP_147497.1| 261 GMEL-SEVEKRREEIKK 276
                                   5555.466666777665 PP

>> PRANC  PRANC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4       6.7   1.5e+03      46      59 ..      29      42 ..       9      87 .. 0.66
   2 ?   10.1   1.0    0.0035      0.79      32      68 ..     207     243 ..     189     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 6.7
                         PRANC 46 ksakkrykliekai 59
                                  +  ++r+kli+++ 
  gi|14600971|ref|NP_147497.1| 29 RLKEERRKLINEVK 42
                                  44445555555443 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0035
                         PRANC  32 kslkiYgklikkiiksakkrykliekaievlnnicsk 68 
                                   +++  Y+++ikk+ ++++kr++ i+++++ ++n+  k
  gi|14600971|ref|NP_147497.1| 207 SKIEEYNERIKKLSEEIEKRSTRIDELSKEIDNLYAK 243
                                   37888***************************98776 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 ?   10.3  10.4    0.0017      0.39     138     225 ..      16      98 ..       4     102 .. 0.79
   2 ?   -0.3  16.9       2.9   6.5e+02     139     224 ..     164     247 ..     116     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0017
                       HAUS6_N 138 askkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeasedaee 218
                                   + k+ ++l++ + + + ++r++++e++a  + r+k +++ +++++k r+lr+e++++ +el        ke+++++ d++ 
  gi|14600971|ref|NP_147497.1|  16 LLKTIEELKEEIVRLKEERRKLINEVKALREERRKASREKREYVEKLRSLREERKKILDELAQ-----LKEERKKTRDELV 91 
                                   45667799999******************99****************************9973.....2333333444455 PP

                       HAUS6_N 219 ekikkvr 225
                                   +k++++r
  gi|14600971|ref|NP_147497.1|  92 IKRDQLR 98 
                                   5655555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.9
                       HAUS6_N 139 skkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeasedaeee 219
                                   + ++ +l++ v+a  ++l+ + +++ +  +    ++e+++ l+ k++e ++++++l++e++  k++ ++ ++ +++d++ +
  gi|14600971|ref|NP_147497.1| 164 ALSTMELQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIE--KRSTRIDELSKEIDNLYA 242
                                   3334455555666666666666666666656666777777777777777777777777666..555555666556655555 PP

                       HAUS6_N 220 kikkv 224
                                   k+++v
  gi|14600971|ref|NP_147497.1| 243 KYREV 247
                                   55555 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   6.5       0.1        23      51     126 ..       8      75 ..       4      99 .. 0.60
   2 ?    5.9   8.4     0.053        12      38     134 ..     170     230 ..     141     288 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.1
                        GldM_N  51 evkkksdelynyiealKeeivkeaggkdedvgeikakd.nldaaselmlaegksgkGkeLkkkineyreellklvnd 126
                                   e kk+ +el ++ie+lKeeiv+  +++ +  +e+ka   +  +as+    e+      e  +k+ + ree +k++++
  gi|14600971|ref|NP_147497.1|   8 EFKKEEEELLKTIEELKEEIVRLKEERRKLINEVKALReERRKASR----EK-----REYVEKLRSLREERKKILDE 75 
                                   6789999**************9999876666666665412222222....22.....45555555555555555555 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.053
                        GldM_N  38 npekakewlekAkevkkksdelynyiealKeeivkeaggkdedvgeikakdnldaaselmlaegksgkGkeLkkkineyre 118
                                    ++++k+++ k k++++  del ++  ++Kee+++ +                                     ki+ey e
  gi|14600971|ref|NP_147497.1| 170 LQAEVKALVIKLKDLNQRIDELRQQAGSVKEELATLSS------------------------------------KIEEYNE 214
                                   23334444444444444444444444444444444444....................................4444444 PP

                        GldM_N 119 ellklvndlakdakli 134
                                   +++kl ++++k+ + i
  gi|14600971|ref|NP_147497.1| 215 RIKKLSEEIEKRSTRI 230
                                   4444444433333222 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   3.0       4.5     1e+03      36      81 ..      17      61 ..       8      79 .. 0.49
   2 ?   12.6   4.1   0.00071      0.16      26      98 ..     171     239 ..     154     240 .. 0.87
   3 ?    4.1   0.2      0.31        70      27      63 ..     242     280 ..     239     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 4.5
                       DUF4665 36 LKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkk 81
                                  LK i+   ke + +l ++  ++ +++k+l ++ ++ +++k++ ++k
  gi|14600971|ref|NP_147497.1| 17 LKTIEEL-KEEIVRLKEERRKLINEVKALREERRKASREKREYVEK 61
                                  4444333.33344455555555555555555444444444444433 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00071
                       DUF4665  26 KaKAkpVttnLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaaellaq 98 
                                    a  k+ + +LK +    ++++ +l ++   ++++l+ ls+k++  +++ +k++++ ek+++ +de  +++ +
  gi|14600971|ref|NP_147497.1| 171 QAEVKALVIKLKDL----NQRIDELRQQAGSVKEELATLSSKIEEYNERIKKLSEEIEKRSTRIDELSKEIDN 239
                                   55667788888888....89*********************************************99888876 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.31
                       DUF4665  27 aKAkpVttnLKkinav..kkekvenldkalvdiqkdlks 63 
                                   aK + V t LK i +   +    ++++k  ++i+k++++
  gi|14600971|ref|NP_147497.1| 242 AKYREVMTRLKDIRIAmaRGMELSEVEKRREEIKKKMEK 280
                                   68899******9988744666788999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3249  (0.181215); expected 358.6 (0.02)
Passed bias filter:                      935  (0.0521501); expected 358.6 (0.02)
Passed Vit filter:                       330  (0.0184059); expected 17.9 (0.001)
Passed Fwd filter:                       234  (0.0130515); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              79  [number of targets reported over threshold]
# CPU time: 2.62u 0.35s 00:00:02.97 Elapsed: 00:00:00.61
# Mc/sec: 1457.69
//
Query:       gi|118431199|ref|NP_147498.2|  [L=262]
Description: GTPase [Aeropyrum pernix K1]
Scores for 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-61  206.4   0.0    6.6e-61  206.2   0.0    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    2.1e-05   25.0   0.0    7.9e-05   23.1   0.0    1.8  2  AAA_16           AAA ATPase domain
    0.00017   20.7   0.2     0.0003   19.8   0.2    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00034   21.1   0.0    0.00064   20.3   0.0    1.5  1  AAA_18           AAA domain
     0.0012   18.7   0.0        0.1   12.3   0.0    2.4  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0017   18.4   0.0     0.0081   16.2   0.0    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0034   17.1   0.1     0.0068   16.1   0.0    1.6  2  AAA_30           AAA domain
     0.0076   16.2   0.1       0.18   11.7   0.1    2.2  2  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.025   14.6   0.0    1.4  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.02   15.1   0.0      0.038   14.2   0.0    1.5  1  AAA_28           AAA domain
      0.032   13.4   0.3      0.056   12.6   0.3    1.3  1  ArsA_ATPase      Anion-transporting ATPase
      0.036   13.3   0.0      0.059   12.6   0.0    1.3  1  Zeta_toxin       Zeta toxin
      0.044   11.7   0.3      0.057   11.3   0.3    1.1  1  Herpes_Helicase  Helicase
      0.048   13.6   0.0       0.13   12.2   0.0    1.6  2  APS_kinase       Adenylylsulphate kinase
      0.055   13.2   0.5       0.11   12.3   0.5    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.056   13.4   0.3       0.48   10.3   0.2    2.3  3  RsgA_GTPase      RsgA GTPase
      0.061   13.4   0.0        0.1   12.7   0.0    1.4  1  DUF87            Helicase HerA, central domain
      0.079   13.0   0.9       0.89    9.6   0.2    2.1  2  Dynamin_N        Dynamin family
      0.079   13.4   0.8        0.2   12.2   0.8    1.7  1  Rnk_N            Rnk N-terminus
       0.13   12.2   0.2       0.24   11.3   0.2    1.4  1  NACHT            NACHT domain
       0.17   11.0   0.0       0.26   10.4   0.0    1.2  1  DUF815           Protein of unknown function (DUF815)
       0.22   10.7   0.0       0.28   10.4   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
        2.1    7.8   4.1        2.1    7.8   0.4    2.4  3  ParA             NUBPL iron-transfer P-loop NTPase


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 !  206.2   0.0   8.4e-64   6.6e-61       1     239 [.       7     248 ..       7     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 8.4e-64
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresld 80 
                                    v+G+aG+GK+++vgal++ +++ g +va++NLDPAae+lpY+++vd r++++++++m++ glgpngalv a++ l +++ 
  gi|118431199|ref|NP_147498.2|   7 VTGTAGAGKSSLVGALADRITSLGANVATLNLDPAAEKLPYDPSVDARDYVSVAELMDK-GLGPNGALVAAVDSLINHVL 85 
                                    89*******************************************************99.*******************8 PP

                     ATP_bind_1  81 wldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhv 160
                                    +++ee++ ++ dy+++DtPGQ+elf ++  +  +++ ++ +++ v ++L+Ds +++++++++s+ll+a+s+ +rl+lP+v
  gi|118431199|ref|NP_147498.2|  86 DIREEIDYYSPDYVVVDTPGQLELFAYRVGGPLVLRGIMGDYNGVNIFLIDSIFIDNAISLVSALLLASSVAVRLGLPQV 165
                                    89****76799********************************************************************* PP

                     ATP_bind_1 161 vvlnkfDllkek.lekeleffedvealslllekee...ekykklaeaiaelleefalvlrflplssekeesiedllslid 236
                                    ++++k+D+l  + +e+ + ++ ++  l+ llek++   ++ k lae++a+++e+++ + ++l++s+ + e+++ l ++ +
  gi|118431199|ref|NP_147498.2| 166 NAVSKADMLLPEvREEVIPRLGEPGFLEFLLEKDKtyeGAGKALAEELARAIETTGFIGEVLQASVLEPETVTLLAAKAQ 245
                                    **********999**********************9999999**********************************9999 PP

                     ATP_bind_1 237 eal 239
                                    ++l
  gi|118431199|ref|NP_147498.2| 246 QIL 248
                                    886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     1e-07   7.9e-05      26      80 ..       4      57 ..       2      97 .. 0.84
   2 ?   -0.9   0.0       2.3   1.8e+03      35      52 ..     205     221 ..     179     250 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-07
                         AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalaree 80
                                   +++++G +G GKsslv +l+++++  g+ +++ + d   +++py++ ++a +   
  gi|118431199|ref|NP_147498.2|  4 YIIVTGTAGAGKSSLVGALADRITSLGANVATLNLDPAAEKLPYDPSVDARDY-V 57
                                   689***********************************9*****998888755.3 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.3
                         AAA_16  35 vGKsslvrellralekdg 52 
                                     GK +l++el+ra+e++g
  gi|118431199|ref|NP_147498.2| 205 AGK-ALAEELARAIETTG 221
                                    333.45555555555442 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 !   19.8   0.2   3.9e-07    0.0003      33      69 ..       6      42 ..       2      45 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.9e-07
                                   EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                           MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                    +tG+ GaGks lv al+ ++++ G  va l +DP++
  gi|118431199|ref|NP_147498.2|  6 IVTGTAGAGKSSLVGALADRITSLGANVATLNLDPAA 42
                                   59*********************************87 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   8.2e-07   0.00064       1      43 [.       5      68 ..       5     128 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.2e-07
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdp 43
                                   I++tGt+G+GK++l  +L++r   +                    +v  rd+++  +l +    
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRItSLganvatlnldpaaeklpydpSVDARDYVSVAELMDKGLG 68
                                   9******************996333556665555666666666666666666666555555444 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   0.00013       0.1       1      34 [.       9      42 ..       9      51 .. 0.92
   2 ?    3.7   0.0      0.06        46      81     119 ..      74     112 ..      69     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34
                                   G   +GKS+l+  L++++++ g +++ ++lD+  
  gi|118431199|ref|NP_147498.2|  9 GTAGAGKSSLVGALADRITSLGANVATLNLDPAA 42
                                   67889**************************975 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.06
                         CLP1_P  81 lalvkelareveekleenkkakasgliIntpGwvkglga 119
                                    +a+v++l+++v    ee + +  + ++++tpG  + +++
  gi|118431199|ref|NP_147498.2|  74 VAAVDSLINHVLDIREEIDYYSPDYVVVDTPGQLELFAY 112
                                    6889999***99999999999***********8876665 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     1e-05    0.0081       2      57 ..       5     107 ..       4     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke................................. 47 
                                    +++ G   +GKS+L+ al ++ ++  ++ +   +d+  +++ ++  +                                 
  gi|118431199|ref|NP_147498.2|   5 IIVTGTAGAGKSSLVGALADRiTSLGANVATLNLDPAAEKLPYDP-Svdardyvsvaelmdkglgpngalvaavdslinh 83 
                                    7899*****************778889*********999998542.2345667777777777777788888888888888 PP

                                    ..............EEEEECGGCS CS
                       MMR_HSR1  48 ..............ielvDtpGli 57 
                                                  +++vDtpG +
  gi|118431199|ref|NP_147498.2|  84 vldireeidyyspdYVVVDTPGQL 107
                                    888888888888889999999954 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.7e-06    0.0068      21      56 ..       5      40 ..       3     105 .. 0.82
   2 ?   -2.7   0.1       5.1     4e+03      28      47 ..     204     235 ..     202     247 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.7e-06
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAptg 56
                                    ++tG AG+GK+ +++al++ +++ g +v+ l    
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSLGANVATLNLDP 40
                                   689***********************9999886554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                         AAA_30  28 GtGKttalkalreaweaag.............g 47 
                                    G+GK  a ++l++a+e+ g             +
  gi|118431199|ref|NP_147498.2| 204 GAGKALA-EELARAIETTGfigevlqasvlepE 235
                                    5666443.4445555555544444444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00023      0.18       2      31 ..       5      34 ..       4      39 .. 0.93
   2 ?    2.1   0.0       0.2   1.6e+02      72     111 ..      71     111 ..      51     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   +++TG  G GK+ lv  +++ + s g +v+
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSLGANVA 34
                                   89********************99999885 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.2
                                    TTEEE-HHHHHHHHHHHHHHHH.HHH-EEEE---STTGGG- CS
                       NTPase_1  72 gkyvvdvesfeelalealrkal.seadviviDEiGkmElks 111
                                    g  v  v+s+ + +l++ ++ +  ++d +v+D  G++El++
  gi|118431199|ref|NP_147498.2|  71 GALVAAVDSLINHVLDIREEIDyYSPDYVVVDTPGQLELFA 111
                                    666666777777666666655578999************97 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.3e-05     0.025       2      44 ..       5      47 ..       4     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-05
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai 44
                                   +i+ ++ G+GK++l+ +La  +   g +V+ + +Dp a+ l +
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSLGANVATLNLDPAAEKLPY 47
                                   79999********************************888773 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.9e-05     0.038       2      26 ..       5      29 ..       4      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
                         AAA_28  2 ivitGgestGKTtlleaLaargypv 26
                                   i++tG+ ++GK++l+ aLa+r ++ 
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSL 29
                                   89*****************984443 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   7.1e-05     0.056       3      41 ..       4      42 ..       2      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTT CS
                    ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAh 41
                                   +i+v+G  G GK+++  a+a +++  g +v  + +DPA 
  gi|118431199|ref|NP_147498.2|  4 YIIVTGTAGAGKSSLVGALADRITSLGANVATLNLDPAA 42
                                   79***********************************95 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.6e-05     0.059      19      57 ..       5      44 ..       3      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                     Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnvvrldpDdlRel 57
                                   i++ G  GAGKs+l  +l+d+++  + nv +l+ D   e 
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITsLGANVATLNLDPAAEK 44
                                   899*******************978999999999976555 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   7.4e-05     0.057      62      86 ..       5      29 ..       2      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.4e-05
                Herpes_Helicase 62 ylitGtAGaGkstsiqalaenldCl 86
                                    ++tGtAGaGks+ + ala+ +  l
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSL 29
                                   579***************9987654 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.13       5      45 ..       5      45 ..       3      64 .. 0.86
   2 ?   -2.4   0.0         5   3.9e+03      11      36 ..     203     227 ..     201     234 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTT CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgL 45
                                   + +tG +g+GKs++  al+ ++++ g +v +L+ d   ++L
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSLGANVATLNLDPAAEKL 45
                                   789**************************999877666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                                    TTSSHHHHHHHHHHHHHHTT--EEEE CS
                     APS_kinase  11 sgsGKstianalekkLvekgisvylL 36 
                                     g+GK ++a++l+++++++g   ++L
  gi|118431199|ref|NP_147498.2| 203 EGAGK-ALAEELARAIETTGFIGEVL 227
                                    68888.58999999988888766665 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   0.5   0.00014      0.11      25      43 ..       5      23 ..       1      34 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                         AAA_29 25 tlltGpsGsGKSTllDAiq 43
                                   +++tG+ G+GKS+l+ A++
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALA 23
                                   689************9975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00061      0.48     102     123 ..       5      26 ..       3      38 .. 0.84
   2 ?   -0.5   0.0       1.3     1e+03     152     161 ..      97     106 ..      89     110 .. 0.80
   3 ?   -2.1   0.0       4.2   3.2e+03      50      99 ..     165     215 ..     145     225 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00061
                                    EEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                    +++ G  G+GKS+L+ al+ + 
  gi|118431199|ref|NP_147498.2|   5 IIVTGTAGAGKSSLVGALADRI 26 
                                    6889*************99864 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                    TEEEESS-SS CS
                    RsgA_GTPase 152 gglliDtPGf 161
                                    + +++DtPG 
  gi|118431199|ref|NP_147498.2|  97 DYVVVDTPGQ 106
                                    6789*****5 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.2
                                    EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--.TTTHTTH.HHHHHHCTT CS
                    RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvs.aktkegl.eelkellkd 99 
                                    v +++K+D+l  e   ee+  +l + g+  +l++  kt eg+ ++l+e+l+ 
  gi|118431199|ref|NP_147498.2| 165 VNAVSKADMLLPEV-REEVIPRLGEPGFLEFLLEkDKTYEGAgKALAEELAR 215
                                    45667777777666.6666666666664433333033334331456666555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013       0.1      28      63 ..       7      43 ..       5      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                          DUF87 28 ilgsTGsGKSntvavLleelle.kkgatililDpHGE 63
                                   + g++G+GKS +v+ L +++ +   ++ +l lDp  E
  gi|118431199|ref|NP_147498.2|  7 VTGTAGAGKSSLVGALADRITSlGANVATLNLDPAAE 43
                                   789******************8877889999998766 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0011      0.89       1      21 [.       5      25 ..       5      38 .. 0.81
   2 ?    1.8   0.0      0.28   2.2e+02      95     110 ..      90     105 ..      60     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                   EEEEEBTTTTHHHHHHHHHTS CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                   i+v G+  +GKSS++ aL  +
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADR 25
                                   89***************9865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.28
                                    EEETTS-SEEEEE--- CS
                      Dynamin_N  95 ilsllvkgltlvDlPG 110
                                      +   +++++vD+PG
  gi|118431199|ref|NP_147498.2|  90 EIDYYSPDYVVVDTPG 105
                                    556678999******9 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   0.00025       0.2      13      38 ..     192     216 ..     192     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                    HHHHHHCTTTT.SSTTHHHHHHHHHCS CS
                          Rnk_N  13 LeaLldsladr.dppaaeaLeaELdRA 38 
                                    Le Ll+   d+ +  a++aL++EL+RA
  gi|118431199|ref|NP_147498.2| 192 LEFLLE--KDKtYEGAGKALAEELARA 216
                                    666888..5555999************ PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00031      0.24       2      24 ..       4      26 ..       3      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                                   CEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                   ++i++G aG GK+ L+  la+ +
  gi|118431199|ref|NP_147498.2|  4 YIIVTGTAGAGKSSLVGALADRI 26
                                   689**************999876 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   0.00033      0.26      56      80 ..       5      29 ..       3      41 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                         DUF815 56 vLLwGarGtGKSslvkallneyaee 80
                                   ++++G+ G+GKSslv al  ++++ 
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSL 29
                                   6899**************9988765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00036      0.28       4      28 ..       5      27 ..       3     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                        DUF2075  4 vlVtGvaGtGKtvvllnllaeledd 28
                                   ++VtG aG+GK+ +  +l+ ++  +
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRI--T 27
                                   89**********9999999988..3 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 ?    7.8   0.4    0.0027       2.1       7      42 ..       5      40 ..       3      72 .. 0.90
   2 ?    0.3   0.1      0.49   3.8e+02     103     120 ..      87     104 ..      70     106 .. 0.80
   3 ?   -2.3   0.0       3.1   2.4e+03      15      57 ..     205     246 ..     204     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                           ParA  7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaDi 42
                                   +++ g  G GKS++   lA  +++ g++v+ l +D 
  gi|118431199|ref|NP_147498.2|  5 IIVTGTAGAGKSSLVGALADRITSLGANVATLNLDP 40
                                   6789999*************************9995 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.49
                           ParA 103 llkdvewgelDyLiiDlP 120
                                    + +++++ + Dy+++D+P
  gi|118431199|ref|NP_147498.2|  87 IREEIDYYSPDYVVVDTP 104
                                    5578999999*******9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.1
                           ParA  15 VGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeek 57 
                                     GK  +a +lA a++++g+   +l a +  p   +ll ++ ++
  gi|118431199|ref|NP_147498.2| 205 AGK-ALAEELARAIETTGFIGEVLQASVLEPETVTLLAAKAQQ 246
                                    566.468899999999999888999999999888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1824.83
//
Query:       gi|118431200|ref|NP_147499.2|  [L=236]
Description: cytochrome c oxidase (aa3-type) subunit II [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-17   61.3   0.4    2.2e-15   56.6   0.0    2.2  2  COX2      Cytochrome C oxidase subunit II, periplasmic 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 !    3.0   0.1    0.0049        88       1      17 [.     106     122 ..     106     130 .. 0.88
   2 !   56.6   0.0   1.2e-19   2.2e-15      44     114 ..     130     202 ..     123     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0049
                           COX2   1 ltikaiGhqwywsyeyt 17 
                                    l++  iG q+ w++ey+
  gi|118431200|ref|NP_147499.2| 106 LVVMVIGFQFGWQFEYS 122
                                    67999***********7 PP

  == domain 2  score: 56.6 bits;  conditional E-value: 1.2e-19
                           COX2  44 vdnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvslli.dreG.vfyGqcselcGvnhssmp 114
                                    + n +v+p +t i + vt+ dv+h+f +p +  k+da+pG ln +++ + d +G v+   c elcG+ hs m 
  gi|118431200|ref|NP_147499.2| 130 TLNYLVVPSDTLIEFRVTSRDVFHAFGIPEFKNKIDAIPGILNSMWIKTpDEPGkVYNAYCYELCGIGHSLMV 202
                                    56889*****************************************98735666578889***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1827.90
//
Query:       gi|118431201|ref|NP_147500.2|  [L=815]
Description: cytochrome c oxidase (aa3-type) subunit I+III [Aeropyrum pernix K1]
Scores for complete 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-133  445.3  60.8   2.1e-133  445.3  60.8    2.9  2  COX1      Cytochrome C and Quinol oxidase polypeptide I
    2.9e-20   73.2  16.3    2.9e-20   73.2  16.3    2.8  2  COX3      Cytochrome c oxidase subunit III
  ------ inclusion threshold ------
        0.2   12.1   0.4       0.44   11.0   0.4    1.5  1  STE       STE like transcription factor


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 !  445.3  60.8  3.6e-137  2.1e-133       1     432 []      23     466 ..      23     466 .. 0.98
   2 ?  -12.4  16.4         3   1.8e+04     142     182 ..     703     738 ..     549     805 .. 0.55

  Alignments for each domain:
  == domain 1  score: 445.3 bits;  conditional E-value: 3.6e-137
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S- CS
                           COX1   1 kigllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardlaf 75 
                                    +igllyl++++++ll++g l+ll+r+qla p     + + y++++t+Hg +m+++fa pf++g++ny+vpl++gardlaf
  gi|118431201|ref|NP_147500.2|  23 DIGLLYLVTSIAFLLIAGSLALLFRVQLAIPksnflTGDAYYEAVTVHGLIMLLWFASPFAFGLANYIVPLQIGARDLAF 102
                                    599**************************997666555****************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHH...CSS-STTTTTTTC.........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           COX1  76 prlnalsfwlvvlgvvllllsll...gaattgwteYapls........evdlwllglllvvvssllgainfivtilkrra 144
                                    prlnals+wl++l++++ll+s++   ga+++gwt Yapl+        + dl+ l+++l+ +s++lg inf+vti+ +ra
  gi|118431201|ref|NP_147500.2| 103 PRLNALSYWLYLLSGLVLLASFFtesGAPNVGWTLYAPLTariytpgiGLDLAALAIFLFSLSVTLGTINFLVTIAAMRA 182
                                    ***********************99999**************************************************** PP

                                    HTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SS.SC.E-HHHHHHHHHHHHTHHHHHHHHHHHHHH CS
                           COX1 145 pgmtvaklplfvwavlatailillalpvlalalllllldrslg.kff.sp.gdplldqhlfWffgHpeVyililpalgiv 221
                                    pg+ ++k+p+f+w++l+t+il+l+a+p l+++ +lllldr+lg +ff +p g +ll++hlfWffgHpeVyil++palg++
  gi|118431201|ref|NP_147500.2| 183 PGIGWFKMPMFTWSILFTVILMLWAFPPLMVGGALLLLDRNLGtEFFlNPaGGALLWDHLFWFFGHPEVYILLFPALGAM 262
                                    ***********************************************7558***************************** PP

                                    HHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCCTTS-CHCH CS
                           COX1 222 yyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkvfnwlatlwrgsirfk 301
                                    + ++++f+g+p+++++ ++ af++ +++sf+vw+HH+f tg++ +++++ s++++li +P+ + v+++++tl++g++ ++
  gi|118431201|ref|NP_147500.2| 263 ADVISTFSGKPIYAKRYILTAFLIATIISFVVWMHHMFITGTNIYTRLFYSITTILISIPFEMAVMSFIFTLYKGRLVYT 342
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--HHHHHHHHHH CS
                           COX1 302 tpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrmlserlaklhfw 381
                                     pmlf++g+++ fiigG tGv l++ +++  + +tywvvaHfH++l+g+v+++l+a++yy++pk+tgr++serl+k+hf 
  gi|118431201|ref|NP_147500.2| 343 VPMLFAVGALLNFIIGGSTGVYLGSIAIDRGFRGTYWVVAHFHYILVGTVTLGLIAGLYYWWPKITGRTYSERLGKIHFA 422
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                           COX1 382 llfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                    l+++G++l+flp+++l  + mprr+++y +     pe+ pln+l+t+g+++
  gi|118431201|ref|NP_147500.2| 423 LAMLGVALTFLPQFAL--MDMPRRYFTY-D----IPEWVPLNQLSTLGAFI 466
                                    *************985..7*********.3....68************996 PP

  == domain 2  score: -12.4 bits;  conditional E-value: 3
                                    HHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHH CS
                           COX1 142 rrapgmtvaklplfvwavlatailillalpvlalallllll 182
                                     ++ +       +++ ++l+t+++++ +l v +++   ll+
  gi|118431201|ref|NP_147500.2| 703 VKRDNY-----LITLSGLLGTLFMAIYFLTVKYFEWKELLI 738
                                    333322.....223445555555555555555444443332 PP

>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.7   9.6         3   1.8e+04     131     172 ..     282     325 ..     223     404 .. 0.67
   2 !   73.2  16.3   4.9e-24   2.9e-20      20     254 ..     571     813 ..     557     815 .] 0.86

  Alignments for each domain:
  == domain 1  score: -7.7 bits;  conditional E-value: 3
                                    HHHHHHHHHH.HHHHHHHHHTTBHH.HHHHHHHHHHHHHHHHHH CS
                           COX3 131 tiillssGvt.vtyahhsliegnrk.kalkgllltillavlftl 172
                                    t+ l+++ ++ v + hh +i+g +  + l   + til+++ f +
  gi|118431201|ref|NP_147500.2| 282 TAFLIATIISfVVWMHHMFITGTNIyTRLFYSITTILISIPFEM 325
                                    55566555543778888888876541445555666666666643 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 4.9e-24
                                    HHHHHHHHHHHHSS-..-HHHHHHHHHHHHHHHHH.HHHHHH..HHTTT-..---HHHHHHHHHHHHHHHHHHHHHHHHH CS
                           COX3  20 llltsalvlflhgykesstllilallslllvmllw.frdiva..eatllG..ehtlavqkGlklGlilfiisevllflal 94 
                                    l+l+++l+l l g   s+ l +l+ ++ ll+   w ++d+ +     l G  eh  + ++ ++  + +fi sev  f ++
  gi|118431201|ref|NP_147500.2| 571 LVLAAGLTLALFGLFVSKPLSYLGAIVFLLSLARWlWKDVKNvfAEELPGyvEHWPFPKDKIRSAMWVFIASEVATFGSI 650
                                    56677788888888888999**********99999788985422233555337999************************ PP

                                    HHHHHHHHHS--GG.GTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHHHHHH CS
                           COX3  95 fwaffhsalsPtve.lGatwpPvGikavnPlevPllntiillssGvtvtyahhsliegnrkkalkgllltillavlftll 173
                                    f a+f   + P+ + l ++wpP     v+ ++v l+ntiil++  +  t a+  + + n   +l+gll t+++a++f+++
  gi|118431201|ref|NP_147500.2| 651 FSAYFFIRFNPVGKfLTEAWPPGY--LVHDVNVGLINTIILFTGTMLFTLAYLGVKRDNYLITLSGLLGTLFMAIYFLTV 728
                                    ***********9764899****64..588999************************************************ PP

                                    HHHHHHH...-SS-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSSB-HHHHHHH.HHHHHHHHHHHHH CS
                           COX3 174 qaveyle...asftisdgvyGsvfylatGlhglhviigtillavallrllkyhltknhhlGfeaai.lywhfvdvvwlfl 249
                                    +++e+ e   a + +  g+y  ++y++tG h lhvi+g +  +  l +l++  l     l    a+ +yw +v++vw ++
  gi|118431201|ref|NP_147500.2| 729 KYFEWKElliAGLGLDAGMYMQAYYVTTGAHALHVILGVLATTYLLVKLFNGNLRGRQALSEVLAVgIYWGIVEIVWTLV 808
                                    **999765558999************************999999999999999998888775555448*********988 PP

                                    HHHTT CS
                           COX3 250 yvsvy 254
                                    +   y
  gi|118431201|ref|NP_147500.2| 809 FPLYY 813
                                    75544 PP

>> STE  STE like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   7.4e-05      0.44      12      41 ..     287     316 ..     275     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.4e-05
                            STE  12 egfiscvlwknlfyitgtdivkilvyklea 41 
                                     ++is v+w ++++itgt+i+  l y +++
  gi|118431201|ref|NP_147500.2| 287 ATIISFVVWMHHMFITGTNIYTRLFYSITT 316
                                    4689*******************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 5380.28
//
Query:       gi|118431202|ref|NP_147501.2|  [L=103]
Description: cytochrome c oxidase (aa3-type) subunit IV [Aeropyrum pernix K1]
Scores for complete 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   41.4   7.5    1.5e-10   41.4   7.5    1.3  2  COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
  ------ inclusion threshold ------
       0.68    9.8   4.6       0.36   10.7   0.2    2.1  2  DUF3487   Protein of unknown function (DUF3487)
       0.76    9.4   5.7        1.1    8.8   5.7    1.3  1  PRA1      PRA1 family protein


Domain annotation for each model (and alignments):
>> COX4_pro  Prokaryotic Cytochrome C oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   7.5   2.5e-14   1.5e-10       2      72 .]      19      88 ..      18      88 .. 0.93
   2 ?   -3.3   0.1       2.2   1.3e+04       7      15 ..      92     100 ..      90     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.5e-14
                       COX4_pro  2 ivfvlllilTaiefalviiklgkllaiiiilvlalvKavlillyFMHLkeekkglrllaliflvflilllv 72
                                    v+++l++  ++e++lv  +    + ++++l++al++  li+l+F HL++e+  +r +++  +v++++l++
  gi|118431202|ref|NP_147501.2| 19 GVWIVLVASAVAEVYLVLEGI-ARNPFVFVLAVALFQSSLIALFFQHLRDEPIIIRGITVSGAVLIAILII 88
                                   69***************5443.9999999999*******************99**************9986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                       COX4_pro   7 llilTaief 15 
                                     ++lT+ ++
  gi|118431202|ref|NP_147501.2|  92 TSVLTCTPY 100
                                    568888776 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.1     0.071   4.3e+02      37      57 ..      20      40 ..      11      62 .. 0.44
   2 ?   10.7   0.2     6e-05      0.36       7      39 ..      62      96 ..      56     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.071
                        DUF3487 37 lvlglllallvgslaliptia 57
                                   + + l++ ++++ ++++ +ia
  gi|118431202|ref|NP_147501.2| 20 VWIVLVASAVAEVYLVLEGIA 40
                                   333333333333222222222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6e-05
                        DUF3487  7 pdrLnrePvVfrGltadEllvla..glglvvglvl 39
                                    + L  eP+++rG+t++  +++a   +++v+ ++ 
  gi|118431202|ref|NP_147501.2| 62 FQHLRDEPIIIRGITVSGAVLIAilIISAVTSVLT 96
                                   57899**********99766555225666665554 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.7   0.00019       1.1      50     109 ..      35      96 ..      15     101 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                           PRA1  50 lllslltnplslivllllvla.wlflyf..lrseplvlfgrelsdrvvlivllvvsvlllflt 109
                                    +l  + +np+  +++++l+ + ++ l+f  lr+ep+++ g ++s  v++++l+ +s +  +lt
  gi|118431202|ref|NP_147501.2|  35 VLEGIARNPFVFVLAVALFQSsLIALFFqhLRDEPIIIRGITVSGAVLIAILI-ISAVTSVLT 96 
                                    34445578887776666665404444445566999988888887765555544.444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); 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:                         3  (0.000167327); expected 0.2 (1e-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: 732.20
//
Query:       gi|118431203|ref|NP_147502.2|  [L=230]
Description: SCO1 protein [Aeropyrum pernix K1]
Scores for 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-10   39.2   0.0    8.5e-10   38.7   0.0    1.2  1  SCO1-SenC        SCO1/SenC
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.048   13.7   0.2    1.5  1  Phage_holin_2_1  Bacteriophage P21 holin S


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 !   38.7   0.0   9.5e-14   8.5e-10      19     132 ..      79     197 ..      69     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 9.5e-14
                      SCO1-SenC  19 legkpslvffgFthCpdvCpttlanmaevldalgeea..ekvqplfiTvDPerDtpevlkeyleafdpriig......lt 90 
                                    +egk+ ++   + +Cpd+C  ++  m++++ +l +e+  ++v ++++ vDP r + e+   y+++  +++        + 
  gi|118431203|ref|NP_147502.2|  79 IEGKVNIIVPQYVRCPDICHYETLIMKSLMIKLFQENslDDVVFVTVEVDPWRGSLEEADMYIKESTASLGFtppwiwVG 158
                                    689*************************99987777547999999999***************99766654456777699 PP

                      SCO1-SenC  91 GskeeiakaakefrvyvekvedeesdytvdHsssvyLvdpdg 132
                                    G+ e +++++k+ ++ v+   +++    + H++ +y+vd++g
  gi|118431203|ref|NP_147502.2| 159 GNMEPLETLYKQLGLSVQLDSSTGL---IVHTAGFYIVDRNG 197
                                    9*************99877666555...***********998 PP

>> 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 ?   13.7   0.2   5.3e-06     0.048      20      55 ..       6      45 ..       1      49 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-06
                Phage_holin_2_1 20 lkqlldklspeeWsa....igvlgglvigllTyltnlYFK 55
                                   l+++l+ + p  W++    + v++gl igl T +t lY K
  gi|118431203|ref|NP_147502.2|  6 LNSILEAIGPFKWAVlvslLVVVSGLSIGLYTAVTGLYPK 45
                                   789999999****873222469****************77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1786.60
//
Query:       gi|14600977|ref|NP_147503.1|  [L=192]
Description: hypothetical protein APE_0797 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-62  209.1   0.0    5.8e-62  208.9   0.0    1.0  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   0.0   3.2e-66   5.8e-62       1     198 []       1     186 [.       1     186 [. 0.99

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 3.2e-66
                                   -EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHH CS
               Methyltrn_RNA_2   1 mrefvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspder 81 
                                   m+ +vv++++++Td++ip+++++G++grldv+ar+++a+l++      +++++++L+g+p ppr++++++s++++v++ er
  gi|14600977|ref|NP_147503.1|   1 MSLYVVISPTGRTDGNIPARGYAGPSGRLDVIARAYNAILEP------NATLAALLMGGPLPPRLLIAPLSCKDIVRS-ER 74 
                                   89****************************************......******************************.** PP

                                   HHHHHHHHHHCHCCTGCCSEEEEETTEEEE---HHHHHHHHHCTSEEEEESTTSEEGGGS---S...SEEEEEE-TT-SHH CS
               Methyltrn_RNA_2  82 niailikkalkaveeikkqekkvrpgltVrkegfealleelsekksiillkekGedisnakiel...nPvFilgdHidlpe 159
                                   +++i++++al+++          r+++tV++eg+eal+++l+++k++ill+ekG+dis++++e+   +P+Fi+g+H+d+p+
  gi|14600977|ref|NP_147503.1|  75 SFMIEASRALRGR----------RSCFTVNDEGVEALASLLRRFKPRILLAEKGGDISSHWGEMcssSPTFIAGSHLDPPH 145
                                   ************9..........9********************************************************* PP

                                   HHHHHHHCTT..SEEEES-SS---HHHHHHHHHHHHHHHHH CS
               Methyltrn_RNA_2 160 eeekllerlk..akrvslgPlsLhadhcvtlihneldkkea 198
                                   + +k+ler+   ++rvs+gPlsLh+dh+++l+++++++++a
  gi|14600977|ref|NP_147503.1| 146 GLIKHLERSLggFLRVSVGPLSLHTDHVFLLVSALRLPMHA 186
                                   *********999************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1430.26
//
Query:       gi|14600978|ref|NP_147504.1|  [L=197]
Description: hypothetical protein APE_0798 [Aeropyrum pernix K1]
Scores for complete 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   32.1   1.8    3.5e-07   30.6   0.0    2.2  2  PEMT         Phospholipid methyltransferase
      2e-05   24.9   0.1      2e-05   24.9   0.1    1.9  2  ICMT         Isoprenylcysteine carboxyl methyltransferase (IC
  ------ inclusion threshold ------
        1.2    8.7   7.7       0.42   10.1   4.8    1.6  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.9      0.21   1.3e+03      69      84 ..      16      31 ..       5      38 .. 0.47
   2 !   30.6   0.0   5.9e-11   3.5e-07      39      97 ..     105     160 ..      91     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                          PEMT 69 itgsaaglllallvll 84
                                  i  ++a+l+++  +l+
  gi|14600978|ref|NP_147504.1| 16 ILAFLAVLVMVSRWLW 31
                                  2233333333333333 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 5.9e-11
                          PEMT  39 mdklvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvylialkfvEeph 97 
                                   ++++v +G+Yr +++P y++ + +flG++L+ +  +  l+++l++++y i+   +Ee  
  gi|14600978|ref|NP_147504.1| 105 EHNIVADGPYRCVRHPVYTAALTMFLGASLVKHYFL--LASALMIAAYTILGV-FEEAR 160
                                   5689**************************987665..666666666666655.66654 PP

>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4      0.92   5.5e+03      68      82 ..      11      25 ..       7      32 .. 0.54
   2 !   24.9   0.1   3.3e-09     2e-05      31      78 ..     104     151 ..      99     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.92
                          ICMT 68 ltalvllalvalllf 82
                                  ++al++la+ a+l++
  gi|14600978|ref|NP_147504.1| 11 VMALIILAFLAVLVM 25
                                  555555555554444 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 3.3e-09
                          ICMT  31 pdhklvksglykylrHPnYllfvilelatllLlcnakltalvllalva 78 
                                    +h++v++g+y+ +rHP Y++ +++ l++ l+ + + l +++++a+++
  gi|14600978|ref|NP_147504.1| 104 REHNIVADGPYRCVRHPVYTAALTMFLGASLVKHYFLLASALMIAAYT 151
                                   68*******************877777766555555444444444433 PP

>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.8     7e-05      0.42      21      68 ..      11      58 ..       1      59 [. 0.67
   2 ?   -1.7   0.0      0.29   1.7e+03      26      35 ..     140     149 ..     120     177 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7e-05
                   Sulf_transp 21 llralllaiavaavgfqllaaaglidlpksafpvvglivGGllFGvGM 68
                                   +  ++la+++  v+++     +++ l+++++ +  ++vGG++ GvG 
  gi|14600978|ref|NP_147504.1| 11 VMALIILAFLAVLVMVSRWLWINIMALDPGPIHPALAVVGGFIVGVGV 58
                                  333334444444444455556677789********************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                   Sulf_transp  26 llaiavaavg 35 
                                   lla a+ +++
  gi|14600978|ref|NP_147504.1| 140 LLASALMIAA 149
                                   2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1604.63
//
Query:       gi|118431204|ref|NP_147505.2|  [L=360]
Description: hypothetical protein APE_0800.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-20   74.6   3.9    1.4e-20   74.2   3.9    1.2  1  DAO            FAD dependent oxidoreductase
    1.5e-05   25.2   0.2    3.1e-05   24.1   0.2    1.5  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    3.1e-05   23.2   0.4    0.00089   18.4   0.7    2.1  2  GIDA           Glucose inhibited division protein A
    8.3e-05   21.5   0.1    0.00013   20.8   0.1    1.3  1  HI0933_like    HI0933-like protein
    8.3e-05   21.9   0.5    0.00021   20.7   0.5    1.8  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00011   21.5   0.3    0.00019   20.8   0.3    1.4  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0002   20.6   0.4    0.00028   20.1   0.4    1.2  1  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.017   15.7   0.1      0.045   14.3   0.1    1.7  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.022   14.0   0.1      0.036   13.3   0.1    1.3  1  FAD_binding_3  FAD binding domain
      0.035   13.4   0.4      0.048   13.0   0.4    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
       0.15   12.0   0.3       0.25   11.2   0.3    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.59    9.3   2.4       0.71    9.1   0.1    2.1  3  Thi4           Thi4 family


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 !   74.2   3.9   9.6e-24   1.4e-20       2     351 ..       5     326 ..       4     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 9.6e-24
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSSTT CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgidi 79 
                                    ++++GGG++Gl +A++++  g  V+++e++   +  a+  ++g++ + ++       la+++le+l +l++l   lg+  
  gi|118431204|ref|NP_147505.2|   5 IAVVGGGVAGLMAAWWASNYGydVVVYEAD-LSSLTATRVSAGIIDPTID-IS----LAPVALETLSLLKRLG--LGL-- 74 
                                    9******************9**********.7777************996.44....56**********9998..453.. PP

                                    SEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.ST.TTSEEEEETTEEEEEHHHHHHHHHHHHH CS
                            DAO  80 dyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lp.gllgalfypdtgqvdpakltaalaraae 157
                                       ++ ll+l  +   +  +++l +ll++ g+ ++ + +ee  +l    ++ g+   l++ +t +vd+ ++  +la+ a 
  gi|118431204|ref|NP_147505.2|  75 ---ESRLLWLH-E---RGSCRRLERLLSDKGIIERSVAGEESIRLGRYtVNlGYGEELHVINTIIVDTGEFY-SLASSA- 145
                                    ...48899994.4...44453333333557875555555544444433322577777999998999999887.456665. PP

                                    HTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTTCTTTSEEEEEEEEEEEEEECCTHST CS
                            DAO 158 alGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gllkeldlpispvrgqvlvlkplseklv 235
                                       v+i+e   v+ +   +   + v   ++ g++ ++da+++aaG+w++++ gl   l  +++  r + l ++       
  gi|118431204|ref|NP_147505.2| 146 -SNVDIVED-SVEYV---G--CGSV-GLKRgGSR-EFDAIIVAAGPWTGFIsGLQ-ALSNMLRVYRCEALIIRA-GG--- 211
                                    .479****9.77766...3..4445.44554664.67************663222.233344555555555522.22... PP

                                    GSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSS.TSCSHHHHHHHHHHHHHHSGGGCG...EEEEEE.EEE CS
                            DAO 236 spaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgddd.pevdeedidellealrklfPqlgd...vlrkwa.Glr 310
                                         ++v   d  ++++ + ++ dg vl  g  +e +++ d  + + + +d+++++  +++ +lg+   ++   a ++ 
  gi|118431204|ref|NP_147505.2| 212 ---GPFAVV-DDILDFYLSIHASGDG-VLGNGCCVEIASPLDgYRYSGDVLDAVISRSIERLEGLGEaelITPVSApCVV 286
                                    ...223333.6667777777777766.6655555455555555899999*************998663334454444888 PP

                                    EETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                            DAO 311 plpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                      +d  p++g  pg +++yl++G  g G+tlap+ ++l++e
  gi|118431204|ref|NP_147505.2| 287 G-RDARPVLGMLPGCSRVYLLAGLDGVGVTLAPVLARLVVE 326
                                    8.9********99999**********************987 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   2.1e-08   3.1e-05       1      27 [.       7      33 ..       7      44 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.1e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                   +vG+G++Gl aA+ ++++g+dv+++e+
  gi|118431204|ref|NP_147505.2|  7 VVGGGVAGLMAAWWASNYGYDVVVYEA 33
                                   8************************97 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   5.9e-07   0.00089       2      35 ..       5      38 ..       4      47 .. 0.87
   2 ?    2.3   0.0     0.048        72     107     152 ..     144     184 ..     136     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.9e-07
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldti 35
                                   + V+GgG AG+ AA+ a++ G++v+ +  +l+++
  gi|118431204|ref|NP_147505.2|  5 IAVVGGGVAGLMAAWWASNYGYDVVVYEADLSSL 38
                                   78***********************997766655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.048
                                    TSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-B CS
                           GIDA 107 nepnleiieeeveeliveekkvkgvvtedgetikakavviatGtfl 152
                                    +  n++i+e++ve +         v +++g   + +a+++a+G++ 
  gi|118431204|ref|NP_147505.2| 144 SASNVDIVEDSVEYVGC-----GSVGLKRGGSREFDAIIVAAGPWT 184
                                    57899**********77.....6699******************43 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   8.9e-08   0.00013       2      32 ..       4      34 ..       3      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.9e-08
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                   +++v+GgG AGlmaA  a++ g +V+++e+ 
  gi|118431204|ref|NP_147505.2|  4 RIAVVGGGVAGLMAAWWASNYGYDVVVYEAD 34
                                   689*************************986 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   0.5   1.4e-07   0.00021       2      31 ..       4      38 ..       3     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.4e-07
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....T CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.....l 31
                                   +++v+GgG+AGl aa  ++++g++v+++e     l
  gi|118431204|ref|NP_147505.2|  4 RIAVVGGGVAGLMAAWWASNYGYDVVVYEadlssL 38
                                   799***********************997544443 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.3   1.3e-07   0.00019      30      65 ..       4      39 ..       1      55 [. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.3e-07
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparle 65
                                   ++ v+GgGvaGl A++ a++ g +V+v++ + + l 
  gi|118431204|ref|NP_147505.2|  4 RIAVVGGGVAGLMAAWWASNYGYDVVVYEADLSSLT 39
                                   789*************************99887765 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   1.9e-07   0.00028       2      46 ..       5      49 ..       4      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.9e-07
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgid 46
                                   + V+G+G+AGL+AA  a++ G +v+v e   +   at  s G id
  gi|118431204|ref|NP_147505.2|  5 IAVVGGGVAGLMAAWWASNYGYDVVVYEADLSSLTATRVSAGIID 49
                                   68**************************99997779999999886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1     3e-05     0.045       1      29 [.       4      32 ..       4      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvve 29
                                   +++vvGgG+ gl++A  ++++g +V v e
  gi|118431204|ref|NP_147505.2|  4 RIAVVGGGVAGLMAAWWASNYGYDVVVYE 32
                                   79***********************9976 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.4e-05     0.036       4      39 ..       5      40 ..       3      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                   +++VG+G aGlm+a   s++G +vv+ e   +    
  gi|118431204|ref|NP_147505.2|  5 IAVVGGGVAGLMAAWWASNYGYDVVVYEADLSSLTA 40
                                   689**********************99876655555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   3.2e-05     0.048       2      30 ..       5      33 ..       4      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                   + VvGGg+aG++AA  A + G  v++ e 
  gi|118431204|ref|NP_147505.2|  5 IAVVGGGVAGLMAAWWASNYGYDVVVYEA 33
                                   78**********************99875 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 ?   11.2   0.3   0.00017      0.25       2      38 ..       5      41 ..       4      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                   +av+G G+ G   a  + + g++Vv+++ + ++l++ 
  gi|118431204|ref|NP_147505.2|  5 IAVVGGGVAGLMAAWWASNYGYDVVVYEADLSSLTAT 41
                                   9**************************9988777665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00048      0.71      20      52 ..       5      36 ..       1      44 [. 0.89
   2 ?   -1.3   0.1      0.71   1.1e+03      12      31 ..     147     166 ..     140     173 .. 0.84
   3 ?   -2.8   0.0         2   2.9e+03      17      32 ..     172     188 ..     169     212 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00048
                                   EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS CS
                           Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvs 52
                                   +++vG+G +GL aa   ++  +  v++ e+ +s
  gi|118431204|ref|NP_147505.2|  5 IAVVGGGVAGLMAAWWASNY-GYDVVVYEADLS 36
                                   89************998877.********9997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.71
                                    HHHHTEEEEEEE--SHHHHH CS
                           Thi4  12 llkyaesDvvivGaGssGLt 31 
                                     ++++e  v  vG Gs GL 
  gi|118431204|ref|NP_147505.2| 147 NVDIVEDSVEYVGCGSVGLK 166
                                    57899999999******996 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2
                                    EEEEEEE--SH.HHHHH CS
                           Thi4  17 esDvvivGaGs.sGLta 32 
                                    e D +iv aG+ +G  +
  gi|118431204|ref|NP_147505.2| 172 EFDAIIVAAGPwTGFIS 188
                                    67889999998434333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2938.84
//
Query:       gi|118431205|ref|NP_147506.2|  [L=267]
Description: 5'(3')-nucleotidase SurE [Aeropyrum pernix K1]
Scores for complete 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-39  135.7   0.0      2e-39  135.4   0.0    1.0  1  SurE             Survival protein SurE
  ------ inclusion threshold ------
      0.023   15.1   0.0      0.051   14.0   0.0    1.6  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      0.038   14.0   0.0      0.059   13.4   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
       0.11   12.5   0.0       0.17   11.9   0.0    1.3  1  Glyco_trans_4_2  Glycosyl transferase 4-like


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 !  135.4   0.0   4.5e-43     2e-39       2     191 ..       5     183 ..       4     186 .. 0.87

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 4.5e-43
                                    EEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHHTT CS
                           SurE   2 LltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklaleel 81 
                                    ++tNDDG++++ +ral+e+la++g++vvv+aP  ++Sg++k++   +  rv + e+  + + +  +  Pa+ v +a++ +
  gi|118431205|ref|NP_147506.2|   5 IVTNDDGVHSRSLRALAESLASRGWDVVVAAPLGNWSGYSKSIGRFRGNRVYRFES-RGVRFFTGDMPPAALVGTAIDIA 83 
                                    69*******************99********************5445555554433.67778877999*********666 PP

                                    TTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSSSS-SSS---HHHHHHHHHHHHTTETTS- CS
                           SurE  82 lkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskkeeekkeedtfeaaakvaaklvekliekl 160
                                       ++pd+VvSGiN+G+Nlg    ++SGT+g+aleaal+g++++++S a+++    +e+d++ +a ++  ++ve+ +e+l
  gi|118431205|ref|NP_147506.2|  84 G--FEPDIVVSGINYGPNLGIYDfFSSGTIGGALEAALRGFKSVSISSACRE----EETDCLPEALSISLAVVETSVETL 157
                                    6..67***************8766*************************963....456899999999999999887877 PP

                                    ...SS-EEEEEEESS.GCG-SEEEE-B--CC CS
                           SurE 161 llekvellnvNvPeleeeeikgvkvtrlgrr 191
                                      +++ l+ vN+P    ++ +g+kvtr +rr
  gi|118431205|ref|NP_147506.2| 158 S-SSAGLMVVNIP----RSPRGFKVTRPCRR 183
                                    5.999********....4668899**99987 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 ?   14.0   0.0   1.1e-05     0.051       5      78 ..      15      91 ..      11     125 .. 0.68
   2 ?   -2.3   0.0       1.2   5.3e+03      38      63 ..     161     187 ..     150     202 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                Glyco_trans_4_4  5 ryvaelaraLaarGheVtvltpapapgape...leedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvh 78
                                   r  ++la++La rG++V+v +p +  + +     + +g rv+r+  +  +  ++d+  ++ +  ++  + + pd+v+
  gi|118431205|ref|NP_147506.2| 15 RSLRALAESLASRGWDVVVAAPLGNWSGYSksiGRFRGNRVYRFESRGVRFFTGDMPPAALVGTAIDIAGFEPDIVV 91
                                   67899****************77766655423344567777777655443222232222223333344566666665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                Glyco_trans_4_4  38 dgvrvhrlpvprrp.spladlaalral 63 
                                    +g+ v+++p ++r+ + ++  ++++++
  gi|118431205|ref|NP_147506.2| 161 AGLMVVNIPRSPRGfKVTRPCRRVPRF 187
                                    455665555444432233334455554 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.3e-05     0.059       6      49 ..      15      64 ..      13     101 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                 Glyco_transf_4  6 rhvleLaraLarrGheVtvvtpgddgpleeev......elvvrvprvplp 49
                                   r+++ La+ La rG++V+v +p ++   + +        +v+r++++  +
  gi|118431205|ref|NP_147506.2| 15 RSLRALAESLASRGWDVVVAAPLGNWSGYSKSigrfrgNRVYRFESRGVR 64
                                   7899****************988877777765444333333333333322 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   3.8e-05      0.17       3      34 ..       4      39 ..       4      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                Glyco_trans_4_2  3 lllanlssvh...tlrlakeLakrgyeVhvitp.kk 34
                                   ++++n + vh   ++ la++La+rg++V+v+ p ++
  gi|118431205|ref|NP_147506.2|  4 AIVTNDDGVHsrsLRALAESLASRGWDVVVAAPlGN 39
                                   68999999994434556**************99544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2064.71
//
Query:       gi|118431206|ref|NP_147507.2|  [L=408]
Description: hypothetical protein APE_0803.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.017   15.6   0.1      0.035   14.5   0.1    1.5  1  Transglut_core  Transglutaminase-like superfamily
      0.027   14.3   0.0         10    6.0   0.0    2.4  2  DAHP_snth_FXD   DAHP synthase ferredoxin-like domain


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.9e-06     0.035      49      72 ..     173     196 ..     151     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.9e-06
                 Transglut_core  49 tgkGncedfaslfvallRalGipa 72 
                                    +  G++e fas+f+a++R lGi+a
  gi|118431206|ref|NP_147507.2| 173 ASGGDSESFASVFAAAARDLGIEA 196
                                    4559******************99 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0012        10       3      30 ..       8      35 ..       8      38 .. 0.82
   2 ?    5.7   0.0    0.0015        13      31      54 ..     163     186 ..     156     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0012
                  DAHP_snth_FXD  3 ivmkkgateeqieevierieelGlkvhv 30
                                   iv+  + t  ++ +v+++ie+lG++v +
  gi|118431206|ref|NP_147507.2|  8 IVLLLQKTGGEVSRVVREIESLGYSVAT 35
                                   56666778889*************9976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0015
                  DAHP_snth_FXD  31 skGeertViGviGdtskldkeqle 54 
                                     +G++ +ViG+ G +s+  +  ++
  gi|118431206|ref|NP_147507.2| 163 AQGADVVVIGASGGDSESFASVFA 186
                                    69***********99987766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 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:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3417.47
//
Query:       gi|14600982|ref|NP_147508.1|  [L=362]
Description: tyrosine recombinase XerC [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-33  115.6   0.0    3.5e-33  114.8   0.0    1.4  1  Phage_integrase  Phage integrase family
    1.9e-05   24.8   1.2    0.00022   21.5   0.1    2.9  3  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    6.1e-05   23.4   0.1       0.11   12.9   0.0    2.5  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
       0.11   11.4   0.2       0.43    9.5   0.1    1.8  2  DUF3435          Protein of unknown function (DUF3435)


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 !  114.8   0.0   7.9e-37   3.5e-33       6     170 ..     128     279 ..     124     281 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 7.9e-37
                                   HHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHH CS
               Phage_integrase   6 deverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellsk 86 
                                    +ve+ll+a+++   i d+l++ +l etGlR+sEllsLr++d+dl +gv++v   +gK +ker+v l+     ll+e+l+ 
  gi|14600982|ref|NP_147508.1| 128 RDVEALLSASRD---IIDALIVSMLAETGLRVSELLSLRLSDVDLGRGVVRV---VGKYGKERIVFLGPLSRMLLEEYLAS 202
                                   6899*******9...*************************************...************************** PP

                                   HCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S.SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHH CS
               Phage_integrase  87 aleeaeksellfaskrgkplsrqtvrkafkraveeagie.kpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiY 166
                                   +         l +  r  +ls q+v+k++k+++++ag++  +++pH lRh+fat+ l++g++l ++q+llGHs+i+ tq Y
  gi|14600982|ref|NP_147508.1| 203 N--------PLPPDSRIIELSYQAVYKRLKSLAKRAGLDpRKVRPHILRHTFATEALRRGMSLAALQRLLGHSDIKVTQLY 275
                                   9........56666677778*******************99**************************************** PP

                                   HCCC CS
               Phage_integrase 167 thva 170
                                    h +
  gi|14600982|ref|NP_147508.1| 276 LHMT 279
                                   **86 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 !   21.5   0.1   4.9e-08   0.00022       9      80 ..      33     105 ..      25     109 .. 0.91
   2 ?    0.5   0.1      0.17   7.6e+02      30      69 ..     223     263 ..     214     267 .. 0.76
   3 ?   -2.1   0.0       1.1   4.8e+03      10      25 ..     335     350 ..     329     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.9e-08
                                   HHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS-----.-----HHHHHHHHHHHHHHH CS
               Phage_int_SAM_1   9 ikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeg.lsatslarrlsalrsFfqfl 80 
                                    + +g s +T+  Yr +L++flk     +  ++ + t     + + e++++g  s+t+++ + + +r+F++++
  gi|14600982|ref|NP_147508.1|  33 LESTGWSSKTIKVYRAALKDFLKSYGRVRVGDASHMTYVQWMSSVSERVRKGvISRTTAHYYSIMVRRFLKWA 105
                                   557789*********************9999*********************99******************8 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                   HHHHHH.TS--TTT--HHHHH.HHHHS----------HHHH CS
               Phage_int_SAM_1  30 lkflaergkesleqlttedvr.aflaeleeeglsatslarr 69 
                                   lk la+r + + ++++++ +r +f  e +++g s + l r 
  gi|14600982|ref|NP_147508.1| 223 LKSLAKRAGLDPRKVRPHILRhTFATEALRRGMSLAALQRL 263
                                   45566669999999999999769999999999887777775 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.1
                                   HTT-S-HHHHHHHHHH CS
               Phage_int_SAM_1  10 kerglspnTlraYrrd 25 
                                   ++ g++p T r Y r 
  gi|14600982|ref|NP_147508.1| 335 IQAGMTPDTSRGYGRV 350
                                   688999*****99885 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 !   12.9   0.0   2.5e-05      0.11       7      42 ..      31      66 ..      27      81 .. 0.77
   2 !    8.3   0.0   0.00069       3.1       7      34 ..      79     106 ..      73     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
               Phage_int_SAM_4  7 ealrlaglserTiksYlsaikrflrflkkkapeelt 42
                                    l++ g s +Tik+Y  a+k+fl+ + + ++ + +
  gi|14600982|ref|NP_147508.1| 31 TILESTGWSSKTIKVYRAALKDFLKSYGRVRVGDAS 66
                                  5689999********************944555444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00069
               Phage_int_SAM_4   7 ealrlaglserTiksYlsaikrflrflk 34 
                                   e  r   +s +T ++Y   ++rfl++  
  gi|14600982|ref|NP_147508.1|  79 ERVRKGVISRTTAHYYSIMVRRFLKWAG 106
                                   5556666899****************85 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.12   5.3e+02      29      55 ..     143     169 ..     135     170 .. 0.90
   2 ?    9.5   0.1   9.5e-05      0.43     171     239 ..     212     279 ..     208     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.12
                       DUF3435  29 llllllaaftsnRpgalleLryrDlel 55 
                                   +l++ + a t+ R + ll+Lr  D+ l
  gi|14600982|ref|NP_147508.1| 143 ALIVSMLAETGLRVSELLSLRLSDVDL 169
                                   689999******************986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.5e-05
                       DUF3435 171 ealtastlnsrlkrlgeiagfe.epitpYklRrgaakalneSgevseaqrnlilqHassrtFlkhYlsqk 239
                                    +l+++++ +rlk+l++ ag++  +++p+ lR   a +  + + +s a  + +l+H+++++  + Yl+  
  gi|14600982|ref|NP_147508.1| 212 IELSYQAVYKRLKSLAKRAGLDpRKVRPHILRHTFATEALR-RGMSLAALQRLLGHSDIKVT-QLYLHMT 279
                                   479******************8478*******987765555.4999999999*******997.4554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2716.69
//
Query:       gi|118431207|ref|NP_147509.2|  [L=540]
Description: delta-1-pyrroline-5-carboxylate dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-100  335.5   0.0   4.8e-100  335.2   0.0    1.0  1  Aldedh         Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.12   11.0   0.0       0.18   10.5   0.0    1.1  1  Adeno_E1B_55K  Adenovirus EB1 55K protein / large t-antigen


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 !  335.2   0.0  5.4e-104  4.8e-100       6     459 ..      53     519 ..      48     522 .. 0.92

  Alignments for each domain:
  == domain 1  score: 335.2 bits;  conditional E-value: 5.4e-104
                                    SSEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHH.HTHHHHHHHHHHHH---H CS
                         Aldedh   6 setievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlle.erkeelaeletletGkpl 83 
                                    +et+e   P+ ++ v+a ++ a++e++++a+++A +a  +w+++++++Ra+++ kaadll+   + e  ++++l+  k+ 
  gi|118431207|ref|NP_147509.2|  53 GETVEIRAPHdKDAVLAVAHLAGEEEIRDAIEKALDAWTKWSEMEWYHRASVFLKAADLLAgPYRLEADAVIMLNHSKTP 132
                                    378999****66777888889****************************************667889999********** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-.SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE- CS
                         Aldedh  84 aearaeveeaidvlryyaelaeklegevlpssegklalvrrePl.GvvgaItPWNfPlllaawklapalaaGNtvvlKPa 162
                                    +ea+ +++e +d+ r+ a +a+ + ++  ++++g+l+ v ++Pl G+v a+ P+Nf  +     +apal+ GN+ ++KP+
  gi|118431207|ref|NP_147509.2| 133 WEAEIDLAELVDFWRFGAYYARFIFEQQPEQAPGELNRVEWRPLeGFVFAVPPFNFFSIGGNLPTAPALV-GNVSIWKPS 211
                                    ***********************9998877789************************************9.********* PP

                                    TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCT......TSEEEEEE CS
                         Aldedh 163 eetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaakn......lkrvtlEl 236
                                      +  s +++++++ eaglP+gv+n+v+  + + ++ +++hp+++ ++ftGs ++  ++ k  a+n      + r++ E+
  gi|118431207|ref|NP_147509.2| 212 RWVIYSNYIIMRILMEAGLPPGVVNFVPF-NTKYSSIVLSHPDFAGLHFTGSYSTFVRLWKMIAQNldkyrnFPRIVGET 290
                                    ***************************99.78899*******************9988877766553333338******* PP

                                    ---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHH CS
                         Aldedh 237 GGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaq 316
                                    GGk+ ++v+++aD+ +av a+++gaf ++GQ+C+aasrl+v++s++ +f e++++++ k+kvg  +d ++ +G++ise+q
  gi|118431207|ref|NP_147509.2| 291 GGKDFIVVHPSADITEAVVATIRGAFEYQGQKCSAASRLFVPKSMWPRFWEAMKAELDKVKVGPVDDFTVFMGAIISEEQ 370
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHH..TTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESS..HHHHHHHHHS CS
                         Aldedh 317 lekvekyveeake..egaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkd..eeeaieiaNd 392
                                    ++k+ +y+e ak+  e++++++Gg   + +++kgyf+ Ptv+   +p+ ++++eEiFGPVl+v+ ++d   +e++ ++ +
  gi|118431207|ref|NP_147509.2| 371 FRKIVSYIEYAKQhpEEYQIIYGG---KYDDSKGYFIWPTVVLTNNPKGKLMTEEIFGPVLTVYVYDDdkYDEILWVVDK 447
                                    *********999855799******...7899***********************************96337899888775 PP

                                    .SSEESEEEEE-SBHHHHHHHHHHS..-SSEEEESSSST--TTT.SEB--CGGGEES-BSH.HHHHHHTEEE CS
                         Aldedh 393 .teyGLaagvftkdleraervaerl..eaGnvyiNdsttgaaea.lpfgGvkqSglGregg.kegleeytev 459
                                      +yGL+++vf+kd e ++++ ++l   aGn yiNd+ tg++ a +pfgG + Sg+++++g    l ++++ 
  gi|118431207|ref|NP_147509.2| 448 aAPYGLTGSVFAKDREAILKAEKALryAAGNFYINDKPTGSIVArQPFGGARWSGTNDKAGwFTNLLRWLNP 519
                                    279******************99996679****************************887756666666665 PP

>> Adeno_E1B_55K  Adenovirus EB1 55K protein / large t-antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     2e-05      0.18     275     369 ..     212     309 ..     204     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2e-05
                  Adeno_E1B_55K 275 kwpefehnvlvrcklhlGaRrGvfspsqcnlsyssvllekesvskvsltgvfdqtvevykilry..deskerlr.aCeCG 351
                                    +w   ++ +++r  +  G   Gv+++   n +yss++l +  +  + +tg++ + v ++k++    d+ ++  r   e G
  gi|118431207|ref|NP_147509.2| 212 RWVIYSNYIIMRILMEAGLPPGVVNFVPFNTKYSSIVLSHPDFAGLHFTGSYSTFVRLWKMIAQnlDKYRNFPRiVGETG 291
                                    56667788899999999*******************************************99773455555445456777 PP

                  Adeno_E1B_55K 352 ashallqlvvlkvteelr 369
                                    +++  ++   +++te+++
  gi|118431207|ref|NP_147509.2| 292 GKDFIVVHPSADITEAVV 309
                                    777777777778887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3885.69
//
Query:       gi|118431208|ref|NP_147510.2|  [L=471]
Description: threonyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for 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-45  152.9   0.0    1.6e-44  152.0   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    4.1e-09   36.5   0.3    9.7e-09   35.3   0.2    1.7  2  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
       0.12   12.3   0.0        3.6    7.5   0.0    2.3  2  DAO_C           C-terminal domain of alpha-glycerophosphate o


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 !  152.0   0.0   2.7e-48   1.6e-44       2     178 ..      97     327 ..      96     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 2.7e-48
                                    EEEETTSEEEEE-SSSHHHHHHHHHHHEE..EBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   2 kledrndreyiLkPtneetfvelirdevl..rskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeasld 77 
                                     ++ + ++e+++kP+n+++++ l+ +ev+  rsk  LP+k++++++++R+E+s +++GLlRvr+F+q+d+++++  +++ 
  gi|118431208|ref|NP_147510.2|  97 LFDIE-GHEFAVKPMNCPYHILLFLNEVAkhRSKLpLPFKVFEFGRVHRYEPSgSIYGLLRVRGFTQDDAHIIVPGGRVI 175
                                    55566.69*******************888888989****************999************************* PP

                                    HHHHHHHHHHHHHHHHT...T...SCEEEEEEGTTSC..........................................B CS
                                    xxxxxxxxxxxxxxxxx...xx..xxxxxxxxxxxxx..........................................x RF
                   tRNA-synt_2b  78 dslrdlikaisriferl...gl..efraiielmsaks..........................................a 110
                                    d+++d++++++ ++erl   g+  e ++++++ms+ks                                          a
  gi|118431208|ref|NP_147510.2| 176 DVVYDVFEEMKLVLERLfklGVssETFKVRLSMSDKSligkefmgskeewegaeealreaasrinekygidivelegeaA 255
                                    ****************966655334599******999******************************************* PP

                                    TTSEEEEEEEEETT..TSEEEEEEEEEEEETHHHHHTTE.EEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                   tRNA-synt_2b 111 dykdkkefeavses..ltkgieigtiqklgtrlserlga.tvldennreksvimicaa.ig.veRllsaileq 178
                                    +y++k++f +++e+  ++k++++gtiq++ ++l++r+++ +v++e++  ++v++i++a +g +eR+l+++le+
  gi|118431208|ref|NP_147510.2| 256 FYGPKLDFIMMVEEsgVSKEWQMGTIQFD-FNLPRRFRLyDVVREEFGIEEVYIIHRAlLGsIERFLGVYLEH 327
                                    *********999974478***********.*********9*******************************98 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   1.1e+04      14      34 ..     181     201 ..     168     218 .. 0.60
   2 !   35.3   0.2   1.6e-12   9.7e-09       1      84 [.     340     430 ..     340     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHTTTSEEEE CS
                 HGTP_anticodon  14 leeyakklaeeLraagirvel 34 
                                    + e++k + e+L + g++ e 
  gi|118431208|ref|NP_147510.2| 181 VFEEMKLVLERLFKLGVSSET 201
                                    556667777777777743333 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 1.6e-12
                                    SEEEEESSSS...HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHH.HTT-SEEEEE-HHHHHHTEEEEEET. CS
                 HGTP_anticodon   1 qvvviplnek...aeeleeyakklaeeLraagirveldd.snesigkkiread.llgipfavvvGekelekgtvtvrdr. 74 
                                    q++vi+++++   ++e+e++a+++a+ L+++g+rv ++  s+  +   +r+ + +++  + v++G+ke++++++ vr + 
  gi|118431208|ref|NP_147510.2| 340 QFAVIAVKTGgevDREIEDLASSIAKGLLDKGFRVAVKGsSKTGLSSDVRHIEsTAKPAVNVFIGAKEVREKVLDVRVFd 419
                                    789******9***888***********************555566666666551688999*****************997 PP

                                    .TTCEEEEEET CS
                 HGTP_anticodon  75 .dtreqervsl 84 
                                     ++++++r+++
  gi|118431208|ref|NP_147510.2| 420 lESMKRRRLAI 430
                                    75555554443 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.026   1.6e+02       9      53 ..     226     269 ..     220     294 .. 0.87
   2 ?    7.5   0.0   0.00059       3.6      23      61 ..     415     451 ..     400     470 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.026
                                    TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHH CS
                          DAO_C   9 vGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelake 53 
                                     Gae+  ++ a ++ ++yg+d  + e  a  YG + + ++ + +e
  gi|118431208|ref|NP_147510.2| 226 EGAEEALREAASRINEKYGIDIVELEGEAAFYGPKLDFIM-MVEE 269
                                    59999999999************************99998.4444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00059
                                    STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHH CS
                          DAO_C  23 aqeygldeevaehLaerYGsraeevlelakedekpelae 61 
                                    ++ + l++   ++La  YG+ a++v +la+++e+  l++
  gi|118431208|ref|NP_147510.2| 415 VRVFDLESMKRRRLAIAYGDAADAVENLAAVAEE--LES 451
                                    55678888889999***********999998875..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3731.67
//
Query:       gi|14600985|ref|NP_147511.1|  [L=327]
Description: hypothetical protein APE_0812 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0001   22.0   0.0     0.0012   18.5   0.0    2.1  1  Q_salvage  Potential Queuosine, Q, salvage protein family
    0.00016   21.1   0.0    0.00025   20.4   0.0    1.2  1  AGOG       N-glycosylase/DNA lyase


Domain annotation for each model (and alignments):
>> Q_salvage  Potential Queuosine, Q, salvage protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-07    0.0012      33     123 ..      61     150 ..      32     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-07
                     Q_salvage  33 rfaveykgkkytgYwsLvaalkraleegipitdpeflsketeeelkkvfrsateeeiplleeRlellreagkvllekfdgs 113
                                    ++   +gk y g   L    +++l+e+  ++++e ls++t e++k++++  ++ + p  + R++llr++g+ l+  ++gs
  gi|14600985|ref|NP_147511.1|  61 PYEAVVDGKLYHGADLLYRLGSKKLQEDPGFFTAERLSRVTVEDVKEWLSVGNA-SPPDPDVRAKLLRDLGRKLMALYQGS 140
                                   55555667778888888888899**************************98855.77999********************* PP

                     Q_salvage 114 fvnlikkank 123
                                   +  li ++++
  gi|14600985|ref|NP_147511.1| 141 AWMLIVESKG 150
                                   *999988765 PP

>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.8e-08   0.00025     165     238 ..     196     279 ..     185     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.8e-08
                                   -TTS-----HHHHHHHHHTTS-SS-HH..HHHHTHCCHC........S.HHHHHHHHHHHHT--HHHHHHHHHHHCCHHHC CS
                          AGOG 165 pfeipiPvDvRiakltktsglielkne..kklarkelvq........eevieaWkevsreseiPplhlDsllWvlgksale 235
                                   p + ++PvD    +l++ +g+++++++  ++++r++ v+         +  +aW+ v+++ +i p  lD +lW++g+ + +
  gi|14600985|ref|NP_147511.1| 196 PHNKELPVDNHLVRLALRMGIVSATEDllEAVKRQREVDtlddvalrLASRRAWRIVAQHGGIDPFILDDFLWAFGRLCCT 276
                                   666789****************998872234555555557878877667789************************98876 PP

                                   CS- CS
                          AGOG 236 led 238
                                   ++ 
  gi|14600985|ref|NP_147511.1| 277 RDA 279
                                   655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2717.10
//
Query:       gi|118431209|ref|NP_147512.2|  [L=358]
Description: hypothetical protein APE_0813.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); 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:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 3121.82
//
Query:       gi|118431210|ref|NP_147514.2|  [L=277]
Description: hypothetical protein APE_0815.1 [Aeropyrum pernix K1]
Scores for complete 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-49  169.0   0.0    1.5e-49  168.5   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.2e-05   24.7   0.0    1.5e-05   24.4   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    2.5e-05   23.8   0.0    3.4e-05   23.4   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00014   21.5   0.0    0.00022   20.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0049   16.4   0.0     0.0095   15.5   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0061   16.5   0.0     0.0094   15.9   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.019   14.6   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.033   13.9   0.0      0.046   13.4   0.0    1.1  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
       0.06   13.1   0.0      0.086   12.6   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase
       0.19   11.5   0.0       0.32   10.8   0.0    1.3  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.0   8.3e-53   1.5e-49       4     198 ..      15     217 ..      12     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 8.3e-53
                                    EEETTEEEEEB-....TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB-.-EEEEEES-.SEEEEEETTEEEEEET CS
                         Met_10   4 eiiGdvvilnlr....eelkeykkvigevildktkvktvlrkvsevegefRtf.elevlaGsdstetihkEngcrfklDv 78 
                                    +iiGd+++++++     ++++ + v ge++    +v++v+  ++ v g f+++ +l +laG+++t t+ +E+g +f +D+
  gi|118431210|ref|NP_147514.2|  15 DIIGDIAVIKKPihggVSIEDLRLVAGELLRRLPHVRSVWLATGPVGGLFKVRrDLLHLAGEKRTSTVYREHGAEFLVDI 94 
                                    79*******9973222467888888899888888****************9752699*********************** PP

                                    TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES CS
                         Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpile 158
                                    skv+  ++l+ E+ r+a+lv++ge+Vv++fAG+G f+i ia  s++++v++id+nP++++++ eni+lN+ve+vv+p+l+
  gi|118431210|ref|NP_147514.2|  95 SKVFITPRLSFEHLRVARLVKPGETVVNMFAGVGVFSIIIALKSRPSKVYSIDINPDAYRLMIENIRLNRVEDVVEPMLG 174
                                    ******************************************************************************** PP

                                    -GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEE CS
                         Met_10 159 Dgrevir...eqladrvvmnlpksaieFldkvlaalkdggvih 198
                                    D++ ++    + +adrv+m+lp+ a ++++++l+al+ +g  h
  gi|118431210|ref|NP_147514.2| 175 DSARIVSeslRGVADRVLMPLPDLALDYIGHALDALRGRGWLH 217
                                    ****998788899**********************99887655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   8.3e-09   1.5e-05      51     116 ..     118     182 ..      65     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 8.3e-09
                                    EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC- CS
                            TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllae 116
                                     +v++ +++ G+ +i  al  +  ++v+  Di++ A+ l+ eN++ln ve++v++  +d + +++e
  gi|118431210|ref|NP_147514.2| 118 ETVVNMFAGVGVFSIIIALK-SRPSKVYSIDINPDAYRLMIENIRLNRVEDVVEPMLGDSARIVSE 182
                                    479999*************9.9999*******************************9999888764 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.9e-08   3.4e-05     156     214 ..     111     170 ..      99     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.9e-08
                           PrmA 156 eklvkegeevlDvGtGSGiLaia.aakLgakkvvavDiDevAvkvakeNaelNkveakle 214
                                     +lvk+ge+v+ + +G G+ +i  a+k   +kv+ +Di++ A +   eN++lN+ve+ +e
  gi|118431210|ref|NP_147514.2| 111 ARLVKPGETVVNMFAGVGVFSIIiALKSRPSKVYSIDINPDAYRLMIENIRLNRVEDVVE 170
                                    4679*****************752788999*************************99775 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 !   20.9   0.0   1.2e-07   0.00022       3      85 ..     119     201 ..     117     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.2e-07
                Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpP 80 
                                    +++ +f+G G  +i +al+   +kv++i+in++   ++ +N ++  v+d + ++lgd   ++++    ++  d v++  P
  gi|118431210|ref|NP_147514.2| 119 TVVNMFAGVGVFSIIIALKsrPSKVYSIDINPDAYRLMIENIRLNRVEDVVEPMLGDSARIVSESLRGVA--DRVLMPLP 196
                                    78999*****98887777644789************************************9999777666..88888777 PP

                Methyltransf_15  81 wGGps 85 
                                        +
  gi|118431210|ref|NP_147514.2| 197 DLALD 201
                                    65555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.3e-06    0.0095      31      84 ..     116     171 ..      97     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.3e-06
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEE CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vev 84 
                                      ++v+ + +G+Gv ++ +a +s   +v  +d++  A ++  en++ n++e  ve 
  gi|118431210|ref|NP_147514.2| 116 PGETVVNMFAGVGVFSIIIALKSRPSKVYSIDINPDAYRLMIENIRLNRVEdvVEP 171
                                    667899*****************999***********************9865555 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.2e-06    0.0094       7      78 ..     109     180 ..     100     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.2e-06
                Methyltransf_18   7 aiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                    ++a+lv++g++v+   +  g+ +i ++ +++ +kv+ +Din+ +++   eni+ +++ed +e +l+d    +
  gi|118431210|ref|NP_147514.2| 109 RVARLVKPGETVVNMFAGVGVFSIIIALKSRPSKVYSIDINPDAYRLMIENIRLNRVEDVVEPMLGDSARIV 180
                                    5899**************************************************************987666 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.019      41     152 ..     116     226 ..     104     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                    CC-EEEETT-TTSHHHH.HHH.HTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                  Cons_hypoth95  41 egarvLDlfaGsGalgl.EAl.SRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                     g++v+++faG G+ ++  Al SR  +k++ ++ ++ a++++ en++  ++e+ ++ +  d+++ +++     ++ d v 
  gi|118431210|ref|NP_147514.2| 116 PGETVVNMFAGVGVFSIiIALkSRP-SKVYSIDINPDAYRLMIENIRLNRVEDVVEPMLGDSARIVSES--LRGVADRVL 192
                                    57889********998625774555.9************************999999999999888777..456789999 PP

                                    E--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEE CS
                  Cons_hypoth95 119 lDPPyakellieevlelleekkllkenalvvvet 152
                                    +  P  + ++i ++l++l+ +++l+    v  e+
  gi|118431210|ref|NP_147514.2| 193 MPLPDLALDYIGHALDALRGRGWLHVYLHVDYER 226
                                    9888777778999999999999998766665555 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 ?   13.4   0.0   2.6e-05     0.046      21      70 ..     117     169 ..     109     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                    -SEEEETT-TTSCCH..HCS...SSCEEEEES-HHHHHHHHHHCCH.SHHHHH CS
                MethyltransfD12  21 gktfvepFaGggaVf..feakkqgkkvlinDinedlinlykalikn.nveeli 70 
                                    g+t+v  FaG g+++  +++k+++ kv++ Din+d + l+   i+  +ve+++
  gi|118431210|ref|NP_147514.2| 117 GETVVNMFAGVGVFSiiIALKSRPSKVYSIDINPDAYRLMIENIRLnRVEDVV 169
                                    6799********8772257888****************998777654666665 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.8e-05     0.086      48     100 ..     118     169 ..     102     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                Methyltransf_16  48 lsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskv 100
                                     +v+ + +G G++ +++a++  + kv+  D++  +  l+ +ni ln+  +++ v
  gi|118431210|ref|NP_147514.2| 118 ETVVNMFAGVGVFSIIIALKSRPSKVYSIDINPdAYRLMIENIRLNR--VEDVV 169
                                    6799999***********************9765***********87..55444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.32       4      54 ..     117     166 ..     115     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld 54 
                                    g +v+   +G G +++ +a + +  ++v++iDi+++a +l+ en + + ++
  gi|118431210|ref|NP_147514.2| 117 GETVVNMFAGVGVFSIIIALKSR-PSKVYSIDINPDAYRLMIENIRLNRVE 166
                                    567888999**********5555.59***********99999998877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2402.54
//
Query:       gi|14600989|ref|NP_147515.1|  [L=188]
Description: hypothetical protein APE_0816 [Aeropyrum pernix K1]
Scores for complete 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   93.5   0.0      4e-26   91.7   0.0    1.7  1  TYW3      Methyltransferase TYW3


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.0   2.3e-30     4e-26      18     212 ..      12     182 ..       3     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 2.3e-30
                                   HHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEESS---HHHHHHHHCS- CS
                          TYW3  18 spkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwlfvsHdpvkeeellaelfgl 98 
                                      G++D++  ++++ in+ +++v tSSC GR++++            + ++++ ++g+++ +++H+p++++e+ + l++ 
  gi|14600989|ref|NP_147515.1|  12 RLIGYLDPGAEKVLARINRPSKIVSTSSCTGRITLI------------EGEAHWLRNGARVAYKTHHPISRSEVERVLRRG 80 
                                   5679********************************............56778888999**********999988888877 PP

                                   -..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTT.EEEEEEE---EEEEEEE.. CS
                          TYW3  99 eeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivslkkk.kvivairsglklevpig.. 176
                                                   + +++k+  +ILH++ +  + A++ll+aA+  Gf++SG++s+ ++ + +++i+s+ +++vp++  
  gi|14600989|ref|NP_147515.1|  81 ---------------FTNLWLKVTGPILHLRVEGWQCAKSLLEAARRNGFKHSGVISIAEDsRLVIEIMSSQSMSVPLVme 146
                                   ...............689***************************************99887999**************96 PP

                                   STS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC- CS
                          TYW3 177 kellvseeylkllvklanerfeenkkrierfeealk 212
                                   +  +v ++ l++l++ an+ + e +  ++ f ++++
  gi|14600989|ref|NP_147515.1| 147 GARIVGDDALDMLIEKANTILVESRIGLDTFSREVE 182
                                   449********************9999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1451.63
//
Query:       gi|118431211|ref|YP_874850.1|  [L=42]
Description: hypothetical protein APE_0816a.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       114  (0.00635841); expected 358.6 (0.02)
Passed bias filter:                      104  (0.00580066); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 349.09
//
Query:       gi|118431212|ref|NP_147516.2|  [L=413]
Description: hypothetical protein APE_0818.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-06   27.3   0.1    4.8e-06   26.5   0.1    1.4  1  Phage_integrase  Phage integrase family
     0.0014   18.6   0.2      0.011   15.7   0.2    2.3  1  Phage_integr_3   Archaeal phage integrase
  ------ inclusion threshold ------
      0.089   11.7   0.0       0.13   11.1   0.0    1.2  1  DUF3435          Protein of unknown function (DUF3435)
       0.11   13.0   1.0        1.2    9.7   0.0    2.9  2  Rnk_N            Rnk N-terminus


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 !   26.5   0.1   1.1e-09   4.8e-06       7     167 ..     228     385 ..     225     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                                    HHHHHHHCCGC.HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECT.HHHHHHHHHHH CS
                Phage_integrase   7 everllaalee.slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravpls.eealellkell 84 
                                    + + +   +e  +++   ++ll ll +tGlR+  + sL ++ l+l ++ ++v    +K+sk ++  +  e +   l+ +l
  gi|118431212|ref|NP_147516.2| 228 QWSDICRVVEAlPHAGAPRALLLLLASTGLRVETAYSLPLDSLKLSERLVWV--WSLKRSKRTYFSFItERVKGELEVYL 305
                                    5666777777777788889*********************************..9*******999887577777888888 PP

                                    HHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-S..SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCH CS
                Phage_integrase  85 skaleeaeksellfaskrgkplsrqtvrkafkraveeagie..kpltpHtlRhsfataLleagvdlrvvqkllGHssist 162
                                    + +     +++l ++ +   +l   + r+  +++ e+ + e   +++   +R+ +a +L  +  ++ ++  ++GH+  + 
  gi|118431212|ref|NP_147516.2| 306 EAR-----RRHLEILGRGSGKLFPYKPRRLREAIYEAMDRElgRRFQLKLIRKRVAEHLSHHL-STLELNVIMGHAPREV 379
                                    888.....67777777755666666666655555555555566789999*********99876.8999********9999 PP

                                    H.HHHH CS
                Phage_integrase 163 t.qiYt 167
                                    + ++Y 
  gi|118431212|ref|NP_147516.2| 380 VeKHYL 385
                                    988885 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   2.4e-06     0.011     103     146 ..     336     387 ..     226     403 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                                    T.........--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CCTTSCHHCHH CS
                 Phage_integr_3 103 k.........vkakyiRkwvatklaelgvpeevidFiqGrkpssvlekhYlnl 146
                                    +         ++ k iRk va  l +    +e  + i+G++p++v ekhYl  
  gi|118431212|ref|NP_147516.2| 336 EamdrelgrrFQLKLIRKRVAEHLSHHLSTLE-LNVIMGHAPREVVEKHYLLR 387
                                    02223334449*************99888888.589**************954 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     3e-05      0.13     200     248 ..     351     397 ..     342     406 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3e-05
                        DUF3435 200 lRrgaakalneSgevseaqrnlilqHassrtFlkhYlsqkvdkdvqavv 248
                                    +R+ +a++l    + s+ + n+i++Ha  ++ +khYl ++  +d+++ +
  gi|118431212|ref|NP_147516.2| 351 IRKRVAEHLSH--HLSTLELNVIMGHAPREVVEKHYLLRDQIEDLRRKY 397
                                    68899999988..***********************9999888887665 PP

>> Rnk_N  Rnk N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.27   1.2e+03      12      23 ..      52      62 ..      50      67 .. 0.62
   2 ?    9.7   0.0   0.00027       1.2       8      37 ..      83     116 ..      80     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.27
                                   HHHHHHHCTTTT CS
                          Rnk_N 12 RLeaLldsladr 23
                                   +Le+Ll+ la +
  gi|118431212|ref|NP_147516.2| 52 ILERLLE-LATD 62
                                   6888888.4333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                                    HHHHHHHHHHHCTTTTSSTTHHH....HHHHHHC CS
                          Rnk_N   8 lDleRLeaLldsladrdppaaea....LeaELdR 37 
                                     D +RL +L++  a+++p+ a+     L aEL+R
  gi|118431212|ref|NP_147516.2|  83 YDVDRLVRLVAEWARANPASAKVfldsLSAELER 116
                                    59*********5555555555555555******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2999.76
//
Query:       gi|118431213|ref|YP_874851.1|  [L=83]
Description: hypothetical protein APE_0818a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 697.33
//
Query:       gi|118431214|ref|NP_147518.2|  [L=129]
Description: hypothetical protein APE_0820.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1137.31
//
Query:       gi|14600993|ref|NP_147519.1|  [L=326]
Description: hypothetical protein APE_0821 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0017   18.2   0.4       0.36   10.8   0.0    2.6  2  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0034   17.0   0.1      0.018   14.7   0.1    2.3  1  GntR           Bacterial regulatory proteins, gntR family
     0.0035   17.5   2.1     0.0035   17.5   2.1    2.7  3  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
  ------ inclusion threshold ------
        0.1   12.4   0.3        1.3    8.8   0.0    2.7  3  LexA_DNA_bind  LexA DNA binding domain
       0.12   10.7   0.0       0.67    8.2   0.0    1.9  2  DUF505         Protein of unknown function (DUF505)
       0.13   11.9   1.5        2.1    8.0   0.0    2.9  3  HTH_24         Winged helix-turn-helix DNA-binding
       0.24   11.3   5.1        2.3    8.2   0.3    3.5  3  MarR_2         MarR family
       0.25   11.0   3.2       0.55    9.9   0.0    2.6  3  HTH_33         Winged helix-turn helix


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.01        23      21      51 ..      48      81 ..      39      84 .. 0.75
   2 !   10.8   0.0   0.00016      0.36      34      62 ..     166     194 ..     139     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.01
                                  CCCHHCHHCCCT...TSSCHCHHHHHHHHHHCTS CS
                          TrmB 21 gpatadeiaeel...gvprskvYevLrsLedkGl 51
                                    +  +eia+++    + r +v ++Lr+L ++G+
  gi|14600993|ref|NP_147519.1| 48 RGLGLSEIAKAVygtSRKRYRVFRILRRLQRMGV 81
                                  555666777764333789999***********97 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00016
                                   SSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                          TrmB  34 vprskvYevLrsLedkGlVerekgrpklY 62 
                                   v+r+ v  +L++L+ +G+Ver ++ +++ 
  gi|14600993|ref|NP_147519.1| 166 VSRNAVWHALKRLSARGVVERLPRGYYRL 194
                                   8999*****************99888765 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   8.1e-06     0.018      36      59 ..     166     189 ..     161     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.1e-06
                                   S-HHHHHHHHHHHHHTTSEEEETT CS
                          GntR  36 VsrttvReALrrLeaeglverrqg 59 
                                   Vsr+ v  AL+rL+a+g+ver ++
  gi|14600993|ref|NP_147519.1| 166 VSRNAVWHALKRLSARGVVERLPR 189
                                   9********************998 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3      0.36   8.1e+02      21      39 ..      58      83 ..      38      86 .. 0.72
   2 !   17.5   2.1   1.6e-06    0.0035      25      48 ..     167     194 ..     165     195 .. 0.85
   3 ?   -3.6   0.4       5.9   1.3e+04      33      42 ..     256     265 ..     255     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.36
                       AbiEi_4 21 a.aGisp.sa.....lrrLvrkGwLv 39
                                  a  G s+ ++     lrrL r G L 
  gi|14600993|ref|NP_147519.1| 58 AvYGTSRkRYrvfriLRRLQRMGVLD 83
                                  44566664448999999999988875 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                       AbiEi_4  25 spsa....lrrLvrkGwLvrlrrGvYal 48 
                                   s++a    l rL  +G ++rl+rG+Y+l
  gi|14600993|ref|NP_147519.1| 167 SRNAvwhaLKRLSARGVVERLPRGYYRL 194
                                   56566666******************97 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.9
                       AbiEi_4  33 vrkGwLvrlr 42 
                                    ++ +L+rl+
  gi|14600993|ref|NP_147519.1| 256 EKARLLERLG 265
                                   6777888887 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 ?   -0.9   0.0      0.65   1.4e+03      43      57 ..      69      83 ..      51      85 .. 0.67
   2 ?    8.8   0.0   0.00058       1.3      39      60 ..     167     188 ..     132     190 .. 0.91
   3 ?   -0.9   0.0      0.62   1.4e+03      55      64 ..     272     281 ..     260     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.65
                                  HHHHHHHHHHTTSEE CS
                 LexA_DNA_bind 43 veehLkaLerKGyie 57
                                  v   L++L+r G+++
  gi|14600993|ref|NP_147519.1| 69 VFRILRRLQRMGVLD 83
                                  456689999999987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00058
                                   .HHHHHHHHHHHHHTTSEE-GG CS
                 LexA_DNA_bind  39 SpsaveehLkaLerKGyierdp 60 
                                   S +av + Lk+L+ +G++er p
  gi|14600993|ref|NP_147519.1| 167 SRNAVWHALKRLSARGVVERLP 188
                                   789****************987 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.62
                                   SEE-GGG-CC CS
                 LexA_DNA_bind  55 yierdpgkpR 64 
                                   yi+r++g+pR
  gi|14600993|ref|NP_147519.1| 272 YIDRKNGAPR 281
                                   89*******9 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.12   2.8e+02     479     521 ..      45      89 ..      33      92 .. 0.79
   2 ?    8.2   0.0    0.0003      0.67     494     524 ..     164     194 ..     146     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.12
                        DUF505 479 iPkrgvsveelveev..deleeeevrealeklearglvevlpdgn 521
                                   + +rg  ++e+ ++v  +  ++ +v + l++l+  g+++ l +g 
  gi|14600993|ref|NP_147519.1|  45 LKRRGLGLSEIAKAVygTSRKRYRVFRILRRLQRMGVLDCLLEGS 89 
                                   4489999999*99997777788899999**********9999885 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0003
                        DUF505 494 deleeeevrealeklearglvevlpdgnvvl 524
                                   + + ++ v +al++l arg+ve lp g++ l
  gi|14600993|ref|NP_147519.1| 164 KRVSRNAVWHALKRLSARGVVERLPRGYYRL 194
                                   6678999********************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 ?   -3.5   0.0       3.7   8.2e+03      18      26 ..      50      58 ..      35      59 .. 0.59
   2 ?    1.8   0.1     0.078   1.7e+02      34      47 ..      69      82 ..      68      83 .. 0.80
   3 ?    8.0   0.0   0.00093       2.1      29      48 .]     166     185 ..     165     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.7
                        HTH_24 18 isqreLAer 26
                                  +  +e+A++
  gi|14600993|ref|NP_147519.1| 50 LGLSEIAKA 58
                                  555677765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.078
                        HTH_24 34 vnrrlkrLeeeGlI 47
                                  v r l+rL+++G++
  gi|14600993|ref|NP_147519.1| 69 VFRILRRLQRMGVL 82
                                  56889999999985 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00093
                        HTH_24  29 lSpstvnrrlkrLeeeGlIk 48 
                                   +S+++v+  lkrL   G+++
  gi|14600993|ref|NP_147519.1| 166 VSRNAVWHALKRLSARGVVE 185
                                   699***************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.032        71      31      50 ..      62      81 ..      30      83 .. 0.73
   2 ?    8.2   0.3     0.001       2.3       9      54 ..     138     187 ..     130     190 .. 0.67
   3 ?   -3.5   0.1       4.4   9.9e+03      45      53 ..     255     263 ..     253     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.032
                                  HTSSHHHHHHHHHHHHHTTS CS
                        MarR_2 31 lglsksavsrilkrLvaaGL 50
                                  +  ++ +v ril+rL++ G 
  gi|14600993|ref|NP_147519.1| 62 TSRKRYRVFRILRRLQRMGV 81
                                  5567899*********9885 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                                   HHHHHHHCTTTSEEEHHHHHH......HHTSSHHHHHHHHHHHHHTTSEEEE CS
                        MarR_2   9 rvLaaLgrrpgrdltvgelar......rlglsksavsrilkrLvaaGLverr 54 
                                    v+aaL+   +   t++ +a+        ++s+ av  +lkrL+a+G ver 
  gi|14600993|ref|NP_147519.1| 138 LVIAALAIQLE--ATPSMIAAyvnhayGKRVSRNAVWHALKRLSARGVVERL 187
                                   55555555555..5666666622222222589999999************96 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.4
                                   HHHTTSEEE CS
                        MarR_2  45 LvaaGLver 53 
                                   L++a L+er
  gi|14600993|ref|NP_147519.1| 255 LEKARLLER 263
                                   777777776 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.2       2.7   6.1e+03      11      35 ..      56      80 ..      52      80 .. 0.54
   2 ?    9.9   0.0   0.00024      0.55       7      34 ..     151     178 ..     149     181 .. 0.93
   3 ?    0.9   0.1      0.17   3.7e+02      29      37 ..     259     267 ..     258     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                        HTH_33 11 aqlieerfgvsysvsgvyrlLkrlG 35
                                  a+ +  + +++y v ++ r L+r+G
  gi|14600993|ref|NP_147519.1| 56 AKAVYGTSRKRYRVFRILRRLQRMG 80
                                  5555555555666656656666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00024
                        HTH_33   7 larlaqlieerfgvsysvsgvyrlLkrl 34 
                                    + +a+++   +g+++s+  v+  Lkrl
  gi|14600993|ref|NP_147519.1| 151 PSMIAAYVNHAYGKRVSRNAVWHALKRL 178
                                   5789***********************8 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.17
                        HTH_33  29 rlLkrlGfs 37 
                                   rlL rlG++
  gi|14600993|ref|NP_147519.1| 259 RLLERLGWR 267
                                   9*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2575.99
//
Query:       gi|14600995|ref|NP_147521.1|  [L=233]
Description: hypothetical protein APE_0824 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-12   46.3   0.1    5.5e-12   45.9   0.1    1.3  1  Peptidase_M48  Peptidase family M48
  ------ inclusion threshold ------
      0.018   15.1   0.5      0.036   14.1   0.5    1.4  1  DUF45          Protein of unknown function DUF45
      0.057   13.2   2.2      0.069   12.9   0.9    1.8  2  Peptidase_U49  Peptidase U49
      0.064   12.8   0.0       0.12   11.9   0.0    1.5  1  DUF2268        Predicted Zn-dependent protease (DUF2268)


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 !   45.9   0.1   1.2e-15   5.5e-12      36     152 ..      70     190 ..      35     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.2e-15
                                   -EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48  36 NAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivsllasillllglallisraeedaagaflda 116
                                    AF +g g    +++ ++L  ++l ee ++++ +HE++Hi+++h++ s    +l +i +  +   + + ++ ++++  +++
  gi|14600995|ref|NP_147521.1|  70 LAFSIGLGGYGIVFIRRELA-DKLPEEVIKFIVAHEVAHIVKNHAIASYTTRQLTKISFDSLKDSIKNLNRTKKSEKPTAN 149
                                   59999999888899999999.*********************************************************999 PP

                                   --HHHHHHHHHHTT.....HHHHHHHHHHHHHHHHTTT.HH CS
                                   xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M48 117 lavliglliillfl.....alSRkrEyqADeagvellkrak 152
                                   l  +i+ l +l ++        +++E++AD ++++++  + 
  gi|14600995|ref|NP_147521.1| 150 LLLIIISLALLAQTtkyeaTTIKEQELEADTLAAKTTGCKP 190
                                   99999999999888***99899*************998444 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   8.1e-06     0.036     160     182 ..      91     112 ..      88     118 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.1e-06
                         DUF45 160 kappevidYVvvHElaHlleknH 182
                                   k+p+evi+++v+HE+aH++  nH
  gi|14600995|ref|NP_147521.1|  91 KLPEEVIKFIVAHEVAHIVK-NH 112
                                   68***************985.44 PP

>> Peptidase_U49  Peptidase U49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9   1.5e-05     0.069      98     133 ..      94     129 ..      85     170 .. 0.82
   2 ?   -0.9   0.0      0.27   1.2e+03     120     137 ..     167     184 ..     147     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                 Peptidase_U49  98 lkalayillHEvaHvvlqeekksteeslreEleaDS 133
                                    +++ +i+ HEvaH+v ++ + s   +    +  DS
  gi|14600995|ref|NP_147521.1|  94 EEVIKFIVAHEVAHIVKNHAIASYTTRQLTKISFDS 129
                                   5799*****************998888777777777 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.27
                 Peptidase_U49 120 steeslreEleaDSfAle 137
                                       ++++EleaD  A +
  gi|14600995|ref|NP_147521.1| 167 EATTIKEQELEADTLAAK 184
                                   556678889999998876 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05      0.12      25      83 ..      56     115 ..      29     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                       DUF2268  25 ilpvneenrklieekgykgglaipdkiflfl.leneyskerlaallaHEyhHvvrlkqle 83 
                                   +++  e+++    e + + gl+  + +f+   l ++  +e ++ ++aHE+ H v  +++ 
  gi|14600995|ref|NP_147521.1|  56 VALFKENEKLPAYELAFSIGLGGYGIVFIRReLADKLPEEVIKFIVAHEVAHIVKNHAIA 115
                                   3455555545555667777777778888888888999999**************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1689.28
//
Query:       gi|118431215|ref|NP_147522.2|  [L=308]
Description: hypothetical protein APE_0825.1 [Aeropyrum pernix K1]
Scores for 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   1.3      0.032   14.2   0.3    2.5  2  Phage_int_SAM_6  Phage integrase SAM-like domain
  ------ inclusion threshold ------
      0.071   12.5   0.1       0.16   11.4   0.0    1.6  2  Glucodextran_C   C-terminal binding-module, SLH-like, of gluc
      0.074   13.1   3.1        2.1    8.4   0.8    2.7  2  DUF4320          Domain of unknown function (DUF4320)


Domain annotation for each model (and alignments):
>> Phage_int_SAM_6  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.31   1.9e+03      73      97 ..     112     135 ..     102     147 .. 0.72
   2 !   14.2   0.3   5.4e-06     0.032      15      79 ..     165     231 ..     153     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.31
                Phage_int_SAM_6  73 nPllklyeyliklelaslkeideel 97 
                                    +P+ kl +++ k   +s+k++deel
  gi|118431215|ref|NP_147522.2| 112 KPISKLLDVCRKH-KKSVKSLDEEL 135
                                    5777887766554.46777777764 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.4e-06
                Phage_int_SAM_6  15 erfvkskltsLsnkqvkdkealakviqelkkgvksie..elekivkeaRniGliGintyanPllkly 79 
                                    + fvk+k+ + + + ++++e+  +  + +k++++  +  ++e  +k++ + G+ Gi++y+  ++ +y
  gi|118431215|ref|NP_147522.2| 165 KEFVKTKVLAPTIRTIHNNESQWTLENIVKEARRIQDeiKMEVKLKDTYKGGMSGIDVYMYAFKLVY 231
                                    689**************99875544444444433333114667789*************99877766 PP

>> Glucodextran_C  C-terminal binding-module, SLH-like, of glucodextranase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.16     190     222 ..     134     166 ..     120     173 .. 0.85
   2 ?   -3.0   0.0      0.66   3.9e+03     172     184 ..     177     189 ..     175     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                 Glucodextran_C 190 idagvaPkviDllapegetQeevLssydvsakk 222
                                       ++a++v+D +++e  +Q+++L+ yd s k+
  gi|118431215|ref|NP_147522.2| 134 ELDEIASRVVDFVVQELGQQYKILETYDNSFKE 166
                                    556899*********************998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.66
                 Glucodextran_C 172 iRkvseeagewrf 184
                                    iR++++++++w++
  gi|118431215|ref|NP_147522.2| 177 IRTIHNNESQWTL 189
                                    7888999999986 PP

>> DUF4320  Domain of unknown function (DUF4320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8   0.00036       2.1      19      91 ..     130     214 ..     126     224 .. 0.63
   2 ?    3.9   0.1    0.0093        56      20      50 ..     255     285 ..     246     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
                        DUF4320  19 ttkqkldtvaselvreaelsGg....vgseteeraaelkeqtglepdisw.skeqtdek.........tgkiqlndevtv 84 
                                    ++  +ld++as++v+ + ++ g    + +++++ ++e  +   l+p+i+   ++   ++          ++iq + +++v
  gi|118431215|ref|NP_147522.2| 130 SLDEELDEIASRVVDFVVQELGqqykILETYDNSFKEFVKTKVLAPTIRTiHNN--ESQwtlenivkeARRIQDEIKMEV 207
                                    566789999999988766554301113344555555554444467777663322..2223456666669*********** PP

                        DUF4320  85 titteak 91 
                                    ++++++k
  gi|118431215|ref|NP_147522.2| 208 KLKDTYK 214
                                    ****998 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0093
                        DUF4320  20 tkqkldtvaselvreaelsGgvgseteeraa 50 
                                     +qkl  +a+ lv+ +e + ++++++ee ++
  gi|118431215|ref|NP_147522.2| 255 FEQKLASYAKDLVDKVEETSSLTRSAEEIKK 285
                                    579*******************999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1366  (0.0761894); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2155.55
//
Query:       gi|14600997|ref|NP_147523.1|  [L=263]
Description: hypothetical protein APE_0826 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.3   1.1         14    5.2   0.3    2.3  2  m04gp34like  Immune evasion protein
        1.8    8.5   5.7        2.5    8.0   1.1    2.9  3  DUF2721      Protein of unknown function (DUF2721)
        8.7    5.9   7.7        4.4    6.9   2.7    2.2  2  Saf_2TM      SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> m04gp34like  Immune evasion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.003        18     226     252 ..      53      79 ..      17      83 .. 0.82
   2 ?    5.2   0.3    0.0023        14     230     266 ..      91     122 ..      84     127 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.003
                                   X......XXXXXXXXXXXXXXXXXXXX CS
                   m04gp34like 226 sdnrallvtilsvivvllivvvllvLa 252
                                   +d + +lv ++ ++v+l+i+vv+ +L 
  gi|14600997|ref|NP_147523.1|  53 MDLKPKLVSVILFVVSLVIIVVSWLLY 79 
                                   44567899**************99875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0023
                                   ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   m04gp34like 230 allvtilsvivvllivvvllvLaylYgpsllrrlssr 266
                                   + ++ti+svi++l  + +  +    Y++++ r l ++
  gi|14600997|ref|NP_147523.1|  91 SGVLTIISVIISLFVLGA--I---YYQAYYTRELAQQ 122
                                   667889999888744433..3...3556666655544 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.1   0.00041       2.5      83     116 ..      46      79 ..      40      82 .. 0.84
   2 ?    0.3   0.1       0.1   6.2e+02      70      85 ..      92     107 ..      86     141 .. 0.64
   3 ?    0.0   0.0      0.12   7.3e+02      24      48 ..     212     235 ..     207     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00041
                       DUF2721  83 llflsallsldlsllaailfvlalllllvslllf 116
                                   l +l ++++l+ +l+ +ilfv++l++++vs ll 
  gi|14600997|ref|NP_147523.1|  46 LSILWEMMDLKPKLVSVILFVVSLVIIVVSWLLY 79 
                                   455668899999******************9986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                       DUF2721  70 lvlsallvvlvvlllf 85 
                                   +vl+++ v+++ ++l 
  gi|14600997|ref|NP_147523.1|  92 GVLTIISVIISLFVLG 107
                                   3444444444444433 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.12
                       DUF2721  24 riadrirqLedeleelaeeeeedee 48 
                                    i dr r L ++l++  +ee + ++
  gi|14600997|ref|NP_147523.1| 212 EILDRTRILLKQLDNPITEETS-KT 235
                                   699*******999976666443.33 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 ?    6.9   2.7   0.00074       4.4      53      87 ..      45      80 ..      41      84 .. 0.84
   2 ?    1.1   0.2     0.045   2.7e+02      67     102 ..      93     124 ..      87     126 .. 0.47

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00074
                       Saf_2TM 53 slevsfssse.ipeivlaiilvigvllivvGavlli 87
                                  sl++ +++ + +p++v++i++v++ ++ivv+ +l i
  gi|14600997|ref|NP_147523.1| 45 SLSILWEMMDlKPKLVSVILFVVSLVIIVVSWLLYI 80
                                  566677888999*******************77766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.045
                       Saf_2TM  67 vlaiilvigvllivvGavllilryvneakrqskkkv 102
                                   vl+ii vi + l+v+Ga+  ++ y    + +++ +v
  gi|14600997|ref|NP_147523.1|  93 VLTIISVIIS-LFVLGAI-YYQAY--YTRELAQQQV 124
                                   4444444444.4555533.34444..2455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2021.11
//
Query:       gi|14600998|ref|NP_147524.1|  [L=54]
Description: hypothetical protein APE_0826a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.7    6.3   6.2        6.5    6.1   6.2    1.1  1  UPF0524   UPF0524 of C3orf70


Domain annotation for each model (and alignments):
>> UPF0524  UPF0524 of C3orf70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.2   0.00036       6.5      35      55 ..      32      52 ..      24      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00036
                       UPF0524 35 hgkcfklhwcchlgwchckyv 55
                                  h  c   h  c +gwc c ++
  gi|14600998|ref|NP_147524.1| 32 HLVCCMAHIVCRVGWCLCMWI 52
                                  778999************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 450.64
//
Query:       gi|118431216|ref|YP_874852.1|  [L=91]
Description: hypothetical protein APE_0826b [Aeropyrum pernix K1]
Scores for 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   17.8   0.8     0.0038   17.5   0.8    1.1  1  DUF996           Protein of unknown function (DUF996)
  ------ inclusion threshold ------
      0.064   13.0   4.2       0.17   11.7   0.2    2.1  2  PQ-loop          PQ loop repeat
       0.47   10.7   7.9       0.57   10.5   0.2    2.1  2  TctB             Tripartite tricarboxylate transporter TctB f
        2.2    8.1   7.6        4.9    6.9   0.8    2.3  2  FeoB_C           Ferrous iron transport protein B C terminus
        4.4    6.3   7.3        5.3    6.1   7.3    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
        4.4    7.8  11.4        2.9    8.4   3.0    2.3  2  DUF2768          Protein of unknown function (DUF2768)
        6.7    6.5   9.4        1.6    8.4   4.0    2.1  2  DUF4750          Domain of unknown function (DUF4750)
        9.1    4.9   5.1         11    4.7   5.1    1.0  1  DUF2207          Predicted membrane protein (DUF2207)


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 !   17.5   0.8   1.7e-06    0.0038      31     100 ..      12      82 ..       5      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.7e-06
                         DUF996  31 iafilsiialvva..ilalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkksyellgk 100
                                    +  i++i+a v++  ++++ +++ + a  + ++g+      + l++l+li +++++ +s +f ++++++lg 
  gi|118431216|ref|YP_874852.1|  12 VDYIIDIVAGVLMafFMVVFGWFLKGAYEVHRAGACD-GLCMNLFVLSLIGFMLATALSLFFSRSILRKLGG 82 
                                    4567777754444235555566666666666665554.449***************************9985 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5     0.038        85      39      59 ..      15      35 ..      14      37 .. 0.85
   2 ?   11.7   0.2   7.6e-05      0.17      22      56 ..      39      73 ..      38      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.038
                        PQ-loop 39 llwllGdilsllylilngfpp 59
                                   ++++++++l +++++++g+ +
  gi|118431216|ref|YP_874852.1| 15 IIDIVAGVLMAFFMVVFGWFL 35
                                   6899999**9***99999875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.6e-05
                        PQ-loop 22 ikNykrkSteGlSilflllwllGdilsllylilng 56
                                   ++ ++   ++Gl +  ++l l+G++l ++ +++++
  gi|118431216|ref|YP_874852.1| 39 YEVHRAGACDGLCMNLFVLSLIGFMLATALSLFFS 73
                                   899*********************99887777665 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.9     0.037        84     112     131 ..      18      36 ..       8      38 .. 0.70
   2 ?   10.5   0.2   0.00025      0.57      76     105 ..      49      73 ..      40      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.037
                           TctB 112 lilavvlallvyllFtklLg 131
                                    ++ +v l ++++++F ++L+
  gi|118431216|ref|YP_874852.1|  18 IVAGV-LMAFFMVVFGWFLK 36 
                                    44555.55555899999997 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00025
                           TctB  76 alllyallleplGfilatalflllllgree 105
                                    +l++ +++l  +Gf+latal l+   +  +
  gi|118431216|ref|YP_874852.1|  49 GLCMNLFVLSLIGFMLATALSLF---F--S 73 
                                    56778999***********5552...1..2 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.0    0.0092        21       5      19 ..      14      28 ..      10      41 .. 0.70
   2 ?    6.9   0.8    0.0022       4.9       1      25 [.      54      78 ..      54      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0092
                         FeoB_C  5 Yllgilvallvalll 19
                                   Y++ i++ +l+a+++
  gi|118431216|ref|YP_874852.1| 14 YIIDIVAGVLMAFFM 28
                                   788888888888776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0022
                         FeoB_C  1 lfslYllgilvallvalllkktt.lk 25
                                   lf+l l+g+++a +++l++++   l+
  gi|118431216|ref|YP_874852.1| 54 LFVLSLIGFMLATALSLFFSR-SiLR 78
                                   6999***************99.5465 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.3    0.0024       5.3     209     261 ..      13      74 ..       9      81 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0024
                ABC2_membrane_3 209 kilgdflvyllqlllilll..afglgipfgnlgl.......llllfllfglayialgyllss 261
                                     +++d ++++l++++++++  +++ ++++   g+       l++l+l+++++++al++++s 
  gi|118431216|ref|YP_874852.1|  13 DYIIDIVAGVLMAFFMVVFgwFLKGAYEVHRAGAcdglcmnLFVLSLIGFMLATALSLFFSR 74 
                                    58888888888888888876433335555544332221222667777788888888887774 PP

>> DUF2768  Protein of unknown function (DUF2768)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.0    0.0013       2.9      34      57 ..       8      33 ..       3      33 .. 0.84
   2 ?    4.3   1.3     0.024        53       7      26 ..      58      77 ..      51      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                        DUF2768 34 ivaliAyilllvsglii..vlvVlsG 57
                                   +va++ yi+ +v+g+++  ++vV+++
  gi|118431216|ref|YP_874852.1|  8 FVAVVDYIIDIVAGVLMafFMVVFGW 33
                                   6899************9444589987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.024
                        DUF2768  7 asiglmflsvlliilsrekl 26
                                     ig+m+  +l+ ++sr  l
  gi|118431216|ref|YP_874852.1| 58 SLIGFMLATALSLFFSRSIL 77
                                   4589************9765 PP

>> DUF4750  Domain of unknown function (DUF4750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.0   0.00073       1.6       9      29 ..      15      35 ..       8      36 .. 0.90
   2 ?    1.0   0.2      0.15   3.4e+02      18      25 ..      55      62 ..      51      81 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00073
                        DUF4750  9 vlrlllalliVlllillgWyl 29
                                   ++ +++ +l+ ++++++gW+l
  gi|118431216|ref|YP_874852.1| 15 IIDIVAGVLMAFFMVVFGWFL 35
                                   7899****************8 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                        DUF4750 18 iVlllill 25
                                   +Vl+li +
  gi|118431216|ref|YP_874852.1| 55 FVLSLIGF 62
                                   55555433 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   5.1    0.0047        11     388     436 ..      18      79 ..       8      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0047
                        DUF2207 388 lgliilglilillallllvll.............lvfllilllillliaiivlllfsrllgr 436
                                    +++++l+ ++++++ ++l ++             ++++++ l++++l+ ++ l++++++l++
  gi|118431216|ref|YP_874852.1|  18 IVAGVLMAFFMVVFGWFLKGAyevhragacdglcMNLFVLSLIGFMLATALSLFFSRSILRK 79 
                                    3344444444444433334346778********99999999999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 684.19
//
Query:       gi|118431217|ref|NP_147525.2|  [L=159]
Description: hypothetical protein APE_0827.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1130.28
//
Query:       gi|14601001|ref|NP_147527.1|  [L=318]
Description: hypothetical protein APE_0830 [Aeropyrum pernix K1]
Scores for complete sequence (score 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       0.45   10.4   0.0    1.8  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


Domain annotation for each model (and alignments):
>> 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 ?   10.4   0.0   2.5e-05      0.45      14      30 ..     143     159 ..     137     172 .. 0.80
   2 ?   -3.2   0.0      0.44   7.8e+03      21      37 ..     209     231 ..     206     233 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.5e-05
               DNA_pol_lambd_f  14 AkkwyakGirtledlra 30 
                                    +k+ ++G+r++edl++
  gi|14601001|ref|NP_147527.1| 143 VSKFRERGFRSIEDLKT 159
                                   57999**********98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.44
               DNA_pol_lambd_f  21 Girtledlra......krakLtr 37 
                                    +  le +r+      ++++Lt 
  gi|14601001|ref|NP_147527.1| 209 ELERLERVRElvkeygGGSSLTV 231
                                   55667777776667765577765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      693  (0.0386525); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2322.66
//
Query:       gi|118431218|ref|NP_147529.2|  [L=134]
Description: hypothetical protein APE_0832.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1102.55
//
Query:       gi|118431219|ref|NP_147530.2|  [L=267]
Description: hypothetical protein APE_0833.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.059   13.7   0.0        0.1   13.0   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.066   12.4   0.0      0.094   11.9   0.0    1.2  1  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.12   12.8   0.0       0.34   11.3   0.0    1.8  1  RNA_helicase  RNA helicase


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 ?   13.0   0.0   1.7e-05       0.1      19      51 ..      33      65 ..      22     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd 51
                                    r+g+ ++v+++G +G GKs  + ++   l ++
  gi|118431219|ref|NP_147530.2| 33 FRTGGFNSVIVYGKQGAGKSVYAIKVVYDLLRR 65
                                   356777**************9885444455555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.6e-05     0.094       4      25 ..      41      62 ..      39      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.6e-05
                        DUF2075  4 vlVtGvaGtGKtvvllnllael 25
                                   v+V G+ G+GK+v +++++++l
  gi|118431219|ref|NP_147530.2| 41 VIVYGKQGAGKSVYAIKVVYDL 62
                                   79******************99 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.6e-05      0.34       1      27 [.      41      67 ..      41      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.6e-05
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklk 27
                                   +++yG++g GKS++a +++ +ll++l+
  gi|118431219|ref|NP_147530.2| 41 VIVYGKQGAGKSVYAIKVVYDLLRRLG 67
                                   689***************999998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2153.79
//
Query:       gi|14601005|ref|NP_147531.1|  [L=221]
Description: hypothetical protein APE_0836 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1829.74
//
Query:       gi|14601006|ref|NP_147532.1|  [L=238]
Description: hypothetical protein APE_0837 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1728.64
//
Query:       gi|14601009|ref|NP_147535.1|  [L=421]
Description: hypothetical protein APE_0840 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.47u 0.19s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3443.03
//
Query:       gi|118431220|ref|YP_874853.1|  [L=96]
Description: hypothetical protein APE_0840a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0011   19.3   0.0     0.0017   18.7   0.0    1.3  1  Tim17     Tim17/Tim22/Tim23/Pmp24 family
  ------ inclusion threshold ------
      0.011   16.1   4.3      0.015   15.6   4.3    1.2  1  DUF3566   Transmembrane domain of unknown function (DUF3566)
      0.018   14.8   0.1      0.041   13.6   0.1    1.6  1  Rz1       Lipoprotein Rz1 precursor
       0.37   10.7   0.8        2.3    8.2   0.6    1.9  2  HlyD      HlyD membrane-fusion protein of T1SS
       0.44   10.9   1.8       0.52   10.6   0.0    1.8  2  Orf78     Orf78 (ac78)
        7.4    6.8   8.0          3    8.1   2.8    2.0  2  HemY_N    HemY protein N-terminus


Domain annotation for each model (and alignments):
>> Tim17  Tim17/Tim22/Tim23/Pmp24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.6e-07    0.0017      10      77 ..      22      91 ..      16      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                          Tim17 10 vlGallGavfglvkgsrradtp..apsker...lreglrsvgkrgpslGknfgvvgglysgiecaleklRgke 77
                                   v+G+++G+++g+ + + +a +   +        ++++l+s+++++  + + + vv++l +++  ++e+lR + 
  gi|118431220|ref|YP_874853.1| 22 VVGWVIGVIWGVWQQLDQATAGtmIE---PpqdWKNMLNSLYSNMLGIWNYLPVVVLLSAVVYIIIESLRRRP 91
                                   89**************8888643333...2556************************************9875 PP

>> DUF3566  Transmembrane domain of unknown function (DUF3566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   4.3   5.1e-06     0.015      21      93 ..       7      86 ..       2      89 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                        DUF3566 21 fllsvalfivlvvavavlylvldalgvfdkvnslvkdlvgee.......ssldleevlslgrvlslaalvgvvnvvllta 93
                                   +++ v +f+++++  +v +++    gv+++++++ + ++ e         ++  +++l +++ l +++l+++v  +++  
  gi|118431220|ref|YP_874853.1|  7 VVAVVGFFVMWLMFQVVGWVIGVIWGVWQQLDQATAGTMIEPpqdwknmLNSLYSNMLGIWNYLPVVVLLSAVVYIIIES 86
                                   444556778889999999***************99866655556777654555678999999999999999999888865 PP

>> Rz1  Lipoprotein Rz1 precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.4e-05     0.041      20      35 ..      45      60 ..      42      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                            Rz1 20 amqpppdwqqlLneii 35
                                   +++pp+dw+ +Ln+  
  gi|118431220|ref|YP_874853.1| 45 MIEPPQDWKNMLNSLY 60
                                   789**********975 PP

>> HlyD  HlyD membrane-fusion protein of T1SS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.6   0.00077       2.3       2      26 ..      11      47 ..      10      53 .. 0.90
   2 ?    0.5   0.0      0.19   5.6e+02      18      33 ..      65      80 ..      61      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00077
                                   SEEEEEEEEEE............EEEEEEEECEEEEE CS
                                   xxxxxxxxxxx............xxxxxxxxxxxxxx RF
                           HlyD  2 lavfvawaala............etdldqvrvgqpve 26
                                   ++ fv+w++++            + +ldq+++g  +e
  gi|118431220|ref|YP_874853.1| 11 VGFFVMWLMFQvvgwvigviwgvWQQLDQATAGTMIE 47
                                   899****************************997665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                                   EEECEEEEEEEGCGEE CS
                                   xxxxxxxxxxxxxxxx RF
                           HlyD 18 qvrvgqpvevrfdAfp 33
                                   ++++ +pv v ++A+ 
  gi|118431220|ref|YP_874853.1| 65 GIWNYLPVVVLLSAVV 80
                                   6889999***999985 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.8      0.74   2.2e+03      68      86 ..       7      25 ..       2      29 .. 0.52
   2 ?   10.6   0.0   0.00018      0.52      60      94 ..      53      90 ..      34      95 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.74
                          Orf78 68 isllavvcvlvllyviyYf 86
                                   +++++ + v+ l++ ++ +
  gi|118431220|ref|YP_874853.1|  7 VVAVVGFFVMWLMFQVVGW 25
                                   4444444555555555444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                          Orf78 60 aqalnil...lisllavvcvlvllyviyYfvilrerqk 94
                                   +++ln l   ++++   + v+vll +++Y++i   r++
  gi|118431220|ref|YP_874853.1| 53 KNMLNSLysnMLGIWNYLPVVVLLSAVVYIIIESLRRR 90
                                   4444444111456667799*************776654 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.8     0.001         3      20      44 ..       6      30 ..       2      45 .. 0.70
   2 ?    1.8   0.2     0.088   2.6e+02      15      38 ..      65      88 ..      60      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                         HemY_N 20 vlllvllfvllylllrllrlllrlp 44
                                    +++v++f++++l+++++++++++ 
  gi|118431220|ref|YP_874853.1|  6 WVVAVVGFFVMWLMFQVVGWVIGVI 30
                                   5778888888888888888887763 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.088
                         HemY_N 15 slvvavlllvllfvllylllrllr 38
                                    ++  + ++vll +++y+++  lr
  gi|118431220|ref|YP_874853.1| 65 GIWNYLPVVVLLSAVVYIIIESLR 88
                                   566777788899999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 797.61
//
Query:       gi|118431221|ref|NP_147538.2|  [L=926]
Description: hypothetical protein APE_0843.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (926 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 6637.28
//
Query:       gi|118431222|ref|NP_147540.2|  [L=123]
Description: hypothetical protein APE_0847.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1042.41
//
Query:       gi|118431223|ref|NP_147541.2|  [L=97]
Description: hypothetical protein APE_0848.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.72   10.0  12.3        0.8    9.8  11.7    1.4  1  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 ?    9.8  11.7   4.5e-05       0.8       7      68 ..      32      95 ..      26      97 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.5e-05
                        DUF1206  7 Gvvylllg.llalqaalg..gggssasgsdgalatlleqpfGrvllglvglgllgyglwqlveAv 68
                                   G+ ++l+g +la+ a+++     +sa ++++++  +l+   Gr +l+lv++  l++ lwq+++A 
  gi|118431223|ref|NP_147541.2| 32 GATFGLFGpVLAVLAVVTvfLKTRSA-SATAVVSLVLAAFLGREWLMLVAALSLAALLWQVWRAS 95
                                   56666666544444444422333344.99**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 848.82
//
Query:       gi|14601017|ref|NP_147543.1|  [L=105]
Description: hypothetical protein APE_0850 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        2.2    8.1   8.1       0.66    9.7   3.1    2.3  2  CTV_P6    Citrus tristeza virus 6-kDa protein


Domain annotation for each model (and alignments):
>> CTV_P6  Citrus tristeza virus 6-kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1   3.7e-05      0.66       5      23 ..       1      19 [.       1      32 [. 0.84
   2 ?    0.7   0.2     0.024   4.2e+02      17      32 ..      84      99 ..      73     103 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.7e-05
                        CTV_P6  5 iqGfLtfLvGiavfsafae 23
                                  +qGf+++LvG av +  a 
  gi|14601017|ref|NP_147543.1|  1 MQGFIAYLVGFAVVAGVAV 19
                                  5************987774 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.024
                        CTV_P6 17 vfsafaeLiiivitiy 32
                                  + +   +L ++ i++ 
  gi|14601017|ref|NP_147543.1| 84 IAALIVGLALLLIAVI 99
                                  2223333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 906.48
//
Query:       gi|118431224|ref|YP_874854.1|  [L=88]
Description: hypothetical protein APE_0850a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        2.9    7.9  12.9        4.7    7.3  12.9    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        4.4    5.9   4.5          5    5.8   4.5    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
        4.8    7.4   7.7          2    8.6   0.2    2.2  2  DUF2613          Protein of unknown function (DUF2613)
          6    6.7  10.9        1.7    8.4   5.3    2.2  2  CTV_P6           Citrus tristeza virus 6-kDa protein


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  12.9    0.0011       4.7      36      83 ..       8      83 ..       3      88 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                Phage_holin_3_6 36 gagllgaagvlallalllllvala..........................lala.a.lwlaalivaavllvlagvl 83
                                   ++g++++ag+ ++l++++ ++  +                          l+ + + l++aaliv++++l++a++ 
  gi|118431224|ref|YP_874854.1|  8 LVGFAIVAGFAVALGFIFGIFNQIvaqlntdpnnpmisqefvdainlaqsLGGTgLtLAIAALIVGLAMLLIAVIR 83
                                   455555666665555555555553568899999999999999888877773333336999*************985 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.5    0.0011         5     388     430 ..      10      83 ..       2      87 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0011
                        DUF2207 388 lgliilglilillallllvll...............................lvfllilllillliaiivlllf 430
                                     ++i++g++++l+++++++                                    l+i +li++l++++++++ 
  gi|118431224|ref|YP_874854.1|  10 GFAIVAGFAVALGFIFGIFNQivaqlntdpnnpmisqefvdainlaqslggtGLTLAIAALIVGLAMLLIAVIR 83 
                                    333444444444444433333666888********************999888888888888888888887776 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00045         2       9      37 ..      12      42 ..       9      52 .. 0.77
   2 ?    1.9   2.4     0.055   2.5e+02       6      22 ..      66      82 ..      61      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                        DUF2613  9 SaVaGivlGvvavfgv..tavvqqdsrPstd 37
                                   ++VaG +++++ +fg+    v+q ++ P++ 
  gi|118431224|ref|YP_874854.1| 12 AIVAGFAVALGFIFGIfnQIVAQLNTDPNNP 42
                                   89************99333577778888776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.055
                        DUF2613  6 aaaSaVaGivlGvvavf 22
                                   a+a+ ++G++  ++av+
  gi|118431224|ref|YP_874854.1| 66 AIAALIVGLAMLLIAVI 82
                                   68888888887777765 PP

>> CTV_P6  Citrus tristeza virus 6-kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.3   0.00038       1.7       5      25 ..       1      21 [.       1      33 [. 0.82
   2 ?    1.5   0.3     0.053   2.4e+02      16      32 ..      69      85 ..      60      87 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00038
                         CTV_P6  5 iqGfLtfLvGiavfsafaeLi 25
                                   +qGf ++LvG a+ + fa  +
  gi|118431224|ref|YP_874854.1|  1 MQGFTAYLVGFAIVAGFAVAL 21
                                   5****************9655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.053
                         CTV_P6 16 avfsafaeLiiivitiy 32
                                   a    +a L+i vi  y
  gi|118431224|ref|YP_874854.1| 69 ALIVGLAMLLIAVIRSY 85
                                   45566788888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 678.35
//
Query:       gi|118431225|ref|NP_147545.2|  [L=424]
Description: hypothetical protein APE_0852.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3442.32
//
Query:       gi|118431226|ref|NP_147548.2|  [L=74]
Description: hypothetical protein APE_0855.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); 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:                         0  (0); expected 0.2 (1e-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: 586.78
//
Query:       gi|14601023|ref|NP_147549.1|  [L=282]
Description: hypothetical protein APE_0856 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2107.18
//
Query:       gi|14601024|ref|NP_147550.1|  [L=534]
Description: hypothetical protein APE_0858 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3945.83
//
Query:       gi|118431227|ref|YP_874855.1|  [L=168]
Description: hypothetical protein APE_0859 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1331.75
//
Query:       gi|14601025|ref|NP_147551.1|  [L=338]
Description: hypothetical protein APE_0860 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy 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:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2775.20
//
Query:       gi|118431228|ref|NP_147553.2|  [L=106]
Description: hypothetical protein APE_0862.1 [Aeropyrum pernix K1]
Scores for complete sequence (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    7.6   5.4        2.6    7.9   2.4    2.2  2  Phage_holin_2_3  Bacteriophage holin family HP1


Domain annotation for each model (and alignments):
>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.4   0.00014       2.6       7      26 ..      50      69 ..      47      71 .. 0.93
   2 ?   -0.4   0.1     0.055   9.9e+02      28      41 ..      84      97 ..      82     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00014
                Phage_holin_2_3  7 aAYisSavavvlGllsLseW 26
                                   +A++s ++ +v G+lsL+ W
  gi|118431228|ref|NP_147553.2| 50 TAFLSPLSMLVWGFLSLTAW 69
                                   8******************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.055
                Phage_holin_2_3 28 iviGIicgvvTfli 41
                                   +v G ++g +T+ i
  gi|118431228|ref|NP_147553.2| 84 LVAGAVMGPLTLYI 97
                                   58899999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 894.25
//
Query:       gi|118431229|ref|NP_147554.2|  [L=135]
Description: hypothetical protein APE_0864.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); 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 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1122.56
//
Query:       gi|118431230|ref|NP_147555.2|  [L=109]
Description: hypothetical protein APE_0865.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 844.06
//
Query:       gi|118431231|ref|NP_147557.2|  [L=325]
Description: hypothetical protein APE_0867.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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       0.21   11.4   0.0    1.2  1  Phage_sheath_1  Phage tail sheath protein subtilisin-like dom


Domain annotation for each model (and alignments):
>> Phage_sheath_1  Phage tail sheath protein subtilisin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.2e-05      0.21     106     144 ..      48      87 ..      42      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                                    HHHHH.STTT--STT....-B-TTEEEESSS--HHHHHHH CS
                 Phage_sheath_1 106 GlcAr.adveqswtarpsngevkgaldlaieltqeerdll 144
                                    Gl+Ar a + + w+ +p++  ++g+  ++  +  e rdll
  gi|118431231|ref|NP_147557.2|  48 GLAARhARSLRQWMRSPNRYDIPGVDSPEVGWWLESRDLL 87 
                                    9******************************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2612.88
//
Query:       gi|118431232|ref|YP_874856.1|  [L=85]
Description: hypothetical protein APE_0867a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      151  (0.00842211); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 630.01
//
Query:       gi|14601034|ref|NP_147560.1|  [L=83]
Description: hypothetical protein APE_0867b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.15   11.3   0.0    1.1  1  Attachment_P66  Borrelia burgdorferi attachment protein P66


Domain annotation for each model (and alignments):
>> Attachment_P66  Borrelia burgdorferi attachment protein P66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.5e-06      0.15      31      54 ..      50      73 ..      36      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.5e-06
                Attachment_P66 31 dkkrelnlafsvgtgiglawnkde 54
                                  +    +n+ fs g++ig  wn+d+
  gi|14601034|ref|NP_147560.1| 50 NYLSFTNVYFSLGCSIGRMWNTDK 73
                                  5556689***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 691.29
//
Query:       gi|118431233|ref|NP_147561.2|  [L=155]
Description: hypothetical protein APE_0870.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.8   8.7       0.57   10.2   1.1    2.5  2  DUF1422   Protein of unknown function (DUF1422)
        2.4    8.0   3.7        1.2    9.0   0.4    2.1  2  B12D      NADH-ubiquinone reductase complex 1 MLRQ subunit


Domain annotation for each model (and alignments):
>> DUF1422  Protein of unknown function (DUF1422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   6.4e-05      0.57       5      45 ..       6      46 ..       2      63 .. 0.84
   2 ?    6.8   1.3   0.00074       6.6      27      59 ..     119     151 ..      85     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.4e-05
                        DUF1422  5 aekktllLaliaGlslngtlsalfsslvpfsifplialvla 45
                                   +++++ +L+li+G+   + l   ++ +++ s++p++a v a
  gi|118431233|ref|NP_147561.2|  6 RHRESYILSLIVGVLSASILWLASKGVISPSVYPIMASVSA 46
                                   568899*******988887777788899********97755 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00074
                        DUF1422  27 lfsslvpfsifplialvlavyclyqrYlnksle 59 
                                     ++ lv  s+ +l+ l+l v+ ly+ + n  l+
  gi|118431233|ref|NP_147561.2| 119 TTMFLVGVSMMSLLILILNVQKLYHDHFNVDLS 151
                                    45667899*****************99998776 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 ?    9.0   0.4   0.00013       1.2       2      23 ..      34      55 ..      33      62 .. 0.87
   2 ?   -1.7   0.2       0.3   2.7e+03      10      22 ..     100     112 ..      99     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00013
                           B12D  2 rpeliPLfvfigagvggavfyl 23
                                    p+++P+++ ++a + g vf +
  gi|118431233|ref|NP_147561.2| 34 SPSVYPIMASVSATLLGFVFTA 55
                                   69***************99976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.3
                           B12D  10 vfigagvggavfy 22 
                                    +++++++++ +fy
  gi|118431233|ref|NP_147561.2| 100 AIVSGAASIFAFY 112
                                    6899999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1186.09
//
Query:       gi|118431234|ref|YP_874857.1|  [L=347]
Description: hypothetical protein APE_0871.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.017   14.6   0.0      0.045   13.3   0.0    1.7  2  Phage_TTP_13  Phage tail tube protein family


Domain annotation for each model (and alignments):
>> Phage_TTP_13  Phage tail tube protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0      0.49   8.8e+03      52      66 ..      66      80 ..      64      89 .. 0.85
   2 ?   13.3   0.0   2.5e-06     0.045      92     135 ..     209     252 ..     193     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.49
                   Phage_TTP_13 52 isdlpegpekslgfi 66
                                   i +lp   ek lg++
  gi|118431234|ref|YP_874857.1| 66 IKELPANGEKYLGIV 80
                                   778999999999986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.5e-06
                   Phage_TTP_13  92 elpnkrtvlmllalsgwemndisapaseviqitvkgkqnklvwg 135
                                     l n+rt+ mll   g ++  i     e+iq + +gk+++l + 
  gi|118431234|ref|YP_874857.1| 209 RLTNQRTIDMLLEKLGIDITKIRGQLYEAIQHAGRGKDQELDFT 252
                                    699***********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2628.97
//
Query:       gi|118431235|ref|NP_147562.2|  [L=66]
Description: hypothetical protein APE_0871a.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.7   0.1       0.15   12.3   0.1    1.2  1  ParG      ParG
       0.13   12.0   0.2       0.21   11.2   0.2    1.3  1  KRAB      KRAB box


Domain annotation for each model (and alignments):
>> ParG  ParG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.15      32      75 ..       7      50 ..       3      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                           ParG 32 GkskrvnvnfdeekhtrfkaacakkGtsitdvinqlvdnwlken 75
                                    k+krv v f +e+           G   +++++++v  wl e+
  gi|118431235|ref|NP_147562.2|  7 AKTKRVQVTFTQEQWELIERFRGVMGNDDAEIVRNIVLSWLAEK 50
                                   699********999875555556678888999*********996 PP

>> KRAB  KRAB box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   2.4e-05      0.21       7      19 ..      12      24 ..      10      28 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                           KRAB  7 VaVdFtqeEWelL 19
                                   V V Ftqe Wel 
  gi|118431235|ref|NP_147562.2| 12 VQVTFTQEQWELI 24
                                   779********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 511.18
//
Query:       gi|118431236|ref|NP_147563.2|  [L=469]
Description: DNA (cytosine-5-)-methyltransferase [Aeropyrum pernix K1]
Scores for complete 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-52  177.8   0.0    9.3e-51  173.1   0.0    2.6  1  DNA_methylase  C-5 cytosine-specific DNA methylase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.1   0.0   5.2e-55   9.3e-51       1     333 [.       4     462 ..       4     464 .. 0.73

  Alignments for each domain:
  == domain 1  score: 173.1 bits;  conditional E-value: 5.2e-55
                                    -EEEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-...............GS--.. CS
                  DNA_methylase   1 lkfidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk..kvsigDitkidkk...............klpe.d 61 
                                    +++i+Lf+G+GG++lg+ + g f++v+a+ei   aa tY++n +   +++gD   ++ +                l++ d
  gi|118431236|ref|NP_147563.2|   4 YSTISLFSGAGGLDLGFVQSGrFRIVFANEILLPAAVTYSRNLGlrLEVCGDEPRVEAQpgtimacdvakldftGLSGvD 83 
                                    579******************************************97888888888888888888888888777888888 PP

                                    -SEEEE---GGGTECTSE....E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEEE CS
                  DNA_methylase  62 iDlLvgGfPCqpfSvaGk....qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYev 137
                                     D+++gG+PCq+fS+ +     ++g++ +rg L++ ++r + + +Pk+f++ENV+gL++ ++g + kvile+++ l  + 
  gi|118431236|ref|NP_147563.2|  84 ADVIIGGPPCQDFSIVRGpdwdRRGINVKRGRLYAHFVRALASLQPKAFVFENVPGLVSANRGLAYKVILEDFARLSIRW 163
                                    ***************9988888*******************************************************888 PP

                                    E......................EEEEEGGGTT-SB--EEEEEEEEEGGG---........................... CS
                  DNA_methylase 138 s......................ykllnasdyGvpQnReRvfivgirkdleln........................... 168
                                    +                      + ++++s+ GvpQ+ReR++i+g+rkdl                              
  gi|118431236|ref|NP_147563.2| 164 DeikrivssngnggkvegyeivfTGIVDFSKLGVPQKRERLVIIGLRKDLAGGgfetisrlraridhvlsgkrwllhryp 243
                                    8889****************99999************************9766888777777777666666666666665 PP

                                    .....-------SS---GGG................................TSGGGTTS-EEBTTTB--GGGSSSTT-E CS
                  DNA_methylase 169 .....vlvkvkefrfpkkkd...........................leasktlrdlleekseldeektalsdklvekee 216
                                         v +  + +r+ +k++                                                  l+ ++++++ 
  gi|118431236|ref|NP_147563.2| 244 ltpieVFEGQPLDRLGDKYKevmlkwegvwdevgterafewkrrvwdR----------------------LTFDIISDYL 301
                                    544443333333333333336653333333333333333333333332......................3333333333 PP

                                    E--.......S---HHHTS--......................B--TTS...-B----S-STT-................ CS
                  DNA_methylase 217 kikkttkaseegypkelsrnr......................idkveelkglsatrrksgrge................ 258
                                    +++  + a+++  ++ l+++                       ++  +e+k  ++ ++++  +e                
  gi|118431236|ref|NP_147563.2| 302 SFNGIKHADKQELEEALMQHEvllkelgyygrpvyslklpdstTEPPYEGKAVVERMKRIPPDEnhefvrgtrwevegrg 381
                                    33333333333333322222234444444444444444444444444444444444444444335556665555556666 PP

                                    .....-B-TTS---EEEETTEEE--T.TTGGG--.B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHH CS
                  DNA_methylase 259 .....klekelaeagklqknkerfkpviekkriR.rLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiake 332
                                         +++  l+ ++++++ +    + +++ r R +Lt rE+arlq+fPd+f f +kk + + qiG++Vp+  +++ia++
  gi|118431236|ref|NP_147563.2| 382 islvyRRIHPLKPSYTVVAYGGGGTHGYHYDRDRaTLTLRERARLQTFPDSFLFYGKKPEIRAQIGEAVPPLAAKRIAEA 461
                                    666663333344444444444444447899999956******************************************99 PP

                                    H CS
                  DNA_methylase 333 i 333
                                    +
  gi|118431236|ref|NP_147563.2| 462 L 462
                                    7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3598.66
//
Query:       gi|118431237|ref|NP_147564.2|  [L=350]
Description: hypothetical protein APE_0874.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2905.98
//
Query:       gi|118431238|ref|NP_147565.2|  [L=223]
Description: U/G and T/G mismatch-specific DNA glycosylase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-14   54.8   0.0    1.5e-14   54.3   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.3e-07   31.7   7.2    3.4e-07   30.4   7.2    1.8  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
    1.5e-05   24.6   0.0    3.7e-05   23.4   0.0    1.7  1  HHH            Helix-hairpin-helix motif


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 !   54.3   0.0   2.5e-18   1.5e-14       1     102 [.      41     171 ..      41     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.5e-18
                                    HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                        HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv.............. 66 
                                    v+a l  +t+   + r++e++ +r   p+p++la+a e+++relir+lG  +++ak ++elA+++               
  gi|118431238|ref|NP_147565.2|  41 VAAFLLRKTTARQVVRVYEEFLRR--YPNPKALASAREDEVRELIRPLGIEHQRAKHLIELAKHIEaryggripcskekl 118
                                    567788899999************..59**************************************************** PP

                                    ...................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHH CS
                                    ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ...................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkl 102
                                                       g p+  +  D ++ ril+r+ ++k  k++ ++  k+
  gi|118431238|ref|NP_147565.2| 119 kelpgvgdyiasevllaacGSPE--PLLDRNMIRILERVLGVKSAKKRPHTDPKM 171
                                    *****************999888..******************987776666555 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 !   30.4   7.2   5.6e-11   3.4e-07       1      17 []     201     217 ..     201     217 .. 1.00

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.6e-11
                  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                    CTARkP C +CPL+D+C
  gi|118431238|ref|NP_147565.2| 201 CTARKPLCTECPLNDIC 217
                                    ***************** PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   6.2e-09   3.7e-05       1      29 [.     106     134 ..     106     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.2e-09
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                    +++g ip+s e L++lPGVG + A  +l 
  gi|118431238|ref|NP_147565.2| 106 RYGGRIPCSKEKLKELPGVGDYIASEVLL 134
                                    699**********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1741.25
//
Query:       gi|14601040|ref|NP_147566.1|  [L=161]
Description: hypothetical protein APE_0878 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1250.15
//
Query:       gi|118431239|ref|NP_147567.2|  [L=477]
Description: hypothetical protein APE_0879.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.072   13.6   0.0        1.1    9.7   0.0    2.3  2  Pox_H7    Late protein H7


Domain annotation for each model (and alignments):
>> Pox_H7  Late protein H7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   6.3e-05       1.1      55     139 ..     155     237 ..     145     239 .. 0.94
   2 ?    1.1   0.0      0.03   5.3e+02      15      45 ..     356     386 ..     346     426 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.3e-05
                                    S-BGGGGGT---EE--HHHHHHTHHHHHHHHHHHHHHHH-HHHHHHH-HHHHHHHHHHT--XXXXXXXXXXXXXXXXXXX CS
                         Pox_H7  55 gflaSdylnaklkkltpdeyaahsaaiakeltaadiilediedyikeskklkrvikvyktkkrkkikeakkklkiAlkkg 134
                                    g  aS+ l+a lk l  d   ++ a ia  l  +++i+e   + i+   k + +  v++ + +  ++e++ +l   +++ 
  gi|118431239|ref|NP_147567.2| 155 GRAASRVLEAALKDLGVDRKLEELAEIAPTLWWVNLIMES--EIIEGLLKFHYLTYVFRDRINAFVAEVEDTLSTIEEHQ 232
                                    6689***********************************9..9***************99******************** PP

                                    XXXXX CS
                         Pox_H7 135 vdydf 139
                                    +dyd+
  gi|118431239|ref|NP_147567.2| 233 ADYDY 237
                                    ****9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.03
                                    TT--HHHHHHHHHHHH----SEEEEEE-TTS CS
                         Pox_H7  15 geLstkDvmvlklellgkaPeetifsvdkdg 45 
                                     ++++ D++v +l+l+g++ + + f+v  ++
  gi|118431239|ref|NP_147567.2| 356 AVITPADIVVAVLRLIGRHGRARDFTVGVED 386
                                    578899**********999998888776444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3456.02
//
Query:       gi|14601042|ref|NP_147568.1|  [L=534]
Description: hypothetical protein APE_0880 [Aeropyrum pernix K1]
Scores for 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-06   25.7   0.1      2e-05   24.6   0.1    1.6  1  AAA_14        AAA domain
    0.00051   20.5   0.0     0.0041   17.5   0.0    2.4  2  AAA           ATPase family associated with various cellular 
     0.0013   19.1   0.0     0.0044   17.4   0.0    1.9  2  AAA_16        AAA ATPase domain
     0.0015   18.2   0.0     0.0037   16.9   0.0    1.6  2  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.025   15.1   0.0       0.28   11.7   0.0    2.4  2  AAA_18        AAA domain
      0.031   14.1   0.0      0.062   13.1   0.0    1.4  1  Bac_DnaA      Bacterial dnaA  protein
      0.049   14.3   0.2       0.13   12.9   0.2    1.7  1  PglD_N        PglD N-terminal domain
      0.059   13.7   0.0       0.11   12.8   0.0    1.5  1  AAA_19        AAA domain
      0.074   12.5   0.0       0.64    9.5   0.0    2.1  2  Autoind_bind  Autoinducer binding domain
      0.079   12.7   0.1       0.41   10.4   0.1    2.0  2  AAA_24        AAA domain
       0.08   12.2   0.0       0.18   11.1   0.0    1.5  1  Zeta_toxin    Zeta toxin
       0.11   12.6   0.0        0.3   11.3   0.0    1.6  1  CwsA          Cell wall synthesis protein CwsA
       0.14   11.9   0.0        1.2    8.9   0.0    2.3  2  PRK           Phosphoribulokinase / Uridine kinase family
        0.2   11.4   0.0       0.35   10.6   0.0    1.4  1  AAA_30        AAA domain
       0.22   11.4   1.3       0.56   10.1   0.4    2.1  2  ATPase_2      ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.7e-08     2e-05       2      88 ..      51     136 ..      50     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.7e-08
                        AAA_14   2 rkilvitGaRrvGKTtllkqlikell.vkkesilyinldderdkkladpekllelilek...lke..ekktylflDEiqev 76 
                                   +++++i G R +GKT ++ ++ik+++  +  ++ y++ d+ ++++++   +l+++i e    l++  + k ++ +D + e+
  gi|14601042|ref|NP_147568.1|  51 KNVIIILGGRGCGKTLVM-RYIKHYFePEGWDYKYFSGDQFKEADAQ---ELMKIISETrdlLENseDYKVIVGIDDVVEA 127
                                   5799***********997.6778888444556777777775555444...4566666654424333345555666766655 PP

                        AAA_14  77 pewekalkslvd 88 
                                   +   +a+++ ++
  gi|14601042|ref|NP_147568.1| 128 S---EAIRDTIK 136
                                   4...34443333 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 ?   -0.5   0.0       1.3   1.5e+03      82      99 ..       3      20 ..       1      31 [. 0.81
   2 !   17.5   0.0   3.5e-06    0.0041       2     121 ..      55     177 ..      54     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                                  HHHHHHHHHHHHHHTTTS CS
                           AAA 82 eervvnqLlteldgvkkk 99
                                  +e  vnqLl++ld  + +
  gi|14601042|ref|NP_147568.1|  3 REVCVNQLLKFLDSIRGR 20
                                  67789********98875 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.5e-06
                                   EEESSTTSSHHHHHHHHHHHH...........THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
                           AAA   2 llyGppGtGKTllakavakel...........gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidala 71 
                                   ++ G  G+GKTl+++ + + +           g +f e ++ el+ k      +++r+l+++ +    ++i+ iD++ +  
  gi|14601042|ref|NP_147568.1|  55 IILGGRGCGKTLVMRYIKHYFepegwdykyfsGDQFKEADAQELM-K----IISETRDLLENSEDY--KVIVGIDDVVEAS 128
                                   78899***************7554333333334667777777777.4....444455666665444..49******99987 PP

                                   HHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESSGGGSTHHHHS CS
                           AAA  72 ksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnrpdkldpallr 121
                                   ++        ++++ nqL++ + ++  +       +    v+g+t+  + l++ l r
  gi|14601042|ref|NP_147568.1| 129 EAI-------RDTIKNQLVPLVVDYAGRiklvisgQ-SERVVGTTTVLHILEDTLGR 177
                                   777.......8999****999999999888888853.36788888888777777665 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   3.7e-06    0.0044      20      88 ..      44     105 ..      28     155 .. 0.64
   2 ?   -2.6   0.0       5.4   6.4e+03      43      75 ..     328     364 ..     321     433 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                        AAA_16  20 rsgrp...elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                   ++++    +++++ G +G+GK+ ++r +++++e +g+ + +   dq+          +a  + el++ + + 
  gi|14601042|ref|NP_147568.1|  44 SKSGAlakNVIIILGGRGCGKTLVMRYIKHYFEPEGWDYKYFSGDQF---------KEAD-AQELMKIISET 105
                                   3333345699*************************888888888888.........2233.32444444443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.4
                        AAA_16  43 ellralekdggif....lrgkcdqlesaipysalaqa 75 
                                   +l+ +l+++++ +    +++   ++ s+++y+ +++ 
  gi|14601042|ref|NP_147568.1| 328 RLYSRLSQQRVAAdvddIKEAIMESASELTYASVVRG 364
                                   4444444443222212222222222222344333333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.1e-06    0.0037       2      96 ..      52     151 ..      51     159 .. 0.78
   2 ?   -3.8   0.0       6.9   8.3e+03      86     102 ..     169     185 ..     165     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.1e-06
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTT.HHHHHHHHHHHTTEEEEESSTTS......CHHHHHHHH CS
                         SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaa.AveQLktlaeklgvpvikkkeea......dpaavakea 75 
                                   nvi+++G  G GKT  +  + ++++ eg +    + D f+ a A+e +k++ e+ +  +++++e+       d +  a+ea
  gi|14601042|ref|NP_147568.1|  52 NVIIILGGRGCGKTLVMRYIKHYFEPEGWDYKYFSGDQFKEAdAQELMKIISETRD--LLENSEDYkvivgiDDVVEASEA 130
                                   89**************************************8835555666666555..55533322123334667778888 PP

                                   HHHHHHTTSSEEEEEE--SST CS
                         SRP54  76 vekakeekidvvlvDTaGrlq 96 
                                   ++   +++   ++vD aGr +
  gi|14601042|ref|NP_147568.1| 131 IRDTIKNQLVPLVVDYAGRIK 151
                                   98999999999999****976 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.9
                                   EEEEEE--SSTTHHHHH CS
                         SRP54  86 vvlvDTaGrlqndkelm 102
                                   ++l DT Gr+ + + l+
  gi|14601042|ref|NP_147568.1| 169 HILEDTLGRSPKAEMLF 185
                                   6899*****99888776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.28       1      78 [.      54     119 ..      54     146 .. 0.84
   2 ?    0.2   0.0      0.89   1.1e+03       9      39 ..     162     204 ..     161     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlv 78 
                                   I++ G  G+GKt + +++ k         +++  +g+ + ++    d++k++d + l+k++++ +   +++e+ k++v
  gi|14601042|ref|NP_147568.1|  54 IIILGGRGCGKTLVMRYI-K---------HYFEPEGWDYKYFSG--DQFKEADAQELMKIISETRDLLENSEDYKVIV 119
                                   899***************.4.........59*************..***********999999999887777777764 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.89
                        AAA_18   9 vGKttlakeLskrlgf............gvnlrdvakenglll 39 
                                   vG tt+ + L++ lg             g++lr+ ++e++ + 
  gi|14601042|ref|NP_147568.1| 162 VGTTTVLHILEDTLGRspkaemlfgeypGEVLRKQFRESYVRK 204
                                   89********888755577777777777777777777766554 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05     0.062      25     106 ..      42     124 ..      38     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                                   HHHHSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHT..T-HHHHHHHHTT-SEEE. CS
                      Bac_DnaA  25 kvaeapgkkynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrd..kkaeefkeklrkvDvLl. 102
                                   ++++  + + n ++i g+ G Gkt +++ i+++ + +  + +  Y ++++F +  ++ l++  ++++++ e+  +  v++ 
  gi|14601042|ref|NP_147568.1|  42 AISKSGALAKNVIIILGGRGCGKTLVMRYIKHYFEPEGWDYK--YFSGDQFKEADAQELMKiiSETRDLLENSEDYKVIVg 120
                                   6788888899************************99888876..*******998888887766677777776666666555 PP

                                   EE-G CS
                      Bac_DnaA 103 iDDi 106
                                   iDD+
  gi|14601042|ref|NP_147568.1| 121 IDDV 124
                                   8887 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00011      0.13       2      65 ..      54     121 ..      53     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                        PglD_N   2 ivIiGaGGhgk.vvadiie....angeyeiigflDdnkk..tevegypvlgkaiellkslseeeyevviAI 65 
                                   i+I+G  G gk  v + i+     +g ++ + f  d+ k  +++e +++++++ +ll++   e+y+v+++I
  gi|14601042|ref|NP_147568.1|  54 IIILGGRGCGKtLVMRYIKhyfePEG-WDYKYFSGDQFKeaDAQELMKIISETRDLLENS--EDYKVIVGI 121
                                   89*********856666651111556.*********9762245666*******9999977..89******9 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.6e-05      0.11       7      34 ..      48      75 ..      41     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-05
                        AAA_19  7 alkekvllvtaGpGtGKTrvlkhivall 34
                                  al+++v+++++G G+GKT v++ i +++
  gi|14601042|ref|NP_147568.1| 48 ALAKNVIIILGGRGCGKTLVMRYIKHYF 75
                                  78899*************9988765444 PP

>> Autoind_bind  Autoinducer binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.33     4e+02      61      91 ..      67      99 ..      67     108 .. 0.78
   2 ?    9.5   0.0   0.00054      0.64      18      61 ..     164     207 ..     160     251 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.33
                                  HHHHHHHCSSEEEEECGGCCCCC..SHHHHHHH CS
                  Autoind_bind 61 vvreaarssspfvWsddllaael..spaarrfl 91
                                  v+r++ + ++p  W+  +++ ++  +++a++++
  gi|14601042|ref|NP_147568.1| 67 VMRYIKHYFEPEGWDYKYFSGDQfkEADAQELM 99
                                  79999***************8888866665554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00054
                                   CSEEEEEEEETTSCESCEEEEEESS-HHHHHHHHHTTGGGT-HH CS
                  Autoind_bind  18 fdrfaygarapskdsaedvlllsnyPaeWlerYveegylaiDPv 61 
                                     ++++ + ++ + s+ + +l+  yP e l+  ++e+y++ DP+
  gi|14601042|ref|NP_147568.1| 164 TTTVLHILEDTLGRSPKAEMLFGEYPGEVLRKQFRESYVRKDPI 207
                                   5667777899999999999************************8 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00034      0.41       2      88 ..      51     138 ..      50     140 .. 0.78
   2 ?   -0.7   0.0      0.82   9.8e+02      56      91 ..     462     497 ..     440     501 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                        AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdie..swedfldevvelaaeladyktlv.iDtidele 78 
                                   k+ i+i G  g GKT +++ + ++  ++  e+  +k   +d+f+++    + ++++e   l ++ +dyk++v iD + e+ 
  gi|14601042|ref|NP_147568.1|  51 KNVIIILGGRGCGKTLVMRYI-KH--YFEPEGwDYKYFSGDQFKEADaqELMKIISETRDLLENSEDYKVIVgIDDVVEAS 128
                                   6789*****************.44..555565557888888888774444555556666669**********9******99 PP

                        AAA_24  79 elclaevirq 88 
                                   e +++ +++q
  gi|14601042|ref|NP_147568.1| 129 EAIRDTIKNQ 138
                                   9999988876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.82
                        AAA_24  56 vvelaaeladyktlviDtideleelclaevirqnek 91 
                                   ++e+++  +d+ ++  D+++el + +++ + ++n  
  gi|14601042|ref|NP_147568.1| 462 YAEIKRIGRDILVVLADSLGELDNSVVKTLADKNAS 497
                                   556689999999**********99999999888765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.18      15      57 ..      50      93 ..      37     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                    Zeta_toxin 15 rPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRel 57
                                   + +i++ G+ G+GK+ +++++k ++e ++ ++  +++D+++e 
  gi|14601042|ref|NP_147568.1| 50 AKNVIIILGGRGCGKTLVMRYIKHYFEpEGWDYKYFSGDQFKEA 93
                                  56677777889***************977889999999999986 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025       0.3      34      91 ..     323     386 ..     306     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                          CwsA  34 qstaeelrrryresrlarelaaaqeai...aqelaaaqevvaglPqaleda...rkkrrrkrpl 91 
                                      ae+l  r  ++r+a+++ + +eai   a el+ a  v  +lP+al      +++ r+++pl
  gi|14601042|ref|NP_147568.1| 323 SEVAERLYSRLSQQRVAADVDDIKEAImesASELTYASVVRGALPEALGIEvpeAEQGRKRKPL 386
                                   567899999****************9966689***************97655667777888775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00098       1.2       1      43 [.      53      95 ..      53     116 .. 0.81
   2 ?   -0.1   0.0      0.54   6.4e+02      10      29 ..     162     181 ..     153     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00098
                           PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldr 43
                                  vI + g  G+Gkt v+r +++ f+ e+   ++  gd+f + d 
  gi|14601042|ref|NP_147568.1| 53 VIIILGGRGCGKTLVMRYIKHYFEPEGWDYKYFSGDQFKEADA 95
                                  688999******************9998888888888777665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.54
                           PRK  10 aGkttvarklekifgrekvk 29 
                                    G+ttv + le+ +gr  + 
  gi|14601042|ref|NP_147568.1| 162 VGTTTVLHILEDTLGRSPKA 181
                                   6*************987654 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   0.00029      0.35      18      48 ..      51      81 ..      40     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggr 48
                                  + v ++ G+ G GKt +++ +++ +e +g +
  gi|14601042|ref|NP_147568.1| 51 KNVIIILGGRGCGKTLVMRYIKHYFEPEGWD 81
                                  4599*******************99998854 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 ?   10.1   0.4   0.00047      0.56      20      74 ..      51     107 ..      45     162 .. 0.66
   2 ?   -3.1   0.0       4.9   5.9e+03     111     152 ..     463     498 ..     448     511 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00047
                      ATPase_2  20 neiyfiYGpegsGKtaLlkeiienl..edkdkyviyyialreesiskldefieeeee 74 
                                   ++++ i G +g+GKt +++ i      e +d++ +  ++++e + ++l + i e+++
  gi|14601042|ref|NP_147568.1|  51 KNVIIILGGRGCGKTLVMRYIKHYFepEGWDYKYFSGDQFKEADAQELMKIISETRD 107
                                   6899***************99887733444444444467777777777777764433 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                      ATPase_2 111 ekikkkgkk.iiiiiDelqklidlglngaellvkeLlnliesl 152
                                   ++ik+ g+  +++++D l +l        +++vk L++   s 
  gi|14601042|ref|NP_147568.1| 463 AEIKRIGRDiLVVLADSLGELD-------NSVVKTLADKNASE 498
                                   5677777776677777766665.......35555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3763.07
//
Query:       gi|14601043|ref|NP_147569.1|  [L=94]
Description: hypothetical protein APE_0880a [Aeropyrum pernix K1]
Scores for 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   18.0   0.0     0.0022   17.8   0.0    1.3  1  DUF1495        Winged helix DNA-binding domain (DUF1495)
     0.0038   17.0   0.0      0.006   16.4   0.0    1.3  1  TetR_N         Bacterial regulatory proteins, tetR family
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.014   15.3   0.0    1.3  1  HTH_45         Winged helix-turn-helix
      0.012   16.1   0.2      0.016   15.6   0.2    1.4  1  HTH_27         Winged helix DNA-binding domain
       0.15   11.8   0.0       0.29   10.9   0.0    1.6  2  LexA_DNA_bind  LexA DNA binding domain


Domain annotation for each model (and alignments):
>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     6e-07    0.0022      56      89 ..      51      84 ..      25      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6e-07
                       DUF1495 56 essLielGLveeeeeseglklYklteeGieivev 89
                                  ++ Li  GLv+ee+ s  +k+ klte+G++++e 
  gi|14601043|ref|NP_147569.1| 51 KDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAEC 84
                                  678********9999****************996 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.7e-06     0.006       8      34 ..      22      47 ..      19      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                                  HHHHHHTTT--HHHHHHHHTSSHHHHH CS
                        TetR_N  8 lfaerGydattvreIAkrAGvskgalY 34
                                   f+++Gy+  +++eI+k+ Gvs+ +++
  gi|14601043|ref|NP_147569.1| 22 EFEKKGYE-PSLAEIVKASGVSEKTFF 47
                                  599*****.66*************997 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0     4e-06     0.014      24      75 ..      34      91 ..      13      93 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4e-06
                        HTH_45 24 kimykanLsykllnkYL.dmLvekgli.....kkskekYvlTekGlelleklkeleel 75
                                  +i++++  s k++   L d L+  gl+     + + ++ +lTekG++l e l++ +++
  gi|14601043|ref|NP_147569.1| 34 EIVKASGVSEKTFFMGLkDRLIRAGLVkeetlSYRVKTLKLTEKGRRLAECLEKCRDV 91
                                  66666666666665555246888888843333556667789********999999876 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.2   4.6e-06     0.016      19      68 .]      30      78 ..      12      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.6e-06
                        HTH_27 19 kkladlcgrlnvedshis.yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   +la+++++  v+  ++     ++L+++GLv++++     r k+++lT+kG
  gi|14601043|ref|NP_147569.1| 30 PSLAEIVKASGVSEKTFFmGLKDRLIRAGLVKEETLS--YRVKTLKLTEKG 78
                                  567777777777777777566679*******554444..6**********9 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 ?   10.9   0.0   8.2e-05      0.29      19      38 ..      23      42 ..      13      65 .. 0.79
   2 ?   -2.8   0.0       1.6   5.8e+03       3      15 ..      73      85 ..      72      88 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.2e-05
                                  HHHHSS---HHHHHHHHTS- CS
                 LexA_DNA_bind 19 ieetgypPsireiaralglk 38
                                   e++gy Ps +ei +a g++
  gi|14601043|ref|NP_147569.1| 23 FEKKGYEPSLAEIVKASGVS 42
                                  589***********998875 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                                  ---HHHHHHHHHH CS
                 LexA_DNA_bind  3 kLTerQrevldli 15
                                  kLTe+ r++ + +
  gi|14601043|ref|NP_147569.1| 73 KLTEKGRRLAECL 85
                                  5777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 743.78
//
Query:       gi|118431240|ref|YP_874858.1|  [L=81]
Description: hypothetical protein APE_0880b [Aeropyrum pernix K1]
Scores for complete 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-09   35.9   0.0    6.7e-09   35.4   0.0    1.2  1  HTH_IclR    IclR helix-turn-helix domain
    9.7e-09   35.0   0.3    1.3e-08   34.6   0.3    1.2  1  MarR_2      MarR family
    8.6e-07   28.7   0.0    1.2e-06   28.3   0.0    1.2  1  HTH_5       Bacterial regulatory protein, arsR family
      8e-06   25.3   0.0    1.3e-05   24.6   0.0    1.3  1  HTH_24      Winged helix-turn-helix DNA-binding
    1.3e-05   25.2   0.1    2.1e-05   24.5   0.1    1.3  1  HTH_20      Helix-turn-helix domain
    6.5e-05   22.7   0.0    8.6e-05   22.3   0.0    1.1  1  TrmB        Sugar-specific transcriptional regulator TrmB
    0.00034   21.0   0.0    0.00042   20.8   0.0    1.1  1  HTH_27      Winged helix DNA-binding domain
     0.0006   19.8   0.0    0.00068   19.6   0.0    1.2  1  HemN_C      HemN C-terminal domain
     0.0039   17.1   0.0     0.0054   16.7   0.0    1.2  1  HTH_Crp_2   Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.017   15.2   0.0    1.2  1  HTH_29      Winged helix-turn helix
      0.014   15.7   0.0      0.024   15.0   0.0    1.4  1  Rrf2        Transcriptional regulator
      0.015   15.6   0.0      0.031   14.5   0.0    1.6  1  DUF4777     Domain of unknown function (DUF4777)
      0.022   14.7   0.5      0.041   13.8   0.1    1.6  2  HTH_1       Bacterial regulatory helix-turn-helix protein, ly
      0.038   14.1   0.2      0.068   13.3   0.0    1.5  2  HTH_28      Helix-turn-helix domain
       0.04   13.7   0.2      0.046   13.5   0.2    1.1  1  DUF742      Protein of unknown function (DUF742)
      0.044   13.8   0.0      0.047   13.7   0.0    1.2  1  HTH_45      Winged helix-turn-helix
       0.05   13.5   0.0      0.063   13.2   0.0    1.1  1  MarR        MarR family
       0.06   13.5   0.0      0.071   13.2   0.0    1.1  1  MotA_activ  Transcription factor MotA, activation domain
      0.072   12.7   0.0      0.085   12.5   0.0    1.1  1  SMC_ScpB    Segregation and condensation complex subunit ScpB


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 !   35.4   0.0   7.1e-12   6.7e-09       5      51 ..      11      57 ..       8      58 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 7.1e-12
                                   HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                   a++iL ala+a+ +l+  e+ + tglp++tv   ++ L  +G+ve+ 
  gi|118431240|ref|YP_874858.1| 11 AAQILLALARADSPLSYGEIVEITGLPPATVDLNVKKLLAEGLVERR 57
                                   89*******************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.3   1.3e-11   1.3e-08       7      54 ..      11      57 ..       7      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.3e-11
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                    a++L+aL+r++ + l+ ge+++ +gl++++v   +k+L a GLverr
  gi|118431240|ref|YP_874858.1| 11 AAQILLALARADSP-LSYGEIVEITGLPPATVDLNVKKLLAEGLVERR 57
                                   589*********98.********************************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 !   28.3   0.0   1.3e-09   1.2e-06       6      46 ..      13      55 ..      11      56 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-09
                                   HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +IL +La+  ++l+ +e++e++gl+++tv+   kkL  +GLVe
  gi|118431240|ref|YP_874858.1| 13 QILLALARadSPLSYGEIVEITGLPPATVDLNVKKLLAEGLVE 55
                                   8********9********************************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 !   24.6   0.0   1.4e-08   1.3e-05       7      48 .]      13      55 ..      13      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.4e-08
                         HTH_24  7 kILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +IL +L + ++ +s+ e+ e +gl+p+tv   +k+L  eGl++
  gi|118431240|ref|YP_874858.1| 13 QILLALARaDSPLSYGEIVEITGLPPATVDLNVKKLLAEGLVE 55
                                   578777776999*****************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   2.2e-08   2.1e-05      14      60 ..      13      60 ..      11      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.2e-08
                                   HHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20 14 rilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                    il aL + + +l+ +e+ e  +l+++t++ ++++L   gLve+++ +
  gi|118431240|ref|YP_874858.1| 13 QILLALaRADSPLSYGEIVEITGLPPATVDLNVKKLLAEGLVERRGRR 60
                                   6899999999**********************************9876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   9.2e-08   8.6e-05      11      60 ..      12      62 ..      11      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.2e-08
                                   CCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                           TrmB 11 akvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                   a++ laL  +  p++  ei e++g+p ++v   +++L+  GlVer+ +r+ 
  gi|118431240|ref|YP_874858.1| 12 AQILLALArADSPLSYGEIVEITGLPPATVDLNVKKLLAEGLVERRGRRYV 62
                                   678899998999*********************************966554 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   4.4e-07   0.00042       3      68 .]       9      67 ..       7      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-07
                         HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                   ++ a++L  +++ + + +  ++++ + +  +++  ++kkL + GLv     e  rr +r+ lT++G
  gi|118431240|ref|YP_874858.1|  9 TPAAQILLALARADSPLSYGEIVEITGLPPATVDLNVKKLLAEGLV-----E--RRGRRYVLTAAG 67
                                   5789999999999999999***************************.....5..9999******99 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.3e-07   0.00068      28      65 ..      32      68 ..      14      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.3e-07
                         HemN_C 28 qrfgldleellaaaleklqeqGLLeldggrlrltprGr 65
                                   + +gl+ + +   +++kl ++GL+e +g+r++lt +Gr
  gi|118431240|ref|YP_874858.1| 32 EITGLPPATV-DLNVKKLLAEGLVERRGRRYVLTAAGR 68
                                   5566664444.889***********************9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.7e-06    0.0054       4      59 ..      12      63 ..      11      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.7e-06
                                   HHHHHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEE CS
                      HTH_Crp_2  4 ArfLlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis.rgrriri 59
                                   A+ Ll la+      + pl+  e+ ++ Gl + tv    ++L  egl++ rgrr ++
  gi|118431240|ref|YP_874858.1| 12 AQILLALARA-----DSPLSYGEIVEITGLPPATVDLNVKKLLAEGLVErRGRRYVL 63
                                   6778888664.....37********************************54565554 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-05     0.017       2      59 ..      12      65 ..      12      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                         HTH_29  2 aqallllaeGvs..tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprnrlse 59
                                   aq+ll+la++ s  +  +i++++gl + tv+  +k   ++G   l +rr ++r+  +l++
  gi|118431240|ref|YP_874858.1| 12 AQILLALARADSplSYGEIVEITGLPPATVDLNVKKLLAEG---LVERR-GRRY--VLTA 65
                                   79***************************************...88754.4554..4665 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.6e-05     0.024      10      61 ..      11      59 ..       5      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                           Rrf2 10 alhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                   a ++ll La+ ++  p+s  ei e ++++p  +   ++kL  +glv+ +rG+
  gi|118431240|ref|YP_874858.1| 11 AAQILLALARADS--PLSYGEIVEITGLPPATVDLNVKKLLAEGLVE-RRGR 59
                                   5556666666555..9******************************8.5665 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.3e-05     0.031       7      65 ..      12      62 ..       8      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                        DUF4777  7 alvlealkvlnrPaTldEivervaerydlseeelkkvVkntLeaAvrhGFlkkengrYs 65
                                   a +l al+  + P+++ Eive    +++l++  +   Vk++L +    G+++++++rY 
  gi|118431240|ref|YP_874858.1| 12 AQILLALARADSPLSYGEIVE----ITGLPPATVDLNVKKLLAE----GLVERRGRRYV 62
                                   789****************95....9****************75....77888888886 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 ?   -2.2   0.0       4.5   4.3e+03       5      13 ..      13      21 ..       8      23 .. 0.61
   2 ?   13.8   0.1   4.3e-05     0.041      39      60 .]      47      68 ..      43      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                                   HHHHHHHHH CS
                          HTH_1  5 rlfvavaee 13
                                   ++++a+a++
  gi|118431240|ref|YP_874858.1| 13 QILLALARA 21
                                   456666665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.3e-05
                                   HHHTS-SEEESSSEEEE-HHHH CS
                          HTH_1 39 eelgvpLfeRtgrglrLTeaGe 60
                                   ++l + L+eR gr+ +LT+aG+
  gi|118431240|ref|YP_874858.1| 47 KLLAEGLVERRGRRYVLTAAGR 68
                                   578899***************7 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.3e-05     0.068       4      51 ..      13      60 ..      12      61 .. 0.85
   2 ?   -2.3   0.0       5.2   4.9e+03      11      22 ..      66      79 ..      63      80 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                         HTH_28  4 eiikllaaGh...svreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                   +i+++la+ +   s+ e+ ++ g+ + tv   +k++ +   +gLv rr+r+
  gi|118431240|ref|YP_874858.1| 13 QILLALARADsplSYGEIVEITGLPPATVDLNVKKLLA---EGLVERRGRR 60
                                   7888888544478*************************...567****986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.2
                         HTH_28 11 aGhsvre..aArel 22
                                   aG+++ e  +A+ +
  gi|118431240|ref|YP_874858.1| 66 AGRARVEslIAEVV 79
                                   56644444566655 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   4.9e-05     0.046      42     110 ..       9      81 .]       4      81 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                         DUF742  42 qpehrailrLcre..plsVaelaAelklPvgvvrvLlsdLldaglltvrapvtd..raaeqpdrelLeevlsG 110
                                    +p ++ +l+L r+  pls  e+   + lP ++v   +  Ll+ gl++ r        a++   ++l++ev+ G
  gi|118431240|ref|YP_874858.1|   9 TPAAQILLALARAdsPLSYGEIVEITGLPPATVDLNVKKLLAEGLVERRGRRYVltAAGRARVESLIAEVVGG 81 
                                    67888899***99999******************************999877666355556667899999866 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.9e-05     0.047      40      68 ..      45      73 ..      12      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-05
                         HTH_45 40 LdmLvekglikkskekYvlTekGlellek 68
                                   +++L+ +gl++ ++  YvlT+ G+  +e+
  gi|118431240|ref|YP_874858.1| 45 VKKLLAEGLVERRGRRYVLTAAGRARVES 73
                                   6899*******************987776 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   6.7e-05     0.063       9      50 ..      15      57 ..       8      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.7e-05
                                   HHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           MarR  9 Lrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRs 50
                                   L  l++ ++ ls  e+ +  g+ ++tv   +++L  +Gl+eR+
  gi|118431240|ref|YP_874858.1| 15 LLALARADSpLSYGEIVEITGLPPATVDLNVKKLLAEGLVERR 57
                                   44455554449999****************************7 PP

>> MotA_activ  Transcription factor MotA, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.5e-05     0.071      18      73 ..      11      66 ..       6      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.5e-05
                                   HHHHHHHHHHSTT.B-HHHHHHT-TTS-HHHHHHHHHHHHHTTSEEEETTEEEE-HH CS
                     MotA_activ 18 tatilitiakkdf.itaaevrevhpdlgnavvnsnigvlikkglveksgdgliitge 73
                                   +a il+++a+ d  ++  e+ e+   l  a v+ n+  l+  glve+ g   ++t  
  gi|118431240|ref|YP_874858.1| 11 AAQILLALARADSpLSYGEIVEIT-GLPPATVDLNVKKLLAEGLVERRGRRYVLTAA 66
                                   688999999999647788999986.6999********************99999865 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     9e-05     0.085      83     130 ..      10      60 ..       5      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                       SMC_ScpB  83 qaaletLaiIaykqpvtraeieeiRGvn...sdsvvrtLlerglieekgrk 130
                                     aa   La+     p++  ei ei G     +d  v++Ll++gl+e++gr+
  gi|118431240|ref|YP_874858.1|  10 PAAQILLALARADSPLSYGEIVEITGLPpatVDLNVKKLLAEGLVERRGRR 60 
                                    45555677777888***********9643338889**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 609.93
//
Query:       gi|118431241|ref|YP_874859.1|  [L=83]
Description: hypothetical protein APE_0880c [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   20.9   0.2      0.078   12.6   0.0    2.0  2  PrpR_N    Propionate catabolism activator


Domain annotation for each model (and alignments):
>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1   0.00026       4.7       9      38 ..       4      33 ..       2      38 .. 0.74
   2 !   12.6   0.0   4.3e-06     0.078      99     126 ..      50      77 ..      45      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00026
                         PrpR_N  9 vvegdleeavelakeleaegvdviiSrGgt 38
                                   +v+ ++ee  +++ +l++ +++vi+S G+t
  gi|118431241|ref|YP_874859.1|  4 IVVYSVEEFRRALSRLARPQTHVIVSDGAT 33
                                   566677777777778888888888888877 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.3e-06
                         PrpR_N  99 iytinseeeaeaavkelkaegvevvvGd 126
                                    +y+ +s ee+ + v+++++eg+ev++G 
  gi|118431241|ref|YP_874859.1|  50 QYSSTSVEEIGSLVEHARREGFEVILGH 77 
                                    799999********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 649.55
//
Query:       gi|14601046|ref|NP_147572.1|  [L=142]
Description: hypothetical protein APE_0883 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.8   7.7       0.09   13.1   7.7    1.3  1  Alanine_zipper  Alanine-zipper, major outer membrane lipoprot
       0.35    9.7   2.8       0.44    9.4   2.8    1.2  1  Spc7            Spc7 kinetochore protein
       0.35   10.1   1.8       0.54    9.5   1.8    1.3  1  CorA            CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> 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 ?   13.1   7.7   1.5e-05      0.09      23      60 ..      99     136 ..      81     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                Alanine_zipper  23 aadeAkskAdeAaarAenAeaaAeeAqkaAeeanerad 60 
                                   a    k++Ad A++  ++A ++A eA+++Ae+a +r++
  gi|14601046|ref|NP_147572.1|  99 ARRRLKAAADRAERVLDAALRDAREALEEAEQALARLK 136
                                   55677999999999999999999999999999999975 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.8   7.4e-05      0.44     176     223 ..      93     140 ..      78     142 .] 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7.4e-05
                          Spc7 176 kaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela 223
                                   + +l +  ++l++aa+  e +  + L+ +re+l+e+++ ++++k+e+a
  gi|14601046|ref|NP_147572.1|  93 HRRLLKARRRLKAAADRAERVLDAALRDAREALEEAEQALARLKEETA 140
                                   778889999***********************************9987 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.8     9e-05      0.54     140     206 ..      76     137 ..      71     142 .] 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 9e-05
                          CorA 140 eledstkkeilrelaqlrrrlvklrralapnrevlkrlla...kaddkllddedkeylrdlldelerlle 206
                                   ++++ +k++ +r+l+ l+rrl k rr l++  +  +r+l+   + d+        e l++ ++ l+rl e
  gi|14601046|ref|NP_147572.1|  76 RVSEIEKAGRARRLIVLHRRLLKARRRLKAAADRAERVLDaalR-DAR-------EALEEAEQALARLKE 137
                                   56666777777777777777777777777777777666662211.111.......123333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1113.73
//
Query:       gi|118431242|ref|YP_874860.1|  [L=76]
Description: hypothetical protein APE_0883a [Aeropyrum pernix K1]
Scores for complete 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   28.4   0.1    3.5e-06   26.7   0.0    1.8  2  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.21   11.6   0.0    1.2  1  RelB      RelB antitoxin


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 !   26.7   0.0   3.9e-10   3.5e-06       3      37 ..      19      53 ..      19      55 .. 0.93
   2 ?   -1.0   0.0      0.22     2e+03      12      19 ..      57      64 ..      57      70 .. 0.57

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.9e-10
                                   EEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  3 sirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   s++ + ++++++d+lar  g +rSe+I+ ++++++
  gi|118431242|ref|YP_874860.1| 19 SFKAPPSMIAEFDRLARQAGLTRSEAIKLLIKHAV 53
                                   678899*************************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.22
                                   HHHHHHHH CS
                          RHH_1 12 erLdelar 19
                                   e+L++la 
  gi|118431242|ref|YP_874860.1| 57 ELLRRLAG 64
                                   44555554 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.3e-05      0.21      14      39 ..      28      53 ..      20      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHCCT--HHHHHHHHHHHHH CS
                           RelB 14 aeatdvlekmGltiSqairlfLekia 39
                                   ae++    + Glt S+ai+l+++  +
  gi|118431242|ref|YP_874860.1| 28 AEFDRLARQAGLTRSEAIKLLIKHAV 53
                                   5778888999***********98644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 671.21
//
Query:       gi|118431243|ref|YP_874861.1|  [L=93]
Description: hypothetical protein APE_0883b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   12.8   0.0      0.054   12.8   0.0    1.1  1  EAP30     EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     3e-06     0.054     121     159 ..      26      68 ..      13      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-06
                          EAP30 121 elyalvnrarggvalvspdDllraiekllvlg......sglsvlq 159
                                    el +++   r g al sp+D+++a+e++lv g      +g  vl+
  gi|118431243|ref|YP_874861.1|  26 ELAKVYS-GR-GPALFSPEDVEKAVEHFLVAGlarldsGGRLVLE 68 
                                    4444443.45.669**************98888888877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.35u 0.19s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 815.21
//
Query:       gi|118431244|ref|YP_874862.1|  [L=76]
Description: hypothetical protein APE_0883c [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 613.24
//
Query:       gi|118431245|ref|NP_147574.2|  [L=108]
Description: hypothetical protein APE_0885.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 879.23
//
Query:       gi|118431246|ref|YP_874863.1|  [L=81]
Description: hypothetical protein APE_0885a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0059   16.6   0.0      0.012   15.7   0.0    1.5  1  DUF1905   Domain of unknown function (DUF1905)


Domain annotation for each model (and alignments):
>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   6.5e-07     0.012       1      54 [.       6      54 ..       6      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.5e-07
                                   EEEE-EE-TT-.S-EEEE--S-HHHHH..-.SS-EEEEEEETT.EEEEEEEESS CS
                        DUF1905  1 FtatlwkwegkggwtfvevPedvseelktggkgsvkVkatidgttfrtslfpmg 54
                                   Ft ++ k +g+   + v +P d ++ +  +g +  kV+++++++++++++    
  gi|118431246|ref|YP_874863.1|  6 FTGRISKRRGQ---VLVLLPRDYWQLF--QGLRGKKVRVRVGEVEYTGRITVIE 54
                                   88888888888...9************..999999************9997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 622.32
//
Query:       gi|118431247|ref|YP_874864.1|  [L=84]
Description: hypothetical protein APE_0885b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       153  (0.00853366); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); 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 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 653.88
//
Query:       gi|118431248|ref|NP_147576.2|  [L=277]
Description: mannosyl-3-phosphoglycerate phosphatase [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.6   0.0       0.49   10.1   0.0    2.0  2  Hydrolase_3  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   2.7e-05      0.49       1      56 [.      10      67 ..      10      93 .. 0.82
   2 ?    1.4   0.0     0.012   2.1e+02     188     221 ..     194     229 ..     149     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.7e-05
                                   EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC...S CS
                    Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgld...l 56
                                   i++DlD TL+  +++  e     ++ l   g+ vv  T  s++++ ++ +++g+     
  gi|118431248|ref|NP_147576.2| 10 IFTDLDNTLVGPGGEAGEAGEVYLEALD-LGYRVVPVTSKSIYEIVELWDSIGVPpgeR 67
                                   89*************8777766666665.******************999999875554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHH..CT--GGGEEEEESSGGGHHHHHH CS
                    Hydrolase_3 188 Kgtalkklake..lnisleeviafGDgeNDieMLea 221
                                    Kg a+ + ++e  l+   + v++ GD+  Di+ +e+
  gi|118431248|ref|NP_147576.2| 194 KGMAIDAALQEplLRPCAKVVVTAGDSSHDIPIIER 229
                                    55566555543214445677999*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2214.87
//
Query:       gi|118431249|ref|NP_147578.2|  [L=388]
Description: mannosyl-3-phosphoglycerate synthase [Aeropyrum pernix K1]
Scores for complete 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-121  404.3   0.0     5e-121  404.1   0.0    1.0  1  Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPG


Domain annotation for each model (and alignments):
>> Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.1   0.0  2.8e-125    5e-121       2     377 ..       6     366 ..       5     376 .. 0.97

  Alignments for each domain:
  == domain 1  score: 404.1 bits;  conditional E-value: 2.8e-125
                  Osmo_MPGsynth   2 pskserlgsvkihdvqrvleLdagkskksnksessetvsvseeeleevesklaivvpiknEelkvlegvlsgiPhdclvi 81 
                                    p+k+e +g+v+i+dv+rvl+Ld++      ks+ ++ v v++ ele+ + +++ivvp+k+E+l +le+vl++iP+++ v+
  gi|118431249|ref|NP_147578.2|   6 PAKFEVFGAVRIYDVSRVLSLDGRP-----KSRPTNLVYVDRGELEDAAFRTVIVVPVKDEDLLTLENVLRSIPTESPVV 80 
                                    6789*******************97.....89999********************************************* PP

                  Osmo_MPGsynth  82 lvSnssreevdkykaevellkefcraterqaiiihQkdpalaeafkaaglkelldetgklirnGKgEgmllgillakllg 161
                                    +vS+s+re+vd++++evel + ++r+ +r++ i++Q dpa++ea++ + l+++++ +g ++r+GKgEgmllg+++a++lg
  gi|118431249|ref|NP_147578.2|  81 VVSASTREPVDRFSNEVELARLISRSLQRDIAIVYQFDPAWSEALSGTPLESMVGASG-RVRKGKGEGMLLGFIVAAALG 159
                                    **********************************************************.********************* PP

                  Osmo_MPGsynth 162 kkyvgFiDaDnyvpgavnEYckafaaglalaksekphamvRikWasKpKvredelvfekeGRvSrvvNrwlNkllseies 241
                                     ++vg++D+Dnyvpg++ EY ++++++l+ a+s  +++mvRi W +K K+  ++++ +k+GRvS+++N +lN  ls +  
  gi|118431249|ref|NP_147578.2| 160 ADFVGYVDSDNYVPGSALEYSWIYYSALSRATS--SYSMVRIVWPYKGKLAASDMYLRKRGRVSTITNGVLNYTLSIY-- 235
                                    *********************************..*******************************************.. PP

                  Osmo_MPGsynth 242 laaeaeteiikTgnaGEhAmtleLalklrfatGyaiEpfelidllekfeskkpaeekeaaekeveilQietrNPHlHeek 321
                                      +++et+iikTgn+GE+A+t++L++++++++G+a+E+++l+++le++    +a ++  a + +e+ Q++ +NPH+H+e+
  gi|118431249|ref|NP_147578.2| 236 --KRIETDIIKTGNSGEQALTVKLGMEMNWGSGFAVETYQLVWMLENCYLGLQAGKCPIAPDYIEVRQVSPLNPHIHAER 313
                                    ..**********************************************99999999************************ PP

                  Osmo_MPGsynth 322 geeHikemlaqglgtiyhsklaeeelkeelleelkeekvleegeeppkervypple 377
                                    g+eHi+em+a +lgti+hs+la+ee+k+++l++lk+ +++e   eppk+++y+p  
  gi|118431249|ref|NP_147578.2| 314 GDEHIAEMTAVSLGTIFHSSLASEEVKSRILDQLKSLGLAE---EPPKPSTYRPAG 366
                                    **********************************9888776...899999999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2795.41
//
Query:       gi|14601053|ref|NP_147579.1|  [L=156]
Description: hypothetical protein APE_0890 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-14   52.6   0.9    7.6e-14   51.2   0.9    1.8  1  DUF3368   Domain of unknown function (DUF3368)
  ------ inclusion threshold ------
      0.022   14.5   1.6       0.75    9.6   0.3    2.5  2  UBA_3     Fungal ubiquitin-associated domain


Domain annotation for each model (and alignments):
>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.9   8.5e-18   7.6e-14       1      45 [.      98     144 ..      98     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 8.5e-18
                       DUF3368   1 vtGTLGiLllAKqrGlIps..vkplldaLiqaGfrispklyaevLrl 45 
                                   v+GT+G+L lA+ +GlI++  + ++l +L+++Gfris+k+++e+L++
  gi|14601053|ref|NP_147579.1|  98 VIGTIGLLRLAYSKGLISKdkLIQALRELKEHGFRISDKIINEALKK 144
                                   89*******************************************98 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0036        32      23      34 ..     116     127 ..     110     134 .. 0.88
   2 ?    9.6   0.3   8.4e-05      0.75      19      39 ..     129     151 ..     125     156 .] 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHS- CS
                         UBA_3  23 kdkvievLkrLg 34 
                                   kdk i++L+ L+
  gi|14601053|ref|NP_147579.1| 116 KDKLIQALRELK 127
                                   9********996 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8.4e-05
                                   HT--.HHHHH.HHHHHS--SS-- CS
                         UBA_3  19 qGFe.kdkvi.evLkrLgiksld 39 
                                    GF   dk+i e+Lk+L++k  +
  gi|14601053|ref|NP_147579.1| 129 HGFRiSDKIInEALKKLNLKAYQ 151
                                   566536999978********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1134.78
//
Query:       gi|118431250|ref|NP_147580.2|  [L=79]
Description: hypothetical protein APE_0890a.1 [Aeropyrum pernix K1]
Scores for 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-17   61.1   0.1    6.8e-17   61.0   0.1    1.1  1  UPF0175   Uncharacterised protein family (UPF0175)


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 !   61.0   0.1   3.8e-21   6.8e-17      15      73 ..      18      76 ..       4      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 3.8e-21
                        UPF0175 15 elerelrialAvklYeegrlSlgkAaelaglsrveflelLarrgiplinydeeeleeDl 73
                                   ++ere+++a Av l+ +g++S  +Aaelag+s ++fl +L+rr i  + y++eel+e+l
  gi|118431250|ref|NP_147580.2| 18 DIEREVKLAYAVDLFLRGIVSVERAAELAGMSLYDFLVELRRRRIQAYPYSDEELREEL 76
                                   689******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 630.21
//
Query:       gi|14601055|ref|NP_147581.1|  [L=162]
Description: hypothetical protein APE_0891 [Aeropyrum pernix K1]
Scores for complete 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   66.8   6.3    1.8e-18   66.8   6.3    1.4  2  CopD        Copper resistance protein D
    1.3e-06   28.3   4.7      2e-06   27.7   4.7    1.2  1  DUF2214     Predicted membrane protein (DUF2214)
    0.00017   21.2   0.0    0.00032   20.3   0.0    1.4  1  DUF3169     Protein of unknown function (DUF3169)
      0.002   18.3   3.4     0.0047   17.2   3.4    1.6  1  UPF0093     Uncharacterised protein family (UPF0093)
  ------ inclusion threshold ------
      0.013   15.8   1.2      0.013   15.8   1.2    1.7  2  DUF4149     Domain of unknown function (DUF4149)
      0.035   13.4   0.2      0.035   13.4   0.2    1.9  2  Urate_ox_N  Urate oxidase N-terminal
        3.3    7.6   9.0       0.25   11.2   1.4    2.7  2  DUF3487     Protein of unknown function (DUF3487)


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   0.1       3.1   7.9e+03      13      19 ..      14      20 ..       4      37 .. 0.57
   2 !   66.8   6.3   7.1e-22   1.8e-18       2     105 .]      52     157 ..      51     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.1
                          CopD 13 aavavvl 19
                                  ++ +v+ 
  gi|14601055|ref|NP_147581.1| 14 ILGVVIW 20
                                  2223322 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 7.1e-22
                          CopD   2 ralrrFsrlalaavavvlvtGvvnallr..vglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqal 80 
                                   ++ +rFs +++++v+vv++tGv+ +++   +g+++l++t+yG +l aKl+l+l+++++++++ +  ++ ++a  ++++ ++
  gi|14601055|ref|NP_147581.1|  52 AISKRFSPMVWISVVVVAATGVLRGARMdvLGYDALTGTTYGLILSAKLILFLAMMVIGVMIGRTGLKLAKAGDPEESLKA 132
                                   5789********************865544559******************************888877755588888888 PP

                          CopD  81 rhrlrrsaalelvlalvvlllaaal 105
                                   + ++r++ ++++++++vv+lla+al
  gi|14601055|ref|NP_147581.1| 133 QTKIRKLSEVNIAIGIVVILLAVAL 157
                                   88********************997 PP

>> DUF2214  Predicted membrane protein (DUF2214)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   4.7   7.7e-10     2e-06       4     145 ..       8     160 ..       5     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.7e-10
                       DUF2214   4 llaylHllailllvaalaaeavllrrel......saeevkrla.....laDlvyglaallvlvtGllrvl.yfgkGlaf.. 70 
                                   +l +lH+l++++ ++  ++  v+lr+        ++e+++rl      +++ +++++ ++v +tG+lr   +   G +   
  gi|14601055|ref|NP_147581.1|   8 FLGWLHILGVVIWIGGSIVLDVILRPGSiksmglTQEQAARLGqaiskRFSPMVWISVVVVAATGVLRGArMDVLGYDAlt 88 
                                   6889*********************984489999999999997333336799****************8866677888833 PP

                       DUF2214  71 .YlhnplFwlKvglfvlvgllslyPtltfirwrkalregelpvvseaevkrlrrivrlellllllipllAalmArG 145
                                     +  +++ +K++lf++++++ ++   t ++    l +   p+ s ++++++r++ ++++++ ++++llA+++ +G
  gi|14601055|ref|NP_147581.1|  89 gTTYGLILSAKLILFLAMMVIGVMIGRTGLK----LAKAGDPEESLKAQTKIRKLSEVNIAIGIVVILLAVALRYG 160
                                   3345689***********9999876666655....888889999****************************9988 PP

>> DUF3169  Protein of unknown function (DUF3169)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.2e-07   0.00032      79     173 ..      37     130 ..       2     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                       DUF3169  79 kkwdeeddeeseeeyeqiekklsiglilssvslilsfllilasyslkiyeeesssklvlifliaivlfliilflkiiiqvr 159
                                   k++    +e+++ + + i k++s + ++s+v++ +  +l +a + +  y+  + ++  li+ + ++lfl+++++ ++i   
  gi|14601055|ref|NP_147581.1|  37 KSMG-LTQEQAARLGQAISKRFSPMVWISVVVVAATGVLRGARMDVLGYDALTGTTYGLILSAKLILFLAMMVIGVMIGRT 116
                                   3333.3345555677********************************999988777777779******************* PP

                       DUF3169 160 ivklikkmnPekkg 173
                                     kl k+ +Pe+  
  gi|14601055|ref|NP_147581.1| 117 GLKLAKAGDPEESL 130
                                   **********9765 PP

>> UPF0093  Uncharacterised protein family (UPF0093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.4   1.8e-06    0.0047       7     143 ..       8     156 ..       3     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
                       UPF0093   7 wikalHiiavisWmAglfyLpRlfVyhaeakeks..eekevlkimerrLlkiimtpamiltlvlGllllalae......gl 79 
                                   ++ +lHi+ v++W+ g ++L  ++     ++ +   e++++l +   + ++ +++++++++ ++G+l  a ++       +
  gi|14601055|ref|NP_147581.1|   8 FLGWLHILGVVIWIGGSIVLDVILRPGSIKSMGLtqEQAARLGQAISKRFSPMVWISVVVVAATGVLRGARMDvlgydaLT 88 
                                   66789***********99998776443333332212445555544444444556777777777775532222234443345 PP

                       UPF0093  80 valssgWlhvKlllvllllayhlvlaklrkklaa....gentksekfyrilNEvptlllivivllvvv 143
                                    ++    l +Kl+l l+++++ ++++++  kla+    +e+ k ++  r l Ev + + iv++ll+v+
  gi|14601055|ref|NP_147581.1|  89 GTTYGLILSAKLILFLAMMVIGVMIGRTGLKLAKagdpEESLKAQTKIRKLSEVNIAIGIVVILLAVA 156
                                   5556678999****************999888863322466788899****************99986 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   1.2     5e-06     0.013       2      84 ..      16     103 ..      15     125 .. 0.64
   2 ?   -1.0   0.2      0.84   2.2e+03      49      51 ..     147     149 ..     104     160 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                       DUF4149   2 slglllGsqlwvtfvvapvlfrsL..prhqf...gelqsklFplyfglglalsvlllltevavg.....seklaseellql 72 
                                    + +++G+ +++ ++  p+  +s+  +++q+   g++ sk F+ + ++++++ + + ++ +a++     ++        + 
  gi|14601055|ref|NP_147581.1|  16 GVVIWIGGSIVLDVILRPGSIKSMglTQEQAarlGQAISKRFSPMVWISVVVVAATGVLRGARMdvlgyDAL-----TGTT 91 
                                   5789*******************5555555511155566668888888888888888888887766665222.....3333 PP

                       DUF4149  73 llllvvllltll 84 
                                   ++l++++ l+l+
  gi|14601055|ref|NP_147581.1|  92 YGLILSAKLILF 103
                                   333333333322 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                       DUF4149  49 svl 51 
                                   +++
  gi|14601055|ref|NP_147581.1| 147 GIV 149
                                   111 PP

>> Urate_ox_N  Urate oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.4e-05     0.035       4      34 ..       2      29 ..       1      51 [. 0.81
   2 ?   -1.3   0.1      0.42   1.1e+03     269     269 ..     118     118 ..      84     158 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                    Urate_ox_N  4 lewlnlllrwlHviaaiaWiGasfyFvaLdn 34
                                  ++++n++l wlH++  + WiG s+   +Ld 
  gi|14601055|ref|NP_147581.1|  2 ADFANIFLGWLHILGVVIWIGGSI---VLDV 29
                                  689*******************96...4444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.42
                    Urate_ox_N 269 f 269
                                   +
  gi|14601055|ref|NP_147581.1| 118 L 118
                                   2 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.3       0.3   7.6e+02      27      43 ..      11      27 ..       4      42 .. 0.65
   2 ?   11.2   1.4   9.7e-05      0.25      15      62 ..      72     117 ..      61     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.3
                       DUF3487 27 vlaglglvvglvlglll 43
                                  +l  lg+v+++  +++l
  gi|14601055|ref|NP_147581.1| 11 WLHILGVVIWIGGSIVL 27
                                  44555566665555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.7e-05
                       DUF3487  15 vVfrGltadEllvlaglglvvglvlglllallvgslaliptialllvl 62 
                                    V+rG+ +d l+  a++g++ gl+l+  l+l++   ++++++++   +
  gi|14601055|ref|NP_147581.1|  72 GVLRGARMDVLGYDALTGTTYGLILSAKLILFLA--MMVIGVMIGRTG 117
                                   69999999*99999*******9999999977777..444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1302.01
//
Query:       gi|118431251|ref|NP_147582.2|  [L=355]
Description: hypothetical protein APE_0892.1 [Aeropyrum pernix K1]
Scores for complete 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-07   31.6   0.0    5.7e-07   29.6   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
      5e-06   27.0   0.0    2.3e-05   24.8   0.0    2.0  1  AAA              ATPase family associated with various cellul
    0.00012   22.5   0.0    0.00024   21.5   0.0    1.5  1  AAA_16           AAA ATPase domain
    0.00015   21.0   0.0    0.00033   19.9   0.0    1.5  2  DUF815           Protein of unknown function (DUF815)
    0.00035   20.8   0.0     0.0013   19.0   0.0    2.0  1  AAA_22           AAA domain
    0.00081   19.1   0.0       0.52   10.0   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0016   18.6   0.0     0.0034   17.6   0.0    1.6  1  AAA_33           AAA domain
      0.003   17.3   0.0      0.092   12.5   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0041   17.2   0.0      0.041   13.9   0.0    2.0  1  AAA_14           AAA domain
     0.0071   16.1   0.0      0.022   14.5   0.0    1.8  2  AAA_30           AAA domain
     0.0074   15.7   0.0      0.034   13.5   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.049   13.2   0.0    1.7  2  AAA_7            P-loop containing dynein motor region
      0.019   14.5   0.0      0.095   12.3   0.0    2.0  2  AAA_25           AAA domain
       0.02   15.2   0.0       0.93    9.8   0.0    2.8  3  AAA_19           AAA domain
      0.024   15.2   0.0      0.043   14.4   0.0    1.4  1  AAA_18           AAA domain
      0.036   14.3   0.0      0.061   13.6   0.0    1.3  1  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.044   13.2   0.0      0.083   12.3   0.0    1.6  1  TniB             Bacterial TniB protein
      0.051   13.3   0.0       0.11   12.3   0.0    1.5  1  AAA_24           AAA domain
       0.06   13.1   0.0       0.15   11.8   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
       0.07   13.2   0.0       0.12   12.4   0.0    1.4  1  MMR_HSR1         50S ribosome-binding GTPase
      0.084   13.4   0.0       0.15   12.6   0.0    1.3  1  ABC_tran         ABC transporter
      0.085   12.8   0.0       0.22   11.4   0.0    1.7  1  NTPase_1         NTPase
       0.13   12.1   0.0       0.22   11.4   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
       0.14   12.1   0.0       0.28   11.1   0.0    1.5  1  Rad17            Rad17 P-loop domain
       0.21   11.3   0.0        1.1    8.9   0.0    2.0  2  IstB_IS21        IstB-like ATP binding protein


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 !   29.6   0.0     8e-10   5.7e-07       2     138 .]      21     174 ..      20     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 8e-10
                                    EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------............... CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraar............... 64 
                                    vlLvGppG+gKs++++++a+    +  +e v l++  + edl     +      +   plvra                 
  gi|118431251|ref|NP_147582.2|  21 VLLVGPPGVGKSTVVRSYAEDSasREGLEFVDLSEARSLEDLDTDSTY---AFLHIYAPLVRAEDlafiarrgegydwtl 97 
                                    8******************99988999****************99998...88999999998888999999********* PP

                                    ...........G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--...-TT-T CS
                          AAA_5  65 ...........egeilvlDEverae.sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld..rslnel 130
                                                  ++++DE++++  +ev+ +L s+  ++r+     ++l +         + v+a++n+++    +++ 
  gi|118431251|ref|NP_147582.2|  98 psrlayltrpgVRGLVFIDEITNVAlPEVQTILFSMVLDKRVAY---NRLSSG--------VEVVAAGNSPRdsPVSQWP 166
                                    ********99977789********99*******98877777772...222222........5566666666654444555 PP

                                    THHHHTT- CS
                          AAA_5 131 spalrsRf 138
                                     p+l++Rf
  gi|118431251|ref|NP_147582.2| 167 PPPLLDRF 174
                                    56666665 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 !   24.8   0.0   3.3e-08   2.3e-05       1     126 [.      21     176 ..      21     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.3e-08
                                    EEEESSTTSSHHHHHHHHHHHH....THEEEEEETTTCSSS...............................STTHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel....gvefleisgsellsk...............................yvgesekk 45 
                                    vll+GppG+GK++++++ a+++    g ef+ +s ++ l++                               y       
  gi|118431251|ref|NP_147582.2|  21 VLLVGPPGVGKSTVVRSYAEDSasreGLEFVDLSEARSLEDldtdstyaflhiyaplvraedlafiarrgegY------- 93 
                                    79*******************8555557788888888886678888888888876666666777544322222....... PP

                                    HHHHHHHHHHTS..............TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                            AAA  46 irelfkeakeka..............kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                                                  +fiDEi ++a  +      +++ + +  l +   +++ +s v v++a+n+
  gi|118431251|ref|NP_147582.2|  94 -----------DwtlpsrlayltrpgVRGLVFIDEITNVALPE------VQTILFSMVLDKRVAYNRLSSGVEVVAAGNS 156
                                    ...........12222222233334234899999999999888......4444444444444444444777999999998 PP

                                    ......GGGSTHHHHSTTSSE CS
                            AAA 112 ......pdkldpallrgRfdr 126
                                           + ++p+ll +Rf  
  gi|118431251|ref|NP_147582.2| 157 prdspvSQWPPPPLL-DRFRL 176
                                    433332233455666.66655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.4e-07   0.00024      26      55 ..      20      50 ..       9     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.4e-07
                         AAA_16 26 lvllsGesGvGKsslvrellr.alekdggif 55
                                    vll+G++GvGKs++vr+ ++ +++++g  f
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAEdSASREGLEF 50
                                   59****************9984555554444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.6e-07   0.00033      45      96 ..      10      63 ..       7      91 .. 0.78
   2 ?   -3.9   0.0       8.7   6.2e+03     182     202 ..     170     190 ..     170     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.6e-07
                         DUF815 45 eqfleglpannvLLwGarGtGKSslvkallneyae.egLrlieveke.dlkelp 96
                                   ++ l+ + a  vLL+G  G+GKS++v++  ++ a+ egL ++++++  +l++l+
  gi|118431251|ref|NP_147582.2| 10 RRILDRYGADRVLLVGPPGVGKSTVVRSYAEDSASrEGLEFVDLSEArSLEDLD 63
                                   67788899********************9987665166*****98641577665 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 8.7
                         DUF815 182 LsdRFGlwlgFykldqeeYle 202
                                    L dRF l +  +++d ee+++
  gi|118431251|ref|NP_147582.2| 170 LLDRFRLLIRVKPPDLEEWVS 190
                                    569999999999999999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-06    0.0013       8      56 ..      21      62 ..      14     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56
                                   ++++G++G+GK+t++r ++e           r ++ fv+l++  s++dl
  gi|118431251|ref|NP_147582.2| 21 VLLVGPPGVGKSTVVRSYAEDSAS-------REGLEFVDLSEARSLEDL 62
                                   689****************99753.......444447777777666666 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00073      0.52      24      61 ..      20      58 ..       8      68 .. 0.79
   2 !    6.8   0.0    0.0069         5      94     122 ..     110     139 ..     105     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00073
                                   -EEEECSTTSSHHHHHHHHHHHST.TTTS-EEEEETTTS CS
                Sigma54_activat 24 svlitGesGtGKellaraiheask.rkekpfvavncaai 61
                                   +vl++G  G+GK+++ r++ e s  r+  +fv +  a  
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAEDSAsREGLEFVDLSEARS 58
                                   79***************9999765155568988876655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0069
                                    TSEEEEETGGGS-H.HHHHHHHHHHHHSEE CS
                Sigma54_activat  94 gGtlfLDeigelpl.elQekLlrvlqegev 122
                                     G +f+Dei+++ l e+Q+ L+ ++ +++v
  gi|118431251|ref|NP_147582.2| 110 RGLVFIDEITNVALpEVQTILFSMVLDKRV 139
                                    599********985489****986544433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.7e-06    0.0034       2      25 ..      21      48 ..      21      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.7e-06
                         AAA_33  2 vllvGlpGsGKstlaerllkklg....a 25
                                   vllvG+pG+GKst+++++++  +     
  gi|118431251|ref|NP_147582.2| 21 VLLVGPPGVGKSTVVRSYAEDSAsregL 48
                                   799***************8766554444 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 !   12.5   0.0   0.00013     0.092      33      55 ..      18      40 ..       9      46 .. 0.85
   2 ?    2.3   0.0      0.18   1.3e+02      82     113 ..     107     139 ..      98     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                         RuvB_N 33 ldhvllyGpPGlGkttlakiiak 55
                                    d vll+GpPG+Gk+t+ +  a+
  gi|118431251|ref|NP_147582.2| 18 ADRVLLVGPPGVGKSTVVRSYAE 40
                                   699*************9876665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.18
                         RuvB_N  82 leekdvlfideihrls.raveevlysamedfrl 113
                                       + ++fidei  ++ ++v+ +l+s + d r+
  gi|118431251|ref|NP_147582.2| 107 PGVRGLVFIDEITNVAlPEVQTILFSMVLDKRV 139
                                    5567799*****998746899999998888765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.8e-05     0.041       5      87 ..      21     134 ..      19     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe...kllelileklke................... 62 
                                    ++++G+  vGK+t+++ +++++  ++e   +++l + r  +  d++        +l  + +                   
  gi|118431251|ref|NP_147582.2|  21 VLLVGPPGVGKSTVVRSYAEDSA-SREGLEFVDLSEARSLEDLDTDstyA----FLHIYAPlvraedlafiarrgegydw 95 
                                    6899***************9998.99999999**9999977666642332....33322223333456666666777777 PP

                         AAA_14  63 ............ekktylflDEiqev..pewekalkslv 87 
                                                  + ++f+DEi +v  pe++++l s+v
  gi|118431251|ref|NP_147582.2|  96 tlpsrlayltrpGVRGLVFIDEITNValPEVQTILFSMV 134
                                    777777777776556778888888875566666665555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     3e-05     0.022      21     107 ..      21     128 ..      10     140 .. 0.59
   2 ?   -2.5   0.0         5   3.6e+03      90     113 ..     290     312 ..     239     316 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                         AAA_30  21 avltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlk.................. 81 
                                    ++l+Gp+G GK+t++++++e  +++ g + + l+   +  ++L +++         +l+ ++                  
  gi|118431251|ref|NP_147582.2|  21 VLLVGPPGVGKSTVVRSYAEDSASReGLEFVDLSEA-RSLEDLDTDST------YAFLHIYAplvraedlafiarrgegy 93 
                                    689***************876666658888777643.22334443333......22222222222222344444444466 PP

                         AAA_30  82 ...........grarlepgtllivDEagmvdtkqlaa 107
                                                  r   + l+ +DE+  v+  ++++
  gi|118431251|ref|NP_147582.2|  94 dwtlpsrlaylT--RPGVRGLVFIDEITNVALPEVQT 128
                                    666666555321..23334666666666666666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5
                         AAA_30  90 tllivDEagmvdtkqlaallkaae 113
                                    tll v Eag ++++++ +l + +e
  gi|118431251|ref|NP_147582.2| 290 TLLSV-EAGRLASQDVVELCRTLE 312
                                    33333.666666666666666655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.7e-05     0.034      19      70 ..      15      66 ..       1     153 [. 0.72
   2 ?   -1.4   0.0       1.8   1.3e+03     188     201 ..     169     182 ..     167     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.7e-05
                   Mg_chelatase 19 aaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeee 70
                                     G   +llvGppG GK+ + +  ++  ++ +  e ++ ++ +s+ + ++++
  gi|118431251|ref|NP_147582.2| 15 RYGADRVLLVGPPGVGKSTVVRSYAEDSASREGLEFVDLSEARSLEDLDTDS 66
                                   468999**************99988888888888888888888887755544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                   Mg_chelatase 188 plldRidlqvevkk 201
                                    plldR+ l ++vk 
  gi|118431251|ref|NP_147582.2| 169 PLLDRFRLLIRVKP 182
                                    9*********9976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.8e-05     0.049      35      58 ..      20      43 ..      16      62 .. 0.82
   2 ?   -2.1   0.0       3.3   2.3e+03      98     113 ..     107     122 ..     100     144 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                          AAA_7 35 pvllvGptGtGKtviikdllkkld 58
                                    vllvGp G+GK+++++++ +   
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAEDSA 43
                                   79***************9877654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                          AAA_7  98 ggkklvvFvDDlnmpa 113
                                    +g + +vF+D++   a
  gi|118431251|ref|NP_147582.2| 107 PGVRGLVFIDEITNVA 122
                                    5666677777765443 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.095      34      64 ..      19      51 ..       6      62 .. 0.82
   2 ?   -1.2   0.0       1.8   1.3e+03      97     140 ..     267     314 ..     245     319 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                         AAA_25 34 elallaGapgtGKttlaldlalava..tGkpwl 64
                                   + +ll+G+pg+GK+t++ + a + a  +G ++ 
  gi|118431251|ref|NP_147582.2| 19 DRVLLVGPPGVGKSTVVRSYAEDSAsrEGLEFV 51
                                   5689*************9999888866666665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                         AAA_25  97 l..rddarllvldlagv.eslpLfakdrggtl.ltadvdaleaaieev 140
                                    +  +d+a l++ + ++  e+ +L+ +  +  + + +dv +l +++e+v
  gi|118431251|ref|NP_147582.2| 267 FlqPDPASLDLSTFPRLdERERLTLLSVEAGRlASQDVVELCRTLEKV 314
                                    255556666666655555555555554333333678888999988876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0013      0.93       9      33 ..      17      41 ..       9      53 .. 0.78
   2 ?    0.8   0.0      0.78   5.6e+02     105     126 ..     112     135 ..      99     141 .. 0.74
   3 ?    0.1   0.0       1.3   9.3e+02      40      75 ..     246     283 ..     237     315 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhival 33
                                    ++ +l++++pG GK++v++   + 
  gi|118431251|ref|NP_147582.2| 17 GADRVLLVGPPGVGKSTVVRSYAED 41
                                   567899*************987765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.78
                         AAA_19 105 llivDEfqdvd..elqyrLlkall 126
                                    l+++DE+ +v   e+q  L++ +l
  gi|118431251|ref|NP_147582.2| 112 LVFIDEITNVAlpEVQTILFSMVL 135
                                    899*******99455555555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.3
                         AAA_19  40 vkpeeillvaftgrAakelrerlaalgae......atTiHrl 75 
                                     ++ +i+++ + +rAa+e r+ l+    +       +T+ rl
  gi|118431251|ref|NP_147582.2| 246 DEAVRIAAMVVGRRAAEEARQFLQ----PdpasldLSTFPRL 283
                                    556789999999*****9998772....11223335666655 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     6e-05     0.043       1      20 [.      21      40 ..      21      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6e-05
                         AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                   +ll G+pGvGK+t+ +  ++
  gi|118431251|ref|NP_147582.2| 21 VLLVGPPGVGKSTVVRSYAE 40
                                   799***********997655 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 ?   13.6   0.0   8.4e-05     0.061       1      28 [.      20      47 ..      20      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-05
                                   EEEEESSTTSSHHHHHHCHCT-CCC-EE CS
                            Roc  1 KvvlvGdsgvGKtsllkrfvedkfseke 28
                                   +v+lvG  gvGK++ ++++ ed+ s++ 
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAEDSASREG 47
                                   689******************9988765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00012     0.083      37      63 ..      20      46 ..      10     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                           TniB 37 nlllvGdsnnGKtmivekFarlhppek 63
                                    +llvG++ +GK+++v+++a++  +++
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAEDSASRE 46
                                   58******************9987655 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   0.00015      0.11       4      22 ..      20      38 ..      18      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   ++l++Gp+g+GK+t+++++
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSY 38
                                   799*************998 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 ?   11.8   0.0   0.00021      0.15      24      39 ..      20      35 ..      11      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                         AAA_29 24 atlltGpsGsGKSTll 39
                                    +ll+Gp G+GKST++
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVV 35
                                   68************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 ?   12.4   0.0   0.00017      0.12       1      22 [.      20      41 ..      20      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                                   EEEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltge 22
                                   +v++vG p vGKSt++++  ++
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAED 41
                                   699************9987765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00021      0.15      13      40 ..      20      47 ..      15      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                                   EEEEEESTTSSHHHHHHHHTTSS--SEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteG 40
                                   +v +vG+ G GKSt+++  a+ +   eG
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAEDSASREG 47
                                   799*************998888777776 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       1      22 [.      20      41 ..      20      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                                   EEEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlel 22
                                   +v++ GppGvGK+T+v+  +e 
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAED 41
                                   58999***********987765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.22      97     122 ..      16      41 ..       5      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                                    CTTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpe 122
                                       + ++lvG+ GvGKSt++ + +++
  gi|118431251|ref|NP_147582.2|  16 YGADRVLLVGPPGVGKSTVVRSYAED 41 
                                    5556789*************988775 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00039      0.28      47      67 ..      20      40 ..       9      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                          Rad17 47 iLLisGPsGCgkstvvkvLsk 67
                                    +L+ GP+G gkstvv+  + 
  gi|118431251|ref|NP_147582.2| 20 RVLLVGPPGVGKSTVVRSYAE 40
                                   46789***********98775 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 ?    8.9   0.0    0.0016       1.1      48      71 ..      19      42 ..      16      67 .. 0.78
   2 ?   -0.7   0.0       1.4   9.9e+02     110     138 ..     111     139 ..      78     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                      IstB_IS21 48 enivllGpsGvGKshlaialgvea 71
                                   + ++l+Gp+GvGKs +  + + + 
  gi|118431251|ref|NP_147582.2| 19 DRVLLVGPPGVGKSTVVRSYAEDS 42
                                   6799**********9988877654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                      IstB_IS21 110 dllilDdlgllpldqaeaellfeviekry 138
                                     l+ +D++  + l + ++ l+  v++kr+
  gi|118431251|ref|NP_147582.2| 111 GLVFIDEITNVALPEVQTILFSMVLDKRV 139
                                    68999999999999999988888999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2653.86
//
Query:       gi|118431252|ref|NP_147584.2|  [L=398]
Description: hypothetical protein APE_0895.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   12.6   0.2       0.17   11.3   0.2    1.7  1  VWA_CoxE  VWA domain containing CoxE-like protein


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 ?   11.3   0.2   9.3e-06      0.17      59      97 ..     259     298 ..     255     379 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.3e-06
                       VWA_CoxE  59 elvllvDvSgSmaaysaiflallhAllqqlprtevfa.Fd 97 
                                    ++ +l+DvS+Sm+   ++ +  ++ +l+   rt+v+a Fd
  gi|118431252|ref|NP_147584.2| 259 RHAVLLDVSASMEGKMRVAVEAAAHALRYPARTRVLAlFD 298
                                    6789**********66666655555555555999885255 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2956.75
//
Query:       gi|118431253|ref|NP_147585.2|  [L=270]
Description: hypothetical protein APE_0896.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.1   0.0       0.22   12.2   0.0    1.4  1  DUF4728   Domain of unknown function (DUF4728)


Domain annotation for each model (and alignments):
>> DUF4728  Domain of unknown function (DUF4728)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.2e-05      0.22      63      89 ..       6      32 ..       1      34 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                        DUF4728 63 lialliifflllvLniyiyygiyslyk 89
                                     a++i  ++l++++i++ +g+ys+++
  gi|118431253|ref|NP_147585.2|  6 GQANPITVVILVAVTIALAMGVYSFFQ 32
                                   5678899999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2120.95
//
Query:       gi|118431254|ref|NP_147586.2|  [L=861]
Description: hypothetical protein APE_0898.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.38
# Mc/sec: 6749.35
//
Query:       gi|118431255|ref|NP_147587.2|  [L=128]
Description: hypothetical protein APE_0900.1 [Aeropyrum pernix K1]
Scores for complete 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   73.4   0.0    1.7e-20   72.9   0.0    1.2  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    5.5e-08   33.0   0.1    8.5e-08   32.4   0.1    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.9e-05   24.8   0.1    4.2e-05   23.6   0.0    1.7  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    0.00029   21.2   0.0    0.00034   21.0   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0049   16.8   0.0     0.0077   16.2   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.049   13.1   0.0      0.051   13.0   0.0    1.1  1  AP_endonuc_2     Xylose isomerase-like TIM barrel
      0.055   13.4   0.0      0.084   12.9   0.0    1.4  1  FR47             FR47-like protein
      0.071   12.6   0.1      0.073   12.5   0.1    1.2  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   7.5e-24   1.7e-20       8      77 ..      24      92 ..      17      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 7.5e-24
                Acetyltransf_CG  8 egeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvptCsyvaaylekhpey 77
                                   e+ ++afl+Y+  ++g++ +  T++p+++rGkG+A+++v++a++ are+gl vvp+Csy+  y+ k+ e 
  gi|118431255|ref|NP_147587.2| 24 EDGSKAFLRYR-IEDGKIYLIETYTPPQHRGKGVARRMVEKAIEIAREKGLEVVPLCSYAVYYFLKNREA 92
                                   35689*****9.8889***************************************************986 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1   3.8e-11   8.5e-08      47      99 ..      30      79 ..      16      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3.8e-11
                                   EEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE.EE CS
                 Acetyltransf_1 47 fisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikki.vl 99
                                   f+++++ +     ++y+++ +  p++rgkG++++++e+++e+are+g++ +  +
  gi|118431255|ref|NP_147587.2| 30 FLRYRIEDG----KIYLIETYTPPQHRGKGVARRMVEKAIEIAREKGLEVVpLC 79
                                   556666666....9*********************************9887444 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   4.2e-05      76     117 ..      42      83 ..      26      90 .. 0.89
   2 ?   -2.1   0.0       1.8   3.9e+03       4      36 ..     102     113 ..      92     122 .. 0.55

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                    EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSH CS
                 Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsllfPssi 117
                                    +  + + p+hrg+gv+++++++a+e +re+g +++ l  +++
  gi|118431255|ref|NP_147587.2|  42 LIETYTPPQHRGKGVARRMVEKAIEIAREKGLEVVPLCSYAV 83 
                                    5667899***************************99988754 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                    EE-GGGHHHHHHHHHHHTT----H..HHHHHHH CS
                 Acetyltransf_9   4 elteedldevlellkyaFqdeespleeireyfr 36 
                                    ++ +edl+                     +y++
  gi|118431255|ref|NP_147587.2| 102 SMSDEDLK---------------------KYYE 113
                                    33333333.....................3333 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.5e-07   0.00034      17      54 ..      30      74 ..      15     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.5e-07
                                   EEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEE CS
                 Acetyltransf_7 17 fialslld..aeitrlaVdpeyrgkGiGraLlea..ae...kgii 54
                                   f+++ ++d   ++++ ++ p++rgkG++r+++e   ++   kg++
  gi|118431255|ref|NP_147587.2| 30 FLRYRIEDgkIYLIETYTPPQHRGKGVARRMVEKaiEIareKGLE 74
                                   55555555445566689***************9534114445533 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.4e-06    0.0077      47      86 ..      34      74 ..       7      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                Acetyltransf_10 47 elrdgs.hisllfVdpeyrgqGigkaLleaveeeaekdgik 86
                                   +++dg+ ++   +  p++rg+G++++++e+++e a+++g++
  gi|118431255|ref|NP_147587.2| 34 RIEDGKiYLIETYTPPQHRGKGVARRMVEKAIEIAREKGLE 74
                                   45444445555699*********************998876 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 ?   13.0   0.0   2.3e-05     0.051       5      93 ..       3      82 ..       1     124 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                                   HHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSE CS
                   AP_endonuc_2  5 aeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapl 86
                                   ++aG++gvE++  + v +++ +d   + lr ++++  +   +++++t +++ +      +   +++ +++aie+a++ G ++
  gi|118431255|ref|NP_147587.2|  3 SSAGAEGVEVRVTSRVIYVPFEDGSKAFLRYRIEDGKIY--LIETYTPPQHRGK----GV---ARRMVEKAIEIAREKGLEV 75
                                   79*****************99999999*********999..7888887777433....33...589*************999 PP

                                   EEEEBCC CS
                   AP_endonuc_2 87 lvlhpGt 93
                                   + l++  
  gi|118431255|ref|NP_147587.2| 76 VPLCSYA 82
                                   9888653 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.8e-05     0.084      20      57 ..      36      75 ..      24      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-05
                                   TTSSEEEE..EE-GGG-SSSHHHHHHHHHHHHHHHS-S-E CS
                           FR47 20 dggelgal..qvlpehrrrGlgsrlvkalakeiaergktv 57
                                   ++g ++ +  ++ p+hr++G ++r+v++ ++  +e+g +v
  gi|118431255|ref|NP_147587.2| 36 EDGKIYLIetYTPPQHRGKGVARRMVEKAIEIAREKGLEV 75
                                   5677777622568*************99888777788665 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   0.1   3.3e-05     0.073      73     100 ..      40      67 ..      15     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.3e-05
                Acetyltransf_15  73 leiYtlyvsekyrgkGlakklLeeslke 100
                                    + + + y+++++rgkG+a++++e++++ 
  gi|118431255|ref|NP_147587.2|  40 IYLIETYTPPQHRGKGVARRMVEKAIEI 67 
                                    4455789****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1129.46
//
Query:       gi|14601062|ref|NP_147588.1|  [L=228]
Description: hypothetical protein APE_0902 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.4   0.1       0.13   12.8   0.1    1.2  1  Stc1      Stc1 domain


Domain annotation for each model (and alignments):
>> Stc1  Stc1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   7.3e-06      0.13      37      68 ..     126     158 ..     111     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.3e-06
                                   ..----TTTS-----.EEE-SSS--EEESTTS- CS
                          Stc1  37 kskikCkectakqat.eleCsaCqktkpldeFs 68 
                                    +k++C +c  k+ t el C +C++t + +eF 
  gi|14601062|ref|NP_147588.1| 126 PTKARCPKCGFKALTpELWCLVCKRTSSEEEFK 158
                                   4699*****99876549*************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 1980.15
//
Query:       gi|118431256|ref|NP_147589.2|  [L=249]
Description: misacylated tRNAala hydrolase AlaX [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-11   43.6   0.5    3.9e-11   42.8   0.5    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    2.6e-10   39.5   0.0    3.3e-10   39.1   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 !   42.8   0.5   4.4e-15   3.9e-11       1      44 []     192     235 ..     192     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 4.4e-15
                                    EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    +r+v+i  ++v++ gG+Hv+nT eIg ++i++ es++k   R+y
  gi|118431256|ref|NP_147589.2| 192 LRIVEIPGVDVQADGGPHVRNTCEIGRVVITKLESKGKRRKRVY 235
                                    69****558*********************************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 !   39.1   0.0   3.7e-14   3.3e-10     473     552 .]      14      94 ..       3      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 3.7e-14
                                    SEEEEEEEEEETTEEEESEEXXXXS.SSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHH CS
                   tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYae.sGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdee 551
                                    +ef+++vee + + vvLdrT+f +   GG + D+G+i+  +++ rv+ + +++ vv h  +  +++l+ g  vk+++d+e
  gi|118431256|ref|NP_147589.2|  14 REFEARVEEASGGRVVLDRTAFHPGpHGGLDTDTGYIFYGDKRYRVVRAAVEGDVVAHYLDSDTATLEPGAVVKGVIDWE 93 
                                    58999999***************9648***************************************************98 PP

                                    H CS
                   tRNA-synt_2c 552 r 552
                                    r
  gi|118431256|ref|NP_147589.2|  94 R 94 
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.19s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2208.92
//
Query:       gi|14601064|ref|NP_147590.1|  [L=118]
Description: hypothetical protein APE_0906 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         0  (0); expected 0.2 (1e-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: 906.82
//
Query:       gi|118431257|ref|NP_147591.2|  [L=554]
Description: thermosome alpha subunit [Aeropyrum pernix K1]
Scores for complete 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-180  601.0  14.9   1.8e-180  600.8  14.9    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
     0.0038   17.1   0.9      0.045   13.6   0.0    3.0  3  RuvB_C          RuvB C-terminal winged helix domain
  ------ inclusion threshold ------
      0.097   13.3   1.2        2.5    8.7   0.1    3.3  2  DnaG_DnaB_bind  DNA primase DnaG DnaB-binding


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 !  600.8  14.9    3e-184  1.8e-180       1     490 [.      34     528 ..      34     529 .. 0.98

  Alignments for each domain:
  == domain 1  score: 600.8 bits;  conditional E-value: 3e-184
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    la+++k++lGP+G+dKmlv+++g+++vTnDGati+ke+ei+hPaakllve+a++qd evGDGTt+vv+Lag+Lle+aekl
  gi|118431257|ref|NP_147591.2|  34 LAEMLKSSLGPRGLDKMLVDAFGDITVTNDGATIVKEMEIQHPAAKLLVEVAKAQDAEVGDGTTSVVVLAGALLEKAEKL 113
                                    79****************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTS..SXXSTHHHHHHHHHHHHHCHCCCS. CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslssk..ltskeaeelsklvvdAvklieene. 157
                                    +++++hpt iiegy ka+e+al+  +e   ++++e +d++ L+++a+t+l sk   t  e++++ ++v+dA++++ e++ 
  gi|118431257|ref|NP_147591.2| 114 LDENLHPTIIIEGYTKAMEEALRLVDEA--AVPVEVEDDSVLRRIAETTLASKfvGTGPERDKIISMVIDAIRTVAEKRp 191
                                    ****************************..666667799**************6557789************66666667 PP

                                    ...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHH CS
                     Cpn60_TCP1 158 ...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeelekle 234
                                       +e+dl+ +k++k++ggsl ds+lv+G+vldk+v++p mpk++enak+l+ld +Le +k+e +t+++++d e+le+++
  gi|118431257|ref|NP_147591.2| 192 dggYEVDLDYVKIEKKKGGSLLDSKLVRGIVLDKEVVHPAMPKRVENAKILVLDAPLEVQKPELTTKIRVTDIEKLESFL 271
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEE CS
                     Cpn60_TCP1 235 kaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakk 314
                                    ++e+++l++++eki+++g+nvv++qkgid++a+hflak+gila+rrvk++d+e++akatGa++v+sl dl+pe lG+a+ 
  gi|118431257|ref|NP_147591.2| 272 EEETRMLRDMVEKIAATGANVVITQKGIDEVAQHFLAKKGILAVRRVKRSDIEKVAKATGAKIVTSLRDLKPEYLGYAEL 351
                                    ******************************************************************************** PP

                                    EEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTS CS
                     Cpn60_TCP1 315 veeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksv 394
                                    vee+k+g++k+++ie+ k++k++tillrga+d+ lde+er+i+dAl+ ++n+++++k+v GGGa+e+ela klke+a++v
  gi|118431257|ref|NP_147591.2| 352 VEERKVGEDKMVFIEGAKNPKSVTILLRGANDMLLDEAERNIKDALHGLRNILREPKIVGGGGAVEVELALKLKEFARTV 431
                                    ******************************************************************************** PP

                                    XCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEE.CCCCTXEEEHHHHHHHHHHH CS
                     Cpn60_TCP1 395 sgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiid.lveagvvDplkvkrqalksA 473
                                     g++qlaiea+a+ALe+ip +Lae aG+d+ e l klr+ h++g k +g++v +g+i++ +++ +v++p+ vk+q++ksA
  gi|118431257|ref|NP_147591.2| 432 GGKQQLAIEAYAEALETIPTVLAESAGMDALEALLKLRSLHSQGYKFAGVNVLEGKIEEdMTKINVYEPVLVKKQVIKSA 511
                                    ********************************************************7644******************** PP

                                    HHHHHHHHCEEEEEXXX CS
                     Cpn60_TCP1 474 teaastiLrideiikak 490
                                    +eaa +iL+id++i a 
  gi|118431257|ref|NP_147591.2| 512 SEAAISILKIDDVIAAA 528
                                    **************985 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 ?   -1.3   0.0      0.35   2.1e+03      21      53 ..      94     127 ..      90     130 .. 0.73
   2 ?   -0.4   0.1      0.18   1.1e+03      25      46 ..     263     284 ..     258     300 .. 0.84
   3 !   13.6   0.0   7.6e-06     0.045      12      55 ..     468     509 ..     456     513 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                                    T--B-HHHHHHHTT--HHHHH.HTTHHHHHHTTS CS
                         RuvB_C  21 ggpvglktlaailgeeketie.dviEPyLlkegl 53 
                                    +g++++ +la +l e+ e++  ++  P ++ eg+
  gi|118431257|ref|NP_147591.2|  94 DGTTSVVVLAGALLEKAEKLLdENLHPTIIIEGY 127
                                    6788899999888777666541678888888776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.18
                                    -HHHHHHHTT--HHHHHHTTHH CS
                         RuvB_C  25 glktlaailgeeketiedviEP 46 
                                     ++ l ++l+ee+ ++ d++E 
  gi|118431257|ref|NP_147591.2| 263 DIEKLESFLEEETRMLRDMVEK 284
                                    5889999999999999999995 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 7.6e-06
                                    HHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEE CS
                         RuvB_C  12 LkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIe 55 
                                    L++l+++   + +g+++l   ++e+ ++i  v+EP+L+k++ I+
  gi|118431257|ref|NP_147591.2| 468 LRSLHSQ-GYKFAGVNVLEGKIEEDMTKIN-VYEPVLVKKQVIK 509
                                    7788877.8899**************9997.**********998 PP

>> DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.31   1.8e+03      28      45 ..      74      91 ..      66     164 .. 0.42
   2 ?    8.7   0.1   0.00042       2.5       9      52 ..     250     291 ..     247     410 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.31
                 DnaG_DnaB_bind 28 edpglallreliealaae 45
                                   ++p+++ll+e+ +a  ae
  gi|118431257|ref|NP_147591.2| 74 QHPAAKLLVEVAKAQDAE 91
                                   455555555554444221 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00042
                 DnaG_DnaB_bind   9 LqhPelagelp..dalaleafedpglallreliealaaepelntaa 52 
                                    +q+Pel +++   d+++le+f +++ ++lr+++e +aa    ++a 
  gi|118431257|ref|NP_147591.2| 250 VQKPELTTKIRvtDIEKLESFLEEETRMLRDMVEKIAA----TGAN 291
                                    89*****765533999999*****************54....3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 4258.86
//
Query:       gi|14601066|ref|NP_147592.1|  [L=260]
Description: dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-47  161.9   0.0    2.5e-47  161.4   0.0    1.1  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    3.6e-33  114.7   0.0    4.6e-33  114.3   0.0    1.1  1  adh_short       short chain dehydrogenase
    2.4e-08   34.1   0.1    5.3e-07   29.7   0.0    2.2  2  KR              KR domain
    0.00038   20.4   0.0    0.00061   19.7   0.0    1.3  1  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.0   5.6e-51   2.5e-47       4     234 .]      17     259 ..      12     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 5.6e-51
                                   TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTT.SEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                  adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelg.aev..lecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                   sg+G+a A +la++Ga+++l  +n+e+ ++++ ++a+ ++ a+v  ++ D++++ ++++l+e+++ ++g+ Dilv + g  
  gi|14601066|ref|NP_147592.1|  17 SGLGFASALELARNGARLLLFSRNREKlEAAASRIASLVSgAQVdiVAGDIREPGDIDRLFEKAR-DLGGADILVYSTGGP 96 
                                   9*************************98888888888776344555*****************76.68************* PP

                                   EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHH CS
                  adh_short_C2  81 pklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvel 159
                                   ++  g+f+e+  e++d+     ++s++ + ++a++ ++++g g++v + sv   r +++ +  ++ +  +++++r+lA el
  gi|14601066|ref|NP_147592.1|  97 RP--GRFMELGVEDWDESYRLLARSAVWVGRRAAEqMVEKGwGRMVYIGSVTLLRPWQDLALSNIMRLPVIGVVRTLALEL 175
                                   **..*************************9999995666669*************************************** PP

                                   GGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEEST CS
                  adh_short_C2 160 gpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDg 231
                                   +p+g++vNav p++i T+ ++++++          +e l+ +++r+p+gr+g+pee a++++fLas++as+itG+++ vDg
  gi|14601066|ref|NP_147592.1| 176 APHGVTVNAVLPSLILTDRVRSLAEerarrsgitVEEALKSMASRIPMGRVGKPEELASVVAFLASEKASFITGAVIPVDG 256
                                   ******************99998875555555556679999**************************************** PP

                                   TGG CS
                  adh_short_C2 232 Glt 234
                                   G +
  gi|14601066|ref|NP_147592.1| 257 GAH 259
                                   *87 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0     1e-36   4.6e-33       1     193 [.       8     201 ..       8     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1e-36
                                   SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                     adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkklgkld 79 
                                   k ++vt +ssG+G a a ela++Ga++++++r+ ekle++a+ + ++  ga++ ++++D+++  ++++l+eka  +lg+ d
  gi|14601066|ref|NP_147592.1|   8 KLAVVTAGSSGLGFASALELARNGARLLLFSRNREKLEAAASRIASLvsGAQVDIVAGDIREPGDIDRLFEKA-RDLGGAD 87 
                                   679*********************************************9************************.789**** PP

                                   EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                     adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                   +Lv  +G  ++g f el  e+w++++ +   +++++ r ++++m+++ +Gr v ++Sv+ + p+  +a        v+g +
  gi|14601066|ref|NP_147592.1|  88 ILVYSTGGPRPGRFMELGVEDWDESYRLLARSAVWVGRRAAEQMVEKGWGRMVYIGSVTLLRPWQDLALSNIMRLPVIGVV 168
                                   ********************************************************************************* PP

                                   HHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                     adh_short 161 rslakelaptgirvnavaPGlvdTdmakelrek 193
                                   r+la elap+g++vnav P l+ Td +++l e+
  gi|14601066|ref|NP_147592.1| 169 RTLALELAPHGVTVNAVLPSLILTDRVRSLAEE 201
                                   *************************99998776 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.2e-10   5.3e-07       4      79 ..      11      84 ..       9     116 .. 0.81
   2 ?    2.4   0.0     0.029   1.3e+02      12      35 ..     123     146 ..     115     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-10
                                  EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                            KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79
                                  ++t G  gLG + a  la++gar l+l+sR+ ++ e+++++ia+l + ga+v++va D+ ++ ++ +l+e++++ +
  gi|14601066|ref|NP_147592.1| 11 VVTAGSSGLGFASALELARNGAR-LLLFSRNREKLEAAASRIASLVS-GAQVDIVAGDIREPGDIDRLFEKARDLG 84
                                  7999*****************97.7899***999999999***9987.***********************98654 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.029
                                   HHHHHHHHHHHHHS-EEEEE-SS. CS
                            KR  12 LGlelarwlaekgarhlvllsRsa 35 
                                   +G+  a++++ekg  ++v+++   
  gi|14601066|ref|NP_147592.1| 123 VGRRAAEQMVEKGWGRMVYIGSVT 146
                                   69999********99999998776 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 !   19.7   0.0   1.4e-07   0.00061      13     106 ..      26     152 ..      15     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-07
                                   HHHHC-T-EEEEEETTHHHCH.......HHHCTTTCEEEE--TT-CCHHHHHHT......T-SE.EEES---TCC...... CS
                NAD_binding_10  13 ellargghevtalvRnpekla.......eleaeeglevvegdvtdvedlaealk......gada.Vvsalggggk...... 73 
                                   el+++ g ++ ++ Rn ekl+       +l + +++++v gd+ ++ d+ + ++      gad+ V+s++g++ +      
  gi|14601066|ref|NP_147592.1|  26 ELARN-GARLLLFSRNREKLEaaasriaSLVSGAQVDIVAGDIREPGDIDRLFEkardlgGADIlVYSTGGPRPGrfmelg 105
                                   45555.6888999999888874444444555789*******************9999999***757888877777876666 PP

                                   ....HHHH............HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
                NAD_binding_10  74 ....deeg............aknivdaakeagvkRfvlvsaigvgdevp 106
                                       d                +++++ + e+g  R+v+++++   + ++
  gi|14601066|ref|NP_147592.1| 106 vedwD--EsyrllarsavwvGRRAAEQMVEKGWGRMVYIGSVTLLRPWQ 152
                                   55553..05588888889999999*****************99886544 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:                      410  (0.022868); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2140.77
//
Query:       gi|14601067|ref|NP_147593.1|  [L=103]
Description: DNA-directed RNA polymerase subunit K [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-11   43.4   0.0    3.4e-11   42.9   0.0    1.3  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 !   42.9   0.0   1.9e-15   3.4e-11       3      48 ..      18      70 ..      16      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.9e-15
                                  TTSS--HHHHHHHHHHHHHHH....HT...........SS-SSSSTTCHHHHTT-S- CS
                  RNA_pol_Rpb6  3 tskvltrYelvriaakRArQieegesl...........etqkpvviAlrEiaegkip 48
                                   +++lt+Ye +ri++ RA Q+    s             + +p++iA  E+++g++p
  gi|14601067|ref|NP_147593.1| 18 GPPYLTKYERARIIGVRAFQL----SIgapplvdperaGSRNPLDIARYEVDNGILP 70
                                  579******************....6555555666664256**************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 865.90
//
Query:       gi|118431258|ref|NP_147594.2|  [L=355]
Description: hypothetical protein APE_0915.1 [Aeropyrum pernix K1]
Scores for 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-11   41.7  14.1    4.4e-07   29.4   1.0    2.5  2  Peptidase_M50  Peptidase family M50


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 !   15.5   7.6   4.4e-07    0.0079       2     109 ..     113     205 ..     112     236 .. 0.82
   2 !   29.4   1.0   2.5e-11   4.4e-07     188     231 ..     240     283 ..     215     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp........LGGyVkmageepeeelse 73 
                                    +++ l++ ++vHE+GH+lv++l++v                   +++Y+i++ p        +G++++m+   p+ +   
  gi|118431258|ref|NP_147594.2| 113 YLVGLLLPLLVHEMGHWLVMRLNRVPA-----------------SLPYMIPAPPlqlgflgtFGAVINMRWLPPTLD--- 172
                                    57899999*****************99.................78*************9999********998877... PP

                                    X....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........x RF
                  Peptidase_M50  74 eeakaflkkspwqrllivlAGplanfilailvfvv.........p 109
                                                +  +++++Gpla+f+ a+ ++vv         p
  gi|118431258|ref|NP_147594.2| 173 ------------SLTVMAVMGPLAGFVAAVPLAVVglqhslllpP 205
                                    ............8889999***********999995544444432 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 2.5e-11
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkpl 231
                                    + s+l+++ ++ +++++lNL+P+ +LDGgh+++ ++ +  ++ +
  gi|118431258|ref|NP_147594.2| 240 VLSPLAFASYVVFIVTFLNLIPVGMLDGGHIVRGVVGERVHQAI 283
                                    448999****************************9998874444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2817.18
//
Query:       gi|118431259|ref|NP_147595.2|  [L=290]
Description: ornithine cyclodeaminase [Aeropyrum pernix K1]
Scores for complete 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-31  108.9   0.0    4.7e-31  107.9   0.0    1.4  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    1.5e-06   28.3   0.0    2.2e-06   27.8   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.026   14.8   0.1      0.046   14.0   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.042   14.4   0.0      0.083   13.5   0.0    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0     1e-34   4.7e-31      51     316 ..      35     280 ..       8     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1e-34
                                    EEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT-- CS
                OCD_Mu_crystall  51 gelevmpaylagrellgvKlvnshpenkksglptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdas 130
                                      l +m a  +g  +++ K+v+++p+n+ + lp v ++++L+ ++ G +++ + a   t  RTaA+sa+a   L      
  gi|118431259|ref|NP_147595.2|  35 SWLGAMVAGGMG--YFSAKIVGVYPGNPSRRLPLVRGVLLLFRSSDGEKVLDIPAEEPTGWRTAAASALALSKLGFGGGG 112
                                    557788888888..****************************************************************** PP

                                    EEEEE--SHHHHHHHHHHCCCS--SEEEEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-G CS
                OCD_Mu_crystall 131 vlaiiGaGvqaetqlealkavldikevriydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilka 210
                                    vl++iGaGvqa+ +l++l+ v+ ++e+ +  r+ e+ e++a++  +  + v      +e  ++ ++v+++T ++ p++  
  gi|118431259|ref|NP_147595.2| 113 VLGVIGAGVQARYHLRVLTSVFRFDEILVASRRVETGERLAREFGG--RRV----GRRELLKRSHVVIAATNSTDPVVEG 186
                                    ******************************************9996..444....5899********************* PP

                                    GGS-TT-EEEE-S--STT--SB-HHHHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTS CS
                OCD_Mu_crystall 211 ewvkpGahinavgadapgkteLdddilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdee 290
                                     ++  Ga++  vga +p  +eLdd++ +ra  +  +   a ee + +               +l + ++G+   R    +
  gi|118431259|ref|NP_147595.2| 187 GLLRRGAYVASVGAPRPV-RELDDQVKRRAGCMLVDSDIACEESDDAC---------GVETVTLRDYVRGVASCR--WGD 254
                                    ****************95.8***********99955555555555555.........234568999*******65..678 PP

                                    EEEEE----HHHHHHHHHHHHHHHCC CS
                OCD_Mu_crystall 291 itlfdsvGlaveDvaaaklvyeraee 316
                                    + +++svG++v D+aaa  +yer+++
  gi|118431259|ref|NP_147595.2| 255 VYVYKSVGTPVFDLAAAIHIYERLRG 280
                                    ***********************986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   4.9e-10   2.2e-06      16      99 ..     115     193 ..     100     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.9e-10
                                    EEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS-SB-HHH CS
                   Shikimate_DH  16 lliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseepilekee 94 
                                     +iGaG  a+  ++ L +  ++++++va R +e  ++la+e++g ++        +ell++++vvi+at+s++p++e + 
  gi|118431259|ref|NP_147595.2| 115 GVIGAGVQARYHLRVLTSVfRFDEILVASRRVETGERLAREFGGRRVG------RRELLKRSHVVIAATNSTDPVVEGGL 188
                                    59**************9988**********************999332......356789****************9888 PP

                                    HHCCH CS
                   Shikimate_DH  95 veeal 99 
                                    +++  
  gi|118431259|ref|NP_147595.2| 189 LRRGA 193
                                    77654 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 ?   14.0   0.1     1e-05     0.046       2      54 ..     115     166 ..     114     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                                    EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE- CS
                Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaial 54 
                                     +iGaG  ++  +++l   f +d ei va+r  e  e+la +  g r+  ++l
  gi|118431259|ref|NP_147595.2| 115 GVIGAGVQARYHLRVLTSVFRFD-EILVASRRVETGERLAREFGGRRVGRREL 166
                                    69********************7.****************9998888877665 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   1.8e-05     0.083       2      69 ..     114     177 ..     113     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav 69 
                                    +g+iGaG +++  ++ l++  ++  ei+va sr  e+ e la+e+g +  +    e+++++ vv+ a 
  gi|118431259|ref|NP_147595.2| 114 LGVIGAGVQARYHLRVLTSV-FRFDEILVA-SRRVETGERLAREFGGRRVG--RRELLKRSHVVIAAT 177
                                    79*********999966665.799****88.***************77777..999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2135.66
//
Query:       gi|14601070|ref|NP_147596.1|  [L=500]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for 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-40  137.9   3.9    8.4e-40  137.5   3.9    1.1  1  Peripla_BP_6  Periplasmic binding protein
    7.1e-33  114.2   0.0    1.1e-32  113.5   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region
    6.2e-10   38.5   0.5    8.7e-10   38.0   0.5    1.1  1  LppC          LppC putative lipoprotein
    0.00085   18.4   0.1     0.0012   18.0   0.1    1.3  1  Peripla_BP_5  Periplasmic binding protein domain
     0.0037   17.3   0.1     0.0071   16.4   0.1    1.5  1  DUF4366       Domain of unknown function (DUF4366)
  ------ inclusion threshold ------
      0.047   13.3   0.7       0.11   12.1   0.1    1.9  3  PrpR_N        Propionate catabolism activator
      0.052   13.7   0.0       0.83    9.8   0.0    2.2  2  MRP-L20       Mitochondrial ribosomal protein subunit L20
      0.063   12.8   0.1        0.6    9.6   0.0    2.4  3  DUF166        Domain of unknown function
       0.14   12.3   1.2       0.43   10.7   1.2    1.8  1  Podoplanin    Podoplanin
       0.26   11.1   1.1       0.71    9.7   1.1    1.8  1  EssA          WXG100 protein secretion system (Wss), protein 


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 !  137.5   3.9   4.7e-43   8.4e-40       1     310 [.      35     357 ..      35     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: 137.5 bits;  conditional E-value: 4.7e-43
                                   EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTE..EEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSH CS
                  Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGr..kielverDdaydpdraaeaarrlvdqdgvdalvgplss 79 
                                   +i+iG+l pl+G+++s+g  + a++q a+e++Na    +    +++l ++D++ +pd+a+++++ lv  +g++ +vgp++s
  gi|14601070|ref|NP_147596.1|  35 TITIGALLPLTGDLQSYGVRAQAAVQVAVEDVNAYLESKNAwfRLDLKVEDTQTKPDVAVQKFNSLVA-QGIKFIVGPMTS 114
                                   79********************************766664445*************************.************ PP

                                   HHHHHHHHHHHHHT-EEEESS-HH..CCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHHHHHH CS
                  Peripla_BP_6  80 avaaavaevlakdgvpvigpaglt..gekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregiaalkaa 158
                                   a ++ + +++++++v++i+p++++   + + ++vf+++p+++ q +a++  la++lg k +++++ ++ +g+ +++a+k++
  gi|14601070|ref|NP_147596.1| 115 AEVKKLKDLADQNNVLIISPSSTAieLKIAGDNVFRFCPTDDVQSKAIGA-LARDLGLKGAVIINRADTWGNGLMEATKEV 194
                                   *******************996664378*********************9.8***************************** PP

                                   HHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-S..........EEEEESSHHHHHHHHHHHHHTT-SSSCEEEE..CCC. CS
                  Peripla_BP_6 159 akaaGgevvgeepvplgttdfsaqvlqikaagad..........avllagtgadlaallkaaaeaGldakrillv..sws. 226
                                   ++ +G+ev   + + +++ +fs ++ q+    ++          + ++a ++  ++ l+ aaa+       + ++  +++ 
  gi|14601070|ref|NP_147596.1| 195 LENEGVEVASVYSYNPESPNFSGIASQANGD-VEslvskygkdkVAVVAIGFKEVVELFSAAADYETLESVLWIGsdGTAq 274
                                   *********99****************9874.4456666666666677778888************997755555444445 PP

                                   -CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTH.CCHHHHHH CS
                  Peripla_BP_6 227 gseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaags.ltreavra 306
                                   +se +  +l+ e    +l++ p f+ + ++a+++ +++++a+ g++  p+++++++y+a+++++ al +ag+  +++++++
  gi|14601070|ref|NP_147596.1| 275 LSEFTTDPLAREFSVSTLFINPLFSPAATEAQEKVRQEVVAKIGEE--PDAYSLAAYDAVWAIALALLQAGPmDNPDEMVN 353
                                   7777888888888889999999888889*****************8..***********************9899999888 PP

                                   HHHH CS
                  Peripla_BP_6 307 ales 310
                                   + ++
  gi|14601070|ref|NP_147596.1| 354 KVKE 357
                                   8776 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 !  113.5   0.0   6.2e-36   1.1e-32       2     346 ..      55     391 ..      54     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 6.2e-36
                                   HHHHHHHHHHHHHT-TTSSTTE.EEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS CS
                  ANF_receptor   2 vleAmklAveeinsdpnllpgi.klgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisyg 81 
                                   ++ A+++Ave++n+  +  +   +l+++++dt+ ++  a++++++++++ ++ ++Gp +s++++ ++ la+++++ +is++
  gi|14601070|ref|NP_147596.1|  55 AQAAVQVAVEDVNAYLESKNAWfRLDLKVEDTQTKPDVAVQKFNSLVAQGIKFIVGPMTSAEVKKLKDLADQNNVLIISPS 135
                                   689************99888878*************************88******************************* PP

                                   ---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEST.... CS
                  ANF_receptor  82 stspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleergicvalkekipe.... 158
                                   st+ el+       ++r  p+d  q++Ai ++ + +g k +++i   d++g+++++a +e le++g++va + ++++    
  gi|14601070|ref|NP_147596.1| 136 STAIELKIAGD--NVFRFCPTDDVQSKAIGALARDLGLKGAVIINRADTWGNGLMEATKEVLENEGVEVASVYSYNPespn 214
                                   *******9888..78**************************************************************9555 PP

                                   ....CHHHCHHHHHHHHHHTT..T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT CS
                  ANF_receptor 159 ....ssnddevvrkllkeiks..karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaeg 233
                                       +s+ + +v++l    ++  k +v v+    +++ el+ aa +    + +  wi+sd+ ++ ++  +++l  +e+   
  gi|14601070|ref|NP_147596.1| 215 fsgiASQANGDVESLV---SKygKDKVAVVAIGFKEVVELFSAAADYETLE-SVLWIGSDGTAQLSEFTTDPL-AREFSVS 290
                                   5555444444444444...4466669*****************77777775.4****************9986.7788666 PP

                                   -EEEEE.--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHCCHH CS
                  ANF_receptor 234 vlgfrl.kdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkpweg 313
                                   +l +   ++p  ++ +e +        +++   + g+e+ +y++a+ YdaV+++a Al +++ +++p      n+ k + +
  gi|14601070|ref|NP_147596.1| 291 TLFINPlFSPAATEAQEKV--------RQEVVAKIGEEPDAYSLAA-YDAVWAIALALLQAGPMDNPDE--MVNKVKELLP 360
                                   6666654566666666666........3566788999999999999.***************6553333..2333333333 PP

                                   HHHHHHHHHT-EEEETTSCEEB-TTSBBE.-EEE CS
                  ANF_receptor 314 gqkllrylrnvnfeGltGdvkfdengdrv.ptyd 346
                                     + +++    +f   tG++ +de gdr+ ++yd
  gi|14601070|ref|NP_147596.1| 361 QITTSDEF--AQFA-ATGKFPLDEGGDRAtADYD 391
                                   33333222..3566.799**********999997 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.5   4.9e-13   8.7e-10     218     382 ..      34     209 ..      22     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 4.9e-13
                                   ----EEEEE--SSTTHHHHHHHHHHHHHHH...........TT--S-EEEEETTTS..-HHHHHHHHHHTT--EEE---SH CS
                          LppC 218 kltkvalLLPlsGklakvaetirdGFlaak........daetqsnaqvkvfDtaae..slediyaqakaagidlvVGPLlk 288
                                   +   ++ LLPl+G+l+  +   ++  + a          ++   + ++kv Dt+++   + + ++ ++a+gi+++VGP+  
  gi|14601070|ref|NP_147596.1|  34 TTITIGALLPLTGDLQSYGVRAQAAVQVAVedvnayleSKNAWFRLDLKVEDTQTKpdVAVQKFNSLVAQGIKFIVGPMTS 114
                                   3346899***********99999999888877767443334445789******9996645566899*************** PP

                                   HHHHHHHHSGG.GTTSEEEES---TT-..--BTTEEE----HHHHHHHHHHHHHHT..T-SSEEEEEESSHHHHHHHHHHH CS
                          LppC 289 qnvdkllaqeqlvqsidvLaLNssdns..raiaqlcyfgLspEdeaesaAsklwad..gvRnplvlvpqndlGrRvveAFn 365
                                    +v+kl + + +    +vL +  s+ +    ia+   f   p d+++s A  ++a   g++ ++++   + +G+  +eA +
  gi|14601070|ref|NP_147596.1| 115 AEVKKLKDLADQ---NNVLIISPSSTAieLKIAGDNVFRFCPTDDVQSKAIGALARdlGLKGAVIINRADTWGNGLMEATK 192
                                   ******988777...4566665544443266*****************998887644699*******************99 PP

                                   HHHHHHHSS--EEEEES CS
                          LppC 366 erwqqlagtdaaielvd 382
                                   e   + + ++a +  ++
  gi|14601070|ref|NP_147596.1| 193 EVLENEGVEVASVYSYN 209
                                   99988888888887776 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 !   18.0   0.1   6.4e-07    0.0012       1     167 [.      36     204 ..      36     360 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.4e-07
                  Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlg..rkieavvvdpasdwelfaekaeklieedkvevvfGcwtSa 79 
                                   i +G L  l+G +      ++ a+++a+e++na    +    +++  v+d +  +++  +k ++l++ +++++++G  tSa
  gi|14601070|ref|NP_147596.1|  36 ITIGALLPLTGDLQSYGVRAQAAVQVAVEDVNAYLESKNawFRLDLKVEDTQTKPDVAVQKFNSLVA-QGIKFIVGPMTSA 115
                                   689*****************************97654442369***********************9.79*********** PP

                  Peripla_BP_5  80 sRkavlpvveelnalLfYpvq..YEGeEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnrilkall 158
                                     k++++  +++n l++ p     E + + +nv+    + + q+ +a+  l+++lg k ++++     +     + +k++l
  gi|14601070|ref|NP_147596.1| 116 EVKKLKDLADQNNVLIISPSStaIELKIAGDNVFRFCPTDDVQS-KAIGALARDLGLKGAVIINRADTWGNGLMEATKEVL 195
                                   ***************99986411566666666666554444443.455556666666666666666666666666666666 PP

                  Peripla_BP_5 159 kakggevvg 167
                                   +++g+ev  
  gi|14601070|ref|NP_147596.1| 196 ENEGVEVAS 204
                                   666666554 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     4e-06    0.0071      90     139 ..     444     497 ..     427     500 .] 0.46

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4e-06
                       DUF4366  90 tdcpv..eepepekeaepee..peeepekksnnglllvvlavaligggaayyfk 139
                                   t+++   +++e++++ +pee  +e+ +e + +++l+ ++++++++ ++aay+f 
  gi|14601070|ref|NP_147596.1| 444 TETSPspTQAETTPTPTPEEteTETAEEGGVSTTLIAAIIIIVIVIAAAAYFFL 497
                                   332223333333333344331133333333345555555555555556666664 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.2e-05      0.11      77     145 ..      61     133 ..      48     144 .. 0.78
   2 ?   -3.7   0.0       4.4   7.9e+03     131     157 ..     164     190 ..     161     192 .. 0.80
   3 ?   -3.2   0.0       3.1   5.6e+03       6      21 ..     237     252 ..     224     262 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                        PrpR_N  77 vgfeniikglktlselldldieiytinseee.aeaavkelkaegvevvvGdgvvadlAek...aGlksvllts 145
                                   v+ e++   l++ ++++ ld+++   ++  + a ++ + l a+g++ +vG++++a++ +    a+ + vl+ s
  gi|14601070|ref|NP_147596.1|  61 VAVEDVNAYLESKNAWFRLDLKVEDTQTKPDvAVQKFNSLVAQGIKFIVGPMTSAEVKKLkdlADQNNVLIIS 133
                                   677777888888899999*****9999888858899*****************99887663334455666666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.4
                        PrpR_N 131 dlAekaGlksvlltsgkesvrqAieeA 157
                                    lA+ +Glk+ ++   +++  + + eA
  gi|14601070|ref|NP_147596.1| 164 ALARDLGLKGAVIINRADTWGNGLMEA 190
                                   589999999999998888887777777 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.1
                        PrpR_N   6 dievvegdleeavela 21 
                                   ++ vv  +++e vel 
  gi|14601070|ref|NP_147596.1| 237 KVAVVAIGFKEVVELF 252
                                   3444444444444444 PP

>> MRP-L20  Mitochondrial ribosomal protein subunit L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.23     4e+02      15      56 ..     119     162 ..     109     170 .. 0.74
   2 ?    9.8   0.0   0.00046      0.83     104     138 ..     277     312 ..     276     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                       MRP-L20  15 srlnlkpeesfgliynPpssapsvsh...tPtkFLPksdprrell 56 
                                   +   l ++ ++ li  P+s+a++  +     + F P++d++ +++
  gi|14601070|ref|NP_147596.1| 119 KLKDLADQ-NNVLIISPSSTAIELKIagdNVFRFCPTDDVQSKAI 162
                                   33344444.455999******99999877788999***9998876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00046
                       MRP-L20 104 kwsrkkLakkFgcsklfvsmvteapk.ekkkeveae 138
                                   ++++  La++F +s+lf++ ++++++ e +++v++e
  gi|14601070|ref|NP_147596.1| 277 EFTTDPLAREFSVSTLFINPLFSPAAtEAQEKVRQE 312
                                   689999*************88755542666666555 PP

>> DUF166  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00033       0.6      40     112 ..      62     135 ..      50     151 .. 0.89
   2 ?   -0.7   0.0      0.47   8.4e+02      81     110 ..     174     204 ..     155     250 .. 0.69
   3 ?   -1.5   0.0      0.83   1.5e+03      34      55 ..     345     366 ..     308     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00033
                        DUF166  40 fiedpeelLpe...lkeaDivia.ytlhpDlllelaekakekkvkalivpaeapkaglrkelkekleelgievavpk 112
                                    +ed++ +L++    +  D+ +   +  pD+ ++  + +  +++k+++ p  + +    k+lk+ ++++++ ++ p 
  gi|14601070|ref|NP_147596.1|  62 AVEDVNAYLESknaWFRLDLKVEdTQTKPDVAVQKFNSLVAQGIKFIVGPMTSAE---VKKLKDLADQNNVLIISPS 135
                                   5899999**9999999****99636789************************999...999***9999999888886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                        DUF166  81 alivpaeapk.aglrkelkekleelgievav 110
                                   a+i+       +gl +  ke le+ g+eva 
  gi|14601070|ref|NP_147596.1| 174 AVIINRADTWgNGLMEATKEVLENEGVEVAS 204
                                   4444433333589999999999999999874 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.83
                        DUF166  34 peeldefiedpeelLpelkeaD 55 
                                    ++ de++++++elLp++  +D
  gi|14601070|ref|NP_147596.1| 345 MDNPDEMVNKVKELLPQITTSD 366
                                   4577899999999999988777 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.2   0.00024      0.43      86     143 ..     434     490 ..     420     494 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                    Podoplanin  86 aestvkakeesqstttlnvvtshstekvgeetet.tvekdGLatvtLvgiivGvllaig 143
                                   +e  + a++e+++++++  +  ++t  + eetet t e++G++t tL+  i+ +++ i+
  gi|14601070|ref|NP_147596.1| 434 QEKFTPAETETETSPSPTQAETTPTP-TPEETETeTAEEGGVST-TLIAAIIIIVIVIA 490
                                   45555667777777766666666644.45555551457777776.55555444555554 PP

>> EssA  WXG100 protein secretion system (Wss), protein EssA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1   0.00039      0.71      73     144 ..     432     498 ..     414     500 .] 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00039
                          EssA  73 LFeeekesneavkdtkesLFsseYevrasasevassetaeEesisktkskiiilliaggvvalaiGlyvvlr 144
                                   LF+e+ +  e+  +t  s  + e   +  + e +++etaeE  +s+t    +i +i+++v+++a   y  lr
  gi|14601070|ref|NP_147596.1| 432 LFQEKFTPAETETETSPSPTQAETTPTP-TPEETETETAEEGGVSTT----LIAAIIIIVIVIAAAAYFFLR 498
                                   5666666665656666666555555555.456678899999999999....99**********999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 3647.22
//
Query:       gi|14601071|ref|NP_147597.1|  [L=254]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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    2.6e-30  105.7   0.0    1.1  1  ABC_tran      ABC transporter
    1.3e-10   41.6   0.1    8.3e-05   22.5   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.7e-09   36.0   0.0    9.2e-09   35.0   0.0    1.5  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    9.6e-07   28.5   0.0      0.013   15.0   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    1.4e-05   24.7   0.0    2.6e-05   23.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    2.5e-05   24.2   0.0    6.4e-05   22.8   0.0    1.6  2  AAA_15        AAA ATPase domain
    3.9e-05   24.2   0.3    5.6e-05   23.7   0.3    1.2  1  AAA_23        AAA domain
    0.00021   20.9   0.0      0.041   13.4   0.0    2.4  2  AAA_25        AAA domain
    0.00065   20.0   0.0     0.0018   18.6   0.0    1.6  1  AAA_22        AAA domain
     0.0013   19.1   0.1     0.0015   19.0   0.1    1.4  1  AAA_16        AAA ATPase domain
     0.0014   18.4   0.0     0.0041   16.9   0.0    1.7  2  AAA_30        AAA domain
     0.0021   18.0   0.1     0.0066   16.4   0.1    1.8  2  RsgA_GTPase   RsgA GTPase
     0.0074   15.9   0.0      0.013   15.1   0.0    1.4  1  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.015   14.2   0.7       0.43    9.3   0.1    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.032   13.3   0.0      0.052   12.6   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
      0.052   14.0   0.1       0.12   12.8   0.1    1.6  1  AAA           ATPase family associated with various cellular 
      0.054   12.8   0.8       0.45    9.8   0.2    2.0  2  ATPase        KaiC
      0.056   13.4   0.0      0.093   12.6   0.0    1.2  1  Rad17         Rad17 P-loop domain
      0.056   13.4   0.0       0.11   12.5   0.0    1.5  1  AAA_5         AAA domain (dynein-related subfamily)
      0.066   13.4   0.1       0.17   12.0   0.1    1.6  1  AAA_33        AAA domain
      0.073   12.6   0.2       0.14   11.8   0.2    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.087   12.7   0.1       0.26   11.2   0.0    1.7  2  ATPase_2      ATPase domain predominantly from Archaea
        0.1   11.4   0.1       0.14   11.0   0.1    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
       0.11   12.0   0.0       0.17   11.3   0.0    1.2  1  AAA_7         P-loop containing dynein motor region
       0.12   11.9   0.0       0.18   11.4   0.0    1.2  1  AAA_27        AAA domain
       0.13   10.9   0.1       0.17   10.5   0.1    1.1  1  AAA_13        AAA domain
       0.13   12.0   0.1       0.18   11.5   0.1    1.3  1  AAA_24        AAA domain
       0.13   12.1   0.1       0.21   11.5   0.1    1.3  1  NACHT         NACHT domain
       0.15   12.4   0.1       0.37   11.1   0.1    1.6  2  AAA_19        AAA domain
       0.15    9.5   0.1        0.2    9.2   0.1    1.0  1  DUF3584       Protein of unknown function (DUF3584)
       0.15   11.8   0.1       0.33   10.7   0.1    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.23   11.2   0.0       0.35   10.6   0.0    1.2  1  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.24   10.6   0.0       0.35   10.1   0.0    1.3  1  Zeta_toxin    Zeta toxin
        0.3   10.2   0.0       0.39    9.8   0.0    1.1  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 !  105.7   0.0     5e-33   2.6e-30       1     136 [.      22     181 ..      22     182 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 5e-33
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                   l++v+l++++g+++ ++G+nG+GK+tL+++++g +kp+ G++l++g+d++   ++e+++  +   +q p+ f +ltv en 
  gi|14601071|ref|NP_147597.1|  22 LDKVNLEIERGKVTLLIGPNGSGKTTLVNVISGFYKPDGGRVLFKGRDITGmSPHEISKLGLVRTFQIPKPFTNLTVLENv 102
                                   789***********************************************989999999999999**************** PP

                                   ..........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                   ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ..........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                                              + +++ ++l ++gl+++ d++      +LSgGq + +++ara++k ++++++DE
  gi|14601071|ref|NP_147597.1| 103 ltaadspgenvylaglarrlwlgfekRAAARAFEILGWVGLDHMWDRRS----GELSGGQMKLLEIARAIMKGAEMIIMDE 179
                                   **********************998888888999*********999999....**************************** PP

                                   TT CS
                                   xx RF
                      ABC_tran 135 pt 136
                                   p 
  gi|14601071|ref|NP_147597.1| 180 PA 181
                                   *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 !   22.5   0.1   1.6e-07   8.3e-05       1      43 [.      34      59 ..      34      94 .. 0.76
   2 !   17.1   0.0   7.2e-06    0.0038     234     294 ..     151     209 ..     144     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.6e-07
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggir 43
                                  +++liGpNgsGK++L   ++++                  +++
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLVNVISGFY-----------------KPD 59
                                  69*****************8875.................444 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 7.2e-06
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvil 294
                                   + elS G+ +ll ++ a+   +     ++ DEp +g +P+l  +++e +k+l+r +g+ +++
  gi|14601071|ref|NP_147597.1| 151 SGELSGGQMKLLEIARAIMKGA---EMIIMDEPAAGVNPRLAGSIMERIKYLAReKGITFLI 209
                                   6789999999999999999877...9***********************9999988888866 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 !   35.0   0.0   1.7e-11   9.2e-09       1      23 []     231     253 ..     231     253 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.7e-11
                  BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                   +vIA+G+P+Ev n+P V e YLG
  gi|14601071|ref|NP_147597.1| 231 KVIASGKPDEVLNNPVVLESYLG 253
                                   79********************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 !   15.0   0.1   2.4e-05     0.013      25      44 ..      33      52 ..      21      56 .. 0.80
   2 !   11.7   0.0   0.00025      0.13     136     213 ..     153     229 ..      70     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                  SEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                  ++t ++GpNGSGK+ l++ i
  gi|14601071|ref|NP_147597.1| 33 KVTLLIGPNGSGKTTLVNVI 52
                                  6899***********99877 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00025
                                   CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-.SCEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                         SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemleka.dklvgvtk 213
                                   +LSgG+ +L+ +a       +k a + ++De +a    +    + e++k  +++k   f++i +r +++++  d+++ +++
  gi|14601071|ref|NP_147597.1| 153 ELSGGQMKLLEIAR----AIMKGAEMIIMDEPAAGVNPRLAGSIMERIKylAREKGITFLIIEHRIGLVKEYvDRVYAMSM 229
                                   79*******88764....4678999************************7666777***********99987789988877 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     5e-08   2.6e-05      13      40 ..      23      50 ..      20      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5e-08
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllD 40
                                  d+  +ei++  +tll+Gp+GsGK+Tl+ 
  gi|14601071|ref|NP_147597.1| 23 DKVNLEIERGKVTLLIGPNGSGKTTLVN 50
                                  66778998666***************95 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.2e-07   6.4e-05      17      48 ..      25      57 ..      21      96 .. 0.84
   2 ?   -1.6   0.0       3.3   1.7e+03     325     354 ..     173     202 ..     159     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.2e-07
                        AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFln 48
                                  v ++++   +t+liG+N+sGK+++++++  F +
  gi|14601071|ref|NP_147597.1| 25 VNLEIERGkVTLLIGPNGSGKTTLVNVISGFYK 57
                                  455555546*******************98877 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                        AAA_15 325 villiEEPEahLHpqaqkvlikllkeland 354
                                     ++++EP a   p +  ++++ +k la++
  gi|14601071|ref|NP_147597.1| 173 EMIIMDEPAAGVNPRLAGSIMERIKYLARE 202
                                   57899************9999999999876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   1.1e-07   5.6e-05      10      39 ..      22      52 ..      14      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-07
                        AAA_23 10 frdqeidFsk.gltlItGpNGaGKTTildAi 39
                                  +++++++ ++ ++tl++GpNG+GKTT+++ i
  gi|14601071|ref|NP_147597.1| 22 LDKVNLEIERgKVTLLIGPNGSGKTTLVNVI 52
                                  467777885548***************9987 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   7.8e-05     0.041      30      50 ..      29      49 ..      25      68 .. 0.89
   2 ?    5.1   0.0     0.029        15     133     188 ..     164     212 ..     111     213 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                        AAA_25 30 lpagelallaGapgtGKttla 50
                                  + +g+++ll+G+ g+GKttl+
  gi|14601071|ref|NP_147597.1| 29 IERGKVTLLIGPNGSGKTTLV 49
                                  579****************97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.029
                        AAA_25 133 leaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                   +++ai +  g+++++ D  ++ +     + + +g+++e+++ +ar++g+++l++ H
  gi|14601071|ref|NP_147597.1| 164 IARAIMK--GAEMIIMDEPAAGV-----NPRLAGSIMERIKYLAREKGITFLIIEH 212
                                   3333333..57777777654433.....23577999******************99 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   3.3e-06    0.0018       4     128 ..      31     210 ..      28     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.3e-06
                        AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..................erpevv.fvtlpsstsskdllrellralg 65 
                                   + ++++++G+ G+GKTtl++ +   ++    ++                    + ++v ++++p++ +  ++l+++l a +
  gi|14601071|ref|NP_147597.1|  31 RGKVTLLIGPNGSGKTTLVNVISGFYK----PDGgrvlfkgrditgmspheiSKLGLVrTFQIPKPFTNLTVLENVLTAAD 107
                                   67899***************9999984....344678899999***88855555555599********************* PP

                        AAA_22  66 lelka.....................................erlsseellealeqalrarav.ielliiDEaqh.lr.s. 105
                                   +++++                                     + ++++    +l + +ra ++  e++i DE    ++ + 
  gi|14601071|ref|NP_147597.1| 108 SPGENvylaglarrlwlgfekraaarafeilgwvgldhmwdrRSGELSGGQMKLLEIARAIMKgAEMIIMDEPAAgVNpRl 188
                                   *99999999999999999999999999999999999998876333333333444555555555677999999888787635 PP

                        AAA_22 106 .eealeeLrsllnlsrkgvqliLv 128
                                      ++e ++ l+   +kg++++++
  gi|14601071|ref|NP_147597.1| 189 aGSIMERIKYLAR--EKGITFLII 210
                                   6999999999999..999988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   2.8e-06    0.0015      23      60 ..      31      68 ..      21     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.8e-06
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkc 60
                                  r+ ++ll+G+ G+GK++lv+ +   ++ dgg +l    
  gi|14601071|ref|NP_147597.1| 31 RGKVTLLIGPNGSGKTTLVNVISGFYKPDGGRVLFKGR 68
                                  55899*****************9999999887765544 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   7.8e-06    0.0041      18      50 ..      32      64 ..      25      87 .. 0.87
   2 ?   -1.3   0.0       2.9   1.5e+03      81      96 ..     156     179 ..      95     199 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.8e-06
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                   +v++l Gp G+GKtt+++++   ++ +ggrv+
  gi|14601071|ref|NP_147597.1| 32 GKVTLLIGPNGSGKTTLVNVISGFYKPDGGRVL 64
                                  469************************997775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                        AAA_30  81 k........grarlepgtllivDE 96 
                                   +        +ra ++ ++++i DE
  gi|14601071|ref|NP_147597.1| 156 GgqmklleiARAIMKGAEMIIMDE 179
                                   044444444333333447777777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.2e-05    0.0066      93     121 ..      25      54 ..      17      68 .. 0.84
   2 ?   -2.2   0.0       6.4   3.4e+03      27      61 ..     185     219 ..     181     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                                   HHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallp 121
                                   ++ +++  k+++l+G+ G GK+tL+n++ +
  gi|14601071|ref|NP_147597.1|  25 VNLEIERgKVTLLIGPNGSGKTTLVNVISG 54 
                                   55556555******************9976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.4
                                   TTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--H CS
                   RsgA_GTPase  27 epelslnlldrfLvlaeekgiepvivlnKiDllee 61 
                                   +p+l  ++++r+  la ekgi+ +i+  +i l++e
  gi|14601071|ref|NP_147597.1| 185 NPRLAGSIMERIKYLAREKGITFLIIEHRIGLVKE 219
                                   47777888899999999999999988777766665 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   0.0   2.5e-05     0.013       2      38 ..      33      69 ..      32      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                         SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                  +v+ll+G++G+GKTt +  ++  +k +g +vl+   D
  gi|14601071|ref|NP_147597.1| 33 KVTLLIGPNGSGKTTLVNVISGFYKPDGGRVLFKGRD 69
                                  589*******************999999999987777 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 ?    9.3   0.1   0.00082      0.43     241     268 ..      28      55 ..      25      65 .. 0.83
   2 ?    2.7   0.0     0.082        43     324     364 ..     155     195 ..     148     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00082
                                   EE-SS.EEEEEE-TTSSHHHHHHHHHHCC CS
                    ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeAlekGv 268
                                    i +G vtl++G++  GK+TL++ ++ G 
  gi|14601071|ref|NP_147597.1|  28 EIERGkVTLLIGPNGSGKTTLVNVIS-GF 55 
                                   588999****************9884.55 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.082
                                   -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHH CS
                    ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqe 364
                                   SG   +  +i++a+  ga+++++DE  + +N  +  + m++
  gi|14601071|ref|NP_147597.1| 155 SGGQMKLLEIARAIMKGAEMIIMDEPAAGVNPRLAGSIMER 195
                                   6777777899***************9999886666666665 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 ?   12.6   0.0   9.9e-05     0.052     126     157 ..      29      60 ..      20      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-05
                         T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksd 157
                                   +++ ++ l+ G+ gsGKttl++++  + + + 
  gi|14601071|ref|NP_147597.1|  29 IERGKVTLLIGPNGSGKTTLVNVISGFYKPDG 60 
                                   5666788999*************998877665 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   0.1   0.00022      0.12       2      20 ..      36      54 ..      35      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00022
                                  EEESSTTSSHHHHHHHHHH CS
                           AAA  2 llyGppGtGKTllakavak 20
                                  ll+Gp G GKT+l++ +  
  gi|14601071|ref|NP_147597.1| 36 LLIGPNGSGKTTLVNVISG 54
                                  8*************99865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00085      0.45       4      36 ..      18      49 ..      17      52 .. 0.86
   2 ?    1.2   0.0      0.37     2e+02     135     163 ..     184     212 ..     157     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00085
                        ATPase  4 gIeglDeilkgGipegrvvlitGepGtGKtifa 36
                                  gI  lD++ +  i +g+v+l+ G  G+GKt+++
  gi|14601071|ref|NP_147597.1| 18 GIVALDKV-NLEIERGKVTLLIGPNGSGKTTLV 49
                                  67778877.47799****************986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                        ATPase 135 ekeavaReilrqlvrvlkklgvTailvse 163
                                    ++ +a +i+ ++++  +++g+T ++++ 
  gi|14601071|ref|NP_147597.1| 184 VNPRLAGSIMERIKYLAREKGITFLIIEH 212
                                   57788899999999999999999999875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00018     0.093      35      66 ..      22      53 ..      19      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                         Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  l+   Le ++ ++ L+ GP G gk+t v+v+s
  gi|14601071|ref|NP_147597.1| 22 LDKVNLEIERGKVTLLIGPNGSGKTTLVNVIS 53
                                  677789999999*****************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 ?   12.5   0.0    0.0002      0.11       3      23 ..      36      56 ..      34      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                                  EEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  3 lLvGppGtgKselaerlaaal 23
                                  lL+Gp G+gK++l+  ++ ++
  gi|14601071|ref|NP_147597.1| 36 LLIGPNGSGKTTLVNVISGFY 56
                                  8*************9998776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00032      0.17       1      16 [.      34      49 ..      34      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
                        AAA_33  1 lvllvGlpGsGKstla 16
                                  ++ll+G++GsGK+tl+
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLV 49
                                  6899**********98 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   0.00026      0.14       2      20 ..      34      52 ..      33      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                                  EEEEEESTTCCHHHHHHHH CS
                          cobW  2 vtvltGflGsGKTtLlnhl 20
                                  vt+l G+ GsGKTtL+n +
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLVNVI 52
                                  899*************976 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 ?   11.2   0.0   0.00049      0.26      15      40 ..      27      52 ..      19      66 .. 0.83
   2 ?   -1.5   0.0       3.6   1.9e+03     136     176 ..     185     223 ..     161     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00049
                      ATPase_2 15 lerepneiyfiYGpegsGKtaLlkei 40
                                  le e+ ++ ++ Gp gsGKt+L++ i
  gi|14601071|ref|NP_147597.1| 27 LEIERGKVTLLIGPNGSGKTTLVNVI 52
                                  5667789999************9976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.6
                      ATPase_2 136 ngaellvkeLlnliesltkekhlcvviclsSeglfiervyn 176
                                   n    l  ++++ i++l +ek +++ i+    gl+ e+v++
  gi|14601071|ref|NP_147597.1| 185 N--PRLAGSIMERIKYLAREKGITFLIIEHRIGLVKEYVDR 223
                                   4..56666777888888888888888888888888886654 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00027      0.14      24      56 ..      31      63 ..      23      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                          DLIC 24 sgksvlvlGedgsGkttliaklqGveeekkGrG 56
                                   gk  l++G +gsGkttl+  + G  ++  Gr 
  gi|14601071|ref|NP_147597.1| 31 RGKVTLLIGPNGSGKTTLVNVISGFYKPDGGRV 63
                                  68999*******************998888875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.17      29      52 ..      28      51 ..      24      60 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                         AAA_7 29 llknkkpvllvGptGtGKtviikd 52
                                   ++++k +ll+Gp G+GKt++++ 
  gi|14601071|ref|NP_147597.1| 28 EIERGKVTLLIGPNGSGKTTLVNV 51
                                  5789999*************9985 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00034      0.18       9      47 ..      14      53 ..       7      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                        AAA_27  9 eryGkf.tdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                  +r+G + +  +++++ e+ +++l++GpN +GK+t+++ is
  gi|14601071|ref|NP_147597.1| 14 KRFGGIvALDKVNLEIERGKVTLLIGPNGSGKTTLVNVIS 53
                                  5666551446788998999***************998876 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00032      0.17      18      39 ..      34      55 ..      24      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                        AAA_13 18 iNliYGwNGaGKTtLSrllrsl 39
                                  + l+ G NG+GKTtL ++++ +
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLVNVISGF 55
                                  56788*************9987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00035      0.18       2      23 ..      32      60 ..      31      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                        AAA_24  2 klkiliyGpsgiGKTtlakel.......g 23
                                  ++  l++Gp+g+GKTtl++ +       g
  gi|14601071|ref|NP_147597.1| 32 GKVTLLIGPNGSGKTTLVNVIsgfykpdG 60
                                  56789************987755555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00041      0.21       2      20 ..      34      52 ..      33      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                                  CEEEEC-TTTCHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                  + +l G++GsGKTtL+  +
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLVNVI 52
                                  6799***********9866 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    0.0007      0.37       9      33 ..      31      55 ..      24      71 .. 0.83
   2 ?   -2.3   0.0       9.4     5e+03      99     110 ..     167     179 ..     112     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0007
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhival 33
                                  + kv l++++ G+GKT++++ i   
  gi|14601071|ref|NP_147597.1| 31 RGKVTLLIGPNGSGKTTLVNVISGF 55
                                  56899************99987655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.4
                        AAA_19  99 klqeee.llivDE 110
                                    + +++ ++i DE
  gi|14601071|ref|NP_147597.1| 167 AIMKGAeMIIMDE 179
                                   2223333555555 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   0.00037       0.2      19      43 ..      34      58 ..      25      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00037
                       DUF3584 19 htnieGtNaaGKTtLlrLiPlFYGe 43
                                   t + G N++GKTtL  +i  FY  
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLVNVISGFYKP 58
                                  57899**************999955 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   0.1   0.00062      0.33       3      23 ..      34      54 ..      32      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00062
                     PduV-EutP  3 killiGkvgsGKttLtqalkg 23
                                    lliG+ gsGKttL + ++g
  gi|14601071|ref|NP_147597.1| 34 VTLLIGPNGSGKTTLVNVISG 54
                                  579************998876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00067      0.35       2      21 ..      38      57 ..      37      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00067
                    ATP_bind_1  2 vGpaGsGKttfvgalseile 21
                                  +Gp GsGKtt+v+ +s +++
  gi|14601071|ref|NP_147597.1| 38 IGPNGSGKTTLVNVISGFYK 57
                                  8************9998776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00067      0.35      12      60 ..      28      76 ..      20     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00067
                    Zeta_toxin 12 sqerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                  + er k+ ll G  G+GK++l + +    +++g+ v +++ d+  + P+
  gi|14601071|ref|NP_147597.1| 28 EIERGKVTLLIGPNGSGKTTLVNVISGFYKPDGGRVLFKGRDITGMSPH 76
                                  55788999****************9999988888888887777666666 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00074      0.39      26      50 ..      35      59 ..      21      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00074
                                  EEEEESTTSSHHHHHHHHHHHCS-- CS
                       G-alpha 26 llllGqseSGKsTilkqlkllykkg 50
                                   ll+G ++SGK+T+++ +  +yk+ 
  gi|14601071|ref|NP_147597.1| 35 TLLIGPNGSGKTTLVNVISGFYKPD 59
                                  589***************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1801.59
//
Query:       gi|14601072|ref|NP_147598.1|  [L=237]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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  106.7   0.0    1.7e-30  106.3   0.0    1.1  1  ABC_tran     ABC transporter
    7.8e-15   55.5   0.1      3e-06   27.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-07   31.1   0.0    1.3e-06   28.0   0.0    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
    1.5e-05   24.9   0.0    0.00039   20.3   0.0    2.0  2  AAA_15       AAA ATPase domain
    1.5e-05   25.3   0.0    6.8e-05   23.2   0.0    1.8  1  AAA_22       AAA domain
    6.5e-05   23.5   0.1    8.9e-05   23.1   0.1    1.3  1  AAA_23       AAA domain
    0.00012   21.7   0.1    0.00029   20.5   0.1    1.6  1  AAA_29       P-loop containing region of AAA domain
    0.00099   19.5   0.0     0.0013   19.2   0.0    1.3  1  AAA_16       AAA ATPase domain
     0.0012   17.7   0.1     0.0028   16.5   0.2    1.5  2  ABC_ATPase   Predicted ATPase of the ABC class
     0.0018   17.9   0.0     0.0028   17.3   0.0    1.2  1  AAA_27       AAA domain
     0.0033   16.4   0.1     0.0068   15.4   0.1    1.4  1  AAA_10       AAA-like domain
     0.0062   15.6   0.6       0.14   11.2   0.0    2.1  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
     0.0066   16.2   0.2      0.017   14.8   0.1    1.7  2  AAA_24       AAA domain
     0.0092   15.9   0.2      0.018   14.9   0.1    1.5  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.095   12.4   0.0    2.0  2  AAA_30       AAA domain
      0.017   14.5   0.2          4    6.7   0.1    2.2  2  ATPase       KaiC
      0.025   14.6   0.0      0.066   13.3   0.0    1.7  2  MMR_HSR1     50S ribosome-binding GTPase
      0.028   14.0   0.2      0.042   13.4   0.2    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.028   14.6   0.0      0.046   13.9   0.0    1.7  1  AAA_33       AAA domain
      0.029   14.6   0.0       0.55   10.5   0.0    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.035   14.1   0.0      0.083   12.9   0.0    1.7  2  AAA_14       AAA domain
      0.049   13.2   0.2       0.11   12.1   0.2    1.8  1  AAA_25       AAA domain
      0.051   12.4   0.0      0.091   11.5   0.0    1.3  1  Adeno_IVa2   Adenovirus IVa2 protein
      0.057   13.3   0.0      0.089   12.7   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
      0.075   13.5   0.1       0.35   11.3   0.0    2.0  2  AAA_17       AAA domain
       0.12   11.7   0.0       0.15   11.3   0.0    1.2  1  Septin       Septin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   2.5e-33   1.7e-30       3     137 .]      23     166 ..      21     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2.5e-33
                                   EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren... 79 
                                   +vsl++ +g +++ivG+nGaGKStLlk++ g ++  +G++l++++d+++  ++ +++  + +++q +++f+eltv+en   
  gi|14601072|ref|NP_147598.1|  23 DVSLEIPRGLITVIVGPNGAGKSTLLKTMFGFTTVYKGRVLFENTDVTHmPPHDRAKIGMTFIFQLENIFRELTVYENlrl 103
                                   89***********************************************788888888888999***************** PP

                                   ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             ++++e++ s +      ++++++++ +LSgG++q++a+a  +++kpk++l+DEpta
  gi|14601072|ref|NP_147598.1| 104 agydlpedVFRDRLEEVFSMFP---RLKERLGQKAGTLSGGERQMLAMAIGIMRKPKVFLIDEPTA 166
                                   **99966555666666666666...5669999999*****************************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 !   26.5   0.1   7.7e-09   5.3e-06       1      41 [.      33      65 ..      33     100 .. 0.69
   2 !   27.2   0.0   4.4e-09     3e-06     234     293 ..     135     191 ..      83     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 7.7e-09
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                  ++v++GpNg+GKS+LL+++ ++  +        ++ +  ++
  gi|14601072|ref|NP_147598.1| 33 ITVIVGPNGAGKSTLLKTMFGFTTV--------YKGRVLFE 65
                                  79*****************776443........33333333 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 4.4e-09
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvi 293
                                   a  lS G +++la++  + r +   +++liDEp +gL Pkl +++l  +++l+++g  v+
  gi|14601072|ref|NP_147598.1| 135 AGTLSGGERQMLAMAIGIMRKP---KVFLIDEPTAGLSPKLAKEVLSYVRILNKEGYTVV 191
                                   6679***************988...9********************88888877777666 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 !   28.0   0.0   1.9e-09   1.3e-06      26     190 ..      33     187 ..      21     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.9e-09
                                   EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH.CCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrse.klsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkr 105
                                   +t+ivGpNG+GKs ll  +   +G+++  k r   + +d+ h     +  ++a++ +tf  + +++  e + ++  r +  
  gi|14601072|ref|NP_147598.1|  33 ITVIVGPNGAGKSTLLKTM---FGFTTVYKGRVLfENTDVTH----MPPHDRAKIGMTFIFQLENIFRELTVYENLRLAGY 106
                                   79*****************...66656655555413344444....58999999999997777775555555555555555 PP

                                   TSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 106 kgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                   +   +++ ++ e  ++   +l e+ g +  +LSgGe++++a+a+      +++  ++l+De  a L  k  k+v ++++  
  gi|14601072|ref|NP_147598.1| 107 DLPEDVFRDRLEEVFSMFPRLKERLGQKAGTLSGGERQMLAMAIG----IMRKPKVFLIDEPTAGLSPKLAKEVLSYVRIL 183
                                   555777777777777777778888888999*********998876....3444457899****************999987 PP

                                   CTTS CS
                                   xxxx RF
                         SMC_N 187 skna 190
                                   +k+ 
  gi|14601072|ref|NP_147598.1| 184 NKEG 187
                                   7664 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.6e-07   0.00039      11      68 ..      15      72 ..      13     102 .. 0.68
   2 ?    2.4   0.0      0.14     1e+02     322     353 ..     154     185 ..     142     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.6e-07
                        AAA_15 11 FRslkd.veidlsee...ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleif 68
                                  +++l+  ++++l+     +tv++G+N++GKS++l+ +  F +      k  + +e+ d+ ++
  gi|14601072|ref|NP_147598.1| 15 YGKLQTlFDVSLEIPrglITVIVGPNGAGKSTLLKTMFGFTTVY----KGRVLFENTDVTHM 72
                                  566666666666666778*****************996666644....45555555555555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.14
                        AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelan 353
                                    k++++li+EP a L p++ k++  + + l +
  gi|14601072|ref|NP_147598.1| 154 RKPKVFLIDEPTAGLSPKLAKEVLSYVRILNK 185
                                   57899***************999888776655 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   9.8e-08   6.8e-05       6     128 ..      32     193 ..      29     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9.8e-08
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevvfvtlpsst 51 
                                    i+v++G+ G+GK+tll++++   + ++                                       e+ +++ ++lp++ 
  gi|14601072|ref|NP_147598.1|  32 LITVIVGPNGAGKSTLLKTMFGFTTVYKGRVLfentdvthmpphdrakigmtfifqlenifreltvyENLRLAGYDLPEDV 112
                                   689*******************98766554449999999999999999999999999999999999888888899999999 PP

                        AAA_22  52 sskdllrellralglelkaerlsseellealeqalrarav.....ielliiDEaqh.lrs....eealeeLrsllnlsrkg 122
                                     +d l+e+++ + + +++  +++   l+  e+++ a a      +++++iDE    l s    +e+l+++ ++ln  + g
  gi|14601072|ref|NP_147598.1| 113 -FRDRLEEVFSMFPRLKER-LGQKAGTLSGGERQMLAMAIgimrkPKVFLIDEPTAgL-SpklaKEVLSYV-RILN--KEG 187
                                   .999999999999987777.666666667777777777777777899******99999.633446666665.5555..777 PP

                        AAA_22 123 vqliLv 128
                                    +++Lv
  gi|14601072|ref|NP_147598.1| 188 YTVVLV 193
                                   777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.3e-07   8.9e-05      21      38 ..      33      50 ..      14      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.3e-07
                        AAA_23 21 ltlItGpNGaGKTTildA 38
                                  +t+I+GpNGaGK+T+l  
  gi|14601072|ref|NP_147598.1| 33 ITVIVGPNGAGKSTLLKT 50
                                  89*************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 !   20.5   0.1   4.2e-07   0.00029      17      39 ..      26      48 ..      19      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.2e-07
                        AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                  +ei  +g +t+++Gp+G+GKSTll
  gi|14601072|ref|NP_147598.1| 26 LEIP-RGlITVIVGPNGAGKSTLL 48
                                  5664.7889**************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.8e-06    0.0013      11      63 ..      17      70 ..      14     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-06
                        AAA_16 11 qLlsale.rvrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                  +L+++++ ++  +r+ +++++G+ G GKs+l+++ +  +++ + g +l +++d  
  gi|14601072|ref|NP_147598.1| 17 KLQTLFDvSLEIPRGLITVIVGPNGAGKSTLLKTMFG-FTTVYkGRVLFENTDVT 70
                                  688888888888999*****************99994.44443366666666666 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 !   16.5   0.2     4e-06    0.0028     240     264 ..      26      51 ..      24      58 .. 0.92
   2 ?   -3.5   0.0       4.8   3.3e+03     325     351 ..     140     166 ..     136     167 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4e-06
                                   EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                                   + ip+G +t+IvG++  GKsTLL+ +
  gi|14601072|ref|NP_147598.1|  26 LEIPRGlITVIVGPNGAGKSTLLKTM 51 
                                   569********************975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.8
                                   HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                    ABC_ATPase 325 GStsqAanimealeagakllLiDEDts 351
                                   G   q  +++  + ++ k++LiDE t+
  gi|14601072|ref|NP_147598.1| 140 GGERQMLAMAIGIMRKPKVFLIDEPTA 166
                                   555556666667778889999999775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     4e-06    0.0028      16      53 ..      23      54 ..      12      70 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4e-06
                        AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAisdllfGi 53
                                  d sl+++  +  +++i+GpN AGKst+l+ +    fG+
  gi|14601072|ref|NP_147598.1| 23 DVSLEIP--RGLITVIVGPNGAGKSTLLKTM----FGF 54
                                  4455555..67789*************9875....454 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   0.1   9.8e-06    0.0068      24      53 ..      34      63 ..      29      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.8e-06
                        AAA_10 24 sliiGdlGnGKSvlakllvlyisllggkal 53
                                  ++i+G+ G+GKS l k+++ + ++ +g++l
  gi|14601072|ref|NP_147598.1| 34 TVIVGPNGAGKSTLLKTMFGFTTVYKGRVL 63
                                  689************************998 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 ?    2.7   0.1     0.073        50      32      49 ..      34      51 ..      14      62 .. 0.78
   2 !   11.2   0.0    0.0002      0.14      74     129 ..     136     195 ..     132     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.073
                                  EEEEE-TTSSHHHHHHHH CS
                          MeaB 32 vGltGvPGaGkstlveal 49
                                    + G  GaGkstl++ +
  gi|14601072|ref|NP_147598.1| 34 TVIVGPNGAGKSTLLKTM 51
                                  5578999*******9875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0002
                                   ----------HCCC....TSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEE CS
                          MeaB  74 GsilGDklRleela....vdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvliet 129
                                   G++ G   ++  +a    +++ vf+   p+ G    la++ +  v++l+  G+ vvl+e 
  gi|14601072|ref|NP_147598.1| 136 GTLSGGERQMLAMAigimRKPKVFLIDEPTAGLSPKLAKEVLSYVRILNKEGYTVVLVEQ 195
                                   66666666777777666689**************************************95 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.5e-05     0.017       4      32 ..      33      68 ..      30      89 .. 0.89
   2 ?   -1.9   0.0       3.4   2.3e+03     107     128 ..     172     193 ..     170     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                        AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidte 32
                                    +i+Gp+g+GK+tl+k++       + ++lf +t+
  gi|14601072|ref|NP_147598.1| 33 ITVIVGPNGAGKSTLLKTMfgfttvyKGRVLFENTD 68
                                  579****************99999888888888777 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                        AAA_24 107 laeefrrllkklqelrknvifi 128
                                   la+e+ ++++ l++ +++v+++
  gi|14601072|ref|NP_147598.1| 172 LAKEVLSYVRILNKEGYTVVLV 193
                                   7899999999999999999997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.6e-05     0.018      99     121 ..      31      53 ..      14      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                   TSEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                   + ++v+vG+ G+GKStL++++ +
  gi|14601072|ref|NP_147598.1|  31 GLITVIVGPNGAGKSTLLKTMFG 53 
                                   4689**************99876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.095      19      43 ..      32      56 ..      27      79 .. 0.84
   2 ?    0.9   0.0      0.48   3.3e+02      62     122 ..     127     193 ..     122     202 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                        AAA_30 19 rvavltGpAGtGKttalkalreawe 43
                                  +++v++Gp G+GK+t+lk++    +
  gi|14601072|ref|NP_147598.1| 32 LITVIVGPNGAGKSTLLKTMFGFTT 56
                                  689**************98765555 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.48
                        AAA_30  62 Laeelgieastiakllkrlk..grarlepg.tllivDEagm.vdtkqlaallkaae...kagakvilv 122
                                   L+e lg +a t+    +++   +   + ++ +++++DE    ++ k ++++l+ ++   k+g +v+lv
  gi|14601072|ref|NP_147598.1| 127 LKERLGQKAGTLSGGERQMLamA-IGIMRKpKVFLIDEPTAgLSPKLAKEVLSYVRilnKEGYTVVLV 193
                                   67777777777776665555642.44556669999999543146566666655443111556666665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0059         4      16      37 ..      28      49 ..      13      71 .. 0.82
   2 ?    5.8   0.0     0.011       7.8     141     186 ..     173     216 ..     144     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0059
                        ATPase 16 ipegrvvlitGepGtGKtifal 37
                                  ip+g ++ i+G  G+GK+++ +
  gi|14601072|ref|NP_147598.1| 28 IPRGLITVIVGPNGAGKSTLLK 49
                                  89***************87644 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                        ATPase 141 ReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgviv 186
                                    +++   vr+l+k g T +lv++  + + ++g  gv    v+g i 
  gi|14601072|ref|NP_147598.1| 173 AKEVLSYVRILNKEGYTVVLVEQNVKASLEIGDKGVLV--VNGRIA 216
                                   46778899***************999999999999975..777776 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   0.0   9.5e-05     0.066       3      22 ..      35      54 ..      33      91 .. 0.76
   2 ?   -1.7   0.0       4.4     3e+03      69      69 ..     178     178 ..     135     217 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                                  EEEESTTSSHHHHHHHHHTS CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                  +ivG   +GKStL+++++g 
  gi|14601072|ref|NP_147598.1| 35 VIVGPNGAGKSTLLKTMFGF 54
                                  79***************983 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                                   H CS
                      MMR_HSR1  69 a 69 
                                   +
  gi|14601072|ref|NP_147598.1| 178 S 178
                                   1 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   0.2     6e-05     0.042       2      21 ..      33      52 ..      32      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-05
                                  EEEEEESTTCCHHHHHHHHH CS
                          cobW  2 vtvltGflGsGKTtLlnhll 21
                                  +tv++G+ G+GK+tLl+++ 
  gi|14601072|ref|NP_147598.1| 33 ITVIVGPNGAGKSTLLKTMF 52
                                  79**************9986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.7e-05     0.046       2      24 ..      34      56 ..      33     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                        AAA_33  2 vllvGlpGsGKstlaerllkklg 24
                                  +++vG++G+GKstl++ +   ++
  gi|14601072|ref|NP_147598.1| 34 TVIVGPNGAGKSTLLKTMFGFTT 56
                                  689************99875444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0008      0.55      25      45 ..     130     150 ..     122     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0008
                       SbcCD_C  25 elsrssgtlSGGekqflayla 45 
                                   +l +++gtlSGGe+q+la+ +
  gi|14601072|ref|NP_147598.1| 130 RLGQKAGTLSGGERQMLAMAI 150
                                   577899********8877654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.083       3      39 ..      32      68 ..      30     104 .. 0.73
   2 ?   -2.5   0.0       7.2     5e+03      64      73 ..     155     164 ..     141     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                        AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinld 39
                                   i vi+G+  +GK+tllk+++    v k ++l+ n d
  gi|14601072|ref|NP_147598.1| 32 LITVIVGPNGAGKSTLLKTMFGFTTVYKGRVLFENTD 68
                                  589****************996555555555555544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.2
                        AAA_14  64 kktylflDEi 73 
                                   k +++++DE 
  gi|14601072|ref|NP_147598.1| 155 KPKVFLIDEP 164
                                   6677888884 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00016      0.11      30      65 ..      28      65 ..      24     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                        AAA_25 30 lpagelallaGapgtGKttlaldlalava..tGkpwlg 65
                                  +p+g +++++G+ g+GK+tl+  +   ++  +G+ +++
  gi|14601072|ref|NP_147598.1| 28 IPRGLITVIVGPNGAGKSTLLKTMFGFTTvyKGRVLFE 65
                                  79999***************977766666566666555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013     0.091      88     111 ..      32      55 ..      22      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                    Adeno_IVa2  88 viGviyGPtGsGksqllrnlissk 111
                                   +i vi GP G+Gks ll+++    
  gi|14601072|ref|NP_147598.1|  32 LITVIVGPNGAGKSTLLKTMFGFT 55 
                                   899***************987654 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 ?   12.7   0.0   0.00013     0.089      20      55 ..      31      66 ..      24     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                      ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyi 55
                                    i +i Gp g GK++Llk +      ++ +v++ +
  gi|14601072|ref|NP_147598.1| 31 GLITVIVGPNGAGKSTLLKTMFGFTTVYKGRVLFEN 66
                                  5799***************98877766666666665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00051      0.35       1      34 [.      37      67 ..      37      82 .. 0.85
   2 ?   -1.4   0.0       4.3     3e+03      66      88 ..     201     223 ..     168     229 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                                  EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHH CS
                        AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreea 34
                                  +G+ G+GK+t++   +  +gft +  G +l+e+ 
  gi|14601072|ref|NP_147598.1| 37 VGPNGAGKSTLL---KTMFGFTTVYKGRVLFENT 67
                                  79**********...6669***********9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.3
                                   HHHHHSSEEEEEE-SEEEETTEE CS
                        AAA_17  66 aeeakkkgvlvdghprikeqagf 88 
                                    e  +k+ ++v+g   ++ +a++
  gi|14601072|ref|NP_147598.1| 201 LEIGDKGVLVVNGRIAFDGPAEE 223
                                   22234555677777777666665 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00022      0.15       8      30 ..      35      57 ..      30      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                                  EEEEBTTSSCCCCCCTTSSSS-- CS
                        Septin  8 mvvGesglGkttlintlfetdli 30
                                  ++vG +g Gk+tl++t+f  + +
  gi|14601072|ref|NP_147598.1| 35 VIVGPNGAGKSTLLKTMFGFTTV 57
                                  689**************975544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 1758.67
//
Query:       gi|14601073|ref|NP_147599.1|  [L=354]
Description: branched-chain amino acid ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-33  114.0  36.0    8.4e-33  113.7  36.0    1.1  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.27   11.2   1.8        1.1    9.3   0.1    2.6  2  TraQ          Type-F conjugative transfer system pilin chaper


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  36.0   9.4e-37   8.4e-33       2     265 ..       7     326 ..       6     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 9.4e-37
                  BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl..........................ll 56 
                                   ++ +l++++++a+++lG++l ++ ++v+n++h  ++ +Gay+aa  +al+  l                          l+
  gi|14601073|ref|NP_147599.1|   7 VFDMLAYSGVIALLSLGITLAYITTRVFNFAHPRIANVGAYAAAASMALYVDLvrdegigrfkvslgplevtglvapdvLA 87 
                                   578999***************************************999999999*********************999999 PP

                  BPD_transp_2  57 lallvallvgaavglllgllvlrlkvdel......iitllllsvlvgltlllltgitsgvkgqssvkellgfagallsfls 131
                                   +++++a+++g++ +l+ ++lvlr  +++       +i++l++ ++v  tl++l++ +s  + +s+v +  +++  l  f  
  gi|14601073|ref|NP_147599.1|  88 VGIVFAVIAGIITALAEYYLVLRPLIERGadflklMIATLAFDFFVIATLFILGTHISVKELVSGVFGRETTSLSLHAFDA 168
                                   999999999999999999999999999988888888888888888888888999999999999988888888887777775 PP

                  BPD_transp_2 132 aviv...............llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGall 197
                                                      l  l+++l +++ll +t++G+++ra  en+++a++lGinv +v +++++isga Ag+aG+l+
  gi|14601073|ref|NP_147599.1| 169 RIDLavlgyklrgimlfsfLGSLAIALMLYILLFKTKLGVKMRASIENPSLAEVLGINVQQVYTIAWIISGATAGFAGFLI 249
                                   4444899***********9889999999***************************************************** PP

                  BPD_transp_2 198 alllgsipp....nigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi.....ptelarvllgalli 265
                                    ++  +++p    +   +++ +a+a  ++Gg+ s++g + G++iig+v++l+++++        t ++++l+ + + 
  gi|14601073|ref|NP_147599.1| 250 LFMGDIVKPvtasSPADEIIVSAFAGSIVGGVNSVFGSIGGGFIIGAVEILISSVITDvtgidVTRYNKMLSMLAVA 326
                                   *********865444556********************************999998666666547777777665544 PP

>> TraQ  Type-F conjugative transfer system pilin chaperone (TraQ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.2     0.093   8.4e+02      17      52 ..      18      55 ..       1      58 [. 0.66
   2 ?    9.3   0.1   0.00012       1.1       3      40 ..      67     107 ..      65     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.093
                          TraQ 17 WvlslGvwfhlvarlv..yrkPelavllaeilavglvl 52
                                   +lslG+ +  ++  v  + +P +a + a   a +++l
  gi|14601073|ref|NP_147599.1| 18 ALLSLGITLAYITTRVfnFAHPRIANVGAYAAAASMAL 55
                                  47899997766555551246899988888888877776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00012
                          TraQ   3 kyklrlPelDvtGlW...vlslGvwfhlvarlvyrkPelav 40 
                                   ++k++l  l+vtGl    vl++G+ f ++a+++    e  +
  gi|14601073|ref|NP_147599.1|  67 RFKVSLGPLEVTGLVapdVLAVGIVFAVIAGIITALAEYYL 107
                                   499**********965669************9988777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 2840.18
//
Query:       gi|118431260|ref|NP_147600.2|  [L=387]
Description: branched-chain amino acid ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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  115.0  26.2    4.4e-33  114.6  26.2    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 !  114.6  26.2   2.4e-37   4.4e-33       3     240 ..      11     290 ..       9     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 2.4e-37
                   BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl............................ 54 
                                    +++++++a+++ +  +l+l  g++G++++g++ f+a+G++v++ l+a+  +                             
  gi|118431260|ref|NP_147600.2|  11 EFIVAYVAVYYVLTSSLNLKAGVTGIPDFGQAMFFAVGGIVVGNLAARIAAAlagmdpslviaentttlevlnseffpnr 90 
                                    678999******************************************9999**************************** PP

                   BPD_transp_2  55 .......lllallvallvgaavglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqs.svkellgfagal 126
                                           l +a++ al++g+++gll  ++ lrl+ d+l+i ll++ ++++++ ++  ++ + + ++  + + ll+++g+ 
  gi|118431260|ref|NP_147600.2|  91 plesiaiLVVAIASALALGGLLGLLASYPALRLRGDYLAIMLLVTAEALRIYTTYSVWLMGSTPTVGlTLPSLLAWTGDP 170
                                    *****************************************************888887776666663444444444443 PP

                   BPD_transp_2 127 lsflsavivllalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallal....llg 202
                                       +s  ++l ++++v++ +++l++++ Gr +rav+++e+a++alG++v +v+  ++v+++alA+laG+l++        
  gi|118431260|ref|NP_147600.2| 171 -GLASILLTLAIAVAVYIYMERLYNSPAGRLMRAVRDDEDASKALGKDVAKVRRNAMVVGSALAALAGVLYSInpllAGS 249
                                    .555566679999**********************************************************852221222 PP

                   BPD_transp_2 203 sipp....nigvglgfnaiaavvlGgagsllgtviGaliigv 240
                                    s+ +    + ++ ++f ++a ++lGg+ s++g+ i++++ g+
  gi|118431260|ref|NP_147600.2| 250 SV-AavsiFDRMLWTFWPWALMILGGMSSNRGVAIASVVTGA 290
                                    22.2467789999************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2940.72
//
Query:       gi|118431261|ref|NP_147603.2|  [L=157]
Description: hypothetical protein APE_0928.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1327.39
//
Query:       gi|118431262|ref|NP_147604.2|  [L=397]
Description: acetyl-CoA acetyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-25   90.1   0.9    1.3e-24   86.9   0.9    2.1  1  Thiolase_N     Thiolase, N-terminal domain
    5.8e-09   35.9   3.8    4.7e-08   32.9   3.6    2.1  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    8.8e-09   35.1   0.1    1.5e-07   31.1   0.1    2.6  2  Thiolase_C     Thiolase, C-terminal domain
    8.5e-06   25.5   0.6    0.00034   20.4   0.4    2.4  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
  ------ inclusion threshold ------
       0.17   12.6   1.2         53    4.6   0.0    3.3  3  PTS_IIB        PTS system, Lactose/Cellobiose specific IIB su


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 !   86.9   0.9   3.7e-28   1.3e-24       1     260 []       5     224 ..       5     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 3.7e-28
                                    EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEE CS
                     Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavt 80 
                                    v+iv++  +++g      +d+++ eL+ ea++++ ++ag++  +vd+v+vGn     ++   +  +   agi    p+ +
  gi|118431262|ref|NP_147604.2|   5 VAIVGTGHSKFGV----RNDVNIAELAWEAMREAASEAGIELRDVDQVVVGNAGGWSSEYLSSIVLLEYAGI-SGKPVYR 79 
                                    6788888888887....9**********************************99999999899899999***.899**** PP

                                    EEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTTSEHHHH CS
                     Thiolase_N  81 vnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafneehmGlt 158
                                    v+ +c+ g +a+ +a ++iaagead v+++GvE+m ++pt   ++++  +g  + + +  +l+ p            +l 
  gi|118431262|ref|NP_147604.2|  80 VEAACATGSAAIKAAHDAIAAGEADLVLVVGVEKMNESPTPIVVEMIgrAGNYFWEFENFGLTFPG---------YYALY 150
                                    ***********************************9999998888873355555555666667776.........789** PP

                                    HHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS CS
                     Thiolase_N 159 aenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGt 238
                                    a  +  +++++ e++ ++Avk+h++a+ ++ka+ F + i              + ++ ++s+ +a +L+ +         
  gi|118431262|ref|NP_147604.2| 151 ATAYMSEFGATEEDLCRVAVKNHHHASMNPKAH-FPRAI--------------TLEQCLQSRYVAWPLKLY--------- 206
                                    *********************************.***99..............8899**************......... PP

                                    -BTTSB--BEEEEEEEEEEEHH CS
                     Thiolase_N 239 vtAgnasqisDGaaavllmses 260
                                        ++s+i+DGaaav+++se+
  gi|118431262|ref|NP_147604.2| 207 ----DSSPITDGAAAVVMASED 224
                                    ....***************986 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   3.6   1.3e-11   4.7e-08     149     208 ..      56     117 ..      27     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.3e-11
                                    HSTTHHHHHHHHH.HT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SH CS
                  ketoacyl-synt 149 vlanviagrisya.lglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltp 208
                                    +++ ++++++ ++  g+ G p++ v++AC+++ +a++aa +++ +gead++l+ Gve + + 
  gi|118431262|ref|NP_147604.2|  56 WSSEYLSSIVLLEyAGISGkPVYRVEAACATGSAAIKAAHDAIAAGEADLVLVVGVEKMNES 117
                                    677777777777667888868999*********************************98765 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   0.0     0.079   2.8e+02      26      50 ..      29      53 ..      13      93 .. 0.82
   2 !   31.1   0.1   4.1e-11   1.5e-07      22     101 ..     258     359 ..     238     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.079
                                   HHHHHHHHHHT--GGGESEEEE--S CS
                     Thiolase_C 26 yaikkvlkkagltvedidlfEinEA 50
                                    a++++ ++ag++++d+d + +  A
  gi|118431262|ref|NP_147604.2| 29 EAMREAASEAGIELRDVDQVVVGNA 53
                                   5788999999*******98877665 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 4.1e-11
                                    GHHHHHHHHHHHHHT--G....GGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH- CS
                     Thiolase_C  22 lgPayaikkvlkkagltv....edidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialG 79 
                                     +   a++++ kk g+++    +  d+  +++AF+   + + +a+++++                    vN+ GG  a G
  gi|118431262|ref|NP_147604.2| 258 RASRLAAERAFKKLGIEIegsyKHFDFANVHDAFTIAEILAYEAMGFAKlgegyklvreeqtyvgglIPVNLDGGLKAKG 337
                                    45678999999***99862222689****************************************9999*********** PP

                                    B-TTTHHHHHHHHHHHHHHHCT CS
                     Thiolase_C  80 HPlGasGaRivvtllselkkeg 101
                                    HP+Ga+G+ ++v  +++l+ + 
  gi|118431262|ref|NP_147604.2| 338 HPIGATGVSMAVEHVRQLQGRV 359
                                    *****************99764 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   9.4e-08   0.00034       3      38 ..      80     115 ..      78     117 .. 0.94
   2 ?    2.8   0.0      0.03   1.1e+02      53      64 ..     212     223 ..     196     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.4e-08
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGG CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetls 38 
                                    ++aaC++  +a++ A+++i++g+a  vLv+g e++ 
  gi|118431262|ref|NP_147604.2|  80 VEAACATGSAAIKAAHDAIAAGEADLVLVVGVEKMN 115
                                    689******************************986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.03
                                    -EEEEEEEEEEE CS
                    ACP_syn_III  53 GDGAgAvvleas 64 
                                     DGA+Avv+  +
  gi|118431262|ref|NP_147604.2| 212 TDGAAAVVMASE 223
                                    6*******9876 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.017        60      16      37 ..      27      48 ..      25      81 .. 0.84
   2 ?   -0.4   0.1      0.54   1.9e+03      33      55 ..      87     110 ..      78     125 .. 0.61
   3 ?    4.6   0.0     0.015        53      20      59 ..     264     299 ..     260     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHCTEEEEETTEE CS
                        PTS_IIB 16 aaeklekaakelgieaegeagv 37
                                   a e++++aa e+gie + + +v
  gi|118431262|ref|NP_147604.2| 27 AWEAMREAASEAGIELRDVDQV 48
                                   5589*********999877766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.54
                                    ETTEE.GGGHHHHHHT-SEEEEEE CS
                        PTS_IIB  33 geagv.eleaeeiaddaDlvllap 55 
                                    g+a + ++ ++  a +aDlvl+  
  gi|118431262|ref|NP_147604.2|  87 GSAAIkAAHDAIAAGEADLVLVVG 110
                                    333343333445556688888765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.015
                                    HHHHHHHCTEEEEETTEEGGGHHHHHHT-SEEEEEESSGG CS
                        PTS_IIB  20 lekaakelgieaegeagveleaeeiaddaDlvllapqvrv 59 
                                     e+a+k+lgie+eg++       + a+  D++ +a  +++
  gi|118431262|ref|NP_147604.2| 264 AERAFKKLGIEIEGSYKH----FDFANVHDAFTIAEILAY 299
                                    589***********9988....666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3141.15
//
Query:       gi|118431263|ref|NP_147605.2|  [L=179]
Description: hypothetical protein APE_0930.1 [Aeropyrum pernix K1]
Scores for complete 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   49.2   0.5      6e-13   48.6   0.5    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    2.6e-08   33.6   0.0    4.9e-08   32.7   0.0    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 !   48.6   0.5   6.7e-17     6e-13       1      64 [.      98     160 ..      98     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 6.7e-17
                                    EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                  OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                    wve++++G++ ++tv++ +p +f+ ++ yvvg+ + +eg  i+a++ g+++  +r Gm+Vr+++
  gi|118431263|ref|NP_147605.2|  98 WVEIPREGVLLTYTVINTKPYTFSHYPDYVVGIGKVAEGLNILAWVRGDPRK-LRRGMKVRLEV 160
                                    ***********************************************98875.********986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   5.5e-12   4.9e-08       1      35 [.      61      95 ..      61      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 5.5e-12
                        DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsdd 35
                                   +++++eg++++++C ++G+ +fPP+  Cp    ++
  gi|118431263|ref|NP_147605.2| 61 FEGLTEGKILATKCVKTGKIYFPPQVDCPDAPDSE 95
                                   699**************************876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1322.69
//
Query:       gi|14601080|ref|NP_147606.1|  [L=294]
Description: diphthine synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-17   64.1   2.3    2.6e-17   63.5   2.3    1.3  1  TP_methylase   Tetrapyrrole (Corrin/Porphyrin) Methylases
  ------ inclusion threshold ------
      0.016   14.8   0.8      0.016   14.8   0.8    2.3  2  Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain


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 !   63.5   2.3   2.9e-21   2.6e-17       2     171 ..      10     177 ..       9     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 2.9e-21
                  TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsr.......aleilldllaeeleleapmgkekepleeayeeiaealaea 75 
                                   l lVG G  +p   T++Al+a+++advv+ +  +        ++++ ++        a  ++ +e ++++ ee ++ ++ +
  gi|14601080|ref|NP_147606.1|  10 LLLVGWGY-APGMQTLEALDAVRRADVVYVES-YtmpgsswLYKSVVEA--------AGEARVVEASRRDLEERSREIVSR 80 
                                   77899999.99999**************8666.2234334544444444........44567899999999*******888 PP

                  TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.....lpglakeee 151
                                   + +   V+++++GDP+v++t+s l+ ++ +  ag+ v+ iPGvs +qaa  ++ ++ + +g ++++       ++++  ++
  gi|14601080|ref|NP_147606.1|  81 ALDAV-VAVVTAGDPMVATTHSSLAAEALE--AGVAVRYIPGVSGVQAARGATMLSFYRFGGTVTLPgpwrgVTPIS-VAR 157
                                   88874.*******************77777..9********************999999999999988866633333.567 PP

                  TP_methylase 152 releallangdtlvllkapr 171
                                   r + +l+a  +t +ll+  +
  gi|14601080|ref|NP_147606.1| 158 RIYLNLCAGLHTTALLDVDE 177
                                   77777777777777775544 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.8   1.8e-06     0.016      11      44 ..      82     115 ..      60     116 .. 0.91
   2 ?   -1.2   0.1      0.18   1.6e+03      36      45 ..     181     190 ..     174     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-06
                 Prot_ATP_OB_N  11 qdgtadVlvggrrmrVavsPlvdaeeLrpGqeVl 44 
                                    d+ + V+++g  m+ + + ++ ae L++G  V+
  gi|14601080|ref|NP_147606.1|  82 LDAVVAVVTAGDPMVATTHSSLAAEALEAGVAVR 115
                                   58999**************************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.18
                 Prot_ATP_OB_N  36 eLrpGqeVlL 45 
                                   +L+pGq V L
  gi|14601080|ref|NP_147606.1| 181 QLSPGQGVSL 190
                                   89****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2223.39
//
Query:       gi|118431264|ref|NP_147607.2|  [L=320]
Description: hypothetical protein APE_0932.1 [Aeropyrum pernix K1]
Scores for complete 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   38.1   0.0    1.3e-08   35.4   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
     0.0013   18.6   0.1          1    9.0   3.8    2.2  2  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.5e-12   1.3e-08       2     162 ..      33     193 ..      32     198 .. 0.77
   2 ?    1.6   0.0     0.036   3.2e+02      91     156 ..     195     256 ..     190     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.5e-12
                                    EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CCT CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vpg 77 
                                    +++ gC+ +C++C+ +   + +  +++ + v ++++ + ++   +g+ + i ++ +p   p++++l + +++l+    +g
  gi|118431264|ref|NP_147607.2|  33 NPYTGCSIGCRYCYATAYiGVKPSTPKRRLVGRLERDLGRI--PPGALVNIGTSSDPYP-PEEEKLGLTRRALEvlaPRG 109
                                    6789************9654455555555555555555555..4556666666666666.666666666666668***** PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGen 156
                                    +r+ ++t gtl  ++ l+ l +++   ++ ++  +     l+ ++ + ++ +e+++a  ++ ++g+++ v + +++p +n
  gi|118431264|ref|NP_147607.2| 110 YRLLITTKGTLYAWRDLDILSRAN-AAITPSITGLGGNSLLRAVEpGAPGQDERIAAAAAAVRSGVPVGVRVDPVIPYVN 188
                                    ************************.666666666666669999*9999*******************9888889****** PP

                                    HHHHHH CS
                                    xxxxxx RF
                    Radical_SAM 157 deelee 162
                                    d+   e
  gi|118431264|ref|NP_147607.2| 189 DDP-HE 193
                                    997.44 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.036
                                    HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                    +e + rl+e+gv  +  +   a ++  l +m r+    e  ++ +++re+g+    ++++ lp e 
  gi|118431264|ref|NP_147607.2| 195 KELVGRLAEAGVRFIVTSTYKARPD-NLSRM-RRALGAEGERLYRLYRERGVY--MHGYIYLPEEV 256
                                    6777788888888888888888888.88888.667777777778888888766..77777777665 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   3.8   0.00011         1     241     265 .]      23      47 ..      16      47 .. 0.89
   2 !    3.6   0.0    0.0052        47      84     204 ..     148     282 ..     113     303 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00011
                        DUF1848 241 eCgCveskDiGayntClhgCvYCYA 265
                                     C C     +  y  C+ gC+YCYA
  gi|118431264|ref|NP_147607.2|  23 LCVCPFKYSLNPYTGCSIGCRYCYA 47 
                                    699999999999************9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0052
                        DUF1848  84 yekelepnvpsleerietfkelseklgkerviwRyDPilltekltvelhlekfeklaeelkgytekvviSfvdl....yk 159
                                      +++ep+ p  +eri++  +  +      v +R DP++ + + + +++ e + +lae+    ++ +v+S ++      +
  gi|118431264|ref|NP_147607.2| 148 LLRAVEPGAPGQDERIAAAAAAVRS--GVPVGVRVDPVIPYVNDDPHELKELVGRLAEA---GVRFIVTSTYKArpdnLS 222
                                    5567888888888888876655443..35688899999988887777766666666554...245555555554222244 PP

                        DUF1848 160 kvkrnl...........kk...k.lelrelseeekeelaeelaeiakklglelatCaeke 204
                                    +++r l           ++       +  l ee +++l++ + e a++lgle atC e  
  gi|118431264|ref|NP_147607.2| 223 RMRRALgaegerlyrlyRErgvYmHGYIYLPEEVRRRLLKPVIEEAARLGLEYATCREGF 282
                                    444444555544444431123213456666677777888888888888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2364.41
//
Query:       gi|14601083|ref|NP_147609.1|  [L=274]
Description: hypothetical protein APE_0934 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2085.10
//
Query:       gi|14601084|ref|NP_147610.1|  [L=337]
Description: glutamate synthase [Aeropyrum pernix K1]
Scores for complete 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-23   82.2   0.0    1.4e-22   80.3   0.0    1.9  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.2e-07   31.0   1.2    5.1e-07   29.8   0.0    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.2e-05   24.4   0.2     0.0062   17.1   0.1    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00022   20.0   0.2    0.00055   18.8   0.3    1.6  2  HI0933_like     HI0933-like protein
    0.00038   19.8   0.5       0.21   10.8   0.2    3.5  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00053   19.3   0.1    0.00096   18.5   0.1    1.3  1  FAD_binding_3   FAD binding domain
     0.0021   17.2   0.1      0.015   14.4   0.1    2.4  3  FAD_binding_2   FAD binding domain
     0.0042   16.4   0.2       0.16   11.2   0.0    2.1  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
     0.0054   16.4   3.5       0.13   11.8   0.1    2.5  3  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.028   14.0   0.1       0.15   11.7   0.1    2.0  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.042   13.2   0.1      0.064   12.6   0.1    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
      0.043   13.2   0.1       0.13   11.6   0.1    1.7  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.066   12.8   0.1       0.12   12.0   0.1    1.3  1  DUF998          Protein of unknown function (DUF998)
       0.12   11.6   0.1       0.23   10.7   0.1    1.4  1  Thi4            Thi4 family
       0.12   12.3   0.4       0.19   11.6   0.4    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
        0.2   10.7   1.6        1.3    8.0   0.6    2.2  2  GIDA            Glucose inhibited division protein A


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 !   80.3   0.0   1.3e-25   1.4e-22       2     294 .]      16     322 ..      15     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.3e-25
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCTCEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                   Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgeevvkidpg 81 
                                    v +iG+GpAGl aa +l+  g++v+++   ++++  g ++   +   + +++ +++ v++l +g  + +l+ ++v+ d  
  gi|14601084|ref|NP_147610.1|  16 TVSIIGAGPAGLGAAGFLRCRGHEVVVY---DMMPEPGGMMMFGIPDDRIPKDNIRKSVRELVEGgARIILN-NKVGRDIS 92 
                                   688*************************...77888888887788888888877776666666665666666.55655555 PP

                                   CEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC........TTBEECCSECHHHHHHCCSS-T.....SEEEEES CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx RF
                   Pyr_redox_2  82 kkkvklekkkegdeekiaydklvlAtGs.sprdlgipGv.......aenvgklvrtldsaealklkllp.....krivvvG 149
                                    +++             a d++++AtG  +pr+lg pG+       a ++  l  +++ a++  l + +      ri+vvG
  gi|14601084|ref|NP_147610.1|  93 LEDIIK-----------ASDAVLIATGTwKPRRLGAPGEdlpwvlpAADW--L-VEVHMARYGYLPWAKvpkvgGRILVVG 159
                                   544444...........45********659*********88887543333..2.34444444444444466999******* PP

                                   -SHHHHHHHHH......HHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.......EEE CS
                                   xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxx RF
                   Pyr_redox_2 150 gGyiGvElAaa......laklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.......kle 217
                                   gG+++ +   +      +++  ++v+l ++r+r +      +++   e+l k+G e    t++ ++ ++g        ++e
  gi|14601084|ref|NP_147610.1| 160 GGLTAADAVHVpltypeFKDGVEKVVLSYRRTRDY----APMRKNEFERLIKMGAEAWELTQPIAFYEEGGrkvvkfvRME 236
                                   *****9998887664433444446*********99....556666667788888888888888888888888755433233 PP

                                   EEETTSCE............EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS-- CS
                                   xxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 218 vvledgee............idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpel 286
                                   ++ +d  +             + d  ++a+G  p +++ +   g+el+++g i++de+  t+ +g++a GDv    +gp l
  gi|14601084|ref|NP_147610.1| 237 LKASDSGRpkpvpiegsefeAEFDWALLAIGEVPTPPFNNGCCGIELNPDGTIKTDENFMTTRKGVFASGDVR---HGPSL 314
                                   4444444488999999999999**************9977*********************************...99999 PP

                                   HHHHHHHH CS
                                   xxxxxxxx RF
                   Pyr_redox_2 287 aqaAvqqG 294
                                   + +A ++G
  gi|14601084|ref|NP_147610.1| 315 IGKALKSG 322
                                   99998876 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 !   29.8   0.0   4.6e-10   5.1e-07       1      38 [.      19      56 ..      19      91 .. 0.80
   2 ?   -1.0   0.3       1.9   2.2e+03       1       8 [.     157     164 ..     157     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.6e-10
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  I+GaG +Gl aA +L+ +g++v+++++ + +GG +   
  gi|14601084|ref|NP_147610.1| 19 IIGAGPAGLGAAGFLRCRGHEVVVYDMMPEPGGMMMFG 56
                                  9********************************98655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                                   EE--SHHH CS
                 NAD_binding_8   1 IvGaGlsG 8  
                                   +vG+Gl++
  gi|14601084|ref|NP_147610.1| 157 VVGGGLTA 164
                                   89***986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.5e-06    0.0062       2      35 ..      17      50 ..      16      91 .. 0.77
   2 ?    4.8   0.0     0.037        42       1      14 [.     154     167 ..     154     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-06
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  v ++G+G  gl +Ag+l+  g++V v ++++++ 
  gi|14601084|ref|NP_147610.1| 17 VSIIGAGPAGLGAAGFLRCRGHEVVVYDMMPEPG 50
                                  679****************************998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.037
                                   EEEEECSSHHHHHH CS
                     Pyr_redox   1 kvvvvGgGyiglEl 14 
                                   +++vvGgG+++ ++
  gi|14601084|ref|NP_147610.1| 154 RILVVGGGLTAADA 167
                                   79********9876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   4.9e-07   0.00055       2      36 ..      16      50 ..      15      55 .. 0.93
   2 ?   -3.0   0.0       1.9   2.1e+03     154     177 ..      99     122 ..      84     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.9e-07
                                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +v +iG+G+AGl aA  ++ rg++V++++ ++++g
  gi|14601084|ref|NP_147610.1| 16 TVSIIGAGPAGLGAAGFLRCRGHEVVVYDMMPEPG 50
                                  688****************************9988 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                                   EESEEEE----SS-GGGT--SHHH CS
                   HI0933_like 154 eadklvlAtGGlSiPklGstgkgy 177
                                   ++d++++AtG     +lG+ g+  
  gi|14601084|ref|NP_147610.1|  99 ASDAVLIATGTWKPRRLGAPGEDL 122
                                   578999****99999999987765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00019      0.21       2      26 ..      19      42 ..      18      48 .. 0.84
   2 ?    4.0   0.0     0.022        25     125     150 ..     100     123 ..      91     170 .. 0.57
   3 ?   -0.2   0.0      0.41   4.6e+02     262     305 .]     263     306 ..     250     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                   Pyr_redox_3  2 IiGaGPaGlaaaielkkagledyli 26
                                  IiGaGPaGl+aa  l+  g  ++++
  gi|14601084|ref|NP_147610.1| 19 IIGAGPAGLGAAGFLRCRGH-EVVV 42
                                  9***********99988887.4555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                   Pyr_redox_3 125 AkkviiAtGefdkPnklnipGeeklv 150
                                   ++ v+iAtG   kP++l+ pGe+  +
  gi|14601084|ref|NP_147610.1| 100 SDAVLIATGT-WKPRRLGAPGEDL-P 123
                                   4679999999.5899999999983.2 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.41
                   Pyr_redox_3 262 vlatGykpdlsflkk.slfeldedgrpvlteeteetnvpglflaG 305
                                   +la+G  p+  f +  +++el+ dg+++ +e+ + t  +g+f  G
  gi|14601084|ref|NP_147610.1| 263 LLAIGEVPTPPFNNGcCGIELNPDGTIKTDENFMTT-RKGVFASG 306
                                   566776666666655799999999999999999877.79999877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   8.6e-07   0.00096       3      31 ..      16      44 ..      15      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.6e-07
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlve 31
                                  +V I+GaGpaGl +a +L+ +G +vv+ +
  gi|14601084|ref|NP_147610.1| 16 TVSIIGAGPAGLGAAGFLRCRGHEVVVYD 44
                                  589*********************99876 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   0.1   1.4e-05     0.015       4      49 ..      19      56 ..      16      90 .. 0.76
   2 ?   -0.7   0.0      0.52   5.8e+02     189     213 ..      96     117 ..      68     131 .. 0.73
   3 ?   -2.2   0.0       1.4   1.6e+03     376     402 ..     289     309 ..     275     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                  EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT CS
                 FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavl 49
                                  +iG+G AGL AA  ++ +G++v+v + ++e         Gg+ + +
  gi|14601084|ref|NP_147610.1| 19 IIGAGPAGLGAAGFLRCRGHEVVVYDMMPE--------PGGMMMFG 56
                                  9*************************9999........55555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.52
                                   EEEES.EEEE-----GG......... CS
                 FAD_binding_2 189 rirak.avvlatgGfgrallkellga 213
                                    i+a  av++atg ++     ++lga
  gi|14601084|ref|NP_147610.1|  96 IIKASdAVLIATGTWKP----RRLGA 117
                                   478888********986....44444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.4
                                   EEBETTSBESTTEEESSBTEEE-STCE CS
                 FAD_binding_2 376 vetdengrvldadgqpipGLYAaGeva 402
                                   ++tden+ +      + +G +A G v 
  gi|14601084|ref|NP_147610.1| 289 IKTDENFMT------TRKGVFASGDVR 309
                                   456666666......888888888876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00015      0.16      30      61 ..      16      47 ..       5      50 .. 0.89
   2 ?    3.1   0.1     0.044        49      22      46 ..     147     170 ..     125     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                  +v +iG+G aGl A+   +  g +V+v+D+ p
  gi|14601084|ref|NP_147610.1| 16 TVSIIGAGPAGLGAAGFLRCRGHEVVVYDMMP 47
                                  689**************************976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.044
                                   EETCB---EEEEESTSHHHHHHHHH CS
                   AlaDh_PNT_C  22 gvpgvepakvlviGgGvaGlqAiat 46 
                                   +vp    +++lv+GgG     A+++
  gi|14601084|ref|NP_147610.1| 147 KVP-KVGGRILVVGGGLTAADAVHV 170
                                   566.3369**********9999875 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00012      0.13       2      35 ..      17      51 ..      16      53 .. 0.91
   2 ?    4.8   0.0     0.015        17     154     205 ..      72     112 ..      58     136 .. 0.74
   3 ?   -2.4   0.1       2.5   2.8e+03       2      10 ..     155     163 ..     154     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                  EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                           DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                  v iiG+G +Gl++A +L  rg  V+++++ +++g g
  gi|14601084|ref|NP_147610.1| 17 VSIIGAGPAGLGAAGFLRCRGheVVVYDMMPEPG-G 51
                                  66***************88899******999998.5 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                                   HHHHHTT-EEEESECEEE.EEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH CS
                           DAO 154 raaealGveilegtevtg.leeedgkvwgverttpgendaadavVnaaGawsd 205
                                   r++ ++G++i+++ +v + ++     +  +      + +a dav +a+G w  
  gi|14601084|ref|NP_147610.1|  72 RELVEGGARIILNNKVGRdIS-----LEDI------I-KASDAVLIATGTWKP 112
                                   678899999999988865343.....3444......2.34599********54 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.5
                                   EEEECTSHH CS
                           DAO   2 vviiGGGii 10 
                                   ++++GGG +
  gi|14601084|ref|NP_147610.1| 155 ILVVGGGLT 163
                                   99*****86 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 ?   11.7   0.1   0.00013      0.15       2      86 ..      16     109 ..      15     139 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                   EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT..S-SS--TTHHHHHHHHCH.......TTTEEEES-HHHH CS
                UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsg..kipiyepgLeelvkkave.......sgrlsfttdveka 73 
                                   ++s+iG+G  Gl  a  l  +ghev++ D+  e   ++  g  +  i   ++++ v++ ve       ++++    ++e  
  gi|14601084|ref|NP_147610.1|  16 TVSIIGAGPAGLGAAGFLRCRGHEVVVYDMMPEPGGMMMFGipDDRIPKDNIRKSVRELVEggariilNNKVGRDISLEDI 96 
                                   79***************************9766433333221122233333333333333210001113333444555666 PP

                                   HHC-SEEEE---- CS
                UDPG_MGDP_dh_N  74 veeadvifiaVgT 86 
                                   ++++d+++ia gT
  gi|14601084|ref|NP_147610.1|  97 IKASDAVLIATGT 109
                                   6677777777776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.7e-05     0.064       2      63 ..      17      74 ..      16      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                  FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiaref 63
                                  v ++G+gpaG+ AA     +G +v++ +  +  GG++  g+  +d+    ++  +++ +re+
  gi|14601084|ref|NP_147610.1| 17 VSIIGAGPAGLGAAGFLRCRGHEVVVYDMMPEPGGMMMFGI--PDDRI--PKDNIRKSVREL 74
                                  679**********************************9877..44442..223455555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00012      0.13      35      71 ..      13      49 ..       5      57 .. 0.91
   2 ?   -1.9   0.0       1.7   1.9e+03      82      98 ..      90     106 ..      83     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                  TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHH CS
                  2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkk 71
                                  +gktv iiG+G  G  +a  l+  g +v++yd  +++
  gi|14601084|ref|NP_147610.1| 13 TGKTVSIIGAGPAGLGAAGFLRCRGHEVVVYDMMPEP 49
                                  79******************************98765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                   ECSHHHHHHH-SEEEE- CS
                  2-Hacid_dh_C  82 lvsleellaesDivslh 98 
                                     sle++++ sD v ++
  gi|14601084|ref|NP_147610.1|  90 DISLEDIIKASDAVLIA 106
                                   4599********99875 PP

>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.12      31      89 ..     115     169 ..     114     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                        DUF998  31 Lgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavaglglvlagvf 89 
                                   Lga+g + +w+  a+++l+ + ++ ++++    +++++ ++g+++l+v+g  +++++v 
  gi|14601084|ref|NP_147610.1| 115 LGAPGEDLPWVLPAADWLVEVHMARYGYL----PWAKVPKVGGRILVVGGGLTAADAVH 169
                                   89***********************9984....899***********999999999974 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0002      0.23      20      59 ..      17      55 ..       9      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                                  EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTT CS
                          Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGawl 59
                                  v i+GaG++GL aa  l  + + +v++ +    pGG +  
  gi|14601084|ref|NP_147610.1| 17 VSIIGAGPAGLGAAGFLRCR-GHEVVVYDMMPEPGGMMMF 55
                                  88***************999.9999999999888887655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00017      0.19       1      32 [.      16      47 ..      16      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                  EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                       3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdise 32
                                  +v +iGaG  G g a  +  +g+eVv++d+ +
  gi|14601084|ref|NP_147610.1| 16 TVSIIGAGPAGLGAAGFLRCRGHEVVVYDMMP 47
                                  699**************************876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6    0.0012       1.3       2      28 ..      17      43 ..      16      54 .. 0.88
   2 ?    0.9   0.0      0.17   1.9e+02      94     151 ..      64     110 ..      58     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                  EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                  v +iG+G AG+ AA  +  +G++v+ +
  gi|14601084|ref|NP_147610.1| 17 VSIIGAGPAGLGAAGFLRCRGHEVVVY 43
                                  89***************9999999987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEEC.EEEE--TT- CS
                          GIDA  94 relyskevteklenepnleiieeeveeliveekkvkgvvtedgetikak.avviatGtf 151
                                   +++++k+v+e +e    + + ++   ++++            + +ika+ av iatGt+
  gi|14601084|ref|NP_147610.1|  64 KDNIRKSVRELVEGGARIILNNKVGRDISL------------EDIIKASdAVLIATGTW 110
                                   566677777777777777777777777766............44555544999****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2301.75
//
Query:       gi|118431265|ref|NP_147611.2|  [L=228]
Description: hypothetical protein APE_0938.1 [Aeropyrum pernix K1]
Scores for complete 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   34.0   0.1    0.00016   21.7   0.0    2.1  2  APH       Phosphotransferase enzyme family
     0.0026   17.4   0.0     0.0033   17.1   0.0    1.2  1  WaaY      Lipopolysaccharide core biosynthesis protein (WaaY)
     0.0084   15.5   0.0      0.056   12.8   0.0    1.9  2  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family


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 !   21.7   0.0   2.7e-08   0.00016      34     106 ..      54     117 ..      44     119 .. 0.90
   2 !   10.3   0.1   8.1e-05      0.49     168     229 ..     122     182 ..     118     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.7e-08
                                    HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHH CS
                            APH  34 aeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalh 106
                                    + ++r+e++++r L++a  pvP+++a++ +    + + ++ eyv+g+++++    + +++++ alg+ la+lh
  gi|118431265|ref|NP_147611.2|  54 EGRLRNELKWYRSLRGA-YPVPRIVAYCIG----EKPLLIREYVDGEPVSN----SLDEDAWKALGSGLARLH 117
                                    56899************.89******9744....446679***********....9****************9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.1e-05
                                    EE-SS-SGGGEEEC..TTEEEEE---...TT-EEEECCHHHHCCHHHCSCHCCCHCHHHHHHHHC CS
                            APH 168 llHgDlhpgNllvdpddgrvtGviDf...edaglgpplyDlavllrswtseldpeflaallraye 229
                                     + gD++pgN++    +     ++Df   +d ++  +++Dl vl+ + t +l   +  ++++a +
  gi|118431265|ref|NP_147611.2| 122 MVLGDPNPGNFIYS-LGEAW--LVDFeqaDDYTPQKAAWDLLVLA-ATTITLASPLKWRFVEAAL 182
                                    678***********.44555..8***7777778888899998888.3344444444444444444 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.5e-07    0.0033     119     189 ..      86     156 ..      47     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-07
                           WaaY 119 imiieyiegielvdmpeiddevkakikqsieklh.qlgmvsgdphrgnfivkkdevriidlsgk.rasaerka 189
                                    ++i ey++g  +++  ++d++  + + + + +lh +lgmv gdp  gnfi + +e  ++d+      + ++ a
  gi|118431265|ref|NP_147611.2|  86 LLIREYVDGEPVSN--SLDEDAWKALGSGLARLHfSLGMVLGDPNPGNFIYSLGEAWLVDFEQAdDYTPQKAA 156
                                    57889999977765..57788888899999***9568*********************998754134445555 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.062   3.7e+02      49      85 ..      47      83 ..      18      92 .. 0.78
   2 !   12.8   0.0   9.4e-06     0.056     115     175 ..      97     153 ..      87     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.062
                            Kdo 49 yrfk.lgrtravrEfrllkrLeeagvavpkpvaagavk 85
                                   yr+   ++ r ++E++  + L+ a  +vp++va+++  
  gi|118431265|ref|NP_147611.2| 47 YRYIySPEGRLRNELKWYRSLRGA-YPVPRIVAYCIGE 83
                                   566656777888888888888876.69******99865 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.4e-06
                            Kdo 115 laeelkrallkavgrliaklh.ragvnHadlyaknillqqeeeeeaeiwliDldkarlrlra 175
                                    ++++l +  +ka+g   a+lh ++g+  +d ++ n+    +e     +wl+D+++a   +++
  gi|118431265|ref|NP_147611.2|  97 VSNSLDEDAWKALGSGLARLHfSLGMVLGDPNPGNFIYSLGE-----AWLVDFEQADDYTPQ 153
                                    6788999**************789****************97.....********9988863 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1707.73
//
Query:       gi|14601086|ref|NP_147612.1|  [L=100]
Description: hypothetical protein APE_0939 [Aeropyrum pernix K1]
Scores for complete 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   31.8   0.6    2.2e-07   31.5   0.6    1.2  1  MJ1316    MJ1316 RNA cyclic group end recognition domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.6   1.2e-11   2.2e-07       6      76 .]      10      84 ..       6      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-11
                        MJ1316  6 dvlnRirWdkeldkskfvvgyldR....fkgikevpleeiswied..flleeeegelaIPlHRiryikr.kgevvWdR 76
                                  + + R++  +  d++++++ y +R     + ++e +le++ ++++  ++l++ +   +IPlHRi +i+  +ge vW+R
  gi|14601086|ref|NP_147612.1| 10 EAVRRVLNYPLEDRGDYSIVYRHRvegvGEVLREARLESVARVDKwaVHLVNGD---SIPLHRIVEIRGpRGETVWRR 84
                                  55667777777899**********655444457889999999999654444444...7**********966*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 805.84
//
Query:       gi|14601087|ref|NP_147613.1|  [L=337]
Description: hypothetical protein APE_0940 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2518.92
//
Query:       gi|14601088|ref|NP_147614.1|  [L=267]
Description: spermidine/putrescine ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-12   46.4  15.8    3.7e-12   46.4  15.8    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 !    3.4   2.5    0.0032        57     110     170 ..       9      79 ..       5      89 .. 0.76
   2 !   46.4  15.8   2.1e-16   3.7e-12       3     183 ..      76     258 ..      74     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0032
                  BPD_transp_1 110 iitglilafggllggavlleflgswpGlgtllleailgydyseis..........nggvlalviavlllnl 170
                                   ++t +ila+++l  + ++l  l s+p +g +   ++ +y + ++            ++++a +++  ll +
  gi|14601088|ref|NP_147614.1|   9 AATYAILAIMYLPIALLALQSLNSSPYIGVWEGLTLKWYGMMMGDerlhaaaynsLAIAAASAVSSTLLGV 79 
                                   58999********************99**999999999999999999999966553333333333333333 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 2.1e-16
                  BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfv....laillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                   llG+ a+  ++r++k+  l++ +++ +l lP ++    l+++l+       ++  +   v+i  + ++++yv+++ + al+
  gi|14601088|ref|NP_147614.1|  76 LLGVAAGlaVRRHGKVG-LVDAIMYPPLVLPEIAeaaaLLLFLT-----ALDVDLGLKTVVIGHTAFNIAYVYVVAAPALQ 150
                                   67788887777777774.77888888888998887544333333.....24555666669999999999999999999997 PP

                  BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.... 154
                                    ++++l+ aar+lGa++ ++++++++P+a+p i +g+ laf++++++++ ++f+  +pG+ t  +   +    +  s    
  gi|14601088|ref|NP_147614.1| 151 -RSSSLEDAARTLGATPARTLVTITIPLAAPAIYAGFTLAFILSFTDFIKTLFTR-GPGIETIPILLWNRARRPGLSefss 229
                                   .6899*************************************************9.7887776666666666666667778 PP

                  BPD_transp_1 155 nggvlalviavlllnlvadilqrlldprv 183
                                   + +++a++ ++l+++l++ + + +l+ r+
  gi|14601088|ref|NP_147614.1| 230 FSYLAAITMVLLAVSLAVALAYVILSTRL 258
                                   88899999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1993.83
//
Query:       gi|14601089|ref|NP_147615.1|  [L=257]
Description: spermidine/putrescine ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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   50.7  16.6    1.8e-13   50.7  16.6    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   2.4      0.12   2.1e+03     155     170 ..      63      78 ..      13      88 .. 0.60
   2 !   50.7  16.6   9.8e-18   1.8e-13      25     174 ..      97     247 ..      91     257 .] 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.12
                  BPD_transp_1 155 nggvlalviavlllnl 170
                                   +++++a+++av+ll l
  gi|14601089|ref|NP_147615.1|  63 AAVAAATALAVMLLAL 78 
                                   2444444444444444 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 9.8e-18
                  BPD_transp_1  25 ivllslPsfv........laillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqi 97 
                                    +l+  P++v        +   lv     l +++ ++++ +i l++ ++p+ +l+  a+++ ++++lveaar+lGa+r ++
  gi|14601089|ref|NP_147615.1|  97 LALFVSPFIVdvllrtlsIK--LV---LTLVGVKPGWTATFIGLVYENLPLGILFAFAGVSGVSRSLVEAARTLGAGRLEV 172
                                   44455555555555543322..22...45678999********************************************** PP

                  BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseisnggvlalviavlllnlvadi 174
                                   +r vv P+alp +++g++++f ++++++v++++lg+ +G  +g+l+ + il+ d          a++++v ll+++a  
  gi|14601089|ref|NP_147615.1| 173 YRSVVAPLALPWLAAGFVVVFLISFTDYVVPSLLGGTTGftVGSLIYHLILSGDRWDLG----SAVTLMVTLLSAAAAY 247
                                   *************************************9999999999999999876433....3333333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1871.88
//
Query:       gi|118431266|ref|NP_147616.2|  [L=342]
Description: spermidine/putrescine ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-34  118.1   0.0    5.5e-34  117.6   0.0    1.2  1  ABC_tran     ABC transporter
      4e-12   46.1   0.6    1.2e-11   44.6   0.6    1.8  1  TOBE_2       TOBE domain
    3.3e-10   40.3   0.0    5.9e-06   26.3   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.2e-06   27.3   0.0      0.005   16.3   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00098   19.5   0.3     0.0025   18.2   0.3    1.7  1  AAA_16       AAA ATPase domain
    0.00098   18.8   0.0     0.0019   17.9   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0023   18.3   0.2      0.018   15.5   0.2    2.1  1  AAA          ATPase family associated with various cellular a
     0.0026   17.3   0.0       0.15   11.6   0.0    2.4  2  AAA_25       AAA domain
     0.0033   17.9   0.0     0.0051   17.3   0.0    1.2  1  AAA_23       AAA domain
     0.0054   17.0   0.3      0.037   14.3   0.3    2.0  1  AAA_22       AAA domain
     0.0064   16.4   0.0     0.0096   15.9   0.0    1.2  1  Rad17        Rad17 P-loop domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.031   14.2   0.0    1.4  2  ATPase_2     ATPase domain predominantly from Archaea
      0.018   14.8   0.0      0.037   13.7   0.0    1.4  1  AAA_30       AAA domain
      0.024   14.6   0.0      0.043   13.7   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.03   14.6   0.1      0.073   13.4   0.1    1.6  1  TOBE         TOBE domain
       0.04   13.8   0.5      0.083   12.8   0.1    1.7  2  NACHT        NACHT domain
       0.12   12.3   0.0       0.28   11.1   0.0    1.6  1  NTPase_1     NTPase
       0.18   12.1   0.0       0.54   10.6   0.0    1.7  2  AAA_19       AAA domain
       0.18   11.8   0.6       0.49   10.4   0.2    1.9  3  AAA_5        AAA domain (dynein-related subfamily)
       0.23   11.7   0.4        3.4    8.0   0.1    2.6  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.24   10.7   0.1       0.56    9.5   0.0    1.5  2  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 !  117.6   0.0   6.4e-37   5.5e-34       1     136 [.      21     166 ..      21     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 6.4e-37
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs+++ e++++a++G++G+GK+t+lk++agllkp  G++ + g d +   l+  r+++g+++q+  lfp++tv++n 
  gi|118431266|ref|NP_147616.2|  21 LRGVSFSFPESSITAVLGPSGCGKTTMLKVIAGLLKPRRGRVFFGGVDYTG--LPPERRSVGFVFQDLALFPHMTVYDNv 98 
                                    678******************************************999999..*************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e ++++e al+++gl+  + + ++++ + LSgGq+qrvalara++ +p++lllDEp 
  gi|118431266|ref|NP_147616.2|  99 afglrargfsggEVRRQVEWALETVGLTP-PREFMGRRVTGLSGGQQQRVALARAIAYEPPVLLLDEPL 166
                                    ****************************9.888888999*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.6   1.4e-14   1.2e-11       2      73 ..     261     336 ..     260     337 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.4e-14
                         TOBE_2   2 aiRPEklrla...aaggan..glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdda 73 
                                    ++RPE+l++    ++ +++  +l+++Ved++++G  +r+ ++  gg+l +v+   ++ +s ++pG++V ++w+pd+ 
  gi|118431266|ref|NP_147616.2| 261 MVRPEDLEIVrngSPVPQGwpRLEAVVEDLVFQGPLIRVELRWRGGRLRAVVPRRTA-SSLPRPGEAVSVTWSPDRG 336
                                    89*******877644443447*************************99666555555.789*************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 !   12.0   0.0   0.00016      0.13       1      24 [.      33      56 ..      33     105 .. 0.78
   2 !   26.3   0.0   6.9e-09   5.9e-06     236     298 ..     138     198 ..     132     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                   ++++ Gp g+GK++ L+ + +l  
  gi|118431266|ref|NP_147616.2| 33 ITAVLGPSGCGKTTMLKVIAGLLK 56
                                   799*****************9964 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 6.9e-09
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                     lS G+++  al+ a+++ +   ++ll+DEp ++L+ k+  rll  lk+l+r  g+  i +TH+
  gi|118431266|ref|NP_147616.2| 138 GLSGGQQQRVALARAIAYEP---PVLLLDEPLSHLDFKIRQRLLAELKRLQRkLGSTMIYVTHD 198
                                    67889988889999999999...*********************99999999899999*****7 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 !    8.9   0.0    0.0011      0.91      23      45 ..      30      52 ..      19      62 .. 0.85
   2 !   16.3   0.0   5.8e-06     0.005     136     210 ..     138     211 ..      99     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                                   TSSEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 23 sksftaivGpNGSGKsnlldAil 45
                                   ++s+ta++Gp G+GK+ +l  i 
  gi|118431266|ref|NP_147616.2| 30 ESSITAVLGPSGCGKTTMLKVIA 52
                                   5689*************998875 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.8e-06
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSH.HHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislre.emlekadklvg 210
                                     LSgG+++ vala  +A    +  p+ llDe  ++LD+k ++++   lk+ + +  + +i +++++ e +e ad+lv 
  gi|118431266|ref|NP_147616.2| 138 GLSGGQQQRVALARAIAY---E-PPVLLLDEPLSHLDFKIRQRLLAELKRLQRKlgSTMIYVTHDQwEAMELADTLVI 211
                                    59******9999987664...3.5999*****************9999987777557888888876467788888775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   2.9e-06    0.0025      24      63 ..      31      70 ..      17     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   ++++ + G+sG+GK+++++ ++  l+ ++g ++ g  d  
  gi|118431266|ref|NP_147616.2| 31 SSITAVLGPSGCGKTTMLKVIAGLLKPRRGRVFFGGVDYT 70
                                   3899******************999999777776666555 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 !   17.9   0.0   2.2e-06    0.0019      14      53 ..      23      63 ..      19      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-06
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvr 53
                                   g ++++ ++++t + GpsG GK+T+l  i+ lL p++ +v 
  gi|118431266|ref|NP_147616.2| 23 GVSFSFPESSITAVLGPSGCGKTTMLKVIAGLLKPRRgRVF 63
                                   5678888888***********************99985554 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 !   15.5   0.2   2.1e-05     0.018       3      24 ..      36      57 ..      34     220 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                   EESSTTSSHHHHHHHHHHHHTH CS
                            AAA  3 lyGppGtGKTllakavakelgv 24
                                   + Gp G+GKT++ k +a  l+ 
  gi|118431266|ref|NP_147616.2| 36 VLGPSGCGKTTMLKVIAGLLKP 57
                                   68***************99863 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00018      0.15      31      73 ..      29      78 ..      14      83 .. 0.79
   2 ?    3.4   0.0     0.058        49     166     192 ..     175     201 ..     148     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                         AAA_25 31 pagelallaGapgtGKttlaldlalava..tGkpwlg.....pvapeqgk 73
                                   p+ +++++ G++g+GKtt++  +a  +   +G+ ++g      ++pe++ 
  gi|118431266|ref|NP_147616.2| 29 PESSITAVLGPSGCGKTTMLKVIAGLLKprRGRVFFGgvdytGLPPERRS 78
                                   8999***************9877766667788877776666655555555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.058
                         AAA_25 166 galvealeriarrtgaavllvhHvgKe 192
                                    ++l++ l+r++r++g + + v H  +e
  gi|118431266|ref|NP_147616.2| 175 QRLLAELKRLQRKLGSTMIYVTHDQWE 201
                                    799********************7776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     6e-06    0.0051      11      41 ..      22      53 ..       6      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6e-06
                         AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAikl 41
                                   r++++ F ++ +t++ Gp G+GKTT l  i  
  gi|118431266|ref|NP_147616.2| 22 RGVSFSFpESSITAVLGPSGCGKTTMLKVIAG 53
                                   7788899999*****************98875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   4.3e-05     0.037       6      38 ..      32      77 ..      30     203 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee.................e 38
                                   +i++v G+sG+GKTt l+ ++  l+ +    +                 +
  gi|118431266|ref|NP_147616.2| 32 SITAVLGPSGCGKTTMLKVIAGLLKPR----RgrvffggvdytglpperR 77
                                   7899*************9988887433....2234455555555555441 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   1.1e-05    0.0096      47      69 ..      33      55 ..      18      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                          Rad17 47 iLLisGPsGCgkstvvkvLskel 69
                                   i  + GPsGCgk+t++kv++  l
  gi|118431266|ref|NP_147616.2| 33 ITAVLGPSGCGKTTMLKVIAGLL 55
                                   67789*************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 ?   14.2   0.0   3.7e-05     0.031      20      53 ..      31      64 ..      24      66 .. 0.83
   2 ?   -3.5   0.0       9.6   8.2e+03     120     147 ..     158     183 ..     154     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                       ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviy 53
                                   ++i  + Gp g+GKt++lk i+  l+    +v++
  gi|118431266|ref|NP_147616.2| 31 SSITAVLGPSGCGKTTMLKVIAGLLKPRRGRVFF 64
                                   578899**************99988776655555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.6
                       ATPase_2 120 iiiiiDelqklidlglngaellvkeLln 147
                                    +++++De     d++++  + l++eL +
  gi|118431266|ref|NP_147616.2| 158 PVLLLDEPLSHLDFKIR--QRLLAELKR 183
                                    78899998888878877..777777755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-05     0.037      19      49 ..      32      62 ..      26      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrv 49
                                    ++++ Gp G GKtt+lk+++ +++ + grv
  gi|118431266|ref|NP_147616.2| 32 SITAVLGPSGCGKTTMLKVIAGLLKPRRGRV 62
                                   478999***************9999886666 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   5.1e-05     0.043      91     123 ..      22      55 ..       5      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                    + ++  + + ++++++G+SG GK+t+++++++ l
  gi|118431266|ref|NP_147616.2|  22 RGVSFSFPEsSITAVLGPSGCGKTTMLKVIAGLL 55 
                                    555555555589****************998765 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.6e-05     0.073       7      53 ..     283     327 ..     282     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-05
                           TOBE   7 lpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgL.apGeeV 53 
                                    l++ V+ ++++g+  +V+++  gg  L A+v+rr a +  L +pGe V
  gi|118431266|ref|NP_147616.2| 283 LEAVVEDLVFQGPLIRVELRWRGGR-LRAVVPRRTASS--LpRPGEAV 327
                                    89***********************.*******98877..33466666 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.8e-05     0.083       3      26 ..      34      57 ..      32      64 .. 0.86
   2 ?   -2.4   0.1       4.5   3.9e+03      90     126 ..     162     196 ..     161     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                                    ++ G++G+GKTt+l+ +a +++ 
  gi|118431266|ref|NP_147616.2| 34 TAVLGPSGCGKTTMLKVIAGLLKP 57
                                   6899**************988875 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.5
                                    STT-SS-TCH.........HHHHHCTTTTT--EEEEE CS
                          NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeaslllt 126
                                    lDe  ++l++k +q++   L++l rk  l ++++ +t
  gi|118431266|ref|NP_147616.2| 162 LDEPLSHLDFKIRQRLLAELKRLQRK--LGSTMIYVT 196
                                    57777777777788888888888777..666666666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.28       4      52 ..      36      86 ..      33      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                   EE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-------EEEEEET CS
                       NTPase_1  4 iTGppGvGKtTlvkkvlellkss..gvkvgGfyteevreggrrigFkivdl 52
                                   + Gp+G GKtT++k ++ llk +   v  gG+       + r +gF   dl
  gi|118431266|ref|NP_147616.2| 36 VLGPSGCGKTTMLKVIAGLLKPRrgRVFFGGVDYTGLPPERRSVGFVFQDL 86
                                   669*****************9773235558888888888888888877766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00063      0.54      10      37 ..      31      58 ..      25      77 .. 0.88
   2 ?   -1.9   0.0       4.5   3.8e+03     105     127 ..     159     183 ..     132     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00063
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvel 37
                                   +++ +v+++ G+GKT++lk i  ll+ +
  gi|118431266|ref|NP_147616.2| 31 SSITAVLGPSGCGKTTMLKVIAGLLKPR 58
                                   67789**************998887755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.5
                         AAA_19 105 llivDE.fqdvd.elqyrLlkallg 127
                                    +l+ DE  + +d +  +rLl +l+ 
  gi|118431266|ref|NP_147616.2| 159 VLLLDEpLSHLDfKIRQRLLAELKR 183
                                    7888986689998889999988874 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 ?   10.4   0.2   0.00057      0.49       4      24 ..      36      57 ..      34      66 .. 0.84
   2 ?   -2.0   0.0       3.9   3.3e+03      57      73 ..     147     164 ..     125     212 .. 0.59
   3 ?   -2.7   0.0       6.1   5.2e+03      22      48 ..     184     212 ..     172     227 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                                   EE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  4 LvGppGtgKselaerlaaal.n 24
                                   ++Gp+G+gK+++ + +a +l  
  gi|118431266|ref|NP_147616.2| 36 VLGPSGCGKTTMLKVIAGLLkP 57
                                   58***************99962 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                                    --------.G-SEEEEES CS
                          AAA_5  57 splvraar.egeilvlDE 73 
                                     +l ra+  e+ +l+lDE
  gi|118431266|ref|NP_147616.2| 147 VALARAIAyEPPVLLLDE 164
                                    444555445666666666 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.1
                                    GB..S--EEEEE--TT--HHHHH--B--. CS
                          AAA_5  22 al..nreveyvqltrdtteedlkgrreik 48 
                                    +     ++ ++  ++++++ +l   + i+
  gi|118431266|ref|NP_147616.2| 184 LQrkLGSTMIYVTHDQWEAMELADTLVIM 212
                                    33333345556667777777777777663 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 ?    8.0   0.1     0.004       3.4       7      85 ..     113     178 ..     110     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.004
                        SbcCD_C   7 RnylsfevevrdedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatll 85 
                                    R++++  +e +  + +++ + r++++lSGG++q    +ala a+a+  +        + +++LDE  s lD + +++ll
  gi|118431266|ref|NP_147616.2| 113 RRQVEWALETVGLTPPREFMGRRVTGLSGGQQQR---VALARAIAY--E--------PPVLLLDEPLSHLDFKIRQRLL 178
                                    555555666665555666688999999***9954...334433332..2........3467777777777777777666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00065      0.56      16      35 ..      28      47 ..      19      52 .. 0.93
   2 ?   -2.7   0.0       3.6   3.1e+03     141     163 ..     174     197 ..     168     207 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00065
                         ATPase 16 ipegrvvlitGepGtGKtif 35
                                   +pe +++ + G +G+GKt++
  gi|118431266|ref|NP_147616.2| 28 FPESSITAVLGPSGCGKTTM 47
                                   8*****************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                         ATPase 141 Reilr.qlvrvlkklgvTailvse 163
                                    R+ l  +l+r  +klg T i v+ 
  gi|118431266|ref|NP_147616.2| 174 RQRLLaELKRLQRKLGSTMIYVTH 197
                                    554440444444888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2422.72
//
Query:       gi|118431267|ref|NP_147617.2|  [L=404]
Description: spermidine/putrescine ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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-33  115.6   0.0    4.6e-33  115.2   0.0    1.1  1  SBP_bac_8    Bacterial extracellular solute-binding protein
    9.8e-24   84.9   0.0    1.3e-23   84.4   0.0    1.1  1  SBP_bac_1    Bacterial extracellular solute-binding protein
    1.5e-22   80.2   0.0    2.2e-22   79.7   0.0    1.2  1  SBP_bac_6    Bacterial extracellular solute-binding protein
    5.2e-07   29.7   0.0    2.8e-06   27.2   0.0    2.0  1  SBP_bac_11   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.31   10.8   2.3        4.7    7.1   0.2    2.3  2  SP_C-Propep  Surfactant protein C, N terminal propeptide


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 !  115.2   0.0   1.3e-36   4.6e-33       5     270 ..      55     318 ..      51     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 1.3e-36
                                    HHHHH-TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS..TTHHH-HHHHHTT..- CS
                      SBP_bac_8   5 efekktgvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl..dnlddltdalaav..g 79 
                                     fe+++g+kv + ++ + +++++ lka    g +   dv++++++ ++ ++e+gl+  l+++  +nl +l++ +a+   +
  gi|118431267|ref|NP_147617.2|  55 IFEERYGIKVVYDEYeSAEEAWPYLKA----GGG-GYDVIIIAHSHVRLAIEQGLVRKLDKSmiPNLSNLDPRIASHpaD 129
                                    69*************777899**9999....333.458999****************9994446******9966666334 PP

                                    -TS..----EEEEEEE-EEEEEHHHHHHS.---BHHHH..HHHHHHHHHH-SEGG---GGGGGGTHHETTEE---H.... CS
                      SBP_bac_8  80 ydgk.lygvPyasetpyvliynkdllekaedpktwdel..laaakklkgkfglpdpasgwlqaallakdgksldddg..g 154
                                       +  y+vPy+++t ++++y +  +e+  +p tw+e+  +++++k+ gk+ l    s +++a+++a +g +++d    +
  gi|118431267|ref|NP_147617.2| 130 P--TqDYAVPYMWGT-TGVAYVEGCVEE--PPSTWKEFlsKSYLEKYSGKVSLLSEFSEVVEAGMIA-LGLDPSDRSswT 203
                                    4..335********9.799********6..********555669*********99999*********.*****99999** PP

                                    HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-H CS
                      SBP_bac_8 155 kdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpknakn 234
                                    ++++++++el+ +lk++   +   ++++  + nGe   ++++++d+  a+++++++g+++p +g++ +++++++p +a +
  gi|118431267|ref|NP_147617.2| 204 EENIDRVVELIIELKPYLAGFYGASQYIPGLVNGELCLAQAWNGDALIAADENPEVGYVAPEDGTLFWVDYMVIPRDAHD 283
                                    ******************96656689****************************************************** PP

                                    HHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT CS
                      SBP_bac_8 235 edlaAldFlkwltspenqaalaektgyipvnksaal 270
                                     + aA  F+++l++pe  a+ +++  y p++k+  l
  gi|118431267|ref|NP_147617.2| 284 VE-AAHLFINFLLEPEIAAMNVKAVWYAPSIKKELL 318
                                    **.6*************************9998665 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 !   84.4   0.0   3.7e-27   1.3e-23      17     313 ..      50     299 ..      37     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 3.7e-27
                                    H.....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEE CS
                      SBP_bac_1  17 a.....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaad 91 
                                    +     fe+  +gikV+++  +s + a      + aG g +Dvi++++++++  +++gl+  ld+ ++++l + +++ a+
  gi|118431267|ref|NP_147617.2|  50 YevlriFEE-RYGIKVVYDEYESAEEAW---PYLKAGGGGYDVIIIAHSHVRLAIEQGLVRKLDKSMIPNLSNLDPRIAS 125
                                    345556988.68*********9999999...7777777779******************************999998888 PP

                                    EEHHHHTHHHHCEEE...ES.EEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHH CS
                      SBP_bac_1  92 klsssvlpkildskv...ly.vPly.aargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtay 166
                                                 ++    y vP++ +++g++Y    +e    +pp tW+e++ +    k +gk     +  +s   +a+
  gi|118431267|ref|NP_147617.2| 126 HP-----------ADptqDYaVPYMwGTTGVAYVEGCVE----EPPSTWKEFLSKSYLEKYSGKVS--LLSEFSEVVEAG 188
                                    85...........33334688****55******555555....3489*****************99..888888888888 PP

                                    HHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHH CS
                      SBP_bac_1 167 yfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaal 246
                                      al l  s  + +  +            +++ +v+      l +elk++ a  ++ +++ + + +Ge  +a +++++al
  gi|118431267|ref|NP_147617.2| 189 MIALGLDPSDRSSWTEE------------NIDRVVE------LIIELKPYLAGFYGASQYIPGLVNGELCLAQAWNGDAL 250
                                    88888888888666655............3444444......559*********************************** PP

                                    HHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHH CS
                      SBP_bac_1 247 aamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspea 313
                                    +a++++p+v+++a+ ++  +                  ++++++ip ++ + eaA+ F++fll+pe 
  gi|118431267|ref|NP_147617.2| 251 IAADENPEVGYVAPEDGTLF------------------WVDYMVIPRDAHDVEAAHLFINFLLEPEI 299
                                    ******************99..................9999***********************95 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 !   79.7   0.0     6e-26   2.2e-22       4     230 ..      86     323 ..      85     329 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 6e-26
                      SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfa...eeglkdp.dgkyypygvgplvlavnkdrlkgrpvPksWaD 79 
                                    +d+i+    + +  +ie+gl+ +ld+  +pn++ +++   +++  dp + + +py +g++++a+ +  +++   P++W++
  gi|118431267|ref|NP_147617.2|  86 YDVII-IAHSHVRLAIEQGLVRKLDKSMIPNLS-NLDpriASHPADPtQDYAVPYMWGTTGVAYVEGCVEEP--PSTWKE 161
                                    58888.88888999***********88888888.45557889*****888888****************655..****** PP

                      SBP_bac_6  80 Lld....Peykgkvalpgnngsdlfealllalyk.........dfgedgvkkllrnlkanlhpaq.mvkaagslesgepa 145
                                    +l+    ++y gkv+l + +     ea + al           ++ +d v +l+ +lk  l   +   +++  l  ge  
  gi|118431267|ref|NP_147617.2| 162 FLSksylEKYSGKVSLLSEFS-EVVEAGMIALGLdpsdrsswtEENIDRVVELIIELKPYLAGFYgASQYIPGLVNGE-- 238
                                    **7344468899999999887.88888888888888******7777*******************99***********.. PP

                      SBP_bac_6 146 vsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvvtnpav 224
                                    + ++ ++ +d+l + +++  +  v PedG+l+++++m+++++    e a  fi+fll+pe++a+ +ka   +P+  ++++
  gi|118431267|ref|NP_147617.2| 239 LCLAQAWNGDALIAADENPEVGYVAPEDGTLFWVDYMVIPRDaHDVEAAHLFINFLLEPEIAAMNVKAVWYAPS-IKKEL 317
                                    ****************999*****************************************88887777665888.77777 PP

                      SBP_bac_6 225 lnelpe 230
                                    l++l e
  gi|118431267|ref|NP_147617.2| 318 LEPLAE 323
                                    766665 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 !   27.2   0.0   7.9e-10   2.8e-06      15     222 ..      51     301 ..      45     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 7.9e-10
                                    HHHHHHHHHH---EEEE.ESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGG...................... CS
                     SBP_bac_11  15 elaaaFeahtgvkvevs.aggsgklarqiadga.rpDvwipassawlellaaaglvqa...................... 70 
                                    e+   Fe+++g+kv++  + ++ ++   +++g   +Dv+i a s +++l++++glv++                      
  gi|118431267|ref|NP_147617.2|  51 EVLRIFEERYGIKVVYDeYESAEEAWPYLKAGGgGYDVIIIAHS-HVRLAIEQGLVRKldksmipnlsnldpriashpad 129
                                    56778********988637777888889999999********96.99********************************9 PP

                                    ...GG-EEEEEEEEEEEESTT-.TT---SHHHHHHS......S--EEEE--T-TTTTHH.HHHHG.....GG--HHHHHH CS
                     SBP_bac_11  71 ...esavplassplviavpkgn.pkkikgwadLlkp......glklavadPttspsGlaalalle.....aagaqellka 135
                                       + avp+   +  +a+ +g   +++++w++ l +      + k+ + + ++s +  a + +l      +   + + ++
  gi|118431267|ref|NP_147617.2| 130 ptqDYAVPYMWGTTGVAYVEGCvEEPPSTWKEFLSKsylekySGKVSLLS-EFSEVVEAGMIALGldpsdR---SSWTEE 205
                                    999999999999999999999746699*****888856664433777776.57777777777777433332...335555 PP

                                    HHHTEEEE.ESSHHHHHHHHHTTT-SEEEEEHHHH..........H..HSTTSSEEEE--TTT--...EEEEEEEE-TT- CS
                     SBP_bac_11 136 lekkvvkl.gessrqlltaveageadagivyesea..........kaaengdkleavylpeglnldpldypaavlkkaak 204
                                      ++vv l  e    l+ + +a ++  g+v+  +           +aa++ +++ +v++ +g+++  +dy ++++++a++
  gi|118431267|ref|NP_147617.2| 206 NIDRVVELiIELKPYLAGFYGASQYIPGLVNGELClaqawngdalIAADENPEVGYVAPEDGTLF-WVDY-MVIPRDAHD 283
                                    5555553322333444444444444444444333322333333355558999************8.8998.77******* PP

                                    -HHHHHHHHHTTSHHHHH CS
                     SBP_bac_11 205 reaAraFlafLrspeaqa 222
                                     eaA  F++fL+ pe  a
  gi|118431267|ref|NP_147617.2| 284 VEAAHLFINFLLEPEIAA 301
                                    **************9776 PP

>> SP_C-Propep  Surfactant protein C, N terminal propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.02        72      44      65 ..      13      34 ..       1      47 [. 0.58
   2 ?    7.1   0.2    0.0013       4.7      31      51 ..     369     390 ..     349     400 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.02
                    SP_C-Propep 44 vvvvlvvvvvlgallmglhmsq 65
                                   +v+v v+  ++ a+lmg   s 
  gi|118431267|ref|NP_147617.2| 13 LVIVAVLAPLVAAVLMGAAASA 34
                                   2444444456677788876654 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0013
                    SP_C-Propep  31 ccplnlkrllivvv.vvvlvvv 51 
                                      p nl   l++vv vvvlvv 
  gi|118431267|ref|NP_147617.2| 369 SQPSNLDSTLVIVVgVVVLVVA 390
                                    4578888777666614444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3104.68
//
Query:       gi|14601092|ref|NP_147618.1|  [L=305]
Description: succinate dehydrogenase iron-sulfur subunit [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-34  117.6   0.0    4.8e-34  116.6   0.0    1.5  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    8.2e-09   35.8   1.7    1.5e-08   34.9   0.3    2.1  2  Fer4_8    4Fe-4S dicluster domain
    3.7e-08   33.8   5.4    4.4e-06   27.1   0.4    2.3  3  Fer4_17   4Fe-4S dicluster domain
    4.6e-07   29.9   0.6    4.6e-07   29.9   0.6    2.1  2  Fer4_10   4Fe-4S dicluster domain
    1.3e-06   28.9   3.6    3.2e-06   27.6   0.5    2.6  2  Fer4_7    4Fe-4S dicluster domain
    1.4e-05   24.7   1.4    1.4e-05   24.7   1.4    3.1  3  Fer4      4Fe-4S binding domain
    4.5e-05   23.3   0.4    4.5e-05   23.3   0.4    2.3  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
     0.0001   22.2   0.8     0.0001   22.2   0.8    2.8  2  Fer4_6    4Fe-4S binding domain
    0.00064   19.7   0.2     0.0012   18.9   0.2    1.4  1  Fer2_4    2Fe-2S iron-sulfur cluster binding domain
     0.0014   19.6  11.2      0.022   15.7   0.5    2.9  3  Fer4_16   4Fe-4S double cluster binding domain
     0.0026   18.0   1.3       0.21   11.8   0.0    2.6  3  Fer4_18   4Fe-4S dicluster domain
     0.0027   17.7   1.1     0.0027   17.7   1.1    3.4  3  Fer4_2    4Fe-4S binding domain
     0.0028   18.0   0.5     0.0028   18.0   0.5    3.0  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.011   15.1   0.1       0.02   14.2   0.1    1.4  1  BRX       Transcription factor regulating root and shoot grow
      0.013   15.7   0.3      0.013   15.7   0.3    2.8  3  Fer4_21   4Fe-4S dicluster domain
      0.013   15.7   1.4      0.013   15.7   1.4    3.0  5  Fer4_9    4Fe-4S dicluster domain
      0.071   13.7   1.2      0.071   13.7   1.2    2.7  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.34   11.7   0.3       0.34   11.7   0.3    2.8  3  Fer4_15   4Fe-4S single cluster domain
          7    7.6   8.2        6.5    7.7   4.2    2.6  2  Fer4_22   4Fe-4S dicluster 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 !  116.6   0.0   5.1e-37   4.8e-34       3     109 .]      20     125 ..      18     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5.1e-37
                        Fer2_3   3 kvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqk 83 
                                    ++++dp  ++g++++qe+eve+ +++tvldaLlkikee+d++l+ r+sCr ++CGsc+++inG+p+laC++++ ++a+++
  gi|14601092|ref|NP_147618.1|  20 VIRKYDP--ESGRSWWQEHEVETYRGMTVLDALLKIKEEQDHSLTLRYSCRMAVCGSCGMTINGTPRLACQTQVAQVARED 98 
                                   6889999..6789*****************************************************************999 PP

                        Fer2_3  84 s.eieleplpkfpvirDLvvDidemle 109
                                   +  +++epl +f+v++DL +D +e++e
  gi|14601092|ref|NP_147618.1|  99 ApVVRVEPLYNFKVVKDLLTDFTEFFE 125
                                   989********************9985 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.1     2e+03      54      57 ..      72      75 ..      36     108 .. 0.75
   2 !   34.9   0.3   1.6e-11   1.5e-08       4      65 .]     164     235 ..     161     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                        Fer4_8 54 cgaC 57
                                  cg+C
  gi|14601092|ref|NP_147618.1| 72 CGSC 75
                                  3333 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 1.6e-11
                        Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaae..........dvqeeqvleeeealwsCttcgaCtevCpvgi 65 
                                    Ci Cg+C +aCp++ +  k+l  +   +a           +v++ + +++ ++++ C+   +C+ vCp+++
  gi|14601092|ref|NP_147618.1| 164 LCIACGLCVAACPIFASDTKFLGPQALSQAYrfvvdprdegYVERLEIVDSIDGVFGCHFAASCSAVCPKEV 235
                                   6***********966664444333333322234444444447788888888******************975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.9   2.8e+03      44      50 ..      70      76 ..      38      99 .. 0.73
   2 !   16.4   0.6     1e-05    0.0098      34      57 ..     153     176 ..     132     179 .. 0.72
   3 !   27.1   0.4   4.7e-09   4.4e-06       2      61 .]     165     236 ..     164     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.9
                       Fer4_17 44 slCieCg 50
                                    C +Cg
  gi|14601092|ref|NP_147618.1| 70 AVCGSCG 76
                                  3333333 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1e-05
                       Fer4_17  34 leeaekeekaslCieCgeCerkCP 57 
                                    ee e+  + slCi Cg+C+++CP
  gi|14601092|ref|NP_147618.1| 153 PEEYEQFYQYSLCIACGLCVAACP 176
                                   34445557999************9 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 4.7e-09
                       Fer4_17   2 CiqCgyClpeCpsyeaydn..epkkllraakl..........glleeaeke...ekaslCieCgeCerkCPqgld 61 
                                   Ci Cg C+++Cp ++   +   p+ l +a+++          ++le        + +  C+    C+++CP+++d
  gi|14601092|ref|NP_147618.1| 165 CIACGLCVAACPIFASDTKflGPQALSQAYRFvvdprdegyvERLEI---VdsiDGVFGCHFAASCSAVCPKEVD 236
                                   **************996653468888888877778766633333333...244589****************997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3         2   1.9e+03      43      51 ..      65      75 ..      50      90 .. 0.68
   2 !   29.9   0.6   4.8e-10   4.6e-07       5      56 .]     161     232 ..     158     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                       Fer4_10 43 ekCtg..cgaC 51
                                  ++C +  cg+C
  gi|14601092|ref|NP_147618.1| 65 YSCRMavCGSC 75
                                  55555555555 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 4.8e-10
                       Fer4_10   5 dddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                   + + Ci Cg Cv+aCP  +                     +++++ e+ e+    ++v  C++  +C ++CP
  gi|14601092|ref|NP_147618.1| 161 QYSLCIACGLCVAACPIFAsdtkflgpqalsqayrfvvdPRDEGYVERLEIVDSIDGVFGCHFAASCSAVCP 232
                                   6688*************88*******************6666666666666666669**************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 ?    1.1   0.2      0.63     6e+02      18      43 ..      52      77 ..      45     101 .. 0.73
   2 !   27.6   0.5   3.4e-09   3.2e-06       2      51 ..     165     234 ..     164     235 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.63
                        Fer4_7 18 eldeeenekgtekveidpekClgCga 43
                                  +++ee++++ t ++  ++  C +Cg+
  gi|14601092|ref|NP_147618.1| 52 KIKEEQDHSLTLRYSCRMAVCGSCGM 77
                                  56677777777778888888888873 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.4e-09
                        Fer4_7   2 CigCgaCvaaCpvkaieldeeenek...............gtekveidpek.....ClgCgaCvavCPtg 51 
                                   Ci Cg CvaaCp  a +++    ++                +e++ei+ +      C +  +C avCP++
  gi|14601092|ref|NP_147618.1| 165 CIACGLCVAACPIFASDTKFLGPQAlsqayrfvvdprdegYVERLEIVDSIdgvfgCHFAASCSAVCPKE 234
                                   ***********988887774322222222222222222222244444322123344888899******97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   1.2       4.9   4.6e+03      11      14 ..      72      75 ..      71      77 .. 0.69
   2 !   24.7   1.4   1.5e-08   1.4e-05       5      20 ..     162     177 ..     159     179 .. 0.88
   3 ?    2.1   0.8       0.2   1.9e+02      14      21 ..     227     234 ..     225     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.9
                                  -THH CS
                          Fer4 11 CGaC 14
                                  CG C
  gi|14601092|ref|NP_147618.1| 72 CGSC 75
                                  7777 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.5e-08
                                   TTTSSS-THHHHHSTT CS
                          Fer4   5 eekCigCGaCvevCPv 20 
                                   +++Ci+CG+Cv +CP 
  gi|14601092|ref|NP_147618.1| 162 YSLCIACGLCVAACPI 177
                                   789************6 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.2
                                   HHHHSTTT CS
                          Fer4  14 CvevCPvg 21 
                                   C  vCP +
  gi|14601092|ref|NP_147618.1| 227 CSAVCPKE 234
                                   ******75 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 !   23.3   0.4   4.8e-08   4.5e-05       9      77 ..      37      91 ..      33      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.8e-08
                                  EEEEETTTHBHHHHHH.....HTTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                          Fer2  9 evevadgettlldaae.....enggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                  eve   g t +lda+      +++ + ++ysC+++ Cg+C  +++            g +      rlaCqt v
  gi|14601092|ref|NP_147618.1| 37 EVETYRGMT-VLDALLkikeeQDHSLTLRYSCRMAVCGSCGMTIN------------GTP------RLACQTQV 91
                                  555555556.777776666654889*****************999............887......8*****87 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.8   1.1e-07    0.0001       4      20 ..     160     176 ..     159     183 .. 0.90
   2 ?    2.7   1.0      0.15   1.5e+02      15      23 ..     227     240 ..     220     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                        Fer4_6   4 idpdkCigCgdCvrvCP 20 
                                   +++++Ci Cg Cv++CP
  gi|14601092|ref|NP_147618.1| 160 YQYSLCIACGLCVAACP 176
                                   6789************* PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
                        Fer4_6  15 CvrvCP.....ega 23 
                                   C +vCP     +ga
  gi|14601092|ref|NP_147618.1| 227 CSAVCPkevdpAGA 240
                                   ******55544455 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 !   18.9   0.2   1.3e-06    0.0012      11      72 ..      36      92 ..      32      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                        Fer2_4 11 kevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpve 72
                                  +ev+ + G tv++All+   +  +s          c +++C  C ++++g p   ac+t+v+
  gi|14601092|ref|NP_147618.1| 36 HEVETYRGMTVLDALLKIKEEQDHSLTL----RYSCRMAVCGSCGMTINGTP-RLACQTQVA 92
                                  7899************999654444443....335*****************.569999986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1         3   2.8e+03      54      60 ..      69      75 ..      31      78 .. 0.65
   2 !   15.7   0.5   2.4e-05     0.022      34      66 ..     145     177 ..     131     178 .. 0.83
   3 !   15.5   4.5   2.6e-05     0.024       2      66 ..     165     233 ..     164     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3
                       Fer4_16 54 itgCdiC 60
                                  ++ C+ C
  gi|14601092|ref|NP_147618.1| 69 MAVCGSC 75
                                  3666666 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.4e-05
                       Fer4_16  34 ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                    t e k l+e++e+ +++  ++ C+ C+++CP+
  gi|14601092|ref|NP_147618.1| 145 PTLEYKLLPEEYEQFYQYSLCIACGLCVAACPI 177
                                   456789999999999999999**********95 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 2.6e-05
                       Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy...ntaekkdlaedeekckkqeaitgCd...iCqdvCPa 66 
                                   C+ Cg C+ +CP  a ++k  +   +  +++y    ++ ++++ e+ e  ++   ++gC     C +vCP 
  gi|14601092|ref|NP_147618.1| 165 CIACGLCVAACPIFASDTK--FLGPQALSQAYrfvVDPRDEGYVERLEIVDSIDGVFGCHfaaSCSAVCPK 233
                                   *************999888..4444444444456667788888888888888999999977779******5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.9   4.6e+03      55      64 ..      66      75 ..      17      89 .. 0.57
   2 !   11.8   0.0   0.00022      0.21      45      73 ..     149     177 ..     122     185 .. 0.70
   3 ?    4.4   0.1     0.045        43      59      77 ..     219     237 ..     204     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                       Fer4_18 55 ekgagdcidc 64
                                  +  ++ c +c
  gi|14601092|ref|NP_147618.1| 66 SCRMAVCGSC 75
                                  2233333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00022
                       Fer4_18  45 kalkekeerkekgagdcidcescvkvcPt 73 
                                    +l  +e ++  + + ci+c+ cv+ cP+
  gi|14601092|ref|NP_147618.1| 149 YKLLPEEYEQFYQYSLCIACGLCVAACPI 177
                                   44555566666777889999999999996 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.045
                       Fer4_18  59 gdcidcescvkvcPtgidi 77 
                                     c    sc +vcP ++d 
  gi|14601092|ref|NP_147618.1| 219 FGCHFAASCSAVCPKEVDP 237
                                   56888899*********95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.7       2.4   2.3e+03      13      16 ..      72      75 ..      64      89 .. 0.68
   2 !   17.7   1.1   2.8e-06    0.0027       8      21 ..     163     176 ..     156     176 .. 0.87
   3 ?    2.3   1.3      0.22   2.1e+02      12      21 ..     220     232 ..     219     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.4
                        Fer4_2 13 CgaC 16
                                  Cg+C
  gi|14601092|ref|NP_147618.1| 72 CGSC 75
                                  5555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.8e-06
                        Fer4_2   8 drCigCgaCvsaCP 21 
                                     Ci+Cg Cv aCP
  gi|14601092|ref|NP_147618.1| 163 SLCIACGLCVAACP 176
                                   57***********9 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.22
                        Fer4_2  12 gCg...aCvsaCP 21 
                                   gC    +C  +CP
  gi|14601092|ref|NP_147618.1| 220 GCHfaaSCSAVCP 232
                                   6766669*999*9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.5     3e-06    0.0028       3      15 ..     164     176 ..     162     193 .. 0.87
   2 ?    2.7   0.5      0.24   2.3e+02       6      16 ..     220     233 ..     219     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                        Fer4_4   3 rCigCgsCvaaCP 15 
                                    Ci Cg CvaaCP
  gi|14601092|ref|NP_147618.1| 164 LCIACGLCVAACP 176
                                   6***********9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.24
                        Fer4_4   6 gCg...sCvaaCPq 16 
                                   gC    sC a+CP 
  gi|14601092|ref|NP_147618.1| 220 GCHfaaSCSAVCPK 233
                                   6775557******5 PP

>> BRX  Transcription factor regulating root and shoot growth via Pin3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.1e-05      0.02      27      49 ..      15      37 ..      11      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                           BRX 27 krvrFSrkrFsekqAeeWWeeNk 49
                                  krvrF  ++++ +  ++WW+e++
  gi|14601092|ref|NP_147618.1| 15 KRVRFVIRKYDPESGRSWWQEHE 37
                                  9********************87 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.5       5.5   5.1e+03      11      19 ..      72      80 ..      66     100 .. 0.61
   2 ?   15.7   0.3   1.3e-05     0.013      39      53 ..     163     177 ..     150     182 .. 0.78
   3 ?    3.6   0.2     0.078        74      43      52 ..     220     232 ..     206     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.5
                       Fer4_21 11 CgkCliaCe 19
                                  Cg+C ++ +
  gi|14601092|ref|NP_147618.1| 72 CGSCGMTIN 80
                                  666655444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                       Fer4_21  39 deCvGCnlCssvCPv 53 
                                   + C++C lC++ CP+
  gi|14601092|ref|NP_147618.1| 163 SLCIACGLCVAACPI 177
                                   679999999999997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.078
                       Fer4_21  43 GCn...lCssvCP 52 
                                   GC+    Cs+vCP
  gi|14601092|ref|NP_147618.1| 220 GCHfaaSCSAVCP 232
                                   5542216****** PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   1.9       5.8   5.5e+03      35      39 ..      71      75 ..      51      92 .. 0.62
   2 ?   -2.9   2.2       8.9   8.4e+03      42      42 ..      75      75 ..      65     104 .. 0.59
   3 ?   15.7   1.4   1.4e-05     0.013      33      47 ..     156     176 ..     129     179 .. 0.73
   4 ?   14.0   6.5   4.5e-05     0.043       2      49 ..     165     234 ..     164     236 .. 0.86
   5 ?    3.9   0.6     0.066        62       6      16 ..     225     235 ..     219     245 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.8
                        Fer4_9 35 aCigC 39
                                   C +C
  gi|14601092|ref|NP_147618.1| 71 VCGSC 75
                                  23333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.9
                        Fer4_9 42 C 42
                                  C
  gi|14601092|ref|NP_147618.1| 75 C 75
                                  2 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.4e-05
                        Fer4_9  33 e......eaCigCgaCveaCp 47 
                                   +      + Ci Cg Cv+aCp
  gi|14601092|ref|NP_147618.1| 156 YeqfyqySLCIACGLCVAACP 176
                                   044555578***********9 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 4.5e-05
                        Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                                   C+ Cg Cv+aCp  +   +  +  a  +a++                         C++  +C ++Cpk+
  gi|14601092|ref|NP_147618.1| 165 CIACGLCVAACPIFASDTKFLGPQALSQAYRFvvdprdegyverleivdsidgvFGCHFAASCSAVCPKE 234
                                   ***********88888777777777777777778888889999999999*****99************96 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.066
                        Fer4_9   6 gaCveaCpagv 16 
                                    +C ++Cp++v
  gi|14601092|ref|NP_147618.1| 225 ASCSAVCPKEV 235
                                   24666665554 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 ?   13.7   1.2   7.5e-05     0.071       6      19 ..     165     177 ..     162     188 .. 0.85
   2 ?   -0.7   0.6       2.4   2.2e+03       6      18 ..     221     233 ..     219     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                       Fer4_13   6 CiacgaCvelaPdv 19 
                                   Ciacg+Cv+++P +
  gi|14601092|ref|NP_147618.1| 165 CIACGLCVAACP-I 177
                                   ************.4 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                       Fer4_13   6 CiacgaCvelaPd 18 
                                   C   ++C +++P+
  gi|14601092|ref|NP_147618.1| 221 CHFAASCSAVCPK 233
                                   666689*****96 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 ?   -0.2   0.0       1.9   1.8e+03      19      41 ..     121     143 ..     117     157 .. 0.73
   2 ?   11.7   0.3   0.00036      0.34       6      25 ..     163     181 ..     159     192 .. 0.87
   3 ?   -1.8   0.5       5.9   5.5e+03       8      20 ..     221     233 ..     220     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                       Fer4_15  19 pevfeldedglasvllddgeiae 41 
                                   +e+fe++ + +++++  d +++e
  gi|14601092|ref|NP_147618.1| 121 TEFFEKHRRVKPYLIRRDVDEQE 143
                                   689*******9988855444333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00036
                       Fer4_15   6 daCigcglCvaeapevfeld 25 
                                   ++Ci cglCva++p +f  d
  gi|14601092|ref|NP_147618.1| 163 SLCIACGLCVAACP-IFASD 181
                                   68***********9.77766 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.9
                       Fer4_15   8 CigcglCvaeape 20 
                                   C   + C a++p+
  gi|14601092|ref|NP_147618.1| 221 CHFAASCSAVCPK 233
                                   8888889998886 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.2    0.0069       6.5      58      93 ..     139     176 ..      66     179 .. 0.69
   2 ?    0.4   0.1       1.3   1.2e+03       2      94 ..     221     233 ..     203     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0069
                       Fer4_22  58 kkerlrqrllhkls..efkekfgesgCvGCgRCieacp 93 
                                     e+ +  l  kl   e+++ ++ s C+ Cg C++acp
  gi|14601092|ref|NP_147618.1| 139 VDEQENPTLEYKLLpeEYEQFYQYSLCIACGLCVAACP 176
                                   44444444555543325566669999***********8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                       Fer4_22   2 ClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfgesgC 82 
                                   C   ++C++vCp                                                                     
  gi|14601092|ref|NP_147618.1| 221 CHFAASCSAVCP--------------------------------------------------------------------- 232
                                   333445555555..................................................................... PP

                       Fer4_22  83 vGCgRCieacpv 94 
                                              +
  gi|14601092|ref|NP_147618.1| 233 -----------K 233
                                   ...........4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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):              19  [number of targets reported over threshold]
# CPU time: 0.49u 0.18s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2566.83
//
Query:       gi|14601093|ref|NP_147619.1|  [L=117]
Description: succinate dehydrogenase subunit D [Aeropyrum pernix K1]
Scores for complete 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   30.7  10.0    3.1e-07   30.4  10.0    1.1  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem
  ------ inclusion threshold ------
        1.9    8.7   8.8         32    4.8   8.8    2.1  1  DPM3      Dolichol-phosphate mannosyltransferase subunit 3 (D


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 !   30.4  10.0   3.5e-11   3.1e-07      22     116 ..       8     102 ..       3     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.5e-11
                       Sdh_cyt  22 lsilhritGvallv.glllllvwlllalslsspesfarv...vallaspiklilllllllallyHllnGiRhllwDlglgl 98 
                                   + +l+ +t+++l+v ++++l    l ++ l++ esf +      ++  +  + lllll++ +l+H++nG+R +l+ +++g 
  gi|14601093|ref|NP_147619.1|   8 MQLLQYVTAALLVVlVSWHLA---LRLPWLHGVESFVHTlmpEVVYREITSFSLLLLLAYTALIHGVNGLRIILLEVHHGE 85 
                                   557899********9999999...56999*******9999986677777777787999999999************98877 PP

                       Sdh_cyt  99 .elesarksalavlalava 116
                                     ++++++ a+++l++  +
  gi|14601093|ref|NP_147619.1|  86 lWDKAVNAAAVLALLV--F 102
                                   6666665555333332..2 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 ?    4.8   8.8    0.0036        32       6      58 ..      52     111 ..       8     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0036
                          DPM3   6 ktlalallllalwlalllrlv.......slplskvqdevvpvlPlwalvlfGayslatlg 58 
                                   ++ ++ llll +++al+ ++        +++  + +d+ v ++ ++al++fGa + +t++
  gi|14601093|ref|NP_147619.1|  52 EITSFSLLLLLAYTALIHGVNglriillEVHHGELWDKAVNAAAVLALLVFGALATYTVV 111
                                   5667777888888888854442222233444489999*****************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 898.28
//
Query:       gi|118431268|ref|NP_147620.2|  [L=119]
Description: succinate dehydrogenase subunit C [Aeropyrum pernix K1]
Scores for complete 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-12   46.1   3.6    6.7e-12   45.5   3.4    1.4  1  Sdh_cyt        Succinate dehydrogenase/Fumarate reductase tra
  ------ inclusion threshold ------
      0.063   13.4   7.0       0.16   12.1   4.5    2.1  1  Ferric_reduct  Ferric reductase like transmembrane component


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 !   45.5   3.4   7.5e-16   6.7e-12      25     120 ..       1     111 [.       1     112 [. 0.71

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 7.5e-16
                        Sdh_cyt  25 lhritGvallvglllllvwlllalslsspesfarvvallas..piklilllllllallyHllnGiRhllwD.lglgl.el 100
                                    +hritGv+ ++ +++++++++ a+++s+ e++ + va l +  pi ++   +++ a+l+H+lnG+R+ll+  l lg  ++
  gi|118431268|ref|NP_147620.2|   1 MHRITGVITAF-FIFFHIISTSAPARSGWEAWLEEVANLDGitPISILF-YIAMGAVLFHGLNGVRLLLVEaLALGIgRP 78 
                                    7**********.*******999998775555544466665676777777.555566666************855666444 PP

                        Sdh_cyt 101 .esa............rksalavlalavalvlv 120
                                     + +            r+   +v+al ++l+++
  gi|118431268|ref|NP_147620.2|  79 eKPKppyiapslrgfqRRLIHIVFALWIILWIA 111
                                    233367888888777666667777777777665 PP

>> Ferric_reduct  Ferric reductase like transmembrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.5   1.8e-05      0.16      36      96 ..       1      53 [.       1     108 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                  Ferric_reduct 36 fHkwlgvlafllallHvilyllnflrfsaldeerlldsllkkpynllGvlalllliilait 96
                                   +H+ +gv++++++++H+i    ++         + ++ +l++ +nl G+  + +l+ +a+ 
  gi|118431268|ref|NP_147620.2|  1 MHRITGVITAFFIFFHIISTSAPAR--------SGWEAWLEEVANLDGITPISILFYIAMG 53
                                   5******************999886........4677777777777777666666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 997.05
//
Query:       gi|118431269|ref|NP_147621.2|  [L=583]
Description: succinate dehydrogenase flavoprotein subunit [Aeropyrum pernix K1]
Scores for 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-108  361.8   0.1   6.5e-108  361.5   0.1    1.1  1  FAD_binding_2   FAD binding domain
      1e-40  138.6   0.4    1.7e-40  138.0   0.4    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    7.7e-05   22.1   0.5      0.005   16.1   0.1    2.7  3  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00079   18.7   0.2      0.028   13.6   0.1    2.2  2  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.019   13.7   0.0          2    7.0   0.0    2.4  2  HI0933_like     HI0933-like protein
      0.022   14.4   5.6      0.024   14.2   0.8    3.0  4  DAO             FAD dependent oxidoreductase
      0.097   12.9   0.7       0.74   10.1   0.2    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
       0.11   11.5   0.1       0.35    9.9   0.0    1.9  2  GIDA            Glucose inhibited division protein A


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 !  361.5   0.1  2.9e-111  6.5e-108       1     416 [.      10     401 ..      10     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 361.5 bits;  conditional E-value: 2.9e-111
                                    SEEEE--SHHHHHHHHHHHH..TTT.-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaae..aGl.kvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                    Dv+V+G+G+AGL+AA+e+++    + +v +v+k + +++++  ++Gg +av ++e      +ds  lh++dt+k++d la
  gi|118431269|ref|NP_147621.2|  10 DVVVVGTGIAGLRAAVEIKRryGDKlDVGLVSKIHLMRSHSISAEGGTAAVIYKEE-----GDSYALHAWDTIKGSDFLA 84 
                                    9******************9543446**************************7776.....7****************** PP

                                    -HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCT.E CS
                  FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarkag.v 156
                                    dq++v +fv+ +pe+v+ Le++g+p+sr++dg+++vr +Gg+s + rtl+ a+d+      tg+  +++l++++++++  
  gi|118431269|ref|NP_147621.2|  85 DQDAVWIFVKLMPEEVRLLEHWGMPWSRRPDGRLAVRAFGGHSVK-RTLF-AGDK------TGFYEMHTLYNKLLQYDgW 156
                                    *********************************************.****.****......******************* PP

                                    EEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCT CS
                  FAD_binding_2 157 dfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalra 236
                                    + +++++a++++vedg+ +G+ + np++g +  ++aka ++atgG+gr           ++ +t a++vtGdg ++alra
  gi|118431269|ref|NP_147621.2| 157 ERYDEWYATNIVVEDGEFRGVFAINPRDGDIYLFKAKAGIIATGGAGR----------LYNFATYAHTVTGDGWGMALRA 226
                                    ************************************************..........********************** PP

                                    TSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.........GGGS-HHHHHHHHH.HHHHTT CS
                  FAD_binding_2 237 gaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.........nelasrdvvsrailekeiaeg 307
                                    g++l+d  +e++qfhPt+l+    +sgiLite++rgeGg+l++++G+rFm         +e+a+rd+vsr i+ +ei eg
  gi|118431269|ref|NP_147621.2| 227 GLPLKD--PEFFQFHPTGLI----PSGILITEGARGEGGYLLNNRGERFMlrkecapkmAEIAPRDIVSRCII-REILEG 299
                                    ******..************....*************************************************.999999 PP

                                    TS.......CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-EEEBET CS
                  FAD_binding_2 308 gs.......eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgGvetde 380
                                    ++        ++v ld++h l++e+++++l+a++e+a++ ++      idp ++p p       v+p +hytmgG++td 
  gi|118431269|ref|NP_147621.2| 300 RGfkddvsgLEYVLLDLRH-LGEEKINERLPAVREIAIRYAG------IDPVEEPLP-------VRPVAHYTMGGIRTDS 365
                                    999*****97799******.**********************......*********.......**************** PP

                                    TSBESTTEEESSBTEEE-STCEESSSSTTS--TTHH CS
                  FAD_binding_2 381 ngrvldadgqpipGLYAaGevaaggvhganrlgGns 416
                                      rvlda+g+ + GL+AaGevaa+++hganrlg+ns
  gi|118431269|ref|NP_147621.2| 366 YYRVLDAEGRWVRGLFAAGEVAAASIHGANRLGSNS 401
                                    ***********************************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 !  138.0   0.4   7.4e-44   1.7e-40       2     128 .]     457     583 .]     456     583 .] 0.97

  Alignments for each domain:
  == domain 1  score: 138.0 bits;  conditional E-value: 7.4e-44
                                    HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHH.HTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTT CS
                 Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrer.lknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGa 80 
                                    +eL+++m k++ v R+eeg++++l ++ +lr+   ++v v+dk++++N++l+ ale an+l+ A a+ak+Al+R ESrGa
  gi|118431269|ref|NP_147621.2| 457 RELRDTMGKYFYVIRDEEGMRRGLLTILKLRKMfREDVYVEDKGRIYNTDLIAALETANMLDAALAVAKAALNRAESRGA 536
                                    79*******************************889******************************************** PP

                                    BEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                 Succ_DH_flav_C  81 HaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                    H+r d+p+rdDenwlkhtl++ +  +++v+++yepv+++t kp eR+Y
  gi|118431269|ref|NP_147621.2| 537 HYRVDYPKRDDENWLKHTLVTAS-GEDDVRIDYEPVRITTWKPVERKY 583
                                    ********************555.5689*******************9 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 !   16.1   0.1   2.2e-06     0.005       1      29 [.       9      40 ..       9      75 .. 0.84
   2 ?   -2.3   0.0      0.89     2e+03      89     113 ..     181     205 ..     157     215 .. 0.74
   3 ?    3.1   0.0     0.021        47     254     279 ..     357     392 ..     335     404 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                                   CSEEEE--SHHHHHHHHHHHH...HTS-EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq...agakvtlv 29
                                   +dvvv+G G+AGl+aa ++++    +++v lv
  gi|118431269|ref|NP_147621.2|  9 HDVVVVGTGIAGLRAAVEIKRrygDKLDVGLV 40
                                   59*******************86658888887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.89
                                    EEECTCEEEEEESEEEE---EEE-B CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  89 kkkegdeekiaydklvlAtGssprd 113
                                    + ++gd   +++++ ++AtG+  r+
  gi|118431269|ref|NP_147621.2| 181 NPRDGDIYLFKAKAGIIATGGAGRL 205
                                    445566667889999*****87665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.021
                                    ETTEEE--TTSBE.....S.STTEEE-GGGC....T CS
                                    xxxxxxxxxxxxx.....x.xxxxxxxxxxx....x RF
                    Pyr_redox_2 254 erggivvdeflrt.....n.vpgiyaiGDva....g 279
                                      ggi +d+++r+       v g++a+G va    +
  gi|118431269|ref|NP_147621.2| 357 TMGGIRTDSYYRVldaegRwVRGLFAAGEVAaasiH 392
                                    46999999999877777756***********55553 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.3e-05     0.028      14      40 ..       5      31 ..       3      58 .. 0.83
   2 ?    2.7   0.0     0.029        64     208     233 ..     373     399 ..     364     400 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                   HHTEEEEEEE--SHHHHHHHHHHHHCT CS
                           Thi4 14 kyaesDvvivGaGssGLtaayylakkp 40
                                   +++e Dvv+vG+G +GL aa  + ++ 
  gi|118431269|ref|NP_147621.2|  5 EIIEHDVVVVGTGIAGLRAAVEIKRRY 31
                                   6799******************99983 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.029
                                    ECEEETTEEE-T.HHHHHHHT-EB--S CS
                           Thi4 208 trevvpnlyvaG.mevaevdganRmGp 233
                                      + v +l++aG +++a ++ganR+G+
  gi|118431269|ref|NP_147621.2| 373 EGRWVRGLFAAGeVAAASIHGANRLGS 399
                                    5567899***99567889*******96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00091         2       1      22 [.       9      30 ..       9      49 .. 0.86
   2 ?    4.2   0.0    0.0066        15     353     408 ..     354     414 ..     319     415 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00091
                                   -SEEEE--SHHHHHHHHHHHHT CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakr 22
                                   +dv+v+G G AGl aA+++++r
  gi|118431269|ref|NP_147621.2|  9 HDVVVVGTGIAGLRAAVEIKRR 30
                                   59***************99654 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0066
                                    -SEEEEEE-GGGB-T.TT-BBTTSTTEEE-GGGB..SEEE-..TTTHHHHHHHHHHHHHHH CS
                    HI0933_like 353 aevTaGGVdlkevss.ktmeskkvpgLffaGEvl..Dvegv..tGGynlqaAwasgyaAGk 408
                                    a  T+GG+++++       e + v gLf aGEv    ++g   +G      +++sg +AG+
  gi|118431269|ref|NP_147621.2| 354 AHYTMGGIRTDSYYRvLDAEGRWVRGLFAAGEVAaaSIHGAnrLGSNSTAECLTSGRIAGM 414
                                    67899****99865414567899**********6224555333677777778888888885 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.8   1.1e-05     0.024       1      87 [.      10     118 ..      10     165 .. 0.68
   2 ?   -2.2   0.0       1.1   2.4e+03     245     265 ..     167     189 ..     146     197 .. 0.79
   3 ?    0.5   0.0      0.16   3.5e+02     290     349 ..     322     387 ..     304     390 .. 0.71
   4 ?   -1.4   0.1      0.62   1.4e+03      36      54 ..     407     425 ..     399     540 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                    EEEEECTSHHHHHHHHHHHHT.T....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH.................... CS
                            DAO   1 dvviiGGGiiGlstAyeLarr.g....VtllekgdiagsgaSgrnsgllhsglrylpeas.................... 55 
                                    dvv++G Gi+Gl +A e  rr g    V l+ k +   s++ ++ +g  +  ++ ++e+                     
  gi|118431269|ref|NP_147621.2|  10 DVVVVGTGIAGLRAAVEIKRRyGdkldVGLVSKIHLMRSHSISAEGGTAAV-IY-KEEGDsyalhawdtikgsdfladqd 87 
                                    9*****************88887899*999999877666666666665555.43.3433334445555666666666665 PP

                                    HHHHHHHHHHHHHHHHHHHHSSTTSEEEEEEE CS
                            DAO  56 elarlslealeelreleeelgididyrrtGll 87 
                                    +++ +++   ee r le   g+++  r+ G l
  gi|118431269|ref|NP_147621.2|  88 AVWIFVKLMPEEVRLLEH-WGMPWSRRPDGRL 118
                                    443444444444444443.3555666666555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                    E..EEETTTTEEEEEETTSEEEE CS
                            DAO 245 e..tdddgrgvyvtprkdgrvlv 265
                                    +   d ++rgv+++ ++dg +++
  gi|118431269|ref|NP_147621.2| 167 IvvEDGEFRGVFAINPRDGDIYL 189
                                    34578899*******999*9997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.16
                                    HHHHHHSGGGCGEEEEEEEEEEE..T.TSSEEEEEEE...TEEEEEEEEECTTTHHHHHHHHHHHH CS
                            DAO 290 ealrklfPqlgdvlrkwaGlrpl..p.dglpligetp...gvkglylatGhsghGltlapatGkll 349
                                    e++++++P+++++  ++aG+ p   p +  p+   t    +++ +y +  ++g+ +    a+G+++
  gi|118431269|ref|NP_147621.2| 322 EKINERLPAVREIAIRYAGIDPVeePlPVRPVAHYTMggiRTDSYYRVLDAEGRWVRGLFAAGEVA 387
                                    678999***999**9*******42222445555553366655666666666666666666666655 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.62
                                    GGGSSEEEEESSSSTHHST CS
                            DAO  36 aSgrnsgllhsglrylpea 54 
                                    +Sgr +g+l++ ++ ++ea
  gi|118431269|ref|NP_147621.2| 407 TSGRIAGMLAAEYALKAEA 425
                                    6666666666666422222 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 ?   10.1   0.2   0.00033      0.74       1      22 [.      13      37 ..      13      57 .. 0.85
   2 ?   -0.2   0.0      0.53   1.2e+03       6      27 ..     411     435 ..     409     438 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00033
                                   EE--SHHHHHHHHHHHCC...TEEE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdv 22
                                   +vG+G++Gl aA +++++   ++dv
  gi|118431269|ref|NP_147621.2| 13 VVGTGIAGLRAAVEIKRRygdKLDV 37
                                   8**************9976555566 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHHCC...TEEEEEE-S CS
                  NAD_binding_8   6 lsGlvaAylLaka...gfdvlllek 27 
                                    ++G++aA ++ ka   g++ + +ek
  gi|118431269|ref|NP_147621.2| 411 IAGMLAAEYALKAearGVEPERFEK 435
                                    7999999775553245888777777 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00016      0.35       1      21 [.      10      30 ..      10      52 .. 0.92
   2 ?   -3.3   0.0       1.6   3.7e+03     120     150 ..     166     201 ..     164     207 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                                   CEEEE-SSHHHHHHHHHHHHT CS
                           GIDA  1 dviViGgGhAGceAAlaaarl 21
                                   dv+V+G G AG+ AA++++r+
  gi|118431269|ref|NP_147621.2| 10 DVVVVGTGIAGLRAAVEIKRR 30
                                   79***************9985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.6
                                    EEEECTTEEEEEEE...TTS-E..EEECEEEE--TT CS
                           GIDA 120 eliveekkvkgvvt...edget..ikakavviatGt 150
                                    +++ve+++ +gv     +dg +  +kaka +iatG 
  gi|118431269|ref|NP_147621.2| 166 NIVVEDGEFRGVFAinpRDGDIylFKAKAGIIATGG 201
                                    566666666665431114444422688899****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 4357.04
//
Query:       gi|118431270|ref|NP_147622.2|  [L=143]
Description: glycine cleavage system protein H [Aeropyrum pernix K1]
Scores for complete 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  160.2   0.2    2.3e-47  159.9   0.2    1.1  1  GCV_H          Glycine cleavage H-protein
    8.7e-06   25.5   0.8    1.8e-05   24.5   0.5    1.7  2  Biotin_lipoyl  Biotin-requiring enzyme
    6.3e-05   22.9   0.0    9.7e-05   22.3   0.0    1.3  1  RnfC_N         RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9   0.2   3.8e-51   2.3e-47       1     120 [.      21     139 ..      21     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 3.8e-51
                                    -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGTT CS
                          GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNeklee 80 
                                    l+yt+++ew + e dgvatvGitdfaq+el d+v velpe+g kvkkge++a+vEs Ka++++yap+sGe+v+vNekl +
  gi|118431270|ref|NP_147622.2|  21 LRYTESDEWARLE-DGVATVGITDFAQKELKDIVGVELPEKGRKVKKGEAVATVESIKATADIYAPLSGEIVDVNEKLLD 99 
                                    69**********5.57**************************************************************** PP

                                    -TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHHH CS
                          GCV_H  81 epeliNkdpyeegWliklklsnleeleeLlsaeeyekllk 120
                                    +peliN+dpy+egW++k+k++++ e e+Ll+ e+y++ ++
  gi|118431270|ref|NP_147622.2| 100 QPELINDDPYGEGWIFKIKVEDPGEFESLLTPEQYVESVR 139
                                    ***********************************99886 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.5   2.9e-09   1.8e-05      22      57 ..      59      94 ..      50     100 .. 0.93
   2 ?   -3.6   0.0       1.8   1.1e+04      54      59 ..     115     120 ..     111     127 .. 0.53

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.9e-09
                                   STTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEES CS
                  Biotin_lipoyl 22 kvGdkVkagqvlaeveamKmemeieapkaGvvkeil 57
                                   ++G kVk+g+ +a+ve+ K++ +i ap +G ++++ 
  gi|118431270|ref|NP_147622.2| 59 EKGRKVKKGEAVATVESIKATADIYAPLSGEIVDVN 94
                                   78******************************9986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.8
                                    EEESST CS
                  Biotin_lipoyl  54 keilvk 59 
                                     +i+v+
  gi|118431270|ref|NP_147622.2| 115 FKIKVE 120
                                    444444 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 !   22.3   0.0   1.6e-08   9.7e-05      47      87 ..      59     100 ..      50     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-08
                         RnfC_N  47 kvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvah 87 
                                    ++g kV+kG+ +a+ e+   +a ++a+ sG+++++++ l  +
  gi|118431270|ref|NP_147622.2|  59 EKGRKVKKGEAVATVESiKATADIYAPLSGEIVDVNEKLLDQ 100
                                    799************9976799*************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1066.54
//
Query:       gi|118431271|ref|NP_147623.2|  [L=240]
Description: hexulose-6-phosphate synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-22   79.6   2.8    2.8e-22   79.4   2.8    1.0  1  OMPdecase       Orotidine 5'-phosphate decarboxylase / HUMPS 
      5e-05   22.9   0.3    8.9e-05   22.1   0.2    1.5  1  His_biosynth    Histidine biosynthesis protein
    0.00055   19.4   0.2     0.0055   16.1   0.2    2.1  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
     0.0024   17.2   0.1       0.17   11.1   0.0    2.4  2  PEP_hydrolase   Phosphoenolpyruvate hydrolase-like


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 !   79.4   2.8   6.3e-26   2.8e-22       3     224 ..      22     227 ..      20     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 6.3e-26
                                    EEEEE-SSSHHHHHHHHHHHGG.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT...SEEEEEEEE-S-HHHHHHHHHS CS
                      OMPdecase   3 LclalDvatarelleladkvgp.sivvlKthydlvegwgfegtgaklaalarkhg...flifeDrKfaDIGntvekqata 78 
                                    L++alD+++ +++++la ++g+   v l+++++l++++g      + +a++r      +++++D K+aD+ ++++ ++  
  gi|118431271|ref|NP_147623.2|  22 LQVALDYTSLWDAVSLASRIGArRGVALEVGTPLLKAHG----ARDSVAALRGVAgeeAPVVVDTKTADASDVEADIV-- 95 
                                    9**************************************....667777777775577********************.. PP

                                    TCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH..H.SHHHHHHHHHHHHHHHTTESEE CS
                      OMPdecase  79 gsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe..k.gytqacveaarehkaedfvmGf 155
                                        ++++ d++tv a+a++ ++k++aeaa + g   ++    +s    l+ ++  + g++  +++   + +++    G+
  gi|118431271|ref|NP_147623.2|  96 ----ASSGGDAFTVVAAAHDVTLKQAAEAAVQRG-VAVYGDLVVSRDPLLDARRvvDaGVHIVLLHLGLDVQRA---LGL 167
                                    ....699**************************7.9******************43245555555555555544...555 PP

                                    ECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                      OMPdecase 156 vaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                     a+++        d +  +   i++   ++++g++++++ +l++ aga+i+i+G +I++++dp  e+e+
  gi|118431271|ref|NP_147623.2| 168 TASSR-------VDLVRRIASEIDA-TIAVAGGVKPREAGALAS-AGASIVIIGGAITGSPDPGREVEK 227
                                    55555.......479*********9.****************99.99*******************998 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2     2e-08   8.9e-05      57     116 ..     168     226 ..     120     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-08
                                    THHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHH CS
                   His_biosynth  57 greanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikela 116
                                      +   dlv++ia+e+++++ v GG++  e + +l +aga+ viig a   +p+  +e+ 
  gi|118431271|ref|NP_147623.2| 168 TASSRVDLVRRIASEIDATIAVAGGVKPRE-AGALASAGASIVIIGGAITGSPDPGREVE 226
                                    4566789*********************99.***************99999888666655 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 ?    1.2   0.0     0.047   2.1e+02      98     120 ..      35      57 ..      23      68 .. 0.82
   2 !   16.1   0.2   1.2e-06    0.0055     151     197 ..     171     215 ..     109     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.047
                                    HHHHHHTTSEEEEEE-TT--GGG CS
                 Ribul_P_3_epim  98 iqeikeaGakaglvlnpatplea 120
                                    ++    +Ga+ g++l+  tpl  
  gi|118431271|ref|NP_147623.2|  35 VSLASRIGARRGVALEVGTPLLK 57 
                                    6677889*************965 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-06
                                    HHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                 Ribul_P_3_epim 151 ekikkvrklidekeldlkievDGGvkldnieqiaeagadvlVagsav 197
                                    +++  vr++++e   d +i v GGvk   + ++a+aga ++++g a+
  gi|118431271|ref|NP_147623.2| 171 SRVDLVRRIASE--IDATIAVAGGVKPREAGALASAGASIVIIGGAI 215
                                    567778888776..99****************************997 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   3.7e-05      0.17     161     204 ..     141     184 ..     132     191 .. 0.86
   2 !    4.1   0.0    0.0052        23     156     195 ..     192     231 ..     173     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.7e-05
                  PEP_hydrolase 161 earamaeaGadvivahlGlttggsigaktalsleeavelvqeia 204
                                    +ar++++aG+ ++ +hlGl  + ++g + ++ ++ + ++++ei 
  gi|118431271|ref|NP_147623.2| 141 DARRVVDAGVHIVLLHLGLDVQRALGLTASSRVDLVRRIASEID 184
                                    79************************999988887777666664 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0052
                  PEP_hydrolase 156 vfneeearamaeaGadvivahlGlttggsigaktalslee 195
                                     ++++ea a+a+aGa ++++   +t + + g + ++ le+
  gi|118431271|ref|NP_147623.2| 192 GVKPREAGALASAGASIVIIGGAITGSPDPGREVEKALES 231
                                    46789***************99999998888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1829.66
//
Query:       gi|14601098|ref|NP_147624.1|  [L=237]
Description: hypothetical protein APE_0954 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-38  132.9   0.0    1.7e-38  132.5   0.0    1.1  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 !  132.5   0.0   9.3e-43   1.7e-38      13     178 ..      17     167 ..       7     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 9.3e-43
                  Creatininase  13 keddvailPvGstEqHGphlplgtDtliaealaervaeklgak....alvlPtlpyGvseehlgfpGTislspetliavlr 89 
                                     +++ +lP+Gs+EqH   lpl+tD+l+aea a+ ++e l+ +    +l+lPt++yG s+e  g+pGT+sls +t   v+r
  gi|14601098|ref|NP_147624.1|  17 PGRALPVLPFGSVEQHC-SLPLATDALLAEAAARGACELLEREhgvaCLLLPTMYYGFSPEWAGYPGTLSLSLSTISGVVR 96 
                                   5667889**********.7****************9999976677779***********999******************* PP

                  Creatininase  90 dileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaaeeseeeegggHAgelE 170
                                   d+lesl  +Gf+r  ++ngHggn+++l+ aare+ +    ++v        +a+  +++          + ++ gH+g++E
  gi|14601098|ref|NP_147624.1|  97 DLLESLRSWGFDRAAIINGHGGNTSVLEAAAREASRSL-SMVVG-------VAS--YWAF--------LPAQDLGHGGDVE 159
                                   ************************************99.66543.......222..2221........233489******* PP

                  Creatininase 171 tSlmlalr 178
                                    Sl+ +l+
  gi|14601098|ref|NP_147624.1| 160 ASLLKHLA 167
                                   *****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1759.06
//
Query:       gi|118431272|ref|YP_874865.1|  [L=93]
Description: hypothetical protein APE_0954a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       203  (0.0113224); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 703.31
//
Query:       gi|14601099|ref|NP_147625.1|  [L=295]
Description: voltage-gated potassium channel [Aeropyrum pernix K1]
Scores for 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-18   64.9   5.1    8.7e-18   64.4   5.1    1.1  1  Ion_trans    Ion transport protein
      1e-17   63.8   5.3    2.8e-17   62.4   5.3    1.7  1  Ion_trans_2  Ion channel
  ------ inclusion threshold ------
        0.1   13.0   0.2        0.4   11.2   0.1    1.9  2  PRA-PH       Phosphoribosyl-ATP pyrophosphohydrolase
       0.12   12.5   0.2       0.24   11.6   0.2    1.3  1  DUF3008      Protein of unknwon function (DUF3008)
        5.2    6.6  11.3      0.044   13.3   1.5    2.3  3  BRI3BP       Negative regulator of p53/TP53


Domain annotation for each model (and alignments):
>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   5.1   2.4e-21   8.7e-18      60     240 ..      62     251 ..      36     253 .. 0.72

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 2.4e-21
                                   HHHHHHCHSHHHHHHHHHHHHHHHHH......HHHH..........................HHHHHHHHHHHHGGGGGGH CS
                     Ion_trans  60 likkrYlrdpwnilDflvvlpsllsl......vlse..........................esllllsvlrlfrvlrllk 108
                                   + +++Yl  +  ++D++ v++ ++++                                    ++l +l ++rl+r+lr+l+
  gi|14601099|ref|NP_147625.1|  62 QLSGEYLVRL-YLVDLILVIILWADYayraykS--GdpagyvkktlyeipalvpagllalieGHLAGLGLFRLVRLLRFLR 139
                                   2256677774.7778888888888775555440..1444455555666667777777777775555555555555555555 PP

                                   HHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHH CS
                     Ion_trans 109 lisrleglrtlvtalirsvkdllnvlllllvvlfifaligvqlfkgklreknecaktwenpnngntnFdnfftallwlfrl 189
                                   ++  +++ + ++ a+++++ ++  + l+ +v+l + + ++  +               e+p ++n++ +++f+al+w++++
  gi|14601099|ref|NP_147625.1| 140 ILLIISRGSKFLSAIADAADKIRFYHLFGAVMLTVLYGAFAIYI-------------VEYP-DPNSSIKSVFDALWWAVVT 206
                                   5555555555899*********8888877777777776664444.............3555.789999************* PP

                                   HTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Ion_trans 190 mttegwgdilyatldekskvaliyfvifiilgsflllNlliaviadnfqel 240
                                   +tt+g+gd+++at  +k      + +i ++l ++  l lli+ +++ fq++
  gi|14601099|ref|NP_147625.1| 207 ATTVGYGDVVPATPIGK------VIGIAVMLTGISALTLLIGTVSNMFQKI 251
                                   *****************......**************************86 PP

>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   5.3   7.9e-21   2.8e-17       3      78 ..     171     249 ..     165     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 7.9e-21
                                   HHHTCHHHHHHHHT.......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ion_trans_2   3 lllvlifgaviysl...eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78 
                                   +l+vl  +++iy++   + +++  s++dal++++vt tT+GYGd+vp t++g+++ i+++l+G++ ++l++ +++++++
  gi|14601099|ref|NP_147625.1| 171 MLTVLYGAFAIYIVeypDPNSSIKSVFDALWWAVVTATTVGYGDVVPATPIGKVIGIAVMLTGISALTLLIGTVSNMFQ 249
                                   455555666666668884445567**************************************************99987 PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   4.5e+03      52      65 ..     152     170 ..     145     173 .. 0.71
   2 ?   11.2   0.1   0.00011       0.4      14      47 ..     256     289 ..     246     293 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                   HHHHHH.....HHHHHHHH CS
                        PRA-PH  52 delaDl.....lYvtygll 65 
                                   +++aD      +Y++ g++
  gi|14601099|ref|NP_147625.1| 152 SAIADAadkirFYHLFGAV 170
                                   4555555556899999987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00011
                                   SS-----HHHHHHHHHHHHHHHHHHHHHT-SCHH CS
                        PRA-PH  14 etPeastaelaslraaligEEavElleaasegdl 47 
                                    +P+ s+a+la +++ + +EE++E++ + ++ ++
  gi|14601099|ref|NP_147625.1| 256 PEPSCSPAKLAEMVSSMSEEEFEEFVRTLKNLRR 289
                                   4688889999999**************9998765 PP

>> DUF3008  Protein of unknwon function (DUF3008)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   6.6e-05      0.24      32      49 ..     267     284 ..     262     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                       DUF3008  32 sMyesMsekeLeelAsTk 49 
                                   +M+ sMse+e ee+ +T 
  gi|14601099|ref|NP_147625.1| 267 EMVSSMSEEEFEEFVRTL 284
                                   8*************9985 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.8       2.4   8.7e+03     105     113 ..      67      75 ..      46      85 .. 0.41
   2 ?   13.3   1.5   1.2e-05     0.044      72     170 ..     107     202 ..      98     209 .. 0.88
   3 ?    1.2   0.3     0.062   2.2e+02     103     151 ..     199     248 ..     195     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.4
                        BRI3BP 105 wllkvvlfl 113
                                   +l+++ l  
  gi|14601099|ref|NP_147625.1|  67 YLVRLYLVD 75 
                                   344444444 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.2e-05
                        BRI3BP  72 vqalllwgllAllayWlLslllgllvallgrvlwllkvvlfllaflyilskeeaeaetaallLlglvavyvLlgslglyak 152
                                   + al+  gllAl+  +l  l l  lv ll r+l +l ++     fl  +++  ++   +   L g v++ vL g +++y++
  gi|14601099|ref|NP_147625.1| 107 IPALVPAGLLALIEGHLAGLGLFRLVRLL-RFLRILLIISRGSKFLSAIADAADK--IRFYHLFGAVMLTVLYGAFAIYIV 184
                                   56788889***********9999999999.9999999999999999999999888..99********************** PP

                        BRI3BP 153 sseesgasleakvrsLer 170
                                   + +++++s++   + L +
  gi|14601099|ref|NP_147625.1| 185 EYPDPNSSIKSVFDALWW 202
                                   **9999999887777755 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.062
                        BRI3BP 103 vlwllkvvlfllaflyilskee.aeaetaallLlglvavyvLlgslglya 151
                                   +lw++ v+  ++ ++ ++ +++ ++    a++L g+ a+ +L g ++ ++
  gi|14601099|ref|NP_147625.1| 199 ALWWAVVTATTVGYGDVVPATPiGKVIGIAVMLTGISALTLLIGTVSNMF 248
                                   68999999999999999988874556678999999999999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2324.42
//
Query:       gi|14601101|ref|NP_147627.1|  [L=261]
Description: hypothetical protein APE_0957 [Aeropyrum pernix K1]
Scores for 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-44  149.5   0.0    1.2e-43  149.1   0.0    1.1  1  NucS      Endonuclease NucS


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 !  149.1   0.0   6.5e-48   1.2e-43       3     213 ..      34     242 ..      32     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 6.5e-48
                          NucS   3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeLkve 83 
                                    ++vv   C+ +yeGr  s   eg++l+++kp Ga+++h  r   P+nWqp+ s+  +   dg l+lk  rr p+e Lk+ 
  gi|14601101|ref|NP_147627.1|  34 SMVVVAGVCSSEYEGRGASVSTEGDKLLIVKPGGAVILHGPRGFRPLNWQPSTSHTEVATADGLLTLKFYRRTPREVLKIA 114
                                   57888899************************************************************************* PP

                          NucS  84 ieevehasayeledveelvldGseaelaeliiehp.dLieeGfkpvareyavaiGivdiLgkdeegklvivelkrrkaevd 163
                                      + + +     ++  + +  +e +l + ++ hp +L++e  +  a e  +++G  d+ g de+g++vive+kr +a+ +
  gi|14601101|ref|NP_147627.1| 115 CGSIWYIAWVRFPEEGAFWMYMTEDDLRKAVALHPrELLGEDIRFFAEEKRTPSGKADLYGVDERGNIVIVEVKRVRADES 195
                                   ********************************99857******************************************** PP

                          NucS 164 aveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldp 213
                                   av+qL+ yv  +    +++kvrG+lvap+i   a++ll+ +glef+++d 
  gi|14601101|ref|NP_147627.1| 196 AVRQLEGYVRDYP---TQAKVRGILVAPDISDAARRLLESRGLEFRRVDL 242
                                   ********97765...4578***************************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2106.71
//
Query:       gi|118431273|ref|YP_874866.1|  [L=94]
Description: small nucleolar RNP protein Sm [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   65.9   0.2    2.3e-18   65.6   0.2    1.1  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.026   14.6   0.1    1.2  1  SM-ATX    Ataxin 2 SM domain
      0.092   11.9   0.0        0.1   11.8   0.0    1.0  1  DUF1615   Protein of unknown function (DUF1615)
        0.1   12.8   0.0       0.22   11.7   0.0    1.7  2  DUF150_C  RimP C-terminal SH3 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 !   65.6   0.2   5.1e-22   2.3e-18       2      66 ..      15      80 ..      14      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 5.1e-22
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET.EEEEEEEEEEEGGGEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk.ekrklglvliRGnnivlis 66
                                    lk+++n++++v+lk+g e++G+L++ D  mNl+L+d++e+ ++++  ++k+g+vli+G+ + +is
  gi|118431273|ref|YP_874866.1| 15 YLKEHLNSQIYVKLKDGSEYVGKLVATDTTMNLILDDAIEVADNGTrLVAKIGRVLIKGSMVEFIS 80
                                   79******************************************9999**************9997 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   5.9e-06     0.026      15      54 ..      23      59 ..      21      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-06
                                   EEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS... CS
                         SM-ATX 15 evevtvknGevyeGifstvslekdfsvvLkmarkvkkans 54
                                   ++ v++k+G+ y G + ++++   ++++L+ a +v++ n+
  gi|118431273|ref|YP_874866.1| 23 QIYVKLKDGSEYVGKLVATDT--TMNLILDDAIEVAD-NG 59
                                   5779*****************..*********99999.33 PP

>> DUF1615  Protein of unknown function (DUF1615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.3e-05       0.1      72     141 ..      20      87 ..       6      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                        DUF1615  72 veaalkkkspdGktykerldavrtekeldelyedliaevllgkklleelnpvttgGpmqvsvafAeehar 141
                                    ++ ++  k +dG  y  +l  v t+  ++ + +d i+ +  g++l++++  v  +G+m   ++f  + a 
  gi|118431273|ref|YP_874866.1|  20 LNSQIYVKLKDGSEYVGKL--VATDTTMNLILDDAIEVADNGTRLVAKIGRVLIKGSMVEFISFDASTAA 87 
                                    5666677888999999988..779999*******************************999999666554 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     5e-05      0.22       9      43 ..      18      49 ..      15      78 .. 0.82
   2 ?   -0.7   0.0      0.35   1.6e+03      24      36 ..      57      69 ..      52      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                       DUF150_C  9 rflGelVkvklklpvegrkkftGkivevdeet.itl 43
                                    +l+ ++ vklk    ++ +++Gk+v+ d ++ ++l
  gi|118431273|ref|YP_874866.1| 18 EHLNSQIYVKLK----DGSEYVGKLVATDTTMnLIL 49
                                   689999******....*************7764333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.35
                       DUF150_C 24 egrkkftGkivev 36
                                   +++ ++++ki +v
  gi|118431273|ref|YP_874866.1| 57 DNGTRLVAKIGRV 69
                                   6778888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 711.73
//
Query:       gi|14601102|ref|NP_147629.1|  [L=175]
Description: methylated-DNA-protein-cysteine methyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-26   90.3   0.0    9.5e-26   89.8   0.0    1.2  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
  ------ inclusion threshold ------
      0.077   12.8   0.0       0.13   12.0   0.0    1.4  1  HTH_38         Helix-turn-helix domain


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 !   89.8   0.0   1.1e-29   9.5e-26       6      81 .]      61     135 ..      58     135 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.1e-29
                                   HHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTT.TTCHHHHHHHHHHTTS CS
                 DNA_binding_1   6 VwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggy.agglerkralLeaEgv 81 
                                   V+ ll+ Ip+GkvttY+ +A++ g   ++raVg++la+np +i vPcHRVv++dg++ggy  gg + k+alL+ Egv
  gi|14601102|ref|NP_147629.1|  61 VYTLLHLIPPGKVTTYSSLARASG--LSPRAVGRILARNPSPIAVPCHRVVRSDGSIGGYsMGGPRVKAALLKLEGV 135
                                   9***********************..**********************************889************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05      0.13      17      37 ..      81     101 ..      77     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                        HTH_38  17 laeGlslreIArrLgrspsTI 37 
                                   +a Gls r+++r+L r+ps I
  gi|14601102|ref|NP_147629.1|  81 RASGLSPRAVGRILARNPSPI 101
                                   688***************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); 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 0.20s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1334.18
//
Query:       gi|14601103|ref|NP_147630.1|  [L=384]
Description: hypothetical protein APE_0960 [Aeropyrum pernix K1]
Scores for 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  135.0   0.0    1.1e-38  132.7   0.0    1.9  2  AAA              ATPase family associated with various cellul
    9.8e-14   50.9   0.0      3e-13   49.4   0.0    1.9  1  AAA_lid_3        AAA+ lid domain
    7.1e-09   35.5   0.0      1e-07   31.8   0.0    2.3  2  Vps4_C           Vps4 C terminal oligomerisation domain
    6.6e-07   29.7   0.0    0.00024   21.4   0.0    3.2  2  AAA_22           AAA domain
    7.5e-07   29.7   0.0    0.00039   20.9   0.0    2.7  2  AAA_16           AAA ATPase domain
    7.6e-07   29.2   0.0    1.2e-05   25.4   0.0    2.3  2  AAA_14           AAA domain
    1.1e-06   28.6   0.0    5.2e-05   23.3   0.0    2.7  1  AAA_5            AAA domain (dynein-related subfamily)
    2.1e-06   28.0   0.0    3.9e-06   27.1   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    2.5e-05   24.1   0.1    0.00021   21.1   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.4e-05   22.2   0.6      0.018   14.6   0.1    2.8  3  AAA_25           AAA domain
    0.00013   21.8   0.1    0.00088   19.1   0.1    2.2  1  AAA_24           AAA domain
    0.00013   22.0   2.6    0.00013   22.0   2.6    2.0  1  MIT              MIT (microtubule interacting and transport) 
    0.00015   21.1   0.0    0.00067   19.0   0.0    2.0  2  TIP49            TIP49 P-loop domain
    0.00095   19.1   0.1        1.7    8.5   0.0    2.6  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0011   19.3   0.0      0.008   16.5   0.0    2.4  2  RNA_helicase     RNA helicase
     0.0019   17.6   0.1     0.0049   16.3   0.0    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0022   18.5   0.1      0.018   15.6   0.1    2.6  2  AAA_18           AAA domain
     0.0022   17.4   0.1        1.5    8.1   0.1    2.6  2  ATPase           KaiC
     0.0056   16.4   0.0     0.0096   15.7   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0063   16.7   0.0      0.019   15.2   0.0    1.9  1  AAA_33           AAA domain
     0.0089   15.6   0.0      0.044   13.3   0.0    2.1  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.018   14.3   0.0       0.24   10.7   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.023   13.8   0.0      0.045   12.8   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.024   14.9   0.1       0.13   12.5   0.0    2.3  2  AAA_28           AAA domain
      0.027   14.2   0.0       0.11   12.2   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
      0.028   14.1   0.3      0.028   14.1   0.3    1.9  1  TPR_11           TPR repeat
      0.039   13.8   0.0      0.078   12.8   0.0    1.5  1  Bac_DnaA         Bacterial dnaA  protein
      0.048   13.6   0.0      0.088   12.7   0.0    1.5  1  NACHT            NACHT domain
      0.056   12.6   0.0       0.52    9.5   0.0    2.1  2  NB-ARC           NB-ARC domain
      0.057   12.7   0.0      0.096   11.9   0.0    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.082   12.8   0.0       0.16   11.9   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
      0.099   11.8   0.0       0.19   10.8   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
        0.1   12.4   1.2       0.15   11.9   0.4    1.7  1  DUF5113          Domain of unknown function (DUF5113)
       0.13   12.3   0.1       0.41   10.7   0.1    1.8  1  PTS_IIA          PTS system, Lactose/Cellobiose specific IIA 
       0.17   12.6   1.3       0.97   10.2   0.1    2.9  2  TPR_6            Tetratricopeptide repeat
       0.17   11.7   0.0       0.28   10.9   0.0    1.3  1  AAA_11           AAA domain
       0.39   10.9   3.8       0.74   10.1   0.4    2.7  2  TPR_2            Tetratricopeptide repeat
       0.82   10.0   4.3        2.4    8.6   0.2    3.1  2  TPR_8            Tetratricopeptide repeat
        1.8    8.5   5.3       0.41   10.6   1.3    2.1  2  TPR_1            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 !  132.7   0.0   2.3e-41   1.1e-38       1     132 []     148     282 ..     148     282 .. 0.96
   2 ?   -0.4   0.0       3.1   1.4e+03      38      74 ..     326     362 ..     310     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 2.3e-41
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgse 78 
                                   +llyGppGtGKT+la+ava+e++ efl +++++++sk++ge+ek++++lf+ a++ka   kp+++fiDE+dal +   gse
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFLYVDAANIMSKWLGEGEKNVKKLFNYARNKAkegKPVVIFIDEVDALLGVH-GSE 227
                                   69****************************************************9999*999************999.999 PP

                                   CHHHHHHHHHHHHHHHHTTTS...SSTEEEEEEESSGGGSTHHHHSTTSSEEEETTS CS
                           AAA  79 seeeervvnqLlteldgvkkk...eskvivigatnrpdkldpallrgRfdrkieiel 132
                                    + e rv nq+l+e+dg ++k    + v vi+atn+p+kld++++ +Rf+++i+++l
  gi|14601103|ref|NP_147630.1| 228 VGGEVRVRNQFLKEMDGIQDKgsrLH-VYVIAATNKPWKLDEPFI-RRFQKRIYVPL 282
                                   99******************977444.9*****************.7*******985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.1
                                   STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                           AAA  38 yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                   + ++ ++ +relf++ k   +p  + + ++ ++ ++r
  gi|14601103|ref|NP_147630.1| 326 VREAYMATVRELFEKGKVDGEPRPITMSDFQEILRRR 362
                                   4556678899999999888888999999999999998 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   6.5e-16     3e-13       1      45 []     304     357 ..     304     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 6.5e-16
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr........gike.itmedfee 45 
                                   dvdl++LAe+ eGy+G D+a ++reA ++++r+        g++  itm+df+e
  gi|14601103|ref|NP_147630.1| 304 DVDLDRLAEMLEGYTGSDIADIVREAYMATVRElfekgkvdGEPRpITMSDFQE 357
                                   9********************************8888777667767*****986 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0         1   4.6e+02      40      54 ..     106     120 ..     102     123 .. 0.81
   2 !   31.8   0.0   2.2e-10     1e-07      26      60 ..     346     381 ..     329     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1
                        Vps4_C  40 karptVskeDLekhe 54 
                                   k +p+V+ +D++ +e
  gi|14601103|ref|NP_147630.1| 106 KEKPSVTFDDIAGLE 120
                                   679999999998766 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2.2e-10
                        Vps4_C  26 eP.pvtlkDflkalkkarptVskeDLekheeFTkef 60 
                                   eP p+t++Df+++l++ rp+V +  L+ +ee+T+ f
  gi|14601103|ref|NP_147630.1| 346 EPrPITMSDFQEILRRRRPSVDHRLLKTYEEWTERF 381
                                   566******************************998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.2e-07   0.00024       8     103 ..     148     220 ..     145     260 .. 0.81
   2 ?    0.7   0.0       1.3   5.8e+02      42      78 ..     277     310 ..     257     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.2e-07
                        AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalra 88 
                                   ++++G++GtGKT+l+  ++++          + e+++v++++ +          +++  e+++   + + l+++ ++ +++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEI---------DGEFLYVDAANIM----------SKWLGEGEK---NVKKLFNYARNKAKE 206
                                   799******************9.........9999***999877..........333334445...888999999999999 PP

                        AAA_22  89 ravielliiDEaqhl 103
                                    +  +++ iDE++ l
  gi|14601103|ref|NP_147630.1| 207 GKP-VVIFIDEVDAL 220
                                   999.99999999996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.3
                        AAA_22  42 vvfvtlpsstsskdllrellralglelkaerlsseel 78 
                                    ++v lps +++k +l++  r+l l ++    ++++l
  gi|14601103|ref|NP_147630.1| 277 RIYVPLPSRETRKRMLEMYTRKLRLAGDV---DLDRL 310
                                   57999999999999999999999987766...44444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   8.4e-07   0.00039      24      55 ..     145     173 ..     117     186 .. 0.83
   2 ?    6.0   0.0     0.031        14     125     146 ..     199     219 ..     186     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.4e-07
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggif 55 
                                   p+ +ll+G++G+GK+ l+ ++++++ ++   f
  gi|14601103|ref|NP_147630.1| 145 PRGILLYGPPGTGKTMLASAVANEIDGE---F 173
                                   599********************99988...3 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                        AAA_16 125 rllallsrderplvlvlDdlqw 146
                                    + +++++ ++p+v+++D+++ 
  gi|14601103|ref|NP_147630.1| 199 YARNKAKE-GKPVVIFIDEVDA 219
                                   33355555.779*******995 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.75   3.5e+02      53      86 ..     101     129 ..      60     137 .. 0.73
   2 !   25.4   0.0   2.5e-08   1.2e-05       5     103 ..     148     262 ..     145     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.75
                        AAA_14  53 lelileklkeekktylflDEiqevpewekalksl 86 
                                   +e++l+     +k  + +D i  ++e++ka+++ 
  gi|14601103|ref|NP_147630.1| 101 PEFVLK-----EKPSVTFDDIAGLEEAKKAIREA 129
                                   344444.....567799*************9986 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 2.5e-08
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd....kkladpekllelileklkeekktylflDEiqev..... 76 
                                   +++ G+  +GKT+l+  +++e      ++ly++  +       + +++ +kl ++ ++k+ke k  ++f+DE+  +     
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEID---GEFLYVDAANIMSkwlgEGEKNVKKLFNYARNKAKEGKPVVIFIDEVDALlgvhg 225
                                   6899***********99997766...9*********9994444334455588999999977768889*********99999 PP

                        AAA_14  77 ..........pewekalkslvdegknldvivtGSnsk 103
                                             +++ k + ++ d+g++l+v+v    +k
  gi|14601103|ref|NP_147630.1| 226 sevggevrvrNQFLKEMDGIQDKGSRLHVYVIAATNK 262
                                   9999999999999999999999999999999876665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.1e-07   5.2e-05       2     138 .]     148     274 ..     147     274 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------......G-SEEEEESGGG CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar......egeilvlDEver 76 
                                   +lL GppGtgK++la  +a  +  e++yv     +++    g+ ++         ++l + ar      ++ ++++DEv+ 
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFLYVDAANIMSKWLGEGEKNV---------KKLFNYARnkakegKPVVIFIDEVDA 219
                                   89***************************98887776655555555.........33333333344455888999999995 PP

                                   --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                         AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                   +     +++      r   l e+++ +++ +  +l  ++via++n++     +l++++++Rf
  gi|14601103|ref|NP_147630.1| 220 LLGVHGSEVGGEVRVRNQFLKEMDGIQDKGS--RLH-VYVIAATNKPW----KLDEPFIRRF 274
                                   4433333333333333333333333333333..222.78888888877....7777777777 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   8.4e-09   3.9e-06       6     105 ..     148     244 ..     146     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 8.4e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKihpke 84 
                                   ill gp g+Gkt+la a+a+ ++     ++  +da +++     e e+ v++l   +    +  +  ++++DE+d      
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDG----EFLYVDAANIMSkwLGEGEKNVKKLFNYARNKAKEGKPVVIFIDEVDALLG-- 222
                                   7999******************95....9***********776788999*****9999999999999********8877.. PP

                                   --------H.HHHHHHHHHHH- CS
                         AAA_2  85 ssgadvSre.gVqrdLLqileg 105
                                     g++v +e  V + +L+ ++g
  gi|14601103|ref|NP_147630.1| 223 VHGSEVGGEvRVRNQFLKEMDG 244
                                   7777777765677777776665 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 !   21.1   0.0   4.6e-07   0.00021      36      65 ..     148     177 ..     111     222 .. 0.79
   2 ?   -0.4   0.0       1.8   8.4e+02       2      34 ..     235     267 ..     234     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.6e-07
                        RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkits 65 
                                   +llyGpPG Gkt la+ +a+e++ ++    
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFLYVD 177
                                   8*********************98875544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                        RuvB_N   2 rPksleeyigqekvkeklkifieaakkreeald 34 
                                   r + l+e  g ++  ++l++++ aa ++  +ld
  gi|14601103|ref|NP_147630.1| 235 RNQFLKEMDGIQDKGSRLHVYVIAATNKPWKLD 267
                                   667777777777777888888888877766666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     4e-05     0.018      36      54 ..     148     166 ..     119     172 .. 0.78
   2 ?    5.1   0.0     0.032        15     122     187 ..     189     258 ..     169     265 .. 0.74
   3 ?   -1.5   0.0       3.3   1.5e+03      84     111 ..     285     313 ..     252     344 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +ll+G+pgtGKt+la+ +a
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVA 166
                                   79*************9987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.032
                        AAA_25 122 ggtlltadvdaleaaieevegvrlvviDplsralgg.densnsdv...galvealeriarrtg.aavllvh 187
                                   g++ ++  ++  +++++e  +++++ iD ++++lg  +++   +v   +++++ ++ i+++    +v ++ 
  gi|14601103|ref|NP_147630.1| 189 GEKNVKKLFNYARNKAKE-GKPVVIFIDEVDALLGVhGSEVGGEVrvrNQFLKEMDGIQDKGSrLHVYVIA 258
                                   555567777778889999.88**************986666666555899999999998875446666665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.3
                        AAA_25  84 delrrRlravg.ealrddarllvldlagv 111
                                    e+r+R+ ++  ++lr+ +++++  la++
  gi|14601103|ref|NP_147630.1| 285 RETRKRMLEMYtRKLRLAGDVDLDRLAEM 313
                                   34666666665455566666665555544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.9e-06   0.00088       5      78 ..     148     221 ..     145     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-06
                        AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdieswedfldevvel..aaeladyktlviDtidele 78 
                                   il+yGp+g+GKT+la+        ++l++d  +    +  + ++   + +++++ +++   +a++ +  +++iD +d l 
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVaneiDGEFLYVDAAN---IMSKWLGE---GEKNVKKLFNYArnKAKEGKPVVIFIDEVDALL 221
                                   89***************9777777777777666...33333333...445566666666554445556688889888875 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 !   22.0   2.6   2.8e-07   0.00013       3      64 ..      10      72 ..       9      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.8e-07
                           MIT  3 kAlelvkkAveeDnagnyeeAlelYkealelLlqalke.kneerrellrekieeYleRaeeLk 64
                                  +A +++ +Av+++++g+ye+A+ +  +a+e+L++++++  +      +r+ i++Y  +++ L+
  gi|14601103|ref|NP_147630.1| 10 SAKKYALAAVDAEKRGDYEAAIVNLNKAIEYLTEIVRNyPDYPLAHIYRRLIAQYRRKVKDLE 72
                                  5889999******************************7699899***********99999997 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.5e-06   0.00067      51      97 ..     146     190 ..     106     212 .. 0.77
   2 ?   -0.1   0.0      0.91   4.2e+02     264     289 ..     194     219 ..     179     222 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.5e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                   r++Ll Gp+gtGkt la a+++e+     f  + ++++ s  +   e
  gi|14601103|ref|NP_147630.1| 146 RGILLYGPPGTGKTMLASAVANEID--GEFLYVDAANIMSKWLGEGE 190
                                   89**********************8..46888888888887665555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.91
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49 264 kkvakyveegkaeivpGvlfiDevhm 289
                                   kk+ +y  +   e  p v+fiDev  
  gi|14601103|ref|NP_147630.1| 194 KKLFNYARNKAKEGKPVVIFIDEVDA 219
                                   33445666666677789******975 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 !    7.8   0.0    0.0059       2.7      23      45 ..     148     170 ..     144     180 .. 0.80
   2 !    8.5   0.0    0.0036       1.7      97     135 ..     188     223 ..     174     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0059
                      ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                   +++YGp g GKt L   ++++ +
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEID 170
                                   689************99999874 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
                      ATPase_2  97 eksklvfkaielllekikkkgkk...iiiiiDelqklidlgl 135
                                   e  k+v+k ++++ +k    +k+   ++i+iDe+  l   g+
  gi|14601103|ref|NP_147630.1| 188 EGEKNVKKLFNYARNK----AKEgkpVVIFIDEVDALL--GV 223
                                   4455555555555554....4444449999***99887..55 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   1.7e-05     0.008       1      32 [.     148     184 ..     148     215 .. 0.72
   2 ?   -1.0   0.0       5.1   2.3e+03      81     106 ..     237     261 ..     232     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.....klkkkd 32 
                                   i+lyGp+g+GK++la  +a+++ +++      ++ ++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFlyvdaANIMSK 184
                                   789*******************999855555333333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.1
                  RNA_helicase  81 pyplnmasleekgtlftSkvvivtsN 106
                                   ++  +m+ +++kg     ++vi+ +N
  gi|14601103|ref|NP_147630.1| 237 QFLKEMDGIQDKGSRLH-VYVIAATN 261
                                   56668999999996554.78888888 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.1e-05    0.0049      25      43 ..     148     166 ..     143     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKtmla++++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVA 166
                                   89*************9875 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     0.018       1      33 [.     148     175 ..     148     293 .. 0.71
   2 ?   -0.9   0.0       4.9   2.2e+03      17      42 ..     309     336 ..     307     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-05
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvak 33 
                                   Ill G+pG+GKt la +++++       ++ ++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEI-----DGEFLY 175
                                   99****************9983.....222222 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.9
                        AAA_18  17 eLskrl.gf.gvnlrdvakenglllevd 42 
                                   +L+++l g+ g  + d+++e ++ + ++
  gi|14601103|ref|NP_147630.1| 309 RLAEMLeGYtGSDIADIVREAYMATVRE 336
                                   6888888889999999999988876554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0032       1.5      21      37 ..     147     163 ..     138     168 .. 0.86
   2 ?    6.4   0.0     0.011       4.9      80     154 ..     170     242 ..     165     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0032
                        ATPase  21 vvlitGepGtGKtifal 37 
                                    +l++G pGtGKt++a 
  gi|14601103|ref|NP_147630.1| 147 GILLYGPPGTGKTMLAS 163
                                   589***********986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
                        ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                    g++ ++da++ +++    ++++++++l +  ++  ke k   + iD +++l    + +++  ++r   ++lk++
  gi|14601103|ref|NP_147630.1| 170 DGEFLYVDAANIMSKWL-GEGEKNVKKLFNYARNKAKEGKPVVIFIDEVDAL-LGVHGSEVGGEVRVRNQFLKEM 242
                                   57889999999987744.499******************************9.6666666666666666666665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.1e-05    0.0096      49      71 ..     147     169 ..     142     221 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.1e-05
                     IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                   +i+l Gp+G+GK+ la a++ e 
  gi|14601103|ref|NP_147630.1| 147 GILLYGPPGTGKTMLASAVANEI 169
                                   689***************98763 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     4e-05     0.019       2      33 ..     148     181 ..     148     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                        AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdt..l 33 
                                   +ll G+pG+GK+ la  ++++ ++++l  d+  +
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFLYVDAanI 181
                                   6789***************999988888887432 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 !   13.3   0.0   9.6e-05     0.044      36      71 ..     148     183 ..     145     220 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                         AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsa 71 
                                   +ll+Gp GtGKt++++ + +++d e + +   n+ +
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFLYVDAANIMS 183
                                   89********************96655555555444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00052      0.24      16      51 ..     145     178 ..     140     183 .. 0.87
   2 ?    0.8   0.0      0.54   2.5e+02     108     133 ..     236     261 ..     230     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                    Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                   P  ill G pG GK+ la+++++e+  +g+++ +d+
  gi|14601103|ref|NP_147630.1| 145 PRGILLYGPPGTGKTMLASAVANEI--DGEFLYVDA 178
                                   67799*******************9..788877775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.54
                    Zeta_toxin 108 dvvkklaealkkaGYevevvvvavkk 133
                                    ++ k ++ ++++G +++v+v+a+ +
  gi|14601103|ref|NP_147630.1| 236 NQFLKEMDGIQDKGSRLHVYVIAATN 261
                                   567788999*************9865 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-05     0.045     117     139 ..     148     170 ..     145     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakavp 139
                                   +++yGp+ tGkt+la+a a+ ++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEID 170
                                   899***************99764 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       5.9   2.7e+03     100     147 ..      16      66 ..       4      73 .. 0.66
   2 ?   12.5   0.0   0.00029      0.13       2      23 ..     148     171 ..     147     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.9
                        AAA_28 100 lea..aarekrydl.vfllppapeidddgeRredleereaiderlrealre 147
                                   l a  a+++  y + ++ l+ a e+ +  +R   +   + i++rl++ +r+
  gi|14601103|ref|NP_147630.1|  16 LAAvdAEKRGDYEAaIVNLNKAIEYLTEIVRNYPDYPLAHIYRRLIAQYRR 66 
                                   333336667778887888888887767777776555577788888877775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00029
                        AAA_28   2 ivitGgestGKTtlleaLaar..g 23 
                                   i + G+++tGKT l++a a++  g
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEidG 171
                                   7899**************987653 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00025      0.11      25      64 ..     148     184 ..     142     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00025
                                   EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TT CS
               Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipee 64 
                                   +l+ G  GtGK++la+a+ ++    +++f+ v+ a+i ++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEI---DGEFLYVDAANIMSK 184
                                   89***************98765...488999999988655 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3     6e-05     0.028       6      23 ..      23      40 ..      23      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                        TPR_11  6 eqGkyeeAieaYkkAlkl 23
                                  ++G+ye+Ai +++kA+++
  gi|14601103|ref|NP_147630.1| 23 KRGDYEAAIVNLNKAIEY 40
                                  59**************95 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00017     0.078      37     180 ..     148     300 ..     145     341 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHH.....HHHHTT-SEEEEE-GGGG... CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeef.....keklrkvDvLliDDiqfl... 109
                                   +++yg+ G Gkt L  a++ne+  ++     +Y+ a + +++ +   +++ ++ f     k k  k  v+ iD++  l   
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEF-----LYVDAANIMSKWLGEGEKNVKKLFnyarnKAKEGKPVVIFIDEVDALlgv 223
                                   79******************997664.....55555555555544433332222211100222223345555555555111 PP

                                   .....TT-HHHHHHHHHHHHHHHTTT-EE...EEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHH.HHHHHHHHH CS
                      Bac_DnaA 110 .....agkektqeelfhtfnalleegkqv...vlssDrsPkeleeledrlrsrfeaGlvvdieppdletr.lailkkkie 180
                                         g  ++++++++ ++ + ++g ++   v+++  +P++   l++ +  rf+  + v +   ++  r l++  +k++
  gi|14601103|ref|NP_147630.1| 224 hgsevGGEVRVRNQFLKEMDGIQDKGSRLhvyVIAATNKPWK---LDEPFIRRFQKRIYVPLPSRETRKRmLEMYTRKLR 300
                                   111105566789999999999999999875557788888886...57788888888877776544443331244445554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00019     0.088       3      25 ..     148     170 ..     146     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                         NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                   ++l G++G GKT+L+  +a ++ 
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEID 170
                                   799**************998875 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0011      0.52      23      48 ..     148     170 ..     145     179 .. 0.86
   2 ?    0.4   0.0      0.64     3e+02     120     147 ..     277     305 ..     271     313 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                   EEEEESTTSSHHHHHHHHCCSHCCCC CS
                        NB-ARC  23 valvGmgGvGKttlakqilnksdeve 48 
                                   + l+G +G GKt la+ + n+   ++
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANE---ID 170
                                   579***************998...44 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.64
                                   ....HHHHCHTTSEEE.EEESBCCCCCCS CS
                        NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanav 147
                                   +i+v+lp+re r r+l + TR+  +a+ v
  gi|14601103|ref|NP_147630.1| 277 RIYVPLPSRETRKRMLeMYTRKLRLAGDV 305
                                   799***********997889988877765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021     0.096       4      26 ..     148     175 ..     145     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                       DUF2075   4 vlVtGvaGtGKtvvllnllael.....e 26 
                                   +l  G +GtGKt++++++++e+      
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIdgeflY 175
                                   6789*****************9554442 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00034      0.16       2      30 ..     148     176 ..     147     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00034
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   +ll g PG++kt+l++a+a+ +d ef  +
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEIDGEFLYV 176
                                   7999*******************999766 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00042      0.19      22      83 ..     108     175 ..      97     218 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                        DUF815  22 vdevklddLvgidkqkealventeqfleglp......annvLLwGarGtGKSslvkallneyaeegLr 83 
                                     +v++dd+ g+++ k+a+ e +   ++          + +LL+G  GtGK  l  a+ ne+  e L 
  gi|14601103|ref|NP_147630.1| 108 KPSVTFDDIAGLEEAKKAIREAIVFPVKRPDlfplgwPRGILLYGPPGTGKTMLASAVANEIDGEFLY 175
                                   5567888888888888888877765444332111222478*********************9998864 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00032      0.15       7      49 ..      10      52 ..       6      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                       DUF5113  7 iandYanlayylnvegeyeeALeyldsaleylNahyekYakkk 49
                                   a++Ya +a  +  +g+ye A+  l++a+eyl +  ++Y +  
  gi|14601103|ref|NP_147630.1| 10 SAKKYALAAVDAEKRGDYEAAIVNLNKAIEYLTEIVRNYPDYP 52
                                  5899****************************99999997665 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00089      0.41      11      45 ..       9      43 ..       6      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00089
                       PTS_IIA 11 GeArslameAlkaakegdfeeaeellkeAeeelke 45
                                  G+A+++a+ A++a k+gd+e+a  +l++A e l+e
  gi|14601103|ref|NP_147630.1|  9 GSAKKYALAAVDAEKRGDYEAAIVNLNKAIEYLTE 43
                                  9****************************998875 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0021      0.97      16      32 ..      34      50 ..      14      51 .. 0.91
   2 ?   -1.2   0.1       9.1   4.2e+03      22      30 ..      56      64 ..      54      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0021
                                  HHHHHHHHHHHHHH-TT CS
                         TPR_6 16 tdkAlealerlikeYPd 32
                                    kA+e+l +++++YPd
  gi|14601103|ref|NP_147630.1| 34 LNKAIEYLTEIVRNYPD 50
                                  569*************9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 9.1
                                  HHHHHHHH- CS
                         TPR_6 22 alerlikeY 30
                                  +++rli +Y
  gi|14601103|ref|NP_147630.1| 56 IYRRLIAQY 64
                                  79****999 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00061      0.28      20      42 ..     148     170 ..     123     211 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00061
                        AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                    l+ GPPGtgKT    ++ +++ 
  gi|14601103|ref|NP_147630.1| 148 ILLYGPPGTGKTMLASAVANEID 170
                                   5899********99998888874 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4    0.0016      0.74       4      30 ..      14      40 ..      11      50 .. 0.88
   2 ?    0.8   0.2       1.5   6.7e+02      18      28 ..     120     130 ..     119     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                         TPR_2  4 lynlGlayyklgdyeeAleafekAlel 30
                                  +   +  ++k+gdye A+  ++kA+e+
  gi|14601103|ref|NP_147630.1| 14 YALAAVDAEKRGDYEAAIVNLNKAIEY 40
                                  666788899****************96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.5
                         TPR_2  18 eeAleafekAl 28 
                                   eeA++a ++A+
  gi|14601103|ref|NP_147630.1| 120 EEAKKAIREAI 130
                                   8********97 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0051       2.4      13      29 ..      23      39 ..      14      40 .. 0.90
   2 ?    1.3   0.4       1.1   5.2e+02      17      28 ..     119     130 ..     119     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0051
                                  HTT-HHHHHHHHHHHHH CS
                         TPR_8 13 klgdyeeAkeyyekale 29
                                  k gdye+A+  ++ka+e
  gi|14601103|ref|NP_147630.1| 23 KRGDYEAAIVNLNKAIE 39
                                  77**************8 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHH CS
                         TPR_8  17 yeeAkeyyekal 28 
                                   +eeAk+++++a+
  gi|14601103|ref|NP_147630.1| 119 LEEAKKAIREAI 130
                                   59********97 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00089      0.41      12      29 ..      22      39 ..      11      41 .. 0.89
   2 ?   -1.9   0.1       7.4   3.4e+03      18      28 ..     120     130 ..     119     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00089
                                  HHTT-HHHHHHHHHHHHH CS
                         TPR_1 12 fklgkydeAleyyekALe 29
                                   k g+y+ A+   +kA+e
  gi|14601103|ref|NP_147630.1| 22 EKRGDYEAAIVNLNKAIE 39
                                  799**************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.4
                                   HHHHHHHHHHH CS
                         TPR_1  18 deAleyyekAL 28 
                                   +eA ++ ++A+
  gi|14601103|ref|NP_147630.1| 120 EEAKKAIREAI 130
                                   89999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 2555.99
//
Query:       gi|118431274|ref|YP_874867.1|  [L=271]
Description: hypothetical protein APE_0962 [Aeropyrum pernix K1]
Scores for 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-06   25.7   0.5     0.0002   21.2   0.1    3.0  3  MarR_2          MarR family
    0.00014   21.4   0.2    0.00036   20.1   0.2    1.7  1  GntR            Bacterial regulatory proteins, gntR family
    0.00023   21.0   0.3    0.00067   19.5   0.1    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00096   19.5   1.3     0.0035   17.7   0.2    2.5  3  Rrf2            Transcriptional regulator
     0.0011   19.1   0.1     0.0025   18.0   0.1    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0031   18.0   0.4     0.0092   16.5   0.1    2.0  2  HTH_27          Winged helix DNA-binding domain
     0.0072   17.0   0.0       0.52   11.0   0.0    2.4  2  RPA_C           Replication protein A C terminal
     0.0088   16.0   0.1      0.021   14.8   0.1    1.7  1  HTH_36          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.6   0.1      0.043   13.6   0.1    2.2  1  IF2_N           Translation initiation factor IF-2, N-termina
      0.011   15.9   0.1      0.032   14.4   0.1    1.8  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.011   15.5   1.2       0.26   11.1   0.1    2.9  3  UBA_3           Fungal ubiquitin-associated domain
      0.012   15.3   0.2      0.047   13.5   0.1    2.1  2  LexA_DNA_bind   LexA DNA binding domain
      0.019   14.5   0.0      0.035   13.7   0.0    1.3  1  DDRGK           DDRGK domain
      0.021   14.8   1.8      0.044   13.8   0.2    2.3  2  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.038   13.9   0.1        0.1   12.5   0.1    1.7  1  MarR            MarR family
      0.044   13.8   0.1       0.48   10.5   0.1    2.5  2  z-alpha         Adenosine deaminase z-alpha domain
      0.044   13.4   0.4      0.044   13.4   0.4    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.061   13.2   0.1       0.14   12.1   0.1    1.6  1  RuvB_C          RuvB C-terminal winged helix domain
      0.066   12.8   0.8       0.16   11.5   0.8    1.6  1  HTH_CodY        CodY helix-turn-helix domain
      0.075   12.9   0.0       0.21   11.4   0.0    1.8  1  HTH_10          HTH DNA binding domain
      0.098   12.9   0.2      0.098   12.9   0.2    2.4  2  PaaX            PaaX-like protein


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 ?    0.8   0.0      0.52   4.5e+02      25      38 ..      34      47 ..      20      49 .. 0.79
   2 ?   -2.4   0.0       5.4   4.6e+03      22      31 ..     137     146 ..     126     148 .. 0.68
   3 !   21.2   0.1   2.3e-07    0.0002      14      57 ..     224     266 ..     220     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.52
                                   HHHHHHHTSSHHHH CS
                         MarR_2 25 gelarrlglsksav 38
                                    e+ +rl+l+k  v
  gi|118431274|ref|YP_874867.1| 34 DEILARLQLTKTEV 47
                                   699*******9765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.4
                                    EEHHHHHHHH CS
                         MarR_2  22 ltvgelarrl 31 
                                     t  e+a+rl
  gi|118431274|ref|YP_874867.1| 137 ATSPEIAARL 146
                                    5888999997 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 2.3e-07
                                    HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                         MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57 
                                    + r++g  ++++ +a++lg++k  + + l+rL+++GL++  +g 
  gi|118431274|ref|YP_874867.1| 224 VKRSGGV-VRISKIAAELGVEKEDIIKSLRRLQQKGLIRIASGR 266
                                    6788885.7*****************************987665 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   4.2e-07   0.00036       8      60 ..     215     266 ..     213     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.2e-07
                                    HHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                           GntR   8 rLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                     +++++ + + r G    + +++aae+gV +  + ++LrrL+++gl+ + +gr
  gi|118431274|ref|YP_874867.1| 215 DIDQKVYEYVKRSGGVV-RISKIAAELGVEKEDIIKSLRRLQQKGLIRIASGR 266
                                    56777777777889999.99****************************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.7   7.5e+03       3      12 ..      39      48 ..      33      65 .. 0.58
   2 !   19.5   0.1   7.9e-07   0.00067      10      58 ..     217     266 ..     214     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.7
                                   HCHHHHHCCC CS
                           TrmB  3 klGLseyEak 12
                                    l L+++E++
  gi|118431274|ref|YP_874867.1| 39 RLQLTKTEVD 48
                                   3444555444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.9e-07
                                    CCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB  10 EakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                    + kvY ++  + g  ++++ia elgv++  + ++Lr+L +kGl+++  gr
  gi|118431274|ref|YP_874867.1| 217 DQKVYEYVKrSGGVVRISKIAAELGVEKEDIIKSLRRLQQKGLIRIASGR 266
                                    66778777756678899***************************998776 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.9   5.9e+03      50      64 ..       7      21 ..       2      23 .. 0.82
   2 ?   -1.4   0.0       3.7   3.2e+03      25      36 ..     136     147 ..     109     159 .. 0.64
   3 !   17.7   0.2   4.1e-06    0.0035      22      62 ..     227     267 ..     220     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.9
                                   HHTTSEEEETTT-TC CS
                           Rrf2 50 rkaglvksvrGkgGG 64
                                   rk g++    G++ G
  gi|118431274|ref|YP_874867.1|  7 RKLGIISWSPGAKAG 21
                                   789999999999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.7
                                    -B-HHHHHHHHT CS
                           Rrf2  25 pvsseeiaerqn 36 
                                     ++s eia+r  
  gi|118431274|ref|YP_874867.1| 136 AATSPEIAARLT 147
                                    366677776654 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4.1e-06
                                    TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                           Rrf2  22 eeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62 
                                    +++ v++++ia++ +++++ + k l++L+++gl++   G++
  gi|118431274|ref|YP_874867.1| 227 SGGVVRISKIAAELGVEKEDIIKSLRRLQQKGLIRIASGRE 267
                                    44569********************************9986 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   2.9e-06    0.0025      13      54 ..     220     262 ..     218     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.9e-06
                                    HHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                 Fe_dep_repress  13 IYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyvey 54 
                                    +Y+  + +++vv+ +++a +L+v++  + ++l++L+++G++  
  gi|118431274|ref|YP_874867.1| 220 VYEYVKrSGGVVRISKIAAELGVEKEDIIKSLRRLQQKGLIRI 262
                                    78888889*******************************9875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.8     5e+03       5      28 ..     160     188 ..     156     199 .. 0.50
   2 !   16.5   0.1   1.1e-05    0.0092      14      62 ..     226     270 ..     220     271 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                         HTH_27   5 qalvLhlir.....hrrrrkkladlcgrl 28 
                                     al++++i       + ++ ++++++++l
  gi|118431274|ref|YP_874867.1| 160 TALTVNNIPvpaatVEIDPEIKREIRRVL 188
                                    56666666622222234444445555544 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-05
                         HTH_27  14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrv 62 
                                    + ++ ++++ ++  l ve+  i++sl++L  kGL+      a++re ++
  gi|118431274|ref|YP_874867.1| 226 RSGGVVRISKIAAELGVEKEDIIKSLRRLQQKGLI----RIASGREATH 270
                                    55667899***************************....3356677665 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 ?    3.5   0.0      0.13   1.1e+02      64      85 ..      27      48 ..      22      56 .. 0.84
   2 !   11.0   0.0   0.00061      0.52      49      97 ..     215     260 ..     179     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.13
                                   STTTEEHHHHHHHSTSXHHHHH CS
                          RPA_C 64 seeGvhvdeiaqklrlsvndvk 85
                                   +eeGv  dei ++l+l + +v 
  gi|118431274|ref|YP_874867.1| 27 GEEGVDYDEILARLQLTKTEVD 48
                                   79************88887775 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00061
                                    HHHHHHHHHHHH.SXSTTT.EEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                          RPA_C  49 alaqqvlnlikqspeseeG.vhvdeiaqklrlsvndvkqavdeLsneGii 97 
                                    + +q v++++k+      G v ++ ia++l+++++d+ + ++ L+++G+i
  gi|118431274|ref|YP_874867.1| 215 DIDQKVYEYVKR----SGGvVRISKIAAELGVEKEDIIKSLRRLQQKGLI 260
                                    567777888777....334279**************************98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.5e-05     0.021      28      55 .]     233     260 ..     220     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                         HTH_36  28 qetlakrlglsknTvsraikeLeqlGyi 55 
                                     + +a+ lg+ k+ +++ ++ L q+G+i
  gi|118431274|ref|YP_874867.1| 233 ISKIAAELGVEKEDIIKSLRRLQQKGLI 260
                                    689***********************98 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 ?   13.6   0.1     5e-05     0.043       4      24 ..     231     251 ..     229     271 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                          IF2_N   4 irVyeLAkeLgvkskevikkL 24 
                                    +r++ +A eLgv+ +++ik L
  gi|118431274|ref|YP_874867.1| 231 VRISKIAAELGVEKEDIIKSL 251
                                    7******************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 ?   14.4   0.1   3.7e-05     0.032       5      38 ..     222     260 ..     218     261 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                        AbiEi_4   5 elasrqvGlfttrelea.aGispsa....lrrLvrkGwL 38 
                                    e + r++G+++ + ++a +G+        lrrL +kG++
  gi|118431274|ref|YP_874867.1| 222 EYVKRSGGVVRISKIAAeLGVEKEDiiksLRRLQQKGLI 260
                                    6678999****************99************98 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.32   2.8e+02      26      41 ..       2      17 ..       1      22 [. 0.84
   2 ?   -1.5   0.1       2.7   2.3e+03      28      52 ..      35      57 ..      34      58 .. 0.72
   3 ?   11.1   0.1   0.00031      0.26      19      38 ..     240     259 ..     235     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.32
                                   HHHHHHHS--SS--SS CS
                          UBA_3 26 vievLkrLgiksldpe 41
                                   vi++ ++Lgi s +p 
  gi|118431274|ref|YP_874867.1|  2 VIDIVRKLGIISWSPG 17
                                   89********887765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                                   HHHHHS--SS--SS--HHHHHHHHH CS
                          UBA_3 28 evLkrLgiksldpednetankileE 52
                                   e+L rL++ +   e +  +n++l E
  gi|118431274|ref|YP_874867.1| 35 EILARLQLTK--TEVDSMKNIVLAE 57
                                   6788999988..4456667888776 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00031
                                    HT--HHHHHHHHHHS--SS- CS
                          UBA_3  19 qGFekdkvievLkrLgiksl 38 
                                     G ek+ +i+ L+rL+ k+l
  gi|118431274|ref|YP_874867.1| 240 LGVEKEDIIKSLRRLQQKGL 259
                                    699*************9986 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 ?   -2.7   0.0       6.3   5.4e+03      52      61 ..       8      17 ..       4      19 .. 0.64
   2 ?   13.5   0.1   5.5e-05     0.047      27      62 ..     232     266 ..     218     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.3
                                   HTTSEE-GGG CS
                  LexA_DNA_bind 52 rKGyierdpg 61
                                   + G+i + pg
  gi|118431274|ref|YP_874867.1|  8 KLGIISWSPG 17
                                   4477777777 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.5e-05
                                    -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                  LexA_DNA_bind  27 sireiaralglkSpsaveehLkaLerKGyierdpgk 62 
                                     i  ia +lg++  + + + L++L++KG+i++ +g+
  gi|118431274|ref|YP_874867.1| 232 RISKIAAELGVE-KEDIIKSLRRLQQKGLIRIASGR 266
                                    5788999***99.8899999************9987 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.2e-05     0.035     100     143 ..     216     260 ..     209     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.2e-05
                                    HHHHHHHHHHH-.SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                          DDRGK 100 lleefinyikek.KvvlleelavkfklktqevierikeLeeqgsl 143
                                    + +++ +y+k +  vv +  +a++++++ +++i+ ++ L+++g +
  gi|118431274|ref|YP_874867.1| 216 IDQKVYEYVKRSgGVVRISKIAAELGVEKEDIIKSLRRLQQKGLI 260
                                    567889999987369**************************9987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       2.3   1.9e+03      20      42 ..     135     157 ..     113     159 .. 0.70
   2 ?   13.8   0.2   5.1e-05     0.044      26      53 ..     235     263 ..     226     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                                    EEHHHHHHHHHTTSSHHHHHHHH CS
                      HTH_Crp_2  20 lpltqeelAsmlGltretvsril 42 
                                    l  t  e+A++l +  +++ r+ 
  gi|118431274|ref|YP_874867.1| 135 LAATSPEIAARLTSIVQSTERVV 157
                                    66777789999988888888876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.1e-05
                                    HHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                      HTH_Crp_2  26 elAsmlGltretvsrilseLkreglis.r 53 
                                     +A+ lG+  e + + l++L+++gli+  
  gi|118431274|ref|YP_874867.1| 235 KIAAELGVEKEDIIKSLRRLQQKGLIRiA 263
                                    69************************952 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012       0.1      18      48 ..     231     261 ..     224     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                    EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  18 lsvseLakklgvskstvtrvldrLekkGlie 48 
                                     ++s++a  lgv+k  + + l+rL +kGli+
  gi|118431274|ref|YP_874867.1| 231 VRISKIAAELGVEKEDIIKSLRRLQQKGLIR 261
                                    789**************************97 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 ?   -0.3   0.0       1.3   1.1e+03      35      47 ..     181     193 ..     168     198 .. 0.76
   2 ?   10.5   0.1   0.00056      0.48       4      51 ..     215     260 ..     213     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHH CS
                        z-alpha  35 kreiNrvLydler 47 
                                    krei rvL +  +
  gi|118431274|ref|YP_874867.1| 181 KREIRRVLSEVSK 193
                                    8999999977655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00056
                                    HHHHHHHHHHHHC-TTCECCHHHH.HHHHCC-HHHHHHHHHHHHHTTSE CS
                        z-alpha   4 eqaekilelLeelgekkaatalal.ergLstpkreiNrvLydlerkgkv 51 
                                    ++ +k+ e+++ +g   ++  + + + +L+ +k +i + L +l++kg +
  gi|118431274|ref|YP_874867.1| 215 DIDQKVYEYVKRSG---GVVRISKiAAELGVEKEDIIKSLRRLQQKGLI 260
                                    789***********...444444426677777*************9965 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.1   5.2e+03       5      12 ..      87      94 ..      86      95 .. 0.79
   2 ?   13.4   0.4   5.1e-05     0.044       2      48 .]     214     261 ..     213     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.1
                         HTH_24  5 drkILelL 12
                                   +++IL++L
  gi|118431274|ref|YP_874867.1| 87 KKRILKAL 94
                                   58999998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.1e-05
                         HTH_24   2 detdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    d++d k++e++++ ++   ++ +A +lg+ +  + + l+rL+++GlI+
  gi|118431274|ref|YP_874867.1| 214 DDIDQKVYEYVKRSGGvVRISKIAAELGVEKEDIIKSLRRLQQKGLIR 261
                                    99***********9999******************************7 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 ?   12.1   0.1   0.00016      0.14       5      65 ..     214     270 ..     211     271 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                    -HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-H CS
                         RuvB_C   5 deldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTk 65 
                                    d++d+k+ + +k+  +gg v+++ +aa lg+eke i++     L ++glI r   GR++T+
  gi|118431274|ref|YP_874867.1| 214 DDIDQKVYEYVKR--SGGVVRISKIAAELGVEKEDIIKSL-RRLQQKGLI-RIASGREATH 270
                                    7899999999998..7*********************887.557777777.6677888885 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 ?   11.5   0.8   0.00019      0.16       3      35 ..     229     261 ..     227     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                       HTH_CodY   3 GrLtaskiaDriGitrsvivnaLrkLesaGiie 35 
                                    G +  skia ++G+ +  i+ +Lr+L   G+i 
  gi|118431274|ref|YP_874867.1| 229 GVVRISKIAAELGVEKEDIIKSLRRLQQKGLIR 261
                                    66678*************************996 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.21      24      50 ..     231     257 ..     221     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                         HTH_10  24 vtlkeLAkelGIskstlsehLrkaesk 50 
                                    v+++++A elG+ k ++ + Lr+ ++k
  gi|118431274|ref|YP_874867.1| 231 VRISKIAAELGVEKEDIIKSLRRLQQK 257
                                    6789*******************9998 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.6   1.3e+03      12      50 ..      75     111 ..      74     121 .. 0.78
   2 ?   12.9   0.2   0.00011     0.098       9      60 ..     220     266 ..     219     271 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                           PaaX  12 dyveprggaiwlgsLirllaelGiseslvRaalsRlaka 50 
                                    d+++ + ++i l++  r+l++l + ++l+  a+ R++ a
  gi|118431274|ref|YP_874867.1|  75 DALHIHAAEIVLKK--RILKALTMYSRLIELAIVRIQDA 111
                                    66777777777776..88999999999999999998765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                           PaaX   9 lygdyveprggaiwlgsLirllaelGiseslvRaalsRlakaGwlvrekegr 60 
                                    +y +yv+ +gg +++++   + aelG++ + +  +l Rl+++G+++  + gr
  gi|118431274|ref|YP_874867.1| 220 VY-EYVKRSGGVVRISK---IAAELGVEKEDIIKSLRRLQQKGLIR-IASGR 266
                                    57.9**********995...789********************875.44454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2075.14
//
Query:       gi|118431275|ref|NP_147631.2|  [L=289]
Description: hypothetical protein APE_0964.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-06   27.6   0.0    2.9e-06   27.1   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    4.9e-06   26.2   0.0    6.5e-06   25.8   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0002   22.0   0.0    0.00068   20.3   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    0.00023   21.8   0.0     0.0019   18.8   0.0    2.5  2  Methyltransf_11  Methyltransferase domain
    0.00065   19.6   0.0     0.0015   18.4   0.0    1.6  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
    0.00087   18.8   0.1     0.0012   18.4   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.037   14.0   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.041   13.2   0.0        1.6    8.0   0.0    2.3  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
       0.11   13.5   0.0       0.25   12.4   0.0    1.6  1  Methyltransf_24  Methyltransferase domain
       0.17   11.6   0.0       0.35   10.6   0.0    1.5  2  Met_10           Met-10+ like-protein
       0.17   11.5   0.0       0.26   10.9   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.21   11.4   0.0       0.39   10.5   0.0    1.4  2  Methyltransf_31  Methyltransferase domain


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 !   27.1   0.0   1.9e-09   2.9e-06      41     125 ..     136     220 ..     125     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.9e-09
                                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T.TTEEEEES-HHHHCTS--SS-EEEEEEE CS
                  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee.etaelkedaleallklakkkeefdivfl 119
                                    +g rvLD + G G  ++ A+ Rga+ ++ ve d+ ++++   n  + +l++ +++++  da+e ++     ++ fd    
  gi|118431275|ref|NP_147631.2| 136 RGFRVLDTCTGLGYTSIAAIARGASLVYTVEVDEIVLQLAALNPWSHRLRDkRIRIILGDAVEVVRDF--GDSAFDALIH 213
                                    5789**********************************888887777777768999999999999888..5679****** PP

                                    --S.SST CS
                  Cons_hypoth95 120 DPP.yak 125
                                    DPP + k
  gi|118431275|ref|NP_147631.2| 214 DPPrFSK 220
                                    ***4444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   4.4e-09   6.5e-06      20     136 ..     124     245 ..     111     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 4.4e-09
                                    HHHHHHH.CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTST. CS
                            MTS  20 sklLlet.lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleeve. 94 
                                    s+ L+++ l  ++  +vlD ++G G+ ++a+ ++  ++ v  v+vd   l++a  n  +++l+   ++++  d++e v  
  gi|118431275|ref|NP_147631.2| 124 SDALAKAsLVVKRGFRVLDTCTGLGYTSIAAIARGASL-VYTVEVDEIVLQLAALNPWSHRLRdkrIRIILGDAVEVVRd 202
                                    5555543245556778**************99988885.999**************999999989999998887765553 PP

                                    ..TS-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS  95 ..ekkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLl 136
                                      +  fd+++  PP  + k t+   + el +e +++L+ gG+L+
  gi|118431275|ref|NP_147631.2| 203 fgDSAFDALIHDPPRFS-KSTSSLYTLELYREFHRILRRGGRLF 245
                                    3389**********555.455788999***************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.7     7e+03      22      38 ..     115     131 ..     109     136 .. 0.80
   2 !   20.3   0.0   4.5e-07   0.00068       1      97 []     140     242 ..     140     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
                                    SEEEEEESSHHHHHHHH CS
                Methyltransf_25  22 akvtgvDiseemleaar 38 
                                    ++v g+D+ +++l++a 
  gi|118431275|ref|NP_147631.2| 115 HRVAGTDPWSDALAKAS 131
                                    68999999999998875 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.5e-07
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCGB..SSSTTTEEEEEEEST.G CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaedl..pfedgsfDlvvssga.l 74 
                                    vLd ++G G +++a+ +r g++ v+ v+++e  l+ a+ +  +++l   +++++ gda ++  +f d+ fD+ +     +
  gi|118431275|ref|NP_147631.2| 140 VLDTCTGLGYTSIAAIAR-GASLVYTVEVDEIVLQLAALNPWSHRLrdkRIRIILGDAVEVvrDFGDSAFDALIHDPPrF 218
                                    9***************99.68*****************77777666677*********8863469*******99955555 PP

                                    GG.SSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  75 hh.lsdedlekalkeiarvLkpgG 97 
                                    +  +s   + ++++e++r+L+ gG
  gi|118431275|ref|NP_147631.2| 219 SKsTSSLYTLELYREFHRILRRGG 242
                                    55455566789************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.8   4.2e+03      19      35 ..     115     131 ..     106     139 .. 0.73
   2 !   18.8   0.0   1.3e-06    0.0019       2      95 ..     142     245 ..     141     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                                    SEEEEEES-HHHHHHHH CS
                Methyltransf_11  19 arvvgvDlskemlklak 35 
                                    +rv g+D++  +l+ a+
  gi|118431275|ref|NP_147631.2| 115 HRVAGTDPWSDALAKAS 131
                                    68888888888887664 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.3e-06
                                    EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCT..SS-TT-EEEEEEES.....- CS
                Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl...kvefvvadaekl..pfednsfDlvvsse.....v 70 
                                    d  +G G+ + a   rg + v++v++++ +l+la  +    +l   +++++ +da ++   f d+ fD+ +        +
  gi|118431275|ref|NP_147631.2| 142 DTCTGLGYTSIAAIARGaSLVYTVEVDEIVLQLAALNPWSHRLrdkRIRIILGDAVEVvrDFGDSAFDALIHDPprfskS 221
                                    55567777777777888899**************7777666667778*********96578********99765543323 PP

                                    CCC-CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  71 lhhvedpekalkeiaRvLkpgGllv 95 
                                            ++ +e++R+L+ gG+l+
  gi|118431275|ref|NP_147631.2| 222 TSS-LYTLELYREFHRILRRGGRLF 245
                                    333.46789*************996 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 !   18.4   0.0   9.8e-07    0.0015      29      91 ..     185     249 ..     165     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.8e-07
                                    TTEEEEEEES-HHHHHHHC-.T-EEEEEE-S..S-TTTSGGGCSHHHHHHHHHHEEEEEEEEES-- CS
                Methyltransf_30  29 eevtlklligdarealkeld.ekadawFlDg..FsPaknPelwseellkelarllkkkgtlatyss 91 
                                     + ++++++gda e++       +da+ +D+  Fs +  + l++ el++e  r+l+ +g+l  y+ 
  gi|118431275|ref|NP_147631.2| 185 RDKRIRIILGDAVEVVRDFGdSAFDALIHDPprFS-KSTSSLYTLELYREFHRILRRGGRLFHYTG 249
                                    56789*************98899*******85566.55789***********************95 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   7.8e-07    0.0012     158     213 ..     133     189 ..     125     212 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.8e-07
                           PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.kl 213
                                    +vk+g +vlD  tG G  +iaa   ga+ v+ v +De+ ++ a+ N    ++++ ++
  gi|118431275|ref|NP_147631.2| 133 VVKRGFRVLDTCTGLGYTSIAAIARGASLVYTVEVDEIVLQLAALNPWSHRLRDkRI 189
                                    689999*************************************99977666666455 PP

>> Methyltransf_18  Methyltransferase 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     0.037       5      79 ..     127     201 ..     123     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                Methyltransf_18   5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagl.edkievrlsdGleklk 79 
                                    L++   +v++g rv+D +t  gy +i+++ +g a+ v+ +++ e  l+ a  n  +++l +++i+++l+d +e+++
  gi|118431275|ref|NP_147631.2| 127 LAKASLVVKRGFRVLDTCTGLGYTSIAAIARG-ASLVYTVEVDEIVLQLAALNPWSHRLrDKRIRIILGDAVEVVR 201
                                    667777899999*****************877.569*****************9999995669********99986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0011       1.6      35     149 ..     123     244 ..     110     249 .. 0.66
   2 ?    2.8   0.0     0.041        61     204     229 ..     263     288 ..     258     289 .] 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                    HHH.HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHH..HHHTSSTEEEEE--TTT-. CS
                Ubie_methyltran  35 Wkk.fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekkl..keegkinieflqanaeeL. 110
                                    W +   +    vkrg +vlD ++G g  ++  +  ++    v  ++++e +L+ +      ++   ++i+ + ++a e+ 
  gi|118431275|ref|NP_147631.2| 123 WSDaLAKASLVVKRGFRVLDTCTGLGYTSI--AAIARGASLVYTVEVDEIVLQLAALNPwsHRLRDKRIRIILGDAVEVv 200
                                    7773444456789************98765..455666667777777777777776554003334459999999999874 PP

                                    .TTS-T-EEEEEEE...S-GGG-S-HH.HHHHHHHHHEEEEEEE CS
                Ubie_methyltran 111 .pfeddsfDvvtvs...fGlrnvtDkl.kaLkeayrvlkpGGrl 149
                                     +f d +fD +      f     + ++ +  +e +r+l+ GGrl
  gi|118431275|ref|NP_147631.2| 201 rDFGDSAFDALIHDpprFSKSTSSLYTlELYREFHRILRRGGRL 244
                                    47889999987543222443333333313347777888888876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.041
                                    HHHHHHHTTEEEEEEEEEGGGTEEEE CS
                Ubie_methyltran 204 lkeliedaGfksveyesltgGvvaih 229
                                    ++ l+++aGf+   +++ + G+va+ 
  gi|118431275|ref|NP_147631.2| 263 VARLLREAGFEVLGFRRRALGLVAVK 288
                                    5789******************9985 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.25      14     100 ..     152     243 ..     141     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                Methyltransf_24  14 llralrrngagrlvavdhdpgaeeaaalare....agldd.rvrlikadseealaslaagsiDllfiDgghaaea..... 83 
                                    +++ +r  ga+ +++v+ d+    + +la+     + l+d r+r+i +d+ e+++++ ++ +D l+ D +   ++     
  gi|118431275|ref|NP_147631.2| 152 IAAIAR--GASLVYTVEVDE---IVLQLAALnpwsHRLRDkRIRIILGDAVEVVRDFGDSAFDALIHDPPRFSKStssly 226
                                    443333..334689999998...5555555344555665538**************************654433212222 PP

                Methyltransf_24  84 vledleallprlapggv 100
                                    +le ++ ++++l++gg 
  gi|118431275|ref|NP_147631.2| 227 TLELYREFHRILRRGGR 243
                                    55556777778888775 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.8   5.7e+03      63      77 ..      49      63 ..      43      67 .. 0.78
   2 ?   10.6   0.0   0.00023      0.35      97     171 ..     133     210 ..     125     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.8
                                   SEEEEEETTEEEEEE CS
                         Met_10 63 tetihkEngcrfklD 77
                                     + + E+g+rf +D
  gi|118431275|ref|NP_147631.2| 49 RAVLVSESGSRFVVD 63
                                   567889999999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00023
                                    T--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-T.TCEEEEES-GGG---...TT-EEE CS
                         Met_10  97 lveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkve.kvvkpileDgrevir...eqladr 171
                                    +v+ g +V+d   G G+ +i++     a+ v++++++    ++   n    ++  k+++ il+D+ ev+r   ++++d 
  gi|118431275|ref|NP_147631.2| 133 VVKRGFRVLDTCTGLGYTSIAAIA-RGASLVYTVEVDEIVLQLAALNPWSHRLRdKRIRIILGDAVEVVRdfgDSAFDA 210
                                    589999**************8765.47889*******999999888887777752679999999999987555555554 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 ?   10.9   0.0   0.00017      0.26      10      88 ..     138     216 ..     130     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                    -EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHH..HHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE CS
                Methyltr_RsmB-F  10 etilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaen..lkrLgvtntivleaDarkidkvlggelfDriLlDa 87 
                                     ++lD c++ G   t ia++ + ++ v+ v++++  l+  a n   +rL  + + ++ +Da ++ ++ g++ fD ++ D 
  gi|118431275|ref|NP_147631.2| 138 FRVLDTCTGLG--YTSIAAIARGASLVYTVEVDEIVLQLAALNpwSHRLRDKRIRIILGDAVEVVRDFGDSAFDALIHDP 215
                                    5799***9887..5789***9***********99877765555338****************************999988 PP

                                    - CS
                Methyltr_RsmB-F  88 P 88 
                                    P
  gi|118431275|ref|NP_147631.2| 216 P 216
                                    7 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       7.4   1.1e+04      95     113 ..      48      66 ..      43      75 .. 0.72
   2 ?   10.5   0.0   0.00026      0.39       3     107 ..     136     244 ..     134     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7.4
                Methyltransf_31  95 eeiervlkpggilliedpr 113
                                    e++  v ++g++++++++ 
  gi|118431275|ref|NP_147631.2|  48 ERAVLVSESGSRFVVDEHA 66 
                                    5666777888999998887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdieeleklledekfDlils 80 
                                    +g rvlD  +G G+ ++++   ++  + v+ ++ +e +++lA  n  ++ l   +++   gd+ e   ++ d+ fD ++ 
  gi|118431275|ref|NP_147631.2| 136 RGFRVLDTCTGLGYTSIAAI--ARGASLVYTVEVDEIVLQLAALNPWSHRLRdkRIRIILGDAVEVVRDFGDSAFDALIH 213
                                    5779**************99..455667****************99999998889**********77569*******988 PP

                Methyltransf_31  81 nevl....naladpdkileeiervlkpggil 107
                                    + +            + ++e +r l+ gg+l
  gi|118431275|ref|NP_147631.2| 214 DPPRfsksTSSLYTLELYREFHRILRRGGRL 244
                                    7333332233333344455777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2069.67
//
Query:       gi|118431276|ref|NP_147632.2|  [L=287]
Description: hypothetical protein APE_0965.1 [Aeropyrum pernix K1]
Scores for complete 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   79.5  30.1    1.2e-13   51.4  16.1    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.051   12.8   5.1      0.017   14.4   1.8    1.8  2  PUNUT     Purine nucleobase transmembrane transport
          3    7.1   8.8       0.79    9.0   2.0    2.4  2  TPT       Triose-phosphate 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 !   51.4  16.1     2e-17   1.2e-13       2     135 ..       5     137 ..       4     139 .. 0.91
   2 !   34.5   6.0   3.4e-12     2e-08       3     136 ..     154     286 ..     152     287 .] 0.84

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 2e-17
                           EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf.. 79 
                                    +g+ la +a+l++a++ vl ++++r++sp  ++f++++ +   l +++ l +++     +  w lll+ ++ ++ ++f  
  gi|118431276|ref|NP_147632.2|   5 IGYALAYAASLLFAVSDVLVRKASRDISPAGILFLSLTSGIPSLAVVSILLGEPT---LPGMWYLLLYCAIGAGHFYFgr 81 
                                    899*********************************9988888888888888888...8888999999998666666655 PP

                           EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                    l+f++a+  ++as a++i+s +P+++ +l+vlllge l    l++++l+ l++++ 
  gi|118431276|ref|NP_147632.2|  82 LFFYTAVAGLGASSAAIIVSATPIMSSFLAVLLLGEDLRPPVLAALILVTLAAYIA 137
                                    ****************************************************9975 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 3.4e-12
                           EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                    ++l a +a+l++a+++v+ +++    ++  l +v +  ++  l ++a +++++      k+ l+ +l + + +++a+   
  gi|118431276|ref|NP_147632.2| 154 AVLAAAAATLIFASTTVAVRWIGFHADSPVLGVVASYTGAYPL-ALATVEARRV--SWGKPALYTALAAGVVVAFAQASR 230
                                    68999****************9888877777777776666665.4444444444..23566788899999********** PP

                           EamA  83 fyalkktsasnaslitslePvftlilsvlll..gekltlkqllgivlillGvllil 136
                                    +++l+ +++ +as+++ l Pv t+++s++     e++++k+++++++++++v++++
  gi|118431276|ref|NP_147632.2| 231 YSSLELIPVPEASVLFGLFPVNTAVISAVAGgeDERPSKKHVVAALMSVAAVAIMF 286
                                    ******************************944479****************9986 PP

>> PUNUT  Purine nucleobase transmembrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.58   3.5e+03     164     183 ..       5      24 ..       3      32 .. 0.69
   2 ?   14.4   1.8   2.8e-06     0.017      74     177 ..      67     166 ..      59     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.58
                          PUNUT 164 igfiltlaasllfaLlLslv 183
                                    ig++l+ aasllfa +  lv
  gi|118431276|ref|NP_147632.2|   5 IGYALAYAASLLFAVSDVLV 24 
                                    67778888888888765555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.8e-06
                          PUNUT  74 lvllyivlGllvavdnllyslgllylpvstfslilatqLaFtaifsalinkqkftrfiinsvvlltisaallalssssdk 153
                                    l+ ++i  G  ++   ++y  + + l +s +++i+++  +++++++ l+    + + ++ +++l+t++a++ a + s+  
  gi|118431276|ref|NP_147632.2|  67 LLYCAIGAGHFYFGRLFFYT-AVAGLGASSAAIIVSATPIMSSFLAVLLLGEDLRPPVLAALILVTLAAYIAARNPSGRP 145
                                    45556666666666666665.5999**********************************************998877776 PP

                          PUNUT 154 paeeskkkyvigfiltlaasllfa 177
                                     ++ s+++ v   +++ aa+l+fa
  gi|118431276|ref|NP_147632.2| 146 LQNVSRSRAV---LAAAAATLIFA 166
                                    6666644433...33333333333 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.0   0.00013      0.79      77     136 ..      79     138 ..       4     170 .. 0.83
   2 ?    2.2   0.7     0.015        92      59     121 ..     205     269 ..     184     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00013
                            TPT  77 lghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalas 136
                                    +g ++   +++    S + ++ ++ Pi +  l+ lllge l   v+ +L+ +     +a+
  gi|118431276|ref|NP_147632.2|  79 FGRLFFYTAVAGLGASSAAIIVSATPIMSSFLAVLLLGEDLRPPVLAALILVTLAAYIAA 138
                                    5566666666666778999*******************************9988777765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.015
                            TPT  59 kisse..flkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllv 121
                                    ++s+    l + l  ++v ++++ +   sl+ ++V  + ++  + P+ t+++s++  ge    ++
  gi|118431276|ref|NP_147632.2| 205 RVSWGkpALYTALAAGVVVAFAQASRYSSLELIPVPEASVLFGLFPVNTAVISAVAGGEDERPSK 269
                                    44444447788899999999999999****************************99888655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2156.37
//
Query:       gi|118431277|ref|NP_147633.2|  [L=724]
Description: hypothetical protein APE_0966.1 [Aeropyrum pernix K1]
Scores for 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   55.7   1.9    1.4e-14   55.1   1.9    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    5.2e-05   23.5   0.0    0.00019   21.7   0.0    1.9  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
      0.002   18.1  30.4     0.0053   16.7  30.4    1.6  1  Mucin          Mucin-like glycoprotein
  ------ inclusion threshold ------
        0.2   11.9  15.8       0.34   11.1  15.8    1.3  1  AJAP1_PANP_C   AJAP1/PANP C-terminus
        2.2    8.7   8.4        4.2    7.8   8.4    1.4  1  MGC-24         Multi-glycosylated core protein 24 (MGC-24), s


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 !   55.1   1.9   3.8e-18   1.4e-14       2     203 ..     168     374 ..     167     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 3.8e-18
                                    EEEEEESBTB......TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS....HHHHHHHHHHHHHHHHTSEEEEEC CS
                    Metallophos   2 rilvigDlHl......algggqlddllkllddllreekpdlvllaGDlvdrg....dlekellellaalvkypipvylll 71 
                                     i++++D+H+       l +  +++ ++l++ l+ e + dlv+++GD+ d g    ++ + ++  +++l+   +p ++++
  gi|118431277|ref|NP_147633.2| 168 VIMHLTDIHFgaidkgILNDVKFARDVALVNTLKYELGLDLVVVTGDISDIGinvsSYRN-WAFAMNQLL---VPTMTVP 243
                                    599********7777755556666666777888888999*************84433333.444444444...599**** PP

                                    -TTS.....CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHC CS
                    Metallophos  72 GNHe.....gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapep 146
                                    GNH+     g+e  ll +yg+++  ++ w  +  ++n+l +        + ++ + g                       
  gi|118431277|ref|NP_147633.2| 244 GNHDwaqvpGLESFLLDFYGKYNVPARYWAAK--WGNFLFIGLDSQS--EGYVEPEG----------------------- 296
                                    ****9988876667777777777778888766..5555555553344..77888888....................... PP

                                    CHHHHHH..HHHHTTCSEEEEEESSESS............CSSSCSCCHHHHH..................HHHHHTT.E CS
                    Metallophos 147 gdewlkd..lekrekadwvivlgHsply............rgsgylfgdeale..................dllkkyg.v 193
                                      ++l++  ++  +++ + i+l H+p+                         +                  d+ ++y+ v
  gi|118431277|ref|NP_147633.2| 297 -LDFLENvlSQYSGEDVVAIILVHHPIFsdpgrykgdpesF-----------RgalygsweskfelverffDIINRYDmV 364
                                    .7888888555555666667777999999666555555550...........444455555555577788888788889* PP

                                    SEEEEESSSS CS
                    Metallophos 194 dlvisGHtHv 203
                                    ++v+sGH+H+
  gi|118431277|ref|NP_147633.2| 365 KVVFSGHIHR 374
                                    *********7 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 !   21.7   0.0   5.3e-08   0.00019       3     130 ..     169     375 ..     167     408 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.3e-08
                  Metallophos_2   3 laiiSDlH...........snldaleavlealke.vgvdaiihaGDl..eeeepevleellela.....pvlaVrGNnD. 62 
                                    +++++D+H            ++++  a+++ lk   g+d+++++GD+   +++ ++ +++         p  +V+GN+D 
  gi|118431277|ref|NP_147633.2| 169 IMHLTDIHfgaidkgilndVKFARDVALVNTLKYeLGLDLVVVTGDIsdIGINVSSYRNWAFAMnqllvPTMTVPGNHDw 248
                                    67888999888888888765566666777777743799********97767777644333332236678**********9 PP

                  Metallophos_2  63 ..............................eevveedvlreaaelgtdl...................peeaelelagek 93 
                                                                                    l                    e    +  ge+
  gi|118431277|ref|NP_147633.2| 249 aqvpglesflldfygkynvparywaakwgnF-----------------LfigldsqsegyvepegldfLENVLSQYSGED 311
                                    9999999999988877777666665555330.................23333333333333222211233333333333 PP

                  Metallophos_2  94 ...vlliHgdpl......................gvkdalaellke...aeegsdvvvcGHtHvp 130
                                       + l+H+                         + k +l e++++    ++ ++vv++GH+H+ 
  gi|118431277|ref|NP_147633.2| 312 vvaIILVHHP-IfsdpgrykgdpesfrgalygswESKFELVERFFDiinRYDMVKVVFSGHIHRD 375
                                    5568888886.55999999*9999*******999555666666666554488888********97 PP

>> Mucin  Mucin-like glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  30.4   1.5e-06    0.0053      47     141 ..     624     717 ..     610     720 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                          Mucin  47 ttttttkppttttttttasttittkttkattttttttttttateaPsdavttaeaPtttttrapsrlrevdGslsssaWv 126
                                    ++ ttt++p + t+t+t+ +t tt  t+atttt+ t  t t+te  s+++t+ +a   +t+ +p +  e  G l ss+ +
  gi|118431277|ref|NP_147633.2| 624 APQTTTTTPPAETATETTEETETT-ETTATTTTSETVETVTTTEETSETTTAGKAGVEETATTPVSPGETAGRLDSSLII 702
                                    456777777777788877777555.55677777788888888999999*****************************988 PP

                          Mucin 127 caPLllavsalayta 141
                                        + a++ +++ a
  gi|118431277|ref|NP_147633.2| 703 LGAAVAAAIIIVAAA 717
                                    777777777666655 PP

>> AJAP1_PANP_C  AJAP1/PANP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  15.8   9.4e-05      0.34      18     104 ..     630     718 ..     613     721 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                   AJAP1_PANP_C  18 tvpnitlstkas.rtttvatttstttrltqrtltvvttpeprrlsttessvsegktvkppkilgdtsG.lavhqii...t 92 
                                    t+p + ++t+++  t t++   +t+t++t++t+ +vtt+e +  +tt  +++ ++t+++p   g+t+G l    ii   +
  gi|118431277|ref|NP_147633.2| 630 TTPPAETATETTeETETTE---TTATTTTSETVETVTTTEETSETTTAGKAGVEETATTPVSPGETAGrLDSSLIIlgaA 706
                                    2333333333331233333...3333445566666666667777899999999**************9344444443333 PP

                   AJAP1_PANP_C  93 itvslimviaal 104
                                    ++ ++i+v aal
  gi|118431277|ref|NP_147633.2| 707 VAAAIIIVAAAL 718
                                    555677777776 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.4    0.0012       4.2      54     102 ..     624     672 ..     607     719 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                         MGC-24  54 aaskstpkptnstaktttkpsstttstsvatsgttnttvtptsqparks 102
                                    a +++t++p ++ta+ tt++++tt++t+++t+++t  tvt t++++ ++
  gi|118431277|ref|NP_147633.2| 624 APQTTTTTPPAETATETTEETETTETTATTTTSETVETVTTTEETSETT 672
                                    4444444444455555555555555555554444444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (724 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.41
# Mc/sec: 5260.89
//
Query:       gi|118431278|ref|NP_147635.2|  [L=400]
Description: hypothetical protein APE_0969.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.9   0.0       0.24   10.9   0.0    2.2  2  ABC_transp_aux  ABC-type uncharacterized transport system
       0.15   11.9   6.5       0.24   11.3   6.5    1.3  1  RIFIN           Rifin
       0.22   10.9   8.8       0.14   11.6   6.0    2.0  2  DUF5305         Family of unknown function (DUF5305)


Domain annotation for each model (and alignments):
>> 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 ?   10.9   0.0   3.9e-05      0.24     186     252 ..      88     152 ..      57     161 .. 0.71
   2 ?    1.9   0.1     0.022   1.3e+02      49      84 ..     145     176 ..     129     186 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.9e-05
                 ABC_transp_aux 186 sedilpedidvlviakptkdlseeelykldqflmnGgkllvfldpvaeeqdslsepsaaprtsnLed 252
                                    + ++l +d+dvl+i + t+ ls++e+ ++  +  +G+k+++++   +   ++++ ++++ +++ Le+
  gi|118431278|ref|NP_147635.2|  88 TPENL-SDVDVLLIGQATSLLSNDEVSAIASWGSQGKKAVWVAGDSDYPAQGSE-TAQQVVNQVLEA 152
                                    34446.89*********************************9987775555444.222222444444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.022
                 ABC_transp_aux  49 evkdlLeeyaaysggkisvefidpspneeeeeeaea 84 
                                     v+++Le +    +++i+++++ ++++e ++e+  +
  gi|118431278|ref|NP_147635.2| 145 VVNQVLEAL----NSNIRIDYVSVEDDESNAERSYR 176
                                    334444433....44999999999988855554433 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.5     4e-05      0.24     236     292 ..     329     388 ..     307     399 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                          RIFIN 236 ekivekaekkaaaaaaeaaaeataeaekaetaaveattas...lqtaiiasivaivvIvL 292
                                      +vek+++++++ ++++++++t++++k+eta+v++t+++   ++++ +a i a v+I+L
  gi|118431278|ref|NP_147635.2| 329 FIVVEKVITQTETVTETVTKTQTETTTKTETATVTETVTQtttVTETNTAVIAAAVIIIL 388
                                    445556666666666666666666666666666555544400034445555666666666 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.17     1e+03      20      35 ..     151     166 ..     121     178 .. 0.48
   2 ?   11.6   6.0   2.3e-05      0.14      88     136 ..     345     399 ..     320     400 .] 0.52

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                        DUF5305  20 ltisesvsinlseynd 35 
                                      +++++ i++  ++d
  gi|118431278|ref|NP_147635.2| 151 EALNSNIRIDYVSVED 166
                                    2345555555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.3e-05
                        DUF5305  88 eikkdetd..eengeitetvtvkespslae....gilliilgllaliglvvlirr 136
                                    +++k++t+  ++++++t+t+tv++  +++e    +i+ +++++la++g++++ +r
  gi|118431278|ref|NP_147635.2| 345 TVTKTQTEttTKTETATVTETVTQTTTVTEtntaVIAAAVIIILAALGAAFFLLR 399
                                    2444444411333444444444444444447677556666666666665555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2007  (0.111942); expected 358.6 (0.02)
Passed bias filter:                      950  (0.0529868); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.40
# Mc/sec: 2990.35
//
Query:       gi|118431279|ref|NP_147637.2|  [L=490]
Description: sodium/solute symporter [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-22   80.1  30.4    2.4e-22   79.4  30.4    1.4  1  SSF       Sodium:solute symporter family
  ------ inclusion threshold ------
       0.19   12.0   4.8       0.35   11.1   0.6    2.6  2  DUF1970   Domain of unknown function (DUF1970)


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4  30.4   2.6e-26   2.4e-22       1     357 [.      38     392 ..      38     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.6e-26
                            SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdyls 76 
                                    ++lagr+ltgf  +++ aa+  s+  +vGl G+++  G++ +++el  l++ ++ll l+  r      + g +   ++l+
  gi|118431279|ref|NP_147637.2|  38 FYLAGRRLTGFLSAMTYAATTYSSFMIVGLVGLAYFTGIGSLVFELAYLVATVILLSLFSRRVWrmsrERGWVSPGEMLA 117
                                    8***********************************************************9987688899********** PP

                            SSF  77 kRfkgkrilvylsalslllvitlklsvdlvggaklielalGln......yetavlllaaltalYtviGGllAvvytdtiq 150
                                      +++     + ++l+ l+ ++ + s++l g a  i  + G +      y +av + ++++  + ++ G + vv+td  q
  gi|118431279|ref|NP_147637.2| 118 DLLGSPW-VALTASLVFLVSLVPYASAQLKGIAETIVAIAGYSpgdntaYMVAVGVALLILLAWSLLAGVRGVVLTDAFQ 196
                                    ***9999.889999***************************75555555999999999999******************* PP

                            SSF 151 avlmlvgalilliivllevGgleslveklkeaapkv.vdlltpdslkllrdpltalslwlglvlGvaglphilvRflaak 229
                                    ++ ml + ++l +   + v + + + e l +++  +  d+           ++  + +   +v+  +  p +++R++  k
  gi|118431279|ref|NP_147637.2| 197 GLWMLTAGSLLFLWLASRVFSKSGASEVLSAMESAGlFDMWS---------ATLLIGFVTPWVFFAVTNPQVVQRLYMPK 267
                                    ******999999999999988888777777777633233333.........333444445578888999*********** PP

                            SSF 230 dakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlAaimstl 309
                                    d +++++ +l+   + ++  +++++i++ a + +     +   e +  +++ p+L   l  +lla+l+   ++Aa +st 
  gi|118431279|ref|NP_147637.2| 268 DEESLRRMILYFFLFGLYYTVLVVAIGFLARAGVEL--GILSIEPQGRDQVTPQLL-SLAHPLLAALVFTSIVAASVSTA 344
                                    ***********9999999999999****99977766..8999999**********8.58999****************** PP

                            SSF 310 tslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaill 357
                                    +s++l+ +s+ ++D+   ++r  ++  ++l ++++ ++ v++++  + 
  gi|118431279|ref|NP_147637.2| 345 DSIILALASSASRDIGLLVLRLDEKGRLRLGYAAAALFTVLMAVFAAT 392
                                    ***********************9999999999888888888776554 PP

>> DUF1970  Domain of unknown function (DUF1970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.3      0.03   2.7e+02       4      21 ..     165     183 ..     162     204 .. 0.72
   2 ?   11.1   0.6   3.9e-05      0.35       7      53 ..     407     457 ..     402     468 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.03
                                    SSHHHHHHHHHHHHHH.HH CS
                        DUF1970   4 kllvvvgvllvllliw.lw 21 
                                      +v vgv l++ll+w l 
  gi|118431279|ref|NP_147637.2| 165 AYMVAVGVALLILLAWsLL 183
                                    56899***********544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.9e-05
                                    HHHHHHHHHHHHHHHHHHTT-S-SS-TT----TT-SS---....S-S---S CS
                        DUF1970   7 vvvgvllvllliwlwirrrpavdvasnweGrtvivyddpq....aGevslp 53 
                                    +++g   v + +w+ +r  pa  vas   G+ +++ +        Gevsl 
  gi|118431279|ref|NP_147637.2| 407 MLLGLAPVTIAAWVGLRVHPALAVASIATGPVLVAANVLYslavGGEVSLS 457
                                    566777799*********************998877754445447777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3437.75
//
Query:       gi|118431280|ref|NP_147638.2|  [L=338]
Description: hypothetical protein APE_0973.1 [Aeropyrum pernix K1]
Scores for complete 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-106  355.4   1.9   2.4e-106  355.3   1.9    1.0  1  DUF1152   Protein of unknown function (DUF1152)


Domain annotation for each model (and alignments):
>> DUF1152  Protein of unknown function (DUF1152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.3   1.9  1.3e-110  2.4e-106       1     295 []      16     311 ..      16     311 .. 0.99

  Alignments for each domain:
  == domain 1  score: 355.3 bits;  conditional E-value: 1.3e-110
                        DUF1152   1 LvlgiGGGGDvvsalvlaellkklgveavlgsvvWeRlvvDplPGPisleelegveaineavaivnaesrairgarsvlp 80 
                                    Lv+g+GGGGD+++a++l++ l++ g e+vlgs+vWeR+vvDp+PGPi++  +eg +++ e++aiv++ +r+ r++ +++p
  gi|118431280|ref|NP_147638.2|  16 LVFGAGGGGDALGAVHLYRRLERIGAEPVLGSIVWERRVVDPTPGPIPVWAIEGSQRLAEHAAIVRGWERVERQGVRFTP 95 
                                    89****************************************************************************** PP

                        DUF1152  81 qlarvakvlneevvlldikkgveglaealeelaeklgidliigvDvGGDvLAkGdEegLrSPLaDalslAalskleee.s 159
                                    q++r+a++l+ e+v+l +++g+ glaeal++la+ +g+d+ii++D GGD+LA+G+Ee+L+SPLaDa+sl++l +++ + +
  gi|118431280|ref|NP_147638.2|  96 QIVRAARALGVEAVALGVDGGSMGLAEALDTLARFYGLDAIIALDSGGDALATGCEEDLWSPLADAVSLSSLLDVKVDvK 175
                                    *****************************************************************************988 PP

                        DUF1152 160 vlavaGpGsDGELseeelleriseiakeggllgilgldeedaellekileeveteAskiplaaakGlrGeveiRkgtrkv 239
                                    +lav+G+G+DGEL+++++l+ri+++a+eggl++++g+++ daelle++ +++++eAsk+pl+a++G++Ge +iR+gtr v
  gi|118431280|ref|NP_147638.2| 176 LLAVHGYGVDGELPRSYVLKRIADVAREGGLVAFTGITRLDAELLENMERDFVSEASKAPLWAFRGEWGERSIRGGTRVV 255
                                    99****************************************************************************** PP

                        DUF1152 240 eltplsalvfyldpkavaelsklaklvagtesleeAeerlnelgiytEldlErdla 295
                                    el+pl+a++ ++d+++va++++l + vag++s+ eA++rlne +iytEl+lE+dla
  gi|118431280|ref|NP_147638.2| 256 ELDPLQATTAIMDVDKVASITSLPHSVAGSRSIYEANARLNERCIYTELNLEEDLA 311
                                    *****************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2593.39
//
Query:       gi|118431281|ref|YP_874868.1|  [L=117]
Description: hypothetical protein APE_0973a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0029   17.0   0.3     0.0039   16.7   0.3    1.1  1  FliD_C          Flagellar hook-associated protein 2 C-terminu
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.023   14.6   0.0    1.6  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,
      0.013   15.2   0.9       0.02   14.6   0.9    1.3  1  Lebercilin      Ciliary protein causing Leber congenital amau
      0.044   13.4   0.1      0.049   13.2   0.1    1.0  1  GCP_N_terminal  Gamma tubulin complex component N-terminal


Domain annotation for each model (and alignments):
>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   8.7e-07    0.0039     172     236 ..      22      88 ..      11      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.7e-07
                                    SHHHHHHHHHHHHH..STT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH CS
                         FliD_C 172 glatrlenllksyv..kssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaalekavs 236
                                    +l  ++++++k y+  + ++g  +++s++ tk++  l++k ++l+k ++ +   l+ ++ ++e+a++
  gi|118431281|ref|YP_874868.1|  22 ELGVQVTDIIKFYIkmGLNKGFAAESSEESTKTLLALSRKLDKLEKDYRMKLTLLEGKYRQMEDAIT 88 
                                    67789999*****977889999******************************************997 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 ?   14.6   0.0   5.1e-06     0.023       4      39 ..       4      39 ..       1      42 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-06
                          RHH_5  4 vnvtLPeelleeLeewAdeegRsvSnlaafLvekal 39
                                   v ++LP+ ++ eL++ A+e g+ v   ++f ++ +l
  gi|118431281|ref|YP_874868.1|  4 VHLSLPDSVYSELKKRAAELGVQVTDIIKFYIKMGL 39
                                   789*******************99999999999887 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 ?   14.6   0.9   4.5e-06      0.02     132     186 ..      47     101 ..      43     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
                     Lebercilin 132 kleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqkl 186
                                      ee+++++  L+rkl+ +ek +r +l+  + k +++++ ++ l e++e l++++
  gi|118431281|ref|YP_874868.1|  47 SSEESTKTLLALSRKLDKLEKDYRMKLTLLEGKYRQMEDAITYLIERVEILEETV 101
                                    568999*********************************************9876 PP

>> GCP_N_terminal  Gamma tubulin complex component N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05     0.049      41     128 ..      14     110 ..       2     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                 GCP_N_terminal  41 rslverllelgtlyrrlrkfveev.........srsesglvlqalaaaldeelteyyrliaqlEsqlledsesiltLlrl 111
                                    ++l +r +elg ++  + kf  +          s+ es+ +l al++ ld++ ++y+  ++ lE ++++ ++ i  L   
  gi|118431281|ref|YP_874868.1|  14 SELKKRAAELGVQVTDIIKFYIKMglnkgfaaeSSEESTKTLLALSRKLDKLEKDYRMKLTLLEGKYRQMEDAITYLIER 93 
                                    577789999999999999999777888888998999*********************************99999888888 PP

                 GCP_N_terminal 112 evwlqetllllrvLanl 128
                                    +  l+et + l++ +++
  gi|118431281|ref|YP_874868.1|  94 VEILEETVMSLKAYSTI 110
                                    88888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 929.27
//
Query:       gi|118431282|ref|YP_874869.1|  [L=57]
Description: hypothetical protein APE_0973b [Aeropyrum pernix K1]
Scores for complete 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-10   39.0   2.8    5.6e-10   38.8   2.8    1.1  1  RHH_1           Ribbon-helix-helix protein, copG family
      2e-05   24.4   2.9    2.7e-05   24.0   2.9    1.1  1  RHH_3           Ribbon-helix-helix domain
     0.0011   19.7   0.0     0.0011   19.6   0.0    1.1  1  PSK_trans_fac   Rv0623-like transcription factor
  ------ inclusion threshold ------
      0.016   15.7   0.2      0.021   15.3   0.2    1.2  1  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
      0.034   14.1   1.6      0.098   12.6   1.6    1.8  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap
      0.085   13.9   0.3       0.11   13.6   0.3    1.3  1  RNase_J_C       Ribonuclease J C-terminal domain
      0.087   12.7   0.2       0.11   12.3   0.2    1.2  1  YmgB            Biofilm development protein YmgB/AriR
      0.092   12.8   0.1       0.15   12.1   0.1    1.4  1  DUF3791         Protein of unknown function (DUF3791)
       0.11   12.4   0.6       0.16   11.9   0.6    1.1  1  RHH_5           CopG-like RHH_1 or ribbon-helix-helix domain,


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   2.8   2.8e-13   5.6e-10       2      38 ..       4      40 ..       3      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.8e-13
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlreyle 38
                                   vs++++e+lle+L+e arr + ++Se+IR+Al+ yl 
  gi|118431282|ref|YP_874869.1|  4 VSFKIEEDLLELLEEYARRKNLTKSEIIRRALEKYLR 40
                                   9**********************************96 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.9   1.4e-08   2.7e-05       5      42 ..       4      41 ..       2      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                          RHH_3  5 ttvsidpelaekLkaLSekTrIprSklldeAiellLek 42
                                   +++ i+++l+e L+++ ++    +S++++ A+e +L++
  gi|118431282|ref|YP_874869.1|  4 VSFKIEEDLLELLEEYARRKNLTKSEIIRRALEKYLRE 41
                                   6899********************************97 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 !   19.6   0.0   5.6e-07    0.0011      12      54 ..      14      54 ..       9      57 .] 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.6e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHH CS
                  PSK_trans_fac 12 rlareLarltgeskteAvrrAleerlerlrreraepllerlla 54
                                   +l +e ar+ + +k e++rrAle++l++    + +p + ++++
  gi|118431282|ref|YP_874869.1| 14 ELLEEYARRKNLTKSEIIRRALEKYLREKP--DMKPYVGKVMK 54
                                   6889**********************9976..66666666655 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   1.1e-05     0.021      43      78 ..       2      37 ..       1      38 [. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                 CopG_antitoxin 43 ksislrlpedlLealkekAnkrdvpyqslikellee 78
                                   + +s++++edlLe l e A+++++  ++ i+ +le+
  gi|118431282|ref|YP_874869.1|  2 RVVSFKIEEDLLELLEEYARRKNLTKSEIIRRALEK 37
                                   579*****************************9986 PP

>> VapB_antitoxin  Bacterial antitoxin of type II TA system, VapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6   4.9e-05     0.098      17      39 ..      21      42 ..       7      46 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                                   XXXXXXXXXXXXXXXXXX----- CS
                 VapB_antitoxin 17 rltglktKrEaVnlALreLiqrr 39
                                   r+ +  tK+E+++ AL+ +++++
  gi|118431282|ref|YP_874869.1| 21 RR-KNLTKSEIIRRALEKYLREK 42
                                   44.3459*************986 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 ?   13.6   0.3   5.4e-05      0.11      30      66 ..      12      49 ..       1      54 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                      RNase_J_C 30 ieealee.kesdwnelkrkirealkkflykktkrrPmI 66
                                   + e lee ++ ++ + ++ ir+al+k+l++k  ++P +
  gi|118431282|ref|YP_874869.1| 12 LLELLEEyARRKNLTKSEIIRRALEKYLREKPDMKPYV 49
                                   44444442445566667889****************87 PP

>> YmgB  Biofilm development protein YmgB/AriR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   5.7e-05      0.11      27      58 ..      13      44 ..       7      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHHT---HHHHHHHHHHHHHHHHHHH- CS
                           YmgB 27 lkLiekLEsesdvvqldvyRqaLElVVgkTpD 58
                                   l+L+e+    +++++ +++R+aLE  +++ pD
  gi|118431282|ref|YP_874869.1| 13 LELLEEYARRKNLTKSEIIRRALEKYLREKPD 44
                                   56777777899*************98887776 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.6e-05      0.15       6      24 ..      15      33 ..      12      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                        DUF3791  6 cIeeyarklglsgkevykl 24
                                   ++eeyar+++l+ +e++++
  gi|118431282|ref|YP_874869.1| 15 LLEEYARRKNLTKSEIIRR 33
                                   78*************9875 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 ?   11.9   0.6   8.2e-05      0.16      10      41 ..      10      41 ..       9      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.2e-05
                          RHH_5 10 eelleeLeewAdeegRsvSnlaafLvekalre 41
                                   e+lle Lee+A     + S  +   +ek+lre
  gi|118431282|ref|YP_874869.1| 10 EDLLELLEEYARRKNLTKSEIIRRALEKYLRE 41
                                   79*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.35u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 497.98
//
Query:       gi|118431283|ref|NP_147639.2|  [L=299]
Description: hypothetical protein APE_0974.1 [Aeropyrum pernix K1]
Scores for complete 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-35  120.2   1.3    3.3e-35  119.6   0.1    2.0  3  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
    5.7e-26   90.7   2.2    2.6e-13   50.2   0.1    2.6  2  CBS              CBS domain
    1.1e-07   32.1   0.1    2.3e-07   31.0   0.1    1.5  1  Rrf2             Transcriptional regulator
    0.00023   21.5   0.0       0.13   12.5   0.0    2.3  2  Pro-kuma_activ   Pro-kumamolisin, activation domain
    0.00037   20.4   0.2     0.0015   18.4   0.0    2.2  1  HTH_11           HTH domain
     0.0012   18.6   0.5      0.026   14.4   0.1    2.9  3  TrmB             Sugar-specific transcriptional regulator Trm
     0.0033   17.6   2.8     0.0053   16.9   0.5    2.3  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
  ------ inclusion threshold ------
      0.023   14.5   0.0       0.14   12.0   0.0    2.3  2  TusA             Sulfurtransferase TusA
      0.025   14.2   0.6       0.12   12.0   0.2    2.3  3  GntR             Bacterial regulatory proteins, gntR family
      0.026   14.9   0.3        0.2   12.0   0.1    2.3  2  Penicillinase_R  Penicillinase repressor
      0.035   14.0   0.0       0.15   11.9   0.0    2.1  2  MarR_2           MarR family
       0.11   12.6   0.0        0.3   11.1   0.0    1.7  1  Put_DNA-bind_N   Putative DNA-binding protein N-terminus
       0.11   12.1   0.3       0.78    9.5   0.0    2.5  3  Sigma70_r4_2     Sigma-70, region 4
       0.12   11.9   0.9       0.23   11.1   0.1    2.0  3  HTH_24           Winged helix-turn-helix DNA-binding
       0.12   12.5   0.0       0.53   10.4   0.0    2.0  2  Sigma70_r3       Sigma-70 region 3
       0.12   12.8   0.1       0.28   11.7   0.1    1.6  1  HTH_27           Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.1   2.9e-38   3.3e-35       1      78 [.       3      80 ..       3      81 .. 0.98
   2 ?   -3.2   0.0         6   6.7e+03      34      45 ..     182     193 ..     170     203 .. 0.58
   3 ?   -3.1   0.0       5.7   6.4e+03       6      15 ..     288     297 ..     286     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2.9e-38
                   HrcA_DNA-bdg  1 eLtsvqkeilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealkiqtl 78
                                   +Lts+q+e+l++L++ly+++kr++K++e+Ae+l+++eGtvRN++++Lk+lgLve+++GP+GGY+Ptlkaye++ +qt 
  gi|118431283|ref|NP_147639.2|  3 MLTSLQREVLETLVSLYERHKRMIKSKEVAEALGKDEGTVRNVIMWLKSLGLVESRTGPAGGYMPTLKAYEVIGVQTP 80
                                   69************************************************************************9985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                   HrcA_DNA-bdg  34 krneGtvRNqlq 45 
                                    +r+  tvR  ++
  gi|118431283|ref|NP_147639.2| 182 SRKLLTVRHDMT 193
                                    444445554443 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.7
                   HrcA_DNA-bdg   6 qkeilqaLie 15 
                                    + +il+aLi 
  gi|118431283|ref|NP_147639.2| 288 RTDILKALIA 297
                                    5789999996 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.2   4.4e-13   4.9e-10       2      52 ..     178     228 ..     177     233 .. 0.91
   2 !   50.2   0.1   2.3e-16   2.6e-13       3      55 ..     243     295 ..     240     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 4.4e-13
                                    HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                            CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                     ++ +r+++tv+ d+t++e+++ + ++g+++ P+Vd+ ++++G +t +D+ 
  gi|118431283|ref|NP_147639.2| 178 NSLISRKLLTVRHDMTVREVAKFLYSHGIRGAPIVDDKNNIIGFITTTDIS 228
                                    56889******************99**********99999*********96 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 2.3e-16
                                    HHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   3 dimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                     +m++ v+t+++d+++ ea++ m + + v+rl V+d  g+++Gi+t++D+l+al
  gi|118431283|ref|NP_147639.2| 243 KYMRKTVFTINEDESIYEAMRYM-DFNgVGRLVVIDYAGRPLGIITRTDILKAL 295
                                    68*********************.8777****667*****************98 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   2.1e-10   2.3e-07       3      66 ..       4      66 ..       1      74 [. 0.91

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.1e-10
                                   --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                           Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                   l+s  + +l +l+ L +++++  ++s+e+ae  +  +  ++ ++  L+  glv+s+ G+ GGy+
  gi|118431283|ref|NP_147639.2|  4 LTSLQREVLETLVSLYERHKRM-IKSKEVAEALGKDEGTVRNVIMWLKSLGLVESRTGPAGGYM 66
                                   56666778999*******9987.****************************************7 PP

>> Pro-kuma_activ  Pro-kumamolisin, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00012      0.13      43      86 ..      21      64 ..       2      75 .. 0.82
   2 !    6.7   0.0    0.0075       8.5      60     108 ..     190     244 ..     186     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                 Pro-kuma_activ 43 nygkhltaeevaelfapseeaidaVrnwLessgiaasrhsdtkg 86
                                   + ++ ++++evae ++  e ++ +V  wL+s g+  sr+ + +g
  gi|118431283|ref|NP_147639.2| 21 RHKRMIKSKEVAEALGKDEGTVRNVIMWLKSLGLVESRTGPAGG 64
                                   3455599****************************999766665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0075
                 Pro-kuma_activ  60 seeaidaVrnwLessgiaasr.hsdtkgwiafsatvaqve.....rllktsfeaY 108
                                    ++ ++ +V ++L s+gi+    ++d++++i f +t+  +      + l++++ +Y
  gi|118431283|ref|NP_147639.2| 190 HDMTVREVAKFLYSHGIRGAPiVDDKNNIIGFITTTDISMliargEDLDATVDKY 244
                                    577999************9997777778888877765433555555555555555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06    0.0015       4      54 ..      14      65 ..      10      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                         HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GY 54
                                   +++ l  +++  i ++e Ae L+  + tvr+ I  L++lg  +es+ g+  GY
  gi|118431283|ref|NP_147639.2| 14 TLVSLYERHKRMIKSKEVAEALGKDEGTVRNVIMWLKSLG-LVESRTGPagGY 65
                                   555566555555****************************.********9999 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   2.3e-05     0.026      24      59 ..      27      67 ..       4      77 .. 0.76
   2 ?    1.0   0.0      0.36     4e+02      49      68 .]      87     107 ..      83     107 .. 0.80
   3 ?   -3.0   0.0       6.3   7.1e+03      19      30 ..     188     199 ..     184     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                                   HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.....T CS
                           TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVerekgr.....p 59
                                   + +e+ae+lg ++ +v +v+  L++ GlVe + g      p
  gi|118431283|ref|NP_147639.2| 27 KSKEVAEALGKDEGTVRNVIMWLKSLGLVESRTGPaggymP 67
                                   678****************************9987555442 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.36
                                    CTSEEEES.STTTEEEE--HH CS
                           TrmB  49 kGlVerek.grpklYravdpe 68 
                                     G V +ek g+ ++Y a+d+e
  gi|118431283|ref|NP_147639.2|  87 YGQVIVEKdGNQYRYAALDME 107
                                    577777775889******986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.3
                                    HHCCCHHCHHCC CS
                           TrmB  19 klgpatadeiae 30 
                                     +  +t++e+a+
  gi|118431283|ref|NP_147639.2| 188 VRHDMTVREVAK 199
                                    567899999996 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 !   16.9   0.5   4.7e-06    0.0053       1      53 [.       3      56 ..       3      59 .. 0.94
   2 ?   -0.7   0.1       1.5   1.7e+03       4      22 ..     239     258 ..     236     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.7e-06
                                   X--HHHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress  1 dLvestEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                   +L++   ++Let+ +l e  k ++k k++ae+L+    +V   +  L++ G+ve
  gi|118431283|ref|NP_147639.2|  3 MLTSLQREVLETLVSLYErHKRMIKSKEVAEALGKDEGTVRNVIMWLKSLGLVE 56
                                   67888889********************************************98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                    HHHHHHH.HHHHHHHHHHSS CS
                 Fe_dep_repress   4 estEdYL.etIYtlseekkv 22 
                                    ++ ++Y+ +t++t++e++++
  gi|118431283|ref|NP_147639.2| 239 ATVDKYMrKTVFTINEDESI 258
                                    66677873599999997665 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.14      14      52 ..      15      54 ..      13      66 .. 0.83
   2 ?   -2.1   0.0       3.1   3.5e+03      32      51 ..     186     205 ..     176     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   HHHHHHHHCCC.GCT-EEEEEESSCHHHHHHHHHHHHHTE CS
                           TusA 14 llklkkalekl.eegevlevladdpaatediprfakklgh 52
                                   l+ l +  +++ ++ ev e l  d+++++++  ++k+lg+
  gi|118431283|ref|NP_147639.2| 15 LVSLYERHKRMiKSKEVAEALGKDEGTVRNVIMWLKSLGL 54
                                   666666667777999***********************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                                    EEESSCHHHHHHHHHHHHHT CS
                           TusA  32 vladdpaatediprfakklg 51 
                                    +++ +  +++ + +f+ ++g
  gi|118431283|ref|NP_147639.2| 186 LTVRHDMTVREVAKFLYSHG 205
                                    56778888999999988777 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   0.00011      0.12      24      59 ..      26      60 ..       7      62 .. 0.87
   2 ?   -2.8   0.0       4.7   5.2e+03      46      58 ..     178     190 ..     177     195 .. 0.80
   3 ?   -1.8   0.0       2.2   2.5e+03      39      51 ..     192     204 ..     184     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                   ---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           GntR 24 LPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                   + + +e+a+++g +  tvR ++  L++ glve+r g
  gi|118431283|ref|NP_147639.2| 26 I-KSKEVAEALGKDEGTVRNVIMWLKSLGLVESRTG 60
                                   5.6799***************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                                    HHHHHTTSEEEET CS
                           GntR  46 rrLeaeglverrq 58 
                                    + L +++l+++r+
  gi|118431283|ref|NP_147639.2| 178 NSLISRKLLTVRH 190
                                    5788999999887 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHT CS
                           GntR  39 ttvReALrrLeae 51 
                                    +tvRe+ + L + 
  gi|118431283|ref|NP_147639.2| 192 MTVREVAKFLYSH 204
                                    8999987776665 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00018       0.2       1      79 [.       4      82 ..       4      92 .. 0.76
   2 ?    0.4   0.0      0.73   8.2e+02      51      65 ..      90     104 ..      85     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                   ---S-SHHHHHHHHHS-.....EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXX CS
                Penicillinase_R  1 lgelEaevmeilwekge.....atvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavk 77
                                   l++l++ev+e+l ++ e     +++kev e+l ++    + TV+ ++  L   gl+++++ g a  Y p+++  e++  ++ 
  gi|118431283|ref|NP_147639.2|  4 LTSLQREVLETLVSLYErhkrmIKSKEVAEALGKD----EGTVRNVIMWLKSLGLVESRT-GPAGGYMPTLKAYEVIGVQTP 80
                                   57788899988865444000136666666666666....*****************9877.***********9999887776 PP

                                   XX CS
                Penicillinase_R 78 ql 79
                                   +l
  gi|118431283|ref|NP_147639.2| 81 TL 82
                                   65 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.73
                                    -EEEEETTEEEEE-- CS
                Penicillinase_R  51 lsrekegrafiYspl 65 
                                    +  ek+g++++Y++l
  gi|118431283|ref|NP_147639.2|  90 VIVEKDGNQYRYAAL 104
                                    6689********997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.15      10      58 ..      14      62 ..       4      64 .. 0.82
   2 ?   -1.9   0.0       2.8   3.1e+03      17      31 ..     190     201 ..     178     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                    L  L+ r  r +  +e+a++lg + ++v +++  L + GLve r+gp+
  gi|118431283|ref|NP_147639.2| 14 TLVSLYERHKRMIKSKEVAEALGKDEGTVRNVIMWLKSLGLVESRTGPA 62
                                   455566666666799*******************************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                                    TTTSEEEHHHHHHHH CS
                         MarR_2  17 rpgrdltvgelarrl 31 
                                    +   d+tv+e+a+ l
  gi|118431283|ref|NP_147639.2| 190 H---DMTVREVAKFL 201
                                    3...38999999866 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027       0.3      15      45 ..      13      43 ..      12      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                   HHHHHHHHTT--EE-HHHHHHHCTS-HHHHH CS
                 Put_DNA-bind_N 15 ryLeelkeegveriSSteLaealgvtaaqvR 45
                                   + L +l e+ +  i S+e aealg ++ +vR
  gi|118431283|ref|NP_147639.2| 13 ETLVSLYERHKRMIKSKEVAEALGKDEGTVR 43
                                   6788999*******************99999 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 ?   -2.0   0.0       2.6   2.9e+03       9      20 ..       2      13 ..       1      14 [. 0.83
   2 ?    9.5   0.0    0.0007      0.78      29      45 ..      28      44 ..      26      47 .. 0.91
   3 ?   -1.4   0.0       1.8     2e+03      23      34 ..     188     199 ..     181     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.6
                                   TTS-HHHHHHHH CS
                   Sigma70_r4_2  9 aeLperqreifl 20
                                    +L+  qre+++
  gi|118431283|ref|NP_147639.2|  2 KMLTSLQREVLE 13
                                   579999***996 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0007
                                   HHHHHHHHT--HHHHHH CS
                   Sigma70_r4_2 29 ykEIAellgisegtVks 45
                                    kE+Ae lg  egtV++
  gi|118431283|ref|NP_147639.2| 28 SKEVAEALGKDEGTVRN 44
                                   69*************97 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.8
                                    HTS---HHHHHH CS
                   Sigma70_r4_2  23 yleglsykEIAe 34 
                                      ++++ +E+A+
  gi|118431283|ref|NP_147639.2| 188 VRHDMTVREVAK 199
                                    447999999997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0002      0.23      15      48 .]      22      56 ..       4      56 .. 0.82
   2 ?   -3.5   0.0       7.1     8e+03      18      26 ..     192     200 ..     191     201 .. 0.81
   3 ?   -3.7   0.2       8.4   9.5e+03       4      12 ..     287     295 ..     286     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                         HTH_24 15 npr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   + r i  +e+Ae+lg   +tv+  +  L++ Gl++
  gi|118431283|ref|NP_147639.2| 22 HKRmIKSKEVAEALGKDEGTVRNVIMWLKSLGLVE 56
                                   6666899*************************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.1
                         HTH_24  18 isqreLAer 26 
                                    ++ re+A+ 
  gi|118431283|ref|NP_147639.2| 192 MTVREVAKF 200
                                    799***986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8.4
                         HTH_24   4 tdrkILelL 12 
                                    t+ +IL++L
  gi|118431283|ref|NP_147639.2| 287 TRTDILKAL 295
                                    677899887 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047      0.53      13      53 ..      18      58 ..       8      64 .. 0.80
   2 ?   -2.4   0.0       4.7   5.2e+03      20      30 ..     191     201 ..     182     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                                   HHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXB CS
                     Sigma70_r3 13 LeqelgrePtpeEiAeeLglseekVrevleaarepvSldlp 53
                                   L+++++r  +  E+Ae+Lg +e  Vr+v++  ++  +++++
  gi|118431283|ref|NP_147639.2| 18 LYERHKRMIKSKEVAEALGKDEGTVRNVIMWLKSLGLVESR 58
                                   777788888899****************9987776666665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                                    XXXHHHHHHHH CS
                     Sigma70_r3  20 ePtpeEiAeeL 30 
                                    + t+ E+A++L
  gi|118431283|ref|NP_147639.2| 191 DMTVREVAKFL 201
                                    44677777765 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 ?   11.7   0.1   0.00025      0.28       1      55 [.       4      62 ..       4      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                         HTH_27  1 ltrqqalvLhlir...hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdea 55
                                   lt +q+ vL+++    +r+ r+++ ++++++l  +  ++ +++  L   GLve+ + +a
  gi|118431283|ref|NP_147639.2|  4 LTSLQREVLETLVslyERHKRMIKsKEVAEALGKDEGTVRNVIMWLKSLGLVESRTGPA 62
                                   688999999999999999******9***************************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2250.36
//
Query:       gi|14601113|ref|NP_147640.1|  [L=262]
Description: hypothetical protein APE_0975 [Aeropyrum pernix K1]
Scores for complete 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-87  292.3   0.7    2.8e-87  292.0   0.7    1.0  1  DUF2192   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.033   14.1   0.0    1.5  1  GSAP-16   gamma-Secretase-activating protein C-term
      0.023   14.4   0.0       0.37   10.5   0.0    2.1  2  ZapD      Cell division protein


Domain annotation for each model (and alignments):
>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.0   0.7   4.7e-91   2.8e-87       4     229 .]      10     241 ..       8     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 292.0 bits;  conditional E-value: 4.7e-91
                       DUF2192   4 ykkrievlvdllsklleee...kltReelvellkkvYeekgiePlrGlskPediYdkElatlYvvgkyGlgleeelkelfd 81 
                                    ++ri++l+d+++++l+e+    ltRe+++e+lk+vY +++i+Pl+G+++P+d+++kEla+lYvvgkyG+gle++++elfd
  gi|14601113|ref|NP_147640.1|  10 IRRRISILMDVWERMLQEWekgGLTRERAIEILKEVYGRERIKPLKGAANPPDLFEKELASLYVVGKYGMGLESDYPELFD 90 
                                   69*****************9999********************************************************** PP

                       DUF2192  82 kifsvEekleealeiilskkkeeavekvkevl.gkidenkvarvlrlvltkvvlgfadeeelikllrkleeafpelektvk 161
                                   k+f+ E+++eea++i+l++k + a+ kv+  l g++den++ar+lrl l++v++gf+++++l +ll++l+eafpe++++++
  gi|14601113|ref|NP_147640.1|  91 KVFHDEIRYEEAIKILLTEKPSTARMKVETLLgGSFDENTIARMLRLKLAEVYFGFSSQDSLKNLLKRLSEAFPEYKEMAS 171
                                   ******************9999999999998899*********************************************** PP

                       DUF2192 162 kyarfyiAfkiaekiaegeirnrlekealkkalalrlgi..ekalPsdeyiaeiakevfkvpkkvlkkvl 229
                                   kyarfyiAfkia++i++ge+r+rl+kea+k+alal++++  +k+lP+d+yi++ia++vfk+++++l+++l
  gi|14601113|ref|NP_147640.1| 172 KYARFYIAFKIADDIQKGEVRDRLTKEATKQALALEFSWlgRKVLPDDTYIRVIAEDVFKLNNRALDSIL 241
                                   **************************************9999************************9997 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 ?   14.1   0.0   5.5e-06     0.033      61     102 ..     208     249 ..     204     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-06
                       GSAP-16  61 ftvLGvrcLplstflqYidngvleltedvvkkllkdlddtee 102
                                   f  LG ++Lp +t+++ i ++v++l+++++  +l + + ++ 
  gi|14601113|ref|NP_147640.1| 208 FSWLGRKVLPDDTYIRVIAEDVFKLNNRALDSILPKSKGRKG 249
                                   889******************************998877655 PP

>> ZapD  Cell division protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.03   1.8e+02     147     191 ..      99     140 ..      87     146 .. 0.88
   2 ?   10.5   0.0   6.1e-05      0.37       3      57 ..     152     207 ..     151     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.03
                                   HHHHHHHHHHHHHHC---EEEEECCCEEEEE-SS..--EEEEEEE CS
                          ZapD 147 leealaliLkllResgefskvvaenGfyqqsleekaaqLlrvrld 191
                                    eea++++L+   ++++++ ++   G++ +++      +lr++l+
  gi|14601113|ref|NP_147640.1|  99 YEEAIKILLTEKPSTARMKVETLLGGSFDENTIA---RMLRLKLA 140
                                   6899*************************99887...99999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.1e-05
                                   HHHHHHHHHHHTT--ST.THHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHHHH CS
                          ZapD   3 LEqlfeqleefleedse.adhhaalralfelldvleRadlksellkeLerqkqkLk 57 
                                   L +l+++l+e+  e +e a++ a +   f++ d +++++++  l+ke  +q  +L+
  gi|14601113|ref|NP_147640.1| 152 LKNLLKRLSEAFPEYKEmASKYARFYIAFKIADDIQKGEVRDRLTKEATKQALALE 207
                                   668999999888776661555677***************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2075.24
//
Query:       gi|118431284|ref|NP_147641.2|  [L=100]
Description: 50S ribosomal protein L14 [Aeropyrum pernix K1]
Scores for 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-05   22.5   0.8    0.00017   21.4   0.3    1.9  1  KOW             KOW motif
     0.0073   16.6   0.0     0.0093   16.3   0.0    1.1  1  XisI            XisI protein
  ------ inclusion threshold ------
      0.015   15.8   0.0       0.02   15.3   0.0    1.3  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 !   21.4   0.3   2.8e-08   0.00017       1      31 [.       7      36 ..       7      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.8e-08
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                            KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                   +G+++  ++G+ +G+++++v++++++ +V+v
  gi|118431284|ref|NP_147641.2|  7 VGRICVKTRGREAGRKCVIVDIIDEN-FVLV 36
                                   6999**********************.4444 PP

>> XisI  XisI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.6e-06    0.0093      29      88 ..      21      82 ..       6      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                                   EEEEEEETTTTEEEEEEEEEE..TTEEEEEEEEEEEEETTEEEEEEE-SS--HHHHHHTTT- CS
                           XisI 29 eeelifDeerdhYlllevgwe..kkkrvygillhldikdgkiwiqedgteegiaeeLveaGv 88
                                   ++++i+D   ++++l++   +  + +r +  + h++i d+k+ iq+   +e++ + L eaG 
  gi|118431284|ref|NP_147641.2| 21 RKCVIVDIIDENFVLVTGPKSltGVRRRRVNIDHIEILDKKVDIQKGASDEEVLKALEEAGL 82
                                   577899999999999876554336677788888**************************997 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.4e-06      0.02       2      38 ..      47      83 ..      46      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.4e-06
                 Ribosomal_L14e  2 RqaiplkrlkLtkivlklprgartgavkkawekadve 38
                                   R  +++ ++++ + ++++++ga+ + v ka+e+a++ 
  gi|118431284|ref|NP_147641.2| 47 RRRVNIDHIEILDKKVDIQKGASDEEVLKALEEAGLA 83
                                   8999*****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 751.52
//
Query:       gi|118431285|ref|NP_147642.2|  [L=172]
Description: cytidylate kinase [Aeropyrum pernix K1]
Scores for 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-21   74.7   0.3    2.6e-10   40.7   0.1    2.0  2  Cytidylate_kin2  Cytidylate kinase-like family
    1.1e-15   58.3   0.0    1.8e-15   57.6   0.0    1.4  1  AAA_17           AAA domain
    4.7e-13   49.8   0.0    5.8e-13   49.5   0.0    1.3  1  AAA_18           AAA domain
    3.6e-09   36.9   0.0    5.1e-09   36.4   0.0    1.3  1  AAA_33           AAA domain
    4.9e-08   33.0   1.7    1.4e-07   31.5   0.2    2.0  2  Cytidylate_kin   Cytidylate kinase
    5.2e-07   29.9   0.1    1.7e-06   28.3   0.1    1.7  1  SKI              Shikimate kinase
    2.1e-05   24.6   0.0    4.3e-05   23.7   0.0    1.5  1  ADK              Adenylate kinase
    3.5e-05   24.1   0.7    0.00015   22.1   0.7    1.9  1  AAA_28           AAA domain
     0.0016   18.8   0.0     0.0026   18.2   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.003   17.9   0.0     0.0048   17.3   0.0    1.3  1  RNA_helicase     RNA helicase
     0.0036   17.2   0.0      0.028   14.3   0.0    2.0  2  NACHT            NACHT domain
     0.0045   17.3   0.0       0.01   16.1   0.0    1.9  1  AAA_22           AAA domain
     0.0052   17.1   0.8         42    4.6   0.3    3.8  3  E3_binding       e3 binding domain
     0.0064   16.9   0.0      0.008   16.6   0.0    1.2  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.019   14.9   0.0    1.4  1  Rad17            Rad17 P-loop domain
       0.02   14.8   0.0      0.037   13.9   0.0    1.5  1  NTPase_1         NTPase
      0.036   14.0   0.0      0.066   13.2   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.037   13.7   0.2        7.3    6.2   0.0    2.1  2  CoaE             Dephospho-CoA kinase
       0.05   13.3   0.0      0.083   12.6   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.055   12.9   0.0      0.074   12.5   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.094   12.1   0.0       0.14   11.5   0.0    1.2  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.098   12.4   0.1       0.13   12.0   0.1    1.2  1  ATP_bind_1       Conserved hypothetical ATP binding protein
        0.1   12.3   0.0       0.15   11.8   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.0   0.1       0.22   11.1   0.1    1.5  1  CobU             Cobinamide kinase / cobinamide phosphate gua
       0.13   12.1   0.0       0.37   10.6   0.0    1.7  2  dNK              Deoxynucleoside kinase


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 !   33.2   0.0   7.6e-11   5.4e-08       4      60 ..       2      60 ..       1      66 [. 0.88
   2 !   40.7   0.1   3.6e-13   2.6e-10      90     178 ..      65     152 ..      55     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 7.6e-11
                Cytidylate_kin2  4 IsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeev.eevdersrlssfl 60
                                   Is+  Gsg++t +++LAe+Lgl +y+   i++ +a+e gls +e+ + ++e +r++  +
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSYYSTgTIFRSIARERGLSLAEMsRLAEEDPRIDLEI 60
                                   89999**********************9*****************66666688776665 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 3.6e-13
                Cytidylate_kin2  90 relaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykkytgqdwgdae 169
                                     ++a+  +vVi    a+ +L+d+   + v++ ap  +rv+r+a+r g+  + a  +  e++  ++ ++k+y+g d++d++
  gi|118431285|ref|NP_147642.2|  65 LDVASRGGVVIDSHLAAWLLRDKA-QYLVLVKAPVWVRVRRIARRDGVPLRRALAETVEREWSQRLRFKRYYGIDVSDTT 143
                                    5677555***************88.899*********************999**************************** PP

                Cytidylate_kin2 170 nYdlvlnts 178
                                     ++l+++ts
  gi|118431285|ref|NP_147642.2| 144 IFHLTVDTS 152
                                    *******98 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   2.5e-18   1.8e-15       2      82 ..       4      81 ..       3     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.5e-18
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEE CS
                         AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghpri 82
                                   G+PGsGK+t++++l+e++g++++s+G ++r+ a+++gl  +  em++l +e + +++ e+ ++  + a+++gv++d h   
  gi|118431285|ref|NP_147642.2|  4 GPPGSGKSTYAKRLAEDLGLSYYSTGTIFRSIARERGL--SLAEMSRLAEE-DPRIDLEIDRRTLDVASRGGVVIDSHLAA 81
                                   9************************************9..78999999855.5569999999999999**********864 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   8.1e-16   5.8e-13       2     119 ..       1     114 [.       1     150 [. 0.89

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 8.1e-16
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                    +++G+pG+GK+t ak+L++ lg+     g++ r++a+e+gl+l +     +e  r+d + + + ld   +        + 
  gi|118431285|ref|NP_147642.2|   1 MISGPPGSGKSTYAKRLAEDLGLsyystGTIFRSIARERGLSLAEMSRLAEEDPRIDLEIDRRTLDVASR--------GG 72 
                                    699*****************99999*********************998888889999996666666555........77 PP

                         AAA_18  77 lvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeak 119
                                    +vid+hla ++  +  ++  v ++a+  ++ +R+++R+  + +
  gi|118431285|ref|NP_147642.2|  73 VVIDSHLAAWLLRDKAQYL-VLVKAPVWVRVRRIARRDGVPLR 114
                                    7******************.*****************976655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   7.1e-12   5.1e-09       3     120 ..       1     134 [.       1     152 [. 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 7.1e-12
                         AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldr...lyqilnelarkalsagrnvildat. 78 
                                    ++ G+pGsGKst+a+rl++ lg    s+ t++r ++ +   s+ + +r++++   +   + ++  +  +++++v++d+  
  gi|118431285|ref|NP_147642.2|   1 MISGPPGSGKSTYAKRLAEDLGLSYYSTGTIFRSIARERGLSLAEMSRLAEEdprIDLEIDRRTLD-VASRGGVVIDSHl 79 
                                    568*********************************988888887777665544455455444433.4567778888887 PP

                         AAA_33  79 .............nlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaa 120
                                                 ++++  + r++++arr gvp r    et e+++ +Rl+ +  
  gi|118431285|ref|NP_147642.2|  80 aawllrdkaqylvLVKAPVWVRVRRIARRDGVPLRRALAETVEREWSQRLRFKRY 134
                                    88988888899988889999******************************96655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2   1.9e-10   1.4e-07       3      38 ..       2      37 ..       1      70 [. 0.84
   2 ?    1.5   0.2      0.28     2e+02     103     207 ..      61     165 ..      43     169 .. 0.56

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.9e-10
                                   EE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHH CS
                 Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldtgalYRalal 38
                                   i GP gsGKs+ a++lae lgl+y +tg+++R +a 
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSYYSTGTIFRSIAR 37
                                   78******************************9984 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                                    HHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHCTSSS-S CS
                 Cytidylate_kin 103 vkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklDkerevgpL 182
                                     ++  +++++++vv++    +  +  +a+  + ++A v +R++R ++           e++++e  +R +  +   ++  
  gi|118431285|ref|NP_147642.2|  61 DRRTLDVASRGGVVIDSHLAAWLLRDKAQYLVLVKAPVWVRVRRIARRDGVPLRRALAETVEREWSQRLRFKRYYGIDVS 140
                                    55556666666777776555555555677777778888888755444422222224444555555555444333333333 PP

                                    ---TT-EEEETTTS-HHHHHHHHHH CS
                 Cytidylate_kin 183 klaedaliidtskltieevvekile 207
                                     ++   l +dts  ++e+    ile
  gi|118431285|ref|NP_147642.2| 141 DTTIFHLTVDTSMYSVEDTYRLILE 165
                                    3333346788888888877776666 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   2.4e-09   1.7e-06       1     137 [.       6     143 ..       6     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2.4e-09
                                    TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleeeglViatGGGavlseenre 80 
                                    +G+GKst +k+lA+ lgl+++ + +++   ++   ++ +     ++  e++ ++  e+ +++  V + GG ++ s+ + +
  gi|118431285|ref|NP_147642.2|   6 PGSGKSTYAKRLAEDLGLSYYSTGTIFRSIAR---ERGLSLAEMSRLAEEDPRIDLEIDRRTLDVASRGGVVIDSHLAAW 82 
                                    69***********************9877666...333333334455555555555566666778899888888888999 PP

                                    HHH.HHSEEEEEE--HHHHHHHHHHTTS...SGGGCSCHHHHHHHHHHHHHHHHHCCSSCE CS
                            SKI  81 llk.ekgiviyLdvsleellerlkadke...RPllqekskeeelleelaereplyeeaadv 137
                                    ll+ + ++++++++++ + ++r+++++    R +l e  ++e+ ++  ++r    + +++ 
  gi|118431285|ref|NP_147642.2|  83 LLRdKAQYLVLVKAPVWVRVRRIARRDGvplRRALAETVEREWSQRLRFKRYYGIDVSDTT 143
                                    99978889******************99788555555555566666666777666655554 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     6e-08   4.3e-05       1      36 [.       2      37 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6e-08
                                   EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                   + G+Pg+GK t a++l++++gl   stG ++R+  +
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSYYSTGTIFRSIAR 37
                                   57******************************8654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.7   2.1e-07   0.00015       4     128 ..       2     162 ..       1     171 [. 0.71

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.1e-07
                         AAA_28   4 itGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcDr 80 
                                    i+G++++GK+t +++La++ g +++    ++r i +e++ +  ++++ +e+  ++     e  ++++   a+++ +++D 
  gi|118431285|ref|NP_147642.2|   2 ISGPPGSGKSTYAKRLAEDlGLSYYstGTIFRSIARERGLSLAEMSRLAEEDPRIDL---EIDRRTLDV-ASRGGVVIDS 77 
                                    99***************9997776655999999999999888877776533333333...233333333.5788888998 PP

                         AAA_28  81 glldtlaYaraygg............................eaeaeleaaarekry......dl.vfllppapei..dd 123
                                     l + l   +a +                             ++e+e+ + +r+kry      d  +f+l ++  +  ++
  gi|118431285|ref|NP_147642.2|  78 HLAAWLLRDKAQYLvlvkapvwvrvrriarrdgvplrralaeTVEREWSQRLRFKRYygidvsDTtIFHLTVDTSMysVE 157
                                    87655443333333667778888888889999999999998668899999999999889999955599999888555688 PP

                         AAA_28 124 dgeRr 128
                                    d+ R 
  gi|118431285|ref|NP_147642.2| 158 DTYRL 162
                                    88874 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 !   18.2   0.0   3.6e-06    0.0026       3      28 ..       2      27 ..       1      57 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.6e-06
                                   EESSTTSSHHHHHHHHHHHHTHEEEE CS
                            AAA  3 lyGppGtGKTllakavakelgvefle 28
                                   ++GppG GK++ ak +a++lg ++++
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSYYS 27
                                   79*****************9877654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.7e-06    0.0048       3      24 ..       2      23 ..       1      39 [. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.7e-06
                   RNA_helicase  3 lyGpsgeGKStlakeLakallk 24
                                   ++Gp+g GKSt+ak+La++l  
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGL 23
                                   89****************9974 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.9e-05     0.028       5      31 ..       2      28 ..       1      47 [. 0.86
   2 ?    0.8   0.0      0.58   4.1e+02      29      64 ..      89     127 ..      77     139 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                                   EEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT  5 lqGeaGsGKTtLlqklalawaegklpq 31
                                   + G++GsGK+t +++la+++  +++  
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSYYST 28
                                   89****************998777655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.58
                                    SCCCC-SEEEEEETTTTTTS-......-HCHHHCCCCTS CS
                          NACHT  29 lpqgafklvFflslrelsrsgna...rsladllfsqlpe 64 
                                    ++ + +k + ++++r++ r+  +   r la+++ +++ +
  gi|118431285|ref|NP_147642.2|  89 QYLVLVKAPVWVRVRRIARRDGVplrRALAETVEREWSQ 127
                                    333446788888888888888777777777777777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-05      0.01      10      33 ..       2      25 ..       1     114 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                         AAA_22 10 vtGesGtGKTtllrrlleqldeea 33
                                   + G++G+GK+t ++rl+e l   +
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSY 25
                                   89***************9886554 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.088        63       7      17 ..      14      24 ..      13      29 .. 0.88
   2 ?    4.2   0.0     0.079        57       8      20 ..      33      45 ..      33      47 .. 0.88
   3 ?    4.6   0.3     0.059        42       7      19 ..     102     114 ..     101     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.088
                                   HHHHHHHCT-- CS
                     E3_binding  7 aRklAkelGid 17
                                   a++lA++lG++
  gi|118431285|ref|NP_147642.2| 14 AKRLAEDLGLS 24
                                   9********95 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.079
                                   HHHHHHCT--TTT CS
                     E3_binding  8 RklAkelGidLsd 20
                                   R +A+e G++L++
  gi|118431285|ref|NP_147642.2| 33 RSIARERGLSLAE 45
                                   789******9986 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.059
                                    HHHHHHHCT--TT CS
                     E3_binding   7 aRklAkelGidLs 19 
                                    +R++A+  G+ L 
  gi|118431285|ref|NP_147642.2| 102 VRRIARRDGVPLR 114
                                    9*********885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05     0.008      29     105 ..       2      79 ..       1     133 [. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                         AAA_16  29 lsGesGvGKsslvrellralekdggiflrgkcdql...esaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                    +sG++G+GKs+ +++l++ l  +  ++ +g+  ++   e++++++   ++++++  +  + d+ + + +++    +++ l
  gi|118431285|ref|NP_147642.2|   2 ISGPPGSGKSTYAKRLAEDLGLS--YYSTGTIFRSiarERGLSLAEMSRLAEEDPRIDLEIDRRTLDVASRGGVVIDSHL 79 
                                    89****************99988..5666666555555666666667777766666666666644444444444444444 PP

>> Rad17  Rad17 P-loop 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     0.019      49      74 ..       1      26 [.       1      47 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                          Rad17 49 LisGPsGCgkstvvkvLskelgiklr 74
                                   +isGP+G gkst  k L+  lg ++ 
  gi|118431285|ref|NP_147642.2|  1 MISGPPGSGKSTYAKRLAEDLGLSYY 26
                                   69********************9984 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.1e-05     0.037       3      33 ..       1      30 [.       1      53 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                                   EEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
                       NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGf 33
                                   +i+GppG+GK+T  k+++e l  s +  +G 
  gi|118431285|ref|NP_147642.2|  1 MISGPPGSGKSTYAKRLAEDLGLS-YYSTGT 30
                                   599****************99544.334444 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 ?   13.2   0.0   9.2e-05     0.066       4      26 ..       2      24 ..       1      33 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.2e-05
                                   EE--SSSSHHHHHHHGGGGBS-- CS
                          AAA_5  4 LvGppGtgKselaerlaaalnre 26
                                   + GppG+gKs+ a+rla+ l+ +
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLS 24
                                   67***************988655 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.01       7.3       5      47 ..       2      45 ..       1      68 [. 0.77
   2 ?    6.0   0.1     0.012       8.5     118     149 ..      84     115 ..      54     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                   EEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHH CS
                           CoaE  5 ltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkk 47
                                   ++G  +sGKst a+++a+ lg+    + ++ r++  +    l++
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEdLGLSYYSTGTIFRSIARERGLSLAE 45
                                   578889**********9889988877777777776666655555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                                    GGGGSSEEEEEE--HHHHHHHHHHCCTSTHHH CS
                           CoaE 118 lekliervlvvdvelelqveRlvardgvseee 149
                                    l+++++  ++v++++  +v+R+ +rdgv    
  gi|118431285|ref|NP_147642.2|  84 LRDKAQYLVLVKAPVWVRVRRIARRDGVPLRR 115
                                    567788999*****************996544 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 ?   12.6   0.0   0.00012     0.083      37      66 ..       1      30 [.       1      67 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                         RuvB_N 37 llyGpPGlGkttlakiiakelgvklkitsg 66
                                   +++GpPG Gk+t ak +a++lg +  +t +
  gi|118431285|ref|NP_147642.2|  1 MISGPPGSGKSTYAKRLAEDLGLSYYSTGT 30
                                   589*******************99887764 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001     0.074       6      26 ..       2      22 ..       1      49 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                   EE--TTSSHHHHHHHHHHHHH CS
                          KTI12  6 ltGlPssGKstrakeLakale 26
                                   ++G P sGKst+ak+La+ l 
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLG 22
                                   89***************9875 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    0.0002      0.14      26      44 ..       1      19 [.       1      28 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                   Mg_chelatase 26 llvGppGsGKtmlakrlps 44
                                   ++ GppGsGK+  akrl++
  gi|118431285|ref|NP_147642.2|  1 MISGPPGSGKSTYAKRLAE 19
                                   578*************975 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 ?   12.0   0.1   0.00018      0.13       1      20 [.       2      21 ..       2      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                     ATP_bind_1  1 vvGpaGsGKttfvgalseil 20
                                   + Gp+GsGK+t+ ++l+e l
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDL 21
                                   67************999865 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 ?   11.8   0.0   0.00021      0.15       2      21 ..       1      20 [.       1      57 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                   +++G pG+GKSt  ++l+++
  gi|118431285|ref|NP_147642.2|  1 MISGPPGSGKSTYAKRLAED 20
                                   689**************988 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00031      0.22       2      33 ..       1      30 [.       1      40 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                           CobU  2 lvtGgarSGKSefAeklaeeskekvvYiATae 33
                                   +++G+  SGKS++A++lae+ +  + Y  T++
  gi|118431285|ref|NP_147642.2|  1 MISGPPGSGKSTYAKRLAEDLG--LSYYSTGT 30
                                   589**************99765..44666666 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00052      0.37       3      27 ..       2      26 ..       1      34 [. 0.89
   2 ?   -1.2   0.0       2.2   1.6e+03     124     144 ..      89     109 ..      74     162 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00052
                                   EEESTTSSHHHHHHHHHCCSTCEEE CS
                            dNK  3 veGnIgaGKstlvklLskklgvkvf 27
                                   ++G+ g+GKst +k+L++ lg   +
  gi|118431285|ref|NP_147642.2|  2 ISGPPGSGKSTYAKRLAEDLGLSYY 26
                                   89*****************997655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                    SEEEEEE--HHHHHHHHHHCT CS
                            dNK 124 dlliYLkasletclerikkRg 144
                                    + l+ +ka++ + ++ri +R+
  gi|118431285|ref|NP_147642.2|  89 QYLVLVKAPVWVRVRRIARRD 109
                                    566667777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1247.29
//
Query:       gi|118431286|ref|YP_874870.1|  [L=90]
Description: 50S ribosomal protein L34 [Aeropyrum pernix K1]
Scores for 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-27   93.9   0.9    5.8e-27   93.8   0.9    1.0  1  Ribosomal_L34e   Ribosomal protein L34e


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.9   3.3e-31   5.8e-27      10      93 ..       3      86 ..       1      87 [. 0.97

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 3.3e-31
                 Ribosomal_L34e 10 rlsYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvkerivr 91
                                   r+  ++rs ++++ +tpgg++v++y+++k+  ++C+ c++ L G+p+ rp +++rlskt+k+++R+YGg+lc++c+ e+i +
  gi|118431286|ref|YP_874870.1|  3 RPGLRSRSLRRVYRRTPGGSTVVHYERRKPGPARCARCGRPLGGVPRGRPPRVRRLSKTAKRPERPYGGVLCSTCLAEMIFE 84
                                   677899**************************************************************************99 PP

                 Ribosomal_L34e 92 af 93
                                   a+
  gi|118431286|ref|YP_874870.1| 85 AI 86
                                   86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 659.86
//
Query:       gi|118431287|ref|NP_147644.2|  [L=431]
Description: amidase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-22   77.6   4.0    9.5e-22   77.6   4.0    1.5  2  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   4.0   5.3e-26   9.5e-22      84     198 ..      86     198 ..      81     208 .. 0.87
   2 ?   -3.1   0.0      0.15   2.7e+03     402     430 ..     371     396 ..     347     404 .. 0.67

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 5.3e-26
                                    HHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHC CS
                        Amidase  84 vverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfc 163
                                    v + L   G+ ++ +T+md +a+g+s+ n+v+g++ NP+++++t GGSSGG AA       +la+++D GGS RiPA ++
  gi|118431287|ref|NP_147644.2|  86 VLKALTTGGFEPYARTSMDILALGTSGFNPVLGDVLNPRNPRYTTGGSSGGAAASALLAPGLLALASDAGGSARIPAGYT 165
                                    67889999*********************************************9888888899***************** PP

                                    TSEEEE--TTSC--TTB--SSTTT-EEEEEESSHH CS
                        Amidase 164 glvGlKPtygrvSragvvalessldvvGplarsve 198
                                    g++GlK    r+ ++g  +++ s +  G l+ s  
  gi|118431287|ref|NP_147644.2| 166 GVLGLK--LRRIDYRGYRGMAPSVEAPGLLSLSMT 198
                                    *****9..677777777777777777777776655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.15
                                    HHGCCTTT...HHHHHTT--EEEEECCCC CS
                        Amidase 402 lynlldftavvvpvnlaglpalsvpagks 430
                                     ++ ++ft    ++n+ +l +ls+p+g s
  gi|118431287|ref|NP_147644.2| 371 TRRAIVFT---SLANTLDLYSLSIPLGPS 396
                                    44455555...999999999999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3355.82
//
Query:       gi|14601117|ref|NP_147645.1|  [L=142]
Description: hypothetical protein APE_0980 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.03   14.4   0.7       0.03   14.4   0.7    2.0  3  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 ?   -2.1   0.3      0.25   4.5e+03      33      38 ..       1       6 [.       1      17 [. 0.81
   2 ?   14.4   0.7   1.7e-06      0.03      16      46 ..      67      97 ..      64     101 .. 0.88
   3 ?   -3.0   0.1      0.47   8.5e+03       4      13 ..     123     132 ..     122     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.25
                        Pox_A9 33 MvmyLv 38
                                  Mv+yL+
  gi|14601117|ref|NP_147645.1|  1 MVVYLI 6 
                                  999998 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.7e-06
                        Pox_A9 16 rlRpNsfafVvlksiisMvmyLvlGvaLlyi 46
                                  r R+  f  +++k+ + M +y vlGv+ l++
  gi|14601117|ref|NP_147645.1| 67 RARSIIFKSIIVKIGLLMAVYTVLGVVALTL 97
                                  667888999*****************99887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.47
                        Pox_A9   4 llrHlfMyfc 13 
                                   l+ H+f +++
  gi|14601117|ref|NP_147645.1| 123 LFAHFFSFLY 132
                                   6788887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1216.82
//
Query:       gi|118431288|ref|NP_147646.2|  [L=202]
Description: adenylate kinase [Aeropyrum pernix K1]
Scores for complete 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-32  112.4   0.1    3.1e-32  111.9   0.1    1.3  1  AAA_17           AAA domain
    1.2e-11   45.3   0.0    2.4e-11   44.3   0.0    1.5  1  AAA_18           AAA domain
    4.5e-06   27.0   0.0    7.6e-06   26.3   0.0    1.4  1  AAA_28           AAA domain
    8.2e-06   26.3   0.5      2e-05   25.1   0.5    1.8  1  AAA_16           AAA ATPase domain
    2.3e-05   24.1   0.4    2.8e-05   23.9   0.4    1.2  1  SRP54            SRP54-type protein, GTPase domain
      5e-05   23.1   0.6      5e-05   23.1   0.6    2.0  2  AAA_30           AAA domain
    6.9e-05   22.8   0.2    0.00031   20.6   0.1    1.8  2  ATP_bind_1       Conserved hypothetical ATP binding protein
    6.9e-05   22.4   0.1    0.00012   21.6   0.1    1.5  1  KTI12            Chromatin associated protein KTI12
    0.00027   21.2   0.3    0.00076   19.8   0.3    1.7  1  AAA_22           AAA domain
    0.00064   19.7   2.7    0.00094   19.1   1.1    2.0  2  NTPase_1         NTPase
     0.0011   18.0   1.1     0.0013   17.8   0.2    1.6  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0014   18.4   0.1      0.002   17.9   0.1    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0017   18.2   0.0     0.0061   16.4   0.0    1.8  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.004   17.3   1.6      0.016   15.3   1.5    2.1  1  AAA_33           AAA domain
     0.0046   17.4   0.6     0.0071   16.8   0.2    1.7  1  AAA              ATPase family associated with various cellul
     0.0049   17.2   2.0     0.0084   16.4   1.8    1.8  1  AAA_19           AAA domain
     0.0055   16.3   1.7      0.007   16.0   0.4    1.8  3  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0076   16.3   0.1     0.0091   16.1   0.1    1.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
  ------ inclusion threshold ------
       0.01   15.9   0.3      0.097   12.8   0.3    2.5  1  MMR_HSR1         50S ribosome-binding GTPase
      0.016   15.0   0.2      0.022   14.6   0.2    1.3  1  CPT              Chloramphenicol phosphotransferase-like prot
      0.017   14.9   0.1      0.032   14.0   0.1    1.4  1  AAA_24           AAA domain
      0.018   14.5   0.0      0.027   14.0   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.022   14.0   0.1      0.032   13.5   0.1    1.4  1  KAP_NTPase       KAP family P-loop domain
      0.024   14.6   0.3      0.043   13.7   0.3    1.5  1  NACHT            NACHT domain
      0.028   14.4   0.0      0.051   13.6   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
      0.029   14.4   0.2      0.049   13.7   0.2    1.7  1  AAA_14           AAA domain
      0.036   14.6   0.1      0.039   14.5   0.1    1.5  1  ABC_tran         ABC transporter
      0.068   13.1   0.0       0.11   12.4   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
       0.07   12.4   0.0       0.12   11.7   0.0    1.3  1  DUF3638          Protein of unknown function (DUF3638)
        0.1   12.5   0.1       0.22   11.4   0.1    1.5  1  RsgA_GTPase      RsgA GTPase
       0.11   12.4   0.0       0.18   11.7   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
       0.12   12.0   0.1        7.9    6.1   0.1    2.4  2  Thymidylate_kin  Thymidylate kinase
       0.12   11.6   0.0       0.15   11.3   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.14   10.1   0.0       0.18    9.7   0.0    1.1  1  Herpes_Helicase  Helicase
       0.19   11.7   0.0       0.25   11.2   0.0    1.2  1  Rad17            Rad17 P-loop domain
       0.37   10.7   2.1       0.84    9.5   0.3    2.4  2  APS_kinase       Adenylylsulphate kinase


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 !  111.9   0.1   6.1e-35   3.1e-32       1     129 [.      11     149 ..      11     157 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 6.1e-35
                                    EE-TTSSHHHHHHHHH.....HHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.....H CS
                         AAA_17   1 lGgPGsGKgtqceklv.....ekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.....k 70 
                                    +G+PG+GK+t++++l+     e ++++++++G+ + ++a + gl+++rd++r+lpl+++ elq+eaa++i  ea     +
  gi|118431288|ref|NP_147646.2|  11 TGVPGVGKTTVIKELQglaekEGVKLHIVNFGSFMLDTAVKLGLVEDRDKIRTLPLRRQLELQREAAKRIVAEAskalgG 90 
                                    7**************6555446779999******************************************8887667755 PP

                                    SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS CS
                         AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdd 129
                                    ++ +++d+h+ +k+ ag+++glpk+vl+elkpd+i ++ea+pee+ +r ++d+tr r d
  gi|118431288|ref|NP_147646.2|  91 DGVLIIDTHALVKTVAGYWPGLPKHVLDELKPDMIAVVEASPEEVAARQARDTTRYRVD 149
                                    5668*****************************************************87 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   4.8e-14   2.4e-11       1     112 [.       8     141 ..       8     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.8e-14
                         AAA_18   1 IlltGtpGvGKttlakeL...skrlgf.......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssa 70 
                                    +++tG+pGvGKtt+ keL   ++++g+       g    d+a + gl++++d+  + + +r  e +++++ +++ e+s+a
  gi|118431288|ref|NP_147646.2|   8 VVVTGVPGVGKTTVIKELqglAEKEGVklhivnfGSFMLDTAVKLGLVEDRDKIRTLPLRRQLELQREAAKRIVAEASKA 87 
                                    79****************8886665667788999********************66666666666666688888888888 PP

                         AAA_18  71 leegknlvidghlaeleseaakdikk............vvLtaspeelleRlek 112
                                    l+  ++l+id h      + ++ +               v++aspee + R ++
  gi|118431288|ref|NP_147646.2|  88 LGGDGVLIIDTHALVKTVAGYWPGLPkhvldelkpdmiAVVEASPEEVAARQAR 141
                                    999**********99999999988779999*******99*********999665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.5e-08   7.6e-06       2      94 ..       8     112 ..       7     163 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.5e-08
                         AAA_28   2 ivitGgestGKTtlleaLa...ar.gypvv.pEaareileekl....akgedalpwv..edllafaervleeqleeeaaa 70 
                                    +v+tG ++ GKTt++++L+   ++ g++ +   ++  +l+        +++d+++    ++ l+++++  +   +  a+a
  gi|118431288|ref|NP_147646.2|   8 VVVTGVPGVGKTTVIKELQglaEKeGVKLHiVNFGSFMLDTAVklglVEDRDKIRTLplRRQLELQREAAK---RIVAEA 84 
                                    8*****************98863369997668888888877774444233333332212455555554333...222333 PP

                         AAA_28  71 ....aankvlfcDrglldtlaYaraygg 94 
                                         +++vl++D+ +l  ++     g 
  gi|118431288|ref|NP_147646.2|  85 skalGGDGVLIIDTHALVKTVAGYWPGL 112
                                    345789*********9998887655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.5   3.9e-08     2e-05      25     107 ..       6      97 ..       1     202 [] 0.60

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.9e-08
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel......lrqlldeaesaeleawr 98 
                                     +v+++G +GvGK+++++el+  +ek+g+ +   ++ ++         ++++ + +l      +r l  + +  ++++++
  gi|118431288|ref|NP_147646.2|   6 KVVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVNFGSF--------MLDTAVKLGLvedrdkIRTLPLRRQLELQREAA 77 
                                    689******************999999766555555555........222222223300000033333332222222333 PP

                         AAA_16  99 ekleeala...........a 107
                                    +++ ++++           +
  gi|118431288|ref|NP_147646.2|  78 KRIVAEASkalggdgvliiD 97 
                                    33333222333344444440 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.4   5.6e-08   2.8e-05       2     145 ..       6     153 ..       5     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.6e-08
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik.kkeeadpaavakeavekak 80 
                                    +v+++ G+ G+GKTt +  L  l +keg k+ +v    f    +  L  + ++ +++ +  +++ + + + ak+ v +a 
  gi|118431288|ref|NP_147646.2|   6 KVVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVNFGSFMLDTAVKLGLVEDRDKIRTLPlRRQLELQREAAKRIVAEAS 85 
                                    6899*****************************************************99964444455566666655554 PP

                                    HTT..SSEEEEEE--SSTTHHHHHHHHHH.HHHHHSSSEEEEEEETTBHTHHHHHHHHH.HHHSSCSEE CS
                          SRP54  81 eek..idvvlvDTaGrlqndkelmeelkk.ikkvvkpdevllvldattgqeavkqakaF.keavgitgv 145
                                    +      v+++DT    ++ + +   l k + + +kpd ++ v++a+ ++ a++qa++  + +v+i+gv
  gi|118431288|ref|NP_147646.2|  86 KALggDGVLIIDTHALVKTVAGYWPGLPKhVLDELKPD-MIAVVEASPEEVAARQARDTtRYRVDIGGV 153
                                    4322256899****999999999999966155566665.566778888888888877541456777776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.6     1e-07     5e-05      19      52 ..       6      39 ..       1     106 [. 0.68
   2 ?   -0.6   0.2       1.9   9.5e+02      49      82 ..     127     169 ..     114     201 .. 0.48

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-07
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvigl 52
                                   +v+v+tG++G GKtt++k+l+ ++e++g +++++
  gi|118431288|ref|NP_147646.2|  6 KVVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIV 39
                                   699************************9766554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.9
                         AAA_30  49 viglAptgkaAkvLaeelgi.....eastiakllkrlk....g 82 
                                    v+ ++p++ aA++ ++ +         + +++l+++ +    +
  gi|118431288|ref|NP_147646.2| 127 VVEASPEEVAARQARDTTRYrvdigGVEGVKRLMENARaasiA 169
                                    5555666666666665443222222333333333333333331 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 !   20.6   0.1   6.3e-07   0.00031       1      33 [.      10      47 ..      10      53 .. 0.86
   2 ?    0.2   0.0       1.1   5.3e+02     197     236 ..     161     200 ..      93     202 .] 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.3e-07
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvN.....LD 33
                                   v+G++G+GKtt +++l+ ++e++g ++++vN     LD
  gi|118431288|ref|NP_147646.2| 10 VTGVPGVGKTTVIKELQGLAEKEGVKLHIVNfgsfmLD 47
                                   89*****************************4444445 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                     ATP_bind_1 197 ykklaeaiaelleefalvlrflplssekeesiedllslid 236
                                     +  a++ia++++  + v  +   + e  +++e+ll+li+
  gi|118431288|ref|NP_147646.2| 161 ENARAASIASAIQYASTVAIVENREGEAAKAAEELLRLIK 200
                                    4456788999999999997777888888888999998887 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   2.4e-07   0.00012       4      41 ..       8      45 ..       6     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.4e-07
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                          KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                   vv+tG+P +GK+t+ keL+   e+e+ + ++++  s+ 
  gi|118431288|ref|NP_147646.2|  8 VVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVNFGSFM 45
                                   9******************************9987776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.3   1.5e-06   0.00076       7      98 ..       7      97 ..       2     103 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-06
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.........erlsseell 79
                                   ++vvtG +G+GKTt++++l+  +++e      ++++  v+  s +    l +++   l +++++          +l++e+  
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELQGLAEKE------GVKLHIVNFGSFM----LDTAVKLGLVEDRDKirtlplrrqLELQREAAK 78
                                   789*****************998543......5555555555555....333333333333333344433334445555555 PP

                         AAA_22 80 ealeqalraravielliiD 98
                                   + +++a++a +  ++liiD
  gi|118431288|ref|NP_147646.2| 79 RIVAEASKALGGDGVLIID 97
                                   5555555555557777777 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.1   1.9e-06   0.00094       2      30 ..       8      36 ..       7      39 .. 0.93
   2 ?   -0.8   0.0       2.6   1.3e+03      92     102 ..      87      97 ..      67     156 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-06
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                   v++TG pGvGKtT++k +  l +++gvk+
  gi|118431288|ref|NP_147646.2|  8 VVVTGVPGVGKTTVIKELQGLAEKEGVKL 36
                                   89*********************999986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.6
                                    HHHHH-EEEE- CS
                       NTPase_1  92 alseadviviD 102
                                    al + +v++iD
  gi|118431288|ref|NP_147646.2|  87 ALGGDGVLIID 97 
                                    45555566665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   2.5e-06    0.0013      30      63 ..       6      39 ..       4      64 .. 0.92
   2 ?   -3.8   0.1        10     5e+03       4      20 ..     177     193 ..     175     199 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                   EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                           MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                   +vv +tGvPG+Gk t++++l     ++G +  ++
  gi|118431288|ref|NP_147646.2|  6 KVVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIV 39
                                   5889*****************9999999999887 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 10
                                    HHHHHH--SHHHHHHHH CS
                           MeaB   4 aitlveserpeakelle 20 
                                     + +ve+++ ea +  e
  gi|118431288|ref|NP_147646.2| 177 TVAIVENREGEAAKAAE 193
                                    56677777774443333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.1e-06     0.002       2      21 ..       9      28 ..       8      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.1e-06
                Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                                   vv GvpG GK+t+i++l   
  gi|118431288|ref|NP_147646.2|  9 VVTGVPGVGKTTVIKELQGL 28
                                   9***************9755 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 ?   -0.8   0.0       2.3   1.1e+03       4      25 ..      15      36 ..      12      41 .. 0.73
   2 !   16.4   0.0   1.2e-05    0.0061      82     170 ..      75     160 ..      65     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.3
                         CLP1_P  4 dsGKSTlarlLlNyalrkgrkp 25
                                    +GK+T+++ L   a ++g k 
  gi|118431288|ref|NP_147646.2| 15 GVGKTTVIKELQGLAEKEGVKL 36
                                   69*****999887777666665 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.2e-05
                         CLP1_P  82 alvkelareveekleenkkakasgliIntpGwvkgl.ga..ellleliealepdvvvvldqeellnelkrdlplskvkvv 158
                                    ++ k+++ e+++        ++++liI+t+ +vk + g+   l +++++ l+pd+++v++ +  ++   r++++++   v
  gi|118431288|ref|NP_147646.2|  75 EAAKRIVAEASKA-----LGGDGVLIIDTHALVKTVaGYwpGLPKHVLDELKPDMIAVVEAS-PEEVAARQARDTTRYRV 148
                                    3344444444422.....336799**********9757776788****************95.34444444554566666 PP

                         CLP1_P 159 klpkspgvvqrs 170
                                     +  ++gv+   
  gi|118431288|ref|NP_147646.2| 149 DIGGVEGVKRLM 160
                                    666666664444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.5   3.3e-05     0.016       1      25 [.       7      36 ..       7     150 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-05
                         AAA_33  1 lvllvGlpGsGKstlaerl...lkklg..a 25
                                   +v++ G+pG+GK+t++++l   ++k+g   
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELqglAEKEGvkL 36
                                   899**************9866455555541 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   1.4e-05    0.0071       1      38 [.       8      69 ..       8     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-05
                                   EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCS.SS....................S CS
                            AAA  1 vllyGppGtGKTllakavakel...gvefleisgsell.sk....................y 38
                                   v+++G pG+GKT+++k +   +   gv++  ++  +++ +                      
  gi|118431288|ref|NP_147646.2|  8 VVVTGVPGVGKTTVIKELQGLAekeGVKLHIVNFGSFMlDTavklglvedrdkirtlplrrQ 69
                                   5789************9988773334666666666666333666666666666666655552 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.8   1.7e-05    0.0084      10      38 ..       5      33 ..       2     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-05
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                    kv++vt+ pG GKT+v+k+   l++++g
  gi|118431288|ref|NP_147646.2|  5 FKVVVVTGVPGVGKTTVIKELQGLAEKEG 33
                                   589***************99876666655 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 !   16.0   0.4   1.4e-05     0.007       2      32 ..       7      39 ..       6      56 .. 0.85
   2 ?   -2.6   0.0       7.3   3.6e+03     128     128 ..     137     137 ..     112     181 .. 0.59
   3 ?   -1.9   0.0       4.4   2.2e+03     104     122 ..     166     184 ..     129     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEE CS
                           cobW  2 vtvltGflGsGKTtLlnhll..enraglklavi 32
                                   v+v+tG +G GKTt++++l   ++++g kl ++
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELQglAEKEGVKLHIV 39
                                   89****************987788888887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.3
                                    H CS
                           cobW 128 e 128
                                     
  gi|118431288|ref|NP_147646.2| 137 A 137
                                    1 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.4
                                    HHHHHCCCECEEEEEEETT CS
                           cobW 104 eelksdltldavvavvDak 122
                                     +++s++++ ++va+v+ +
  gi|118431288|ref|NP_147646.2| 166 ASIASAIQYASTVAIVENR 184
                                    4555566666666666654 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 !   16.1   0.1   1.8e-05    0.0091       2      83 ..       8     184 ..       7     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                                    EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                           CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                    +++ +  GvGKTt+   L  +  ++g +   v ++  +  +a+  gl++d+++                           
  gi|118431288|ref|NP_147646.2|   8 VVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVNFGSFMLDTAVKLGLVEDRDKirtlplrrqlelqreaakrivaeaska 87 
                                    6777778************************************************************************* PP

                                    ...................................................................CCHCCCHHHHHHC CS
                                    ...................................................................xxxxxxxxxxxxx RF
                           CbiA  55 ...................................................................dlkrllellealg 67 
                                                                                                       ++krl e ++a +
  gi|118431288|ref|NP_147646.2|  88 lggdgvliidthalvktvagywpglpkhvldelkpdmiavveaspeevaarqardttryrvdiggveGVKRLMENARAAS 167
                                    *********99999999999999999999999999999999999999999999999999999999998888888888877 PP

                                    HCHHHH...EEEEEEEE CS
                                    xxxxxx.xxxxxxxxxx RF
                           CbiA  68 kkkall.lkiagvvlnr 83 
                                    +  a +    + +v nr
  gi|118431288|ref|NP_147646.2| 168 IASAIQyASTVAIVENR 184
                                    77666665555666665 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   0.3   0.00019     0.097       2      82 ..       8     128 ..       7     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                                    EEEEESTTSSHHHHHHHHHT...STEEESSSTTSSSSE.EEEEEEETTEE.............................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg...ekaivsdkpgtTrdi.negrvklkgke.............................. 47 
                                    v++ G p vGK+t+i+ l g   +        g+ ++i n+g + l+                                 
  gi|118431288|ref|NP_147646.2|   8 VVVTGVPGVGKTTVIKELQGlaeK-------EGVKLHIvNFGSFMLDT-Avklglvedrdkirtlplrrqlelqreaakr 79 
                                    899***************873331.......23333322222222111.0111111122234444444444444455555 PP

                                    .............EEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEE CS
                       MMR_HSR1  48 .............ielvDtpGliegaseek.glgkaflaleeadlillv 82 
                                                 + ++Dt  l+++    + gl k++l+  + d+i++v
  gi|118431288|ref|NP_147646.2|  80 ivaeaskalggdgVLIIDTHALVKTVAGYWpGLPKHVLDELKPDMIAVV 128
                                    5555555555555666666666655555556666666666665555444 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   4.3e-05     0.022       2     134 ..       6     146 ..       5     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.3e-05
                                    -EEEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHHS-GGGGT.....STTSEEEETTSEEE-HHHHHHHHHHHHHH CS
                            CPT   2 riilLnGgsssGKsslaralqevldepwlhlgvDafvealppkrqd.....eadglefeteleeigpeldlllaalyeav 76 
                                    ++++  G++  GK+++ + lq ++++  ++l + +f   +++  ++     + d ++  + + + + +++++ + ++ea 
  gi|118431288|ref|NP_147646.2|   6 KVVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVNFGSFMLDTAVKlglveDRDKIRTLPLRRQLELQREAAKRIVAEAS 85 
                                    699**********************9999999988888887777766666688999999999999999999999999999 PP

                                    HHHHHTT-EEEEEE--TTTHH..HHHHHHHHHTTS-EEEEE.EE--HHHHHHHHHHHTSSS CS
                            CPT  77 aamaraGnnvivDdvilekew..lvdllrrllsgldvllVG.vrcplevlerRelergdRe 134
                                    +a    G  +i  +++++  +   + l +++l +l+  ++  v ++ e++++R+++ + R+
  gi|118431288|ref|NP_147646.2|  86 KALGGDGVLIIDTHALVKTVAgyWPGLPKHVLDELKPDMIAvVEASPEEVAARQARDTTRY 146
                                    9999999966655776665443346677788888876666514677777777777766665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   6.4e-05     0.032       4      22 ..       7      25 ..       5      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.4e-05
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                    ++++G +g+GKTt++kel
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKEL 25
                                   789**************99 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 ?   14.0   0.0   5.5e-05     0.027      35      72 ..       7      44 ..       3      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                          AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                    v+++G  G+GKt++ik+l    +ke ++ +++nf + 
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVNFGSF 44
                                   5899****************9999**********9875 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 ?   13.5   0.1   6.4e-05     0.032      22      64 ..       7      47 ..       2     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                     KAP_NTPase 22 vvgLygkWGsGKssllnkledelkefakpvrflfaefnawsfk 64
                                   vv+++g  G+GK++++++l+   +++   v++++++f ++  +
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELQGLAEKE--GVKLHIVNFGSFMLD 47
                                   8999999*******************..9********999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   8.7e-05     0.043       2      31 ..       7      36 ..       6     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.7e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpq 31
                                   +v+++G +G+GKTt +++l  ++ ++  + 
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELQGLAEKEGVKL 36
                                   89****************988887776555 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    0.0001     0.051       2      46 ..       8      55 ..       7      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                                   EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrre 46
                                   v++ G pG+gK++++++l  +    + ++++v++ +++  + +k ++ 
  gi|118431288|ref|NP_147646.2|  8 VVVTGVPGVGKTTVIKELQGLAekeGVKLHIVNFGSFMLDTAVKLGLV 55
                                   6889***************99998899999999999888887776665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   9.8e-05     0.049       3      23 ..       6      26 ..       4     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.8e-05
                         AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                   k++v+tG+  vGKTt++k+l 
  gi|118431288|ref|NP_147646.2|  6 KVVVVTGVPGVGKTTVIKELQ 26
                                   89***************9984 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   7.8e-05     0.039      12      44 ..       6      38 ..       3     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.8e-05
                                   SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 12 ekvaivGenGaGKStLlkllagllkpteGeill 44
                                   ++v+++G  G GK+t++k l gl +++  ++++
  gi|118431288|ref|NP_147646.2|  6 KVVVVTGVPGVGKTTVIKELQGLAEKEGVKLHI 38
                                   7899*******************9876555544 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   0.0   0.00021      0.11      18      46 ..       3      31 ..       1     105 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                       ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienled 46
                                    p ++++++G  g+GKt+++ke+    e+
  gi|118431288|ref|NP_147646.2|  3 HPFKVVVVTGVPGVGKTTVIKELQGLAEK 31
                                   6889*****************98655544 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00023      0.12      50     136 ..      15      97 ..      13     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                        DUF3638  50 GeGKssvIvPivaaaladgkkLvrvivlkpllkqmaqlLvskLggllnr.rvyhlpfsRslklteekaeairklleeclk 128
                                    G GK++vI  +  +a ++g kL  v +   +l++++     kLg + +r +++ lp++R+l+l++e a++i + +++ l 
  gi|118431288|ref|NP_147646.2|  15 GVGKTTVIKELQGLAEKEGVKLHIVNFGSFMLDTAV-----KLGLVEDRdKIRTLPLRRQLELQREAAKRIVAEASKALG 89 
                                    678888888887777777778877777777666654.....6777777746***************************** PP

                        DUF3638 129 eggvllvq 136
                                      gvl++ 
  gi|118431288|ref|NP_147646.2|  90 GDGVLIID 97 
                                    ****9986 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   0.00044      0.22     100     123 ..       6      29 ..       2      43 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                                    SEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpel 123
                                    k++v+ G  GvGK+t+i++l++ +
  gi|118431288|ref|NP_147646.2|   6 KVVVVTGVPGVGKTTVIKELQGLA 29 
                                    789*****************9854 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.18       2      39 ..       8      48 ..       7      68 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                          AAA_3  2 vllegvPGlaktllvkal...akaldlefkriqftpdllPs 39
                                   v+++gvPG++kt+++k+l   a++ +++++ + f + +l +
  gi|118431288|ref|NP_147646.2|  8 VVVTGVPGVGKTTVIKELqglAEKEGVKLHIVNFGSFMLDT 48
                                   7899**********998622266667777777777766655 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.016       7.9       3      26 ..      12      35 ..      10      43 .. 0.84
   2 ?    3.6   0.0      0.09        45     112     145 ..     114     149 ..     109     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                   ESTTSSHHHHHHHHHHHHHHTTE. CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik 26
                                   G+ G+GKtt+++ l    ++eg k
  gi|118431288|ref|NP_147646.2| 12 GVPGVGKTTVIKELQGLAEKEGVK 35
                                   999***********9998888876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.09
                                    GGTTS..E-SEEEEEESSHHHHHTSCCTTSSTTTSH CS
                Thymidylate_kin 112 edvll..kPdltflldvdpevalkRlakrdeldeee 145
                                    ++vl   kPd++  ++ +pe+ ++R a+  ++++ +
  gi|118431288|ref|NP_147646.2| 114 KHVLDelKPDMIAVVEASPEEVAARQARDTTRYRVD 149
                                    55555669*****************99988877755 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.15       2      21 ..       6      25 ..       5      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                        DUF2075  2 avvlVtGvaGtGKtvvllnl 21
                                   +vv+VtGv+G GKt v  +l
  gi|118431288|ref|NP_147646.2|  6 KVVVVTGVPGVGKTTVIKEL 25
                                   69************998766 PP

>> Herpes_Helicase  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00037      0.18      57      80 ..       3      26 ..       1      30 [. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                Herpes_Helicase 57 lPFsaylitGtAGaGkstsiqala 80
                                    PF++ ++tG  G Gk+t i+ l+
  gi|118431288|ref|NP_147646.2|  3 HPFKVVVVTGVPGVGKTTVIKELQ 26
                                   5*******************9875 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    0.0005      0.25      44      66 ..       4      26 ..       1      58 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                          Rad17 44 kkriLLisGPsGCgkstvvkvLs 66
                                   + ++++++G +G gk+tv+k+L 
  gi|118431288|ref|NP_147646.2|  4 PFKVVVVTGVPGVGKTTVIKELQ 26
                                   567999**************984 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0017      0.84       4      37 ..       7      40 ..       5     102 .. 0.80
   2 ?   -0.8   0.1       2.6   1.3e+03      55      79 ..     157     181 ..     137     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                     APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLd 37
                                   vv +tG+ g GK+t+ ++l+   +++g++  +++
  gi|118431288|ref|NP_147646.2|  7 VVVVTGVPGVGKTTVIKELQGLAEKEGVKLHIVN 40
                                   7899****************99999998877655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.6
                                    HHHHHHHHHHHHHHHHHHTT-EEEE CS
                     APS_kinase  55 dRkenirrvaevaklladaglivlv 79 
                                    +R ++  r a +a+ ++ a+++++v
  gi|118431288|ref|NP_147646.2| 157 KRLMENARAASIASAIQYASTVAIV 181
                                    4445555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.36
# Mc/sec: 1665.56
//
Query:       gi|118431289|ref|NP_147647.2|  [L=457]
Description: preprotein translocase subunit SecY [Aeropyrum pernix K1]
Scores for 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-63  212.4  12.8      1e-62  212.1  12.8    1.1  1  SecY             SecY translocase
    2.2e-11   43.4   1.2    7.6e-11   41.7   1.2    2.0  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.1  12.8   1.2e-66     1e-62       1     306 []      73     433 ..      73     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 212.1 bits;  conditional E-value: 1.2e-66
                                    BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC............ CS
                           SecY   1 sifaLGImPyitasIilqLl.tvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg............ 65 
                                    ++++LGI+P++tas+i+q+l ++     +++k +  ++egr+k+++++++l++++a+++a++++++ g            
  gi|118431289|ref|NP_147647.2|  73 TLMELGIGPIVTASLIIQVLvGA-----KIIKlDLaDPEGRRKFTSAQKVLALAFAALEAVAFTVG-Grywvgtaiepgp 146
                                    89******************999.....666655569*************************8866.359999******* PP

                                    HH.HHHHHHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHCCHSS-.HHHH..........SS........... CS
                           SecY  66 lalllivlqltagtvllmwLgEqite.kGiGnGisllifagivarlpkalsg.liel..........ale.......... 123
                                    l ++l+ lql++g++l+++++E++++ +GiG+ isl+i+ag++++++ ++ g ++ +          + +          
  gi|118431289|ref|NP_147647.2| 147 LDYALVSLQLFLGALLVIYFDEVMQKgWGIGSAISLFILAGVAQGVVWSIFGtIPGVaqdyglvpaiI-Snpdltllarp 225
                                    999********************************************555542554444455555441.14445556678 PP

                                    .THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHHHH.............. CS
                           SecY 124 gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfasslla.............. 189
                                    + ++ l+ +++tl+ i+l+vy++ ++++ip+++++    +g +s++Pl+++y  +iPi+++  l++              
  gi|118431289|ref|NP_147647.2| 226 NGFPDLTGFFTTLAAIILLVYLQAMRVEIPITSERF---KGIRSRVPLQFIYVTNIPILLVGILVSdlllvqrlladylg 302
                                    779*****************************9965...69*****************9999999988777777666666 PP

                                    .......HHHCCCCS..........TCCC.S..THHHHHHHHHHHHHHHHHHHHTCT.THHHHHHHCCHHTBSSSCTTT. CS
                           SecY 190 .......lpstiaqfl.........lall.s..psvlyvvlyvlliifFayfyteit.fnpkevaenlkksggfipgir. 248
                                           + s+i   +         ++ + +  ++++ ++  ++l i+F y+++ei+ +np+e ae l k g  ipg+r 
  gi|118431289|ref|NP_147647.2| 303 vesrayqIYSSI---VyylspprgvVQSIaDpvKTAVFIASWTVLSIVFGYMWVEIAgLNPREQAERLIKGGLAIPGMRs 379
                                    666555522222...133355554422221355567888899999999******************************** PP

                                    TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                           SecY 249 pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                    + + ++++L++++  +t++++l++a++++++d++ga  +g  +gt+lL++Vg++ +++
  gi|118431289|ref|NP_147647.2| 380 DPRVLERVLRRYIYPLTFLSSLIVAALVIVADIFGA--YG--TGTGLLLAVGIINQYY 433
                                    99**********************************..66..9***********9986 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   1.2   8.4e-15   7.6e-11       1      35 []      38      72 ..      38      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 8.4e-15
                                   HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                   +lY+++s+iPLyGi+ +++  +  + R+ifAs+ G
  gi|118431289|ref|NP_147647.2| 38 VLYFIMSNIPLYGIPPQNIGGQVDLQRIIFASSAG 72
                                   79*************99****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); 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:                         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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.35
# Mc/sec: 3904.63
//
Query:       gi|118431290|ref|NP_147648.2|  [L=333]
Description: hypothetical protein APE_0985.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 2880.91
//
Query:       gi|118431291|ref|NP_147649.2|  [L=238]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Aeropyrum pernix K1]
Scores for complete 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-44  151.2   0.0    2.7e-44  151.0   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   1.5e-48   2.7e-44       2     191 ..      15     227 ..      14     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 1.5e-48
                                    HHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSS...S-S...... CS
                  DHBP_synthase   2 eaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmve...ene...... 72 
                                    +a+++l++G +v+++D ++re+e+dL++ A +vt+++v ++++ a+Glic+ ++e++ + L+Lp+++e   + +      
  gi|118431291|ref|NP_147649.2|  15 RAVDSLRNGMPVMIYDGDRREGEVDLVYYAGSVTWREVYTLRTLAGGLICFVTSERVGRLLGLPFAQElllS-Qeslapl 93 
                                    6999**************************************************************965552.1578999 PP

                                    ........STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T.............T--GGGEEEEEEEEEEEE-TTGG CS
                  DHBP_synthase  73 ........dkhktaftvsvdaaegttTGIsaaDRalTirkladp.............kakpedfrrPGhvfplrareggv 131
                                            d+   af+++v++  +++TGIs++DR  Ti+ l++              +   e+f +PGhv +l ar+  +
  gi|118431291|ref|NP_147649.2|  94 asktpgygDP--PAFSIWVNHV-SVKTGISDEDRGITISGLHRVvekaysglvgearRMLREEFMSPGHVPILLARS--L 168
                                    9999997666..9********9.9*****************99556899****99886677***************7..* PP

                                    GTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                  DHBP_synthase 132 leRrghTEaavdLarlaglkpaavicellnddgtmarrdeleefakkhglkiitiedlie 191
                                     +RrghTE++v+L rlagl+p  vi+e+l ++  ++ ++e+e++a++  ++++++e+++e
  gi|118431291|ref|NP_147649.2| 169 DRRRGHTELTVALGRLAGLPPSFVIAEMLGERW-SLGLREAEAIARERRIPLLRGEEIVE 227
                                    *********************99******9885.9***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1910.19
//
Query:       gi|14601122|ref|NP_147650.1|  [L=155]
Description: riboflavin synthase [Aeropyrum pernix K1]
Scores for complete 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   34.2   0.2    2.4e-08   33.9   0.2    1.1  1  DMRL_synthase   6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
       0.15   11.0   0.0       0.19   10.7   0.0    1.1  1  SHR3_chaperone  ER membrane protein SH3


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.2   2.7e-12   2.4e-08      26     136 ..      23     128 ..       6     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.7e-12
                                   HHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHHHCTS-EEEEEE CS
                 DMRL_synthase  26 elkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyvaeavskglmrvsldtgvPvifgvl 106
                                   e+ ++     +i++ tVPG  +lp aak++++  ++ ++vi+lG v r e ++  y a++v  gl+ v++ tg+ vi  v 
  gi|14601122|ref|NP_147650.1|  23 EVLRRRLPGYRIVRHTVPGIKDLPGAAKRILSM-GC-EGVITLGWVGRREADKLSYLAASV--GLIMVEVLTGKIVID-VT 98 
                                   3444444557899******************94.45.*****************9998766..899999999976665.55 PP

                                   EESSHHCCHHCCTSTCCCHHHHHHHHHHHH CS
                 DMRL_synthase 107 tvdteeqaleraggkagnkGeeaaeaalem 136
                                     ++e++a e   + a ++++++ae+   +
  gi|14601122|ref|NP_147650.1|  99 VHEDEAEAPEELAAIAVDRARKHAENLAAL 128
                                   566666666666455688888888777665 PP

>> SHR3_chaperone  ER membrane protein SH3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.2e-05      0.19     110     176 ..      56     123 ..      50     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.2e-05
                SHR3_chaperone 110 glrtvtegawgevdredslkvlaasn.tilalvLvGVlvLQaGqwYaerkeqeeleefeeeeaeeaaa 176
                                   g + v++  w    + d+l+ laas  +i++ vL+G +v+ ++    e +  eel++++ ++a+++a+
  gi|14601122|ref|NP_147650.1|  56 GCEGVITLGWVGRREADKLSYLAASVgLIMVEVLTGKIVIDVTVHEDEAEAPEELAAIAVDRARKHAE 123
                                   6666777778888999*********7267777**********99999999999999887777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1168.21
//
Query:       gi|118431292|ref|NP_147652.2|  [L=354]
Description: H/ACA RNA-protein complex component Cbf5p [Aeropyrum pernix K1]
Scores for 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-25   90.8   0.1    7.2e-22   78.4   0.1    3.1  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
    1.5e-19   69.8   0.0    3.4e-19   68.8   0.0    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    2.6e-18   65.7   0.6    4.7e-18   64.9   0.6    1.4  1  PUA       PUA domain
    1.3e-15   57.2   0.3    2.8e-15   56.1   0.3    1.5  1  DKCLD     DKCLD (NUC011) domain
    0.00035   20.8   0.0    0.00083   19.6   0.0    1.6  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> 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 !   78.4   0.1     2e-25   7.2e-22       1     149 []      77     190 ..      77     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 2e-25
                                    HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHH CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleev 80 
                                    kr+l+++++Gh+GtLDp++tGvL+va++++T+++  +++++KeY+++++l+                     +e++l+ev
  gi|118431292|ref|NP_147652.2|  77 KRMLGVSRAGHGGTLDPKVTGVLPVALERMTRIIGTVMHSSKEYVCVMQLHRPV------------------EEDRLREV 138
                                    899***********************************************8654..................445699** PP

                                    HHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                         TruB_N  81 lkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                    lk f+Gei+q pp  S+vk                 r+ r+ ++ ++elle++ +++ l+v+c++GtY+
  gi|118431292|ref|NP_147652.2| 139 LKLFEGEIYQKPPLRSSVK-----------------RALRTRRVFRIELLEYTGKYALLRVDCEAGTYM 190
                                    *******************.................899*****************************6 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 !   68.8   0.0   9.4e-23   3.4e-19       1      62 [.     191     257 ..     191     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 9.4e-23
                                    HHHHHHHHHHTTS-EEEEEEEEEEETTE..GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGG CS
                       TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf..deedmvtledLedavllyke..dee.LdrlllPlesa 62 
                                    R+Lc DiG++Lg+gAh++eLRR+r+gpf  d   mv+l+d++ av  ++e  +++ L+r+++P e  
  gi|118431292|ref|NP_147652.2| 191 RKLCWDIGLVLGVGAHMRELRRIRTGPFseDSGLMVRLDDVAYAVIRWREegKDDlLRRVVIPGEYS 257
                                    9***************************988889****************654448*******9875 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.6   1.3e-21   4.7e-18       1      73 [.     262     334 ..     262     335 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1.3e-21
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                    ++v v d+Av+ l++ga+L apGv  ve+ +e+g +Va+++ +gel+++G+a+ s++e+ ++++g++v   r+
  gi|118431292|ref|NP_147652.2| 262 PKVLVRDSAVESLTHGAQLAAPGVAAVEEGVEKGGMVALMTLKGELIGLGKALASAQEMLEAERGIVVSPTRI 334
                                    699*****************************************************************98887 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.3   7.8e-19   2.8e-15      10      58 .]      25      73 ..      18      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 7.8e-19
                                   XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                          DKCLD 10 nydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                   n++++l + ++ t+ ++G+ P++Rp++ y++yG+i +DKP +P+SHEVV
  gi|118431292|ref|NP_147652.2| 25 NTSRILYKYDEPTDPRYGYLPHERPLDVYLRYGMIVVDKPPGPTSHEVV 73
                                   77889999999*************************************9 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.3e-07   0.00083       1      64 [.     263     329 ..     263     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-07
                        UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgkivv 64 
                                    kv v+ +a ++++ G ++   ++  ++e+v+++++v+++  +ge++G+Gk+  +       +++ivv
  gi|118431292|ref|NP_147652.2| 263 KVLVRDSAVESLTHGAQLAAPGVAAVEEGVEKGGMVALMTLKGELIGLGKALASAqeMlEAERGIVV 329
                                    799************************************************9988753344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2886.82
//
Query:       gi|118431293|ref|NP_147653.2|  [L=244]
Description: S-methyl-5-thioadenosine phosphorylase [Aeropyrum pernix K1]
Scores for 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-36  123.5   0.1    8.8e-36  123.3   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 !  123.3   0.1   4.9e-40   8.8e-36       2     203 ..      17     214 ..      16     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 4.9e-40
                                    EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHH.HHHHHHHHHHC--SEEEEEEEEE CS
                      PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaa.vvaeirllkefgvkaiiriGtaG 80 
                                    +++ vg+pg++e la   le+ +  ++ rg k++tG+ +g +v+i+++GiG p+aa v  e+r+l    +++++r Gt+G
  gi|118431293|ref|NP_147653.2|  17 LVVAVGDPGRAERLATGLLEDARLVSSARGLKVYTGSFNGSEVTIATHGIGGPSAAvVFEELRMLG---AEVLVRLGTSG 93 
                                    7999****************************************************7777777777...*********** PP

                                    ESSTTT-TT-EEEEEE...EEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-C CS
                      PNP_UDP_1  81 glnpdlkvGDvvipdd...ainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyae 157
                                    gl +dl++GDvv++     +++  g  ++ g++   ++ p+s+d+ + + +++ l     +lg +v+  +v+++d fyae
  gi|118431293|ref|NP_147653.2|  94 GLSKDLRLGDVVVAAGagcYWGSGGSIQYAGERP--MCLPASPDPILTAGIYRGLSS---RLGDRVVLAPVMSSDAFYAE 168
                                    ****************554466666666554322..555555555555555555555...9******************* PP

                                    HHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTB CS
                      PNP_UDP_1 158 teaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaag 203
                                    t++++ ++r+lg +aveME + ++ ++  +g + a++ +vsdl+  
  gi|118431293|ref|NP_147653.2| 169 TPEAAGRWRSLGMAAVEMELHTLFSISWIRGFRSAGVLIVSDLLLP 214
                                    ******************************************7765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1761.69
//
Query:       gi|14601126|ref|NP_147654.1|  [L=258]
Description: hypothetical protein APE_0994 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.2   0.0       0.24   10.7   0.0    1.1  1  HPS3_C    Hermansky-Pudlak syndrome 3, C-terminal


Domain annotation for each model (and alignments):
>> HPS3_C  Hermansky-Pudlak syndrome 3, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.4e-05      0.24      47      82 ..     208     243 ..     197     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.4e-05
                        HPS3_C  47 merhaemllvygfieePrLLlkkkekavvPtelalq 82 
                                   +++h+e+ lv gfie  r+L+ + ++++v  +la  
  gi|14601126|ref|NP_147654.1| 208 LNQHSETELVNGFIEALRILMDRVRNTLVALALASA 243
                                   799*******************99999988888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2061.72
//
Query:       gi|118431294|ref|NP_147655.2|  [L=448]
Description: glycerate kinase [Aeropyrum pernix K1]
Scores for complete 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-71  239.0   0.0    6.3e-71  238.6   0.0    1.2  1  DUF4147   Domain of unknown function (DUF4147)
    9.4e-31  106.2   0.0    1.8e-30  105.3   0.0    1.5  1  MOFRL     MOFRL family
  ------ inclusion threshold ------
        0.1   13.1   0.1       0.28   11.7   0.1    1.8  1  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 !  238.6   0.0   1.1e-74   6.3e-71       6     229 .]      17     240 ..      12     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: 238.6 bits;  conditional E-value: 1.1e-74
                                    HHHHHHTTSHHHHHHTTHHHH--.......-SEEEEEESTTHHHHH.HHHH.HHHG..EEEEEEETT-----TT-EEEEE CS
                        DUF4147   6 feaaveavdpeklvkralslkeeeldlskkkrvvvvgaGKAaaama.aaleeealk..sgvvvvkkghaeekerievlea 82 
                                    +++av +v  ++ ++  +++  ee  l  ++r vv+++GK +++ma  ale   l+  +gvvv ++g + + e +ev+e+
  gi|118431294|ref|NP_147655.2|  17 LREAVGRVLEASRLDWRVRRLLEERGL-CRSRAVVLALGKGSLQMArGALE--CLEpeGGVVVKPRGMTGNVEGLEVVEG 93 
                                    455555555554444444331111122.46899*************77888..5666588888899999999******** PP

                                    -SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHHHHHHHTTBSS CS
                        DUF4147  83 ahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqelNtVRkhlsai 162
                                    +hplPde s++a r++le+a +++e+d v+vl+SGGgSAl ++P+eg+ led+++++ +Ll+sGasI+e+NtVRkhls+i
  gi|118431294|ref|NP_147655.2|  94 SHPLPDEWSLRAGRRLLEWAGSAGEGDNVVVLVSGGGSALAEVPMEGLALEDLREVNMLLLKSGASIHEINTVRKHLSRI 173
                                    ******************************************************************************** PP

                                    TTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..-HHHHHHH. CS
                        DUF4147 163 kGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklpesvrelLe 229
                                    kGGrLa+ a+parv+ +  SDV+gd+ld+IASGPtvpd++t+ dala+le+y+l++++p++v +lLe
  gi|118431294|ref|NP_147655.2| 174 KGGRLAATAYPARVLGVYASDVPGDRLDMIASGPTVPDPTTYGDALAVLERYGLRDSAPPRVVALLE 240
                                    ***************************************************************9996 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0     3e-34   1.8e-30       2     108 ..     324     430 ..     323     431 .. 0.98

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 3e-34
                                    EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--HHHH CS
                          MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagldakea 81 
                                    +ll+gGEttvtv+g G+GGrn+elala++l+++  + ++ +++l+++tDGiDG +daaGa++ +    ++++agld+ ++
  gi|118431294|ref|NP_147655.2| 324 ALLAGGETTVTVRGGGRGGRNMELALAWSLAMAYWSPEAPAAILAMDTDGIDGRSDAAGAVAWPWLPVALRDAGLDPYQL 403
                                    79*********************************99999**************************************** PP

                                    HHTT-HHHHHHHTT-EE-----S---- CS
                          MOFRL  82 LanndsyeffeklgallktgpTgtNVn 108
                                    La+nds ++f+ +g+l+ tg TgtN+n
  gi|118431294|ref|NP_147655.2| 404 LADNDSERAFAYAGSLVSTGLTGTNLN 430
                                    *************************98 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 ?   11.7   0.1   4.8e-05      0.28      88     125 ..     294     335 ..     263     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                                    HHHHHHHHHHHHHHHHHHHHHCT..ECE..EEEESHHHHHHH CS
                          NBD_C  88 lerageriaaalaeiarrlverg..vrr..lviaGGdtssav 125
                                    le +++++++ala+ia ++++rg  v++   ++aGG+t+  v
  gi|118431294|ref|NP_147655.2| 294 LEGESREVGRALASIALEALDRGvpVKPpaALLAGGETTVTV 335
                                    4455999*************88556666679********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3317.15
//
Query:       gi|118431295|ref|YP_874871.1|  [L=98]
Description: hypothetical protein APE_0996a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       155  (0.00864521); expected 358.6 (0.02)
Passed bias filter:                      148  (0.00825478); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 761.10
//
Query:       gi|118431296|ref|NP_147656.2|  [L=151]
Description: hypothetical protein APE_1000.1 [Aeropyrum pernix K1]
Scores for 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-12   45.9   0.0    8.2e-12   45.5   0.0    1.2  1  LEA_2            Late embryogenesis abundant protein


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   4.6e-16   8.2e-12       3      99 ..      55     149 ..      53     151 .] 0.93

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.6e-16
                                    EEEESSSS-EEEEEEEEEEEESS....SEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEE CS
                          LEA_2   3 rvrNPNsfgvrydgleldlsyng....qrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytl 78 
                                    +++NP sfg+r+++le++++++     +++a+ ts +++++++++++t+ + vsv     +r+l+a++    g el +++
  gi|118431296|ref|NP_147656.2|  55 SIENPTSFGFRVERLEVRVYASSgsglEEVAVLTSKSPVYLAPGSSSTVYMDVSVGI---LRALAAVI---GGAELVVEV 128
                                    79******************9555779****************************99...89******...9******** PP

                                    EEEEE.EEETTTSCEEEEEEE CS
                          LEA_2  79 rgrlkvlgkpilgsvtvpvkv 99 
                                    ++++k + +pi +++tvp + 
  gi|118431296|ref|NP_147656.2| 129 EVEAKPYLGPIPFTQTVPSCN 149
                                    *****************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1129.48
//
Query:       gi|118431297|ref|NP_147657.2|  [L=387]
Description: hypothetical protein APE_1001.1 [Aeropyrum pernix K1]
Scores for 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  40.6      6e-06   26.2  40.6    3.2  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 ?   -1.6   0.4       0.1   1.8e+03     105     115 ..      22      32 ..       3      42 .. 0.44
   2 !   26.2  40.6   3.3e-10     6e-06       3     232 ..      75     289 ..      71     297 .. 0.60
   3 ?   -4.4   6.2       0.7   1.3e+04       1      57 [.     293     358 ..     293     374 .. 0.47

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.1
                           GT87 105 laaaiKltPal 115
                                    laaa+  ++++
  gi|118431297|ref|NP_147657.2|  22 LAAALAMLGLA 32 
                                    22222111111 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 3.3e-10
                           GT87   3 YPPfaallfapl..allp....yglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfGqi 76 
                                    YPP+  ll +    + +p    ++  +++ al+ +a+ ll++  + rr      + v+ al   a+al p +    + + 
  gi|118431297|ref|NP_147657.2|  75 YPPLVGLLWLLSvnTRIPgltgLESHYIVQALAAAAMGLLSVEAV-RR-----LAGVKRAL---AAALLPSMAVYSVYNW 145
                                    666665554433113344221233334444443333333334444.33.....56788887...89999999999999** PP

                           GT87  77 nllllllvlldllllrrrrpllaGlliGlaaaiKltPalfll.ylll..rrrwralaaaaatalvltalpllllppssle 153
                                    +ll ++ +l++l + rr+r  +aGll+Gl+ a Kl+P+l ++ ++++  rr  +a+a+a+a++++ +++  +l+p   +e
  gi|118431297|ref|NP_147657.2| 146 DLLAAAPMLWGLYMFRRGRVTAAGLLLGLGGAAKLLPLLAAApLPVVagRRGVKAAATAFAVTAASFLAVEALAP-GFIE 224
                                    ***************************************999655554345556666664444444444444444.4455 PP

                           GT87 154 yfletlfdtseriaedvgnqsllslagllaralalglsavtllwlvlvllv.valaavaawrlrrrerllalaaallval 232
                                    +f++    + +  a ++   s   +  ++ +++   l       ++++l++ ++laa+aa rl+r ++++a   +l + l
  gi|118431297|ref|NP_147657.2| 225 AFYR----H-H--AGWYIEGS---WLLVFGDPFSEEL-----RRVAQALAAlAVLAALAASRLLRLDPVTAAFVTLSAYL 289
                                    5555....4.4..45556666...4445555333344.....34555555556666666666666666666654444444 PP

  == domain 3  score: -4.4 bits;  conditional E-value: 0.7
                           GT87   1 FtYPPfaallfaplallp...yglalalwallnlaalllalrlllrrlgral......asavalal 57 
                                    ++Y P + ll a lal +    + ++ ++++  +aa++++l++ ++    +       a+ v++ l
  gi|118431297|ref|NP_147657.2| 293 YVYTPQMNLLPALLALSTplfTPSLYPILLAQDTAATAVILTWHTTPNPLDPlapptiATYVKTTL 358
                                    567777777777776655553334444444444555555444444332222245555533333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 3062.71
//
Query:       gi|118431298|ref|NP_147659.2|  [L=530]
Description: hypothetical protein APE_1003.1 [Aeropyrum pernix K1]
Scores for complete 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   53.8   0.4    1.9e-12   47.3   0.4    2.1  1  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.062   13.3   2.2       0.12   12.5   0.3    2.2  2  PA             PA domain


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.4   2.2e-16   1.9e-12       9     195 ..     209     382 ..     202     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.2e-16
                                    TCESEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSG.........SSHHHH CS
                  Peptidase_M28   9 katdevlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEa.........gllGSk 79 
                                    +    v+l gAH+D++++       G +Dn  gva  +e+a  l  +g  +  g  +++f+aEE          +  GS+
  gi|118431298|ref|NP_147659.2| 209 GR-GGVVLAGAHLDHWYT-------GFTDNILGVAQAVETAGRLRGRG--LAAG--VVVFGAEEHgmpgmaswyWAAGSR 276
                                    44.479***********9.......99******************744..5555..5789*************99***** PP

                                    HHHH..HHC.CCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTT CS
                  Peptidase_M28  80 afak..akp.elkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflka 156
                                     +a   +++ ++++++a++n+D +g +         ++  + +++ l+a a +   +             + D ++ + a
  gi|118431298|ref|NP_147659.2| 277 SYAGllRESgAAEEVEAYVNFDVAGYRCLV-----ASGAPQLVGHALEAGAVERCCE-----------CPECDSIMMAWA 340
                                    ***9974447*************8876433.....4567777777777666655442...........2346******** PP

                                    T--EEEE...CTSSS-TTTTSTTSSGGGB-HHHHHHHHHHHH CS
                  Peptidase_M28 157 gvpvldl...aetgfpevyHtprDtldnidkdtlariaelvl 195
                                    g+p+l+l      g +e yHtprDt+d+ ++dt+++  e++ 
  gi|118431298|ref|NP_147659.2| 341 GIPTLSLhslWCPGVQEAYHTPRDTPDRASWDTAWTAVEAAV 382
                                    *******777777889*****************998877665 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.3e-05      0.12       4      81 ..      91     173 ..      82     184 .. 0.72
   2 ?   -0.7   0.1      0.16   1.4e+03      47      57 ..     250     260 ..     204     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                             PA   4 plVyscfagygisadfe..gvdvkGkivLvqr......tfaeKarnAqaaGAagviivndge....lgaatgasgnegep 71 
                                    plV    +g+ ++a+ +  gvd  G++v+  r      + +  a  A++aGA+++++ + ++    +g++ g s  +g+p
  gi|118431298|ref|NP_147659.2|  91 PLV---LEGDPSHAS-SwrGVDAGGRVVVA-RapgvvdDLKAAALLAAEAGAEALLVESRDPrvivTGGDWGYSVSAGSP 165
                                    666...455554444.25789988999999.557655455999999***********95555577655555566666666 PP

                             PA  72 dgitiPavgv 81 
                                      + iP++ v
  gi|118431298|ref|NP_147659.2| 166 --TPIPVAVV 173
                                    ..99999887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.16
                             PA  47 Aagviivndge 57 
                                    Aagv+++  +e
  gi|118431298|ref|NP_147659.2| 250 AAGVVVFGAEE 260
                                    88999996444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 4291.74
//
Query:       gi|118431299|ref|NP_147661.2|  [L=309]
Description: hypothetical protein APE_1007.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0003   20.1   1.4        0.5    9.8   0.0    2.3  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.2   1.3       0.12   11.9   0.0    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.016   15.2   0.5        1.8    8.7   0.0    2.4  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.022   14.5   2.0        4.3    7.2   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.05   13.2   0.8        7.2    6.3   0.1    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.074   13.1   0.3       0.15   12.1   0.3    1.5  1  DZR             Double zinc ribbon
        0.1   12.1   6.4       0.35   10.4   0.4    2.3  2  Mu-like_Com     Mu-like prophage protein Com
       0.18   12.0   3.6        7.1    6.8   0.4    2.4  2  UPF0547         Uncharacterised protein family UPF0547
       0.23   11.2   6.4        1.8    8.3   1.0    2.6  2  zf-CCHC_5       GAG-polyprotein viral zinc-finger
        0.3   11.0   1.4        8.6    6.4   0.1    2.3  2  zinc_ribbon_4   zinc-ribbon domain
       0.41   10.1   3.5        1.9    8.0   3.6    2.0  1  DUF2688         Protein of unknown function (DUF2688)
          1    9.1   5.8        9.8    5.9   0.4    2.7  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        1.3    8.9   8.9        3.5    7.6   1.5    2.5  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
        1.3    8.9   9.0        3.9    7.4   1.3    2.7  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.4    9.0   5.5        6.3    6.9   0.3    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.4    9.6   5.7         11    6.8   0.5    2.6  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        3.4    7.8   7.4        3.2    7.8   0.1    3.3  4  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        6.8    6.5   6.4          9    6.1   0.7    2.6  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00051       0.5       3      14 ..     232     243 ..     231     246 .. 0.77
   2 !    9.0   0.3   0.00092      0.92       4      16 ..     259     273 ..     258     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00051
                    zf-ribbon_3   3 vrCPnCGaplss 14 
                                    +rCP+CG+++++
  gi|118431299|ref|NP_147661.2| 232 TRCPRCGTVVAT 243
                                    59******6554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00092
                    zf-ribbon_3   4 rCPnCGa.p.lssdd 16 
                                    rCP+CGa + ++ ++
  gi|118431299|ref|NP_147661.2| 259 RCPRCGAgIpVKGGW 273
                                    8******98677776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.12      15      30 ..     227     242 ..     225     245 .. 0.88
   2 ?    1.6   0.4       0.2     2e+02       2       7 ..     259     264 ..     258     267 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                    TSTTCEEESSSSBEEE CS
                   TF_Zn_Ribbon  15 pergelvCtdCGlVle 30 
                                    ++r +++C++CG+V+ 
  gi|118431299|ref|NP_147661.2| 227 YSRLDTRCPRCGTVVA 242
                                    7899**********95 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                    EETTTT CS
                   TF_Zn_Ribbon   2 kCPnCg 7  
                                    +CP Cg
  gi|118431299|ref|NP_147661.2| 259 RCPRCG 264
                                    466666 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 ?    8.7   0.0    0.0018       1.8       2      13 ..     232     243 ..     232     245 .. 0.86
   2 ?    4.5   0.1     0.038        38       3      11 ..     259     267 ..     259     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                         zf-ACC   2 tKCpsCgemlyk 13 
                                    t+Cp+Cg+++ +
  gi|118431299|ref|NP_147661.2| 232 TRCPRCGTVVAT 243
                                    79******9976 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                         zf-ACC   3 KCpsCgeml 11 
                                    +Cp+Cg+ +
  gi|118431299|ref|NP_147661.2| 259 RCPRCGAGI 267
                                    6*****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 ?    6.6   0.1    0.0066       6.6      16      21 ..     234     239 ..     231     242 .. 0.62
   2 ?    7.2   0.3    0.0043       4.3       1       9 [.     259     267 ..     259     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0066
                  zinc_ribbon_2  16 CpyCGt 21 
                                    Cp+CGt
  gi|118431299|ref|NP_147661.2| 234 CPRCGT 239
                                    555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
                  zinc_ribbon_2   1 fCpnCGael 9  
                                    +Cp+CGa +
  gi|118431299|ref|NP_147661.2| 259 RCPRCGAGI 267
                                    588888866 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.016        16       4      13 ..     233     242 ..     231     246 .. 0.83
   2 ?    6.3   0.1    0.0072       7.2       5      14 ..     260     269 ..     257     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.016
                         zf_UBZ   4 lCerCgkeip 13 
                                     C+rCg+ + 
  gi|118431299|ref|NP_147661.2| 233 RCPRCGTVVA 242
                                    5*****9986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0072
                         zf_UBZ   5 CerCgkeipe 14 
                                    C+rCg+ ip+
  gi|118431299|ref|NP_147661.2| 260 CPRCGAGIPV 269
                                    ******9996 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   0.00016      0.15      14      39 ..     233     268 ..     223     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                            DZR  14 fCseCgtklkavaa..........edrCpsCgekvd 39 
                                     C++Cgt +    +            rCp+Cg+ ++
  gi|118431299|ref|NP_147661.2| 233 RCPRCGTVVATRREglldamqlasGGRCPRCGAGIP 268
                                    6*******975555999999999999*****98765 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00035      0.35      23      37 ..     230     244 ..     226     259 .. 0.79
   2 ?    4.6   0.8     0.021        21      26      32 ..     259     265 ..     247     272 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                    Mu-like_Com  23 ltiKCPRCGtLnHlk 37 
                                    l  +CPRCGt+   +
  gi|118431299|ref|NP_147661.2| 230 LDTRCPRCGTVVATR 244
                                    5679******86555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                    Mu-like_Com  26 KCPRCGt 32 
                                    +CPRCG 
  gi|118431299|ref|NP_147661.2| 259 RCPRCGA 265
                                    7*****7 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.016        16       3      10 ..     234     241 ..     232     243 .. 0.59
   2 ?    6.8   0.4    0.0072       7.1       2      12 ..     259     269 ..     259     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                        UPF0547   3 CPeCeakv 10 
                                    CP+C + v
  gi|118431299|ref|NP_147661.2| 234 CPRCGTVV 241
                                    66666655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0072
                        UPF0547   2 vCPeCeakvPv 12 
                                    +CP+C a +Pv
  gi|118431299|ref|NP_147661.2| 259 RCPRCGAGIPV 269
                                    6********98 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 ?    5.1   0.4     0.019        19       4       9 ..     233     238 ..     231     240 .. 0.88
   2 ?    8.3   1.0    0.0018       1.8       3      11 ..     258     266 ..     256     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.019
                                    B-TTT- CS
                      zf-CCHC_5   4 lCpRCk 9  
                                    +CpRC+
  gi|118431299|ref|NP_147661.2| 233 RCPRCG 238
                                    9****9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0018
                                    -B-TTT-SS CS
                      zf-CCHC_5   3 glCpRCkkg 11 
                                    g+CpRC+ g
  gi|118431299|ref|NP_147661.2| 258 GRCPRCGAG 266
                                    9******87 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0086       8.6      27      34 ..     233     240 ..     227     242 .. 0.65
   2 ?    3.2   0.2     0.088        87      27      32 ..     259     264 ..     258     267 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0086
                  zinc_ribbon_4  27 rCskCghv 34 
                                    rC++Cg+v
  gi|118431299|ref|NP_147661.2| 233 RCPRCGTV 240
                                    55555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.088
                  zinc_ribbon_4  27 rCskCg 32 
                                    rC++Cg
  gi|118431299|ref|NP_147661.2| 259 RCPRCG 264
                                    455555 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.6    0.0019       1.9       8      41 ..     232     263 ..     230     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0019
                        DUF2688   8 TqCrRCGkslstlsrSLlGldeLkqklGdICsdC 41 
                                    T+C RCG+ + t +  Ll  d+++   G+ C  C
  gi|118431299|ref|NP_147661.2| 232 TRCPRCGTVVATRREGLL--DAMQLASGGRCPRC 263
                                    99************9996..67777778888777 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 ?    5.9   0.4    0.0098       9.8       6      14 ..     234     242 ..     232     248 .. 0.75
   2 ?    5.2   0.7     0.017        17       6      11 ..     260     265 ..     251     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0098
                  zf-NADH-PPase   6 CgrCGapte 14 
                                    C+rCG+ ++
  gi|118431299|ref|NP_147661.2| 234 CPRCGTVVA 242
                                    999999765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                  zf-NADH-PPase   6 CgrCGa 11 
                                    C+rCGa
  gi|118431299|ref|NP_147661.2| 260 CPRCGA 265
                                    999998 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 ?    7.6   1.5    0.0035       3.5       3      13 ..     233     243 ..     233     247 .. 0.82
   2 ?    5.2   1.0      0.02        20       3      10 ..     259     266 ..     257     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0035
                                    B-TTT--BBEE CS
                   zf-FPG_IleRS   3 pCpRCwryier 13 
                                    +CpRC++++++
  gi|118431299|ref|NP_147661.2| 233 RCPRCGTVVAT 243
                                    5******9877 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                                    B-TTT--B CS
                   zf-FPG_IleRS   3 pCpRCwry 10 
                                    +CpRC+  
  gi|118431299|ref|NP_147661.2| 259 RCPRCGAG 266
                                    7****975 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 ?    7.4   1.3     0.004       3.9      12      21 ..     232     241 ..     232     247 .. 0.83
   2 ?    5.0   1.2     0.023        23      11      19 ..     257     265 ..     256     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.004
                        DUF35_N  12 qrCpdCGtvq 21 
                                    +rCp CGtv+
  gi|118431299|ref|NP_147661.2| 232 TRCPRCGTVV 241
                                    69******97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.023
                        DUF35_N  11 gqrCpdCGt 19 
                                    g+rCp CG+
  gi|118431299|ref|NP_147661.2| 257 GGRCPRCGA 265
                                    789999996 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.8     0.037        37      20      27 ..     233     240 ..     214     249 .. 0.79
   2 ?    6.9   0.3    0.0063       6.3       9      25 ..     248     264 ..     245     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.037
                  Zn_Tnp_IS1595  20 vCPhCgsr 27 
                                    +CP+Cg  
  gi|118431299|ref|NP_147661.2| 233 RCPRCGTV 240
                                    6*****54 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0063
                  Zn_Tnp_IS1595   9 lLealrWpngfvCPhCg 25 
                                    lL a+  ++g +CP+Cg
  gi|118431299|ref|NP_147661.2| 248 LLDAMQLASGGRCPRCG 264
                                    577888899999****9 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 ?    6.8   0.5     0.011        11       3      14 ..     232     243 ..     231     247 .. 0.78
   2 ?    4.7   0.6     0.048        48       3      11 ..     258     266 ..     256     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.011
                        zf-ISL3   3 hrCPnCgsktvv 14 
                                    +rCP+Cg ++++
  gi|118431299|ref|NP_147661.2| 232 TRCPRCGTVVAT 243
                                    69*****99664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.048
                        zf-ISL3   3 hrCPnCgsk 11 
                                     rCP+Cg+ 
  gi|118431299|ref|NP_147661.2| 258 GRCPRCGAG 266
                                    69*****86 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 ?   -1.9   0.0       3.6   3.6e+03      11      20 ..      43      52 ..      42      55 .. 0.84
   2 ?   -3.2   0.1       9.1   9.1e+03       8      17 ..     149     158 ..     149     158 .. 0.83
   3 ?    7.8   0.1    0.0032       3.2       1      14 [.     233     247 ..     233     252 .. 0.84
   4 ?    2.7   0.3      0.13   1.3e+02       1       7 [.     259     265 ..     259     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.6
                 DNA_ligase_ZBD 11 ReegeaiyRC 20
                                   R+ g+a  RC
  gi|118431299|ref|NP_147661.2| 43 RPGGGASSRC 52
                                   66799999** PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.1
                 DNA_ligase_ZBD   8 avvReegeai 17 
                                    a+ R+ +ea+
  gi|118431299|ref|NP_147661.2| 149 ALARTVEEAV 158
                                    5789999996 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0032
                 DNA_ligase_ZBD   1 hCPvCGsavv.Reeg 14 
                                    +CP CG+ v  R eg
  gi|118431299|ref|NP_147661.2| 233 RCPRCGTVVAtRREG 247
                                    5*******9988776 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.13
                 DNA_ligase_ZBD   1 hCPvCGs 7  
                                    +CP CG+
  gi|118431299|ref|NP_147661.2| 259 RCPRCGA 265
                                    5****96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.6      0.12   1.2e+02      16      21 ..     233     238 ..     233     240 .. 0.85
   2 ?    6.1   0.7     0.009         9      15      22 ..     258     265 ..     253     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                   Rubredoxin_2  16 rCpsCg 21 
                                    rCp Cg
  gi|118431299|ref|NP_147661.2| 233 RCPRCG 238
                                    899998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.009
                   Rubredoxin_2  15 GrCpsCgs 22 
                                    GrCp Cg+
  gi|118431299|ref|NP_147661.2| 258 GRCPRCGA 265
                                    9*****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2270.73
//
Query:       gi|14601135|ref|NP_147663.1|  [L=90]
Description: hypothetical protein APE_1007a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-09   37.5   0.4    2.6e-09   36.8   0.4    1.4  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    5.1e-05   23.1   0.9    0.00011   22.0   0.9    1.6  1  Nudix_N_2        Nudix N-terminal
    0.00015   21.4   3.1    0.00055   19.5   3.2    1.9  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0012   18.3   1.7     0.0032   16.9   1.7    1.7  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0056   16.6   0.4      0.013   15.4   0.4    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
       0.01   15.2   1.0      0.017   14.5   0.0    1.8  1  zf-TFIIB         Transcription factor zinc-finger
      0.012   15.0   3.4       0.23   10.9   0.5    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.039   14.0   0.7      0.092   12.8   0.7    1.6  1  DZR              Double zinc ribbon
      0.041   13.6   5.9       0.54   10.0   1.7    2.3  2  zinc_ribbon_2    zinc-ribbon domain
        0.1   13.0   2.2       0.27   11.6   1.9    1.9  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.6   0.5       0.33   11.1   0.5    1.8  1  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.11   12.7   0.3       0.22   11.7   0.3    1.5  1  IBR              IBR domain, a half RING-finger domain
       0.35   10.5   1.9       0.67    9.6   0.7    2.0  1  zf-C2H2_12       Zinc-finger C2H2-type
       0.62   10.6   7.5        5.4    7.6   4.7    2.6  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.96    9.7   4.0        3.6    7.8   4.0    2.0  1  Ribosomal_S27    Ribosomal protein S27a
        1.8    9.4   4.1         11    6.9   0.1    2.4  2  zinc_ribbon_15   zinc-ribbon family
        2.1    8.6   5.5       0.66   10.2   0.4    2.4  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.4   2.4e-12   2.6e-09       1      33 [.       1      33 [.       1      36 [. 0.94

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.4e-12
                                  EEBESTTTSBEEEEECSCCCEEEESSSS-EEES CS
                RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepa 33
                                  +kFCpkCg  +lp++d e++ + C +CgY  +a
  gi|14601135|ref|NP_147663.1|  1 MKFCPKCGGVMLPRKDGEKRLLVCGSCGYTIEA 33
                                  9******************99********9887 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.9   1.1e-07   0.00011       1      31 [.       2      30 ..       2      31 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-07
                                  -B-TTT--B-EEE--TT-SS-E.EEETTTTEE CS
                     Nudix_N_2  1 kFCsqCGtpvelripdgDnreR.lvCpaCgti 31
                                  kFC++CG+ +   +p  D + R lvC +Cg++
  gi|14601135|ref|NP_147663.1|  2 KFCPKCGGVM---LPRKDGEKRlLVCGSCGYT 30
                                  9******974...44444444428******95 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 !   19.5   3.2   5.3e-07   0.00055       4      29 ..       2      29 ..       1      31 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.3e-07
                 zf-NADH-PPase  4 rFCgrCGaptepaeggwar..vCpaCgl 29
                                  +FC++CG+ + p ++g +r  vC +Cg+
  gi|14601135|ref|NP_147663.1|  2 KFCPKCGGVMLPRKDGEKRllVCGSCGY 29
                                  7**************9887669****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 !   16.9   1.7     3e-06    0.0032       3      31 ..       4      33 ..       3      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                                  ETTTTCEEC.HEETSTTCEEESSSSBEEEE CS
                  TF_Zn_Ribbon  3 CPnCgstnl.veDpergelvCtdCGlVled 31
                                  CP+Cg+ +l   D e   lvC++CG+ +e 
  gi|14601135|ref|NP_147663.1|  4 CPKCGGVMLpRKDGEKRLLVCGSCGYTIEA 33
                                  *******965888888889*******9985 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 !   15.4   0.4   1.3e-05     0.013      30      58 ..       3      33 ..       2      34 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                OrfB_Zn_ribbon 30 tCseCgsknke..alsgrtfkCpnCgfeadr 58
                                   C++Cg ++ +  + ++r+++C +Cg+++ +
  gi|14601135|ref|NP_147663.1|  3 FCPKCGGVMLPrkDGEKRLLVCGSCGYTIEA 33
                                  5*******9988899************9875 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.017      22      37 ..       4      19 ..       2      22 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
                      zf-TFIIB 22 CpqCrGvWldrgelek 37
                                  Cp+C+Gv+l r++ ek
  gi|14601135|ref|NP_147663.1|  4 CPKCGGVMLPRKDGEK 19
                                  ***********98665 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   0.5   0.00022      0.23      17      25 ..       2      10 ..       1      11 [. 0.65
   2 ?    4.8   0.1     0.019        20      18      24 ..      23      29 ..      19      31 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                   zf-ribbon_3 17 nvCpyCGtk 25
                                  ++Cp+CG++
  gi|14601135|ref|NP_147663.1|  2 KFCPKCGGV 10
                                  577777765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                   zf-ribbon_3 18 vCpyCGt 24
                                  vC +CG+
  gi|14601135|ref|NP_147663.1| 23 VCGSCGY 29
                                  7*****8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   8.7e-05     0.092      13      40 ..       2      33 ..       1      37 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
                           DZR 13 rfCseCgtklkavaa....edrCpsCgekvdp 40
                                  +fC++Cg  + + ++      +C sCg+ +++
  gi|14601135|ref|NP_147663.1|  2 KFCPKCGGVMLPRKDgekrLLVCGSCGYTIEA 33
                                  79999999865444478889999999998765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.7   0.00052      0.54      14      20 ..       2       8 ..       1       9 [. 0.86
   2 ?    5.3   0.1     0.016        16       2      10 ..      24      32 ..      23      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00052
                 zinc_ribbon_2 14 kFCpyCG 20
                                  kFCp+CG
  gi|14601135|ref|NP_147663.1|  2 KFCPKCG 8 
                                  8999998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                 zinc_ribbon_2  2 CpnCGaelq 10
                                  C +CG++++
  gi|14601135|ref|NP_147663.1| 24 CGSCGYTIE 32
                                  999999886 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 ?   11.6   1.9   0.00026      0.27       4      37 ..       2      34 ..       1      75 [. 0.76
   2 ?   -0.1   0.0       1.2   1.3e+03      14      27 ..      59      72 ..      55      82 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
               Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCga....s 37
                                  k CP Cgg     +++ ++        C  Cg+     
  gi|14601135|ref|NP_147663.1|  2 KFCPKCGGVMLPRKDGEKR-----LLVCGSCGYtieaK 34
                                  66*****976666666555.....9********44431 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
               Lar_restr_allev 14 vlersqrvvaeigq 27
                                  v++++qr ++ei+q
  gi|14601135|ref|NP_147663.1| 59 VVKKRQREKEEIEQ 72
                                  67777777777766 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 ?   11.1   0.5   0.00031      0.33       4      26 .]       4      27 ..       3      27 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                        zf-ACC  4 CpsCgemly.kkeLernlyVCPkC 26
                                  Cp+Cg +++ +k+ e+ l VC +C
  gi|14601135|ref|NP_147663.1|  4 CPKCGGVMLpRKDGEKRLLVCGSC 27
                                  ****986555***********999 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 ?   11.7   0.3   0.00021      0.22      19      47 ..       2      30 ..       1      31 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                           IBR 19 kwCprpdCeaiiekseg.cks.vtCskCgfe 47
                                  k Cp  +C++++ + ++ +k+ + C +Cg+ 
  gi|14601135|ref|NP_147663.1|  2 KFCP--KCGGVMLPRKDgEKRlLVCGSCGYT 30
                                  79**..******766664333478****986 PP

>> zf-C2H2_12  Zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7   0.00063      0.67      17      64 ..      16      72 ..      11      76 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00063
                    zf-C2H2_12 17 dpqrrglvCmvCgeslas........lklstikrHIrqvHP.eslslseeekeaile 64
                                  d+++r lvC  Cg +             ++++k H++++   + ++ +++eke i +
  gi|14601135|ref|NP_147663.1| 16 DGEKRLLVCGSCGYTIEAkpedlsryKGVEKVKDHVLTTKTvNVVKKRQREKEEIEQ 72
                                  899**********98653111111113488888888776541344455556666655 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 ?    7.6   4.7    0.0051       5.4       7      32 ..       3      27 ..       1      54 [. 0.61
   2 ?    7.6   2.1    0.0053       5.6       5      19 ..      21      35 ..      19      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0051
               Zn_ribbon_recom  7 rCgeCGspmtrrkrkgkrhyYrCsty 32
                                  +C +CG+ m  rk  g+++  +C+++
  gi|14601135|ref|NP_147663.1|  3 FCPKCGGVMLPRKD-GEKRLLVCGSC 27
                                  79999999999987.67766666654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0053
               Zn_ribbon_recom  5 llrCgeCGspmtrrk 19
                                  ll+Cg CG +   + 
  gi|14601135|ref|NP_147663.1| 21 LLVCGSCGYTIEAKP 35
                                  8*******9976654 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.0    0.0034       3.6      18      45 .]       2      30 ..       1      30 [. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                                  -B-SS-S-TTSBEEECTT...E.EEESSTTTE CS
                 Ribosomal_S27 18 keCpreCGaGvfMAehkd...R.kyCGkCglT 45
                                  k Cp+ C  G  M   kd   R   CG+Cg+T
  gi|14601135|ref|NP_147663.1|  2 KFCPK-C--GGVMLPRKDgekRlLVCGSCGYT 30
                                  78***.9..5555555665874258******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 ?    3.9   0.7     0.087        92      79      86 .]       1       8 [.       1       8 [. 0.88
   2 ?    6.9   0.1      0.01        11      33      64 ..      17      48 ..      10      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.087
                zinc_ribbon_15 79 fkyCpkCg 86
                                  +k+CpkCg
  gi|14601135|ref|NP_147663.1|  1 MKFCPKCG 8 
                                  58*****9 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                zinc_ribbon_15 33 kkkpylacskCkslleaskelgkeiekkesse 64
                                   +k +l+c +C++++ea+ e  ++ +  e+++
  gi|14601135|ref|NP_147663.1| 17 GEKRLLVCGSCGYTIEAKPEDLSRYKGVEKVK 48
                                  45788999999999999987777766655554 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 ?   10.2   0.4   0.00063      0.66      24      36 ..       2      14 ..       1      19 [. 0.88
   2 ?    1.0   0.8      0.47   4.9e+02      26      31 ..      24      29 ..      15      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                  NOB1_Zn_bind 24 kFCpkCGnktLkr 36
                                  kFCpkCG  +L r
  gi|14601135|ref|NP_147663.1|  2 KFCPKCGGVMLPR 14
                                  7******999977 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                  NOB1_Zn_bind 26 CpkCGn 31
                                  C +CG 
  gi|14601135|ref|NP_147663.1| 24 CGSCGY 29
                                  444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1649  (0.0919739); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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):              17  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 703.98
//
Query:       gi|118431300|ref|NP_147664.2|  [L=168]
Description: hypothetical protein APE_1009.1 [Aeropyrum pernix K1]
Scores for 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-47  158.8   0.0    7.9e-47  158.6   0.0    1.0  1  DUF371    Domain of unknown function (DUF371)


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.6   0.0   4.4e-51   7.9e-47       2     132 ..       8     138 ..       7     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.6 bits;  conditional E-value: 4.4e-51
                                    EEE--TT-----SSEEEEES-S---TT-TTEEEBS-S--GGGS-HHHHHHHS----EEEEEEE-SS-EEEEEEE--TT-- CS
                         DUF371   2 karGHenvkaehksTleitkddeltprgdCIigveadkaaadlseelkealkeeeatitvtlevgeledeitgrGspklt 81 
                                    +a+GH+nv+a+h++T+eit+dd+ltprgdCIig++++ ++++l++ +k++ ++ +++i v+l +++++d+ +grG+p l+
  gi|118431300|ref|NP_147664.2|   8 QAWGHPNVRATHRTTFEITSDDYLTPRGDCIIGIRSSVTPRSLPQWFKSIARSPDSIIVVVLCSEGVCDTAVGRGHPGLS 87 
                                    79****************************************************************************** PP

                                    ---SSEEEEESSS---TTEEEBS-S--GGGS-HHHHHHHHTT-EEEEEEEE CS
                         DUF371  82 lenerdlvvRkSdyvddrTllvkadkaaadldrelveaLkkgaeltvelev 132
                                    l + r++v+R+S++v ++T+++ ++kaaadl+r+l+e+L++ga l+v ++v
  gi|118431300|ref|NP_147664.2|  88 LGDGRRMVFRRSSFVGPETVMIGSSKAAADLRRDLIEMLRRGAALRVGMTV 138
                                    **********************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1251.43
//
Query:       gi|118431301|ref|NP_147666.2|  [L=260]
Description: protein-L-isoaspartate O-methyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-66  223.9   0.0    2.1e-66  223.7   0.0    1.0  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    5.8e-11   42.4   0.0    7.7e-11   42.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.3e-07   30.0   0.0    1.1e-06   29.3   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      2e-06   27.6   0.0      3e-06   27.0   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    7.5e-06   26.5   0.0    1.9e-05   25.2   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    1.1e-05   25.3   0.0    1.6e-05   24.8   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.5e-05   24.8   0.0    2.3e-05   24.2   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00014   21.4   0.0    0.00023   20.8   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00016   20.8   0.0    0.00023   20.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00018   20.8   0.0    0.00027   20.2   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    0.00019   20.6   0.0    0.00026   20.2   0.0    1.1  1  Fibrillarin      Fibrillarin
    0.00037   21.5   0.0    0.00073   20.5   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
     0.0014   18.6   0.0     0.0021   18.0   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
     0.0019   18.2   0.0     0.0026   17.8   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
     0.0029   17.0   0.0     0.0045   16.4   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.033   14.0   0.0      0.071   12.9   0.0    1.7  2  Methyltransf_23  Methyltransferase domain
      0.074   12.7   0.0       0.12   12.0   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.12   11.5   0.0       0.18   10.9   0.0    1.1  1  DREV             DREV methyltransferase
       0.16   11.3   0.0       0.21   10.8   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
       0.28   10.5   0.0        0.4   10.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.7   0.0   2.3e-69   2.1e-66       5     208 ..      40     244 ..      36     246 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.7 bits;  conditional E-value: 2.3e-69
                                    HHHHHHHHTTS---HHHHHHHHHS-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TT CS
                           PCMT   5 alieelkkkgviksdkvaealeevdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGs 84 
                                    +++e+l+++g+++s +v+ea++ v+R+ fvp +++ +aYed pl+ig ++tiSap +v+++l+ll+ ++g++vL+vG+Gs
  gi|118431301|ref|NP_147666.2|  40 RMVEQLRRSGLVTSRRVLEAMARVPRHLFVPPEYRGMAYEDRPLPIGHGQTISAPGVVGRMLQLLDPQPGEKVLDVGAGS 119
                                    699***************************************************************************** PP

                                    SHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-SEEEEEESSBBSS--HHHHHTE CS
                           PCMT  85 Gyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaPYdaihvgaaapeiPealidQL 163
                                    Gy++a+la+lv + grv ++eri+el+e a++nl+k +++  v vvvgDG kG +++aPY +i v+aaap+ P++l++QL
  gi|118431301|ref|NP_147666.2| 120 GYQSALLAELVTPGGRVYAVERIPELAEYARENLEKTGYRgVVEVVVGDGSKGLPQHAPYHRIKVAAAAPKPPKPLVEQL 199
                                    ***************************************97889************************************ PP

                                    EEEEEEEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                           PCMT 164 keGGrlvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                    ++GGr+v+P+g+   Q l+ ++k+ dg+v  ++  ev+fvpl ++
  gi|118431301|ref|NP_147666.2| 200 APGGRMVIPIGTPDLQILTIIEKTPDGRVRERRDIEVLFVPLIGE 244
                                    ******************************************876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   8.6e-14   7.7e-11       3      73 ..     108     177 ..     106     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 8.6e-14
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.lekllede 73 
                                     g +vlD+G+G+G+ +  lae++ p+++v+ +++ +e  e+Aren++k g+   ve+ +gd  + l+++   +
  gi|118431301|ref|NP_147666.2| 108 PGEKVLDVGAGSGYQSALLAELVTPGGRVYAVERIPELAEYARENLEKTGYRgVVEVVVGDGSKgLPQH---A 177
                                    6789************************************************999********999976...3 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.2e-09   1.1e-06       1      61 [.     112     176 ..     112     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.2e-09
                                    EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfe 61 
                                    vLd+G+G+G  ++ la+ + + ++v++v+  +e+ e+are++e+ g+   ve+v+gd ++ lp++
  gi|118431301|ref|NP_147666.2| 112 VLDVGAGSGYQSALLAELVtPGGRVYAVERIPELAEYARENLEKTGYrgVVEVVVGDGSKgLPQH 176
                                    9*****************9846**********************999999*******97746654 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 !   27.0   0.0   3.3e-09     3e-06       2      70 ..     102     171 ..     101     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.3e-09
                                    HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTC CS
                Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDark 70 
                                    +lL+pq++e++lD+ a+ G + +++ael+ + g+v+Av++  e ++   enl++ g +  + v+ +D++k
  gi|118431301|ref|NP_147666.2| 102 QLLDPQPGEKVLDVGAGSGYQSALLAELVTPGGRVYAVERIPELAEYARENLEKTGYRgVVEVVVGDGSK 171
                                    68******************************************************99667888889876 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.2e-08   1.9e-05       1      54 [.     113     171 ..     113     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.2e-08
                                    EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaek 54 
                                    LdvG+G+G+ ++ la+ +   +rv++v+  +e+ ++a+e+ ++ g    ve+vv+d +k
  gi|118431301|ref|NP_147666.2| 113 LDVGAGSGYQSALLAELVtpgGRVYAVERIPELAEYARENLEKTGYrgVVEVVVGDGSK 171
                                    8**************777777************************999999****9987 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-08   1.6e-05      33     100 ..     101     168 ..      88     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-08
                          GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrD 100
                                     + L+ +pG +v++ G+Gsg  s  +a  v+P G+++++e   + ae are++++++  ++v v + D
  gi|118431301|ref|NP_147666.2| 101 LQLLDPQPGEKVLDVGAGSGYQSALLAELVTPGGRVYAVERIPELAEYARENLEKTGYRGVVEVVVGD 168
                                    45677799**************************************************9999998776 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.6e-08   2.3e-05      98     167 ..     106     176 ..      98     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.6e-08
                                    --TT-EEEETT-TTTCCHHHCCHHT.TSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT CS
                         Met_10  98 veegevVvdvfAGiGpfaipiakys.kakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireq 167
                                     ++ge V+dv AG G+ +  +a +   + rv+a++  Pe  +y +en++      vv+++ +Dg + ++++
  gi|118431301|ref|NP_147666.2| 106 PQPGEKVLDVGAGSGYQSALLAELVtPGGRVYAVERIPELAEYARENLEKTGYRGVVEVVVGDGSKGLPQH 176
                                    489*************99888876515689*********************************98876655 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.5e-07   0.00023      23      94 ..     100     174 ..      98     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.5e-07
                                    HHHHCHCCTCSEEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST CS
                            MTS  23 LletlpkelsgkvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle..vevvasdvleeve 94 
                                    +l+ l+ +  +kvlD+G+G G+ +a la+  +p  +v +v+   +  e a+enle+++ +  vevv  d+ + ++
  gi|118431301|ref|NP_147666.2| 100 MLQLLDPQPGEKVLDVGAGSGYQSALLAELvTPGGRVYAVERIPELAEYARENLEKTGYRgvVEVVVGDGSKGLP 174
                                    6899999999****************9997267888***********************9999999999988776 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.5e-07   0.00023      18      84 ..      96     168 ..      89     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                                    HHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S- CS
                         RrnaAD  18 vineIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls...kdeklkvvhqD 84 
                                    v+ + l+ l++++  +vl++g+G G +++ La+ +     v ++E  ++La+  +++l+     + ++vv  D
  gi|118431301|ref|NP_147666.2|  96 VVGRMLQLLDPQPGEKVLDVGAGSGYQSALLAELVtpgGRVYAVERIPELAEYARENLEktgYRGVVEVVVGD 168
                                    6778889999*************************99999****************99955445556666666 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     3e-07   0.00027      46     114 ..     107     175 ..      88     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                                    HT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHH CS
                 Methyltransf_3  46 vnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLee 114
                                        +vl++G   Gy    +a  + + G++ a++  +e +e a++ ++k g+   +e+ +gd+ k L +
  gi|118431301|ref|NP_147666.2| 107 QPGEKVLDVGAGSGYQSALLAELVTPGGRVYAVERIPELAEYARENLEKTGYRGVVEVVVGDGSKGLPQ 175
                                    45578**********99999999999************************************9998866 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.9e-07   0.00026      66     107 ..     104     145 ..      93     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                    -S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                    Fibrillarin  66 lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                    l  ++g+kvL +Ga+sG   + ++++v++ g+vyave  p  
  gi|118431301|ref|NP_147666.2| 104 LDPQPGEKVLDVGAGSGYQSALLAELVTPGGRVYAVERIPEL 145
                                    55689********************************98864 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.1e-07   0.00073       2      66 ..     114     177 ..     113     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.1e-07
                Methyltransf_24   2 EiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealasla 66 
                                     +G+ sG+ +++l++++   g  r++av+  p+ ae a+++++++g++ +v+++++d ++ l+++a
  gi|118431301|ref|NP_147666.2| 114 DVGAGSGYQSALLAELVTPGG--RVYAVERIPElAEYARENLEKTGYRGVVEVVVGDGSKGLPQHA 177
                                    57888***********99998..6******99766667888888**************99999876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.3e-06    0.0021      14      81 ..     108     176 ..      98     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                Methyltransf_18  14 kgsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsdGleklkee 81 
                                    +g++v+D+G+  gy ++ l++      +v+a++  ++  e a+en+ek+g++  +ev+++dG + l ++
  gi|118431301|ref|NP_147666.2| 108 PGEKVLDVGAGSGYQSALLAELvTPGGRVYAVERIPELAEYARENLEKTGYRGVVEVVVGDGSKGLPQH 176
                                    589***********99999975145679**********************************9998655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.9e-06    0.0026      15      78 ..      99     158 ..      92     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                Methyltransf_32  15 kllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78 
                                    ++l+   + ++ ++v+DvGaG gY s  la   +  + +v++++   el+e a++  ek g  +
  gi|118431301|ref|NP_147666.2|  99 RMLQL-LDPQPGEKVLDVGAGSGYQSALLAE-LVTPGGRVYAVERIPELAEYARENLEKTG--Y 158
                                    55555.57788899****************9.55579*****************9999988..5 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     5e-06    0.0045      44     109 ..     105     171 ..      99     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
                                    -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT CS
                Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaee 109
                                     +++g+kvlDv +G+g  ++ l++ v   g+v  ++  +++ + +++ l+++g+   +e +++++ +
  gi|118431301|ref|NP_147666.2| 105 DPQPGEKVLDVGAGSGYQSALLAELVTPGGRVYAVERIPELAEYARENLEKTGYRgVVEVVVGDGSK 171
                                    67899*************************************************9788999998865 PP

>> Methyltransf_23  Methyltransferase 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     0.071      16      62 ..     103     161 ..      93     236 .. 0.78
   2 ?   -2.4   0.0       4.2   3.7e+03     107     117 ..     197     207 ..     193     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                Methyltransf_23  16 llpklraggrvLdiGcGtGillevlrengf...svtgvDlspeaveiae..........k 62 
                                    ll+  ++g +vLd+G+G+G+ + +l+e ++    v++v+  pe+ e a+           
  gi|118431301|ref|NP_147666.2| 103 LLD-PQPGEKVLDVGAGSGYQSALLAELVTpggRVYAVERIPELAEYARenlektgyrgV 161
                                    443.68899***********9999988877677999999999888877665555555550 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                Methyltransf_23 107 tllkpgGylll 117
                                    + l+pgG++++
  gi|118431301|ref|NP_147666.2| 197 EQLAPGGRMVI 207
                                    56888888876 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.12      41     107 ..     108     176 ..      97     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                    CC-EEEETT-TTS...HHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS CS
                  Cons_hypoth95  41 egarvLDlfaGsG...alglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallkl 107
                                     g++vLD+ aGsG   al  E +  g  ++++ve+ +e ++  +enle+++ ++ +++++ d ++ l+++
  gi|118431301|ref|NP_147666.2| 108 PGEKVLDVGAGSGyqsALLAELVTPG-GRVYAVERIPELAEYARENLEKTGYRGVVEVVVGDGSKGLPQH 176
                                    46789*******97778899*99999.99*************************9999999998888776 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.18      95     141 ..     109     162 ..      98     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                           DREV  95 dkklldlGaGdGeitkrvaptfee...vyat....elsetmrdrlkkkkynvls 141
                                     +k+ld+GaG G  +  +a+ +     vya     el+e  r++l+k +y+ + 
  gi|118431301|ref|NP_147666.2| 109 GEKVLDVGAGSGYQSALLAELVTPggrVYAVeripELAEYARENLEKTGYRGVV 162
                                    679*****************9987777***833335899999*******99654 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00024      0.21      54     116 ..     100     164 ..      96     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                    HHTTTT--TT-EEEEES-TTSHHHHHHHHHH..--EEEEEES-HHHHHHHHHHHHTS-SSS-EEE CS
                           CMAS  54 ileklelkpGmtlLdiGcGWGslvrravery..dvkvvglTlSkeqaklakkrvdeldlerkvev 116
                                    +l+ l+ +pG+++Ld+G+G G+     +e    + +v ++    e a++a++++++++ +  vev
  gi|118431301|ref|NP_147666.2| 100 MLQLLDPQPGEKVLDVGAGSGYQSALLAELVtpGGRVYAVERIPELAEYARENLEKTGYRGVVEV 164
                                    6778899************9986655544321177788888778888888888888877777666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00044       0.4     160     215 ..     107     164 ..      99     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00044
                           PrmA 160 kegeevlDvGtGSGiLa..iaaakLgakkvvavDiDevAvkvakeNaelNkveaklev 215
                                    ++ge+vlDvG+GSG  +  +a +     +v+av   +   + a+eN+e+ + +  +ev
  gi|118431301|ref|NP_147666.2| 107 QPGEKVLDVGAGSGYQSalLAELVTPGGRVYAVERIPELAEYARENLEKTGYRGVVEV 164
                                    789***********98733344444567899998888888888888887776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2002.47
//
Query:       gi|118431302|ref|NP_147667.2|  [L=170]
Description: hypothetical protein APE_1013.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-07   31.7   0.9    4.1e-07   30.8   0.9    1.4  1  Pilin_N   Archaeal Type IV pilin, N-terminal


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 !   30.8   0.9   2.3e-11   4.1e-07       1      78 [.       5      90 ..       5      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.3e-11
                        Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl.asneekapqasievk...idssastgkna....vslehkgGdsidtkdlki 74
                                   +++SpVi  +++va+ + +   +a+  +gl  s ++ +pq++++     +++ ++t++++    ++++++gG s ++  ++i
  gi|118431302|ref|NP_147667.2|  5 RGISPVIATVIIVAVAIAISIAVAGWLFGLwGSFATGSPQIQVSAAkvvYETINNTDNDEieakLYINNSGGSSDTLIRIEI 86
                                   69***************99999********9999*********555555333333333334568********9988887777 PP

                        Pilin_N 75 vlns 78
                                     n+
  gi|118431302|ref|NP_147667.2| 87 SGNN 90
                                   7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1292.88
//
Query:       gi|118431303|ref|NP_147668.2|  [L=291]
Description: hypothetical protein APE_1014.1 [Aeropyrum pernix K1]
Scores for complete 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-27   95.1   0.0    5.2e-27   94.8   0.0    1.0  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   2.9e-31   5.2e-27       2     255 .]       9     287 ..       8     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.9e-31
                                    EEEE-TTS.CCCTTTHHHHHHHHHHTTEEEEEEE-SSG.................GGHHHHHHHHTT.TTTEEEEE---G CS
                     TatD_DNase   2 DaHcHlds.kefeedreeileraeeagvaavvvvgtss.................kdskavlelakkypnkvyavlGiHP 63 
                                    DaH+H++  + +   + e+ +r++++g+   +  ++++                 + + +  + a++   +v + +GiHP
  gi|118431303|ref|NP_147668.2|   9 DAHMHTNPtRGL--GAREVARRFRREGGWFAALLTLTTwsyglaptgveayrrmyEIHLRECRAAREEGLRVACFAGIHP 86 
                                    ********5444..455555999999999998777777789999999999999855677999999999************ PP

                                    GGGGC...........C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEE CS
                     TatD_DNase  64 nevde...........asedlleelkel.anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHl 131
                                    +evd+           a e+ le+++ l + +++  + ++Ge+G+ +y++++      e v+ee  ++A e ++ l++Hl
  gi|118431303|ref|NP_147668.2|  87 AEVDRmidkhrqppekALETALEAVEVLrRLCREGAIDGVGEVGRQHYRTSPLRVAIAEVVLEEAAAAALEEGCLLQLHL 166
                                    *****999999987765666669999998889***************9999999999999******************** PP

                                    ES....-HHHHHHHHHHCGGCCS...EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE-- CS
                     TatD_DNase 132 rk....aeedlleilkeaaeaka...kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiET 204
                                    ++    + e++ +il++a++++a    v++H+   +  +ak+++ +gy  +++g+ +     +l e ++a +    ++E+
  gi|118431303|ref|NP_147668.2| 167 ENegpaTVETVDRILRRAGATGArrgMVIFHH--ATLRVAKEAVARGYNATIPGV-P-----KLLEHAAANEPPDYMVES 238
                                    *****9999**********99999999999*9..889999**************5.3.....367777777777889*** PP

                                    -TTSSEECCCTT.SE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     TatD_DNase 205 DaPyltpkpyrg.krnepanvayvveklaelkaltleelaeitaeNakrlfk 255
                                    D  yl++ p r+ ++ ep+ +a+ ++++a  + +t e++ ++  + ++r+f+
  gi|118431303|ref|NP_147668.2| 239 D--YLDD-PARPgAVVEPWKMAQKLREIASRTPETREWVRRTNIDLVERVFQ 287
                                    *..9999.99999*****************************9999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2305.97
//
Query:       gi|14601141|ref|NP_147669.1|  [L=959]
Description: leucyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-60  203.8   0.0      5e-41  140.6   0.0    2.7  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
      2e-23   82.8   0.1    2.2e-10   39.9   0.0    3.9  4  tRNA-synt_1g   tRNA synthetases class I (M)
      1e-21   77.5   0.1    1.9e-21   76.6   0.1    1.4  1  Anticodon_1    Anticodon-binding domain of tRNA
    4.5e-11   42.6   0.0      4e-09   36.3   0.0    2.3  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    1.6e-08   34.3   0.0    0.00016   21.1   0.0    2.3  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.077   13.5   3.5         14    6.2   0.2    3.2  3  RecX           RecX family


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 !  140.6   0.0   1.7e-44     5e-41       1     305 [.      10     325 ..      10     339 .. 0.87
   2 !   59.7   0.0   5.2e-20   1.6e-16     320     590 ..     397     664 ..     395     679 .. 0.73

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 1.7e-44
                   tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea.kv 80 
                                   k++e+W e+ +f++    +  +++f ++ + Pyv+  +H+G a++    di+ rykrm+G++vl+  Gw   G +i + ++
  gi|14601141|ref|NP_147669.1|  10 KWQERWREARLFEAD--PQPGRRKFFITFPYPYVNAYPHLGSAFTILRVDIMARYKRMRGYNVLFPQGWHATGGPIVSsAL 88 
                                   5899*********99..666799**************************************************99854144 PP

                   tRNA-synt_1  81 ekklgake.kkerkklgree.....frekvrewkaeyaeeirkqvkrlGvsvDfdreylT..ldkeleeavkevfvrladk 153
                                     + g  +  k+  ++g  e     fr   r w++ +++ +r++++r G+s+D+ re  T  l++ ++  +++ + +l +k
  gi|14601141|ref|NP_147669.1|  89 RVREGDPRiIKTLRDMGIPEediprFR-DPRYWVEFFTKAWRRDLERYGMSIDWRREFYTtsLNPAYSRFIEWQYLKLREK 168
                                   544444432367789997542222133.4589*************************987568899*************** PP

                   tRNA-synt_1 154 gliyrgkklvnwstklktalselEv..eykdkk.dalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv.... 227
                                   g + +g ++v w++k + ++ + +   ey   + + ++ ++f   d+      + T +PeT++g t + v+p+  y     
  gi|14601141|ref|NP_147669.1| 169 GFVGKGRHPVVWCPKEQKVVGDHDRpdEYAGISpQEAVIIKFRGRDGL--VYPALTYRPETVFGVTNLWVHPDATYLvaev 247
                                   ***********************9986666654345566666655554..58899*********************97884 PP

                   tRNA-synt_1 228 itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyev 305
                                     +e++i+ e+  ++l+++ +   ile+++g+ L g+ v +p  +r++p++   +v  + GtGvV   Pah + Dy +
  gi|14601141|ref|NP_147669.1| 248 DGEERWIIGEQAARELADQGHRVVILERIEGRRLLGRIVVNPADGREVPVLPASFVRPDLGTGVVMSVPAHAPYDYVA 325
                                   456889**********************************************************************86 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 5.2e-20
                   tRNA-synt_1 320 dgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvp..fcerskkpiiyrateqWfvrvke..ladaalkave 396
                                   +g + e+++ f+glkv +a++kvve l+e+g+ l++ +   +v   ++ r+++ i   + +qWf   ++   ++ a +av 
  gi|14601141|ref|NP_147669.1| 397 EGIMLETTGRFSGLKVAEAKEKVVEWLEERGAALRIYTLPQEVYcrCGARTHVKI---VEDQWFLLYSKpeWKALAREAVA 474
                                   688999*****************************99988877411344555544...689****9998556666667888 PP

                   tRNA-synt_1 397 kvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkek 477
                                   +++f p   ++ ++ ++e  +dW++  +   G+++p  ++   e     +++ +++  + ++ +++        +k + e 
  gi|14601141|ref|NP_147669.1| 475 RMEFLPGHVRRDFEAIIEALRDWAFTHKGELGTPLPWDREWVIE-SLS-DSTIYMAYYTIAKYTQH-------PEKYGVEP 546
                                   ************************************53333322.222.12222222111211111.......12222233 PP

                   tRNA-synt_1 478 gelekdedvlDvWFsSgswpfst...lgyp....eedteelkkffpadmlleGlDiirgWvarlillslaltgsePf.kev 550
                                   + l   ++v+D  F  +  p  +    g p    ee ++e+   +p dm ++G D i   +   i+  +a++ +e + + +
  gi|14601141|ref|NP_147669.1| 547 EML--TPEVFDYVFLGAGDPGEVsrrSGIPqgllEEMRREFLYWYPLDMRISGKDLIPNHLVFFIFHHTAIFPRELWpRAI 625
                                   333..689999998665443222111233311114678899999***************************9999663678 PP

                   tRNA-synt_1 551 lvhglvrdeeGrKmSKslgNvidpldvikkygadalRltl 590
                                    v+g v+   G KmSKs+gN i   + ++  gada R++ 
  gi|14601141|ref|NP_147669.1| 626 GVNGWVLV-AGEKMSKSKGNFILLRQALDWWGADATRWAE 664
                                   8****996.5***************************963 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 !   39.9   0.0   7.3e-14   2.2e-10       2      57 ..      33      88 ..      32     100 .. 0.94
   2 ?    2.8   0.0     0.013        40      67     132 ..     121     190 ..     114     198 .. 0.79
   3 ?    0.4   0.1     0.073   2.2e+02     156     245 ..     427     517 ..     411     543 .. 0.63
   4 !   33.9   0.0   4.8e-12   1.4e-08     286     368 ..     594     680 ..     578     698 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 7.3e-14
                                  EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH CS
                  tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe 57
                                  ++t + pY+n+ +HlG + +++  Di+aRykr+rg++vlf  g  + G pi  +A 
  gi|14601141|ref|NP_147669.1| 33 FITFPYPYVNAYPHLGSAFTILRVDIMARYKRMRGYNVLFPQGWHATGGPIVSSAL 88
                                  89**********************************************99998885 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHTT---S...E.EEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                  tRNA-synt_1g  67 vekvheeikelfkklnisfd...k.ygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                   ve ++++ +++++++++s d   + y+++ + + +++ +  + kl ekg++ +++  +++cpk+++   d
  gi|14601141|ref|NP_147669.1| 121 VEFFTKAWRRDLERYGMSIDwrrEfYTTSLNPAYSRFIEWQYLKLREKGFVGKGRHPVVWCPKEQKVVGD 190
                                   5556677777777777777644432555567888999999***********************9998877 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.073
                                   SSB-E................EEE..EEEEEE-GGG..GHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SS CS
                  tRNA-synt_1g 156 gkkleptelinpksaisgskpevke.tehlffklsk..fekklkewieeeekeleenvkkivkewlkegLkdlaisrdldw 233
                                   g+ l   +l + +   +g++  vk  ++++f+  sk  ++   +e +++ e  l+ +v++  ++++++ L+d+a + + + 
  gi|14601141|ref|NP_147669.1| 427 GAALRIYTLPQEVYCRCGARTHVKIvEDQWFLLYSKpeWKALAREAVARME-FLPGHVRRDFEAIIEA-LRDWAFTHKGEL 505
                                   555555555555555566666655413445544443103344455552222.4788888888888887.************ PP

                                   S-EETTECCEEE CS
                  tRNA-synt_1g 234 GipvPgaekkvl 245
                                   G p+P + + v+
  gi|14601141|ref|NP_147669.1| 506 GTPLPWDREWVI 517
                                   *****6666555 PP

  == domain 4  score: 33.9 bits;  conditional E-value: 4.8e-12
                                   EEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHH..HHHHHS-TTS CS
                  tRNA-synt_1g 286 hfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRY..ylaaeapekk 362
                                    + gkd i+ H +f+    ++   +   p+++ +++++ v g+K+SkS+g+++  ++al+   ad+ R+  +la + +  +
  gi|14601141|ref|NP_147669.1| 594 RISGKDLIPNHLVFFIFHHTAifPRELWPRAIGVNGWVLVAGEKMSKSKGNFILLRQALDWWGADATRWaeVLAGADSGLD 674
                                   567************9999998767779****************************************9445666888888 PP

                                   -EEE-H CS
                  tRNA-synt_1g 363 Dldfsw 368
                                   D++f+ 
  gi|14601141|ref|NP_147669.1| 675 DANFEP 680
                                   888875 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 !   76.6   0.1   6.4e-25   1.9e-21       1     134 [.     713     831 ..     713     870 .. 0.81

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 6.4e-25
                   Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfm 81 
                                   drw+ s+ln+++++vt+ +ee +f++a+ ++++ +++++ +wyl+ +  +              +l+ ++e  + l+aPf+
  gi|14601141|ref|NP_147669.1| 713 DRWFESRLNSTIARVTRLMEEANFKTALVEAWYKLQESY-RWYLRRSGGEPRE----------DLLRRFIEVQTLLIAPFA 782
                                   9****************************9999866665.******9877533..........89**************** PP

                   Anticodon_1  82 PfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkair 134
                                   P+++Ee+w    e +g++ + + a+wpe ++++  +e  e++ e ++++++ +r
  gi|14601141|ref|NP_147669.1| 783 PHTAEEAW----EAMGREGFASTASWPEpDESKISPEV-EAAEETVQAVLEDAR 831
                                   ********....99*************96655554444.334444333333333 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 !   36.3   0.0   1.3e-12     4e-09      27     126 ..     222     323 ..     204     328 .. 0.84
   2 ?    3.8   0.0     0.012        36     153     185 .]     393     424 ..     372     424 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.3e-12
                 tRNA-synt_1_2  27 ttrpdtlfGvtfvalapehp.lveklaekkkelaafieevkkksesereletkekeGv.ftglkaihPitgekipiwvany 105
                                   t rp+t+fGvt + + p+   lv ++  +++ +    +  +  ++ +r +  ++ eG    g  +++P +g+++p+  a +
  gi|14601141|ref|NP_147669.1| 222 TYRPETVFGVTNLWVHPDATyLVAEVDGEERWIIGEQAARELADQGHRVVILERIEGRrLLGRIVVNPADGREVPVLPASF 302
                                   88**************997538999977777776655555666666666666677888689******************** PP

                 tRNA-synt_1_2 106 vlmeygtgavmavPahdqrDf 126
                                   v  + gtg+vm+vPah   D+
  gi|14601141|ref|NP_147669.1| 303 VRPDLGTGVVMSVPAHAPYDY 323
                                   ****************98887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.012
                 tRNA-synt_1_2 153 eeayteegilvnsg.efdglkskeakekiakkle 185
                                   +e y  egi+++++ +f+glk++eakek++++le
  gi|14601141|ref|NP_147669.1| 393 REFY--EGIMLETTgRFSGLKVAEAKEKVVEWLE 424
                                   2233..899998766***************9986 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 !   10.6   0.0   8.4e-05      0.25      19      52 ..      41      74 ..      30     137 .. 0.90
   2 !   21.1   0.0   5.5e-08   0.00016     206     279 ..     589     663 ..     579     677 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.4e-05
                                  TTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                  tRNA-synt_1e 19 vydashlGhaRslvafDilrrilqalgYdvqfvq 52
                                  v  + hlG a +++ +Di++r+ +++gY+v f q
  gi|14601141|ref|NP_147669.1| 41 VNAYPHLGSAFTILRVDIMARYKRMRGYNVLFPQ 74
                                  77899*************************9976 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 5.5e-08
                                   SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHH CS
                  tRNA-synt_1e 206 seidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRll 279
                                     +d+   G+DL+  h    +  ++a f  + + +    ng++ + gekmsks +nfi+++++l  + + + R++
  gi|14601141|ref|NP_147669.1| 589 YPLDMRISGKDLIPNHLVFFIFHHTAIFPrELWPRAIGVNGWVLVAGEKMSKSKGNFILLRQALDWWGADATRWA 663
                                   568999999999988888999999999995667788889**************************9999999987 PP

>> RecX  RecX family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0047        14      36      86 ..      86     135 ..      82     171 .. 0.84
   2 ?    6.2   0.2    0.0046        14      50     106 ..     367     427 ..     363     431 .. 0.84
   3 ?   -1.8   0.7       1.4   4.1e+03      44      74 ..     869     899 ..     853     924 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                                   HHHHH----HHHHHHHHHTTT--HHHHHHHHTTS-HHHHHHHHHHHHHHHT CS
                          RecX  36 srlrsrgyGprrikqeLkqkGiseelieqaleeldeeeqarelaekklkkl 86 
                                   s lr  + G  ri + L+  Gi+ee+i +  +  ++ e  ++++++ l+++
  gi|14601141|ref|NP_147669.1|  86 SALR-VREGDPRIIKTLRDMGIPEEDIPRFRDPRYWVEFFTKAWRRDLERY 135
                                   5554.678999***********************************99988 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0046
                                   HHHHTTT--HHHHHHHHTTS-HHHHHHHHHHHHHHHTTTS-H....HHHHHHHHHHHHHTT CS
                          RecX  50 qeLkqkGiseelieqaleeldeeeqarelaekklkklkkeed....ekekqklvrfLarrG 106
                                   +e +++G+++++  + l+e ++e  are +e  + +++ + +     ++k+k+v++L  rG
  gi|14601141|ref|NP_147669.1| 367 EEVRRRGVESQMDREKLDEATREVYAREFYEGIMLETTGRFSglkvAEAKEKVVEWLEERG 427
                                   7899**************99999999998888877774333355559***********999 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.4
                                   -HHHHHHHHHTTT--HHHHHHHHTTS-HHHH CS
                          RecX  44 GprrikqeLkqkGiseelieqaleeldeeeq 74 
                                    + +++++ k  G+++  +++ +++l++  +
  gi|14601141|ref|NP_147669.1| 869 MKEALREAFKVEGVDKREAARLVQQLSRAPE 899
                                   3446677777788888877777776555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (959 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); 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:                         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: 0.74u 0.27s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 6473.44
//
Query:       gi|118431304|ref|NP_147671.2|  [L=303]
Description: dihydrodipicolinate synthase [Aeropyrum pernix K1]
Scores for 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-49  165.9   0.0    1.1e-48  165.5   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 !  165.5   0.0   5.9e-53   1.1e-48       4     285 ..       5     288 ..       3     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 5.9e-53
                                    EEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSHH CS
                          DHDPS   4 giitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnsts 83 
                                    ++i+++vtp  + g +dk+a++ l+  l ++gvdg++v GttGE  +l  +e+++ +  +++ a     ++agv +   +
  gi|118431304|ref|NP_147671.2|   5 KVIVPMVTPL-RGGSVDKNAASWLASRLSESGVDGVFVPGTTGEWYLLDPHERAEAFFAVASSAIAGLRLVAGVSGYRPE 83 
                                    58999****7.68*****************************************9999999999999************* PP

                                    HHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHH.HCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE CS
                          DHDPS  84 eaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaii.eatdlpvilYnvpsrtgadlspetvkrLaelenivgvKe 162
                                    e+ +la++a+  Ga++v+av+P Y +ps+  l +++ +i   a++lp+ +Y +p+r g  l++e+v+ L+e   + g+K+
  gi|118431304|ref|NP_147671.2|  84 ESYRLAEEAAGHGAHAVMAVPPIYFRPSTDFLREFYGEIKrRAGGLPTYIYIFPERMGYTLAVEQVESLVEAGVVDGIKA 163
                                    ****************************************99************************************** PP

                                    -SS-CTHHH..HHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          DHDPS 163 avgdleevi..kikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllpli 240
                                    +v d  ++     +ke ++++ +++G  e+l ++   G+dGv+ + sn+a++++ +l + l++G ++ +a l+ ++l+l 
  gi|118431304|ref|NP_147671.2| 164 TVTDAAYIAglAAVKERNPEFEVLAGGLEMLVHTSLSGGDGVVDAYSNVAPKLAVELAESLEKGSVERVAGLQGRVLKLS 243
                                    *****887622557888*************************************************************** PP

                                    HHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHH CS
                          DHDPS 241 kilfaepnvilvktalellGlvveatlrkPltpleeeekeeleal 285
                                     il ++++++ +k++l++lG + +  +rkPl pl++ e ++ +++
  gi|118431304|ref|NP_147671.2| 244 RILGKRSLPAVLKAVLHVLGAPITGEVRKPLKPLTQPEANATANA 288
                                    ***********************************9888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2255.99
//
Query:       gi|118431305|ref|NP_147673.2|  [L=211]
Description: heme exporter protein A [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-19   69.9   0.0    4.1e-19   69.4   0.0    1.2  1  ABC_tran      ABC transporter
      3e-05   24.5   0.2    5.7e-05   23.6   0.2    1.4  1  AAA_16        AAA ATPase domain
      5e-05   23.2   0.5      0.028   14.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0019   18.4   0.0      0.003   17.7   0.0    1.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0061   14.2   0.1     0.0075   13.9   0.1    1.0  1  DUF3584       Protein of unknown function (DUF3584)
     0.0081   16.1   0.3      0.065   13.1   0.0    2.0  2  NACHT         NACHT domain
     0.0096   15.6   0.1      0.016   14.9   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.015   15.6   0.2       0.68   10.2   0.2    2.0  2  AAA_22        AAA domain
      0.032   14.0   0.1      0.083   12.6   0.1    1.6  2  AAA_30        AAA domain
      0.036   14.6   0.0      0.049   14.1   0.0    1.1  1  AAA_23        AAA domain
       0.05   13.8   0.1      0.083   13.1   0.1    1.3  1  AAA_28        AAA domain
      0.053   12.6   0.1       0.08   12.0   0.1    1.2  1  T2SSE         Type II/IV secretion system protein
      0.068   12.9   0.1        6.2    6.6   0.1    2.1  2  DEAD          DEAD/DEAH box helicase
      0.083   12.5   0.1       0.12   12.0   0.1    1.2  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.088   12.4   0.4       0.16   11.5   0.4    1.4  1  AAA_25        AAA domain
       0.13   11.0   0.1       0.17   10.7   0.1    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
       0.18   12.2   0.0       0.26   11.7   0.0    1.2  1  RNA_helicase  RNA helicase
       0.23   10.7   0.1       0.35   10.1   0.1    1.2  1  Zeta_toxin    Zeta toxin
       0.29   11.0   0.0        0.6   10.0   0.0    1.5  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 !   69.4   0.0   4.4e-22   4.1e-19       1     136 [.      20     156 ..      20     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 4.4e-22
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vsl l +ge v++ G nG+GK+tLl+l agl +p  G++ +          +  r  +g++ ++p +  +ltv en 
  gi|118431305|ref|NP_147673.2|  20 LRGVSLALGPGEAVVVSGANGSGKTTLLRLSAGLAEPSRGRVSWG-------CPRGPRGCVGYVGHTPMVYGDLTVWENv 92 
                                    6789**************************************555.......57789**********************9 PP

                                    ...........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   +   +++a + lgl++   + +    s+LS G+++r+ ++rall +p+llllDE++
  gi|118431305|ref|NP_147673.2|  93 effsslhggslG---DyplAAEAWRLLGLEKYGSHLA----SQLSFGWRRRLDVVRALLGEPRLLLLDEAF 156
                                    888777665433...1556899999999999888888....****************************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.2   6.1e-08   5.7e-05      24     161 ..      30     173 ..      19     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.1e-08
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa.......ipy....sa.laqalareellrqlldeaes 91 
                                    +e+v++sG+ G+GK++l+r  +  +e ++g + +g  +   ++       +p+    ++ + ++ ++++l    l  +  
  gi|118431305|ref|NP_147673.2|  30 GEAVVVSGANGSGKTTLLRLSAGLAEPSRGRVSWGCPRGP-RGcvgyvghTPMvygdLTvWENVEFFSSLHGGSLG-DYP 107
                                    399*******************999999888877776665.55555666666666764424444434344444444.466 PP

                         AAA_16  92 aeleawrekleealaavpelagaea...srllellkrllallsrderplvlvlD.dlqwadeaslqllaaLlrl 161
                                     ++eawr   +e ++  ++la++++   +r l+++++ll      ++p +l+lD  +  +d++  ++l+ Llrl
  gi|118431305|ref|NP_147673.2| 108 LAAEAWRLLGLEKYG--SHLASQLSfgwRRRLDVVRALL------GEPRLLLLDeAFTGLDQGASEALSRLLRL 173
                                    689999999999998..7777777777777777777777......77788888834668888888888888876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     3e-05     0.028       3      22 ..      34      53 ..      33      69 .. 0.83
   2 !    7.4   0.1    0.0035       3.3     235     296 ..     127     185 ..     119     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   v+ G+NgsGK++LL++  +l
  gi|118431305|ref|NP_147673.2| 34 VVSGANGSGKTTLLRLSAGL 53
                                   666***********976555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0035
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                    ++lS G +r l ++ all  +   +lll+DE  +gL+  + + l +ll+++  +g  +++tT
  gi|118431305|ref|NP_147673.2| 127 SQLSFGWRRRLDVVRALLGEP---RLLLLDEAFTGLDQGASEALSRLLRLALGEGLALLMTT 185
                                    567777777777888888777...************************99999999999999 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 !   17.7   0.0   3.2e-06     0.003      63      89 ..     146     172 ..     125     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-06
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                     +rl++LDEAF +lD+  +++l +ll+
  gi|118431305|ref|NP_147673.2| 146 EPRLLLLDEAFTGLDQGASEALSRLLR 172
                                    48******************9999986 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1     8e-06    0.0075      13      36 ..      26      49 ..      18      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8e-06
                        DUF3584 13 eldldghtnieGtNaaGKTtLlrL 36
                                    l + + + + G+N++GKTtLlrL
  gi|118431305|ref|NP_147673.2| 26 ALGPGEAVVVSGANGSGKTTLLRL 49
                                   566778899**************8 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   6.9e-05     0.065       3      18 ..      33      48 ..      31      59 .. 0.87
   2 ?    1.0   0.0      0.37   3.5e+02      90     127 ..     152     185 ..     120     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.9e-05
                                   EEEEC-TTTCHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlq 18
                                   v++ G++GsGKTtLl+
  gi|118431305|ref|NP_147673.2| 33 VVVSGANGSGKTTLLR 48
                                   89************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.37
                                    STT-SS-TCH.........HHHHHCTTTTT--EEEEEE CS
                          NACHT  90 lDelvtdlgqkekqpvrtlLselirkkllpeasllltv 127
                                    lDe+ t l+q     + + Ls+l+r +l  +  ll+t+
  gi|118431305|ref|NP_147673.2| 152 LDEAFTGLDQ----GASEALSRLLRLALGEGLALLMTT 185
                                    5788888888....888899999999998888888886 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 !   14.9   0.1   1.7e-05     0.016      16      39 ..      24      47 ..      18      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   ++ + + +a++++G++GsGK+Tll
  gi|118431305|ref|NP_147673.2| 24 SLALGPGEAVVVSGANGSGKTTLL 47
                                   55666677999************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00072      0.68       7      25 ..      32      50 ..      28      83 .. 0.89
   2 ?    3.7   0.0     0.072        68      83     117 ..     137     175 ..      89     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00072
                         AAA_22  7 ilvvtGesGtGKTtllrrl 25
                                    +vv G  G+GKTtllr  
  gi|118431305|ref|NP_147673.2| 32 AVVVSGANGSGKTTLLRLS 50
                                   579*************975 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.072
                         AAA_22  83 eqalrarav.ielliiDEaqh.lr..seealeeLrslln 117
                                     + +ra    ++ll++DEa   l+    eal+ L +l+ 
  gi|118431305|ref|NP_147673.2| 137 LDVVRALLGePRLLLLDEAFTgLDqgASEALSRLLRLAL 175
                                    333444444789*******99997543888888877765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   8.8e-05     0.083      17      49 ..      29      61 ..      22      69 .. 0.80
   2 ?   -1.8   0.0       2.3   2.1e+03      83      99 ..     141     157 ..     116     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.8e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrv 49
                                   +   +v+ G+ G+GKtt+l+  + ++e + grv
  gi|118431305|ref|NP_147673.2| 29 PGEAVVVSGANGSGKTTLLRLSAGLAEPSRGRV 61
                                   445899**************9999998886666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                         AAA_30  83 rarlepgtllivDEagm 99 
                                    ra l + +ll+ DEa  
  gi|118431305|ref|NP_147673.2| 141 RALLGEPRLLLLDEAFT 157
                                    44556668888888744 PP

>> AAA_23  AAA 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     0.049      22      37 ..      33      48 ..      12      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                         AAA_23 22 tlItGpNGaGKTTild 37
                                   ++++G NG+GKTT+l+
  gi|118431305|ref|NP_147673.2| 33 VVVSGANGSGKTTLLR 48
                                   6899**********96 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.8e-05     0.083       2      17 ..      33      48 ..      32      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.8e-05
                         AAA_28  2 ivitGgestGKTtlle 17
                                   +v++G+ ++GKTtll+
  gi|118431305|ref|NP_147673.2| 33 VVVSGANGSGKTTLLR 48
                                   9*************96 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   0.1   8.4e-05      0.08     131     149 ..      32      50 ..      20      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.4e-05
                          T2SSE 131 lilvsGgTgsGKttllyal 149
                                     ++vsG+ gsGKttll   
  gi|118431305|ref|NP_147673.2|  32 AVVVSGANGSGKTTLLRLS 50 
                                    689************9654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0066       6.2      13      31 ..      29      47 ..      21      53 .. 0.81
   2 ?    4.3   0.0     0.033        31     119     147 ..     144     172 ..     123     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0066
                                   TTCEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                           DEAD 13 gggdvlvaaeTGsGKTlaf 31
                                    g+ v+v+++ GsGKT+  
  gi|118431305|ref|NP_147673.2| 29 PGEAVVVSGANGSGKTTLL 47
                                   6889************875 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.033
                                    CTTEEEEEEETHHHHHHTTTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 119 lsqvrflVlDEadrlldqgfsdfinriln 147
                                    l + r+l lDEa + ldqg s+ ++r+l+
  gi|118431305|ref|NP_147673.2| 144 LGEPRLLLLDEAFTGLDQGASEALSRLLR 172
                                    78889*******************99876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.12       2      18 ..      32      48 ..      31      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                   EEEEEESTTCCHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLln 18
                                   ++v++G  GsGKTtLl+
  gi|118431305|ref|NP_147673.2| 32 AVVVSGANGSGKTTLLR 48
                                   689************98 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00017      0.16      23      65 ..      17      64 ..      15      77 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                         AAA_25 23 rwlvkg...llpagelallaGapgtGKttlaldlalava...tGkpwlg 65
                                   rw+++g    l  ge +++ Ga g+GKttl+  l++ +a   +G+  +g
  gi|118431305|ref|NP_147673.2| 17 RWVLRGvslALGPGEAVVVSGANGSGKTTLL-RLSAGLAepsRGRVSWG 64
                                   56777644446789***************85.55655555556665555 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   0.00018      0.17      21      55 ..      26      60 ..       7      62 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                           DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                    l  g +v+v G +gsGkttl+    G+ e+ +Gr
  gi|118431305|ref|NP_147673.2| 26 ALGPGEAVVVSGANGSGKTTLLRLSAGLAEPSRGR 60
                                   5777999***************9999999999997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00027      0.26       1      62 [.      33      90 ..      33     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdgYtgqevvvidDfgqvk 62
                                   ++++G++g GK+tl +  ++ l+    ++++++v +  +     + gY g++ +v+ D+  ++
  gi|118431305|ref|NP_147673.2| 33 VVVSGANGSGKTTLLRL-SAGLA----EPSRGRVSWgCPRGPRGCVGYVGHTPMVYGDLTVWE 90
                                   689************98.55555....7888999987788889999********999997766 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00037      0.35      18      37 ..      32      51 ..      29      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00037
                     Zeta_toxin 18 lillgGqpGAGKselaellk 37
                                   +++++G+ G+GK++l++l++
  gi|118431305|ref|NP_147673.2| 32 AVVVSGANGSGKTTLLRLSA 51
                                   799*************9876 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 ?   -3.2   0.0       6.9   6.5e+03     216     225 ..       7      16 ..       6      17 .. 0.86
   2 ?   10.0   0.0   0.00064       0.6      17      41 ..      27      51 ..      23      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.9
                       ATPase_2 216 feeiyryvGG 225
                                    +e++++++GG
  gi|118431305|ref|NP_147673.2|   7 LENVWKMLGG 16 
                                    589******9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00064
                       ATPase_2 17 repneiyfiYGpegsGKtaLlkeii 41
                                    +p e +++ G  gsGKt+Ll+ ++
  gi|118431305|ref|NP_147673.2| 27 LGPGEAVVVSGANGSGKTTLLRLSA 51
                                   578899***************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1702.91
//
Query:       gi|14601146|ref|NP_147674.1|  [L=220]
Description: heme exporter protein B [Aeropyrum pernix K1]
Scores for 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   8.6     0.0002   20.7   8.6    2.0  2  ABC2_membrane_2  ABC-2 family transporter protein
    0.00021   20.5   5.9    0.00026   20.2   5.9    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0046   16.9   5.5      0.026   14.5   5.8    1.9  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 ?    1.7   0.1     0.022   1.3e+02       2      32 ..       7      36 ..       6      47 .. 0.83
   2 !   20.7   8.6   3.4e-08    0.0002      81     214 ..      56     181 ..      48     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.022
               ABC2_membrane_2  2 aiakkEfrdlvrsrrfllltvllplidvala 32
                                  ++++kE   + r++++l++ +l+ l   a+a
  gi|14601146|ref|NP_147674.1|  7 WLVRKEALLAARNPVLLATQALFTLA-IAVA 36
                                  79999999999999999999999998.5555 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.4e-08
               ABC2_membrane_2  81 mavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledl 161
                                   +a l+ + aa +++++  +E e gTl++l ++Pv  + ++l+K + ++a+   i +++la      ++ +  + +++l+ +
  gi|14601146|ref|NP_147674.1|  56 LAALMLFQAAFTAYTSYIREAEWGTLEALRTSPVDPGLVYLAKTLYSAAS---IFLTTLAF---LPVYAVLASPPIPLWGY 130
                                   55666677******************************************...77777776...33466788999999999 PP

               ABC2_membrane_2 162 lllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivly 214
                                   l l   ++l+ ll+   +++ l S+ +  sr++a+l   +++v +  ++ v++
  gi|14601146|ref|NP_147674.1| 131 LMLGEWILLSSLLL--GGVASLSSAMLSYSRNQALLTPTILAVVSAPYMRVAS 181
                                   99999999999966..9999999999999999999998888888877776664 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 !   20.2   5.9   4.3e-08   0.00026     163     279 ..      52     171 ..      22     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.3e-08
               ABC2_membrane_3 163 lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllil.ll.afglgipfg.nlgl 240
                                   l ++++++++f  a+ + +s+++E e +++e + +s+v+p   +l+k l +++  +l++l +l ++ +++   p    +g+
  gi|14601146|ref|NP_147674.1|  52 LPPMLAALMLFQAAFTAYTSYIREAEWGTLEALRTSPVDPGLVYLAKTLYSAASIFLTTLAFLpVYaVLA--SPPIpLWGY 130
                                   5679999999999999999********************************9999999988773335888..555557777 PP

               ABC2_membrane_3 241 ll.llfllfglayialgyllsslfknsetaqilifivil.l 279
                                   l+   ++l + +++  ++ lss++ +++  q+l++++il +
  gi|14601146|ref|NP_147674.1| 131 LMlGEWILLSSLLLGGVASLSSAMLSYSRNQALLTPTILaV 171
                                   66555666666666666777777777777777777777633 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2       0.1   6.1e+02      90     136 ..      10      57 ..       9      62 .. 0.63
   2 !   14.5   5.8   4.3e-06     0.026      56     174 ..      58     172 ..      20     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.1
               ABC2_membrane_4  90 srtklllaKlivllllsvllmlvtflitvlfallsgf.vgfsvklvle 136
                                    + +ll+a   vll + +l++l+ ++++ +++  s   +gfs  ++l 
  gi|14601146|ref|NP_147674.1|  10 RKEALLAARNPVLLATQALFTLAIAVAAGAVEHSSLLgPGFSLPPMLA 57 
                                   567788888888888888888887777766644333215566555555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.3e-06
               ABC2_membrane_4  56 lllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvle 136
                                   +l+l+ + +   a ++  rE + +tl  L+t Pv    ++laK ++ +  ++l +l+     + +  ++ ++++   + l 
  gi|14601146|ref|NP_147674.1|  58 ALMLFQAAF--TAYTSYIREAEWGTLEALRTSPVDPGLVYLAKTLYSAASIFLTTLA----FLPVYAVLASPPIPLWGYLM 132
                                   333444444..444555699999********************99876544444433....33333344445554444444 PP

               ABC2_membrane_4 137 llkkcl.elgllvffavlpiialvl.lkksyvlpliltlv 174
                                   l  ++l    ll  +a+l   +l++  ++  ++p il++v
  gi|14601146|ref|NP_147674.1| 133 LGEWILlSSLLLGGVASLSSAMLSYsRNQALLTPTILAVV 172
                                   4444441333333445555556666355566788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1833.36
//
Query:       gi|118431306|ref|NP_147675.2|  [L=463]
Description: hypothetical protein APE_1031.1 [Aeropyrum pernix K1]
Scores for 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-10   39.8   0.0    6.8e-09   36.3   0.0    2.3  2  VWA_2     von Willebrand factor type A domain
    1.4e-09   38.4   0.0    9.9e-09   35.7   0.0    2.0  2  VWA       von Willebrand factor type A domain
    1.3e-07   31.2   2.1    1.3e-07   31.2   2.1    2.3  3  VWA_CoxE  VWA domain containing CoxE-like protein
    8.1e-06   25.9   0.0    2.2e-05   24.5   0.0    1.7  2  VWA_3     von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.16   12.6   0.5       0.41   11.2   0.1    1.9  2  ATP-cone  ATP cone domain


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.22   7.9e+02      25      70 ..     186     233 ..     166     245 .. 0.68
   2 !   36.3   0.0   1.9e-12   6.8e-09       2     107 .]     299     407 ..     298     407 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                          VWA_2  25 kdaveallkslpgdrvglvtfsdgpevlipl..tkdkakilnalrnle 70 
                                    ++ v++ll+ +     ++++f+++ e ++    ++d +++l+ +++++
  gi|118431306|ref|NP_147675.2| 186 AKNVKQLLSMMGAGDTSVLAFDENIEFILRIarETDVSRVLENVQGIR 233
                                    444555566666566778888888887777733477777777666665 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1.9e-12
                          VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallk.slp.gdrvglvtfsd..gpevlipltkdkakilnalrnleak..ggg 75 
                                     ++lD SgSm +      +++ a++ + al+  sl+ + r++   f++   p +++ + + ++++l+ ++ l a   ggg
  gi|118431306|ref|NP_147675.2| 299 YVLLDKSGSMVGA-----KIDWARAVAVALFRrSLAeNRRFSARFFDSvtYPAIHLRPRSKPRDFLELVKYLAAVkaGGG 373
                                    689*******998.....899999988888885778466*********7558999999999****9999999999999** PP

                          VWA_2  76 tnlaaaLqlarkalkkrr..kgekrvivlitDge 107
                                    t+++aa+++a + +++++  +++ + ivlitDge
  gi|118431306|ref|NP_147675.2| 374 TDITAAIKTAADDISRTPrgEQRISDIVLITDGE 407
                                    ************99988888899999******96 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.27   9.5e+02      81     117 ..     168     203 ..     161     234 .. 0.65
   2 !   35.7   0.0   2.8e-12   9.9e-09       2     142 ..     298     434 ..     298     445 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.27
                                    HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS CS
                            VWA  81 tgkalkyaleklfkssagaRenakkviilltdGksnd 117
                                    + +a+++ale++ k ++   +n+k+++ ++  G+++ 
  gi|118431306|ref|NP_147675.2| 168 LREAVEKALESVEKDARA-AKNVKQLLSMMGAGDTSV 203
                                    556777777777666666.336888887777776654 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 2.8e-12
                                    EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SGGGGSSC- CS
                            VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnl.kysgggttn 80 
                                    i+++lD Sgsm + +++ ++  +  l+++     e+ r++   f s +++ ++l+  s+  ++l+ ++ l  ++ gg t+
  gi|118431306|ref|NP_147675.2| 298 IYVLLDKSGSMVGAKIDWARAVAVALFRRSL--AENRRFSARFFDSVTYPAIHLRPRSKPRDFLELVKYLaAVKAGGGTD 375
                                    89***************99999999998888..79*********************9988*********99667777777 PP

                                    HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHHHHHHGCTEEEEEEEESSS CS
                            VWA  81 tgkalkyaleklfkssagaRenakkviilltdGksndgdpkeaaneakeqgikvfavGvgna 142
                                    + +a+k a++ + +  +g  e+  + i+l+tdG++   +++ + +++k+++ ++++v ++ +
  gi|118431306|ref|NP_147675.2| 376 ITAAIKTAADDISRTPRG--EQRISDIVLITDGEDRL-NIDVVEDSLKRSDARLHTVIIQGH 434
                                    ******************..777899*********77.999999999999999999987554 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.6       2.6   9.4e+03       4      26 ..     124     139 ..     116     145 .. 0.54
   2 ?   -1.1   0.2      0.29     1e+03      90     122 ..     200     232 ..     192     241 .. 0.84
   3 !   31.2   2.1   3.8e-11   1.3e-07      43     184 ..     267     430 ..     222     452 .. 0.67

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 2.6
                       VWA_CoxE   4 klaalllglarrrrrrkrrrrgr 26 
                                    +la+ll++l+r+        rgr
  gi|118431306|ref|NP_147675.2| 124 RLARLLSRLQRPQ-------RGR 139
                                    4555555555555.......222 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.29
                       VWA_CoxE  90 rtevfaFdtrlvdlTralrerDpaeaLarvsaa 122
                                    +t+v+aFd ++  + r  re D  ++L++v+ +
  gi|118431306|ref|NP_147675.2| 200 DTSVLAFDENIEFILRIARETDVSRVLENVQGI 232
                                    789999*99999999999999999999999855 PP

  == domain 3  score: 31.2 bits;  conditional E-value: 3.8e-11
                       VWA_CoxE  43 e..............lvelvrrkprerkprelvllvDvSgSmaaysaiflallhAllqqlp..rtevf..aFdtrlvdlT 104
                                    +                 l +rk  +++  ++ +l+D SgSm      +++ ++ +l +++  + + f   F ++++   
  gi|118431306|ref|NP_147675.2| 267 QlilpdeyfwasfssSKLLLYRKVLDSSRGPIYVLLDKSGSMVGAKIDWARAVAVALFRRSlaENRRFsaRFFDSVTYPA 346
                                    244555555555555555666666666677999*********99777777766655555554633333124667777777 PP

                       VWA_CoxE 105 ralrerDpaeaLarv.saaved.lgGgTrigaalaeflelvtrp..aLsrravvvlvsDglergdreellaelarlvrra 180
                                     +lr r+  + + ++ +  +    gGgT+i aa++++++ ++r+    +r + +vl++Dg++r +++ +++ l+r  +r 
  gi|118431306|ref|NP_147675.2| 347 IHLRPRSKPRDFLELvKYLAAVkAGGGTDITAAIKTAADDISRTprGEQRISDIVLITDGEDRLNIDVVEDSLKRSDARL 426
                                    788666554444444343333349*************9999875113356699******************999977776 PP

                       VWA_CoxE 181 rrlv 184
                                    + ++
  gi|118431306|ref|NP_147675.2| 427 HTVI 430
                                    6655 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   4.3e+03      81     106 ..     173     198 ..     164     216 .. 0.56
   2 !   24.5   0.0     6e-09   2.2e-05       4     131 ..     299     429 ..     296     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                          VWA_3  81 egaLkealrqpakpgevrsvilltDg 106
                                    e+aL+ + +  +  ++v++++ + + 
  gi|118431306|ref|NP_147675.2| 173 EKALESVEKDARAAKNVKQLLSMMGA 198
                                    33333333333444555555555544 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6e-09
                          VWA_3   4 vivvDvsssmsaen..klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslgasnle 81 
                                     +++D s sm + +   + + a  ++ r+L +n +++ + f++ + p +      ++++  e+ +++++ ++  g+++  
  gi|118431306|ref|NP_147675.2| 299 YVLLDKSGSMVGAKidWARAVAVALFRRSLAENRRFSARFFDSVTYPAIHLRPRSKPRDFLELVKYLAAVKA-GGGTDIT 377
                                    57899999999888755566677888899**************999***99999******************.******* PP

                          VWA_3  82 gaLkeal....rqpakpgevrsvilltDgssaqge.ervsdlisrarekirfhal 131
                                    +a+k+a+    r+p+  ++++ ++l+tDg  ++   + v+d+++r  +++r+h++
  gi|118431306|ref|NP_147675.2| 378 AAIKTAAddisRTPRGEQRISDIVLITDGE-DRLNiDVVEDSLKR--SDARLHTV 429
                                    ****99844445789999************.55551455555544..46666665 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012      0.41      12      41 ..     162     190 ..     161     224 .. 0.76
   2 ?   -2.9   0.0       2.9     1e+04      18      36 ..     376     400 ..     375     424 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                    E--HHHHHHHHHHHHHH-HHHHHHHHHHHH CS
                       ATP-cone  12 pfdvekIkraiekAcegseeeideiaeeve 41 
                                    +fd+ek+++a+ekA+e++e+++++  ++v 
  gi|118431306|ref|NP_147675.2| 162 EFDEEKLREAVEKALESVEKDARAA-KNVK 190
                                    7****************55554333.4443 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHH......-HHHHHHH CS
                       ATP-cone  18 IkraiekAceg......seeeidei 36 
                                    I++ai+ A+         e++i++i
  gi|118431306|ref|NP_147675.2| 376 ITAAIKTAADDisrtprGEQRISDI 400
                                    5666666655555522222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.23s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3257.96
//
Query:       gi|118431307|ref|NP_147676.2|  [L=379]
Description: hypothetical protein APE_1035.1 [Aeropyrum pernix K1]
Scores for complete 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   0.0    2.7e-27   95.5   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    9.4e-09   35.0   0.1    3.2e-08   33.3   0.0    1.9  2  AAA_lid_8        AAA lid domain
    1.9e-06   27.8   0.0    3.1e-06   27.1   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    3.5e-05   23.3   1.5    0.00046   19.6   0.0    3.0  4  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00011   22.6   0.0    0.00045   20.6   0.0    2.1  2  AAA              ATPase family associated with various cellul
     0.0024   18.1   0.0      0.015   15.6   0.0    2.4  2  AAA_22           AAA domain
     0.0027   18.1   0.2     0.0097   16.3   0.0    1.9  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.016   14.9   0.0       0.13   12.0   0.0    2.2  1  Sigma54_activat  Sigma-54 interaction domain
      0.016   14.3   0.0      0.033   13.3   0.0    1.6  1  MCM              MCM P-loop domain
      0.038   13.5   0.0      0.074   12.6   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.066   13.6   0.2        6.9    7.1   0.0    2.6  2  EF-hand_14       EF-hand domain
      0.095   12.4   0.0       0.22   11.2   0.0    1.7  1  AAA_30           AAA domain
       0.12   12.4   0.3       0.42   10.7   0.0    2.0  2  HTH_46           Winged helix-turn-helix DNA binding


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 !   95.5   0.0     2e-30   2.7e-27       1     138 []      40     167 ..      40     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 2e-30
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESGGG CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEver 76 
                                    +v+++G+pGt+Ks la+r a++ln++++ ++ltr+t++++l+g++++    +sl+++++ r  r    e+ei++lDEv++
  gi|118431307|ref|NP_147676.2|  40 HVVMIGEPGTAKSALARRAAELLNARFFKYLLTRFTEPSELFGPLDL----RSLREGKYIRITRgklpEAEIAFLDEVFN 115
                                    79********************************************9....9********9999**************** PP

                                    --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                          AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                    a+s+vln+Llsl+ er ++  +g  +++++       +++i+++n+++ ++ e  +al++Rf
  gi|118431307|ref|NP_147676.2| 116 ANSAVLNTLLSLMQERIVY--DGYSEIRVPI------WSIIGASNRVP-EEPE-LEALYDRF 167
                                    *******************..********99......***********.6666.8******9 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   2.3e-11   3.2e-08      16      71 ..     235     290 ..     223     291 .. 0.91
   2 ?   -2.2   0.0       2.9     4e+03       2      18 ..     301     317 ..     300     338 .. 0.63

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.3e-11
                      AAA_lid_8  16 eeeaiyvSDRRwkkivkllkasAylngrdevnlsDllllkhclWnepeqkekvkki 71 
                                    ee+++ v DRR  ki+k   a+A+lngr++ ++sDl++lk+++ ++pe+ +k++ i
  gi|118431307|ref|NP_147676.2| 235 EEKGLHVTDRRKGKILKAVAAHALLNGRSSAEESDLIVLKYTVPKDPEDFDKINII 290
                                    678899**********************************************9866 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                      AAA_lid_8   2 vlelileiknkleeeee 18 
                                    vl  + ei++++e+ + 
  gi|118431307|ref|NP_147676.2| 301 VLRELEEIRKNVENAQS 317
                                    66778889999866544 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 !   27.1   0.0   2.2e-09   3.1e-06       1     116 [.      40     157 ..      40     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.2e-09
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvf.anllladeinrappk 77 
                                    hv++ g PG+ak  l++  a+ l+++f +  +t    Ps++ G   +++ +  k +++++G +  a++ + de+  a++ 
  gi|118431307|ref|NP_147676.2|  40 HVVMIGEPGTAKSALARRAAELLNARFFKYLLTRFTEPSELFGPLDLRSLRegKYIRITRGKLPeAEIAFLDEVFNANSA 119
                                    9******************************************86555433347889****99537999*********** PP

                          AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqe 116
                                    +  +ll  m+er v  + +  ++p  + ++ + n + +e
  gi|118431307|ref|NP_147676.2| 120 VLNTLLSLMQERIVYDGYSEIRVP-IWSIIGASNRVPEE 157
                                    ***********9887666665555.46666666666555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.3e-07   0.00046       6      48 ..      22      64 ..      19      73 .. 0.90
   2 ?    0.4   0.0      0.26   3.6e+02     109     130 ..     107     128 ..      92     134 .. 0.81
   3 ?   -1.6   0.0         1   1.4e+03      98     130 ..     192     223 ..     167     230 .. 0.73
   4 ?   -2.2   0.2       1.7   2.3e+03     121     141 ..     303     323 ..     288     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                   Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                   +G++e+   l++a + g +++++G pG+ K+ la+r ++ll +
  gi|118431307|ref|NP_147676.2| 22 VGRHEQALMLTLALISGEHVVMIGEPGTAKSALARRAAELLNA 64
                                   6888999999***999999*******************99975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.26
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePl 130
                                    + fLDE+ + ++ vl++L + +
  gi|118431307|ref|NP_147676.2| 107 IAFLDEVFNANSAVLNTLLSLM 128
                                    78**************997655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1
                   Mg_chelatase  98 kpGeislahnGvLfLDElpefkrkvlevLRePl 130
                                    ++Ge   a + ++ + El e++++v+ v  +P+
  gi|118431307|ref|NP_147676.2| 192 EKGEYE-AAKPIMSMAELREINKHVMSVDVSPV 223
                                    555543.56779999999999999998766665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.7
                   Mg_chelatase 121 kvlevLRePledgevtisrak 141
                                    + le +R+ +e+ + +i+r +
  gi|118431307|ref|NP_147676.2| 303 RELEEIRKNVENAQSVITRMQ 323
                                    458899999999999999976 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 !   20.6   0.0   3.3e-07   0.00045       1     124 [.      41     167 ..      41     174 .. 0.73
   2 ?   -2.0   0.1       3.3   4.5e+03     111     111 ..     321     321 ..     283     364 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS........STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk........yvgesekkirelfkeakeka..kpsilfiDEidal 70 
                                    v+++G pGt K++la+  a+ l+++f++  ++++++         + + +e k   + +     +  +  i f+DE+ + 
  gi|118431307|ref|NP_147676.2|  41 VVMIGEPGTAKSALARRAAELLNARFFKYLLTRFTEPselfgpldLRSLREGKYIRITR---G-KlpEAEIAFLDEVFNA 116
                                    5789*******************************665666555533333333333332...2.134469*******998 PP

                                    HHHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESS.GGGSTHHHHSTTS CS
                            AAA  71 aksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnr.pdkldpallrgRf 124
                                    +++            +n+Ll+ +++   +            +iga+nr p++++ + l +Rf
  gi|118431307|ref|NP_147676.2| 117 NSAV-----------LNTLLSLMQERIVYdgyseirVPIWSIIGASNRvPEEPELEALYDRF 167
                                    7766...........********999988899988744467999999975555533332776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
                                    S CS
                            AAA 111 r 111
                                    r
  gi|118431307|ref|NP_147676.2| 321 R 321
                                    3 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   1.1e-05     0.015       6      61 ..      39      85 ..      36     133 .. 0.87
   2 ?   -1.2   0.0       1.6   2.3e+03      44      74 ..     274     300 ..     248     352 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrell 61
                                    ++v +Ge+Gt K+ l+rr +e l         +++++++ l+  t++++l+  l 
  gi|118431307|ref|NP_147676.2| 39 EHVVMIGEPGTAKSALARRAAELL---------NARFFKYLLTRFTEPSELFGPLD 85
                                   57899*******************.........9************9999998775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                         AAA_22  44 fvtlpsstsskdllrellralglelkaerls 74 
                                    ++t+p++   +d+  ++  +l +elk+  ++
  gi|118431307|ref|NP_147676.2| 274 KYTVPKDP--EDF-DKINIILMEELKT-KDR 300
                                    44444443..333.4455555544444.222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   7.1e-06    0.0097       1      60 [.      20      74 ..      20      91 .. 0.76
   2 ?   -2.6   0.0       4.5   6.2e+03     153     153 ..     331     331 ..     288     366 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.1e-06
                         AAA_16  1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkc 60
                                   ++vGR e+  +L+ al    sg  e v+ +Ge+G+ Ks+l+r++++ l+++ + +l +++
  gi|118431307|ref|NP_147676.2| 20 PFVGRHEQALMLTLAL---ISG--EHVVMIGEPGTAKSALARRAAELLNARFFKYLLTRF 74
                                   5899999976665544...455..89*******************888777233355555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.5
                         AAA_16 153 q 153
                                    +
  gi|118431307|ref|NP_147676.2| 331 D 331
                                    2 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.2e-05      0.13      21     145 ..      37     155 ..      24     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.2e-05
                                    SSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEE CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfLD 100
                                    +  +v++ Ge Gt K+ lar   e  + +  +++    ++ +e     +L   ++G +       +G++ +a+  + fLD
  gi|118431307|ref|NP_147676.2|  37 SGEHVVMIGEPGTAKSALARRAAELLNARFFKYLLTRFTEPSELFGPLDLRSLREGKYIRI---TRGKLPEAE--IAFLD 111
                                    45789999***********998887774444444444333333333344555555655433...348888776..78*** PP

                                    TGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-H CS
                Sigma54_activat 101 eigelplelQekLlrvlqegevervGsskeikvdvriiaatnedl 145
                                    e+ + + ++ + Ll ++qe+ v+  G s+ +     ii a+n+ +
  gi|118431307|ref|NP_147676.2| 112 EVFNANSAVLNTLLSLMQERIVYD-GYSEIRVPIWSIIGASNRVP 155
                                    *******************99876.44444444456666666655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.4e-05     0.033      54      85 ..      35      66 ..      21     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                                   BCSS-EEEEEESSTSTHHHHHHHHHHHSSSEE CS
                            MCM 54 lrgdinvllvgdpgtaKsqlLkyveklaprav 85
                                   l++  +v+++g+pgtaKs+l +++++l++   
  gi|118431307|ref|NP_147676.2| 35 LISGEHVVMIGEPGTAKSALARRAAELLNARF 66
                                   56677****************99998876654 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 ?   12.6   0.0   5.4e-05     0.074      23      69 ..      28      74 ..      20      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                          AAA_7 23 syllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                     +l+l l ++ +v+++G+ Gt+K++++++  + l+ + +++l   f
  gi|118431307|ref|NP_147676.2| 28 ALMLTLALISGEHVVMIGEPGTAKSALARRAAELLNARFFKYLLTRF 74
                                   56788889999******************999988877777666665 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.005       6.9      18      52 ..     226     260 ..     219     285 .. 0.84
   2 ?    3.9   0.1     0.049        67      33      53 ..     324     344 ..     298     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.005
                     EF-hand_14  18 svakllkaLaetGirkdDpRLkellkklkkvekek 52 
                                    s+ +l+  L+e+G++ +D R  ++lk++  +   +
  gi|118431307|ref|NP_147676.2| 226 SLIRLFVLLEEKGLHVTDRRKGKILKAVAAHALLN 260
                                    6889**********************998876655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.049
                     EF-hand_14  33 kdDpRLkellkklkkvekeks 53 
                                    + DpRL + ++ lk  +++ +
  gi|118431307|ref|NP_147676.2| 324 SFDPRLTDYFRSLKATRNRVA 344
                                    56***********99887754 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   0.00016      0.22       4      45 ..      25      65 ..      23     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                         AAA_30  4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaa 45
                                   +eQa +++ +l sg+  +v+ G +Gt K+ + + ++e+++a+
  gi|118431307|ref|NP_147676.2| 25 HEQALMLTLALISGE-HVVMIGEPGTAKSALARRAAELLNAR 65
                                   699999999999997.9999****************999876 PP

>> HTH_46  Winged helix-turn-helix DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.42      44      61 ..      86     103 ..      85     107 .. 0.90
   2 ?   -3.7   0.1       9.2   1.3e+04      39      49 ..     119     129 ..     117     132 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                         HTH_46  44 LseLkkggyIeierGkLv 61 
                                    L +L++g+yI+i rGkL 
  gi|118431307|ref|NP_147676.2|  86 LRSLREGKYIRITRGKLP 103
                                    679*************95 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.2
                         HTH_46  39 simkvLseLkk 49 
                                     ++++L +L +
  gi|118431307|ref|NP_147676.2| 119 AVLNTLLSLMQ 129
                                    45555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2409.66
//
Query:       gi|118431308|ref|NP_147677.2|  [L=136]
Description: cytidine deaminase [Aeropyrum pernix K1]
Scores for 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-14   51.5   0.0    8.6e-14   51.3   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    5.7e-10   39.5   0.3    5.7e-10   39.5   0.3    1.4  2  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
     0.0001   22.0   0.6      0.021   14.4   0.0    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 !   51.3   0.0   1.4e-17   8.6e-14       6      93 ..       8     101 ..       5     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.4e-17
                                    HHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE.....EE CS
                dCMP_cyt_deam_1   6 kllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv.....tl 79 
                                     l+  a++ a +a+ ++s+f+VGa++ +++ +++ g+n e+ ++  t++AE++A+ ka+++g+  + +  +y       +
  gi|118431308|ref|NP_147677.2|   8 DLVGAAVEQAGRAYaPYSRFRVGAAVRTSDGRVYGGCNVENSSYGLTVCAERTAVFKAVSEGSRGVVEVAVYAadsdePV 87 
                                    677789**********************99*******************************8667777777878*9999* PP

                                    --BHHHHHHHHHHT CS
                dCMP_cyt_deam_1  80 ePCsmCakaiiqsg 93 
                                     PC+ C +++ ++ 
  gi|118431308|ref|NP_147677.2|  88 PPCGACLQVLSEFA 101
                                    **********9984 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 !   39.5   0.3   9.6e-14   5.7e-10      45     109 ..       7      71 ..       1      88 [. 0.86
   2 ?   -3.3   0.1       1.6   9.6e+03       1       9 [.     121     129 ..     121     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 9.6e-14
                                    -HHHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHHTT-- CS
                dCMP_cyt_deam_2  45 delkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvlggke 109
                                    ++l+ aA+++a ++yapys+   G a+ t+dg+vy G  +E+  +  +  + ++A+ ++v +g +
  gi|118431308|ref|NP_147677.2|   7 EDLVGAAVEQAGRAYAPYSRFRVGAAVRTSDGRVYGGCNVENSSYGLTVCAERTAVFKAVSEGSR 71 
                                    46899*****************************************************9995543 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.6
                                    HHHHSTT-- CS
                dCMP_cyt_deam_2   1 LsslLPhsF 9  
                                    Ls+lLP +F
  gi|118431308|ref|NP_147677.2| 121 LSQLLPMAF 129
                                    789***999 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 !    6.3   0.1    0.0011       6.7      56      87 ..      36      67 ..      15      71 .. 0.86
   2 !   14.4   0.0   3.5e-06     0.021     148     177 ..      81     110 ..      68     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
                LmjF365940-deam 56 greelvrgvNlEvSmPtGSlCsErnaigkala 87
                                   +  +++ g N+E S      C+Er a+ ka++
  gi|118431308|ref|NP_147677.2| 36 SDGRVYGGCNVENSSYGLTVCAERTAVFKAVS 67
                                   4557999********************99875 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.5e-06
                LmjF365940-deam 148 arksnPLkPCGaCeewLkkiaevnpdfkvl 177
                                    a  + P+ PCGaC + L   a+  p + ++
  gi|118431308|ref|NP_147677.2|  81 ADSDEPVPPCGACLQVLSEFARGDPRVYMI 110
                                    45669****************999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1074.92
//
Query:       gi|118431309|ref|NP_147678.2|  [L=222]
Description: hypothetical protein APE_1040.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.34   10.7   2.1       0.43   10.3   0.1    2.3  3  DUF5353   Family of unknown function (DUF5353)
       0.99    7.6   9.9        1.3    7.2   9.9    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF5353  Family of unknown function (DUF5353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.51   4.6e+03      30      41 ..      25      36 ..      22      39 .. 0.78
   2 ?   -2.5   0.2       0.5   4.4e+03      17      21 ..     149     153 ..     136     174 .. 0.56
   3 ?   10.3   0.1   4.8e-05      0.43       5      32 ..     180     209 ..     176     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.51
                        DUF5353 30 arGeLtwkvvgl 41
                                   ++G  +w+vv+ 
  gi|118431309|ref|NP_147678.2| 25 EEGDSSWRVVAQ 36
                                   688899999975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.5
                        DUF5353  17 lsagL 21 
                                    l+a+L
  gi|118431309|ref|NP_147678.2| 149 LAALL 153
                                    23332 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 4.8e-05
                        DUF5353   5 pvvvgNavlvavlsagLGfg..AYrkyarG 32 
                                    pvv +  +l+a+ sa+LGf+  AY  y+r 
  gi|118431309|ref|NP_147678.2| 180 PVVDSYSILMALYSAVLGFAaaAYSSYTRR 209
                                    8999999************73369999886 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   9.9   0.00015       1.3      77     183 ..     109     215 ..      98     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00015
                        DUF2070  77 ltelivviisllaillsall..qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly..fspe 152
                                    ++ ++++ii+l+++++  +   qa ++ a v +lal+ +    +l a +++sl   +    + + ++++++++y  + ++
  gi|118431309|ref|NP_147678.2| 109 AARVLASIIFLASAAYIGVEgiQAPSTPAAVTTLALASFALAALLAASTHYSLYLLA----VSTGASLAIATAYrpVVDS 184
                                    566778888888888777778877777777777666666555555555555555333....3333333333333345799 PP

                        DUF2070 153 sfllllllslifalavylfivvvdrplkrnl 183
                                    +++l++l+s++++ a++++  +  r++ r l
  gi|118431309|ref|NP_147678.2| 185 YSILMALYSAVLGFAAAAYSSYTRRKFYRML 215
                                    999***********************99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1658.07
//
Query:       gi|14601151|ref|NP_147679.1|  [L=143]
Description: hypothetical protein APE_1041 [Aeropyrum pernix K1]
Scores for 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-22   78.5   2.0    7.5e-22   78.2   2.0    1.1  1  Sm_multidrug_ex  Putative small multi-drug export protein
    0.00099   19.6   6.7     0.0021   18.5   6.7    1.4  1  SNARE_assoc      SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> Sm_multidrug_ex  Putative small multi-drug export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   2.0   8.4e-26   7.5e-22       1     121 []       2     130 ..       2     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 8.4e-26
               Sm_multidrug_ex   1 Elrgaiplgillgldpllallvsvlgn.llpvplillf..lrklle.llkkkkl...lkklfekleekaekkseki.ekyg 73 
                                   E r+a+++g+ lgl +l++l++s +g  +l ++l+  +  +++l+e l+++k+l    + ++  l++ a +++ ++ e+yg
  gi|14601151|ref|NP_147679.1|   2 EPRYALLVGLGLGLGLLESLALSAAGVlVLGLLLYTAIdtVDRLMEaLCSRKRLgvnPGCIYLALRSSAARRAGGYvERYG 82 
                                   88*************************555555555668899999988888887867788999999998886666637*** PP

               Sm_multidrug_ex  74 flGLllFvaiPLpgTGawtGsliasllglkkkkallaillGvliaglI 121
                                   ++GL++F+aiPLp TG+++G+l+a+llg++  + l+++llG +++ +I
  gi|14601151|ref|NP_147679.1|  83 WAGLIVFIAIPLPATGMYSGALAAALLGIRGPRLLASLLLGGYLSLAI 130
                                   ******************************************999876 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   6.7   2.4e-07    0.0021       2     118 ..       3     135 ..       3     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-07
                   SNARE_assoc   2 PsevllvaaGvlfglllgtlvtslgallGaslayllgrylgr..............kalrrkllsekrvkalerlverygf 68 
                                   P ++llv +G+ +gll  + ++++g+l+ ++l y ++  + r                    +l + +++++  +veryg+
  gi|14601151|ref|NP_147679.1|   3 PRYALLVGLGLGLGLLESLALSAAGVLVLGLLLYTAIDTVDRlmealcsrkrlgvnPGCIYLALRSSAARRAGGYVERYGW 83 
                                   67889999999999999999999999999999***99999999999888888887744445567777888899******** PP

                   SNARE_assoc  69 lallllrllpivPrdlvn...yvaGltrvsfkrFflatfiGsipwalvyaylG 118
                                     l+++  +p  P + +    ++a+l++++  r ++  ++G  + + ++a++G
  gi|14601151|ref|NP_147679.1|  84 AGLIVFIAIPL-PATGMYsgaLAAALLGIRGPRLLASLLLGGYLSLAITAVVG 135
                                   **********6.565555599***************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1140.23
//
Query:       gi|118431310|ref|NP_147680.2|  [L=144]
Description: hypothetical protein APE_1042.1 [Aeropyrum pernix K1]
Scores for 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   17.3   0.7      0.016   15.6   0.3    2.0  2  DUF760        Protein of unknown function (DUF760)
  ------ inclusion threshold ------
      0.081   13.4   0.1        7.6    7.0   0.0    2.2  2  Phage_TAC_12  Phage tail assembly chaperone protein, TAC


Domain annotation for each model (and alignments):
>> DUF760  Protein of unknown function (DUF760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   1.7e-06     0.016      32      77 ..      41      84 ..      10      90 .. 0.76
   2 ?   -0.7   0.0      0.22   1.9e+03      18      36 ..     118     136 ..     101     142 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                         DUF760 32 hvsgllgslepslqfqtliqisrdklaqLlawsmllGYfLrgleqR 77
                                   ++++ll+ +  +++ +   ++ r ++++++   m++GY+L +++q 
  gi|118431310|ref|NP_147680.2| 41 TLDALLQLA--EMGDEIFNSLARPEVMKMIGNLMMMGYMLSQIDQP 84
                                   455555544..6888888899999******************9985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                         DUF760  18 sephspevleaikehvsgl 36 
                                    + ++spe+    k +++g+
  gi|118431310|ref|NP_147680.2| 118 KTMTSPEMAALLKALIAGV 136
                                    4567888888888777776 PP

>> Phage_TAC_12  Phage tail assembly chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0051        46      64     105 ..       3      44 ..       1      61 [. 0.86
   2 ?    7.0   0.0   0.00085       7.6      28      63 ..     103     138 ..      95     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0051
                   Phage_TAC_12  64 kkkrpsrdeieealekvdeekdleklfddvlkelkksnltkk 105
                                    +  ++++++i + le v+e++++ +   +++ +lkks+ +  
  gi|118431310|ref|NP_147680.2|   3 HGAQVGDEKILKLLELVEENYEALATTIELVAALKKSGTLDA 44 
                                    5679999*******9999999988888899999999987765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00085
                   Phage_TAC_12  28 kveginfgeGlsllvpgLesgdpevLvevlyaalsh 63 
                                    ++ + ++g+G++ l+  + s ++++L+++l a++s 
  gi|118431310|ref|NP_147680.2| 103 EAAATEKGMGIRELMKTMTSPEMAALLKALIAGVSC 138
                                    366889************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1116.35
//
Query:       gi|14602197|ref|NP_147681.1|  [L=381]
Description: dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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   83.7   0.0    1.3e-22   80.4   0.0    2.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.7e-06   27.1   0.0        0.8   10.3   0.0    3.6  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.3e-05   24.2   0.1     0.0075   15.9   0.4    2.2  2  DAO             FAD dependent oxidoreductase
    0.00011   22.4   0.3    0.00041   20.5   0.2    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00027   19.9   0.1    0.00046   19.2   0.1    1.3  1  Trp_halogenase  Tryptophan halogenase
    0.00053   20.0   0.1       0.14   12.1   0.1    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
    0.00079   18.2   0.0      0.067   11.9   0.1    2.3  2  HI0933_like     HI0933-like protein
     0.0096   15.0   0.0      0.015   14.4   0.0    1.3  1  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
       0.19   10.8   0.1       0.74    8.8   0.1    1.8  2  GIDA            Glucose inhibited division protein A


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 !   80.4   0.0   6.6e-26   1.3e-22       1     278 [.       2     284 ..       2     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 6.6e-26
                                   CSEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCTCEE CS
                                   xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgeevvk 77 
                                   k++vv+GgGp+Gl aa +la+    +a++tl+ +++  +++ ++l  +++g +e+++i++   +kl+++ i+++++ +v +
  gi|14602197|ref|NP_147681.1|   2 KKIVVLGGGPGGLVAAYNLARllrGKAEITLI-DKTGYHLFPPSLLWVMVGQREPEDIMRPL-SKLEKHgIKVVTA-SVES 79 
                                   589******************9877*******.888899999***9***********99954.4444444999999.**** PP

                                   EEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T..SEEEEES-SHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                   Pyr_redox_2  78 idpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp..krivvvGgGyiGvE 156
                                   idp++ kv        ++ +++yd+lv+  Gs+pr   ++++ ++v+    t++ a   ++kl       ++vG+      
  gi|14602197|ref|NP_147681.1|  80 IDPDNNKVAT------SGGEFEYDYLVVSLGSTPRPELMKAD-DTVCSP-WTVEGALDCRRKLAGfkSGRIIVGAWSWPYK 152
                                   *****99999......2447************9998888888.777766.999999999999999876679***9777666 PP

                                   HHHH....HHHHT-.............EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEE CS
                                   xxxx....xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 157 lAaa....laklgk.............evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvl 220
                                   +  a    +                  +vt+v+  +++++++++ +++a +  l   Gv +k g ++ e++g      +v 
  gi|14602197|ref|NP_147681.1| 153 CPPApfetA----FlvkylleqrggdaQVTVVHFWKKPMEPFGPTMAEAFQSFLDMYGVGFKGGVEPMEARGGR----LVA 225
                                   655543321....122344556666779**********************************999998888555....9** PP

                                   TTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BES.STTEEE-GGGC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxx RF
                   Pyr_redox_2 221 edgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtn.vpgiyaiGDva 278
                                   ++geei++dl v+a   +p ++ +e  lg e   +g++ vd++  r+    +++ +GD++
  gi|14602197|ref|NP_147681.1| 226 SSGEEIEYDLAVFAPPHEPPKPVAESPLGDES-LGGYMRVDKRTlRSPrYGNVFGVGDII 284
                                   ***********************987888887.89******98877766*********98 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0004       0.8       1      30 [.       3      35 ..       3      45 .. 0.82
   2 ?    4.7   0.0     0.022        44      48      73 ..      63      87 ..      48      92 .. 0.83
   3 !    7.5   0.0    0.0031       6.2      23      57 ..     175     209 ..     164     222 .. 0.83
   4 ?   -2.5   0.0       3.9   7.9e+03      11      36 ..     289     315 ..     288     325 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0004
                                  EEEEECSSHHHHHHHHHHHHTT...SEEEEEES CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelg...kkVtvver 30
                                  k+vv+GgG  gl +A +la+l    +++t+++ 
  gi|14602197|ref|NP_147681.1|  3 KIVVLGGGPGGLVAAYNLARLLrgkAEITLIDK 35
                                  79****************995435568899876 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                                  HHHHHTTEEEECSEEEEEEEEETTSE CS
                     Pyr_redox 48 eklekngievllntkveeiegsedgv 73
                                   klek+gi+v++ ++ve+i+ ++++v
  gi|14602197|ref|NP_147681.1| 63 SKLEKHGIKVVT-ASVESIDPDNNKV 87
                                  589*******99.5799999999983 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0031
                                   SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEE CS
                     Pyr_redox  23 kkVtvversdkllrllDeeaskilqeklekngiev 57 
                                   ++Vtvv+  +k++  +++++++++q  l   g+ +
  gi|14602197|ref|NP_147681.1| 175 AQVTVVHFWKKPMEPFGPTMAEAFQSFLDMYGVGF 209
                                   79**********************99888777766 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 3.9
                                   HHHHHHHHHHTTSEEEEEESSSSSS.T CS
                     Pyr_redox  11 glElAgalaelgkkVtvversdkll.r 36 
                                   gl +Ag++a+++++    + +d++l  
  gi|14602197|ref|NP_147681.1| 289 GLGMAGIFAHFQAEYVASQIADEILgT 315
                                   778899999988887777777777744 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   3.7e-06    0.0075       1      29 [.       3      36 ..       3      39 .. 0.88
   2 !    6.0   0.0    0.0039       7.7     154     203 ..      63     106 ..      49     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.7e-06
                                  EEEEECTSHHHHHHHHHHHH..TT...EEEEESS CS
                           DAO  1 dvviiGGGiiGlstAyeLar..rg...Vtllekg 29
                                  ++v+ GGG  Gl +Ay Lar  rg   +tl++k 
  gi|14602197|ref|NP_147681.1|  3 KIVVLGGGPGGLVAAYNLARllRGkaeITLIDKT 36
                                  59****************98445899******95 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0039
                                   HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                           DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                   +++e++G+++++   v++++ +++   +v  +t+ ge +++d++V++ G  
  gi|14602197|ref|NP_147681.1|  63 SKLEKHGIKVVTA-SVESIDPDNN---KV--ATSgGE-FEYDYLVVSLGST 106
                                   6889********9.*****66544...56..666455.578******9965 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 !   20.5   0.2   2.1e-07   0.00041       1      28 [.       6      36 ..       6      39 .. 0.87
   2 ?   -2.7   0.0       3.7   7.3e+03      39      56 ..     351     368 ..     347     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                                  EE--SHHHHHHHHHHHCC...TEEEEEE-SS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekr 28
                                  ++G+G +GlvaAy La+    +++++l++k 
  gi|14602197|ref|NP_147681.1|  6 VLGGGPGGLVAAYNLARLlrgKAEITLIDKT 36
                                  89***************5565669*****95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                                   CETTCEECTS---EEETT CS
                 NAD_binding_8  39 evpgvrvdygahifhgsg 56 
                                   e+p++++  g+++f++ +
  gi|14602197|ref|NP_147681.1| 351 EYPDCVILGGMRAFRPLK 368
                                   668888889999999875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.3e-07   0.00046       1      33 [.       3      35 ..       3      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-07
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                  kiv++GGG+ G +aA  la+ l+gk+e+tl+++
  gi|14602197|ref|NP_147681.1|  3 KIVVLGGGPGGLVAAYNLARLLRGKAEITLIDK 35
                                  79*****************************87 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1     7e-05      0.14       1      35 [.       5      37 ..       5      42 .. 0.92
   2 !    5.3   0.0    0.0092        18     114     155 ..      67     105 ..      56     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                 NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpse 35
                                  ++ G+Gp Gl ++ +L++    + + eitl+d+++
  gi|14602197|ref|NP_147681.1|  5 VVLGGGPGGLVAAYNLARLL--RGKAEITLIDKTG 37
                                  578****************9..**********975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0092
                 NAD_binding_9 114 gvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                   +  ++v++a+v++++++++++    ++g ++++d++v+ lG 
  gi|14602197|ref|NP_147681.1|  67 KHGIKVVTASVESIDPDNNKV---ATSGGEFEYDYLVVSLGS 105
                                   45799************9995...789***********9995 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   3.4e-05     0.067       2      32 ..       3      36 ..       2      40 .. 0.83
   2 !    4.1   0.0     0.008        16     117     170 ..      63     111 ..      51     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                  SEEEE--SHHHHHHHHHH...HHTT--EEEE-SS CS
                   HI0933_like  2 dviviGgGaAGlmaAisa...akrgkrVllleka 32
                                  +++v+GgG+ Gl aA ++    + +++++l++k+
  gi|14602197|ref|NP_147681.1|  3 KIVVLGGGPGGLVAAYNLarlLRGKAEITLIDKT 36
                                  79*************9994434678899999986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.008
                                   HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GGG CS
                   HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPkl 170
                                   ++l++ g+k+ +  +v+s++ ++    +v+t s++e+e d+lv+++G++  P+l
  gi|14602197|ref|NP_147681.1|  63 SKLEKHGIKVVT-ASVESIDPDN---NKVAT-SGGEFEYDYLVVSLGSTPRPEL 111
                                   678889999865.5799995544...45999.9**************9888865 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   7.7e-06     0.015       2      33 ..       4      38 ..       3      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-06
                                  EEEE--SHHHHHHHHHHHH..TTT.-EEEEESSSG CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaae..aGl.kvavvekeqe 33
                                  ++V G+G +GL+AA+++a+  +G+ ++++++k+++
  gi|14602197|ref|NP_147681.1|  4 IVVLGGGPGGLVAAYNLARllRGKaEITLIDKTGY 38
                                  79*****************999999******9987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00037      0.74       1      21 [.       3      23 ..       3      39 .. 0.88
   2 ?   -0.9   0.0      0.34   6.8e+02     107     150 ..      67     105 ..      59     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                                  CEEEE-SSHHHHHHHHHHHHT CS
                          GIDA  1 dviViGgGhAGceAAlaaarl 21
                                  +++V+GgG  G+ AA+++arl
  gi|14602197|ref|NP_147681.1|  3 KIVVLGGGPGGLVAAYNLARL 23
                                  689****************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                                   TSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                          GIDA 107 nepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                   + + +++++++ve+++++++kv+    ++g +++ +  v++ G+
  gi|14602197|ref|NP_147681.1|  67 K-HGIKVVTASVESIDPDNNKVA----TSGGEFEYDYLVVSLGS 105
                                   4.6799*********99888875....45555666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2730.69
//
Query:       gi|14601153|ref|NP_147682.1|  [L=249]
Description: NADH dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-22   80.7   1.9    1.8e-21   76.9   1.9    2.1  1  Nitroreductase  Nitroreductase family
      7e-05   22.5   0.0       0.15   11.6   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 !   76.9   1.9     2e-25   1.8e-21       3     170 .]      19     171 ..      17     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2e-25
                                   H--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGG...HHH CS
                Nitroreductase   3 kRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrke...elk 80 
                                   + rSiRk+ ++p+p+e+++ +leaarraP+   l+ w  v v d+ +r+++a+a+ ++  ++ a +++++  + +   +l 
  gi|14601153|ref|NP_147682.1|  19 RHRSIRKYVKKPLPEEHVSLLLEAARRAPTDATLHLWSAVRVVDDGVRRRIADAIGQEHVYE-AGEFFIFLADFYrlkRLL 98 
                                   57**************************************999999*********9998887.555566665533344555 PP

                                   HHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SE CS
                Nitroreductase  81 lkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeee 161
                                   +++ + l++ +  +++                 +a++dag+aa+n+ ++A+alG+g+c+igg+ +aae + +ll lp++  
  gi|14601153|ref|NP_147682.1|  99 EYRGEELGRVDRALLV-----------------FAAIDAGLAAENMAVMAEALGYGTCFIGGVQNAAELIIELLALPEKTY 162
                                   5555555555555555.................********************************************9999 PP

                                   EEEEEEEE- CS
                Nitroreductase 162 ivvliavGy 170
                                   ++  +++Gy
  gi|14601153|ref|NP_147682.1| 163 PLFGLTIGY 171
                                   999999998 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00011      0.98       5      43 ..      16      54 ..      12      72 .. 0.83
   2 !   11.6   0.0   1.6e-05      0.15      83     137 ..     119     176 ..     115     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00011
                                  HHHH--B---B--S---HHHHHHHHH-----S...S--- CS
                TM1586_NiRdase  5 aiekRhsvRkYkdealeeelleelkeaieeinkesglel 43
                                       +s+RkY +++l+ee ++ l ea+++  ++++l+l
  gi|14601153|ref|NP_147682.1| 16 VFARHRSIRKYVKKPLPEEHVSLLLEAARRAPTDATLHL 54
                                  444446*********************999988887776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHHHHHTT-EEEEES--SST..............T-S-EEEEE-BS--- CS
                TM1586_NiRdase  83 kaGYygeqlvLkltalGlgtcWvggtykkkkakvel...kkgeklvivIalGyaktkl 137
                                    aG   e++   + alG gtc++gg ++  +  +el   +++   +  +++Gy++++ 
  gi|14601153|ref|NP_147682.1| 119 DAGLAAENMAVMAEALGYGTCFIGGVQNAAELIIELlalPEKTYPLFGLTIGYPAEDP 176
                                   68999********************999977655541113344444556777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1931.85
//
Query:       gi|118431311|ref|NP_147683.2|  [L=319]
Description: zinc metalloprotease HtpX [Aeropyrum pernix K1]
Scores for 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-37  126.6   0.0    1.8e-36  125.8   0.0    1.4  1  Peptidase_M48   Peptidase family M48
  ------ inclusion threshold ------
      0.011   14.9   0.1      0.026   13.7   0.0    1.6  2  Peptidase_M56   BlaR1 peptidase M56
        1.1    7.5   3.6       0.59    8.3   0.1    1.9  2  DUF2070         Predicted membrane protein (DUF2070)
          3    7.2   7.9      0.075   12.4   1.2    1.7  2  Zn_peptidase_2  Putative neutral zinc metallopeptidase


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 !  125.8   0.0     4e-40   1.8e-36       4     194 ..      70     308 ..      68     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 125.8 bits;  conditional E-value: 4e-40
                                    SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsvv 82 
                                    e+++ ++ve+la+++gl  +++kv+v +++  NAFa+g      ++++t+gLl +ll ++e++aVl+HE+GH+khr+++v
  gi|118431311|ref|NP_147683.2|  70 EEWIVAEVEQLARRSGL--KPPKVVVSEMNMPNAFAYGSPIAGsYVAVTRGLL-RLLPKDEVRAVLAHEVGHLKHRDVTV 146
                                    68999************..7777777777777*******99999*********.************************** PP

                                    HHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT.........HHHHHHHHHHHHHHHHTTT.HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  83 slivsllasillllglallisraeedaagafldalavliglliillfl.........alSRkrEyqADeagvellkrakd 153
                                     l  sl++  ++l+g++l+ +   +   g   ++ + l+++  +ll +          + R rEy+AD++++ ++  ++ 
  gi|118431311|ref|NP_147683.2| 147 ILALSLIPIAAFLIGRTLVWAGILGGGGGERRGNPMALVAVGAALLAAgmvfqlivsHFNRLREYYADAHSALVTGSPRS 226
                                    **************9998765433322222222222222222222222223334688*********************** PP

                                    HHHHHHHHHHHTT--S---HHHH.........................................HHS-SS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.........................................xxxxxxxxxxxxxxxx RF
                  Peptidase_M48 154 lvraliklakdlerqdvsaslrs.........................................ellstHPplleRiqal 192
                                    l+ral+++++ +e ++   ++ +                                         el+stHPp ++R++ l
  gi|118431311|ref|NP_147683.2| 227 LQRALARIHAAYEHNPHLVEEARsnemasmlfivapltsltasplvdvdylverlkeqetnplvELFSTHPPVSKRLRFL 306
                                    **************876655555578889999999999999999999999999999999999*****************9 PP

                                    HH CS
                                    xx RF
                  Peptidase_M48 193 ke 194
                                    ++
  gi|118431311|ref|NP_147683.2| 307 DR 308
                                    87 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.9e-06     0.026     104     216 ..      37     148 ..      26     158 .. 0.67
   2 ?   -2.6   0.0      0.55   2.5e+03     107     138 ..     183     212 ..     182     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-06
                  Peptidase_M56 104 illliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrnikirlsssidsPavlgllkp.... 179
                                    +l+l+ ++++l+     +++  +++  +  ++    +e ++ ++++  ++ +l +++k+++s +++ P  +++  p    
  gi|118431311|ref|NP_147683.2|  37 MLSLLALAMVLV---QWLFSPYIINMVYRTREPLPGEEWIVAEVEQLARRSGL-KPPKVVVS-EMNMPNAFAYGSPiags 111
                                    555555555555...44444444443333444444555677888888888884.45555544.56888888887763333 PP

                  Peptidase_M56 180 rIvlPadflkklsdeeleyillHElaHlkrkDllvnl 216
                                    ++ +   +l+ l ++e   +l+HE  Hlk++D+ v l
  gi|118431311|ref|NP_147683.2| 112 YVAVTRGLLRLLPKDEVRAVLAHEVGHLKHRDVTVIL 148
                                    5889999999999*******************97654 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.55
                  Peptidase_M56 107 liWivgalilllyliaallvlkkrfvrklgkl 138
                                    ++++vga++l++ +++ l v +  f r ++ +
  gi|118431311|ref|NP_147683.2| 183 ALVAVGAALLAAGMVFQLIVSH--FNRLREYY 212
                                    6788899998888888888766..44444333 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.0     0.072   3.2e+02      41      91 ..       5      55 ..       2      69 .. 0.61
   2 ?    8.3   0.1   0.00013      0.59      15     114 ..     143     259 ..     133     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.072
                        DUF2070 41 illfglpalvaflltlpvlrilggrltykrslflalltelivviisllail 91
                                   +l+++  ++v + +  ++l+ + g   +  +++l+ll++ +v++  l++  
  gi|118431311|ref|NP_147683.2|  5 VLALIGGYIVVLGVAAWALDAFTGLSGTGVAFMLSLLALAMVLVQWLFSPY 55
                                   455555566666666666666666666666666666666666665544443 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00013
                        DUF2070  15 kvsllliillalligllaflssk...............lfgillfglpalvaflltlpvlrilggrltykrslflallte 79 
                                     v+++l++ l+ ++++l  +                   ++++++g  +l+a+++++ +++ +++  +y   ++ al+t 
  gi|118431311|ref|NP_147683.2| 143 DVTVILALSLIPIAAFLIGRTLVwagilgggggerrgnPMALVAVGAALLAAGMVFQLIVSHFNRLREYYADAHSALVTG 222
                                    4677777778888777777777799**************************************999999999*****999 PP

                        DUF2070  80 livviisllaillsall..qalvllalvlslalvfal 114
                                     + ++   la + +a+   + lv  a    +a+++++
  gi|118431311|ref|NP_147683.2| 223 SPRSLQRALARIHAAYEhnPHLVEEARSNEMASMLFI 259
                                    9888888877777766666555555555555555555 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 ?   -3.6   0.8       1.3   5.9e+03     146     152 ..      34      40 ..       6      59 .. 0.52
   2 ?   12.4   1.2   1.7e-05     0.075      89     158 ..     130     201 ..     127     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                 Zn_peptidase_2 146 iilfala 152
                                    +++++  
  gi|118431311|ref|NP_147683.2|  34 VAFMLSL 40 
                                    3222222 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.7e-05
                 Zn_peptidase_2  89 avAAHevGhaiqhaegyaplklrsalvpvvnigsklslillliglllslss...lllligiilfalavlfqlv 158
                                    av AHevGh ++h++   +l l    + +  ig +l+++ +l g   +       l+ +g +l+a+ ++fql+
  gi|118431311|ref|NP_147683.2| 130 AVLAHEVGH-LKHRDVTVILALSLIPIAAFLIGRTLVWAGILGGGGGERRGnpmALVAVGAALLAAGMVFQLI 201
                                    899******.578888888888777777777888999999988877755557856*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.36
# Mc/sec: 2623.95
//
Query:       gi|118431312|ref|NP_147685.2|  [L=284]
Description: translation initiation factor eIF-2B subunit [Aeropyrum pernix K1]
Scores for complete 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   83.7   0.0      3e-23   82.4   0.0    1.6  1  IF-2B     Initiation factor 2 subunit family
     0.0005   20.0   1.4    0.00086   19.3   1.4    1.4  1  T2SSF     Type II secretion system (T2SS), protein F
     0.0026   17.7   0.3     0.0045   16.9   0.3    1.3  1  YjeF_N    YjeF-related protein N-terminus


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 !   82.4   0.0   5.1e-27     3e-23      76     226 ..      74     219 ..      19     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.4 bits;  conditional E-value: 5.1e-27
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHH CS
                          IF-2B  76 kksliekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLv 155
                                      +l e++++l++ +eea +  ++ aae+++   ++ T++ s++v  ++ aa+       V+v+EsrP  +G  +a  L+
  gi|118431312|ref|NP_147685.2|  74 PGELAEALRRLMDYVEEAGREAAERAAEFLSGAGAVSTVSFSRAVQLTILAARPRV----VYVLESRPGGEGVAMARHLR 149
                                    445999*********************************************99966....******************** PP

                                    HTTXEEEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTS CS
                          IF-2B 156 qagipvtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfserv 226
                                    q g++  +++dsa++   s+  ++v+ GAd+   +G++ nk GT+ lA +A +  ++  +v es+k++ r+
  gi|118431312|ref|NP_147685.2| 150 QSGVNAVVLPDSAAGLAVSR-SNAVVFGADAAGLDGCLRNKLGTLPLAASAAALGVEAVAVFESYKIVSRA 219
                                    ********************.9*********************************************9985 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 !   19.3   1.4   1.4e-07   0.00086      14     110 ..       4     110 ..       3     123 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-07
                                    -HHHHHHHHHHHHS...SHHHHHHHHHHHHHHHTTSSHH.....HHHC.T-TT..TS-HHHHHHHHHHHHHT-HHHHHHH CS
                          T2SSF  14 plveaLellaeeae...ngplaeelkriarrlraGgsls.....eale.rtps.sefpelvvqlirageeggnLaevLer 83 
                                    +l+ea++ +++e     + +++   + ++++l++G +l+     ++l+   p    +  l+  + r+  + g Lae+L+r
  gi|118431312|ref|NP_147685.2|   4 GLEEAVREVSRERIrgaSWAISTLARGLLEDLESGRTLDcdrasQVLRtTLPGmGSLEVLAEVVERLCNRPGELAEALRR 83 
                                    58999999999999999999****************98444333666664444445699999999999************ PP

                                    HHHHHHHHHHHHHHHHHHHHTTXXXXX CS
                          T2SSF  84 laeyleeerelrrkllaallepllllv 110
                                    l +y+ee  + +++++a++l+ +  + 
  gi|118431312|ref|NP_147685.2|  84 LMDYVEEAGREAAERAAEFLSGAGAVS 110
                                    *******************99876665 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   7.5e-07    0.0045       6      58 ..      89     157 ..      84     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.5e-07
                         YjeF_N   6 enagravaevlrallg................nspaekkvlvlvGsgnnGgdglaaArhLaqegakVtv 58 
                                    e agr++ae + + l                 +  a++  +v v + + Gg g+a+ArhL+q g+++ v
  gi|118431312|ref|NP_147685.2|  89 EEAGREAAERAAEFLSgagavstvsfsravqlTILAARPRVVYVLESRPGGEGVAMARHLRQSGVNAVV 157
                                    778888888777777778888888888888886666666677777889******************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2424.21
//
Query:       gi|118431313|ref|NP_147686.2|  [L=490]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-30  106.9   2.2    1.5e-30  106.5   0.0    2.0  2  Peripla_BP_2     Periplasmic binding protein
    3.6e-06   27.0   2.5     0.0061   16.6   0.1    2.4  2  DUF1664          Protein of unknown function (DUF1664)
    1.1e-05   25.5   9.6    4.4e-05   23.5   6.2    2.6  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    1.2e-05   25.7   3.3       0.06   13.8   0.8    3.3  3  NPV_P10          Nucleopolyhedrovirus P10 protein
    1.6e-05   24.4   2.1      0.073   12.4   1.0    2.1  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
    1.6e-05   25.0   0.2       0.16   12.2   0.0    3.0  2  DUF948           Bacterial protein of unknown function (DUF94
    1.8e-05   24.2   6.2    2.9e-05   23.6   6.2    1.2  1  Tropomyosin      Tropomyosin
    2.1e-05   24.6   4.5        0.1   12.6   0.1    2.2  2  Laminin_II       Laminin Domain II
    2.3e-05   24.4   3.3    0.00082   19.4   0.3    3.2  3  DUF2730          Protein of unknown function (DUF2730)
    2.8e-05   24.3   0.9      0.017   15.4   0.0    2.6  2  KxDL             Uncharacterized conserved protein
    2.9e-05   23.1   8.7    5.9e-05   22.1   8.4    1.5  1  Spc7             Spc7 kinetochore protein
    4.3e-05   23.7  17.3     0.0026   17.9   7.5    4.0  3  ABC_tran_CTD     ABC transporter C-terminal domain
    8.5e-05   22.7   8.2    0.00027   21.1   8.1    1.8  1  Tropomyosin_1    Tropomyosin like
    9.3e-05   20.8   5.0     0.0074   14.5   0.9    1.8  1  EzrA             Septation ring formation regulator, EzrA
    9.9e-05   22.0   0.7    0.00016   21.4   0.7    1.2  1  DUF4795          Domain of unknown function (DUF4795)
    0.00012   22.5   3.9       0.17   12.4   0.8    2.3  2  DUF16            Protein of unknown function DUF16
    0.00019   21.8   4.2       0.37   11.2   0.0    2.5  2  Snapin_Pallidin  Snapin/Pallidin
     0.0002   19.7   5.8    0.00026   19.4   5.8    1.0  1  FPP              Filament-like plant protein, long coiled-coi
    0.00022   21.6  10.0    0.00043   20.7  10.0    1.4  1  HrpB7            Bacterial type III secretion protein (HrpB7)
    0.00027   21.3  13.1     0.0038   17.5  13.1    2.0  1  ATG16            Autophagy protein 16 (ATG16)
    0.00032   20.8   3.2      0.027   14.5   1.2    2.5  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    0.00036   19.7   1.6     0.0012   17.9   1.6    1.6  1  TelA             Toxic anion resistance protein (TelA)
    0.00039   20.6   7.5       0.14   12.5   1.7    3.1  3  BLOC1_2          Biogenesis of lysosome-related organelles co
    0.00065   19.1   8.4        0.2   10.9   8.4    2.1  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
    0.00068   20.0   9.6        1.1    9.7   0.2    5.0  4  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00086   19.4   7.1      0.015   15.4   7.1    2.1  1  Nup54            Nucleoporin complex subunit 54
    0.00091   19.8  10.2     0.0019   18.8  10.2    1.5  1  APG6_N           Apg6 coiled-coil region
    0.00094   19.5  10.3       0.61   10.5   0.8    4.3  4  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0011   17.7   0.8     0.0015   17.2   0.8    1.2  1  Zw10             Centromere/kinetochore Zw10
     0.0013   17.4   1.3       0.81    8.2   0.0    2.2  2  FapA             Flagellar Assembly Protein A
     0.0015   17.6   2.9     0.0043   16.1   2.9    1.6  1  IFT57            Intra-flagellar transport protein 57
     0.0018   18.4   2.8       0.49   10.6   0.7    3.4  3  XhlA             Haemolysin XhlA
     0.0019   17.8   0.4       0.95    8.9   0.0    2.1  2  Allexi_40kDa     Allexivirus 40kDa protein
      0.002   17.4   8.3      0.044   13.0   0.3    2.1  2  HAP1_N           HAP1 N-terminal conserved region
      0.002   17.5   3.9     0.0063   15.9   3.9    1.7  1  GAS              Growth-arrest specific micro-tubule binding
     0.0021   17.3   0.1     0.0039   16.4   0.0    1.4  1  Taxilin          Myosin-like coiled-coil protein
     0.0022   17.8   5.0        3.6    7.4   0.1    3.2  2  SKA2             Spindle and kinetochore-associated protein 2
     0.0025   16.5   4.1     0.0035   16.0   4.1    1.1  1  CCDC154          Coiled-coil domain-containing protein 154
     0.0025   17.0   1.7     0.0088   15.2   1.7    1.8  1  FH2              Formin Homology 2 Domain
      0.003   16.3   1.1     0.0043   15.8   1.1    1.1  1  AAA_13           AAA domain
     0.0032   17.0  16.2      0.064   12.8  16.4    2.0  1  MscS_porin       Mechanosensitive ion channel porin domain
     0.0033   16.8   5.4     0.0065   15.8   5.4    1.4  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
     0.0037   15.2   6.2      0.005   14.7   6.2    1.1  1  Myosin_tail_1    Myosin tail
     0.0038   16.4   3.1       0.12   11.5   0.1    2.2  2  RmuC             RmuC family
     0.0039   16.8   1.2     0.0062   16.1   1.2    1.2  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0041   16.6   3.1     0.0059   16.1   3.1    1.1  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0055   15.8   5.7        0.2   10.7   5.9    2.0  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0057   16.3   9.0      0.022   14.4   9.0    1.8  1  Filament         Intermediate filament protein
     0.0058   17.0   8.5      0.069   13.6   3.6    2.4  2  ZapB             Cell division protein ZapB
     0.0076   16.5   3.4      0.069   13.4   3.8    2.0  1  DUF5082          Domain of unknown function (DUF5082)
     0.0081   14.8   1.9      0.012   14.2   1.9    1.1  1  FUSC             Fusaric acid resistance protein family
     0.0084   16.2  12.5       0.17   11.9   0.8    2.3  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
     0.0089   15.9   6.7      0.014   15.2   6.7    1.2  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0099   15.5   1.1      0.019   14.6   1.1    1.4  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
  ------ inclusion threshold ------
      0.011   16.2   5.8      0.031   14.7   5.8    1.8  1  TBCC_N           Tubulin-specific chaperone C N-terminal doma
      0.011   15.4   4.7      0.029   14.0   1.8    2.3  2  TMP_2            Prophage tail length tape measure protein
      0.012   15.8   0.9      0.025   14.7   0.9    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.013   13.1   6.4      0.017   12.7   6.4    1.1  1  DUF3584          Protein of unknown function (DUF3584)
      0.015   15.5   8.4       0.53   10.5   5.6    2.4  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.016   15.2  10.0        2.4    8.3   0.2    2.3  2  DHR10            Designed helical repeat protein 10 domain
      0.016   14.4   1.4      0.086   12.1   0.7    1.7  2  TMPIT            TMPIT-like protein
      0.019   14.1   3.6      0.029   13.5   3.6    1.2  1  CCDC144C         CCDC144C protein coiled-coil region
       0.02   14.6   7.6      0.033   13.9   7.6    1.2  1  Laminin_I        Laminin Domain I
      0.022   14.8   5.0       0.86    9.7   1.9    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
      0.026   14.9  11.6       0.13   12.6  11.6    2.0  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
      0.028   14.4   7.4       0.27   11.2   4.4    2.8  3  FlxA             FlxA-like protein
      0.029   14.6  10.7       0.16   12.2   4.4    2.3  2  FliJ             Flagellar FliJ protein
      0.029   14.2  10.6      0.075   12.9   0.8    4.0  3  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
      0.029   14.4   4.3      0.029   14.4   1.6    2.2  1  Phasin           Poly(hydroxyalcanoate) granule associated pr
       0.03   13.6   9.6       0.15   11.4   6.9    2.0  2  Dynamitin        Dynamitin
      0.031   13.6   8.0        0.1   11.9   8.0    1.6  1  DUF4763          Domain of unknown function (DUF4763)
      0.031   14.4   2.1       0.21   11.8   2.1    2.1  1  SesA             N-terminal domain on NACHT_NTPase and P-loop
      0.032   14.5   6.4        1.5    9.1   0.2    2.7  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.036   14.3   6.4        5.4    7.3   0.4    3.4  3  JIP_LZII         JNK-interacting protein  leucine zipper II
      0.036   14.2   1.7        1.2    9.3   0.1    2.2  2  BLOC1S3          Biogenesis of lysosome-related organelles co
      0.036   12.3   1.9      0.048   11.9   1.9    1.1  1  Cast             RIM-binding protein of the cytomatrix active
      0.036   14.4   3.2      0.065   13.6   0.9    2.2  1  TBCA             Tubulin binding cofactor A
      0.039   13.4   5.3      0.065   12.6   5.3    1.4  1  HBM              Helical bimodular sensor domain
      0.039   14.1   9.2        5.8    7.1   1.1    3.6  3  HR1              Hr1 repeat
       0.04   14.5   7.3       0.36   11.4   4.1    3.0  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.041   14.6   0.7       0.58   10.9   0.2    2.4  2  Occludin_ELL     Occludin homology domain
      0.042   14.4   4.3       0.39   11.3   4.4    2.1  1  DUF2408          Protein of unknown function (DUF2408)
      0.042   13.9   7.3       0.17   12.0   1.4    2.2  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.043   13.6   1.3       0.23   11.3   0.7    2.0  2  Phage_GP20       Phage minor structural protein GP20
      0.043   12.7   0.2      0.066   12.1   0.2    1.3  1  DUF677           Protein of unknown function (DUF677)
      0.044   13.9   0.7       0.12   12.5   0.7    1.8  1  DUF4363          Domain of unknown function (DUF4363)
      0.044   12.9   7.0       0.28   10.3   7.1    2.0  1  Tmemb_cc2        Predicted transmembrane and coiled-coil 2 pr
      0.047   13.4   1.9       0.43   10.3   0.6    2.2  2  DUF4201          Domain of unknown function (DUF4201)
      0.048   12.0   5.4      0.065   11.6   5.4    1.1  1  MAD              Mitotic checkpoint protein
      0.048   14.1   6.3        2.5    8.6   6.3    2.6  1  Spectrin         Spectrin repeat
       0.05   13.3   5.5        1.5    8.5   0.1    2.1  2  DUF745           Protein of unknown function (DUF745)
       0.05   13.7  15.1       0.48   10.5   8.1    3.3  3  TolA_bind_tri    TolA binding protein trimerisation
      0.051   13.9   3.6       0.06   13.7   1.5    1.9  1  Muted            Organelle biogenesis, Muted-like protein
      0.051   13.5   8.8         28    4.7   0.3    3.9  2  Prefoldin_2      Prefoldin subunit
      0.052   12.9  10.8       0.17   11.2   5.2    2.1  2  DUF3450          Protein of unknown function (DUF3450)
      0.052   14.2   7.7        3.5    8.3   3.0    2.4  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
      0.056   11.6   3.2       0.15   10.2   2.0    2.0  2  COG6             Conserved oligomeric complex COG6
      0.059   13.6  11.3       0.96    9.7   1.6    3.5  3  Spc24            Spc24 subunit of Ndc80
      0.059   13.0   2.1        6.2    6.5   0.2    3.6  3  DUF4988          Domain of unknown function
      0.062   13.2   1.7       0.12   12.3   1.2    1.7  2  Sec8_exocyst     Sec8 exocyst complex component specific doma
      0.062   12.2   6.4       0.39    9.5   1.4    2.0  2  DUF812           Protein of unknown function (DUF812)
      0.064   12.8  12.3        2.4    7.7   9.5    2.3  2  PspA_IM30        PspA/IM30 family
      0.065   13.1   4.0          5    7.0   0.1    2.3  2  Sec34            Sec34-like family
      0.068   13.2   0.3        3.1    7.8   0.0    2.3  2  DUF4446          Protein of unknown function (DUF4446)
      0.068   13.5  11.0        4.2    7.8   0.6    4.2  4  Csm1_N           Csm1 N-terminal domain
      0.075   13.7   3.7       0.59   10.8   0.7    2.5  2  YabA             Initiation control protein YabA
      0.078   11.1   7.9       0.16   10.0   7.9    1.4  1  HOOK             HOOK protein
      0.094   12.2  17.2       0.09   12.2   6.6    3.5  3  DUF4349          Domain of unknown function (DUF4349)
       0.11   12.7   2.4       0.41   10.8   1.7    1.8  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.11   12.3   1.6        5.9    6.7   0.4    2.2  2  SPAM             Salmonella surface presentation of antigen g
       0.11   11.8   5.4       0.68    9.2   6.5    1.6  2  DUF4407          Domain of unknown function (DUF4407)
       0.12   12.7   1.8         79    3.6   1.2    3.2  3  V-SNARE_C        Snare region anchored in the vesicle membran
       0.12   12.6  13.5       0.37   11.1   6.7    2.6  2  DUF4164          Domain of unknown function (DUF4164)
       0.12   12.0   0.0         10    5.8   0.0    2.3  2  DUF2576          Protein of unknown function (DUF2576)
       0.12   12.0   0.1       0.18   11.5   0.1    1.2  1  LUC7             LUC7 N_terminus
       0.13   12.7  13.4       0.33   11.3   2.8    3.5  2  DASH_Hsk3        DASH complex subunit Hsk3 like
       0.14   11.1   0.0       0.21   10.5   0.0    1.2  1  LMBR1            LMBR1-like membrane protein
       0.14   12.4   6.7        5.2    7.3   0.3    2.1  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.14   10.9   5.6        0.2   10.4   5.6    1.2  1  Tektin           Tektin family
       0.14   12.1   3.5       0.18   11.8   1.6    1.8  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
       0.14   12.6   6.9       0.36   11.3   6.9    1.6  1  Fez1             Fez1
       0.15   11.5   5.2       0.35   10.3   5.2    1.6  1  DUF2884          Protein of unknown function (DUF2884)
       0.15   11.0   1.7       0.24   10.3   1.7    1.3  1  Vps53_N          Vps53-like, N-terminal
       0.16   11.5   4.2        1.3    8.5   0.6    2.1  2  CENP-K           Centromere-associated protein K
       0.17   11.6   0.5       0.26   11.0   0.5    1.3  1  CR6_interact     Growth arrest and DNA-damage-inducible prote
       0.17   11.7   0.0       0.31   10.8   0.0    1.4  1  Spc29            Spindle Pole Component 29
       0.18   11.3   0.3       0.48    9.8   0.3    1.6  1  DUF3829          Protein of unknown function (DUF3829)
       0.18   11.6   0.4        2.5    8.0   0.0    2.8  2  DASH_Duo1        DASH complex subunit Duo1
       0.19   12.1   8.1       0.13   12.6   1.6    3.1  3  CCDC-167         Coiled-coil domain-containing protein 167
       0.19   11.8   0.1        0.4   10.8   0.1    1.6  1  Col_cuticle_N    Nematode cuticle collagen N-terminal domain
       0.19   11.3   1.1       0.35   10.5   1.1    1.3  1  Miff             Mitochondrial and peroxisomal fission factor
        0.2   11.8   1.7         17    5.5   0.1    2.7  3  DUF148           Domain of unknown function DUF148
        0.2    9.6   0.1        0.3    9.0   0.1    1.2  1  Prominin         Prominin
       0.21   11.3   0.4         23    4.7   0.0    2.5  2  DUF4525          Domain of unknown function (DUF4525)
       0.22   11.4   1.6       0.37   10.7   1.6    1.3  1  STAT_alpha       STAT protein, all-alpha domain
       0.23   11.4  11.9        1.4    8.8   9.6    2.2  2  YscO             Type III secretion protein YscO
       0.24   11.5   2.1       0.45   10.6   1.6    1.7  1  Mating_N         Mating-type protein beta 1
       0.25   10.6   7.4       0.79    9.0   7.4    1.8  1  CorA             CorA-like Mg2+ transporter protein
       0.26   11.1   6.1      0.082   12.7   3.5    1.5  1  Alpha-E          A predicted alpha-helical domain with a cons
       0.26   11.0   5.6        8.7    6.0   0.3    3.2  4  LXG              LXG domain of WXG superfamily
       0.27   11.3   5.2       0.92    9.6   2.6    2.4  2  COG2             COG (conserved oligomeric Golgi) complex com
       0.28   11.0   2.2         12    5.7   0.5    2.3  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.28   10.6   2.9       0.44    9.9   2.4    1.4  1  DUF4618          Domain of unknown function (DUF4618)
       0.28   11.2   2.2        3.6    7.6   0.3    2.1  2  DUF1043          Protein of unknown function (DUF1043)
        0.3   10.8   4.7       0.59    9.8   4.7    1.5  1  YkyA             Putative cell-wall binding lipoprotein
       0.31   11.9   4.6         24    5.8   0.5    3.3  2  Rho_Binding      Rho Binding
       0.31   10.9   3.4         15    5.5   0.1    2.8  2  Nuc_N            Nuclease N terminal
       0.31   10.8   2.3        1.5    8.5   2.3    1.8  1  TACC_C           Transforming acidic coiled-coil-containing p
       0.32   10.8   2.1        3.4    7.4   1.1    2.2  2  SKA1             Spindle and kinetochore-associated protein 1
       0.32   11.1   3.8       0.64   10.1   2.3    2.1  1  RP-C_C           Replication protein C C-terminal region
       0.34   10.4   8.0       0.96    9.0   8.0    1.7  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.35   11.0   8.0         11    6.2   0.5    3.0  2  Uds1             Up-regulated During Septation
       0.39   10.8   1.9        1.4    9.0   0.0    2.6  1  Bap31_Bap29_C    Bap31/Bap29 cytoplasmic coiled-coil domain
       0.45    9.8   1.7         20    4.4   0.1    2.1  2  TraF_2           F plasmid transfer operon, TraF, protein
       0.46    9.6   2.2        1.5    7.9   0.2    2.3  2  phiKZ_IP         phiKZ-like phage internal head proteins
       0.55   10.6   7.2        5.1    7.4   7.2    2.1  1  OmpH             Outer membrane protein (OmpH-like)
       0.55   10.2   9.0         11    6.0   1.5    3.6  4  Prefoldin        Prefoldin subunit
       0.56   10.9  14.9        1.4    9.6   2.4    3.8  3  SlyX             SlyX
       0.57    9.0   3.0        1.1    8.0   3.0    1.4  1  Apt1             Golgi-body localisation protein domain
       0.57    8.7   4.1       0.77    8.2   4.1    1.1  1  Macoilin         Macoilin family
       0.59   10.2  11.7        1.7    8.8   1.1    3.8  3  PspB             Phage shock protein B
       0.62    8.9   2.5        1.6    7.5   2.5    1.6  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.63    9.3   3.3        1.1    8.6   3.3    1.3  1  DUF1978          Domain of unknown function (DUF1978)
       0.66    9.5   3.5        1.7    8.2   3.6    1.6  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
       0.68   10.4   6.7        5.4    7.5   6.7    2.0  1  T3SSipB          Type III cell invasion protein SipB
       0.69   10.0   5.5        8.7    6.5   0.7    3.6  2  Swi5             Swi5
        0.7   10.4   3.5       0.19   12.2   0.5    1.6  1  GPS2_interact    G-protein pathway suppressor 2-interacting d
       0.71   10.0   3.7        1.4    9.0   3.7    1.4  1  Spore_III_AB     Stage III sporulation protein AB (spore_III_
       0.87    9.2   4.4        4.8    6.8   1.3    2.3  2  GrpE             GrpE
        0.9    9.5   5.4         12    5.9   0.2    2.2  2  Sipho_Gp157      Siphovirus Gp157
       0.96    9.7   8.8         10    6.4   0.2    3.6  3  WXG100           Proteins of 100 residues with WXG
       0.99    9.8   7.9        6.4    7.2   4.3    3.2  2  DUF4200          Domain of unknown function (DUF4200)
        1.1    9.6   4.7         19    5.7   0.5    2.6  2  Tup_N            Tup N-terminal
        1.3    9.4   6.8        2.7    8.3   0.9    2.5  2  Rx_N             Rx N-terminal domain
        1.4    9.1   4.1          2    8.6   0.4    2.7  1  Cnn_1N           Centrosomin N-terminal motif 1
        1.4    8.7  11.9       0.41   10.4   1.5    3.4  3  DivIC            Septum formation initiator
        1.5    8.3   9.0         39    3.7   9.0    2.1  1  DegS             Sensor protein DegS
        1.5    9.3  11.2       0.16   12.5   0.4    3.0  2  HSCB_C           HSCB C-terminal oligomerisation domain
        1.6    8.1   3.9        5.6    6.3   2.2    2.4  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
        1.7    9.4   5.2         32    5.3   5.2    2.3  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        1.7    9.2   4.8        2.9    8.4   2.3    2.2  2  FadA             Adhesion protein FadA
        1.7    9.1   7.5         25    5.3   2.0    3.4  3  UPF0184          Uncharacterised protein family (UPF0184)
        1.8    7.2   6.9        6.3    5.4   3.2    2.4  2  Dor1             Dor1-like family
        1.9    8.9   8.6         43    4.6   1.8    3.8  3  LPP              Lipoprotein leucine-zipper
        2.2    8.5   5.9         16    5.7   0.1    2.6  2  Med9             RNA polymerase II transcription mediator com
        2.2    8.4   6.7        2.1    8.4   1.5    2.7  2  DivIVA           DivIVA protein
        2.2    8.1   3.5        3.6    7.4   1.9    1.6  2  DUF724           Protein of unknown function (DUF724)
        2.4    8.5  21.5         12    6.3   1.1    4.6  3  HalX             HalX domain
        2.5    8.6  13.7        1.7    9.2   4.6    3.2  2  BMFP             Membrane fusogenic activity
        2.6    8.6   8.2         35    5.0   5.3    2.6  2  HisKA_3          Histidine kinase
        2.8    7.8   6.9    1.3e+02    2.4   6.9    2.6  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
        3.2    7.6   7.9        1.4    8.8   2.9    2.2  2  DASH_Spc19       Spc19
        3.3    7.5   7.1    1.4e+02    2.3   7.1    3.0  1  Dynactin_p22     Dynactin subunit p22
        3.6    7.3   8.2        7.3    6.3   8.2    1.5  1  FAM184           Family with sequence similarity 184, A and B
        4.1    7.5  12.4          1    9.4   1.8    3.6  4  DUF2205          Short coiled-coil protein
        4.7    6.6   8.3         11    5.4   8.3    1.5  1  Golgin_A5        Golgin subfamily A member 5
        5.4    7.3   8.0         23    5.3   7.2    2.1  1  THOC7            Tho complex subunit 7
          6    7.1  10.6        8.4    6.7   7.9    2.2  2  Cortex-I_coil    Cortexillin I, coiled coil
        8.3    6.5   7.1         21    5.2   0.9    2.8  2  Sec2p            GDP/GTP exchange factor Sec2p
        9.6    6.3   8.9        2.6    8.1   2.7    2.6  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        9.9    6.5   8.3         38    4.6   5.4    3.0  2  Plasmid_RAQPRD   Plasmid protein of unknown function (Plasmid


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 ?   -0.4   0.5       7.8     7e+02     101     135 ..     102     136 ..      77     161 .. 0.77
   2 !  106.5   0.0   1.7e-32   1.5e-30       1     234 [.     184     420 ..     184     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 7.8
                                    HHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT CS
                   Peripla_BP_2 101 iralgellgledeaeklvaeidsklaaaksaidse 135
                                    +r+l+ l+++ +  ++ ++ +++  a+a++++d++
  gi|118431313|ref|NP_147686.2| 102 ARELASLTQQLEDLQARIQALEESGAEAGERLDQL 136
                                    57777777777777777777777777777777776 PP

  == domain 2  score: 106.5 bits;  conditional E-value: 1.7e-32
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT....TS-BSBESSSB-HHHHHHH--SEEEE-GGG....GGGHH CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..aivevgadgeidvEklaalkPDlvilskgl.gltdedee 77 
                                    i+s +ps te+l+ +Ga+d+vvgvd ++ +p + ++++e  ++ ++g+++++++E+++ l PDlv++ ++   + +  + 
  gi|118431313|ref|NP_147686.2| 184 IVSMAPSATETLYYVGALDRVVGVDQYSDFPPELNEAKEagEVEVIGGYWNPSIEAILSLEPDLVVGVASVpNHIQVKKV 263
                                    89**********************************999********************************99999999* PP

                                    HHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TT CS
                   Peripla_BP_2  78 llksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsn 157
                                    l + gip++  + s+  e++ e+++ +g+++g+   a ++v ++d ++aaa+  ++   p +++v+ + ++   +v g +
  gi|118431313|ref|NP_147686.2| 264 LSAYGIPVILLPDSSL-EDVRESMMIVGKATGEVVGAYEAVLKFDMAVAAAGLLLEGVEPVETAVVVWPNP--LFVVGGG 340
                                    **************96.*****************************************************9..999**** PP

                                    STTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH...HHHT-S--HHHHT-S..HHHHTSHHHHTT-EE CS
                   Peripla_BP_2 158 syigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr...aeadnktgleflken..pllaelpAvkngrVy 232
                                    ++  ++++ +g+ n++ +  ++++ ++s E +l++dpdvi+ +g           + e+l+++  +++ e+ Av++gr+y
  gi|118431313|ref|NP_147686.2| 341 TWEHEVIELAGGVNVYGD--TQGWPQVSYESLLEADPDVIILMGGhgnSGVTVEGFIEALESQlgEAAWEIDAVASGRIY 418
                                    ***************999..9************************776333444455666655656666*********** PP

                                    EE CS
                   Peripla_BP_2 233 al 234
                                     l
  gi|118431313|ref|NP_147686.2| 419 VL 420
                                    98 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   6.8e-05    0.0061      62     119 ..      34      91 ..      22      96 .. 0.88
   2 !   10.2   0.3    0.0066      0.59      71     122 ..     101     152 ..      92     161 .. 0.39

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-05
                        DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                      L s+++ ++++ +e +e  +e++   ++ r+d+++i + +es+++ v+++e++l +
  gi|118431313|ref|NP_147686.2|  34 ASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGS 91 
                                    5789999999999999999999999999999999999999999999999999999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0066
                        DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                    v ++l + ++  +++++ +++++e  +e ge ++++  a ++l+++l+++ee
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    3333333333333333333333333333333333333333333333333332 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 !   23.5   6.2   4.9e-07   4.4e-05      18     105 ..      32     128 ..      28     136 .. 0.81
   2 ?    1.5   0.2       3.1   2.8e+02      60      84 ..     132     156 ..     124     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.9e-07
                 CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr.........sekeeLeke 88 
                                    + +sL+ +ve+L+   e++ e++e+v    E+s+  +e++ + +e ++ + +++e  L +           +e  +L+++
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAAtqsdldavaRELASLTQQ 111
                                    6689***********************************88888888888777765554444444444444********* PP

                 CENP-F_leu_zip  89 lqkkqervseLeslnss 105
                                    l++ q r++ Le++  +
  gi|118431313|ref|NP_147686.2| 112 LEDLQARIQALEESGAE 128
                                    ************98665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 3.1
                 CENP-F_leu_zip  60 eieelaeelreleldLvalrsekee 84 
                                     +++la  l++l++ L++l +  +e
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASLEERVDE 156
                                    5677777777777777777766555 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1    0.0017      0.15      11      66 ..      31      90 ..      26      99 .. 0.67
   2 !   13.8   0.8   0.00067      0.06      10      63 ..      65     117 ..      62     127 .. 0.76
   3 !   10.2   2.0    0.0093      0.83      12      61 ..      97     150 ..      93     167 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0017
                        NPV_P10 11 adikavddkVdalqqqvddvqenlpdvt....elnekLdaqsaqLaeletkvenIqdiLn 66
                                   ++ + + ++V+ l+++ ++++e l++v+         +++++ +L+++++ v++I++ L 
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQgafeSSRGDIESIASSLESIQDRVSKIEERLG 90
                                   5555555566666666666555555555111124568******************99886 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00067
                        NPV_P10  10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                    r di+ + + ++++q++v +++e l      ++ Lda + +La+l +++e+ q 
  gi|118431313|ref|NP_147686.2|  65 RGDIESIASSLESIQDRVSKIEERLGS-AATQSDLDAVARELASLTQQLEDLQA 117
                                    678999999999999999999988877.55677777777777777777777664 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0093
                        NPV_P10  12 dikavddkVdalqqqvddvqenlpdvte....lnekLdaqsaqLaeletkvenI 61 
                                    d  av   + +l qq++d+q+ ++ ++e      e+Ld+++ +L++l++ + + 
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEEsgaeAGERLDQLAMALQDLQARLASL 150
                                    556666666666666666666666665411114567777777777777755443 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0013      0.12     107     171 ..      43     106 ..      33     108 .. 0.89
   2 !   12.4   1.0   0.00082     0.073     106     154 ..     107     155 ..      98     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0013
                     FmiP_Thoc5 107 laeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkqhelaslLP 171
                                    l++ ++e++e+ ++++ + e+++  ++s+++ L+s+++ +++++e lg   t +++ ++ a++L 
  gi|118431313|ref|NP_147686.2|  43 LNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAAT-QSDLDAVARELA 106
                                    78899*******************************************6555.777777777775 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00082
                     FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealg 154
                                    +l +ql++l+++ ++le+  +e  ++L++L+ +L++l++ ++ l+e ++
  gi|118431313|ref|NP_147686.2| 107 SLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVD 155
                                    6889***************************************999875 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0    0.0018      0.16       5      83 ..      10      88 ..       7      94 .. 0.85
   2 ?    9.3   0.2     0.014       1.3      31      88 ..      94     151 ..      88     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0018
                         DUF948  5 IaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83
                                   IaA+  vv  i+l v +  + + l ++++++e+l+ + ++i++ +e++    +    d+++   +++++ + v ++ e 
  gi|118431313|ref|NP_147686.2| 10 IAAGIAVVALIILGVGFYAIYQELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEER 88
                                   777777777888899999999**************99999999999999999998889999888888888888888776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.014
                         DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                    +++ ++ + +++ ++++++edl a +++l e   e  e++d+l  a++dl + +++l+
  gi|118431313|ref|NP_147686.2|  94 TQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLE 151
                                    56678889999999999999999999999999999***************99999886 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   6.2   3.3e-07   2.9e-05       6     119 ..      43     158 ..      38     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.3e-07
                    Tropomyosin   6 veeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeeler..teerleealekLeeaekaadeserarKvl 83 
                                    +++  +e++e+le+++   e+ +  +e+  +  ++++ r++++ee l +  t+++l+   ++L  ++++ ++ +  + +l
  gi|118431313|ref|NP_147686.2|  43 LNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSaaTQSDLDAVARELASLTQQLEDLQARIQAL 122
                                    67889*****************************************9752278999************************ PP

                    Tropomyosin  84 EnrelkdeekleeleaqlkeakeiaeeadrkyeEva 119
                                    E++ ++  e+l++l ++l++ + +  + +++++Ev 
  gi|118431313|ref|NP_147686.2| 123 EESGAEAGERLDQLAMALQDLQARLASLEERVDEVY 158
                                    ************************999999999995 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1    0.0012       0.1      12      67 ..      33      88 ..      27      96 .. 0.62
   2 !   12.5   1.6    0.0013      0.11      11      71 ..      97     157 ..      91     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0012
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--T CS
                     Laminin_II 12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekl 67
                                   +++  +q+++l+++ e+++e+l+e+++  e    ++++    +++ ++ v+k+e+ 
  gi|118431313|ref|NP_147686.2| 33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEER 88
                                   44555666666666666666666666666666666666666666666666666654 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0013
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                     Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71 
                                     + +v + la l q+le +++ ++ +++s +e  e ++++ +a++d +     Le+ ++++
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    4567778888888888888888888888888888888888888888888888888877765 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   0.0       4.8   4.3e+02      63      89 ..      31      57 ..      27      64 .. 0.64
   2 !   19.4   0.3   9.2e-06   0.00082      32      91 ..      65     124 ..      63     127 .. 0.96
   3 ?    1.8   0.1       2.8   2.5e+02      65      89 ..     133     157 ..     128     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 4.8
                        DUF2730 63 kdlekLkllladlrgelkaleaevrql 89
                                   ++l++L+ ++++l+ + ++++++++++
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEV 57
                                   466666666666666666666666655 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 9.2e-06
                        DUF2730  32 redleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91 
                                    r d+e++a ++e+++ r++++e ++ +  t++dl+++  +la l  +l++l+a++++l+ 
  gi|118431313|ref|NP_147686.2|  65 RGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    889*****************************************************9985 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 2.8
                        DUF2730  65 lekLkllladlrgelkaleaevrql 89 
                                    l++L + l+dl+++l  le++v+++
  gi|118431313|ref|NP_147686.2| 133 LDQLAMALQDLQARLASLEERVDEV 157
                                    5566666666666666666666654 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   0.00019     0.017      22      79 ..      33      90 ..      30      95 .. 0.89
   2 ?    6.8   0.3     0.089       7.9      31      81 ..     107     157 ..      90     162 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 0.00019
                           KxDL 22 sgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79
                                   ++ l ++ + L +  ++ +e l++++  f++   ++ ++ + Lesi+ ++++++++l 
  gi|118431313|ref|NP_147686.2| 33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLG 90
                                   56777888889999999************************************99886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.089
                           KxDL  31 eLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklakk 81 
                                     L+++ + +q+r + l++  ++  + l ++   L+ ++ ++ sl++++ + 
  gi|118431313|ref|NP_147686.2| 107 SLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    344444455555555555555555555555555555555555555555544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   8.4   6.7e-07   5.9e-05     143     259 ..      35     156 ..      33     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.7e-07
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles.....idkeeLeelreelaelkaeiee 217
                                    +l++++egl++ +e+++++ ee++ + ++ +   +++ + le++q+++ ++e+      ++ +L ++ +ela+l +++e 
  gi|118431313|ref|NP_147686.2|  35 SLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEErlgsaATQSDLDAVARELASLTQQLED 114
                                    67888899999999999999999999999999999999999999998888888888767788899999999999999999 PP

                           Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                    ++++++ l+e  +e  e++++l+   ++l++++a+ e+ ++e
  gi|118431313|ref|NP_147686.2| 115 LQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    999999999999999999998888888888888888877665 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.28        25      45      69 .]      28      52 ..      24      57 .. 0.86
   2 !   12.3   4.5    0.0017      0.15      10      69 .]      68     124 ..      62     124 .. 0.80
   3 !   17.9   7.5     3e-05    0.0026       8      62 ..     103     159 ..     100     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.28
                   ABC_tran_CTD 45 elsaeleeleaeLeelyerWeeLee 69
                                   ++ +el+ l+++ e l  r+ee +e
  gi|118431313|ref|NP_147686.2| 28 AIYQELASLRSQVEGLNTRYEEISE 52
                                   6778999999999999999999876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0017
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLee 69 
                                    +e + + +e+++ + +++e++l +++       l ++ +el+ l ++Le l +r   Lee
  gi|118431313|ref|NP_147686.2|  68 IESIASSLESIQDRVSKIEERLGSAATQ---SDLDAVARELASLTQQLEDLQARIQALEE 124
                                    68899999****************9843...35788888888888888888777777665 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 3e-05
                   ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelye 62 
                                    rel+ l +++e L+++i++le+  a+++   d+   +l++l+a+l+ le+  +e y+
  gi|118431313|ref|NP_147686.2| 103 RELASLTQQLEDLQARIQALEESGAEAGERLDQlaMALQDLQARLASLEERVDEVYA 159
                                    788888888888888888888888888755444445688888888888888888775 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   8.1     3e-06   0.00027       2     118 ..      33     155 ..      32     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3e-06
                  Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakek......aeesekkktnn 75 
                                    l sL+   e   +++ee+ e++ e +   ++   +i+s+   ++ +++ v k+ee+l  a ++      a e +++ ++ 
  gi|118431313|ref|NP_147686.2|  33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQsdldavARELASLTQQL 112
                                    77999999999*******************************************99966555411111156777888899 PP

                  Tropomyosin_1  76 ealtrkiqlLEeeleesdkkLkettekLretdvkaeelERkvk 118
                                    e l+ +iq LEe   e+ ++L +    L++ +++   lE +v 
  gi|118431313|ref|NP_147686.2| 113 EDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVD 155
                                    9************999999999999999998888777777665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.9   8.3e-05    0.0074     344     407 ..      31      94 ..      27     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.3e-05
                                    TTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 344 eklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrk 407
                                    ++l +l ++++ l+++yee+ e lee + a+ + + ++e++ ++le i++++ +i+e l+s   
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAAT 94 
                                    5677899999*********************************************999998754 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.7   1.8e-06   0.00016       9     128 ..      33     156 ..      23     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.8e-06
                        DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq.fD 87 
                                    l  l++++e l +++e+++e+ +e+++  e  + ++e++ +++e  +++  +   +ee l  +a  ++L++++ +   + 
  gi|118431313|ref|NP_147686.2|  33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSK---IEERLGSAATQSDLDAVARELAsLT 109
                                    667899999******************************9999999999998...8888888888888888885544666 PP

                        DUF4795  88 eakkeLekmleellekleeqeealkkaldtLq......eelkekldr 128
                                    + +++L+  ++ l e+  e+ e+l+++   Lq       +l+e++d+
  gi|118431313|ref|NP_147686.2| 110 QQLEDLQARIQALEESGAEAGERLDQLAMALQdlqarlASLEERVDE 156
                                    66666666666666666666666666666555333333377777764 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1    0.0052      0.46      41      99 ..      31      89 ..      23      94 .. 0.70
   2 !   12.4   0.8    0.0019      0.17      42     102 ..      97     157 ..      91     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0052
                                   HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                          DUF16 41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99
                                   +++++l  q++ l+   e+  e ++e +   +  + +++++ ++le+i + + ki++Rl
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89
                                   55666677777777777777777777777777777777777777777777777777777 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0019
                                    HHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                          DUF16  42 kvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                     +d+   +++ l+q+ e ++++i+ l++     ge+l+++  +l+ +   L+++++R+D++
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    5566667788888888888889988888888888888888888888888888888888875 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0042      0.37      31      86 ..      35      89 ..      27      92 .. 0.73
   2 !   10.3   1.9     0.008      0.71      13      75 ..      96     157 ..      91     161 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0042
                Snapin_Pallidin 31 eLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86
                                    L++q++ ln++++e++e  e ev   +++ +  + +i   ++s+++r++k+++R+
  gi|118431313|ref|NP_147686.2| 35 SLRSQVEGLNTRYEEISESLE-EVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89
                                   578888888888888888777.7777777777777777777777777777777776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.008
                Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssl 75 
                                    ++ld++  +l++l+q+ e+L+++++ l e+ +e+ e  + ++   l+  +++L++++ r+ ++
  gi|118431313|ref|NP_147686.2|  96 SDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLD-QLAMALQDLQARLASLEERVDEV 157
                                    445555555555555555555555555555555555555.44455555555555555555554 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 !   19.4   5.8   2.9e-06   0.00026     695     814 ..      31     152 ..      27     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-06
                            FPP 695 eeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrate...le 771
                                    +el +l+s+ e l+++ ++ +e+le+++  ++ s   ++++ s Les+++  s++e+ l + + ++++l+  a+e   l+
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAA-TQSDLDAVARElasLT 109
                                    7999*****************************************************998765.5566776554411178 PP

                            FPP 772 aelnelkqkieaLeveLeeekksheeleakckelqeqlervek 814
                                    ++l+ l+ +i+aLe+   e  +   +l ++ ++lq +l + e+
  gi|118431313|ref|NP_147686.2| 110 QQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    99***********************************999874 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 !   20.7  10.0   4.8e-06   0.00043      15     126 ..      45     157 ..      33     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.8e-06
                          HrpB7  15 rreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspf..siadylacrayrdvlegrvraae 92 
                                     r+e++ + le+ + a ++   ++++ ++ +e  +d+v ++eerl +++t s  +  ++ +++++   ++ l++r++a+e
  gi|118431313|ref|NP_147686.2|  45 TRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSD-LdaVARELASLTQQLEDLQARIQALE 123
                                    6899*********************************************9997.523788999***************** PP

                          HrpB7  93 aelaaarqaldaaedavaatarkiaRndaqidac 126
                                    +  a a ++ld+ + a++  ++++a+++ ++d +
  gi|118431313|ref|NP_147686.2| 124 ESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    *******************************976 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  13.1   4.3e-05    0.0038      19     148 ..      28     156 ..      26     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-05
                          ATG16  19 eliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqkl..aqlreelaelyks 96 
                                    +++q    L  +++ l+++ ++++++ ++++    s++ + e+ as+ +   + ++++++ e++l  a+++++l ++ ++
  gi|118431313|ref|NP_147686.2|  28 AIYQELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLE---SIQDRVSKIEERLgsAATQSDLDAVARE 104
                                    4455555555555555566566655555555533333333344444333...344555555555433789********** PP

                          ATG16  97 rgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                     + l+q+l +l++ +q+lee+  e  erl++l    ++l+ +l+++ee++ e
  gi|118431313|ref|NP_147686.2| 105 LASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    ************************************************9988 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 ?    8.2   0.0     0.027       2.4      49     108 ..      28      89 ..       7      94 .. 0.72
   2 !   14.5   1.2    0.0003     0.027      28     108 ..      36     119 ..      26     125 .. 0.43
   3 !   13.0   3.5   0.00087     0.078      36     102 ..      71     155 ..      68     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.027
                   Baculo_PEP_C  49 alsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstL 108
                                    a+ ++l sl + + + l+t  ++++++l ++q   ++ r +++++ s l +++  v  i++ L
  gi|118431313|ref|NP_147686.2|  28 AIYQELASLRS-QVEGLNTRYEEISESLEEVQgafESSRGDIESIASSLESIQDRVSKIEERL 89 
                                    55566666444.334688888888888888888888888888888888888887777776655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.0003
                   Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq.dtlrneLtnlnsiltnLlssvtN 103
                                    + +q+   l+t  ++i ++L++++ +++s+  ++++    l++  +++++   +l   + +++L+++  +l++L+ ++  
  gi|118431313|ref|NP_147686.2|  36 LRSQV-EGLNTRYEEISESLEEVQGAFESSRGDIESiasSLESIQDRVSKIEERLGsAATQSDLDAVARELASLTQQLED 114
                                    34444.44555555555555555555555544444333333333333333333333433344444444444444444444 PP

                   Baculo_PEP_C 104 instL 108
                                    +++ +
  gi|118431313|ref|NP_147686.2| 115 LQARI 119
                                    44333 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00087
                   Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldt........rldtlltnLtdalnalq..........dtlrneLtnlnsiltnL 97 
                                    +a+ l++i+ ++++++e+l s+ ++ d          l+++l+ L++ ++al+          d+l  +L+ l++ l++L
  gi|118431313|ref|NP_147686.2|  71 IASSLESIQDRVSKIEERLGSAATQSDLdavarelaSLTQQLEDLQARIQALEesgaeagerlDQLAMALQDLQARLASL 150
                                    67788888888888888888877655545566644444444444444455554877555555555555555555555555 PP

                   Baculo_PEP_C  98 lssvt 102
                                       v 
  gi|118431313|ref|NP_147686.2| 151 EERVD 155
                                    55544 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.6   1.4e-05    0.0012      48     158 ..      31     146 ..      27     161 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-05
                           TelA  48 klLseLvkelkeldpdelkeekkl.gllplfkkaknkieklfakYekaeeqidkIvkeLekgqde.....llkdnaaLdq 121
                                    + L++L+ ++++l+ +  + +++l ++ + f++ +  ie+++++ e++++ + kI ++L ++ ++       +  a+L q
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLeEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQsdldaVARELASLTQ 110
                                    78999********9986654577745555999999999999999999999999999999776554111113444555555 PP

                           TelA 122 lyeknleyfkeLekyiaaGekkleeldekllpeleak 158
                                      e + + +++Le+  a + ++l++l  + l+ l+a+
  gi|118431313|ref|NP_147686.2| 111 QLEDLQARIQALEESGAEAGERLDQLAMA-LQDLQAR 146
                                    55555666666665544444445555422.3333333 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2    0.0017      0.15      40      90 ..      30      81 ..      26      89 .. 0.84
   2 !   12.5   1.7    0.0016      0.14      12      80 ..      58     125 ..      57     142 .. 0.82
   3 ?    8.0   2.1     0.038       3.4      32      83 ..     101     156 ..      99     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0017
                        BLOC1_2 40 kdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeyske 90
                                    +++asl++++e ln +yee+++ l++++ ++e +  ++e+++s L+++  +
  gi|118431313|ref|NP_147686.2| 30 YQELASLRSQVEGLNTRYEEISESLEEVQgAFESSRGDIESIASSLESIQDR 81
                                   578999**********************856899999999999999987554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0016
                        BLOC1_2  12 eaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                    ++ +e+++ d++ +    e+ + ++ k+++++ s++++ ++l++   el+++ qq+++++++++ Lee 
  gi|118431313|ref|NP_147686.2|  58 QGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQ-SDLDAVARELASLTQQLEDLQARIQALEES 125
                                    66778888888899999999999999****99998776.689999**********************85 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.038
                        BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqq....idqiekqvteLeeavse 83 
                                    ++++ ++l++++++l++ +++l+e  +e  + l+q    ++++++++++Lee v+e
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEAGERLDQlamaLQDLQARLASLEERVDE 156
                                    67788889999999999999999988877777766222257888888888888876 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 !   10.9   8.4    0.0023       0.2      10     102 ..      14     125 ..       8     163 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0023
                           HemX  10 lallvalavgaglyylgqqqvqeltaevaelqqqlaaleqqlaq..................veaekeqkqeleerlqql 71 
                                    +a++  + +g+g+y + q   ++l+++v+ l+++ ++++++l++                  +e+ + + +++eerl  +
  gi|118431313|ref|NP_147686.2|  14 IAVVALIILGVGFYAIYQE-LASLRSQVEGLNTRYEEISESLEEvqgafessrgdiesiassLESIQDRVSKIEERLGSA 92 
                                    3333333355556655544.458888888888888888888888888888899998888777555555555555555544 PP

                           HemX  72 ..aeklealekeleqlqkqleelqqqlskvsga 102
                                      +++l+a ++el++l++qle lq+++++++ +
  gi|118431313|ref|NP_147686.2|  93 atQSDLDAVARELASLTQQLEDLQARIQALEES 125
                                    335566666666666666666666666665543 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 ?    8.0   0.2     0.041       3.6       7      34 ..      31      58 ..      28      64 .. 0.83
   2 ?    9.2   0.9     0.018       1.6       2      39 ..      47      84 ..      46      91 .. 0.87
   3 ?    9.7   0.2     0.012       1.1       1      40 [.      81     122 ..      81     128 .. 0.87
   4 ?    4.9   0.1      0.39        35       1      40 [.     118     157 ..     118     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.041
                      FlaC_arch  7 nklsklsteletvkkeneelsksveelk 34
                                   ++l +l +++e + +  ee+s+s+ee++
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQ 58
                                   7888999999999999999999999886 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.018
                      FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelkenVkd 39
                                    +e+ + l++++  +e+ + ++e++ +s+e ++++V +
  gi|118431313|ref|NP_147686.2| 47 YEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSK 84
                                   67899999999999999999999999999999999976 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.012
                      FlaC_arch   1 ridelEnklsklst..eletvkkeneelsksveelkenVkdl 40 
                                    r+ ++E++l++  t   l+ v +e+ +l +++e+l+ +++ l
  gi|118431313|ref|NP_147686.2|  81 RVSKIEERLGSAATqsDLDAVARELASLTQQLEDLQARIQAL 122
                                    8999*****999988889999999999999999999988765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.39
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                    ri+ lE+   +   +l+ +   +++l+  +  l+e+V ++
  gi|118431313|ref|NP_147686.2| 118 RIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    6677777777777778888888888888888888888776 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   7.1   0.00017     0.015      44     138 ..      67     159 ..      18     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHH CS
                          Nup54  44 evaqhrerlkeisdrleeleqkh.qletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaq 122
                                     ++   + l++i+dr++++e++  ++ t++ l+ ++++ + l+++l  l ++++ l+ +g    +  ++l+  l++l+a+
  gi|118431313|ref|NP_147686.2|  67 DIESIASSLESIQDRVSKIEERLgSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQAR 146
                                    45566667778888888887664268888999999999999999999999999999888888888888999999988888 PP

                                    HS-HHH.HHHHHHHHH CS
                          Nup54 123 lndpaqlkgrvnelwa 138
                                    l    +l+ rv+e+ a
  gi|118431313|ref|NP_147686.2| 147 LA---SLEERVDEVYA 159
                                    88...57899999876 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  10.2   2.1e-05    0.0019      21     127 ..      40     155 ..      28     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-05
                         APG6_N  21 aekerdaYeeflkklkkekkeeek.......qdeeleeleeeleklekee..eelleeLkelekereeleaelaaleeel 91 
                                    +e     Yee  + l++ +   e+         ++le+++++++k+e+    ++ ++ L+++ +e ++l ++l++l++  
  gi|118431313|ref|NP_147686.2|  40 VEGLNTRYEEISESLEEVQGAFESsrgdiesIASSLESIQDRVSKIEERLgsAATQSDLDAVARELASLTQQLEDLQARI 119
                                    4444445555555555554444445666666788999999999999998722455778********************** PP

                         APG6_N  92 ealeeeeerfwreynelqlelleleeeldsleaqye 127
                                    +alee  ++  ++  +l++ l++l+ +l+sle +++
  gi|118431313|ref|NP_147686.2| 120 QALEESGAEAGERLDQLAMALQDLQARLASLEERVD 155
                                    ********************************9987 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 ?    4.3   0.1      0.56        50      31      59 ..      31      59 ..      28      70 .. 0.85
   2 ?    4.2   0.0      0.62        55      32      58 ..      67      93 ..      60      98 .. 0.83
   3 ?    6.3   0.6      0.14        12      20      51 ..      92     123 ..      84     130 .. 0.73
   4 !   10.5   0.8    0.0069      0.61      24      57 ..     124     157 ..     120     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.56
                            CLZ 31 ekverLessLeaLqtrlarLlaeyessqr 59
                                   + + +L s++e L+tr++ + + +e++q 
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQG 59
                                   56789999**********99999999886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.62
                            CLZ 32 kverLessLeaLqtrlarLlaeyessq 58
                                    +e++ ssLe++q+r+ ++ + + s++
  gi|118431313|ref|NP_147686.2| 67 DIESIASSLESIQDRVSKIEERLGSAA 93
                                   588999999999999999999888765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.14
                            CLZ  20 akagaeqkeleekverLessLeaLqtrlarLl 51 
                                    a+ +++ + + + + +L ++Le Lq r++ L 
  gi|118431313|ref|NP_147686.2|  92 AATQSDLDAVARELASLTQQLEDLQARIQALE 123
                                    45557777788888899999999999988875 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0069
                            CLZ  24 aeqkeleekverLessLeaLqtrlarLlaeyess 57 
                                    +   e+ e++++L  +L+ Lq rla L + ++++
  gi|118431313|ref|NP_147686.2| 124 ESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    566788999****************999888776 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.8   1.7e-05    0.0015      12     103 ..      36     124 ..      30     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-05
                           Zw10  12 lekkisklekkveeikeevskmivkkYseflelsssaeellerveslskeidalkkkven.eieqdlkaaveelaelkqq 90 
                                    l+++++ l+++ ee    +s+ +++  + f  +    e + + +es+++ ++ + +++++   ++dl+a++ ela l+qq
  gi|118431313|ref|NP_147686.2|  36 LRSQVEGLNTRYEE----ISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSaATQSDLDAVARELASLTQQ 111
                                    55555555665555....556667777889999999999*******************9988999*************** PP

                           Zw10  91 lkekevvlellea 103
                                    l+  ++ ++ le+
  gi|118431313|ref|NP_147686.2| 112 LEDLQARIQALEE 124
                                    ****999998865 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0     0.009      0.81     316     401 ..      10      89 ..       2      97 .. 0.70
   2 ?    7.9   0.4     0.011         1     336     403 ..      95     156 ..      91     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.009
                           FapA 316 lGselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeele 395
                                    +++ + +   i +g+ + ++ ++l+ l+ ++e l+ + e++ +++++++  +      +  + +++++  ++e+++++++
  gi|118431313|ref|NP_147686.2|  10 IAAGIAVVALIILGVGFYAIYQELASLRSQVEGLNTRYEEISESLEEVQG-A-----FESSRGDIESIASSLESIQDRVS 83 
                                    5555666677788999999999999***************9999999998.2.....23335555555555555555555 PP

                           FapA 396 eleeel 401
                                    ++ee+l
  gi|118431313|ref|NP_147686.2|  84 KIEERL 89 
                                    555554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                           FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelke 403
                                    ++ l+++ +el +l ++le+l+++i+ l++++ae        e l++l  +++ l+ +l++lee+ +e
  gi|118431313|ref|NP_147686.2|  95 QSDLDAVARELASLTQQLEDLQARIQALEESGAEA------GERLDQLAMALQDLQARLASLEERVDE 156
                                    56778899999999999999999999999944433......255555555555555555555555444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.9   4.8e-05    0.0043     223     327 ..      37     146 ..      29     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-05
                          IFT57 223 rahleqmkkhkksieeslpetksqlkklhedis...ktlekiesrEkylnsqleellqe..yreaqeelsevkekykqls 297
                                    r+++e +++  ++i+esl+e++ +++    di+    +le i+ r + ++++l +  ++  + ++ +el+++++++++l+
  gi|118431313|ref|NP_147686.2|  37 RSQVEGLNTRYEEISESLEEVQGAFESSRGDIEsiaSSLESIQDRVSKIEERLGSAATQsdLDAVARELASLTQQLEDLQ 116
                                    55566666666666777777776666666554411145666666666677766665544447788888888888888888 PP

                          IFT57 298 egvseltrelaeiseelekvkqemeergss 327
                                    +++++l++  ae  e+l+++   +++ +++
  gi|118431313|ref|NP_147686.2| 117 ARIQALEESGAEAGERLDQLAMALQDLQAR 146
                                    888888888888888887777777766655 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       2.2     2e+02       5      47 ..      32      74 ..      29      80 .. 0.59
   2 !   10.6   0.7    0.0055      0.49       2      46 ..      78     124 ..      65     125 .. 0.80
   3 !   10.0   0.1    0.0085      0.76       5      46 ..     104     145 ..     100     150 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 2.2
                           XhlA  5 rlerietkldnleervdkleekaaeaeekiknleedlkklesn 47
                                   +l+ + ++++ l++r +++ e  +e++   ++   d++++ s+
  gi|118431313|ref|NP_147686.2| 32 ELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASS 74
                                   5666666666666666666666666666666666666666554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0055
                           XhlA   2 ikerlerietkldnlee..rvdkleekaaeaeekiknleedlkkles 46 
                                    i++r+ +ie++l +  +  ++d + +  a   ++++ l+ ++  le+
  gi|118431313|ref|NP_147686.2|  78 IQDRVSKIEERLGSAATqsDLDAVARELASLTQQLEDLQARIQALEE 124
                                    78888888888888888788888888888888888888888888876 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0085
                           XhlA   5 rlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                    +l+ + ++l++l+ r++ lee  aea e++++l   l +l++
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQA 145
                                    6889999**************************999999986 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.011      0.95      54     135 ..       7      90 ..       6      97 .. 0.75
   2 ?    7.8   0.2     0.024       2.1      75     139 ..      93     159 ..      88     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.011
                   Allexi_40kDa  54 LthishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaeta..sdskllkklesietsleelh 131
                                    Lthi+  +  +   +  v   +  ++L+ lr++++ l++  +++++  ++++   e+   + ++++ +lesi+ ++ ++ 
  gi|118431313|ref|NP_147686.2|   7 LTHIAAGIAVVALIILGVGFYAIYQELASLRSQVEGLNTRYEEISESLEEVQGAFESSrgDIESIASSLESIQDRVSKIE 86 
                                    78888888888777777888899999******************998887765544431144566778888888888888 PP

                   Allexi_40kDa 132 akld 135
                                    ++l 
  gi|118431313|ref|NP_147686.2|  87 ERLG 90 
                                    8774 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.024
                   Allexi_40kDa  75 sqttlLselrdalrtltklldklksvekklelsaetasds..kllkklesietsleelhakldelss 139
                                    ++++ L  +  +l  lt++l++l++  + le+s  +a ++  +l+  l+ ++ +l +l +++de+ +
  gi|118431313|ref|NP_147686.2|  93 ATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERldQLAMALQDLQARLASLEERVDEVYA 159
                                    5667788999999999999999999999998887766554226777888899999999999988866 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 !   13.0   0.3   0.00049     0.044     237     298 ..      31      92 ..      27      99 .. 0.93
   2 ?    7.7   3.1      0.02       1.8     231     293 ..      97     159 ..      91     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00049
                         HAP1_N 237 eeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLhea 298
                                    +e +sL++q+  l+++ +e+++  ee++   ++s+   +++++ L+ +q++ + +e+ L +a
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSA 92 
                                    6999***************************************************9999766 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.02
                         HAP1_N 231 elerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaeveg 293
                                    +l+   +e +sL+ q+ dlq +++ l +   e  ++L     a ++L+a L  l+e+  ev  
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVYA 159
                                    666778999999999999999999998888888888877777778999999999999999865 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 !   15.9   3.9     7e-05    0.0063      29     153 ..      34     156 ..      30     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7e-05
                            GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkweh 108
                                     sl++++e l+++ e+ +  l+e++   ++ +  ++     +e  + ++ + e+ +   +++++ l  + +el +l+++ 
  gi|118431313|ref|NP_147686.2|  34 ASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEE-RLGSAATQSDLDAVARELASLTQQL 112
                                    689********************************************9999998.77788999***************** PP

                            GAS 109 evleqrfekvekerdelykkfeaaiqevqqktglknllLekklka 153
                                    e l+ r++++e++  e  ++ ++  +   q+ + +   Le ++++
  gi|118431313|ref|NP_147686.2| 113 EDLQARIQALEESGAEAGERLDQLAMA-LQDLQARLASLEERVDE 156
                                    ************888888888885554.45566666667766665 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.4e-05    0.0039     209     300 ..      31     124 ..      27     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.4e-05
                        Taxilin 209 etekelkeqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklEketnlwkskfek..tnkallemaeertekkk 286
                                    ++ ++l++q++  + ++ee+ ++L+    +F++ + ++e ++++++++ +  +++ ++  +  t+  l ++a e    ++
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSaaTQSDLDAVARELASLTQ 110
                                    67789*****************************************************875227889************* PP

                        Taxilin 287 eieklkkkiqkLek 300
                                    ++e+l+ +iq Le+
  gi|118431313|ref|NP_147686.2| 111 QLEDLQARIQALEE 124
                                    ************96 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 ?    7.4   0.1      0.04       3.6      39     102 ..      32      99 ..      25     105 .. 0.72
   2 ?    5.0   0.2      0.22        20      38      66 ..     131     159 ..     122     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.04
                           SKA2  39 NpvkLlerlkkvkeelqaLkeqceellaekk...elidkirttlvanrellqqLqasaelppls.eee 102
                                    +++ L ++++ +++++++++e +ee++ + +     i++i ++l + +  + +++++++  +++ + +
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRYEEISESLEEVQGAFEssrGDIESIASSLESIQDRVSKIEERLGSAATQsDLD 99 
                                    45677788888888888888888888765443336799999999999999999999996665442444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.22
                           SKA2  38 eNpvkLlerlkkvkeelqaLkeqceella 66 
                                    e + +L   l++++++l++L+e+++e++a
  gi|118431313|ref|NP_147686.2| 131 ERLDQLAMALQDLQARLASLEERVDEVYA 159
                                    5556788999****************986 PP

>> CCDC154  Coiled-coil domain-containing protein 154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   4.1     4e-05    0.0035      27     154 ..      31     161 ..      27     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4e-05
                        CCDC154  27 aevvslrghkerceaallsllrellqlrasvqlqdseLkklrqevkraavaPeKealelsgaqnqnqmqaLdkrLvevre 106
                                    +e++slr + e+ ++    + + l ++++  +    +++ + + ++ +    +K++ +l +a  q+ ++a+ + L  + +
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQ 110
                                    699***************************************************************************** PP

                        CCDC154 107 altqir.rkqalqdserkkaeq..eaglrlakLtdklkqeeqareaacsaL 154
                                    +l +++ r qal++s  ++ e+  +++  l+ L+ +l   e+  ++++++L
  gi|118431313|ref|NP_147686.2| 111 QLEDLQaRIQALEESGAEAGERldQLAMALQDLQARLASLEERVDEVYASL 161
                                    *****956699*999877766522667778888888887777777776665 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.7   9.9e-05    0.0088     254     347 ..      44     139 ..      28     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.9e-05
                                    HTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCT..TSSTT-THHHHHHHHHHHHHHHHHHHH CS
                            FH2 254 reklpevldfsseLknvkkaakvnleslekevkklekglkklekelessek..keepsdkflevlkeflkeaeeklkkle 331
                                     ++++e+++  +e +   ++++ ++es++++++ ++++++k+e+ l s ++  + +   + l++l++ l++ + +++ le
  gi|118431313|ref|NP_147686.2|  44 NTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATqsDLDAVARELASLTQQLEDLQARIQALE 123
                                    55788899999999999999******************************955555556667789999999999999999 PP

                                    HHHHHHHHHHHHHHHH CS
                            FH2 332 eelkeakelvkelveY 347
                                    e   ea e++++l+  
  gi|118431313|ref|NP_147686.2| 124 ESGAEAGERLDQLAMA 139
                                    9999999999988765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   4.8e-05    0.0043     337     464 ..      36     158 ..      28     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-05
                         AAA_13 337 LkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykk 416
                                    L++  + l+ + +e+++  +le+v++  es   ++++i  + ++   +v+++ee+  +a+++  l+ v+    el  +++
  gi|118431313|ref|NP_147686.2|  36 LRSQVEGLNTRYEEISE--SLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVA---RELASLTQ 110
                                    55555667888888888..88999999999999999999999999999999999999999999998877...67888889 PP

                         AAA_13 417 kykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeein 464
                                    ++++l++ i+ le++ +e+ ++l +l+   ++L+++l + ++ ++e+ 
  gi|118431313|ref|NP_147686.2| 111 QLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVY 158
                                    999999999999999999999999999999999999999999999875 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 !   12.8  16.4   0.00072     0.064      93     207 ..      32     154 ..      28     156 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00072
                     MscS_porin  93 qlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage........alsqaqrtalqaelaaleaq 164
                                    +l++l++q   ln++  e++ ++e++q +  + r  ++ i + L+s +++ +        a +q+  +a   ela+l++q
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSkieerlgsAATQSDLDAVARELASLTQQ 111
                                    56666666666666666666666666666666666666666666333333222233344455556666666666666666 PP

                     MscS_porin 165 ieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqell 207
                                    +e l+   +      + +  ++d+l+  +q+l+++l+ L+e++
  gi|118431313|ref|NP_147686.2| 112 LEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERV 154
                                    6666666666666666666666666666666666666666655 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   5.4   7.2e-05    0.0065      75     171 ..      34     134 ..      31     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-05
                 ALIX_LYPXL_bnd  75 aelraelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaalpssssa....aasesveeqirklrsllekld 150
                                    a+lr++++ + +  ee ses + v+ ++++++ d+e ++++ e++++ +++ +++    a++++ ++++r+l sl ++l+
  gi|118431313|ref|NP_147686.2|  34 ASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERlgsaATQSDLDAVARELASLTQQLE 113
                                    689**********************************************954444344244678888888********** PP

                 ALIX_LYPXL_bnd 151 elkaereqllkdlkekaendD 171
                                    +l+a+ + l+++  e+ e+ D
  gi|118431313|ref|NP_147686.2| 114 DLQARIQALEESGAEAGERLD 134
                                    ***999999987666655555 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   6.2   5.7e-05     0.005     410     529 ..      36     157 ..      31     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-05
                  Myosin_tail_1 410 leaqlqelqvklseserqreelaekvsklqaelesvsslleeaegksiklskdv..sslesqlqDtqellqeetrqkLal 487
                                    l +q++ l+++++e   + ee++   +  + ++es+ s+le+ + + +k++  +  ++ +s+l+ +   l   t+q  +l
  gi|118431313|ref|NP_147686.2|  36 LRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLgsAATQSDLDAVARELASLTQQLEDL 115
                                    5689*******************************************99999872245789999999999999999999* PP

                  Myosin_tail_1 488 ssrlrqleeeknalkeqleeeeeakknvekqlstlqaqlsdl 529
                                     +r+++lee  +   e+l+  + a ++++ +l++l+ ++ ++
  gi|118431313|ref|NP_147686.2| 116 QARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    ************99****999999999999999998888775 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1    0.0013      0.12     223     287 ..      28      92 ..      14      96 .. 0.59
   2 ?    5.5   0.6     0.091       8.1     231     274 ..     101     143 ..      90     162 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0013
                           RmuC 223 aqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaekl.kelgvk 287
                                    a+ ++ + + ++++ l +++e++ e+le+++ ++e+++ ++++++++l ++i+ ++ k+ ++lg +
  gi|118431313|ref|NP_147686.2|  28 AIYQELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSL-ESIQDRVSKIeERLGSA 92 
                                    455555555555555666666666666666666666666666644444.78888888884446655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.091
                           RmuC 231 iaellgelydkfekfgedleklgkklekaqksydkavkklegni 274
                                    +a++l++l +++e +++++++l+++  +a + +d+++  l + +
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMAL-QDL 143
                                    4444444444444444444444444444444444333333.222 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 !   16.1   1.2     7e-05    0.0062     145     256 ..      36     154 ..      26     165 .. 0.36

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7e-05
                   Exonuc_VII_L 145 leeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq........lkkkrerlee 216
                                    l++q+e l+ r+e+   + lee +  +e+ + +++s  + le+ ++r++++eerl +a +++        l++ +++le 
  gi|118431313|ref|NP_147686.2|  36 LRSQVEGLNTRYEEIS-ESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSdldavareLASLTQQLED 114
                                    4444444444443322.233333333333333333333333344444444444443332222311111113333333333 PP

                   Exonuc_VII_L 217 lkerlk...ekleekkerlkklkerle....lleekkerleeleekl 256
                                    l++r++   e+ +e+ erl       +     l++ + rl++lee++
  gi|118431313|ref|NP_147686.2| 115 LQARIQaleESGAEAGERL-------DqlamALQDLQARLASLEERV 154
                                    3322211221112222222.......222223444444444444444 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 !   16.1   3.1   6.7e-05    0.0059     175     289 ..      45     154 ..      28     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.7e-05
                         HMMR_N 175 akekevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqle 254
                                    ++  e+s   e++++  ++   ++e+  + +  ++++ +++e+      + +  l +   el ++++qle  + +i++le
  gi|118431313|ref|NP_147686.2|  45 TRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEER-LGSAATQSDLDAVARELASLTQQLEDLQARIQALE 123
                                    44445555555555555555556666666666666666555554.555566678999999******************** PP

                         HMMR_N 255 ellkekndeiesLkssLeekeqelskqvkdlnekc 289
                                    e  +e+ + + +L  +L++ +  l     +l+e++
  gi|118431313|ref|NP_147686.2| 124 ESGAEAGERLDQLAMALQDLQARL----ASLEERV 154
                                    ******999999998888766543....3333333 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   5.9    0.0022       0.2      24     123 ..      61     152 ..      25     160 .. 0.40

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0022
                          Atg14  24 lyelrerlaklksekeslkkkiekalegke......eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                    +++ r ++ ++ s  es++ +++k++e+        + +  ++++ +++++              l+ l+++++ l ++ 
  gi|118431313|ref|NP_147686.2|  61 FESSRGDIESIASSLESIQDRVSKIEERLGsaatqsDLDAVARELASLTQQ--------------LEDLQARIQALEESG 126
                                    344444444555555555555555544444222222222222333333333..............333333333333333 PP

                          Atg14  98 eekkkklaklsdklkkRrsdleslqn 123
                                    +e+ ++l +l  +l + +++l+sl++
  gi|118431313|ref|NP_147686.2| 127 AEAGERLDQLAMALQDLQARLASLEE 152
                                    33333333333333333333333333 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   9.0   0.00024     0.022     156     274 ..      39     157 ..      28     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00024
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..-HHHHHHHHHHHHHHHHHHH CS
                       Filament 156 lvevdaarkldLteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrs..akeeitelrrqiqsleiele 233
                                    +ve  ++r  +++e l+e++  +e    ++r ++e+   s le +q+ ++k +e l s  +++++  + r++ sl+ +le
  gi|118431313|ref|NP_147686.2|  39 QVEGLNTRYEEISESLEEVQGAFE----SSRGDIESI-ASSLESIQDRVSKIEERLGSaaTQSDLDAVARELASLTQQLE 113
                                    556666667777777777777666....578888876.6779************9986225789**************** PP

                                    HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHH CS
                       Filament 234 slkkqkasleaqlaeleerl...eaeleklqeklseleeelaei 274
                                    +l++  ++le++ ae+ erl   +++l++lq+ l++lee + e+
  gi|118431313|ref|NP_147686.2| 114 DLQARIQALEESGAEAGERLdqlAMALQDLQARLASLEERVDEV 157
                                    **************99988622267999**********999886 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2      0.24        21      19      61 ..      32      88 ..      28      92 .. 0.56
   2 !   13.6   3.6   0.00078     0.069      15      65 ..     107     157 ..      98     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.24
                           ZapB 19 titlLqmeieeLkeeneelkeenrele..............eeneqlkeereawqer 61
                                   ++++L+ ++e L  + ee +e  +e++              +++e  ++  ++++er
  gi|118431313|ref|NP_147686.2| 32 ELASLRSQVEGLNTRYEEISESLEEVQgafessrgdiesiaSSLESIQDRVSKIEER 88
                                   456677777777777777777777777444444433333335555555555555555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00078
                           ZapB  15 kaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    ++ ++++ Lq +i++L+e  +e  e+ ++l   ++ l++  ++++er++ +
  gi|118431313|ref|NP_147686.2| 107 SLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    567788889999999999999999999999999999999988888888876 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   3.8   0.00078     0.069      11     122 ..      32     144 ..      28     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00078
                        DUF5082  11 qiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs.nlessyqtyvdkldel 89 
                                    + a+lrs++++l+    r +e +++l++++ ++++++ ++e ++ s es + + ++ ++   s  ++s+ +++ ++l +l
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNT---RYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSaATQSDLDAVARELASL 108
                                    44555555555553...4448999*****************************99999999889**************99 PP

                        DUF5082  90 idaiee...EIerLenqiseaqgvldtlqsqlnslk 122
                                     +++e+    I+ Le++  ea   ld+l ++l++l+
  gi|118431313|ref|NP_147686.2| 109 TQQLEDlqaRIQALEESGAEAGERLDQLAMALQDLQ 144
                                    9988754448************************96 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.9   0.00013     0.012     220     324 ..      32     150 ..      24     173 .. 0.47

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00013
                           FUSC 220 alrrllsrmlallallsslarllarlraeeaaavpelaallaelaal.......eaaaaaealeaalaalrarlralrra 292
                                     l++l+s++  l +++ ++ + l++++ + + ++ +++ +   l+++       e++  ++a++ +l+a+ ++l++l ++
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIqdrvskiEERLGSAATQSDLDAVARELASLTQQ 111
                                    45566666666666666666666666666665555544444444444444666633334444444444444444444444 PP

                           FUSC 293 le.......adadtaalllarlaellaelaqllaslral 324
                                    le       a  + +a++ +rl++l  +l++l+a l++l
  gi|118431313|ref|NP_147686.2| 112 LEdlqariqALEESGAEAGERLDQLAMALQDLQARLASL 150
                                    441111111222223333333333333333333333322 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.8    0.0019      0.17      57     118 ..      31      95 ..      28      98 .. 0.75
   2 ?    7.3   7.1     0.053       4.7      58     115 ..      97     157 ..      86     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0019
                     TPR_MLP1_2  57 kelqalreelnelkaeiaelkaeaesakaeleese...esweeqkeelekelselekriedlneq 118
                                    +el++lr++++ l+++++e+ +++e+++ ++e s+   es+++  e++++++s++e+r+    +q
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRgdiESIASSLESIQDRVSKIEERLGSAATQ 95 
                                    78999999999999999999999999999999998333455566667777888888887666666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.053
                     TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleesees...weeqkeelekelselekriedl 115
                                    +l a+  el++l++++++l+a+ ++++++ +e+ e    ++   + l+ +l++le+r++++
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERldqLAMALQDLQARLASLEERVDEV 157
                                    5555555555555555555555555554444444430003445677888888888888886 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 !   15.2   6.7   0.00016     0.014      22     144 ..      31     152 ..      28     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.00016
                       KASH_CCD  22 eenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnk..qlekenqs 99 
                                    +e ++L+ +ve  +   + ++e +ee ++   s+       ++++  le ++  v+++eE+  ++++q+    + +e  s
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSR---GDIESIASSLESIQDRVSKIEERLGSAATQSDldAVARELAS 107
                                    57889999999999999999999999999888865...56678999****************9999998622699***** PP

                       KASH_CCD 100 LiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhelee 144
                                    L++++e+Lq +++ l     e  ++l +L++  ++L+ +l +lee
  gi|118431313|ref|NP_147686.2| 108 LTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    *************99999999*******************99987 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 !   14.6   1.1   0.00021     0.019      12     122 ..      33     144 ..      25     161 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00021
                  PI3K_P85_iSH2  12 leklseklrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfs.keaqehEieklqenl 90 
                                    l+ l  + + ++  ++e s+++++++ ++++ + +i+     le  ++ ++  ee +   ++ s  +a  +E  +l+++l
  gi|118431313|ref|NP_147686.2|  33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSdLDAVARELASLTQQL 112
                                    33444444455555555555555555555555555555555555555555444444443333221244566666666666 PP

                  PI3K_P85_iSH2  91 eqlksrlkelhsskekLeedlkqqkeeerele 122
                                    e+l++r++ l++s ++  e l q +   + l+
  gi|118431313|ref|NP_147686.2| 113 EDLQARIQALEESGAEAGERLDQLAMALQDLQ 144
                                    66666666666665555555555444444443 PP

>> TBCC_N  Tubulin-specific chaperone C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   5.8   0.00035     0.031       3     108 ..      43     157 ..      41     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00035
                         TBCC_N   3 LekReqerqeqlekrkeereseaveeekvdsFlkaFteekaaieellesve.......esadksklkqkldeitaeiqeL 75 
                                    L+ R +e  e le+ + + es+  + e+++s l++++++  +iee+l s+         + + ++l+q+l++++a+iq+L
  gi|118431313|ref|NP_147686.2|  43 LNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAAtqsdldaVARELASLTQQLEDLQARIQAL 122
                                    88999999999999999999999999***********************9988888766777788999999999999999 PP

                         TBCC_N  76 qkllaessmfLpsY..dlrsaqealskLkesleea 108
                                    +++ ae+   L +    l+  q+ l +L+e+++e 
  gi|118431313|ref|NP_147686.2| 123 EESGAEAGERLDQLamALQDLQARLASLEERVDEV 157
                                    99999888888765114677777777777777776 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1       1.5   1.3e+02      73     135 ..      12      74 ..       2      90 .. 0.75
   2 ?   14.0   1.8   0.00032     0.029     110     163 ..      93     146 ..      68     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.5
                          TMP_2  73 ltlaAaavgalalAyykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaea 135
                                    +++a++a++ l++ +y   +e+ ++++++ +++      +++Le++  + +   g ++++a++
  gi|118431313|ref|NP_147686.2|  12 AGIAVVALIILGVGFYAIYQELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASS 74 
                                    677788999999999999999999999999998877777777777666655555555555544 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00032
                          TMP_2 110 lTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaeleka 163
                                    +T+s L+a+a+++a  +++ ++ ++ ++al ++G+ +ge+l+++a a  +l++ 
  gi|118431313|ref|NP_147686.2|  93 ATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQAR 146
                                    69999******************************************9999875 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   0.00028     0.025      67     166 ..      51     155 ..       8     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00028
                        UPF0242  67 kskleekeaklteldeglktkeealeelqeeeeeLkee..ldakeeelerlkeenqqLqekleaiae...dfeelklele 141
                                    ++ lee +    + + +++ ++ +le  q++  + +e+   +a ++ l    +e ++L ++le+ ++     ee+  e+ 
  gi|118431313|ref|NP_147686.2|  51 SESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERlgSAATQSDLDAVARELASLTQQLEDLQAriqALEESGAEAG 130
                                    23455555555566678888888999999999998888663344555555555555555555555552223566667788 PP

                        UPF0242 142 eqLaekqellqeyqetieeqrsvle 166
                                    e+L++    lq++q+ + ++ + ++
  gi|118431313|ref|NP_147686.2| 131 ERLDQLAMALQDLQARLASLEERVD 155
                                    8888888888888887776665554 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   6.4   0.00019     0.017     357     477 ..      37     154 ..      28     162 .. 0.35

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                        DUF3584 357 rseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrlkaaieealealesqlrkqleaqk 436
                                    rs++e l+ +++ + e+ ++vq +++  +  i+ + +  le +++r+ +i e      aa +++l+a+  +l   l +q 
  gi|118431313|ref|NP_147686.2|  37 RSQVEGLNTRYEEISESLEEVQGAFESSRGDIE-SIASSLESIQDRVSKIEERLGS--AATQSDLDAVARELA-SLTQQL 112
                                    333333444444444444444444444443332.2333333333333333333222..333333333333333.333333 PP

                        DUF3584 437 eelneeekelesrlselklrldsat.ateEeleqieeadeal 477
                                    e+l+ + + le++ +e+  rld+   a ++++ +++  +e++
  gi|118431313|ref|NP_147686.2| 113 EDLQARIQALEESGAEAGERLDQLAmALQDLQARLASLEERV 154
                                    333333333333333333333332202233333333333333 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 ?    6.9   0.2     0.081       7.2      64     102 ..      31      69 ..      27      73 .. 0.89
   2 ?   10.5   5.6     0.006      0.53      21     106 ..      61     145 ..      52     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.081
                    TMF_TATA_bd  64 keleelekeleelqeryetlLellGeksEeveELraDva 102
                                    +el++l++++e l++rye++ e l e +   e  r D++
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIE 69 
                                    68899*********************9999988888886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.006
                    TMF_TATA_bd  21 irrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraD 100
                                      +  g+++s+ ++le+++   ++++e  +   ++  +l++ ++el++l+++le+lq r ++l e   e  E+ ++L + 
  gi|118431313|ref|NP_147686.2|  61 FESSRGDIESIASSLESIQDRVSKIEER-LGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMA 139
                                    5555677777888888887766666555.5555677789999************************************** PP

                    TMF_TATA_bd 101 vaDlKe 106
                                    ++Dl +
  gi|118431313|ref|NP_147686.2| 140 LQDLQA 145
                                    ***986 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 ?    8.3   0.2     0.027       2.4      45     101 ..      40      96 ..      28     102 .. 0.81
   2 ?    7.7   8.4     0.039       3.5      11      86 ..      82     153 ..      74     159 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.027
                          DHR10  45 ieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqa 101
                                    +e    ++ee ++ l+e + a e+ + + + + +  e +q ++++ ee+l  +  q+
  gi|118431313|ref|NP_147686.2|  40 VEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQS 96 
                                    444456889999999999999999999999999999999999999999998887776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.039
                          DHR10  11 laelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrq 86 
                                    +++ E++     ++ d l+ v ++l+s++++le+++a +++lee+ +++ e    l+++   l++l+++ + l+ +
  gi|118431313|ref|NP_147686.2|  82 VSKIEERLGSAATQSD-LDAVARELASLTQQLEDLQARIQALEESGAEAGER---LDQLAMALQDLQARLASLEER 153
                                    5555555555544444.67788888888888888888888888877665543...333333444444444444444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   0.00097     0.086       6      87 ..      35     117 ..      30     126 .. 0.50
   2 ?   11.9   0.4    0.0011     0.096       3      95 ..      67     161 ..      66     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00097
                          TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkkvlke 84 
                                    +l+++++ l+++ +e+ ++lee++   ++ + +i++    l++++++++k++++++ + +++ ++ +++el++ +++l++
  gi|118431313|ref|NP_147686.2|  35 SLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGsAATQSDLDAVARELASLTQQLED 114
                                    55555555555555555555555555555555555555555555555555555543233444455555555555555554 PP

                          TMPIT  85 ves 87 
                                    +++
  gi|118431313|ref|NP_147686.2| 115 LQA 117
                                    443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0011
                          TMPIT   3 eweelekefkeleetakeykqkleelskl..qskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                    ++e++++++++++++ ++++++l + +++   +++++e+++ +++l++l+++++ l++s ++e  e++++l+  l++ ++
  gi|118431313|ref|NP_147686.2|  67 DIESIASSLESIQDRVSKIEERLGSAATQsdLDAVARELASLTQQLEDLQARIQALEES-GAEAGERLDQLAMALQDLQA 145
                                    5789999999******9999999776554116799**********************99.57899999999999999999 PP

                          TMPIT  81 vlkevesllpkk.ngl 95 
                                     l+++e+   +   +l
  gi|118431313|ref|NP_147686.2| 146 RLASLEERVDEVyASL 161
                                    9888887665555555 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.6   0.00033     0.029     152     283 ..      32     157 ..      26     161 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00033
                       CCDC144C 152 qLskaeskansLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnkyiakqe..sleerlaqlqse 229
                                    +L+       sL  +++ +++ + e +  le+vq   + ++  i  + + +++ +++v+k  ++    +++  l  + +e
  gi|118431313|ref|NP_147686.2|  32 ELA-------SLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGsaATQSDLDAVARE 104
                                    444.......4444444444444444444555555555555555555555555555555555543300456778888888 PP

                       CCDC144C 230 nmlLrqqLedaqnkadakekvvidiqdqfqdivkkLqaesekqvllleernkeL 283
                                     + L qqLed q + +a e    ++ +++++    Lq + + +   leer  e+
  gi|118431313|ref|NP_147686.2| 105 LASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQ-DLQARLASLEERVDEV 157
                                    8888888888888888888888888888866666655.6666777777776665 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   7.6   0.00037     0.033      47     180 ..      31     156 ..      28     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00037
                      Laminin_I  47 kelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlneneealpssklseelae 126
                                    +el sL +++e L ++ ++ +++ ++v+ + e   + +++ a   + ++d ++ i e+       ++a+ +s+l++   e
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL------GSAATQSDLDAVARE 104
                                    57788888888888888888888888888888888888888888888888888888887......77999********** PP

                      Laminin_I 127 aqrlLeelrsRdftkqleeaeaelkaAqkLLsrvqtllqklqeenkaLkealrd 180
                                      +l ++l   d+++  ++ e+  ++A + L +    lq lq+ + +L+e + +
  gi|118431313|ref|NP_147686.2| 105 LASLTQQL--EDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    ********..89************************************998865 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.068       6.1      67     136 ..      31     100 ..      28     106 .. 0.89
   2 ?    9.7   1.9    0.0096      0.86      58     109 ..     101     152 ..      96     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.068
                           ADIP  67 aeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqyahel 136
                                     e+++l+s++e l t++e+    l+ vq +  + + ++++  + l + ++ +++ +  l + +tq   + 
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDA 100
                                    578999999***********************************************99999999987665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0096
                           ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleq 109
                                    +++++ +l+  +e lq++i+ l+++ ++   +l+++  ++++l+++l++le+
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    4556666667777777777777777777777777777777777777777665 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 ?   12.6  11.6    0.0015      0.13       4     105 ..      55     156 ..      28     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0015
                    Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEld 83 
                                    +e++   +s +   e+  ++l+s ++++ + e+    +a +s  + +  e  +l+++le+l+a++++ +e+  e+ + ld
  gi|118431313|ref|NP_147686.2|  55 EEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLD 134
                                    45555555555566666777777777777777775555667778899999999999****************99999*** PP

                    Uso1_p115_C  84 DLLlllgDleeKvekykarLke 105
                                     L + l Dl+++++++++r  e
  gi|118431313|ref|NP_147686.2| 135 QLAMALQDLQARLASLEERVDE 156
                                    ******************9876 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3       2.2   1.9e+02      18      40 ..      32      55 ..      27      88 .. 0.62
   2 ?    6.9   4.3     0.069       6.1      13      68 ..      69     122 ..      57     124 .. 0.67
   3 ?   11.2   4.4    0.0031      0.27       6      69 ..      92     151 ..      88     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 2.2
                           FlxA 18 qiasLqkQiknlqkqLkelses.d 40
                                   ++asL+ Q++ l+   +e+ses +
  gi|118431313|ref|NP_147686.2| 32 ELASLRSQVEGLNTRYEEISESlE 55
                                   566777777777777777766642 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.069
                           FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaql 68 
                                    +++as ++s+q  ++++++ L + +++++l++         + +Q+++lqa I+ l
  gi|118431313|ref|NP_147686.2|  69 ESIASSLESIQDRVSKIEERLGSAATQSDLDAV--ARELASLTQQLEDLQARIQAL 122
                                    567888888888888888888888888444444..444556666666666666655 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0031
                           FlxA   6 asssssssgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlq 69 
                                    a+++s  +  a ++asL++Q+++lq  ++ l es ++      ++ +++   +q+lqa +a l+
  gi|118431313|ref|NP_147686.2|  92 AATQSDLDAVARELASLTQQLEDLQARIQALEESGAEA----GERLDQLAMALQDLQARLASLE 151
                                    55555556678888999999999999999999993333....3466666777777777776654 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4      0.15        14       5      70 ..      31      91 ..      28      98 .. 0.61
   2 ?   12.2   4.4    0.0018      0.16       1      63 [.      99     156 ..      99     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.15
                           FliJ  5 reLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaq 70
                                   +eLa+ + +++  + + ee+ + ++e q  ++++       ++  + + +++++++++++++ l  
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSR-----GDIESIASSLESIQDRVSKIEERLGS 91
                                   56666666666666666666666666666666666.....66666666666666666666665554 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0018
                           FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaq 63 
                                    d+ areLa+  ++l++ ++++++le+  +e  ++l + a      +l+ +qa +++l+e++++
  gi|118431313|ref|NP_147686.2|  99 DAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLA-----MALQDLQARLASLEERVDE 156
                                    6889**********************************9.....9*************99886 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       9.1   8.1e+02      22      40 ..      38      56 ..      35      59 .. 0.84
   2 ?   12.9   0.8   0.00084     0.075      19      43 ..     100     124 ..      99     125 .. 0.92
   3 ?    4.3   0.4       0.4        36      22      44 ..     131     153 ..     127     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 9.1
                                   HHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil 22 seiqaLtqkLeavtkRlea 40
                                   s+++ L+++ e++++ le 
  gi|118431313|ref|NP_147686.2| 38 SQVEGLNTRYEEISESLEE 56
                                   678899*******998886 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00084
                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil  19 kVeseiqaLtqkLeavtkRlealEn 43 
                                    +V  e+ +Ltq+Le+   R++alE 
  gi|118431313|ref|NP_147686.2| 100 AVARELASLTQQLEDLQARIQALEE 124
                                    688999*****************95 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil  22 seiqaLtqkLeavtkRlealEnk 44 
                                    +++++L   L +   Rl+ lE +
  gi|118431313|ref|NP_147686.2| 131 ERLDQLAMALQDLQARLASLEER 153
                                    78999999*************98 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 ?   14.4   1.6   0.00033     0.029      53     125 ..      48     116 ..      28     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00033
                         Phasin  53 kvaeekleevresvkskveevkekaeeqwdklekafdervakaLsrlg.vpsredveaLsarvdeLtkelekla 125
                                    +++ e+le    +v+ ++e+ +  +e+  ++le+ +++rv+k+ +rlg  ++++d++a+++++ +Lt++le l+
  gi|118431313|ref|NP_147686.2|  48 EEISESLE----EVQGAFESSRGDIESIASSLES-IQDRVSKIEERLGsAATQSDLDAVARELASLTQQLEDLQ 116
                                    33444444....4444555555555555677776.5789********9457999***************99876 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.21        19     337     383 ..      31      77 ..      27      78 .. 0.90
   2 ?   11.4   6.9    0.0017      0.15     208     282 ..      73     153 ..      67     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.21
                      Dynamitin 337 qtLteleeeqkeiseelkslkelLekveeslkenletvkkNveslee 383
                                    q L+ l ++ + +++  ++ +e Le+v+ ++++++  +++  +sle+
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLES 77 
                                    789999999999999********************999998888875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0017
                      Dynamitin 208 akiaelekRLaeLEklvGlssesldelsanlk.prplletlsrLeaklslL......qtahLDaierRlksllaeldela 280
                                    +++ ++  R++++E+ +G+  ++ ++l+a     ++l+++l++L+a++++L        + LD++   l+ l a+l +l+
  gi|118431313|ref|NP_147686.2|  73 SSLESIQDRVSKIEERLGSAATQ-SDLDAVAReLASLTQQLEDLQARIQALeesgaeAGERLDQLAMALQDLQARLASLE 151
                                    56777889999999999998876.44444443389999999999999999977666555678888888888888888887 PP

                      Dynamitin 281 ek 282
                                    e 
  gi|118431313|ref|NP_147686.2| 152 ER 153
                                    75 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.0    0.0011       0.1      22     153 ..      39     156 ..      27     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0011
                        DUF4763  22 qseqldveeeisseselpaeqe.eeeeeldLdeiydelekiKqrvlelrskLalnvpecPeidecvdedlelelltseqp 100
                                    q+e+l++  e  ses ++  q   e++  d+++i   le i  rv++++++L+               + +l++   +  
  gi|118431313|ref|NP_147686.2|  39 QVEGLNTRYEEISESLEE-VQGaFESSRGDIESIASSLESIQDRVSKIEERLGSA-----------ATQSDLDA---VAR 103
                                    566666655555555343.44559*****************************44...........22222222...446 PP

                        DUF4763 101 eileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlne 153
                                    e+  L ++   L+ +++ l+++  +  + l +l + l+ ++ rl++l++r +e
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    67778888888888888888888888888888888888888888888877776 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.1    0.0023      0.21      21     101 ..      61     142 ..      15     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0023
                           SesA  21 ikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapapad..srleryrka 98 
                                     ++ +  ++ ++++L+ +q+  ++++++l s+  ++d ++ +   l+s  ++++ l++  ++++++ a+  +rl++   a
  gi|118431313|ref|NP_147686.2|  61 FESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDA-VARELASLTQQLEDLQARIQALEESGAEagERLDQLAMA 139
                                    5555666677888888888888888888888888887554.888888888888888888888855544444787888888 PP

                           SesA  99 vrs 101
                                    ++ 
  gi|118431313|ref|NP_147686.2| 140 LQD 142
                                    765 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 ?    9.1   0.2     0.017       1.5      32      93 ..      27      92 ..      25      98 .. 0.78
   2 ?    7.6   4.5     0.048       4.3      16      94 ..      83     158 ..      67     163 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 32 leldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkel 93
                                   ++++++  +l++++e l+++  e+s++ ++   +      d+e++  + ++++++++++e++l  +
  gi|118431313|ref|NP_147686.2| 27 YAIYQELASLRSQVEGLNTRYEEISESLEEVQGAFessrGDIESIASSLESIQDRVSKIEERLGSA 92
                                   67899999*****************99998887654556777777777777777777777777655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.048
                                    HHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  16 eklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkele 94 
                                     k+++R +++a+  +l ++ ++  +l ++le+lqa+  +l ++ ++a    e  ++l    ++l+++l+ le++++e+ 
  gi|118431313|ref|NP_147686.2|  83 SKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAG---ERLDQLAMALQDLQARLASLEERVDEVY 158
                                    233444455555555555556666666666666666655555443333...4456666666666666666666666665 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 ?    7.3   0.4      0.06       5.4      15      70 ..      34      89 ..      26      90 .. 0.83
   2 ?    7.1   0.2     0.067         6      41      68 ..      97     124 ..      94     126 .. 0.89
   3 ?    0.9   0.0         6   5.4e+02      45      64 ..     136     155 ..     130     161 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.06
                       JIP_LZII 15 teLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70
                                   + L+   + Ln+  +++ + ++e +   e+ r ++es+ +++e++++r++++Ee l
  gi|118431313|ref|NP_147686.2| 34 ASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89
                                   55666666677777888888999999999************************976 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.067
                       JIP_LZII  41 ereiLreEleslqkakerlesrikelEe 68 
                                    + +++  El sl++++e l+ ri++lEe
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEE 124
                                    5667889********************8 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 6
                       JIP_LZII  45 LreEleslqkakerlesrik 64 
                                    L + l+ lq+ +++le+r+ 
  gi|118431313|ref|NP_147686.2| 136 LAMALQDLQARLASLEERVD 155
                                    44445555555555555555 PP

>> BLOC1S3  Biogenesis of lysosome-related organelles complex 1 subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1     0.013       1.2     106     166 ..      37      96 ..      32     102 .. 0.86
   2 ?    4.4   0.4      0.42        38     120     162 ..     101     143 ..      92     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.013
                        BLOC1S3 106 rkdvkeavsqvysaaskelesvtsqLnksqsaiqnashsirlilddlkavsekldiitscs 166
                                    r+ v e ++  y++ s+ le+v+    +s+  i+ +++s+ +i+d++ +++e+l + +++s
  gi|118431313|ref|NP_147686.2|  37 RSQV-EGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQS 96 
                                    5555.457788******************************************98877665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.42
                        BLOC1S3 120 askelesvtsqLnksqsaiqnashsirlilddlkavsekldii 162
                                      +el+s+t+qL   q+ iq    s   + ++l++++ +l+++
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDL 143
                                    5799********************************9999986 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.9   0.00054     0.048     338     448 ..      31     143 ..      21     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00054
                           Cast 338 qRAaiLqtevdalrlrleekeqlLnkktkqlqdlteekstlageirdlkdml.dvkeRkvnvl.qkkienLqeqlrdkdk 415
                                    q  a L + v+ l++r+ee  + L++ +  +++ + +  ++a+ ++ ++d + +++eR      q+ ++ +   l    +
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVsKIEERLGSAAtQSDLDAVARELASLTQ 110
                                    7778899******************************************987257777654435999************* PP

                           Cast 416 qlaelkervkslqtDssntDtALatleeaLsek 448
                                    ql++l+ r+++l++  +++   L  l  aL + 
  gi|118431313|ref|NP_147686.2| 111 QLEDLQARIQALEESGAEAGERLDQLAMALQDL 143
                                    *************99999888888888888775 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.9   0.00073     0.065      12      71 ..     102     161 ..      94     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00073
                           TBCA  12 vKEeasYekEleeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekL 71 
                                    ++E as  + le+ +ar++ l++ g+e   +l +   +l++ +a +  l++r+++ +++L
  gi|118431313|ref|NP_147686.2| 102 ARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVYASL 161
                                    68999******************9977799*************************99987 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.3   0.00073     0.065      31     128 ..      58     153 ..      30     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00073
                                    HHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HBM  31 RlqyelsngdataaavqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaer 110
                                    +  +e+s+gd   + +  +l+ +++ + k+++++ s++++ +L++ +  ++ + +++++l+a +++ +++ +e  ++ ++
  gi|118431313|ref|NP_147686.2|  58 QGAFESSRGDI--ESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQ 135
                                    55677777764..5688999999999999999999999999999999999999999999999999999999999999999 PP

                                    HHHHHHHHHHHHHCS-S- CS
                            HBM 111 aleaideleaevlqtpea 128
                                    +  a++ l+a+++ + e 
  gi|118431313|ref|NP_147686.2| 136 LAMALQDLQARLASLEER 153
                                    999999999888776554 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0      0.14        12      35      66 ..      52      83 ..      38      86 .. 0.91
   2 ?    7.1   1.1     0.065       5.8      39      66 ..      93     120 ..      87     123 .. 0.86
   3 ?    4.4   0.4      0.46        41      46      64 ..     128     146 ..     120     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.14
                            HR1 35 kvrqeaeselsesnskielLreqLeelqasvq 66
                                   ++++e++   ++s+  ie + ++Le +q++v+
  gi|118431313|ref|NP_147686.2| 52 ESLEEVQGAFESSRGDIESIASSLESIQDRVS 83
                                   589*************************9875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.065
                            HR1  39 eaeselsesnskielLreqLeelqasvq 66 
                                    + +s l+   ++++ L++qLe+lqa+ q
  gi|118431313|ref|NP_147686.2|  93 ATQSDLDAVARELASLTQQLEDLQARIQ 120
                                    5688899999***************876 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.46
                            HR1  46 esnskielLreqLeelqas 64 
                                    e+  ++++L ++L++lqa+
  gi|118431313|ref|NP_147686.2| 128 EAGERLDQLAMALQDLQAR 146
                                    45569************96 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 ?   11.4   4.1     0.004      0.36       3      72 ..      61     127 ..      25     137 .. 0.68
   2 ?    8.7   1.1     0.029       2.6       6      60 ..     101     157 ..      99     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.004
                   Syntaxin-6_N   3 FfevkeeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknps 72 
                                    F + + ++++ ++++es+ +r +++ e      s   ++  + + ++l s+ ++ledL+  ++++e++ +
  gi|118431313|ref|NP_147686.2|  61 FESSRGDIESIASSLESIQDRVSKIEERL---GSAATQSDLDAVARELASLTQQLEDLQARIQALEESGA 127
                                    33444455555555555555554444433...34444445555566778999***********9998765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.029
                   Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledL 60 
                                    v++e  +  +++e l +r + l e++ +  ++ ++l  + ++L++ l s+e+ +++ 
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEagERLDQLAMALQDLQARLASLEERVDEV 157
                                    566666666777777777777666666654467777777777777777777777765 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2    0.0065      0.58      23      98 ..      46     121 ..      25     124 .. 0.91
   2 ?    6.2   0.1       0.2        17      27      73 ..     101     147 ..      92     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0065
                   Occludin_ELL  23 eYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklike 98 
                                    +Y e+ ++leev+  f+  + ++++ + + + +++++++i +++ +   +++  +  +++  L ++L+ + ++i+ 
  gi|118431313|ref|NP_147686.2|  46 RYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQA 121
                                    6999999999999999999999999999999999999999999999999999999999999999999999999986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.2
                   Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdp 73 
                                    + +el+++++++++L++++++l+e+  e  ++ +++   +++l+   
  gi|118431313|ref|NP_147686.2| 101 VARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARL 147
                                    45677777777788888888887777777777777777777776544 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.4    0.0044      0.39      10     125 ..      28     150 ..      22     162 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0044
                        DUF2408  10 piyekLvsirrsLlslaakskaeeakesee.............vkeelkelkeeLkkieskrdeegkFkseegke...vv 73 
                                    +iy++L s+r ++  l+++ ++ +++ +e              ++++l++++++++kie++  +        +++   +v
  gi|118431313|ref|NP_147686.2|  28 AIYQELASLRSQVEGLNTRYEEISESLEEVqgafessrgdiesIASSLESIQDRVSKIEERLGS------AATQSdldAV 101
                                    6899999999999999999988744444437888885555555555555555555555554444......3332200144 PP

                        DUF2408  74 ekgqavlngLlddcfdlvedlkaqdgeekkvasslqpiYdrLleikttLenL 125
                                     ++ a l + l+d    ++ l+++     +  ++l+++   L++++  L +L
  gi|118431313|ref|NP_147686.2| 102 ARELASLTQQLEDLQARIQALEES---GAEAGERLDQLAMALQDLQARLASL 150
                                    444444444445555555555444...3566666666666666666666555 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 ?   12.0   1.4    0.0019      0.17      26     108 ..      31     113 ..      25     114 .. 0.88
   2 ?    7.1   4.6     0.063       5.6      26      79 ..     103     156 ..      67     162 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0019
                          Mod_r  26 pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspdallarLqtava 105
                                    +e+ +l+++ e l +  e++ e+  + +  +e  r ++++  ++l+++++++ + e++l ++  + ++da+ + L   ++
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQ 110
                                    56778999999999999999998888899******************************999999999999999999888 PP

                          Mod_r 106 eae 108
                                    + e
  gi|118431313|ref|NP_147686.2| 111 QLE 113
                                    877 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.063
                          Mod_r  26 pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefee 79 
                                     e+ +l++++e+l a +++l e+  +  ++l++l   lq+    l++le++++e
  gi|118431313|ref|NP_147686.2| 103 RELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    223344444444444444444444444444444444444444444444444444 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 ?    0.7   0.0       4.7   4.2e+02      20      62 ..      33      79 ..      28      87 .. 0.50
   2 ?   11.3   0.7    0.0026      0.23       3      68 ..      82     150 ..      80     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 4.7
                     Phage_GP20 20 ldeveeerdtlkeqlkdrdkqLed....LkkkakdneeLqkqieelq 62
                                   l+++ ++++ l+++ ++  ++Le+    ++ + +d e++   +e++q
  gi|118431313|ref|NP_147686.2| 33 LASLRSQVEGLNTRYEEISESLEEvqgaFESSRGDIESIASSLESIQ 79
                                   44555555555555555555555422223444455555555555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0026
                     Phage_GP20   3 ikkvmkaengkditkakldeveeerdtlkeqlkdrdkqLedLkkkakdn....eeLqkqieelqaknkka 68 
                                    + k+  +  g+  t+++ld v  e  +l++ql+d +  ++ L+++  ++    ++L  ++++lqa ++  
  gi|118431313|ref|NP_147686.2|  82 VSKIE-ERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAgerlDQLAMALQDLQARLASL 150
                                    56776.888899999****************************995544111144555666666665554 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   0.2   0.00074     0.066     217     319 ..      18     134 ..       5     154 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00074
                         DUF677 217 avPleavgkwva................sawkkyeealkrqkeivssmekgievakkdvenisilverleseiksilktv 280
                                    a+ + +vg + a                +++++  e+l   +++ +s +  ie     +e+i+  v+++e +  s   + 
  gi|118431313|ref|NP_147686.2|  18 ALIILGVG-FYAiyqelaslrsqveglnTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQS 96 
                                    33344444.22234445322222222225555556666666666666666666666666666666666666665555555 PP

                         DUF677 281 e.fAvekeeneaavklaleeikkkvekltekieevgeeaa 319
                                    + +Av +e   a+  + le+++  ++ l e   e ge+ +
  gi|118431313|ref|NP_147686.2|  97 DlDAVAREL--ASLTQQLEDLQARIQALEESGAEAGERLD 134
                                    434555544..55566666666666666665555555555 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7    0.0013      0.12       7      75 ..      43     113 ..      35     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0013
                        DUF4363   7 lkkstdelsekleeleeai..enedweeakekleelekeWekkkkklsifiehdeldeietslaklkayie 75 
                                    l++ ++e+se+lee++ a   + +d e+ ++ le+++++ +k ++ l      ++ld +  +la+l++ +e
  gi|118431313|ref|NP_147686.2|  43 LNTRYEEISESLEEVQGAFesSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLE 113
                                    6788999999999999999778899*****************************************99766 PP

>> Tmemb_cc2  Predicted transmembrane and coiled-coil 2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.1    0.0031      0.28     186     274 ..      64     155 ..      31     159 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0031
                      Tmemb_cc2 186 ssssvesssadsnsnseestasasksaesesqeklekileelqeikeeqerleeelerlkeqlkkel...kllkqaLqee 262
                                    s  ++es++++ +s ++  ++ +++  ++ +q++l+++ +el+++ ++ e l++++++l+e+  +     + l++aLq+ 
  gi|118431313|ref|NP_147686.2|  64 SRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGerlDQLAMALQDL 143
                                    22222222222222222222222344445555555566666666665555555555555543322222225556666666 PP

                      Tmemb_cc2 263 ryryerLEeqln 274
                                    + r   LEe ++
  gi|118431313|ref|NP_147686.2| 144 QARLASLEERVD 155
                                    666666666655 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6    0.0049      0.43      77     175 ..      31     133 ..      27     135 .. 0.70
   2 ?    8.2   0.5     0.021       1.8      84     137 ..      96     149 ..      90     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0049
                        DUF4201  77 halthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg....llrvPaLlkDYdktke 152
                                    ++l+ l+     l++ ++e  ++l+e +   ++ r  +++     + ++++ +k+++++g    + +  a+ ++     +
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGsaatQSDLDAVARELASLTQ 110
                                    88899999999999999999999999988888877777766666666655555555555511115566777777777777 PP

                        DUF4201 153 kveekrksvkkLrrkvkilemrl 175
                                    ++e+++++++ L+++  ++ +rl
  gi|118431313|ref|NP_147686.2| 111 QLEDLQARIQALEESGAEAGERL 133
                                    77777777777777777776665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.021
                        DUF4201  84 eklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggl 137
                                      l+++++el+ l ++l+++++r+++l+++  ++ ++ d+l    ++l+++++ 
  gi|118431313|ref|NP_147686.2|  96 SDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLAS 149
                                    567889999999999999999999999999999999999999999999888765 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.4   0.00073     0.065      99     213 ..      33     154 ..      29     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00073
                            MAD  99 laearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqli......qqlekkqkelaeaeqri 172
                                    la++r   + l+ + +e  +++e+ + ++++ + ++e++   l+  + ++s++e++       ++l++  +ela   q++
  gi|118431313|ref|NP_147686.2|  33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLgsaatqSDLDAVARELASLTQQL 112
                                    56666667778888899999999999999999999999999999999999999999888888888999999999999999 PP

                            MAD 173 keLefeiqsqeddslivknsksel.aripelekelerlreen 213
                                     +L+ +iq  e++ ++  +  ++l + + +l++ l+ l+e+ 
  gi|118431313|ref|NP_147686.2| 113 EDLQARIQALEESGAEAGERLDQLaMALQDLQARLASLEERV 154
                                    999999999888888887777777788888888888888875 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.3     0.028       2.5      27     104 ..      48     134 ..      26     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.028
                                    SSCSSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHH......HHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  27 edlgkdleevqallk....khkaleaelaaqqervkaln......elaeklldeghsaseeieerleelnerWeeLkela 96 
                                    e+++++leevq   +    + + +   l++ q+rv +++      +++++l d+   + + ++++le+l+ r ++L+e  
  gi|118431313|ref|NP_147686.2|  48 EEISESLEEVQGAFEssrgDIESIASSLESIQDRVSKIEerlgsaATQSDL-DAVARELASLTQQLEDLQARIQALEESG 126
                                    666788888888888888888888888888888888888766644444444.5556777888888888888888888887 PP

                                    HHHHHHHH CS
                       Spectrin  97 aerkqkLe 104
                                    ae  ++L 
  gi|118431313|ref|NP_147686.2| 127 AEAGERLD 134
                                    77777775 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1     0.017       1.5     101     159 ..      35      93 ..      27     103 .. 0.73
   2 ?    4.8   4.2      0.24        21     100     157 ..      99     156 ..      91     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.017
                         DUF745 101 qaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkear 159
                                    + ++q+e l++ +++++e+le+++ + +++  ++++ ++ le+ + Rv +++++l +a 
  gi|118431313|ref|NP_147686.2|  35 SLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAA 93 
                                    55677788888888888888888888888888888888888888888888888876664 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.24
                         DUF745 100 kqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlke 157
                                    + + ++l++l++ l+  +++++ +e+  a+a + l++ ++ l++ ++R+++L+++++e
  gi|118431313|ref|NP_147686.2|  99 DAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    4445556666666666666666666666666666666666666666666666666554 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 ?    5.2   0.2      0.24        22      31      54 ..      30      53 ..      26      76 .. 0.84
   2 ?   10.5   8.1    0.0054      0.48       1      70 [.      77     141 ..      77     146 .. 0.90
   3 ?    2.5   6.4       1.7   1.5e+02       2      42 ..     115     155 ..     107     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.24
                  TolA_bind_tri 31 qqelreLRGqiEelqyqleqleer 54
                                    qel++LR q+E l+ + e++ e 
  gi|118431313|ref|NP_147686.2| 30 YQELASLRSQVEGLNTRYEEISES 53
                                   589999999999999998888765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0054
                  TolA_bind_tri   1 sledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkle 70 
                                    s++drv+++E+ l +        q+ l+a  +el++L  q+E+lq +++ lee   +  + lD++  +l+
  gi|118431313|ref|NP_147686.2|  77 SIQDRVSKIEERLGS-----AATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQ 141
                                    5799*********99.....7899*****************************99999999999887776 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 1.7
                  TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiE 42 
                                    l++r++ LE+  +   + l +l + l++lq+ l++L   ++
  gi|118431313|ref|NP_147686.2| 115 LQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVD 155
                                    67888888888888888888888888888888888865555 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.5   0.00068      0.06      29     111 ..      61     155 ..      57     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00068
                          Muted  29 FEekRgdrev..elLenikklvnelkeqllpkcles...........mkenLselnkkleaalekverllqkeleeekrk 95 
                                    FE+ Rgd e+  ++Le+i+  v++++e+l    ++s           + ++L++l+++++a+ e+  +  ++ l++  + 
  gi|118431313|ref|NP_147686.2|  61 FESSRGDIESiaSSLESIQDRVSKIEERLGSAATQSdldavarelasLTQQLEDLQARIQALEESGAEAGER-LDQLAMA 139
                                    9******9974468**************99999998777744444444444444444444444444444444.4444444 PP

                          Muted  96 seqlqekeeerkaewe 111
                                     ++lq++   ++++++
  gi|118431313|ref|NP_147686.2| 140 LQDLQARLASLEERVD 155
                                    4444444444444443 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2      0.47        42      62     100 ..      52      90 ..      49      96 .. 0.83
   2 ?    4.7   0.3      0.31        28      61      99 ..     123     161 ..     120     163 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.47
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelkeelq 100
                                    e +ee++   e+    i+++ ++le+++ ++++++e l 
  gi|118431313|ref|NP_147686.2|  52 ESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLG 90 
                                    667888899999999999999999999999999999875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                    ee  +e  er+++l + ++ l+ +l +le++++e+ ++l
  gi|118431313|ref|NP_147686.2| 123 EESGAEAGERLDQLAMALQDLQARLASLEERVDEVYASL 161
                                    455555666777777777777777777777777766555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2      0.17        15      46      92 ..      33      79 ..      28      90 .. 0.46
   2 ?   11.2   5.2    0.0019      0.17      13      77 ..      93     157 ..      88     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.17
                        DUF3450 46 kqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92
                                    ++l ++++ l+++ e+++   e+++   +s + +i+s+  ++e+i+
  gi|118431313|ref|NP_147686.2| 33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQ 79
                                   33344444444444444444444444444444444444444444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0019
                        DUF3450  13 alaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasq 77 
                                    a +++ld++  e ++ +++ ++ q++i++l++  +e  +++ +l   l++l++  + le+ v+++
  gi|118431313|ref|NP_147686.2|  93 ATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    33667777777777777777777777777777777777777777777777777777777666654 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 ?    8.1   0.2     0.047       4.2      43      89 ..      43      89 ..      28      93 .. 0.78
   2 ?    8.3   3.0     0.039       3.5      50      93 ..      94     137 ..      84     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.047
                 HIP1_clath_bdg 43 aerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssql 89
                                    + + ee +e le+++  +e++r +++++ ssLes +   ++++++l
  gi|118431313|ref|NP_147686.2| 43 LNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89
                                   456678889999999999999*******9999999998888777666 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.039
                 HIP1_clath_bdg  50 qkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                     ++ l+++ rel++  ++l+ l++ ++  e+sg++  ++l++L 
  gi|118431313|ref|NP_147686.2|  94 TQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLA 137
                                    57789999999999999999999999999999999999999886 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0    0.0017      0.15      30      99 ..      52     123 ..      32     128 .. 0.86
   2 ?    5.0   1.0     0.067         6      38      94 ..      97     153 ..      83     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0017
                           COG6  30 kineefleefqpvaeqLkriesdveklnelcdemkkklssakeet..sdlleeaeeLkeekkklelkqkllk 99 
                                    ++ ee+  +f+  +  +++i s++e++++ +++++++l sa +++  + + +e ++L++++++l+ + + l+
  gi|118431313|ref|NP_147686.2|  52 ESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSdlDAVARELASLTQQLEDLQARIQALE 123
                                    4557788889999999**********************99988887799***************99988876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.067
                           COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelk 94 
                                    ++++va++L ++ +++e+l++ ++ ++++  +a e+ ++l    ++L++++++le++
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEER 153
                                    667777777778888888888888887777777777777777777777777777776 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3      0.41        36      18      43 ..      31      56 ..      27      76 .. 0.77
   2 ?    9.7   1.6     0.011      0.96      10      43 ..      95     128 ..      86     135 .. 0.84
   3 ?    4.6   0.3      0.42        37      11      37 ..     131     157 ..     128     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.41
                          Spc24 18 selesleselaelkeeleeleeesee 43
                                   +el sl+s+ + l++++ee++e+ ee
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEE 56
                                   68899999999999999999998888 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.011
                          Spc24  10 akelsdleselesleselaelkeeleeleeesee 43 
                                    + +l+ + +el sl+++l++l+++++ lee++ e
  gi|118431313|ref|NP_147686.2|  95 QSDLDAVARELASLTQQLEDLQARIQALEESGAE 128
                                    5567788899********************9998 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.42
                          Spc24  11 kelsdleselesleselaelkeeleel 37 
                                    + l++l ++l++l+++la+l+e+++e+
  gi|118431313|ref|NP_147686.2| 131 ERLDQLAMALQDLQARLASLEERVDEV 157
                                    568899999999999999999999987 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       1.4   1.2e+02       3      30 ..      31      58 ..      28      71 .. 0.66
   2 ?    0.9   0.0       3.5   3.1e+02       3      25 ..      73      95 ..      71     105 .. 0.82
   3 ?    6.5   0.2     0.069       6.2       1      48 [.     108     156 ..     108     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 1.4
                        DUF4988  3 ddvndlkdrvaaleeqvkelndniealk 30
                                   +++ +l+++v+ l+++++e+ +++e ++
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQ 58
                                   4556666666666666666666666554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 3.5
                        DUF4988  3 ddvndlkdrvaaleeqvkelndn 25
                                   + +++++drv+ +ee++ +  ++
  gi|118431313|ref|NP_147686.2| 73 SSLESIQDRVSKIEERLGSAATQ 95
                                   678999********999887665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.069
                        DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkll.eegkviteveensdg 48 
                                    l ++++dl+ r++alee   e  + +++l+  l + +  + ++ee+ d 
  gi|118431313|ref|NP_147686.2| 108 LTQQLEDLQARIQALEESGAEAGERLDQLAMALqDLQARLASLEERVDE 156
                                    67899***********999999999998876552445556666666666 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 ?   12.3   1.2    0.0013      0.12      54     128 ..      48     124 ..      22     136 .. 0.80
   2 ?    3.3   0.1      0.78        70      76     121 ..     107     152 ..     102     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0013
                   Sec8_exocyst  54 eaLqevvnehhqaFnssiasYskilssiqesqekvselKesleea..kkklstkkkeLkelnarsakykevieiLda 128
                                    e++ e  +e + aF ss +  ++i ss+++ q++vs++ e+l +a  +++l +   eL  l ++   ++  i+ L++
  gi|118431313|ref|NP_147686.2|  48 EEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAatQSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    3444555666899*****************************765226789999************99999999985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.78
                   Sec8_exocyst  76 kilssiqesqekvselKesleeakkklstkkkeLkelnarsakyke 121
                                    ++ +++++ q ++++l es +ea + l +    L++l+ar a ++e
  gi|118431313|ref|NP_147686.2| 107 SLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    56788999999**************************999877665 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.092       8.2     321     367 ..      43      89 ..      28      98 .. 0.56
   2 ?    9.5   1.4    0.0044      0.39     329     381 ..     102     154 ..      91     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.092
                         DUF812 321 eeelkkkreeeleelqeqieeleskieeleeeikklessikqveeel 367
                                     + + ++ +e+lee+q  +e+ + +ie++++ +++++++++++ee l
  gi|118431313|ref|NP_147686.2|  43 LNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89 
                                    33334444555666666666666666666666666666666666554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0044
                         DUF812 329 eeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekev 381
                                     +el++l +q+e+l+++i++lee  ++  +++ q+  +l+ +++  + le+ v
  gi|118431313|ref|NP_147686.2| 102 ARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERV 154
                                    46999***********************************9999999999877 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.13        12      91     131 ..      31      71 ..      27      84 .. 0.81
   2 ?    7.7   9.5     0.027       2.4      61     139 ..      76     151 ..      69     161 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.13
                      PspA_IM30  91 aeikslekqaealetqlaqqrsaveqlrkqlealetkieel 131
                                    +e++sl +q+e+l+t +++  ++ e+++++ e     ie +
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESI 71 
                                    78999999***************999999988777766655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.027
                      PspA_IM30  61 eeqkeqakklekkAkaALtkgeeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellk 139
                                    e+ ++++ k e++  +A t+       ++++e++sl++q+e+l++  + ++++ +++ + l++l++ +++l+a    l 
  gi|118431313|ref|NP_147686.2|  76 ESIQDRVSKIEERLGSAATQS---DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLE 151
                                    444444444444444444444...3345666666666666666666666666666666666666666666666554443 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.057         5       3      53 ..      31      81 ..      27      92 .. 0.54
   2 ?    6.9   0.6     0.061       5.4       4      65 ..      97     158 ..      92     164 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.057
                          Sec34  3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqllee 53
                                   ++L s +++++ l ++ +e+ e+Lee++  f+s   + +s+ ++ e++ + 
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDR 81
                                   455555555555555556666666666555555555555555555544333 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.061
                          Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65 
                                     L++  +e+ +l +q+++++  ++ lee+  +  e+  +l  a ++l +   +lee ++e+ 
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVY 158
                                    45555555666666666666666666666666666666666666666555555555555555 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.035       3.1       6      78 ..      15      92 ..       9      98 .. 0.61
   2 ?    3.2   0.1      0.88        79      26      79 ..     107     158 ..      94     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.035
                        DUF4446  6 lavlvvillillivllvklkklkkkykklmk.....gkdgksleellkekleeveelkeeseelekeieeleeklkks 78
                                   ++v ++il + + +++ +l +l+++++ l +      ++ ++++ ++++   ++e++ ++ e+++++++++ee+l ++
  gi|118431313|ref|NP_147686.2| 15 AVVALIILGVGFYAIYQELASLRSQVEGLNTryeeiSESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSA 92
                                   344444455555555566666666666665522111224455556678888888888899999999999998888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.88
                        DUF4446  26 klkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkksl 79 
                                    +l+++++ l+   + + lee  +e  e++++l  + ++l++++++lee++++ +
  gi|118431313|ref|NP_147686.2| 107 SLTQQLEDLQA--RIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVY 158
                                    33333333332..45566666666666666666666666666666666666555 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.46        41      41      64 ..      31      54 ..      28      62 .. 0.86
   2 ?    2.1   0.1       2.8   2.5e+02      43      65 ..      68      90 ..      57     100 .. 0.59
   3 ?    7.8   0.6     0.047       4.2      35      69 ..      97     131 ..      93     132 .. 0.80
   4 ?    4.3   0.1      0.56        50      35      59 ..     132     156 ..     130     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.46
                         Csm1_N 41 qeiesLkeqlaeleekvkeleerr 64
                                   qe+ sL+ q++ l+++ +e+ e+ 
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESL 54
                                   89999*********9999988875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 2.8
                         Csm1_N 43 iesLkeqlaeleekvkeleerrk 65
                                   ies+   l++++ +v+++eer  
  gi|118431313|ref|NP_147686.2| 68 IESIASSLESIQDRVSKIEERLG 90
                                   55555555555555555555443 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.047
                         Csm1_N  35 kletkdqeiesLkeqlaeleekvkeleerrkkqeE 69 
                                    +l+   +e+ sL +ql+ l+++++ lee+ +++ E
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGE 131
                                    57777889999999999999999999998777665 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.56
                         Csm1_N  35 kletkdqeiesLkeqlaeleekvke 59 
                                    +l++    ++ L+++la+lee+v+e
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASLEERVDE 156
                                    56777778999**********9987 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       1.8   1.6e+02       6      38 ..      29      61 ..      26      97 .. 0.61
   2 ?   10.8   0.7    0.0066      0.59       5      57 ..     100     152 ..      96     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA  6 lfdkleeleeqleelleeleelkeelaelleen 38
                                   ++++l++l +q+e l+++ ee+ e+l+e+    
  gi|118431313|ref|NP_147686.2| 29 IYQELASLRSQVEGLNTRYEEISESLEEVQGAF 61
                                   667777777777777777777777776665444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0066
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXX CS
                           YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeek 57 
                                     + ++l++l++qle+l++++++l+e+ ae  e+ ++L +  + l+ rl++ e+
  gi|118431313|ref|NP_147686.2| 100 AVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    5678999***************************************9965444 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.9    0.0018      0.16     182     283 ..      48     153 ..      28     160 .. 0.36

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                           HOOK 182 delaQrcheldkqlsllqeEknaLlaenkklqerlsele....ngeesgtiqltskkylelqkqleqlqeelfrlEtard 257
                                    +e++  ++e++     +  + +++++  +++q+r+s++e    +   ++ ++ +++ + +l++qle lq  +  lE++  
  gi|118431313|ref|NP_147686.2|  48 EEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEerlgSAATQSDLDAVARELASLTQQLEDLQARIQALEESGA 127
                                    22222222222222222222333333333333333333333333333333333333334444444444444444444444 PP

                           HOOK 258 dyrlkceelekevlelqqrneeltsl 283
                                    +   ++++l   +++lq r   l++ 
  gi|118431313|ref|NP_147686.2| 128 EAGERLDQLAMALQDLQARLASLEER 153
                                    44444444444444444443333333 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.9     0.098       8.8      96     147 ..      34      83 ..      28      86 .. 0.74
   2 ?   12.2   6.6     0.001      0.09      94     144 ..      74     124 ..      67     129 .. 0.87
   3 ?    2.9   0.4      0.69        62      87     106 ..     139     158 ..     130     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.098
                        DUF4349  96 kaleasedrllallek.aksvedlleiereLsevqaeieslegqlryLdnqva 147
                                    ++l+ +++ l + +e+ ++s+e   e++ + ++ + +ies+ ++l++++++v+
  gi|118431313|ref|NP_147686.2|  34 ASLRSQVEGLNTRYEEiSESLE---EVQGAFESSRGDIESIASSLESIQDRVS 83 
                                    5555555555555544344444...68999*********************97 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.001
                        DUF4349  94 RlkaleasedrllallekaksvedlleiereLsevqaeieslegqlryLdn 144
                                     l++ ++ + ++++ l  a++ +dl ++ reL++ ++++e l++++++L++
  gi|118431313|ref|NP_147686.2|  74 SLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    466777778888888999*******************************97 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.69
                        DUF4349  87 qyvDleaRlkaleasedrll 106
                                     + Dl+aRl++le+ +d + 
  gi|118431313|ref|NP_147686.2| 139 ALQDLQARLASLEERVDEVY 158
                                    45677777777777777655 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 ?   10.2   1.1    0.0071      0.63      36     130 ..      32     124 ..      27     128 .. 0.56
   2 ?   10.8   1.7    0.0046      0.41      35     126 ..      59     155 ..      48     160 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0071
                                    HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH..HHHHHHHHHHHH CS
                      Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe..snirvLqnvles 113
                                    +l++l++++e ++ +++e++e  +e++   ++         + i +s +++++++++++e++ +    s + +    l s
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDI----ESIASSLESIQDRVSKIEERLGSAAtqSDLDAVARELAS 107
                                    4555555555555555555555555554444333333....345555555555777777777655544667777777777 PP

                                    HHHHHHHHHHHHHHHHH CS
                      Fib_alpha 114 neqkiqkLeqdidqker 130
                                    + q++++L+  i+++e+
  gi|118431313|ref|NP_147686.2| 108 LTQQLEDLQARIQALEE 124
                                    77777777777777665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0046
                                    HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                      Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.....dnvikksskeleeeilrlketidaqesnirvLqn 109
                                       e+ + ++e+i++s +++++ v++i++ l ++ ++++          +++  ++l+ +i+ l+e+  +  +++ +L  
  gi|118431313|ref|NP_147686.2|  59 GAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDavareLASLTQQLEDLQARIQALEESGAEAGERLDQLAM 138
                                    44555566677777777777777777777777777666632221112333333455666777777777777788888888 PP

                                    HHHHHHHHHHHHHHHHH CS
                      Fib_alpha 110 vlesneqkiqkLeqdid 126
                                     l++++ +++ Le+ +d
  gi|118431313|ref|NP_147686.2| 139 ALQDLQARLASLEERVD 155
                                    88888888888888877 PP

>> SPAM  Salmonella surface presentation of antigen gene type M protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.29        26      62      95 ..      25      58 ..      23      69 .. 0.90
   2 ?    6.7   0.4     0.066       5.9      58     102 ..      93     137 ..      62     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.29
                           SPAM 62 elyallrkqaivrrqlkeLeLqlvaiqekrselq 95
                                   ++ya+ + +a +r q++ L+ +  +i e   e+q
  gi|118431313|ref|NP_147686.2| 25 GFYAIYQELASLRSQVEGLNTRYEEISESLEEVQ 58
                                   68************************99988877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.066
                           SPAM  58 ldreelyallrkqaivrrqlkeLeLqlvaiqekrselqkekeels 102
                                      +++l a+ r +a + +ql++L+ ++ a++e   e  ++ ++l 
  gi|118431313|ref|NP_147686.2|  93 ATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLA 137
                                    4567899*************************9988877777765 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   6.5    0.0076      0.68     140     250 ..      31     136 ..      26     160 .. 0.49
   2 ?    2.5   0.1      0.85        76     131     174 ..     129     172 ..     121     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0076
                        DUF4407 140 aqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaalrael 219
                                    +++a+l+++++ +++r+++  + ++ e++g++ +    ++    + ++ ++   +++++l ++ ++    ++l+a  +el
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLE-EVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQ----SDLDAVAREL 105
                                    5678888888888888888777777.8888874442333344444444444444444444444444....3333333333 PP

                        DUF4407 220 aeleaerakeraasqaaaaaddGllarleal 250
                                    a+l++++++ +a+ qa +++ +  ++rl+ l
  gi|118431313|ref|NP_147686.2| 106 ASLTQQLEDLQARIQALEESGAEAGERLDQL 136
                                    4444443333333333333333333333322 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.85
                        DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtg 174
                                    + ++l++l   +++lqa ++++e+r+d+ +a +   ++   gtg
  gi|118431313|ref|NP_147686.2| 129 AGERLDQLAMALQDLQARLASLEERVDEVYASLYFPVTVVDGTG 172
                                    56788899999999999999999999998888777666655665 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 ?    2.1   0.0       2.6   2.3e+02      26      55 ..      28      57 ..      25      59 .. 0.91
   2 ?    3.3   0.0       1.1        99      36      54 ..      73      91 ..      65      94 .. 0.88
   3 ?    3.6   1.2      0.89        79       6      55 ..     108     157 ..     103     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 2.6
                      V-SNARE_C 26 ailedLhsQretLkrarsklhnvanrlgks 55
                                   ai ++L+s r++ ++ +++  +++++l  +
  gi|118431313|ref|NP_147686.2| 28 AIYQELASLRSQVEGLNTRYEEISESLEEV 57
                                   8999********************999766 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 1.1
                      V-SNARE_C 36 etLkrarsklhnvanrlgk 54
                                   ++L++++++++ + +rlg 
  gi|118431313|ref|NP_147686.2| 73 SSLESIQDRVSKIEERLGS 91
                                   78***************96 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.89
                      V-SNARE_C   6 esdrlknShrivdetisiGaailedLhsQretLkrarsklhnvanrlgks 55 
                                     +++l++ +  +  ++++Ga+  e L++  + L++ +++l  + +r++ +
  gi|118431313|ref|NP_147686.2| 108 LTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    678888889999999***************************99999875 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.7    0.0041      0.37      10      79 ..      65     136 ..      56     139 .. 0.78
   2 ?    6.4   0.5      0.12        11       5      26 ..     135     156 ..     134     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0041
                        DUF4164  10 ltrLeaaldsLEkavdr..rleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaa 79 
                                      ++e    sLE+  dr  ++e+    ++ ++++ a++++ + L ++L + +ar ++lee  +E+ +rL+ +
  gi|118431313|ref|NP_147686.2|  65 RGDIESIASSLESIQDRvsKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQL 136
                                    56677777777765554224444444488899999999999****************************975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.12
                        DUF4164   5 eleaaltrLeaaldsLEkavdr 26 
                                    +l+ al++L+a l sLE++vd+
  gi|118431313|ref|NP_147686.2| 135 QLAMALQDLQARLASLEERVDE 156
                                    4556666777777777766665 PP

>> DUF2576  Protein of unknown function (DUF2576)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.54        48      16      33 ..      29      46 ..      27      49 .. 0.91
   2 ?    5.8   0.0      0.12        10      12      33 ..      97     118 ..      91     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.54
                        DUF2576 16 ikreLnsLrrnvhDLCtr 33
                                   i +eL sLr  v  L tr
  gi|118431313|ref|NP_147686.2| 29 IYQELASLRSQVEGLNTR 46
                                   778************999 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.12
                        DUF2576  12 DrDqikreLnsLrrnvhDLCtr 33 
                                    D D + reL sL +   DL +r
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQAR 118
                                    6789**************9877 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     0.002      0.18      81     150 ..      63     134 ..      36     185 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.002
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           LUC7  81 yeeeflrfleklledvdrkiqkgkqrleltqeekeeeeeaka..kkqeqlkeleekiekllaeaeelgeeGk 150
                                      +  ++ + + le ++ +++k ++rl   +++++  + a++  + ++ql++l+++i+ l +   e+ge+ +
  gi|118431313|ref|NP_147686.2|  63 SSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARElaSLTQQLEDLQARIQALEESGAEAGERLD 134
                                    3344578899999**************865555543333333459999***********9999999998743 PP

>> DASH_Hsk3  DASH complex subunit Hsk3 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.8    0.0037      0.33       1      23 [.     102     124 ..     102     125 .. 0.94
   2 ?    6.2   0.7      0.15        13       5      25 ..     134     154 ..     132     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0037
                      DASH_Hsk3   1 qRqyshLasqLaqLqaNLadtee 23 
                                    +R+++ L +qL+ Lqa+++ +ee
  gi|118431313|ref|NP_147686.2| 102 ARELASLTQQLEDLQARIQALEE 124
                                    69******************997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.15
                      DASH_Hsk3   5 shLasqLaqLqaNLadteell 25 
                                     +La  L+ Lqa+La +ee +
  gi|118431313|ref|NP_147686.2| 134 DQLAMALQDLQARLASLEERV 154
                                    58999*************977 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0023      0.21     173     318 ..      16     154 ..       6     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0023
                          LMBR1 173 vllilllGyGlvelPrslwreiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilk 252
                                    v++++ lG+G+ ++  +l+      l ++ + l+++ +++++++ee +  +e+   +++ + +s+++ +   + +++i +
  gi|118431313|ref|NP_147686.2|  16 VVALIILGVGFYAIYQELAS-----LRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQ---DRVSKIEE 87 
                                    77899999999999555544.....55555555556666666666666666655555555555553333...23333333 PP

                          LMBR1 253 kvPeeiaeklks....nenkteeslaklekqlikalqkrertekqwkrlleka.lelediiknksskekef 318
                                       +     + +         + sl++  ++l+ ++q  e++ ++  + l++  ++l+d+    +s e+++
  gi|118431313|ref|NP_147686.2|  88 RLGS----AATQsdldAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLaMALQDLQARLASLEERV 154
                                    2222....222222212222333444444455555666666666655555554344555555544444444 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 ?    7.3   0.3     0.059       5.2      57     112 ..      31      85 ..      28     100 .. 0.72
   2 ?    6.9   2.8     0.074       6.6      85     144 ..      99     158 ..      83     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.059
                  Jnk-SapK_ap_N  57 eeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelka 112
                                    +el +L+++ e  +   ++  e lee+  ++e+ r ++++  ++le+ +++++ k+
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVS-KI 85 
                                    46677777777777777778888888888888888888888888887777776.33 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.074
                  Jnk-SapK_ap_N  85 dqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretell 144
                                    d++ +e   l +++e+l+ +++ le    +a ++l +l    ++l+ + ++l+er  e+ 
  gi|118431313|ref|NP_147686.2|  99 DAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVY 158
                                    445555566666666666666666666666666666666666666666666666666665 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.6    0.0023       0.2     248     362 ..      35     148 ..      31     155 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0023
                         Tektin 248 alrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveEvk 327
                                    +lr ++e ++   +++ e l++v+   ++   +ie++ +++++ ++ +   + Rl   +    ++ +  e   +L++ ++
  gi|118431313|ref|NP_147686.2|  35 SLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVAREL-ASLTQQLE 113
                                    6899999999999****************************************************999988.89****** PP

                         Tektin 328 eleetieaLkeklaeaeaslkaLertrleleedia 362
                                    +l++ i+aL+e+ aea + l++L    ++l+  +a
  gi|118431313|ref|NP_147686.2| 114 DLQARIQALEESGAEAGERLDQLAMALQDLQARLA 148
                                    ***********************999999987765 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6     0.002      0.18      47     152 ..      35     138 ..      28     140 .. 0.82
   2 ?    7.4   1.2     0.044       3.9      77     136 ..      95     157 ..      93     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.002
                       MIP-T3_C  47 vsaseiekLresiQkltksvnPLgklldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlaeleeaI 126
                                    + +s++e L +   +++ s       ++    Di+s +  Le+ ++    ++ e     +at+++l+ +  +la l +++
  gi|118431313|ref|NP_147686.2|  35 SLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRV--SKIEERLGSAATQSDLDAVARELASLTQQL 112
                                    55678888888888888888888888999999**********987755..55555566789******************* PP

                       MIP-T3_C 127 kdqkekisnvrakilkNeakiqkllk 152
                                    +d + +i+++ ++  +  +++++l++
  gi|118431313|ref|NP_147686.2| 113 EDLQARIQALEESGAEAGERLDQLAM 138
                                    ********999887777777777766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.044
                       MIP-T3_C  77 qdDidsMqrELemWrseyrqqa...eelaeerrateealeplkaqlaeleeaIkdqkekisnv 136
                                    q D+d+ +rEL++ +++ +  +   ++l+e  ++  e l++l   l++l++ ++  +e++++v
  gi|118431313|ref|NP_147686.2|  95 QSDLDAVARELASLTQQLEDLQariQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    789999999999999987665511145555555566666777778999999888888888877 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.9     0.004      0.36      31     152 ..      31     155 ..      28     162 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.004
                           Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekl..eeelkelreelselsl 108
                                    +e+ +l++q+  l+++ ee  e+++e++ ++e+   ++e + + l+  +++++ ++e+++++  +++l  + +el++l++
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAatQSDLDAVARELASLTQ 110
                                    68899999999999999999999999999999999999999999999999999999998765115677788888888776 PP

                           Fez1 109 eeeeaalesdeakaqrqe.aeeleelkreverlraeLkeerqkke 152
                                    + e+ +++ ++ ++  +e  e+l++l   ++ l+a+L+  +++ +
  gi|118431313|ref|NP_147686.2| 111 QLEDLQARIQALEESGAEaGERLDQLAMALQDLQARLASLEERVD 155
                                    666665554444444333356788888888888888877666554 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.2    0.0039      0.35     145     223 ..      77     151 ..      29     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0039
                        DUF2884 145 lveesiGsilsalgsemlesegdnleafeqrmeklgekieeeveeqakalekkaealCeslkeldaleqqLqkkipeLk 223
                                     +++ +++i + lgs+ ++s+ d   a+++++++l +++e +++++ +ale+ + +  e+l++l+ + q+Lq+++ +L+
  gi|118431313|ref|NP_147686.2|  77 SIQDRVSKIEERLGSAATQSDLD---AVARELASLTQQLE-DLQARIQALEESGAEAGERLDQLAMALQDLQARLASLE 151
                                    24556777777777777777755...8***********98.6999***************************9998876 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7    0.0027      0.24      18     112 ..      52     151 ..      34     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0027
                        Vps53_N  18 qslanidelikklqeeikklddeiksvvraqanvgek.....gkealeeaqkaieelfqkikeikdkaekseemvkeitr 92 
                                    +sl++++   ++ +++i+ +  +++s+++  + + e+     ++ +l+ + + + +l+q++++++ + +  ee+  e  +
  gi|118431313|ref|NP_147686.2|  52 ESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERlgsaaTQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGE 131
                                    5666666666666666666666666655554444332211115678999******************************* PP

                        Vps53_N  93 dIkqLDiAKknlttsiTtlk 112
                                     + qL +A ++l + +  l+
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASLE 151
                                    ********999998887775 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3      0.27        24      99     147 ..      40      88 ..      26     105 .. 0.83
   2 ?    8.5   0.6     0.015       1.3      14      72 ..     100     157 ..      91     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.27
                         CENP-K  99 lsiiqsknkklkedLkrEqewleeqqeilesLkektkelkkqvvafsek 147
                                    ++ ++ + +++ e L++ q   e  + ++es+ ++ + +++ v+++ e+
  gi|118431313|ref|NP_147686.2|  40 VEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEER 88 
                                    4556778899******************************999999887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.015
                         CENP-K  14 ellkeceelwkeleecqskLsllgtetlvesdaqlslliarvklLtaeleqwekktpei 72 
                                     + +e  +l ++le+ q++++ l +e+  e   +l+ l + ++ L+a l+ +e+++ e+
  gi|118431313|ref|NP_147686.2| 100 AVARELASLTQQLEDLQARIQAL-EESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    5667778899***********99.777779999*********************99887 PP

>> CR6_interact  Growth arrest and DNA-damage-inducible proteins-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5    0.0029      0.26     106     153 ..      93     140 ..      43     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0029
                   CR6_interact 106 rrkaReeeiakkleKlpqliadlkakiakreaeaqaakerkerlveev 153
                                     ++   + +a++l+ l+q ++dl+a+i++ e+  ++a er ++l    
  gi|118431313|ref|NP_147686.2|  93 ATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMAL 140
                                    3333445789*******************************9997655 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0035      0.31      94     164 ..      83     157 ..      35     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0035
                          Spc29  94 pkisspglapsdesrldsiyssvkkivelekklddqkleIkeLkr.......eleqqrtvnseLqekvaeleeevkrl 164
                                    +ki++ + + + +s ld + +++ +   l ++l+d + +I++L+         l+q  +  + Lq ++a lee+v+++
  gi|118431313|ref|NP_147686.2|  83 SKIEERLGSAATQSDLDAVARELAS---LTQQLEDLQARIQALEEsgaeageRLDQLAMALQDLQARLASLEERVDEV 157
                                    5677777777888999999999999...99999999999999986222222258888888888888888888888653 PP

>> DUF3829  Protein of unknown function (DUF3829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3    0.0054      0.48      12      95 ..      41     121 ..      31     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0054
                        DUF3829  12 klyNaldgriqeslarYfswvgneekgptgkektiyglydlkecleklkaaaaskpameelDeaakkliaaleklaplld 91 
                                    + +N++ + i+esl++ +  + ++  g++  e++ ++l+++++   k+++ + s    ++lD+ a+ l+  +++l++l  
  gi|118431313|ref|NP_147686.2|  41 EGLNTRYEEISESLEEVQGAF-ESSRGDI--ESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQA 117
                                    556888888888888888888.5556666..5555566888888888888888888888999999999888888888887 PP

                        DUF3829  92 eada 95 
                                     ++a
  gi|118431313|ref|NP_147686.2| 118 RIQA 121
                                    7766 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.028       2.5       7      37 ..      52      82 ..      35      89 .. 0.67
   2 ?    0.1   0.1       7.6   6.8e+02      11      36 ..     100     125 ..      92     144 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.028
                      DASH_Duo1  7 eqLrkinevienviesLkkaksniervketv 37
                                   e+L+++  ++e+++++++++ s +e+++ +v
  gi|118431313|ref|NP_147686.2| 52 ESLEEVQGAFESSRGDIESIASSLESIQDRV 82
                                   5566666666666666666666666666655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 7.6
                      DASH_Duo1  11 kinevienviesLkkaksniervket 36 
                                     + + + +++++L++ +  i+ ++e+
  gi|118431313|ref|NP_147686.2| 100 AVARELASLTQQLEDLQARIQALEES 125
                                    55555555555555555555555554 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 ?    0.8   0.1         7   6.2e+02       3      24 ..      37      58 ..      29      65 .. 0.71
   2 ?   12.6   1.6    0.0014      0.13       5      61 ..      67     122 ..      63     127 .. 0.92
   3 ?    0.3   0.0       9.9   8.8e+02       6      27 ..     140     161 ..     135     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 7
                       CCDC-167  3 aseIdkleeklascrerLeave 24
                                    s++++l+ + +++ e+Le+v 
  gi|118431313|ref|NP_147686.2| 37 RSQVEGLNTRYEEISESLEEVQ 58
                                   4677777777777777777775 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0014
                       CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksL 61 
                                    +I+++  +l+s+++r+ ++e rl ++  +++  +++ +E+asl++qle+ + + + L
  gi|118431313|ref|NP_147686.2|  67 DIESIASSLESIQDRVSKIEERLGSAATQSD-LDAVARELASLTQQLEDLQARIQAL 122
                                    69999******************99988887.8999***************999887 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 9.9
                       CCDC-167   6 IdkleeklascrerLeaverrl 27 
                                    +++l+ +las++er+++v  +l
  gi|118431313|ref|NP_147686.2| 140 LQDLQARLASLEERVDEVYASL 161
                                    5788999999999999997776 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0045       0.4       2      33 ..      10      41 ..       9      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0045
                  Col_cuticle_N  2 vavalStvailsslitlpsiyndiqsfqsevl 33
                                   +a+++++va++++ + +  iy+++ s++s+v+
  gi|118431313|ref|NP_147686.2| 10 IAAGIAVVALIILGVGFYAIYQELASLRSQVE 41
                                   6999**************************97 PP

>> Miff  Mitochondrial and peroxisomal fission factor Mff
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1    0.0039      0.35     190     267 ..      45     128 ..      29     133 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0039
                           Miff 190 rayqqvlevldenr.....lrggsaskssslskhdslreelstldssleltp....ddvtvvdaasLrrqiiklnrRLql 260
                                     +y++++e+l+e +     +rg  +s    +s+ +s++  +s++++ l  ++     d+   ++asL +q+  l  R+q+
  gi|118431313|ref|NP_147686.2|  45 TRYEEISESLEEVQgafesSRGDIES---IASSLESIQDRVSKIEERLGSAAtqsdLDAVARELASLTQQLEDLQARIQA 121
                                    35889999999998875533333233...3333334444555555444433322224556669***************** PP

                           Miff 261 lEeenke 267
                                    lEe   e
  gi|118431313|ref|NP_147686.2| 122 LEESGAE 128
                                    **97665 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.19        17      35      73 ..      48      86 ..      28     105 .. 0.75
   2 ?    5.3   0.2      0.24        21      15      70 ..      89     144 ..      86     150 .. 0.75
   3 ?    0.9   0.1       5.5   4.9e+02      33      62 ..     132     161 ..     115     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.19
                         DUF148 35 deykefeakvkaqkeevkknvtavisnLssvqekleaIl 73
                                   +e++e  ++v+ + e+ +  ++++ s+L+s+q+++++I 
  gi|118431313|ref|NP_147686.2| 48 EEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIE 86
                                   56677778899999999999*****************96 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.24
                         DUF148  15 ltiaeieeqleawaeky.gvtdeykefeakvkaqkeevkknvtavisnLssvqekle 70 
                                    l  a ++++l+a a +  ++t+++++++a+++a +e+  +++ + + +L+ + ++l+
  gi|118431313|ref|NP_147686.2|  89 LGSAATQSDLDAVARELaSLTQQLEDLQARIQALEES-GAEAGERLDQLAMALQDLQ 144
                                    5567788899999999889***********9998765.4555566666666666665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 5.5
                         DUF148  33 vtdeykefeakvkaqkeevkknvtavisnL 62 
                                      d+++   ++++a+ ++++++v++v ++L
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASLEERVDEVYASL 161
                                    557888888999999999999999998877 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0034       0.3     249     693 ..      34     132 ..      16     162 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0034
                       Prominin 249 keakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsn.lCqseeCskilssleiekldtskcl..dqlpnvdevle 325
                                     + + q e +n   +e+ +s ++ + ++++ + d+++++s+ +  + + ski+++l     +++ +   ++l +++++le
  gi|118431313|ref|NP_147686.2|  34 ASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSlESIQDRVSKIEERLGSAATQSDLDAvaRELASLTQQLE 113
                                    44444444444444444444444444444444444444444322234444444444443333333323344444444444 PP

                       Prominin 326 aleevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktfd 405
                                    +l+  +++                                                                        
  gi|118431313|ref|NP_147686.2| 114 DLQARIQA------------------------------------------------------------------------ 121
                                    44433332........................................................................ PP

                       Prominin 406 dvvekyekyrwliglivcsllllivvililgLlcGilGlsrtatptdrgcskntGasfLlvgvglsFlffsllmlvvllt 485
                                                                                                                    
  gi|118431313|ref|NP_147686.2|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                       Prominin 486 FlvGlnvyklvCeplesneLfrvlDtpgllpeldLsrllskklkknltisevikaCkanesifkvLrlnnlydieellni 565
                                                                                                                    
  gi|118431313|ref|NP_147686.2|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                       Prominin 566 kklteeiqkelenlkvdlsnlelLteeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsngkk 645
                                                                                                                    
  gi|118431313|ref|NP_147686.2|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                       Prominin 646 nlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqes 693
                                                                         l+e++ + +e+
  gi|118431313|ref|NP_147686.2| 122 -------------------------------------LEESGAEAGER 132
                                    .....................................22222222222 PP

>> DUF4525  Domain of unknown function (DUF4525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.38        34      37     102 ..      30      89 ..       5     100 .. 0.80
   2 ?    4.7   0.0      0.25        23      83     108 ..     135     160 ..     106     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.38
                        DUF4525  37 ressaelreqildlskryvkalaeenknvmdgengaslagyadlkrtiavllddilqrlvklenkv 102
                                     +  a lr+q+  l  ry     ee  + ++  +ga  ++  d+  +ia  l+ i  r++k+e+++
  gi|118431313|ref|NP_147686.2|  30 YQELASLRSQVEGLNTRY-----EEISESLEEVQGAFESSRGDIE-SIASSLESIQDRVSKIEERL 89 
                                    566788999999999999.....6777777777777778888875.79999************987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.25
                        DUF4525  83 tiavllddilqrlvklenkvdylvvn 108
                                     +a+ l d+  rl+ le++vd +  +
  gi|118431313|ref|NP_147686.2| 135 QLAMALQDLQARLASLEERVDEVYAS 160
                                    58999****************87654 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6    0.0041      0.37      19      94 ..      48     148 ..      28     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0041
                     STAT_alpha  19 eqdirkLedeqeeFdfqyqelqkl.........................eqeraesekkelkkqkellqqmlnaLdqkRk 73 
                                    e+  ++Le++q  F+     ++++                         + + + +e ++l++q e lq+ ++aL ++ +
  gi|118431313|ref|NP_147686.2|  48 EEISESLEEVQGAFESSRGDIESIasslesiqdrvskieerlgsaatqsDLDAVARELASLTQQLEDLQARIQALEESGA 127
                                    33333455555555555555555555555555556666666999887775566777778899999999999999****** PP

                     STAT_alpha  74 elvdklkellnlleslqekll 94 
                                    e  ++l +l + l+ lq++l 
  gi|118431313|ref|NP_147686.2| 128 EAGERLDQLAMALQDLQARLA 148
                                    *****************9985 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.51        46      73     107 ..      31      65 ..      28      87 .. 0.70
   2 ?    8.8   9.6     0.016       1.4      28     127 ..      56     157 ..      52     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  73 qqvalLrekeaelekqveeakqqleaerealrqar 107
                                    q++a+Lr +++ l ++ ee+ + le+   a ++ r
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSR 65 
                                    67788888888888888888888877665555544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHTTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  28 eareaheqaresladyrawraqeearl..yaeiigklvllkelekvkqqvalLrekeaelekqveeakqqleaerealrq 105
                                    e++ a e++r +++ +   ++  ++r+  ++e  g+++ +++l++v +++a+L ++ ++l+ +++ +++   ++ e+l+q
  gi|118431313|ref|NP_147686.2|  56 EVQGAFESSRGDIESIASSLESIQDRVskIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQ 135
                                    5555556666666666666655555544488999********************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHH CS
                           YscO 106 arkelqearraveKfaelarlv 127
                                    +  +lq  +  ++ ++e ++ v
  gi|118431313|ref|NP_147686.2| 136 LAMALQDLQARLASLEERVDEV 157
                                    *****99987777776666655 PP

>> Mating_N  Mating-type protein beta 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.6     0.005      0.45      12      90 ..      48     123 ..      38     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.005
                       Mating_N  12 edvrqtLdalrkdFfssLrgesealstFlsawskfdellqschdsL.seeTleliysfssliatvssgllelesekeaie 90 
                                    e+++++L+ ++  F ss rg+   +++ +s+ ++ ++++++++++L s+ T+ +++ ++  +a+++++l +l+++ +a+e
  gi|118431313|ref|NP_147686.2|  48 EEISESLEEVQGAFESS-RGD---IESIASSLESIQDRVSKIEERLgSAATQSDLDAVARELASLTQQLEDLQARIQALE 123
                                    56777777777777665.444...47899*****************556899*****************99999888776 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.4    0.0088      0.79     120     211 ..      68     157 ..      26     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0088
                           CorA 120 vdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkeylrdll 198
                                    +++++  le + +++ ++e++l +  ++++l+ +a+   +l+ l ++l ++++ +++l +  a++++  d+ +  l+dl+
  gi|118431313|ref|NP_147686.2|  68 IESIASSLESIQDRVSKIEERLGSAATQSDLDAVAR---ELASLTQQLEDLQARIQALEEsGAEAGERLDQLAMALQDLQ 144
                                    577888899999999999999988888888888777...9***************6666665555555556667799999 PP

                           CorA 199 delerllemleal 211
                                     +l++l+e ++ +
  gi|118431313|ref|NP_147686.2| 145 ARLASLEERVDEV 157
                                    9999988888765 PP

>> Alpha-E  A predicted alpha-helical domain with a conserved ER motif.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.5   0.00092     0.082     219     292 ..      70     158 ..      67     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00092
                        Alpha-E 219 Slafqleeleealaalsp...aeseegrsseaerllgellaelr..ladieelle..........glhelldelqeelae 283
                                    S+a +le+++++++++++   +++++++ +++ r l+ l ++l+   a+i+ l e          +l+  l++lq++la+
  gi|118431313|ref|NP_147686.2|  70 SIASSLESIQDRVSKIEErlgSAATQSDLDAVARELASLTQQLEdlQARIQALEEsgaeagerldQLAMALQDLQARLAS 149
                                    999*************885554445555566666666666666654344554442567788888899999********** PP

                        Alpha-E 284 lsdaiserY 292
                                    l +++ e Y
  gi|118431313|ref|NP_147686.2| 150 LEERVDEVY 158
                                    ***999988 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.32        28       6      35 ..      34      63 ..      30      67 .. 0.88
   2 ?   -0.5   0.0       9.7   8.7e+02      12      33 ..      68      89 ..      65      97 .. 0.71
   3 ?    6.0   0.3     0.097       8.7       6      39 ..      92     125 ..      87     131 .. 0.86
   4 ?    0.2   0.0       5.9   5.2e+02      11      36 ..     132     157 ..     127     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.32
                            LXG  6 aelieaieqlkseleelkeqleqlkkaiqk 35
                                   a+l +++e l++++ee +e+le+++ a+++
  gi|118431313|ref|NP_147686.2| 34 ASLRSQVEGLNTRYEEISESLEEVQGAFES 63
                                   789999999**************9999886 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 9.7
                            LXG 12 ieqlkseleelkeqleqlkkai 33
                                   ie++ s+le+ ++ ++++++++
  gi|118431313|ref|NP_147686.2| 68 IESIASSLESIQDRVSKIEERL 89
                                   6777778888888888877765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.097
                            LXG   6 aelieaieqlkseleelkeqleqlkkaiqklvel 39 
                                    a+ ++ ++++  el++l++qle+l+++iq l e+
  gi|118431313|ref|NP_147686.2|  92 AATQSDLDAVARELASLTQQLEDLQARIQALEES 125
                                    5678999**********************97655 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 5.9
                            LXG  11 aieqlkseleelkeqleqlkkaiqkl 36 
                                     ++ql  +l++l+  l +l+++++++
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASLEERVDEV 157
                                    56777777777777777777777775 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 ?    9.6   2.6      0.01      0.92      59     127 ..      49     120 ..      26     125 .. 0.63
   2 ?    6.1   2.7      0.12        11      61     129 ..      72     150 ..      70     161 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.01
                           COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr...ellklllkldevve 127
                                    ++S++L  +q + e  + +++++ + +es+++ +s+ ee++ s   +    + +r    l + l +l+++++
  gi|118431313|ref|NP_147686.2|  49 EISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARelaSLTQQLEDLQARIQ 120
                                    567777777777777777777777777777777777777776666666555555523344444444444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.12
                           COG2  61 SghLvglqeeleevesplaaa..rkkvesvreklsereeeveskleeakeleekr........ellklllkldevvekl 129
                                     ++L ++q++++++e  l +a  ++++++v ++l+   +++e+  +  ++lee          +l  +l++l++++ +l
  gi|118431313|ref|NP_147686.2|  72 ASSLESIQDRVSKIEERLGSAatQSDLDAVARELASLTQQLEDLQARIQALEESGaeagerldQLAMALQDLQARLASL 150
                                    5677777777777777665431155666666666666666655544444444443333444444444444444444444 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.29        26     134     176 ..      42      84 ..      28      85 .. 0.77
   2 ?    5.7   0.5      0.13        12     101     147 ..     106     152 ..      95     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.29
                   Bacillus_HBL 134 klakdsknFktdvdeltsilagdsgvisqlqneiedlqgkikk 176
                                     l+   ++ ++ ++e++   +++ g+i+ +   +e++q+ ++k
  gi|118431313|ref|NP_147686.2|  42 GLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSK 84 
                                    35556667788999************************99986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.13
                   Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvd 147
                                    a+l+++le+Lq+ iq  +++  +  + L +l+ +l+  ++ + +  +
  gi|118431313|ref|NP_147686.2| 106 ASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    67899999999999999999999999999988887765555554444 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.4     0.005      0.44     128     226 ..      53     150 ..      46     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.005
                        DUF4618 128 qlqqlkdsqqdeldeleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieelee 207
                                    +l++++   +    ++e ++ + le++++++ k +e+l +++++  l+a  + L   t++ ++l+  i+   e   e  e
  gi|118431313|ref|NP_147686.2|  53 SLEEVQGAFESSRGDIESIA-SSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGE 131
                                    45555555555555665554.56999999********************************************9999999 PP

                        DUF4618 208 eipeLkaeveqLqaqaeep 226
                                    ++++L  ++++Lqa+ +  
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASL 150
                                    9999999999999887644 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.041       3.6       4      89 ..      15      99 ..      12     117 .. 0.73
   2 ?    3.1   1.1         1        90      31      77 ..     103     152 ..      98     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.041
                        DUF1043  4 glvvGiiiGalilrltnsklkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlpelee 85
                                   ++v+ ii+G+  + + ++  ++ ++  + l++  +e++e  +e++  f++s+  +e++a++ + +++ ++k +e+L +++++
  gi|118431313|ref|NP_147686.2| 15 AVVALIILGVGFYAIYQEL-ASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQ 95
                                   4444455555544444433.444444456888888999999999999*****************************887777 PP

                        DUF1043 86 qelf 89
                                    +l 
  gi|118431313|ref|NP_147686.2| 96 SDLD 99
                                   7764 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 1
                        DUF1043  31 kelekakaeleeqk...qeledHfaqsaelLetlaedyqkLyqhlaksse 77 
                                    +el + +++le+ +   q le+  a++ e L++la   q+L+  la+ +e
  gi|118431313|ref|NP_147686.2| 103 RELASLTQQLEDLQariQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    55555555555444222667777888888888888888888888887655 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.7    0.0066      0.59      48     155 ..      46     157 ..      28     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0066
                           YkyA  48 efdkikklsdealenveeReellekekesieeakeefekikeeieei....edeelkkeaeelieameeryeaydklyka 123
                                    ++++i++  +e++   e  +  +e+   s+e+ ++ ++ki+e + +     + +++  e+ +l +++e+ ++ +++l ++
  gi|118431313|ref|NP_147686.2|  46 RYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAatqsDLDAVARELASLTQQLEDLQARIQALEES 125
                                    368899999999999999999999999999999999999999987777776788999999999***************** PP

                           YkyA 124 YkealeldkeLYemLkkeeltleeleeqieki 155
                                      ea e   +L   L++ ++ l  lee+++++
  gi|118431313|ref|NP_147686.2| 126 GAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    99999999999999999999999999999987 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.34        30       1      36 [.      36      71 ..      31      89 .. 0.73
   2 ?    5.8   0.5      0.27        24       3      34 ..      96     127 ..      94     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.34
                    Rho_Binding  1 Ltkdvenlakekeelnkklkkleeelekakeeeeei 36
                                   L+++ve l++  ee+++ l++++ ++e  + + e+i
  gi|118431313|ref|NP_147686.2| 36 LRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESI 71
                                   677888888888888888888888888888333333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.27
                    Rho_Binding   3 kdvenlakekeelnkklkkleeelekakeeee 34 
                                    +d++ +a e   l+++l++l+ ++++++e+ +
  gi|118431313|ref|NP_147686.2|  96 SDLDAVARELASLTQQLEDLQARIQALEESGA 127
                                    67888899999999999999999999885333 PP

>> Nuc_N  Nuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5      0.21        19      35      50 ..      72      87 ..      56      96 .. 0.82
   2 ?    5.5   0.1      0.17        15      40      56 ..     114     130 ..     109     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.21
                          Nuc_N 35 kaSKAkiQsrIsklEk 50
                                   + S  +iQ+r+sk+E+
  gi|118431313|ref|NP_147686.2| 72 ASSLESIQDRVSKIEE 87
                                   567779********97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.17
                          Nuc_N  40 kiQsrIsklEkeGvkgt 56 
                                    ++Q rI+ lE+ G +++
  gi|118431313|ref|NP_147686.2| 114 DLQARIQALEESGAEAG 130
                                    79***********9998 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.3     0.017       1.5      21     132 ..      37     153 ..      29     161 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.017
                         TACC_C  21 eeeiqelkkkveelkkenqemkkivaefektiaql...ieekqkqkelakkeiqkvl..eekeqlladlnsveksfsdlf 95 
                                     ++++ l+ ++ee  +  +e +  +++  + i+ +   +e+ q + ++ ++ +  +   ++ ++++ +l s+ ++++dl 
  gi|118431313|ref|NP_147686.2|  37 RSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIassLESIQDRVSKIEERLGSAAtqSDLDAVARELASLTQQLEDLQ 116
                                    33444555555555555555555555444333333000333333333333333222222555555555666655566665 PP

                         TACC_C  96 kryekqkevlegykkneeslkkcaeeylarvkkeeqR 132
                                     r++ + e   +  +  ++l    +++ ar++  e+R
  gi|118431313|ref|NP_147686.2| 117 ARIQALEESGAEAGERLDQLAMALQDLQARLASLEER 153
                                    5555555555555555555555555555555555555 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.54        48      37      81 ..      45      89 ..      26      99 .. 0.42
   2 ?    7.4   1.1     0.038       3.4      19      64 ..      92     137 ..      76     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.54
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXX CS
                           SKA1 37 ellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshl 81
                                      +++ + l+e + a ++ + +ie  + + e++q   +++ ++l
  gi|118431313|ref|NP_147686.2| 45 TRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89
                                   444444444444444444444444443333333333333333333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.038
                                    .....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           SKA1  19 allkedlskieaevsaleellnklkkelqeeeeaikklkkeieasl 64 
                                    a++++dl ++  e+ +l+++l++l++++q  ee   ++ + +++ +
  gi|118431313|ref|NP_147686.2|  92 AATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLA 137
                                    5568899999999999999999999999877665555554444443 PP

>> RP-C_C  Replication protein C C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.3    0.0071      0.64       3      55 ..      76     128 ..      74     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0071
                         RP-C_C   3 eqleqrfralverlprkatlaeleelleelealreevenalesalkaenssan 55 
                                    e++++r++++ erl  +at ++l ++++el++l +++e++  + +  e+s a+
  gi|118431313|ref|NP_147686.2|  76 ESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAE 128
                                    689***********************************998777766666655 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 ?    9.0   8.0     0.011      0.96      59     124 ..      91     156 ..      29     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.011
                   HAUS-augmin3  59 sdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeeke 124
                                    s  +q+d +++  +l+ ++++le+L++ +q+L++  a   +rl++L ++  +lq +l +lee+ +e
  gi|118431313|ref|NP_147686.2|  91 SAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    222346667777777777778888888888888888888888888888888888777777776554 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3      0.15        13      74     119 ..      44      89 ..      29      94 .. 0.84
   2 ?    6.2   0.5      0.12        11      20      53 ..      95     129 ..      91     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.15
                           Uds1  74 rsnskssreslakaeeelaeserkvdelaselekleeraaevrrrL 119
                                    +++ ++++esl++ + + ++s   ++ +as le++++r  ++++rL
  gi|118431313|ref|NP_147686.2|  44 NTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERL 89 
                                    56667788999999****************************9998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.12
                           Uds1  20 leeVeelkkelkaLeerlealrkkL.aletklrda 53 
                                    + +++++ +el++L+++le l++++ ale +  +a
  gi|118431313|ref|NP_147686.2|  95 QSDLDAVARELASLTQQLEDLQARIqALEESGAEA 129
                                    56778888888888888888887762355555555 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.016       1.4      15      41 ..      31      57 ..      28      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.016
                  Bap31_Bap29_C 15 kDlealKkQaeglakEYDrLadehskl 41
                                   ++l  l++Q egl+  Y   ++  ++ 
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEV 57
                                   68999*************999987765 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.23        20      31      77 ..      38      91 ..      28     102 .. 0.75
   2 ?    4.4   0.3      0.23        20      31      90 ..     103     161 ..      96     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.23
                         TraF_2 31 gdvdnlvDkiDdlsdildgleaavnaasad......etq.vdeaaddlnalLed 77
                                   ++v++l+ +++++s++l+++++a +++  d      + + +++++ ++++ L +
  gi|118431313|ref|NP_147686.2| 38 SQVEGLNTRYEEISESLEEVQGAFESSRGDiesiasSLEsIQDRVSKIEERLGS 91
                                   57999*************999999998887666554333466666666665555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.23
                         TraF_2  31 gdvdnlvDkiDdlsdildgleaavnaasadetqvdeaaddlnalLedlggdgylkasagv 90 
                                    ++   l+ +++dl++++ +le+++++a ++  q+  a++dl+a L++l++    ++ a +
  gi|118431313|ref|NP_147686.2| 103 RELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERV-DEVYASL 161
                                    5666788899999999999999988877775558889999999999888766.4444444 PP

>> phiKZ_IP  phiKZ-like phage internal head proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2     0.016       1.5      52     107 ..      40      94 ..      29     101 .. 0.72
   2 ?    1.1   0.2         2   1.8e+02     262     305 ..     103     147 ..      93     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                       phiKZ_IP  52 ledlkeklkeagkkakelikkiietlkdaavritsgierlskridkLeerlkslkk 107
                                    +e+l+++ +e+ ++  e+ + ++e  +  + +i s++e++ +r++k+eerl+s+ +
  gi|118431313|ref|NP_147686.2|  40 VEGLNTRYEEISESLEEV-QGAFESSRGDIESIASSLESIQDRVSKIEERLGSAAT 94 
                                    566666666666554444.344566666678999******************9954 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 2
                       phiKZ_IP 262 arlkelkellkrlgdvkqgakkikavd.drikqlaeavrknerre 305
                                    ++l  l + l++l++++q  +++ a+  +r+ qla a  ++++r 
  gi|118431313|ref|NP_147686.2| 103 RELASLTQQLEDLQARIQALEESGAEAgERLDQLAMALQDLQARL 147
                                    333344444555556666666666665588888888877666554 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   7.2     0.057       5.1       9      89 ..      70     156 ..      26     166 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.057
                                    HHHHHSHHHHHHHHHHHHHH.........HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHH CS
                           OmpH   9 kileespegkaaqeqlekkf.........kklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqk 79 
                                    +i ++ +  ++  +++e+            + + el+++ ++l++lq+++q+ +++   +e+ + l+++  +lq+ +q++
  gi|118431313|ref|NP_147686.2|  70 SIASSLESIQDRVSKIEERLgsaatqsdlDAVARELASLTQQLEDLQARIQALEES--GAEAGERLDQLAMALQD-LQAR 146
                                    44444444444444444444442222222333444444444444444444322222..22222225555555555.4444 PP

                                    HHHHHHHHHH CS
                           OmpH  80 aqelqkkqqe 89 
                                       l+++  e
  gi|118431313|ref|NP_147686.2| 147 LASLEERVDE 156
                                    4555554444 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1      0.25        23       3      30 ..      31      58 ..      29      67 .. 0.88
   2 ?    0.8   0.1       4.7   4.2e+02      86     104 ..      68      86 ..      55     100 .. 0.50
   3 ?    6.0   1.5      0.12        11      81     116 ..     107     142 ..      92     146 .. 0.63
   4 ?    1.8   0.1       2.4   2.1e+02      92     118 ..     132     158 ..     122     162 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.25
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  3 eeleslqaelaqlkeaieelektletlk 30
                                   +el+sl+++++ l+++ ee+ ++le ++
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQ 58
                                   7999999************999999987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 4.7
                                    HHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  86 leelekqlekleeeleklk 104
                                    +e++ ++le++++ + k+ 
  gi|118431313|ref|NP_147686.2|  68 IESIASSLESIQDRVSKIE 86 
                                    3333333333333333333 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  81 llkkkleelekqlekleeeleklkdqittleanlaq 116
                                     l ++le+l++ ++ lee+ +++ +++++l ++l+ 
  gi|118431313|ref|NP_147686.2| 107 SLTQQLEDLQARIQALEESGAEAGERLDQLAMALQD 142
                                    455666666666666666666666666666666665 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 2.4
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  92 qlekleeeleklkdqittleanlaqly 118
                                     l++l  +l++l++++ +le+ ++++y
  gi|118431313|ref|NP_147686.2| 132 RLDQLAMALQDLQARLASLEERVDEVY 158
                                    444444444555555444444444444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1       1.4   1.3e+02      30      56 ..      30      56 ..      26      69 .. 0.79
   2 ?    9.6   2.4     0.015       1.4       2      46 ..      79     125 ..      78     132 .. 0.61
   3 ?    9.1   2.9     0.022         2       1      45 [.     115     159 ..     115     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                           SlyX 30 qqqidrlqrqlrllaerlkeleessga 56
                                    q+++ l+ q++ l+ r +e++es ++
  gi|118431313|ref|NP_147686.2| 30 YQELASLRSQVEGLNTRYEEISESLEE 56
                                   688999999999999999999888765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.015
                                    HHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           SlyX   2 eerleeLEikl..afqedtieeLndvvaeqqqqidrlqrqlrllaer 46 
                                    ++r+ ++E++l  a ++  +++  +++a   qq++ lq+++++l+e 
  gi|118431313|ref|NP_147686.2|  79 QDRVSKIEERLgsAATQSDLDAVARELASLTQQLEDLQARIQALEES 125
                                    56677777776445566666666666666666666666666666654 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.022
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllae 45 
                                    l++r+++LE+  a   + +++L  ++ + q +++ l++++++++ 
  gi|118431313|ref|NP_147686.2| 115 LQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEVYA 159
                                    578999999999999999999999999999999999999988775 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.0     0.012       1.1      56     151 ..      26     141 ..      24     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                           Apt1  56 YyalydivtdLLlysePlek...erserlekim..lasdfsdleglpemvkklqerirqleeikehfqieskyldkegwe 130
                                    +ya+y+ + +L   +e l+    e se le++   ++s + d+e+++++++++q+r+ ++ee   +   +s+ ld   + 
  gi|118431313|ref|NP_147686.2|  26 FYAIYQELASLRSQVEGLNTryeEISESLEEVQgaFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSD-LDAVAR- 103
                                    5666666666666666444344499999***99888899999******************886555555554.666665. PP

                           Apt1 131 drlklekelaece.................eeLfllmk 151
                                    ++++l+++l++++                 ++L ++++
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQariqaleesgaeagerlDQLAMALQ 141
                                    77777777777774444555555666644444444444 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.1    0.0087      0.77     531     632 ..      32     136 ..      27     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0087
                       Macoilin 531 eikkLekelklkeeqirelelkvqelr.kykesekdtevLlsaLsamqdknehLensL.saetrlkLdLfs.aLGdakrq 607
                                    e+  L+ ++   + + +e+    +e++  ++ s+ d e + s+L+ +qd+  ++e+ L sa t+  Ld  +  L    +q
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRYEEISESLEEVQgAFESSRGDIESIASSLESIQDRVSKIEERLgSAATQSDLDAVArELASLTQQ 111
                                    666677777655566666665566665257999**********************999899*******8763699999** PP

                       Macoilin 608 leiaqgqlrqkekeikdLkakiaev 632
                                    le +q++++  e+  ++  +++ ++
  gi|118431313|ref|NP_147686.2| 112 LEDLQARIQALEESGAEAGERLDQL 136
                                    *****99999988877777776665 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       4.4   3.9e+02      41      64 ..      66      89 ..      54      95 .. 0.79
   2 ?    8.8   1.1     0.019       1.7      40      62 ..     102     124 ..      90     125 .. 0.86
   3 ?    5.2   0.3      0.24        22      40      65 ..     130     155 ..     126     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 4.4
                           PspB 41 krLeellekAekleeRietLEriL 64
                                     +e+++ + e +++R++ +E+ L
  gi|118431313|ref|NP_147686.2| 66 GDIESIASSLESIQDRVSKIEERL 89
                                   567888888999999999999765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.019
                           PspB  40 ekrLeellekAekleeRietLEr 62 
                                     ++L++l+++ e l++Ri++LE+
  gi|118431313|ref|NP_147686.2| 102 ARELASLTQQLEDLQARIQALEE 124
                                    578******************96 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.24
                           PspB  40 ekrLeellekAekleeRietLEriLd 65 
                                     +rL++l+   + l++R+ +LE+ +d
  gi|118431313|ref|NP_147686.2| 130 GERLDQLAMALQDLQARLASLEERVD 155
                                    689*******************8766 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 ?    7.5   2.5     0.017       1.6     180     243 ..      68     129 ..      29     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.017
                     Fmp27_WPPW 180 leeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseess 243
                                    +e++ +++e+++++++++e++  +  ++++++++++ +e+++l ++le l++ ++ l+es +++
  gi|118431313|ref|NP_147686.2|  68 IESIASSLESIQDRVSKIEERLGS--AATQSDLDAVARELASLTQQLEDLQARIQALEESGAEA 129
                                    456777777777777777777777..67777777777777777777777777777777766543 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.3     0.012       1.1     114     232 ..      31     147 ..      27     162 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.012
                        DUF1978 114 qeierveeRlkelealYpevseskeeteaqekvelevdLetalgsiEeeyrevvrdQedywKeeekkelersaElrekgt 193
                                    qe+   +  ++ l+ +Y e+ses ee ++    +   d+e +  s+E+    v +  e       + +l+     re   
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESS-RGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAV--ARELAS 107
                                    677788899*****************99876664.5566666666665555555555555444444453322..222222 PP

                        DUF1978 194 kvks.eEleeqlesleellkesseeLevlekhilkvekea 232
                                      ++ e+l+  ++ lee   e  e+L++l + +++++  +
  gi|118431313|ref|NP_147686.2| 108 LTQQlEDLQARIQALEESGAEAGERLDQLAMALQDLQARL 147
                                    2222356666666666666666666666555555554433 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 ?    8.2   3.6     0.019       1.7     194     253 ..      59     124 ..      31     159 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.019
                      Phage_GPO 194 arfadveeavelvAeevkelsekveall......aleaelaalkkeveklkaeleaLkekLsktda 253
                                      f + +  +e +A+++++++++v++ +      a++++l a+ +e+++l+++le+L++++++ ++
  gi|118431313|ref|NP_147686.2|  59 GAFESSRGDIESIASSLESIQDRVSKIEerlgsaATQSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    334444444555555555555555444333333344444444555555555555555554443333 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 ?    7.5   6.7      0.06       5.4      27     146 ..      33     156 ..      20     161 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.06
                                    HHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........HHTT----- CS
                        T3SSipB  27 laawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqk.........rlkeLaPde 97 
                                    la  +++ ++ ++  +++S+ l+++ ++ +    d+e  +  +++++  + + ++++  a +          l +L    
  gi|118431313|ref|NP_147686.2|  33 LASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATqsdldavarELASL---- 108
                                    5555666666666666666666666666666666666666666666666666665555544423222222222222.... PP

                                    ----CHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        T3SSipB  98 PekakleaaeqQagaaadalqadealqKkldaasklsekakakekevDd 146
                                     ++ +  +a++Qa +    ++a e l+    a + l+ +  ++e++vD+
  gi|118431313|ref|NP_147686.2| 109 TQQLEDLQARIQALE-ESGAEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    111111123333331.222333344444444555555555555555555 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.5      0.92        82       3      30 ..      31      58 ..      29     107 .. 0.74
   2 ?    6.5   0.7     0.097       8.7       2      45 ..     109     152 ..     101     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.92
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Swi5  3 aeikeleeqleelekelaelkeelkekk 30
                                   +e+++l++q+e l++ ++e++e l+e +
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYEEISESLEEVQ 58
                                   6788899999999999999999988765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.097
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                           Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                    ++++++l++++++le++ ae+ e+l++ + + + ++  +  L e
  gi|118431313|ref|NP_147686.2| 109 TQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    68888999999999999999999999888888888888887776 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5    0.0021      0.19      22      66 ..      84     128 ..      64     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0021
                  GPS2_interact  22 lvpsrlsKdeLlqnidkvDREiakveqqiskLkkkqkeleeeaak 66 
                                    ++  rl      +++d v RE+a   qq++ L+ + + lee+ a+
  gi|118431313|ref|NP_147686.2|  84 KIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAE 128
                                    445566666666789*************************98776 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 ?    9.0   3.7     0.015       1.4       5     148 ..      14     155 ..      11     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.015
                                    XXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS- CS
                   Spore_III_AB   5 allillactgiGfalakrlkrrlkeleelkralellegeirygatpLpealeklaeksesplseffeevaerleekeges 84 
                                    +++++l+  g+Gf++   + ++l  l+   + l+    ei+ + +  + a+e+    +es +++ +e++ +r+++ e++ 
  gi|118431313|ref|NP_147686.2|  14 IAVVALIILGVGFYA---IYQELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIES-IASSLESIQDRVSKIEERL 89 
                                    555555555555554...344555566666666666666666666666666666655555.5555677777776666666 PP

                                    HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT--SHH..HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Spore_III_AB  85 feeaweeavekllkklaLkkedkeilkelgeslgysdre..gqlkalelaleeleeeieeareeak 148
                                     + a ++ ++   ++la   +++e l++  + l +s +e  + l +l++al++l+++++ ++e+ +
  gi|118431313|ref|NP_147686.2|  90 GSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEagERLDQLAMALQDLQARLASLEERVD 155
                                    666677777777777777777777777777777766555227888999**********99999865 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1       0.9        80      13      46 ..      32      65 ..      27      95 .. 0.63
   2 ?    6.8   1.3     0.054       4.8       6      54 ..     104     152 ..      94     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.9
                                   HHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHH CS
                           GrpE 13 eeeeleeeleelekevkelkekllrllaefenlr 46
                                   e+++l++++e l+++++e++e+l++ +  fe  r
  gi|118431313|ref|NP_147686.2| 32 ELASLRSQVEGLNTRYEEISESLEEVQGAFESSR 65
                                   4555555555566666666555555555554433 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.054
                                    .CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHH CS
                           GrpE   6 eeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekeke 54 
                                    e +++++++e+l++++++le+  +e+ e+l++l+  ++ l+ r++   e
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    5678899999999999999999999999999999988888888866544 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2      0.13        12       3      62 ..      27      87 ..      26      96 .. 0.68
   2 ?    5.2   1.2      0.22        19       8      63 ..     104     153 ..      97     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.13
                    Sipho_Gp157  3 yelaeqykellelleeedvdeeeeeikdtLesleeeieeK...aeniakviknleaeaeaike 62
                                   y + +++++l +++e ++++   eei + Le+ ++++e+    +e ia  +++++ +++ i+e
  gi|118431313|ref|NP_147686.2| 27 YAIYQELASLRSQVEGLNTRY--EEISESLEEVQGAFESSrgdIESIASSLESIQDRVSKIEE 87
                                   778888888888888887765..7999999999988887611155555555555555555544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.22
                    Sipho_Gp157   8 qykellelleeedvdeeeeeikdtLesleeeieeKaeniakviknleaeaeaikee 63 
                                    ++++l ++le+++      +  ++Le+   e  e++++ a+ ++ l+a+ + ++e+
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQ------ARIQALEESGAEAGERLDQLAMALQDLQARLASLEER 153
                                    4444444444443......3345788888999999999999999999998888776 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 ?    6.4   0.2      0.11        10      24      78 ..      30      86 ..      27      95 .. 0.62
   2 ?    2.3   5.0       2.3     2e+02      12      78 ..      57     123 ..      50     143 .. 0.61
   3 ?    1.8   5.0       3.2   2.8e+02      12      38 ..     101     123 ..      90     161 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 24 edelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkqaa 78
                                    +el++l+++v+ l+  ++   ++ ++ q++fe  +  ++ ++  Le+i++ + ++ 
  gi|118431313|ref|NP_147686.2| 30 YQELASLRSQVEGLNTRYEeiSESLEEVQGAFESSRGDIESIASSLESIQDRVSKIE 86
                                   456666666666666666655555566666666666666666666666666666655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  12 aaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                    +  +f ++++++e++ ++l++ +d ++   +   + a q+ ++ + ++++ l ++Le+++  +++  
  gi|118431313|ref|NP_147686.2|  57 VQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALE 123
                                    5555666666666666666666666655555445555555666666666666666666666555544 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 3.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                         WXG100  12 aaarfqkqaeeledelqrlkaevdalq 38 
                                    +a+    + ++l+++l++l+a ++al+
  gi|118431313|ref|NP_147686.2| 101 VAR----ELASLTQQLEDLQARIQALE 123
                                    333....33444444444444444442 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.3     0.071       6.4      16     102 ..      37     125 ..      29     131 .. 0.73
   2 ?    2.0   0.1         3   2.7e+02      80     105 ..     131     156 ..     127     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.071
                        DUF4200  16 eakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklk..kekeaeikklkaeietlk 93 
                                      + e ++++ e++++  ee++ + +  + d++     l++++++ ++ +++  + + +   +  ++e++ l++++e+l+
  gi|118431313|ref|NP_147686.2|  37 RSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSdlDAVARELASLTQQLEDLQ 116
                                    4555556666777777777777777777777777777788888877777777766655541157899************* PP

                        DUF4200  94 seiekleek 102
                                    ++i+ lee 
  gi|118431313|ref|NP_147686.2| 117 ARIQALEES 125
                                    *******96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 3
                        DUF4200  80 aeikklkaeietlkseiekleeklee 105
                                    + + +l   +++l+++++ lee+++e
  gi|118431313|ref|NP_147686.2| 131 ERLDQLAMALQDLQARLASLEERVDE 156
                                    5678999999************9987 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2      0.36        32      38      64 ..      30      56 ..      26      63 .. 0.92
   2 ?    5.7   0.5      0.21        19       6      60 ..      98     152 ..      94     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.36
                          Tup_N 38 iqElqqirqtlyeLeeahrkikqqYEe 64
                                   +qEl+++r+++  L++++++i ++ Ee
  gi|118431313|ref|NP_147686.2| 30 YQELASLRSQVEGLNTRYEEISESLEE 56
                                   69********************99997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.21
                          Tup_N   6 LdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikq 60 
                                    Ldav  E  +l+q+++ l+a+ + +e + ++  + l+q+  +l +L+++  ++ +
  gi|118431313|ref|NP_147686.2|  98 LDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    8999999999999999999999999999888888899998888888887666655 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.9     0.031       2.7       9      70 ..      50     114 ..      35     115 .. 0.78
   2 ?    4.5   4.1      0.49        44       7      74 ..      83     156 ..      82     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.031
                           Rx_N   9 LadllaeeakllkgvkeeleklkdeLesiqavLedaeerqi...kdeavkeWlkelrdlaydaeD 70 
                                    +++ l+e    +++ ++++e++ + Lesiq  +++ eer     + + +++  +el  l  ++eD
  gi|118431313|ref|NP_147686.2|  50 ISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGsaaTQSDLDAVARELASLTQQLED 114
                                    5666666668899999*********************9654333566677777777777777776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.49
                           Rx_N   7 qkLadllaeea..kllkgvkeeleklkdeLesiqavLedaeerqikd....eavkeWlkelrdlaydaeDvlDe 74 
                                    +k+++ l + a  + l  v +el +l ++Le +qa ++  ee   +     +++ + l++l+    ++e  +De
  gi|118431313|ref|NP_147686.2|  83 SKIEERLGSAAtqSDLDAVARELASLTQQLEDLQARIQALEESGAEAgerlDQLAMALQDLQARLASLEERVDE 156
                                    556666666666688999***********************955533323367777777777777777766666 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4     0.022         2      22      69 ..      81     129 ..      77     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.022
                         Cnn_1N  22 riyfLeerleklse.eqkeellkenielkveveslqkelkekkkllrea 69 
                                    r+   eerl   ++ ++ +++ +e+  l +++e+lq  +++++++  ea
  gi|118431313|ref|NP_147686.2|  81 RVSKIEERLGSAATqSDLDAVARELASLTQQLEDLQARIQALEESGAEA 129
                                    5667899999888877889999********************9987766 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       2.2   1.9e+02      16      41 ..      30      55 ..      13      74 .. 0.56
   2 ?   10.4   1.5    0.0046      0.41      16      45 ..      95     124 ..      90     129 .. 0.89
   3 ?    1.9   0.4       2.2     2e+02      27      49 ..     134     156 ..     128     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 2.2
                                   XXHHHHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC 16 llaykqlkqeiaalqaelaklkaene 41
                                   ++ + +l+++++ l+  ++++++  e
  gi|118431313|ref|NP_147686.2| 30 YQELASLRSQVEGLNTRYEEISESLE 55
                                   33444455555555555555554444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0046
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLea 45 
                                    ++++ ++ +e+a l+++l+ l+a++++Le+
  gi|118431313|ref|NP_147686.2|  95 QSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    678889999******************996 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHHHHHHHHHHCC CS
                          DivIC  27 aalqaelaklkaeneeLeaevkd 49 
                                    ++l   l+ l+a+ ++Le++v++
  gi|118431313|ref|NP_147686.2| 134 DQLAMALQDLQARLASLEERVDE 156
                                    56666777777777777777765 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   9.0      0.44        39      27     152 ..      31     157 ..      30     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.44
                           DegS  27 keverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkysee..eikeaYeeakelqvelallrekEkqlr 104
                                    +e+++l++++e l+++ +e+ ++ ++++    ++r     + ++ ++ ++   +i+e   +a ++q +l  + ++ ++l 
  gi|118431313|ref|NP_147686.2|  31 QELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRvsKIEERLGSA-ATQSDLDAVARELASLT 109
                                    68888888888888888888888888888888888888888888888877422566666555.56888888888889999 PP

                           DegS 105 erRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledl 152
                                    ++ ++l+ r++ l+e+   A + + q++++l+ L+  l +++e+++++
  gi|118431313|ref|NP_147686.2| 110 QQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    999999999999999999999999999999999999999999888765 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4    0.0018      0.16      11      65 ..      49     108 ..      49     109 .. 0.78
   2 ?    1.9   2.5       3.6   3.2e+02      26      49 ..     120     143 ..     107     161 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0018
                                    HHHHHHHCGGGSSSH.....HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                         HSCB_C  11 elrEeleeaeeaadk.....eeleelkaeveerieeleaeleeafekkdleaaadllrrl 65 
                                    e+ E+lee++ a +      e ++   + ++ r+ ++e++l +a  ++dl+a+a++l  l
  gi|118431313|ref|NP_147686.2|  49 EISESLEEVQGAFESsrgdiESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASL 108
                                    789******555444554447777778888889999999999999888******999766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 3.6
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                         HSCB_C  26 eeleelkaeveerieeleaeleea 49 
                                    ++lee  ae  er+++l  +l+++
  gi|118431313|ref|NP_147686.2| 120 QALEESGAEAGERLDQLAMALQDL 143
                                    344444444444444443333333 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       2.9   2.6e+02      32      39 ..      62      69 ..       9      99 .. 0.47
   2 ?    6.3   2.2     0.063       5.6      31      77 ..      98     143 ..      66     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.9
                    Helo_like_N 32 rsrdktvr 39
                                    s++ ++ 
  gi|118431313|ref|NP_147686.2| 62 ESSRGDIE 69
                                   22222222 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.063
                    Helo_like_N  31 frsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpllrC 77 
                                    +    +++  L+++le+L++ +++Lee + ae+ + l +L + l+  
  gi|118431313|ref|NP_147686.2|  98 LDAVARELASLTQQLEDLQARIQALEE-SGAEAGERLDQLAMALQDL 143
                                    556678899999***************.7789999999999988765 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.2      0.36        32      22      80 ..      75     123 ..      26     162 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.36
                        DUF2203  22 lralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                    l + ++++ ++ee+l            a+ +++l++++ e+ +l++++e+l + ++ le
  gi|118431313|ref|NP_147686.2|  75 LESIQDRVSKIEERLG----------SAATQSDLDAVARELASLTQQLEDLQARIQALE 123
                                    2222222222222332..........333333333333333333333333333333332 PP

>> FadA  Adhesion protein FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.3     0.033       2.9       3      80 ..      41     121 ..      33     137 .. 0.84
   2 ?    3.5   1.7       1.1        99       2      53 ..     105     152 ..     104     160 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.033
                           FadA   3 naLeaelqkLekk.eeqr..ykkekakaeaaaaklakkkelkakieeklakleadsevrfykdeYkellkeyksllkele 79 
                                    + L+  ++++ ++ ee +  +++ +   e+ a +l+  ++   kiee+l  ++++s+      e  +l +++++l+++++
  gi|118431313|ref|NP_147686.2|  41 EGLNTRYEEISESlEEVQgaFESSRGDIESIASSLESIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQ 120
                                    66788888887652666689*******************************999**************999999998877 PP

                           FadA  80 k 80 
                                    +
  gi|118431313|ref|NP_147686.2| 121 A 121
                                    5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 1.1
                           FadA   2 lnaLeaelqkLekkeeqrykkekakaeaaaaklakkkelkakieeklaklea 53 
                                    l +L+++l++L+    +r +  ++   +a ++l++  ++ + ++++la le+
  gi|118431313|ref|NP_147686.2| 105 LASLTQQLEDLQ----ARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    566777777775....456666666666777777777777777777777665 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       8.1   7.2e+02      27      48 ..      67      88 ..      50      92 .. 0.73
   2 ?    5.3   2.0      0.28        25      29      66 ..      92     129 ..      69     135 .. 0.84
   3 ?    4.3   0.2      0.61        55      35      60 ..     133     158 ..     127     162 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 8.1
                        UPF0184 27 EyeainsmLDqinsaLDalEer 48
                                   ++e i s+L+ i+  + ++Eer
  gi|118431313|ref|NP_147686.2| 67 DIESIASSLESIQDRVSKIEER 88
                                   5677888888888888888887 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.28
                        UPF0184  29 eainsmLDqinsaLDalEernDdlnskLrELlesnRqi 66 
                                    +a  s LD++   L  l ++ +dl+++++ L es  ++
  gi|118431313|ref|NP_147686.2|  92 AATQSDLDAVARELASLTQQLEDLQARIQALEESGAEA 129
                                    677899*************************9997665 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.61
                        UPF0184  35 LDqinsaLDalEernDdlnskLrELl 60 
                                    LDq+  aL +l  r  +l+ ++ E+ 
  gi|118431313|ref|NP_147686.2| 133 LDQLAMALQDLQARLASLEERVDEVY 158
                                    66666666666666666666655543 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.46        41      50      86 ..      28      64 ..      25      91 .. 0.61
   2 ?    5.4   3.2     0.071       6.3       5      72 ..      94     157 ..      90     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.46
                           Dor1 50 airqelediraqledLvlklpkLteectrfskkaeei 86
                                   ai+qel ++r q+e L  + ++++e+ ++++ + e++
  gi|118431313|ref|NP_147686.2| 28 AIYQELASLRSQVEGLNTRYEEISESLEEVQGAFESS 64
                                   5666666666666666666666666666666555544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.071
                           Dor1   5 sskpleelekepelLaeeaeeilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkL 72 
                                    ++++l++  +e ++L+++ e ++a iq+L  +     ++a+e l+++   l+d++a l++L +++++ 
  gi|118431313|ref|NP_147686.2|  94 TQSDLDAVARELASLTQQLEDLQARIQALEESG----AEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    678999999999999999999999999998765....7889999999999999999999998888765 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5      0.59        53       4      32 ..      35      63 ..      32     106 .. 0.80
   2 ?    4.6   1.8      0.48        43       8      46 ..      97     135 ..      94     139 .. 0.81
   3 ?    3.0   0.1       1.5   1.3e+02       2      26 ..     133     157 ..     132     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.59
                            LPP  4 eLssqVsqLkskvdqlssdvnsakaaaqa 32
                                    L sqV+ L++  +++s+ +++++ a ++
  gi|118431313|ref|NP_147686.2| 35 SLRSQVEGLNTRYEEISESLEEVQGAFES 63
                                   57788888998888888887777766554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.48
                            LPP   8 qVsqLkskvdqlssdvnsakaaaqaakeEAaRANqRlDN 46 
                                    ++ +  ++ ++l++++++++a +qa  e  a A +RlD 
  gi|118431313|ref|NP_147686.2|  97 DLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQ 135
                                    666677788889999999999999999999999999995 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 1.5
                            LPP   2 ldeLssqVsqLkskvdqlssdvnsa 26 
                                    ld+L+  +++L++  ++l++ v+++
  gi|118431313|ref|NP_147686.2| 133 LDQLAMALQDLQARLASLEERVDEV 157
                                    89*****************999876 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 ?    5.7   0.1      0.18        16      35      79 ..      33      81 ..      28      92 .. 0.67
   2 ?    3.4   2.4      0.91        81      23      78 ..     100     152 ..      84     156 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.18
                           Med9 35 Lkkarelirelpg....idrsveeqeaeieeleeqlakKrelLkkyknr 79
                                   L + r++++ l      i++s ee +   e+ +  ++   + L+++++r
  gi|118431313|ref|NP_147686.2| 33 LASLRSQVEGLNTryeeISESLEEVQGAFESSRGDIESIASSLESIQDR 81
                                   5566666666666666677777777777777777777766666666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.91
                           Med9  23 dletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                     +  ++++l ++L+   + i+    +++s +e  +++++l   l+  ++ L+++ +
  gi|118431313|ref|NP_147686.2| 100 AVARELASLTQQLEDLQARIQA---LEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    4555555666666666666666...5555555555555555555555555555555 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       5.8   5.2e+02      36      66 ..      28      58 ..      24      62 .. 0.74
   2 ?    8.4   1.5     0.023       2.1      21      79 ..      99     157 ..      91     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 5.8
                                   HHHHHHHHHHHHHHCCCCTXXXXXXXXXXXX CS
                         DivIVA 36 allkeneelkekvkeleeklkeykeleetLk 66
                                   a+++e ++l+++v+ l+++ +e +e  e+++
  gi|118431313|ref|NP_147686.2| 28 AIYQELASLRSQVEGLNTRYEEISESLEEVQ 58
                                   5678888888888888888887777666655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.023
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  21 deVdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeev 79 
                                    d V + L+++++++e+l  + ++l+e  +e+ e+l++ + + ++L+  l + +e  +ev
  gi|118431313|ref|NP_147686.2|  99 DAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEERVDEV 157
                                    45555566666666666666666666666666677777777777776666666666665 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.9     0.041       3.6     100     179 ..      43     124 ..      31     129 .. 0.88
   2 ?    7.3   1.5     0.043       3.8      95     177 ..      73     157 ..      66     161 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.041
                         DUF724 100 lkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk..ekkeaadkeiarlkseaekleeeledv 177
                                    l+++++++ e +++++  +e  + + +++ ++++ ++ +++++e++l ++   ++ +a ++e+a+l ++ e+l+ ++++ 
  gi|118431313|ref|NP_147686.2|  43 LNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAAtqSDLDAVARELASLTQQLEDLQARIQAL 122
                                    67899999999999999999999999*******************9988875577789999*************999998 PP

                         DUF724 178 eq 179
                                    e+
  gi|118431313|ref|NP_147686.2| 123 EE 124
                                    86 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.043
                         DUF724  95 nkLlslkdeqtklleerkkl..ekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaeklee 172
                                    + L s++d+ +k++e++  +  ++++   + e ++l +++++l+ +i+ le+  a + e+ ++ +  + +l++  ++lee
  gi|118431313|ref|NP_147686.2|  73 SSLESIQDRVSKIEERLGSAatQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLEE 152
                                    44556777777777766543113445555566666666666666666666666666666666666666666666666666 PP

                         DUF724 173 eledv 177
                                    ++++v
  gi|118431313|ref|NP_147686.2| 153 RVDEV 157
                                    55544 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.1      0.13        12      10      60 ..      31      77 ..      27      83 .. 0.73
   2 ?    0.8   0.1       6.8   6.1e+02      39      59 ..      77      99 ..      71     108 .. 0.59
   3 ?    3.2   9.3       1.3   1.1e+02       4      56 ..     104     159 ..     101     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.13
                           HalX 10 qelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldeldd 60
                                   qel +L+s +  L + +     ++se  +e ++ +e+ r +++ ++++l++
  gi|118431313|ref|NP_147686.2| 31 QELASLRSQVEGLNTRYE----EISESLEEVQGAFESSRGDIESIASSLES 77
                                   777888888888877777....57888888888888888888888877766 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 6.8
                           HalX 39 eLearleelraqldetlde..ld 59
                                    +++r+  ++++l   +++  ld
  gi|118431313|ref|NP_147686.2| 77 SIQDRVSKIEERLGSAATQsdLD 99
                                   56677777777776666662222 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 1.3
                           HalX   4 eYdeelqelfaLasKravLeaekseaeLadse...eYqeLearleelraqldetld 56 
                                    e+ +  q+l+ L+++ ++Le + +ea  + ++   + q+L+arl++l++++de+ +
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQARIQALEESGAEAGERLDQlamALQDLQARLASLEERVDEVYA 159
                                    55666788888888888888777665443333333789999***********9865 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.6     0.019       1.7      47      77 .]      94     124 ..      44     124 .. 0.89
   2 ?    3.5   1.3       1.1     1e+02      52      74 ..     134     156 ..     131     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.019
                           BMFP  47 tREEFdvqrevlartrekleaLearvaaLEa 77 
                                    t  ++d+++  la   ++le L+ar++aLE+
  gi|118431313|ref|NP_147686.2|  94 TQSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    56689************************95 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 1.1
                           BMFP  52 dvqrevlartrekleaLearvaa 74 
                                    d ++  l+  +++l++Le+rv++
  gi|118431313|ref|NP_147686.2| 134 DQLAMALQDLQARLASLEERVDE 156
                                    55666777888888888888876 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.99        89      13      59 ..      29      71 ..      28      92 .. 0.73
   2 ?    5.0   5.3      0.39        35      11      61 ..      99     148 ..      99     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.99
                                   HHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3 13 vgqsLsaiklqlelakrllekdpekaaeqlreieelarealqevRrl 59
                                   + q+L++++ q+e +++++e    ++ e l+e++ + +++ +++  +
  gi|118431313|ref|NP_147686.2| 29 IYQELASLRSQVEGLNTRYE----EISESLEEVQGAFESSRGDIESI 71
                                   5699***********97774....66666666666666655555444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.39
                                    HHHHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3  11 DsvgqsLsaiklqlelakrllekdpekaaeqlreieelarealqevRrllh 61 
                                    D v+ +L++++ qle +++++++ +e  ae+ +++ + +  alq++ + l+
  gi|118431313|ref|NP_147686.2|  99 DAVARELASLTQQLEDLQARIQALEESGAEAGERLDQ-LAMALQDLQARLA 148
                                    899******************9887744444444433.3345555555555 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 ?    2.4   6.9       1.4   1.3e+02     108     155 ..      77     124 ..      29     161 .. 0.56

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.4
                           FTA4 108 esweveekeaeeepleallerYaelrarLielserrqqlqarlarlrk 155
                                      ++   k +e+  + a++ + + ++ +L++l ++++ lqar++ l++
  gi|118431313|ref|NP_147686.2|  77 SIQDRVSKIEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEE 124
                                    333333344444445566666666666666666666666666666654 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.9     0.015       1.4      66     157 .]      30     122 ..      28     125 .. 0.79
   2 ?    1.2   0.3       3.3     3e+02      70      99 ..     127     156 ..     121     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.015
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX.XXXXXXXXXXXXX CS
                     DASH_Spc19  66 eellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk.ltkeelerlkkLk 144
                                     + l  +++++e l++r e++ + le  +g  ++++ + ++ ++s es +++ ++ +++  +++++    + +++l  L 
  gi|118431313|ref|NP_147686.2|  30 YQELASLRSQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSAATQsDLDAVARELASLT 109
                                    5677889999************************9999999999998888777666655555444443333459999999 PP

                                    XXXXXXXXXXXXX CS
                     DASH_Spc19 145 qkKerLkytlerL 157
                                    q+ e L+ +++ L
  gi|118431313|ref|NP_147686.2| 110 QQLEDLQARIQAL 122
                                    9999999998865 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     DASH_Spc19  70 ekaekeleklerreetLkaklelqegrlsn 99 
                                     +a + l++l+   + L+a+l+ +e r+++
  gi|118431313|ref|NP_147686.2| 127 AEAGERLDQLAMALQDLQARLASLEERVDE 156
                                    567778888888888888888888888765 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   7.1       1.5   1.4e+02      14     110 ..      38     124 ..      28     157 .. 0.39

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 1.5
                   Dynactin_p22  14 krvlGeekekekedesiidsLakvqkklssavskrekikellkkl....eelekyLdpeyedseelpdevKleliLaeed 89 
                                    ++v G +       e+i +sL++vq + +s   + e+i + l+ +    +++e+ L ++ ++s+       l+   a + 
  gi|118431313|ref|NP_147686.2|  38 SQVEGLNTR----YEEISESLEEVQGAFESSRGDIESIASSLESIqdrvSKIEERLGSAATQSD-------LD---AVAR 103
                                    555444443....345666677777666666555555443333331000223333333222222.......22...2223 PP

                   Dynactin_p22  90 eLkktaalleqlqeLkpvlds 110
                                    eL + +++le+lq   + l++
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQARIQALEE 124
                                    333333333333333333333 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.2     0.082       7.3      95     189 ..      44     155 ..      28     161 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.082
                         FAM184  95 sqkvvelsreveevkrkFeeklrqfaqlqeqle..................qekekaLeelrkkhreeveeLlkeqeaqs 156
                                    ++++ e+s+ +eev+ +Fe    +++++++ le                  q    a+ +  ++ ++++e+L+ + +a +
  gi|118431313|ref|NP_147686.2|  44 NTRYEEISESLEEVQGAFESSRGDIESIASSLEsiqdrvskieerlgsaatQSDLDAVARELASLTQQLEDLQARIQALE 123
                                    34555555555555555555555555555555588777777766666655533333333333334677777777777777 PP

                         FAM184 157 ekllkeqekleekhkaeveklkeeveelekekk 189
                                    e+ ++  e+l + +++ +++l++++ +le+   
  gi|118431313|ref|NP_147686.2| 124 ESGAEAGERLDQ-LAMALQDLQARLASLEERVD 155
                                    766666666644.45566777766666665544 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       5.4   4.8e+02      19      43 ..      34      58 ..      29      67 .. 0.87
   2 ?    2.2   0.3         2   1.8e+02      11      44 ..      51      87 ..      43      89 .. 0.71
   3 ?    1.6   0.6         3   2.7e+02       9      35 ..      97     122 ..      90     125 .. 0.59
   4 ?    9.4   1.8     0.011         1       8      42 ..     120     157 ..     116     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 5.4
                        DUF2205 19 erLqqqakeLqssLqaLaervdeVk 43
                                   + L++q++ L+   ++++e  +eV+
  gi|118431313|ref|NP_147686.2| 34 ASLRSQVEGLNTRYEEISESLEEVQ 58
                                   6799999999999999999999996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 2
                        DUF2205 11 eklerearerLqq...qakeLqssLqaLaervdeVke 44
                                   ++  +e + + ++    ++++ ssL+++ +rv ++ e
  gi|118431313|ref|NP_147686.2| 51 SESLEEVQGAFESsrgDIESIASSLESIQDRVSKIEE 87
                                   5555555555555555788999**********99865 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 3
                        DUF2205   9 dveklerearerLqqqakeLqssLqaL 35 
                                    d++++ re  + L qq + Lq+  qaL
  gi|118431313|ref|NP_147686.2|  97 DLDAVAREL-ASLTQQLEDLQARIQAL 122
                                    555555543.55667777777666666 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.011
                        DUF2205   8 edveklerearerLqq...qakeLqssLqaLaervdeV 42 
                                    + +e+ + ea erL+q     + Lq+ L +L ervdeV
  gi|118431313|ref|NP_147686.2| 120 QALEESGAEAGERLDQlamALQDLQARLASLEERVDEV 157
                                    568899999999999955456778899**********9 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 ?    5.4   8.3      0.12        11      69     190 ..      32     151 ..      27     161 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.12
                      Golgin_A5  69 qieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekei 148
                                    ++ +lr++++ l++++    e++ e l+e++ ++e++r   e++ + le++++ ++ +ee l  +   +qs +    +e+
  gi|118431313|ref|NP_147686.2|  32 ELASLRSQVEGLNTRY----EEISESLEEVQGAFESSRGDIESIASSLESIQDRVSKIEERLGSA--ATQSDLDAVAREL 105
                                    4555555555555555....333444555555555666666666666666666666666665533..3333344444444 PP

                      Golgin_A5 149 eklrnqlttk....slsssseselesRlkqLtesLiqKQtvlEals 190
                                     +l++ql       +  + s +e  +Rl qL  +L   Q+ l +l+
  gi|118431313|ref|NP_147686.2| 106 ASLTQQLEDLqariQALEESGAEAGERLDQLAMALQDLQARLASLE 151
                                    4444444332110122233555666666666666666555555554 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.2      0.26        23      31     100 ..      55     135 ..      27     148 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.26
                          THOC7  31 a.........esteeeleqlkedllldfaafelsie..rlqllakanerereryeaekeeieseieavreeieelkaqLe 99 
                                    +           + e++++  e+++ ++++ e  +    +q  ++a +re ++++++ e++++ i+a++e+ +e  ++L+
  gi|118431313|ref|NP_147686.2|  55 EevqgafessRGDIESIASSLESIQDRVSKIEERLGsaATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLD 134
                                    12223333333444555555555555555555555555666666666666666666666666666666666666666666 PP

                          THOC7 100 e 100
                                    +
  gi|118431313|ref|NP_147686.2| 135 Q 135
                                    5 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 ?    1.9   0.4       2.8   2.5e+02      45      76 ..      32      63 ..      28      86 .. 0.55
   2 ?    6.7   7.9     0.094       8.4       5      93 ..      59     152 ..      55     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Cortex-I_coil 45 llasleseaaerekrlreleakldealknlel 76
                                    lasl+s+ +  + r  e+   l+e+   +e 
  gi|118431313|ref|NP_147686.2| 32 ELASLRSQVEGLNTRYEEISESLEEVQGAFES 63
                                   46666666666666666666666665544443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.094
                                    XXXXXXXXXH...HHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Cortex-I_coil   5 erleasknel...anklaglensle..sekvsreelikqkdelesllasleseaaerekrlreleakldealknlelekl 79 
                                     ++e+s+ ++   a+ l ++++ +    e++         d +   lasl ++ ++ + r++ le    ea   l++  +
  gi|118431313|ref|NP_147686.2|  59 GAFESSRGDIesiASSLESIQDRVSkiEERLGSAATQSDLDAVARELASLTQQLEDLQARIQALEESGAEAGERLDQLAM 138
                                    56777776541115555555553331145555555556667888999********************************* PP

                                    HHHHHHHHHHHHHH CS
                  Cortex-I_coil  80 arlelesrlsktek 93 
                                    a  +l++rl+ +e 
  gi|118431313|ref|NP_147686.2| 139 ALQDLQARLASLEE 152
                                    *********99874 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       5.4   4.8e+02      43      86 ..      38      81 ..      33      88 .. 0.79
   2 ?    5.2   0.9      0.23        21      55      86 ..      94     125 ..      77     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 5.4
                                   HHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXX CS
                          Sec2p 43 kekealekkneklkeqLkeketlleslqeqLkeLkevlekmeee 86
                                    + e l+++ e++ e L+e +  +es+  + ++  + le+++++
  gi|118431313|ref|NP_147686.2| 38 SQVEGLNTRYEEISESLEEVQGAFESSRGDIESIASSLESIQDR 81
                                   55667788999999999999999999998888888888888776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.23
                                    HHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXX CS
                          Sec2p  55 lkeqLkeketlleslqeqLkeLkevlekmeee 86 
                                     ++ L+     l+sl +qL++L+  ++ +ee 
  gi|118431313|ref|NP_147686.2|  94 TQSDLDAVARELASLTQQLEDLQARIQALEES 125
                                    56667777778888888888888888887765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4       4.6   4.1e+02      37      60 ..      35      58 ..      30      92 .. 0.60
   2 ?    8.1   2.7     0.029       2.6      20      67 ..     104     151 ..      92     157 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 4.6
                     TMF_DNA_bd 37 kLrkknkelekeikelkkklekle 60
                                   +Lr++++ l++  +e ++ le+++
  gi|118431313|ref|NP_147686.2| 35 SLRSQVEGLNTRYEEISESLEEVQ 58
                                   344444444444444444444433 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.029
                     TMF_DNA_bd  20 EGekLskkelklnntikkLrkknkelekeikelkkkleklekeleele 67 
                                    E+  L  +  +l + i  L +  +e+ + +++l   l++l+  l++le
  gi|118431313|ref|NP_147686.2| 104 ELASLTQQLEDLQARIQALEESGAEAGERLDQLAMALQDLQARLASLE 151
                                    445555555555555555555555555555555555555555555555 PP

>> Plasmid_RAQPRD  Plasmid protein of unknown function (Plasmid_RAQPRD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1         9     8e+02       6      29 ..      65      88 ..      60     102 .. 0.73
   2 ?    4.6   5.4      0.43        38       7      39 ..     103     134 ..      98     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 9
                 Plasmid_RAQPRD  6 reeLakllkqLdqlqalveraeaq 29
                                   r +++++++ L+++q  v++ e++
  gi|118431313|ref|NP_147686.2| 65 RGDIESIASSLESIQDRVSKIEER 88
                                   667888899999998888877665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.43
                 Plasmid_RAQPRD   7 eeLakllkqLdqlqalveraeaqakqeekaRvh 39 
                                    +eLa+l +qL++lqa ++ +e++ +++  +R+ 
  gi|118431313|ref|NP_147686.2| 103 RELASLTQQLEDLQARIQALEESGAEA-GERLD 134
                                    69*******************999988.56554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1413  (0.0788109); expected 358.6 (0.02)
Passed bias filter:                     1218  (0.0679346); expected 358.6 (0.02)
Passed Vit filter:                       420  (0.0234257); expected 17.9 (0.001)
Passed Fwd filter:                       209  (0.0116571); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             201  [number of targets reported over threshold]
# CPU time: 1.75u 0.33s 00:00:02.08 Elapsed: 00:00:00.53
# Mc/sec: 2765.43
//
Query:       gi|118431314|ref|NP_147689.2|  [L=320]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-65  220.6  37.4    2.8e-65  220.4  37.4    1.1  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
      0.037   13.5  16.4      0.059   12.9  16.4    1.5  1  ABC-3     ABC 3 transport family
        3.2    7.6  10.4       0.24   11.3   1.7    2.5  2  Colicin   Colicin pore forming domain


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 !  220.4  37.4   4.7e-69   2.8e-65      40     310 ..      44     310 ..       7     312 .. 0.94

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 4.7e-69
                          FecCD  40 elrlprvlaallvGaaLavaGallQtvtrNpLadPsilGissgaalgavlalllllgslslfalplaaflgallalllvl 119
                                     +rl r+ a ++vGa+Lav+Ga+lQ+ +rNpL+dP++lGis+ga+l+++l+lll  g ++  ++  aa++g+l+a+llvl
  gi|118431314|ref|NP_147689.2|  44 LYRLLRTSASIVVGASLAVSGASLQQALRNPLVDPYLLGISTGASLAVALSLLL--GLAGPLGIGSAALAGGLAAFLLVL 121
                                    58***************************************************9..6999******************** PP

                          FecCD 120 llarkrkgasplkliLaGiavsallsaltsllllllneealesilfwllGslsgaswskvllllvllllllllllllark 199
                                    + a + +g++   li++G+a s+l+++lt+ll+l   +++l  +l+w++Gs+++++   ++ ++  l+l++l+l++ ++ 
  gi|118431314|ref|NP_147689.2| 122 ATA-RLAGMTGSGLIIVGVAYSYLFGSLTTLLVLS-FPDKLTGALYWIFGSVAYVDRGILATAAGGLALATLYLAASSKA 199
                                    ***.*****************************99.789***************************************** PP

                          FecCD 200 ldllalgdetAkslGvnvervrllllllvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllla 279
                                    l++l+lg+e A+ lG+ ver+r  ++ ++ +++a++val+Gp+gF+GL +P iarll  a+++++l++sa +Ga l l++
  gi|118431314|ref|NP_147689.2| 200 LEALSLGEEAARGLGIGVERLRAGVATASLVAVAASVALAGPVGFIGLTAPWIARLLGAARFQHILVASAPMGAGLALAS 279
                                    *******************************************************8888********************* PP

                          FecCD 280 dllarlllsptelpvgivtaliGapffiyll 310
                                    d+lar+l+sp+elp+  + +liG+p+++y  
  gi|118431314|ref|NP_147689.2| 280 DILARTLASPAELPLTPIASLIGVPILVYAA 310
                                    ****************************976 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  16.4   9.8e-06     0.059      42     223 ..      87     274 ..      51     309 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-06
                          ABC-3  42 alpGvalayllgvn..lllg.ailvgliaavalellkrktk.lked..taigivlsvfl.alglvlvslikkskvdldsy 114
                                    a   val +llg+   l +g a+l+g +aa+ l+l +++   +     +++g+  s  + +l  +lv   ++   +   +
  gi|118431314|ref|NP_147689.2|  87 ASLAVALSLLLGLAgpLGIGsAALAGGLAAFLLVLATARLAgMTGSglIIVGVAYSYLFgSLTTLLVLSFPDKLTGALYW 166
                                    5556888888888766444414444444444444433333312222124678888988845777777777879999999* PP

                          ABC-3 115 LfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkllllalialavvvalqavGviLvia 194
                                    +fG+++ +++  l + a   a+  l+l    k l ++++ ee A+  g+ v++l+   ++   +av++++ ++G +  i 
  gi|118431314|ref|NP_147689.2| 167 IFGSVAYVDRGILATAAGGLALATLYLAASSKALEALSLGEEAARGLGIGVERLRAGVATASLVAVAASVALAGPVGFIG 246
                                    ***********************************************************************999988887 PP

                          ABC-3 195 lliiPaatArrltrslesllivAillglv 223
                                     l++P ++ ++ + +++++l+ ++ +g+ 
  gi|118431314|ref|NP_147689.2| 247 -LTAPWIARLLGAARFQHILVASAPMGAG 274
                                    .5889777777778999999888877764 PP

>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.7     0.063   3.8e+02     126     167 ..      78     123 ..      53     152 .. 0.72
   2 ?   11.3   1.7     4e-05      0.24     104     161 ..     198     247 ..     167     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.063
                        Colicin 126 Plfvkvea.iaagiaasflssiafalavg.tpl..gilgfalliav 167
                                    P+++ + +  + ++a s+l ++a  l +g ++l  g+ +f l++a+
  gi|118431314|ref|NP_147689.2|  78 PYLLGISTgASLAVALSLLLGLAGPLGIGsAALagGLAAFLLVLAT 123
                                    5666665534556777777777777777742222234455555543 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4e-05
                        Colicin 104 kaidaekLleefkiavetGnWkPlfvkveaiaagiaasflssiafalavgtplgilgf 161
                                    ka++a +L ee++ +        l + ve + ag+a + l+++a ++a+++p+g +g 
  gi|118431314|ref|NP_147689.2| 198 KALEALSLGEEAARG--------LGIGVERLRAGVATASLVAVAASVALAGPVGFIGL 247
                                    555555555555544........4466999*************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2460.29
//
Query:       gi|118431315|ref|NP_147690.2|  [L=249]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-24   86.6   0.0    2.5e-24   86.3   0.0    1.1  1  ABC_tran     ABC transporter
      3e-18   66.7   0.8    4.7e-11   43.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      2e-07   30.7   0.0    0.00067   19.2   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00063   20.3   0.0     0.0009   19.8   0.0    1.1  1  AAA_23       AAA domain
    0.00076   19.9   0.1     0.0021   18.4   0.1    1.6  1  AAA_16       AAA ATPase domain
     0.0016   18.1   0.1     0.0032   17.2   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0033   17.2   0.0     0.0043   16.8   0.0    1.5  1  AAA_30       AAA domain
     0.0096   15.9   0.0      0.016   15.1   0.0    1.4  1  NACHT        NACHT domain
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.016   14.8   0.1    1.4  1  AAA_25       AAA domain
      0.015   12.8   0.0      0.019   12.5   0.0    1.0  1  DUF3584      Protein of unknown function (DUF3584)
       0.02   15.1   0.0       0.12   12.5   0.0    2.0  2  AAA_33       AAA domain
      0.026   14.8   0.0      0.066   13.5   0.0    1.8  1  AAA_22       AAA domain
      0.032   13.9   0.0      0.067   12.9   0.0    1.4  2  AAA_15       AAA ATPase domain
      0.033   14.4   0.1      0.057   13.7   0.1    1.4  1  AAA_28       AAA domain
       0.05   13.6   0.1      0.085   12.9   0.1    1.3  1  AAA_5        AAA domain (dynein-related subfamily)
      0.052   14.0   0.0       0.12   12.8   0.0    1.6  2  AAA          ATPase family associated with various cellular a
      0.071   12.7   0.0       0.12   12.0   0.0    1.3  1  SRP54        SRP54-type protein, GTPase domain
        0.1   11.4   0.0       0.15   10.9   0.0    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
       0.15   12.6   0.1       0.24   12.0   0.1    1.3  1  AAA_18       AAA domain
       0.26   11.2   0.0       0.49   10.3   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.32    9.6   0.0       0.42    9.2   0.0    1.0  1  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 !   86.3   0.0     3e-27   2.5e-24       1     136 [.      22     164 ..      22     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3e-27
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs++l +g++va++G+nG+GK+tLl+llag  kp  G++++ g +  +     +r+ +g+ p  p+++p+l++ e  
  gi|118431315|ref|NP_147690.2|  22 LRGVSFSLDPGSLVALLGPNGSGKTTLLRLLAGIIKPSRGRVEVCGSPPGR-----VRRMLGYAPASPEVDPRLKAVEVa 96 
                                    678***************************************888777766.....*******************88889 PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    + ee+ +al ++g  el+ +++     +LS Gq++ v la +l+++p l llDEp 
  gi|118431315|ref|NP_147690.2|  97 llyrygvsegvawgrRDWEEVLAALGEMGVGELAWRRW----GELSSGQRRLVILAGVLARRPGLALLDEPH 164
                                    ***********955555555666666666666666666....*****************************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 !   22.1   0.4   1.3e-07   0.00011       2      22 ..      35      55 ..      34      64 .. 0.87
   2 !   43.0   0.0   5.5e-14   4.7e-11     225     300 ..     125     196 ..      82     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    +l GpNgsGK++LL++l ++
  gi|118431315|ref|NP_147690.2| 35 VALLGPNGSGKTTLLRLLAGI 55
                                   689***************887 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 5.5e-14
                         AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                      g   ++ + elS+G++rl  l+  l+r++   +l l+DEp ++L+ + +rr+  +l++l+  +a ++ tTH+pl
  gi|118431315|ref|NP_147690.2| 125 GVGELAWRRWGELSSGQRRLVILAGVLARRP---GLALLDEPHSFLDVSNMRRVTLVLRSLRG-RATIVYTTHDPL 196
                                    556677899********************99...9**************************99.***********7 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00063      0.54      26      41 ..      34      49 ..      25      54 .. 0.85
   2 !   19.2   0.0   7.8e-07   0.00067     136     210 ..     136     206 ..      74     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                                   EEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnll 41
                                   + a++GpNGSGK+ ll
  gi|118431315|ref|NP_147690.2| 34 LVALLGPNGSGKTTLL 49
                                   6789*********986 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 7.8e-07
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                    +LS G++ Lv la ++A    ++  l llDe  + LD +n+++v  +l++ + +a ++ ++++      ad+++ 
  gi|118431315|ref|NP_147690.2| 136 ELSSGQRRLVILAGVLA----RRPGLALLDEPHSFLDVSNMRRVTLVLRSLRGRATIVYTTHDPLAAMAADSVIM 206
                                    69********9999987....6778***************************99999999999888888888765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06    0.0009      12      39 ..      24      52 ..      19      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                         AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAi 39
                                   ++++ +++  l+++ GpNG+GKTT+l+ +
  gi|118431315|ref|NP_147690.2| 24 GVSFSLDPgSLVALLGPNGSGKTTLLRLL 52
                                   556777773599**************876 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   2.5e-06    0.0021      24      55 ..      31      63 ..      23      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                         AAA_16 24 p.elvllsGesGvGKsslvrellralekdggif 55
                                   p +lv l G+ G+GK++l+r l+  ++ ++g +
  gi|118431315|ref|NP_147690.2| 31 PgSLVALLGPNGSGKTTLLRLLAGIIKPSRGRV 63
                                   34899******************8888875544 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 !   17.2   0.1   3.7e-06    0.0032      14      39 ..      24      49 ..      21      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                   g ++++d+ + + l Gp+GsGK+Tll
  gi|118431315|ref|NP_147690.2| 24 GVSFSLDPGSLVALLGPNGSGKTTLL 49
                                   567888988899*************8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.1e-06    0.0043      18      52 ..      32      66 ..      26     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvigl 52
                                     +++l Gp G+GKtt+l+ l+ +++ + grv ++
  gi|118431315|ref|NP_147690.2| 32 GSLVALLGPNGSGKTTLLRLLAGIIKPSRGRVEVC 66
                                   468899********************996555544 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   1.9e-05     0.016       2      23 ..      34      55 ..      33      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                   CEEEEC-TTTCHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                   lv+l G++GsGKTtLl+ la  
  gi|118431315|ref|NP_147690.2| 34 LVALLGPNGSGKTTLLRLLAGI 55
                                   799*************998865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.8e-05     0.016      14      57 ..      14      56 ..       3     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                         AAA_25 14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalav 57
                                   +++++pp +r +   l   g+l++l G+ g+GKttl+  la  +
  gi|118431315|ref|NP_147690.2| 14 RYNTSPPVLRGVSFSL-DPGSLVALLGPNGSGKTTLLRLLAGII 56
                                   5666777777666666.78*****************98877655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05     0.019       7      37 ..      22      52 ..      16      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                        DUF3584  7 lkGrvaeldldghtnieGtNaaGKTtLlrLi 37
                                   l+G+   ld+   + + G N++GKTtLlrL+
  gi|118431315|ref|NP_147690.2| 22 LRGVSFSLDPGSLVALLGPNGSGKTTLLRLL 52
                                   5677777888888999**************7 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.12       1      20 [.      34      53 ..      34      91 .. 0.93
   2 ?    0.3   0.0      0.82     7e+02      65     106 ..     150     193 ..     110     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                         AAA_33  1 lvllvGlpGsGKstlaerll 20
                                   lv l G++GsGK+tl++ l+
  gi|118431315|ref|NP_147690.2| 34 LVALLGPNGSGKTTLLRLLA 53
                                   78899**********99875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.82
                         AAA_33  65 kalsagrnvildat..nlsrrerarflklarrlgvpvrivvvet 106
                                      +++ + ++ld +  +l+ ++++r+  ++r l  + +iv+ + 
  gi|118431315|ref|NP_147690.2| 150 VLARRPGLALLDEPhsFLDVSNMRRVTLVLRSLRGRATIVYTTH 193
                                    44566666888888778899999999999998888888888665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.7e-05     0.066       6      26 ..      33      53 ..      29     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                   +++++ G+ G+GKTtllr l+
  gi|118431315|ref|NP_147690.2| 33 SLVALLGPNGSGKTTLLRLLA 53
                                   67899*************987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.8e-05     0.067      22      47 ..      30      56 ..      22      64 .. 0.78
   2 ?   -3.3   0.0       6.7   5.7e+03     359     366 ..     188     195 ..     172     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.8e-05
                         AAA_15 22 see.ltvliGkNnsGKSsilealdlFl 47
                                   ++  l  l G+N+sGK+++l++l  ++
  gi|118431315|ref|NP_147690.2| 30 DPGsLVALLGPNGSGKTTLLRLLAGII 56
                                   3434999**************996555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.7
                         AAA_15 359 viitTHSp 366
                                    +++tTH p
  gi|118431315|ref|NP_147690.2| 188 IVYTTHDP 195
                                    89****98 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.6e-05     0.057       2      20 ..      35      53 ..      34      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   ++++G+ ++GKTtll+ La
  gi|118431315|ref|NP_147690.2| 35 VALLGPNGSGKTTLLRLLA 53
                                   89****************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 ?   12.9   0.1   9.9e-05     0.085       2      24 ..      35      58 ..      34      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                                   EEEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                   v L+Gp G+gK++l + la  +  
  gi|118431315|ref|NP_147690.2| 35 VALLGPNGSGKTTLLRLLAGIIkP 58
                                   569****************99851 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   0.00014      0.12       2      23 ..      36      57 ..      35      88 .. 0.86
   2 ?   -2.1   0.0       5.9     5e+03      38      71 ..     133     167 ..     113     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                                   EEESSTTSSHHHHHHHHHHHHT CS
                            AAA  2 llyGppGtGKTllakavakelg 23
                                    l Gp G GKT+l + +a  ++
  gi|118431315|ref|NP_147690.2| 36 ALLGPNGSGKTTLLRLLAGIIK 57
                                   699**************98765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.9
                                    STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHH CS
                            AAA  38 yvgesekkirelfkeakeka.kpsilfiDEidala 71 
                                     +ge ++  r l+  a   a +p   ++DE +++ 
  gi|118431315|ref|NP_147690.2| 133 RWGELSSGQRRLVILAGVLArRPGLALLDEPHSFL 167
                                    45666666666666666666667777888877765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.12       3      28 ..      34      59 ..      32      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                   EEEEEESTTSSHHHHHHHHHHHHHHT CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                                   +++l+G++G+GKTt l  La ++k +
  gi|118431315|ref|NP_147690.2| 34 LVALLGPNGSGKTTLLRLLAGIIKPS 59
                                   5789************9999988866 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00017      0.15      24      55 ..      31      62 ..      23      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                           DLIC 24 sgksvlvlGedgsGkttliaklqGveeekkGr 55
                                    g  v +lG +gsGkttl+  l G+ ++ +Gr
  gi|118431315|ref|NP_147690.2| 31 PGSLVALLGPNGSGKTTLLRLLAGIIKPSRGR 62
                                   5667899******************9999997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00028      0.24       1      19 [.      35      53 ..      35      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                         AAA_18  1 IlltGtpGvGKttlakeLs 19
                                   ++l G+ G+GKttl + L+
  gi|118431315|ref|NP_147690.2| 35 VALLGPNGSGKTTLLRLLA 53
                                   6899************995 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00058      0.49      97     121 ..      29      54 ..      14      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                                    CTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallp 121
                                    l+  ++++l+G+ G GK+tL+  l++
  gi|118431315|ref|NP_147690.2|  29 LDPgSLVALLGPNGSGKTTLLRLLAG 54 
                                    55548899**************9987 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      23      39 ..      39      55 ..      30      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00049
                         AAA_13 23 GwNGaGKTtLSrllrsl 39
                                   G NG+GKTtL rll+ +
  gi|118431315|ref|NP_147690.2| 39 GPNGSGKTTLLRLLAGI 55
                                   99***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1730.21
//
Query:       gi|118431316|ref|NP_147691.2|  [L=231]
Description: hypothetical protein APE_1056.1 [Aeropyrum pernix K1]
Scores for 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-48  162.3   0.0    1.6e-47  161.2   0.0    1.5  2  AMMECR1   AMMECR1
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.038   14.0   0.0    1.4  1  DUF454    Protein of unknown function (DUF454)


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 ?   -2.2   0.0       0.3   2.7e+03      73      85 ..      11      23 ..       9      26 .. 0.86
   2 !  161.2   0.0   1.8e-51   1.6e-47       1     165 [.      29     202 ..      29     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.3
                                   TS----HHHHTTE CS
                        AMMECR1 73 RFspvtaeElpel 85
                                   R +p+++eEl++ 
  gi|118431316|ref|NP_147691.2| 11 RGPPIEPEELDDA 23
                                   899*******985 PP

  == domain 2  score: 161.2 bits;  conditional E-value: 1.8e-51
                                    HHHHHHHHHHHTTSS-S-HH---HHHHSEEEEEEEEEEE.....CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS--- CS
                        AMMECR1   1 lklareaieealkeekkleeeakeelkekaglFVtlkekkg...eLRGCiGtleperpLaeevaenAlaaAfeDpRFspv 77 
                                    +++ar+a+ee ++++++l+ ea  +l +++++FVtl++++g   eLRGCiG ++p  pL+e+v+ +A++aA +DpRF+p+
  gi|118431316|ref|NP_147691.2|  29 VRIARRAVEEWVEHGRRLDVEAGGKLGRPGAAFVTLERRSGdgwELRGCIGVVRPVLPLVEAVVTAAVDAASSDPRFEPL 108
                                    689**********************************7767899************************************ PP

                                    -HHHHTTEEEEEEEE---EE-....-..GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS-TTCC CS
                        AMMECR1  78 taeElpeleveVsvLtepepi....v..ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKaglrpdew 151
                                    ++eEl++++veV+vL+++ep+    +  ++ +evg hGl++ek  + ++lLPqvav++gwd+  fl+ ++ Kagl++++w
  gi|118431316|ref|NP_147691.2| 109 SREELDRVRVEVTVLGSMEPLpkkpHerPALVEVGLHGLYVEKPPYAGLLLPQVAVDEGWDPILFLTWACIKAGLPGTCW 188
                                    *********************6543133455************************************************* PP

                                    CSTTSEEEEE-EEE CS
                        AMMECR1 152 kdseikltryevek 165
                                     +++++++r+++ +
  gi|118431316|ref|NP_147691.2| 189 LREDVEIYRFRAAV 202
                                    9*********9875 PP

>> DUF454  Protein of unknown function (DUF454)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.3e-06     0.038      15      45 ..      76     106 ..      74     111 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-06
                         DUF454  15 GviGivlPlLPTtpFlLlAafcfarssprlh 45 
                                    G+iG+v P+LP +  ++ Aa+  a s pr++
  gi|118431316|ref|NP_147691.2|  76 GCIGVVRPVLPLVEAVVTAAVDAASSDPRFE 106
                                    99***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1736.91
//
Query:       gi|14601163|ref|NP_147692.1|  [L=346]
Description: tRNA-modifying enzyme [Aeropyrum pernix K1]
Scores for 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-20   71.1   0.0    1.2e-19   70.4   0.0    1.4  1  Wyosine_form  Wyosine base formation
    2.3e-16   60.6   0.0    3.9e-16   59.9   0.0    1.3  1  Radical_SAM   Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   1.4e-23   1.2e-19       2      63 .]     251     311 ..     250     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.4e-23
                                   HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                  Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                   a+p++vE+K+y++vG sr+rL+++n+ +he v++ ++rl++ ++ Y +l e+r Srvvll+r
  gi|14601163|ref|NP_147692.1| 251 AQPTYVEIKSYMWVGASRMRLSKANMAEHEYVRKVSERLSELTG-YPILGESRASRVVLLSR 311
                                   89******************************************.**************986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.0   4.3e-20   3.9e-16       6     161 ..      64     239 ..      60     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 4.3e-20
                                   EESS--TTTSCCTT............................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGG CS
                                   xxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   6 gCnlrCsfCarpet............................vrregrgrslsveeileevkelkaekgvkevilgggepl 58 
                                   +C ++C +C+r +                             +rr   g+   ++   +++ e+ +++ v++ +++ gep+
  gi|14601163|ref|NP_147692.1|  64 WCWNACLHCWRIRPqdlgvdldetkltivddpkwlvdeliriHRRLISGYKGHPRVDPKKFWEA-WNP-VHVTLSLTGEPT 142
                                   7**********99999************************************************.**9.************ PP

                                   GSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  59 lypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmnrghtfeevlealek 136
                                   lyp + +ll++ +++   g++ +++t g++p  ++l+ l e +  +++++lea+d++    + +++  +  +e ++e+le+
  gi|14601163|ref|NP_147692.1| 143 LYPMLSDLLKEVHRR---GMTSFLVTRGVRP--DILADLEEEP-SQLYVSLEAWDKKsynYFTRPL-VPRAWELTMETLEM 216
                                   **************8...************5..7888888855.*************888888888.99************ PP

                                   HHHTTSETEEEEEEEBTTTSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 137 lreagikrvvdrivglpGendeele 161
                                   + +   + + +ri+++ G+nd + e
  gi|14601163|ref|NP_147692.1| 217 MPSFTSP-TAIRITLVAGFNDTD-E 239
                                   ****999.*************87.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 00:00:00.39
# Mc/sec: 2687.08
//
Query:       gi|118431317|ref|NP_147693.2|  [L=337]
Description: thioredoxin reductase [Aeropyrum pernix K1]
Scores for complete 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-50  170.6   0.3    4.9e-50  170.4   0.3    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-23   83.4   0.0    2.1e-18   66.6   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.3e-14   54.5   2.4    4.9e-12   46.2   0.4    2.9  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.1e-07   29.5   9.2      0.017   14.2   0.1    4.6  5  FAD_binding_2   FAD binding domain
    4.8e-07   28.8   0.9      0.026   13.2   0.0    3.1  3  HI0933_like     HI0933-like protein
    3.5e-06   26.4   3.5      0.038   13.1   0.2    3.9  4  GIDA            Glucose inhibited division protein A
    6.8e-05   22.6   7.7     0.0096   15.5   0.0    3.0  3  DAO             FAD dependent oxidoreductase
    8.5e-05   21.8   0.1      0.095   11.8   0.0    3.0  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00023   20.5   0.6     0.0064   15.8   0.1    2.7  2  Thi4            Thi4 family
      0.002   17.4   0.9      0.058   12.6   0.1    2.4  2  FAD_binding_3   FAD binding domain
  ------ inclusion threshold ------
      0.021   14.8   0.7        6.1    6.8   0.0    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
       0.13   11.6   7.6       0.09   12.1   0.5    3.0  3  FAD_oxidored    FAD dependent oxidoreductase
       0.14   11.2   0.1       0.14   11.2   0.1    1.9  3  Lycopene_cycl   Lycopene cyclase protein
       0.31   11.3   0.2       0.31   11.3   0.2    2.5  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4   0.3   3.8e-53   4.9e-50       1     294 []      19     311 ..      19     311 .. 0.86

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 3.8e-53
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgielllg 72 
                                    +d v++G+GpAGl+aa++  +  + +++v    + ++g+  l++++  +++ +  ++         + + ++++i +  +
  gi|118431317|ref|NP_147693.2|  19 YDTVIVGAGPAGLSAAIYTTRFLMSTLIV---SMDVGGQLNLTNWIDDYPGMGGLEAsklvesfkSHAEMFGAKIVTGVQ 95 
                                    689**************************...556899999999999999999988895555554333333333222222 PP

                                    .CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-S CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  73 .eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgG 151
                                     ++v ++d g+  + ++   ++ + ++++ +++lA Gs+ r+lg+pG+ae +g++v+++  ++a   k ++  +vvvGgG
  gi|118431317|ref|NP_147693.2|  96 vKTVDRLDDGW--FLVR---GSRGLEVKARTVILAVGSRRRKLGVPGEAELAGRGVSYCSVCDAPLFKGKD-AVVVVGGG 169
                                    12244444444..6663...37799****************************************999998.9******* PP

                                    HHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE.EEETTSCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx.xxxxxxxx RF
                    Pyr_redox_2 152 yiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle.vvledgee 225
                                      ++E A  l+ +  +v+lv++r+ +       ++ ++ e+ +k+ ++e+ l + v+ei+g+++     ++  v+++++e
  gi|118431317|ref|NP_147693.2| 170 DSALEGALLLSGYVGKVYLVHRRQGFR------AKPFYVEEARKKpNIEFILDSIVTEIRGRDRvesvVVKnKVTGEEKE 243
                                    *************99***********7......5565555555555*****************99876556899999999 PP

                                    EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 226 idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                    + +d +++ +G +p +el+ e++gle+d+ g +vvde++rt++pgi+a+GD+++   g++++++A ++G
  gi|118431317|ref|NP_147693.2| 244 LRVDGIFIEIGSEPPKELF-EAIGLETDSMGNVVVDEWMRTSIPGIFAAGDCTSMWPGFRQVVTAAAMG 311
                                    *******************.*********************************99**********9998 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     9e-06     0.011       1      29 [.      22      49 ..      22      68 .. 0.75
   2 !   66.6   0.0   1.6e-21   2.1e-18      83     305 .]      75     292 ..      67     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-06
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                                   +I+GaGPaGl+aai   ++ + + li+  
  gi|118431317|ref|NP_147693.2| 22 VIVGAGPAGLSAAIYTTRFLM-STLIVSM 49
                                   7***************99999.5677754 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 1.6e-21
                    Pyr_redox_3  83 aleYlrevaksfelpiklfeeVesvkkedeg.fevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkhyskvk 157
                                    ++e +++ a+ f  +i +  +V++v++ d+g f v+ s++ +++A++vi+A G   + +kl++pGe +     + y  v 
  gi|118431317|ref|NP_147693.2|  75 LVESFKSHAEMFGAKIVTGVQVKTVDRLDDGwFLVRGSRGlEVKARTVILAVGS--RRRKLGVPGEAElagRGVSYCSVC 152
                                    56667778899999*************65555*******99************9..999*******97444467888888 PP

                    Pyr_redox_3 158 efhkya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevk 236
                                    ++  ++ ++ vvV+Gg++Sa + Al l  +  +V +v+r++  +++         p + ++     k+ +i+++ ++ v+
  gi|118431317|ref|NP_147693.2| 153 DAPLFKgKDAVVVVGGGDSALEGALLLSGYVGKVYLVHRRQGFRAK---------PFYVEEA---RKKPNIEFILDSIVT 220
                                    8877885567999***************************976665.........4443333...334446666666666 PP

                    Pyr_redox_3 237 eikeke..eeykvk.tedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    ei+ ++  e++ vk + +g++ e + d +++ +G +p  +++++ ++e+d+ g +v++ e++ t +pg+f aG
  gi|118431317|ref|NP_147693.2| 221 EIRGRDrvESVVVKnKVTGEEKELRVDGIFIeIGSEPPKELFEAIGLETDSMGNVVVD-EWMRTSIPGIFAAG 292
                                    66543311233333233445555566778887*****************888887765.79**********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 ?    6.4   0.0      0.01        13       2      28 ..      21      47 ..      20      51 .. 0.82
   2 ?   -0.7   0.0       1.7   2.1e+03      49      72 ..      81     105 ..      68     111 .. 0.71
   3 !   46.2   0.4   3.8e-15   4.9e-12       2      80 ..     163     235 ..     162     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                                   EEEECSSHHHHHHHHHHHHTTSEEEEE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvv 28
                                    v+vG+G  gl +A + +++  ++ +v
  gi|118431317|ref|NP_147693.2| 21 TVIVGAGPAGLSAAIYTTRFLMSTLIV 47
                                   69*************999986665555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.7
                                    HHHHT.TEEEECSEEEEEEEEETTS CS
                      Pyr_redox  49 klekn.gievllntkveeiegsedg 72 
                                    ++ ++ g +++++ +v+ ++  +dg
  gi|118431317|ref|NP_147693.2|  81 SHAEMfGAKIVTGVQVKTVDRLDDG 105
                                    3444468899999999999887776 PP

  == domain 3  score: 46.2 bits;  conditional E-value: 3.8e-15
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEEET CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvklkd 80 
                                    vvvvGgG+++lE A  l+ +  kV++v+r+  ++      a     e+ +k+ +ie++l++ v+ei+g ++ vesv++k+
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGALLLSGYVGKVYLVHRRQGFR------AKPFYVEEARKKpNIEFILDSIVTEIRGRDR-VESVVVKN 235
                                    8*********************************......************9*****************9.*****985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.3e-05     0.017       1      29 [.      20      48 ..      20      57 .. 0.83
   2 ?    0.4   0.0      0.21   2.7e+02     174     204 ..      91     131 ..      71     161 .. 0.76
   3 ?    1.5   0.4     0.098   1.3e+02       2      36 ..     163     197 ..     162     202 .. 0.86
   4 ?    2.3   0.1     0.053        68     148     193 ..     202     247 ..     197     256 .. 0.83
   5 !   12.6   0.0   4.1e-05     0.052     373     408 ..     264     300 ..     256     305 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEE CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavve 29
                                   D +++G+G AGL+AA+  ++   ++++v+
  gi|118431317|ref|NP_147693.2| 20 DTVIVGAGPAGLSAAIYTTRFLMSTLIVS 48
                                   89**************7776666777776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                                    EEEEEEEET..........TTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 174 vtGavvenp..........esgrevrirakavvlatgGfgr 204
                                    vtG+ v+            +++r  +++a+ v+la g   r
  gi|118431317|ref|NP_147693.2|  91 VTGVQVKTVdrlddgwflvRGSRGLEVKARTVILAVGSRRR 131
                                    78888887678888888889999999*********999888 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.098
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36 
                                    v+V+G+G + L  Al ++    kv +v   q f+ 
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGALLLSGYVGKVYLVHRRQGFRA 197
                                    9**************99888888999998888775 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.053
                                    HHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES CS
                  FAD_binding_2 148 vesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirak 193
                                    ve+ark + ++f     ++e+ +  +rv  +vv+n+ +g+e ++r +
  gi|118431317|ref|NP_147693.2| 202 VEEARKKPnIEFILDSIVTEI-RGRDRVESVVVKNKVTGEEKELRVD 247
                                    567777778999999999999.7688**********99999887765 PP

  == domain 5  score: 12.6 bits;  conditional E-value: 4.1e-05
                                    S-EEEBETTSBE..STTEEESSBTEEE-STCEESSSST CS
                  FAD_binding_2 373 mgGvetdengrv..ldadgqpipGLYAaGevaaggvhg 408
                                    + G+etd  g+v  ++   + ipG +AaG ++ ++  g
  gi|118431317|ref|NP_147693.2| 264 AIGLETDSMGNVvvDEWMRTSIPGIFAAGDCT-SMWPG 300
                                    56666666666665555666***********9.65555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0     7e-05      0.09       2      20 ..      20      38 ..      19      60 .. 0.83
   2 !   13.2   0.0     2e-05     0.026     107     164 ..      71     128 ..      68     136 .. 0.96
   3 ?    0.8   0.1      0.12   1.5e+02       3      34 ..     163     194 ..     161     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7e-05
                                   SEEEE--SHHHHHHHHHHH CS
                    HI0933_like  2 dviviGgGaAGlmaAisaa 20
                                   d++++G+G+AGl aAi   
  gi|118431317|ref|NP_147693.2| 20 DTVIVGAGPAGLSAAIYTT 38
                                   89*************9775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2e-05
                                    -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                    HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    +a+++v+ ++++++  g k+ +  +vk+v++ +dg f v+ + + e++a++++lA+G+
  gi|118431317|ref|NP_147693.2|  71 EASKLVESFKSHAEMFGAKIVTGVQVKTVDRLDDGWFLVRGSRGLEVKARTVILAVGS 128
                                    699**************************************9**************97 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.12
                                    EEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                    v+v+GgG + l +A+ ++    +V l+ + + 
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGALLLSGYVGKVYLVHRRQG 194
                                    9*************999999999999887765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2     3e-05     0.038       2      29 ..      21      52 ..      20     101 .. 0.68
   2 ?    1.3   0.0      0.11   1.5e+02     129     166 ..     107     143 ..      88     152 .. 0.71
   3 ?    1.6   0.0     0.089   1.1e+02       2      28 ..     163     189 ..     162     237 .. 0.88
   4 !    8.7   0.0   0.00063      0.81     349     391 ..     280     325 ..     264     326 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE....E CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLi....t 29
                                    +++G+G AG+ AA+ + r  +++l++     
  gi|118431317|ref|NP_147693.2| 21 TVIVGAGPAGLSAAIYTTRFLMSTLIVsmdvG 52
                                   69**********************99955542 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                                    EEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESS CS
                           GIDA 129 kgvvtedgetikakavviatGtflkgkihigekelsaG 166
                                      v+ ++g ++ka++v++a G+  + k  +  ++  aG
  gi|118431317|ref|NP_147693.2| 107 FLVRGSRGLEVKARTVILAVGS-RRRKLGVPGEAELAG 143
                                    558889999************9.555555544444455 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.089
                                    EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                    v+V+GgG + +e Al ++    kv L+
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGALLLSGYVGKVYLV 189
                                    99************9998888888887 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00063
                                    TSBBSSSBTEEE-CGGGTB.-SH...HHHHHHHHHHHHHHHHHHCTS CS
                           GIDA 349 tLetkkvkgLflAGqinGt.eGY...eEaaaqGllAGinaarkakgk 391
                                     ++t+ ++g+f+AG+ + +  G+   + aaa+G +A+  a  ++++k
  gi|118431317|ref|NP_147693.2| 280 WMRTS-IPGIFAAGDCTSMwPGFrqvVTAAAMGAVAAYSAYTYLQEK 325
                                    56676.9**********997785333789***********9999886 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.5   0.00026      0.33       1      20 [.      20      39 ..      20      56 .. 0.78
   2 !   15.5   0.0   7.5e-06    0.0096     137     203 ..      64     129 ..      55     156 .. 0.82
   3 ?   -2.1   0.3       1.7   2.2e+03       2      28 ..     163     191 ..     161     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                                   EEEEECTSHHHHHHHHHHHH CS
                            DAO  1 dvviiGGGiiGlstAyeLar 20
                                   d vi+G+G +Gls+A + +r
  gi|118431317|ref|NP_147693.2| 20 DTVIVGAGPAGLSAAIYTTR 39
                                   89***************966 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.5e-06
                                    ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                            DAO 137 ypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                    yp+ g +++ kl+ ++ + ae  G++i++g +v+ +++ d ++w +    + g +++a++v++a G  
  gi|118431317|ref|NP_147693.2|  64 YPGMGGLEASKLVESFKSHAEMFGAKIVTGVQVKTVDRLD-DGWFLV-RGSrGLEVKARTVILAVGSR 129
                                    5666778999**************************8754.468884.444477766799*****954 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                                    EEEECTSHHHHHHHHHHHHT.T.EEEEES CS
                            DAO   2 vviiGGGiiGlstAyeLarr.g.Vtllek 28 
                                    vv++GGG   l  A+ L+   g V l+ +
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGALLLSGYvGkVYLVHR 191
                                    89****96666666666544445666555 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 !    5.3   0.0    0.0071         9       2      22 ..      18      38 ..      17      49 .. 0.88
   2 !   11.8   0.0   7.4e-05     0.095     132     229 ..     106     196 ..      77     199 .. 0.68
   3 ?    1.1   0.0      0.13   1.7e+02     284     339 ..     200     254 ..     197     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0071
                    K_oxygenase  2 ilDligiGiGpsnLsLaille 22
                                    +D +++G+Gp+ Ls ai + 
  gi|118431317|ref|NP_147693.2| 18 EYDTVIVGAGPAGLSAAIYTT 38
                                   69*************999765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7.4e-05
                    K_oxygenase 132 lltveskdaegeeeelearnlvlgvGtepk...iPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeife 208
                                     + v+      +  e++ar+++l+vG+++    +P  +e       v   s         + k+ ++VvG+G Sa e + 
  gi|118431317|ref|NP_147693.2| 106 WFLVRG----SRGLEVKARTVILAVGSRRRklgVPGEAELAG--RGVSYCSVCDAPL--FKGKDAVVVVGGGDSALEGAL 177
                                    555554....3567899*********7664344788887433..5666666655555..78999***********99766 PP

                    K_oxygenase 209 dllrrqkkvelklvtrseale 229
                                     l       ++ lv r+++++
  gi|118431317|ref|NP_147693.2| 178 LLSGYVG--KVYLVHRRQGFR 196
                                    5555444..777788887775 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.13
                    K_oxygenase 284 lyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                    +y ++ +++++++++ ++ v++++ + +    + ++n+ +gee++l+vd +++  G
  gi|118431317|ref|NP_147693.2| 200 FYVEEARKKPNIEFILDSIVTEIRGRDR-VESVVVKNKVTGEEKELRVDGIFIEIG 254
                                    6788888888999999999999998874.677889999999999999999987555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1     5e-06    0.0064      17      39 ..      18      40 ..      13      58 .. 0.80
   2 ?    2.0   0.1     0.082     1e+02      19      39 ..     162     182 ..     156     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5e-06
                                   EEEEEEE--SHHHHHHHHHHHHC CS
                           Thi4 17 esDvvivGaGssGLtaayylakk 39
                                   e D vivGaG++GL+aa y ++ 
  gi|118431317|ref|NP_147693.2| 18 EYDTVIVGAGPAGLSAAIYTTRF 40
                                   789**************998775 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.082
                                    EEEEE--SHHHHHHHHHHHHC CS
                           Thi4  19 DvvivGaGssGLtaayylakk 39 
                                     vv+vG+G s L  a  l+  
  gi|118431317|ref|NP_147693.2| 162 AVVVVGGGDSALEGALLLSGY 182
                                    499**********99988765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   4.5e-05     0.058       1      18 [.      18      35 ..      18      48 .. 0.87
   2 ?    3.0   0.1     0.038        49       3      35 ..     162     194 ..     160     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.5e-05
                                   EEEEEEE--SHHHHHHHH CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlal 18
                                   e+d++IVGaGpaGl++a 
  gi|118431317|ref|NP_147693.2| 18 EYDTVIVGAGPAGLSAAI 35
                                   5799************96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                     V++VG+G + l  allLs +  +v lv +r+ 
  gi|118431317|ref|NP_147693.2| 162 AVVVVGGGDSALEGALLLSGYVGKVYLVHRRQG 194
                                    599******************556888888875 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 ?    6.0   0.1    0.0083        11       1      14 [.      22      35 ..      22      44 .. 0.89
   2 ?    6.8   0.0    0.0048       6.1     123     155 ..      95     128 ..      73     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0083
                  NAD_binding_9  1 aivGaGprGlavle 14
                                   +ivGaGp+Gl+++ 
  gi|118431317|ref|NP_147693.2| 22 VIVGAGPAGLSAAI 35
                                   7*********9985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0048
                  NAD_binding_9 123 evvdleeradgq.avlladgaslaadaVvLAlGh 155
                                    +v  +++ +dg+  v+ ++g +++a+ V+LA+G 
  gi|118431317|ref|NP_147693.2|  95 QVKTVDRLDDGWfLVRGSRGLEVKARTVILAVGS 128
                                    788999999**856778999************95 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5     7e-05      0.09       1      30 [.      20      49 ..      20     121 .. 0.79
   2 ?   -2.8   0.4       2.3   2.9e+03       2      16 ..     163     177 ..     163     193 .. 0.70
   3 ?    2.8   0.0     0.047        60      95     132 ..     204     242 ..     196     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                   D v+vG+gpaG+ AAi   r   ++l+v+ 
  gi|118431317|ref|NP_147693.2| 20 DTVIVGAGPAGLSAAIYTTRFLMSTLIVSM 49
                                   789*****************9999999974 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                   FAD_oxidored   2 vvVvGGgpaGvaAAi 16 
                                    vvVvGGg + +  A+
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGAL 177
                                    89*****98877776 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.047
                   FAD_oxidored  95 emlaeagvtvllntrlvevekegkriesvtveske.g.rk 132
                                    e  ++++++ +l++ ++e++ ++ r+esv+v++k  g +k
  gi|118431317|ref|NP_147693.2| 204 EARKKPNIEFILDSIVTEIRGRD-RVESVVVKNKVtGeEK 242
                                    555889***************98.*******998766444 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00011      0.14       1      55 [.      20      71 ..      20      87 .. 0.81
   2 ?   -1.1   0.0       0.6   7.7e+02     107     143 ..      94     130 ..      66     142 .. 0.74
   3 ?   -4.5   0.6       6.4   8.2e+03       2      15 ..     163     176 ..     163     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgale 55
                                   D v++GaGpAgls A   t+  +   +v+++ + +l   n   W d   ++g+le
  gi|118431317|ref|NP_147693.2| 20 DTVIVGAGPAGLSAAIYTTRFLMSTLIVSMDVGGQL---NLTNWIDDYPGMGGLE 71
                                   88*************999888777778888888877...3346888877777766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                  Lycopene_cycl 107 akvesveeeeageslvvleggrkirarlvvdarglas 143
                                     +v+ v   ++g  lv  + g +++ar+v+ a g  +
  gi|118431317|ref|NP_147693.2|  94 VQVKTVDRLDDGWFLVRGSRGLEVKARTVILAVGSRR 130
                                    45666766677677777777889*******9999433 PP

  == domain 3  score: -4.5 bits;  conditional E-value: 6.4
                  Lycopene_cycl   2 vvviGaGpAglslA 15 
                                    vvv+G+G   l  A
  gi|118431317|ref|NP_147693.2| 163 VVVVGGGDSALEGA 176
                                    899****8887655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00025      0.31       1      17 [.      23      39 ..      23      56 .. 0.84
   2 ?   -2.9   0.0       6.7   8.6e+03       6      40 ..      67     101 ..      66     115 .. 0.54
   3 ?   -1.2   0.3         2   2.5e+03       1      18 [.     165     182 ..     165     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                                   EE--SHHHHHHHHHHHC CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLak 17
                                   IvGaG +Gl+aA + ++
  gi|118431317|ref|NP_147693.2| 23 IVGAGPAGLSAAIYTTR 39
                                   9***********88766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
                                    HHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                  NAD_binding_8   6 lsGlvaAylLakagfdvlllekrdrlGGraasyev 40 
                                    ++Gl a  l    + + + + +   +G +++++++
  gi|118431317|ref|NP_147693.2|  67 MGGLEASKLVESFKSHAEMFGAKIVTGVQVKTVDR 101
                                    55555555555445555555555555555555544 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2
                                    EE--SHHHHHHHHHHHCC CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLaka 18 
                                    +vG+G s+l  A lL+ +
  gi|118431317|ref|NP_147693.2| 165 VVGGGDSALEGALLLSGY 182
                                    89***9999888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2428.83
//
Query:       gi|14601165|ref|NP_147694.1|  [L=115]
Description: hypothetical protein APE_1063 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.02   14.7   0.5      0.043   13.6   0.5    1.6  1  HTH_23           Homeodomain-like domain
      0.025   14.6   1.9      0.041   13.9   0.4    2.0  2  HTH_29           Winged helix-turn helix
       0.05   13.6   0.1      0.075   13.0   0.1    1.4  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
      0.052   13.5   0.4      0.085   12.8   0.4    1.3  1  HTH_11           HTH domain
       0.11   12.5   0.0       0.16   11.9   0.0    1.2  1  HTH_36           Helix-turn-helix 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 ?   13.6   0.5   1.2e-05     0.043      25      49 ..      42      66 ..      37      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                        HTH_23 25 reLgvsrrTvyrwlkryreeGlegl 49
                                  ++L v++rT +r++kr r+ G++ l
  gi|14601165|ref|NP_147694.1| 42 ERLCVTKRTARRIVKRLRRIGAARL 66
                                  689*************998777765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.2e-05     0.041      20      44 ..      42      66 ..      31      73 .. 0.85
   2 ?   -0.9   0.0      0.49   1.7e+03      30      42 ..      85      97 ..      84     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                        HTH_29 20 kllglsrrtvyrwlkrfeegGlaal 44
                                  ++l++++rt +r++kr +  G+a l
  gi|14601165|ref|NP_147694.1| 42 ERLCVTKRTARRIVKRLRRIGAARL 66
                                  78*******************9987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.49
                        HTH_29 30 yrwlkrfeegGla 42
                                  +r+ +++ eg+l+
  gi|14601165|ref|NP_147694.1| 85 RRVAEAYIEGRLR 97
                                  6777777777653 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 ?   13.0   0.1   2.1e-05     0.075      24      40 ..      76      92 ..      56      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
               Ribonuc_red_lgN 24 ivEspqqmfmRvAlala 40
                                   vEsp+++f+RvA a  
  gi|14601165|ref|NP_147694.1| 76 TVESPEELFRRVAEAYI 92
                                  79***********9865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   2.4e-05     0.085      21      47 ..      40      67 ..      37      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                        HTH_11 21 LAeeLnvSrrtvrrdIkaLeelg.vpIe 47
                                  L e+L v++rt rr +k+L+ +g +++e
  gi|14601165|ref|NP_147694.1| 40 LRERLCVTKRTARRIVKRLRRIGaARLE 67
                                  679********************75555 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.16      29      53 ..      38      62 ..      29      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                        HTH_36 29 etlakrlglsknTvsraikeLeqlG 53
                                  e l +rl++ k+T++r++k L++ G
  gi|14601165|ref|NP_147694.1| 38 EILRERLCVTKRTARRIVKRLRRIG 62
                                  56789****************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 888.25
//
Query:       gi|14601166|ref|NP_147695.1|  [L=242]
Description: hypothetical protein APE_1064 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.25   11.8   1.3         14    6.2   0.1    2.4  2  DUF4687   Domain of unknown function (DUF4687)


Domain annotation for each model (and alignments):
>> DUF4687  Domain of unknown function (DUF4687)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1    0.0034        61      58      87 ..       5      34 ..       2      43 .. 0.94
   2 ?    6.2   0.1   0.00079        14      30      58 ..      85     113 ..      75     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0034
                       DUF4687 58 avrpsvrtesrrataggrsptrlikGrdld 87
                                  +vrp++ t   r +a+  +  r  kGr++d
  gi|14601166|ref|NP_147695.1|  5 SVRPNIDTRGGREPAAPGGYGRPCKGRAPD 34
                                  79*************************998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00079
                       DUF4687  30 asalamvsGDsllvarPeailpglvprqa 58 
                                    +++a+ sGD+  v++P  +    +p qa
  gi|14601166|ref|NP_147695.1|  85 LVEWALSSGDAWAVTAPTVVAVRAGPGQA 113
                                   4789**************99988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1800.07
//
Query:       gi|118431318|ref|NP_147696.2|  [L=378]
Description: succinyl-CoA synthetase subunit beta [Aeropyrum pernix K1]
Scores for complete 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-50  171.3   0.0    2.6e-50  170.8   0.0    1.2  1  ATP-grasp_2  ATP-grasp domain
    2.3e-14   53.5   0.0    4.6e-14   52.5   0.0    1.5  1  Ligase_CoA   CoA-ligase
    4.2e-05   23.1   0.3     0.0017   17.9   0.0    2.4  2  ATP-grasp_5  ATP-grasp 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 !  170.8   0.0   4.3e-54   2.6e-50       1     201 [.       2     196 ..       2     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 4.3e-54
                                    BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSS.SEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSE CS
                    ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgek.elvvKaQvlaGGRGKagGvklvkskeeakeaakellgke 79 
                                    +l+E++akeil+ ygv++p + ++   +++++++++ g +  lvvK+Qvl+ GRGKagG+klv+s+e+a ++a el  k 
  gi|118431318|ref|NP_147696.2|   2 KLYEFEAKEILRMYGVETPPSVLVMPGDDVAAKIREAGLEpPLVVKSQVLVAGRGKAGGIKLVESVEDAVRVAGELWRKP 81 
                                    69***************************99999999865279************************************* PP

                                    EE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHH CS
                    ATP-grasp_2  80 lvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqa 159
                                    ++       G    ++lve+a++ + ElY si++Dr+++++v++aS+ GG+diEe+a +kPe i++  +dp  gl+ ++a
  gi|118431318|ref|NP_147696.2|  82 IK-------GILPGALLVEKAVPHDAELYTSIIIDRSERRPVILASRFGGMDIEEIAREKPESIVRHYVDPFLGLRGYEA 154
                                    **.......*********************************************************************** PP

                                    HHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                    ATP-grasp_2 160 reiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                    r + k++gl+++l+++ a++++ ly++f++l+a+lvE NPL+
  gi|118431318|ref|NP_147696.2| 155 RMVGKAIGLSGRLLNSYASFLQVLYRVFTALEAELVESNPLA 196
                                    *****************************************8 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   7.7e-18   4.6e-14       3     142 ..     260     367 ..     258     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 7.7e-18
                                    SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEE CS
                     Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldiv 82 
                                    nG++L++++mdl+ +               g+ +++++d+G++a            + + +a+  l++ p+ + i+++++
  gi|118431318|ref|NP_147696.2| 260 NGAGLTMATMDLVYHF--------------GGRPANFLDIGGGAR----------AELVKKAVSFLLEFPKAEKIFINVF 315
                                    8***************..............***************..........7************************ PP

                                    ESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE- CS
                     Ligase_CoA  83 lGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiass 142
                                    +G+ + +++a ++++a++e       +p+v+r+ Gt ++     e++++leeag+  ++ 
  gi|118431318|ref|NP_147696.2| 316 GGITRGDEVARGIVAAVRESG---SSKPLVVRLSGTREE-----EGRRILEEAGIYAYTD 367
                                    ********************7...***************.....99*******9977665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.8e-07    0.0017      10     120 ..       3     109 ..       1     132 [. 0.72
   2 ?    2.9   0.1     0.011        63     201     222 .]     190     211 ..     172     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-07
                    ATP-grasp_5  10 Lteaeakelleaygipvvetrlassaeeaveaaeeigy..pvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeiler 87 
                                    L+e+eake+l+ yg++++++ l+   +++++ ++e g   p v+K ++  +  + ++gG++l     e+v++a++   e 
  gi|118431318|ref|NP_147696.2|   3 LYEFEAKEILRMYGVETPPSVLVMPGDDVAAKIREAGLepPLVVKSQV-LVAGRGKAGGIKL----VESVEDAVRVAGEL 77 
                                    99********************99999999999888762157777664.37899********....55666666655555 PP

                    ATP-grasp_5  88 vkekspeariegvlVqemakrggrElivgvteD 120
                                     ++  ++     +lV++ ++ +  El  ++  D
  gi|118431318|ref|NP_147696.2|  78 WRKPIKGILPGALLVEKAVP-HDAELYTSIIID 109
                                    55533332223344666666.666666666555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.011
                    ATP-grasp_5 201 ldinPllveeegvvalDarirl 222
                                    ++ nPl + +++vv lDari +
  gi|118431318|ref|NP_147696.2| 190 VESNPLAIVGDKVVPLDARIIV 211
                                    688****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2973.55
//
Query:       gi|118431319|ref|NP_147697.2|  [L=292]
Description: succinyl-CoA synthetase subunit alpha [Aeropyrum pernix K1]
Scores for 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-32  109.9   1.8    9.2e-32  109.6   0.4    1.9  2  CoA_binding    CoA binding domain
      3e-19   69.4   0.1    5.1e-19   68.6   0.1    1.4  1  Ligase_CoA     CoA-ligase
    4.8e-15   55.6   0.0    4.4e-14   52.5   0.0    2.1  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    7.1e-11   42.6   0.2    1.5e-10   41.6   0.1    1.6  2  CoA_binding_2  CoA binding domain
     0.0043   17.9   0.1      0.011   16.5   0.1    1.7  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
       0.11   12.7   0.1         21    5.3   0.0    3.1  3  DUF5130        Domain of unknown function (DUF5130)


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 !  109.6   0.4   3.1e-35   9.2e-32       1      96 []       6     100 ..       6     100 .. 0.98
   2 ?   -1.5   0.0       1.4   4.3e+03       8      15 ..     176     183 ..     145     198 .. 0.61

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 3.1e-35
                                    CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEES-HHHHHHHH CS
                    CoA_binding   1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavitvPaesaqeav 79 
                                    d++t+v+v+G++g+  +g +h k +l+yg+k+v+gv+p+k+g+ev+g+pvy+sv+e+ +++ e+++++++vPa++a +av
  gi|118431319|ref|NP_147697.2|   6 DSETRVLVQGITGR--EGSFHAKAMLEYGTKVVAGVTPGKGGSEVHGVPVYDSVKEALAEHpEINTSIVFVPAPFAPDAV 83 
                                    579***********..*********************************************77***************** PP

                                    HHHHHTT-SEEEEESST CS
                    CoA_binding  80 delveagikgiviiteg 96 
                                     e+v+agi+++v+iteg
  gi|118431319|ref|NP_147697.2|  84 YEAVDAGIRLVVVITEG 100
                                    ***************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                    EETTTSHH CS
                    CoA_binding   8 viGagglg 15 
                                    viG+gg  
  gi|118431319|ref|NP_147697.2| 176 VIGIGGDP 183
                                    45555553 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.1   1.7e-22   5.1e-19       1     151 [.     152     272 ..     152     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.7e-22
                                    EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEE CS
                     Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilld 80 
                                    ++++GtL+ye  ++++ +              g +q+++i++G+d            + +++ealk +++dp++++++l 
  gi|118431319|ref|NP_147697.2| 152 VSRSGTLTYEISYMLTRQ--------------GIGQSTVIGIGGDPIV---------GLSFTEALKLFQEDPQTEALVLI 208
                                    689***************..............***************8.........9********************** PP

                                    EEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHH CS
                     Ligase_CoA  81 ivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraak 151
                                    +++G g  e+ aae++k+ + +k      pv+a++aG +a+p +++++a+a+   g  +++ k +alr a+
  gi|118431319|ref|NP_147697.2| 209 GEIG-GDMEERAAEMIKKGEFTK------PVIAYIAGRTAPPEKRMGHAGAIIMMGTGTYEGKVKALREAG 272
                                    ****.*****************9......**************************************9987 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 ?    0.6   0.0      0.15   4.5e+02      50      77 ..      86     115 ..      82     120 .. 0.81
   2 !   52.5   0.0   1.5e-17   4.4e-14       2     129 ..     147     280 ..     146     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.15
                   Succ_CoA_lig  50 aedpetkvillylEsi..rdgrkflsaarr 77 
                                    a d  ++++++  E+i  +d  +f++ ar+
  gi|118431319|ref|NP_147697.2|  86 AVDAGIRLVVVITEGIpvHDTMRFVNYARQ 115
                                    568999********9833578999999986 PP

  == domain 2  score: 52.5 bits;  conditional E-value: 1.5e-17
                   Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsaarra 78 
                                    G++a++s SG+l  ++  +++++g+g s+v+ +G    + +++++ l+ ++edp+t++++l  E  +d  ++ ++++++ 
  gi|118431319|ref|NP_147697.2| 147 GGVAVVSRSGTLTYEISYMLTRQGIGQSTVIGIGGdpIVGLSFTEALKLFQEDPQTEALVLIGEIGGDmEERAAEMIKKG 226
                                    99********************************94458899**********************99996799******** PP

                   Succ_CoA_lig  79 arkkpvvvlksGrseagaraaashtgal....agsdavvdaafrqaGvlrvdsle 129
                                      +kpv+++ +Gr++  ++  + h ga+    +g ++   +a+r+aGv ++++  
  gi|118431319|ref|NP_147697.2| 227 EFTKPVIAYIAGRTAPPEKR-MGHAGAIimmgTGTYEGKVKALREAGVEVAETPF 280
                                    *************8776655.5777776333357788888999999999888765 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1     5e-14   1.5e-10      13     114 ..      18     129 ..       9     131 .. 0.85
   2 ?   -3.3   0.0       4.2   1.3e+04      84     105 ..     254     275 ..     242     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5e-14
                                    TSHHHHHHHHHHHHT--EEE.ESSS-..SEETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE- CS
                  CoA_binding_2  13 gkfgykvlryllehglpvvp.Vnpke..eeilgekvyaslaed...pepvdlvdvftppeatpeivkealalgakavwlq 86 
                                    g+ g   ++ +le g +vv+ V+p +  +e++g++vy s++e+     ++ +  vf+p+  +p+ v ea+++g++ v++ 
  gi|118431319|ref|NP_147697.2|  18 GREGSFHAKAMLEYGTKVVAgVTPGKggSEVHGVPVYDSVKEAlaeHPEINTSIVFVPAPFAPDAVYEAVDAGIRLVVVI 97 
                                    55666667777777766664499*9999*************8556778889*************************9999 PP

                                    TT....---HHHHHHHHHTT-EEE.ES-HHHH CS
                  CoA_binding_2  87 pg....sedeeaaelaeeagirvvgdrCilve 114
                                     +         ++++a+++g +++g++C++ +
  gi|118431319|ref|NP_147697.2|  98 TEgipvHDTMRFVNYARQKGATIIGPNCPGAI 129
                                    99899888999*****************9975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                    EE-TT---HHHHHHHHHTT-EE CS
                  CoA_binding_2  84 wlqpgsedeeaaelaeeagirv 105
                                    +++     e  +++++eag++v
  gi|118431319|ref|NP_147697.2| 254 IMMGTGTYEGKVKALREAGVEV 275
                                    4444444444556777777776 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 !   16.5   0.1   3.8e-06     0.011       2     114 ..      10     118 ..       9     122 .. 0.81
   2 ?   -3.0   0.0       4.2   1.3e+04      17      43 ..     194     220 ..     183     237 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-06
                                    EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHH.HHHTCTTESEEEE-S-GGGHHHHH CS
                   GFO_IDH_MocA   2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdle.elladpeidavivatpngtheela 79 
                                    rv++ G+ G+ gs h++++ e   +++vva + p++  +e      gv++y++++ +l+++pei+  iv +p+    + +
  gi|118431319|ref|NP_147697.2|  10 RVLVQGItGREGSFHAKAMLEY--GTKVVAGVTPGKGGSEV----HGVPVYDSVKeALAEHPEINTSIVFVPAPFAPDAV 83 
                                    78899998999*****999988..99**********99996....6*******763677777****************** PP

                                    HHHHHTT-...EEEEESSS-SSHHHHHHHHHHHHHHTS CS
                   GFO_IDH_MocA  80 kaaleagk...hvllEKPlattveeakelvelaekkgk 114
                                     +a+ ag+    v+ E  +  +v +  + v++a++kg 
  gi|118431319|ref|NP_147697.2|  84 YEAVDAGIrlvVVITE-GI--PVHDTMRFVNYARQKGA 118
                                    ********76334444.23..66777777777777765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.2
                                    HHHHHTTTTEEEEEEECSSHHHHHHHH CS
                   GFO_IDH_MocA  17 rplnesqrleevvalldpdaeraeava 43 
                                    + ++e  ++e +v + +++    e++a
  gi|118431319|ref|NP_147697.2| 194 KLFQEDPQTEALVLIGEIGGDMEERAA 220
                                    345555555555555555555444444 PP

>> DUF5130  Domain of unknown function (DUF5130)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.43   1.3e+03      59     111 ..      62     117 ..      57     122 .. 0.70
   2 ?    3.0   0.0     0.036   1.1e+02      38      72 ..     191     225 ..     184     238 .. 0.83
   3 ?    5.3   0.0    0.0072        21       8      35 ..     260     287 ..     254     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.43
                        DUF5130  59 gedtaaaareilakvpepenavLiavsPnqraiev.vsGaevad..rvadrvaqlG 111
                                     e +  +++ ++  +p + +av  av    r ++v   G  v+d  r  + + q+G
  gi|118431319|ref|NP_147697.2|  62 AEHPEINTSIVFVPAPFAPDAVYEAVDAGIRLVVViTEGIPVHDtmRFVNYARQKG 117
                                    56667777888889999999999999999887765146777776334445555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                        DUF5130  38 daLkeasrkakvrfavyiGdlgedtaaaareilak 72 
                                    +aLk   ++ +    v iG++g d   +a e+++k
  gi|118431319|ref|NP_147697.2| 191 EALKLFQEDPQTEALVLIGEIGGDMEERAAEMIKK 225
                                    6777777888888889**************99987 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0072
                        DUF5130   8 tssGrisavrelgelsvelPfskddlva 35 
                                    t  G++ a re+g  + e+Pf+  +lv+
  gi|118431319|ref|NP_147697.2| 260 TYEGKVKALREAGVEVAETPFEVPELVR 287
                                    789**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2175.91
//
Query:       gi|14601169|ref|NP_147698.1|  [L=539]
Description: DNA repair helicase [Aeropyrum pernix K1]
Scores for complete 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-22   78.7   0.0    6.4e-22   78.0   0.0    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    2.7e-21   76.3   0.0    4.8e-21   75.5   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
    9.6e-16   58.1   0.0    1.9e-15   57.2   0.0    1.5  1  Helicase_C     Helicase conserved C-terminal domain
    4.9e-07   29.7   0.0    1.2e-06   28.5   0.0    1.6  2  DEAD           DEAD/DEAH box helicase
    1.8e-06   27.7   0.1    5.5e-06   26.2   0.1    1.9  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
     0.0037   17.6   0.0      0.031   14.6   0.0    2.6  3  AAA_22         AAA domain
     0.0037   16.0   0.0      0.033   12.9   0.0    2.1  2  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.045   13.5   0.0      0.085   12.6   0.0    1.4  1  P2_N           Viral coat protein P2 N-terminal domain


Domain annotation for each model (and alignments):
>> 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 !   78.0   0.0   2.8e-25   6.4e-22      34     182 ..     396     536 ..     387     537 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 2.8e-25
                 ERCC3_RAD25_C  34 kkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflsk 114
                                    k  ++ +  +k+ra+e L++   +rg k+ivf+      +e+a++    +++G  +++ r + l kf++ +   ++++  
  gi|14601169|ref|NP_147698.1| 396 MK-EIVQLSESKIRAVEKLVREELSRGSKVIVFTQYRRQAEEIARRTGALLLHGGLERRVREATLAKFRALK-AGALVVTT 474
                                   33.45566789**********************************************************985.6678899* PP

                 ERCC3_RAD25_C 115 vgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrq 182
                                   vgD+ +D+P+anv i +s  +gsrrq  qrlGr+Lr+ ++     ++a  Y ++++ t e   s++r+
  gi|14601169|ref|NP_147698.1| 475 VGDEGLDIPDANVGILVSG-TGSRRQFIQRLGRLLRPGEG-----KRAVLYEVIARGTGEELQSRRRR 536
                                   ***************9986.79***************887.....79*************99999886 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 !   75.5   0.0   2.2e-24   4.8e-21       3     171 .]     166     306 ..     164     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.2e-24
                                   EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                        ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                   elr+yQeea+e+++     k   rg+i+++TG+GKT+va a+++++   +      l++v +++ + q++++f++f++ + 
  gi|14601169|ref|NP_147698.1| 166 ELRDYQEEALEAWR-----KAGGRGVIVLPTGAGKTVVAiAAVAWAGVWS------LIVVYTRDHVRQWIDAFRRFTDAHS 235
                                   79***********9.....5678****************66666666654......99*******************9986 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEE CS
                        ResIII  83 keigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavll 163
                                       + + g++k+        + i+vtt+q++++++        + l   f+++++DEaH++ a +++++i+ + ++ +++
  gi|14601169|ref|NP_147698.1| 236 --LVGAYYGEEKRL-------APITVTTYQTAYRHI--------DRLAPLFPFLVFDEAHHIPA-DKFKRIASASPAPYRM 298
                                   ..677777777777.......7**************........889999**************.**************** PP

                                   EEESS-S- CS
                        ResIII 164 glTATper 171
                                   gl+AT+er
  gi|14601169|ref|NP_147698.1| 299 GLSATIER 306
                                   *****985 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 !   57.2   0.0   8.4e-19   1.9e-15       2     110 ..     406     510 ..     405     511 .. 0.92

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 8.4e-19
                                   HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                    Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                   k++a+ +l+ ++ ++g+k+++f+++++++e  ++    +   ++ lhg l+ + re++l++f++ +   L+ t+v+ +G+d
  gi|14601169|ref|NP_147698.1| 406 KIRAVEKLVrEELSRGSKVIVFTQYRRQAE--EIA---RRTGALLLHGGLERRVREATLAKFRALKAGALVVTTVGDEGLD 481
                                   67778888778889***************6..555...558899*******************99999************* PP

                                   STTESEEEESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                   ip++n+ i ++   + +++iqr GR  R 
  gi|14601169|ref|NP_147698.1| 482 IPDANVGILVSGTGSRRQFIQRLGRLLRP 510
                                   *************************9996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   5.1e-10   1.2e-06       2     170 ..     169     305 ..     168     310 .. 0.79
   2 ?   -3.6   0.0       3.6   8.2e+03      38      63 ..     412     437 ..     394     454 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 5.1e-10
                                   HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                   d+Q+ea+++    gg  ++  +TG+GKT +++ +v           g   liv+ tr  ++q ++ +++f++  +     +
  gi|14601169|ref|NP_147698.1| 169 DYQEEALEAWRkAGGRGVIVLPTGAGKTVVAIAAVA--------WAGVWSLIVVYTRDHVRQWIDAFRRFTDAHS-----L 236
                                   79******999777799999**********888888........67999***********************533.....3 PP

                                   ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                   +g  a+  + ++l   + i+v+t +   ++++ +      + flV+DEa+ +  ++f++  ++  +               
  gi|14601169|ref|NP_147698.1| 237 VG--AYYGEEKRL---APITVTTYQTAYRHID-RL--APLFPFLVFDEAHHIPADKFKRIASASPAPY------------R 297
                                   33..333455567...99***********996.33..46679**********9987776665522222............6 PP

                                   EEEESSBS CS
                                   xxxxxxxx RF
                          DEAD 163 ivlSATlp 170
                                   + lSAT++
  gi|14601169|ref|NP_147698.1| 298 MGLSATIE 305
                                   77777766 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                                   HHHHSTTSTS-EEEEEESSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  38 ivyetkgktgpkalivePtreLaeqt 63 
                                   ++++++ ++g k+++ +  r  ae++
  gi|14601169|ref|NP_147698.1| 412 KLVREELSRGSKVIVFTQYRRQAEEI 437
                                   33333444444444444444444444 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   2.4e-09   5.5e-06      19      57 .]     114     149 ..     102     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.4e-09
                                   .-CT.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                       XPB_DRD  19 slpfvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57 
                                   slp   +D  +++yRap + Y +l+ea++++g+ +eDrv
  gi|14601169|ref|NP_147698.1| 114 SLP---YDREARAYRAPPIMYPRLREAFERRGLKVEDRV 149
                                   466...9*******************************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.4e-05     0.031       7     112 ..     184     288 ..     179     303 .. 0.74
   2 ?   -2.7   0.0         3   6.8e+03      60      84 ..     340     361 ..     316     379 .. 0.57
   3 ?   -2.3   0.0       2.2   4.8e+03      48      68 ..     510     530 ..     485     536 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseell.ealeq 84 
                                    +v++ ++G+GKT+++   + ++  +       + +v +t  +   + d +r++  a  l + +  e++++  +  ++ + 
  gi|14601169|ref|NP_147698.1| 184 RGVIVLPTGAGKTVVAIAAVAWAGVW-------SLIVVYTRDHVRQWIDAFRRFTDAHSLVGAYygEEKRLAPITvTTYQT 257
                                   5677889****************866.......333455555555899999999888888777788666666666444444 PP

                        AAA_22  85 alrarav....ielliiDEaqhlrseealeeL 112
                                   a r+ ++     ++l+ DEa+h+ +++ ++ +
  gi|14601169|ref|NP_147698.1| 258 AYRHIDRlaplFPFLVFDEAHHI-PADKFKRI 288
                                   4444444777*************.87777766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
                        AAA_22  60 llralglelkaerlsseellealeq 84 
                                   + r +++el++   ++++l+e l +
  gi|14601169|ref|NP_147698.1| 340 VIRRVKVELEE---EEKRLYEDLKR 361
                                   44444444444...33333322222 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                        AAA_22  48 psstsskdllrellralglel 68 
                                   p++++++ l++ ++r +g+el
  gi|14601169|ref|NP_147698.1| 510 PGEGKRAVLYEVIARGTGEEL 530
                                   333344444555555555544 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 !   12.9   0.0   1.5e-05     0.033      64     214 ..     191     303 ..     161     322 .. 0.74
   2 ?    1.4   0.0     0.045     1e+02     252     312 ..     306     368 ..     295     403 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                   TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH--------- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N  64 mGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkva 143
                                   +G+GKTv ++a ++                ++ +  Livv + + ++qW + ++r++   +l   +yg++k          
  gi|14601169|ref|NP_147698.1| 191 TGAGKTVVAIAAVA----------------WAGVWSLIVVYTrDHVRQWIDAFRRFTDAHSLVGAYYGEEK---------- 245
                                   78888888888888................5556678999888*******************777777653.......... PP

                                   --------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 144 pklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGT 214
                                       + + + +ttY++  r+       + l  +   ++v DE+h +   + k    +s   + +r+ l++T
  gi|14601169|ref|NP_147698.1| 246 ----RLAPITVTTYQTAYRHI------DRLAPL-FPFLVFDEAHHIPADKFKRIASAS--PAPYRMGLSAT 303
                                   ....35789999999999777......666555.457889999999877655544444..67777777777 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.045
                                   HHHHHHHHHHTT-STTEE---GGGT..--S---EEEEEEEEE--HHHHHHHH........... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        SNF2_N 252 qaekgrsrLlqllqrlmlrrakkdv..eknlPpkteeiiflklskverksYnrllevlrkkal 312
                                    ++ + ++ ++l+  ++ +++  ++  + +l+p + + + ++l+++e+++Y++l+ + r  a+
  gi|14601169|ref|NP_147698.1| 306 REDGRHEEVYSLVGGVVYSSSPGELtrKGYLAPFVIRRVKVELEEEEKRLYEDLKRKYRILAR 368
                                   445566788999999999999999975557**********************77766665544 PP

>> P2_N  Viral coat protein P2 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.8e-05     0.085      21      96 ..     367     443 ..     364     463 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                          P2_N  21 piGptYekIvLelggtakaqItrirvklNgkeiiqvsgadldklnaykglaadagflvidFtdisak.tkagqrlga 96 
                                   + G+++ekI+      +++ I++irv    kei+q+s ++++++++  +   + g  vi Ft+ + + ++ ++r+ga
  gi|14601169|ref|NP_147698.1| 367 ARGRSFEKILEDARRGDPTAIEAIRVNTRMKEIVQLSESKIRAVEKLVREELSRGSKVIVFTQYRRQaEEIARRTGA 443
                                   56788888887788888********************************************9865441444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 3935.74
//
Query:       gi|14601171|ref|NP_147700.1|  [L=163]
Description: hypothetical protein APE_1078 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   10.6   0.0       0.18   10.2   0.0    1.1  1  DUF2863   Protein of unknown function (DUF2863)
       0.38   11.6   1.5         23    6.1   0.2    2.7  3  HEAT_PBS  PBS lyase HEAT-like repeat


Domain annotation for each model (and alignments):
>> DUF2863  Protein of unknown function (DUF2863)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     2e-05      0.18     282     323 ..      42      83 ..      37      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2e-05
                       DUF2863 282 eaaelraviaafgeerleEyRigftlresneviyGvvWpllg 323
                                     +el+av+aa +   ++E  i ++  +  +v y v W++ +
  gi|14601171|ref|NP_147700.1|  42 GEEELHAVVAALEKMGVDEALIRLSSAGGLQVFYHVSWSMED 83 
                                   5689**********************************9854 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 ?    3.9   0.1     0.012   1.1e+02       3      21 ..      47      65 ..      46      68 .. 0.85
   2 ?    6.1   0.2    0.0025        23       4      25 ..      88     108 ..      86     109 .. 0.90
   3 ?   -3.1   0.0         2   1.8e+04       7      13 ..     137     143 ..     137     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                                  HHHHHHHHHCTSGGGHHHH CS
                      HEAT_PBS  3 raAakaLgqlgdeeaipaL 21
                                  +a + aL ++g +ea+ +L
  gi|14601171|ref|NP_147700.1| 47 HAVVAALEKMGVDEALIRL 65
                                  7999********9998666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0025
                                   HHHHHHHHCTSGGGHHHHHHHC CS
                      HEAT_PBS   4 aAakaLgqlgdeeaipaLleaL 25 
                                   aAa  L  +gd e  p+Ll+a 
  gi|14601171|ref|NP_147700.1|  88 AAALVLRGCGD-EWGPRLLKAA 108
                                   9**********.****999996 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2
                                   HHHHHCT CS
                      HEAT_PBS   7 kaLgqlg 13 
                                   kaL +lg
  gi|14601171|ref|NP_147700.1| 137 KALEKLG 143
                                   6888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1235.34
//
Query:       gi|118431320|ref|NP_147701.2|  [L=235]
Description: hypothetical protein APE_1080.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-06   27.3   0.1    4.3e-06   26.3   0.1    1.5  1  Pribosyltran  Phosphoribosyl transferase domain
    0.00089   19.0   0.1     0.0035   17.1   0.2    2.0  2  HTH_IclR      IclR helix-turn-helix domain
     0.0017   18.4   0.0     0.0032   17.5   0.0    1.5  1  HTH_3         Helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.4   0.0      0.018   14.6   0.0    1.4  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.019   14.4   0.0       0.03   13.8   0.0    1.3  1  UPRTase       Uracil phosphoribosyltransferase
      0.078   12.5   0.2        0.2   11.2   0.2    1.7  1  Sigma70_r4    Sigma-70, region 4
      0.083   12.8   0.0       0.41   10.6   0.0    2.0  2  HTH_5         Bacterial regulatory protein, arsR family
       0.13   12.5   0.0       0.95    9.7   0.0    2.2  2  HTH_17        Helix-turn-helix 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 !   26.3   0.1   1.9e-09   4.3e-06      27     120 ..     111     210 ..      96     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.9e-09
                                    -GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.............EE----TT.SEEEEE-SEESSS CS
                   Pribosyltran  27 ngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.....rlledpag.kkVliVDDildtG 100
                                    +g  d++v+++ gGv+fa+++a     pla+ r+++   ++  e++      +      +l  ++g +  +iVDD+   G
  gi|118431320|ref|NP_147701.2| 111 RGLFDAIVAPEVGGVTFATAVAMVSRKPLAIARRSRMGWERFVEIPVYRDPATveyyyLNLDYLRGvEAAIIVDDFGVRG 190
                                    56789***************************************987665555*****777777763789********** PP

                                    HHHHHHHHHHHCC-BSEEEE CS
                   Pribosyltran 101 gTllaalelLkekgpeevri 120
                                     Tl  ++e+L+ +g e+ ++
  gi|118431320|ref|NP_147701.2| 191 ATLAGFVEALEGHGIEVKGV 210
                                    **************974333 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 !   17.1   0.2   1.6e-06    0.0035      12      38 ..      16      42 ..      11      44 .. 0.90
   2 ?   -3.0   0.0         3   6.7e+03      28      46 ..     186     204 ..     182     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.6e-06
                                   -CTTBSS-BHHHHHHHHTS-HHHHHHH CS
                       HTH_IclR 12 laeapqeltlselArrtglpkStvhRl 38
                                   l++a++ +tl+el++ +glp S+v+R+
  gi|118431320|ref|NP_147701.2| 16 LRSARRFMTLRELSEVLGLPVSAVSRY 42
                                   6778888*******************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3
                                    HTS-HHHHHHHHHHHHHTT CS
                       HTH_IclR  28 tglpkStvhRlLqtLvelG 46 
                                    +g+  +t  +++  L+ +G
  gi|118431320|ref|NP_147701.2| 186 FGVRGATLAGFVEALEGHG 204
                                    5666677788888888887 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0032      10      47 ..      23      60 ..      20      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHH CS
                          HTH_3 10 lsqeeLAeklGvsrstisriEnGernPsletlkklaka 47
                                   ++++eL+e+lG+++s++sr+ n +  Ps+e + ++ + 
  gi|118431320|ref|NP_147701.2| 23 MTLRELSEVLGLPVSAVSRYSNLKLLPSVESARRIIEG 60
                                   899*****************************999886 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     8e-06     0.018      15      37 ..      19      42 ..      14      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8e-06
                         HTH_24 15 npr.isqreLAerlglSpstvnrr 37
                                     r ++ reL+e lgl++s+v+r+
  gi|118431320|ref|NP_147701.2| 19 ARRfMTLRELSEVLGLPVSAVSRY 42
                                   55569*****************98 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.3e-05      0.03      93     159 ..     151     215 ..     137     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.3e-05
                        UPRTase  93 rvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsv 159
                                    r++++ ++r+++t e   yy +L      + ++++D     G+++a +++ L  +g++++ + ++  
  gi|118431320|ref|NP_147701.2| 151 RFVEIPVYRDPATVE--YYYLNLDYLRGVEAAIIVDDFGVRGATLAGFVEALEGHGIEVKGVYLMVG 215
                                    688999*****9976..9*******99********************************99987765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   8.9e-05       0.2       8      39 ..       9      41 ..       7      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.9e-05
                                   HHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHH CS
                     Sigma70_r4  8 rerevlelrf.geglTleEIgerlgiSrerVrq 39
                                   r r  l lr   + +Tl E++e+lg++ ++V++
  gi|118431320|ref|NP_147701.2|  9 RYRAALILRSaRRFMTLRELSEVLGLPVSAVSR 41
                                   557777777777889****************97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00018      0.41      16      35 ..      23      42 ..      12      42 .. 0.86
   2 ?   -1.4   0.0      0.99   2.2e+03      14      24 ..      82      92 ..      79      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                   EEHHHHHHHHTS-HHHHHHH CS
                          HTH_5 16 lcvcelaeelglsqstvShH 35
                                   ++  el+e lgl+ s+vS++
  gi|118431320|ref|NP_147701.2| 23 MTLRELSEVLGLPVSAVSRY 42
                                   8999**************85 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.99
                                   SSEEHHHHHHH CS
                          HTH_5 14 gelcvcelaee 24
                                   +e++v +++ +
  gi|118431320|ref|NP_147701.2| 82 REATVYDISSA 92
                                   799*****986 PP

>> HTH_17  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   0.00042      0.95       1      31 [.      22      52 ..      22      60 .. 0.84
   2 ?   -0.3   0.0      0.55   1.2e+03      16      30 ..     128     141 ..     124     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00042
                         HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaak 31
                                   ++t  E++e Lg+ +s v r+ + + lp + 
  gi|118431320|ref|NP_147701.2| 22 FMTLRELSEVLGLPVSAVSRYSNLKLLPSVE 52
                                   69*******************9999998873 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.55
                         HTH_17  16 stvyrlirrgelpaa 30 
                                    +t+  +++r++l a 
  gi|118431320|ref|NP_147701.2| 128 ATAVAMVSRKPL-AI 141
                                    69999******9.54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1886.97
//
Query:       gi|118431321|ref|NP_147702.2|  [L=308]
Description: signal recognition particle protein [Aeropyrum pernix K1]
Scores for 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-74  247.7   0.0    9.1e-74  247.3   0.0    1.1  1  SRP54            SRP54-type protein, GTPase domain
    5.5e-09   36.1   0.6    1.7e-08   34.5   0.2    2.0  2  SRP54_N          SRP54-type protein, helical bundle domain
    8.5e-06   25.6   0.7    1.5e-05   24.8   0.7    1.4  1  AAA_30           AAA domain
    8.9e-05   22.9   0.2    0.00025   21.5   0.1    1.9  1  AAA_16           AAA ATPase domain
     0.0008   19.8   0.0     0.0013   19.1   0.0    1.3  1  AAA_19           AAA domain
     0.0009   18.9   0.1     0.0014   18.3   0.1    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0014   18.9   0.0     0.0029   17.9   0.0    1.5  1  AAA_22           AAA domain
     0.0022   17.0   4.3     0.0028   16.7   1.5    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0063   15.9   0.0      0.012   15.0   0.0    1.4  1  ATPase           KaiC
     0.0093   16.4   0.0      0.018   15.5   0.0    1.7  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   15.5   0.4      0.064   13.0   0.4    2.1  1  AAA_24           AAA domain
      0.015   15.7   0.1      0.032   14.7   0.1    1.6  1  AAA_17           AAA domain
      0.017   15.0   0.0       0.03   14.2   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.018   15.1   0.0      0.061   13.4   0.0    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.03   14.6   0.1       0.18   12.1   0.0    2.1  2  AAA_28           AAA domain
      0.045   13.9   0.1      0.088   13.0   0.1    1.6  1  AAA_33           AAA domain
      0.052   13.5   1.7        0.3   11.0   0.3    2.3  2  NTPase_1         NTPase
      0.062   12.6   0.0       0.13   11.5   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.093   12.5   0.3        1.1    9.0   0.1    2.7  4  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
       0.15   11.7   0.1       0.85    9.3   0.0    2.0  2  Thymidylate_kin  Thymidylate kinase
       0.22   11.0   0.0       0.34   10.4   0.0    1.2  1  AAA_7            P-loop containing dynein motor region


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 !  247.3   0.0   1.1e-76   9.1e-74       2     196 .]     114     308 .]     113     308 .] 0.99

  Alignments for each domain:
  == domain 1  score: 247.3 bits;  conditional E-value: 1.1e-76
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                     vil++G++G+GKTtt+aK+a +l+k g +++++aaDtfRa+A+eQL+++aeklgvp+++ + + dpa+va++av++a++
  gi|118431321|ref|NP_147702.2| 114 LVILFLGVNGTGKTTTIAKVAYMLRKAGVTPVIAAADTFRAGAQEQLAVHAEKLGVPIVRGRYGGDPASVAYDAVKHAES 193
                                    69****************************************************************************** PP

                                    TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHH CS
                          SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaals 161
                                    +++ +vlvDTaGr++ d++l+eel+ki +vvkpd ++lv+d++tg++av+qa+ F+eavg++gvi+tk+D+d kgG+++s
  gi|118431321|ref|NP_147702.2| 194 RGFCAVLVDTAGRMHVDSNLVEELRKIVRVVKPDYKILVVDSLTGNDAVEQARLFDEAVGVDGVIVTKVDADPKGGTLVS 273
                                    ******************************************************************************** PP

                                    HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                    +a+++ +Pi +ig+G+++edl++fdp+++v++llg
  gi|118431321|ref|NP_147702.2| 274 VAHAIRKPILYIGTGQRYEDLRPFDPQKIVDQLLG 308
                                    ********************************995 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 !   34.5   0.2     2e-11   1.7e-08      15      75 .]      26      85 ..      16      85 .. 0.90
   2 ?   -2.1   0.0       5.4   4.6e+03      20      53 ..     211     219 ..     200     229 .. 0.61

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2e-11
                                   SSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
                        SRP54_N 15 kskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75
                                   +++++ edle +l+++   L+e+DV++++++++++ vk+   g  ++++++ v+k+v+d+L
  gi|118431321|ref|NP_147702.2| 26 YKELKPEDLEPVLDDILIDLVESDVALEAAESIVAGVKEGLTG-YRVRRGEPVEKVVRDAL 85
                                   5789***********************************9888.99*************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.4
                                    HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHH CS
                        SRP54_N  20 eedleealkeleeaLleaDVgvkvvkklienvkk 53 
                                      ++ee                         ++k
  gi|118431321|ref|NP_147702.2| 211 SNLVEE-------------------------LRK 219
                                    444444.........................222 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.7   1.8e-08   1.5e-05      15     140 ..     110     251 ..     102     263 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.8e-08
                         AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaag.grviglAptgkaAkvLaeelgieastiakllkrlk............ 81 
                                    +++ +v +  G+ GtGKtt++++++ ++++ag  +vi++A t +a ++  e+l ++a+ +   + r +            
  gi|118431321|ref|NP_147702.2| 110 GGRPLVILFLGVNGTGKTTTIAKVAYMLRKAGvTPVIAAADTFRAGAQ--EQLAVHAEKLGVPIVRGRyggdpasvayda 187
                                    5556788899*********************76899999999998664..445555555554444444455555555554 PP

                         AAA_30  82 .grarlepg.tllivDEagmv..dtkqlaallkaaeka..gakvilvGDerQlasVeaGgvlrdl 140
                                     ++a+ ++g   ++vD ag +  d++ +++l k+++    + k+++v      ++Ve+ +++++ 
  gi|118431321|ref|NP_147702.2| 188 vKHAE-SRGfCAVLVDTAGRMhvDSNLVEELRKIVRVVkpDYKILVVDSLTGNDAVEQARLFDEA 251
                                    32122.23457788888887656666565555555442126777777666666666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.9e-07   0.00025      12     148 ..     101     240 ..      80     253 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.9e-07
                         AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql..esaipysalaqalareellrqllde 88 
                                    L++  +r + grp ++l+ G  G+GK++ + +++  l+k+ g++ + + +d +  +++  +++ a+ l    ++r     
  gi|118431321|ref|NP_147702.2| 101 LAAEARRRCGGRPLVILFLGVNGTGKTTTIAKVAYMLRKA-GVTpVIAAADTFraGAQEQLAVHAEKL-GVPIVRGRYGG 178
                                    5566678999************************666666.444566666666222222333355555.33444444444 PP

                         AAA_16  89 aesaeleawrekleeala....avpelagaea....srllellkrllallsrderplvlvlDdlqwad 148
                                     + a++++++ k  e+ +        ++ a++    s l e+l+++++  ++d +  +lv+D l   d
  gi|118431321|ref|NP_147702.2| 179 -DPASVAYDAVKHAESRGfcavL---VDTAGRmhvdSNLVEELRKIVRVVKPDYK--ILVVDSLTGND 240
                                    .3335555555555555564432...22222244578888888888888888666..78888776555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-06    0.0013      12     127 ..     115     253 ..     104     264 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                         AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrA..akelrerlaalgae..................... 68 
                                    v+l ++  GtGKT+++ ++  +l ++g v   +++++a t rA   ++l+   ++lg++                     
  gi|118431321|ref|NP_147702.2| 115 VILFLGVNGTGKTTTIAKVAYMLRKAG-V--TPVIAAADTFRAgaQEQLAVHAEKLGVPivrgryggdpasvaydavkha 191
                                    56778999********87666666666.6..5666666666651166777777777777888888888888877776666 PP

                         AAA_19  69 .........atTiHrlalldfddlltealelleeaeeekklqeee.llivDEfqdvd.elqyrLlkallg 127
                                              +T  r   +++d+ l   +e l++    + ++  + +l+vD     d   q rL+++ +g
  gi|118431321|ref|NP_147702.2| 192 esrgfcavlVDTAGR---MHVDSNL---VEELRK--IVRVVKPDYkILVVDSLTGNDaVEQARLFDEAVG 253
                                    655544333222222...3444444...334343..3445555556999999999998888888887765 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 !   18.3   0.1   1.6e-06    0.0014       2     158 ..     115     271 ..     114     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-06
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCC...CT.EEEETTTTECCHCTT-HHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellret...gveivelenGciCctlredllkeleal 76 
                                    v+++ G  G+GKTt + ++    ++ag    +   +    +  ++l  ++   gv+iv    G+ + +++ d++k+    
  gi|118431321|ref|NP_147702.2| 115 VILFLGVNGTGKTTTIAKVAymLRKAGVTPVIAAADTFRAGAQEQLAVHAeklGVPIVRGRYGGDPASVAYDAVKH---A 191
                                    67788999**********9988788888888889999999988888866623455577777777777766665554...4 PP

                                    HHHHTT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCH CS
                           cobW  77 eereerldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDllde 155
                                    e+r   + ++l+ t G ++     + + +++ + ++ d ++ vvD+    ++  ++++++++     d ++++K+D  ++
  gi|118431321|ref|NP_147702.2| 192 ESRG--FCAVLVDTAGRMHVDSNlVEELRKIVRVVKPDYKILVVDSLTG-NDAVEQARLFDEA-VGVDGVIVTKVDADPK 267
                                    5555..999*******6666665255599999**************554.5555555555555.567999******9887 PP

                                    C... CS
                           cobW 156 e.al 158
                                      +l
  gi|118431321|ref|NP_147702.2| 268 GgTL 271
                                    7444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.4e-06    0.0029       7     118 ..     115     223 ..     107     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-06
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka..erlsseellea 81 
                                    +++  G  GtGKTt+++++++ l         +++v  v ++++t   + ++ l   +++lg++  +  ++++   +   
  gi|118431321|ref|NP_147702.2| 115 VILFLGVNGTGKTTTIAKVAYMLR--------KAGVTPVIAAADTfraGAQEQLAVHAEKLGVPIVRgrYGGDPASVAYD 186
                                    68889******************4........999999999999988888888888899999998889977787777766 PP

                         AAA_22  82 leqalraravielliiDEaqhlr.seealeeLrsllnl 118
                                      +++++r+   ++++D a ++    +++eeLr+++ +
  gi|118431321|ref|NP_147702.2| 187 AVKHAESRGF-CAVLVDTAGRMHvDSNLVEELRKIVRV 223
                                    6666666666.7**********5559******999875 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 !   16.7   1.5   3.3e-06    0.0028      26     147 ..     110     221 ..      95     228 .. 0.77
   2 ?   -2.5   0.1       2.3     2e+03     115     132 ..     246     264 ..     237     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                                    -S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTTEEEEEE-----HHH CS
                           MeaB  26 aGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdegvfiRslpsrGalGG 105
                                     Gr  v+ + Gv G+Gk t++ +++  lr++G    + a D   +f  G+    + +l+ +a + gv i     rG+ GG
  gi|118431321|ref|NP_147702.2| 110 GGRPLVILFLGVNGTGKTTTIAKVAYMLRKAGVTPVIAAAD---TFRAGA----QEQLAVHAEKLGVPI----VRGRYGG 178
                                    47999***************************988777777...566665....566666666666654....5888888 PP

                                    H.HHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEE CS
                           MeaB 106 l.aaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfv 147
                                      a  + ++v+  e+ Gf  vl++t G    + +++e    +v
  gi|118431321|ref|NP_147702.2| 179 DpASVAYDAVKHAESRGFCAVLVDTAGRMHVDSNLVEELRKIV 221
                                    6266788999999999999999999997776666666555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                                    HHH.HHTT-SEEEEEEESS CS
                           MeaB 115 lll.eaaGfDvvlietvGv 132
                                    +l+ ea+G D v++  v +
  gi|118431321|ref|NP_147702.2| 246 RLFdEAVGVDGVIVTKVDA 264
                                    5552689999999988865 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.4e-05     0.012      21     133 ..     115     241 ..     110     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                         ATPase  21 vvlitGepGtGKtifalqFlikgaekygepgvfvtveepa....edlrenakslGwdlekleeeg..klaiidasesaee 94 
                                    v+l  G+ GtGKt+  ++ ++   +k g   v+ + +       e+l  +a++lG+ + + +  g    +  da+++ae 
  gi|118431321|ref|NP_147702.2| 115 VILFLGVNGTGKTTTIAKVAYML-RKAGVTPVIAAADTFRagaqEQLAVHAEKLGVPIVRGRYGGdpASVAYDAVKHAES 193
                                    78999**********99999987.55598888888887666788*************98765555115667788888776 PP

                         ATPase  95 saee........kdkedle.elieelaeaikeika..krvviDsitglay 133
                                    +            +++ ++ +l+eel+++++ +k   k +v+Ds+tg + 
  gi|118431321|ref|NP_147702.2| 194 R--GfcavlvdtAGRMHVDsNLVEELRKIVRVVKPdyKILVVDSLTGNDA 241
                                    4..245889988777777537************9999********99743 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 !   15.5   0.0   2.1e-05     0.018       1      70 [.     116     207 ..     116     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                    EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS....................STTHHHHHHHHHHHHHHHTS CS
                            AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellsk....................yvgesekkirelfkeakeka 57 
                                    +l+ G  GtGKT+++  va  l   gv+ +   + +++                      y g+ ++   + +k+a++  
  gi|118431321|ref|NP_147702.2| 116 ILFLGVNGTGKTTTIAKVAYMLrkaGVTPVIAAADTFRAGaqeqlavhaeklgvpivrgrYGGDPASVAYDAVKHAESRG 195
                                    699****************9974334554444444444223344444444444444444455555555556666555554 PP

                                    TSEEEEEETGGGH CS
                            AAA  58 kpsilfiDEidal 70 
                                      + +++D + ++
  gi|118431321|ref|NP_147702.2| 196 -FCAVLVDTAGRM 207
                                    .566666655555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.4   7.5e-05     0.064       3      75 ..     114     237 ..     112     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.5e-05
                         AAA_24   3 lkiliyGpsgiGKTtlakel.........gpkplfidtek.Glksldadkfpdie....................swedf 52 
                                    l il  G +g+GKTt++++          +p ++  dt++ G+++  a + +++                     +    
  gi|118431321|ref|NP_147702.2| 114 LVILFLGVNGTGKTTTIAKVaymlrkagvTPVIAAADTFRaGAQEQLAVHAEKLGvpivrgryggdpasvaydavK---- 189
                                    679999*************988888774433333345555555555444444443555555555554444333331.... PP

                         AAA_24  53 ldevvel..............................aaeladyktlviDtid 75 
                                                                         +  ++dyk+lv+D+++
  gi|118431321|ref|NP_147702.2| 190 -----HAesrgfcavlvdtagrmhvdsnlveelrkivRVVKPDYKILVVDSLT 237
                                    .....224445666667778888888888888888899999999999999987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.7e-05     0.032       1     108 [.     119     232 ..     119     255 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                                    EE-TTSSHHHHHHHHH...HHHTEE.EEEHHHHHHHHHHTTTSHSSHHHHC..TSHHHHHHHHHHHHHHHHHHHHHSSE. CS
                         AAA_17   1 lGgPGsGKgtqceklv...ekygft.hlsaGdllreeakrgglakardemr..klpleekkelqkeaaekiaeeakkkg. 73 
                                    lG+ G GK+t ++k++   +k g+t ++ a d +r+ a+++ ++ + +++    +  +   +    a +++++++ ++g 
  gi|118431321|ref|NP_147702.2| 119 LGVNGTGKTTTIAKVAymlRKAGVTpVIAAADTFRAGAQEQLAV-HAEKLGvpIVRGRYGGDPASVAYDAVKHAE-SRGf 196
                                    79*************9666677765499*********9877554.444443233344444455566666666654.3443 PP

                                    ..EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                         AAA_17  74 ..vlvdghprikeqagfldglpkevleelkpdaiill 108
                                      vlvd+  r+  ++ ++++l  ++++ +kpd  il+
  gi|118431321|ref|NP_147702.2| 197 caVLVDTAGRMHVDSNLVEELR-KIVRVVKPDYKILV 232
                                    4479999999877777777665.57888888665554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.6e-05      0.03       1      54 [.     112     165 ..     112     172 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.6e-05
                                    S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHH CS
                     APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfsee 54 
                                    r++v+++ G+ g+GK+t   +++ +L++ g++ ++   d+ R g +++L+ ++e
  gi|118431321|ref|NP_147702.2| 112 RPLVILFLGVNGTGKTTTIAKVAYMLRKAGVTPVIAAADTFRAGAQEQLAVHAE 165
                                    5789*************999************************9999987765 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 ?   13.4   0.0   7.2e-05     0.061       9      88 ..     123     266 ..     120     284 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                    G+GKTt+ a+ a  l ++g   +   aD+ +       g +++++                                   
  gi|118431321|ref|NP_147702.2| 123 GTGKTTTIAKVAYMLRKAGVTPVIAAADTFR------AGAQEQLAVhaeklgvpivrgryggdpasvaydavkhaesrgf 196
                                    9****************98875555555542......2333333333344555555599999999999999999999999 PP

                                    ...........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS.. CS
                                    ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ...........................................dlkrllellealgkkkalllkiagvvlnrvdgen 88 
                                                                               d+    +l+ + +++        gv++++vd + 
  gi|118431321|ref|NP_147702.2| 197 cavlvdtagrmhvdsnlveelrkivrvvkpdykilvvdsltgnDAVEQARLFDEAVGV-------DGVIVTKVDADP 266
                                    9999999999999999999888888888888888888777777666667777555554.......799999988875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.98   8.3e+02      80     102 ..      18      40 ..       7      88 .. 0.86
   2 ?   12.1   0.0   0.00021      0.18       2      43 ..     116     164 ..     115     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.98
                         AAA_28  80 rglldtlaYarayggeaeaelea 102
                                    rg++dtlaY +   ++ e+ l++
  gi|118431321|ref|NP_147702.2|  18 RGIVDTLAYKELKPEDLEPVLDD 40 
                                    89999999999999998888877 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00021
                         AAA_28   2 ivitGgestGKTtlleaLa...ar.g.ypvv..pEaareileeklakge 43 
                                    i ++G  +tGKTt++++ a   ++ g +pv+  ++++r   +e+la + 
  gi|118431321|ref|NP_147702.2| 116 ILFLGVNGTGKTTTIAKVAymlRKaGvTPVIaaADTFRAGAQEQLAVHA 164
                                    7899**************9665225636666667777777777776555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1    0.0001     0.088       1      34 [.     115     153 ..     115     234 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlr 34 
                                    ++l+ G++G+GK+t + ++   l+k g   v+ + dt+r
  gi|118431321|ref|NP_147702.2| 115 VILFLGVNGTGKTTTIAKVaymLRKAGvtPVIAAADTFR 153
                                    89**************99944444444655555555544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00035       0.3       6      29 ..     120     143 ..     115     146 .. 0.89
   2 ?    1.4   0.1      0.31   2.6e+02      84     131 ..     183     233 ..     150     267 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                                    --TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1   6 GppGvGKtTlvkkvlellkssgvk 29 
                                    G  G+GKtT + kv+ +l++ gv+
  gi|118431321|ref|NP_147702.2| 120 GVNGTGKTTTIAKVAYMLRKAGVT 143
                                    889****************99985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHH-..EEEE---STTGGG-HHHHH..HHHHHHTTTSEEEEE CS
                       NTPase_1  84 lalealrkalsead..viviDEiGkmElkskkfke..aveevLksekpvlav 131
                                    +a +a+++a s  +   +++D  G+m + s+ ++e  ++ +v+k++  +l+v
  gi|118431321|ref|NP_147702.2| 183 VAYDAVKHAES-RGfcAVLVDTAGRMHVDSNLVEElrKIVRVVKPDYKILVV 233
                                    55556665542.2223567899999999888776422466666666666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015      0.13      13      56 ..     110     154 ..     100     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                     Zeta_toxin  13 qerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRe 56 
                                    + rP +il  G  G GK++++++++  l+ ++   v   +D++R+
  gi|118431321|ref|NP_147702.2| 110 GGRPLVILFLGVNGTGKTTTIAKVAYMLRkAGVTPVIAAADTFRA 154
                                    489**********************99985555677778888885 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 ?   -3.0   0.0       6.6   5.7e+03      28      55 ..       6      33 ..       4      38 .. 0.81
   2 ?    9.0   0.1    0.0013       1.1       1      43 [.     130     172 ..     130     182 .. 0.83
   3 ?   -2.7   0.0       5.4   4.6e+03      25      52 ..     211     242 ..     203     247 .. 0.52
   4 ?   -0.4   0.0         1   8.7e+02      11      26 ..     278     293 ..     271     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.6
                                   HHHHHHHHHHHT-EEEEEGGGTTSS-TT CS
                   TPP_enzyme_M 28 seelrelaeklgiPvvttlmgkgviped 55
                                   +e+l++ +e++   +v+tl+ k + ped
  gi|118431321|ref|NP_147702.2|  6 REALNRASEHIARGIVDTLAYKELKPED 33
                                   6788889999999999999988888876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHH-S.SEEEEE-CHHCHTTGHHHHHHHHHHHT-EEE CS
                   TPP_enzyme_M   1 iekaaellkaak.rpvilvGggvarsgaseelrelaeklgiPvv 43 
                                    i+k+a +l++a   pvi +     r+ga+e+l+  aeklg+P+v
  gi|118431321|ref|NP_147702.2| 130 IAKVAYMLRKAGvTPVIAAADTF-RAGAQEQLAVHAEKLGVPIV 172
                                    68999999999845666666655.5*****************98 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.4
                                    TTGHHHHHHHHH....HHT-EEEEEGGGTTSS CS
                   TPP_enzyme_M  25 sgaseelrelae....klgiPvvttlmgkgvi 52 
                                    s+  eelr+ ++     ++i vv++l g +++
  gi|118431321|ref|NP_147702.2| 211 SNLVEELRKIVRvvkpDYKILVVDSLTGNDAV 242
                                    55555555554422223456666666666555 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1
                                    -SSEEEEE-CHHCHTT CS
                   TPP_enzyme_M  11 akrpvilvGggvarsg 26 
                                     ++p++++G g ++++
  gi|118431321|ref|NP_147702.2| 278 IRKPILYIGTGQRYED 293
                                    589*******988765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     0.001      0.85       3      26 ..     120     143 ..     118     150 .. 0.88
   2 ?   -0.6   0.0       1.1   9.3e+02     101     125 ..     208     233 ..     203     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                                    ESTTSSHHHHHHHHHHHHHHTTE. CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik 26 
                                    G++G+GKtt +++++  l+++g  
  gi|118431321|ref|NP_147702.2| 120 GVNGTGKTTTIAKVAYMLRKAGVT 143
                                    9***************99999865 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                                    TTTCHHHHHHGGGTTS.E-SEEEEEE CS
                Thymidylate_kin 101 gvdldlvlslnedvll.kPdltflld 125
                                    +vd +lv +l++ v   kPd+ +l+ 
  gi|118431321|ref|NP_147702.2| 208 HVDSNLVEELRKIVRVvKPDYKILVV 233
                                    58889999999988778999999875 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    0.0004      0.34      36      65 ..     116     145 ..     111     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                          AAA_7  36 vllvGptGtGKtviikdllkkldkekylsl 65 
                                    +l+ G  GtGKt++i ++   l k  ++++
  gi|118431321|ref|NP_147702.2| 116 ILFLGVNGTGKTTTIAKVAYMLRKAGVTPV 145
                                    79***************9999887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2122.42
//
Query:       gi|118431322|ref|NP_147703.2|  [L=151]
Description: prefoldin subunit alpha [Aeropyrum pernix K1]
Scores for complete 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-23   81.7   1.5    4.9e-23   81.3   1.5    1.2  1  Prefoldin        Prefoldin subunit
     0.0033   17.3   7.9       0.15   12.0   0.6    2.2  2  Prefoldin_2      Prefoldin subunit
     0.0068   16.0   2.8      0.096   12.3   0.9    2.1  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0087   16.1   6.4       0.15   12.0   0.2    2.1  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
  ------ inclusion threshold ------
      0.013   15.9   4.6      0.033   14.5   4.6    1.6  1  CCDC-167         Coiled-coil domain-containing protein 167
      0.015   14.9   3.1      0.073   12.7   3.0    1.9  1  BAR              BAR domain
      0.015   14.7   1.8      0.015   14.7   1.8    1.9  2  vATP-synt_E      ATP synthase (E/31 kDa) subunit
      0.018   15.2   4.0      0.098   12.8   1.7    2.1  2  Fib_alpha        Fibrinogen alpha/beta chain family
      0.031   14.2   2.7        0.8    9.6   0.4    2.2  2  Takusan          Takusan
      0.079   13.5   1.3        2.7    8.6   0.2    2.2  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.084   13.3   0.1        2.3    8.7   0.0    2.1  2  MtrB             Tetrahydromethanopterin S-methyltransferase 
      0.088   13.1   0.1       0.11   12.7   0.1    1.3  1  HHH_6            Helix-hairpin-helix motif
        0.1   12.4   6.9       0.31   10.8   0.4    2.2  2  Nsp1_C           Nsp1-like C-terminal region
       0.11   12.6   5.5       0.96    9.6   0.2    2.4  2  Med9             RNA polymerase II transcription mediator com
       0.12   12.5   0.3       0.12   12.5   0.3    1.6  2  DUF4715          Domain of unknown function (DUF4715)
       0.13   12.1   5.2        3.4    7.5   0.1    2.1  2  CK2S             Casein Kinase 2 substrate
       0.16   11.8   5.8        1.9    8.3   0.2    2.3  2  CdvA             CdvA-like coiled-coil domain
       0.17   12.1   7.8        2.9    8.2   2.6    2.2  2  Spc24            Spc24 subunit of Ndc80
       0.18   12.0   1.6       0.33   11.2   0.2    1.8  2  EIAV_Rev         Rev protein of equine infectious anaemia vir
       0.24   11.9   7.5        1.7    9.1   1.7    2.3  2  Snapin_Pallidin  Snapin/Pallidin
       0.26   10.6   0.4       0.49    9.7   0.1    1.5  2  ThrE             Putative threonine/serine exporter
       0.27   11.7   9.9       0.19   12.3   1.8    2.2  2  APG6_N           Apg6 coiled-coil region
       0.33   11.1   6.4        1.3    9.2   1.5    2.2  2  TRPM_tetra       Tetramerisation domain of TRPM
       0.47   11.6   2.8        1.7    9.8   0.2    2.2  2  DUF5320          Family of unknown function (DUF5320)
       0.66   10.0   3.5        7.5    6.6   0.1    2.1  2  DUF1664          Protein of unknown function (DUF1664)
        1.3    9.5  12.0       0.22   11.9   2.2    2.6  2  V-SNARE          Vesicle transport v-SNARE protein N-terminus
        1.4    9.2  10.2        1.2    9.4   3.3    2.2  2  Cortex-I_coil    Cortexillin I, coiled coil
        1.7    8.9   8.5       0.44   10.8   5.5    1.5  1  Cor1             Cor1/Xlr/Xmr conserved region
        1.8    9.3   8.8         16    6.2   0.2    2.3  2  DUF4404          Domain of unknown function (DUF4404)
          2    8.6  13.4        2.7    8.2   6.3    2.1  2  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
        2.4    6.7   6.3        2.8    6.4   2.1    2.0  2  FapA             Flagellar Assembly Protein A
        3.1    8.1   9.1        1.3    9.3   0.6    2.3  2  THOC7            Tho complex subunit 7
        3.3    8.2  10.1          4    7.9   1.1    2.5  2  DUF4140          N-terminal domain of unknown function (DUF41
        5.8    6.4  13.7        4.5    6.8   7.3    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3


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 !   81.3   1.5   9.2e-26   4.9e-23       2     118 ..      19     135 ..      18     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 9.2e-26
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHH CS
                      Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiel 81 
                                    + ++++lq  laql+ +++++++++et+++   +d ++++  + + + ++ka++ ++ k++v+lG ++y++++  +A+e+
  gi|118431322|ref|NP_147703.2|  19 RDQIAELQGVLAQLELRLRSVQAAKETVEKAAGQDGETLFPGDPELNTILKARLLEPGKAIVHLGLNVYAKLDTAKATEI 98 
                                    679***************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqly 118
                                    l kk++ l+++le+l++el+kl+++++++ + l++l+
  gi|118431322|ref|NP_147703.2|  99 LAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALT 135
                                    ********************************99875 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   1.4    0.0021       1.1       2      42 ..      10      50 ..       9      55 .. 0.91
   2 !   12.0   0.6   0.00029      0.15      53     102 ..      85     134 ..      67     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                    Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelelld 42
                                   e+++++q +++q+ +l+  ++qle +l+ ++ ++e++e+++
  gi|118431322|ref|NP_147703.2| 10 EIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVEKAA 50
                                   788999*****************************999875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00029
                                    TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                    Prefoldin_2  53 dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                    +v  k d ++++e L ++++ l+  ++tl+++l+kl ++ ++  + lq++
  gi|118431322|ref|NP_147703.2|  85 NVYAKLDTAKATEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQAL 134
                                    56778899999999********************9999988887777776 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 ?    3.8   0.0     0.074        39      86     123 ..      11      48 ..       2      67 .. 0.61
   2 !   12.3   0.9   0.00018     0.096     116     148 ..     101     133 ..      88     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.074
                  PI3K_P85_iSH2  86 lqenleqlksrlkelhsskekLeedlkqqkeeereleR 123
                                    +  +l+ +++++ el+   ++Le  l++  + + ++e+
  gi|118431322|ref|NP_147703.2|  11 IAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVEK 48 
                                    44445555555555555555555555555555555544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00018
                  PI3K_P85_iSH2 116 eeereleReinalkpellqLqkrkdkylewLkt 148
                                    ++e  l R++ +lk el +L+++ d+yl+ L+ 
  gi|118431322|ref|NP_147703.2| 101 KKEDALKRSLETLKQELDKLSRTHDQYLQLLQA 133
                                    5677899**********************9985 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 !   12.0   0.2   0.00029      0.15      51      91 ..      12      52 ..       5      57 .. 0.87
   2 ?    6.6   1.7     0.014       7.1      46      77 ..     102     133 ..      86     150 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                 CENP-F_leu_zip 51 kaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91
                                    a+++ ++++i el+  l +lel L +++  ke++ek   +
  gi|118431322|ref|NP_147703.2| 12 AAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVEKAAGQ 52
                                   56788899***************************998776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                 CENP-F_leu_zip  46 eaEtskaevetlkeeieelaeelreleldLva 77 
                                      +  k  +etlk+e+++l+++  +  + L+a
  gi|118431322|ref|NP_147703.2| 102 KEDALKRSLETLKQELDKLSRTHDQYLQLLQA 133
                                    22223444455555555554444444444444 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 ?   14.5   4.6   6.2e-05     0.033       2      76 ..      11     135 ..      10     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.2e-05
                       CCDC-167   2 vaseIdkleeklascrerLeaverrlrkeelseee............................................. 36 
                                    +a +++ + +++a+++  L ++e rlr+++  +e                                              
  gi|118431322|ref|NP_147703.2|  11 IAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETvekaagqdgetlfpgdpelntilkarllepgkaivhlglnvyakl 90 
                                    7899999************************************************************************* PP

                       CCDC-167  37 .....ResleeEeaslkeqleenekeLksLrkeNrksmllsvall 76 
                                          e l + e++lk  le+  +eL +L + + +   l+ al+
  gi|118431322|ref|NP_147703.2|  91 dtakaTEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALT 135
                                    **9998999999999999999999999999999998877777765 PP

>> BAR  BAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.0   0.00014     0.073     133     219 ..      20     138 ..       3     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                            BAR 133 kefkeiqkerkklehkrlDyDaakarlkklktkkskkakde................................ekaeeel 180
                                    +++ e+q  +++le ++    aak++++k+  ++ +++                                   +ka+e l
  gi|118431322|ref|NP_147703.2|  20 DQIAELQGVLAQLELRLRSVQAAKETVEKAAGQDGETLFPGdpelntilkarllepgkaivhlglnvyakldtAKATEIL 99 
                                    55555555555556555556666666665554444333322555666666666666666666666666666678999999 PP

                            BAR 181 rkAqqkfeesneelkaeLpnllalevefvnqlqafveaq 219
                                     k +++  +s e lk+eL++l+ ++ ++++ lqa+   q
  gi|118431322|ref|NP_147703.2| 100 AKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQ 138
                                    999999999************999999999999997655 PP

>> 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 ?   -0.2   0.2         1   5.5e+02      61      93 ..      12      44 ..       2      53 .. 0.58
   2 ?   14.7   1.8   2.9e-05     0.015      64     104 ..      96     136 ..      88     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHH CS
                    vATP-synt_E 61 karlkvLkareevleevfeeaekkLaeveedkd 93
                                   +a+l++ + +   l+ v+ ++e +L+ v+  k+
  gi|118431322|ref|NP_147703.2| 12 AAQLQMIRDQIAELQGVLAQLELRLRSVQAAKE 44
                                   555555555555566666666666666665553 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.9e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTSHHCCCCHHHHHHC CS
                    vATP-synt_E  64 lkvLkareevleevfeeaekkLaeveedkdeYkellkkLiv 104
                                     ++L  +e+ l++ +e ++++L+++++++d+Y +ll+ L  
  gi|118431322|ref|NP_147703.2|  96 TEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTA 136
                                    478999*******************************9965 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 ?    2.7   0.0      0.24   1.3e+02      32     119 ..      17      37 ..       5      57 .. 0.46
   2 ?   12.8   1.7   0.00019     0.098      23      75 ..      96     148 ..      92     151 .] 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.24
                                    CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                      Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                     ++++                                                                   i +Lq+vl
  gi|118431322|ref|NP_147703.2|  17 MIRDQ-------------------------------------------------------------------IAELQGVL 29 
                                    22333...................................................................33333333 PP

                                    HHHHHHHH CS
                      Fib_alpha 112 esneqkiq 119
                                     ++e ++ 
  gi|118431322|ref|NP_147703.2|  30 AQLELRLR 37 
                                    33332222 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00019
                                    HHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  23 qdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn 75 
                                    +++l k+e  +k++le+l++el+++s+++ +  +l ++++   +++q+ ++++
  gi|118431322|ref|NP_147703.2|  96 TEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQAGQQQK 148
                                    57899********************************9999988888877754 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.056        30      15      41 ..       4      30 ..       2      35 .. 0.87
   2 ?    9.6   0.4    0.0015       0.8      12      50 ..     103     141 ..      92     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.056
                        Takusan 15 akkklEeLkleLrkitreRdELrdiLa 41
                                   ++   Ee+  +L+ i  +  EL+  La
  gi|118431322|ref|NP_147703.2|  4 QMPSPEEIAAQLQMIRDQIAELQGVLA 30
                                   556679******************998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                        Takusan  12 keqakkklEeLkleLrkitreRdELrdiLalytegslnd 50 
                                    +  +k  lE+Lk eL k++r  d   + L+  t g+  +
  gi|118431322|ref|NP_147703.2| 103 EDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQ 141
                                    45578899**********999999999999998887655 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 ?    4.0   0.0      0.14        73      44      81 ..       9      46 ..       4      52 .. 0.72
   2 ?    8.6   0.2    0.0052       2.7      34      63 ..      94     123 ..      78     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.14
                   Syntaxin-6_N 44 teLrkalrsiewdledLeetvriveknpskfkidekel 81
                                   +e+ ++l+ i+ ++ +L+ + + +e   + ++  ++++
  gi|118431322|ref|NP_147703.2|  9 EEIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETV 46
                                   57788888899999999888877776655555555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0052
                   Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLeet 63 
                                    + +e l + ++ L+++l++++++l+ L +t
  gi|118431322|ref|NP_147703.2|  94 KATEILAKKEDALKRSLETLKQELDKLSRT 123
                                    457889999999***************998 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.31   1.6e+02      27      55 ..      11      39 ..       4      58 .. 0.80
   2 ?    8.7   0.0    0.0043       2.3      17      54 ..      96     133 ..      79     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.31
                           MtrB 27 vllsldpvleeidkLekiaddlvnsLdpe 55
                                   +  +l+ + ++i++L+ +  +l+  L   
  gi|118431322|ref|NP_147703.2| 11 IAAQLQMIRDQIAELQGVLAQLELRLRSV 39
                                   67889999*******99999988777654 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0043
                           MtrB  17 gvvaearedvvllsldpvleeidkLekiaddlvnsLdp 54 
                                      + +++ed +  sl+ +++e+dkL  + d++ + L+ 
  gi|118431322|ref|NP_147703.2|  96 TEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQA 133
                                    346678899*********************99988865 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00021      0.11      20      78 ..      74     132 ..      30     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                          HHH_6  20 eedga.irlGLaaikglgeaaaerivaeRekegpfksledlarrvdslnkrqleaLakaG 78 
                                    e ++a + lGL+   +l +a a +i+a++e +   +sle l +++d+l++++ + L    
  gi|118431322|ref|NP_147703.2|  74 EPGKAiVHLGLNVYAKLDTAKATEILAKKE-DALKRSLETLKQELDKLSRTHDQYLQLLQ 132
                                    3555589********************998.9999**********997666544444443 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 ?   10.8   0.4   0.00059      0.31      74     107 ..       9      42 ..       2      53 .. 0.84
   2 ?    5.0   1.3     0.039        21      70     113 ..     100     143 ..      71     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00059
                         Nsp1_C  74 nkidqeLeyiesqqdeLeslLdnyEkeleellsk 107
                                    ++i  +L++i  q  eL+ +L+++E +l ++++ 
  gi|118431322|ref|NP_147703.2|   9 EEIAAQLQMIRDQIAELQGVLAQLELRLRSVQAA 42 
                                    68999********************999887744 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.039
                         Nsp1_C  70 eqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesqks 113
                                     +++ ++ ++Le ++++ d L++  d+y + l++l + ++ q++
  gi|118431322|ref|NP_147703.2| 100 AKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQA 143
                                    45566777777777777777777777777777777766665555 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0018      0.96      51      77 ..       7      33 ..       5      51 .. 0.65
   2 ?    4.9   1.3     0.052        27      42      74 ..      99     132 ..      84     143 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                           Med9 51 sveeqeaeieeleeqlakKrelLkkyk 77
                                   s+ee  a+++  ++q+a  + +L+++ 
  gi|118431322|ref|NP_147703.2|  7 SPEEIAAQLQMIRDQIAELQGVLAQLE 33
                                   566666666666666666666666654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.052
                           Med9  42 irelpg.idrsveeqeaeieeleeqlakKrelLk 74 
                                    +++ ++ + rs e+ ++e+++l+   ++  +lL+
  gi|118431322|ref|NP_147703.2|  99 LAKKEDaLKRSLETLKQELDKLSRTHDQYLQLLQ 132
                                    4444444566666666666666555555555554 PP

>> DUF4715  Domain of unknown function (DUF4715)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.4   2.8e+03      73      92 ..      15      34 ..       7      50 .. 0.63
   2 ?   12.5   0.3   0.00022      0.12      41      99 ..      89     147 ..      62     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.4
                        DUF4715 73 ihrledaycemsralveqee 92
                                   ++ + d   e+++ l++ e 
  gi|118431322|ref|NP_147703.2| 15 LQMIRDQIAELQGVLAQLEL 34
                                   45566777777777776543 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00022
                        DUF4715  41 clpsqadleillqkvagvqreledfkkealkaihrledaycemsralv.eqeeqaarvkq 99 
                                     l +    eil +k   ++r le +k+e l+ + r  d y ++ +al+  q  q a  +q
  gi|118431322|ref|NP_147703.2|  89 KLDTAKATEILAKKEDALKRSLETLKQE-LDKLSRTHDQYLQLLQALTaGQAAQQAGQQQ 147
                                    56677788******************99.78899**********9996256777766555 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0065       3.4      59      93 ..      16      50 ..       7      74 .. 0.86
   2 ?    6.5   1.5     0.013       7.1      74     115 ..     105     146 ..      85     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0065
                           CK2S 59 rLrekqlealeevlakLrekleelqkvrdsleklv 93
                                   ++++ q+++l+ vla+L+  l ++q +++++ek+ 
  gi|118431322|ref|NP_147703.2| 16 QMIRDQIAELQGVLAQLELRLRSVQAAKETVEKAA 50
                                   56788999**********************99986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                           CK2S  74 kLrekleelqkvrdsleklvrdalqlyeekadklslkelier 115
                                     L+  le+l++  d+l++ + + lql++  ++ + ++++ ++
  gi|118431322|ref|NP_147703.2| 105 ALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQAGQQ 146
                                    578888888888888888888888888888877666666655 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0037       1.9      43      70 ..       9      36 ..       8      48 .. 0.91
   2 ?    5.9   1.1      0.02        11      77     114 ..     103     140 ..      84     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0037
                           CdvA 43 eklkkrlkeledqikslekalanlkisy 70
                                   e++ ++l+ ++dqi++l+ +la+l+++ 
  gi|118431322|ref|NP_147703.2|  9 EEIAAQLQMIRDQIAELQGVLAQLELRL 36
                                   68999*******************9975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                           CdvA  77 EeaYksaieairellesaleekeeikklleklsklele 114
                                    E+a k++ e ++++l+++++  ++  +ll+ l + +++
  gi|118431322|ref|NP_147703.2| 103 EDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAA 140
                                    44555555555555555555555555555555444444 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0069       3.7       9      49 ..      11      62 ..       9      93 .. 0.50
   2 ?    8.2   2.6    0.0054       2.9       6      43 ..      89     126 ..      86     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0069
                          Spc24  9 iakelsdleselesleselaelkeeleeleeesee.keser..........v 49
                                   ia +l+ + +++ +l+  la+l+ +l+ ++  +e  ++++            
  gi|118431322|ref|NP_147703.2| 11 IAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETvEKAAGqdgetlfpgdP 62
                                   6667777777777777777777777777776666642222212222344431 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0054
                          Spc24   6 kfriakelsdleselesleselaelkeeleeleeesee 43 
                                    k+++ak+ + l ++ ++l+ +l+ lk+el++l++   +
  gi|118431322|ref|NP_147703.2|  89 KLDTAKATEILAKKEDALKRSLETLKQELDKLSRTHDQ 126
                                    78889999999999999999999999999999887665 PP

>> EIAV_Rev  Rev protein of equine infectious anaemia virus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00062      0.33      48      80 ..      16      48 ..       3      55 .. 0.82
   2 ?   -0.1   0.1       1.9     1e+03      56      90 ..      95     129 ..      65     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00062
                       EIAV_Rev 48 rwlreqvlqaevlqerlewrirgvqqaakelek 80
                                   + +r+q+ + + +  +le r+r vq a   +ek
  gi|118431322|ref|NP_147703.2| 16 QMIRDQIAELQGVLAQLELRLRSVQAAKETVEK 48
                                   689*********************876666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.9
                       EIAV_Rev  56 qaevlqerlewrirgvqqaakelekvnkeiwrelq 90 
                                     +e+l ++ +   r ++   +el+k+ +   + lq
  gi|118431322|ref|NP_147703.2|  95 ATEILAKKEDALKRSLETLKQELDKLSRTHDQYLQ 129
                                    45666666666667777777788887776655555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.029        15      54      88 ..       4      38 ..       1      49 [. 0.75
   2 ?    9.1   1.7    0.0032       1.7      23      51 ..      97     125 ..      88     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.029
                Snapin_Pallidin 54 vlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88
                                   ++p  +e a+ L+ i+ ++ +l+ +l +l+ R+  
  gi|118431322|ref|NP_147703.2|  4 QMPSPEEIAAQLQMIRDQIAELQGVLAQLELRLRS 38
                                   46777777788888888888888888888887765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0032
                Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkeleeaqe 51 
                                    + l ++ ++L+ +l++l+++L++l+++++
  gi|118431322|ref|NP_147703.2|  97 EILAKKEDALKRSLETLKQELDKLSRTHD 125
                                    55788999******************999 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.3   2.3e+03      88     103 ..       7      22 ..       2      45 .. 0.66
   2 ?    9.7   0.1   0.00093      0.49      80     119 ..     101     140 ..      85     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.3
                           ThrE  88 sleeaeerLdeIersk 103
                                    s+ee+ ++L+ I  + 
  gi|118431322|ref|NP_147703.2|   7 SPEEIAAQLQMIRDQI 22 
                                    6777777777776554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00093
                           ThrE  80 reiaageisleeaeerLdeIerskpryprwlvvlaaglaa 119
                                    ++  a + sle ++++Ld+++r +++y ++l++l ag aa
  gi|118431322|ref|NP_147703.2| 101 KKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAA 140
                                    444445789***************************9887 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.3     0.096        51      50      89 ..       9      48 ..       2      57 .. 0.54
   2 ?   12.3   1.8   0.00035      0.19      11      94 ..     110     141 ..      68     150 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.096
                         APG6_N 50 eeleeeleklekeeeelleeLkelekereeleaelaalee 89
                                   ee+  +l+ ++++ +el+  L++le   ++++a+ ++ e+
  gi|118431322|ref|NP_147703.2|  9 EEIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVEK 48
                                   4445555555555555555555555555555554444443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00035
                         APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90 
                                    le+l+++l+++ + +d+Y++ l+ l++ +                                                   
  gi|118431322|ref|NP_147703.2| 110 LETLKQELDKLSRTHDQYLQLLQALTAGQAA------------------------------------------------- 140
                                    4555555555555555555555555544333................................................. PP

                         APG6_N  91 leal 94 
                                        
  gi|118431322|ref|NP_147703.2| 141 ---Q 141
                                    ...2 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.075        39      12      43 ..       9      40 ..       8      48 .. 0.86
   2 ?    9.2   1.5    0.0024       1.3      22      55 ..     100     133 ..      93     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.075
                     TRPM_tetra 12 EnmsmkveevneKenlikaSLqsldfrLgkLe 43
                                   E++  +++ + +     +  L +l++rL+ ++
  gi|118431322|ref|NP_147703.2|  9 EEIAAQLQMIRDQIAELQGVLAQLELRLRSVQ 40
                                   78889999999999999999999999999887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0024
                     TRPM_tetra  22 neKenlikaSLqsldfrLgkLedlsaltvdtLkv 55 
                                     +Ke + k+SL +l + L kL   +++ ++ L+ 
  gi|118431322|ref|NP_147703.2| 100 AKKEDALKRSLETLKQELDKLSRTHDQYLQLLQA 133
                                    689******************9999999988876 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.91   4.8e+02      69      98 ..       9      38 ..       2      39 .. 0.77
   2 ?    9.8   0.2    0.0032       1.7      66      99 .]      87     120 ..      71     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.91
                        DUF5320 69 askeeekelLeeqaeaLeeeleaikkrlke 98
                                   ++  ++ +++++q++ L+  l++++ rl++
  gi|118431322|ref|NP_147703.2|  9 EEIAAQLQMIRDQIAELQGVLAQLELRLRS 38
                                   555678899999999999999999988865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0032
                        DUF5320  66 taeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                    +a+ ++ + +e+L ++++aL+++le++k++l++l
  gi|118431322|ref|NP_147703.2|  87 YAKLDTAKATEILAKKEDALKRSLETLKQELDKL 120
                                    5666788899********************9876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.014       7.5      77     111 ..      10      44 ..       3      51 .. 0.63
   2 ?    4.2   0.7      0.08        42      57      84 ..      99     126 ..      84     148 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.014
                        DUF1664  77 eqkeiskeikeevtevredlseigedvesvkeave 111
                                    e ++  + i+++++e+++ l++++  ++sv++a e
  gi|118431322|ref|NP_147703.2|  10 EIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKE 44 
                                    45555566666666666666666666666666555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.08
                        DUF1664  57 laatkrhLssridrvdkkldeqkeiske 84 
                                    la+  + L++ ++++ ++ld+ +++  +
  gi|118431322|ref|NP_147703.2|  99 LAKKEDALKRSLETLKQELDKLSRTHDQ 126
                                    3333333444444444444443333333 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 ?   11.9   2.2   0.00041      0.22      16      57 ..       3      44 ..       1      50 [. 0.83
   2 ?    4.4   0.3     0.094        50      55      75 ..     102     122 ..      92     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00041
                        V-SNARE 16 sslag.eerkaalreiekkldeaeelldqMelEvrnlpssera 57
                                   ++ ++ ee  a+l+ i  ++ e++ +l q+el +r+++ +++ 
  gi|118431322|ref|NP_147703.2|  3 QQMPSpEEIAAQLQMIRDQIAELQGVLAQLELRLRSVQ-AAKE 44
                                   55667788899**************************7.4443 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.094
                        V-SNARE  55 erasykaklreykselkklkk 75 
                                      +++k  l+  k+el+kl +
  gi|118431322|ref|NP_147703.2| 102 KEDALKRSLETLKQELDKLSR 122
                                    567889999999999999876 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 ?    4.4   0.6     0.079        42      31      70 ..       7      46 ..       2      85 .. 0.77
   2 ?    9.4   3.3    0.0023       1.2      12      55 ..      97     141 ..      85     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.079
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Cortex-I_coil 31 sreelikqkdelesllasleseaaerekrlreleakldea 70
                                   s ee++ q + +++ +a l++  a+ e rlr ++a  + +
  gi|118431322|ref|NP_147703.2|  7 SPEEIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETV 46
                                   5677777888888888888888888888888888765544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0023
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHH CS
                  Cortex-I_coil  12 nelanklaglenslesekvsreelikqkdelesllasles.eaae 55 
                                    + la+k  +l++sle+ k   ++l +  d+  +ll++l   +aa+
  gi|118431322|ref|NP_147703.2|  97 EILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAgQAAQ 141
                                    4589999***********************999998886414444 PP

>> Cor1  Cor1/Xlr/Xmr conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.5   0.00083      0.44      65     121 ..      92     148 ..      87     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00083
                           Cor1  65 eeklsnlfqqqqkllqqarvvqeqrlkeikqlydqFlksledLekehekllsdeqse 121
                                    + k ++++ +++  l+++  + +q l+++   +dq+l+ l++L   +  +++ +q++
  gi|118431322|ref|NP_147703.2|  92 TAKATEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQAGQQQK 148
                                    578999*********************************************999975 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.031        16      12      60 ..      11      57 ..       5      71 .. 0.73
   2 ?    5.6   4.0     0.047        25       1      31 [.     106     136 ..     106     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.031
                        DUF4404 12 LeqnesldeetralLeslaedieellaeedaaaeeeelaerlneaverF 60
                                   ++ + ++  ++ a+L+ +  ++e +l++ +aa+e+  +++ + +  e+ 
  gi|118431322|ref|NP_147703.2| 11 IAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKET--VEKAAGQDGETL 57
                                   55666677789999************999999998..555555555555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.047
                        DUF4404   1 LkelLekLheeLeqnesldeetralLeslae 31 
                                    Lk++Le+L++eL++ +++ ++  +lL++l  
  gi|118431322|ref|NP_147703.2| 106 LKRSLETLKQELDKLSRTHDQYLQLLQALTA 136
                                    7999**********************99975 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 ?    5.0   0.6     0.048        25      38      76 ..      12      50 ..       7      56 .. 0.81
   2 ?    8.2   6.3    0.0051       2.7      34      86 ..      96     148 ..      87     151 .] 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.048
                         CENP-Q 38 eaqLspelhslelLeaeiekeeralerdyeaLreLekna 76
                                    aqL++ ++++++L+  + ++e  l + ++a ++ ek a
  gi|118431322|ref|NP_147703.2| 12 AAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVEKAA 50
                                   578888888899998888888888888888888888776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0051
                         CENP-Q  34 kaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerkek 86 
                                    +  l ++ +++++sle L++e++k+ r+  +  + L+ L +   a+++ +++k
  gi|118431322|ref|NP_147703.2|  96 TEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQAGQQQK 148
                                    55677888999999999999*99999999999999999999888888876554 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.077        40     382     418 ..      10      45 ..       2      61 .. 0.48
   2 ?    6.4   2.1    0.0054       2.8     319     371 ..      91     142 ..      68     151 .] 0.53

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.077
                           FapA 382 klletkeklkeeleeleeelkelkeeleskkeeakik 418
                                    ++  +++ ++++++el+  l++l+ +l+s  ++ak  
  gi|118431322|ref|NP_147703.2|  10 EIAAQLQMIRDQIAELQGVLAQLELRLRSV-QAAKET 45 
                                    333334444444444444444444444444.222222 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0054
                           FapA 319 elgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekq 371
                                    +  ++tei +  +  +lk++l+ l++el +l +  +++ + ++ l + +a +q
  gi|118431322|ref|NP_147703.2|  91 DTAKATEILAKKE-DALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQ 142
                                    3333344444333.666666666666666666666666666666665333222 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.6    0.0024       1.3      78     116 ..       9      47 ..       4      53 .. 0.80
   2 ?    2.8   2.5      0.25   1.3e+02      84     107 ..     103     126 ..      84     149 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                          THOC7  78 eeieseieavreeieelkaqLeearatranrkeydelae 116
                                    eei ++++++r++i+el+  L +    ++++++  e +e
  gi|118431322|ref|NP_147703.2|   9 EEIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVE 47 
                                    689999999999999999999998888888777666655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.25
                          THOC7  84 ieavreeieelkaqLeearatran 107
                                      a++ + e lk++L++  +t+++
  gi|118431322|ref|NP_147703.2| 103 EDALKRSLETLKQELDKLSRTHDQ 126
                                    234566667777777766666654 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 ?    7.9   1.1    0.0076         4      60      96 ..       8      44 ..       2      47 .. 0.73
   2 ?    4.8   2.3     0.074        39      65      89 ..      97     125 ..      74     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0076
                        DUF4140 60 reaeeeelkalraeleeledelaaledelaaaearla 96
                                   +e+ +++l+ +r+++ el+  la+le +l++++a ++
  gi|118431322|ref|NP_147703.2|  8 PEEIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKE 44
                                   3333335999999999999999999999999988765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.074
                        DUF4140  65 e....elkalraeleeledelaaledela 89 
                                    e    + +al+++le+l++el++l+++ +
  gi|118431322|ref|NP_147703.2|  97 EilakKEDALKRSLETLKQELDKLSRTHD 125
                                    23333567888888888888887776554 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 ?    3.9   0.4     0.063        33      89     132 ..      10      53 ..       7      82 .. 0.76
   2 ?    6.8   7.3    0.0085       4.5      64     117 ..      94     147 ..      82     151 .] 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.063
                   HAUS-augmin3  89 eLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkea 132
                                    e   + + +  +  +Lq + a+l+ +lr++++++++++k   + 
  gi|118431322|ref|NP_147703.2|  10 EIAAQLQMIRDQIAELQGVLAQLELRLRSVQAAKETVEKAAGQD 53 
                                    55667788888999999999999999999999988888766555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0085
                   HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrk 117
                                    +++e l +  ++++ sle L+qel++L ++ +  l+ l+ L++  a++q ++++
  gi|118431322|ref|NP_147703.2|  94 KATEILAKKEDALKRSLETLKQELDKLSRTHDQYLQLLQALTAGQAAQQAGQQQ 147
                                    456667777788899999999999999999999999999999988888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1795  (0.100117); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1079.17
//
Query:       gi|118431323|ref|YP_874872.1|  [L=88]
Description: 50S ribosomal protein LX [Aeropyrum pernix K1]
Scores for complete 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-13   49.3   0.4    1.1e-12   48.1   0.4    1.5  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.4     6e-17   1.1e-12      71     121 .]      13      63 ..       2      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 6e-17
                                    ........TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                 Ribosomal_L18A  71 iwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                    +++  d + ++++f  ++r+l++e+a+e+vYs+lgsrh+++r++I+I +ve
  gi|118431323|ref|YP_874872.1|  13 MLISHDRYPEWRKFEVYVRALKREHALEKVYSDLGSRHKLRRKHIRIRSVE 63 
                                    57889999****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 676.49
//
Query:       gi|14601175|ref|NP_147705.1|  [L=233]
Description: translation initiation factor IF-6 [Aeropyrum pernix K1]
Scores for 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-67  227.4   0.8    1.2e-67  227.1   0.8    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 !  227.1   0.8   6.9e-72   1.2e-67       1     197 []      11     210 ..      11     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 6.9e-72
                                   .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-..E.EEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHH CS
                         eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkv..e.vvettiagsrlvGslvvgNsngllvpstvtdeelek 78 
                                   +ls++g+++iGv++++ ++y+l p +++++ v++i+e+L+v  e vv+ ++ g+rlvG+l++gNs+g+l+p+ v d+e+e 
  gi|14601175|ref|NP_147705.1|  11 KLSLYGNPNIGVYLTASDSYVLAPDDIGADDVRTISEVLGVamErVVRLRVLGMRLVGVLTTGNSRGILLPEGV-DREVEL 90 
                                   6899************************************74436**************************987.99**** PP

                                   HHHHHH.---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT- CS
                         eIF-6  79 lkeslk.leverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpka 158
                                   ++++l+ +ev +++++ +AlGNvi++ND+++l +p l+ke+ ++++d+Lgvevv+g++ag+ tvGsa+vvtn+g+l hp+a
  gi|14601175|ref|NP_147705.1|  91 VRKALEgVEVGIVPTRSNALGNVIVCNDRACLASPGLEKEALKTVSDTLGVEVVEGSVAGVYTVGSAIVVTNRGGLAHPDA 171
                                   *****99************************************************************************** PP

                                   -HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                         eIF-6 159 teeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                   +eeel++l++++kv++eagT+N+G+++v++glvaN+ ga
  gi|14601175|ref|NP_147705.1| 172 SEEELKFLSDVFKVPFEAGTINFGVEFVRTGLVANSYGA 210
                                   ************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1829.93
//
Query:       gi|118431324|ref|NP_147706.2|  [L=104]
Description: 50S ribosomal protein L31 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-18   65.4   0.3    5.2e-18   65.1   0.3    1.1  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 !   65.1   0.3   2.9e-22   5.2e-18       4      80 ..       6      81 ..       4      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.9e-22
                 Ribosomal_L31e  4 treytInihkrihgvgfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrlsrkrnedEds 80
                                   t  y++n  +r+++ ++++ra rA++++++f++++++  +v id++Ln+++w+++ +++p+r+++ +s +++e E++
  gi|118431324|ref|NP_147706.2|  6 TWVYVVN-LRRVYWGRRTRRAIRAVRMVREFVRRHTKADEVVIDNELNNYIWSRSREKPPARVKIIVSIREEEPEEG 81
                                   7789***.89****************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 877.61
//
Query:       gi|118431325|ref|YP_874873.1|  [L=51]
Description: 50S ribosomal protein L39 [Aeropyrum pernix K1]
Scores for complete 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   67.8  11.0    5.6e-19   67.5  11.0    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5  11.0   3.1e-23   5.6e-19       1      42 []       9      50 ..       9      50 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 3.1e-23
                  Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                   +KlrLa+alk+Nr++P+Wv+++t r++r n  rRhWRr+kLk
  gi|118431325|ref|YP_874873.1|  9 RKLRLARALKSNRAIPVWVVIRTSRRIRFNLLRRHWRRSKLK 50
                                   7****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 408.81
//
Query:       gi|118431326|ref|YP_874874.1|  [L=115]
Description: DNA-binding protein [Aeropyrum pernix K1]
Scores for complete 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-22   78.7  12.5    4.2e-22   78.5  12.5    1.0  1  dsDNA_bind      Double-stranded DNA-binding domain
    1.2e-05   24.7   7.9    1.5e-05   24.5   7.9    1.0  1  Radial_spoke_3  Radial spoke protein 3
  ------ inclusion threshold ------
      0.026   14.9   7.5      0.036   14.5   7.5    1.2  1  NINJA_B         Putative nuclear localisation signal
       0.37   10.9   3.2       0.52   10.4   3.2    1.1  1  MAS20           MAS20 protein import receptor
        8.3    6.4  10.6        9.8    6.1  10.6    1.0  1  DUF4192         Domain of unknown function (DUF4192)
        8.8    6.0  15.9         11    5.6  15.9    1.2  1  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 !   78.5  12.5   1.4e-25   4.2e-22       1     111 []      12     115 .]      12     115 .] 0.91

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.4e-25
                                    XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--S CS
                     dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGq 80 
                                    ir++++ elq++ ++++      +++e+q++   +++k aiL+++L+++AreRL+++rlv+pe aea en +iql+q+G+
  gi|118431326|ref|YP_874874.1|  12 IRRRKMLELQRRLEEER------RREEEQAR--LRAQKDAILRRLLTSKARERLANLRLVRPEIAEAAENAVIQLVQTGR 83 
                                    8**********988643......44555555..89********************************************* PP

                                    S-----HHHHHHHHHHHS-.--XXXXX..XXX CS
                     dsDNA_bind  81 lrskvteeqLkeLLeqvae.kkketkivisrr 111
                                    ++  v++++L+++L ++++ ++++ +i i+r+
  gi|118431326|ref|YP_874874.1|  84 ITPPVDDDTLVQILLELDRsTRRDFEIRIKRK 115
                                    *******************88888***99996 PP

>> Radial_spoke_3  Radial spoke protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   7.9     5e-09   1.5e-05     163     252 ..       7      98 ..       4     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 5e-09
                 Radial_spoke_3 163 rafeelRnaelaevqrLeeqekrlreekerrlkqqkealkk..eketaekiaaralakqylaellpsvlesLedsgyfyd 240
                                    +++ee R   + e+qr  e+e+r++ee+ r ++q+ + l++    +++e++a+ +l++  +ae  ++++ +L ++g ++ 
  gi|118431326|ref|YP_874874.1|   7 DELEEIRRRKMLELQRRLEEERRREEEQARLRAQKDAILRRllTSKARERLANLRLVRPEIAEAAENAVIQLVQTGRITP 86 
                                    6789********************************99987447899********************************* PP

                 Radial_spoke_3 241 pverdveteflp 252
                                    pv  d   ++l 
  gi|118431326|ref|YP_874874.1|  87 PVDDDTLVQILL 98 
                                    **9988777765 PP

>> NINJA_B  Putative nuclear localisation signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   7.5   1.2e-05     0.036      13      77 ..      10      76 ..       6      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                        NINJA_B 13 EEwrkRkEmqsLrRmeAKRrRsEkqrnknsgegevske..eeakdrrrgraslvlPrWsaaaksgll 77
                                   EE r+Rk ++  rR+e  RrR E q  + ++++ +     + ++  r ++ +lv P  + aa+ +++
  gi|118431326|ref|YP_874874.1| 10 EEIRRRKMLELQRRLEEERRREEEQARLRAQKDAILRRllTSKARERLANLRLVRPEIAEAAENAVI 76
                                   99*********************99666566555544311223335556666777777776666655 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.2   0.00017      0.52      18      82 ..      13      82 ..      11      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                          MAS20 18 kRrsdpefkkklrerrkkqakaakeeeeaekaekkk..kealeeakee....lptdaeevekfFleevqlG 82
                                   +Rr+  e +++l+e+r++++++a+ ++++++  ++   +  ++e  ++     p+ ae+ e+ +++ vq+G
  gi|118431326|ref|YP_874874.1| 13 RRRKMLELQRRLEEERRREEEQARLRAQKDAILRRLltS-KARERLANlrlvRPEIAEAAENAVIQLVQTG 82
                                   79999*************997775555555555544742.3444444445534488899999999999998 PP

>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  10.6    0.0033       9.8     149     238 ..      15     107 ..       8     111 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0033
                        DUF4192 149 eelearlapvegaaaraaqrraaeraaaaleralarprdaerrsdpaevrraaleavraalarvaagaglsda...eeaa 225
                                    +++ ++ + +e +++r++++++++++++a+ r+l++ +++er ++ + vr +  ea++ a+ ++ +  + +++   ++++
  gi|118431326|ref|YP_874874.1|  15 RKMLELQRRLEEERRREEEQARLRAQKDAILRRLLTSKARERLANLRLVRPEIAEAAENAVIQLVQTGRITPPvddDTLV 94 
                                    44444444444553444444445555555555555555555557778888888888888887777766655555558*** PP

                        DUF4192 226 rlavaLtdvrvRD 238
                                    ++ + L++++ RD
  gi|118431326|ref|YP_874874.1|  95 QILLELDRSTRRD 107
                                    **********999 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 ?    5.6  15.9    0.0038        11       5      47 ..       8      51 ..       4      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0038
                        Casc1_N  5 eeEeeRlraeeeererleeerrekeereql.aaeqarrkeelee 47
                                   e Ee R r+  e ++rleeerr++ee+ +l a+++a++   l++
  gi|118431326|ref|YP_874874.1|  8 ELEEIRRRKMLELQRRLEEERRREEEQARLrAQKDAILRRLLTS 51
                                   349**********************9999977777766655533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1400  (0.0780858); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 872.49
//
Query:       gi|14601178|ref|NP_147710.1|  [L=153]
Description: 30S ribosomal protein S19 [Aeropyrum pernix K1]
Scores for complete 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-52  177.1   0.0    1.5e-52  176.9   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.099   12.6   0.4        1.4    8.9   0.0    2.6  4  HTH_12          Ribonuclease R winged-helix domain
       0.11   12.4   0.2          1    9.3   0.0    2.4  2  MarR_2          MarR family
       0.22   10.5   0.0        0.3   10.0   0.0    1.1  1  DUF4788         Domain of unknown function (DUF4788)


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 !  176.9   0.0   3.4e-56   1.5e-52       4     136 ..       6     140 ..       3     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 3.4e-56
                                   SHHHHHHHHHS--S--.-S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGG.GGS----SS-SSS----- CS
                Ribosomal_S19e   4 dVpaeelikalaeeLk.ksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrg.pvGverlrkvYGgkkrrg 82 
                                   +Vpa+ li+++a++Lk k  ++++P+wa ++Ktg +ke++p+d+dW+yvRaAsilRk+y ++ p+G+e++r++YGg+++rg
  gi|14601178|ref|NP_147710.1|   6 EVPADLLIRRVARKLKeKYPQVKPPAWAYFAKTGPHKERPPTDRDWWYVRAASILRKLYKSPePIGIETFRTIYGGRQNRG 86 
                                   8***************8889****************************************877****************** PP

                                   --THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                Ribosomal_S19e  83 vrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                   ++p+hf+ka gsv rkilqqLe++glv k  ++gr+++++G++lld++a+e+++
  gi|14601178|ref|NP_147710.1|  87 SAPEHFRKAGGSVPRKILQQLEEAGLVVKVPGRGRTISPAGRSLLDTTAREIME 140
                                   ***************************888899*******************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 ?   -2.9   0.0       1.6     7e+03      47      54 ..      12      19 ..       9      23 .. 0.51
   2 ?    0.8   0.0      0.11   4.7e+02       2      17 ..      58      73 ..      57      78 .. 0.86
   3 ?    8.9   0.0   0.00031       1.4      36      66 .]     101     131 ..      94     131 .. 0.89
   4 ?   -3.5   0.0       2.4   1.1e+04      17      25 ..     136     144 ..     134     148 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                        HTH_12 47 ltrrvgya 54
                                  l+rrv + 
  gi|14601178|ref|NP_147710.1| 12 LIRRVARK 19
                                  55555443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                        HTH_12  2 eILkilaesdkpigak 17
                                   IL+ l +s +pig +
  gi|14601178|ref|NP_147710.1| 58 SILRKLYKSPEPIGIE 73
                                  59***********965 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00031
                        HTH_12  36 RyrLrkleergltrrvgyagreltEkGleeL 66 
                                   R  L+ lee gl+ +v   gr++   G ++L
  gi|14601178|ref|NP_147710.1| 101 RKILQQLEEAGLVVKVPGRGRTISPAGRSLL 131
                                   7779*************99****98887765 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.4
                        HTH_12  17 keiaeeLkk 25 
                                   +ei eeL k
  gi|14601178|ref|NP_147710.1| 136 REIMEELVK 144
                                   556565544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00022         1      40      59 ..     102     119 ..     101     122 .. 0.87
   2 ?    0.1   0.1      0.17   7.7e+02      20      35 ..     128     146 ..     119     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00022
                                   HHHHHHHHTTSEEEEESSSS CS
                        MarR_2  40 rilkrLvaaGLverrpgpeD 59 
                                   +il+ L++aGLv+++pg   
  gi|14601178|ref|NP_147710.1| 102 KILQQLEEAGLVVKVPG--R 119
                                   699************98..4 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.17
                                   S...EEEHHHHHHHHTSSH CS
                        MarR_2  20 r...dltvgelarrlglsk 35 
                                   r   d t++e+ ++l  ++
  gi|14601178|ref|NP_147710.1| 128 RsllDTTAREIMEELVKTR 146
                                   2455669999999886555 PP

>> DUF4788  Domain of unknown function (DUF4788)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   6.7e-05       0.3      52      94 ..      99     141 ..      94     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.7e-05
                       DUF4788  52 sPkeLrqsLeekGipvtvryngkvlGtgtlsfpqefidkieke 94 
                                    P ++ q+Lee G++v v  +g+++  +  s+ +++ ++i +e
  gi|14601178|ref|NP_147710.1|  99 VPRKILQQLEEAGLVVKVPGRGRTISPAGRSLLDTTAREIMEE 141
                                   799*************************999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); 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:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1125.93
//
Query:       gi|14601179|ref|NP_147711.1|  [L=107]
Description: hypothetical protein APE_1091 [Aeropyrum pernix K1]
Scores for complete 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   55.6   1.8    5.5e-15   55.3   1.8    1.1  1  CRS1_YhbY  CRS1 / YhbY (CRM) domain
  ------ inclusion threshold ------
       0.15   11.7   3.0       0.19   11.4   3.0    1.1  1  CCDC85     CCDC85 family


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   1.8   6.1e-19   5.5e-15      10      84 .]       8      86 ..       2      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 6.1e-19
                     CRS1_YhbY 10 rhlairlkpkvkiGkaGvtkevvdeiheklkteelvkvkc.....egppalnmkrmaeiLeektgglviqrsgtsivLYR 84
                                   ++a++ ++ v iGkaGvt ev++ei+ +l+++e+vkvk+     +  ++  ++++a+ ++  +g+ +  ++g +++LYR
  gi|14601179|ref|NP_147711.1|  8 VRRAHHGRADVIIGKAGVTREVLREIDARLEKKEVVKVKMlktalK-REEGGRRELARRVAGSLGARLMGVRGYTFILYR 86
                                  46799************************************99964.45666***************************9 PP

>> CCDC85  CCDC85 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.0   2.1e-05      0.19      19      76 ..       3      62 ..       1      65 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.1e-05
                        CCDC85 19 elvrrLRraeaekvsllvergrlikevnrrLqqhL..leiRelkevnqkLqednqelrdl 76
                                   +  r+Rra+  +  +++ ++ + +ev r+++  L  +e+ ++k +   L+ ++  +r+l
  gi|14601179|ref|NP_147711.1|  3 SVRTRVRRAHHGRADVIIGKAGVTREVLREIDARLekKEVVKVKMLKTALKREEGGRREL 62
                                  55679**************************99994459*************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 800.84
//
Query:       gi|118431327|ref|NP_147712.2|  [L=163]
Description: ribonuclease P protein component 4 [Aeropyrum pernix K1]
Scores for 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-13   49.1   0.0    7.4e-13   48.6   0.0    1.2  1  Rpr2       RNAse P Rpr2/Rpp21/SNM1 subunit domain
  ------ inclusion threshold ------
      0.047   13.7   0.1      0.093   12.8   0.1    1.4  1  DZR        Double zinc ribbon
        0.2   11.6   3.3        6.2    6.8   0.4    2.6  2  Nudix_N_2  Nudix N-terminal


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 !   48.6   0.0   1.2e-16   7.4e-13      18      90 .]      36     100 ..      22     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.2e-16
                                    HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                           Rpr2  18 palsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90 
                                       +r++a+ql +++  +++r p+ vkr +Ck+C++ lipg+t++vr++++   +         +vvtCl+Cg
  gi|118431327|ref|NP_147712.2|  36 TGEARRVAEQLFQLAASTRVRPPRRVKRLFCKNCRTPLIPGLTARVRLRSQGGMS--------YTVVTCLSCG 100
                                    5568999*****************************************8644432........368******7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.6e-05     0.093      13      35 ..      64     100 ..      56     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                            DZR  13 rfCseCgtklkavaa..............edrCpsCg 35 
                                     fC++C+t+l +  +                +C sCg
  gi|118431327|ref|NP_147712.2|  64 LFCKNCRTPLIPGLTarvrlrsqggmsytVVTCLSCG 100
                                    5********9966668999*********99******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 ?    4.6   0.1     0.005        30      22      30 ..      63      71 ..      51      77 .. 0.73
   2 ?    6.8   0.4     0.001       6.2      24      32 ..      95     103 ..      94     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.005
                                   EEEETTTTE CS
                      Nudix_N_2 22 RlvCpaCgt 30
                                   Rl C++C t
  gi|118431327|ref|NP_147712.2| 63 RLFCKNCRT 71
                                   777777754 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.001
                                    EETTTTEEE CS
                      Nudix_N_2  24 vCpaCgtih 32 
                                    +C +Cg+ih
  gi|118431327|ref|NP_147712.2|  95 TCLSCGWIH 103
                                    6*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1229.78
//
Query:       gi|118431328|ref|NP_147713.2|  [L=602]
Description: ATP-dependent DNA ligase [Aeropyrum pernix K1]
Scores for 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-62  209.9   0.1    6.9e-62  208.7   0.0    1.6  2  DNA_ligase_A_M   ATP dependent DNA ligase domain
    2.8e-37  128.7   0.0    4.3e-37  128.1   0.0    1.3  1  DNA_ligase_A_N   DNA ligase N terminus
    3.5e-26   91.7   0.0    8.6e-26   90.4   0.0    1.7  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    0.00022   21.6   0.1    0.00034   20.9   0.1    1.3  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
       0.13   12.3   1.1        4.3    7.4   0.0    3.0  3  DNA_ligase_OB_2  DNA ligase OB-like 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 !  208.7   0.0   1.9e-65   6.9e-62       1     204 []     239     439 ..     239     439 .. 0.97
   2 ?   -3.1   0.0       1.4   4.9e+03     130     149 ..     493     512 ..     486     521 .. 0.75

  Alignments for each domain:
  == domain 1  score: 208.7 bits;  conditional E-value: 1.9e-65
                                    -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                 DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                    pmLAe+ ++  ++l+k++ + ++vE+KyDGeRaq+hk++++v+++SRrl++it+ +p++v+++++ +k+   ++i++GE+
  gi|118431328|ref|NP_147713.2| 239 PMLAERGRDPAEILRKVG-GRAVVEYKYDGERAQIHKKDGEVYIYSRRLENITRMFPDVVEMARKGLKAG--EAIVEGEI 315
                                    9***************95.5555********************************************998..8******* PP

                                    EEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEE CS
                 DNA_ligase_A_M  81 vavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaesle 160
                                    vavd+++ ei+pfq+l++r k+k++++++++e+++ +f+FD Ly+dge+lt +pl eRr+ L+ei+  ++  ++laes+e
  gi|118431328|ref|NP_147713.2| 316 VAVDPDNYEIQPFQVLMQR-KRKHDIHRVMREVPVAVFLFDALYVDGEDLTSKPLPERRRRLKEIV-VETPLWRLAESIE 393
                                    *******************.78899*****************************************.88999******** PP

                                    ESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 161 vkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                    ++d eel  ++ +ai+eg+EG++vK    ds+Y++g r++ w+K+K
  gi|118431328|ref|NP_147713.2| 394 TSDPEELWTFFLKAIEEGAEGVMVKAvhRDSVYTAGVRGWLWVKLK 439
                                    **************************8889**************99 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                                    HTTSCHHHHHHHHHHHB--B CS
                 DNA_ligase_A_M 130 ltdeplkeRrklLeeilkes 149
                                    +tde+l+ + ++L++ + + 
  gi|118431328|ref|NP_147713.2| 493 FTDEELDRMNEMLKKHIIPR 512
                                    78999999999999988333 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 !  128.1   0.0   1.2e-40   4.3e-37       1     173 []       2     188 ..       2     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 128.1 bits;  conditional E-value: 1.2e-40
                                    BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS-.-----HHHHHHHHHHHHT-- CS
                 DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgr.eygigesllakalaealgls 75 
                                    pF+ +ae+f+++e+  ++r++ + +l+++f+++   +p  + ++++L    l Pd++g  e+g+ge+ll+ka+a a++ +
  gi|118431328|ref|NP_147713.2|   2 PFKPVAEAFASMER-ITSRTQLTLLLTRLFKST---PPGAIGIVVYLiqgkLGPDWKGLpELGVGEKLLVKAIALAYKAT 77 
                                    7999**********.888999*********664...7889*****************999******************** PP

                                    HHHHHHHHHHHS-HHHHHHHHHCCHHHH............------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHH CS
                 DNA_ligase_A_N  76 kkkikdalakvgDlgevaeevlskrstl............akkspltieevnelLdklaaa.gkgsedekkkilkkllkr 142
                                    ++ ++  +++vgDlg+vae++ ++ +++               + lt++ v+++L ++a a g+gs+d k ++l++ll+ 
  gi|118431328|ref|NP_147713.2|  78 EERVERLYKSVGDLGSVAERLSREYRSRaaravtleafmaGGGEALTVRRVYNTLYRIAMAqGEGSRDIKLRLLAGLLAD 157
                                    ********************9988777778888888888878888**************999****************** PP

                                    S-HHHHHHHHHHHCT---SS--HHHHHHHHH CS
                 DNA_ligase_A_N 143 aspeEakyliriilkdlriglsektvldala 173
                                    a p Eaky++r+++++lr+g+++ tvldala
  gi|118431328|ref|NP_147713.2| 158 AEPVEAKYIVRFVEGRLRVGVGDATVLDALA 188
                                    *****************************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 !   90.4   0.0   2.4e-29   8.6e-26       1      99 []     464     573 ..     464     573 .. 0.88

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 2.4e-29
                                    GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG.GGEECTTCESS---HHHHTTEEE-TT-EEEEEESEE CS
                 DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk.elerkkppfaekvpeeekrdvWvePelvveVkfaei 77 
                                    rgg+++sll+++yd  ++ + +v+kv+tGf+d+el++++++lk  +  +k+p    v+ + ++dvWveP+lv+e+ +ae+
  gi|118431328|ref|NP_147713.2| 464 RGGKLSSLLMAAYDpdRDVFPTVCKVATGFTDEELDRMNEMLKkHIIPRKHPR---VESRIEPDVWVEPALVAEILGAEL 540
                                    6899**********86677***********************96444444444...444555569*************** PP

                                    ECTSSSTT...........EECT-EEEEE-TTS CS
                 DNA_ligase_A_C  78 tasgkyka...........slRfPrfkrlReDk 99 
                                    t s+ +++           s+RfPrf+r+R+Dk
  gi|118431328|ref|NP_147713.2| 541 TLSPMHTCclntvrpgvgiSIRFPRFIRWRDDK 573
                                    ********************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   9.6e-08   0.00034       3     154 ..     259     429 ..     257     439 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.6e-08
                                    EEEEEE-SSEEEEEEEETT.EEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES..........SS CS
                     RNA_ligase   3 vvvtEKlDGtnfriylvke.vgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig.........hsi 72 
                                     vv+ K DG++++i++ ++ v++ sR+ +        + f   +++ rk+    l+  e i+ GE++          +  
  gi|118431328|ref|NP_147713.2| 259 AVVEYKYDGERAQIHKKDGeVYIYSRRLEN-----ITRMFPDVVEMARKG----LKAGEAIVEGEIVAvdpdnyeiqP-- 327
                                    5899************9546*******999.....445566666666666....554579********8664433320.. PP

                                    ..TTSS......................EEEEEEEEEEE.CTTBECE--HHHH..HHHHHCCTB..EEEEE.SSHHHHHC CS
                     RNA_ligase  73 kygglpk.....................efyvFdifdir.dkeeqrylspdev..ealakglgtvpvlyegkflaaeell 128
                                                                  ++Fd + ++ ++ + + l+ +++  +++  ++   +++++ ++++ eel 
  gi|118431328|ref|NP_147713.2| 328 ------FqvlmqrkrkhdihrvmrevpvAVFLFDALYVDgEDLTSKPLPERRRrlKEIVVETPLWRLAESIETSDPEELW 401
                                    ......233333444456777888888899********987778888876665233333333234444333444555555 PP

                                    CC..HHHHTC--EEEEEESSSSBE.TTE CS
                     RNA_ligase 129 ell.lskgnkrEGlVikpeselyk.nkg 154
                                    +++ +  ++ +EG+ +k +++    + g
  gi|118431328|ref|NP_147713.2| 402 TFFlKAIEEGAEGVMVKAVHRDSVyTAG 429
                                    5543444569*******99765444444 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.65   2.3e+03      42      51 ..     259     268 ..     253     271 .. 0.82
   2 ?    7.4   0.0    0.0012       4.3       2      36 ..     460     500 ..     459     522 .. 0.70
   3 ?    1.7   0.3     0.073   2.6e+02      57      66 .]     561     570 ..     555     570 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.65
                                    -EEEEEEE-T CS
                DNA_ligase_OB_2  42 kiitykyqel 51 
                                    ++++yky+++
  gi|118431328|ref|NP_147713.2| 259 AVVEYKYDGE 268
                                    689****997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                                    ...EEEEEEEEEEEEE.TTEE......EEE-SS--HHHHHH CS
                DNA_ligase_OB_2   2 GkGkykgmlGallvetkkgkr......fkiGsGlsdaqRen 36 
                                    G+Gk  g+l +ll+   + +r       k+++G++d++  +
  gi|118431328|ref|NP_147713.2| 460 GRGKRGGKLSSLLMAAYDPDRdvfptvCKVATGFTDEELDR 500
                                    99************99864433344459********98554 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.073
                                    -EEEEEEEE- CS
                DNA_ligase_OB_2  57 pRfPsflrvR 66 
                                     RfP+f r+R
  gi|118431328|ref|NP_147713.2| 561 IRFPRFIRWR 570
                                    5*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4473.90
//
Query:       gi|14601183|ref|NP_147715.1|  [L=388]
Description: RNA (cytosine-C(5)-)-methyltransferase [Aeropyrum pernix K1]
Scores for 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-30  103.8   0.0    1.4e-29  103.1   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    1.7e-17   63.1   1.7    3.3e-17   62.2   1.7    1.5  1  PUA              PUA domain
  ------ inclusion threshold ------
       0.07   14.2   0.0       0.75   10.8   0.0    2.4  1  Methyltransf_24  Methyltransferase domain
       0.11   12.6   0.0       0.16   12.1   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.13   11.4   0.0        0.2   10.7   0.0    1.2  1  Fibrillarin      Fibrillarin
       0.18   12.1   0.0       0.63   10.3   0.0    1.8  2  UPF0113          UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.0   4.8e-33   1.4e-29       3     199 ..     195     385 ..     193     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 4.8e-33
                                   HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC....EE CS
               Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg..elfD 81 
                                   +L+p+++  ++Dl aaPGgK +h+a+l   ++++vA+d+  +++ r+ e+l+rLg   + v+ +D r+ ++ l g    +D
  gi|14601183|ref|NP_147715.1| 195 ALDPRPGWVVVDLNAAPGGKVSHVAQLAGREAVIVAIDR-PSKVGRLRETLERLGAGWVRVVGGDSRRASRLLPGlaGRVD 274
                                   89************************************8.5789***************************99887789** PP

                                   EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEE CS
               Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvel 162
                                    +L+D PC+  gvi +  dvk++r+    a+ ++ q   ++ a+ ll++gG l YsTC++   Ene  +++a +     +l
  gi|14601183|ref|NP_147715.1| 275 AVLVDPPCTNIGVIPKVFDVKTLRDS---AAASRYQWMFVEEAWRLLRRGGLLAYSTCTLSSLENELIVARAEELG--FRL 350
                                   ********************999866...566778999*****************************998763322..222 PP

                                   ESSBSTTSTTSSECEEC.TSEEE-TTTTSS-SEEEEEE CS
               Methyltr_RsmB-F 163 vetelsepkglklgeea.gtlrllPhtenkdgffiakl 199
                                   +    s + + + g+ +    r  Ph++ + gff+a l
  gi|14601183|ref|NP_147715.1| 351 TW---SWGLRPSRGRRSwLGFRWEPHRDGTPGFFLAIL 385
                                   22...222222222222244566788888888887765 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   1.7   1.1e-20   3.3e-17       1      72 [.      93     163 ..      93     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.1e-20
                                   CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                           PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                   +rvv d+ A + +l g++L+apGvv ++g +e+gd+V+iv+++g++v+ G+a +s+ e++++ +g +v++ +
  gi|14601183|ref|NP_147715.1|  93 KRVVADKVASESVLMGSDLYAPGVVYARG-VERGDEVVIVAPNGRVVGGGVAVMSWREMRRAGRGLAVRVTK 163
                                   58***************************.**************************************9875 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.75      16     101 ..     220     324 ..     181     326 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
               Methyltransf_24  16 ralrrngagrlvavdhdpgaeeaaalare..aglddrvrlikads...eealaslaagsiDllfiDgghaa.......... 81 
                                   +++ r     +va+d      ++++l ++     + +vr++ +ds   + +l++la g++D +++D + +           
  gi|14601183|ref|NP_147715.1| 220 QLAGRE--AVIVAIDRPS---KVGRLRETleRLGAGWVRVVGGDSrraSRLLPGLA-GRVDAVLVDPPCTNigvipkvfdv 294
                                   222222..2455555555...4444444442344568****999954455566777.99**99999998887777777777 PP

               Methyltransf_24  82 ..........eavledleallprlapggvv 101
                                             +    ++e ++++l++gg++
  gi|14601183|ref|NP_147715.1| 295 ktlrdsaaasRYQWMFVEEAWRLLRRGGLL 324
                                   777777665455556678888888888876 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.2e-05      0.16      21      74 ..     200     263 ..     186     361 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.2e-05
                                   TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS.......HHH..TTEEEECS-CCCSS CS
                          FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm.......apl..pgvttiqgditdpe 74 
                                   pg  vvDl aaPGg    ++q  g ++++va+D   ++       + l   +v+++ gd ++ +
  gi|14601183|ref|NP_147715.1| 200 PGWVVVDLNAAPGGKVSHVAQLAGREAVIVAIDRpSKVgrlretlERLgaGWVRVVGGDSRRAS 263
                                   7788******************9999*******8444455543332224446666677665554 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.7e-05       0.2      69     109 ..     199     239 ..     189     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
                                   -TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHH CS
                   Fibrillarin  69 kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlr 109
                                   ++g  v+ l aa G  vsHv+ + g+e+v+ a++  ++v+r
  gi|14601183|ref|NP_147715.1| 199 RPGWVVVDLNAAPGGKVSHVAQLAGREAVIVAIDRPSKVGR 239
                                   567789999************************99988877 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00021      0.63       2      55 ..      95     147 ..      94     160 .. 0.87
   2 ?   -1.9   0.0       1.4   4.2e+03      12      40 ..     181     206 ..     179     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00021
                       UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt 55 
                                   vv ++ a++++L G d++  ++++ + +v++++ vv++  ng+++G G++  + 
  gi|14601183|ref|NP_147715.1|  95 VVADKVASESVLMGSDLYAPGVVYAR-GVERGDEVVIVAPNGRVVGGGVAVMSW 147
                                   56778899***************999.9999*****************997754 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                       UPF0113  12 FLYGrdvlkesilkitesvkenqvvvVln 40 
                                   ++YG+ v+   + +  ++ +   + vV++
  gi|14601183|ref|NP_147715.1| 181 LVYGQSVTSMYVARALDPRP---GWVVVD 206
                                   68999998888877776655...444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2775.89
//
Query:       gi|14601184|ref|NP_147716.1|  [L=139]
Description: hypothetical protein APE_1102 [Aeropyrum pernix K1]
Scores for complete 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-18   65.5   0.0    6.1e-18   65.1   0.0    1.2  1  PIN_6           PIN domain of ribonuclease
     0.0022   17.5   1.2     0.0029   17.1   1.1    1.3  1  PIN_5           PINc domain ribonuclease
     0.0086   16.6   0.1      0.019   15.5   0.1    1.6  1  PIN             PIN domain
  ------ inclusion threshold ------
       0.02   15.3   0.1      0.042   14.2   0.1    1.5  1  GHMP_kinases_C  GHMP kinases C terminal


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 !   65.1   0.0   1.4e-21   6.1e-18       1      89 []      16     103 ..      16     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.4e-21
                         PIN_6   1 lVlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellp..lelevrePspesvkkvtefakktGDlsvLSktD 79 
                                   +VlD+ga+i+    +  +l  +l t p+V++E+rd+ +r+ lell+   +lev  Ps++++++++e a++ G l  LS +D
  gi|14601184|ref|NP_147716.1|  16 IVLDTGAFIAG---KAAALPGRLATPPRVLEEVRDRGSRSLLELLQstGRLEVLAPSTRALERAREEARRAGVLGRLSGAD 93 
                                   7********99...55667899***********************9544******************************** PP

                         PIN_6  80 ievlALtyeL 89 
                                   +evlAL+++L
  gi|14601184|ref|NP_147716.1|  94 LEVLALALDL 103
                                   *******997 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.1   6.4e-07    0.0029     127     193 ..      59     132 ..      28     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.4e-07
                         PIN_5 127 keeeeeevgelikklRekYrealRkGilD..saeDldvllLAkEL.....daavvssDeGikkwaeklGlrlve 193
                                   ++ + e+++   + l +   ea R G+l   s  Dl+vl LA +L       av ++D  ++++a +lGl +v+
  gi|14601184|ref|NP_147716.1|  59 STGRLEVLAPSTRALERAREEARRAGVLGrlSGADLEVLALALDLawqgcRVAVATDDYTLQRLAARLGLGVVR 132
                                   4445666667777777777789999999766899*********9944333368999**************9986 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.2e-06     0.019      28     120 ..      31     123 ..      16     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.2e-06
                                   S.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHH CS
                           PIN  28 l.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAke 103
                                   l ++l+t++ vl+E++   +r          l+ell+   +l++l  +++++e+a+e a+++g    l+ +D+ ++A+A+ 
  gi|14601184|ref|NP_147716.1|  31 LpGRLATPPRVLEEVRDRGSR---------SLLELLQSTGRLEVLAPSTRALERAREEARRAGvlgrLSGADLEVLALALD 102
                                   248888999999999888877.........99999999*****************************************88 PP

                                   HT-E....EE.ESSTHHHHHH CS
                           PIN 104 hgik....liatfDedfrrva 120
                                      +    ++at D  + r+a
  gi|14601184|ref|NP_147716.1| 103 LAWQgcrvAVATDDYTLQRLA 123
                                   877777787888888888876 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 ?   14.2   0.1   9.3e-06     0.042      11      56 ..      51      92 ..      38      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.3e-06
                GHMP_kinases_C 11 ellgellnlsqrselkavvgilppeleellealselGalgaklsGa 56
                                  ++l ell +  r   ++v+++++++le++ e+++++G   ++lsGa
  gi|14601184|ref|NP_147716.1| 51 RSLLELLQSTGR---LEVLAPSTRALERAREEARRAG-VLGRLSGA 92
                                  456677777777...78********************.88999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1061.06
//
Query:       gi|118431329|ref|NP_147717.2|  [L=280]
Description: inorganic polyphosphate/ATP-NAD kinase [Aeropyrum pernix K1]
Scores for complete 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-36  126.0   0.3    9.1e-35  120.3   0.2    2.1  2  NAD_kinase  ATP-NAD kinase
  ------ inclusion threshold ------
      0.039   13.6   0.0      0.086   12.5   0.0    1.5  1  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0027        24       2      40 ..       5      40 ..       4      50 .. 0.90
   2 !  120.3   0.2     1e-38   9.1e-35      82     289 ..      61     259 ..      59     262 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0027
                                   EEEEESSCGGTCSHHHHHHHHHHHCT-..EEEEECCGGC CS
                     NAD_kinase  2 vgivvnpikkeaieraeevarwLldalsrvlevtveekl 40
                                   vg+vv++++  a+++a+ v++ L+++   ++ev+v+e +
  gi|118431329|ref|NP_147717.2|  5 VGLVVKRRSGIAEDVARLVVKELVES---GVEVLVDETV 40
                                   9********99999999999999999...9****99976 PP

  == domain 2  score: 120.3 bits;  conditional E-value: 1e-38
                                    EEEEE-HHHHHHHHHHHHHCT-EE.EEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE......E CS
                     NAD_kinase  82 iivvGGDGTaldvarllqkaeiPv.lgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskgeediadi 160
                                    ++vvGGDGT l+ +  l + e P+ +++ aG+kgfl ++e  +a e l+++leg++r     + ++++  + ++     +
  gi|118431329|ref|NP_147717.2|  61 VVVVGGDGTLLRTFLRLGERESPLfMTIKAGKKGFLLDVERYEAVERLRDFLEGRFREVVYPRYRVYLEGEARA-----C 135
                                    89**********98777776777649*******************************99999999999999994.....4 PP

                                    EEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS--- CS
                     NAD_kinase 161 viensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivpicPhslssr 240
                                          + + + +++++++++ +++ vd+ l+ ++  dg++vst  Gstaysls Ggp+i+P+++ i+++p++P  l  r
  gi|118431329|ref|NP_147717.2| 136 ------MFNDTAVTANNAKMARVHVFVDGDLAMNIDGDGVVVSTTAGSTAYSLSGGGPIIDPRLDVIVLTPLNPVQLFLR 209
                                    ......4445789******************************************************************* PP

                                    -EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEE CS
                     NAD_kinase 241 piVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfkl 289
                                     iVv+s s+++++ +   + +++ +dG++ +el+pg++v + ++ + +++
  gi|118431329|ref|NP_147717.2| 210 SIVVPSGSRVTVEASvYSNPLVVNIDGQYVYELEPGGIVDIERCGSGVRI 259
                                    *************99999999********************999776665 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.6e-06     0.086      15      73 ..      16      75 ..       5      89 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-06
                                   HHHHHHHCHHHHHHCTCEEEEEE--.STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHH CS
                       DAGK_cat 15 gekllrkvrelleeagveleliete.epgdakelakeakeegvdlivvaGGDGtvsevln 73
                                   +e+++r v + l e gve+ + et  +p        +++++   ++vv+GGDGt+   + 
  gi|118431329|ref|NP_147717.2| 16 AEDVARLVVKELVESGVEVLVDETVdYPSLSGFPRFSISRDPPGRVVVVGGDGTLLRTFL 75
                                   55666777777777777777777663333333335567777779**********976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2183.04
//
Query:       gi|118431330|ref|NP_147718.2|  [L=344]
Description: hypothetical protein APE_1106.1 [Aeropyrum pernix K1]
Scores for complete 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-37  129.2   0.0      2e-37  128.9   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.1e-08   34.8   0.0    1.9e-08   34.0   0.0    1.4  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
      8e-05   22.2   0.0    0.00013   21.5   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    9.5e-05   23.0   0.0    0.00018   22.1   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    0.00071   19.3   0.0     0.0013   18.4   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0014   18.3   0.0     0.0022   17.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0015   18.1   0.0     0.0023   17.5   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.025   14.2   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.057   13.4   0.0      0.093   12.7   0.0    1.3  1  EF_assoc_2       EF hand associated
      0.068   12.3   0.1      0.099   11.8   0.1    1.1  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
      0.074   12.4   0.0        0.1   12.0   0.0    1.1  1  DNA_methylase    C-5 cytosine-specific DNA methylase


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 !  128.9   0.0   1.2e-40     2e-37       2     193 ..      85     281 ..      84     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 1.2e-40
                                    EEEEETTEEEEEB-TT...SSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEET CS
                         Met_10   2 kfeiiGdvvilnlree...lkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDv 78 
                                    +++ +Gd+++  +re    ++ey++    ++ ++ +v++v+ k+ +  ge+R+++l +laG+++t t+h+E g +f++D+
  gi|118431330|ref|NP_147718.2|  85 GYSLVGDIAVFSRREGgpgVEEYRRAAEALMREQPRVRAVYLKEAT-VGELRVQRLVHLAGEERTWTVHREFGLEFEVDI 163
                                    6999*********9853337889887655555555**********9.7******************************** PP

                                    TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT..-TTCEEEE CS
                         Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNk..vekvvkpi 156
                                    ++ yf+++l++E++ +a+ v ege+V+d+f G+G f+i  a + +a+ v+a d+nP++  +  +n ++N+  +  +v+++
  gi|118431330|ref|NP_147718.2| 164 ARAYFNPRLANEHRLVAESVGEGERVLDMFSGVGGFSIHTASLRRAS-VVASDINPHAALLAARNARRNRrrLRGRVSVL 242
                                    *****************************************976666.9********************644899***** PP

                                    ES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEE CS
                         Met_10 157 leDgrevir..eqladrvvmnlpksaieFldkvlaalkd 193
                                     +D++ + r  + ++  ++mn+p+ ++ F  ++++ +  
  gi|118431330|ref|NP_147718.2| 243 RADAALLPRilQPVFTTIIMNHPTASHMFAWEACRLASS 281
                                    ******99998999**************98877776655 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 !   34.0   0.0   1.2e-11   1.9e-08       1      41 [.       4      44 ..       4      46 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.2e-11
                                   EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S CS
                         Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvke 41
                                   c+ V+  +gE+++++L+++glLd ++K+ ++++ l++Pv +
  gi|118431330|ref|NP_147718.2|  4 CVAVKTVDGERAIRLLRAAGLLDTGFKPARSGGRLMLPVED 44
                                   9**************************************76 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   7.7e-08   0.00013     158     215 ..     182     239 ..     177     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 7.7e-08
                           PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev 215
                                     v ege+vlD+  G G  +i  a L  ++vva Di++ A   a++Na++N+ + + +v
  gi|118431330|ref|NP_147718.2| 182 SVGEGERVLDMFSGVGGFSIHTASLRRASVVASDINPHAALLAARNARRNRRRLRGRV 239
                                    567899********************************************87664444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.1e-07   0.00018       1      80 [.     189     274 ..     189     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT....TEEEEESBCCGBSS.STTTEEEEEEEST.G CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl....nvefvqgdaedlpf.edgsfDlvvssga.l 74 
                                    vLd+  G G ++++ a    +a+v++ Di++ +   a+++a++++     +v+++++da  lp   +  f  +++++   
  gi|118431330|ref|NP_147718.2| 189 VLDMFSGVGGFSIHTASL-RRASVVASDINPHAALLAARNARRNRRrlrgRVSVLRADAALLPRiLQPVFTTIIMNHPtA 267
                                    8***************99.68**********9998888888874445588************962444777777754444 PP

                                    GG.SSHH CS
                Methyltransf_25  75 hh.lsde 80 
                                    +h +  e
  gi|118431330|ref|NP_147718.2| 268 SHmFAWE 274
                                    4434333 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.9e-07    0.0013      39     122 ..     183     265 ..     163     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.9e-07
                                    CHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--T..TTEEEEES-HHHHCTS--SS-EEEE CS
                  Cons_hypoth95  39 eiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelklee..etaelkedaleallklakkkeefdi 116
                                     +eg+rvLD+f+G G+ ++  +S   +++v+ + +++a+ +  +n ++ + +   ++++l+ da+   + l   +++f  
  gi|118431330|ref|NP_147718.2| 183 VGEGERVLDMFSGVGGFSIHTASLRRASVVASDINPHAALLAARNARRNRRRLrgRVSVLRADAALLPRIL---QPVFTT 259
                                    3899*******************9999***********999999998877555547777777776544433...456666 PP

                                    EEE--S CS
                  Cons_hypoth95 117 vflDPP 122
                                    + ++ P
  gi|118431330|ref|NP_147718.2| 260 IIMNHP 265
                                    665555 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 !   17.6   0.0   1.4e-06    0.0022       3      43 ..     188     229 ..     186     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNae 43 
                                     +lD+fsG GG +i+ a     +v+a++in++   +a++Na+
  gi|118431330|ref|NP_147718.2| 188 RVLDMFSGVGGFSIHTASLrRASVVASDINPHAALLAARNAR 229
                                    79*************99876789*****************98 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   1.4e-06    0.0023      31     106 ..     185     265 ..     160     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC....EEEEE-ST..TTTSTTS-EEEEEE- CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle....vevvasdv..leeveekkfdlivsN 104
                                    + ++vlD+ +G+G  +++ a+    a+v++ d++ +A  +a +n+++n+ +    v+v+  d+  l  + +  f +i++N
  gi|118431330|ref|NP_147718.2| 185 EGERVLDMFSGVGGFSIHTASLRR-ASVVASDINPHAALLAARNARRNRRRlrgrVSVLRADAalLPRILQPVFTTIIMN 263
                                    4678***************99665.59*********************98877777777766411455556778888888 PP

                                    -- CS
                            MTS 105 PP 106
                                     P
  gi|118431330|ref|NP_147718.2| 264 HP 265
                                    77 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 ?   14.2   0.0   1.5e-05     0.025       8      88 ..     185     265 ..     179     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                    TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHH....HHTT--SEEEEES-CTCCHHHHCC..EEEE CS
                Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenl....krLgvtntivleaDarkidkvlggelfDri 83 
                                    e+e++lD+ ++ Gg   h a l   ++ vvA d+n + +   a+n     +rL  + + vl+aDa   +++l   +f  i
  gi|118431330|ref|NP_147718.2| 185 EGERVLDMFSGVGGFSIHTASL--RRASVVASDINPHAALLAARNArrnrRRLRGR-VSVLRADAALLPRILQ-PVFTTI 260
                                    799*******************..999*********98766665551100566665.9999999999988877.478888 PP

                                    EEEE- CS
                Methyltr_RsmB-F  84 LlDaP 88 
                                    ++  P
  gi|118431330|ref|NP_147718.2| 261 IMNHP 265
                                    77777 PP

>> EF_assoc_2  EF hand associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05     0.093      46      82 ..     145     181 ..     131     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                     EF_assoc_2  46 hettWtvLrkFgYddsLsLkeeflhPkldvpedssve 82 
                                     e tWtv r+Fg + ++++++ +++P+l  ++   +e
  gi|118431330|ref|NP_147718.2| 145 EERTWTVHREFGLEFEVDIARAYFNPRLANEHRLVAE 181
                                    599************************9988776665 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     6e-05     0.099      78     179 ..     142     242 ..     133     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                Methyltrans_SAM  78 lvgeldespvvvesglkyqldigrnq.nfglfldmrlgrdwvqenakdknvlnlfaytcgfsvaaiaggaskvvnvdma. 155
                                    l+ge     v  e gl +++di r   n  l  + rl  + v    ++ +vl++f+   gfs+ + +     vv  d+  
  gi|118431330|ref|NP_147718.2| 142 LAGEERTWTVHREFGLEFEVDIARAYfNPRLANEHRLVAESV---GEGERVLDMFSGVGGFSIHTASLRRASVVASDINp 218
                                    67777766677899**********852555555555544444...46799*************99999999999999873 PP

                Methyltrans_SAM 156 rgslnkgrdnhrlnghdl.rrvsfl 179
                                    +++l   r+  r n   l +rvs l
  gi|118431330|ref|NP_147718.2| 219 HAALLAARNARR-NRRRLrGRVSVL 242
                                    566666665544.444441466665 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 ?   12.0   0.0   6.1e-05       0.1       2      36 ..     188     222 ..     187     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                                    EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHH CS
                  DNA_methylase   2 kfidLfaGiGGfrlgleaagfecvaaseidkkaak 36 
                                    +++d+f+G+GGf++  ++     v+as+i+++aa 
  gi|118431330|ref|NP_147718.2| 188 RVLDMFSGVGGFSIHTASLRRASVVASDINPHAAL 222
                                    689****************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2802.07
//
Query:       gi|118431331|ref|NP_147719.2|  [L=387]
Description: fructose-1,6-bisphosphatase [Aeropyrum pernix K1]
Scores for 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-189  627.7   0.0   7.2e-189  627.5   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 !  627.5   0.0    4e-193  7.2e-189       2     361 .]       7     366 ..       6     366 .. 1.00

  Alignments for each domain:
  == domain 1  score: 627.5 bits;  conditional E-value: 4e-193
                       FBPase_3   2 vtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeate 81 
                                    +t+svikaD+GslaGh++vh++ + ++++vl+eak+kg+++ fyvt+ GDD++limth kgvdn e+h+law af+eat+
  gi|118431331|ref|NP_147719.2|   7 TTVSVIKADIGSLAGHHRVHPDTILAASRVLAEAKRKGVIKSFYVTNAGDDLQLIMTHFKGVDNPEIHELAWTAFREATK 86 
                                    79****************************************************************************** PP

                       FBPase_3  82 vakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpklh 161
                                    vak+l+ly+aGqDlL+dafsGn++GlGPgvae+ef eR+sep+vvf+aDktepgafnlplykifadpfntaGlvidp+lh
  gi|118431331|ref|NP_147719.2|  87 VAKDLGLYAAGQDLLSDAFSGNIRGLGPGVAEMEFVERPSEPIVVFMADKTEPGAFNLPLYKIFADPFNTAGLVIDPRLH 166
                                    ******************************************************************************** PP

                       FBPase_3 162 eGfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkDDPvaivRaqs 241
                                    +Gf fevlDv e k+++l+apee+ydllal+g+++ryv+krvy+k+d eiaavvs+erlsliaG+YvGkDDPv+ivRaqs
  gi|118431331|ref|NP_147719.2| 167 DGFIFEVLDVFEGKAVELRAPEEIYDLLALIGTPSRYVVKRVYRKSDREIAAVVSSERLSLIAGRYVGKDDPVMIVRAQS 246
                                    ******************************************************************************** PP

                       FBPase_3 242 glPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDlfddpafdeaReka 321
                                    g+Pavgevlepfa+phlvaGwmrGsh+gplmPv lkd+k++rfdgpprv+algfq+k+g+l+gp+DlfddpafdeaR++a
  gi|118431331|ref|NP_147719.2| 247 GFPAVGEVLEPFAFPHLVAGWMRGSHHGPLMPVGLKDSKVSRFDGPPRVIALGFQVKNGELIGPADLFDDPAFDEARRQA 326
                                    ******************************************************************************** PP

                       FBPase_3 322 aeiadelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                    + iad++Rr+Gpf+phrl +ee+eYttlpevl++lk+rf+
  gi|118431331|ref|NP_147719.2| 327 QMIADYIRRHGPFMPHRLGPEEMEYTTLPEVLKRLKDRFK 366
                                    **************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2970.47
//
Query:       gi|14601188|ref|NP_147720.1|  [L=174]
Description: hypothetical protein APE_1113 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 00:00:00.38
# Mc/sec: 1363.38
//
Query:       gi|118431332|ref|NP_147721.2|  [L=307]
Description: methionine aminopeptidase [Aeropyrum pernix K1]
Scores for 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-35  120.2   0.2      1e-34  120.1   0.2    1.2  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 !  120.1   0.2   5.6e-39     1e-34       3     203 ..       9     205 ..       7     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 120.1 bits;  conditional E-value: 5.6e-39
                                    HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEEEE CS
                  Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlvli 79 
                                    + +a+ria++a+e+++  ++ g + r +++++e++  +r  +  +afp  + ++  + ++hytp   +d ++  g +v++
  gi|118431332|ref|NP_147721.2|   9 LLEAGRIAAEAREYAAGLVEAGASCRRVCELVEEK--IRSLGAVPAFP--CNISLDSVAAHYTPglrDDCSIGGGSVVKL 84 
                                    569************999***************98..56666789***..8888888888****8877888********* PP

                                    EEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS CS
                  Peptidase_M24  80 dagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl 159
                                    d+ga ++gy++D+++Tv +G     +r l+ea  e+++aa+k +kpG+++ +i++a+++ ++++g+ k+++++ GH + +
  gi|118431332|ref|NP_147721.2|  85 DVGAAVEGYIADTAVTVDLG--G-GHRSLVEASVEGLRAAMKVLKPGARFYDIGRAVEQAVRRRGF-KVVKNLSGHTIDR 160
                                    *****************766..3.3789**************************************.************9 PP

                                    .SSSEEEEEESS...STTCSSB--TTBEEEEEE...EEEEETTTEEEEEBE CS
                  Peptidase_M24 160 .evhdegpsvsr...esndgrkleeGmvftiEp...giyfapgeggvried 203
                                      +h +  s+++   ++   +++++Gm+f+iEp         g g vr   
  gi|118431332|ref|NP_147721.2| 161 yTIHAG-LSIPNygdRTAWIHRIRPGMTFAIEPfatN-----GRGMVREGS 205
                                    9***98.666653333335566***********4330.....444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2386.74
//
Query:       gi|14601190|ref|NP_147722.1|  [L=242]
Description: hypothetical protein APE_1117 [Aeropyrum pernix K1]
Scores for complete 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-24   87.1   0.3    1.2e-23   83.8   0.4    2.2  2  Lactamase_B_3  Beta-lactamase superfamily domain
    1.9e-23   83.0   0.2    2.7e-23   82.6   0.2    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    7.7e-15   55.4   3.3    9.7e-15   55.1   3.3    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.16   11.3   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.4   2.7e-27   1.2e-23       1     163 []       3     199 ..       3     199 .. 0.74
   2 ?   -3.4   0.0       1.8   8.1e+03      59      74 ..     223     238 ..     217     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 2.7e-27
                 Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppa...eeaDlvlisqaledHa.hletlkqlaenvkvlee.......... 67 
                                   +lt+lgh++f le +g +ilvDP+  n +   ++   e +Dl++i++++ dH  ++ ++++ +  +kvl+           
  gi|14601190|ref|NP_147722.1|   3 RLTYLGHAAFQLEAGGRKILVDPWLSNPKSPVKPeevEGVDLIVITHSHFDHLgDVGKIAAKNPGAKVLAVyevadlaaee 83 
                                   69**********************885555554455799*************62666777766667777774444444444 PP

                 Lactamase_B_3  68 .........geslevggleiravatsh...........................davggsergenngflleqdgltiyhlG 112
                                            +                +                           ++   s  g   g ++  ++ ++yh G
  gi|14601190|ref|NP_147722.1|  84 iaketgaskD----------------ElfnagrviganiggpvvlqdlglkvafTPATHSSVGVAAGAVIITGEGRVYHAG 148
                                   4444444431................0333333333333333355555555554444455556677778888999****** PP

                 Lactamase_B_3 113 hlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                   +++ ++++    e+ ++ v l+P+gg++t+++ ea++++++++p + +Pmh
  gi|14601190|ref|NP_147722.1| 149 DTGVTMDMRLVGEIYKPHVALLPIGGHFTMDPVEAAKAVELIRPLVAIPMH 199
                                   **************************************************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                 Lactamase_B_3  59 aenvkvleegeslevg 74 
                                    ++v++l++ges+e++
  gi|14601190|ref|NP_147722.1| 223 PTQVRILKPGESYEFD 238
                                   4599999999999875 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 !   82.6   0.2     6e-27   2.7e-23       1     201 []      19     200 ..      19     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 6e-27
                                   SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EE..EEEE.EEHHHHHHCCTTCGHHH CS
                 Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkk..lply.apkgvlavleanfvyla 78 
                                   r iL+D++++     +++  Pv+  +e++ +d++++th+H+DHl ++  +++  p    l +y + +  ++++++++ +  
  gi|14601190|ref|NP_147722.1|  19 RKILVDPWLS-----NPKS-PVK-PEEVEGVDLIVITHSHFDHLGDVGKIAAKNPGAkvLAVYeVADLAAEEIAKETGASK 92 
                                   78********.....5554.554.6789************************76654456666655555555555544433 PP

                                   CHTT..TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHHCT CS
                 Lactamase_B_2  79 leee..pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerlgg 156
                                   +  e   a +v   ++g+++ l+d gl++ +tpa h+s          ++G +i +g+ rvy++gDtg +   ++  ++++
  gi|14601190|ref|NP_147722.1|  93 D--ElfNAGRVIGANIGGPVVLQDLGLKVAFTPATHSSVG-------VAAGAVIITGEGRVYHAGDTGVTMdMRLVGEIYK 164
                                   3..1447899999*************************98.......99****999************6663557789999 PP

                                   -SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                 Lactamase_B_2 157 adllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                   + ++ll+i+         ++++++p ea++a++ +++ +++++H+
  gi|14601190|ref|NP_147722.1| 165 PHVALLPIG---------GHFTMDPVEAAKAVELIRPLVAIPMHY 200
                                   *********.........9999**********************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 !   55.1   3.3   2.2e-18   9.7e-15      11     183 ..      14     191 ..       5     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 2.2e-18
                                   EEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHH CS
                   Lactamase_B  11 iegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaa 91 
                                   +e +g+ iL+D+ +s++++        +  + + vd +++TH+H+DH G++g+++ + + +++    e + l  ee  +++
  gi|14601190|ref|NP_147722.1|  14 LEAGGRKILVDPWLSNPKSPV------KPEEVEGVDLIVITHSHFDHLGDVGKIAAKNPGAKVLAVYEVADLAAEEIAKET 88 
                                   7899****************9......69*************************987665555555555555555555555 PP

                                   HHCCHH..TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........ CS
                   Lactamase_B  92 srkgll..lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl........ 162
                                   ++ +++   ag ++ +++  + +l++ ++ + ++++t+  +  + ++v+  g+g+v  +GD++ + +  ++++        
  gi|14601190|ref|NP_147722.1|  89 GASKDElfNAGRVIGANIGGPVVLQDLGLKVAFTPATHSSVGVAAGAVIITGEGRVYHAGDTGVTMDMRLVGEiykphval 169
                                   6666657999999999999999*********************************************************** PP

                                   ..TTCEEE-SHCHHHHHHHHHH CS
                   Lactamase_B 163 .tlrgaevrdpsdaekyldsll 183
                                    +++g++++dp++a+k+ + ++
  gi|14601190|ref|NP_147722.1| 170 lPIGGHFTMDPVEAAKAVELIR 191
                                   ****************997666 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 ?   11.3   0.0   3.7e-05      0.16       2      57 ..      14      63 ..      13      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                 Lactamase_B_6  2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallya 57
                                  Le  + kiL+D+  ++ k    s +k   + ++ vdli+++h+  +hlG    + a
  gi|14601190|ref|NP_147722.1| 14 LEAGGRKILVDPWLSNPK----SPVK--PEEVEGVDLIVITHSHFDHLGDVGKIAA 63
                                  566677899998666542....3455..5669*****************6544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1931.79
//
Query:       gi|118431333|ref|NP_147723.2|  [L=614]
Description: ATPase RIL [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-38  132.9   0.0    2.5e-18   66.9   0.0    2.6  2  ABC_tran         ABC transporter
    2.8e-15   56.9   2.1     0.0093   15.8   0.0    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.1e-13   50.7   1.6    2.9e-13   49.4   1.6    1.8  1  RLI              Possible Fer4-like domain in RNase L inhibit
    7.5e-11   41.9   0.6      0.016   14.7   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.4e-08   34.4  14.1      6e-05   22.9   4.8    2.3  2  Fer4_6           4Fe-4S binding domain
    1.2e-07   31.3   5.7    1.2e-07   31.3   5.7    2.9  3  Fer4             4Fe-4S binding domain
    5.7e-07   29.6   9.3    6.6e-05   23.0   0.8    2.3  2  Fer4_10          4Fe-4S dicluster domain
    1.6e-06   28.5   0.0      0.039   14.4   0.0    2.7  2  AAA              ATPase family associated with various cellul
    2.7e-05   24.6   1.6      0.072   13.5   0.2    3.1  3  AAA_16           AAA ATPase domain
    4.7e-05   23.5   0.0       0.42   10.9   0.0    2.7  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
    4.8e-05   23.6   1.1       0.18   12.0   0.1    3.9  2  AAA_33           AAA domain
    5.9e-05   23.1  10.1    0.00012   22.1  10.1    1.5  1  Fer4_21          4Fe-4S dicluster domain
    0.00012   22.0   0.6        0.1   12.5   0.0    2.4  2  NACHT            NACHT domain
    0.00016   22.0   0.9       0.97    9.7   0.0    3.8  3  AAA_22           AAA domain
    0.00037   20.4   2.4    0.00037   20.4   2.4    2.4  2  Fer4_2           4Fe-4S binding domain
    0.00041   20.9   0.2        1.1    9.7   0.0    2.2  2  AAA_23           AAA domain
    0.00042   20.8  10.5    0.00074   20.1   1.3    2.3  3  Fer4_7           4Fe-4S dicluster domain
    0.00068   19.7   8.0     0.0012   18.9   8.0    1.4  1  Fer4_9           4Fe-4S dicluster domain
    0.00075   19.3   0.7       0.12   12.1   0.1    2.3  2  AAA_24           AAA domain
      0.001   19.0   0.4       0.34   10.9   0.1    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0012   18.6   3.4       0.35   10.6   0.0    3.3  3  AAA_30           AAA domain
     0.0015   19.4   4.0      0.033   15.1   0.1    2.3  2  Fer4_16          4Fe-4S double cluster binding domain
     0.0026   18.3   0.0        4.2    7.9   0.0    2.8  2  AAA_18           AAA domain
     0.0041   17.1   2.8       0.26   11.2   0.0    3.1  3  NTPase_1         NTPase
     0.0043   17.4   0.0        1.5    9.2   0.0    2.3  2  RNA_helicase     RNA helicase
      0.005   16.5   0.4        2.4    8.0   0.0    2.7  2  AAA_29           P-loop containing region of AAA domain
     0.0061   16.6   0.0       0.83    9.7   0.0    2.9  2  AAA_14           AAA domain
     0.0078   16.1   0.1        3.4    7.6   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
     0.0081   17.0   4.5     0.0081   17.0   4.5    2.3  2  Fer4_3           4Fe-4S binding domain
     0.0084   16.1   0.0        4.2    7.2   0.0    2.7  2  Rad17            Rad17 P-loop domain
     0.0093   15.7   0.0        5.9    6.5   0.0    2.8  2  Thymidylate_kin  Thymidylate kinase
  ------ inclusion threshold ------
      0.012   14.8   0.0        1.3    8.1   0.0    2.2  2  NB-ARC           NB-ARC domain
      0.012   15.4   0.0       0.15   11.8   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.012   15.2   2.8        1.8    8.2   0.2    2.3  2  SRP54            SRP54-type protein, GTPase domain
      0.013   15.8   0.3         11    6.3   0.0    3.0  3  AAA_28           AAA domain
      0.016   15.7   2.5      0.016   15.7   2.5    2.3  2  Fer4_4           4Fe-4S binding domain
      0.021   14.8   1.6        3.4    7.7   0.0    3.1  3  AAA_5            AAA domain (dynein-related subfamily)
       0.03   14.4   1.6         12    6.0   0.0    3.1  3  MMR_HSR1         50S ribosome-binding GTPase
      0.053   13.4   0.5         11    5.9   0.0    2.4  2  MobB             Molybdopterin guanine dinucleotide synthesis
      0.082   13.4   3.8      0.098   13.1   0.2    2.2  2  Fer4_8           4Fe-4S dicluster domain
       0.11   12.2   0.0        4.5    6.9   0.0    2.4  2  AAA_15           AAA ATPase domain
       0.21   11.4   0.0       0.85    9.5   0.0    1.9  2  ATPase_2         ATPase domain predominantly from Archaea
       0.31   10.6   6.1        3.1    7.3   1.5    3.1  2  AAA_25           AAA domain
        0.4   11.0   2.8         21    5.4   0.1    2.8  2  AAA_19           AAA domain
       0.45   11.1   7.8       0.31   11.6   1.7    2.2  2  Fer4_17          4Fe-4S dicluster domain
       0.59    9.4   2.6        7.9    5.7   0.3    2.7  3  ATPase           KaiC
        3.2    8.4   4.2        6.5    7.4   4.2    1.5  1  AFP              Insect antifreeze protein repeat


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 !   66.9   0.0   6.6e-21   2.5e-18      10     136 ..     105     248 ..     103     249 .. 0.77
   2 !   63.1   0.0   9.5e-20   3.6e-17       8     137 .]     380     507 ..     374     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 6.6e-21
                                    TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                       ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.......... 79 
                                    eg++v+++G+nG+GK+t l++lag+lkp+ G+++  + +++e+ +++  +e+++++ +  ++ +l+v+ +          
  gi|118431333|ref|NP_147723.2| 105 EGQVVGLLGRNGTGKTTALRILAGELKPNLGRVEGGEPEWDEILKRFRGSELQTYFRK-LVDGKLRVAHKiqyvelvprr 183
                                    89*******************************7777777777777777777777777.455555555556666777777 PP

                                    .........HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .........xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             ++ +e   + ++++++gl+++ d+ v    ++LSgG+ q++ ++++l ++++++++DEp+
  gi|118431333|ref|NP_147723.2| 184 lkgrvrdllKRADErgvALELAEQVGLDKVFDRDV----RQLSGGELQKMLIVAVLSRDANVYIFDEPS 248
                                    76667777844444244666666666666555555....*****************************7 PP

  == domain 2  score: 63.1 bits;  conditional E-value: 9.5e-20
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...... RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren...... 79 
                                    l+ ge++++ G+nG GK+t++++lag lkp eG +        +    + + ++++ pq   p+  p+ tv++       
  gi|118431333|ref|NP_147723.2| 380 LYGGEVIGVAGPNGIGKTTFVRTLAGALKPVEGAV--------Y--PYVEDLRVSYKPQYisPESLPDATVEQVlkaanp 449
                                    6779*******************************........2..2355666777777777889999999888776666 PP

                                    ....HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ....xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ....esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           ++   +++++++l++l +++v    ++LSgG+ q+va+a+al+++++++llDEp+a
  gi|118431333|ref|NP_147723.2| 450 ailaP-GSWlNLELVKRMRLDKLLERRV----RTLSGGELQKVAVAAALAREADVYLLDEPSA 507
                                    66632.3334678899999999999999....*****************************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 !   14.7   0.2   5.1e-05      0.02       2      33 ..     109     134 ..     108     157 .. 0.73
   2 !   12.5   0.0   0.00024     0.092     228     287 ..     212     268 ..     147     284 .. 0.68
   3 !   10.7   0.1   0.00087      0.33       3      22 ..     387     406 ..     385     431 .. 0.85
   4 !   15.8   0.0   2.4e-05    0.0093     175     280 ..     452     526 ..     415     533 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-05
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdveglt 33 
                                     +l G+Ng+GK++ L++l      ++++++  
  gi|118431333|ref|NP_147723.2| 109 VGLLGRNGTGKTTALRIL------AGELKPNL 134
                                    689***************......55555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00024
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                    +  ++++r+lS G ++   +++ l r++    ++++DEp + L+ +   r ++l+  ++r
  gi|118431333|ref|NP_147723.2| 212 KVFDRDVRQLSGGELQKMLIVAVLSRDA---NVYIFDEPSSYLDIRERMRMARLIAGAAR 268
                                    34456789*********66666666666...89***********9888888888755555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00087
                         AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                    ++ GpNg GK+++ ++l ++
  gi|118431333|ref|NP_147723.2| 387 GVAGPNGIGKTTFVRTLAGA 406
                                    689**************877 PP

  == domain 4  score: 15.8 bits;  conditional E-value: 2.4e-05
                         AAA_21 175 yfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallra 254
                                    +++++ ++  l +++r  kl e ++++l                                   S G ++  a+++al+r 
  gi|118431333|ref|NP_147723.2| 452 LAPGSWLNLELVKRMRLDKLLERRVRTL-----------------------------------SGGELQKVAVAAALARE 496
                                    5555555555555555555555555555...................................***************** PP

                         AAA_21 255 lkkgsllliDEpEngLHP.......kllrrlle 280
                                    +   +++l+DEp + L+        +++rr++e
  gi|118431333|ref|NP_147723.2| 497 A---DVYLLDEPSAYLDVeervgvaRAIRRIVE 526
                                    *...9************9988877777777775 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 !   49.4   1.6   7.6e-16   2.9e-13       2      35 .]       8      38 ..       7      38 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 7.6e-16
                                   -EEEES---------TTHHHHHTTSEEEESS--S CS
                            RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                   rlA++d+d C+PKKC++ +c+  cpv  +++g++
  gi|118431333|ref|NP_147723.2|  8 RLAVIDYDSCKPKKCSY-ECIAVCPV--NKSGRG 38
                                   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 ?    5.3   0.0      0.03        11       4      39 ..      89     121 ..      86     127 .. 0.84
   2 !   14.7   0.0   4.2e-05     0.016     136     212 ..     220     293 ..     146     299 .. 0.80
   3 ?    2.9   0.1      0.17        64      27      43 ..     386     402 ..     379     407 .. 0.83
   4 !   14.2   0.0   5.8e-05     0.022     135     197 ..     477     537 ..     428     557 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.03
                                    EEEEESETTEECEEEEEETTSSEEEEEESTTSSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   4 rleienFksyagktvilpfsksftaivGpNGSGKsn 39 
                                    r  +++Fk +   +  +p + ++  ++G+NG GK+ 
  gi|118431333|ref|NP_147723.2|  89 RYGVNGFKLF---RLPIPREGQVVGLLGRNGTGKTT 121
                                    5668899999...599999999************96 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.2e-05
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                    +LSgGe +     L++A+ + + a +y++De  + LD +++ ++a+l+  +    a ++v+ ++  +l  ++ lv + 
  gi|118431333|ref|NP_147723.2| 220 QLSGGELQK---MLIVAVLS-RDANVYIFDEPSSYLDIRERMRMARLIAGAARPgAYVMVVEHDLAVLDYVSDLVHIL 293
                                    89***9643...35666665.67889**********************955544499999999888888877777765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.17
                                    EEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsnlldA 43 
                                      + GpNG GK+ ++  
  gi|118431333|ref|NP_147723.2| 386 IGVAGPNGIGKTTFVRT 402
                                    5799********99865 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 5.8e-05
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivisl 197
                                     +LSgGe + va+a  +A    + a +yllDe  a LD +++  va+ ++   ++ +a  +v+ +
  gi|118431333|ref|NP_147723.2| 477 RTLSGGELQKVAVAAALA----READVYLLDEPSAYLDVEERVGVARAIRriVETREAAALVVEH 537
                                    48*****99999887766....7789*********************999332344466666655 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   1.8   1.4e-05    0.0052       2      22 ..      10      33 ..       9      41 .. 0.89
   2 !   22.9   4.8   1.6e-07     6e-05       2      24 .]      51      73 ..      50      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-05
                         Fer4_6  2 veidpdkCi..gC.gdCvrvCPeg 22
                                   ++id+d+C    C ++C++vCP +
  gi|118431333|ref|NP_147723.2| 10 AVIDYDSCKpkKCsYECIAVCPVN 33
                                   79******9888*9********75 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.6e-07
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   ++i +d+CigC  Cv++CP++ai
  gi|118431333|ref|NP_147723.2| 51 PVIYEDACIGCALCVKACPFDAI 73
                                   67779****************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       4.7   1.8e+03       2       8 ..      11      17 ..      10      18 .. 0.87
   2 ?    4.5   1.2     0.087        33      13      21 ..      25      33 ..      24      33 .. 0.90
   3 !   31.3   5.7   3.1e-10   1.2e-07       1      24 []      51      74 ..      51      74 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.7
                                   EEETTTS CS
                           Fer4  2 videekC 8 
                                   vid++ C
  gi|118431333|ref|NP_147723.2| 11 VIDYDSC 17
                                   8****** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.087
                                   HHHHHSTTT CS
                           Fer4 13 aCvevCPvg 21
                                   +C+ vCPv+
  gi|118431333|ref|NP_147723.2| 25 ECIAVCPVN 33
                                   6******98 PP

  == domain 3  score: 31.3 bits;  conditional E-value: 3.1e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                   +vi e+ CigC +Cv++CP++AI+
  gi|118431333|ref|NP_147723.2| 51 PVIYEDACIGCALCVKACPFDAIY 74
                                   689********************6 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.1   0.00085      0.32       2      35 ..      10      44 ..       9      52 .. 0.71
   2 !   23.0   0.8   1.7e-07   6.6e-05       2      27 ..      51      76 ..      50      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00085
                        Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeasee 35
                                   +vid d+C   +C  +C ++CP+  +++g   +++ +
  gi|118431333|ref|NP_147723.2| 10 AVIDYDSCkpKKCSyECIAVCPV--NKSGRGVAIDAD 44
                                   699*****6669999********..444444444444 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.7e-07
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl.tsvg 27
                                   +vi +d Ci+C+ CvkaCP+d+    +
  gi|118431333|ref|NP_147723.2| 51 PVIYEDACIGCALCVKACPFDAiY-IV 76
                                   67889***************8852.22 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   0.0    0.0001     0.039       3      34 ..     111     142 ..     109     199 .. 0.81
   2 !   11.3   0.0   0.00089      0.34       3      23 ..     388     408 ..     386     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.0001
                                    EESSTTSSHHHHHHHHHHHHTHEEEEEETTTC CS
                            AAA   3 lyGppGtGKTllakavakelgvefleisgsel 34 
                                    l G  GtGKT++ + +a el+ ++ +++g e 
  gi|118431333|ref|NP_147723.2| 111 LLGRNGTGKTTALRILAGELKPNLGRVEGGEP 142
                                    88******************999888777664 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00089
                                    EESSTTSSHHHHHHHHHHHHT CS
                            AAA   3 lyGppGtGKTllakavakelg 23 
                                    + Gp G+GKT++++ +a  l+
  gi|118431333|ref|NP_147723.2| 388 VAGPNGIGKTTFVRTLAGALK 408
                                    68***************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0043       1.6      24      88 ..     106     194 ..      96     284 .. 0.61
   2 !   13.5   0.2   0.00019     0.072      25      55 ..     384     414 ..     361     537 .. 0.72
   3 ?   -1.7   0.0       8.5   3.2e+03      25      35 ..     548     558 ..     540     558 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0043
                         AAA_16  24 pelvllsGesGvGKsslvrellralekd.......................ggif...lrgkcdqlesaipysa.laqal 76 
                                    +++v l G  G+GK++ +r l+ +l+ +                         +f   + gk +    +i y+  + + l
  gi|118431333|ref|NP_147723.2| 106 GQVVGLLGRNGTGKTTALRILAGELKPNlgrveggepewdeilkrfrgselQTYFrklVDGKLRVA-HKIQYVElVPRRL 184
                                    378899****************99999966666665555555555544333223333333333333.3344544233333 PP

                         AAA_16  77 areellrqllde 88 
                                     + + +r+ll +
  gi|118431333|ref|NP_147723.2| 185 -K-GRVRDLLKR 194
                                    .3.444444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00019
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggif 55 
                                    e++ + G+ G+GK++ vr+l+ al+  +g +
  gi|118431333|ref|NP_147723.2| 384 EVIGVAGPNGIGKTTFVRTLAGALKPVEGAV 414
                                    8889*****************8777664333 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 8.5
                         AAA_16  25 elvllsGesGv 35 
                                    +++l++Ge+Gv
  gi|118431333|ref|NP_147723.2| 548 RIMLVTGEPGV 558
                                    799*******7 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 !    9.8   0.0    0.0024      0.93      19      47 ..     207     235 ..     195     264 .. 0.84
   2 !   10.9   0.0    0.0011      0.42       9      48 ..     457     494 ..     451     520 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0024
                        SbcCD_C  19 edgkekelsrssgtlSGGekqflaylala 47 
                                    + g +k ++r++++lSGGe q+++ +a++
  gi|118431333|ref|NP_147723.2| 207 QVGLDKVFDRDVRQLSGGELQKMLIVAVL 235
                                    456677799**************999986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0011
                        SbcCD_C   9 ylsfevevrdedgkekelsrssgtlSGGekqflaylalaa 48 
                                    +l++e+ +r     +k l+r+++tlSGGe q++a  a +a
  gi|118431333|ref|NP_147723.2| 457 WLNLELVKR--MRLDKLLERRVRTLSGGELQKVAVAAALA 494
                                    566666666..4444569************7765544443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.014       5.4       2      28 ..     109     137 ..     108     284 .. 0.60
   2 !   12.0   0.1   0.00047      0.18       2      24 ..     386     408 ..     385     536 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.014
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avll 28 
                                    v l G +G+GK+t ++ l+ +l+    ++
  gi|118431333|ref|NP_147723.2| 109 VGLLGRNGTGKTTALRILAGELKpnLGRV 137
                                    6678999*********9999998554444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00047
                         AAA_33   2 vllvGlpGsGKstlaerllkklg 24 
                                    + + G++G GK+t+++ l+ +l+
  gi|118431333|ref|NP_147723.2| 386 IGVAGPNGIGKTTFVRTLAGALK 408
                                    5678**************99988 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  10.1   3.2e-07   0.00012       1      57 [.      10      73 ..      10      75 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.2e-07
                        Fer4_21  1 AridedkCi..gCg.kCliaCedt.shq..aieid.aktvlkvv.edeCvGCnlCssvCPvedci 57
                                   A+id d+C   +C  +C+ +C+ + s    ai+ d a++  +v+ ed C+GC+lC++ CP  d+i
  gi|118431333|ref|NP_147723.2| 10 AVIDYDSCKpkKCSyECIAVCPVNkSGRgvAIDADmASRGKPVIyEDACIGCALCVKACPF-DAI 73
                                   7788888853378647*****9652444125544422345577669**************7.777 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2     0.011       4.1       2      25 ..     108     131 ..     107     135 .. 0.87
   2 !   12.5   0.0   0.00026       0.1       2      25 ..     385     408 ..     384     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                                    CEEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawa 25 
                                    +v l G++G GKTt l+ la +++
  gi|118431333|ref|NP_147723.2| 108 VVGLLGRNGTGKTTALRILAGELK 131
                                    67799************9998776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00026
                                    CEEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawa 25 
                                    ++ + G++G+GKTt+++ la a++
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTLAGALK 408
                                    56689**************98876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5     0.014       5.2      10      30 ..     111     131 ..     104     302 .. 0.68
   2 !    9.7   0.0    0.0025      0.97       8      37 ..     386     415 ..     381     530 .. 0.71
   3 ?   -1.4   0.0       6.7   2.5e+03       5      16 ..     547     558 ..     545     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                         AAA_22  10 vtGesGtGKTtllrrlleqld 30 
                                    + G  GtGKTt lr l+ +l+
  gi|118431333|ref|NP_147723.2| 111 LLGRNGTGKTTALRILAGELK 131
                                    7899**********9998883 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0025
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee 37 
                                    + v G+ G+GKTt +r+l+  l+ ++ a +
  gi|118431333|ref|NP_147723.2| 386 IGVAGPNGIGKTTFVRTLAGALKPVEGAVY 415
                                    6689**************999977665555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 6.7
                         AAA_22   5 agilvvtGesGt 16 
                                    ++i++vtGe+G+
  gi|118431333|ref|NP_147723.2| 547 DRIMLVTGEPGV 558
                                    689********7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   2.2      0.27     1e+02       3      21 ..      10      31 ..       8      32 .. 0.77
   2 !   20.4   2.4   9.8e-07   0.00037       2      21 ..      50      69 ..      49      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.27
                         Fer4_2  3 vvvdtdrCi.g.Cg.aCvsaCP 21
                                   +v+d d+C    C+  C+ +CP
  gi|118431333|ref|NP_147723.2| 10 AVIDYDSCKpKkCSyECIAVCP 31
                                   6789999953359779****** PP

  == domain 2  score: 20.4 bits;  conditional E-value: 9.8e-07
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                   ++v+ +d+CigC  Cv+aCP
  gi|118431333|ref|NP_147723.2| 50 KPVIYEDACIGCALCVKACP 69
                                   68999*************** PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0     0.003       1.1      20      39 ..     107     126 ..      91     231 .. 0.78
   2 !    8.9   0.2     0.005       1.9      24      43 ..     388     407 ..     379     409 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.003
                         AAA_23  20 gltlItGpNGaGKTTildAi 39 
                                     ++ + G NG+GKTT l+ +
  gi|118431333|ref|NP_147723.2| 107 QVVGLLGRNGTGKTTALRIL 126
                                    577899*********99866 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.005
                         AAA_23  24 ItGpNGaGKTTildAiklaL 43 
                                    + GpNG GKTT+++ +  aL
  gi|118431333|ref|NP_147723.2| 388 VAGPNGIGKTTFVRTLAGAL 407
                                    68**********99888776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.6      0.14        52      32      51 ..      11      33 ..       6      34 .. 0.73
   2 !   14.5  12.8   0.00011     0.041       4      52 .]      21      72 ..      15      72 .. 0.76
   3 !   20.1   1.3   1.9e-06   0.00074       1      21 [.      57      77 ..      57      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                         Fer4_7 32 eidpekCl..gCga.CvavCPtg 51
                                   +id+++C    C   C+avCP++
  gi|118431333|ref|NP_147723.2| 11 VIDYDSCKpkKCSYeCIAVCPVN 33
                                   567788853367544******97 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.00011
                         Fer4_7  4 gCg.aCvaaCpvkaieldeeenek..gtekveidpekClgCgaCvavCPtga 52
                                   +C   C a+Cpv+      + +++   + k++i ++ C+gC  Cv++CP++a
  gi|118431333|ref|NP_147723.2| 21 KCSyECIAVCPVNKSGRGVAIDADmaSRGKPVIYEDACIGCALCVKACPFDA 72
                                   46557******7766655443443224589999****************997 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 1.9e-06
                         Fer4_7  1 rCigCgaCvaaCpvkaielde 21
                                   +CigC  Cv+aCp +ai++ +
  gi|118431333|ref|NP_147723.2| 57 ACIGCALCVKACPFDAIYIVN 77
                                   5****************9874 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   8.0   3.2e-06    0.0012       4      51 .]      21      73 ..      15      73 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.2e-06
                         Fer4_9  4 gCga.CveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkgai 51
                                   +C + C+++Cp +      +++ a               +aCigC  Cv+aCp +ai
  gi|118431333|ref|NP_147723.2| 21 KCSYeCIAVCPVNKS----GRGVAIDADMASrgkpviyeDACIGCALCVKACPFDAI 73
                                   355346666665544....3333332222223447899999************9987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.037        14       3      22 ..     107     126 ..     105     137 .. 0.83
   2 !   12.1   0.1    0.0003      0.12       4      22 ..     385     403 ..     383     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.037
                         AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                    + + + G +g+GKTt ++ l
  gi|118431333|ref|NP_147723.2| 107 QVVGLLGRNGTGKTTALRIL 126
                                    67899**********98766 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0003
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     i + Gp+giGKTt++++l
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTL 403
                                    5889*************99 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.037        14      19      44 ..     106     131 ..      83     139 .. 0.79
   2 !   10.9   0.1   0.00088      0.34      19      44 ..     383     408 ..     370     424 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.037
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                    g+v+ L G  G+GKTt  r la +l+
  gi|118431333|ref|NP_147723.2| 106 GQVVGLLGRNGTGKTTALRILAGELK 131
                                    78899**************9998875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00088
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                    g+vi   G+ G GKTt+vr la al+
  gi|118431333|ref|NP_147723.2| 383 GEVIGVAGPNGIGKTTFVRTLAGALK 408
                                    6789999**************99984 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   0.00092      0.35      18      42 ..     106     130 ..      98     144 .. 0.81
   2 ?   -0.2   0.1       1.8   6.9e+02      85     122 ..     235     276 ..     185     278 .. 0.63
   3 ?    6.3   0.4     0.019       7.2      19      46 ..     384     411 ..     377     538 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00092
                         AAA_30  18 drvavltGpAGtGKttalkalreaw 42 
                                     +v+ l G+ GtGKttal+ l+  +
  gi|118431333|ref|NP_147723.2| 106 GQVVGLLGRNGTGKTTALRILAGEL 130
                                    469999*************997655 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                         AAA_30  85 rlepgtllivDEagmv....dtkqlaallkaaekagakvilv 122
                                      ++++++i DE +          +a+l++ a++ ga v++v
  gi|118431333|ref|NP_147723.2| 235 LSRDANVYIFDEPSSYldirERMRMARLIAGAARPGAYVMVV 276
                                    234459999999776554444445777777777778887766 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.019
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaag 46 
                                     v  + Gp G GKtt +++l+ a++  +
  gi|118431333|ref|NP_147723.2| 384 EVIGVAGPNGIGKTTFVRTLAGALKPVE 411
                                    478899**************99988664 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.7      0.13        50       4      15 ..      21      33 ..      14      49 .. 0.78
   2 !   15.1   0.1   8.7e-05     0.033       2      18 ..      58      74 ..      54      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.13
                        Fer4_16  4 tCgk.CaevCPtn 15
                                   +C   C+ vCP+n
  gi|118431333|ref|NP_147723.2| 21 KCSYeCIAVCPVN 33
                                   6766688888877 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.7e-05
                        Fer4_16  2 CgtCgkCaevCPtnaik 18
                                   C++C  C+++CP +ai 
  gi|118431333|ref|NP_147723.2| 58 CIGCALCVKACPFDAIY 74
                                   99999999999999985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.014       5.5       1      22 [.     109     130 ..     109     199 .. 0.81
   2 ?    7.9   0.0     0.011       4.2       1      22 [.     386     407 ..     386     449 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                         AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                    ++l G  G+GKtt  + L+ +l
  gi|118431333|ref|NP_147723.2| 109 VGLLGRNGTGKTTALRILAGEL 130
                                    6789999***********8776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                         AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                    I+++G+ G GKtt+ + L+  l
  gi|118431333|ref|NP_147723.2| 386 IGVAGPNGIGKTTFVRTLAGAL 407
                                    89***************98766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.067        26       3      32 ..     110     139 ..     108     141 .. 0.82
   2 !   11.2   0.0   0.00068      0.26       2      29 ..     386     409 ..     385     422 .. 0.83
   3 ?   -2.3   0.0       9.3   3.6e+03      94     103 ..     495     504 ..     478     545 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.067
                                    EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                     + G+ G+GKtT ++ ++ +lk +  +v+G
  gi|118431333|ref|NP_147723.2| 110 GLLGRNGTGKTTALRILAGELKPNLGRVEG 139
                                    5779***********999999877656655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00068
                                    EEEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvk 29 
                                    + + Gp G+GKtT+v+ ++ +lk    +
  gi|118431333|ref|NP_147723.2| 386 IGVAGPNGIGKTTFVRTLAGALK----P 409
                                    6799***************9996....4 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.3
                                    HHH-EEEE-- CS
                       NTPase_1  94 seadviviDE 103
                                    +eadv+++DE
  gi|118431333|ref|NP_147723.2| 495 READVYLLDE 504
                                    6788888887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.045        17       3      26 ..     111     134 ..     109     158 .. 0.78
   2 !    9.2   0.0     0.004       1.5       3      23 ..     388     408 ..     386     429 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.045
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkkl 26 
                                    l G++g+GK+t+ + La +l  +l
  gi|118431333|ref|NP_147723.2| 111 LLGRNGTGKTTALRILAGELKPNL 134
                                    68*************999988655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.004
                   RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                                    + Gp+g+GK+t++++La al 
  gi|118431333|ref|NP_147723.2| 388 VAGPNGIGKTTFVRTLAGALK 408
                                    78*************998875 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 !    8.0   0.0    0.0063       2.4      16      39 ..      99     123 ..      91     128 .. 0.85
   2 ?    5.8   0.1      0.03        11      26      43 ..     387     404 ..     379     415 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                         AAA_29  16 tieidlkg.atlltGpsGsGKSTll 39 
                                    +++i ++g ++ l G++G+GK+T l
  gi|118431333|ref|NP_147723.2|  99 RLPIPREGqVVGLLGRNGTGKTTAL 123
                                    577888898999***********76 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.03
                         AAA_29  26 lltGpsGsGKSTllDAiq 43 
                                     ++Gp+G GK+T++  ++
  gi|118431333|ref|NP_147723.2| 387 GVAGPNGIGKTTFVRTLA 404
                                    579*********996655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.16        63       3      39 ..     107     140 ..     105     191 .. 0.72
   2 !    9.7   0.0    0.0022      0.83       3      43 ..     384     423 ..     382     452 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.16
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinld 39 
                                    +++ + G   +GKTt l+ l+ el     +   ++  
  gi|118431333|ref|NP_147723.2| 107 QVVGLLGRNGTGKTTALRILAGELK---PNLGRVEGG 140
                                    788999999********99998776...555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43 
                                    +++ + G+  +GKTt++++l+  l  + e  +y  ++d r 
  gi|118431333|ref|NP_147723.2| 384 EVIGVAGPNGIGKTTFVRTLAGALK-PVEGAVYPYVEDLRV 423
                                    68999***************98888.667777766666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.027        10      99     130 ..     106     137 ..      97     141 .. 0.87
   2 !    7.6   0.0    0.0089       3.4     100     124 ..     384     408 ..     377     419 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                                    TSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgev 130
                                    ++++ l+G  G GK+t +  l++el+ + g v
  gi|118431333|ref|NP_147723.2| 106 GQVVGLLGRNGTGKTTALRILAGELKPNLGRV 137
                                    68999******************998877766 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0089
                                    SEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpele 124
                                    +++ ++G+ G+GK+t++ +l++ l+
  gi|118431333|ref|NP_147723.2| 384 EVIGVAGPNGIGKTTFVRTLAGALK 408
                                    677799**************98765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   4.0       0.2        78       4      14 ..      22      33 ..      17      34 .. 0.82
   2 !   17.0   4.5   2.1e-05    0.0081       1      15 []      58      72 ..      58      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.2
                         Fer4_3  4 Cg.aCvevCPvg 14
                                   C+  C  vCPv+
  gi|118431333|ref|NP_147723.2| 22 CSyECIAVCPVN 33
                                   8558******97 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.1e-05
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gC +Cv++CP +A
  gi|118431333|ref|NP_147723.2| 58 CIGCALCVKACPFDA 72
                                   ************998 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   0.0     0.011       4.2      43      73 ..     105     134 ..      76     141 .. 0.75
   2 ?    5.5   0.0     0.039        15      49      68 ..     387     406 ..     379     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                          Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgikl 73 
                                    +  +++ + G  G gk+t++++L+ el ++l
  gi|118431333|ref|NP_147723.2| 105 E-GQVVGLLGRNGTGKTTALRILAGELKPNL 134
                                    3.5688889***************9998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.039
                          Rad17  49 LisGPsGCgkstvvkvLske 68 
                                     ++GP G gk+t v+ L+  
  gi|118431333|ref|NP_147723.2| 387 GVAGPNGIGKTTFVRTLAGA 406
                                    589*************9965 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.015       5.9       3      50 ..     113     158 ..     112     213 .. 0.76
   2 ?    6.0   0.0     0.022       8.2       3      23 ..     390     410 ..     388     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                                    ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkee 50 
                                    G +G+GKtt +++l+  lk +  + v   ep+  ei + +r++ l ++
  gi|118431333|ref|NP_147723.2| 113 GRNGTGKTTALRILAGELKPNLGR-VEGGEPEWDEILKRFRGSEL-QT 158
                                    779***************999865.77777777777777777766.44 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.022
                                    ESTTSSHHHHHHHHHHHHHHT CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkee 23 
                                    G +G GKtt++++l+ +lk  
  gi|118431333|ref|NP_147723.2| 390 GPNGIGKTTFVRTLAGALKPV 410
                                    99*************999865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.047        18      19      36 ..     107     122 ..      98     131 .. 0.85
   2 ?    8.1   0.0    0.0035       1.3      22      60 ..     385     424 ..     378     479 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.047
                                    CSEEEEEEESTTSSHHHH CS
                         NB-ARC  19 qslvvalvGmgGvGKttl 36 
                                    q  vv+l G+ G GKtt 
  gi|118431333|ref|NP_147723.2| 107 Q--VVGLLGRNGTGKTTA 122
                                    4..9************95 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0035
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEEEEE CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg.rFdsvawvvvs 60 
                                    v+++ G  G+GKtt ++     ++ veg  ++ v  + vs
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTLAGALKPVEGaVYPYVEDLRVS 424
                                    89***************99999999998778877777666 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.87   3.3e+02       1      24 [.     108     131 ..     108     153 .. 0.78
   2 ?   11.8   0.0   0.00039      0.15       1      31 [.     385     413 ..     385     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.87
                            PRK   1 vIgvagsSGaGkttvarklekifg 24 
                                    v+g+ g  G Gktt  r l   ++
  gi|118431333|ref|NP_147723.2| 108 VVGLLGRNGTGKTTALRILAGELK 131
                                    78999*********9998876665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00039
                            PRK   1 vIgvagsSGaGkttvarklekifgrekvkaa 31 
                                    vIgvag+ G Gktt+ r+l  +++   v+ a
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTLAGALK--PVEGA 413
                                    8******************99988..55544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0095       3.6       3      26 ..     108     131 ..     106     137 .. 0.84
   2 ?    8.2   0.2    0.0046       1.8       3      26 ..     385     408 ..     383     415 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0095
                                    EEEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54   3 villvGlqGaGKTttlaKLaallk 26 
                                    v+ l+G +G+GKTt+l  La  lk
  gi|118431333|ref|NP_147723.2| 108 VVGLLGRNGTGKTTALRILAGELK 131
                                    67799**********999997766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0046
                                    EEEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54   3 villvGlqGaGKTttlaKLaallk 26 
                                    vi ++G++G+GKTt +  La  lk
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTLAGALK 408
                                    67799************9998776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.028        11       4      21 ..     111     128 ..     108     174 .. 0.87
   2 ?    6.3   0.0     0.028        11       4      22 ..     388     406 ..     385     441 .. 0.81
   3 ?   -1.6   0.1       7.6   2.9e+03     100     140 ..     488     520 ..     477     541 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.028
                         AAA_28   4 itGgestGKTtlleaLaa 21 
                                    ++G  +tGKTt l+ La 
  gi|118431333|ref|NP_147723.2| 111 LLGRNGTGKTTALRILAG 128
                                    78999***********94 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.028
                         AAA_28   4 itGgestGKTtlleaLaar 22 
                                    + G+ + GKTt ++ La  
  gi|118431333|ref|NP_147723.2| 388 VAGPNGIGKTTFVRTLAGA 406
                                    68**************943 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 7.6
                         AAA_28 100 leaaarekrydlvfllppapeidddgeRredleereaider 140
                                     +aaa +++ d ++l +p++++ d +eR         ++++
  gi|118431333|ref|NP_147723.2| 488 AVAAALAREADVYLLDEPSAYL-DVEER-------VGVARA 520
                                    4455666667777777777777.33333.......333333 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   3.4       2.2   8.5e+02       8      17 .]      23      33 ..      14      34 .. 0.68
   2 ?   15.7   2.5   4.2e-05     0.016       2      16 ..      56      70 ..      55      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 2.2
                         Fer4_4  8 g.sCvaaCPqg 17
                                      C+a+CP++
  gi|118431333|ref|NP_147723.2| 23 SyECIAVCPVN 33
                                   345******75 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.2e-05
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   + CigC  Cv aCP+
  gi|118431333|ref|NP_147723.2| 56 DACIGCALCVKACPF 70
                                   79************7 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 ?    4.0   0.3      0.12        47       4      23 ..     111     130 ..     109     139 .. 0.85
   2 ?    7.7   0.0    0.0089       3.4       5      24 ..     389     409 ..     387     424 .. 0.82
   3 ?   -0.6   0.0       3.2   1.2e+03      37      73 ..     467     504 ..     438     507 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                                    EE--SSSSHHHHHHHGGGGB CS
                          AAA_5   4 LvGppGtgKselaerlaaal 23 
                                    L+G  GtgK++  + la  l
  gi|118431333|ref|NP_147723.2| 111 LLGRNGTGKTTALRILAGEL 130
                                    99*********999988655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0089
                                    E--SSSSHHHHHHHGGGGB.S CS
                          AAA_5   5 vGppGtgKselaerlaaal.n 24 
                                     Gp G+gK+++++ la al  
  gi|118431333|ref|NP_147723.2| 389 AGPNGIGKTTFVRTLAGALkP 409
                                    5***************99962 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 3.2
                                    -HHHHH--B--..........--------G-SEEEEES CS
                          AAA_5  37 teedlkgrreik.ngttslvdsplvraaregeilvlDE 73 
                                    + ++l+ rr  + +g++  +  ++   are+++++lDE
  gi|118431333|ref|NP_147723.2| 467 RLDKLLERRVRTlSGGELQKVAVAAALAREADVYLLDE 504
                                    44444444443332222222233333455777777776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.065        25       2      23 ..     109     131 ..     108     140 .. 0.84
   2 ?    6.0   0.0     0.031        12       2      23 ..     386     407 ..     385     428 .. 0.86
   3 ?    0.3   0.0       1.9   7.3e+02      44      84 ..     495     536 ..     468     553 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.065
                                    EEEEESTTSSHHHHHHHHHTS.T CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.k 23 
                                    v+++Gr  +GK+t ++ l ge k
  gi|118431333|ref|NP_147723.2| 109 VGLLGRNGTGKTTALRILAGElK 131
                                    89***************999743 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                                    EEEEESTTSSHHHHHHHHHTST CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgek 23 
                                    ++++G    GK+t++++l g+ 
  gi|118431333|ref|NP_147723.2| 386 IGVAGPNGIGKTTFVRTLAGAL 407
                                    899***************9974 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.9
                                    TTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCT.SEEEEEEE CS
                       MMR_HSR1  44 kgkeielvDtpGliegaseekglgkaflaleea.dlillvvd 84 
                                    ++ +++l+D p  + + +e+ g+++a++++ e+ ++++lvv+
  gi|118431333|ref|NP_147723.2| 495 READVYLLDEPSAYLDVEERVGVARAIRRIVETrEAAALVVE 536
                                    357899999999775455666999999998886477777775 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 ?    5.5   0.1     0.038        14       1      25 [.     108     132 ..     108     138 .. 0.86
   2 ?    5.9   0.0      0.03        11       1      24 [.     385     408 ..     385     414 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.038
                           MobB   1 vlgivgksgsGKTtLleklipelka 25 
                                    v+g+ g++g+GKTt l  l  elk 
  gi|118431333|ref|NP_147723.2| 108 VVGLLGRNGTGKTTALRILAGELKP 132
                                    6899************999998875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.03
                           MobB   1 vlgivgksgsGKTtLleklipelk 24 
                                    v+g++g +g GKTt++  l  +lk
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTLAGALK 408
                                    689**************9988876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5         2   7.5e+02      56      64 ..      25      33 ..      13      49 .. 0.71
   2 ?   13.1   0.2   0.00026     0.098       3      17 ..      56      70 ..      54      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2
                         Fer4_8 56 aCtevCpvg 64
                                   +C  vCpv+
  gi|118431333|ref|NP_147723.2| 25 ECIAVCPVN 33
                                   366666664 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00026
                         Fer4_8  3 ekCieCgaCqsaCpv 17
                                   ++Ci+C +C +aCp+
  gi|118431333|ref|NP_147723.2| 56 DACIGCALCVKACPF 70
                                   58***********94 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.012       4.5      25      43 ..     108     126 ..      91     130 .. 0.74
   2 ?    2.2   0.0      0.32   1.2e+02      30      43 ..     390     403 ..     384     405 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                         AAA_15  25 ltvliGkNnsGKSsileal 43 
                                    +  l G+N++GK+++l++l
  gi|118431333|ref|NP_147723.2| 108 VVGLLGRNGTGKTTALRIL 126
                                    77799***********998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
                         AAA_15  30 GkNnsGKSsileal 43 
                                    G+N++GK+++++ l
  gi|118431333|ref|NP_147723.2| 390 GPNGIGKTTFVRTL 403
                                    9*********9866 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.2     2e+03      25      41 ..     111     127 ..     105     133 .. 0.78
   2 ?    9.5   0.0    0.0022      0.85      22      96 ..     385     473 ..     381     503 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.2
                       ATPase_2  25 iYGpegsGKtaLlkeii 41 
                                    + G+ g GKt+ l+ ++
  gi|118431333|ref|NP_147723.2| 111 LLGRNGTGKTTALRILA 127
                                    679********998665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0022
                       ATPase_2  22 iyfiYGpegsGKtaLlkeiienledkdk.yviyyialreesiskldefieeeeekkklekal...............gia 85 
                                    ++ + Gp g+GKt++++ ++  l+  +     y+ +lr ++  ++ +   e+  +  +e++l               ++ 
  gi|118431333|ref|NP_147723.2| 385 VIGVAGPNGIGKTTFVRTLAGALKPVEGaVYPYVEDLRVSYKPQYISP--ESLPDATVEQVLkaanpailapgswlnLEL 462
                                    66688*****************97766525679999999888888777..333333333333333455677777766666 PP

                       ATPase_2  86 vpkaeleeilk 96 
                                    v++ +l+++l+
  gi|118431333|ref|NP_147723.2| 463 VKRMRLDKLLE 473
                                    66666666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.087        33      32      50 ..     105     123 ..     101     137 .. 0.86
   2 ?    7.3   1.5    0.0082       3.1      28      58 ..     378     408 ..     376     547 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.087
                         AAA_25  32 agelallaGapgtGKttla 50 
                                    +g ++ l G+ gtGKtt++
  gi|118431333|ref|NP_147723.2| 105 EGQVVGLLGRNGTGKTTAL 123
                                    788999***********87 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0082
                         AAA_25  28 gllpagelallaGapgtGKttlaldlalava 58 
                                    g l  ge++ +aG+ g GKtt++  la a+ 
  gi|118431333|ref|NP_147723.2| 378 GALYGGEVIGVAGPNGIGKTTFVRTLAGALK 408
                                    5667899***************999987765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.055        21      10      34 ..     106     130 ..     102     138 .. 0.82
   2 ?    4.7   0.3     0.095        36      11      35 ..     384     408 ..     378     417 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.055
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivall 34 
                                     +v+ +++  GtGKT+ l+    +l
  gi|118431333|ref|NP_147723.2| 106 GQVVGLLGRNGTGKTTALRILAGEL 130
                                    678999***********99776665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.095
                         AAA_19  11 kvllvtaGpGtGKTrvlkhivallv 35 
                                    +v+ v ++ G GKT+ +++    l+
  gi|118431333|ref|NP_147723.2| 384 EVIGVAGPNGIGKTTFVRTLAGALK 408
                                    678899999********99887766 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.4     0.024       9.2       4      58 ..      21      70 ..      17      72 .. 0.66
   2 ?   11.6   1.7   0.00082      0.31       1      17 [.      57      73 ..      57      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                        Fer4_17  4 qCgy.ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58
                                   +C+y C+++Cp ++  +     ++ +a +++ ++     + + Ci+C +C+++CP 
  gi|118431333|ref|NP_147723.2| 21 KCSYeCIAVCPVNKSGRG----VAIDADMASRGKP--VIYEDACIGCALCVKACPF 70
                                   577778888887766554....5555555433332..3466899999999999996 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00082
                        Fer4_17  1 rCiqCgyClpeCpsyea 17
                                   +Ci+C+ C+++Cp+ ++
  gi|118431333|ref|NP_147723.2| 57 ACIGCALCVKACPFDAI 73
                                   59999999999997555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.21        79      18      34 ..     105     121 ..      90     124 .. 0.87
   2 ?    5.7   0.3     0.021       7.9      13      37 ..     377     401 ..     365     415 .. 0.84
   3 ?   -2.1   0.0       5.3     2e+03      17      29 ..     545     557 ..     541     558 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                         ATPase  18 egrvvlitGepGtGKti 34 
                                    eg+vv + G  GtGKt+
  gi|118431333|ref|NP_147723.2| 105 EGQVVGLLGRNGTGKTT 121
                                    6899************7 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                         ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                    +g ++ g+v+ ++G  G GKt+f+ 
  gi|118431333|ref|NP_147723.2| 377 EGALYGGEVIGVAGPNGIGKTTFVR 401
                                    5789999****************86 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.3
                         ATPase  17 pegrvvlitGepG 29 
                                     ++r++l+tGepG
  gi|118431333|ref|NP_147723.2| 545 VSDRIMLVTGEPG 557
                                    5789********9 PP

>> AFP  Insect antifreeze protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.2     0.017       6.5       1      11 [.      57      67 ..      57      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                            AFP  1 tCTgsknCteA 11
                                   +C+g+++C++A
  gi|118431333|ref|NP_147723.2| 57 ACIGCALCVKA 67
                                   8********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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):              47  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.41
# Mc/sec: 4486.28
//
Query:       gi|118431334|ref|NP_147725.2|  [L=372]
Description: hypothetical protein APE_1123.1 [Aeropyrum pernix K1]
Scores for complete 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-144  480.1   4.4   4.4e-144  479.9   4.4    1.0  1  DUF1512   Protein of unknown function (DUF1512)


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.9   4.4  2.4e-148  4.4e-144       2     356 .]      15     371 ..      14     371 .. 0.99

  Alignments for each domain:
  == domain 1  score: 479.9 bits;  conditional E-value: 2.4e-148
                        DUF1512   2 isliifllllillllglnqklqlavllrdiekklakleklaeeakkkvvellkklgkedpkklverlleffviePvdleP 81 
                                    is+++++l++i l++g+nq++q+++++rdi++kl +le++a++a++++ve++ ++g++d+++lv+rl++ffvi+Pvd+eP
  gi|118431334|ref|NP_147725.2|  15 ISQLLLVLIFIALFTGANQRIQVYLWSRDIRSKLVILESFANDARRRAVEYMVSKGAKDAESLVSRLADFFVISPVDIEP 94 
                                    8999999999999******************************************************************* PP

                        DUF1512  82 tgivkrlehllrtsedklkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllqlqmllpll 161
                                    ++i++rlehl++ +++++k++v++++peadev+rs++e+aleiasal++i+k+vrH+ll+++kt+n++l++qlq+++p++
  gi|118431334|ref|NP_147725.2|  95 VDIIRRLEHLVNLRSRRFKEEVARHMPEADEVSRSKAEVALEIASALSFIHKYVRHILLTGEKTRNWILIMQLQLIMPMI 174
                                    ******************************************************************************** PP

                        DUF1512 162 lklaeayekalkaflkgkPvGDgaGplvaakllekkekksleaakdtviaevelegrkvivvkaeGpgstvGrlgeavek 241
                                    lk+a++y++al+ flkg+P+GD+aGp+va++l+ +++++ ++++++tv++ +++egr+v++vkaeGpgs+vGr+g+a+e+
  gi|118431334|ref|NP_147725.2| 175 LKIADTYRRALNDFLKGVPIGDSAGPMVALRLAGRGARW-ERIEEETVYTVADVEGRRVYIVKAEGPGSSVGRPGSATER 253
                                    ***********************************9999.99************************************** PP

                        DUF1512 242 ivekl...kekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatkygipldaviikmsleeAitaMtke 318
                                    ++ekl   ++k++l++tvDAalkLEGEetgsva+GvG+aiGd+G+eki++Er+a+kygi l+av+ikm leeAi  Mt++
  gi|118431334|ref|NP_147725.2| 254 LIEKLvaqGRKPRLLVTVDAALKLEGEETGSVADGVGAAIGDIGPEKIRFERIAVKYGIALRAVAIKMGLEEAILGMTEK 333
                                    ****988899********************************************************************** PP

                        DUF1512 319 iaeavdkavervkeiikektkegetvivvGvGNtvGva 356
                                    i+++v+kavervk+ii+ ++k+g+ v+vvGvGNtvGv+
  gi|118431334|ref|NP_147725.2| 334 IVKGVEKAVERVKDIIRGESKPGDIVVVVGVGNTVGVG 371
                                    ************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2614.50
//
Query:       gi|14601197|ref|NP_147729.1|  [L=109]
Description: hypothetical protein APE_1127 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 819.33
//
Query:       gi|14601199|ref|NP_147731.1|  [L=572]
Description: methionyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-154  513.7   0.0     3e-154  513.5   0.0    1.0  1  tRNA-synt_1g    tRNA synthetases class I (M)
      3e-14   52.2   0.0    9.4e-08   30.8   0.1    3.3  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
      5e-09   36.3   0.0    8.5e-09   35.5   0.0    1.4  1  Anticodon_1     Anticodon-binding domain of tRNA
     0.0024   17.3   0.0      0.072   12.4   0.0    2.1  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
       0.04   14.0   0.3      0.066   13.3   0.3    1.4  1  TerY_C          TerY-C metal binding domain
      0.097   11.6   0.0        1.4    7.8   0.0    2.1  2  tRNA-synt_1f    tRNA synthetases class I (K)
       0.36   10.9   5.7        0.5   10.4   5.0    1.5  1  DZR             Double zinc ribbon
        1.6    9.1   3.8       0.55   10.6   1.0    1.7  1  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        1.7    8.5   4.8        7.5    6.5   2.3    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        4.3    7.6   7.0        2.6    8.3   0.3    2.8  2  zf-RING_7       C4-type zinc ribbon domain
        9.6    6.3   8.1         14    5.8   2.2    2.7  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        9.7    6.9   7.9         17    6.1   0.3    3.1  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109


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 !  513.5   0.0    2e-157    3e-154       1     391 []       4     398 ..       4     398 .. 0.99

  Alignments for each domain:
  == domain 1  score: 513.5 bits;  conditional E-value: 2e-157
                                   EEEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1g   1 vlvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkk 80 
                                   ++vt+a+pY+n ++HlG l+ +v+saDi+aRy rlrg++v+fv+g+DehGtpiel+A+k+gv+p+el+++vhe   +++++
  gi|14601199|ref|NP_147731.1|   4 YVVTSAWPYVNHVPHLGTLIgSVLSADIYARYLRLRGRQVVFVSGSDEHGTPIELEARKKGVHPKELTDQVHEYDVKMWRE 84 
                                   58******************************************************************************* PP

                                   TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E. CS
                  tRNA-synt_1g  81 lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkklep 161
                                   + isfd+y+rt+s  hke+v e++kkl+e+g+i ++e    yc++d+ flpdr+vegtCP+c++e+argdqc+ecg+ l+p
  gi|14601199|ref|NP_147731.1|  85 YRISFDNYSRTESPVHKEFVMEFMKKLEENGYIFSQEEVLPYCERDKIFLPDRFVEGTCPYCGYEKARGDQCDECGRLLHP 165
                                   ********************************************************************************* PP

                                   ...............EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..TE CS
                  tRNA-synt_1g 162 telinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..ga 240
                                   tel+np++a++gskp++k+t+h+f +l++++++l +w+ e++ el+++vkk++ +w+ +gLk+++++rdl+wG+p P  ga
  gi|14601199|ref|NP_147731.1| 166 TELKNPRCALCGSKPVYKSTRHWFIDLRRVQDRLLKWL-ESHGELQDSVKKYSINWVAQGLKPRSVTRDLSWGVPAPfkGA 245
                                   **************************************.77779************************************* PP

                                   CCEEE-HHHHHHHHHHHTTTTT-....TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE CS
                  tRNA-synt_1g 241 ekkvlYVWldAligYisatkela.kkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvvah 318
                                   e+k++YVW+dAl+gY+satkel+  ++g++e+wk++W  d+ ++ v+figkd+i+FH+i++Pa+ l+    + lp +++a+
  gi|14601199|ref|NP_147731.1| 246 EGKTIYVWFDALLGYVSATKELFiMRRGDPEEWKSWW-WDSGTRTVYFIGKDNIPFHAIILPALFLAshDPYVLPWRISAT 325
                                   **********************999999*********.889***********************99988899********* PP

                                   --EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                  tRNA-synt_1g 319 eyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                   eyl++eg+++SkSr+++v+++eale  +ad++R+ la+ +pe +D++f+w++f + vN+eL+d++gn+vnRvl
  gi|14601199|ref|NP_147731.1| 326 EYLMYEGQQFSKSRRIGVWIDEALEIAPADYWRWALARMRPEARDTNFTWKEFYRIVNTELNDDIGNFVNRVL 398
                                   ***********************************************************************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   6.3e-11   9.4e-08      24     167 ..       3     128 ..       1     140 [. 0.75
   2 !   16.6   0.0   1.2e-06    0.0018     348     433 ..     158     242 ..     149     264 .. 0.85
   3 ?   -2.1   0.0      0.56   8.3e+02     560     601 ..     331     373 ..     300     374 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.3e-11
                   tRNA-synt_1  24 efilvdgPPyvtGslHiGhalaktlk.divirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrek 103
                                   +++++   Pyv+  +H+G  + ++l  di  ry r++G +v +v G D +G +ie +  kk g + k         e +++
  gi|14601199|ref|NP_147731.1|   3 KYVVTSAWPYVNHVPHLGTLIGSVLSaDIYARYLRLRGRQVVFVSGSDEHGTPIELEARKK-GVHPK---------ELTDQ 73 
                                   79999999****************955999**************************99998.44443.........55555 PP

                   tRNA-synt_1 104 vrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwst 167
                                   v+e+  ++  e+         ++ fd+   T ++  +e v+e +++l ++g i+  + +++++ 
  gi|14601199|ref|NP_147731.1|  74 VHEYDVKMWREY---------RISFDNYSRTESPVHKEFVMEFMKKLEENGYIFSQEEVLPYCE 128
                                   555554443333.........2445566666666666667777777777777777777777765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.2e-06
                   tRNA-synt_1 348 ekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwW 427
                                   e g+ll+  ++e++ p c   +   +y++t  Wf+ + +++d +lk +e+     +s +k   +w+++  +   + R++ W
  gi|14601199|ref|NP_147731.1| 158 ECGRLLH--PTELKNPRCALCGSKPVYKSTRHWFIDLRRVQDRLLKWLESHGELQDSVKKYSINWVAQgLKPRSVTRDLSW 236
                                   5666665..56788999999999999***********************999899998898899997637899******** PP

                   tRNA-synt_1 428 Ghripl 433
                                   G++ p+
  gi|14601199|ref|NP_147731.1| 237 GVPAPF 242
                                   ***996 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.56
                   tRNA-synt_1 560 eGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                   eG+  SKs    +  ++ ++   ad  R++l+ + +  rd+n+
  gi|14601199|ref|NP_147731.1| 331 EGQQFSKSRRIGVWIDEALEIAPADYWRWALArMRPEARDTNF 373
                                   7999999999998888999999999999999988888888886 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 !   35.5   0.0   5.7e-12   8.5e-09       5     135 ..     422     560 ..     418     568 .. 0.80

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 5.7e-12
                   Anticodon_1   5 lselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.raaqevllevletllrllaPfmPfi 84 
                                   + ++ +++  v e++e  r+++a   + e       + yl+ ++p+   +++ ++  +a ++ l++++tl  llaPf+P  
  gi|14601199|ref|NP_147731.1| 422 VERVRRAAWAVAEDLEAIRIKRATEGILEI-AR-EGNAYLNRTQPWKLLSQDREEgVRALSAALYAVKTLAHLLAPFTPDA 500
                                   5678888999*******************5.44.46**********9887776667668899******************* PP

                   Anticodon_1  85 tEelwqreeeelgkkesimlaewpe.kaeel..ekel..e.........eeevellkeivkairk 135
                                   ++ lw     +lg   s++ a w e  + +l    ++            +  +e+++eiv+ +r+
  gi|14601199|ref|NP_147731.1| 501 ADRLW----SMLGLAGSVHEAVWDEwLDRPLpgG-ARivRveplfqklpDDFLERVDEIVEDARR 560
                                   *****....99*************8777666641.223313456667887777777778777766 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 !   12.4   0.0   4.8e-05     0.072      19     125 ..      13     121 ..       4     135 .. 0.80
   2 ?    2.5   0.0     0.051        77     244     283 ..     325     364 ..     307     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                                   TTS--BHHHH.HHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB- CS
                  tRNA-synt_1e  19 vydashlGha.RslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptle 98 
                                   v    hlG    s+++ Di +r+l+ +g +v fv+   +    i ++ar+++ + kel++++ e   k  ++  +   +  
  gi|14601199|ref|NP_147731.1|  13 VNHVPHLGTLiGSVLSADIYARYLRLRGRQVVFVSGSDEHGTPIELEARKKGVHPKELTDQVHEYDVKMWREYRISFDN-Y 92 
                                   66778999862577799*******************9999999***************999887777777888887744.4 PP

                                   -BGGGGHHH..HHHHHHHHHHTTSEEE-T CS
                  tRNA-synt_1e  99 prvsekvde..iielvekliekgyaYavs 125
                                   +r    v++  ++e+++kl e+gy ++++
  gi|14601199|ref|NP_147731.1|  93 SRTESPVHKefVMEFMKKLEENGYIFSQE 121
                                   4444444332389***********99877 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.051
                                   E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                  tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                   +++l+ eg++ sks +  + i ++l+   +   R++l+  
  gi|14601199|ref|NP_147731.1| 325 TEYLMYEGQQFSKSRRIGVWIDEALEIAPADYWRWALARM 364
                                   6799************************999999999865 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.4e-05     0.066      75     126 ..     141     194 ..     101     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.4e-05
                        TerY_C  75 pgCPhCgnalafa.vC.eCgkllCidgeeeatCpwCgkevkfgeaseegfdvnR 126
                                   ++CP+Cg + a    C eCg+ll  ++ ++  C+ Cg++  ++++ +  +d++R
  gi|14601199|ref|NP_147731.1| 141 GTCPYCGYEKARGdQCdECGRLLHPTELKNPRCALCGSKPVYKSTRHWFIDLRR 194
                                   69*****98886436747*********************999977666777777 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     0.099   1.5e+02      37      70 ..      17      51 ..      13      55 .. 0.90
   2 ?    7.8   0.0    0.0009       1.4     277     316 ..     330     369 ..     306     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.099
                  tRNA-synt_1f 37 iHiGnlr.evltadlvaralrkrgeevrlilisDd 70
                                  +H+G+l   vl+ad+ ar lr rg +v ++  sD+
  gi|14601199|ref|NP_147731.1| 17 PHLGTLIgSVLSADIYARYLRLRGRQVVFVSGSDE 51
                                  8****8549******************99999987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0009
                  tRNA-synt_1f 277 kggekmssSkGnvltledwlevaepevlrflilrrkPkka 316
                                    +g++ s+S+  ++ ++++le+a+ +  r+ ++r +P+ +
  gi|14601199|ref|NP_147731.1| 330 YEGQQFSKSRRIGVWIDEALEIAPADYWRWALARMRPEAR 369
                                   45679********************************854 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.0   0.00033       0.5       1      37 [.     143     179 ..     143     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                           DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCgek 37 
                                   Cp Cg e +++   C+eCg  l +++  + rC  Cg+k
  gi|14601199|ref|NP_147731.1| 143 CPYCGYE-KARGDQCDECGRLLHPTELkNPRCALCGSK 179
                                   9****99.556668******99854448999****987 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 ?   10.6   1.0   0.00037      0.55       4      40 ..     142     179 ..     139     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                       zf-Di19   4 tCPyCgkeltvkeLveHved.eHrveskevvCPvCaek 40 
                                   tCPyCg e +    ++ +    H+ e k+  C +C +k
  gi|14601199|ref|NP_147731.1| 142 TCPYCGYEKARGDQCDECGRlLHPTELKNPRCALCGSK 179
                                   9*****9888888888886527*************865 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.15   2.2e+02      13      31 ..     135     150 ..     132     153 .. 0.79
   2 ?    6.5   2.3     0.005       7.5       4      30 ..     156     179 ..     156     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.15
                                   EEECSCCCEEEESSSS-EE CS
                RNA_POL_M_15KD  13 pkedkegknfeCrqCgYee 31 
                                   p++ +eg+   C  CgYe+
  gi|14601199|ref|NP_147731.1| 135 PDRFVEGT---CPYCGYEK 150
                                   56667787...999***96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                   ESTTTSBEEEEECSCCCEEEESSSS-E CS
                RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYe 30 
                                   C +Cg lL p+e k  +   C+ Cg++
  gi|14601199|ref|NP_147731.1| 156 CDECGRLLHPTELKNPR---CALCGSK 179
                                   9**************98...****985 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.6      0.29   4.3e+02      25      30 ..     142     147 ..     141     147 .. 0.94
   2 ?    8.3   0.3    0.0017       2.6      25      33 .]     155     163 ..     151     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.29
                                   E-TTT- CS
                     zf-RING_7  25 tCpeCG 30 
                                   tCp+CG
  gi|14601199|ref|NP_147731.1| 142 TCPYCG 147
                                   8****9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                                   E-TTT--EE CS
                     zf-RING_7  25 tCpeCGRIL 33 
                                   +C+eCGR+L
  gi|14601199|ref|NP_147731.1| 155 QCDECGRLL 163
                                   7******98 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.2    0.0092        14      15      30 ..     134     152 ..     130     169 .. 0.73
   2 ?    2.3   1.3      0.11   1.6e+02      16      34 ..     169     186 ..     157     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0092
                 Zn_Tnp_IS1595  15 Wpng...fvCPhCgsrkay 30 
                                    p++    +CP+Cg++ka+
  gi|14601199|ref|NP_147731.1| 134 LPDRfveGTCPYCGYEKAR 152
                                   566644346*****88764 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.11
                 Zn_Tnp_IS1595  16 pngfvCPhCgsrkayrikt 34 
                                   +n ++C  Cgs+ +y+ ++
  gi|14601199|ref|NP_147731.1| 169 KN-PRCALCGSKPVYKSTR 186
                                   44.55*******8887765 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 ?    3.9   1.0     0.059        88       3      14 ..     141     152 ..     140     158 .. 0.82
   2 ?    6.1   0.3     0.012        17       2      17 ..     170     185 ..     169     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.059
                       zf-ISL3   3 hrCPnCgsktvv 14 
                                    +CP+Cg  +++
  gi|14601199|ref|NP_147731.1| 141 GTCPYCGYEKAR 152
                                   59*****98876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                       zf-ISL3   2 phrCPnCgsktvvkhg 17 
                                    +rC  Cgsk+v+k  
  gi|14601199|ref|NP_147731.1| 170 NPRCALCGSKPVYKST 185
                                   589********99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3944.72
//
Query:       gi|118431335|ref|NP_147732.2|  [L=118]
Description: 30S ribosomal protein S24 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-19   69.1   0.0    3.2e-19   68.6   0.0    1.1  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 !   68.6   0.0   1.8e-23   3.2e-19       4      73 ..      40     109 ..      37     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.8e-23
                                    EE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTS CS
                 Ribosomal_S24e   4 vlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRngl 73 
                                    + H+ k+tp +  +r+kla+ + vd + ++++ ++t +G g +++ +++Yds+e+a +fEpk++++Rng 
  gi|118431335|ref|NP_147732.2|  40 LHHELKPTPMRIMLRQKLAEVLGVDIKRIYIRYIKTGYGAGLSKVRVHVYDSPERALSFEPKYIIERNGG 109
                                    56788***************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 944.41
//
Query:       gi|118431336|ref|YP_874875.1|  [L=63]
Description: 30S ribosomal protein S27 [Aeropyrum pernix K1]
Scores for complete 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   53.7   3.4    2.2e-14   53.3   3.4    1.2  1  Ribosomal_S27    Ribosomal protein S27a
    4.1e-05   23.5   3.1    5.4e-05   23.1   3.1    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0004   20.3   0.7    0.00046   20.1   0.7    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.3   0.3      0.012   15.3   0.3    1.2  1  TackOD1          Thaumarchaeal output domain 1
      0.016   15.1   0.3      0.036   13.9   0.3    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.024   14.6   2.8      0.043   13.7   2.8    1.5  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.03   14.5   0.1       0.03   14.5   0.1    1.2  1  zf-piccolo       Piccolo Zn-finger
      0.031   14.6   1.5        2.1    8.8   0.1    2.1  2  GFA              Glutathione-dependent formaldehyde-activatin
      0.046   13.6   1.7        1.9    8.4   0.5    2.2  2  HalOD2           Halobacterial output domain 2
      0.055   13.1   5.4       0.21   11.2   0.3    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.066   13.4   2.0      0.096   12.9   1.2    1.6  2  DUF2387          Probable metal-binding protein (DUF2387)
      0.083   12.9   0.7      0.083   12.9   0.7    1.1  1  DUF1451          Zinc-ribbon containing domain
      0.092   12.7   3.9       0.43   10.5   3.9    1.9  1  Nudix_N_2        Nudix N-terminal
       0.11   12.0   5.9       0.21   11.1   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.11   12.7   2.8       0.56   10.4   0.3    2.4  3  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.14   12.6   2.8       0.22   11.9   2.8    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.22   12.2   6.7       0.66   10.7   0.9    2.3  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.24   11.0   2.6       0.55    9.9   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.48   10.2   5.5        1.8    8.4   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
        5.5    6.8   9.4        6.3    6.6   1.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding 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 !   53.3   3.4   2.5e-17   2.2e-14       1      45 []      11      56 ..      11      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.5e-17
                                   SSSSCCESS.SSSEEESS-B-SS-S-TTSBEEECTT...EEEESSTTTE CS
                  Ribosomal_S27  1 vlkyYkvdd.sgkverlrkeCpreCGaGvfMAehkd...RkyCGkCglT 45
                                   v+k+Y+vd+ +g ++ ++++Cpr C  G +MA+h     R++CGkCg+T
  gi|118431336|ref|YP_874875.1| 11 VHKLYEVDYeKGVIKLKNRRCPR-C--GSIMAHHMKpveRWHCGKCGYT 56
                                   89*******99************.*..*******97777*********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 !   23.1   3.1     6e-08   5.4e-05      18      46 .]      28      56 ..      21      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6e-08
                  Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCrkq 46
                                   +++CP+Cgs  a+ +k  ++++C +C+++
  gi|118431336|ref|YP_874875.1| 28 NRRCPRCGSIMAHHMKPVERWHCGKCGYT 56
                                   467***********************985 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 !   20.1   0.7   5.1e-07   0.00046      15      55 ..      15      56 ..       5      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-07
                 OrfB_Zn_ribbon 15 yGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfe 55
                                   y + +e+        +C++Cgs++ +  +  ++++C +Cg++
  gi|118431336|ref|YP_874875.1| 15 YEVDYEKGVIKLKNRRCPRCGSIMAHhMKPVERWHCGKCGYT 56
                                   5555555555555679**********9999**********97 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   1.4e-05     0.012      88     116 ..      29      57 ..       3      63 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                        TackOD1  88 evCpkCkSidieeqelihhftCgnvgpee 116
                                      Cp C+Si  ++ + ++ ++Cg+ g +e
  gi|118431336|ref|YP_874875.1|  29 RRCPRCGSIMAHHMKPVERWHCGKCGYTE 57 
                                    57999999988777777777777666543 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 ?   13.9   0.3     4e-05     0.036       4      31 ..      31      57 ..      29      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                                   ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                 RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                   Cp Cg+ +    +    +  C +CgY e
  gi|118431336|ref|YP_874875.1| 31 CPRCGSIMAHHMKPVE-RWHCGKCGYTE 57
                                   ********98776544.357******75 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.8   4.8e-05     0.043       6      34 ..      30      58 ..      30      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                 Zn_ribbon_SprT  6 rCtgCgreythhlsi.rrhnYrCrrCk.gtL 34
                                   rC++Cg+   hh +   r  ++C++C+  ++
  gi|118431336|ref|YP_874875.1| 30 RCPRCGSIMAHHMKPvER--WHCGKCGyTEF 58
                                   8*****999999999999..******97766 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   3.3e-05      0.03      26      53 ..      26      53 ..       4      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                     zf-piccolo 26 CkkqvCnlCGFnptphltekkeWlclnC 53
                                    k+  C  CG  +  h++ ++ W c +C
  gi|118431336|ref|YP_874875.1| 26 LKNRRCPRCGSIMAHHMKPVERWHCGKC 53
                                   57788*****777777777********9 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0023       2.1      42      61 ..      21      40 ..       1      44 [. 0.63
   2 ?    7.3   0.1    0.0068       6.1      42      62 ..      40      60 ..      37      63 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                            GFA 42 dsgnkvtrsfCpeCgsplys 61
                                   +   k++++ Cp+Cgs + +
  gi|118431336|ref|YP_874875.1| 21 KGVIKLKNRRCPRCGSIMAH 40
                                   344577889*******9886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0068
                            GFA 42 dsgnkvtrsfCpeCgsplyse 62
                                   ++ ++v+r+ C +Cg + +++
  gi|118431336|ref|YP_874875.1| 40 HHMKPVERWHCGKCGYTEFVT 60
                                   567899*********887764 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.033        29      33      41 ..      30      38 ..      20      42 .. 0.77
   2 ?    8.4   0.5    0.0022       1.9      32      40 ..      48      56 ..      45      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.033
                         HalOD2 33 kCtrCGevq 41
                                   +C rCG ++
  gi|118431336|ref|YP_874875.1| 30 RCPRCGSIM 38
                                   788888875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                         HalOD2 32 WkCtrCGev 40
                                   W+C++CG +
  gi|118431336|ref|YP_874875.1| 48 WHCGKCGYT 56
                                   *******87 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00024      0.21       3      11 ..      28      36 ..      26      41 .. 0.80
   2 ?    4.4   0.7     0.033        30       6      10 ..      50      54 ..      49      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                  zf-NADH-PPase  3 hrFCgrCGa 11
                                   +r C+rCG+
  gi|118431336|ref|YP_874875.1| 28 NRRCPRCGS 36
                                   799999998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.033
                  zf-NADH-PPase  6 CgrCG 10
                                   Cg+CG
  gi|118431336|ref|YP_874875.1| 50 CGKCG 54
                                   77777 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.6   2.4e+03      49      62 ..       3      16 ..       1      27 [. 0.63
   2 ?   12.9   1.2   0.00011     0.096      11      44 ..      31      61 ..      29      63 .] 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                        DUF2387 49 vakelktrvnkdee 62
                                   ++kelkt v k  e
  gi|118431336|ref|YP_874875.1|  3 EKKELKTYVHKLYE 16
                                   56778887776654 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                        DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelse 44
                                   CPrC    +i++++  +ve   C +Cg+t+  ++
  gi|118431336|ref|YP_874875.1| 31 CPRCG---SIMAHHMKPVERWHCGKCGYTEFVTK 61
                                   99997...59*******************97765 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   9.2e-05     0.083     103     144 ..      18      59 ..       1      62 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.2e-05
                        DUF1451 103 vyqsGevvglGtlvCekCgkel.alkkteeippCpkCgateFr 144
                                     y+ G v+ l + +C +Cg  + +  k+ e  +C kCg teF 
  gi|118431336|ref|YP_874875.1|  18 DYEKG-VIKLKNRRCPRCGSIMaHHMKPVERWHCGKCGYTEFV 59 
                                    45555.67788899*****97724567888889*********7 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.9   0.00048      0.43       3      31 ..      31      56 ..      29      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                                   -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                   C+ CG+ +++++      eR  C +Cg++
  gi|118431336|ref|YP_874875.1| 31 CPRCGSIMAHHMK---PVERWHCGKCGYT 56
                                   *********9995...689********97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00023      0.21       3      11 ..      29      37 ..      27      39 .. 0.84
   2 ?    3.3   1.4     0.063        57      18      24 ..      49      55 ..      48      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                    zf-ribbon_3  3 vrCPnCGap 11
                                   +rCP+CG++
  gi|118431336|ref|YP_874875.1| 29 RRCPRCGSI 37
                                   79*****95 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.063
                    zf-ribbon_3 18 vCpyCGt 24
                                   +C +CG+
  gi|118431336|ref|YP_874875.1| 49 HCGKCGY 55
                                   6999997 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.3   8.3e+03      23      31 ..      12      20 ..       8      23 .. 0.60
   2 ?    2.5   0.1      0.19   1.7e+02       1       8 [.      30      37 ..      30      46 .. 0.78
   3 ?   10.4   0.3   0.00063      0.56      37      49 ..      49      61 ..      47      63 .] 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.3
                 zinc_ribbon_13 23 skifdvqnk 31
                                    k+++v+ +
  gi|118431336|ref|YP_874875.1| 12 HKLYEVDYE 20
                                   566666554 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                 zinc_ribbon_13  1 kCpKCgnt 8 
                                   +Cp+Cg+ 
  gi|118431336|ref|YP_874875.1| 30 RCPRCGSI 37
                                   59***975 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00063
                 zinc_ribbon_13 37 sCknCgYtelYka 49
                                    C +CgYte+  +
  gi|118431336|ref|YP_874875.1| 49 HCGKCGYTEFVTK 61
                                   599******9766 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   2.8   0.00025      0.22       5      40 ..      30      57 ..      24      63 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpw 40
                                    CP Cg+   ++  +          +C +Cg+  ++
  gi|118431336|ref|YP_874875.1| 30 RCPRCGSIMAHHMKPVE------RWHCGKCGY--TE 57
                                   7*****98777666544......569*****9..33 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 ?   10.7   0.9   0.00074      0.66       3      18 ..      29      44 ..      27      47 .. 0.77
   2 ?    5.3   0.7     0.035        32       2      13 ..      47      58 ..      46      63 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00074
                        zf-ISL3  3 hrCPnCgsktvvkhgk 18
                                   +rCP+Cgs +++ +  
  gi|118431336|ref|YP_874875.1| 29 RRCPRCGSIMAHHMKP 44
                                   79******98887765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.035
                        zf-ISL3  2 phrCPnCgsktv 13
                                   +++C +Cg +  
  gi|118431336|ref|YP_874875.1| 47 RWHCGKCGYTEF 58
                                   689999999843 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00061      0.55       4      17 ..      30      43 ..      27      44 .. 0.84
   2 ?    1.3   0.3      0.29   2.6e+02       3       9 ..      48      54 ..      46      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00061
                         zf_UBZ  4 lCerCgkeipesel 17
                                    C+rCg+ + ++++
  gi|118431336|ref|YP_874875.1| 30 RCPRCGSIMAHHMK 43
                                   6*******999876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                         zf_UBZ  3 ylCerCg 9 
                                   + C +Cg
  gi|118431336|ref|YP_874875.1| 48 WHCGKCG 54
                                   7799998 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   0.1    0.0021       1.8      15      20 ..      30      35 ..      24      38 .. 0.66
   2 ?    2.9   2.4      0.11        96      16      21 ..      50      55 ..      49      56 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                  zinc_ribbon_2 15 FCpyCG 20
                                    Cp+CG
  gi|118431336|ref|YP_874875.1| 30 RCPRCG 35
                                   466665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                  zinc_ribbon_2 16 CpyCGt 21
                                   C +CG+
  gi|118431336|ref|YP_874875.1| 50 CGKCGY 55
                                   666665 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   1.7      0.03        27      16      22 ..      30      36 ..      30      36 .. 0.89
   2 ?    6.6   1.1    0.0071       6.3       1       9 [.      48      56 ..      48      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
                   Rubredoxin_2 16 rCpsCgs 22
                                   rCp Cgs
  gi|118431336|ref|YP_874875.1| 30 RCPRCGS 36
                                   8****97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0071
                   Rubredoxin_2  1 YvCsqCGfe 9 
                                   ++C +CG++
  gi|118431336|ref|YP_874875.1| 48 WHCGKCGYT 56
                                   689999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 473.79
//
Query:       gi|14601201|ref|NP_147734.1|  [L=349]
Description: DNA-binding/iron metalloprotein/AP endonuclease [Aeropyrum pernix K1]
Scores for complete 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  238.4   0.2    1.4e-70  238.1   0.2    1.0  1  Peptidase_M22   Glycoprotease family
     0.0045   16.7   0.0      0.031   14.0   0.0    2.1  3  Carbam_trans_N  Carbamoyltransferase N-terminus
  ------ inclusion threshold ------
      0.015   15.0   0.5      0.046   13.5   0.5    1.9  1  DUF348          G5-linked-Ubiquitin-like domain


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 !  238.1   0.2   2.3e-74   1.4e-70      11     270 ..      39     305 ..      33     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 2.3e-74
                                   EEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHHH CS
                 Peptidase_M22  11 kelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhle 91 
                                   ++++++ GG++P+++++ +s +  ++++eal eag+s++d+da+av+ gPG++++LrvG+++A++l+ +++kPlv+Vnh  
  gi|14601201|ref|NP_147734.1|  39 RRWTPREGGILPREVAEFFSLHAGEAVAEALGEAGVSIADVDAVAVALGPGMGPALRVGATVARALSAKYGKPLVPVNHAV 119
                                   5678999************************************************************************** PP

                                   HHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SS...CCH.HHHHHHCTCS.. CS
                 Peptidase_M22  92 ahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpyp...ggp.kieklakegkki 168
                                   ah++aar++++ ++Pv+l+v Gg+t+v+   +gry+ +getld+a+g+ ld +ar  g+  p   gg+ +++++a+ g  +
  gi|14601201|ref|NP_147734.1| 120 AHVEAARFTTGLRDPVALYVAGGNTTVVSFVAGRYRTFGETLDIALGNLLDTFAREAGIAPPyvaGGLhAVDRCAEGGGFV 200
                                   *********999******************99***************************9854447778999999988666 PP

                                   ......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCH CS
                 Peptidase_M22 169 e.fprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeee 246
                                   e +p+++kg+d+sfsG+ ta+l++l++ +  +d+++ + e +++++ve+ter+l+++++++  + GGvaan+ L+e+++ +
  gi|14601201|ref|NP_147734.1| 201 EgIPYVVKGQDVSFSGILTAALRLLKRgArLSDVCYTLREVAFSSVVEVTERCLAHTGKRQATLTGGVAANRVLNEKMSLM 281
                                   669**********************77637************************************************966 PP

                                   HHHTTSEEEXXXHHHHSSXCHHHH CS
                 Peptidase_M22 247 aeelglkliiPplkyctdnaamia 270
                                   a  +g+ +   + ++  dn++mia
  gi|14601201|ref|NP_147734.1| 282 AGLHGAVYRPVDVRLSGDNGVMIA 305
                                   66675555555778*********8 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.1     6e+02      46      66 ..      63      83 ..      11      90 .. 0.84
   2 ?   -3.5   0.0         1   6.2e+03     121     143 ..     109     131 ..     100     147 .. 0.73
   3 !   14.0   0.0   5.1e-06     0.031     256     313 ..     222     279 ..     209     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.1
                Carbam_trans_N 46 kaidyaleeagvelsdiDqiv 66
                                  +a++ al+eagv+  d+D ++
  gi|14601201|ref|NP_147734.1| 63 EAVAEALGEAGVSIADVDAVA 83
                                  689999************876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1
                Carbam_trans_N 121 rkdvslyeHhlsHaaSaystSpF 143
                                    k++  ++H ++H+  a +t + 
  gi|14601201|ref|NP_147734.1| 109 GKPLVPVNHAVAHVEAARFTTGL 131
                                   56677788888888888777665 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 5.1e-06
                Carbam_trans_N 256 lrlkearekdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNsall 313
                                   lrl +  ++ +d+  +++++    vvev++   ++++ r+ +l+GGva+N +lN ++ 
  gi|14601201|ref|NP_147734.1| 222 LRLLKRGARLSDVCYTLREVAFSSVVEVTERCLAHTGKRQATLTGGVAANRVLNEKMS 279
                                   44444444446999****************************************9984 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   7.7e-06     0.046      19      40 ..      65      86 ..      61      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-06
                                  HHHHHHHTT----TT-EEES-T CS
                        DUF348 19 VgdlLeeagitlgeqDkVsPsL 40
                                  V+++L eag+++ ++D V ++L
  gi|14601201|ref|NP_147734.1| 65 VAEALGEAGVSIADVDAVAVAL 86
                                  9******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2800.87
//
Query:       gi|118431337|ref|NP_147735.2|  [L=231]
Description: protein kinase [Aeropyrum pernix K1]
Scores for complete 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-08   33.2   0.8     0.0007   19.6   0.0    2.3  2  APH       Phosphotransferase enzyme family
    1.3e-06   28.1   0.0    1.9e-06   27.6   0.0    1.3  1  RIO1      RIO1 family
    0.00028   20.6   0.0    0.00033   20.4   0.0    1.2  1  WaaY      Lipopolysaccharide core biosynthesis protein (WaaY)
     0.0012   18.3   0.0     0.0014   18.0   0.0    1.2  1  Pkinase   Protein kinase domain
     0.0078   15.6   0.0      0.073   12.4   0.0    2.2  1  Kdo       Lipopolysaccharide kinase (Kdo/WaaP) family


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 !   14.1   0.3     9e-06     0.032      34     108 ..      58     129 ..      48     130 .. 0.83
   2 !   19.6   0.0     2e-07    0.0007     164     229 ..     127     196 ..     115     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9e-06
                                    HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS..HHHHHHHHHHHHHHHHHHCCHHCH CS
                            APH  34 aeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr..klsaaqlpellealgeflaalhqv 108
                                      ++rre+++ ++ ++agv++P++la       +g    ++eyv+g  l +        ++ l+e++g  l+ lh++
  gi|118431337|ref|NP_147735.2|  58 RLRTRREARVIAAARAAGVSAPALLA---VFPSLG--LIVMEYVEGPLLKDviDRRGLGAGGLVEEAGYNLGLLHRA 129
                                    56799*********************...455555..89***********977555667788889999999999987 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2e-07
                                    S-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH......HHCSCHCC.......CHCHHHHHHHHC CS
                            APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll......rswtseld.......peflaallraye 229
                                     +++++HgD+ + N +v+ ++g v  +iD ++a  +  + D av l                      e++  + r+y+
  gi|118431337|ref|NP_147735.2| 127 HRAGVVHGDPTTSNYIVR-GGGVV--LIDYGLAEFSSSVEDRAVDLhlfrraV------EsthaplaGELYSLYTRGYL 196
                                    4899**************.88999..********9999999999883333220......22233333555555555555 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.2e-10   1.9e-06      47     150 ..      53     154 ..      28     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.2e-10
                                    HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEE..TTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHH CS
                           RIO1  47 prklvklwaekEfrnLkrleeagvpvPkpielk..rhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklyk 123
                                      +lv+l +++E r + ++++agv++P  +++      +vme+++  g   p lkdv  ++   +  + e   +   l++
  gi|118431337|ref|NP_147735.2|  53 AERLVRLRTRREARVIAAARAAGVSAPALLAVFpsLGLIVMEYVE--G---PLLKDVIdRRGLGAGGLVEEAGYNLGLLH 127
                                    56799***********************9999622578*******..5...55566552234444444444556677888 PP

                                    TSTEEESS-STTSEEEETTEEEE--GT CS
                           RIO1 124 eaglvHaDLSeyNvlvdedkvviIDvs 150
                                    +ag+vH+D    N +v  ++vv+ID +
  gi|118431337|ref|NP_147735.2| 128 RAGVVHGDPTTSNYIVRGGGVVLIDYG 154
                                    *************************75 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   9.2e-08   0.00033     118     190 ..      89     167 ..      40     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.2e-08
                           WaaY 118 yimiieyiegielvdmpeid....devkakikqsieklhqlgmvsgdphrgnfivkkdevriid..lsgkrasaerkak 190
                                     ++++ey+eg  l d+ +        + ++    +  lh+ g+v gdp   n+iv++++v +id  l+  ++s e +a 
  gi|118431337|ref|NP_147735.2|  89 GLIVMEYVEGPLLKDVIDRRglgaGGLVEEAGYNLGLLHRAGVVHGDPTTSNYIVRGGGVVLIDygLAEFSSSVEDRAV 167
                                    5688999999999998776411114566777788999**************************9333444555555555 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     4e-07    0.0014      74     152 ..      90     163 ..      53     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-07
                                    EEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                        Pkinase  74 ylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesss 152
                                    ++v+eyveg  l+d++ r+g  +      ++++    l  lH++g++H D  ++N ++   g + ++D+Gla+  +s +
  gi|118431337|ref|NP_147735.2|  90 LIVMEYVEGPLLKDVIDRRGLGAG----GLVEEAGYNLGLLHRAGVVHGDPTTSNYIVR-GGGVVLIDYGLAEFSSSVE 163
                                    79**************98666554....555666666789*******************.88999*******9877655 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0     2e-05     0.073      34     173 ..      37     160 ..      21     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                            Kdo  34 kyyrggllgklskdlyrfklgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwa 113
                                    + y+ +  +  ++ ++  +l r+r +rE r++ + ++agv +p  +a            l+++e +eg   L+d++ +  
  gi|118431337|ref|NP_147735.2|  37 AVYKARVRKPYMHPRLAERLVRLRTRREARVIAAARAAGVSAPALLAVFP------SLGLIVMEYVEGPL-LKDVIDR-- 107
                                    5566666666677777788999*********************9998643......45689999999975.7777776.. PP

                            Kdo 114 elaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrl 173
                                       +     l+++ g     lhragv H+d    n  ++ ++     ++liD   a+  +
  gi|118431337|ref|NP_147735.2| 108 --RGLGAGGLVEEAGYNLGLLHRAGVVHGDPTTSNYIVRGGG-----VVLIDYGLAEFSS 160
                                    ..688889999999999999**********999999999888.....8888877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1935.77
//
Query:       gi|118431338|ref|NP_147736.2|  [L=188]
Description: deoxyribonucleotide triphosphate pyrophosphatase [Aeropyrum pernix K1]
Scores for complete 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-47  162.4   0.0    1.3e-47  162.2   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 !  162.2   0.0     7e-52   1.3e-47       1     187 []       5     181 ..       5     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 162.2 bits;  conditional E-value: 7e-52
                                    EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE---.-BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTTTB CS
                     Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeve.Etq.gtfeenalkKaraaae.aglpvladDsgLevdaLnglP 77 
                                    i+++TgN+gKl+e++e+l+e ++ev++++       + E+q +++ee+al  ar a++  + p+ ++D gL+++aLng+P
  gi|118431338|ref|NP_147736.2|   5 ILLVTGNRGKLEEAREVLREYGVEVEQAQ-----AWKlEVQsESLEEIALRAARVAYAqLRRPLAVEDAGLFINALNGFP 79 
                                    799***************99888888662.....22239999************888635788***************** PP

                                    GGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEET CS
                     Ham1p_like  78 GvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpe 157
                                    G+ys++  +     + ++  +l+ le++ +dr+A f++++a+++p   +e++f+Gev G+i++eprg++gfG+DpiFvpe
  gi|118431338|ref|NP_147736.2|  80 GPYSSYAYK-----TIGIPGVLRLLEGA-ADRGACFKAAVAYVAP--LVERVFTGEVCGSIAREPRGSQGFGFDPIFVPE 151
                                    *****9963.....45778888888743.48*************8..6668****************************6 PP

                                    T-SS.BTTTS.CHHHHHHSHHHHHHHHHHHH CS
                     Ham1p_like 158 egek.tfaelskeeknaiShRgkAlekllef 187
                                    + ++ tfael +  kn+iShR++A+++l e+
  gi|118431338|ref|NP_147736.2| 152 G-YSsTFAELGPGVKNRISHRARAFRRLGEW 181
                                    4.566**********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1438.04
//
Query:       gi|14601204|ref|NP_147737.1|  [L=150]
Description: 30S ribosomal protein S15 [Aeropyrum pernix K1]
Scores for complete 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   82.8   0.0    2.6e-23   81.8   0.0    1.6  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    1.2e-17   63.9   0.1    1.6e-17   63.5   0.1    1.2  1  Ribosomal_S15    Ribosomal protein S15


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 !   81.8   0.0   2.9e-27   2.6e-23       5      60 .]       3      58 ..       1      58 [. 0.97

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 2.9e-27
                                  SSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
               Ribosomal_S13_N  5 hsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                  ++r+kG+S+S+rP + ++p+Wl +++ee+e li +lakkG+ pS+IG+iLRDqyG+
  gi|14601204|ref|NP_147737.1|  3 KRREKGQSHSTRPPHPQPPQWLVFTPEEIELLIAELAKKGYGPSMIGIILRDQYGI 58
                                  4899***************************************************9 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.1   1.8e-21   1.6e-17       3      80 ..      71     146 ..      69     147 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.8e-21
                                   HHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCTS CS
                 Ribosomal_S15   3 elikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklgl 80 
                                   e+++e + h+     +++++ +l+++++nl++hl+e++kD+h+++gL+ l+sk+r+l+kY+kr+ v  +++k+  e ++l
  gi|14601204|ref|NP_147737.1|  71 EVLREKGLHP----PLPEDLLMLIRKAVNLRRHLDEHPKDYHAKKGLIDLESKIRRLVKYYKRRGVlpPDWKYDPEAAKL 146
                                   6788889999....99*********************************************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 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:                        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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1134.01
//
Query:       gi|118431339|ref|NP_147738.2|  [L=454]
Description: aspartate kinase [Aeropyrum pernix K1]
Scores for 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-43  147.4   0.0    8.7e-43  146.6   0.0    1.3  1  AA_kinase  Amino acid kinase family
    3.6e-08   33.1   0.1    1.8e-07   30.8   0.0    2.2  2  ACT        ACT domain
    2.3e-05   24.1   0.0    0.00024   20.8   0.0    2.5  2  ACT_7      ACT domain


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.0   1.5e-46   8.7e-43       2     238 ..       8     282 ..       7     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 1.5e-46
                                    EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH...........TCCCCCHHHC...... CS
                      AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal...........ksglssgelaa..... 64 
                                    +vVvK+GGs+l    +  + ++ + +  l esg ++vvV+++ +++td+ll+                            
  gi|118431339|ref|NP_147738.2|   8 LVVVKFGGSVLNGSPG--FLAAGRLVLGLLESGLEPVVVVSAvKGVTDALLSSferrdpgvggaV---------Gktyls 76 
                                    79**********6666..555555555555***********************776666553330.........133334 PP

                                    ......................E..HHHHHHHHH..........HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE CS
                      AA_kinase  65 ...................glrstleeagevatr..........dalaslgerlvaallaaglpavglsaaaldateagr 115
                                                       ++ s+l  a+    +          d+++s gerl+aal+a +l+  g+ a++l+  eag+
  gi|118431339|ref|NP_147738.2|  77 iarelglppesvrdvslasAEVSKLLWAA----EvlgqwtprvrDLVVSYGERLSAALMAGLLRRLGVEARWLGGGEAGI 152
                                    45555555666566755554444444444....255559999************************************** PP

                                    ..........HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSS CS
                      AA_kinase 116 ........degsdgnvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdG 184
                                             ++  g  e v +e +e +le+gvvpv++gf g+++eg+   lgrg+sD +a+llA algA +++++tdV+G
  gi|118431339|ref|NP_147738.2| 153 vtdgefgdATPLYGYTEGVIRERLEPMLEEGVVPVVAGFTGATREGDttlLGRGGSDLTATLLASALGAGRVVLYTDVPG 232
                                    *999777777777777777799999999**************************************************** PP

                                    CESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEE CS
                      AA_kinase 185 VydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvv 238
                                    +++ dp++v   r++  +s++ea e     a+ G + +hp++++++  gg  v 
  gi|118431339|ref|NP_147738.2| 233 ILSGDPRVVGEPRRVGYMSYEEAWE----VARLGLRKFHPRTFEPLIAGGLGVE 282
                                    *************************....*******************985544 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.38   2.3e+03       6      15 ..     226     235 ..     224     236 .. 0.80
   2 !   30.8   0.0     3e-11   1.8e-07       6      64 ..     322     374 ..     317     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.38
                                    EEESSTTHHH CS
                            ACT   6 gvpDrPGlLa 15 
                                    +  D+PG+L+
  gi|118431339|ref|NP_147738.2| 226 LYTDVPGILS 235
                                    567*****98 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 3e-11
                                    EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                    +++++ G L+r++g+la rg+Ni  i q +s      ++ + +vvde+dl++++e+l +
  gi|118431339|ref|NP_147738.2| 322 SMAGKRGFLSRLAGLLAGRGVNILAIRQPPS------ETAIELVVDERDLPAAVEELGA 374
                                    68999**************************......99*****************976 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.15     9e+02       4      25 ..       6      26 ..       4      28 .. 0.86
   2 !   20.8   0.0   4.1e-08   0.00024       4      61 ..     311     370 ..     308     373 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.15
                                   EEEEEEEE-S-.---SS--HHH CS
                          ACT_7  4 dgwiklsvvgsglpfdvtGiva 25
                                   ++ +++++ gs l++ ++G++a
  gi|118431339|ref|NP_147738.2|  6 NDLVVVKFGGSVLNG-SPGFLA 26
                                   678899*****9999.****99 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.1e-08
                                    EEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHH CS
                          ACT_7   4 dgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAve 61 
                                    +g++ l v g+++++   G++++la+ La  g++i++i    +++ + ++V+e+dl +Ave
  gi|118431339|ref|NP_147738.2| 311 RGVARLVVRGPSMAG-KRGFLSRLAGLLAGRGVNILAIRqppSETAIELVVDERDLPAAVE 370
                                    6788999******99.*******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3572.51
//
Query:       gi|14601206|ref|NP_147739.1|  [L=349]
Description: aspartate-semialdehyde dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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  113.1   0.0    2.1e-32  112.7   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    1.9e-26   92.9   0.0    2.9e-26   92.3   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


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 !  112.7   0.0   2.4e-36   2.1e-32       1     183 [.     157     328 ..     157     329 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 2.4e-36
                                   HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHH CS
               Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkav 81 
                                   LkP++da ++l++v+vat+qa+SGaG+                     gv+g+ i +N+ip+i +ee k e e+r++l+ +
  gi|14601206|ref|NP_147739.1| 157 LKPIVDA-AGLREVHVATMQAISGAGR--------------------RGVPGYGIVDNIIPHIPGEEGKVEAESRKILGSL 216
                                   8*****9.99*****************....................6********************************* PP

                                   HHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS............TTEEEEESSHCHHSSHHH CS
               Semialdhyde_dhC  82 aetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa............pevkvvvneeedrPtpaa 150
                                      + + + ++ v at +rVPvl Gh+e v++k++ ++ e  e+ e+l++             p + ++v   edrP+p++
  gi|14601206|ref|NP_147739.1| 217 RGGRLEPAAFS-VAATTTRVPVLEGHLEVVYLKTA-RPMEPGEAVEALESYrgipqelglptaPPKPLRVLRGEDRPQPRL 295
                                   **********8.**********************6.888888888888888888999******9999999999*******9 PP

                                   HTTC..SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
               Semialdhyde_dhC 151 vagg..tnsvsVGRirkdemgdeglklvvvgDNll 183
                                   ++    +++vsVGR++  e g   l +vv+g+Nl+
  gi|14601206|ref|NP_147739.1| 296 DRAAggGMTVSVGRVEAKEGGW--LRMVVLGHNLV 328
                                   987677*************777..**********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 !   92.3   0.0   3.2e-30   2.9e-26       1     119 [.       2     128 ..       2     130 .. 0.95

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 3.2e-30
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGC..TT-SEEEE- CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeel..kevdivfla 73 
                                   ++a++Ga+G vGq++lrlLe hp++e+++++ss  +aG   aea         + + + ++++ +++ +l  ++v++vf+a
  gi|14601206|ref|NP_147739.1|   2 RAAVLGASGLVGQVFLRLLEGHPYFEVAAVASSPGKAGLDAAEAIDwilpggPPGYLEGMRMSRPEPGALraEGVELVFSA 82 
                                   579**********************************************9*988999999999988888888********* PP

                                   SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                Semialdhyde_dh  74 lpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                   lp+++++el+p+la +g+ v+++ss++Rl++d+++v  evn+ +++
  gi|14601206|ref|NP_147739.1|  83 LPSQAAAELEPALAREGFEVFSNSSNMRLDPDIPLVNGEVNPGHLA 128
                                   ******************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2539.46
//
Query:       gi|118431340|ref|NP_147740.2|  [L=332]
Description: homoserine dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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  106.6   0.0    1.6e-30  106.3   0.0    1.1  1  Homoserine_dh  Homoserine dehydrogenase


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0     9e-35   1.6e-30       1     173 []     143     316 ..     143     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 9e-35
                                    --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHHCTT CS
                  Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarlafgl 80 
                                    P+i+ l+  l+g r+ r+ G+lngt+nyil+ + e g  ++e+++ a +lG+ae+Dp++D+ G+D a K+ i+a+ + g 
  gi|118431340|ref|NP_147740.2| 143 PLIDLLRVGLAGRRVLRVVGVLNGTSNYILNLLME-GVPLEEAVEAAVRLGIAEPDPSADLRGVDLALKASIVAQTL-GC 220
                                    99********************************6.999**************************************.** PP

                                    T--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE....CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEEEEEEE CS
                  Homoserine_dh  81 eveledvevegiskltaedikeakeegkvlklvasa....vearVkpelvpkshplasvkgsenavlvetdrlgelviqG 156
                                    +v + dv v g     a      + +g  l++ a++    ++a+++++l  + + l+s+ gs na ++  +   ++++ G
  gi|118431340|ref|NP_147740.2| 221 PVGPGDVVVGGTVYDAAGWAPGLRGAGAALRYTARVdvagCRAEIGLTLHGAGSRLYSLPGSLNAAVIGLEDS-TIYLEG 299
                                    *******999988777777888999**********8876669*************************998875.8***** PP

                                    S-SSHHHHHHHHHHHHH CS
                  Homoserine_dh 157 pgaGaepTAsavlsDll 173
                                    pgaG  +TA+ +lsDl+
  gi|118431340|ref|NP_147740.2| 300 PGAGLGVTAATLLSDLV 316
                                    ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2429.00
//
Query:       gi|118431341|ref|NP_147741.2|  [L=435]
Description: hypothetical protein APE_1147.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.53u 0.20s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3115.75
//
Query:       gi|118431342|ref|YP_874876.1|  [L=85]
Description: hypothetical protein APE_1147a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 677.23
//
Query:       gi|118431343|ref|NP_147748.2|  [L=214]
Description: 30S ribosomal protein S3 [Aeropyrum pernix K1]
Scores for complete 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-65  221.0   0.0    1.3e-65  220.8   0.0    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.14   12.1   0.0    1.2  1  ELYS            Nuclear pore complex assembly


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 !  220.8   0.0   1.5e-69   1.3e-65       6     202 .]       6     195 ..       2     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 220.8 bits;  conditional E-value: 1.5e-69
                                    -S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSEEEE CS
                 Ribosomal_S3Ae   6 vvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgknalt 85 
                                    ++D+++ K+W++v aP lfg++ +G+t++       ++++kl+grv+e++l D+t+d+ + +++k+++++ +v+g++a+t
  gi|118431343|ref|NP_147748.2|   6 IRDTWRLKKWFKVVAPPLFGETVLGTTPA-------DDPDKLIGRVMETTLFDITGDY-SYVHVKMYFQVVRVEGDTAYT 77 
                                    79***************************.......*********************9.778****************** PP

                                    EEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-HHHH CS
                 Ribosomal_S3Ae  86 nFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldlkel 165
                                    +Fkg+el rD++r l+r++ss+++ i++v tkDgy lrv+++afT++r   +k+sqk+aIrk+m+ei++++a+e++l+el
  gi|118431343|ref|NP_147748.2|  78 RFKGHELLRDYIRGLTRRKSSKVTGIFNVWTKDGYGLRVTAMAFTRQR---CKTSQKSAIRKVMQEIVEQKARESTLDEL 154
                                    ************************************************...***************************** PP

                                    HHHHTT....THHHHHHHHHHTTTS-EEEEEEEEEEEEE-S CS
                 Ribosomal_S3Ae 166 vkklip....eslgkeiekeakkIyplrnveirKvkvlkkP 202
                                    ++ +++     sl+  i ++a+kIyplr+vei K+k+l  P
  gi|118431343|ref|NP_147748.2| 155 IQLMVFsdheGSLAYLIDESARKIYPLRKVEIAKSKLLWVP 195
                                    ****9654456899***********************9765 PP

>> ELYS  Nuclear pore complex assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.5e-05      0.14     163     210 ..     116     164 ..      75     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                           ELYS 163 teAfsfqRslsdkekreelleelvelclee..aarklkeLlelpldeeEe 210
                                    + A +f+R+++++  ++  ++++++ ++e+  +++ l+eL++l   ++ e
  gi|118431343|ref|NP_147748.2| 116 VTAMAFTRQRCKT-SQKSAIRKVMQEIVEQkaRESTLDELIQLMVFSDHE 164
                                    6799999999988.45544444444444444437889*****97555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1623.61
//
Query:       gi|118431344|ref|NP_147749.2|  [L=352]
Description: hypothetical protein APE_1156.1 [Aeropyrum pernix K1]
Scores for complete 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-79  264.2   0.6    4.9e-79  263.7   0.6    1.2  1  SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
    3.6e-28   98.5   0.0    6.4e-28   97.7   0.0    1.4  1  THUMP          THUMP domain
  ------ inclusion threshold ------
        2.1    8.6   3.9        0.5   10.6   0.4    1.8  2  Mtf2_C         Polycomb-like MTF2 factor 2


Domain annotation for each model (and alignments):
>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.7   0.6   8.2e-83   4.9e-79       1     173 []     169     340 ..     169     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 263.7 bits;  conditional E-value: 8.2e-83
                  SPOUT_MTase_2   1 kvvlvqlpYlgdlkaakelgeriGRavqafevkeliiapkekvdayelaeflrgvreGqesRyeiqkksygrevrkvpvl 80 
                                    +v++vq+pYlg+l+a++++g+riGR+vq+fev+el++ap++ vda++laefl+gv+eG+esR+e+q+ksy+r++r+vpv+
  gi|118431344|ref|NP_147749.2| 169 RVAVVQMPYLGPLDACRNMGVRIGREVQNFEVRELVVAPTGLVDARQLAEFLQGVFEGVESRFEVQRKSYHRRARRVPVY 248
                                    799***************************************************************************** PP

                  SPOUT_MTase_2  81 vqdlyqlvrkrrkkellivtdPeGeeisevkeelaealrkakevvvlvGsReGiPkGlfrfadfvvDlaPgvtlateyai 160
                                    +qdl+qlvr+rr+ e++iv++PeGe+is+v+++l+e++r +++v+vlvGsReGiP G++r+ad+vvD+aPg+tl+t+ya+
  gi|118431344|ref|NP_147749.2| 249 LQDLHQLVRDRRG-EPIIVMEPEGEHISRVADRLWEMFRGSRRVNVLVGSREGIPLGVYRYADLVVDIAPGITLSTDYAA 327
                                    *************.****************************************************************** PP

                  SPOUT_MTase_2 161 aaalialvtvlee 173
                                    a+al+a++tvl e
  gi|118431344|ref|NP_147749.2| 328 ASALVAIATVLYE 340
                                    *********9875 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.0   1.1e-31   6.4e-28      13     143 ..      23     148 ..      13     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 1.1e-31
                                    H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEE CS
                          THUMP  13 nverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkr 92 
                                    +++ +++g +++v++++ ++pe d++l+ e++  a    rv++v +v +a+le++ +aa e+ + ++ ++ e FaVr++r
  gi|118431344|ref|NP_147749.2|  23 RARPIPRGFKGLVLVYGCRDPEADARLILERVVEAD---RVLVVHAVSRASLEEMAAAAAEAARGRIGGG-ECFAVRTTR 98 
                                    567789999*******************99999988...***************************9776.5******** PP

                                    SSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                          THUMP  93 rgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                    rg+h  +ts+++n +vG+a++++tg+ V+le+Pd+vv veii+d a+isi 
  gi|118431344|ref|NP_147749.2|  99 RGSH-GYTSVDVNVVVGDAVRRATGACVNLESPDKVVAVEIIQDLALISIY 148
                                    ****.*******************************************996 PP

>> Mtf2_C  Polycomb-like MTF2 factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   8.3e-05       0.5      15      37 ..      82     104 ..      80     109 .. 0.88
   2 ?   -3.8   0.2       2.7   1.6e+04      25      32 ..     238     245 ..     237     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-05
                         Mtf2_C  15 aanRiasGEkfavlAkRvtpnGk 37 
                                    a +Ri  GE fav+  R++ +G 
  gi|118431344|ref|NP_147749.2|  82 ARGRIGGGECFAVRTTRRGSHGY 104
                                    449***************99995 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.7
                         Mtf2_C  25 favlAkRv 32 
                                    +  +A+Rv
  gi|118431344|ref|NP_147749.2| 238 YHRRARRV 245
                                    66799998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2593.36
//
Query:       gi|118431345|ref|NP_147750.2|  [L=522]
Description: hypothetical protein APE_1158.1 [Aeropyrum pernix K1]
Scores for complete 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   50.3   0.0    8.4e-13   49.0   0.0    1.7  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.092   12.8   0.0       0.27   11.3   0.0    1.8  1  B12-binding  B12 binding domain
       0.64   10.7   3.1         28    5.4   0.0    3.2  3  GTP-bdg_M    GTP-binding GTPase Middle Region


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.4e-16   8.4e-13       2     166 ..     197     357 ..     196     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.4e-16
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiri 80 
                                    +++rgC ++C+fC  ++     ++ r++s+e ++++++e+ ++ + +  vi+ +   ++++   e+l  +++     + +
  gi|118431345|ref|NP_147750.2| 197 ETSRGCGRGCRFCMEGT---VFRPRRDRSLEVLKHLLREG-VRVNgAQRVIFYSLVFFDNRASDEILWYAVED----LGL 268
                                    689*************9...7*******************.56666999999999999999999999999985....555 PP

                                    EEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTS CS
                                    xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGen 156
                                      +++ ++ +   +e + ++++ g  +v++  e+++   + + + ++ + + +l a++++   gi     + i+g+pGe 
  gi|118431345|ref|NP_147750.2| 269 QASVPSLRAEtltWERAGLIARGGQRTVTIAPETGSCT-IARAILKPIGGDITLWAVDNALGQGITGvKLYLITGFPGEG 347
                                    5555555544666************************9.77777788999****************9999********** PP

                                    HHHHHHHHHH CS
                                    xxxxxxxxxx RF
                    Radical_SAM 157 deeleellel 166
                                    +e+l ++++l
  gi|118431345|ref|NP_147750.2| 348 EEDLAQTRDL 357
                                    ******9987 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.5e-05      0.27      53     118 ..      60     129 ..      47     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.5e-05
                    B12-binding  53 dvvglSalltsqleavkelvel.......lkrirprvkvvvGGahpsldpeetleaklgiddvvvgegedale 118
                                    ++v++S+ +   ++++ + +e+       + r   +  v++GG+++++ p+ +l   l +d v vge e  +e
  gi|118431345|ref|NP_147750.2|  60 RAVLVSLPYEIMYADMVRALEQlglnpwaRGRGEGDPLVIAGGPAATANPAPLLD--L-VDAVLVGELEPVAE 129
                                    57888888888888888888888888885444445889**************997..4.59999**9886655 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 ?   -1.4   0.0      0.64   3.8e+03      37      62 ..     341     366 ..     323     368 .. 0.72
   2 ?    3.6   0.4     0.017     1e+02      51      67 ..     395     411 ..     392     416 .. 0.89
   3 ?    5.4   0.0    0.0046        28       7      34 ..     424     451 ..     421     466 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.64
                                    ..XXXXXXXXXHHHHHHHHHHHHHHH CS
                      GTP-bdg_M  37 igtrGpGetkleldrrlireriaklk 62 
                                     g+ G+Ge  l   r l  + +++++
  gi|118431345|ref|NP_147750.2| 341 TGFPGEGEEDLAQTRDLALRVVERVR 366
                                    45889999999998888777666666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHH CS
                      GTP-bdg_M  51 rrlireriaklkkeLek 67 
                                    rrl++eri++l ++L++
  gi|118431345|ref|NP_147750.2| 395 RRLLEERINRLSRALRR 411
                                    9*************986 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0046
                                    HHHHHHHHHHHHHHHHHCXXXXXXXXX. CS
                      GTP-bdg_M   7 aklQVelAqlkyllprLeglgkelsrqg 34 
                                    a +QV+lA+   ++ r++  ++++ rq+
  gi|118431345|ref|NP_147750.2| 424 AEVQVALARGGREMARVVVEWARMPRQT 451
                                    899***************99*9999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.55u 0.21s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3868.75
//
Query:       gi|118431346|ref|NP_147751.2|  [L=123]
Description: ribonuclease P protein component 2 [Aeropyrum pernix K1]
Scores for complete 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   40.4   0.0    3.2e-10   40.2   0.0    1.0  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 !   40.2   0.0   1.8e-14   3.2e-10       1      99 [.      14     109 ..      14     112 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.8e-14
                                    EEEEEEEEESS......-..HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--E CS
                  RNase_P_Rpp14   1 RYllveilypdeeeelte..ksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitk 78 
                                    RY+++e+l+ d +    +   ++ +a+r    + fG   l+ ++   +++y++++++ +++ + r++   ++aaL l++ 
  gi|118431346|ref|NP_147751.2|  14 RYVAFEVLSLDGPP---PgkGEFEEALRGVYLKAFGAESLALARP--RIVYYEEESGRGVVAVVRDYRYHILAALGLVRM 88 
                                    9**********743...244*************************..9******************************** PP

                                    ETTEEEEEEEEEEESSHHHHH CS
                  RNase_P_Rpp14  79 iegrpvvfrvvrvsGTikkae 99 
                                     +gr+v++ ++r+sGT+k a 
  gi|118431346|ref|NP_147751.2|  89 AGGRRVLVVPLRTSGTVKGAL 109
                                    *****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 914.65
//
Query:       gi|14601219|ref|NP_147752.1|  [L=410]
Description: translation-associated GTPase [Aeropyrum pernix K1]
Scores for complete 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  112.6   0.0    2.2e-32  111.9   0.0    1.3  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    2.5e-18   66.2   0.0    1.2e-17   64.1   0.0    2.0  2  MMR_HSR1       50S ribosome-binding GTPase
    4.5e-17   61.9   0.0    8.3e-17   61.0   0.0    1.4  1  TGS            TGS domain
    2.6e-06   27.0   0.0    0.00022   20.8   0.1    2.5  2  FeoB_N         Ferrous iron transport protein B
     0.0095   16.1   0.0       0.46   10.7   0.0    2.3  1  YchF-GTPase_C  Protein of unknown function (DUF933)


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 !  111.9   0.0   6.2e-36   2.2e-32       2     112 .]     231     338 ..     230     338 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 6.2e-36
                    MMR_HSR1_C   2 lNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdlvl 82 
                                   +NK+D+p a+en+e+l ++yp    vvp+sA aEl+Lr++a++g ++Y+pgd df++k+ +   l  k  kaLe +r+ v+
  gi|14601219|ref|NP_147752.1| 231 ANKVDVPGAEENVERLGSSYPGIP-VVPASALAELMLRRLAREGRVRYIPGDPDFTVKDPGG--LGGKALKALELVRERVM 308
                                   7********************877.*********************************9966..***************** PP

                    MMR_HSR1_C  83 krygsTGVqealnaavfelldlivVYPVed 112
                                   kr+g+TGV++a+n+avf++ld+i+VYPVed
  gi|14601219|ref|NP_147752.1| 309 KRWGGTGVVQAINTAVFDVLDMIAVYPVED 338
                                   ****************************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 !   64.1   0.0   3.2e-21   1.2e-17       3      87 ..       9     121 ..       7     143 .. 0.83
   2 ?   -1.7   0.0      0.83     3e+03      79      79 ..     214     214 ..     152     249 .. 0.57

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3.2e-21
                                   EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE..........................EEEEECGGCS CS
                      MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke..........................ielvDtpGli 57 
                                   ++vG++NvGKSt++ a t+  ++++++p++T+++n g     +k+                          ++l+D++Gl+
  gi|14601219|ref|NP_147752.1|   9 GLVGKTNVGKSTFFAAATEVPVKIENRPFVTIEPNVGVGY-ARKRcahvelglprcdpvnslciegwrfipVKLLDVAGLV 88 
                                   89***********************************665.322356677777788888888888888888********99 PP

                                   SHHHHHHHHHHHHHHHHC.TSEEEEEEETT..T CS
                      MMR_HSR1  58 egaseekglgkaflalee.adlillvvdas..e 87 
                                    ga++++glg++fl+  + ad++llvvdas  +
  gi|14601219|ref|NP_147752.1|  89 PGAHRGRGLGNRFLDDVRkADALLLVVDASgsT 121
                                   9*************96665*********98441 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.83
                                   E CS
                      MMR_HSR1  79 i 79 
                                    
  gi|14601219|ref|NP_147752.1| 214 R 214
                                   1 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   2.3e-20   8.3e-17       7      59 ..     346     404 ..     340     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2.3e-20
                                   TSSEEE....EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                           TGS   7 dGkvpd....lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                   +G++      ++rg+t++D+Ay+Ih++l+k+f+yA   +  qrvg  ++L+dgdvv+Iv
  gi|14601219|ref|NP_147752.1| 346 EGRILPdvilVKRGSTPRDLAYRIHTDLGKTFLYAVNAKtkQRVGEGYRLQDGDVVKIV 404
                                   55544347779***************************9*******************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   6.3e-08   0.00022       3      43 ..       8      48 ..       6      60 .. 0.86
   2 ?    3.5   0.0     0.013        47      95     152 ..     213     269 ..     207     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.3e-08
                                  EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEE CS
                        FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklk 43
                                  + lvG+ nvGk+t+f a t++  k+ N p vt+e + g   
  gi|14601219|ref|NP_147752.1|  8 LGLVGKTNVGKSTFFAAATEVPVKIENRPFVTIEPNVGVGY 48
                                  579*******************************9988654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.013
                                   HHHHHHH.HHTTSSEEEEEETHHHHHHTTEEE-HHHHHH.HHTS-EEEEBTTTTBTHHHH CS
                        FeoB_N  95 LyLtlql.lelgvpvvlalnmideaekkgieidlkkLse.kLgvpvvktsakkkegieel 152
                                   L L+++l le g+p v+  n++d+    g e ++++L +   g+pvv++sa  +  +++l
  gi|14601219|ref|NP_147752.1| 213 LRLFVKLvLERGKPAVILANKVDVP---GAEENVERLGSsYPGIPVVPASALAELMLRRL 269
                                   66666653799*********99985...55567888865156999999999887766666 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00013      0.46      17      47 ..     356     386 ..     354     405 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                 YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevikye 47 
                                   +k+g+t  + A  iH+D+ k+F+ a   k +
  gi|14601219|ref|NP_147752.1| 356 VKRGSTPRDLAYRIHTDLGKTFLYAVNAKTK 386
                                   6889999999************998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2905.67
//
Query:       gi|118431347|ref|NP_147753.2|  [L=233]
Description: RNA-associated protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-23   82.0   0.0    3.8e-23   81.4   0.0    1.3  1  SBDS         Shwachman-Bodian-Diamond syndrome (SBDS) protein
    5.5e-18   65.1   0.0    8.4e-18   64.5   0.0    1.3  1  SBDS_C       SBDS protein C-terminal domain
     0.0062   15.3   0.0     0.0093   14.7   0.0    1.2  1  HI0933_like  HI0933-like protein


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 !   81.4   0.0   6.3e-27   3.8e-23       5      88 .]      10      93 ..       6      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 6.3e-27
                                   EEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--HHH CS
                           SBDS  5 vrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsaee 86
                                   + ++  +krFei+v ++ + +y+e+ ++dL++vl +++i+++++kG +as +e++kafgt++   ++++ILk+Geiq+++e+
  gi|118431347|ref|NP_147753.2| 10 AWMEVRGKRFEILVRPELAFRYKEKGDVDLEDVLWTDTIYRDVRKGLKASPEEVKKAFGTSDPRRVAEKILKEGEIQLTEEQ 91
                                   5567789**************************************************************************9 PP

                                   HH CS
                           SBDS 87 rk 88
                                   r+
  gi|118431347|ref|NP_147753.2| 92 RR 93
                                   96 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   1.4e-21   8.4e-18       2      87 ..     100     185 ..      99     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.4e-21
                                    HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CCCHH CS
                         SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikdkil 81 
                                    +++ii+++a+++++p+t+rp++  +Ie al+e+++ +++ + a+sQa e+++++ + +pi+ ar  l++++p     ++ 
  gi|118431347|ref|NP_147753.2| 100 RRQIISYIARNAIDPTTGRPIPEARIEAALEEVRFPINLWRDAESQAVEAVRLIARVMPIRLARALLEVKIPPPHSGRAY 179
                                    789********************************************************************966644444 PP

                                    HHHHHH CS
                         SBDS_C  82 klieqv 87 
                                    +++  +
  gi|118431347|ref|NP_147753.2| 180 QALMRM 185
                                    444443 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.6e-06    0.0093     258     354 ..      29     124 ..      21     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-06
                                    .-TT--EEEECSTTS-...HHHHHHHHHHHTTTSBHHHHHTTTS-HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHH CS
                    HI0933_like 258 kkeeetleidllPdldaeelkaalekekekeskkslknalaellpkrlvevlleealieeedkklaqlskkelkklaeal 337
                                     +++e+  +dl   l ++++ + ++k  ++++ +++k+a+ +  p+r++e +l+e +i+ ++++ ++l +++++++++++
  gi|118431347|ref|NP_147753.2|  29 FRYKEKGDVDLEDVLWTDTIYRDVRKGLKASP-EEVKKAFGTSDPRRVAEKILKEGEIQLTEEQRRRLLEAKRRQIISYI 107
                                    56677777888888888999999999998888.9********************************************** PP

                                    HSEEE--SEE--TTT-S CS
                    HI0933_like 338 kaltvkvngteglrkae 354
                                     +  + ++  +++ +a 
  gi|118431347|ref|NP_147753.2| 108 ARNAIDPTTGRPIPEAR 124
                                    ********999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1830.47
//
Query:       gi|118431348|ref|NP_147754.2|  [L=251]
Description: hypothetical protein APE_1169.1 [Aeropyrum pernix K1]
Scores for 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   91.8   0.0    6.7e-26   91.4   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.9e-14   54.1   1.5    1.4e-13   51.8   1.5    1.8  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 !   91.4   0.0   7.5e-30   6.7e-26       1     164 [.       1     203 [.       1     204 [. 0.82

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 7.5e-30
                  Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellelapvlaVrGNnD................ 62 
                                    M+++i+SD+H+nl aleavlea+ +   d ++ +GDl  ++  p  + ++l+ +  ++VrGN+D                
  gi|118431348|ref|NP_147754.2|   1 MRVLIVSDVHGNLPALEAVLEAAGRF--DEVLALGDLvdYGPWPGEVIDVLRGLGARIVRGNHDhavgygvdcrcgeeth 78 
                                    9*********************9999..********999999999888999988**********9999999999987665 PP

                  Metallophos_2  63 .......eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl..................gvkdalaellkeaee 117
                                           e++ ++ +++     ++++ ++  lel+ + vl +Hg p                   g++    +l ++++ 
  gi|118431348|ref|NP_147754.2|  79 wlsvwfrENITQRLLGDG----DRRFLAKLPLELRLDGVLAVHGCPRnplycylypwmgreslldGLRRPGVRLGRQGAV 154
                                    543333222222333322....2333566666666667*******98**********99998888666666666666555 PP

                  Metallophos_2 118 gsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtde 164
                                    +++  v++GHtHv+   + +g++vvnPGs+g+prdgdp+ +ya+ld+++
  gi|118431348|ref|NP_147754.2| 155 VEEaTVLVGHTHVQFHLTLDGRRVVNPGSAGQPRDGDPRaGYAMLDLES 203
                                    5556******************************************986 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   1.5   1.5e-17   1.4e-13       1     122 [.       1     118 [.       1     168 [. 0.72

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.5e-17
                                    EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS...CH CS
                    Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe...gf 77 
                                    +r+l+++D+H     g+l++l+++l+ +    + d vl +GDlvd g+++ e+++ l+ l++      +++GNH+   g 
  gi|118431348|ref|NP_147754.2|   1 MRVLIVSDVH-----GNLPALEAVLEAAG---RFDEVLALGDLVDYGPWPGEVIDVLRGLGA-----RIVRGNHDhavG- 66 
                                    89********.....**********9995...55****99**********************.....9*******8552. PP

                                    HHHHHHHHHHHHHHHHHHEHH...........HCEEETSEEEEEETTEEEEEEEES CS
                    Metallophos  78 eeellnkygylgifsepwrsd...........aevfnnlplaslgsgslkvlllhG 122
                                     +++  + g+++++  +w ++             ++  lpl    +g   vl +hG
  gi|118431348|ref|NP_147754.2|  67 -YGVDCRCGEETHWLSVWFREnitqrllgdgdRRFLAKLPLELRLDG---VLAVHG 118
                                    .4566666666666666666544444433333444444454443333...666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1871.98
//
Query:       gi|118431349|ref|YP_874877.1|  [L=87]
Description: hypothetical protein APE_1169a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   15.5   3.7      0.034   14.2   1.0    2.3  3  DUF1206   Domain of Unknown Function (DUF1206)
      0.048   14.0   0.2       0.06   13.7   0.2    1.1  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


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 ?   14.2   1.0   3.8e-06     0.034      32      60 ..      10      38 ..       2      45 .. 0.87
   2 ?    0.2   0.4      0.09   8.1e+02      31      44 ..      43      56 ..      36      72 .. 0.60
   3 ?    1.6   0.1     0.033   2.9e+02      10      24 ..      57      75 ..      48      86 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                        DUF1206 32 sdgalatlleqpfGrvllglvglgllgyg 60
                                    ++ la+ +e p+G++ l+ ++l l++++
  gi|118431349|ref|YP_874877.1| 10 LREILAWAGENPGGPFALAFMALLLMAAV 38
                                   57789******************999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.09
                        DUF1206 31 gsdgalatlleqpf 44
                                   gs++   +l+e+ +
  gi|118431349|ref|YP_874877.1| 43 GSEDLANRLAEYAY 56
                                   55555555555543 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.033
                        DUF1206 10 ylllgllalqaalg....g 24
                                   y l+++++l +a +     
  gi|118431349|ref|YP_874877.1| 57 YSLVAAVLLELASTilsrD 75
                                   6777888877777533222 PP

>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   6.7e-06      0.06      20      75 ..      14      67 ..      12      74 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                           MnhB 20 lllrGhnsPGGGFqgGlilaaalillylafglee.lekllrvklaprileglgllla 75
                                   l+++G+ +PGG F+ + ++ + ++ ++la+g+e+ +++l +    ++ l+++ ll  
  gi|118431349|ref|YP_874877.1| 14 LAWAGE-NPGGPFALAFMALLLMAAVALARGSEDlANRLAEYA--YYSLVAAVLLEL 67
                                   566674.6**************************444444444..455555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 673.67
//
Query:       gi|118431350|ref|NP_147756.2|  [L=354]
Description: hypothetical protein APE_1173.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2802.79
//
Query:       gi|118431351|ref|NP_147759.2|  [L=464]
Description: hypothetical protein APE_1177.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.37
# Mc/sec: 3804.93
//
Query:       gi|14601228|ref|NP_147761.1|  [L=187]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Aeropyrum pernix K1]
Scores for complete 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  206.6   0.0    2.2e-61  206.5   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    9.6e-05   22.0   0.0    0.00013   21.6   0.0    1.1  1  Cupin_1          Cupin
     0.0007   19.3   0.0     0.0012   18.5   0.0    1.3  1  Cupin_2          Cupin domain


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.5   0.0   3.6e-65   2.2e-61       2     169 .]       9     178 ..       8     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.5 bits;  conditional E-value: 3.6e-65
                                   -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEEE CS
               dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaVD 82 
                                   +ei++++li+ ++f+D RGff+e ++++ f ++g++ +f+q nls+s kgv+RGlH+q +p++q+klv+v+ G+vldvaVD
  gi|14601228|ref|NP_147761.1|   9 LEIPDIVLIKYERFSDPRGFFAELYKRTPFLAEGIPYDFIQVNLSYSYKGVVRGLHYQLKPHEQGKLVYVLYGRVLDVAVD 89 
                                   68******************************************************************************* PP

                                   -BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---.....SS.B-- CS
               dTDP_sugar_isom  83 lRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw.....eelilS 158
                                   +RkgSp +gk+v++eL+     +l+ip+gfahGf++l+d a +lY+vt+ y ++ser+i+wnDp+l+i+w     +++i+S
  gi|14601228|ref|NP_147761.1|  90 IRKGSPWYGKHVSAELK--PGMALWIPPGFAHGFQALED-ALFLYLVTKEYFKDSERCIKWNDPNLEIKWpiiddDKVIVS 167
                                   ****************9..99****************98.9*******99*************************99**** PP

                                   HHHHT-B-HHH CS
               dTDP_sugar_isom 159 ekDkaapslae 169
                                    kD++ p l+e
  gi|14601228|ref|NP_147761.1| 168 GKDRNCPPLKE 178
                                   *******9985 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.1e-08   0.00013      40     112 ..      54     132 ..      47     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.1e-08
                                   E..TTEEEEEEEESSS-E...EEEEEESEEEEEEEETTSS.....EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEE CS
                       Cupin_1  40 l.epgglllPhyhpnate...iayvlqGegrvgfvvpgng....nrdfhkklreGdvfvvPaglvhfqynsgdepavaivv 112
                                   + ++g ++ +hy  + +e   ++yvl G+++ + v   +g     +  +++l++G ++++P+g++h +++   e+a+ +++
  gi|14601228|ref|NP_147761.1|  54 YsYKGVVRGLHYQLKPHEqgkLVYVLYGRVLDVAVDIRKGspwyGKHVSAELKPGMALWIPPGFAHGFQAL--EDALFLYL 132
                                   5566777777887655533339*********77777776689988888999*******************9..55555544 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     2e-07    0.0012      14      63 ..      68     127 ..      61     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-07
                                   ECSSSEEEEEEEEESE.EEEEEC........TE..EEEEETTEEEEE-TT-EEEEEE-SSS CS
                       Cupin_2  14 hrHpgedeffyVleGe.geltvd........ge..eveleaGdsvyfpagtpHrfrNtgde 63 
                                     H++   ++yVl G+ + + vd        g+    el++G ++ +p+g  H+f   +d+
  gi|14601228|ref|NP_147761.1|  68 KPHEQG-KLVYVLYGRvLDVAVDirkgspwyGKhvSAELKPGMALWIPPGFAHGFQALEDA 127
                                   569999.*********99999**99987777557799******************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1386.57
//
Query:       gi|118431352|ref|NP_147762.2|  [L=300]
Description: dTDP-4-dehydrorhamnose reductase [Aeropyrum pernix K1]
Scores for complete 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-86  289.3   0.0    2.9e-86  289.1   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    1.5e-28   99.9   0.0    1.9e-28   99.6   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
    5.7e-18   65.4   0.1    1.2e-17   64.3   0.1    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.1e-13   49.5   0.3    1.3e-08   34.4   0.0    2.7  2  NAD_binding_4    Male sterility protein
      7e-13   48.4   0.0    5.5e-11   42.1   0.0    2.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    6.5e-09   35.2   0.0    1.1e-08   34.5   0.0    1.4  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0015   18.5   0.0     0.0028   17.6   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.027   14.4   0.2       0.72    9.7   0.2    2.7  3  KR               KR domain
      0.047   13.2   0.0       0.21   11.1   0.0    2.0  2  NmrA             NmrA-like family
      0.054   12.9   0.0       0.13   11.7   0.0    1.6  1  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.1   0.0   1.6e-89   2.9e-86       1     285 [.       1     294 [.       1     296 [. 0.97

  Alignments for each domain:
  == domain 1  score: 289.1 bits;  conditional E-value: 1.6e-89
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                    mk+lvtG++G+lG++L++ql ++g++v+++ ++            +++l+d++++++l++++kpd+v+++AAyt+vD +E
  gi|118431352|ref|NP_147762.2|   1 MKLLVTGGTGLLGYNLVQQLLKKGYSVYPTYNKntpfklagarwsKVNLEDPSQLTQLFRDIKPDAVIHTAAYTDVDGCE 80 
                                    89****************************55569********************************************* PP

                                    HSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH..H-SSEEEE CS
                  RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla..agkkaliv 146
                                     ++e+ay++n  a++++A++aa++g+lLi+vStDyVFdG+k + Y+e+++++P+n+YG +Kl+GE a l+  +++++l+v
  gi|118431352|ref|NP_147762.2|  81 LHRERAYRINFLASMTVARLAARHGSLLIYVSTDYVFDGDKGM-YREEEAPNPINYYGLSKLLGEVATLSamDKENVLVV 159
                                    ****************************************776.*************************95566799*** PP

                                    EE-SEESS...SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHH CS
                  RmlD_sub_bind 147 Rtswvyge...kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlef 223
                                    R+s +yg     ++nf  ++l+++ + ee++ + Dq+ sPT++  l++ l+++le++++     gv+Hla+e+ +s+lef
  gi|118431352|ref|NP_147762.2| 160 RVSGLYGYsptGKRNFGINVLEKLLRGEEVRAFYDQYLSPTYTYFLSRRLIDVLEREIR-----GVLHLAGER-LSRLEF 233
                                    ******99787899********************************************8.....*******98.****** PP

                                    HHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHHH CS
                  RmlD_sub_bind 224 ArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlkel 285
                                    A+ i+k +gad+e +kpis++e++ pA+RP++S+Ldt+++++  g++l++++e++k++++ +
  gi|118431352|ref|NP_147762.2| 234 AQLIAKVLGADAELIKPISMKEANLPARRPRDSSLDTTMAKKL-GLELPSQEESVKHFVNIY 294
                                    ****************************************999.9*************9876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   1.1e-31   1.9e-28       2     201 ..       4     190 ..       3     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 1.1e-31
                                    EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHHHH CS
                      Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaass 81 
                                    lVtG+tG++G +lv++ll+kgy v    ++++ ++ a    +++ +++l d+s+l++lf++ +pdavih Aa+ +v+   
  gi|118431352|ref|NP_147762.2|   4 LVTGGTGLLGYNLVQQLLKKGYSVYPTYNKNTPFKLA---GARWSKVNLEDPSQLTQLFRDIKPDAVIHTAAYTDVDGCE 80 
                                    9*****************************8888755...558************************************* PP

                                    HSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT CS
                      Epimerase  82 edpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyg 161
                                     ++++ +++n+  +++++  a ++g   l+++s++ v+  d+ + +ee++     +p + Y+++Kl+ge  + ++ ++  
  gi|118431352|ref|NP_147762.2|  81 LHRERAYRINFLASMTVARLAARHGS-LLIYVSTDYVFDGDKGMYREEEA----PNPINYYGLSKLLGEVATLSAMDKE- 154
                                    **************************.************99996466666....79******************99999. PP

                                    -EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEE CS
                      Epimerase 162 lnaiilrlfnlyGprngegevsrvipalirkilegkqevt 201
                                     n++++r++ lyG    ++  +++   +++k+l+g+ ev 
  gi|118431352|ref|NP_147762.2| 155 -NVLVVRVSGLYGYS--PTGKRNFGINVLEKLLRGE-EVR 190
                                    .8************9..5557888888888888888.665 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 !   64.3   0.1   6.7e-21   1.2e-17       1     194 [.       4     177 ..       4     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 6.7e-21
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG++G  G +l+++Ll+kgy v+ + ++++ f+      la           ++ k++l+D s+l++l+++++pd+v+
  gi|118431352|ref|NP_147762.2|   4 LVTGGTGLLGYNLVQQLLKKGYSVYPTYNKNTPFK------LAG---------ARWSKVNLEDPSQLTQLFRDIKPDAVI 68 
                                    9*************************998888877......332.........2467899******************** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlya 160
                                    + AA   Vd    + e+ +++n+l+ +++  ++ ++g      ++ +St+ v+    +  ++E+   +P + Y+ +Kl  
  gi|118431352|ref|NP_147762.2|  69 HTAAYTDVDGCELHRERAYRINFLASMTVARLAARHGS----LLIYVSTDYVFDGD-KGMYREEEAPNPINYYGLSKLLG 143
                                    **********99999**************999999985....7999*******444.5788899999************* PP

                                    HHHHHHHHHHH---EEEEEE-EEESTTS-TTSCC CS
                  GDP_Man_Dehyd 161 dwivvnyreayglfavngilfnhesprrgetfvt 194
                                    +  + +  ++ ++ +v       +sp  +++f  
  gi|118431352|ref|NP_147762.2| 144 EVATLSAMDKENVLVVRVSGLYGYSPTGKRNFGI 177
                                    *********9999999888888888887777755 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   4.1e-05     0.073       1      21 [.       5      25 ..       5      31 .. 0.88
   2 !   34.4   0.0   7.2e-12   1.3e-08      89     216 ..      65     174 ..      51     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.1e-05
                                   EE-TTSHHHHHHHHHHHHHS- CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                   +TG+TG LG  L+++LL++  
  gi|118431352|ref|NP_147762.2|  5 VTGGTGLLGYNLVQQLLKKGY 25
                                   7****************9865 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 7.2e-12
                                    -EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......HHH--E CS
                  NAD_binding_4  89 dviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeekldede 165
                                    d++ih aA +++d+   + ++++r+N ++   v +la++  +l  l++vST yv + ++g                    
  gi|118431352|ref|NP_147762.2|  65 DAVIHTAAYTDVDGcelHRERAYRINFLASMTVARLAARHGSL--LIYVSTDYVFDGDKGMY-----------------R 125
                                    89**********998666778*****************77666..******88888887532.................3 PP

                                    EEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST--- CS
                  NAD_binding_4 166 raklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwin 216
                                    +++  +  n Y  sK l+E    +a+  ++ +v++vR+s ++g s tG  n
  gi|118431352|ref|NP_147762.2| 126 EEEAPNPINYYGLSKLLGEVATLSAM--DKENVLVVRVSGLYGYSPTGKRN 174
                                    456677889*****************..567789***********999655 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   3.1e-14   5.5e-11       2     156 ..       4     154 ..       3     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.1e-14
                                    EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
                Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                    lvtG++G +G +lv+q+lkk  +    ++++    ++++       +  k          +++d ++l+++++++k+d+v
  gi|118431352|ref|NP_147762.2|   4 LVTGGTGLLGYNLVQQLLKKGYSVYPTYNKNT--PFKLAGAR---WS--K---------VNLEDPSQLTQLFRDIKPDAV 67 
                                    89**************9999876554444332..22333221...11..2.........3578***************** PP

                                    EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEG......G.......GSS--SHHHHHHHHHHHH CS
                Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStD......K.......AvnPtnvmGatKrlaekl 148
                                    +h+AA+  V  +e +   a + N l++++v++ a ++g + ++++StD      K       A nP+n +G++K+l e  
  gi|118431352|ref|NP_147762.2|  68 IHTAAYTDVDGCELHRERAYRINFLASMTVARLAARHG-SLLIYVSTDyvfdgdKgmyreeeAPNPINYYGLSKLLGEVA 146
                                    **********************************9998.6799***9855555534444444789*************98 PP

                                    HHHGGG-- CS
                Polysacc_synt_2 149 lqalakes 156
                                    + ++ +++
  gi|118431352|ref|NP_147762.2| 147 TLSAMDKE 154
                                    87766555 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 !   34.5   0.0     6e-12   1.1e-08       1     162 [.       4     152 ..       4     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 6e-12
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegv..dvvihlaslvd 78 
                                    +vtGg+G lG +lv++L++ +      v+   ++++     +k+  +   ++ + d ++l++  +++  d+vih+a+++d
  gi|118431352|ref|NP_147762.2|   4 LVTGGTGLLGYNLVQQLLKKGY----SVYPTYNKNTP----FKLAGARWSKVNLEDPSQLTQLFRDIkpDAVIHTAAYTD 75 
                                    69*****************995....44444444433....555555599999************984469********* PP

                      3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklv 157
                                    v g +l++++ +++n     +v   + ++g   l+Y+S+ + v++    + +   +Ee    +++ + y  sK l E + 
  gi|118431352|ref|NP_147762.2|  76 VDGcELHRERAYRINFLASMTVARLAARHG-SLLIYVST-DYVFD--GDKGMY-REEEA---PNPINYYGLSKLLGEVAT 147
                                    ***99**********************999.79****98.77888..445555.44544...456677999999999888 PP

                      3Beta_HSD 158 lkaNg 162
                                    l+a +
  gi|118431352|ref|NP_147762.2| 148 LSAMD 152
                                    88877 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 !   17.6   0.0   1.6e-06    0.0028       1     102 [.       7     117 ..       7     178 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-..SEEEES---TCC..... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkga..daVvsalggggk..... 73 
                                    G+tG  G  lv++ll++g ++v     +   ++ l   +g++  +++++d+++l++ ++++  daV+ +++ ++      
  gi|118431352|ref|NP_147762.2|   7 GGTGLLGYNLVQQLLKKG-YSVYPTYNKNTPFK-L---AGARWSKVNLEDPSQLTQLFRDIkpDAVIHTAAYTDVdgcel 81 
                                    9****************5.99988777777776.4...69*******************99667****997666655554 PP

                                    .HHHH......HHHHHHHHHHCT--EEEEEEETTTT CS
                 NAD_binding_10  74 .deeg......aknivdaakeagvkRfvlvsaigvg 102
                                     +e++      a  +v+ + + + + +++vs+  v 
  gi|118431352|ref|NP_147762.2|  82 hRERAyrinflASMTVARLAARHGSLLIYVSTDYVF 117
                                    433335556665555555555555666666665555 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0004      0.72       4      24 ..       4      24 ..       2      28 .. 0.92
   2 ?   -0.7   0.0      0.66   1.2e+03      57      92 ..      44      74 ..      38      87 .. 0.78
   3 ?    0.3   0.0      0.31   5.6e+02      78      90 ..     213     225 ..     206     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0004
                                   EEETTTSHHHHHHHHHHHHHH CS
                             KR  4 litGGlGgLGlelarwlaekg 24
                                   l+tGG+G LG  l+++l++kg
  gi|118431352|ref|NP_147762.2|  4 LVTGGTGLLGYNLVQQLLKKG 24
                                   9******************99 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.66
                                   E----TT-HHHHHHHHHHHHHHSS---EEEE----- CS
                             KR 57 vvaaDvsdkdavealleeikaeeppikGvihaAgvl 92
                                   + ++ + d++++++l+++ik ++     vih+A  +
  gi|118431352|ref|NP_147762.2| 44 WSKVNLEDPSQLTQLFRDIKPDA-----VIHTAAYT 74
                                   56778889999999999998555.....88888765 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.31
                                    HSS---EEEE--- CS
                             KR  78 eeppikGvihaAg 90 
                                     e++i+Gv+h Ag
  gi|118431352|ref|NP_147762.2| 213 LEREIRGVLHLAG 225
                                    4579********8 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.21       2      63 ..       4      60 ..       3      82 .. 0.73
   2 ?   -1.0   0.0      0.59   1.1e+03     204     228 ..     220     244 ..     210     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                   EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHT CS
                           NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealk 63
                                   lv+G+TG +G  +v+ llk+g++v      ++ ++ + +k aG+   k +l+d + l ++++
  gi|118431352|ref|NP_147762.2|  4 LVTGGTGLLGYNLVQQLLKKGYSVY-----PTYNKNTPFKLAGARWSKVNLEDPSQLTQLFR 60
                                   8**********************96.....44444555566666666666666666666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                                    EEEE-SEEE-HHHHHHHHHHHHTS- CS
                           NmrA 204 riklagntlsgneivelfekkigkt 228
                                    +++lag+ ls  e ++l+ k++g  
  gi|118431352|ref|NP_147762.2| 220 VLHLAGERLSRLEFAQLIAKVLGAD 244
                                    57899****************9975 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.1e-05      0.13       4     120 ..       4     102 ..       2     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                                    EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE CS
                      adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvn 83 
                                    lvtG+++ +G++++++l+k+G++v+ + +++ +      +l      a   +v+++d +++ +l++++     k d++++
  gi|118431352|ref|NP_147762.2|   4 LVTGGTGLLGYNLVQQLLKKGYSVYPTYNKNTPF-----KLAG----ARWSKVNLEDPSQLTQLFRDI-----KPDAVIH 69 
                                    8***********************9855555544.....3332....566677888888888887777.....4566666 PP

                                    ---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHH CS
                      adh_short  84 NAGitgsgpfselseeewervievNltgvflltravl 120
                                     A+ t      + +e   er + +N+ + + ++r+++
  gi|118431352|ref|NP_147762.2|  70 TAAYT----DVDGCELHRERAYRINFLASMTVARLAA 102
                                    66663....3344444456666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2168.97
//
Query:       gi|14601230|ref|NP_147763.1|  [L=330]
Description: dTDP-glucose 4,6-dehydratase [Aeropyrum pernix K1]
Scores for complete 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-77  260.4   0.0    3.3e-77  260.1   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.6e-69  234.0   0.0      2e-69  233.8   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.5e-20   72.7   0.0    2.8e-20   72.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    5.2e-20   71.6   0.0    6.4e-20   71.3   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      6e-16   58.4   0.0    7.1e-15   54.9   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.2e-13   49.5   0.0    4.6e-12   45.7   0.0    2.2  1  NAD_binding_4    Male sterility protein
     0.0001   21.8   0.0     0.0002   20.9   0.0    1.4  1  adh_short        short chain dehydrogenase
    0.00095   19.4   0.0     0.0021   18.3   0.0    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0059   16.5   0.0      0.011   15.7   0.0    1.3  1  KR               KR domain
  ------ inclusion threshold ------
       0.15   12.2   0.0       0.27   11.4   0.0    1.4  1  DapB_N           Dihydrodipicolinate reductase, N-terminus


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 !  260.1   0.0   1.8e-80   3.3e-77       1     331 [.       4     303 ..       4     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 260.1 bits;  conditional E-value: 1.8e-80
                                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                 GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                   L+TG+aGfiGs +++++++     + +  +++++++gr+e+l +     + +++ +++gD+ D+++  r+l e +pd v+n
  gi|14601230|ref|NP_147763.1|   4 LVTGGAGFIGSSFVRYIVNTTD--WEVLVYDKLTYAGRLENLHD-----VIDRIGFMRGDIADEEQFGRVLTEFEPDVVVN 77 
                                   9*****************9843..44556889999******975.....3479**************************** PP

                                   --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSS..B-TTS-----SHHHHHHHHH CS
                 GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevp..qtEttpfyPrsPYaaaKlya 160
                                   +AA+ hVd+s+++P+ ++++n++G++++Leair+    +++ ++++St+EvYG++ ++    tE+ p++P sPY+a+K++ 
  gi|14601230|ref|NP_147763.1|  78 FAAETHVDRSINEPAPFMRTNIIGVFTILEAIRKR--IDQIVLLHVSTDEVYGDLWNTGkeATESDPLNPSSPYSASKASG 156
                                   *********************************95..479***************76552379****************** PP

                                   HHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS CS
                 GDP_Man_Dehyd 161 dwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdk 241
                                   d ++++y ++ygl   + +  n+++p++    v+++i+r++ ri++gk + +++G+++++Rdw++v+D+++a++ +l+++ 
  gi|14601230|ref|NP_147763.1| 157 DLLIKAYGRTYGLKYRIVRPCNNYGPYQ---HVEKLIPRTIIRILHGKPP-VIYGDGSQIRDWLYVEDTARAIHVVLEKGV 233
                                   ***************************6...799*************965.569************************996 PP

                                   ---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH----S CS
                 GDP_Man_Dehyd 242 pedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgWkpk 322
                                          +ge ++v + +  ++++++ +i  +             gk +  + + + rpge++++++ ++k++ +LgW p 
  gi|14601230|ref|NP_147763.1| 234 -------DGEIYNVCGGMASTVKDIVVNILES------------MGKPRDYLVYGKSRPGEDRRYAMKCDKIR-NLGWAPH 294
                                   .......8*****************9988654............355566677899****************9.9****** PP

                                   S-HHHHHHH CS
                 GDP_Man_Dehyd 323 vsfeelvre 331
                                   v+++e+++ 
  gi|14601230|ref|NP_147763.1| 295 VTLKEGLKI 303
                                   ******985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.8   0.0   1.1e-72     2e-69       1     241 []       3     241 ..       3     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 1.1e-72
                                   EEEETTTSHHHHHHHHHHHHCT.SEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                     Epimerase   1 ilVtGatGfiGsalvkallekg.yevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                   +lVtG++GfiGs +v+++ + + +ev++ d+l++a++ ++l+d+     ++++d+ d++++ r++ e++pd+v+++Aa+ +
  gi|14601230|ref|NP_147763.1|   3 VLVTGGAGFIGSSFVRYIVNTTdWEVLVYDKLTYAGRLENLHDVidriGFMRGDIADEEQFGRVLTEFEPDVVVNFAAETH 83 
                                   79******************9999********************************************************* PP

                                   HHHHHHSHHHHHHHHTHHHHHHHHHHHHH..TCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                     Epimerase  77 vaassedpadfieknlqgtlnlleaarka..gvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                   v++s+++pa f+++n++g+ ++lea+rk+  ++  ll++s++evYG+  ++  +e t+++pl+p+spY+a+K+ g+ l++a
  gi|14601230|ref|NP_147763.1|  84 VDRSINEPAPFMRTNIIGVFTILEAIRKRidQI-VLLHVSTDEVYGDLWNT-GKEATESDPLNPSSPYSASKASGDLLIKA 162
                                   ***************************998455.***************97.9**************************** PP

                                   HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTE CS
                     Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkge 236
                                   y ++ygl++ i+r++n+yGp+   ++v+++ip+ i +il+gk + +++gdg++ Rd+lyveD a+ai+ vle+   g +ge
  gi|14601230|ref|NP_147763.1| 163 YGRTYGLKYRIVRPCNNYGPY---QHVEKLIPRTIIRILHGK-PPVIYGDGSQIRDWLYVEDTARAIHVVLEK---GVDGE 236
                                   *********************...99****************.******************************...999** PP

                                   EEEES CS
                     Epimerase 237 iyniG 241
                                   iyn++
  gi|14601230|ref|NP_147763.1| 237 IYNVC 241
                                   ***96 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 !   72.6   0.0   1.6e-23   2.8e-20       1     233 [.       1     261 [.       1     306 [. 0.85

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 1.6e-23
                                   EEEEEESTTSHHHHHHHHHC.TTTSEEEEEE-TT...................T--TTSHHHHHHHHHHH--SEEEE---- CS
                 RmlD_sub_bind   1 mkilvtGanGqlGseLakql.aeeglevlaltre...................eldltdaeavaellkeakpdvvvnaAAy 61 
                                   m++lvtG+ G +Gs  ++ + +  ++evl  ++                    + d++d+e+  ++l e++pdvvvn AA 
  gi|14601230|ref|NP_147763.1|   1 MRVLVTGGAGFIGSSFVRYIvNTTDWEVLVYDKLtyagrlenlhdvidrigfmRGDIADEEQFGRVLTEFEPDVVVNFAAE 81 
                                   89*************988651669*******98899********************************************* PP

                                   --HHHHHHSHHHHHHHHTHHHHHHHHHHHHC..T-EEEEEEEGGGS-S-..TTS-B-TTS----SSHHHHHHHHHHHHHHH CS
                 RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaav..galLihvStDyVFdGe..kkrpYeeddetsPlnvYGrtKlaGEqavla 138
                                   t vD+  +e++  ++ n  +v ++ ea +++  +++L+hvStD V+     + ++ +e+d+ +P + Y ++K+ G   ++a
  gi|14601230|ref|NP_147763.1|  82 THVDRSINEPAPFMRTNIIGVFTILEAIRKRidQIVLLHVSTDEVYGDLwnTGKEATESDPLNPSSPYSASKASGDLLIKA 162
                                   ***************************998755899**********7646677779************************9 PP

                                   ....H-SSEEEEEE-SEESS...SSS-HHHHHHHHHHH-SEE.EEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE CS
                 RmlD_sub_bind 139 ....agkkalivRtswvyge...kgknfvktmlrlakereel.kvvaDqlgsPTsardlAevllqllekaaeekelagvyH 211
                                       +g k+ ivR    yg     +k   +t++r ++ + ++      q++   +++d A+++  +lek ++     ++y 
  gi|14601230|ref|NP_147763.1| 163 ygrtYGLKYRIVRPCNNYGPyqhVEKLIPRTIIRILHGKPPViYGDGSQIRDWLYVEDTARAIHVVLEKGVD----GEIYN 239
                                   6655667899****9999884334567889999988666655144557999999999999999999999997....78888 PP

                                   ---BS-EEHHHHHHHHHHHHCH CS
                 RmlD_sub_bind 212 lanegetswlefArailkeaga 233
                                   + +  + +  ++   il+++g+
  gi|14601230|ref|NP_147763.1| 240 VCGGMASTVKDIVVNILESMGK 261
                                   8888777777777777777766 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 !   71.3   0.0   3.5e-23   6.4e-20       1     230 [.       4     231 ..       4     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 3.5e-23
                     3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskv.nvkkviegDvtdkdkleealegv..dvvihlaslvd 78 
                                   +vtGgaGF+G++ v+ +v++ + +ev v+D+ +    le+l+ v +++ ++ gD+ d+++  ++l +   dvv+  a+ + 
  gi|14601230|ref|NP_147763.1|   4 LVTGGAGFIGSSFVRYIVNTTD-WEVLVYDKLTYAGRLENLHDViDRIGFMRGDIADEEQFGRVLTEFepDVVVNFAAETH 83 
                                   69*******************7.*******9888888888777615555****************976348********** PP

                     3Beta_HSD  79 vag.kltedeimkvnvkGTrnvleacvka.gvrvlvYtSsaevvgpnslgeeilngdEeleyesl.hqdaypesKalaEkl 156
                                   v     +   +m+ n+ G  ++lea +k  +  vl+++S+ ev g+         g+E +e ++l ++++y+ sKa   +l
  gi|14601230|ref|NP_147763.1|  84 VDRsINEPAPFMRTNIIGVFTILEAIRKRiDQIVLLHVSTDEVYGD-----LWNTGKEATESDPLnPSSPYSASKASG-DL 158
                                   *9834556789**************987613445678888888887.....67779999988776599*******976.67 PP

                     3Beta_HSD 157 vlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlak..lglalfkigdeevlsdrvYvgNvawa.hilAar 230
                                   ++ka grt      l    +Rp   yG+++++ +   +++++  +g+  + +gd +++ d+ Yv+  a a h++  +
  gi|14601230|ref|NP_147763.1| 159 LIKAYGRT---Y-GLKYRIVRPCNNYGPYQHVEKLIPRTIIRilHGKPPVIYGDGSQIRDWLYVEDTARAiHVVLEK 231
                                   77899933...3.4777789*********9876555555554226668899****************9873665555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0     4e-18   7.1e-15       1     251 [.       3     263 ..       3     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 4e-18
                                   EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
               Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                   vlvtG++G iGs++vr i++++  +++++++  ++    + e+ +++ + ++ +    + gd++d+e+  ++l+e+++dvv
  gi|14601230|ref|NP_147763.1|   3 VLVTGGAGFIGSSFVRYIVNTTDWEVLVYDKLTYAG---RLENLHDVID-RIGF----MRGDIADEEQFGRVLTEFEPDVV 75 
                                   8****************************9876543...3332233333.4544....48********************* PP

                                   EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEE..EEEGGG................SS--SHHHHHHHH CS
               Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvl..iStDKA................vnPtnvmGatKrl 144
                                   ++ AA  hV    ++p+  ++tN++g  +++e ai+++++++vl  +StD                   nP + + a+K+ 
  gi|14601230|ref|NP_147763.1|  76 VNFAAETHVDRSINEPAPFMRTNIIGVFTILE-AIRKRIDQIVLlhVSTDEVygdlwntgkeatesdpLNPSSPYSASKAS 155
                                   **************************998887.67889999997447***7522222222223333335788899999999 PP

                                   HHHHHHHGGG--SSS--EEEEEEE-EETTGTTSS...HHHHHHHHHTT.SSEEES-TT-EEEEE-HHHHHHHHHHHHHH-- CS
               Polysacc_synt_2 145 aekllqalakeseekktkfvvvRfGNVlgSrGSv...iplFkkqikeg.gpvtvTdpemtRyfmtieeavqLvlqalalak 221
                                    ++l+ a+ ++      k+ +vR  N  g    v   ip    +i +g  pv   d + +R ++ +e++++ +   l+++ 
  gi|14601230|ref|NP_147763.1| 156 GDLLIKAYGRTY---GLKYRIVRPCNNYGPYQHVeklIPRTIIRILHGkPPVIYGDGSQIRDWLYVEDTARAIHVVLEKGV 233
                                   999999999998...799*****999999876654448988889999945688899************************* PP

                                   SS-EEEE--.-EEEHHHHHHHH........ CS
               Polysacc_synt_2 222 ggeifvldmGepvkivdlakalielsglee 251
                                   +gei+ +  G + +++d++ +++e +g+  
  gi|14601230|ref|NP_147763.1| 234 DGEIYNVCGGMASTVKDIVVNILESMGKPR 263
                                   *********************999998543 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   2.6e-15   4.6e-12       1     204 [.       5     177 ..       5     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.6e-15
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG--HHHH CS
                 NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLseedl 81 
                                   +TG+ GF+G+ +++ +++tt+  +  +lv  k   + + Rl       +l +     + +ri ++ GD+++++      ++
  gi|14601230|ref|NP_147763.1|   5 VTGGAGFIGSSFVRYIVNTTD-WE--VLVYDK--LTYAGRL------ENLHD-----VIDRIGFMRGDIADEE------QF 63 
                                   79***************9996.24..444433..4566777......33443.....458*********9653......44 PP

                                   HHHHH..H--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H.... CS
                 NAD_binding_4  82 qelae..evdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegek 157
                                    ++    e dv+++ aA +++d++++e   ++r+N+ G+  +le  +k+  + vllhvST  v+g+  ++           
  gi|14601230|ref|NP_147763.1|  64 GRVLTefEPDVVVNFAAETHVDRSINEpapFMRTNIIGVFTILEAIRKRIDQIVLLHVSTDEVYGDLWNT----------- 133
                                   4443301679***************998889*************999877777*******8888777755........... PP

                                   ..HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE- CS
                 NAD_binding_4 158 eekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRps 204
                                       +e ++++  + +  Y+ sKa ++ l+++++r  gl+  ivRp 
  gi|14601230|ref|NP_147763.1| 134 ---GKEATESDPLNPSSPYSASKASGDLLIKAYGRTYGLKYRIVRPC 177
                                   ...57889999999*******************************96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.1e-07    0.0002       3     166 ..       3     166 ..       1     175 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                   EEEESTTSHHHHHHHHHHHH.TT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                     adh_short   3 vlvtGassGIGraiakelak.eGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                   vlvtG+++ IG  +++ +++  +++v+v+d+   +    +++l++  +++ ++++D++d+e+  +++ +      + dv+v
  gi|14601230|ref|NP_147763.1|   3 VLVTGGAGFIGSSFVRYIVNtTDWEVLVYDKLTYAG--RLENLHDVIDRIGFMRGDIADEEQFGRVLTEF-----EPDVVV 76 
                                   9***************99852799**9999885544..88889988889**************9999998.....66**** PP

                                   E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.........HCTTEEEEEEEEGGG.TSB-TTBHHHHHHH CS
                     adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpaml.........kqssGrIvnvsSvag.kvpvagvaaYsAsK 153
                                   n A+ t  +     s +e    + +N+ gvf + +a+ + ++         ++  G+  n++  a+   p++  ++YsAsK
  gi|14601230|ref|NP_147763.1|  77 NFAAET--HVDR--SINEPAPFMRTNIIGVFTILEAIRKRIDqivllhvstDEVYGDLWNTGKEATeSDPLNPSSPYSASK 153
                                   ***993..4444..4444556677777777777777766654555889999999***********97789999******** PP

                                   HHHHHHHHHHHHH CS
                     adh_short 154 aavagltrslake 166
                                   a  + l+++  + 
  gi|14601230|ref|NP_147763.1| 154 ASGDLLIKAYGRT 166
                                   *999999987765 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 !   18.3   0.0   1.2e-06    0.0021       3      80 ..       5      82 ..       3      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                  EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-SSGG CS
               Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnlsppi 80
                                  + G+ G++G++++++++++ d+  e+ v d+     + +  +    r+ ++  d++++e+   ++l+e   d+vvn +  +
  gi|14601230|ref|NP_147763.1|  5 VTGGaGFIGSSFVRYIVNTTDW--EVLVYDKLTYAGRLENLHDVIDRIGFMRGDIADEEQ-FGRVLTEFepDVVVNFAAET 82
                                  55555*****************..9***999766655555455789**************.***************98765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.9e-06     0.011       3      76 ..       3      71 ..       2      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.9e-06
                                  EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHH CS
                            KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeik 76
                                  +l+tGG+G +G +++r +++    ++++  +      + + ++++l++   ++ +++ D++d+++  ++l+e++
  gi|14601230|ref|NP_147763.1|  3 VLVTGGAGFIGSSFVRYIVNTTDWEVLVYDKL-----TYAGRLENLHDVIDRIGFMRGDIADEEQFGRVLTEFE 71
                                  69***********************9999888.....45568999***999*****************999987 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.27       1      81 [.       1      85 [.       1     104 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTC..STTTTTBHHHHSSSS--S-BEBSSHHHHHHH..-SEEEE-S-HHH CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrke..selegkdagellglgklgvavtddleevlek..advliDFTtpea 79
                                  ++v+v+G +G +G++ v+ + +++d e+    + +      + +d+ + +g+ + ++a ++++ +vl++   dv++ F + + 
  gi|14601230|ref|NP_147763.1|  1 MRVLVTGGAGFIGSSFVRYIVNTTDWEVLVYDKLTYagRLENLHDVIDRIGFMRGDIADEEQFGRVLTEfePDVVVNFAAETH 83
                                  89*********************99997654333332133344577788888899999999*******98899*****98776 PP

                                  HH CS
                        DapB_N 80 vl 81
                                  v 
  gi|14601230|ref|NP_147763.1| 84 VD 85
                                  65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2341.09
//
Query:       gi|14601231|ref|NP_147764.1|  [L=355]
Description: glucose-1-phosphate thymidylyltransferase [Aeropyrum pernix K1]
Scores for complete 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-41  142.0   0.0    2.9e-41  141.7   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    1.2e-10   41.9   0.0    1.8e-10   41.4   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0038   17.0   0.0     0.0061   16.3   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
     0.0045   17.3   3.3       0.02   15.2   2.2    2.1  2  Bactofilin       Polymer-forming cytoskeletal
  ------ inclusion threshold ------
       0.32   10.8   3.1        2.4    8.0   0.1    3.4  3  Hexapep          Bacterial transferase hexapeptide (six repea


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   0.0   8.1e-45   2.9e-41       1     244 [.       3     236 ..       3     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 8.1e-45
                                   EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
               NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                   k++ILa G+G+RL+P t +++k l+p lgk ++iq+ +  l++ ++++ i v+  +    ++e l+e s+fg + ++++++
  gi|14601231|ref|NP_147764.1|   3 KGLILAAGEGSRLRPFTFSRPKHLIPLLGK-PIIQYAIDDLVSINVRD-IGVVVGYFGDKIKEFLGEDSRFGAKFTYIVQK 81 
                                   689***************************.*****************.77777799999********************* PP

                                   S--BGGHHHHHTHH..HHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEE CS
               NTP_transferase  82 egkgtAdAvalaae..lledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrve 160
                                   ++ g+A+A++ a++  ++++e     +++Lg+++l +  +++ vk+  e+++  +v +++++v+++ ++G++   + g++ 
  gi|14601231|ref|NP_147764.1|  82 KRLGIAHAIYRAIKqgFIDKE----FIVYLGDNILSG-GISRHVKSWGEAGS--EVHILLTKVRDPGRFGIAVLRD-GKIL 154
                                   *********988762244444....488898888888.**************..9*****************9998.8*** PP

                                   EEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHH CS
               NTP_transferase 161 rfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslle 240
                                   ++vEKP+e   s+la+ G+Y+f    l+ +a   l++++rge eitd+++  +++g++    l +++  W+DvGt + ll+
  gi|14601231|ref|NP_147764.1| 155 KLVEKPQEHI-SDLAVVGVYMFRDPELVAKAFsTLKPSWRGEYEITDLIQWFVDKGYKVTFSLVTGW--WKDVGTYEGLLD 232
                                   ********99.***********87666666666**************************999999*6..***********9 PP

                                   HHHH CS
               NTP_transferase 241 anek 244
                                   a   
  gi|14601231|ref|NP_147764.1| 233 AIYL 236
                                   9765 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 !   41.4   0.0     5e-14   1.8e-10       1      98 [.       4     112 ..       4     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5e-14
                                   EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-E..EE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrv..vededpg 69 
                                   ++iLA+G++sR+      ++K l+pl gkp++++++d l + +v+++ vv+g+  +++++ l    r+g+++  ++++ + 
  gi|14601231|ref|NP_147764.1|   4 GLILAAGEGSRLRpftfsRPKHLIPLLGKPIIQYAIDDLVSINVRDIGVVVGYfgDKIKEFLgedSRFGAKFtyIVQK-KR 83 
                                   69**********7554436**********************************9988887663333445554115554.58 PP

                                   -SHHHHHHHHHHH.H.SSSCEEEEETT-TT CS
                  NTP_transf_3  70 kgplaslaaalra.aadadavlvlacDmPl 98 
                                    g++++++ a+++    ++ ++v ++D +l
  gi|14601231|ref|NP_147764.1|  84 LGIAHAIYRAIKQgF-IDKEFIVYLGDNIL 112
                                   9*********99853.56777777777655 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 !   16.3   0.0   1.7e-06    0.0061       4      52 ..       5      55 ..       2      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.7e-06
                                  EEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE- CS
                          IspD  4 vipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvs 52
                                  +i AAG+G+R++     +pK ++ l g+++++ ++d l +  +v  i vvv 
  gi|14601231|ref|NP_147764.1|  5 LILAAGEGSRLRpftFSRPKHLIPLLGKPIIQYAIDDLVS-INVRDIGVVVG 55
                                  799*******96333699********************99.67788888775 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.9   2.3e-05     0.082      20      49 ..     244     271 ..     239     275 .. 0.87
   2 !   15.2   2.2   5.6e-06      0.02       8      95 ..     252     341 ..     250     344 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                    Bactofilin  20 ridGkveGdieakgklvvgeggkvegnika 49 
                                   r++Gk+eG++  +g++vv+eg+ veg+++ 
  gi|14601231|ref|NP_147764.1| 244 RVEGKIEGEV--RGRVVVEEGAIVEGTVHG 271
                                   8999999999..667************985 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.6e-06
                    Bactofilin   8 kikGelevegdlridGkveGdieakgklvvgeggkvegnikaee..vvvaGtvkGnveaee.kvelkktakveGdikaksl 85 
                                   +++G + ve++  ++G+v+G  + ++++ +g++g ve  ++ e+   +++Gtv  ++  +e ++ l+ +a++  ++  ++ 
  gi|14601231|ref|NP_147764.1| 252 EVRGRVVVEEGAIVEGTVHGPAYIGKDVYIGRSGLVEHYVSMEQgsRIISGTVARSMILDEsELYLN-KARLVDSVVGPKS 331
                                   6889999999999999999999999999999999999999985444889999998888887555555.5666666666665 PP

                    Bactofilin  86 eieegavfeG 95 
                                    i+++ ++ G
  gi|14601231|ref|NP_147764.1| 332 IIKSNREIYG 341
                                   5666555555 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.13   4.5e+02      16      30 ..     253     267 ..     252     270 .. 0.78
   2 ?    8.0   0.1   0.00067       2.4      16      30 ..     269     283 ..     268     289 .. 0.88
   3 ?   -0.2   0.0      0.27   9.6e+02       2      13 ..     325     336 ..     324     345 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.13
                                   EETTEEE-TTEEEET CS
                       Hexapep  16 iggnVkIGdnvkIga 30 
                                   ++g V++ ++++++ 
  gi|14601231|ref|NP_147764.1| 253 VRGRVVVEEGAIVEG 267
                                   678889999998876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00067
                                   EETTEEE-TTEEEET CS
                       Hexapep  16 iggnVkIGdnvkIga 30 
                                   ++g++ IG++v+Ig+
  gi|14601231|ref|NP_147764.1| 269 VHGPAYIGKDVYIGR 283
                                   789999*******98 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.27
                                   EEEETTEEE-TT CS
                       Hexapep   2 tvIGsnvlIgpf 13 
                                   +v+G +++I ++
  gi|14601231|ref|NP_147764.1| 325 SVVGPKSIIKSN 336
                                   455555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2771.44
//
Query:       gi|14601232|ref|NP_147765.1|  [L=522]
Description: hypothetical protein APE_1182 [Aeropyrum pernix K1]
Scores for complete 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-68  232.3   0.0    1.6e-68  231.9   0.0    1.1  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
  ------ inclusion threshold ------
        0.4   11.0   2.1       0.53   10.6   0.6    2.0  2  DUF1947       Domain of unknown function (DUF1947)


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.9   0.0   1.8e-72   1.6e-68       1     354 [.       3     439 ..       3     442 .. 0.87

  Alignments for each domain:
  == domain 1  score: 231.9 bits;  conditional E-value: 1.8e-72
                                   EEEEEETT-BTTHHHHHG.S.TSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEE CS
                  Phosphodiest   1 vlvislDGlradlldrla.e.llpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvf 79 
                                   +++++lDG+++++l++la +  ++nla+L+k+++++  lr+++P++T +++ sl+TGl+Pg++Giv+  f+ rk++ey+ +
  gi|14601232|ref|NP_147765.1|   3 TVLLGLDGCTWSILRPLAeKgVMHNLAKLMKQCSWGI-LRSTIPPITGAAWPSLATGLNPGKTGIVD--FLGRKGQEYRLY 80 
                                   69****************879****************.*****************************..*******98888 PP

                                   ETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC...........TBHHSBTCT........CSTTSC CS
                  Phosphodiest  80 vtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs..........etppryled.......dfnakvp 143
                                     +    + w++g+ +wd +  + +++ a++f+p ++++y+++++lvs          ++p++++ d       df+ +v+
  gi|14601232|ref|NP_147765.1|  81 PAD----SSWYRGYAFWDLLSVE-NKRIAVFFYPLTYPPYPIKGVLVSgigtpslkpkSYPQEVT-DeilssfpDFRVYVD 155
                                   877....669*************.*****************************988854444444.469999********* PP

                                   HHHHHHHHHHHHHHHCHTHSHHHHHCT.........SSESEEEEEECCCHHHHHHH-TT..SHH....HHHHHHHHHHHHH CS
                  Phosphodiest 144 ledkvdkavlqtwldaafakvvlekel.........ekpdlllvyleetDtvgHkfGpd..spe....vedalrrvDkaig 209
                                   ++d + ++v   ++++ +++++++k++         + +d +++++++tD+++H++ ++  +p+    +e++ +r+ k i+
  gi|14601232|ref|NP_147765.1| 156 YHDEKYNDVD-LFISDVMRHLEITKRMvksyvlgkyGLYDNITFIVSATDWIQHRL-WHlmDPKhplyHEEQSKRYSKKID 234
                                   ***7777799.9****************99999666666*****************.**99999***************** PP

                                   HHHHHHHHT.TGTTTEE......EEEEES---EEEHTTSEEEGGGTSTGGHGEEEEECBHHS.SSE.....EEEEESTEE. CS
                  Phosphodiest 210 dLlealder.glsaetn......iilvSDHGmadvsddkvielndlleekgllhlkdegkggakal.....iainpkare. 277
                                   dL++++de+ g++ae++      +++vSDHG++++   +v++l+++l +kg+++l+++g+++a+ l     ia +++a++ 
  gi|14601232|ref|NP_147765.1| 235 DLWSLVDETvGFFAEYAhsekayLMIVSDHGFGSN--LGVFNLARWLVTKGYMKLRRGGSWKASILsygirIAKKLRADDl 313
                                   ***********************************..***************************99***99********** PP

                                   E.CCCTTHHHHHHHHH................................HTCHHCCH....ST.HTT.....TEEEEEGGGS CS
                  Phosphodiest 278 lnrvaeaeaeevyael................................kakleelr....kk.ege.....alavylkeai 316
                                   ++rv ++++ e+++ l                                ++kl++++    kk + e      ++vy++e++
  gi|14601232|ref|NP_147765.1| 314 AKRVLRGRVREYVQSLgltglinfteskaialghsitfggiyvlkskeREKLIDELtgelKKiPEEfkidvGVNVYRREDL 394
                                   **************************9666666666666666666655333333333333443444444445555555543 PP

                                   -GGGCHS....TTS-SEEE.EE-TTEEEESSTTCS.......SBS-SEE- CS
                  Phosphodiest 317 pkrlhyk....krapdlvl.vadpgwsitskdkpd.......eyeikgth 354
                                         +    k +pdl++ ++d+++sit++ + +       ++++ g+h
  gi|14601232|ref|NP_147765.1| 395 Y-----SgdklKLLPDLIIgIDDWSFSITEDLHSPllelrpwSPRHTGAH 439
                                   3.....03444**********************99888877777777777 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6     6e-05      0.53       3      45 ..     355     398 ..     355     407 .. 0.79
   2 ?   -3.7   0.0       1.8   1.6e+04      56      65 ..     465     474 ..     463     474 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6e-05
                                   EE--HHHHHHHHHHHHTTT---TT--..-EEEE-S..S-EEEEET CS
                       DUF1947   3 HfLSkKeakeileklkekyisislesdkiEieeek..keklYlin 45 
                                   ++L++Ke+++++++l  +  +i+ e + i+++ +   +e lY  +
  gi|14601232|ref|NP_147765.1| 355 YVLKSKEREKLIDELTGELKKIPEEFK-IDVGVNVyrREDLYSGD 398
                                   79**********************996.77765432256666555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                                   EEE-HHHHHH CS
                       DUF1947  56 liPtLklLlk 65 
                                   + Pt+ +L k
  gi|14601232|ref|NP_147765.1| 465 VAPTILYLHK 474
                                   67****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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 0.23s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 4201.03
//
Query:       gi|14601233|ref|NP_147766.1|  [L=309]
Description: hypothetical protein APE_1183 [Aeropyrum pernix K1]
Scores for complete 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-15   56.5   0.0    7.4e-15   55.4   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    1.7e-08   34.5   0.0    3.1e-08   33.6   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    9.9e-08   32.6   0.0    4.5e-07   30.5   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
    3.2e-07   31.0   0.0    1.2e-06   29.2   0.0    2.0  2  Methyltransf_12  Methyltransferase domain
    1.5e-06   28.1   0.0    2.6e-06   27.3   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    4.7e-06   26.1   0.0    1.2e-05   24.8   0.0    1.6  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      2e-05   24.5   0.0    3.7e-05   23.7   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
     0.0063   15.5   0.0     0.0094   14.9   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
  ------ inclusion threshold ------
      0.095   11.2   0.0       0.11   11.1   0.0    1.1  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m


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 !   55.4   0.0   3.7e-18   7.4e-15      48      96 .]      67     115 ..      37     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 3.7e-18
                                   TTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
               Methyltransf_11  48 vvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96 
                                   + +++eklpf+++sfD+v+s+evl+hv+++++a+ ei+RvLk gG+lv+
  gi|14601233|ref|NP_147766.1|  67 LISNVEKLPFRSESFDIVISTEVLEHVHNWRSAICEIKRVLKVGGILVL 115
                                   5789******************************************985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   1.5e-11   3.1e-08      46     122 ..      52     120 ..      17     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.5e-11
               Methyltransf_23  46 svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllsepla 122
                                   +++g Dl +         k +++   + ++ ++ +++fd+++++evlehv+++ +++  i++ lk gG l+l++ + 
  gi|14601233|ref|NP_147766.1|  52 NYIGLDLHE--------QKGYVDLISNVEKLPFRSESFDIVISTEVLEHVHNWRSAICEIKRVLKVGGILVLTTRGP 120
                                   455555543........3455555666677778999*************************************9764 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.3e-10   4.5e-07      53      97 .]      69     111 ..      47     111 .. 0.93
   2 ?   -1.5   0.0       2.2   4.3e+03      37      70 ..     245     274 ..     235     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.3e-10
                                   SBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
               Methyltransf_25  53 gdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                    ++e+lpf ++sfD+v+s+ +l+h++  +++ a+ ei+rvLk gG
  gi|14601233|ref|NP_147766.1|  69 SNVEKLPFRSESFDIVISTEVLEHVH--NWRSAICEIKRVLKVGG 111
                                   689***************888***98..8**************99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                   HHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
               Methyltransf_25  37 areraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                   a++     +++ +f++++  +l  +d +f +v +
  gi|14601233|ref|NP_147766.1| 245 AEKC----HVSTSFIECNSLRLAKKDLHFYIVSL 274
                                   3333....36788888888888888888877765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   5.9e-10   1.2e-06      42      99 .]      42     113 ..      36     113 .. 0.91
   2 ?   -2.9   0.0       5.8   1.2e+04      27      45 ..     249     267 ..     248     270 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.9e-10
               Methyltransf_12  42 krennnnnnvelealdlldldgg..............ssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99 
                                   ++  +n +nv++  ldl++++g               +sfD+v++ +vl+h+ ++r+++ +i+++Lk gG+l
  gi|14601233|ref|NP_147766.1|  42 DWVTYNIANVNYIGLDLHEQKGYvdlisnveklpfrsESFDIVISTEVLEHVHNWRSAICEIKRVLKVGGIL 113
                                   5667788999999999998888899999999999************************************86 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
               Methyltransf_12  27 Dispsaiedakeklakren 45 
                                    +s+s+ie  + +lak++ 
  gi|14601233|ref|NP_147766.1| 249 HVSTSFIECNSLRLAKKDL 267
                                   6899999988899888765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.3e-09   2.6e-06      60     111 ..      68     117 ..      51     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.3e-09
               Methyltransf_31  60 qgdieeleklledekfDlilsnevlnaladpdkileeiervlkpggillied 111
                                   ++++e+l+  +  e+fD+++s evl ++ +  +++ ei+rvlk ggil++++
  gi|14601233|ref|NP_147766.1|  68 ISNVEKLP--FRSESFDIVISTEVLEHVHNWRSAICEIKRVLKVGGILVLTT 117
                                   57888888..99************************************9875 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.1e-09   1.2e-05     103     173 ..      67     136 ..      47     146 .. 0.88
   2 ?   -2.1   0.0      0.99     2e+03      94     142 ..     246     294 ..     242     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.1e-09
                                   EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.H CS
               Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskev 173
                                   l +n e+Lpf  +sfD+v  +  l  v +   a+ e+ rvlk+GG+l vl +  +  pl   +++ + +++
  gi|14601233|ref|NP_147766.1|  67 LISNVEKLPFRSESFDIVISTEVLEHVHNWRSAICEIKRVLKVGGIL-VLTTRGPGFPLHAYPHDYWRFDI 136
                                   579***************99999**********************86.68888899999988888887765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.99
                                   HHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHH CS
               Ubie_methyltran  94 eegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrv 142
                                   e+  ++  f+  n+ +L  +d  f +v +  G +      k Lk  yr+
  gi|14601233|ref|NP_147766.1| 246 EKCHVSTSFIECNSLRLAKKDLHFYIVSLIKGSKTSRTFYKILKFRYRI 294
                                   5666677899999999999998888888888888777777777777776 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.9e-08   3.7e-05      95     156 ..      52     115 ..      42     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.9e-08
                                   .EEEEESS-SSTTEE.ES-TTS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_8  95 kvrsfdlvavnervv.acdlakvPledesvdvavfclsl.mgtnladflkeanrvlkvGGllkv 156
                                   + + +dl+  +  v    ++ k+P   es d+++    l  + n+++ + e++rvlkvGG+l +
  gi|14601233|ref|NP_147766.1|  52 NYIGLDLHEQKGYVDlISNVEKLPFRSESFDIVISTEVLeHVHNWRSAICEIKRVLKVGGILVL 115
                                   45678999988888624678**************998884589******************975 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 !   14.9   0.0   4.7e-06    0.0094     168     220 ..      65     118 ..      51     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.7e-06
                                   EEE---GGGS-T.---EEEEEEES-GGG-S-HHHHHHHHHCTEEEEEEEEEEEE CS
                Methyltransf_9 168 hllplgieqlpe.leafdtvfsmGvlyhrrsPldhllqlkdqlvkgGelvletl 220
                                   ++l   +e+lp   e+fd+v s  vl h +     + ++k  l+ gG lvl t 
  gi|14601233|ref|NP_147766.1|  65 VDLISNVEKLPFrSESFDIVISTEVLEHVHNWRSAICEIKRVLKVGGILVLTTR 118
                                   4566789****889*************************************985 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 ?   11.1   0.0   5.3e-05      0.11     172     219 ..      71     117 ..      62     225 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.3e-05
               Methyltransf_29 172 tkrlpyPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvlsa 219
                                    ++lp+ s+sfd++  +  + ++ ++    + e++Rvl+ gG +vl++
  gi|14601233|ref|NP_147766.1|  71 VEKLPFRSESFDIVISTEVL-EHVHNWRSAICEIKRVLKVGGILVLTT 117
                                   479**********9877665.55666677899*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2326.10
//
Query:       gi|14601234|ref|NP_147767.1|  [L=357]
Description: glycosyl transferase [Aeropyrum pernix K1]
Scores for 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-15   55.6   0.1    8.4e-15   55.0   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    7.4e-09   35.8   0.0    2.8e-08   33.9   0.0    1.8  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.046   13.1   0.0    1.2  1  Anp1             Anp1
      0.063   13.2   0.0      0.082   12.8   0.0    1.4  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 !   55.0   0.1   1.9e-18   8.4e-15       1     130 [.       7     143 ..       7     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.9e-18
                                   EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH...C-TTEEEEEESSS-HHHHHHHHHHHH CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak...edprvrvirreenvGkagalnaglra 77 
                                   s++++t+N +k++ ++l+ l +  +p++ +++i+vD++S D+t  ++ ++ k   e  ++rv+ +++n G+ +++n g+ +
  gi|14601234|ref|NP_147767.1|   7 SIIVVTHNSSKYIDKLLADLSSLdYPRELLQVIFVDNASWDDTLRLIFDYLKknlEIRNIRVLELKNNIGFPAGVNVGITY 87 
                                   8***************************************************9*************999************ PP

                                   --SS....EEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC- CS
               Glycos_transf_2  78 atgd....yilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernk 130
                                   a       yi++++ D+ +  + +l++ +  + k  +++ ++++  ++ e+++  + +
  gi|14601234|ref|NP_147767.1|  88 ALKTwnprYIVIMNPDVRILNKaFLKESILLMRK--YKISCASPIIFKLEENRDYKIQ 143
                                   *9999999*********999998********999..6678888877777777776655 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 !   33.9   0.0   6.2e-12   2.8e-08       1     216 [.       4     239 ..       4     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.2e-12
               Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetle.vaeelaaalpdvrvrvvvnarnl.gstgksr 77 
                                   p  ++++V+t n ++++ ++l++l++ +ypr  ++v++v++ s ++tl+  ++ l ++l+   +rv+  ++n   + g   
  gi|14601234|ref|NP_147767.1|   4 PK-VSIIVVTHNSSKYIDKLLADLSSLDYPRelLQVIFVDNASWDDTLRlIFDYLKKNLEIRNIRVLELKNNIgFPAGVNV 83 
                                   55.9*************************99999********999998747*********668999999877725678888 PP

               Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfl.l.nrstl............vsalgalefae 143
                                   ++  al++ +++++++++ D+++  + +lk +  +++  k+ ++    f  + nr++             +++ g   ++ 
  gi|14601234|ref|NP_147767.1|  84 GITYALKTWNPRYIVIMNPDVRIlNKAFLKESILLMRKYKISCASPIIFKlEeNRDYKiqwalglldnsgTAFMGFYDLDY 164
                                   99*********************6666777766666555677777555442324553356688888877655554445556 PP

               Glyco_tranf_2_3 144 rhlrflaarralg.vltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfpss 216
                                   +  ++l+   +l  vl ++ ++  i+ + ++ +++l+  lfl  +D+e++lrl+  gf+ + +  + v +++ +s
  gi|14601234|ref|NP_147767.1| 165 DTVNRLSSKITLIpVLWITFALAIIDSDAVRKTGLLRSnLFLYYEDIEYSLRLMLKGFQCYSLLIPSVAHAESES 239
                                   66666666655543888777*************9999999*******************9987777666665544 PP

>> Anp1  Anp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05     0.046      23      78 ..       6      59 ..       3     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                          Anp1 23 vLiltplrdaekflpeyfenllkltyphelidLaflvsdtsegdktlealeeelkk 78
                                  v i++  ++++k++++++  l++l+yp+el+++ f+ + +   d+tl+ + ++lkk
  gi|14601234|ref|NP_147767.1|  6 VSIIVVTHNSSKYIDKLLADLSSLDYPRELLQVIFVDNASW--DDTLRLIFDYLKK 59
                                  667777889**********************9988876666..9999999998876 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 ?   12.8   0.0   1.8e-05     0.082      41     143 ..     153     254 ..      96     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
               Glyco_trans_2_3  41 anwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes. 120
                                   ++ +  +++l ++    +  ++  +l  v+ ++ + a+++ +a+++ g  +++ +   ED + +lrl+ kG++++    + 
  gi|14601234|ref|NP_147767.1| 153 GTAFMGFYDLDYD--TVNRLSSKITLIPVLWITFALAIIDSDAVRKTGLLRSNLFLYYEDIEYSLRLMLKGFQCYSLLIPs 231
                                   5555556666664..23334566667777778888999**********99999******************9996653332 PP

               Glyco_trans_2_3 121 lvkekspltlraalrQrkRwayG 143
                                   + + +s++  + +l +  R ++ 
  gi|14601234|ref|NP_147767.1| 232 VAHAESESLRDPELSRNIRALFV 254
                                   35555555555566666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2590.36
//
Query:       gi|118431353|ref|NP_147768.2|  [L=429]
Description: hypothetical protein APE_1186.1 [Aeropyrum pernix K1]
Scores for complete 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   28.4   0.2    2.2e-06   27.3   0.2    1.6  1  Glycos_transf_1  Glycosyl transferases group 1
    0.00097   19.6   0.0     0.0022   18.4   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2   2.5e-10   2.2e-06       9     126 ..     228     349 ..     222     400 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.5e-10
                                    TTTTTT-EEEEEESS-TTTTT.HHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCGGGEEECCH CS
                Glycos_transf_1   9 lgknekkkiilsvgrlekeKg.vdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdnviflgevs 82 
                                    ++  +k + ++++grl++ Kg ++++i+ ++ l ++ n n++  i+      + ++ ++  + ++++++  +v++l ++ 
  gi|118431353|ref|NP_147768.2| 228 YNSVQKVYDVIYIGRLDPSKGsFKNFITFLRNLAER-NLNIRAAIITsclkeELPYIERSLSGIKQYNN-VKVEVLVNKT 305
                                    566678889***********96799********998.************98888898999999999999.99*******9 PP

                                    SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTT CS
                Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasnagg 126
                                    + ++  +++++ ++v+ s+ + f +++lE++  g+ via n++ 
  gi|118431353|ref|NP_147768.2| 306 PIEVYRIISRSRALVMLSTLDVFNLAILESLVHGIHVIALNNPR 349
                                    9999999999*****************************99875 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 !   18.4   0.0   2.4e-07    0.0022       3     103 ..     236     348 ..     235     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.4e-07
                                    EEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---.....HHHHHHHTT-T...TEEEE---....THHHHHHH CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgp.rp..eeleelaagle..erveftGfv....edlaella 71 
                                    +++++Grl++ +  ++ ++  +  l++++  +r  i+  ++ ++  + +e+ ++g++  ++v++   v     ++ ++++
  gi|118431353|ref|NP_147768.2| 236 DVIYIGRLDPSKGSFKNFITFLRNLAERNlnIRAAIIT-SClKEelPYIERSLSGIKqyNNVKVEVLVnktpIEVYRIIS 314
                                    589*****776556699999999999885569999999.443322445554444555446677777675443359999** PP

                                    H-SEEEE--..---SHHHHHHHHTT-EEEE-TGG CS
                Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvg 103
                                    +++ +v+ s    f+l++lE++ +g+ v+a + +
  gi|118431353|ref|NP_147768.2| 315 RSRALVMLStlDVFNLAILESLVHGIHVIALNNP 348
                                    *********8789*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3149.99
//
Query:       gi|118431354|ref|NP_147769.2|  [L=767]
Description: hypothetical protein APE_1187.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 4972.96
//
Query:       gi|14601237|ref|NP_147770.1|  [L=383]
Description: glycosyl transferase, group 1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-09   35.5   0.0    1.2e-08   34.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    5.1e-07   30.2   0.0    8.8e-07   29.4   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.033   14.4   0.0      0.079   13.2   0.0    1.6  2  SAM35            SAM35, subunit of SAM coomplex


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 !   34.7   0.0     2e-12   1.2e-08      13     159 ..     198     346 ..     190     359 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 2e-12
                                   TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSSHHHHHHC CS
               Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.redleellkn 92 
                                    k + i+++g l+k Kgvd l+++++++ k+  +++ ++i+G+g   +++ +++ e   +++vi++g ++ + +l    ++
  gi|14601237|ref|NP_147770.1| 198 RKSNDIVYIGSLSKDKGVDILLELVKTFTKN-GNDTIIHIVGKGLLYEKIFERIGEI--NKRVIYYGPQPlKRALQIASRA 275
                                   57899************************99.**********999999999998865..55*********77777777777 PP

                                   ESEEEEEESS.BSS...-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
               Glycos_transf_1  93 adifvlpsis.Egf...GivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                   +  +vl+  s E++   ++ +  ++aa +pvi   +  ++ +v+  + G +v + ++  +  +++ +led+
  gi|14601237|ref|NP_147770.1| 276 SLGVVLTRPSyESLttdPMKPKVYLAAHTPVILPEYFEISSYVNRFKAGMVVGKLKPSYILSKVKVALEDS 346
                                   6556666555677733366666789**********************999998888888887777777776 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 !   29.4   0.0   1.5e-10   8.8e-07       2     118 ..     201     329 ..     200     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.5e-10
                                   EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEE CS
               Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfv 77 
                                   ++i+++G+l  + kgvd+lle v+   k+ +   ++ivG+g   + ++ e++ ++++rv++ G    +   ++ ++a++ v
  gi|14601237|ref|NP_147770.1| 201 NDIVYIGSL-SKDKGVDILLELVKTFTKNgNdTIIHIVGKGLlYE-KIFERIGEINKRVIYYGPQplKRALQIASRASLGV 279
                                   579******.556**********99997774699*****998664.77779988999******997666778889999999 PP

                                   E...--.---...SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--T CS
               Glyco_trans_1_4  78 a...Ps.egf...glkllEamaaglpvVatdvggiaevv..gengllvpp 118
                                   +   Ps e++   ++k   ++aa +pv+  +   i+ +v   ++g++v +
  gi|14601237|ref|NP_147770.1| 280 VltrPSyESLttdPMKPKVYLAAHTPVILPEYFEISSYVnrFKAGMVVGK 329
                                   9555558654556***************9988777777754367777754 PP

>> SAM35  SAM35, subunit of SAM coomplex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.079      28      91 ..      57     126 ..      35     166 .. 0.76
   2 ?   -3.3   0.0       1.7     1e+04      56      76 ..     277     294 ..     252     313 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
                         SAM35  28 aakkeiesrsyeF.....egnskseksendtfkLgvynv.feesetdsvLatdPlclfaqLalckknnlk 91 
                                   ++ ++i +rs++F     +  s +   +  +++L++ ++  e ++ d ++a+dP++ +++++l +kn ++
  gi|14601237|ref|NP_147770.1|  57 EKGEKIFERSFHFpsintRIPSLEIAAKIIEYTLSIISItAEAKHYDIAIAQDPITATIAIMLKQKNYIS 126
                                   45566888999998776555666666677789*******6667778888******************764 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                         SAM35  56 LgvynvfeesetdsvLatdPl 76 
                                   Lgv  v+ +  + + L+tdP+
  gi|14601237|ref|NP_147770.1| 277 LGV--VL-TRPSYESLTTDPM 294
                                   444..22.2333445666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2866.14
//
Query:       gi|14602202|ref|NP_147771.1|  [L=283]
Description: glycosyl transferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-24   86.4   0.0      3e-24   85.8   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    2.5e-10   40.6   0.0    5.8e-10   39.4   0.0    1.6  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.6e-06   26.3   0.0    9.1e-06   25.3   0.0    1.5  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
       0.04   14.4   0.1        4.4    7.9   0.1    2.2  2  YflT             Heat induced stress protein YflT
      0.068   13.7   0.0       0.14   12.7   0.0    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
        0.1   11.9   0.0       0.15   11.4   0.0    1.2  1  F420_ligase      F420-0:Gamma-glutamyl ligase


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 !   85.8   0.0   9.9e-28     3e-24       1     113 [.      20     123 ..      20     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 9.9e-28
                                   EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS CS
               Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd 81 
                                   s+viptyN ektl  tles+++q +y+++e+i+vD+ StD+tv+i+e++     + rvi+ + + G+  a+  g  +a+g+
  gi|14602202|ref|NP_147771.1|  20 SIVIPTYNSEKTLSLTLESIKRQ-TYKNIEVIIVDNYSTDGTVKIAEKY-----NARVIQTS-G-GLLWARYLGHLHAKGE 92 
                                   8**********************.*************************.....9*******.5.9*************** PP

                                   EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEE CS
               Glycos_transf_2  82 yilflDaDdepdpdwleklvealekdgadvvl 113
                                   + l+lD+D + +   +e+ v+   + g+d+ +
  gi|14602202|ref|NP_147771.1|  93 VELLLDSDQILEHTAIERGVKMVRR-GYDALI 123
                                   **********************999.666554 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 !   39.4   0.0     2e-13   5.8e-10       4     138 ..      19     140 ..      17     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2e-13
               Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84 
                                   +++++pt+n e++l  +les+ +q+y ++ev++v++ s+++t++ ae     + +   rv+++     s+g  +a + +  
  gi|14602202|ref|NP_147771.1|  19 VSIVIPTYNSEKTLSLTLESIKRQTYKNIEVIIVDNYSTDGTVKIAEK----YNA---RVIQT-----SGGLLWARYLGHL 87 
                                   89******************************************8875....644...78744.....358899999**** PP

               Glyco_tranf_2_3  85 avksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalga 138
                                   ++k+++ ll+D+D ++e ++++r +  + +++++a+   + ++ ++tlv+ l +
  gi|14602202|ref|NP_147771.1|  88 HAKGEVELLLDSDQILEHTAIERGVKMV-RRGYDALILEETSYKPRTLVQWLFY 140
                                   ***************************9.99******99999999999876533 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 !   25.3   0.0     3e-09   9.1e-06       1     106 [.      20     115 ..      20     132 .. 0.83
   2 ?   -3.5   0.0       1.9   5.6e+03     240     258 ..     205     223 ..     191     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3e-09
               Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskae 81 
                                   s+vip ++se++  +  ++  ++ +  ++ie+i+vd++S++     v+   + n +v      +++ +l  ar +G  +a+
  gi|14602202|ref|NP_147771.1|  20 SIVIPTYNSEKT--LSLTLESIKRQTYKNIEVIIVDNYSTDG---TVKIAEKYNARVI-----QTSGGLLWARYLGHLHAK 90 
                                   79**********..66677665555558**************...4555556666666.....4566999*********** PP

               Glyco_tranf_2_2  82 sdlvlFlDaDcfissDkfekilkli 106
                                   +++ l lD+D       +e+ +k++
  gi|14602202|ref|NP_147771.1|  91 GEVELLLDSDQILEHTAIERGVKMV 115
                                   **********999988888887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
               Glyco_tranf_2_2 240 aalglvvfhlYheepksed 258
                                   + lg+    +Yh ep+s++
  gi|14602202|ref|NP_147771.1| 205 EKLGIISNAIYHVEPESLK 223
                                   4678888889999998865 PP

>> YflT  Heat induced stress protein YflT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0015       4.4       2      58 ..      24      81 ..      23     102 .. 0.84
   2 ?    4.5   0.0     0.016        49      70      96 ..     224     250 ..     204     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                          YflT  2 gvyeneeellsaieelkaeGyneddiyvvak.dkdrlerlaentdaetettseeglwd 58
                                   +y++e++l   +e++k++ y++ + ++v +   d + ++ae+++a +++ts   lw 
  gi|14602202|ref|NP_147771.1| 24 PTYNSEKTLSLTLESIKRQTYKNIEVIIVDNySTDGTVKIAEKYNARVIQTSGGLLWA 81
                                  58999******************999999873567799************98655554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.016
                          YflT  70 elrekleslGltedeaeeyeeeldeGk 96 
                                   ++  k+ ++G+te ++ +y+ el + k
  gi|14602202|ref|NP_147771.1| 224 QVVRKFYRYGITEMNLTQYYPELSKKK 250
                                   455699**************9998766 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.7e-05      0.14       2      46 ..      27      72 ..      26     143 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
               Glyco_tranf_2_4  2 neadiLpeflahhlalgfdr..ilvydndstDgtrailkelpevkll 46
                                  n +++L  +l+ +++  +++  ++++dn stDgt +i +++ +++++
  gi|14602202|ref|NP_147771.1| 27 NSEKTLSLTLESIKRQTYKNieVIIVDNYSTDGTVKIAEKY-NARVI 72
                                  788888899999888888754499*************9995.33333 PP

>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.9e-05      0.15     146     192 ..      27      76 ..       6     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                                   -HHHHHHHHHHHHHHHHS---EEEE.....EEEEEETTEECEEEEEEEEE CS
                   F420_ligase 146 dpdksaeeikkklkertgkdveVliyg...kDpegriweladpvvaigts 192
                                   +++k+ +   +++k++t k++eV+i++   +D +++i e +++ v   + 
  gi|14602202|ref|NP_147771.1|  27 NSEKTLSLTLESIKRQTYKNIEVIIVDnysTDGTVKIAEKYNARVIQTSG 76 
                                   556666666789***************************99888755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2236.54
//
Query:       gi|118431355|ref|NP_147772.2|  [L=206]
Description: hypothetical protein APE_1190.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   54.1   0.0    2.3e-14   53.8   0.0    1.1  1  Methyltransf_21  Methyltransferase FkbM domain
    0.00012   21.9   0.1    0.00015   21.6   0.1    1.3  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.056   13.9   0.0       0.16   12.4   0.0    1.7  2  MtrB             Tetrahydromethanopterin S-methyltransferase 


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   3.8e-18   2.3e-14       1     172 [.      14     167 ..      14     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 3.8e-18
                Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndv....glyelivegksggkyfpfavg 76 
                                    dvGa+ig     ++      +   +v+++EP+p    +++ l+ n   +a  n+v    +l   iv+ k          +
  gi|118431355|ref|NP_147772.2|  14 DVGAHIG-----LYSL-VVSNYAHRVISVEPHPI---NYKLLKIN--KIA--NNVegmlTLNAAIVGTK----TDRTKLC 76 
                                    9******.....2222.2477999**********...******99..344..44411113333344333....5555556 PP

                Methyltransf_21  77 dtngfstssvlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeG.aqkglkrcqpnlivvEvhkfkefe 155
                                    +++++++ss++ +++++  ++++++l +++e +  ++  llk+ +EGaE++++++ + ++l+ +   +  +Evh      
  gi|118431355|ref|NP_147772.2|  77 ESTHSGGSSIMIESPSKCYRIQTKHLNELIESYTGNDKVLLKMNIEGAEFDIFKSvDPNLLRSVERIV--MEVHLRY--- 151
                                    6666666666667****************************************999999998854444..7999865... PP

                Methyltransf_21 156 telfdeirqflrecgyr 172
                                      +   i+ +l+++g+ 
  gi|118431355|ref|NP_147772.2| 152 -GSLNIIVNKLKSAGFS 167
                                    .6677777778888875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   2.5e-08   0.00015     101     153 ..       9      59 ..       5     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-08
                                    T-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCE CS
                         Met_10 101 gevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvv 153
                                    g +V+dv A iG ++++++    a+rv++++  P  +k+lk n   N+ve ++
  gi|118431355|ref|NP_147772.2|   9 GFTVLDVGAHIGLYSLVVSN--YAHRVISVEPHPINYKLLKINKIANNVEGML 59 
                                    668****************9..67889**************999999999876 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05      0.16      18      67 ..      25      74 ..      14      85 .. 0.87
   2 ?   -2.5   0.0       1.2   7.3e+03      57      70 ..     104     117 ..     102     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                           MtrB 18 vvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgRek 67
                                   vv++ ++ v+ ++ +p++ ++ k++kia++++ +L+ + a++++  +R k
  gi|118431355|ref|NP_147772.2| 25 VVSNYAHRVISVEPHPINYKLLKINKIANNVEGMLTLNAAIVGTKTDRTK 74
                                   67788899****************************99999988888876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                           MtrB  57 allesypgRektlv 70 
                                    +l+esy g +k+l+
  gi|118431355|ref|NP_147772.2| 104 ELIESYTGNDKVLL 117
                                    67889999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1684.82
//
Query:       gi|14601239|ref|NP_147773.1|  [L=363]
Description: glycosyl transferase, group 1 [Aeropyrum pernix K1]
Scores for complete 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  144.9   0.0    2.3e-42  144.4   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    7.2e-30  104.2   0.0      2e-29  102.7   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-27   96.7   1.7    2.7e-27   95.8   1.7    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
      4e-16   59.8   1.6      8e-16   58.9   1.6    1.5  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    6.6e-10   39.2   0.0    1.4e-09   38.2   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.4   0.0   6.5e-46   2.3e-42      10     171 ..     180     339 ..     173     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.4 bits;  conditional E-value: 6.5e-46
                                   TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
               Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                   g ++ +++il  gr++ +K++d+l+ka++ +k+ + p+++l+i+G g++e+++++la++le   +v+flg++s+++++ ++
  gi|14601239|ref|NP_147773.1| 180 GSKDPRPTILWAGRIKMYKNLDHLLKAYRIVKQ-EIPDAQLIIIGTGDQEQKMRELAKKLEP-RDVHFLGKMSEQEKIMWM 258
                                   5678899**********************9975.6***************************.88**************** PP

                                   HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
               Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                   ++a i+v +s+ Eg+Gi+++EA a+++p+ia+n++g+++ vk+ etG+lv+p+n+e+la+ai++ll+d+ lr++l+ena++
  gi|14601239|ref|NP_147773.1| 259 QRAWIIVSTSMIEGWGITITEAAACKIPAIAYNVPGLRDSVKHMETGILVEPGNIEQLAKAIAWLLTDNSLRNKLSENAYN 339
                                   *******************************************************************************86 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 ?   -2.1   0.0       1.3   4.7e+03      17      55 ..     125     162 ..     119     177 .. 0.60
   2 !  102.7   0.0   5.5e-33     2e-29       1     134 []     185     326 ..     185     326 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                   HHHHHHHH.HHHH.H.HEEEEEES---..HHHHHHHTT-T. CS
               Glyco_trans_1_4  17 vdllleav.pllrkk.dvrlvivGdgprpeeleelaaglee 55 
                                   + +++  + + ++ k   r++ v ++  ++el +++ g+++
  gi|14601239|ref|NP_147773.1| 125 LAWIVSRAeKTIA-KiYRRFIAVSQS-TKKELAKRL-GIDP 162
                                   6677777744444.424688888865.445787666.5553 PP

  == domain 2  score: 102.7 bits;  conditional E-value: 5.5e-33
                                   SEEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.T.EEEE---..THHHHHHHH-SEE CS
               Glyco_trans_1_4   1 rpvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleer.veftGfv..edlaellaaadvf 76 
                                   rp+il+ Gr+ + +k++d ll+a   ++++  d++l+i+G g+++++++ela++le+r v+f+G++  +++  ++++a++ 
  gi|14601239|ref|NP_147773.1| 185 RPTILWAGRI-KMYKNLDHLLKAYRIVKQEipDAQLIIIGTGDQEQKMRELAKKLEPRdVHFLGKMseQEKIMWMQRAWII 264
                                   699*******.767**************99855*********96679*99999999999*******9777*********** PP

                                   EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
               Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                   v +s  eg+g+++ Ea+a+++p +a +v+g+++ v   e+g+lv+pg+ e+la+ai+ Ll+d
  gi|14601239|ref|NP_147773.1| 265 VSTSmiEGWGITITEAAACKIPAIAYNVPGLRDSVkhMETGILVEPGNIEQLAKAIAWLLTD 326
                                   *********************************998769*********************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   1.7   7.6e-31   2.7e-27       1     170 []      16     176 ..      16     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 7.6e-31
                Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvv..Hah 79 
                                   +GG+e+ ++e+ar+L ++GheV v++ ++++ ++ee   v +++r+  ++ +r+ + l +++++r++ +  ++Dv+   + 
  gi|14601239|ref|NP_147773.1|  16 AGGAEVRLYEIARRLVKMGHEVMVLCEKVSRLPGEE---VLEGIRIK-RSGGRASIHLLAPLYVRKHGH--EYDVIvdDIA 90 
                                   59**********************************...55555555.444566666667777777666..9****66333 PP

                Glyco_transf_4  80 spaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekit 160
                                   ++++++     l   ++ p+V+ +H+   +  +    kpl  ++ + e+ +++  +r+iavS++t++el++r+g++p++i+
  gi|14601239|ref|NP_147773.1|  91 HAVPWYSP---LV--TKTPVVAQIHHVHQDVVYIELPKPLAWIVSRAEKTIAKIYRRFIAVSQSTKKELAKRLGIDPDRIA 166
                                   33443333...33..799**********9777778889999999999********************************** PP

                Glyco_transf_4 161 VipnGvDler 170
                                   V+pnGvDle+
  gi|14601239|ref|NP_147773.1| 167 VVPNGVDLEK 176
                                   ********85 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 !   58.9   1.6   2.2e-19     8e-16       1     160 []      17     171 ..      17     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.2e-19
               Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll.rqrrerpdvvh.. 78 
                                   gG++++ +e+ar+L++ GheV vl+ +  + + e++ +g+r+ r   +++         ++ l+ l  r +   +dv++  
  gi|14601239|ref|NP_147773.1|  17 GGAEVRLYEIARRLVKMGHEVMVLCEKVSRLPGEEVLEGIRIKRSGGRAS---------IHLLAPLYvRKHGHEYDVIVdd 88 
                                   8************************9999999988889999977544433.........3444333346678999999877 PP

               Glyco_trans_4_4  79 .ahs..ptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvseaeaeelra.lgvpadrv 154
                                    ah   ++++l+ +       +  ++++h++ +  +   ++++++ ++e+++++  +++++vs++  +el+  lg+++dr+
  gi|14601239|ref|NP_147773.1|  89 iAHAvpWYSPLVTKTPV----VAQIHHVHQDVVYIElPKPLAWIVSRAEKTIAKIYRRFIAVSQSTKKELAKrLGIDPDRI 165
                                   65654366777665555....667888887665533367889999**************************99******** PP

               Glyco_trans_4_4 155 vvvpng 160
                                   +vvpng
  gi|14601239|ref|NP_147773.1| 166 AVVPNG 171
                                   *****8 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   3.9e-13   1.4e-09       9      91 ..     271     354 ..     258     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 3.9e-13
               Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhra 87 
                                   e+    + Eaaac ++a++   +gl++ ++  +++il+e  + e+la++i+ ll++  +r++++e+a++   + +++d+ a
  gi|14601239|ref|NP_147773.1| 271 EGWGITITEAAACKIPAIAYNVPGLRDSVKHMETGILVEpgNIEQLAKAIAWLLTDNSLRNKLSENAYNY-AQSFSWDNTA 350
                                   66677899*************************************************************9.899*****99 PP

               Glyco_trans_1_2  88 eqll 91 
                                    ++l
  gi|14601239|ref|NP_147773.1| 351 ITFL 354
                                   8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); 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:                         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: 00:00:00.41
# Mc/sec: 2660.46
//
Query:       gi|14601240|ref|NP_147774.1|  [L=290]
Description: glycosyl transferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-10   41.3   0.0      2e-10   40.7   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00051   20.0   0.0     0.0016   18.3   0.0    1.8  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.012   15.2   0.0       0.31   10.5   0.0    2.3  2  Glyco_transf_21  Glycosyl transferase family 21


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 !   40.7   0.0   3.4e-14     2e-10       1     129 [.       4     137 ..       4     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.4e-14
                                   EEEEEESS-TTTHHHHHHHHHHH.......GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHH CS
               Glycos_transf_2   1 svviptyNeektlletlesllaq.......dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnag 74 
                                   svvip+  e +tl e ++ l++          +  +eii+v D     t +   +lak +   + + ++++ Gk+g++ ++
  gi|14601240|ref|NP_147774.1|   4 SVVIPVAKEGNTLYERIH-LINKhfnslssSHKFSYEIILVSDIFHKPTLKAMIRLAK-ENVAKCLLLTQRIGKGGSIKNA 82 
                                   8*****************.88888*****99999**********96666666666665.6777777888778********* PP

                                   HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
               Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiern 129
                                   +  ++gdyi++lDaD  + p ++ + v  + + g d+++++r+++  +  ++   
  gi|14601240|ref|NP_147774.1|  83 IPFSRGDYIVILDADIPVRPIFINQAVVLAMNLGIDLIIANRVYRTHSLLRRVLS 137
                                   **************************9999999**********998887776665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-07    0.0016       4     138 ..       3     141 ..       2     213 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-07
               Glyco_tranf_2_3   4 lavlVptfneedvlge...vlesllaq.e..y.prvevvvvvdesdaetle.vaeelaaalpdvrvrvvvnarnlgstgks 76 
                                   ++v++p+++e  +l e   +++ + ++ +  +  ++e+++v d   + tl+ +++    a ++v  +++  +++    gk 
  gi|14601240|ref|NP_147774.1|   3 VSVVIPVAKEGNTLYErihLINKHFNSlSssHkFSYEIILVSDIFHKPTLKaMIRL---AKENV-AKCLLLTQRI---GKG 76 
                                   79*********976664665554443212113366*******99999998625554...33344.5788777754...577 PP

               Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpv..flln.rstlvsalga 138
                                    ++++a++  ++d+++++D+D  v P ++ +++ ++   +++ + +++  +++   ++++s++++
  gi|14601240|ref|NP_147774.1|  77 GSIKNAIPFSRGDYIVILDADIPVRPIFINQAVVLAMNLGIDLIIANRvyRTHSlLRRVLSVAYN 141
                                   7788***************************9999866666665544422444235555555554 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.015        92      14      64 ..      21      70 ..      15      75 .. 0.83
   2 ?   10.5   0.0   5.2e-05      0.31      23     111 ..      80     166 ..      72     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.015
               Glyco_transf_21 14 gvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVt 64
                                  ++ +K +n l    +  y+++++sD  +  + +++ +l+++    k+ l+t
  gi|14601240|ref|NP_147774.1| 21 HLINKHFNSLSSSHKFSYEIILVSDIFHKPTLKAMIRLAKENVA-KCLLLT 70
                                  55579999999999***********9999999999999988774.666666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.2e-05
               Glyco_transf_21  23 lqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqaklsglgfavG 103
                                    +a++  + d++vi+D+d+ v+p ++++ +   +  ++ l+ +  +++++++l +++ ++  n l ++l   ++  +   G
  gi|14601240|ref|NP_147774.1|  80 KNAIPFSRGDYIVILDADIPVRPIFINQAVVLAMNLGIDLIIAN-RVYRTHSLLRRVLSVAYNSLVNLLFK-TGLRDHQAG 158
                                   566777899*****************987777666799998875.56677888888888888888877777.555566666 PP

               Glyco_transf_21 104 ksmalrre 111
                                     ++ rr+
  gi|14601240|ref|NP_147774.1| 159 LKILSRRA 166
                                   66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2228.74
//
Query:       gi|118431356|ref|NP_147775.2|  [L=143]
Description: hypothetical protein APE_1193.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 1056.45
//
Query:       gi|118431357|ref|NP_147776.2|  [L=101]
Description: hypothetical protein APE_1194.1 [Aeropyrum pernix K1]
Scores for 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   18.0   0.1     0.0028   17.7   0.1    1.2  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
     0.0029   16.6   0.0      0.003   16.5   0.0    1.0  1  LMBR1            LMBR1-like membrane protein
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.012   15.3   0.0    1.0  1  DUF4131          Domain of unknown function (DUF4131)
      0.021   13.7   0.0      0.025   13.4   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
      0.043   13.9   0.1      0.051   13.7   0.1    1.1  1  DUF2614          Zinc-ribbon containing domain
       0.21   11.3   3.0        0.3   10.8   3.0    1.2  1  RPN7             26S proteasome subunit RPN7
       0.36   10.5   2.1       0.57    9.9   2.1    1.3  1  DUF1673          Protein of unknown function (DUF1673)
       0.98    9.8   7.6         90    3.5   7.6    2.1  1  DPM2             Dolichol phosphate-mannose biosynthesis regu


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   1.2e-06    0.0028      41     109 ..       8      75 ..       5      85 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                Phage_holin_3_6  41 gaagvlallalllllvalalalaalwlaali.vaavllvla..gvlalvglkklkkakplpertieelkedv 109
                                    g +++++ la++++ + l+++     + ++i ++++ +v++  g+la++g+  +     +p + iee+++ +
  gi|118431357|ref|NP_147776.2|   8 GFGLLIGSLAIIIVYAYLVFFT-EKIWEFVIkLTGFAAVAGffGLLAWIGYVLATT---PPPKPIEEIEKEI 75 
                                    4445555555555555555444.377888886655555554558888888885555...3556777776655 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-06     0.003     132     218 ..      11      95 ..       3     101 .] 0.69

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-06
                          LMBR1 132 lllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvel.Prslwreiksdldeelkklyfeaa 210
                                    ll+  + ++++y ++++  ++++   ++   l   a + G + l+  +Gy l+ + P + + ei+++++eelkkl+ e++
  gi|118431357|ref|NP_147776.2|  11 LLIGSLAIIIVYAYLVFFTEKIW---EFVIKLTGFAAVAGFFGLLAWIGYVLATTpPPKPIEEIEKEIEEELKKLEQEIK 87 
                                    33333333333333333445555...7777777888888****************86677788************88887 PP

                          LMBR1 211 klntekee 218
                                      n+   e
  gi|118431357|ref|NP_147776.2|  88 HENQATGE 95 
                                    77755544 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   5.3e-06     0.012       8      82 ..      11      93 ..       6      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.3e-06
                        DUF4131  8 vllalllllllllllllrr.......rprrrvllllllllllallgfalrapqpna..ndlsqllesgqeviveGvvaslpe 80
                                   +l+++l++++++++l++          +   ++++++++ lla++g++l +  p++  +++++ +e ++   +e ++  + +
  gi|118431357|ref|NP_147776.2| 11 LLIGSLAIIIVYAYLVFFTekiwefvIKLTGFAAVAGFFGLLAWIGYVLATTPPPKpiEEIEKEIE-EELKKLEQEIKHENQ 91
                                   789999999999999887788888887788889999999999999999887766664455555554.555556666665555 PP

                        DUF4131 81 lt 82
                                    t
  gi|118431357|ref|NP_147776.2| 92 AT 93
                                   55 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.025      96     185 ..      13      96 ..       3     101 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                        DUF2254  96 LGtfigtfvYsllvlrairteeevpqlsvlvalllaivsvllLiyFihhlarsiqvsnviarveeelrkailearedeee 175
                                    +G     +vY+ lv+++ +    + ++ + ++ + a++  + L+++i  +  +    + i+++e+e++++++  + ++e 
  gi|118431357|ref|NP_147776.2|  13 IGSLAIIIVYAYLVFFTEK----IWEFVIKLTGFAAVAGFFGLLAWIGYVLATTPPPKPIEEIEKEIEEELK--KLEQEI 86 
                                    5666667788888888877....88899999****************************************2..222233 PP

                        DUF2254 176 eeeeeakdee 185
                                    + e++a+ ee
  gi|118431357|ref|NP_147776.2|  87 KHENQATGEE 96 
                                    3333333332 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.3e-05     0.051       8      62 ..       5      59 ..       2      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                        DUF2614  8 kirtfalllvfiglivmyigllfkeselllvlflllGlllvlastvvyfwiGlls 62
                                   +i  f ll+   ++i++y  l+f ++++   ++ l G+ +v   + +  wiG + 
  gi|118431357|ref|NP_147776.2|  5 RIVGFGLLIGSLAIIIVYAYLVFFTEKIWEFVIKLTGFAAVAGFFGLLAWIGYVL 59
                                   778899999999********99999999999999******************764 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.0   0.00014       0.3       4      37 ..      67     100 ..      65     101 .] 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           RPN7   4 wveelrkknekeleeLdaelkdakenlgkeeirr 37 
                                     +ee++k+ e+el++L++e+k   +  g+ee r+
  gi|118431357|ref|NP_147776.2|  67 PIEEIEKEIEEELKKLEQEIKHENQATGEEESRE 100
                                    589******************9999999999875 PP

>> DUF1673  Protein of unknown function (DUF1673)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.1   0.00025      0.57     146     203 ..       6      59 ..       2      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                        DUF1673 146 vlrwllrllllviflliavllillsyvesiagelqlgevvssfisgllllllwliylq 203
                                    ++ + l +  l i++++a l+ ++  +++++ +l    + ++ ++g++ ll+w  y +
  gi|118431357|ref|NP_147776.2|   6 IVGFGLLIGSLAIIIVYAYLVFFTEKIWEFVIKL----TGFAAVAGFFGLLAWIGYVL 59 
                                    5567777777888888888888888888888888....68999999999999999975 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 ?    3.5   7.6      0.04        90       2      27 ..       4      29 ..       3      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.04
                           DPM2  2 dklvGlllllvalllfvYYtiwvill 27
                                   d++vG++ll+ +l++ + Y   v+++
  gi|118431357|ref|NP_147776.2|  4 DRIVGFGLLIGSLAIIIVYAYLVFFT 29
                                   89999999999999999998888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2639  (0.147192); expected 358.6 (0.02)
Passed bias filter:                     1461  (0.0814881); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 739.58
//
Query:       gi|118431358|ref|NP_147777.2|  [L=183]
Description: adenylylsulfate kinase [Aeropyrum pernix K1]
Scores for complete 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-59  199.0   0.0    4.7e-59  198.8   0.0    1.0  1  APS_kinase       Adenylylsulphate kinase
    2.8e-11   43.4   0.0    3.2e-11   43.2   0.0    1.1  1  KTI12            Chromatin associated protein KTI12
    4.1e-11   43.2   0.0    4.9e-11   43.0   0.0    1.2  1  AAA_33           AAA domain
    2.2e-07   31.4   0.0    3.1e-07   31.0   0.0    1.2  1  AAA_18           AAA domain
    6.8e-07   29.4   0.0    9.8e-07   28.9   0.0    1.2  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    6.9e-06   25.2   0.0    9.6e-06   24.8   0.0    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    9.2e-06   25.5   0.0    1.3e-05   25.0   0.0    1.3  1  AAA_30           AAA domain
    1.2e-05   25.1   0.0    2.5e-05   24.0   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
    2.2e-05   24.4   0.2    5.3e-05   23.2   0.0    1.7  2  NTPase_1         NTPase
    0.00014   22.2   0.2    0.00043   20.6   0.1    1.7  2  AAA_28           AAA domain
    0.00022   20.8   0.0    0.00026   20.5   0.0    1.2  1  ParA             NUBPL iron-transfer P-loop NTPase
     0.0003   21.2   0.0    0.00035   21.0   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0003   21.2   0.0    0.00058   20.3   0.0    1.5  1  AAA_17           AAA domain
    0.00039   20.1   0.0    0.00054   19.6   0.0    1.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00058   19.8   0.1     0.0013   18.7   0.1    1.6  1  NACHT            NACHT domain
    0.00085   19.3   0.0      0.001   19.0   0.0    1.2  1  AAA_31           AAA domain
    0.00091   19.1   0.0     0.0014   18.5   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0011   19.0   0.0     0.0016   18.4   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0018   17.6   0.0     0.0029   16.9   0.0    1.3  1  Zeta_toxin       Zeta toxin
     0.0031   17.8   0.0     0.0051   17.1   0.0    1.5  1  AAA_22           AAA domain
     0.0035   16.7   0.0     0.0073   15.6   0.0    1.7  1  6PF2K            6-phosphofructo-2-kinase
     0.0043   17.2   0.5     0.0098   16.0   0.1    1.8  2  SKI              Shikimate kinase
     0.0046   16.7   0.0     0.0092   15.7   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
     0.0055   17.2   0.0      0.012   16.2   0.0    1.4  1  ABC_tran         ABC transporter
     0.0061   16.0   0.0      0.012   15.0   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0063   16.9   0.0      0.016   15.6   0.0    1.7  2  AAA              ATPase family associated with various cellul
     0.0073   15.9   0.0      0.015   14.9   0.0    1.5  1  AAA_25           AAA domain
     0.0079   16.0   0.0      0.013   15.3   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.029   14.1   0.0    1.3  1  AAA_24           AAA domain
      0.026   14.9   0.0      0.046   14.1   0.0    1.4  1  RNA_helicase     RNA helicase
      0.027   14.2   0.0      0.047   13.4   0.0    1.5  1  CoaE             Dephospho-CoA kinase
      0.053   13.6   0.0       0.13   12.3   0.0    1.7  1  AAA_14           AAA domain
      0.053   12.8   0.0      0.075   12.3   0.0    1.2  1  MipZ             ATPase MipZ
      0.062   12.8   0.0        0.1   12.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.073   14.1   0.0       0.11   13.5   0.0    1.4  1  LytR_C           LytR cell envelope-related transcriptional a
      0.075   13.4   0.1       0.12   12.7   0.1    1.4  1  AAA_19           AAA domain
      0.077   12.2   0.0       0.14   11.3   0.0    1.4  1  NB-ARC           NB-ARC domain
      0.092   12.9   0.0        0.2   11.7   0.0    1.7  1  Cytidylate_kin2  Cytidylate kinase-like family
      0.098   11.7   0.0       0.15   11.1   0.0    1.3  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.12   11.8   0.0       0.14   11.5   0.0    1.1  1  IPT              Isopentenyl transferase
       0.12   12.1   0.0       0.22   11.2   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
       0.16   11.8   0.0       0.36   10.6   0.0    1.6  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
       0.16   11.7   0.0       0.25   11.1   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
       0.16   11.8   0.0        0.3   11.0   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
       0.17   11.1   0.0       0.17   11.1   0.0    1.2  1  KAP_NTPase       KAP family P-loop domain


Domain annotation for each model (and alignments):
>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.8   0.0   1.2e-61   4.7e-59       1     156 [.       9     165 ..       9     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 198.8 bits;  conditional E-value: 1.2e-61
                                    S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                     APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRkenirrvaevaklladaglivlva 80 
                                    +g+vvwltGl gsGK+tia++l+  L+++g++v++LdGd  R+ ++++ gf++e+R  +++r+a +a+lla++g+iv+++
  gi|118431358|ref|NP_147777.2|   9 KGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVSEGAGFTREERLRHLKRIAWIARLLARNGVIVICS 88 
                                    689***************************************************************************** PP

                                    ----SHHHHHHHHHHHHCH.TEEEEEEEE--HHHHHHHTTTSHHHHHHTTSSSSHTTTSS-----SS-SEEEETTTS CS
                     APS_kinase  81 fisPyreeReaarelleea.lkfievfvdtplevceerDpkglYkkareGeikeftGidspYeaPenpelvvdtdke 156
                                    f+sPy+++R+++r+++ee+ + f+e++v+++le+  +rDpkglYkka +Ge+++ftGi++pYe+Penp+lv+dt+++
  gi|118431358|ref|NP_147777.2|  89 FVSPYKQARNMVRRIVEEEgIPFLEIYVKASLEEVIRRDPKGLYKKALKGELENFTGITDPYEPPENPQLVLDTESN 165
                                    ****************9888*****************************************************9876 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   8.1e-14   3.2e-11       4     141 ..      13     154 ..      11     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.1e-14
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHH.HHHHHHHHHHTT.S.EEEE-S--- CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRs.slrsavkrdLskek.vVIvDslny 81 
                                    v ltGlP sGK+t+a +La+ l++e+++v v+d +  +++ ++ +   +e++lR+ + ++ ++r L ++  +VI+  +  
  gi|118431358|ref|NP_147777.2|  13 VWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVSEGAGFTREERLRHlKRIAWIARLLARNGvIVICSFVSP 92 
                                    679******************************9999988888666666666666266788*****99962689999999 PP

                                    SHHHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHHHHTT-S..S-HHH..HHHHHHH---TT CS
                          KTI12  82 ikgfRYeLyciakaakttlcvvyvvapldvlvkwneereekeeyekel..ldaLiqRyeePd 141
                                    +k  R  +  i+ +  +++  +yv+a+l+++++++ +   k+  + el  +  ++  ye P+
  gi|118431358|ref|NP_147777.2|  93 YKQARNMVRRIVEEEGIPFLEIYVKASLEEVIRRDPKGLYKKALKGELenFTGITDPYEPPE 154
                                    *******************************9999665555444433222666666666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   1.2e-13   4.9e-11       1     115 [.      12     127 ..      12     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.2e-13
                         AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil 75 
                                    +v+l GlpGsGK+t a+rl   l+k+g  +++l+ d +r+++ +    + +++ r l+r+  ++++     l a+++vi+
  gi|118431358|ref|NP_147777.2|  12 VVWLTGLPGSGKTTIATRLadlLQKEGyrVEVLDGDWARTTVSEGAGFTREERLRHLKRIA-WIAR-----LLARNGVIV 85 
                                    799***************955566666999************9844433333333333333.3333.....447788999 PP

                         AAA_33  76 datnlsr..rerarflklarrlgvpvrivvvetdeetlkeRl 115
                                       ++s+  ++r  +++++++ g p++ ++v+++ e+  +R 
  gi|118431358|ref|NP_147777.2|  86 ICSFVSPykQARNMVRRIVEEEGIPFLEIYVKASLEEVIRRD 127
                                    999999644778899*********************999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   7.9e-10   3.1e-07       1     109 [.      13     126 ..      13     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 7.9e-10
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                    ++ltG pG+GKtt+a +L+++l+     v++ d  + + ++ e     + +++rl+  k+ +++  l +       ++++
  gi|118431358|ref|NP_147777.2|  13 VWLTGLPGSGKTTIATRLADLLQKegyRVEVLDGDWARTTVSEGA--GFTREERLRHLKRIAWIARLLAR------NGVI 84 
                                    78****************888622222333333333333333333..44777777777777777777775......58** PP

                         AAA_18  78 vidghlaeleseaakdikk..........vvLtaspeelleR 109
                                    vi ++++ + ++++  +            ++++as ee ++R
  gi|118431358|ref|NP_147777.2|  85 VICSFVSPYKQARNMVRRIveeegipfleIYVKASLEEVIRR 126
                                    ******999987665444478*******************99 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 !   28.9   0.0   2.4e-09   9.8e-07       9     110 ..      20     113 ..      14     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.4e-09
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH...CCHCCCHHH..HHHCHCHHHH..EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep...dlkrllell..ealgkkkalllkiagvvlnr 83 
                                    G+GKTt+a+ La +l+++g+rV ++D D  ++  +  eg    +e+    lkr   ++  ++l  +     + + v+   
  gi|118431358|ref|NP_147777.2|  20 GSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVS--EGAGFTREErlrHLKR---IAwiARLLAR-----NGVIVICSF 89 
                                    9***************************9977766..7777777773344444...3333666655.....234444444 PP

                                    ESS...-TTCHHHHHHHHHHCTS-EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  84 vdgeneetllkealeelkqrygvpvlg 110
                                    v +   +++ +++++++ ++ g+p+l 
  gi|118431358|ref|NP_147777.2|  90 VSP---YKQARNMVRRIVEEEGIPFLE 113
                                    444...455555555555555888886 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 !   24.8   0.0   2.4e-08   9.6e-06      30      68 ..      11      49 ..       4      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.4e-08
                                   EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--- CS
                           MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPs 68
                                    vv ltG+PG+Gk t+  +l+  l+++G+rv vl  D +
  gi|118431358|ref|NP_147777.2| 11 IVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWA 49
                                   6899*****************************987755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.2e-08   1.3e-05      18      94 ..      10      85 ..       3     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.2e-08
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgieastiakllkrlkgrarlepgtlliv 94
                                     v+ ltG +G+GKtt+ + l+++++++g+rv +l      A++ ++e++g++ +   + lkr ++ arl +++ +iv
  gi|118431358|ref|NP_147777.2| 10 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDW--ARTtVSEGAGFTREERLRHLKRIAWIARLLARNGVIV 85
                                   46899****************************995444..4333888888877777777777776666666655554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.2e-08   2.5e-05       3      42 ..      12      51 ..      10      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.2e-08
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa 42
                                   v+ l Gl G+GKTt +++La+ll+keg++v +   D  R 
  gi|118431358|ref|NP_147777.2| 12 VVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWART 51
                                   6889****************************99999987 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.3e-07   5.3e-05       2      31 ..      13      42 ..      12      61 .. 0.93
   2 ?   -1.4   0.0       4.9     2e+03     120     150 ..      76     109 ..      62     126 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-07
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   v +TG pG+GKtT+  ++++ll+++g++v+
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLADLLQKEGYRVE 42
                                   789************************995 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.9
                                    HHHT.TTSEEEE..E--SS--SHHHHHHHT-TT- CS
                       NTPase_1 120 evLk.sekpvla..vihrrkdlalveeirerkdv 150
                                    ++L+ ++++v+   v + ++  ++v++i e++++
  gi|118431358|ref|NP_147777.2|  76 RLLArNGVIVICsfVSPYKQARNMVRRIVEEEGI 109
                                    4455344444431133344455666666665554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.1e-06   0.00043       2      58 ..      13      77 ..      12      82 .. 0.76
   2 ?   -1.1   0.0       4.9     2e+03     139     161 ..      98     121 ..      93     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.1e-06
                         AAA_28  2 ivitGgestGKTtlleaLa...ar.gyp..vv.pEaareileekl.akgedalpwvedllafaer 58
                                   + +tG +++GKTt++ +La   ++ gy+  v+  + ar+ ++e++ +++e+ l++ +++ ++a++
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLAdllQKeGYRveVLdGDWARTTVSEGAgFTREERLRHLKRIAWIARL 77
                                   679****************665226777446799*****99999977777777776666666554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.9
                         AAA_28 139 erlrealrelgipviivp.sgdve 161
                                    +++r +++e gip++++  ++++e
  gi|118431358|ref|NP_147777.2|  98 NMVRRIVEEEGIPFLEIYvKASLE 121
                                    678899999999999987666666 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 !   20.5   0.0   6.5e-07   0.00026       5      55 ..      11      61 ..       7     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.5e-07
                           ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgvee 55
                                   +++ l g  G GK+t+a+ lA  L+k+g++v +lD D     + +  g ++
  gi|118431358|ref|NP_147777.2| 11 IVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVSEGAGFTR 61
                                   455567888****************************87777766666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.7e-07   0.00035      26      82 ..      12      84 ..       6     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.7e-07
                         AAA_16 26 lvllsGesGvGKsslvrellralekd..................ggiflrgkcdqlesaipysa.laqalareell 82
                                   +v l+G +G+GK++++++l++ l+k+                  g+ f+r++  ++   + ++a +a++lar++++
  gi|118431358|ref|NP_147777.2| 12 VVWLTGLPGSGKTTIATRLADLLQKEgyrvevldgdwarttvseGAGFTREERLRH---LKRIAwIARLLARNGVI 84
                                   588*****************999999654444444444333333333333333333...44455566666665555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.5e-06   0.00058       1      47 [.      16      66 ..      16     129 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.5e-06
                                   EE-TTSSHHHHHHHHH.....HHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC CS
                         AAA_17  1 lGgPGsGKgtqceklv.....ekygfthlsaGdllreeakrgglakardemr 47
                                   +G+PGsGK+t++ +l+     e y +++l  Gd  r ++++g   + ++++r
  gi|118431358|ref|NP_147777.2| 16 TGLPGSGKTTIATRLAdllqkEGYRVEVLD-GDWARTTVSEGAGFTREERLR 66
                                   7**************855544678888888.*****9998885422222222 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-06   0.00054       2      41 ..      12      53 ..      11      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHC CS
                           cobW  2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsi 41
                                   v+ ltG +GsGKTt+ ++l    +++g+++ v+ ++   + +
  gi|118431358|ref|NP_147777.2| 12 VVWLTGLPGSGKTTIATRLAdlLQKEGYRVEVLDGDWARTTV 53
                                   6789************999988899***********987655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.2e-06    0.0013       2      28 ..      12      38 ..      11      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.2e-06
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaegk 28
                                   +v+l+G +GsGKTt + +la++++++ 
  gi|118431358|ref|NP_147777.2| 12 VVWLTGLPGSGKTTIATRLADLLQKEG 38
                                   79*********************9986 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.5e-06     0.001      12      61 ..      20      70 ..      11     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-06
                         AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlD.pQanattglgiekneiektlye 61
                                   G GKTT ++ la  l k+g++v + D D + +  + g+g++++e+ ++l +
  gi|118431358|ref|NP_147777.2| 20 GSGKTTIATRLADLLQKEGYRVEVLDGDwARTTVSEGAGFTREERLRHLKR 70
                                   99**************************44566677888777775555544 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 !   18.5   0.0   3.6e-06    0.0014       2      33 ..      13      44 ..      12      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-06
                           MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                   + ++g  gsGKTt+ ++l   l+++g+rv ++
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLADLLQKEGYRVEVL 44
                                   678999***********************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 !   18.4   0.0   4.1e-06    0.0016       2      40 ..      13      52 ..      12      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.1e-06
                                   EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHH CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteed 40
                                   v L G pG+gK+++a rla +l +  + +  l  d+ +++
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLADLLqKEGYRVEVLDGDWARTT 52
                                   5699******************766666666666666655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.3e-06    0.0029      15      57 ..       9      52 ..       2      70 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.3e-06
                     Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRel 57
                                   + +++ l G pG+GK+++a+ l+d l+++g  v +ld+D  R+ 
  gi|118431358|ref|NP_147777.2|  9 KGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVeVLDGDWARTT 52
                                   567899*********************65555526788888875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-05    0.0051       9      39 ..      14      40 ..       8     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-05
                         AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeer 39
                                    +tG +G+GKTt + rl++ l++e +    r
  gi|118431358|ref|NP_147777.2| 14 WLTGLPGSGKTTIATRLADLLQKEGY----R 40
                                   589*****************976544....3 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-05    0.0073      12      48 ..       9      45 ..       1     129 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                                   S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                          6PF2K 12 sklvivlvGLpargKtyiskkltrylkwlgvrtkvFn 48
                                   + +v+ l GLp  gKt+i+++l   l+  g+r  v +
  gi|118431358|ref|NP_147777.2|  9 KGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLD 45
                                   568899*********************9999988865 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       9.5   3.8e+03      82      92 ..       7      16 ..       3      17 .. 0.76
   2 !   16.0   0.1   2.5e-05    0.0098       1     101 [.      19     126 ..      19     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.5
                                   HHHHSEEEEEE CS
                            SKI 82 lkekgiviyLd 92
                                   + ekgiv++L 
  gi|118431358|ref|NP_147777.2|  7 I-EKGIVVWLT 16
                                   4.49*****95 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.5e-05
                                    TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHH.HHHHCCCSSEEEEE-TTGGGSHHHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsev.lkelleeeglViatGGGavlseenr 79 
                                    +G+GK+t++ +lA+ l+ e + +  l  + ++++++e      ee+ r l + + +++ll+++g+++ +   ++ ++ +r
  gi|118431358|ref|NP_147777.2|  19 PGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVSEGAGFTREERLRHLKRIAwIARLLARNGVIVICSFVSPYKQ-AR 97 
                                    69***********99876555555555555555555555555679999999877699*****999999955555443.44 PP

                                    HHHH....HHSE...EEEEE--HHHHHHH CS
                            SKI  80 ellk....ekgi...viyLdvsleeller 101
                                    ++++    e+gi    iy+++slee+++r
  gi|118431358|ref|NP_147777.2|  98 NMVRriveEEGIpflEIYVKASLEEVIRR 126
                                    44444555887755569999999999987 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-05    0.0092       3      28 ..      17      43 ..      15      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                                   ESTTSSHHHHHHHHHHHHHHTTE..EE CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vv 28
                                   Gl G+GKtt+a  l++ l++eg++  v
  gi|118431358|ref|NP_147777.2| 17 GLPGSGKTTIATRLADLLQKEGYRvEV 43
                                   999********************9555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     3e-05     0.012       8      51 ..       7      50 ..       4      75 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-05
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                   +++g +v ++G  G+GK+t++  la ll+++  ++++ + d+ +
  gi|118431358|ref|NP_147777.2|  7 IEKGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWAR 50
                                   78999***********************9887778666655555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     3e-05     0.012      25      48 ..      13      36 ..      10      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpp 48
                                   + l+G pGsGKt +a+rl+ ll +
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLADLLQK 36
                                   5699****************9976 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   4.1e-05     0.016       2      29 ..      14      41 ..      13      89 .. 0.70
   2 ?   -1.6   0.0       8.8   3.5e+03      14      40 ..      99     125 ..      94     137 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-05
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEE CS
                            AAA  2 llyGppGtGKTllakavakelgveflei 29
                                    l+G pG GKT++a  +a  l+ e +++
  gi|118431358|ref|NP_147777.2| 14 WLTGLPGSGKTTIATRLADLLQKEGYRV 41
                                   699***************9996433322 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 8.8
                                    HHHHHHHHHTHEEEEEETTTCSSSSTT CS
                            AAA  14 lakavakelgvefleisgsellskyvg 40 
                                    +++ +++e g++flei ++  l++++ 
  gi|118431358|ref|NP_147777.2|  99 MVRRIVEEEGIPFLEIYVKASLEEVIR 125
                                    567788888899999888877766555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.8e-05     0.015      29      54 ..       6      31 ..       3      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-05
                         AAA_25 29 llpagelallaGapgtGKttlaldla 54
                                   ++ +g ++ l+G pg+GKtt+a+ la
  gi|118431358|ref|NP_147777.2|  6 CIEKGIVVWLTGLPGSGKTTIATRLA 31
                                   6889*******************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 !   15.3   0.0   3.3e-05     0.013       2      35 ..      16      49 ..      15      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.3e-05
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPA 35
                                   +G +GsGKtt+  +l+++l+++g++v+v+  D A
  gi|118431358|ref|NP_147777.2| 16 TGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWA 49
                                   699***********************99876655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.2e-05     0.029       2      29 ..      10      44 ..       9      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-05
                         AAA_24  2 klkiliyGpsgiGKTtlakel.......gpkplfi 29
                                   ++ ++++G +g+GKTt+a++l       g+++ ++
  gi|118431358|ref|NP_147777.2| 10 GIVVWLTGLPGSGKTTIATRLadllqkeGYRVEVL 44
                                   6789***************9966655555555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   0.00012     0.046       1      25 [.      13      37 ..      13      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00012
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                   +wl+G +g GK+t+a++La+ l+k+
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLADLLQKE 37
                                   7****************99988865 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00012     0.047       2      41 ..      12      56 ..      11      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                   EEEEEESTTSSHHHHHHHHHH......TT-EEEEHHHHHHHTTCCT CS
                           CoaE  2 ivgltGgiasGKstvanlfad......lgvpivDaDlvArqvvepg 41
                                   +v ltG  +sGK+t+a ++ad      + v+++D D  Ar  v +g
  gi|118431358|ref|NP_147777.2| 12 VVWLTGLPGSGKTTIATRLADllqkegYRVEVLDGDW-ARTTVSEG 56
                                   789************9988763211344689999996.55555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00033      0.13       4     107 ..      12     126 ..       9     145 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                         AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd.........kkladpe......kllelileklke...ekk 65 
                                    ++ +tG+  +GKTt++ +l++ l  +  ++  ++ d  r+         +     e      k +  i     +   ++ 
  gi|118431358|ref|NP_147777.2|  12 VVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWARTtvsegagftR-----EerlrhlKRIAWIA----RllaRNG 82 
                                    789**************999544433333333333333333333333221.....11111111222222....1332356 PP

                         AAA_14  66 tylflDEiqevpewekalkslvdeg..knldvivtGSnskllsk 107
                                     +++   ++ +++++++++++v+e+  + l+++v  S+  ++ +
  gi|118431358|ref|NP_147777.2|  83 VIVICSFVSPYKQARNMVRRIVEEEgiPFLEIYVKASLEEVIRR 126
                                    66666677888888888888888766777788888887776655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019     0.075      10      44 ..      19      53 ..      11      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                   TTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH CS
                           MipZ 10 GGsGksttavhvavaLlkkGarvaaidldlrqrtl 44
                                    GsGk+t+a  +a  L k+G rv ++d d  + t+
  gi|118431358|ref|NP_147777.2| 19 PGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTV 53
                                   59*************************99877776 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   0.00025       0.1      28      65 ..       5      42 ..       1      54 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
                          AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldkekylsl 65
                                   ++++++  v l+G  G+GKt+i+++l + l+ke y + 
  gi|118431358|ref|NP_147777.2|  5 KCIEKGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVE 42
                                   67899999***********************9999876 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 ?   13.5   0.0   0.00028      0.11       9      44 ..      20      52 ..      18      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00028
                         LytR_C  9 gtgvsGlAarvadaLeerGftvgevg.nagnadeett 44
                                   g+g++ +A r+ad+L+++G++v   + +++     tt
  gi|118431358|ref|NP_147777.2| 20 GSGKTTIATRLADLLQKEGYRVEVLDgDWAR----TT 52
                                   89******************88875524433....34 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    0.0003      0.12      12      38 ..      12      38 ..       5      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0003
                         AAA_19 12 vllvtaGpGtGKTrvlkhivallvelg 38
                                   v+ +t+ pG+GKT++ +    ll+++g
  gi|118431358|ref|NP_147777.2| 12 VVWLTGLPGSGKTTIATRLADLLQKEG 38
                                   7889*********99888888877766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.14      20      40 ..      10      30 ..       4      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                                   SEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 20 slvvalvGmgGvGKttlakqi 40
                                    +vv l G +G+GKtt+a+  
  gi|118431358|ref|NP_147777.2| 10 GIVVWLTGLPGSGKTTIATRL 30
                                   48999*************876 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00051       0.2       4      45 ..      15      56 ..      12     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00051
                Cytidylate_kin2  4 IsreyGsgGetigeaLAekLglpfydreiieevakelglsee 45
                                   +++  Gsg++ti+ +LA+ L+ + y  e+++    ++ +se 
  gi|118431358|ref|NP_147777.2| 15 LTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVSEG 56
                                   66778***************9999999998866666666554 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.15      47      71 ..      20      44 ..      11      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                                   -HSHHHHHHHHHHHTTTS..-EEEE CS
                           LpxK 47 GtGKTPlvialvkllqarglkvgvl 71
                                   G+GKT ++  l++llq++g++v vl
  gi|118431358|ref|NP_147777.2| 20 GSGKTTIATRLADLLQKEGYRVEVL 44
                                   9*********************997 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00035      0.14       6      71 ..      15      84 ..      10     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00035
                            IPT  6 ifGatttGKtaeaikla...ketgapvivlDRvqcyselavgsGrpleeelegtrRiylddrsls.eGvi 71
                                   + G  ++GKt  a +la   +++g+ v vlD   + + ++ g+G   ee+l+ ++Ri  + r l+ +Gvi
  gi|118431358|ref|NP_147777.2| 15 LTGLPGSGKTTIATRLAdllQKEGYRVEVLDGDWARTTVSEGAGFTREERLRHLKRIAWIARLLArNGVI 84
                                   5678899*******99966689**********************************97777766426776 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 ?   11.2   0.0   0.00055      0.22      42      78 ..       5      41 ..       1      53 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00055
                      IstB_IS21 42 sfiekkenivllGpsGvGKshlaialgveavraglsv 78
                                   + iek   + l+G +G GK+ +a+ l+    ++g++v
  gi|118431358|ref|NP_147777.2|  5 KCIEKGIVVWLTGLPGSGKTTIATRLADLLQKEGYRV 41
                                   6678888899*****************9999999998 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 ?   10.6   0.0   0.00091      0.36       4      33 ..      20      49 ..      17      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00091
                         CLP1_P  4 dsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                    sGK+T+a+ L++ + ++g+++ ++D D  
  gi|118431358|ref|NP_147777.2| 20 GSGKTTIATRLADLLQKEGYRVEVLDGDWA 49
                                   79*************************975 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00062      0.25       3      43 ..      14      54 ..      12      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00062
                            PRK  3 gvagsSGaGkttvarklekifgrekvkaaeiegdsflrldr 43
                                    ++g  G+Gktt+a +l +++++e+ +  + +gd   ++++
  gi|118431358|ref|NP_147777.2| 14 WLTGLPGSGKTTIATRLADLLQKEGYRVEVLDGDWARTTVS 54
                                   589999****************9998866666666655555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00075       0.3       2      32 ..      13      43 ..      12      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00075
                          AAA_3  2 vllegvPGlaktllvkalakaldlefkriqf 32
                                   v l+g+PG +kt+++  la+ l+ e  r+ +
  gi|118431358|ref|NP_147777.2| 13 VWLTGLPGSGKTTIATRLADLLQKEGYRVEV 43
                                   56899******************99999865 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.17      18      47 ..       8      37 ..       2     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                     KAP_NTPase 18 atpivvgLygkWGsGKssllnkledelkef 47
                                   +++ivv L+g  GsGK+++ ++l d l+++
  gi|118431358|ref|NP_147777.2|  8 EKGIVVWLTGLPGSGKTTIATRLADLLQKE 37
                                   679***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1285.38
//
Query:       gi|118431359|ref|NP_147778.2|  [L=265]
Description: hypothetical protein APE_1196.1 [Aeropyrum pernix K1]
Scores for 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   96.4  32.4    2.5e-27   96.1  32.4    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
        6.8    4.8  11.8       0.69    8.1   4.4    2.0  2  DUF2070   Predicted membrane protein (DUF2070)


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 !   96.1  32.4   2.8e-31   2.5e-27       2     234 ..      13     247 ..      12     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 2.8e-31
                           TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrg..nvdwrlllllllgsliGal 78 
                                    ++ gl+a+ ++  lG+G+gl+a+P+L+++ l+p++a+a++l+a+v++s+++++a+r +g       +ll+l+++sl+G++
  gi|118431359|ref|NP_147778.2|  13 FMSGLIASSLDYGLGLGFGLLATPILVVMgLDPRQAIAAALVAQVISSATALIAWRSHGakPPSTDVLLVLIASSLAGVV 92 
                                    789*************************669**************************9832335789************* PP

                           TauE  79 lGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvliggl.vGllsGllGiGgGfllvplllll 157
                                    lG+++++ll ++  ++++ v+l+ +a l +++++ s   +++r  ++++++l gg+ +Gl  +l G+G  ++lv+   + 
  gi|118431359|ref|NP_147778.2|  93 LGSVFMSLLGDAEALAIYTVALAGIATLYMATATDSYSLEVRRLGRRPITIL-GGFlGGLSKALSGGGFSPILVASQRV- 170
                                    *******999885566666666655555544444344444555555555555.55549999999999999988888885. PP

                           TauE 158 lglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfallllvlgv 234
                                     g++ k +  +  l+  +  la+a++y +ag++ + +++ l++g++lG+ll+ rl+r +++r+  +l++l l+++ +
  gi|118431359|ref|NP_147778.2| 171 SGVDYKASLVAIPLVKPLAFLAAAVIYSWAGYMEPYTAASLTAGSILGSLLAPRLSRLIPRRWAHALVGLALAAAML 247
                                    89999997666666777888889999999********************************9999999999888766 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.4   7.7e-05      0.69      90     200 ..       8     127 ..       4     139 .. 0.76
   2 ?    1.4   0.8    0.0085        76     130     182 ..     179     236 ..     142     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 7.7e-05
                        DUF2070  90 illsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly........fspesflllllls 161
                                    +l +++++ l+  +l  +l l f+l    +++v++ ++++a++ al+  +++ +++++          s++  l+l+++s
  gi|118431359|ref|NP_147778.2|   8 YLSAVFMSGLIASSLDYGLGLGFGLLATPILVVMGLDPRQAIAAALVAQVISSATALIAwrshgakpPSTDVLLVLIASS 87 
                                    55554457777788888899999999999999999999999999999999988888888899**9986778888999999 PP

                        DUF2070 162 lifalavylfivvv.drplkrnlgvsaldllsaFlahile 200
                                    l+ +++  +f+ ++ d    +++ v    +   ++a+ ++
  gi|118431359|ref|NP_147778.2|  88 LAGVVLGSVFMSLLgDAEALAIYTVALAGIATLYMATATD 127
                                    9999888888766525666666666666666666666555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.0085
                        DUF2070 130 avlpaliqpllailllvly.....fspesfllllllslifalavylfivvvdrplkrn 182
                                     v++ l+ pl++++++v+y     ++p++++ l + s++  l++  + +++ r++ ++
  gi|118431359|ref|NP_147778.2| 179 LVAIPLVKPLAFLAAAVIYswagyMEPYTAASLTAGSILGSLLAPRLSRLIPRRWAHA 236
                                    2366799999999999999888887888888888888888887777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1866.71
//
Query:       gi|118431360|ref|NP_147779.2|  [L=383]
Description: sulfate adenylyltransferase [Aeropyrum pernix K1]
Scores for 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-86  287.2   0.1    8.7e-86  286.8   0.1    1.1  1  ATP-sulfurylase  ATP-sulfurylase
    1.1e-48  164.9   0.0      2e-48  164.1   0.0    1.4  1  PUA_2            PUA-like domain
  ------ inclusion threshold ------
      0.033   14.1   0.1      0.065   13.2   0.1    1.4  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.8   0.1   1.5e-89   8.7e-86       2     210 ..     169     376 ..     168     378 .. 0.98

  Alignments for each domain:
  == domain 1  score: 286.8 bits;  conditional E-value: 1.5e-89
                                    CCB.-HHHHHHHHHHTT-SSEEEEEESS---HHHHHHHHHHHHHTSEEEEEEEB-SB-STTSTTHHHHHHHHHHHHHHHS CS
                ATP-sulfurylase   2 eyrltPaevreefkekgwdkVvAfqtrnplHraHeellkraleeeadglllhplvgptkpgdvpaevrvrayealieeyl 81 
                                    +y l P e+r  fkekgw++V+Afqtrn++H +He+++k al+  +dgll+hpl g++k gd+++ev++rayeali +y+
  gi|118431360|ref|NP_147779.2| 169 RYTLWPVETRVLFKEKGWRTVAAFQTRNVPHLGHEYVQKAALT-FVDGLLVHPLAGWKKRGDYRDEVIIRAYEALITHYY 247
                                    7999***************************************.8*********************************** PP

                                    -GGGEEE-BB-SB---SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STCSS-TTHHHHHHHHCHHHCTSEEEE---EEEET CS
                ATP-sulfurylase  82 pkdrvvlallplamryaGprEallhaiirknyGcthfivGrdhagvgdfYgpydaqellakvagelgiepvkfeeavYck 161
                                    p+ +vvl++l ++m yaGprEa+ hai+rkn+G+thfivGrdhagvg++Ygpy+a e++++++ +lgi+p++++ea+Yc+
  gi|118431360|ref|NP_147779.2| 248 PRGVVVLSVLRMNMNYAGPREAVHHAIVRKNFGATHFIVGRDHAGVGSYYGPYEAWEIFREFP-DLGITPLFVREAYYCR 326
                                    **************************************************************9.6*************** PP

                                    TTTEEEECCCC.GCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHHH CS
                ATP-sulfurylase 162 kegevasektc.hkkeevesisgtelrkllregeeipewfsrpevlkvLr 210
                                    ++g++++ek c h++e +++isgt+lr++l +ge++pe ++rpev++ + 
  gi|118431360|ref|NP_147779.2| 327 RCGGMVNEKVCpHGDEYRVRISGTRLREMLGRGERPPEYMMRPEVADAII 376
                                    **********************************************9886 PP

>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.0   3.4e-52     2e-48       2     158 ..       4     161 ..       3     162 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 3.4e-52
                                    S-TTSS----B--CHHHHHHHHHHHTS-EEE--HHHHHHHHHHHTTTTTT-SCC--HHHHHHHHHHSEETTS-E-SS--- CS
                          PUA_2   2 kphggkLvelvvedeekeellkeakelpsielskrelqdlellaeGgfsPLegFmreedyesvleemrLadgllwsiPiv 81 
                                    +phgg+Lv++v++++++e  +++ +e+p++e+  +++ d e la G+fsPLegFm e+dy+svl++mrL+++l w+iPiv
  gi|118431360|ref|NP_147779.2|   4 RPHGGRLVRRVLSGRRREIFESQYREMPRLEVPLERAIDAEDLARGVFSPLEGFMVEDDYLSVLSRMRLSNDLPWTIPIV 83 
                                    7******************************************************************************* PP

                                    EEEECCHCHH..HTT-SEEEEEETTTEEEEEEEEEEEEE-HHHHHHHHHHS---TTSHHHHHHCTS-SEEEEEEEEE-S CS
                          PUA_2  82 Ldvseedakk..lkegdrvaLkdkegellAileveeiyeldkeeeaekvfgttdeaHPgvkkvleqgevlvgGkvevle 158
                                    Ld+++e + +  +++gd++ L+++ g ++A+l+ e+iy++dk  +aekvf+t+d++HPgv++++++g++l+gG++e+++
  gi|118431360|ref|NP_147779.2|  84 LDANREWVLNegVSAGDDIILTYH-GLPIAVLTLEDIYSWDKGLHAEKVFKTRDPNHPGVEATYKRGDILLGGRLELIQ 161
                                    ******986667************.***************************************************997 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05     0.065      22      35 ..     320     333 ..     314     336 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                 Zn_ribbon_SprT  22 rhnYrCrrCkgtLr 35 
                                    r++Y+CrrC+g+ +
  gi|118431360|ref|NP_147779.2| 320 REAYYCRRCGGMVN 333
                                    899*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2850.49
//
Query:       gi|14601246|ref|NP_147780.1|  [L=458]
Description: hypothetical protein APE_1199 [Aeropyrum pernix K1]
Scores for complete 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  202.4   0.0    1.8e-59  202.1   0.0    1.0  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
     0.0059   16.0   0.0      0.012   15.1   0.0    1.4  1  Sulfatase     Sulfatase


Domain annotation for each model (and alignments):
>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.1   0.0     2e-63   1.8e-59       1     357 []       4     405 ..       4     405 .. 0.92

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 2e-63
                                   EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEET CS
                  Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfvt 81 
                                   +lvi+lD++++ l++++++l pnl++L++  v+++ l++  P++T+p++  ++ G++ ge G++g++ + +++    ++v+
  gi|14601246|ref|NP_147780.1|   4 LLVIGLDSVPPLLIEKFRDLIPNLQSLLN--VKGK-LLSGHPPITVPMWGVMLAGRSAGELGVYGFRHRRPGDVGT-SYVV 80 
                                   69**************999**********..****.*******************************999999986.9999 PP

                                   TTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC...........TBHHSBTCT.........CSTTS.. CS
                  Phosphodiest  82 ededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvs..........etppryled........dfnakv.. 142
                                   ++++    + ++++wd++    gl++ ++++p ++++++ +++ vs            +p+ l++        d+  +v  
  gi|14601246|ref|NP_147780.1|  81 TSRS----IAEGWVWDDLGLRLGLRSLVIGVPPGYPARRVRGWFVScfltpgvdgaFAWPPGLKReilkasggDYVFDVky 157
                                   9887....************************************************8888888788888999955555511 PP

                                   CHHHHHHHHHHHHH..HHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TT..SHH..............HHHHHHHHH CS
                  Phosphodiest 143 pledkvdkavlqtw..ldaafakvvlekelekpdlllvyleetDtvgHkfGpd..spe..............vedalrrvD 205
                                    +edk + ++++ w   +++f+ v + ++++ +d+ + ++ +tD+v+H f ++  +pe              ++++++ vD
  gi|14601246|ref|NP_147780.1| 158 RVEDKES-VRKSLWrlAKTQFKVVKYLLSSKPWDFAMYMHIGTDRVHHAF-WKywDPEhprypgegnpyenvLPEYYSLVD 236
                                   5555555.3444556699999999999888********************.9779************************** PP

                                   HHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTSTGGH.....................GEEEEECBHHS. CS
                  Phosphodiest 206 kaigdLlealderglsaetniilvSDHGmadvsddkvielndlleekg.....................llhlkdegkgga 265
                                   k+ig+Lle+l+ +     t++i+vSDHG++++  ++++ +n++lee+g                     +++++++++gg+
  gi|14601246|ref|NP_147780.1| 237 KHIGQLLESLPGD-----TDVIVVSDHGAKAM--KGAFAINQWLEEEGylslkeepkrpgadleasmidWDRTMAWAWGGY 310
                                   ***********99.....**************..*********************************************** PP

                                   SSEEEEEESTEE.E.CCCTTHHHHHHHHHHTCHHCCHSTHTT..TEEEEEGG.GS-GGGCHSTTS-SEEE.EE-TTEEEES CS
                  Phosphodiest 266 kaliainpkare.lnrvaeaeaeevyaelkakleelrkkege..alavylke.aipkrlhykkrapdlvl.vadpgwsits 341
                                   +++++in+k+re ++ v ++e+++v+++lk+++e++r ++ge    ++y+++  +p+  +  + apdl++ +++ +w++++
  gi|14601246|ref|NP_147780.1| 311 YSRVYINLKGREpRGIVGREEYWSVVEQLKRDIEKIRGPNGErwENKAYHPSeLYPE-VR--GDAPDLMVyLDNLSWRPAG 388
                                   *************************************66898899999999945665.55..9****************** PP

                                   STTCS.SBS-SEE--SS CS
                  Phosphodiest 342 kdkpd.eyeikgthGyd 357
                                   + +++ +y  ++++G+d
  gi|14601246|ref|NP_147780.1| 389 TIGWPsTYLEENDRGPD 405
                                   *****999999999986 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-06     0.012     171     265 ..     191     272 ..     172     284 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-06
                                   SSEEEEEEE-TTSSSTCTCGGHTCCGSTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                     Sulfatase 171 kpfflylatlapHappeapdeyakkyatffddgseaarqlleaylnsveyvDdligrvlaaLeenglldntlvvftSDhga 251
                                      ++++ t  +H+++    +y +  + +++  ++ ++++l +y+     vD++ig++l+ L       +t v+++SDhga
  gi|14601246|ref|NP_147780.1| 191 FAMYMHIGTDRVHHAF---WKYWDPEHPRYPGEGNPYENVLPEYYSL---VDKHIGQLLESL-----PGDTDVIVVSDHGA 260
                                   4445666677777655...4443443334433344455788888876...699*********.....99999********* PP

                                   CCCGHHTTSSSCTT CS
                     Sulfatase 252 sleesngplrggkg 265
                                       ++g++ ++++
  gi|14601246|ref|NP_147780.1| 261 KA--MKGAFAINQW 272
                                   99..7787777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3530.84
//
Query:       gi|118431361|ref|NP_147781.2|  [L=416]
Description: nucleotidyl transferase [Aeropyrum pernix K1]
Scores for complete 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   86.3   0.0    3.1e-24   85.9   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.8e-13   49.0  14.2    3.2e-05   23.5   1.5    4.0  3  Hexapep          Bacterial transferase hexapeptide (six repea
    2.6e-10   40.9   0.6    3.8e-10   40.3   0.6    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.026   14.3   5.0       0.76    9.6   0.4    3.4  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0     7e-28   3.1e-24       3     243 ..       7     231 ..       5     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 7e-28
                                    EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHH.HHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsr.lansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    v+LaGG+G+RLwP++ t+ak+lvp+lg+ +l+   l   la   ++e  vvl  ++  +v e +++   fg  v ++ + 
  gi|118431361|ref|NP_147781.2|   7 VVLAGGRGERLWPVSETRAKPLVPILGE-PLVCRHLRLgLATGLFDE-AVVLVGYRGGEVVEAVRACG-FG-GVRFVEQG 82 
                                    89**************************.777766665155566777.99****************99.77.6******* PP

                                    S--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEE CS
                NTP_transferase  82 egkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrver 161
                                       gt +Av+ ++e l+ e     + ++ gD++ +  +  ++++a++ +      +++ +ve+a+ yG+  +++ g v+ 
  gi|118431361|ref|NP_147781.2|  83 GALGTGHAVRRVLEELGGEGV---FTFVYGDVYLDSRFYGLLASAEAPS------VLAGWVEDARWYGLLDVGD-GLVRG 152
                                    *******************95...******************9987655......589999************9.89*** PP

                                    EECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHH CS
                NTP_transferase 162 fvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllea 241
                                     vEKP+e++   ++  G +  + + l  l + le+++rge e+td+l+++ +eg   + +  +++ +W DvG + ++l+a
  gi|118431361|ref|NP_147781.2| 153 VVEKPREPR-GGWVFLGGFKVDGSFLGLL-RGLEPSPRGEVEVTDALEALAREGVLRALVGGEGW-GWVDVGRPWDVLRA 229
                                    *********.8899999888877766666.78*************************99999999.8*******999999 PP

                                    HH CS
                NTP_transferase 242 ne 243
                                    n+
  gi|118431361|ref|NP_147781.2| 230 NR 231
                                    86 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.6   7.9e-09   3.5e-05       3      36 .]     261     294 ..     259     294 .. 0.93
   2 !    9.4   0.3   0.00019      0.85       3      34 ..     314     344 ..     312     346 .. 0.77
   3 !   23.5   1.5   7.2e-09   3.2e-05       1      36 []     371     406 ..     371     406 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.9e-09
                                    EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                     I  ++ Ig+ +v+ g++ IG+++++g+g+ ++g
  gi|118431361|ref|NP_147781.2| 261 YIARGARIGAHSVVEGPAYIGPGARVGPGAHVRG 294
                                    68899*************************9986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00019
                                    EEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    vI +++   +  ++ g+ ++G++v +gag+v 
  gi|118431361|ref|NP_147781.2| 314 VIMEGARAPHLNYV-GDSVVGEHVNLGAGTVT 344
                                    67777777777788.6666**********996 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 7.2e-09
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    ++vIG  ++ g ++ i+++V IG+++ + +g+v+g+
  gi|118431361|ref|NP_147781.2| 371 GAVIGGYAQTGINVSIMPGVRIGPRALVYPGCVVGR 406
                                    589*******************************96 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.6   8.6e-14   3.8e-10       2     126 ..       7     138 ..       6     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 8.6e-14
                                    EEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHC..HHHHHHTTC...TS-EEE-TTSS- CS
                   NTP_transf_3   2 viLAGGrSsRm.....ggdKallplggkpllervldalraag.vdevvvvggde..evlaalarl...gvrvvededpgk 70 
                                    v+LAGGr+ R+      + K+l+p+ g+pl+ r+l+   a g +de vv +g++  ev +a++     gvr+ve+     
  gi|118431361|ref|NP_147781.2|   7 VVLAGGRGERLwpvseTRAKPLVPILGEPLVCRHLRLGLATGlFDEAVVLVGYRggEVVEAVRACgfgGVRFVEQG-GAL 85 
                                    9**********7776446******************9999985799999999954566666665533369999997.589 PP

                                    SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSE CS
                   NTP_transf_3  71 gplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyege 126
                                    g++++++  l++++++  + ++ +D+ +l++ ++  l+ a   +++  + ++ + +
  gi|118431361|ref|NP_147781.2|  86 GTGHAVRRVLEELGGEGVFTFVYGDV-YLDSRFYGLLASAE--APSVLAGWVEDAR 138
                                    *************99999999****9.67999988877763..4444444444444 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 ?    3.8   0.1     0.011        47       8      29 ..     266     289 ..     260     293 .. 0.82
   2 ?    0.5   0.0      0.11   5.1e+02       4      15 ..     332     343 ..     331     344 .. 0.76
   3 ?    9.6   0.4   0.00017      0.76      11      33 ..     381     405 ..     380     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.011
                                    -EE-TT-EE..SEEE-TT-EE-TT CS
                      Hexapep_2   8 CliGanagi..GvslGdncvvgaG 29 
                                      iGa +++  +  +G ++ vg+G
  gi|118431361|ref|NP_147781.2| 266 ARIGAHSVVegPAYIGPGARVGPG 289
                                    679999998855999999999999 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                                    E-TT-EE-TT-E CS
                      Hexapep_2   4 IGdnCliGanag 15 
                                    +G+ +++Ga  +
  gi|118431361|ref|NP_147781.2| 332 VGEHVNLGAGTV 343
                                    789999998754 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00017
                                    -TT-EE..SEEE-TT-EE-TT-EE- CS
                      Hexapep_2  11 Ganagi..GvslGdncvvgaGvvit 33 
                                    G n  i  Gv +G ++ v++G+v+ 
  gi|118431361|ref|NP_147781.2| 381 GINVSImpGVRIGPRALVYPGCVVG 405
                                    55745559***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3533.61
//
Query:       gi|118431362|ref|NP_147783.2|  [L=617]
Description: isomerizing glucosamine--fructose-6-phosphate aminotransferase [Aeropyrum pernix K1]
Scores for complete 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-41  140.8   0.0    3.3e-27   94.9   0.0    2.5  2  SIS         SIS domain
    1.2e-19   70.8   0.0    2.7e-19   69.7   0.0    1.5  1  GATase_6    Glutamine amidotransferase domain
    3.9e-13   49.4   0.0    1.1e-12   47.9   0.0    1.8  2  GATase_7    Glutamine amidotransferase domain
    0.00038   19.4   0.0    0.00058   18.9   0.0    1.2  1  GATase_4    Glutamine amidotransferases class-II
    0.00084   19.4   0.0      0.006   16.6   0.0    2.3  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
  ------ inclusion threshold ------
      0.057   13.4   1.5        0.1   12.6   0.1    2.2  2  SIS_2       SIS domain
      0.095   13.1   0.5       0.78   10.2   0.0    2.7  3  DUF4350     Domain of unknown function (DUF4350)


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 !   94.9   0.0   1.3e-30   3.3e-27       3     129 ..     298     423 ..     296     425 .. 0.96
   2 !   43.6   0.0   9.2e-15   2.4e-11       2      87 ..     470     554 ..     469     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 1.3e-30
                                    CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                            SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                    a a r++++GaGts+++++ + ++l +++gi+ + + ase +  + + +d +++v+++s+sget d+++a+++ + rga+
  gi|118431362|ref|NP_147783.2| 298 AGAGRLLIVGAGTSFHAGLVGHYYLSRLAGILGHPVVASE-HKVYTPGVDGETVVVAVSQSGETYDTLEAVREWRGRGAR 376
                                    5689************************************.88889********************************** PP

                                    EEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                            SIS  83 iiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                    +i++T+  gs+l read++ly++a+pe++va+tk+++aq+++l++l 
  gi|118431362|ref|NP_147783.2| 377 VIGVTNVVGSALDREADVTLYLRAGPEIGVAATKTFLAQTILLQTLS 423
                                    ******************************************99885 PP

  == domain 2  score: 43.6 bits;  conditional E-value: 9.2e-15
                                    HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTS CS
                            SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerga 81 
                                    L  a ++y++G+G  + +a+e+alk++e+++i++e+++a+e khg++al++++  v ++++s+ ++++  +a ++k+rga
  gi|118431362|ref|NP_147783.2| 470 LKGAGSMYIIGRGLGGRLAMEAALKVKEVSYIHAEAYPAGESKHGPIALVEPGFKVYVVATSD-SPEVMGNAIEMKARGA 548
                                    677899******************************************************776.7889999999999999 PP

                                    EEEEEE CS
                            SIS  82 kiiaIT 87 
                                     + +++
  gi|118431362|ref|NP_147783.2| 549 SVTVVA 554
                                    886554 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   1.1e-22   2.7e-19      10     133 ..      66     196 ..      56     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.1e-22
                       GATase_6  10 vedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.eelG... 85 
                                     +++v+++H+R+a++g +++  a+P +   gr+++vhNG i+ny +lr+el+a +g+++ s++Dte++++l+ e+lG   
  gi|118431362|ref|NP_147783.2|  66 LRGRVGIGHTRWATHGPPNDVNAHPHTDCGGRVAVVHNGVIRNYASLRRELEA-RGHRLVSETDTELVAHLIeEYLGrgy 144
                                    4778**************77777******************************.****************9977788999 PP

                       GATase_6  86 .....eevl.erlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafas 133
                                           +l + lrG +a a+    +++++ ++r +   +pl+++  e+  a+as
  gi|118431362|ref|NP_147783.2| 145 sfleaLSLLgRVLRGSYALALLHLgEPDKVYFLRYK---SPLVVGLGEGVNAVAS 196
                                    9965545555699******99999999999888443...7888777766666666 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   4.3e-16   1.1e-12      13     122 ..      88     202 ..      74     203 .. 0.86
   2 ?   -2.2   0.0       1.4   3.7e+03      24      48 ..     352     376 ..     343     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.3e-16
                       GATase_7  13 aQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfAfaiw 83 
                                    a P + + +gr+++v+nG i Ny +lr+eLea+ghr  +++Dte++++l+e+         e +  + + l+G++A+a++
  gi|118431362|ref|NP_147783.2|  88 AHPHT-DCGGRVAVVHNGVIRNYASLRRELEARGHRLVSETDTELVAHLIEEylgrgysflEALSLLGRVLRGSYALALL 166
                                    55667.5799********************************************99998877777777899********* PP

                       GATase_7  84 d.eeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    +  e ++++  R    + PL +g  +g   ++aS + a+l
  gi|118431362|ref|NP_147783.2| 167 HlGEPDKVYFLRY---KSPLVVGLGEG-VNAVASDITAVL 202
                                    9656669999999...59999999975.889999988875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                       GATase_7  24 lvivfnGeiyNykelreeLeakghr 48 
                                    +++  +Ge y++ e  +e + +g r
  gi|118431362|ref|NP_147783.2| 352 VAVSQSGETYDTLEAVREWRGRGAR 376
                                    4566789999999988887777654 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.2e-07   0.00058      57     133 ..      51     132 ..      20     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.2e-07
                       GATase_4  57 esplaelvreyp...iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTD 129
                                      ++ e+vr+     ++ ++ + H R at+G  ++ n+hp + + +gr     HnG +++y+  +    +  ++ v +TD
  gi|118431362|ref|NP_147783.2|  51 AGKIGEVVRRTGvlsLRGRVGIGHTRWATHGPPNDVNAHPHT-DCGGRVA-VVHNGVIRNYASLRreleARGHRLVSETD 128
                                    55788999998754478899********************97.5667655.57******9887665556667889***** PP

                       GATase_4 130 sEla 133
                                    +El+
  gi|118431362|ref|NP_147783.2| 129 TELV 132
                                    **87 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 !   16.6   0.0   2.3e-06     0.006       5     141 ..     463     606 ..     459     612 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.3e-06
                                    HHHHHHHHTT.SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH... CS
                     bact-PGI_C   5 akqlAlelag.klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeeh. 82 
                                    a++ A  l+g   + i+g  +l + +A+ ++ + +e + i+a a    e++h  i+++    e + ++++v   d+ e  
  gi|118431362|ref|NP_147783.2| 463 AREAASLLKGaGSMYIIG-RGLGGRLAMEAALKVKEVSYIHAEAYPAGESKHGPIALV----EPGFKVYVVATSDSPEVm 537
                                    677788888876667778.899999999999999999999999999999999999999....334444444444333222 PP

                                    ................HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S- CS
                     bact-PGI_C  83 ..........prvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtp 141
                                                v+ +a    +l + +g++v ++ ++g++ l   +sl+ ++ + +++lA++rg+DP +
  gi|118431362|ref|NP_147783.2| 538 gnaiemkargASVTVVAPSDLQLDTPEGIEVLKMPPTGGETLLDPYSLTPYFQLLAYHLAVARGYDPDK 606
                                    3332222111333333333345556679999999999******************************86 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.9e-05       0.1     105     137 ..     349     381 ..     289     382 .. 0.88
   2 ?   -1.8   0.2       1.1   2.8e+03      22      58 ..     460     496 ..     446     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-05
                                    -EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2 105 DvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                     v + +S+sG+    +ea+++ + rg++vi++t
  gi|118431362|ref|NP_147783.2| 349 TVVVAVSQSGETYDTLEAVREWRGRGARVIGVT 381
                                    477889**************************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT CS
                          SIS_2  22 ekaaeliadslenggkvlvfGsGhSaalaeelaarag 58 
                                    e aa+  a+ l+  g  ++ G G    la+e+a ++ 
  gi|118431362|ref|NP_147783.2| 460 EGAAREAASLLKGAGSMYIIGRGLGGRLAMEAALKVK 496
                                    5688888889999999999999999999999887765 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.8   1.2e+04      40      66 ..     100     124 ..      95     124 .. 0.68
   2 ?   10.2   0.0   0.00031      0.78      34      66 ..     347     378 ..     322     381 .. 0.80
   3 ?   -1.1   0.0         1   2.6e+03      14      36 ..     543     565 ..     541     580 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.8
                        DUF4350  40 vvapdlrlteeelaallewvarGntlv 66 
                                    vv++++  ++++l++ le  arG +lv
  gi|118431362|ref|NP_147783.2| 100 VVHNGVIRNYASLRRELE--ARGHRLV 124
                                    677776556677777777..7888886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00031
                        DUF4350  34 edgtllvvapdlrlteeelaallewvarGntlv 66 
                                    ++++++ v++    t+++l+a++ew  rG++++
  gi|118431362|ref|NP_147783.2| 347 GETVVVAVSQS-GETYDTLEAVREWRGRGARVI 378
                                    56677777777.77789**************97 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                        DUF4350  14 LeaqGvevrrvrkpfd.alegedg 36 
                                    ++a+G++v+ v  p+d +l+ ++g
  gi|118431362|ref|NP_147783.2| 543 MKARGASVT-VVAPSDlQLDTPEG 565
                                    789999999.45555558877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.36
# Mc/sec: 5162.30
//
Query:       gi|118431363|ref|NP_147784.2|  [L=363]
Description: nucleotidyl transferase [Aeropyrum pernix K1]
Scores for complete 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   52.3   8.9    1.3e-05   24.7   0.9    4.4  3  Hexapep          Bacterial transferase hexapeptide (six repea
    7.1e-11   42.7   3.2      9e-11   42.4   0.4    2.2  2  NTP_transf_3     MobA-like NTP transferase domain
      1e-09   38.4   0.1    4.6e-09   36.2   0.1    2.0  1  NTP_transferase  Nucleotidyl transferase
    2.1e-05   24.2   6.5      0.087   12.6   0.9    3.9  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
     0.0072   16.1   0.0     0.0096   15.7   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


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 !   18.8   0.6   2.7e-07   0.00098       2      36 .]     233     267 ..     232     267 .. 0.92
   2 !   24.7   0.9   3.6e-09   1.3e-05       1      34 [.     274     307 ..     274     309 .. 0.93
   3 !   10.0   0.0   0.00016      0.57       1      31 [.     320     359 ..     320     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.7e-07
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    +vI  ++ +   +vi g+V+I +++ +g+g+v+ g
  gi|118431363|ref|NP_147784.2| 233 AVISAKARVARSSVIQGGVVIEEDAEVGEGAVVEG 267
                                    688899999999********************975 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.6e-09
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                    ++v+G n+++gp++v+ +++++Gd v I++ v +
  gi|118431363|ref|NP_147784.2| 274 GAVVGRNSVVGPGVVLEEGAVVGDLVSIERSVML 307
                                    589***************************9876 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00016
                                    TEEEETTEEE-T.........TEEEETTEEE-TTEEEETT CS
                        Hexapep   1 stvIGsnvlIgp.........faviggnVkIGdnvkIgag 31 
                                    ++vIG++++I p          +v+++ + +G+++++++g
  gi|118431363|ref|NP_147784.2| 320 GVVIGDGAYIAPlaaatnregCTVVAPKTRLGPRATLEPG 359
                                    5789999999999999999999999999999999999887 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 !   42.4   0.4   2.5e-14     9e-11       1     120 [.       3     128 ..       3     160 .. 0.78
   2 ?   -0.5   0.0       0.4   1.4e+03     102     124 ..     327     349 ..     301     358 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.5e-14
                                    EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT...-CEEEEECSH.CHHHHHHTTCTS-EEE-TTSS-SH CS
                   NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraag..vdevvvvggd.eevlaalarlgvrvvededpgkgp 72 
                                    av+LAGG ++R+      ++K+ lpl+gkpl+ +++++++ +   +d+ v+v+++ ++  +   ++ +++ve++  g+g 
  gi|118431363|ref|NP_147784.2|   3 AVVLAGGVGKRLlpltrERPKPYLPLAGKPLYMYAVEQVAMVRslLDRAVMVTPPgHPTPPGSLPSWLDTVEQQ--GEGV 80 
                                    79**********7776556*****************99977743379*****9994444433333335555554..89** PP

                                    HHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEE CS
                   NTP_transf_3  73 laslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvv 120
                                     a+la+al+++++ + v+v  +     +  lv+++l+ +  ++++ v 
  gi|118431363|ref|NP_147784.2|  81 EAGLATALKRLGGGEEVVVSFVGYLARPNTLVRHVLDFYSVTRYKLVL 128
                                    ****************99998888777777777777776666665555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.4
                                    HHHHHHHHCHHHHTSSEEEEESS CS
                   NTP_transf_3 102 elverllaaaaasgadvvvptye 124
                                    + ++ l+aa  ++g+ vv+p+++
  gi|118431363|ref|NP_147784.2| 327 AYIAPLAAATNREGCTVVAPKTR 349
                                    34555666666666666666554 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.1   1.3e-12   4.6e-09       2      55 ..       3      57 ..       2     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.3e-12
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH..TT-SEEEEEEET CS
                NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan..sgieeiivvltq 55
                                   av+LaGG G+RL PLtr+++k+ +p +gk +l  + ++++a   s  ++ ++v+ +
  gi|118431363|ref|NP_147784.2|  3 AVVLAGGVGKRLLPLTRERPKPYLPLAGK-PLYMYAVEQVAMvrSLLDRAVMVTPP 57
                                   89***************************.99999999987655777777776655 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.8    0.0016       5.7      14      32 ..     245     265 ..     242     267 .. 0.84
   2 !   12.6   0.9   2.4e-05     0.087      17      33 ..     274     290 ..     268     297 .. 0.60
   3 !    4.7   0.0     0.007        25      16      27 ..     319     330 ..     313     331 .. 0.85
   4 ?   -3.3   0.0       2.2   7.8e+03      19      29 ..     349     359 ..     347     359 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0016
                                    -EE..SEEE-TT-EE-TT-EE CS
                      Hexapep_2  14 agi..GvslGdncvvgaGvvi 32 
                                    ++i  Gv +++++ vg G v+
  gi|118431363|ref|NP_147784.2| 245 SVIqgGVVIEEDAEVGEGAVV 265
                                    668999***********9998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.4e-05
                                    SEEE-TT-EE-TT-EE- CS
                      Hexapep_2  17 GvslGdncvvgaGvvit 33 
                                    G  +G+n+vvg+Gvv+ 
  gi|118431363|ref|NP_147784.2| 274 GAVVGRNSVVGPGVVLE 290
                                    45566666666666664 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.007
                                    ESEEE-TT-EE- CS
                      Hexapep_2  16 iGvslGdncvvg 27 
                                     Gv +Gd++ ++
  gi|118431363|ref|NP_147784.2| 319 EGVVIGDGAYIA 330
                                    59*******998 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.2
                                    EE-TT-EE-TT CS
                      Hexapep_2  19 slGdncvvgaG 29 
                                     lG ++++++G
  gi|118431363|ref|NP_147784.2| 349 RLGPRATLEPG 359
                                    45556666655 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.7e-06    0.0096       2      54 ..       2      58 ..       1     129 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.7e-06
                                   EEEEECTTSSCTT...-SSS-GGGSEETTEEHHHHHHHHHHCTTT.EEEEEEEE-GG CS
                           IspD  2 vvvipAAGsGkRm...kaglpKqflelkgqtllehtvdallaska.vdkivvvvsed 54
                                    +v+ A G+GkR+     ++pK +l l+g++l   +v+ ++  ++ +d+ v+v ++ 
  gi|118431363|ref|NP_147784.2|  2 EAVVLAGGVGKRLlplTRERPKPYLPLAGKPLYMYAVEQVAMVRSlLDRAVMVTPPG 58
                                   689*********644479*******************98776665157777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2709.65
//
Query:       gi|14601251|ref|NP_147785.1|  [L=265]
Description: hypothetical protein APE_1209 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2160.19
//
Query:       gi|118431364|ref|YP_874878.1|  [L=65]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for 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   26.9   0.0    7.6e-06   26.6   0.0    1.1  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   4.2e-10   7.6e-06       3      39 ..      19      55 ..      18      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.2e-10
                                   HHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHH CS
                  Acyl-CoA_dh_N  3 eqealrdtvrefaeeelaphaaewdeegefprelwkk 39
                                   e++ lr++vrefae+ ++p+a+e+d  +++pr+l+  
  gi|118431364|ref|YP_874878.1| 19 EHRLLRKSVREFAEKTVRPRAREIDVGNQYPRDLLPV 55
                                   8***********************99889**997443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 537.49
//
Query:       gi|118431365|ref|YP_874879.1|  [L=141]
Description: hypothetical protein APE_1209b [Aeropyrum pernix K1]
Scores for complete 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   62.6   0.8    5.9e-17   62.3   0.8    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 !   62.3   0.8   3.3e-21   5.9e-17       2     119 ..       5     140 ..       4     141 .] 0.92

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 3.3e-21
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....................SCHCHHHHHHHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....................rkskrekaaelve 60 
                                    ++D++++i++++++e++  +++ l +  e +ts + l+E++y+l +                     +  +   +a+l +
  gi|118431365|ref|YP_874879.1|   5 FVDANIFIRIIFNREHS--LLEYLIG-TEPYTSTHLLEEAAYKLIAlsiiesegpvsvykigklfekGAAEDTIRARLAA 81 
                                    9**************99..4555555.**************************************976777777777777 PP

                                    HHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  61 lllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                    l  +++ l+i+p + ++++e  +i+l+y+llp Dal +A +k++ ik i+t D+df+++
  gi|118431365|ref|YP_874879.1|  82 LDKIAEKLNIIPPTYSDFRESMKISLEYKLLPSDALTVAIMKREEIKEILTLDNDFKQI 140
                                    7777****************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1177.00
//
Query:       gi|118431366|ref|NP_147787.2|  [L=73]
Description: hypothetical protein APE_1209c.1 [Aeropyrum pernix K1]
Scores for 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-17   61.9   4.2    6.9e-17   61.6   4.2    1.2  1  DUF104    Protein of unknown function DUF104
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.18   11.8   0.0    1.2  1  DUF5016   Domain of unknown function (DUF5016)


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   4.2   7.7e-21   6.9e-17       1      47 [.       1      50 [.       1      70 [. 0.74

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 7.7e-21
                         DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIee...akeilkklkgilk 47
                                   MskvI+++YE+GvLKPLe++ L+EGeev+++I++    +e  ++l  +l 
  gi|118431366|ref|NP_147787.2|  1 MSKVIRVKYEGGVLKPLEPLVLSEGEEVEVVIRRrvfGEEDYRELVDFLS 50
                                   9*********************************6663333333333333 PP

>> DUF5016  Domain of unknown function (DUF5016)
   #    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      69     108 ..      21      59 ..       5      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                        DUF5016  69 llfdeesvseevirtktsGtytgaifvPlykniPdGkatl 108
                                    +l ++e+v e vir +  G  + +  v ++ ++P+Gka+l
  gi|118431366|ref|NP_147787.2|  21 VLSEGEEV-EVVIRRRVFGEEDYRELVDFLSELPKGKAEL 59 
                                    55555555.89***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 549.68
//
Query:       gi|14601253|ref|NP_147788.1|  [L=56]
Description: hypothetical protein APE_1209d [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 435.80
//
Query:       gi|118431367|ref|YP_874880.1|  [L=91]
Description: acyl-CoA dehydrogenase, partial [Aeropyrum pernix K1]
Scores for complete 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-16   60.9   1.1    1.7e-16   60.8   1.1    1.0  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
     0.0038   17.5   0.6     0.0044   17.3   0.6    1.0  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 !   60.8   1.1   1.8e-20   1.7e-16      33     118 ..       2      88 ..       1      91 [] 0.95

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1.8e-20
                                    HHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------.HHHHHHHHHHHHHHHHHHHHHHHHHHG CS
                  Acyl-CoA_dh_1  33 aleyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpd.raeasmaKlfaselaqevadlamqllG 111
                                    a+e++ +  +fg+p+   q+vr+++++ma+++++++ l+y+aa++ d+g+p+    as+aKl as +a+e+a+ a+ +lG
  gi|118431367|ref|YP_874880.1|   2 AYEWSLSSMSFGRPIHRLQAVRFQIVDMAVKTRSMKTLAYTAARLRDQGDPRyVWMASAAKLHASIAANEIAAAAVRILG 81 
                                    568899999*******************************************9889999********************* PP

                                    GGTTSGG CS
                  Acyl-CoA_dh_1 112 gaGylee 118
                                    g Gy +e
  gi|118431367|ref|YP_874880.1|  82 GLGYVKE 88 
                                    ****876 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 !   17.3   0.6   4.9e-07    0.0044      28     114 ..      10      89 ..       5      91 .] 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-07
                                    TTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCGG CS
                  Acyl-CoA_dh_2  28 assgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedraearraaalavelaiaavdalfeaaGg 107
                                    +s+g+++   +a+ +++ ++a + ++ ++l + aa+     +++g++   + +  a++a+++a+  a +++ a++++ Gg
  gi|118431367|ref|YP_874880.1|  10 MSFGRPIHRLQAVRFQIVDMAVKTRSMKTLAYTAARL----RDQGDP---RYVWMASAAKLHASIAANEIAAAAVRILGG 82 
                                    6789999999**********************99999....888877...6899999999******************** PP

                                    GGGBTT- CS
                  Acyl-CoA_dh_2 108 salrkes 114
                                     ++ kes
  gi|118431367|ref|YP_874880.1|  83 LGYVKES 89 
                                    ***9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 697.54
//
Query:       gi|118431368|ref|YP_874881.1|  [L=32]
Description: acyl-CoA dehydrogenase, partial [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0034   17.6   0.1     0.0034   17.6   0.1    1.0  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.9e-07    0.0034     124     148 ..       1      25 [.       1      27 [. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-07
                                    HHHHTHHHHHSSS-HHHHHHHHHHH CS
                  Acyl-CoA_dh_1 124 lyrdarvlrigeGtseiqrniiarr 148
                                    +yrda++l+ige t+eiqr i+++ 
  gi|118431368|ref|YP_874881.1|   1 MYRDAKLLEIGEWTNEIQRWIMGKM 25 
                                    7********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); 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 0.22s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 240.34
//
Query:       gi|118431369|ref|NP_147790.2|  [L=571]
Description: hypothetical protein APE_1210.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   0.2      0.023   14.7   0.2    1.5  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> 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 ?   14.7   0.2   1.3e-06     0.023      47     134 ..     210     300 ..     186     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-06
                   Baculo_PEP_C  47 Lnalsedlksllaeldt..rldtlltnLtdalnalqdtlrneLtnlnsiltnLlss.vtNinstLnnllqalnnldlgal 123
                                    L++  ++ ++ll+ l +  ++++l+++L +a+ ++  + r +L +l++++ ++    + N+   +n +++a+  ++ g  
  gi|118431369|ref|NP_147790.2| 210 LDEEVQRYRKLLSRLGEidHIEELVERLRRAIEKIYRSERRRLAGLQKDVVSMDKLiISNLTLNINDIVSAVYDVNIGYA 289
                                    44444555566666665779*******************************99875279*****************9999 PP

                   Baculo_PEP_C 124 sqeledaldtv 134
                                        + +++t 
  gi|118431369|ref|NP_147790.2| 290 YLNMRRSIETL 300
                                    88888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3857.20
//
Query:       gi|118431370|ref|NP_147791.2|  [L=124]
Description: hypothetical protein APE_1211.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00038   20.5   0.8    0.00058   19.9   0.3    1.6  2  HTH_20    Helix-turn-helix domain
  ------ inclusion threshold ------
       0.14   12.0   1.5         20    5.1   0.0    2.9  3  HTH_5     Bacterial regulatory protein, arsR family


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 !   19.9   0.3   6.4e-08   0.00058       5      58 ..      28      86 ..      21      89 .. 0.89
   2 ?   -2.6   0.0      0.67     6e+03      39      48 ..     104     113 ..      95     118 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.4e-08
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHT.....S-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20  5 eALahPvRrrilraLaraegltaselaerld.....lskntlsyHLrvLeeagLvevvr 58
                                    +L+h+ R  il+a a  ++++ + l+  l+     + +ntl +H r+L eagL+++ +
  gi|118431370|ref|NP_147791.2| 28 GLLSHRLRILILAATAAYGEASWTSLKTILEsllgpVNPNTLAFHTRKLMEAGLLRRAG 86
                                   5799***********99************9556667*******************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.67
                                    HHHHHHHHHH CS
                         HTH_20  39 ntlsyHLrvL 48 
                                    ++l + +++L
  gi|118431370|ref|NP_147791.2| 104 AELAKEMEKL 113
                                    4455555555 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   0.6       0.2   1.8e+03      32      39 ..      30      37 ..      27      40 .. 0.76
   2 ?    5.1   0.0    0.0022        20      28      46 ..      65      83 ..      63      84 .. 0.83
   3 ?    4.6   0.0    0.0033        30       8      27 ..      92     112 ..      92     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.2
                                   HHHHHHHH CS
                          HTH_5 32 vShHLkkL 39
                                   +Sh L++L
  gi|118431370|ref|NP_147791.2| 30 LSHRLRIL 37
                                   78888887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0022
                                   -HHHHHHHHHHHHHTTSEE CS
                          HTH_5 28 sqstvShHLkkLreaGLVe 46
                                   ++ t+  H +kL+eaGL++
  gi|118431370|ref|NP_147791.2| 65 NPNTLAFHTRKLMEAGLLR 83
                                   666888899********85 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0033
                                    HHHHTTSS.EEHHHHHHHHTS CS
                          HTH_5   8 LklLaege.lcvcelaeelgl 27 
                                    +++Lae++ + + ela+e+++
  gi|118431370|ref|NP_147791.2|  92 VYMLAEEPdREIAELAKEMEK 112
                                    699***999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 974.97
//
Query:       gi|118431371|ref|NP_147793.2|  [L=1362]
Description: surface layer-associated protease precursor [Aeropyrum pernix K1]
Scores for complete 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-24   86.3   0.0    4.8e-23   81.9   0.0    2.4  1  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 !   81.9   0.0   2.7e-27   4.8e-23       1     286 [.     182     778 ..     182     789 .. 0.75

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.7e-27
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag........................................ 40 
                                    g+gv+++v+DtGvd s p+l      e k+      +  g                                        
  gi|118431371|ref|NP_147793.2| 182 GEGVVIGVIDTGVDFSGPGLG-----EDKI----AFSPEGlplivdygmvflaaplyvevdpdsgsgavdfqglytveag 252
                                    79*****************98.....3344....3444447788999999****************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                   Peptidase_S8  41 ................................................................................ 40 
                                                                                                                    
  gi|118431371|ref|NP_147793.2| 253 pagvgllvkrsggfasiaylspeggyssgyveysleppvlpqevvdaalqggappryglavsenmaytldggllwyrmtv 332
                                    *****************999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................GGEETT-SS-TT-SC- CS
                                    ................................................................xxxxxxxxxxxxxxxx RF
                   Peptidase_S8  41 ................................................................fngadsettstnward 56 
                                                                                                                    
  gi|118431371|ref|NP_147793.2| 333 pglvadadadglydtiyldastavyhlasaarqagltlypapsaadysfegekpvtpasplagyD--------------- 397
                                    99977777777777776666666666666666666666666666666655555555555555550............... PP

                                    S...........................................................................SS.. CS
                                    x...........................................................................xxxx RF
                   Peptidase_S8  57 d...........................................................................ngns 61 
                                                                                                                +g  
  gi|118431371|ref|NP_147793.2| 398 ArgdgdidlpvgalagytvdlsgaalgmatgilgemaaglpeggatllptedlpagyllpgmdfwrgsyavfhtddDG-- 475
                                    055555555555555555555555555555555555555555555555555555555555555555555444332245.. PP

                                    ..HHHHHHHHHH-B.............SSSSSB-SSTTSEEE..EEE-SSTTSB-HH..HHHHHH............... CS
                                    xxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx............... RF
                   Peptidase_S8  62 ieHGthvAGiaaan...........apeegekngvapgakil..svkvldtsggsmetgtelira............... 113
                                      HGt  A++aa+             +    ++g ap+a+++  s+ ++ +   +  tg  +++a               
  gi|118431371|ref|NP_147793.2| 476 --HGTKAASTAAGRefifraetglgLEVRMLVSGTAPEARLAasSFYIYEQAMLTL-TGHVMVDAgtgeplwippwmggv 552
                                    ..************666655555444444456666666666666555554444443.45777777888999888888888 PP

                                    ................HHHHHH..CT-SEEEE-EESCETTCHHCHHHHHH.....HHHHHH.CCT-EEEEE--SS-T-HH CS
                                    ................xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 114 ................ieeaae..dkvdvinmslgestslpktgrsieal.....ainravnkkgvlvviSaGNngktgs 170
                                                    +e+a      vd+  +s+g  +sl+ + +++  l     +i+  + + gv   i+aGN g    
  gi|118431371|ref|NP_147793.2| 553 dpwdrldprlngggvkAEWAWTgtPLVDLTTNSWG-ISSLQYYADKPLGLeevslFIDSITLETGVPHFIAAGNGG---- 627
                                    8888888888888888555544226788*******.8888888887766678899*********************.... PP

                                    EEE-TTCEECTTTSTTCEEEEEES....................TTSSB-TT--B-TT.......-EEEE-S-CCCCCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 171 slqagspvgtpstsknvitvgayt....................tegkiapfSsrGpssdgklkpdivapGgnivstwsr 230
                                      + + +v +p+t++ +++v+a+t                      g+ a+fS rGps++g+ kp ++a Gg  + t   
  gi|118431371|ref|NP_147793.2| 628 --PGLGTVTAPATARLAVAVAAATdmaylsliqpgylpllaglgGYGDPAYFSARGPSHAGAPKPGLAAIGGFAYTTGRS 705
                                    ..9*********************************************************************93333333 PP

                                    CCHHHTTTHH.......EEEE-SHHHCHHHHHHHHHHHHHHHTT.--HHH........HHHHHHCCS-EE...... CS
                                    xxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx........xxxxxxxxxxxx....xx RF
                   Peptidase_S8 231 qsnnsaglss.......yqsmsGTSmAsPnaagaaAlllsalpk.ltpet........vraallntAqdl....gk 286
                                     ++ +    +         ++ GTSmA+P+aagaaAl ++al++ l +e         v +al +tAq+     g+
  gi|118431371|ref|NP_147793.2| 706 LDHYTG---GrldpraaPLLFGGTSMATPMAAGAAALAIQALKEsLGVERlgleewlrVYTALSMTAQWRglpwGE 778
                                    332222...135588885689*******************99998444445555566699*******997666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.78u 0.26s 00:00:01.04 Elapsed: 00:00:00.44
# Mc/sec: 9313.94
//
Query:       gi|14601261|ref|NP_147796.1|  [L=533]
Description: surface layer protein [Aeropyrum pernix K1]
Scores for complete 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   49.0  32.2    6.8e-07   28.5  18.2    3.1  3  Spc7             Spc7 kinetochore protein
    4.1e-13   49.3  17.7    0.00045   20.4   0.7    6.1  6  XhlA             Haemolysin XhlA
    1.4e-11   44.5  21.4      0.016   15.6   0.0    6.9  8  FlaC_arch        Flagella accessory protein C (FlaC)
    1.6e-11   44.5  31.0    8.9e-06   25.9   3.1    4.4  4  Tropomyosin_1    Tropomyosin like
      2e-11   43.3  33.1    3.4e-08   32.6   7.4    2.1  2  AAA_13           AAA domain
    4.3e-11   42.9  21.0    3.6e-05   23.8   4.9    4.4  4  DUF1664          Protein of unknown function (DUF1664)
    1.6e-10   41.1  25.9    9.6e-05   22.1  11.5    3.2  3  Filament         Intermediate filament protein
    3.9e-10   39.9  37.0    7.5e-06   26.0  14.5    3.2  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    5.1e-10   39.6  26.7     0.0012   19.0   8.5    3.4  3  ADIP             Afadin- and alpha -actinin-Binding
    6.2e-10   39.3  23.2    0.00012   22.1  12.8    4.0  4  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    1.1e-09   38.9  43.0    0.00025   21.4  19.0    4.0  4  ATG16            Autophagy protein 16 (ATG16)
    3.1e-09   36.8  16.5    0.00031   20.5  12.9    2.4  2  DUF4201          Domain of unknown function (DUF4201)
    3.8e-09   36.7  26.9    0.00062   19.8   7.3    4.2  4  Laminin_II       Laminin Domain II
    5.5e-09   34.8  18.5    1.2e-07   30.4   1.4    2.5  2  EzrA             Septation ring formation regulator, EzrA
    8.7e-09   35.9  41.4    8.2e-05   23.2   1.2    5.6  6  SlyX             SlyX
    1.1e-08   35.0  51.4    1.4e-05   24.8  28.2    3.7  3  MscS_porin       Mechanosensitive ion channel porin domain
    1.1e-08   34.7  34.7      0.002   17.6   1.6    3.0  3  Tropomyosin      Tropomyosin
    2.1e-08   34.5  27.7       0.14   12.6   8.7    5.5  4  NPV_P10          Nucleopolyhedrovirus P10 protein
      5e-08   31.6  27.9    0.00035   18.9  21.3    2.3  2  FPP              Filament-like plant protein, long coiled-coi
    7.1e-08   32.3  26.1    0.00024   20.8   4.5    3.3  3  DUF4795          Domain of unknown function (DUF4795)
    7.4e-08   31.8  21.9    1.5e-05   24.3   8.7    2.7  3  Atg14            Vacuolar sorting 38 and autophagy-related su
    8.2e-08   31.6  26.2    5.6e-06   25.5  24.1    2.1  2  DUF812           Protein of unknown function (DUF812)
    9.7e-08   31.9  26.2      0.037   14.0   1.2    6.0  6  Prefoldin_2      Prefoldin subunit
    1.4e-07   31.7  36.5    0.00079   19.6   0.8    5.4  5  ABC_tran_CTD     ABC transporter C-terminal domain
    1.5e-07   29.7  31.3    0.00097   17.1   9.4    2.9  3  Myosin_tail_1    Myosin tail
    2.8e-07   30.4  44.5    1.1e-06   28.4  14.9    2.6  2  Lebercilin       Ciliary protein causing Leber congenital ama
    1.1e-06   28.5  30.4     0.0032   17.4   0.4    5.4  5  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    1.8e-06   27.9  18.7    0.00059   19.7   6.6    3.1  3  DUF724           Protein of unknown function (DUF724)
    2.3e-06   28.2  25.0    0.00088   19.8  19.8    2.2  2  Fez1             Fez1
    2.4e-06   27.8  27.4      0.042   14.2   1.1    5.3  5  BLOC1_2          Biogenesis of lysosome-related organelles co
    2.4e-06   27.1  24.3    0.00011   21.6   9.2    3.4  3  GAS              Growth-arrest specific micro-tubule binding
    2.4e-06   27.4  31.7     0.0009   19.0  16.1    3.2  3  DUF745           Protein of unknown function (DUF745)
    2.5e-06   27.5  21.4     0.0066   16.5   0.8    5.0  4  DUF2730          Protein of unknown function (DUF2730)
    3.3e-06   27.6  39.9      0.019   15.3   1.9    4.6  3  HrpB7            Bacterial type III secretion protein (HrpB7)
    3.5e-06   26.7  25.9    0.00062   19.3   2.3    2.5  2  HMMR_N           Hyaluronan mediated motility receptor N-term
    4.5e-06   26.9  36.3      0.045   14.1   0.6    6.2  6  CLZ              C-terminal leucine zipper domain of cyclic n
    4.7e-06   26.1  32.0     0.0014   18.0  12.4    3.7  3  DUF3450          Protein of unknown function (DUF3450)
    5.7e-06   26.3  44.9     0.0038   17.3   1.4    5.5  6  TolA_bind_tri    TolA binding protein trimerisation
    5.9e-06   26.5  25.2      0.002   18.3  13.0    3.5  2  FliJ             Flagellar FliJ protein
    6.1e-06   26.7  23.8      0.016   15.7   3.6    4.5  2  DUF16            Protein of unknown function DUF16
    6.4e-06   25.2  26.4     0.0004   19.2  13.5    4.2  3  Tektin           Tektin family
    6.6e-06   26.2  38.3      0.016   15.2   3.4    4.2  4  DHR10            Designed helical repeat protein 10 domain
    7.2e-06   26.2  27.5     0.0011   19.1   2.5    3.2  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
    8.2e-06   25.0  18.8    0.00095   18.2   5.5    2.8  3  IFT57            Intra-flagellar transport protein 57
    1.4e-05   25.2  31.2     0.0016   18.6  12.1    3.1  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
    1.4e-05   25.3  16.2      0.005   17.0   6.3    3.6  5  Fib_alpha        Fibrinogen alpha/beta chain family
    1.5e-05   24.9  25.7        0.6   10.0   0.0    6.3  7  Prefoldin        Prefoldin subunit
    1.7e-05   24.7  21.7     0.0021   17.9  17.7    2.3  2  TACC_C           Transforming acidic coiled-coil-containing p
    1.7e-05   24.5  28.7    0.00049   19.8   5.6    4.4  4  PspA_IM30        PspA/IM30 family
      2e-05   23.7  33.4    0.00013   21.0  32.2    2.1  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
    2.2e-05   24.3  23.1       0.79    9.5   0.2    5.0  2  Phage_GP20       Phage minor structural protein GP20
    2.3e-05   24.7  25.9      0.014   15.8   7.4    4.9  3  Snapin_Pallidin  Snapin/Pallidin
    2.3e-05   23.7  17.6      0.012   14.7   4.0    3.1  3  FH2              Formin Homology 2 Domain
    2.6e-05   24.6  33.6      0.063   13.7  10.1    4.1  4  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
    3.5e-05   23.9  27.8     0.0019   18.3  11.0    3.2  3  Nup54            Nucleoporin complex subunit 54
    3.5e-05   24.0  20.8      0.057   13.7   0.6    5.1  7  DUF948           Bacterial protein of unknown function (DUF94
    3.7e-05   21.5  31.2    8.9e-05   20.2  31.1    1.6  1  DUF3584          Protein of unknown function (DUF3584)
    4.6e-05   23.5  39.8     0.0012   18.9  14.5    4.3  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    4.8e-05   23.1  20.9       0.37   10.3  21.0    2.6  1  Exonuc_VII_L     Exonuclease VII, large subunit
    5.6e-05   23.3  22.9       0.12   12.6   7.3    4.6  6  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
    5.7e-05   22.6  34.1      0.048   13.0   2.4    4.0  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
    8.4e-05   22.4  20.6    0.00037   20.3  18.8    2.2  2  SHE3             SWI5-dependent HO expression protein 3
    9.1e-05   22.5  22.1     0.0035   17.4   3.3    3.1  2  BRE1             BRE1 E3 ubiquitin ligase
     0.0001   22.6  22.0       0.43   11.0   2.4    4.8  4  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
    0.00011   20.6  30.4     0.0014   16.9  11.0    2.4  3  HOOK             HOOK protein
    0.00012   21.9  28.6    0.00021   21.1  27.8    1.8  1  Laminin_I        Laminin Domain I
    0.00013   21.3  35.0     0.0012   18.1  35.0    2.6  1  HAP1_N           HAP1 N-terminal conserved region
    0.00013   20.5  28.3     0.0013   17.2  20.9    2.4  2  MAD              Mitotic checkpoint protein
    0.00015   20.6  12.7      0.028   13.0   6.3    2.9  3  FapA             Flagellar Assembly Protein A
    0.00019   22.0  42.8     0.0033   17.9  15.8    3.6  3  APG6_N           Apg6 coiled-coil region
     0.0002   21.7  34.5      0.031   14.7  10.7    4.9  5  ZapB             Cell division protein ZapB
    0.00023   21.8  21.3       0.25   12.0   2.0    4.6  4  YabA             Initiation control protein YabA
    0.00024   21.2  26.7       0.11   12.6   4.5    4.5  4  COG2             COG (conserved oligomeric Golgi) complex com
    0.00025   21.3  29.7      0.061   13.6  12.2    3.8  3  THOC7            Tho complex subunit 7
    0.00039   19.6  17.0    0.00069   18.8  17.0    1.4  1  APG17            Autophagy protein Apg17
     0.0005   19.4  14.8       0.26   10.5   0.0    3.0  2  TMPIT            TMPIT-like protein
    0.00056   19.8  30.9      0.026   14.3  10.7    2.4  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    0.00058   18.7  19.0    0.00058   18.7  19.0    1.9  2  WEMBL            Weak chloroplast movement under blue light
    0.00062   19.8  15.4    0.00062   19.8  15.4    2.6  2  Rootletin        Ciliary rootlet component, centrosome cohesi
    0.00081   19.9  26.6     0.0033   17.9   2.3    3.4  3  Spectrin         Spectrin repeat
      0.001   18.7  21.8     0.0039   16.7   8.6    2.6  3  Leu_zip          Leucine zipper
      0.001   19.1  20.5        0.8    9.6   0.8    4.7  4  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
      0.001   18.5  25.6        5.4    6.3  25.6    2.8  1  DUF4407          Domain of unknown function (DUF4407)
      0.001   17.4  25.8     0.0014   17.0  25.8    1.1  1  Cast             RIM-binding protein of the cytomatrix active
     0.0011   18.6  20.1       0.12   11.9   3.0    3.6  3  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0011   18.1  17.8       0.11   11.6   0.2    4.1  4  RmuC             RmuC family
     0.0013   19.0  32.2       0.49   10.6  12.9    3.8  4  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0014   18.3   3.0       0.13   11.7   2.8    3.2  2  WASH_WAHD        WAHD domain of WASH complex
     0.0014   18.6  23.6      0.022   14.8   0.7    4.7  4  Med9             RNA polymerase II transcription mediator com
     0.0016   16.7  21.2      0.004   15.4   1.7    3.6  3  COG6             Conserved oligomeric complex COG6
     0.0017   18.5  27.6      0.018   15.1   4.0    4.4  3  DivIVA           DivIVA protein
     0.0018   18.4  22.5      0.016   15.4   6.9    3.9  4  COG5             Golgi transport complex subunit 5
     0.0023   17.6  31.7      0.031   13.9   9.0    3.1  4  HAUS-augmin3     HAUS augmin-like complex subunit 3
     0.0024   17.1  19.9       0.81    8.8   0.0    2.8  2  Taxilin          Myosin-like coiled-coil protein
     0.0024   18.1  19.8      0.057   13.7   3.9    4.2  4  Tup_N            Tup N-terminal
     0.0025   18.0  33.9       0.66   10.3   3.6    5.6  5  Spc24            Spc24 subunit of Ndc80
     0.0026   18.5  23.5       0.26   12.0   0.4    3.7  3  DUF4472          Domain of unknown function (DUF4472)
     0.0026   18.1  21.5      0.039   14.3   5.0    3.6  3  DUF4200          Domain of unknown function (DUF4200)
     0.0027   17.2  31.1      0.037   13.5  12.8    2.8  3  Golgin_A5        Golgin subfamily A member 5
      0.003   17.7  28.2      0.017   15.3   9.7    4.0  3  Uds1             Up-regulated During Septation
     0.0032   18.2  10.6        1.1   10.0   1.0    4.2  5  Occludin_ELL     Occludin homology domain
     0.0036   17.9  16.5      0.008   16.7   5.3    3.2  2  ING              Inhibitor of growth proteins N-terminal hist
     0.0041   16.6  10.2     0.0041   16.6  10.2    3.1  3  Rab5-bind        Rabaptin-like protein
     0.0044   16.9  33.4       0.14   12.0   0.6    7.6  7  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
     0.0044   17.2  13.4     0.0044   17.2  13.4    3.9  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0044   16.7  11.8        2.8    7.6   0.1    5.4  5  DUF4988          Domain of unknown function
     0.0045   16.9  16.9       0.62    9.9   3.1    3.8  4  SKA1             Spindle and kinetochore-associated protein 1
     0.0051   17.3  27.8       0.15   12.6   7.0    3.0  2  T3SSipB          Type III cell invasion protein SipB
     0.0053   16.9  23.3        0.4   10.9   2.1    4.5  4  Cnn_1N           Centrosomin N-terminal motif 1
     0.0059   16.4  30.9      0.022   14.6  24.6    2.4  2  ERM              Ezrin/radixin/moesin family
     0.0071   15.8   1.8     0.0071   15.8   1.8    2.7  3  DegS             Sensor protein DegS
     0.0077   15.9   6.8       0.25   11.0   2.6    2.4  2  IL11             Interleukin 11
     0.0078   16.5  16.3       0.14   12.5   4.9    4.1  3  KxDL             Uncharacterized conserved protein
  ------ inclusion threshold ------
      0.012   15.6  36.0       0.15   12.0   1.3    4.3  4  YscO             Type III secretion protein YscO
      0.013   15.6   0.3      0.013   15.6   0.3    4.4  3  MbeD_MobD        MbeD/MobD like
      0.013   15.8  16.9       0.19   12.0   0.6    2.2  2  zf-C4H2          Zinc finger-containing protein
      0.013   15.8  25.4        0.8   10.0   2.9    4.4  4  Rx_N             Rx N-terminal domain
      0.013   15.2   9.2        1.2    8.9   0.6    4.5  4  RPW8             Arabidopsis broad-spectrum mildew resistance
      0.013   15.3  32.9      0.093   12.5   2.8    4.9  4  Nsp1_C           Nsp1-like C-terminal region
      0.014   15.3   9.8        4.1    7.3   0.5    3.6  3  LMP              LMP repeated region
      0.018   12.9  16.2      0.041   11.7  15.7    1.7  1  Nup88            Nuclear pore component
      0.019   14.6   0.1      0.034   13.8   0.1    1.4  1  DUF1411          Protein of unknown function (DUF1411)
       0.02   13.4   6.7        0.2   10.0   0.0    3.1  3  Hemagglutinin    Haemagglutinin
      0.021   14.6  33.7       0.38   10.5   4.3    5.8  6  DivIC            Septum formation initiator
      0.021   14.4   0.7      0.021   14.4   0.7    3.2  2  DUF2968          Protein of unknown function (DUF2968)
      0.022   14.5  21.7      0.055   13.2   5.4    2.6  2  LXG              LXG domain of WXG superfamily
      0.022   14.3  16.9       0.42   10.1   5.4    3.2  4  Allexi_40kDa     Allexivirus 40kDa protein
      0.023   14.3   2.7        2.7    7.7   0.1    4.0  3  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
      0.023   14.7  19.1      0.034   14.1   0.6    4.4  4  Noelin-1         Neurogenesis glycoprotein
      0.023   14.6  32.3       0.97    9.4   0.6    4.6  4  Sec2p            GDP/GTP exchange factor Sec2p
      0.024   15.2  27.6          2    9.0  10.1    4.9  4  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.025   12.6  15.1       0.12   10.3   6.6    2.4  3  Prominin         Prominin
      0.025   14.0   8.1      0.093   12.2   1.4    3.2  3  DUF3829          Protein of unknown function (DUF3829)
      0.028   13.6  10.0       0.19   10.9   3.6    2.8  2  ISG65-75         Invariant surface glycoprotein
      0.042   14.1  19.8       0.45   10.8   1.9    4.4  4  DUF5082          Domain of unknown function (DUF5082)
      0.052   13.2  25.4         20    4.7   5.9    3.7  3  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
      0.056   12.9  47.3      0.017   14.5   8.2    4.3  2  DUF4349          Domain of unknown function (DUF4349)
      0.056   12.9  23.5       0.23   10.9  13.0    3.7  2  DUF4618          Domain of unknown function (DUF4618)
      0.056   12.6  27.4      0.072   12.2   1.0    2.4  2  CCDC144C         CCDC144C protein coiled-coil region
      0.057   12.7  20.2         12    5.1   0.1    3.8  3  FmiP_Thoc5       Fms-interacting protein/Thoc5
      0.059   13.2  22.2       0.44   10.4   0.5    3.6  3  Sec34            Sec34-like family
      0.064   13.9  33.0       0.95   10.1   5.7    4.5  6  BST2             Bone marrow stromal antigen 2
      0.065   14.0  24.9        4.3    8.2   0.2    5.6  4  Rho_Binding      Rho Binding
      0.067   13.4   1.8      0.095   12.9   0.5    2.0  1  Big_3_5          Bacterial Ig-like domain (group 3)
      0.068   13.0  20.2       0.99    9.2   6.3    3.6  4  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.069   13.1  35.9       0.79    9.6   0.7    4.9  4  Wtap             WTAP/Mum2p family
       0.07   12.0  18.8       0.55    9.0   6.0    3.0  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.073   13.2  18.1        9.9    6.3   0.1    5.9  9  bZIP_1           bZIP transcription factor
      0.074   11.5  23.7       0.11   10.9  22.4    1.6  1  BicD             Microtubule-associated protein Bicaudal-D
      0.075   11.6  34.9        1.2    7.6  17.0    2.6  2  FUSC             Fusaric acid resistance protein family
       0.08   12.8  27.2        0.1   12.5   5.5    3.0  3  CEP63            Centrosomal protein of 63 kDa
      0.085   12.5  24.0        1.6    8.4   0.6    4.4  4  GrpE             GrpE
      0.086   13.3   5.8         13    6.3   0.1    4.5  5  MtrB             Tetrahydromethanopterin S-methyltransferase 
      0.087   13.0  14.3        2.2    8.5   5.1    3.2  3  RasGAP_C         RasGAP C-terminus
      0.092   12.8  42.4      0.042   13.9   1.4    5.9  3  Cep57_CLD_2      Centrosome localisation domain of PPC89
      0.096   12.8  23.9        4.7    7.4   1.6    6.2  6  TRPM_tetra       Tetramerisation domain of TRPM
      0.097   13.0  27.4       0.46   10.8   1.0    3.2  1  OmpH             Outer membrane protein (OmpH-like)
      0.097   12.3  10.5       0.15   11.7   0.1    3.9  3  Phage_tail_NK    Sf6-type phage tail needle knob or tip of so
      0.099   12.0  31.0       0.11   12.0   3.9    4.0  4  DUF3552          Domain of unknown function (DUF3552)
       0.11   12.9  13.5      0.067   13.6   3.7    4.0  3  Flagellin_C      Bacterial flagellin C-terminal helical regio
       0.11   12.9  13.6         26    5.3   0.2    4.0  2  MitMem_reg       Maintenance of mitochondrial structure and f
       0.12   12.4  18.9       0.21   11.7   3.5    3.3  2  MCU              Mitochondrial calcium uniporter
       0.13   10.9  30.2       0.13   10.9   3.1    2.1  2  GOLGA2L5         Putative golgin subfamily A member 2-like pr
       0.15   11.9  17.0       0.21   11.4   1.6    3.6  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.15   11.5  17.9       0.09   12.2   6.7    3.2  3  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.16   12.7  17.4    2.1e+02    2.5  17.4    3.0  1  AATF-Che1        Apoptosis antagonizing transcription factor
       0.17   12.2  21.7        1.7    9.0   4.1    4.5  4  DUF641           Plant protein of unknown function (DUF641)
       0.17   12.4  17.3        6.5    7.4   0.3    3.9  4  Hrs_helical      Hepatocyte growth factor-regulated tyrosine 
       0.17   12.2  42.4       0.12   12.6   5.7    4.3  4  DUF4164          Domain of unknown function (DUF4164)
       0.17   12.0  18.6       0.31   11.2   3.4    3.9  4  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.19   11.1  15.5        1.4    8.3   5.6    3.6  3  FliD_C           Flagellar hook-associated protein 2 C-termin
        0.2   11.5  14.6        3.8    7.3   6.5    3.5  3  Spc29            Spindle Pole Component 29
        0.2   12.3  37.5        0.3   11.7  12.2    4.0  6  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        0.2   12.1  31.6        2.7    8.5   2.2    6.8  5  LPP              Lipoprotein leucine-zipper
       0.21   10.8  18.0       0.99    8.6  10.2    2.8  3  MPS2             Monopolar spindle protein 2
       0.22    9.8  16.1       0.11   10.8  12.0    2.0  1  Gp58             gp58-like protein
       0.23   11.9  27.7        0.5   10.8   9.7    3.0  3  CENP-H           Centromere protein H (CENP-H)
       0.23   11.1   0.2        2.7    7.7   0.1    2.4  2  DUF2576          Protein of unknown function (DUF2576)
       0.26   10.6  23.3       0.12   11.8  11.5    3.6  2  Cluap1           Clusterin-associated protein-1
       0.27   10.3  31.3       0.64    9.1  17.6    2.7  2  DUF4686          Domain of unknown function (DUF4686)
       0.28   11.1   3.8          2    8.4   0.1    3.6  1  ApoC-I           Apolipoprotein C-I (ApoC-1)
       0.29   10.0  13.0        2.6    6.8   1.9    3.6  4  FemAB            FemAB family
       0.29   11.4  26.1        6.5    7.1   0.4    4.9  5  WXG100           Proteins of 100 residues with WXG
       0.32   11.7  22.1        1.7    9.4   5.0    3.8  5  DUF2203          Uncharacterized conserved protein (DUF2203)
       0.32   10.0  12.4      0.057   12.4   5.3    2.3  2  MT               Microtubule-binding stalk of dynein motor
       0.39   11.1  36.7        1.2    9.5   1.0    6.6  7  Csm1_N           Csm1 N-terminal domain
       0.41    9.5  10.7       0.69    8.7  10.7    1.4  1  LMBR1            LMBR1-like membrane protein
       0.42    8.5  14.7         45    1.8  14.7    2.4  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.43   10.5  22.9       0.39   10.6   0.2    6.1  4  HSBP1            Heat shock factor binding protein 1
       0.45   10.2   5.7        1.2    8.7   0.4    3.7  2  Nup54_57_C       NUP57/Nup54 C-terminal domain
       0.46   10.3   0.0       0.46   10.3   0.0    4.1  5  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
       0.47   11.2  23.1        2.2    9.0   5.1    4.4  1  FliD_N           Flagellar hook-associated protein 2 N-termin
       0.48   10.3  19.6       0.79    9.5   0.8    4.1  4  DUF1465          Protein of unknown function (DUF1465)
        0.5   10.6  16.6          3    8.1   9.2    3.4  4  SesA             N-terminal domain on NACHT_NTPase and P-loop
        0.5   10.8  40.7        2.1    8.9   1.7    6.9  2  DUF4140          N-terminal domain of unknown function (DUF41
       0.51   10.2   2.8         12    5.7   0.5    2.4  2  Vip3A_N          Vegetative insecticide protein 3A N terminal
       0.58    9.4  27.0      0.099   11.9  12.5    2.9  4  CorA             CorA-like Mg2+ transporter protein
        0.7    9.2  24.4       0.29   10.4   8.5    3.4  3  DUF4763          Domain of unknown function (DUF4763)
       0.76    9.8  11.4        3.5    7.6   0.4    4.1  4  DUF4446          Protein of unknown function (DUF4446)
       0.76   10.1  18.3         11    6.4   1.5    3.4  3  Troponin         Troponin
       0.82    9.6   4.5         25    4.8   4.5    2.4  1  DUF2400          Protein of unknown function (DUF2400)
       0.99    8.5  23.6       0.33   10.1   1.4    3.9  3  DLP_helical      Dynamin-like helical domain
          1    8.0  13.8       0.73    8.5   1.7    2.8  3  Vps52            Vps52 / Sac2 family
        1.1    9.4  14.2        6.2    7.0   1.4    5.2  3  YojJ             Bacterial membrane-spanning protein N-termin
        1.4    9.1   5.7        2.2    8.4   0.0    3.4  2  SMODS            Second Messenger Oligonucleotide or Dinucleo
        1.4    8.8  15.8         15    5.5   0.7    5.7  5  DASH_Dam1        DASH complex subunit Dam1
        1.4    7.8  23.0       0.24   10.3   3.2    3.5  3  Vps53_N          Vps53-like, N-terminal
        1.5    7.6   3.0         11    4.6   0.1    2.4  2  Baculo_gp64      Baculovirus gp64 envelope glycoprotein famil
        1.6    8.9  15.7         13    6.0   0.2    5.4  4  Vps51            Vps51/Vps67
        1.6    9.2  24.8       0.56   10.6   0.9    5.9  6  UPF0184          Uncharacterised protein family (UPF0184)
        1.7    8.8  26.0         98    3.1  22.8    3.1  2  MutS_III         MutS domain III
        1.7    7.5  20.9       0.15   11.0   1.2    3.0  3  TTKRSYEDQ        Predicted coiled-coil domain-containing prot
        1.9    8.6  20.9       0.12   12.5   5.6    3.5  4  CREPT            Cell-cycle alteration and expression-elevate
          2    7.7  15.9        0.9    8.8   5.0    2.8  3  FAM76            FAM76 protein
        2.3    6.8   8.9        3.3    6.4   5.4    2.0  2  HlyD_2           HlyD family secretion protein
        2.4    8.1  18.3          1    9.4   5.0    3.1  2  YscO-like        YscO-like protein
        2.5    7.6  14.5        3.4    7.2   0.1    2.8  2  PTRF_SDPR        PTRF/SDPR family
        2.9    8.6   5.5         61    4.3   0.6    3.3  3  DUF4665          Domain of unknown function (DUF4665)
        2.9    7.2   9.4         44    3.4   9.4    2.6  1  ZnuA             Zinc-uptake complex component A periplasmic
        2.9    8.3   5.4         23    5.5   2.1    3.6  2  L31              Mitochondrial ribosomal protein L31
        3.1    7.7  23.0        1.7    8.6   6.7    3.2  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
        3.2    7.8  15.6          3    7.9   0.2    3.6  4  LidA_Long_CC     LidA long coiled-coil domain
        3.5    7.8  21.2         15    5.7   1.9    5.1  2  Swi5             Swi5
        3.9    7.5  24.5        4.3    7.4  15.6    2.6  2  SYCE1            Synaptonemal complex central element protein
        4.3    7.8  28.2          5    7.5   3.8    5.0  4  CCDC-167         Coiled-coil domain-containing protein 167
        4.4    8.0  15.4        9.1    7.0   3.3    3.3  3  Cytochrom_B562   Cytochrome b562
        4.5    7.1  16.7        5.1    7.0   4.5    3.9  4  Sec8_exocyst     Sec8 exocyst complex component specific doma
        4.7    5.4  14.9         14    3.9  14.9    1.5  1  SpecificRecomb   Site-specific recombinase
        4.8    7.4  29.9       0.47   10.6   5.9    4.7  4  DMPK_coil        DMPK coiled coil domain like
        5.1    7.0   9.8         21    5.0   0.6    4.0  4  GP41             Retroviral envelope protein
        5.2    7.2  12.2        1.8    8.7   2.1    4.0  3  Prefoldin_3      Prefoldin subunit
        5.5    7.5   5.0         30    5.1   0.6    2.6  2  Arm-DNA-bind_5   Arm DNA-binding domain
        5.8    6.2  14.4       0.31   10.3   5.1    2.7  2  DUF1978          Domain of unknown function (DUF1978)
        5.9    6.5  16.0        3.9    7.0   4.1    2.6  3  LUC7             LUC7 N_terminus
        6.1    7.3  11.2        2.9    8.3   2.7    3.2  3  DUF3037          Protein of unknown function (DUF3037)
        6.7    6.3   7.6         31    4.2   0.0    4.8  2  YvrJ             YvrJ protein family
        7.5    6.8  12.5         57    4.0   0.2    4.9  3  DUF3782          Protein of unknown function (DUF3782)
          8    6.1  21.4       0.12   12.0   7.8    2.6  3  YkyA             Putative cell-wall binding lipoprotein
        8.1    6.7  28.3       0.59   10.4   0.5    5.9  4  JIP_LZII         JNK-interacting protein  leucine zipper II
        8.2    6.8   9.2    1.9e+03   -0.8   9.2    3.1  0  HCMV_UL139       Human Cytomegalovirus UL139 protein
        8.6    6.6  32.1       0.62   10.3   2.0    4.3  5  Cortex-I_coil    Cortexillin I, coiled coil
        9.3    6.3  36.9         23    5.0   7.9    4.2  4  FlxA             FlxA-like protein
        9.6    6.5  15.2         28    5.0   0.4    5.4  3  HALZ             Homeobox associated leucine zipper


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 ?    5.2   0.0      0.11       8.3     192     256 ..     230     294 ..     213     300 .. 0.86
   2 !   26.9  10.3   2.8e-08   2.1e-06     145     258 ..     292     408 ..     288     413 .. 0.57
   3 !   28.5  18.2   9.2e-09   6.8e-07     143     259 ..     388     500 ..     387     507 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.11
                          Spc7 192 elesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                     e++ +++++ l e+l+ +++ +e +   l++l+e++ +le ++e+l+ q s+l +++ + e+ 
  gi|14601261|ref|NP_147796.1| 230 IAEEVASAYVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDR 294
                                   45668889999999*************************************99999998877765 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 2.8e-08
                          Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkel 222
                                   e++++++e   e +e + e l+ ++++++++ ++l e le+l +++e+le+   + +++L ++ e++++l + ++++++el
  gi|14601261|ref|NP_147796.1| 292 EDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEArvgSVEDRLSQAEEDIDSLTTSLDSLRTEL 372
                                   555666666666666666666666666666666666666666666666666555445666666666666666666666666 PP

                          Spc7 223 aelqeqleeleekieelkeqkseleeeiaeaervle 258
                                   ++l ++l+e ++++e+l+++ +++ + +++ ++ l 
  gi|14601261|ref|NP_147796.1| 373 EDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLA 408
                                   666666666666666666666666666666555443 PP

  == domain 3  score: 28.5 bits;  conditional E-value: 9.2e-09
                          Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkela 223
                                    l+ +l+++ +  ++L+++ + ++e l++l+e  a+l++e+e+lq+   e++     +L +lr++++++  e+e++ ++l 
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEID----RRLGQLRSTVDAVRLEVESLGEKLV 464
                                   6889999999************************************998854....49*********************** PP

                          Spc7 224 elqeqleeleekieelkeqkseleeeiaeaervlee 259
                                   + +e+ ++++++ie+ ++q++el++++ e+ r  ++
  gi|14601261|ref|NP_147796.1| 465 QAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   ****************************88887665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.97        72       3      46 ..     243     286 ..     241     291 .. 0.76
   2 !   13.6   0.0   0.00078     0.058       3      46 ..     292     335 ..     290     337 .. 0.95
   3 !   14.9   0.3   0.00031     0.023       4      45 ..     328     369 ..     327     372 .. 0.75
   4 !   15.2   0.6   0.00025     0.018       3      47 ..     355     399 ..     355     401 .. 0.94
   5 !   20.4   0.7   6.1e-06   0.00045       3      46 ..     383     426 ..     381     429 .. 0.93
   6 ?    8.6   0.8      0.03       2.2      13      46 ..     456     489 ..     444     492 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.97
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                   +erl  +e+ +++l+  +d lee+    e  ++ l+ +l++l s
  gi|14601261|ref|NP_147796.1| 243 EERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDS 286
                                   67888888888888888888888888888777777777777765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00078
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                   ++r++ ie++l+  e  +++l    + + ++++ l edl++l s
  gi|14601261|ref|NP_147796.1| 292 EDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSS 335
                                   89**************************************9976 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 0.00031
                          XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                   e+le + +++++le rv  +e++ + aee i++l+  l++l 
  gi|14601261|ref|NP_147796.1| 328 EDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLR 369
                                   677778888888888888888888888888888888887775 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 0.00025
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkklesn 47 
                                   +e++  + t ld+l +++++l  + aea+++++ l+ +l++  s+
  gi|14601261|ref|NP_147796.1| 355 EEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVAST 399
                                   689999**********************************99887 PP

  == domain 5  score: 20.4 bits;  conditional E-value: 6.1e-06
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                   +  le ++t+ld   +++++l+++ a+aee+++ l+edl++l++
  gi|14601261|ref|NP_147796.1| 383 QASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQA 426
                                   56899*************************************97 PP

  == domain 6  score: 8.6 bits;  conditional E-value: 0.03
                          XhlA  13 ldnleervdkleekaaeaeekiknleedlkkles 46 
                                   +++l+e++ + eek+ +++++i+  + ++ +l  
  gi|14601261|ref|NP_147796.1| 456 VESLGEKLVQAEEKNQRQDASIEDFQSQIQELRT 489
                                   788999*************************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 ?    3.7   0.1       1.1        83      15      40 ..     245     270 ..     238     284 .. 0.55
   2 ?    9.7   0.0     0.015       1.1       2      39 ..     260     297 ..     259     298 .. 0.95
   3 !   15.6   0.0   0.00022     0.016       1      40 [.     287     326 ..     287     328 .. 0.95
   4 !   11.6   0.4    0.0038      0.28       1      40 [.     336     375 ..     336     375 .. 0.86
   5 !   13.3   0.2    0.0011      0.08       3      40 ..     366     403 ..     364     407 .. 0.93
   6 ?    9.4   0.6     0.018       1.3       4      36 ..     409     441 ..     401     452 .. 0.72
   7 ?    2.5   3.3       2.6   1.9e+02       3      36 ..     429     462 ..     427     487 .. 0.67
   8 ?    3.7   0.6       1.1        82       6      32 ..     467     493 ..     462     497 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 1.1
                     FlaC_arch  15 eletvkkeneelsksveelkenVkdl 40 
                                   +l+ v++  e+l   ++ l+e+V dl
  gi|14601261|ref|NP_147796.1| 245 RLSLVEQAVEDLGLALDSLEERVGDL 270
                                   44445555555555555555554433 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.015
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkd 39 
                                   +d+lE+++++l+  +e +  ++++l + v  l+++V d
  gi|14601261|ref|NP_147796.1| 260 LDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVAD 297
                                   589********************************987 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 0.00022
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   r++ lE ++ +++ +le v+ ++e+ls  v+ + ++ + l
  gi|14601261|ref|NP_147796.1| 287 RVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQAL 326
                                   899********************************98866 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 0.0038
                     FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   r+++lE ++++++ +l+ +++++++l +s++ l  + +dl
  gi|14601261|ref|NP_147796.1| 336 RVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDL 375
                                   8999999999999999999999999999999998777665 PP

  == domain 5  score: 13.3 bits;  conditional E-value: 0.0011
                     FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   d+l ++l++lst+l+ +++++e+l++ ++++  + ++l
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQL 403
                                   88999**************************9998876 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.018
                     FlaC_arch   4 elEnklsklsteletvkkeneelsksveelken 36 
                                   + E+ l+ l   l+++++e e l++s+ e++++
  gi|14601261|ref|NP_147796.1| 409 TAEESLQALTEDLASLQAEVETLQQSIVEIDRR 441
                                   457777777777777777777777777777765 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 2.6
                     FlaC_arch   3 delEnklsklsteletvkkeneelsksveelken 36 
                                   ++l++ + +++ +l+ ++++ + ++ +ve l e+
  gi|14601261|ref|NP_147796.1| 429 ETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEK 462
                                   5566666666666666666666666666665543 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 1.1
                     FlaC_arch   6 Enklsklsteletvkkeneelsksvee 32 
                                   E+k ++ + ++e  +++++el+++++e
  gi|14601261|ref|NP_147796.1| 467 EEKNQRQDASIEDFQSQIQELRTQLDE 493
                                   7888899999************99986 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2    0.0018      0.14      26      90 ..     263     331 ..     252     333 .. 0.49
   2 !   25.9   3.1   1.2e-07   8.9e-06       2      69 ..     323     390 ..     322     393 .. 0.95
   3 !   14.3   3.8   0.00047     0.035      11      63 ..     388     440 ..     386     447 .. 0.91
   4 ?    9.5   5.3     0.014         1       2      64 ..     442     504 ..     441     514 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0018
                 Tropomyosin_1  26 leqenlekeqeiksLtkknqqleeevekleeklkeakekaeese....kkktnnealtrkiqlLEeele 90 
                                   le++  + e  +++Lt +++ l++ v  le+++ + +  +e+ e     ++   +a+++++q L e+le
  gi|14601261|ref|NP_147796.1| 263 LEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEgsleDLSGAVDAMSQQLQALAEDLE 331
                                   333444444444444444444444444444444444444333320000244456688888888888887 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.2e-07
                 Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeese 69 
                                   l++L  + e+   ++e+le++v + e++  + e++i sLt+ ++ l  e+e l+++l ea++++e+ +
  gi|14601261|ref|NP_147796.1| 323 LQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLN 390
                                   78999999******************************************************999865 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 0.00047
                 Tropomyosin_1  11 eaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeake 63 
                                   +  ++ +++ + +++l+q+    e+ ++ Lt+ +  l++eve+l++++ e  +
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDR 440
                                   567899*****************************************998765 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.014
                 Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakek 64 
                                   l +L+   ++    +e l ek+ ++e++n++++  i++ + ++q+l  ++++   + +++ ++
  gi|14601261|ref|NP_147796.1| 442 LGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   667888888888888888999999999999999999999999999988888766555554444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   7.4   4.6e-10   3.4e-08     308     469 ..     280     444 ..     231     465 .. 0.72
   2 !   24.9  17.6     1e-07   7.7e-06     280     463 ..     315     501 ..     312     508 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4.6e-10
                        AAA_13 308 avsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksve.lesvkakiesikklvaeineliakhNekvan 387
                                   ++s  +s+  a e+ +++++ ++ea+e +L+ l+ a++a  +++ + +e les+++++e ++  v ++++  ++  e +++
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEdLESLSSRVEDLEARVGSVEDRLSQAEEDIDS 360
                                   334456666778888888888888888888888888888888887755558888888888888888888888888888888 PP

                        AAA_13 388 leeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinke 466
                                   l+++  +++++le     ++e+++ l+ +++ +++++ ++++l+++l+ +e+ l++l e+ + L++++++ ++++ ei + 
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLStrLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRR 441
                                   888888888888865423678888888888888888888888888888888888888888888888888888888888887 PP

                        AAA_13 467 Lka 469
                                   L +
  gi|14601261|ref|NP_147796.1| 442 LGQ 444
                                   765 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1e-07
                        AAA_13 280 efeekqerLekliekveskkselleklkavsd.easensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svele 358
                                   ++++  ++L+ l+e++es +s++ e l+a +   +++ s++eed++ l++ ++ l+++L+ l+ +l +    +   +  l+
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLESLSSRV-EDLEARVGsVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDlNTRLD 394
                                   57788899********9998655.7777777625889999**************************99998888867789* PP

                        AAA_13 359 svkakiesikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeea 437
                                   +v++ ++++++ +a+++e+ ++  e  a+l++e+e++++++      + +l+s +d+   ++++l +++ ++e++ + + a
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDrrLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDA 475
                                   *************************************9998653213799******************************* PP

                        AAA_13 438 elkkleeeikeLekqlrdekpaaeei 463
                                    ++  + +i+eL++ql ++++ a++ 
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQELRTQLDEKTREAQQT 501
                                   *******************9999875 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0049      0.36      63     122 ..     241     300 ..     211     309 .. 0.64
   2 !   20.8   0.4   4.2e-06   0.00031      43     122 ..     274     349 ..     269     358 .. 0.69
   3 !   23.8   4.9   4.8e-07   3.6e-05      38     120 ..     360     445 ..     355     449 .. 0.70
   4 ?    3.4   2.1      0.97        72      54     105 ..     449     500 ..     442     511 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0049
                       DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                    L++r+  v++ +++   +  +++e v +++  ++++  +++s+++ v  le ++++ie+
  gi|14601261|ref|NP_147796.1| 241 PLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEG 300
                                   466666666666666666666666666666666666666666666666666666666664 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 4.2e-06
                       DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                   ve+++ ql ++ +        L++r++ ++ +l++++   ++++  v++++++l+++ ed+es+++ ve+le+++ ++e+
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSR----VGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVED 349
                                   55555555554444....44577777888888888888888888888888888888888888888888888888777775 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 4.8e-07
                       DUF1664  38 slsdavesvskqleqvseslaatkr...hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                   sl+  ++s+ ++le++s+ la+++    +L+ r+d+v ++l++ ++  +  +e ++++ edl++++ +ve++++ + +++ 
  gi|14601261|ref|NP_147796.1| 360 SLTTSLDSLRTELEDLSTRLAEAQAsleDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDR 440
                                   577778888888888888888887611145567777777777777777777777777777777777777777777777777 PP

                       DUF1664 116 kleri 120
                                   +l ++
  gi|14601261|ref|NP_147796.1| 441 RLGQL 445
                                   77666 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.97
                       DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                    ++++   + L +++ + ++k + q + +++ +++++e+r +l+e  ++ ++
  gi|14601261|ref|NP_147796.1| 449 VDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   4444444455555555555555566666666666666666555555554444 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   0.00012    0.0087     195     277 ..     244     329 ..     224     333 .. 0.76
   2 !   22.1  11.5   1.3e-06   9.6e-05     180     288 ..     325     431 ..     308     433 .. 0.82
   3 !    9.6  10.8    0.0085      0.63     198     280 ..     415     500 ..     412     507 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 0.00012
                                   XXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHH CS
                      Filament 195 skleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerlea...eleklqeklseleeela 272
                                   ++l+ +++a+e  + al s +e + +l   ++ l+ +l+sl +   +le+++a++e rlea    le+l  +++++ ++l+
  gi|14601261|ref|NP_147796.1| 244 ERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAvegSLEDLSGAVDAMSQQLQ 324
                                   46677889999999999***************************************9987511145555555555555555 PP

                                   HHHHH CS
                      Filament 273 eiree 277
                                    + e+
  gi|14601261|ref|NP_147796.1| 325 ALAED 329
                                   55554 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.3e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHH CS
                      Filament 180 elaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerle...ael 257
                                   +l     e++e   +s++e+l+  + + ++ l++a+e+i  l  +++sl++ele+l    a  +a+l++l+ rl+   + l
  gi|14601261|ref|NP_147796.1| 325 AL----AEDLE-SLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDqvaSTL 400
                                   33....33444.4689*******************************************************9875111678 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Filament 258 eklqeklseleeelaeireemarqlreYqeL 288
                                   ++lq+ l+  ee l+ + e++a    e + L
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   899999999***********99988887665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0085
                                   XXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
                      Filament 198 eelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleae...leklqeklseleeelaeir 275
                                   + l+e  ++ ++++++ ++ i e+ r++ +l++ +++++ + +sl ++l  +ee+ +++   +e++q++++el ++l e  
  gi|14601261|ref|NP_147796.1| 415 QALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQdasIEDFQSQIQELRTQLDEKT 495
                                   5677888888999999999************************99998877666555441116777778888877777665 PP

                                   HHHHH CS
                      Filament 276 eemar 280
                                   +e ++
  gi|14601261|ref|NP_147796.1| 496 REAQQ 500
                                   55554 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 ?    8.9   0.4      0.02       1.4      55     114 ..     247     306 ..     229     310 .. 0.82
   2 !   26.0  14.5     1e-07   7.5e-06       6     131 ..     296     421 ..     292     423 .. 0.94
   3 !   17.8  17.1   3.4e-05    0.0025      20     127 ..     394     502 ..     392     507 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.02
                CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekE 114
                                   + +++ +e l   l  le  + +l    e+L+ +l    +rv  Le +  ++e  le  E
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVE 306
                                   446778888888888888888888899999999999999999999999999999998877 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1e-07
                CENP-F_leu_zip   6 lhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLe 86 
                                     ++++L ++e + + L + v+++ ++l+ + e++e++   +E+  a v ++++ + + +e    l++ L++lr e e+L 
  gi|14601261|ref|NP_147796.1| 296 ADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   56889999999999******************************************************************* PP

                CENP-F_leu_zip  87 kelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeL 131
                                     l + q   ++L+++  ++ ++l+++ q  +  +e+ +a  e L
  gi|14601261|ref|NP_147796.1| 377 TRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDL 421
                                   ***************************999999999998888777 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.4e-05
                CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLe 100
                                   d++    ++L++ l ++ee++++++ +  + +aevetl++ i e+ ++l +l++ ++a+r e e+L ++l +  e+ +  +
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQD 474
                                   566677899************************************************************************ PP

                CENP-F_leu_zip 101 slnsslenlleekEqe.kvqmkeeskaa 127
                                   ++ ++++++++e+  + + + +e++++a
  gi|14601261|ref|NP_147796.1| 475 ASIEDFQSQIQELRTQlDEKTREAQQTA 502
                                   **********999888667777777666 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0     0.002      0.15      62     129 ..     274     341 ..     246     345 .. 0.80
   2 !   19.0   8.5   1.6e-05    0.0012      46     125 ..     334     414 ..     333     416 .. 0.91
   3 !   13.8  12.2   0.00061     0.045      53     139 ..     412     498 ..     405     506 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.002
                          ADIP  62 irkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqik 129
                                   +++l+  +++l s++  l++++++ e +l++v+  + +l  ++ + +q+l+ ++e+l+ l + +++++
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLE 341
                                   55666677888888999999999999999999999999999999999999999999988888887766 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.6e-05
                          ADIP  46 qardrdleqr.eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                    +r +dle+r  s+++++++ e +i++l+++ ++l t+le+l ++la +qa + +l+++l +  ++l+++++ l+  +  l
  gi|14601261|ref|NP_147796.1| 334 SSRVEDLEARvGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESL 414
                                   67888999884599*********************************************************9998776665 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00061
                          ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqya 133
                                   e  ++l+e++ +l+ae e lq++i   +++l ql++ +++v  +  +l  kl ++e+k++++  +++  ++++q+++tq+ 
  gi|14601261|ref|NP_147796.1| 412 ESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLD 492
                                   567899*************************************************************************99 PP

                          ADIP 134 helkkk 139
                                     ++  
  gi|14601261|ref|NP_147796.1| 493 EKTREA 498
                                   888865 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 !   15.3   0.2    0.0002     0.015      17     116 ..     276     331 ..     220     333 .. 0.49
   2 !   21.9   3.3   1.9e-06   0.00014      35     112 ..     311     390 ..     305     394 .. 0.72
   3 !   22.1  12.8   1.7e-06   0.00012      24     120 ..     357     454 ..     339     473 .. 0.63
   4 ?    3.8   1.0      0.73        54      34      85 ..     443     493 ..     441     527 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.0002
                  Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnL 97 
                                   dLt +L+++    + + ++l+  +++ie                                         +L++++  l +L
  gi|14601261|ref|NP_147796.1| 276 DLTLQLSSL---DSRV-GALEDRVADIE----------------------------------------GRLEAVEGSLEDL 312
                                   222222222...2333.33444444444........................................4444444444444 PP

                  Baculo_PEP_C  98 lssvtNinstLnnllqaln 116
                                      v  + + L+ l ++l+
  gi|14601261|ref|NP_147796.1| 313 SGAVDAMSQQLQALAEDLE 331
                                   4444444444444444443 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.9e-06
                  Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnnll 112
                                   +l+ ++da+ +qL+al+edl+sl++ +++   r+ ++ ++L++a   +  +l++ L++l ++l +L + ++  +++L+ l 
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDleaRVGSVEDRLSQAEEDID-SLTTSLDSLRTELEDLSTRLAEAQASLEDLN 390
                                   68889999*************9998777655566666666666666664.7777777777777777777777777766654 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1.7e-06
                  Baculo_PEP_C  24 airlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssv 101
                                   +i ++++++   l t l+++ t+L + +++l++l + ld+    l++l ++L +a  +l ++l+++L +l++++ +L+ s+
  gi|14601261|ref|NP_147796.1| 357 DIDSLTTSL-DSLRTELEDLSTRLAEAQASLEDLNTRLDQvasTLQQLQQRLATAEESL-QALTEDLASLQAEVETLQQSI 435
                                   343344443.4444444444444444444444444433333334444444444444444.599999999999999999999 PP

                  Baculo_PEP_C 102 tNinstLnnllqalnnldl 120
                                     i   L  l ++++++ l
  gi|14601261|ref|NP_147796.1| 436 VEIDRRLGQLRSTVDAVRL 454
                                   9999999999999988744 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.73
                  Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrn 85 
                                   +ql +++da+  ++++l e+l ++ +  ++r d++++  ++++++l ++l++
  gi|14601261|ref|NP_147796.1| 443 GQLRSTVDAVRLEVESLGEKLVQAEE-KNQRQDASIEDFQSQIQELRTQLDE 493
                                   67777777777777777777766333.3333333333333333333333322 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0071      0.52      69     152 ..     232     315 ..     211     319 .. 0.84
   2 !   20.9   9.2   4.7e-06   0.00035     103     178 ..     315     390 ..     310     392 .. 0.87
   3 !   21.4  19.0   3.3e-06   0.00025      79     176 ..     375     472 ..     373     476 .. 0.67
   4 ?    1.3   5.5       4.7   3.5e+02      68     102 ..     469     503 ..     464     512 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0071
                         ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                   +++ sa+++ le++l+ + + +++l  +   l++r+ +l+ ++++l  +l++ ++r+ +le+++a++e +l+  e  l+++
  gi|14601261|ref|NP_147796.1| 232 EEVASAYVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDL 312
                                   456789999999999999999999999999999999999999999999999999999999999999999999988888877 PP

                         ATG16 150 ekl 152
                                     +
  gi|14601261|ref|NP_147796.1| 313 SGA 315
                                   655 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.7e-06
                         ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkle 178
                                    + +++++lq+l e l++ ++r+++lea++ ++e++l++ ee +  +++ ++ l+ El+ L  +l  a + l++l+
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLN 390
                                   5778999999999999999999999999999999999999999999999999999999999999999998888775 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 3.3e-06
                         ATG16  79 leqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDE 159
                                   l+++la+ ++ l++l  +  + a+ l++l++ l++ ee+l++ +e la+l+ae+++l++ + + + +l +++ +v++++ E
  gi|14601261|ref|NP_147796.1| 375 LSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLE 455
                                   556666777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                         ATG16 160 lsaLqlqlnqaEeklrk 176
                                   +++L  +l qaEek+++
  gi|14601261|ref|NP_147796.1| 456 VESLGEKLVQAEEKNQR 472
                                   77777777777777665 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 4.7
                         ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaq 102
                                   +n++q+a+i++ ++++++lr++l e  ++ +++a+
  gi|14601261|ref|NP_147796.1| 469 KNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   34456666666666666666666666666666655 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.2e-05    0.0031      32     139 ..     270     376 ..     258     382 .. 0.69
   2 !   20.5  12.9   4.2e-06   0.00031       6     120 ..     384     497 ..     379     507 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.2e-05
                       DUF4201  32 keelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrk 112
                                   +e   e+Ltl +  +l   + al++++++ +  L++   +  + + a+  + + l++l++ l+ l ++ +++e+r  ++++
  gi|14601261|ref|NP_147796.1| 270 LEFAVEDLTL-QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVED 349
                                   5555555555.4566667777777777777777777777777777777777777888888888888888888888888888 PP

                       DUF4201 113 elykvklerdklrkqneklkqqggllr 139
                                   +l++++++ d l +  + l++++++l+
  gi|14601261|ref|NP_147796.1| 350 RLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   888888888888888888887777764 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.2e-06
                       DUF4201   6 nelsklrlklislkhqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkekl 86 
                                   + l++l+ +l +  ++l+++q++l + ee   +Lt +d  +lq+e+++l++ I e +  L +l++++     +++ l ekl
  gi|14601261|ref|NP_147796.1| 384 ASLEDLNTRLDQVASTLQQLQQRLATAEESLQALT-EDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKL 463
                                   668888889999999******************98.59******************************************* PP

                       DUF4201  87 hmleselselkkelkekeerlaklrkelykvkle 120
                                      e++++++  ++++ + ++++lr +l +   e
  gi|14601261|ref|NP_147796.1| 464 VQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   **************************99876655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1     0.026         2      18      78 ..     238     298 ..     222     304 .. 0.51
   2 !   18.9   0.9   1.5e-05    0.0011       5      81 ..     295     371 ..     292     374 .. 0.91
   3 !   19.8   7.3   8.4e-06   0.00062      16     103 ..     369     453 ..     363     458 .. 0.93
   4 ?    3.9   2.7      0.67        50       6      49 ..     464     507 ..     453     524 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.026
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHH CS
                    Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkel 78 
                                    +apl+++l+ +++ ++ +   ++  +e v d+  a++d   + + L+  +  L+d++  +
  gi|14601261|ref|NP_147796.1| 238 YVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADI 298
                                   3455555555555555555555555555555555555555555555555555555555554 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.5e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                    Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                   +a+++  +++v+  l++ls  ++ ++++l+ +++++e     v+d+   + ++++  ++ e+ ++ L   l +l++ 
  gi|14601261|ref|NP_147796.1| 295 VADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTE 371
                                   688999999*********************************************************99999998765 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 8.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                    Laminin_II  16 leqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                      l++ls++l + +++l+ +n+ ++++   ++++++ ++ A++s + L++ +  L + +++l+q  ++   + + + +++
  gi|14601261|ref|NP_147796.1| 369 RTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE---IDRRLGQLR 446
                                   56799************************************************************9999...999999999 PP

                                   HHHHHHH CS
                    Laminin_II  97 elIaqAR 103
                                     + + R
  gi|14601261|ref|NP_147796.1| 447 STVDAVR 453
                                   9888776 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.67
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkd 49 
                                    +a+e+ +   + +++ + ++++++ +l e  r++++t   ++ 
  gi|14601261|ref|NP_147796.1| 464 VQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   33444444444455555555555555555555555555555544 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   1.4   1.6e-09   1.2e-07     345     492 ..     252     397 ..     247     401 .. 0.94
   2 !    8.4  10.7     0.007      0.51      60     157 ..     398     496 ..     394     507 .. 0.51

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.6e-09
                                   THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelke 425
                                    +++l   l++le+++ +le ++e+ +   S+l +++  le+++++ie ++e ++ sl++l        +ql+ + ++l++
  gi|14601261|ref|NP_147796.1| 252 AVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLES 332
                                   577888899************************************************************************ PP

                                   HHHHSSS-SS-S-TTTHHHHSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHHHHHH CS
                          EzrA 426 ikrkieksnLPgiPesyleelkeasdeieelakeLekkpinikevnkrldeardlveklyektneli 492
                                   + +++e+ +      s+ ++l++a++ i+ l  +L+  + +++++++rl ea+  +e l+++ +++ 
  gi|14601261|ref|NP_147796.1| 333 LSSRVEDLE--ARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVA 397
                                   *****9865..6668999*****************************************99988875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.007
                                   HHHHHHHHHHHHHHHHHTHHHHHT-GGGT--S-..SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHH CS
                          EzrA  60 ekfeewkkkwdeiktkklpeieellfeaeelld..kykfkkakkklaeleeeldeveekikkileelkelteseeknreei 138
                                   +++++++++  + ++ +l++++e l  +++ ++  + ++ ++ ++l +l++++d v+ +++++ e+l +  e+++++ + i
  gi|14601261|ref|NP_147796.1| 398 STLQQLQQRLATAEE-SLQALTEDLASLQAEVEtlQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASI 477
                                   455555555555544.55555555554444443113345555555555555555555555555555555555555555555 PP

                                   HHHHHHHHHHHHT--TTTT CS
                          EzrA 139 eklkekYrelrkkllanrf 157
                                   e+ +++ +elr++l ++  
  gi|14601261|ref|NP_147796.1| 478 EDFQSQIQELRTQLDEKTR 496
                                   5555555555555555544 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.068         5       7      53 ..     241     287 ..     236     290 .. 0.89
   2 !   23.2   1.2   1.1e-06   8.2e-05       1      56 [.     291     346 ..     291     357 .. 0.92
   3 ?    6.9   8.2      0.13       9.5       2      55 ..     355     408 ..     348     412 .. 0.76
   4 ?    9.8  10.5     0.016       1.2       3      56 ..     370     423 ..     368     427 .. 0.91
   5 ?   10.0   6.0     0.014         1       2      60 ..     411     469 ..     410     472 .. 0.91
   6 ?    3.2   3.4       1.9   1.4e+02      28      54 ..     472     500 ..     470     509 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.068
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX   7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                    LE++l+  e+++e+L  ++   ++++  l+  ++ l+ +l++l+++
  gi|14601261|ref|NP_147796.1| 241 PLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSR 287
                                   69********************9999999999999999999998876 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                          SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                   le+r+ ++E +l   e  +e+L+ +v +  qq+++l + l+ l  r+++le++ g+
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGS 346
                                   69*************************************************99775 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                          SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                   ee ++ L + l  +   +e+L+  +ae q  ++ l ++l+++a  l++l+++ +
  gi|14601261|ref|NP_147796.1| 355 EEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLA 408
                                   667777777777777888888888888888888888888888888888887765 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                          SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                   + le+L ++la  +  +e+Ln  + + + ++++lq++l+  +e l++l e+ ++
  gi|14601261|ref|NP_147796.1| 370 TELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLAS 423
                                   679********************************************9998765 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXX CS
                          SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgaseae 60 
                                   ee l++L + la ++  +e+L++ ++e ++++ +l+  +++++ ++++l e+  ++e++
  gi|14601261|ref|NP_147796.1| 411 EESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEK 469
                                   789999******************************************99998866654 PP

  == domain 6  score: 3.2 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHHHHHHT-..XXXXXXX CS
                          SlyX  28 eqqqqidrlqrqlrllaerl..keleess 54 
                                   +q+  i+  q q+++l+ +l  k++e+++
  gi|14601261|ref|NP_147796.1| 472 RQDASIEDFQSQIQELRTQLdeKTREAQQ 500
                                   78999999999999999999543333333 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 ?    9.2   2.1     0.011       0.8      80     138 ..     274     332 ..     242     335 .. 0.61
   2 !   24.8  28.2   1.9e-07   1.4e-05      35     171 ..     305     434 ..     297     435 .. 0.81
   3 !   12.4  30.1    0.0011     0.083      34     162 ..     395     518 ..     394     529 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.011
                    MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLns 138
                                    e+L  +l +  s++ +l+ + a+++ +l + + ++e +  +  +++q+lq++  +L+s
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLES 332
                                   34555555555566666666666666666666666666666666666666665555544 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.9e-07
                    MscS_porin  35 skkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrp 115
                                    +  +e+l  a+d   ++l++l ++le+l      +s+ ++ +      e rl q++++  +l++ l +l ++l  l+tr+
  gi|14601261|ref|NP_147796.1| 305 VEGSLEDLSGAVDAMSQQLQALAEDLESL------SSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRL 379
                                   44556666667777777777777777777......666666677788999******************************* PP

                    MscS_porin 116 eraqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqe 171
                                   ++aq+ l + ++rl+++ + L++++++  a +++  +al   la+l+a++e l+q+
  gi|14601261|ref|NP_147796.1| 380 AEAQASLEDLNTRLDQVASTLQQLQQRL-ATAEESLQALTEDLASLQAEVETLQQS 434
                                   *******************999995444.8888888889999**********9996 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.0011
                    MscS_porin  34 kskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilak..lsleeLeqrllqtssqlqelqeqlaqlnsqlvelq 112
                                   + ++ +++lq+++++a + l++l+++l++l +++ e+ ++++ +    l +L + ++++  ++++l e+l q++++ + + 
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEESLQALTEDLASL-QAEVETLQQSIVEidRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQD 474
                                   567789************************.44444444444331134566666666666666666666666666666666 PP

                    MscS_porin 113 trperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaelaale 162
                                    ++e  q+q+ e r++l+e +++ ++t       s a r++  a  a+l 
  gi|14601261|ref|NP_147796.1| 475 ASIEDFQSQIQELRTQLDEKTREAQQT------ASTASRWSMAAAGASLI 518
                                   666666666666666666666655555......55555555555444443 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.6   2.7e-05     0.002     138     233 ..     234     328 ..     216     331 .. 0.89
   2 !   14.8   5.1   0.00018     0.014       2      74 ..     322     394 ..     321     396 .. 0.91
   3 !   14.9  16.2   0.00018     0.013       2     113 ..     392     507 ..     391     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-05
                   Tropomyosin 138 aaeskiveLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRaeeAErsvqkLekevdrledeleaeke 218
                                    a + ++ Lee+L  v + + +L  + +   er  + e ++++L+ +L     R  + E +v+ +e  ++++e +le    
  gi|14601261|ref|NP_147796.1| 234 VASAYVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSG 314
                                   45667889***********************************************************************99 PP

                   Tropomyosin 219 kykaiseeLdqtlae 233
                                     +a+s++L q+lae
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQL-QALAE 328
                                   999999999.55543 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 0.00018
                   Tropomyosin   2 klkqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaad 74 
                                   +l+++ e+l++ + r e++++++ + e++  +ae++  +l+ ++  l  ele  ++rl+ea++ Le+++ + d
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLD 394
                                   68999999*******************************************************9999877655 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 0.00018
                   Tropomyosin   2 klkqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqllee...elerteerleealekLeeaekaades.er 78 
                                   +l qv  +l++ ++rl++a+++l++ ++  ++ +aEv++l+++i  ++    +l++t + +    e L e   +a+e+ +r
  gi|14601261|ref|NP_147796.1| 392 RLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRrlgQLRSTVDAVRLEVESLGEKLVQAEEKnQR 472
                                   6789999999999*****************************999999833356677788888899999999999999788 PP

                   Tropomyosin  79 arKvlEnrelkdeekleeleaqlkeakeiaeeadr 113
                                       +E+ + +  e   +l+++ +ea++ a  a r
  gi|14601261|ref|NP_147796.1| 473 QDASIEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   8999*************************999977 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1     0.023       1.7       6      62 ..     246     299 ..     236     303 .. 0.85
   2 !   12.6   8.7     0.002      0.14       6      65 ..     323     386 ..     279     408 .. 0.76
   3 ?    9.7   5.3     0.015       1.1      14      63 ..     387     433 ..     384     444 .. 0.78
   4 ?    4.1   2.9      0.89        66      15      65 ..     444     491 ..     433     502 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.023
                       NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIq 62 
                                   L ++ ++++++   +d+l+++v d++  ++d   l+ +L ++   + +le+ v +I+
  gi|14601261|ref|NP_147796.1| 246 LSLVEQAVEDLGLALDSLEERVGDLEFAVED---LTLQLSSLDSRVGALEDRVADIE 299
                                   5567789999999999999999999998877...88999999999999999999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.002
                       NPV_P10   6 LlvIradikavddkVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                   L    +d + ++++V+ l+++v    d++++  +d++ l++ Ld++ ++L++l+t + + q  L
  gi|14601261|ref|NP_147796.1| 323 LQALAEDLESLSSRVEDLEARVgsveDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASL 386
                                   6667778888888888888888555555555556677777777777777777777666555544 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.015
                       NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                   +++++++d + + ++++q+ l +    +e L+a+++ La+l+++ve+ q+
  gi|14601261|ref|NP_147796.1| 387 EDLNTRLDQVASTLQQLQQRLAT---AEESLQALTEDLASLQAEVETLQQ 433
                                   57888889999999999998888...458888899999998888888764 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.89
                       NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                   ++ + Vda+  +v+++ e+l + +   ek ++q a+++++++++++    L
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAE---EKNQRQDASIEDFQSQIQELRTQL 491
                                   344555555555655555555533...444445555555555555444333 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5   3.8e-05    0.0028     716     833 ..     258     356 ..     229     365 .. 0.50
   2 !   18.9  21.3   4.8e-06   0.00035     693     842 ..     361     517 ..     352     520 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-05
                           FPP 716 enleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeeekkshe 796
                                     l+sl  +  + E  +++l+++L+sl    + +e+ +   +   e +e  +++l   +  + q+++aL ++Le+ ++  e
  gi|14601261|ref|NP_147796.1| 258 LALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVE 338
                                   234444444444444555555555555555555555555555555555555555555555555555555555555555555 PP

                           FPP 797 eleakckelqeqlervekkevskssaeeedkklkqek 833
                                   +lea++  ++ +l ++e                    
  gi|14601261|ref|NP_147796.1| 339 DLEARVGSVEDRLSQAE-------------------E 356
                                   55555555555544443...................3 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.8e-06
                           FPP 693 lkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkes.kslaet......qlkcmkesyesletr 766
                                   l+  l +l+ e e+l ++l++a+++le l+++l +   +l++l++ L++++es + l+e+      +++  ++s  +++ r
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESlQALTEDlaslqaEVETLQQSIVEIDRR 441
                                   44556666667777777777777777777777777777777777777777666233444322221145556667778999* PP

                           FPP 767 ateleaelnelkqkieaLeveLeeekksheeleakckelqeqlervekkevskssaeeedkklkqekeiaAAaeKL 842
                                   + +l++ +  ++ ++e+L ++L + ++  + + a++++ q q++  +++   k  ++++   + + + +aAA   L
  gi|14601261|ref|NP_147796.1| 442 LGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSMAAAGASL 517
                                   **********************************************9888889999999999*********98766 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   4.5   3.3e-06   0.00024       8     146 ..     245     387 ..     233     390 .. 0.81
   2 !   10.9   4.0    0.0034      0.25       7      55 ..     391     439 ..     383     442 .. 0.88
   3 !   11.8   3.2    0.0018      0.13       9      69 ..     442     502 ..     436     513 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.3e-06
                       DUF4795   8 llkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDe 88 
                                    l+ +++a+e+l   l++lee+v +le   ed+  +l +l + + +le++ ad       +a+    e+L   v  d + +
  gi|14601261|ref|NP_147796.1| 245 RLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVAD--IEGRLEAVEGSLEDLSGAV--DAMSQ 321
                                   4788899**********************************************..344667899999*******..77888 PP

                       DUF4795  89 akkeLekmleellekle.......eqeealkkaldtLqeelkekld..rlelepLkeqleerlkelq 146
                                    +++L + le+l +++e       ++e++l +a +++  +l++ ld  r ele+L+++l e   +l+
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLESLSSRVEdlearvgSVEDRLSQAEEDID-SLTTSLDslRTELEDLSTRLAEAQASLE 387
                                   88888888888888877333333366666666666665.9999999999999999999987766665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0034
                       DUF4795   7 ellkklqeaieklqeelekleekvkelekrledkekklealkkqieele 55 
                                   + l+++ +++++lq++l+  ee+ + l ++l+ ++ ++e+l+++i e +
  gi|14601261|ref|NP_147796.1| 391 TRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEID 439
                                   4499999************************************997765 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0018
                       DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeela 69 
                                   l +l++++  +  e+e+l ek  + e++ ++++ ++e  ++qi+el+++ ++k+  +++ a
  gi|14601261|ref|NP_147796.1| 442 LGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   7899*********************************************999998777665 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   0.7   4.1e-06    0.0003      26     125 ..     276     386 ..     240     387 .. 0.71
   2 !   24.3   8.7     2e-07   1.5e-05      22     133 ..     328     436 ..     326     439 .. 0.93
   3 !   15.2  15.9   0.00012    0.0086      23     147 ..     385     505 ..     382     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-06
                         Atg14  26 elrerlaklksekeslkkkiekalegke...........eaeqledkiknkkakleelksliadlrerlqelkdklsqlkk 95 
                                   +l  +l +l s+  +l+ ++ +++ + e           +++  +++++ ++++le+l s+++dl++r+  ++d+lsq  +
  gi|14601261|ref|NP_147796.1| 276 DLTLQLSSLDSRVGALEDRVADIEGRLEavegsledlsgAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEE 356
                                   445556666666666666666555555577786667777667777777777778888888888888887777777777777 PP

                         Atg14  96 eieekkkklaklsdklkkRrsdleslqnel 125
                                    i+     l +l+ +l +   +l+ +q +l
  gi|14601261|ref|NP_147796.1| 357 DIDSLTTSLDSLRTELEDLSTRLAEAQASL 386
                                   777777777777777776666666666655 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2e-07
                         Atg14  22 erlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkk 102
                                   e+l++l  r+ +l ++  s++ ++++a+e  +   +l++ ++++++ le+l ++ a+ ++ l+ l+++l+q  + +++ ++
  gi|14601261|ref|NP_147796.1| 328 EDLESLSSRVEDLEARVGSVEDRLSQAEEDID---SLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   68999999999999999999999999999999...99999999999999999999999999******************** PP

                         Atg14 103 klaklsdklkkRrsdleslqneleerrkkqi 133
                                   +la+  ++l   ++dl+slq e+e  +++++
  gi|14601261|ref|NP_147796.1| 406 RLATAEESLQALTEDLASLQAEVETLQQSIV 436
                                   ************************9999987 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 0.00012
                         Atg14  23 rlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkk 103
                                   +l++l++rl ++ s+ ++l++++  a+e+ +    l++++ +++a +e+l++ i ++ +rl +l+ +++  + e+e   +k
  gi|14601261|ref|NP_147796.1| 385 SLEDLNTRLDQVASTLQQLQQRLATAEESLQ---ALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEK 462
                                   899***************************9...89999999999999999999999999999999999999999999999 PP

                         Atg14 104 laklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqkl 147
                                   l +  +k+ +  +++e  q++++e r+++ +k+  + ++++ + 
  gi|14601261|ref|NP_147796.1| 463 LVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTR-EAQQTASTA 505
                                   9999999999999999999999999876555554.444444443 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.021       1.6     334     421 ..     241     332 ..     227     342 .. 0.67
   2 !   25.5  24.1   7.6e-08   5.6e-06     313     475 ..     339     501 ..     265     509 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.021
                        DUF812 334 elqeqieeleskieeleeeikklessikqveeeleeekeeneelekev.klkkktlel...lpdaeeniekLqalveasaq 410
                                    l+e+++ +e+ +e l   +++le+++  +e ++e +  + + l + v +l+ +++++   l+  e+++e L  +v+a +q
  gi|14601261|ref|NP_147796.1| 241 PLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVgALEDRVADIegrLEAVEGSLEDLSGAVDAMSQ 321
                                   566666667777777777777777777777777777777776666666345666666544456678888888888888888 PP

                        DUF812 411 rlvelakqWek 421
                                   +l+ la+  e+
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLES 332
                                   88888877764 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 7.6e-08
                        DUF812 313 elakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd 393
                                    l++++ + e++  + ee++++l + +++l+ ++e l+  +++ ++s++ ++  l++  ++ ++l++ +++++  l+ l  
  gi|14601261|ref|NP_147796.1| 339 DLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQAL-- 417
                                   3337788999999***************************************************************999.. PP

                        DUF812 394 aeeniekLqalveasaqrlvelakqWekhRvpl...ieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeel 471
                                     e ++ Lqa+ve+ +q++ve+ ++  + R+++     e ++l e+  + e++ +r+ + i+ ++++++e+  +l +k  +
  gi|14601261|ref|NP_147796.1| 418 -TEDLASLQAEVETLQQSIVEIDRRLGQLRSTVdavRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   .899**************************8752215699***********************************999988 PP

                        DUF812 472 lkqL 475
                                    +q 
  gi|14601261|ref|NP_147796.1| 498 AQQT 501
                                   8885 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       3.9   2.9e+02      62      89 ..     258     285 ..     245     289 .. 0.56
   2 ?    8.6   0.0     0.024       1.8      62     103 ..     286     327 ..     278     330 .. 0.86
   3 !   11.0   1.3    0.0041       0.3      61     103 ..     341     383 ..     319     385 .. 0.78
   4 !   14.0   1.2    0.0005     0.037      60     104 ..     361     405 ..     359     407 .. 0.92
   5 !   11.5   0.5    0.0029      0.21      59      99 ..     409     449 ..     406     453 .. 0.91
   6 ?    2.4   4.7       2.1   1.5e+02      74     102 ..     466     494 ..     455     505 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 3.9
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  62 evkeeLeerketlekeiktlekqlekle 89 
                                    +++ Leer  +le  ++ l+ ql++l 
  gi|14601261|ref|NP_147796.1| 258 LALDSLEERVGDLEFAVEDLTLQLSSLD 285
                                   2455666666666666666666666655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                   Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                   +    Le+r +++e +++++e +le+l   ++ + ++lq++ 
  gi|14601261|ref|NP_147796.1| 286 SRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALA 327
                                   556689*******************************99975 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0041
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                   Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                   e     +e+r+ ++e+ i++l+ +l++l++ele+l + l +++
  gi|14601261|ref|NP_147796.1| 341 EARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQ 383
                                   4444567888888888888888888888888888888887765 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 0.0005
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                   Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeelqkklq 104
                                   +++ ++ L +++e+l++++++ + +le+l+++l+++ ++lq+++q
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   6678899***********************************998 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.0029
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                   + ee ++ L e++++l++e++tl++++ ++ ++l +l++++
  gi|14601261|ref|NP_147796.1| 409 TAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTV 449
                                   568999*****************************999876 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                   Prefoldin_2  74 lekeiktlekqleklekeleelkeelqkk 102
                                   +e++ ++   ++e+ + +++el+++l +k
  gi|14601261|ref|NP_147796.1| 466 AEEKNQRQDASIEDFQSQIQELRTQLDEK 494
                                   44444444444444444444444444333 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 ?    8.4   0.3     0.034       2.5      10      58 ..     260     310 ..     228     312 .. 0.79
   2 !   19.6   0.8   1.1e-05   0.00079      10      68 ..     281     341 ..     275     342 .. 0.87
   3 !   16.4   4.2   0.00011    0.0079       9      63 ..     329     378 ..     326     396 .. 0.80
   4 !   10.6   9.3     0.007      0.51       7      60 ..     383     431 ..     380     437 .. 0.93
   5 ?    4.9   4.2      0.41        30       8      61 ..     440     495 ..     437     508 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.034
                  ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLe 58 
                                   l+ le++   LE   ++l+ +l++ +       +++a++  +le++e  Le
  gi|14601261|ref|NP_147796.1| 260 LDSLEERVGDLEFAVEDLTLQLSSLDSRVGAleDRVADIEGRLEAVEGSLE 310
                                   788999999999999999999998884422234556666666666666665 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.1e-05
                  ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleaeLeelyerWeeLe 68 
                                   l  l+++  aLE + a++e +l++ e   +d   ++ + s++l++l ++Le l +r e Le
  gi|14601261|ref|NP_147796.1| 281 LSSLDSRVGALEDRVADIEGRLEAVEGSlEDLsGAVDAMSQQLQALAEDLESLSSRVEDLE 341
                                   77888999999999999999999999985555899*********************99998 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 0.00011
                  ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                    le l ++ e LE++  ++e++l+++e     e +  l++ l+ l++eLe l  r
  gi|14601261|ref|NP_147796.1| 329 DLESLSSRVEDLEARVGSVEDRLSQAE-----EDIDSLTTSLDSLRTELEDLSTR 378
                                   5999999*****************999.....66777777777777777777665 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.007
                  ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                   q  le l  ++++    +++l+++la +e     e l++l++ l+ l+ae e+l
  gi|14601261|ref|NP_147796.1| 383 QASLEDLNTRLDQVASTLQQLQQRLATAE-----ESLQALTEDLASLQAEVETL 431
                                   7789**********************999.....99***************997 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.41
                  ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpely.sdp..eklaelsaeleeleaeLeely 61 
                                   r+l +l ++ +a   e ++l ++l ++e   +    + + + + +++el+++L+e++
  gi|14601261|ref|NP_147796.1| 440 RRLGQLRSTVDAVRLEVESLGEKLVQAEEKnQ-RqdASIEDFQSQIQELRTQLDEKT 495
                                   56667777777777777888887777774422.234669999999999999999987 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.2   3.1e-05    0.0023     375     474 ..     242     341 ..     229     345 .. 0.92
   2 !   17.1   9.4   1.3e-05   0.00097     358     460 ..     344     446 ..     340     452 .. 0.93
   3 !    9.7   6.3    0.0023      0.17     426     487 ..     440     501 ..     436     509 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.1e-05
                 Myosin_tail_1 375 lekakqaLesenkelqaelkslqqakqdseqkrkkleaqlqelqvklseserqreelaekvsklqaelesvsslleeaegk 455
                                   le     +e+ +++l   l sl++   d e     l  ql+ l++++   e + ++++ +++ ++  le++s++++ + ++
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQ 322
                                   666667789999********************************************************************* PP

                 Myosin_tail_1 456 siklskdvsslesqlqDtq 474
                                      l+ d++sl+s+++D +
  gi|14601261|ref|NP_147796.1| 323 LQALAEDLESLSSRVEDLE 341
                                   ****************986 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.3e-05
                 Myosin_tail_1 358 leelseqleqakrskaslekakqaLesenkelqaelkslqqakqdseqkrkkleaqlqelqvklseserqreelaekvskl 438
                                   + +++++l qa     sl  +  +L +e ++l++ l   q++ +d +++  ++ + lq+lq +l+ +e + + l+e ++ l
  gi|14601261|ref|NP_147796.1| 344 VGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASL 424
                                   668899*************************************************************************** PP

                 Myosin_tail_1 439 qaelesvsslleeaegksikls 460
                                   qae+e++++++ e + +  +l 
  gi|14601261|ref|NP_147796.1| 425 QAEVETLQQSIVEIDRRLGQLR 446
                                   ***********99998876665 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0023
                 Myosin_tail_1 426 rqreelaekvsklqaelesvsslleeaegksiklskdvsslesqlqDtqellqeetrqkLal 487
                                   r+  +l   v  ++ e+es+ + l +ae+k+ +    ++  +sq+q+ + +l+e tr+  + 
  gi|14601261|ref|NP_147796.1| 440 RRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   55566778899999******************************************986555 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 !   28.4  14.9   1.5e-08   1.1e-06      12     193 .]     266     442 ..     258     442 .. 0.86
   2 !   16.1  21.6   8.8e-05    0.0065      63     192 ..     366     497 ..     365     498 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.5e-08
                    Lebercilin  12 kikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklke 92 
                                   ++ +L+  +++l  +l+ l+    +L++     e +L+ +e++ ++L+  ++ +++ +++l e+l  +  ++++le ++ +
  gi|14601261|ref|NP_147796.1| 266 RVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGS 346
                                   667777788888888888888888888888888999********************************************* PP

                    Lebercilin  93 keaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevk 173
                                    e++l +++++++ l     d    e e+L+++L+e++a le+ + ++++       + ++ +++la+ +++ +++ e+++
  gi|14601261|ref|NP_147796.1| 347 VEDRLSQAEEDIDSLTTSL-DSLRTELEDLSTRLAEAQASLEDLNTRLDQVA----STLQQLQQRLATAEESLQALTEDLA 422
                                   ***************9944.33345888899999999998888888887554....4556678899999************ PP

                    Lebercilin 174 alqeeierlkqklkeKereL 193
                                   +lq+e+e+l+q++ e +r L
  gi|14601261|ref|NP_147796.1| 423 SLQAEVETLQQSIVEIDRRL 442
                                   ***************99986 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.8e-05
                    Lebercilin  63 arhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknL.aereeLqkkLeeleakleekeekike 142
                                   ++ + E++ l +rl ++q++ ++l+ +l +  + l++l++ l + ++    + L ++ + Lq ++e+l++ + e ++++ +
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESL--QALtEDLASLQAEVETLQQSIVEIDRRLGQ 444
                                   5667788899999999999999999999999999999999998888844..344145689********************* PP

                    Lebercilin 143 Lerk...leleeksfrrqlaaekkktkeaqeevkalqeeierlkqklkeKere 192
                                   L+     ++le +s   +l + ++k +   +++++ q++i++l+++l eK+re
  gi|14601261|ref|NP_147796.1| 445 LRSTvdaVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   *98622268999***************************************97 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 ?    3.2   0.0       1.2        86      34      70 ..     259     295 ..     242     299 .. 0.68
   2 !   17.4   0.4   4.3e-05    0.0032      30      74 .]     311     355 ..     302     355 .. 0.92
   3 ?    9.5   1.4     0.013      0.96      32      72 ..     355     395 ..     353     397 .. 0.87
   4 !   10.8   4.8    0.0051      0.37      22      69 ..     387     434 ..     386     439 .. 0.90
   5 ?    3.5   3.5      0.95        70      24      73 ..     445     494 ..     442     502 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.2
                    TMF_DNA_bd  34 tikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                   ++++L + + +le  +++l+ +l++l++ +  le+r 
  gi|14601261|ref|NP_147796.1| 259 ALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRV 295
                                   4566667777777777777777777777777777766 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.3e-05
                    TMF_DNA_bd  30 klnntikkLrkknkelekeikelkkkleklekeleeleerlkeae 74 
                                   +l+ +++ + ++++ l +++++l++++e+le  + + e+rl++ae
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAE 355
                                   6788999************************************98 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.013
                    TMF_DNA_bd  32 nntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                   ++ i++L   +  l +e+++l+ +l++ + +le l+ rl++
  gi|14601261|ref|NP_147796.1| 355 EEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   67799999999999999999999999999999999999986 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.0051
                    TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                   e+L    ++   t+ +L++ ++ +e++++ l++ l++l+ e+e+l+++
  gi|14601261|ref|NP_147796.1| 387 EDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   667777778889**********************************97 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.95
                    TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                   L+++ ++ +  + +L +k+ ++e++ ++++  +e+ +++++el+  l+e+
  gi|14601261|ref|NP_147796.1| 445 LRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEK 494
                                   55555555666666667777777777777777777777777776666654 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0066      0.49      97     178 ..     281     362 ..     244     369 .. 0.56
   2 !   19.7   6.6     8e-06   0.00059      67     181 ..     327     442 ..     322     448 .. 0.91
   3 !    9.7   4.0    0.0094      0.69      99     162 ..     444     507 ..     440     517 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0066
                        DUF724  97 Llslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledv 177
                                   L sl ++   l+++  ++e ++e  e + + l+  +d ++++ + l + l++l ++ e+ ++++ +++   +++ee++++ 
  gi|14601261|ref|NP_147796.1| 281 LSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSL 361
                                   444555555555555555555555555555555555555555555555555555555555555555555555555555554 PP

                        DUF724 178 e 178
                                    
  gi|14601261|ref|NP_147796.1| 362 T 362
                                   4 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 8e-06
                        DUF724  67 rseleslkeslaeLekhGFdVkalqsrl.nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerql 146
                                   ++ lesl+  + +Le+   +V+  +s+  +++ sl ++ ++l++e+++l  +++e++++ + l++ +d++ ++ ++l+++l
  gi|14601261|ref|NP_147796.1| 327 AEDLESLSSRVEDLEARVGSVEDRLSQAeEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRL 407
                                   578999999*******988888877777577999*********************************************** PP

                        DUF724 147 allkekkeaadkeiarlkseaekleeeledveqeF 181
                                   a++ e  +a  +++a+l++e+e+l++++ ++ ++ 
  gi|14601261|ref|NP_147796.1| 408 ATAEESLQALTEDLASLQAEVETLQQSIVEIDRRL 442
                                   ***************************99887765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0094
                        DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiar 162
                                   +l++  + ++ e + l +k+ ++e+++++ +++i++++++i+el++ql+ + ++ ++ ++  +r
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   6667777777788888999999999999999999999999999999998777555555554444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.3   0.00056     0.042      39     147 ..     273     382 ..     243     385 .. 0.71
   2 !   19.8  19.8   1.2e-05   0.00088      35     155 ..     367     502 ..     353     509 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00056
                          Fez1  39 qlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesde 119
                                    + +l+ +l++ ++++  le+++ + +  le +e  l+  +  ++ +++++++l e+l++l +++++l+++  + + + ++
  gi|14601261|ref|NP_147796.1| 273 AVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQ 353
                                   667888889999999999999999999999999999999999999999999999999999988888866554444333333 PP

                          Fez1 120 akaqrqe.aeeleelkreverlraeLkee 147
                                   a++  ++ +++l++l+ e+e l ++L+e 
  gi|14601261|ref|NP_147796.1| 354 AEEDIDSlTTSLDSLRTELEDLSTRLAEA 382
                                   33332223556666777777776666654 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.2e-05
                          Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa. 114
                                   +l+++l +l+++l e ++++++l+++l++ +  l++++++l+ ++++ + l e + +l++e++ l++++ e  ++  + + 
  gi|14601261|ref|NP_147796.1| 367 SLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRs 447
                                   577777777777777777777777777777777777777777777777777777777777777777777776655555446 PP

                          Fez1 115 ...............lesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqa 155
                                                  l + e k+qrq+  ++e+ ++++++lr++L e+ ++ ++ a
  gi|14601261|ref|NP_147796.1| 448 tvdavrleveslgekLVQAEEKNQRQD-ASIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   677777777777777555666888888.799**************99888766654 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1     0.017       1.2      36      95 ..     239     295 ..     229     296 .. 0.78
   2 !   14.2   1.1   0.00057     0.042      38      95 ..     297     351 ..     289     381 .. 0.52
   3 ?    7.5   1.8     0.067         5      27      69 ..     363     405 ..     352     413 .. 0.44
   4 !   13.0   3.0    0.0013     0.093      39      94 ..     393     448 ..     391     452 .. 0.88
   5 ?    2.7   2.2       2.1   1.6e+02      20      75 ..     461     492 ..     449     508 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.017
                       BLOC1_2  36 ykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   ++ l+++++ +e+ +e+l     +l+++ +++ ++e  v++L+   s LD+ + +LE+++
  gi|14601261|ref|NP_147796.1| 239 VAPLEERLSLVEQAVEDLGL---ALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRV 295
                                   55566666777777777777...8888889999999999999999999999999999987 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00057
                       BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                   +++ +++ +e +le+l+    +++ + qq++++ +++++L + v+ L++ + + E+++
  gi|14601261|ref|NP_147796.1| 297 DIEGRLEAVEGSLEDLSG---AVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRL 351
                                   444445555555555444...4555555555555555555555555555554444443 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.067
                       BLOC1_2  27 klNeaasekykklkdvaaslekkleklnekyeelqpylqqidq 69 
                                   +   +  ++ ++l++++a+++++le+ln + +++++ lqq++q
  gi|14601261|ref|NP_147796.1| 363 TSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   2222333334444444444444444444444444444444433 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.0013
                       BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                   l++va+ l++  ++l   +e+lq + + +  ++++v++L++ + e+D    +L + 
  gi|14601261|ref|NP_147796.1| 393 LDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRST 448
                                   67888999999999999999999999999999999999999999999999999765 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 2.1
                       BLOC1_2  20 edyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                   e++   e+ N+++ +                        +++ + +qi+++ +q++
  gi|14601261|ref|NP_147796.1| 461 EKLVQAEEKNQRQDA------------------------SIEDFQSQIQELRTQLD 492
                                   333333333333333........................33333333333333333 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1      0.04       2.9      86     160 ..     259     332 ..     233     338 .. 0.46
   2 !   21.6   9.2   1.6e-06   0.00011      31     167 ..     291     430 ..     286     432 .. 0.82
   3 ?    5.4   4.4      0.14        10      42      92 ..     456     506 ..     442     513 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.04
                           GAS  86 slknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEk 160
                                   +l++l++r+ +le  ++dl+++  +l  r+ ++e+   +++ + ea+   +   +g     + ++l+al e+lE+
  gi|14601261|ref|NP_147796.1| 259 ALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDA-MSQQLQALAEDLES 332
                                   344444455555555555555555555555555555555544444433333333333322.33444444444443 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.6e-06
                           GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekd....kqslknlkarlkelekelkdlkwe 107
                                   l + +++++ + e+ e  l+++s     ++++L+++ e++e L  ++++ e        +l ++++ + +l+  l +l+ e
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARvgsvEDRLSQAEEDIDSLTTSLDSLRTE 371
                                   667778888888888888888888888888888888888888888888777651111468999****************** PP

                           GAS 108 hevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqlee 167
                                    e l+ r+++++++ ++l+ + +++  ++q + + +    e  l+al+e+l + +a++e+
  gi|14601261|ref|NP_147796.1| 372 LEDLSTRLAEAQASLEDLNTRLDQVASTLQ-QLQQRLATAEESLQALTEDLASLQAEVET 430
                                   *********************999666555.57888899999999999999999998876 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.14
                           GAS  42 eernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlka 92 
                                    e+   +l +++++n+r    ++  + +++eLr ql +  ++ q+ +++ +
  gi|14601261|ref|NP_147796.1| 456 VESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTAS 506
                                   444555666677777777777777777777777777777777777666655 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       7.3   5.4e+02     120     157 ..     228     265 ..     211     275 .. 0.77
   2 !   16.8   2.4   5.8e-05    0.0043      65     165 ..     289     389 ..     281     398 .. 0.91
   3 !   19.0  16.1   1.2e-05    0.0009      63     179 ..     399     515 ..     396     519 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 7.3
                        DUF745 120 lenaeqvaagaqqelaektqlleaAkkRveeLkkqlke 157
                                    e ae+va+   + l+e+ +l+e+A + +      l+e
  gi|14601261|ref|NP_147796.1| 228 REIAEEVASAYVAPLEERLSLVEQAVEDLGLALDSLEE 265
                                   566899999999999*******9998766665555555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.8e-05
                        DUF745  65 eqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAk 145
                                     le+ +++ e  ++ ++ sl+  + +++a ++  +   + le+l++ ++  ++++ ++e+  ++a++++++ t+ l++ +
  gi|14601261|ref|NP_147796.1| 289 GALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLR 369
                                   57999999999999999*****99999**999999999******************************************* PP

                        DUF745 146 kRveeLkkqlkearkdlekt 165
                                   + +e L+++l+ea++ le+ 
  gi|14601261|ref|NP_147796.1| 370 TELEDLSTRLAEAQASLEDL 389
                                   **********9999988865 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.2e-05
                        DUF745  63 lveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqllea 143
                                    ++ql+q l+ ae+ +q  ++ l+s +a +++ +++  ++ + l +l+++++a++ ++e++ +   +a+++ + + + +e+
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIED 479
                                   589****************************************************************************** PP

                        DUF745 144 AkkRveeLkkqlkearkdlektkkaAykAacAAqeA 179
                                    +++++eL++ql+e  ++ ++t + A++ ++AA+ A
  gi|14601261|ref|NP_147796.1| 480 FQSQIQELRTQLDEKTREAQQTASTASRWSMAAAGA 515
                                   *********************************988 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.4    0.0085      0.63      38      91 ..     277     328 ..     229     335 .. 0.75
   2 !   16.5   0.8     9e-05    0.0066      35      94 ..     337     394 ..     333     397 .. 0.88
   3 !   10.3   3.1    0.0076      0.56      36      94 ..     394     450 ..     391     464 .. 0.82
   4 ?    0.6   0.4       8.3   6.2e+02      34      74 ..     455     493 ..     449     510 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0085
                       DUF2730  38 laekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91 
                                   l+ ++++ d+r+ +le +v+++  +  le+++  l+dl g ++a+++++++l+ 
  gi|14601261|ref|NP_147796.1| 277 LTLQLSSLDSRVGALEDRVADI--EGRLEAVEGSLEDLSGAVDAMSQQLQALAE 328
                                   4445566666777777777666..455677777777777777777777777654 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9e-05
                       DUF2730  35 leklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvd 94 
                                   +e l+  v + + rl+++e  +++L t   l++L+++l+dl  +l +++a+++ l++++d
  gi|14601261|ref|NP_147796.1| 337 VEDLEARVGSVEDRLSQAEEDIDSLTTS--LDSLRTELEDLSTRLAEAQASLEDLNTRLD 394
                                   677888999****************875..779999999999999999999999998765 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0076
                       DUF2730  36 eklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvd 94 
                                    ++a ++++ ++rl+++e +++ L  ++dl++L+ +++ l+  + ++++++ ql+  vd
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESLQAL--TEDLASLQAEVETLQQSIVEIDRRLGQLRSTVD 450
                                   577788899999999999999998..678899999988888888888888888887765 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 8.3
                       DUF2730  34 dleklaekveendkrlteletkvenLPtakdlekLklllad 74 
                                   ++e+l ek+ + +++ ++ ++++e++  ++++++L+++l +
  gi|14601261|ref|NP_147796.1| 455 EVESLGEKLVQAEEKNQRQDASIEDF--QSQIQELRTQLDE 493
                                   55555555555555555555555554..3344444444444 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 ?    8.3   0.2     0.038       2.8      78     135 ..     236     293 ..     208     297 .. 0.81
   2 !   15.3   1.9   0.00026     0.019      83     144 ..     297     358 ..     294     360 .. 0.95
   3 !   12.7  24.4    0.0017      0.13      20     149 ..     347     475 ..     346     500 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.038
                         HrpB7  78 rayrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrr 135
                                    ay++ le+r+  +e++++ +  ald  e++v   + ++  +  q+   + r+ +l++
  gi|14601261|ref|NP_147796.1| 236 SAYVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALED 293
                                   58****************************9999999999999999999999988876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 0.00026
                         HrpB7  83 vlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaerareda 144
                                    +egr++a+e  l+ + +a+da  ++++a a+ + ++ ++++  ++r+  +++ + +a+ed+
  gi|14601261|ref|NP_147796.1| 297 DIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDI 358
                                   5799*******************************************************997 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.0017
                         HrpB7  20 lraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvraaeaelaaarq 100
                                   +++ l++a ++ +++ ++l +  +++e   +++++ +++l+dl t     ++  +++++  ++ +e+ ++a+ + la +++
  gi|14601261|ref|NP_147796.1| 347 VEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLD-QVASTLQQLQQRLATAEESLQALTEDLASLQA 426
                                   678899999999999999999999999999999999999999999886.78899999999999999999999999999999 PP

                         HrpB7 101 aldaaedavaatarkiaRndaqidacrerierlrraaeraredaadEEa 149
                                   +++  ++ + + +r+++ +++ +da+r  +e l +++ +a+e+++  +a
  gi|14601261|ref|NP_147796.1| 427 EVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDA 475
                                   9999999999999999999999999999999999999999999886665 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 !   19.3   2.3   8.4e-06   0.00062     185     299 ..     275     389 ..     260     395 .. 0.77
   2 !   13.1  18.4   0.00066     0.048     187     309 ..     382     504 ..     374     507 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.4e-06
                        HMMR_N 185 edmeaklqvtqknLeeskakvaqLkeklvslekek....ieekseteklleyieelsnvseqlekykldiaqleellkekn 261
                                   ed++ +l +++    +   +va ++ +l ++e           + +++l +  e l+++s ++e  + ++ ++e+ l++++
  gi|14601261|ref|NP_147796.1| 275 EDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLedlsGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAE 355
                                   788999999999999999999999999987665431111455566799999999999999999999999999********* PP

                        HMMR_N 262 deiesLkssLeekeqelskqvkdlnekckllekekeel 299
                                   ++i sL +sL+   +    + +dl++++ + ++++e+l
  gi|14601261|ref|NP_147796.1| 356 EDIDSLTTSLDSLRT----ELEDLSTRLAEAQASLEDL 389
                                   ***999999987666....5555555555555555544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00066
                        HMMR_N 187 meaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesL 267
                                    +a l+ +++ L++  ++++qL+++l + e+  +   ++   l +++e l++ + ++     ++ ql++++++   e+esL
  gi|14601261|ref|NP_147796.1| 382 AQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEI---DRRLGQLRSTVDAVRLEVESL 459
                                   5677899999****************9999999999999999999999999999999...999****************** PP

                        HMMR_N 268 kssL...eekeqelskqvkdlnekckllekekeelvreeeekeqt 309
                                    ++L   eek+q  ++ ++d ++++++l ++++e+ re+++ ++t
  gi|14601261|ref|NP_147796.1| 460 GEKLvqaEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   *9995556778888999****************999998887766 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 ?    6.5   0.3      0.15        11      29      69 ..     249     292 ..     237     299 .. 0.59
   2 !   14.1   0.6   0.00061     0.045      13      70 ..     289     342 ..     282     350 .. 0.72
   3 !   13.5   3.0   0.00091     0.067      26      63 ..     351     388 ..     339     400 .. 0.54
   4 ?    8.6   4.0     0.031       2.3      19      55 ..     379     415 ..     375     421 .. 0.75
   5 ?    7.3   4.8     0.083       6.1      25      61 ..     399     435 ..     392     448 .. 0.78
   6 ?    3.4   3.6       1.3        99      15      57 ..     459     501 ..     453     506 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.15
                           CLZ  29 leekverLessLeaLqtrlarLlaeyessq...rkLkqRitkLE 69 
                                   +e+ ve L  +L++L+ r+  L   +e      + L +R+ +LE
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERVGDLEFAVEDLTlqlSSLDSRVGALE 292
                                   56666666666666666666664433333300033445555555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00061
                           CLZ  13 glLDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLEk 70 
                                   g L+ ++a+ +   + +e  +e L ++++a+ ++l+ L +++es    L +R+++LE+
  gi|14601261|ref|NP_147796.1| 289 GALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLES----LSSRVEDLEA 342
                                   66777777777777788888888888888888888888887776....5566666665 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00091
                           CLZ  26 qkeleekverLessLeaLqtrlarLlaeyessqrkLkq 63 
                                     ++ee +++L +sL++L t l+ L + + ++q+ L+ 
  gi|14601261|ref|NP_147796.1| 351 LSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLED 388
                                   44566666666666666666666665555555544432 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.031
                           CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlaeye 55 
                                    a+a+a  ++l+++++++ s+L++Lq+rla   + ++
  gi|14601261|ref|NP_147796.1| 379 LAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQ 415
                                   5778888888889999999999999999887666655 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.083
                           CLZ  25 eqkeleekverLessLeaLqtrlarLlaeyessqrkL 61 
                                   + ++l++++   e+sL+aL+  la L ae+e+ q+ +
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSI 435
                                   5578999999999999999999999999999999865 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 1.3
                           CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyess 57 
                                   L e+  +a+++++  +  +e ++s+++ L t+l    +e +++
  gi|14601261|ref|NP_147796.1| 459 LGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   5566778888999999999999999999999988777776655 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   0.00089     0.066      37     114 ..     251     328 ..     244     336 .. 0.78
   2 !   18.0  12.4   1.9e-05    0.0014      12     114 ..     317     419 ..     312     422 .. 0.94
   3 ?    5.0  12.2      0.18        13      14      95 ..     417     498 ..     413     509 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00089
                       DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfve 114
                                   + +++l    ++l++++ +l+  +e+l+++ + l++ v ++e ++a++e ++e +e   ++l+   + m ++L+ + e
  gi|14601261|ref|NP_147796.1| 251 QAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAE 328
                                   666777777778888888888888888888888888888888888888888888888888888888888888877644 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.9e-05
                       DUF3450  12 galaatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                    a++++l+++ +  e+  +  ++ ++++ +++d  ++ ++++ +l++ l+sl+ + e l+  +a++++++++l+++++++ 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVA 397
                                   45699**************************************************************************** PP

                       DUF3450  93 eierelvpllekmidrLeqfve 114
                                    + ++l++ l +  ++L+ + e
  gi|14601261|ref|NP_147796.1| 398 STLQQLQQRLATAEESLQALTE 419
                                   *****************99876 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.18
                       DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                   l ++l+++++e e  +++  ++ ++  +l    + +  e+++l e+l ++e +n+++++++++ +++i++l++q++e ++ 
  gi|14601261|ref|NP_147796.1| 417 LTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   456777778888888888888888888888888888888888888888888888888888888888888888887775554 PP

                       DUF3450  95 e 95 
                                   +
  gi|14601261|ref|NP_147796.1| 498 A 498
                                   4 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 ?    2.4   0.1       2.3   1.7e+02       6      54 ..     239     287 ..     236     288 .. 0.82
   2 !   17.3   1.4   5.2e-05    0.0038       2      54 ..     291     343 ..     290     344 .. 0.97
   3 !   15.0   9.3   0.00026     0.019       1      72 [.     332     403 ..     332     408 .. 0.95
   4 ?    7.9  11.3     0.043       3.2       2      71 ..     389     458 ..     385     462 .. 0.85
   5 ?    5.9   5.4      0.19        14       2      55 ..     417     470 ..     416     475 .. 0.87
   6 ?    6.5   7.3      0.12       8.6       6      51 ..     456     501 ..     451     505 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 2.3
                 TolA_bind_tri   6 varLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleer 54 
                                   va LE+ l+  +q+  +l   l++l++ + +L   +E+l+ ql++l  r
  gi|14601261|ref|NP_147796.1| 239 VAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSR 287
                                   6678888888888888899999999999999999999999999887665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.2e-05
                 TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleer 54 
                                   ledrva +E  lea + +l +l   ++a++q+l+ L  ++E l+ ++e+le r
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEAR 343
                                   8************************************************9987 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 0.00026
                 TolA_bind_tri   1 sledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleag 72 
                                   sl +rv+ LE  + + +  l +  + +++l + l++LR ++E+l+ +l +++    dl + lD++ + l++ 
  gi|14601261|ref|NP_147796.1| 332 SLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQL 403
                                   6899*************************************************************9999875 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.043
                 TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                   l++r++++   l++ +q l    + l+al ++l++L+ ++E lq  + ++ +r  +l   +D++  ++e+
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVES 458
                                   6788888888888888888888999999999999999999999999999999999999999988777766 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.19
                 TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQ 55 
                                   l + +a+L   +e  +q+++e+ ++l +l++ ++  R ++E l  +l q+ee+ 
  gi|14601261|ref|NP_147796.1| 417 LTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKN 470
                                   5678899999999999999**********************9999999998864 PP

  == domain 6  score: 6.5 bits;  conditional E-value: 0.12
                 TolA_bind_tri   6 varLErilearsqlllelqqqlealqqelreLRGqiEelqyqleql 51 
                                   v++L ++l + ++ + ++   +e+ q++++eLR q++e + + +q+
  gi|14601261|ref|NP_147796.1| 456 VESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   66676666666799999999**********************9997 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0    0.0011     0.082       4      92 ..     292     375 ..     289     377 .. 0.85
   2 !   18.3  13.0   2.7e-05     0.002       2     106 ..     374     474 ..     366     479 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0011
                          FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqe 84 
                                   + ++a ++ +l++ e  le l    + +++ql++ a     ++l  +++  + l+ ++ + +  l+qae++++     + +
  gi|14601261|ref|NP_147796.1| 292 EDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALA-----EDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDS 367
                                   567788888999999999999999999999999998.....9999999999999999999999999999999999998888 PP

                          FliJ  85 arqerkkl 92 
                                    r e++ l
  gi|14601261|ref|NP_147796.1| 368 LRTELEDL 375
                                   88888765 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.7e-05
                          FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82 
                                   +  ++Laeaq+ l++ + +l+++ +++q++q++l+ +      + l+++ + +++l+ +++ ++q++    +++ + r+  
  gi|14601261|ref|NP_147796.1| 374 DLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAE-----ESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTV 449
                                   5678999***********************99999999.....************************************** PP

                          FliJ  83 qearqerkkl.ekLkerekkeeqke 106
                                    + r e+++l ekL + e+k++++ 
  gi|14601261|ref|NP_147796.1| 450 DAVRLEVESLgEKLVQAEEKNQRQD 474
                                   *********9888888888887765 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1    0.0017      0.13      35     103 ..     280     341 ..     232     348 .. 0.54
   2 !   15.7   3.6   0.00022     0.016      31      99 ..     339     407 ..     308     411 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0017
                                   HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                         DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                   +L  ++ +v +l+ +++ +e   e+ +  +++l+  ++       ++ + l+ ++e L++++ R+  +e
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVD-------AMSQQLQALAEDLESLSSRVEDLE 341
                                   33344444444444444444444444444444444444.......444455555555555555544444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 0.00022
                                   .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                         DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                   + ++r+  +e+++++ +e i+ l+   + +  ++++l+ +    +++l+ ++  l+ ++ tLq++++Rl
  gi|14601261|ref|NP_147796.1| 339 DLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRL 407
                                   334455555555555555666666666666666655555554444445566666666666666666666 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0     0.023       1.7      47      94 ..     262     309 ..     250     314 .. 0.91
   2 !   19.2  13.5   5.5e-06    0.0004     247     381 ..     324     448 ..     312     450 .. 0.73
   3 ?    1.1   4.1       1.8   1.3e+02     242     296 ..     445     499 ..     442     507 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.023
                        Tektin  47 rLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeepl 94 
                                   +LeeR+ d+ef  e L  +l+ l++ + aLe+    +e  lea+e  l
  gi|14601261|ref|NP_147796.1| 262 SLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSL 309
                                   7999***************************99999999999998776 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 5.5e-06
                        Tektin 247 ealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveEvk 327
                                   +al++ +e + +  + le     v+++++++e++i++L  ++++    l    tRl + +             + L++ ++
  gi|14601261|ref|NP_147796.1| 324 QALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQA----------SLEDLNTRLD 394
                                   3455555555555566666666666666666666666666666666666666666666322..........233488999* PP

                        Tektin 328 eleetieaLkeklaeaeaslkaLertrleleediavKansl.fiDeekclelRks 381
                                   ++ +t+++L+++la ae+sl+aL +  ++l+ +++  ++s+ +iD+ +  +lR++
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIvEIDR-RLGQLRST 448
                                   ***********************************99999758**9.99999976 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.8
                        Tektin 242 aeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplk 296
                                    +++ +a r  +e + +   + ee+ ++    i++ + +i+eL+ ++++k++  +
  gi|14601261|ref|NP_147796.1| 445 LRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQ 499
                                   5667777777888888888888888888888888888888888888888887655 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 ?    3.2   0.1       1.2        86      55      98 ..     249     292 ..     242     312 .. 0.65
   2 !   15.2   3.4   0.00022     0.016      17     105 ..     280     369 ..     273     374 .. 0.77
   3 !   14.9  19.2   0.00029     0.021       3     102 ..     322     422 ..     321     433 .. 0.84
   4 ?    6.1  14.1      0.15        11      28     113 ..     414     503 ..     413     507 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.2
                         DHR10  55 akkklkelrdaleekeielrelerkeerlqrqlenaeeklerlr 98 
                                   +++ +++l  al+++e+++ +le   e l+ ql++   +   l+
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALE 292
                                   55666666667777777777777777777777776666554443 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 0.00022
                         DHR10  17 karelqakidalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeekler 96 
                                   +   l  ++ al++  +d++  ++++e  +e+   +++  +++l++l + le+++ ++++le++   ++ +l++aee ++ 
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGsLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDS 360
                                   556677777777777788888888888746666678888899999999999999999999999999999999999999999 PP

                         DHR10  97 lreqaeekr 105
                                   l+ + +  r
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLR 369
                                   987766555 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 0.00029
                         DHR10   3 slaeekeelaelErkarelqaki....dalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerk 79 
                                   +l++  e l++l  +  +l+a++    d l+++e+d+ s+++ l+ + +el+ l   + +l+e+++ le+++++l ++ ++
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLESLSSRVEDLEARVgsveDRLSQAEEDIDSLTTSLDSLRTELEDL---STRLAEAQASLEDLNTRLDQVAST 399
                                   66777778888888888888887333355789*****************98765...67999******************* PP

                         DHR10  80 eerlqrqlenaeeklerlreqae 102
                                    ++lq++l+ aee l+ l+e+ +
  gi|14601261|ref|NP_147796.1| 400 LQQLQQRLATAEESLQALTEDLA 422
                                   ******************99866 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.15
                         DHR10  28 lqvvekdlrsciklleeieael....akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                   lq +++dl+s+ + +e++++ +    ++l + ++++++ r ++e+++++l + e k +r    +e  + +++ lr q +ek
  gi|14601261|ref|NP_147796.1| 414 LQALTEDLASLQAEVETLQQSIveidRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEK 494
                                   677777777777776666666522223455666777778888888888888888888888888888888888888888888 PP

                         DHR10 105 reaakarle 113
                                    ++a+++  
  gi|14601261|ref|NP_147796.1| 495 TREAQQTAS 503
                                   888888765 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 ?    4.1   0.0       0.6        44     148     186 ..     243     281 ..     232     286 .. 0.87
   2 !   19.1   2.5   1.5e-05    0.0011      78     178 ..     289     392 ..     279     397 .. 0.78
   3 ?    8.6  16.9     0.026       1.9      71     173 ..     394     499 ..     390     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.6
                       UPF0242 148 qellqeyqetieeqrsvlekrqdqieqLeskVrDlnyEi 186
                                   +e+l+  ++ +e++   l++ ++++++Le  V+Dl+  +
  gi|14601261|ref|NP_147796.1| 243 EERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQL 281
                                   5778889999*************************9766 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.5e-05
                       UPF0242  78 teldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelkleleeqLaekqellqeyq 155
                                    +l++ ++ +e  le ++   e+L   +da++++l+ l e+ ++L+++ e+  +    +e+ + ++ee ++  ++ l+ ++
  gi|14601261|ref|NP_147796.1| 289 GALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEArvgSVEDRLSQAEEDIDSLTTSLDSLR 369
                                   4455677888889999999***************************99888666555777777777777777777777777 PP

                       UPF0242 156 etieeqrsvlekrqdqieqLesk 178
                                    ++e++   l + q+  e+L+++
  gi|14601261|ref|NP_147796.1| 370 TELEDLSTRLAEAQASLEDLNTR 392
                                   77777777777777777777766 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.026
                       UPF0242  71 eekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelkleleeqLaekq 148
                                   ++  + l++l++ l+t ee+l+ l+e+   L+ e++  ++ + +  ++  qL++   a+        e + ++ee+ +++ 
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLeveSLGEKLVQAEEKNQRQD 474
                                   566678888889999999999999999999999999999999999999999998777766533344466778899999999 PP

                       UPF0242 149 ellqeyqetieeqrsvlekrqdqie 173
                                     ++++q +i+e+r  l+++  + +
  gi|14601261|ref|NP_147796.1| 475 ASIEDFQSQIQELRTQLDEKTREAQ 499
                                   99****************9987765 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0037      0.27     252     326 ..     268     342 ..     240     345 .. 0.65
   2 !   18.2   5.5   1.3e-05   0.00095     227     320 ..     352     448 ..     342     463 .. 0.56
   3 ?    1.2   3.7         2   1.5e+02     280     326 ..     457     503 ..     439     509 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0037
                         IFT57 252 edisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergs 326
                                    d++ ++e ++ + + l+s++  l +   + + +l++v+ ++++ls+ v +++++l+ + e+le++++++e+ ++
  gi|14601261|ref|NP_147796.1| 268 GDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEA 342
                                   444555555555555566666666666666677777888888888888888888888888888888888877665 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-05
                         IFT57 227 eqmkkhkksieeslpetksqlkklhedisk...tlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvselt 304
                                    q ++  +s+++sl +++++l++l++ +++   +le +++r  ++ s l++l q + +a+e+l++++e++  l+++v+ l+
  gi|14601261|ref|NP_147796.1| 352 SQAEEDIDSLTTSLDSLRTELEDLSTRLAEaqaSLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   444444455555556666666666654433111455555555555556666666666666666666666666666666666 PP

                         IFT57 305 relaeiseelekvkqe 320
                                   +   ei+ +l ++ + 
  gi|14601261|ref|NP_147796.1| 433 QSIVEIDRRLGQLRST 448
                                   6666665555555444 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2
                         IFT57 280 reaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergs 326
                                   +++ e+l +++ek +   +++++ + + +e+ ++l++  +e ++  s
  gi|14601261|ref|NP_147796.1| 457 ESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   45556666666666666666666666666666666666666655444 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 ?    1.4   0.0       4.2   3.1e+02      28      83 ..     239     294 ..     228     305 .. 0.67
   2 !   18.6  12.1   2.2e-05    0.0016       5      92 ..     320     408 ..     316     417 .. 0.93
   3 ?    8.1  15.1     0.036       2.6      17     111 ..     402     502 ..     401     525 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 4.2
                         Mod_r  28 vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqe 83 
                                   v  l+e+++ ++++ e+l  +  sle+++ +l   +++   +l +l +++ ++e +
  gi|14601261|ref|NP_147796.1| 239 VAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDR 294
                                   45566777777777777777677777777777777777777777777776666655 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.2e-05
                         Mod_r   5 keeLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqel 84 
                                   +++Lq+l ed e l+++v++l  +v +++++++++++ + sl  +  sl++ele+l+ +l+e+  +l+ l++++++  + l
  gi|14601261|ref|NP_147796.1| 320 SQQLQALAEDLESLSSRVEDLeARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTL 400
                                   589******************888********************99999******************************** PP

                         Mod_r  85 dellqkfs 92 
                                   ++l q++ 
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLA 408
                                   **998765 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.036
                         Mod_r  17 klealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekef...eekeqeldellqkfsp 93 
                                   +l++++ t+ +++++l+e++ +l ae e l ++  +   +l +lrs + + + e+++l +++   eek+q++d+ +++f++
  gi|14601261|ref|NP_147796.1| 402 QLQQRLATAeESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLvqaEEKNQRQDASIEDFQS 482
                                   567777788677999999999998888888777777799999999999999999888887542227888889999999987 PP

                         Mod_r  94 d..allarLqtavaeaeeeS 111
                                   +   l+++L ++++ea + +
  gi|14601261|ref|NP_147796.1| 483 QiqELRTQLDEKTREAQQTA 502
                                   73355666666666655544 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 ?    6.8   0.0     0.097       7.1      81     123 ..     300     342 ..     241     345 .. 0.52
   2 !   15.4   0.2   0.00021     0.015      32     127 ..     290     381 ..     275     385 .. 0.70
   3 !   17.0   6.3   6.7e-05     0.005      26     130 ..     326     426 ..     317     429 .. 0.77
   4 !   15.7   7.4   0.00017     0.013      28     131 ..     363     469 ..     359     475 .. 0.82
   5 ?    6.0   3.8      0.17        13      34      97 ..     432     495 ..     428     507 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.097
                                   HHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  81 ksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeq 123
                                      + +e   ++l   +da  +++++L + les+++++++Le 
  gi|14601261|ref|NP_147796.1| 300 GRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEA 342
                                   2223333444566666666667777777777777777776665 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 0.00021
                                   CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHH CS
                     Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvle 112
                                    ++++++++e +le ++ s ++ +  v +++++l++  +      + +++  ++le ++  +++++++ e+ i  L++ l+
  gi|14601261|ref|NP_147796.1| 290 ALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDL----ESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLD 366
                                   34556666666666666666666666655555554433333....356666788999999********************* PP

                                   HHHHHHHHHHHHHHH CS
                     Fib_alpha 113 sneqkiqkLeqdidq 127
                                   s++ ++++L +  ++
  gi|14601261|ref|NP_147796.1| 367 SLRTELEDLSTRLAE 381
                                   ********9987765 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 6.7e-05
                                   CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
                     Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                                   l +  ++++ ++e+le ++ +++++ ++aee + ++++sl +  ++ +d ++ + + + +le    +l+ ++d+  s++++
  gi|14601261|ref|NP_147796.1| 326 LAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLE----DLNTRLDQVASTLQQ 402
                                   44455566777777788888888888888888888888887777777777777777777777....788889999999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 107 LqnvlesneqkiqkLeqdidqker 130
                                   Lq+ l + e+++q L +d +++++
  gi|14601261|ref|NP_147796.1| 403 LQQRLATAEESLQALTEDLASLQA 426
                                   999999999999999999988876 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 0.00017
                                   CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCHHHHHHHCCHHHHH CS
                     Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksske...leeeilrlketidaqesnir 105
                                   +   +++++le+l  +l+e++ s ++ ++   ++ ++l++ q+  +  ++ ++ ++++   l+ e+++l+++i++  +++ 
  gi|14601261|ref|NP_147796.1| 363 TSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDlasLQAEVETLQQSIVEIDRRLG 443
                                   5556788899999999999999999999999999988888888877777777777766111567999************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 106 vLqnvlesneqkiqkLeqdidqkerk 131
                                   +L++++++ + +++ L ++  q e+k
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEK 469
                                   ****************9999888776 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.17
                                   CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH CS
                     Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketi 97 
                                   ++++ ++ ++l +++++   ++  v+++ ++l +++++++ +d  i++++++++e  ++l+e+ 
  gi|14601261|ref|NP_147796.1| 432 QQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKT 495
                                   4445555555555555555555555555555555555555555555555555544444444433 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       4.8   3.5e+02      74     109 ..     255     290 ..     249     293 .. 0.81
   2 !   10.0   0.0    0.0082       0.6      82     118 ..     291     327 ..     283     329 .. 0.93
   3 ?    5.7   0.1      0.18        14      81     116 ..     339     374 ..     328     378 .. 0.69
   4 ?    9.4   2.8     0.013      0.96      77     119 ..     363     405 ..     355     410 .. 0.84
   5 ?    9.5   2.8     0.012       0.9      82     114 ..     403     435 ..     400     441 .. 0.91
   6 ?    1.4   0.2       3.8   2.8e+02      74     113 ..     430     469 ..     428     474 .. 0.67
   7 ?    4.5   3.4      0.43        32      85     113 ..     476     504 ..     464     509 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 4.8
                                   EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqitt 109
                                   +l  A + l++++ +le ++e+l+ +l  l +++  
  gi|14601261|ref|NP_147796.1| 255 DLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGA 290
                                   566689999999999999999999999998887655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0082
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqly 118
                                   l+++++++e  le +e +le+l+ +++ + ++l++l+
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALA 327
                                   899*******************************986 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  81 llkkkleelekqlekleeeleklkdqittleanlaq 116
                                    l+ ++ ++e+ l + ee+++ l++ +++l+ +l+ 
  gi|14601261|ref|NP_147796.1| 339 DLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELED 374
                                   566667777777777777777777777777666654 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  77 eAiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                    + + l  +le+l+  l + +++le+l ++++++  +l+ql+q
  gi|14601261|ref|NP_147796.1| 363 TSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   5667888899999999999999999999999999999999987 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanl 114
                                   l+++l+++e++l+ l+e+l+ l+++++tl++ +
  gi|14601261|ref|NP_147796.1| 403 LQQRLATAEESLQALTEDLASLQAEVETLQQSI 435
                                   899**************************9875 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 3.8
                                   EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittlean 113
                                   +l+++i  ++++l +l+++++ +  e+e l +++ ++e++
  gi|14601261|ref|NP_147796.1| 430 TLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEK 469
                                   4556666677777777777777777777777777766665 PP

  == domain 7  score: 4.5 bits;  conditional E-value: 0.43
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  85 kleelekqlekleeeleklkdqittlean 113
                                    +e+ ++q+++l  +l++++++++++  +
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   45555555555555555555555555555 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 !   17.0   0.1   5.4e-05     0.004       5     130 ..     255     383 ..     251     389 .. 0.85
   2 !   17.9  17.7   2.9e-05    0.0021       5     192 ..     311     500 ..     310     505 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.4e-05
                        TACC_C   5 dldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefe...ktiaqlieekqkqkelakkeiqkvleekeqlla 82 
                                   dl  al  ++e v + e  +++l+ + + l+ ++  +++ va+ e   ++++  +e+        ++++q + e+ e l++
  gi|14601261|ref|NP_147796.1| 255 DLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEgrlEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSS 335
                                   5556677777778888888999999999999999999999999983333566667888888899999999999******** PP

                        TACC_C  83 dlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkee 130
                                    ++++e  +  +  r+ +  e ++ + +  +sl+++ e++ +r+++++
  gi|14601261|ref|NP_147796.1| 336 RVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQ 383
                                   ****************************************99998765 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.9e-05
                        TACC_C   5 dldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqk...elakkeiqkvleekeqlla 82 
                                   dl  a+ ++ ++ +   e+++ l+++ve+l++++   ++ +++ e+ i  l+++ +  +   e  +  ++++++  e l++
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRtelEDLSTRLAEAQASLEDLNT 391
                                   6667888888999998899999****************************9998876551014455677888888888999 PP

                        TACC_C  83 dlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeekLekAneeiaqvrskakaeta 163
                                    l +v  ++++l +r+    e l+ + +  +sl++++e + + + + ++R  +L+ + +  ++   e + +   +a++  +
  gi|14601261|ref|NP_147796.1| 392 RLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDA-VRLEVESLGEKLVQAEEKNQ 471
                                   9999***************************************************88775.44444555555556666667 PP

                        TACC_C 164 alqasLrkeqlkvqSLeksleqKtkenee 192
                                      as+   q ++q L  +l++Kt+e ++
  gi|14601261|ref|NP_147796.1| 472 RQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   7789**********************985 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1      0.32        24      86     143 ..     227     282 ..     226     287 .. 0.83
   2 !   19.8   5.6   6.6e-06   0.00049      26     157 ..     261     395 ..     245     399 .. 0.81
   3 !   18.9  15.2   1.2e-05   0.00088      12     136 ..     345     471 ..     344     472 .. 0.90
   4 ?    3.5   7.0       0.6        44      94     148 ..     457     511 ..     455     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.32
                     PspA_IM30  86 Arealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarek 143
                                   Are+++e +s+   ++ le+ l+ +++ave+l  +l+ le ++ +l+  +e l ++++
  gi|14601261|ref|NP_147796.1| 227 AREIAEEVASA--YVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLS 282
                                   67777777765..589999999999***************999999988887777765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 6.6e-06
                     PspA_IM30  26 kileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAka...ALtkgeeeLArealaeikslekqaeal 103
                                   + le+ + d++ ++++++ +l ++  r  +le+++++ + ++++ e + +    A ++ +++L +++++ ++sl + +e+l
  gi|14601261|ref|NP_147796.1| 261 DSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDlsgAVDAMSQQL-QALAEDLESLSSRVEDL 340
                                   678999999999999999999999999999999999999999988866443122444446665.6677889********** PP

                     PspA_IM30 104 etqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaq.eavqkslgk 157
                                   e+ +  +++   q+++ ++ l t ++ l+++ e l  r++ a+a  e+++++l++
  gi|14601261|ref|NP_147796.1| 341 EARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASlEDLNTRLDQ 395
                                   ****************************************999975778887776 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.2e-05
                     PspA_IM30  12 aniselldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekk...AkaALtkgeeeLArea 89 
                                   +++ + l++ae+  + l   +  ++ el+++ + la++ a+   l ++l++ +  +++l+++   A++ L++  e+LA  +
  gi|14601261|ref|NP_147796.1| 345 GSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRlatAEESLQALTEDLAS-L 424
                                   57888899999999999999**************************9999887766666654444999**********7.6 PP

                     PspA_IM30  90 laeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakke 136
                                    ae ++l++++ + +  l q+rs+v+ +r ++e l  k+ ++++k +
  gi|14601261|ref|NP_147796.1| 425 QAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQ 471
                                   6799***************************************9976 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.6
                     PspA_IM30  94 kslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaq 148
                                   +sl +++ + e++ ++q +++e+ + q+++l t+++e+ ++ +  +++++  +++
  gi|14601261|ref|NP_147796.1| 457 ESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSMA 511
                                   56677778888999999999999*********99999999988887777655544 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 !   21.0  32.2   1.7e-06   0.00013      64     290 ..     270     493 ..     242     499 .. 0.86
   2 ?    2.2   6.0      0.85        63     175     232 ..     444     501 ..     440     517 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-06
                      CALCOCO1  64 ykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearirELEeDiktltqr 144
                                    + + e+l  + + l srv  l++ ++  +   e +e   ++l+ + ++++++ +al+e  e  ++r+ +LE  + ++ +r
  gi|14601261|ref|NP_147796.1| 270 LEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDR 350
                                   455566777788889999999999999999999999999999999999999999999999999999999999999999999 PP

                      CALCOCO1 145 alekEteLeRlkerakkalaqrkeeeaerkqlqakleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttA 225
                                     + E +++ l+     + + + +  +   + qa le  ++ l ++++ lq+l++ la  + +++ L ++++ l+ +++t 
  gi|14601261|ref|NP_147796.1| 351 LSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   99999999999999999999999999999999999999999999************************************* PP

                      CALCOCO1 226 qrkeaenEallkelrslqerlaaSerkvegLkeeLssvaaqrdrtqaeLHqaRleaAqltlqLad 290
                                   q+ ++e +  l +lrs+ + +     +ve L+e L ++  + +r  a +     +  +l +qL +
  gi|14601261|ref|NP_147796.1| 432 QQSIVEIDRRLGQLRSTVDAVR---LEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDE 493
                                   *********9999999988765...5899999999999888888888777777777778777766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.85
                      CALCOCO1 175 qlqakleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaen 232
                                   ql++ +++ + e++sl + l ++ ++ +++d+++   q++i++l+++L++  r   ++
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   5677788888999999999999999999999999999999999999999876655444 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 ?    9.5   0.2     0.011      0.79      19      65 ..     301     344 ..     226     361 .. 0.67
   2 ?    1.0  19.9       4.6   3.4e+02      14      84 ..     357     426 ..     339     504 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.011
                    Phage_GP20  19 kldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqakn 65 
                                   +l+ ve   ++l + +++  +qL+ L   a+d e+L   +e+l+a +
  gi|14601261|ref|NP_147796.1| 301 RLEAVEGSLEDLSGAVDAMSQQLQAL---AEDLESLSSRVEDLEARV 344
                                   34444444444444444444444444...223444444444443333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 4.6
                    Phage_GP20  14 dit..kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldna 84 
                                   di    ++ld++ +e ++l ++l++++ +LedL +     +++  ++++lq+ +++a++  +a  +dl+  +a
  gi|14601261|ref|NP_147796.1| 357 DIDslTTSLDSLRTELEDLSTRLAEAQASLEDLNTR---LDQVASTLQQLQQRLATAEESLQALTEDLASLQA 426
                                   554456788899999999999999999999999777...7777778888888888888877776666654443 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.4   0.00028      0.02      12      81 ..     299     367 ..     280     373 .. 0.52
   2 !   15.8   7.4   0.00018     0.014      11      90 .]     354     432 ..     345     432 .. 0.88
   3 ?    4.6   4.4       0.6        44       9      65 ..     429     487 ..     426     490 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.00028
               Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqk 81 
                                   e  l++++ +l++l    +++++ql+ l+e+L++l+   e ++ +++ +  ++L++++ ++ sl ++l +
  gi|14601261|ref|NP_147796.1| 299 EGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVE-DLEARVGSVEDRLSQAEEDIDSLTTSLDS 367
                                   3334445555555555555555555555555555544444.44444445555555555555555555555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 0.00018
               Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekLq 90 
                                    e ++d l+++l +lr++ e+L+ +l + +++L++l+   + +v ++l++ +++L++++  +++l e l +l++ +e Lq
  gi|14601261|ref|NP_147796.1| 354 AEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLD-QVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   57789999999999999999999999999999999999998.99999999999999999999999999999999999886 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.6
               Snapin_Pallidin   9 ellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKL 65 
                                   e+l+ ++ e+d +l +lr + ++++ ++++l ekL ++ee ++  +++++d+++ ++ L
  gi|14601261|ref|NP_147796.1| 429 ETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQrqDASIEDFQSQIQEL 487
                                   78999********************************9999997334555555555544 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   0.00022     0.016     274     344 ..     277     347 ..     243     363 .. 0.81
   2 !   14.7   4.0   0.00017     0.012     276     345 ..     363     432 ..     348     440 .. 0.90
   3 ?    1.8   3.2       1.4     1e+02     285     343 ..     442     504 ..     430     512 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00022
                                   CTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FH2 274 akvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkel 344
                                     ++l sl++ v +le++++++e  le+ e + e+    ++++++ l+  +e+l++l++  ++++++v ++
  gi|14601261|ref|NP_147796.1| 277 LTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSV 347
                                   5689999999999**************9999999999999*******999999999999999999988776 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 0.00017
                                   S-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FH2 276 vnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelv 345
                                    +l+sl++e+++l+++l++++ +le+ ++  ++    l++l++ l++aee+l+ l e+l +++++v++l 
  gi|14601261|ref|NP_147796.1| 363 TSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   489*************************************************************999886 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHHHCCT....TSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FH2 285 vkklekglkklekelessek....keepsdkflevlkeflkeaeeklkkleeelkeakelvke 343
                                   + +l++ +++++ e+es  +    +ee++++  +++++f ++ +e   +l e+ +ea++++ +
  gi|14601261|ref|NP_147796.1| 442 LGQLRSTVDAVRLEVESLGEklvqAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   445555555555555554444454445666666666666666666666666666666665544 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   0.0      0.17        12       6      72 ..     242     306 ..     237     313 .. 0.83
   2 !   13.7  10.1   0.00085     0.063      11     104 ..     317     408 ..     307     409 .. 0.91
   3 ?    6.0  17.3      0.19        14       3      84 ..     400     479 ..     394     507 .. 0.78
   4 ?    1.9   4.8       3.7   2.7e+02       6      37 ..     473     504 ..     468     528 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.17
                   Uso1_p115_C   6 leseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeek 72 
                                   le++ + +++  e+l   l+sl++++ +le +   ++ + q ++l++++ +le+++ +++ +l++ +
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLEFA--VEDLTLQLSSLDSRVGALEDRVADIEGRLEAVE 306
                                   68889999999999999999999999999999..888888888888888888888888888877765 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00085
                   Uso1_p115_C  11 aslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDLLlllgD 91 
                                     ++++ ++l  +l+sls+++e+le      + e + +++e+ +++l+  l+ lr el++   +  e+q+ l+DL   l +
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEAR--VGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   567899999999*************99..99999*****************************************999999 PP

                   Uso1_p115_C  92 leeKvekykarLk 104
                                     + ++++++rL 
  gi|14601261|ref|NP_147796.1| 396 VASTLQQLQQRLA 408
                                   9999999999986 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.19
                   Uso1_p115_C   3 aseleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEld 83 
                                   +++l+++ a++++  ++l  +l sl+ ++e l+q+    +++ +  +l++++++++ e+e l ++l +++ek++ + + ++
  gi|14601261|ref|NP_147796.1| 400 LQQLQQRLATAEESLQALTEDLASLQAEVETLQQS--IVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIE 478
                                   67889999999999999999999999999999999..9999999*********************9999999976644444 PP

                   Uso1_p115_C  84 D 84 
                                   D
  gi|14601261|ref|NP_147796.1| 479 D 479
                                   4 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 3.7
                   Uso1_p115_C   6 leseaaslkdeneklkaelqslskalesleqk 37 
                                      + ++++++ ++l ++l+++++++++++++
  gi|14601261|ref|NP_147796.1| 473 QDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   55667889999999999999999999999988 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   0.00014      0.01      34     139 ..     242     343 ..     239     344 .. 0.95
   2 !   18.3  11.0   2.6e-05    0.0019      32     134 ..     338     443 ..     336     455 .. 0.80
   3 ?    0.8   4.4       6.7   4.9e+02      36      71 ..     468     503 ..     456     511 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHH CS
                         Nup54  34 LakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelra 114
                                   L++R+ + +++v+ +  +l+++++r+ +le +   +++ +l  + +r  +l+ R+  +  +le ++ +   l+   +++++
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLE-FAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQ 321
                                   899***************************.************************************************** PP

                                   HHHHHHHHHS-HHH.HHHHHHHHHH CS
                         Nup54 115 rletleaqlndpaqlkgrvnelwar 139
                                   +l++l ++l+   +l++rv++l ar
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLE---SLSSRVEDLEAR 343
                                   *******999...578999999876 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-.......SS-- CS
                         Nup54  32 edLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsr.......gyal 105
                                   edL+ Rv   ++ ++q++e ++++ ++l++l+  +  ++s+rl++a+     l +Rl ++++ l+ l++r        +al
  gi|14601261|ref|NP_147796.1| 338 EDLEARVGSVEDRLSQAEEDIDSLTTSLDSLR-TELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRlataeesLQAL 417
                                   899****************************9.99999*************************999977745544445588 PP

                                   -SSHHHHHHHHHHHHHHHS-HHH.HHHHH CS
                         Nup54 106 daeEeelrarletleaqlndpaqlkgrvn 134
                                   +++  +l+a++etl++++ +   + +r+ 
  gi|14601261|ref|NP_147796.1| 418 TEDLASLQAEVETLQQSIVE---IDRRLG 443
                                   88888888888888877763...333333 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 6.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Nup54  36 kRvkaQqkevaqhrerlkeisdrleeleqkhqlets 71 
                                   ++ + Q++ ++ ++++++e++++l+e  ++ q+++s
  gi|14601261|ref|NP_147796.1| 468 EKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   577889999999999999999999998866665554 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 ?    1.7   0.0       4.1     3e+02      24      61 ..     256     293 ..     239     307 .. 0.54
   2 !   11.2   0.1    0.0047      0.35      21      87 ..     281     347 ..     270     353 .. 0.74
   3 !   13.7   0.6   0.00077     0.057      23      88 ..     311     376 ..     304     377 .. 0.93
   4 !   12.1   1.4    0.0023      0.17      24      78 ..     347     404 ..     345     405 .. 0.84
   5 ?    8.9   4.9     0.025       1.8      19      58 ..     398     437 ..     375     467 .. 0.48
   6 ?    5.8   1.2      0.22        16      23      84 ..     444     505 ..     435     509 .. 0.71
   7 ?    3.8   1.5      0.95        70      28      58 ..     477     507 ..     463     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 4.1
                        DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelle 61 
                                   l+  ld++++++ +le  v+ ++ ++  l + v +l +
  gi|14601261|ref|NP_147796.1| 256 LGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALED 293
                                   34455556666666665555555555555555554322 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0047
                        DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                   l +l + + +++++++++e +++++   +edl   v ++ ++++   e++++l + v+dl + v ++
  gi|14601261|ref|NP_147796.1| 281 LSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSV 347
                                   6667777778888888888888888888888888888877777777777777777777777777655 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00077
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                    l+  +d+++++++ l +++++++  vedl a v  + + +++  e++d+lt+++  l + +++l+
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   577899*************************************************99999999886 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.0023
                        DUF948  24 lkktldeaaatieelekqvdpilkevedl...lakvnelledvneklekvdplteava 78 
                                   +++ l++a++ i++l+  +d++ +e+edl   la++++ led+n +l++v +  ++++
  gi|14601261|ref|NP_147796.1| 347 VEDRLSQAEEDIDSLTTSLDSLRTELEDLstrLAEAQASLEDLNTRLDQVASTLQQLQ 404
                                   567789999*************999999844466777799999999999999988877 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.025
                        DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvne 58 
                                    +l +l++ l  a+++++ l++++ ++  eve+l + + e
  gi|14601261|ref|NP_147796.1| 398 STLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE 437
                                   2333444444444444444444444444444444444333 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.22
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesv 84 
                                   +l++t+d+++  +e+l++++ +  ++ ++  a +++ +++++e   ++d+ t ++++++ + 
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTA 505
                                   67777777777777777777777777777777777777777777777777777777776665 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.95
                        DUF948  28 ldeaaatieelekqvdpilkevedllakvne 58 
                                   ++ ++++i+el+ q+d+ ++e++++ +++ +
  gi|14601261|ref|NP_147796.1| 477 IEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   5677889999999999999999999888765 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2  31.1   1.2e-06   8.9e-05     257     516 ..     239     506 ..     226     522 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-06
                       DUF3584 257 leslelrLsllkgelkadeerlaekqe...evqeakaelkqqlrtled...elkeaidelnqelsaakaklaakeseleal 331
                                   ++ le+rLsl+++++++   +l +  e   + + a ++l  ql++l++   +l+++++  +++l+a ++ l+  +  ++a+
  gi|14601261|ref|NP_147796.1| 239 VAPLEERLSLVEQAVEDLGLALDSLEErvgDLEFAVEDLTLQLSSLDSrvgALEDRVADIEGRLEAVEGSLEDLSGAVDAM 319
                                   455677777777777776555444444000445566777888888877222456777788999999999999999999999 PP

                       DUF3584 332 eeqkkkyedadieklka...dld.qlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklker...lea 405
                                    +q ++   +d+e+l+    dl+ +++s+++ l+++ee++d lt++  ++  +++ +   + e  ++ le+l+ r   ++ 
  gi|14601261|ref|NP_147796.1| 320 SQQLQAL-AEDLESLSSrveDLEaRVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAE-AQASLEDLNTRldqVAS 398
                                   9999885.45666666511155534689***************************99887765.45566666666111444 PP

                       DUF3584 406 ireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelek 486
                                   + ++ ++++a++ee l+al + l   l+a+ e l++   e+ +rl++l   +d++  + E l   e+ ++a ek q++  +
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQALTEDLA-SLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLG--EKLVQAEEKNQRQDAS 476
                                   455555669999999999999998.88888888999999999999988888888887776654..4455555666666666 PP

                       DUF3584 487 aeaevealqaeeeqlrkkrdeadealqkae 516
                                    e+ +++ q+ ++ql++k  ea+++ + a+
  gi|14601261|ref|NP_147796.1| 477 IEDFQSQIQELRTQLDEKTREAQQTASTAS 506
                                   666777777777777777777776666655 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.8     0.073       5.4      58     117 ..     280     342 ..     242     343 .. 0.78
   2 !   15.2   6.6   0.00022     0.016      12     116 ..     276     383 ..     265     385 .. 0.75
   3 !   18.9  14.5   1.6e-05    0.0012       4     100 ..     345     441 ..     342     461 .. 0.90
   4 ?    9.3  21.2     0.015       1.1       5     111 ..     395     501 ..     393     508 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.073
                    TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaelee...seesweeqkeelekelselekriedlne 117
                                   +l++l +++  l++++a+++ ++e+++ +le    +  ++++q ++l ++l++l +r+edl++
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDlsgAVDAMSQQLQALAEDLESLSSRVEDLEA 342
                                   566677777777777777777777777655541115567788889999999999999999975 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 0.00022
                    TPR_MLP1_2  12 slkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleesee 92 
                                   +l+ + +++++++ +l++ +   + ++++ + + e       + +++lqal e+l++l +++++l+a++ s++  l+++ee
  gi|14601261|ref|NP_147796.1| 276 DLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEE 356
                                   555555556666666666666666666666666666666667789***********************************8 PP

                    TPR_MLP1_2  93 ...sweeqkeelekelselekriedln 116
                                      s+++  ++l++el++l +r+ + +
  gi|14601261|ref|NP_147796.1| 357 didSLTTSLDSLRTELEDLSTRLAEAQ 383
                                   444566778889999999999999987 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 1.6e-05
                    TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                                    s+e+ +++++e+++++++ l +l+++le  + +++eaq + e   +   + + +lq+l ++l+++++ ++ l++++ s++
  gi|14601261|ref|NP_147796.1| 345 GSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQ 425
                                   5789999************************************************************************** PP

                    TPR_MLP1_2  85 aeleeseesweeqkee 100
                                   ae+e+ ++s+ e   +
  gi|14601261|ref|NP_147796.1| 426 AEVETLQQSIVEIDRR 441
                                   ****999998765544 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.015
                    TPR_MLP1_2   5 sleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85 
                                   ++ +++++l+++ + ae+ lq+l edl + ++++++ qq+  +      +   ++ a+r e+++l +++ ++++++++  a
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDA 475
                                   677899*********************************9999999999999***************************** PP

                    TPR_MLP1_2  86 eleeseesweeqkeelekelselekr 111
                                   ++e  +++++e +++l+++ +e+++ 
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQELRTQLDEKTREAQQT 501
                                   *******************9999985 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 !   10.3  21.0     0.005      0.37     172     257 ..     331     422 ..     227     528 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.005
                  Exonuc_VII_L 172 eklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k.........ekleekkerlkklkerlell 242
                                   e+l+sr+++ e+++ + ++rl+++ee++++ l+++l++ r++le l++rl +         ++l++ +++l++l++rl+  
  gi|14601261|ref|NP_147796.1| 331 ESLSSRVEDLEARVGSVEDRLSQAEEDIDS-LTTSLDSLRTELEDLSTRLaEaqasledlnTRLDQVASTLQQLQQRLA-- 408
                                   222222222222222222222222222222.222222222222222211111110000111111112222222211111.. PP

                  Exonuc_VII_L 243 eekkerleeleekle 257
                                    +++e+l++l+e l+
  gi|14601261|ref|NP_147796.1| 409 -TAEESLQALTEDLA 422
                                   .11111111111111 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 ?    1.3   0.0       5.2   3.8e+02      55     105 ..     230     282 ..     227     284 .. 0.74
   2 ?    2.3   0.0       2.7     2e+02      70     100 ..     282     312 ..     243     320 .. 0.73
   3 ?    9.1   0.4     0.021       1.5      36     103 ..     293     364 ..     282     365 .. 0.64
   4 !   12.2   5.0    0.0022      0.16      24     104 ..     316     393 ..     302     407 .. 0.75
   5 ?    8.5   5.8      0.03       2.2      29     102 ..     349     419 ..     349     435 .. 0.62
   6 !   12.6   7.3    0.0017      0.12      25     104 ..     408     484 ..     393     488 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 5.2
                                   HHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS- CS
                  Seryl_tRNA_N  55 lskeIgkakkkk..edaeeliaevkelkeelkaleaelkeleaeleklllaiP 105
                                   +++e+++a  +   e  + + + v++l+  l+ le+++ +le ++e+l+l++ 
  gi|14601261|ref|NP_147796.1| 230 IAEEVASAYVAPleERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLS 282
                                   5566666666666344444456789999999******9999999999999885 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 2.7
                                   CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Seryl_tRNA_N  70 eeliaevkelkeelkaleaelkeleaelekl 100
                                   ++l  +v +l ++++++e +l+++e  le+l
  gi|14601261|ref|NP_147796.1| 282 SSLDSRVGALEDRVADIEGRLEAVEGSLEDL 312
                                   4566677777777777777777777777765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                  Seryl_tRNA_N  36 ekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekllla 103
                                   ++   ++ +le++      ls ++  ++++     ed e+l  +v++l +++  +e++l+++e+++++l+++
  gi|14601261|ref|NP_147796.1| 293 DRVADIEGRLEAVEGSLEDLSGAVDAMSQQLqalaEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTS 364
                                   444444444444444444445554444444444457889999999999999999999999999998888765 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.0022
                                   CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                  Seryl_tRNA_N  24 dkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                    +a  ++l +l e  ++l +++e+l a+  ++    ++a    ed+++l  + ++l +el++l+++l+e++a le+l +++
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAE---EDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRL 393
                                   4555677888888999999999999999999998888887...57788888888888888888888888888887776654 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.03
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                  Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                   d+l +++e   +l + l++l++e   ls   ++a ++    e+l  + +++   l++l+++l+++e+ l++l+ 
  gi|14601261|ref|NP_147796.1| 349 DRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASL---EDLNTRLDQVASTLQQLQQRLATAEESLQALTE 419
                                   57778888888888999999999999999999888876...334444444444444444444444444444332 PP

  == domain 6  score: 12.6 bits;  conditional E-value: 0.0017
                                   CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                  Seryl_tRNA_N  25 kadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                   +   ++l +l e   +lq+e+e lq+   e+ +  g++       ++++ ev++l+e+l ++e++ +  +a +e++ ++i
  gi|14601261|ref|NP_147796.1| 408 ATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRST---VDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQI 484
                                   44446788899999999********************9975...7999***************************99988 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 !   12.8   1.2   0.00071     0.052      32     113 ..     276     355 ..     204     355 .. 0.75
   2 !   13.0   2.4   0.00065     0.048      36     102 ..     315     378 ..     304     383 .. 0.77
   3 !   11.5   9.0    0.0018      0.13      32     100 ..     381     446 ..     373     454 .. 0.67
   4 ?    3.7   9.5      0.41        30      38     112 ..     436     513 ..     431     524 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00071
                          HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga.erkdWlLae 111
                                   +lt + ++l++++ ale+ +a     + + + +e +l++l+++++a +++l++l+++le+l++++++++++  + + +L++
  gi|14601261|ref|NP_147796.1| 276 DLTLQLSSLDSRVGALEDRVAD---IEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARvGSVEDRLSQ 353
                                   3344445555555555555555...45566667777777788888888888888888888888888887777555556777 PP

                          HemX 112 Ad 113
                                   A+
  gi|14601261|ref|NP_147796.1| 354 AE 355
                                   75 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00065
                          HemX  36 evaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                    v++++qql+al + l++   + ++ ++le+r+   +++l+++e+ +++l+ +l++l+++l+++s +
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLES---LSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTR 378
                                   446777777777777777...7778888888999999999999999999999999999999888765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0018
                          HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvs 100
                                   e++a+ ++l+++l ++ ++l+q   ++++ ++ ee+lq+l+e+l++l++e+e+lq+++ e+ ++l ++ 
  gi|14601261|ref|NP_147796.1| 381 EAQASLEDLNTRLDQVASTLQQ---LQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLR 446
                                   4455556666666666666666...66677777777777777777777777777777777777777665 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.41
                          HemX  38 aelqqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkdWlLaeA 112
                                    e++ +l +l +++++    ve++ e+  + ee+ q ++ ++e+ ++++++l  ql+e +++ ++  +++++ W +a A
  gi|14601261|ref|NP_147796.1| 436 VEIDRRLGQLRSTVDAvrleVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ-TASTASRWSMAAA 513
                                   55666666666666663333444444444555555555555555555555555555555555544.4448888888877 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 ?    2.1   0.0       1.8   1.3e+02      48     106 ..     247     305 ..     233     318 .. 0.67
   2 !   20.3  18.8     5e-06   0.00037       6     197 ..     310     503 ..     305     509 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH CS
                          SHE3  48 aslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssasetel 106
                                   + + +  + L+  L+  e r+ dle  +++l+ +  +l  +  +l++r+ + + + +++
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAV 305
                                   55555556677777777777777777777777777777777777777766555554444 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 5e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SHE3   6 esLHeqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelk 86 
                                   e L   +Da+++++ +L +  + L+++ e  +++  ++ + l+++ ++ d L++ L+     l dl + l+e + s e+l+
  gi|14601261|ref|NP_147796.1| 310 EDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLN 390
                                   667778999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX CS
                          SHE3  87 lekkqlkkrlenssaseteleeelerlkvqYdal...vdsqkeYkehYqqeieeLkesleklklenekqleelqerissnd 164
                                   ++ +q+   l++++++ ++ ee l+ l  +  +l   v++ ++     ++ + +L+  +++ +le e   e+l +   +n+
  gi|14601261|ref|NP_147796.1| 391 TRLDQVASTLQQLQQRLATAEESLQALTEDLASLqaeVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQ 471
                                   9999999999999999999999999998777666211444444445678999***************66666666655555 PP

                                   .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SHE3 165 kdidtkldsynnkkknlesieeeknkkllkkle 197
                                      d+++++++++ ++l     ek+++ +++ +
  gi|14601261|ref|NP_147796.1| 472 -RQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   .88*************99988888887776655 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   3.3   4.8e-05    0.0035       4      82 ..     315     393 ..     305     403 .. 0.66
   2 !   10.0  10.6    0.0094      0.69       5      94 ..     400     489 ..     396     497 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-05
                          BRE1   4 ELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkele 82 
                                    ++ ++++ ++l e l+++ + +++le ++  +e   ++a++ + ++  s d+l++el  L++ l+  + + e+L+ + 
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRL 393
                                   4566777777777777777777777777777777777777777777777777777777777777777777777766543 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0094
                          BRE1   5 LvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekef 85 
                                   L++l++    ++e+l++++++l++l+ ++  l++ + + d+   +++   da++ e+  L ++l +  e+ ++   + ++f
  gi|14601261|ref|NP_147796.1| 400 LQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDF 480
                                   677777777777777777777777777777777777777777777777777777777777777666666666666666666 PP

                          BRE1  86 vrklkelek 94 
                                   +++++el  
  gi|14601261|ref|NP_147796.1| 481 QSQIQELRT 489
                                   666666654 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 ?    4.4   0.0      0.66        49      13      54 ..     292     333 ..     280     335 .. 0.87
   2 !   10.9   0.2    0.0062      0.46      14      55 ..     335     376 ..     330     386 .. 0.84
   3 !   11.0   2.4    0.0058      0.43      12      54 ..     395     438 ..     384     450 .. 0.84
   4 ?    7.4   2.4     0.076       5.6      13      52 ..     453     492 ..     441     501 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.66
                        CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkeeeleti 54 
                                   ++ + +++ +l+a e +l++ +  +d + ++++   e+le +
  gi|14601261|ref|NP_147796.1| 292 EDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESL 333
                                   678899999************************999999965 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0062
                        CC2-LZ  14 eeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletis 55 
                                   + +e+L+a++ + e+ l++ +e+id l++++ + ++ele +s
  gi|14601261|ref|NP_147796.1| 335 SRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   6799*********************************99544 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0058
                        CC2-LZ  12 k.keeieeLkaqlqaaeealaakqeeidelkeeikkkeeeleti 54 
                                   +  + +++L+++l +aee+l+a  e++  l++e++  ++ + +i
  gi|14601261|ref|NP_147796.1| 395 QvASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEI 438
                                   4467899**************************99988866555 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.076
                        CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkeeele 52 
                                   + e+e+L ++l +aee+ ++++  i++ + +i++ +++l+
  gi|14601261|ref|NP_147796.1| 453 RLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLD 492
                                   6799****************************99998876 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   3.9   0.00015     0.011     476     585 ..     263     369 ..     228     379 .. 0.64
   2 !   16.9  11.0   1.9e-05    0.0014     477     591 ..     299     417 ..     280     419 .. 0.80
   3 !    9.5  20.6    0.0032      0.24     163     287 ..     382     501 ..     366     507 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00015
                          HOOK 476 eeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkk 556
                                    ee++ +l+   ed   ++++L++   + ++r+ ++e ++e ++ +l++  +  +    + ++l+++ e l+++ + ++  
  gi|14601261|ref|NP_147796.1| 263 LEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDA---MSQQLQALAEDLESLSSRVEDL 340
                                   24555556666666666666666666666666666666666666666655555553...6777788888888888888888 PP

                          HOOK 557 keqleelepklssnkqkieeleeaLkkkd 585
                                   ++ + ++e +ls++ + i++l + L    
  gi|14601261|ref|NP_147796.1| 341 EARVGSVEDRLSQAEEDIDSLTTSLDSLR 369
                                   88888888888888888888888776655 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.9e-05
                          HOOK 477 eekltelqelledanrrkneLetenrlanqrileLeaqveelqkal...qeqgskaed.ssllkkkleehleklkevqeel 553
                                   e +l++++  led    ++ + ++ ++  + +++L+++ve+l+ +    ++  s+ae+   +l   l+++  +l+++   l
  gi|14601261|ref|NP_147796.1| 299 EGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVgsvEDRLSQAEEdIDSLTTSLDSLRTELEDLSTRL 379
                                   667888888888888888888888888888888888888888765411133445554426679999*************** PP

                          HOOK 554 qkkkeqleelepklssnkqkieeleeaLkkkdedlkam 591
                                   ++ ++ le+l+ +l++ ++  ++l++ L   +e l+a+
  gi|14601261|ref|NP_147796.1| 380 AEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQAL 417
                                   *****************************999999987 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0032
                          HOOK 163 ldsqlrklleelkeaqeekdelaQrcheldkqlsllqeEknaLlaenkklqerlselengeesgtiqltskkylelqkqle 243
                                   ++ +l +l + l+++++  ++l+Qr+   ++ l++l+e+ ++L+ae ++lq+ + e++  +  g++    +    ++ ++e
  gi|14601261|ref|NP_147796.1| 382 AQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEID--RRLGQL---RSTVDAVRLEVE 457
                                   444555666677788888899********************************99999..444444...445566777788 PP

                          HOOK 244 qlqeelfrlEtarddyrlkceelekevlelqqrneeltslaeEa 287
                                   +l e l+++E+  +     +e+ + +++el+++ +e t+ a+ +
  gi|14601261|ref|NP_147796.1| 458 SLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   88888888887766666677777888888887777777766654 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  27.8   2.8e-06   0.00021      13     231 ..     266     491 ..     256     518 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-06
                     Laminin_I  13 apykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikk 93 
                                   ++  ++  +edlt +L++  s   a ++++   e+ le ++   e L + +  ++++ q + ++ e  +++ ++L++ +  
  gi|14601261|ref|NP_147796.1| 266 RVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGS 346
                                   566788899************************************************************************ PP

                     Laminin_I  94 ladnikeilekvatlne..neealpssklseelaeaqrlLeelrsR.d.ftkqleeaeaelkaAqkLLsrvqtllqklqee 170
                                   ++d ++ + e +  l    +   +  ++ls  laeaq  Le l  R d     l++  + l+ A++ L+   + l +lq+e
  gi|14601261|ref|NP_147796.1| 347 VEDRLSQAEEDIDSLTTslDSLRTELEDLSTRLAEAQASLEDLNTRlDqVASTLQQLQQRLATAEESLQALTEDLASLQAE 427
                                   ************999997677788889****************99974699****************************** PP

                     Laminin_I 171 nkaLkeal...rdsLaeyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevseek 231
                                    ++L++++     +L++     ++ r  +e   +k  +a++ n++  a +++++++ +e++ + 
  gi|14601261|ref|NP_147796.1| 428 VETLQQSIveiDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQL 491
                                   ****9975222679******************************************99987553 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 !   18.1  35.0   1.6e-05    0.0012      41     304 ..     229     500 ..     193     504 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-05
                        HAP1_N  41 eqieet.leYflLcservsqvtktyeDievvtrLLeEkerDLelaAr....IGqsLlkrNsvLternekLeeqLesareei 116
                                   e +ee+   Y++   er s v ++ eD  + +  LeE+  DLe a+        sL  r  +L++r+  +e +Le ++ + 
  gi|14601261|ref|NP_147796.1| 229 EIAEEVaSAYVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEdltlQLSSLDSRVGALEDRVADIEGRLEAVEGSL 309
                                   4555541468888899****************************9853211124666777778888888888888888888 PP

                        HAP1_N 117 aqlrhelslkddLLqlysdseeeseeeseeseelreeesleslqklvqldlLqeklreLeeeNekLreeasqLktetdtlE 197
                                   + l+  +    + Lq ++++ e  ++  e  e    + +  ++q    +d L   l +L  e e L ++   L++ + +lE
  gi|14601261|ref|NP_147796.1| 310 EDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTR---LAEAQASLE 387
                                   888888888888888888875554444444333333334456667777888888888887777766543...333344444 PP

                        HAP1_N 198 ekEqqL......vldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaske 272
                                   +   +L      ++++ + l++a+++++ l+e+la+ + e+e+ q+ i+++  ++ +l+  +  +  e e l ++L  + e
  gi|14601261|ref|NP_147796.1| 388 DLNTRLdqvastLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEE 468
                                   4333331111115666777788888888888888888888888888888888888888888889999************** PP

                        HAP1_N 273 aqrqLtaELqdlqekyaevegmLheaqeevke 304
                                    +++  a ++d+q++ +e  + L e+  e+++
  gi|14601261|ref|NP_147796.1| 469 KNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   *************************9988876 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       1.2        92     440     477 ..     243     280 ..     229     286 .. 0.87
   2 !   17.2  20.9   1.7e-05    0.0013       2     161 ..     342     504 ..     341     513 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                           MAD 440 keevdslkkkleeLelerqrLreqkeelElelerreLq 477
                                   +e ++ + + +e+L l  ++L+e+   lE  +e  +Lq
  gi|14601261|ref|NP_147796.1| 243 EERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQ 280
                                   67788999************************999987 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 1.7e-05
                           MAD   2 aelieskaaleqlknelkqkelehkrarielekkasalkr...qleeesdrnqelqkrikllekreeekeealreqiElar 79 
                                   a++ + + +l+q+++++    ++ ++ r ele  ++ l++    le    r  ++   +++l++r +++ee+l++ +E   
  gi|14601261|ref|NP_147796.1| 342 ARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEaqaSLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLA 422
                                   666788999**********************999988776212466667788888899*********************** PP

                           MAD  80 lkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlek 160
                                   +++   e+l++   e + +l ++r + +a++ e++ l +++ ++e + ++++  +e++q + ++l+++l e ++  qq  +
  gi|14601261|ref|NP_147796.1| 423 SLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   *************************************99999999999999999999999999999988887777766554 PP

                           MAD 161 k 161
                                    
  gi|14601261|ref|NP_147796.1| 504 T 504
                                   4 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0     0.003      0.22     330     410 ..     279     353 ..     199     365 .. 0.59
   2 !   13.0   6.3   0.00038     0.028     332     416 ..     365     441 ..     351     472 .. 0.62
   3 !    8.5   4.3    0.0089      0.65     333     414 ..     415     493 ..     408     515 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.003
                          FapA 330 ldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                   l+  +l++++ +le+++ ++e +le ++ +++ l+           +++ql+ l e++e+l++++e+le++  +++++l +
  gi|14601261|ref|NP_147796.1| 279 LQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSG------AVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQ 353
                                   222333344444444444444444444444444443......223355666666666666666666666666666665555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00038
                          FapA 332 epelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskk 412
                                     +l+ +l++l ++l e +++le+l+ +++++ ++       ++ ++ l+ ++e++++l+e+l++l++e ++l++++ +  
  gi|14601261|ref|NP_147796.1| 365 LDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTL------QQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEI- 438
                                   347888888888888888888888888888888733......33446666666666666666666666666666666554. PP

                          FapA 413 eeak 416
                                    + +
  gi|14601261|ref|NP_147796.1| 439 -DRR 441
                                   .333 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0089
                          FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskke 413
                                   ++l e l+ l+ e+e l++++ ++++++ +l+++   +++  e ++  +kl ++ ek +++ +++e+ + +++e   +  +
  gi|14601261|ref|NP_147796.1| 415 QALTEDLASLQAEVETLQQSIVEIDRRLGQLRST--VDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQL-D 492
                                   5677888999999999999999999999999994..3455666666666666666555555555444444444433333.2 PP

                          FapA 414 e 414
                                   e
  gi|14601261|ref|NP_147796.1| 493 E 493
                                   2 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  14.3     0.023       1.7      16     126 ..     286     393 ..     228     394 .. 0.67
   2 !   17.9  15.8   4.5e-05    0.0033      14     124 ..     347     454 ..     343     457 .. 0.85
   3 !   11.5  19.6    0.0046      0.34       9     108 ..     398     501 ..     396     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.023
                        APG6_N  16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96 
                                   +++ ++e+   + e  l+ ++ + ++       +++  ++l++l ++ e+l +  ++le+   ++e+ l+++ee  + l  
  gi|14601261|ref|NP_147796.1| 286 SRVGALEDRVADIEGRLEAVEGSLED---LSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTT 363
                                   33333333333333333333333222...3456666677777777777777777777777777777777777777777777 PP

                        APG6_N  97 eeerfwreynelqlelleleeeldsleaqy 126
                                     +   +e  +l++ l+e +  l+ l++++
  gi|14601261|ref|NP_147796.1| 364 SLDSLRTELEDLSTRLAEAQASLEDLNTRL 393
                                   777777777777777777777777777665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.5e-05
                        APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                   ++ +l+qae+++d++++ l+ l++e ++ +   + l+e++ +le+l+   ++  + L++l++  +  e+ l+al+e l+ l
  gi|14601261|ref|NP_147796.1| 347 VEDRLSQAEEDIDSLTTSLDSLRTELEDLS---TRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASL 424
                                   57899******************9966654...799999999999999999999999999999999999999999999999 PP

                        APG6_N  95 eeeeerfwreynelqlelleleeeldslea 124
                                   ++e e   ++  e ++ l +l    d++  
  gi|14601261|ref|NP_147796.1| 425 QAEVETLQQSIVEIDRRLGQLRSTVDAVRL 454
                                   999999999988888888888888877765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0046
                        APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleaela 85 
                                   + l++l+++l++ae+  +a++e l+ l++e ++ ++     d  l +l+  +++++ e e+l e+L ++e+++++ +a ++
  gi|14601261|ref|NP_147796.1| 398 STLQQLQQRLATAEESLQALTEDLASLQAEVETLQQsiveIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIE 478
                                   5799**************************888766888888888889999999999999999999999999999999999 PP

                        APG6_N  86 aleeelealeeeeerfwreynel 108
                                   + +++ ++l  + +++ re ++ 
  gi|14601261|ref|NP_147796.1| 479 DFQSQIQELRTQLDEKTREAQQT 501
                                   99999999999999999998775 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2    0.0047      0.35       5      65 ..     280     340 ..     259     345 .. 0.90
   2 ?    7.4   3.0     0.082         6      11      62 ..     321     379 ..     315     382 .. 0.63
   3 ?    9.1   5.7     0.024       1.8       6      62 ..     351     407 ..     345     408 .. 0.82
   4 !   14.7  10.7   0.00042     0.031       5      65 ..     385     445 ..     381     446 .. 0.94
   5 ?    3.3   5.9       1.5   1.1e+02      23      71 .]     445     493 ..     443     509 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0047
                          ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                   +L+ L s++ ++ d+++    ++e+++   e l+   +++++++++l e+ e++ +r++ L
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDL 340
                                   68899999999999999999999999999999999999999****************9987 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.082
                          ZapB  11 skiqkaidtitlLqmeieeLkeen.......eelkeenreleeeneqlkeereawqerl 62 
                                   ++ q++ + +++L+ ++e+L++++       ++ +e ++ l+ +++ l++e e +  rl
  gi|14601261|ref|NP_147796.1| 321 QQLQALAEDLESLSSRVEDLEARVgsvedrlSQAEEDIDSLTTSLDSLRTELEDLSTRL 379
                                   56778888888888888888888833333335555555555577777777777776666 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.024
                          ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerl 62 
                                   L+q E+ i+++ + +++L+ e+e+L  + +e +   + l+  ++q   + +++q+rl
  gi|14601261|ref|NP_147796.1| 351 LSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRL 407
                                   677788888888999999999999999998888888888888888888888888887 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 0.00042
                          ZapB   5 lLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    Le L ++ ++   t+++Lq++++  +e  ++l+e  + l++e+e l++   ++ +rl +L
  gi|14601261|ref|NP_147796.1| 385 SLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQL 445
                                   69***********************************************999999999765 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 1.5
                          ZapB  23 LqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgklee 71 
                                   L+  +++++ e+e+l e+  + ee+n++  +  e +q+ ++ L  +l+e
  gi|14601261|ref|NP_147796.1| 445 LRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDE 493
                                   6666677777777777777777777777777777777777777666654 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1       4.3   3.2e+02      18      18 ..     289     289 ..     236     328 .. 0.50
   2 !   12.0   2.0    0.0034      0.25       4      74 ..     331     401 ..     295     403 .. 0.70
   3 !   10.6   2.0     0.009      0.66       5      52 ..     388     435 ..     384     439 .. 0.91
   4 ?    7.8   3.3      0.07       5.2       6      68 ..     438     500 ..     435     511 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 4.3
                                   H CS
                          YabA  18 e 18 
                                   +
  gi|14601261|ref|NP_147796.1| 289 G 289
                                   2 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXX CS
                          YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLa 74 
                                   ++l +++e+le +++++ ++l++ +e++ +l+   ++L++e e l +rl+e++++ ++ +++l++  + L+
  gi|14601261|ref|NP_147796.1| 331 ESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQ 401
                                   34556666666666666666776677777777666777777777777666666666666666666555555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.009
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                   +l ++l+++ ++l++l+++l++ +e+l++l+e+ a+L++e e+l++ +
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSI 435
                                   7889999***********************************999876 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXX CS
                          YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelse 68 
                                   + ++l +l ++++++  e+e+l e+l++  e+n++  +  e ++++++e +++ +ek++e ++
  gi|14601261|ref|NP_147796.1| 438 IDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   6678999**************************998887666665553333332222222222 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 ?    3.0   0.5       1.3        99      63      92 ..     280     309 ..     229     325 .. 0.51
   2 !   10.0   1.2    0.0092      0.68      60     110 ..     319     369 ..     317     373 .. 0.89
   3 !   12.6   4.5    0.0015      0.11      59     129 ..     374     445 ..     373     449 .. 0.91
   4 ?    8.2   1.8     0.033       2.4      59     113 ..     458     512 ..     449     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1.3
                          COG2  63 hLvglqeeleevesplaaarkkvesvrekl 92 
                                   +L +l++++  +e  +a +  ++e+v+ +l
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGSL 309
                                   333333333333333333333333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0092
                          COG2  60 lSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakele 110
                                   +S++L+ l e+le ++s ++ +  +v sv++ ls++ee+++s      +l+
  gi|14601261|ref|NP_147796.1| 319 MSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLR 369
                                   6999**********************************9999877776666 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.0015
                          COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllkldevvekl 129
                                   +lS++L   q++le +++ l ++ + ++++++ l+ +ee +++  e+ ++l+++   l ++++++d+++ +l
  gi|14601261|ref|NP_147796.1| 374 DLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVeTLQQSIVEIDRRLGQL 445
                                   59**************************************************99945556788999998887 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.033
                          COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                   sl+++Lv  +e+ ++ + +++ ++++++++r +l+e+ +e ++  + a++  ++ 
  gi|14601261|ref|NP_147796.1| 458 SLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSMAA 512
                                   6899999999999999999999999999999999999999999998888877766 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   4.6     0.012      0.86      36     104 ..     317     385 ..     229     388 .. 0.75
   2 !   13.6  12.2   0.00083     0.061       7     117 ..     350     462 ..     348     465 .. 0.88
   3 !   10.6  16.0    0.0073      0.54       5     107 ..     404     500 ..     401     502 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.012
                         THOC7  36 eeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLeearat 104
                                   ++  q  ++l  d++++ + +e l++   + e    + e++ + + +++ ++r+e e+l ++L ea+a 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQAS 385
                                   344455566667777777777777777777777777777777777788888888888888888888875 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00083
                         THOC7   7 RLlnveerplkrltkrllklltsla..esteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseie 85 
                                   RL    e  +  lt +l++l t+l+  ++  +e ++  edl +++ +  +++++lq  +++ e+  + ++++ + +++e e
  gi|14601261|ref|NP_147796.1| 350 RLSQ-AEEDIDSLTTSLDSLRTELEdlSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVE 429
                                   7777.44589999999999999988998889************************************************** PP

                         THOC7  86 avreeieelkaqLeearat.ranrkeydelaek 117
                                    ++++i+e   +L + r t  a r e++ l ek
  gi|14601261|ref|NP_147796.1| 430 TLQQSIVEIDRRLGQLRSTvDAVRLEVESLGEK 462
                                   ***************997614456666666555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0073
                         THOC7   5 ksRLlnveerplkrltkrllklltslaesteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseie 85 
                                   ++RL + ee  l+ lt+ l +l ++      e l+q   ++  ++ +++++++ + l  ++  ++  + e+++++ +++ie
  gi|14601261|ref|NP_147796.1| 404 QQRLATAEE-SLQALTEDLASLQAE-----VETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIE 478
                                   589999555.999999999996666.....79************************************************* PP

                         THOC7  86 avreeieelkaqLeearatran 107
                                   + +++i+el++qL+e+ ++ ++
  gi|14601261|ref|NP_147796.1| 479 DFQSQIQELRTQLDEKTREAQQ 500
                                   ***************9988775 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8  17.0   9.3e-06   0.00069      87     316 ..     256     500 ..     217     507 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.3e-06
                                   HHHHHHHHHTSS-TTS..........STGGGCS-..-TTTTHHHHHHHHH...HHHHHHHHHHHHTTHH..HHHHHHHHHH CS
                         APG17  87 LektlekLrktkvepsfrpegee...ktLlDFvd..edsveelkealkes...idelqaaqkkldssllefdtdlrelkke 159
                                   L   l++L++   ++ f  e+ +    +L   v   ed v +++ +l+++    ++l+ a + ++++l+++ +dl++l+++
  gi|14601261|ref|NP_147796.1| 256 LGLALDSLEERVGDLEFAVEDLTlqlSSLDSRVGalEDRVADIEGRLEAVegsLEDLSGAVDAMSQQLQALAEDLESLSSR 336
                                   444444444444444444333333333333333333445555555553333337777777788888888888888888888 PP

                                   H..............-------.STCCHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHH................S- CS
                         APG17 160 l..............sksksks.essslipellkelesleeemAs...lLesLtnHfDqcvkAvkltegggalrraaaels 222
                                   +              s+ +++  +  +++++l +ele+l++++A+    Le L    Dq+ + ++++++  a    +a   
  gi|14601261|ref|NP_147796.1| 337 VedlearvgsvedrlSQAEEDIdSLTTSLDSLRTELEDLSTRLAEaqaSLEDLNTRLDQVASTLQQLQQRLA----TA--- 410
                                   888888888888877434444458889999999***********84445999999******99999998764....22... PP

                                   CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHH CS
                         APG17 223 eeereelleVlekDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeefl 303
                                   e    e l+ l++D a l++ v++lq+++ e+ +   +l+++ ++++  +++l + l + ee +++ ++ ++ f+++ + l
  gi|14601261|ref|NP_147796.1| 411 E----ESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQEL 487
                                   2....45******************************************************98888888888777766666 PP

                                   HH...HHHHHHHH CS
                         APG17 304 erweeekekieek 316
                                   +++ +ek++ +++
  gi|14601261|ref|NP_147796.1| 488 RTQLDEKTREAQQ 500
                                   6655555443333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0036      0.26       6      83 ..     290     373 ..     278     379 .. 0.60
   2 ?    3.9  12.8      0.37        27       6      87 ..     367     447 ..     362     519 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0036
                         TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelkerkk 80 
                                    le+++ ++e + + ++ +le+ls   +++s++++   ++l++l+s++++l+++v+      ++ ee +++l+++l++ ++
  gi|14601261|ref|NP_147796.1| 290 ALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGsvedrlSQAEEDIDSLTTSLDSLRT 370
                                   556666666666666677777777777777777777777777777777777776543444444444555555555555555 PP

                         TMPIT  81 vlk 83 
                                    l+
  gi|14601261|ref|NP_147796.1| 371 ELE 373
                                   444 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.37
                         TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkeve 86 
                                   +l++e+++l+++  e +++le+l++  +++++++++ ++rl   ++sl+ l++++ ++ + eve+l++++ e+++ l ++ 
  gi|14601261|ref|NP_147796.1| 367 SLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDL-ASLQAEVETLQQSIVEIDRRLGQLR 446
                                   5666666666666666666666666666666666666666666666666666664.3455556666666655555544443 PP

                         TMPIT  87 s 87 
                                   s
  gi|14601261|ref|NP_147796.1| 447 S 447
                                   3 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 !   14.3  10.7   0.00036     0.026      10     144 ..     267     405 ..     258     411 .. 0.70
   2 ?    8.9  19.8     0.016       1.2       8     125 ..     384     498 ..     377     510 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00036
                      KASH_CCD  10 vadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklk....stQqalqkaklleeEleelkalvkeleEkrarl 86 
                                   v dL+++   L  + s+L   v + e+  a +   +e+  + l      +   +q+ ++l+e+le l   v++le +  ++
  gi|14601261|ref|NP_147796.1| 267 VGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEdlsgAVDAMSQQLQALAEDLESLSSRVEDLEARVGSV 347
                                   566666667777777777777766666665555555544444441111455667778888888888888888888888888 PP

                      KASH_CCD  87 kaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhelee 144
                                   + + +q+e + +sL++ ++sL  e++ l +   e +  l++L +  +++ + l++l++
  gi|14601261|ref|NP_147796.1| 348 EDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   8888888888888888888888888888888888888888888777776666655554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.016
                      KASH_CCD   8 stvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlka 88 
                                   ++++dL++   + a   ++L++ + taee+ + Lte++  L+  +  +Qq++++   ++  l +l+ +v  +  + ++l  
  gi|14601261|ref|NP_147796.1| 384 ASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE---IDRRLGQLRSTVDAVRLEVESLGE 461
                                   466777777777777788888888888888888888888888888888888775...455666666666666666666666 PP

                      KASH_CCD  89 qnkqlekenqsLiakiesLqeenikllaekdelkkkl 125
                                   +  q+e  nq   a ie+ q +++ l+++ de  +  
  gi|14601261|ref|NP_147796.1| 462 KLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREA 498
                                   6666666666666666666666666655555544443 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 !   18.7  19.0   7.9e-06   0.00058     238     432 ..     242     439 ..     227     442 .. 0.86
   2 ?    0.4   5.3       2.6   1.9e+02      39      96 ..     444     501 ..     437     510 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.9e-06
                         WEMBL 238 LneellsakdlkskletasallldLkaeLaayvesklkeeaeeeeee...kksetsikealasarkELeevkaniekakde 315
                                   L+e+l+  ++  + l  a + l +   +L   ve+   + ++ +++    +    +i+  l+     Le++   ++ + ++
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVgalEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQ 322
                                   66666666666666666777777777777666664444444333333455888899999********************** PP

                         WEMBL 316 vklLkvaaasLrseLekekaeLaslrqregmasiavssLeaelsrtkselelvqakekearekmvelpkeLqeAaqeaeeA 396
                                   +++L    +sL s +e   a++ s+  r + a   + sL   l++ ++ele + ++ +ea+  +++l   L++ a  +++ 
  gi|14601261|ref|NP_147796.1| 323 LQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQL 403
                                   ********************************************************************************* PP

                         WEMBL 397 kslAqaareelrkakeeaeqakaavstvesrLeavl 432
                                   ++   +a+e l+  +e+    +a+v+t++  + ++ 
  gi|14601261|ref|NP_147796.1| 404 QQRLATAEESLQALTEDLASLQAEVETLQQSIVEID 439
                                   ****************************99887765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.6
                         WEMBL  39 lveeeLdkvqeeipeykkqaeaaeaaksqvleeLestkrlieeLklnLekaqteeaqA 96 
                                   ++ + +d v+ e+ +  +++ +ae++ ++    +e+ +  i+eL+++L+    e++q 
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   5667788888888888888888888888888888888888888888888877777775 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  15.4   8.4e-06   0.00062       5     127 ..     317     437 ..     278     450 .. 0.90
   2 ?    2.7   6.1       1.5   1.1e+02      91     138 ..     457     504 ..     436     520 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.4e-06
                     Rootletin   5 qayqeaqqrqaqLvskLqaKvlqYkkrcseleqrllektselektkltlllssareleeeesadleealakLeeErqrsek 85 
                                   +a +++ q  a+ +++L ++v +   r++++e+rl +   e + ++lt++l s r+  e+ s+ l ea a Le+   r ++
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQA--EEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   6667777777888999********************95..555555666778899999999******************** PP

                     Rootletin  86 laqvnslLreqleearqaneaLtedlqkltkdwerlreeleq 127
                                   +a++ + L++ l  a+++ +aLtedl  l++++e l++++ +
  gi|14601261|ref|NP_147796.1| 396 VASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE 437
                                   *************************************98765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 1.5
                     Rootletin  91 slLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeea 138
                                   + L e+l +a+++n++   +++  ++++++lr++l++k +e ++   +
  gi|14601261|ref|NP_147796.1| 457 ESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   678899999999999999999999999999999999999988876655 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       2.3   1.7e+02      49     104 ..     252     303 ..     237     304 .. 0.66
   2 !   17.9   2.3   4.5e-05    0.0033      17     105 .]     302     388 ..     286     388 .. 0.70
   3 ?    6.7  13.7      0.13       9.9       3     101 ..     393     496 ..     391     501 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  49 elaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkelaaerkqkLe 104
                                    +++    +++l+e   +l    ++a e+++ +l+ l++r  +L++++a+ + +Le
  gi|14601261|ref|NP_147796.1| 252 AVEDLGLALDSLEERVGDL----EFAVEDLTLQLSSLDSRVGALEDRVADIEGRLE 303
                                   4444444444444444444....344688999999999999999999998888887 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.5e-05
                                   HHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  17 ieekeellssedlgkdleevqallkkhkaleaelaaqqervkaln....elaeklldeghsaseeieerleelnerWeeLk 93 
                                   +e  e  l     +    +v a+ ++++al ++l++   rv++l+     ++++l ++ +++ + ++++l+ l++  e+L+
  gi|14601261|ref|NP_147796.1| 302 LEAVEGSL-----EDLSGAVDAMSQQLQALAEDLESLSSRVEDLEarvgSVEDRLSQA-EEDIDSLTTSLDSLRTELEDLS 376
                                   33333333.....222346677777********************5554444444333.4666788889999999999999 PP

                                   HHHHHHHHHHHH CS
                      Spectrin  94 elaaerkqkLee 105
                                   +++ae +++Le+
  gi|14601261|ref|NP_147796.1| 377 TRLAEAQASLED 388
                                   999999999985 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHH..CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHTTHTTHHH CS
                      Spectrin   3 lqqfaqdadeleeWieekeell..ssedlgkdleevqallkkhkaleaelaaqqervkaln....elaeklldeghsasee 77 
                                   l q a+ +++l++ +  +ee l   +edl++  +ev++l++   ++ + l + +  v+a+      l+ekl+++ ++++++
  gi|14601261|ref|NP_147796.1| 393 LDQVASTLQQLQQRLATAEESLqaLTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRleveSLGEKLVQA-EEKNQR 472
                                   6778888999999999999999667788899999999999999999999********999999999*****666.366777 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                      Spectrin  78 ieerleelnerWeeLkelaaerkq 101
                                     +++e+ +++ +eL+++++e+ +
  gi|14601261|ref|NP_147796.1| 473 QDASIEDFQSQIQELRTQLDEKTR 496
                                   777777777777777777776654 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.4    0.0085      0.63     112     243 ..     232     358 ..     221     360 .. 0.67
   2 !   16.7   8.6   5.3e-05    0.0039     129     237 ..     324     436 ..     313     444 .. 0.71
   3 !   10.3  15.0    0.0047      0.35      80     216 ..     369     503 ..     367     519 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0085
                       Leu_zip 112 eelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeis 191
                                   ee+ ++ ++Pl+e     L+++ +e L    + L+er+ +lE  ++++  + s l++ + +l++++ + + + e  + +++
  gi|14601261|ref|NP_147796.1| 232 EEVASAYVAPLEE--RLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEaVEGSLE 310
                                   5556666788888..578888888888888888888888888888888888888888888877777666544442455555 PP

                       Leu_zip 192 kleeklaelkldlektleektasaksleedlastkhelLkvqeqLelaekeL 243
                                   +l+  + ++     ++l++ +++ +sl++ + +   ++ +v+++L++ae+++
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMS----QQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDI 358
                                   5555555554....44445555556666666666777777777777777766 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.3e-05
                       Leu_zip 129 eLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlek.. 206
                                   + L  ++e L    e L++r+ ++E+++ +a e+   l+++l++l++el++ +++ +  ++++++l+++l ++ + l++  
  gi|14601261|ref|NP_147796.1| 324 QALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAeAQASLEDLNTRLDQVASTLQQlq 404
                                   457778888888889999999999999999999999999999999999988766544356666777766666655555411 PP

                       Leu_zip 207 .tleektasaksleedlastkhelLkvqeqLe 237
                                     l + ++s ++l+edlas + e+  +q+ + 
  gi|14601261|ref|NP_147796.1| 405 qRLATAEESLQALTEDLASLQAEVETLQQSIV 436
                                   15556667777888899998888877777654 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0047
                       Leu_zip  80 qaDiselenReLlEkiaefEekefkssnkkeseelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqatsal 160
                                   ++++ +l  R L E  a++E+ +++ ++  ++ ++ +++L+  +e  + + L  +++ L+ e e+L++ + e+++++ ++ 
  gi|14601261|ref|NP_147796.1| 369 RTELEDLSTR-LAEAQASLEDLNTRLDQVASTLQQLQQRLATAEE--SLQALTEDLASLQAEVETLQQSIVEIDRRLGQLR 446
                                   5666667666.89999***********999999*********999..59999***************************99 PP

                       Leu_zip 161 eeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlektleektasak 216
                                   +   +++ ++++l ++l +++++++ ++++i++ +++++el+++l+++++e +++a+
  gi|14601261|ref|NP_147796.1| 447 STVDAVRLEVESLGEKLVQAEEKNQrQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   999999999999988876665554447999****************99888766654 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 ?    9.4   0.0     0.012      0.91     104     155 ..     292     344 ..     264     347 .. 0.70
   2 ?    9.6   0.8     0.011       0.8     110     155 ..     348     393 ..     339     397 .. 0.92
   3 ?    5.2   2.6      0.25        18     108     155 ..     388     435 ..     382     442 .. 0.77
   4 ?    6.4   2.0      0.11       7.8     111     164 ..     461     514 ..     444     525 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.012
                   EMP24_GP25L 104 ykdsak.kekletleselkkleekldsikreqkylrereerlrdtnestnsrv 155
                                   ++ +a+ +  le +e +l+ l+  +d + +++++l e  e+l   +e+++ rv
  gi|14601261|ref|NP_147796.1| 292 EDRVADiEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   23334447778888888888888888888888888888888888888887776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.011
                   EMP24_GP25L 110 kekletleselkkleekldsikreqkylrereerlrdtnestnsrv 155
                                   ++ l++ e+ ++ l ++lds+++e++ l +r ++ ++ +e++n+r+
  gi|14601261|ref|NP_147796.1| 348 EDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRL 393
                                   6889999************************************985 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.25
                   EMP24_GP25L 108 akkekletleselkkleekldsikreqkylrereerlrdtnestnsrv 155
                                   + ++ l+++ s+l++l+++l   ++ +++l e  ++l++ +e +++ +
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSI 435
                                   456788888888888888888888888888888888888888776655 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.11
                   EMP24_GP25L 111 ekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqll 164
                                   ekl + e++ ++ + ++++++++++ lr++ ++  + +++t s   +ws++  +
  gi|14601261|ref|NP_147796.1| 461 EKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSMAAAG 514
                                   677777777777788888888888888888888888888888888888777655 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  25.6     0.074       5.4     116     239 ..     354     504 ..     226     528 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.074
                       DUF4407 116 qqeeakelkeqlaaa......ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekka 190
                                   ++e++++l+++l++       l+++lae++a +++l++ +d+  ++l++l++ ++                 +++ ++ ++
  gi|14601261|ref|NP_147796.1| 354 AEEDIDSLTTSLDSLrteledLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLA---------------TAEESLQALTE 419
                                   2223333333333223334444444444444444444444444444444444443...............33344444444 PP

                       DUF4407 191 qldaaqaelaelkakld....................................atarlaalraelaeleaerakeraasqa 235
                                   +l+ +qae+++l++++                                     ++a +++ +++++el++++++++++ q+
  gi|14601261|ref|NP_147796.1| 420 DLASLQAEVETLQQSIVeidrrlgqlrstvdavrleveslgeklvqaeeknqrQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   444444444444444335555555555555599999999999999999999999999999999999999999998888888 PP

                       DUF4407 236 aaaa 239
                                   +a+ 
  gi|14601261|ref|NP_147796.1| 501 TAST 504
                                   7764 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  25.8   1.9e-05    0.0014     320     580 ..     247     504 ..     238     511 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-05
                          Cast 320 sDckqHievLkesltAkeqRAaiLqtevdalrlrleekeqlLnkktkqlqdlteekstlageirdlkdmldvkeRkvnvlq 400
                                   s   q +e L  +l   e R   L   v+ l l+l   ++ +   ++++ d++    + +g ++dl   +d    +++ l 
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALA 327
                                   5566788888888889999999999999999999999999999999999999999999999***********9******** PP

                          Cast 401 kkienLqeqlrdkdkqlaelkervkslqtDssntDtALatleeaLsekervierLkeqreredrerleeleslkkenkelk 481
                                     +e+L+  + d +  + +  +r+ + ++D     t L  l   L   e +  rL e +++ + +    l+++   +++l+
  gi|14601261|ref|NP_147796.1| 328 EDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTEL---EDLSTRLAEAQASLE-DLNTRLDQVASTLQQLQ 404
                                   ***********************9999999876666666666555...556677777655544.34556889999999999 PP

                          Cast 482 eklsalqaeltekesslldlkekasslassglkkdsklksleiavekkkeecskleaqlkkaqeaeeae.ranpeitdrik 561
                                   ++l +  ++l+   + l +l+ + ++l++s+++ d +l +l  +v+  + e++ l  +l +a+e ++++    ++++++i+
  gi|14601261|ref|NP_147796.1| 405 QRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQdASIEDFQSQIQ 485
                                   99999999999999999*******************************************999998887356799****** PP

                          Cast 562 lLekevarkkeessksqae 580
                                    L ++++ k  e++++ + 
  gi|14601261|ref|NP_147796.1| 486 ELRTQLDEKTREAQQTAST 504
                                   ******9999999887665 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 !    9.9   0.8    0.0069      0.51      78     137 ..     318     377 ..     239     381 .. 0.89
   2 !   11.9   3.0    0.0017      0.12      86     137 ..     382     433 ..     378     435 .. 0.94
   3 ?    6.5   4.5     0.075       5.6      79     142 ..     431     494 ..     425     507 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0069
                 PI3K_P85_iSH2  78 aqehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqk 137
                                   a ++  + l e le l sr++ l++   ++e+ l q  e+  +l  ++ +l+ el  L+ 
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLST 377
                                   4578899999*****************************************999999875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0017
                 PI3K_P85_iSH2  86 lqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqk 137
                                    q +le+l+ rl+++ s+ ++L++ l +  e+ + l  ++ +l+ e+ +Lq+
  gi|14601261|ref|NP_147796.1| 382 AQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQ 433
                                   57899******************************************99986 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.075
                 PI3K_P85_iSH2  79 qehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdky 142
                                    ++ i +++  l ql+s ++ ++ + e+L e+l q  e+++  + +i   ++++++L+ + d+ 
  gi|14601261|ref|NP_147796.1| 431 LQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEK 494
                                   4555666667777777777777788999******************************998875 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.028         2     231     279 ..     284     338 ..     266     342 .. 0.73
   2 !   11.6   0.2    0.0015      0.11     223     281 ..     318     375 ..     315     385 .. 0.78
   3 !   10.0   1.8    0.0045      0.34     220     269 ..     385     434 ..     373     453 .. 0.66
   4 ?    2.4   4.5      0.96        71       2      55 ..     444     497 ..     442     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.028
                          RmuC 231 iaellgelydkfekfgedleklgkklekaqksydkavkkle......gnilrkae 279
                                   + +++g+l d+++ ++ +le+++ +le+++ ++d + ++l+      +++++++e
  gi|14601261|ref|NP_147796.1| 284 LDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQalaedlESLSSRVE 338
                                   5567889999999999999999999999999999977777666655555555544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0015
                          RmuC 223 aqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaekl 281
                                   a++++ + +ae l++l +++e +++++ +++++l++a++++d++ ++l +++ +++e+l
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSL-DSLRTELEDL 375
                                   788999999999999999999999999999999999999999977777.5555555554 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0045
                          RmuC 220 rqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkk 269
                                     e+++ + +++a++l++l +++++ +e+l++l + l ++q +++++ ++
  gi|14601261|ref|NP_147796.1| 385 SLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   45667777777777777777777777777777777777777777773333 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.96
                          RmuC   2 qleellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaen 55 
                                   ql ++++ ++ ++e++ ek+ + +++++++ +s++   +++qel +ql++++++
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   577888888999999999999999999999999999999999998888887765 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 ?    7.1   0.0     0.081       5.9      67     128 ..     243     304 ..     232     315 .. 0.85
   2 !   10.6  12.9    0.0066      0.49      38     140 ..     309     407 ..     302     420 .. 0.67
   3 ?    8.2   9.4     0.037       2.7      38     106 ..     365     433 ..     362     450 .. 0.67
   4 ?    2.7  13.9       1.8   1.4e+02      54     136 ..     416     501 ..     408     510 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.081
                 Jnk-SapK_ap_N  67 erekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeae 128
                                   e++ +l ++a e+l ++ d++ee+  +l+ +ve+l+ +   l+ ++ +++d+++++e + + 
  gi|14601261|ref|NP_147796.1| 243 EERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEA 304
                                   56667778888999999999999999999999999999999999999999999999987555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0066
                 Jnk-SapK_ap_N  38 LeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadq 118
                                   Le l    ++ +++l+ l e+le+L ++ e+  +     e++l ++e+ +++ +  l++  ++le+   +l     +a+  
  gi|14601261|ref|NP_147796.1| 309 LEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLA----EAQAS 385
                                   666777777888888888888888888888888888888888888888887777777666666666666666....55555 PP

                 Jnk-SapK_ap_N 119 lsrleekeaelkkeysklhere 140
                                   l++l+ + +++ +  ++l++r 
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRL 407
                                   6666666666655556655532 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.037
                 Jnk-SapK_ap_N  38 LeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenr 106
                                   L+sl ++ e  +++l e ++ le+L t++++ ++  ++ +++l  +e++++  +++l +  +++e+ ++
  gi|14601261|ref|NP_147796.1| 365 LDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQ 433
                                   788888888888888888888888888888888888888888877777777666665554444444333 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 1.8
                 Jnk-SapK_ap_N  54 elreeleqLeteyerekelrkraeeeleeie...dqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkk 131
                                    l e+l +L+ e e  ++   + +++l ++    d+++ e + l ek+ q ee+n++ ++ +++++ q+++l  + +e ++
  gi|14601261|ref|NP_147796.1| 416 ALTEDLASLQAEVETLQQSIVEIDRRLGQLRstvDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTR 496
                                   444444444444444444444444333333211133444444455555555555555554555555555554444444444 PP

                 Jnk-SapK_ap_N 132 eyskl 136
                                   e +++
  gi|14601261|ref|NP_147796.1| 497 EAQQT 501
                                   44443 PP

>> WASH_WAHD  WAHD domain of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       5.5   4.1e+02      44      75 ..     274     305 ..     247     319 .. 0.60
   2 !   11.7   2.8    0.0018      0.13      22     160 ..     315     452 ..     306     501 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 5.5
                     WASH_WAHD  44 vernreklqaineRveiaqakiaklkeskkai 75 
                                   ve+   +l++++ Rv   ++++a +++  +a+
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAV 305
                                   45555555555555555555555555555443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0018
                     WASH_WAHD  22 aadaL.eyLnkvlndvfgridarvernreklqaineRveiaqakiaklkeskkaikiyspakyPa.sdllqkyestftatn 100
                                   a+da+ + L+  ++d ++ +++rve+  +++ ++++R+++a+++i+ l +s  +            ++ ++ +e + t  +
  gi|14601261|ref|NP_147796.1| 315 AVDAMsQQLQALAED-LESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRlAEAQASLEDLNTRLD 394
                                   556652345555555.578999*****************************999877544222233778888888889999 PP

                     WASH_WAHD 101 siaavekefsyrlkskpeqleekalqeklkffhvkveekletekeveeGlgtlpkkiksv 160
                                   ++a + ++ ++rl   +e    +al e l   + +ve+ ++++ e+++ lg+l++ +  v
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEES--LQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAV 452
                                   9999999999999998886..68999999999999999999999****999999887765 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 ?    5.8   0.1       0.2        15      19      78 ..     279     342 ..     265     344 .. 0.73
   2 !   14.8   0.7    0.0003     0.022      15      78 ..     332     391 ..     323     393 .. 0.88
   3 ?    6.2   6.6      0.15        11      33      78 ..     377     426 ..     368     449 .. 0.48
   4 ?    5.3   7.1      0.29        22      20      80 .]     427     484 ..     420     501 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.2
                          Med9  19 lsskdletktgelrhkLkkarelirelpg....idrsveeqeaeieeleeqlakKrelLkkykn 78 
                                   l+   l++ +g+l ++   +   ++ ++g    ++  v+ + +++++l e l+   +  +++  
  gi|14601261|ref|NP_147796.1| 279 LQLSSLDSRVGALEDRVADIEGRLEAVEGsledLSGAVDAMSQQLQALAEDLESLSSRVEDLEA 342
                                   5556677777777777777777777777666668888888888888888888888877777766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 0.0003
                          Med9  15 kdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                   + + + ++dle+ +g++ ++L++a e i++   +  s ++   e+e+l+ +la  ++ L++++ 
  gi|14601261|ref|NP_147796.1| 332 SLS-SRVEDLEARVGSVEDRLSQAEEDIDS---LTTSLDSLRTELEDLSTRLAEAQASLEDLNT 391
                                   444.8899**********************...99************************99976 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.15
                          Med9  33 hkLkkarelirelpg....idrsveeqeaeieeleeqlakKrelLkkykn 78 
                                   ++L +a + ++ l      +  + ++ ++++++ ee+l++  e L++++ 
  gi|14601261|ref|NP_147796.1| 377 TRLAEAQASLEDLNTrldqVASTLQQLQQRLATAEESLQALTEDLASLQA 426
                                   44444444444444444444444444444444444444444444444443 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.29
                          Med9  20 sskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkyknrv 80 
                                   +++ l++++ e+  +L + r+ ++    +   ve+  +++ + ee+++++ + ++++++++
  gi|14601261|ref|NP_147796.1| 427 EVETLQQSIVEIDRRLGQLRSTVDA---VRLEVESLGEKLVQAEEKNQRQDASIEDFQSQI 484
                                   5566777777777777777777776...666666666666666666666666666666653 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.7   5.5e-05     0.004      37      96 ..     321     380 ..     315     387 .. 0.92
   2 ?    7.3   3.8     0.016       1.2      41      93 ..     381     433 ..     378     438 .. 0.81
   3 ?    2.4   3.3      0.48        36      41      94 ..     437     490 ..     429     507 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-05
                          COG6  37 eefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqk 96 
                                   +++q++ae L++++s+ve+l++ + +++++ls+a+e+ ++l+++ ++L++e+++l+++  
  gi|14601261|ref|NP_147796.1| 321 QQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLA 380
                                   7899***************************************************99865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.016
                          COG6  41 pvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklel 93 
                                   +++ +L+ +++++++ +++ ++++++l +a+e+ + l+e+ ++L++e + l++
  gi|14601261|ref|NP_147796.1| 381 EAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQ 433
                                   67788888888999999999999999999999999999999988888887654 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.48
                          COG6  41 pvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelk 94 
                                   +++++L +++s+v++    ++++ +kl +a+e++++   ++e+++++ ++l+++
  gi|14601261|ref|NP_147796.1| 437 EIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQ 490
                                   455555555555555555555555555555555555555555555555555544 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.8    0.0065      0.48      26      69 ..     322     365 ..     313     386 .. 0.87
   2 !   15.1   4.0   0.00024     0.018      24      73 ..     390     439 ..     385     448 .. 0.90
   3 ?    4.0   5.5      0.68        51      27      85 ..     449     507 ..     441     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0065
                                   HHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXX CS
                        DivIVA  26 FLdqvakdyeallkeneelkekvkeleeklkeykeleetLkktl 69 
                                    L+ +a+d+e+l +++e+l+++v   e++l++ +e  ++L  +l
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSL 365
                                   5999*******************************999999887 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  24 deFLdqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaq 73 
                                   +  Ldqva+++++l ++ ++ +e +++l+e+l++ +   etL++++v   
  gi|14601261|ref|NP_147796.1| 390 NTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEID 439
                                   5669******************************************9765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.68
                                   HHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA  27 LdqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakk 85 
                                    d v  ++e+l ++  + +ek ++++ ++++++++ ++L+  l    + a+++ ++a++
  gi|14601261|ref|NP_147796.1| 449 VDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   6889999********************************99997776666666666554 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.7       0.1       7.6      69     107 ..     318     356 ..     251     370 .. 0.56
   2 !   14.1   8.6   0.00054      0.04      29     123 ..     345     435 ..     337     438 .. 0.78
   3 !   15.4   6.9   0.00021     0.016      27     113 ..     371     453 ..     366     461 .. 0.82
   4 ?    8.6   5.3     0.027         2      29     111 ..     422     507 ..     418     513 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.1
                                   XXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHH CS
                          COG5  69 slssvlselksslesLsasyerlkskvlepyeeaeklqs 107
                                     s+ l+ l + lesLs+ +e l+  v    +++++ ++
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEE 356
                                   222245555555555555555555555555555555555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00054
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHH CS
                          COG5  29 ldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsal 109
                                    +++ +l++ ++di+ l++ l++l t+    L +  ++ ++++++l++l+++l+++ + +++l++ + +  e+++ l++ l
  gi|14601261|ref|NP_147796.1| 345 GSVEDRLSQAEEDIDSLTTSLDSLRTE----LEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDL 421
                                   566777888888888888888776554....43444555666779999999999999999999999999999999999999 PP

                                   HHHHHHHHHHHHHH CS
                          COG5 110 krlhqtldLlrral 123
                                   ++l+  +++l +++
  gi|14601261|ref|NP_147796.1| 422 ASLQAEVETLQQSI 435
                                   99999999998776 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 0.00021
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHH CS
                          COG5  27 teldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklq 106
                                   + +dlst+l+  +  +++l++rl+q  ++     l++l++++ + + +l+ l++ l+sL+a +e l++ ++e   ++ +l+
  gi|14601261|ref|NP_147796.1| 371 ELEDLSTRLAEAQASLEDLNTRLDQVAST-----LQQLQQRLATAEeSLQALTEDLASLQAEVETLQQSIVEIDRRLGQLR 446
                                   567999999999999****9999997655.....5666666655555************************9999999999 PP

                                   HHHHHHH CS
                          COG5 107 salkrlh 113
                                   s+   ++
  gi|14601261|ref|NP_147796.1| 447 STVDAVR 453
                                   8877665 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.027
                                   XXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHH CS
                          COG5  29 ldlstplkrlnydiqeldkrl...rqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklq 106
                                   ++l++++++l++ i e+d+rl   r+ + +  le+ +  +k  ++++ ++  + s+e+ ++ ++ l++++ e+  ea++  
  gi|14601261|ref|NP_147796.1| 422 ASLQAEVETLQQSIVEIDRRLgqlRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   57899**************8611155667777888888888889999********************************99 PP

                                   HHHHH CS
                          COG5 107 salkr 111
                                   s+++r
  gi|14601261|ref|NP_147796.1| 503 STASR 507
                                   99887 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 !   10.4   0.5    0.0048      0.35      70     151 ..     250     331 ..     231     346 .. 0.51
   2 !   13.9   9.0   0.00042     0.031      64     157 ..     314     407 ..     297     409 .. 0.88
   3 !   12.3  14.5    0.0013     0.095      49     155 ..     340     450 ..     325     455 .. 0.84
   4 ?    6.1  17.1     0.099       7.3      50     160 ..     397     504 ..     393     517 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0048
                  HAUS-augmin3  70 evileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnavLqql 150
                                   e+ +e+++ +l  Le+ + +L+   + ++ +l+ L+  + +l+++  + e + +++++ l+++  ++ a + +++a+ ++l
  gi|14601261|ref|NP_147796.1| 250 EQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDL 330
                                   444555555555555555555555555555555555555555555555555555555555555544444444444332222 PP

                  HAUS-augmin3 151 t 151
                                    
  gi|14601261|ref|NP_147796.1| 331 E 331
                                   2 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00042
                  HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetn 144
                                    +v++++++l+++ e+le L + +++L+    + + rl++ +  + sl+  l +l +e +  + +l eaq++l+  n +++
  gi|14601261|ref|NP_147796.1| 314 GAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLD 394
                                   6899999************************************************************************99 PP

                  HAUS-augmin3 145 avLqqlteeakql 157
                                   +v ++l++  ++l
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRL 407
                                   9988888866666 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0013
                  HAUS-augmin3  49 LeeaLktiepsdlkq.edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkk 128
                                   Le    ++e++ ++  ed ++l+ +l+ +++ le+L + l e+q   + ++ rl++   +  +lqq+l + ee+ ++ +++
  gi|14601261|ref|NP_147796.1| 340 LEARVGSVEDRLSQAeEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTED 420
                                   5555555554444447999************************************************************** PP

                  HAUS-augmin3 129 lkeaqee...lraenaetnavLqqlteeak 155
                                   l  +q+e   l++ + e+++ L ql +++ 
  gi|14601261|ref|NP_147796.1| 421 LASLQAEvetLQQSIVEIDRRLGQLRSTVD 450
                                   999998733367889999999999988775 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.099
                  HAUS-augmin3  50 eeaLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklk 130
                                   +  L++++      +    +e++l++++e+l  L++e+++Lq+    + +rl +L  ++ +   e ++l e+  +a++k++
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQ------QRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQ 471
                                   44555555......7788889999**********************************99999999999999877777777 PP

                  HAUS-augmin3 131 eaq...eelraenaetnavLqqlteeakqlaey 160
                                   + +   e++++++ e++++L++ t ea+q a+ 
  gi|14601261|ref|NP_147796.1| 472 RQDasiEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   666111567889999999999999999998875 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0     0.011      0.81     195     304 ..     265     374 ..     242     378 .. 0.73
   2 ?    7.1  18.3     0.037       2.7       5     130 ..     371     502 ..     369     510 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.011
                       Taxilin 195 keakeltkkvkalketekelkeqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklEketnlwkskfektnkall 275
                                   +++ +l+  v++l+ + ++l +++   +++  ++++ L+  +   +     ++ m+++++ l ++ +++ s+ e+ ++ + 
  gi|14601261|ref|NP_147796.1| 265 ERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVG 345
                                   556666666777777777777777777777777777777777777788888888888888888888888888888888888 PP

                       Taxilin 276 emaeertekkkeieklkkkiqkLeklcra 304
                                   ++ +   + +++i++l+  +++L++  + 
  gi|14601261|ref|NP_147796.1| 346 SVEDRLSQAEEDIDSLTTSLDSLRTELED 374
                                   87777778888888888888888765554 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.037
                       Taxilin   5 qlkeslsklespeekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaels....kaalaksKLekLcRelqk 81 
                                   +l+ + ++l++ +  le L +++ ++ +  ++lq+ l  +++ l++l+++  +lqae +      +    +L +L   ++ 
  gi|14601261|ref|NP_147796.1| 371 ELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVEtlqqSIVEIDRRLGQLRSTVDA 451
                                   566777888888888888888888888888888888888888888888888888888751111455677889999999999 PP

                       Taxilin  82 qnkklk..eeskqrareeeekrkelaekfqakLkdiqaqieekserneklr 130
                                    + +++   e + +a+e+++++++  e fq++++++++q++ek  + ++++
  gi|14601261|ref|NP_147796.1| 452 VRLEVEslGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   8888883334444455555666677899**************999998876 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1       1.3        95       6      37 ..     316     347 ..     309     362 .. 0.72
   2 !   13.7   3.9   0.00077     0.057       4      69 ..     363     431 ..     360     439 .. 0.80
   3 ?    1.6   0.2       4.9   3.6e+02       6      33 ..     414     441 ..     409     448 .. 0.50
   4 ?    8.7   2.2     0.028         2       4      42 ..     447     488 ..     444     501 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 1.3
                         Tup_N   6 LdavkqEfdalsqeasslkaqkdeyelkiqsq 37 
                                    da  q  +al+++++sl ++ +++e+++ s 
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSV 347
                                   67777888888888888888888888877654 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00077
                         Tup_N   4 elLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikq...qYEeeiarL 69 
                                     Ld +++E + ls+ +   +a+ +++++++ + ++ lqq++q l   ee+ +++ +   + + e++ L
  gi|14601261|ref|NP_147796.1| 363 TSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEdlaSLQAEVETL 431
                                   579******************************************998887766554111334444444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 4.9
                         Tup_N   6 LdavkqEfdalsqeasslkaqkdeyelk 33 
                                   L+a+ ++  +l+ e+++l+++  e++++
  gi|14601261|ref|NP_147796.1| 414 LQALTEDLASLQAEVETLQQSIVEIDRR 441
                                   4455555555555555554444444443 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.028
                         Tup_N   4 elLdavkqEfdalsqeasslka..qkdeyelk.iqsqiqElq 42 
                                      dav+ E ++l +++ + ++  q+++     +qsqiqEl 
  gi|14601261|ref|NP_147796.1| 447 STVDAVRLEVESLGEKLVQAEEknQRQDASIEdFQSQIQELR 488
                                   578**************9976633777777777888888875 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0         2   1.5e+02       9      40 ..     263     294 ..     242     306 .. 0.79
   2 ?    5.2   0.5      0.32        24      12      42 ..     308     338 ..     290     349 .. 0.57
   3 !   10.3   3.6    0.0089      0.66       9      49 ..     347     387 ..     339     402 .. 0.60
   4 ?    7.6   6.2      0.06       4.4       5      43 ..     399     437 ..     382     459 .. 0.77
   5 ?    4.9   5.2       0.4        30       5      43 ..     462     500 ..     435     521 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 2
                         Spc24   9 iakelsdleselesleselaelkeeleeleee 40 
                                   + + + dle ++e+l+ +l++l +++  le+ 
  gi|14601261|ref|NP_147796.1| 263 LEERVGDLEFAVEDLTLQLSSLDSRVGALEDR 294
                                   45667788888888888888888888877764 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.32
                         Spc24  12 elsdleselesleselaelkeeleeleeese 42 
                                   +l+dl  ++++++++l+ l e le l++  e
  gi|14601261|ref|NP_147796.1| 308 SLEDLSGAVDAMSQQLQALAEDLESLSSRVE 338
                                   4455555555555555555555555555433 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0089
                         Spc24   9 iakelsdleselesleselaelkeeleeleeeseekeserv 49 
                                   +   ls++e++++sl+++l++l++ele+l++   e +++++
  gi|14601261|ref|NP_147796.1| 347 VEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLE 387
                                   55566777777777777777777777777776666333332 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.06
                         Spc24   5 ekfriakelsdleselesleselaelkeeleeleeesee 43 
                                   +++++++ l  +e++l++l++ la+l++e+e+l+++ +e
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE 437
                                   567888889999999999999999999999999999888 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.4
                         Spc24   5 ekfriakelsdleselesleselaelkeeleeleeesee 43 
                                   +++++ ++++ +++++e+ +s+ +el+++l+e  +e ++
  gi|14601261|ref|NP_147796.1| 462 KLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   556666666777777777777777777777776666665 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.4    0.0036      0.26      32      97 ..     283     348 ..     243     357 .. 0.85
   2 !   11.3   7.4    0.0059      0.43      25     104 ..     353     432 ..     347     435 .. 0.84
   3 ?    2.2   7.1       4.2   3.1e+02      35     103 ..     426     501 ..     422     506 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0036
                       DUF4472  32 elknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekek 97 
                                    l ++v ale rv ++e + e  + + ++l+  ++++ ++ ++l+e + +l +++ +le+   + +
  gi|14601261|ref|NP_147796.1| 283 SLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVE 348
                                   577888899999999999999999999999999999999999999999999999888887766655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0059
                       DUF4472  25 qheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqels 104
                                   q+e+++  l++ + +l  ++ +l+ + ++a+ + ++l++rl+++ +  ++l++++++ ++++qal++++ + +++ + l+
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   77888888888888889999999999999999999999999999999999999999999999999999988888877776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 4.2
                       DUF4472  35 nkvlalenrvlelelerek.......aaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqel 103
                                    +v +l+++++e++ +  +        + e +sl e+l ++ee++++  +     ++++q+l++++++++++ q+ 
  gi|14601261|ref|NP_147796.1| 426 AEVETLQQSIVEIDRRLGQlrstvdaVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   4555555666666655555555555588899999999999999999999999999999999999999988888876 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.6    0.0033      0.24      33     106 ..     316     389 ..     297     391 .. 0.88
   2 !   14.3   5.0   0.00053     0.039      11     101 ..     361     447 ..     346     454 .. 0.47
   3 ?    6.4  14.1      0.15        11       9     105 ..     401     500 ..     398     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0033
                       DUF4200  33 eeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekleey 106
                                    +++ ++ q l edl+ +   +++ +a+    + +  + ++ +++ +  +  l++e+e+l +++++ ++ le++
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDL 389
                                   56778888999999999999999999999999999999999999999999999999999999999999999876 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00053
                       DUF4200  11 vqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeiet 91 
                                   ++ +l+  + e     e l++r +e +++ + l+ +l ++   l++ +++ a a++  +  ++   + +ae++ l+++i++
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTE----LEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE 437
                                   22222222222....233333333333333344444444445555555556666666666666666666666666666655 PP

                       DUF4200  92 lkseieklee 101
                                   +  ++ +l  
  gi|14601261|ref|NP_147796.1| 438 IDRRLGQLRS 447
                                   5555555555 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.15
                       DUF4200   9 fevqealeakkeeiqrleeal...kqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklk 86 
                                   +++q+ l++++e +q l e l   + + e l+++  e+ ++l ++   +     + +   +k  + ++++++ +a i++++
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLaslQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQ 481
                                   6899999999999998887661115555666666678899999999999999999999999999***************** PP

                       DUF4200  87 aeietlkseiekleeklee 105
                                   ++i++l++++++  ++ ++
  gi|14601261|ref|NP_147796.1| 482 SQIQELRTQLDEKTREAQQ 500
                                   *******999988777665 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 ?    6.4   0.5     0.074       5.4     127     213 ..     253     336 ..     228     343 .. 0.71
   2 !   13.5  12.8    0.0005     0.037      45     150 ..     340     444 ..     328     449 .. 0.62
   3 !   10.6  20.3    0.0037      0.28      45     170 ..     382     506 ..     380     511 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.074
                     Golgin_A5 127 eeelvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqLtesLiqKQtvlEalsteknslvlQLeRleqqi 207
                                    e+l  +  +l++r+ d e  +e+l+ ql++    +s    le+R+  +   L +    lE ls   +++  QL+ l +++
  gi|14601261|ref|NP_147796.1| 253 VEDLGLALDSLEERVGDLEFAVEDLTLQLSSL---DSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDL 330
                                   45666666778888888888888888888654...3456788888888888888888888888888888888888887777 PP

                     Golgin_A5 208 kevqse 213
                                   ++++s 
  gi|14601261|ref|NP_147796.1| 331 ESLSSR 336
                                   777665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0005
                     Golgin_A5  45 lsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelry 125
                                   l+a + +++++  +++e++ +l++++++lrtel+dl ++  aea+     l++l+++l++  ++ +++++ l+  +e l++
  gi|14601261|ref|NP_147796.1| 340 LEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRL-AEAQA---SLEDLNTRLDQVASTLQQLQQRLATAEESLQA 416
                                   4556667777778888999999999999999999998877.44433...45566666666667777777777777777777 PP

                     Golgin_A5 126 leeelvrska...tlqsrikdrekeiek 150
                                   l e+l   +a   tlq+ i + ++ + +
  gi|14601261|ref|NP_147796.1| 417 LTEDLASLQAeveTLQQSIVEIDRRLGQ 444
                                   7777765544001344444444444444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0037
                     Golgin_A5  45 lsaeldelkqerdllreelqklnqqieqlrtelqdlea...qqqaeaeslreqlqeleeqleeerkakeeveaelerlkee 122
                                   ++a l++l+ + d++ + lq+l+q++ +    lq l +   + qae+e+l++ + e++ +l + r++  +v+ e+e+l e+
  gi|14601261|ref|NP_147796.1| 382 AQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEdlaSLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEK 462
                                   567788888888999999999999998888888877642225789************************************ PP

                     Golgin_A5 123 lryleeelvrskatlqsrikdrekeieklrnqlttkslsssseseles 170
                                   l  +ee ++r+ a+    i+d +++i++lr ql  k+ +  + +   s
  gi|14601261|ref|NP_147796.1| 463 LVQAEEKNQRQDAS----IEDFQSQIQELRTQLDEKTREAQQTASTAS 506
                                   ****9999988655....667778899999999988887766655555 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   5.7   0.00081      0.06      23     119 ..     274     386 ..     248     386 .. 0.83
   2 !   15.3   9.7   0.00023     0.017      29     119 ..     357     442 ..     353     449 .. 0.71
   3 ?    1.8   3.0       3.4   2.5e+02      83     114 ..     462     493 ..     446     505 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00081
                          Uds1  23 VeelkkelkaLeerlealrkkLa.letklrdaarsLsrlyssskksak................ssaarsnskssreslak 86 
                                   Ve+l  +l++L++r+ al+ ++a +e +l +   sL+ l+ +  + ++                +  +  +  s ++ l +
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVAdIEGRLEAVEGSLEDLSGAVDAMSQqlqalaedleslssrvEDLE-ARVGSVEDRLSQ 353
                                   89999999999999999999986599999999999999997666665589999999999888763333.33334457899* PP

                          Uds1  87 aeeelaeserkvdelaselekleeraaevrrrL 119
                                   aee++++++++ d l +ele l++r+ae + +L
  gi|14601261|ref|NP_147796.1| 354 AEEDIDSLTTSLDSLRTELEDLSTRLAEAQASL 386
                                   **************************9999876 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 0.00023
                          Uds1  29 elkaLeerlealrkkLa.letklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvdelaselekl 108
                                   ++ +L++ l++lr++L+ l t+l +a  sL+ l+ + + +       s+ ++ ++ la+aee+l+++++    l++e+e+l
  gi|14601261|ref|NP_147796.1| 357 DIDSLTTSLDSLRTELEdLSTRLAEAQASLEDLN-TRLDQ-----VASTLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   5678999999999999669999999999999999.66666.....445555555666666666666666666666666666 PP

                          Uds1 109 eeraaevrrrL 119
                                   ++   e++rrL
  gi|14601261|ref|NP_147796.1| 432 QQSIVEIDRRL 442
                                   66666666665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 3.4
                          Uds1  83 slakaeeelaeserkvdelaselekleeraae 114
                                   +l +aee+ +  ++++++++s++++l++++ e
  gi|14601261|ref|NP_147796.1| 462 KLVQAEEKNQRQDASIEDFQSQIQELRTQLDE 493
                                   55566777777777777777777766665544 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       1.8   1.3e+02      33      98 ..     276     339 ..     258     342 .. 0.58
   2 ?    8.0   0.1     0.064       4.7      26      97 ..     311     380 ..     307     383 .. 0.79
   3 ?   10.0   1.0     0.015       1.1      26      97 ..     367     429 ..     359     440 .. 0.47
   4 ?    7.4   0.7     0.096       7.1      27      70 ..     389     432 ..     376     463 .. 0.54
   5 ?    5.7   2.6      0.33        25      26      90 ..     423     492 ..     419     502 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1.8
                  Occludin_ELL  33 evskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklike 98 
                                   +++ ++s L++++ +l+++   ++ + e +  ++++l  + +  ++ ++++ L e L+ + +++++
  gi|14601261|ref|NP_147796.1| 276 DLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDL--SGAVDAMSQQLQALAEDLESLSSRVED 339
                                   4444555555555555555555555555555555555..555666666666677666666666655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.064
                  Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklik 97 
                                   +l   ++++s++++ L ++l++l+ + +  + ++ ++ +++++ +  ++  +  + ++ L+ +L+ + ++++
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAE--EDIDSLTTSLDSLRTELEDLSTRLA 380
                                   577789999999999999999999999999999999899988884..5555666777788888877776665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.015
                  Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklik 97 
                                   +l +ele++s +++e ++ l++l+++ ++++++ ++++q+++           ++ ++ L e L+ + + ++
  gi|14601261|ref|NP_147796.1| 367 SLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATA---------EESLQALTEDLASLQAEVE 429
                                   34444555555555555555555555555555555555555444.........4444444444444444443 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.096
                  Occludin_ELL  27 lhaeleevskkfseLerelkelkegskeykkieeeilqeykklk 70 
                                   l+++l++v++++++L+++l +++e+ +  ++  ++++ e + l+
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   55555555555555555555555555443333333344444332 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.33
                  Occludin_ELL  26 elhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkkrceyLkekLs 90 
                                   +l+ae+e++++ + e++r+l +l+ + +    e++++ e+++q  +k ++ d++  + + ++++L+ +L+
  gi|14601261|ref|NP_147796.1| 423 SLQAEVETLQQSIVEIDRRLGQLRSTVDavrlEVESLGEKLVQAEEKNQRqDASIEDFQSQIQELRTQLD 492
                                   6888999999999999999998888888788888888888777777666657778888888888888775 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.4       0.8        59       4      75 ..     318     388 ..     308     412 .. 0.46
   2 !   16.7   5.3   0.00011     0.008       2      84 ..     414     502 ..     413     507 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.8
                                   HHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING   4 dyldsvenLPlelqrnltelreiDakvqellkei...dskiekflkngslqknekeeelsriqeelkeaqellde 75 
                                    +++++++L ++l+ + +++ +++a+v ++ +++   ++ i+++     ++ ++ + el+++   l eaq +l++
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLsqaEEDIDSLT----TSLDSLRTELEDLSTRLAEAQASLED 388
                                   455566666666666666666666665554444433244444444....23333333333333333333333333 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 0.00011
                                   HHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHTS..S-HHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING   2 LedyldsvenLPlelqrnltelreiDakvqellkei.......dskiekflkngslqknekeeelsriqeelkeaqellde 75 
                                   L+ +++++ +L++e++ + + + eiD ++ +l+  +       +s  ek++ + ++++++++ ++++ q++++e+   lde
  gi|14601261|ref|NP_147796.1| 414 LQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVdavrlevESLGEKLV-QAEEKNQRQDASIEDFQSQIQELRTQLDE 493
                                   77889**********************998888888655666566666666.54556666666666*************** PP

                                   HHHHHHHHH CS
                           ING  76 Kiqlaqqal 84 
                                   K   aqq++
  gi|14601261|ref|NP_147796.1| 494 KTREAQQTA 502
                                   **9999986 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.7     0.081       5.9      30     123 ..     247     343 ..     237     358 .. 0.74
   2 !   16.6  10.2   5.6e-05    0.0041     198     284 ..     350     433 ..     336     436 .. 0.85
   3 ?    2.9  10.7      0.81        60     189     270 ..     419     500 ..     415     507 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.081
                     Rab5-bind  30 ellrraneqLekerkdkkeLedslkelseetskqvselakrvkksEllleeLqqafs...kakrniqeqlavlvksreqve 107
                                   +l ++a e+L  +++  +e    l+ + e+ + q+s l +rv + E + +++++  +   ++ +++   +  + ++++ ++
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEaveGSLEDLSGAVDAMSQQLQALA 327
                                   677888888888888888888888888999999999999999999999999998665111455666667777777788888 PP

                     Rab5-bind 108 delvrLqkdyesLlGk 123
                                   ++l  L+   e L  +
  gi|14601261|ref|NP_147796.1| 328 EDLESLSSRVEDLEAR 343
                                   8888888888877655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.6e-05
                     Rab5-bind 198 eierlkeelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqrLqtE 278
                                    +++  e+   i+sl + l+ ++ e e+l + lae+++ l++l+t+ +++ + l++l++  a++e+ ++   +   +Lq E
  gi|14601261|ref|NP_147796.1| 350 RLSQAEED---IDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAE 427
                                   34444444...556999**************************************************************** PP

                     Rab5-bind 279 LDvseq 284
                                   +++ +q
  gi|14601261|ref|NP_147796.1| 428 VETLQQ 433
                                   988665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.81
                     Rab5-bind 189 EnlEetlqleierlkeelasissl....kveleeikvekeslekslae....ktrq...ldklqtikselEeqlkelekek 258
                                   E+l ++lq+e+e l++ +  i+ +    +  ++ +++e esl + l +    ++rq   ++++q+ ++el +ql e ++  
  gi|14601261|ref|NP_147796.1| 419 EDL-ASLQAEVETLQQSIVEIDRRlgqlRSTVDAVRLEVESLGEKLVQaeekNQRQdasIEDFQSQIQELRTQLDEKTR-- 496
                                   444.578888888888887776541111556677778887765543220001111122255555555555555555444.. PP

                     Rab5-bind 259 aaveqlvleekn 270
                                           e ++
  gi|14601261|ref|NP_147796.1| 497 --------EAQQ 500
                                   ........4444 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       6.4   4.7e+02      20      42 ..     249     271 ..     247     274 .. 0.92
   2 ?    3.1   0.0       1.2        86      23      44 ..     273     294 ..     271     295 .. 0.91
   3 ?    7.1   0.1     0.067         5      19      41 ..     304     326 ..     302     329 .. 0.93
   4 !   12.0   0.6    0.0019      0.14      21      44 ..     320     343 ..     317     344 .. 0.90
   5 ?    5.7   0.4      0.18        13      19      39 ..     353     380 ..     352     384 .. 0.66
   6 ?    9.7   1.6      0.01      0.75      20      45 .]     382     407 ..     380     407 .. 0.92
   7 ?    3.7   0.8      0.77        57      20      42 ..     410     432 ..     408     435 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 6.4
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil  20 VeseiqaLtqkLeavtkRlealE 42 
                                   Ve+++++L   L++  +R+ +lE
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERVGDLE 271
                                   999***************99998 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil  23 eiqaLtqkLeavtkRlealEnk 44 
                                   ++++Lt +L++  +R+ alE++
  gi|14601261|ref|NP_147796.1| 273 AVEDLTLQLSSLDSRVGALEDR 294
                                   5899****************98 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.067
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil  19 kVeseiqaLtqkLeavtkRleal 41 
                                   +Ve ++++L+   +a+++ l+al
  gi|14601261|ref|NP_147796.1| 304 AVEGSLEDLSGAVDAMSQQLQAL 326
                                   79*******************98 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil  21 eseiqaLtqkLeavtkRlealEnk 44 
                                   ++++qaL + Le+ ++R+e+lE +
  gi|14601261|ref|NP_147796.1| 320 SQQLQALAEDLESLSSRVEDLEAR 343
                                   5789******************88 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHH.......HHHHHHHHH CS
                Matrilin_ccoil  19 kVeseiqaLtqk.......LeavtkRle 39 
                                   ++e++i++Lt+        Le+ + Rl+
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSldslrteLEDLSTRLA 380
                                   6778888888863344444777777776 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.01
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil  20 VeseiqaLtqkLeavtkRlealEnkl 45 
                                   ++ ++++L+++L+ v++ l++l+ +l
  gi|14601261|ref|NP_147796.1| 382 AQASLEDLNTRLDQVASTLQQLQQRL 407
                                   7899******************9986 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.77
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                Matrilin_ccoil  20 VeseiqaLtqkLeavtkRlealE 42 
                                   +e+++qaLt+ L++    +e+l+
  gi|14601261|ref|NP_147796.1| 410 AEESLQALTEDLASLQAEVETLQ 432
                                   799*********99888888776 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   3.7     0.041         3      31     104 ..     270     340 ..     242     354 .. 0.47
   2 !   17.2  13.4   5.9e-05    0.0044      12     106 ..     335     433 ..     331     437 .. 0.87
   3 ?    4.2   7.7      0.65        48      18      90 ..     425     494 ..     423     505 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.041
                   TMF_TATA_bd  31 lkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDl 104
                                   l+  +e l+ + +++ + + +l    +++++ +++le +e +le+l+   +++ + l+  +E  e L   v+Dl
  gi|14601261|ref|NP_147796.1| 270 LEFAVEDLTLQLSSLDSRVGALE---DRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDL 340
                                   55555555555555554444443...333334444444444444444444444444444444444444444443 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.9e-05
                   TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklm....keneelkelkkeleelekeleelqeryetlLellG 88 
                                   + ve l++++ + E  l++++e++ +l+++ d++r e+ +l+    +   +l++l+++l+++ + l++lq+r+ t+ e l+
  gi|14601261|ref|NP_147796.1| 335 SRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLStrlaEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQ 415
                                   5699*********************************988872222455667888999999999***************** PP

                   TMF_TATA_bd  89 eksEeveELraDvaDlKe 106
                                     +E    L+a+v+ l +
  gi|14601261|ref|NP_147796.1| 416 ALTEDLASLQAEVETLQQ 433
                                   *************98865 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.65
                   TMF_TATA_bd  18 sseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGek 90 
                                   ++e+  l+  + ++ ++l +l +  d++r e+ +l    e+l +++++++ + +++e+ q++ ++l + l ek
  gi|14601261|ref|NP_147796.1| 425 QAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLG---EKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEK 494
                                   444444444444555544444444444444444332...3344444444444444444444444444444444 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       2.9   2.1e+02       5      29 ..     260     284 ..     249     287 .. 0.85
   2 ?    6.7   0.0      0.07       5.2       2      29 ..     285     312 ..     277     328 .. 0.60
   3 ?    7.6   0.1     0.038       2.8       1      30 [.     333     362 ..     326     370 .. 0.73
   4 ?    1.6   0.3       2.5   1.9e+02       1      33 [.     368     400 ..     368     412 .. 0.83
   5 ?    3.4   0.8      0.74        54       6      44 ..     401     440 ..     396     473 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 2.9
                       DUF4988   5 vndlkdrvaaleeqvkelndnieal 29 
                                   +++l++rv  le +v++l  ++++l
  gi|14601261|ref|NP_147796.1| 260 LDSLEERVGDLEFAVEDLTLQLSSL 284
                                   7899999999999999998888877 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.07
                       DUF4988   2 eddvndlkdrvaaleeqvkelndnieal 29 
                                   +++v +l+drva +e ++++++ ++e l
  gi|14601261|ref|NP_147796.1| 285 DSRVGALEDRVADIEGRLEAVEGSLEDL 312
                                   4455555555555555555555555544 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.038
                       DUF4988   1 leddvndlkdrvaaleeqvkelndniealk 30 
                                   l ++v+dl+ rv ++e ++++ +++i++l 
  gi|14601261|ref|NP_147796.1| 333 LSSRVEDLEARVGSVEDRLSQAEEDIDSLT 362
                                   456777777777777777777777777775 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 2.5
                       DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkll 33 
                                   l+ +++dl  r a  ++ +++ln+ +++++  l
  gi|14601261|ref|NP_147796.1| 368 LRTELEDLSTRLAEAQASLEDLNTRLDQVASTL 400
                                   67899*******************998876655 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.74
                       DUF4988   6 ndlkdrvaaleeqvkelndniealkkll.eegkvitevee 44 
                                   ++l++r a+ ee +++l +++++l++ + + ++ i+e+++
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLASLQAEVeTLQQSIVEIDR 440
                                   5666666666666666666666666555344455555544 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       5.9   4.4e+02      21      57 ..     242     278 ..     228     289 .. 0.69
   2 ?    8.1   0.1     0.029       2.1      20      58 ..     318     356 ..     274     366 .. 0.49
   3 !    9.9   3.1    0.0084      0.62      16      90 ..     321     395 ..     309     412 .. 0.42
   4 ?    5.3  11.6       0.2        15      18     110 ..     379     485 ..     367     516 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 5.9
                                   ...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SKA1  21 lkedlskieaevsaleellnklkkelqeeeeaikklk 57 
                                   l+e ls +e++v+ l   l++l++++ + e a ++l+
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLT 278
                                   5667777777777777777777777777776666665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.029
                                   ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SKA1  20 llkedlskieaevsaleellnklkkelqeeeeaikklkk 58 
                                   ++++ l+++ +++++l + +++l++++ + e+ ++++++
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEE 356
                                   223333333333333333333333333333333333333 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0084
                                   ........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXX CS
                          SKA1  16 qdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassa 90 
                                   q+ ++l edl+ +++ v+ le  + +++++l + ee i++l+  ++  +++ e l+  +++  + l++ ++   +
  gi|14601261|ref|NP_147796.1| 321 QQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   333333444444444444444444444444444444444444333333333333333333333333333333222 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.2
                                   ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          SKA1  18 pallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpkktaassaeesksssp 98 
                                    a ++  l+++++ + ++ ++l++l+++l++ ee ++ l++++   + + e lq+   ++ ++l + +++  a++ + +s 
  gi|14601261|ref|NP_147796.1| 379 LAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESL 459
                                   455677888889999999999999999999999999999988877777777799999999998888777777665555444 PP

                                   XXXXXXXXXXX................X CS
                          SKA1  99 eeeeeteskke................k 110
                                    e+    +++e                +
  gi|14601261|ref|NP_147796.1| 460 GEKL--VQAEEknqrqdasiedfqsqiQ 485
                                   4333..2222201233333333333331 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 !   12.6   7.0     0.002      0.15      17      93 ..     306     382 ..     291     410 .. 0.73
   2 ?    9.4  12.8     0.019       1.4      15     113 ..     409     504 ..     407     530 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.002
                                   HHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                       T3SSipB  17 nkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                   + SL++L+  ++a  ++ +a  e ++ lS  ++++      + d l +a e +d++    d +   +++  +rl e 
  gi|14601261|ref|NP_147796.1| 306 EGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEA 382
                                   569******************************99999999999999999988888777776666555555544443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.019
                                   HHHHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--- CS
                       T3SSipB  15 lgnkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaP 95 
                                   +++ SL++L++ la  +a  +  q+   ++   l ++ s  +++  ++e   ek+ qa+ + +  ++ +++ q +++eL  
  gi|14601261|ref|NP_147796.1| 409 TAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRT 489
                                   5789***************************************************************************32 PP

                                   ------CHHHHHHHHH.. CS
                       T3SSipB  96 dePekakleaaeqQagaa 113
                                      +  +  ++ qQ +  
  gi|14601261|ref|NP_147796.1| 490 ---QLDEKTREAQQTAST 504
                                   ...223333333333322 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 ?    5.2   0.3      0.32        24      35      72 ..     307     357 ..     242     358 .. 0.69
   2 !   10.9   2.1    0.0054       0.4       8      71 ..     329     391 ..     319     395 .. 0.84
   3 !   10.8   2.2    0.0057      0.42      24      70 ..     401     446 ..     392     449 .. 0.84
   4 ?    3.6   3.1         1        76      20      69 ..     453     501 ..     450     505 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.32
                        Cnn_1N  35 e.............eqkeellkenielkveveslqkelkekkkllreaeka 72 
                                                 +q ++l + +  l  +ve+l+  + + +++l +ae++
  gi|14601261|ref|NP_147796.1| 307 GsledlsgavdamsQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEED 357
                                   133344434445555667777777777777777777777777777777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0054
                        Cnn_1N   8 qidkLkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaek 71 
                                    ++ L+    dL  r+   e+rl + +e ++++l  ++  l++e+e+l   l e + +l+++++
  gi|14601261|ref|NP_147796.1| 329 DLESLSSRVEDLEARVGSVEDRLSQAEE-DIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNT 391
                                   5566666667888888899999999888.9***************************9999876 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0057
                        Cnn_1N  24 yfLeerleklseeqkeellkenielkveveslqkelkekkkllreae 70 
                                   + L++rl   + e+ ++l + +  l+ eve+lq+++ e +++l ++ 
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAE-ESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLR 446
                                   45666666555.599*************************9998875 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 1
                        Cnn_1N  20 KLriyfLeerleklse..eqkeellkenielkveveslqkelkekkkllrea 69 
                                   +L++  L e+l + +e  + +++  ++  + + ++++l+ +l+ek+++ ++ 
  gi|14601261|ref|NP_147796.1| 453 RLEVESLGEKLVQAEEknQ-RQD--ASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   5777778888877777422.222..223478888888888888888877775 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.9     0.032       2.3      10     132 ..     242     364 ..     235     368 .. 0.90
   2 !   14.6  24.6    0.0003     0.022       2     151 ..     353     500 ..     352     515 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.032
                           ERM  10 leerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaele 90 
                                   leerL  +++ +e    aL   ee++  L+   + +  +   L+ +  ++e   + ++ + e+ e + e+l   +++++++
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQ 322
                                   899999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                           ERM  91 aarleeeserkeeeaerLkeeleeareaeeeakekllealst 132
                                   ++ l+e+ e   + +e L++++  +++++ +a+e +  ++++
  gi|14601261|ref|NP_147796.1| 323 LQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTS 364
                                   999999999999999999999999999999999988877765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.0003
                           ERM   2 eaerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekekler 82 
                                   +ae + + l   L +l+ e e     L e++   e L+ ++ ++    ++L+q+ a aee  q+l e+ +  ++e e l++
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQ 433
                                   68888899999********************************************************************** PP

                           ERM  83 klreaeleaarleeeserkeeeaerLkeeleeareaeeeakekllealstpsks.eseenveeseteeee 151
                                    + e ++++ +l++ +++   e+e L e+l +a+e+++++ + + ++ s+ ++  +   + +e+++e ++
  gi|14601261|ref|NP_147796.1| 434 SIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELrT---QLDEKTREAQQ 500
                                   ******************************************99999999953331...22222222222 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.4    0.0042      0.31      86     154 ..     274     342 ..     263     345 .. 0.92
   2 !   15.8   1.8   9.6e-05    0.0071      87     154 ..     317     384 ..     308     387 .. 0.93
   3 ?    6.5  18.0     0.073       5.4      23     155 ..     366     497 ..     347     502 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0042
                          DegS  86 akelqvelallrekEkqlrerRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledlkq 154
                                   +++l ++l+ l ++   l +r  ++e rL+ ++ ++e     v  ++  l+ L +dl+++s+++edl+ 
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEA 342
                                   56888999999999999************************************************9986 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.6e-05
                          DegS  87 kelqvelallrekEkqlrerRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledlkq 154
                                   +++  +l+ l e  ++l +r ++le r+ ++++ + +Ae+ + ++++ l+ L+++l+++s++l +++ 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQA 384
                                   56778999999999*************************************************99986 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.073
                          DegS  23 EsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYeeakelqvelallrekEkql 103
                                   +s r+e+e+l++ l+e +  ++++ ++ d++++  ++ ++rLa+ + + +  +e ++ +   e+++lq +++   ++  ql
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTE-DLASLQAEVETLQQSIVEIDRRLGQL 445
                                   678**********************************************99886.7899999******************* PP

                          DegS 104 rerRdelerrLkklketierAeklvsqvgvvlnyLsgdlkqvsekledlkqk 155
                                   r+  d +  ++++l e + +Ae+  ++    ++  +++++++ ++l++  ++
  gi|14601261|ref|NP_147796.1| 446 RSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   ********************************************99876554 PP

>> IL11  Interleukin 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   2.6    0.0034      0.25      45     141 ..     328     430 ..     309     442 .. 0.71
   2 ?    8.3   0.4     0.022       1.6      46     139 ..     420     518 ..     417     532 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0034
                          IL11  45 ksLPalsnsasdlssl..evkstLsqLhtdlksyekHfdWLkkvskk...skhslepklgelisklkrLlkslqllmskle 120
                                   ++L +ls++++dl++    v++ Lsq + d+ s    +d L++  +    + + ++ +l++l ++l+++++ lq+l ++l+
  gi|14601261|ref|NP_147796.1| 328 EDLESLSSRVEDLEARvgSVEDRLSQAEEDIDSLTTSLDSLRTELEDlstRLAEAQASLEDLNTRLDQVASTLQQLQQRLA 408
                                   5788999******9853479**********************998864434455567788888888888888887777776 PP

                          IL11 121 aprvpv..vspslppssatawev 141
                                     +     ++  l++  + + e 
  gi|14601261|ref|NP_147796.1| 409 TAEESLqaLTEDLASL-QAEVET 430
                                   5443322244555444.333333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.022
                          IL11  46 sLPalsnsasdlss..levkstLsqLhtdlksyekHfdWLkk....vskkskhslepklgelisklkrLlkslqllmskle 120
                                   +L +l+ +++ l++  +e+   L qL++ +   +  ++ L +    +++k++   + ++++ +s++++L ++l++   + +
  gi|14601261|ref|NP_147796.1| 420 DLASLQAEVETLQQsiVEIDRRLGQLRSTVDAVRLEVESLGEklvqAEEKNQ-RQDASIEDFQSQIQELRTQLDEKTREAQ 499
                                   5677777777775333899999999999999999999887541111444444.45599********************999 PP

                          IL11 121 aprvpvvspslppssataw 139
                                   +++++ +  s+++  a+  
  gi|14601261|ref|NP_147796.1| 500 QTASTASRWSMAAAGASLI 518
                                   9999988887777665555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.11       8.4      37      78 ..     303     344 ..     287     348 .. 0.82
   2 ?    9.8   0.2     0.013      0.96      11      79 ..     312     380 ..     301     384 .. 0.66
   3 !   12.5   4.9    0.0018      0.14      10      73 ..     374     437 ..     365     445 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.11
                          KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                   + ++  l++l+  +    + l+ + +dLes+ ++++ l+a++
  gi|14601261|ref|NP_147796.1| 303 EAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   5667788889999999999*******************9986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.013
                          KxDL  11 ldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                   l+ ++++ +q ++ l +  + L+   + +++r+ ++++r+ q  +++ ++   L+s++  ++ l ++la
  gi|14601261|ref|NP_147796.1| 312 LSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLA 380
                                   445555555555555555566666666677777777777777777777777777777777777777766 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0018
                          KxDL  10 dldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirs 73 
                                   dl++ la  +  +  ln    ++    +++q+rla +++ ++  t++l +++++ e++++ i  
  gi|14601261|ref|NP_147796.1| 374 DLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE 437
                                   4444444444455555555555555555555555555555555555555555555555555555 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.3     0.002      0.15      68     127 ..     274     333 ..     269     342 .. 0.86
   2 ?   10.5   1.4    0.0059      0.43      68     112 ..     316     360 ..     312     380 .. 0.68
   3 ?    7.9  10.3     0.037       2.7      66     141 ..     356     431 ..     351     434 .. 0.86
   4 ?    0.8  24.5       5.7   4.2e+02      24     144 ..     377     497 ..     371     513 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.002
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YscO  68 lekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlv 127
                                   +e++  q+++L  ++  le++v++++ +lea +  l++++ ++ + +++++ +ae  + +
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESL 333
                                   788889999999999999999999999999999999999999999999999888876655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0059
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YscO  68 lekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqe 112
                                   ++++ qq+++L e  ++l ++ve++++++   +++l qa++ +  
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDS 360
                                   677777777777777777777777777777777777777766544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.037
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YscO  66 kelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqerkEeq 141
                                   ++++ +   + +Lr + ++l ++++ea++ le   ++l+q    lq+ ++ ++  +e  + + ++ + +q   E +
  gi|14601261|ref|NP_147796.1| 356 EDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   789999999999999999*********9999999999999999999999999998888888888877777666655 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 5.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          YscO  24 qalaeareaheqaresladyrawraqeearlyaeiigklvllkelekvkqqvalLrekeaelekqveeakqqleaerealr 104
                                    +laea++ +e+   +l+++  +++q ++rl  +  +  +l+++l  ++++v  L++   e   ++ +++ +++a r +++
  gi|14601261|ref|NP_147796.1| 377 TRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVE 457
                                   689999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG CS
                          YscO 105 qarkelqearraveKfaelarlvraeasrqqerkEeqelE 144
                                   ++ ++l +a+ + ++ ++  +++++  + ++ ++ e   E
  gi|14601261|ref|NP_147796.1| 458 SLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   9999999999999999999999999999999999887655 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       7.4   5.5e+02      46      66 ..     262     282 ..     233     289 .. 0.69
   2 ?   15.6   0.3   0.00017     0.013      11      65 ..     290     344 ..     285     353 .. 0.90
   3 ?    1.2   6.9       5.5   4.1e+02       3      65 ..     402     463 ..     372     468 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 7.4
                     MbeD_MobD  46 aLseqvtgLsqQVesLseqvr 66 
                                    L+e+v +L   Ve+L  q++
  gi|14601261|ref|NP_147796.1| 262 SLEERVGDLEFAVEDLTLQLS 282
                                   577777777777777776665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 0.00017
                     MbeD_MobD  11 AlEqLQqdYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqv 65 
                                   AlE   +d e rl++ e + ++l   ++ +++++ aL e  + Ls  Ve+L  +v
  gi|14601261|ref|NP_147796.1| 290 ALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   89999999*******************************************9887 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 5.5
                     MbeD_MobD   3 elekqLLsAlEqLQqdYeqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqv 65 
                                   +l+++L  A E+LQ+  +  l   +   + lq+ +    r +++L+  v+     VesL e++
  gi|14601261|ref|NP_147796.1| 402 QLQQRLATAEESLQA-LTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKL 463
                                   688888888888886.56678888888888888888888888899999999999999998876 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6    0.0026      0.19       9     106 ..     278     376 ..     273     398 .. 0.73
   2 ?    8.0  10.1     0.043       3.2       8     103 ..     396     498 ..     390     508 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0026
                       zf-C4H2   9 tleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeey 89 
                                   tl+l++l +++ +  + + + e  le ++  le L+    a +++L+ + +D+++l s +++ e      +++ +++ e++
  gi|14601261|ref|NP_147796.1| 278 TLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDI 358
                                   678888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                       zf-C4H2  90 kklkeevnelrse.lgle 106
                                   + l +++++lr+e   l+
  gi|14601261|ref|NP_147796.1| 359 DSLTTSLDSLRTElEDLS 376
                                   888888888888733333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.043
                       zf-C4H2   8 ktleleklknklakevealekeekcleeykkelelLeq...EkmaHveeLrl....IhaDinalEsvikeaeeekekslek 81 
                                     + l++l+++la++ e+l++ ++ l + ++e+e+L+q   E    + +Lr     ++  +++l + + +aee+++++ ++
  gi|14601261|ref|NP_147796.1| 396 VASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQsivEIDRRLGQLRStvdaVRLEVESLGEKLVQAEEKNQRQDAS 476
                                   567899*******************************95556677777887432235667888889999************ PP

                       zf-C4H2  82 akklyeeykklkeevnelrsel 103
                                   ++ + +++++l+++++e  +e 
  gi|14601261|ref|NP_147796.1| 477 IEDFQSQIQELRTQLDEKTREA 498
                                   ****************988874 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.8     0.012      0.86       3      71 ..     271     340 ..     270     343 .. 0.91
   2 ?    7.3   0.3     0.078       5.7      12      47 ..     350     392 ..     340     399 .. 0.67
   3 ?   10.0   2.9     0.011       0.8       2      47 ..     396     441 ..     395     453 .. 0.91
   4 ?    2.8   1.5       1.9   1.4e+02      22      64 ..     444     487 ..     440     504 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.012
                          Rx_N   3 sallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaee.rqikdeavkeWlkelrdlaydaeDv 71 
                                   +++++ L+  l++  +++  +++ +  ++ +Le++++ Led +   +  ++++++  ++l  l+  +eD+
  gi|14601261|ref|NP_147796.1| 271 EFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGaVDAMSQQLQALAEDLESLSSRVEDL 340
                                   6788888888999999***************************9455599******************96 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.078
                          Rx_N  12 llaeea.......kllkgvkeeleklkdeLesiqavLedaeer 47 
                                    l++         ++l +++ ele l ++L   qa Led   r
  gi|14601261|ref|NP_147796.1| 350 RLSQAEedidsltTSLDSLRTELEDLSTRLAEAQASLEDLNTR 392
                                   4444444455666777788888888888888888888887665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.011
                          Rx_N   2 vsallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaeer 47 
                                   v + lq+L + la   ++l+ + e+l +l+ e e++q+ + + ++r
  gi|14601261|ref|NP_147796.1| 396 VASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRR 441
                                   6789*************************************99997 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 1.9
                          Rx_N  22 gvkeeleklkdeLesiqavLedaeerqi.kdeavkeWlkelrdl 64 
                                   ++++ ++  + e es+   L +aee+++ +d +++   +++++l
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQrQDASIEDFQSQIQEL 487
                                   56666777777777777777788775554777777777777776 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1         1        76      50      73 ..     315     338 ..     254     356 .. 0.60
   2 ?    8.9   0.6     0.016       1.2      43      76 ..     350     383 ..     318     389 .. 0.79
   3 ?    3.5   0.1       0.7        52      51      77 ..     386     412 ..     382     419 .. 0.87
   4 ?    2.5   0.4       1.4   1.1e+02      13      76 ..     428     467 ..     421     498 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1
                          RPW8  50 eieklnkeldrpreeieeLkklLe 73 
                                    ++ ++++l+   e++e+L ++ e
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLESLSSRVE 338
                                   344455555555555555544444 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.016
                          RPW8  43 ritPvvkeieklnkeldrpreeieeLkklLekae 76 
                                   r++   ++i++l++ ld+ r e+e+L  +L +a+
  gi|14601261|ref|NP_147796.1| 350 RLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQ 383
                                   45556689**********************9997 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.7
                          RPW8  51 ieklnkeldrpreeieeLkklLekaek 77 
                                   +e ln++ld+  + +++L+++L  ae+
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRLATAEE 412
                                   799********************9987 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 1.4
                          RPW8  13 lgellkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkklLekae 76 
                                   ++ l + i+e  ++  + +s+++                          r e+e+L ++L +ae
  gi|14601261|ref|NP_147796.1| 428 VETLQQSIVEIDRRLGQLRSTVDA------------------------VRLEVESLGEKLVQAE 467
                                   444444444444444444444444........................4444444444444443 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 ?    5.2   0.2      0.24        18      74     104 ..     240     270 ..     228     280 .. 0.85
   2 ?   12.5   2.8    0.0013     0.093      18     112 ..     289     383 ..     280     387 .. 0.91
   3 ?    3.5   5.8      0.82        60      56     107 ..     383     434 ..     378     441 .. 0.66
   4 ?    6.3   5.0      0.11       8.2      58     106 ..     455     503 ..     452     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.24
                        Nsp1_C  74 nkidqeLeyiesqqdeLeslLdnyEkeleel 104
                                   + ++++L+++e+  ++L   Ld++E+++ +l
  gi|14601261|ref|NP_147796.1| 240 APLEERLSLVEQAVEDLGLALDSLEERVGDL 270
                                   6799**********************98776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0013
                        Nsp1_C  18 ktldelinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyE 98 
                                     l++ +   +  Le  e   e+ +  v +  + L    e +++L s v++ e+    ++++L+  e++ d L++ Ld++ 
  gi|14601261|ref|NP_147796.1| 289 GALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLR 369
                                   578899999999999999999999999****************************************************** PP

                        Nsp1_C  99 keleellsklesqk 112
                                   +ele+l+ +l+ ++
  gi|14601261|ref|NP_147796.1| 370 TELEDLSTRLAEAQ 383
                                   ******98887766 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.82
                        Nsp1_C  56 gekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsk 107
                                      +++L++ + ++ ++ +++ q+L   e++ + L++ L+++ +e+e+l+++
  gi|14601261|ref|NP_147796.1| 383 QASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   4455667777777777777777777777777777777777777777776655 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.11
                        Nsp1_C  58 kIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleells 106
                                   ++++L +++++ae+++++ d ++e ++sq +eL + Ld+  +e+++  s
  gi|14601261|ref|NP_147796.1| 455 EVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   578999*******************************988777776655 PP

>> LMP  LMP repeated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1      0.14        11      31      83 ..     323     374 ..     290     384 .. 0.77
   2 ?    6.3   0.7      0.11       8.2      12      65 ..     392     447 ..     380     462 .. 0.76
   3 ?    7.3   0.5     0.056       4.1       7      49 ..     475     517 ..     469     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.14
                           LMP  31 nqalnsnntasmqsakssLdakvteitkkLekFnkdkeakFkeLeqtRkdiee 83 
                                    qal  ++ +s+ s  + L+a+v  ++++L + ++d +     L+  R ++e+
  gi|14601261|ref|NP_147796.1| 323 LQAL-AEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELED 374
                                   3344.578889999999999999999999999999988888888888877776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.11
                           LMP  12 nDkeiqkakkeLekeiqkanqaln..snntasmqsakssLdakvteitkkLekFnk 65 
                                   +  +++ + ++L++ +  a+++l+   ++ as+q+  + L++ + ei+ +L + + 
  gi|14601261|ref|NP_147796.1| 392 RLDQVASTLQQLQQRLATAEESLQalTEDLASLQAEVETLQQSIVEIDRRLGQLRS 447
                                   4455667777888888888888763358999****************999987765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.056
                           LMP   7 akLiDnDkeiqkakkeLekeiqkanqalnsnntasmqsakssL 49 
                                   a + D  ++iq+++++L+++ ++a+q+       sm +a  sL
  gi|14601261|ref|NP_147796.1| 475 ASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSMAAAGASL 517
                                   66789999****************************9999988 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  15.7   0.00055     0.041     546     707 ..     330     489 ..     313     498 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00055
                         Nup88 546 lkkqelvreeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkv...lkrlnsklpvl 623
                                   l+  +   e++e rv  ++++ +q +e++ sl  + +sl+ + e l +++ e++   e+l  r+++v   l++l+++l + 
  gi|14601261|ref|NP_147796.1| 330 LESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVastLQQLQQRLATA 410
                                   5555555688999*************************************************9998833355555555555 PP

                         Nup88 624 seaeremkkelekikeklkslknalkqvkkkldkqrkqiakskeeekksslelsekqkktikeiLk..eegeeieelikqv 702
                                    e+ +++ + l++++ ++++l++++ ++ ++l + r+ +++ + e       +++  +k ++   k   +  +ie+  +q+
  gi|14601261|ref|NP_147796.1| 411 EESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLE-------VESLGEKLVQAEEKnqRQDASIEDFQSQI 484
                                   555555666666666666666666666666655555555554333.......33333333322221002222344444444 PP

                         Nup88 703 kdikk 707
                                   +++++
  gi|14601261|ref|NP_147796.1| 485 QELRT 489
                                   44443 PP

>> DUF1411  Protein of unknown function (DUF1411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   0.00046     0.034      70     133 ..     353     419 ..     307     461 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00046
                       DUF1411  70 kklkalsdltktentektslsdisvklgpikksm...nlrvkdvdvdlellnkriavllkkvtnygP 133
                                   +  +++ +lt++ +  +t+l+d+s +l++++ s+   n r+ +v   l+ l++r+a+  + +   + 
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLedlNTRLDQVASTLQQLQQRLATAEESLQALTE 419
                                   3337889999*********************996333799****************97666655544 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.6   1.9e+02     389     422 ..     251     284 ..     242     294 .. 0.83
   2 ?   10.0   0.0    0.0028       0.2     363     413 ..     295     345 ..     291     361 .. 0.90
   3 ?    3.9   0.8      0.19        14     384     448 ..     386     450 ..     362     464 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.6
                                   TEEEBXSSXXTTTTHHHHHHHHHHHHHHHHHHHH CS
                 Hemagglutinin 389 kqleavgkelnelekrieeldkkvddgfldvity 422
                                   + +e +g +l+ le+r+ +l+  v+d+ l + + 
  gi|14601261|ref|NP_147796.1| 251 QAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSL 284
                                   56788999******************99987665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0028
                                   EEXHHHHHHHHHHHHHHHHHHHHHTTTEEEBXSSXXTTTTHHHHHHHHHHH CS
                 Hemagglutinin 363 aadkkstqeainkitkkvnsliekenkqleavgkelnelekrieeldkkvd 413
                                    ad +   ea+++  +++   ++ + +ql+a++++l+ l  r+e+l+ +v 
  gi|14601261|ref|NP_147796.1| 295 VADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVG 345
                                   58999999***************************************9985 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.19
                                   HHHTTTEEEBXSSXXTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Hemagglutinin 384 iekenkqleavgkelnelekrieeldkkvddgfldvityniellvllenerildfedsnvknlee 448
                                    e  n++l++v+  l +l++r+   ++ ++ +  d+ + ++e+  l +    +d +  ++++  +
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVD 450
                                   46678999999999999999999999999999999999999998887766666655555555555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1       1.4   1.1e+02      22      52 ..     270     300 ..     244     307 .. 0.71
   2 ?    9.2   0.3     0.014         1      19      48 ..     316     345 ..     309     350 .. 0.87
   3 ?    4.6   0.2      0.37        27      19      49 ..     351     381 ..     345     394 .. 0.70
   4 ?   10.5   4.3    0.0052      0.38      16      56 ..     397     437 ..     391     443 .. 0.86
   5 ?    2.0   6.5       2.4   1.8e+02      20      57 ..     457     494 ..     447     501 .. 0.78
   6 ?    2.0   2.7       2.3   1.7e+02      18      50 ..     476     508 ..     470     510 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                         DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                   l+  +++l+ +l +l  +  +Le++v+d + 
  gi|14601261|ref|NP_147796.1| 270 LEFAVEDLTLQLSSLDSRVGALEDRVADIEG 300
                                   4445677777888888888888888877754 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevk 48 
                                   + ++ q+++al ++l++l+ + e+Lea+v 
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVG 345
                                   567899*********************995 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.37
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                         DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkd 49 
                                   ++q +++i+ l+  l++l+ e e+L  ++++
  gi|14601261|ref|NP_147796.1| 351 LSQAEEDIDSLTTSLDSLRTELEDLSTRLAE 381
                                   5566777777777777777777777666554 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0052
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                         DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56 
                                    ++++ql+q +a+ ++ l++l+++ ++L+aev+ L+++   
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE 437
                                   6899*******************************866554 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                         DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyi 57 
                                    +l +++++ +++++++ a +e+ ++++++L+ + d  
  gi|14601261|ref|NP_147796.1| 457 ESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEK 494
                                   56778899999999999999999999999998655554 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 2.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                         DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                   ++ + +++i++l  +l++++ e ++ ++  +++
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQELRTQLDEKTREAQQTASTASRW 508
                                   456677888888888888888887777776666 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   0.00029     0.021      91     177 ..     278     364 ..     272     367 .. 0.95
   2 ?    5.1  13.4      0.21        16      92     174 ..     370     452 ..     363     459 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00029
                       DUF2968  91 taelaeveirrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqi 171
                                   t +l++ + r   le   a +e  ++a e  +e L+  ++ + qQ qa+ae  +++ + ++ Lea   +++++l+++++ i
  gi|14601261|ref|NP_147796.1| 278 TLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDI 358
                                   7899***************************************************************************** PP

                       DUF2968 172 rqLqaq 177
                                   ++L   
  gi|14601261|ref|NP_147796.1| 359 DSLTTS 364
                                   **9865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.21
                       DUF2968  92 aelaeveirrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqir 172
                                   +el +  +r ++ +a  + l+  + + ++ +++Lq+ la a++  qa++e  +++++e+++L++   ++ ++l +l+  ++
  gi|14601261|ref|NP_147796.1| 370 TELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVD 450
                                   456667777777777777777777777777777777777777777777777777777777777777777777777777776 PP

                       DUF2968 173 qL 174
                                   + 
  gi|14601261|ref|NP_147796.1| 451 AV 452
                                   65 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.4   0.00075     0.055      66     191 ..     291     405 ..     284     411 .. 0.71
   2 ?    7.1  21.7     0.056       4.1       7     187 ..     318     503 ..     315     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00075
                           LXG  66 lqdlieqyeefLkkikealesvepssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkds 146
                                   l+d ++++e +L+ + ++le++  + +++  ++ L+  l+ +l+ +++ +e+l+ ++ +    v d +s  e d++++++s
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAM--SQQLQ-ALAEDLESLSSRVEDLEARVGS----VEDRLSQAEEDIDSLTTS 364
                                   56667888888999999999976665554..34455.6667777777777777777766....88888888********** PP

                           LXG 147 lqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLee 191
                                   l++ + ++++  + l ++ ++    l++l+  l+++++++++L++
  gi|14601261|ref|NP_147796.1| 365 LDSLRTELEDLSTRLAEAQAS----LEDLNTRLDQVASTLQQLQQ 405
                                   *******99888888776655....55555555555555555544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.056
                           LXG   7 elieaieqlkseleelkeqleqlkkaiqklveledslkGkaaeaiknfyadlhlplltslqdlieqyeefLkkikealesv 87 
                                   ++ +++++l + le+l++ +e+l++++ +   +ed+l+ +a e i +  ++     l+sl++ +e+ +++L++ +++le+ 
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGS---VEDRLS-QAEEDIDSLTTS-----LDSLRTELEDLSTRLAEAQASLED- 388
                                   55566666666666666666666666666...899998.888888777777.....999999999999999999999999. PP

                           LXG  88 epssngfide..dfLeqelenglkkakevteelkdeinkil.................asvsdivslpelddsevkdslqk 149
                                       n+++d+  + L+ +l+++l  a+e++++l++ + +                    + + +v+ ++l+ +++ ++l +
  gi|14601261|ref|NP_147796.1| 389 ---LNTRLDQvaSTLQ-QLQQRLATAEESLQALTEDLASLQaevetlqqsiveidrrlGQLRSTVDAVRLEVESLGEKLVQ 465
                                   ...4456655337788.9999999999999999999999557888888888888899999999999999999999999999 PP

                           LXG 150 akkkvqetiekledfdqeqksalanlesdlkalktyvs 187
                                   a++k q++   +edf  + +++ ++l+++ ++++++ s
  gi|14601261|ref|NP_147796.1| 466 AEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   99999999999999999999999999999998888765 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.38        28      77     145 ..     278     327 ..     242     344 .. 0.48
   2 ?   10.1   5.4    0.0056      0.42      74     157 ..     317     403 ..     302     420 .. 0.64
   3 ?    9.2   4.9      0.01      0.76      57     134 ..     354     435 ..     344     440 .. 0.62
   4 ?    5.3   4.2      0.17        12      74     149 ..     436     506 ..     413     522 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.38
                  Allexi_40kDa  77 ttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetses 145
                                   t +Ls l +++ +l++ + +++                    +le++e sle+l   +d +s++ +   
  gi|14601261|ref|NP_147796.1| 278 TLQLSSLDSRVGALEDRVADIE-------------------GRLEAVEGSLEDLSGAVDAMSQQLQALA 327
                                   3334444444444444444444...................4455555555555555555544443322 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0056
                  Allexi_40kDa  74 lsqttlLselrdalrtltklldklksvekklelsaetasd..skllkklesietsleelhakldelsssetseseg.Psss 151
                                    +++++L+ l ++l+ l++ +++l++   ++e++ ++a++   +l+++l+s+ t+le+l ++l e  +s ++ +++  +++
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEdiDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRlDQVA 397
                                   456777888888888888888888888777776665554411456778888888888888888888777776655534444 PP

                  Allexi_40kDa 152 ptkass 157
                                   +t ++ 
  gi|14601261|ref|NP_147796.1| 398 STLQQL 403
                                   433332 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.01
                  Allexi_40kDa  57 ishdvdsiinklnpvs..llsqttlLselrdalrtltklldklksvekklelsaetasds..kllkklesietsleelhak 133
                                    ++d+ds+ ++l+++   l   +t L+e +++l+ l++ ld+++s+ ++l+++  ta++s   l+++l+s++ ++e+l++ 
  gi|14601261|ref|NP_147796.1| 354 AEEDIDSLTTSLDSLRteLEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESlqALTEDLASLQAEVETLQQS 434
                                   456677777777665411334567777888888888888888877777776666555443114556677777777777666 PP

                  Allexi_40kDa 134 l 134
                                   +
  gi|14601261|ref|NP_147796.1| 435 I 435
                                   5 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.17
                  Allexi_40kDa  74 lsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhakldelsssetsesegPs 149
                                   +     L +lr+++ +++ ++++l ++  + e++++++       ++e  + +++el ++lde +++++++ ++ s
  gi|14601261|ref|NP_147796.1| 436 VEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQ-----DASIEDFQSQIQELRTQLDEKTREAQQTASTAS 506
                                   33445566666666666666666665554444333222.....235777888888999999888888877776654 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       6.1   4.5e+02       2      34 ..     260     292 ..     259     298 .. 0.79
   2 ?    7.7   0.1     0.037       2.7       2      48 ..     330     376 ..     329     381 .. 0.91
   3 ?    2.4   0.1       1.7   1.2e+02       4      33 ..     388     417 ..     385     444 .. 0.54

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 6.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlE 34 
                                   l +leer+  le  +++++ + +  + ++  lE
  gi|14601261|ref|NP_147796.1| 260 LDSLEERVGDLEFAVEDLTLQLSSLDSRVGALE 292
                                   568999999999999999888888777666555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.037
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXX CS
                    Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlEnHleTlRkamlaLa 48 
                                   l++l  r+  le  +  v+++ ++ +e ++ l   l+ lR  + +L+
  gi|14601261|ref|NP_147796.1| 330 LESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   789999**********************************9987776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRl 33 
                                   dl  rl +++   q++ ++  + +e+l+ l
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQQRLATAEESLQAL 417
                                   555666666666666666666655555543 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       6.5   4.8e+02      41      88 ..     246     293 ..     240     304 .. 0.73
   2 ?   14.1   0.6   0.00046     0.034      34      96 ..     316     378 ..     310     382 .. 0.93
   3 ?    2.6   3.4       1.8   1.3e+02      40      87 ..     385     432 ..     368     442 .. 0.57
   4 ?    3.5   3.7      0.97        72      28      93 ..     432     501 ..     426     507 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 6.5
                      Noelin-1  41 lrqllekvqnlsqsievldlRtsrdlqy.vrktetllktlesklkvvee 88 
                                   l  +++ v++l   ++ l++R   dl++ v++   +l++l+s++  +e+
  gi|14601261|ref|NP_147796.1| 246 LSLVEQAVEDLGLALDSLEERV-GDLEFaVEDLTLQLSSLDSRVGALED 293
                                   5556667788888888888885.56765478888888899888877765 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00046
                      Noelin-1  34 rDarsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrkelsak 96 
                                    Da s+ql+ l e  + ls  +e l+ R  +  + ++++e+ +++l++ l++++ + + ls++
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTR 378
                                   5999************************************************99998888876 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 1.8
                      Noelin-1  40 qlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvve 87 
                                    l +l  +   ++ ++++l++R + + + ++   + l +l++++++++
  gi|14601261|ref|NP_147796.1| 385 SLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   455555555555555666666555555555555555555555555554 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.97
                      Noelin-1  28 aqdvCsrDarsrqlrqlle....kvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrkel 93 
                                   +q++ + D r  qlr+ ++    +v+ l +++ + +++ +r+   +++ ++++++l+++l++ + + ++ 
  gi|14601261|ref|NP_147796.1| 432 QQSIVEIDRRLGQLRSTVDavrlEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   677777888888888766512225678888888899999999999***************9887776654 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1       1.8   1.3e+02      51      83 ..     259     291 ..     243     299 .. 0.76
   2 ?    9.4   0.6     0.013      0.97      12      87 ..     263     337 ..     259     342 .. 0.85
   3 ?    8.6  13.5     0.024       1.7       9      85 ..     358     433 ..     336     440 .. 0.81
   4 ?    4.7   3.5      0.39        29      40      89 ..     451     500 ..     443     503 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 1.8
                                   HHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTX CS
                         Sec2p  51 kneklkeqLkeketlleslqeqLkeLkevlekm 83 
                                     ++l+e++ + e  +e+l  qL++L + +  +
  gi|14601261|ref|NP_147796.1| 259 ALDSLEERVGDLEFAVEDLTLQLSSLDSRVGAL 291
                                   567888888889999999999998887766555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXXX CS
                         Sec2p  12 aekekkklekEledLtasLFeeANkmVaaarkekealekkneklkeqLkeketlleslqeqLkeLkevlekmeees 87 
                                    e+   +le  +edLt +L     + V a + + +++e + e ++  L++    ++++++qL+ L e le+++++ 
  gi|14601261|ref|NP_147796.1| 263 LEERVGDLEFAVEDLTLQLS-SLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRV 337
                                   67788889999999999985.5677888888899999****************************99999988765 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXX CS
                         Sec2p   9 reeaekekkklekEledLtasLFeeANkmVaaarkekealekkneklkeqLkeketlleslqeqLkeLkevlekmee 85 
                                     +  ++ ++l +EledL+++L  eA     + + + +++    ++l+++L+ +e+ l++l e+L++L+  +e++++
  gi|14601261|ref|NP_147796.1| 358 IDSLTTSLDSLRTELEDLSTRL-AEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQ 433
                                   4555666778899999999999.578888888889999999999999999999999999999999999888877765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXXXXX CS
                         Sec2p  40 aarkekealekkneklkeqLkeketlleslqeqLkeLkevlekmeeesee 89 
                                   a r e e+l +k  + +e+ + +++ +e+ q+q +eL++ l + + e ++
  gi|14601261|ref|NP_147796.1| 451 AVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   55667777778888888888888999999999999999988877776655 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 ?    6.6   1.3      0.16        12      36      84 ..     288     336 ..     226     347 .. 0.65
   2 ?    8.0   0.6     0.055         4      36      70 ..     316     350 ..     294     361 .. 0.68
   3 ?    1.2  10.6       7.5   5.6e+02      20      75 ..     333     390 ..     322     419 .. 0.40
   4 ?    9.0  10.1     0.027         2      11      98 ..     390     487 ..     382     491 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.16
                  Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84 
                                      l++   +++  l+ +e  ledL  +v++++++ +    d + ls+r
  gi|14601261|ref|NP_147796.1| 288 VGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSR 336
                                   4455555666666677777777777777766655444333333333333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.055
                  Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLeetvrivekn 70 
                                    + ++++ + L + l+s++  +edLe  v+ ve  
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDR 350
                                   45667777788888888888888888888888765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 7.5
                  Syntaxin-6_N  20 lyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriveknpskfk 75 
                                   l +r e+l     s  ++ ++ +e  + L ++l+s++++ledL    + ++++ ++ +
  gi|14601261|ref|NP_147796.1| 333 LSSRVEDLEARVGSveDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLN 390
                                   4444444333333322233333333444444444444444444444322222111111 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.027
                  Syntaxin-6_N  11 qkslnkaeslyrrwe.rlledtss.s....tseeldetrteLrkalrsiewdledLeetvriv....eknpskfkidekel 81 
                                   +  l++++s++++ + rl + ++s +       +l+   + L++++ +i+  l +L+ tv++v    e+  +k    e++ 
  gi|14601261|ref|NP_147796.1| 390 NTRLDQVASTLQQLQqRLATAEESlQalteDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVrlevESLGEKLVQAEEKN 470
                                   5556666666666642333333333143334566666677788999999999999*9999988554466667877777777 PP

                  Syntaxin-6_N  82 srrrafveevreevkem 98 
                                   +r+ a +e+++++++e+
  gi|14601261|ref|NP_147796.1| 471 QRQDASIEDFQSQIQEL 487
                                   888999*******9987 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.3     0.023       1.7     244     709 ..     312     359 ..     259     381 .. 0.52
   2 ?   10.3   6.6    0.0016      0.12     626     704 ..     365     459 ..     359     470 .. 0.44
   3 ?    2.8   1.4       0.3        22     229     288 ..     444     503 ..     431     513 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.023
                      Prominin 244 llenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcldqlpnvdevl 324
                                   l  +                                                                             
  gi|14601261|ref|NP_147796.1| 312 LSGA----------------------------------------------------------------------------- 315
                                   2222............................................................................. PP

                      Prominin 325 ealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkiprealdavisdlenterssktfd 405
                                                                                                                    
  gi|14601261|ref|NP_147796.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                      Prominin 406 dvvekyekyrwliglivcsllllivvililgLlcGilGlsrtatptdrgcskntGasfLlvgvglsFlffsllmlvvlltF 486
                                                                                                                    
  gi|14601261|ref|NP_147796.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                      Prominin 487 lvGlnvyklvCeplesneLfrvlDtpgllpeldLsrllskklkknltisevikaCkanesifkvLrlnnlydieellnikk 567
                                                                                                                    
  gi|14601261|ref|NP_147796.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                      Prominin 568 lteeiqkelenlkvdlsnlelLteeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsngkknlk 648
                                                                                                                    
  gi|14601261|ref|NP_147796.1|   - ---------------------------------------------------------------------------------   -
                                   ................................................................................. PP

                      Prominin 649 qslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraenflk 709
                                                    v+ ++++++ l + +++l+++ +dl++++  + +++++ae+ ++
  gi|14601261|ref|NP_147796.1| 316 -----------------VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDID 359
                                   .................33333333333333333333333333333333333333333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0016
                      Prominin 626 letlaekleelanelsngk.................knlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensd 689
                                   l++l ++le+l+++l +++                 ++l+q+l ++ ++l+a+ ++l   l+++v++l++s+ ++d++  +
  gi|14601261|ref|NP_147796.1| 365 LDSLRTELEDLSTRLAEAQasledlntrldqvastlQQLQQRLATAEESLQALTEDL-ASLQAEVETLQQSIVEIDRRLGQ 444
                                   555555555555555555455511111111111222344555555555555554443.23555555555555555555555 PP

                      Prominin 690 lqesikkllaavera 704
                                   l+++++ +  +ve++
  gi|14601261|ref|NP_147796.1| 445 LRSTVDAVRLEVESL 459
                                   555555555554443 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.3
                      Prominin 229 tlesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqals 288
                                   +l+s+v  +  e+e+l+e+l +a+e+ +  +++ ++ +++ ++Lr+ l +  r+ +q++s
  gi|14601261|ref|NP_147796.1| 444 QLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   6888888888899***********999999999999999999999999999888888776 PP

>> DUF3829  Protein of unknown function (DUF3829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.85        63     189     246 ..     289     343 ..     276     351 .. 0.83
   2 ?   12.2   1.4    0.0013     0.093     145     264 ..     321     431 ..     317     447 .. 0.75
   3 ?    2.5   0.9       1.1        83     186     243 ..     447     501 ..     428     519 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.85
                       DUF3829 189 aklkkklddlekaleklekaskeekrkkpalesfkssakeflaaarkiirrirdkepy 246
                                    +l+  ++d+e +le+ e++ ++      a++++ ++++++ ++++++ +r++d e+ 
  gi|14601261|ref|NP_147796.1| 289 GALEDRVADIEGRLEAVEGSLEDLSG---AVDAMSQQLQALAEDLESLSSRVEDLEAR 343
                                   57888899999999999999999855...99999999999999999999999997765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0013
                       DUF3829 145 eelekikkdermikyytlklmieakqlidlidrdkitakneldlaklkkklddlekaleklekaskeekrkkpalesfkss 225
                                   ++l+++ +d ++ +  +  l   +  + d +++ +      +d+  l+++ld l+++le+l++  +e +   ++le+++  
  gi|14601261|ref|NP_147796.1| 321 QQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAE------EDIDSLTTSLDSLRTELEDLSTRLAEAQ---ASLEDLNTR 392
                                   55556665555555555556666666666677777......9**********************88883...79******* PP

                       DUF3829 226 akeflaaarkiirrirdkepysdsdkellksadsvegsp 264
                                   + ++ ++++++++r+++ e   +  +e+l s + + ++ 
  gi|14601261|ref|NP_147796.1| 393 LDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   ***************998877776666666555555554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 1.1
                       DUF3829 186 ldlaklkkklddlekaleklekaskeekrkkpalesfkssakeflaaarkiirrirdk 243
                                     + ++  +++ l + l+++e++ +    +++++e+f+s+++e+ +++++ +r++++ 
  gi|14601261|ref|NP_147796.1| 447 STVDAVRLEVESLGEKLVQAEEKNQR---QDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   55556666666666677777776333...568999******99999999988865554 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1       0.4        30      59     128 ..     291     360 ..     282     367 .. 0.77
   2 ?   10.9   3.6    0.0026      0.19      50     136 ..     429     515 ..     411     526 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.4
                      ISG65-75  59 tkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaek 128
                                    +d++a ie  +e+v+  +e+l + ++ + ++ ++ ++d e l + +e+ +a + + +++  +a e + +
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDS 360
                                   5778888888888888888888888888888888888888888888888888888888888777777655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0026
                      ISG65-75  50 etadyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaekas 130
                                   et ++ + e++++l+++ +++++v+ +ve l++ l +a+ek++ +++ +e+ +++++e   + +++ ++a++++++a + s
  gi|14601261|ref|NP_147796.1| 429 ETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWS 509
                                   666777789999*********************99999*************************************999988 PP

                      ISG65-75 131 kkakea 136
                                     a+ a
  gi|14601261|ref|NP_147796.1| 510 MAAAGA 515
                                   877655 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.037       2.7      13     120 ..     240     346 ..     232     349 .. 0.80
   2 ?   10.8   1.9    0.0062      0.45      17     120 ..     300     395 ..     290     398 .. 0.57
   3 ?    8.7   6.7     0.027         2       4     119 ..     336     450 ..     333     453 .. 0.67
   4 ?    1.7  10.1       3.9   2.9e+02       6     106 ..     401     504 ..     396     508 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.037
                       DUF5082  13 aelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdkldelidai 93 
                                   a l+++++ +e+ +e L  a ++l++    l+ + ++l+ +l s +s  G  e+ + +i+  le +++ + ++l  ++da+
  gi|14601261|ref|NP_147796.1| 240 APLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLE-AVEGSLEDLSGAVDAM 319
                                   5567777778888888888888888888888888888888888888888888888888888764.7899999999999999 PP

                       DUF5082  94 eeEIerLenqiseaqgvldtlqsqlns 120
                                   ++  + L+++++++++ ++ l+  ++s
  gi|14601261|ref|NP_147796.1| 320 SQQLQALAEDLESLSSRVEDLEARVGS 346
                                   999999999999999999888887766 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0062
                       DUF5082  17 seiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvdkldel...idaie 94 
                                   +          rL+++  +l+d + ++++  ++l+  + + es+  + e + +  + ++e+  ++ ++++d+l    d++ 
  gi|14601261|ref|NP_147796.1| 300 G----------RLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVE-DLEARVGSVEDRLSQAEEDIDSLttsLDSLR 369
                                   4..........55555555555555555555555555555555554433.2333333444444444444444411156777 PP

                       DUF5082  95 eEIerLenqiseaqgvldtlqsqlns 120
                                   +E e+L + + eaq +l+ l++ l++
  gi|14601261|ref|NP_147796.1| 370 TELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   88899999999999999888888876 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.027
                       DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirsnlessyqtyvd 84 
                                   + ++l+a++++ + ++++ ee+I  L +  ++l +e   l++  + l++  +s e ++ ++ +++ + +++l++   t ++
  gi|14601261|ref|NP_147796.1| 336 RVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTE---LEDLSTRLAEAQASLEDLN-TRLDQVASTLQQLQQRLATAEE 412
                                   5678999999*************9998655555554...4444455555555544443.4445555666655555555555 PP

                       DUF5082  85 kldel...idaieeEIerLenqiseaqgvldtlqsqln 119
                                    l +l    ++++ E+e+L+++i e  + l++l s ++
  gi|14601261|ref|NP_147796.1| 413 SLQALtedLASLQAEVETLQQSIVEIDRRLGQLRSTVD 450
                                   55555111367899999999999999999999998876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 3.9
                       DUF5082   6 sklqaqiaelrseiaaleekIerLk....eaktklsdekeslkqkkkklekplnssesWkGk.eennydgirsnlessyqt 81 
                                   ++lq++ a +++ ++al e+++ L+    +  +++++ + +l q ++ +    ++ es+  k  +++++++r+  + s++ 
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLASLQaeveTLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKlVQAEEKNQRQ--DASIED 479
                                   5788999999999999999999999888778888888899999999999999999999888877777777776..467888 PP

                       DUF5082  82 yvdkldelidaieeEIerLenqise 106
                                   +++++ el  +++e++++ +++ s+
  gi|14601261|ref|NP_147796.1| 480 FQSQIQELRTQLDEKTREAQQTAST 504
                                   8888888888888888877776665 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 ?    0.6   0.0       4.9   3.6e+02     193     242 ..     243     289 ..     215     305 .. 0.54
   2 ?    4.6  12.2      0.28        21     174     248 ..     358     435 ..     269     447 .. 0.64
   3 ?    4.7   5.9      0.26        20     191     258 ..     437     501 ..     429     512 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 4.9
                     Phage_GPO 193 darfadveeavelvAeevkelsekveallaleaelaalkkeveklkaele 242
                                   ++r + ve+ave++  ++ +l+e+v    +le ++++l+ ++++l++++ 
  gi|14601261|ref|NP_147796.1| 243 EERLSLVEQAVEDLGLALDSLEERVG---DLEFAVEDLTLQLSSLDSRVG 289
                                   34555555555555555555555555...333333333333333333333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.28
                     Phage_GPO 174 geslferikal......lskkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekL 248
                                     sl++++ +l      ls++ ++ +a   d++  +++vA+++++l+++++   ++e++l+al++++++l+ae+e+L++++
  gi|14601261|ref|NP_147796.1| 358 IDSLTTSLDSLrteledLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLA---TAEESLQALTEDLASLQAEVETLQQSI 435
                                   334444444433332333444444456666666666666666666666666...455566666666666666666666655 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.26
                     Phage_GPO 191 sddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsktdakekqr 258
                                   + d r  +++++v++v  ev++l ek+    ++e++++  ++++e+ ++++++L+++L+++ ++++q 
  gi|14601261|ref|NP_147796.1| 437 EIDRRLGQLRSTVDAVRLEVESLGEKLV---QAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   4588999999999999999999999988...77788888889999*************9988755443 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   8.2   0.00024     0.017      61     146 ..     256     344 ..     211     346 .. 0.87
   2 ?    6.6   0.7     0.065       4.8     120     145 ..     346     371 ..     344     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00024
                       DUF4349  61 ldafldelaelgkvtsrstsaeDVTeqyvDleaRlkaleasedrllallek.aksvedll....eiereLsevqaeiesle 136
                                   l  +ld+l+   +v + +  +eD+T q+  l++R+ ale+ ++ ++  le   +s+edl     + +++L+   +++esl 
  gi|14601261|ref|NP_147796.1| 256 LGLALDSLE--ERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAvEGSLEDLSgavdAMSQQLQALAEDLESLS 334
                                   455566666..567788999*****************************88799****97444467999************ PP

                       DUF4349 137 gqlryLdnqv 146
                                   ++ + L+ +v
  gi|14601261|ref|NP_147796.1| 335 SRVEDLEARV 344
                                   *******998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.065
                       DUF4349 120 eiereLsevqaeieslegqlryLdnq 145
                                   ++e++Ls+ +++i+sl+++l +L+ +
  gi|14601261|ref|NP_147796.1| 346 SVEDRLSQAEEDIDSLTTSLDSLRTE 371
                                   69*******************99875 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  13.0    0.0031      0.23      65     219 ..     291     452 ..     242     457 .. 0.65
   2 ?    4.6  14.7      0.26        19      62     165 ..     397     502 ..     382     530 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0031
                       DUF4618  65 leqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLstY.kDkeYpvkav..qIanlvrqlqqlk...dsqqde 139
                                   le+  a+++   e +e  le+L   ++++ +++q l e+l+ Ls+   D e  v +v  ++++  ++++ l    ds + e
  gi|14601261|ref|NP_147796.1| 291 LEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRvEDLEARVGSVedRLSQAEEDIDSLTtslDSLRTE 371
                                   555566666667777777788888888888888888888887776414666666666333566666666665222345666 PP

                       DUF4618 140 ldeleelikevleklskkiqk..kkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveq 218
                                   l++l+  + e  ++l++   +  +    l++l ++ l+  +e+L++ t + ++l+ e+e+ ++ i e+  ++ +L+++v++
  gi|14601261|ref|NP_147796.1| 372 LEDLSTRLAEAQASLEDLNTRldQVASTLQQL-QQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDA 451
                                   66666666666666654322200223334444.334444566777777777777777777777777777777777776666 PP

                       DUF4618 219 L 219
                                    
  gi|14601261|ref|NP_147796.1| 452 V 452
                                   5 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.26
                       DUF4618  62 kkqleqakaeLqeweek...eekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqde 139
                                   ++ l+q+++ L + ee    + ++l++L+ ++e l++ + +    l  L++  D       +++++l ++l q ++++q++
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQQRLATAEESlqaLTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDA----VRLEVESLGEKLVQAEEKNQRQ 473
                                   3345555655555555411145688899999999999999999999999999995....46899***99999999887765 PP

                       DUF4618 140 ...ldeleelikevleklskkiqkkkekl 165
                                      +++++  i+e +++l +k+++ ++  
  gi|14601261|ref|NP_147796.1| 474 dasIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   33377888888888888888887766543 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.0   0.00098     0.072     137     238 ..     265     366 ..     246     371 .. 0.88
   2 ?    8.9  26.4    0.0098      0.72      55     245 ..     313     499 ..     303     507 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00098
                      CCDC144C 137 fdvsnlkdknevLsqqLskaeskansLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnkyiakqe 217
                                     v +l  ++e L+ qLs  +s++  Le+ + +++  L      le +    +   +q++ l + +++  ++v+   a+  
  gi|14601261|ref|NP_147796.1| 265 ERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVG 345
                                   556667777899999****************************************************************** PP

                      CCDC144C 218 sleerlaqlqsenmlLrqqLe 238
                                   s+e+rl+q++++   L   L+
  gi|14601261|ref|NP_147796.1| 346 SVEDRLSQAEEDIDSLTTSLD 366
                                   ********9998877777776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0098
                      CCDC144C  55 tktvfqyngqLnvlkaentmlnskLekekqnkerleaevesyrsrLaaAiqdheqsqtskrdlelalqrer...dewlrlq 132
                                     +v  +++qL++l  + + l+s++       e lea v s+  rL+ A +d++   ts   l  +l+       e +   
  gi|14601261|ref|NP_147796.1| 313 SGAVDAMSQQLQALAEDLESLSSRV-------EDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLStrlAEAQASL 386
                                   4444445555555555555555555.......8899999999999999999999998887666665543330013444555 PP

                      CCDC144C 133 dklnfdvsnlkdknevLsqqLskaeskansLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnkyi 213
                                   + ln  + ++  + + L+q+L++ae  ++ L ++l  ++ ++   +  + ++ r l q ++ +  +    ++  ek+ +  
  gi|14601261|ref|NP_147796.1| 387 EDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAE 467
                                   666777777777777777777778888888888877777777776666667777777777777777777777777777777 PP

                      CCDC144C 214 akqesleerlaqlqsenmlLrqqLedaqnkad 245
                                   +k++  +  +  +qs+   Lr qL++   +a+
  gi|14601261|ref|NP_147796.1| 468 EKNQRQDASIEDFQSQIQELRTQLDEKTREAQ 499
                                   77777777777778877788888877766665 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1       0.3        22     106     162 ..     276     332 ..     239     340 .. 0.80
   2 ?    5.1   0.1      0.16        12     110     155 ..     301     346 ..     290     363 .. 0.68
   3 ?    3.5  16.6      0.49        36     106     247 ..     360     499 ..     332     509 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.3
                    FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerk 162
                                   +l  ql++l +++ +le+ ++  + +L++ +  L++l+ a+  + ++l+   +  ++
  gi|14601261|ref|NP_147796.1| 276 DLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLES 332
                                   567788888888888888888888888888888888888888888888764444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.16
                    FmiP_Thoc5 110 qlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealgl 155
                                    l+++e + + l+ ++    ++L++L++ L+sl++ ++ l+  +g 
  gi|14601261|ref|NP_147796.1| 301 RLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGS 346
                                   5667777777777777888888888888888888888777777663 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.49
                    FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkqhelaslLPkPLYvlYvqleayke 186
                                   +l + l++l ++ + l+   +e ++ L+ L+++L+++++++++lq+ l        + +e+ + L + L  l +++e +++
  gi|14601261|ref|NP_147796.1| 360 SLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLA-------TAEESLQALTEDLASLQAEVETLQQ 433
                                   5666677777777777777777777777777777777777777777775.......5667777777777888888888888 PP

                    FmiP_Thoc5 187 avd......kkleveIeGdveeakafnkssnsaeekkaeaessdsdsesq..eekekkkkkrekqkeek 247
                                   +         +l+ ++     e +++ ++ ++aeek++++++s +d +sq  e +++ ++k ++   ++
  gi|14601261|ref|NP_147796.1| 434 SIVeidrrlGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQiqELRTQLDEKTRE---AQ 499
                                   8732333333333333333355556668888888888888888888888854222333333322...22 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5     0.006      0.44      18      83 ..     301     367 ..     284     374 .. 0.61
   2 ?    9.5   7.3     0.012      0.87       4      69 ..     378     443 ..     375     468 .. 0.86
   3 ?    2.6   5.7       1.6   1.2e+02       4      69 ..     420     485 ..     418     507 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.006
                         Sec34  18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe.eldpitrkLns 83 
                                   ++++++ +Le+l+  ++++s++ ++l e+ e+l +  ++le  + ++e++L+  e ++d++t++L+s
  gi|14601261|ref|NP_147796.1| 301 RLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEeDIDSLTTSLDS 367
                                   5566666666666666666666666666666666666666666666666665432135555555544 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.012
                         Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                   +L + ++++++l +++d++ ++L++l+++  + +e+ ++l e+  +l +e + l++   ei+ +L 
  gi|14601261|ref|NP_147796.1| 378 RLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLG 443
                                   789999*******************************************************99995 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 1.6
                         Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                    L s ++e+++l +++ e+ + L +l++ +++v  + +sl e+  q  e+++r +   e+ +++++
  gi|14601261|ref|NP_147796.1| 420 DLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQ 485
                                   678888999999999999999999999999999999999998888888888877777777776665 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2       1.7   1.3e+02      39      90 ..     280     331 ..     240     332 .. 0.69
   2 ?    3.7   0.2       1.2        92      51      84 ..     306     339 ..     275     348 .. 0.54
   3 ?    2.4   1.1       3.2   2.4e+02      46      83 ..     329     366 ..     316     374 .. 0.46
   4 ?    5.7   5.2       0.3        22      22      85 ..     340     403 ..     337     405 .. 0.84
   5 ?    9.3  10.1     0.023       1.7      20      90 ..     401     471 ..     397     472 .. 0.94
   6 ?   10.1   5.7     0.013      0.95      47      91 .]     456     500 ..     449     500 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          BST2  39 qaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                   q ++ ++ v  L++     + + +  +  +++l g +  + q+Lq   +++e
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLE 331
                                   4445555555555555555555555566677788888888888887777765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 1.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2  51 kasLekekaqsqkqqakvqelqgeikkLnqkLqd 84 
                                   + sLe        + +++q l +++++L  +++d
  gi|14601261|ref|NP_147796.1| 306 EGSLEDLSGAVDAMSQQLQALAEDLESLSSRVED 339
                                   3344444444444445555555555555555555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2  46 tvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLq 83 
                                    +++L++  e  +a+    + ++ + +++i +L+ +L+
  gi|14601261|ref|NP_147796.1| 329 DLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLD 366
                                   33344444444444444444444455555555555555 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          BST2  22 LerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqda 85 
                                   Le++    ++ l +ae ++ +    + +L+  Le   ++  ++qa +++l+  + + +  Lq+ 
  gi|14601261|ref|NP_147796.1| 340 LEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQL 403
                                   5666666788999999999999999999999999999999999999999999999999988876 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.023
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          BST2  20 rlLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                   + L+++L+ a+esl+    + a+ +  v+tL++s+ +   +  + ++ v   + e+++L +kL +ae++ +
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQ 471
                                   78***********************************999999999********************99876 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                          BST2  47 vvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaever 91 
                                   v++L + L + + ++q+q a ++++q +i++L  +L+++  e ++
  gi|14601261|ref|NP_147796.1| 456 VESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   788999999999**************************9999875 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.072       5.3       1      39 [.     326     361 ..     326     366 .. 0.84
   2 ?    8.2   0.2     0.058       4.3       1      32 [.     361     392 ..     361     398 .. 0.86
   3 ?    7.0   2.5      0.15        11       1      40 [.     389     432 ..     389     444 .. 0.81
   4 ?    3.6   4.2       1.6   1.2e+02       1      44 [.     445     492 ..     445     501 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.072
                   Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekakeeeeeiekl 39 
                                   L +d+e l++  e+l++++ ++e++l++a+   e+i++l
  gi|14601261|ref|NP_147796.1| 326 LAEDLESLSSRVEDLEARVGSVEDRLSQAE---EDIDSL 361
                                   6789************************97...455554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.058
                   Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekakee 32 
                                   Lt++++ l++e e+l+ +l +++ +le +++ 
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLSTRLAEAQASLEDLNTR 392
                                   789999********************998854 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.15
                   Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekake....eeeeieklk 40 
                                   L+++++++a+  ++l+++l ++ee+l++++e     ++e+e+l+
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEdlasLQAEVETLQ 432
                                   778999**********************9954554555555555 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 1.6
                   Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekake....eeeeieklkasye 44 
                                   L+++v+ ++ e e l +kl ++ee+ +++ +     +++i++l+++ +
  gi|14601261|ref|NP_147796.1| 445 LRSTVDAVRLEVESLGEKLVQAEEKNQRQDAsiedFQSQIQELRTQLD 492
                                   678899999**********99999998887434445666666664444 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5    0.0013     0.095       5      68 ..     129     193 ..     125     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0013
                                   ETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS-EE--TTS..EEEEEEE-SS-EEEEEEEEEE CS
                       Big_3_5   5 tagqtvtltatVtaasggtptGtVtftdggttlgtavllsanG..tAtltvsalaaGthsitAtYs 68 
                                   ++g    lta+V + +gg ++   ++  gg+t++   + + +G  +A++tv+ l+ G h++  +Y+
  gi|14601261|ref|NP_147796.1| 129 QVGVGEVLTAEVEGLGGGGVSYAYQLRMGGVTVAVVYPDD-SGraVASFTVPPLPSGVHTVELVYT 193
                                   5666677888888887788888888888999998888877.676688999999***********97 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0         2   1.5e+02     121     174 ..     249     302 ..     239     305 .. 0.88
   2 ?    7.9   4.4     0.035       2.6      97     173 ..     327     406 ..     303     409 .. 0.73
   3 ?    9.2   6.3     0.013      0.99     102     174 ..     360     435 ..     354     450 .. 0.67
   4 ?    7.9   5.6     0.035       2.6     101     174 ..     415     491 ..     408     494 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 2
                  Bacillus_HBL 121 vkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                   v+q +++L    ++l++ + +++ +v+ lt  l++ +  + +l+ +++d++g +
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRL 302
                                   67888888888899999999*************************999998865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.035
                  Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklk...lklakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                   ++d ++l++++e+L++ + + +    q  +++ +l    ++l  + ++++t ++e+++ l+  +  ++q+  ++++lq+ 
  gi|14601261|ref|NP_147796.1| 327 AEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTtslDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQR 406
                                   37778888899999988887776655555555555400055667888899999999999999999999999999999886 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.013
                  Bacillus_HBL 102 ellellekLqeeiqqnq...kevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                   +l+  l  L++e+   +   +e+++++++L+   +++a+  +++++ ++++++ l++   +++ lq+e+e+lq++i
  gi|14601261|ref|NP_147796.1| 360 SLTTSLDSLRTELEDLStrlAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSI 435
                                   5566666666665444411145555555555555566666777777888888888888888888888888888877 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.035
                  Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklkl...klakdsknFktdvdeltsilagdsgvisqlqneiedlqgki 174
                                   + l+e+l  Lq+e+ + q+++ +    L +l++   ++  +++++ +++ ++++  + +++ i++ q +i++l+ ++
  gi|14601261|ref|NP_147796.1| 415 QALTEDLASLQAEVETLQQSIVEIDRRLGQLRStvdAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQL 491
                                   678999*******9999998766666666666511166679*******************************99886 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.7     0.011      0.79     104     155 ..     229     280 ..     227     281 .. 0.94
   2 ?    7.9   0.3     0.037       2.7     111     155 ..     292     336 ..     289     337 .. 0.95
   3 ?    3.8  16.5      0.69        51      55     156 .]     365     463 ..     338     484 .. 0.70
   4 ?    1.9   2.1       2.5   1.9e+02      15      71 ..     472     500 ..     464     519 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.011
                          Wtap 104 ELgkvleegrvakLeselalqkkfveelkkaleeleelleeleeevevlqst 155
                                   E+++ + ++ va+Le++l+l ++ ve+l  al  lee + +le  ve+l+ +
  gi|14601261|ref|NP_147796.1| 229 EIAEEVASAYVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQ 280
                                   8899999****************************************99876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.037
                          Wtap 111 egrvakLeselalqkkfveelkkaleeleelleeleeevevlqst 155
                                   e+rva +e++l++ +  +e+l  a   + + l+ l e++e l+s 
  gi|14601261|ref|NP_147796.1| 292 EDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSR 336
                                   79****************************************986 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.69
                          Wtap  55 fsrlrkeleeaenkleeaqeeLqalkftpdsqtGkrLmakcrvLeqENeELgkvleegrvakLeselalqkkfveelkkal 135
                                   +  lr ele+ +++l+eaq+ L+ l++  d   ++ L +  ++L    e L  ++ ++ +a+L+ e++ +++ + e+ ++l
  gi|14601261|ref|NP_147796.1| 365 LDSLRTELEDLSTRLAEAQASLEDLNTRLDQ-VASTLQQLQQRLATAEESL--QALTEDLASLQAEVETLQQSIVEIDRRL 442
                                   5678888888888888888888888776664.5566666666666666666..5556667777777777777777777777 PP

                          Wtap 136 eeleelleeleeevevlqstl 156
                                    +l+  ++ ++ eve l ++l
  gi|14601261|ref|NP_147796.1| 443 GQLRSTVDAVRLEVESLGEKL 463
                                   777777777777777666654 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 2.5
                          Wtap  15 akeqelqelksslqelkqslqppsssqlrqvllDPAvnlvfsrlrkeleeaenklee 71 
                                   ++++++ +++s++qel+++l +++                            ++ ++
  gi|14601261|ref|NP_147796.1| 472 RQDASIEDFQSQIQELRTQLDEKT----------------------------REAQQ 500
                                   455666666666666666655533............................22222 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 ?    9.0   6.0    0.0075      0.55     172     240 ..     343     407 ..     240     419 .. 0.63
   2 ?    3.3  12.0      0.42        31     176     259 ..     389     481 ..     381     515 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0075
                    Fmp27_WPPW 172 qkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkese 240
                                       +e+Rl++ ee+i++l+++l++l ++ e     l++++ e +  +++l+++l+ + ++l++l+++ 
  gi|14601261|ref|NP_147796.1| 343 RVGSVEDRLSQAEEDIDSLTTSLDSLRTELED----LSTRLAEAQASLEDLNTRLDQVASTLQQLQQRL 407
                                   22223333333333333333333333333333....444444444444444444444444444444433 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.42
                    Fmp27_WPPW 176 leeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkeseesse......... 244
                                   l+ Rl+++ + +++l+++l ++e++ +      ++l++e+e+l++ i e++++l  l+++++ ++ + e  +         
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALtedLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVE--Slgeklvqae 467
                                   688999999999999999999988887733333444555555555555555555555555555444443..1445555442 PP

                    Fmp27_WPPW 245 ..........eeeskskelsaasts 259
                                             e           + +
  gi|14601261|ref|NP_147796.1| 468 eknqrqdasiE-----------DFQ 481
                                   22222222220...........111 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       2.7     2e+02      26      59 ..     237     270 ..     236     275 .. 0.89
   2 ?    3.0   0.0       1.5   1.1e+02      26      57 ..     265     296 ..     259     303 .. 0.68
   3 ?    2.2   0.0       2.7     2e+02      28      63 ..     288     323 ..     282     324 .. 0.86
   4 ?    5.6   0.1      0.22        17      28      60 ..     309     341 ..     301     345 .. 0.88
   5 ?    6.3   0.1      0.13       9.9      27      61 ..     329     363 ..     326     366 .. 0.90
   6 ?    2.9   1.6       1.6   1.2e+02      27      61 ..     371     405 ..     350     408 .. 0.78
   7 ?    5.1   0.7      0.34        25      29      62 ..     401     434 ..     397     438 .. 0.91
   8 ?    3.7   0.2      0.89        66      29      57 ..     422     450 ..     409     457 .. 0.55
   9 ?    1.9   0.6       3.3   2.4e+02      27      63 ..     455     491 ..     452     492 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                   a+++ Le+r +  e+  ++L   l++l++ v  L
  gi|14601261|ref|NP_147796.1| 237 AYVAPLEERLSLVEQAVEDLGLALDSLEERVGDL 270
                                   79999***********************998766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkeve 57 
                                   +++  Le  v+ L+ + +sL s+++ l++ v+
  gi|14601261|ref|NP_147796.1| 265 ERVGDLEFAVEDLTLQLSSLDSRVGALEDRVA 296
                                   45556777777777777777777777777666 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                   + +Le+rv+ +e+  ++    le l+  v+ + +++
  gi|14601261|ref|NP_147796.1| 288 VGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQL 323
                                   6689********999999999999999888887775 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                    e L+  v+a++++ ++L++ le+l+  ve L+
  gi|14601261|ref|NP_147796.1| 309 LEDLSGAVDAMSQQLQALAEDLESLSSRVEDLE 341
                                   5789999999999999*******9999999887 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                     e L++rv+ Le+   s  ++l++ ++++++L +
  gi|14601261|ref|NP_147796.1| 329 DLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTT 363
                                   5789**************************99965 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                   e e L++r ++ ++  ++L  +l++ + + ++L++
  gi|14601261|ref|NP_147796.1| 371 ELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   66777777777777777888888888888888876 PP

  == domain 7  score: 5.1 bits;  conditional E-value: 0.34
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  29 eeLerrvkaLekeNksLkseleelkkevekLksk 62 
                                   ++L++r ++ e+  ++L + l +l+ eve+L++ 
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   79***************************99875 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  29 eeLerrvkaLekeNksLkseleelkkeve 57 
                                   + L+ +v++L++   +   +l++l+ +v+
  gi|14601261|ref|NP_147796.1| 422 ASLQAEVETLQQSIVEIDRRLGQLRSTVD 450
                                   34555555555555555555555555554 PP

  == domain 9  score: 1.9 bits;  conditional E-value: 3.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                   e+e L ++  + e++N+     +e  + ++++L++++
  gi|14601261|ref|NP_147796.1| 455 EVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQL 491
                                   789999999999*****9999***********99885 PP

>> BicD  Microtubule-associated protein Bicaudal-D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  22.4    0.0015      0.11     268     436 ..     318     493 ..     312     507 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0015
                          BicD 268 kLkqqLiqverekvsLlatlqesqkqLekskgalseqkekvnrLtehlealrklqaskerqaaedkekerdsned.gdeye 347
                                    + qqL  +  +  sL+++++++  ++   ++ ls+ +e +++Lt  l++lr    + e  ++   e+ + s ed  +  +
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRT---ELEDLSTRLAEA-QASLEDlNTRLD 394
                                   5789************************************************9...223322222333.333333023333 PP

                          BicD 348 vdingkevlecklkvaveelaelkeelktlkakyeklee..........rykeekarlraeiqelkeklrslekaskqdke 418
                                       + + l+ +l +a e l+ l e+l +l+a+ e+l++          + +   +  r e+++l ekl ++e+  +++ +
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQsiveidrrlgQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDA 475
                                   33456677899999999888888888888888888877754444444444555566778899***********99999999 PP

                          BicD 419 kiaelekelkklrkvase 436
                                    i +++++++ lr+  +e
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQELRTQLDE 493
                                   9********999875444 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  17.8     0.018       1.3     179     330 ..     314     423 ..     259     434 .. 0.44
   2 ?    7.6  17.0     0.016       1.2     200     323 ..     400     529 ..     399     533 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.018
                          FUSC 179 geegaeareaararlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaal 259
                                   g+ +a +  +++++la+d+  l++ ++ +++  ++     ++l ++  ++ +l+++l+sl+++l++l+++ a+a+++l++l
  gi|14601261|ref|NP_147796.1| 314 GAVDAMS--QQLQALAEDLESLSSRVEDLEARVGS---VEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDL 389
                                   2222222..33333333333333333333322222...3333444444444444444444444444444444443333333 PP

                          FUSC 260 laelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa 330
                                     +l++                                     ++++l++l ++la + +sl+al+++ a+
  gi|14601261|ref|NP_147796.1| 390 NTRLDQ-------------------------------------VASTLQQLQQRLATAEESLQALTEDLAS 423
                                   333333.....................................3333333333333333333333332222 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.016
                          FUSC 200 lealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaal.....eaaaaaeal 275
                                   l++l + +a+  ++++a ++ l++l++++ +l +++ ++ r+l +lr++ +a + e++ l ++l ++     ++ a+ e+ 
  gi|14601261|ref|NP_147796.1| 400 LQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAeeknqRQDASIEDF 480
                                   67777778888888899999************************************999999999999999977789999* PP

                          FUSC 276 eaalaalrarlralrrale.adadtaalllarlaellaelaqllaslra 323
                                   + ++++lr++l++  r+++  ++ ++++ +a++   l +la++ a++++
  gi|14601261|ref|NP_147796.1| 481 QSQIQELRTQLDEKTREAQqTASTASRWSMAAAGASLIALAAAAAAIAR 529
                                   ***********87777777466666777788888888888888887766 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4       1.4     1e+02     213     261 ..     285     333 ..     229     340 .. 0.50
   2 ?   12.5   5.5    0.0014       0.1      25     101 ..     339     415 ..     333     423 .. 0.86
   3 ?    7.1   8.2      0.06       4.4      27      96 ..     425     497 ..     421     504 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 1.4
                         CEP63 213 elelerLrllveelgkskrvlleekqeleeelresekqlqvleeeksel 261
                                   +  +  L+ +v+++ ++ + ++   ++l+ ++ + ++qlq+l e++++l
  gi|14601261|ref|NP_147796.1| 285 DSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESL 333
                                   2333334444444444444444444444444444445555554444444 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0014
                         CEP63  25 eWeaqtraletrlkireeeLasarnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsklkrsyekLq 101
                                   + ea++  +e rl++ ee++ s+ + ld+  +E + l  +l e++++ ++l ++ +q  + l++  ++l   +e Lq
  gi|14601261|ref|NP_147796.1| 339 DLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQ 415
                                   668889999********************************************999987777776677776666666 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.06
                         CEP63  27 eaqtraletrlkireeeLasarnaldekhkEvgllrqqleelekekq...elvakyeqqlqklreelsklkrs 96 
                                   +a+++ l+ ++   ++ L ++r+++d+   Ev+ l ++l ++e+++q   +  ++++ q+q+lr +l++ +r 
  gi|14601261|ref|NP_147796.1| 425 QAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQrqdASIEDFQSQIQELRTQLDEKTRE 497
                                   567888999999999*********************98887776655111446678899******99987765 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.68        50      13      50 ..     301     338 ..     250     344 .. 0.76
   2 ?    8.4   0.6     0.021       1.6       6      51 ..     350     395 ..     345     402 .. 0.86
   3 ?    7.0   1.4     0.055       4.1      13      48 ..     399     434 ..     394     458 .. 0.78
   4 ?    4.1   5.6      0.45        33       5      46 ..     461     502 ..     455     516 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.68
                                   HHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHH CS
                          GrpE  13 eeeeleeeleelekevkelkekllrllaefenlrkrte 50 
                                   ++e+ e  le+l   v++++++l+ l++++e l  r+e
  gi|14601261|ref|NP_147796.1| 301 RLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVE 338
                                   44556666777777888888888888888888877776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.021
                                   .CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHH CS
                          GrpE   6 eeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtek 51 
                                   +  ++e+++++l + l++l++e+++l+ +l +++a +e l+ r+++
  gi|14601261|ref|NP_147796.1| 350 RLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   567889999999999***********************99999876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.055
                                   HHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHH CS
                          GrpE  13 eeeeleeeleelekevkelkekllrllaefenlrkr 48 
                                   ++++l+++l+++e+ +++l+e+l  l+ae+e l++ 
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   567888888888888888888888888888877764 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.45
                                   ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHH CS
                          GrpE   5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlr 46 
                                   e+ +++e++++ +++ +e+++++++el  +l+++  e+++  
  gi|14601261|ref|NP_147796.1| 461 EKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   566788899999999999999999999999999999988755 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       1.9   1.4e+02      22      54 ..     230     262 ..     219     272 .. 0.84
   2 ?    6.3   0.1      0.18        13      17      65 ..     247     294 ..     238     299 .. 0.81
   3 ?    4.6   0.1      0.59        44      13      65 ..     285     336 ..     279     348 .. 0.79
   4 ?    1.9   0.1         4     3e+02      25      54 ..     366     395 ..     343     413 .. 0.56
   5 ?    1.2   0.1       6.7   4.9e+02      30      61 ..     385     416 ..     374     434 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 1.9
                          MtrB  22 aredvvllsldpvleeidkLekiaddlvnsLdp 54 
                                    +e+v    ++p++e++  +e++++dl  +Ld 
  gi|14601261|ref|NP_147796.1| 230 IAEEVASAYVAPLEERLSLVEQAVEDLGLALDS 262
                                   5678888999*****************988886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.18
                          MtrB  17 gvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgR 65 
                                   ++v++a ed + l ld ++e++ +Le +++dl  +L+   + +++ ++R
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVED-LGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDR 294
                                   667777775.57899******************9999887777776666 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.59
                          MtrB  13 dpetgvvaearedvvllsldpvleeidkLekiaddlvnsLdpetallesypgR 65 
                                   d  +g ++   +d +   l+ v+  +++L  ++d++ ++L+   + les   R
  gi|14601261|ref|NP_147796.1| 285 DSRVGALEDRVAD-IEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSR 336
                                   6666666666554.466789999999999999999999999999999998888 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 4
                          MtrB  25 dvvllsldpvleeidkLekiaddlvnsLdp 54 
                                   d + ++l+++ +++++ ++  +dl + Ld 
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEAQASLEDLNTRLDQ 395
                                   333334444444444444444444444444 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 6.7
                          MtrB  30 sldpvleeidkLekiaddlvnsLdpetalles 61 
                                   sl+++++++d++ ++ ++l + L+  ++ l++
  gi|14601261|ref|NP_147796.1| 385 SLEDLNTRLDQVASTLQQLQQRLATAEESLQA 416
                                   67777777777777777777777776666655 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       1.8   1.3e+02      37      84 ..     308     355 ..     299     364 .. 0.72
   2 ?    6.5   1.3      0.11       8.5      40      91 ..     353     404 ..     344     425 .. 0.75
   3 ?    8.5   5.1     0.029       2.2      26      93 ..     430     497 ..     409     515 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 1.8
                      RasGAP_C  37 dirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvl 84 
                                    +  ++ + + + ++l++l e l++Ls++ + le ++ s ++ ++++ 
  gi|14601261|ref|NP_147796.1| 308 SLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAE 355
                                   555556666677888888888888888888888888888888777765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.11
                      RasGAP_C  40 nkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkk 91 
                                   + ++ +++ +  l+sl++ l++Ls + +  +  le++++ +++v ++l++ +
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQ 404
                                   5555666777788999999999999999999999999999999999998764 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.029
                      RasGAP_C  26 nyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgk 93 
                                    +q+ + eI + + ++++  + ++ E+esl e l + +ekn+     +e++++ i++ + ql +k ++
  gi|14601261|ref|NP_147796.1| 430 TLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTRE 497
                                   567777899999999***********************************************999643 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 ?   13.9   1.4   0.00057     0.042       1      58 [.     284     341 ..     284     343 .. 0.96
   2 ?    6.4   8.3      0.13       9.8       1      63 [.     340     402 ..     340     408 .. 0.84
   3 ?    3.4   0.6       1.1        81       3      21 ..     482     500 ..     480     506 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00057
                   Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealr 58 
                                   L++ v +L++r   ++ +l++ e+ l++L+   d + +qL+   e+l++L+++ve l+
  gi|14601261|ref|NP_147796.1| 284 LDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLE 341
                                   788899*************************************************996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.13
                   Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELke 63 
                                   Lea v + ++rL+++++ + +  + l++L++E +   ++L +A   l++L  +++  +  L+ 
  gi|14601261|ref|NP_147796.1| 340 LEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQ 402
                                   678888889999999999999999999999999999999999999999999999888776654 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 1.1
                   Cep57_CLD_2   3 aevktLqnrLdsltrklqv 21 
                                   +++++L+++Ld  tr++q 
  gi|14601261|ref|NP_147796.1| 482 SQIQELRTQLDEKTREAQQ 500
                                   689*********9999885 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1      0.32        23      18      44 ..     267     293 ..     243     303 .. 0.77
   2 ?    5.6   0.2      0.23        17      11      44 ..     274     293 ..     264     326 .. 0.61
   3 ?    5.9   0.8      0.19        14       9      48 ..     335     378 ..     320     382 .. 0.62
   4 ?    5.9   2.0      0.18        13      17      47 ..     371     401 ..     355     410 .. 0.65
   5 ?    7.4   1.6     0.063       4.7      10      47 ..     378     416 ..     373     424 .. 0.80
   6 ?    5.9   0.2      0.19        14      25      43 ..     428     446 ..     418     454 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.32
                    TRPM_tetra  18 veevneKenlikaSLqsldfrLgkLed 44 
                                   v++++  +   +  L+sld+r g Led
  gi|14601261|ref|NP_147796.1| 267 VGDLEFAVEDLTLQLSSLDSRVGALED 293
                                   444444555566679999999999999 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.23
                    TRPM_tetra  11 vEnmsmkveevneKenlikaSLqsldfrLgkLed 44 
                                   vE+++++              L+sld+r g Led
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQ--------------LSSLDSRVGALED 293
                                   4444444..............5555555555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.19
                    TRPM_tetra   9 ERvEnmsmkveevneKenlikaSLqs....ldfrLgkLedlsal 48 
                                    RvE++  +v+ v+++ +  ++ + s    ld+    Ledls +
  gi|14601261|ref|NP_147796.1| 335 SRVEDLEARVGSVEDRLSQAEEDIDSlttsLDSLRTELEDLSTR 378
                                   47777777777777776666554444000144444566777766 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.18
                    TRPM_tetra  17 kveevneKenlikaSLqsldfrLgkLedlsa 47 
                                    +e+++ +    +aSL +l +rL ++    +
  gi|14601261|ref|NP_147796.1| 371 ELEDLSTRLAEAQASLEDLNTRLDQVASTLQ 401
                                   5667777777777777777777766433333 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.063
                    TRPM_tetra  10 RvEnmsmkveevneKenlikaSLqsldfrLgkLed.lsa 47 
                                   R  + +  +e++n +   + ++Lq+l +rL+  e+ l a
  gi|14601261|ref|NP_147796.1| 378 RLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEEsLQA 416
                                   667778889*********************988773444 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.19
                    TRPM_tetra  25 enlikaSLqsldfrLgkLe 43 
                                   + + ++S+ ++d rLg+L 
  gi|14601261|ref|NP_147796.1| 428 VETLQQSIVEIDRRLGQLR 446
                                   7889*************95 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.0    0.0062      0.46      29     107 ..     310     398 ..     290     399 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0062
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTTS................-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          OmpH  29 kklqaeleakekelqklqeelqkkakkle...............keekeqelqkkeqelqqkqqqkaqelqkkqqellkpi 94 
                                   ++l  +++a+ ++lq+l+e+l+  +   +                 ++e++++ + + l   ++ + ++l  + +e++++ 
  gi|14601261|ref|NP_147796.1| 310 EDLSGAVDAMSQQLQALAEDLESLS---SrvedlearvgsvedrLSQAEEDIDSLTTSLDS-LRTELEDLSTRLAEAQAS- 385
                                   5555566777777777777775322...123356667777777555555558888888888.888889999999888885. PP

                                   HHHHHHHHHHHHH CS
                          OmpH  95 ldkinkaikevak 107
                                   l+ +n+ +++va+
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVAS 398
                                   8888888888875 PP

>> Phage_tail_NK  Sf6-type phage tail needle knob or tip of some Caudovirales
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     0.002      0.15       4      30 ..     280     306 ..     274     310 .. 0.93
   2 ?    3.2   0.4      0.81        60       3      27 ..     335     359 ..     323     363 .. 0.57
   3 ?    2.5   0.3       1.3        98       2      27 ..     355     380 ..     354     396 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.002
                                   XXXXXXXXXXXXXXXXXXXXXHHHHHH CS
                 Phage_tail_NK   4 dissldtrvqslesqvsdhetridale 30 
                                   ++ssld+rv +le +v+d e r++a+e
  gi|14601261|ref|NP_147796.1| 280 QLSSLDSRVGALEDRVADIEGRLEAVE 306
                                   589**********************98 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.81
                                   XXXXXXXXXXXXXXXXXXXXXXHHH CS
                 Phage_tail_NK   3 sdissldtrvqslesqvsdhetrid 27 
                                   s +  l++rv s+e ++s+ e  id
  gi|14601261|ref|NP_147796.1| 335 SRVEDLEARVGSVEDRLSQAEEDID 359
                                   3344455555555555555555555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 1.3
                                   XXXXXXXXXXXXXXXXXXXXXXXHHH CS
                 Phage_tail_NK   2 esdissldtrvqslesqvsdhetrid 27 
                                   e di sl t ++sl +++ d  tr+ 
  gi|14601261|ref|NP_147796.1| 355 EEDIDSLTTSLDSLRTELEDLSTRLA 380
                                   78*********************985 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2      0.21        15      81     131 ..     282     332 ..     244     344 .. 0.52
   2 ?   12.0   3.9    0.0014      0.11      78     135 ..     342     399 ..     331     403 .. 0.88
   3 ?    5.9   5.9       0.1       7.3      78     132 ..     384     438 ..     381     453 .. 0.81
   4 ?    4.9   7.0      0.21        15      76     131 ..     452     507 ..     443     521 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.21
                       DUF3552  81 qrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeelee 131
                                   ++l+ R+   e+++   e  le  e sle+    +++ +q+l++  e+le+
  gi|14601261|ref|NP_147796.1| 282 SSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLES 332
                                   333333333333333334444444444444444444444444444444433 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0014
                       DUF3552  78 nelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelvee 135
                                   + + ++e+Rl q ee +d  ++sl++  ++le+   +l++ ++sle  +++l+++ ++
  gi|14601261|ref|NP_147796.1| 342 ARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVAST 399
                                   566789********************************************99997665 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.1
                       DUF3552  78 nelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleel 132
                                   + l+ l++Rl q   tL++ ++ l   eesl++ +++l++ ++++e+ ++++ e+
  gi|14601261|ref|NP_147796.1| 384 ASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEI 438
                                   5677888999999999999999999999999999999999999999888887664 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.21
                       DUF3552  76 rrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeelee 131
                                    r e+++l ++l+q ee+ +r+++s+e+ +++++e + +l++k+++ +++ +++++
  gi|14601261|ref|NP_147796.1| 452 VRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   5789999*************************************999999888765 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 ?    2.1   0.0       3.3   2.5e+02       4      35 ..     274     305 ..     271     320 .. 0.82
   2 ?   13.6   3.7   0.00091     0.067       5      77 ..     331     405 ..     327     408 .. 0.86
   3 ?    4.2   2.5      0.76        56       4      41 ..     386     423 ..     383     441 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 3.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaq 35 
                                   v++ + +l++  s +Ga + R+ +   +l+a 
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAV 305
                                   677788999************99887777765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00091
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHHH..HHHHHHHHHHHHHHHHHHHHHHHCTC CS
                   Flagellin_C   5 deaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrledvDp..aeestrvtklqiliqasyallaqanq 77 
                                   ++ ++ ++   + +G+v+ Rl++a + ++  ++ l++ +++led  +  ae+ + +++l++ ++   + l q++q
  gi|14601261|ref|NP_147796.1| 331 ESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTrlAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   6677889999**********************************8644499**********99977777777776 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.76
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHH CS
                   Flagellin_C   4 vdeaitdldkvrselGavqnRlesaitnlkaqsenlka 41 
                                   +++  t ld+v+s+l   q+Rl  a ++l+a +e l++
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLAS 423
                                   567789999999**********9999999998887655 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2      0.36        26      20      42 ..     317     339 ..     227     374 .. 0.60
   2 ?    2.4  10.3       2.8     2e+02      21      68 ..     374     420 ..     349     507 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.36
                    MitMem_reg  20 stlstglnrqyyslkilqerldl 42 
                                    ++s++l++  + l+ l++r+++
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVED 339
                                   22233333333333333333333 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 2.8
                    MitMem_reg  21 tlstglnrqyyslkilqerldlikdYlkkveegelpvnheilrnlqkl 68 
                                   +lst+l + + sl+ l++rld++ + l++++ ++l   +e l+ l + 
  gi|14601261|ref|NP_147796.1| 374 DLSTRLAEAQASLEDLNTRLDQVASTLQQLQ-QRLATAEESLQALTED 420
                                   4445555555555555555555555544444.2221222222222111 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   7.7       1.1        79      26      84 ..     378     442 ..     276     454 .. 0.76
   2 ?   11.7   3.5    0.0028      0.21      31     108 ..     452     529 ..     441     531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1.1
                                   X.........XXXXXXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCG CS
                           MCU  26 e.........eeakvllrvkqlvkalesalnveeeqlkkereleekleelreelepleekkeeidekA 84 
                                   +         +  ++l++v +++++l++ l ++   +++ ++l+e+l++l++e+e l++   eid++ 
  gi|14601261|ref|NP_147796.1| 378 RlaeaqasleDLNTRLDQVASTLQQLQQRLATA---EESLQALTEDLASLQAEVETLQQSIVEIDRRL 442
                                   044333333222455666666666666666444...67778889999999999999999999999875 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0028
                                   XXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHGGGHHHHHHHHTHHHHH CS
                           MCU  31 vllrvkqlvkalesalnveeeqlkkereleekleelreelepleekkeeidekAerrtrrllwagLallavqlgilar 108
                                   v l+v++l ++l +a + ++ q  + ++ +++++elr +l++  ++ ++ ++ A+r++ + + a L++la+  +++ar
  gi|14601261|ref|NP_147796.1| 452 VRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSMAAAGASLIALAAAAAAIAR 529
                                   44455555566666667777777788889999999******999999****************************999 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 ?   10.9   3.1    0.0017      0.13      31     149 ..     246     366 ..     236     371 .. 0.71
   2 ?    6.1  20.1     0.049       3.6     189     332 ..     361     504 ..     356     514 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0017
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXX CS
                      GOLGA2L5  31 veqlseqvkllkeekeksvsqvqeLeaslaeLknqaavkpaeeeaqppagPseee...qrlqeeleqLqkekealagqlqa 108
                                   +  + + v+ l    ++  ++v +Le ++ +L  q     +   a      ++ e   ++++ +le L   ++a+++qlqa
  gi|14601261|ref|NP_147796.1| 246 LSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGA-LEDRVADIEgrlEAVEGSLEDLSGAVDAMSQQLQA 325
                                   444445555566666666777778888888877776555544422.2333444440004556789999************* PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      GOLGA2L5 109 qvrDneqLsrlnqeqeerLlelereaerwseeaedrkriLe 149
                                      D e+Ls  +++ e+r+  +e ++ + +e+ +     L+
  gi|14601261|ref|NP_147796.1| 326 LAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLD 366
                                   ***********************999999988776655555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.049
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      GOLGA2L5 189 ltsalqseqhvkkelakklGqlqeelgelketlelksqeaqslqeqrdqylahlqqYvaayqqlasekeelhkqlllqtql 269
                                   lt++l+s +   ++l+ +l + q +l++l  +l++  +  q+lq++       lq  +     l +e e+l++ ++   + 
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRR 441
                                   7888888888889999****************************9999999****************************** PP

                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      GOLGA2L5 270 mdrlqheevqgkvalelarkeLqeaqerLealakenqqLkaqlsllaapseGdgveseekeee 332
                                   + +l+      + ++e   ++L +a+e+ ++     ++ ++q+++l ++ +    e +++   
  gi|14601261|ref|NP_147796.1| 442 LGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   ******9999************************************98887666666665444 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 ?    3.7   0.1      0.64        47     118     166 ..     283     331 ..     208     337 .. 0.67
   2 ?   11.4   1.6    0.0029      0.21      87     165 ..     326     407 ..     312     414 .. 0.61
   3 ?    3.5   5.7      0.73        54      89     167 ..     429     507 ..     412     512 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.64
                                   HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal 118 egselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqave 166
                                   +  + v   ++ +++i  + + v+ ++++++ a++ +s+ ++  ++ +e
  gi|14601261|ref|NP_147796.1| 283 SLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLE 331
                                   3344445555566666666777777777777777777776666666555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0029
                                   HHHHHHHH...H..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  87 aakeieal...iieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                                    a+++e+l   ++++++ + ++ + l+++++ +++ ++  ++ +++l++++++ ae +++++++++  ++ ++++++ +q 
  gi|14601261|ref|NP_147796.1| 326 LAEDLESLssrVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQR 406
                                   444444431113444455555556666666667777777777777777777777777777777777777777777777766 PP

                                   H CS
                     MCPsignal 165 v 165
                                   +
  gi|14601261|ref|NP_147796.1| 407 L 407
                                   5 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.73
                                   HHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MCPsignal  89 keiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqavee 167
                                   + +++ i+ei +   +  ++++ +r +ve+  e+  +++e+ ++  +++++ ++++qe+ +  +e+++ +++++++ ++
  gi|14601261|ref|NP_147796.1| 429 ETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   445677999999999999***********99999999999999999*************************99987765 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 ?    5.7   0.7      0.12       8.6      15      82 ..     319     382 ..     302     384 .. 0.78
   2 ?   12.2   6.7    0.0012      0.09      26     126 ..     368     468 ..     359     481 .. 0.86
   3 ?    1.5   0.2       2.2   1.7e+02      89     135 ..     484     531 ..     475     532 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.12
                     Mce4_CUP1  15 LnatLsAvaeALeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdna 82 
                                   +++ L+A+ae Le     l   ++dl++ +  +++rl q++edi +l++  d      +dl + L++a
  gi|14601261|ref|NP_147796.1| 319 MSQQLQALAEDLE----SLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEA 382
                                   4455555555554....456678999999999***************999999999999999888765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0012
                     Mce4_CUP1  26 LeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavgl 106
                                   L+   e l + l+++++ L++lN+rl+q+ + +++l++  ++ +++ + l + L+++    +T+++   e+d+ l ++ ++
  gi|14601261|ref|NP_147796.1| 368 LRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRST 448
                                   55555677788999***********************************************************99999998 PP

                     Mce4_CUP1 107 sntgadllerngdnLirlaa 126
                                    + ++  +e+ g++L+++ +
  gi|14601261|ref|NP_147796.1| 449 VDAVRLEVESLGEKLVQAEE 468
                                   88888888888888877765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 2.2
                     Mce4_CUP1  89 iveqqaeLdalllaavglsntgadl.lerngdnLirlaadlrptlelL 135
                                   i+e +++Ld+   +a ++++t++++ +++ g++Li laa++ + +++L
  gi|14601261|ref|NP_147796.1| 484 IQELRTQLDEKTREAQQTASTASRWsMAAAGASLIALAAAAAAIARVL 531
                                   666677777777777777766665436777777777777776666665 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  17.4       2.9   2.1e+02      45     128 ..     397     494 ..     242     509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 2.9
                     AATF-Che1  45 lesseefeealeeaekalkklleslleLreelleqneikkla.......................eskeeeekkkskrkrk 102
                                    ++ ++++++l++ae++l++l e+l +L+ e     e  +l+                        ++ +e+  ++++k+ 
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQQRLATAEESLQALTEDLASLQAEV----E--TLQqsiveidrrlgqlrstvdavrleVESLGEKLVQAEEKN- 470
                                   22245677888888888888888888888888....2..11133456668899999999999997333333333333333. PP

                     AATF-Che1 103 kkkkeetsleelwkeleklekalkpf 128
                                     ++++ s+e++ +++++l ++l++ 
  gi|14601261|ref|NP_147796.1| 471 --QRQDASIEDFQSQIQELRTQLDEK 494
                                   ..345568888888888887777654 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 ?    7.2   1.0     0.081         6      74     127 ..     324     377 ..     309     392 .. 0.64
   2 ?    9.0   4.1     0.023       1.7      70     121 ..     390     441 ..     370     447 .. 0.80
   3 ?    8.1   6.6     0.042       3.1      53     124 ..     400     472 ..     397     478 .. 0.82
   4 ?    1.9   3.8       3.6   2.7e+02      80     123 ..     456     499 ..     444     504 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.081
                        DUF641  74 seleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkklek 127
                                   ++l+  ++ + s ++ +e++v ++e  l++ +++i++L  +L++++ + + l+ 
  gi|14601261|ref|NP_147796.1| 324 QALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLST 377
                                   455555566666667777777777777777777777777777666665555543 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.023
                        DUF641  70 eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeks 121
                                   +++  ++++ +q++++ l+t e  +++l ++l + ++e+e L++++ e+ ++
  gi|14601261|ref|NP_147796.1| 390 NTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRR 441
                                   3667789999***********************************9998876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.042
                        DUF641  53 lselkrlyrkkqkkkas.eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkk 124
                                   l +l+++  + +++ ++ +++ ++l+ae++++++ +   + ++ +l++ ++a + e+e+L ekL +ae++n++
  gi|14601261|ref|NP_147796.1| 400 LQQLQQRLATAEESLQAlTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQR 472
                                   55666666665554443358889999*****999999999**************************9999986 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 3.6
                        DUF641  80 iqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnk 123
                                   ++ + ++l   e   ++ +a ++  +s+i+eL+ +L+e +++ +
  gi|14601261|ref|NP_147796.1| 456 VESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQ 499
                                   44444555555555566666777777777777777777776655 PP

>> Hrs_helical  Hepatocyte growth factor-regulated tyrosine kinase substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3     0.088       6.5       4      73 ..     282     349 ..     274     381 .. 0.63
   2 ?    5.6   5.6      0.31        23       3      79 ..     330     404 ..     321     421 .. 0.71
   3 ?    3.0   5.4         2   1.5e+02      30      82 ..     397     453 ..     363     458 .. 0.64
   4 ?    4.1   9.7      0.89        66       5      91 ..     395     486 ..     393     504 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.088
                   Hrs_helical   4 ealkssveifvnrmksnsarGrsianDsavqslFqkltamhsqllkriqeqeekraeyeslqdklaqike 73 
                                   ++l s v  +++r+ + + r   +  + ++++l   + am +ql +  +++e   +++e l+ ++  +++
  gi|14601261|ref|NP_147796.1| 282 SSLDSRVGALEDRVADIEGRLEAV--EGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVED 349
                                   567777888888887776665555..56666666667777777666666666666666666666655554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.31
                   Hrs_helical   3 lealkssveifvnrmksnsarGrsianDsavqslFqkltamhsqllkriqeqeekraeyeslqdklaqikeareald 79 
                                   le+l+s ve ++ r+ s++ r  +  +++ ++sl ++l +++++l +   ++ e +a++e l+ +l+q+  + + l+
  gi|14601261|ref|NP_147796.1| 330 LESLSSRVEDLEARVGSVEDRLSQ--AEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQ 404
                                   344555555555555555555444..455699999999999999999999999999999999999999987666554 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 2
                   Hrs_helical  30 DsavqslFqkltamhsqllkriqeqeekraeyeslqdklaqik....earealdalr 82 
                                    s++q+l q+l + ++ l + ++++   +ae+e lq+++ +i     + r+++da+r
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDrrlgQLRSTVDAVR 453
                                   368999999999999999999999999999999999999887422225677777776 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.89
                   Hrs_helical   5 alkssveifvnrmksnsarGrsianDsa.....vqslFqkltamhsqllkriqeqeekraeyeslqdklaqikearealda 80 
                                   ++ s ++++++r+  +++  + +++D a     v++l q++ +++ +l +  ++ +  r e+esl +kl q +e  +  da
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQQRLATAEESLQALTEDLAslqaeVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDA 475
                                   566777777777777777777777774333334899999999999999999999999999999999999999999999999 PP

                   Hrs_helical  81 lreehkeklrr 91 
                                     e++++++++
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQE 486
                                   99999988875 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       1.7   1.3e+02       6      24 ..     249     267 ..     244     275 .. 0.90
   2 ?   12.6   5.7    0.0017      0.12      10      87 ..     281     362 ..     273     364 .. 0.86
   3 ?    9.9  11.9     0.012      0.87       3      86 ..     369     452 ..     367     455 .. 0.92
   4 ?    1.0   5.0       7.3   5.4e+02      22      61 ..     462     501 ..     453     532 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1.7
                       DUF4164   6 leaaltrLeaaldsLEkav 24 
                                   +e+a ++L  aldsLE++v
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERV 267
                                   68999***********987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.0017
                       DUF4164  10 ltrLeaaldsLEkav...drrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86 
                                   l+ L+  + +LE++v   + rlea +   ++l   + a+ +  + Lae+L + + r + le+    v +rL  a e i ++
  gi|14601261|ref|NP_147796.1| 281 LSSLDSRVGALEDRVadiEGRLEAVEGSlEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSL 361
                                   56778888888887522267888877777*************************************************987 PP

                       DUF4164  87 L 87 
                                   +
  gi|14601261|ref|NP_147796.1| 362 T 362
                                   6 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.012
                       DUF4164   3 tkeleaaltrLeaaldsLEkavdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaiet 82 
                                   ++ele+  trL +a  sLE+ ++ rl++ +++ ++l+++++  +e  + L e+L + +a+ ++l++   E+ rrL  +  t
  gi|14601261|ref|NP_147796.1| 369 RTELEDLSTRLAEAQASLED-LNTRLDQVASTlQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRST 448
                                   6799***************8.577888877777*********************************************999 PP

                       DUF4164  83 irav 86 
                                   + av
  gi|14601261|ref|NP_147796.1| 449 VDAV 452
                                   9887 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 7.3
                       DUF4164  22 kavdrrleaerkrdeleaeiealgedrsRLaeeLdqaear 61 
                                   k v++  +++r+ +++e   ++++e r++L+e+  +a+  
  gi|14601261|ref|NP_147796.1| 462 KLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   4444444455555555555566666666666655444433 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       3.7   2.7e+02      37      98 ..     222     284 ..     211     306 .. 0.60
   2 ?    7.1   0.8     0.073       5.4      30     104 ..     307     374 ..     280     383 .. 0.52
   3 ?   11.2   3.4    0.0041      0.31      49     107 ..     375     447 ..     357     452 .. 0.55
   4 ?    3.3   0.9       1.1        81      54     107 ..     446     496 ..     442     529 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 3.7
                                   HHHHHHHHHCTTT....THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHH CS
               Cob_adeno_trans  37 saiglarallaee....eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeidel 98 
                                   ++ig ar++++e      + l+e+L+ +++ + dlg +l + e+++ + ++    ve+l  ++ +l
  gi|14601261|ref|NP_147796.1| 222 ATIGGAREIAEEVasayVAPLEERLSLVEQAVEDLGLALDSLEERVGDLEFA---VEDLTLQLSSL 284
                                   7788888777666777767788888888888888888885333333333333...22222222222 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.073
                                   HHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS-- CS
               Cob_adeno_trans  30 GtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpp 104
                                   G+++ l+ a+  + +    + ++l+e+Le++ +++ dl a + +    +++ +  ee+++ l + +d+l++el+ 
  gi|14601261|ref|NP_147796.1| 307 GSLEDLSGAVDAMSQ----QLQALAEDLESLSSRVEDLEARVGSV---EDRLSQAEEDIDSLTTSLDSLRTELED 374
                                   444444444443332....23455666666666666666666422...122222233455555555555555554 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.0041
                                   T..........THHHHHHHHHHHHHHHHHHHHHHT.....-BTCCG-S--HHHHHHHHHHHHHHHHHS--EES CS
               Cob_adeno_trans  49 e..........eeelkeaLeeiqneLfdlgaelatp....ekkkekkkiteeeveelekeideleaelpplks 107
                                               e+l+++L ++ + L +l++ lat     ++ +e+ +  ++eve+l++ i e++ +l +l+s
  gi|14601261|ref|NP_147796.1| 375 LstrlaeaqasLEDLNTRLDQVASTLQQLQQRLATAeeslQALTEDLASLQAEVETLQQSIVEIDRRLGQLRS 447
                                   2333333355556667777777777777777777664443223333333355578888888888888877765 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EES CS
               Cob_adeno_trans  54 keaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplks 107
                                   ++++  +  e+ +lg++l      +ek++ +++++e+ +++i+el+++l++ ++
  gi|14601261|ref|NP_147796.1| 446 RSTVDAVRLEVESLGEKLVQA---EEKNQRQDASIEDFQSQIQELRTQLDEKTR 496
                                   555666666777778887533...333334445577777777777777764332 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.6     0.019       1.4     122     238 ..     254     400 ..     243     433 .. 0.55
   2 ?   -0.3   6.7       7.8   5.8e+02     172     220 ..     388     438 ..     379     486 .. 0.61
   3 ?    0.7   2.1       3.9   2.9e+02     200     233 ..     467     500 ..     450     507 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.019
                                   GGGTEEEXTT.T..XXEEEXHHHHHHHHHHHHHHHHHH....................HTTTSS.......SXSHHHHHHH CS
                        FliD_C 122 adlGistnkn.k..GkLelDeekLkkalkenpssveel....................Fsgstsqektvtsdsglatrlen 179
                                   +dlG+ +++  +  G Le+  e L+ +l++  s v +l                    +                    ++
  gi|14601261|ref|NP_147796.1| 254 EDLGLALDSLeErvGDLEFAVEDLTLQLSSLDSRVGALedrvadiegrleavegsledL--------------------SG 314
                                   68888888875478888888888888888888888888444444444444444433332....................22 PP

                                   HHHHHHSTT.SHHH............................HHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                        FliD_C 180 llksyvkssngtlq............................tasknltkqikdldkkiedldkrletleerlkkqfaale 232
                                   +++ +++   ++l+                            +++++lt+ +++l ++ edl+ rl + +++l+   ++l+
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQL-QALAedleslssrvedlearvgsvedrlsqaeEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLD 394
                                   222222222.22221111111111122222223333333344444555555555555555555555555555555555555 PP

                                   HHHHHH CS
                        FliD_C 233 kavskl 238
                                   +++s l
  gi|14601261|ref|NP_147796.1| 395 QVASTL 400
                                   444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 7.8
                                   SHHHHHHHHHHHHHSTT.SHHHHHHHH...XXXXHHHHHHHHHHHHHCHHHH CS
                        FliD_C 172 glatrlenllksyvkssngtlqtaskn...ltkqikdldkkiedldkrletl 220
                                    l trl+++++++ + + + l+ta+++   lt+++ +l+ ++e+l++++ ++
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQ-QRLATAEESlqaLTEDLASLQAEVETLQQSIVEI 438
                                   34455555555555444.4444333331113334444444444444444444 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 3.9
                                   XXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                        FliD_C 200 tkqikdldkkiedldkrletleerlkkqfaalek 233
                                   +++ ++ d  ied+++++++l  +l ++  + ++
  gi|14601261|ref|NP_147796.1| 467 EEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   4455566666666666666666666666554444 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.32        24     122     170 ..     256     308 ..     236     339 .. 0.80
   2 ?    7.3   6.5     0.052       3.8      68     166 ..     356     447 ..     317     453 .. 0.74
   3 ?    2.2   3.3       1.8   1.4e+02     119     184 ..     435     505 ..     432     514 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.32
                         Spc29 122 lekklddqkleIkeLkreleqqrtvnseLqekvaeleeev....krlaalehS 170
                                   l   ld+ ++++  L+ ++e+     s L ++v  le++v     rl+a+e S
  gi|14601261|ref|NP_147796.1| 256 LGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVadieGRLEAVEGS 308
                                   455799999999****************************7777677777777 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.052
                         Spc29  68 adskkktelDdkLRrQLReglsrkPppkisspglapsdesrldsiyssvkkivelekklddqkleIkeLkreleqqrtvns 148
                                   +d    t+  d LR  L +  +r+ +++ s+  l      rld++ s +++   l++ l   ++++++L   l   ++  +
  gi|14601261|ref|NP_147796.1| 356 EDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLN----TRLDQVASTLQQ---LQQRLATAEESLQALTEDLASLQAEVE 429
                                   34444455567899999999999988888777776....689999988888...999999999999999999999999999 PP

                         Spc29 149 eLqekvaeleeevkrlaa 166
                                   +Lq+ + e+++++ +l++
  gi|14601261|ref|NP_147796.1| 430 TLQQSIVEIDRRLGQLRS 447
                                   999999999999877775 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 1.8
                         Spc29 119 ivelek.......klddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaalehSnrkfrsyssapsns 184
                                   ive+++        +d  +le+++L  +l q +  n+     ++ +++++++l++  +   k+r  ++  s+ 
  gi|14601261|ref|NP_147796.1| 435 IVEIDRrlgqlrsTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDE--KTREAQQTASTA 505
                                   45555545555558899999999999999999999999999999999999888765444..666666555554 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6      0.61        45      16      99 .]     247     333 ..     240     333 .. 0.76
   2 ?    8.9   2.8     0.031       2.3      39      99 .]     315     375 ..     296     375 .. 0.80
   3 ?   11.0   7.9    0.0069      0.51      37      94 ..     348     405 ..     331     410 .. 0.81
   4 ?   11.7  12.2     0.004       0.3      31      99 .]     360     431 ..     353     431 .. 0.81
   5 ?    8.8   5.9     0.033       2.4      41      99 .]     401     459 ..     397     459 .. 0.88
   6 ?    3.4   8.0       1.5   1.1e+02      15      77 ..     442     507 ..     436     522 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.61
                HIP1_clath_bdg  16 svarqaqeeverekkeleeelerlk...eeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                   s   qa e++  + + lee++ +l+   e+ + +l+   + + +L+  +++ + +l+ +++sLe+   + + +s+ql+aL 
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVEDLGLALDSLEERVGDLEfavEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALA 327
                                   5666777777777777777655443211666677778888888999999999999************************99 PP

                HIP1_clath_bdg  94 aEkesL 99 
                                   +  esL
  gi|14601261|ref|NP_147796.1| 328 EDLESL 333
                                   877665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.031
                HIP1_clath_bdg  39 lkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaEkesL 99 
                                   + +  +++l+  +e le+L + +e+ +a++ +++  L++ e+  + l+++l++L++E e L
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDL 375
                                   334556778888999*****************************************98876 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0069
                HIP1_clath_bdg  37 erlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqa 94 
                                   e+  ++ae+ ++  ++ l++L++ele+ +++la++++sLe+ ++  +q++s+l++Lq+
  gi|14601261|ref|NP_147796.1| 348 EDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   33334566667788999***************************************97 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.004
                HIP1_clath_bdg  31 eleeelerlkee...aerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaEkesL 99 
                                    l+++l++l+ e    + +l+e +  le L++ l +    l++l++ L++ e+s + l++ la+LqaE e+L
  gi|14601261|ref|NP_147796.1| 360 SLTTSLDSLRTEledLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   455555555554111456788999********************************************9987 PP

  == domain 5  score: 8.8 bits;  conditional E-value: 0.033
                HIP1_clath_bdg  41 eeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaEkesL 99 
                                   ++ +++l+  +e l++L ++l++ +ae+++l++s+ +  +   ql s+++a + E esL
  gi|14601261|ref|NP_147796.1| 401 QQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESL 459
                                   677888999999999999*************9999999999999999999998888776 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 1.5
                HIP1_clath_bdg  15 lsvarqaqeeverekkeleeelerlkeeaerkle...eqkeelekLkreleakraelarlkssLes 77 
                                   l + r + + v  e + l e+l +++e+++r+ +   + ++++++L+++l +k  e ++  s+ ++
  gi|14601261|ref|NP_147796.1| 442 LGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDAsieDFQSQIQELRTQLDEKTREAQQTASTASR 507
                                   556666777777788888888988888888775444488999999********9999998887655 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.53        39       2      32 ..     274     304 ..     273     307 .. 0.84
   2 ?    8.5   2.2     0.036       2.7       3      30 ..     317     344 ..     308     357 .. 0.61
   3 ?    7.0   2.2       0.1       7.4       4      49 ..     353     398 ..     349     402 .. 0.90
   4 ?    3.9   1.3      0.99        73       9      35 ..     386     412 ..     379     413 .. 0.88
   5 ?    3.3   0.9       1.4   1.1e+02       3      30 ..     478     505 ..     476     515 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.53
                           LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                   ++ L+ q+s+L s v +l++ v++++  ++a
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEA 304
                                   678999************9999988766665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.036
                           LPP   3 deLssqVsqLkskvdqlssdvnsakaaa 30 
                                   d +s+q+++L ++ ++lss v++++a +
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   5566666666666666666655555544 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.1
                           LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaakeEAaRANqRlDNiaq 49 
                                   +  +++ +L +  d+l  +++++++ +++a++  +  N RlD +a+
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVAS 398
                                   55689*************************************9887 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.99
                           LPP   9 VsqLkskvdqlssdvnsakaaaqaake 35 
                                   +++L++  dq++s ++++++ +++a e
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRLATAEE 412
                                   578****************99999876 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 1.4
                           LPP   3 deLssqVsqLkskvdqlssdvnsakaaa 30 
                                   +   sq+++L ++ d+ + +++++++ a
  gi|14601261|ref|NP_147796.1| 478 EDFQSQIQELRTQLDEKTREAQQTASTA 505
                                   5567899999999888888877776655 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6      0.21        16     144     199 ..     322     377 ..     310     387 .. 0.82
   2 ?    4.9   1.7      0.17        13     156     207 ..     355     406 ..     332     412 .. 0.81
   3 ?    8.6  10.2     0.013      0.99     153     246 ..     408     497 ..     384     504 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.21
                          MPS2 144 kkqesPeklrrsnrklkaLevrveslkdELeakdevlrekeRelleLkkrlseyke 199
                                   + q+  e l +   ++  Le+rv s++d L++ +e +      l  L+  l+++  
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLST 377
                                   555556667777889999*******************9999999999999998865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.17
                          MPS2 156 nrklkaLevrveslkdELeakdevlrekeRelleLkkrlseykekYellqre 207
                                    + + +L + ++sl+ ELe+    l+e +  l +L+ rl++     + lq++
  gi|14601261|ref|NP_147796.1| 355 EEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQR 406
                                   5566789999999999999999999999999999999999998888888887 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.013
                          MPS2 153 rrsnrklkaLevrveslkdELeakdevlrekeRelleLkkrlseykekYellqrefslykarrveksqnslktai.khevi 232
                                       + l+aL   ++sl+ E+e  ++ + e +R l +L+++++  +   e+l ++    +a + +++q++   +i + +  
  gi|14601261|ref|NP_147796.1| 408 ATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLV--QAEEKNQRQDA---SIeDFQSQ 483
                                   34567889999******************************************9987..44444444444...44145777 PP

                          MPS2 233 isElkrklqeqtei 246
                                   i+El+ +l e+t+ 
  gi|14601261|ref|NP_147796.1| 484 IQELRTQLDEKTRE 497
                                   9*********9975 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  12.0    0.0015      0.11     174     330 ..     298     450 ..     283     462 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0015
                          Gp58 174 ieGlkatlasdklglkaeiqasaqgLsqkyddeirkLsakitttss..GtteayeskLddlraeftrsnqGmrveleskis 252
                                   ieG  + ++    +l   ++a +q+L q   ++++ Ls+++  +    G +e   s+ ++     t+s   +r+ele  +s
  gi|14601261|ref|NP_147796.1| 298 IEGRLEAVEGSLEDLSGAVDAMSQQL-QALAEDLESLSSRVEDLEArvGSVEDRLSQAEEDIDSLTTSLDSLRTELED-LS 376
                                   66666667777778899999999998.5678889999999998876225555555555666778999999*******7.55 PP

                          Gp58 253 GlqstqqstakqisqeiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlqstvsdpnsklesrvtqLadlie 330
                                      +  q++ + ++ ++ + ++ + ++qq l++    lq   ++ +sL+  v+ lq+++ +    ++ r+ qL++ ++
  gi|14601261|ref|NP_147796.1| 377 TRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVE----IDRRLGQLRSTVD 450
                                   5455566666777777777777777777777777777777777777777777777766654....5567777777665 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 ?    6.7   0.8      0.13       9.5       2      41 ..     324     363 ..     260     372 .. 0.65
   2 ?   10.8   9.7    0.0068       0.5       2      92 ..     324     417 ..     316     418 .. 0.85
   3 ?    1.5  16.5       5.1   3.8e+02      15      88 ..     414     504 ..     392     512 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.13
                        CENP-H   2 lplieqrdelssellklsqelrelqeeltevekenlrlkr 41 
                                   ++l e  + lss++++l++ + +++++l+++e+++ +l++
  gi|14601261|ref|NP_147796.1| 324 QALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTT 363
                                   2333334444444444444444444444444444433333 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0068
                        CENP-H   2 lplieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksr 79 
                                   ++l e  + lss++++l++ + +++++l+++e+++ +l++   +l +el+ l+   ++ +   e+l+ +l+++ + l++ +
  gi|14601261|ref|NP_147796.1| 324 QALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQaslEDLNTRLDQVASTLQQLQ 404
                                   66778888999999999999999***********99999999999999965555444444469889999999999999999 PP

                        CENP-H  80 qrwrvvknvasai 92 
                                   qr  +  + ++a+
  gi|14601261|ref|NP_147796.1| 405 QRLATAEESLQAL 417
                                   9999999888876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 5.1
                        CENP-H  15 llklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.................eklkeelekleaelkks 78 
                                   l++l+++l++lq+e+++++++++++ r+  +l +++   + e es                   e+ ++++++l+++l+++
  gi|14601261|ref|NP_147796.1| 414 LQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGeklvqaeeknqrqdasiEDFQSQIQELRTQLDEK 494
                                   344444444444444444444444444444444444322222222222244443333333466766777777777777777 PP

                        CENP-H  79 rqrwrvvknv 88 
                                    ++++ +  +
  gi|14601261|ref|NP_147796.1| 495 TREAQQTAST 504
                                   7766655555 PP

>> DUF2576  Protein of unknown function (DUF2576)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       7.4   5.4e+02      19      36 ..     329     346 ..     323     350 .. 0.86
   2 ?    7.7   0.1     0.037       2.7       7      33 ..     352     378 ..     350     383 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 7.4
                       DUF2576  19 eLnsLrrnvhDLCtrsGt 36 
                                   +L sL   v DL +r G 
  gi|14601261|ref|NP_147796.1| 329 DLESLSSRVEDLEARVGS 346
                                   799************996 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.037
                       DUF2576   7 sqhDyDrDqikreLnsLrrnvhDLCtr 33 
                                   sq + D D +   L+sLr    DL tr
  gi|14601261|ref|NP_147796.1| 352 SQAEEDIDSLTTSLDSLRTELEDLSTR 378
                                   8999999*******************9 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  11.5    0.0016      0.12     127     259 ..     318     450 ..     285     458 .. 0.71
   2 ?   -0.4   4.3         8   5.9e+02     159     211 ..     447     500 ..     439     507 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0016
                        Cluap1 127 qlaseitekgasLydlLekevelreartkals.rqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkk 206
                                   ++++++   +  L + L+  ve  ear   ++ r  + ee   +l+++++++++ele+++++l++ ++  + L++++++  
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDL-ESLSSRVEDLEARVGSVEdRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVA 397
                                   3444444444444.4455555555555555551333444444678888889999999999999999999999999999999 PP

                        Cluap1 207 qeleraqkrLqslqsvrPafmdeyekleeeLqelyeeYvekfrnlsylekqle 259
                                   + l++ q+rL++ ++   a  ++   l++e ++l +  ve  r l  l++ ++
  gi|14601261|ref|NP_147796.1| 398 STLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVD 450
                                   99999999999998888899999999999988888888888888888777766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 8
                        Cluap1 159 rqleleeie.kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeler 211
                                   ++++  ++e ++l e++ +++e+ ++  +++e+ +s+ ++L ++++ k++e ++
  gi|14601261|ref|NP_147796.1| 447 STVDAVRLEvESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   444444444234556666666666666666666666666666666666666655 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  17.6    0.0087      0.64      68     264 ..     243     438 ..     229     451 .. 0.65
   2 ?    6.1   6.2     0.072       5.3      58     110 ..     450     502 ..     436     508 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0087
                       DUF4686  68 qqklldseklcssltaelkhlqqkireLelev..lkqaqs..lksqnsLqeklaqekskvaeaeekileLqqkLeqa.hkv 143
                                   +++l+ +e+ +  l   l++l++++ +Le  v  l+ + s     +  L++++a+   ++ + e  + +L    ++  +++
  gi|14601261|ref|NP_147796.1| 243 EERLSLVEQAVEDLGLALDSLEERVGDLEFAVedLTLQLSslDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMsQQL 323
                                   677777888888888888888888888886551133333322334455666666666666666666666766666664444 PP

                       DUF4686 144 rltearilekkqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlk 224
                                   +   a + + + L +++++++    ++  +l         L ++ + L++ ++ l  + a+ + +  ++++r++q    l+
  gi|14601261|ref|NP_147796.1| 324 Q---ALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQ 401
                                   4...44556666666666666666666666666666666666666666666666666666666666666667777777777 PP

                       DUF4686 225 klenekrksdehlksnqeLsekLsslqqekealqeelqqv 264
                                   +l++   + +e   s q L+e L slq e e+lq+ + ++
  gi|14601261|ref|NP_147796.1| 402 QLQQRLATAEE---SLQALTEDLASLQAEVETLQQSIVEI 438
                                   77777777666...5699***************9966544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.072
                       DUF4686  58 ikikaElkqaqqklldseklcssltaelkhlqqkireLelevlkqaqslksqn 110
                                     +++E++ + +kl++ e++   + a +++ q++i+eL+ ++ +++++ +++ 
  gi|14601261|ref|NP_147796.1| 450 DAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTA 502
                                   56899************************************988888877665 PP

>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1     0.027         2       7      30 ..     476     499 ..     472     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.027
                                   SC....HHHCHHHHHHHHHHCCHC CS
                        ApoC-I   7 afeslpdklkEfgktledKaraai 30 
                                   ++e ++ +++E+  +l +K+r+a 
  gi|14601261|ref|NP_147796.1| 476 SIEDFQSQIQELRTQLDEKTREAQ 499
                                   6799*****************985 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.23        17     243     300 ..     301     360 ..     291     386 .. 0.61
   2 ?    5.9   2.6     0.065       4.8     244     304 ..     358     420 ..     353     431 .. 0.72
   3 ?    6.8   1.9     0.035       2.6     239     293 ..     388     444 ..     369     452 .. 0.56
   4 ?    3.0   3.1      0.51        37     245     297 ..     450     504 ..     434     527 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.23
                         FemAB 243 ylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefiek 300
                                   +l+ +++ le+l+  ++ + ++l+   e  ++  ++++ le  + s+e++l++aee i++
  gi|14601261|ref|NP_147796.1| 301 RLEAVEGSLEDLSGAVDAMSQQLQALAEdlESLSSRVEDLEARVGSVEDRLSQAEEDIDS 360
                                   555555555555555555555555555556666666666666666666666666665544 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.065
                         FemAB 244 lkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefiekdgee 304
                                   +++l++ l+ l+++l++l  +l++++   +  +++l+++ ++l++l+++l+ aee  ++  e+
  gi|14601261|ref|NP_147796.1| 358 IDSLTTSLDSLRTELEDLSTRLAEAQAslEDLNTRLDQVASTLQQLQQRLATAEESLQALTED 420
                                   567777777777777777777777777777888888888888888888888888876665554 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.035
                         FemAB 239 nlaeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelke 293
                                   +l+++l+++++ l++l+++la+ ee+l+  +e  ++ +  +++l++ + + +++l++
  gi|14601261|ref|NP_147796.1| 388 DLNTRLDQVASTLQQLQQRLATAEESLQALTEdlASLQAEVETLQQSIVEIDRRLGQ 444
                                   345555555555555555555555555555555555555555555555555555555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.51
                         FemAB 245 kelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeef 297
                                   + ++ + e l +kl + eek+++++   +  +++++el  ql++ ++e +++ + 
  gi|14601261|ref|NP_147796.1| 450 DAVRLEVESLGEKLVQAEEKNQRQDAsiEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   4445556666777777777766666678888888888888888888887777663 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 ?    7.1   0.4     0.089       6.5      48      85 ..     304     341 ..     273     342 .. 0.86
   2 ?    4.8   3.3      0.44        32      10      84 ..     317     389 ..     315     391 .. 0.67
   3 ?    3.8   5.8      0.93        68      54      86 .]     380     412 ..     342     424 .. 0.74
   4 ?    3.1   4.9       1.5   1.1e+02       5      37 ..     399     431 ..     390     469 .. 0.62
   5 ?    6.5   6.0      0.14        10       2      80 ..     424     504 ..     423     508 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.089
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  48 afqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                   a ++ +e +  a++ + ++L+ ++e l++ ++++ed +
  gi|14601261|ref|NP_147796.1| 304 AVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLE 341
                                   66777888899999999999999999999999999987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100  10 rqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafeda 84 
                                   +++++++q+ ae+le++ +r++   + ++s    +  ++ ++ ++ ++ +++ l ++Le++s  l +a +++ed 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGS--VEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDL 389
                                   455555555555555555555555555544..3555567788889999999999999999999999999998885 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.93
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100  54 eewkqaaqklvdaLeeisealkqaanafedaDe 86 
                                   +e ++++++l++ L++++++l+q  ++++ a+e
  gi|14601261|ref|NP_147796.1| 380 AEAQASLEDLNTRLDQVASTLQQLQQRLATAEE 412
                                   455666677777777777777777777776664 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                        WXG100   5 dpeelrqaaarfqkqaeeledelqrlkaevdal 37 
                                   + ++l+q  a++ ++ + l++ l++l+aev+ l
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   344444444444455555555555555555554 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.14
                                   HCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCT..HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        WXG100   2 ikvdpeelrqaaarfqkqaeeledelqrlkaevdalqsgWs..GaaadafqaefeewkqaaqklvdaLeeisealkqaana 80 
                                   ++++ e l+q++ ++++  ++l++ +++++ ev++l+++     +  ++ +a +e ++ ++q+l ++L+e +++ +q+a++
  gi|14601261|ref|NP_147796.1| 424 LQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVqaEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   7999********************************9988856777889999999*****************999999976 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       6.5   4.8e+02      12      85 ..     246     317 ..     226     322 .. 0.67
   2 ?    5.8   0.2      0.29        21      12      80 ..     281     348 ..     269     353 .. 0.58
   3 ?    8.4   0.3     0.047       3.4      15      80 ..     316     376 ..     302     380 .. 0.64
   4 ?    9.4   5.0     0.023       1.7      16      86 ..     366     438 ..     351     448 .. 0.62
   5 ?    4.3   5.1      0.87        64      13      71 ..     436     500 ..     428     507 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 6.5
                       DUF2203  12 LpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdleaglvD 85 
                                   L l+++ +e+l  + + lee++ +le a ++ +  + ++l +++ +le+++ ++  ++e++   + dl  g vD
  gi|14601261|ref|NP_147796.1| 246 LSLVEQAVEDLGLALDSLEERVGDLEFAVEDLTL-QLSSLDSRVGALEDRVADIEGRLEAVEGSLEDL-SGAVD 317
                                   5555555555555555555555555555555433.377888888888888888888888888888888.47777 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.29
                       DUF2203  12 Lpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdle 80 
                                   L  l++++ +l +  +++e    +le+ + + e  +    ++ ++l++l++ +e+l +++e+l + v ++e
  gi|14601261|ref|NP_147796.1| 281 LSSLDSRVGALEDRVADIEG---RLEAVEGSLEDLSgaVDAMSQQLQALAEDLESLSSRVEDLEARVGSVE 348
                                   44444444444444444444...444444333322245788888888888888888888888888776665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.047
                       DUF2203  15 lkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdle 80 
                                   ++ + ++l+al+++le+l++++e+ +a+       + e +l+++e+ i++l++ +++l  e+ dl+
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEAR-----VGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   4455556666666666666666666666.....556677777777777777777777777666665 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.023
                       DUF2203  16 kelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdleaglvDF 86 
                                   ++l +el +l ++l+e++++le+ +++ ++ +   ++l+++l+++e+++++l+e + +l +ev  l++ +v+ 
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEAQASLEDLNTRLDQVAstLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEI 438
                                   3333333344444444444444444443333366888888888888888888888888888888888887765 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.87
                       DUF2203  13 pllkelleelr....alrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeiee 71 
                                    +++++l +lr    a+r e+e+l e+l +a++++++++   +  +++++el+++++e ++e ++
  gi|14601261|ref|NP_147796.1| 436 VEIDRRLGQLRstvdAVRLEVESLGEKLVQAEEKNQRQDasIEDFQSQIQELRTQLDEKTREAQQ 500
                                   55555555555222255566666666776666666666666778888888888888888887766 PP

>> MT  Microtubule-binding stalk of dynein motor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.3   0.00077     0.057       9     103 ..     329     426 ..     321     438 .. 0.88
   2 ?    1.3   0.8       1.9   1.4e+02     215     277 ..     448     507 ..     431     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00077
                            MT   9 klqstaaqvddlkaklaaqevelkqknedadkliq...vvgvetekvskekaiadeeekkvavinkevkkkqkdceedlak 86 
                                    l+s +++v+dl a++ + e  l q +ed d l      +  e e +s   a a+   + ++   ++v+   ++ ++ la 
  gi|14601261|ref|NP_147796.1| 329 DLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTsldSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLAT 409
                                   6899****************************97511156789999********999999********************* PP

                            MT  87 aepallaaqealntlnk 103
                                   ae +l a  e l +l+ 
  gi|14601261|ref|NP_147796.1| 410 AEESLQALTEDLASLQA 426
                                   *******9999998865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.9
                            MT 215 dvepkrqalekanaelaaaqeklaaikakiaelnanlaeltaafekatadklkcqqeaeatar 277
                                    v+  r  +e   ++l +a+ek  +  a i ++++++ el ++++  t +    qq a +++r
  gi|14601261|ref|NP_147796.1| 448 TVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREA---QQTASTASR 507
                                   577778888889999999999999999999999999999999998888764...555554444 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       8.7   6.4e+02      32      61 ..     242     271 ..     240     278 .. 0.84
   2 ?    2.2   0.0       3.1   2.3e+02      22      51 ..     274     303 ..     260     315 .. 0.48
   3 ?    9.5   1.0     0.016       1.2      33      70 .]     320     357 ..     311     360 .. 0.84
   4 ?    3.9   5.6      0.95        70      10      63 ..     346     399 ..     345     413 .. 0.50
   5 ?    5.1   4.3      0.38        28      32      61 ..     403     432 ..     388     437 .. 0.63
   6 ?    1.9   6.9       3.8   2.8e+02      32      63 ..     403     434 ..     402     470 .. 0.78
   7 ?    2.8   6.7       2.1   1.6e+02      33      66 ..     467     500 ..     453     504 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 8.7
                        Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkele 61 
                                   L+++l+  +q +e L   l++lee+v +le
  gi|14601261|ref|NP_147796.1| 242 LEERLSLVEQAVEDLGLALDSLEERVGDLE 271
                                   678888999999999999999999987765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 3.1
                        Csm1_N  22 vsklvhENsvLsqkletkdqeiesLkeqla 51 
                                   v+ l+   s L+ ++   ++++  ++ +l+
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLE 303
                                   444444444444444444444444444444 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.016
                        Csm1_N  33 sqkletkdqeiesLkeqlaeleekvkeleerrkkqeEe 70 
                                   sq+l+   + +esL  +++ le++v + e+r +++eE+
  gi|14601261|ref|NP_147796.1| 320 SQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEED 357
                                   78888888888999999999999998888888888885 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.95
                        Csm1_N  10 sVqerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                   sV++rl +A+  +  l+     L+++le  ++++ + ++ l+ l++++++  + 
  gi|14601261|ref|NP_147796.1| 346 SVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVAST 399
                                   677777777777776666555555555554444444444444444444443332 PP

  == domain 5  score: 5.1 bits;  conditional E-value: 0.38
                        Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkele 61 
                                   L+q+l t ++ +++L e la+l+++v+ l+
  gi|14601261|ref|NP_147796.1| 403 LQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   566666666666666666666666666655 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 3.8
                        Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                   L+q+l t ++ +++L e la+l+++v+ l+++
  gi|14601261|ref|NP_147796.1| 403 LQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   67777777777777777777777777777654 PP

  == domain 7  score: 2.8 bits;  conditional E-value: 2.1
                        Csm1_N  33 sqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                   ++k++ +d  ie  + q++el+++++e   ++++
  gi|14601261|ref|NP_147796.1| 467 EEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   567888999****************998776665 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.7    0.0094      0.69     198     358 ..     361     521 ..     285     530 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0094
                         LMBR1 198 ldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslaklek 278
                                   l   l++l++e++ l+t+++ea+  ledl++++ ++ +++++ +++    ee l+   e++a+      ++  e+l+++  
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASL-----QAEVETLQQSIV 436
                                   5567889999999999999999999999999999999999998877799999999888887777.....445555555555 PP

                         LMBR1 279 qlikalqkrertekqwkrlleka....lelediiknksskekefkssessrrgefakqg.klkltptleyywaklllplvl 354
                                   ++ ++l + + t +  +  +e      ++ e+  + ++ + ++f+s+ ++ r+++ +++ +   t ++   w++++ ++ l
  gi|14601261|ref|NP_147796.1| 437 EIDRRLGQLRSTVDAVRLEVESLgeklVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTrEAQQTASTASRWSMAAAGASL 517
                                   555555555555555555555551100333333333333333333333322222222223333444455555555555555 PP

                         LMBR1 355 lils 358
                                   ++l+
  gi|14601261|ref|NP_147796.1| 518 IALA 521
                                   5554 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 ?    1.8  14.7      0.61        45      12      97 ..     373     440 ..     253     512 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.61
                    V_ATPase_I  12 rDlnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenl 92 
                                   +Dl++ +++ q +  +   r+d++  +l+ l++ ++                    e++l+ l+e+l +l++e+++l+++ 
  gi|14601261|ref|NP_147796.1| 373 EDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLAT------------------AEESLQALTEDLASLQAEVETLQQSI 435
                                   2222222222222222222222222222222222222..................11112222222222222222222222 PP

                    V_ATPase_I  93 eklkk 97 
                                    ++ +
  gi|14601261|ref|NP_147796.1| 436 VEIDR 440
                                   22222 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 ?    3.3   0.1         1        76      29      47 ..     260     278 ..     251     282 .. 0.74
   2 ?   10.6   0.2    0.0052      0.39       6      45 ..     304     346 ..     302     355 .. 0.82
   3 ?    2.3   0.9       2.1   1.6e+02      23      39 ..     366     382 ..     346     394 .. 0.54
   4 ?    5.5   1.1      0.21        15       7      43 ..     396     435 ..     393     443 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1
                         HSBP1  29 iDdMssriDdLEksiadlm 47 
                                   +D +++r+ dLE  ++dl+
  gi|14601261|ref|NP_147796.1| 260 LDSLEERVGDLEFAVEDLT 278
                                   6777888888888887776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0052
                         HSBP1   6 vVenlLqqlqdkFqtmsdqi...lsriDdMssriDdLEksiad 45 
                                   +Ve  L++l+   ++ms+q+    + ++ +ssr++dLE+ + +
  gi|14601261|ref|NP_147796.1| 304 AVEGSLEDLSGAVDAMSQQLqalAEDLESLSSRVEDLEARVGS 346
                                   799999999999999999972225689999********98765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 2.1
                         HSBP1  23 dqilsriDdMssriDdL 39 
                                   d++ + ++d+s+r+ + 
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEA 382
                                   23333455555555555 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.21
                         HSBP1   7 VenlLqqlqdkFqtmsdqi...lsriDdMssriDdLEksi 43 
                                   V  +Lqqlq++  t ++++   ++ +  ++  ++ L++si
  gi|14601261|ref|NP_147796.1| 396 VASTLQQLQQRLATAEESLqalTEDLASLQAEVETLQQSI 435
                                   7789**********97765111445555566677777766 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       7.6   5.6e+02      17      26 ..     367     376 ..     364     377 .. 0.82
   2 ?    8.7   0.4     0.017       1.2       9      24 ..     478     493 ..     477     497 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 7.6
                    Nup54_57_C  17 HLkKElEsik 26 
                                    L++ElE+++
  gi|14601261|ref|NP_147796.1| 367 SLRTELEDLS 376
                                   59*****987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.017
                    Nup54_57_C   9 eDYekQLqHLkKElEs 24 
                                   eD + Q+q L+++l++
  gi|14601261|ref|NP_147796.1| 478 EDFQSQIQELRTQLDE 493
                                   9*************97 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0062      0.46       2      62 ..     284     344 ..     283     346 .. 0.91
   2 ?    0.3   0.1       8.2   6.1e+02       5      58 ..     343     396 ..     340     401 .. 0.68
   3 ?    1.3   0.6       4.1     3e+02      23      59 ..     389     425 ..     367     429 .. 0.85
   4 ?    3.8   1.8      0.67        50       2      58 ..     403     459 ..     396     463 .. 0.85
   5 ?    0.3   3.0       8.3   6.1e+02       3      60 ..     432     489 ..     430     492 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0062
                 TRAF_BIRC3_bd   2 lekklsaLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqLerti 62 
                                   l  ++ aLe +va  E+     +   e  s +++a+++q ++  e  e+L+ +v++Le  +
  gi|14601261|ref|NP_147796.1| 284 LDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   56789999999999999999999999*******************************9766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 8.2
                 TRAF_BIRC3_bd   5 klsaLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqL 58 
                                   ++   e ++   E  +  L    ++  t++e+++   +++q   e L++++ q 
  gi|14601261|ref|NP_147796.1| 343 RVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQV 396
                                   555566666666666666666777888888888888888888888888777665 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 4.1
                 TRAF_BIRC3_bd  23 LnrEverssttieaverqrrldqekieaLekKvrqLe 59 
                                   Ln   +++++t++++++  + ++e  +aL++ +++L+
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQ 425
                                   6777889999999999999999999999999888887 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.67
                 TRAF_BIRC3_bd   2 lekklsaLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqL 58 
                                   l+++l++ e+ ++      + L+ Eve  +  i ++ r   + + +++a+   v++L
  gi|14601261|ref|NP_147796.1| 403 LQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESL 459
                                   667777777777777677789999***************999999999999988887 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 8.3
                 TRAF_BIRC3_bd   3 ekklsaLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqLer 60 
                                   ++ + +++++++     V     Eve+   ++ + e+ ++     ie  +  +++L+ 
  gi|14601261|ref|NP_147796.1| 432 QQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRT 489
                                   6667777777777777777788899*99999988888888888999999999999985 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.1      0.03       2.2      21      72 ..     461     510 ..     447     528 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.03
                                   XXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXXGGGGGXEEEEECSTTT CS
                        FliD_N  21 dkleqkktklewkqsayrelnsklsnlksalsalsksstfsakkatssdesv 72 
                                   +kl q+++k++ + + +++++s++++l+++l+  +k+ + ++++ t+s  s+
  gi|14601261|ref|NP_147796.1| 461 EKLVQAEEKNQRQDASIEDFQSQIQELRTQLD--EKTREAQQTASTASRWSM 510
                                   578999999********************775..222222221122221122 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1       2.3   1.7e+02     100     149 ..     273     322 ..     233     325 .. 0.64
   2 ?    9.5   0.8     0.011      0.79      96     144 ..     318     366 ..     299     375 .. 0.55
   3 ?    7.7   3.8     0.041         3      82     153 ..     397     466 ..     381     467 .. 0.81
   4 ?    0.7   0.2       5.7   4.2e+02      22      49 ..     485     512 ..     481     518 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 2.3
                                   ------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXX CS
                       DUF1465 100 avaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeqler 149
                                   av++L  +l +L +r  +L +rv+ ++ +l + + + e  + +v++  ++
  gi|14601261|ref|NP_147796.1| 273 AVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQ 322
                                   45566666666666666666666666666665555554445555555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.011
                                   ----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXX CS
                       DUF1465  96 sdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpva 144
                                     +++++ L e+l++L +r e+L +rv +++++l++ +e+ ++ +  ++
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLD 366
                                   3344555555555555555555555555555555555555444344444 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.041
                                   SSSS-------..-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXXXXXX CS
                       DUF1465  82 asekkrvklaaaeasdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeqlerLeaa 153
                                   as  ++++++   a+++e+++ L e+l++L ++ e+L++ ++++dr+l + +++ +a   +v+++ e+L +a
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQQRL--ATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQA 466
                                   44444444444..89999******************************999999988888888888877765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 5.7
                                   HHHHHHHTTHHHHHHCTS-HHHHHHHHH CS
                       DUF1465  22 eetaayldgegreeskalsreaalayas 49 
                                   +e ++ ld+++re+++++s +++ ++a+
  gi|14601261|ref|NP_147796.1| 485 QELRTQLDEKTREAQQTASTASRWSMAA 512
                                   6889999***999999999988887776 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1       4.7   3.5e+02      21      48 ..     309     336 ..     274     343 .. 0.51
   2 ?    6.6   0.8      0.12       8.6       8      71 ..     316     381 ..     308     389 .. 0.68
   3 ?    8.1   9.2      0.04         3      15      86 ..     380     455 ..     358     491 .. 0.71
   4 ?    1.8   1.8       3.5   2.6e+02      21      89 ..     428     500 ..     423     515 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 4.7
                          SesA  21 ikglpeaFrevgkrLplvqetLedaksq 48 
                                   +++l  a ++ +++L+ + e Le+  s+
  gi|14601261|ref|NP_147796.1| 309 LEDLSGAVDAMSQQLQALAEDLESLSSR 336
                                   3334444444444444444444443333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.12
                          SesA   8 veaaiklydaikd.ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa.ikpvlescke 71 
                                   v+a+++  +a+ + +++l    ++ ++r+  v++ L++a++ ++s + + d+  + ++++ ++  e
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEdLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTeLEDLSTRLAE 381
                                   566665555554438999999999999999999999999999999999888755444433333333 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.04
                          SesA  15 ydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesa....ikpvlesckekatkleeifekvapa 86 
                                    +a  ++++l   +++v++ L+ +q+ L +a+++l++ ++d ++ +a    +++++ + + ++ +l +  ++v+ +
  gi|14601261|ref|NP_147796.1| 380 AEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAevetLQQSIVEIDRRLGQLRSTVDAVRLE 455
                                   3444458999999999999999999999999999999999999999999999999999999999999999998322 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 3.5
                          SesA  21 ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa....ikpvlesckekatkleeifekvapapad 89 
                                   +++l++++ e+ +rL  ++ t ++++ ++es  ++  + ++       ++e+ ++++++l + +++ ++++++
  gi|14601261|ref|NP_147796.1| 428 VETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEknqrQDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   5566777777777777777777777777766555544433344556677777777777777766665333332 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 ?    1.5   8.4       5.5   4.1e+02      53      94 ..     294     343 ..     162     361 .. 0.72
   2 ?    8.9   1.7     0.028       2.1      61      96 ..     353     387 ..     345     396 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 5.5
                       DUF4140  53 qvervpnreaeee........elkalraeleeledelaaledelaaaear 94 
                                   +v+  + r ++ e        +++a+ ++l++l ++l+ l+++ + +ear
  gi|14601261|ref|NP_147796.1| 294 RVADIEGRLEAVEgsledlsgAVDAMSQQLQALAEDLESLSSRVEDLEAR 343
                                   33333333333333344466645555555555555555555555555554 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.028
                       DUF4140  61 eaeeeelkalraeleeledelaaledelaaaearla 96 
                                   +aee+ +++l+ +l++l++el++l+ +la a+a+l+
  gi|14601261|ref|NP_147796.1| 353 QAEED-IDSLTTSLDSLRTELEDLSTRLAEAQASLE 387
                                   33333.666777777777777777777666666654 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 ?    3.7   0.0       0.7        52      45      66 ..     293     314 ..     281     341 .. 0.78
   2 ?    5.7   0.5      0.17        12      68     142 ..     366     442 ..     341     469 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.7
                       Vip3A_N  45 qllndisgkldgvngslndlia 66 
                                   + + di g+l+ v+gsl+dl  
  gi|14601261|ref|NP_147796.1| 293 DRVADIEGRLEAVEGSLEDLSG 314
                                   5578999************954 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.17
                       Vip3A_N  68 gnlntelskeilkianeqnqvlndvnnkldaintmlrvylpkitsm...lsdvmkqnyalslqieylskqlqeisdkl 142
                                     l tel     ++a+ q   l+d+n++ld + ++l+    ++++    l+ +  +  +l  ++e l + + ei  +l
  gi|14601261|ref|NP_147796.1| 366 DSLRTELEDLSTRLAEAQA-SLEDLNTRLDQVASTLQQLQQRLATAeesLQALTEDLASLQAEVETLQQSIVEIDRRL 442
                                   5678888877777776665.5899999999999988876666654311144444555555666777777777776665 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.0    0.0056      0.41     113     225 ..     260     375 ..     233     378 .. 0.73
   2 ?   11.9  12.5    0.0013     0.099     117     227 ..     313     426 ..     285     433 .. 0.77
   3 ?    6.1  10.2     0.081         6     120     218 ..     358     459 ..     350     463 .. 0.53
   4 ?    3.6  11.5      0.47        35     121     217 ..     394     500 ..     389     510 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0056
                          CorA 113 yrlldeivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddklldded 190
                                   +  l+e v +l+ ++e+l  +l  l++++   +++ ++i ++l +++ +l  l  a+ ++ + l++l +  +  +   ++ 
  gi|14601261|ref|NP_147796.1| 260 LDSLEERVGDLEFAVEDLTLQLSSLDSRVgaLEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEdLESLSSRVEDL 340
                                   455666667777777777777777777777777777788888888887777776666666666655555544555555666 PP

                          CorA 191 keylrdlldelerllemlealrerleslqdtyssl 225
                                   + +   ++d+l++++e++++l   l+sl+ ++  l
  gi|14601261|ref|NP_147796.1| 341 EARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDL 375
                                   68899999999999999999999999999888766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0013
                          CorA 117 deivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkeyl 194
                                      vd + ++l++l e+l+ l++++   + +  +  ++l+q ++++  l ++l  +r+ l++l +  a++    ++ + +l
  gi|14601261|ref|NP_147796.1| 313 SGAVDAMSQQLQALAEDLESLSSRVedLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTrLAEAQASLEDLNTRL 393
                                   567899999999999999999999977777778888999999999999999999999999877774333333333444568 PP

                          CorA 195 rdlldelerllemlealrerleslqdtysslls 227
                                   +++ + l++l++ l +  e l+ l + ++sl++
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESLQALTEDLASLQA 426
                                   888888888888888888888888877777766 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.081
                          CorA 120 vdrlfellekleeeldeledel.edstkkeil.relaqlrrrlvklrralapnrevlkrlla.kaddkllddedkeylrdl 197
                                   +d+l + l+ l +el++l+++l e + + e+l  +l q+  +l +l++ la+ +e l++l +  a    + ++ ++ + ++
  gi|14601261|ref|NP_147796.1| 358 IDSLTTSLDSLRTELEDLSTRLaEAQASLEDLnTRLDQVASTLQQLQQRLATAEESLQALTEdLASLQAEVETLQQSIVEI 438
                                   566677777777777777777763333333330344445566666666666666666444442111111222222235666 PP

                          CorA 198 ldelerllemlealrerlesl 218
                                     +l +l  +++a+r  +esl
  gi|14601261|ref|NP_147796.1| 439 DRRLGQLRSTVDAVRLEVESL 459
                                   666666777777776666665 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.47
                          CorA 121 drlfellekleeeldeledel.........edstkkeilrelaqlrrrlvklrralapnrevlk....rllakaddklldd 188
                                   d+++ +l++l ++l  +e+ l          + + + + ++++++ rrl++lr+ + + r  ++    +l++ +++++  d
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESLqaltedlasLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVEslgeKLVQAEEKNQRQD 474
                                   555566666666666666666665555588788888888888888888888888888888777744445555555555555 PP

                          CorA 189 edkeylrdlldelerllemlealrerles 217
                                   +    ++d +++++ l  +l+   + +++
  gi|14601261|ref|NP_147796.1| 475 AS---IEDFQSQIQELRTQLDEKTREAQQ 500
                                   55...999999999987777754444443 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.66        48     115     154 ..     294     333 ..     242     349 .. 0.61
   2 ?   10.4   8.5    0.0039      0.29      57     155 ..     315     411 ..     303     419 .. 0.74
   3 ?    0.6   8.7       3.8   2.8e+02      50     126 ..     420     501 ..     410     507 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.66
                       DUF4763 115 qlaelqqhlkasrkslkelreslcqekkrlrklqkrlnel 154
                                   ++a+++ +l+a + sl++l   +    ++l++l++ l+ l
  gi|14601261|ref|NP_147796.1| 294 RVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESL 333
                                   4444444444444444444444444444444444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0039
                       DUF4763  57 elekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelresl 137
                                    ++++ q+++ l + L   +    e d ++     +++l++ + +i  L  +   Lr +l++l+ +l + ++sl++l+++l
  gi|14601261|ref|NP_147796.1| 315 AVDAMSQQLQALAEDLES-LSSRVE-DLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRL 393
                                   444444444444444442.222222.666667777777777999************************************* PP

                       DUF4763 138 cqekkrlrklqkrlneld 155
                                    q  ++l++lq+rl   +
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAE 411
                                   ************997655 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 3.8
                       DUF4763  50 dLdeiydelekiKqrvlelrskLalnvp...ecPei..decvdedlele.lltseqpeileLqrnnhkLrqqlaelqqhlk 124
                                   dL + ++e+e++ q   e++++L+ +++   +   +  ++  ++ +++e +++ +   i + q + + Lr ql+e ++  +
  gi|14601261|ref|NP_147796.1| 420 DLASLQAEVETLQQSIVEIDRRLG-QLRstvDAVRLevESLGEKLVQAEeKNQRQDASIEDFQSQIQELRTQLDEKTREAQ 499
                                   555555555555555555555555.22211133333433333333333303333456788888888888888887776666 PP

                       DUF4763 125 as 126
                                   ++
  gi|14601261|ref|NP_147796.1| 500 QT 501
                                   55 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.83        61      43      70 ..     319     346 ..     260     359 .. 0.62
   2 ?    4.5   0.3      0.44        33      40      72 ..     358     390 ..     330     409 .. 0.46
   3 ?    7.6   0.4     0.047       3.5      26      86 ..     395     453 ..     382     456 .. 0.76
   4 ?    0.6   1.3       6.8     5e+02      41      80 ..     457     496 ..     452     507 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.83
                       DUF4446  43 leellkekleeveelkeeseelekeiee 70 
                                   + ++l+   e++e+l++++e+le+++ +
  gi|14601261|ref|NP_147796.1| 319 MSQQLQALAEDLESLSSRVEDLEARVGS 346
                                   3333444444444444444444444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.44
                       DUF4446  40 gksleellkekleeveelkeeseelekeieele 72 
                                    +sl + l +  +e+e+l+++ +e ++++e+l+
  gi|14601261|ref|NP_147796.1| 358 IDSLTTSLDSLRTELEDLSTRLAEAQASLEDLN 390
                                   223333333333333333333333333333333 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.047
                       DUF4446  26 klkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkvglvr 86 
                                   ++ + +++l+  ++ ++ ee l+  +e++ +l++e+e+l+++i e++++l +  ++v  vr
  gi|14601261|ref|NP_147796.1| 395 QVASTLQQLQ--QRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVR 453
                                   3444444443..3677889999999999999999999999999999999999888888777 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 6.8
                       DUF4446  41 ksleellkekleeveelkeeseelekeieeleeklkkslq 80 
                                   +sl e+l +  e+ ++ +++ e+ +++i+el+++l+++ +
  gi|14601261|ref|NP_147796.1| 457 ESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTR 496
                                   5666666666677777777777777777777776666554 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.5      0.14        11      43      93 ..     317     370 ..     242     383 .. 0.70
   2 ?    4.7   6.1      0.46        34      16     111 ..     318     414 ..     308     439 .. 0.52
   3 ?    5.4   8.7      0.29        21      19      95 ..     405     491 ..     394     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.14
                                   X.XXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Troponin  43 glseeqlqelckklh...eridkleeekydieekvakkdkeieelkkkvndlrG 93 
                                   ++  +qlq+l+++l    +r++ le     +e   ++ +++i+ l+ ++ +lr 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLEslsSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRT 370
                                   223356666655544111455555555556677777777777777766666654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.46
                                   HHHTXXXXXXXXXXXXXXXXXXXX.XXX.XX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Troponin  16 lkfeqrkkeeerlrvLkerieplkeldglse....eqlqelckklheridkleeekydieekvakkdkeieelkkkvndlr 92 
                                   +  +q +  +e l++L+ r+e l++  g s      q +e    l   +d l  e +d+ +  a+ ++  e+l+ ++ ++ 
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVG-SVedrlSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVA 397
                                   5566666667777777777777764444.2234554444444444445555555555555555555555555555544444 PP

                                   XXXXXXXXXXX---THHHH CS
                      Troponin  93 GkfkkpalKkvrktadekl 111
                                   +  ++  l++   ta+e l
  gi|14601261|ref|NP_147796.1| 398 STLQQ--LQQRLATAEESL 414
                                   43332..222233333333 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.29
                                   TXXXXXXXXXXXXXXXXXXXX.XXX.XX............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Troponin  19 eqrkkeeerlrvLkerieplkeldglse............eqlqelckklheridkleeekydieekvakkdkeieelkkk 87 
                                   +    +ee l++L e   +l+++ +                ql++ +   +  ++ l e+  + eek +++d+ ie+ + +
  gi|14601261|ref|NP_147796.1| 405 QRLATAEESLQALTEDLASLQAEVE--TlqqsiveidrrlGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQ 483
                                   4445677778888888888875444..2335888889999***************************************** PP

                                   XXXXXXXX CS
                      Troponin  88 vndlrGkf 95 
                                   +++lr + 
  gi|14601261|ref|NP_147796.1| 484 IQELRTQL 491
                                   *****875 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   4.5      0.34        25      71     147 ..     436     510 ..     310     512 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.34
                       DUF2400  71 ffnsedllallkalkelleksgsLeeaflkaeeeeeeleealeafreafle.kekrtrkleflipspekksacKRlnm 147
                                   +  +++l +l +++ ++  + +sL e +++aee++++  +++e+f+++++e +   t+  e+    ++++s++ R+ m
  gi|14601261|ref|NP_147796.1| 436 VEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQElR---TQLDEKTREAQQTASTASRWSM 510
                                   33344555566666666666667766666688888888999999999999842...3333334455556777777777 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.4    0.0045      0.33      70     130 ..     317     380 ..     286     388 .. 0.82
   2 ?    4.5   4.6      0.23        17      73     118 ..     390     435 ..     366     458 .. 0.57
   3 ?    2.9   4.1      0.71        53      72     114 ..     459     501 ..     445     511 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0045
                   DLP_helical  70 dvlerqlpeaeerleelekevekleesakriekelaelkkeieearie...lreelkayfsdLi 130
                                   d +++ql+   e le l++ ve+le ++   e++l++++++i    +    lr+el+++ ++L 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSldsLRTELEDLSTRLA 380
                                   8999************************************998777651115677777777665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.23
                   DLP_helical  73 erqlpeaeerleelekevekleesakriekelaelkkeieeariel 118
                                   + +l ++ + l++l++ ++ +ees++ ++++la+l+ e+e+ ++ +
  gi|14601261|ref|NP_147796.1| 390 NTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSI 435
                                   3344444444555555555555555555555555555554444443 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.71
                   DLP_helical  72 lerqlpeaeerleelekevekleesakriekelaelkkeieea 114
                                   l+++l +aee+ +++++ +e+ +++ ++++++l e  +e +++
  gi|14601261|ref|NP_147796.1| 459 LGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   4455566666666666666666666666666666666665555 PP

>> Vps52  Vps52 / Sac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.13       9.5      16      72 ..     288     344 ..     274     359 .. 0.79
   2 ?    8.5   1.7    0.0099      0.73      13      80 ..     327     394 ..     316     397 .. 0.82
   3 ?    3.0   7.0      0.47        35      17      97 ..     387     468 ..     381     507 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.13
                         Vps52  16 iaslhnqiaaidsvleqledlLeeFqsdlssissdikklqekSnelqlrLenrkave 72 
                                   ++ l +++a+i+  le +e +Le+    ++ +s++++ l e   +l++r e  +a  
  gi|14601261|ref|NP_147796.1| 288 VGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   567788999999999999999999999999999999999999999999888776543 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0099
                         Vps52  13 seniaslhnqiaaidsvleqledlLeeFqsdlssissdikklqekSnelqlrLenrkaveaklsklvd 80 
                                   +e ++sl+ +++++++ +  +ed L++ ++d++s+++ ++ l+    +l+ rL   +a    l   +d
  gi|14601261|ref|NP_147796.1| 327 AEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLD 394
                                   46788999999999999999999999999999999999999999999999999999998877766655 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.47
                         Vps52  17 aslhnqiaaidsvleqledlLeeFqsdlssissdikklqekSnelqlrLenrkaveaklsklvddlivp.pelidvIiegk 96 
                                   ++l  +++++ s l+ql + L   ++ l+ ++ d+  lq     lq  +       ++l + vd + +  + l +++++++
  gi|14601261|ref|NP_147796.1| 387 EDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEvESLGEKLVQAE 467
                                   455556666666777777777666666666666666666666666666666666666666666665443122333333333 PP

                         Vps52  97 v 97 
                                    
  gi|14601261|ref|NP_147796.1| 468 E 468
                                   3 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 ?    4.0   0.1      0.71        52      14      55 ..     298     342 ..     295     347 .. 0.76
   2 ?    3.7   0.2      0.91        67      17      54 ..     350     383 ..     338     385 .. 0.54
   3 ?    7.0   1.4     0.084       6.2      15      57 ..     383     425 ..     380     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.71
                          YojJ  14 lkeeLeqiekeleev...lkaldeedeClLcelesirekfaelet 55 
                                   +   Le +e++le+    ++a+ ++ + l  +les+   +++le+
  gi|14601261|ref|NP_147796.1| 298 IEGRLEAVEGSLEDLsgaVDAMSQQLQALAEDLESLSSRVEDLEA 342
                                   566778888777665222788889999999999999999999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.91
                          YojJ  17 eLeqiekeleevlkaldeedeClLcelesirekfaele 54 
                                    L+q+e++++   ++ld     l +ele++ + +ae++
  gi|14601261|ref|NP_147796.1| 350 RLSQAEEDIDSLTTSLD----SLRTELEDLSTRLAEAQ 383
                                   34444444444444444....35567777777777666 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.084
                          YojJ  15 keeLeqiekeleevlkaldeedeClLcelesirekfaeletla 57 
                                   +  Le+  ++l++v  +l++ +++l +  es++   ++l +l 
  gi|14601261|ref|NP_147796.1| 383 QASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQ 425
                                   5678999999999999999999999999888888877776654 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 ?    8.4   0.0      0.03       2.2       3      47 ..     319     363 ..     318     367 .. 0.90
   2 ?    0.9   0.1         6   4.4e+02       4      35 ..     411     442 ..     389     453 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.03
                         SMODS   3 vssqFkeflsnielsqttkdsissrvkaitkrLnkdfrelkskia 47 
                                   +s+q++++++++e  ++++++++ rv+++++rL++ +++++s ++
  gi|14601261|ref|NP_147796.1| 319 MSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTT 363
                                   5799*******99999*********************99998664 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 6
                         SMODS   4 ssqFkeflsnielsqttkdsissrvkaitkrL 35 
                                   ++ ++++ +++   q +++++++++ +i +rL
  gi|14601261|ref|NP_147796.1| 411 EESLQALTEDLASLQAEVETLQQSIVEIDRRL 442
                                   34455566664444666666666666666666 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.94        69       9      37 ..     306     334 ..     249     338 .. 0.73
   2 ?    5.4   0.6      0.22        16       2      24 ..     320     342 ..     319     368 .. 0.82
   3 ?    1.5   0.4       3.5   2.6e+02       8      23 ..     361     376 ..     349     390 .. 0.44
   4 ?    5.5   0.7       0.2        15       5      37 ..     383     415 ..     375     423 .. 0.77
   5 ?    3.7   0.1      0.72        53       3      25 ..     412     434 ..     410     458 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.94
                     DASH_Dam1   9 aDsletLdknledLqqihesLsdfNeSFa 37 
                                   + sle+L+  ++ ++q  ++L++  eS++
  gi|14601261|ref|NP_147796.1| 306 EGSLEDLSGAVDAMSQQLQALAEDLESLS 334
                                   44444444444444444444444444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.22
                     DASH_Dam1   2 epafaeLaDsletLdknledLqq 24 
                                   +++++ La+ le L++++edL+ 
  gi|14601261|ref|NP_147796.1| 320 SQQLQALAEDLESLSSRVEDLEA 342
                                   67899999999999999999986 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 3.5
                     DASH_Dam1   8 LaDsletLdknledLq 23 
                                   L+ sl+ L++ ledL+
  gi|14601261|ref|NP_147796.1| 361 LTTSLDSLRTELEDLS 376
                                   3333333333333322 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.2
                     DASH_Dam1   5 faeLaDsletLdknledLqqihesLsdfNeSFa 37 
                                    a+L+D  + Ld+  + Lqq++++L++  eS+ 
  gi|14601261|ref|NP_147796.1| 383 QASLEDLNTRLDQVASTLQQLQQRLATAEESLQ 415
                                   466777777778888889999999999888875 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.72
                     DASH_Dam1   3 pafaeLaDsletLdknledLqqi 25 
                                   ++++ L++ l+ L++ +e Lqq 
  gi|14601261|ref|NP_147796.1| 412 ESLQALTEDLASLQAEVETLQQS 434
                                   66777788888888888777764 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.6      0.13       9.8      27      97 ..     295     368 ..     273     379 .. 0.67
   2 ?   10.3   3.2    0.0033      0.24      52     109 ..     379     436 ..     365     441 .. 0.78
   3 ?    2.4   5.6      0.82        60      13      86 ..     435     504 ..     426     510 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.13
                       Vps53_N  27 ikklqeeikklddeiksvvraqanvg...ekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqL 97 
                                   ++ +++ ++ ++ +++ +  a   ++   +   e+le + + +e+l+  + ++ d+  ++ee +  +t  +  L
  gi|14601261|ref|NP_147796.1| 295 VADIEGRLEAVEGSLEDLSGAVDAMSqqlQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSL 368
                                   45566666666655555444444444000445578888899999999999999999999999999999877666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0033
                       Vps53_N  52 gekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqLDiAKknlttsiT 109
                                     +++ +le++++ + ++ + +++++++ + +ee+++ +t+d+  L      l +si 
  gi|14601261|ref|NP_147796.1| 379 LAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIV 436
                                   4567899999999999999999999999999999999999999999887777777775 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.82
                       Vps53_N  13 llpteqslanidelikklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseem 86 
                                   ++  +  l ++ ++++ ++ e++ l +++ ++++++     +   ++e+ q+ i+el  ++ e    a+++ ++
  gi|14601261|ref|NP_147796.1| 435 IVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQ----RQDASIEDFQSQIQELRTQLDEKTREAQQTAST 504
                                   4445677888889999999999999998888877766....444789***************999999999776 PP

>> Baculo_gp64  Baculovirus gp64 envelope glycoprotein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.44        32     283     332 ..     359     408 ..     336     414 .. 0.81
   2 ?    4.6   0.1      0.15        11     282     338 ..     418     470 ..     408     516 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTHH CS
                   Baculo_gp64 283 ddlmalseelayelellkasieeldarirklseilddlivsvakvderli 332
                                   d l +  + l  ele l + ++e +a ++ l+  ld++ +++ ++++rl 
  gi|14601261|ref|NP_147796.1| 359 DSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLA 408
                                   45555556677889999999999999999999999999999999888884 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.15
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTHHHHHTTS CS
                   Baculo_gp64 282 kddlmalseelayelellkasieeldarirklseilddlivsvakvderliGrlika 338
                                    +dl +    l  e e l+ si e+d r+ +l   +d +   v  + e+l+    k+
  gi|14601261|ref|NP_147796.1| 418 TEDLAS----LQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKN 470
                                   333333....34589*******************************99999766555 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       3.1   2.3e+02      63      77 ..     319     333 ..     290     349 .. 0.58
   2 ?    6.0   0.2      0.17        13      55      85 ..     353     383 ..     346     385 .. 0.84
   3 ?    5.4   0.3      0.26        19      55      85 ..     381     411 ..     377     413 .. 0.84
   4 ?    4.3   0.2      0.58        43      58      84 ..     412     438 ..     406     452 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 3.1
                         Vps51  63 mksemdkldqklsel 77 
                                   m+++++ l++ l++l
  gi|14601261|ref|NP_147796.1| 319 MSQQLQALAEDLESL 333
                                   333333333333333 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.17
                         Vps51  55 sasdtIrkmksemdkldqklselkqaiskia 85 
                                   +a ++I ++ +++d+l+++l++l+ ++ + +
  gi|14601261|ref|NP_147796.1| 353 QAEEDIDSLTTSLDSLRTELEDLSTRLAEAQ 383
                                   6889999999999999999999999887765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.26
                         Vps51  55 sasdtIrkmksemdkldqklselkqaiskia 85 
                                   +a   ++++++ +d+++++l++l+q++   +
  gi|14601261|ref|NP_147796.1| 381 EAQASLEDLNTRLDQVASTLQQLQQRLATAE 411
                                   67788999*****************998765 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.58
                         Vps51  58 dtIrkmksemdkldqklselkqaiski 84 
                                   + ++ + +++ +l++++++l+q+i +i
  gi|14601261|ref|NP_147796.1| 412 ESLQALTEDLASLQAEVETLQQSIVEI 438
                                   555555555555555555555555443 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1       3.2   2.3e+02      31      54 ..     249     272 ..     242     279 .. 0.78
   2 ?    2.9   0.1         2   1.5e+02      29      57 ..     275     303 ..     270     315 .. 0.85
   3 ?    4.3   2.0      0.72        53      22      45 ..     317     340 ..     290     357 .. 0.52
   4 ?    2.1   0.4       3.5   2.5e+02      33      58 ..     356     381 ..     345     386 .. 0.67
   5 ?   10.6   0.9    0.0077      0.56      26      61 ..     384     419 ..     376     433 .. 0.85
   6 ?    1.0   0.9       7.8   5.8e+02      26      63 ..     433     470 ..     418     504 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 3.2
                       UPF0184  31 insmLDqinsaLDalEernDdlns 54 
                                   + + ++ +  aLD lEer  dl+ 
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERVGDLEF 272
                                   56677888999*******999875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 2
                       UPF0184  29 eainsmLDqinsaLDalEernDdlnskLr 57 
                                   e++   L  ++s + alE+r  d++++L+
  gi|14601261|ref|NP_147796.1| 275 EDLTLQLSSLDSRVGALEDRVADIEGRLE 303
                                   666677889999999***********996 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.72
                       UPF0184  22 efgeeEyeainsmLDqinsaLDal 45 
                                   ++ ++ ++a+ + L+ ++s +++l
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDL 340
                                   233344444444444444444444 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 3.5
                       UPF0184  33 smLDqinsaLDalEernDdlnskLrE 58 
                                   + +D + + LD l    +dl ++L E
  gi|14601261|ref|NP_147796.1| 356 EDIDSLTTSLDSLRTELEDLSTRLAE 381
                                   44577777777777777777777766 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0077
                       UPF0184  26 eEyeainsmLDqinsaLDalEernDdlnskLrELle 61 
                                   + +e++n  LDq+ s+L +l +r    +  L+ L e
  gi|14601261|ref|NP_147796.1| 384 ASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTE 419
                                   5689*******************8888888877765 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 7.8
                       UPF0184  26 eEyeainsmLDqinsaLDalEernDdlnskLrELlesn 63 
                                   + + +i+  L q+ s++Da+    ++l  kL    e n
  gi|14601261|ref|NP_147796.1| 433 QSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKN 470
                                   55667888888888888888877777777776655555 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1         3   2.2e+02      50      89 ..     241     279 ..     222     294 .. 0.72
   2 ?    3.1  22.8       1.3        98      49     152 ..     296     469 ..     293     530 .. 0.44

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 3
                                   HHHHHHHHHHH.T..TT.HHHHHHHHTT---HHHHHHHHHT CS
                                   xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MutS_III  50 eInaRldaVee.leneelreelrellrrlpDleRllsrisl 89 
                                    +++Rl++Ve  +e  +l  +l +l +r++Dle ++  ++l
  gi|14601261|ref|NP_147796.1| 241 PLEERLSLVEQaVE--DLGLALDSLEERVGDLEFAVEDLTL 279
                                   589*******9784..5445554444458899877776655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHH.T..TT.HHHHH...HHHTT.---HHHHHHHHHTT---...........HHHHHHHHHHHHHHHTTTTT CS
                                   xxxxxxxxxxxx.xxxxxxxxxxx...xxxxx.xxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx RF
                      MutS_III  49 eeInaRldaVee.leneelreelr...ellrr.lpDleRllsrislgkak...........ardlkallealkaleelval 113
                                   ++I+ Rl+aVe  le+ +   ++    ++l+   +Dle l sr+   +a+            +d+ +l ++l++l    + 
  gi|14601261|ref|NP_147796.1| 296 ADIEGRLEAVEGsLEDLS--GAVDamsQQLQAlAEDLESLSSRVEDLEARvgsvedrlsqaEEDIDSLTTSLDSLRTELED 374
                                   689999999997675333..3333223667775558888888776653332221111111111233333333332222222 PP

                                   ---SSTHHHHH...............HHHHHHHHHHB-SS--SSGGGS--B-T............................ CS
                                   xxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                      MutS_III 114 lekeklaesee...............eslaelleeaideeplalekegedlra............................ 151
                                   l++  ++ + +               +                  + ++ l++                            
  gi|14601261|ref|NP_147796.1| 375 LSTRLAEAQASledlntrldqvastlQ------------------QLQQRLATaeeslqaltedlaslqaevetlqqsive 437
                                   222222111112112222222222220..................111111111112222333333222222222234444 PP

                                   ...............................H CS
                                   ...............................x RF
                      MutS_III 152 ...............................i 152
                                                                  +
  gi|14601261|ref|NP_147796.1| 438 idrrlgqlrstvdavrleveslgeklvqaeeK 469
                                   44444444555555555555555555555551 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 ?   11.0   1.2    0.0021      0.15     427     520 ..     274     363 ..     269     366 .. 0.93
   2 ?    6.4   4.8     0.052       3.8     425     484 ..     377     436 ..     372     450 .. 0.84
   3 ?   -0.4   1.1       6.1   4.5e+02     445     487 ..     453     495 ..     433     511 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0021
                     TTKRSYEDQ 427 iaeLtsqlqlaDskavhfhaecraLakRlalaekskeklteelklakqnisrlqDelattkrsYedqLsmmsdhLcsmnek 507
                                   +++Lt ql   Ds+  ++   +  ++ Rl+  e s e+l+  + + +q+++ l ++l+  ++  ed    +   + s+ ++
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVED----LEARVGSVEDR 350
                                   899******************************************************999988887....567899***** PP

                     TTKRSYEDQ 508 LtkqreeidtLkl 520
                                   L++  e+id+L  
  gi|14601261|ref|NP_147796.1| 351 LSQAEEDIDSLTT 363
                                   **********975 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.052
                     TTKRSYEDQ 425 ariaeLtsqlqlaDskavhfhaecraLakRlalaekskeklteelklakqnisrlqDela 484
                                   +r+ae  + l   +++  +  + ++ L++Rla ae+s + lte+l++ + +++ lq  ++
  gi|14601261|ref|NP_147796.1| 377 TRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIV 436
                                   56777777777777777788889999****************************998776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 6.1
                     TTKRSYEDQ 445 haecraLakRlalaekskeklteelklakqnisrlqDelattk 487
                                     e+ +L  +l +ae+ +++    ++  +++i++l+  l   +
  gi|14601261|ref|NP_147796.1| 453 RLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKT 495
                                   4566666666666666666666666666666666666655444 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1         2   1.5e+02      60     137 ..     263     342 ..     232     352 .. 0.58
   2 ?    4.5   0.2      0.49        36      52     109 ..     311     368 ..     280     375 .. 0.58
   3 ?   12.5   5.6    0.0017      0.12      43     115 ..     369     444 ..     356     452 .. 0.70
   4 ?    1.2   2.8       5.1   3.8e+02      52     105 ..     448     501 ..     439     510 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 2
                         CREPT  60 laeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsLP.dLtelpd.vtggla 137
                                   l+e ++ Le  +e+ +   + l++ + a+ +++a+ e +le ++  le ++ + + + +++q L  dL++l++ v++ +a
  gi|14601261|ref|NP_147796.1| 263 LEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAeDLESLSSrVEDLEA 342
                                   44444444444454444445555555556666666666666666666666666666666666664355555553444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.49
                         CREPT  52 qveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekv 109
                                     + a+ ++++  + L+++le  ++  + le+ + ++ ++l++aee +++l + l+ +
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSL 368
                                   4444555555555555555555555555555555555555555555555555555444 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.0017
                         CREPT  43 keeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaee...kleelkeklekvksvrke 115
                                   + e e l++   ea++ l++ n+rL++  +  ++l++ l++  e++++l ++ ++   ++e l++ + +++    +
  gi|14601261|ref|NP_147796.1| 369 RTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASlqaEVETLQQSIVEIDRRLGQ 444
                                   578999*********************9999999999999887777666554444000444444444444444444 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 5.1
                         CREPT  52 qveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkek 105
                                   +v+     ++   ++L +  e+ ++    +edf+++++el ++ +ek +e ++ 
  gi|14601261|ref|NP_147796.1| 448 TVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   444444455555555555555555555666677776666666666666666655 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0         3   2.2e+02     208     296 ..     247     334 ..     227     338 .. 0.78
   2 ?    1.7   4.2       1.9   1.4e+02     220     296 ..     336     411 ..     316     415 .. 0.74
   3 ?    8.8   5.0     0.012       0.9     222     296 ..     415     495 ..     411     499 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 3
                         FAM76 208 ksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirel 288
                                   + +++++ d  +a+  L+e++  l+  +e    +l++ d  + +l     + e +l+  ++ + ++ +  +++++++ ++l
  gi|14601261|ref|NP_147796.1| 247 SLVEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEA-VEGSLEDLSGAVDAMSQQLQAL 326
                                   4677788888899999999999999999999999999999999999888888877765.5666667777888888888888 PP

                         FAM76 289 lkevaels 296
                                     ++ +ls
  gi|14601261|ref|NP_147796.1| 327 AEDLESLS 334
                                   87777666 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.9
                         FAM76 220 avtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkevaels 296
                                    v++L+ ++ s + +l+q ++++ +    + +l++el++  ++l e    + ++ +++++++ ++ ++l++ +a+ +
  gi|14601261|ref|NP_147796.1| 336 RVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQA-SLEDLNTRLDQVASTLQQLQQRLATAE 411
                                   4677788888888888888888888888888888888777777665444.445667888999999999999888765 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.012
                         FAM76 222 tqLkeeiaslkkqleqkdqellekdkkitelkaelleke...kelreklkeleke...akekieklekkirellkevaels 296
                                   + L e++asl+ ++e+ +q+++e d+ + +l++     +   ++l ekl + e++    +++ie ++++i+el+ ++ e +
  gi|14601261|ref|NP_147796.1| 415 QALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRlevESLGEKLVQAEEKnqrQDASIEDFQSQIQELRTQLDEKT 495
                                   6799***************************98765544112345567766555411155689999*******99876655 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1       1.1        83     101     145 ..     324     373 ..     313     395 .. 0.53
   2 ?    6.4   5.4     0.044       3.3     101     207 ..     394     500 ..     385     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.1
                        HlyD_2 101 eklkekletlnerikeien.....neaieniekdiekldreInvlekdik 145
                                   + l+e le l  r++++e      ++ +++ e+di+ l  +++ l+++++
  gi|14601261|ref|NP_147796.1| 324 QALAEDLESLSSRVEDLEArvgsvEDRLSQAEEDIDSLTTSLDSLRTELE 373
                                   44455555555555555541111122234445555555555555555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.044
                        HlyD_2 101 eklkekletlnerikeienneaieniekdiekldreInvlekdikesikn.ed.ikkieelKeelnalldkKkllygsksl 179
                                   ++ +++l++l++r+   e++   +++ +d   l+ e+++l++ i e+ +  ++  + ++ ++ e+++l +k    +++++ 
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESL--QALTEDLASLQAEVETLQQSIVEIDRRlGQlRSTVDAVRLEVESLGEKLVQAEEKNQR 472
                                   5678899*******9999887..999*****************99876542441578999*99999998888888888889 PP

                        HlyD_2 180 sgkdleqlkkkkkeienklesskevika 207
                                   +++++e  +++ +e++ +l+++++  + 
  gi|14601261|ref|NP_147796.1| 473 QDASIEDFQSQIQELRTQLDEKTREAQQ 500
                                   999*****************99876655 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.8     0.018       1.3      25     160 ..     264     406 ..     237     407 .. 0.69
   2 ?    9.4   5.0     0.014         1      23     145 ..     318     438 ..     310     455 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..H---...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     YscO-like  25 kdkkkaLekEkeklrkleeerdkvkkhkkaKvaqlreeld..kGtt...sdkikkmkryikvvkeelkqeekkvekQkekV 100
                                   ++++  Le   e+l    + +d ++   +++va++   l+  +G+    s ++  m + ++ ++e+l+    +ve+ + +V
  gi|14601261|ref|NP_147796.1| 264 EERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEavEGSLedlSGAVDAMSQQLQALAEDLESLSSRVEDLEARV 344
                                   455555666666666666666666666666666655544411344311145788999999999999999999999999999 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHT CS
                     YscO-like 101 kvAerkvEqareelakkrkeveklekhkeewlkevkkeeekreeleq..dEiGsvlflarqr 160
                                      e ++ qa+e++      ++ l+++ e+    + + +++ e+l++  d + s l +++qr
  gi|14601261|ref|NP_147796.1| 345 GSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTrlDQVASTLQQLQQR 406
                                   99999999999999999999999999999999999888888887765446777777666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     YscO-like  23 vvkdkkkaLekEkeklrkleeerdkvkkhkkaKvaqlreeldkGttsdkikkmkryikvvkeelkqeekkvekQkekVkvA 103
                                   +++++ +aL+++ e l  + e+++ ++   +++++q  e +d  tts  +  +++ ++ ++ +l++ +  +e+ + +    
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTS--LDSLRTELEDLSTRLAEAQASLEDLNTRLDQV 396
                                   67777778888888888888888888888888888888888777775..44445555555555555555555555555555 PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     YscO-like 104 erkvEqareelakkrkeveklekhkeewlkevkkeeekreel 145
                                   +  + q ++ la ++  +++l+++    + ev   ++++ e+
  gi|14601261|ref|NP_147796.1| 397 ASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEI 438
                                   555555555555555555555555555555555555555444 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.047       3.4      26      93 ..     289     356 ..     273     364 .. 0.83
   2 ?    3.3   8.1      0.73        54      11      94 ..     386     469 ..     381     484 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.047
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     PTRF_SDPR  26 krlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklEa 93 
                                     lE+r a++e+ ++++ g l  L+ +  + s++++ l e     s++v ++ +r+   + ++ + E+
  gi|14601261|ref|NP_147796.1| 289 GALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEE 356
                                   56899999999999999999999999999999999999999999999999999999877777766665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.73
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     PTRF_SDPR  11 LdkvvgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkkl 91 
                                   L+ + + +d+v ++ ++l +r a  e++++++  dl+ L  +  +  +++  +  +  +  ++v  vr ++e    ++ + 
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQA 466
                                   78899999*******************************999999999999999999999999999999999887776555 PP

                                   HHH CS
                     PTRF_SDPR  92 Ean 94 
                                   E++
  gi|14601261|ref|NP_147796.1| 467 EEK 469
                                   544 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0       1.7   1.2e+02      47      95 ..     316     364 ..     301     368 .. 0.82
   2 ?    2.3   0.2       3.5   2.6e+02      46      93 ..     385     432 ..     362     438 .. 0.60
   3 ?    4.3   0.6      0.82        61      44      98 ..     432     486 ..     415     487 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1.7
                       DUF4665  47 venldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaael 95 
                                   v  ++++l+ + +dl+sls++++  + +   v+++  + ++++d+ +  
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTS 364
                                   7899****************99988888888888888888888876655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 3.5
                       DUF4665  46 kvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaa 93 
                                     e+l+  l ++   l++l ++l++ ++  + ++++    +++v+  +
  gi|14601261|ref|NP_147796.1| 385 SLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   455666666666666666666666665555555555555555555444 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.82
                       DUF4665  44 kekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaaellaq 98 
                                   ++ + ++d+ l +++  + ++  ++++  +k  ++++k++ + +++++ + ++++
  gi|14601261|ref|NP_147796.1| 432 QQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQE 486
                                   678999*************999999999999999999999999999998888776 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 ?    3.4   9.4      0.59        44     123     220 ..     374     484 ..     315     504 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.59
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS...........HHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx RF
                          ZnuA 123 tyeanaaayiekLeeldaeireelaeipeekrklvtthdafgylarayglevagiagiste...........aaqiaalie 192
                                   ++++++a+ +++Le+l++++ ++ +++++ ++ l t++++++ l+++    +a + +++++            +++ a++ 
  gi|14601261|ref|NP_147796.1| 374 DLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSiveidrrlgqlRSTVDAVRL 454
                                   47889999*********************999**************99999998888888889999999999999999999 PP

                                   HHHHTT-SEEEEET.TS.-THHHHHHHHHH CS
                                   xxxxxxxxxxxxxx.xx.xxxxxxxxxxxx RF
                          ZnuA 193 eikeagvkaifvep.la.spklaetlaeea 220
                                   e++++g k + +e+ ++ +++++e+ ++++
  gi|14601261|ref|NP_147796.1| 455 EVESLGEKLVQAEEkNQrQDASIEDFQSQI 484
                                   999999999999986334777777777665 PP

>> L31  Mitochondrial ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       7.3   5.4e+02      24      57 ..     348     381 ..     335     388 .. 0.79
   2 ?    5.5   2.1      0.32        23      14      66 ..     378     432 ..     370     509 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 7.3
                           L31  24 rkRlkavDevieavkeslkkkgvslkalekakae 57 
                                    +Rl + +e i+ +++sl +  ++l+ l++  ae
  gi|14601261|ref|NP_147796.1| 348 EDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAE 381
                                   6799999999999999999988888888766654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.32
                           L31  14 rlsktqk..arqrkRlkavDevieavkeslkkkgvslkalekakaelpkesemsp 66 
                                   rl+++q     + +Rl +v + ++++++ l++++ sl+al++  a+l+ e e  +
  gi|14601261|ref|NP_147796.1| 378 RLAEAQAslEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   555555411356899*****************99999999999999888877655 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.7     0.023       1.7      40     134 ..     318     415 ..     287     418 .. 0.78
   2 ?    2.2  10.1       2.2   1.6e+02      42     134 ..     411     499 ..     404     506 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.023
                      MIP-T3_C  40 sakkeravsaseiekLresiQkltksvnPLgklldfiqdDidsMqrELemWrseyrqqaeelaeerratee...aleplka 117
                                   +  ++ +  a+++e+L + + +l   v      l  +++Dids++  L++ r e +  ++ lae+++  e     l+++  
  gi|14601261|ref|NP_147796.1| 318 AMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDlntRLDQVAS 398
                                   345566677899*******************************************99999999998876641115666777 PP

                      MIP-T3_C 118 qlaeleeaIkdqkekis 134
                                    l++l++ ++  +e ++
  gi|14601261|ref|NP_147796.1| 399 TLQQLQQRLATAEESLQ 415
                                   89999988877776665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 2.2
                      MIP-T3_C  42 kkeravsaseiekLresiQkltksvnPLgklldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlael 122
                                   +++ +   +++ +L+ ++ +l +s+  + + l      +d+   E e+  ++  q++e+ +++    + ++e+ + q++el
  gi|14601261|ref|NP_147796.1| 411 EESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQ----DASIEDFQSQIQEL 487
                                   556667789999999999999999999999999999999999999999877766665554444....56677778888888 PP

                      MIP-T3_C 123 eeaIkdqkekis 134
                                     ++ ++  + +
  gi|14601261|ref|NP_147796.1| 488 RTQLDEKTREAQ 499
                                   888877766655 PP

>> LidA_Long_CC  LidA long coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       6.6   4.9e+02       6      52 ..     304     342 ..     285     359 .. 0.47
   2 ?    2.4   0.3         2   1.4e+02       3      48 ..     350     390 ..     334     397 .. 0.49
   3 ?    4.5   4.5      0.43        32       4      59 ..     379     433 ..     376     441 .. 0.87
   4 ?    7.9   0.2     0.041         3       2      33 ..     475     506 ..     474     528 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 6.6
                                   HHHHHHHHHHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHHHHHH CS
                  LidA_Long_CC   6 kieeriaklekkldkqaeeIneliesgsdgkeeearkllhelnglnl 52 
                                   ++e  +++l+  +d+  ++++ l+e+         + l ++++ l++
  gi|14601261|ref|NP_147796.1| 304 AVEGSLEDLSGAVDAMSQQLQALAED--------LESLSSRVEDLEA 342
                                   33333333333333333333333333........3333344444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 2
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHH CS
                  LidA_Long_CC   3 kiekieeriaklekkldkqaeeIneliesgsdgkeeearkllheln 48 
                                   +  + ee i++l++ ld  ++e+++l +        ea++ l++ln
  gi|14601261|ref|NP_147796.1| 350 RLSQAEEDIDSLTTSLDSLRTELEDLSTR-----LAEAQASLEDLN 390
                                   33344444444444444444444444443.....334555555555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.43
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  LidA_Long_CC   4 iekieeriaklekkldkqaeeIneliesgsdgkeeearkllhelnglnlqvaglkd 59 
                                    ++ ++ +++l++ ld+ a ++++l +      ee+ ++l ++l  l+++v++l++
  gi|14601261|ref|NP_147796.1| 379 LAEAQASLEDLNTRLDQVASTLQQLQQR-LATAEESLQALTEDLASLQAEVETLQQ 433
                                   6788999**********99999998877.66778999*****************97 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.041
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S- CS
                  LidA_Long_CC   2 ekiekieeriaklekkldkqaeeIneliesgs 33 
                                   + ie+++++i++l+++ld++++e ++ +++ s
  gi|14601261|ref|NP_147796.1| 475 ASIEDFQSQIQELRTQLDEKTREAQQTASTAS 506
                                   6799*******************999988755 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2       1.1        81       2      43 ..     320     361 ..     263     363 .. 0.78
   2 ?    5.7   1.9      0.21        15       2      45 ..     362     405 ..     350     406 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                          Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklL 43 
                                   ++++++l e le+l + +++l+++ ++ +d     ++ I+ L
  gi|14601261|ref|NP_147796.1| 320 SQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSL 361
                                   455666666666666666666666666656666666666655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                          Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                   ++++ +l+ +le l + lae+++ l++ ++  + v + +++L++
  gi|14601261|ref|NP_147796.1| 362 TTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQ 405
                                   56777888888888888888888888888888888888888886 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 ?    5.4   1.3      0.23        17       8      64 ..     331     387 ..     324     396 .. 0.71
   2 ?    7.4  15.6     0.058       4.3       3     110 ..     389     496 ..     385     507 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.23
                         SYCE1   8 edLinrineLQqakkksseELgeaqalkealkrElDsLnaEkvhLeevlnkKqealr 64 
                                   e L +r+++L      +++ L++a++  ++l   lDsL++E   L   l + q  l+
  gi|14601261|ref|NP_147796.1| 331 ESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLE 387
                                   667777777777667777888888888888888888888887777766666666555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.058
                         SYCE1   3 lepqiedLinrineLQqakkksseELgeaqalkealkrElDsLnaEkvhLeevlnkKqealriLqlhcqekeseaqrkqel 83 
                                   l+ +++++ + +++LQq    ++e L+   +   +l+ E + L++  v+++  l + + ++  ++l+ +   ++  + +e 
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEK 469
                                   56788888999***********************************************************99999999999 PP

                         SYCE1  84 seeckqrieeltskiqeeklkrrklrl 110
                                   ++ ++  ie ++s+iqe +++  +   
  gi|14601261|ref|NP_147796.1| 470 NQRQDASIEDFQSQIQELRTQLDEKTR 496
                                   999999**********98776554444 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 ?    4.6   0.1      0.56        42       5      28 ..     287     310 ..     239     314 .. 0.83
   2 ?    7.5   0.4     0.071       5.3       6      55 ..     288     341 ..     277     343 .. 0.61
   3 ?    7.5   3.8     0.068         5       3      61 ..     334     389 ..     314     392 .. 0.71
   4 ?    6.1   9.2      0.19        14       7      62 ..     359     446 ..     354     450 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.56
                      CCDC-167   5 eIdkleeklascrerLeaverrlr 28 
                                    +  le+++a+++ rLeave +l+
  gi|14601261|ref|NP_147796.1| 287 RVGALEDRVADIEGRLEAVEGSLE 310
                                   455678888888888888887776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.071
                      CCDC-167   6 IdkleeklascrerLeaverrlrk....eelseeeResleeEeaslkeqleene 55 
                                   +  le+++a+++ rLeave +l++    +   +++ ++l e ++sl++++e+ e
  gi|14601261|ref|NP_147796.1| 288 VGALEDRVADIEGRLEAVEGSLEDlsgaVDAMSQQLQALAEDLESLSSRVEDLE 341
                                   556788888888888888887776222222333336666677777777766655 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.068
                      CCDC-167   3 aseIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksL 61 
                                    s +++le ++ s+++rL + e  + + + s    +sl +E++ l+++l e +  L+ L
  gi|14601261|ref|NP_147796.1| 334 SSRVEDLEARVGSVEDRLSQAEEDIDSLTTSL---DSLRTELEDLSTRLAEAQASLEDL 389
                                   34566666666666666666666666555554...488899999999999999999887 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.19
                      CCDC-167   7 dkleeklascrerLeaverrlrkeelseee................................ResleeEeaslkeqleene 55 
                                   d+l  +l s+r +Le++ +rl +++ s e+                                  sl+ E ++l++ + e +
  gi|14601261|ref|NP_147796.1| 359 DSLTTSLDSLRTELEDLSTRLAEAQASLEDlntrldqvastlqqlqqrlataeeslqaltedLASLQAEVETLQQSIVEID 439
                                   555555555555555555555555555555555544444444447777777777766676666777788888888888888 PP

                      CCDC-167  56 keLksLr 62 
                                   ++L +Lr
  gi|14601261|ref|NP_147796.1| 440 RRLGQLR 446
                                   8888887 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4       1.2        91      10      74 ..     320     378 ..     299     391 .. 0.44
   2 ?    7.0   3.3      0.12       9.1      20      92 ..     356     433 ..     339     441 .. 0.69
   3 ?    6.3   2.3       0.2        15      21      78 ..     448     501 ..     431     512 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 1.2
                Cytochrom_B562  10 kkalkqvakaddaeelkkalkelraaaedakeatpsklek....dseeqkdYqeGldklidqldkaeal 74 
                                   +++l+++  a+d e+l++ +++l+a + + +        +     +e+ +     ld l ++l+++++ 
  gi|14601261|ref|NP_147796.1| 320 SQQLQAL--AEDLESLSSRVEDLEARVGSVE--------DrlsqAEEDIDSLTTSLDSLRTELEDLSTR 378
                                   2222222..2233333333333333333222........222224444444455555555555444443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.12
                Cytochrom_B562  20 ddaeelkkalkelraaaedakeatp...sklekdseeqkdYqeGldklidqldkaealaka..gkleeakaalkelkd 92 
                                   +d+++l+++l++lr+  ed ++  +   ++le+ + + ++    l++l++ l++ae++++a  ++l+  +a++++l++
  gi|14601261|ref|NP_147796.1| 356 EDIDSLTTSLDSLRTELEDLSTRLAeaqASLEDLNTRLDQVASTLQQLQQRLATAEESLQAltEDLASLQAEVETLQQ 433
                                   566666666666666666655544300125667888888999999999999999999888644777788888888875 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.2
                Cytochrom_B562  21 daeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaealakag 78 
                                   ++++++ ++++l +   +a+e++      +++  +d+q  +++l +qld+  ++a++ 
  gi|14601261|ref|NP_147796.1| 448 TVDAVRLEVESLGEKLVQAEEKNQ----RQDASIEDFQSQIQELRTQLDEKTREAQQT 501
                                   344455556666666666666665....377888888888888888888887777765 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 ?    2.6   0.1       1.5   1.1e+02      85     140 ..     285     338 ..     275     350 .. 0.64
   2 ?    7.0   4.5     0.069       5.1      76     140 ..     367     429 ..     343     431 .. 0.62
   3 ?    6.4   4.9       0.1       7.7      72     119 ..     384     431 ..     366     455 .. 0.57
   4 ?    1.5   3.7       3.3   2.5e+02      76     133 ..     430     488 ..     408     497 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 1.5
                  Sec8_exocyst  85 qekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkkvpdkie 140
                                    ++v +l +++++ +  l++ + +L++l+    ++++ ++ L   e+l+++ +++e
  gi|14601261|ref|NP_147796.1| 285 DSRVGALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALA--EDLESLSSRVE 338
                                   5666677777777777777777777777766666666666664..34444444444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.069
                  Sec8_exocyst  76 kilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkkvpdkie 140
                                   ++   +++  ++++e + sle+ ++ l +  ++L++l++r a+ +e ++ L   e+l+++  ++e
  gi|14601261|ref|NP_147796.1| 367 SLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALT--EDLASLQAEVE 429
                                   3444455555666666666666666666666666666666666666666664..45555555555 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.1
                  Sec8_exocyst  72 asYskilssiqesqekvselKesleeakkklstkkkeLkelnarsaky 119
                                   as + +   +++ ++++++l+++l+ a+++l++  ++L  l+a+  ++
  gi|14601261|ref|NP_147796.1| 384 ASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETL 431
                                   333444444555555555555555555555555555555555555554 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 3.3
                  Sec8_exocyst  76 kilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiL.daieelk 133
                                    +++si e  +++ +l+  + + + +++   ++L + ++++++++  ie   ++i+el+
  gi|14601261|ref|NP_147796.1| 430 TLQQSIVEIDRRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFqSQIQELR 488
                                   45666677778888999999999999999999999999999999999987624677775 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  14.9      0.18        14     139     306 ..     319     491 ..     308     528 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.18
                SpecificRecomb 139 aeklreellealevlsvqiaalglepelrrrlpeleeeespFlalqrelealleayeaaledeeeaeedlkhlrvlldqcr 219
                                   +++  ++l e le ls+++   +le  + ++ ++l+++e+   +l+ +l++l+++ e+  ++ +ea+++l++l++ ldq  
  gi|14601261|ref|NP_147796.1| 319 MSQQLQALAEDLESLSSRVE--DLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVA 397
                                   45556778888999999998..999999**************************999999999999999************ PP

                SpecificRecomb 220 eavdrvrkhleenGvsvs.lvfllerlrqrleRlee.Lldlll.....eeeeeeraralveLlkelveaeaekrsvrellr 293
                                   +++++++++l+++  s++ l+  l  l++++e l++ ++++       +++ ++ + ++ +L ++lv+ae++++   + ++
  gi|14601261|ref|NP_147796.1| 398 STLQQLQQRLATAEESLQaLTEDLASLQAEVETLQQsIVEIDRrlgqlRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIE 478
                                   **********99999985467777777777666654133333355655678888899999999999999888776665555 PP

                SpecificRecomb 294 enielLarkvver 306
                                   +  + + +  ++ 
  gi|14601261|ref|NP_147796.1| 479 DFQSQIQELRTQL 491
                                   5555444444444 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 ?    2.3   0.6       2.6   1.9e+02      40      60 ..     322     342 ..     290     343 .. 0.77
   2 ?    3.8   1.0      0.85        62      29      59 ..     346     376 ..     332     378 .. 0.82
   3 ?   10.6   5.9    0.0064      0.47      16      59 ..     389     432 ..     381     434 .. 0.94
   4 ?    6.1   1.3      0.16        12      31      60 ..     460     489 ..     438     490 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 2.6
                     DMPK_coil  40 knreLeeeleqLkkemEelra 60 
                                   + ++L e+le+L  ++E l a
  gi|14601261|ref|NP_147796.1| 322 QLQALAEDLESLSSRVEDLEA 342
                                   557788888888888888776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.85
                     DMPK_coil  29 afeskLkeaEkknreLeeeleqLkkemEelr 59 
                                   ++e +L  aE     L   l++L+ e+E l 
  gi|14601261|ref|NP_147796.1| 346 SVEDRLSQAEEDIDSLTTSLDSLRTELEDLS 376
                                   6899************************975 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0064
                     DMPK_coil  16 lqeeLekvkaanlafeskLkeaEkknreLeeeleqLkkemEelr 59 
                                   l+ +L +v  + ++ + +L  aE   ++L e+l++L+ e+E l+
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQ 432
                                   6789*************************************998 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.16
                     DMPK_coil  31 eskLkeaEkknreLeeeleqLkkemEelra 60 
                                     kL  aE kn+   + +e  + ++ elr 
  gi|14601261|ref|NP_147796.1| 460 GEKLVQAEEKNQRQDASIEDFQSQIQELRT 489
                                   459************************996 PP

>> GP41  Retroviral envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       1.2        90      36      61 ..     241     266 ..     221     271 .. 0.88
   2 ?    0.7   0.1       5.7   4.2e+02      34      62 ..     295     323 ..     270     328 .. 0.76
   3 ?    2.5   0.0       1.7   1.2e+02      16      60 ..     316     363 ..     308     371 .. 0.78
   4 ?    5.0   0.6      0.28        21      13      62 ..     369     428 ..     359     434 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 1.2
                                   HHHHHHHCHHHH..........HHHH CS
                          GP41  36 kleaRlsAleevvrvlgedvaslktr 61 
                                    le+Rls +e+ v +lg  ++sl++r
  gi|14601261|ref|NP_147796.1| 241 PLEERLSLVEQAVEDLGLALDSLEER 266
                                   69*******************99987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 5.7
                                   HHHHHHHHHCHHHH..........HHHHH CS
                          GP41  34 dkkleaRlsAleevvrvlgedvaslktrm 62 
                                      +e Rl+A+e  + +l   v+++ ++ 
  gi|14601261|ref|NP_147796.1| 295 VADIEGRLEAVEGSLEDLSGAVDAMSQQL 323
                                   56788899999999889988888887775 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHHHH...HHHHHHHHHCHHHH..........HHH CS
                          GP41  16 vdglqrnvlkvleeqqel...dkkleaRlsAleevvrvlgedvaslkt 60 
                                   vd++++++    e  ++l      leaR+  +e+ + +  ed++sl t
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQALAEDLESLssrVEDLEARVGSVEDRLSQAEEDIDSLTT 363
                                   566666666666666666777788999**9999999999999999876 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.28
                                   HHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHCHHHH..........HHHHH CS
                          GP41  13 atlvdglqrnvlkvleeqqel..........dkkleaRlsAleevvrvlgedvaslktrm 62 
                                   +t +++l+  + ++  + ++l           ++l++Rl   ee ++ l ed+asl+   
  gi|14601261|ref|NP_147796.1| 369 RTELEDLSTRLAEAQASLEDLntrldqvastLQQLQQRLATAEESLQALTEDLASLQAEV 428
                                   45566666666666666666677777777777899****99999999*****99998765 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.1     0.024       1.8       5      98 ..     321     414 ..     317     415 .. 0.88
   2 ?    5.6   4.0      0.21        16       3      92 ..     364     464 ..     362     472 .. 0.57
   3 ?    0.7   2.3       7.6   5.6e+02      19      86 ..     419     458 ..     413     508 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.024
                   Prefoldin_3   5 yklreweaeydglkeeisalkeeddateedllriardfegslvtekEveeilGekqgvtrskqQvvdlisrRiDYVkqnik 85 
                                   ++l+   +++++l   +++l+++  + e+ l + ++d ++     + +++ l + ++   ++q  ++ ++ R+D V   ++
  gi|14601261|ref|NP_147796.1| 321 QQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQ 401
                                   6788888899999999999999999999999999999999999999999888888887778888999************** PP

                   Prefoldin_3  86 tlekrleaaenkl 98 
                                    l++rl++ae+ l
  gi|14601261|ref|NP_147796.1| 402 QLQQRLATAEESL 414
                                   **********988 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.21
                   Prefoldin_3   3 slyklreweaeydglkeeisalkeeddateedllriardfegslvtekEveeilGe....kqgvtrskqQvvdlisrR... 76 
                                   sl++lr+  +++++  +e +a  e+ ++  ++++++ ++++ +l t++E  + l e     q    + qQ +  i+rR   
  gi|14601261|ref|NP_147796.1| 364 SLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEdlasLQAEVETLQQSIVEIDRRlgq 444
                                   667777777777776666666556677777777777777777777777755555552222334456667777777777222 PP

                   Prefoldin_3  77 ....iDYVkqniktlekrle 92 
                                       +D V+  +++l  +l 
  gi|14601261|ref|NP_147796.1| 445 lrstVDAVRLEVESLGEKLV 464
                                   22223555555555544444 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 7.6
                   Prefoldin_3  19 eeisalkeeddateedllriardfegslvtekEveeilGekqgvtrskqQvvdlisrRiDYVkqnikt 86 
                                   e++ +l++e ++ ++++++i r ++    t                            +D V+  +++
  gi|14601261|ref|NP_147796.1| 419 EDLASLQAEVETLQQSIVEIDRRLGQLRST----------------------------VDAVRLEVES 458
                                   555555555555555555555544432111............................2222223333 PP

>> Arm-DNA-bind_5  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3       1.2        86      47      85 ..     379     417 ..     350     421 .. 0.82
   2 ?    5.1   0.6      0.41        30      48      80 ..     471     503 ..     445     508 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 1.2
                Arm-DNA-bind_5  47 vkerepntlelnskirqerekledivrklrqkektaell 85 
                                   + e +   ++ln  ++q  + l+++ ++l ++e+++++l
  gi|14601261|ref|NP_147796.1| 379 LAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQAL 417
                                   44556668999*****************99999977765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.41
                Arm-DNA-bind_5  48 kerepn..tlelnskirqerekledivrklrqkek 80 
                                   +++  +  +++ +s+i++ r++l+++ r+ +q  +
  gi|14601261|ref|NP_147796.1| 471 QRQ--DasIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   233..155999******************999765 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       2.8   2.1e+02     151     228 ..     255     333 ..     242     338 .. 0.59
   2 ?   10.3   5.1    0.0042      0.31     150     238 ..     337     420 ..     322     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.8
                       DUF1978 151 dLetalgsiEeeyrevvrdQedywKeeekkelersa..ElrekgtkvkseEleeqlesleellkesseeLevlekhilkv 228
                                   dL  al+s+Ee+        ed   ++ + +  r    E r  +++ + e +e +le l   ++ +s++L+ l  +++ +
  gi|14601261|ref|NP_147796.1| 255 DLGLALDSLEERVGDLEFAVEDLTLQLSSLD-SRVGalEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESL 333
                                   5556666666665555545555554444444.333301334445555557777788888888888888888887777665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0042
                       DUF1978 150 v.dLetalgsiEeeyrevvrdQedywKeeekkelersaElrekgtkvkseEleeqlesleellkesseeLevlekhilkve 229
                                   v dLe   gs+E ++ +  +d ++    +++       El++  t+    E++ +le l+ +l+++   L++l++ +  +e
  gi|14601261|ref|NP_147796.1| 337 VeDLEARVGSVEDRLSQAEEDIDSLTTSLDSLR----TELEDLSTRLA--EAQASLEDLNTRLDQVASTLQQLQQRLATAE 411
                                   2499*********************99999988....99998888777..******************************* PP

                       DUF1978 230 keataevek 238
                                   ++++a +e 
  gi|14601261|ref|NP_147796.1| 412 ESLQALTED 420
                                   *99998875 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.1     0.054       3.9      83     178 ..     327     424 ..     316     438 .. 0.64
   2 ?    4.5   1.8      0.33        24      86     134 ..     386     434 ..     365     462 .. 0.48
   3 ?    3.9   4.2      0.49        36      87     147 ..     443     503 ..     437     513 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.054
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX.XXXXXXX CS
                          LUC7  83 eeflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgee.GkVdea.qklmkev 161
                                   +e l+ l++ +ed++ ++   ++rl++ +e+ ++ +++  +   +l++l+ ++ +  a  e l ++ ++V    q+l +++
  gi|14601261|ref|NP_147796.1| 327 AEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRlDQVASTlQQLQQRL 407
                                   56688899999***************9999998877776677788888888888888888877655244444313333344 PP

                                   XXXXXXXXXXXXXXXXX CS
                          LUC7 162 eelkeekeeleqqyeaa 178
                                    + +e  ++l+++  + 
  gi|14601261|ref|NP_147796.1| 408 ATAEESLQALTEDLASL 424
                                   44444444444444443 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.33
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXX CS
                          LUC7  86 lrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleek 134
                                   l++l+  l++v    q+ +qrl+  +e+ ++ +e  a+ q+++++l+++
  gi|14601261|ref|NP_147796.1| 386 LEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQS 434
                                   3333444444444444444444433333333333322222233332222 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.49
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXX CS
                          LUC7  87 rfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelge 147
                                    +l+++++ v+  ++   ++l + +e++++++++ ++ q q++el  +++++ +ea++ ++
  gi|14601261|ref|NP_147796.1| 443 GQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTAS 503
                                   5678889999999999999999999999988888889999**********99999999875 PP

>> DUF3037  Protein of unknown function (DUF3037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0       2.2   1.6e+02      38      87 ..     285     342 ..     248     350 .. 0.58
   2 ?    8.3   2.7      0.04       2.9      31     114 ..     334     422 ..     327     436 .. 0.71
   3 ?    1.2   1.1       6.2   4.6e+02      52      97 ..     465     510 ..     423     524 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 2.2
                       DUF3037  38 eaRlralfpel.....dlealeeelkaleeicegeka.agpiak..ldlaerfrwlta 87 
                                    +R+ al +++      lea+e  l+ l+  +   ++  ++ a+  ++l++r++ l+a
  gi|14601261|ref|NP_147796.1| 285 DSRVGALEDRVadiegRLEAVEGSLEDLSGAVDAMSQqLQALAEdlESLSSRVEDLEA 342
                                   3555555544444444445555555555555533333223333334555555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.04
                       DUF3037  31 kvrleldeaRlralfpel.....dlealeeelkaleeicegekaagpiakldlaerfrwltaprstviqtsevhtgltedp 106
                                   + r+e+ eaR+ ++ ++l     d++ l   l++l+  +e+ +   ++a+ +l+++ ++l +  st+ q+++  ++ +e++
  gi|14601261|ref|NP_147796.1| 334 SSRVEDLEARVGSVEDRLsqaeeDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESL 414
                                   445555555555555555555557788888888888888888777778888888888888888888888888888888888 PP

                       DUF3037 107 eaelerLf 114
                                   +a  e+L 
  gi|14601261|ref|NP_147796.1| 415 QALTEDLA 422
                                   77777775 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 6.2
                       DUF3037  52 aleeelkaleeicegekaagpiakldlaerfrwltaprstviqtse 97 
                                   + ee+ ++ ++++e+ +++ ++ +++l e +r+ +++ st+ ++s 
  gi|14601261|ref|NP_147796.1| 465 QAEEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTASRWSM 510
                                   2223333333333333333444445555555555555555555554 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.42        31      19      34 ..     298     313 ..     298     315 .. 0.94
   2 ?    2.1   0.2         2   1.5e+02      20      35 ..     355     370 ..     351     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.42
                          YvrJ  19 iEkkLdeLtksIeeLs 34 
                                   iE++L++   s e+Ls
  gi|14601261|ref|NP_147796.1| 298 IEGRLEAVEGSLEDLS 313
                                   8**************8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 2
                          YvrJ  20 EkkLdeLtksIeeLse 35 
                                   E+ +d+Lt+s + L++
  gi|14601261|ref|NP_147796.1| 355 EEDIDSLTTSLDSLRT 370
                                   7789********9987 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.0       1.2        91      17      41 ..     323     347 ..     303     418 .. 0.64
   2 ?    4.0   0.2      0.77        57       2      33 ..     413     444 ..     405     448 .. 0.59
   3 ?    1.4   1.2       4.8   3.5e+02       2      32 ..     462     492 ..     461     508 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 1.2
                       DUF3782  17 leelekeieklertigaLGaRWGlv 41 
                                   l+ l + +e+l+++++ L aR G v
  gi|14601261|ref|NP_147796.1| 323 LQALAEDLESLSSRVEDLEARVGSV 347
                                   4444444444444444444443332 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.77
                       DUF3782   2 elekleeeeeetkedleelekeieklertiga 33 
                                   +l++l e+ ++++ ++e l+++i +++r++g 
  gi|14601261|ref|NP_147796.1| 413 SLQALTEDLASLQAEVETLQQSIVEIDRRLGQ 444
                                   45555555666666666666666666666554 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 4.8
                       DUF3782   2 elekleeeeeetkedleelekeieklertig 32 
                                   +l + ee++++++  +e+++++i++l++ ++
  gi|14601261|ref|NP_147796.1| 462 KLVQAEEKNQRQDASIEDFQSQIQELRTQLD 492
                                   6778889999999999999999999988765 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.5     0.011      0.78      61     170 ..     296     404 ..     244     410 .. 0.43
   2 ?   12.0   7.8    0.0017      0.12      34     157 ..     316     440 ..     289     453 .. 0.61
   3 ?    0.5  12.0       5.7   4.2e+02      12     105 ..     406     500 ..     397     507 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.011
                          YkyA  61 enveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryeaydklykaYkealeldkeLYemLk 139
                                   + +e R e +e   e ++ a +++   +++++ +  + e+l + +e+l+  + + ++  ++  ++  +++++  +L ++L+
  gi|14601261|ref|NP_147796.1| 296 ADIEGRLEAVEGSLEDLSGAVDAM---SQQLQALaeDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELE 373
                                   444444444444333222222222...222222211122233333333333333333333333333333333333333333 PP

                          YkyA 140 keeltleeleeqiekiNesyeevkeaneqFn 170
                                   + ++ l e ++ +e++N+  ++v ++ +q++
  gi|14601261|ref|NP_147796.1| 374 DLSTRLAEAQASLEDLNTRLDQVASTLQQLQ 404
                                   3333333333333333333333333333333 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0017
                          YkyA  34 eqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelieamee 112
                                      + +++ +   ++++ +++ ++++ + v   e++l++ +e i++    ++++++e+e++     e++  +e+l++ +++
  gi|14601261|ref|NP_147796.1| 316 VDAMSQQLQA-LAEDLESLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLstRLAEAQASLEDLNTRLDQ 395
                                   4444444433.3355566666666666677777777777777777777777777777777744455666666666666666 PP

                          YkyA 113 ryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNe 157
                                     ++ ++l ++  +a e+ + L e L + ++++e+l++ i +i +
  gi|14601261|ref|NP_147796.1| 396 VASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDR 440
                                   666666666666666666666666666666666666666666655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 5.7
                          YkyA  12 eavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeie 92 
                                    ++++E+++++  e L +l+++ + l ++i+e +  ++ ++ + +d +   ve   e+l + +e  ++    +e+ +++i+
  gi|14601261|ref|NP_147796.1| 406 RLATAEESLQALTEDLASLQAEVETLQQSIVEID-RRLGQLRSTVDAVRLEVESLGEKLVQAEEKNQRQDASIEDFQSQIQ 485
                                   3455566666666666666666666666666533.2246666666666666666666666666666666666666666666 PP

                          YkyA  93 ei..edeelkkeaee 105
                                   e+  + +e+  ea++
  gi|14601261|ref|NP_147796.1| 486 ELrtQLDEKTREAQQ 500
                                   664333333334443 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       5.7   4.2e+02      35      62 ..     274     301 ..     249     310 .. 0.54
   2 ?   10.4   0.5    0.0079      0.59      30      70 ..     311     351 ..     303     352 .. 0.84
   3 ?    6.0   0.9      0.18        13      36      69 ..     359     392 ..     356     401 .. 0.50
   4 ?    1.6   5.6       4.1   3.1e+02      29      69 ..     387     427 ..     372     443 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 5.7
                      JIP_LZII  35 vdeLtsereiLreEleslqkakerlesr 62 
                                   v++Lt + ++L + + +l++  + +e r
  gi|14601261|ref|NP_147796.1| 274 VEDLTLQLSSLDSRVGALEDRVADIEGR 301
                                   4444444444444444444444444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0079
                      JIP_LZII  30 dLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                   dL   vd ++++ ++L e+lesl +  e le r+  +E+ l
  gi|14601261|ref|NP_147796.1| 311 DLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRL 351
                                   66677999999999999999999999999999999999876 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.18
                      JIP_LZII  36 deLtsereiLreEleslqkakerlesrikelEee 69 
                                   d Lt+  ++Lr Ele l + +++ + ++++l   
  gi|14601261|ref|NP_147796.1| 359 DSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTR 392
                                   5555555555555555555555555554444433 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 4.1
                      JIP_LZII  29 ddLIarvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                   +dL +r+d+  s  + L++ l + ++++++l + ++ l++e
  gi|14601261|ref|NP_147796.1| 387 EDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAE 427
                                   45555555555555555555555555555555554444444 PP

>> HCMV_UL139  Human Cytomegalovirus UL139 protein
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.9      0.34        25       7      73 ..     249     315 ..     242     332 .. 0.84
   2 ?   10.3   2.0    0.0084      0.62       6      75 ..     290     359 ..     287     362 .. 0.89
   3 ?    4.8   9.8      0.42        31      13      92 ..     332     411 ..     324     417 .. 0.64
   4 ?    6.4   8.4      0.14        10       7      72 ..     368     433 ..     356     448 .. 0.69
   5 ?    4.6   4.9       0.5        37       7      74 ..     389     456 ..     387     465 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.34
                                   XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil   7 leasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealkn 73 
                                   +e + ++l   l +le+ +     + e+l  q   l+s + +le++ a+ e rl  +e  l++    
  gi|14601261|ref|NP_147796.1| 249 VEQAVEDLGLALDSLEERVGDLEFAVEDLTLQLSSLDSRVGALEDRVADIEGRLEAVEGSLEDLSGA 315
                                   4777889999999999999999999999999*************99999999999999999987555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0084
                                   XXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil   6 rleasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealknle 75 
                                   +le   +++  +l ++e sle    + + + +q + l + l sl s+ ++ e r+  +e +l +a  +++
  gi|14601261|ref|NP_147796.1| 290 ALEDRVADIEGRLEAVEGSLEDLSGAVDAMSQQLQALAEDLESLSSRVEDLEARVGSVEDRLSQAEEDID 359
                                   5777788999999999999999999999999****************99999999999999998877776 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.42
                                   XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil  13 elanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealknleleklarlelesrlskte 92 
                                   +l++++  le  + s      +     d l  +l sl++e ++   rl+e +a l++    l++   +  +l+ rl+  e
  gi|14601261|ref|NP_147796.1| 332 SLSSRVEDLEARVGSVEDRLSQAEEDIDSLTTSLDSLRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAE 411
                                   34444444444444333333333345566777888888888888888888888888888888877777777888887766 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.14
                                   XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil   7 leasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealk 72 
                                   l +  ++l+++la  + sle   +  ++++   ++l++ la+ e+  +   + l+ l+a ++   +
  gi|14601261|ref|NP_147796.1| 368 LRTELEDLSTRLAEAQASLEDLNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQ 433
                                   444456777777777777777777777777777777777777777777777777777777765444 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.5
                                   XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil   7 leasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealknl 74 
                                   l++  +++a+ l  l++ l +   s + l      l+  + +l++   e ++rl +l++ +d +  ++
  gi|14601261|ref|NP_147796.1| 389 LNTRLDQVASTLQQLQQRLATAEESLQALTEDLASLQAEVETLQQSIVEIDRRLGQLRSTVDAVRLEV 456
                                   55566788999999999999999999999999999999999999999999999999999998765444 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2       2.7     2e+02      20      39 ..     317     336 ..     306     351 .. 0.69
   2 ?    4.8   8.1      0.37        27      13      73 ..     352     408 ..     341     415 .. 0.68
   3 ?    5.0   7.9      0.32        23      13      68 ..     394     445 ..     390     450 .. 0.79
   4 ?    1.7  18.1       3.5   2.6e+02      24      86 ..     433     505 ..     408     516 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 2.7
                          FlxA  20 asLqkQiknlqkqLkelses 39 
                                    ++ +Q++ l + L++ls+ 
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSR 336
                                   45566666666666666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.37
                          FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqa 73 
                                   s+ +++i sL+  +++l  +L++ls+       e ++  + + + ++q+ + ++qlqq  a
  gi|14601261|ref|NP_147796.1| 352 SQAEEDIDSLTTSLDSLRTELEDLSTR----LAEAQASLEDLNTRLDQVASTLQQLQQRLA 408
                                   567788888888888888888888888....333445556666667777777776666544 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.32
                          FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaql 68 
                                   ++ as +++Lq+ +++++++L+ l+e+   + +   +  +++q+ I  +   + ql
  gi|14601261|ref|NP_147796.1| 394 DQVASTLQQLQQRLATAEESLQALTED-LASLQ---AEVETLQQSIVEIDRRLGQL 445
                                   578999*********************.44444...55777777777777776666 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 3.5
                          FlxA  24 kQiknlqkqLkelses......deltkeekk....kqqqliqaQIqqlqaQIaqlqqqqaekaqekqqsekee 86 
                                   + i ++   L +l ++      + ++  ek     ++ q   a I++ q+QI+ l  q +ek++e+qq++ ++
  gi|14601261|ref|NP_147796.1| 433 QSIVEIDRRLGQLRSTvdavrlEVESLGEKLvqaeEKNQRQDASIEDFQSQIQELRTQLDEKTREAQQTASTA 505
                                   3333333333344333433333222222332444466666677888888888888888888888888776654 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2       1.4     1e+02      15      41 ..     317     343 ..     310     345 .. 0.73
   2 ?    5.0   0.4      0.38        28      15      35 ..     359     379 ..     355     390 .. 0.73
   3 ?    3.5   0.4       1.1        85      23      39 ..     416     432 ..     411     443 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.4
                          HALZ  15 daLksdydsLkkenekLkaelqeLkek 41 
                                   da+  + ++L ++ e+L + ++ L ++
  gi|14601261|ref|NP_147796.1| 317 DAMSQQLQALAEDLESLSSRVEDLEAR 343
                                   677777778888888888888877765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.38
                          HALZ  15 daLksdydsLkkenekLkael 35 
                                   d+L+++ dsL+ e e L + l
  gi|14601261|ref|NP_147796.1| 359 DSLTTSLDSLRTELEDLSTRL 379
                                   677777777777777776655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 1.1
                          HALZ  23 sLkkenekLkaelqeLk 39 
                                   +L ++  +L+ae+++L 
  gi|14601261|ref|NP_147796.1| 416 ALTEDLASLQAEVETLQ 432
                                   56666667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2501  (0.139495); expected 358.6 (0.02)
Passed bias filter:                     1318  (0.0735122); expected 358.6 (0.02)
Passed Vit filter:                       419  (0.02337); expected 17.9 (0.001)
Passed Fwd filter:                       326  (0.0181828); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             243  [number of targets reported over threshold]
# CPU time: 3.59u 0.41s 00:00:04.00 Elapsed: 00:00:00.81
# Mc/sec: 1997.53
//
Query:       gi|118431372|ref|NP_147798.2|  [L=359]
Description: hypothetical protein APE_1219.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2719.11
//
Query:       gi|14601264|ref|NP_147799.1|  [L=311]
Description: hypothetical protein APE_1220 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   4.2      0.016   15.2   0.6    2.2  2  DUF4714   Domain of unknown function (DUF4714)
       0.28    9.4   8.4       0.34    9.1   8.4    1.3  1  DUF2070   Predicted membrane protein (DUF2070)
        1.5    8.2  10.1        2.2    7.6  10.1    1.3  1  DUF373    Domain of unknown function (DUF373)


Domain annotation for each model (and alignments):
>> DUF4714  Domain of unknown function (DUF4714)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.6   2.7e-06     0.016      81     114 ..     111     146 ..      67     155 .. 0.77
   2 ?    0.9   0.2     0.068   4.1e+02      79     100 ..     232     255 ..     224     262 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-06
                       DUF4714  81 grgafllllallvltclalaila..vylsvlqsesl 114
                                   g g+fllll  ++l+ + + +la  vylsv+qs  l
  gi|14601264|ref|NP_147799.1| 111 GPGGFLLLLMTVLLAVIMFFLLAalVYLSVVQSTLL 146
                                   5699****999999999988887679*******876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.068
                       DUF4714  79 vhgrga..fllllallvltclala 100
                                     +r a   ll l  l+lt l+la
  gi|14601264|ref|NP_147799.1| 232 TTARTAaaALLALVSLILTWLSLA 255
                                   455554004555556899*99998 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.4   5.7e-05      0.34      38     195 ..     120     300 ..      49     311 .] 0.57

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 5.7e-05
                       DUF2070  38 lfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall.qalvllalvls.......... 107
                                   ++ +l++++ +l+a+l++l v++++   l  + s +l      +++ ++ l+ +++a+   a+vl+ l+l+          
  gi|14601264|ref|NP_147799.1| 120 MTVLLAVIMFFLLAALVYLSVVQST---LLGRVSSVLGWGLDGFMARLTGLGGAVFAFStVAFVLYILALAlplpglytly 197
                                   3333333333444444444444443...55566677777777777777777777776666666666666666666666666 PP

                       DUF2070 108 .....lalvfalrllvlvavsdesllkav...lpaliqpllailllvly........fspesfllllllslifalavylfi 172
                                        + ++f     +++a++  +ll+++    p+++ +++a+ll++ +        ++   + +     l +a++++++ 
  gi|14601264|ref|NP_147799.1| 198 qrypeYEIYFTAIATIYLATTALTLLWSLlhaPPTTARTAAAALLAL-VsliltwlsLAHPEVTIGPTGPLGMAAGLAILY 277
                                   66666555555555555555555555555332122222222222222.134455544444444455555555555555556 PP

                       DUF2070 173 vvvdrplkrnlgvsaldllsaFl 195
                                   v ++r++++ +g +al+  +  l
  gi|14601264|ref|NP_147799.1| 278 VEMERRIRERYGEEALEEARTVL 300
                                   66778888888888887666666 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  10.1   0.00037       2.2     163     269 ..     115     220 ..     107     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00037
                        DUF373 163 lllliyallll......lglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligiis 237
                                   +lll++++ll       l    +  ++ ++llG +  + G gld  +++l+     ++  +++ fv y++al+l l g++ 
  gi|14601264|ref|NP_147799.1| 115 FLLLLMTVLLAvimfflLAALVYLSVVQSTLLGRVSSVLGWGLDGFMARLTGLGGAVFAFSTVAFVLYILALALPLPGLYT 195
                                   44444444443444443667788899999**************************************************99 PP

                        DUF373 238 gyislesvss.....asvssglltlilafiygavewl 269
                                    y+ + +++      a           + iy a++ l
  gi|14601264|ref|NP_147799.1| 196 LYQRYPEYEIyftaiA-----------T-IYLATTAL 220
                                   9888555554332211...........1.22211111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2126.62
//
Query:       gi|14601265|ref|NP_147800.1|  [L=356]
Description: hypothetical protein APE_1221 [Aeropyrum pernix K1]
Scores for complete 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-26   91.4   1.1      8e-26   89.8   1.1    1.9  1  PDDEXK_10        PD-(D/E)XK nuclease superfamily
    2.4e-22   78.8   0.8    2.4e-22   78.8   0.8    5.0  4  DUF3782          Protein of unknown function (DUF3782)
    2.5e-06   27.6  19.4       0.35   11.1   2.3    4.8  5  XhlA             Haemolysin XhlA
    0.00065   20.0  20.5     0.0042   17.4   2.7    3.6  4  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0012   18.4  45.5        0.1   12.2   3.5    5.5  6  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
     0.0015   18.7  37.3       0.32   11.2   9.3    3.5  3  Tropomyosin_1    Tropomyosin like
     0.0016   19.2  31.9       0.16   12.7   8.7    3.3  3  DUF4472          Domain of unknown function (DUF4472)
     0.0025   17.2  47.3      0.087   12.2  34.1    2.9  3  GAS              Growth-arrest specific micro-tubule binding
     0.0049   15.1  30.4     0.0054   15.0  19.3    2.1  2  EzrA             Septation ring formation regulator, EzrA
     0.0056   17.0  49.3      0.084   13.2  11.2    4.7  5  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0083   16.6  26.2       0.43   11.1   3.8    3.5  3  DUF16            Protein of unknown function DUF16
  ------ inclusion threshold ------
      0.014   14.1  27.1       0.09   11.4  11.3    2.2  2  FapA             Flagellar Assembly Protein A
      0.018   15.1   0.4        2.2    8.3   0.4    2.7  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.019   13.8  33.1       0.35    9.7  21.4    2.5  2  Spc7             Spc7 kinetochore protein
      0.031   13.6  44.6       0.18   11.1  44.6    2.0  1  Tropomyosin      Tropomyosin
      0.032   13.5  22.8      0.076   12.2   7.6    2.1  2  TMPIT            TMPIT-like protein
      0.039   14.2  51.6       0.28   11.4  17.6    2.6  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.049   13.4  54.9      0.014   15.2  33.7    2.2  2  ERM              Ezrin/radixin/moesin family
       0.06   13.4  43.2       0.41   10.7  20.1    3.3  2  Nup54            Nucleoporin complex subunit 54
      0.063   13.4  42.7      0.073   13.2  12.3    3.3  4  ADIP             Afadin- and alpha -actinin-Binding
      0.075   13.8  33.0       0.33   11.7  11.9    3.5  4  Occludin_ELL     Occludin homology domain
       0.14   12.0  35.0       0.38   10.5   7.3    4.1  4  SKA2             Spindle and kinetochore-associated protein 2
       0.18    9.5  49.4       0.26    9.0  49.4    1.1  1  Myosin_tail_1    Myosin tail
       0.23   11.3  31.3         16    5.3   7.4    4.4  4  DUF1465          Protein of unknown function (DUF1465)
       0.23   11.2  29.5       0.17   11.7  10.1    2.3  2  DUF724           Protein of unknown function (DUF724)
       0.28   10.6  53.5       0.51    9.7  19.4    3.3  3  DUF3552          Domain of unknown function (DUF3552)
       0.31   11.1  29.9       0.19   11.8   2.0    4.1  4  BRE1             BRE1 E3 ubiquitin ligase
       0.33   11.2  45.9        1.1    9.6  17.2    3.2  3  Troponin         Troponin
        0.4   10.7  19.8        1.8    8.6   6.6    3.6  3  DUF1664          Protein of unknown function (DUF1664)
       0.46    9.7  24.2    1.8e+04   -5.4  24.2    2.4  0  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.47   10.3  21.5        6.2    6.7   0.6    5.9  8  DASH_Dam1        DASH complex subunit Dam1
       0.82   10.3  52.5        1.4    9.5  11.6    4.0  3  SlyX             SlyX
        1.2    9.1  35.6        1.2    9.1   5.2    3.5  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        1.3    8.5  35.2        1.1    8.8  16.8    2.2  2  Exonuc_VII_L     Exonuclease VII, large subunit
        1.4    9.2  51.9       0.17   12.2   9.7    4.2  3  ABC_tran_CTD     ABC transporter C-terminal domain
        1.5    8.4  24.6         21    4.6  15.9    3.2  2  DUF4795          Domain of unknown function (DUF4795)
        1.9    8.0  38.4        5.6    6.4  22.8    2.4  2  Leu_zip          Leucine zipper
        2.1    7.9  17.9    4.4e+02    0.3  17.9    2.4  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
        2.9    8.1  23.7         20    5.4  12.0    3.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
        3.6    7.6  15.8        0.8    9.7   1.8    3.7  3  Laminin_II       Laminin Domain II
        3.6    7.2   5.8         57    3.3   1.0    3.9  3  DUF4988          Domain of unknown function
          5    4.9  14.8       0.51    8.2   3.5    2.1  2  Prominin         Prominin
        5.7    6.9  42.0        5.6    7.0   3.0    5.0  6  Prefoldin_2      Prefoldin subunit
        9.2    6.5  46.7        1.6    8.9   7.3    5.2  4  bZIP_1           bZIP transcription factor
        9.6    6.7  20.0        2.3    8.7   0.9    4.7  4  FlaC_arch        Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   1.1     2e-28     8e-26       1      74 []     281     349 ..     281     349 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 2e-28
                     PDDEXK_10   1 sevelDvvvkdgkvilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgie 74 
                                   s ve+Dvvvkdg+++lvEiks+++++D+a+++r++ lYe+a+gvk +rl++v++f+d+r    ++a+Aerlg+e
  gi|14601265|ref|NP_147800.1| 281 SIVEVDVVVKDGQHVLVEIKSQVTQADVAEMHRIGLLYERAEGVK-PRLVIVGGFVDER----ARALAERLGVE 349
                                   67*******************************************.*************....*********97 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   5.4      0.17        66       1      47 [.      55     101 ..      55     103 .. 0.93
   2 ?    5.9   5.1     0.036        14       2      46 ..     105     148 ..     103     162 .. 0.77
   3 ?    0.1   5.8       2.4   9.4e+02       1      37 [.     160     196 ..     146     203 .. 0.74
   4 !   78.8   0.8   6.1e-25   2.4e-22       1      78 []     202     280 ..     201     280 .. 0.98

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
                       DUF3782   1 eelekleeeeeetkedleelekeieklertigaLGaRWGlvsEeafR 47 
                                   e++eklee++ +++e+  +le++  kle++++ L +R+  + E+ +R
  gi|14601265|ref|NP_147800.1|  55 ERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLR 101
                                   6789**********************************999999877 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.036
                       DUF3782   2 elekleeeeeetkedleelekeieklertigaLGaRWGlvsEeaf 46 
                                   +++kl+e+ ++++++  +le+++++le+++++L  R+ l  E+ f
  gi|14601265|ref|NP_147800.1| 105 RFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERY-LRLEQRF 148
                                   5788888888888888889999999999999988888.5555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2.4
                       DUF3782   1 eelekleeeeeetkedleelekeieklertigaLGaR 37 
                                   e+++kle+++ +++e+ ++le++  kle++++ L  R
  gi|14601265|ref|NP_147800.1| 160 ERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEER 196
                                   4667777777777777777777777777777766555 PP

  == domain 4  score: 78.8 bits;  conditional E-value: 6.1e-25
                       DUF3782   1 eelekleeeeeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv.kVekwlyyDkeGeVygyP 78 
                                   +++++leee ++++e++ ++e+++ ++ r+++++++R+G+++EeafR+++k+++ee+lg+  V +w+++DkeG+Vyg+P
  gi|14601265|ref|NP_147800.1| 202 QRFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIAHRFGILTEEAFRSAMKHVVEEVLGAgVVGRWIHHDKEGIVYGHP 280
                                   5789**************************************************************************9 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   2.0    0.0011      0.44       1      46 [.      52      97 ..      52      99 .. 0.94
   2 !   10.7   0.3    0.0011      0.45       3      46 ..      96     139 ..      94     142 .. 0.90
   3 !   11.0   0.2   0.00097      0.39       2      48 ..     123     169 ..     122     170 .. 0.92
   4 !    8.3   1.1    0.0066       2.6       2      44 ..     144     186 ..     142     188 .. 0.85
   5 !   11.1   2.3   0.00088      0.35       2      45 ..     172     215 ..     171     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                          XhlA  1 eikerlerietkldnleervdkleekaaeaeekiknleedlkkles 46
                                  e++er e++e+++  leer ++lee++ + ee+ + le++  +le+
  gi|14601265|ref|NP_147800.1| 52 ELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEE 97
                                  578999**********************************999997 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0011
                          XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                   +er  r+e++  +l+er ++le+++ + ee+ + le +  +le+
  gi|14601265|ref|NP_147800.1|  96 EERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEE 139
                                   5666799******************************9999997 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00097
                          XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesnq 48 
                                   ++er +r+e++  +leer  +le++  + ee+   lee+  kle+ q
  gi|14601265|ref|NP_147800.1| 123 LEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQ 169
                                   589999***********999**********************99876 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0066
                          XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                   +++r +r+e++   leer +kle+++   ee+ + lee+  kl
  gi|14601265|ref|NP_147800.1| 144 LEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKL 186
                                   5789999999999999999999999999999999999875555 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00088
                          XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                   ++er +r+e+++ +le+r +klee+  + e++ + lee+  +l 
  gi|14601265|ref|NP_147800.1| 172 LEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLS 215
                                   78999******************************999988776 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 ?    6.6   1.0     0.024       9.6      60      95 ..      50      85 ..      26      86 .. 0.91
   2 !   11.1   4.3   0.00097      0.39      34      94 ..      55     119 ..      50     122 .. 0.86
   3 !   17.4   2.7     1e-05    0.0042      20      95 ..      83     162 ..      80     163 .. 0.65
   4 !   11.3   6.5   0.00082      0.33      21      95 ..     133     211 ..     127     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.024
                       BLOC1_2 60 lqpylqqidqiekqvteLeeavseLDeyskeLEakf 95
                                  ++++l++ +++e++  +Lee  s+L+e   +LE++f
  gi|14601265|ref|NP_147800.1| 50 FKELLERFEKLEERQLRLEERFSQLEERQIKLEERF 85
                                  78899999999999999**********999999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00097
                       BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidq....iekqvteLeeavseLDeyskeLEak 94 
                                   e+++kl+++   le+ +++l+e++ +l++ +q +++    +e++  +Le   ++LDe  ++LE++
  gi|14601265|ref|NP_147800.1|  55 ERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKrfqrLEERHLRLERRFQKLDERFQRLEQR 119
                                   7999999999**************99999998876433339999999***************986 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1e-05
                       BLOC1_2  20 edyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidq....iekqvteLeeavseLDeyskeLEakf 95 
                                   e ++lLek  ++ +e+   l+++ ++l + +++l++++  l++ +q+++q    +e++  +Le+  ++L+e  + LE++f
  gi|14601265|ref|NP_147800.1|  83 ERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQrfqsLEERYLRLEQRFQRLEERFRLLEERF 162
                                   45666666666666666666666666666666666666665555555443222278888889999999999999998887 PP

  == domain 4  score: 11.3 bits;  conditional E-value: 0.00082
                       BLOC1_2  21 dyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqid....qiekqvteLeeavseLDeyskeLEakf 95 
                                    ++ Le+   + +++++ l+++   le+ ++kl++++ +l++ +q+++    ++e++ ++Lee   +L++  ++LE+ f
  gi|14601265|ref|NP_147800.1| 133 RFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEerqlKLEQRFQKLEERHLKLEQRFQRLEEEF 211
                                   5666777777778888888888888888888888888888888888873333477777777777777777777777766 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   7.1    0.0067       2.7       2      35 ..      71     104 ..      56     110 .. 0.91
   2 ?    7.0   4.7     0.011       4.3       4      35 ..      87     118 ..      84     128 .. 0.74
   3 !    8.1   3.8    0.0051         2       4      35 ..     101     132 ..      99     140 .. 0.92
   4 !   10.4   3.6   0.00093      0.37       4      34 ..     122     152 ..     112     153 .. 0.67
   5 !   10.1   3.1    0.0012      0.48       2      35 ..     148     181 ..     147     183 .. 0.95
   6 !   12.2   3.5   0.00026       0.1       1      35 [.     189     223 ..     189     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0067
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlEn 35 
                                   + +leer ++le+ fql++k+++r +e+  RlE+
  gi|14601265|ref|NP_147800.1|  71 FSQLEERQIKLEERFQLLEKRFQRLEERHLRLER 104
                                   6789999999999999999999999999999998 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRlEn 35 
                                    le+r  +le+ +  ++ ++++ +e+ +RlE+
  gi|14601265|ref|NP_147800.1|  87 LLEKRFQRLEERHLRLERRFQKLDERFQRLEQ 118
                                   57778888888888888888888888888875 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0051
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRlEn 35 
                                   +le+r  +l + fq +++++ r +e+ +RlE+
  gi|14601265|ref|NP_147800.1| 101 RLERRFQKLDERFQRLEQRQLRLEERFQRLEQ 132
                                   699****************************7 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00093
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRlE 34 
                                   +leer  +le+ fq +++++ r +++ +RlE
  gi|14601265|ref|NP_147800.1| 122 RLEERFQRLEQRFQSLEERYLRLEQRFQRLE 152
                                   4677777777777777777777777777776 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlEn 35 
                                   +++leer   le+ fq++++++   +e+ +RlE 
  gi|14601265|ref|NP_147800.1| 148 FQRLEERFRLLEERFQKLEQRQLHLEERFQRLEE 181
                                   789*****************************95 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00026
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    Vac_Fusion   1 dlkdleerllvlekdfqlvikcckrvnealkRlEn 35 
                                   ++++leer l+le+ fq ++++++r +e++ R+E+
  gi|14601265|ref|NP_147800.1| 189 RFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQ 223
                                   5789******************************7 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  12.0     0.012       4.9      87     140 ..      58     115 ..      51     118 .. 0.86
   2 !   11.2   9.3   0.00079      0.32      16      87 ..     106     181 ..     105     181 .. 0.71
   3 !    8.8   7.5    0.0042       1.7      19      69 ..     172     222 ..     167     252 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                 Tropomyosin_1  87 eeleesdkkLkettekLretdvkaee....lERkvkaLeqerdewekkyeeleekyke 140
                                   e lee + +L+e   +L+e ++k ee    lE++ ++Le+++   e+++++l+e+++ 
  gi|14601265|ref|NP_147800.1|  58 EKLEERQLRLEERFSQLEERQIKLEErfqlLEKRFQRLEERHLRLERRFQKLDERFQR 115
                                   8999999************99999986666799***************9999999875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00079
                 Tropomyosin_1  16 aeeleekvKeleqenlekeqeiksLtkknqqleee...vekleeklkeakekaeesekkktnne.altrkiqlLEe 87 
                                    ++l e+ ++leq++l+ e+  + L+++ q lee    +e+  ++l+e  + +ee  +k  +    l+ + q LEe
  gi|14601265|ref|NP_147800.1| 106 FQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERylrLEQRFQRLEERFRLLEERFQKLEQRQlHLEERFQRLEE 181
                                   5678888889999999999999999999999998622245555566666666777666666655688899999987 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0042
                 Tropomyosin_1  19 leekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeese 69 
                                   lee+ ++le+++l+ eq  ++L+++  +le+   +lee+ +   e +   e
  gi|14601265|ref|NP_147800.1| 172 LEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVE 222
                                   555555555555555555555555555555555555555444444333333 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1  10.4    0.0026         1      39     104 ..      59     124 ..      50     132 .. 0.64
   2 !   12.7   8.7   0.00041      0.16      34     104 ..      96     166 ..      94     169 .. 0.79
   3 !    8.9   9.3    0.0062       2.5      41      99 ..     159     217 ..     155     245 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0026
                       DUF4472  39 alenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqels 104
                                   +le+r l le + ++++e + +l+er++ le+  ++lee+   l++++q+l + f++ +++q +l+
  gi|14601265|ref|NP_147800.1|  59 KLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLE 124
                                   456666666666666666666666666666666666666666666666666666666666665553 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00041
                       DUF4472  34 knkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqels 104
                                   + + l+le r   l+ + +++++ +  l+er++ le+  ++lee+y  l++++q le+ f   +++ q+l+
  gi|14601265|ref|NP_147800.1|  96 EERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLE 166
                                   55667888888888888888888888888888888888888888888888888888888888888888875 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0062
                       DUF4472  41 enrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkk 99 
                                   e+r   le ++ +++e  q l+er+ +le+  ++lee+   l++++q le+ef +  ++
  gi|14601265|ref|NP_147800.1| 159 EERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSER 217
                                   55555555555555555566666666666666666666666666666666555554443 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 ?    4.7  17.6     0.043        17      75     150 ..      52     126 ..      24     129 .. 0.63
   2 !   12.2  34.1   0.00022     0.087      29     156 ..      51     181 ..      47     184 .. 0.90
   3 !   10.8   8.8   0.00058      0.23      85     129 ..     174     218 ..     171     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.043
                           GAS  75 kqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekk 150
                                   + l+++ek  ++  +l++r ++le+   +l++  + le+rf+++e+   +l+++f++ ++e +q+ + ++l Le +
  gi|14601265|ref|NP_147800.1|  52 ELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQK-LDERFQRLEQRQLRLEER 126
                                   445555555555555566666666665566666666666666666665666665555.555555555555555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                           GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrk...ql.knyekdkqslknlkarlkelekelkdlk 105
                                   k+l e  e+l++++ r e ++s+++++  +l+e  + +e+  ++L++   +l ++++k  +++++l++r  +le+ +++l+
  gi|14601265|ref|NP_147800.1|  51 KELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEErhlRLeRRFQKLDERFQRLEQRQLRLEERFQRLE 131
                                   67888999*************************************9943322246777778889999999*********** PP

                           GAS 106 wehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqe 156
                                   +  ++le+r+ ++e+ +++l+++f+  ++e +qk + ++l Le + ++l+e
  gi|14601265|ref|NP_147800.1| 132 QRFQSLEERYLRLEQRFQRLEERFRL-LEERFQKLEQRQLHLEERFQRLEE 181
                                   ************************87.9********************998 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00058
                           GAS  85 qslknlkarlkelekelkdlkwehevleqrfekvekerdelykkf 129
                                   +++++l++r  +le+ +++l++ h  leqrf+++e+e+ +l+++ 
  gi|14601265|ref|NP_147800.1| 174 ERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERV 218
                                   67899************************************9986 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5  11.0    0.0051         2     343     425 ..      54     136 ..      24     143 .. 0.54
   2 !   15.0  19.3   1.3e-05    0.0054     302     431 ..     107     233 ..     103     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0051
                                   STTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA 343 leklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkel 423
                                   le++++le++  +le+++ +lee+  + +  +  l++++++lee+  ++e + ++++e ++ l++  +r +e+ ++++++ 
  gi|14601265|ref|NP_147800.1|  54 LERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRF 134
                                   344444444444444444444444444444444444444444444444444444444444444444444444444444443 PP

                                   HH CS
                          EzrA 424 ke 425
                                   ++
  gi|14601265|ref|NP_147800.1| 135 QS 136
                                   33 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   HHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTH CS
                          EzrA 302 keveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeele 382
                                   ++ ++++++l+++  +le+ ++ l++  + l+++Y    +  ++++ le+++  le+++++le++  + +  + +l+e++ 
  gi|14601265|ref|NP_147800.1| 107 QKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYL---RLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQL 184
                                   456677777777777777777777777777777774...34689999********************************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                          EzrA 383 eleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkie 431
                                   +le++ +++ee++ ++++ ++ l+++ +r  e++ ++++ l ++ r ++
  gi|14601265|ref|NP_147800.1| 185 KLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVNMMRMMN 233
                                   *****************************************99999886 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 !    9.4  13.8    0.0033       1.3       6      71 .]      51     119 ..      50     119 .. 0.88
   2 !   13.2  11.2   0.00021     0.084      14      71 .]     108     168 ..     104     168 .. 0.88
   3 ?    2.7  17.4      0.41   1.6e+02      28      69 ..     143     194 ..     123     196 .. 0.38
   4 !    8.7  13.8    0.0057       2.3      14      71 .]     157     210 ..     153     210 .. 0.90
   5 ?    4.8  11.4     0.088        35      15      56 ..     172     213 ..     171     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0033
                           CLZ   6 reILlKdglLDeeaakagaeqkeleekverLessLeaLqtrlarLlaey...essqrkLkqRitkLEkk 71 
                                   +e+L +   L+e+    ++   +lee+  +Le++ + L++r++rL + +   e   +kL +R ++LE++
  gi|14601265|ref|NP_147800.1|  51 KELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHlrlERRFQKLDERFQRLEQR 119
                                   68999999*****99999999************************9976222667789999*****985 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00021
                           CLZ  14 lLDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrk...LkqRitkLEkk 71 
                                    LDe+++  ++ q  lee+ +rLe++ ++L+ r+ rL + ++  +++   L++R +kLE++
  gi|14601265|ref|NP_147800.1| 108 KLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERfrlLEERFQKLEQR 168
                                   79***********************************999887776644488999999985 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.41
                           CLZ  28 eleekverLessLeaLqtrlarL..........laeyessqrkLkqRitkLE 69 
                                    le++ +rLe++   L+ r+++L           + +e+ q kL+qR +kLE
  gi|14601265|ref|NP_147800.1| 143 RLEQRFQRLEERFRLLEERFQKLeqrqlhleerFQRLEERQLKLEQRFQKLE 194
                                   3333333333333333333333311111111111223555666666666666 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0057
                           CLZ  14 lLDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLEkk 71 
                                   lL+e+++k ++ q  lee+ +rLe++   L++r+++L    e+ + kL+qR ++LE++
  gi|14601265|ref|NP_147800.1| 157 LLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKL----EERHLKLEQRFQRLEEE 210
                                   899***********************99999999887....67789*********985 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.088
                           CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyes 56 
                                   L+e+++  ++ q +le++ ++Le++   L++r++rL +e+  
  gi|14601265|ref|NP_147800.1| 172 LEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRR 213
                                   677777777888888888888888888888888888777754 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  10.8     0.037        15      32     102 ..      81     151 ..      24     152 .. 0.69
   2 ?    7.6   9.1     0.013       5.2      32      81 ..     144     193 ..     117     195 .. 0.60
   3 !   11.1   3.8    0.0011      0.43      34      99 ..     174     239 ..     171     244 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.037
                                   BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
                         DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                                    ++r++ +e++ + l+e+  +le   +k++e+ ++l+++q   +e+++++++ ++++ e   ++++R+ ++
  gi|14601265|ref|NP_147800.1|  81 LEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRL 151
                                   34555556666666666666666666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.013
                                   BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
                         DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkv 81 
                                    +qr++++e++ + l+e+++kleq   +++e+ ++l+++q + +++++k+
  gi|14601265|ref|NP_147800.1| 144 LEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKL 193
                                   35666666666666666666666666666666666666666666666654 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0011
                                   HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                         DUF16  34 qrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                   +r++++e++  kl+++++kle+   k++++ ++l++e    +e++ +v+++l  +++ +++i  R+
  gi|14601265|ref|NP_147800.1| 174 ERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIAHRF 239
                                   455666666666666666666666666666666666666666666666666666666666666665 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  10.7     0.006       2.4     334     411 ..      59     130 ..      43     141 .. 0.53
   2 ?   11.4  11.3   0.00023      0.09     333     423 ..     135     225 ..     122     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.006
                          FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                   +l e++ +lee+  +lee++ kl++++++l+k        ++ +e + +l++  +kl e+ + le+++ +l+e++++ 
  gi|14601265|ref|NP_147800.1|  59 KLEERQLRLEERFSQLEERQIKLEERFQLLEK------RFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRL 130
                                   33333344444444445555555555555554......3444556666666666666666666666666666666655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00023
                          FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskk 412
                                   ++l e++ +le++ ++lee+ + l+++++kl++ +   ++  ++ +e + kl++  +kl+e+  +le+++++l+ee+++  
  gi|14601265|ref|NP_147800.1| 135 QSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLhLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRL- 214
                                   45555555555555555555555555566665544444555667777778888888888888888888888888888888. PP

                          FapA 413 eeakikvnkei 423
                                   +e  ++v++ +
  gi|14601265|ref|NP_147800.1| 215 SERVLRVEQAL 225
                                   55566666655 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 ?    8.3   0.4    0.0055       2.2      36     120 ..     144     237 ..      58     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0055
                  Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinst 107
                                   l++ ++ +e+++  l+e++++l + + +      rl++   +L++  ++l+    +l+++ + l+ +   L   v  ++++
  gi|14601265|ref|NP_147800.1| 144 LEQRFQRLEERFRLLEERFQKLEQRQLHleerfqRLEERQLKLEQRFQKLEerhLKLEQRFQRLEEEFRRLSERVLRVEQA 224
                                   445555555555555555555433322244444456666666666666666555567777777888888888888888888 PP

                  Baculo_PEP_C 108 Lnnllqalnnldl 120
                                   L n++  +n +++
  gi|14601265|ref|NP_147800.1| 225 LVNMMRMMNTIAH 237
                                   8887777777743 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4  19.1    0.0011      0.43     140     247 ..      63     166 ..      39     169 .. 0.61
   2 ?    9.7  21.4   0.00087      0.35     142     248 ..     114     216 ..     101     239 .. 0.36

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                          Spc7 140 LkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk 220
                                    + +lee++++lee + +Le++ ++l++  ++lee++ +le++++kl e+ + le+    +L+ l e++++l++  +++++
  gi|14601265|ref|NP_147800.1|  63 RQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQ---RQLR-LEERFQRLEQRFQSLEE 139
                                   34467788888888888888888888888888888888888888888886665554...3332.33344444444444445 PP

                          Spc7 221 elaelqeqleeleekieelkeqksele 247
                                   ++ +l+++ ++lee++  l+e+ ++le
  gi|14601265|ref|NP_147800.1| 140 RYLRLEQRFQRLEERFRLLEERFQKLE 166
                                   555555555555555555555555544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00087
                          Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                   ++le++   lee  ++Le++ + l+e + +le+++++lee+++ l+e+ ++le+  +  Lee  ++l+e + ++e++ ++l
  gi|14601265|ref|NP_147800.1| 114 QRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQ-RQLHLEERFQRLEERQLKLEQRFQKL 193
                                   222222222333333333333333333333333333333333333333333332.34444444444444444444333333 PP

                          Spc7 223 aelqeqleeleekieelkeqkselee 248
                                   +e+     +le++++ l+e+ ++l e
  gi|14601265|ref|NP_147800.1| 194 EERHL---KLEQRFQRLEEEFRRLSE 216
                                   33222...222222222333322222 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  44.6   0.00046      0.18      56     227 ..      64     225 ..      50     237 .. 0.41

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00046
                   Tropomyosin  56 eerleealekLeeaekaadeserarKvlEnrelkdeekleeleaqlkeakeiaeeadrkyeEvarklvvvesdLeraeera 136
                                   + rlee  ++Lee + +          lE+r +  e + ++le++    +++ +  d++++  +++   +e+ ++r e+r 
  gi|14601265|ref|NP_147800.1|  64 QLRLEERFSQLEERQIK----------LEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRF 134
                                   22222222222222111..........233333333333333333333333333333333333333334444444444444 PP

                   Tropomyosin 137 eaaeskiveLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRaeeAErsvqkLekevdrledeleaek 217
                                   ++ e++   Le++++   +  + Le   +k  +r+ + ee+ + Lee+  + e+R ++ E +  kLe+   rle+e +   
  gi|14601265|ref|NP_147800.1| 135 QSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLS 215
                                   444555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                   Tropomyosin 218 ekykaiseeL 227
                                   e+  ++++ L
  gi|14601265|ref|NP_147800.1| 216 ERVLRVEQAL 225
                                   5555554444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.0    0.0023       0.9       5      99 ..      51     144 ..      49     145 .. 0.93
   2 ?   12.2   7.6   0.00019     0.076       4      90 ..     141     226 ..     138     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0023
                         TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                   +el ++f++lee++ +++++  +l++ q k+ ++ +  +kr ++l+++  +l+++  ++ +e++++l+++  + ++ ++++
  gi|14601265|ref|NP_147800.1|  51 KELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRF-QKLDERFQRLEQRQLRLEERFQRL 130
                                   789999**********************************************9997.5888999***************** PP

                         TMPIT  86 esllpkknglylkl 99 
                                   e+ + + + +yl+l
  gi|14601265|ref|NP_147800.1| 131 EQRFQSLEERYLRL 144
                                   ***99999999986 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                         TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                     +le++f++lee+++ ++++ ++l++ q ++ ++ ++ ++r  +l+++++kl+++ + + e+++++l+ee+++ ++ + +
  gi|14601265|ref|NP_147800.1| 141 YLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEER-HLKLEQRFQRLEEEFRRLSERVLR 220
                                   56899*************************************************99.578899999*****9999999999 PP

                         TMPIT  85 vesllp 90 
                                   ve+ l 
  gi|14601265|ref|NP_147800.1| 221 VEQALV 226
                                   999886 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 ?   11.4  17.6   0.00071      0.28      54     143 ..      22     116 ..      16     121 .. 0.92
   2 ?    5.8  30.3     0.038        15      42     141 ..     117     219 ..     106     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00071
                 Jnk-SapK_ap_N  54 elreeleqLeteyerekelrkrae.....eeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeael 129
                                   + ++e+e++   +er +e+r +       +el+e  +++ee++  l+e+++qlee++ +le +++ ++++ +rlee++  l
  gi|14601265|ref|NP_147800.1|  22 LSKREIEKILRTLERDREFRYALMgllgfKELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRL 102
                                   568999999999*****999999999******************************************************* PP

                 Jnk-SapK_ap_N 130 kkeysklheretel 143
                                   +++ +kl er + l
  gi|14601265|ref|NP_147800.1| 103 ERRFQKLDERFQRL 116
                                   *******9976554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.038
                 Jnk-SapK_ap_N  42 asrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqw...eeerkelqekveqleeenrelelkaknaadql 119
                                    +r+ + e++ ++l++ +++Le++y r  +  +r ee++ ++e+ +   e+++  l+e++++lee++ +le+++++++++ 
  gi|14601265|ref|NP_147800.1| 117 EQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFqklEQRQLHLEERFQRLEERQLKLEQRFQKLEERH 197
                                   233334444555666666666666666666666666555555544311144555566666666666666666666666666 PP

                 Jnk-SapK_ap_N 120 srleekeaelkkeysklheret 141
                                    +le++ + l++e  +l+er  
  gi|14601265|ref|NP_147800.1| 198 LKLEQRFQRLEEEFRRLSERVL 219
                                   6666666666666666666444 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  24.6     0.092        37      12      95 ..      55     138 ..      49     140 .. 0.43
   2 ?   15.2  33.7   3.5e-05     0.014       3     115 ..     116     228 ..     114     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.092
                           ERM  12 erLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaa 92 
                                   er ++l+e   + +e  ++ ee+  +L+e+ + +e+  ++Le+++ ++e+  q+l e+ ++ e+ + +le++ ++ e++++
  gi|14601265|ref|NP_147800.1|  55 ERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQ 135
                                   444444444444444444444444444444444444444444444444444444444444444444444444444444444 PP

                           ERM  93 rle 95 
                                    le
  gi|14601265|ref|NP_147800.1| 136 SLE 138
                                   444 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.5e-05
                           ERM   3 aerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerk 83 
                                    e+++ +leer ++l++ ++  +e   + e++ ++L+e+ r +ee  ++Leq++ ++ee  qrl+e++ k e+  +kle++
  gi|14601265|ref|NP_147800.1| 116 LEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEER 196
                                   577888888888888888888888888888888888888888888888888888888888888888877777777777777 PP

                           ERM  84 lreaeleaarleeeserkeeeaerLkeeleea 115
                                     + e++++rleee +r  e + r ++ l ++
  gi|14601265|ref|NP_147800.1| 197 HLKLEQRFQRLEEEFRRLSERVLRVEQALVNM 228
                                   77777777777777777666666665555443 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  20.1     0.001      0.41      29     132 ..      48     150 ..      41     156 .. 0.73
   2 ?    4.8  17.7      0.07        28      31     102 ..     148     218 ..     146     261 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                                   ECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSH CS
                         Nup54  29 kGFedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeE 109
                                    GF++L +R ++ ++   +++er +++++r  +le ++ + + +r +++  rh  l++R+ +l  + + l++r+  l++  
  gi|14601265|ref|NP_147800.1|  48 LGFKELLERFEKLEERQLRLEERFSQLEERQIKLE-ERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERF 127
                                   69999999999999999999999999999999999.666667777777777777777777777777777777777777777 PP

                                   HHHHHHHHHHHHHHS-HHH.HHH CS
                         Nup54 110 eelrarletleaqlndpaqlkgr 132
                                   ++l++r+++le++  + +q  +r
  gi|14601265|ref|NP_147800.1| 128 QRLEQRFQSLEERYLRLEQRFQR 150
                                   77777777777765543332333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.07
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S CS
                         Nup54  31 FedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrg 102
                                   F+ L++R ++ ++  +++++r   +++r + le ++ql++ +r +k+  rh +l++R+ rl      l+ r 
  gi|14601265|ref|NP_147800.1| 148 FQRLEERFRLLEERFQKLEQRQLHLEERFQRLE-ERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERV 218
                                   666666666666666666666666777777776.66777777777777777777776666655444443333 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  15.8      0.17        66      57     122 ..      52     117 ..      26     128 .. 0.60
   2 ?    7.7  16.2    0.0088       3.5      43     122 ..      86     166 ..      85     173 .. 0.82
   3 ?    6.7  15.6     0.018       7.2      56     119 ..     128     191 ..     116     192 .. 0.75
   4 ?   13.2  12.3   0.00018     0.073      58     127 ..     158     227 ..     156     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                          ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                   +l e+ +kle    rl+ ++++l+++  +le + +l++++ + le +  +le+  +++ e +qrl+
  gi|14601265|ref|NP_147800.1|  52 ELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLE 117
                                   455566666666666666666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0088
                          ADIP  43 sLlqardrdleqres.lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                   +Ll +r + le+r + l+++ +kl+   +rl+++  rl+++ ++le++ ++++++   le++ ++le+  + + e +q+l+
  gi|14601265|ref|NP_147800.1|  86 QLLEKRFQRLEERHLrLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLE 166
                                   567777666666664267788999999999999999999999999999999999999999999999999999999999987 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.018
                          ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelq 119
                                   + l+++ ++le  + rl+++++rl+++   le + + +++++ +le + ++le+   ++ + +q
  gi|14601265|ref|NP_147800.1| 128 QRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQ 191
                                   6788888999999999999999999999999999999999999998888888776666666665 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00018
                          ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqq 127
                                   l+e+ +kle    +l+ +++rl+++  +le++ + +++++ +le++ ++le+  ++++e + r ++al +
  gi|14601265|ref|NP_147800.1| 158 LEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVN 227
                                   899************************************************************9998876 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8  12.8      0.24        94      36      95 ..      69     133 ..      47     140 .. 0.37
   2 ?   11.7  11.9   0.00084      0.33      22      97 ..      90     163 ..      82     166 .. 0.85
   3 ?    9.7  17.3    0.0034       1.4       7      96 ..     124     218 ..     119     223 .. 0.74
   4 ?    4.2   0.1      0.18        73      16      50 ..     203     237 ..     201     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.24
                  Occludin_ELL  36 kkfseLerelkelkegsk....eykkieee...ilqeykklkkdpeyqekkkrceyLkekLshiKkl 95 
                                   ++fs+Le++  +l+e+ +    +++++ee+   + ++++kl  d+++q+ ++r   L+e+ + + ++
  gi|14601265|ref|NP_147800.1|  69 ERFSQLEERQIKLEERFQllekRFQRLEERhlrLERRFQKL--DERFQRLEQRQLRLEERFQRLEQR 133
                                   33333333333333332222222222222200022222222..444444444444444444444443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00084
                  Occludin_ELL  22 keYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKklik 97 
                                   k++++l+++   ++++f++L+++ ++l++++ + +++ +++ q++++l  +++y++ ++r++ L+e+ + + ++ +
  gi|14601265|ref|NP_147800.1|  90 KRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSL--EERYLRLEQRFQRLEERFRLLEERFQ 163
                                   678899999999999999999999999999999999999999999999..88999999999999999888877655 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0034
                  Occludin_ELL   7 aeqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkkrc 82 
                                   +e  +r ++ F++  ++Y +l+++++ ++++f+ Le++ ++l++++     +++++ee+ l+  ++++k ++++++ ++r+
  gi|14601265|ref|NP_147800.1| 124 EERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLhleeRFQRLEERQLKLEQRFQKlEERHLKLEQRF 204
                                   56678889999999999****************999999999999885555555555552222233333578888888888 PP

                  Occludin_ELL  83 eyLkekLshiKkli 96 
                                   + L+e+ + + +++
  gi|14601265|ref|NP_147800.1| 205 QRLEEEFRRLSERV 218
                                   88888888877777 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.18
                  Occludin_ELL  16 eFnkeYkeYkelhaeleevskkfseLerelkelke 50 
                                    F++  +e+++l +++  v++ + ++ r++++ ++
  gi|14601265|ref|NP_147800.1| 203 RFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIAH 237
                                   45555556666666666666666666666655544 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 ?    4.6   3.9      0.07        28      40      76 ..      50      86 ..      18      98 .. 0.76
   2 ?   -0.0  10.6       1.8   7.3e+02      22      73 ..      64     118 ..      58     132 .. 0.60
   3 ?    6.1  10.1     0.024       9.4      16      77 ..     114     178 ..     101     179 .. 0.78
   4 ?   10.5   7.3   0.00096      0.38      24      95 ..     171     241 ..     169     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.07
                          SKA2 40 pvkLlerlkkvkeelqaLkeqceellaekkelidkir 76
                                    +Ller++k+ e+   L+e++ +l +++ +l ++++
  gi|14601265|ref|NP_147800.1| 50 FKELLERFEKLEERQLRLEERFSQLEERQIKLEERFQ 86
                                  568999*****************99999988887765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.8
                          SKA2  22 qhrLekefqqsypdna..eNpvkLl.erlkkvkeelqaLkeqceellaekkelid 73 
                                   q rLe++f+q  +++   e+  +Ll +r++++ e++  L++++++l ++ ++l +
  gi|14601265|ref|NP_147800.1|  64 QLRLEERFSQLEERQIklEERFQLLeKRFQRLEERHLRLERRFQKLDERFQRLEQ 118
                                   6788888888888776674444444245666666666666666666555554443 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.024
                          SKA2  16 sdLdyvqhrLekefqqsypdna...eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirt 77 
                                   + L+  q rLe++fq+  ++ +   e  ++L +r++++ e++  L+e++++l +++  l +++++
  gi|14601265|ref|NP_147800.1| 114 QRLEQRQLRLEERFQRLEQRFQsleERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQR 178
                                   34666778899999988887777888899**************************9999888765 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00096
                          SKA2  24 rLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidki...rttlvanrellqqLqasael 95 
                                    Le++fq+  +++    +kL +r++k+ e++ +L+++++ l +e ++l +++   ++ lv+++ ++  + ++ ++
  gi|14601265|ref|NP_147800.1| 171 HLEERFQRLEERQ----LKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVlrvEQALVNMMRMMNTIAHRFGI 241
                                   6888888877776....7**************************9988776511167899999999988888766 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  49.4   0.00066      0.26       5     168 ..      62     225 ..      58     232 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00066
                 Myosin_tail_1   5 eelqakeeeLkkvkekqqkaekelkelekkqqqlleeklaLqeqLqaetelfaeaeemRaRLaarkqeleeilhdleaRle 85 
                                   e     ee  ++ +e+q k+e++++ lek+ q+l e +l L+ + q   e f+  e+ + RL+ r q le+ ++ le R  
  gi|14601265|ref|NP_147800.1|  62 ERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYL 142
                                   444556788999********************************************************************* PP

                 Myosin_tail_1  86 eeeeraqqlqsekkkmqqniqdleeqldeeeaaRqkLqlekvtleaklkkleedilvledqnnklskekklleeRiaelts 166
                                     e+r q+l++  + ++++ q+le++  + e+  q+L   +  le + +klee  l le++ ++l+ e + l eR+  +++
  gi|14601265|ref|NP_147800.1| 143 RLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQ 223
                                   **********99999*********9766677788*****************************************998887 PP

                 Myosin_tail_1 167 nl 168
                                    l
  gi|14601265|ref|NP_147800.1| 224 AL 225
                                   66 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.3      0.11        44     108     152 ..      50      90 ..      17      96 .. 0.70
   2 ?    2.1  13.7      0.39   1.5e+02      78     154 .]      62     134 ..      56     155 .. 0.66
   3 ?    3.4  10.3      0.16        63      96     151 ..     122     180 ..     114     194 .. 0.59
   4 ?    5.3   7.4     0.039        16      95     147 ..     177     229 ..     163     245 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXXXXX CS
                       DUF1465 108 lqeLierserLyervrrLdrelreeaeaaeaaenpvaeqlerLea 152
                                   ++eL+er e+L er  rL++++++ +e++     +++e++++Le+
  gi|14601265|ref|NP_147800.1|  50 FKELLERFEKLEERQLRLEERFSQLEERQI----KLEERFQLLEK 90 
                                   677777777777777777777777666552....34444444444 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.39
                                   TTTTSSSS-------..-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXXXXXXX CS
                       DUF1465  78 eeqaasekkrvklaaaeasdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeqlerLeaaf 154
                                   e q++ e++  +l++ + + +e ++ L++++q L er  rL +r ++Ld+++++ ++++      ++e+++rLe+ f
  gi|14601265|ref|NP_147800.1|  62 ERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQL----RLEERFQRLEQRF 134
                                   555555555555665556667777777777777777777777777777777776666553....4555555555544 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.16
                                   ----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX....XXXXXXXXXXXX CS
                       DUF1465  96 sdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaa...enpvaeqlerLe 151
                                   + +e +++L++++q+L er  rL +r +rL++++r  +e+ ++    + +++e+++rLe
  gi|14601265|ref|NP_147800.1| 122 RLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLeqrQLHLEERFQRLE 180
                                   44556666666666666666666666666666655443333222223556666666665 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.039
                                   -----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXX CS
                       DUF1465  95 asdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeql 147
                                   ++ +e   +L++++q+L er  +L +r +rL++e+r+ +e+  + e+++ + +
  gi|14601265|ref|NP_147800.1| 177 QRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVNMM 229
                                   44444444555555555555556666666665555555555444444444444 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  10.1   0.00042      0.17     102     184 ..      55     137 ..      38     141 .. 0.92
   2 ?    5.2  11.6     0.042        17      69     150 ..     147     229 ..     139     256 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00042
                        DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFe 182
                                   ++ +kl+e++ +le+++++ e+++ klee ++ lek+ ++le++  +l ++ ++ d++  rl++ + +lee+ ++ eq+F+
  gi|14601265|ref|NP_147800.1|  55 ERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQ 135
                                   6778999999***********************************9999******************************** PP

                        DUF724 183 av 184
                                   ++
  gi|14601265|ref|NP_147800.1| 136 SL 137
                                   97 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                        DUF724  69 eleslkeslaeLekhGFdVkalqsrl.nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlal 148
                                    +++l e +  Le+     ++ q +l ++   l ++q kl+++ +kle++  + e++ ++leee++ l++++l++e+ l+ 
  gi|14601265|ref|NP_147800.1| 147 RFQRLEERFRLLEERFQKLEQRQLHLeERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVN 227
                                   455555555555555555555555553334456666666666666666666666666666666666666666666666554 PP

                        DUF724 149 lk 150
                                   + 
  gi|14601265|ref|NP_147800.1| 228 MM 229
                                   44 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  16.1     0.098        39      71     132 ..      51     112 ..      24     114 .. 0.89
   2 ?    4.9  18.0     0.039        15      89     142 ..      97     150 ..      92     168 .. 0.40
   3 ?    9.7  19.4    0.0013      0.51      78     174 ..     146     246 ..     142     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.098
                       DUF3552  71 kelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleel 132
                                   kel er ++l++ + Rl+++  +L++++ +le++ + le++ ++l++++ +le++ ++l+e 
  gi|14601265|ref|NP_147800.1|  51 KELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDER 112
                                   68888999999999999999999999999999999999999999999999999999988875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                       DUF3552  89 qkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLer 142
                                   ++  +L+r+ ++l+++ ++le+++ +l+++ q+le++ ++lee + + +q+++r
  gi|14601265|ref|NP_147800.1|  97 ERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQR 150
                                   444444444444444444444444444444444444444444433222222222 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0013
                       DUF3552  78 nelqrlekR...llqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLerisg..LtkeeAke 153
                                   + +qrle+R   l+++ ++L++++ +le++ ++lee++ +l+q+ q+lee++ +le+  ++ ++e+ r+s+  L  e+A  
  gi|14601265|ref|NP_147800.1| 146 QRFQRLEERfrlLEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSErvLRVEQALV 226
                                   567888888555678888999999999999999999999999999999999999999999999999999977789999977 PP

                       DUF3552 154 illeeveeelkheaAkmikei 174
                                    +++ + + + h  +++  e 
  gi|14601265|ref|NP_147800.1| 227 NMMRMM-NTIAHRFGILTEEA 246
                                   766544.45666666665555 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   6.5       1.6   6.3e+02       7      42 ..      73     108 ..      50     118 .. 0.39
   2 ?    4.8  11.6     0.075        30       7      80 ..     101     174 ..      88     184 .. 0.86
   3 ?    4.5  11.2      0.09        36       8      67 ..     158     217 ..     144     235 .. 0.55
   4 ?   11.8   2.0   0.00048      0.19       7      59 ..     185     237 ..     184     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.6
                          BRE1   7 klekafeelseqlskkvkeltileekklrleaekak 42 
                                   +le+   +l+e  + + k +++lee+ lrle   +k
  gi|14601265|ref|NP_147800.1|  73 QLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQK 108
                                   233333333333333333333333333333333333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.075
                          BRE1   7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLke 80 
                                   +le+ f++l+e  + + +   +lee+ +rle+  +  ++ y  ++   + le   + L +  +K  + +  L+e
  gi|14601265|ref|NP_147800.1| 101 RLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEE 174
                                   68999999999999999999999999999999999999999999999999999999999999998888888877 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.09
                          BRE1   8 lekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkl 67 
                                   le+ f++l++    + + +++lee++l+le+  +k ++    ++   + le e ++L++ 
  gi|14601265|ref|NP_147800.1| 158 LEERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSER 217
                                   455555555555555555555555555555555555555555555555555555555443 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00048
                          BRE1   7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalen 59 
                                   kle+ f++l+e   k+ + +++lee+  rl+    + +q   + mr ++++  
  gi|14601265|ref|NP_147800.1| 185 KLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIAH 237
                                   79*********************************************999875 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  20.7     0.055        22      22     102 ..      58     134 ..      50     141 .. 0.91
   2 ?    1.2   9.8       1.1   4.2e+02      22      66 ..     114     154 ..     107     164 .. 0.62
   3 ?    9.6  17.2    0.0026       1.1      22      92 ..     149     222 ..     142     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.055
                                   XXXXXXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Troponin  22 kkeeerlrvLkerieplkeldglseeqlqelckklheridkleeekydieekvakkdkeieelkkkvndlrGkfkkpalKk 102
                                   +k eer+  L+er  +l+ +++    +l+e+ + l +r ++lee + ++e+  +k d+  + l+++ + l  +f++ +++ 
  gi|14601265|ref|NP_147800.1|  58 EKLEERQLRLEERFSQLE-ERQ---IKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRF 134
                                   7889**************.999...9*********************************************99*9998885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                                   XXXXXXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXX CS
                      Troponin  22 kkeeerlrvLkerieplkeldglseeqlqelckklheridkleee 66 
                                   ++ e+r+  L+er ++l+  +    + l+e++ +l +r ++lee 
  gi|14601265|ref|NP_147800.1| 114 QRLEQRQLRLEERFQRLE-QRF---QSLEERYLRLEQRFQRLEER 154
                                   444666666777777776.555...67777777777777777653 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0026
                                   XXXXXXXXXXXXXXXXXX.XXX.XX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Troponin  22 kkeeerlrvLkerieplkeldglse....eqlqelckklheridkleeekydieekvakkdkeieelkkkvndlr 92 
                                   ++ eer r L+er ++l+  ++l      + l+e++ kl +r +klee + ++e+  ++ ++e + l+ +v+ + 
  gi|14601265|ref|NP_147800.1| 149 QRLEERFRLLEERFQKLE-QRQLHLeerfQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVE 222
                                   667999999999999999.888777788999********************************999999998775 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.5     0.018         7      62     124 .]      58     120 ..      49     120 .. 0.78
   2 ?    8.6   6.6    0.0045       1.8      48     124 .]     107     183 ..      72     183 .. 0.72
   3 ?    6.0   0.3     0.028        11      49      94 ..     199     244 ..     191     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                       DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                   ++L++r  r++++  + +e + +++e  + +++  ++++e    +++ +++l+++ +r+e++Q
  gi|14601265|ref|NP_147800.1|  58 EKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQ 120
                                   567777777888888888888888888888888888888888888888999999999988887 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0045
                       DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                   ++l++  + l++ + +L++r +r++++ ++ +e    +++  ++++e  + ++e ++++++   +le++ +r+ee+Q
  gi|14601265|ref|NP_147800.1| 107 QKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQ 183
                                   45666666677777777777777777777777777777777777777777777777777777777777777777766 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.028
                       DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevre 94 
                                   +leq  + l++  r+Ls+r+ rv++ l +++++ + i++    + e
  gi|14601265|ref|NP_147800.1| 199 KLEQRFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIAHRFGILTE 244
                                   6888899999999999999999999999999999999877666555 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3      0.29   1.2e+02       2      31 ..      54      83 ..      53      87 .. 0.80
   2 ?    2.5   0.1      0.32   1.3e+02       8      31 ..      81     104 ..      77     108 .. 0.82
   3 ?    3.1   0.1      0.21        83       1      30 [.      88     117 ..      88     120 .. 0.76
   4 ?    3.7   0.2      0.14        55       3      24 ..     111     132 ..     101     141 .. 0.47
   5 ?    4.4   0.1     0.082        33       2      30 ..     124     152 ..     123     156 .. 0.67
   6 ?    5.6   0.2     0.035        14       1      30 [.     144     173 ..     144     175 .. 0.88
   7 ?    6.7   0.6     0.015       6.2       1      32 [.     172     204 ..     172     206 .. 0.91
   8 ?    2.7   0.2      0.27   1.1e+02       1      28 [.     207     234 ..     200     240 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.29
                     DASH_Dam1  2 epafaeLaDsletLdknledLqqihesLsd 31
                                   ++f++L++    L++++++L++ + +L++
  gi|14601265|ref|NP_147800.1| 54 LERFEKLEERQLRLEERFSQLEERQIKLEE 83
                                  678999999999999999999987777765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.32
                     DASH_Dam1   8 LaDsletLdknledLqqihesLsd 31 
                                   L++  + L+k++++L++ h +L++
  gi|14601265|ref|NP_147800.1|  81 LEERFQLLEKRFQRLEERHLRLER 104
                                   778888999999999999988887 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                     DASH_Dam1   1 lepafaeLaDsletLdknledLqqihesLs 30 
                                   le++f++L++    L++++++L++  ++L+
  gi|14601265|ref|NP_147800.1|  88 LEKRFQRLEERHLRLERRFQKLDERFQRLE 117
                                   577888888888888888888887666665 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.14
                     DASH_Dam1   3 pafaeLaDsletLdknledLqq 24 
                                   ++f++L+     L++++++L+q
  gi|14601265|ref|NP_147800.1| 111 ERFQRLEQRQLRLEERFQRLEQ 132
                                   3344444444444444444444 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.082
                     DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLs 30 
                                   e++f++L+   + L++++ +L+q  ++L+
  gi|14601265|ref|NP_147800.1| 124 EERFQRLEQRFQSLEERYLRLEQRFQRLE 152
                                   66777777777777777777777666665 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.035
                     DASH_Dam1   1 lepafaeLaDsletLdknledLqqihesLs 30 
                                   le++f++L++  + L++++++L+q + +L+
  gi|14601265|ref|NP_147800.1| 144 LEQRFQRLEERFRLLEERFQKLEQRQLHLE 173
                                   6789******************99877765 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.015
                     DASH_Dam1   1 lepafaeLaDsletLdknledLqqihesLsd.f 32 
                                   le++f++L++   +L++++++L++ h +L++ f
  gi|14601265|ref|NP_147800.1| 172 LEERFQRLEERQLKLEQRFQKLEERHLKLEQrF 204
                                   6899**********************9999855 PP

  == domain 8  score: 2.7 bits;  conditional E-value: 0.27
                     DASH_Dam1   1 lepafaeLaDsletLdknledLqqihes 28 
                                   le++f++L++ +  +++ l ++ ++ ++
  gi|14601265|ref|NP_147800.1| 207 LEEEFRRLSERVLRVEQALVNMMRMMNT 234
                                   4555666666666666655555555555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  12.3      0.43   1.7e+02       3      54 ..      55     106 ..      53     115 .. 0.86
   2 ?    8.7  12.7    0.0065       2.6       1      54 [.     116     169 ..     116     171 .. 0.95
   3 ?    9.5  11.6    0.0036       1.4       1      53 [.     172     224 ..     172     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.43
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                          SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                   er+e+LE++   +e+   +L +  ++ +++ + l++++++l+er   le + 
  gi|14601265|ref|NP_147800.1|  55 ERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRF 106
                                   8999999999999999999999999999999999999999999988777664 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0065
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                          SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                   le+r  +LE++   +e+  ++L +   + +q+ +rl++++rll+er+++le+++
  gi|14601265|ref|NP_147800.1| 116 LEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQ 169
                                   5889999*******************************************9875 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0036
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                          SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                   leer+++LE++   +e+  ++L +   + +q+ +rl++++r+l er+  +e++
  gi|14601265|ref|NP_147800.1| 172 LEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQA 224
                                   69*********************************************888776 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   9.5     0.074        29      15      72 ..      51     108 ..      50     110 .. 0.94
   2 ?    9.1   5.2    0.0031       1.2      20      74 .]     112     166 ..     107     166 .. 0.90
   3 ?    5.3   8.5     0.047        19      22      72 ..     163     213 ..     163     222 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.074
                    TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                   ++L+e  ekL+  +l+l++  ++L +   +le+  + l+k+ ++le+   +le+r+++
  gi|14601265|ref|NP_147800.1|  51 KELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQK 108
                                   5899999**********************************************99876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0031
                    TMF_DNA_bd  20 EGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkeae 74 
                                     ++L+  +l+l++   +L +  + le+   +l+++ ++le+ +  leer+++ e
  gi|14601265|ref|NP_147800.1| 112 RFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLE 166
                                   56899********************************************998765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.047
                    TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                   +kL+  +l+l++   +L +   +le+  ++l+++  kle+ +++lee++++
  gi|14601265|ref|NP_147800.1| 163 QKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRR 213
                                   566666666666666666666666666666666666666666666666554 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 ?    8.8  16.8    0.0028       1.1     151     251 ..      52     153 ..       2     159 .. 0.48
   2 ?    7.8  18.5    0.0054       2.1     147     240 ..     125     219 ..     121     257 .. 0.39

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                  Exonuc_VII_L 151 elerrlekaikrlleekkqrleklasrl...kspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleek 228
                                   el +r+ek  +r+l+  ++r+++l++r    ++  +lle++ qrl+e + rler   ++l+++ +rle+ + rl+e++++ 
  gi|14601265|ref|NP_147800.1|  52 ELLERFEKLEERQLR-LEERFSQLEERQiklEERFQLLEKRFQRLEERHLRLER-RFQKLDERFQRLEQRQLRLEERFQRL 130
                                   222233333333333.22334444333211144445666666666666666666.55566666666666666665666666 PP

                  Exonuc_VII_L 229 kerlkklkerlelleekkerlee 251
                                   ++r+++l+er  +le++ +rlee
  gi|14601265|ref|NP_147800.1| 131 EQRFQSLEERYLRLEQRFQRLEE 153
                                   66666665555545544444443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0054
                  Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq..lkkkrerleelkerlkekl 225
                                   e++++le+r+++  +r+l+  +qr+++l++r++  ee++++ +qr  +leer++r  ++q  l+++ ++lee + +l++++
  gi|14601265|ref|NP_147800.1| 125 ERFQRLEQRFQSLEERYLR-LEQRFQRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQlkLEQRFQKLEERHLKLEQRF 204
                                   3344444444333333332.3334444444443333333333333333333333311111112222222222222222333 PP

                  Exonuc_VII_L 226 eekkerlkklkerle 240
                                   ++ +e++++l+er+ 
  gi|14601265|ref|NP_147800.1| 205 QRLEEEFRRLSERVL 219
                                   333333333333322 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 ?    2.9  15.5      0.34   1.3e+02      10      68 ..      50     103 ..      18     104 .. 0.87
   2 ?   12.2   9.7   0.00042      0.17       7      69 .]     103     160 ..     101     160 .. 0.94
   3 ?    4.9  13.5     0.079        31      14      69 .]     159     209 ..     155     229 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.34
                  ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLe 68 
                                   ++el ++ e+LEe++  le+++++ e     e+  +l ++ + le+  ++l+er + Le
  gi|14601265|ref|NP_147800.1|  50 FKELLERFEKLEERQLRLEERFSQLE-----ERQIKLEERFQLLEKRFQRLEERHLRLE 103
                                   458999*****************998.....999999999*************999997 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00042
                  ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLee 69 
                                   +r++++l+++ ++LE+++  le++++  e     ++++ l +++ +le+  ++l+er+  Lee
  gi|14601265|ref|NP_147800.1| 103 ERRFQKLDERFQRLEQRQLRLEERFQRLE-----QRFQSLEERYLRLEQRFQRLEERFRLLEE 160
                                   799***********************988.....99*********************999986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.079
                  ABC_tran_CTD  14 eaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWeeLee 69 
                                   e++ ++LE+++  le++++  e     e+  +l ++ ++le+   +l++r+  Lee
  gi|14601265|ref|NP_147800.1| 159 EERFQKLEQRQLHLEERFQRLE-----ERQLKLEQRFQKLEERHLKLEQRFQRLEE 209
                                   5555556666666655555444.....33334444444444444444444333333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5  17.9      0.24        94       9     148 ..      50     189 ..      30     195 .. 0.78
   2 ?    4.6  15.9     0.052        21      12     121 ..     123     234 ..      97     260 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.24
                       DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDea 89 
                                   +k+l e +ekl+e++ +lee+ ++le+r+ ++e+ ++ l+k  ++le++    e   ++l+e   ++ L++ +    ++e+
  gi|14601265|ref|NP_147800.1|  50 FKELLERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDER--FQRLEQRQ--LRLEER 126
                                   4667789999999999********************************998877777777776..77777777..7799** PP

                       DUF4795  90 kkeLekmleellekleeqeealkkaldtLq..eelkekld..rlelepLkeqleerlkelqke 148
                                   +++Le+ +++l e+    e++ +++ +  +  ee ++kl+  +l le+  ++leer  +l+++
  gi|14601265|ref|NP_147800.1| 127 FQRLEQRFQSLEERYLRLEQRFQRLEERFRllEERFQKLEqrQLHLEERFQRLEERQLKLEQR 189
                                   ********9999999999999999999988767777777755444444444444444444444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.052
                       DUF4795  12 lqeaieklqeelekleekvkelekrledkekklealkkqieelekvk...adkeeveeelaekadkeaLatkvsrdqfDea 89 
                                   l+e ++ l+++ ++lee+  +le+r +++e+ +  l++  ++le++    +++++  ee ++k   +  +    + +++++
  gi|14601265|ref|NP_147800.1| 123 LEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQlhlEERFQRLEERQLKLEQRFQKLEERHLKLEQR 203
                                   34666777777777777777777777777777777777777777777655555555444444443332222222355**** PP

                       DUF4795  90 kkeLekmleellekleeqeealkkaldtLqee 121
                                   +++Le+ ++ l e++  +e+al  ++  ++  
  gi|14601265|ref|NP_147800.1| 204 FQRLEEEFRRLSERVLRVEQALVNMMRMMN-T 234
                                   **************9999999988887766.3 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  22.8     0.014       5.6      89     208 ..      51     166 ..      45     169 .. 0.87
   2 ?    5.8  17.5     0.022       8.8      65     166 ..     130     235 ..     127     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                       Leu_zip  89 ReLlEkiaefEekefkssnkkeseelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqatsaleekskleka 169
                                   +eLlE+  ++Ee++++ +++ ++ e+++ kLe   e   ++LL+k  +rL+e   +L+ r+++l+++ +++ + + +le+ 
  gi|14601265|ref|NP_147800.1|  51 KELLERFEKLEERQLRLEERFSQLEERQIKLE---E--RFQLLEKRFQRLEERHLRLERRFQKLDERFQRLEQRQLRLEER 126
                                   79***************988888888888875...5..699**************************************** PP

                       Leu_zip 170 lkelqkelgekkdeke.nskeiskleeklaelkldlektl 208
                                    ++l+++ ++ +++    ++++++lee++  l+  ++k  
  gi|14601265|ref|NP_147800.1| 127 FQRLEQRFQSLEERYLrLEQRFQRLEERFRLLEERFQKLE 166
                                   ***9998887765544378999999999999999888765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                       Leu_zip  65 lrqlfsqAEkwhLklqaDiselenRe.Ll.EkiaefEekefkssnkkeseelkkkkLePlneg.G.gaeLLkkeierLkee 141
                                   l+q f+  E  +L+l+     le R  Ll E+ +++E+++++ +++ +  e+++ kLe   +        L++  +rL+ee
  gi|14601265|ref|NP_147800.1| 130 LEQRFQSLEERYLRLEQRFQRLEERFrLLeERFQKLEQRQLHLEERFQRLEERQLKLEQRFQKlEeRHLKLEQRFQRLEEE 210
                                   7899********************96677256999********99988888888887654444120344478889****** PP

                       Leu_zip 142 nekLkerlkelEkqatsaleekskl 166
                                    ++L+er+ ++E+ + ++++  + +
  gi|14601265|ref|NP_147800.1| 211 FRRLSERVLRVEQALVNMMRMMNTI 235
                                   ************9998887765555 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 ?    0.3  17.9       1.1   4.4e+02     143     248 ..      59     170 ..       9     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                     Phage_GPO 143 plakrkqspenlftaavetalefeeeeeeeegeslferikal...lskkkksddarfadveeavelvAeevkelsekveal 220
                                    l++r+ + e+ f++ +e ++++ee+ +  e  + f+r+++    l+++ ++ d+rf+ +e+   ++ e++++l++++++l
  gi|14601265|ref|NP_147800.1|  59 KLEERQLRLEERFSQLEERQIKLEERFQLLE--KRFQRLEERhlrLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSL 137
                                   5677777778888888888888888776655..333333332222555556668888888888888888888888888855 PP

                     Phage_GPO 221 l....aleaelaalkkeveklkaeleaLkek.L 248
                                   +    +le++++ l+++++ l++++++L+++ L
  gi|14601265|ref|NP_147800.1| 138 EerylRLEQRFQRLEERFRLLEERFQKLEQRqL 170
                                   545555555555555555555555555555432 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  12.0      0.05        20      28     130 ..      55     160 ..      49     164 .. 0.76
   2 ?    4.7   4.7     0.078        31      80     128 ..     166     214 ..     159     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.05
                                   CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHCCCHHHHHHHCCHHHHH CS
                     Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikkss...keleeeilrlketidaqesnir 105
                                   +  ++++++  +le++++++++++ + ee  + +++  ++ ++ +   ++ ++k+    ++le+++lrl+e+ ++ e++ +
  gi|14601265|ref|NP_147800.1|  55 ERFEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEERHLRLERRFQKLDerfQRLEQRQLRLEERFQRLEQRFQ 135
                                   4445555666678888888888888888888888887777666666666666666522267999***************** PP

                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 106 vLqnvlesneqkiqkLeqdidqker 130
                                    L + + ++eq+ q+Le+    +e+
  gi|14601265|ref|NP_147800.1| 136 SLEERYLRLEQRFQRLEERFRLLEE 160
                                   ****************998776665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.078
                                   HHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  80 kksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                   ++ + +lee+ +rl+e+  + e++ ++L + + ++eq+ q+Le++   +
  gi|14601265|ref|NP_147800.1| 166 EQRQLHLEERFQRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRL 214
                                   4556678888888888888888888888888888888888888776554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.5       1.5     6e+02      61      80 ..      78      97 ..      50     108 .. 0.57
   2 ?    9.7   1.8     0.002       0.8      18      91 ..     105     175 ..     100     183 .. 0.82
   3 ?    5.2   0.9     0.052        21      14      82 ..     178     246 ..     172     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                                  XXXX--TTTTTGGGHHHHHH CS
                    Laminin_II 61 vkkLeklapqLldklkelkq 80
                                    kLe+  + L++++++l++
  gi|14601265|ref|NP_147800.1| 78 QIKLEERFQLLEKRFQRLEE 97
                                  33455555555555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.002
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHH CS
                    Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdn 91 
                                     ++l+++ +++++   ++++  ++ ++  +++ +     ++  + Le+    L++++++l+q++ +   l + 
  gi|14601265|ref|NP_147800.1| 105 RFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRLEERFRLLEERFQKLEQRQLH---LEER 175
                                   5678888888999999999999999999999999999999999999999999999999999999988...5444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.052
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                    Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                     +e   +l+q+ ++++e   ++++  ++ +e+ + +++ +  ++++ +++ + ++ +  ++  l +  
  gi|14601265|ref|NP_147800.1| 178 RLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIAHRFGILTEEA 246
                                   556667778888888888888999999999999999999999999999999999999999987776655 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       0.8   3.2e+02       2      30 ..      68      96 ..      60     104 .. 0.74
   2 ?    3.3   1.0      0.14        57       5      29 ..     127     151 ..      81     181 .. 0.73
   3 ?    1.9   0.1      0.39   1.6e+02       1      31 [.     186     216 ..     179     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.8
                       DUF4988  2 eddvndlkdrvaaleeqvkelndniealk 30
                                  e++ ++l++r   lee+ + l++ ++ l+
  gi|14601265|ref|NP_147800.1| 68 EERFSQLEERQIKLEERFQLLEKRFQRLE 96
                                  56667777777777777777777776664 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                       DUF4988   5 vndlkdrvaaleeqvkelndnieal 29 
                                    + l++r ++lee++  l++ ++ l
  gi|14601265|ref|NP_147800.1| 127 FQRLEQRFQSLEERYLRLEQRFQRL 151
                                   4445555555555555544444444 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.39
                       DUF4988   1 leddvndlkdrvaaleeqvkelndniealkk 31 
                                   le++ ++l++r   le++ + l++++  l++
  gi|14601265|ref|NP_147800.1| 186 LEQRFQKLEERHLKLEQRFQRLEEEFRRLSE 216
                                   5677778888888888888888887777754 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   4.2      0.12        48     626     706 ..      60     139 ..      50     152 .. 0.79
   2 ?    8.2   3.5    0.0013      0.51     645     742 ..     163     258 ..     140     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                      Prominin 626 letlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraen 706
                                   le+ + +lee  ++l++++ +l+++++   + +++++ e++l+le+  +kl ++ ++l++++  l+e++++l ++ +++e+
  gi|14601265|ref|NP_147800.1|  60 LEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLE-ERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSLEE 139
                                   4455556777777777777888888888888888886.5678999999999999999999999999999999998888764 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                      Prominin 645 knlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraenflkkngseiinneskklld 725
                                   ++l+q+  +  + +++++ e+ l+le+  +kl+++  kl+++ + l+e++++l ++v r e+ l + + +++n+ ++++  
  gi|14601265|ref|NP_147800.1| 163 QKLEQRQLHLEERFQRLE-ERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVN-MMRMMNTIAHRFGI 241
                                   333333333333344443.456789999999999999999999999999999*****999999976.56789999999999 PP

                      Prominin 726 rileqfeeYidwvieev 742
                                     +e f++ +++v eev
  gi|14601265|ref|NP_147800.1| 242 LTEEAFRSAMKHVVEEV 258
                                   99999999999998887 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   7.9      0.13        52      64     100 ..      57      93 ..      22      98 .. 0.76
   2 ?    7.0   3.0     0.014       5.6      60     100 ..      95     135 ..      93     137 .. 0.85
   3 ?    1.9  10.3      0.54   2.2e+02      74     100 ..     123     149 ..     107     169 .. 0.47
   4 ?    3.1  11.8      0.22        88      65     101 ..     163     199 ..     149     206 .. 0.87
   5 ?    5.9   6.8     0.031        12      65     101 ..     177     213 ..     171     218 .. 0.86
   6 ?    4.4   3.4     0.086        34      65     101 ..     191     227 ..     185     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  64 keeLeerketlekeiktlekqleklekeleelkeelq 100
                                    e+Leer+ +le++ ++le+++ kle++++ l++  q
  gi|14601265|ref|NP_147800.1|  57 FEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQ 93 
                                   5789999999999999999999999999999998766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeelq 100
                                   +ee + +Le r  +l+++ ++le+++ +le++++ l++  q
  gi|14601265|ref|NP_147800.1|  95 LEERHLRLERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQ 135
                                   56667789999999999999****99999999999998776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.54
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2  74 lekeiktlekqleklekeleelkeelq 100
                                   le++ ++le++ ++le+++  l++  q
  gi|14601265|ref|NP_147800.1| 123 LEERFQRLEQRFQSLEERYLRLEQRFQ 149
                                   333333333333333333333333222 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   ++Le+r+  le++ ++le+++ kle+++++l+e + k
  gi|14601265|ref|NP_147800.1| 163 QKLEQRQLHLEERFQRLEERQLKLEQRFQKLEERHLK 199
                                   789****************************997754 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.031
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   ++Leer+ +le++ ++le++  kle++++ l+ee + 
  gi|14601265|ref|NP_147800.1| 177 QRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRR 213
                                   7899999999999999999999999999999999775 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.086
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelqk 101
                                   ++Leer+ +le++ ++le++ ++l +++  +++ l +
  gi|14601265|ref|NP_147800.1| 191 QKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVN 227
                                   5778888888888888888888888887777777655 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   7.6     0.034        14      25      61 ..      61      97 ..      50     100 .. 0.91
   2 ?    1.8  10.6      0.65   2.6e+02      22      59 ..     114     151 ..      91     156 .. 0.60
   3 ?   -0.1  10.7       2.6     1e+03      22      59 ..     149     186 ..     138     189 .. 0.73
   4 ?    8.9   7.3    0.0041       1.6      22      60 ..     177     215 ..     175     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.034
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 25 qaeieeLerrvkaLekeNksLkseleelkkevekLks 61
                                  ++++ +Le+r+++Le+   +L ++ + l+k  + L++
  gi|14601265|ref|NP_147800.1| 61 EERQLRLEERFSQLEERQIKLEERFQLLEKRFQRLEE 97
                                  78999*************************9998875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.65
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  22 qRKqaeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                   qR ++++ +Le+r++ Le+  +sL ++  +l+   + L
  gi|14601265|ref|NP_147800.1| 114 QRLEQRQLRLEERFQRLEQRFQSLEERYLRLEQRFQRL 151
                                   44455555555555555555555555555555555544 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  22 qRKqaeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                   qR +++   Le+r+++Le+    L ++ ++l++   kL
  gi|14601265|ref|NP_147800.1| 149 QRLEERFRLLEERFQKLEQRQLHLEERFQRLEERQLKL 186
                                   56667777788888888888888888888887776665 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0041
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1  22 qRKqaeieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                   qR ++++ +Le+r+++Le+   +L ++ ++l++e   L 
  gi|14601265|ref|NP_147800.1| 177 QRLEERQLKLEQRFQKLEERHLKLEQRFQRLEEEFRRLS 215
                                   78899****************************998775 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 ?    1.1   0.9       1.3   5.2e+02       2      40 ..      57      95 ..      56      98 .. 0.75
   2 ?    4.3   0.1      0.13        53       5      40 ..     102     137 ..      98     141 .. 0.89
   3 ?    4.5   0.8      0.11        45       5      19 ..     144     158 ..     122     188 .. 0.52
   4 ?    8.7   0.9    0.0058       2.3       2      48 ..     190     236 ..     185     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.3
                     FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelkenVkdl 40
                                   ++lE++  +l+ +++ +++ + +l++  + l++++++l
  gi|14601265|ref|NP_147800.1| 57 FEKLEERQLRLEERFSQLEERQIKLEERFQLLEKRFQRL 95
                                  567788888888888888888888888888888777765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.13
                     FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                   lE +++kl+ +++ +++ +  l++  ++l+++++ l
  gi|14601265|ref|NP_147800.1| 102 LERRFQKLDERFQRLEQRQLRLEERFQRLEQRFQSL 137
                                   899999999999999999999999999999998876 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.11
                     FlaC_arch   5 lEnklsklsteletv 19 
                                   lE+++++l+ ++  +
  gi|14601265|ref|NP_147800.1| 144 LEQRFQRLEERFRLL 158
                                   333333333333333 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0058
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdllsLYEvVs 48 
                                    ++lE++  kl+ +++ +++e+  ls+ v ++++   +++ +  +++
  gi|14601265|ref|NP_147800.1| 190 FQKLEERHLKLEQRFQRLEEEFRRLSERVLRVEQALVNMMRMMNTIA 236
                                   56788888889999999999999999999999999999998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1595  (0.088962); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                       198  (0.0110436); expected 17.9 (0.001)
Passed Fwd filter:                       118  (0.00658152); 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: 1.63u 0.39s 00:00:02.02 Elapsed: 00:00:00.55
# Mc/sec: 1939.65
//
Query:       gi|118431373|ref|NP_147802.2|  [L=389]
Description: cystathionine beta-synthase [Aeropyrum pernix K1]
Scores for complete 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-60  203.6   0.7    1.3e-59  202.0   0.7    1.6  1  PALP       Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
        0.3   10.7   0.9       0.46   10.1   0.0    1.7  3  SDH_alpha  Serine dehydratase alpha chain


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 !  202.0   0.7   1.5e-63   1.3e-59       3     292 ..      15     355 ..      13     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 1.5e-63
                                    GCSSS--EEEECCTC...CCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHH CS
                           PALP   3 lgigpTPlvrlprls...kelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaal 76 
                                    + +g+TPl+rl r++   +  gv+l+ KlE +np+gS+KdR   y+l++++     +++ +++e ++GN+g++lA+aa +
  gi|118431373|ref|NP_147802.2|  15 DLVGGTPLLRLGRVErffRLEGVELYGKLEMFNPGGSVKDRIGLYMLMDARSRglvEEGAVIIEPTAGNTGVGLALAAIH 94 
                                    6789**********9666666677*************************888889999********************** PP

                                    HT-EEEEEEETTS-HHHHHHHHHTT-EEEEE...............................CCHHHHHHHHHHHHHHH. CS
                           PALP  77 lGlkvtivvpadaspekvallrllGaevvev...............................ggdydeavaaaaelaae. 124
                                    +G++++ v+p+++s ek + lr++Ga v+++                               gg++   v+++++l +e 
  gi|118431373|ref|NP_147802.2|  95 YGFRLVAVMPSKMSVEKELILRAYGAYVIRTptavppesplsyyrvaeavrnllwmiggrpgGGEVRKVVEKVQTLVREe 174
                                    *******************************9999999999999999999999999999988777899999999888889 PP

                                    ...............STTCEE--TTTSHHHHHH.HHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEE CS
                           PALP 125 ...............gegaylvsqfdnptvieg.ygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvi 188
                                                   ++ ay+ +q++np++  +  +t+g Ei+ q+gg++d+v++++G+ g+i+G+a++lk ++p+vr++
  gi|118431373|ref|NP_147802.2| 175 rvedlrsileasvepTPYAYIPNQYSNPANPRAhEETTGREIWMQTGGRVDVVYAGMGTRGTITGVARYLKRAKPSVRIV 254
                                    99999999999***9***************************************************************** PP

                                    EEEECTT..CGGTTCCS..S.SS..B...SSS.CCSTCS.CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B CS
                           PALP 189 gvepegs..dalarslragrrvtvpvs..dtiadglavg.spselafelldrlvdeivtvsdeealeamrllarregivv 263
                                    gv+pegs  + + +++   ++++  ++  +  ++g++ +  ps+ +++l+    de+v v+d++a++++r lar eg+++
  gi|118431373|ref|NP_147802.2| 255 GVDPEGSiySLVKKGM---SPHEAAKHarPYKVEGIGEDfIPSTIDLSLV----DEVVVVTDQQAFSMARMLARLEGVLA 327
                                    *****54224555555...33333333679*********99999999877....66777********************* PP

                                    -HHHHHHHHHH.HHHHHHCCTTCEEEEEEE CS
                           PALP 264 epssaaalaal.klreagelkegdrvvvil 292
                                    + ss+aal a+ k  + +++++    vvil
  gi|118431373|ref|NP_147802.2| 328 GGSSGAALYAAvKHIKTRRVRGV--AVVIL 355
                                    **999998888788888888777..45544 PP

>> SDH_alpha  Serine dehydratase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   5.1e-05      0.46      71     111 ..      50      95 ..      21     124 .. 0.74
   2 ?   -3.7   0.1      0.86   7.7e+03      95     115 ..     226     246 ..     220     255 .. 0.78
   3 ?   -3.0   0.0      0.53   4.7e+03      76     102 ..     307     333 ..     259     338 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.1e-05
                      SDH_alpha  71 krlldklsaaAlavaemnaa..ggrvvtaptsGaaGi...lPavlv 111
                                     ++ d++ ++ l +a+  +   +g v++ pt+G+ G+   l a+ +
  gi|118431373|ref|NP_147802.2|  50 GSVKDRIGLYMLMDARSRGLveEGAVIIEPTAGNTGVglaLAAIHY 95 
                                    3345899999*******9964489*************954444433 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.86
                      SDH_alpha  95 vtaptsGaaGilPavlvalle 115
                                    v  ++ G  G +  v+ +l +
  gi|118431373|ref|NP_147802.2| 226 VVYAGMGTRGTITGVARYLKR 246
                                    567899999999999999665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.53
                      SDH_alpha  76 klsaaAlavaemnaaggrvvtaptsGa 102
                                    ++   A+++a+m a    v +   sGa
  gi|118431373|ref|NP_147802.2| 307 VTDQQAFSMARMLARLEGVLAGGSSGA 333
                                    555667777787777777777666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2766.90
//
Query:       gi|14601268|ref|NP_147803.1|  [L=384]
Description: cystathionine gamma-synthase [Aeropyrum pernix K1]
Scores for 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-153  509.1   0.0   5.8e-153  508.9   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    6.6e-09   35.4   0.0    9.3e-09   34.9   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    8.9e-07   28.2   0.0    3.3e-06   26.3   0.0    1.7  2  Aminotran_5      Aminotransferase class-V
      9e-07   28.5   0.0    1.5e-06   27.8   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0021   17.4   0.0     0.0045   16.3   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.061   11.8   0.0        0.1   11.1   0.0    1.3  1  Met_gamma_lyase  Methionine gamma-lyase


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.9   0.0    2e-156  5.8e-153       2     382 .]       6     382 ..       5     382 .. 0.99

  Alignments for each domain:
  == domain 1  score: 508.9 bits;  conditional E-value: 2e-156
                                   HHHHHTTTTCHT.TTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHH CS
               Cys_Met_Meta_PP   2 Tllvhagqekde.qtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAia 81 
                                   T++vhag++++e  +g v+ pi+l+ ty  +      a+ e+gy+YsR+ nptr++le+++aaLe++  ala+ssG+aA a
  gi|14601268|ref|NP_147803.1|   6 TKAVHAGEDPREtLHGDVVHPIHLSVTYWKR----SVAEAEEGYVYSRTSNPTRDALEKKLAALENARYALAFSSGLAAEA 82 
                                   99*******999789*************999....56777889************************************** PP

                                   HHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHH CS
               Cys_Met_Meta_PP  82 aailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiakl 162
                                   ++ilall++Gd+iv+ ddlYggt+rl+++v+ ++gi+v++vd  d+ ++eka+++ t++++lEtptnpllk++Di++ a++
  gi|14601268|ref|NP_147803.1|  83 TVILALLREGDHIVAFDDLYGGTKRLFQRVMARFGIKVTYVDARDPGNIEKALTPATRMIWLETPTNPLLKLTDIRAAAEI 163
                                   ********************************************************************************* PP

                                   HHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHHHH CS
               Cys_Met_Meta_PP 163 akkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawlll 243
                                   a  ag+ +vvDntfa+p++qrpl+lgaDivvhSaTKyl+Ghsd++aG+++v++  e+ ++lk++qna+Gav  p d++ll+
  gi|14601268|ref|NP_147803.1| 164 ASRAGAYLVVDNTFATPYFQRPLELGADIVVHSATKYLSGHSDLLAGAVMVNS-SEVYEKLKYHQNAVGAVPPPLDSYLLM 243
                                   ****************************************************9.999999********************* PP

                                   HHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SSSEE CS
               Cys_Met_Meta_PP 244 rGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlklfsl 324
                                   r lkTL+lR+e hq+nA+k+Ae+Le+hpkv +v Ypgl++hpqh lak+q++g++g+lsFelk+++ +a +fv++l++++l
  gi|14601268|ref|NP_147803.1| 244 RSLKTLALRMEWHQHNAMKIAEHLESHPKVDRVIYPGLSTHPQHSLAKRQMTGYSGMLSFELKGGAGAAVRFVESLRIIAL 324
                                   ******************************************************************99************* PP

                                   CSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
               Cys_Met_Meta_PP 325 aeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqale 382
                                   aeslGgvesl+e+p  mthasip+eer ++g+td+l+RlsvGiEd++Dli+D++qal+
  gi|14601268|ref|NP_147803.1| 325 AESLGGVESLVEIPSLMTHASIPREERLKKGITDGLVRLSVGIEDLEDLIEDIEQALK 382
                                   ********************************************************96 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 !   34.9   0.0   3.1e-12   9.3e-09      31     284 ..      41     266 ..      28     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.1e-12
                                   HHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                 Aminotran_1_2  31 alaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                   a++g  + ++++++  ++le++la + +        +  a+ ++sG  a + ++ +ll+   gd i+++d  y+  k+ ++
  gi|14601268|ref|NP_147803.1|  41 AEEGYVYSRTSNPT-RDALEKKLAALEN--------ARYALAFSSGLAAEATVILALLR--EGDHIVAFDDLYGGTKRLFQ 110
                                   55555556666666.8999999999999........555**********9999999999..*************9988887 PP

                                   HT....TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                 Aminotran_1_2 112 ls....ggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                         g++v ++          d  ++e+al+        t++i++e+p NP    ++l ++++ +++a + +++l+vD 
  gi|14601268|ref|NP_147803.1| 111 RVmarfGIKVTYVD-------ARDPGNIEKALTP------ATRMIWLETPTNPL---LKLTDIRAAAEIASRAGAYLVVDN 175
                                   54222266777777.......6799********9......899**********6...666666666666************ PP

                                   TTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEE.EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHH CS
                 Aminotran_1_2 189 aYagfvfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilg.naavvsqlrklsrpfls..ssllqaavaaals 265
                                   ++a+ +f+        +++ +   +++v s  K + G   +  G++ + +++v + l+  ++++    + l +++++ +l+
  gi|14601268|ref|NP_147803.1| 176 TFATPYFQR------PLELGA---DIVVHSATKYLsGHSDLLAGAVMVnSSEVYEKLKYHQNAVGAvpPPLDSYLLMRSLK 247
                                   *******93......344444...489999999997777777789999677999999988888777766666777888888 PP

                                   HHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 266 dallkqseleemrqrlqkr 284
                                   +  l++++++ ++ +++++
  gi|14601268|ref|NP_147803.1| 248 TLALRMEWHQHNAMKIAEH 266
                                   8888888888888888776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.1e-09   3.3e-06      46     203 ..      56     201 ..      31     205 .. 0.88
   2 ?   -0.9   0.0      0.21   6.3e+02     269     327 ..     259     316 ..     246     373 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.1e-09
                                   HHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSC CS
                   Aminotran_5  46 eearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeege 126
                                   ++ ++k+a+l na+  + + f sG + a ++v+l+l   l++gd+iv  +  + ++    q+++ r g+kv+++ + + g 
  gi|14601268|ref|NP_147803.1|  56 DALEKKLAALENAR--YALAFSSGLA-AEATVILAL---LREGDHIVAFDDLYGGTKRLFQRVMARFGIKVTYVDARDPG- 129
                                   45688999999999..5888888877.889999999...9***********************************96555. PP

                                   BEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTT CS
                   Aminotran_5 127 ldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKll 203
                                       ++ek+l++ t+++ +    n +  + ++ + +++a ++ga+++vD + a +  +  + +lg+D+++ s+ K+l
  gi|14601268|ref|NP_147803.1| 130 ----NIEKALTPATRMIWLETPTNPLLKLTDIRAAAEIASRAGAYLVVDNTFATPYFQRPL-ELGADIVVHSATKYL 201
                                   ....5669******************************************99999988776.79***********76 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.21
                                   HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHH CS
                   Aminotran_5 269 eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatl 327
                                   +++++++  + + +    ++ +l+  p+  l++ ++    ++++sf +kg   + v+ +
  gi|14601268|ref|NP_147803.1| 259 NAMKIAEHLESHPKVDRVIYPGLSTHPQHSLAK-RQMTGYSGMLSFELKGGAGAAVRFV 316
                                   566777777888888999999999999999966.7899999999999999988887655 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 !   27.8   0.0   4.9e-10   1.5e-06      15     158 ..      43     186 ..      34     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.9e-10
                                   TSS-SSS..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH....HHHHTT-EEEE CS
               DegT_DnrJ_EryC1  15 ksgwlts..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan....avlelgakpvf 89 
                                   ++  +++  +p+ +++Ek++aa  ++++a+a+ssG aA + ++ al   +gd ++     + +t      + ++ g k+ +
  gi|14601268|ref|NP_147803.1|  43 EGYVYSRtsNPTRDALEKKLAALENARYALAFSSGLAAEATVILALL-REGDHIVAFDDLYGGTKRlfqrVMARFGIKVTY 122
                                   4444444559*****************************99999975.459*************8622225677899**** PP

                                   E-B-TTTSSB-GGGCGGG--TTEEEE...EEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEEC CS
               DegT_DnrJ_EryC1  90 vDvdpdtynidpaaieaaitertkaI...lpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkv 158
                                   vD        dp +ie+a+t+ t+ I   +p + + +  d+ a  +ia++ g +++ D   A  + y ++++
  gi|14601268|ref|NP_147803.1| 123 VDAR------DPGNIEKALTPATRMIwleTPTNPLLKLTDIRAAAEIASRAGAYLVVDNTFA--TPYFQRPL 186
                                   **99......****************666689999999*******************96544..44555555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.5e-06    0.0045      27     168 ..      48     175 ..      32     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-06
                                   CCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSST.THHHHC.C--EEEEE-EBT CS
               Beta_elim_lyase  27 sYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdet.gaiael.agvklrdlknke 105
                                   s   ++t  +Le+++a+l  + +al + +G aA++  + +ll+ g+ +++ ++         g+ + l + v++r + +k 
  gi|14601268|ref|NP_147803.1|  48 SRTSNPTRDALEKKLAALENARYALAFSSGLAAEATVILALLREGDHIVAFDD-------LyGGTKRLfQRVMAR-FGIKV 120
                                   455788999*********************************88887765444.......345555443444333.22222 PP

                                   T..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
               Beta_elim_lyase 106 a..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                   +     d+ ++e+a+++       +++i l++ +n      ++l  +r++a+ia + g  l++D 
  gi|14601268|ref|NP_147803.1| 121 TyvDARDPGNIEKALTP------ATRMIWLETPTNP----LLKLTDIRAAAEIASRAGAYLVVDN 175
                                   22245678899999999......499*********5....9*********************995 PP

>> Met_gamma_lyase  Methionine gamma-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05       0.1      48     242 ..      43     219 ..      35     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
               Met_gamma_lyase  48 tGyGyddl...GrdtldkvyaevfgaeaalvrpqlvsGthaiatalfgvlrpgdellaitGkPydtleeviGlrgegqgsl 125
                                    Gy y       rd+l+k  a + +a  a     + sG  a at++ + lr gd+++a     +d l    G++   q  +
  gi|14601268|ref|NP_147803.1|  43 EGYVYSRTsnpTRDALEKKLAALENARYA---LAFSSGLAAEATVILALLREGDHIVA-----FDDLYG--GTKRLFQRVM 113
                                   57777654111577777777776666665...5799*******************997.....565543..66666999** PP

               Met_gamma_lyase 126 kdfgikykevdlleegkvdieavkeaikektkliliqrskGyserkslsieeieeiiklvkeinedvivfvdncyGefvee 206
                                     fgik   vd ++ g     ++++a+++ t++i +       + + l++ +i+ + ++  +      + vdn +      
  gi|14601268|ref|NP_147803.1| 114 ARFGIKVTYVDARDPG-----NIEKALTPATRMIWLETP----TNPLLKLTDIRAAAEIASRAGA--YLVVDNTFATP-YF 182
                                   ******9999999866.....56799*********9876....57999*****998887665544..4458**99864.45 PP

               Met_gamma_lyase 207 kePtevGadliaGsliknpGGgi.aktGGyiaGkeel 242
                                   + P e+Gad++  s  k   G     +G  ++   e+
  gi|14601268|ref|NP_147803.1| 183 QRPLELGADIVVHSATKYLSGHSdLLAGAVMVNSSEV 219
                                   78************99998775413444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 2920.26
//
Query:       gi|118431374|ref|NP_147804.2|  [L=243]
Description: CRISPR-associated protein [Aeropyrum pernix K1]
Scores for complete 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-11   43.5   0.3    6.3e-11   42.8   0.3    1.3  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.3   3.5e-15   6.3e-11       6      86 .]     130     237 ..     128     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.5e-15
                                    EE-EE..TEEESS--HHHHHHHHHHHHHHHTSS........................EECHHH....HH.HEEEEEEEE- CS
                    CRISPR_Cas6   6 Ptrfk..krkgllpsprlvfssllrrwnalaglkgk.....................ptveee....le.gGfvGevkys 57 
                                    Pt  +  +r  l+psp++++ s+++++ + +gl++k                               ++  +f+G+++y+
  gi|118431374|ref|NP_147804.2| 130 PTIYMfrSRPILYPSPQRLVYSVFSALARHTGLSLKgyantlasnvellgwngrvglY----SigrdRKvRAFYGRATYA 205
                                    6665555788899*************99999999888887766555454444444441....044445555********4 PP

                                    -...HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                    CRISPR_Cas6  58 g...eleelekllrfaeylgvGkktafGlGkv 86 
                                    +   ++e l+ ++++a++l+vGk++++G+G+v
  gi|118431374|ref|NP_147804.2| 206 AtarYVELLQLVMEAAQVLHVGKSRGIGFGAV 237
                                    44678889999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 2016.11
//
Query:       gi|14601271|ref|NP_147806.1|  [L=374]
Description: CRISPR-associated protein [Aeropyrum pernix K1]
Scores for 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-119  397.4   0.0   7.7e-119  397.1   0.0    1.0  1  Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
  ------ inclusion threshold ------
      0.056   13.1   0.1          8    6.1   0.0    3.0  3  DUF4131   Domain of unknown function (DUF4131)
       0.18   12.0   0.0       0.31   11.2   0.0    1.3  1  ArnB_C    Archaellum regulatory network B, C-terminal domain


Domain annotation for each model (and alignments):
>> Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.1   0.0  1.3e-122  7.7e-119       1     354 [.       3     368 ..       3     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 397.1 bits;  conditional E-value: 1.3e-122
                      Cas_Csa4   1 kelytPghseildtlImygivrslaragvvelrvertGerYvievevDvrnkn...........leegLrealeevlsghe 70 
                                   ++lytPgh+ ++dtlI+ygi+r+la++g+v+++ver+GerYv++  vD++n++           ++++L+e++++v++g+e
  gi|14601271|ref|NP_147806.1|   3 CILYTPGHNLYTDTLILYGIARLLAWSGKVSGEVERVGERYVVK--VDADNCHpvsqlpesirlALRLLQEEQQQVFLGDE 81 
                                   79******************************************..*****************99**************** PP

                      Cas_Csa4  71 algrrkiisdadisagafisdlqrlnrvyrelesilnnle.klkasvksels...........kkkqaeargrkkklltvp 139
                                                  g+f+sdl+rl+r+++++esilnnl+ +++a++ s+++           kk+q+e+rgrkk+l+t++
  gi|14601271|ref|NP_147806.1|  82 ---------------GTFYSDLYRLARGSKVGESILNNLRiRVAAKILSNDAnilekyvspghKKLQGEFRGRKKGLVTLV 147
                                   ...............***********************************99***************************** PP

                      Cas_Csa4 140 ltLmPsagkyllkslkkk..eekpyrvcklcyalawlGfhYyastikikdGesvvvvtlapseevslidllalkdlkekls 218
                                   l+L+P++gk++++slk++  +ekpy+vc++cy+l++lGfhY+++t++ kdGes+vv tl+p+++ sl+d+lal++++e++s
  gi|14601271|ref|NP_147806.1| 148 LPLGPLYGKFYTWSLKPRrlTEKPYVVCPYCYFLSVLGFHYGSYTYQ-KDGESKVV-TLSPHHA-SLEDVLALSQSFEAAS 225
                                   ***********************************************.********.*******.**************** PP

                      Cas_Csa4 219 vlqpalvnsreall.kalllyllslgalellteskftvlvYalefkvgnnqrirsfrevelsk....lldfiaelkardfa 294
                                   +++pa++++r++l+ ++l+ly+lslg+++l+++s+f+vl+  +ef+v+nn    +fr+v++++    ll++ia++k++ +a
  gi|14601271|ref|NP_147806.1| 226 IWMPAILRYRNSLTgPGLSLYVLSLGETLLSSSSHFEVLY--GEFSVDNN----TFRVVDVGRlpgvLLTSIAIIKYH-MA 299
                                   ****************************************..********....9********99999**********.** PP

                      Cas_Csa4 295 stiklvddllredleillr..Lieal.......lygdlrevysalrvlkkagvrldaelvdalaeilae 354
                                   s+++l+d+++r+d+++l+r  L+ ++       lyg+lre++s+l+++k++++r+ a+++d+lae+la+
  gi|14601271|ref|NP_147806.1| 300 SWPRLIDFIARRDPGLLHRiaLTLSFevgneyaLYGILREILSLLNDDKSQEARYLAKQLDRLAEGLAM 368
                                   *******************7788888*****************************************98 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.028   1.7e+02      78     136 ..      35      92 ..       8      99 .. 0.78
   2 ?    6.1   0.0    0.0013         8      26      65 ..     159     204 ..     142     219 .. 0.69
   3 ?    1.1   0.0     0.046   2.8e+02     120     153 ..     325     358 ..     313     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.028
                       DUF4131  78 lpeltgsgtrfvlevervlsagktkpvsgrvlvtvpkspae..glrpGdrlrltgrlkrpr 136
                                   ++   + g r+v++v+  ++     ++++++++ ++  ++e  ++  Gd+ ++   l+r  
  gi|14601271|ref|NP_147806.1|  35 EV--ERVGERYVVKVDA-DNCHPVSQLPESIRLALRLLQEEqqQVFLGDEGTFYSDLYRLA 92 
                                   44..4446788888875.8888888899999999999999888889999999888888876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0013
                       DUF4131  26 r...rprrrv...llllllllllallgfalrapqpnandlsqlles 65 
                                       +prr +    +++ ++++l +lgf++ +++ +++  s+++++
  gi|14601271|ref|NP_147806.1| 159 TwslKPRRLTekpYVVCPYCYFLSVLGFHYGSYTYQKDGESKVVTL 204
                                   1334344433555*************************99999876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.046
                       DUF4131 120 lrpGdrlrltgrlkrprpatNpggFDyraYLarq 153
                                   ++ G++ +l g l+++ +  N      ++YLa+q
  gi|14601271|ref|NP_147806.1| 325 FEVGNEYALYGILREILSLLNDDKSQEARYLAKQ 358
                                   6789***************************987 PP

>> ArnB_C  Archaellum regulatory network B, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.3e-05      0.31       2      40 ..     326     364 ..     325     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.3e-05
                                   HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                        ArnB_C   2 dvinEyrYyellkkysealeagnlkeATrilqeleeiAe 40 
                                   +v nEy +y  l+++ ++l+ ++ +eA   +++l ++Ae
  gi|14601271|ref|NP_147806.1| 326 EVGNEYALYGILREILSLLNDDKSQEARYLAKQLDRLAE 364
                                   5779*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3171.97
//
Query:       gi|14601272|ref|NP_147807.1|  [L=282]
Description: CRISPR-associated protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0025   18.0   0.0     0.0034   17.5   0.0    1.3  1  HD_6      HD domain
  ------ inclusion threshold ------
      0.084   13.1   0.1       0.37   11.0   0.0    2.2  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-07    0.0034      48      77 ..      60      88 ..      14     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-07
                                  HHHHHHHHHHHHCCCGGGSSHHHHTTS--- CS
                          HD_6 48 ealrrllaflaalHDlGKaspaFqakvpel 77
                                  + l + +a+ ++lHD+GKa pa+q+k+  +
  gi|14601272|ref|NP_147807.1| 60 SVLGDPVAVAIVLHDIGKAVPAYQKKRI-M 88
                                  44556689999**************992.2 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.1e-05      0.37      28      74 ..      66     106 ..      55     168 .. 0.74
   2 ?   -1.8   0.0      0.39   3.5e+03      27      35 ..     231     239 ..     219     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                                   HHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHH CS
                            HD  28 lllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrl 74 
                                   + +a  lHDiGk ++  ++      ++++++ +++  e+++ ++ +l
  gi|14601272|ref|NP_147807.1|  66 VAVAIVLHDIGKAVPA-YQK-----KRIMRGRVQYRHELVSGALSLL 106
                                   67999*********55.343.....3455555555555555554444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.39
                                   HHHHHHHHT CS
                            HD  27 llllaaLlH 35 
                                   ++++a++lH
  gi|14601272|ref|NP_147807.1| 231 RARVAGILH 239
                                   6899***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2481.28
//
Query:       gi|14601273|ref|NP_147808.1|  [L=570]
Description: CRISPR-associated helicase Cas3 [Aeropyrum pernix K1]
Scores for complete 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   72.7   0.0      7e-20   71.5   0.0    1.5  2  DEAD        DEAD/DEAH box helicase
    2.2e-05   24.8   0.1    4.3e-05   23.8   0.1    1.4  1  Helicase_C  Helicase conserved C-terminal domain
     0.0042   17.1   0.0       0.01   15.9   0.0    1.6  1  ResIII      Type III restriction enzyme, res subunit


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 !   71.5   0.0   1.2e-23     7e-20       4     175 ..      39     223 ..      37     224 .. 0.83
   2 ?   -3.2   0.0         1   6.1e+03      49      94 ..     267     310 ..     261     328 .. 0.60

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.2e-23
                                   HHHHHHHHH......TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                   xxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD   4 Qaeaiplil......gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                   Qa+a ++i        gg v++ a+TG+GKT++f+ p+l+++++ k+  + + ++veP+++L++ ++++lk+++++++   
  gi|14601273|ref|NP_147808.1|  39 QAKAAEEICriayesPGGVVFLGAPTGAGKTEVFMAPLLASFAS-KRPIAARGFLVEPMHSLIKAMVDRLKTSIETLG--- 115
                                   666666666666677789************************88.9*****************************866... PP

                                   EEEETTSSHHHHHHHHHTTCSEEEEEH.........HHHHHHH.....HCTSSH....CTTEEEEEEETHHHHHHT..TTH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx.....xxxxxx....xxxxxxxxxxxxxxxxxx..xxx RF
                          DEAD  79 lliiggvaardqlskldngvdivvgtp.........grlddll.....stgkln....lsqvrflVlDEadrlldq..gfs 139
                                     + +++ ++ q + l  ++ i+v+tp         +r+ ++l     +tg+++    l+  ++ V+DEa+ ++d+     
  gi|14601273|ref|NP_147808.1| 116 --VSEDHGETVQPTFL-YTAPITVTTPdtyfygfaaSRVYRILthegvETGRFSmpvgLQATSYTVFDEAHLVQDEvfLSP 193
                                   ..34567788899999.9*********7777777666666655899999999888999******************54446 PP

                                   HHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD 140 dfinrilnqlpqitcdgklqrqvivlSATlpkdvkk 175
                                   + ++ ++++l+++   g     ++v SATlp+ +k+
  gi|14601273|ref|NP_147808.1| 194 RLLSLVVAALARA--GGL----IVVSSATLPSYYKT 223
                                   6788888888433..222....9********88775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1
                                   EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          DEAD  49 kalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl 94 
                                   k l+++ t +    +++ lk+++++ +  vll+ +  ++rd+ sk+
  gi|14601273|ref|NP_147808.1| 267 KGLVLVNTVSKSIRVYKSLKTRCSNSK--VLLLHSLFKRRDKNSKI 310
                                   556666666666677777777777643..44444444444444443 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 !   23.8   0.1   7.1e-09   4.3e-05      18     110 ..     267     363 ..     258     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.1e-09
                                   EEEEEESSHH...HHHHHHHHHHHT.TSTEEEEST...TSTHHHHHHHHHHHHTTSSS.EE.EESGGGTSSSTSTTESEEE CS
                    Helicase_C  18 kilifvntid...rlekvklllekk.gikvavlhg...elpqnereeileqfnkgesd.vL.iatdvaerGidipkvnlVi 89 
                                   k l+ vnt++   r++  k l+++  + kv+ lh+   +  +n+++e l++  k++ + v+ +at+v+e G+d+ + + + 
  gi|14601273|ref|NP_147808.1| 267 KGLVLVNTVSksiRVY--KSLKTRCsNSKVLLLHSlfkRRDKNSKIELLQKLLKEQDNgVIaVATQVLEVGVDL-DFEALY 344
                                   5688899998655555..77743336899999999444577888888888887655555666************.355554 PP

                                   ESSSSSSHHHHHHHHTTSSST CS
                    Helicase_C  90 nfdlprnvtsyiqriGRtgRa 110
                                      +   ++s+iqr GR+gR 
  gi|14601273|ref|NP_147808.1| 345 TETA--PIDSVIQRLGRIGRR 363
                                   4444..499***********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 !   15.9   0.0   1.7e-06      0.01       7     146 ..      38     187 ..       5     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHHT......TTSEEE.EEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                        ResIII   7 yQeeaienlleklkskrdkrgl.ikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkflseayke 84 
                                    Q++a e++      +    ++ + ++TG+GKT v  a l +++++k+++  + +++ p  sl++ + +++k  +++   +
  gi|14601273|ref|NP_147808.1|  38 SQAKAAEEICRIAY-ESPGGVVfLGAPTGAGKTEVFmAPLLASFASKRPIAaRGFLVEPMHSLIKAMVDRLKTSIETLGVS 117
                                   45555555553322.33333334889*******99879999999999998888899999************9998876422 PP

                                   ..GEEEESSS-B--.......-SEEEEEHHHHHHTH.....................HHHTTT-SEEEEETGGGTTS CS
                        ResIII  85 ..igkkvsgdkkkakekdstnkkilvttiqsldadseee.............eeeseellrdrfdviiiDEaHrlga 146
                                     +g+ v+            ++ i+vtt ++                      + s   + ++  + ++DEaH +++
  gi|14601273|ref|NP_147808.1| 118 edHGETVQPTFLY-------TAPITVTTPDTYFYGFAASrvyrilthegvetGRFSMPVGLQATSYTVFDEAHLVQD 187
                                   3344444444444.......455555555554444422234444444467666677777777777999999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3867.60
//
Query:       gi|118431375|ref|NP_147810.2|  [L=282]
Description: CRISPR-associated protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   15.0   0.0      0.046   14.2   0.0    1.4  1  FliX      Class II flagellar assembly regulator


Domain annotation for each model (and alignments):
>> FliX  Class II flagellar assembly regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.6e-06     0.046      59      94 ..      97     132 ..      59     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-06
                           FliX  59 vdedeterrrravrrgetlLDkLdelklalLdGevs 94 
                                    v e + e+     +rg+++LD+L ++  alL G+++
  gi|118431375|ref|NP_147810.2|  97 VLEPDSEEGSTRENRGNRVLDELSRISDALLRGYIT 132
                                    44556666777789*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.19s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2299.37
//
Query:       gi|14601276|ref|NP_147811.1|  [L=347]
Description: CRISPR-associated negative autoregulator [Aeropyrum pernix K1]
Scores for complete 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-70  235.9   0.0    4.9e-70  235.7   0.0    1.0  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 !  235.7   0.0   2.7e-74   4.9e-70       1     268 [.       6     281 ..       6     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 2.7e-74
                                   EEEEEE-------------------EEEEEE--T.T--EEEEEE-THHHHHHHHHHHHHHHHTS.TTSSBHHHHTT----- CS
                          DevR   1 isgrvvvnveaLNmdesvGNytehrkvpvvlkee.ykvrtvpaiSgeslkHayfetlvklaken.nlpvcelckrvegdgg 79 
                                   ++grv+vnv  L +++++GNy +h +++v+++ +  kv++vp+++g+slkH++++++++++++  + +++elckr+ g +g
  gi|14601276|ref|NP_147811.1|   6 VAGRVRVNVAVLTGHGTAGNYSMHARARVYCCGDsSKVYEVPVLTGNSLKHWHAYYAAQVYQALgGSMLNELCKRGIGLRG 86 
                                   579***************************99999*****************************99*************** PP

                                   -TT--EEEBTTSEESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEEE--BEE-TTTTTTT...-----------.... CS
                          DevR  80 vikfatekklkekelkvekeiikecvveDvfGfLitekeksvkRkspvkfsyavpveesekav...vdaqfharydl.... 153
                                   +  +++ +  + + ++ e+e+ik+++ +D++GfLi+e+++++kR+s ++fs+a+pv+++e  +   + +++h+r+d+    
  gi|14601276|ref|NP_147811.1|  87 YNVDTNLEGER-RLATRESEAIKDFC-NDLHGFLIAERGRQLKRDSLARFSFAIPVLNNEVLEnieKFSVTHNRVDPlqrr 165
                                   ****9888665.999***********.*********************************9889999**********8888 PP

                                   .------------------HHHHHSSEEEEEEEEEGGGTTS-TTS--EE---S-HHHHHHHHHHHHHTHHHHHH------- CS
                          DevR 154 .lenrarkkgeeeekqnifqvEehsalYalsfvlDldriGkpevkkskieyvleeeerkkRikaalkallnlLsgsfgakr 233
                                    + +++++++++++++++f++E++s+lY++s+++Dl+++++p +++++   +++eeer++R++a+l al++lL g+  +k+
  gi|14601276|ref|NP_147811.1| 166 rAGEESNSQETGATEMMVFKQEYSSGLYGISASFDLEYLCRPLYESEEGGSACDEEERMRRARASLLALAYLLGGA-ASKQ 245
                                   88889999999************************************************************99999.99** PP

                                   -------EEEEEEEE--SSS------TT.TTHHHHH CS
                          DevR 234 arllPvfeveslvaavskkpfpvfpirl.edyveee 268
                                   ar+lP+ +ve+lv+av++kp+p+ +++  e+yve++
  gi|14601276|ref|NP_147811.1| 246 ARALPIAMVEELVVAVCNKPVPNAVHGSyENYVEKT 281
                                   *************************8888*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2623.08
//
Query:       gi|118431376|ref|NP_147812.2|  [L=131]
Description: CRISPR-associated protein [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.7   0.0       0.05   13.4   0.0    1.1  1  DUF2785   Protein of unknown function (DUF2785)


Domain annotation for each model (and alignments):
>> DUF2785  Protein of unknown function (DUF2785)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-06      0.05      76     130 ..      29      79 ..      25     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-06
                        DUF2785  76 dlldellkepelkradailllelivkkltrtqsvlaadEdeRlatailalleknk 130
                                    d++d l++ p   +++  ll  l vk+++ ++s++  +E eR      ++l++ k
  gi|118431376|ref|NP_147812.2|  29 DITDTLASRPSSYEEQLALLARLAVKVYKDLESFYNKGEGERVE----EALKRLK 79 
                                    99****************************************94....4444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1034.28
//
Query:       gi|118431377|ref|NP_147813.2|  [L=240]
Description: CRISPR-associated DNA-binding protein [Aeropyrum pernix K1]
Scores for 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   21.3   0.2    0.00031   20.6   0.2    1.3  1  MarR           MarR family
    0.00026   20.8   0.6    0.00054   19.8   0.6    1.5  1  MarR_2         MarR family
    0.00056   19.7   0.3     0.0013   18.6   0.3    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0015   18.8   0.2     0.0027   18.0   0.2    1.4  1  Rrf2           Transcriptional regulator
     0.0026   17.6   0.2     0.0057   16.5   0.2    1.5  1  HxlR           HxlR-like helix-turn-helix
     0.0074   16.8   0.5      0.014   15.9   0.5    1.5  1  HTH_27         Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.034   14.1   0.3      0.068   13.2   0.3    1.5  1  HTH_Crp_2      Crp-like helix-turn-helix domain
      0.054   14.0   0.0        0.1   13.1   0.0    1.4  1  Carbpep_Y_N    Carboxypeptidase Y pro-peptide
      0.063   13.1   0.7       0.14   12.0   0.7    1.6  1  HTH_IclR       IclR helix-turn-helix domain
      0.099   12.6   0.1       0.23   11.5   0.1    1.5  1  Dimerisation2  Dimerisation domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   1.7e-07   0.00031       4      49 ..     174     219 ..     171     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                                    HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49 
                                     +++++++l+  g ++v+ +a+ l+vs++ + r+l++Le k li++
  gi|118431377|ref|NP_147813.2| 174 KELLVVETLAGLGRARVKSIARSLQVSRTLADRLLRKLESKKLISS 219
                                    688999***********************************99986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.6     3e-07   0.00054      12      54 ..     180     220 ..     171     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3e-07
                                    HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                      L+  ++   +v+ +ar l++s+  + r+l++L+++ L+  +
  gi|118431377|ref|NP_147813.2| 180 ETLAGLGR--ARVKSIARSLQVSRTLADRLLRKLESKKLISSE 220
                                    55555555..7****************************9654 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   7.3e-07    0.0013      15      66 ..     180     232 ..     172     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.3e-07
                                    HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                           TrmB  15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66 
                                     +L  lg+a+++ ia+ l v+r+ + + Lr+Le+k l+  e  gr klY+ +d
  gi|118431377|ref|NP_147813.2| 180 ETLAGLGRARVKSIARSLQVSRTLADRLLRKLESKKLISSEVrGRGKLYSLTD 232
                                    578889********************************988746678887665 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   1.5e-06    0.0027      23      67 ..     185     230 ..     173     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                                    CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE.ETTT-TCEEE CS
                           Rrf2  23 eepvsseeiaerqnispsylekilakLrkaglvks.vrGkgGGyrL 67 
                                     + +++++ia++ ++s++ + ++l+kL+ ++l+ s vrG+g  y+L
  gi|118431377|ref|NP_147813.2| 185 LGRARVKSIARSLQVSRTLADRLLRKLESKKLISSeVRGRGKLYSL 230
                                    455889***************************9956898766666 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   3.2e-06    0.0057       8      73 ..     176     238 ..     172     240 .] 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-06
                                    HHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGH CS
                           HxlR   8 llilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrsle 73 
                                    ll++ +l   g+ R + ++r l ++s+ +  + Lr+Le+++li+ ev  +      Yslt+ G  l 
  gi|118431377|ref|NP_147813.2| 176 LLVVETLAGlGRARVKSIARSL-QVSRTLADRLLRKLESKKLISSEVRGRGKL---YSLTDLGYMLV 238
                                    56666676679***********.99988878889**********999887766...*****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 !   15.9   0.5   7.6e-06     0.014       5      68 .]     175     234 ..     171     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.6e-06
                         HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                    + lv+++++  ++r++ + +++ l+v+ + +   l+kL+ k L+    +e  +r k+++lTd G
  gi|118431377|ref|NP_147813.2| 175 ELLVVETLA-GLGRARVKSIARSLQVSRTLADRLLRKLESKKLI---SSEVRGRGKLYSLTDLG 234
                                    678899999.9*********************************...666779*********87 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 ?   13.2   0.3   3.8e-05     0.068      25      62 ..     191     233 ..     183     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                                    HHHHHHTTSSHHHHHHHHHHHHHTTSEE...ETEE..EEES-H CS
                      HTH_Crp_2  25 eelAsmlGltretvsrilseLkreglis...rgrr..irildl 62 
                                    + +A+ l ++r    r+l++L+ ++lis   rgr+    ++dl
  gi|118431377|ref|NP_147813.2| 191 KSIARSLQVSRTLADRLLRKLESKKLISsevRGRGklYSLTDL 233
                                    579*************************864344345556665 PP

>> Carbpep_Y_N  Carboxypeptidase Y pro-peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.8e-05       0.1      56     103 ..      50      97 ..      39     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-05
                    Carbpep_Y_N  56 nnvfekiskvlneplkeltseakkiWsemelkfPdavsklkfktkpkk 103
                                     +++ek ++++ +++++l  e++++W + +   P  v k++  ++ + 
  gi|118431377|ref|NP_147813.2|  50 VDAVEKLKNMIIDAYGDLHVETRDVWLDPSNGIPRGVAKMRRVVEEAA 97 
                                    4779************************************98876655 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 ?   12.0   0.7   7.7e-05      0.14       8      48 ..     178     217 ..     174     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                                    HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                    + + la  +++ +++ +Ar + ++++ + RlL+ L+  +++
  gi|118431377|ref|NP_147813.2| 178 VVETLAGLGRA-RVKSIARSLQVSRTLADRLLRKLESKKLI 217
                                    67889999997.************************99987 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00013      0.23      20      79 ..     175     233 ..     173     237 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                  Dimerisation2  20 eLgvFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntel 79 
                                    eL v ++L+  +  +++ +a++l++s    +rLl+ + + +L ++e +  +++lYs t+l
  gi|118431377|ref|NP_147813.2| 175 ELLVVETLAGLGRARVKSIARSLQVSRTLADRLLRKLESKKLISSEVRG-RGKLYSLTDL 233
                                    688889999999999*****************************88555.579*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1785.09
//
Query:       gi|118431378|ref|NP_147814.2|  [L=199]
Description: CRISPR-associated Cas4 family protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-10   40.9   0.0    5.6e-10   39.6   0.0    1.6  1  Cas_Cas4  Domain of unknown function DUF83
    4.1e-08   33.4   0.0    6.1e-07   29.6   0.0    2.0  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
     0.0011   18.4   0.0     0.0014   18.0   0.0    1.2  1  Csa1      CRISPR-associated exonuclease Csa1


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 !   39.6   0.0   9.3e-14   5.6e-10       2     161 ..       4     189 ..       3     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 9.3e-14
                       Cas_Cas4   2 gtkiqyyliCkrklwlisheitleensetvelGkllhe............esyerekkevel.se....sikiDvve.ke 63 
                                    +++++ y++C+r ++++++     +  e ++l + +               +  +e+ +v l s+    +++ D v  + 
  gi|118431378|ref|NP_147814.2|   4 VSMLKEYAYCPRVAYYMEVLRPSYRPTEPMNLSREIYSvdhvrgilrssgFRIVKEEWAVPLrSKrlglQGVADGVVvEG 83 
                                    68999*************988888888888888888776677777766553333444667776558888999**888577 PP

                       Cas_Cas4  64 keklvvvEvKkskkk......eeaa.klQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeiee 135
                                      +++vvE K s +       +  +  +Q  +Y+l Le ++g +++  ++  ++  k+  v++++ lr+ + + ++++++
  gi|118431378|ref|NP_147814.2|  84 SLGIIVVEAKLSVRSnrwlhtRGRHvIFQAAAYALALEeTRGYSVDYLAIVSLEDSKTYVVKMSPSLRRDVIRLADDMNK 163
                                    889999****99888778887555569***********9*******88888888889999******************** PP

                       Cas_Cas4 136 iissekppkvkkkkiCkkCayaelCl 161
                                     ++    p++k  ++C +C ++ +C 
  gi|118431378|ref|NP_147814.2| 164 TLDDGLEPPPKPGRKCVACRFRRVCQ 189
                                    *************************7 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 ?    2.0   0.1     0.027   1.6e+02       4      29 ..       4      31 ..       4      48 .. 0.80
   2 !   29.6   0.0     1e-10   6.1e-07     111     255 .]      51     189 ..      35     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.027
                       PDDEXK_1  4 vsrletfleCplrfflryllgl..reee 29
                                   vs l+ ++ Cp+  ++  +l+   r++e
  gi|118431378|ref|NP_147814.2|  4 VSMLKEYAYCPRVAYYMEVLRPsyRPTE 31
                                   6889********9999999998665544 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1e-10
                       PDDEXK_1 111 krgfrpvalelefg..gekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkegl.....QlllYllalaegee 182
                                    + gfr+v+ e ++   ++++ L+G  D v  + +  + +++ K +    +s +  +l ++      Q ++Y+lal+e+  
  gi|118431378|ref|NP_147814.2|  51 SSGFRIVKEEWAVPlrSKRLGLQGVADGVVvEGSLGIIVVEAKLSV---RSNR--WLHTRGrhvifQAAAYALALEETRG 125
                                    345888888955556357888*******99555559*******655...3333..3333333346*************33 PP

                       PDDEXK_1 183 lkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilag.efparpskkCeyCpyksvCr 255
                                    +     +  +++++le+   ++  vvk  +  + +  +l+++++++   + +g e p++p++kC  C +++vC+
  gi|118431378|ref|NP_147814.2| 126 YS----VDYLAIVSLED---SKTYVVKMSPSLRRDVIRLADDMNKT---LDDGlEPPPKPGRKCVACRFRRVCQ 189
                                    32....44444445522...33445555555555555555555555...557779******************8 PP

>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-07    0.0014     209     290 ..     112     189 ..      63     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-07
                           Csa1 209 alaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidivekesDPGl..akkCsskClfl 286
                                      a YalalE + +  vD+ +++s+        k+++v++s+slR+  +   d + + ++++ +P     +kC   C f+
  gi|118431378|ref|NP_147814.2| 112 QAAAYALALEETRGYSVDYLAIVSLE-----DSKTYVVKMSPSLRRDVIRLADDMNKTLDDGLEPPPkpGRKCV-ACRFR 185
                                    5689**************98888764.....346789999*********************9987541145775.699** PP

                           Csa1 287 evCk 290
                                    +vC+
  gi|118431378|ref|NP_147814.2| 186 RVCQ 189
                                    ***6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1423.24
//
Query:       gi|118431379|ref|YP_874882.1|  [L=92]
Description: CRISPR-associated Cas2 family protein [Aeropyrum pernix K1]
Scores for 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-14   51.3   0.1    1.2e-13   51.0   0.1    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.026   14.0   0.0      0.028   13.9   0.0    1.0  1  CutC         CutC family
      0.055   13.5   0.1       0.06   13.4   0.1    1.1  1  DUF4385      Domain of unknown function (DUF4385)
       0.14   11.1   0.0       0.16   10.9   0.0    1.0  1  DUF4616      Domain of unknown function (DUF4616)


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 !   51.0   0.1   2.7e-17   1.2e-13       2      69 ..       3      69 ..       1      75 [. 0.92

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.7e-17
                                   EEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEE CS
                    CRISPR_Cas2  2 lvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriyklt 69
                                   +vl++YDi +++ +r k a+ l + Gf rvQ+SV++ +  ++ +++  + l+++ d+ +d+i+++ + 
  gi|118431379|ref|YP_874882.1|  3 YVLIAYDI-SNDSKRLKAAQKLLQMGFARVQKSVYIAKGGRSLAKEAYRALQRLADSGKDKIMVMVIP 69
                                   78******.***************************************************99987765 PP

>> CutC  CutC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.3e-06     0.028     121     178 ..       6      70 ..       1      79 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-06
                           CutC 121 rAfDvvad..peealeqlielgverv.....LtsGqkssalegleklaeLveqaaerieimagaG 178
                                     A+D ++d  + +a ++l+++g++rv     + +G++s a e+   l+ L +  +++i +m   G
  gi|118431379|ref|YP_874882.1|   6 IAYDISNDskRLKAAQKLLQMGFARVqksvyIAKGGRSLAKEAYRALQRLADSGKDKIMVMVIPG 70 
                                    68999998556789***********955555578**************************98655 PP

>> DUF4385  Domain of unknown function (DUF4385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05      0.06      62     116 ..       7      60 ..       1      68 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                        DUF4385  62 eyleeddfvGaDmaRkflqmGytRarRYa.nhkgGkkykkekeeeeleeeeedeek 116
                                    +y  ++d      a+k lqmG+ R ++     kgG+  +  ke  +  ++ +d+ k
  gi|118431379|ref|YP_874882.1|   7 AYDISNDSKRLKAAQKLLQMGFARVQKSVyIAKGGRSLA--KEAYRALQRLADSGK 60 
                                    6777777788889***********988651468999885..444555555555555 PP

>> DUF4616  Domain of unknown function (DUF4616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.5e-05      0.16      50      90 ..      17      57 ..       7      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                        DUF4616 50 vqsseqllhliyqrvekavslaeaalslakannellkrlqe 90
                                   ++++++ll + + rv+k+v +a+   slak    +l+rl +
  gi|118431379|ref|YP_874882.1| 17 LKAAQKLLQMGFARVQKSVYIAKGGRSLAKEAYRALQRLAD 57
                                   678999********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 720.90
//
Query:       gi|118431380|ref|NP_147815.2|  [L=327]
Description: CRISPR-associated Cas1 family protein [Aeropyrum pernix K1]
Scores for complete 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-59  200.1   0.0    4.9e-59  199.8   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 !  199.8   0.0   2.7e-63   4.9e-59       2     247 ..       4     253 ..       3     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 2.7e-63
                                    EEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSSS CS
                       Cas_Cas1   2 yvteqgaylrkkgerlvvekegeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlep.eesg 79 
                                    +v e+g+++r+ ++ lvve++   kk +  +++e+++i ++ vs+s++a+r++a+ gi++vfl+++g++++rl+p   ++
  gi|118431380|ref|NP_147815.2|   4 VVAEPGSRIRVARGALVVETKAG-KKVVVESSVERVIISSSrVSISSAAVRAAAKMGIDLVFLDWDGSPVARLYPpIINK 82 
                                    799******************88.788888999**9999999*********************************999** PP

                                    THHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-......HSHHHHHH CS
                       Cas_Cas1  80 nvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleellekleka......esleeLrg 153
                                    +v++r+ Q+ a  +e+ r  +a ++v++k++nq ++l++++r+r +e+l+ea  e+e l  +  ++        +++L+ 
  gi|118431380|ref|NP_147815.2|  83 TVATRIGQFSA--NERLRRLIAAELVSAKIYNQGQTLKYIARQRADERLREAGYEVELLSGEPLRIadedgpGFRDKLLS 160
                                    *********99..778899*************************999999999999998887777778899999****** PP

                                    HHHHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHH CS
                       Cas_Cas1 154 iEGeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDL 233
                                    iE++a+++Y+++++++l+ ++ f+gR  r++ Dp+Na L++gY++lys v +++  vgLdPy+G++H++++g+psL lD 
  gi|118431380|ref|NP_147815.2| 161 IEARASRRYWQCIAEILPGRLGFSGRD-RGALDPFNAALNYGYGMLYSIVEKSLLLVGLDPYLGVFHSEKSGKPSLTLDA 239
                                    **************************5.788************************************************* PP

                                    HHHHHHHHCHHHHH CS
                       Cas_Cas1 234 mEefRpllvDrlvl 247
                                    +E+fR+++vDr++ 
  gi|118431380|ref|NP_147815.2| 240 IEPFRAPIVDRILA 253
                                    ***********864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2469.69
//
Query:       gi|118431381|ref|NP_147816.2|  [L=260]
Description: CRISPR-associated protein [Aeropyrum pernix K1]
Scores for 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-88  297.5   0.0    1.1e-61  208.8   0.0    2.0  2  Csa1      CRISPR-associated exonuclease Csa1


Domain annotation for each model (and alignments):
>> Csa1  CRISPR-associated exonuclease Csa1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   3.8e-29   6.8e-25       9      96 ..       4      87 ..       1      91 [. 0.96
   2 !  208.8   0.0   5.9e-66   1.1e-61     127     290 ..      89     259 ..      84     260 .] 0.98

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 3.8e-29
                           Csa1  9 rlLkrlkklsaskeveeElRGWnwnePPvkprslvklslsdvvsgyCetkRdvYLkrvlgvrgeeekklllGaaiHeavaka 90
                                   r+L++l+++sa + v++ElRGW+wn+  v pr++++++lsdv+ g+C+++Rd+YL+rvl++r++ ++ l+lGa++Hea+  +
  gi|118431381|ref|NP_147816.2|  4 RGLWDLVRSSAGDGVYAELRGWKWNV--VGPRYAARPTLSDVT-GVCPVGRDTYLRRVLNTRVN-GGLLRLGALVHEAFLLP 81
                                   89************************..***************.********************.99*************** PP

                           Csa1 91 leelkk 96
                                   ++++++
  gi|118431381|ref|NP_147816.2| 82 FKAHRV 87
                                   **9986 PP

  == domain 2  score: 208.8 bits;  conditional E-value: 5.9e-66
                           Csa1 127 kakelykylasrvsaelsevr...skfekatedsvaarv..iPvlvefkvdGsllGlsslvrvDafililp..lvvelkv 199
                                    +a+++++yl++rv+a+ +e+r   + feka+e+s+aarv  iPv+ve++v+G+++Gls++vr+D+++ i+p  lv++ + 
  gi|118431381|ref|NP_147816.2|  89 DAYRMFNYLLRRVRARGNEIRvmnAVFEKAVEFSAAARVdgIPVAVEPNVPGGPVGLSDYVRPDLLVGIMPvdLVLAGHG 168
                                    799******************9999*********************************************9889****** PP

                           Csa1 200 gsykeehelalaGYalalEsqleiPvDfGvlisvtvngevklkaelvaisdslRkefleeRdraidivekesDPGlakkC 279
                                    +++ +++ela+aGYala+E+++++PvD+Gv++ ++vn+++k+ ++lv+++d+lR++fle+Rd++++i+e++sDPGl+++C
  gi|118431381|ref|NP_147816.2| 169 DRWVARKELAIAGYALAVEAWTGNPVDYGVVVGLRVNDGLKIVWRLVRVDDHLRTRFLERRDAVARIIEYRSDPGLPEAC 248
                                    ******************************************************************************** PP

                           Csa1 280 sskClflevCk 290
                                    ++ C+f+evC 
  gi|118431381|ref|NP_147816.2| 249 PPGCVFREVCG 259
                                    **********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1950.67
//
Query:       gi|118431382|ref|YP_874883.1|  [L=88]
Description: hypothetical protein APE_1241a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.4   0.0      0.095   12.3   0.0    1.1  1  Peptidase_C47  Staphopain peptidase C47


Domain annotation for each model (and alignments):
>> Peptidase_C47  Staphopain peptidase C47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.3e-06     0.095      26      68 ..      21      63 ..      11      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-06
                  Peptidase_C47 26 Gytmsallnatkntnkynaedvmrflypelreqdlqftgltpn 68
                                    +tm+  ++ t  tn y+  ++m  l p l+e++ q+  +t++
  gi|118431382|ref|YP_874883.1| 21 DWTMTVKIEFTIRTNPYRLPQIMLQLMPILEEHNAQHLNVTAE 63
                                   589******************************9998887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 679.45
//
Query:       gi|118431383|ref|NP_147820.2|  [L=583]
Description: hypothetical protein APE_1244.1 [Aeropyrum pernix K1]
Scores for complete 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   37.5   0.2    3.3e-09   36.4   0.2    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
    2.9e-06   27.1   0.4    6.3e-06   26.0   0.4    1.5  1  Abhydrolase_1  alpha/beta hydrolase fold
     0.0079   14.9   0.0      0.011   14.4   0.0    1.2  1  AXE1           Acetyl xylan esterase (AXE1)
  ------ inclusion threshold ------
      0.068   12.3   2.9        0.1   11.6   2.9    1.2  1  DUF2048        Abhydrolase domain containing 18
       0.12   11.9   0.5       0.24   11.0   0.1    1.6  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
       0.39   10.6   1.0       0.66    9.8   1.0    1.2  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.2   1.1e-12   3.3e-09       4     103 ..     102     220 ..      99     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.1e-12
                    Hydrolase_4   4 kavvvlvHGlaehsgrya......elaeaLaaqGfavyalDhrGhGrse.............gkrghvpsfddyvdDlaa 64 
                                    +a v+lvHGl+     ++      ++a++La +Gf+v+a+D+ GhG+s+              + g++  ++ y+  ++a
  gi|118431383|ref|NP_147820.2| 102 RAWVLLVHGLGGDHTFFEeplggyRVAYDLALRGFKVLAIDAAGHGESCipggeswrdkaltLEPGEFFLYHVYLSGVRA 181
                                    899*******99988888333333479******************************99998777777788888888888 PP

                    Hydrolase_4  65 fvekvkeehpelplfllGhSmGGliallyllrypdkva.g 103
                                    +  +++   +   + ++G SmGGl++ +++  +p+ va +
  gi|118431383|ref|NP_147820.2| 182 VEAALELGAEPGGIAVMGVSMGGLTSYTVASLHPA-VAlA 220
                                    86666655555589*****************9999.4423 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.4   2.1e-09   6.3e-06       2      96 ..     104     216 ..     103     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.1e-09
                                    EEEEE-STTTCGGGGTTGH....HHHHHHHTTSEEEEEEETTSTTSSSTTTGB................CHHSHHHHHHH CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerg....lapaLakdgfdvillDlrGvgySspapacin...............ddygtasvadd 62 
                                    +++++hGl+g +  + e++    +a++La +gf v+++D  G+g+S  +  + +                +  + s  + 
  gi|118431383|ref|NP_147820.2| 104 WVLLVHGLGGDHTFFEEPLggyrVAYDLALRGFKVLAIDAAGHGESCIPGGE-SwrdkaltlepgefflYHVYL-SGVRA 181
                                    79********888866665222267777777***************777765.247788888886665422233.34555 PP

                                    HH.HHHHHCTTSSEEEEEETHHHHHHHHHHHHHGG CS
                  Abhydrolase_1  63 ld.rildalgddkltlvGhSmGGmialayaaeype 96 
                                    ++ ++      + ++++G SmGG+++ ++a+++p 
  gi|118431383|ref|NP_147820.2| 182 VEaALELGAEPGGIAVMGVSMGGLTSYTVASLHPA 216
                                    552556666777888******************96 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.8e-06     0.011     138     205 ..     157     224 ..      31     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.8e-06
                                    STTTTT.TSTTT-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES CS
                           AXE1 138 fiirGl.ldkeklyyrrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvady 205
                                    +  + l l++ +++  +v+l  vr+ve++ +l   ++  +av+G s GG  + +va+l++ ++ +v+ +
  gi|118431383|ref|NP_147820.2| 157 WRDKALtLEPGEFFLYHVYLSGVRAVEAALELG-AEPGGIAVMGVSMGGLTSYTVASLHPAVALAVPIV 224
                                    4444441468889999**************997.5899**********************999888765 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.9   3.5e-05       0.1     175     209 ..     192     226 ..     178     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                        DUF2048 175 yGplgltGlSmGGhmaslaasnwpkplvlvpclsw 209
                                    +G +++ G+SmGG  +  +as++p  +  vp+++ 
  gi|118431383|ref|NP_147820.2| 192 PGGIAVMGVSMGGLTSYTVASLHPAVALAVPIVAS 226
                                    7999***************************9986 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.2   3.6e+03      53      71 ..     131     149 ..      91     159 .. 0.82
   2 ?   11.0   0.1   7.9e-05      0.24     100     136 ..     192     227 ..     167     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.2
                                    HHHTT-EEEEEE-TTSTTS CS
                  Peptidase_S15  53 fvarGYavVvqdvrGtggS 71 
                                    ++ rG+ v+  d+ G+g+S
  gi|118431383|ref|NP_147820.2| 131 LALRGFKVLAIDAAGHGES 149
                                    7789999999999999988 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.9e-05
                                    EEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S CS
                  Peptidase_S15 100 nGkVgmtGiSYlGttqllaaatgvpalkaivpeaais 136
                                     G ++++G+S +G t++ +a+  +pa++ +vp++a  
  gi|118431383|ref|NP_147820.2| 192 PGGIAVMGVSMGGLTSYTVAS-LHPAVALAVPIVASG 227
                                    699******************.99********99854 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 ?    9.8   1.0   0.00022      0.66      22      57 ..     193     228 ..     188     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00022
                                    SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB CS
                         BAAT_C  22 dkigllGiSkGgelalllasflkkisavvlingsav 57 
                                     +i+++G+S Gg +   +as ++++  +v i++s  
  gi|118431383|ref|NP_147820.2| 193 GGIAVMGVSMGGLTSYTVASLHPAVALAVPIVASGC 228
                                    68***************************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4383.20
//
Query:       gi|118431384|ref|NP_147821.2|  [L=326]
Description: zinc-binding dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-26   91.1   0.0    6.1e-26   90.4   0.0    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.9e-13   50.6   0.0    2.8e-13   50.0   0.0    1.2  1  ADH_zinc_N    Zinc-binding dehydrogenase
    9.5e-06   25.2   0.0    1.3e-05   24.8   0.0    1.2  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    2.5e-05   25.3   0.0    3.9e-05   24.7   0.0    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.043   13.4   0.0      0.077   12.6   0.0    1.4  1  IlvN          Acetohydroxy acid isomeroreductase, NADPH-bindi
       0.26   10.9   0.0       0.48   10.1   0.0    1.4  1  AAT           Acyl-coenzyme A:6-aminopenicillanic acid acyl-t


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0     2e-29   6.1e-26       2     104 ..      25     122 ..      24     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 2e-29
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                    g++l++ +a+giCg+D  +++g + +  k pl++GHE++Gev+e  +++    vG+rVv e++++c +C+ C+eg +++C
  gi|118431384|ref|NP_147821.2|  25 GWALVRSRAVGICGTDKAFYRG-TYPLFKKPLVPGHEVSGEVVEGPEDL----VGSRVVSEINFACLRCEVCREGLYTHC 99 
                                    799*******************.8********************66665....9************************** PP

                                    TTBEETTTSS-SSSBSEEEECGG CS
                          ADH_N  82 eeakllgvsldGgfaeyvvvpek 104
                                    +++k+lg+++dGg+aey+++p  
  gi|118431384|ref|NP_147821.2| 100 PRKKTLGIDFDGGMAEYFTAPPW 122
                                    ******************99865 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   9.2e-17   2.8e-13       4     129 ..     168     290 ..     166     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 9.2e-17
                                    HHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEE CS
                     ADH_zinc_N   4 laavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkllkpg 82 
                                    +++ q + a+G+   i++ +++ k+ + ++lG +++  +   + v++  e  gg g++ vfe++Gs++ l+ a++l++p+
  gi|118431384|ref|NP_147821.2| 168 HLTAQTLTAYGFkPAIVARPDSPKAVFFRRLGLEVLTPE---EAVKAASETPGGLGFHMVFETTGSNQGLSIATALARPR 244
                                    678999******77888899999*********6555555...69************************************ PP

                                    EEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  83 GrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                    G + v  +++ge +f+    + ke++++G+ +gs ++efkeal+ll+
  gi|118431384|ref|NP_147821.2| 245 GVVHVKSTPGGEAVFSQTLAVVKEIRLIGTRCGS-HREFKEALRLLE 290
                                    ***********999***9999*************.9********986 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 !   24.8   0.0   4.3e-09   1.3e-05      33     211 ..     157     325 ..     132     326 .] 0.79

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.3e-09
                    Glu_dehyd_C  33 salvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipea..seemdlvvEaTGs 110
                                     + vlG+G +  L++ +l+a   g++   +++r   ++p++ + ++lG    +  e+ v+  +e+     + +v+E+TGs
  gi|118431384|ref|NP_147821.2| 157 AVAVLGTGFMAHLTAQTLTA--YGFK-PAIVAR--PDSPKAVFFRRLGLEVLTP-EEAVKAASETpgGLGFHMVFETTGS 230
                                    468***************97..7998.568887..45689999*****998874.66777776661145789******** PP

                    Glu_dehyd_C 111 akhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtkvv 190
                                     + +  a+   +p Gv+     p +++v  ++ ++      +   l+G+   + r+f++a++ L++ +   ++  vtk  
  gi|118431384|ref|NP_147821.2| 231 NQGLSIATALARPRGVVHVKSTPGGEAVFSQTLAVV-----KEIRLIGTRCGSHREFKEALRLLESGE---VEPQVTKFR 302
                                    ****9999999*********9999987666655555.....55679**************99987655...7889***** PP

                    Glu_dehyd_C 191 dldeleeAfe..dddetiKtvve 211
                                     l+e+ eAfe   d e++K vv 
  gi|118431384|ref|NP_147821.2| 303 SLEEAPEAFEasLDRESMKIVVT 325
                                    *********83346788999986 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 !   24.7   0.0   1.3e-08   3.9e-05      16     121 ..     214     313 ..     200     324 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.3e-08
                                    HHH-TT-EEEEEES-HHHHH.HHHHHHE.EEEEEE.EE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHH CS
                   ADH_zinc_N_2  16 aatggegvDvvldtvggealleaslkvl.pggGrl.vsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileel 93 
                                    +  gg g+  v++t+g+++ l+ +  +l +++G + v    p      ++  + +  + vk   l+ ++ +  +++++e 
  gi|118431384|ref|NP_147821.2| 214 ETPGGLGFHMVFETTGSNQGLSIAT-ALaRPRGVVhVKS-TP-----GGEAVFSQTLAVVKEIRLIGTRCG-SHREFKEA 285
                                    4556789*********777755554.5547867763332.32.....333334455577777777766667.6777**** PP

                                    HHHHHHHH----EEEEEEGGGHHHHHHH CS
                   ADH_zinc_N_2  94 aalieeGklrpvvdrvfpleeaaeAhry 121
                                    ++l+e+G+++p v++  +leea+eA+++
  gi|118431384|ref|NP_147821.2| 286 LRLLESGEVEPQVTKFRSLEEAPEAFEA 313
                                    **************9999********97 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 ?   12.6   0.0   2.6e-05     0.077       6      61 ..     157     212 ..     154     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                    -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT- CS
                           IlvN   6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkka 61 
                                     +av+G G  +h  a+ l   g++ ++  r +s ++   ++ g+evlt +eavk+a
  gi|118431384|ref|NP_147821.2| 157 AVAVLGTGFMAHLTAQTLTAYGFKPAIVARPDSPKAVFFRRLGLEVLTPEEAVKAA 212
                                    69****************************************************98 PP

>> AAT  Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00016      0.48      73     108 ..     191     225 ..     182     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                    ----HHHHHHH.--SHHHHHHTHHHHTTTS-SEEEE CS
                            AAT  73 prafitRllLekcesveeAvellkeipraaginyiv 108
                                    ++ f++Rl Le   + eeAv+++ e p + g+++++
  gi|118431384|ref|NP_147821.2| 191 KAVFFRRLGLE-VLTPEEAVKAASETPGGLGFHMVF 225
                                    6789*******.*********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2656.07
//
Query:       gi|14601287|ref|NP_147822.1|  [L=871]
Description: hypothetical protein APE_1248 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (871 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.22s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 6370.25
//
Query:       gi|14601291|ref|NP_147826.1|  [L=306]
Description: hypothetical protein APE_1253 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-32  111.2   0.0    9.7e-32  110.3   0.0    1.4  1  ABC_tran      ABC transporter
    7.6e-11   42.4   0.3    4.2e-06   26.8   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.6e-06   26.2   0.0     0.0037   16.7   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
      2e-05   23.8   0.4      0.029   13.4   0.0    2.2  2  T2SSE         Type II/IV secretion system protein
    0.00052   19.9   0.0     0.0011   19.0   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
     0.0013   18.4   0.0     0.0027   17.4   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0016   18.8   2.8     0.0077   16.6   2.8    2.2  1  AAA_16        AAA ATPase domain
     0.0059   16.3   1.8      0.008   15.9   0.0    2.2  3  AAA_30        AAA domain
     0.0091   16.5   0.0      0.023   15.2   0.0    1.6  2  AAA_23        AAA domain
     0.0093   16.2   0.3      0.045   14.0   0.0    2.3  3  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.025   14.2   0.0    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.027   14.7   0.5       0.15   12.3   0.0    2.4  3  AAA_28        AAA domain
      0.031   14.2   0.0       0.58   10.1   0.0    2.2  2  NTPase_1      NTPase
      0.043   13.7   0.0      0.087   12.7   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
      0.044   13.7   0.2       0.13   12.1   0.1    1.8  2  NACHT         NACHT domain
      0.051   13.3   0.0        0.1   12.3   0.0    1.5  1  AAA_24        AAA domain
      0.051   13.5   0.0      0.086   12.7   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.054   13.1   3.6       0.19   11.3   0.2    2.4  2  AAA_25        AAA domain
      0.099   12.5   0.1       0.48   10.3   0.0    2.3  3  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.12   11.6   0.5       0.46    9.6   0.1    1.9  2  NB-ARC        NB-ARC domain
       0.14   11.6   0.0       0.34   10.3   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.14   12.4   0.2       0.71   10.2   0.0    2.0  2  AAA_19        AAA domain
       0.18   10.6   0.0       0.25   10.1   0.0    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
       0.19   11.8   0.1       0.49   10.5   0.1    1.7  1  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 !  110.3   0.0   1.3e-34   9.7e-32       1     136 [.      30     175 ..      30     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 1.3e-34
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvr 77 
                                   l++vsl++ +ge++ai+G++G+GK+tLl+++ag  +p++G++ +dg ++++    + +++  +++g+++q+++l p+lt+ 
  gi|14601291|ref|NP_147826.1|  30 LREVSLSVARGEVLAIMGPSGSGKTTLLNIIAGVDRPNAGRVIVDGFEVSSaggeELRRFRLERVGYVFQQHNLIPTLTAL 110
                                   679**********************************************999996666777799***************** PP

                                   HH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  78 en..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   en          + + + +++l+++gl +++ +      ++LSgG++qr+a+a al+++p+++++DEpt
  gi|14601291|ref|NP_147826.1| 111 ENillpmalagkANRLRGQELLRRVGLGGKERRYP----EELSGGEQQRLAVAVALANDPPIIVADEPT 175
                                   *********987666779***********666655....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2     6e-05     0.045       3      23 ..      44      64 ..      42      94 .. 0.74
   2 !   26.8   0.0   5.6e-09   4.2e-06     227     301 ..     138     210 ..      98     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                        AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                  ++ Gp gsGK++LL ++ ++ 
  gi|14601291|ref|NP_147826.1| 44 AIMGPSGSGKTTLLNIIAGVD 64
                                  789**************8873 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5.6e-09
                        AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                   g+   + + elS G ++ la+++al+ ++   ++++ DEp   L+ +  +r++++l +e++++g  v+ltTH+p +
  gi|14601291|ref|NP_147826.1| 138 GGKERRYPEELSGGEQQRLAVAVALANDP---PIIVADEPTGELDIATGERIVRILlEEAHSRGKTVVLTTHDPRV 210
                                   56666778889*******9*******999...*********************9998888889**********975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0033       2.5      25      44 ..      41      60 ..      29      63 .. 0.83
   2 !   16.7   0.0   4.9e-06    0.0037     134     210 ..     145     219 ..      90     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0033
                                  SEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                  ++ ai+Gp GSGK+ ll+ i
  gi|14601291|ref|NP_147826.1| 41 EVLAIMGPSGSGKTTLLNII 60
                                  5779**********998765 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-06
                                   TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvg 210
                                   +e+LSgGe++ +a+a+ +A    +  p+ + De   +LD +  ++++++l e+ ++    ++ ++++ ++ + ad++  
  gi|14601291|ref|NP_147826.1| 145 PEELSGGEQQRLAVAVALA----NDPPIIVADEPTGELDIATGERIVRILLEEAHSrgKTVVLTTHDPRVARMADRVAV 219
                                   569*******998888776....678*******************9998865443322556666677777776776654 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 !   13.4   0.0   3.9e-05     0.029     124     151 ..      35      62 ..      22      86 .. 0.79
   2 !    8.4   0.1    0.0013      0.98     132     198 ..     189     255 ..     179     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                         T2SSE 124 kavrerglilvsGgTgsGKttllyallk 151
                                    +v++  ++ + G+ gsGKttll+++  
  gi|14601291|ref|NP_147826.1|  35 LSVARGEVLAIMGPSGSGKTTLLNIIAG 62 
                                   456666777899************9865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                         T2SSE 132 ilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLRl 198
                                   il+  + + GKt++l +    ++   +r+ ++ED +   +  + +++  +  ++v+++++++a++R+
  gi|14601291|ref|NP_147826.1| 189 ILLEEAHSRGKTVVLTTHDPRVARMADRVAVIEDGRLRGVYSPSRIAGATGFGEVEAEKAVEAVMRR 255
                                   566666789***************************99999999999999999************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.4e-06    0.0011      96     123 ..      37      64 ..      13      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.4e-06
                                   HCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpel 123
                                   + ++++ +++G+SG GK+tL+n +++ +
  gi|14601291|ref|NP_147826.1|  37 VARGEVLAIMGPSGSGKTTLLNIIAGVD 64 
                                   45669******************99865 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 !   17.4   0.0   3.7e-06    0.0027      17      40 ..      35      58 ..      29      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                        AAA_29 17 ieidlkgatlltGpsGsGKSTllD 40
                                  +++ + ++  ++GpsGsGK+Tll 
  gi|14601291|ref|NP_147826.1| 35 LSVARGEVLAIMGPSGSGKTTLLN 58
                                  5666555999************95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.8     1e-05    0.0077       6      63 ..      24      79 ..      22     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                        AAA_16  6 eeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                  +e + +L+++  +v++g  e++ + G+sG+GK++l++ ++  + + + g ++   ++ +
  gi|14601291|ref|NP_147826.1| 24 GERIVALREVSLSVARG--EVLAIMGPSGSGKTTLLNIIA-GVDRPNaGRVIVDGFEVS 79
                                  55556666666667777..89***************9988.455554466666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05     0.008      17      51 ..      40      73 ..      12     128 .. 0.89
   2 ?   -2.0   0.0       3.4   2.5e+03     105     121 ..     187     203 ..     147     214 .. 0.67
   3 ?   -2.2   0.2       3.9   2.9e+03     157     184 ..     259     288 ..     242     295 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                        AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                  g  v ++ Gp G+GKtt+l+ ++ + + + grvi+
  gi|14601291|ref|NP_147826.1| 40 G-EVLAIMGPSGSGKTTLLNIIAGVDRPNAGRVIV 73
                                  3.4999******************99999778875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.4
                        AAA_30 105 laallkaaekagakvil 121
                                   ++ ll++a+++g +v+l
  gi|14601291|ref|NP_147826.1| 187 VRILLEEAHSRGKTVVL 203
                                   34455555555555554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.9
                        AAA_30 157 qkeseeraaalalregdae..ealealadr 184
                                    +e + r+a +++r+g++   + +e + + 
  gi|14601291|ref|NP_147826.1| 259 DAERRLREAEDRFRRGEVGidALVETYTRV 288
                                   345677788888888888764444555444 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   3.1e-05     0.023      21      40 ..      42      61 ..      26      63 .. 0.86
   2 ?   -2.6   0.0       8.6   6.4e+03     174     174 ..     269     269 ..     226     302 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.1e-05
                        AAA_23 21 ltlItGpNGaGKTTildAik 40
                                  + +I Gp G+GKTT+l+ i 
  gi|14601291|ref|NP_147826.1| 42 VLAIMGPSGSGKTTLLNIIA 61
                                  568*************9885 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.6
                        AAA_23 174 k 174
                                   +
  gi|14601291|ref|NP_147826.1| 269 D 269
                                   1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     6e-05     0.045       6      23 ..      41      58 ..      37      93 .. 0.90
   2 ?   -1.7   0.0       4.4   3.3e+03      60      99 ..     131     173 ..     114     203 .. 0.58
   3 ?   -2.0   0.0       5.5   4.1e+03      96     104 ..     256     265 ..     242     303 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-05
                        AAA_22  6 gilvvtGesGtGKTtllr 23
                                   +l+++G+sG+GKTtll+
  gi|14601291|ref|NP_147826.1| 41 EVLAIMGPSGSGKTTLLN 58
                                  6899************97 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                        AAA_22  60 llralglelkaerlsseell.ealeqalrarav...ielliiDE 99 
                                   llr +gl++k+ r   eel     ++ + a a    +++++ DE
  gi|14601291|ref|NP_147826.1| 131 LLRRVGLGGKE-RRYPEELSgGEQQRLAVAVALandPPIIVADE 173
                                   55555555555.33333333222222222222233455555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.5
                        AAA_22  96 iiDEaqh.lr 104
                                   i+D+a++ lr
  gi|14601291|ref|NP_147826.1| 256 ILDDAERrLR 265
                                   4444444442 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   0.0   3.4e-05     0.025       2      33 ..      42      73 ..      41      89 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                                  EEEEEESTTCCHHHHHHHHHCT--SS-EEEEE CS
                          cobW  2 vtvltGflGsGKTtLlnhllenraglklaviv 33
                                  v+ + G+ GsGKTtLln +    + +   viv
  gi|14601291|ref|NP_147826.1| 42 VLAIMGPSGSGKTTLLNIIAGVDRPNAGRVIV 73
                                  67899************998555555555555 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    0.0002      0.15       3      21 ..      44      64 ..      42     102 .. 0.76
   2 ?   -1.7   0.0         4     3e+03     145     145 ..     194     194 ..     141     224 .. 0.61
   3 ?   -1.0   0.2       2.4   1.8e+03      55      70 ..     252     267 ..     232     298 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                        AAA_28  3 vitGgestGKTtlleaLa..a 21
                                  +i+G++++GKTtll+ +a  +
  gi|14601291|ref|NP_147826.1| 44 AIMGPSGSGKTTLLNIIAgvD 64
                                  79*************999441 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4
                        AAA_28 145 l 145
                                    
  gi|14601291|ref|NP_147826.1| 194 A 194
                                   2 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.4
                        AAA_28  55 faervleeqleeeaaa 70 
                                   + +r+l+ + +++++a
  gi|14601291|ref|NP_147826.1| 252 VMRRILDDAERRLREA 267
                                   3333333333333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00078      0.58       2      36 ..      43      79 ..      42      95 .. 0.74
   2 ?    1.7   0.0      0.28   2.1e+02      94     152 ..     164     225 ..     130     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00078
                                  EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEE CS
                      NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyte 36
                                  ++i Gp+G+GKtTl++ ++ + + +   v v+Gf ++
  gi|14601291|ref|NP_147826.1| 43 LAIMGPSGSGKTTLLNIIAGVDRPNagRVIVDGFEVS 79
                                  5789***********9998665433225778888665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.28
                                   HHH-EEEE--.-STTGGG-HH..HHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EE CS
                      NTPase_1  94 seadviviDE.iGkmElkskk..fkeaveevLksekpvlavihrrkdlalveeirerkdvkv 152
                                   +++ +iv DE  G++   + +  ++  +ee+ +++k v+ + h ++  ++ +++   +d+++
  gi|14601291|ref|NP_147826.1| 164 NDPPIIVADEpTGELDIATGEriVRILLEEAHSRGKTVVLTTHDPRVARMADRVAVIEDGRL 225
                                   56668888886677776653311344456666689999999999987778888777666665 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 ?   12.7   0.0   0.00012     0.087       7      41 ..      29      61 ..      24      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                      ATPase_2  7 elkeleeilerepneiyfiYGpegsGKtaLlkeii 41
                                  +l+e+   + r   e++ i Gp gsGKt+Ll+ i+
  gi|14601291|ref|NP_147826.1| 29 ALREVSLSVAR--GEVLAIMGPSGSGKTTLLNIIA 61
                                  56666555555..7899**************9776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00018      0.13       2      21 ..      42      61 ..      41      63 .. 0.89
   2 ?   -3.0   0.0         8     6e+03     111     134 ..     189     212 ..     179     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                  CEEEEC-TTTCHHHHHHHHH CS
                         NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                  ++++ G++GsGKTtLl  +a
  gi|14601291|ref|NP_147826.1| 42 VLAIMGPSGSGKTTLLNIIA 61
                                  7899************8776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8
                                   HHHCTTTTT--EEEEEEECCCHHH CS
                         NACHT 111 elirkkllpeasllltvrpralrd 134
                                    l+++++ ++ +++lt++  ++ +
  gi|14601291|ref|NP_147826.1| 189 ILLEEAHSRGKTVVLTTHDPRVAR 212
                                   577788888888888887766655 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   0.00014       0.1       4      22 ..      42      60 ..      39      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                        AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   ++i+Gpsg+GKTtl++ +
  gi|14601291|ref|NP_147826.1| 42 VLAIMGPSGSGKTTLLNII 60
                                  689************9876 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   0.00012     0.086      35      66 ..      30      61 ..      18      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                         Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  l+  +L  ++ ++L i GPsG gk+t +++++
  gi|14601291|ref|NP_147826.1| 30 LREVSLSVARGEVLAIMGPSGSGKTTLLNIIA 61
                                  556678888889****************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00026      0.19      31      50 ..      38      57 ..      33      88 .. 0.93
   2 ?    2.3   0.4      0.14   1.1e+02      56     135 ..     179     254 ..     177     292 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                        AAA_25 31 pagelallaGapgtGKttla 50
                                  ++ge+ +++G++g+GKttl+
  gi|14601291|ref|NP_147826.1| 38 ARGEVLAIMGPSGSGKTTLL 57
                                  79****************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                        AAA_25  56 avatGkpwlg...pvapeqgkVlyvsaEdsed.elrrRlravgealrddarllvldlagveslpLfakdrggtlltadvda 132
                                   ++atG+       + a+ +gk++++ + d++  +++ R++ +        rl+ ++ ++   +   a+++g+  ++ +v+a
  gi|14601291|ref|NP_147826.1| 179 DIATGERIVRillEEAHSRGKTVVLTTHDPRVaRMADRVAVIEDG-----RLRGVYSPS---RIAGATGFGEVEAEKAVEA 251
                                   678888887788855678999999999999633667777655544.....344443222...1222222233223333333 PP

                        AAA_25 133 lea 135
                                   +++
  gi|14601291|ref|NP_147826.1| 252 VMR 254
                                   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 ?   10.3   0.0   0.00064      0.48       1      18 [.      42      59 ..      42      85 .. 0.90
   2 ?   -2.5   0.0         6   4.5e+03      10      33 ..     197     220 ..     190     222 .. 0.71
   3 ?   -2.5   0.0       5.9   4.4e+03      74      99 ..     256     285 ..     233     300 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                          MobB  1 vlgivgksgsGKTtLlek 18
                                  vl+i+g sgsGKTtLl+ 
  gi|14601291|ref|NP_147826.1| 42 VLAIMGPSGSGKTTLLNI 59
                                  799************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6
                          MobB  10 sGKTtLleklipelkarglrvgti 33 
                                    GKT  l+   p +++   rv++i
  gi|14601291|ref|NP_147826.1| 197 RGKTVVLTTHDPRVARMADRVAVI 220
                                   688888887777777776666666 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.9
                          MobB  74 l.eeaelsleellarlse....vDlvlvEGf 99 
                                   + ++ae +l+e  +r+++    +D  lvE +
  gi|14601291|ref|NP_147826.1| 256 IlDDAERRLREAEDRFRRgevgID-ALVETY 285
                                   345555555555555533333333.244444 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00062      0.46      22      40 ..      42      60 ..      32      64 .. 0.87
   2 ?   -0.9   0.0         1   7.7e+02     127     147 ..     194     214 ..     181     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                                  EEEEEESTTSSHHHHHHHH CS
                        NB-ARC 22 vvalvGmgGvGKttlakqi 40
                                  v+a++G  G+GKttl++ i
  gi|14601291|ref|NP_147826.1| 42 VLAIMGPSGSGKTTLLNII 60
                                  89*************8755 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                   HCHTTSEEEEEESBCCCCCCS CS
                        NB-ARC 127 arenrlrvllTTRdeevanav 147
                                   a++++  v+lTT d  va  +
  gi|14601291|ref|NP_147826.1| 194 AHSRGKTVVLTTHDPRVARMA 214
                                   567788899****99997654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00046      0.34      13      64 ..      31      82 ..      22     105 .. 0.75
   2 ?   -2.8   0.0       4.6   3.4e+03       4      21 ..     147     164 ..     141     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                  Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasva 64
                                  r + +++a g  l ++Gp+GsGKt l + ++++  p   + +++  +++s  
  gi|14601291|ref|NP_147826.1| 31 REVSLSVARGEVLAIMGPSGSGKTTLLNIIAGVDRPNAGRVIVDGFEVSSAG 82
                                  6678888999999*************99998886666666666666655555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.6
                  Mg_chelatase   4 dvkGqeeakraleiaaaG 21 
                                   ++ G e+++ a+ +a a 
  gi|14601291|ref|NP_147826.1| 147 ELSGGEQQRLAVAVALAN 164
                                   455666666666666654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00095      0.71       8      30 ..      38      60 ..      31      70 .. 0.85
   2 ?   -0.1   0.0       1.4   1.1e+03       3      63 ..     156     218 ..     154     287 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                        AAA_19  8 lkekvllvtaGpGtGKTrvlkhi 30
                                  ++ +vl+++++ G+GKT++l+ i
  gi|14601291|ref|NP_147826.1| 38 ARGEVLAIMGPSGSGKTTLLNII 60
                                  567899************99876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                        AAA_19   3 eave.alkekvllvtaGpGtGKTrvl..khivallvelggvkpeeillvaftgrAakelrerla 63 
                                    av+ al++++ +++a   tG   +   + iv++l+e+ +   ++++l +     + ++++r+a
  gi|14601291|ref|NP_147826.1| 156 LAVAvALANDPPIIVADEPTGELDIAtgERIVRILLEEAHSRGKTVVLTTHDP-RVARMADRVA 218
                                   55555666666666666556654443114566666666665544444444443.3456666664 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00034      0.25      26      56 ..      41      71 ..      29      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                          DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGrG 56
                                    + ++G +gsGkttl+  + Gv+ ++ Gr 
  gi|14601291|ref|NP_147826.1| 41 EVLAIMGPSGSGKTTLLNIIAGVDRPNAGRV 71
                                  45669********************999985 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   0.1   0.00066      0.49       2      21 ..      43      62 ..      42      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                                  EEEEESTTSSHHHHHHHHHT CS
                      MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   ai+G + +GK+tL+n + g
  gi|14601291|ref|NP_147826.1| 43 LAIMGPSGSGKTTLLNIIAG 62
                                  58**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2152.50
//
Query:       gi|118431385|ref|NP_147827.2|  [L=249]
Description: hypothetical protein APE_1255.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-25   88.3   0.0    8.7e-25   87.8   0.0    1.2  1  ABC_tran         ABC transporter
    4.7e-16   59.5   0.0    1.7e-08   34.6   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.2e-05   23.1   0.0        0.2   11.1   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0052   16.5   0.0     0.0065   16.2   0.0    1.4  1  AAA_30           AAA domain
     0.0069   16.9   0.0       0.01   16.3   0.0    1.2  1  AAA_23           AAA domain
     0.0078   16.5   0.0      0.018   15.3   0.0    1.7  1  AAA_22           AAA domain
     0.0097   15.5   0.0      0.015   14.9   0.0    1.2  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.018   15.4   0.0      0.024   15.0   0.0    1.4  1  AAA_16           AAA ATPase domain
       0.04   14.1   0.0      0.071   13.3   0.0    1.5  1  AAA_33           AAA domain
      0.062   13.1   0.0       0.14   11.9   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.063   12.9   0.0        0.1   12.2   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.087   11.8   0.2       0.14   11.2   0.2    1.2  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.092   12.8   0.0       0.18   11.9   0.0    1.4  1  MMR_HSR1         50S ribosome-binding GTPase
       0.11   12.0   0.1       0.44   10.1   0.1    1.9  2  AAA_25           AAA domain
       0.18   11.7   0.0       0.29   11.0   0.0    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
        0.2   10.7   0.1       0.39    9.7   0.0    1.4  2  T2SSE            Type II/IV secretion system protein
       0.24   11.1   0.0        0.4   10.3   0.0    1.4  1  Thymidylate_kin  Thymidylate 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 !   87.8   0.0   8.2e-28   8.7e-25       1     137 []      24     166 ..      24     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 8.2e-28
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    lk+vsl++ +g+++++vG+nGaGK+tL+++l+gl++ + G++ l g+++++    sl +++++lp++ +  +++t +e  
  gi|118431385|ref|NP_147827.2|  24 LKDVSLTVPRGSVYGVVGPNGAGKTTLFRTLLGLYRADRGRVALLGEPVER-AGGSLFRRVAYLPEDGEPYRNMTGHEFl 102
                                    79*************************************************.88888899**************99999* PP

                                    ......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                          +  e++e +l++ +       +++++ +s+S+G+++r+ +a++l+ kp+l +lDEpta
  gi|118431385|ref|NP_147827.2| 103 rlyasiYGVEDLEGYLEEASRLSGLGGRLGERVRSYSKGMRRRLLVAAMLALKPSLAVLDEPTA 166
                                    9*9998555557777766666666666777777*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.3e-08   4.6e-05       2      29 ..      37      67 ..      36      94 .. 0.72
   2 !   34.6   0.0   1.6e-11   1.7e-08     195     301 ..     128     200 ..      80     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.3e-08
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdv 29
                                    +++GpNg+GK++L+++l +l r+   +  +
  gi|118431385|ref|NP_147827.2| 37 YGVVGPNGAGKTTLFRTLLGLYRAdrgRVAL 67
                                   579******************9875554444 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 1.6e-11
                         AAA_21 195 veielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                     +                                     +r+ S G++r   l++a+l++ +  sl ++DEp +gL+P  
  gi|118431385|ref|NP_147827.2| 128 GGR--------------------------------LGERVRSYSKGMRRR-LLVAAMLALKP--SLAVLDEPTAGLDPVY 172
                                    433................................33445778*******.77777776665..9*************** PP

                         AAA_21 275 lrrllellkelsr.ngaQviltTHSpll 301
                                       + +llke s+ +g+ v+l++H+ + 
  gi|118431385|ref|NP_147827.2| 173 SVGIRRLLKEYSErHGVTVLLSSHNMYE 200
                                    ********888888**********9875 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 !    9.9   0.0   0.00042      0.45      26      44 ..      36      54 ..      25      65 .. 0.83
   2 !   11.1   0.0   0.00019       0.2     150     215 ..     148     212 ..     140     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                   +  +vGpNG+GK+ l+  +
  gi|118431385|ref|NP_147827.2| 36 VYGVVGPNGAGKTTLFRTL 54
                                   6679**********99876 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                                    HHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 150 lfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkve 215
                                    + A+ + kp +l +lDe  a LD  +   + +llke s++  + v   +++m+e  + +  +t+ +
  gi|118431385|ref|NP_147827.2| 148 VAAMLALKP-SLAVLDEPTAGLDPVYSVGIRRLLKEYSERHGVTVLLSSHNMYEVESVCSEITMIS 212
                                    334555555.699*****************************************999999999865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.2e-06    0.0065      19      53 ..      35      69 ..      27     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.2e-06
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglA 53
                                    v  ++Gp G+GKtt+ ++l  +++a+ grv++l 
  gi|118431385|ref|NP_147827.2| 35 SVYGVVGPNGAGKTTLFRTLLGLYRADRGRVALLG 69
                                   57789**********************98999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.9e-06      0.01      21      38 ..      36      53 ..      25      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-06
                         AAA_23 21 ltlItGpNGaGKTTildA 38
                                   ++ ++GpNGaGKTT+++ 
  gi|118431385|ref|NP_147827.2| 36 VYGVVGPNGAGKTTLFRT 53
                                   56789**********975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.018       9      91 ..      38     140 ..      33     199 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee................erpevv..fvtlpsst......sskdllrellral 64 
                                     v+G+ G+GKTtl r+ll  + ++    +                     +    +lp+++      +  ++lr  ++++
  gi|118431385|ref|NP_147827.2|  38 GVVGPNGAGKTTLFRTLLGLYRAD----RgrvallgepveraggsL----FrrVAYLPEDGepyrnmTGHEFLRLYASIY 109
                                    599***************998432....233557776666544431....133233333333444557777777777777 PP

                         AAA_22  65 glelka....erlsseellealeqalrarav 91 
                                    g+e  +    e  +++ l  +l + +r++++
  gi|118431385|ref|NP_147827.2| 110 GVEDLEgyleEASRLSGLGGRLGERVRSYSK 140
                                    7766667776333333333444444444443 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 !   14.9   0.0   1.4e-05     0.015       2      30 ..      36      66 ..      35      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                   EEEEEESTTCCHHHHHHHHH..CT--SS-EE CS
                           cobW  2 vtvltGflGsGKTtLlnhll..enraglkla 30
                                   v++++G+ G+GKTtL ++ll   +++  ++a
  gi|118431385|ref|NP_147827.2| 36 VYGVVGPNGAGKTTLFRTLLglYRADRGRVA 66
                                   7899***************986444444555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.3e-05     0.024      25      63 ..      35      74 ..      23     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                   ++  ++G+ G GK++l r+ll  +++d+g + l g+ ++ 
  gi|118431385|ref|NP_147827.2| 35 SVYGVVGPNGAGKTTLFRTLLGLYRADRGRVaLLGEPVER 74
                                   56669****************9999998777688877776 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       4      32 ..      39      72 ..      36     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                         AAA_33  4 lvGlpGsGKstlaerllkklg.....avllssdt 32
                                   +vG++G+GK+tl + ll         + ll +++
  gi|118431385|ref|NP_147827.2| 39 VVGPNGAGKTTLFRTLLGLYRadrgrVALLGEPV 72
                                   79************99632222234566666666 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 ?   11.9   0.0   0.00013      0.14      19      39 ..      31      51 ..      22      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                         AAA_29 19 idlkg.atlltGpsGsGKSTll 39
                                   +  +g ++ ++Gp+G+GK+Tl+
  gi|118431385|ref|NP_147827.2| 31 VP-RGsVYGVVGPNGAGKTTLF 51
                                   44.4448889**********97 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.8e-05       0.1       3      43 ..      36      76 ..      34      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.8e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTT CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaa 43
                                   v+ +vG++GaGKTt    L  l++++  +v+l    + Ra+
  gi|118431385|ref|NP_147827.2| 36 VYGVVGPNGAGKTTLFRTLLGLYRADRGRVALLGEPVERAG 76
                                   5668****************999999999988776666665 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 ?   11.2   0.2   0.00013      0.14      18      76 ..      23      79 ..       9      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                   HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------- CS
                           MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsi 76
                                   +l+ ++ +  r  v G+ G  GaGk tl   l   +r+   rva+l  +P  +++GGs+
  gi|118431385|ref|NP_147827.2| 23 VLKDVSLTVPRGSVYGVVGPNGAGKTTLFRTLLGLYRADRGRVALLG-EP-VERAGGSL 79
                                   678888888999*******************99999999999*9986.44.35566665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.18       3      22 ..      38      57 ..      36      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                   EEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                   ++vG   +GK+tL+++l+g 
  gi|118431385|ref|NP_147827.2| 38 GVVGPNGAGKTTLFRTLLGL 57
                                   79***************984 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00042      0.44      23      50 ..      21      51 ..      19      75 .. 0.86
   2 ?   -1.3   0.0       1.3   1.3e+03     172     188 ..     180     196 ..     177     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                         AAA_25 23 rwlvkg...llpagelallaGapgtGKttla 50
                                   rw++k+    +p+g++  ++G+ g+GKttl 
  gi|118431385|ref|NP_147827.2| 21 RWVLKDvslTVPRGSVYGVVGPNGAGKTTLF 51
                                   67777655568******************95 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                         AAA_25 172 leriarrtgaavllvhH 188
                                    l++ ++r+g++vll  H
  gi|118431385|ref|NP_147827.2| 180 LKEYSERHGVTVLLSSH 196
                                    5677899******9998 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 ?   11.0   0.0   0.00027      0.29       2      33 ..      37      68 ..      36      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                           MobB  2 lgivgksgsGKTtLleklipelkarglrvgti 33
                                    g+vg +g+GKTtL   l+   +a   rv+++
  gi|118431385|ref|NP_147827.2| 37 YGVVGPNGAGKTTLFRTLLGLYRADRGRVALL 68
                                   589******************99999999875 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 ?    9.7   0.0   0.00037      0.39     134     168 ..      39      73 ..      28      78 .. 0.92
   2 ?   -3.5   0.0       4.1   4.4e+03     110     138 ..     218     246 ..     207     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                          T2SSE 134 vsGgTgsGKttllyallkeinksderivtvEDpvE 168
                                    v G+ g GKttl  +ll    ++  r+ ++  pvE
  gi|118431385|ref|NP_147827.2|  39 VVGPNGAGKTTLFRTLLGLYRADRGRVALLGEPVE 73 
                                    78*************************99999998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.1
                          T2SSE 110 aeealkekiaevlrkavrerglilvsGgT 138
                                    ++++  e+++++ +++++e ++ lv+Gg 
  gi|118431385|ref|NP_147827.2| 218 YSGSPGEAVRRTGASSLEEAYVALVTGGG 246
                                    55555566666666777777888999986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00038       0.4       3      47 ..      41      85 ..      39     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                                   ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll 47
                                   G +GaGKtt  ++l   +++   +v l  ep +   G+++r++  
  gi|118431385|ref|NP_147827.2| 41 GPNGAGKTTLFRTLLGLYRADRGRVALLGEPVERAGGSLFRRVAY 85
                                   899***************999988999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1791.69
//
Query:       gi|14601293|ref|NP_147828.1|  [L=439]
Description: hypothetical protein APE_1257 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-13   48.5   6.1      1e-12   47.8   6.1    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    3.6e-06   26.5  16.1    1.8e-05   24.2  16.1    2.2  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.072   12.6   0.2      0.072   12.6   0.2    2.6  3  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 !   47.8   6.1   1.7e-16     1e-12      15     338 ..      45     401 ..      23     407 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.7e-16
               ABC2_membrane_3  15 vlllglifsnsve..ddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdidgilvipkgfskdl 93 
                                   ++++g+i  ++ +   +    +avvd+d+++lsq +++al a         + s eea     + ++ ++lvip+gf  +l
  gi|14601293|ref|NP_147828.1|  45 AIFAGSITPQTGSggIPGLEGLAVVDLDGTPLSQAVATALGAAA-------AGSVEEAL----QAGYKMVLVIPEGFASTL 114
                                   2222222222222122444445********************55.......56688884....689*************** PP

               ABC2_membrane_3  94 lkgesatvtvlinssnlnss.............kailnalnsllqqlnasalvlqseatstsaninvestql.eeelsnva 160
                                   +kg +a ++++i++  ++ s              a++ a++ l +q ++           +++ + ve+ +l   e + + 
  gi|14601293|ref|NP_147828.1| 115 QKGGQARLELYIQAGEVLRSqgllgffsysglsGALEGAVDLLAKQALGI--------PTAEDLVRVEEKPLgILEGNPAS 187
                                   ************99999888789998887666555555555555554433........33566677777777433334444 PP

               ABC2_membrane_3 161 sflvgliliilifitasfiav....siveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...l..afgl. 231
                                   + lv ++l++++fit+sf+++     +  ++e+r++el+l +++++  y+ +++ g + ++ + ll + +   +  +++  
  gi|14601293|ref|NP_147828.1| 188 HLLVLFMLLMASFITGSFLLQvsaiTVGYDREQRTLELLLATPLRTRGYVAVRLAGAASMASVGLLSLAAsllImmVYAAv 268
                                   4455577777788998888886665778*************************8777666665554433332234344446 PP

               ABC2_membrane_3 232 ..........................gipfgnlglllllfllfglayialgyllssl....fknsetaqilifivilllsg 282
                                                             + + g+++++l  + + +l +++lg+ l+++    +k++ ta+++ +++++ +++
  gi|14601293|ref|NP_147828.1| 269 ripqevgggvtsgelasllgeaaerlAPTPGQVLVALASIAVTALYTLTLGLILGFVgagdVKSAQTASGMSVFILF-ILL 348
                                   99**********************766666699************************97777777777765555555.666 PP

               ABC2_membrane_3 283 ffgglfpledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavv 338
                                   + ++ +p+  lp+a+   + + P++a   + l  ++gd+ + i++    la++a++
  gi|14601293|ref|NP_147828.1| 349 LPLAAIPFR-LPHAIP--LALHPITAAPAAYLAYANGDYAMAIGMLASTLAGSALA 401
                                   666666665.666555..66777777778888888888555555444444444444 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 !   24.2  16.1   2.9e-09   1.8e-05       6     253 ..      13     383 ..      10     418 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.9e-09
               ABC2_membrane_2   6 kEfrdlvrsrrfllltvllpli......................dvalaylkdlgsslqseakaikeatlaleyveaasas 64 
                                   kE+++ +r+r++l + v+ p +                       + +  l+ l+  +  + +  ++ ++al +++a+s +
  gi|14601293|ref|NP_147828.1|  13 KELKEVLRDRTLLFNLVISPMLgvvvwivvveaifagsitpqtgSGGIPGLEGLAVVDLDGTPLSQAVATALGAAAAGSVE 93 
                                   9*******************************************999*********************************9 PP

               ABC2_membrane_2  65 deaedtdqdlkv..................................................................... 76 
                                   +++++++++  v                                                                     
  gi|14601293|ref|NP_147828.1|  94 EALQAGYKMVLVipegfastlqkggqarlelyiqagevlrsqgllgffsysglsgalegavdllakqalgiptaedlvrve 174
                                   999999999988********************************************************************* PP

               ABC2_membrane_2  77 ...................vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiaval 138
                                                      + ++++++ + + +  +a  +  ++e++Tl+llL++P   + +++  + g + ++ +++++l
  gi|14601293|ref|NP_147828.1| 175 ekplgilegnpashllvlfMLLMASFITGSFLLQVSAITVGYDREQRTLELLLATPLRTRGYVAVRLAGAASMASVGLLSL 255
                                   ***************9997667777888888999999999999**************999999999887776655588888 PP

               ABC2_membrane_2 139 latvll.......................alaiilalgivlaledllllvvasvlllllvvflalglllSsv....arssr 192
                                    a++l+                       +l+  +a   +++ +++l+ ++++ +++l++  l+lgl l  v    ++s++
  gi|14601293|ref|NP_147828.1| 256 AASLLImmvyaavripqevgggvtsgelaSLLGEAAERLAPTPGQVLVALASIAVTALYT--LTLGLILGFVgagdVKSAQ 334
                                   888888*******************99877777777777777788887777777777755..8899999988444456666 PP

               ABC2_membrane_2 193 eaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilags 253
                                   +a  ++++++++l++    + +++  +              + l p+ a  +++ +  +g+
  gi|14601293|ref|NP_147828.1| 335 TASGMSVFILFILLLPLAAIPFRLPHAIP------------LALHPITAAPAAYLAYANGD 383
                                   66666666666666666555555444443............33445555555555555544 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 ?   -3.1   0.3      0.82   4.9e+03     180     190 ..      33      43 ..      18      52 .. 0.41
   2 ?   12.6   0.2   1.2e-05     0.072      36     112 ..     194     269 ..     186     287 .. 0.71
   3 ?   -0.6   2.9      0.14   8.4e+02      90     137 ..     304     351 ..     299     358 .. 0.49

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.82
               ABC2_membrane_5 180 yilliillvii 190
                                   ++ +++ +v++
  gi|14601293|ref|NP_147828.1|  33 MLGVVVWIVVV 43 
                                   22222222222 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.2e-05
               ABC2_membrane_5  36 vllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvt 112
                                   +ll+ s+++  ++ ++   t+ yD+ +++  +ll +P++ + +V+ +  +++ +  +++l  l++++++++++  v 
  gi|14601293|ref|NP_147828.1| 194 MLLMASFITGSFLLQVSAITVGYDREQRTLELLLATPLRTRGYVAVRLAGAASMASVGLLS-LAASLLIMMVYAAVR 269
                                   2344555555555555557899*************************77776665555554.455555666666554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.14
               ABC2_membrane_5  90 iliailitlllliiavlikgnvtisevllsiliglvialiflaivlPl 137
                                    l++i +t+l+++  +li g v   +v  + +++ + ++i+++++lPl
  gi|14601293|ref|NP_147828.1| 304 ALASIAVTALYTLTLGLILGFVGAGDVKSAQTASGMSVFILFILLLPL 351
                                   344444444444446666666555555444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3160.13
//
Query:       gi|118431386|ref|NP_147829.2|  [L=184]
Description: hypothetical protein APE_1258.1 [Aeropyrum pernix K1]
Scores for complete 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   74.5   8.0    1.1e-20   74.5   8.0    1.4  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 !   74.5   8.0   6.4e-25   1.1e-20       1     130 [.       8     142 ..       8     143 .. 0.94
   2 ?   -2.4   0.0      0.39     7e+03      10      21 ..     149     160 ..     147     179 .. 0.47

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 6.4e-25
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...CCC.HHHHHH CS
                    Hemerythrin   1 aivealdeeHralrallerlraladaaaevhga...lrklaelldelvdeleaHhaaEEellfPlle..drpggravldv 75 
                                    + v+ l ++Hr++++ l+ l++++d +a+ + +     +la++l+e++d    Hha+EE+ lfP +e  ++p  ++++++
  gi|118431386|ref|NP_147829.2|   8 HLVDSLVDDHRYILQALDLLEEAVDLMARGRLPpstVGRLARFLEEFADG--CHHAKEEAALFPCMEarGHPFREGGIER 85 
                                    578999********************77777777****************..**************************** PP

                                    HHHHHHHHHHHHHHHHHHCHTCG..GSTCHHHHHHHHHHHHHHHHHHHHHHHTHHHH CS
                    Hemerythrin  76 lereHdeirelleelrellkgle..epsaaafaelleeladllreHiakEesilfpl 130
                                    l+ eH ++r ll++l++ l++le  e+s + +++ ++++ +l+r+Hi++E+ +lf +
  gi|118431386|ref|NP_147829.2|  86 LTCEHGVARYLLRGLQRELERLErgEGSVEKARDYAARYVELIRRHIDVEDLELFER 142
                                    ****************999999977778888888********************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.39
                                    HHHHHHHHHHHH CS
                    Hemerythrin  10 Hralrallerlr 21 
                                    H +++++++r++
  gi|118431386|ref|NP_147829.2| 149 HGEMLEEARRID 160
                                    555555555442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1456.87
//
Query:       gi|14601295|ref|NP_147830.1|  [L=209]
Description: hypothetical protein APE_1260 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-28  100.6   5.1    1.4e-28  100.3   5.1    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
      1e-06   28.4   0.2    1.3e-06   28.0   0.2    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.088   12.7   0.0        0.1   12.5   0.0    1.2  1  Lactamase_B_3  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 !  100.3   5.1   2.3e-32   1.4e-28       2     197 .]      10     188 ..       9     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 2.3e-32
                                   CCCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                   Lactamase_B   2 gpdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                   g+++vn+y+   +g+++++D+G+++  + +      ++l+ +d+  v lTH+H+DH++g+++l+ +  v+ ++ +    a 
  gi|14601295|ref|NP_147830.1|  10 GVLQVNTYVAAAGGECLVVDPGGPEVLEAL------ERLGCRDI-VVALTHGHFDHVAGVEHLAARGAVVAAHPQTPRVAE 83 
                                   789************************998......57777777.578********************************* PP

                                   HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC. CS
                   Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridlt 163
                                    +  ++   ++ +    gv+++++dv + ++ + ++ +++l+++++pgh+++h+v++++ ++++ftGD++++g++gr+d  
  gi|14601295|ref|NP_147830.1|  84 AYADLGVKMGYLK----GVPRISVDVELVDGSTLRAAGLSLKAIHTPGHSPDHIVLYDQARGLAFTGDLIFRGSIGRVDIA 160
                                   *****99999985....7**************************************************************9 PP

                                   TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                   Lactamase_B 164 lrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                   l+++e++ +s+a+  +       +l+  ++++ gH
  gi|14601295|ref|NP_147830.1| 161 LGDGEAMARSLARIVR-------ELPRGTRLLpGH 188
                                   9999999999998888.......555555444488 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 !   28.0   0.2   2.2e-10   1.3e-06      30     143 ..      46     148 ..      26     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.2e-10
                                   SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT.TTEEEEEE-....TTSEEEECSTTEEE CS
                 Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee.pavnvheld....wgesfelgdgglei 105
                                   +i  V lth+H+DH+ag+ +l++ r+  + + a++++ +v ea  +  ++    ++v++  +d     g +++ +  gl++
  gi|14601295|ref|NP_147830.1|  46 DIV-VALTHGHFDHVAGVEHLAA-RG--AVVAAHPQTPRVAEAYADLGVKMGYlKGVPRISVDvelvDGSTLRAA--GLSL 120
                                   555.99*****************.33..23447777777777765544444446344444444333245555555..899* PP

                                   EEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS- CS
                 Lactamase_B_2 106 tatparhksgrrldrnagdtlGlriegggkrvyyigDt 143
                                   +a+  ++ s+             ++ ++ + ++++gD+
  gi|14601295|ref|NP_147830.1| 121 KAIHTPGHSPD----------HIVLYDQARGLAFTGDL 148
                                   ********999..........34444444555555554 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 ?   12.5   0.0   1.7e-05       0.1       5      67 ..      12      74 ..       8     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                 Lactamase_B_3  5 lghnsflletagarilvDPfkanlgyeppa.eeaD.lvlisqaledHah.letlkqlaenvkvlee 67
                                  l  n+++   +g  ++vDP+ +++  + ++    D +v +++++ dH + +e l++   +  v++ 
  gi|14601295|ref|NP_147830.1| 12 LQVNTYVAAAGGECLVVDPGGPEVLEALERlGCRDiVVALTHGHFDHVAgVEHLAA---RGAVVAA 74
                                  6789999999**********99776666663333426679*******762333333...4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1543.15
//
Query:       gi|14601296|ref|NP_147831.1|  [L=286]
Description: cation efflux protein CzrB [Aeropyrum pernix K1]
Scores for complete 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   50.0  10.9    4.9e-13   49.3  10.9    1.4  1  Cation_efflux  Cation efflux family


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3  10.9   2.8e-17   4.9e-13       3     198 ..       8     189 ..       6     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 2.8e-17
                 Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgl.lllgla 82 
                                   l+ll+ ++ a+v++++ l+ +S all+d+   ++ +++ l +l  l++s+ ppd+++pfG+grl + g  ++ +   ++++
  gi|14601296|ref|NP_147831.1|   8 LGLLLSVAGAAVKIAGSLVYGSKALLVDGATCVAGIAAGLAALYWLRASKAPPDADHPFGHGRLAFGGVSFTLVaYGVAAG 88 
                                   789999*********************************************************998777666663333333 PP

                 Cation_efflux  83 vfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvillf 163
                                   + l + a     ++++ ++  g a++++l+ ++++ a++ + r      + ++  a a  + + ++ s++  ++a++ + f
  gi|14601296|ref|NP_147831.1|  89 FGLAYLA-----RPEPYSVGLGAAVLGVLGLILYSGAVAAFRR------SPIVGGAMAAFTASEVFESIVSTLAAVGGFGF 158
                                   3333322.....4667788888888888888888888777776......45666667777888999999999999999998 PP

                 Cation_efflux 164 nlksgplaDpvaslligliilysalkllkeslseL 198
                                       g+l+D +++ +i +++ly  +  +++ + +L
  gi|14601296|ref|NP_147831.1| 159 ----GYLVDYLGAWAIEAYLLYELVLHARSMVHQL 189
                                   ....789****************999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2225.01
//
Query:       gi|118431387|ref|NP_147833.2|  [L=347]
Description: glyoxylate reductase [Aeropyrum pernix K1]
Scores for 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-37  126.0   0.0    1.3e-36  125.6   0.0    1.2  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
    8.9e-16   57.8   0.0    1.1e-15   57.5   0.0    1.0  1  2-Hacid_dh    D-isomer specific 2-hydroxyacid dehydrogenase, 


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 !  125.6   0.0   1.5e-40   1.3e-36       2     178 .]     109     289 ..     108     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 1.5e-40
                                    HHHHHHHTTHHHHHHHH...HTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHH CS
                   2-Hacid_dh_C   2 alllallrrlaeadeev...regewksekallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeee 77 
                                    a++la+lr + +++ ++    ++ w  +++l g  ++g+ vG++G+GrIGq+va +l+a+g+   ++y+rs+k+   e+ 
  gi|118431387|ref|NP_147833.2| 109 AAVLAALRGVVAGHMYTprwAREGW--PSHLAGFLVRGRSVGLLGAGRIGQSVAFKLAALGAgPFYYYSRSRKPGL-EAV 185
                                    7899999999999988866545558..9**********************************999******99998.999 PP

                                    HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSS CS
                   2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeee 157
                                    lg++  +  el+++s i+++ lplt etr+l++a  l+++++ga+ +N++RGg+ +  a+ ++  +++  +++lDv+ ee
  gi|118431387|ref|NP_147833.2| 186 LGAKRLEPRELFSRSMILVNSLPLTGETRGLVTAGLLRLLPRGAVYVNVGRGGTEEPGAVEAVASEREDLYFVLDVHPEE 265
                                    9******************************************************************************* PP

                                    SSGTCH...HHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 158 plpeds...pllelpnviltPHia 178
                                    plp++s   +l   p+v++tPHia
  gi|118431387|ref|NP_147833.2| 266 PLPPSSgrmRLHGNPRVVMTPHIA 289
                                    ***98666699************8 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 !   57.5   0.0   1.2e-19   1.1e-15      39     134 .]      44     321 ..      20     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.2e-19
                                    TESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                     2-Hacid_dh  39 dadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt................ 102
                                    +a  ++++  t+v+a +l+    L++i++ ++G+D+vD++aa+  G+ V+n p++ te+vAE++                
  gi|118431387|ref|NP_147833.2|  44 RASRVFINAFTPVDAGLLRDKGCLELIVLTSTGFDHVDVEAAAGVGVCVANQPEVITEAVAEYVvaavlaalrgvvaghm 123
                                    466678888899******************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|118431387|ref|NP_147833.2| 124 ytprwaregwpshlagflvrgrsvgllgagrigqsvafklaalgagpfyyysrsrkpgleavlgakrleprelfsrsmil 203
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|118431387|ref|NP_147833.2| 204 vnslpltgetrglvtagllrllprgavyvnvgrggteepgaveavaseredlyfvldvhpeeplppssgrmrlhgnprvv 283
                                    ******************************************************************************** PP

                                    ......T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                    ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 ......aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                          ++++e++ + +  aa + +++l+ + + n+vn
  gi|118431387|ref|NP_147833.2| 284 mtphiaGSSRESMTATRLLAAMQARDYLERGCVWNPVN 321
                                    ******************************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2604.84
//
Query:       gi|118431388|ref|NP_147834.2|  [L=428]
Description: oxidoreductase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-41  142.8   1.8    2.3e-41  142.6   1.8    1.0  1  DAO            FAD dependent oxidoreductase
    2.9e-05   23.5   0.2     0.0072   15.6   0.1    2.2  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00038   20.6   1.8    0.00094   19.4   1.8    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00098   18.3   2.4     0.0014   17.8   2.4    1.5  1  FAD_binding_2  FAD binding domain
     0.0012   18.1   0.3     0.0024   17.1   0.3    1.4  1  Thi4           Thi4 family
     0.0052   17.3   0.6       0.41   11.2   0.5    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.11   11.7   0.0       0.16   11.2   0.0    1.2  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.14   10.8   0.2        1.3    7.7   0.4    2.0  2  HI0933_like    HI0933-like protein


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 !  142.6   1.8     1e-44   2.3e-41       1     351 [.       5     393 ..       5     394 .. 0.73

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 1e-44
                                    EEEEECTSHHHHHHHHHHHHT.T..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHH.HHHHHHHHHHHS CS
                            DAO   1 dvviiGGGiiGlstAyeLarr.g..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslea.leelreleeelg 76 
                                    d v++G+G++Gl++Ay+L    g  V+++++g+ +gsg Sgr+ + ++  ++++  +    rl++ + ++++++ ++  g
  gi|118431388|ref|NP_147834.2|   5 DYVVVGAGVVGLAAAYYLKVWsGgsVLVVDAGHAPGSGDSGRSMAAFRTFFSSTM-N----RLVAGStVRLFEDAQRG-G 78 
                                    89****************544546*************************876444.4....88886648888999987.9 PP

                                    STTSEEEEEEEEEESSHHHHHHHHHHHHHH.HHTTT...TEEEEEHHHHHHHSTT.ST.............TTSEEEEET CS
                            DAO  77 ididyrrtGllslaadeeelealdkllall.leagl...daelldaeevrelepa.lp.............gllgalfyp 138
                                     d+++ ++G+l+++ d   +e++ ++++++ +eag    d+ ++ +ee++++  + ++             ++ ga++ +
  gi|118431388|ref|NP_147834.2|  79 EDLGLVKSGYLFVY-D---RERW-REVEEPlREAGEegrDYLIIPPEELERRLGMnTRvsdgeeaevlgvgDVEGAVLIR 153
                                    9************7.5...6777.44555544444422144468888888888776224567788899999999****** PP

                                    TEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..............EECTEEE.EEEEEEEE--GGG CS
                            DAO 139 dtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve..............rttpgen.daadavVnaaGaw 203
                                    ++g +d++k++ +++r+a  +Gve+++g++v+g+e +     g+e              + ++g++ +  +++V+aaG+w
  gi|118431388|ref|NP_147834.2| 154 SAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEgeplpwqearasaaVLSDGTRvEVGEKLVVAAGVW 233
                                    **********************************88553334444556666555554432222444334467******** PP

                                    HH.HHHTTCTT..TSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE........EEETTTTEEEEE.ETTSEEEEEESSE. CS
                            DAO 204 sd.llgllkel..dlpispvrgqvlvlkplseklvspaailpvpe........tdddgrgvyvtp.rkdgrvlvGgtad. 270
                                    s+ ll   ++l  d   +p +  v++++  +e l   + i+ + +         +   + v v+p +++g+++v  ++  
  gi|118431388|ref|NP_147834.2| 234 SNrLL---NPLgiDTFSRPKKRMVFRVSASTEGL---RRIMREGDlagagappLIILPKRVLVRPaPREGSFWVQLSDNl 307
                                    **888...66655545599********6666633...3344444453333333333333344444336677887777768 PP

                                    ..EETTCSSTSCSHHHHHH.HHHHHHHHSGGGCGEEE..EEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHH CS
                            DAO 271 ..eesgdddpevdeedide.llealrklfPqlgdvlr..kwaGlrp.lpdglpligetpgvkglylatGhsghGltlapa 344
                                      +++ ++dp+++e+ +   +l+ l+ ++Pq++d      waG+++   d +p++ e p+ +g+++a+G sg+G++ +  
  gi|118431388|ref|NP_147834.2| 308 grPFALEEDPQPEEHYYSLaILPILSLYLPQFQDAYPsgGWAGHYDiSFDANPVVFE-PWESGIVVAAGTSGSGIMKSDS 386
                                    86444444445554444448***********98866445*******559********.8888****************** PP

                                    HHHHHHH CS
                            DAO 345 tGkllae 351
                                    +G+++a 
  gi|118431388|ref|NP_147834.2| 387 IGRVAAA 393
                                    ***9985 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.2e-06    0.0072       1      37 [.       4      40 ..       4      81 .. 0.88
   2 !    5.9   0.0    0.0029       6.6     189     252 ..     167     245 ..     127     287 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-06
                                   CSEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq.agakvtlvelegtcln 37
                                   +d+vv+G+G+ Glaaa +l+  +g+ v++v + g+ ++
  gi|118431388|ref|NP_147834.2|  4 FDYVVVGAGVVGLAAAYYLKVwSGGSVLVV-DAGHAPG 40
                                   589******************88*******.6666665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0029
                                    HHHHHHHTTEEEEESCEEEEEEETTE...............EEE.EEETTSCEEEE.SEEEE-S-EEES-HHCSHCCT-E CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...............xxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 189 leealekeGvevklgtsvkeidgnge...............kle.vvledgeeida.dlvvvavGvrpstelleeklgle 251
                                    + ++    Gve+ +g +v+ ++ +++               +++  vl+dg+++++ + +vva+Gv  ++ l  + lg+ 
  gi|118431388|ref|NP_147834.2| 167 YYRRASGAGVEFIFGRRVVGVELKPRvelgiegeplpwqeaRASaAVLSDGTRVEVgEKLVVAAGVWSNRLL--NPLGID 244
                                    444555555555555555555544444455555555555331114555555553331455555555555433..344443 PP

                                    E CS
                                    x RF
                    Pyr_redox_2 252 l 252
                                    +
  gi|118431388|ref|NP_147834.2| 245 T 245
                                    3 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 !   19.4   1.8   4.2e-07   0.00094       1      33 [.       8      42 ..       8      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.2e-07
                                   EE--SHHHHHHHHHHHC.CTEEEEEE-SSSSSS.G CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLak.agfdvlllekrdrlG.G 33
                                   +vGaG+ Gl+aAy+L+   g +vl++++++ +G G
  gi|118431388|ref|NP_147834.2|  8 VVGAGVVGLAAAYYLKVwSGGSVLVVDAGHAPGsG 42
                                   8**************9856***********99954 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.4   6.2e-07    0.0014       1      76 [.       5      81 ..       5     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-07
                                   SEEEE--SHHHHHHHHHHHH.TTT-EEEEESSSGGGS.GGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT- CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaae.aGlkvavvekeqefgg.atawsqGgidavlspeqkkagikdspelhrtdtlkaldel 76
                                   D +V+G+G+ GLaAA+ ++   G +v+vv+ +++ g+  +  s + +    s++++++    s +  ++d++ ++ +l
  gi|118431388|ref|NP_147834.2|  5 DYVVVGAGVVGLAAAYYLKVwSGGSVLVVDAGHAPGSgDSGRSMAAFRTFFSSTMNRLVA-GSTVRLFEDAQRGGEDL 81
                                   88****************977999*********999989999999999999999999977.77999999999988655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   1.1e-06    0.0024      19      60 ..       5      46 ..       2      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60
                                   D v+vGaG  GL+aayyl    +  v+++++  +pG G  + 
  gi|118431388|ref|NP_147834.2|  5 DYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGR 46
                                   89****************9999**************997665 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   0.5   0.00018      0.41       3      34 ..       7      39 ..       5      51 .. 0.83
   2 ?    3.8   0.0     0.039        87      28      71 ..     151     192 ..     136     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                   EEECSSHHHHHHHHHHHH.TTSEEEEEESSSSS CS
                      Pyr_redox  3 vvvGgGyiglElAgalae.lgkkVtvversdkl 34
                                   vvvG+G++gl +A +l+   g +V vv+++  +
  gi|118431388|ref|NP_147834.2|  7 VVVGAGVVGLAAAYYLKVwSGGSVLVVDAGHAP 39
                                   9***************99677889888877665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.039
                                    EESSSSSSTTSSHHHHHHHHHHHHHT...TEEEECSEEEEEEEEETT CS
                      Pyr_redox  28 versdkllrllDeeaskilqeklekn...gievllntkveeiegsed 71 
                                    + rs  +l     +a+k++  + ++    g+e++++++v+ +e +++
  gi|118431388|ref|NP_147834.2| 151 LIRSAGFL-----DAEKVVDYYYRRAsgaGVEFIFGRRVVGVELKPR 192
                                    55666666.....6777777777666677***********9997665 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 ?   11.2   0.0   7.2e-05      0.16       1      52 [.       7      59 ..       7      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni...gnsiyrypkemtfispsfts 52
                                   +++GaG  Glaaa+ lk     ++l+++ g++   g+s +   + +tf+s+    
  gi|118431388|ref|NP_147834.2|  7 VVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHApgsGDSGRSMAAFRTFFSST--M 59
                                   79****************9999*******96433377888888888888853..4 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4   0.00058       1.3       2      36 ..       5      40 ..       4      42 .. 0.90
   2 ?    0.4   0.0     0.089     2e+02     107     146 ..     159     198 ..     157     234 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00058
                                   SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisa.akrgkrVlllekakklg 36
                                   d +v+G+G  Gl aA  +    g +Vl++++++++g
  gi|118431388|ref|NP_147834.2|  5 DYVVVGAGVVGLAAAYYLkVWSGGSVLVVDAGHAPG 40
                                   789*************9956799********99988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.089
                                    -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEE CS
                    HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvk 146
                                    +ae++vd + ++++ agv++   ++v +ve +   ++ ++
  gi|118431388|ref|NP_147834.2| 159 DAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIE 198
                                    599************************9976665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3098.02
//
Query:       gi|118431389|ref|NP_147835.2|  [L=149]
Description: hypothetical protein APE_1270.1 [Aeropyrum pernix K1]
Scores for 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-14   52.0   0.0      9e-14   51.5   0.0    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
      1e-06   28.7   0.0    1.7e-06   28.0   0.0    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0012   19.0   0.0     0.0017   18.6   0.0    1.5  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.034   14.0   0.1      0.047   13.6   0.1    1.2  1  Cas_Cas5d       CRISPR-associated protein (Cas_Cas5)
       0.12   12.7   0.0       0.23   11.8   0.0    1.4  1  BolA            BolA-like protein


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 !   51.5   0.0   2.5e-17     9e-14       7      82 ..      24      93 ..      18     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.5e-17
                                   HHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCC CS
                   NTP_transf_2  7 elkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledp 82
                                   +l e+ +++ v+lfGSyarG++++ SDiD++vv+p++  r    ++l+++     ++ee  g+e+ l+t e++++ 
  gi|118431389|ref|NP_147835.2| 24 KLLERLGDVTVILFGSYARGDFNRWSDIDIIVVSPRF--R--GVRILDRYDMVSGAVEE--GVEAILMTPEEFREA 93
                                   4556667******************************..4..67889999999999999..*******99999863 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   4.6e-10   1.7e-06      15      42 ..      33      60 ..      22      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.6e-10
                                   STTEEEEEE-S------EEEEEEEESS- CS
                        Polbeta 15 laylFGSrakgkareeSDiDlavllkek 42
                                    ++lFGS+a+g++++ SDiD+ v+  + 
  gi|118431389|ref|NP_147835.2| 33 TVILFGSYARGDFNRWSDIDIIVVSPRF 60
                                   689********************98766 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 !   18.6   0.0   4.7e-07    0.0017       1      54 [.       2      62 ..       2     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.7e-07
                                   -EEHHHHHH.HHHHHH..HHHHHH-TT...-EEEE-HHHHTT-.SEESSEEEEEEBTTBST CS
                 DNA_pol_B_palm  1 riPreEvea.lealvk..kaakeldpe...vevivcGSYRRga.essGDvDvlitkkdaks 54
                                   riPre  +a lealvk  ++a++l ++   v+vi  GSY Rg  +   D+D+++  ++++ 
  gi|118431389|ref|NP_147835.2|  2 RIPRERLSAwLEALVKakSSASKLLERlgdVTVILFGSYARGDfNRWSDIDIIVVSPRFRG 62
                                   89**9998735666763234455555455599*********9736789******9998765 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 ?   13.6   0.1   1.3e-05     0.047     125     183 ..      88     139 ..      69     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHTTSSSSESSSTTSEEEECESETTT.CESSHHHCCHSSCEBSSSBSEEEEEE CS
                      Cas_Cas5d 125 eelaralrkpvwplyLGrkecivpvepveaekvgeeegledalkelppkvegilglmle 183
                                    ee+++alrkpvw ++L r +  + v+ +       +  +e+al+++pp+ e  l++m++
  gi|118431389|ref|NP_147835.2|  88 EEFREALRKPVWGHALARSSA-IVVDRLGL-----AREVEEALGRRPPSLE-DLEAMVR 139
                                    89*******************.66666664.....5677788888885554.2556665 PP

>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.4e-05      0.23      31      60 ..      51      80 ..      41      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                           BolA 31 FkvvivseaFegkslvarhRlvyalLkeel 60
                                    ++ +vs++F g + ++r  +v  +++e +
  gi|118431389|ref|NP_147835.2| 51 IDIIVVSPRFRGVRILDRYDMVSGAVEEGV 80
                                   5799******************99998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); 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:                         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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1176.00
//
Query:       gi|118431390|ref|NP_147836.2|  [L=139]
Description: hypothetical protein APE_1272.1 [Aeropyrum pernix K1]
Scores for complete 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-34  117.8   0.1    3.3e-34  117.5   0.1    1.0  1  HEPN            HEPN domain
  ------ inclusion threshold ------
      0.028   13.8   0.6        1.6    8.2   0.2    2.4  2  Enolase_like_N  Enolase N-terminal domain-like
       0.35   11.2   2.7          5    7.5   0.1    3.1  3  TPR_12          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 !  117.5   0.1   5.6e-38   3.3e-34       3     117 ..      10     130 ..       8     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 5.6e-38
                                    HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHHHC CS
                           HEPN   3 ewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeLek 82 
                                    +wlr+A+++le+ ++++e g+y++acf+a qaae+++KA+l + g e   +hdl +L+++++ + +  +e++e++ +L+k
  gi|118431390|ref|NP_147836.2|  10 RWLRQAKHTLESIRVDYEGGFYSWACFKANQAAEYSIKAVLRAAGLE-SFGHDLMALWRRARSLCQPLQEMEECIAVLNK 88 
                                    8*********************************************9.******************************** PP

                                    CCHHCCCTSS--S.......--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  83 ayiesrYpdakee.......yteedaeealkdaeevlelvee 117
                                    +y + rYpda+++       yt++daeeal++a +v+++vee
  gi|118431390|ref|NP_147836.2|  89 LYLPPRYPDAWPGgaapfenYTRRDAEEALECASRVYRAVEE 130
                                    **************************************9987 PP

>> Enolase_like_N  Enolase N-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0    0.0076        46      36      48 ..       3      15 ..       2      18 .. 0.84
   2 ?    8.2   0.2   0.00027       1.6      28      48 ..     101     121 ..      94     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0076
                 Enolase_like_N 36 YddaeaarWlaaa 48
                                   +d +ea rWl+ a
  gi|118431390|ref|NP_147836.2|  3 FDCEEAVRWLRQA 15
                                   5779******987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00027
                 Enolase_like_N  28 gEfspFleYddaeaarWlaaa 48 
                                    g  +pF +Y+ ++a++ l++a
  gi|118431390|ref|NP_147836.2| 101 GGAAPFENYTRRDAEEALECA 121
                                    6789**************999 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.11   6.7e+02      60      71 ..       4      15 ..       3      17 .. 0.78
   2 ?    1.1   0.0     0.081   4.9e+02       4      29 ..      64      89 ..      60      91 .. 0.76
   3 ?    7.5   0.1   0.00084         5      16      41 ..     111     136 ..     108     139 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                         TPR_12 60 ryeeAlelleea 71
                                   + eeA+++l++a
  gi|118431390|ref|NP_147836.2|  4 DCEEAVRWLRQA 15
                                   678888888887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.081
                         TPR_12  4 talnnlaavlrr.lgrydeAlelleka 29
                                   +++ ++a  l++ l++++e+++ l+k 
  gi|118431390|ref|NP_147836.2| 64 ALW-RRARSLCQpLQEMEECIAVLNKL 89
                                   444.78888877799999999999886 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00084
                         TPR_12  16 lgrydeAlellekaleiarrllGpdh 41 
                                    + + +eAle+  ++++++++ lG++ 
  gi|118431390|ref|NP_147836.2| 111 RRDAEEALECASRVYRAVEECLGEEC 136
                                    56899**************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 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:                        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 0.21s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1208.10
//
Query:       gi|118431391|ref|NP_147837.2|  [L=390]
Description: nicotinate phosphoribosyltransferase [Aeropyrum pernix K1]
Scores for complete 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   86.0   0.0    3.3e-24   85.6   0.0    1.2  1  QRPTase_C   Quinolinate phosphoribosyl transferase, C-termina
    1.1e-05   25.7   0.0    1.9e-05   25.0   0.0    1.4  1  NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal d
    3.1e-05   24.0   0.0    7.3e-05   22.8   0.0    1.6  1  QRPTase_N   Quinolinate phosphoribosyl transferase, N-termina
     0.0082   16.5   0.0      0.031   14.6   0.0    1.9  2  NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N
  ------ inclusion threshold ------
       0.17   11.3   0.0       0.25   10.7   0.0    1.2  1  BtpA        BtpA family


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 !   85.6   0.0   9.1e-28   3.3e-24       1     169 []     120     309 ..     120     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 9.1e-28
                                    HHHHHHHHHHHHHCT.SSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHHHH CS
                      QRPTase_C   1 iAtltarmveaaksa.kvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveavks 72 
                                    iAt++ar+  aa +  +v +++ R  +P++++++ +A+l+GG d         +lg++   +++++ i+++gs+vea+++
  gi|118431391|ref|NP_147837.2| 120 IATKAARVRLAAGRGkTVLFFGLRALHPAVQPAADRAALVGGLDgvsgvlsREYLGVEPRGTMPHALIIVFGSQVEAWRA 199
                                    8*******9999876589999*****************************99**************************** PP

                                    HHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEESS--T CS
                      QRPTase_C  73 vreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr....vlievSGgvtl 138
                                    + e  ++e +    v++  +e  e+ ++a+       +++LD++s+    ++++vee+ ++ +++    v+i+vSGg+ +
  gi|118431391|ref|NP_147837.2| 200 FAETFKEETPviALVDTFWDEREEALMAARelgevLAGVRLDTPSSrrGRMRDIVEEVrWALDIHgykhVKIFVSGGLDE 279
                                    *****999887567888777777777776678777789******997789*******989999889999*********** PP

                                    TTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                      QRPTase_C 139 enveeyaksgvdvisvgalthsvkalDislk 169
                                    e v+e+++   d ++vg+ +  ++ +Dis++
  gi|118431391|ref|NP_147837.2| 280 ERVAELRDVA-DGFGVGTTIAAAPNIDISMD 309
                                    *********9.******************97 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 !   25.0   0.0   5.3e-09   1.9e-05      46      86 ..     347     387 ..     307     390 .] 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.3e-09
                     NAPRTase_C  46 eitpsrvekLlkkvfkdGklvyelpsleeireyvkeqlael 86 
                                      +p+ +e+L++k++++G+l + lpsl+eir+yv +ql++l
  gi|118431391|ref|NP_147837.2| 347 GEEPEGCEPLTRKYLEEGRLAQSLPSLDEIRSYVLKQLENL 387
                                    4568889********************************98 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 !   22.8   0.0     2e-08   7.3e-05      25      86 ..      56     115 ..      41     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2e-08
                                    SSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHH CS
                      QRPTase_N  25 keegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllq 86 
                                     e++v+aGle+a ++++    ++v +  ++G+ +e++d l+ +eG+ +++   E  +L ll 
  gi|118431391|ref|NP_147837.2|  56 YEWAVYAGLEEALALLQGK-PVTV-YSLPEGTVFERKDPLMVVEGRFQDIILFETALLGLLR 115
                                    699***********99966.5554.666******************************9996 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.25   8.9e+02       3      52 ..      22      72 ..      21      77 .. 0.83
   2 !   14.6   0.0   8.8e-06     0.031      79     123 ..      68     113 ..      64     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.25
                     NAPRTase_N  3 tDlYkltmaqavfkkgp.dvevvfelffRkkpfkgeyaivagleevieyle 52
                                   tD Y +    +  k g   ++v++e+   + p ++e a++aglee++  l+
  gi|118431391|ref|NP_147837.2| 22 TDIYFVRTRRVAEKYGVgGKRVRMEVHAYSLPRGYEWAVYAGLEEALALLQ 72
                                   67777777777777777788999999999999999**********998886 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.8e-06
                     NAPRTase_N  79 Lrtfrfkpse.vaveeeevvfpgepeirveGpwieaillEtplLai 123
                                    L+ ++ kp + ++++e++v++ ++p + veG   ++il+Et+lL +
  gi|118431391|ref|NP_147837.2|  68 LALLQGKPVTvYSLPEGTVFERKDPLMVVEGRFQDIILFETALLGL 113
                                    55666677775778888889999********************976 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.1e-05      0.25     200     238 ..     267     306 ..     245     315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.1e-05
                           BtpA 200 k.vkvlvgsGvseenlekllsiadGvivgtsikkdGkian 238
                                    k vk++v  G +ee +++l ++adG+ vgt+i    +i  
  gi|118431391|ref|NP_147837.2| 267 KhVKIFVSGGLDEERVAELRDVADGFGVGTTIAAAPNIDI 306
                                    3599***************************987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3343.83
//
Query:       gi|14601303|ref|NP_147838.1|  [L=467]
Description: tryptophanase [Aeropyrum pernix K1]
Scores for 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-86  287.9   0.0    9.8e-86  287.7   0.0    1.0  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.018   14.3   0.0      0.038   13.3   0.0    1.6  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.078   11.7   0.0       0.12   11.1   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
       0.11   11.2   0.0       0.55    8.9   0.0    2.1  3  SepSecS          O-phosphoseryl-tRNA(Sec) selenium transferas


Domain annotation for each model (and alignments):
>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.7   0.0   2.2e-89   9.8e-86       1     292 [.      52     427 ..      52     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 287.7 bits;  conditional E-value: 2.2e-89
                                   E-S-GGG----HHHHHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT- CS
               Beta_elim_lyase   1 DLlSDsvtkgteamsdaq.aaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepa 80 
                                   DLl+Ds   gt++ms +q aa+m+Gde+Y+++++++r+ dav++++g + +l+v+qG+aA++il+  ll+r ++ iv  pa
  gi|14601303|ref|NP_147838.1|  52 DLLTDS---GTGSMSIYQwAALMTGDEAYAGARSWFRFRDAVRDVLGLDLVLPVHQGRAAERILYGELLRRRNARIV--PA 127
                                   9*****...************************************************************88887765..8* PP

                                   HHHHSSTTHHHHCC--EEEEE-EBTT.........TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHH CS
               Beta_elim_lyase  81 hihfdetgaiaelagvklrdlknkea.........GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelre 152
                                   ++hfd+ +a+   +g  + dl++++a         G++d+++le+++ke+++   ++++i+l +TnntagGq+vs+++++ 
  gi|14601303|ref|NP_147838.1| 128 NTHFDTGRAVILNQGGVPLDLPSPQAsrreaypfkGDIDVARLERLLKERSR---DVAFILLVITNNTAGGQPVSMDNVKT 205
                                   *************9999********************************666...************************** PP

                                   HHHHHHHCT-EEEEEETTHHHHH............HHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH........ CS
               Beta_elim_lyase 153 vaaiakkygiplhlDgARfanaa............kslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel...... 215
                                   v+++a++yg+pl++D +Rfa++a            +s++ i++em+sy D+++ms+kKd+lan+Gg++a+rd +l      
  gi|14601303|ref|NP_147838.1| 206 VRELADAYGLPLVMDICRFAENAylvkerdpryrgWSVRDIAREMISYGDHFVMSAKKDGLANIGGFIATRDPSLyedlaa 286
                                   *************************************************************************99****** PP

                                   .................................HHHHHHHHHHHHT---SSTHHHHH........................ CS
               Beta_elim_lyase 216 ...............................edylaerveqrkylggglrqagvlaa........................ 241
                                                                  edyl++rveq++ylg+ l+++gv+++                        
  gi|14601303|ref|NP_147838.1| 287 rvvleegyvtygglagrdleaiaqglrevveEDYLRHRVEQVRYLGELLSSQGVPIVepvgghavyvdvlealpemprshy 367
                                   ********************************************************************************* PP

                                   ............HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEECCGTTCCEEEEE. CS
               Beta_elim_lyase 242 ..........leagiraleeglaslerdhktaeqlaeklelvrlaiprrvytqehldyvaa 292
                                             le g+ra+ +g+  ++r+ +++e  ++++el+rla+prr+yt++h++yvaa
  gi|14601303|ref|NP_147838.1| 368 padalaaalyLESGVRAVGLGALAFARE-ENGEIVYPEFELLRLAVPRRTYTNSHMEYVAA 427
                                   *********************9999988.88****************************97 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 ?   13.3   0.0   8.5e-06     0.038      27     147 ..      85     223 ..      66     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.5e-06
                                   HHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHH.HHHTT-EEEEE........-B-TTTSS CS
               DegT_DnrJ_EryC1  27 eFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatana.vlelgakpvfv........Dvdpdtyn 98 
                                   +F  a+++ lg + +++v  G aA  +++  l   +++  Ivp++t + t  a +l+ g +p  +        +  p    
  gi|14601303|ref|NP_147838.1|  85 RFRDAVRDVLGLDLVLPVHQGRAAERILYGELLR-RRNARIVPANTHFDTGRAvILNQGGVPLDLpspqasrrEAYPFKGD 164
                                   6788888888888888888888888888877644.4677788888888777651566777776542222222244455689 PP

                                   B-GGGCGGG--TTE...EEEEEB....-GGGB---HHH...HHHHHHHCT-EEEEE-TT CS
               DegT_DnrJ_EryC1  99 idpaaieaaitert...kaIlpV....hlyGqvadmda...lkaiaakhglkvieDaAh 147
                                   id+a++e+++ er+   + Il+V     + Gq++ md+   ++++a+++gl+++ D + 
  gi|14601303|ref|NP_147838.1| 165 IDVARLERLLKERSrdvAFILLVitnnTAGGQPVSMDNvktVRELADAYGLPLVMDICR 223
                                   **************88855655533326789**999872225789***********885 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.6e-05      0.12      94     203 ..     108     220 ..     100     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHH--TTEEEEEESS--HHHHHHHHHS.-EEEEEE...--E.B-TTS-BE---GGGGSHHHHHHHHHHSTTTGSE CS
                      OKR_DC_1  94 snkvvlnavltpgdlvlvdRNcHKSiehalvls.gatPvyl...epe.rnalgiiggidlkefeeetlkekikevpdakap 169
                                   + +++   +l + +  +v+ N+H    +a++l+ g +P+ l   +++ r+a+ + g id      + l++ +ke + + a+
  gi|14601303|ref|NP_147838.1| 108 AERILYGELLRRRNARIVPANTHFDTGRAVILNqGGVPLDLpspQASrREAYPFKGDIDV-----ARLERLLKERSRDVAF 183
                                   556666667777777789999999999977664388999885432345999*********.....99************** PP

                                   SEEEEESS-TTSE...EE-HHHHHHHHTTSESEEEEE CS
                      OKR_DC_1 170 rlavitnsTYdGv...lynakeivdkleklsdrilfD 203
                                    l+vitn T  G    + n+k++ ++++ ++ ++ +D
  gi|14601303|ref|NP_147838.1| 184 ILLVITNNTAGGQpvsMDNVKTVRELADAYGLPLVMD 220
                                   ************7333568888888999998888887 PP

>> SepSecS  O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.75   3.4e+03     224     265 ..      52      93 ..      42      96 .. 0.79
   2 ?    8.9   0.0   0.00012      0.55     139     198 ..     165     233 ..     157     286 .. 0.67
   3 ?   -1.3   0.0      0.15   6.8e+02     217     257 ..     334     375 ..     315     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.75
                                   CCCEECCHCCCCESSCHCCCCCHCCCHCHCTSCHCCCCCCCH CS
                       SepSecS 224 nllvpvGgaiiaasdesfikeiskeypgrasaapskdvlisl 265
                                   +ll+ +G +++   +   ++   ++y+g  s    +d++ ++
  gi|14601303|ref|NP_147838.1|  52 DLLTDSGTGSMSIYQWAALMTGDEAYAGARSWFRFRDAVRDV 93 
                                   899999999999999999999999999988877666666665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00012
                                   EHHHHHHHHHHCCTCCC..EEEEEE.CSSTTTTB----HHHHHHHHHCCT--EEEE......GCCCCT- CS
                       SepSecS 139 tdvedveeiiekkreev..ilavls.tlsffaprspDdvkeiakiCaeydvPhlvN......gAYaiqs 198
                                   +dv   e+ ++++  +v  il v++  + + +p s D+vk + ++ ++y++P+++       +AY +++
  gi|14601303|ref|NP_147838.1| 165 IDVARLERLLKERSRDVafILLVITnNTAGGQPVSMDNVKTVRELADAYGLPLVMDicrfaeNAYLVKE 233
                                   577788888988888872233344415667789999****************99742222226666654 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.15
                                   ECCCHCHCCCEECCHCCCCESSCHCCCCCHC.CCHCHCTSCH CS
                       SepSecS 217 vvksldknllvpvGgaiiaasdesfikeisk.eypgrasaap 257
                                    ++s +  ++ pvGg  ++    + + e+ + +yp  a+aa+
  gi|14601303|ref|NP_147838.1| 334 LLSSQGVPIVEPVGGHAVYVDVLEALPEMPRsHYPADALAAA 375
                                   57888888999*********9999999997626998888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3476.29
//
Query:       gi|118431392|ref|YP_874884.1|  [L=93]
Description: hypothetical protein APE_1275a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   15.4   0.5        1.5    8.6   0.2    2.0  2  Oleosin   Oleosin


Domain annotation for each model (and alignments):
>> Oleosin  Oleosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0   0.00073        13      56     101 ..       7      52 ..       5      57 .. 0.84
   2 ?    8.6   0.2   8.6e-05       1.5      60      87 ..      58      85 ..      52      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00073
                        Oleosin  56 vagflasgafgvaalsslswlykyvrgkhpagadkldqakrrladk 101
                                    v ++l+ +   +  l  +sw ++++ +++ +g d  ++ k ++a++
  gi|118431392|ref|YP_874884.1|   7 VYAILSGAIALILSLKLVSWWIETASRRRLVGRDMNKYDKPEVAEA 52 
                                    55677777778889999*********99999999999999988875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 8.6e-05
                        Oleosin 60 lasgafgvaalsslswlykyvrgkhpag 87
                                   +++gafg+ +l +l wl + + g+h +g
  gi|118431392|ref|YP_874884.1| 58 VVAGAFGLLMLEALLWLTRVAWGSHGTG 85
                                   679*****************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 728.24
//
Query:       gi|14601304|ref|NP_147839.1|  [L=98]
Description: hypothetical protein APE_1275b [Aeropyrum pernix K1]
Scores for 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   0.0    0.00022   21.5   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


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 !   21.5   0.0   1.2e-08   0.00022     136     164 ..      14      43 ..       7      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-08
                 Metallophos_2 136 ggvlvvnPGsvgeprdgdpe.tyaildtde 164
                                   gg +vvnPGsvg+prdgdp+ +y ++d ++
  gi|14601304|ref|NP_147839.1|  14 GGAIVVNPGSVGQPRDGDPRaSYTVIDAEK 43 
                                   7899****************9***999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 808.88
//
Query:       gi|118431393|ref|YP_874885.1|  [L=38]
Description: hypothetical protein APE_1275c [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       100  (0.00557756); expected 358.6 (0.02)
Passed bias filter:                       83  (0.00462937); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.20s 00:00:00.50 Elapsed: 00:00:00.33
# Mc/sec: 340.92
//
Query:       gi|14601305|ref|NP_147840.1|  [L=371]
Description: hypothetical protein APE_1276 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 3198.39
//
Query:       gi|14601306|ref|NP_147841.1|  [L=188]
Description: hypothetical protein APE_1277 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 1399.57
//
Query:       gi|14601307|ref|NP_147842.1|  [L=135]
Description: hypothetical protein APE_1278 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0064   16.4   0.6     0.0064   16.4   0.6    2.1  2  Herpes_pp38    Herpesvirus pp38 phosphoprotein
  ------ inclusion threshold ------
       0.46    9.5  16.5       0.59    9.1  16.5    1.1  1  Acyl_transf_3  Acyltransferase family
       0.84    9.3  24.7        1.1    8.9  24.7    1.1  1  Yip1           Yip1 domain


Domain annotation for each model (and alignments):
>> Herpes_pp38  Herpesvirus pp38 phosphoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.27   1.6e+03      30      35 ..      39      44 ..      16      47 .. 0.68
   2 !   16.4   0.6   1.1e-06    0.0064      11      57 ..      50      96 ..      45     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                   Herpes_pp38 30 aGtLvG 35
                                  aGtLvG
  gi|14601307|ref|NP_147842.1| 39 AGTLVG 44
                                  678887 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-06
                   Herpes_pp38 11 viLivsakiLllGsCisFaaGtLvGktadvkvPlcdsvnLllAFlAG 57
                                  + L     +L++G  + F +    G+ + v +P   +vnLl AF+AG
  gi|14601307|ref|NP_147842.1| 50 IYLALMVGMLVVGNILFFLSSFRGGRVSRVLTPPVIAVNLLWAFIAG 96
                                  556666778*************************************9 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  16.5   9.9e-05      0.59     159     276 ..      16     125 ..       7     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 9.9e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 159 kshlllllilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllsllllalilla 239
                                     ++ll+l+ llll +v+ r+ + g+  +v +l+++  l++ ++++G +l+ ++  ++ + ++ +   ++++ ll++++++
  gi|14601307|ref|NP_147842.1|  16 VLGFLLALGSLLLLGYVYTRASGAGTLVGVIVLAIYLALMVGMLVVGNILFFLSSFRGGRVSRVLTPPVIAVNLLWAFIAG 96 
                                   5789***************************************************************************** PP

                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Acyl_transf_3 240 lfgqtdggglvasvliqsaslllvslgimllllllfa 276
                                   + +++        +l +  + ++ ++g++l++l ++ 
  gi|14601307|ref|NP_147842.1|  97 ANAMG--------SLRSGDTGAAAAAGLLLVFLVALT 125
                                   *****........455555555555555555544443 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  24.7   0.00018       1.1      57     170 ..       7     122 ..       2     129 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00018
                          Yip1  57 ltlssllgaiiggylglllgllllalllhliakllggkgsfkqtlsvvgya..llPlilgaliaillllllgt.....lll 130
                                   l+ +s+l++++g++l+ l +llll+++++     + g g++  ++ ++ y   ++ +++ + i+++l+ + g+     l  
  gi|14601307|ref|NP_147842.1|   7 LSYISALAGVLGFLLA-LGSLLLLGYVYTR----ASGAGTLVGVIVLAIYLalMVGMLVVGNILFFLSSFRGGrvsrvLTP 82 
                                   6678999999999997.9999999999999....66****888777777777788888888887877777777******** PP

                          Yip1 131 lvgllaliWslvllylglkaahnlskkkallaalilllll 170
                                    v+++ l+W++++ ++++ ++   +++ a++a l+l+ l+
  gi|14601307|ref|NP_147842.1|  83 PVIAVNLLWAFIAGANAMGSLRSGDTGAAAAAGLLLVFLV 122
                                   ***********************99999999999833332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1049.43
//
Query:       gi|118431394|ref|NP_147843.2|  [L=220]
Description: pyrimidine nucleotide reductase [Aeropyrum pernix K1]
Scores for complete 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-38  131.8   0.0    2.9e-38  131.7   0.0    1.0  1  RibD_C    RibD C-terminal domain
  ------ inclusion threshold ------
        1.5    8.9   8.4        7.3    6.7   0.4    3.4  3  DUF834    Domain of unknown function (DUF834)


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.0   3.3e-42   2.9e-38       1     192 [.       4     199 ..       4     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 3.3e-42
                                    -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEE CS
                         RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrv 80 
                                    py  ++++++lDG++a  +g s  +++ e+ +  h++ra ada++vG++t   d p+ltvr++ +         r+p+rv
  gi|118431394|ref|NP_147843.2|   4 PYTFIFSTATLDGRIASITGYSL-LSCREDFELQHKYRASADAVMVGSRTAVLDRPRLTVRLARG---------RSPLRV 73 
                                    6778999****************.*****************************************.........8***** PP

                                    EEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCC.....E......SE-HHHHHHHHHHT.T--EEEEEETHHHHH CS
                         RibD_C  81 Vvdstlrvpldakvltddaptlvatteeadkekveklk.....v......rvdlkelleeLker.girsllveGGatLag 148
                                    Vvds l+vp+d++ l+++  ++++t e  ++e+++ +      v      +vdl+++++ L+er g+r l+veGG+ L+ 
  gi|118431394|ref|NP_147843.2|  74 VVDSGLKVPPDVAGLRRG--SVLVTAEGHSRERLKPYLergveVveagrgKVDLERAVAVLRERlGVRVLMVEGGGGLNC 151
                                    *************99988..88888888888887777678866269999******************************* PP

                                    HHHHTTT-SEEEEEEESCE--TTSBCSSSSST-SS.....EEEEEEEEE CS
                         RibD_C 149 sllraglvDelrlyiaPkllGgagktlfdgegfka.....lklklvkse 192
                                    ++l++glvDe+r +iaP+++Gg g  l +  g+       ++l l +++
  gi|118431394|ref|NP_147843.2| 152 AMLEKGLVDEVRATIAPYIFGG-GVGLAECPGVFDgrdrrVELALQHTR 199
                                    **********************.77776655554444544566665555 PP

>> DUF834  Domain of unknown function (DUF834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.061   5.5e+02      20      40 ..     115     134 ..     110     137 .. 0.72
   2 ?    6.7   0.4   0.00081       7.3      11      36 ..     142     167 ..     134     168 .. 0.89
   3 ?    4.9   0.2    0.0029        26      19      33 ..     181     195 ..     172     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.061
                         DUF834  20 avfggnepaAGllLglAePtv 40 
                                    +v  g+++  +l++++A++++
  gi|118431394|ref|NP_147843.2| 115 VVEAGRGK-VDLERAVAVLRE 134
                                    55555555.469*****9998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00081
                         DUF834  11 rvdgdgGvpavfggnepaAGllLglA 36 
                                     v g+gG+  +  +++ +++++ + A
  gi|118431394|ref|NP_147843.2| 142 MVEGGGGLNCAMLEKGLVDEVRATIA 167
                                    599******************98876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0029
                         DUF834  19 pavfggnepaAGllL 33 
                                    p+vf+g++++ +l+L
  gi|118431394|ref|NP_147843.2| 181 PGVFDGRDRRVELAL 195
                                    99***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1850.41
//
Query:       gi|118431395|ref|YP_874886.1|  [L=97]
Description: hypothetical protein APE_1279a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.7   0.0       0.12   11.6   0.0    1.1  1  EAP30     EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.9e-06      0.12     121     159 ..      27      69 ..      17      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.9e-06
                          EAP30 121 elyalvnrarggvalvspdDllraiekllvlg......sglsvlq 159
                                    el +++   r g al sp+D+++a+e++l  g      +g  vl+
  gi|118431395|ref|YP_874886.1|  27 ELAKVYS-GR-GPALFSPEDVEKAVEHFLIAGlarldsGGRLVLE 69 
                                    4444443.46.669**************55555566666677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 753.98
//
Query:       gi|14601310|ref|NP_147845.1|  [L=643]
Description: hypothetical protein APE_1281 [Aeropyrum pernix K1]
Scores for 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   22.4   3.8     0.0021   18.3   3.8    2.9  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.8   1.2e-07    0.0021       1     119 [.      61     270 ..      61     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHHHHHHHHHHHHH...........................................HHHHHHHHHHHHHTTTT CS
                            HD   1 rleHsleVaklarrlaedlge...........................................eedrellllaaLlHDiG 38 
                                   r+eHsl+Va+ +rr  +++ +                                           +  +  +++aaLlHD G
  gi|14601310|ref|NP_147845.1|  61 RFEHSLGVAYTMRRALHHIVKnveeivlpsvaeyiedeyplkgglqkrlqgiathlirdvtnalRNMEGEAVVAALLHDSG 141
                                   79*************9999999******************************************88888899********* PP

                                   HHHHTS..HHH............HHHCTCCHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHTTCCHHHHHHHH. CS
                            HD  39 kgpfgdafekk............eeefekflaHekvgaeilrevekrlgld........ledvaklirehheswegkkrp. 98 
                                   ++  ++  e++             +e   +++He+ + +i++++   + +         l  v+++ r    + e++kr  
  gi|14601310|ref|NP_147845.1| 142 HIMASHIAEQAlhdplimvapraVRELPLLEEHEDLTIKIVSKLADEDVEIlyggrrvdLRRVVEILRLAYSRGEWEKRCi 222
                                   ******999888887777766552225566678888888888886665333566666665555555544444444444446 PP

                                   .....................H......HHHCCTSCHHHHHHHHHHHH CS
                            HD  99 .....................r......glaerqlslearivklaDrl 119
                                                        r      +  + ql ++ ++v++aD++
  gi|14601310|ref|NP_147845.1| 223 rdaeyqaptapgglgesarasRyatvaaMCIIAQLLSSGIDVDRADYI 270
                                   666666666666666655544134445566666777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4604.89
//
Query:       gi|118431396|ref|NP_147846.2|  [L=166]
Description: hypothetical protein APE_1284.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1281.63
//
Query:       gi|118431397|ref|NP_147847.2|  [L=333]
Description: hypothetical protein APE_1285.1 [Aeropyrum pernix K1]
Scores for 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-39  133.9   0.0    1.1e-38  133.4   0.0    1.1  1  Hist_deacetyl   Histone deacetylase domain
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.34   10.8   0.0    1.5  1  AAA_31          AAA domain
       0.19   12.0   0.0        0.4   10.9   0.0    1.5  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C


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 !  133.4   0.0   1.9e-42   1.1e-38       1     277 [.      14     272 ..      14     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 1.9e-42
                                    SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskllddd 80 
                                    h e+p+Rl+++l++l++s +lld le+ ++p   +  ++++vH++ Y++ +       ++     +           d d
  gi|118431397|ref|NP_147847.2|  14 HIEEPRRLDKALKALKKS-RLLDMLEK-VDPGFQSLRVFETVHDPLYIKGILAEL---EAAL---DS-------YFIDSD 78 
                                    7899*************9.99988885.99999999999*********9986422...2222...11.......246789 PP

                                    THCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-B......TTBSS-HHHHHHHHHHHCC-SS-E CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  81 tpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseas......GFClvNnvaiaikylqakhelkrv 154
                                    t++sp+t  a ++ +++v +a ++v++g   +a+vl rPpgHHa    ++      G ClvN++a  + +l+   +  +v
  gi|118431397|ref|NP_147847.2|  79 TYISPGTQAALEALAASVEQASEHVAEG--GKALVLGRPPGHHAGVAGPGlgapslGACLVNAAASLAYRLAG-RG-LKV 154
                                    **************************99..**************766655677779************99999.33.4** PP

                                    EEEE-SSS--HHHHHHCTT...-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 155 ailDvDvHhGnGteeafys...dpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                    +ilD+D+ hGnGt+e+++     +++++l++H+  ++ +P tg+   +    g g++ln+ l+eg+gd+ +l+++ e l+
  gi|118431397|ref|NP_147847.2| 155 LILDFDANHGNGTQEILQAlpmGDRLFHLDMHQDWRKSFPWTGEPGVT----GDGTALNIVLPEGSGDDIVLALI-EGLE 229
                                    ******************744469*********************988....5999************8777776.5678 PP

                                    HHHCCH--SEEEEEE-STTBTTS.TT-S-BB-HHHHHHHHHHHCCCH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgd.plgelnlsvegykeltkklaela 277
                                    p+++e +Pd+++vs+GfD+++gd pl   +l+ + ++ l +     a
  gi|118431397|ref|NP_147847.2| 230 PLVNESEPDAVVVSMGFDGYSGDsPLTLTKLTSHTFHALGRL----A 272
                                    ***********************8888889999888776553....3 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.6e-05      0.34      19      46 ..     140     168 ..     135     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.6e-05
                         AAA_31  19 svnlaaalaklgkkvLlvDlDpQ.anatt 46 
                                    +  la+ la +g kvL+ D+D+  +n t+
  gi|118431397|ref|NP_147847.2| 140 AASLAYRLAGRGLKVLILDFDANhGNGTQ 168
                                    678******************86145454 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 ?   10.9   0.0   6.7e-05       0.4      18      60 ..     139     187 ..     136     202 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.7e-05
                 CobA_CobO_BtuR  18 AAlGlalRalgaglkvlvvqFlKgekesgElaalkkl.......eieler 60 
                                    AA  la R +g+glkvl++ F  ++   g +++l++l       ++++++
  gi|118431397|ref|NP_147847.2| 139 AAASLAYRLAGRGLKVLILDFDANH-GNGTQEILQALpmgdrlfHLDMHQ 187
                                    9999*****************9994.589999999986655433344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2609.86
//
Query:       gi|14601313|ref|NP_147848.1|  [L=469]
Description: hypothetical protein APE_1286 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.59   10.4   3.6        1.6    9.0   0.1    3.2  4  Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen


Domain annotation for each model (and alignments):
>> Myco_19_kDa  Mycobacterium 19 kDa lipoprotein antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.051   9.1e+02      41      85 ..      93     136 ..      81     150 .. 0.55
   2 ?   -2.0   0.0      0.24   4.3e+03      60      80 ..     165     185 ..     162     188 .. 0.70
   3 ?    9.0   0.1   9.1e-05       1.6      41      97 ..     254     317 ..     229     330 .. 0.80
   4 ?   -1.9   0.1      0.22   3.9e+03      70      84 ..     392     406 ..     373     442 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.051
                   Myco_19_kDa  41 sgvsavltdgdeptvesvgigdvd.Gftltyaegtgggsaevtkdg 85 
                                   + ++a l+   e+++e+ +ig ++   t+++ +++  g  e+t dg
  gi|14601313|ref|NP_147848.1|  93 DALQASLEAVGEVNIEECDIGSLEkTLTINVVASE--GVFEATLDG 136
                                   55555555555566666666665323344443333..445555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.24
                   Myco_19_kDa  60 igdvd.Gftltyaegtgggsae 80 
                                   +++ d Gf++ty+ +  g+ a 
  gi|14601313|ref|NP_147848.1| 165 LEESDgGFAGTYQGSLAGS-AS 185
                                   5566449****99888664.54 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 9.1e-05
                   Myco_19_kDa  41 sgvsavltdgdeptvesvgigdvdGf........tltyaegtgggsaevtkdgntYtitGtaega 97 
                                    +v+ +++d+++pt+e  +i++++G           +++eg+ g +a +t+    +t+ G+a++ 
  gi|14601313|ref|NP_147848.1| 254 VQVEFEVSDSEPPTIEF-TIDTTEGElfsriaaaLAGVQEGEAGLEASLTVSEGEFTLRGQATAN 317
                                   34555666778888775.5999999989999987566899999988****************875 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.22
                   Myco_19_kDa  70 yaegtgggsaevtkd 84 
                                   y +g +++s+evtk+
  gi|14601313|ref|NP_147848.1| 392 YIDGAVTDSVEVTKE 406
                                   444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.54u 0.20s 00:00:00.74 Elapsed: 00:00:00.36
# Mc/sec: 3928.86
//
Query:       gi|118431398|ref|NP_147849.2|  [L=1283]
Description: nitrate reductase alpha subunit [Aeropyrum pernix K1]
Scores for 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-133  444.0   0.0   7.1e-133  443.7   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.8e-19   69.2   0.1    5.3e-19   68.3   0.1    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0021   17.8   3.9     0.0039   17.0   3.9    1.5  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 !  443.7   0.0  1.2e-136  7.1e-133       1     432 []     140     863 ..     140     863 .. 0.98

  Alignments for each domain:
  == domain 1  score: 443.7 bits;  conditional E-value: 1.2e-136
                                    B--S-EEEC..................................TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEE CS
                  Molybdopterin   1 RlkyPmvRk..................................qargeGkFvrvsWdeAleliaaslkytikkygpdrva 46 
                                    R+kyP+vRk                                   arg G++vr+ Wd++le+ia++l+ytikkygpdr++
  gi|118431398|ref|NP_147849.2| 140 RVKYPYVRKpllelwrearssysdpveawagivedpdkrsryvRARGLGGWVRADWDTVLEIIASALVYTIKKYGPDRIF 219
                                    9******************************************************************************* PP

                                    EEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHS CS
                  Molybdopterin  47 gfssgplmsmeslaslkkllsllggknlsfydwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreer 126
                                    gf ++p+ms +s+as++++++l+gg+++sfydwyadlppas+  ++++++++++es     d+ n+ +ii +G+N++ +r
  gi|118431398|ref|NP_147849.2| 220 GFTPIPAMSPVSYASGARFIELIGGSMGSFYDWYADLPPASP--QVWGEQTDVPESA----DWFNAAYIINFGTNIPMTR 293
                                    ******************************************..89***********....******************* PP

                                    HHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCC CS
                  Molybdopterin 127 pilnarirkaalkkkakvivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpll 206
                                    +++ a++  ++++k++k++v++p+++e ++fad w++ik gtd+a+a++m+hvil+e +v  +   +++y+k+ td p+l
  gi|118431398|ref|NP_147849.2| 294 TPD-AQFFTEVRYKGTKIVVVSPDFSEHTRFADVWVPIKEGTDGAFAISMAHVILREYYVERQVDFFIDYVKRFTDLPFL 372
                                    ***.***********************99*************************************************** PP

                                    CEECCS.......................................................................... CS
                  Molybdopterin 207 vtleee.......................................................................... 212
                                     +le                                                                            
  gi|118431398|ref|NP_147849.2| 373 IVLEPYeggyrpgkflrlsdlhpeeyysegysgepnkewkllvydsntgrprlvngsigyrwdgsgkwnlkledpitgep 452
                                    9998878************************************************************************* PP

                                    ................................................................................ CS
                  Molybdopterin 213 ................................................................................ 212
                                                                                                                    
  gi|118431398|ref|NP_147849.2| 453 vdpklsliddsdevvmvkfpvfgasfgekgivergvpakrvkladgsealvatvfdllaaylgvdrglpgdypagyddkk 532
                                    ******************************************************************************** PP

                                    ..........HHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESS. CS
                  Molybdopterin 213 ..........tgkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnG. 281
                                              tg+++e  +r are a+ a kt+g+ m+++G g+nh++++d +yra+++L++l+g+ g++gGgwah++G 
  gi|118431398|ref|NP_147849.2| 533 pftpawqediTGVSRELAIRLAREWADTAVKTRGRVMVMLGPGVNHWFHSDLHYRAILTLVKLTGAEGRNGGGWAHYVGq 612
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                  Molybdopterin 282 ................................................................................ 281
                                                                                                                    
  gi|118431398|ref|NP_147849.2| 613 ekirtiagwaklafaldwvlpprhqnspsfyyvhtdqwrydrlttdyyegpwsdvrekmkcshpmdcnikaarlgwlpfy 692
                                    **************************************************************999999999999999999 PP

                                    ......CTTHHHCHHHHTCCTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH........ CS
                  Molybdopterin 282 ......qlilagaaekvgalpvllsvkslkeekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgn........ 347
                                           l la +a++ g+ pv+  v+ lk++++k+a+e+p+   n  r  fv+r+nll+ssgk+++y+l++        
  gi|118431398|ref|NP_147849.2| 693 pqfnrsTLDLAAEARRLGKDPVQHVVDLLKSGQLKLAIEDPDAPENWIRVMFVWRANLLGSSGKGHEYFLKHllgspmaq 772
                                    9999999999999999999999999999999************************************************9 PP

                                    ...HHHHSTTSCCCH..CHHH.CSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEE.EEESSS-STT-BE CS
                  Molybdopterin 348 ..npevdhadeneve..kale.kldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqh.lkqavsppgeaks 421
                                      ++evd + ++ev+   a+e kldl+v++d+r+++t  yaDi+LPaatwyEk dl+++d + f h + +av+p +e+ks
  gi|118431398|ref|NP_147849.2| 773 pmSEEVDRSLIKEVVwrAAPEgKLDLLVAIDFRMATTPIYADIVLPAATWYEKYDLSMTDLHTFLHpFTPAVDPLWESKS 852
                                    9988888887777752134448********************************************************** PP

                                    HHHHHHHHHHH CS
                  Molybdopterin 422 dwkIlkaLakk 432
                                    dw+I+k+La+k
  gi|118431398|ref|NP_147849.2| 853 DWDIFKELARK 863
                                    ********975 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.1   8.8e-23   5.3e-19       1      98 [.    1130    1236 ..    1130    1241 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 8.8e-23
                                     EEEEEE-BTTBSTTTT.TCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEE CS
                Molydop_binding    1 lrLitgrsldqlhsqt.rtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmp 77  
                                     lr+ t++ ++ +hs + ++ ++l l + ++ vv++n edA+  Gi+d+d+Ve+ +++G +++r+++++r+++Gv++m+
  gi|118431398|ref|NP_147849.2| 1130 LRYLTPHGKWNIHSEFwDNLKMLTLFRGGQ-VVWLNDEDARWAGIEDNDWVEIVNDNGVIVARVATSPRIPKGVAIMY 1206
                                     6899*************************9.*********************************************** PP

                                     SSHCC..............S-GHCTS--SC CS
                Molydop_binding   78 fgwwe.........agekggnaNaltddat 98  
                                     +++++         +g+kgg  N++t++++
  gi|118431398|ref|NP_147849.2| 1207 HAQERhiyvrpsklTGKKGGIHNSVTRADL 1236
                                     ***99*********************8775 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 !   17.0   3.9   6.6e-07    0.0039       1      26 []      15      40 ..      15      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-07
                     TAT_signal  1 klSRRdFLKgsAAaaAAaalggcaaa 26
                                   klSRR FLK  AAa+ +  lg +a+a
  gi|118431398|ref|NP_147849.2| 15 KLSRRGFLKVLAAAGLLSSLGPLASA 40
                                   69*******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.25s 00:00:00.96 Elapsed: 00:00:00.39
# Mc/sec: 9851.99
//
Query:       gi|118431399|ref|NP_147850.2|  [L=464]
Description: nitrate reductase beta subunit [Aeropyrum pernix K1]
Scores for complete 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-36  123.0   7.9    4.3e-36  123.0   7.9    1.6  1  Fer4_11         4Fe-4S dicluster domain
      3e-24   84.5   0.0    4.8e-24   83.9   0.0    1.3  1  Nitr_red_bet_C  Respiratory nitrate reductase beta C-terminal
    3.8e-06   26.7  15.6      0.043   13.9   1.2    3.8  3  Fer4_2          4Fe-4S binding domain
    4.6e-06   27.1  18.2    0.00018   22.0   5.6    3.2  3  Fer4_7          4Fe-4S dicluster domain
    5.3e-05   23.3  20.5    0.00093   19.3   7.7    3.2  3  Fer4_10         4Fe-4S dicluster domain
    0.00042   20.4  20.2     0.0031   17.7   5.9    3.1  3  Fer4_9          4Fe-4S dicluster domain
     0.0007   20.1   6.4      0.032   14.8   0.1    3.3  3  Fer4_13         4Fe-4S single cluster domain of Ferredoxin I
     0.0011   19.7   7.1      0.063   14.0   0.4    3.3  3  Fer4_15         4Fe-4S single cluster domain
     0.0041   17.1  14.6        1.9    8.7   0.2    3.7  3  Fer4_6          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.062   13.1  19.3       0.11   12.4   2.1    4.4  4  Fer4            4Fe-4S binding domain
       0.14   12.3  17.9       0.14   12.3   1.4    2.8  3  Fer4_21         4Fe-4S dicluster domain
       0.46   11.1  16.5        1.3    9.6   0.2    3.5  2  Fer4_17         4Fe-4S dicluster domain
       0.61   10.6   0.0       0.61   10.6   0.0    3.5  1  Fer4_8          4Fe-4S dicluster domain
        2.2    8.4   6.6        3.2    7.9   1.3    3.0  3  Fer4_19         Divergent 4Fe-4S mono-cluster


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 !  123.0   7.9   3.4e-39   4.3e-36       1      99 [.     162     259 ..     162     260 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 3.4e-39
                        Fer4_11   1 vewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrvea 80 
                                    v++++lp++C+hCl+p+C+a++p+++++k++e+G+Vl+d+++++ ++r++v+acPyk+v++n++tgk+ekC +c++r+e+
  gi|118431399|ref|NP_147850.2| 162 VFMFYLPRICNHCLNPSCLAACPRKSVYKRPEDGIVLIDQTRCR-GYRQCVQACPYKKVYYNWKTGKSEKCIFCFPRIET 240
                                    579****************************************9.*********************************** PP

                        Fer4_11  81 Gllpacvescptgalnfgd 99 
                                    G++p+c  +c+++++++g+
  gi|118431399|ref|NP_147850.2| 241 GQPPVCALTCVGKIRYVGV 259
                                    ****************996 PP

>> Nitr_red_bet_C  Respiratory nitrate reductase beta C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   3.8e-27   4.8e-24       1      80 [.     345     428 ..     345     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 3.8e-27
                 Nitr_red_bet_C   1 LsPvvsaveagkld.eeadgllpaveslRiPveYLAnLltAGdeepvekaLkrllamRaymRaknvegea...deavlee 76 
                                    L Pvv+++++++   ++ d++lp++++lRiP++YLAn+++AG+ee+v+kaLkrlla+R + R+ +veg++   ++ vlee
  gi|118431399|ref|NP_147850.2| 345 LNPVVTVLDRNGKYsADYDSILPTIDKLRIPIRYLANMFAAGNEEEVRKALKRLLAIREFFRQIEVEGKSrseAAWVLEE 424
                                    89******998887799999**********************************************99884445667888 PP

                 Nitr_red_bet_C  77 vglt 80 
                                     glt
  gi|118431399|ref|NP_147850.2| 425 NGLT 428
                                    8876 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   1.2   3.4e-05     0.043       4      20 ..       9      25 ..       6      27 .. 0.85
   2 !   12.4   1.7    0.0001      0.13       3      21 ..     164     184 ..     162     185 .. 0.89
   3 !    8.5   0.3    0.0018       2.4       5      22 .]     199     216 ..     195     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                         Fer4_2  4 vvdtdrCigCgaCvsaC 20
                                   v + d+CigC +C   C
  gi|118431399|ref|NP_147850.2|  9 VMVLDKCIGCHTCSLTC 25
                                   66789********9999 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0001
                         Fer4_2   3 vvvdtdrCigCg..aCvsaCP 21 
                                    +++ +++C++C   +C+ aCP
  gi|118431399|ref|NP_147850.2| 164 MFYLPRICNHCLnpSCLAACP 184
                                    578899*****889******* PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0018
                         Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                    +d  rC g + Cv+aCP+
  gi|118431399|ref|NP_147850.2| 199 IDQTRCRGYRQCVQACPY 216
                                    6666666656*******5 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.2   0.00012      0.15       1      15 [.      14      28 ..       5      61 .. 0.75
   2 !   22.0   5.6   1.4e-07   0.00018       2      50 ..     171     216 ..     170     219 .. 0.90
   3 ?    6.1   8.4     0.013        17       1      48 [.     203     250 ..     203     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                         Fer4_7  1 rCigCgaCvaaCpvk 15
                                   +CigC+ C  +C++ 
  gi|118431399|ref|NP_147850.2| 14 KCIGCHTCSLTCKNV 28
                                   577777777777654 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.4e-07
                         Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                    C +C    C aaCp k ++ ++e   +    v id+++C g ++Cv++CP+
  gi|118431399|ref|NP_147850.2| 171 CNHCLnpSCLAACPRKSVYKRPE---D--GIVLIDQTRCRGYRQCVQACPY 216
                                    999*5559***********9997...3..5899*****************8 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.013
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgC.........gaCvavC 48 
                                    rC g ++Cv+aCp+k ++++ +         ++++ekC++C          +C+ +C
  gi|118431399|ref|NP_147850.2| 203 RCRGYRQCVQACPYKKVYYNWK---------TGKSEKCIFCfprietgqpPVCALTC 250
                                    799999************9987.........45666777764444443333455555 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   0.00023       0.3       3      23 ..       9      27 ..       7      62 .. 0.73
   2 !   19.3   7.7   7.3e-07   0.00093       5      56 .]     167     215 ..     163     215 .. 0.93
   3 !   12.3   6.5   0.00011      0.14       2      49 ..     197     235 ..     196     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                        Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                   v   d+Ci+C +C   C  ++
  gi|118431399|ref|NP_147850.2|  9 VMVLDKCIGCHTCSLTC--KN 27
                                   56679***********9..33 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.3e-07
                        Fer4_10   5 dddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +  C +C    C +aCP      +  +++ e++ v ++  +C g  +Cv+aCP
  gi|118431399|ref|NP_147850.2| 167 LPRICNHCLnpSCLAACPR-----KSVYKRPEDGIVLIDQTRCRGYRQCVQACP 215
                                    5789****9899*******.....99999************************9 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00011
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg 49 
                                    v id+ +C + ++Cv+aCP+         ++ + + + +k+ekC++c+
  gi|118431399|ref|NP_147850.2| 197 VLIDQTRCRGYRQCVQACPY---------KKVYYNWKTGKSEKCIFCF 235
                                    689*****************.........5555555566688899995 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.6   0.00016      0.21       1      20 [.      14      33 ..       8      46 .. 0.76
   2 !   17.7   5.9   2.4e-06    0.0031       2      49 ..     171     217 ..     170     220 .. 0.91
   3 ?    3.1   8.1     0.081     1e+02       2      46 ..     204     250 ..     204     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                         Fer4_9  1 kCtgCgaCveaCpagvvved 20
                                   kC+gC++C   C++  ++++
  gi|118431399|ref|NP_147850.2| 14 KCIGCHTCSLTCKNVWTNRE 33
                                   69999999999976555544 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.4e-06
                         Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    C+ C +  C +aCp + v ++   +++ ++++   +C g ++Cv+aCp +
  gi|118431399|ref|NP_147850.2| 171 CNHCLNpsCLAACPRKSVYKRPEDGIVLIDQT---RCRGYRQCVQACPYK 217
                                    9***8667******************999886...8************85 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.081
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaC 46 
                                    C g ++Cv+aCp++ v + ++++k +       +Ci+C           C+  C
  gi|118431399|ref|NP_147850.2| 204 CRGYRQCVQACPYKKVYYNWKTGKSE-------KCIFCFPrietgqppvCALTC 250
                                    555579****************9988.......5**997666666666666666 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.5e-05     0.032       4      29 ..      13      38 ..      12      58 .. 0.88
   2 ?   -1.6   0.5       3.3   4.2e+03      11      18 ..     178     185 ..     171     197 .. 0.65
   3 !    7.3   0.1    0.0055       7.1       1      17 [.     199     215 ..     199     228 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                        Fer4_13  4 dtCiacgaCvelaPdvFeeddeggas 29
                                   d+Ci+c++C  ++ +v    + ++++
  gi|118431399|ref|NP_147850.2| 13 DKCIGCHTCSLTCKNVWTNREGQEYA 38
                                   79***************999887765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                        Fer4_13  11 aCvelaPd 18 
                                    +C +++P 
  gi|118431399|ref|NP_147850.2| 178 SCLAACPR 185
                                    57777773 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0055
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    +D+ +C +  +Cv+++P
  gi|118431399|ref|NP_147850.2| 199 IDQTRCRGYRQCVQACP 215
                                    89*************** 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 !    8.0   0.3    0.0038       4.9       6      25 ..      13      32 ..      12      46 .. 0.87
   2 !   14.0   0.4   4.9e-05     0.063       1      19 [.     197     215 ..     197     236 .. 0.89
   3 ?   -2.7   0.0       8.3   1.1e+04      40      54 ..     299     313 ..     291     314 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0038
                        Fer4_15  6 daCigcglCvaeapevfeld 25
                                   d+Cigc  C   +++v ++ 
  gi|118431399|ref|NP_147850.2| 13 DKCIGCHTCSLTCKNVWTNR 32
                                   89************998776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.9e-05
                        Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                    V +D+++C g  +Cv+++p
  gi|118431399|ref|NP_147850.2| 197 VLIDQTRCRGYRQCVQACP 215
                                    78****************6 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.3
                        Fer4_15  40 aegevpddeeeaaqe 54 
                                     e  vpd+ +eaa++
  gi|118431399|ref|NP_147850.2| 299 RESGVPDNFIEAARK 313
                                    345899999999987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   1.3    0.0031         4       7      19 ..      13      25 ..       8      32 .. 0.90
   2 !    7.9   1.3    0.0026       3.4       8      20 ..     170     184 ..     164     189 .. 0.84
   3 !    8.7   0.2    0.0015       1.9       1      21 [.     196     216 ..     196     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0031
                         Fer4_6  7 dkCigCgdCvrvC 19
                                   dkCigC  C   C
  gi|118431399|ref|NP_147850.2| 13 DKCIGCHTCSLTC 25
                                   9********9999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0026
                         Fer4_6   8 kCigC.gd.CvrvCP 20 
                                     C++C ++ C ++CP
  gi|118431399|ref|NP_147850.2| 170 ICNHClNPsCLAACP 184
                                    7****666******* PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0015
                         Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                    +v id+ +C g + Cv +CP+
  gi|118431399|ref|NP_147850.2| 196 IVLIDQTRCRGYRQCVQACPY 216
                                    57899***************8 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.1   8.3e-05      0.11       5      18 ..      12      25 ..       8      27 .. 0.87
   2 ?    0.4   0.2      0.53   6.8e+02      14      20 ..     179     185 ..     178     188 .. 0.86
   3 ?    8.6   0.2    0.0014       1.7       3      20 ..     199     216 ..     197     217 .. 0.82
   4 ?    1.8   0.5      0.19   2.4e+02       6      11 ..     229     234 ..     227     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                                   TTTSSS-THHHHHS CS
                           Fer4  5 eekCigCGaCvevC 18
                                    +kCigC +C   C
  gi|118431399|ref|NP_147850.2| 12 LDKCIGCHTCSLTC 25
                                   69********9999 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.53
                                    HHHHSTT CS
                           Fer4  14 CvevCPv 20 
                                    C  +CP 
  gi|118431399|ref|NP_147850.2| 179 CLAACPR 185
                                    99****6 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0014
                                    EETTTSSS-THHHHHSTT CS
                           Fer4   3 ideekCigCGaCvevCPv 20 
                                    id+ +C g  +Cv++CP+
  gi|118431399|ref|NP_147850.2| 199 IDQTRCRGYRQCVQACPY 216
                                    77888888889******8 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.19
                                    TTSSS- CS
                           Fer4   6 ekCigC 11 
                                    ekCi+C
  gi|118431399|ref|NP_147850.2| 229 EKCIFC 234
                                    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 ?   12.3   1.4   0.00011      0.14      37      51 ..      11      25 ..       2      30 .. 0.65
   2 ?    8.1   5.1    0.0022       2.9       8      53 ..     171     216 ..     168     220 .. 0.73
   3 ?   -3.0   0.1       6.4   8.2e+03       5      11 ..     228     234 ..     227     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                        Fer4_21 37 vedeCvGCnlCssvC 51
                                   v d+C+GC+ Cs  C
  gi|118431399|ref|NP_147850.2| 11 VLDKCIGCHTCSLTC 25
                                   456666666666666 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0022
                        Fer4_21   8 CigC..gkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCPv 53 
                                    C +C   +Cl aC+    + + + ++  + ++ + +C G   C++ CP 
  gi|118431399|ref|NP_147850.2| 171 CNHClnPSCLAACPR---KSVYKRPEDGIVLIdQTRCRGYRQCVQACPY 216
                                    4555224799****6...66667777666555388*************6 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.4
                        Fer4_21   5 edkCigC 11 
                                    ++kCi C
  gi|118431399|ref|NP_147850.2| 228 SEKCIFC 234
                                    5678877 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2     0.001       1.3      43      57 ..      12      26 ..       2      58 .. 0.75
   2 ?   -1.9  11.6       4.1   5.3e+03       2      58 ..     171     216 ..     170     234 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                        Fer4_17 43 aslCieCgeCerkCP 57
                                    ++Ci+C+ C+  C 
  gi|118431399|ref|NP_147850.2| 12 LDKCIGCHTCSLTCK 26
                                   566666666666664 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                        Fer4_17   2 CiqCgy..ClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                    C++C    Cl++Cp+   y+  ++ ++        ++        +C + ++C+++CP+
  gi|118431399|ref|NP_147850.2| 171 CNHCLNpsCLAACPRKSVYKRPEDGIVLI------DQ-------TRCRGYRQCVQACPY 216
                                    77777555777777777766655533322......11.......245555555555554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00048      0.61       2      18 ..      12      28 ..      11      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                         Fer4_8  2 lekCieCgaCqsaCpvl 18
                                   l+kCi+C  C  +C  +
  gi|118431399|ref|NP_147850.2| 12 LDKCIGCHTCSLTCKNV 28
                                   57999999999999633 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3       0.3   3.8e+02      12      32 ..      12      32 ..       3      39 .. 0.84
   2 ?   -0.9   0.0       1.4   1.8e+03       1      12 [.     118     129 ..     118     131 .. 0.87
   3 ?    7.9   1.3    0.0025       3.2      10      55 ..     166     215 ..     159     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.3
                        Fer4_19 12 relCihsgnCvkglpevFdpk 32
                                    + Ci+   C  + ++v+   
  gi|118431399|ref|NP_147850.2| 12 LDKCIGCHTCSLTCKNVWTNR 32
                                   578**************9865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                        Fer4_19   1 yegeeitiednr 12 
                                    y+ge+i++++ +
  gi|118431399|ref|NP_147850.2| 118 YSGEKIDVQWGP 129
                                    89*******976 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0025
                        Fer4_19  10 dnrelCihs..gnCvk..glpevFdpkrkpwikpdeasteeiievverCP 55 
                                    + + +C+h    +C      ++v++  +++++  d++  +  ++ v+ CP
  gi|118431399|ref|NP_147850.2| 166 YLPRICNHClnPSCLAacPRKSVYKRPEDGIVLIDQTRCRGYRQCVQACP 215
                                    5567788852235766334579***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3909.85
//
Query:       gi|14601316|ref|NP_147851.1|  [L=321]
Description: nitrate reductase gamma subunit [Aeropyrum pernix K1]
Scores for complete 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-39  134.9   0.0      1e-38  133.7   0.0    1.5  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 !  133.7   0.0   5.8e-43     1e-38       1     249 []      52     248 ..      52     248 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 5.8e-43
                                   -HHHHTS-EEEEE-EE--GGGG--S-----EEEEEEEE-SSEEE.EEEEEE----.......-S--STT----EEEEEEES CS
                         EB_dh   1 aadWskappveislsgqklvipvpgkeevkpvtVkAaydgeniy.frleWkdptksalpsevgegkeddeyedkvAvmfdd 80 
                                   +++W++++++eisl +q++v+p++g e+v++++V+Aa  +e i+ ++leW+dpt      +v+++   dey+dkvAv+f+ 
  gi|14601316|ref|NP_147851.1|  52 DSFWQQMEKAEISLVSQNIVYPMTGYEDVRTLRVAAAVSSEGILaIYLEWEDPTM-----DVPQPGGIDEYPDKVAVQFPL 127
                                   589**************************************9977**********.....********************* PP

                                   ............STT--GGG..........T-BTTB-EEEEEEETT-SS-EEEEESSTTS.EE-GGGGG............ CS
                         EB_dh  81 dqaGcwgtchegarglpgapakeeatgskymgtagsfvdlwqWkagrseplglvddgyvl.eerqndkg.ktnytynvene 159
                                              + ++lp+++          mgta+++v ++ W+a+ s++   + + y + +e++++ g +++ t+++e  
  gi|14601316|ref|NP_147851.1| 128 -----------SSDSLPYIC----------MGTAEQPVSIVLWSASGSTETLIAGSAYGMsPEHREALGlHSVPTSPIELV 187
                                   ...........*********..........*******************99999988888899999999899999999999 PP

                                   .................................---EEEEEEETTEEEEEEEEES---TTS..---TTEEEEEEEEEE-GG CS
                         EB_dh 160 kdepaamfskegfraddenesvpfdpewkegdtadvkaeakykdGkWtVelvRpLkagnpldvalepgkvydvafAvwdgk 240
                                     e+                             + + ++a ykdGkW+V+l+Rp  + ++l  +lepg++++vafAvw+g+
  gi|14601316|ref|NP_147851.1| 188 PPEA-----------------------------QVWGSNAVYKDGKWMVVLYRPTGSIHELVPTLEPGSETSVAFAVWQGS 239
                                   9888.............................9***************************55****************** PP

                                   GT--TT-SE CS
                         EB_dh 241 agershhks 249
                                   ++e +++ks
  gi|14601316|ref|NP_147851.1| 240 KAEVGGKKS 248
                                   *****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2697.10
//
Query:       gi|14601317|ref|NP_147852.1|  [L=244]
Description: hypothetical protein APE_1298 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.9    7.1   8.7        5.1    7.3   0.8    2.6  2  TMEM191C  TMEM191C family


Domain annotation for each model (and alignments):
>> TMEM191C  TMEM191C family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.8   0.00028       5.1      44      72 ..      39      67 ..      32      81 .. 0.80
   2 ?    3.9   0.9    0.0032        57      66      92 ..     132     158 ..     111     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00028
                      TMEM191C 44 lfGgagaaalrlwalgalqtllllPlgfl 72
                                  l+  ag +a+ l +l++l tll lPl + 
  gi|14601317|ref|NP_147852.1| 39 LITVAGVTAVNLSVLASLATLLALPLYME 67
                                  677889999****************9754 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0032
                      TMEM191C  66 llPlgflalpllylvlvksdavraglp 92 
                                   +l l++l+lpl y+ +++s ++ +g  
  gi|14601317|ref|NP_147852.1| 132 VLNLLWLVLPLAYIAVTRSVSIPRGKS 158
                                   578899999999999999998877743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); 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:                         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: 1727.22
//
Query:       gi|118431400|ref|NP_147854.2|  [L=178]
Description: nitrate reductase delta subunit [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-11   42.4   0.2    8.7e-11   42.0   0.2    1.1  1  Nitrate_red_del  Nitrate reductase delta subunit
  ------ inclusion threshold ------
      0.098   12.6   0.0       0.34   10.9   0.0    1.9  2  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_


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 !   42.0   0.2   9.7e-15   8.7e-11       9     136 ..      38     148 ..      31     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 9.7e-15
                Nitrate_red_del   9 eealaelaealaaededllelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgestlevrefyrqaglevaeefneppD 88 
                                    +ea+a + e+l  e+ dl++  +eY+++F     +++s y+  Yl + k +++g+  lev+  y++ +l+ + +  e p 
  gi|118431400|ref|NP_147854.2|  38 GEAAALIMEFL--EKLDLERADEEYVAVFE--MPPKCSIYAHTYLLKGKEDMVGQLLLEVKSHYKAKQLDMPVDR-EIPT 112
                                    56677799999..9****************..7999*********97778********************66665.6699 PP

                Nitrate_red_del  89 HlaveLeflahLaereaeaeeaeeaealleaqkafleehllpWlpefa 136
                                    +l+++Le+la    +e             +a + f +++l+pW++e+a
  gi|118431400|ref|NP_147854.2| 113 YLPAMLEYLALVY-DEDP-----------KAARRFAKKYLQPWVGELA 148
                                    **********555.4444...........79*************9986 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.17   1.5e+03      55      71 ..       4      20 ..       1      27 [. 0.81
   2 ?   10.9   0.0   3.8e-05      0.34      28      69 ..      71     112 ..      43     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.17
                Phage_rep_org_N 55 taemlalifnreletvr 71
                                   t ++l++if+ + e+++
  gi|118431400|ref|NP_147854.2|  4 TLKTLSIIFSYPSEDLE 20
                                   78999***999988876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 3.8e-05
                Phage_rep_org_N  28 viwlkllvlaGKlnenGelylsenipytaemlalifnrelet 69 
                                     i+ + ++l GK +  G+l l+ +  y a++l + ++re+ t
  gi|118431400|ref|NP_147854.2|  71 SIYAHTYLLKGKEDMVGQLLLEVKSHYKAKQLDMPVDREIPT 112
                                    58999999******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1360.80
//
Query:       gi|118431401|ref|NP_147855.2|  [L=260]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-31  107.5   0.0    1.1e-30  106.9   0.0    1.2  1  ABC_tran     ABC transporter
    8.9e-18   65.1   0.1    1.4e-08   34.9   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-06   27.9   0.1    1.5e-05   24.5   0.1    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
      4e-06   27.5   0.0      6e-06   26.9   0.0    1.3  1  AAA_23       AAA domain
    0.00013   21.7   0.1    0.00023   20.8   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
    0.00015   21.6   0.1    0.00033   20.5   0.0    1.5  2  AAA_15       AAA ATPase domain
     0.0004   20.8   0.1    0.00062   20.2   0.1    1.4  1  AAA_16       AAA ATPase domain
    0.00044   20.5   0.6     0.0068   16.7   0.6    2.2  1  AAA_22       AAA domain
     0.0014   18.4   0.1     0.0038   17.0   0.1    1.7  1  AAA_30       AAA domain
     0.0017   18.8   0.0     0.0028   18.1   0.0    1.5  1  AAA          ATPase family associated with various cellular a
     0.0062   16.5   0.1       0.01   15.7   0.1    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0067   16.0   0.1      0.017   14.7   0.0    1.6  2  AAA_27       AAA domain
  ------ inclusion threshold ------
      0.013   14.3   0.1      0.082   11.7   0.2    1.9  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.039   14.0   0.1      0.091   12.8   0.1    1.6  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.049   13.1   0.0       0.33   10.4   0.0    2.0  2  PhoH         PhoH-like protein
      0.062   12.5   0.0        0.1   11.8   0.0    1.2  1  DUF2813      Protein of unknown function (DUF2813)
      0.066   13.2   0.0       0.15   12.1   0.0    1.6  1  AAA_5        AAA domain (dynein-related subfamily)
      0.077   13.2   0.2       0.39   11.0   0.1    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.092   13.0   0.6       0.19   11.9   0.3    1.7  1  AAA_28       AAA domain
      0.097   12.8   0.0       0.26   11.5   0.0    1.7  2  AAA_33       AAA domain
      0.099   11.5   0.0       0.13   11.1   0.0    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
      0.099   12.4   0.0       0.15   11.8   0.0    1.3  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
        0.1   12.2   0.3       0.22   11.1   0.3    1.5  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
        0.1   12.5   0.1       0.18   11.7   0.1    1.3  1  NACHT        NACHT domain
       0.16   11.6   0.0       0.32   10.6   0.0    1.6  1  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 !  106.9   0.0   1.5e-33   1.1e-30       2     136 ..      22     168 ..      21     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1.5e-33
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke.qeleslrkeigvlpqepqlfpelt 75 
                                    kn+sl++++g+++ ++G+nGaGK+tLlk+++g  k      t G+i+l+g+d+++ ++ e++r+ + ++ +  ++f+elt
  gi|118431401|ref|NP_147855.2|  22 KNLSLSVEKGSITCLIGPNGAGKTTLLKAVSGVIKYergrvTRGSIQLEGEDITNrEPDEIARRGVIYVMEGRRIFKELT 101
                                    8*********************************996666677777*******99999********************** PP

                                    HHHH.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     +en         +s+++i  +ls +      ++++++++ +LSgG++q++a+a+all +pkll+lDEp+
  gi|118431401|ref|NP_147855.2| 102 TEENlvsvayaagASRDDIRSVLSYFP---RLKERLGEKAGNLSGGEQQMLAIAMALLYRPKLLMLDEPS 168
                                    ********9966666666666666666...5669999999*****************************5 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 !   34.9   0.0   1.9e-11   1.4e-08       1     107 [.      33     133 ..      33     140 .. 0.91
   2 !   28.7   0.1   1.5e-09   1.1e-06     234     293 ..     138     195 ..     133     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.9e-11
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrler 80 
                                    +++liGpNg+GK++LL+a +++   +++ +g+ +      +i+     +++++p++ ++ +++  +++g r+  +l+ e+
  gi|118431401|ref|NP_147855.2|  33 ITCLIGPNGAGKTTLLKAVSGV---IKYERGRVTRG----SIQLEGEDITNREPDEIARRGVI-YVMEGRRIFKELTTEE 104
                                    79********************...88888888888....***********************.**************** PP

                         AAA_21  81 sqv..eeklssvetllesgllldkrslee 107
                                    + v  +   ++++++ +s l  ++r +e+
  gi|118431401|ref|NP_147855.2| 105 NLVsvAYAAGASRDDIRSVLSYFPRLKER 133
                                    ***99999999999999998888888876 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.5e-09
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvi 293
                                    a +lS G +++la++ all+++   +ll +DEp +gL Pk+++ ++  +k l+r +g  ++
  gi|118431401|ref|NP_147855.2| 138 AGNLSGGEQQMLAIAMALLYRP---KLLMLDEPSLGLAPKITSQIYATIKMLHReEGLTIL 195
                                    5789******************...99*******************999888886666665 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 !   24.5   0.1   2.1e-08   1.5e-05      24     184 ..      31     184 ..      20     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.1e-08
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH...CCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrse...klsdlihkskekasvkkaeveitfdnedkk.lkiekeevsi 99 
                                     s+t+++GpNG+GK+ ll A++ v+  +  +  r +   + +d+ +    ++  + a+  +++  e+++ +k+ ++e ++
  gi|118431401|ref|NP_147855.2|  31 GSITCLIGPNGAGKTTLLKAVSGVIKYERGRVTRGSiqlEGEDITN----REPDEIARRGVIYVMEGRRiFKELTTEENL 106
                                    4689******************999999887766552112334433....344444444455545666546666777788 PP

                                    EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       ++  g s+  i      +  ++e l +   +  +LSgGe++++a+a+ +    ++p+ l +lDe    L  k ++++
  gi|118431401|ref|NP_147855.2| 107 VSVAYAAGASRDDIRSVLSYFPRLKERLGE---KAGNLSGGEQQMLAIAMAL---LYRPK-LLMLDEPSLGLAPKITSQI 179
                                    888899999888888877777888877766...5679********9999874...45555.5567776666666666666 PP

                                    HHHHH CS
                                    xxxxx RF
                          SMC_N 180 aellk 184
                                       +k
  gi|118431401|ref|NP_147855.2| 180 YATIK 184
                                    66665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.4e-09     6e-06      13      62 ..      24      78 ..      14     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.4e-09
                         AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrks....grgfeksd 62
                                    ++  +k  +t+++GpNGaGKTT+l A+  +   e +r  r+s    g+++ +++
  gi|118431401|ref|NP_147855.2| 24 LSLSVEKgSITCLIGPNGAGKTTLLKAVSGVIKYERGRVTRGSiqleGEDITNRE 78
                                   4555544269******************999866677777766555544444444 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 !   20.8   0.1   3.2e-07   0.00023      17      45 ..      26      54 ..      20      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.2e-07
                         AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqal 45
                                   ++++ kg +t l+Gp+G+GK+Tll A++ +
  gi|118431401|ref|NP_147855.2| 26 LSVE-KGsITCLIGPNGAGKTTLLKAVSGV 54
                                   5555.4569***************999866 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.6e-07   0.00033      15      44 ..      22      52 ..      20     109 .. 0.82
   2 ?   -2.3   0.0       3.9   2.8e+03     324     351 ..     159     186 ..     137     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.6e-07
                         AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileald 44
                                   k+ ++++++  +t+liG+N++GK+++l+a  
  gi|118431401|ref|NP_147855.2| 22 KNLSLSVEKGsITCLIGPNGAGKTTLLKAVS 52
                                   66667777768*****************965 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.9
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkel 351
                                    +++l+++EP + L p+  ++++ ++k l
  gi|118431401|ref|NP_147855.2| 159 PKLLMLDEPSLGLAPKITSQIYATIKML 186
                                    4569999999999888888877777655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   8.6e-07   0.00062      22     107 ..      31     129 ..      21     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.6e-07
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa........ipysalaqalareellrqlldeaesae 93 
                                    g  +++ l+G+ G GK++l++++   ++ ++g ++rg  +  +++        i++  ++ + + ++++++l +e++  +
  gi|118431401|ref|NP_147855.2|  31 G--SITCLIGPNGAGKTTLLKAVSGVIKYERGRVTRGSIQLEGEDitnrepdeIARRGVIYVMEGRRIFKELTTEENLVS 108
                                    3..7899***********************99998888888866644445555555665555556688888888855555 PP

                         AAA_16  94 leawrekleeala.......a 107
                                    +++++ + ++ ++        
  gi|118431401|ref|NP_147855.2| 109 VAYAAGASRDDIRsvlsyfpR 129
                                    555544444444433334441 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   9.5e-06    0.0068       4      38 ..      30      92 ..      27     205 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.5e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee................................e 38
                                   + +i++++G+ G+GKTtll+ +    +  ++  +                                e
  gi|118431401|ref|NP_147855.2| 30 KGSITCLIGPNGAGKTTLLKAVSGVIK--YE--RgrvtrgsiqlegeditnrepdeiarrgviyvmE 92
                                   6799****************9865432..11..1224455555566666666555555555555550 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   5.3e-06    0.0038      17      49 ..      30      62 ..      24      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.3e-06
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrv 49
                                   +  +++l Gp G+GKtt+lka+  +++ + grv
  gi|118431401|ref|NP_147855.2| 30 KGSITCLIGPNGAGKTTLLKAVSGVIKYERGRV 62
                                   445999******************999986666 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 !   18.1   0.0   3.9e-06    0.0028       2      44 ..      35      95 ..      34     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.9e-06
                                   EEESSTTSSHHHHHHHHHHHHTHE.......EEEEETTTCSSS...........STTHHHH CS
                            AAA  2 llyGppGtGKTllakavakelgve.......fleisgsellsk...........yvgesek 44
                                   +l+Gp G GKT+l kav   ++ e        ++++g ++++            yv e+ +
  gi|118431401|ref|NP_147855.2| 35 CLIGPNGAGKTTLLKAVSGVIKYErgrvtrgSIQLEGEDITNRepdeiarrgviYVMEGRR 95
                                   79*****************997554444455677777777765666666666664433333 PP

>> RsgA_GTPase  RsgA GTPase
   #    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      96     130 ..      27      62 ..      14      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                                    HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                     +++ ++++l+G+ G+GK+tL++a+ +  + + g v
  gi|118431401|ref|NP_147855.2|  27 SVEKgSITCLIGPNGAGKTTLLKAVSGVIKYERGRV 62 
                                    555559******************998877766665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.4e-05     0.017      18      47 ..      23      52 ..      20      56 .. 0.89
   2 ?   -3.7   0.0        10   7.2e+03     140     169 ..     102     131 ..      99     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                   +l++s e+ +++ ++GpN AGK+t+l+A+s
  gi|118431401|ref|NP_147855.2| 23 NLSLSVEKGSITCLIGPNGAGKTTLLKAVS 52
                                   678888899999****************98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 10
                         AAA_27 140 aegelgqlLfeasaGlaslrevleaLeaea 169
                                    +e++l ++ ++a+a+  ++r+vl  + + +
  gi|118431401|ref|NP_147855.2| 102 TEENLVSVAYAAGASRDDIRSVLSYFPRLK 131
                                    566777777888888888888877655554 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 ?   11.7   0.2   0.00011     0.082     240     265 ..      26      52 ..      22      58 .. 0.89
   2 ?   -0.1   0.0      0.42     3e+02     298     348 ..     116     166 ..     100     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                    EEE-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAle 265
                                    + + kG +t ++G++  GK+TLL+A++
  gi|118431401|ref|NP_147855.2|  26 LSVEKGsITCLIGPNGAGKTTLLKAVS 52 
                                    5688999******************86 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.42
                                    EEE--TTTB---CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEG CS
                     ABC_ATPase 298 kgvDispFinnLPegkdttkfstedASGStsqAanimealeagakllLiDE 348
                                    ++ Di++ ++  P  k+       + SG   q  +i+ al  + kll++DE
  gi|118431401|ref|NP_147855.2| 116 SRDDIRSVLSYFPRLKERLGEKAGNLSGGEQQMLAIAMALLYRPKLLMLDE 166
                                    56789999999999999889999999************************9 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00013     0.091      18      46 ..      28      58 ..      18      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                   H..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE 18 l..gdvilLeGdLGaGKTtlvrglakalgve 46
                                   +  g++ +L G+ GaGKTtl +++   +++e
  gi|118431401|ref|NP_147855.2| 28 VekGSITCLIGPNGAGKTTLLKAVSGVIKYE 58
                                   2337789***************998776665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00045      0.33      16      51 ..      28      64 ..      20      84 .. 0.75
   2 ?    0.2   0.0      0.61   4.4e+02      47      84 ..     118     157 ..     102     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                                   HHH-SEEEEE--TTSSTTHH.HHHHHHHHHHTTS-SE CS
                           PhoH 16 lkkndivfaiGpaGtGKtyl.avalavealkkkkvkr 51
                                   ++k +i++ iGp G+GKt l   + +v  +++++v+r
  gi|118431401|ref|NP_147855.2| 28 VEKGSITCLIGPNGAGKTTLlKAVSGVIKYERGRVTR 64
                                   56888************86515566777777666654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.61
                                    TS-SEEEEEE-S--T..T----SS---------TTTHHHH CS
                           PhoH  47 kkvkriiltrpavea..geelGflpgdleekvdpylrply 84 
                                    ++++ ++   p ++   ge+ G l g +++ +++ ++ ly
  gi|118431401|ref|NP_147855.2| 118 DDIRSVLSYFPRLKErlGEKAGNLSGGEQQMLAIAMALLY 157
                                    4555555555666433599*******99999999999888 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.1      14      48 ..      21      57 ..      18      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                        DUF2813 14 inrLSlslee..ntvLiGENaWGKSSLldALslilnv 48
                                   i+ LSls+e+   t LiG N  GK  Ll+A s +++ 
  gi|118431401|ref|NP_147855.2| 21 IKNLSLSVEKgsITCLIGPNGAGKTTLLKAVSGVIKY 57
                                   899999999722578****************988775 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 ?   12.1   0.0   0.00021      0.15       3      25 ..      35      57 ..      33      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                                   EEE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  3 lLvGppGtgKselaerlaaalnr 25
                                   +L+Gp G gK++l + ++ +++ 
  gi|118431401|ref|NP_147855.2| 35 CLIGPNGAGKTTLLKAVSGVIKY 57
                                   9***************9999843 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   0.1   0.00055      0.39      25      71 ..     133     166 ..     119     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                        SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDE 71 
                                    +l +++g+lSGGe+q+l     a a+a ly+         +l++LDE
  gi|118431401|ref|NP_147855.2| 133 RLGEKAGNLSGGEQQML-----AIAMALLYRP--------KLLMLDE 166
                                    466789********654.....4444455554........3555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00027      0.19       3      20 ..      35      52 ..      33      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                   +++G+ ++GKTtll+a +
  gi|118431401|ref|NP_147855.2| 35 CLIGPNGAGKTTLLKAVS 52
                                   89*************987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00036      0.26       3      20 ..      35      52 ..      33      87 .. 0.87
   2 ?   -2.5   0.0       7.1   5.1e+03      18      38 ..     185     206 ..     182     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                         AAA_33  3 llvGlpGsGKstlaerll 20
                                    l+G++G+GK+tl++ + 
  gi|118431401|ref|NP_147855.2| 35 CLIGPNGAGKTTLLKAVS 52
                                   689**********99875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.1
                         AAA_33  18 rllkklg.avllssdtlrrrlf 38 
                                     l++++g ++ll++ ++r++l+
  gi|118431401|ref|NP_147855.2| 185 MLHREEGlTILLAEQNARKALE 206
                                    5788888899999999999886 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.13      29      87 ..      35      98 ..      25     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                           DLIC 29 lvlGedgsGkttliaklqGveeekkGrG....leylyldvkdedrddltrlnv.wildGdlyhk 87
                                    ++G +g+Gkttl+  + Gv ++ +Gr     ++    d+ + + d+ +r +v ++++G    k
  gi|118431401|ref|NP_147855.2| 35 CLIGPNGAGKTTLLKAVSGVIKYERGRVtrgsIQLEGEDITNREPDEIARRGViYVMEGRRIFK 98
                                   589***********************85111122223344555556666665435666666555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00022      0.15       5      31 ..      35      60 ..      31      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                      PduV-EutP  5 lliGkvgsGKttLtqalkgeelkYkkt 31
                                    liG+ g+GKttL +a++g  +kY++ 
  gi|118431401|ref|NP_147855.2| 35 CLIGPNGAGKTTLLKAVSG-VIKYERG 60
                                   69***************98.4788765 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 ?   11.1   0.3    0.0003      0.22       2      20 ..      33      51 ..      32      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                                   EEEEEESTTCCHHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnhl 20
                                   +t l G+ G+GKTtLl+++
  gi|118431401|ref|NP_147855.2| 33 ITCLIGPNGAGKTTLLKAV 51
                                   68899***********986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00025      0.18       3      21 ..      34      52 ..      32      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00025
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                    +l G++G GKTtLl+ + 
  gi|118431401|ref|NP_147855.2| 34 TCLIGPNGAGKTTLLKAVS 52
                                   799************9875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00044      0.32      31      51 ..      29      49 ..      22      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                         AAA_25 31 pagelallaGapgtGKttlal 51
                                    +g+++ l+G+ g+GKttl+ 
  gi|118431401|ref|NP_147855.2| 29 EKGSITCLIGPNGAGKTTLLK 49
                                   6899**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1668.22
//
Query:       gi|118431402|ref|NP_147857.2|  [L=427]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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  220.7   0.2    5.1e-65  220.4   0.2    1.1  1  Peripla_BP_6  Periplasmic binding protein
  ------ inclusion threshold ------
       0.09   12.7   0.0       0.17   11.8   0.0    1.4  1  AidB_N        Adaptive response protein AidB N-terminal domai


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 !  220.4   0.2   5.7e-69   5.1e-65       1     339 [.      45     399 ..      45     403 .. 0.91

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 5.7e-69
                                    EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET...TE..EEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE CS
                   Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGin...Gr..kielverDdaydpdraaeaarrlvdqdgvdalvg 75 
                                    +i++Gll++++Gp++++gk++  ga++af+++N++G i+   G+   i+++ rD+ay+p++a e +r++ d+ gv a++g
  gi|118431402|ref|NP_147857.2|  45 TINVGLLVDETGPTSDVGKGYSLGAELAFKYFNEKG-IYtkdGVrvNINYIKRDYAYNPTTAEEYYREFRDRYGVIAIIG 123
                                    79********************************97.7767776558********************************* PP

                                    -BSHHHHHHHHHHHHHHT-EEEESS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEES.SHHHHHHHHH CS
                   Peripla_BP_6  76 plssavaaavaevlakdgvpvigpagltgekcspyvfslgpsysaqasalveylakelggkkvalvyad.yafgregiaa 154
                                     +++a+++ +++ +++d++ +i+++ ++   ++p +f+++p+ys+qa +++ +la+e+g  k+al y+   a++r++i a
  gi|118431402|ref|NP_147857.2| 124 -WGTADTEKLSDQVDTDKITYISASYSAKLLVKPFNFYPAPDYSTQACSGLAFLASEFGQGKLALAYDSkVAYSRSPIGA 202
                                    .7*****************************************************************888********** PP

                                    HHHHHHCCTEEEEEEEEE-TTH..HHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHHH CS
                   Peripla_BP_6 155 lkaaakaaGgevvgeepvplgt..tdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsgseedl 232
                                    +k+aa ++G++vvg++++pl +  +d + +++++ aa +d+v++++t +++  l +a+a++Glda ++l   w+++e + 
  gi|118431402|ref|NP_147857.2| 203 IKKAAPSLGLQVVGDYDLPLRAteADAERIAREMLAADPDYVWCGNTISSCSLLGRAMAKVGLDA-FLLTNVWGFDERSP 281
                                    *******************9887899999***********************************9.89999********* PP

                                    HHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHH....TTGGC--HHHHHHHHHHHHHHHHHHCCTHCC.....HHH CS
                   Peripla_BP_6 233 kalggeaaegvlavtpyfpdldnpavrafvaayeaay....ggapppsqfaaggyiaadlllealkaagslt.....rea 303
                                    + +g+++  +v++++p+ + + ++ v+ +++ +eaa      + ++ ++  ++g+++++ll++a++++ s +     +ea
  gi|118431402|ref|NP_147857.2| 282 QLIGEGGYGKVFGISPFIYPMFGQDVEGIQTIFEAARmngvSE-DQINLRVVQGFVNVWLLIKAIESVTSQDlqergGEA 360
                                    ******************************9999985453333.469********************9643333444*** PP

                                    HHHHHHHS-BE..CCCTC.CBEECTTSBEE--EEEEEE- CS
                   Peripla_BP_6 304 vraaleslgfd..gllgp.lkftaedhqasrpvyvvqvd 339
                                    +++ale+ +fd  g++++ +++ +  h a r+v++ ++ 
  gi|118431402|ref|NP_147857.2| 361 LKEALEANTFDlgGITADtIDYEPGFHLAYRKVFIIKLG 399
                                    **********97667765155558899999999998765 PP

>> AidB_N  Adaptive response protein AidB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17      39      82 ..     346     389 ..     333     398 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                         AidB_N  39 ellgsaevlelarlanrnpPrlrthDrfGrRiDevefhpayhal 82 
                                    e+++s++++e++ +a +++ + +t+D  G  +D+++++p++h  
  gi|118431402|ref|NP_147857.2| 346 ESVTSQDLQERGGEALKEALEANTFDLGGITADTIDYEPGFHLA 389
                                    578999************************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2765.40
//
Query:       gi|118431403|ref|NP_147858.2|  [L=345]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for 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  38.1      2e-32  112.4  38.1    2.0  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
          5    6.1   6.0        1.2    8.2   0.3    2.6  3  TMEM237       Transmembrane protein 237


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 ?    2.0   0.3      0.01        94      47      74 ..      15      41 ..       8      42 .. 0.77
   2 !  112.4  38.1   2.3e-36     2e-32       2     267 ..      44     319 ..      43     320 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.01
                   BPD_transp_2 47 llalllsllllallvallvgaavglllg 74
                                   ++ +++   ++al++a+++++a+ +++g
  gi|118431403|ref|NP_147858.2| 15 AIFRYPI-HWAALILAVVAAVAAPFVIG 41
                                   5555555.79999999999999988886 PP

  == domain 2  score: 112.4 bits;  conditional E-value: 2.3e-36
                   BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlk 81 
                                     lnll++ +i+ iaA+Gl+++ g+aG+i+l+h+++m++Gay++a ++  l+ +  ++l++a l++a++g +l l++ rlk
  gi|118431403|ref|NP_147858.2|  44 YLNLLVVMMIFWIAAIGLNITLGLAGQISLAHAALMGIGAYTVANAALHLGVNSVAILPIAGLAAALLGIILSLPSFRLK 123
                                    689***************************************************************************** PP

                   BPD_transp_2  82 vdeliitllllsvlvgltlllltgitsgvkg..qssvkellgfagallsflsavivllalllvlavllllrrtrfGralr 159
                                    + +l+++ l+  +++ +++     i  ++++  +++ k+llg++ +  + l  +i +++ ++++++   + r+++Gra++
  gi|118431403|ref|NP_147858.2| 124 EYYLAMASLAAQLILEYVY---SRIDPDQYTpvPPETKTLLGISLTEPTALYYFILAIT-VVMALAAANIGRSSLGRAMK 199
                                    ****987665544444444...5555555541034555555555555554444444444.44555556689********* PP

                   BPD_transp_2 160 avgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGga.....gsllgtvi 233
                                    av++n  a++a Ginv  vk+++f+i+g+ Ag+aG l+a ++ +i +  + +  +++ + +v++Gg      gsllg+++
  gi|118431403|ref|NP_147858.2| 200 AVRDNDVASEAIGINVQLVKATAFAIGGFYAGVAGGLYAIYSSGIGWeGFTLVNSIELLGMVLIGGPgrvvwGSLLGVLV 279
                                    *******************************************************************6666666666666 PP

                   BPD_transp_2 234 Galiigvvksllltllgi......ptelarvllgallilv 267
                                      +   +++s ++ ll        +++ ++++lg l++++
  gi|118431403|ref|NP_147858.2| 280 MRTGWTMMESTITPLLAGiglsiiASSAKYIVLGFLIVAF 319
                                    66666677776666655588888889********999986 PP

>> TMEM237  Transmembrane protein 237
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.3   0.00014       1.2     139     165 ..     169     195 ..     140     211 .. 0.84
   2 ?   -0.1   0.1     0.045   4.1e+02      75     107 ..     203     234 ..     196     253 .. 0.74
   3 ?   -1.9   0.1      0.16   1.5e+03      89     110 ..     282     303 ..     275     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00014
                        TMEM237 139 qslfYlllalstvsalDrldLakasta 165
                                     +l+Y++la+ +v+al   ++++ s  
  gi|118431403|ref|NP_147858.2| 169 TALYYFILAITVVMALAAANIGRSSLG 195
                                    489*************99999998765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.045
                        TMEM237  75 ptllttrdvairvhkafrvlglflhGlLAGial 107
                                     +++ ++ ++i+v+   +  ++++ G+ AG+a 
  gi|118431403|ref|NP_147858.2| 203 DNDVASEAIGINVQL-VKATAFAIGGFYAGVAG 234
                                    556667777777764.588899********995 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.16
                        TMEM237  89 kafrvlglflhGlLAGialwni 110
                                     ++ ++  ++  lLAGi l  i
  gi|118431403|ref|NP_147858.2| 282 TGWTMMESTITPLLAGIGLSII 303
                                    5788888889999999987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2576.09
//
Query:       gi|14601324|ref|NP_147859.1|  [L=294]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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   93.6  36.6    1.3e-26   93.4  36.6    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 !   93.4  36.6   7.1e-31   1.3e-26       2     267 ..      12     278 ..      11     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 7.1e-31
                  BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkv 82 
                                   +++++ +++++ ++AlG+++v+++   in+++ ++++l+ay+a++++ + ++ ll+a+++al++++av +++++ v++  +
  gi|14601324|ref|NP_147859.1|  12 VFQGVLMGLLYSLIALGYNIVYRVNKSINFAVPEVVLLAAYLAWIASIATGN-LLAAVAIALAASIAVSMAMERFVAKPLL 91 
                                   57889999*******************************************9.**************************** PP

                  BPD_transp_2  83 deliitllllsvlvgltllll..tgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGralrav 161
                                    ++ i+l++ ++ ++++l  +    +++ v+  +  +e+ +     l +      l  +++++ +++l r+t+fG a+r v
  gi|14601324|ref|NP_147859.1|  92 GRPPIALIGATLGLFYMLKGVvlIVGKGEVAVLPFYPEVYRLGFLTLGTNDVIALLGSIAVLAGIIVLHRKTSFGAAMRGV 172
                                   ***88777555555555522200556666777777777777777777777655557788888888888899********** PP

                  BPD_transp_2 162 geneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgagsllgtviGaliigvvk 242
                                   +e+ e a+a G++v+r+ l+ ++++g+++gla++ll+  ++++p      + + a+aa +++g+ sl g+v+G++ +g+++
  gi|14601324|ref|NP_147859.1| 173 AEDAEGAAAYGLPVRRLMLAGWALAGLVSGLAALLLSIKTQVSP--DLEFFAIIALAASLIAGLDSLGGIVVGGVFLGLAE 251
                                   ********************************************..555677889************************** PP

                  BPD_transp_2 243 sllltllgi..ptelarvllgallilv 267
                                   + ++  l    p   +++ +++l++++
  gi|14601324|ref|NP_147859.1| 252 QIASKTLDPylPGIGRDIAFFILFLVL 278
                                   *77777766766666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2352.62
//
Query:       gi|14601325|ref|NP_147860.1|  [L=651]
Description: fatty-acid--CoA ligase [Aeropyrum pernix K1]
Scores for 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-91  305.3   0.0    6.9e-91  304.9   0.0    1.1  1  AMP-binding  AMP-binding enzyme


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 !  304.9   0.0   3.8e-95   6.9e-91       1     422 [.      27     489 ..      27     490 .. 0.89

  Alignments for each domain:
  == domain 1  score: 304.9 bits;  conditional E-value: 3.8e-95
                                   HHHHHHHSTTSEEEEE..CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                   AMP-binding   1 leeqaaktpdkvalvd..sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                   le++a+++p++va+ +  +g ++++T+r+++ rv  +A +L++lG+++gd+ a++  n+p wv+  ++++ +G+ ++ ++ 
  gi|14601325|ref|NP_147860.1|  27 LEWRARTQPGRVAFRWkrYGIWRRYTWRDYYLRVAYAALALENLGLGPGDTGAFITFNRPSWVIYEVGVQLLGGRAMGIYR 107
                                   689***********88999************************************************************** PP

                                   TS-HHHHHHHHHHHTESEEE............E..TCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCT CS
                   AMP-binding  80 tltaeelayiledseakvli............a..tvdselleklleaaakleavklvivldadellkeeelkeeeeseek 146
                                   ++ ++e+ y+l++ +ak+++            +  +vd++ +++++  ++++ +v +++v+  d ++  ++l+++ +++++
  gi|14601325|ref|NP_147860.1| 108 DSLSDEVGYLLDSGDAKFVLvegqeqldrvldSgvDVDKIIVDEAKGLHQYRGMVGSKLVTFGDVMRLGRKLYSDGGDQQV 188
                                   *************************999887626778888899************************************99 PP

                                   TS-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHT CS
                   AMP-binding 147 aekpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllalls 227
                                   +  +    el+pd ++ ++ TSGTTG PK +m+s +n++a++++l  +t + ++ed +++s+lp a+i ++++++ ++++ 
  gi|14601325|ref|NP_147860.1| 189 K--K-LMGELEPDMVCGLFTTSGTTGLPKLAMISFKNMLAMAHQL--NTVDPVREDWEYVSFLPTAWIGEQMMSIPYHMIG 264
                                   7..3.44479*******************************9997..56677889************************** PP

                                   T-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHH.......HH.CCCHHCHHHHC.................... CS
                   AMP-binding 228 GatvvllpkdaaldpklllelieklkvtviagvPrvleal.......le.sgalkaakkak.................... 280
                                   G++v ++++      ++l+++++++ +++++++Prv+e++       ++ ++++k     +                    
  gi|14601325|ref|NP_147860.1| 265 GFKVNFPETP-----HTLWRDFREIAPHFMFSPPRVWERIakdimarVDdADPIK-----Raafrlaykigyeaarrrlvk 335
                                   ******8844.....4578*********************777766644333333.....022333444557777778888 PP

                                   .........................CGTT-SEEE...EESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTC CS
                   AMP-binding 281 .........................dlsslrlvl...lggeplspellrffralfgeevlegYGlTEttgvvtvlpleedk 333
                                                            d  +l+ ++   +gg+ + ++ + f+++l+ + + ++YG+TE +g+++ ++ ++d+
  gi|14601325|ref|NP_147860.1| 336 grsrpptlwralyylaywlalravlDKAGLKRIVrayTGGAMIGEDYVIFYHSLGVN-LKQIYGQTEVAGIAV-VH-PDDD 413
                                   88888888888888888888888874444444433339****************987.**************9.77.5666 PP

                                   TSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEE CS
                   AMP-binding 334 kklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivg 414
                                   +++ +vGkplp +evki+++           Ge+l+r+p +mkgY+k++eata++++  ++wlrTGD+g+l+edG+l++++
  gi|14601325|ref|NP_147860.1| 414 VRPDTVGKPLPLTEVKIAED-----------GEILMRSPAMMKGYYKNEEATAKTIV--DGWLRTGDVGVLTEDGHLKVLD 481
                                   899**************987...........9************************9..57******************** PP

                                   ECCCEEEE CS
                   AMP-binding 415 Rkkdlikl 422
                                   R+k++i+l
  gi|14601325|ref|NP_147860.1| 482 RAKEIIIL 489
                                   ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4733.51
//
Query:       gi|14601326|ref|NP_147861.1|  [L=250]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-30  104.7   0.0    7.4e-30  104.2   0.0    1.2  1  ABC_tran      ABC transporter
    4.5e-08   32.8   0.9    7.1e-08   32.2   0.0    1.8  2  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    2.4e-06   27.6   0.7    0.00093   19.1   0.4    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0004   21.0   0.1    0.00061   20.4   0.1    1.3  1  AAA_23        AAA domain
     0.0029   17.3   0.0     0.0053   16.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0051   16.9   1.0      0.038   14.1   1.0    2.3  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0064   16.2   0.0     0.0085   15.8   0.0    1.4  1  AAA_30        AAA domain
     0.0093   15.4   0.5      0.092   12.2   0.0    2.0  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.027   14.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.036   14.5   0.0      0.068   13.5   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.044   13.5   0.0      0.062   13.0   0.0    1.2  1  AAA_15        AAA ATPase domain
      0.094   12.2   1.0        0.2   11.1   1.0    1.6  1  KdpD          Osmosensitive K+ channel His kinase sensor doma
      0.098   12.2   2.0       0.56    9.8   0.1    2.3  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.11   12.1   0.0       0.14   11.8   0.0    1.1  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.14   12.6   0.2        5.5    7.4   0.0    2.2  2  AAA           ATPase family associated with various cellular 
       0.14   12.2   0.6          1    9.4   0.6    2.0  1  Dynamin_N     Dynamin family
       0.17   10.7   2.9        4.7    5.9   0.5    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 !  104.2   0.0     7e-33   7.4e-30       1     137 []      17     178 ..      17     178 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 7e-33
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                   l+nvs+++++ge+++i+G+nGaGK++Ll++++g +kp+ G++ ++g+d++  +++++    ++  +q+++lf  +tv en 
  gi|14601326|ref|NP_147861.1|  17 LDNVSVEVRRGEILGIIGPNGAGKTSLLNVITGVYKPQRGRVYFKGRDITGlKPHQRITLGLSRTFQHSELFHSMTVLENi 97 
                                   79*************************************************9***************************** PP

                                   ...........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                   ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                                              e++e++e++++ l+l+e +++++      L  G +++v la al+++p+++l+D
  gi|14601326|ref|NP_147861.1|  98 mvrlhpwtrgsilekalwafrakrwevEARERAEHVIDLLDLHEHRHSPI----GALPPGIQKKVDLAGALAQNPEVVLMD 174
                                   ***********************999999999************999999....*************************** PP

                                   STTT CS
                                   xxxx RF
                      ABC_tran 134 Epta 137
                                   Ep+a
  gi|14601326|ref|NP_147861.1| 175 EPMA 178
                                   **85 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 ?   -2.6   0.1       5.5   5.8e+03      13      18 ..     166     171 ..     165     171 .. 0.80
   2 !   32.2   0.0   6.7e-11   7.1e-08       1      23 []     227     249 ..     227     249 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.5
                  BCA_ABC_TP_C  13 ndPrVi 18 
                                    +P+V+
  gi|14601326|ref|NP_147861.1| 166 QNPEVV 171
                                   59*995 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 6.7e-11
                  BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                   +vI eG+P E ++d+rV++AYLG
  gi|14601326|ref|NP_147861.1| 227 KVIFEGPPHEAVADERVRKAYLG 249
                                   79********************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 !   19.1   0.4   8.8e-07   0.00093       2      22 ..      30      50 ..      29      77 .. 0.83
   2 !    6.4   0.0    0.0064       6.8     234     286 ..     147     196 ..     143     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.8e-07
                        AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                   ++iGpNg+GK++LL  + ++
  gi|14601326|ref|NP_147861.1| 30 LGIIGPNGAGKTSLLNVITGV 50
                                  58**************99876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0064
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkels 286
                                   +  l+ G ++   l+ al++ +    ++l DEp +gL  +  + +++ + e+s
  gi|14601326|ref|NP_147861.1| 147 IGALPPGIQKKVDLAGALAQNP---EVVLMDEPMAGLSKEEKEDIVRAIIETS 196
                                   5667788888889******999...9***********9977777777775555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   5.8e-07   0.00061      11      40 ..      18      48 ..       8      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.8e-07
                        AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAik 40
                                  ++++++  +  +  I+GpNGaGKT++l+ i+
  gi|14601326|ref|NP_147861.1| 18 DNVSVEVRRgEILGIIGPNGAGKTSLLNVIT 48
                                  56666664425778**************998 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 !   16.5   0.0     5e-06    0.0053      13      50 ..      18      55 ..      15      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5e-06
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  d+ ++e+++ ++  ++Gp+G+GK++ll  i+ +  p++
  gi|14601326|ref|NP_147861.1| 18 DNVSVEVRRGEILGIIGPNGAGKTSLLNVITGVYKPQR 55
                                  66788898666999*************99998888877 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.0   3.6e-05     0.038       3      38 ..      31      67 ..      29     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                                  EEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEE CS
                      MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivsdkpgtTrdine 38
                                  +i+G   +GK++L+n +tg  k + ++  ++ rdi+ 
  gi|14601326|ref|NP_147861.1| 31 GIIGPNGAGKTSLLNVITGVyKPQRGRVYFKGRDITG 67
                                  89****************9666666666666666654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     8e-06    0.0085      20      67 ..      29      83 ..      19     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-06
                        AAA_30 20 vavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLaeelg 67
                                  +  + Gp G+GKt +l++++ +++ + g      +++ gl p ++    L++ ++
  gi|14601326|ref|NP_147861.1| 29 ILGIIGPNGAGKTSLLNVITGVYKPQrGrvyfkgRDITGLKPHQRITLGLSRTFQ 83
                                  67799*******************9966888888888888888888887776554 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 !   12.2   0.0   8.8e-05     0.092      26      44 ..      29      47 ..      14      55 .. 0.84
   2 ?    1.4   0.1      0.17   1.8e+02     161     211 ..     170     220 ..     160     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
                                  EEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxx RF
                         SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                  +  i+GpNG+GK++ll+ i
  gi|14601326|ref|NP_147861.1| 29 ILGIIGPNGAGKTSLLNVI 47
                                  567************9887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.17
                                   EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                   ++l+De  a L +++ + +++ + e+s+++   ++ ++++m    d + +v
  gi|14601326|ref|NP_147861.1| 170 VVLMDEPMAGLSKEEKEDIVRAIIETSETMHTTMVLIEHDMEVVTDVCDRV 220
                                   5789*************9999999999987777666666665555555444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.6e-05     0.027      96     123 ..      23      51 ..       7      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                                   HCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpel 123
                                   +++  ++  ++G+ G+GK++L+n++++  
  gi|14601326|ref|NP_147861.1|  23 EVRRgEILGIIGPNGAGKTSLLNVITGVY 51 
                                   444448999***************99865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.5e-05     0.068      18      54 ..      23      57 ..      14     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-05
                        AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggi 54
                                   vr+g  e++ ++G+ G GK+sl++ +   ++ ++g 
  gi|14601326|ref|NP_147861.1| 23 EVRRG--EILGIIGPNGAGKTSLLNVITGVYKPQRGR 57
                                  45555..8999*************9988766666433 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   5.9e-05     0.062      16      43 ..      19      47 ..      16      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.9e-05
                        AAA_15 16 dveidlsee.ltvliGkNnsGKSsileal 43
                                  +v++++    +  +iG+N++GK+s+l+++
  gi|14601326|ref|NP_147861.1| 19 NVSVEVRRGeILGIIGPNGAGKTSLLNVI 47
                                  55555555557789************999 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.0   0.00019       0.2      69     122 ..     154     203 ..     122     231 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                          KdpD  69 eleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagidVittv 122
                                     +++dl  +la++pevvl+De     ++g ++e++ + v++++e      tt+
  gi|14601326|ref|NP_147861.1| 154 IQKKVDLAGALAQNPEVVLMDEP----MAGLSKEEKEDIVRAIIETSETMHTTM 203
                                   46899****************94....334445555555666666666666654 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00053      0.56       3      21 ..      30      48 ..      28      58 .. 0.81
   2 ?    1.2   0.3      0.23   2.4e+02      79     124 ..     184     228 ..     173     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00053
                                  EEEEESTTCCHHHHHHHHH CS
                          cobW  3 tvltGflGsGKTtLlnhll 21
                                  +++ G+ G+GKT+Lln ++
  gi|14601326|ref|NP_147861.1| 30 LGIIGPNGAGKTSLLNVIT 48
                                  6899***********9886 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                                   HHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH CS
                          cobW  79 reerldviliEttGlaePapvafteeelksdltldavvavvDaknl 124
                                   ++e++ + +iEt+  ++ ++v + e++++  + +   v+v+D  ++
  gi|14601326|ref|NP_147861.1| 184 EKEDIVRAIIETSETMHTTMV-LIEHDMEVVTDVCDRVVVMDYGKV 228
                                   335677779999999999999.456666666666666777776665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.14       1      84 [.      13     213 ..      13     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                   SSHHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE................................ CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................ RF
                   ATP-synt_ab   1 GirvlDal.fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg................................ 48 
                                   G+ +lD + + + +G+ ++i+g +g Gkt +++ ++   + ++  +y                                  
  gi|14601326|ref|NP_147861.1|  13 GVTALDNVsVEVRRGEILGIIGPNGAGKTSLLNVITGVYKPQRGRVYFKgrditglkphqritlglsrtfqhselfhsmtv 93 
                                   66677765256778999****************999987777678888779999999999999999999999999999999 PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                   ATP-synt_ab  49 ................................................................................. 48 
                                                                                                                    
  gi|14601326|ref|NP_147861.1|  94 lenimvrlhpwtrgsilekalwafrakrweveareraehvidlldlhehrhspigalppgiqkkvdlagalaqnpevvlmd 174
                                   999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                   ...ESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HH CS
                                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  49 ...iGergnevaevleefpegtimkrtvlvantsnepva 84 
                                       G  ++e +++++ + e++   +t++v+ + ++ v+
  gi|14601326|ref|NP_147861.1| 175 epmAGLSKEEKEDIVRAIIETSETMHTTMVLIEHDMEVV 213
                                   999999999999999999997766677777777777665 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    0.0052       5.5       3      20 ..      32      49 ..      30      95 .. 0.84
   2 ?    3.5   0.0     0.085        89      39      92 ..     147     195 ..     114     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0052
                                  EESSTTSSHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavak 20
                                  ++Gp G GKT+l + +  
  gi|14601326|ref|NP_147861.1| 32 IIGPNGAGKTSLLNVITG 49
                                  68**********998865 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.085
                                   TTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                           AAA  39 vgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                   +g+ +  i++ ++ a + a +p ++++DE  a  +++      e+e++v ++++ 
  gi|14601326|ref|NP_147861.1| 147 IGALPPGIQKKVDLAGALAqNPEVVLMDEPMAGLSKE------EKEDIVRAIIET 195
                                   6666677788888887778889*******87777777......455555555444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6   0.00099         1       2      28 ..      31      57 ..      30     216 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00099
                                  EEEEBTTTTHHHHHHHHHTS--S---S CS
                     Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgp 28
                                   ++G   +GK+S+ln ++g     rg 
  gi|14601326|ref|NP_147861.1| 31 GIIGPNGAGKTSLLNVITGVYKPQRGR 57
                                  6899*************9986554555 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   0.1    0.0086       9.1     242     270 ..      24      52 ..      20      60 .. 0.85
   2 ?    5.9   0.5    0.0044       4.7     357     412 ..     172     224 ..     165     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0086
                                   E-SS.EEEEEE-TTSSHHHHHHHHHHCCSE CS
                    ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlekGvyn 270
                                   +++G +  I+G++  GK+ LL+ + +Gvy+
  gi|14601326|ref|NP_147861.1|  24 VRRGeILGIIGPNGAGKTSLLNVI-TGVYK 52 
                                   67888999**************98.58886 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0044
                                   ---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                    ABC_ATPase 357 irDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                   + De m+ l ++eke i   v  + e  +++  +++l+   ++  +dv d+v++m+
  gi|14601326|ref|NP_147861.1| 172 LMDEPMAGLSKEEKEDI---VRAIIETSETMHTTMVLIEHDMEVVTDVCDRVVVMD 224
                                   56999999998888765...7777788888999**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 1895.27
//
Query:       gi|14601327|ref|NP_147862.1|  [L=529]
Description: fatty-acid--CoA ligase [Aeropyrum pernix K1]
Scores for complete 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-57  194.2   0.0    3.6e-57  193.9   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    2.9e-09   37.7   0.2    6.2e-09   36.7   0.2    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.9   0.0     4e-61   3.6e-57      13     422 ..      58     447 ..      48     448 .. 0.86

  Alignments for each domain:
  == domain 1  score: 193.9 bits;  conditional E-value: 4e-61
                                   EEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                   AMP-binding  13 alvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                   al+++++g  +T++ l + ++r++ +L+s+Gv +g  Va++++n +e ++  la+l  Ga +v ++p +  e+l+++le  
  gi|14601327|ref|NP_147862.1|  58 ALIQGETGYCYTWKSLASFIERIGGWLQSKGVSHGAQVAVASENLIEAIAFSLAVLASGARLVLIDPLTVGEDLEWQLEGR 138
                                   6777778888******************99************************************************976 PP

                                   TESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.-TSCCCS-BTTSEEEEEEE--SSS CS
                   AMP-binding  94 eakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae.kpeeeeelkpddlayiiYTSGTTG 172
                                   +    +    s+  le+++ea ++ +  ++vi l++++ + e    e  + +e+   +   e+ ++pdd  + iY  G  G
  gi|14601327|ref|NP_147862.1| 139 RGLETL--AASRGfLERNREAVSRIDNISTVIELSSNPQPLEVGGVEVLGLNEVLSsTAALEDDVEPDDDSFSIYYAGIAG 217
                                   655555..3455559********9999999999998887766444444444433315344556799*************** PP

                                   S-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT CS
                   AMP-binding 173 kPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklk 253
                                   +   +++sh  l    +   +  + +++++ v l   p+ h++gl ++l ++l++G+tvv l++++++   l ++l++ l+
  gi|14601327|ref|NP_147862.1| 218 RTMQAIHSHLGLWMGSKV--FAATAGIDRETVSLLATPFTHVLGLQASLVAPLIQGGTVVALQRWNPR---LAARLVSSLR 293
                                   *********998665333..3344556678899******************************99883...34789***** PP

                                   -SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCT CS
                   AMP-binding 254 vtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkk 334
                                   ++++agvP ++++ll+ g           s+lrl++++g+pl+pel+r+f + +g ++l++YG++E ++ ++  + ++  +
  gi|14601327|ref|NP_147862.1| 294 INYLAGVPLMFQQLLDLG---------ATSGLRLAISAGAPLPPELQRRFGRETGIPLLQAYGMSESLILTF-QT-PKIAE 363
                                   ****************75.........4568***********************99*************997.44.55557 PP

                                   STTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEE CS
                   AMP-binding 335 klgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgR 415
                                     g++G plpgvev ++ ++ g + p+  +Gel+v+ p+vmkgY  + e++++af+  ++wlrTGD+ +++++G +++ g 
  gi|14601327|ref|NP_147862.1| 364 IEGTIGVPLPGVEVSLLGDD-GLLSPPPGVGELVVQAPWVMKGYEFE-EENSKAFI--DGWLRTGDVIEITDRGVMFFRGV 440
                                   99****************99.666666669**************977.999****9..57**********999******** PP

                                   CCCEEEE CS
                   AMP-binding 416 kkdlikl 422
                                    k +ik 
  gi|14601327|ref|NP_147862.1| 441 RKRIIKY 447
                                   *****97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   6.9e-13   6.2e-09       2      64 ..     457     519 ..     456     521 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6.9e-13
                                   HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEE CS
                 AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvv 64 
                                   +E +l shp+V ea V G p    G+++va Vvl++gs+ ++e+L+++v++++  y++ ++v+
  gi|14601327|ref|NP_147862.1| 457 LEVILESHPDVLEARVWGEPAGDVGQIPVASVVLRAGSSVTPEDLMEYVNQRVSFYKKIRRVE 519
                                   6999******************************99976689**************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 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:                        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 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3810.78
//
Query:       gi|118431404|ref|NP_147863.2|  [L=178]
Description: hypothetical protein APE_1313.1 [Aeropyrum pernix K1]
Scores for 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-07   29.2   6.8    8.4e-07   29.2   6.8    1.9  2  DUF4129   Domain of unknown function (DUF4129)


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 ?   -2.2   0.1      0.29   5.3e+03      10      22 ..       6      18 ..       5      19 .. 0.79
   2 !   29.2   6.8   4.7e-11   8.4e-07       6      69 .]     115     175 ..     110     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.29
                        DUF4129 10 aergldrrpgeTp 22
                                   a+++++ +p eT+
  gi|118431404|ref|NP_147863.2|  6 ARHVIPLPPVETT 18
                                   4559999999996 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 4.7e-11
                        DUF4129   6 lraLaergldrrpgeTprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                     + + +rg + ++++TprE a ++    ++  +++++++++++  YG++++s+e +rr+++++r
  gi|118431404|ref|NP_147863.2| 115 YEKALARGARIARSMTPREAAGEA---EAAGLRAREIVDIYYDGVYGPHEPSEEMVRRAWRLVR 175
                                    44455579****************...334459999************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1377.43
//
Query:       gi|118431405|ref|YP_874887.1|  [L=368]
Description: hypothetical protein APE_1315 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.13   12.7   0.0       0.28   11.7   0.0    1.6  1  DUF4350    Domain of unknown function (DUF4350)
       0.76   10.0   8.9        1.2    9.4   4.8    2.6  2  TetR_C_31  Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.1e-05      0.28       1      63 [.      40     106 ..      40     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                        DUF4350   1 skspnGtralaelLeaq.Gvevrrvrkpfdalegedg...tllvvapdlrlteeelaallewvarGn 63 
                                    ++s +G++ ++e ++++ ++ + r    +++l+ e+g   +++v+apd  +t+ee   l  ++++G 
  gi|118431405|ref|YP_874887.1|  40 NPSVYGASEFYEAAREAyDAVLVRSIGELEELAVEGGasiVYVVIAPDKPFTYEEYLVLSSLASQGR 106
                                    6888*************6666688888999998777777899******99****9999999999996 PP

>> TetR_C_31  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.038   3.4e+02      70      89 ..       4      23 ..       2      36 .. 0.75
   2 ?    9.4   4.8   0.00013       1.2      18      59 ..     307     349 ..     289     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.038
                                   HHHHHHHHHHHHHHHHHHSG CS
                      TetR_C_31 70 aarllvaaldGllldrLagp 89
                                   +a ll+a ++Gl+l+  a +
  gi|118431405|ref|YP_874887.1|  4 RAILLFAIITGLVLSGAAVD 23
                                   56789*********998886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00013
                                    CT.THHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_31  18 la.drertlAryelfleaarrPeLraalarlrralrealaall 59 
                                    l+ +  + lA+y+l  +a+r+P Lraal+ +++  ++ l++ll
  gi|118431405|ref|YP_874887.1| 307 LGdEMLEKLALYALQEAARRDPILRAALTFGVALRLRPLRRLL 349
                                    555666779********************99999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2703.19
//
Query:       gi|14601331|ref|NP_147866.1|  [L=306]
Description: hypothetical protein APE_1317 [Aeropyrum pernix K1]
Scores for 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-64  213.8   0.0      9e-64  213.2   0.0    1.3  1  AAA_3            ATPase family associated with various cellul
    6.8e-17   61.8   0.0    1.1e-16   61.1   0.0    1.3  1  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-15   57.1   4.2    1.7e-15   56.6   0.1    2.6  3  AAA_lid_2        AAA lid domain
    1.3e-06   28.9   0.0    2.5e-06   28.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
    4.4e-06   26.0   0.0    6.9e-06   25.3   0.0    1.3  1  MCM              MCM P-loop domain
    3.9e-05   23.4   0.0    0.00037   20.3   0.0    2.1  1  Sigma54_activat  Sigma-54 interaction domain
      5e-05   23.1   0.0    0.00045   20.0   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00019   21.9   0.2    0.00047   20.6   0.2    1.7  2  AAA_16           AAA ATPase domain
     0.0002   20.8   1.2      0.023   14.1   0.4    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.047   13.4   0.6       0.27   10.9   0.6    2.0  1  AAA_30           AAA domain
      0.071   13.7   0.0       0.12   13.0   0.0    1.4  1  AAA_18           AAA domain
       0.15   12.7   0.2       0.49   11.1   0.0    1.9  1  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal
       0.16   12.1   0.0        0.3   11.2   0.0    1.6  1  AAA_33           AAA domain
       0.18   11.8   0.0       0.32   11.0   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


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 !  213.2   0.0     7e-67     9e-64       1     130 [.      35     164 ..      35     165 .. 1.00

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 7e-67
                         AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsa 81 
                                   hvllegvPG+akt++++a+a+a +l+f+riqftpd+lPsd++Gt+v+++++ ef f++Gpvfan++lade+nra+p+tqsa
  gi|14601331|ref|NP_147866.1|  35 HVLLEGVPGVAKTTMARAIARATGLRFSRIQFTPDMLPSDVIGTMVYDQRTGEFVFRRGPVFANVVLADEVNRANPRTQSA 115
                                   9******************************************************************************** PP

                         AAA_3  82 lleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                   +leam+e qvtv geth+lp+pf+vlat nPie eG+yplpeaqldrf+
  gi|14601331|ref|NP_147866.1| 116 FLEAMQEGQVTVWGETHRLPSPFIVLATMNPIELEGVYPLPEAQLDRFM 164
                                   ************************************************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 !   61.1   0.0   8.4e-20   1.1e-16       1     138 []      35     163 ..      35     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 8.4e-20
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraes 79 
                                   +vlL G pG++K+++a+ +a+a++ ++  +q+t d+ ++d++g + ++   g+ +++ +p+      + +++ DEv+ra++
  gi|14601331|ref|NP_147866.1|  35 HVLLEGVPGVAKTTMARAIARATGLRFSRIQFTPDMLPSDVIGTMVYDqrTGEFVFRRGPVF-----ANVVLADEVNRANP 110
                                   79*********************************************988899999999999.....9************* PP

                                   HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                         AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    +++++l  + e ++   +g +    ++      f v+at+np +  ++ +l +a ++Rf
  gi|14601331|ref|NP_147866.1| 111 RTQSAFLEAMQEGQVT-VWGETHRLPSP------FIVLATMNPIElEGVYPLPEAQLDRF 163
                                   ***************9.67777776777......***********999999999999998 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.3      0.24     3e+02      29      48 ..      27      46 ..      25      59 .. 0.78
   2 ?   -3.7   0.0       8.7   1.1e+04      40      51 ..     198     209 ..     196     210 .. 0.78
   3 !   56.6   0.1   1.3e-18   1.7e-15       2      72 ..     227     298 ..     226     299 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.24
                     AAA_lid_2 29 lAalegrdyVtpeDvkeaap 48
                                  lAal++r +V+ e v  +a+
  gi|14601331|ref|NP_147866.1| 27 LAALAARGHVLLEGVPGVAK 46
                                  89999999999887766665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.7
                     AAA_lid_2  40 peDvkeaaplVL 51 
                                   peD+ +a + V+
  gi|14601331|ref|NP_147866.1| 198 PEDIVAAQEAVW 209
                                   899999888876 PP

  == domain 3  score: 56.6 bits;  conditional E-value: 1.3e-18
                     AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                   +t +h+ ++lg s+r a+l ++  Ar lA+l+g  yVtp++vkeaa+ +L+HRl+   e++ eg + e++ve+
  gi|14601331|ref|NP_147866.1| 227 ETHKHPGVSLGGSPR-AALSIMMLARGLALLDGLGYVTPDHVKEAARAALPHRLIltTEAKLEGLKPESVVED 298
                                   7899***********.****************************************99999999888888876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.9e-09   2.5e-06       1     111 [.      36     146 ..      36     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.9e-09
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHH...HHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkire...lfkeakekakpsilfiDEidalaksrsg 76 
                                   vll G pG+ KT++a+a+a+ +g +f +i+  +++l s+++g +  + r    +f++    a   +++ DE+ + +++   
  gi|14601331|ref|NP_147866.1|  36 VLLEGVPGVAKTTMARAIARATGLRFSRIQFtPDMLpSDVIGTMVYDQRTgefVFRRGPVFA--NVVLADEVNRANPRT-- 112
                                   79************************999963677778888877666554222677766665..9**********9999.. PP

                                   CCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS CS
                           AAA  77 seseeeervvnqLlteldgvkkk........eskvivigatnr 111
                                            ++++l+++++ +           s++iv+++ n 
  gi|14601331|ref|NP_147866.1| 113 ---------QSAFLEAMQEGQVTvwgethrlPSPFIVLATMNP 146
                                   .........6666666666666666666665888888888776 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   5.4e-09   6.9e-06      55     174 ..      31     147 ..       9     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 5.4e-09
                                   CSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSS...SSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGG CS
                           MCM  55 rgdinvllvgdpgtaKsqlLkyveklapravytsgkgs...saagLtaavvrdeetgefvleaGalvladkGvcciDefdk 132
                                    ++ +vll g pg+aK+++ +++++ +    +  ++ +     ++   ++v d++tgefv+  G +      v++ De+++
  gi|14601331|ref|NP_147866.1|  31 AARGHVLLEGVPGVAKTTMARAIARAT-GLRFSRIQFTpdmLPSDVIGTMVYDQRTGEFVFRRGPVFAN---VVLADEVNR 107
                                   55679****************999654.333444443300044677888999************98754...9******** PP

                                   STCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--S CS
                           MCM 133 mkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpk 174
                                    + +++sa +Eam + ++++   G +  L++   vla +np+
  gi|14601331|ref|NP_147866.1| 108 ANPRTQSAFLEAMQEGQVTVW--GETHRLPSPFIVLATMNPI 147
                                   ******************997..66799************98 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.9e-07   0.00037      13     141 ..      24     144 ..      16     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                   HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTT CS
               Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekad 93 
                                   + + ++ + + +vl++G  G+ K+++arai +a+  + +  +++    +p++++ + ++  + G F      ++G + +  
  gi|14601331|ref|NP_147866.1|  24 RLVLAALAARGHVLLEGVPGVAKTTMARAIARATGLRFS-RIQFTPDMLPSDVIGTMVYDQRTGEFV----FRRGPVFA-- 97 
                                   556667778899******************987764433.466666677888888888888887775....46666543.. PP

                                   TSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEE CS
               Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaat 141
                                     +++ De+++ ++++Q+ +l+++qeg+v+  G+++  +  + ++a+ 
  gi|14601331|ref|NP_147866.1|  98 -NVVLADEVNRANPRTQSAFLEAMQEGQVTVWGETHRLPSPFIVLATM 144
                                   .47899*****************************9999877555443 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.5e-07   0.00045      32      86 ..      32      87 ..      14     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.5e-07
                        RuvB_N 32 aldhvllyGpPGlGkttlakiiakelgvkl.kitsgPvlekagdlaalltnleekd 86
                                  a  hvll G PG+ ktt+a+ ia+  g ++ +i  +P +  +  + +++ + ++++
  gi|14601331|ref|NP_147866.1| 32 ARGHVLLEGVPGVAKTTMARAIARATGLRFsRIQFTPDMLPSDVIGTMVYDQRTGE 87
                                  457*********************99988734555666655544455555544444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.2   3.6e-07   0.00047       3      59 ..      17      65 ..      15     122 .. 0.83
   2 ?   -2.0   0.0       3.2   4.1e+03     138     159 ..      99     121 ..      88     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-07
                        AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgk 59
                                  vG+e+e++ +l+al +      + vll G +Gv K++++r+++ra       f r +
  gi|14601331|ref|NP_147866.1| 17 VGKEREIRLVLAALAAR-----GHVLLEGVPGVAKTTMARAIARATG---LRFSRIQ 65
                                  9********9**99833.....79*******************7433...3354444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                        AAA_16 138 vlvlDdlqwadeaslql.laaLl 159
                                   v++ D++ +a + ++++ l+a+ 
  gi|14601331|ref|NP_147866.1|  99 VVLADEVNRANPRTQSAfLEAMQ 121
                                   67788899999988888555554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.4   1.8e-05     0.023       5      43 ..      16      54 ..      12      58 .. 0.92
   2 ?    5.1   0.0      0.01        13     109     159 ..      99     147 ..      88     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                  Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlp 43
                                  ++G+e+  r +  a a + ++ll G pG  Kt +a++++
  gi|14601331|ref|NP_147866.1| 16 IVGKEREIRLVLAALAARGHVLLEGVPGVAKTTMARAIA 54
                                  899********************************9985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                   v++ DE+   + ++  ++ e +++g+vt+   ++  + p+ f ++a+mNp 
  gi|14601331|ref|NP_147866.1|  99 VVLADEVNRANPRTQSAFLEAMQEGQVTVWGETH--RLPSPFIVLATMNPI 147
                                   6788*************************87665..67999********96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00021      0.27      12      42 ..      29      57 ..      22     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                        AAA_30 12 alltsgdrvavltGpAGtGKttalkalreaw 42
                                  al++ g   ++l+G++G  Ktt+ +a+++a 
  gi|14601331|ref|NP_147866.1| 29 ALAARG--HVLLEGVPGVAKTTMARAIARAT 57
                                  344444..699****************9886 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     9e-05      0.12       1      38 [.      36      71 ..      36     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                        AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakengll 38
                                  +ll G+pGv Ktt+a+++++ +  g + + + +  ++l
  gi|14601331|ref|NP_147866.1| 36 VLLEGVPGVAKTTMARAIARAT--GLRFSRIQFTPDML 71
                                  799*****************99..55555554444444 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.49      55      90 ..     236     271 ..     221     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                Mg_chelatase_C  55 lglsaRaydrilkvArTiADLegseeieeehlaeAl 90 
                                   lg s Ra+  i+ +Ar +A L+g   ++++h++eA+
  gi|14601331|ref|NP_147866.1| 236 LGGSPRAALSIMMLARGLALLDGLGYVTPDHVKEAA 271
                                   56689******************************7 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024       0.3       2      28 ..      36      64 ..      36     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                        AAA_33  2 vllvGlpGsGKstlaerllkklg..avll 28
                                  vll G+pG+ K+t a+ +++++g  + ++
  gi|14601331|ref|NP_147866.1| 36 VLLEGVPGVAKTTMARAIARATGlrFSRI 64
                                  7899***************9999774444 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   0.0   0.00025      0.32      11      46 ..      27      60 ..       7      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                  HHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE 11 gkklakalgdvilLeGdLGaGKTtlvrglakalgve 46
                                   ++la+  +  +lLeG  G+ KTt++r++a+a g++
  gi|14601331|ref|NP_147866.1| 27 LAALAA--RGHVLLEGVPGVAKTTMARAIARATGLR 60
                                  334433..557********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2197.80
//
Query:       gi|118431406|ref|NP_147867.2|  [L=415]
Description: hypothetical protein APE_1319.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-23   81.5   0.0    8.9e-23   80.4   0.0    1.7  1  DUF58      Protein of unknown function DUF58
  ------ inclusion threshold ------
       0.05   13.3   0.3        2.4    7.8   0.6    2.3  2  Kinocilin  Kinocilin protein


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 !   80.4   0.0   9.9e-27   8.9e-23       1      83 [.     194     276 ..     194     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 9.9e-27
                          DUF58   1 gldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqllde 80 
                                    g +f++lReY+pgD++r I+W++tAR g+l+vre   e++ ++++vld+s em  g  g +++++a++++++la+ + ++
  gi|118431406|ref|NP_147867.2| 194 GYEFLELREYQPGDDPRMIHWPSTARAGTLVVRETAMETRLNLTIVLDASGEMWIGGPGASPIDHAARLTLALAALAWES 273
                                    579**************************************************************************999 PP

                          DUF58  81 gdr 83 
                                    g  
  gi|118431406|ref|NP_147867.2| 274 GGT 276
                                    876 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.6   0.00027       2.4      26      63 ..      11      50 ..       2      72 .. 0.75
   2 ?    2.5   0.0     0.012   1.1e+02      48      78 ..     218     248 ..     215     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00027
                      Kinocilin 26 siiigvsvskaaa.avgg.ifigaaglgllllaypflkar 63
                                   s++++ s+s+aaa a g  i++ +  +g+l+l + fl a+
  gi|118431406|ref|NP_147867.2| 11 SLLLASSLSSAAAlATGDpILLASGLVGILVLGFSFLYAK 50
                                   788889999998835555455555557**********875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.012
                      Kinocilin  48 aglgllllaypflkarfnldrilpaignlri 78 
                                    a  g l++    +++r+nl  +l a g++ i
  gi|118431406|ref|NP_147867.2| 218 ARAGTLVVRETAMETRLNLTIVLDASGEMWI 248
                                    5668888889999**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3076.89
//
Query:       gi|118431407|ref|NP_147868.2|  [L=240]
Description: hypothetical protein APE_1322.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1678.81
//
Query:       gi|14601334|ref|NP_147869.1|  [L=66]
Description: hypothetical protein APE_1322a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.7   0.0       0.12   12.5   0.0    1.2  1  AAA_33    AAA domain


Domain annotation for each model (and alignments):
>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-06      0.12       5      34 ..       6      37 ..       5      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-06
                        AAA_33  5 vGlpGsGKstlaerllkklg..avllssdtlr 34
                                   G+pGsGKs+l   +l++ g  ++ +s  t++
  gi|14601334|ref|NP_147869.1|  6 LGHPGSGKSFLGGLVLAASGivFFGISVYTIY 37
                                  5***********99999999655556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 522.07
//
Query:       gi|118431408|ref|YP_874888.1|  [L=56]
Description: hypothetical protein APE_1322b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.5   1.2      0.039   14.2   1.2    1.1  1  DUF1947   Domain of unknown function (DUF1947)


Domain annotation for each model (and alignments):
>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.2   2.2e-06     0.039       7      41 ..       3      35 ..       1      43 [. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-06
                                   HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EE CS
                        DUF1947  7 kKeakeileklkekyisislesdkiEieeekkekl 41
                                   kKe+ ++++ +++ky + ++ +  +Ei+e+k+ k+
  gi|118431408|ref|YP_874888.1|  3 KKEKIKFFDLVAKKYYETDNYE--VEIKETKRGKF 35
                                   9**************7766666..*******8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 426.19
//
Query:       gi|118431409|ref|NP_147870.2|  [L=151]
Description: ssDNA-binding protein [Aeropyrum pernix K1]
Scores for 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-10   38.5   0.3    1.2e-09   38.0   0.3    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.013   15.4   0.0    1.1  1  REPA_OB_2        Replication protein A OB domain
       0.02   14.6   0.0      0.023   14.4   0.0    1.1  1  CDC24_OB3        Cell division control protein 24, OB domain 
      0.058   12.6   0.0       0.07   12.3   0.0    1.0  1  PS-DH            Polyketide synthase dehydratase


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 !   38.0   0.3   2.8e-13   1.2e-09       1      70 [.      18      90 ..      18      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.8e-13
                                   EEEEEEEEEEE.......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEE CS
                tRNA_anti-codon  1 VtvaGrvtsis.......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkv 70
                                   V++ Grv  +        +r+ + ++ +++ D++gr++v+l+     + a +lkeG  vr++G ++++++g+++++v
  gi|118431409|ref|NP_147870.2| 18 VSISGRVLETGepkmvetKRGPATLSEAVVGDESGRVKVTLWG----SHAGTLKEGEAVRIEGAWTTSYRGKVQVNV 90
                                   89*****************************************....************************999988 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.9e-06     0.013      17      94 ..      22      95 ..       9      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                      REPA_OB_2 17 gvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFggr.slsllssst 94
                                   g v +++e + + +k +    +  e  + Desg+ v+vtlWg++a +++  e + v + g+  + + g+ ++++ + st
  gi|118431409|ref|NP_147870.2| 22 GRVLETGEPKMVETKRGP--ATLSEAVVGDESGR-VKVTLWGSHAGTLK--EGEAVRIEGAWTTSYRGKvQVNVGREST 95
                                   556666666777777665..55567788899996.9**********976..7788999999999999952566665555 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.1e-06     0.023       1      76 [.      10      83 ..      10     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                      CDC24_OB3  1 DLrekmlnvtLlGrvvaifr.eknsek.kkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsgLatsetk 76
                                   DLre   nv++ Grv +  + +  ++k   ++ +   + D++G +++tlw     ++ + l+ G+ v ++g  t++ +
  gi|118431409|ref|NP_147870.2| 10 DLREGLRNVSISGRVLETGEpKMVETKrGPATLSEAVVGDESGRVKVTLWGS---HAGT-LKEGEAVRIEGAWTTSYR 83
                                   99****************665556666678889999*************976...3334.777999999887776655 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.07      66     162 ..      15     123 ..       8     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                                    EEEEEE----.B--SS-EEEEEEEEE-TTS-E.........EEEEEEE-SS-TT...........EEEEEEEEEE----- CS
                          PS-DH  66 lrdvsilkalvlpedepvevqlslepeedgad.....rawvefeifSregggee..........wtehatGtvrlaegaa 130
                                    lr+vsi+  + l+ +ep+ v++   p++ +++     + +v+++++   +g+ +          wt+ ++G+v+++ g++
  gi|118431409|ref|NP_147870.2|  15 LRNVSISGRV-LETGEPKMVETKRGPATLSEAvvgdeSGRVKVTLWGSHAGTLKegeavriegaWTTSYRGKVQVNVGRE 93 
                                    7888887666.8888899999999888777778888888888888877777766789999999***************99 PP

                                    ..--B--HHHHHHHS-SEE....E-HHHHHHHHH CS
                          PS-DH 131 ..aaavdlealqarcaepaslrsvssaefYerla 162
                                       ++vd e+++++++ p+      +++ Y+ + 
  gi|118431409|ref|NP_147870.2|  94 stIEKVDSEDVPQAEDIPE----EMPEAQYRGFG 123
                                    6655666666644444443....34445566654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1106.57
//
Query:       gi|14601336|ref|NP_147871.1|  [L=174]
Description: hypothetical protein APE_1324 [Aeropyrum pernix K1]
Scores for complete 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-14   53.1   0.0    4.8e-14   52.6   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.2e-07   30.7   0.0    5.9e-07   30.2   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    1.7e-05   25.1   0.0    4.7e-05   23.7   0.0    1.7  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.3e-05   24.3   0.0    4.1e-05   23.4   0.0    1.4  1  FR47             FR47-like protein
    0.00019   21.6   0.0    0.00022   21.4   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00067   19.3   0.0    0.00093   18.8   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
    0.00092   19.2   0.0     0.0012   18.8   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.9e-17   4.8e-14      24     116 ..      48     140 ..      18     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.9e-17
                                   HHHHHHSTTCEEEEEEET...TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEE CS
                Acetyltransf_1  24 feesfsleaegllvaeed...geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlav 101
                                   + +++  + ++l+++ ed   ge++G++  + +       a+  ++ V+++y+g+GlGs L   ++ +++  g+kk++ +v
  gi|14601336|ref|NP_147871.1|  48 YIDRLLHDRCTLVIVAEDlatGEIVGMAESFVDEK---TGAAEGGIIVREDYQGHGLGSILASVMISILKPAGVKKLYGYV 125
                                   333344456677778888999*******9999999...899999************************************* PP

                                   ETTEHHHHHHHHHTT CS
                Acetyltransf_1 102 eedndaairlYeklG 116
                                    +dn++ai l +klG
  gi|14601336|ref|NP_147871.1| 126 LSDNQRAISLARKLG 140
                                   ***********8899 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.3e-10   5.9e-07       1     137 [.       8     141 ..       8     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.3e-10
                Acetyltransf_3   1 RLlLrplteeDlealfel...rsdpe.vmrylpepltleeaeewlerawaeeseeegygwaivl..kdtgv.iGsvglrdl 74 
                                   R+ +r l++ D ++l ++   +s+++  +r+    + +   + +++     +  ++ ++++iv    +tg+ +G++  + +
  gi|14601336|ref|NP_147871.1|   8 RVRIRGLCPGDRDKLIRFyksLSEETiYTRF---FAVVRYFDPYID-----RLLHDRCTLVIVAedLATGEiVGMAESF-V 79 
                                   6677777777777776552223333322233...222334444444.....3345778888865565556559999666.4 PP

                Acetyltransf_3  75 eeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                   +e++++ae g++++++++g+G+++  ++ ++ ++ +  g+++l+  +  +N++ i +++klG 
  gi|14601336|ref|NP_147871.1|  80 DEKTGAAEGGIIVREDYQGHGLGSILASVMISIL-KPAGVKKLYGYVLSDNQRAISLARKLGA 141
                                   666677****************************.7778***********************7 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   6.7e+03      65      72 ..      22      29 ..      12      29 .. 0.77
   2 !   23.7   0.0   1.8e-08   4.7e-05       5      73 ..      60     140 ..      50     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                                  HHHHHHHT CS
                Acetyltransf_7 65 aikfYekl 72
                                   i+fY++l
  gi|14601336|ref|NP_147871.1| 22 LIRFYKSL 29
                                  48999986 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.8e-08
                                   EEEEEET..TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEE.EE.EEEE..THHHHHHHHHH CS
                Acetyltransf_7   5 vfVaedd..gkivGfialslld...aeitrlaVdpeyrgkGiGraLlea..ae...kgii.le.qlel..naekaikfYek 71 
                                   v+Vaed   g+ivG++   +++   a ++++ V+++y+g+G+G+ L  +   +    g++ l+ +  +  ++++ai++ +k
  gi|14601336|ref|NP_147871.1|  60 VIVAEDLatGEIVGMAESFVDEktgAAEGGIIVREDYQGHGLGSILASVmiSIlkpAGVKkLYgY--VlsDNQRAISLARK 138
                                   667777699*****8886666687666666****************8853411345443322222..22244477777666 PP

                                   TT CS
                Acetyltransf_7  72 lG 73 
                                   lG
  gi|14601336|ref|NP_147871.1| 139 LG 140
                                   65 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.6e-08   4.1e-05      22      81 ..      85     145 ..      66     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.6e-08
                                   SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEEE CS
                          FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfekie 81 
                                    + g++ v+++ ++ Glgs l++ ++  +  +g k++  +v  +N+++i+l  klG + ++
  gi|14601336|ref|NP_147871.1|  85 AAEGGIIVREDYQGHGLGSILASVMISILKPAGvKKLYGYVLSDNQRAISLARKLGARTLR 145
                                   445899*********************9999883566779999*************88775 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   8.6e-08   0.00022       8     142 ..      18     149 ..      11     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 8.6e-08
                Acetyltransf_4   8 Dakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvae...sdrivGyaylgqfkkrakdwkaelsvyla 85 
                                   D +++ + y+   ++t  t+      v +f+  +++l  + + +  vae    ++ivG+a    ++   k+++ae  + + 
  gi|14601336|ref|NP_147871.1|  18 DRDKLIRFYKSLSEETIYTRF--FAVVRYFDPYIDRLLHDRCTLVIVAEdlaTGEIVGMAESF-VDE--KTGAAEGGIIV- 92 
                                   666666666665555545533..245678888888885555666666665999******9877.777..9**********. PP

                Acetyltransf_4  86 erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkk 142
                                   ++d +  glg+ l  +++ +lk  ++++l+  + s+n+ +i ++ +lG + ++++ +
  gi|14601336|ref|NP_147871.1|  93 REDYQGHGLGSILASVMISILKPAGVKKLYGYVLSDNQRAISLARKLGARTLREQPG 149
                                   58********99999999******************************999888765 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.6e-07   0.00093     164     233 ..      67     140 ..      53     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.6e-07
               GNAT_acetyltran 164 kngeivsgasSys.vyekgieieidTkedyrrkgLAtivaaalile...clkrglyPsWDaaneaSvaLaekLG 233
                                     geiv +a S++   ++++e  i  +edy+++gL +i+a+ +i+    +  ++ly +   +n+ +++La+kLG
  gi|14601336|ref|NP_147871.1|  67 ATGEIVGMAESFVdEKTGAAEGGIIVREDYQGHGLGSILASVMISIlkpAGVKKLYGYVLSDNQRAISLARKLG 140
                                   458**********55677899********************998751115567788888899***********9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.7e-07    0.0012      24     107 ..      50     142 ..      25     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.7e-07
               Acetyltransf_10  24 eri.eegealllvaeeg...gkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp 95 
                                   +r+ ++  +l++vae +   g+ivG++e   d++     + ++V+++y+g G+g+ L   +++ ++ +g k+    v +++
  gi|14601336|ref|NP_147871.1|  50 DRLlHDRCTLVIVAE-DlatGEIVGMAESfVDEKtgaAEGGIIVREDYQGHGLGSILASVMISILKPAGVKKlYGYVLSDN 129
                                   444133334455555.44669******776666667788999**************************9999988888888 PP

               Acetyltransf_10  96 .yavpfYeklGFk 107
                                     a+++ +klG +
  gi|14601336|ref|NP_147871.1| 130 qRAISLARKLGAR 142
                                   7888888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); 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:                         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: 1292.14
//
Query:       gi|118431410|ref|NP_147872.2|  [L=383]
Description: hypothetical protein APE_1326.1 [Aeropyrum pernix K1]
Scores for 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-06   26.1   0.0    4.7e-05   23.8   0.0    2.2  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.6e-09   4.7e-05       3     165 ..      52     219 ..      50     221 .. 0.74
   2 ?   -1.9   0.0      0.21   3.7e+03     116     135 ..     340     358 ..     321     367 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.6e-09
                                    EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEE..SSTGGGSTTHHHHHHHHHHTC... CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxx..xxxxxxxxxxxxxxxxxxxxx... RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelk.aekg.vkevilg..ggepllypdfvellerlakla... 74 
                                    ++ gC+++C +C+++ +     + ++ ls +e++  +  +  + +g +++++ +    ep+++    +++e l   +   
  gi|118431410|ref|NP_147872.2|  52 TGVGCSYGCLYCYIYDMgFTGKPQPYPLSGDELALALALNPyVAPGpKGTLLAFgsVTEPFMRETAWRAIEYLESTRrwl 131
                                    578*************9766666667777777776666666788886776666634678888855555555555555666 PP

                                    ..CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  75 ..vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                         i++     g+l+ e+++e+ +++    v ++  +++  k l++      +ee++e + +l eag+  + +  +++
  gi|118431410|ref|NP_147872.2| 132 gnPQQISTKTALRGGLL-ERFIEAADPR--IDVLVSMTTLSRWKALEPG--ASPPEERIEFMGRLVEAGLSATLFLRPII 206
                                    77788888888888888.6666666663..3666777777776555555..6889****************9******** PP

                                    TTTSHHHHHHHHH CS
                                    xxxxxxxxxxxxx RF
                    Radical_SAM 153 pGendeeleelle 165
                                    pG++d+e e++l+
  gi|118431410|ref|NP_147872.2| 207 PGVTDREAEDILS 219
                                    ********99986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.21
                                    HHHHHHTCTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 116 kvlklmnrghtfeevleale 135
                                    +v+  + rgh++e+vl++ +
  gi|118431410|ref|NP_147872.2| 340 PVKVSV-RGHSVEAVLRGGR 358
                                    344455.7777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2799.70
//
Query:       gi|118431411|ref|NP_147873.2|  [L=680]
Description: hydantoin utilization protein A [Aeropyrum pernix K1]
Scores for complete 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-97  326.5   1.0    4.7e-96  321.5   0.1    2.1  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    4.4e-47  160.1   0.0    1.4e-46  158.4   0.0    1.8  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
      0.003   18.0   0.9      0.021   15.2   0.1    2.3  2  FtsA            Cell division protein FtsA
     0.0087   15.6   0.0        0.7    9.3   0.0    2.3  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.017   13.8   1.1       0.78    8.3   0.1    2.2  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 !    3.7   0.1    0.0087        31      82      99 ..       6      22 ..       3      39 .. 0.85
   2 !  321.5   0.1   1.3e-99   4.7e-96       1     289 [.     200     496 ..     200     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0087
                 Hydantoinase_A 82 ItfDmGGTstDvslikdg 99
                                   +++D+GGT tD+ +++ g
  gi|118431411|ref|NP_147873.2|  6 VGVDVGGTFTDIVVFD-G 22
                                   789*********9988.4 PP

  == domain 2  score: 321.5 bits;  conditional E-value: 1.3e-99
                 Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekk 80 
                                    rt+t+vvnA+l+pil++yl+++  +l++rg+k  l+vmqs+Gg++ ++ea ++p+ +i+SGP aG+v++a++s+l+++++
  gi|118431411|ref|NP_147873.2| 200 RTSTTVVNAVLKPILSTYLQELHRQLRDRGFKGVLLVMQSNGGVAGVEEAVGRPAAFIESGPSAGAVAVAYFSRLQRVDR 279
                                    89****************************************************************************** PP

                 Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrvgpesag 148
                                    +++fDmGGT++++s i+dge+ev+  +e+            +g++vr+p +d+++v+agGg+i++vd gg+l+vgp sag
  gi|118431411|ref|NP_147873.2| 280 ALGFDMGGTTAKASSIIDGEPEVVDTYEVggrvhmgrlirgSGYPVRYPHIDLAEVSAGGGTIAWVDPGGALQVGPMSAG 359
                                    ******************************************************************************** PP

                 Hydantoinase_A 149 adpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarraf.eelakelnlkveevAegilsvavenman 227
                                    adpgpacy+ Gg ++tvTDanl+LGrl+   ++    g  +l ++la+ a+   +a++++l+v e+A++i+++a+  m +
  gi|118431411|ref|NP_147873.2| 360 ADPGPACYGLGGSKPTVTDANLILGRLPDV-LA----GGLRLSRRLAEDAVkGRVAEPMGLDVVEAAWAIVRIANAIMSR 434
                                    ***************************987.66....999***********99*************************** PP

                 Hydantoinase_A 228 avrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvre 289
                                    a+r +s erg dp+ +t+++fGGaG++haa+laee+gv++vi+pp +gv+salG+++Ad+++
  gi|118431411|ref|NP_147873.2| 435 ALRLVSLERGRDPRGFTMYAFGGAGPLHAAELAEEMGVSRVIIPPFPGVFSALGLLVADYKH 496
                                    ***********************************************************987 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 !  158.4   0.0     4e-50   1.4e-46       1     176 [.       5     178 ..       5     180 .. 0.96
   2 ?   -2.1   0.0      0.74   2.7e+03     127     156 ..     207     236 ..     193     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 4e-50
                     Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg...e 77 
                                    r+g+DvGGTfTD+v++d++   ++vlK+l+tp+ ++eg+++ l+++l+      + ++v++++TT+ tN +l + g   +
  gi|118431411|ref|NP_147873.2|   5 RVGVDVGGTFTDIVVFDGG---LRVLKVLTTPKRPVEGVMNGLSRALGT----LEGVEVLVHATTIGTNLFLGQVGlqaP 77 
                                    79***************65...9***********************987....789************************ PP

                     Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiav 155
                                    r+aL++++gfrd++eigrqnrp l++   +  kplv+++ ++ v++r+  dg ++++ld ++vre +++l ++gv+ +av
  gi|118431411|ref|NP_147873.2|  78 RIALFVNEGFRDIVEIGRQNRPSLYNPLYRrpKPLVPRDLRIGVRGRIGPDGVEIERLDVDAVREWAARLCREGVRVYAV 157
                                    *************************9655599************************************************ PP

                     Hydant_A_N 156 vllhSylnpehElrvaeiare 176
                                    ++lhS++np hE+ +a+++ e
  gi|118431411|ref|NP_147873.2| 158 SFLHSHRNPLHEKMAAQAVGE 178
                                    ***************998866 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.74
                     Hydant_A_N 127 gevlkpldeeevrealkalkaagvesiavv 156
                                      vlkp+    ++e  ++l+++g++++  v
  gi|118431411|ref|NP_147873.2| 207 NAVLKPILSTYLQELHRQLRDRGFKGVLLV 236
                                    568889999999999999999999988655 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.8e-06     0.021       1      43 [.       6      50 ..       6      53 .. 0.87
   2 ?    0.7   0.1       0.2   7.2e+02       3      31 ..     283     311 ..     281     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                                   EEEEE-SSSEEEEEEETTEEEEEEEES-...-HHHHHHHHHHHHT- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                           FtsA  1 alvDiGagktdvavaedgalvhlrvigv...ggngitkdiakalrt 43
                                   ++vD+G++ td++v+++g l+ l+v+ +   + +g+ +++++al+t
  gi|118431411|ref|NP_147873.2|  6 VGVDVGGTFTDIVVFDGG-LRVLKVLTTpkrPVEGVMNGLSRALGT 50
                                   69*************994.66677777799999*********9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                                    EEE-SSSEEEEEEETTEEEEEEEES--HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           FtsA   3 vDiGagktdvavaedgalvhlrvigvggn 31 
                                     D+G+++ +++ + dg++  +++  vgg+
  gi|118431411|ref|NP_147873.2| 283 FDMGGTTAKASSIIDGEPEVVDTYEVGGR 311
                                    5***************9999999999885 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00019       0.7       1      35 [.       6      40 ..       6     238 .. 0.84
   2 !    4.5   0.0    0.0059        21       1      61 [.     281     527 ..     281     600 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                                   EEEEE-SSEEEEEEEETTTEEEEEEEE--TTS-HH CS
                    BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgitnsanlesv 35
                                   vG+D+G+T t  v++d    vl+   t  + +e+v
  gi|118431411|ref|NP_147873.2|  6 VGVDVGGTFTDIVVFDGGLRVLKVLTTPKRPVEGV 40
                                   8***************9988888877777655544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0059
                                    EEEEE-SSEEEEE.EEETTTEEEEEEEE--.................................................. CS
                    BcrAD_BadFG   1 vGiDgGsTttkav.lmdekgevlgrgitns.................................................. 29 
                                    +G D+G+Tt ka  ++d + ev+ ++  ++                                                  
  gi|118431411|ref|NP_147873.2| 281 LGFDMGGTTAKASsIIDGEPEVVDTYEVGGrvhmgrlirgsgypvryphidlaevsagggtiawvdpggalqvgpmsaga 360
                                    799********963677777788888888777777777777888888888888888888888888888888888888888 PP

                                    ................................................................................ CS
                    BcrAD_BadFG  30 ................................................................................ 29 
                                                                                                                    
  gi|118431411|ref|NP_147873.2| 361 dpgpacyglggskptvtdanlilgrlpdvlagglrlsrrlaedavkgrvaepmgldvveaawaivrianaimsralrlvs 440
                                    88888888888888888888888888888888888887777777777777777777777777777777777777777777 PP

                                    .......................................................TTS-HHH.........HHHHHHHHH CS
                    BcrAD_BadFG  30 .......................................................anlesvrfeaaekvleealtealer 54 
                                                                                            +l+++  + a +v ++ l+ ++e+
  gi|118431411|ref|NP_147873.2| 441 lergrdprgftmyafggagplhaaelaeemgvsrviippfpgvfsalgllvadykHSLHAPVARPASSVSQDELDRVFEK 520
                                    77777777777777777777777777777777777777777777777777777766666555555666666677777777 PP

                                    HT--GGG CS
                    BcrAD_BadFG  55 ageeead 61 
                                    ++e +++
  gi|118431411|ref|NP_147873.2| 521 LRERADE 527
                                    7776666 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1    0.0038        14       4      53 ..       8      53 ..       5      64 .. 0.74
   2 ?    8.3   0.1   0.00022      0.78     224     272 ..     257     303 ..     235     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0038
                           MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtvee..edvleGleealeelee 53
                                   +D+G t+T ++++d      r+l   + +Tt ++  e v++Gl++al  le 
  gi|118431411|ref|NP_147873.2|  8 VDVGGTFTDIVVFDGG---LRVL---KVLTTPKRpvEGVMNGLSRALGTLEG 53
                                   7999999999999993...3444...45555555567899999999888875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00022
                           MutL 224 impTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegspeke 272
                                    i   P+A   av  +++   ++++ +l++D+GG+T    s+++g+pe  
  gi|118431411|ref|NP_147873.2| 257 IESGPSAGAVAVAYFSR--LQRVDRALGFDMGGTTAKASSIIDGEPEVV 303
                                    55667788888888888..345789********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 4700.68
//
Query:       gi|14601339|ref|NP_147874.1|  [L=562]
Description: hydantoin utilization protein B [Aeropyrum pernix K1]
Scores for complete 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-185  617.6   0.4   1.6e-185  617.5   0.4    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.5   0.4  8.7e-190  1.6e-185       1     516 []       4     520 ..       4     520 .. 0.97

  Alignments for each domain:
  == domain 1  score: 617.5 bits;  conditional E-value: 8.7e-190
                Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekf..eg.el 78 
                                   D + ++v+r++   + eemg +l++ta+Spnik+r D  ca+++++g+lvaqa+hipvh+gsm+  vka+++++  eg +l
  gi|14601339|ref|NP_147874.1|   4 DRVAVDVVRHAAIYASEEMGVVLRNTAYSPNIKDRSDHTCAILTPEGDLVAQAEHIPVHIGSMAVGVKAAVDYLrrEGeDL 84 
                                   8899*******************************************************************888753358* PP

                Hydantoinase_B  79 kpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveegelee 159
                                   +pGDv+++NdPy  gtHl+D+++++Pv+ +g++v+ va++aHh+DiGG +pGs+  +a+e+ +EGl+ippvk+ ++g+l++
  gi|14601339|ref|NP_147874.1|  85 EPGDVVAVNDPYIAGTHLNDVMLLKPVYSRGRMVAIVANKAHHVDIGGLHPGSIGGSARELLQEGLIIPPVKISRGGRLDD 165
                                   ********************************************************************************* PP

                Hydantoinase_B 160 dvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpd.gtyeaedyld 239
                                   ++l+ll++nvRtp++++gDlkAq+aa++vgerr+ el+ +yG++ + +a++eil +ae+ +r+++++l   g+++aed+l+
  gi|14601339|ref|NP_147874.1| 166 GLLRLLESNVRTPRYLRGDLKAQLAALNVGERRVVELASRYGEEFLLEAWREILGHAEAYARRRIEDLGVeGVWSAEDVLE 246
                                   ******************************************************************99877********97 PP

                Hydantoinase_B 240 d.g..ipikvtvti.dgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpegsllnps 316
                                     g    +k t++i  g +++vDftgtspqv++++Na++ vt +a++++l+++vd+d+p+N+G++r++e+++pegsl+np+
  gi|14601339|ref|NP_147874.1| 247 LsGgeAVVKSTLSIlPGGRVRVDFTGTSPQVDEPVNAVYGVTVAATTFALKTVVDPDMPVNQGFFRAVEIEAPEGSLVNPR 327
                                   7556778888887647778************************************************************** PP

                Hydantoinase_B 317 epaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgkdGasavhvh 397
                                   +pa+v+ggn+etsqr++dvv+ ala+alp rv+Aas+g+m+n+++g      g  +++yet+a+G GArp +dG ++vh++
  gi|14601339|ref|NP_147874.1| 328 RPAPVSGGNTETSQRIADVVFMALAKALPGRVPAASCGSMTNVMLG------GPGWAFYETVACGEGARPVRDGYDGVHTN 402
                                   **********************************************......5568************************* PP

                Hydantoinase_B 398 mtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfapwGlaGGepGargrvvl 478
                                   mtnt nt+vE +E++yPvl+ r+elr ds G+G++rGG+Gvvr ++++  ++t+++ ++r +++pwGl+GG pG++ +   
  gi|14601339|ref|NP_147874.1| 403 MTNTLNTPVERMETEYPVLFVRYELRADSEGPGRWRGGLGVVRAFKLTGGRATLTLYGQRCRTRPWGLEGGSPGEPAA--- 480
                                   *************************************************99***************************... PP

                Hydantoinase_B 479 nllvr..geeenlggkatvelkagdvlvietpGGGGyGdp 516
                                   ++lv+  g++++lg +atve+++gd+++i+tpGGGGyGdp
  gi|14601339|ref|NP_147874.1| 481 HYLVKkdGSRVELGCTATVEIEEGDTVYIQTPGGGGYGDP 520
                                   6666667999****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4261.90
//
Query:       gi|14601340|ref|NP_147875.1|  [L=103]
Description: hypothetical protein APE_1333 [Aeropyrum pernix K1]
Scores for 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   61.3   1.8    8.6e-17   61.0   1.8    1.1  1  ABM              Antibiotic biosynthesis monooxygenase
     0.0026   17.2   0.0     0.0028   17.1   0.0    1.0  1  Dehydratase_hem  Haem-containing dehydratase
      0.003   17.9   1.0     0.0095   16.3   1.0    1.8  1  DUF1330          Domain of unknown function (DUF1330)
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.013   15.2   0.1    1.1  1  DUF3291          Domain of unknown function (DUF3291)


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 !   61.0   1.8   1.9e-20   8.6e-17       4      78 .]       5      78 ..       2      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.9e-20
                                  EEEEEE.ESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHHHHH CS
                           ABM  4 viaeir.vkpgqaeafldafaeavesllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaahea 78
                                  + ++ir   p++ +++++af+ +++ l+++++G+++ ++l   +d+ evvvi++Wes++++e++++s +f++ah++
  gi|14601340|ref|NP_147875.1|  5 IANYIRaETPEAFDKVIEAFTGRAG-LVERMEGFRSLQVLA-NRDRLEVVVITVWESREHFERWVESREFEEAHKR 78
                                  6678885578999************.77************8.999999**************************86 PP

>> Dehydratase_hem  Haem-containing dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.2e-07    0.0028      35      84 ..      35      83 ..       8     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-07
               Dehydratase_hem 35 alvetlsvtdeddalnsavwiaYWkskeayeawlasssvaefwaslpede 84
                                  + + +l+v  ++d l++ v i+ W+s+e++e+w +s +++e +++ ++++
  gi|14601340|ref|NP_147875.1| 35 EGFRSLQVLANRDRLEVVV-ITVWESREHFERWVESREFEEAHKRARRRR 83
                                  4456788999*********.**********************99987764 PP

>> DUF1330  Domain of unknown function (DUF1330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.0   2.1e-06    0.0095      42      81 ..      41      80 ..       2      90 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                       DUF1330 42 evlEGdeeptrlvvieFpsveaarawyeSpeYqaakalRq 81
                                  +vl  + + + +v+  ++s+e++++w eS e+++a +  +
  gi|14601340|ref|NP_147875.1| 41 QVLANRDRLEVVVITVWESREHFERWVESREFEEAHKRAR 80
                                  3333333345678889******************985433 PP

>> DUF3291  Domain of unknown function (DUF3291)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.8e-06     0.013      24      91 ..      16      85 ..       4      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-06
                       DUF3291 24 aldeinalaeaspGfvwrleeeegdatalrafeddllivnlsvWeslealrafv....Yksehaevlrrrre 91
                                  a d++ ++ +   G+v r+e+   ++ ++ a +d l +v ++vWes e+ + +v    ++++h+++ rrr e
  gi|14601340|ref|NP_147875.1| 16 AFDKVIEAFTGRAGLVERMEG--FRSLQVLANRDRLEVVVITVWESREHFERWVesreFEEAHKRARRRRLE 85
                                  567777888888899999954..444566677788899*************998555567777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 785.33
//
Query:       gi|118431412|ref|NP_147876.2|  [L=341]
Description: N-terminal deblocking aminopeptidase [Aeropyrum pernix K1]
Scores for complete 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-88  297.1   0.0    1.2e-88  296.9   0.0    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    2.9e-11   43.4   0.0    4.7e-09   36.2   0.0    2.2  2  Peptidase_M28  Peptidase family M28
    8.4e-11   42.0   0.1    2.4e-10   40.5   0.1    1.8  1  Peptidase_M20  Peptidase family M20/M25/M40
    0.00061   18.7   0.0    0.00081   18.3   0.0    1.1  1  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.42   10.9   0.0    1.9  2  DUF3247        Protein of unknown function (DUF3247)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.9   0.0   3.5e-92   1.2e-88       1     292 []      44     332 ..      44     332 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.9 bits;  conditional E-value: 3.5e-92
                                    S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTE.EEEEEEEE--CGGCH. CS
                  Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkg.kisGvigskppHllk. 78 
                                    Gn++++ +g   ep+++ aAHmDe+Gf+++ + +dG l f+k+GG+d+++l+gq+v+il + g +i+Gvig++ppHl+  
  gi|118431412|ref|NP_147876.2|  44 GNVVVNPSG--GEPRLLAAAHMDELGFVITGVGDDGLLAFRKLGGIDDRILPGQHVEILLDGGaRIEGVIGITPPHLQLd 121
                                    99***9999..9*****************************************************************995 PP

                                    HHHHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTEC.EEETTHHHHHHHHHHHHHHHHHCTSS-S.S CS
                  Peptidase_M42  79 eeerkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangk.ivskalDdragvavllellkelkeeele.a 156
                                    + e +k+l+++el+iDiga+s++eaeelG+++ +++vf+k++++la+g+ ++s+ +Ddragva+llel+k+++e +++  
  gi|118431412|ref|NP_147876.2| 122 RGEAEKPLRWHELRIDIGAQSRAEAEELGVKPLQPAVFKKHWSTLAGGRaLASRGFDDRAGVALLLELAKRIAEGRVDaG 201
                                    777888888*********************************************************************88 PP

                                    EEEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSSTTS-CEEEEEETTCCSHHHHHHHHHHHHHHT CS
                  Peptidase_M42 157 tvylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeaklgkGpvirvkDasgiyhpklrkkllelAkkn 236
                                     + l++tvqEEvGlrGa+++a+++kp++++avD++a+++   + +++   g+Gpv+r+ D+++i+++ l++ l+e+A+++
  gi|118431412|ref|NP_147876.2| 202 GIALAWTVQEEVGLRGASYVASRMKPKAFLAVDTMACCHPAVTGHTR--PGGGPVVRALDNQHITPRWLVELLEEAARSA 279
                                    9999**********************************999999999..******************************* PP

                                    T--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                  Peptidase_M42 237 nipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                    ++++q+ +++gg+tDA+a+++t  gvp+a+i+ip++y+Hs++ev+ l+dle + kL
  gi|118431412|ref|NP_147876.2| 280 GLELQY-ATAGGTTDAAAFQRT--GVPSAAIGIPLKYTHSTAEVLYLSDLEGALKL 332
                                    ******.999*********999..***************************99987 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0     0.005        18       2      39 ..      46      77 ..      45      81 .. 0.78
   2 !   36.2   0.0   1.3e-12   4.7e-09      20     163 ..     162     307 ..     155     323 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.005
                                   EEEEESTTCESEEEEEEEE--B-TTTTCCT---TTTTH CS
                  Peptidase_M28  2 viatlegkatdevlllgAHyDsvgvgrgpifvGAdDnA 39
                                   v++  +g++   +ll +AH+D +g+    ++ G+ D++
  gi|118431412|ref|NP_147876.2| 46 VVVNPSGGE--PRLLAAAHMDELGF----VITGVGDDG 77
                                   555554444..589***********....789999998 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 1.3e-12
                                    E--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCS.SEEEEEEEESSCSGSSHHHHHHHHHHCCCTTEEEEEEEC CS
                  Peptidase_M28  20 HyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrp.krgvrflffdaEEagllGSkafakakpelkkiaavlnlD 98 
                                    H+ +++ gr+    G dD A gva+lLela+ +a+ g r    g+ ++++  EE gl G+++ a     + k +a+l +D
  gi|118431412|ref|NP_147876.2| 162 HWSTLAGGRALASRGFDDRA-GVALLLELAKRIAE-G-RVdAGGIALAWTVQEEVGLRGASYVA----SRMKPKAFLAVD 234
                                    66666654222445777776.*************7.6.45499*********************....578889999999 PP

                                    S-SSSS--EEE.........HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEE CS
                  Peptidase_M28  99 mvgsggkellf.........esgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldl 163
                                     ++  ++++           ++  ++++   ++l +l ++++r+a  + ++++   g++D+++f++ gvp + +
  gi|118431412|ref|NP_147876.2| 235 TMACCHPAVTGhtrpgggpvVRALDNQHITPRWLVELLEEAARSAGLE-LQYATAGGTTDAAAFQRTGVPSAAI 307
                                    999999999987788888876667777777777778888888875444.566667899************9988 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   6.8e-14   2.4e-10      35     204 ..     176     336 ..     154     339 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.8e-14
                                    TTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  35 addmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgileagklaigv 114
                                      d+ +gv+ +le+++++++      g i l+ ++ EE+g +Ga +++     r k++a++++  +   ++   + + ++
  gi|118431412|ref|NP_147876.2| 176 GFDDRAGVALLLELAKRIAEGR-VDAGGIALAWTVQEEVGLRGASYVAS----RMKPKAFLAVDTMACCHPAVTG-HTRP 249
                                    57999************77765.569************988********....7788887765544444444222.4455 PP

                                    EEEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEE.SSGGCTTSTTTEEEH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxx RF
                  Peptidase_M20 115 vkvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifg.pgsglaHspnEyvdl 191
                                    +   v   ++    ++    lv++l+eaa+++ g++ +  + g g+tda+ f   g+p++  +g p  +  Hs  E + l
  gi|118431412|ref|NP_147876.2| 250 GGGPVV--RALDNQHITPRWLVELLEEAARSA-GLELQYATAG-GTTDAAAFqrTGVPSA-AIGiPL-KYTHSTAEVLYL 323
                                    544444..2333334443577**********8.*999999***.********77777988.478688.99********** PP

                                    HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxx RF
                  Peptidase_M20 192 edlekgikvlarl 204
                                    +dle ++k+l++l
  gi|118431412|ref|NP_147876.2| 324 SDLEGALKLLEHL 336
                                    *********9987 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.3e-07   0.00081     335     429 ..     247     334 ..     215     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.3e-07
                                    --TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EEBSTTSSSE CS
                  Peptidase_M18 335 pllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaqlsmHSire 414
                                      +++G+v++   nq+  t    ++ll+e+a+ a+ +lQ+++      +G+t+ + +  +tG+    +G++    HS  e
  gi|118431412|ref|NP_147876.2| 247 TRPGGGPVVRALDNQHI-TPRWLVELLEEAARSAGLELQYAT------AGGTTDAAAFQRTGVPSAAIGIPLKYTHSTAE 319
                                    46799*****9999985.677889***************986......79999999************************ PP

                                    EEECCHHHHHHHHHH CS
                  Peptidase_M18 415 ltgskdveeavklfk 429
                                    +   +d+e a+kl++
  gi|118431412|ref|NP_147876.2| 320 VLYLSDLEGALKLLE 334
                                    **********99986 PP

>> DUF3247  Protein of unknown function (DUF3247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.42      25      75 ..      92     142 ..      88     149 .. 0.84
   2 ?   -2.0   0.0       1.2   4.5e+03      35      51 ..     193     209 ..     173     212 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                    TTTT-EEEEEETTS-EEEEEECC--.-EEEEE-TT--EEEEEEEEEE-SSTT CS
                        DUF3247  25 ldseervaleledGrqlaGtvavrp.tvqiyrdeqereGvnallrlddldds 75 
                                    l+++  v ++l+ G ++ G + + p  +q+ r e e+      lr+d  ++s
  gi|118431412|ref|NP_147876.2|  92 LPGQ-HVEILLDGGARIEGVIGITPpHLQLDRGEAEKPLRWHELRIDIGAQS 142
                                    5554.69***************985379**********9999***9976665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                    ETTS-EEEEEECC---E CS
                        DUF3247  35 ledGrqlaGtvavrptv 51 
                                    + +Gr  aG +a+  tv
  gi|118431412|ref|NP_147876.2| 193 IAEGRVDAGGIALAWTV 209
                                    23445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2610.85
//
Query:       gi|14602204|ref|NP_147877.1|  [L=549]
Description: phytoene dehydrogenase [Aeropyrum pernix K1]
Scores for 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-19   68.0   3.6    1.1e-17   64.5   3.6    2.2  1  Amino_oxidase    Flavin containing amine oxidoreductase
    3.1e-11   43.4   0.2    3.1e-11   43.4   0.2    2.1  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    6.5e-10   39.1  10.3    1.2e-08   35.0  10.0    2.6  1  DAO              FAD dependent oxidoreductase
    2.5e-09   36.7   6.5      3e-06   26.6   0.9    2.2  2  FAD_binding_2    FAD binding domain
    2.7e-09   36.9   1.1    7.3e-09   35.5   0.3    1.8  2  FAD_oxidored     FAD dependent oxidoreductase
    6.3e-07   28.9   0.0    1.3e-06   27.9   0.0    1.4  1  Thi4             Thi4 family
    6.6e-07   28.4   0.3    0.00013   20.8   0.2    2.1  2  HI0933_like      HI0933-like protein
      1e-06   28.1   0.5    2.1e-05   23.8   0.2    2.1  2  GIDA             Glucose inhibited division protein A
    1.3e-05   24.6   0.2    0.00015   21.1   0.1    2.1  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00011   22.7   1.1    0.00085   19.8   0.8    2.3  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00014   21.3   1.4    0.00014   21.3   1.4    1.6  2  FAD_binding_3    FAD binding domain
     0.0054   15.8   0.0     0.0097   15.0   0.0    1.4  1  Lycopene_cycl    Lycopene cyclase protein
  ------ inclusion threshold ------
      0.013   14.3   0.8      0.025   13.4   0.1    1.7  2  Trp_halogenase   Tryptophan halogenase
      0.015   14.7   0.6      0.025   13.9   0.0    1.6  2  GMC_oxred_N      GMC oxidoreductase
       0.26   11.2   0.4       0.44   10.4   0.4    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.35   10.1   1.0       0.65    9.2   1.0    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain


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 !   64.5   3.6   9.6e-21   1.1e-17       3     318 ..      18     352 ..      18     511 .. 0.64

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 9.6e-21
                                   HHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEET.TEEEESS--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEEEEETT CS
                 Amino_oxidase   3 GLaaArqLlsaGfdVtvlEardrvGGRirtvrsd.GylielGamwftgagnpllellkelgledslslpdpgapkrvlskg 82 
                                   GL+aA+ L+++G++V +lEar+r+GG ++++    G+++  Ga ++  +  +   l++e g+e +++l   ++  +v+  +
  gi|14602204|ref|NP_147877.1|  18 GLTAASVLARRGLRVALLEARERLGGLAASYSPWpGFTAPFGAYVLGLYPRW---LMREAGIEGRVRLLPKDPGMTVVLGE 95 
                                   9*************************999988779********999985554...67888999999955556678888877 PP

                                   EECC.........TTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHH CS
                 Amino_oxidase  83 gref.........pgdlspv.paewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgd 153
                                   gr             ++s+v pa  ea+l+   ++          ++   +l   + ++ ++ s++   + +  ++r p  
  gi|14602204|ref|NP_147877.1|  96 GRALrvygdarrtSREFSRVsPADGEAYLR---WA-------RLWSALGVLLE--EVYSHPPLSPREVVEHAYRAARTPLV 164
                                   777788777777777777777777777777...33.......33333333333..11133344444444433344444444 PP

                                   HHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE.......................TTHTHH CS
                 Amino_oxidase 154 vevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllp.......................rgGlsq 211
                                     +++  +e   +     a ++++ ++++ +a++al ++  + +++++ + +                       +gG+++
  gi|14602204|ref|NP_147877.1| 165 GRIVEEALEAAQWMLTAPAARILGEWFESWEARAALVEDALVGEMAAPSTPGtgivlahhylgvstgrrgewayvKGGMGR 245
                                   344444444333333334445555555888888888888888888888665599*************************** PP

                                   HHHHHHH..TTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESE.EEE-S-HHHHHSSEEES.CCSHHHHHHHHHS.E CS
                 Amino_oxidase 212 lpealae..elrgldirlntrVkeikr.egdgvtvtledgevveaDa.VvvTvplgvlkailfsP.plpdekaeairnl.g 286
                                   l++alae  ++ g +i +++rV+e+   +g  v+v+++dg+v++a++ V+ ++++ +l     s  +l +  a+ ir l  
  gi|14602204|ref|NP_147877.1| 246 LIHALAEaaREAGASIETGARVSEVLVeSGRAVGVRTWDGRVYRARKaVLWAASIKTLP----SVvELDRGLARRIRTLeS 322
                                   ***************************66666***********88776999********....224566688999999999 PP

                                   EEEEEEEEEEESSGGSGCST..SECECECCCEEE CS
                 Amino_oxidase 287 fgsvnkvilefdrkfwedna..lgqgvlvseltt 318
                                   +g ++k++l+ +++  + ++  +    l ++l+t
  gi|14602204|ref|NP_147877.1| 323 SGASSKIVLAAREPLKPAEEyrW----LGEDLYT 352
                                   9*************933332211....2222222 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 !   43.4   0.2   2.7e-14   3.1e-11       1      50 [.      11      61 ..      11      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.7e-14
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE.TTCEECTS-- CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev.pgvrvdygah 50
                                  +vG+G  Gl+aA+ La++g++v lle+r+rlGG aasy+  pg+++  ga 
  gi|14602204|ref|NP_147877.1| 11 VVGGGHNGLTAASVLARRGLRVALLEARERLGGLAASYSPwPGFTAPFGAY 61
                                  8*************************************9988988877775 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0  10.0   1.1e-11   1.2e-08       1     205 [.       8     303 ..       8     343 .. 0.60

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.1e-11
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSS.....STHHSTH..HHHHHHHHH.HHHH.H CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsgl.....rylpeas..elarlslea.leel.r 69 
                                   dvv++GGG  Gl++A  Larrg  V+lle+++++g  +aS   +  +++ +              +   l++ea +e + r
  gi|14602204|ref|NP_147877.1|   8 DVVVVGGGHNGLTAASVLARRGlrVALLEARERLGGlAASYSPWPGFTAPFgayvlG-----LypR--WLMREAgIEGRvR 81 
                                   9******************************99996688888886666656443321.....1221..2333332444445 PP

                                   HHHHHHSSTTSEEEEEEEEEESS..........HHHHHHHH........................................ CS
                           DAO  70 eleeelgididyrrtGllslaad..........eeeleald........................................ 100
                                    l ++ g+ + + +   l ++ d                                                          
  gi|14602204|ref|NP_147877.1|  82 LLPKDPGMTVVLGEGRALRVYGDarrtsrefsrV------Spadgeaylrwarlwsalgvlleevyshpplsprevvehay 156
                                   5555555555555555555543233333333330......14444444445555555555555555555555555555555 PP

                                   ................................HHHHHHHHTTTTEEEEEHHHHHHHS.TTST...............TTSE CS
                           DAO 101 ................................kllallleagldaelldaeevrele.palp...............gllg 133
                                                                   +++++++   ++a l++ ++v e++ p +p               g +g
  gi|14602204|ref|NP_147877.1| 157 raartplvgriveealeaaqwmltapaarilgEWFESWE---ARAALVEDALVGEMAaPSTPgtgivlahhylgvstGRRG 234
                                   555555555555555555556666666655555555552...333344444444444232224446666777766554444 PP

                                   EEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHH CS
                           DAO 134 alfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsd 205
                                    + y  +g     +l++ala+aa+++G+ i +g++v ++  e+g+++gv   t  g++ +a +av  aa + + 
  gi|14602204|ref|NP_147877.1| 235 EWAYVKGGM---GRLIHALAEAAREAGASIETGARVSEVLVESGRAVGV--RTWdGRVyRARKAVLWAASIKTL 303
                                   455555566...889999********************978899*****..44449885553458888876664 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.9   2.7e-09     3e-06       1      38 [.       8      46 ..       8      50 .. 0.91
   2 !   13.1   0.5   3.3e-05     0.037      88     198 ..     183     297 ..     143     306 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.7e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS.GG CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg.at 38
                                  Dv+V+G+G  GL+AA  +a++Gl+va++e  ++ gg a+
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVLARRGLRVALLEARERLGGlAA 46
                                  9*******************************9998544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.3e-05
                                   THHHHHHHHHHTT----B............CCTS...SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHT CS
                 FAD_binding_2  88 aapeavdeLeelgvpfsr............tedg...pvdvrelGglsatartlhdaadarretlvtghallarlvesark 153
                                   aa+   +++e++ ++               ++ g   +++   lG  + + r  + a+++     +   +l+++l+e+ar+
  gi|14602204|ref|NP_147877.1| 183 AARILGEWFESWEARAALvedalvgemaapSTPGtgiVLAHHYLGVSTGR-RGEW-AYVK-----GGMGRLIHALAEAARE 256
                                   33333344555533333322222222222222223444444444444444.6666.5555.....577899********** PP

                                   CTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEES.EEEE- CS
                 FAD_binding_2 154 agvdfqerteadeLivedgrvtGavvenpesgrevrirak.avvla 198
                                   ag  + + +++ e++ve+gr++G+  +   +gr   +ra+ av+ a
  gi|14602204|ref|NP_147877.1| 257 AGASIETGARVSEVLVESGRAVGVRTW---DGRV--YRARkAVLWA 297
                                   ************************988...5554..4577677766 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.3   6.5e-12   7.3e-09       1      40 [.       8      47 ..       8      58 .. 0.96
   2 ?   -0.6   0.0      0.58   6.5e+02      93     136 ..     250     290 ..     237     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 6.5e-12
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllts 40
                                  DvvVvGGg  G++AA   ar+G +v+L+e r++lGGl++s
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVLARRGLRVALLEARERLGGLAAS 47
                                  9***********************************9986 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.58
                  FAD_oxidored  93 leemlaeagvtvllntrlvevekegkriesvtveskegrktirA 136
                                   l e  +eag  + +++r++ev +e +r  +v++++   ++++rA
  gi|14602204|ref|NP_147877.1| 250 LAEAAREAGASIETGARVSEVLVESGRAVGVRTWD---GRVYRA 290
                                   45556899999999999999999877999999987...555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   1.1e-09   1.3e-06      18      55 ..       7      43 ..       4      62 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                   Dvv+vG+G  GLtaa +la++ +l+va+le++  +GG
  gi|14602204|ref|NP_147877.1|  7 FDVVVVGGGHNGLTAASVLARR-GLRVALLEARERLGG 43
                                  6*********************.*********999998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   1.2e-07   0.00013       1      36 [.       7      42 ..       7      44 .. 0.95
   2 !    5.6   0.0     0.005       5.6     110     160 ..     245     295 ..     239     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +dv+v+GgG  Gl aA  +a+rg rV+lle+ ++lg
  gi|14602204|ref|NP_147877.1|  7 FDVVVVGGGHNGLTAASVLARRGLRVALLEARERLG 42
                                  59*****************************99987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.005
                                   HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE CS
                   HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvl 160
                                   ++++al ++++eag ++++  +v++v  e+++++ v+t +++ ++a+k vl
  gi|14602204|ref|NP_147877.1| 245 RLIHALAEAAREAGASIETGARVSEVLVESGRAVGVRTWDGRVYRARKAVL 295
                                   5799**********************************8899999988887 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   1.9e-08   2.1e-05       1      34 [.       8      40 ..       8      51 .. 0.83
   2 ?    2.4   0.0      0.06        67     117     148 ..     266     297 ..     260     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.9e-08
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldt 34
                                  dv+V+GgGh G+ AA  +ar+G++v+L+ +  ++
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVLARRGLRVALL-EARER 40
                                  79*************************9.44444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.06
                                   -EEEEEECTTEEEEEEETTS-EEEECEEEE-- CS
                          GIDA 117 eveeliveekkvkgvvtedgetikakavviat 148
                                   +v+e++ve+++  gv+t dg++++a++ v+ +
  gi|14602204|ref|NP_147877.1| 266 RVSEVLVESGRAVGVRTWDGRVYRARKAVLWA 297
                                   7999**********************999855 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.3e-07   0.00015       1      33 [.       7      39 ..       7      61 .. 0.82
   2 ?    1.2   0.0      0.16   1.8e+02     187     234 ..     248     297 ..     237     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                  +dvvv+GgG+ Gl+aa  la+ g++v+l+e+++
  gi|14602204|ref|NP_147877.1|  7 FDVVVVGGGHNGLTAASVLARRGLRVALLEARE 39
                                  589999999999999999999999999997444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                                   HHHHHHHHHTTEEEEESCEEEEEEETTE.EEEEEETTSCEEEES.EEEE- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxx RF
                   Pyr_redox_2 187 aaleealekeGvevklgtsvkeidgnge.klevvledgeeidad.lvvva 234
                                    al+ea ++ G  + +g++v e+  ++   + v + dg+++ a+  v++a
  gi|14602204|ref|NP_147877.1| 248 HALAEAAREAGASIETGARVSEVLVESGrAVGVRTWDGRVYRARkAVLWA 297
                                   5778999999*************999995555999999998876145555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.8   7.6e-07   0.00085       2      35 ..       9      42 ..       8      47 .. 0.94
   2 ?    0.1   0.0       1.1   1.2e+03      45      77 ..     249     281 ..     245     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.6e-07
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  vvvvGgG  gl +A++la+ g +V ++e++++l 
  gi|14602204|ref|NP_147877.1|  9 VVVVGGGHNGLTAASVLARRGLRVALLEARERLG 42
                                  8******************************997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                     Pyr_redox  45 ilqeklekngievllntkveeiegsedgvesvk 77 
                                   +l+e  ++ g  + ++++v e+  ++    +v+
  gi|14602204|ref|NP_147877.1| 249 ALAEAAREAGASIETGARVSEVLVESGRAVGVR 281
                                   577889999999********9997776555666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.4   1.2e-07   0.00014       3      34 ..       8      39 ..       6      43 .. 0.94
   2 ?   -3.3   0.0       3.6     4e+03     107     130 ..     246     269 ..     244     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                  dV++VG+G  Gl++a++L+++G rv l+e r+
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVLARRGLRVALLEARE 39
                                  8****************************987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.6
                                   HHHHHHHHHHHHTEEETCSEEEEC CS
                 FAD_binding_3 107 leriLvehaeerglqvrfkteves 130
                                   l  +L+e+a+e+g++++ +++v  
  gi|14602204|ref|NP_147877.1| 246 LIHALAEAAREAGASIETGARVSE 269
                                   5678999999****9999998865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.6e-06    0.0097       1      36 [.       8      41 ..       8      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.6e-06
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  Dvvv+G+G  gl  A  l  a+ gl+v l+ea + l
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVL--ARRGLRVALLEARERL 41
                                  9***************99..***********98876 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.2e-05     0.025       1      34 [.       8      38 ..       8      72 .. 0.94
   2 ?   -1.6   0.1      0.84   9.4e+02     157     201 ..     247     291 ..     240     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                  ++v+vGGG  G +aA++la+ +   l+v l+e+ 
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVLARRG---LRVALLEAR 38
                                  69******************99...999999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.84
                                   HHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-S CS
                Trp_halogenase 157 akfLrrvaearGvtrvegkvvevqldedgrveslrledgrevead 201
                                    + L + a ++G  +  g  v+ +l e+gr  ++r+ dgr++ a+
  gi|14602204|ref|NP_147877.1| 247 IHALAEAAREAGASIETGARVSEVLVESGRAVGVRTWDGRVYRAR 291
                                   567889999999999999999999999999999999999988765 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.2   2.4e+03       1      30 [.       7      35 ..       7      40 .. 0.71
   2 ?   13.9   0.0   2.3e-05     0.025     198     252 ..     249     295 ..     233     309 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                   GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvl 30
                                  +d +v+ggG  g + A+ L+  +  +v +l
  gi|14602204|ref|NP_147877.1|  7 FDVVVVGGGHNGLTAASVLARRG-LRVALL 35
                                  578999***99999777776543.455555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.3e-05
                   GMC_oxred_N 198 wLrpalerpnleiltgakaekiilegrkkravGVeasdkkgtvkrlvvaakevvv 252
                                    L +a ++ ++ i tga+++ +++e  ++ravGV++ d           a++ v+
  gi|14602204|ref|NP_147877.1| 249 ALAEAAREAGASIETGARVSEVLVE--SGRAVGVRTWDGRVY------RARKAVL 295
                                   577888888****************..*******98775443......3333444 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 ?   10.4   0.4   0.00039      0.44       2      32 ..       9      39 ..       8      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdise 32
                                  v v+G G  G   a+v+a++gl+V l++ +e
  gi|14602204|ref|NP_147877.1|  9 VVVVGGGHNGLTAASVLARRGLRVALLEARE 39
                                  89************************99876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.0   0.00058      0.65      30      61 ..       8      39 ..       2      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00058
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                   v+v+GgG  Gl A+++ ++ g +V +l+ r+
  gi|14602204|ref|NP_147877.1|  8 DVVVVGGGHNGLTAASVLARRGLRVALLEARE 39
                                  69************************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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):              16  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 4192.33
//
Query:       gi|118431413|ref|NP_147878.2|  [L=227]
Description: hypothetical protein APE_1337.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.0  22.4      0.011   16.0  22.4    3.0  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 ?   16.0  22.4   6.2e-07     0.011      27     135 .]      22     144 ..      17     144 .. 0.55
   2 ?    0.5   1.2     0.038   6.8e+02      36      78 ..     146     183 ..     142     214 .. 0.42

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.2e-07
                         DUF996  27 snaliafilsiialvva.....ilalllvlgalatalelpgleeaaslilllllvliiayvlliis.......avflkks 94 
                                    ++++ + il +  lvv      +++l++  ++++ + +l++++     il+++ +l++ ++ll+i+       av +k+ 
  gi|118431413|ref|NP_147878.2|  22 RRVFLSYILFLMVLVVWlgvlgAFLLVGLTFEALLGSGLEAFT-----ILGVVTALLASVLLLVIAgyifyrgAVDIKDG 96 
                                    4444444444444444422225444444444444455555444.....44444444444433333300000003334444 PP

                         DUF996  95 yellgk.......rtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                    ++++g+       ++g +l+ ++g l ++Ga+LtivlvG++il +++i
  gi|118431413|ref|NP_147878.2|  97 VARVGEprvrsdlALGAELLYIGGVLTLVGAVLTIVLVGVLILAVGNI 144
                                    45555444444446899*****************************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.038
                         DUF996  36 siialvvailalllvlgalatalelpgleeaaslilllllvli 78 
                                    ++i++ v++  l +v  +l t l+++ +  a+      ll++i
  gi|118431413|ref|NP_147878.2| 146 ALIGIGVIAYRLRGVHPELETPLNITLVGVALH-----LLSYI 183
                                    444444444444444444444444443333332.....11111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 1604.05
//
Query:       gi|118431414|ref|NP_147879.2|  [L=224]
Description: hypothetical protein APE_1339.1 [Aeropyrum pernix K1]
Scores for complete sequence (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    6.9   9.7       0.25   10.4   3.3    2.0  2  DUF973    Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   3.9      0.12   2.2e+03      77      77 ..      94      94 ..      21     140 .. 0.49
   2 ?   10.4   3.3   1.4e-05      0.25      59     121 ..     130     193 ..     119     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.12
                         DUF973 77 l 77
                                   +
  gi|118431414|ref|NP_147879.2| 94 Y 94
                                   1 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 1.4e-05
                         DUF973  59 liaaii.liiiasvllilgllkirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivs 121
                                    + ++++ l   ++ l   g++ ++ g++i++   r  g+  t++tl+l+ga +++ig+++ ++ 
  gi|118431414|ref|NP_147879.2| 130 IAGSVLlLLGAGLTLATAGFIVFQAGLAIMAYGARSRGGPDTSMTLLLVGASLALIGAAVGVSA 193
                                    333444244456677788999*********999**************************88843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1614.33
//
Query:       gi|118431415|ref|NP_147880.2|  [L=1370]
Description: reverse gyrase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-69  235.3   0.0    2.7e-66  224.3   0.0    2.7  2  Topoisom_bac    DNA topoisomerase
    1.5e-20   73.3   0.0    3.2e-20   72.3   0.0    1.6  1  Toprim          Toprim domain
    1.4e-10   41.2   0.0    2.7e-10   40.3   0.0    1.4  1  DEAD            DEAD/DEAH box helicase
    1.8e-10   40.1   6.2    1.8e-10   40.1   6.2    2.1  2  zf_Rg           Reverse gyrase zinc finger
    3.9e-10   40.1   0.0    2.6e-06   27.7   0.1    3.5  3  Helicase_C      Helicase conserved C-terminal domain
     0.0013   18.8   5.8       0.37   10.9   0.5    2.8  2  Zn-ribbon_8     Zinc ribbon domain
      0.009   14.6   0.0       0.02   13.5   0.0    1.5  1  Terminase_GpA   Phage terminase large subunit (GpA)
  ------ inclusion threshold ------
      0.015   15.2   4.8        1.6    8.7   0.4    2.5  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.017   15.1   4.1       0.23   11.5   0.4    2.4  2  DZR             Double zinc ribbon
       0.02   14.9   0.0      0.039   14.0   0.0    1.4  1  ResIII          Type III restriction enzyme, res subunit
      0.024   13.4   0.2      0.044   12.6   0.2    1.3  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
      0.074   13.1   3.1       0.22   11.5   0.3    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.089   12.4   0.0       0.17   11.5   0.0    1.4  1  Terminase_6     Terminase-like family
       0.43   10.7   2.3         26    5.0   0.1    2.4  2  DUF1272         Protein of unknown function (DUF1272)
       0.98    9.2  13.4      0.023   14.4   0.9    2.6  2  zinc_ribbon_2   zinc-ribbon domain
        4.5    7.4   6.7       0.73    9.9   0.0    2.8  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        6.5    6.3   7.6        1.1    8.8   0.0    3.1  3  AAA_25          AAA domain
        7.8    6.5  14.5      0.073   13.0   1.0    3.0  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


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 ?   -3.0   0.0       2.7   2.6e+03       8      24 ..     198     214 ..     194     220 .. 0.89
   2 !  224.3   0.0   2.7e-69   2.7e-66       3     412 ..     841    1312 ..     839    1313 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                   Topoisom_bac   8 daaeaRrelDwliGinl 24 
                                     aa aR+ +D+l G+++
  gi|118431415|ref|NP_147880.2| 198 TAAFARKYADRLSGYRF 214
                                    6999**********987 PP

  == domain 2  score: 224.3 bits;  conditional E-value: 2.7e-69
                   Topoisom_bac    3 nenlvdaaeaRrelDwliGinlsrlltk......klk.....................g.kkvlsaGRVqtptLaliv 52  
                                     ++nlvda+ +Rr+ D++iG++ls+ll+         k                     +   +lsaGRVqtptL+++v
  gi|118431415|ref|NP_147880.2|  841 DDNLVDAQVVRRVEDRWIGFTLSPLLWCdfwpryC-KrvleeygekrphmdrercakyKaYYNLSAGRVQTPTLGWVV 917 
                                     89*************************98887750.2556677777777777777765246899************** PP

                   Topoisom_bac   53 eRereienFvpeeyweve.atlkkekkeke.....kkkkkkkerikdkeeaeaileklkkk.eakvesvekkek.kk. 121 
                                     +R+ ++++ v   y  v+  +l      ++     ++  ++ +r+ d+       + +  +  + v++v +ke+ +  
  gi|118431415|ref|NP_147880.2|  918 DRTLAYRKKVWL-YRVVHdSQL-----LFAvrsddPEVPESVKRVLDNWVKHHKKTGI--EpWLDVKAVVEKEEwTAl 987 
                                     *****9988533.333321222.....2222222355666666666666555555566..348999999888885558 PP

                   Topoisom_bac  122 ppplpfdtttLqkeasrklglsakktlsiaqkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekl 199 
                                     ppp p++t+t++++a+r lgl+++++++iaq+L+e  glitY+RTdstr+s+   ++ ++e+l+++    + + a +l
  gi|118431415|ref|NP_147880.2|  988 PPPPPYTTDTMLRDANRLLGLGSAEAMRIAQDLFEW-GLITYHRTDSTRVSDRG-MQVAREWLETR----FGGLAGQL 1059
                                     9999*******************************6.****************9.9********98....55677788 PP

                   Topoisom_bac  200 lkktkkksvvknkkveaHeAIrPteelpklkels...............ddekklYelIvrrflaslmkdakyeettv 262 
                                     +  ++++    ++  +aHeAIrP++ ++  ++l+               + + +lY+lI+rrf+as+m++a   ++ +
  gi|118431415|ref|NP_147880.2| 1060 YR-PRRW----GEG-GAHEAIRPVRPIDV-ERLQllveegvielpgtltRRHLRLYDLIFRRFMASQMREADALRVVY 1130
                                     87.5555....555.8********99993.556666889999999*99977778************************ PP

                   Topoisom_bac  263 klev............eeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleekkTkppkryte 328 
                                     +l+v              e  +    + + +Gf+ v ++ + +      p+l eg e  +  +++e ++  +  +yte
  gi|118431415|ref|NP_147880.2| 1131 RLRVpeldgytltlerVVEIGRPGDAEGVTRGFTLVWPYVRPQ------PRLVEGREAWIR-ARVEGRQVPKAYPYTE 1201
                                     **88766444443322111112222344568999998887665......6799***97655.59************** PP

                   Topoisom_bac  329 asLikamekagiGtpaTraeiieklvergYverk......k.kslvptelGkalvell.ekf.kd............. 384 
                                     ++++++m+++giG+p+T+a+i+e+l++r+Yv +       + + +v+t+ G+++++ l e++ +              
  gi|118431415|ref|NP_147880.2| 1202 GEIVEEMKTRGIGRPSTYAKIVETLFRRRYVIEVsreegrGaGFVVATSRGINVYNYLtEELrSAdeeeyggriagil 1279
                                     ******************************987644455434569**********99865443112344555555555 PP

                   Topoisom_bac  385 .....lvspelTaeleekLdeIaegkadakevl 412 
                                          lvs++ T+ele+++d +++g a++++vl
  gi|118431415|ref|NP_147880.2| 1280 rrvpsLVSEDRTRELERQMDMVEKGDASRDDVL 1312
                                     555559************************998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   3.2e-23   3.2e-20       2     103 .]     649     825 ..     648     825 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 3.2e-23
                                    EEEESSHHHHHHHHHTHT...................STEEEEEEESSSSEEEHS......................... CS
                         Toprim   2 lvivEgpsdaktiakalg...................sgfqavtaslGhildlet......................... 37 
                                    l +vE+p++a+tia+++g                   ++ ++++as Gh++dl+                          
  gi|118431415|ref|NP_147880.2| 649 LLVVESPNKARTIARFFGqpsvrllpgggrvyevatgDKILMIMASGGHVFDLVVrvdgrdleaaggepehaifgvlryr 728
                                    89****************************************************************************** PP

                                    .......TTEEEEE.........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHH CS
                         Toprim  38 .......efkpvye.........................eiedkkkvlkalkelakradeiilatDpDreGeaiawelle 85 
                                            + pvy+                          i++  ++++ l++ a +ade+++ tDpD+eGe+i+w+++ 
  gi|118431415|ref|NP_147880.2| 729 lggngaaAYTPVYTsikrcldcgyqfvdeasrcprcgseLIRNSLSTVEDLRRVAWEADEVYVGTDPDTEGEKIGWDVAL 808
                                    *******888888888888888888999999**99*99889999999999****************************** PP

                                    HHTHHHTTTEEEEEESSS CS
                         Toprim  86 vlkellenkigrvefsei 103
                                    +l++++++ i+r+ef+e+
  gi|118431415|ref|NP_147880.2| 809 ALRPYAPD-IKRLEFHEV 825
                                    ********.*******96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   2.8e-13   2.7e-10       4     139 ..      95     231 ..      93     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.8e-13
                                    HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST......SE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx RF
                           DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid......lr 77 
                                    Q+   + + +g+++ + a+TG GKT+  + + l  +y    k+g +  iv Pt+ La +++++l+++ + ++      l 
  gi|118431415|ref|NP_147880.2|  95 QRTWAKRLARGDSFSIIAPTGVGKTTFGAAASL--FYA--CKKGMRSYIVLPTTTLAANVARKLESMVESTGcgrvrlLV 170
                                    666667778899999***********9887777..775..99***************************97777844333 PP

                                    EEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTH CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  78 vlliiggvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfs 139
                                    +++ ++ +++r+ ++++++g  di+v+t     +  +  +l+  ++r++ +D +d +l + +s
  gi|118431415|ref|NP_147880.2| 171 IHSKLKTSERREAMERFEKGdFDILVTTAAFARKYAD--RLSGYRFRLVFVDDVDAVLRSARS 231
                                    334466888899999998889********99998664..666778888999****99988443 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   6.2   1.8e-13   1.8e-10       5      34 ..      11      40 ..       8      44 .. 0.94
   2 ?   -1.4   0.1       1.6   1.6e+03       9      17 ..     760     768 ..     758     774 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.8e-13
                          zf_Rg  5 vfeklCPNCgGdisdeRlekGLpCkrClPk 34
                                   v++ lCPNCgG+ s+eRl +GLpC rClP 
  gi|118431415|ref|NP_147880.2| 11 VYRYLCPNCGGPNSEERLSRGLPCPRCLPR 40
                                   8999*************************5 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                          zf_Rg   9 lCPNCgGdi 17 
                                     CP Cg ++
  gi|118431415|ref|NP_147880.2| 760 RCPRCGSEL 768
                                    6****9887 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 !   27.7   0.1   2.6e-09   2.6e-06      14      78 ..     132     203 ..     123     284 .. 0.82
   2 ?    5.5   0.0     0.022        21      38      85 ..     389     437 ..     355     454 .. 0.72
   3 ?    2.3   0.0      0.21   2.1e+02      94     110 ..     558     574 ..     554     575 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.6e-09
                                    TTTSEEEEEESSHHHHHH....HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                     Helicase_C  14 eeggkilifvntidrlek....vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                    ++g +++i+++t++ + +    ++ + e+     ++ +v+h++l+++er+e++e+f kg++d+L++t + +r
  gi|118431415|ref|NP_147880.2| 132 KKGMRSYIVLPTTTLAANvarkLESMVESTgcgRVRLLVIHSKLKTSERREAMERFEKGDFDILVTTAAFAR 203
                                    6777888888888833333223333333336878*********************************99776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.022
                                    HTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTST.TE CS
                     Helicase_C  38 kkgikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidip.kv 85 
                                    + g+k+ ++h+    ++ +e l++f +ge+dvL+        + rG+d+p +v
  gi|118431415|ref|NP_147880.2| 389 RAGVKAEAYHA----KKPLELLDRFAEGEIDVLVGVANyygtLVRGLDLPaRV 437
                                    33566655555....8999**************98875555577888888445 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.21
                                    SSSHHHHHHHHTTSSST CS
                     Helicase_C  94 prnvtsyiqriGRtgRa 110
                                      ++++y q++GRt R 
  gi|118431415|ref|NP_147880.2| 558 VPDPATYLQASGRTSRL 574
                                    56899*********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 !    9.4   0.5    0.0011       1.1       3      32 ..      11      37 ..      11      44 .. 0.80
   2 !   10.9   0.5   0.00038      0.37       7      37 ..     746     769 ..     741     771 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                    Zn-ribbon_8  3 iYeYrCeeCghefevlqsisdapltaCPeC 32
                                   +Y Y C +Cg    + + +      +CP+C
  gi|118431415|ref|NP_147880.2| 11 VYRYLCPNCGGPNSEERLSR---GLPCPRC 37
                                   6*********9999888655...556**** PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00038
                    Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgsevr 37 
                                    rC +Cg +f             CP+Cgse+ 
  gi|118431415|ref|NP_147880.2| 746 RCLDCGYQFVDE-------ASRCPRCGSELI 769
                                    7*****999822.......346******875 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     2e-05      0.02      37     148 ..     109     229 ..     102     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                  Terminase_GpA  37 vfvkpaqvGkTelllnwigyvidndpapmlvvqptkdlarefskerldpliesspe.......lrerlas..srrsdntl 107
                                    +++ p+ vGkT+++ ++     +++     +v+pt +la +++ ++l+ ++es+         + ++l++   r+  +++
  gi|118431415|ref|NP_147880.2| 109 SIIAPTGVGKTTFGAAASLFYACKKGMRSYIVLPTTTLAANVA-RKLESMVESTGCgrvrllvIHSKLKTseRREAMERF 187
                                    5678999*****999888887778888888999***9998877.9********986222222244555556444555666 PP

                  Terminase_GpA 108 lskrfrggmllliga...nsasnlrsksaryvvldevDaypenv 148
                                    ++ +f+  +l++++a   + a +l+  ++r+v++d+vDa+ +++
  gi|118431415|ref|NP_147880.2| 188 EKGDFD--ILVTTAAfarKYADRLSGYRFRLVFVDDVDAVLRSA 229
                                    666788..666665522255789***************986655 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 ?    8.7   0.4    0.0016       1.6      31      53 ..      16      38 ..      14      47 .. 0.89
   2 ?    7.7   0.4    0.0033       3.3      23      56 ..     738     768 ..     730     775 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                 OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCg 53
                                   C++Cg  n+e++ +r + Cp+C 
  gi|118431415|ref|NP_147880.2| 16 CPNCGGPNSEERLSRGLPCPRCL 38
                                   **********************7 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                 OrfB_Zn_ribbon  23 npayTS.ktCseCgsknkealsgrtfkCpnCgfea 56 
                                     p yTS k+C  Cg++  +    +  +Cp+Cg e+
  gi|118431415|ref|NP_147880.2| 738 TPVYTSiKRCLDCGYQFVD----EASRCPRCGSEL 768
                                    689999678******9999....8999*****886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.041        41      29      48 ..      14      37 ..       3      43 .. 0.65
   2 ?   11.5   0.4   0.00024      0.23      29      49 .]     745     765 ..     733     772 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
                            DZR 29 drCpsCgekvdpearf....CpeC 48
                                   + Cp+Cg ++++e       Cp C
  gi|118431415|ref|NP_147880.2| 14 YLCPNCGGPNSEERLSrglpCPRC 37
                                   567777776665543345555555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00024
                            DZR  29 drCpsCgekvdpearfCpeCG 49 
                                    +rC  Cg++   ea+ Cp CG
  gi|118431415|ref|NP_147880.2| 745 KRCLDCGYQFVDEASRCPRCG 765
                                    566666666666666666665 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 ?   14.0   0.0   3.9e-05     0.039      16     139 ..      99     220 ..      73     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                                    T......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG...........GEEE CS
                         ResIII  16 leklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.......igkk 88 
                                    ++ l   r   + i ++TG+GKT   a++   ++ k++  +  ++ p+++l     ++++++ +++          ++k 
  gi|118431415|ref|NP_147880.2|  99 AKRL--ARGDSFSIIAPTGVGKTTFGAAASLFYACKKG-MRSYIVLPTTTLAANVARKLESMVESTGCGrvrllviHSKL 175
                                    4444..466778899********999777666666645.49999************999999998865578888865555 PP

                                    ESSS-B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEE CS
                         ResIII  89 vsgdkkka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiD 139
                                    +++++++a ++ ++ + +ilvtt   + +         ++l+  rf ++++D
  gi|118431415|ref|NP_147880.2| 176 KTSERREAmERFEKGDFDILVTTAAFARKYA-------DRLSGYRFRLVFVD 220
                                    5555555556667777777777765443333.......55666666666666 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   4.4e-05     0.044     499     537 ..     736     782 ..     730     783 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                    -EEEEE--EEEETT.--..EESSSB-TTT--B...E....EEEEEES CS
                           NRDD 499 gYfsinpkidvCnecgy..kgeiekCpkCgse...ee...vevirRi 537
                                     Y  + + i++C +cgy    e  +Cp+Cgse   ++   ve +rR+
  gi|118431415|ref|NP_147880.2| 736 AYTPVYTSIKRCLDCGYqfVDEASRCPRCGSElirNSlstVEDLRRV 782
                                    577778899********66666699*****87555224457777776 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 ?    1.1   0.2       0.4     4e+02      70      92 ..      13      37 ..       6      41 .. 0.72
   2 ?   11.5   0.3   0.00022      0.22      72      96 ..     746     768 ..     737     778 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.4
                                   EEEETTTS-EEECHH.H.HHS-TTT CS
                           HypA 70 kvrCreCgkefelee.k.alrCpkC 92
                                   ++ C +Cg   ++e+ +  l Cp+C
  gi|118431415|ref|NP_147880.2| 13 RYLCPNCGGPNSEERlSrGLPCPRC 37
                                   5678889877766654346788888 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00022
                                    EETTTS-EEECHHHHHS-TTTSSS- CS
                           HypA  72 rCreCgkefeleekalrCpkCgsad 96 
                                    rC +Cg++f  e  a rCp+Cgs+ 
  gi|118431415|ref|NP_147880.2| 746 RCLDCGYQFVDE--ASRCPRCGSEL 768
                                    8********977..459*****975 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.17       3     105 ..     111     222 ..     109     233 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                    EE-SSS-HHHHHHHHHHHHHHSSSS.-EEEEEESSHHHHHHHHH......HHHHHHHTS-TTTS--EEEE..-SSEEEE. CS
                    Terminase_6   3 lggrqsGKTfagarellrhalgrgprnqvflsasktqareeggq......fekgigelakeildiefees..aknlvvl. 73 
                                     ++ ++GKT+ ga+  l++a+++g  ++ ++ +++t a +   +      ++ g g+++   ++ +++ s  ++ +  + 
  gi|118431415|ref|NP_147880.2| 111 IAPTGVGKTTFGAAASLFYACKKGM-RSYIVLPTTTLAANV-ARklesmvESTGCGRVRLLVIHSKLKTSerREAMERFe 188
                                    6899********************7.999999***999995.33477777555555555554444444220022333334 PP

                                    .TTS-EEEEES.....SHHHHHTS--SEEEEESG CS
                    Terminase_6  74 .snGaslhflslese.taggiqGaqidliyfDEl 105
                                      ++  l  +++ ++  a++  G +++l+++D+ 
  gi|118431415|ref|NP_147880.2| 189 kGDFDILVTTAAFARkYADRLSGYRFRLVFVDDV 222
                                    4222222222222223667777777777777775 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.026        26      39      49 ..      11      21 ..       5      26 .. 0.83
   2 ?    4.8   0.2     0.029        29      32      53 ..     747     770 ..     735     772 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.026
                        DUF1272 39 vlenvCPncgG 49
                                   v++  CPncgG
  gi|118431415|ref|NP_147880.2| 11 VYRYLCPNCGG 21
                                   56789*****9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.029
                        DUF1272  32 CaeCaeevl..envCPncgGelvk 53 
                                    C +C  + +  +++CP cg el++
  gi|118431415|ref|NP_147880.2| 747 CLDCGYQFVdeASRCPRCGSELIR 770
                                    88888888844578*******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 ?   -1.3   5.8         2     2e+03       2       9 ..      16      23 ..      15      37 .. 0.66
   2 ?   14.4   0.9   2.3e-05     0.023       1      23 []     746     768 ..     746     768 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                  zinc_ribbon_2  2 CpnCGael 9 
                                   CpnCG ++
  gi|118431415|ref|NP_147880.2| 16 CPNCGGPN 23
                                   66666555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.3e-05
                  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                    +C  CG++  d+a  Cp+CG++l
  gi|118431415|ref|NP_147880.2| 746 RCLDCGYQFVDEASRCPRCGSEL 768
                                    699*****************997 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 ?    9.9   0.0   0.00073      0.73       1      12 [.     760     771 ..     760     790 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00073
                 DNA_ligase_ZBD   1 hCPvCGsavvRe 12 
                                    +CP CGs+++R+
  gi|118431415|ref|NP_147880.2| 760 RCPRCGSELIRN 771
                                    5*********97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.1      28      61 ..     100     133 ..      81     234 .. 0.64
   2 ?   -1.2   0.4       1.3   1.3e+03      86     146 ..     246     306 ..     237     307 .. 0.63
   3 ?   -0.5   0.4      0.78   7.8e+02      72     138 ..     583     643 ..     575     654 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                         AAA_25  28 gllpagelallaGapgtGKttlaldlalavatGk 61 
                                      l++g+   +++++g+GKtt+    +l +a  k
  gi|118431415|ref|NP_147880.2| 100 KRLARGDSFSIIAPTGVGKTTFGAAASLFYACKK 133
                                    45678999999****************9999444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                         AAA_25  86 lrrRlravgealrddarllvldlagv.eslpLfakdrggtl.ltadvdaleaaieeveg..vrlv 146
                                    +++ l+ ++ + r++arl  l  +++ e++  +++ r+  l +++ +++lea+ie++ g  + l+
  gi|118431415|ref|NP_147880.2| 246 IEKGLEVLRLQ-REQARLVGLL-QSQrEEV--REEARKKLLeVKRRLERLEAEIEARRGrtASLI 306
                                    55555655555.4566666664.4433444..466666666899999999999999876655555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.78
                         AAA_25  72 gkVlyvsaEdsedelrrRlravg.ealrddarllvldlagveslpLfakdrggtlltadvdaleaaie 138
                                      V++v++E    +l +R++++   ++r+ ++l++ ++       L++ d + +++ ++v+ l + +e
  gi|118431415|ref|NP_147880.2| 583 LSVVVVDNEPVMRGLMKRVSWMAeVDWRRFEDLDLQSI-------LREIDEDREKVRRVVKGLYRGVE 643
                                    67999999999999999*99544233333333333333.......33333333334444444444444 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.088        87      25      35 ..      13      23 ..      13      25 .. 0.82
   2 ?   13.0   1.0   7.4e-05     0.073      12      33 ..     745     766 ..     743     768 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.088
                        DUF35_N 25 ravCphCgsdd 35
                                   r  Cp+Cg+ +
  gi|118431415|ref|NP_147880.2| 13 RYLCPNCGGPN 23
                                   678*****976 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.4e-05
                        DUF35_N  12 qrCpdCGtvqfPPravCphCgs 33 
                                     rC dCG  ++     Cp+Cgs
  gi|118431415|ref|NP_147880.2| 745 KRCLDCGYQFVDEASRCPRCGS 766
                                    6********99999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); 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):              18  [number of targets reported over threshold]
# CPU time: 0.98u 0.33s 00:00:01.31 Elapsed: 00:00:00.53
# Mc/sec: 7745.69
//
Query:       gi|14601345|ref|NP_147881.1|  [L=306]
Description: hypothetical protein APE_1343 [Aeropyrum pernix K1]
Scores for 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-13   48.1   0.0    1.2e-12   47.8   0.0    1.1  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   6.5e-17   1.2e-12      10     182 ..      11     190 ..       2     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 6.5e-17
                                   STTHHHHHHHHHHHHHHHHHHT.TESEEEEETTTTTBS........SSHHHHHHHHB......HSSSHHHHHHHHHHHHHT CS
                  CN_hydrolase  10 kaadleanlqklleliaeAark.gadLivlPElfitgy........keeahfleaAe......aglgetlallaalarkng 75 
                                   k a +  n  ++  li+++++   +dLivlP +  tg         k + + +e+Ae         g+++ ++++ ++++g
  gi|14601345|ref|NP_147881.1|  11 KLAAKRSNARRHSILIDKVVSTrTVDLIVLPAYPFTGPligyyppsKARLKLRELAEkiseknIPAGPSVSFMSRWSQEYG 91 
                                   66777889999999999999999********99988878999****99999******999999889*************** PP

                                   EEEEEE.EEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS.-SSS-EEEETTE....EEEE CS
                  CN_hydrolase  76 iavvig.liereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfep.gdgipvfdtpvg....kiGa 150
                                   +++ +g +ier  +++++  y t vl ++dg+++gkyrK+ L        t  er +  + g++  +f+++v      +G+
  gi|14601345|ref|NP_147881.1|  92 VYILGGpIIER--AGPRI--YVTTVLTSPDGSIAGKYRKVSL--------TEEERDMGISpGKEPGIFKLKVNgsdvSLGV 160
                                   ******9****..9****..*********************7........67777777774444666766666667799** PP

                                   EEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCC CS
                  CN_hydrolase 151 aiCyeigfpellralalkgaeilvnlserapv 182
                                      ++   pe+ r l+l g +i+v ++  +p+
  gi|14601345|ref|NP_147881.1| 161 FSDEDLATPEIFRHLQLGGSKIIVGTI--FPY 190
                                   ***********************9944..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2127.83
//
Query:       gi|118431416|ref|NP_147882.2|  [L=91]
Description: hypothetical protein APE_1343a.1 [Aeropyrum pernix K1]
Scores for 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-06   26.3   5.0    7.5e-06   26.2   5.0    1.0  1  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.14   11.6   0.0    1.1  1  DUF4892   Domain of unknown function (DUF4892)


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 !   26.2   5.0   8.4e-10   7.5e-06       3      82 ..       9      91 .]       7      91 .] 0.82

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 8.4e-10
                           EamA  3 gillallaalfwaiyfvlskil..lrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafll 81
                                   g+l+  laa++w++++v+ ++l     ++ +tlt vrf +a+ l  + a++ ++ +  +   + +++  +lgllg++ ++++
  gi|118431416|ref|NP_147882.2|  9 GLLFPALAAVSWGTNAVAGRYLvgGGHIDGVTLTLVRFALATPLIGLSAFYIARERlLNTEGRLLFWSSVLGLLGITGFNIF 90
                                   788889****************556667889***********9998877777777733555555888899999999998877 PP

                           EamA 82 f 82
                                   f
  gi|118431416|ref|NP_147882.2| 91 F 91
                                   5 PP

>> DUF4892  Domain of unknown function (DUF4892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.6e-05      0.14      56      91 ..      41      76 ..      23      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                        DUF4892 56 ltavtyrlpaehsaaeaftqarealleqgaellywc 91
                                   lt v + l +   +  af  are ll+ + +ll+w 
  gi|118431416|ref|NP_147882.2| 41 LTLVRFALATPLIGLSAFYIARERLLNTEGRLLFWS 76
                                   677888888899999********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 721.61
//
Query:       gi|14601347|ref|NP_147883.1|  [L=197]
Description: hypothetical protein APE_1345 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-24   86.4  32.4    2.4e-23   82.8  20.2    2.0  2  EamA          EamA-like transporter family
  ------ inclusion threshold ------
      0.036   13.0   6.3       0.91    8.4   0.2    2.4  2  CRT-like      CRT-like, chloroquine-resistance transporter-li


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 !    9.9   4.2   8.5e-05      0.77      90     136 ..       2      48 ..       1      49 [. 0.95
   2 !   82.8  20.2   2.7e-27   2.4e-23       2     136 ..      59     194 ..      58     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.5e-05
                          EamA  90 sasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   +as+ +l+t+l+  +t i +v+l  ek tl+  +g++++++G++l+l
  gi|14601347|ref|NP_147883.1|   2 DASITALVTALATPLTYIAAVVLGLEKATLLATAGAFISVAGTYLVL 48 
                                   69999****************************************97 PP

  == domain 2  score: 82.8 bits;  conditional E-value: 2.7e-27
                          EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafll 81 
                                   +g lla+ aal+w iy+++ ++ l+ ++   + f+++l+++++ ++ +   + +   +  l + +l+l++++++++l++ l
  gi|14601347|ref|NP_147883.1|  59 IGFLLAFGAALSWVIYTLILRVKLAGYDQNVVMFWTSLFGTVFTVPAYIALAPRGgLEVGLLEAALILYVAAVPGALGYTL 139
                                   799*****************************************99866665555548888889999************** PP

                          EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                   ++ ++++++as+ ++++ l+P+ ++il++lllge+l++kq +g+ li++G++ ++
  gi|14601347|ref|NP_147883.1| 140 WNLGVERVGASKSAVFIPLVPLTAAILGWLLLGETLSIKQAIGATLIIAGIVAVV 194
                                   ***************************************************9887 PP

>> CRT-like  CRT-like, chloroquine-resistance transporter-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.5   0.00025       2.3      96     142 ..       5      51 ..       2     117 .. 0.88
   2 ?    8.4   0.2    0.0001      0.91     110     139 ..     165     194 ..     142     197 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00025
                      CRT-like  96 lqvllnqaiipitllasllllkerysliqylGAlviilgvvvvlips 142
                                   +  l++ +++p+t +a+++l  e+  l+   GA++ ++g  +vl+p+
  gi|14601347|ref|NP_147883.1|   5 ITALVTALATPLTYIAAVVLGLEKATLLATAGAFISVAGTYLVLSPQ 51 
                                   7789999********************************99998875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0001
                      CRT-like 110 lasllllkerysliqylGAlviilgvvvvl 139
                                   ++  lll e  s+ q +GA++ii+g+v v+
  gi|14601347|ref|NP_147883.1| 165 ILGWLLLGETLSIKQAIGATLIIAGIVAVV 194
                                   5667899*******************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1616.40
//
Query:       gi|118431417|ref|NP_147884.2|  [L=656]
Description: acetyl-coenzyme A synthetase [Aeropyrum pernix K1]
Scores for 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-77  258.6   0.0    1.1e-76  258.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    8.3e-22   78.0   0.6    1.7e-21   76.9   0.6    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    6.9e-12   45.1   0.7    6.9e-12   45.1   0.7    1.7  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
       0.05   14.0   0.4          4    7.8   0.0    3.4  4  Lambda_tail_I  Bacteriophage lambda tail assembly protein I


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 !  258.2   0.0   2.4e-80   1.1e-76       9     422 ..      97     530 ..      90     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 258.2 bits;  conditional E-value: 2.4e-80
                                    TTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HH CS
                    AMP-binding   9 pdkvalvd...sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvplnptltae 84 
                                      + a+++   +ge +++TY +l+++v+r+A+ L    G++ gd+Vai++p++pe ++a+la++k+Gav++p+ +++ ++
  gi|118431417|ref|NP_147884.2|  97 GHREAFTWvgeDGEVRRYTYLQLKDEVDRMAKLLSqDYGLGVGDVVAIYAPMMPESIAAMLAAMKVGAVASPIFSGFAPP 176
                                    56778877889999*********************99******************************************* PP

                                    HHHHHHHHHTESEEE..........E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT.S... CS
                    AMP-binding  85 elayiledseakvli..........a.tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseeka.e... 148
                                    ++a  l+  ea+vl+          + +   ++ ++++ + a+   av++viv+ + +++  + + +++e+++ a     
  gi|118431417|ref|NP_147884.2| 177 AVAERLKLGEARVLVtvdgylrrgrRiA--LKEqADQAVKLAG--GAVEHVIVVRRLGIDVPWVE-GRDEWYDRAiAgka 251
                                    *****************99998664232..2222444444444..789999****9999998555.55556655541567 PP

                                    -TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHH..HHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHH CS
                    AMP-binding 149 kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslk..letr.fklkeddvvlsilplahifglilellla 224
                                       e+eel+p+++a++++TSGTTG+PKG+++sh +++++  ++++  l+ +  + + +d++++i ++ +++g  + +l++
  gi|118431417|ref|NP_147884.2| 252 GSAEPEELDPEHPALLLFTSGTTGRPKGAVISHaGAILQPGKEHYfnLDIHpAWRGGEDRLWWITDIGWMMGP-WQVLGS 330
                                    4457789**************************777777777766554444433456***************7.****** PP

                                    HHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHH..HHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHH CS
                    AMP-binding 225 llsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleal..lesgalkaakkakdlsslrlvllggeplspellr 301
                                     l Ga+  ++++  + + + ++++li++++vt++  + +v+++l  ++s++    ++++dlss+r +   gep+  +++ 
  gi|118431417|ref|NP_147884.2| 331 QLLGASHLMAEGAIDyPYKSRVWRLIQEHRVTHFGFAATVARMLraVASDT----VEDYDLSSIRAFGNTGEPIDHATWM 406
                                    ***************55599999*********************4444433....3467*******999*********** PP

                                    HHHHHHTC...EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-S CS
                    AMP-binding 302 ffralfge...evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmk 376
                                    ++ +++g+   +++++ G TE  g++   p +    k+ +   p  gv++ + D+e g+pv +ge+G l+v++p  ++++
  gi|118431417|ref|NP_147884.2| 407 WVMEKLGGwrrPLINLSGGTEVFGCILL-PSPVVPLKPTTLWGPALGVDADVFDDE-GRPV-RGEPGYLVVKKPfpSMTR 483
                                    **********99**************84.44444345555656668*********9.****.8**********9889*** PP

                                    EBTT-HHHHHHHEEET.CC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 377 gYlkkpeataeafdse.gr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                    g +k+pe+  ++++s  ++ w++ GD + +dedG  +i+gR++d+ik+
  gi|118431417|ref|NP_147884.2| 484 GLWKDPERYIKTYWSRfPGvWYH-GDYALVDEDGFWYILGRADDVIKV 530
                                    **************845576999.***********************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.6   3.9e-25   1.7e-21       1      76 []     539     616 ..     539     616 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 3.9e-25
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH....HT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk....elgpyavpkkvvfvdelpktrsGK 76 
                                    e+Es+l++ p+Vaeaa++Gvp+++kGe++++f v+k g++  +eeL +++rk    ++g+  +p++vv+v+elpktrsGK
  gi|118431417|ref|NP_147884.2| 539 ELESVLTQLPEVAEAACIGVPHPIKGEVIACFLVPKGGYD--AEELASKARKavvdRFGKPFAPEHVVIVSELPKTRSGK 616
                                    89*********************************97763..36666666666666***********************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 !   45.1   0.7   1.5e-15   6.9e-12       1      55 []      30      87 ..      30      87 .. 0.95
   2 ?   -4.0   0.0       3.3   1.5e+04       9      16 ..     511     518 ..     509     519 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.5e-15
                                   HHHHHHHHHH-HHHHHHHHHCC..S--SB--S-SECSTTTC.T-EESTT-EE-HHHHH CS
                         ACAS_N  1 ykelykeSiedpeaFWaeqake..ldWekpfdkvldgskgp.fikWFeGGklNicyNc 55
                                   y+el ++S ed ++FW++  +   ++W+++++ v+d s g  +++W+ GG lN++yN+
  gi|118431417|ref|NP_147884.2| 30 YEELVRRSSEDLKWFWGNLPEWlgVEWFREPKAVVDLSRGVeWAQWYRGGLLNAAYNV 87
                                   99******************9556****************99***************6 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.3
                                    HH-HHHHH CS
                         ACAS_N   9 iedpeaFW 16 
                                    + d ++FW
  gi|118431417|ref|NP_147884.2| 511 LVDEDGFW 518
                                    56899*** 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 ?    7.8   0.0    0.0009         4      24      68 ..      28      76 ..      20      94 .. 0.87
   2 ?   -1.7   0.0      0.84   3.8e+03      49      73 ..      96     121 ..      77     122 .. 0.82
   3 ?    2.0   0.0      0.06   2.7e+02      20      63 ..     214     256 ..     191     264 .. 0.78
   4 ?   -3.2   0.0       2.5   1.1e+04      73      86 .]     563     576 ..     561     576 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0009
                  Lambda_tail_I 24 ktleeairalssqldafkellq....rskfavrvagvdVgesvpvdrya 68
                                   k++ee++r+ s++l  f   l       +f  + a vd +  v+ +++ 
  gi|118431417|ref|NP_147884.2| 28 KSYEELVRRSSEDLKWFWGNLPewlgVEWFREPKAVVDLSRGVEWAQWY 76
                                   89*************9987777777799****************99996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.84
                  Lambda_tail_I  49 favrvagvdVgesvpvdrya.etlkd 73 
                                    ++ r+a+  Vge ++v ry   +lkd
  gi|118431417|ref|NP_147884.2|  96 YGHREAFTWVGEDGEVRRYTyLQLKD 121
                                    678899999******99998666665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.06
                  Lambda_tail_I  20 veavktleea..iralssqldafkellqrskfavrvagvdVgesvp 63 
                                    ++a++  e +  +r+l+++++  +    + +++  +ag   g  +p
  gi|118431417|ref|NP_147884.2| 214 KLAGGAVEHVivVRRLGIDVPWVEGR--DEWYDRAIAGKA-GSAEP 256
                                    55666666541168999999999777..999999999988.77776 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 2.5
                  Lambda_tail_I  73 dgkvvtivpvpaGg 86 
                                     g+v+   +vp Gg
  gi|118431417|ref|NP_147884.2| 563 KGEVIACFLVPKGG 576
                                    599*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4979.58
//
Query:       gi|118431418|ref|YP_874889.1|  [L=90]
Description: hypothetical protein APE_1346a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.5   0.0       0.18   12.3   0.0    1.3  1  CoA_binding_2  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 ?   12.3   0.0     1e-05      0.18      14      64 ..       4      54 ..       1      81 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                   SHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S- CS
                  CoA_binding_2 14 kfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftp 64
                                   +f + +l+    hg+ v+p  p ++e l +   ++ a+ +  vd++ v ++
  gi|118431418|ref|YP_874889.1|  4 RFLRDILSRRDPHGYYVIPLKPEARETLSRMRLPRDAKIVDGVDVILVKLR 54
                                   555667777777*****************9999999965677887776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 728.85
//
Query:       gi|118431419|ref|NP_147886.2|  [L=146]
Description: molybdenum cofactor biosynthesis protein MoaC [Aeropyrum pernix K1]
Scores for 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-47  158.5   2.6      1e-46  158.4   2.6    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.4   2.6   5.8e-51     1e-46       1     136 []       6     146 .]       6     146 .] 0.98

  Alignments for each domain:
  == domain 1  score: 158.4 bits;  conditional E-value: 5.8e-51
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    mvd+++ke ++r+AvA+g+++l++et+++i+e++++kGdv++va +a+++a+K+t++lipl+Hp+p++kve e++++  +
  gi|118431419|ref|NP_147886.2|   6 MVDITAKEPVRREAVASGFISLKRETVKAIREGRVEKGDVISVASVAAVLAVKETPRLIPLTHPIPIEKVEPEVRVR--D 83 
                                    9*************************************************************************887..7 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEESS CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsgG 136
                                    + ve++++v t++ktGvemEAL +v++a+ltv+DmvK+++k+       +vi+ v++  K++G
  gi|118431419|ref|NP_147886.2|  84 DGVEVRVRVATTAKTGVEMEALAGVTAALLTVWDMVKSLEKDetgnypdTVITGVKVEVKRKG 146
                                    9****************************************99*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1240.41
//
Query:       gi|118431420|ref|NP_147888.2|  [L=1321]
Description: ATP-dependent helicase [Aeropyrum pernix K1]
Scores for 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   44.9   0.0    2.4e-11   43.7   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
    2.5e-11   43.9   0.0    1.3e-09   38.3   0.0    2.4  2  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
       0.04   13.9   0.0       0.08   12.9   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit


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 !   43.7   0.0   4.1e-15   2.4e-11      15     171 ..     614     769 ..     595     774 .. 0.78

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 4.1e-15
                                    CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT...TSTSEEEEEETTSSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk...yidlrvlliiggvaardql 91 
                                       ++ ++TG+GK+l f+ p+    y      g  +l+v+P+++L++++ + +  ++    yid +    ++ +a+ + l
  gi|118431420|ref|NP_147888.2| 614 SVTIAVMPTGYGKSLLFQAPARGLAY---LGYGALTLVVTPLKALMRDQTRAALGRGLaacYIDSS----LSLKARGEVL 686
                                    557899****************9887...58899**************999986665522334433....3334444444 PP

                                    HHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCTTST.TTSEEEEEES CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                           DEAD  92 skldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqitcdgk.lqrqvivlSA 167
                                    ++   g +d+++  p+r+ d   ++ ++  ++ + VlDEa++ + +   f++ +  ++++l++   ++      +++l+A
  gi|118431420|ref|NP_147888.2| 687 RAAAMGlIDLLYIAPERFEDARIREVVEGGRLALAVLDEAHTASRWgeTFRNSYLYMAKTLASLRLEEGwPP--ILALTA 764
                                    4444557*************777788889*****************989************77766655444..999**9 PP

                                    SBS.H CS
                                    xxx.x RF
                           DEAD 168 Tlp.k 171
                                    T++ +
  gi|118431420|ref|NP_147888.2| 765 TATlD 769
                                    99844 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 ?    2.9   0.0     0.022   1.3e+02      38      70 ..     665     697 ..     637     701 .. 0.73
   2 !   38.3   0.0   2.2e-13   1.3e-09      41     110 ..     884     954 ..     857     955 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.022
                                    HTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEE CS
                     Helicase_C  38 kkgikvavlhgelpqnereeileqfnkgesdvL 70 
                                     +g+ +++++++l+ + r e+l++   g +d+L
  gi|118431420|ref|NP_147888.2| 665 GRGLAACYIDSSLSLKARGEVLRAAAMGLIDLL 697
                                    34899*******************999999876 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 2.2e-13
                                    STEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  41 ikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                     +v+v+hg++  + r+ + e+  + + + +++at++ ++G+di +++   ++ + ++v++++q iGR+gR 
  gi|118431420|ref|NP_147888.2| 884 CEVLVYHGQMGEKRRKMVEERAAEPRGRkIIVATKAFGMGVDIRNLRWTLHLFPSDSVEDLVQEIGRAGRD 954
                                    57899*****************9655444*****************************************6 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 ?   12.9   0.0   1.3e-05      0.08       3     151 ..     592     737 ..     591     768 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHH.HHHHHHGGGGTGG. CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprksll.eqtleefkkflsea 81 
                                    +lr+ Qe +++++   + s      + +m+TG GK+l+  + ++ l+  g+   +l++ p k+l+ +qt+ ++ + l  +
  gi|118431420|ref|NP_147888.2| 592 RLRPGQEAVLRRISRVYASLSPSVTIAVMPTGYGKSLLFQAPARGLAYLGYGALTLVVTPLKALMrDQTRAALGRGLAAC 671
                                    5899*********9888878899999**************99*9999999999*********986368888887777777 PP

                                    ...GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS..TTTH CS
                         ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak.kswr 151
                                    y + + +++ +++  ++ +   +++l +  +++  ++      +e  + +r  + + DEaH +++  +++r
  gi|118431420|ref|NP_147888.2| 672 YIDSSLSLKARGEVLRAAAMGLIDLLYIAPERFEDAR-----IREVVEGGRLALAVLDEAHTASRWgETFR 737
                                    7665555555555554566667777777777777777.....88889999999999999998887543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.77u 0.24s 00:00:01.01 Elapsed: 00:00:00.42
# Mc/sec: 9399.42
//
Query:       gi|14601355|ref|NP_147891.1|  [L=173]
Description: hypothetical protein APE_1357 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1323.57
//
Query:       gi|118431421|ref|NP_147892.2|  [L=235]
Description: hypothetical protein APE_1358.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1809.31
//
Query:       gi|118431422|ref|NP_147893.2|  [L=173]
Description: PadR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete 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-21   74.5   0.1    6.8e-21   74.0   0.1    1.3  1  PadR          Transcriptional regulator PadR-like family
     0.0001   22.1   0.0    0.00016   21.5   0.0    1.2  1  AphA_like     Putative AphA-like transcriptional regulator
    0.00074   20.1   0.0     0.0011   19.6   0.0    1.2  1  RTP           Replication terminator protein
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.15   12.1   0.0    1.2  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 !   74.0   0.1   1.5e-24   6.8e-21       1      74 [.      24      99 ..      24     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.5e-24
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S..TSSS-EEEEEESHCCCHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees..gegpprkyYrlTdaGrrela 74
                                   +L +l+e+p +Gyei++++ee ++g++++ +G+lYp+L++L++egl+  e+ +   ++g++r +Y+lT++G r+la
  gi|118431422|ref|NP_147893.2| 24 VLRVLAERPYHGYEIMNRIEEITNGVWRPAPGTLYPLLDQLKREGLIRVERMDRkgVKGGRRIVYALTEDGWRRLA 99
                                   89*********************************************9888777678999***********99987 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 !   21.5   0.0   3.5e-08   0.00016       8      95 ..      16     107 ..      11     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.5e-08
                      AphA_like   8 pkeavrLvvLGlieraplryselagavrhlvsriagPsldLlgsslellreeGLv..eavdGeGme..dnalLaiteaGr 83 
                                     +e +r  vL +++  p    e+ + +  + + ++ P    l+  l++l+ eGL+  e +d +G+   + +  a+te+G 
  gi|118431422|ref|NP_147893.2|  16 IRESLRQLVLRVLAERPYHGYEIMNRIEEITNGVWRPAPGTLYPLLDQLKREGLIrvERMDRKGVKggRRIVYALTEDGW 95 
                                    58999*************************************************63378*****9733567789****** PP

                      AphA_like  84 relqaLltanlr 95 
                                    r+l +++ ++ r
  gi|118431422|ref|NP_147893.2|  96 RRLADIMFEKAR 107
                                    ******987765 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.4e-07    0.0011      13      89 ..      23      98 ..      16     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHHH CS
                            RTP 13 ylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkeka 89
                                    +++++++++ +g+++++++  e  +  ++P++ ++y  l++l  +g+++ ++  ++++k    ++Y lt++G  ++
  gi|118431422|ref|NP_147893.2| 23 LVLRVLAERPYHGYEIMNRIE-EITNGVWRPAPGTLYPLLDQLKREGLIRVERMDRKGVKGGRRIVYALTEDGWRRL 98
                                   578999999*9*******995.678888*********************99999999***99999******997654 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.4e-05      0.15      26      70 ..      56      99 ..      25     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                   Replic_Relax 26 tarrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarlla 70
                                   t++  L +L+++gl++       +g++g  +++vYaLt+ G r la
  gi|118431422|ref|NP_147893.2| 56 TLYPLLDQLKREGLIRVeR-MDRKGVKG-GRRIVYALTEDGWRRLA 99
                                   678889********99843.33356666.56**********99884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1341.32
//
Query:       gi|118431423|ref|NP_147894.2|  [L=260]
Description: oxidoreductase [Aeropyrum pernix K1]
Scores for 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-24   84.6   0.0    1.1e-23   84.0   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    6.2e-20   71.5   0.0    7.6e-20   71.2   0.0    1.1  1  adh_short     short chain dehydrogenase
    3.4e-07   30.4   0.1    5.1e-07   29.8   0.1    1.2  1  KR            KR domain
  ------ inclusion threshold ------
       0.14   11.7   0.3       0.74    9.4   0.0    2.2  3  Sigma70_r4    Sigma-70, region 4


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 !   84.0   0.0   2.6e-27   1.1e-23       3     231 ..      13     252 ..       9     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 2.6e-27
                                    TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                   adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                     +g+G+++A+ala+ G+++v++ +++ea +k+++e+ e +g +v  l  D +++ +ve++v ++v++fg++D +v + g 
  gi|118431423|ref|NP_147894.2|  13 SRGLGFHAARALASLGCNLVIVARGREAlEKSAKEISEGFGVDVepLVGDLRKKGHVENAVIHAVQTFGRVDAVVAAYGN 92 
                                    59*****************************************999*********************************9 PP

                                    -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAvel 159
                                      +    + e+++e++ +a +  l s+ +l ka++ + ++++ ++ lss+     ++   +  a++a+l  l++++A+ l
  gi|118431423|ref|NP_147894.2|  93 ISREPLTLREAEWEDWIEAAALYLASTSSLFKALASYNTAKATVILLSSFTVAEPMDPLIVSDAVRAGLSRLVKSAAR-L 171
                                    99967778899***************************************8888888888***************887.6 PP

                                    GGGTEEEEEEEE--BHCTGGGGSTT..........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                   adh_short_C2 160 gpkgiRvNavspgpikTlaasgikg..........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                     p++iR      g  kT+ a +  +          ++  ++e+e  +pl r g  +e  e++ +L+     y+ G+t+v 
  gi|118431423|ref|NP_147894.2| 172 YPDRIRPILLILGSFKTPGAMRTLEriarsrgeslENVWRREVEMLSPLARSGGLDEFEEVIRMLVRSP-DYMHGATVVF 250
                                    67799988877666666543222221222322232333666777889******************9765.8********* PP

                                    ST CS
                   adh_short_C2 230 Dg 231
                                    Dg
  gi|118431423|ref|NP_147894.2| 251 DG 252
                                    98 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   1.7e-23   7.6e-20       4     190 ..       8     194 ..       7     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.7e-23
                                    EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    lv G+s+G+G   a++la+ G+++v+v+r  e+le+ ake+ e  g ++ ++ +D++++  ve++v +av+ +g++d++v
  gi|118431423|ref|NP_147894.2|   8 LVLGGSRGLGFHAARALASLGCNLVIVARGREALEKSAKEISEGfGVDVEPLVGDLRKKGHVENAVIHAVQTFGRVDAVV 87 
                                    799***************************************************************************** PP

                                    E---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHH CS
                      adh_short  83 nNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavaglt 160
                                    +  G    ++ +  e + e+w +  ++ l ++ +l +a++ +  +  +++++  sS +  +p+  +++  A  a++  l+
  gi|118431423|ref|NP_147894.2|  88 AAYGNisREPLTLREAEWEDWIEAAALYLASTSSLFKALASY--NTAKATVILLSSFTVAEPMDPLIVSDAVRAGLSRLV 165
                                    ****94444444556666666666777788888888888888..89********************************** PP

                                    HHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 161 rslakelaptgirvnavaPGlvdTdmakel 190
                                    +s+a+ + + +ir + +  G ++T+ a+++
  gi|118431423|ref|NP_147894.2| 166 KSAARLYPD-RIRPILLILGSFKTPGAMRT 194
                                    **9986665.6*************988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1   1.1e-10   5.1e-07       4     137 ..       8     142 ..       7     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.1e-10
                                    EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS--- CS
                             KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppik 83 
                                    l+ GG  gLG + ar la+ g  +lv+++R  +a e+s+++i+  e  g++ve +  D+ +k +ve+++ ++ ++++++ 
  gi|118431423|ref|NP_147894.2|   8 LVLGGSRGLGFHAARALASLGC-NLVIVARGREALEKSAKEIS--EGFGVDVEPLVGDLRKKGHVENAVIHAVQTFGRVD 84 
                                    899****************995.45555665345555554454..567******************************** PP

                                    EEEE---------T..TT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEH CS
                             KR  84 GvihaAgvlrdkll..eemtaedleqvlapKvkGawnLhelled..esldffvlfSSi 137
                                     v+ a g +  ++l   e + ed+ ++ a  ++ +  L ++l++  +    ++l+SS 
  gi|118431423|ref|NP_147894.2|  85 AVVAAYGNISREPLtlREAEWEDWIEAAALYLASTSSLFKALASynTAKATVILLSSF 142
                                    ******9999887511678888999999988888888888888754555566777775 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.4   1.8e+03      21      32 ..      43      54 ..      32      57 .. 0.77
   2 ?   -3.3   0.0       1.5   6.7e+03      19      25 ..      96     102 ..      87     103 .. 0.63
   3 ?    9.4   0.0   0.00017      0.74      18      45 ..     190     217 ..     180     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.4
                                   --HHHHHHHHTS CS
                     Sigma70_r4 21 lTleEIgerlgi 32
                                    + +EI+e +g+
  gi|118431423|ref|NP_147894.2| 43 KSAKEISEGFGV 54
                                   578999999987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                                    TT--HHH CS
                     Sigma70_r4  19 eglTleE 25 
                                    e+lTl E
  gi|118431423|ref|NP_147894.2|  96 EPLTLRE 102
                                    5666665 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00017
                                    TTT--HHHHHHHHTS-HHHHHHHHHHHH CS
                     Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAl 45 
                                    g  +Tle I++  g S+e V ++e + l
  gi|118431423|ref|NP_147894.2| 190 GAMRTLERIARSRGESLENVWRREVEML 217
                                    7789******************998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1814.03
//
Query:       gi|118431424|ref|NP_147895.2|  [L=161]
Description: hypothetical protein APE_1362.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   10.5   0.0       0.12   10.3   0.0    1.0  1  Nup188    Nucleoporin subcomplex protein binding to Pom34


Domain annotation for each model (and alignments):
>> Nup188  Nucleoporin subcomplex protein binding to Pom34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.6e-06      0.12     770     836 ..      40     107 ..      30     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.6e-06
                         Nup188 770 gqsllniiesgsdnlesielsdisgqlydqliqlslslanllisirssln.lspSplEkaLfsqspk.L 836
                                    ++ + +i++    ++++i lsd+sg ++++ ++ s+++  l+i++rs+ + +   +lE+++ + +++ +
  gi|118431424|ref|NP_147895.2|  40 AAKIARILTKYFYTIDYIALSDLSGGECETSVNGSFDI-DLVIKVRSPAEaYALATLEEIIDNAVKEaF 107
                                    5568889999999************************8.8**********96668***99988777653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1256.09
//
Query:       gi|118431425|ref|NP_147896.2|  [L=273]
Description: hypothetical protein APE_1363.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-40  138.4   0.0    6.5e-40  136.8   0.0    1.7  1  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.8   0.0   3.7e-44   6.5e-40       2     197 ..      73     265 ..      72     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 3.7e-44
                   RNA_Me_trans   2 yviEhleeelseWvllEYrhiakevgaenliltslskasleslpeelkslaklelekesveellkelkevkkekvclLDp 81 
                                    +v+E le++ s+W+l E  + +  + +    ++   ++  + l         +++ +++v  ++++ +++++  ++lLD 
  gi|118431425|ref|NP_147896.2|  73 IVVELLEDTPSRWLLEELLESYLFAVQMGYRFAVTGAT--NPL-------VYAAVRRAGVPVFMERGYSLNRPGCILLDL 143
                                    89***************888887776766555544442..222.......34566778********************** PP

                   RNA_Me_trans  82 kaekelspedaeefdvflfGGIlGddpprdRTselrkkg...fegRrLGpvqmttDtAvrvtklvvedkvkleeieyvde 158
                                    +++k+l+pe+a++++++++GGI+Gd+pp++RT+ l+++    +++R+LGp+q+++D+Av+++ lv+e +++l+eie+ + 
  gi|118431425|ref|NP_147896.2| 144 WSPKRLEPEEASSASYIIVGGIMGDHPPKGRTYLLSSQVytaCAKRNLGPEQLSVDGAVKTAILVAE-GYRLDEIEFEEG 222
                                    *************************************999999*********************999.************ PP

                   RNA_Me_trans 159 pelkfnk.....kesvempfrYvkdeegkpllpegmlellkkdl 197
                                    +e+++++     +++ve+p++Y+k   g++l+++++l+ll++++
  gi|118431425|ref|NP_147896.2| 223 VEVEVESpvrgvSARVELPYAYPK-VGGRILVSQRLLSLLSRGI 265
                                    ***********99***********.9**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); 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: 00:00:00.37
# Mc/sec: 2215.27
//
Query:       gi|118431426|ref|NP_147897.2|  [L=241]
Description: hypothetical protein APE_1364.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.3   0.3        7.8    6.3   0.0    2.4  2  DUF3670   SNF2 Helicase protein
      0.081   12.7   1.2        0.4   10.5   0.1    2.6  3  CheR_N    CheR methyltransferase, all-alpha domain
       0.36   10.9   0.1       0.36   10.9   0.1    3.3  4  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0036        21      81     114 ..       9      46 ..       7      66 .. 0.80
   2 ?    6.3   0.0    0.0013       7.8      89     122 ..     160     193 ..     155     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0036
                        DUF3670  81 eLseeEldrLaeakr..pLvrlrg..qWvevdpeelrr 114
                                    +L++eE++rL e++r  +   + +  +Wv+ +++e r+
  gi|118431426|ref|NP_147897.2|   9 KLTKEEFERLREQARrhGFASVTDyvRWVLAQHAEGRE 46 
                                    79**********98855666666655677777776665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                        DUF3670  89 rLaeakrpLvrlrgqWvevdpeelrraleflkrr 122
                                     L + +  + ++ g++v+vd++  +r ++ l++ 
  gi|118431426|ref|NP_147897.2| 160 SLEKRGAVVLNIEGKYVAVDKNYWERFRSILEEL 193
                                    56666777889*****************999984 PP

>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   6.6e-05       0.4      29      50 ..      17      38 ..      16      41 .. 0.90
   2 ?   -0.4   0.0      0.16   9.8e+02      24      34 ..      62      72 ..      61      75 .. 0.81
   3 ?   -2.8   0.0      0.89   5.3e+03      29      43 ..     215     229 ..     214     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.6e-05
                                   HHHHHHHTTT-SSSHHHHHHTS CS
                         CheR_N 29 RlsrRmralglksfeeYldlLr 50
                                   Rl+   r++g++s+++Y++ + 
  gi|118431426|ref|NP_147897.2| 17 RLREQARRHGFASVTDYVRWVL 38
                                   899999************9886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.16
                                   HHHHTHHHHHH CS
                         CheR_N 24 allkrRlsrRm 34
                                   a+l+rR+  ++
  gi|118431426|ref|NP_147897.2| 62 ASLERRIMDLL 72
                                   689***98776 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.89
                                    HHHHHHHTTT-SSSH CS
                         CheR_N  29 RlsrRmralglksfe 43 
                                    Rl r m + g++ f+
  gi|118431426|ref|NP_147897.2| 215 RLFREMVRAGIAVFD 229
                                    788888888887776 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 ?   10.9   0.1   5.9e-05      0.36       2      36 ..       6      41 ..       6      43 .. 0.89
   2 ?   -3.1   0.3       1.5   9.1e+03       9      20 ..      91     102 ..      91     105 .. 0.64
   3 ?    0.3   0.4      0.13   7.7e+02       4      37 ..     176     209 ..     176     211 .. 0.85
   4 ?   -2.1   0.1      0.73   4.4e+03      28      35 ..     216     223 ..     215     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.9e-05
                                   EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlrey 36
                                   + i+l +e+ erL+e arr g  S+ + +R  l+++
  gi|118431426|ref|NP_147897.2|  6 IKIKLTKEEFERLREQARRHGfASVTDYVRWVLAQH 41
                                   689**********************99999777776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHH CS
                          RHH_1   9 ellerLdelarr 20 
                                    e++e+L+  +r+
  gi|118431426|ref|NP_147897.2|  91 EMIETLELARRD 102
                                    567777666555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.13
                                    EEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1   4 irldeellerLdelarrrgrSrSelIReAlreyl 37 
                                    + +d+++ er++ + +++++S S + ++ ++e l
  gi|118431426|ref|NP_147897.2| 176 VAVDKNYWERFRSILEELDVSDSIAAERIIAEKL 209
                                    6789999999999999999999999999998877 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.73
                                    HHHHHHHH CS
                          RHH_1  28 lIReAlre 35 
                                    l+Re++r+
  gi|118431426|ref|NP_147897.2| 216 LFREMVRA 223
                                    57888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1803.67
//
Query:       gi|118431427|ref|NP_147898.2|  [L=241]
Description: GTP cyclohydrolase III [Aeropyrum pernix K1]
Scores for 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-98  328.0   0.3    3.6e-98  327.8   0.3    1.0  1  GCH_III   GTP cyclohydrolase III
  ------ inclusion threshold ------
      0.076   13.1   0.8       0.18   11.9   0.0    2.0  2  DUF5132   Protein of unknown function (DUF5132)
      0.089   11.7   0.0       0.11   11.3   0.0    1.1  1  RdRP_4    Viral RNA-directed RNA-polymerase
       0.13   12.6   0.0       0.22   11.8   0.0    1.4  1  mCpol     minimal CRISPR polymerase domain


Domain annotation for each model (and alignments):
>> GCH_III  GTP cyclohydrolase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.8   0.3    8e-102   3.6e-98       2     246 .]      10     241 .]       9     241 .] 0.99

  Alignments for each domain:
  == domain 1  score: 327.8 bits;  conditional E-value: 8e-102
                                    EEEEETTHHHHCCSSS---HHHHHHHHHHHHHHHHHHHHTTT-EEE-TTSSEEEEE-TT--HHHHHHHHHHHHHHSSS-E CS
                        GCH_III   2 tviqidnYgpWtvepaprreadlqalqarlyadlqkelaardGlvfatRfDnllaitngidleehkRiqesirnrypvtv 81 
                                    +v+   +Y++Wt+e++++re+++q+lq+++ya++qke+a+++G+v+++R+D++l+i+++++++eh+R++++i+++++v+v
  gi|118431427|ref|NP_147898.2|  10 AVVEQVGYREWTEELGSDREWIIQTLQSDIYAAAQKEAAGYGGFVLPIRYDIMLLISSNMGVQEHARVLDAIAGLSKVKV 89 
                                    6777789************************************************************************* PP

                                    EEEEEEESSHHHHHHHHHHHHHHH--TT-TT----EEES---SS--EEEEEEEETTHHHHTTTTS-HHHHHHHHHHHHHH CS
                        GCH_III  82 smgigaaetPldaleaaseaLreagsaqdeeRkevlsvdelvtegyvqiahiDinnitgtltdivsavrtylevnkvkak 161
                                    +m+++++++Plda+e+a++aLr++++++++eR+e        +e+y++iahiD+nn+t ++t+++++vrty+ev++++ak
  gi|118431427|ref|NP_147898.2|  90 RMASYCGVKPLDAVERAWNALRRREERLIYERCE--------GEEYTAIAHIDLNNVT-AITRAEGPVRTYYEVMDLMAK 160
                                    **********************************........9***************.********************* PP

                                    HHHHHHTTT---EEEETTEEEEE-TT--HHHHHHHHHHHHHHHS-.....-EEEEEEEESSHHHHHHHHHHHHHHHHTTS CS
                        GCH_III 162 lakklekegallqfiGGDnilavcneleeedvldiinevkekvdv.....dlkaGiGiadtaedaaaladeaLeeiRgkl 236
                                    ++k++ek+ga++q++GGDnila         vl+++++vke+vd+     dlkaGiGia+ta++++ala+eaL+eiR+k+
  gi|118431427|ref|NP_147898.2| 161 ISKVAEKIGAITQYLGGDNILA---------VLPLNGSVKETVDMllvrsDLKAGIGIAPTARASLALAAEALHEIRSKI 231
                                    **********************.........************************************************* PP

                                    SSSSEEEEET CS
                        GCH_III 237 vegplvvakq 246
                                    ++gplvv++q
  gi|118431427|ref|NP_147898.2| 232 NPGPLVVKAQ 241
                                    *******986 PP

>> DUF5132  Protein of unknown function (DUF5132)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1         4   1.8e+04      16      24 ..      39      47 ..      38      49 .. 0.44
   2 ?   11.9   0.0     4e-05      0.18       5      34 ..     198     227 ..     198     229 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 4
                        DUF5132 16 lyeearkaa 24
                                   +y+ a+k a
  gi|118431427|ref|NP_147898.2| 39 IYAAAQKEA 47
                                   344444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4e-05
                        DUF5132   5 LvkgvvKtgiglyeearkaaaevGEeLeDl 34 
                                    Lv++ +K gig++  ar  +a + E L+ +
  gi|118431427|ref|NP_147898.2| 198 LVRSDLKAGIGIAPTARASLALAAEALHEI 227
                                    9**************************976 PP

>> RdRP_4  Viral RNA-directed RNA-polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.4e-05      0.11      27     138 ..      67     197 ..      26     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.4e-05
                         RdRP_4  27 a......nill.daiatslksnlsalafllgrillavtsrekdkaarillrtieaytnekygvprryrlyeaawansa.. 97 
                                    +      + +  daia++ k   + +++   + l av  + ++ ++r+   + e+++ e y +++++ l++++ ++ a  
  gi|118431427|ref|NP_147898.2|  67 SnmgvqeHARVlDAIAGLSKVKVRMASYCGVKPLDAVERAWNALRRREERLIYERCEGEEYTAIAHIDLNNVTAITRAeg 146
                                    04444444445588888888887777777777777776668889999999999**********************999** PP

                         RdRP_4  98 .........dylkaleqvvksyg.aklsspmstlvelvpLygrgattkdle 138
                                             d ++++++v +++g  + +  +  + +  pL+g+ ++t+d+ 
  gi|118431427|ref|NP_147898.2| 147 pvrtyyevmDLMAKISKVAEKIGaITQYLGGDNILAVLPLNGSVKETVDML 197
                                    ******999999999999999995333445566666777*********986 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     5e-05      0.22      30      81 ..     152     204 ..     135     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5e-05
                          mCpol  30 kevkeaikklkkllkdelgasvifaaGDsilaksslee..dllvelsrvyqkit 81 
                                     ev + + k++k+ +++ ga   + +GD+ila  +l+   ++ v++  v + ++
  gi|118431427|ref|NP_147898.2| 152 YEVMDLMAKISKVAEKI-GAITQYLGGDNILAVLPLNGsvKETVDMLLVRSDLK 204
                                    57888899999999999.999*************99877777777766655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1903.13
//
Query:       gi|118431428|ref|NP_147899.2|  [L=147]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-33  115.6   0.2    1.7e-33  115.4   0.2    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.2   9.6e-38   1.7e-33       2     139 ..       7     139 ..       6     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 9.6e-38
                                    EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHH CS
                  DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfey 81 
                                    +riaiVv++fn ++t  + e+a+d+++ +g+  e   v++ PG+f+ p+++++l+++++++dav +lG+vi+G+t+h+e+
  gi|118431428|ref|NP_147899.2|   7 IRIAIVVSEFNYDVTRVMEEKAIDHARFLGA--EVSLVARSPGTFDTPFIVSRLLATHSEVDAVAVLGAVIKGDTKHDEV 84 
                                    79****************************7..59999******************65559******************* PP

                                    HHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHH CS
                  DMRL_synthase  82 vaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanl 139
                                    va++++++l ++s+++g+Pv+ g++ +  ++ +a+era    ++++++a+e+a+++a+ 
  gi|118431428|ref|NP_147899.2|  85 VAHQAARKLLDLSIEYGKPVTLGIIGPGaSRLEAIERA----EEYARRAVESAVKLARR 139
                                    ***************************999********....89***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1046.64
//
Query:       gi|14601365|ref|NP_147901.1|  [L=726]
Description: cell division protein CDC48 [Aeropyrum pernix K1]
Scores for complete 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-101  336.3   0.0    1.8e-51  174.0   0.0    2.5  2  AAA              ATPase family associated with various cellul
    9.1e-37  124.6   4.4    9.1e-18   63.8   0.3    2.7  2  AAA_lid_3        AAA+ lid domain
    4.7e-29  100.4   0.2    3.7e-28   97.5   1.1    2.1  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    8.8e-17   61.3   0.0    2.7e-08   33.7   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.7e-16   58.5   0.0    9.1e-09   35.7   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
    9.2e-15   55.4   0.1      1e-06   29.3   0.0    3.5  2  AAA_16           AAA ATPase domain
    2.8e-14   52.6   2.7    2.2e-13   49.8   0.4    3.0  3  CDC48_2          Cell division protein 48 (CDC48), domain 2
    3.5e-12   46.1   0.7    5.1e-05   23.2   0.0    3.1  2  Vps4_C           Vps4 C terminal oligomerisation domain
    3.1e-11   43.4   1.3    0.00022   21.2   0.2    3.9  2  AAA_5            AAA domain (dynein-related subfamily)
    4.8e-11   43.0   0.0    0.00015   22.0   0.0    2.6  2  AAA_33           AAA domain
      5e-11   42.4   0.0    9.7e-05   21.7   0.0    2.6  2  TIP49            TIP49 P-loop domain
    1.7e-10   41.3   1.2     0.0047   17.2   0.0    4.2  4  AAA_22           AAA domain
    3.9e-10   39.9   0.0    5.6e-05   23.2   0.0    2.4  2  AAA_14           AAA domain
    1.8e-08   34.3   0.1       0.01   15.6   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
    2.7e-08   34.4   0.3     0.0015   19.1   0.0    2.9  2  AAA_18           AAA domain
    2.8e-08   34.2   0.0     0.0029   17.8   0.0    2.7  2  AAA_28           AAA domain
    2.4e-07   31.1   0.0      0.004   17.5   0.0    2.6  2  RNA_helicase     RNA helicase
    9.3e-07   28.8   0.0     0.0071   16.1   0.0    2.5  2  AAA_24           AAA domain
    1.2e-06   28.1   3.0      0.017   14.5   0.1    2.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.6e-06   27.0   0.0      0.043   13.8   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    4.7e-06   26.1   2.4      0.091   12.1   0.0    3.5  4  ATPase           KaiC
    1.6e-05   24.6   0.0       0.49   10.1   0.0    3.4  3  Sigma54_activat  Sigma-54 interaction domain
      3e-05   24.6   0.0       0.47   11.0   0.0    2.8  2  ABC_tran         ABC transporter
      3e-05   24.0   0.0     0.0039   17.1   0.0    2.9  2  Bac_DnaA         Bacterial dnaA  protein
    3.7e-05   23.0   0.0       0.13   11.4   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    3.8e-05   23.3   0.0       0.22   11.0   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    3.9e-05   22.9   0.5      0.049   12.7   0.0    2.5  2  Parvo_NS1        Parvovirus non-structural protein NS1
      5e-05   23.2   0.0       0.16   11.8   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    5.6e-05   22.6   0.0      0.017   14.3   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    7.1e-05   22.4   1.0        0.2   11.1   0.1    2.7  2  PhoH             PhoH-like protein
    7.3e-05   22.7   0.8       0.71    9.8   0.1    3.7  4  NACHT            NACHT domain
     0.0001   22.3   0.1       0.03   14.2   0.0    3.0  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00012   21.5   0.0       0.32   10.3   0.0    2.7  2  Zeta_toxin       Zeta toxin
    0.00022   20.8  10.5       0.51    9.9   0.0    4.5  3  AAA_25           AAA domain
    0.00039   20.9   0.0        0.7   10.3   0.0    3.3  2  AAA_17           AAA domain
     0.0011   19.1   0.0          2    8.5   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0014   18.5   0.0        1.4    8.7   0.0    2.3  2  AAA_11           AAA domain
     0.0014   18.4   0.5        2.6    7.7   0.0    3.0  2  AAA_30           AAA domain
     0.0019   18.5   0.6        3.6    7.9   0.0    3.0  3  AAA_19           AAA domain
     0.0022   17.1   0.0       0.18   10.7   0.0    2.9  3  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0022   17.4   0.1        2.3    7.6   0.0    2.6  2  IPT              Isopentenyl transferase
     0.0038   17.2   0.0          2    8.3   0.0    2.6  3  Rad17            Rad17 P-loop domain
     0.0047   17.0   0.1       0.47   10.5   0.0    2.9  2  DUF1905          Domain of unknown function (DUF1905)
     0.0082   15.9   0.9        2.1    8.0   0.0    2.9  2  Cytidylate_kin   Cytidylate kinase
     0.0094   16.1   0.0        1.5    8.9   0.0    2.7  2  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.017   15.2   0.5       0.36   10.9   0.1    2.6  2  Molydop_binding  Molydopterin dinucleotide binding domain
      0.017   15.2   0.0        2.5    8.2   0.0    2.6  2  SKI              Shikimate kinase
      0.019   14.2   0.0        4.4    6.4   0.0    2.5  2  NB-ARC           NB-ARC domain
      0.019   14.9   2.0         23    4.9   0.0    4.1  3  NTPase_1         NTPase
       0.03   14.0   0.4         38    3.9   0.0    3.9  4  Guanylate_kin    Guanylate kinase
      0.033   13.1   0.0        8.6    5.1   0.0    2.5  2  AFG1_ATPase      AFG1-like ATPase
      0.043   12.9   0.0        2.1    7.3   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.053   13.3   0.0        6.5    6.5   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.069   12.9   0.0        4.7    6.9   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.072   13.0   0.3        5.1    7.1   0.0    2.5  2  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
      0.094   12.5   0.0         18    5.2   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
       0.22   11.5   0.0         21    5.0   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit


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 !  174.0   0.0   5.6e-54   1.8e-51       1     131 [.     221     350 ..     221     351 .. 0.98
   2 !  159.9   0.0   1.4e-49   4.3e-47       1     131 [.     496     627 ..     496     628 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.0 bits;  conditional E-value: 5.6e-54
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHH CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsesee 81 
                                   +llyGppGtGKTllaka+a+e+g++f++i+g+e++sky gese+++re+fkea+e+a psi+fiDEida+a++r++ + e+
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGAYFISINGPEIMSKYYGESEQRLREIFKEAEENA-PSIIFIDEIDAIAPKREEVTGEV 300
                                   69******************************************************9.*********************** PP

                                   HHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  82 eervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   e+rvv+qLlt +dg+k++ ++vivigatnrpd +dpal+r gRfdr+iei+
  gi|14601365|ref|NP_147901.1| 301 EKRVVAQLLTLMDGLKER-GRVIVIGATNRPDAIDPALRRpGRFDREIEIR 350
                                   *****************6.77***************************986 PP

  == domain 2  score: 159.9 bits;  conditional E-value: 1.4e-49
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgses 79 
                                   vll+GppGtGKTllakava+e+g++f+ + g+e+lsk+vgese+ ir++f++a++ a p ++f+DEida+a++r  + ++s
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESERAIRKIFERARQAA-PAVVFFDEIDAIAPARgaRFDTS 575
                                   79******************************************************9.****************9777799 PP

                                   HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                           AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                   ++++r+vnq+l+e+dg +   s+v+vigatnrpd ldpallr gRfdr i+++
  gi|14601365|ref|NP_147901.1| 576 GVTDRIVNQMLAEMDGIQPL-SNVVVIGATNRPDILDPALLRpGRFDRLIYVP 627
                                   *******************6.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.4   1.3e-19   4.2e-17       1      45 []     373     436 ..     373     436 .. 0.89
   2 !   63.8   0.3   2.9e-20   9.1e-18       1      45 []     650     696 ..     650     696 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.3e-19
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr...................gikeitmedfee 45 
                                   dvdl++LAe+T+Gy+GADlaal +eAa++Alrr                   ++ ++tm+df+e
  gi|14601365|ref|NP_147901.1| 373 DVDLDKLAEMTHGYTGADLAALAKEAAMAALRRfiregkinfeakeipatvlKELKVTMKDFME 436
                                   9********************************9888888888888888855555799999976 PP

  == domain 2  score: 63.8 bits;  conditional E-value: 2.9e-20
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfee 45 
                                   dvdl++LAe+TeGy+GAD++a++reA+++ lr++++  +++m++f e
  gi|14601365|ref|NP_147901.1| 650 DVDLEKLAEMTEGYTGADIEAVVREAVMAKLREKLEvgKVEMRHFLE 696
                                   9***********************************877******75 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 !   97.5   1.1   1.2e-30   3.7e-28       1      84 [.       7      91 ..       7      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 1.2e-30
                                  CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                       CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveieg.krkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                  +LrV+ea+++dvgr+ivrid+++ ++lg+e gd+v++++ +r+ va+vwp++p+deg+giIrmdg++R+ +gv++Gd+VtV+k
  gi|14601365|ref|NP_147901.1|  7 ELRVSEAYPRDVGRKIVRIDRQTAARLGVEVGDFVKVSKgDRSVVAVVWPLRPDDEGRGIIRMDGYLRAALGVTVGDTVTVEK 89
                                  59***********************************988999**************************************** PP

                                  E- CS
                       CDC48_N 83 ae 84
                                  ae
  gi|14601365|ref|NP_147901.1| 90 AE 91
                                  98 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   8.7e-11   2.7e-08      34     104 ..     219     297 ..     196     343 .. 0.85
   2 !   24.5   0.0     6e-08   1.9e-05      36     145 ..     496     610 ..     487     623 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 8.7e-11
                        RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl 104
                                     +llyGpPG Gkt lak +a+e+g+ + +  gP +      e ++ l  ++++ ee+   ++fidei  ++++ eev 
  gi|14601365|ref|NP_147901.1| 219 KGILLYGPPGTGKTLLAKALANEIGAYFISINGPEImskyygESEQRLREIFKEAEENapSIIFIDEIDAIAPKREEVT 297
                                   569*******************************984433334457799999998876447*************99985 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 6e-08
                        RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl.ysa 107
                                   vll+GpPG Gkt lak +a+e g+++ +  gP +      e ++ +  ++ + ++    v+f dei  +++a    +  s 
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEIlskwvgESERAIRKIFERARQAapAVVFFDEIDAIAPARGARFdTSG 576
                                   9*******************************8744333344566777776665542269999999988877654441344 PP

                        RuvB_N 108 medfrldivigkGpsarsikldlpkftlvgattragll 145
                                   + d  ++ ++ +  + +     l++  ++gat r  +l
  gi|14601365|ref|NP_147901.1| 577 VTDRIVNQMLAEMDGIQ----PLSNVVVIGATNRPDIL 610
                                   55555555555544433....45666666666666665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   2.9e-11   9.1e-09       6     105 ..     221     314 ..     216     318 .. 0.91
   2 !   20.0   0.0   1.9e-06   0.00059       6      92 ..     496     576 ..     491     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.9e-11
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----. CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk. 83 
                                   ill gp g+Gkt+lakala+ + +     +i ++  e++     + + ++++  ++  ++aee+   i+++DEid i+pk 
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGA----YFISINGPEIMS----KYYGESEQRLREIFKEAEENApsIIFIDEIDAIAPKr 293
                                   8999******************96....************....********************9**************97 PP

                                   ---------HHHHHHHHHHHH- CS
                         AAA_2  84 essgadvSregVqrdLLqileg 105
                                   e+ + +v +  V+  LL +++g
  gi|14601365|ref|NP_147901.1| 294 EEVTGEVEK-RVVAQLLTLMDG 314
                                   777777766.577778999987 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.9e-06
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                   +ll gp g+Gkt+laka+a    +    ++i +   e+l     + + +++   ++   +a +    +v++DEid i+p +
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGA----NFIAVRGPEILS----KWVGESERAIRKIFERARQAApaVVFFDEIDAIAPAR 568
                                   6788****************9995....9**999999999....44444444445555555555588************87 PP

                                   -------- CS
                         AAA_2  85 ssgadvSr 92 
                                    ++ d S+
  gi|14601365|ref|NP_147901.1| 569 GARFDTSG 576
                                   77777775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   3.2e-09     1e-06      24     141 ..     218     324 ..     209     332 .. 0.75
   2 !   20.0   0.2   2.3e-06   0.00073      24      93 ..     493     552 ..     483     601 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.2e-09
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                   p  +ll+G++G+GK+ l+++l++++    ++f++ +  +  ++  y    q l r e++++ +++   a    + +++++ 
  gi|14601365|ref|NP_147901.1| 218 PKGILLYGPPGTGKTLLAKALANEIG---AYFISINGPEI-MSKYYGESEQRL-R-EIFKEAEEN---APSIIFIDEIDAI 289
                                   4889******************9777...89********9.333333344444.4.454444444...4445555666666 PP

                        AAA_16 105 laavpelagaeasrllellkrllallsrderplvlvl 141
                                   +    e++g+ ++r+ ++l  l++ l++++r  v+v+
  gi|14601365|ref|NP_147901.1| 290 APKREEVTGEVEKRVVAQLLTLMDGLKERGR--VIVI 324
                                   668888888888***********99999776..5554 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.3e-06
                        AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesae 93 
                                   p+ vll G++G+GK+ l+++++++  ++   f++ +  +      +s ++    + + +r++ ++a++a+
  gi|14601365|ref|NP_147901.1| 493 PRGVLLFGPPGTGKTLLAKAVATESGAN---FIAVRGPEI-----LSKWVGES-E-RAIRKIFERARQAA 552
                                   599*******************877766...666665555.....33455555.3.44455554433333 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 ?    0.9   0.0       1.3     4e+02      33      58 ..       5      34 ..       2      38 .. 0.87
   2 ?   -1.5   0.0       6.9   2.2e+03      19      28 ..      79      88 ..      74     106 .. 0.76
   3 !   49.8   0.4   6.9e-16   2.2e-13       1      63 [.     108     169 ..     108     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.3
                                  CEEEEEEEECCCC....SCEEECTSCCEEE CS
                       CDC48_2 33 eiklvVvstePkg....pvgitetTeielg 58
                                   ++l+V +  P +    +v+i+++T  +lg
  gi|14601365|ref|NP_147901.1|  5 SVELRVSEAYPRDvgrkIVRIDRQTAARLG 34
                                  6899*********************87765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.9
                                  E-TTEEEEEC CS
                       CDC48_2 19 vtkGdlvvfe 28
                                  vt+Gd+v++e
  gi|14601365|ref|NP_147901.1| 79 VTVGDTVTVE 88
                                  6778888765 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 6.9e-16
                                   ..SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                       CDC48_2   1 ridgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                   r+  d+++y+k  +l +p++ G+++ ++++   ++lvVvst+P+  v +te+Te+e+++kpv+
  gi|14601365|ref|NP_147901.1| 108 RFGRDFVEYVKEFLLRKPISRGETIIVPVL-EGLPLVVVSTQPAHFVYVTEATEVEIREKPVR 169
                                   6889999**********************9.56****************************97 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 !   19.8   0.1   1.8e-06   0.00056      10      45 ..     410     445 ..     408     448 .. 0.92
   2 !   23.2   0.0   1.6e-07   5.1e-05      22      58 ..     682     718 ..     668     720 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.8e-06
                        Vps4_C  10 gaiemtwmdipsdkllePpvtlkDflkalkkarptV 45 
                                   g+i    ++ip+  l+e +vt+kDf++a+k  rpt 
  gi|14601365|ref|NP_147901.1| 410 GKINFEAKEIPATVLKELKVTMKDFMEAMKMIRPTL 445
                                   77888999**************************95 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.6e-07
                        Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                   +kl   +v++++fl+alkk+ p+ +keD+ ++e+  k
  gi|14601365|ref|NP_147901.1| 682 EKLEVGKVEMRHFLEALKKVPPSLTKEDILRYERLAK 718
                                   677777**************************98665 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 !   21.2   0.2   7.1e-07   0.00022       2     136 ..     221     339 ..     220     340 .. 0.69
   2 !   17.8   0.1   8.2e-06    0.0026       1      87 [.     495     574 ..     495     617 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.1e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H. CS
                         AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes. 79 
                                   +lL GppGtgK+ la+ la  +++ +  +++++ +++     + +           ++ ++a+   ++i+++DE++ + + 
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGAYFISINGPEIMSKYYGESEQR---------LREIFKEAEenAPSIIFIDEIDAIAPk 292
                                   89*****************************99887643333333.........35555566657899********88761 PP

                                   ..HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                         AAA_5  80 ..evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                     ev++++ +          ++ +l++  ++    r+ vi+++n++d     ++palr+
  gi|14601365|ref|NP_147901.1| 293 reEVTGEVEKRVVA------QLLTLMDGLKE--RGRVIVIGATNRPD----AIDPALRR 339
                                   11444444333333......55555544432..12289999999999....88888876 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 8.2e-06
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                   +vlL GppGtgK+ la+ +a   ++++  v +++      ++ ++    g+ ++   ++ + ar   ++++++DE++ + +
  gi|14601365|ref|NP_147901.1| 495 GVLLFGPPGTGKTLLAKAVATESGANFIAVRGPE------ILSKWV---GESERAIRKIFERARqaAPAVVFFDEIDAIAP 566
                                   59*******************9999999999987......555666...33333334444455547888999999998877 PP

                                   HHHHHHHH CS
                         AAA_5  80 evlnsLls 87 
                                   +  +++ +
  gi|14601365|ref|NP_147901.1| 567 ARGARFDT 574
                                   66555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.7e-07   0.00015       2      80 ..     221     329 ..     221     386 .. 0.78
   2 !   18.6   0.0   5.1e-06    0.0016       2      46 ..     496     542 ..     496     638 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.7e-07
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrvl 52 
                                   +ll G+pG+GK+ la+ l+++ g  ++ ++ ++++++++g+ +q+++                               +v+
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGayFISINGPEIMSKYYGESEQRLReifkeaeenapsiifideidaiapkreeVTGEVE 301
                                   6789*******************9778899*********998888887777777777777777777777776654333466 PP

                        AAA_33  53 drlyqilnelarkalsagrnvildatnl 80 
                                   +r+ ++l  l +   ++gr +++ atn+
  gi|14601365|ref|NP_147901.1| 302 KRVVAQLLTLMDGLKERGRVIVIGATNR 329
                                   6677777677766666666666666664 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.1e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                   vll G+pG+GK+ la+ ++ + g  ++ ++ ++++++ +g+ ++ ++
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGanFIAVRGPEILSKWVGESERAIR 542
                                   7899*******************999999999988877775555444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   3.1e-07   9.7e-05      51      98 ..     219     264 ..     211     302 .. 0.90
   2 !   17.8   0.0   4.8e-06    0.0015      51      99 ..     494     540 ..     485     551 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.1e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                   +++Ll Gp+gtGkt la a+++e+g    f++++g e+ s     +e 
  gi|14601365|ref|NP_147901.1| 219 KGILLYGPPGTGKTLLAKALANEIG--AYFISINGPEIMSKYYGESEQ 264
                                   89***********************..79*********9987777764 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.8e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevl 99 
                                   r+vLl Gp+gtGkt la a++ e g    f+a+ g e+ s  v  +e  
  gi|14601365|ref|NP_147901.1| 494 RGVLLFGPPGTGKTLLAKAVATESG--ANFIAVRGPEILSKWVGESERA 540
                                   89********************988..78***********999888843 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.5e-05    0.0047       8      30 ..     221     243 ..     216     270 .. 0.77
   2 ?    5.2   0.0     0.075        23      73     131 ..     261     327 ..     251     333 .. 0.70
   3 !   14.2   0.1   0.00012     0.039       8      29 ..     496     517 ..     491     531 .. 0.84
   4 ?   -0.6   0.0       4.7   1.5e+03      79     104 ..     541     565 ..     528     605 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                   ++++G++GtGKT+l++ l+++  
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIG 243
                                   89*****************9974 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.075
                        AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGtp 131
                                    s+++l+e + +a +++    ++ iDE++ +   +        ++++ +L +l++  +   ++i++G +
  gi|14601365|ref|NP_147901.1| 261 ESEQRLREIFKEAEENAPS--IIFIDEIDAIApkReevtgeveKRVVAQLLTLMDGLKERGRVIVIGAT 327
                                   5566666666666666655..**********88624556667788888888888876666677777765 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 0.00012
                        AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                   ++++G++GtGKT+l++ ++ + 
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATES 517
                                   689*************998875 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 4.7
                        AAA_22  79 lealeqalraravielliiDEaqhlr 104
                                   ++++ + +r++a  +++  DE++ + 
  gi|14601365|ref|NP_147901.1| 541 IRKIFERARQAAP-AVVFFDEIDAIA 565
                                   3333333444444.8*******9985 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.8e-07   5.6e-05       5     102 ..     221     328 ..     218     352 .. 0.79
   2 !   14.2   0.0   0.00011     0.034       5      76 ..     496     564 ..     493     587 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-07
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev......... 76 
                                   +++ G+  +GKT l+k l++e       ++ in  +   k + ++e+ l++i+++++e+  +++f+DEi  +         
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIG---AYFISINGPEIMSKYYGESEQRLREIFKEAEENAPSIIFIDEIDAIapkreevtg 298
                                   7899***************8888...89999999998888877766445555554455699***********999999999 PP

                        AAA_14  77 ...pewekalkslvd.egknldvivtGSns 102
                                      +++   l  l+d  +++++viv G  +
  gi|14601365|ref|NP_147901.1| 299 eveKRVVAQLLTLMDgLKERGRVIVIGATN 328
                                   888888888888888533678888888765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00011
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT l+k ++ e+     +++ +   +   k   ++e+ ++ i+e++++    ++f+DEi  +
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESG---ANFIAVRGPEILSKWVGESERAIRKIFERARQAAPAVVFFDEIDAI 564
                                   6899***************9999...999999999999988888888888888886666999*******877 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 !   15.6   0.0   3.2e-05      0.01      47      70 ..     218     241 ..     206     250 .. 0.88
   2 !   15.3   0.0   4.1e-05     0.013      48      72 ..     494     518 ..     483     560 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.2e-05
                     IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                    ++i+l Gp+G+GK+ la al+ e
  gi|14601365|ref|NP_147901.1| 218 PKGILLYGPPGTGKTLLAKALANE 241
                                   5789*****************976 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.1e-05
                     IstB_IS21  48 enivllGpsGvGKshlaialgveav 72 
                                    +++l+Gp+G+GK+ la a+++e  
  gi|14601365|ref|NP_147901.1| 494 RGVLLFGPPGTGKTLLAKAVATESG 518
                                   6799****************98765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   4.8e-06    0.0015       1      32 [.     221     273 ..     221     328 .. 0.61
   2 !   12.4   0.0   0.00056      0.18       1      26 [.     496     519 ..     496     552 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.8e-06
                        AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdva 32 
                                   Ill G+pG+GKt lak+L+++  ++                     +++ + a
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIgAYfisingpeimskyygeseqrLREIFKEA 273
                                   99*****************9985557866666666666666644333333333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00056
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgv 26 
                                   +ll G+pG+GKt lak+++ +   g 
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATES--GA 519
                                   799**************98775..33 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.3e-06    0.0029       2      47 ..     221     271 ..     220     313 .. 0.72
   2 !   13.5   0.0    0.0002     0.063       2      47 ..     496     542 ..     495     577 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.3e-06
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakgedalp 47 
                                   i + G+++tGKT l++aLa++ g   +    pE++ +++ e  ++ +++ +
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEiGAYFIsingPEIMSKYYGESEQRLREIFK 271
                                   7899***************88855544224777777776665555554444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0002
                        AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalp 47 
                                   + ++G+++tGKT l++a a + g + ++  + eil++   + e+a++
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATEsGANFIAVRGPEILSKWVGESERAIR 542
                                   6799***************7666666655555555444444444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-05     0.004       1      31 [.     221     251 ..     221     293 .. 0.78
   2 !   10.9   0.0    0.0015      0.46       1      24 [.     496     519 ..     496     568 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-05
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkk 31 
                                   i+lyGp+g+GK++lak La+++   + +++ 
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGAYFISING 251
                                   789******************9976633333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0015
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallk 24 
                                   ++l+Gp+g+GK++lak +a++   
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGA 519
                                   679**************8887654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.3e-05    0.0071       5      77 ..     221     289 ..     218     303 .. 0.71
   2 !   10.1   0.0    0.0016      0.49       5      22 ..     496     513 ..     493     569 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-05
                        AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                   il+yGp+g+GKT lak l  +  + fi +++   ++  + +   es + +++ ++e +++ +  ++++iD id +
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALanEIGAYFISING--PEIMSKYYG--ESEQRLREIFKEAEENAP--SIIFIDEIDAI 289
                                   89****************7655566666666..223333322..366788888887777766..78888888876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0016
                        AAA_24   5 iliyGpsgiGKTtlakel 22 
                                   +l++Gp+g+GKT lak  
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAV 513
                                   79*************987 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.4e-05     0.017      25      43 ..     221     239 ..     217     245 .. 0.90
   2 !   13.0   0.1   0.00016     0.049      25      43 ..     496     514 ..     493     516 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt+lak+l+
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALA 239
                                   89**************996 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll+GppG+GKt+lak+++
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVA 514
                                   79*************9875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00014     0.043      19      59 ..     218     258 ..     188     269 .. 0.74
   2 !   10.3   0.0    0.0016      0.51      21      51 ..     495     527 ..     462     530 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00014
                                   TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEE CS
                          TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeY 59 
                                    + ilL+G+ G+GKT l+++la+++g    +++ P   ++++Y
  gi|14601365|ref|NP_147901.1| 218 PKGILLYGPPGTGKTLLAKALANEIGAYfiSINGP--EIMSKY 258
                                   3449*********************9876677776..455555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0016
                                   EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                          TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                    +lL G+ G+GKT l++++a + g +  +v+ P
  gi|14601365|ref|NP_147901.1| 495 GVLLFGPPGTGKTLLAKAVATESGANfiAVRGP 527
                                   39*******************999887677665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00081      0.25      11      38 ..     209     237 ..     207     246 .. 0.85
   2 ?    0.2   0.0       1.2   3.8e+02     108     152 ..     263     313 ..     247     327 .. 0.65
   3 ?   -2.6   0.0       9.3   2.9e+03     170     202 ..     397     429 ..     388     446 .. 0.67
   4 !   12.1   0.0   0.00029     0.091      10      40 ..     483     514 ..     481     524 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00081
                        ATPase  11 il.kgGipegrvvlitGepGtGKtifalq 38 
                                   i+ + Gi   + +l++G pGtGKt++a+ 
  gi|14601365|ref|NP_147901.1| 209 IFkHLGIEPPKGILLYGPPGTGKTLLAKA 237
                                   565668888899**************975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                        ATPase 108 ieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlk 152
                                    ++l+e+ ke ++   + + iD i+++    +e + +v ++ + ql++ + 
  gi|14601365|ref|NP_147901.1| 263 EQRLREIFKEAEEnapSIIFIDEIDAIapkREEVTGEVEKRVVAQLLTLMD 313
                                   456666666665544588999999999421222233344556666666665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.3
                        ATPase 170 aaggygveefivdgvivLdlkeieeelvRtlei 202
                                   +a   ++  fi +g i  + kei  ++ + l++
  gi|14601365|ref|NP_147901.1| 397 EAAMAALRRFIREGKINFEAKEIPATVLKELKV 429
                                   455566777777777777777777755555444 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00029
                        ATPase  10 eil.kgGipegrvvlitGepGtGKtifalqFl 40 
                                   ei+ k Gi   r vl+ G pGtGKt++a+  +
  gi|14601365|ref|NP_147901.1| 483 EIFeKMGIRPPRGVLLFGPPGTGKTLLAKAVA 514
                                   57767899999****************98755 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0016      0.49      23      58 ..     219     251 ..     208     330 .. 0.86
   2 !   10.0   0.0    0.0016      0.51      23      52 ..     494     520 ..     483     538 .. 0.82
   3 ?   -1.9   0.0       7.5   2.4e+03      90     108 ..     549     567 ..     540     606 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEET CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavnc 58 
                                     +l+ G  GtGK+lla+a+ ++     + f+++n 
  gi|14601365|ref|NP_147901.1| 219 KGILLYGPPGTGKTLLAKALANEIG---AYFISING 251
                                   569****************987554...56776665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0016
                                   S-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekp 52 
                                     vl+ G  GtGK+lla+a+ ++s    ++
  gi|14601365|ref|NP_147901.1| 494 RGVLLFGPPGTGKTLLAKAVATESG---AN 520
                                   569****************987765...44 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.5
                                   HHTTTSEEEEETGGGS-HH CS
               Sigma54_activat  90 ekadgGtlfLDeigelple 108
                                   ++a   ++f+Dei  + ++
  gi|14601365|ref|NP_147901.1| 549 RQAAPAVVFFDEIDAIAPA 567
                                   5677889999999988765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0022      0.69       6      36 ..     213     243 ..     211     320 .. 0.78
   2 !   11.0   0.0    0.0015      0.47       8      70 ..     490     551 ..     487     602 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0022
                                   EEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllk 36 
                                   l +++ + + + G+ G+GK+ L+k+la++  
  gi|14601365|ref|NP_147901.1| 213 LGIEPPKGILLYGPPGTGKTLLAKALANEIG 243
                                   5677788899****************99875 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0015
                                   EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pql 70 
                                   +++ + v ++G+ G+GK+ L+k++a ++   +  i ++g ++ ++   ++++ i+ +++   q 
  gi|14601365|ref|NP_147901.1| 490 IRPPRGVLLFGPPGTGKTLLAKAVATESG--ANFIAVRGPEILSKWVGESERAIRKIFERaRQA 551
                                   56666789*****************9985..577888888888888888888888888874444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-05    0.0039      37     180 ..     221     366 ..     216     384 .. 0.78
   2 ?    3.3   0.0       0.2        64      37      61 ..     496     520 ..     489     531 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-05
                                   EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-H... CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagke... 113
                                   +++yg+ G Gkt L ka++ne+ + +     + +++ e +++     +++  e fke   ++  ++ iD+i  +a k    
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGAYF-----ISINGPEIMSKYYGESEQRLREIFKEAEENApSIIFIDEIDAIAPKReev 296
                                   79******************998766.....457888888888888888999999998875527899*******9885222 PP

                                   ......HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHH CS
                      Bac_DnaA 114 ......ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkie 180
                                         ++  +l+++++ l e g+ +v+ +   P +++    r   rf++   ++i ppd+  r++ilk + +
  gi|14601365|ref|NP_147901.1| 297 tgevekRVVAQLLTLMDGLKERGRVIVIGATNRPDAIDPAL-RRPGRFDR--EIEIRPPDKRARAEILKVHTR 366
                                   22111134457889999999**************9987654.33578877..6899************85544 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.2
                                   EEEE-SSSSSHHHHHHHHHHHHHHH CS
                      Bac_DnaA  37 lfiygevGlGktHLlkaignevlen 61 
                                   ++++g+ G Gkt L ka++ e  +n
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGAN 520
                                   799***************9887665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00042      0.13      45      83 ..     210     248 ..     162     324 .. 0.68
   2 !    9.1   0.0    0.0021      0.66      24      82 ..     455     522 ..     442     562 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00042
                        DUF815  45 eqfleglpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                    ++l  +p + +LL+G  GtGK  l kal ne+ +  + 
  gi|14601365|ref|NP_147901.1| 210 FKHLGIEPPKGILLYGPPGTGKTLLAKALANEIGAYFIS 248
                                   34556678899********************99876644 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                        DUF815  24 evklddLvgidkqkealventeqfleg.........lpannvLLwGarGtGKSslvkallneyaeegL 82 
                                   ev+++d+ g+++ k+al e +e  l++         +p + vLL+G  GtGK  l ka+ +e  ++ +
  gi|14601365|ref|NP_147901.1| 455 EVRWSDIGGLEEAKQALREAVEWPLKHpeifekmgiRPPRGVLLFGPPGTGKTLLAKAVATESGANFI 522
                                   56667777777777777666654333211111112257789******************999887764 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00069      0.22      32      58 ..     217     243 ..     208     295 .. 0.87
   2 !    9.5   0.0     0.002      0.64      34      56 ..     494     516 ..     483     525 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00069
                         AAA_7  32 nkkpvllvGptGtGKtviikdllkkld 58 
                                     k +ll+Gp GtGKt+++k l +++ 
  gi|14601365|ref|NP_147901.1| 217 PPKGILLYGPPGTGKTLLAKALANEIG 243
                                   56789***************9998876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                         AAA_7  34 kpvllvGptGtGKtviikdllkk 56 
                                   + vll Gp GtGKt+++k + ++
  gi|14601365|ref|NP_147901.1| 494 RGVLLFGPPGTGKTLLAKAVATE 516
                                   679*************9986654 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00015     0.049     117     141 ..     221     245 ..     216     250 .. 0.90
   2 !    7.7   0.0    0.0053       1.7     117     136 ..     496     515 ..     489     520 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                     Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                   +++yGp+ tGkt la+a+a+ +  y
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGAY 245
                                   89*****************987765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0053
                     Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                   v+++Gp+ tGkt la+a a+
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVAT 515
                                   8899*************987 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00052      0.16       2      31 ..     221     250 ..     220     307 .. 0.83
   2 !    8.5   0.0    0.0054       1.7       2      30 ..     496     524 ..     495     568 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00052
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                   +ll g PG++ktll+kala+ +++ f  i 
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIGAYFISIN 250
                                   7999******************99987764 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0054
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   vll g PG++ktll+ka+a+  +++f  +
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGANFIAV 524
                                   7999***************9999988665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.5e-05     0.017       4      69 ..     221     279 ..     218     305 .. 0.72
   2 ?    6.0   0.0     0.019       5.9       6      25 ..     498     517 ..     494     549 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-05
                       DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafeklss 69 
                                   +l  G +GtGKt+++ +l++e+        a ++s N+p+++ +++ + +++  ++ +kea e+  s
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEI-------GAYFISINGPEIMsKYYGESEQRL-REIFKEAEENAPS 279
                                   6789******************.......888999999987735555555555.6666655554433 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.019
                       DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                     G +GtGKt+++ ++++e 
  gi|14601365|ref|NP_147901.1| 498 LFGPPGTGKTLLAKAVATES 517
                                   5699*********9999886 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0028      0.88      23      40 ..     222     239 ..     214     244 .. 0.86
   2 !   11.1   0.1   0.00063       0.2      22      42 ..     496     516 ..     489     524 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0028
                                   EEE--TTSSTTHHHHHHH CS
                          PhoH  23 faiGpaGtGKtylavala 40 
                                      Gp GtGKt+la ala
  gi|14601365|ref|NP_147901.1| 222 LLYGPPGTGKTLLAKALA 239
                                   578***********9998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00063
                                   EEEE--TTSSTTHHHHHHHHH CS
                          PhoH  22 vfaiGpaGtGKtylavalave 42 
                                   v  +Gp GtGKt+la a+a e
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATE 516
                                   6789*************9976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0022      0.71       3      24 ..     221     242 ..     219     245 .. 0.90
   2 ?    0.1   0.0       2.1   6.6e+02      62     125 ..     259     323 ..     253     366 .. 0.58
   3 !    7.9   0.1    0.0082       2.6       3      23 ..     496     516 ..     494     520 .. 0.88
   4 ?   -1.4   0.0       6.3     2e+03      62      99 ..     534     570 ..     527     591 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0022
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                   ++l G++G GKT L++ la ++
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEI 242
                                   7899**************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.1
                                   CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT--EEEE CS
                         NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllpeaslll 125
                                   + e++++ +e++++  e++ ++ + +D +D ++ + ++      +++v   L +l+ + l  + ++++
  gi|14601365|ref|NP_147901.1| 259 YGESEQRLREIFKEAEENAPSIIF-IDEIDAIAPKREEvtgeV-EKRVVAQLLTLMDG-LKERGRVIV 323
                                   667777788888888888888877.488888888777787743.44444444466666.333334443 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0082
                                   EEEEC-TTTCHHHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                   v+l G++G GKT L++ +a++
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATE 516
                                   7899************99976 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 6.3
                                   CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                         NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq 99 
                                     e+++++++ + ++++++  ++  +D +D ++   g+
  gi|14601365|ref|NP_147901.1| 534 VGESERAIRK-IFERARQAAPAVVFFDEIDAIAPARGA 570
                                   4455555655.888999999999999**9999887776 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 !   14.2   0.0   9.7e-05      0.03      13     122 ..     211     324 ..     207     334 .. 0.66
   2 ?    4.2   0.0      0.11        35      23      43 ..     496     516 ..     483     524 .. 0.82
   3 ?   -1.9   0.0       8.1   2.5e+03     108     130 ..     539     564 ..     517     573 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.7e-05
                      ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialr..eesiskldefieeeeekkklekal......... 82 
                                   + l  ep + +++YGp g GKt L k ++++         y+i+++  e+ ++++ e+      +++l++ +         
  gi|14601365|ref|NP_147901.1| 211 KHLGIEPPKGILLYGPPGTGKTLLAKALANEIG------AYFISINgpEIMSKYYGES------EQRLREIFkeaeenaps 279
                                   556667888899***************999983......3444444004444444444......22222222222455555 PP

                      ATPase_2  83 .....giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                         i+    + ee+  e  k v +++  l++ +k++g+ i+i
  gi|14601365|ref|NP_147901.1| 280 iifidEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKERGRVIVI 324
                                   566664444444555667788899999999999999999987666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                      ATPase_2  23 yfiYGpegsGKtaLlkeiien 43 
                                   ++++Gp g GKt L k ++++
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATE 516
                                   789***********9998876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 8.1
                      ATPase_2 108 lllekikkkgkk...iiiiiDelqkl 130
                                   ++++ki +++++    ++++De+  +
  gi|14601365|ref|NP_147901.1| 539 RAIRKIFERARQaapAVVFFDEIDAI 564
                                   44555555555556578888998766 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     0.001      0.32      14      50 ..     216     250 ..     207     264 .. 0.86
   2 !    8.2   0.0    0.0043       1.3      16      49 ..     493     524 ..     482     529 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.001
                    Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                   e Pk ill G pG GK+ la++l++e+  +  ++ ++
  gi|14601365|ref|NP_147901.1| 216 EPPKGILLYGPPGTGKTLLAKALANEI--GAYFISIN 250
                                   6799**********************9..56666665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0043
                    Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                   P  +ll G pG GK+ la+++++e   + n++ +
  gi|14601365|ref|NP_147901.1| 493 PRGVLLFGPPGTGKTLLAKAVATES--GANFIAV 524
                                   77899*******************8..7777766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0016      0.51      36      54 ..     221     239 ..     215     242 .. 0.89
   2 ?    4.4   0.1     0.076        24     128     176 ..     264     312 ..     252     327 .. 0.84
   3 !    9.0   1.2     0.003      0.95      36      65 ..     496     523 ..     472     601 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0016
                        AAA_25  36 allaGapgtGKttlaldla 54 
                                   +ll+G+pgtGKt la  la
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALA 239
                                   69************98887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.076
                        AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                   + ++++ +++ee + +  + iD ++++ +  e+   +v +++v++l  + 
  gi|14601365|ref|NP_147901.1| 264 QRLREIFKEAEE-NAPSIIFIDEIDAIAPKREEVTGEVeKRVVAQLLTLM 312
                                   456788899999.77***************99999998899999887664 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.003
                        AAA_25  36 allaGapgtGKttlaldlalavatGkpwlg 65 
                                   +ll+G+pgtGKt la  +a  + +G ++  
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVA--TESGANFIA 523
                                   689*********9985444..445565544 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0022       0.7       1      26 [.     224     249 ..     224     305 .. 0.77
   2 ?    6.7   0.0     0.028       8.9       1      24 [.     499     522 ..     499     599 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0022
                                   EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                   +G+PG GK+ +++ l+ ++g  ++s 
  gi|14601365|ref|NP_147901.1| 224 YGPPGTGKTLLAKALANEIGAYFISI 249
                                   7******************9888775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.028
                                   EE-TTSSHHHHHHHHHHHHTEEEE CS
                        AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                   +G+PG GK+ +++ ++ + g  ++
  gi|14601365|ref|NP_147901.1| 499 FGPPGTGKTLLAKAVATESGANFI 522
                                   6***********999998876655 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.012       3.6      24      46 ..     221     243 ..     216     296 .. 0.76
   2 !    8.5   0.0    0.0064         2      24      79 ..     496     562 ..     491     571 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                                   EEEEEETT--HHHHHHCC--TTS CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsg 46 
                                   ++l G++G+gk+l A++L+++ g
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIG 243
                                   799***************98754 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0064
                                   EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.........HHHHHH...TTTSEEEEEE-T CS
               Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp.........ldlleq...akggtLylkdia 79 
                                   v+l G++G+gk+l A++ + +sg +   +v    + +           +++e+   a +++ ++ +i+
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATESGANFI-AVRGPEILSKwvgeseraiRKIFERarqAAPAVVFFDEID 562
                                   9*****************999987532.2222222211223333444444444222466666666666 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0043       1.4      20      41 ..     221     242 ..     208     280 .. 0.78
   2 ?    7.4   0.0     0.011       3.3      19      41 ..     495     517 ..     468     554 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0043
                        AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                    l+ GPPGtgKT    +l +++
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEI 242
                                   5899********8887777776 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                        AAA_11  19 itliqGPPGtgKTktivellsql 41 
                                    +l+ GPPGtgKT    ++  + 
  gi|14601365|ref|NP_147901.1| 495 GVLLFGPPGTGKTLLAKAVATES 517
                                   46899********7666655555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0082       2.6      22      40 ..     222     240 ..     208     250 .. 0.83
   2 ?    7.3   0.1     0.011       3.4      21      40 ..     496     515 ..     484     526 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0082
                        AAA_30  22 vltGpAGtGKttalkalre 40 
                                   +l Gp+GtGKt + kal++
  gi|14601365|ref|NP_147901.1| 222 LLYGPPGTGKTLLAKALAN 240
                                   789**********999976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                        AAA_30  21 avltGpAGtGKttalkalre 40 
                                   ++l Gp+GtGKt + ka++ 
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVAT 515
                                   6788*********9999864 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.016       5.2      11      31 ..     219     239 ..     215     280 .. 0.84
   2 ?   -1.6   0.0       9.7   3.1e+03      98     125 ..     273     300 ..     255     314 .. 0.67
   3 ?    7.9   0.0     0.012       3.6      12      31 ..     495     514 ..     488     572 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                        AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                   k +l+ ++pGtGKT + k+  
  gi|14601365|ref|NP_147901.1| 219 KGILLYGPPGTGKTLLAKALA 239
                                   56899*********9877665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.7
                        AAA_19  98 kklqeeellivDEfqdvdelqyrLlkal 125
                                    + ++  ++++DE+  + +   ++  ++
  gi|14601365|ref|NP_147901.1| 273 AEENAPSIIFIDEIDAIAPKREEVTGEV 300
                                   3333455999***999887766665555 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.012
                        AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                    +l+ ++pGtGKT + k++ 
  gi|14601365|ref|NP_147901.1| 495 GVLLFGPPGTGKTLLAKAVA 514
                                   5899*********8877655 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 !   10.7   0.0   0.00059      0.18      37      69 ..     223     255 ..     215     262 .. 0.88
   2 ?    2.5   0.0      0.19        59      34      62 ..     495     523 ..     470     563 .. 0.87
   3 ?   -1.6   0.1       3.2     1e+03     217     266 ..     669     720 ..     664     722 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                         AAA_6  37 paGpagtGKtEtvkdLakalakqvvvfncsdql 69 
                                   ++Gp gtGKt   k La++++ +++ +n  + +
  gi|14601365|ref|NP_147901.1| 223 LYGPPGTGKTLLAKALANEIGAYFISINGPEIM 255
                                   68***********************99977655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                         AAA_6  34 ggapaGpagtGKtEtvkdLakalakqvvv 62 
                                   g  + Gp gtGKt   k +a + +  ++ 
  gi|14601365|ref|NP_147901.1| 495 GVLLFGPPGTGKTLLAKAVATESGANFIA 523
                                   55678999****99999999887776665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
                         AAA_6 217 ksvlkaagelk.re..epeeseeelllralrdvnlpklvaeDvplfkglisdl 266
                                   ++v++ a  +k re  e  + e   +l+al++v  p l++eD+  +++l ++l
  gi|14601365|ref|NP_147901.1| 669 EAVVREAVMAKlREklEVGKVEMRHFLEALKKV-PPSLTKEDILRYERLAKEL 720
                                   566666555531331245577999999999998.799******9999998876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.011       3.6       5      32 ..     222     249 ..     219     251 .. 0.91
   2 !    7.6   0.0    0.0073       2.3       5      31 ..     497     523 ..     494     531 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.011
                           IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                   l++G+ +tGKt  a +la+e ga  i++
  gi|14601365|ref|NP_147901.1| 222 LLYGPPGTGKTLLAKALANEIGAYFISI 249
                                   89********************988875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0073
                           IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                   l+fG+ +tGKt  a ++a e ga  i+
  gi|14601365|ref|NP_147901.1| 497 LLFGPPGTGKTLLAKAVATESGANFIA 523
                                   89********************99987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0062         2      47      80 ..     220     252 ..     193     273 .. 0.80
   2 ?   -1.5   0.0       6.6   2.1e+03     141     177 ..     254     288 ..     252     295 .. 0.70
   3 ?    5.5   0.0     0.046        15      46      79 ..     494     527 ..     481     568 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0062
                         Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewlnpv 80 
                                    +L+ GP+G gk+   k L+ e g  ++  +n+ 
  gi|14601365|ref|NP_147901.1| 220 GILLYGPPGTGKTLLAKALANEIGAYFIS-INGP 252
                                   46889*****************9987765.4554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.6
                         Rad17 141 lPnkfyrds.dalrevirkylrssealplilviteies 177
                                   + +k+y++s ++lre+ +++     a p i+ i ei+ 
  gi|14601365|ref|NP_147901.1| 254 IMSKYYGESeQRLREIFKEAEEN--A-PSIIFIDEIDA 288
                                   66888888878999988876433..3.55667777775 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.046
                         Rad17  46 riLLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                   r +L+ GP+G gk+   k ++ e g +++    p
  gi|14601365|ref|NP_147901.1| 494 RGVLLFGPPGTGKTLLAKAVATESGANFIAVRGP 527
                                   557899****************999988876665 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.34   1.1e+02      52      81 ..      15      44 ..       9      44 .. 0.88
   2 !   10.5   0.0    0.0015      0.47      50      81 ..      57      88 ..      54      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.34
                                  ESSTT-EEEEE-HHHHHHHT--TTSEEEEE CS
                       DUF1905 52 pmgkggyiLpvkaavrkaigkeaGdtvtve 81
                                  p + g+ i+ ++++  +++g+e+Gd v+v+
  gi|14601365|ref|NP_147901.1| 15 PRDVGRKIVRIDRQTAARLGVEVGDFVKVS 44
                                  55558999*******************995 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0015
                                  EEESSTT-EEEEE-HHHHHHHT--TTSEEEEE CS
                       DUF1905 50 lfpmgkggyiLpvkaavrkaigkeaGdtvtve 81
                                  l p+++g+ i+ ++  +r+a+g+++Gdtvtve
  gi|14601365|ref|NP_147901.1| 57 LRPDDEGRGIIRMDGYLRAALGVTVGDTVTVE 88
                                  568889999*********************96 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0066       2.1       3      28 ..     223     248 ..     221     251 .. 0.89
   2 ?    5.4   0.0     0.042        13       5      27 ..     500     522 ..     496     525 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0066
                                   EE-STTSSHHHHHHHHHHHHT-EEEE CS
                Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                   + GP g+GK  +a+ala+++g+ +++
  gi|14601365|ref|NP_147901.1| 223 LYGPPGTGKTLLAKALANEIGAYFIS 248
                                   67*******************99875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.042
                                   -STTSSHHHHHHHHHHHHT-EEE CS
                Cytidylate_kin   5 GPagsGKssvaralaeklglkyl 27 
                                   GP g+GK  +a+a+a++ g++++
  gi|14601365|ref|NP_147901.1| 500 GPPGTGKTLLAKAVATESGANFI 522
                                   9****************999987 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0047       1.5       8      66 ..     227     289 ..     221     326 .. 0.68
   2 ?    4.2   0.0      0.14        43       8      55 ..     502     549 ..     498     601 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0047
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde...rsrlssflskllaa 66 
                                    G+g++ +++aLA++ g  f++ + +e ++k  g se+ + e ++e   ++++  f++++ a 
  gi|14601365|ref|NP_147901.1| 227 PGTGKTLLAKALANEIGAYFISINGPEIMSKYYGESEQRLrEIFKEaeeNAPSIIFIDEIDAI 289
                                   69********************99888888888888888764444432255555555555444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.14
               Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevdersr 55 
                                    G+g++ +++a+A++ g +f+  + +e ++k  g se  ++++ er+r
  gi|14601365|ref|NP_147901.1| 502 PGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESERAIRKIFERAR 549
                                   59*********************9999999999999999977777544 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0012      0.36      23      54 ..      13      45 ..       2      56 .. 0.74
   2 ?    1.6   0.0      0.89   2.8e+02      32      53 ..      67      88 ..      56     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                                  HHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEE CS
               Molydop_binding 23 rlakpep.evveinpedAaalGikdGdlVeves 54
                                  ++ ++ + + v+i  ++Aa+lG++ Gd V+v+ 
  gi|14601365|ref|NP_147901.1| 13 AYPRDVGrKIVRIDRQTAARLGVEVGDFVKVSK 45
                                  4444455689********************975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.89
                                  EEEEHHHHHHHT--TT-EEEEE CS
               Molydop_binding 32 veinpedAaalGikdGdlVeve 53
                                  +++     aalG++ Gd+V+ve
  gi|14601365|ref|NP_147901.1| 67 IRMDGYLRAALGVTVGDTVTVE 88
                                  5666666699**********98 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0     0.008       2.5       1      44 [.     227     275 ..     227     277 .. 0.70
   2 ?    4.4   0.0      0.12        37       1      22 [.     502     523 ..     502     551 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.008
                                   TTSSHHHHHHHHHHHHTSEEEEHHH..HHHHHHT...S-HHHHHHHHHH CS
                           SKI   1 mGaGKstvGkllAkklglefiDlDe..liekrtg...ksiaeifeeege 44 
                                   +G+GK+ ++k+lA+++g  fi +    +++k  g   ++ +eif+e  e
  gi|14601365|ref|NP_147901.1| 227 PGTGKTLLAKALANEIGAYFISINGpeIMSKYYGeseQRLREIFKEAEE 275
                                   69******************98753315566555333556677766655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.12
                                   TTSSHHHHHHHHHHHHTSEEEE CS
                           SKI   1 mGaGKstvGkllAkklglefiD 22 
                                   +G+GK+ ++k++A + g +fi 
  gi|14601365|ref|NP_147901.1| 502 PGTGKTLLAKAVATESGANFIA 523
                                   69*****************985 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.014       4.4      23      43 ..     221     241 ..     206     249 .. 0.82
   2 ?    4.9   0.0     0.039        12      23      43 ..     496     516 ..     486     522 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.014
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   + l+G +G GKt lak   n+
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANE 241
                                   789************998876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                                   EEEEESTTSSHHHHHHHHCCS CS
                        NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                   v l G +G GKt lak +  +
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATE 516
                                   6789************99876 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     0.073        23       2      24 ..     221     243 ..     220     255 .. 0.82
   2 ?    1.3   0.2      0.89   2.8e+02      81     118 ..     262     300 ..     253     318 .. 0.73
   3 ?    4.8   0.0     0.077        24       2      23 ..     496     517 ..     495     548 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.073
                                   EEEE--TTSSHHHHHHHHHHHH. CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                   +++ GppG+GKt l k +++++ 
  gi|14601365|ref|NP_147901.1| 221 ILLYGPPGTGKTLLAKALANEIG 243
                                   6788**********999999875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.89
                                   HHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHH CS
                      NTPase_1  81 feelalealrkal.seadviviDEiGkmElkskkfkeav 118
                                    e+   e++++a  + + +i iDEi  +  k +++  +v
  gi|14601365|ref|NP_147901.1| 262 SEQRLREIFKEAEeNAPSIIFIDEIDAIAPKREEVTGEV 300
                                   566777778887745566*******77666555555555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.077
                                   EEEE--TTSSHHHHHHHHHHHH CS
                      NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                   v++ GppG+GKt l k v+ + 
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVATES 517
                                   6788********9999998765 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.12        38       4      30 ..     220     246 ..     218     254 .. 0.86
   2 ?    1.3   0.0      0.74   2.3e+02      75      95 ..     255     275 ..     249     297 .. 0.79
   3 ?    3.2   0.0       0.2        63       3      30 ..     494     521 ..     492     529 .. 0.87
   4 ?   -0.6   0.0       2.8   8.8e+02      77      96 ..     532     551 ..     525     567 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                                   EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                    + l gp g+Gk  l kaL +e   +f
  gi|14601365|ref|NP_147901.1| 220 GILLYGPPGTGKTLLAKALANEIGAYF 246
                                   6899***************99988877 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.74
                                   TTEEEEEEHHHHHHHHHTTSE CS
                 Guanylate_kin  75 sgnlygtsveaieevlekgki 95 
                                    +++yg+s +  +e+++++ +
  gi|14601365|ref|NP_147901.1| 255 MSKYYGESEQRLREIFKEAEE 275
                                   679*************99876 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.2
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                 Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                   r v l gp g+Gk  l ka+ +e   +f
  gi|14601365|ref|NP_147901.1| 494 RGVLLFGPPGTGKTLLAKAVATESGANF 521
                                   6789***************999988777 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.8
                                   EEEEEEHHHHHHHHHTTSEE CS
                 Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                   +  g+s  ai++++e ++++
  gi|14601365|ref|NP_147901.1| 532 KWVGESERAIRKIFERARQA 551
                                   567999*********99984 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.027       8.6      58      79 ..     214     235 ..     186     242 .. 0.85
   2 ?    5.0   0.0     0.029       9.2      58      79 ..     489     510 ..     463     516 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.027
                   AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                     ep++g+ l+G+ G GKt l 
  gi|14601365|ref|NP_147901.1| 214 GIEPPKGILLYGPPGTGKTLLA 235
                                   468****************985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                   AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                     +p+rg+ l G+ G GKt l 
  gi|14601365|ref|NP_147901.1| 489 GIRPPRGVLLFGPPGTGKTLLA 510
                                   5679***************985 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0067       2.1     129     156 ..     218     245 ..     153     253 .. 0.84
   2 ?    2.9   0.0      0.15        48     131     152 ..     495     516 ..     400     524 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0067
                         T2SSE 129 rglilvsGgTgsGKttllyallkeinks 156
                                    + il+ G+ g+GKt l+ al +ei ++
  gi|14601365|ref|NP_147901.1| 218 PKGILLYGPPGTGKTLLAKALANEIGAY 245
                                   4679******************999775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                         T2SSE 131 lilvsGgTgsGKttllyallke 152
                                    +l+ G+ g+GKt l+ a+ +e
  gi|14601365|ref|NP_147901.1| 495 GVLLFGPPGTGKTLLAKAVATE 516
                                   57888*********99988765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.021       6.5       2      24 ..     219     241 ..     218     247 .. 0.88
   2 ?    4.2   0.0      0.11        34       4      23 ..     496     515 ..     493     518 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                     PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                   k ill G+ g+GKt L++al +e
  gi|14601365|ref|NP_147901.1| 219 KGILLYGPPGTGKTLLAKALANE 241
                                   6699****************987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                     PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                   +ll+G+ g+GKt L++a+  
  gi|14601365|ref|NP_147901.1| 496 VLLFGPPGTGKTLLAKAVAT 515
                                   89**************9876 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.13        41       4      71 ..     224     286 ..     221     291 .. 0.75
   2 ?    6.9   0.0     0.015       4.7       4      71 ..     499     561 ..     496     567 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
               Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+ l + l+++    + +++   e+ ++   +++++  + ++++++++       i+++DE+
  gi|14601365|ref|NP_147901.1| 224 YGPPGTGKTLLAKALANEIgAYFISING-PEIMSKYYGESEQRLREIFKEAEENAP-----SIIFIDEI 286
                                   588*************998844444444.477777777888888888888888764.....38999987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
               Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++   + ++ + +a+       ++++DE+
  gi|14601365|ref|NP_147901.1| 499 FGPPGTGKTLLAKAVATESgANFIAVRG-PEILSKWVGESERAIRKIFERARQAAP-----AVVFFDEI 561
                                   588*************999*88888888.9******98888887777777777665.....48999997 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.26        80      43      68 ..      29      54 ..      23      62 .. 0.76
   2 ?    7.1   0.0     0.016       5.1      46      65 ..      76      95 ..      71     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.26
                                  XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                 DNA_ligase_OB 43 eierkdirigdtVvvekaGdvIPevv 68
                                    +r+++++gd V v+k+   +  vv
  gi|14601365|ref|NP_147901.1| 29 TAARLGVEVGDFVKVSKGDRSVVAVV 54
                                  56799************987654443 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                                  XXXXXXXXXXXXXXXXXXXX CS
                 DNA_ligase_OB 46 rkdirigdtVvvekaGdvIP 65
                                   +++ +gdtV+veka +v P
  gi|14601365|ref|NP_147901.1| 76 ALGVTVGDTVTVEKAEKVEP 95
                                  5799***********99876 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     0.087        27      21      39 ..     218     235 ..     209     240 .. 0.77
   2 ?    5.2   0.0     0.056        18      21      42 ..     493     513 ..     483     515 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.087
                        AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                   +kg +ll Gp G+GK+ l 
  gi|14601365|ref|NP_147901.1| 218 PKG-ILLYGPPGTGKTLLA 235
                                   456.9**********8765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.056
                        AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                   ++g +ll Gp G+GK+ l  A+
  gi|14601365|ref|NP_147901.1| 493 PRG-VLLFGPPGTGKTLLAKAV 513
                                   356.9**********8776555 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 ?    5.0   0.0     0.068        21      22      47 ..     216     241 ..     188     249 .. 0.74
   2 ?    3.5   0.0      0.21        65      22      46 ..     491     515 ..     464     560 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.068
                                   .TTSEEEEEESTTSTHHHHHHHHHHH CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklier 47 
                                   +  k +l+  + GtGKTl+a +l+ +
  gi|14601365|ref|NP_147901.1| 216 EPPKGILLYGPPGTGKTLLAKALANE 241
                                   778899999**********9887765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.21
                                   .TTSEEEEEESTTSTHHHHHHHHHH CS
                        ResIII  22 krdkrglikmaTGtGKTlvaaklie 46 
                                   +  + +l+  + GtGKTl+a +++ 
  gi|14601365|ref|NP_147901.1| 491 RPPRGVLLFGPPGTGKTLLAKAVAT 515
                                   555677788999******9955544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        57  (0.00317921); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              57  [number of targets reported over threshold]
# CPU time: 0.83u 0.28s 00:00:01.10 Elapsed: 00:00:00.45
# Mc/sec: 4881.60
//
Query:       gi|118431429|ref|NP_147903.2|  [L=176]
Description: hypothetical protein APE_1372.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1324.55
//
Query:       gi|14601368|ref|NP_147904.1|  [L=453]
Description: hypothetical protein APE_1373 [Aeropyrum pernix K1]
Scores for 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-36  123.5  24.8      9e-36  123.5  24.8    3.1  2  DUF4010   Domain of unknown function (DUF4010)
    4.5e-11   43.2  15.1    4.5e-11   43.2  15.1    3.3  3  MgtC      MgtC family


Domain annotation for each model (and alignments):
>> DUF4010  Domain of unknown function (DUF4010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.0  15.8         2   1.8e+04       7      48 ..      58      98 ..      55     184 .. 0.70
   2 !  123.5  24.8     1e-39     9e-36       2     210 .]     198     417 ..     197     417 .. 0.93

  Alignments for each domain:
  == domain 1  score: -10.0 bits;  conditional E-value: 2
                       DUF4010  7 sfagYvalrllgarrGllltgllGGlvSStAvtlslarrske 48
                                  s +gYv +    +  G+++++l++Gl   t + l+l    ++
  gi|14601368|ref|NP_147904.1| 58 SATGYVSSYTASQ-YGVVFAALIAGLGAATITLLTLLFAYTR 98
                                  5678887766655.9999999999999999998888655554 PP

  == domain 2  score: 123.5 bits;  conditional E-value: 1e-39
                       DUF4010   2 lisaisfagYvalrllgarrGllltgllGGlvSStAvtlslarrskeepelarllaagillAnavmllrvllivavvnpal 82 
                                   +i+a+sf++Y+a+r++g  rG++++ +lG++v+S+Av++s+a+r +    +++++++++++A +vm lr++ + ++   al
  gi|14601368|ref|NP_147904.1| 198 AIVAVSFTSYIASRIWGV-RGFVTSIILGSIVNSEAVVASIASRRDI---DRGVVFQAVVAALSVMQLRIAGLGLL---AL 271
                                   599***************.****************************...899******************99999...55 PP

                       DUF4010  83 lvala.................lpllalallallvaalllrrrekeeeeeelelenPlelksAlkfallfalilll....a 142
                                   lv                    l llal+++a +va+++++  ek e++  + +++Pl+++ A++ a++f+l++ll    +
  gi|14601368|ref|NP_147904.1| 272 LVGGGfpqgevvlhfrdnilpwLILLALMTIASIVAWASTLALEKVENKG-VIPGTPLQWGVAVRGAVAFLLLTLLfdaaS 351
                                   5544455666667777777555669999*********************9.************************988889 PP

                       DUF4010 143 kaaqeyfGdaglyalaalsGladvdAitlslarlaaegtlsaataalaillavlsntlvKavlalviG 210
                                   +a++ y+G+ ++++l++++G+++++A++lsla l+  ++l a+t++++il ++l  t++K+++++++G
  gi|14601368|ref|NP_147904.1| 352 RALSGYTGNIAFLTLSIIGGFISANATLLSLAGLL--TRLGADTFTVGILGIALGATFNKILYTRAVG 417
                                   99********************************9..7**************************9987 PP

>> MgtC  MgtC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2  15.1     5e-15   4.5e-11       2     119 ..      16     149 ..      15     151 .. 0.83
   2 ?   -1.8   1.0      0.41   3.7e+03      64      64 ..     226     226 ..     164     284 .. 0.63
   3 ?    1.6   6.3     0.039   3.5e+02      53     107 ..     334     387 ..     294     418 .. 0.62

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 5e-15
                          MgtC   2 llAlllGlliGleRel......rek....aaGlRTfaLvalgaalfvllslelae..srvaaqvvsgigflg..agvilke 68 
                                   +  ll+G+liG+eRe+      + +      G+R + +++l +++  ++s+++a+    v+a +++g+g  +   +++l  
  gi|14601368|ref|NP_147904.1|  16 ATGLLVGALIGIERERaqlvgkS-EksgsIPGFRSMGFMGLYGSATGYVSSYTASqyGVVFAALIAGLGAATitLLTLLFA 95 
                                   6789************6555431.14666********************99998899778888887777766665555555 PP

                          MgtC  69 kega...kvkglTTaaslwvtaaiGllvglglyllavvatvlvllllallrele 119
                                   +++    +  g+TT +++++t++ Gl+ g+gl+l++v++ v+  llla + ++ 
  gi|14601368|ref|NP_147904.1|  96 YTRMirlRAMGFTTYVVILLTFVAGLMSGMGLILEGVAVGVIGGLLLASKYPVV 149
                                   55556789***********************************99999988775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.41
                          MgtC  64 v 64 
                                    
  gi|14601368|ref|NP_147904.1| 226 S 226
                                   1 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.039
                          MgtC  53 vvsgigflgagvilkekegakvkglTTaaslwvtaaiGllvglglyllavvatvl 107
                                   v  +++fl   +++    +++ +g T  +++++  +iG  + ++  ll++++ ++
  gi|14601368|ref|NP_147904.1| 334 VRGAVAFLLLTLLF-DAASRALSGYTGNIAFLTLSIIGGFISANATLLSLAGLLT 387
                                   33334444444444.5555688888888888888888888888877777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3424.16
//
Query:       gi|118431430|ref|YP_874890.1|  [L=87]
Description: hypothetical protein APE_1373a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.1   0.0      0.071   12.9   0.0    1.2  1  PAS_5     PAS domain
       0.12   12.1   0.0       0.15   11.8   0.0    1.2  1  SpoVS     Stage V sporulation protein S (SpoVS)


Domain annotation for each model (and alignments):
>> PAS_5  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     8e-06     0.071      36      64 ..      17      45 ..       3      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8e-06
                          PAS_5 36 lLgdvFilerdaegelrfRlAGtrlcall 64
                                    L+ + ++e++++g +r+R  G+ +c+l+
  gi|118431430|ref|YP_874890.1| 17 DLAITLVVECKERGRVRLRAVGSEVCTLF 45
                                   467788*********************98 PP

>> SpoVS  Stage V sporulation protein S (SpoVS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.6e-05      0.15       3      36 ..       7      40 ..       5      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                                   EEE-TT--HHHHHHHHHHHHHHTSEEEEEE-SHH CS
                          SpoVS  3 LkvssksnpnkvagAiagvlrekgkvevqaiGag 36
                                   ++v    np+ +a  ++   +e+g+v ++a+G +
  gi|118431430|ref|YP_874890.1|  7 IRVKDGVNPEDLAITLVVECKERGRVRLRAVGSE 40
                                   7999999*************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 733.09
//
Query:       gi|118431431|ref|NP_147906.2|  [L=1215]
Description: reverse gyrase [Aeropyrum pernix K1]
Scores for 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-81  272.3   0.0      1e-80  271.8   0.0    1.2  1  Topoisom_bac    DNA topoisomerase
    2.9e-22   78.8   0.0    8.9e-22   77.3   0.0    1.9  2  Toprim          Toprim domain
    9.7e-13   47.3   1.9    9.7e-13   47.3   1.9    1.8  1  zf_Rg           Reverse gyrase zinc finger
    1.3e-11   44.6   0.0    3.4e-11   43.2   0.0    1.8  1  DEAD            DEAD/DEAH box helicase
    2.4e-05   24.4   0.0    5.1e-05   23.3   0.0    1.4  1  ResIII          Type III restriction enzyme, res subunit
    0.00017   21.2   2.6    0.00017   21.2   2.6    1.9  2  zinc_ribbon_2   zinc-ribbon domain
    0.00071   20.0   0.0      0.026   15.0   0.0    3.1  2  Toprim_4        Toprim domain
     0.0016   18.0   0.0     0.0053   16.3   0.0    1.9  1  AAA_25          AAA domain
     0.0023   17.7   0.1      0.013   15.3   0.1    2.2  2  AAA_30          AAA domain
     0.0026   18.4   0.2     0.0077   16.9   0.2    1.8  1  CarD_CdnL_TRCF  CarD-like/TRCF domain
     0.0026   18.1   0.0       0.14   12.5   0.0    3.4  4  Helicase_C      Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.015   15.3   0.4      0.015   15.3   0.4    2.1  2  DZR             Double zinc ribbon
      0.065   13.0   0.0       0.17   11.6   0.0    1.6  1  IstB_IS21       IstB-like ATP binding protein
      0.077   13.8   0.8       0.12   13.2   0.2    1.6  1  zinc_ribbon_15  zinc-ribbon family
       0.11   12.1   5.2       0.14   11.8   0.7    3.1  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.16   12.3   0.1          1    9.6   0.1    2.4  1  AAA_22          AAA domain
       0.17   12.2   0.0       0.48   10.7   0.0    1.8  1  AAA_19          AAA domain
        3.6    7.1  11.9       0.33   10.4   4.1    2.3  2  zf-ribbon_3     zinc-ribbon domain
        4.3    7.3  10.7       0.35   10.8   5.4    1.9  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !  271.8   0.0   1.1e-83     1e-80       3     412 ..     799    1189 ..     797    1190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 271.8 bits;  conditional E-value: 1.1e-83
                   Topoisom_bac    3 nenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekkek 80  
                                     +++l++a+++Rr++D++iG++ls  l++k + k +l aGRVqtp+L++iv+R+re ++   + y  +  +l ++++  
  gi|118431431|ref|NP_147906.2|  799 EKSLIEAQKVRRIVDRWIGFHLSTHLKLKFS-KPWLGAGRVQTPVLGWIVDRYREWQDT--RGYLVIF-KLSSGGR-- 870 
                                     6789***********************9777.7***********************997..8899995.5433332.. PP

                   Topoisom_bac   81 ekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYeka 158 
                                             + +++++   + l+++  + ++v+++  k+++++pp p++t++ + +asrklglsa  +++iaq+L+e+ 
  gi|118431431|ref|NP_147906.2|  871 -------TSYFTQNRLEVENLKRV--EWLEVVDIAGKTEERNPPPPYTTDEYLYDASRKLGLSAGLAMKIAQDLFES- 938 
                                     .......23333333333444445..4799*******99997777*******************************7. PP

                   Topoisom_bac  159 glitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkels... 233 
                                     glitY+RTdstr+s++  +k +le+la++ g  +++    +  +++++    ++  +aHeAIrP++ ++ + +l+   
  gi|118431431|ref|NP_147906.2|  939 GLITYHRTDSTRVSPTG-VKLALEYLASR-G--LEG----EA-QPRGW----GEG-GAHEAIRPVRPIDAQ-DLErav 1001
                                     *****************.9********95.3..222....33.36666....555.9*********99953.444467 PP

                   Topoisom_bac  234 ............ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeel 299 
                                                 + + ++Y++I+rrf+as+mk+a+ + ++++l+++e  f+  g   +  G+  v + + +e     l
  gi|118431431|ref|NP_147906.2| 1002 lsgsiripirltRLHIRVYDMIFRRFIASQMKPATLDIVEATLQAGETVFNHAGVARVRGGYALVNPPRVEE----WL 1075
                                     89999****99955556************************************************9865544....49 PP

                   Topoisom_bac  300 pelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverk.k.kslvptelGkal 375 
                                      +l+ g++++v++  +   k +    y  ++++k+m ++giG+p+T+a+ ie+  ++gYv ++ k ++l+pt++G ++
  gi|118431431|ref|NP_147906.2| 1076 ARLSPGDRIDVED--VLVVKSSLKRLYRAGDIVKMMREHGIGRPSTYAKAIEQNRRHGYVIESkKmRYLIPTKTGVSI 1151
                                     9************..777888999***********************************998856999********** PP

                   Topoisom_bac  376 vell.ekfkdlvspelTaeleekLdeIaegkadakevl 412 
                                     ++ l + fk+lvs+++T++lee+L+++++g +++++vl
  gi|118431431|ref|NP_147906.2| 1152 YDYLsNGFKKLVSVDTTRRLEEALERVEKGVEKPEAVL 1189
                                     ****8888***************************998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0        10   9.4e+03      38      75 ..     196     233 ..     166     248 .. 0.58
   2 !   77.3   0.0   9.4e-25   8.9e-22       2     103 .]     620     783 ..     619     783 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 10
                                    TTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHH CS
                         Toprim  38 efkpvyeeiedkkkvlkalkelakradeiilatDpDre 75 
                                     + p+y+    + + +++l ++++++++i+l+t   +e
  gi|118431431|ref|NP_147906.2| 196 LLHPQYKFDLAIVDDVDSLLRNSRNVERILLLTGFSEE 233
                                    44477774445555566677777888888888866666 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 9.4e-25
                                    EEEESSHHHHHHHHHTHT........................STEEEEEEESSSSEEEHS...................T CS
                         Toprim   2 lvivEgpsdaktiakalg........................sgfqavtaslGhildlet...................e 38 
                                    l +vE+p++a+tia + g                           +++t+++Gh++dl+t                    
  gi|118431431|ref|NP_147906.2| 620 LLVVESPTKARTIAWFWGrpgkrrigrsviyeasvsdpetgdVHILQITSTRGHLTDLTTdsvgskygvdedgggyrayY 699
                                    89**************99*******************************************9999999999999555550 PP

                                    TEEEEE.........................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT CS
                         Toprim  39 fkpvye.........................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen 93 
                                                                      d k+v+++l++la+++dei++atDpDreGe+iaw+++ +++++++n
  gi|118431431|ref|NP_147906.2| 700 -----StikrcldcgaqhtssspfcprcgspRQVDSKSVVEILRKLASEVDEIVIATDPDREGEKIAWDVFLAVRPYNPN 774
                                    .....455555557777778888999999999999************************************999****** PP

                                    TEEEEEESSS CS
                         Toprim  94 kigrvefsei 103
                                     ++r +f+e+
  gi|118431431|ref|NP_147906.2| 775 -VRRGRFHEV 783
                                    .******995 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   1.9     1e-15   9.7e-13       2      35 ..       5      38 ..       4      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1e-15
                          zf_Rg  2 ikavfeklCPNCgGdisdeRlekGLpCkrClPke 35
                                   ++av+  lC NCgG+i ++RlekGLpC rClP +
  gi|118431431|ref|NP_147906.2|  5 VNAVYMGLCYNCGGNIDEDRLEKGLPCARCLPSP 38
                                   679*****************************86 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   3.6e-14   3.4e-11       3     145 ..      88     224 ..      86     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 3.6e-14
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                     Q++  + +++g+++ + a+TG GK++   + +          ++ ++l+++Pt+ L++q++ +l ++   i   + + +
  gi|118431431|ref|NP_147906.2|  88 AQRSWAKRLVKGDSFAIIAPTGVGKSTLLTVYAAYVA----AVKRGRVLYLVPTENLVRQVYAKLDQVEPGIATAYYSRM 163
                                    58888889999***************99888777444....56777*************************998888999 PP

                                    TTSSHHHHHHHHHTT.CSEEEEEHHHHHHHH...HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHH CS
                                    xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  83 ggvaardqlskldng.vdivvgtpgrlddll...stgklnlsqvrflVlDEadrlldqgfsdfinri 145
                                      +a+++ l+k+ +g ++++v+t+g l + +   +       ++ + ++D +d ll +  s+ ++ri
  gi|118431431|ref|NP_147906.2| 164 PAKARESSLEKIASGgARLIVATTGFLSRRFdllHP----QYKFDLAIVDDVDSLLRN--SRNVERI 224
                                    99**********8667********999985522122....446778**********98..5555554 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 !   23.3   0.0   5.4e-08   5.1e-05      13     140 ..      90     210 ..      77     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.4e-08
                                    HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG........GEEE CS
                         ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke....igkk 88 
                                    +++++ l   +   + i ++TG+GK+ +++  +++++   k+ ++l lvp+++l+ q + ++ ++ +  +++       k
  gi|118431431|ref|NP_147906.2|  90 RSWAKRLV--KGDSFAIIAPTGVGKSTLLTVYAAYVAA-VKRGRVLYLVPTENLVRQVYAKLDQVEPGIATAyysrMPAK 166
                                    55555553..55678899*******9888777777666.5667****************999999998776654432222 PP

                                    ESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
                         ResIII  89 vsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                                     ++    +  ++++s  ++++v+t+  l+++       +    + +fd+ i+D 
  gi|118431431|ref|NP_147906.2| 167 ARE----SslEKIASGGARLIVATTGFLSRRF------DLLHPQYKFDLAIVDD 210
                                    222....1234577999999999998888888......7777777888888876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       2.8   2.7e+03      16      20 ..      13      17 ..       6      20 .. 0.72
   2 !   21.2   2.6   1.8e-07   0.00017       1      22 [.     704     725 ..     704     725 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.8
                  zinc_ribbon_2 16 CpyCG 20
                                   C +CG
  gi|118431431|ref|NP_147906.2| 13 CYNCG 17
                                   99999 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.8e-07
                  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                    +C  CGa++   ++FCp+CG+p
  gi|118431431|ref|NP_147906.2| 704 RCLDCGAQHTSSSPFCPRCGSP 725
                                    699*****************97 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.75   7.1e+02      46      77 ..     213     245 ..     197     252 .. 0.77
   2 !   15.0   0.0   2.8e-05     0.026      49      71 ..     739     761 ..     724     777 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.75
                       Toprim_4  46 nlveaekkvkevilaldgDaeGeataerlae.l 77 
                                    +l+++  +v++++l++  ++e  ++a+ l++ +
  gi|118431431|ref|NP_147906.2| 213 SLLRNSRNVERILLLTGFSEETVEAAHSLVKaR 245
                                    344466789*******************99942 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.8e-05
                       Toprim_4  49 eaekkvkevilaldgDaeGeata 71 
                                    +  ++v+e+++a+d+D eGe+ a
  gi|118431431|ref|NP_147906.2| 739 KLASEVDEIVIATDPDREGEKIA 761
                                    256789**************988 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.7e-06    0.0053      25      78 ..      92     135 ..      72     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.7e-06
                         AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvs 78 
                                    + k+l ++g+  ++++++g+GK+tl++  a+ va           ++g+Vly++
  gi|118431431|ref|NP_147906.2|  92 WAKRL-VKGDSFAIIAPTGVGKSTLLTVYAAYVAAV---------KRGRVLYLV 135
                                    44455.6999999*********************63.........567888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.3e-05     0.013       4      66 ..      87     148 ..      84     194 .. 0.83
   2 ?   -1.3   0.0       1.6   1.5e+03      41      82 ..     466     519 ..     458     570 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                         AAA_30   4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeel 66 
                                    + Q++ +++l++++    ++ +p G GK+t+l+++++ ++a   grv+ l pt++  +++ ++l
  gi|118431431|ref|NP_147906.2|  87 SAQRSWAKRLVKGDS--FAIIAPTGVGKSTLLTVYAAYVAAVkRGRVLYLVPTENLVRQVYAKL 148
                                    679999999998885..8999**************9999998679********99998877554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                         AAA_30  41 aweaa.ggrviglAptgkaAkv..Laeelgieastiakllkrlk.........g 82 
                                    ++e+    +++ lA  gk  ++   +e++gi ++t  +l+++l           
  gi|118431431|ref|NP_147906.2| 466 LLEKViDTSIVSLAARGKLEAQgpAGEAAGIISETAPRLVDWLVaearlqgglL 519
                                    555555566777777776544447889999999999999999885555444440 PP

>> CarD_CdnL_TRCF  CarD-like/TRCF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   8.2e-06    0.0077       3      87 ..    1102    1184 ..    1100    1190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.2e-06
                 CarD_CdnL_TRCF    3 vGDyV.vhedhGiGriegiekrevegaekeylvleyadkkgdklyvPvdqldlirkyiskeepkldklg....gkrwe 75  
                                      GD V + ++hGiGr     k  +e++++  +v+e ++   ++ ++P++   +i  y+s++    +kl     ++r e
  gi|118431431|ref|NP_147906.2| 1102 AGDIVkMMREHGIGRPSTYAKA-IEQNRRHGYVIESKK---MRYLIPTKTGVSIYDYLSNG---FKKLVsvdtTRRLE 1172
                                     6788856799*********766.8888999******98...*******99999*****999...45555444677779 PP

                 CarD_CdnL_TRCF   76 ktkekakkgvke 87  
                                     ++ e+++kgv++
  gi|118431431|ref|NP_147906.2| 1173 EALERVEKGVEK 1184
                                     999999998875 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 !   12.5   0.0   0.00015      0.14       9      74 ..     121     187 ..     113     201 .. 0.79
   2 ?   -2.7   0.0       7.7   7.3e+03      59      84 ..     385     414 ..     382     425 .. 0.76
   3 ?    0.7   0.0      0.71   6.7e+02      98     110 ..     541     553 ..     525     554 .. 0.83
   4 ?   -1.9   0.0       4.5   4.3e+03      52      74 ..     730     752 ..     718     757 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                    HHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                     Helicase_C   9 llkleeeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                     +   +++g++l  v+t + + +    l + + gi + ++++++p++ re +le+  +g  ++++at+
  gi|118431431|ref|NP_147906.2| 121 AYVAAVKRGRVLYLVPTENLVRQvYAKLDQVEpGIAT-AYYSRMPAKARESSLEKIASGGARLIVATT 187
                                    434678999**********775454555444445655.77888*******************999985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.7
                                    HHHHHTTSSSEEEESGG....GTSSSTSTT CS
                     Helicase_C  59 leqfnkgesdvLiatdv....aerGidipk 84 
                                    +e+f +ge +vLi        + rG+d+p+
  gi|118431431|ref|NP_147906.2| 385 VEAFARGEARVLIGMASrygvIVRGLDLPE 414
                                    578999999999876544444888999886 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.71
                                    HHHHHHHTTSSST CS
                     Helicase_C  98 tsyiqriGRtgRa 110
                                     +yiq++GR+ R 
  gi|118431431|ref|NP_147906.2| 541 PTYIQASGRVSRL 553
                                    58********996 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 4.5
                                    HHHHHHHHHHHHTTSSS.EEEESG CS
                     Helicase_C  52 qnereeileqfnkgesd.vLiatd 74 
                                    +++  eil++  + e+d ++iatd
  gi|118431431|ref|NP_147906.2| 730 SKSVVEILRKL-ASEVDeIVIATD 752
                                    56677899999.678888*****8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4      0.71   6.7e+02      15      40 ..      13      22 ..       6      40 .. 0.59
   2 ?   15.3   0.4   1.6e-05     0.015      29      49 .]     703     723 ..     686     730 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.71
                            DZR 15 CseCgtklkavaaedrCpsCgekvdp 40
                                   C++Cg +++                +
  gi|118431431|ref|NP_147906.2| 13 CYNCGGNID----------------E 22
                                   555555544................2 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.6e-05
                            DZR  29 drCpsCgekvdpearfCpeCG 49 
                                    +rC  Cg++ ++ + fCp CG
  gi|118431431|ref|NP_147906.2| 703 KRCLDCGAQHTSSSPFCPRCG 723
                                    677777777777777777776 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   0.00017      0.17      46      92 ..      98     146 ..      70     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                      IstB_IS21  46 kkenivllGpsGvGKshlai..algveavraglsvlfvrvedLveelkr 92 
                                    k ++++++ p+GvGKs l +  a  v+av++g   + v +e+Lv+++ +
  gi|118431431|ref|NP_147906.2|  98 KGDSFAIIAPTGVGKSTLLTvyAAYVAAVKRGRVLYLVPTENLVRQVYA 146
                                    67899**********998651255679999999999999*****99865 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   0.00012      0.12      64      86 .]     701     723 ..     666     723 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                 zinc_ribbon_15  64 ekkeCknCgkeveeefkyCpkCg 86 
                                    + k+C +Cg++ ++++ +Cp+Cg
  gi|118431431|ref|NP_147906.2| 701 TIKRCLDCGAQHTSSSPFCPRCG 723
                                    389*******************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 ?   -0.4   0.2      0.98   9.2e+02      22      31 ..     703     712 ..     701     712 .. 0.88
   2 ?   11.8   0.7   0.00015      0.14       2      12 ..     715     725 ..     714     730 .. 0.87
   3 ?   -0.2   0.0      0.86   8.1e+02      14      23 ..    1050    1059 ..    1046    1069 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.98
                  zf-NADH-PPase  22 rvCpaCgleh 31 
                                    ++C +Cg+ h
  gi|118431431|ref|NP_147906.2| 703 KRCLDCGAQH 712
                                    79*****988 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                  zf-NADH-PPase   2 thrFCgrCGap 12 
                                    +++FC+rCG+p
  gi|118431431|ref|NP_147906.2| 715 SSPFCPRCGSP 725
                                    789*******9 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.86
                  zf-NADH-PPase   14 epaeggwarv 23  
                                     + +++g arv
  gi|118431431|ref|NP_147906.2| 1050 VFNHAGVARV 1059
                                     5555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0011         1       7      56 ..     101     144 ..      95     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl 56 
                                    + ++++++G+GK+tll  ++    ++      +++ v++ +p ++  +++
  gi|118431431|ref|NP_147906.2| 101 SFAIIAPTGVGKSTLLTVYAAYVAAV------KRGRVLYLVPTENLVRQV 144
                                    678*************9998876555......555555555555544444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00051      0.48       5      75 ..      93     161 ..      89     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                         AAA_19   5 ve.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                    ++  +k + ++++a+ G GK+++l+   a++ ++++    ++l + +t+  ++++  +l++++  + T  + 
  gi|118431431|ref|NP_147906.2|  93 AKrLVKGDSFAIIAPTGVGKSTLLTVYAAYVAAVKR---GRVLYLVPTENLVRQVYAKLDQVEPGIATAYYS 161
                                    5446788999***************99999999995...589999999999999999888777777776554 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.0      0.31   2.9e+02      18      26 .]      12      20 ..      10      20 .. 0.84
   2 ?   10.4   4.1   0.00035      0.33       4      25 ..     704     725 ..     703     725 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.31
                    zf-ribbon_3 18 vCpyCGtkl 26
                                    C++CG+ +
  gi|118431431|ref|NP_147906.2| 12 LCYNCGGNI 20
                                   5*****875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                    zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtk 25 
                                    rC  CGa + +s+ ++Cp CG++
  gi|118431431|ref|NP_147906.2| 704 RCLDCGAqH-TSSSPFCPRCGSP 725
                                    7888***88.***********86 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   5.4   0.00037      0.35      11      34 ..     702     725 ..     701     728 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00037
                        DUF35_N  11 gqrCpdCGtvqfPPravCphCgsd 34 
                                    + rC dCG+ +    ++Cp+Cgs 
  gi|118431431|ref|NP_147906.2| 702 IKRCLDCGAQHTSSSPFCPRCGSP 725
                                    67********88888*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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):              19  [number of targets reported over threshold]
# CPU time: 0.83u 0.25s 00:00:01.08 Elapsed: 00:00:00.41
# Mc/sec: 8917.22
//
Query:       gi|118431432|ref|NP_147907.2|  [L=312]
Description: hypothetical protein APE_1380.1 [Aeropyrum pernix K1]
Scores for complete 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-23   82.6   0.0    5.6e-23   82.0   0.0    1.3  1  ABC_tran     ABC transporter
    3.1e-15   56.8   0.2    9.2e-09   35.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.2e-06   27.8   0.0    6.9e-06   26.7   0.0    1.6  1  DUF4162      Domain of unknown function (DUF4162)
    5.3e-06   27.1   0.2    9.1e-06   26.3   0.2    1.3  1  AAA_23       AAA domain
    9.5e-06   25.2   0.0     0.0085   15.6   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0014   18.4   0.3      0.071   12.8   0.2    2.8  2  AAA_30       AAA domain
       0.01   15.6   0.0      0.018   14.8   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.033   14.5   0.0       0.39   11.0   0.1    2.4  3  AAA_19       AAA domain
       0.04   14.2   0.3       0.19   12.0   0.1    2.1  2  AAA_22       AAA domain
      0.049   13.8   0.0       0.35   11.0   0.0    2.3  1  AAA_33       AAA domain
       0.05   14.0   0.2      0.088   13.2   0.2    1.8  1  AAA_16       AAA ATPase domain
      0.059   13.0   0.0       0.11   12.0   0.0    1.4  1  AAA_27       AAA domain
      0.074   12.6   0.9       0.14   11.7   0.9    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.086   12.9   0.1        1.8    8.6   0.2    2.2  2  AAA_14       AAA domain
      0.086   12.7   0.3        1.2    9.0   0.1    2.3  2  NTPase_1     NTPase
       0.09   11.4   0.0        5.3    5.5   0.1    2.0  2  AAA_13       AAA domain
      0.095   12.4   0.0        1.1    8.8   0.1    2.0  2  AAA_15       AAA ATPase domain
      0.095   12.6   0.0       0.24   11.3   0.0    1.6  1  RsgA_GTPase  RsgA GTPase
       0.14   11.2   0.4       0.24   10.4   0.4    1.3  1  T2SSE        Type II/IV secretion system protein
       0.23   11.4   0.5       0.53   10.2   0.5    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 !   82.0   0.0   6.3e-26   5.6e-23       2     136 ..      21     163 ..      20     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 6.3e-26
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB...HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt...vre 78 
                                    +nv++++  g +++++G+nGaGK+tLlk+++gl+kp +Geil++g + ++   e+l  +ig++p+ p +   +t   + e
  gi|118431432|ref|NP_147907.2|  21 RNVEFTFTSG-ILGVLGPNGAGKTTLLKTILGLVKPSAGEILVEGVNPRSPGFEKLLPRIGYVPELPVVPLWTTpciLLE 99 
                                    6888998877.89*****************************************************77776666432334 PP

                                    H..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +          e+++++ +al+ +gl +  +t++     +LS+G ++rv +a+a++ +++ll+lDEp 
  gi|118431432|ref|NP_147907.2| 100 TlarlegytsvEARVRAREALEVVGLAGECETPI----GKLSKGARKRVLVAQAFIGERELLVLDEPY 163
                                    49******99999999************999999....*****************************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 !   19.3   0.2     9e-07   0.00081       3      22 ..      33      52 ..      31      75 .. 0.80
   2 !   35.5   0.0     1e-11   9.2e-09     231     297 ..     130     193 ..     128     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9e-07
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++ GpNg+GK++LL+++ +l
  gi|118431432|ref|NP_147907.2| 33 GVLGPNGAGKTTLLKTILGL 52
                                   689**************887 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 1e-11
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    e+p+ +lS G ++   ++ a++  +    ll++DEp +gL+P+++ r+ ell+  +r+ga vi+++H
  gi|118431432|ref|NP_147907.2| 130 ETPIGKLSKGARKRVLVAQAFIGER---ELLVLDEPYSGLDPEWVYRVRELLRTVAREGATVIVSSH 193
                                    6789999999999978888888777...9***********************999999********* PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   7.7e-09   6.9e-06       1      81 []     216     303 ..     216     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.7e-09
                                    E-HHHHHTTS.-SSEEEEE....-------..---EEEE-TT.S-EEEEE-------------.----EEEEEEEE---H CS
                        DUF4162   1 GtleeiKrsy.gknrieve....adaeelleepgveeveeeg.gelelkledeeaanellkal.tsgveirsFeeeePsL 73 
                                    G++ee+++ + g+ ri ++    + a e+l+  g+   + ++ g+l++ +e+ +++ ++l+ l ++++ei ++++e++sL
  gi|118431432|ref|NP_147907.2| 216 GSIEELRAWLsGTPRIILSvaepERAVEVLRRGGFNAYTINKgGQLVVAVEGADDPARVLSLLlAENIEISEYRVEKASL 295
                                    999*****999999***9986655578888888888888777799******************88*************** PP

                                    HHHHHHHH CS
                        DUF4162  74 ndIFiekv 81 
                                    ++ ++++v
  gi|118431432|ref|NP_147907.2| 296 EEAYLKLV 303
                                    **998876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2     1e-08   9.1e-06      10      39 ..      20      49 ..      15      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1e-08
                         AAA_23 10 frdqeidFskgltlItGpNGaGKTTildAi 39
                                   +r++e+ F +g+  + GpNGaGKTT+l  i
  gi|118431432|ref|NP_147907.2| 20 YRNVEFTFTSGILGVLGPNGAGKTTLLKTI 49
                                   89************************9866 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   0.0   9.5e-06    0.0085      13      44 ..      18      49 ..      12      66 .. 0.90
   2 !    7.9   0.0    0.0021       1.9     155     213 ..     150     209 ..      72     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-06
                                   EECEEEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 13 yagktvilpfsksftaivGpNGSGKsnlldAi 44
                                   ya ++v+  f++++  ++GpNG+GK+ ll  i
  gi|118431432|ref|NP_147907.2| 18 YAYRNVEFTFTSGILGVLGPNGAGKTTLLKTI 49
                                   7778999**********************999 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0021
                                    CCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvtk 213
                                     +  + l +lDe  + LD + v +v ell++   + a +iv s+  + le+  + v v k
  gi|118431432|ref|NP_147907.2| 150 FIGERELLVLDEPYSGLDPEWVYRVRELLRTVAREgATVIVSSHILRELEDIATHVLVLK 209
                                    45667799**********************76555499*****98888888777666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   7.9e-05     0.071      14      49 ..      27      60 ..      13     192 .. 0.76
   2 ?    2.0   0.0      0.16   1.4e+02      40      75 ..     223     257 ..     217     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.9e-05
                         AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                    tsg  +  + Gp G+GKtt+lk++  +++ + g++
  gi|118431432|ref|NP_147907.2| 27 FTSG--ILGVLGPNGAGKTTLLKTILGLVKPSAGEI 60
                                   3444..88899*************988888774443 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                         AAA_30  40 eaweaaggrviglAptgkaAkvLaeelgieastiak 75 
                                    + +    + ++ +A  ++a +vL+++ g++a+ti+k
  gi|118431432|ref|NP_147907.2| 223 AWLSGTPRIILSVAEPERAVEVLRRG-GFNAYTINK 257
                                    4444446777899***********88.*******98 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   0.0     2e-05     0.018      12      49 ..      20      56 ..      16      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                         AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   +++ +++++ +g+  + Gp+G+GK+Tll  i  l  p+
  gi|118431432|ref|NP_147907.2| 20 YRNVEFTFT-SGILGVLGPNGAGKTTLLKTILGLVKPS 56
                                   556667776.678889************8887777665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00043      0.39       5      35 ..      23      54 ..      19      67 .. 0.85
   2 ?   -0.2   0.0       1.3   1.1e+03      97     132 ..     148     188 ..     101     191 .. 0.73
   3 ?   -1.4   0.0       2.9   2.6e+03      31      72 ..     218     255 ..     209     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                         AAA_19  5 ve.alkekvllvtaGpGtGKTrvlkhivallv 35
                                   ve ++++++l v+++ G GKT++lk+i+ l++
  gi|118431432|ref|NP_147907.2| 23 VEfTFTSGILGVLGPNGAGKTTLLKTILGLVK 54
                                   555788999*****************998776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.3
                         AAA_19  97 ekklqeeellivDE.fqdvd.elqyr...Llkallgekkkl 132
                                    + ++ e+ell+ DE ++ +d e  yr   Ll++++ e++++
  gi|118431432|ref|NP_147907.2| 148 QAFIGERELLVLDEpYSGLDpEWVYRvreLLRTVAREGATV 188
                                    45666777999999888899765553222788887666544 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                         AAA_19  31 vallvelggvkpeeillvaftgrAakelrerlaalgaeatTi 72 
                                    +++l +  +  p+ il va  +rA++ lr      g +a+Ti
  gi|118431432|ref|NP_147907.2| 218 IEELRAWLSGTPRIILSVAEPERAVEVLRRG----GFNAYTI 255
                                    5556666666778889999999999888743....3455555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021      0.19       4      26 ..      28      50 ..      23      74 .. 0.87
   2 ?   -1.2   0.0       2.5   2.3e+03      91     117 ..     150     179 ..     136     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                         AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                   t gil v G+ G+GKTtll+++l
  gi|118431432|ref|NP_147907.2| 28 TSGILGVLGPNGAGKTTLLKTIL 50
                                   5689999*************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                         AAA_22  91 v...ielliiDEaqh.lrseealeeLrslln 117
                                        +ell++DE    l  +e +  +r+ll 
  gi|118431432|ref|NP_147907.2| 150 FigeRELLVLDEPYSgL-DPEWVYRVRELLR 179
                                    34667899999966666.5555555555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00039      0.35       4      76 ..      34     191 ..      31     213 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                         AAA_33   4 lvGlpGsGKstlaerl...lkklgavllssdt................................................ 32 
                                    + G++G+GK+tl++ +   +k+ ++++l + +                                                
  gi|118431432|ref|NP_147907.2|  34 VLGPNGAGKTTLLKTIlglVKPSAGEILVEGVnprspgfekllprigyvpelpvvplwttpcilletlarlegytsvear 113
                                    57***********9963335555566666666666677777777777777777777777777766666666666666666 PP

                         AAA_33  33 ..........................lrrrlfgtdqqskt..............dytrvldrlyqilnelarkalsagrn 72 
                                                              +r+r+ +                      y+ + +++ ++++el+r ++++g++
  gi|118431432|ref|NP_147907.2| 114 vrarealevvglagecetpigklskgARKRVLV------AqafigerellvldePYSGLDPEWVYRVRELLRTVAREGAT 187
                                    665555555555555555544444443332222......02222223333344355556666666666777777777777 PP

                         AAA_33  73 vild 76 
                                    vi+ 
  gi|118431432|ref|NP_147907.2| 188 VIVS 191
                                    7665 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   0.2   9.8e-05     0.088      25      51 ..      30      56 ..      19     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.8e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                   +++ + G+ G GK++l++++l  ++ +
  gi|118431432|ref|NP_147907.2| 30 GILGVLGPNGAGKTTLLKTILGLVKPS 56
                                   67889**************99655555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.11      10      49 ..      13      52 ..      10      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                         AAA_27 10 ryGk.ftdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   r+G+ ++ r+++f   ++++  ++GpN AGK+t+l+ i  l
  gi|118431432|ref|NP_147907.2| 13 RFGQrYAYRNVEFT-FTSGILGVLGPNGAGKTTLLKTILGL 52
                                   56642566777777.57888889************999766 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   0.9   0.00016      0.14       3      21 ..      32      50 ..      30      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                   EEEEESTTCCHHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhll 21
                                   +++ G+ G+GKTtLl+++l
  gi|118431432|ref|NP_147907.2| 32 LGVLGPNGAGKTTLLKTIL 50
                                   67889************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2     0.002       1.8       3      23 ..      30      50 ..      28      62 .. 0.88
   2 ?    1.8   0.0      0.25   2.3e+02      61     112 ..     151     204 ..     132     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                         AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                    il + G+  +GKTtllk+++
  gi|118431432|ref|NP_147907.2| 30 GILGVLGPNGAGKTTLLKTIL 50
                                   68999************9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.25
                         AAA_14  61 keekktylflDEiqev..pewekalkslvdeg.knldvivtGSnskllskeiats 112
                                     + ++++l+lDE      pew   +++l+++  +++  ++  S+ +  +++iat+
  gi|118431432|ref|NP_147907.2| 151 IG-ERELLVLDEPYSGldPEWVYRVRELLRTVaREGATVIVSSHILRELEDIATH 204
                                    34.7889999997653449999999999997668899999999999888888875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0014       1.2       4      26 ..      34      56 ..      32      69 .. 0.81
   2 ?    1.1   0.0      0.37   3.3e+02      43      88 ..     246     302 ..     235     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                                   EE--TTSSHHHHHHHHHHHH... CS
                       NTPase_1  4 iTGppGvGKtTlvkkvlellkss 26
                                   + Gp G GKtTl+k +l l+k s
  gi|118431432|ref|NP_147907.2| 34 VLGPNGAGKTTLLKTILGLVKPS 56
                                   569*************9999865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.37
                                    ---EEEEEET.T--EEEEEETT...........---SSEETTEEE-HHHHHHHHHHH CS
                       NTPase_1  43 rrigFkivdlasgeegiLarve...........akreprvgkyvvdvesfeelalea 88 
                                    rr gF+  ++++g +   a ++             +++++++y v+  s+ee  l+ 
  gi|118431432|ref|NP_147907.2| 246 RRGGFNAYTINKGGQLVVAVEGaddparvlsllLAENIEISEYRVEKASLEEAYLKL 302
                                    788999999988888888887777777777777778888888888888888877665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.006       5.3      23      38 ..      36      51 ..      33      63 .. 0.82
   2 ?    3.7   0.0     0.021        19     524     570 ..     151     194 ..     143     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.006
                         AAA_13 23 GwNGaGKTtLSrllrs 38
                                   G NGaGKTtL + +  
  gi|118431432|ref|NP_147907.2| 36 GPNGAGKTTLLKTILG 51
                                   99********887765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                         AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                    ig+ +  v+D P S LD + ++ v  l+++++    + + ++++ H 
  gi|118431432|ref|NP_147907.2| 151 IGERELLVLDEPYSGLDPEWVYRVRELLRTVA---REGATVIVSSHI 194
                                    6788899************************9...666778887775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0013       1.1      14      47 ..      20      53 ..      19      66 .. 0.84
   2 ?    1.2   0.0      0.27   2.4e+02     316     364 ..     153     193 ..     104     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                         AAA_15 14 lkdveidlseeltvliGkNnsGKSsilealdlFl 47
                                   +++ve  + + +  + G+N++GK+++l+ +  + 
  gi|118431432|ref|NP_147907.2| 20 YRNVEFTFTSGILGVLGPNGAGKTTLLKTILGLV 53
                                   7788888888888899************996665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                         AAA_15 316 kkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    ++        +l+++EP   L p+  + + +ll+ +a+++   vi+++H
  gi|118431432|ref|NP_147907.2| 153 ER-------ELLVLDEPYSGLDPEWVYRVRELLRTVAREGA-TVIVSSH 193
                                    33.......699****************************8.9****99 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      0.24      89     129 ..      19      59 ..       3      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                    THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S- CS
                    RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpelelktge 129
                                    ++++++  +++ +  ++G+ G+GK+tL++++l+  + + ge
  gi|118431432|ref|NP_147907.2|  19 AYRNVEFTFTSGILGVLGPNGAGKTTLLKTILGLVKPSAGE 59 
                                    5677888888999999**************99876666665 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 ?   10.4   0.4   0.00027      0.24     132     160 ..      32      60 ..      23      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                          T2SSE 132 ilvsGgTgsGKttllyallkeinksderi 160
                                    + v G+ g GKttll ++l  ++ s  +i
  gi|118431432|ref|NP_147907.2|  32 LGVLGPNGAGKTTLLKTILGLVKPSAGEI 60 
                                    5588******************9986665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00059      0.53       5      22 ..      34      51 ..      31      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                                   EEC-TTTCHHHHHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlqklal 22
                                   + G++G GKTtLl+ +  
  gi|118431432|ref|NP_147907.2| 34 VLGPNGAGKTTLLKTILG 51
                                   78************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2285.39
//
Query:       gi|118431433|ref|NP_147908.2|  [L=307]
Description: hypothetical protein APE_1381.1 [Aeropyrum pernix K1]
Scores for 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   22.1   5.1    0.00012   22.1   5.1    2.4  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.18   11.6   0.3       0.53   10.1   0.3    1.8  1  Pam17            Mitochondrial import protein Pam17


Domain annotation for each model (and alignments):
>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   5.1   1.3e-08   0.00012       2     172 ..      10     188 ..       9     196 .. 0.68
   2 ?   -0.5   0.5      0.11     1e+03     110     150 ..     193     235 ..     182     259 .. 0.42

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-08
                ABC2_membrane_4   2 iktEflKlkrskivwllvlaallvpllallyfnllgktgldp.aefyslsvf........gftll.....lllplilgi. 66 
                                    ++ E+l l ++k v + ++a++++p+l+ l+   ++++++     +  l+ f        g  ll          +lg+ 
  gi|118431433|ref|NP_147908.2|  10 LSYEVLRLVKRKAVAF-MAAMAVLPVLGALIAGFIASREIGGeRLWAVLMGFdigtgamtG--LLaavgvAGWAWLLGVv 86 
                                    6788899988887777.66777788877666666666665442222222222222222121..11222222234456653 PP

                ABC2_membrane_4  67 iasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgl 146
                                    i++ l+     ++ l   +++P  r+ + +aK+++  l+s++++ v+ li+++ ++++g+ + ++ l   l    ++lg+
  gi|118431433|ref|NP_147908.2|  87 IGGDLFASDIRDGSLQLFMLRPARRV-YPIAKIAAAGLFSIAFYTVASLIVLISSIILGGWQRDWWLA-PLTG--FILGV 162
                                    789*******************9999.99******************************999998653.3334..45566 PP

                ABC2_membrane_4 147 lvffavlpiialvllkksyvlplilt 172
                                    +++ ++l   ++ ++++s ++++il 
  gi|118431433|ref|NP_147908.2| 163 GLYPVILTSSIFGIVTRSPIAGMILG 188
                                    66666666677788889988888874 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.11
                ABC2_membrane_4 110 mlvtflitvlf..allsgfvgfsvklvl.ellkkclelgllvff 150
                                    +l+ +++++ +   l++g++  ++++ + ++ k++l+ g++ ++
  gi|118431433|ref|NP_147908.2| 193 LLTGMAVSFGLsiILIVGGI-GNIEAWIsFIEKEILVSGAIPYL 235
                                    22222222222002222323.22333220223345555555554 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   5.9e-05      0.53      18      99 ..       9      94 ..       2     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.9e-05
                          Pam17 18 kltwneffklrkkrrrielvasivtallglllgaavlstleidp.tqqilglDplv.vlglatlasgalG..wllGpvlgsa 95
                                    l+++    +++k   +  ++ ++  l++l++g+    ++  +   + ++g+D  + +++   +a+g++G  wllG v+g  
  gi|118431433|ref|NP_147908.2|  9 ILSYEVLRLVKRKAVAFMAAMAVLPVLGALIAGFIASREIGGERlWAVLMGFDIGTgAMTGLLAAVGVAGwaWLLGVVIGGD 90
                                   566666666677777777778888888888888888888888998999*****854234444455555553379*******9 PP

                          Pam17 96 vfkl 99
                                   +f+ 
  gi|118431433|ref|NP_147908.2| 91 LFAS 94
                                   9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2434.57
//
Query:       gi|14601373|ref|NP_147909.1|  [L=450]
Description: NCS1 nucleoside transporter [Aeropyrum pernix K1]
Scores for 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-21   74.2  30.5      9e-21   74.2  30.5    1.5  2  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 !   74.2  30.5     5e-25     9e-21      11     372 ..      15     369 ..       7     373 .. 0.79
   2 ?   -3.2   0.6      0.14   2.6e+03      53      74 ..     396     417 ..     391     440 .. 0.55

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 5e-25
                Transp_cyt_pur  11 tlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpilsRasfGirgsllpll 91 
                                   +l++ +i ++++ +++++ +g +++ lgL++ +++l+ +vgnl++a+++al+g+aG k  + fp ++  s G       ++
  gi|14601373|ref|NP_147909.1|  15 ALEYTFIMFSMASCLPLFFLGPIAFNLGLSLQEALLAALVGNLVVAVAMALNGHAGIKHKIDFPEQAVRSLGELTGKAAVV 95 
                                   7899********************************************************************666667899 PP

                Transp_cyt_pur  92 lrvviaivwfgvqawiGsealllmlgkifgkwleigg.ailgtsltelvtffifwvvslv.ivllgvskirkffviaallv 170
                                   +r+++  +wfgv a+ G+ al+l+l  + g    + g a+l  ++  + ++++  + s++ ++ lgv+ i k  ++a +l+
  gi|14601373|ref|NP_147909.1|  96 MRGLVGAMWFGVEAYNGALALNLILLFALG----LTGaALLEKATVLIPAALVLYLGSMYlVLKLGVKGIGKAATLAGPLL 172
                                   99*************************999....3332555555555555555555555515569**************** PP

                Transp_cyt_pur 171 pvaafgfliwalvkaegGpvldkavklgkselflsavagvlagfatlilnapDFtryaktkkssvkiqlvavpllftllll 251
                                    + +  + iw+       + + k+v l  s +fl  +a     +at+++n++D +r ak+  +      ++v+l+++   l
  gi|14601373|ref|NP_147909.1| 173 LLYFAWLWIWMKNSGFQPSEAPKGVGLL-SSAFLIYLAIQTNWWATVAVNISDLSREAKSWGALW----IGVMLGMVGGQL 248
                                   **97555555544443333333343333.348999999999************998666555544....444444444444 PP

                Transp_cyt_pur 252 igilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanllsagldl.aallPkkinikrgsliaavi 331
                                   ig   +   + +  +    p++i+ +f + a  +l  + +a+   +++   + l+++ d+ + +++  ++ kr+sl  a++
  gi|14601373|ref|NP_147909.1| 249 IGTYLSYELVLL--TGKTLPQEIITEFAPGAIAVLLGLAFAFLAPWTTDLTANLPPMIDIlKSIFG--MSWKRASLLSAAA 325
                                   444433333333..3344588889999999777777788888777777776667777776155555..************* PP

                Transp_cyt_pur 332 alvivpwkllsssskl...ftaflsllavflspvagviiadyfv 372
                                   + v +pw ll ++ ++   +t+f   ++v+l+p+ g ++a  +v
  gi|14601373|ref|NP_147909.1| 326 GFVLAPWWLLDNAPQIvgyVTSFAASYGVILGPILGALLAAHWV 369
                                   ***************9999******************9998887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.14
                Transp_cyt_pur  53 ligaifvallglaGakyGlpfp 74 
                                   ++++++  +lg++ + +G+pfp
  gi|14601373|ref|NP_147909.1| 396 IVSYAIAYPLGMVTSVLGVPFP 417
                                   5555555556666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3546.12
//
Query:       gi|14601375|ref|NP_147911.1|  [L=219]
Description: UDP pyrophosphate synthetase [Aeropyrum pernix K1]
Scores for 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-34  117.4   0.1    7.3e-31  107.4   0.1    2.0  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 !  107.4   0.1     4e-35   7.3e-31       1     223 [.      10     217 ..      10     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 4e-35
                                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHT..T-SEEEEEEEEGGGG.GS-HHHHHHHHHHHHHHHHHHHHHH CS
                  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclel..gvkvvtvYafSteNf.kRskeevdalmellkeellkeelke 78 
                                   i DGNrRwA  rg e+   ++  G++++k+il+++ ++   ++ v +Y++S +N+ kRs++e++ l++++++  ++++++e
  gi|14601375|ref|NP_147911.1|  10 IPDGNRRWASLRG-ENLYIAYYTGYRNVKRILTYIRDFypAIRSVYLYVLSRDNCsKRSRAELSILYRIMRR-SIERDIAE 88 
                                   78***********.88888****************998778*************978*************65.999999** PP

                                   HHHTTEEEEEESSGG..GS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSGGGHSHHHHH CS
                  Prenyltransf  79 llkegvrvrviGdle..llpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkkeeideetle 157
                                   + k g+++ ++Gd++  +lp++++e+l+                  ++ gs  +  + v  l+ +   e ++   + +tl 
  gi|14601375|ref|NP_147911.1|  89 IEKGGASLVIVGDINhpNLPDNIRESLAPYHFDM-----------YLKKGSLPDGRRVVAGLCYDPFWEIEH--YTPKTLP 156
                                   ************9985578888888776554443...........344444444444444444433222222..3456777 PP

                                   CTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHT CS
                  Prenyltransf 158 khlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrf 223
                                   ++l       ++Dl+iRt+Ge+RlS F+   + y+elyf+d+lWPdf++edl +a++ +++r+r +
  gi|14601375|ref|NP_147911.1| 157 SRLL-----DEIDLVIRTGGEKRLSSFFPLLTRYAELYFIDKLWPDFTREDLDRAVQWFSTRRRPM 217
                                   7887.....47***************************************************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1645.70
//
Query:       gi|118431434|ref|NP_147912.2|  [L=418]
Description: NADP-dependent glutamate dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-72  242.3   1.9      7e-72  242.1   1.9    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    3.9e-52  175.6   0.0    8.1e-52  174.5   0.0    1.6  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    0.00017   21.0   0.2    0.00032   20.1   0.2    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0061   15.7   0.0      0.009   15.2   0.0    1.2  1  CoA_transf_3     CoA-transferase family III
  ------ inclusion threshold ------
      0.014   12.9   0.1       0.02   12.4   0.1    1.1  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
      0.018   15.4   0.1      0.033   14.6   0.1    1.6  1  NAD_binding_7    Putative NAD(P)-binding
       0.03   13.1   0.0      0.041   12.6   0.0    1.2  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
      0.088   12.9   1.4       0.26   11.3   1.4    1.8  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.1   1.9   3.1e-75     7e-72       1     243 []     180     416 ..     180     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 242.1 bits;  conditional E-value: 3.1e-75
                                    T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHH CS
                  ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieell 80 
                                    GG ++r  +Tg+Gv++ ++ +++k+ +  leg++va++G+Gnvg yaa++l+e+gak+vavsDs+G iydpeG+d ee l
  gi|118431434|ref|NP_147912.2| 180 GGLNARIVSTGYGVAVSTRVAAEKFLGG-LEGRTVAVQGYGNVGYYAAKFLAEMGAKIVAVSDSRGGIYDPEGIDPEEAL 258
                                    99**********************8888.*************************************************** PP

                                    HHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHH CS
                  ELFV_dehydrog  81 elkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeilee 160
                                    ++k+++++v++y+       ++i+   e+lel+vdilvP+A++++i+ ena+ +ik  +k++ EgAN+ptt++A++il +
  gi|118431434|ref|NP_147912.2| 259 KVKRSTGTVANYQ---R--GKKISTM-EILELPVDILVPAAIEEVITDENAD-RIK--AKIISEGANGPTTTAAEKILVK 329
                                    *************...2..3789996.9************************.***..********************** PP

                                    TT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T....HHHHHHHHHHHHHH CS
                  ELFV_dehydrog 161 agvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe....lvkganiagfekva 236
                                    +gvlv+pd++aNaGGV++S +E+++n ++  +t+ee  +kl+++m e +k+v+++ e++ ++    l+++a+++++e+v 
  gi|118431434|ref|NP_147912.2| 330 KGVLVLPDILANAGGVIMSHIEWVNNRMGGWITDEEALKKLEQKMVENTKTVITYWEKNLKPeensLRDAAYMIAVERVF 409
                                    *********************************************************977767888************** PP

                                    HHHHHCT CS
                  ELFV_dehydrog 237 eamkaqG 243
                                    +amk +G
  gi|118431434|ref|NP_147912.2| 410 RAMKLRG 416
                                    ****998 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 !  174.5   0.0   3.6e-55   8.1e-52       1     129 [.      34     161 ..      34     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 3.6e-55
                                    -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GG CS
                ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpk 80 
                                    p+rvlqv+v++k+d+G+++++ g+r+qh+salgP+kGG+R+hp+v+++ev aL+++mt+Kn+l++lp+GG+kggv+++pk
  gi|118431434|ref|NP_147912.2|  34 PDRVLQVRVTIKMDDGTVKTFLGWRSQHNSALGPYKGGVRYHPNVTMNEVIALSMWMTWKNSLAGLPYGGGKGGVRVNPK 113
                                    789***************************************************************************** PP

                                    GS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
                ELFV_dehydrog_N  81 klseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                     ls++ele + r++ ++++ +++G ++D+pApDv+t+++ m+w+ dey+
  gi|118431434|ref|NP_147912.2| 114 ILSPRELELLSRKYFESIS-DIVGVDQDIPAPDVYTDPQVMSWFLDEYN 161
                                    *******************.****************************8 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 !   20.1   0.2   1.4e-07   0.00032      33      69 ..     207     243 ..     185     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                                    -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                   2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrsk 69 
                                     l+g+tv++ G+G++G  +ak l+++g+k++a++ s+
  gi|118431434|ref|NP_147912.2| 207 GLEGRTVAVQGYGNVGYYAAKFLAEMGAKIVAVSDSR 243
                                    599*****************************99875 PP

>> CoA_transf_3  CoA-transferase family III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     4e-06     0.009       1      68 [.     208     279 ..     208     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-06
                   CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkg..DpaRkvgpsee...kgesayflavnrnKrsval 68 
                                    L+G +V   ++  +G +a+++LA++GA+++ v ++++g  D    + p+e    k++++ +++++r+K+  ++
  gi|118431434|ref|NP_147912.2| 208 LEGRTVAVQGYGNVGYYAAKFLAEMGAKIVAVSDSRGGiyD-PEGIDPEEAlkvKRSTGTVANYQRGKKISTM 279
                                    7899999999999*********************9755222.2234444447888888888888888886665 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   8.8e-06      0.02    1050    1099 ..     302     351 ..     300     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.8e-06
                        Bac_GDH 1050 ngkelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                     n+  ++ak+++EG+N   t  +     +kg+ +  D + N++GV +S  E
  gi|118431434|ref|NP_147912.2|  302 NADRIKAKIISEGANGPTTTAAEKILVKKGVLVLPDILANAGGVIMSHIE 351 
                                     7889************99999999999********************988 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.5e-05     0.033       5      40 ..     208     243 ..     206     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                    l+g++v v G G+v++  ++ l+e gak++ v+   
  gi|118431434|ref|NP_147912.2| 208 LEGRTVAVQGYGNVGYYAAKFLAEMGAKIVAVSDSR 243
                                    789****************************99886 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 ?   12.6   0.0   1.8e-05     0.041     269     303 ..     207     241 ..     197     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                    HHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEE CS
                 Oxidored_nitro 269 ylagkrvaiygdpdrvvalarllkelGmevvaagt 303
                                     l+g++va+ g++   +  a++l+e+G+++va++ 
  gi|118431434|ref|NP_147912.2| 207 GLEGRTVAVQGYGNVGYYAAKFLAEMGAKIVAVSD 241
                                    589*****************************975 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.4   0.00012      0.26      21      50 ..     208     237 ..     197     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEE CS
                  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvi 50 
                                    l G+++ v GyG+vG  +a+ l ++Ga+++
  gi|118431434|ref|NP_147912.2| 208 LEGRTVAVQGYGNVGYYAAKFLAEMGAKIV 237
                                    5699***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 2973.74
//
Query:       gi|118431435|ref|NP_147913.2|  [L=194]
Description: hypothetical protein APE_1387.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1448.17
//
Query:       gi|118431436|ref|NP_147914.2|  [L=295]
Description: hypothetical protein APE_1388.1 [Aeropyrum pernix K1]
Scores for 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-73  244.2   0.1    1.1e-72  243.9   0.1    1.1  1  DUF1028       Family of unknown function (DUF1028)
    1.7e-27   95.5   0.7    8.7e-27   93.3   0.0    2.3  3  PG_binding_2  Putative peptidoglycan binding domain
  ------ inclusion threshold ------
      0.037   14.2   0.0      0.099   12.9   0.0    1.7  1  PG_binding_1  Putative peptidoglycan binding domain
       0.18   12.3   1.8         15    6.2   0.4    2.7  2  RuvA_C        RuvA, C-terminal domain
       0.19   11.9   0.0       0.38   10.9   0.0    1.5  1  POTRA_TamA_1  POTRA domain TamA domain 1


Domain annotation for each model (and alignments):
>> DUF1028  Family of unknown function (DUF1028)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.9   0.1   3.1e-76   1.1e-72       1     193 []       2     199 ..       2     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.9 bits;  conditional E-value: 3.1e-76
                                    EEEEEEE-TTT--EEEEEEESSS-HHHHHEEEETTTEEEEEESS--HHHHHHHHHHHHTT--HHHHHHHHHHT-TTGGG- CS
                        DUF1028   1 TfSivardpetgelGvAvaskslaVgalvpfaragvGavatQaltnpelgekglelleagasaeealeallaadegrelR 80 
                                    TfSiva++petge+GvAvask++a g++vp+++ gvGavatQ+++n+++g+ +l+lle g+++++a+e +l  d+ re R
  gi|118431436|ref|NP_147914.2|   2 TFSIVAVNPETGEVGVAVASKFIAAGSIVPWVQLGVGAVATQSWANVKFGPALLRLLELGYTPRRAVEMVLTGDSRREMR 81 
                                    9******************************************************************************* PP

                                    EEEEEETTS-EEEEE-TTS-S-EEEE.ETTEEEEEES-S-TCHHHHHHHHH.....S-HHHHHHHHHHHHHHT------- CS
                        DUF1028  81 QlavvdakgetaaftGeeclewaghrtgenyavaGNlLageevleamaeafeategepLaerLlaALeaGeaaGGDkrgr 160
                                    Q++vv+  ge++aftG+ec+e+agh++g+++av+GN+L+g+ev+e+ma+a+e+t+g +L ++LlaAL+aG++aGGD+rgr
  gi|118431436|ref|NP_147914.2|  82 QIGVVSSGGEAYAFTGRECIEYAGHIVGDGFAVQGNILTGPEVIESMAKAYESTKG-ELVDKLLAALAAGDRAGGDRRGR 160
                                    ***************************************************99999.9********************** PP

                                    -EEEEEEEE..........TTEEEEEEEE--SS-HHHHH CS
                        DUF1028 161 qSAallVvr......esedeskpyvdLrvddhedpiaeL 193
                                    +SAa++V++      + e+   +yvdLrvd+h+d+++eL
  gi|118431436|ref|NP_147914.2| 161 ESAAVIVYKpcggygGCEEGVGKYVDLRVDHHPDAVNEL 199
                                    **************98888899**************998 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 ?   -0.2   0.0      0.36   1.3e+03      25      45 ..      57      78 ..      54      82 .. 0.61
   2 ?   -3.5   0.0       3.7   1.3e+04      12      25 ..     134     147 ..     129     149 .. 0.64
   3 !   93.3   0.0   2.4e-30   8.7e-27       1      74 []     209     282 ..     209     282 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                   PG_binding_2 25 LsrLGy.ydgeaggafrealrd 45
                                   L +LGy   ++ + +++   r+
  gi|118431436|ref|NP_147914.2| 57 LLELGYtPRRAVEMVLTGDSRR 78
                                   8899994445555555555555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.7
                   PG_binding_2  12 vlaedvaeevqaaL 25 
                                      +++ ++++ aaL
  gi|118431436|ref|NP_147914.2| 134 STKGELVDKLLAAL 147
                                    45666777777777 PP

  == domain 3  score: 93.3 bits;  conditional E-value: 2.4e-30
                   PG_binding_2   1 tllerkpeeervlaedvaeevqaaLsrLGyydgeaggafrealrdALrafiaveNFEnraradgeidrlVlayl 74 
                                    t+ler++++++v+ edva+e+++aL++LGyy+g+++g+++++l +AL++++a++NFEn++r+dg+i+++V+++l
  gi|118431436|ref|NP_147914.2| 209 TILEREDPSDVVKIEDVAGELEKALAALGYYKGPFTGRASKELLQALESWMAINNFENKIRRDGYIWGTVYRFL 282
                                    799*********************************************************************98 PP

>> PG_binding_1  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.8e-05     0.099       7      35 ..     228     256 ..     223     258 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHTT--.SSSSSB--HHHHHHHH CS
                   PG_binding_1   7 elqryLsrlGylsgpadgtfgpateeaVk 35 
                                    el+++L++lGy++gp +g+ ++++ +a+ 
  gi|118431436|ref|NP_147914.2| 228 ELEKALAALGYYKGPFTGRASKELLQALE 256
                                    89*****************9999988875 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.014        49      10      24 ..      57      71 ..      53      73 .. 0.89
   2 ?    6.2   0.4    0.0041        15       1      15 [.     224     238 ..     224     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                                   HHHCTS-HHHHHHHH CS
                         RuvA_C 10 LlaLGYkekeaekAv 24
                                   Ll LGY+++ a ++v
  gi|118431436|ref|NP_147914.2| 57 LLELGYTPRRAVEMV 71
                                   899******998876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0041
                                    HHHHHHHHHHHHCTS CS
                         RuvA_C   1 daledaveALlaLGY 15 
                                    d+ ++++ AL aLGY
  gi|118431436|ref|NP_147914.2| 224 DVAGELEKALAALGY 238
                                    57899********** PP

>> POTRA_TamA_1  POTRA domain TamA domain 1
   #    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      40      60 ..     225     245 ..     212     260 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                   POTRA_TamA_1  40 aeeeirkALralGYYqptief 60 
                                    +  e +kAL alGYY+  ++ 
  gi|118431436|ref|NP_147914.2| 225 VAGELEKALAALGYYKGPFTG 245
                                    667899*********976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2364.06
//
Query:       gi|118431437|ref|NP_147915.2|  [L=748]
Description: ABC transporter substrate-binding protein precursor [Aeropyrum pernix K1]
Scores for complete 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-63  213.9   5.4    5.7e-63  213.1   5.4    1.4  1  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 !  213.1   5.4   3.2e-67   5.7e-63       1     374 [.     273     726 ..     273     729 .. 0.96

  Alignments for each domain:
  == domain 1  score: 213.1 bits;  conditional E-value: 3.2e-67
                                    SEEESSEEEEEEEETTTTEEEEEE-TT-B.-TTSS....B-SHHHHHHHHHHHHTGGGHCTTHHHHHC............ CS
                      SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvk.FsDGt....pltAeDvvfsferlldpdtasgyasllee............ 63 
                                    e++p LA + w  ++D +++ f +R gvk F +++    ++tA Dv f++ r+++    ++++ + ++            
  gi|118431437|ref|NP_147915.2| 273 ELTPELAVA-WAHNEDSTEWYFVIRGGVKaFDNWNnktyDVTAVDVLFTIWRIARLSLDPSWMITEFVdvnnsqvlteee 351
                                    579******.7*****************9999998899***********************9999888************ PP

                                    ..........................TCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHHHHGC............... CS
                      SBP_bac_5  64 ..........................dqdikkveavddytvrftlkkpnalfltllaavpasiak............... 102
                                                                +  +       +v+++l  p+a+ l+++a++  s+                 
  gi|118431437|ref|NP_147915.2| 352 fnqllgqggiyasyggfsgevksldeLLQAFGYSGGTAGVVKIKLYYPYAPILSIFADPFTSVIPmkyifdnveelqgky 431
                                    ************************9999999999************************99999999************** PP

                                    ...................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTST.........TTSCSSSSE CS
                      SBP_bac_5 103 ...................kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYw.........gggkpkldr 154
                                                         + +++ +     +kp+ tGPY +k++k g++i+le np+Yw         g++kp+ + 
  gi|118431437|ref|NP_147915.2| 432 eealeasnygknpaaweayIGTGENEPSHILLHQKPIATGPYYVKDYKEGSYIILEYNPYYWnkelwqdlyGQDKPQHEL 511
                                    *************99998877777777788999*************************************999******* PP

                                    EEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE......EEEEEEEEEEEEEETTTSTGGGSHHHHHHHH CS
                      SBP_bac_5 155 iefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv......lyespgggvtylafNtkkppfddkrvRqAls 228
                                     +f +  d+ +r++ ++sG++ d   +p++ +e +k +  +          ++ ++ + ++++N  k+pf++++vRqAl+
  gi|118431437|ref|NP_147915.2| 512 AIFLINDDAVSRIETMKSGQA-DTGAIPLDRLEDIKGYALEGTnfqiivEEKGLSPVIVFIVLNAMKEPFNNTKVRQALM 590
                                    ******9999999999*****.9999*********8888777788999999999************************** PP

                                    HHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSH CS
                      SBP_bac_5 229 yAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlllasgsp 308
                                    yAi++++i + v+ gy ++ n++lp ++ g++++  ++y ++++ kA++l+ke G++ +d++        + + ++ g++
  gi|118431437|ref|NP_147915.2| 591 YAIPFDQIKTSVYAGYIERLNGVLPAGFLGHNDDIVTQY-EFNIVKARELIKESGINPSDYT--------IKIWYNKGNT 661
                                    *************************************98.69******************95........99******** PP

                                    HHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTC CS
                      SBP_bac_5 309 aekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssg 374
                                     ++++a++++  + ++G++v v++++w  t l+r+++gdfd+++ gw +dy dpdn+  p++++++
  gi|118431437|ref|NP_147915.2| 662 QREKVANMLKTIWGNLGFNVVVEPLEW-PTLLSRTEKGDFDVWIVGWAPDYLDPDNYAGPLFYGGT 726
                                    ***************************.*******************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.25s 00:00:00.93 Elapsed: 00:00:00.42
# Mc/sec: 5314.24
//
Query:       gi|118431438|ref|NP_147917.2|  [L=332]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-37  129.1  14.3    1.6e-37  129.1  14.3    1.9  2  BPD_transp_1    Binding-protein-dependent transport system in
  ------ inclusion threshold ------
        1.7    6.2   4.3        2.6    5.6   4.3    1.2  1  ACR_tran        AcrB/AcrD/AcrF 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 ?   -4.9   4.4         2   1.8e+04     146     146 ..      70      70 ..       5     115 .. 0.52
   2 !  129.1  14.3   1.8e-41   1.6e-37       1     185 []     116     332 .]     116     332 .] 0.98

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 2
                   BPD_transp_1 146 l 146
                                     
  gi|118431438|ref|NP_147917.2|  70 F 70 
                                    1 PP

  == domain 2  score: 129.1 bits;  conditional E-value: 1.8e-41
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..................................vil 46 
                                    gi+lGi++al r  ++d ++r++  v+ s+P+f+la ll++vf                                   + 
  gi|118431438|ref|NP_147917.2| 116 GIPLGIISALTRDTIIDAAIRIMALVGISVPIFWLAYLLIFVFytkyrlitlagtpeppysitgiplidsiimldaaTFE 195
                                    89***************************************************************************999 PP

                   BPD_transp_1  47 silghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggav 126
                                    ++l  + +p+++l+  s+++++rl+r+++l++++ d+ve++ a+G++    +r ++l+n+ +pi+t l+l fggll+ga 
  gi|118431438|ref|NP_147917.2| 196 DVLRRYTIPAFTLAYPSIGFVARLVRNSFLDAMSGDYVEFMDARGLPSTWKYR-HILRNSSIPIVTVLGLIFGGLLTGAP 274
                                    **********************************************8766555.************************** PP

                   BPD_transp_1 127 lleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                    ++e++++ pGlg +ll++i++ydy + + ggvl+++i++l +nl++di ++++dprvr+
  gi|118431438|ref|NP_147917.2| 275 ITETIFGLPGLGKFLLDSINNYDYLSLM-GGVLFVGIIYLTVNLLVDITYAIIDPRVRY 332
                                    ****************************.****************************95 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   4.3   0.00029       2.6     890     922 ..     111     143 ..     100     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00029
                                    HHHHTTHHHHHHHHHHHHHHTT--BSHHHHHHH CS
                       ACR_tran 890 llilltvPlalvGallalllrglelsviaqvGl 922
                                    ++ill +Pl++++al+  ++ ++++ ++a+vG+
  gi|118431438|ref|NP_147917.2| 111 FIILLGIPLGIISALTRDTIIDAAIRIMALVGI 143
                                    89******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2540.19
//
Query:       gi|14601382|ref|NP_147918.1|  [L=387]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-28   99.5  14.3    1.9e-28   99.5  14.3    2.2  3  BPD_transp_1  Binding-protein-dependent transport system inne
    3.9e-05   23.5   0.8    3.9e-05   23.5   0.8    3.9  5  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
       0.25   11.3   0.1       0.25   11.3   0.1    2.3  3  PIG-P         PIG-P


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 ?   -1.0   0.0       0.2   1.2e+03      36      49 ..      61      74 ..      33      87 .. 0.60
   2 ?   -2.7   0.1       0.7   4.2e+03      18      40 ..     136     158 ..     126     161 .. 0.60
   3 !   99.5  14.3   3.1e-32   1.9e-28       1     185 []     163     378 ..     163     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                  BPD_transp_1 36 aillvlvfvilsil 49
                                  ++ lv +fvi+ ++
  gi|14601382|ref|NP_147918.1| 61 GVALVIAFVIIAVI 74
                                  22222222222333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.7
                  BPD_transp_1  18 kllrpliivllslPsfvlaillv 40 
                                   +ll+++ +  ++  ++v++++ v
  gi|14601382|ref|NP_147918.1| 136 DLLSRILYGARTSFIVVILVMAV 158
                                   55555555555555555555544 PP

  == domain 3  score: 99.5 bits;  conditional E-value: 3.1e-32
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf............................vilsilghli 53 
                                   gillG++++ +r++++d++++++++v+l++P ++lai l +v+                            +       l+
  gi|14601382|ref|NP_147918.1| 163 GILLGLFSG-YRGGVVDEVIMRVVDVFLAFPGLILAIALSAVLpsrldpiiinnelllgtllrlfalkpedA--LPMVRLV 240
                                   89*******.********************************************************987431..3344788 PP

                  BPD_transp_1  54 lpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw 134
                                     vi+l ++ ++ y+rl+r ++l++++  +veaaralG ++  i+  ++lPn+l p++  l l fg+++   + l+flg  
  gi|14601382|ref|NP_147918.1| 241 VVVIALWIVWWPVYARLVRGMVLSARENTYVEAARALGIPTHSILLGHILPNILGPVLVYLTLDFGAVILVEAGLSFLG-- 319
                                   889****************************************************************************.. PP

                  BPD_transp_1 135 pGlgtllleailgydyseis..........nggvlalviavlllnlvadilqrlldprvrk 185
                                     lg +   a +g+ +  ++          +++ la+++ vl +nl+ d+l ++ dpr+r+
  gi|14601382|ref|NP_147918.1| 320 --LGAVPPIADWGRIIYDGAqyypnawwlvFFPGLAILFTVLGFNLLGDALRDIMDPRTRR 378
                                   ..***********999988889************************************985 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 !   23.5   0.8   6.5e-09   3.9e-05       4      51 .]      46     102 ..      45     102 .. 0.84
   2 ?    1.5   0.9     0.048   2.9e+02      22      36 ..     149     162 ..     147     167 .. 0.74
   3 ?   -2.5   1.0      0.89   5.3e+03      22      32 ..     194     204 ..     187     219 .. 0.57
   4 ?   -2.4   0.3       0.8   4.8e+03      27      32 ..     242     247 ..     236     256 .. 0.49
   5 ?   -2.4   0.1      0.85   5.1e+03      19      34 ..     351     366 ..     348     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.5e-09
                        OppC_N   4 qdawrrFkrNklAvvglvilllllliaifaPliaPydp........qdli.qnllpP 51 
                                   + +++ + r ++ ++g ++++++++ia+++P+iaP ++        +d++  +l+pP
  gi|14601382|ref|NP_147918.1|  46 KLTLYALNRSPIGLLGVALVIAFVIIAVIGPYIAPLGYndqlvycvTDFDaVRLAPP 102
                                   567788899*************************99988888887777763358888 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.048
                        OppC_N  22 illlllliaifaPli 36 
                                   +++++l++a ++P+i
  gi|14601382|ref|NP_147918.1| 149 FIVVILVMA-VGPWI 162
                                   566666666.78998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.89
                        OppC_N  22 illlllliaif 32 
                                   ++l+++l a++
  gi|14601382|ref|NP_147918.1| 194 LILAIALSAVL 204
                                   34555555555 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.8
                        OppC_N  27 lliaif 32 
                                   ++ia++
  gi|14601382|ref|NP_147918.1| 242 VVIALW 247
                                   222222 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 0.85
                        OppC_N  19 glvilllllliaifaP 34 
                                   gl+il ++l + ++++
  gi|14601382|ref|NP_147918.1| 351 GLAILFTVLGFNLLGD 366
                                   7899988888777665 PP

>> PIG-P  PIG-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2         2   1.2e+04      50      61 ..      67      78 ..      59      94 .. 0.56
   2 ?   -3.2   1.2       1.2   7.5e+03      13      23 ..     240     250 ..     233     263 .. 0.60
   3 ?   11.3   0.1   4.1e-05      0.25      35      60 ..     336     361 ..     329     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2
                         PIG-P 50 ayllmlvlyiyv 61
                                  a+++++v+  y+
  gi|14601382|ref|NP_147918.1| 67 AFVIIAVIGPYI 78
                                  334444444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                         PIG-P  13 stlafllyllw 23 
                                   ++++++l+++w
  gi|14601382|ref|NP_147918.1| 240 VVVVIALWIVW 250
                                   34444445554 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 4.1e-05
                         PIG-P  35 gityypnryWalavpayllmlvlyiy 60 
                                   g++yypn +W +++p + + ++++ +
  gi|14601382|ref|NP_147918.1| 336 GAQYYPNAWWLVFFPGLAILFTVLGF 361
                                   789************99987777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2844.94
//
Query:       gi|14601383|ref|NP_147919.1|  [L=333]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-23   82.1   0.0    6.9e-23   81.7   0.0    1.2  1  ABC_tran     ABC transporter
    6.4e-21   74.6   0.3    1.2e-20   73.8   0.3    1.5  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    6.1e-08   32.8   0.1    8.9e-06   25.7   0.2    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0082   16.4   0.8       0.11   12.7   0.8    2.1  1  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.025   14.2   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.05   13.4   0.0       0.11   12.3   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      0.063   13.7   0.0       0.13   12.7   0.0    1.5  1  AAA_16       AAA ATPase domain
       0.14   12.1   0.0       0.26   11.3   0.0    1.4  1  AAA_5        AAA domain (dynein-related subfamily)
        4.5    6.7   6.3        1.1    8.7   2.8    1.8  2  GETHR        GETHR pentapeptide repeat (5 copies)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   3.5e-26   6.9e-23       2     136 ..      30     193 ..      29     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 3.5e-26
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEE........EETTCEGGG.B-HHHCCHCEEEE-SS.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx........xxxxxxxxx.xxxxxxxxxxxxxxxx.. RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGei........lldgkdlke.qeleslrkeigvlpqe.. 67 
                                   ++vs+ + +ge++ +vGe+G+GKS   ++l++l  p     eG+i        ++d  +l+e + +++  +ei++++q+  
  gi|14601383|ref|NP_147919.1|  30 EDVSFRICRGETYCLVGETGCGKSVTSRALTRLIYPpgriVEGKIyyypepgrRVDIMSLDEkELRRIRGEEIAYIFQDps 110
                                   79********************************99787778888776666664444444444445577789*******99 PP

                                   --S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                   xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  68 pqlfpeltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                   + l+p +t++ +               e  +++  +l+++ +++ ++++vks p++LSgG+kqr ++  +l ++pkll++D
  gi|14601383|ref|NP_147919.1| 111 AALDPLYTIGYQvgetmlahgrvrslrEGVRRAVGVLKTVLMPD-PEKRVKSYPHELSGGMKQRGVIGISLSNRPKLLIAD 190
                                   999****999999999***9999888777777999999999999.888999****************************** PP

                                   STT CS
                                   xxx RF
                      ABC_tran 134 Ept 136
                                   Ept
  gi|14601383|ref|NP_147919.1| 191 EPT 193
                                   **9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.3   5.9e-24   1.2e-20       1      65 []     245     309 ..     245     309 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 5.9e-24
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                   vE++p+++lf++plHPYT+aL+r+vp + ++ ++le i+g++p+l   + GC+F+pRCp a + C
  gi|14601383|ref|NP_147919.1| 245 VEEAPVDELFSNPLHPYTRALIRAVPNPLAKIENLEHIPGTVPNLITPPPGCRFHPRCPLAFDRC 309
                                   8**************************************************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.012        23       3      41 ..      43      65 ..      42     124 .. 0.67
   2 !   25.7   0.2   4.4e-09   8.9e-06     233     302 ..     162     229 ..     154     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.012
                        AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                  +l+G  g+GKS   +al  l                  +
  gi|14601383|ref|NP_147919.1| 43 CLVGETGCGKSVTSRALTRLIY----------------P 65
                                  69***************99854................3 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 4.4e-09
                        AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                    ++elS G+k+  +++ + l+ ++  +ll+ DEp + L+  +++ +++ll +l+r +g  ++l TH+  l+
  gi|14601383|ref|NP_147919.1| 162 YPHELSGGMKQR-GVIGISLSNRP--KLLIADEPTTALDVTIQAQIMDLLTQLKReHGLTLLLITHNLGLV 229
                                   57899*******.**********9..79999*******************88888899*********9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.8   5.6e-05      0.11       8      29 ..      42      63 ..      38     229 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                        AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                   +++Ge+G+GK+++ r l++  
  gi|14601383|ref|NP_147919.1| 42 YCLVGETGCGKSVTSRALTRLI 63
                                  589***************9975 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 ?   14.2   0.0   1.2e-05     0.025       6      36 ..      31      61 ..      26      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                  HHHS-EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  6 DalfpivqGqrtlipgafgvGktvisqslsk 36
                                  D+ f i++G++ +++g+ g+Gk+v s++l++
  gi|14601383|ref|NP_147919.1| 31 DVSFRICRGETYCLVGETGCGKSVTSRALTR 61
                                  78899********************998876 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   5.3e-05      0.11      16      50 ..      33      67 ..      27      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  +++i + +++ l+G++G GKS    A++ l++p+ 
  gi|14601383|ref|NP_147919.1| 33 SFRICRGETYCLVGETGCGKSVTSRALTRLIYPPG 67
                                  5667655599**********************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.3e-05      0.13      18      63 ..      35      77 ..      24     154 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                        AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                  r+++g  e   l+Ge G+GKs   r+l r +    g  ++gk   +
  gi|14601383|ref|NP_147919.1| 35 RICRG--ETYCLVGETGCGKSVTSRALTRLIYPP-GRIVEGKIYYY 77
                                  55666..56779****************988887.77777776666 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 ?   11.3   0.0   0.00013      0.26       3      23 ..      43      63 ..      41      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                  EEE--SSSSHHHHHHHGGGGB CS
                         AAA_5  3 lLvGppGtgKselaerlaaal 23
                                  +LvG++G+gKs  ++ l +++
  gi|14601383|ref|NP_147919.1| 43 CLVGETGCGKSVTSRALTRLI 63
                                  9****************9998 PP

>> GETHR  GETHR pentapeptide repeat (5 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.8   0.00056       1.1      10      22 ..      38      52 ..      37      55 .. 0.75
   2 ?   -3.4   0.1       3.3   6.5e+03      16      18 ..     124     126 ..     124     127 .. 0.33

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00056
                         GETHR 10 RGETvR..GEThRGe 22
                                  RGET +  GET +G+
  gi|14601383|ref|NP_147919.1| 38 RGETYClvGETGCGK 52
                                  777777778888886 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.3
                         GETHR  16 GET 18 
                                   GET
  gi|14601383|ref|NP_147919.1| 124 GET 126
                                   222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2442.17
//
Query:       gi|118431439|ref|NP_147920.2|  [L=344]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-29  102.5   0.0    3.5e-29  102.0   0.0    1.2  1  ABC_tran   ABC transporter
    8.9e-20   71.0   0.2    1.5e-19   70.3   0.2    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.7e-08   34.7   1.0    1.3e-05   25.2   0.2    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
      3e-05   23.6   0.3    0.00071   19.1   0.0    2.0  2  SMC_N      RecF/RecN/SMC N terminal domain
    0.00072   19.8   0.0     0.0021   18.4   0.0    1.7  1  AAA_22     AAA domain
    0.00085   18.7   0.5     0.0032   16.8   0.2    1.9  2  ATPase     KaiC
  ------ inclusion threshold ------
       0.03   13.8   0.1       0.42   10.0   0.0    2.1  2  TniB       Bacterial TniB protein
      0.033   14.6   0.0        0.8   10.1   0.0    2.2  1  AAA        ATPase family associated with various cellular act
      0.052   13.8   0.0       0.57   10.5   0.0    2.1  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
      0.065   12.8   0.0        3.3    7.2   0.0    2.1  2  AAA_25     AAA domain
       0.11   11.1   0.5        2.4    6.7   0.1    2.0  2  AAA_13     AAA domain
       0.17   12.3   1.2        0.4   11.0   1.2    1.8  1  AAA_16     AAA ATPase domain
       0.18   11.6   0.5       0.35   10.6   0.5    1.4  1  AAA_29     P-loop containing region of AAA domain
        0.4   10.1   3.2        2.2    7.7   0.3    2.1  2  Pox_A32    Poxvirus A32 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 !  102.0   0.0   2.8e-32   3.5e-29       1     137 []      52     203 ..      52     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 2.8e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpelt 75 
                                    ++nv++ + +g+++++vGe+G+GK+t+ +++++l++pt G+i +dg d+ +   + l+++r++ ++++q+   +l+p++t
  gi|118431439|ref|NP_147920.2|  52 VDNVTIGIPRGKTLGLVGESGSGKTTFGRVILRLEEPTGGRIFFDGIDVMKlrgRGLKEFRRRAQIIFQDpyGSLNPRKT 131
                                    589**********************************************99999****************8889****** PP

                                    HHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    + +           +  +  e ++s l +++l++t++++ p+++SgGq+qr+a+ar+l+ kp++++lDEpt+
  gi|118431439|ref|NP_147920.2| 132 IFNLiaepikvhgiKVGDLQEYIVSLLYQVGLNETHLYRYPHEFSGGQRQRIAIARVLALKPEFIVLDEPTS 203
                                    9999999999888755555777777777777888***9********************************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 !   70.3   0.2   1.2e-22   1.5e-19       1      65 []     254     321 ..     254     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.2e-22
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE g+++++f++plHPYTk Ll+s+p +d+e        +ikge+ps+ + ++GC+F++RCp a+++C
  gi|118431439|ref|NP_147920.2| 254 VEFGEAEEVFEKPLHPYTKVLLESIPVPDPEVAkrrSRIRIKGEPPSPINPPSGCRFRTRCPIAVDKC 321
                                    8**************************9998776678899**************************** 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 !    8.2   0.1    0.0016         2       3      22 ..      66      85 ..      65     109 .. 0.79
   2 !   25.2   0.2     1e-08   1.3e-05     226     301 ..     164     237 ..     108     239 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +l+G  gsGK+++ + +  l
  gi|118431439|ref|NP_147920.2| 66 GLVGESGSGKTTFGRVILRL 85
                                   69***************887 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1e-08
                         AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                    n+    + ++e+S G+++ +a++  l+  +    ++++DEp + L+ ++++ +l llk+l+r      ++ +H+  +
  gi|118431439|ref|NP_147920.2| 164 NETHLYRYPHEFSGGQRQRIAIARVLALKP---EFIVLDEPTSALDVSVQAQILNLLKDLQRkYSLTYLFISHDLGV 237
                                    444446789999******944444444433...9**************************99888888*****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 ?    2.1   0.1     0.086   1.1e+02      26      41 ..      64      79 ..      46      88 .. 0.77
   2 !   19.1   0.0   5.6e-07   0.00071     136     212 ..     174     248 ..     146     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.086
                                   EEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnll 41
                                      +vG+ GSGK+ + 
  gi|118431439|ref|NP_147920.2| 64 TLGLVGESGSGKTTFG 79
                                   4569********9876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.6e-07
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvt 212
                                    ++SgG+++ +a+a ++A++      + +lDe  +aLD +  +++ +llk  + +    ++ is++ ++++ ++  + v+
  gi|118431439|ref|NP_147920.2| 174 EFSGGQRQRIAIARVLALKP----EFIVLDEPTSALDVSVQAQILNLLKDLQRKysLTYLFISHDLGVVRYMSDYIAVM 248
                                    79**************9864....499**********************666553478999999999999998888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0021      10     128 ..      67     231 ..      61     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.....................erpevvfvtlpsst..sskdllrellralgl 66 
                                    ++GesG+GKTt  r +l+  +    ++                      +r+ ++ ++ p ++   +k++++ +++ +++
  gi|118431439|ref|NP_147920.2|  67 LVGESGSGKTTFGRVILRLEE----PTGgriffdgidvmklrgrglkefRRRAQIIFQDPYGSlnPRKTIFNLIAEPIKV 142
                                    89***********99999873....3335577888999999999999995555554454444446777789999999998 PP

                         AAA_22  67 elka..............erlsseellealeqalrarav...........ielliiDEaqh.lr...seealeeLrslln 117
                                     + +               +l++ +l+++ ++ +  ++            +e++++DE    l+   ++++l+ L++l+ 
  gi|118431439|ref|NP_147920.2| 143 HGIKvgdlqeyivsllyqVGLNETHLYRYPHEFSGGQRQriaiarvlalkPEFIVLDEPTSaLDvsvQAQILNLLKDLQR 222
                                    888899999999999999777777777777777777777888888999999********999989655**********99 PP

                         AAA_22 118 lsrkgvqliLv 128
                                      +++++ +++
  gi|118431439|ref|NP_147920.2| 223 --KYSLTYLFI 231
                                    ..888887776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   2.5e-06    0.0032       3      36 ..      47      79 ..      45      85 .. 0.89
   2 ?   -0.9   0.0      0.67   8.6e+02     139     163 ..     208     233 ..     186     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                         ATPase  3 tgIeglDeilkgGipegrvvlitGepGtGKtifa 36
                                    +++  D+++  Gip+g++  ++Ge+G+GKt+f+
  gi|118431439|ref|NP_147920.2| 47 AYVKAVDNVT-IGIPRGKTLGLVGESGSGKTTFG 79
                                   5788889986.8*********************9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.67
                         ATPase 139 vaReilrqlvrvl.kklgvTailvse 163
                                     + +++ +l++ l +k+ +T +++s 
  gi|118431439|ref|NP_147920.2| 208 SVQAQILNLLKDLqRKYSLTYLFISH 233
                                    45567777777777999999999986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.14   1.8e+02      34      51 ..      61      78 ..      57      91 .. 0.80
   2 ?   10.0   0.0   0.00033      0.42     107     156 ..     180     227 ..     155     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                           TniB 34 rmpnlllvGdsnnGKtmi 51
                                   r + l lvG+s  GKt+ 
  gi|118431439|ref|NP_147920.2| 61 RGKTLGLVGESGSGKTTF 78
                                   5567889*********86 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00033
                           TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkip 156
                                     ++ +++   +lk++ +++DE  ++l   ++ q ++ln+lk L+++++++
  gi|118431439|ref|NP_147920.2| 180 RQRIAIARVLALKPEFIVLDEPTSAL--DVSVQAQILNLLKDLQRKYSLT 227
                                    4555666677899*************..6777889*********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 ?   10.1   0.0   0.00062       0.8       3      66 ..      67     200 ..      65     239 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00062
                                    EESSTTSSHHHHHHHHHHH...HT..HEEEEEETTTCSSS........................................ CS
                            AAA   3 lyGppGtGKTllakavake...lg..vefleisgsellsk........................................ 37 
                                    l+G  G GKT++ + + +    +g  + f  i++++l+                                          
  gi|118431439|ref|NP_147920.2|  67 LVGESGSGKTTFGRVILRLeepTGgrIFFDGIDVMKLRGRglkefrrraqiifqdpygslnprktifnliaepikvhgik 146
                                    89**************9984442233445556666666552222344444444444444444444444444444444444 PP

                                    ........................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  38 ........................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                            y  e +   r+ ++ a+  a kp  +++DE
  gi|118431439|ref|NP_147920.2| 147 vgdlqeyivsllyqvglnethlyrYPHEFSGGQRQRIAIARVLAlKPEFIVLDE 200
                                    444555555555555555555555555555555555555555555555555555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00045      0.57      56      89 ..     191     218 ..     149     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                        SbcCD_C  56 saegrepalrlvfLDEAFsklDeesiatllelle 89 
                                           ++++++LDE  s lD   +a++l+ll+
  gi|118431439|ref|NP_147920.2| 191 L------KPEFIVLDEPTSALDVSVQAQILNLLK 218
                                    3......589*********************997 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0026       3.3      30      49 ..      59      78 ..      52     120 .. 0.93
   2 ?    3.5   0.0     0.036        47     137     188 ..     188     233 ..     158     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0026
                         AAA_25 30 lpagelallaGapgtGKttl 49
                                   +p+g++  l+G +g+GKtt+
  gi|118431439|ref|NP_147920.2| 59 IPRGKTLGLVGESGSGKTTF 78
                                   699****************8 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                         AAA_25 137 ieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                    + +  +++++v+D  ++al+ + +     +++++ l++++r++  + l++ H
  gi|118431439|ref|NP_147920.2| 188 VLAL-KPEFIVLDEPTSALDVSVQ-----AQILNLLKDLQRKYSLTYLFISH 233
                                    3442.4899999999999998888.....89******************999 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.034        43      23      41 ..      69      87 ..      67      97 .. 0.86
   2 ?    6.7   0.1    0.0018       2.4     526     578 ..     192     242 ..     183     253 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.034
                         AAA_13 23 GwNGaGKTtLSrllrslel 41
                                   G  G+GKTt+ r++  le+
  gi|118431439|ref|NP_147920.2| 69 GESGSGKTTFGRVILRLEE 87
                                   778***********99875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0018
                         AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                    k + +v+D P S LD  ++  + +l+k+   +k +   lfi+ H l   ++++
  gi|118431439|ref|NP_147920.2| 192 KPEFIVLDEPTSALDVSVQAQILNLLKDLQ-RKYSLTYLFIS-HDLGVVRYMS 242
                                    7889*************************7.89999999997.8887777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.2   0.00031       0.4      22      52 ..      58      90 ..      46     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                         AAA_16 22 grp..elvllsGesGvGKsslvrellralekd.g 52
                                   g p    + l+GesG+GK++  r +lr le+  g
  gi|118431439|ref|NP_147920.2| 58 GIPrgKTLGLVGESGSGKTTFGRVILR-LEEPtG 90
                                   4444488899***********999995.555533 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   0.5   0.00027      0.35      13      38 ..      53      78 ..      50      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00027
                         AAA_29 13 dghtieidlkg.atlltGpsGsGKSTl 38
                                   d+ ti i  +g +  l+G+sGsGK+T+
  gi|118431439|ref|NP_147920.2| 53 DNVTIGIP-RGkTLGLVGESGSGKTTF 78
                                   55677776.453677**********96 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3    0.0017       2.2      16      33 ..      65      82 ..      62      86 .. 0.83
   2 ?    2.9   0.2      0.05        64      30      67 ..     213     256 ..     209     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                        Pox_A32 16 lalvGgsGsGktvyLlsL 33
                                   l lvG+sGsGkt++ + +
  gi|118431439|ref|NP_147920.2| 65 LGLVGESGSGKTTFGRVI 82
                                   679**********96655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.05
                        Pox_A32  30 LlsLlrtlvkkykhifLltp......vknseYdkyvwPdhinkv 67 
                                    +l+Ll+ l +ky   +L+++       + s+Y   ++   i + 
  gi|118431439|ref|NP_147920.2| 213 ILNLLKDLQRKYSLTYLFIShdlgvvRYMSDYIAVMYLGKIVEF 256
                                    689***************99777754456667666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 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:                        78  (0.00435049); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2430.82
//
Query:       gi|118431440|ref|NP_147921.2|  [L=419]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Aeropyrum pernix K1]
Scores for complete 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-58  198.6   0.0    1.6e-58  198.4   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0   8.9e-63   1.6e-58       3     417 .]       6     409 ..       4     409 .. 0.90

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 8.9e-63
                                    CSS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-H CS
                  EPSP_synthase   3 kgkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeape 82 
                                    k++++ ge+ +p+sk  +  al ++ La g+s+i+++L s+Dv++ + a+r++g+ ++k   e + +++++   +  +p 
  gi|118431440|ref|NP_147921.2|   6 KPSQIGGEIIAPSSKGHTIAALFASLLAGGRSKISEPLYSRDVDTAIYAVRRFGGLVQKG--ERDLIVDSP--PRPWWP- 80 
                                    68899*************9998888888888***********************877666..456666666..566666. PP

                                    HHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET.SS-BEEEEET CS
                  EPSP_synthase  83 elvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg.lklkgveika 161
                                      v++++ s t+lr  +  +ala+g + + Gd   ++ P+++l  aL+++Gae+   +g   +p++vkg l  +  e + 
  gi|118431440|ref|NP_147921.2|  81 -RVVNCRRSSTVLRHSIVTAALAPGISLVYGDSHTNSTPVSELAGALKKIGAEVVTTNG--RPPVAVKGpLARGCCEGET 157
                                    .6************888888888889*****************************7766..********98888888888 PP

                                    SSTTHHHHHHHHHHHTTSBS.EEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHH CS
                  EPSP_synthase 162 evsSqqvtsllllaallaeg.tteleelasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAa 240
                                      +S + + + ll a    g  ++  +  s  ++   l++l+ fg+ki+   ++  i++  k+  pg  y v+gD+ +Aa
  gi|118431440|ref|NP_147921.2| 158 VGASDGESLAALLLASPLLGfAIKRAGTHSWHHVAVALHVLRGFGAKISF--DGG-IYYPDKPYGPG-AYAVPGDYVNAA 233
                                    8888776544444443445879999999**********************..555.77766666888.************ PP

                                    HHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBHGGGHHHHH CS
                  EPSP_synthase 241 yflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeaptlavlaafa 320
                                     +l+a+ai+g ++tv+ ++++  qG + +l+ il ++ga+++++e+++ vvg+ +l++ + d+++ p +ap+lavlaa a
  gi|118431440|ref|NP_147921.2| 234 PLLLAGAIAG-RITVRRLDPEDPQGEKVFLN-ILAQAGAKLKAGESSVEVVGTGSLEGFEADVSETPSLAPVLAVLAAYA 311
                                    *********9.***************99999.************************************************ PP

                                    HHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEET..TEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEE CS
                  EPSP_synthase 321 egttviegiaelrvketdrlaamateLrklGaeveeee..dgliiipaekqlkgaevesydDhRiamalalaglvaegev 398
                                    +g++vi+gi++lr ke  +l+ ++++Lr+l ++++ +   d l++++    ++g++ + y+D R+ ma+a+agl++++ v
  gi|118431440|ref|NP_147921.2| 312 KGRSVIKGISHLRLKEGGNLKPLMSNLRRLKVKAKPRCggDCLEVYGEGY-VEGGTAKGYGDPRMTMAFAVAGLASRKGV 390
                                    *********************************99875559999777766.***************************** PP

                                    EEETTHHHHHHSSSHHHHH CS
                  EPSP_synthase 399 eiddiectdksfpefeekL 417
                                    +++ ++  +  +p+f+e+L
  gi|118431440|ref|NP_147921.2| 391 RVTGASRYRDYYPGFVEDL 409
                                    ****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2955.22
//
Query:       gi|118431441|ref|NP_147922.2|  [L=108]
Description: hypothetical protein APE_1405.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00052   20.5   6.1     0.0011   19.4   6.1    1.5  1  DUF3209         Protein of unknown function (DUF3209)
     0.0065   16.4   8.0       0.01   15.8   8.0    1.3  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
     0.0075   16.3   0.4       0.81    9.8   0.2    2.0  2  Spo0A_C         Sporulation initiation factor Spo0A C termina
  ------ inclusion threshold ------
      0.027   12.7   2.8      0.029   12.5   2.8    1.0  1  HSP70           Hsp70 protein
      0.031   14.2   0.6       0.12   12.4   0.2    2.1  2  SNARE           SNARE domain
      0.052   13.8   0.2       0.21   11.9   0.0    2.0  2  DUF4777         Domain of unknown function (DUF4777)
      0.061   13.2   8.6      0.022   14.7   6.2    1.4  2  ARGLU           Arginine and glutamate-rich 1
      0.068   13.2   2.6      0.075   13.1   2.6    1.2  1  CFAP91          Cilia- and flagella-associated protein 91
      0.071   12.8   1.9       0.46   10.2   0.5    1.9  2  MukF_M          MukF middle domain
      0.093   12.9   0.2       0.16   12.1   0.2    1.4  1  DUF2294         Uncharacterized conserved protein (DUF2294)
      0.094   12.8   0.4       0.18   11.9   0.3    1.5  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
       0.11   12.2   0.4       0.12   12.1   0.4    1.1  1  DUF1678         Protein of unknown function (DUF1678)
       0.13   11.6   0.9       0.16   11.2   0.8    1.3  1  Cas_Csa4        CRISPR-associated protein (Cas_Csa4)
       0.17   11.1   0.8       0.18   11.0   0.8    1.0  1  TMPIT           TMPIT-like protein
       0.22   11.9   9.0       0.66   10.4   9.0    1.8  1  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C
       0.68    9.6   7.7        1.9    8.1   7.7    1.7  1  GrpE            GrpE


Domain annotation for each model (and alignments):
>> DUF3209  Protein of unknown function (DUF3209)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   6.1     1e-06    0.0011      15     112 ..       8     104 ..       4     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1e-06
                                    HHTT.--GGGCHHHHHHHTTTTTT-HHHHHHH..H--SHH.HHHHHHHHHHHHHHHHHHH....STT-HHHHHHHHHHHH CS
                        DUF3209  15 nvlgvkdeaerrHaeaEleaeleepgpikala..eAkdla.elerhldaalvdLeeevaktdeddpeldYlRgrlvavrd 91 
                                    + l+v d+++rr +e+ +e +    g+i++ a  eAk l+ e+ r+l+aal++Le+ +a+t+++ ++++  R   v  + 
  gi|118431441|ref|NP_147922.2|   8 KALDVIDSTARRLDEKSIELA----GDIASTAdsEAKRLEkEVGRLLEAALAELESALASTEDELAREAKSRVEAVRKEL 83 
                                    567777888887777766543....667766633799996379*****************99999988877777777777 PP

                                    HHHHHHHHHHHHHHHHHHHHH CS
                        DUF3209  92 aeralkrlveeleallddlee 112
                                     e+a ++ ++++ea+l++le+
  gi|118431441|ref|NP_147922.2|  84 KEAAERNWSNGIEAFLRELEN 104
                                    88888999999********97 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   8.0   8.9e-06      0.01       4      81 ..       8      89 ..       4     108 .] 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.9e-06
                                   HCCCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHH CS
                 Apolipoprotein  4 esldelkayaeeleeqlaplaqelrdrlskeleelrarl....raeleevrarlepyrdevqeqlgqnleelrqrlapytee 81
                                   + ld ++++a  l e+  +la +++ +   e++ l +++    +a l e+ ++l++  de+  + ++++e++r++l++++e+
  gi|118431441|ref|NP_147922.2|  8 KALDVIDSTARRLDEKSIELAGDIASTADSEAKRLEKEVgrllEAALAELESALASTEDELAREAKSRVEAVRKELKEAAER 89
                                   5566667777777777777777777777777777777776666666666666677777777777777777777777766653 PP

>> Spo0A_C  Sporulation initiation factor Spo0A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.017        19      20      68 ..       6      54 ..       2      64 .. 0.87
   2 !    9.8   0.2   0.00072      0.81      43      78 ..      66     101 ..      54     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.017
                        Spo0A_C 20 lreaielvledpellesitkelypevAkkykttpsrVeraIrhaIevaW 68
                                   l++a+ ++ +  ++l++ + el  ++A + +++++r e+++    e+a 
  gi|118431441|ref|NP_147922.2|  6 LAKALDVIDSTARRLDEKSIELAGDIASTADSEAKRLEKEVGRLLEAAL 54
                                   7788888889999999***********************9988888775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                        Spo0A_C  43 pevAkkykttpsrVeraIrhaIevaWekgnkeklee 78 
                                     e+A++ k+ +++V +++++a e+ W++g +  l+e
  gi|118431441|ref|NP_147922.2|  66 DELAREAKSRVEAVRKELKEAAERNWSNGIEAFLRE 101
                                    589*************************98777665 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.8   2.6e-05     0.029     502     588 ..      20     104 ..       3     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                    SBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHH CS
                          HSP70 502 lseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeiea 581
                                    l+e+ ie +  d  ++a++++k+ e+ e    +e+ + +le++l+ +++++ +++k++ve+  +eLke++e++ ++ iea
  gi|118431441|ref|NP_147922.2|  20 LDEKSIE-LAGDIASTADSEAKRLEK-EVGRLLEAALAELESALASTEDELAREAKSRVEAVRKELKEAAERNWSNGIEA 97 
                                    4444443.666666677777666666.99999*************************************99888888888 PP

                                    HHHHHHH CS
                          HSP70 582 kteelkk 588
                                     + el++
  gi|118431441|ref|NP_147922.2|  98 FLRELEN 104
                                    8888876 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.6   2.9e+03       8      26 ..      33      51 ..      29      53 .. 0.54
   2 ?   12.4   0.2    0.0001      0.12      12      35 ..      71      94 ..      66      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHHHHHHH CS
                          SNARE  8 tnVenaqsnveraqkeLkk 26
                                   +  ++   ++e+  ++L  
  gi|118431441|ref|NP_147922.2| 33 STADSEAKRLEKEVGRLLE 51
                                   4444445566666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHHHHHHHHHHHHCTXX CS
                          SNARE 12 naqsnveraqkeLkkavkyqksnR 35
                                   +a s+ve+++keLk a+++ +sn+
  gi|118431441|ref|NP_147922.2| 71 EAKSRVEAVRKELKEAAERNWSNG 94
                                   689*****************9995 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.21      24      52 ..      26      54 ..      24      56 .. 0.94
   2 ?    0.7   0.1      0.56   6.2e+02      21      50 ..      53      85 ..      52      89 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                        DUF4777 24 EivervaerydlseeelkkvVkntLeaAv 52
                                   E+++ +a+  d + ++l+k+V ++LeaA 
  gi|118431441|ref|NP_147922.2| 26 ELAGDIASTADSEAKRLEKEVGRLLEAAL 54
                                   8999***********************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.56
                        DUF4777 21 TldEivervaerydlseeelk...kvVkntLea 50
                                   +l E+  ++a+ +d+  +e+k   + V++ L++
  gi|118431441|ref|NP_147922.2| 53 ALAELESALASTEDELAREAKsrvEAVRKELKE 85
                                   567777778888888888888444555555555 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.4   4.9e+03      10      18 ..      14      22 ..       8      26 .. 0.73
   2 ?   14.7   6.2   1.9e-05     0.022       4      68 ..      38     101 ..      35     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                          ARGLU 10 eevarRvee 18
                                   + +arR++e
  gi|118431441|ref|NP_147922.2| 14 DSTARRLDE 22
                                   667788776 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                          ARGLU   4 esklieeevarRveeavakrVeeelekrkeeiekeverrveearkkmekqveeelerereaelee 68 
                                    e k +e ev r +e+a+a ++e  l+  ++e+ +e + rve  rk++++  e++  +  ea l+e
  gi|118431441|ref|NP_147922.2|  38 EAKRLEKEVGRLLEAALA-ELESALASTEDELAREAKSRVEAVRKELKEAAERNWSNGIEAFLRE 101
                                    899************997.69****************************9999988877777776 PP

>> CFAP91  Cilia- and flagella-associated protein 91
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.6   6.7e-05     0.075      87     141 ..      38      92 ..       4     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                         CFAP91  87 ewaereeeiqelqeeRlellkkllkkreeeqeeanekrleklkeklekekekkle 141
                                    e +  e+e+ +l e+ l+ l+ +l + e+e ++++++r+e+++++l+++ e++ +
  gi|118431441|ref|NP_147922.2|  38 EAKRLEKEVGRLLEAALAELESALASTEDELAREAKSRVEAVRKELKEAAERNWS 92 
                                    45777*******************************************9998765 PP

>> MukF_M  MukF middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00041      0.46      44     110 ..       6      69 ..       2      77 .. 0.85
   2 ?    4.7   0.5      0.02        23      29      83 ..      39      97 ..      32     107 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MukF_M  44 vaeildridltqrvmdeqqqqvkeeiaellnkdWreaisscekllsetsstlrelqdtleaaGdklq 110
                                    +a+ ld id t r +de+  ++  +ia+  + + +   ++  +ll+   ++l el  +l ++ d+l 
  gi|118431441|ref|NP_147922.2|   6 LAKALDVIDSTARRLDEKSIELAGDIASTADSEAKRLEKEVGRLLE---AALAELESALASTEDELA 69 
                                    57889***********************999999999899999886...467888888888777775 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                                   HHHHHHHTHHHHHHTHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHGGGGHHH CS
                         MukF_M 29 ekaWrknvfarlkysvaeildri....dltqrvmdeqqqqvkeeiaellnkdWreaiss 83
                                    k  +k+v   l+ ++ae+ + +    d   r    + ++v++e+ e  +++W + i++
  gi|118431441|ref|NP_147922.2| 39 AKRLEKEVGRLLEAALAELESALasteDELAREAKSRVEAVRKELKEAAERNWSNGIEA 97
                                   45555555555555555544433111133345555666778888888888888887754 PP

>> DUF2294  Uncharacterized conserved protein (DUF2294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00014      0.16      38      84 ..      54      98 ..      42     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                        DUF2294 38 ivrlegvlTpaEkfLaetkeGrelvkqvRteLveeikpelkelieei 84
                                     +le  l  +E  La++++  + v++vR+eL e+++ +  + ie  
  gi|118431441|ref|NP_147922.2| 54 LAELESALASTEDELAREAK--SRVEAVRKELKEAAERNWSNGIEAF 98
                                   56788889999999999888..89**************999999976 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 ?   11.9   0.3   0.00016      0.18      29      88 ..      24      84 ..      18     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                   Baculo_PEP_C 29 nvqilaqlatlldaietqLn.alsedlksllaeldtrldtlltnLtdalnalqdtlrneLt 88
                                   ++++++++a++ d+ +++L+ ++   l+++lael+++l+++ ++L +  ++  +++r+eL+
  gi|118431441|ref|NP_147922.2| 24 SIELAGDIASTADSEAKRLEkEVGRLLEAALAELESALASTEDELAREAKSRVEAVRKELK 84
                                   6788999999999999999625888889999999999999999999998888889999886 PP

>> DUF1678  Protein of unknown function (DUF1678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00011      0.12      78     150 ..      31     107 ..      16     108 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                        DUF1678  78 lvsldrkevlklaralrralrsvlktl....lteleelvkkkvrrvlarllalefdarrlgspgirdvleelpdrle 150
                                    + s    e  +l +++ r l + l +l        +el+++  +rv a+ + l+  a r  s gi+  l+el + l+
  gi|118431441|ref|NP_147922.2|  31 IASTADSEAKRLEKEVGRLLEAALAELesalASTEDELAREAKSRVEAVRKELKEAAERNWSNGIEAFLRELENLLR 107
                                    555555555666666666666666666555255567899***************999999999*********88765 PP

>> Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00015      0.16      82     135 ..      30      83 ..       3      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                       Cas_Csa4  82 disagafisdlqrlnrvy.relesilnnleklkasvkselskkkqaeargrkkkl 135
                                    di  ++  s+ +rl++   r+le++l +le   as++ el+++ ++  ++  k+l
  gi|118431441|ref|NP_147922.2|  30 DIA-STADSEAKRLEKEVgRLLEAALAELESALASTEDELAREAKSRVEAVRKEL 83 
                                    444.45589999**98888**********************87777777666655 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.8   0.00016      0.18       4      87 ..       3      88 ..       1     103 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                          TMPIT  4 weelekefkeleetakeykqkleelsklq.skcskeikkqkkrlke.lksslkklkksvkeeeeeeveelkeelkerkkvlk 83
                                   +e+l+k ++ + +ta+++ +k+ el+  + s+  +e+k+ +k++ + l+++l +l++++ + e+e ++e k++++  +k lk
  gi|118431441|ref|NP_147922.2|  3 VEKLAKALDVIDSTARRLDEKSIELAGDIaSTADSEAKRLEKEVGRlLEAALAELESALASTEDELAREAKSRVEAVRKELK 84
                                   7889999999999999999998888766515556677888888876256789999999888888888888888888887777 PP

                          TMPIT 84 eves 87
                                   e ++
  gi|118431441|ref|NP_147922.2| 85 EAAE 88
                                   6654 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 ?   10.4   9.0   0.00059      0.66       7      86 ..      22     106 ..       2     107 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00059
                    Uso1_p115_C   7 eseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleae.nkklekeleklraelkeekekekek.....qk 80 
                                    e++ + + d ++++ +e++ l+k++  l ++ a+++ es   ++e+e + + ++++e++r+elke++e++  +       
  gi|118431441|ref|NP_147922.2|  22 EKSIELAGDIASTADSEAKRLEKEVGRLLEA-ALAELESALASTEDElAREAKSRVEAVRKELKEAAERNWSNgieafLR 100
                                    5555666677777888888888888888887.444444444444444155566799999999999998885446766777 PP

                    Uso1_p115_C  81 EldDLL 86 
                                    El+ LL
  gi|118431441|ref|NP_147922.2| 101 ELENLL 106
                                    777776 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.7    0.0017       1.9      11      68 ..      44     102 ..       2     107 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                                    HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTT.TTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                           GrpE  11 edeeeeleeeleelekevkelkekllrllae.fenlrkrtekekeeakkfaiekfakdL 68 
                                    ++    le+ l+ele+ +++ +++l r+++  +e +rk +++ +e   + +ie f+++L
  gi|118431441|ref|NP_147922.2|  44 KEVGRLLEAALAELESALASTEDELAREAKSrVEAVRKELKEAAERNWSNGIEAFLREL 102
                                    22223355557778888888888887765541557777777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1499  (0.0836076); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 845.65
//
Query:       gi|118431442|ref|NP_147923.2|  [L=346]
Description: hypothetical protein APE_1406.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   0.0      0.018   14.5   0.0    1.6  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit


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 ?   14.5   0.0     1e-06     0.018       5     133 ..      12     133 ..       9     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-06
                                    HHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HHHHHH CS
                 vATP-synt_AC39   5 vramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsrefld 84 
                                    +ra  s l ++++y++L+++esl+++++  + + +     +e+    s +++e ++ + +a+ + k  +++p ++r  + 
  gi|118431442|ref|NP_147923.2|  12 IRAVLSMLPDPSQYRELMESESLQEALSTASAPAFPG--VKEA---RSITSLEPLMWRDFASIVVKAVKLSPAKARYAVG 86 
                                    789999999*******************888888888..3444...4788************************99**** PP

                                    HHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.SSSS-HHHHHHHHHS CS
                 vATP-synt_AC39  85 yllyrydidNvklllrgklsgdldleeleeklhplgelsaldldkliea 133
                                    + ++  d   v+ +l ++  g+++lee+ +   p  +++  +l++++++
  gi|118431442|ref|NP_147923.2|  87 FNVMIEDAKDVISVLYSIRVGNASLEEISKL--PTSSVEGTTLNNIVST 133
                                    ***************9999975677887443..3345555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2768.01
//
Query:       gi|118431443|ref|YP_874891.1|  [L=89]
Description: hypothetical protein APE_1406a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0005   19.7   0.0    0.00074   19.2   0.0    1.2  1  HTH_41    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.1e-08   0.00074       3      38 ..      20      55 ..      19      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.1e-08
                         HTH_41  3 GdRlktIeelakeleLSvGlvQkALklLeddkaisl 38
                                   G+R++tI + a  +++++G +   L lL +++ i l
  gi|118431443|ref|YP_874891.1| 20 GERMETIVNAAPAFGIGRGDINDCLGLLAASGLIRL 55
                                   9*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); 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 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 702.37
//
Query:       gi|118431444|ref|NP_147924.2|  [L=266]
Description: hypothetical protein APE_1407.1 [Aeropyrum pernix K1]
Scores for complete 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   0.1    6.1e-06   26.3   0.1    1.4  1  FdhE             Protein involved in formate dehydrogenase fo
    0.00017   22.2   0.5    0.00035   21.2   0.5    1.5  1  zinc_ribbon_15   zinc-ribbon family
  ------ inclusion threshold ------
      0.016   15.2   1.7       0.79    9.8   2.4    2.6  2  DZR              Double zinc ribbon
      0.018   14.9   3.4        1.5    8.8   0.2    2.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.039   14.0   0.1        3.1    7.9   0.0    2.4  2  Elf1             Transcription elongation factor Elf1 like
      0.059   13.8   5.7        1.4    9.3   1.3    2.5  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.11   12.6  15.7       0.53   10.4   0.2    3.9  3  UPF0547          Uncharacterised protein family UPF0547
       0.12   12.4   5.6         32    4.6   0.4    3.5  3  Nudix_N_2        Nudix N-terminal
       0.12   11.8   0.5        0.9    9.0   0.5    2.2  1  NMD3             NMD3 family
       0.16   11.8   5.1      0.071   13.0   1.9    2.0  2  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
       0.17   12.5   5.7        5.2    7.8   0.1    3.0  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.31   11.2   7.4         18    5.5   5.2    3.1  3  Zn-ribbon_8      Zinc ribbon domain
       0.38   10.5   9.8        5.9    6.8   0.1    3.5  3  zinc_ribbon_2    zinc-ribbon domain
       0.49   10.3   5.1         14    5.6   5.4    2.5  2  Prok-RING_4      Prokaryotic RING finger family 4
       0.62   10.1   3.0        5.3    7.1   1.0    3.0  3  HypA             Hydrogenase/urease nickel incorporation, met
       0.89    9.3  17.8         12    5.6   0.1    4.3  4  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.96    9.5  12.0         14    5.7   6.4    3.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.2    8.7   7.5          5    6.7   0.1    3.3  3  zf-ribbon_3      zinc-ribbon domain
        1.3    8.6   5.6        2.5    7.8   0.1    3.0  3  zf_UBZ           Ubiquitin-Binding Zinc Finger
        1.4    8.5  12.8        4.6    6.8   1.7    3.0  2  TF_Zn_Ribbon     TFIIB zinc-binding
        1.5    9.2   8.1        5.7    7.3   8.1    2.0  1  zf-LITAF-like    LITAF-like zinc ribbon domain
        1.8    8.6   7.5        5.8    7.0   0.2    3.2  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        3.9    7.9   9.5       0.98    9.8   5.3    2.2  3  zf-RING_2        Ring finger domain
        4.3    7.6   9.4       0.52   10.5   0.6    2.7  3  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
        6.1    6.8  12.4        4.6    7.2   0.4    3.5  3  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
        6.2    6.8   9.2        9.2    6.2   5.8    2.7  3  zf-C3HC4_2       Zinc finger, C3HC4 type (RING finger)
        8.2    6.4  10.1         14    5.6   6.8    2.7  3  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)


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 !   26.3   0.1   9.1e-09   6.1e-06     155     249 ..     140     231 ..     114     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 9.1e-09
                                    T--TTSSS-.-TT-SS-TTT---EEEEEEE-------EEEEEETTT--EEE--TTS..-TTT---SS-EEE------C-E CS
                           FdhE 155 aldakalaelaeekglCPvCgsaPvasvvriggeaeglRylhCslCeteWhvvRvk..CsnCeetkelaylsledekaav 232
                                    +l+++   + +  ++ CPvCg + + ++vr g+   g  y+ C +C   W v+R +  C  C++t  l+   + d++  +
  gi|118431444|ref|NP_147924.2| 140 ELKRQGY-SWSGISHRCPVCGLE-SETMVRKGD---G-YYMVCHMCFFTWLVSRGIpvCPRCGSTVPLEVGIFTDKSRRI 213
                                    5544444.44445789****976.678898887...5.5***************8555********************** PP

                                    EEEEETTTT.EEEEEEET CS
                           FdhE 233 kAesCdeCh.sYlkilyq 249
                                        C  C  s++ +l+q
  gi|118431444|ref|NP_147924.2| 214 GLGFCSRCGySWRILLDQ 231
                                    ********7356666555 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.5   5.3e-07   0.00035       2      73 ..     154     223 ..     153     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.3e-07
                 zinc_ribbon_15   2 lCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgk 73 
                                    +Cp Cg  s++ ++k + +  ++ + +f+w  ++ + +c +C+s+++ +   g  ++k++++    C++Cg 
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLESETMVRKGDGYYMVCHMCFFTWLVSRGIPVCPRCGSTVPLEV--GIFTDKSRRIGLGFCSRCGY 223
                                    7**********************************************997..66666666677999999986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.2      0.62   4.1e+02      29      35 ..     153     159 ..     137     179 .. 0.68
   2 ?    9.8   2.4    0.0012      0.79       8      37 ..     185     224 ..     152     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.62
                            DZR  29 drCpsCg 35 
                                    +rCp Cg
  gi|118431444|ref|NP_147924.2| 153 HRCPVCG 159
                                    5666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                            DZR   8 lppdarfCseCgtklkavaa..........edrCpsCgek 37 
                                    ++ +  +C++Cg++++ +              +C++Cg++
  gi|118431444|ref|NP_147924.2| 185 VSRGIPVCPRCGSTVPLEVGiftdksrrigLGFCSRCGYS 224
                                    5555568999999987544488999999999999999986 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 ?    8.8   0.2    0.0023       1.5      28      56 ..     152     183 ..     144     184 .. 0.88
   2 ?    6.5   0.3     0.012         8      31      56 ..     192     225 ..     190     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                 OrfB_Zn_ribbon  28 SktCseCgsknke...alsgrtfkCpnCgfea 56 
                                    S +C++Cg ++++   + +g  ++C  C f++
  gi|118431444|ref|NP_147924.2| 152 SHRCPVCGLESETmvrKGDGYYMVCHMCFFTW 183
                                    899**********9888888889999998875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                 OrfB_Zn_ribbon  31 CseCgsknke........alsgrtfkCpnCgfea 56 
                                    C++Cgs++          ++   +  C++Cg+++
  gi|118431444|ref|NP_147924.2| 192 CPRCGSTVPLevgiftdkSRRIGLGFCSRCGYSW 225
                                    *******9988999987777788899****9976 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.11        72      23      51 ..     154     179 ..     143     185 .. 0.79
   2 ?    7.9   0.0    0.0046       3.1      24      56 ..     192     226 ..     191     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                           Elf1  23 dCpfCnheksvevkldkkekiaevsCkvC 51 
                                    +Cp+C+ e   + ++ +k +  ++ C++C
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLE---SETMVRKGDGYYMVCHMC 179
                                    68888888...667777777777778887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0046
                           Elf1  24 CpfCnheksvevkl..dkkekiaevsCkvCgesfe 56 
                                    Cp+C+++  +ev +  dk+++i+   C+ Cg s +
  gi|118431444|ref|NP_147924.2| 192 CPRCGSTVPLEVGIftDKSRRIGLGFCSRCGYSWR 226
                                    ******998887762266667*********98866 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 ?    9.3   1.3    0.0022       1.4       5      34 ..     154     179 ..     152     188 .. 0.84
   2 ?    6.0   0.2     0.023        15       5      36 ..     191     223 ..     187     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadC 34 
                                     CP Cg + +   +++  +    ++ C+ C
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLESETMVRKGDGY----YMVCHMC 179
                                    6*****9998888888887....9****99 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.023
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigq.cvyCadCga 36 
                                     CP Cg+   le    +++++     +C  Cg+
  gi|118431444|ref|NP_147924.2| 191 VCPRCGSTVPLEVGIFTDKSRRIgLGFCSRCGY 223
                                    6******99998887777654446788888888 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.64   4.2e+02      16      21 ..     154     159 ..     152     161 .. 0.79
   2 ?   10.4   0.2    0.0008      0.53       2      14 ..     191     203 ..     191     205 .. 0.86
   3 ?   10.1   0.8   0.00097      0.65      16      24 ..     217     225 ..     215     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.64
                        UPF0547  16 fCphCG 21 
                                    +Cp CG
  gi|118431444|ref|NP_147924.2| 154 RCPVCG 159
                                    688888 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0008
                        UPF0547   2 vCPeCeakvPvaa 14 
                                    vCP+C ++vP+ +
  gi|118431444|ref|NP_147924.2| 191 VCPRCGSTVPLEV 203
                                    7*********865 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00097
                        UPF0547  16 fCphCGyvF 24 
                                    fC+ CGy++
  gi|118431444|ref|NP_147924.2| 217 FCSRCGYSW 225
                                    9******** PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.4     0.048        32       3      19 ..     155     171 ..     154     182 .. 0.82
   2 ?    4.5   0.1     0.049        33       3      11 ..     192     200 ..     191     211 .. 0.78
   3 ?    4.0   0.1     0.072        48       2       8 ..     217     223 ..     216     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.048
                                    -TTT--B-EEE--TT-S CS
                      Nudix_N_2   3 CsqCGtpvelripdgDn 19 
                                    C+ CG + e+ + +gD 
  gi|118431444|ref|NP_147924.2| 155 CPVCGLESETMVRKGDG 171
                                    9******9999999996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.049
                                    -TTT--B-E CS
                      Nudix_N_2   3 CsqCGtpve 11 
                                    C+ CG++v 
  gi|118431444|ref|NP_147924.2| 192 CPRCGSTVP 200
                                    888888765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.072
                                    B-TTT-- CS
                      Nudix_N_2   2 FCsqCGt 8  
                                    FCs CG 
  gi|118431444|ref|NP_147924.2| 217 FCSRCGY 223
                                    9****95 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.5    0.0014       0.9       1      45 [.     155     199 ..     155     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                           NMD3   1 CcrCGkeieeling......lCedCllkevditegiekievevCkeCgryl 45 
                                    C+ CG e+e+++++      +C  C+++   +++g     + vC++Cg+  
  gi|118431444|ref|NP_147924.2| 155 CPVCGLESETMVRKgdgyymVCHMCFFTWL-VSRG-----IPVCPRCGSTV 199
                                    99****997777667888987777777665.3443.....33566666544 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 ?   13.0   1.9   0.00011     0.071       3      47 ..     153     199 ..     151     201 .. 0.89
   2 ?   -1.6   0.1         4   2.6e+03      25      33 ..     217     225 ..     215     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                    SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH..TT-B-TTT--B- CS
                     zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllk..rkkkCpiCrrpi 47 
                                    + C++C  + +++v    g+ ++C+ C+ ++l     + Cp C + +
  gi|118431444|ref|NP_147924.2| 153 HRCPVCGLESETMVRKGDGYYMVCHMCFFTWLVsrGIPVCPRCGSTV 199
                                    57*******9999999999999******9999778999*****8865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                                    E-HHHHHHH CS
                     zf-C3HC4_3  25 lCeeCaekl 33 
                                    +C++C  ++
  gi|118431444|ref|NP_147924.2| 217 FCSRCGYSW 225
                                    799997765 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 ?    6.3   0.3     0.023        15       3      17 ..     153     169 ..     151     178 .. 0.79
   2 ?    7.8   0.1    0.0079       5.2       3      12 ..     190     200 ..     189     213 .. 0.72
   3 ?   -1.1   0.1       4.8   3.2e+03       4       9 ..     217     222 ..     215     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                        zf-ISL3   3 hrCPnCgsk..tvvkhg 17 
                                    hrCP Cg    t+v++g
  gi|118431444|ref|NP_147924.2| 153 HRCPVCGLEseTMVRKG 169
                                    9******8866556655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0079
                        zf-ISL3   3 hrCPnCgsk.t 12 
                                    ++CP+Cgs+ +
  gi|118431444|ref|NP_147924.2| 190 PVCPRCGSTvP 200
                                    68******954 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.8
                        zf-ISL3   4 rCPnCg 9  
                                     C +Cg
  gi|118431444|ref|NP_147924.2| 217 FCSRCG 222
                                    699999 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   0.1      0.12        79      28      36 ..     154     162 ..     143     166 .. 0.71
   2 ?    5.5   5.2     0.028        18       6      36 ..     174     199 ..     152     201 .. 0.63
   3 ?   -1.4   0.0         4   2.6e+03       8      13 ..     218     223 ..     217     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                    Zn-ribbon_8  28 aCPeCgsev 36 
                                     CP Cg e 
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLES 162
                                    388888654 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                    Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsev 36 
                                      C++C   f+ l+s      ++CP+Cgs+v
  gi|118431444|ref|NP_147924.2| 174 MVCHMCF--FTWLVSRG---IPVCPRCGSTV 199
                                    3455555..55555433...677*****976 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4
                    Zn-ribbon_8   8 CeeCgh 13 
                                    C +Cg 
  gi|118431444|ref|NP_147924.2| 218 CSRCGY 223
                                    888885 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.23   1.5e+02       2       6 ..     155     159 ..     153     162 .. 0.69
   2 ?    6.8   0.1    0.0088       5.9       2      10 ..     192     200 ..     191     203 .. 0.78
   3 ?    5.1   1.6      0.03        20      15      21 ..     217     223 ..     216     224 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.23
                  zinc_ribbon_2   2 CpnCG 6  
                                    Cp CG
  gi|118431444|ref|NP_147924.2| 155 CPVCG 159
                                    66666 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0088
                  zinc_ribbon_2   2 CpnCGaelq 10 
                                    Cp+CG +++
  gi|118431444|ref|NP_147924.2| 192 CPRCGSTVP 200
                                    999998876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.03
                  zinc_ribbon_2  15 FCpyCGt 21 
                                    FC++CG+
  gi|118431444|ref|NP_147924.2| 217 FCSRCGY 223
                                    7777776 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 ?    2.4   0.2      0.21   1.4e+02      31      37 ..     153     159 ..     145     167 .. 0.75
   2 ?    5.6   5.4     0.021        14      18      38 ..     173     197 ..     155     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                    Prok-RING_4  31 ssCPlCq 37 
                                     +CP+C 
  gi|118431444|ref|NP_147924.2| 153 HRCPVCG 159
                                    37****7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                    Prok-RING_4  18 HlvCkeCfdskdls....sCPlCqr 38 
                                     +vC+ Cf  +  s     CP C +
  gi|118431444|ref|NP_147924.2| 173 YMVCHMCFFTWLVSrgipVCPRCGS 197
                                    58*********99986667777765 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 ?    2.4   0.0      0.24   1.6e+02      86     100 ..     152     166 ..     138     174 .. 0.62
   2 ?    7.1   1.0    0.0079       5.3      71      95 ..     153     198 ..     146     205 .. 0.67
   3 ?   -0.7   0.0       2.1   1.4e+03      72      81 ..     217     226 ..     210     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.24
                                    HHS-TTTSSS-EEEE CS
                           HypA  86 alrCpkCgsadveiv 100
                                    + rCp Cg ++ ++v
  gi|118431444|ref|NP_147924.2| 152 SHRCPVCGLESETMV 166
                                    347999987744433 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0079
                                    EEETTTS-EEECHHHHH......................S-TTTSSS CS
                           HypA  71 vrCreCgkefeleekal......................rCpkCgsa 95 
                                     rC +Cg e e+  +                         Cp+Cgs+
  gi|118431444|ref|NP_147924.2| 153 HRCPVCGLESETMVR-KgdgyymvchmcfftwlvsrgipVCPRCGST 198
                                    577777777764432.123345677777777777777779****985 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.1
                                    EETTTS-EEE CS
                           HypA  72 rCreCgkefe 81 
                                     C++Cg++++
  gi|118431444|ref|NP_147924.2| 217 FCSRCGYSWR 226
                                    6999999987 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 ?    5.1   0.3     0.026        17      19      30 ..     150     161 ..     149     162 .. 0.79
   2 ?    4.8   2.3     0.033        22       6      27 ..     155     179 ..     152     179 .. 0.78
   3 ?    5.6   0.1     0.019        12       6      11 ..     192     197 ..     190     203 .. 0.84
   4 ?    3.4   4.0     0.094        62       5      10 ..     217     222 ..     216     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.026
                  zf-NADH-PPase  19 gwarvCpaCgle 30 
                                    g + +Cp Cgle
  gi|118431444|ref|NP_147924.2| 150 GISHRCPVCGLE 161
                                    56679*****98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                  zf-NADH-PPase   6 CgrCG..aptepaeg.gwarvCpaC 27 
                                    C+ CG  ++t++ +g g+ +vC+ C
  gi|118431444|ref|NP_147924.2| 155 CPVCGleSETMVRKGdGYYMVCHMC 179
                                    8888877777888887888998877 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.019
                  zf-NADH-PPase   6 CgrCGa 11 
                                    C+rCG+
  gi|118431444|ref|NP_147924.2| 192 CPRCGS 197
                                    999998 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.094
                  zf-NADH-PPase   5 FCgrCG 10 
                                    FC+rCG
  gi|118431444|ref|NP_147924.2| 217 FCSRCG 222
                                    *****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 ?    3.8   1.5     0.086        57      19      31 ..     153     166 ..     147     182 .. 0.66
   2 ?    5.7   6.4     0.022        14      18      45 ..     188     223 ..     174     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.086
                  Zn_Tnp_IS1595  19 fvCPhCgsr.kayr 31 
                                    ++CP Cg + +   
  gi|118431444|ref|NP_147924.2| 153 HRCPVCGLEsETMV 166
                                    68*****8854444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.022
                  Zn_Tnp_IS1595  18 g.fvCPhCgsrkayrikt.......rglfqCkeCrk 45 
                                    g +vCP+Cgs+ + ++          gl  C++C++
  gi|118431444|ref|NP_147924.2| 188 GiPVCPRCGSTVPLEVGIftdksrrIGLGFCSRCGY 223
                                    369*******95544433334666566667777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.09        60       4       9 ..     154     159 ..     153     162 .. 0.87
   2 ?    6.7   0.1    0.0076         5       5      10 ..     192     197 ..     183     203 .. 0.67
   3 ?    1.2   0.5       0.4   2.7e+02       4       9 ..     217     222 ..     217     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.09
                    zf-ribbon_3   4 rCPnCG 9  
                                    rCP CG
  gi|118431444|ref|NP_147924.2| 154 RCPVCG 159
                                    799998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0076
                    zf-ribbon_3   5 CPnCGa 10 
                                    CP+CG+
  gi|118431444|ref|NP_147924.2| 192 CPRCGS 197
                                    666665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.4
                    zf-ribbon_3   4 rCPnCG 9  
                                    +C++CG
  gi|118431444|ref|NP_147924.2| 217 FCSRCG 222
                                    477776 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.9   2.6e+03       3       9 ..     153     159 ..     152     163 .. 0.79
   2 ?    7.8   0.1    0.0038       2.5       4      14 ..     191     201 ..     191     202 .. 0.89
   3 ?    2.2   0.1       0.2   1.3e+02       4       9 ..     217     222 ..     215     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.9
                         zf_UBZ   3 ylCerCg 9  
                                    + C+ Cg
  gi|118431444|ref|NP_147924.2| 153 HRCPVCG 159
                                    57**9*9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0038
                         zf_UBZ   4 lCerCgkeipe 14 
                                    +C+rCg+++p 
  gi|118431444|ref|NP_147924.2| 191 VCPRCGSTVPL 201
                                    7*******996 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.2
                         zf_UBZ   4 lCerCg 9  
                                    +C+rCg
  gi|118431444|ref|NP_147924.2| 217 FCSRCG 222
                                    7****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.7    0.0069       4.6       2      25 ..     154     179 ..     153     179 .. 0.87
   2 ?    5.4   3.7     0.019        13       2      27 ..     191     223 ..     190     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0069
                                    EETTTTCEE.CHEETSTTCE.EESSS CS
                   TF_Zn_Ribbon   2 kCPnCgstn.lveDpergel.vCtdC 25 
                                    +CP+Cg ++ + +    g + vC  C
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLESeTMVRKGDGYYmVCHMC 179
                                    7*****98889999999999999988 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                                    EETTTTCEE.C....HEE.TSTTCE.EESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgstn.l....veD.pergel.vCtdCGl 27 
                                    +CP Cgst  l     +D   r  l +C++CG+
  gi|118431444|ref|NP_147924.2| 191 VCPRCGSTVpLevgiFTDkSRRIGLgFCSRCGY 223
                                    7******86678887556677777778888885 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 ?    7.3   8.1    0.0086       5.7       7      49 ..     154     193 ..     150     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0086
                  zf-LITAF-like   7 dCpaCqqrvvTsveyksgkltwllalllclfgcllccliPfcv 49 
                                     Cp C+ +++T v++  g +     + +c+f++l+   iP+c 
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLESETMVRKGDGYYMV---CHMCFFTWLVSRGIPVCP 193
                                    7************998887665...555555553444455443 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.6       0.3     2e+02       5      25 ..     155     179 ..     151     183 .. 0.80
   2 ?    7.0   0.2    0.0087       5.8       3      15 ..     190     207 ..     188     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.3
                 PhnA_Zn_Ribbon   5 CplCaSeytY....edgallvCpeC 25 
                                    Cp C+ e++      dg  +vC +C
  gi|118431444|ref|NP_147924.2| 155 CPVCGLESETmvrkGDGYYMVCHMC 179
                                    8888777776678889999****99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0087
                 PhnA_Zn_Ribbon   3 pkCplCaSeytY.....e 15 
                                    p Cp C+S +++      
  gi|118431444|ref|NP_147924.2| 190 PVCPRCGSTVPLevgifT 207
                                    779999999999555551 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.14        95      33      43 ..     148     158 ..     147     159 .. 0.84
   2 ?    9.8   5.3    0.0015      0.98       2      43 ..     154     195 ..     153     196 .. 0.80
   3 ?   -2.3   0.1       9.2   6.1e+03      25      33 ..     217     225 ..     215     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.14
                      zf-RING_2  33 wlrssstCPlC 43 
                                    w   s++CP+C
  gi|118431444|ref|NP_147924.2| 148 WSGISHRCPVC 158
                                    7788899**** PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssst..CPlC 43 
                                     Cp+C   l+s+  v++ +  ++ ++ C+ +wl s+    CP C
  gi|118431444|ref|NP_147924.2| 154 RCPVCG--LESETMVRKGDGYYMVCHMCFFTWLVSRGIpvCPRC 195
                                    6****5..577777776654456899******9999999***99 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 9.2
                      zf-RING_2  25 fhreClerw 33 
                                    f+  C   w
  gi|118431444|ref|NP_147924.2| 217 FCSRCGYSW 225
                                    888887666 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 ?   -1.6   0.1       4.6   3.1e+03      26      31 ..     155     160 ..     152     168 .. 0.73
   2 ?   10.5   0.6   0.00078      0.52       5      33 ..     170     199 ..     166     215 .. 0.76
   3 ?    2.3   0.4      0.28   1.8e+02      24      31 ..     216     223 ..     205     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.6
                   NOB1_Zn_bind  26 CpkCGn 31 
                                    Cp CG 
  gi|118431444|ref|NP_147924.2| 155 CPVCGL 160
                                    999995 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00078
                   NOB1_Zn_bind   5 kswvlrChaCfkvt.kdmtkkFCpkCGnkt 33 
                                      + + Ch Cf +         Cp+CG+  
  gi|118431444|ref|NP_147924.2| 170 DGYYMVCHMCFFTWlVSRGIPVCPRCGSTV 199
                                    56999******98845578889*****865 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.28
                   NOB1_Zn_bind  24 kFCpkCGn 31 
                                     FC++CG 
  gi|118431444|ref|NP_147924.2| 216 GFCSRCGY 223
                                    6******6 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 ?    4.4   1.5     0.053        35       2      18 ..     153     169 ..     152     179 .. 0.73
   2 ?    7.2   0.4    0.0069       4.6       3      12 ..     191     200 ..     190     203 .. 0.81
   3 ?    1.2   0.2      0.52   3.4e+02      23      27 ..     217     221 ..     214     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.053
                                    SB-TTT--BBEEEECTT CS
                   zf-FPG_IleRS   2 epCpRCwryiervgqag 18 
                                    ++Cp+C+   e+++  g
  gi|118431444|ref|NP_147924.2| 153 HRCPVCGLESETMVRKG 169
                                    58*****9988877633 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0069
                                    B-TTT--BBE CS
                   zf-FPG_IleRS   3 pCpRCwryie 12 
                                    +CpRC+ +++
  gi|118431444|ref|NP_147924.2| 191 VCPRCGSTVP 200
                                    6*****9876 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.52
                                    E-TTT CS
                   zf-FPG_IleRS  23 fCprC 27 
                                    fC rC
  gi|118431444|ref|NP_147924.2| 217 FCSRC 221
                                    77777 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 ?    1.1   0.7      0.53   3.5e+02      35      40 .]     153     158 ..     148     158 .. 0.79
   2 ?    6.2   5.8     0.014       9.2       1      40 []     154     195 ..     154     195 .. 0.83
   3 ?    0.2   0.1         1   6.9e+02      21      29 ..     216     224 ..     214     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.53
                     zf-C3HC4_2  35 neCPlC 40 
                                     +CP+C
  gi|118431444|ref|NP_147924.2| 153 HRCPVC 158
                                    589999 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                     zf-C3HC4_2   1 kCpiCldmlkdpsvvtpCgHvfCqkCilrsLeekn..eCPlC 40 
                                    +Cp+C  + ++ ++        C +C+ ++L +     CP C
  gi|118431444|ref|NP_147924.2| 154 RCPVCGLESETMVRKGDGYYMVCHMCFFTWLVSRGipVCPRC 195
                                    5999999988754444888899*********9988789**99 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1
                     zf-C3HC4_2  21 vfCqkCilr 29 
                                    +fC+ C   
  gi|118431444|ref|NP_147924.2| 216 GFCSRCGYS 224
                                    59****876 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 ?   -1.1   0.4       2.6   1.8e+03      36      41 .]     153     158 ..     147     158 .. 0.74
   2 ?    5.6   6.8     0.021        14      21      41 .]     175     195 ..     155     195 .. 0.82
   3 ?   -0.1   0.1       1.3   8.5e+02      21      30 ..     217     226 ..     216     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.6
                                    B--TTT CS
                       zf-C3HC4  36 vkCPlC 41 
                                      CP+C
  gi|118431444|ref|NP_147924.2| 153 HRCPVC 158
                                    469998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.021
                                    B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4  21 fCskCirkilksrkkvkCPlC 41 
                                    +C++C  ++l sr+   CP C
  gi|118431444|ref|NP_147924.2| 175 VCHMCFFTWLVSRGIPVCPRC 195
                                    8**********999999**** PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.3
                                    B-CHHHHHHH CS
                       zf-C3HC4  21 fCskCirkil 30 
                                    fCs C  +++
  gi|118431444|ref|NP_147924.2| 217 FCSRCGYSWR 226
                                    9****87775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      688  (0.0383736); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):              27  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1793.13
//
Query:       gi|14601389|ref|NP_147925.1|  [L=252]
Description: hypothetical protein APE_1408 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.41
# Mc/sec: 1843.82
//
Query:       gi|118431445|ref|NP_147926.2|  [L=331]
Description: hypothetical protein APE_1409.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.19   11.8   0.1       0.19   11.8   0.1    4.3  5  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> 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 ?   -1.4   0.8      0.14   2.5e+03      20      33 ..      11      24 ..       9      27 .. 0.84
   2 ?   11.8   0.1     1e-05      0.19       5      31 ..      36      62 ..      33      64 .. 0.88
   3 ?   -1.0   0.6       0.1   1.8e+03      22      32 ..      77      87 ..      74      94 .. 0.58
   4 ?   -1.2   0.4      0.12   2.2e+03      15      28 ..     113     126 ..     112     127 .. 0.81
   5 ?   -0.5   1.2     0.075   1.3e+03      19      28 ..     163     172 ..     156     176 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.14
                   CytB6-F_Fe-S 20 ialtaaaaLyPvvk 33
                                    a t + +L Pvv+
  gi|118431445|ref|NP_147926.2| 11 TAFTVTVLLFPVVA 24
                                   68899999999985 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1e-05
                   CytB6-F_Fe-S  5 DmsrRqllNlllvGaialtaaaaLyPv 31
                                   + +rR     ++v a+alta++++y+ 
  gi|118431445|ref|NP_147926.2| 36 STGRREYVASIVVSAAALTASSLIYGF 62
                                   5689999999***************96 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.1
                   CytB6-F_Fe-S 22 ltaaaaLyPvv 32
                                   ++aaaaL  ++
  gi|118431445|ref|NP_147926.2| 77 VPAAAALAAYA 87
                                   45555554443 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.12
                   CytB6-F_Fe-S  15 llvGaialtaaaaL 28 
                                    +lv+ +a t+a+ L
  gi|118431445|ref|NP_147926.2| 113 FLVALLASTTASSL 126
                                    68899999999876 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.075
                   CytB6-F_Fe-S  19 aialtaaaaL 28 
                                    ++al+a+a +
  gi|118431445|ref|NP_147926.2| 163 VAALPATAYI 172
                                    4566666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2438.34
//
Query:       gi|118431446|ref|YP_874892.1|  [L=31]
Description: hypothetical protein APE_1409a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       109  (0.00607954); expected 358.6 (0.02)
Passed bias filter:                       93  (0.00518713); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 254.62
//
Query:       gi|118431447|ref|NP_147927.2|  [L=461]
Description: NADH dehydrogenase subunit N [Aeropyrum pernix K1]
Scores for 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-23   81.4  25.8    6.2e-23   81.4  25.8    3.4  2  Proton_antipo_M  Proton-conducting membrane transporter
  ------ inclusion threshold ------
       0.52    9.6   1.0        0.9    8.8   1.0    1.3  1  Tmpp129          Putative transmembrane protein precursor


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   2.7     0.019   1.7e+02     106     144 ..      26      65 ..       3     125 .. 0.63
   2 !   81.4  25.8   6.9e-27   6.2e-23       6     291 ..     133     408 ..     128     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.019
                Proton_antipo_M 106 pdayveaPtpvsallAatlvkagvlllirllllla.vssn 144
                                    p +yv++P     + A t+v++ ++ll+++  +++ ++++
  gi|118431447|ref|NP_147927.2|  26 PAVYVASPSLRRYIQALTAVAVLAFLLAAIATVYHvFAYG 65 
                                    5556666665555555555555555555555555543322 PP

  == domain 2  score: 81.4 bits;  conditional E-value: 6.9e-27
                Proton_antipo_M   6 llylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllll 85 
                                    l+  ++ + ++++y+++gl +++ +s++A++ ++ ++ l+ l++ + i+++y+       + l++            l+ 
  gi|118431447|ref|NP_147927.2| 133 LILASWLVLSVATYIIAGLPGDR-DSVAAAVRYIYVGTLATLFIAVWIAAFYAGLR----PPLAL----------EALAV 197
                                    6667888999**********888.9***************9999999988886444....22332..........35788 PP

                Proton_antipo_M  86 llllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla......vssneisqlllilaiisml 159
                                    +++++++ +K++++p+h W+p++y  a     a++A+ + k++ l+++++l+         + + +++ l+++ a+++m 
  gi|118431447|ref|NP_147927.2| 198 VAIMASIGFKLGAFPFHWWVPNVYGRADGRAIAIVAG-VAKLAFLGILVRLVYTLsggltpFEADALALLIAASAVATMT 276
                                    8**********************************88.7899999988777665557666667778888999999***** PP

                Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialav.........atqygveaaiihllthalfkallFllagsviyerektr 230
                                    lg++ al++ d++ +lAySsi++ Gy+l+++++         +  ++++++ ++ +++a+ ka lF la         ++
  gi|118431447|ref|NP_147927.2| 277 LGNVSALNTGDLRAMLAYSSIAQTGYLLVGMVAvanlmsaglNPTIALAGIGLQAVAYAVAKAPLFSLA---------AE 347
                                    ******************************998422222111223445555556666666666666666.........45 PP

                Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasv 291
                                    +  +++g+   + + a+ ++vll sl G+Pp+ gF++k++++  a+++s+il++la+v s+
  gi|118431447|ref|NP_147927.2| 348 TGGRVKGILRGDWVSAVSVAVLLASLLGIPPLVGFWGKLYMFLPATSYSSILVLLALVNSG 408
                                    56778999999*******************************************9988775 PP

>> Tmpp129  Putative transmembrane protein precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0    0.0001       0.9      41     109 ..      46     112 ..      28     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0001
                        Tmpp129  41 sltllvhsllplgYflgllllsk......vkaeelleletlwkvllllsvllailalvlvvywsskkwsnhPiak 109
                                    +++ ++ +++  +Y               + a+++  +++l +v+ll ++ la++++++  y++ ++w +hP + 
  gi|118431447|ref|NP_147927.2|  46 AVLAFLLAAIATVYH-------VfaygnlTMANNMIVHDKLSSVMLLGAA-LAAALAYIQAYYKAEEWPTHPGYY 112
                                    223333333333444.......2333444446677777777776666555.7888888889***********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3118.79
//
Query:       gi|118431448|ref|NP_147928.2|  [L=701]
Description: NuoL-like protein [Aeropyrum pernix K1]
Scores for complete 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-51  175.9  29.6    4.3e-48  164.0  27.7    4.9  4  Proton_antipo_M  Proton-conducting membrane transporter
    9.1e-15   54.5   2.7    9.1e-15   54.5   2.7    3.3  2  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 ?   -2.7   1.5      0.29   2.6e+03      39      79 ..      96     136 ..      91     141 .. 0.65
   2 !   20.4   0.0   2.7e-08   0.00025       1      30 [.     142     171 ..     142     176 .. 0.93
   3 !  164.0  27.7   4.8e-52   4.3e-48      32     293 .]     192     483 ..     189     483 .. 0.84
   4 ?   -1.4   0.8      0.12     1e+03      90     132 ..     570     585 ..     519     619 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.29
                Proton_antipo_M  39 flltllgsliLLlgilllynltgtlefeelskalelglnsl 79 
                                    ++   +++++LL+++  +  ++g+  f   + ++++ ++s+
  gi|118431448|ref|NP_147928.2|  96 VMSLVVSWISLLIAVYSIKYMEGDWGFGRYFFMISFFVGSM 136
                                    55556788888888888888888877766666655444444 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.7e-08
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpk 30 
                                    a++L+l+++g+E+++l++y Lig w+++++
  gi|118431448|ref|NP_147928.2| 142 ADNLVLMFVGWEGTGLASYALIGHWYTDEE 171
                                    79************************9976 PP

  == domain 3  score: 164.0 bits;  conditional E-value: 4.8e-52
                Proton_antipo_M  32 leAslklflltllgsliLLlgilllynltgtlefeelskal....elglnslelllllllllvgllvKsaqvplhlWlpd 107
                                    +++++ ++l t++g++ +L+gi++ly  +gtl+++el++++       +++  l l+ll++++g+l+Ksaqvp+h Wl+ 
  gi|118431448|ref|NP_147928.2| 192 SHSAVRAILFTRIGDIGFLIGIAALYLTAGTLSIPELASTAhvwiAEFAAQGVLPLILLIFTLGALAKSAQVPFHEWLVT 271
                                    5689999**********************************5554333444455577778889***************** PP

                Proton_antipo_M 108 ayveaPtpvsall.Aatlvkagvlllirllllla..........vss..neisqlllilaiismllgslvalaqtdiKrl 174
                                    a + +Ptpvsal+ Aat+vkagv+ ++r+ +++           v s  + +  l++++a++++ll sl+al+  ++K +
  gi|118431448|ref|NP_147928.2| 272 A-MTGPTPVSALIhAATMVKAGVYFVLRFAPIIVagalaagapeVLSgvGSYFTLIAWIAVLTALLLSLMALVSDELKLI 350
                                    *.*****************************987665433333322311345567899********************** PP

                Proton_antipo_M 175 lAySsishlGymlialavatqy...............gveaaiihllthalfkallFllagsviyerektrdirayggLa 239
                                    lA+S+ s+lGym++a+a+++++               +v+a + hl++ha+fka+lFl+ag vi++  ++r i+++gg+a
  gi|118431448|ref|NP_147928.2| 351 LAFSTASQLGYMILAAAAGGVIasvlaggealelageAVAAGLGHLVSHAVFKAALFLAAGWVIHAA-HSRFIDNMGGFA 429
                                    ***************99977652222222212222114566688*******************9998.9*********** PP

                Proton_antipo_M 240 kkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvlt 293
                                     +m ++a+++ ++ lslaG+Pp++gF+ k ++ + a+++++++  la ++++lt
  gi|118431448|ref|NP_147928.2| 430 RYMKLTAAAFWLAGLSLAGVPPLSGFFTKEEVVAIAYKAEPVIGGLAALTALLT 483
                                    *****************************************9999998888776 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.12
                Proton_antipo_M  90 vgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlll 132
                                    +g                            +A++++ ag++++
  gi|118431448|ref|NP_147928.2| 570 AG---------------------------VIASIALVAGLYMV 585
                                    22...........................22444444444444 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 !   54.5   2.7     1e-18   9.1e-15       4      58 .]      78     130 ..      76     130 .. 0.92
   2 ?    0.1   0.2     0.096   8.6e+02      20      44 ..     560     584 ..     545     593 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1e-18
                Proton_antipo_N   4 WlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayls 58 
                                    W++  +l + +g ++D+l a+m lvv+++sll+ +YSi+YM++d+g+ R+f+++s
  gi|118431448|ref|NP_147928.2|  78 WIP--HLGVGWGSYIDGLAAVMSLVVSWISLLIAVYSIKYMEGDWGFGRYFFMIS 130
                                    666..45699*****************************************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.096
                Proton_antipo_N  20 klsalmllvvtfvsllvhlYSigYM 44 
                                    k++ l   vv +v + + l +  YM
  gi|118431448|ref|NP_147928.2| 560 KVTSLTYSVVAGVIASIALVAGLYM 584
                                    6788899999999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.22s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 5104.78
//
Query:       gi|14601393|ref|NP_147929.1|  [L=513]
Description: NuoM-like protein [Aeropyrum pernix K1]
Scores for complete 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-57  194.2  22.7    5.6e-57  193.2  22.1    1.8  1  Proton_antipo_M  Proton-conducting membrane transporter
    0.00048   20.1   3.6     0.0068   16.5   0.1    3.1  2  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 !  193.2  22.1   6.2e-61   5.6e-57       2     278 ..     142     423 ..     141     439 .. 0.91

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 6.2e-61
               Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal.....elgln 77 
                                    + ll+ ++lEl ll+++lLi+++++  ++  A l+++ +  +g l+LL g+ ++   tgt ++ ++         + +  
  gi|14601393|ref|NP_147929.1| 142 LNFLLFIIFLELSLLSSFLLIAFYGYGDRRRIALLYFVWTHIAGALALLGGLYYVI-KTGTFDVATVEGGRivyfsSPADR 221
                                   6899**********************977777766666666666666666666665.678777777665555577688999 PP

               Proton_antipo_M  78 slelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiis 157
                                   s  + ++ + ll+g+lvK+a++ +h+Wlp a+ eaPtp+sall+  l  +g+++++r+   +     ++++ ll+ la+++
  gi|14601393|ref|NP_147929.1| 222 SVYAAIAGVSLLLGMLVKMAVFGVHMWLPYAHAEAPTPISALLSPNLIGLGGYGIARFAAAFYpWLLEDLKPLLVGLAFVT 302
                                   999****************************************999*************9999899*************** PP

               Proton_antipo_M 158 mllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggL 238
                                   +++g+lval+q d KrllAySsis++Gyml+al++    g++aa + +l ha+ ka lF+ ag +i e +  r+i+++ggL
  gi|14601393|ref|NP_147929.1| 303 IVYGGLVALSQLDFKRLLAYSSISQMGYMLLALSTLHPLGFAAASLIFLGHAVGKAVLFMTAGVFITEAHGLRNIARMGGL 383
                                   ***********************************99******************************************** PP

               Proton_antipo_M 239 akkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                   a   P++a++ l+++l laG+Pp  gF++++++  +++++
  gi|14601393|ref|NP_147929.1| 384 ARLYPLTAAAALIGFLHLAGIPPAFGFWGELYLTLSVLNY 423
                                   *******************************998777765 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   7.6e-07    0.0068      14      45 ..      74     105 ..      70     129 .. 0.90
   2 ?    2.8   0.6     0.014   1.3e+02      17      40 ..     426     450 ..     419     457 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.6e-07
               Proton_antipo_N  14 igfllDklsalmllvvtfvsllvhlYSigYMa 45 
                                   +++ +D++s  ++l v++v++lv +Y  +YM+
  gi|14601393|ref|NP_147929.1|  74 VALAVDGFSYPFVLGVSVVTALVAVYGYKYME 105
                                   5789***************************6 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.014
               Proton_antipo_N  17 llDklsalmllvvtfvsllvh.lYS 40 
                                   + D +s+  l+++ +v++ v   YS
  gi|14601393|ref|NP_147929.1| 426 YSDAVSLGLLAIILIVAFTVTaAYS 450
                                   5699**************9952466 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3733.55
//
Query:       gi|118431449|ref|NP_147930.2|  [L=101]
Description: NuoK-like protein [Aeropyrum pernix K1]
Scores for 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-11   42.9   9.6    3.8e-11   42.5   9.6    1.1  1  Oxidored_q2    NADH-ubiquinone/plastoquinone oxidoreductase c
     0.0079   16.1   1.6     0.0079   16.1   1.6    1.4  1  DUF485         Protein of unknown function, DUF485
  ------ inclusion threshold ------
      0.017   14.4   5.3      0.021   14.2   5.3    1.1  1  NADHdh         NADH dehydrogenase
      0.041   12.9   4.6      0.051   12.6   4.6    1.1  1  ArAE_2_N       Putative ER transporter, 6TM, N-terminal
        1.3    8.9   7.1       0.11   12.3   2.8    1.4  2  Amastin        Amastin surface glycoprotein


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 !   42.5   9.6   1.1e-14   3.8e-11       2     103 ..       9      96 ..       8      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.1e-14
                                    HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHH CS
                    Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaet 81 
                                    + ll+a+l +iG yg+  +rnl+++li+ e++ na  l+++l+ +++                +  + ++++iv++ +e+
  gi|118431449|ref|NP_147930.2|   9 VVLLAAVLAAIGSYGLAGSRNLVRQLISAEVLFNAFLLIVILVLSKS-------------SLAANVLGIMLVIVVS-GEI 74 
                                    5799***************************************9998.............8888888999999999.*** PP

                                    HHHHHHHHHHHHHSSS-BCCG- CS
                    Oxidored_q2  82 avgLallvrlyreygtddvqel 103
                                    +v++al+ +lyr  gt++++ l
  gi|118431449|ref|NP_147930.2|  75 IVVVALVAALYRRLGTLETEPL 96 
                                    ******************9987 PP

>> DUF485  Protein of unknown function, DUF485
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.6   2.2e-06    0.0079      12      85 ..      27      98 ..      22      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                         DUF485 12 krrrfafpltaiflvvYfgfvllvafapdllatkvgegnitvglllgllqivltflltglYvrrAnrefDplae 85
                                   +r+ +  +++a +l+  f++++++ ++++ la++v+ g i + +++   +iv++ l+++lY r    e +pl e
  gi|118431449|ref|NP_147930.2| 27 SRNLVRQLISAEVLFNAFLLIVILVLSKSSLAANVL-G-IMLVIVVSGEIIVVVALVAALYRRLGTLETEPLEE 98
                                   56777777888889999999****************.8.9999999999************9999888888876 PP

>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.3   5.8e-06     0.021     109     192 ..       7      86 ..       2      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
                                    CHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHH CS
                         NADHdh 109 gvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiveaqeeiwfillqllafiiflialla 188
                                    +v+++l a +a+   Y l G+   + q+is Ev +   ll+v+l+ ++ sl   v       ++++ + + ii+++al+a
  gi|118431449|ref|NP_147930.2|   7 QVVVLLAAVLAAIGSYGLAGSRNLVRQLISAEVLFNAFLLIVILVLSKSSLAANVLGI----MLVIVVSGEIIVVVALVA 82 
                                    46667777889999********9***************************99997632....344447778888888877 PP

                                    CCTC CS
                         NADHdh 189 etnr 192
                                     + r
  gi|118431449|ref|NP_147930.2|  83 ALYR 86 
                                    7655 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 ?   12.6   4.6   1.4e-05     0.051      27      76 ..      40      89 ..      30      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                       ArAE_2_N 27 wvaiiLmvipptarwlGtaayLllivsvivpsGggsvivfilialllllg 76
                                    + ++L+++  ++++ + aa  l i++viv+sG+ +v+v++++al+  lg
  gi|118431449|ref|NP_147930.2| 40 LFNAFLLIVILVLSKSSLAANVLGIMLVIVVSGEIIVVVALVAALYRRLG 89
                                   4556677777899*******************************987665 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.5   5.3e+03      76      80 ..      11      15 ..       4      24 .. 0.44
   2 ?   12.3   2.8     3e-05      0.11      69     120 ..      33      86 ..      29      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                        Amastin 76 laaal 80
                                   l+aa+
  gi|118431449|ref|NP_147930.2| 11 LLAAV 15
                                   11111 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3e-05
                        Amastin  69 siisilvlaaalllsvllllccsslk..wvclllnivsvvtllivwalmvavyy 120
                                    ++is  vl+ a+ll v+l+l+ ssl   ++ ++l+iv     ++v al++a+y+
  gi|118431449|ref|NP_147930.2|  33 QLISAEVLFNAFLLIVILVLSKSSLAanVLGIMLVIVVSGEIIVVVALVAALYR 86 
                                    679*****************9988761145556777777777888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1183  (0.0659825); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 765.84
//
Query:       gi|118431450|ref|NP_147931.2|  [L=160]
Description: NuoJ-like protein [Aeropyrum pernix K1]
Scores for 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-16   58.6  11.3    5.3e-16   58.6  11.3    1.3  1  Oxidored_q3    NADH-ubiquinone/plastoquinone oxidoreductase c
  ------ inclusion threshold ------
       0.48    9.1   6.9       0.16   10.7   4.3    1.5  1  DUF2207        Predicted membrane protein (DUF2207)


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 !   58.6  11.3   5.9e-20   5.3e-16       2     143 ..      21     155 ..      20     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 5.9e-20
                                    HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHHH CS
                    Oxidored_q3   2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaall 81 
                                    +++v+ ++ +vys  +L+l+ +++a+++ llg +++a+++++vYvGA +++++ ++++l   +   +e++ ++  laa++
  gi|118431450|ref|NP_147931.2|  21 SMFVVRHRDMVYSSAALALVGLSTAAVVGLLGFPLVAVFLVIVYVGAAVMFIIVSVSML---GGGGREEWDEWRGLAAAA 97 
                                    6899******************************************************5...667889999999999999 PP

                                    HHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHH CS
                    Oxidored_q3  82 igllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaiv 143
                                    +++  ++ll ++ +     ++  + +++ n+e+i+ +l  + + ++++++  L ++++  i+
  gi|118431450|ref|NP_147931.2|  98 AAFSTVTLLGFIGGL----WQLYTPPQPVNLETIALVLTRDLYPVVIVLAAGLAATILEGIA 155
                                    999999999999664....4455678999*********998888888888888888887776 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.3   1.8e-05      0.16     380     451 ..      31      93 ..       5      95 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                        DUF2207 380 lkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrrteeGaellakwkgF 451
                                     +++ al+l+++  + +++ll++ l+    vfl+i+ ++ ++++iiv + +      +   G+e++++w+g+
  gi|118431450|ref|NP_147931.2|  31 VYSSAALALVGLSTAAVVGLLGFPLV---AVFLVIVYVGAAVMFIIVSVSM------LGGGGREEWDEWRGL 93 
                                    33333433333333333333322222...4555555555555555555544......5679*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1269.65
//
Query:       gi|118431451|ref|NP_147932.2|  [L=186]
Description: NADH dehydrogenase subunit I [Aeropyrum pernix K1]
Scores for 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   51.1  13.9      8e-09   35.0   3.3    2.2  2  Fer4      4Fe-4S binding domain
    4.9e-12   46.3  20.9    3.5e-09   37.1  11.4    1.6  2  Fer4_7    4Fe-4S dicluster domain
    1.8e-10   40.8  21.0    3.6e-07   30.2  12.9    2.0  2  Fer4_10   4Fe-4S dicluster domain
    7.2e-10   38.5  14.4    1.3e-05   25.1   2.7    2.2  2  Fer4_6    4Fe-4S binding domain
    2.8e-09   37.8   5.2    0.00083   20.2   0.1    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    3.9e-09   36.5  19.6    7.8e-08   32.4   9.4    1.8  2  Fer4_9    4Fe-4S dicluster domain
    5.4e-08   32.8   8.2    8.4e-08   32.2   8.2    1.3  1  Fer4_21   4Fe-4S dicluster domain
    2.6e-07   31.1   3.2     0.0039   17.7   0.1    2.2  2  Fer4_17   4Fe-4S dicluster domain
    8.2e-07   28.8  11.1     0.0027   17.7   2.5    2.4  2  Fer4_2    4Fe-4S binding domain
    3.6e-06   27.1  11.8     0.0039   17.6   1.4    2.2  2  Fer4_4    4Fe-4S binding domain
    1.3e-05   25.5   8.4    0.00059   20.2  10.7    2.0  2  Fer4_8    4Fe-4S dicluster domain
    7.9e-05   23.3   3.6       0.18   12.6   0.1    2.3  2  Fer4_15   4Fe-4S single cluster domain
    0.00012   22.6  10.6      0.096   13.2   0.5    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00027   21.1   5.6      0.058   13.6   0.4    2.2  2  Fer4_18   4Fe-4S dicluster domain
     0.0015   19.3  15.2      0.032   15.2   2.8    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.12   13.3  12.2        1.6    9.6   1.8    2.2  3  Fer4_22   4Fe-4S dicluster domain
          4    7.6   7.1        5.1    7.3   2.5    2.2  2  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


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 !   21.9   2.9     1e-07   0.00011       2      23 ..      60      81 ..      59      82 .. 0.89
   2 !   35.0   3.3   7.6e-12     8e-09       1      24 []     103     126 ..     103     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1e-07
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                   + ++ kCi C aC+ +CP  A 
  gi|118431451|ref|NP_147932.2| 60 ILNKAKCISCAACARICPSAAM 81
                                   67999*************9986 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 7.6e-12
                                    EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                    +vi++ +Ci+CG+Cv++CP++A++
  gi|118431451|ref|NP_147932.2| 103 PVINYQRCIFCGYCVDICPTEALY 126
                                    69********************85 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1  11.4   3.3e-12   3.5e-09       1      52 []      65     124 ..      65     124 .. 0.74
   2 !   21.4   1.9   2.7e-07   0.00028       1      22 [.     109     130 ..     109     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3.3e-12
                         Fer4_7   1 rCigCgaCvaaCpvkaield........eeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +Ci C aC++ Cp+ a+++         e e++ +++ ++i++++C++Cg Cv+ CPt+a
  gi|118431451|ref|NP_147932.2|  65 KCISCAACARICPSAAMKMIrvpvphpkEPEKKVTKQFPVINYQRCIFCGYCVDICPTEA 124
                                    7****************988333332211222223355699*****************87 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.7e-07
                         Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                    rCi Cg+Cv+ Cp++a++  ++
  gi|118431451|ref|NP_147932.2| 109 RCIFCGYCVDICPTEALYHVNY 130
                                    8***************997654 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2  12.9   3.4e-10   3.6e-07       2      56 .]      59     121 ..      58     121 .. 0.81
   2 !   22.3   1.0   9.8e-08    0.0001       2      23 ..     103     124 ..     102     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.4e-10
                        Fer4_10   2 vvidddtCirCgkCvkaCPadl........tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +++++ +Ci C++C + CP+ +         + +  +++  ++   +++++C++cg+Cv++CP
  gi|118431451|ref|NP_147932.2|  59 IILNKAKCISCAACARICPSAAmkmirvpvPHPKEPEKKVTKQFPVINYQRCIFCGYCVDICP 121
                                    68899***************88*****99544444444455555556***************9 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 9.8e-08
                        Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                    +vi+ ++Ci Cg Cv+ CP+ +
  gi|118431451|ref|NP_147932.2| 103 PVINYQRCIFCGYCVDICPTEA 124
                                    58999**************965 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   4.1   1.1e-06    0.0011       5      23 ..      62      80 ..      61      81 .. 0.90
   2 !   25.1   2.7   1.2e-08   1.3e-05       1      24 []     102     125 ..     102     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                         Fer4_6  5 dpdkCigCgdCvrvCPega 23
                                   ++ kCi+C +C+r+CP +a
  gi|118431451|ref|NP_147932.2| 62 NKAKCISCAACARICPSAA 80
                                   578*************877 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.2e-08
                         Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                    +++i++++Ci Cg Cv++CP+ a+
  gi|118431451|ref|NP_147932.2| 102 FPVINYQRCIFCGYCVDICPTEAL 125
                                    69*******************996 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.1   2.5e-06    0.0026       1      30 [.      65      94 ..      65     107 .. 0.75
   2 !   20.2   0.1   7.9e-07   0.00083       1      25 [.     109     133 ..     109     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.5e-06
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearec 30
                                   +C++C +Ca +CP++a+k+ + ++  ++e 
  gi|118431451|ref|NP_147932.2| 65 KCISCAACARICPSAAMKMIRVPVPHPKEP 94
                                   6****************9875555554444 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 7.9e-07
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekei 25 
                                    rC+ Cg C+++CPt+a+ + ++  i
  gi|118431451|ref|NP_147932.2| 109 RCIFCGYCVDICPTEALYHVNYHDI 133
                                    6***************998855554 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.5   6.4e-06    0.0068      34      50 ..      64      80 ..      39      81 .. 0.74
   2 !   32.4   9.4   7.4e-11   7.8e-08       1      50 [.      65     124 ..      65     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.4e-06
                         Fer4_9 34 eaCigCgaCveaCpkga 50
                                    +Ci+C aC+ +Cp+ a
  gi|118431451|ref|NP_147932.2| 64 AKCISCAACARICPSAA 80
                                   68************986 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 7.4e-11
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkga 50 
                                    kC++C aC + Cp+ ++++ +++     + +++          ++Ci+Cg Cv++Cp++a
  gi|118431451|ref|NP_147932.2|  65 KCISCAACARICPSAAMKMIRVPVPHPKEPEKKvtkqfpvinyQRCIFCGYCVDICPTEA 124
                                    7****************99999999888877779999********************986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   8.2   7.9e-11   8.4e-08       3      54 ..      61     123 ..      59     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.9e-11
                        Fer4_21   3 idedkCigCgkCliaCedtshqai..........eidaktvlkvv.edeCvGCnlCssvCPve 54 
                                    ++++kCi+C  C+  C+ ++++ i          e++  ++++v+  ++C+ C  C+++CP+e
  gi|118431451|ref|NP_147932.2|  61 LNKAKCISCAACARICPSAAMKMIrvpvphpkepEKKVTKQFPVInYQRCIFCGYCVDICPTE 123
                                    6899********************888888765544444566887479*************74 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.4   5.3e-05     0.056       1      16 [.      65      80 ..      60     106 .. 0.67
   2 !   17.7   0.1   3.7e-06    0.0039       1      29 [.     109     137 ..     109     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-05
                        Fer4_17  1 rCiqCgyClpeCpsye 16
                                   +Ci+C++C++ Cps +
  gi|118431451|ref|NP_147932.2| 65 KCISCAACARICPSAA 80
                                   5777777777777754 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.7e-06
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraa 29 
                                    rCi CgyC++ Cp+ + y  + + ++++ 
  gi|118431451|ref|NP_147932.2| 109 RCIFCGYCVDICPTEALYHVNYHDIVYDN 137
                                    7*************999988877777763 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.5   9.6e-06      0.01       4      21 ..      60      77 ..      57      78 .. 0.89
   2 !   17.7   2.5   2.6e-06    0.0027       3      22 .]     103     122 ..     101     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.6e-06
                         Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                     + ++Ci+C aC   CP
  gi|118431451|ref|NP_147932.2| 60 ILNKAKCISCAACARICP 77
                                   57899************* PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.6e-06
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    +v++ +rCi Cg Cv+ CP+
  gi|118431451|ref|NP_147932.2| 103 PVINYQRCIFCGYCVDICPT 122
                                    799****************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 !   14.5   3.2   3.6e-05     0.038       2      16 ..      64      78 ..      63      82 .. 0.90
   2 !   17.6   1.4   3.7e-06    0.0039       1      16 [.     107     122 ..     107     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                    +Ci C +C ++CP+
  gi|118431451|ref|NP_147932.2| 64 AKCISCAACARICPS 78
                                   58************6 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.7e-06
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    ++rCi Cg Cv++CP+
  gi|118431451|ref|NP_147932.2| 107 YQRCIFCGYCVDICPT 122
                                    58*************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2  10.7   5.6e-07   0.00059       4      64 ..      65     123 ..      63     124 .. 0.85
   2 !   15.1   0.5   2.2e-05     0.023       3      22 ..     108     127 ..     106     160 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.6e-07
                         Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    kCi C aC   Cp++  +  + +   ++e ++ ++++q      + ++C  cg C++ Cp++
  gi|118431451|ref|NP_147932.2|  65 KCISCAACARICPSAAMKMiRVPVPHPKEPEK-KVTKQF--PVINYQRCIFCGYCVDICPTE 123
                                    8************8888888888888888888.777776..347899*************85 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-05
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtk 22 
                                    ++Ci Cg+C + Cp+     
  gi|118431451|ref|NP_147932.2| 108 QRCIFCGYCVDICPTEALYH 127
                                    68***********9433333 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.5   0.00034      0.36       1      20 [.      59      78 ..      59      84 .. 0.87
   2 !   12.6   0.1   0.00017      0.18       3      20 ..     105     122 ..     104     152 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                        Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                   + +++ +Ci+c++C++ +p 
  gi|118431451|ref|NP_147932.2| 59 IILNKAKCISCAACARICPS 78
                                   568899************96 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00017
                        Fer4_15   3 vDrdaCigcglCvaeape 20 
                                    ++ ++Ci cg Cv+ +p+
  gi|118431451|ref|NP_147932.2| 105 INYQRCIFCGYCVDICPT 122
                                    7889************94 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 !   13.1   3.9    0.0001      0.11       2      18 ..      62      78 ..      61      79 .. 0.91
   2 !   13.2   0.5   9.1e-05     0.096       1      18 [.     105     122 ..     105     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                        Fer4_13  2 DrdtCiacgaCvelaPd 18
                                   ++ +Ci+c+aC+ ++P 
  gi|118431451|ref|NP_147932.2| 62 NKAKCISCAACARICPS 78
                                   6899************6 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.1e-05
                        Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                    ++ ++Ci cg Cv+++P 
  gi|118431451|ref|NP_147932.2| 105 INYQRCIFCGYCVDICPT 122
                                    57789************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.6    0.0007      0.73      58      73 ..      63      78 ..      57      87 .. 0.85
   2 !   13.6   0.4   5.5e-05     0.058      57      74 ..     106     123 ..      88     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0007
                        Fer4_18 58 agdcidcescvkvcPt 73
                                   +++ci+c +c ++cP 
  gi|118431451|ref|NP_147932.2| 63 KAKCISCAACARICPS 78
                                   6889999999999996 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.5e-05
                        Fer4_18  57 gagdcidcescvkvcPtg 74 
                                    +   ci c++cv++cPt+
  gi|118431451|ref|NP_147932.2| 106 NYQRCIFCGYCVDICPTE 123
                                    5678************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 !    9.8   4.7    0.0015       1.6       1      13 [.      66      78 ..      66      80 .. 0.91
   2 !   15.2   2.8     3e-05     0.032       1      15 []     110     124 ..     110     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                         Fer4_3  1 CtgCgaCvevCPv 13
                                   C+ C aC + CP+
  gi|118431451|ref|NP_147932.2| 66 CISCAACARICPS 78
                                   ************8 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+ Cg Cv+ CP+ A
  gi|118431451|ref|NP_147932.2| 110 CIFCGYCVDICPTEA 124
                                    ************876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   3.6    0.0044       4.6       1      16 [.      65      80 ..      65     102 .. 0.80
   2 ?    9.6   1.8    0.0015       1.6      70      94 ..      98     122 ..      90     124 .. 0.71
   3 ?    8.9   1.7    0.0026       2.8       1      20 [.     109     128 ..     109     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0044
                        Fer4_22  1 rClsCgaCtlvCptCs 16
                                   +C+sC+aC+ +Cp+  
  gi|118431451|ref|NP_147932.2| 65 KCISCAACARICPSAA 80
                                   7************865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                        Fer4_22  70 lsefkekfgesgCvGCgRCieacpv 94 
                                    +++    ++ + C+ Cg C++ cp+
  gi|118431451|ref|NP_147932.2|  98 VTKQFPVINYQRCIFCGYCVDICPT 122
                                    4445555578888888888888886 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0026
                        Fer4_22   1 rClsCgaCtlvCptCsCfdv 20 
                                    rC+ Cg C  +Cpt   ++v
  gi|118431451|ref|NP_147932.2| 109 RCIFCGYCVDICPTEALYHV 128
                                    7999********99766655 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 ?    4.5   1.0     0.035        37      67      89 ..      58      80 ..      41      91 .. 0.77
   2 ?    7.3   2.5    0.0049       5.1      46      86 ..      72     121 ..      70     131 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.035
                                   EEEE-CCC--S--HHHHH-TT-- CS
                         ETF_QO 67 klqinaqnCvhCktCdikdpsqn 89
                                    + +n + C+ C +C    ps  
  gi|118431451|ref|NP_147932.2| 58 FIILNKAKCISCAACARICPSAA 80
                                   466899*********87777655 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0049
                                    HHHH-TTS-EEEEE.........TTTTSSEEEEE-CCC--S--HHHHH-T CS
                         ETF_QO  46 eqryCPagvyeive.........deeakekklqinaqnCvhCktCdikdp 86 
                                    ++r+CP++  ++++         +++ +++  +in q C+ C  C    p
  gi|118431451|ref|NP_147932.2|  72 CARICPSAAMKMIRvpvphpkepEKKVTKQFPVINYQRCIFCGYCVDICP 121
                                    678899988888876666554322334455558*********99954445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1403.09
//
Query:       gi|118431452|ref|NP_147933.2|  [L=375]
Description: NADH dehydrogenase subunit H [Aeropyrum pernix K1]
Scores for 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-78  261.7  23.2    1.1e-77  261.4  23.2    1.0  1  NADHdh    NADH dehydrogenase
  ------ inclusion threshold ------
       0.29   11.0   4.6       0.16   11.8   0.8    2.5  2  PGG       Domain of unknown function


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 !  261.4  23.2   1.2e-81   1.1e-77       9     297 ..      26     334 ..      18     336 .. 0.93

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 1.2e-81
                                    HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT..TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS CS
                         NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGpl..GllqplaDalKlllKediipkkadkllfllapvlalilallafavi 86 
                                     +ll++++++++eRk +Ar+q+R+GP  ++p+  Gll+++aD++++++++ iip+++d + fl+ap++ +++++l fav+
  gi|118431452|ref|NP_147933.2|  26 GALLIAIVAVWFERKAAARVQRRIGPYWASPRlgGLLHLVADMMRYMFQQVIIPRTVDYFPFLVAPIVGMAVSILPFAVV 105
                                    4566677***********************9777********************************************** PP

                                    -SSS.......SSS--...TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S CS
                         NADHdh  87 Pfge.......vladl...nvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllags 156
                                    P+++               +++lll+la+s+l ++++++aGwa+n++++++G++R+a ++++yE++ +lslla+++++gs
  gi|118431452|ref|NP_147933.2| 106 PLTAnpsywplP---PglmEYSLLLALAISTLPPIFLIVAGWAANNPFTIVGGVREAFIILAYELIAILSLLAPAITVGS 182
                                    *99445555431...133466*********************************************************** PP

                                    S-HHHHHHCCCTT.-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHH CS
                         NADHdh 157 lslseiveaqeei.wfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsala 235
                                    +++ eiv+aq    wfi+l++laf++ +ia+ ++t+ +PF++pe+e E+vaG++tEYsg+ +al + + y++ +++s++a
  gi|118431452|ref|NP_147933.2| 183 FNIVEIVQAQGFFkWFIILNPLAFLAAVIAIAMSTSAFPFEIPESEPEVVAGPFTEYSGILYALNMGGAYMRRFAFSLIA 262
                                    **********7558****************************************************************** PP

                                    HHHCT.SS-HCCS..........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                         NADHdh 236 vllFlgGwllpfs..........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                    +l+ lgGw + ++          + l++++K++l+ + + ++ra++ R+R+dq+++l+w  +lpl+l+++ll
  gi|118431452|ref|NP_147933.2| 263 SLVLLGGWYPVVPgegvvmgyllPSLVVVAKAALVTLAISFLRAVYGRYRLDQALDLAWRLVLPLTLLAILL 334
                                    ********8877799999999999999*****************************************9997 PP

>> PGG  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   1.8e-05      0.16      48      77 ..     190     219 ..     185     254 .. 0.81
   2 ?   -1.3   0.2       0.2   1.8e+03      64     113 ..     256     307 ..     253     310 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                            PGG  48 akkaafkvFvisnaiAlvaSlvvvvlllis 77 
                                    + +  fk F+i+n +A++a+++++ + +++
  gi|118431452|ref|NP_147933.2| 190 QAQGFFKWFIILNPLAFLAAVIAIAMSTSA 219
                                    45568********************99843 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.2
                            PGG  64 lvaSlvvvvlll..isslvedeakslpkklrvllvllvlsllsllvaFaagl 113
                                    +++Sl++ ++ll  +  +v  e   +   l  l v+  ++l++l+++F+ ++
  gi|118431452|ref|NP_147933.2| 256 FAFSLIASLVLLggWYPVVPGEGVVMGYLLPSLVVVAKAALVTLAISFLRAV 307
                                    5566666666662222224555555555566666666677777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2948.12
//
Query:       gi|14601398|ref|NP_147934.1|  [L=414]
Description: NADH dehydrogenase subunit D [Aeropyrum pernix K1]
Scores for complete 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-85  285.0   0.0    5.9e-85  284.6   0.0    1.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


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 !  284.6   0.0   3.3e-89   5.9e-85       2     271 .]     143     414 .]     143     414 .] 0.93

  Alignments for each domain:
  == domain 1  score: 284.6 bits;  conditional E-value: 3.3e-89
                                   TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSS CS
                Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkg 82 
                                   lG+ t++++a+ +Re +++l e++tGaRlt+sy ++GG +rD+p+++ ++ ++++++++k+lde+ k++ +n+++++R++g
  gi|14601398|ref|NP_147934.1| 143 LGHSTMYMWAMGDREVFIELAEALTGARLTHSYPIPGGARRDIPADFPDMARRAVRYMRKRLDEYAKIFLNNPVIRSRLEG 223
                                   69******************************************************************************* PP

                                   SS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--... CS
                Complex1_49kDa  83 vgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpe.. 161
                                   vgv+ k+ a e+g++Gp++R+sG++yD+R ++pY+aY e+df+vpv eegD+++R++vrveE++qSl+Iieqa+e+l++  
  gi|14601398|ref|NP_147934.1| 224 VGVIPKKAAAEMGIVGPNARGSGIDYDVRLVHPYDAYPEIDFEVPVFEEGDALARTYVRVEEIKQSLRIIEQAVEWLEKhp 304
                                   *************************************************************************99997634 PP

                                   .S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTT CS
                Complex1_49kDa 162 .gpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlq 241
                                    +p++ +    ++p+ ++   + e    +   +   +kvp+g ++ + E+++Ge+++y+ sdg+ +pyr++i ++s  n+ 
  gi|14601398|ref|NP_147934.1| 305 rEPIVDKYLYGKYPPLHKKVLEAEGRA-KLLPTVAAMKVPPGRAIGRAETGRGETVYYVESDGGVNPYRVRIVTASARNVI 384
                                   366666666666666555555555544.45666799********************************************* PP

                                   THHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                Complex1_49kDa 242 aleellkgellaDvvailgsldivlgevDR 271
                                   a++++l g++++D++ai+gsld++ +e+DR
  gi|14601398|ref|NP_147934.1| 385 AFKYVLPGHRVMDIPAIYGSLDYFPPEADR 414
                                   *****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.49u 0.19s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3416.53
//
Query:       gi|14601399|ref|NP_147935.1|  [L=189]
Description: NuoC-like protein [Aeropyrum pernix K1]
Scores for 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-32  111.0   0.0    6.8e-32  110.7   0.0    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.032   14.4   0.0    1.2  1  Glyoxalase_3    Glyoxalase-like domain
      0.042   13.4   0.0        1.8    8.1   0.0    2.1  2  RITA            RBPJ-interacting and tubulin associated prote


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 !  110.7   0.0   1.1e-35   6.8e-32       3     121 ..      54     176 ..      52     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.1e-35
                                   --HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--....S-.-EEEEEE.....-S-BEE--TTT-STH CS
                Complex1_30kDa   3 vepedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsl....eknerirvkvevde.eepevpSvtdlfpga 77 
                                   v+ +dl+++a++lk+    gfd+++++t +D+  e++f+vvyh++s+     k   + + ve+++ e+p++pS+++++ +a
  gi|14601399|ref|NP_147935.1|  54 VSVDDLVRAAEALKT---VGFDHVVSITTIDYLkEKKFRVVYHVSSYldaaLKGAIVGLGVELPRvEKPSIPSLSQIWISA 131
                                   7889**********9...9************8889************65443337777888888867************** PP

                                   HHHHHHHHHHSHHBCTTSSTSS-SSSSTT.SSS-TTSTTS----- CS
                Complex1_30kDa  78 dwyEREayDmfGivfeghpdlrrillped.feghPLRkdfplsge 121
                                   +++ERE+y++fGi+feghpdlr +ll     e+ PLRkdf +++e
  gi|14601399|ref|NP_147935.1| 132 EFQEREVYEFFGIEFEGHPDLRPFLLTPPvAEKRPLRKDFVVREE 176
                                   **********************999955537999******99875 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.3e-06     0.032      59     120 ..      31      92 ..      12     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-06
                  Glyoxalase_3  59 paperprlfgldrlakgeglhtlalrtddidataarlraaGvdeagrrvrpdg.gdlrwrllf 120
                                   +++ ++r ++++r ++g+g++++++++dd+ ++a++l+  G+d+ ++ ++ d  ++ ++r+++
  gi|14601399|ref|NP_147935.1|  31 EEALKERGIQFKR-EDGKGFVDFIVSVDDLVRAAEALKTVGFDHVVSITTIDYlKEKKFRVVY 92 
                                   2223334444445.78**************************966666666655556666665 PP

>> RITA  RBPJ-interacting and tubulin associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0003       1.8      95     138 ..      84     126 ..      74     137 .. 0.82
   2 ?    3.3   0.0    0.0089        53     130     148 ..     146     164 ..     132     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0003
                          RITA  95 kknkYRlishtpsYCDEsLFgsrpeetsweapwmkkedaaklrp 138
                                   k  k+R++ h +sY D +L g+   + + e p+++k  ++ l  
  gi|14601399|ref|NP_147935.1|  84 KEKKFRVVYHVSSYLDAALKGAIV-GLGVELPRVEKPSIPSLSQ 126
                                   6679***************99865.8888888888888777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0089
                          RITA 130 kedaaklrpLlwtPPatpr 148
                                    e+ + lrp l+tPP++ +
  gi|14601399|ref|NP_147935.1| 146 FEGHPDLRPFLLTPPVAEK 164
                                   567789**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1541.86
//
Query:       gi|118431453|ref|NP_147936.2|  [L=199]
Description: NuoB-like protein [Aeropyrum pernix K1]
Scores for complete 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   72.3   0.1    4.5e-20   71.8   0.1    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 !   71.8   0.1   2.5e-24   4.5e-20      44     131 .]      79     160 ..      51     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 2.5e-24
                                    TTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHH CS
                    Oxidored_q6  44 keadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpea 123
                                    ++ +++++eG+vt+k++ a++l++e+++++k+ ia+G+CA +GG++  +n+++ +    +  +v+p+di+ipGCPp+pe 
  gi|118431453|ref|NP_147936.2|  79 RQTNLIIIEGTVTKKMACAVRLTWEQMPHPKFAIAMGACALDGGLF--YNSYNIV----KPWQVLPIDIYIPGCPPRPEG 152
                                    38899*****************************************..7733333....44668**************** PP

                                    HHHHHHHH CS
                    Oxidored_q6 124 iletllal 131
                                    +++++++l
  gi|118431453|ref|NP_147936.2| 153 VARAIVEL 160
                                    ***99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1690.72
//
Query:       gi|118431454|ref|NP_147938.2|  [L=138]
Description: NADH dehydrogenase subunit A [Aeropyrum pernix K1]
Scores for 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   22.2   0.7    0.00019   21.5   0.1    1.6  2  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch


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 ?   -0.4   0.1     0.074   1.3e+03      70      81 ..      24      35 ..       7      43 .. 0.48
   2 !   21.5   0.1   1.1e-08   0.00019      14      92 ..      47     126 ..      27     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.074
                                   HHHHHHHHHHHH CS
                    Oxidored_q4 70 glfgliemllFl 81
                                    ++g + +++Fl
  gi|118431454|ref|NP_147938.2| 24 LVVGATVAVVFL 35
                                   233333333333 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.1e-08
                                    ----HHHHS-SSSS--SS-.--.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHHHHHH CS
                    Oxidored_q4  14 kkpnkeklspYEcGfepvg.earlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillvglvYew 92 
                                    +k +++k   Y++G  p   + r ++s+++  + +lFl  +  v+++  + ++ +e+ +  l+ ++  lli +  l+Y +
  gi|118431454|ref|NP_147938.2|  47 EKIEARKYLRYDAGNPPRPgDFRRKVSMQYLGYLILFLAVEPIVILMALILIAPREALARVLFLYVAILLIYAPLLYYGI 126
                                    223445999********76489*******************999999999998886655555666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1055.84
//
Query:       gi|14601403|ref|NP_147939.1|  [L=736]
Description: elongation factor EF-2 [Aeropyrum pernix K1]
Scores for 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-65  218.3   0.1    9.4e-65  217.8   0.1    1.2  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    9.1e-33  112.6   0.1    5.1e-31  107.0   0.0    3.2  3  EFG_IV           Elongation factor G, domain IV
    1.1e-23   83.1   0.1    2.5e-23   82.0   0.1    1.6  1  EFG_II           Elongation Factor G, domain II
    7.9e-23   80.3   0.0    3.4e-22   78.3   0.0    2.1  2  EFG_C            Elongation factor G C-terminus
    1.1e-13   51.3   0.1    3.1e-13   49.9   0.1    1.9  1  GTP_EFTU_D2      Elongation factor Tu domain 2
    0.00011   22.3   0.1    0.00026   21.1   0.1    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.035   14.1   0.3       0.14   12.2   0.0    2.1  2  HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
      0.039   13.4   0.1       0.48    9.8   0.0    2.2  2  SRPRB            Signal recognition particle receptor beta su
      0.048   13.6   0.0      0.092   12.6   0.0    1.4  1  Dak2             DAK2 domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.8   0.1   4.7e-68   9.4e-65       2     193 ..      20     259 ..      19     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 217.8 bits;  conditional E-value: 4.7e-68
                                   CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.T.TCSSEEEEEEEESSS CS
                      GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.k.etkkylinliDtPGH 80 
                                   +irnigii+hvDhGKtT++d+Ll+++g+is+  + a+e+ vlD l+ E++rgiT+ksa++sl+ + e+k y inliDtPGH
  gi|14601403|ref|NP_147939.1|  20 QIRNIGIIAHVDHGKTTTSDSLLAAAGIISE--RIAGEALVLDYLNVEKQRGITVKSANVSLYhEyEGKPYVINLIDTPGH 98 
                                   79*****************************..6678899***********************6269************** PP

                                   GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH........ CS
                      GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk........ 153
                                   vdFs +v+r+lrvlDga++vvdaveGv++qte+v+r+al+e+v++i+fiNK+Drl++elk  +e+++q++ +         
  gi|14601403|ref|NP_147939.1|  99 VDFSGKVTRSLRVLDGAIVVVDAVEGVMTQTETVIRQALEERVRPILFINKVDRLIKELKLPPEKIQQRFVEIikevnnli 179
                                   **********************************************************************55566665555 PP

                                   ....HHHHHHHHHTTT..........TTEEEEEEBTTTTBTHH....................................HH CS
                      GTP_EFTU 154 ....eeklekygekge..........kevpvvfgSalkgegvk....................................tl 184
                                       e                     +   v+fgSa++++g++                                    tl
  gi|14601403|ref|NP_147939.1| 180 dlyaE----------PefrkkwkldpNAGMVAFGSAKDKWGISvpqvkkkgitfreiiqayekgkeavaelskkmplheTL 250
                                   44442..........044555556557899**********9999999999****************************99* PP

                                   HHHHHHHSH CS
                      GTP_EFTU 185 lealvellp 193
                                   l+++++++p
  gi|14601403|ref|NP_147939.1| 251 LDMVIKFVP 259
                                   *****9998 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 ?    1.2   0.0      0.15     3e+02      11      64 ..     231     284 ..     219     303 .. 0.81
   2 ?   -0.4   0.0      0.48   9.5e+02       2      20 ..     467     485 ..     466     509 .. 0.69
   3 !  107.0   0.0   2.5e-34   5.1e-31      11     119 ..     516     622 ..     510     624 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.15
                                   S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHH CS
                        EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyiea 64 
                                   ++ ke++ +l k+ + + +  + ++++ P++++++   + ++  g ++ e+ +a
  gi|14601403|ref|NP_147939.1| 231 EKGKEAVAELSKKMPLHETLLDMVIKFVPNPREAQRYRIPKIWKGDINSEIGQA 284
                                   34455788899999*****************99999999999999998888666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.48
                                   CCESCEE.SS-CCHCCCCC CS
                        EFG_IV   2 qVayrEtirkpvkereekl 20 
                                    V yrEt+r+++  +e+k 
  gi|14601403|ref|NP_147939.1| 467 IVVYRETVRQQSRVFEGKS 485
                                   589***9999988666654 PP

  == domain 3  score: 107.0 bits;  conditional E-value: 2.5e-34
                                   S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEEE CS
                        EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtLl 91 
                                   ++ k+r+++l++++g+d ++a++i++i+++     n+fvd+t g+q+++e+++++ +Gf+ alkeGpla epv++vkv+L+
  gi|14601403|ref|NP_147939.1| 516 QDPKDRARILADKAGWDYNEARKIWAIDEN----INVFVDKTAGVQYLREVKDTIIAGFRLALKEGPLAAEPVRGVKVVLH 592
                                   67788************************7....8********************************************** PP

                                   EEE--T..TTC-HHHHHHHHCHHHHHHHHC CS
                        EFG_IV  92 dgslhe..vdsseaafkpaarralkeallk 119
                                   d+++he  v+++++++ pa+r+a+++++l+
  gi|14601403|ref|NP_147939.1| 593 DAVIHEdpVHRGPGQLYPAVRNAIWAGILD 622
                                   *************************99876 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 !   82.0   0.1   1.2e-26   2.5e-23       1      73 [.     391     463 ..     391     465 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.2e-26
                        EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevel 73 
                                   ++ePv+++a+ep + +d  k+ +aL++l+ EDp l v+ +eeT+e++lsGmG lHlei+++ l+++++vev+ 
  gi|14601403|ref|NP_147939.1| 391 VSEPVVTIAVEPVKIQDLPKMIEALRKLTIEDPNLVVKINEETGEYLLSGMGPLHLEIALTMLREKFGVEVKA 463
                                   689********************************************************************87 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 ?   -2.1   0.0       2.1   4.1e+03       3      24 ..     343     364 ..     341     373 .. 0.77
   2 !   78.3   0.0   1.7e-25   3.4e-22       2      88 ..     627     712 ..     626     713 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                                   EEEEEEEEEEEECCCCCCHHHH CS
                         EFG_C   3 lEPivkveievpeeyvgkvisd 24 
                                   + P+ +v+ e+p  ++g+v++ 
  gi|14601403|ref|NP_147939.1| 343 MGPFREVTKEIPAGNIGAVMGF 364
                                   66889999999*******9964 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 1.7e-25
                                   EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE-- CS
                         EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevp 82 
                                   llEP++k++i++p ey+++++  l+++rG+i+++e++ + +++i a iP+ae++++a eLrs+T+G++ + +ef g+++vp
  gi|14601403|ref|NP_147939.1| 627 LLEPLQKLDIRAPMEYLSNITAVLTRKRGRIINVETT-GVMARIIAAIPVAESFDLAGELRSATAGRAFWGVEFYGWAPVP 706
                                   8************************************.******************************************* PP

                                   HHHHHH CS
                         EFG_C  83 gdklde 88 
                                    ++l++
  gi|14601403|ref|NP_147939.1| 707 DQMLQD 712
                                   *99876 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 !   49.9   0.1   1.6e-16   3.1e-13       1      73 [.     307     373 ..     307     374 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 1.6e-16
                                   EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                   G va+grv+sGtl+ G+ev++  +  +kk   +r  ++   +++ +e+ ++ +aG+i a+ g ed +++G+t+
  gi|14601403|ref|NP_147939.1| 307 GLVATGRVFSGTLRSGEEVYL--LNAGKK---SRLLQVSIYMGPFREVTKEIPAGNIGAVMGFED-VRAGETV 373
                                   679******************..888899...*********************************.*****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 !   21.1   0.1   1.3e-07   0.00026       2     113 ..      24     148 ..      23     149 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE.....................EEEEECGGCSSHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke.....................ielvDtpGliega 60 
                                   ++i+ +   GK+t   +l+ +   i ++++g  +   + +v+++  +                     i+l+DtpG ++  
  gi|14601403|ref|NP_147939.1|  24 IGIIAHVDHGKTTTSDSLLAAaGIISERIAGEALVLDYLNVEKQ--RgitvksanvslyheyegkpyvINLIDTPGHVD-- 100
                                   788888999*********99733456778888888888888722..2344555666666666777777********666.. PP

                                   HHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                      MMR_HSR1  61 seekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                         gk  ++l+  d +++vvda e+ +++ +  + + lee+ +p il +n
  gi|14601403|ref|NP_147939.1| 101 ----FSGKVTRSLRVLDGAIVVVDAVEGVMTQTETVIRQALEERVRP-ILFIN 148
                                   ....344444444457********99665666656666666655555.55555 PP

>> HIGH_NTase1_ass  Cytidyltransferase-related C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.5   6.9e+03      18      47 ..     397     427 ..     394     429 .. 0.76
   2 ?   12.2   0.0   6.8e-05      0.14      94     173 ..     498     575 ..     484     587 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.5
               HIGH_NTase1_ass  18 hikikPykivdlet.kevlledkLeeDnyvi 47 
                                   +i++ P ki+dl +  e l +  +e  n v+
  gi|14601403|ref|NP_147939.1| 397 TIAVEPVKIQDLPKmIEALRKLTIEDPNLVV 427
                                   5899999**9996515788777777777775 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6.8e-05
               HIGH_NTase1_ass  94 mlPeetievlkeelendnpledirdeekiletvneldldelldlnlldeklankliekrpyesieeikeaiprgfskhyk 173
                                    l eeti+++++   +++  +d +d  +il     +d++e  ++  +de++   + +++  + ++e+k++i +gf    k
  gi|14601403|ref|NP_147939.1| 498 PLNEETITLIQNGAVTED--QDPKDRARILADKAGWDYNEARKIWAIDENINVFVDKTAGVQYLREVKDTIIAGFRLALK 575
                                   577899999988887766..78899**************************************************86665 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 ?    9.8   0.0   0.00024      0.48      15      84 ..      54     120 ..      44     124 .. 0.77
   2 ?    0.8   0.0      0.14   2.8e+02     124     144 ..     124     144 ..     119     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                   SHHHHHHHHHHS.S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEE CS
                         SRPRB  15 GKTslftrLttd.svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvD 84 
                                   G  +++  L  + +   tv S + s+ +++ + k   ++liD PGh+ +  k++ +    + l g + vvD
  gi|14601403|ref|NP_147939.1|  54 GEALVLDYLNVEkQRGITVKSANVSLYHEY-EGKPYVINLIDTPGHVDFSGKVTRS---LRVLDGAIVVVD 120
                                   666666666665245568888888888888.7788999************999888...566677777777 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                                   STT---HHHHHHHHHHHHHHH CS
                         SRPRB 124 lflakspklikdaLEkElnki 144
                                    ++++++++i++aLE+ +  i
  gi|14601403|ref|NP_147939.1| 124 GVMTQTETVIRQALEERVRPI 144
                                   57899**********988766 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.6e-05     0.092      67     115 ..     218     266 ..     203     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                   ...TT---HHHHHHHHHHHHHHHH---TTSSSTHHHHHHHHHHHHT... CS
                          Dak2  67 keeldaedlaaalkaaleaiqavgkarpgdkTmlDvlrpavealekakd 115
                                   k+ ++  ++ +a +++ ea+ +++k  p + T+lD+++++v + ++a+ 
  gi|14601403|ref|NP_147939.1| 218 KKGITFREIIQAYEKGKEAVAELSKKMPLHETLLDMVIKFVPNPREAQR 266
                                   55589************************************99998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5389.70
//
Query:       gi|118431455|ref|NP_147940.2|  [L=248]
Description: repair endonuclease XPF [Aeropyrum pernix K1]
Scores for complete 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-22   79.2   0.0    5.2e-22   78.7   0.0    1.2  1  ERCC4           ERCC4 domain
    1.6e-11   44.6   0.1    3.8e-11   43.4   0.1    1.6  1  HHH_5           Helix-hairpin-helix domain
    4.5e-10   38.9   0.0    5.8e-06   25.9   0.1    2.4  2  HHH             Helix-hairpin-helix motif
    9.5e-10   38.4   0.0    3.9e-09   36.5   0.0    1.9  2  HHH_2           Helix-hairpin-helix motif
    2.8e-05   24.3   0.1      0.087   13.1   0.1    2.5  2  HHH_3           Helix-hairpin-helix motif
    5.9e-05   23.2   0.2      0.017   15.4   0.0    2.5  2  IMS_HHH         IMS family HHH motif
     0.0013   19.3   0.0       0.02   15.5   0.0    2.3  1  5_3_exonuc      5'-3' exonuclease, C-terminal SAM fold
     0.0013   19.0   0.1        2.1    8.8   0.0    2.6  2  HHH_8           Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.011   16.1   0.1      0.029   14.7   0.0    1.9  2  Transposase_20  Transposase IS116/IS110/IS902 family
      0.056   13.2   0.3       0.33   10.8   0.3    2.2  3  RNA_pol_A_CTD   Bacterial RNA polymerase, alpha chain C termi


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 !   78.7   0.0   2.9e-25   5.2e-22       1     155 [.      17     136 ..      17     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 2.9e-25
                                    EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHH CS
                          ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqv 80 
                                    +D re++s ++   le+lgv+v++++lp gdy l+   +++               ++verk+ +d++ s+ dgrl+eq+
  gi|118431455|ref|NP_147940.2|  17 VDVREERSPVPSI-LESLGVQVIPKQLPMGDY-LV---SDS---------------IIVERKTSSDFAKSLFDGRLFEQA 76 
                                    799**99******.******************.**...***...............************************ PP

                                    HHHHH.H-SEEEEEEES...-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHHH CS
                          ERCC4  81 srlkrngykkpillveg...ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewlan 155
                                    srl++ +y+ ++++veg     +y+                   r ++++a+++lqld+g+++  t +++ ta ++ +
  gi|118431455|ref|NP_147940.2|  77 SRLAE-HYETVFIIVEGppvPRRYRG----------------RER-SLYAAMAALQLDYGIRLMNTMDPKGTALVIES 136
                                    *****.***********542222222................445.5***********************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 !   43.4   0.1   2.1e-14   3.8e-11       4      53 ..     168     216 ..     166     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.1e-14
                                    HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                          HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                    L+s +GiG++tA ++l+  ++s+e +  a+++e++k+ GiG+k+Ae i+ 
  gi|118431455|ref|NP_147940.2| 168 LQSFPGIGRRTAERILER-FGSLERFFTASKAEISKVEGIGEKRAEEIKK 216
                                    899***************.***************************9975 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00022      0.39      17      29 ..     172     184 ..     168     185 .. 0.87
   2 !   25.9   0.1   3.3e-09   5.8e-06       1      29 [.     188     216 ..     188     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                                    TT-SHHHHHHHHH CS
                            HHH  17 PGVGpktAeaIls 29 
                                    PG+G+ tAe+Il+
  gi|118431455|ref|NP_147940.2| 172 PGIGRRTAERILE 184
                                    ***********96 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.3e-09
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIls 29 
                                    sle+ ++as +e+ +++G+G+k+Ae I  
  gi|118431455|ref|NP_147940.2| 188 SLERFFTASKAEISKVEGIGEKRAEEIKK 216
                                    68999*********************976 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.1     2e+03      15      25 ..      75      85 ..      74      87 .. 0.84
   2 !   36.5   0.0   2.2e-12   3.9e-09       9      58 ..     172     221 ..     165     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                          HHH_2 15 tAklLakrFks 25
                                    A  La+++++
  gi|118431455|ref|NP_147940.2| 75 QASRLAEHYET 85
                                   5899*****97 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 2.2e-12
                          HHH_2   9 rhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFene 58 
                                    + +G +tA+ + +rF+sl+++ +as  e+++v++iGe+ A++i++ + ++
  gi|118431455|ref|NP_147940.2| 172 PGIGRRTAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKILMTP 221
                                    889****************************************9988776 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0013       2.3      16      32 ..     168     184 ..     159     192 .. 0.91
   2 !   13.1   0.1   4.8e-05     0.087      10      30 ..     194     214 ..     192     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                          HHH_3  16 LqklpGlgpklAknIva 32 
                                    Lq +pG+g ++A++I++
  gi|118431455|ref|NP_147940.2| 168 LQSFPGIGRRTAERILE 184
                                    99*************97 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.8e-05
                          HHH_3  10 tAsaeeLqklpGlgpklAknI 30 
                                    tAs++e++k++G+g+k A++I
  gi|118431455|ref|NP_147940.2| 194 TASKAEISKVEGIGEKRAEEI 214
                                    9******************99 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.6e-06     0.017      14      31 ..     169     187 ..     168     187 .. 0.91
   2 ?    5.2   0.1     0.017        30      12      29 ..     199     216 ..     195     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.6e-06
                        IMS_HHH  14 tkipGiGgklgek.LeklG 31 
                                     ++pGiG++++e+ Le +G
  gi|118431455|ref|NP_147940.2| 169 QSFPGIGRRTAERiLERFG 187
                                    68*************9887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                        IMS_HHH  12 pitkipGiGgklgekLek 29 
                                    +i+k+ GiG k +e+++k
  gi|118431455|ref|NP_147940.2| 199 EISKVEGIGEKRAEEIKK 216
                                    6999**********9887 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 !   15.5   0.0   1.1e-05      0.02      23      56 ..     171     210 ..     168     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                     5_3_exonuc  23 vpgiGektAakLlkeygsleeilenld.elke.....kkl 56 
                                     pgiG +tA ++l+++gsle  + + + e+++     +k+
  gi|118431455|ref|NP_147940.2| 171 FPGIGRRTAERILERFGSLERFFTASKaEISKvegigEKR 210
                                    59********************997655544432333333 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0012       2.1      49      65 ..     168     184 ..     152     186 .. 0.78
   2 !    7.5   0.1    0.0029       5.1      44      67 ..     196     218 ..     188     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                                    CTTSTT--HHHHHHHHH CS
                          HHH_8  49 ltklpgiGkkiaakiee 65 
                                    l+++pgiG ++a++i e
  gi|118431455|ref|NP_147940.2| 168 LQSFPGIGRRTAERILE 184
                                    699***********976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0029
                                    HHTTHCTTSTT--HHHHHHHHHHH CS
                          HHH_8  44 sleeeltklpgiGkkiaakieeil 67 
                                    s ++e++k+ giG+k a++i+ il
  gi|118431455|ref|NP_147940.2| 196 S-KAEISKVEGIGEKRAEEIKKIL 218
                                    3.33599*************9997 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.029       3      33 ..     167     197 ..     165     212 .. 0.92
   2 ?   -3.2   0.0       6.3   1.1e+04      40      52 ..     219     231 ..     219     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                 Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakq 33 
                                    +L+s pGiG+ ta ++l + g l+rf +a +
  gi|118431455|ref|NP_147940.2| 167 ILQSFPGIGRRTAERILERFGSLERFFTASK 197
                                    8************************987755 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.3
                 Transposase_20  40 lapvenqSGkkkr 52 
                                    ++p+++++G+ +r
  gi|118431455|ref|NP_147940.2| 219 MTPYKRSTGGGRR 231
                                    5799999998776 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 ?   -3.1   0.0       3.9     7e+03      18      35 ..     115     132 ..     107     143 .. 0.65
   2 ?   -0.7   0.0      0.67   1.2e+03      47      63 ..     168     184 ..     157     188 .. 0.84
   3 ?   10.8   0.3   0.00018      0.33      41      65 ..     194     218 ..     184     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                                    HT--HHHHHHHHHTT--B CS
                  RNA_pol_A_CTD  18 LeLSvRslNcLkragikt 35 
                                    L+  +R +N ++  g   
  gi|118431455|ref|NP_147940.2| 115 LDYGIRLMNTMDPKGTAL 132
                                    666677777776666544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.67
                                    HTTSSS-SSHHHHHHHH CS
                  RNA_pol_A_CTD  47 LlkikNlGkKSleEIke 63 
                                    L++++ +G+++ e I e
  gi|118431455|ref|NP_147940.2| 168 LQSFPGIGRRTAERILE 184
                                    78999******999887 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00018
                                    HS-HHHHTTSSS-SSHHHHHHHHHH CS
                  RNA_pol_A_CTD  41 klseeeLlkikNlGkKSleEIkekL 65 
                                    + s++e++k++ +G+K  eEIk+ L
  gi|118431455|ref|NP_147940.2| 194 TASKAEISKVEGIGEKRAEEIKKIL 218
                                    57899******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1811.36
//
Query:       gi|118431456|ref|NP_147941.2|  [L=348]
Description: hypothetical protein APE_1437.1 [Aeropyrum pernix K1]
Scores for complete 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-13   50.0   0.0    4.9e-13   49.2   0.0    1.4  1  DHH       DHH family
    2.8e-08   34.3   0.6    6.4e-08   33.1   0.6    1.6  1  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 !   49.2   0.0   5.5e-17   4.9e-13       3     101 .]      24     167 ..      22     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.5e-17
                                    EEE-ECSSSHHHHHHHHHHHH.............................................CECS--TCGGCGCC CS
                                    xxxxxxxxxxxxxxxxxxxxx.............................................xxxxxxxxxxxxxx RF
                            DHH   3 livghknpDtDsigSaialan.............................................llvDhneksqaveg 37 
                                    ++++h+n D D++g+a+++++                                             ++vD  + sq + +
  gi|118431456|ref|NP_147941.2|  24 AVITHRNADPDAVGAALVVREvlralrmnpclyspegisrqskrlleavgeefgplcspdenpliaVVVDAANLSQIAGA 103
                                    689******************7777666666666666666666666666666666666666666666****999998766 PP

                                    H.HCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  38 e.akeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                    e + + a   ++iDHH++g ++++ a++ ++++ +gs +e++++ + e ++ +++++a++ l gi
  gi|118431456|ref|NP_147941.2| 104 EsLFRAARLKVVIDHHERG-SIHEEADVALVDPGAGSSSELAVKTAVEAGTPLRPSVATAALGGI 167
                                    6377888889*********.9**************************************999887 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.6   7.1e-12   6.4e-08      59     123 ..     249     315 ..     227     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 7.1e-12
                                    HHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEEETCEEEEEEE CS
                          DHHA1  59 aadklksklkkpvivfvakeegdkvkvsarskkd....gvdagelakeaaaklgggGGGHdlAaGagip 123
                                    +a  l +  + + ++++++e+ ++ ++s+r+++     gv a+++a+ +a+k+gg GGGHd A  a ip
  gi|118431456|ref|NP_147941.2| 249 VAKSLVD--EAADVAVAVAERTSEFRLSVRVSPLalekGVTARAIASMLAEKFGGEGGGHDEAGMAHIP 315
                                    4555666..55888999999888*********99**************************999777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2529.48
//
Query:       gi|118431457|ref|YP_874893.1|  [L=110]
Description: hypothetical protein APE_1437a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.3   0.1       0.78    9.8   0.1    1.9  2  DUF5345   Family of unknown function (DUF5345)


Domain annotation for each model (and alignments):
>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   4.4e-05      0.78      15      39 ..       5      29 ..       2      32 .. 0.91
   2 ?    0.2   0.0      0.04   7.2e+02      15      36 ..      59      82 ..      50      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.4e-05
                        DUF5345 15 etPsleeleqllaeekerkrkrlrr 39
                                   ++Ps++ le+ l e +er rkrl +
  gi|118431457|ref|YP_874893.1|  5 KEPSTQGLEEALLELEERIRKRLQK 29
                                   57********************987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.04
                        DUF5345 15 et..Psleeleqllaeekerkrkr 36
                                   e+  P le l++++++  e++ kr
  gi|118431457|ref|YP_874893.1| 59 EAvrPGLEGLQDIVDAIVEEEVKR 82
                                   333489999999888766555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 877.45
//
Query:       gi|14601406|ref|NP_147942.1|  [L=123]
Description: prefoldin beta subunit [Aeropyrum pernix K1]
Scores for 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-25   87.0   9.9    8.1e-25   86.8   9.9    1.0  1  Prefoldin_2      Prefoldin subunit
     0.0018   18.1   3.1      0.033   14.0   0.6    2.1  2  Nsp1_C           Nsp1-like C-terminal region
     0.0034   18.0   4.2     0.0047   17.5   4.2    1.2  1  DUF2408          Protein of unknown function (DUF2408)
     0.0034   17.3   7.5      0.004   17.0   4.4    2.0  2  Prefoldin        Prefoldin subunit
     0.0051   17.2   1.3      0.043   14.2   0.5    2.0  2  YlqD             YlqD protein
  ------ inclusion threshold ------
      0.063   12.9   2.2      0.063   12.9   2.2    2.5  2  Nup54_57_C       NUP57/Nup54 C-terminal domain
      0.073   13.1   6.2       0.14   12.2   6.2    1.5  1  Laminin_II       Laminin Domain II
      0.077   13.1   4.8        3.4    7.8   4.6    2.0  2  ADIP             Afadin- and alpha -actinin-Binding
       0.14   11.7   6.0       0.18   11.3   6.0    1.2  1  CENP-K           Centromere-associated protein K
       0.15   12.4   8.6       0.15   12.4   5.3    2.1  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.25   12.1   5.3        1.3    9.7   5.3    2.0  1  Occludin_ELL     Occludin homology domain
       0.25   11.4  13.6        4.4    7.3  13.5    2.0  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.38   11.4  10.9          1   10.0   6.5    2.1  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
       0.49   10.6  11.3          2    8.7   7.3    2.1  2  Cortex-I_coil    Cortexillin I, coiled coil
       0.83   10.1   5.9        3.4    8.1   2.8    2.1  2  DASH_Dad2        DASH complex subunit Dad2
       0.91   10.1  16.5       0.86   10.1  10.2    2.0  2  APG6_N           Apg6 coiled-coil region
        1.2    9.9   5.3          5    7.9   3.3    2.4  2  Vir_act_alpha_C  Virulence activator alpha C-term
        1.2   10.2   7.3       0.66   11.1   3.6    2.1  2  DUF5320          Family of unknown function (DUF5320)
        1.3    7.6  11.8        1.3    7.7   2.9    2.0  2  FbpA             Fibronectin-binding protein A N-terminus (Fb
        3.1    8.3   6.0         52    4.4   6.0    2.2  1  DUF4140          N-terminal domain of unknown function (DUF41
        4.8    7.0   8.8        7.7    6.4   8.8    1.3  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
        4.8    7.5   7.9        5.7    7.2   4.8    2.0  2  Spc24            Spc24 subunit of Ndc80
        5.2    5.9  10.8        4.5    6.1   6.2    1.9  1  Spc7             Spc7 kinetochore 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 !   86.8   9.9     1e-27   8.1e-25       2     105 ..      11     114 ..      10     115 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 1e-27
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHH CS
                   Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktle 82 
                                   ++  k+ +l+++l+ ++ +++++e+ l e+e+vl+ele l+ed++ y+l G vlvk++k+ev e+L++rke+le ++k l+
  gi|14601406|ref|NP_147942.1|  11 AKYTKYLKLRETLSVVMREKATVEAGLAEVESVLKELEGLPEDAELYRLTGFVLVKKSKNEVVEDLNKRKEDLELKLKVLK 91 
                                   7889***************************************************************************** PP

                                   HHHHHHHHHHHHHHHHHHCCTS- CS
                   Prefoldin_2  83 kqleklekeleelkeelqkklqq 105
                                   +q+e+l+kele +++el+ +lq+
  gi|14601406|ref|NP_147942.1|  92 SQEEHLKKELERIESELRRLLQG 114
                                   *******************9986 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 ?    4.7   0.1     0.032        25      61      91 ..      18      48 ..       3      57 .. 0.65
   2 !   14.0   0.6   4.2e-05     0.033      66     107 ..      73     114 ..      64     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.032
                        Nsp1_C 61 kLysevleaeqeqnkidqeLeyiesqqdeLe 91
                                  kL++ +  + +e++ ++  L  +es  +eLe
  gi|14601406|ref|NP_147942.1| 18 KLRETLSVVMREKATVEAGLAEVESVLKELE 48
                                  4555555556666666666666666666665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.2e-05
                        Nsp1_C  66 vleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsk 107
                                   v++ ++ ++ ++ +L++++sq + L++ L+++E+el +ll+ 
  gi|14601406|ref|NP_147942.1|  73 VEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRLLQG 114
                                   4566788899***************************99865 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   4.2     6e-06    0.0047       2     118 ..       3     111 ..       2     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6e-06
                       DUF2408   2 eelspelepiyekLvsirrsLlslaakskaeeakeseevkeelkelkeeLkkieskrdeegkFkseegkevvekgqavlng 82 
                                   e+l+pe+e+ y+k +++r +L+ ++ ++ka+       v++ l e+++ Lk++e   ++ + +  +    v++++++v+++
  gi|14601406|ref|NP_147942.1|   3 ERLPPEVEAKYTKYLKLRETLS-VVMREKAT-------VEAGLAEVESVLKELEGLPEDAELYRLTGFVLVKKSKNEVVED 75 
                                   789**************98875.66677776.......79999***********9999989998877767888889***** PP

                       DUF2408  83 LlddcfdlvedlkaqdgeekkvasslqpiYdrLlei 118
                                   L ++  dl  +lk  +++e++++++l+ i ++L ++
  gi|14601406|ref|NP_147942.1|  76 LNKRKEDLELKLKVLKSQEEHLKKELERIESELRRL 111
                                   *******99999999989999***999998888765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.43   3.3e+02       8      34 ..      26      52 ..      18      62 .. 0.68
   2 !   17.0   4.4   5.2e-06     0.004      69     119 ..      63     113 ..      60     114 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.43
                                  HHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                     Prefoldin  8 lqaelaqlkeaieelektletlktlkk 34
                                  + +e a++++ + e+e++l+ l+ l +
  gi|14601406|ref|NP_147942.1| 26 VMREKATVEAGLAEVESVLKELEGLPE 52
                                  556667777777777777777777665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.2e-06
                                   EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Prefoldin  69 yyveksleeAiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                   + v+ks++e +e l+k++e+le  l++l+ + e lk++++ +e +l++l q
  gi|14601406|ref|NP_147942.1|  63 VLVKKSKNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRLLQ 113
                                   5799******************************************99976 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.36   2.8e+02      63      95 ..      24      56 ..       6      60 .. 0.79
   2 !   14.2   0.5   5.5e-05     0.043      12      55 ..      63     106 ..      61     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.36
                          YlqD 63 eqvekekserlekkkqllqqleqvqkLelgsev 95
                                  + v +ek+ +++  +++++ l++++ L+ ++e+
  gi|14601406|ref|NP_147942.1| 24 SVVMREKATVEAGLAEVESVLKELEGLPEDAEL 56
                                  556788899999999999999999999999997 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
                          YlqD  12 ivTeklKeelqqqlqaqieqldkelqqLefqakrlikeikkqsa 55 
                                   ++ +k+K+e+ ++l++++e l+ +l+ L+ q+++l ke+++ + 
  gi|14601406|ref|NP_147942.1|  63 VLVKKSKNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIES 106
                                   56789*********************************998665 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.7   5.4e+02      21      28 ..      39      46 ..      38      53 .. 0.69
   2 ?   12.9   2.2     8e-05     0.063      16      28 ..      95     107 ..      91     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.7
                    Nup54_57_C 21 ElEsikkD 28
                                  E+Es+ k+
  gi|14601406|ref|NP_147942.1| 39 EVESVLKE 46
                                  67777665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8e-05
                    Nup54_57_C  16 qHLkKElEsikkD 28 
                                    HLkKElE+i ++
  gi|14601406|ref|NP_147942.1|  95 EHLKKELERIESE 107
                                   7*********988 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.2   0.00018      0.14      49      96 ..      61     105 ..      17     112 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                   XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                    Laminin_II  49 dankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                    +  + ++ ++ v +L+k  ++L+ klk lk +ee+   l++++++i 
  gi|14601406|ref|NP_147942.1|  61 GFVLVKKSKNEVVEDLNKRKEDLELKLKVLKSQEEH---LKKELERIE 105
                                   44444555667799**********************...999999995 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.084        65      68     108 ..       8      48 ..       2      52 .. 0.85
   2 ?    7.8   4.6    0.0043       3.4      71     114 ..      68     111 ..      65     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.084
                          ADIP  68 eierlqskierlktqleqlerelalvqakerqlekklktle 108
                                   e e + +k+ +l + l+   re a+v+a +++ e  lk+le
  gi|14601406|ref|NP_147942.1|   8 EVEAKYTKYLKLRETLSVVMREKATVEAGLAEVESVLKELE 48 
                                   56667788889999999999999999999999999999987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0043
                          ADIP  71 rlqskierlktqleqlerelalvqakerqlekklktleqklkne 114
                                   +++  +e l ++ e+le +l++++++e +l+k+l++ e+ l+++
  gi|14601406|ref|NP_147942.1|  68 SKNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRL 111
                                   55667889999999999999999999999999999999998876 PP

>> CENP-K  Centromere-associated protein K
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.0   0.00023      0.18      44     116 ..      29     104 ..       5     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                        CENP-K  44 sdaqlslliarvklLtaeleqwekktpeiislneevllalgkee....lqklksqLelvlsiiqsknkklkedLkrE 116
                                   ++a ++  +a v  + +ele + +  +e+  l+  vl++ +k+e    l+k k++Lel l++++s++++lk++L+r 
  gi|14601406|ref|NP_147942.1|  29 EKATVEAGLAEVESVLKELEGLPE-DAELYRLTGFVLVKKSKNEvvedLNKRKEDLELKLKVLKSQEEHLKKELERI 104
                                   555566666666666777766654.56777888899999999763333799************************94 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 ?    0.9   0.1      0.78   6.1e+02      17      34 ..      31      48 ..      15      53 .. 0.65
   2 ?   12.4   5.3    0.0002      0.15       2      41 ..      73     112 ..      72     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.78
                     FlaC_arch 17 etvkkeneelsksveelk 34
                                  +tv++ + e+++ ++el+
  gi|14601406|ref|NP_147942.1| 31 ATVEAGLAEVESVLKELE 48
                                  566666666666665554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0002
                     FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                   +++l ++ ++l+ +l+ +k++ e+l+k++e+++ + ++ll
  gi|14601406|ref|NP_147942.1|  73 VEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRLL 112
                                   6788999999****************************98 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.3    0.0017       1.3      18      92 ..      10     104 ..       6     111 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                  Occludin_ELL  18 nkeYkeYkelhaeleevskkfseLe..........relkelkegsk........eykkieeeilqeykklkk..dpeyqek 78 
                                   +++Y++Y +l + l+ v+++ + +e          +el+ l+e+ +         +kk ++e++++++k k+  + + +  
  gi|14601406|ref|NP_147942.1|  10 EAKYTKYLKLRETLSVVMREKATVEaglaevesvlKELEGLPEDAElyrltgfvLVKKSKNEVVEDLNKRKEdlELKLKVL 90 
                                   689999999999999999999999966766666666666666666555555555566666666666666666222333444 PP

                  Occludin_ELL  79 kkrceyLkekLshi 92 
                                   k + e+Lk++L+ i
  gi|14601406|ref|NP_147942.1|  91 KSQEEHLKKELERI 104
                                   66666666666655 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 ?    5.7   0.2     0.018        14      59     106 ..       7      54 ..       1      57 [. 0.81
   2 ?    7.3  13.5    0.0056       4.4       6      96 ..      17     108 ..      14     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                CENP-F_leu_zip  59 eeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnssl 106
                                    e+e   ++  +l+  L+ + +ek ++e  l +  +  +eLe l ++ 
  gi|14601406|ref|NP_147942.1|   7 PEVEAKYTKYLKLRETLSVVMREKATVEAGLAEVESVLKELEGLPEDA 54 
                                   555665667778999999999********************9987775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0056
                CENP-F_leu_zip   6 lhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkee.ieelaeelreleldLvalrsekeeL 85 
                                   l+++e L  + r+++ ++    + e+ l+++e   e+++l   t    v++ k+e +e l+++ ++lel+L+ l+s+ e+L
  gi|14601406|ref|NP_147942.1|  17 LKLRETLSVVMREKATVEAGLAEVESVLKELEGLPEDAELYRLTGFVLVKKSKNEvVEDLNKRKEDLELKLKVLKSQEEHL 97 
                                   666667777777777777666666666666666666666555555555665554426889999999999999999999999 PP

                CENP-F_leu_zip  86 ekelqkkqerv 96 
                                   +kel+   ++ 
  gi|14601406|ref|NP_147942.1|  98 KKELERIESEL 108
                                   99999766655 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 ?    3.7   0.1      0.12        92      54      93 ..       2      41 ..       1      50 [. 0.81
   2 ?   10.0   6.5    0.0013         1      25      71 ..      65     111 ..      63     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                HIP1_clath_bdg 54 lekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93
                                  +e+L  e+eak ++  +l+++L+   ++++++++ la+ +
  gi|14601406|ref|NP_147942.1|  2 VERLPPEVEAKYTKYLKLRETLSVVMREKATVEAGLAEVE 41
                                  6888899999999999999999988888888888877765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                HIP1_clath_bdg  25 verekkeleeelerlkeeaerkleeqkeelekLkreleakraelarl 71 
                                   v++ k+e+ e+l++ ke+ e kl+  k++ e+Lk+ele+ + el rl
  gi|14601406|ref|NP_147942.1|  65 VKKSKNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRL 111
                                   6889***************************************9987 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 ?    4.2   0.1     0.063        49      41      69 ..      18      46 ..       8      62 .. 0.73
   2 ?    8.7   7.3    0.0026         2      27      72 ..      68     113 ..      52     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.063
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil 41 elesllasleseaaerekrlreleaklde 69
                                  +l+++l+++  e+a  e  l+e+e+ l+e
  gi|14601406|ref|NP_147942.1| 18 KLRETLSVVMREKATVEAGLAEVESVLKE 46
                                  57778888888888888888888887766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Cortex-I_coil  27 sekvsreelikqkdelesllasleseaaerekrlreleakldealk 72 
                                   s+    e+l k+k++le  l++l+s++++ +k l  +e+ l   l+
  gi|14601406|ref|NP_147942.1|  68 SKNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRLLQ 113
                                   445556899******************************9988876 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.092        72      24      65 ..      19      60 ..      13      82 .. 0.72
   2 ?    8.1   2.8    0.0044       3.4       4      42 ..      76     115 ..      73     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.092
                     DASH_Dad2 24 lakqleeLeeklstladgteavasVlanWqnvlraismaslk 65
                                  l++ l+ +  + +t++ g + v+sVl++ +   + +++++l+
  gi|14601406|ref|NP_147942.1| 19 LRETLSVVMREKATVEAGLAEVESVLKELEGLPEDAELYRLT 60
                                  677788888889999***********9988777666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0044
                     DASH_Dad2   4 iaeKraELe.aLkqlrdlsdslakqleeLeeklstladgt 42 
                                   +++ +++Le +Lk l+++ ++l+k+le++e +l+ l +g+
  gi|14601406|ref|NP_147942.1|  76 LNKRKEDLElKLKVLKSQEEHLKKELERIESELRRLLQGG 115
                                   56777778768**********************9998886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5       0.1        81      65      95 ..      18      48 ..       3      55 .. 0.67
   2 ?   10.1  10.2    0.0011      0.86      52      95 ..      69     112 ..      63     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                        APG6_N 65 elleeLkelekereeleaelaaleeeleale 95
                                  +l e L  + +e++ +ea la+ e+ l++le
  gi|14601406|ref|NP_147942.1| 18 KLRETLSVVMREKATVEAGLAEVESVLKELE 48
                                  4556666666777777777777777666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
                        APG6_N  52 leeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                    +e +e+l+k +e+l+ +Lk l++++e l++el+ +e+el++l 
  gi|14601406|ref|NP_147942.1|  69 KNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRLL 112
                                   3445899999****************************999985 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 ?    1.9   0.0      0.48   3.7e+02      19      46 ..      21      52 ..       2      64 .. 0.63
   2 ?    7.9   3.3    0.0064         5      14      46 ..      66     104 ..      53     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.48
               Vir_act_alpha_C 19 alieeLerrreeheekLaeyeeieerl....e 46
                                  +++  + r ++  e+ Lae e+  ++l    e
  gi|14601406|ref|NP_147942.1| 21 ETLSVVMREKATVEAGLAEVESVLKELeglpE 52
                                  44555566666666666666666666655552 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0064
               Vir_act_alpha_C  14 vldpealieeLerrreeheekLaeyeeieerl......e 46 
                                     ++++++e+L++r+e  e kL+ +++ ee+l       
  gi|14601406|ref|NP_147942.1|  66 KKSKNEVVEDLNKRKEDLELKLKVLKSQEEHLkkelerI 104
                                   568999********************9999996655441 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1         2   1.5e+03      70      99 .]      18      47 ..       4      47 .. 0.77
   2 ?   11.1   3.6   0.00084      0.66      66      99 .]      78     111 ..      56     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2
                       DUF5320 70 skeeekelLeeqaeaLeeeleaikkrlkel 99
                                  + +e+ ++  +++++ e+ l+++++ lkel
  gi|14601406|ref|NP_147942.1| 18 KLRETLSVVMREKATVEAGLAEVESVLKEL 47
                                  556777788889999999999999999886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00084
                       DUF5320  66 taeaskeeekelLeeqaeaLeeeleaikkrlkel 99 
                                   +++++ e + ++L++q+e L++ele i+++l++l
  gi|14601406|ref|NP_147942.1|  78 KRKEDLELKLKVLKSQEEHLKKELERIESELRRL 111
                                   56677788899******************99875 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 ?    7.7   2.9    0.0016       1.3     383     422 ..      10      56 ..       5      84 .. 0.78
   2 ?    1.8   6.5      0.11        83     389     437 ..      65     109 ..      60     116 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......T CS
                          FbpA 383 qkyfkkykKlkraveaveeqieetkeeleylesveaale.......q 422
                                   ++ ++ky Kl+++   v  + + +++ l+ +esv ++le        
  gi|14601406|ref|NP_147942.1|  10 EAKYTKYLKLRETLSVVMREKATVEAGLAEVESVLKELEglpedaeL 56 
                                   678***********************************955554440 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.11
                                   HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHT-.-HHHHHHHHHHHH CS
                          FbpA 389 ykKlkra.veaveeqieetkeeleylesveaaleqaesledleeikeELi 437
                                   +kK k+  ve ++++ e  + +l+ l+s e+ l+     ++le i+ EL+
  gi|14601406|ref|NP_147942.1|  65 VKKSKNEvVEDLNKRKEDLELKLKVLKSQEEHLK-----KELERIESELR 109
                                   5666655246677777777777777777777777.....88999999995 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 ?    4.4   6.0     0.066        52      65      89 ..      75     109 ..       2     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.066
                       DUF4140  65 e..........elkalraeleeledelaaledela 89 
                                   +          +lk l+++ e l++el+++e+el+
  gi|14601406|ref|NP_147942.1|  75 DlnkrkedlelKLKVLKSQEEHLKKELERIESELR 109
                                   12222222334566666666666666666666665 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 ?    6.4   8.8    0.0099       7.7     122     192 ..       9     105 ..       3     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0099
                          FTA4 122 leallerYaelrarLielserrqqlqarlarlrklkallepflgs............edpqesvqenlvtrdge....... 183
                                    ea+ ++Y +lr+ L  + +++ +++a la+ +++ ++le + +             ++++++v e+l  r+++       
  gi|14601406|ref|NP_147942.1|   9 VEAKYTKYLKLRETLSVVMREKATVEAGLAEVESVLKELEGLPEDaelyrltgfvlvKKSKNEVVEDLNKRKEDlelklkv 89 
                                   478889***********************************966699**********999999999999999997888888 PP

                          FTA4 184 .......leaElermR 192
                                          l++Eler+ 
  gi|14601406|ref|NP_147942.1|  90 lksqeehLKKELERIE 105
                                   8888888777777754 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2       0.4   3.1e+02      17      43 ..      27      53 ..      10      78 .. 0.46
   2 ?    7.2   4.8    0.0073       5.7       8      42 ..      75     109 ..      66     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.4
                         Spc24 17 eselesleselaelkeeleeleeesee 43
                                   +e   +e+ lae ++ l+ele   e+
  gi|14601406|ref|NP_147942.1| 27 MREKATVEAGLAEVESVLKELEGLPED 53
                                  333333333333333333333333322 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0073
                         Spc24   8 riakelsdleselesleselaelkeeleeleeese 42 
                                   ++ k  +dle +l+ l+s+ + lk+ele +e+e  
  gi|14601406|ref|NP_147942.1|  75 DLNKRKEDLELKLKVLKSQEEHLKKELERIESELR 109
                                   57788899999999999999999999999998765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   6.2    0.0057       4.5     141     186 ..      66     111 ..      57     117 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0057
                          Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeelekl 186
                                   k++ +e +e+l++ ke Le + + l++  + l++e +++e+el++l
  gi|14601406|ref|NP_147942.1|  66 KKSKNEVVEDLNKRKEDLELKLKVLKSQEEHLKKELERIESELRRL 111
                                   6666777788888888888888888888888888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1900  (0.105974); expected 358.6 (0.02)
Passed bias filter:                     1020  (0.0568911); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 879.28
//
Query:       gi|118431458|ref|YP_874894.1|  [L=93]
Description: hypothetical protein APE_1440a [Aeropyrum pernix K1]
Scores for 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   21.8   0.0    0.00019   21.5   0.0    1.1  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 !   21.5   0.0     1e-08   0.00019      11      67 ..      12      69 ..       2      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-08
                                   HHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH CS
                           Pcc1 11 erlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslg 67
                                     + ++++r+L+ ++  + +    ++l  ++  ++++++A ++  LR+  n+fl ++ 
  gi|118431458|ref|YP_874894.1| 12 GTDSEAIYRSLEAEARQRGPSkGVVKLGMDDGCVVLHIRARDLAGLRAITNSFLLLIH 69
                                   446899********7776654466678899***********************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 685.60
//
Query:       gi|118431459|ref|NP_147944.2|  [L=280]
Description: small conductance mechanosensitive channel MscS [Aeropyrum pernix K1]
Scores for complete 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  172.1   0.4    1.4e-50  171.7   0.4    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 !  171.7   0.4   7.7e-55   1.4e-50       4     206 .]      65     260 ..      62     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 7.7e-55
                                    HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSE CS
                     MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrt 83 
                                    +++++++++ +++l+ lgv+++all++ G++gl+l+lal+ l+sn+++G+ l+ ek++ iGDl+ ig+++G+V++i++ +
  gi|118431459|ref|NP_147944.2|  65 TYYMVLFLTAVAALQALGVELTALLVAGGFAGLVLSLALQPLFSNFFSGLYLYGEKSLVIGDLISIGGFIGRVVEISTMS 144
                                    6899**************************************************************************** PP

                                    EEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE CS
                     MS_channel  84 tkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldef 163
                                    t++rt dg++v iPns ++++ ++N+s+ s  rr++++ +++y +d   + k++ ++ +al++ + vlkd+ ++v+  e+
  gi|118431459|ref|NP_147944.2| 145 TRVRTLDGEVVRIPNSRIINDYMVNYSK-SAVRRLTFKASIAYRED---IGKAINTISNALESIYLVLKDPSPEVYASEL 220
                                    ****************************.*****************...99***************************** PP

                                    -SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT--- CS
                     MS_channel 164 gdsslnfevrvfvktvvpeeylsvqseinlrikkileeegiei 206
                                    gds++ + v+v+v+t   + +++   ++++++ ++l +egiei
  gi|118431459|ref|NP_147944.2| 221 GDSGVIIDVKVWVPT---DYWYQASMQVIKTVREALAREGIEI 260
                                    ***************...***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2241.93
//
Query:       gi|14601408|ref|NP_147945.1|  [L=239]
Description: hypothetical protein APE_1442 [Aeropyrum pernix K1]
Scores for 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-28   97.4   0.0    8.9e-28   96.9   0.0    1.2  1  DUF432    Protein of unknown function (DUF432)


Domain annotation for each model (and alignments):
>> DUF432  Protein of unknown function (DUF432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   4.9e-32   8.9e-28       1     123 []      60     182 ..      60     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 4.9e-32
                        DUF432   1 PvnlpkeitkyllveleeplvvepkseveiyvkvpveigvfikskkeveliDvfsl.skkkYaLYGspesGviaryvksev 80 
                                   P++ p ++t+++l+++e ++vv+p+se+++y+ +pv+ ++++   +e +++Dv+++ +k+   LYG+pesGv+ar + s+v
  gi|14601408|ref|NP_147945.1|  60 PIFKPLYVTRFILLRIEPRIVVSPGSERTFYTLIPVDTAIYAFPGDEPTIVDVIPMdDKPSLVLYGPPESGVVARLAISSV 140
                                   8999****************************************************99*********************** PP

                        DUF432  81 yseppeldpleeavveleikNetdevvevskivfdalglklyy 123
                                   + +p e ++l++a++++ +kN + + v++s+i++d++ lkly+
  gi|14601408|ref|NP_147945.1| 141 SPRP-EEPSLGRALARIAVKNISGTPVTLSRILLDSAPLKLYF 182
                                   **95.56***********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1901.09
//
Query:       gi|118431460|ref|NP_147946.2|  [L=180]
Description: hypothetical protein APE_1443.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1571.43
//
Query:       gi|14601410|ref|NP_147947.1|  [L=86]
Description: 50S ribosomal protein L37 [Aeropyrum pernix K1]
Scores for complete 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-32  110.7   3.1      3e-32  110.6   3.1    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    2.7e-05   24.0   2.0    3.9e-05   23.5   2.0    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00096   19.5   0.6     0.0014   19.0   0.6    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0037   17.1   2.3     0.0055   16.6   2.3    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0061   16.0   0.6      0.009   15.5   0.6    1.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
       0.02   15.2   2.2       0.19   12.1   0.3    2.2  2  DUF4379          Probable Zinc-ribbon domain
      0.037   14.2   1.1       0.47   10.6   0.1    2.1  2  Zn-ribbon_8      Zinc ribbon domain
       0.11   13.0   1.6       0.28   11.7   0.1    2.1  2  zf-H2C2_2        Zinc-finger double domain
       0.12   12.5   0.6       0.22   11.6   0.6    1.5  1  Elf1             Transcription elongation factor Elf1 like
       0.25   12.0   6.7       0.73   10.6   0.4    2.5  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.27   11.3   0.7          3    7.9   0.0    2.0  2  CpXC             CpXC protein
        1.5    8.8   5.7         11    6.0   1.9    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
        2.1    8.7   9.0          7    7.0   9.0    1.8  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        2.2    8.3   8.8         16    5.5   8.8    2.0  1  HalOD2           Halobacterial output domain 2


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 !  110.6   3.1   2.3e-35     3e-32       1      82 [.       3      85 ..       3      86 .] 0.98

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 2.3e-35
                                  XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSS.EEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH-XXX CS
               Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgkt.kvkRkavgiwkCkkcgktvaGgAytpettsaktvksairr 82
                                  rtk+vg aG+yg+rYG+s+rkrv++i +++++ ++Cpfcg+t +v+R++vg+w+C+kcg+t+aG+Aytp+   ak++k+ i r
  gi|14601410|ref|NP_147947.1|  3 RTKVVGPAGRYGPRYGVSVRKRVRDILARRYQPHECPFCGSTgTVRRVSVGVWSCRKCGNTWAGAAYTPRSGLAKYFKRYIVR 85
                                  79****************************************9***********************************99865 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 !   23.5   2.0   3.1e-08   3.9e-05      18      45 ..      35      62 ..      26      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.1e-08
                 Zn_Tnp_IS1595 18 gfvCPhCgsr.kayriktrglfqCkeCrk 45
                                   + CP+Cgs+ +++r++  g++ C++C+ 
  gi|14601410|ref|NP_147947.1| 35 PHECPFCGSTgTVRRVSV-GVWSCRKCGN 62
                                  356*******99999996.********86 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 !   19.0   0.6   1.1e-06    0.0014       5      36 ..      37      62 ..      34      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
               Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga 36
                                   CPfCg+ +++ r   +v+      +C +Cg 
  gi|14601410|ref|NP_147947.1| 37 ECPFCGSTGTVRRVSVGVW------SCRKCGN 62
                                  7*************88876......8999997 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 !   16.6   2.3   4.3e-06    0.0055      28      56 ..      35      64 ..      15      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.3e-06
                OrfB_Zn_ribbon 28 SktCseCgsknke.alsgrtfkCpnCgfea 56
                                    +C+ Cgs+++  ++s  ++ C++Cg ++
  gi|14601410|ref|NP_147947.1| 35 PHECPFCGSTGTVrRVSVGVWSCRKCGNTW 64
                                  579********9999************986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.6   7.1e-06     0.009       2      27 ..      37      62 ..      36      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.1e-06
                                  EETTTTCEECHEETSTTCEEESSSSB CS
                  TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                   CP Cgst +v+  + g   C +CG+
  gi|14601410|ref|NP_147947.1| 37 ECPFCGSTGTVRRVSVGVWSCRKCGN 62
                                  5************************7 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       0.1   1.3e+02      45      56 .]      31      41 ..      14      41 .. 0.57
   2 ?   12.1   0.3   0.00015      0.19      29      40 ..      54      65 ..      46      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.1
                       DUF4379 45 nrtkgssk...CpkC 56
                                   r     +   Cp C
  gi|14601410|ref|NP_147947.1| 31 RRY----QpheCPFC 41
                                  222....2455***9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00015
                       DUF4379 29 wWkCakCgheWe 40
                                   W C+kCg++W 
  gi|14601410|ref|NP_147947.1| 54 VWSCRKCGNTWA 65
                                  6**********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 ?   10.6   0.1   0.00037      0.47      26      39 ..      34      50 ..      22      51 .. 0.75
   2 ?    2.5   0.1      0.13   1.6e+02       8      13 ..      57      62 ..      54      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                   Zn-ribbon_8 26 lta.CPeCgs..evrrv 39
                                  +++ CP Cgs  +vrrv
  gi|14601410|ref|NP_147947.1| 34 QPHeCPFCGStgTVRRV 50
                                  5666******9777775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                   Zn-ribbon_8  8 CeeCgh 13
                                  C++Cg+
  gi|14601410|ref|NP_147947.1| 57 CRKCGN 62
                                  888886 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 ?   11.7   0.1   0.00022      0.28      14      23 ..      35      44 ..      30      46 .. 0.87
   2 ?   -0.4   0.1       1.4   1.8e+03      17      21 ..      57      61 ..      54      63 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                     zf-H2C2_2 14 pyeCplCdka 23
                                  p+eCp+C+ +
  gi|14601410|ref|NP_147947.1| 35 PHECPFCGST 44
                                  9******987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                     zf-H2C2_2 17 CplCd 21
                                  C +C+
  gi|14601410|ref|NP_147947.1| 57 CRKCG 61
                                  77776 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   0.00017      0.22      22      54 ..      36      63 ..      18      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                          Elf1 22 FdCpfCnheksvevkldkkekiaevsCkvCges 54
                                   +CpfC+++ +v+     + ++++ sC++Cg +
  gi|14601410|ref|NP_147947.1| 36 HECPFCGSTGTVR-----RVSVGVWSCRKCGNT 63
                                  58*******8874.....678999******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 ?   10.6   0.4   0.00057      0.73       1      14 [.      34      48 ..      34      52 .. 0.79
   2 ?    5.1   0.1     0.029        37       2      11 ..      54      63 ..      53      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00057
                       zf-ISL3  1 aphrCPnCgsk.tvv 14
                                  +ph CP Cgs+ tv+
  gi|14601410|ref|NP_147947.1| 34 QPHECPFCGSTgTVR 48
                                  69*********6543 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.029
                       zf-ISL3  2 phrCPnCgsk 11
                                  ++ C++Cg++
  gi|14601410|ref|NP_147947.1| 54 VWSCRKCGNT 63
                                  589*****97 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0023         3      27      49 ..      25      47 ..      20      52 .. 0.87
   2 ?    2.6   0.1       0.1   1.3e+02      35      46 ..      52      63 ..      46      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                          CpXC 27 keklldgslfeatCpkCgatakl 49
                                  + ++l+ +++ ++Cp Cg t+++
  gi|14601410|ref|NP_147947.1| 25 VRDILARRYQPHECPFCGSTGTV 47
                                  5689999************9987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                          CpXC 35 lfeatCpkCgat 46
                                  +  + C kCg+t
  gi|14601410|ref|NP_147947.1| 52 VGVWSCRKCGNT 63
                                  567999999987 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.024        31       1      12 [.      36      47 ..      36      50 .. 0.85
   2 ?    6.0   1.9    0.0086        11      30      38 ..      56      64 ..      54      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.024
                       TFIIS_C  1 akCpkCgsreay 12
                                  ++Cp Cgs+ ++
  gi|14601410|ref|NP_147947.1| 36 HECPFCGSTGTV 47
                                  68*****99876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0086
                       TFIIS_C 30 kCtkCghrW 38
                                   C kCg++W
  gi|14601410|ref|NP_147947.1| 56 SCRKCGNTW 64
                                  699999999 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 ?    7.0   9.0    0.0055         7       3      33 ..      35      61 ..      33      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0055
                                  EE--TTTT-TTTEE.ETT....S-EEETTTTB CS
                Prim_Zn_Ribbon  3 hspCPvCGGrDrFr.fddkdgrGtwfCrqCgg 33
                                  + +CP CG+ +  r  +     G w Cr+C g
  gi|14601410|ref|NP_147947.1| 35 PHECPFCGSTGTVRrVSV----GVWSCRKC-G 61
                                  579********9998888....********.4 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   8.8     0.013        16      24      45 ..      47      68 ..      34      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                        HalOD2 24 yrqLGayvWkCtrCGevqaaAd 45
                                  +r+    vW C +CG++ a+A 
  gi|14601410|ref|NP_147947.1| 47 VRRVSVGVWSCRKCGNTWAGAA 68
                                  5667778***********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 732.28
//
Query:       gi|14601411|ref|NP_147948.1|  [L=276]
Description: exosome complex RNA-binding protein Rrp42 [Aeropyrum pernix K1]
Scores for 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-32  110.8   0.0    9.2e-31  107.1   0.0    2.0  2  RNase_PH    3' exoribonuclease family, domain 1
    8.3e-12   45.0   0.7    1.6e-11   44.0   0.2    1.8  2  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0     1e-34   9.2e-31       3     132 .]      38     171 ..      36     171 .. 0.95
   2 ?    1.7   0.1     0.039   3.5e+02      26      91 ..     196     265 ..     179     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 1e-34
                                   EEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHH CS
                      RNase_PH   3 RslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrlle 83 
                                   R+++ietg++++a+GSa+++lG+t+v+a+v++++ + p+++  +++g+l+v+ e+ p+as+ ++  g p++ +iel+r+++
  gi|14601411|ref|NP_147948.1|  38 RNVKIETGIIEKAEGSALVKLGKTQVIAGVKAGVGA-PFKD-TPNQGVLTVHAEFVPLASPVFEP-GPPDENAIELARVVD 115
                                   99********************************99.7888.556799***************77.9************** PP

                                   HHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  84 ralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                   r+lr+++ +        ++++ + + +d++++++dg +l+da+++a+++ L++a++p
  gi|14601411|ref|NP_147948.1| 116 RSLREVGAVdleslvirPGEKVWVLWVDLYIIDHDG-NLFDASMLATMAVLLTARLP 171
                                   ********88899999999999**************.******************98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.039
                                   EEEEEEEEEEEEE......E-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC- CS
                      RNase_PH  26 tkvlasvtgpiee......rpseer.ddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsil 91 
                                   t v+++ t+ i        +++ee+ +d+   l++ v+    + g  +++g  s +e +++ ++  +l++s +
  gi|14601411|ref|NP_147948.1| 196 TRVVTVTTAKIDRyivvdpNIEEEAvSDVR--LVTAVDENGRIVGL-QKTGMGSLTEADIETMIGYSLEASKV 265
                                   777777777776655554334444444444..66666655444333.45689999999999999999999875 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 ?   -2.9   0.0      0.79   7.1e+03      38      50 ..     178     189 ..     162     195 .. 0.71
   2 !   44.0   0.2   1.8e-15   1.6e-11       3      63 ..     198     258 ..     196     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.79
                                   TSEEEEEEEECSS CS
                    RNase_PH_C  38 tkevvtlmkeggs 50 
                                   t+e+  ++keg++
  gi|14601411|ref|NP_147948.1| 178 TGEI-IISKEGEG 189
                                   4444.77777776 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 1.8e-15
                                   -EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHH CS
                    RNase_PH_C   3 viavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaiel 63 
                                   v+ vt +k+d ++v+Dp+ eEe++s+ +l  av++++++v l+k+g ++l+e +++ +i  
  gi|14601411|ref|NP_147948.1| 198 VVTVTTAKIDRYIVVDPNIEEEAVSDVRLVTAVDENGRIVGLQKTGMGSLTEADIETMIGY 258
                                   899****************************************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2123.49
//
Query:       gi|14601412|ref|NP_147949.1|  [L=246]
Description: exosome complex exonuclease Rrp41 [Aeropyrum pernix K1]
Scores for 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-37  127.0   0.0      9e-37  126.5   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    3.7e-10   39.7   0.2    5.9e-10   39.0   0.2    1.4  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0     1e-40     9e-37       1     132 []      25     154 ..      25     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1e-40
                                   EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                      RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                   +lR+++++ g+l +a+GSa++e+G t vla+v+gp+e+++++   +d   al v++ +apf++ er++   ps++eiels+
  gi|14601412|ref|NP_147949.1|  25 DLRPVRMQVGILHNADGSALVEFGRTRVLAAVYGPREPHQRFYVlPDR-AALRVRYHMAPFSTDERKS-PAPSRREIELSK 103
                                   58************************************7776666543.57***************66.78********** PP

                                   HHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                      RNase_PH  81 lleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                   ++ +al+p++l e++p++ id++++vl++dg ++  a+++aaslALadagip
  gi|14601412|ref|NP_147949.1| 104 VVREALEPVVLAEEFPRTVIDVFLEVLQADG-GTRTAAVTAASLALADAGIP 154
                                   *******************************.*******************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 !   39.0   0.2   6.6e-14   5.9e-10       1      66 [.     157     221 ..     157     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.6e-14
                                   S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                    RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                   a+v++v+vgk+ + +v+D +  E+ ++e+d+++a a +  ++tl++++g  l+ e++  a+ +A++
  gi|14601412|ref|NP_147949.1| 157 ALVGGVAVGKIQGVLVVDVDELEDMYGEADMPVAAAPDIGEITLLQLNGV-LTGEEFRTALAMALR 221
                                   68************************************************.************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1857.15
//
Query:       gi|14601413|ref|NP_147950.1|  [L=235]
Description: exosome complex RNA-binding protein Rrp4 [Aeropyrum pernix K1]
Scores for complete 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   27.8   0.0    4.7e-06   26.9   0.0    1.5  1  KH_6      KH domain
    5.9e-06   26.0   0.1    1.9e-05   24.4   0.1    1.8  1  KH_1      KH domain
    0.00038   20.2   0.3     0.0008   19.2   0.3    1.5  1  KH_2      KH domain
    0.00041   20.6   0.2     0.0057   17.0   0.0    2.7  3  S1        S1 RNA binding domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0     1e-09   4.7e-06       1      45 [.     149     196 ..     149     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1e-09
                          KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvksesp 45 
                                   G ++e+s+ +v+R++     +L++L+++  + i v +NGri + ++++
  gi|14601413|ref|NP_147950.1| 149 GKIVEISPAKVPRVIgrkMSMLKTLEEKTECKIFVARNGRIHLECPNE 196
                                   7789***********555444455556699*************99986 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   4.2e-09   1.9e-05       4      37 ..     152     185 ..     150     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.2e-09
                                   EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES CS
                          KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk 37 
                                   +++   +v+r+IG++ s++k ++e+t +kI v +
  gi|14601413|ref|NP_147950.1| 152 VEISPAKVPRVIGRKMSMLKTLEEKTECKIFVAR 185
                                   5788889************************874 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   1.8e-07    0.0008      27      69 ..     150     192 ..     136     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-07
                                   EEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                          KH_2  27 viiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                    i+ i  ++  +vIG++ s++k+++++ + +i + ++++++l+
  gi|14601413|ref|NP_147950.1| 150 KIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLE 192
                                   589999**************************9*****99997 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.3     1e+04      26      37 ..      50      61 ..      34      61 .. 0.73
   2 !   17.0   0.0   1.3e-06    0.0057       2      68 ..      64     133 ..      63     138 .. 0.95
   3 ?    0.0   0.0      0.25   1.1e+03       5      17 ..     144     156 ..     142     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.3
                                  TTEEEEEEGGGS CS
                            S1 26 ngvegfvpasel 37
                                  +g ++fv ++e+
  gi|14601413|ref|NP_147950.1| 50 GGGRAFVKLKEI 61
                                  577788888876 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                                   STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS...CEESCHHHCEETTEEEEEEEEEEETTTT CS
                            S1   2 pekgevveGeVtsvtkgGafVelgngvegfvpaselsrd...arvedpdevlkvGdevkvkvlkvdkdrr 68 
                                   p++g+vv G ++sv  ++ fV++  +  + +++ +   +   + v+d    lkvGd +k+kv  +dk+r 
  gi|14601413|ref|NP_147950.1|  64 PQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFLGRpfnPAVDDMQSLLKVGDYIKAKVVAFDKTRS 133
                                   799********************************999999999************************96 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.25
                                   TCEEEEEEEEEET CS
                            S1   5 gevveGeVtsvtk 17 
                                   g +v G+++++++
  gi|14601413|ref|NP_147950.1| 144 GRIVRGKIVEISP 156
                                   889******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1806.58
//
Query:       gi|14601414|ref|NP_147951.1|  [L=258]
Description: proteasome subunit alpha [Aeropyrum pernix K1]
Scores for complete 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-60  203.1   0.1    1.1e-59  201.1   0.0    1.8  2  Proteasome      Proteasome subunit
    6.6e-11   41.7   2.2    7.4e-11   41.5   0.5    2.0  2  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
      0.035   13.3   0.0      0.047   12.9   0.0    1.1  1  SabA_adhesion   SabA N-terminal extracellular adhesion 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 !  201.1   0.0   1.9e-63   1.1e-59       1     178 [.      35     209 ..      35     220 .. 0.95
   2 ?   -0.2   0.1       0.1   6.1e+02     145     168 ..     226     249 ..     215     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.9e-63
                                   HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                    Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                   vkkG+t++Gik+++gvv+aa+kr      l++ ++++Ki+kiddhigvafaG+ +D+r+l+++ar+   ++rl yg+p+pv
  gi|14601414|ref|NP_147951.1|  35 VKKGWTSLGIKTNEGVVIAAEKRFI--GPLVDIDDIDKIYKIDDHIGVAFAGMGGDGRILIDYARVFTVRHRLLYGEPPPV 113
                                   79***********************..66669999********************************************** PP

                                   HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                    Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                   e +++ va+ +qaytq++g+rpfgv+l++agv+ +g+ ++y++dp G+y++ k a+aiGsg+++a +++ek+y++d++lee
  gi|14601414|ref|NP_147951.1| 114 ELVAKVVADVKQAYTQHGGVRPFGVALIFAGVNPDGTTKVYRTDPGGQYFSFK-AIAIGSGEQVANEMFEKHYRSDMSLEE 193
                                   ****************************************************8.*************************** PP

                                   HHHHHHHHHHHHHHHB CS
                    Proteasome 163 avelavkalkealerd 178
                                   a +la+k+l++++++ 
  gi|14601414|ref|NP_147951.1| 194 ATKLALKILYAIIRKT 209
                                   ***********99844 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHSTTBSHHHHHHHHH CS
                    Proteasome 145 aaktalekeykedltleeavelav 168
                                    a+  ++++++ ++t+e+ +e++ 
  gi|14601414|ref|NP_147951.1| 226 LAYITVKERMFTKMTKEQVKEIVD 249
                                   567778999999999999999986 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 !   41.5   0.5   1.2e-14   7.4e-11       1      23 []      12      34 ..      12      34 .. 0.99
   2 ?   -2.1   0.0      0.55   3.3e+03      11      15 ..      88      92 ..      88      96 .. 0.63

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.2e-14
                Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                  YDr+ t+FSP+G L+QV YA++A
  gi|14601414|ref|NP_147951.1| 12 YDRAATIFSPEGDLYQVRYAFEA 34
                                  **********************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.55
                Proteasome_A_N 11 dGRLf 15
                                  dGR++
  gi|14601414|ref|NP_147951.1| 88 DGRIL 92
                                  78876 PP

>> SabA_adhesion  SabA N-terminal extracellular adhesion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-06     0.047      89     173 ..     157     244 ..     141     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-06
                 SabA_adhesion  89 eenngkqifendpaqngttitCnryesgkngklsieeyekl..neAYqiiqkA.lknqaglpaLndkgeklevnvtkenrr 166
                                   + ++++ +f+    + g +++ + +e+   + +s+ee  kl  +  Y ii+k  + +++ ++ L d+ e   + v+++   
  gi|14601414|ref|NP_147951.1| 157 DPGGQYFSFKAIAIGSGEQVANEMFEKHYRSDMSLEEATKLalKILYAIIRKTvEDKEKAIATLPDQVELAYITVKERMFT 237
                                   456677788888899999999999****************722568*******8888************999998886655 PP

                 SabA_adhesion 167 tadinre 173
                                     ++++ 
  gi|14601414|ref|NP_147951.1| 238 KMTKEQV 244
                                   5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1059  (0.0590663); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1805.47
//
Query:       gi|118431461|ref|NP_147952.2|  [L=211]
Description: ribonuclease P protein component 3 [Aeropyrum pernix K1]
Scores for complete 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-12   46.1   0.0    9.6e-12   44.8   0.0    1.6  1  RNase_P_p30      RNase P subunit p30
  ------ inclusion threshold ------
      0.064   13.7   0.2       0.11   12.9   0.2    1.3  1  DraK_HK_N        DraK Histidine Kinase N-terminal domain
      0.083   12.8   0.0       0.15   11.9   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.0   1.6e-15   9.6e-12       2     208 ..       5     193 ..       4     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 1.6e-15
                                    EEEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH..HHSSEEEEEEES-H.. CS
                    RNase_P_p30   2 dlnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsglkllsRvtlvvsdpskl. 80 
                                    d+ +++++++   + + ++t+ +lgyt+vai  +   e  + + +                  +l++R  +++s+ + + 
  gi|118431461|ref|NP_147952.2|   5 DISVKPQTEQC--S-EVLRTAGRLGYTAVAIPPESADECMSLEGDGI---------------PRLYRRGYVEASTRRDVr 66 
                                    55555555543..3.49*****************9977777766666...............89*************888 PP

                                    HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-.EEEEESHHHHHS-HHHHHH CS
                    RNase_P_p30  81 qrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergv.afEinyspllrdsglaRrn 159
                                    ++ +k++  +d ++v+P t +a r a+ n +v ii  d ++      ++ t++  ++rg  a+E+++ +l  ++g + + 
  gi|118431461|ref|NP_147952.2|  67 RAAEKLAGVVDFIVVKPLTLEAARYAAANKRVHIIRVDGSN--LWAADRGTAEIMAQRGWgALEVSLRNLTLNPG-SPAA 143
                                    9**************************************87..4447999998666665439*************.9999 PP

                                    HHHHHHHHHHHHHH.--EEEE--BSSGGG---HHHHHHHHHHHT--HHHH CS
                    RNase_P_p30 160 fisnarkllrltrg.kgvviSSgAesplelRnpydiinLlktlGLeedra 208
                                    + + a  l r+      v++ S+Ae p el++py  ++L+++lG+  ++a
  gi|118431461|ref|NP_147952.2| 144 WRALAVVLRRSFAYgVHVFLASDAEEPHELWSPYSGASLAALLGVPWSHA 193
                                    877776666665558*****************************987766 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 ?   12.9   0.2   1.9e-05      0.11       2      53 ..      56     105 ..      56     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                    ---SSHHHHHHHHHHHHHHHHHHHHHHTS---HHHHTTT-SS-SEEEEE-TT CS
                      DraK_HK_N   2 lvessaqervesraqrlasivdsrlaagepitaelLeeqvpgdryvvVripg 53 
                                    +ve s++++v+  a++la++vd+ +   +p+t e+ + +   +r   +r+ g
  gi|118431461|ref|NP_147952.2|  56 YVEASTRRDVRRAAEKLAGVVDFIVV--KPLTLEAARYAAANKRVHIIRVDG 105
                                    599********************999..889999999998888877777766 PP

>> Transketolase_C  Transketolase, C-terminal 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      0.15      23     110 ..      64     141 ..      59     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                    HHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCSSEEEEEEE- CS
                Transketolase_C  23 ealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdgldapvkrvggp 102
                                     + +Aae+L      a Vvd + vkpl  e  + ++++++  ++  +++   +     a+++a++++  l++  +++++ 
  gi|118431461|ref|NP_147952.2|  64 DVRRAAEKL------AGVVDFIVVKPLTLEAARYAAANKRVHIIRVDGSNLWAADRGTAEIMAQRGWGALEVSLRNLTLN 137
                                    566777777......79****************9999999999999***99*******************9999999987 PP

                                    SSSSSSGH CS
                Transketolase_C 103 dviepgsa 110
                                        pgs+
  gi|118431461|ref|NP_147952.2| 138 ----PGSP 141
                                    ....4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1645.91
//
Query:       gi|118431462|ref|NP_147953.2|  [L=153]
Description: hypothetical protein APE_1451.1 [Aeropyrum pernix K1]
Scores for 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-37  126.5   0.1      8e-37  126.2   0.1    1.1  1  RNA_binding     RNA binding
  ------ inclusion threshold ------
      0.039   13.7   0.1      0.074   12.8   0.1    1.4  1  Bac_A_amyl_C    Bacterial Alpha amylase C-terminal domain
       0.12   12.2   1.1       0.35   10.8   0.4    2.0  2  Planc_extracel  Planctomycete extracellular


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 !  126.2   0.1   1.3e-40     8e-37       2     117 ..       7     125 ..       6     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 1.3e-40
                                    EEEEEEE-TTC-HHHHHHHHHTTSTTS..E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHHHH CS
                    RNA_binding   2 ievrafvhaTEdeekVlealsnllpee..eveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeLlk 78 
                                    +e+r+ vhaTEd+ekV +alsn+lp +  ++e+ e   eGhygn+i+++++++++ +   kvl+ +l++l ++++++Ll+
  gi|118431462|ref|NP_147953.2|   7 LEARVSVHATEDREKVVRALSNILPLSggKIEVVEDVFEGHYGNQIRVITVRIKDGRTaSKVLEDILSKLPSHDRRYLLE 86 
                                    689**********************99**999*************************9********************** PP

                                    CCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEE CS
                    RNA_binding  79 eleervdekgklylrldKQaaylgklslvegddvIkvki 117
                                    +leervd++g+ly+r++KQ+aylg+ +++egddvI++ +
  gi|118431462|ref|NP_147953.2|  87 TLEERVDKNGVLYIRVSKQDAYLGEARIYEGDDVIRIAV 125
                                    ************************************987 PP

>> Bac_A_amyl_C  Bacterial Alpha amylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.2e-05     0.074      21      59 ..      25      63 ..      15      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                   EEEEEE-TT--EEEEE--S-SEEEEETTTSEEEEEETTE CS
                   Bac_A_amyl_C 21 klvGiFsLkgkegevkvdlpDGsYkNlidgseveVkdGk 59
                                   +l  i +L g + ev  d+  G Y N i   +v +kdG+
  gi|118431462|ref|NP_147953.2| 25 ALSNILPLSGGKIEVVEDVFEGHYGNQIRVITVRIKDGR 63
                                   5667999*******************************8 PP

>> Planc_extracel  Planctomycete extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   5.8e-05      0.35       6      21 ..      76      91 ..      74      91 .. 0.90
   2 ?   -1.9   0.0       0.6   3.6e+03       6      12 ..     127     133 ..     125     134 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                 Planc_extracel  6 srsqrRRLrlEsLEsR 21
                                    +s++RR +lE+LE R
  gi|118431462|ref|NP_147953.2| 76 LPSHDRRYLLETLEER 91
                                   5899**********98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.6
                 Planc_extracel   6 srsqrRR 12 
                                    ++++rR+
  gi|118431462|ref|NP_147953.2| 127 FQGGRRK 133
                                    5788997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1149.79
//
Query:       gi|14601417|ref|NP_147954.1|  [L=225]
Description: 50S ribosomal protein L15 [Aeropyrum pernix K1]
Scores for complete 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-83  278.4   6.1    3.3e-83  278.1   6.1    1.1  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.1   6.1   1.8e-87   3.3e-83       1     190 [.       4     192 ..       4     193 .. 0.98

  Alignments for each domain:
  == domain 1  score: 278.1 bits;  conditional E-value: 1.8e-87
                                   -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS-- CS
                Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktgr 81 
                                   ++y+y++  wkk+ +  + el++ rl e+r++p++ rve+ptrldrAr+LGYkakqG++v+rvrvr+Ggr+k  ++ ++gr
  gi|14601417|ref|NP_147954.1|   4 SMYHYIAREWKKPYEGLHGELMKARLLEWRRQPSILRVEKPTRLDRARALGYKAKQGVIVARVRVRKGGRRK--PRPNKGR 82 
                                   79**********************************************************************..******* PP

                                   -GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGTTGGGGT CS
                Ribosomal_L15e  82 kpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhkhRelrG 162
                                   +pkr+gv+ + paksl+ iaeer++rk+pnl vLnSY+vgeDg+yk+yEvilvDp+h+ai+nd+++nw+++ +hk+R +rG
  gi|14601417|ref|NP_147954.1|  83 RPKRMGVYGFAPAKSLRLIAEERAQRKYPNLVVLNSYYVGEDGRYKWYEVILVDPNHPAIKNDPELNWVTTGKHKGRPFRG 163
                                   ********************************************************************************* PP

                                   -SHHHHHHTT-S-SS..TT-TTTSS-TGG CS
                Ribosomal_L15e 163 ltsagkksRGlrkkg.lkgaekirgsrra 190
                                   ltsagkk+RGlrk++ lkg++k+++ ++a
  gi|14601417|ref|NP_147954.1| 164 LTSAGKKMRGLRKSRgLKGTHKYKWKKKA 192
                                   ***********975449*****9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1711.75
//
Query:       gi|118431463|ref|NP_147955.2|  [L=838]
Description: cation-transporting ATPase [Aeropyrum pernix K1]
Scores for complete 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-54  183.5   0.9    4.8e-54  182.6   0.1    1.9  2  E1-E2_ATPase   E1-E2 ATPase
    3.9e-45  154.7   3.0    8.7e-45  153.6   1.0    2.2  2  Hydrolase      haloacid dehalogenase-like hydrolase
    2.8e-24   85.3   1.3    4.2e-12   46.3   0.1    3.0  2  HMA            Heavy-metal-associated domain
    0.00023   21.7   0.1    0.00077   19.9   0.0    2.1  2  HAD            haloacid dehalogenase-like hydrolase
    0.00033   20.5   0.1     0.0031   17.3   0.1    2.2  2  Hydrolase_3    haloacid dehalogenase-like hydrolase
     0.0047   17.0   0.0      0.058   13.5   0.0    2.6  2  Hydrolase_6    Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.049   13.5   0.5         23    4.9   0.0    4.1  4  DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
       0.05   13.3   1.3        4.5    7.0   0.5    3.7  4  Cupin_3        Protein of unknown function (DUF861)
       0.11   12.6   0.1        1.4    8.9   0.0    2.6  2  HAD_2          Haloacid dehalogenase-like hydrolase


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 !  182.6   0.1   2.4e-57   4.8e-54       1     180 [.     288     466 ..     288     467 .. 0.98
   2 ?   -2.8   0.1       1.9   3.8e+03      23      33 ..     714     724 ..     709     738 .. 0.75

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 2.4e-57
                                    SSS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-E CS
                   E1-E2_ATPase   1 kllpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsge 80 
                                    kl+p++a+v+r+ +e+e+d++e++pGD+v++++g+r+p+Dg +v+g+a vdes+ TGE  pvek+ gd v +G++v sg 
  gi|118431463|ref|NP_147955.2| 288 KLKPQKARVLRGRREVEVDVSEVKPGDLVVVRQGERIPVDGYVVQGKAYVDESVFTGEPIPVEKKPGDLVLAGSMVSSGW 367
                                    5899**************************************************************************** PP

                                    EEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS- CS
                   E1-E2_ATPase  81 akavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiP 160
                                    +++ +t+t  dt +++iarl++++++ k ++q+ +d+++++++++vl+ia l+f ++l+lg+   +a++ra +++++++P
  gi|118431463|ref|NP_147955.2| 368 LHISATRTSGDTAIDRIARLIAYSQAGKMDIQRLADRVSGMFFWAVLCIASLTFTAWLFLGGLE-TAIIRAASVFLISCP 446
                                    ***********************************************************99976.*************** PP

                                    TTHHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 161 caLplavplalalgarrlak 180
                                    caL+la+p+a ++g++ +a+
  gi|118431463|ref|NP_147955.2| 447 CALGLATPTASSAGVGVAAR 466
                                    ****************9998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                                    --TTSEEEEET CS
                   E1-E2_ATPase  23 lvpGDivllka 33 
                                    ++ GDivl+k 
  gi|118431463|ref|NP_147955.2| 714 VEAGDIVLIKG 724
                                    78999999985 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.32   6.4e+02      94     146 ..      99     149 ..      27     159 .. 0.74
   2 !  153.6   1.0   4.4e-48   8.7e-45       3     210 .]     485     701 ..     483     701 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.32
                                    HHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  94 qsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpe 146
                                      +g  +++ +     v+   +p+  kpe  e++++L++ag++  ++ g +  
  gi|118431463|ref|NP_147955.2|  99 KMKGVAEVYASHTNKTVVVRYNPHATKPE--EVLEALRKAGYKAEMAEGKSLV 149
                                    44555555556666666777777666666..8899999999988888887655 PP

  == domain 2  score: 153.6 bits;  conditional E-value: 4.4e-48
                                    EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH......HHCHHHHHHHHHHHHH....HHHHHHHHHETTTE..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx..... RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletg......sehpigkalvaaakar....sgaltgfatfigrg..... 67 
                                     vvfDk+GTLt g p+v  v +    +++++le++      sehp+++a++ a+ ++    +++ ++ ++f+g g     
  gi|118431463|ref|NP_147955.2| 485 IVVFDKTGTLTLGMPRVAAVEAVDGYSEKEILELAasaekwSEHPLARAIIDAYMEVagrgPEDPDNAEVFPGMGvyaev 564
                                    69***************888888899************************88888887965445599999********** PP

                                    ...HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEE CS
                                    ...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 ...ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvllt 141
                                        + +g+++ ++      + l++  +++qs+g t +++  +++  +v++i d+  ++pea+e+v +L + g++v +lt
  gi|118431463|ref|NP_147955.2| 565 ggrSVVVGNRKIMDGFeVDIKTLEKIAEEWQSRGATTVFVaiDGKPAGVIAIRDE--PRPEARETVDWLEKLGLKVMMLT 642
                                    ****************9667778888888888888888888**************..*********************** PP

                                    SSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 142 gdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    gd++ ta+++a++l+           ie+  a++spegk ++ireLq k++ v+mVGDgvnDa+ la+A+
  gi|118431463|ref|NP_147955.2| 643 GDSEGTARAIARELD-----------IEEyRAGVSPEGKAEVIRELQKKGHVVVMVGDGVNDAPSLARAD 701
                                    ***************...........7777**************************************98 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.1   2.1e-15   4.2e-12       2      62 .]      11      71 ..      10      71 .. 0.97
   2 !   37.0   0.2   1.7e-12   3.5e-09       2      62 .]      79     139 ..      78     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.1e-15
                            HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62
                                   ++++gmhCa C  +vek+L +lpgV +++ d +t+++++ +++ s+ l+++++ai++ gy+
  gi|118431463|ref|NP_147955.2| 11 LSIKGMHCATCGLTVEKALRSLPGVVEASADPVTGEAVIAYEPGSVRLSDVVKAIRSVGYD 71
                                   5799*******************************************************96 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 1.7e-12
                            HMA   2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                    +rv+ m     ++ ve++L++++gV +v  +  +ktv+V++++ +tk+++++ea++kagyk
  gi|118431463|ref|NP_147955.2|  79 IRVPSMSSIDDERVVEETLLKMKGVAEVYASHTNKTVVVRYNPHATKPEEVLEALRKAGYK 139
                                    56666666666899**********************************************7 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.6   9.2e+03     115     158 ..      93     133 ..      90     149 .. 0.46
   2 !   19.9   0.0   3.9e-07   0.00077      86     187 ..     620     697 ..     535     698 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.6
                            HAD 115 vepll.aelgadevlatelevddrltge..lglegkpvrgegkvaal 158
                                    ve++l +  g+ ev+a+      + ++   +++ ++ ++ e+ + al
  gi|118431463|ref|NP_147955.2|  93 VEETLlKMKGVAEVYAS------HTNKTvvVRYNPHATKPEEVLEAL 133
                                    55555455557777777......444442122222222222222222 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.9e-07
                            HAD  86 ldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaae 165
                                     +p+a+e +++  + G +v +++g  +  ++++++el+    + +       + ++       v  egk+ ++re l+++
  gi|118431463|ref|NP_147955.2| 620 PRPEARETVDWLEKLGLKVMMLTGDSEGTARAIARELD----IEE-------YRAG-------VSPEGKAEVIRE-LQKK 680
                                    349***********************************....999.......5555.......688899999999.4444 PP

                            HAD 166 gegidleevvayGDspsDlpll 187
                                    g     + vv +GD+++D p l
  gi|118431463|ref|NP_147955.2| 681 G-----HVVVMVGDGVNDAPSL 697
                                    4.....448999******9976 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       0.3   5.9e+02      17      57 ..     621     661 ..     616     665 .. 0.88
   2 !   17.3   0.1   1.6e-06    0.0031     194     239 ..     672     717 ..     668     723 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.3
                                    -HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSE CS
                    Hydrolase_3  17 sektkeaikklkekgikvviATGRslravlpvleelgldlp 57 
                                     ++++e++  l++ g kv+  TG s  +++ +++el+++ +
  gi|118431463|ref|NP_147955.2| 621 RPEARETVDWLEKLGLKVMMLTGDSEGTARAIARELDIEEY 661
                                    578889999999***********************999865 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.6e-06
                                    HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHS CS
                    Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaA 239
                                    +++ el+ +   v+ +GDg ND + L +a++g+A++na++   +a 
  gi|118431463|ref|NP_147955.2| 672 EVIRELQKKGHVVVMVGDGVNDAPSLARADVGIAVANATDVSVEAG 717
                                    567788888899***************************9766665 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.66   1.3e+03      29      59 ..     111     141 ..      96     149 .. 0.77
   2 !   13.5   0.0   2.9e-05     0.058       7      51 ..     612     656 ..     610     694 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.66
                                    TT-EEEEEE---SS-HHHHHHHHHHTT---- CS
                    Hydrolase_6  29 agkpvvllTNnsskseeeyakkleklgvdit 59 
                                    ++k+vv+  N    ++ee+++ l+k g++++
  gi|118431463|ref|NP_147955.2| 111 TNKTVVVRYNPHATKPEEVLEALRKAGYKAE 141
                                    5677777778888888899999999888765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.9e-05
                                    TTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                    Hydrolase_6   7 GvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                    Gv+   d++ p+a e++++l++ g +v++lT  s  + +++a +l
  gi|118431463|ref|NP_147955.2| 612 GVIAIRDEPRPEARETVDWLEKLGLKVMMLTGDSEGTARAIAREL 656
                                    99999*****************************99999888776 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.59   1.2e+03      16      33 ..      60      77 ..      56     108 .. 0.58
   2 ?    4.9   0.0     0.012        23       4      35 ..     116     147 ..     114     149 .. 0.83
   3 ?    3.2   0.0      0.04        79      13      35 ..     623     645 ..     613     648 .. 0.85
   4 ?   -2.2   0.0       1.9   3.8e+03       8      27 ..     664     683 ..     662     689 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.59
                  DAHP_snth_FXD 16 evierieelGlkvhvskG 33
                                   +v++ i++ G++v + + 
  gi|118431463|ref|NP_147955.2| 60 DVVKAIRSVGYDVVLAEA 77
                                   567777777776665543 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                  DAHP_snth_FXD   4 vmkkgateeqieevierieelGlkvhvskGee 35 
                                    v++ +    + eev+e +++ G+k+++ +G++
  gi|118431463|ref|NP_147955.2| 116 VVRYNPHATKPEEVLEALRKAGYKAEMAEGKS 147
                                    556666677789*****************985 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.04
                  DAHP_snth_FXD  13 qieevierieelGlkvhvskGee 35 
                                    + +e ++++e+lGlkv + +G +
  gi|118431463|ref|NP_147955.2| 623 EARETVDWLEKLGLKVMMLTGDS 645
                                    668999***********999975 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.9
                  DAHP_snth_FXD   8 gateeqieevierieelGlk 27 
                                    g+++e   evi++++++G  
  gi|118431463|ref|NP_147955.2| 664 GVSPEGKAEVIRELQKKGHV 683
                                    77888889999999999964 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 ?   -2.6   0.0       2.3   4.6e+03      11      38 ..     139     167 ..     134     169 .. 0.63
   2 ?    7.0   0.5    0.0022       4.5      30      60 ..     295     322 ..     289     341 .. 0.77
   3 ?    1.7   0.1      0.11   2.1e+02      30      55 ..     329     358 ..     322     367 .. 0.87
   4 ?    0.3   0.0      0.29   5.9e+02      40      60 ..     706     726 ..     701     740 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.3
                                    EEEEECEEEEECESS.EEEEEEEECEEEE CS
                        Cupin_3  11 iwectpGkfrltyee.dEfcyileGevkv 38 
                                    + e+  Gk  ++ e+ +E   +l G +++
  gi|118431463|ref|NP_147955.2| 139 KAEMAEGKSLVEAEAeEERRLLLDGLISI 167
                                    66777777777777755666666666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0022
                                    EEEECEEEEEETTTEEEEEETTEEEEE-TTE CS
                        Cupin_3  30 yileGevkvtpeggetvelraGDlvvlpkgl 60 
                                     +l+G+ +v++      e+++GDlvv+++g 
  gi|118431463|ref|NP_147955.2| 295 RVLRGRREVEV---DVSEVKPGDLVVVRQGE 322
                                    58999999999...66789**********98 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.11
                                    EEEECEEEEEET..TTEE..EEEETTEEEE CS
                        Cupin_3  30 yileGevkvtpe..gget..velraGDlvv 55 
                                    y+++G+  v +    ge+  ve ++GDlv 
  gi|118431463|ref|NP_147955.2| 329 YVVQGKAYVDESvfTGEPipVEKKPGDLVL 358
                                    9******999999999998899999**985 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.29
                                    ETTTEEEEEETTEEEEE-TTE CS
                        Cupin_3  40 peggetvelraGDlvvlpkgl 60 
                                    +++  +v ++aGD+v ++ +l
  gi|118431463|ref|NP_147955.2| 706 VANATDVSVEAGDIVLIKGDL 726
                                    55667799*******988766 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   3.4e+03      82      97 ..     124     139 ..      87     144 .. 0.65
   2 ?    8.9   0.0   0.00072       1.4      80     173 ..     620     702 ..     617     707 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                          HAD_2  82 dgvkelLeeLkeagyk 97 
                                       +e+Le L++agyk
  gi|118431463|ref|NP_147955.2| 124 TKPEEVLEALRKAGYK 139
                                    3446788888888887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00072
                          HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvG 159
                                    p ++++e++++L++ g+k+   T  s+ +++   ++l+ie+y            +   pe  ++++++l+ k + v++vG
  gi|118431463|ref|NP_147955.2| 620 PRPEARETVDWLEKLGLKVMMLTGDSEGTARAIARELDIEEYRAG--------VS---PEGKAEVIRELQKKGHVVVMVG 688
                                    678899999999999999999999999999999999999888433........33...6777899999999********* PP

                          HAD_2 160 DsptDieaakkagi 173
                                    D  +D  +  +a +
  gi|118431463|ref|NP_147955.2| 689 DGVNDAPSLARADV 702
                                    ****9988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.43
# Mc/sec: 5891.14
//
Query:       gi|14601419|ref|NP_147956.1|  [L=173]
Description: hypothetical protein APE_1457 [Aeropyrum pernix K1]
Scores for complete 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  105.4   0.0    2.8e-30  105.1   0.0    1.0  1  Ferritin      Ferritin-like domain
    1.3e-07   32.1   2.0     0.0028   18.0   0.1    2.0  2  Rubrerythrin  Rubrerythrin
     0.0015   18.8   0.0     0.0019   18.4   0.0    1.1  1  Ferritin_2    Ferritin-like domain
  ------ inclusion threshold ------
      0.019   14.8   0.1       0.96    9.2   0.0    2.0  2  COQ7          Ubiquinone biosynthesis protein COQ7
      0.099   12.1   0.0       0.13   11.7   0.0    1.1  1  DUF3845       Domain of Unknown Function with PDB structure


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 !  105.1   0.0   7.8e-34   2.8e-30       1     138 [.      19     162 ..      19     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 7.8e-34
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHH.HHHHHHHHHHHHTTS....SHHHHHH.....C-SS CS
                      Ferritin   1 ikaLneqladeltaayqylamawyvkgpgleglaeffdeqaeeer.ehadklaerilalGgtpvltraelee.....ieap 75 
                                   ik L +++ade++a y+y++ a  vkgp+ e+++e f+++aeee  +ha+++aer+++++ +p+ + a+l+e     +++ 
  gi|14601419|ref|NP_147956.1|  19 IKRLLSAFADEWVAGYYYMYTALAVKGPHAETISEIFMKEAEEEIgKHAKMIAERLQDFDVDPPRDFAKLYEisgckYPPL 99 
                                   68899****************************************9**************************999887777 PP

                                   SSCS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Ferritin  76 kefg.sveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallek 138
                                   +e+  +v+ ++ aa+++e +++++++el +l++   Dpat++++ed+l+++ +h  el +ll+k
  gi|14601419|ref|NP_147956.1| 100 PEDPyDVDGFIIAAVKAEICAIKAYKELFDLTHGT-DPATEELAEDLLRDETRHRTELVNLLTK 162
                                   77666*****************************8.*************************987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   7.8e-07    0.0028       3      59 ..      22      80 ..      20      95 .. 0.91
   2 !   13.9   0.2   1.5e-05     0.052       5      57 ..     112     164 ..     109     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.8e-07
                                  HHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHH.HHHHHHHHHHHHHCSTT CS
                  Rubrerythrin  3 LekAiagEssarrlYkelaekak.egypqiaelFeelAeeE.reHakilnklleklepe 59
                                  L  A+a E  a  +Y++ a  +k    + i+e+F + AeeE  +Hak++++ l++++ +
  gi|14601419|ref|NP_147956.1| 22 LLSAFADEWVAGYYYMYTALAVKgPHAETISEIFMKEAEEEiGKHAKMIAERLQDFDVD 80
                                  789********************99****************559***********9876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   HHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCS CS
                  Rubrerythrin   5 kAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnkllekle 57 
                                   +A+++E+ a++ Ykel + +    p ++el e+l ++E +H+  l +ll k  
  gi|14601419|ref|NP_147956.1| 112 AAVKAEICAIKAYKELFDLTHGTDPATEELAEDLLRDETRHRTELVNLLTKEG 164
                                   699***************999999*******************9999998855 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.2e-07    0.0019      10     135 ..      26     161 ..      18     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-07
                    Ferritin_2  10 lnlEyleaafYtaalegaslddkalldaevrevaeeiakhee.aHveflkaaleGaaavakptfdf..............a 75 
                                    + E ++  +Y + + +     k+   +++ e++ + a++e+ +H++++++ l+ +  v+ p  df              +
  gi|14601419|ref|NP_147956.1|  26 FADEWVAGYYYMYTALAV----KGPHAETISEIFMKEAEEEIgKHAKMIAERLQ-DFDVD-PPRDFaklyeisgckypplP 100
                                   555666666666666654....67777777787777777776369999999995.66666.45566777888999999877 PP

                    Ferritin_2  76 fdpfadeksflalaavlEdvgvsAYlgaaplls..nkelltaaasIlsvEArHaavirtllg 135
                                    dp+ d + f+ +a   E  +++AY+    l +  +++  ++a  +l +E rH + + +ll 
  gi|14601419|ref|NP_147956.1| 101 EDPY-DVDGFIIAAVKAEICAIKAYKELFDLTHgtDPATEELAEDLLRDETRHRTELVNLLT 161
                                   7777.678899999999***********9988766999****************99998886 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.013        46      11      62 ..      27      80 ..      19      94 .. 0.69
   2 ?    9.2   0.0   0.00027      0.96      13      61 ..     117     165 ..     109     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.013
                          COQ7 11 aGElgAvaiYkgqlavlakkdpe.lkpllkemleqEk.eHlatfeellkerrvr 62
                                  a E  A + Y   +++++  ++e + +++ + +e+E  +H ++++e+l++ +v 
  gi|14601419|ref|NP_147956.1| 27 ADEWVAGYYYMYTALAVKGPHAEtISEIFMKEAEEEIgKHAKMIAERLQDFDVD 80
                                  557778888888888775555553555555555555437888888888877765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00027
                          COQ7  13 ElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellkerrv 61 
                                   E++A   Yk   +  + +dp +++l ++ l++E++H   + +ll+++++
  gi|14601419|ref|NP_147956.1| 117 EICAIKAYKELFDLTHGTDPATEELAEDLLRDETRHRTELVNLLTKEGI 165
                                   99***********************************999999998876 PP

>> DUF3845  Domain of Unknown Function with PDB structure
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.7e-05      0.13     138     195 ..      22      81 ..      13      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                                   EEE--SSSEEEEEEEEEEESSSS-SSGGG-TTEEEEEEGGGTEEE-T..TSSEEEEEEEE CS
                       DUF3845 138 eltlsgdewmidyvyaqlaslfqpyppaafeevflckggesfaelds..frrtytfdiey 195
                                    l   +dew+  y y+  a   +     +  e+f+  ++e++++     ++r+  fd++ 
  gi|14601419|ref|NP_147956.1|  22 LLSAFADEWVAGYYYMYTALAVKGPHAETISEIFMKEAEEEIGKHAKmiAERLQDFDVDP 81 
                                   567789*******999888777766666789*********99987652279999**9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1291.48
//
Query:       gi|14601420|ref|NP_147957.1|  [L=461]
Description: mercuric reductase [Aeropyrum pernix K1]
Scores for 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-51  172.9   0.2    1.1e-50  172.6   0.2    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      4e-33  114.0   0.4    7.4e-33  113.1   0.4    1.5  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    2.5e-12   46.9   4.7    1.6e-07   31.0   0.5    2.9  3  FAD_oxidored   FAD dependent oxidoreductase
    3.8e-10   40.2   4.9    3.5e-09   37.1   0.0    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      7e-10   38.5  12.6    1.1e-05   24.7   4.8    3.6  4  GIDA           Glucose inhibited division protein A
      8e-08   31.9   0.5    0.00039   19.8   0.0    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.4e-06   26.4   1.6    3.4e-06   26.4   1.6    2.9  3  FAD_binding_2  FAD binding domain
    0.00034   19.4   7.8     0.0018   17.1   3.0    2.7  3  HI0933_like    HI0933-like protein
  ------ inclusion threshold ------
      0.012   14.9   2.0        1.7    7.8   0.3    2.5  2  Thi4           Thi4 family
       0.13   11.5   3.3       0.64    9.3   1.8    2.4  3  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
       0.44    9.7   6.6        1.9    7.7   0.1    2.3  2  FAD_binding_3  FAD binding domain
       0.68    9.4  10.6        0.5    9.9   6.2    2.5  3  DAO            FAD dependent oxidoreductase
        5.2    6.9   7.1       0.92    9.4   0.1    2.5  3  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
        5.9    5.8   5.6        2.9    6.8   2.5    2.0  2  Lycopene_cycl  Lycopene cyclase protein
         10    6.5   7.6          4    7.8   2.4    2.5  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.6   0.2   8.8e-54   1.1e-50       1     294 []       6     318 ..       6     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: 172.6 bits;  conditional E-value: 8.8e-54
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.............HHHHCHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxx RF
                   Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.............evvkklnq 65 
                                   +d++viGgG+AG++a   +a+ ga v+lv+   l+gtc+n+gc++sk +l   + a+ a              +v + l++
  gi|14601420|ref|NP_147957.1|   6 YDIIVIGGGAAGFSAVVAAAEGGASVLLVSegpLGGTCVNFGCVPSKHVLYNLSTARKAGlkislsealegarKVSETLRK 86 
                                   69***************************8899**************99999999998989***********988888888 PP

                                   H.CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEE.SEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.. CS
                                   x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                   Pyr_redox_2  66 g.ielllgeevvkidpgkkkvklekkkegdeekiay.dklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.. 142
                                   + +e ll++ +v++ +g++++k    +e d++++ y ++ ++A G+++ +++ipG++e   k  r+ld+ + + +   p  
  gi|14601420|ref|NP_147957.1|  87 EkYESLLDSLGVDYLRGRARFKAPGIVEADGREVRYrKAAIIAVGARTWRPPIPGLKEAE-KAGRILDNERLFGEGPPPdm 166
                                   88******7799999*********************999*****************5555.5559***99999999999** PP

                                   SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEEEEET CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                   Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge..klevvle 221
                                   ++++v+Gg + GvE A+ +a+ g +++l+++  rll+  ++e++ +++++le +Gvev++ +++ ++++     ++++++ 
  gi|14601420|ref|NP_147957.1| 167 ESVAVIGGRAQGVEAAQIFARSGLKTVLLQRSGRLLPRDEPEAGVYMKRVLEGDGVEVRTSARPLRVESVRGavRIDYETP 247
                                   ********************************************************************9999555558887 PP

                                   TSCE.EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 222 dgee.idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                   +g   ++a+++ +a+G++p  ++l+ e++g+ + ++g+ivv+e+l    pg+ya+GD++   gg++l ++A ++G
  gi|14601420|ref|NP_147957.1| 248 QGPAsVEASYIYLATGRKPVLDGLGlENVGVRVSSDGFIVVNEKL-MASPGVYAAGDCI---GGIQLEPVAAREG 318
                                   77667****************************************.569**********...*********9998 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 !  113.1   0.4   6.2e-36   7.4e-33       1     109 [.     337     445 ..     337     446 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 6.2e-36
                                   BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHH CS
                 Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelav 81 
                                   ip++vftdpe+asvGlte e+ ++ + + + +++++++ ra++++ + gfvK+v+d +t+kv G+h+++p+a+e+i+e+a+
  gi|14601420|ref|NP_147957.1| 337 IPRAVFTDPEFASVGLTERELARKLGVCACRTVDITQIPRARIMGYETGFVKMVVDPRTKKVAGVHMMAPQAAEAIHEAAF 417
                                   79****************999999999****************************************************** PP

                                   HHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                 Pyr_redox_dim  82 aikagltvedladtihihPtlsealkea 109
                                   ++kag+tv+d++dtihi P++se +k a
  gi|14601420|ref|NP_147957.1| 418 ILKAGMTVDDVIDTIHIFPSISEGIKYA 445
                                   ***********************99977 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.5   1.4e-10   1.6e-07       1      43 [.       7      48 ..       7      93 .. 0.83
   2 !   15.6   0.7   6.4e-06    0.0076       2      34 ..     169     201 ..     168     201 .. 0.95
   3 ?   -0.4   0.0      0.46   5.5e+02      92     144 ..     212     263 ..     204     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.4e-10
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv 43
                                  D++V+GGg+aG+ A +aAa+ Ga+vlLv+e + lGG+  + + 
  gi|14601420|ref|NP_147957.1|  7 DIIVIGGGAAGFSAVVAAAEGGASVLLVSEGP-LGGTCVNFGC 48
                                  9***************************9987.8998877555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.4e-06
                  FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvl 34 
                                   v V+GG + Gv AA   ar+G k++L++++g+l
  gi|14601420|ref|NP_147957.1| 169 VAVIGGRAQGVEAAQIFARSGLKTVLLQRSGRL 201
                                   89***************************9876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.46
                  FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                    ++ +l+++gv+v + +r+ +ve        +  e+ +g   ++A+++  ATg
  gi|14601420|ref|NP_147957.1| 212 YMKRVLEGDGVEVRTSARPLRVESVR-GAVRIDYETPQGPASVEASYIYLATG 263
                                   57788999**************9973.699999999999******99987776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   2.1      0.14   1.7e+02       2      30 ..       8      36 ..       7      39 .. 0.89
   2 !   37.1   0.0   2.9e-12   3.5e-09       1      71 [.     168     238 ..     168     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                  ++v+GgG  g  +  a+ae g++V +v  
  gi|14601420|ref|NP_147957.1|  8 IIVIGGGAAGFSAVVAAAEGGASVLLVSE 36
                                  89***********9999999999999876 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.9e-12
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                     Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                   +v+v+Gg   g+E+A+++a+ g k+ +++rs +ll+  ++ea+ ++++ le  g+ev++++++ ++e    
  gi|14601420|ref|NP_147957.1| 168 SVAVIGGRAQGVEAAQIFARSGLKTVLLQRSGRLLPRDEPEAGVYMKRVLEGDGVEVRTSARPLRVESVRG 238
                                   699***************************************************************95543 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   4.8   9.6e-09   1.1e-05       1      45 [.       7      53 ..       7      67 .. 0.93
   2 ?   -1.7   0.0      0.97   1.2e+03     126     150 ..     107     132 ..      59     154 .. 0.68
   3 !   13.2   0.0   2.9e-05     0.035       2      30 ..     169     197 ..     168     205 .. 0.90
   4 ?    3.6   0.1     0.024        29     353     385 ..     293     326 ..     279     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 9.6e-09
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsig 45
                                  d+iViGgG AG+ A +aaa+ Ga+vlL+   +  +t+++ +C ps  
  gi|14601420|ref|NP_147957.1|  7 DIIVIGGGAAGFSAVVAAAEGGASVLLVseGPLGGTCVNFGCVPSKH 53
                                  79**************************888899**********975 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.97
                                   TEEEEEEETTS-EEEEC.EEEE--TT CS
                          GIDA 126 kkvkgvvtedgetikak.avviatGt 150
                                    k  g+v +dg++++ + a +ia G+
  gi|14601420|ref|NP_147957.1| 107 FKAPGIVEADGREVRYRkAAIIAVGA 132
                                   46678999999988766599999998 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 2.9e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                          GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                   v ViGg   G+eAA   ar+G+k++L++ 
  gi|14601420|ref|NP_147957.1| 169 VAVIGGRAQGVEAAQIFARSGLKTVLLQR 197
                                   89************************954 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.024
                                   SSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHH CS
                          GIDA 353 kkvkgLflAGqinGteGYeEaaa..qGllAGinaa 385
                                    + +g+++AG+  G   ++E +a   G +A++na 
  gi|14601420|ref|NP_147957.1| 293 MASPGVYAAGDCIGGI-QLEPVAarEGYVAALNAL 326
                                   5679*********998.677666689*******96 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 !    7.9   2.7    0.0014       1.6       1      38 [.       9      45 ..       9      50 .. 0.87
   2 !   19.8   0.0   3.3e-07   0.00039     161     305 .]     163     302 ..     115     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyr 38
                                  i+iG+G+aG +a +++ + g  ++l +  g +g +  +
  gi|14601420|ref|NP_147957.1|  9 IVIGGGAAGFSAVVAAAEGGA-SVLLVSEGPLGGTCVN 45
                                  89******************9.7899988888876665 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.3e-07
                   Pyr_redox_3 161 kyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikek 241
                                   +  ++ v+ViGg   +v+aA  ++r g +  ++ r+  +  ++ +p++    ++ +r+ e    + ++v + a+  +++  
  gi|14601420|ref|NP_147957.1| 163 PPDMESVAVIGGRAQGVEAAQIFARSGLKTVLLQRSGRLLPRD-EPEA---GVYMKRVLE---GDGVEVRTSARPLRVESV 236
                                   556899*****************************99888886.5554...334444444...344777777776666666 PP

                   Pyr_redox_3 242 eeeykvk..tedgkkvevkddvvla.tGykpdlsf..lkkslfeldedgrpvlteeteetnvpglflaG 305
                                      +++   t++g   +v+  ++++ tG kp l+   l++ ++  ++dg++v++e+ + +  pg++ aG
  gi|14601420|ref|NP_147957.1| 237 RGAVRIDyeTPQGPA-SVEASYIYLaTGRKPVLDGlgLENVGVRVSSDGFIVVNEKLMAS--PGVYAAG 302
                                   666655532778755.5566666555******99845677999***************99..****998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   1.6   2.8e-09   3.4e-06       1      36 [.       7      41 ..       7      85 .. 0.93
   2 ?   -1.0   0.6      0.61   7.3e+02       2      30 ..     169     197 ..     168     201 .. 0.90
   3 ?    1.1   0.2      0.14   1.6e+02     387     404 ..     290     307 ..     276     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.8e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  D+iViG+G+AG +A ++aae G++v++v+ ++  gg
  gi|14601420|ref|NP_147957.1|  7 DIIVIGGGAAGFSAVVAAAEGGASVLLVSEGPL-GG 41
                                  9****************************9986.44 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.61
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                 FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvek 30 
                                   v ViG+ + G  AA   a+ Glk++++  
  gi|14601420|ref|NP_147957.1| 169 VAVIGGRAQGVEAAQIFARSGLKTVLLQR 197
                                   89**********************99976 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                                   TEEESSBTEEE-STCEES CS
                 FAD_binding_2 387 adgqpipGLYAaGevaag 404
                                   ++  + pG YAaG +++g
  gi|14601420|ref|NP_147957.1| 290 EKLMASPGVYAAGDCIGG 307
                                   4445689********944 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.0   1.5e-06    0.0018       1      32 [.       6      37 ..       6      44 .. 0.91
   2 ?    3.8   0.2     0.016        19       2      34 ..     168     200 ..     167     204 .. 0.90
   3 ?   -0.9   0.0      0.43   5.1e+02      98     165 ..     198     265 ..     195     282 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                  +d+iviGgGaAG+ a ++aa+ g++Vll+ ++
  gi|14601420|ref|NP_147957.1|  6 YDIIVIGGGAAGFSAVVAAAEGGASVLLVSEG 37
                                  589*************************9776 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                   HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                   +v+viGg a G+ aA   a+ g +++ll +  +
  gi|14601420|ref|NP_147957.1| 168 SVAVIGGRAQGVEAAQIFARSGLKTVLLQRSGR 200
                                   699***********************9988755 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.43
                                   TTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE....TTEEEEESEEEE----S CS
                   HI0933_like  98 sgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvkt...kseeeleadklvlAtGGl 165
                                   sgrl p+++  + +   +++ l+  gv++r++ +  +ve+ ++  +r+++   ++  ++ea+++ lAtG +
  gi|14601420|ref|NP_147957.1| 198 SGRLLPRDEPEAGV--YMKRVLEGDGVEVRTSARPLRVESVRGA-VRIDYetpQGPASVEASYIYLATGRK 265
                                   56666666332222..4567788899*****9999999765544.676663255778999*******9966 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0015       1.7      17      47 ..       5      34 ..       3      64 .. 0.78
   2 ?    5.9   0.1    0.0054       6.4      19      50 ..     168     198 ..     165     201 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                                  EEEEEEE--SHHHHHHHHHHHHCTTS-EEEE CS
                          Thi4 17 esDvvivGaGssGLtaayylakkpdlkvail 47
                                  e D++++G+G++G +a    a+  +  v+++
  gi|14601420|ref|NP_147957.1|  5 EYDIIVIGGGAAGFSAVVAAAEG-GASVLLV 34
                                  78*************98777765.6555544 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0054
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                          Thi4  19 DvvivGaGssGLtaayylakkpdlkvailers 50 
                                    v+++G+ + G+ aa+++a++ +lk+++l rs
  gi|14601420|ref|NP_147957.1| 168 SVAVIGGRAQGVEAAQIFARS-GLKTVLLQRS 198
                                   5899*****************.******9886 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.8   0.00054      0.64      31      56 ..       8      33 ..       4      38 .. 0.90
   2 ?    0.3   0.0      0.29   3.5e+02      30      57 ..     168     195 ..     159     204 .. 0.85
   3 ?   -3.9   0.0       5.8     7e+03     132     156 ..     327     350 ..     322     354 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00054
                                  EEEESTSHHHHHHHHHHHHTT-EEEE CS
                   AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtv 56
                                  ++viGgG aG +A+ +a++ ga+V +
  gi|14601420|ref|NP_147957.1|  8 IIVIGGGAAGFSAVVAAAEGGASVLL 33
                                  89********************9965 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEE CS
                   AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvl 57 
                                    v viGg   G++A+++ ++ g k+++l
  gi|14601420|ref|NP_147957.1| 168 SVAVIGGRAQGVEAAQIFARSGLKTVLL 195
                                   699*************999988877665 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 5.8
                                   T-SBTT--TBBTTSEEEEETTEEEE CS
                   AlaDh_PNT_C 132 GGnvetsrltthgepvveekgvvhy 156
                                   GGnve + +t   + v+++ +   +
  gi|14601420|ref|NP_147957.1| 327 GGNVE-MDYTVIPRAVFTDPEFASV 350
                                   99999.8888888888776665555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.2     0.021        25       1      31 [.       5      35 ..       5      37 .. 0.91
   2 ?    7.7   0.1    0.0016       1.9       3      48 ..     168     215 ..     167     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.021
                                  EEEEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                 FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlve 31
                                  e+d++++G+G aG+++    +e G +v+lv 
  gi|14601420|ref|NP_147957.1|  5 EYDIIVIGGGAAGFSAVVAAAEGGASVLLVS 35
                                  5799*************99999999999985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC..SSS--EEEHH CS
                 FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvv..lpradglnqr 48 
                                   +V+++G+   G+ +a++ ++ G ++vl+ +  +  +  +p a++  +r
  gi|14601420|ref|NP_147957.1| 168 SVAVIGGRAQGVEAAQIFARSGLKTVLLQRSGRLLPrdEPEAGVYMKR 215
                                   599**************************9887654114466666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.2   0.00042       0.5       1      36 [.       7      42 ..       7      85 .. 0.84
   2 ?   -2.1   0.0       1.9   2.2e+03     157     166 ..      94     103 ..      47     143 .. 0.52
   3 ?    0.7   0.0      0.27   3.2e+02     188     270 ..     284     370 ..     210     419 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                  d+++iGGG +G s+  ++a+ g  V+l+  g  +g g+
  gi|14601420|ref|NP_147957.1|  7 DIIVIGGGAAGFSAVVAAAEGGasVLLVSEG-PLG-GT 42
                                  8*****************9988******999.666.44 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                   HHTT-EEEES CS
                           DAO 157 ealGveileg 166
                                    +lGv+ l+g
  gi|14601420|ref|NP_147957.1|  94 DSLGVDYLRG 103
                                   3344444444 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.27
                                   EEE.EEEEEEEE--GGGHH.HH.HTTCTTT.SEEEEEEEEEEEEEECCTHSTGSGCSEEEEE.EEETTTTEEEEEE....T CS
                           DAO 188 gen.daadavVnaaGawsd.ll.gllkeld.lpispvrgqvlvlkplseklvspaailpvpe.tdddgrgvyvtpr....k 259
                                   g + +  +++  + G+++     g    ++  p+ ++ g+v +l+ l  + ++ + + p  + td ++ +v +t r    k
  gi|14601420|ref|NP_147957.1| 284 GFIvVN-EKLMASPGVYAAgDCiG---GIQlEPVAAREGYVAALNALGGNVEMDYTVIPRAVfTDPEFASVGLTERelarK 360
                                   444223.44555556665332222...222246677777777777777777676655555555666666666666544422 PP

                                   TSEEEEEESSE CS
                           DAO 260 dgrvlvGgtad 270
                                    g v+++ t d
  gi|14601420|ref|NP_147957.1| 361 LG-VCACRTVD 370
                                   23.66666654 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 ?   -0.1   1.8      0.62   7.4e+02       2      29 ..       8      35 ..       7      39 .. 0.90
   2 ?    9.4   0.1   0.00077      0.92       2      43 ..     169     210 ..     168     240 .. 0.83
   3 ?   -2.9   0.0       4.5   5.3e+03     129     142 ..     395     408 ..     391     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.62
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE- CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvd 29
                                  + viG G  G +   ++a+ g +V lv 
  gi|14601420|ref|NP_147957.1|  8 IIVIGGGAAGFSAVVAAAEGGASVLLVS 35
                                  679***********999**9****9985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00077
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHH CS
                       3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekie 43 
                                   vaviG    G + a++fa++gl++vl+++s + l + + ++ 
  gi|14601420|ref|NP_147957.1| 169 VAVIGGRAQGVEAAQIFARSGLKTVLLQRSGRLLPRDEPEAG 210
                                   9**************************999887766665555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.5
                                   GGGEEEEEE-SSTT CS
                       3HCDH_N 129 perviglHFfnPpp 142
                                    ++v+g+H + P  
  gi|14601420|ref|NP_147957.1| 395 TKKVAGVHMMAPQA 408
                                   56788888888864 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.5    0.0024       2.9       1      34 [.       7      38 ..       7      45 .. 0.82
   2 ?   -1.4   0.1      0.77   9.2e+02       2      34 ..     169     199 ..     168     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0024
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                  D++viG+G+Ag s    +++a+ g +v+l+  +p
  gi|14601420|ref|NP_147957.1|  7 DIIVIGGGAAGFSAV--VAAAEGGASVLLVSEGP 38
                                  9**********9855..44599999999995554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.77
                 Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieasp 34 
                                   v+viG+ + g+  A+    a+ glk vl++ s 
  gi|14601420|ref|NP_147957.1| 169 VAVIGGRAQGVEAAQIF--ARSGLKTVLLQRSG 199
                                   89****999**999999..999***99997765 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 ?    7.8   2.4    0.0033         4       1      28 [.      10      37 ..      10      51 .. 0.87
   2 ?    0.4   0.2      0.64   7.6e+02       1      30 [.     171     200 ..     171     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0033
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                  ++G+G++G +a  ++a+ g++vll+  +
  gi|14601420|ref|NP_147957.1| 10 VIGGGAAGFSAVVAAAEGGASVLLVSEG 37
                                  8**********************99666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.64
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                 NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                   ++G+ + G  aA+  a+ g++ +ll+++ r
  gi|14601420|ref|NP_147957.1| 171 VIGGRAQGVEAAQIFARSGLKTVLLQRSGR 200
                                   799999999999999*****9999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 3465.58
//
Query:       gi|118431464|ref|YP_874895.1|  [L=141]
Description: HTH-type transcriptional regulator LysM [Aeropyrum pernix K1]
Scores for complete 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-15   57.1   0.3      2e-15   56.5   0.3    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.1e-14   53.9   1.1    2.2e-14   53.0   0.5    1.8  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    2.1e-14   52.8   1.2    3.4e-14   52.1   1.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    7.8e-07   28.9   0.2    2.5e-06   27.3   0.2    1.8  2  MarR_2          MarR family
    4.7e-06   26.4   2.9    6.9e-06   25.9   0.7    2.1  2  HTH_11          HTH domain
    8.6e-05   22.5   0.1    0.00016   21.6   0.1    1.5  1  HTH_20          Helix-turn-helix domain
    9.5e-05   22.3   0.2    0.00021   21.1   0.2    1.6  1  MarR            MarR family
    0.00011   22.0   0.1    0.00019   21.2   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00014   21.5   0.1    0.00026   20.7   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
    0.00026   20.8   0.2    0.00036   20.3   0.2    1.2  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00041   20.2   0.1    0.00079   19.3   0.1    1.5  1  HTH_36          Helix-turn-helix domain
    0.00066   19.7   0.7      0.001   19.1   0.7    1.2  1  NapD            NapD protein
    0.00081   19.0   1.4     0.0011   18.6   0.4    1.7  2  Sigma70_r4_2    Sigma-70, region 4
    0.00093   18.9   0.9     0.0021   17.8   0.5    1.8  2  HTH_23          Homeodomain-like domain
     0.0016   18.6   0.2     0.0036   17.4   0.2    1.6  1  HTH_28          Helix-turn-helix domain
     0.0018   18.2   0.1     0.0033   17.4   0.1    1.3  1  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0023   17.4   0.2     0.0044   16.5   0.2    1.4  1  Sigma70_r4      Sigma-70, region 4
     0.0086   15.8   0.0      0.018   14.8   0.0    1.5  1  DUF4423         Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.017   15.6   0.2      0.032   14.7   0.2    1.5  1  HTH_27          Winged helix DNA-binding domain
      0.018   14.9   0.0      0.033   14.1   0.0    1.4  1  RuvB_C          RuvB C-terminal winged helix domain
      0.023   15.0   0.2      0.076   13.4   0.1    1.9  2  Rrf2            Transcriptional regulator
      0.031   14.5   0.0      0.058   13.6   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
      0.032   14.0   0.1      0.053   13.3   0.1    1.4  1  LexA_DNA_bind   LexA DNA binding domain
      0.049   13.7   0.1       0.13   12.4   0.0    1.6  2  DUF2250         Uncharacterized protein conserved in archaea 
      0.059   13.4   0.0        0.1   12.7   0.0    1.3  1  FeoC            FeoC like transcriptional regulator
      0.061   13.3   0.0       0.11   12.4   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.062   13.1   0.3       0.21   11.4   0.2    2.0  1  HTH_8           Bacterial regulatory protein, Fis family
      0.064   13.3   0.1        1.2    9.2   0.1    2.8  3  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.065   13.4   0.1       0.14   12.3   0.1    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.085   12.6   0.2       0.28   11.0   0.1    1.8  2  HTH_39          Helix-turn-helix domain
       0.13   12.3   0.1       0.23   11.5   0.1    1.3  1  Replic_Relax    Replication-relaxation
       0.15   12.5   0.1       0.19   12.1   0.1    1.2  1  GcrA            GcrA cell cycle regulator


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 !   56.5   0.3   3.7e-18     2e-15       1      75 []      69     140 ..      69     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 3.7e-18
                                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                 AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                    +lv++++ +  ++ +++e++a++  V+ +  vtGdyd++++++++d+e+++r+++  ++ ++gv +t t+ivl++
  gi|118431464|ref|YP_874895.1|  69 ILVRTNNAK--PVPQVAERIAAYMHVEKVMEVTGDYDIIAIATAQDIEDINRLIDY-IRGIEGVHSTYTMIVLRE 140
                                    678888666..9*****************************************866.****************85 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 !   53.0   0.5     4e-17   2.2e-14       1      41 [.       6      46 ..       6      47 .. 0.99
   2 ?   -1.8   0.0       5.1   2.8e+03      32      39 ..      80      87 ..      78      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4e-17
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                   LDe D+k+L++L +++R+sy+ +A+++G++es+v++R++rL
  gi|118431464|ref|YP_874895.1|  6 LDEKDLKLLSILKRNSRASYSYIARELGITESAVRKRIKRL 46
                                   8***************************************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.1
                  HTH_AsnC-type 32 stvlrRvr 39
                                   ++v++R++
  gi|118431464|ref|YP_874895.1| 80 PQVAERIA 87
                                   67999986 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 !   52.1   1.2   6.1e-17   3.4e-14       1      48 []       6      53 ..       6      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.1e-17
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   lde+d+k+L++L++n+r s++ +A++lg++ s+v++r+krL++ G+++
  gi|118431464|ref|YP_874895.1|  6 LDEKDLKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVVR 53
                                   79********************************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.2   4.4e-09   2.5e-06       9      53 ..      12      54 ..       4      59 .. 0.87
   2 ?   -1.7   0.0         5   2.8e+03      24      35 ..      83      94 ..      70      94 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.4e-09
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                    +L  L r+ +   + + +ar+lg++ sav +++krLv+ G v+r
  gi|118431464|ref|YP_874895.1| 12 KLLSILKRNSR--ASYSYIARELGITESAVRKRIKRLVRLGVVRR 54
                                   57777888887..89****************************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 5
                                   HHHHHHHHTSSH CS
                         MarR_2 24 vgelarrlglsk 35
                                   +  +a++++++k
  gi|118431464|ref|YP_874895.1| 83 AERIAAYMHVEK 94
                                   557899999876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.7   1.2e-08   6.9e-06       3      44 ..      11      51 ..       9      61 .. 0.86
   2 ?   -0.1   0.1       1.6   9.2e+02      34      50 ..     111     127 ..     110     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.2e-08
                         HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   l++l +L + ++  s +++A+eL++++++vr++Ik+L  lgv
  gi|118431464|ref|YP_874895.1| 11 LKLLSIL-KRNSRASYSYIARELGITESAVRKRIKRLVRLGV 51
                                   6899999.555559***********************99883 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                         HTH_11  34 rdIkaLeelgvpIesep 50 
                                    +dI++++ l + I +  
  gi|118431464|ref|YP_874895.1| 111 QDIEDINRLIDYIRGIE 127
                                    69999999998887765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   2.9e-07   0.00016      13      56 ..      11      54 ..       6      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.9e-07
                                   HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   +++l+ L+r+  ++ s +a++l+++ + ++++++ L++ g v++
  gi|118431464|ref|YP_874895.1| 11 LKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVVRR 54
                                   6899************************************9985 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   3.8e-07   0.00021       5      50 ..      10      55 ..       6      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-07
                                   HHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           MarR  5 qfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                    +++L il+++  +s s +a+ lg++ s+v + ++rL++ G ++R 
  gi|118431464|ref|YP_874895.1| 10 DLKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVVRRF 55
                                   6899****************************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   3.5e-07   0.00019       5      56 ..       5      56 ..       1      68 [. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.5e-07
                                   HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   GL e + k    L ++ +a+ + ia+elg+ +s v + +++L++ G+V+r  
  gi|118431464|ref|YP_874895.1|  5 GLDEKDLKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVVRRFT 56
                                   99**********************************************9965 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 !   20.7   0.1   4.7e-07   0.00026       6      50 ..      11      54 ..       8      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.7e-07
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   l +L +l +  ++ + s +Ar++g++ S+v+  ++ Lv+lG v++
  gi|118431464|ref|YP_874895.1| 11 LKLLSILKRNSRA-SYSYIARELGITESAVRKRIKRLVRLGVVRR 54
                                   7899999999998.9****************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   6.4e-07   0.00036       1      46 [.       7      53 ..       7      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.4e-07
                                   SHHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   d++ lk+L++L +++ ++ + +a+elg+++s+v+   k+L  +G+V+
  gi|118431464|ref|YP_874895.1|  7 DEKDLKLLSILKRNSrASYSYIARELGITESAVRKRIKRLVRLGVVR 53
                                   56679********665999**************************96 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.4e-06   0.00079      26      53 ..      23      50 ..      12      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                         HTH_36 26 psqetlakrlglsknTvsraikeLeqlG 53
                                   +s++++a+ lg+ ++ v++ ik L++lG
  gi|118431464|ref|YP_874895.1| 23 ASYSYIARELGITESAVRKRIKRLVRLG 50
                                   79*************************9 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   1.8e-06     0.001       7      68 ..      70     133 ..      67     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                           NapD   7 vVqa.rperlaavkaalaalpgvE.vhasdeegklVvviEaesedeladtieaiealpgVlsas 68 
                                    +V++ + + +++v++++aa  +vE v  ++++  ++ +  a++ +++ + i+ i+ ++gV+s+ 
  gi|118431464|ref|YP_874895.1|  70 LVRTnNAKPVPQVAERIAAYMHVEkVMEVTGDYDIIAIATAQDIEDINRLIDYIRGIEGVHSTY 133
                                    67773445599*************67778888*****************************985 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 !   18.6   0.4     2e-06    0.0011      28      49 ..      24      45 ..      16      48 .. 0.89
   2 ?   -2.6   0.0       7.9   4.4e+03      31      38 ..      85      92 ..      82      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                                   -HHHHHHHHT--HHHHHHHHHH CS
                   Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                   sy  IA++lgi+e++V++r++R
  gi|118431464|ref|YP_874895.1| 24 SYSYIARELGITESAVRKRIKR 45
                                   8999****************99 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.9
                                   HHHHHHT- CS
                   Sigma70_r4_2 31 EIAellgi 38
                                    IA+++++
  gi|118431464|ref|YP_874895.1| 85 RIAAYMHV 92
                                   69999987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5   3.7e-06    0.0021       6      43 ..      11      48 ..       7      55 .. 0.78
   2 ?   -2.3   0.0       7.6   4.3e+03      20      26 ..      79      85 ..      68      92 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-06
                         HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkryre 43
                                    +l+ +l    ++s++ IAreLg++++ v++ +kr ++
  gi|118431464|ref|YP_874895.1| 11 LKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVR 48
                                   455555555559******************99999765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.6
                         HTH_23 20 vreIAre 26
                                   v+++A++
  gi|118431464|ref|YP_874895.1| 79 VPQVAER 85
                                   5555554 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   6.4e-06    0.0036      13      40 ..      22      50 ..      13      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.4e-06
                         HTH_28 13 h.svreaArelgisrrtvyrWikryeegG 40
                                   + s++ +Arelgi+++ v++ ikr+   G
  gi|118431464|ref|YP_874895.1| 22 RaSYSYIARELGITESAVRKRIKRLVRLG 50
                                   458999******************86655 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 !   17.4   0.1   5.9e-06    0.0033       6      45 ..       9      47 ..       7      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-06
                        HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                    +lkLl++L   +++ +++ +a eLg++e++++++i  L 
  gi|118431464|ref|YP_874895.1|  9 KDLKLLSILKR-NSRASYSYIARELGITESAVRKRIKRLV 47
                                   689******99.************************9885 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   7.8e-06    0.0044      21      44 ..      23      46 ..       5      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.8e-06
                                   --HHHHHHHHTS-HHHHHHHHHHH CS
                     Sigma70_r4 21 lTleEIgerlgiSrerVrqiekrA 44
                                    +++ I+++lgi++++Vr ++kr 
  gi|118431464|ref|YP_874895.1| 23 ASYSYIARELGITESAVRKRIKRL 46
                                   68999*****************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 !   14.8   0.0   3.2e-05     0.018      36      70 ..      22      54 ..      11      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                        DUF4423 36 kadpeelakrlrpkisaeevekalefLlklgllkk 70
                                   +a+++ +a+ l+  i+++ v+k +++L++lg++++
  gi|118431464|ref|YP_874895.1| 22 RASYSYIARELG--ITESAVRKRIKRLVRLGVVRR 54
                                   589999******..******************987 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 ?   14.7   0.2   5.8e-05     0.032      11      51 ..      16      55 ..       7      61 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.8e-05
                         HTH_27 11 lirhrrrrkkladlcgrlnvedshisyslkkLtekGLvert 51
                                    +  r+ r++ + +++ l ++ s++ + +k+L++ G+v r 
  gi|118431464|ref|YP_874895.1| 16 IL-KRNSRASYSYIARELGITESAVRKRIKRLVRLGVVRRF 55
                                   34.4888999999*************************776 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 ?   14.1   0.0   5.8e-05     0.033       2      54 ..       4      52 ..       3      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-05
                                   T---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSE CS
                         RuvB_C  2 lGLdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglI 54
                                    GLde+d k+L++lk   +++ ++ + +a  lg++++ + + i   L++ g +
  gi|118431464|ref|YP_874895.1|  4 RGLDEKDLKLLSILK---RNSRASYSYIARELGITESAVRKRIKR-LVRLGVV 52
                                   5*************9...789****************99998854.5666655 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00014     0.076      15      56 ..      15      53 ..      10      56 .. 0.82
   2 ?   -1.4   0.0       5.7   3.2e+03      44      44 ..      94      94 ..      66     115 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                                   HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                    +L++   ++ +s + ia++ +i +s ++k +++L + g+v+
  gi|118431464|ref|YP_874895.1| 15 SILKR---NSRASYSYIARELGITESAVRKRIKRLVRLGVVR 53
                                   34444...44489***************************97 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.7
                                   H CS
                           Rrf2 44 k 44
                                   k
  gi|118431464|ref|YP_874895.1| 94 K 94
                                   2 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0    0.0001     0.058       3      44 ..      11      52 ..      10      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                         HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYi 44
                                   l++ls+L  +++a+++++  +l++t+++  + +k L   g +
  gi|118431464|ref|YP_874895.1| 11 LKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVV 52
                                   899*******************************99888755 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.4e-05     0.053      27      58 ..      24      54 ..       5      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.4e-05
                                   -HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                  LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyier 58
                                   s   iar+lg++  sav ++ k+L r G+++r
  gi|118431464|ref|YP_874895.1| 24 SYSYIARELGIT-ESAVRKRIKRLVRLGVVRR 54
                                   55679*******.9****************98 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00024      0.13       7      56 ..       7      56 ..       2      59 .. 0.81
   2 ?   -1.8   0.0       6.3   3.5e+03      15      43 ..      93     120 ..      81     126 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                        DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                   de++lk+l +lk+        ia+el i  + vr+ +k+L +lG + r +
  gi|118431464|ref|YP_874895.1|  7 DEKDLKLLSILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVVRRFT 56
                                   5667777777777655444579***********************99865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.3
                        DUF2250  15 khlkkanvdYaksiakeleipleevrell 43 
                                    + + ++  dY   ia  +  ++e +++l+
  gi|118431464|ref|YP_874895.1|  93 EKVMEVTGDYD-IIAIATAQDIEDINRLI 120
                                    44555666664.45566666666666555 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00018       0.1       7      46 ..      15      54 ..      11      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                           FeoC  7 eyleergrvslkeLsrhfkaspealeamLeqwvrkGrvek 46
                                   + l+++ r+s + ++r++ ++++a+++ +  +vr G v++
  gi|118431464|ref|YP_874895.1| 15 SILKRNSRASYSYIARELGITESAVRKRIKRLVRLGVVRR 54
                                   57899*******************************9987 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0002      0.11      20      37 ..      29      46 ..      10      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                                   HHHHTS-HHHHHHHHHHH CS
                          HTH_1 20 AeeLglsqpavsrqikrL 37
                                   A+eLg++ +av ++ikrL
  gi|118431464|ref|YP_874895.1| 29 ARELGITESAVRKRIKRL 46
                                   9****************9 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 ?   11.4   0.2   0.00037      0.21      25      42 .]      29      46 ..      26      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                                   HHHHTS-HHHHHHHHHHT CS
                          HTH_8 25 ArlLGisRrtLyrKLkkY 42
                                   Ar+LGi+ + +++++k++
  gi|118431464|ref|YP_874895.1| 29 ARELGITESAVRKRIKRL 46
                                   9***************96 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0022       1.2      26      46 ..      21      41 ..      11      41 .. 0.78
   2 ?   -0.4   0.0       2.1   1.2e+03       6      18 ..      82      94 ..      80     111 .. 0.74
   3 ?   -0.8   0.0       2.8   1.6e+03       7      20 ..     116     129 ..     115     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0022
                                   -EE-HHHHHHHCTS-HHHHHH CS
                 Put_DNA-bind_N 26 eriSSteLaealgvtaaqvRK 46
                                   +r S + +a++lg+t++ vRK
  gi|118431464|ref|YP_874895.1| 21 SRASYSYIARELGITESAVRK 41
                                   5677778*************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHH CS
                 Put_DNA-bind_N  6 tikRLplYlryLe 18
                                   + +R + Y+++ +
  gi|118431464|ref|YP_874895.1| 82 VAERIAAYMHVEK 94
                                   6788888887644 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 2.8
                                    HHHHHHHHHHHHHH CS
                 Put_DNA-bind_N   7 ikRLplYlryLeel 20 
                                    i+RL  Y r +e +
  gi|118431464|ref|YP_874895.1| 116 INRLIDYIRGIEGV 129
                                    78999999977755 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 ?   12.3   0.1   0.00026      0.14      20      52 ..      20      52 ..      12      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00026
                                   HSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                 Fe_dep_repress 20 kkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                   ++ ++ + +a++L++  s V + +k+L + G v
  gi|118431464|ref|YP_874895.1| 20 NSRASYSYIARELGITESAVRKRIKRLVRLGVV 52
                                   56688899*******************998876 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0005      0.28       5      42 ..      12      51 ..       9      64 .. 0.89
   2 ?   -1.3   0.0       3.5   1.9e+03       5      10 ..      85      90 ..      72     113 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0005
                         HTH_39  5 rilaaLrqhgsittleamrelditr..laaRIkeLrekGy 42
                                   ++l++L++ ++ +  +  rel+it+   ++RIk+L + G 
  gi|118431464|ref|YP_874895.1| 12 KLLSILKRNSRASYSYIARELGITEsaVRKRIKRLVRLGV 51
                                   78999*99999999999********767799*****9996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.5
                         HTH_39  5 rilaaL 10
                                   ri a++
  gi|118431464|ref|YP_874895.1| 85 RIAAYM 90
                                   555555 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0004      0.23       4      46 ..      17      58 ..      14      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                   Replic_Relax  4 LaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkr 46
                                   L++   ++ ++iar l  +++a +r+r++rL +lg+++r++ +
  gi|118431464|ref|YP_874895.1| 17 LKRNSRASYSYIARELGITESA-VRKRIKRLVRLGVVRRFTLE 58
                                   5556667889************.****************9876 PP

>> GcrA  GcrA cell cycle regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00034      0.19      20      55 ..      24      60 ..      15     124 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00034
                           GcrA 20 SasqiaaqlggvsRnAViGkvhRL...glsgrakalept 55
                                   S+s ia++lg ++ +AV  +++RL   g+++r +  e +
  gi|118431464|ref|YP_874895.1| 24 SYSYIARELG-ITESAVRKRIKRLvrlGVVRRFTL-EYR 60
                                   99*******9.******887776521155554332.322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1099.47
//
Query:       gi|118431465|ref|NP_147959.2|  [L=270]
Description: acetylglutamate kinase [Aeropyrum pernix K1]
Scores for complete 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-35  122.9   1.9    1.7e-35  122.8   1.9    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 !  122.8   1.9   9.5e-40   1.7e-35       3     235 ..       7     246 ..       5     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 9.5e-40
                                    EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHHHHHH CS
                      AA_kinase   3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeagevat 78 
                                     VvK+GGs+ +   +  l+r+a++ia l+++g +lvvVhGgg+++d+++++ +g+++++       + r+t+ e++ev  
  gi|118431465|ref|NP_147959.2|   7 AVVKIGGSIAS---R--LERVADEIAVLAREGLRLVVVHGGGKVVDEYSRR-MGVEPRYVLHpsgvRSRYTSWEELEVYV 80 
                                    7*******999...6..999*******************************.*******9999***************** PP

                                    HHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..................HHHTTTCEEECCHHHHHHHTT-EEE CS
                      AA_kinase  79 rdalaslgerlvaallaaglpavglsaaaldateagr................degsdgnvesvdaeaieelleagvvpv 142
                                    +++++ l+++++++l++ gl+  +l++ + +++ea+r                  g++g++e+vd+  +  +l++ v ++
  gi|118431465|ref|NP_147959.2|  81 MVMAGLLATSISSELASRGLKVLSLTGLDGLSVEARRrerivivnergrpqaiPGGYTGKIERVDSMFVGSMLQQ-VDVI 159
                                    *************************************************************************99.5666 PP

                                    EESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHH CS
                      AA_kinase 143 ltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGm 219
                                    l   +++ +eg+    +++++D++aa l +al+A  l ++tdV+GV  +       +r++++i+v+ea+e  +  a  Gm
  gi|118431465|ref|NP_147959.2| 160 LYSPVAYGREGDrvvALNVDGDQMAASLSAALKA-PLALVTDVPGVILD-------GRVVDRIRVSEARE-IAAKAGVGM 230
                                    66667799999999*88*****************.99999******633.......39999999999999.7778999** PP

                                    HHCHHHHHHHHHCTT- CS
                      AA_kinase 220 kvkhpaalaaarrggi 235
                                    + k++ a++a+ +g  
  gi|118431465|ref|NP_147959.2| 231 NRKILMAAKAVSEGSP 246
                                    ***********99955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2082.33
//
Query:       gi|14601422|ref|NP_147960.1|  [L=355]
Description: N-acetyl-gamma-aminoadipyl-phosphate reductase/N-acetyl-gamma-glutamyl-phosphate reductase [Aeropyrum pernix K1]
Scores for complete 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-31  107.9   0.0    6.9e-31  107.2   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00044   20.5   0.1     0.0028   17.9   0.1    2.1  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
        0.1   13.1   0.0       0.28   11.7   0.0    1.7  2  CoA_binding_2    CoA binding domain


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 !  107.2   0.0   1.1e-34   6.9e-31       1     120 [.       6     144 ..       6     145 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 1.1e-34
                                   EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTT.TECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkalee.gkdlkvedvdeeelkevdivflalpagvsk 80 
                                   +++i+Ga+G++G ellr+L++hp ve+ +++s++  aGk+++ a+++l++ ++ lk++++d+ ++ evd+vf alp+gv +
  gi|14601422|ref|NP_147960.1|   6 RAGILGASGMTGGELLRILASHPGVEVEWATSREY-AGKPVHTAHPHLRGfYTGLKYTSIDKIDIGEVDVVFNALPHGVGA 85 
                                   579********************************.**********8776367899999********************** PP

                                   HHHHHHHHTTSEEEESSSTTTTST...................TSEBE-HHHHGGGGGG CS
                Semialdhyde_dh  81 elapklaeagvkviDlssdfRlkd...................davyvlpevnreaikk 120
                                   +++++++e+gv+v+Dls+d+Rl+d                   +a+y lpe++ e+++ 
  gi|14601422|ref|NP_147960.1|  86 SIVAEAYENGVRVVDLSADYRLRDqslypklygfkhprpdlleEAIYALPEIYGEKLRG 144
                                   *****************************************************999875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   4.7e-07    0.0028       3     114 ..       9     110 ..       7     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.7e-07
                                   EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE-SSGGG CS
               Sacchrp_dh_NADP   3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnlsppis 81 
                                   i+Ga G++G  +++ la h  v  e+  a+  +   + +  +     +     +  +y++ ++++ + e d+v n++p   
  gi|14601422|ref|NP_147960.1|   9 ILGAsGMTGGELLRILASHPGV--EVEWATSREYAGKPVH-T--AHPHLRGFYTGLKYTS-IDKIdIGEVDVVFNALPHGV 83 
                                   89******************99..4544444443333333.2..2334444567777888.7777799************* PP

                                   HHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHH CS
               Sacchrp_dh_NADP  82 sldvlkaCietgvhyvdtsiskeertnyalrea 114
                                   ++++++ ++e+gv++vd s        y+lr++
  gi|14601422|ref|NP_147960.1|  84 GASIVAEAYENGVRVVDLSA------DYRLRDQ 110
                                   *****************998......6666665 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.7e-05      0.28      21      83 ..      33      99 ..      29     114 .. 0.86
   2 ?   -3.6   0.0       2.5   1.5e+04      66      81 ..     217     232 ..     214     250 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                                  HHHHHHT--EEEESSS-SEETTEE...S----T.....T--EEEE-S-HHHHGGGHHHHHHH--SEE CS
                 CoA_binding_2 21 ryllehglpvvpVnpkeeeilgek...vyaslae.dpepvdlvdvftppeatpeivkealalgakav 83
                                  ++  ++++   pV+  ++ + g     +y s+++ d ++vd+v+ ++p  + ++iv ea + g+++v
  gi|14601422|ref|NP_147960.1| 33 EWATSREYAGKPVHTAHPHLRGFYtglKYTSIDKiDIGEVDVVFNALPHGVGASIVAEAYENGVRVV 99
                                  6777777777888888888888555679*****988****************************998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.5
                                   HHHGGGHHHHHHH--S CS
                 CoA_binding_2  66 eatpeivkealalgak 81 
                                   +++++++++++ +g++
  gi|14601422|ref|NP_147960.1| 217 AEAVQVLRDLVGRGIR 232
                                   4455555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2855.86
//
Query:       gi|118431466|ref|YP_874896.1|  [L=56]
Description: lysine biosynthesis protein LysW [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.039   13.6   4.0       0.65    9.7   0.3    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.045   13.3   3.7      0.077   12.5   3.7    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.64   10.1   4.2       0.89    9.6   4.2    1.5  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma


Domain annotation for each model (and alignments):
>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3   0.00011      0.65       8      20 ..       5      17 ..       1      25 [. 0.77
   2 ?    5.4   0.3    0.0024        14      12      23 ..      29      40 ..      27      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                                   E-TTT--EEEECC CS
                Desulfoferrod_N  8 kCevCGniVeVle 20
                                   kC vCG  VeV e
  gi|118431466|ref|YP_874896.1|  5 KCPVCGLDVEVPE 17
                                   9*********976 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0024
                                   T--EEEECC--S CS
                Desulfoferrod_N 12 CGniVeVleaGg 23
                                   CG + e++e Gg
  gi|118431466|ref|YP_874896.1| 29 CGVVLEIVESGG 40
                                   **********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 ?   12.5   3.7   1.3e-05     0.077       2      31 ..       5      35 ..       4      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                                   EETTTTCEE.CHEETSTTCEEESSSSBEEEE CS
                   TF_Zn_Ribbon  2 kCPnCgstn.lveDpergelvCtdCGlVled 31
                                   kCP+Cg +  + eD  +gelv  dCG+Vle 
  gi|118431466|ref|YP_874896.1|  5 KCPVCGLDVeVPEDVVSGELVEHDCGVVLEI 35
                                   9*****9555999999*************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 ?    9.6   4.2   0.00015      0.89       1      14 [.       5      18 ..       5      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                 DNA_ligase_ZBD  1 hCPvCGsavvReeg 14
                                   +CPvCG  v+ +e+
  gi|118431466|ref|YP_874896.1|  5 KCPVCGLDVEVPED 18
                                   6******9998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 474.09
//
Query:       gi|14601423|ref|NP_147961.1|  [L=286]
Description: ribosomal protein S6 modification protein RimK [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-27   94.7   0.0    6.5e-27   94.4   0.0    1.1  1  RimK         RimK-like ATP-grasp domain
    1.5e-06   28.4   0.0    2.9e-06   27.4   0.0    1.4  1  ATP-grasp_3  ATP-grasp domain
     0.0006   19.1   0.0      0.035   13.3   0.0    2.1  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
     0.0033   17.0   0.0      0.023   14.2   0.0    2.0  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
     0.0033   17.0   0.0     0.0074   15.9   0.0    1.6  2  ATP-grasp    ATP-grasp domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.015   15.1   0.0    1.2  1  GARS_A       Phosphoribosylglycinamide synthetase, 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 !   94.4   0.0   2.2e-30   6.5e-27       2     187 ..      91     279 ..      90     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.2e-30
                                   H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...GGG--... CS
                          RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...lkeai... 76 
                                   +dK+ s+ lL ++++++p++  + d++ +    e i  +fP v K   gs G  v l +++ ++  + ea   ++  +   
  gi|14601423|ref|NP_147961.1|  91 QDKVWSHMLLSRRGVPTPRSYTILDPQAVPYAAEAI--GFPAVFKPARGSWGKLVSLLRDKSEASLLSEAleyVQGDLklg 169
                                   79*********************************9..6************************998888844434444889 PP

                                   EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEEEEETT. CS
                          RimK  77 lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDllrakr. 156
                                   lvqey+++  ++diR + ++d v aa+ r +    F +nl  Gg a ++ ++ + ++l ++a +a+++ v GvD++++ r 
  gi|14601423|ref|NP_147961.1| 170 LVQEYVDK-PGRDIRSFCIGDTVPAAIYRYGSG--FATNLAAGGRAAPAPVTGDVEDLTLRACEALGVEVGGVDIVESTRd 247
                                   ******95.689******************877..*****************************************98654 PP

                                   .EEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                          RimK 157 .gllvlEvnsspglekiektlgidiakkliea 187
                                    gllvlEvn s + ++  + +g+++a+ ++++
  gi|14601423|ref|NP_147961.1| 248 gGLLVLEVNPSTEFKNTVRVTGVNVAALIADY 279
                                   48*************************99987 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   9.8e-10   2.9e-06       2     156 ..      91     257 ..      90     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.8e-10
                                   TSHHHHHHHHTTT.S---....-EESS--.......SSSEEEEESS-------B--SS--TTE................EE CS
                   ATP-grasp_3   2 sdKlktykkLkeagvkvPtkleaeeleee.......ekklvvKprdGaggesvrvveekeeaeaaieeve.........lv 66 
                                   +dK+ +   L+++gv++P  ++   ++ +         + v Kp++G+ g+ v++ ++k ea    e +e         lv
  gi|14601423|ref|NP_147961.1|  91 QDKVWSHMLLSRRGVPTPRSYTILDPQAVpyaaeaiGFPAVFKPARGSWGKLVSLLRDKSEASLLSEALEyvqgdlklgLV 171
                                   699999999*********555555555555555555899********************99988777777888******** PP

                                   EE---..SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEE.. CS
                   ATP-grasp_3  67 qefie..GkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlv.. 143
                                   qe+++  G+++   +++d+   ++ a+ r   ++a+ +++  G  +p++   + +v++l  +++e+l g + + GvD+v  
  gi|14601423|ref|NP_147961.1| 172 QEYVDkpGRDIRSFCIGDT---VPAAIYRYGSGFAT-NLAAGGRAAPAP--VTGDVEDLTLRACEAL-G-VEVGGVDIVes 244
                                   ****744777777777766...56666665555533.388899999999..7899************.5.5578*****87 PP

                                   ESS.SEEEEEEES CS
                   ATP-grasp_3 144 lkdeepyviEvNP 156
                                    +d+++ v+EvNP
  gi|14601423|ref|NP_147961.1| 245 TRDGGLLVLEVNP 257
                                   788*********9 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 !   13.3   0.0   1.2e-05     0.035       9      85 ..      80     152 ..      78     169 .. 0.82
   2 ?    3.6   0.0     0.011        33     230     265 ..     223     258 ..     215     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                   ATPgrasp_ST   9 kyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredq 85 
                                    +N+ +++   +dK+    l++r+g+++p+ + +++ qa   ++ea  +++ +  v Kpa+gs+Gk ++ + +++++
  gi|14601423|ref|NP_147961.1|  80 TVNSSHAIMASQDKVWSHMLLSRRGVPTPRSYTILDPQAVPYAAEA--IGF-P-AVFKPARGSWGKLVSLLRDKSEA 152
                                   58999999999*************************9977665555..466.3.49**********99998665544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.011
                   ATPgrasp_ST 230 elaakaaeklpglgylGwDiv.ldeekgplllElNar 265
                                   +l+ +a e  +g+ + G+Div  ++++g+l+lE+N  
  gi|14601423|ref|NP_147961.1| 223 DLTLRACE-ALGVEVGGVDIVeSTRDGGLLVLEVNPS 258
                                   67777888.89999******94578999*******65 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 !   14.2   0.0   7.7e-06     0.023       1     178 [.      92     257 ..      92     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                                   SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS CS
                   CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnk 81 
                                   Dk+ ++ +l++ +vp+ +s +    + + +  +a+ ig+P + k+a g  Gk   + r+++e + l+++al+  +   g+ 
  gi|14601423|ref|NP_147961.1|  92 DKVWSHMLLSRRGVPTPRSYTI--LDPQAVPYAAEAIGFPAVFKPARGSWGKLVSLLRDKSEAS-LLSEALEYVQ---GDL 166
                                   7888888999999*****9999..89999999****************************9965.6667777664...443 PP

                                   -E.EEEE--SSS.EEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                   CPSase_L_D2  82 qv.lvekslkgp.keiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                   ++ lv++++++p ++i    + D+   +i+        +l  +     AP+++  d e       ++++++++gv+ +  v
  gi|14601423|ref|NP_147961.1| 167 KLgLVQEYVDKPgRDIRSFCIGDTVPAAIYRYGSGFATNLAAGG--RAAPAPVTGDVE-----DLTLRACEALGVEVG-GV 239
                                   33377777777656677777777666666666555555555544..345555444332.....233344555555443.35 PP

                                   EEEEETTTTEEEEEEEES CS
                   CPSase_L_D2 161 eflldpkskeyyviEvNt 178
                                   + + + +++   v+EvN+
  gi|14601423|ref|NP_147961.1| 240 DIVESTRDGGLLVLEVNP 257
                                   555555556666666666 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-06    0.0074       3      61 ..     102     159 ..     100     176 .. 0.87
   2 ?   -3.0   0.0       1.6   4.8e+03     125     158 ..     224     257 ..     213     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-06
                                   TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC CS
                     ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal 61 
                                   + g+p+pr +++ + +++  aae++g+p+v K +  g+ Gk  s++r++++++ + eal
  gi|14601423|ref|NP_147961.1| 102 RRGVPTPRSYTILDPQAVPYAAEAIGFPAVFK-PARGSWGKLVSLLRDKSEASLLSEAL 159
                                   679*****************************.999999**********9998887776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.6
                                   HHHHHHHHHTSSEEEEEEEEEE.TTCTEEEEEEES CS
                     ATP-grasp 125 iakkiveeLggvGvfavElFvl.edgellvnElap 158
                                   ++ +++e+Lg+  v +v + +  +dg llv E+ p
  gi|14601423|ref|NP_147961.1| 224 LTLRACEALGV-EVGGVDIVEStRDGGLLVLEVNP 257
                                   55555555543.34455554432566688888776 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 ?   15.1   0.0     5e-06     0.015       2      64 ..      92     153 ..      91     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                                   BHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHH CS
                        GARS_A   2 sKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeeal 64 
                                   +K +++ ll++ g+pt++  ++ dp+++    e+ +++a V K+++ + gK v++ ++++ea 
  gi|14601423|ref|NP_147961.1|  92 DKVWSHMLLSRRGVPTPRSYTILDPQAVPYAAEAIGFPA-VFKPARGSWGKLVSLLRDKSEAS 153
                                   79*************************************.*******************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2237.66
//
Query:       gi|14601424|ref|NP_147962.1|  [L=388]
Description: acetyl-lysine aminotransferase/acetylornithine aminotransferase [Aeropyrum pernix K1]
Scores for 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-87  291.5   0.0    3.1e-86  289.6   0.0    1.7  1  Aminotran_3  Aminotransferase class-III
     0.0059   15.9   0.0     0.0099   15.2   0.0    1.3  1  CCB2_CCB4    Cofactor assembly of complex C subunit B, CCB2/C
  ------ inclusion threshold ------
      0.015   14.2   0.0      0.025   13.6   0.0    1.3  1  Aminotran_5  Aminotransferase class-V


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 !  289.6   0.0   5.1e-90   3.1e-86      12     406 .]      17     382 ..      11     382 .. 0.94

  Alignments for each domain:
  == domain 1  score: 289.6 bits;  conditional E-value: 5.1e-90
                                   EEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEE CS
                   Aminotran_3  12 vitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvfl 92 
                                    i k+   y++d  g++ylD  ++  ++ lGh++P++v+av  qa +l+  s   +++ +++++  +  ++ap   +++++
  gi|14601424|ref|NP_147962.1|  17 RIVKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAAS-SSFSTPSLEEALTEFSRIAPPWAEEIVF 96 
                                   57889999****************************************9999.9999999********************* PP

                                   ESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHH CS
                   Aminotran_3  93 ansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkenee 173
                                    n+G+eAve+AlK+a        at k  i+a+k++fHGrtl++lsvt++ + y+++++ +   + +   +          
  gi|14601424|ref|NP_147962.1|  97 LNTGTEAVEAALKAAWL------ATGKRGIVALKNSFHGRTLASLSVTWN-PRYRRGVPVLDTRFLSPSTD---------- 160
                                   *****************......***************************.******99887776654444.......... PP

                                   HHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS-- CS
                   Aminotran_3 174 eeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvsp 254
                                             ++ek   +++aA+ivEpiqgegG +   +e  ++lre +++ ++lli+DE+qtGfGrTG ++A+e++gv+p
  gi|14601424|ref|NP_147962.1| 161 --------PGEVEKLVPEDTAAIIVEPIQGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHESLGVEP 233
                                   ........24566777***************************************************************** PP

                                   SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT- CS
                   Aminotran_3 255 DlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelgaalkegLeelqkky 335
                                   D+mt +K+++gGlp+savl ++ v  +la+g hgsT ++npl +a+++a+ + + ee + ++a+++ga l+  L++  +  
  gi|14601424|ref|NP_147962.1| 234 DIMTAGKSIAGGLPASAVLSREGVLATLASGRHGSTHAANPLSMAAVAAASRFLREEGVPDKARAAGALLEGLLRDRIEGL 314
                                   ***************************************************************************999999 PP

                                   TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHH.CTEE-EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
                   Aminotran_3 336 evikevRgkGlmiaielkeeaevkekeilkkake.kGvlilsaGdnvirllppliitdeeidelleilkkal 406
                                     ++ vRg Glm+++el  +       +l  ++e + vl l +G +v+rllpp+ i+ e+++ ++  l++++
  gi|14601424|ref|NP_147962.1| 315 RLVRGVRGEGLMLGVELRLDPG----PVLRCLQEsERVLALRSGATVVRLLPPYSISREDAEMVVYGLERCI 382
                                   9****************99988....45554444267999**********************9998888875 PP

>> CCB2_CCB4  Cofactor assembly of complex C subunit B, CCB2/CCB4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.7e-06    0.0099      66     189 ..      72     225 ..      43     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                     CCB2_CCB4  66 evfelaedlsdalkeeLaWaseaLltnTnarsvvvlydgevll..rrGilaekkekvkpgailkrvlkkq.....keiyLv 139
                                   ++  l+e l++  +    Wa e+++ nT +++v  + +   l   +rGi+a k++    g  l+++  +      + +   
  gi|14601424|ref|NP_147962.1|  72 STPSLEEALTEFSRIAPPWAEEIVFLNTGTEAVEAALKAAWLAtgKRGIVALKNS--FHGRTLASLSVTWnpryrRGVPVL 150
                                   455666777777777778***************99998877754479*****955..444444444333334444778888 PP

                     CCB2_CCB4 140 dlklypGrvef....dylpentqsvlvqpl.....................gdegvlilgsntpraftkkdeaWi 189
                                   d++++ + +      +++pe+t +++v+p+                     ++ g+l+++ + + +f +  + W 
  gi|14601424|ref|NP_147962.1| 151 DTRFLSPSTDPgeveKLVPEDTAAIIVEPIqgeggltkiyaelakalreaaDRVGALLIFDEIQTGFGRTGRVWA 225
                                   8885555554446679**************988888888888888888888888888888888888888888886 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.1e-06     0.025      57     179 ..      87     215 ..      58     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-06
                                   T-STGGGEEEESSHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEE....EEEEEBETTSCBEGGGH CS
                   Aminotran_5  57 naeseeeiiftsGtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgak....vkvipldeegeldldel 132
                                     +++eei+f+  +tea++++++++  +    ++ iv  ++  h+ +++   +     ++    v   ++    + d+ e+
  gi|14601424|ref|NP_147962.1|  87 APPWAEEIVFLNTGTEAVEAALKAA--WlATGKRGIVALKNSFHGRTLASLSVTWNPRYRrgvpVLDTRF-LSPSTDPGEV 164
                                   45788*****************999..5367778899999999999988777765444440000433333.234567999* PP

                                   HHH--TTEEEEEEESBETTTTEB--HHHHHHHHHH.T...T-EEEEE-TTT CS
                   Aminotran_5 133 ekllnektklvaithvsnvtGtiqpveeigklakk.k...galvlvDaaqa 179
                                   ekl+ e+t+++++  ++ + G  +  +e++k++++ +   gal++ D  q+
  gi|14601424|ref|NP_147962.1| 165 EKLVPEDTAAIIVEPIQGEGGLTKIYAELAKALREaAdrvGALLIFDEIQT 215
                                   *********************999988888887764133589999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3148.72
//
Query:       gi|77640972|ref|NP_147963.2|  [L=350]
Description: acetyl-lysine deacetylase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-21   76.6   0.1    1.1e-20   74.2   0.1    1.8  1  Peptidase_M20  Peptidase family M20/M25/M40
      3e-12   46.4   0.1    6.3e-12   45.4   0.2    1.6  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 !   74.2   0.1   1.3e-24   1.1e-20       2     205 ..      69     343 ..      68     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.3e-24
                                   EEEES-BSSTTCGGGSSSTTSEEETTT.EEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20   2 lgsHlDvVpeeetdgwttpfslteedG.klyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakal 81 
                                   l +HlD+Vp +         +++ e G  l+GrGa+d kg ++a++  l+    eg+    +  +l  + EEg + Ga +l
  gi|77640972|ref|NP_147963.2|  69 LVGHLDTVP-GRL-------EARLE-GyTLWGRGAVDAKGPLAAMILGLHLASSEGL--SCSSAVLGLVGEEGDSPGAWSL 138
                                   679******.333.......33434.867********************98888885..78***********999****** PP

                                   HHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                 Peptidase_M20  82 legleerekvdavfelhieepgileagklaigvv............................................... 115
                                   +       + d  + ++++ep++ +    ++ ++                                               
  gi|77640972|ref|NP_147963.2| 139 VS------RGDTPLHIIVGEPTGGD----GVAIGyrgsltieiectgheghssnpergaadmlvkalasilerdsratvtr 209
                                   **......667777799********....345556699******************************************* PP

                                   ...........................................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEE CS
                                   ...........................................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 116 ...........................................kvevelleggapvtln.dsplvkalaeaaeelfgekve 152
                                                                              ++  + ++   pv+++ +++ ++al ++++ + g+k++
  gi|77640972|ref|NP_147963.2| 210 lkagtaanitpgralatvnmrfnepglealqlaselcsslhqhRCHCSSISLLHPVKTSlSNATARALVASLRTA-GVKPR 289
                                   ******************************************758888889999*****9999999999**9998.***** PP

                                   EEEESSSBHTHHHH.TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 153 livsgpggtdarff.agiptvmifgpgs.glaHspnEyvdledlekgikvlarll 205
                                    +v+  g++d++ +  ++ ++  +gpg+  l+H+ +E++++ d++k++ ++ r+l
  gi|77640972|ref|NP_147963.2| 290 IVVKR-GTSDMNVLsIATESIAAYGPGDpRLSHTKHENIRVGDIVKAAMIYSRTL 343
                                   *****.********533356667****88**********************9987 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.2   7.1e-16   6.3e-12       2      85 ..     162     232 ..     161     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 7.1e-16
                                   EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEE CS
                     M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidi 82 
                                   g +G+++ +i+++g+ gHs++p++g  A  +l+++la++ + +           +  +vt +++G+a+n++p++a a++++
  gi|77640972|ref|NP_147963.2| 162 GYRGSLTIEIECTGHEGHSSNPERG--AADMLVKALASILERD-----------SRATVTRLKAGTAANITPGRALATVNM 229
                                   779**********************..**************95...........7799*********************** PP

                                   EHH CS
                     M20_dimer  83 Rll 85 
                                   R++
  gi|77640972|ref|NP_147963.2| 230 RFN 232
                                   *65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2887.77
//
Query:       gi|118431467|ref|NP_147964.2|  [L=269]
Description: hypothetical protein APE_1470.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-39  135.8   0.0      3e-39  134.7   0.0    1.5  1  QueC      Queuosine biosynthesis protein QueC
    0.00025   20.7   0.0    0.00036   20.2   0.0    1.3  1  ThiI      Thiamine biosynthesis protein (ThiI)


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 !  134.7   0.0   3.3e-43     3e-39       1     209 [.       5     236 ..       5     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 3.3e-43
                                    EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT-..........-.-EEEEE-GGGGGGS.C CS
                           QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelg..........veehkildldllkelg.g 69 
                                    +av ++SGG DS t +++ +++g  v+al+f+Ygq++++e+ +a+k+ ++++          v eh+ +d++++k+l  g
  gi|118431467|ref|NP_147964.2|   5 RAVSIVSGGPDSFTYTLIWLSRGCSVHALSFNYGQKASREVLTARKLLEKADelasergwgrVLEHRLVDISFMKSLWrG 84 
                                    69*************************************************99*********88***********97648 PP

                                    GGG-----------...--------TTHHHHHHHHHHHHH....HHHT-SEEE..E---S-STT-........-GGGSHH CS
                           QueC  70 saLtdeeievpkeeleeeelpntfVpaRNliflslaasya....ealgaeaii..iGvneedfsg........YPDcrde 135
                                    + Ltdee+ev++     + +p++ Vp RN+++ls+aa+ya    e+ ++++++  +G+++ d++         YPDc++e
  gi|118431467|ref|NP_147964.2|  85 TQLTDEEVEVKE-----DYAPSVVVPIRNVVMLSIAAAYAysllEEEDVDRVVvtYGAQRGDIKPrpdtgeplYPDCSPE 159
                                    999999998888.....89********************9333334466665511688888876333334555******* PP

                                    HHHHHHHHHHHH...HTS--EEE-TTTT.--HHHHHHHHH.HTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                           QueC 136 fvkalnkalnlg...edkkieieaPlid.lsKaeivklgk.elgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                     ++al++a +l      +++e+  P  + lsK++ +k +   +g  +  t+sCY +++  ++Cg+C++C+ R+++f++a
  gi|118431467|ref|NP_147964.2| 160 CIEALQAAFRLChfrGMRRLEVWSPSREgLSKSDLLKWAYgTVGKLIYDTWSCYLNGK--YHCGRCESCINRHRAFKDA 236
                                    ***********98885599******87449******9986257788999*****9954..5***************986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     4e-08   0.00036       5      75 ..       5      80 ..       2     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4e-08
                           ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseea...iekveklaellae..yqtslevklvvvdfkev 75
                                   ++++++SgG DS   + + l+RGc v+++ ++     s e+   ++ +ek+ el +e  ++  le +lv ++f + 
  gi|118431467|ref|NP_147964.2|  5 RAVSIVSGGPDSFTYTLIWLSRGCSVHALSFNYGQKASREVltaRKLLEKADELASErgWGRVLEHRLVDISFMKS 80
                                   6899***************************644444444311023333444444432234456677777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2255.76
//
Query:       gi|118431468|ref|NP_147965.2|  [L=101]
Description: GTP cyclohydrolase I [Aeropyrum pernix K1]
Scores for complete 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   40.7   0.0    2.3e-10   40.5   0.0    1.1  1  QueF             QueF-like protein
    0.00036   20.0   0.0    0.00038   19.9   0.0    1.1  1  GTP_cyclohydroI  GTP cyclohydrolase I
  ------ inclusion threshold ------
       0.16   10.5   0.0       0.18   10.3   0.0    1.0  1  LEF-9            Late expression factor 9 (LEF-9)


Domain annotation for each model (and alignments):
>> QueF  QueF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   3.8e-14   2.3e-10       1      59 [.      16      74 ..      16      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 3.8e-14
                           QueF  1 PDfatlvirYvpdkkvvelkslklYlisfrnrgifhEevvnrilddlvealkPkwlevv 59
                                   PD  ++ i+Yv+++ ++e  sl  +l sfr  +i++E+  ++i+ +l e lkP+++ v+
  gi|118431468|ref|NP_147965.2| 16 PDSYDVEIEYVSRDACLEALSLASWLESFRGVKISQEQLAHEIALTLKELLKPEYVCVK 74
                                   88889*************************************************98775 PP

>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   6.3e-08   0.00038      82     143 ..      21      82 ..       7      96 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.3e-08
                                    EEEEEE-TTEEE-HHHHHHHHHHHHSSEE-HHHHHHHHHHHHHHHH--SEEEEEEEEEEHHH CS
                GTP_cyclohydroI  82 ahvaYiPkkkviGlSklaRivdvvarrlqvQErlteqiadaleevlkpkgvavvieaehlCm 143
                                    +++ Y++++  +    la   + +      QE+l+++ia +l+e lkp+ v v ++++h  +
  gi|118431468|ref|NP_147965.2|  21 VEIEYVSRDACLEALSLASWLESFRGVKISQEQLAHEIALTLKELLKPEYVCVKLTGSHGRV 82 
                                    556666655554444466666777777778*****************************755 PP

>> LEF-9  Late expression factor 9 (LEF-9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     3e-05      0.18     414     465 ..      20      74 ..      14      87 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3e-05
                          LEF-9 414 etdvevvaerai...tslnsyisshnkvkvsgadiyhntvvllslflknnsvcyk 465
                                    + ++e v+  a     sl s++ s   vk+s  ++ h+  + l+ +lk ++vc k
  gi|118431468|ref|NP_147965.2|  20 DVEIEYVSRDACleaLSLASWLESFRGVKISQEQLAHEIALTLKELLKPEYVCVK 74 
                                    5678888877752225899**********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 806.58
//
Query:       gi|14601428|ref|NP_147966.1|  [L=309]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Aeropyrum pernix K1]
Scores for complete 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  103.1   0.3    1.9e-29  102.5   0.3    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    3.4e-20   71.9   0.2      8e-20   70.8   0.2    1.6  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.3   2.1e-33   1.9e-29       2     153 .]      49     196 ..      48     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 2.1e-33
                                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   iGc+ +           + y++ s++++ +G+++p+A+G+kla+p+ +v++  GDG+++ i + +++   rrnl+itv+++
  gi|14601428|ref|NP_147966.1|  49 IGCSGR----------TTYYVKgSNFHALHGRAIPVATGVKLANPHLNVIVAGGDGDLMGIgGGHFVALGRRNLNITVLLF 119
                                   566665..........555666999******************************************************** PP

                                   E-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   +N++yg+t+gq   + p+  k+k+   +++ ++++++ la a+G +  ar   +++++l+e +k+a++++g al+++
  gi|14601428|ref|NP_147966.1| 120 DNAVYGLTKGQaapTLPAWVKTKALSMPNIHDNINPVLLAFAAGYTfIARGYAYHTQQLKELIKTAVRHRGAALVDI 196
                                   ***********9988888888988888889****************8888889999*******************97 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 !   70.8   0.2   8.9e-24     8e-20       1      64 [.     200     274 ..     200     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 8.9e-24
                                   XTTTXSSSXSXXXXX-EEEGGGS.T---EE.........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT. CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleed.gyDpsd.........lekAlekalewgdkiplGifYk.eekptyeerleel 64 
                                   C+t+N++ T +wY+er+y+++++ gyDp             +  +k++e+gd+iplGi+Y  ++++++eerle++
  gi|14601428|ref|NP_147966.1| 200 CPTYNNIMTNKWYEERIYYVDQEeGYDPIIrtpeefqkkAPAIAAKLMEFGDRIPLGILYWnQTRESFEERLEKI 274
                                   **********************88******9*****9977777899**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2470.15
//
Query:       gi|118431469|ref|NP_147967.2|  [L=642]
Description: 2-oxoacid:ferredoxin oxidoreductase alpha subunit [Aeropyrum pernix K1]
Scores for complete 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-56  190.5   0.1    6.1e-56  189.8   0.1    1.4  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.5e-43  147.4   0.0    9.6e-43  146.3   0.0    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    2.7e-11   43.6   0.0      1e-10   41.8   0.0    2.0  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    5.5e-07   29.5   0.0    1.7e-06   27.9   0.0    1.8  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.034   13.8   0.2       0.17   11.5   0.1    2.1  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
      0.038   14.0   1.0        1.4    8.9   0.0    3.3  3  RHH_3            Ribbon-helix-helix 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 !  189.8   0.1     2e-59   6.1e-56       2     226 ..     251     497 ..     250     502 .. 0.88

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 2e-59
                                    HHHHCTEEEEEE--BTTTCC...HHHHHCHCCCCCTT........EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECC CS
                          POR_N   2 aaiaagvdviaaYPITPsse...iaeelaellakgev........gdvevvqmesEigaisaviGAaaaGaraaTaTSgq 70 
                                    ++i +g+ vi++YPITPss+    +e+++    +g +          v +vqme+E+++i+av+GAaaaGara T+TSg+
  gi|118431469|ref|NP_147967.2| 251 GKIVGGLGVITYYPITPSSDealYVEKHSYISIDGPLaeklgydkIAVAIVQMEDELASINAVLGAAAAGARASTTTSGP 330
                                    56778899************775555555555555559999998755899****************************** PP

                                    HHHHCCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHC CS
                          POR_N  71 GllLmienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekv 145
                                    G++Lm e++ la+ +e+Pvv+++ +Ra+pstg+++rt q+Dl+  +     d + ivlas+++ eaf +a++Afn+Ae++
  gi|118431469|ref|NP_147967.2| 331 GFSLMNEAVSLAVEAEIPVVVTLWMRAGPSTGMPTRTGQQDLLHSIfsghgDAPKIVLASGDHVEAFYDAIKAFNWAEEF 410
                                    ******************************************************************************** PP

                                    TSEEEEEEEHHHH.HEEEEEEC-SGG..GS-----SBXXXXXXXX........SXXXBXXTXXTSSXXEEESBXBXTTSX CS
                          POR_N 146 rvPvivlfDgfllshevekvelpdee.delklikekleeyerkey........aldpekpiargtaanpdtglehrekgn 216
                                    ++Pvi+l+D++l+s +v+  + +d +  ++ + + kl ++ +++y        +++p+  +  g a++  tgleh+e+g+
  gi|118431469|ref|NP_147967.2| 411 QTPVIHLLDKYLASSMVSLAR-EDLDpSKVPITRGKLLDNPPADYrryevvedGISPRARL--GSATMVITGLEHDEYGY 487
                                    *************77776554.556668888888888888888888888899899999887..9999************* PP

                                    BXXXXHHHHH CS
                          POR_N 217 eaedaaekvv 226
                                    ++ed +   +
  gi|118431469|ref|NP_147967.2| 488 ATEDPVMREI 497
                                    ***9444433 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3   0.0   3.2e-46   9.6e-43       2     176 ..      13     215 ..      10     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 3.2e-46
                                    TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                            POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                    G G+++ag+i +k+++  Gy+v+++rey+s+i+G+hsy+h+r++++ + +s++  ++d ++aldae++++h+ +++pggi
  gi|118431469|ref|NP_147967.2|  13 GGGIESAGQIAIKSMVLLGYEVLGSREYHSNIMGAHSYYHLRVQQH-RPRSLK-LPVDGVLALDAESVFTHFRDVRPGGI 90 
                                    99*******************************************9.889999.************************** PP

                                    EEEECTCGTT-CCHHHCTS-HHHHHHH.......................T-EEEEE-HHHHHHHCCC.........CCH CS
                            POR  82 iiynseelkpdelkkakeeerelkerl.......................gvrvygvdatkiakeiggn........era 130
                                    ++y+++++++++ + +++ + +lk+rl                       g+r++g+++++++k ++          +ra
  gi|118431469|ref|NP_147967.2|  91 LVYDPGTKSTRVDAIQPM-AGPLKKRLkslfdsrgmqpvvesavklaeeaGARIVGLPLKEMLKTLSERtgapvarvSRA 169
                                    *****9888888888776.566777778************************************5444455577777*** PP

                                    HHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                            POR 131 aNtvmlGalaallglplealeeaikkrfpkkkeviekNlkafragy 176
                                    +Nt++l+ ++ +lg+p+e++e+ai+ +f++k++vi++N++a+r ++
  gi|118431469|ref|NP_147967.2| 170 LNTLGLASMLYMLGVPVEYIEKAISLQFAGKEKVINMNVEAVRIAV 215
                                    *******************************************987 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.4     1e+04      26      39 ..     251     264 ..     247     283 .. 0.82
   2 !   41.8   0.0   3.4e-14     1e-10       1      95 [.     527     614 ..     527     621 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.4
                                    T--EEEEEES--BS CS
                        PFOR_II  26 gikvGllrlrtlrP 39 
                                    g  vG l ++t++P
  gi|118431469|ref|NP_147967.2| 251 GKIVGGLGVITYYP 264
                                    67799999999999 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 3.4e-14
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGG CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkk 80 
                                    A v++v +Gs+ + + +a ++lR+eg+++ + ++r+l+PFP + ++e+l++v+kv+ +++n      Gql++  +a+++ 
  gi|118431469|ref|NP_147967.2| 527 ASVALVSFGSTKQPILEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQNL----LGQLAMLLRAHTSI 602
                                    789***********************************************************....48888888888765 PP

                                    GTSEEEEEE--GGG- CS
                        PFOR_II  81 skvkvvnfvaglgGr 95 
                                    +   + + + +++Gr
  gi|118431469|ref|NP_147967.2| 603 K---PDSSIVKINGR 614
                                    5...44445555555 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   5.6e-10   1.7e-06       9      70 ..     526     587 ..     517     592 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.6e-10
                                    TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEE CS
                Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveea 70 
                                    +  v+lv++Gs+ +  leA e+L++eg++a+   +r + p+  ++++e+++  +++++ve++
  gi|118431469|ref|NP_147967.2| 526 EASVALVSFGSTKQPILEALEMLRDEGVRARFAQVRLLYPFPGRLVEEMLEGVEKVIMVEQN 587
                                    778********************************************************986 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 ?   -1.7   0.0      0.64   1.9e+03     116     167 ..     105     154 ..      90     158 .. 0.77
   2 ?   11.5   0.1   5.5e-05      0.17      36     106 ..     293     362 ..     284     414 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.64
                                    CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEHHHCC-E CS
                   TPP_enzyme_N 116 qlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpkdvllee 167
                                    ++ ++ p+ k    + +++ ++++++ A++ a  ++ g+  + lp+  +l++
  gi|118431469|ref|NP_147967.2| 105 IQPMAGPLKKRLKSLFDSRGMQPVVESAVKLA--EEAGARIVGLPLKEMLKT 154
                                    55677788888888888899999999999999..888888888888877765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.5e-05
                                    CT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH CS
                   TPP_enzyme_N  36 eeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg 106
                                      +  + +v++ +E + ++a  g a a     +  +tsgpG+  +  a+  A  + iP++v    r+  ++g
  gi|118431469|ref|NP_147967.2| 293 YDKiAVAIVQMEDELASINAVLGAAAAG--ARASTTTSGPGFSLMNEAVSLAVEAEIPVVVTLWMRAGPSTG 362
                                    5555677888888888888888888776..468899*************************98777776666 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00047       1.4      15      30 ..     150     165 ..     147     166 .. 0.89
   2 ?    1.3   0.0      0.11   3.3e+02      30      38 ..     187     195 ..     182     198 .. 0.87
   3 ?   -1.6   0.2       0.9   2.7e+03      30      39 ..     569     578 ..     569     579 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00047
                          RHH_3  15 ekLkaLSekTrIprSk 30 
                                    e+Lk+LSe+T+ p+++
  gi|118431469|ref|NP_147967.2| 150 EMLKTLSERTGAPVAR 165
                                    89*********99986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.11
                          RHH_3  30 klldeAiel 38 
                                    +++++Ai+l
  gi|118431469|ref|NP_147967.2| 187 EYIEKAISL 195
                                    8******97 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.9
                          RHH_3  30 klldeAiell 39 
                                    +l++e++e +
  gi|118431469|ref|NP_147967.2| 569 RLVEEMLEGV 578
                                    79*****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.57u 0.21s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 5193.97
//
Query:       gi|118431470|ref|YP_874897.1|  [L=102]
Description: hypothetical protein APE_1473a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 864.73
//
Query:       gi|14601431|ref|NP_147969.1|  [L=308]
Description: hypothetical protein APE_1477 [Aeropyrum pernix K1]
Scores for 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  154.1  27.3    8.7e-43  146.1  14.7    2.0  2  Lys_export  Lysine exporter LysO


Domain annotation for each model (and alignments):
>> Lys_export  Lysine exporter LysO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   4.8     1e-06     0.018       5     103 ..      19     117 ..      15     119 .. 0.81
   2 !  146.1  14.7   4.8e-47   8.7e-43       1     189 [.     118     300 ..     118     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-06
                    Lys_export   5 iaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggllaalllglslk 85 
                                   +aG+++G++++   + ++e+l   +  +L+f +G  +gss +l +++  l  ++l+  l  +++  +++lla+   + s+ 
  gi|14601431|ref|NP_147969.1|  19 VAGVVAGAYMRGAYSRAVEHLLYPVVWALVFTIGAGVGSSIDLERAAGILYGSILIAILPGAASVAVAALLAGNSSQESVG 99 
                                   89**********99999************************9888866666666666666666666666666667788999 PP

                    Lys_export  86 eslavasGfGwYSLsgil 103
                                    +  va G   YS  +++
  gi|14601431|ref|NP_147969.1| 100 IGSQVAGGSSLYSSPAVI 117
                                   999999999999976666 PP

  == domain 2  score: 146.1 bits;  conditional E-value: 4.8e-47
                    Lys_export   1 llaliaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggllaalllg 81 
                                   l++++aG++ G+l+ ++   + + +s++lLy+Llf+ G+ +g    l+ +  + ++ +lll+l++++g ++gg++aa++lg
  gi|14601431|ref|NP_147969.1| 118 LAFFLAGLASGWLTGSS---FPDVVSTLLLYILLFQAGYLVGGAAGLRGM-LRGGRLGLLLALSCLVGGVIGGAAAAFVLG 194
                                   589*********76665...6899********************997777.67788899999******************* PP

                    Lys_export  82 lslkeslavasGfGwYSLsgilitelkgaelGtiallanllREllalllipllakrfgklaaisvaGatsmDttLPiitks 162
                                   +sl+ ++a+++  GwYSL+g+l+    ++++G++al+ n+lRE + ++++plla+r++  +a++++Gat+mDt LP+i  s
  gi|14601431|ref|NP_147969.1| 195 WSLEAGVAMGVSSGWYSLAGPLLYT-IDPYYGAVALVGNMLREAFHIVVYPLLARRIPI-QAVAFGGATTMDTGLPVILAS 273
                                   ***********************87.7****************************9987.78******************* PP

                    Lys_export 163 sgkevvvlaivhGvilsllvPilvslf 189
                                   sg+++++ a+v+G++l+ll  +l++l+
  gi|14601431|ref|NP_147969.1| 274 SGERAALPAFVQGALLTLLLSLLLPLY 300
                                   ************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2420.37
//
Query:       gi|118431471|ref|NP_147970.2|  [L=221]
Description: hypothetical protein APE_1478.1 [Aeropyrum pernix K1]
Scores for complete 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   89.3  18.4    1.3e-23   83.6  13.3    2.0  2  DUF389    Domain of unknown function (DUF389)


Domain annotation for each model (and alignments):
>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2   7.8e-05       1.4      63     100 ..      29      66 ..      13      67 .. 0.73
   2 !   83.6  13.3   7.2e-28   1.3e-23       1     140 [.      68     206 ..      68     208 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.8e-05
                         DUF389  63 semlsrtepnlvdllvAlasGaagalallsgnssslvG 100
                                    +e   r++++l++ l+A ++G+++   +++g+   lvG
  gi|118431471|ref|NP_147970.2|  29 DEANDRSSVDLLQALLAAIAGVVALAGIITGSMILLVG 66 
                                    56677777777788888888877777777777777777 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 7.2e-28
                         DUF389   1 MlisPlmgpilaiafglvigdrkllrrglknlliglllallvgflfglllplkvlg.eeelptsemlsrtepnlvdllvA 79 
                                    Ml+sP+++pi+++a+gl+ g+ +++ rg ++lli ++lal+ ++++++++ +     + ++  +  ++ ++p+++dl++ 
  gi|118431471|ref|NP_147970.2|  68 MLLSPILSPIYSAAVGLSFGRLEIAVRGGFSLLILTFLALASSTTAAAIVSVF--LpGPDAVLEAARQAYTPHYIDLIIG 145
                                    ***********************************************665443..334555558999************* PP

                         DUF389  80 lasGaagalallsgnssslvGvaIaaaLlPPavnaGlglalgewalalgslllllvNivgI 140
                                    la Gaa+ la + + ++ l+Gva+aaaL+PP+++ Glgla+ +++l lgsl+    N++g+
  gi|118431471|ref|NP_147970.2| 146 LALGAAVSLAAVARLNEPLIGVAVAAALIPPLAALGLGLAFLDYELSLGSLAKASANMAGL 206
                                    *********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1818.46
//
Query:       gi|118431472|ref|NP_147971.2|  [L=180]
Description: ADP-ribose pyrophosphatase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-19   70.0   0.7    2.3e-19   69.7   0.7    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 !   69.7   0.7   1.3e-23   2.3e-19       3     115 ..      33     146 ..      31     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.3e-23
                                    EEEEEEE.EEETTSE..EEEEEESSSSTTT.E..ESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEE CS
                          NUDIX   3 rravgvv.llnekge..vLlvrrskkpfpg.W..elPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapyd 75 
                                    + +v+v+ l +++ge  v+lvr++ +p  g W  e P+G++++gEtpe+AA+REleEE+Gl+a  l+++ g       ++
  gi|118431472|ref|NP_147971.2|  33 PDSVAVLpLVEKDGEwhVVLVRQF-RPSIGkWtlEAPAGTLKEGETPEAAAARELEEEAGLKAkALVRVGG-------GH 104
                                    578999999999999*********.8888899555****************************88889998.......33 PP

                                    EEEEEEEEEEEEEE..EEECSGCSSTSTTT.EEEEEEEEHHHH CS
                          NUDIX  76 gpygdeheilyvfl..eevegelepndene.vsevrwvpleel 115
                                     + g  +e++++fl    ++ge+ p+ e+e +++v  ++l e+
  gi|118431472|ref|NP_147971.2| 105 VSPGYSTEYIHLFLaySLEKGEMSPE-EHEvIEGVVEMRLSEA 146
                                    33334778999999899999999999.7772555556777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1406.63
//
Query:       gi|118431473|ref|NP_147972.2|  [L=279]
Description: hypothetical protein APE_1483.1 [Aeropyrum pernix K1]
Scores for 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-63  211.9   0.0    8.2e-63  211.6   0.0    1.0  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 !  211.6   0.0   4.6e-67   8.2e-63       4     204 ..      66     276 ..      63     277 .. 0.97

  Alignments for each domain:
  == domain 1  score: 211.6 bits;  conditional E-value: 4.6e-67
                                    --SEEEEEEEEE-TT---EEEEE--B-SS-.-TTSS-TT-B--B-HHHHHHHHHHHHGGG...GGSTT-EEEE--S-SS- CS
                 tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlge.aelGGkpeelapaaPrllkallralkkia...ekleefevtlEatHHGP 79 
                                    +++++i+lS+H++esg+++LTvH+ Gn++e ++lGG+p ela+a+P+l+kall +l+k +   ++ e +evtlEatHHGP
  gi|118431473|ref|NP_147972.2|  66 QASAVIVLSKHRAESGRKSLTVHHPGNPTEdNSLGGRPMELAVAYPALAKALLISLAKASretGLAESYEVTLEATHHGP 145
                                    6789******************************************************99999999************** PP

                                    ----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--...----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGG CS
                 tRNA_deacylase  80 telkvPslFvEiGSteeeWkdedaaeavaeavlellese...eekekvlvgiGGgHYaprftklvletevavGhilskya 156
                                    t+ ++P++F+E+GStee+W+++  +e++a av e++++    e+++ ++ g+GG+HY+p++t+l le+++++Gh ++ ya
  gi|118431473|ref|NP_147972.2| 146 TTPSKPVVFAELGSTEEDWRNPLGWETLALAVEEAIKTLpqiERECIPAAGFGGTHYVPKHTRLQLESGYCIGHTIPRYA 225
                                    ***********************************999999999************************************ PP

                                    GGG.--HHHHHHHHHHH...T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                 tRNA_deacylase 157 lee.lkeevikqaleks..egadvalidkkslkseqkeaieelleelgiev 204
                                    ++  +++ev+k+a+ ks  + a+val++kkslks q++++ee+ ee g +v
  gi|118431473|ref|NP_147972.2| 226 FDRgVTAEVLKNAILKSypGPARVALVEKKSLKSPQRRMVEEASEEAGAKV 276
                                    9987999****************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2092.90
//
Query:       gi|118431474|ref|NP_147973.2|  [L=669]
Description: 3-hydroxyacyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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  242.7   0.0    5.6e-72  242.1   0.0    1.3  1  ECH_1           Enoyl-CoA hydratase/isomerase
    2.1e-64  216.7   2.5      4e-64  215.8   2.5    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    2.6e-51  172.2   0.7    1.8e-25   89.4   0.1    2.6  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
      5e-42  144.6   0.3    1.8e-38  132.9   0.0    2.7  3  ECH_2           Enoyl-CoA hydratase/isomerase
    0.00066   19.9   0.2     0.0026   18.0   0.2    2.1  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.014   14.7   0.6      0.061   12.7   0.1    2.1  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.053   12.8   0.1      0.094   12.0   0.1    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.11   12.4   0.0         19    5.1   0.0    2.9  2  OAM_alpha       D-ornithine 4,5-aminomutase alpha-subunit
       0.14   11.3   0.1       0.26   10.5   0.1    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
       0.17   11.9   2.5        1.6    8.7   0.7    3.3  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


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 !  242.1   0.0   3.1e-75   5.6e-72       3     250 ..     421     668 ..     419     669 .] 0.99

  Alignments for each domain:
  == domain 1  score: 242.1 bits;  conditional E-value: 3.1e-75
                                    ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                          ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                    e+ +a i lnrP+++Na+s++++ El qal +le+   vrav+LtG ++aF+aGad+++ a+  + +   ++ +++el  
  gi|118431474|ref|NP_147973.2| 421 EKPIAWIVLNRPDKLNAISPKMIMELSQALDELEERSDVRAVILTGAGRAFSAGADVTAFAQVTPIDILRFSRKFQELTL 500
                                    567999************************************************************************** PP

                                    HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EEEHH CS
                          ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkkisaq 162
                                    k++   kpvi a++G+a+gGGlela+  Di+ia+++a  g++e++lG+ipgaggtq+lar  G ++A+e++++g+ i a 
  gi|118431474|ref|NP_147973.2| 501 KIQFYTKPVIVAIKGYALGGGLELAMSGDIRIASEDAMLGQPEINLGFIPGAGGTQRLARLAGPARAKELIMTGDMIPAS 580
                                    ******************************************************************************** PP

                                    HHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHHHHHHHT CS
                          ECH_1 163 ealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeGlqaflE 242
                                    +a+k+G+v++vvp e l++ea +la klaek+p al+++k a++  le++  ++l++ea lf+ +fs++d+ eG++aflE
  gi|118431474|ref|NP_147973.2| 581 DAEKMGIVNRVVPPELLEQEASSLALKLAEKPPIALAAAKYAIDFGLESNIWAGLQLEASLFSVLFSTEDVIEGVTAFLE 660
                                    ******************************************************************************** PP

                                    CSH----- CS
                          ECH_1 243 krkpefed 250
                                    krkp+f++
  gi|118431474|ref|NP_147973.2| 661 KRKPKFKG 668
                                    ******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 !  215.8   2.5   2.2e-67     4e-64       1     179 [.       7     195 ..       7     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 2.2e-67
                                    EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEE.........EES CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalaris.........ftt 71 
                                    +++v+GaGtmG+gia+++a ag++V l di+ ++l++al++i+ slekl+ekg++  e+ve++++ri+         +++
  gi|118431474|ref|NP_147973.2|   7 TITVVGAGTMGHGIAELAAIAGFKVYLADINIDILNNALQRIRWSLEKLAEKGRIR-ESVETVMSRITpivsvrdgeYSE 85 
                                    69*****************************************************9.99999999997666666666899 PP

                                    -HHHHH.C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEE CS
                        3HCDH_N  72 dleeav.dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvv 150
                                    dl++a  + d++iEa++E+lelK+++fa  +k+ak++ailasnTSsl+i+e+a+a++rpe+v+g+HFfnPp lm+LvEvv
  gi|118431474|ref|NP_147973.2|  86 DLAKALsESDFMIEAIPEKLELKQQLFAFADKHAKETAILASNTSSLPITEIAAATSRPEKVVGMHFFNPPVLMPLVEVV 165
                                    ******9************************************************************************* PP

                                    E-TT--HHHHHHHHHHHHHTT-EEEEE.CS CS
                        3HCDH_N 151 rgekTseetvatvvelakkigktpvvv.kd 179
                                    +gekTseetva++v+lakk+gk++vvv kd
  gi|118431474|ref|NP_147973.2| 166 KGEKTSEETVAATVDLAKKMGKQTVVVkKD 195
                                    ***************************666 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   0.1     1e-28   1.8e-25       1      97 []     198     292 ..     198     292 .. 0.95
   2 !   80.7   0.0   5.2e-26   9.3e-23      12      97 .]     320     405 ..     315     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 1e-28
                                    TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHH CS
                          3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspllekl 80 
                                    GF+vnR+l++l++ a+ lve+g  ++ ++Da++++ lGlpmG+fel+d+ g+dv +++ e++ ++ g r ++ + ++e+ 
  gi|118431474|ref|NP_147973.2| 198 GFIVNRILGRLMESACLLVERGGYTVVQVDATAKYLLGLPMGVFELADYSGIDVFYYVFEAMSRR-GFRSAK-CSIFEEK 275
                                    9***********************************************************77777.555455.9****** PP

                                    HHTT--BGGGTBSSSBC CS
                          3HCDH  81 veagrlgrktgkgfyky 97 
                                    ++ag++g k+gkg+y y
  gi|118431474|ref|NP_147973.2| 276 FKAGEYGVKAGKGIYSY 292
                                    ***************98 PP

  == domain 2  score: 80.7 bits;  conditional E-value: 5.2e-26
                                    HHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGGGT CS
                          3HCDH  12 lneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrlgrktg 91 
                                    +nea +l+ e va+ ediD+a++lglG+p G+fe +d++gld +  +le +++ +g ++++p pll+k+ve+gr+grk+g
  gi|118431474|ref|NP_147973.2| 320 INEAAWLLREDVATREDIDKAVKLGLGWPKGVFEYADEFGLDRVVEALERIKRDFGVDHAEPDPLLKKMVEEGRIGRKAG 399
                                    89****************************************************************************** PP

                                    BSSSBC CS
                          3HCDH  92 kgfyky 97 
                                    kgfy+y
  gi|118431474|ref|NP_147973.2| 400 KGFYEY 405
                                    ****98 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.77   1.4e+03     174     253 ..      42     119 ..      21     142 .. 0.55
   2 !  132.9   0.0     1e-41   1.8e-38       2     184 ..     425     604 ..     424     607 .. 0.95
   3 !   10.0   0.0   0.00024      0.44     249     318 ..     601     667 ..     597     669 .] 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.77
                                    GGGHHHHHHHHHTT..........--------......----SHHHHHHHHHHHT.-S..-TTTHHHHHH.T..--SHHH CS
                          ECH_2 174 seklealeeaLaelessd..eeaveevleelaeeaeeeeeeselaekreaidrlfsad..sveeiveaLekaeaeedewa 249
                                    +++l++++ +L++l ++   +e+ve+v+++++  ++ +  + e     e ++++ s++   +e+i e+Le  +++  ++a
  gi|118431474|ref|NP_147973.2|  42 NNALQRIRWSLEKLAEKGriRESVETVMSRITPIVSVR--DGE---YSEDLAKALSESdfMIEAIPEKLEL-KQQLFAFA 115
                                    44455555555555444344555555555544333332..223...3455666665553567888888873.33444444 PP

                                    HHHH CS
                          ECH_2 250 kktl 253
                                    +k +
  gi|118431474|ref|NP_147973.2| 116 DKHA 119
                                    4443 PP

  == domain 2  score: 132.9 bits;  conditional E-value: 1e-41
                                    EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHHHHH CS
                          ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYklny 81 
                                    ++i Lnrp++lNa+s +m+ +l++al+e e+ ++v++v+l+gag +af+AG Dv a+++    +     +f r+  +l  
  gi|118431474|ref|NP_147973.2| 425 AWIVLNRPDKLNAISPKMIMELSQALDELEERSDVRAVILTGAG-RAFSAGADVTAFAQVTPIDIL---RFSRKFQELTL 500
                                    689***************************************99.*************99988654...5999999**** PP

                                    HHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH---B-HH CS
                          ECH_2  82 liatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTGarlkga 160
                                     i+ y+kpv+  + G+++GgG+ l+++g +r+++e++++  PE+++G++P  Gg+  L+rl g + ++ l +TG+ + ++
  gi|118431474|ref|NP_147973.2| 501 KIQFYTKPVIVAIKGYALGGGLELAMSGDIRIASEDAMLGQPEINLGFIPGAGGTQRLARLAGpARAKELIMTGDMIPAS 580
                                    *************************************************************99788************** PP

                                    HHHHTTS--EE--GGGHHHHHHHH CS
                          ECH_2 161 dalaaglathyvpseklealeeaL 184
                                    da ++g+ + +vp e le+ +++L
  gi|118431474|ref|NP_147973.2| 581 DAEKMGIVNRVVPPELLEQEASSL 604
                                    *************99888766555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                          ECH_2 249 akktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                    a++ + +l+++ P++l+++  +++ g + + +   l+ E  l + l++++D++eGv+a l +  +kPk+k
  gi|118431474|ref|NP_147973.2| 601 ASSLALKLAEKPPIALAAAKYAIDFGLESN-IWAGLQLEASLFSVLFSTEDVIEGVTAFLEK--RKPKFK 667
                                    667778899********************5.***************************9955..577775 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 !   18.0   0.2   1.4e-06    0.0026       2      89 ..       8     100 ..       7     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS..H CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...akaaesieelvasldvvitmvkagkavdevieg..l 76 
                                    i ++G G+MG+ +a+  + ag+kv++ + + + +++++++    ++ +++   + +s+++v+  ++    v++   +  l
  gi|118431474|ref|NP_147973.2|   8 ITVVGAGTMGHGIAELAAIAGFKVYLADINIDILNNALQRIrwsLEKLAEKGRIRESVETVMSRITPIVSVRDGEYSedL 87 
                                    89****************************99999999886666445555555555555555555555555432111246 PP

                                    CCC--TT-EEEE- CS
                  NAD_binding_2  77 lealkkgdilidg 89 
                                    ++al+++d++i+ 
  gi|118431474|ref|NP_147973.2|  88 AKALSESDFMIEA 100
                                    6666666666654 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 ?   12.7   0.1   3.4e-05     0.061      37      70 ..       6      39 ..       3      61 .. 0.81
   2 ?   -0.7   0.0      0.44   7.8e+02      80     122 ..      82     124 ..      68     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                   kt+ ++G+G +G+ +a++++  g+kv+  d + +
  gi|118431474|ref|NP_147973.2|  6 KTITVVGAGTMGHGIAELAAIAGFKVYLADINID 39
                                   89**************************998865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.44
                                    CEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEE CS
                   2-Hacid_dh_C  80 velvsleellaesDivslhlpltpetrhlinaeelakmkkgai 122
                                     + ++l ++l+esD+ + ++p + e ++ + a + ++ k++ai
  gi|118431474|ref|NP_147973.2|  82 EYSEDLAKALSESDFMIEAIPEKLELKQQLFAFADKHAKETAI 124
                                    4567999********9999998777766666655556665555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.2e-05     0.094      21      69 ..       3      46 ..       1     102 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                                   CEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                    AlaDh_PNT_C 21 GgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69
                                   G v+     +++v+G+G+ G   ++ a+  g kV++ D++++ l++  +
  gi|118431474|ref|NP_147973.2|  3 GEVK-----TITVVGAGTMGHGIAELAAIAGFKVYLADINIDILNNALQ 46
                                   5565.....899*****************************99987655 PP

>> OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.032        58      56      96 ..     374     414 ..     358     428 .. 0.86
   2 ?    5.1   0.0     0.011        19      62     102 ..     583     623 ..     577     633 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.032
                                    TT--HHHHHHHHHHHHHTTGGGG-HHHHHHHHHHHTT--HH CS
                      OAM_alpha  56 mGlssleakaivekvlekgllgkGaGhvvyrlakeknidir 96 
                                     G++  e   +++k++e+g +g+ aG+  y++ + ++ +++
  gi|118431474|ref|NP_147973.2| 374 FGVDHAEPDPLLKKMVEEGRIGRKAGKGFYEYGEVEEKKME 414
                                    699999999*********************99988877765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHTTGGGG-HHHHHHHHHHHTT--HHHHHHHH CS
                      OAM_alpha  62 eakaivekvlekgllgkGaGhvvyrlakeknidireageal 102
                                    e + iv++v+  +ll++ a  + ++la++  i +  a  a+
  gi|118431474|ref|NP_147973.2| 583 EKMGIVNRVVPPELLEQEASSLALKLAEKPPIALAAAKYAI 623
                                    6778*************************999999887665 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 ?   10.5   0.1   0.00014      0.26     143     211 ..       6      74 ..       2     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                    SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidg 211
                                    k i+vvG+G  G  +A  +a +g +v+l + +  +l++  ++++  le+  ek  ++  ++t++ +i++
  gi|118431474|ref|NP_147973.2|   6 KTITVVGAGTMGHGIAELAAIAGFKVYLADINIDILNNALQRIRWSLEKLAEKGRIRESVETVMSRITP 74 
                                    5799***********************999999999888889999999999988888888888877775 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 ?    8.7   0.7   0.00091       1.6       2      80 ..       8     104 ..       7     129 .. 0.63
   2 ?   -1.5   0.0       1.2   2.2e+03      53      86 ..     171     205 ..     163     212 .. 0.74
   3 ?   -1.8   0.0       1.5   2.8e+03     125     140 ..     556     571 ..     552     576 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00091
                                    EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.................HHHHHHHHHSSBT.TTBTT----TTEEEES-H CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvree.................elieeineehenv.kyLpgiklpenlvattdl 63 
                                    i+v+GaG  G  +A + a +g +v l   +                  ++  +i+e+ e v   +  i    + + ++dl
  gi|118431474|ref|NP_147973.2|   8 ITVVGAGTMGHGIAELAAIAGFKVYLADINIdilnnalqrirwsleklAEKGRIRESVETVmSRITPIVSVRDGEYSEDL 87 
                                    9********************77766655555555555555555542333333444333321112223333344678889 PP

                                    HHHHTT--EEEE---HH CS
                 NAD_Gly3P_dh_N  64 aealkgadiivlvvPsq 80 
                                    a+al+++d+++ ++P +
  gi|118431474|ref|NP_147973.2|  88 AKALSESDFMIEAIPEK 104
                                    99999999999998876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                    --TTEEEES-HHHHHTT--EEEE.---HHHHHHHH CS
                 NAD_Gly3P_dh_N  53 lpenlvattdlaealkgadiivl.vvPsqalrevl 86 
                                     +e++ at dla+ + + +++v   vP  +++++l
  gi|118431474|ref|NP_147973.2| 171 SEETVAATVDLAKKMGKQTVVVKkDVPGFIVNRIL 205
                                    56899999999999998888885247776666666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.5
                                    --EEEEESS--HHHHH CS
                 NAD_Gly3P_dh_N 125 ekvavlsGpslAeEva 140
                                    +++a l+Gp  A+E++
  gi|118431474|ref|NP_147973.2| 556 QRLARLAGPARAKELI 571
                                    56899*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 4792.14
//
Query:       gi|118431475|ref|YP_874898.1|  [L=88]
Description: hypothetical protein APE_1484a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 664.13
//
Query:       gi|118431476|ref|NP_147974.2|  [L=340]
Description: threonine synthase [Aeropyrum pernix K1]
Scores for complete 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  185.2   2.4    2.5e-54  184.7   2.4    1.1  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.06   13.1   1.3       0.11   12.3   1.3    1.4  1  zinc_ribbon_2  zinc-ribbon domain
       0.13   12.2   4.4       0.92    9.4   0.1    2.4  2  zf-FPG_IleRS   Zinc finger found in FPG and IleRS
       0.13   12.1   0.2       0.22   11.4   0.2    1.3  1  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)


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 !  184.7   2.4   5.6e-58   2.5e-54       4     294 .]      47     323 ..      45     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 184.7 bits;  conditional E-value: 5.6e-58
                                    CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                           PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                    g+g TPlv++          +++KlE+lnp+gSfKdRg+ y l  +    g + vv+ ssGN+g+++A+++a+lGlk+++
  gi|118431476|ref|NP_147974.2|  47 GEGSTPLVEAGE-------GVYAKLEYLNPSGSFKDRGVGYSLRMASLL-GYDCVVVDSSGNTGLSTALYSARLGLKARV 118
                                    789999998877.......4***********************998888.****************************** PP

                                    EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEEE CS
                           PALP  84 vvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavvv 163
                                    +vp++asp+k+al+r+ Gae+ve ++  ++a+   ae++ae + +++++++ np+ ieg +++g E++ +  g+ d v++
  gi|118431476|ref|NP_147974.2| 119 YVPRGASPGKKALIRATGAELVEAESREEAARL--AEAEAE-KCFHVAHPT-NPLFIEGVKSLGRELAGEAAGDTD-VLA 193
                                    ************************664444444..599999.999999999.9***************66667999.9** PP

                                    E-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCC.S..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEE CS
                           PALP 164 pvGgGgliaGiaaglkerrpdvrvigvepegsdalarsl.ragrrvtvpvsdtiadglavgspselafelldrlvdeivt 242
                                    pv++G l+ Gi++gl e+r+  r+++v++  + +l + + + g +  v+     a  la +   e+  ++++++++ +v 
  gi|118431476|ref|NP_147974.2| 194 PVSSGTLLLGIYRGLEEERGRFRLVAVQSPAAYSLKGLVpELGWVGGVEGRLLDALLLARPPRLEEMARAVRESGGGVVV 273
                                    ***************************99877777777756666666666566666667778888888999********* PP

                                    EEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                           PALP 243 vsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                    v d ++  a+r+     g +vepssaa++aa   lre++ l++    +++ltg
  gi|118431476|ref|NP_147974.2| 274 VGDGAIPGAVREAV-QRGFLVEPSSAAVFAAHeVLREKKWLSGR--SLLVLTG 323
                                    **************.9999*************888888888888..7777776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.3   2.4e-05      0.11       2      23 .]      11      34 ..      11      34 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                  zinc_ribbon_2  2 CpnCGaelqdnakF..CpyCGtpl 23
                                   Cp+CG +l +++    Cp+C+ pl
  gi|118431476|ref|NP_147974.2| 11 CPRCGIKLREGEYRpwCPRCRGPL 34
                                   *********988888*****8765 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   0.9     0.015        69       4       8 ..      11      15 ..      10      20 .. 0.65
   2 ?    9.4   0.1    0.0002      0.92       4      16 ..      27      39 ..      27      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.015
                                   -TTT- CS
                   zf-FPG_IleRS  4 CpRCw 8 
                                   CpRC+
  gi|118431476|ref|NP_147974.2| 11 CPRCG 15
                                   55555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0002
                                   -TTT--BBEEEEC CS
                   zf-FPG_IleRS  4 CpRCwryiervgq 16
                                   CpRC++++e vg+
  gi|118431476|ref|NP_147974.2| 27 CPRCRGPLEAVGL 39
                                   *********9997 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 ?   11.4   0.2   4.8e-05      0.22      22      49 ..       8      36 ..       5      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                                   EEEE-HHHHHHHHH..TT-B-TTT--B--E CS
                     zf-C3HC4_3 22 HlvlCeeCaekllk..rkkkCpiCrrpiek 49
                                   Hl  C +C  kl++   ++ Cp Cr p e 
  gi|118431476|ref|NP_147974.2|  8 HL-WCPRCGIKLREgeYRPWCPRCRGPLEA 36
                                   77.9********999999*******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2480.56
//
Query:       gi|118431477|ref|NP_147976.2|  [L=220]
Description: precorrin-2 dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-20   72.5   0.0    7.4e-20   71.3   0.0    1.6  2  NAD_binding_7    Putative NAD(P)-binding
    0.00088   20.1   0.1     0.0018   19.1   0.1    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0037   16.6   1.6     0.0063   15.8   1.0    1.6  2  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0073   16.1   0.1      0.013   15.2   0.1    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.028   13.8   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.021   14.2   1.0      0.099   12.0   0.9    1.9  2  ThiF             ThiF family
      0.032   13.3   2.1      0.052   12.6   2.1    1.3  1  FAD_binding_2    FAD binding domain
      0.034   14.6   0.5      0.096   13.1   0.5    1.8  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.039   13.2   1.9      0.059   12.6   1.9    1.3  1  FAD_binding_3    FAD binding domain
      0.061   13.2   0.4       0.14   12.0   0.4    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.094   12.4   0.2       0.27   10.9   0.2    1.8  2  ApbA             Ketopantoate reductase PanE/ApbA
        0.1   12.3   0.1       0.19   11.4   0.1    1.5  1  PPR_1            PPR repeat
       0.11   12.1   0.0       0.19   11.3   0.0    1.4  1  Glyco_trans_4_5  Glycosyl-transferase family 4
       0.12   12.0   0.0       0.21   11.1   0.0    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.16   12.0   0.0       0.27   11.3   0.0    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.35   11.4   3.1        1.2    9.7   3.1    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   6.6e-23   7.4e-20       2     103 ..       7     116 ..       6     117 .. 0.88
   2 ?   -2.3   0.0       5.4     6e+03      19      35 ..     141     157 ..     137     195 .. 0.66

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 6.6e-23
                  NAD_binding_7   2 fldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee...........lekdlegadlviaatd 70 
                                    +l+++g +vlvvGgG v+ r++  l+++gakv vv+ e   +++el+++ae+            +++++ +a +v++at+
  gi|118431477|ref|NP_147976.2|   7 VLRVRGARVLVVGGGGVGGRRAVLLASKGAKVRVVSLE---FSQELLRAAERLgielieggfgeARRHIPWASIVVIATP 83 
                                    5789**********************************...99988887765544444444333578899********** PP

                  NAD_binding_7  71 drelneriaeaakarrilvnvadkpelcdfifp 103
                                    ++ + e+ia++a ++++lvnva ++ l++  fp
  gi|118431477|ref|NP_147976.2|  84 HTGEAEEIAREALKAGKLVNVAADHRLGNLLFP 116
                                    ************99******************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.4
                  NAD_binding_7  19 Aarkvrklleagakvtv 35 
                                    A++k+  ll+ + +v  
  gi|118431477|ref|NP_147976.2| 141 ALEKIIELLDGDEEVEC 157
                                    56666666666665544 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 !   19.1   0.1   1.6e-06    0.0018       2      88 ..      14     103 ..      13     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                                    EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS.HHHHHTCT.TESEEEE-S-G.GGHHHH CS
                   GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd.leelladp.eidavivatpn.gtheel 78 
                                    rv+++G+G +g + +  l +s ++++v  +  + +++  ++ae++g+e  +  + e  ++   + +v++atp  g+ ee+
  gi|118431477|ref|NP_147976.2|  14 RVLVVGGGGVGGRRA-VLLAS-KGAKVRVVSLEFSQELLRAAERLGIELIEGgFGEARRHIpWASIVVIATPHtGEAEEI 91 
                                    89********88887.67777.9*****9999****************88877445544433899*******9899**** PP

                                    HHHHHHTT-..E CS
                   GFO_IDH_MocA  79 akaaleagk..h 88 
                                    a++al+agk  +
  gi|118431477|ref|NP_147976.2|  92 AREALKAGKlvN 103
                                    ********9444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   5.6e-06    0.0063      26      77 ..      10      63 ..       6     106 .. 0.65
   2 ?   -1.7   0.0       1.3   1.5e+03      35      68 ..     127     160 ..     119     184 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                                   B---EEEEESTS.HHHHHHHHHH.HHTT-EEEEEESSHHHHHHHHHTTTCECEE CS
                    AlaDh_PNT_C 26 vepakvlviGgG.vaGlqAiata.kglgakVtvlDvrparleqleslgakfvev 77
                                   v+ a+vlv+GgG v G  A+  a kg + +V+ l+ +++ l+  e lg + +e 
  gi|118431477|ref|NP_147976.2| 10 VRGARVLVVGGGgVGGRRAVLLAsKGAKVRVVSLEFSQELLRAAERLGIELIEG 63
                                   789******876166666766552344555566788899999999998886654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                    STSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                    AlaDh_PNT_C  35 GgGvaGlqAiatakglgakVtvlDvrparleqle 68 
                                    G+   G++ +a+ ++l+ ++++lD ++++   le
  gi|118431477|ref|NP_147976.2| 127 GVTSLGVSGLAARRALEKIIELLDGDEEVECLLE 160
                                    4444444455555667777777777777655555 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 !   15.2   0.1   1.2e-05     0.013      73     116 ..      11      55 ..       3      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                    TT-EEEEES-.TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHH CS
                           PCMT  73 kgarvLevGs.GsGyltavlarlvgekgrvvsierikelveeakr 116
                                    +garvL vG+ G G + avl    g+k rvvs+e ++el ++a+r
  gi|118431477|ref|NP_147976.2|  11 RGARVLVVGGgGVGGRRAVLLASKGAKVRVVSLEFSQELLRAAER 55 
                                    699*****8626899*************************99986 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.5e-05     0.028      32     111 ..       8      94 ..       2     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                                    S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEEC.....SHHHHHHH-SEEEE-S--STT CS
                   2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelv.....sleellaesDivslhlpltpe 104
                                     +++g +v ++G G +G + a +l++ g+kv +++   ++e   ++e+lg+el      +    + ++ iv++++p t e
  gi|118431477|ref|NP_147976.2|   8 LRVRGARVLVVGGGGVGGRRAVLLASKGAKVRVVSLEFSQELlrAAERLGIELIeggfgEARRHIPWASIVVIATPHTGE 87 
                                    5789******************************9998877677666677664422112677889999999999999999 PP

                                    TTTSBSH CS
                   2-Hacid_dh_C 105 trhlina 111
                                     +++  +
  gi|118431477|ref|NP_147976.2|  88 AEEIARE 94 
                                    8886544 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   8.8e-05     0.099      13      42 ..       7      36 ..       3      45 .. 0.87
   2 ?   -0.2   0.0      0.45   5.1e+02     188     233 ..     125     174 ..      70     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                                   HHHHHTSEEEEE--SHHHHHHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 13 qekLrdskvllvGaGglGsellknLalsGv 42
                                     ++r ++vl+vG Gg+G   +++La  G 
  gi|118431477|ref|NP_147976.2|  7 VLRVRGARVLVVGGGGVGGRRAVLLASKGA 36
                                   568999********************9886 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.45
                                    B-HHHHHHHHHHHHHHHHHHH....TTBCGGGCCEEEECCTTTTEEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 188 aiatttavvaglaalellkll....sgkeklenslltqvdllesrfenve 233
                                    +++ t   v+glaa+ +l+ +    +g e+ e  l t  +l++  fe ve
  gi|118431477|ref|NP_147976.2| 125 LVGVTSLGVSGLAARRALEKIiellDGDEEVECLLETHGRLKRLLFEVVE 174
                                    46666666777777777766656666666666666666777777666666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.1   4.6e-05     0.052       2      35 ..      15      48 ..      14      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                   v+V+G+G+ G + A+ +a +G+kv vv+ e++++
  gi|118431477|ref|NP_147976.2| 15 VLVVGGGGVGGRRAVLLASKGAKVRVVSLEFSQE 48
                                   9****************************99876 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 ?   13.1   0.5   8.5e-05     0.096       1     104 [.      14     112 ..      14     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                                    EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCH.HHH CS
                 Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpa.gvs 79 
                                    +v +vG+ G  G++ + l ++  +v +v l  s++    + ae+ +   e  +  + +     +  + iv+ a+p+ g +
  gi|118431477|ref|NP_147976.2|  14 RVLVVGGGGVGGRRAVLLASKGAKVRVVSLEFSQE--LLRAAERLG--IELIEGGFGE-ARRHIPWASIVVIATPHtGEA 88 
                                    6899**99999999999988999999999988887..344444444..3466666777.56788899********95689 PP

                                    HHHHHHHHHTTSEEEESSSTTTTST CS
                 Semialdhyde_dh  80 kelapklaeagvkviDlssdfRlkd 104
                                    +e+a+++++ag  ++  ++d+Rl +
  gi|118431477|ref|NP_147976.2|  89 EEIAREALKAGK-LVNVAADHRLGN 112
                                    9**********7.789999999866 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.9   5.2e-05     0.059       3      31 ..      14      42 ..      12      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlve 31
                                    Vl+VG+G +G   a lL+++G +v++v 
  gi|118431477|ref|NP_147976.2| 14 RVLVVGGGGVGGRRAVLLASKGAKVRVVS 42
                                   79************************995 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 ?   12.0   0.4   0.00013      0.14       2      36 ..      15      51 ..      14      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S..-HHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi..seeale 36
                                   v v+G G +G   a ++as+g +V++v    s+e l+
  gi|118431477|ref|NP_147976.2| 15 VLVVGGGGVGGRRAVLLASKGAKVRVVSLefSQELLR 51
                                   78**********************9997742444444 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00024      0.27       1      27 [.      15      41 ..      15      94 .. 0.77
   2 ?   -1.5   0.0       1.5   1.7e+03      82     110 ..     139     167 ..     124     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtli 27
                                   ++++G G++G+  a+ La +ga+v ++
  gi|118431477|ref|NP_147976.2| 15 VLVVGGGGVGGRRAVLLASKGAKVRVV 41
                                   68*****************99995544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                    HHHHHHHGGGECTCEEEEEESSSSCHHHH CS
                           ApbA  82 eealeeikplldpntvvlllqNGlgheee 110
                                      ale+i +lld +  v +l+++ g +++
  gi|118431477|ref|NP_147976.2| 139 RRALEKIIELLDGDEEVECLLETHGRLKR 167
                                    56788888888888888888877776655 PP

>> PPR_1  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00017      0.19      17      27 ..     195     205 ..     193     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                    HHHTS-HHHHH CS
                          PPR_1  17 lCkaGrvdeAf 27 
                                    lC++Grv+eA+
  gi|118431477|ref|NP_147976.2| 195 LCREGRVEEAM 205
                                    8*********8 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.19      25      79 ..      28      82 ..      25     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                Glyco_trans_4_5 25 atlLrsvgaevvvltlskkggllkeladrgikvleakaeelfklalkaDlvvlnt 79
                                   a+lL s ga+v v++l+  ++ll+ +++ gi+++e    e+ +    a +vv+ t
  gi|118431477|ref|NP_147976.2| 28 AVLLASKGAKVRVVSLEFSQELLRAAERLGIELIEGGFGEARRHIPWASIVVIAT 82
                                   899*******************************997777767667777777666 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   0.00019      0.21       2      48 ..      14      62 ..      13      73 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                   EEEEE--STTHHHHHHHHHHCT..SEEEEE-S-HHHHHHHCTTS-SS-- CS
                 UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig..hevigvDideekvdklnsgkipiye 48
                                   ++ v+G G vG+  a++la++g  + v+ +  ++e  ++ ++  i+++e
  gi|118431477|ref|NP_147976.2| 14 RVLVVGGGGVGGRRAVLLASKGakVRVVSLEFSQELLRAAERLGIELIE 62
                                   899*******************444445555666666665555555555 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.27      10      85 ..      10      84 ..       5     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                   .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHH.HHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                   Shikimate_DH 10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlera.kelaeelkgeeiealkleelkellaeadvvisatas 85
                                   +++++vl++G G ++ + a  L++kg+k v v+  ++++   + ae+l g e+    + e ++++  a +v++at +
  gi|118431477|ref|NP_147976.2| 10 VRGARVLVVGGGGVGGRRAVLLASKGAK-VRVVSLEFSQElLRAAERL-GIELIEGGFGEARRHIPWASIVVIATPH 84
                                   6789***********************9.7777554443303334444.5567777899999999999999999865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1    0.0011       1.2       1      30 [.      14      43 ..      14      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvver 30
                                   +v+vvGgG +g   A  la  g+kV vv  
  gi|118431477|ref|NP_147976.2| 14 RVLVVGGGGVGGRRAVLLASKGAKVRVVSL 43
                                   79***********************99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 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:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1719.32
//
Query:       gi|14601439|ref|NP_147977.1|  [L=240]
Description: uroporphyrinogen-III synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   54.3   0.1    1.4e-14   54.1   0.1    1.0  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   0.1   7.6e-19   1.4e-14      10     230 ..      26     226 ..      18     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 7.6e-19
                                   TTEEEEE---EECCECCHHHHHHHHHT.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHHHHHHT CS
                          HEM4  10 rGaeplelPlieiepaedraelraalddleagkydwliftSanavealfealkreeedvkalaslkvaavGpaTaraLeel 90 
                                   +G+  + +P++ ++ +e +   +++l++l   +  +l +tS+++ e l+     + e+++a    +v+avGp+Tar+L e 
  gi|14601439|ref|NP_147977.1|  26 LGGSTFWIPVMGFREVEGW--RNSLLRALR--RCPVLGITSPRGAELLAR----APEVLEAA--ERVYAVGPQTARVLVEM 96 
                                   6888888999999984332..334445555..788************444....44566654..59************995 PP

                                   .T---SEE-..SSSHHHHGGGS-.---EEE.EEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHHHHHTT- CS
                          HEM4  91 .glrvdlvpseegtaegLaeelaeslagkr.vlllrgeiarddlaegLeergaevdevevYetvpaeeepeelkealkage 169
                                    g++++ vps+ +++ ++++e  ++ ag+r ++l r+   ++ l +g e  g++v e  vYe       + e+ e+  + +
  gi|14601439|ref|NP_147977.1|  97 aGVKPV-VPSSGYSVSSMLKE--AEAAGERcIVLARS---KAGLGKGVEGVGLRVLEEAVYEP----VIRREMLEEAARLK 167
                                   388885.***99999999994..34555664666666...699********************....44555555555668 PP

                                   -SEEEESSHHHHHHHHHH-S-HHHHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHH CS
                          HEM4 170 vdavvftSpstvrnllellkdegdelkevkvaaiGptTaealkklglkvdvvaeeptaegl 230
                                   vd+ ++tS + +r  +++l++   + +   ++aiG +Ta a+ ++  ++ +v++ ++ e l
  gi|14601439|ref|NP_147977.1| 168 VDVAILTSGEIARMYCRALEKG--GGGAGGYVAIGVSTALAASSCPPRPLCVPSSARREEL 226
                                   ********************98..788889***********************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1802.09
//
Query:       gi|14601440|ref|NP_147978.1|  [L=202]
Description: hypothetical protein APE_1494 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.038   14.3   0.0      0.054   13.8   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.09   13.1   0.0        2.1    8.7   0.0    2.5  3  SpoU_sub_bind    RNA 2'-O ribose methyltransferase substrate 
       0.18   11.5   0.0       0.95    9.1   0.0    1.9  2  DNase-RNase      Bifunctional nuclease


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     9e-06     0.054      41      97 ..      27      83 ..      13     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                  HCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG..GHHHHHHHHHHHT-EEE CS
               Sacchrp_dh_NADP 41 aakalgvrfeaialdaenyeavLaallkegdlvvnlsppi..ssldvlkaCietgvhyv 97
                                  +a  ++  +   +++++++e++  ++ ++gdlvv+l+p       +v +a++e+g++ v
  gi|14601440|ref|NP_147978.1| 27 LA--RKLGVRVDTVQIKEVESMGGRVFNQGDLVVSLLPARggHLYTVDEAAREAGARHV 83
                                  22..6777777788889999999*****************85555999*******9876 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00035       2.1      35      65 ..      24      54 ..       3      58 .. 0.74
   2 ?   -2.4   0.0      0.98   5.8e+03      35      52 ..      57      74 ..      52      78 .. 0.80
   3 ?    1.4   0.0     0.067     4e+02      28      51 ..     119     143 ..     112     149 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00035
                 SpoU_sub_bind 35 llklakkrgikvelvdkekLdklsgtanHQG 65
                                    +la+k+g++v++v  ++ + + g++  QG
  gi|14601440|ref|NP_147978.1| 24 AARLARKLGVRVDTVQIKEVESMGGRVFNQG 54
                                  34566777****************9999888 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.98
                 SpoU_sub_bind 35 llklakkrgikvelvdke 52
                                  +++l+ +rg + ++vd++
  gi|14601440|ref|NP_147978.1| 57 VVSLLPARGGHLYTVDEA 74
                                  677888899999999986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.067
                 SpoU_sub_bind  28 adkrleellklakkr.gikvelvdk 51 
                                   + ++l+e+ ++++++ g +velv+ 
  gi|14601440|ref|NP_147978.1| 119 QREDLGEIASRLAAAtGARVELVSI 143
                                   5556788888888888******986 PP

>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00016      0.95      51      78 ..      18      45 ..       6      65 .. 0.88
   2 ?   -0.2   0.0      0.12   7.2e+02      56      77 ..     126     147 ..     115     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00016
                                  --HHHHHHHHHHHTTEEEEEEEEEEEET CS
                   DNase-RNase 51 PlthDLlasllealgakvervvItdled 78
                                   l  DL a l ++lg++v+ v+I+++e 
  gi|14601440|ref|NP_147978.1| 18 RLVEDLAARLARKLGVRVDTVQIKEVES 45
                                  5789********************9985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                                   HHHHHHHHTTEEEEEEEEEEEE CS
                   DNase-RNase  56 LlasllealgakvervvItdle 77 
                                   +   l  a+ga+ve v I+d++
  gi|14601440|ref|NP_147978.1| 126 IASRLAAATGARVELVSISDVK 147
                                   5667889999********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 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:                        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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1592.19
//
Query:       gi|118431478|ref|NP_147979.2|  [L=326]
Description: hypothetical protein APE_1495.1 [Aeropyrum pernix K1]
Scores for complete 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  141.7   0.0    3.1e-41  141.5   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 !  141.5   0.0   1.8e-45   3.1e-41       2     293 ..      12     305 ..      11     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 1.8e-45
                                    EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE...--SSSTT CS
                   Aldo_ket_red   2 lglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKv...dlrdaei 77 
                                    l +G  +l++  + +++ eal++lr a + G+++fDtA+vYg+g  e+llGea+         v++atKv    ++ + +
  gi|118431478|ref|NP_147979.2|  12 LAYGVYSLTGMyGSVEPGEALAILRFARSLGVEHFDTADVYGNGLGERLLGEAFPG----GRGVFVATKVgydFYSGGRP 87 
                                    78899999988999******************************************....99********9855555678 PP

                                    SSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--.HHHHHHH.HHTTT- CS
                   Aldo_ket_red  78 ksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfs.veqleka.kkkkkv 155
                                     +++ +e ++++l++sl+rLg++ vDll++H+p  ++ +  e++++l   ++eG+i   G++  +  +  e+a ++ +  
  gi|118431478|ref|NP_147979.2|  88 VRRYDREYLEKALRRSLERLGVESVDLLYIHNPPLEVLRGGEIYRFLSWARREGLIGMGGIALGPeTDVAEEAlEAVSHS 167
                                    899***********************************9***********************555588888887666777 PP

                                    -EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHH CS
                   Aldo_ket_red 156 kivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelsel 235
                                    ++ avq  yn+l+++    ++  +++ gv+ +a  p +gG l++  +++e  e+ + +++l+r+ ++++++  + +++ l
  gi|118431478|ref|NP_147979.2| 168 EVEAVQFVYNMLEQEPGYTIAAWARERGVAAVARVPHAGGVLDESITPSEA-EKLSDHRSLRRRGWYRWAFRVYGRMKPL 246
                                    8889********99999999999999*****************88886666.667888889999**************** PP

                                    HHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG-.---HHHHHHHHHHH CS
                   Aldo_ket_red 236 akehgvslaqlalryalsqpavgivipgasnieqlednldalel.klseeevaeldell 293
                                     +    ++ q a++++ls+ +v +v++ a++ e+l + ++  ++ +l+ ++v+e+++++
  gi|118431478|ref|NP_147979.2| 247 LEGLPGTPGQKAIAFILSSAPVDSVVLIARSRERLVEYVSPESTlQLPRSVVEEIRRIY 305
                                    ******************************************777***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2415.16
//
Query:       gi|14601442|ref|NP_147980.1|  [L=78]
Description: hypothetical protein APE_1495a [Aeropyrum pernix K1]
Scores for complete 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-12   45.4   0.3    6.3e-12   45.0   0.3    1.2  1  RHH_1           Ribbon-helix-helix protein, copG family
    2.7e-05   24.3   0.0    2.7e-05   24.3   0.0    1.2  1  RHH_8           Ribbon-Helix-Helix transcriptional regulator 
    4.3e-05   23.8   0.0    5.4e-05   23.5   0.0    1.1  1  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t
     0.0057   16.5   0.1     0.0083   16.0   0.1    1.3  1  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.3   1.4e-15   6.3e-12       2      39 .]       4      42 ..       3      42 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 1.4e-15
                                  EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHHH CS
                         RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyler 39
                                  v+++++e++++ +del+r+++ +SrSe+IR A+re+l+r
  gi|14601442|ref|NP_147980.1|  4 VTVKMPEMYVKGIDELVRAGRySSRSEVIRIAVRELLKR 42
                                  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 !   24.3   0.0     6e-09   2.7e-05       6      45 ..       4      43 ..       2      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6e-09
                         RHH_8  6 vtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLakh 45
                                  vt+ +  + +  iD Lv+ G Ys+R+++ir a+r+ L+++
  gi|14601442|ref|NP_147980.1|  4 VTVKMPEMYVKGIDELVRAGRYSSRSEVIRIAVRELLKRE 43
                                  788888899999***********************99875 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.2e-08   5.4e-05       8      44 ..       7      43 ..       2      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                                  ---HHHHHHHHHHHCTTS-SSHHHHHHHHHHHHHHHH CS
                ParD_antitoxin  8 vLgehfsafidsqvaaGrYgsaseviraaLrLLeere 44
                                   + e +   id  v aGrY s sevir a+r L +re
  gi|14601442|ref|NP_147980.1|  7 KMPEMYVKGIDELVRAGRYSSRSEVIRIAVRELLKRE 43
                                  566778888**********************887776 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 !   16.0   0.1   1.9e-06    0.0083      12      39 ..      16      43 ..      14      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
                                  XXXXXXXXXXXXXXXXXXXXXXX----- CS
                VapB_antitoxin 12 laeAirltglktKrEaVnlALreLiqrr 39
                                  ++e +r ++++ ++E+++ A+reL++r+
  gi|14601442|ref|NP_147980.1| 16 IDELVRAGRYSSRSEVIRIAVRELLKRE 43
                                  6788999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 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:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 592.25
//
Query:       gi|118431479|ref|NP_147981.2|  [L=324]
Description: hypothetical protein APE_1497.1 [Aeropyrum pernix K1]
Scores for complete 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  117.5   0.1    1.2e-16   60.6   0.0    2.3  2  AsnC_trans_reg2  AsnC-like ligand binding domain
    1.3e-05   24.6   0.0       0.14   11.8   0.0    2.8  2  HTH_24           Winged helix-turn-helix DNA-binding
    0.00025   20.8   0.0      0.032   14.0   0.0    2.5  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0073   16.4   0.0       0.86    9.8   0.0    3.0  3  LAL_C2           L-amino acid ligase C-terminal domain 2
     0.0085   16.0   0.0       0.14   12.0   0.0    2.5  2  MarR_2           MarR family
  ------ inclusion threshold ------
       0.04   14.1   0.0         15    5.7   0.0    2.6  3  Helicase_C_3     Helicase conserved C-terminal domain
      0.049   13.6   0.0        8.9    6.4   0.0    2.5  2  HTH_36           Helix-turn-helix domain
      0.076   13.1   0.0        3.8    7.6   0.0    2.7  2  HTH_20           Helix-turn-helix domain
      0.076   13.1   0.0         75    3.5   0.0    3.7  4  DUF3791          Protein of unknown function (DUF3791)
       0.14   11.9   0.0        1.2    9.0   0.0    2.2  2  LexA_DNA_bind    LexA DNA binding domain
       0.15   12.1   0.0         16    5.5   0.0    2.7  2  HTH_1            Bacterial regulatory helix-turn-helix protei
       0.17   11.9   0.0       0.73    9.9   0.0    2.0  2  HTH_Crp_2        Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0     5e-18   7.4e-15       5      82 .]      69     145 ..      65     145 .. 0.94
   2 !   60.6   0.0   7.9e-20   1.2e-16       1      82 []     233     319 ..     233     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 5e-18
                AsnC_trans_reg2   5 kanalvawkvpeerveevaevvaelpevtHcYeRew.pynlyfmvharseeeveevlaeiaaatgledyevLpstrefK 82 
                                    + +alva+ +  er+ e+a+ +   p vtH+Y+R++  yn+++++  +++ee+ + ++e a++++++d+  L+s +++K
  gi|118431479|ref|NP_147981.2|  69 T-AALVAFAA-GERYRELANLFRGDPDVTHNYLRNHpVYNVWIVIKRPTREELLRAVDEAARKVDVKDWIALFSRKTYK 145
                                    4.89999996.77**********************967****************************************9 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 7.9e-20
                AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRe......wpynlyfmvharseeeveevlaeiaaatgledyev 74 
                                    k+Gf++na+v+++ pe   ee++ + aelp  tH+++Re      w++ +yfmvha+s+e+++ vl+e +a++  +d + 
  gi|118431479|ref|NP_147981.2| 233 KAGFTENAMVVME-PEGGGEETCVRAAELPYSTHVVLREsyppgaWRHICYFMVHATSKERINMVLEEAKAKCRPRDAMA 311
                                    79***********.9***********************5555666*********************************** PP

                AsnC_trans_reg2  75 LpstrefK 82 
                                    ++s++++K
  gi|118431479|ref|NP_147981.2| 312 IFSLEDLK 319
                                    ****9998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   9.1e-05      0.14      22      48 .]      29      55 ..      26      55 .. 0.92
   2 !   10.0   0.0   0.00032      0.48      24      47 ..     199     222 ..     194     223 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.1e-05
                         HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlIk 48
                                   + A+ +glSp    +rlk+L ++G++k
  gi|118431479|ref|NP_147981.2| 29 DAARSVGLSPEKAVERLKELAKAGIVK 55
                                   6699*********************97 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00032
                         HTH_24  24 AerlglSpstvnrrlkrLeeeGlI 47 
                                    Aerlg+S+  v+ ++k L ++G++
  gi|118431479|ref|NP_147981.2| 199 AERLGISVDEVLSQVKLLLDKGVL 222
                                    9*********************96 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   2.2e-05     0.032       1      41 [.       5      48 ..       5      49 .. 0.95
   2 ?    4.2   0.0     0.025        37      19      39 ..     194     214 ..     193     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                  HTH_AsnC-type  1 LDeiDrkILeaLqed...aRisyaeLAervGlSestvlrRvrrL 41
                                   L e D+ +L +Lq +      +  + A+ vGlS++ + +R++ L
  gi|118431479|ref|NP_147981.2|  5 LSEKDIDLLMELQYNfqlTPDPIGDAARSVGLSPEKAVERLKEL 48
                                   6789*************************************987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                  HTH_AsnC-type  19 syaeLAervGlSestvlrRvr 39 
                                    +y+  Aer+G+S ++vl  v+
  gi|118431479|ref|NP_147981.2| 194 PYSHAAERLGISVDEVLSQVK 214
                                    67788***********97665 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 ?   -1.4   0.0       1.9   2.8e+03      56      71 ..      35      50 ..      33      57 .. 0.82
   2 !    9.8   0.0   0.00058      0.86      48      75 ..     105     132 ..      95     133 .. 0.86
   3 ?    2.7   0.0     0.097   1.5e+02      42      73 ..     273     304 ..     271     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                         LAL_C2 56 gdtaeeaeaaaeeaaa 71
                                   g ++e+a+++++e+a+
  gi|118431479|ref|NP_147981.2| 35 GLSPEKAVERLKELAK 50
                                   6689999999998876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00058
                         LAL_C2  48 rlGyviatgdtaeeaeaaaeeaaaeiri 75 
                                    +  +++++ +t+ee+++a++eaa+++++
  gi|118431479|ref|NP_147981.2| 105 YNVWIVIKRPTREELLRAVDEAARKVDV 132
                                    56699********************997 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.097
                         LAL_C2  42 prssgdrlGyviatgdtaeeaeaaaeeaaaei 73 
                                    p+ ++  + y ++++ ++e     +eea a+ 
  gi|118431479|ref|NP_147981.2| 273 PPGAWRHICYFMVHATSKERINMVLEEAKAKC 304
                                    566788999******************98875 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   9.6e-05      0.14       8      53 ..      10      56 ..       5      58 .. 0.86
   2 ?    0.7   0.0      0.33     5e+02      26      49 ..     197     220 ..     191     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.6e-05
                                   HHHHHHHHCTTTSEE...EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  8 arvLaaLgrrpgrdl...tvgelarrlglsksavsrilkrLvaaGLver 53
                                    ++L++L  +    l    +g+ ar  gls+  +  +lk+L +aG v r
  gi|118431479|ref|NP_147981.2| 10 IDLLMELQYNFQ--LtpdPIGDAARSVGLSPEKAVERLKELAKAGIVKR 56
                                   678888888876..444599**************************987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.33
                                    HHHHHHTSSHHHHHHHHHHHHHTT CS
                         MarR_2  26 elarrlglsksavsrilkrLvaaG 49 
                                      a+rlg+s   v   +k L ++G
  gi|118431479|ref|NP_147981.2| 197 HAAERLGISVDEVLSQVKLLLDKG 220
                                    579******999999999999998 PP

>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.013        20      41      73 ..      20      53 ..      14      60 .. 0.80
   2 ?   -3.3   0.0       6.2   9.3e+03      21      42 ..      68      89 ..      62      90 .. 0.69
   3 ?    5.7   0.0      0.01        15      44      91 ..     115     162 ..     108     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                   Helicase_C_3 41 yrltplSl.rrAldaGltaeeiiefLerlskypv 73
                                   ++ltp  +  +A+++Gl+ e+ +e L++l+k  +
  gi|118431479|ref|NP_147981.2| 20 FQLTPDPIgDAARSVGLSPEKAVERLKELAKAGI 53
                                   67777777346899****************9776 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.2
                   Helicase_C_3 21 araaLaafAelesrpehahtyr 42
                                    +aaL afA  e+  e+a  +r
  gi|118431479|ref|NP_147981.2| 68 KTAALVAFAAGERYRELANLFR 89
                                   5677888888887777776665 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.01
                   Helicase_C_3  44 tplSlrrAldaGltaeeiiefLerlskypvPqaleylirdvarryGkl 91 
                                    t++ l rA+d    + ++ ++++ +s+     +++y++r+ ++r G+ 
  gi|118431479|ref|NP_147981.2| 115 TREELLRAVDEAARKVDVKDWIALFSRKTYKLSVKYDLREGISRSGRY 162
                                    788899********************779999************9985 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0059       8.9      32      55 .]      31      54 ..      30      54 .. 0.89
   2 ?    4.6   0.0     0.021        32      32      53 ..     199     220 ..     196     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0059
                         HTH_36 32 akrlglsknTvsraikeLeqlGyi 55
                                   a+  gls ++++  +keL+++G++
  gi|118431479|ref|NP_147981.2| 31 ARSVGLSPEKAVERLKELAKAGIV 54
                                   5667******************85 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                         HTH_36  32 akrlglsknTvsraikeLeqlG 53 
                                    a+rlg+s++ v + +k+L ++G
  gi|118431479|ref|NP_147981.2| 199 AERLGISVDEVLSQVKLLLDKG 220
                                    89****************9998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0026       3.8      28      57 ..      28      57 ..      11      59 .. 0.85
   2 ?    2.3   0.0      0.12   1.8e+02      30      54 ..     198     222 ..     194     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0026
                                   HHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 28 selaerldlskntlsyHLrvLeeagLvevv 57
                                   ++ a+ ++ls+  +  +L++L++ag+v++ 
  gi|118431479|ref|NP_147981.2| 28 GDAARSVGLSPEKAVERLKELAKAGIVKRI 57
                                   5667777999999**************975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.12
                                    HHHHHTS-HHHHHHHHHHHHHCTTE CS
                         HTH_20  30 laerldlskntlsyHLrvLeeagLv 54 
                                     aerl++s  ++  +++ L + g +
  gi|118431479|ref|NP_147981.2| 198 AAERLGISVDEVLSQVKLLLDKGVL 222
                                    79*****************998865 PP

>> DUF3791  Protein of unknown function (DUF3791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.05        75       7      27 ..      27      47 ..      26      51 .. 0.90
   2 ?   -2.8   0.0       4.5   6.7e+03      19      37 ..      82     102 ..      74     103 .. 0.77
   3 ?    1.9   0.0      0.16   2.4e+02       9      23 ..     197     211 ..     196     222 .. 0.85
   4 ?    2.5   0.0     0.098   1.5e+02      36      53 ..     280     297 ..     279     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.05
                        DUF3791  7 Ieeyarklglsgkevykllkk 27
                                   I + ar  gls+++++++lk+
  gi|118431479|ref|NP_147981.2| 27 IGDAARSVGLSPEKAVERLKE 47
                                   67889**************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                        DUF3791  19 kevykllk.ksgvl.dylidc 37 
                                    +e ++l++ + +v+ +yl ++
  gi|118431479|ref|NP_147981.2|  82 RELANLFRgDPDVThNYLRNH 102
                                    677888888888888888765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.16
                        DUF3791   9 eyarklglsgkevyk 23 
                                    + a++lg+s++ev+ 
  gi|118431479|ref|NP_147981.2| 197 HAAERLGISVDEVLS 211
                                    579*********985 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.098
                        DUF3791  36 dcYevlHtqSkeyivedi 53 
                                     cY + H +Ske i   +
  gi|118431479|ref|NP_147981.2| 280 ICYFMVHATSKERINMVL 297
                                    69**********986655 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 ?    9.0   0.0   0.00077       1.2      30      58 ..      29      56 ..      20      58 .. 0.87
   2 ?   -0.5   0.0      0.72   1.1e+03      32      56 ..     199     222 ..     196     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00077
                                   HHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                  LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyier 58
                                   + ar +gl+ p+ + e+Lk L++ G+++r
  gi|118431479|ref|NP_147981.2| 29 DAARSVGLS-PEKAVERLKELAKAGIVKR 56
                                   568999997.99**************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.72
                                    HHHHTS-.HHHHHHHHHHHHHTTSE CS
                  LexA_DNA_bind  32 aralglkSpsaveehLkaLerKGyi 56 
                                    a++lg++    v ++ k L  KG++
  gi|118431479|ref|NP_147981.2| 199 AERLGIS-VDEVLSQVKLLLDKGVL 222
                                    6777875.8899999********97 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.05        75      18      37 ..      29      48 ..      27      51 .. 0.89
   2 ?    5.5   0.0     0.011        16      17      37 ..     196     216 ..     192     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.05
                                   HHHHHHTS-HHHHHHHHHHH CS
                          HTH_1 18 rAAeeLglsqpavsrqikrL 37
                                    AA+ +gls+  +  ++k+L
  gi|118431479|ref|NP_147981.2| 29 DAARSVGLSPEKAVERLKEL 48
                                   6****************998 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                                    HHHHHHHTS-HHHHHHHHHHH CS
                          HTH_1  17 trAAeeLglsqpavsrqikrL 37 
                                    + AAe+Lg+s   v  q+k L
  gi|118431479|ref|NP_147981.2| 196 SHAAERLGISVDEVLSQVKLL 216
                                    78********99999999865 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 ?    9.9   0.0   0.00049      0.73      26      53 ..      29      56 ..      11      64 .. 0.89
   2 ?   -2.0   0.0       2.4   3.6e+03      28      50 ..     199     221 ..     189     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00049
                                   HHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                      HTH_Crp_2 26 elAsmlGltretvsrilseLkreglisr 53
                                   + A+ +Gl++e     l+eL ++g+++r
  gi|118431479|ref|NP_147981.2| 29 DAARSVGLSPEKAVERLKELAKAGIVKR 56
                                   66999********************995 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                                    HHHTTSSHHHHHHHHHHHHHTTS CS
                      HTH_Crp_2  28 AsmlGltretvsrilseLkregl 50 
                                    A++lG++   v    + L ++g+
  gi|118431479|ref|NP_147981.2| 199 AERLGISVDEVLSQVKLLLDKGV 221
                                    89999999888888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2518.77
//
Query:       gi|118431480|ref|NP_147982.2|  [L=411]
Description: threonine dehydratase [Aeropyrum pernix K1]
Scores for complete 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-84  284.2   5.2    1.6e-84  283.8   5.2    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
     0.0055   16.4   0.0      0.018   14.8   0.0    2.0  1  ACT       ACT domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.063   13.3   0.0    1.8  1  ACT_6     ACT domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.8   5.2   2.7e-88   1.6e-84       3     294 .]      27     313 ..      25     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 283.8 bits;  conditional E-value: 2.7e-88
                                    GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                           PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvt 82 
                                     g+  TPl ++  ls+ +g++++lKlE+l++tgSfK+Rg  + l r+ e+ + ++vv+as+GNh++++A+aa+ +Glk++
  gi|118431480|ref|NP_147982.2|  27 RGAHVTPLDKSTTLSRITGAEVYLKLENLQKTGSFKVRGPLFKLGRALEKGSVEGVVAASAGNHAQGVAYAASFYGLKSV 106
                                    56778*****************************************55555***************************** PP

                                    EEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEE CS
                           PALP  83 ivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavv 162
                                    iv+p+ a+p+kv+++r++Gaevv+ g+ +dea ++a+++a+e +g+ lv++fd+p +++g gti++E +eq  gk+d+v+
  gi|118431480|ref|NP_147982.2| 107 IVMPELAPPAKVKATRSYGAEVVLHGRVVDEAFKLAEKIAEE-RGYMLVHPFDDPEIMAGNGTIAWEAYEQG-GKFDTVI 184
                                    ******************************************.*************************7666.6****** PP

                                    EE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEE CS
                           PALP 163 vpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdeivt 242
                                    vpvGgGgli+G++  +++  p v+vigve+e ++++ +s+++g++ +v+v++++adgl +++p++l+ ++++ lvd++v+
  gi|118431480|ref|NP_147982.2| 185 VPVGGGGLISGVVSVVRKLMPGVKVIGVEAEAAPKFVESFKEGKPIEVEVTHSLADGLVTKKPGRLTYPIVKHLVDKVVA 264
                                    ******************************************************************************** PP

                                    EEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                           PALP 243 vsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                    v++ e+++am ll +r +i++e ++aa++aal    a+ +k++ +++vi++g
  gi|118431480|ref|NP_147982.2| 265 VDEHEIASAMYLLLERSKILAEGAGAAGVAAL---LARVVKPKGKTLVIVSG 313
                                    ********************************...88888888889999998 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     3e-06     0.018       8      60 ..     343     399 ..     334     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-06
                                    ESSTTHHHHHHHHHHHTTSEEEEEEEEEESTT....ECEEEEEEEEEEHHHHHHHHH CS
                            ACT   8 pDrPGlLarvfgaladrgiNidsieqrssedk....vagivfvvivvdeedleevle 60 
                                    pD PG L +v+ ++a+   N++ i + + +++     a+ ++v +v++   l e+le
  gi|118431480|ref|NP_147982.2| 343 PDIPGQLYKVLEVIAEKRCNVVDIIHDRLHPRispgMARVTIVLEVPERMLLFELLE 399
                                    7************************99999888765555555555555555555555 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.063      10      46 ..     343     379 ..     334     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                          ACT_6  10 pdrpGltasLtsvlaefgvnilDieqavihgrlsLgl 46 
                                    pd pG++ ++++v+ae ++n++Di   ++h r s g+
  gi|118431480|ref|NP_147982.2| 343 PDIPGQLYKVLEVIAEKRCNVVDIIHDRLHPRISPGM 379
                                    799*********************8888887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3407.81
//
Query:       gi|118431481|ref|NP_147983.2|  [L=133]
Description: ribonuclease UK114 [Aeropyrum pernix K1]
Scores for complete 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-39  135.2   0.0    1.2e-39  135.0   0.0    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.0   6.7e-44   1.2e-39       2     119 ..      12     127 ..      11     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 6.7e-44
                                    TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGHHH CS
                  Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladiedfae 81 
                                    e+ap++++pYsqav++g +++vsGq+p++petg l eg ++e +++al+nlka+++ ag s++d+Vkvtv+++di++f e
  gi|118431481|ref|NP_147983.2|  12 ETAPKPVGPYSQAVESGCFMFVSGQIPINPETGALEEGGFKESAKRALDNLKAIVEGAGYSMDDIVKVTVYITDISRFSE 91 
                                    579***************************************************************************** PP

                                    HHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEE CS
                  Ribonuc_L-PSP  82 vnevyaeafdelkeaParsaveVaaLpkgakvEIeaia 119
                                    +nevy e+f+ ++  Par++v+VaaLp ga +E+ea+ 
  gi|118431481|ref|NP_147983.2|  92 FNEVYREYFNRPY--PARAVVGVAALPLGAPLEVEAVL 127
                                    ************7..********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1016.19
//
Query:       gi|118431482|ref|NP_147984.2|  [L=164]
Description: hypothetical protein APE_1503.1 [Aeropyrum pernix K1]
Scores for 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-11   41.9   0.0      4e-09   36.3   0.0    2.1  1  DOT1             Histone methylation protein DOT1
    5.7e-10   39.8   0.0    7.5e-10   39.4   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    6.7e-08   32.6   0.0    8.8e-08   32.2   0.0    1.1  1  Methyltransf_18  Methyltransferase domain
    6.7e-08   31.9   0.0    8.3e-08   31.6   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.7e-07   31.1   0.1    2.5e-07   30.6   0.1    1.3  1  Methyltransf_31  Methyltransferase domain
    1.2e-06   29.0   0.0    1.6e-06   28.7   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    3.5e-05   23.2   0.0    4.4e-05   22.9   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    3.8e-05   23.5   0.1     0.0013   18.4   0.1    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    4.2e-05   23.0   0.0    5.1e-05   22.7   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00011   22.1   0.0    0.00014   21.7   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00013   21.5   0.0    0.00017   21.1   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
    0.00013   21.6   0.0    0.00017   21.1   0.0    1.1  1  MTS              Methyltransferase small domain
    0.00076   18.9   0.0      0.001   18.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0014   18.2   0.0     0.0017   17.9   0.0    1.2  1  TrmK             tRNA (adenine(22)-N(1))-methyltransferase
     0.0014   18.0   0.0     0.0018   17.7   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0044   17.7   0.0     0.0058   17.3   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
     0.0057   16.7   0.0     0.0069   16.4   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
     0.0073   15.5   0.0       0.01   15.0   0.0    1.1  1  Methyltransf_20  Putative methyltransferase
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.014   15.0   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.017   15.0   0.0       0.02   14.7   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
      0.037   13.6   0.0      0.045   13.3   0.0    1.1  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.041   14.9   0.0      0.055   14.5   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
       0.13   11.8   0.1       0.16   11.6   0.1    1.2  1  MetW             Methionine biosynthesis protein MetW
       0.14   11.8   0.0       0.18   11.5   0.0    1.1  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


Domain annotation for each model (and alignments):
>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   5.4e-12     4e-09      25     156 ..      13     129 ..       8     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.4e-12
                                    -B-HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EE CS
                           DOT1  25 EllpeflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakie 104
                                     + pe++ ++l+ ++lk++dvF+DLG G G+vv+ a  ++++k++v vE  d+  + a+k++ee        G+   +ie
  gi|118431482|ref|NP_147984.2|  13 PTRPELIPKILELLDLKEDDVFYDLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEEE-------GVS-DRIE 84 
                                    57899***********************************************9999888877653.......332.2344 PP

                                    EESS-STT-HHHHHHGGG-SEEEE--TT--HHHHHHHH.HHHTT--TT-EEEE CS
                           DOT1 105 firksFvenekveeiieeadvilvNNfaFdaelnkqlk.ellqdlkegtkiis 156
                                    fi+++F      ++ +++a+ +++      +++n++lk +l  +l++gt+i++
  gi|118431482|ref|NP_147984.2|  85 FINNDFF-----KTPLKDATAVYM---YLLTSVNESLKpKLARELRDGTRIVT 129
                                    4444433.....333344444433...22344555553144455666666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0     1e-12   7.5e-10       3      90 ..      36     122 ..      34     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1e-12
                                    EET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   3 dlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    dlGcG Gr+++++ k+   +k ++v+  ++++++ar++aeeeg+  ++ef++ d+ + p++d+   +v++ + l  ++++
  gi|118431482|ref|NP_147984.2|  36 DLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVsdRIEFINNDFFKTPLKDA--TAVYM-YLLTSVNES 112
                                    9***************878*****************************************995..45555.445666666 PP

                                    HHHHHHHHHH CS
                Methyltransf_25  81 dlekalkeia 90 
                                      +k+ +e++
  gi|118431482|ref|NP_147984.2| 113 LKPKLARELR 122
                                    6666666665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.2e-10   8.8e-08      13      78 ..      29      94 ..      19     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.2e-10
                Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78
                                   ++++++ D G+  g + i++vk+ ++kk++ ++ ++  +++a++++e++g++d+ie++ +d +++ 
  gi|118431482|ref|NP_147984.2| 29 KEDDVFYDLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVSDRIEFINNDFFKTP 94
                                   467899***************************************************999877665 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.1e-10   8.3e-08      16      92 ..      16      97 ..      14     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.1e-10
                                   HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHH CS
                         RrnaAD 16 kkvineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpe 92
                                   + +i +Il+ l+l+e++  +++g G G    e +k    k+ v +E + +L+k+ +kk +    + +++ +++Df k+ ++ 
  gi|118431482|ref|NP_147984.2| 16 PELIPKILELLDLKEDDVFYDLGCGDGRVVIEAVKKTrvKKAVCVETRDDLVKEARKKAEeegVSDRIEFINNDFFKTPLKD 97
                                   67899**********************988777665557********************999999**********9987765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.1   3.4e-10   2.5e-07       3      72 ..      30      97 ..      28     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.4e-10
                Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklled 72
                                   ++ +++DlGCG G+ ++e+ ++    ++ v ++   + ++ Ar++a++ g++ ++eF   d+++ +  l+d
  gi|118431482|ref|NP_147984.2| 30 EDDVFYDLGCGDGRVVIEAVKKT-RVKKAVCVETRDDLVKEARKKAEEEGVSdRIEFINNDFFKTP--LKD 97
                                   677899**************654.45789*********************999**********988..665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   2.1e-09   1.6e-06       2      66 ..      36     104 ..      35     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.1e-09
                                    EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEE CS
                Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvv 66 
                                    d+GcG Gr++ +  k+   ++ v+v++ + ++k a++ka+eeg+  ++ef+  d+ k+p++d++    +
  gi|118431482|ref|NP_147984.2|  36 DLGCGDGRVVIEAVKKTrvKKAVCVETRDDLVKEARKKAEEEGVsdRIEFINNDFFKTPLKDATAVYMY 104
                                    9*******99988855558*******************************************7543333 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.9e-08   4.4e-05      53     133 ..      21     103 ..      17     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.9e-08
                                    HHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-E.EEEEE-HHHHHHHHHHS.-----TTEEEEES-TTTS-----SE CS
                 Methyltransf_2  53 kvleafdleglkslvDvGGGtGalakaivsayPtik.vivfDlpeVveaAkehl.sageeervefvgGdffkdslPeaDa 130
                                    k+le  dl++  +++D+G G G ++ ++v++    k v+v    + v++A+++  + g ++r+ef++ dffk +l +a a
  gi|118431482|ref|NP_147984.2|  21 KILELLDLKEDDVFYDLGCGDGRVVIEAVKKTRVKKaVCVETRDDLVKEARKKAeEEGVSDRIEFINNDFFKTPLKDATA 100
                                    799*******************888777776665551555566789******9978999*************99999999 PP

                                    EEE CS
                 Methyltransf_2 131 ill 133
                                    + +
  gi|118431482|ref|NP_147984.2| 101 VYM 103
                                    887 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.8e-06    0.0013      19     116 ..      21      94 ..      12     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                                    HHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHH CS
                        UPF0020  19 alvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaek 98 
                                     +++l ++k++++++D  CG G + IEa    ++++                       k ++++    +v+ ar++ae+
  gi|118431482|ref|NP_147984.2|  21 KILELLDLKEDDVFYDLGCGDGRVVIEAVK--KTRV----------------------KKAVCVETRDDLVKEARKKAEE 76 
                                    578888899999999999999999999743..3333......................2478****************** PP

                                    TT-GGGEEEEE--GGG-- CS
                        UPF0020  99 agvgdliefsqadaakLr 116
                                     gv+d+ief + d+ k +
  gi|118431482|ref|NP_147984.2|  77 EGVSDRIEFINNDFFKTP 94 
                                    *********999987766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.8e-08   5.1e-05      44     120 ..      27     103 ..      19     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.8e-08
                                    -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEE CS
                Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvv 120
                                      k+   + D+ +G g + ++  ++ + k k v ++  ++++k+++kk++eeg++ +ief++ +  + p +d +  ++
  gi|118431482|ref|NP_147984.2|  27 DLKEDDVFYDLGCGDGRVVIEAVKKTRVK-KAVCVETRDDLVKEARKKAEEEGVSdRIEFINNDFFKTPLKDATAVYM 103
                                    567778899***********999998877.5667899*****************999*******99999999765443 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 !   21.7   0.0   1.8e-07   0.00014      58     136 ..      15      93 ..       9     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.8e-07
                                    -HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGT CS
                           PCMT  58 aphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkG 136
                                     p ++ ++lell+lk+ +   ++G+G G   ++ a    ++ ++v +e   +lv+ea+++ ++++++ ++ ++  D  k 
  gi|118431482|ref|NP_147984.2|  15 RPELIPKILELLDLKEDDVFYDLGCGDGRV-VIEAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVSdRIEFINNDFFKT 93 
                                    5888999*********************63.33333333445899******************99987888888886554 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.3e-07   0.00017       4      64 ..      33      91 ..      30     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-07
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSS.EEEEES-CCCHH CS
                 Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkN.lrilrgdalkvl 64
                                   v+ ++GcG G+++++  kk   k+ + +E r ++v+++ kk+e+++++  ++ +++d   ++
  gi|118431482|ref|NP_147984.2| 33 VFYDLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVSDrIEFINND---FF 91
                                   899******************************************886524444444...44 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.3e-07   0.00017      24      94 ..      23      95 ..      20     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.3e-07
                                   HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST CS
                            MTS 24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve 94
                                   le l+ ++++   DlGcG G + +++ k++   + ++v+     ++ a++ +e+++++  +e++++d +++  
  gi|118431482|ref|NP_147984.2| 23 LELLDLKEDDVFYDLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVSdrIEFINNDFFKTPL 95
                                   5667777777889********************************************999*******998765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06     0.001      53     120 ..      21      89 ..      17     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                                    HHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E.EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES- CS
                           CMAS  53 lileklelkpGmtlLdiGcGWGslvrraverydvk.vvglTlSkeqaklakkrvdeldlerkvevklld 120
                                     ile l+lk+ +   d+GcG G +v++av++  vk  v +   ++  k a+k+ +e++++++ e    d
  gi|118431482|ref|NP_147984.2|  21 KILELLDLKEDDVFYDLGCGDGRVVIEAVKKTRVKkAVCVETRDDLVKEARKKAEEEGVSDRIEFINND 89 
                                    58999**************************99963688888999999**********99998866655 PP

>> TrmK  tRNA (adenine(22)-N(1))-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.3e-06    0.0017       1      60 [.      34      93 ..      34     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                           TrmK  1 laDiGsDHAyLpiylvknnkvsvaiagevnegplesAkknvkkskleekievrlgdGlav 60
                                   ++D+G+  ++  i++vk+ +v+ a+ +e  +   ++A+k+ ++++ +++ie + +d ++ 
  gi|118431482|ref|NP_147984.2| 34 FYDLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVSDRIEFINNDFFKT 93
                                   58***************************************************9998864 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.5e-06    0.0018     154     257 ..      22     128 ..      17     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.5e-06
                           PrmA 154 aleklvkegeevl.DvGtGSGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadv 229
                                    +le l  +++ v+ D+G+G G   i a++k   kk+v v + +  vk a++ ae  +v++++e  ++++ +k   + a  
  gi|118431482|ref|NP_147984.2|  22 ILELLDLKEDDVFyDLGCGDGRVVIeAVKKTRVKKAVCVETRDDLVKEARKKAEEEGVSDRIEF-INNDFFKtpLKDATA 100
                                    67778777887777*******88884567899******************************87.667777645567888 PP

                           PrmA 230 ivaNILaevlielaedikklvkegglli 257
                                    +    L +v  +l +++++ +++g++++
  gi|118431482|ref|NP_147984.2| 101 VYMYLLTSVNESLKPKLARELRDGTRIV 128
                                    9999999999999999999999998877 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.8e-06    0.0058       2      72 ..      36     103 ..      35     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.8e-06
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                    ++GcG+G+++ +  +k++ ++ ++v+   + ++ a++k  +  +   +++e+ ++d ++++ +    +v++
  gi|118431482|ref|NP_147984.2|  36 DLGCGDGRVVIEAVKKTRVKKAVCVETRDDLVKEARKKAEE--EGVSDRIEFINNDFFKTPLK-DATAVYM 103
                                    89******************************555555444..45788*****9998887765.5555555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   9.2e-06    0.0069      14      94 ..      20      95 ..      14     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.2e-06
                Methyltransf_32 14 akllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeats 94
                                    k+l+   + +++    D+G+G g         +     k v+++++++lv++a+k ae+ g  +++r++f++++  ++  
  gi|118431482|ref|NP_147984.2| 20 PKILEL-LDLKEDDVFYDLGCGDGRVVIEAVK-K-TRVKKAVCVETRDDLVKEARKKAEEEG--VSDRIEFINNDFFKTPL 95
                                   555555.4566778889******976544444.3.3467899********************..99*****9998877655 PP

>> Methyltransf_20  Putative 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      0.01     120     197 ..      18      92 ..      15     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                Methyltransf_20 120 llekaverlkaegrpvrildiaaGhGryvldalekaeervesillrdyselnveqGraliaekglediarfekgdafd 197
                                    l+ k +e l  ++++v   d+ +G Gr v++a++k+    ++++  +  +  v++ r+ ++e+g++d ++f ++d f 
  gi|118431482|ref|NP_147984.2|  18 LIPKILELLDLKEDDV-FYDLGCGDGRVVIEAVKKTRV--KKAVCVETRDDLVKEARKKAEEEGVSDRIEFINNDFFK 92 
                                    6666677777776666.68**************99876..4444455566779********************99996 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.9e-05     0.014      44     107 ..      33      97 ..      20     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                    EEEETT-TTSHHHHHHHHTT.-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS CS
                  Cons_hypoth95  44 rvLDlfaGsGalglEAlSRg.akkavlvekdkeavkilkenleelkleeetaelkedaleallkl 107
                                     + Dl +G G + +EA+    +kkav+ve+ +  vk  +++ ee +++++++ +++d ++  lk 
  gi|118431482|ref|NP_147984.2|  33 VFYDLGCGDGRVVIEAVKKTrVKKAVCVETRDDLVKEARKKAEEEGVSDRIEFINNDFFKTPLKD 97 
                                    578999***********87438***************************9999999998877665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.7e-05      0.02       8      69 ..      17      91 ..      12     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                Methyltransf_23  8 elsdklerllpklraggrvLdiGcGtGillevl..rengfsvtgvDlspeaveiae............kakkaqkd 69
                                   el  k+++ll+ l+++    d+GcG+G++  ++  ++++++ + v+ ++ +v++a+            +++++ + 
  gi|118431482|ref|NP_147984.2| 17 ELIPKILELLD-LKEDDVFYDLGCGDGRVVIEAvkKTRVKKAVCVETRDDLVKEARkkaeeegvsdriEFINNDFF 91
                                   56778889997.99999999*******9888886556677************999866666666655544444444 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.1e-05     0.045       5      61 ..      35     102 ..      32     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.1e-05
                Methyltransf_15   5 lDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe.........l 61 
                                     Dl +G G  vi+  ++   +k +++e+  + ++ a + ae  gvsd+i ++  d+f+          
  gi|118431482|ref|NP_147984.2|  35 YDLGCGDGRVVIEAVKKtrVKKAVCVETRDDLVKEARKKAEEEGVSDRIEFINNDFFKtplkdatavY 102
                                    58889999999887665568999**********************************95555555440 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.4e-05     0.055       4      61 ..      38      93 ..      36     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-05
                Methyltransf_24  4 GvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseea 61
                                   G  +G    ++ +a+++++  + v+v++  +  +ea++ a+e+g++dr+++i+ d++++
  gi|118431482|ref|NP_147984.2| 38 G--CGDGR-VVIEAVKKTRVKKAVCVETRDDlVKEARKKAEEEGVSDRIEFINNDFFKT 93
                                   5..33333.455788888889*******88777889999999*************9665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00021      0.16      15      56 ..      32      74 ..      20     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                           MetW 15 srvldlGcGdGel.lellkeekqvdgrGleldeegvaecvakG 56
                                       dlGcGdG + +e +k+++  ++  +e+ ++ v+e+ +k 
  gi|118431482|ref|NP_147984.2| 32 DVFYDLGCGDGRVvIEAVKKTRVKKAVCVETRDDLVKEARKKA 74
                                   4567*******86278999999999*********999987763 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 ?   11.5   0.0   0.00023      0.18       8      97 ..      18     110 ..      16     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                    THHHHHCCS-..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCH.SHHHHHHHHH.TCTTGGC.T CS
                MethyltransfD12   8 llpeIkelipkdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykalikn.nveelikelekllekeelen 84 
                                    l+p I el++ + +++f+++ +G g V +ea k  ++kk++   + +dl+  ++++ ++  v + i+ + + ++k+ l++
  gi|118431482|ref|NP_147984.2|  18 LIPKILELLDLKEDDVFYDLGCGDGRVVIEAVKktRVKKAVCVETRDDLVKEARKKAEEeGVSDRIEFINNDFFKTPLKD 97 
                                    899*******9999***************998889*******************88877877777777777777777778 PP

                                    SHHHHHHHHHHHH CS
                MethyltransfD12  85 ereyfyelreefn 97 
                                     +  +++l ++ n
  gi|118431482|ref|NP_147984.2|  98 ATAVYMYLLTSVN 110
                                    8888888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1237.10
//
Query:       gi|118431483|ref|NP_147985.2|  [L=248]
Description: hypothetical protein APE_1505.1 [Aeropyrum pernix K1]
Scores for complete 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-88  294.4   0.0    5.5e-88  294.2   0.0    1.0  1  ATPase    KaiC
    6.2e-06   25.1   0.0    1.3e-05   24.0   0.0    1.4  1  GvpD      GvpD gas vesicle protein
    3.9e-05   23.3   0.0    5.7e-05   22.8   0.0    1.3  1  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.021   13.9   0.0      0.032   13.3   0.0    1.3  1  T2SSE     Type II/IV secretion system protein
      0.047   12.5   0.0      0.069   12.0   0.0    1.1  1  PPV_E1_C  Papillomavirus helicase
      0.059   12.6   0.0        0.1   11.8   0.0    1.4  1  Rad51     Rad51


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 !  294.2   0.0   1.8e-91   5.5e-88       1     230 [.       5     237 ..       5     238 .. 0.99

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 1.8e-91
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80 
                                    vktgI+g+D+il+gGip+++vvl++G+pGtGK+if+ q+l++g+++ gepgvfv++ee+++++r n++++Gwd++++e++
  gi|118431483|ref|NP_147985.2|   5 VKTGIPGMDDILYGGIPRRNVVLLSGGPGTGKSIFSYQYLWNGLRE-GEPGVFVALEEHPVQVRINMAQFGWDVREYERQ 83 
                                    79*****************************************999.********************************* PP

                         ATPase  81 gklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                    g++a++da++s++++a++      +d ed+  li+ l+eai++++akrv +Ds+++l y +k+ +aR++++ l+rvl++l
  gi|118431483|ref|NP_147985.2|  84 GLFAVVDAFTSGIGEAAKkeryvvTDPEDVGLLIDVLKEAIRDVGAKRVAVDSVSTL-YLAKPVLARRTVMLLKRVLSGL 162
                                    **************9998999*999********************************.********************** PP

                         ATPase 155 gvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvleek 230
                                    g+T+ilvs++s++e+++gg+gve+ ++dg+i+Ldl+e+++elvR+l+i+kmRgtkhs+++hpfeIt++gi v+++k
  gi|118431483|ref|NP_147985.2| 163 GTTSILVSQVSVTERGFGGPGVEH-AADGIIRLDLDEVDGELVRSLIIWKMRGTKHSMRRHPFEITDKGIIVYPDK 237
                                    ************************.************************************************986 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   4.4e-09   1.3e-05      13     207 ..      26     228 ..      21     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.4e-09
                           GvpD  13 llikGaPGtGktlftlrgl.dvlrresdvlyvstrvd..detvseay....fsgeaeld...ktalldllkdpleldldv 82 
                                    +l+ G PGtGk +f  ++l + lr+ ++ ++v+      +  ++ a     +    e +     a++d +  +++   ++
  gi|118431483|ref|NP_147985.2|  26 VLLSGGPGTGKSIFSYQYLwNGLREGEPGVFVALEEHpvQVRINMAQfgwdV---REYErqgLFAVVDAFTSGIGEAAKK 102
                                    6899*************99568999999999987665114445544433333...4444112557779999999877666 PP

                           GvpD  83 d..vPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlares.gvrlvlvletaan 159
                                    +  v  +  d+  l++ ++e         +a+ds  +   yla+       + ++k  l  l   s  v  v+v+e    
  gi|118431483|ref|NP_147985.2| 103 EryVVTDPEDVGLLIDVLKEAIRDVGAKRVAVDS--VSTLYLAKPVLARRTVMLLKRVLSGLGTTSiLVSQVSVTERGFG 180
                                    422777788999999998764444445568****..556689999999999********999877625789999998765 PP

                           GvpD 160 .srleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftlad 207
                                       +e+ +dG++ l++ e   g l+r+l + k+rG +   r +Pf ++d
  gi|118431483|ref|NP_147985.2| 181 gPGVEHAADGIIRLDLDEV-DGELVRSLIIWKMRGTKHSMRRHPFEITD 228
                                    1569************987.7************************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.9e-08   5.7e-05      13     155 ..       3     141 ..       1     175 [. 0.70

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                         AAA_25  13 adlaapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlr 91 
                                    +++++ +p  ++++ g +p+  ++ll G pgtGK+ + ++     + +G+           + ++v++E+   ++r  ++
  gi|118431483|ref|NP_147985.2|   3 DRVKTGIPGMDDILYGGIPRRNVVLLSGGPGTGKSIFSYQYLWNGLrEGE-----------PGVFVALEEHPVQVRINMA 71 
                                    567888999999*****************************999995555...........6799999999999999999 PP

                         AAA_25  92 avgeal...rddarllvld........lagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                    + g ++   ++++  +v+d        +a + e+  ++++++ g      +d l +ai++v g++ v +D++s ++
  gi|118431483|ref|NP_147985.2|  72 QFGWDVreyERQGLFAVVDaftsgigeAA-KkERYVVTDPEDVG----LLIDVLKEAIRDV-GAKRVAVDSVSTLY 141
                                    99977644433233333333333333211.11222222223333....3345577777775.58888888887765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.032     118     150 ..      12      44 ..       5      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                          T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyall 150
                                    ++++l   + +r ++l+sGg g+GK+++ y  l
  gi|118431483|ref|NP_147985.2|  12 MDDILYGGIPRRNVVLLSGGPGTGKSIFSYQYL 44 
                                    7788999999******************99876 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05     0.069     257     281 ..      18      42 ..      10      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                       PPV_E1_C 257 kgvPkknclvllGppntGkslfams 281
                                     g+P++n+++l G p tGks+f++ 
  gi|118431483|ref|NP_147985.2|  18 GGIPRRNVVLLSGGPGTGKSIFSYQ 42 
                                    489*******************975 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.5e-05       0.1      18      56 ..       4      42 ..       1      45 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                                   EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                          Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                   ++ tG   +D++L GGi+  ++  + G  ++Gk+ ++++
  gi|118431483|ref|NP_147985.2|  4 RVKTGIPGMDDILYGGIPRRNVVLLSGGPGTGKSIFSYQ 42
                                   689*******************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1922.46
//
Query:       gi|118431484|ref|NP_147986.2|  [L=433]
Description: inosine-5'-monophosphate dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-105  353.0   0.0   1.8e-105  352.8   0.0    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    4.9e-09   36.0   1.5    0.00043   19.8   2.0    2.6  2  NMO           Nitronate monooxygenase
    2.1e-07   30.3   7.2    6.4e-07   28.7   5.8    2.2  2  FMN_dh        FMN-dependent dehydrogenase
    6.5e-05   22.3   2.1    0.00011   21.6   2.1    1.3  1  DHO_dh        Dihydroorotate dehydrogenase
    9.6e-05   21.7   2.4    0.00014   21.2   2.4    1.2  1  Glu_synthase  Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.025   14.0   1.6       0.17   11.3   1.7    2.0  1  His_biosynth  Histidine biosynthesis protein
      0.026   13.9   1.5      0.058   12.7   1.5    1.5  1  ThiG          Thiazole biosynthesis protein ThiG


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 !  352.8   0.0  6.9e-109  1.8e-105       2     345 .]      14     428 ..      13     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 352.8 bits;  conditional E-value: 6.9e-109
                                    --GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH   2 ltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvkr 81 
                                    ltfddv ++p+ s+v+p++v+l+++++++i +++Plvs++mdtvte +mA alar G++gvih+n+  eeqa++v+ vk+
  gi|118431484|ref|NP_147986.2|  14 LTFDDVAILPGLSTVEPHDVELSSRVSRSIFVSTPLVSSPMDTVTEWRMAAALARLGAVGVIHRNMPREEQARHVSMVKS 93 
                                    8******************************************************************************9 PP

                                    S.....................................................................TTSXBXTTSX CS
                                    x.....................................................................xxxxxxxxxx RF
                          IMPDH  82 s.....................................................................pnaakdekgr 92 
                                                                                                          p  + d +gr
  gi|118431484|ref|NP_147986.2|  94 VspspwsevprirlpdglenyslileeldagaavvfgddgikgylvlerpdaqlwlekarylslyltrirPFPTIDGEGR 173
                                    9*********************************************************************99999***** PP

                                    B-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHH.HHHT.T-SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxx RF
                          IMPDH  93 llvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegaka.Liea.gadav 170
                                    l+vgaav+  +  l+r++ l ++g+d+lv+d+ah h+++ l+ ++++ k+v +++v+aGn+ t+eg+ + L++a ++ ++
  gi|118431484|ref|NP_147986.2| 174 LVVGAAVSPFD--LDRARLLEKSGADFLVIDVAHLHNRNALSSLSRLVKEV-SIDVVAGNLGTREGVLDtLARAeEVAGL 250
                                    **********5..9************************************9.7*************9762665426999* PP

                                    EE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 171 kvGiGpGsiCttrvvagvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAlaaGadavmlGsllagteEsp 246
                                    ++Gi +GsiC t +vag+ vp ltAv++++ a ++ g    +p+iaDGG+++ gd +kA+ aGa+avm G+l+ag +Esp
  gi|118431484|ref|NP_147986.2| 251 RMGISSGSICSTGEVAGAAVPTLTAVMNAVLALEELGlagrIPIIADGGVRNAGDAAKAIIAGASAVMGGRLFAGADESP 330
                                    ***********************************998899*************************************** PP

                                    SEEEEETTEEEEEEEETTSHHHHHH-.SS-TTS-..--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 247 geviliegrkyKeyrGmgslgamkkg.skdryfqkkeklvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieel 325
                                    g  i + ++ yK yrGm+s gam+++ + dry + ++k v+eGveg vpy g+v +++++l++gl++++gy+Ga+++++ 
  gi|118431484|ref|NP_147986.2| 331 GPRIRVGDKLYKPYRGMASRGAMERRfAVDRYSR-QAKAVEEGVEGLVPYTGPVVKTLYELAEGLKAALGYAGAQDVTSA 409
                                    ***********************665599***75.56*****************************************98 PP

                                    HHH-EEEEE-HHHHHHHS-- CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 326 kekakfvritaaglkeshvH 345
                                    + kak+ r+t +g +e ++H
  gi|118431484|ref|NP_147986.2| 410 W-KAKLARVTPTGSREIRPH 428
                                    7.89*************999 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.4e-05     0.036       8     162 ..      43     201 ..      36     243 .. 0.72
   2 !   19.8   2.0   1.7e-07   0.00043     181     235 ..     273     333 ..     247     418 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                            NMO   8 lkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkaltdkPfgvnlflpkkdaadraekykkel 87 
                                    + +  p+v ++m  +++ r+aaa +  G+ Gv+    +   + a  +  vk++   P     ++  +d +++   y  +l
  gi|118431484|ref|NP_147986.2|  43 IFVSTPLVSSPMDTVTEWRMAAALARLGAVGVIH-RNMPREEQARHVSMVKSVSPSPWSEVPRIRLPDGLEN---YSLIL 118
                                    557899***************************9.77777899999*******9999988877777777777...66666 PP

                            NMO  88 eeaalelnieegvr......fyrkvevvl.dekvevvsfgfglpteevvar.lkeagvvliptissvkearkvearGaDa 159
                                    ee  +++++  g+         ++ +  l  ek++  s+ +   ++++ +  + ++ v + ++    + ar +e++GaD 
  gi|118431484|ref|NP_147986.2| 119 EELDAGAAVVFGDDgikgylVLERPDAQLwLEKARYLSLYLTRIRPFPTIDgEGRLVVGAAVSPFDLDRARLLEKSGADF 198
                                    66666666666555554655333333333034666777666666555544303333333333334566777777777777 PP

                            NMO 160 liv 162
                                    l++
  gi|118431484|ref|NP_147986.2| 199 LVI 201
                                    776 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.7e-07
                            NMO 181 lfaLvpqvldavd.......iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakd 235
                                    l+a+++ vl   +       iP+iA GG+ ++ + a a+ +GAs+v  g  f +++es+ + 
  gi|118431484|ref|NP_147986.2| 273 LTAVMNAVLAL-EelglagrIPIIADGGVRNAGDAAKAIIAGASAVMGGRLFAGADESPGPR 333
                                    33333333333.25777788**************************8888899999998765 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   0.1     0.042   1.1e+02      79     108 ..     240     269 ..     227     277 .. 0.81
   2 !   28.7   5.8   2.5e-10   6.4e-07     256     304 ..     268     324 ..     262     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.042
                                    HHHHHHHHHTS-EEEETT-SS-HHHHHHHH CS
                         FMN_dh  79 alaraaakagipfvlstvastsleevaaaa 108
                                     lara + ag+ +++s+ + +s  eva aa
  gi|118431484|ref|NP_147986.2| 240 TLARAEEVAGLRMGISSGSICSTGEVAGAA 269
                                    37899999******************9754 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2.5e-10
                                    -HHHCHHHHHHHH..........SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                         FMN_dh 256 atidvLpeiveav........ggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                    a++ +L ++++av        +gri++++DgG+r+  D++kA+  GA+av+ GR f+
  gi|118431484|ref|NP_147986.2| 268 AAVPTLTAVMNAVlaleelglAGRIPIIADGGVRNAGDAAKAIIAGASAVMGGRLFA 324
                                    66666777766665556665567*******************************985 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   2.1   4.1e-08   0.00011     217     273 ..     261     320 ..     219     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.1e-08
                                    SSEEEEEGGGHHHH..HHHHHHHHHH.TTT.S-EEEESS--SHHHHHHHHHHTECEEEES CS
                         DHO_dh 217 ktGGlsGkalkdia..lkvirelykr.lkkeipiIgvGGiesgeDalekieaGAslvqvy 273
                                    +tG ++G+a+  +   ++ + +l +  l ++ipiI+ GG+  + Da   i aGAs+v  +
  gi|118431484|ref|NP_147986.2| 261 STGEVAGAAVPTLTavMNAVLALEELgLAGRIPIIADGGVRNAGDAAKAIIAGASAVMGG 320
                                    478888888865431245677776643789**************************9765 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 !   21.2   2.4   5.4e-08   0.00014     250     303 ..     267     320 ..     208     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.4e-08
                                    HB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-S CS
                   Glu_synthase 250 haGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgig 303
                                     a +P+++a+ +++ +l e gl  r+ +iadGg++ + d +ka++ GA av  g
  gi|118431484|ref|NP_147986.2| 267 GAAVPTLTAVMNAVLALEELGLAGRIPIIADGGVRNAGDAAKAIIAGASAVMGG 320
                                    3458*********************************************99766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.7   6.6e-05      0.17     182     223 ..     282     323 ..     184     327 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.6e-05
                                    HHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHH CS
                   His_biosynth 182 ltkelaeavkipviasGGvgsledlkelksegvdavivgsal 223
                                    +++el  a +ip+ia GGv++  d +++  +g++av+ g+++
  gi|118431484|ref|NP_147986.2| 282 ALEELGLAGRIPIIADGGVRNAGDAAKAIIAGASAVMGGRLF 323
                                    245666678899****************99999999999887 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.5   2.2e-05     0.058     172     210 ..     288     326 ..     266     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                                    HH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTS CS
                           ThiG 172 eeakvPvivDAGigspsdaaqamelGadavllntavaea 210
                                       ++P+i D G++++ daa+a+  Ga+av+     a a
  gi|118431484|ref|NP_147986.2| 288 LAGRIPIIADGGVRNAGDAAKAIIAGASAVMGGRLFAGA 326
                                    4558**************************976655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3441.45
//
Query:       gi|118431485|ref|NP_147988.2|  [L=153]
Description: hypothetical protein APE_1509.1 [Aeropyrum pernix K1]
Scores for complete 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-18   65.7   0.4    5.1e-18   65.4   0.4    1.1  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain


Domain annotation for each model (and alignments):
>> DUF296  Plants and Prokaryotes Conserved (PCC) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.4   2.8e-22   5.1e-18       1     106 [.      11     128 ..      11     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.8e-22
                                    TEEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT....EE-......S-EEEEEEEEEEEETT. CS
                         DUF296   1 rphvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee....kll......grfeilslsGtilpdg. 68 
                                    r++++++++Ged+++ ++++a+ ++   a+v ++iG ++++t ++++ +e    +++        +e+ +++G+i++++ 
  gi|118431485|ref|NP_147988.2|  11 RVYAVKIDEGEDVHSVLSSLAEAEDLGFAMV-TGIGGMAEATvAFYSPPEatyyTVDvkppegRVIEVAAMTGNIVKTSq 89 
                                    6899**************************9.**************99999877222667775689***********434 PP

                                    ...EEEEEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE-C CS
                         DUF296  69 ...lHlhvslagedgqvvgGhlaegplvaattvevvvaefe 106
                                       +H+hv+l+ ++g+ + Ghl++g  v+   +ev+v e++
  gi|118431485|ref|NP_147988.2|  90 gysVHIHVALGVSPGKSISGHLVKG--VVKPFMEVFVVELV 128
                                    589*********99*********99..559*******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1190.24
//
Query:       gi|118431486|ref|NP_147989.2|  [L=255]
Description: hypothetical protein APE_1510.1 [Aeropyrum pernix K1]
Scores for complete 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   50.2   0.1    5.2e-06   26.8   0.0    4.1  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     5e-05       0.9       7      51 ..      13      56 ..       7      60 .. 0.80
   2 !   26.8   0.0   2.9e-10   5.2e-06       8      55 ..      79     124 ..      74     126 .. 0.89
   3 ?    2.3   0.0     0.013   2.4e+02      11      33 ..     143     164 ..     131     176 .. 0.77
   4 !    5.8   0.0    0.0011        19      17      54 ..     207     243 ..     195     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5e-05
                                   SSCEEEETTSBHHHHHHHHH...HHTSSEEEEEETTT.BEEEEEEHHHH CS
                            CBS  7 rdvvtvppdttleealelmr...ekgvsrlPVVdedg.klvGivtlrDl 51
                                    + +t+ p+t+l++a+  +    +   +r+  V + g  + G+v   D+
  gi|118431486|ref|NP_147989.2| 13 APAITFEPSTSLGDAVSALLvlhK---HRI-LV-GRGvAVTGVVEPGDI 56
                                   5789************99654534...7**.88.688558899999998 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 2.9e-10
                                    SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    ++++v  dt+++ea+elm+++g+s l  Vd  g + G++t  D+l+a+
  gi|118431486|ref|NP_147989.2|  79 RPPVVGGDTPVGEAAELMVRTGLSTL-LVDLGG-VTGVFTSWDVLQAI 124
                                    5679999****************999.887566.************98 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.013
                                    EEETTSBHHHHHHHHHHHTSSEE CS
                            CBS  11 tvppdttleealelmrekgvsrl 33 
                                     v+pd+++e  le m++ g +++
  gi|118431486|ref|NP_147989.2| 143 RVSPDEPVEAGLEAMASFG-RAI 164
                                    699***********97644.344 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0011
                                    BHHHHHHHHHHHTSSEEEEEETTT.BEEEEEEHHHHHHH CS
                            CBS  17 tleealelmrekgvsrlPVVdedg.klvGivtlrDllra 54 
                                     l+e++  m++++  r+ VV  +g k++  + + D++ra
  gi|118431486|ref|NP_147989.2| 207 ALSEVVAAMVDAAT-RVAVV-HSGwKPLASLDEGDIVRA 243
                                    58999****99996.*****.7999***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1895.79
//
Query:       gi|14601452|ref|NP_147990.1|  [L=307]
Description: hypothetical protein APE_1512 [Aeropyrum pernix K1]
Scores for complete 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-06   27.0   0.1    8.4e-06   26.1   0.1    1.5  1  GHMP_kinases_C  GHMP kinases C terminal
     0.0089   16.3   0.7       0.02   15.1   0.7    1.7  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 !   26.1   0.1   9.4e-10   8.4e-06       5      81 ..     201     277 ..     196     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9.4e-10
                GHMP_kinases_C   5 lergdlellgellnlsqrs......elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                   + rgdl+   e+l ++q+       e   + ++  + l ++++++s++G   +kl ++++Gpt++++  +++ a+  ar l
  gi|14601452|ref|NP_147990.1| 201 IARGDLDIALEGLSSMQAGtgllfqEV--QGAVFRRDLMNIVDEASRNG---VKLAQSSWGPTLYTIS-HESTADSDARML 275
                                   667888888888888888888896444..88999999************...***************9.999999888877 PP

                GHMP_kinases_C  80 re 81 
                                   r+
  gi|14601452|ref|NP_147990.1| 276 RA 277
                                   65 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 !   15.1   0.7   2.3e-06      0.02       3      42 ..      72     111 ..      70     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.3e-06
                                   EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHH CS
                GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallglsleeakla 42 
                                   +i s+ P + GLGS + l++a+ +Allal gl+ + + la
  gi|14601452|ref|NP_147990.1|  72 KIASRPPRHMGLGSTTQLSLAASMALLALKGLRPSIPSLA 111
                                   67788899**********************9773223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2422.04
//
Query:       gi|118431487|ref|NP_147991.2|  [L=247]
Description: hypothetical protein APE_1514.1 [Aeropyrum pernix K1]
Scores for complete 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      3e-10   40.7   0.5    1.4  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 !   40.7   0.5   1.6e-14     3e-10       1     111 [.       5     126 ..       5     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.6e-14
                                    EEEEEESS-TTTTT....THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTC...TS-.EEE-TTSS CS
                   NTP_transf_3   1 aviLAGGrSsRmgg....dKallplggkpllervldalraagvdevvvvggd...eevlaalarl...gvr.vvededpg 69 
                                    +++LA+G S+R+ g    +K  + ++g pll + + +l+ agvd+v+vv+ +   + v + + ++   +v+ v+  + + 
  gi|118431487|ref|NP_147991.2|   5 GLVLAAGFSRRFRGllgvHKVAAGVRGYPLLCYPVTSLALAGVDRVFVVASQfnlN-VVELVLGHcpfRVSgVLISSLST 83 
                                    69**********877778*******************************9886532.33333322222333357777789 PP

                                    -SHHHHHHHHHHHH...SSSCEEEEETT-TT--HHHHHHHHHCH CS
                   NTP_transf_3  70 kgplaslaaalraaa..dadavlvlacDmPlltpelverllaaa 111
                                     g + sl  +lr+a+  ++  ++v ++D+++ +p++ +rl++a 
  gi|118431487|ref|NP_147991.2|  84 LGNGFSLVEGLREAGlrGSRCLAVSMADHVY-PPSIARRLIEAG 126
                                    *************77779999********98.99******9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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: 0.41u 0.19s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 2119.10
//
Query:       gi|118431488|ref|NP_147993.2|  [L=212]
Description: CDP-alcohol phosphatidyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-11   42.6   2.7    7.9e-11   42.6   2.7    2.4  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 !   42.6   2.7   4.4e-15   7.9e-11       2      66 .]      36      99 ..      35      99 .. 0.88
   2 ?   -0.8   1.1      0.16   2.8e+03       5       5 ..     174     174 ..     104     207 .. 0.59

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 4.4e-15
                                   -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   +Pn+++l+++l + +a+l +++  +l+++ ll+ ++s++D++DG +ARrl+  s+ G +lD ++D
  gi|118431488|ref|NP_147993.2| 36 TPNMLSLISFLTAAAAAL-FIAGGQLLVGGLLVQLSSVLDGVDGIVARRLRAASKAGGFLDTMLD 99
                                   8**********9888885.556666788888888******************999******9998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                                    H CS
                CDP-OH_P_transf   5 a 5  
                                    +
  gi|118431488|ref|NP_147993.2| 174 V 174
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1812.37
//
Query:       gi|14601456|ref|NP_147994.1|  [L=392]
Description: inositol-3-phosphate synthase [Aeropyrum pernix K1]
Scores for complete 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-20   72.1   0.0    5.7e-20   71.6   0.0    1.2  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
      0.041   13.9   0.1      0.099   12.7   0.1    1.6  1  Radical_SAM_C   Radical_SAM C-terminal domain


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 !   71.6   0.0   6.3e-24   5.7e-20       1     109 []     214     319 ..     214     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 6.3e-24
                                   SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE-GGG CS
                Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kYvpyl 78 
                                   G+T l   L+e+l+er+ +v si+++Ni+Gn D+++l+ +e++ +K+++Kssvv+di++++  +y      i    ++++l
  gi|14601456|ref|NP_147994.1| 214 GATPLTADLLEHLAERNRRVLSIAQFNIGGNLDFLALTLPEKNIMKEKTKSSVVKDILGYDVPHY------IkptGFLEPL 288
                                   99**********************************************************66544......33369***** PP

                                   TTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                Inos-1-P_synth  79 gDsKvaldeieseiflggkntielkleceDS 109
                                   gD+K+  ++i  ++f g + +++++++++DS
  gi|14601456|ref|NP_147994.1| 289 GDKKFVSMHIAWKTFNGLEDELVVNMRINDS 319
                                   ******************************9 PP

>> 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 ?   12.7   0.1   1.1e-05     0.099      31      57 ..     112     138 ..     108     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                 Radical_SAM_C  31 leeyvdlvadilellppdirvhRltgd 57 
                                   +ee+v++vad l++l+pd++++ +t +
  gi|14601456|ref|NP_147994.1| 112 MEEAVEIVADRLQHLRPDVVINVITTE 138
                                   79*******************988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2866.78
//
Query:       gi|118431489|ref|YP_874899.1|  [L=108]
Description: hypothetical protein APE_1517a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0034   17.1   3.4     0.0059   16.3   3.4    1.4  1  Antimicrobial21  Plant antimicrobial peptide
     0.0079   15.8   1.1       0.71    9.6   0.1    2.2  2  zf-Tim10_DDP     Tim10/DDP family zinc finger


Domain annotation for each model (and alignments):
>> Antimicrobial21  Plant antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.4   6.6e-07    0.0059       1      27 [.      68      96 ..      68      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.6e-07
                Antimicrobial21  1 egrdrCrkkC.qhHh.DpwkkqqCVqdCr 27
                                   eg +rC k C + H     ++q C++ C 
  gi|118431489|ref|YP_874899.1| 68 EGECRCLKEClEKHGiGKEETQDCMDACI 96
                                   699*************************7 PP

>> zf-Tim10_DDP  Tim10/DDP family zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   7.9e-05      0.71      29      51 ..      59      81 ..      35      82 .. 0.77
   2 !    5.3   0.1    0.0017        15      20      30 ..      88      98 ..      85     107 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.9e-05
                   zf-Tim10_DDP 29 gkypgssLdsseesCldnCvdry 51
                                   ++ + ssL  +e  Cl+ C +++
  gi|118431489|ref|YP_874899.1| 59 PELRVSSLEEGECRCLKECLEKH 81
                                   666789***************97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0017
                   zf-Tim10_DDP 20 tekCfkkCigk 30
                                   t+ C++ Ci++
  gi|118431489|ref|YP_874899.1| 88 TQDCMDACIES 98
                                   67788888844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 880.96
//
Query:       gi|118431490|ref|NP_147996.2|  [L=136]
Description: hypothetical protein APE_1520.1 [Aeropyrum pernix K1]
Scores for 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-33  113.3   0.0    8.5e-33  112.9   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   4.7e-37   8.5e-33       1     113 [.      20     131 ..      20     132 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 4.7e-37
                                    E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHHH-S CS
                        UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssllgs 79 
                                    d+t +vee+++  g  +Gl++v+++htta++++nE+ +p+++eD+ e++++l  +  +++hn   + na+aHl ++++g 
  gi|118431490|ref|NP_147996.2|  20 DVTGKVEEWLSTVGGVNGLLVVYVPHTTAAVAVNEA-EPRLMEDIVEFIRELTKPGgPWKHNL-VDVNAHAHLGNTIIGD 97 
                                    79*********************************9.****************9999*****4.457************* PP

                                    EEEEEEETTEE---TTEEEEEEESS-SSEEEEEE CS
                        UPF0047  80 sltipvedgklalGtwqsiylveldgpreRkvvv 113
                                    s +ipv+ g+l lGtwq+i++ve+dgpreR+v++
  gi|118431490|ref|NP_147996.2|  98 SRVIPVVGGRLSLGTWQRILFVEMDGPRERTVNL 131
                                    *******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1038.54
//
Query:       gi|118431491|ref|NP_147997.2|  [L=325]
Description: replication factor C small subunit [Aeropyrum pernix K1]
Scores for complete 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   79.3   0.2    7.9e-22   77.5   0.0    2.1  1  Rep_fac_C        Replication factor C C-terminal domain
    1.9e-16   60.3   0.1    2.7e-13   50.0   0.1    2.2  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    3.7e-16   59.8   0.0    7.6e-16   58.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
    3.4e-08   33.4   0.0    8.8e-08   32.1   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.5e-08   32.7   0.0    1.5e-07   31.5   0.0    1.6  1  Rad17            Rad17 P-loop domain
    4.5e-07   30.4   0.1     0.0065   16.9   0.0    2.7  2  AAA_16           AAA ATPase domain
      6e-07   29.4   0.0    1.3e-06   28.3   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
    1.2e-06   28.7   0.5    7.5e-05   23.0   0.1    2.8  2  AAA_assoc_2      AAA C-terminal domain
    3.1e-06   27.5   0.1      0.071   13.4   0.0    3.0  3  AAA_22           AAA domain
    7.7e-06   26.5   0.1    0.00011   22.8   0.0    2.5  2  AAA_18           AAA domain
    1.6e-05   24.9   0.0     0.0001   22.3   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    2.6e-05   24.1   0.0    0.00021   21.1   0.0    2.2  2  DNA_pol3_delta   DNA polymerase III, delta subunit
    0.00014   21.3   0.0     0.0044   16.4   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00022   21.3   0.0    0.00057   19.9   0.0    1.7  2  AAA_14           AAA domain
    0.00079   19.5   0.0     0.0022   18.0   0.0    1.8  1  ResIII           Type III restriction enzyme, res subunit
     0.0011   19.2   0.0     0.0024   18.1   0.0    1.7  1  AAA_28           AAA domain
     0.0012   18.4   0.1        0.2   11.1   0.0    2.4  2  PhoH             PhoH-like protein
     0.0012   18.4   0.0     0.0022   17.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0013   18.0   0.0     0.0025   17.0   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
     0.0013   17.8   0.0     0.0093   15.0   0.0    2.0  2  T2SSE            Type II/IV secretion system protein
     0.0013   18.5   0.0      0.003   17.3   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
     0.0016   17.9   0.0     0.0031   16.9   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0021   18.2   0.0     0.0053   16.9   0.0    1.9  1  AAA_33           AAA domain
     0.0025   17.9   0.0      0.014   15.5   0.0    2.1  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.003   17.0   0.1      0.055   12.9   0.0    2.4  2  TniB             Bacterial TniB protein
     0.0037   16.9   0.1      0.052   13.1   0.0    2.7  3  AAA_25           AAA domain
     0.0052   17.1   0.0      0.013   15.9   0.0    1.7  1  RNA_helicase     RNA helicase
     0.0052   16.3   0.0     0.0092   15.5   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
     0.0055   16.4   0.1       0.19   11.4   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
     0.0064   16.2   0.3      0.096   12.4   0.0    2.7  3  AAA_30           AAA domain
     0.0069   16.2   0.0      0.013   15.3   0.0    1.5  1  AAA_11           AAA domain
     0.0098   15.6   0.0      0.014   15.1   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
  ------ inclusion threshold ------
       0.02   14.1   0.0       0.05   12.8   0.0    1.6  2  TIP49            TIP49 P-loop domain
      0.025   14.5   0.0       0.37   10.7   0.0    2.2  2  NTPase_1         NTPase
       0.03   14.2   0.0       0.11   12.4   0.0    1.9  2  APS_kinase       Adenylylsulphate kinase
      0.031   14.0   0.0      0.066   12.9   0.0    1.5  1  AAA_24           AAA domain
      0.041   13.1   0.1       0.54    9.4   0.1    2.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.044   13.1   0.0       0.31   10.3   0.0    2.0  2  ATPase           KaiC
      0.049   13.6   0.0       0.24   11.3   0.0    2.1  1  NACHT            NACHT domain
      0.051   13.9   0.1       0.42   10.9   0.0    2.1  2  AAA_19           AAA domain
      0.053   12.8   0.0        0.1   11.9   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.079   13.1   0.1       0.28   11.3   0.1    2.0  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.11   12.3   0.0         15    5.3   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
       0.11   12.3   0.1        8.1    6.2   0.0    2.4  2  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.11   12.9   0.0       0.22   11.9   0.0    1.5  1  DUF5613          Domain of unknown function (DUF5613)
       0.14   12.3   0.0       0.45   10.6   0.0    1.8  1  Torsin           Torsin
       0.14   11.8   0.4        5.3    6.7   0.1    2.7  2  AraC_N           AraC-type transcriptional regulator N-termin
       0.16   11.6   0.0       0.32   10.6   0.0    1.4  1  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   2.1e-24   7.9e-22       2      87 ..     228     314 ..     227     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 2.1e-24
                                    -HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS...S-HHHHHHHHHHHHHHHHHHHCTH-HHH CS
                      Rep_fac_C   2 hpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq.eelpeaqkleilellgeiekrlveGasehl 80 
                                    +p e++e+l+++l+gdf++a++ lr+ ++e+G+s+ed+ +q+hr +++   ++pe++++   ++lge+++rlveG+++ +
  gi|118431491|ref|NP_147997.2| 228 KPREVREMLATALKGDFTAARSLLRKIMIEYGMSGEDVARQIHRELFSTeLKMPEELRVLAADYLGEVHYRLVEGSDDDI 307
                                    699********************************************99877**************************** PP

                                    HHHHHHH CS
                      Rep_fac_C  81 qlsalla 87 
                                    qlsa+la
  gi|118431491|ref|NP_147997.2| 308 QLSAFLA 314
                                    *****98 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 !   50.0   0.1   7.2e-16   2.7e-13       2     163 .]      24     164 ..      23     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 7.2e-16
                DNA_pol3_delta2   2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivieteeker 81 
                                    q+++++ l++ +k+ ++ h +Lf+G+ g+gk ++a +la+ l+ e+ ++            + + +       +++e+  
  gi|118431491|ref|NP_147997.2|  24 QKHVVERLKQFVKQRNMPH-LLFAGPPGTGKTTAAHALAHDLFGENYRQY-----------MLELN-------ASDER-- 82 
                                    7889999999999999998.89*********************9999844...........33333.......34455.. PP

                DNA_pol3_delta2  82 sikldqirelieel..srkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkf 159
                                       ++ ire  +e+  sr+p e   ki+++++a++mt+ A+ al +++E  s+ + fiLi++ ++k++++i+SRc  ++f
  gi|118431491|ref|NP_147997.2|  83 --GINVIREKVKEFarSRTPPEIPFKIVLLDEADNMTSDAQQALRRLMELYSSVTRFILIANYPSKIIDPIQSRCAFFRF 160
                                    ..45555544444412678999********************************************************** PP

                DNA_pol3_delta2 160 spls 163
                                    +pls
  gi|118431491|ref|NP_147997.2| 161 QPLS 164
                                    *985 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 !   58.7   0.0     2e-18   7.6e-16       1     128 [.      43     159 ..      43     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2e-18
                                    EEEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksr 74 
                                    +l+ GppGtGKT++a+a+a++l      +++le+++s+ +   +    +k++e+ ++    + p +i+++DE+d+++++ 
  gi|118431491|ref|NP_147997.2|  43 LLFAGPPGTGKTTAAHALAHDLfgenyRQYMLELNASDER--GINVIREKVKEFARSRTPPEIPfKIVLLDEADNMTSDA 120
                                    699******************9766545889*********..88888888888887754444677***********9999 PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                            AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                               +++L + ++ +++    + +i+++n+p+k+ +++  +R+    
  gi|118431491|ref|NP_147997.2| 121 -----------QQALRRLMELYSSV---TRFILIANYPSKIIDPIQ-SRCAFFR 159
                                    ...........9********99994...78****************.9*98665 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 !   32.1   0.0   2.3e-10   8.8e-08       2      57 ..      14      64 ..      13      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.3e-10
                         RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                   rP+sl++ + q++v e+lk f++   +  +++ h+l++GpPG Gktt a+ +a++l
  gi|118431491|ref|NP_147997.2| 14 RPRSLDDIVDQKHVVERLKQFVK---Q--RNMPHLLFAGPPGTGKTTAAHALAHDL 64
                                   9******************9985...4..4678********************997 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0     4e-10   1.5e-07       8      81 ..       8      77 ..       5     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4e-10
                          Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewlnpvs 81
                                   lW+eky+P  ++++   k+ +e +k+++k   +++     LL +GP+G gk+t+ + L+  l g ++r+++  ++
  gi|118431491|ref|NP_147997.2|  8 LWVEKYRPRSLDDIVDQKHVVERLKQFVKQRNMPH-----LLFAGPPGTGKTTAAHALAHDLfGENYRQYMLELN 77
                                   7***********************99999887775.....6******************9754888998876555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.7e-05    0.0065      10      51 ..      29      67 ..      22      77 .. 0.75
   2 !   10.7   0.0    0.0013       0.5     116     169 ..      82     139 ..      65     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-05
                         AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                   e+L++ ++   +   + +l+ G++G+GK++ + +l++ l ++
  gi|118431491|ref|NP_147997.2| 29 ERLKQFVK---QRNMPHLLFAGPPGTGKTTAAHALAHDLFGE 67
                                   44444444...333489*****************99987665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0013
                         AAA_16 116 a..srllellkrll.allsrderp.lvlvlDdlqwadeaslqllaaLlrllesk.pllv 169
                                    +  + ++e++k+++ +++++ e p  +++lD+++   ++ +q+l+ L++l +s  ++++
  gi|118431491|ref|NP_147997.2|  82 RgiNVIREKVKEFArSRTPP-EIPfKIVLLDEADNMTSDAQQALRRLMELYSSVtRFIL 139
                                    24578888999999444444.66658999*******************99877446555 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 !   28.3   0.0   3.5e-09   1.3e-06       1      87 [.      42     129 ..      42     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.5e-09
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGp..vfanllladeinrappkt 78 
                                    h+l+ g PG++kt++++ala+ l  e  r q+  +l  sd  G++v++ek kef  ++ p  +  +++l de +  ++ +
  gi|118431491|ref|NP_147997.2|  42 HLLFAGPPGTGKTTAAHALAHDLFGENYR-QYMLELNASDERGINVIREKVKEFARSRTPpeIPFKIVLLDEADNMTSDA 120
                                    99*******************99888887.999*********************99888766889*************** PP

                          AAA_3  79 qsalleame 87 
                                    q al   me
  gi|118431491|ref|NP_147997.2| 121 QQALRRLME 129
                                    ****99887 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 !   23.0   0.1     2e-07   7.5e-05       3      34 ..     179     210 ..     177     224 .. 0.88
   2 ?    2.9   0.0      0.38   1.4e+02       9      72 ..     230     299 ..     225     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2e-07
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaa 34 
                                    + +++e++al+a+ e+++GD+Rka+n+L++a 
  gi|118431491|ref|NP_147997.2| 179 EGVDYEEEALDAIYEISEGDMRKAINVLQAAS 210
                                    67899************************886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.38
                                    XXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHH CS
                    AAA_assoc_2   9 ddalealaeladGDaRkaLnlLE...laaeaaeak...egkieitledleealqrkalryDkagdehYdl 72 
                                    ++++e+la++ +GD  +a  lL    +   ++ ++   + ++e+ + +l+   + ++l  D  g+ hY l
  gi|118431491|ref|NP_147997.2| 230 REVREMLATALKGDFTAARSLLRkimIEYGMSGEDvarQIHRELFSTELKMPEELRVLAADYLGEVHYRL 299
                                    6889999999999965555555531033333332232333333444444444445567888888888876 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   0.00019     0.071       7      29 ..      42      64 ..      35      99 .. 0.75
   2 !   11.7   0.0   0.00063      0.23      78     129 ..      87     141 ..      62     145 .. 0.67
   3 ?   -1.4   0.0       7.1   2.6e+03      57      59 ..     251     253 ..     213     296 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00019
                         AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                   +l+  G++GtGKTt +  l++ l
  gi|118431491|ref|NP_147997.2| 42 HLLFAGPPGTGKTTAAHALAHDL 64
                                   78899*************99987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00063
                         AAA_22  78 llealeqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                    ++e++ + +r+r       +++++DEa+++ + +a + Lr+l++l ++ +++iL+ 
  gi|118431491|ref|NP_147997.2|  87 IREKVKEFARSRTPpeipFKIVLLDEADNM-TSDAQQALRRLMELYSSVTRFILIA 141
                                    335555555555558888899*********.8777777777777777888888886 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 7.1
                         AAA_22  57 lre 59 
                                    lr+
  gi|118431491|ref|NP_147997.2| 251 LRK 253
                                    222 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.9e-07   0.00011       3      44 ..      45      85 ..      43     133 .. 0.80
   2 ?    0.6   0.0       2.1   7.7e+02      27      68 ..     171     210 ..     118     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-07
                         AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                    +G+pG+GKtt a++L+  l fg+n+r++  e + ++e+  +
  gi|118431491|ref|NP_147997.2| 45 FAGPPGTGKTTAAHALAHDL-FGENYRQYMLELNASDERGIN 85
                                   79**************8887.899999999998888777666 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.1
                         AAA_18  27 nlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                                    +lr +a ++g  +e+++   d   ++ e+ + k+++ l+++s
  gi|118431491|ref|NP_147997.2| 171 RLRYIAENEGVDYEEEAL--DAIYEISEGDMRKAINVLQAAS 210
                                    445555555555555555..8888888888888888887765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.8e-07    0.0001       1      90 [.      42     129 ..      42     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.8e-07
                                    EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------.......G-SEEEEE CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraar.......egeilvlD 72 
                                    ++l  GppGtgK++ a  la+ l + ++  ++l  + + e  +  ++  ++ +++         r         +i++lD
  gi|118431491|ref|NP_147997.2|  42 HLLFAGPPGTGKTTAAHALAHDLfGENYRQYMLELNASDERGINVIR--EKVKEFA--------RsrtppeiPFKIVLLD 111
                                    6899*****************99999999998887766665433333..3444444........33334455789***** PP

                                    SGGG--HHHHHHHHHHHH CS
                          AAA_5  73 EveraesevlnsLlslle 90 
                                    E +++ s+++++L +l+e
  gi|118431491|ref|NP_147997.2| 112 EADNMTSDAQQALRRLME 129
                                    *************99987 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 !   21.1   0.0   5.5e-07   0.00021      59     170 ..     106     207 ..     104     208 .. 0.90
   2 ?   -0.2   0.0         2   7.4e+02     146     173 ..     228     255 ..     216     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.5e-07
                                    EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHH CS
                 DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkr 138
                                    +iv+l+ +      ++ + + +++L ++++ ++  t +ilia+       k+++ ++++   +++++l+++++++ + ++
  gi|118431491|ref|NP_147997.2| 106 KIVLLDEA------DNMTSDAQQALRRLMELYSSVTRFILIAN----YPSKIIDPIQSRCAFFRFQPLSKQDVIERLRYI 175
                                    56666666......6688999999******************9....34589**************************** PP

                                    HHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                 DNA_pol3_delta 139 aqelglkiekealelLlelvennlsaikqele 170
                                    a+++g++ e+eal+ ++e +e++++ + + l+
  gi|118431491|ref|NP_147997.2| 176 AENEGVDYEEEALDAIYEISEGDMRKAINVLQ 207
                                    *************************9988776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                                    E-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                 DNA_pol3_delta 146 iekealelLlelvennlsaikqelekLa 173
                                      +e+ e+L+ ++ ++++a+ + l k++
  gi|118431491|ref|NP_147997.2| 228 KPREVREMLATALKGDFTAARSLLRKIM 255
                                    567899*************999998876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0044      21      59 ..      39      78 ..      17     101 .. 0.72
   2 ?    2.7   0.0      0.19        72     109     149 ..     107     146 ..     105     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                   Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlp.sllpplseeealevak 59
                                      +ll++GppG+GKt  a++l+  l+ +  ++ +le ++
  gi|118431491|ref|NP_147997.2| 39 NMPHLLFAGPPGTGKTTAAHALAhDLFGENYRQYMLELNA 78
                                   4569****************99625777777788888765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefpar 149
                                    +++LDE+ ++++++ ++LR+ +e  + +++r    +++p++
  gi|118431491|ref|NP_147997.2| 107 IVLLDEADNMTSDAQQALRRLMELYS-SVTRFILIANYPSK 146
                                    678*****************999654.56666666666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       6.9   2.6e+03      70      91 ..      18      39 ..      11      47 .. 0.75
   2 !   19.9   0.0   1.5e-06   0.00057       5      92 ..      43     133 ..      39     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.9
                         AAA_14 70 lDEiqevpewekalkslvdegk 91
                                   lD i   +++ + lk++v++++
  gi|118431491|ref|NP_147997.2| 18 LDDIVDQKHVVERLKQFVKQRN 39
                                   7888888889999999998873 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.5e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelileklke..ekktylflDEiqev.pew 79 
                                    l+  G+  +GKTt ++ l+++l+    ++ +l++n  der  +   + k+ e+ +++  +     ++++lDE+ ++ +++
  gi|118431491|ref|NP_147997.2|  43 LLFAGPPGTGKTTAAHALAHDLFgeNYRQYMLELNASDERGINVIRE-KVKEFARSRT-PpeIPFKIVLLDEADNMtSDA 120
                                    56789999***********9999766677778888888777665533.5666666663.33434567******987368* PP

                         AAA_14  80 ekalkslvdegkn 92 
                                    ++al++l++ ++ 
  gi|118431491|ref|NP_147997.2| 121 QQALRRLMELYSS 133
                                    *******996633 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 !   18.0   0.0     6e-06    0.0022       8      57 ..      24      73 ..      21     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6e-06
                                   HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                         ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekf 57
                                   Q++++e+l++ +k+++  ++l++ + GtGKT  a +l+  l+ +++++ +
  gi|118431491|ref|NP_147997.2| 24 QKHVVERLKQFVKQRNMPHLLFAGPPGTGKTTAAHALAHDLFGENYRQYM 73
                                   99**********988888***********************999887644 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.5e-06    0.0024       4      57 ..      45      96 ..      42     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.5e-06
                         AAA_28  4 itGgestGKTtlleaLaargypvvpEaareileeklakgedalpwv.edllafae 57
                                   + G+++tGKTt + aLa      + E +r+++ e+ a++e+ ++   e++ +fa+
  gi|118431491|ref|NP_147997.2| 45 FAGPPGTGKTTAAHALAH---DLFGENYRQYMLELNASDERGINVIrEKVKEFAR 96
                                   78**************95...4667777777777777777777766555666655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00053       0.2       8      46 ..      23      67 ..      19      83 .. 0.77
   2 ?    5.0   0.0     0.038        14     120     137 ..     105     122 ..      77     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                                   HHHHHHHHHH....H-S..EEEEE--TTSSTTHHHHHHHHHHHHT CS
                           PhoH  8 eQkeylealk....knd..ivfaiGpaGtGKtylavalavealkk 46
                                    Qk+++e lk    + +   +  +Gp GtGKt  a ala +++ +
  gi|118431491|ref|NP_147997.2| 23 DQKHVVERLKqfvkQRNmpHLLFAGPPGTGKTTAAHALAHDLFGE 67
                                   577777777766642223467789**************9988765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.038
                                    SEEEEE-SGGG--HHHHH CS
                           PhoH 120 dafvilDEAQnttkeqmk 137
                                     ++v+lDEA n+t+   +
  gi|118431491|ref|NP_147997.2| 105 FKIVLLDEADNMTSDAQQ 122
                                    479*********987644 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 !   17.5   0.0   5.9e-06    0.0022      32      72 ..      39      79 ..      20     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-06
                          AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                   n  ++l+ Gp GtGKt+ ++ l + l  e+y   +++++a+
  gi|118431491|ref|NP_147997.2| 39 NMPHLLFAGPPGTGKTTAAHALAHDLFGENYRQYMLELNAS 79
                                   334899***************************99999985 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.6e-06    0.0025      30     104 ..      18      93 ..       5     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-06
                         DUF815  30 LvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLr..lievekedlkelpklvellre 104
                                    L +i +q +++ve  +qf+++++  ++L+ G  GtGK +  +al +++  e+ r  ++e++ +d + ++ + e+++e
  gi|118431491|ref|NP_147997.2|  18 LDDIVDQ-KHVVERLKQFVKQRNMPHLLFAGPPGTGKTTAAHALAHDLFGENYRqyMLELNASDERGINVIREKVKE 93 
                                    4455444.5688999*******************************9998884433788888777777777777765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-05    0.0093     104     153 ..      17      64 ..       8      86 .. 0.84
   2 ?    0.0   0.0      0.95   3.6e+02     233     262 ..     117     147 ..     116     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                          T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                    +ldd++ ++++ e++++++++   +   +l++G+ g+GKtt + al + +
  gi|118431491|ref|NP_147997.2|  17 SLDDIVDQKHVVERLKQFVKQR--NMPHLLFAGPPGTGKTTAAHALAHDL 64 
                                    6888888888889999999888..7888***************9988765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.95
                          T2SSE 233 ansaagalerLeqlgaeveaa.elkssilav 262
                                    + +a++al+rL +l + v ++  ++++  ++
  gi|118431491|ref|NP_147997.2| 117 TSDAQQALRRLMELYSSVTRFiLIANYPSKI 147
                                    6789**********98866651445555555 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 !   17.3   0.0   7.9e-06     0.003      41      84 ..      32      77 ..      15     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.9e-06
                      IstB_IS21 41 lsfiekke..nivllGpsGvGKshlaialgveavraglsvlfvrve 84
                                    +f+++++   +++ Gp+G+GK+  a al+++   ++++ + + ++
  gi|118431491|ref|NP_147997.2| 32 KQFVKQRNmpHLLFAGPPGTGKTTAAHALAHDLFGENYRQYMLELN 77
                                   456665542268999*****************99999987766654 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.4e-06    0.0031       3      59 ..       5      60 ..       3      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.4e-06
                                   HHHHTSHHHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE  3 levleskkfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntL 59
                                   le+l+ +k+r +s   +v+  +++ + +  + +++m+ hll aG +g+GK+ta ++L
  gi|118431491|ref|NP_147997.2|  5 LEMLWVEKYRPRSLDDIVDQKHVVERLKQFVKQRNMP-HLLFAGPPGTGKTTAAHAL 60
                                   67778888888888888888888888899999*****.***************9998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-05    0.0053       3      32 ..      44      73 ..      43     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-05
                         AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt 32
                                   l+ G+pG+GK+t a+ l+  l ++  ++  
  gi|118431491|ref|NP_147997.2| 44 LFAGPPGTGKTTAAHALAHDLFGENYRQYM 73
                                   799**************9888855555544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.7e-05     0.014       5     104 ..      42     129 ..      38     135 .. 0.83
   2 ?   -0.8   0.0       3.9   1.5e+03      19      60 ..     232     276 ..     219     283 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-05
                                    -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...EEEEETGGG-- CS
                          AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...ivllDEidKih 81 
                                     +l++gp g+Gkt +a ala  lf     +  r  + el  ++e    v r+++++ +  +   +    ivllDE d  +
  gi|118431491|ref|NP_147997.2|  42 HLLFAGPPGTGKTTAAHALAHDLFG----ENYRQYMLELNASDERGINVIREKVKEFARSRTPPEIpfkIVLLDEADNMT 117
                                    689*********************4....6677778888887778888888888888888777777899*********** PP

                                    -----------HHHHHHHHHHHH CS
                          AAA_2  82 pkessgadvSregVqrdLLqile 104
                                    +           + q++L +++e
  gi|118431491|ref|NP_147997.2| 118 S-----------DAQQALRRLME 129
                                    9...........77777777776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.9
                                    HHHHHHHHTT-......-EEEEEGGG---.----THHHHHHHHHT CS
                          AAA_2  19 lakalaellfv..kkekkliradaselle.eeevehlvsrligap 60 
                                    + ++la  l+   +  ++l r+ + e+   +e+v++ + r++ + 
  gi|118431491|ref|NP_147997.2| 232 VREMLATALKGdfTAARSLLRKIMIEYGMsGEDVARQIHRELFST 276
                                    455555555444466788888888888554888888888877665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00015     0.055      23      54 ..      28      59 ..      18      73 .. 0.86
   2 ?    1.4   0.0      0.48   1.8e+02     117     143 ..     102     128 ..      69     135 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                           TniB 23 LeeLleypkrkrmpnlllvGdsnnGKtmivek 54
                                    e+L ++ k+  mp+ll++G++ +GKt+ ++ 
  gi|118431491|ref|NP_147997.2| 28 VERLKQFVKQRNMPHLLFAGPPGTGKTTAAHA 59
                                   4778889999*****************98876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.48
                           TniB 117 elkvrvLiiDEihnllagsarkqrefl 143
                                    e+  +++++DE +n+ +  +++ r+++
  gi|118431491|ref|NP_147997.2| 102 EIPFKIVLLDEADNMTSDAQQALRRLM 128
                                    567899999999999866666555554 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   0.00014     0.052      36      57 ..      43      64 ..      15     136 .. 0.91
   2 ?   -0.4   0.0       1.9   7.1e+02     126     157 ..     195     226 ..     166     245 .. 0.79
   3 ?   -0.7   0.0       2.4   8.9e+02      78     133 ..     261     316 ..     259     323 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                         AAA_25 36 allaGapgtGKttlaldlalav 57
                                    l+aG+pgtGKtt+a  la+++
  gi|118431491|ref|NP_147997.2| 43 LLFAGPPGTGKTTAAHALAHDL 64
                                   5789**************9986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                         AAA_25 126 ltadvdaleaaieevegvrlvviDplsralgg 157
                                     ++d+++ +++++++  ++ v +D ++r++g 
  gi|118431491|ref|NP_147997.2| 195 SEGDMRKAINVLQAASYLGKVTVDAVYRVVGM 226
                                    46788899999999777999999999999886 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.4
                         AAA_25  78 saEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdal 133
                                    s+Ed + +++r l  +  ++++  r+l+ d+ g+   +L++  +++ +l a++++l
  gi|118431491|ref|NP_147997.2| 261 SGEDVARQIHRELFSTELKMPEELRVLAADYLGEVHYRLVEGSDDDIQLSAFLAWL 316
                                    68999999999999999999766666666655554556666555554466666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.4e-05     0.013       2      27 ..      44      77 ..      43     155 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.4e-05
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl........k 27
                                   ++ Gp+g+GK+t+a+ La++l ++         +
  gi|118431491|ref|NP_147997.2| 44 LFAGPPGTGKTTAAHALAHDLFGENyrqymlelN 77
                                   689******************9665455555542 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-05    0.0092       1      41 [.      40      80 ..      40     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-05
                                   E.EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                          KTI12  1 MpLvvltGlPssGKstrakeLakaleeekrsvvviddeslg 41
                                   Mp +++ G P +GK+t+a+ La+ l  e+++ ++++ ++  
  gi|118431491|ref|NP_147997.2| 40 MPHLLFAGPPGTGKTTAAHALAHDLFGENYRQYMLELNASD 80
                                   999************************99999998876665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00052      0.19       9      57 ..      25      77 ..      21      86 .. 0.73
   2 ?    1.8   0.0      0.46   1.7e+02      96     118 ..     107     129 ..     106     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00052
                                   HHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHH.HH.HSTTTTS-EEEEE CS
                Sigma54_activat  9 kelleqikkvaktd..lsvlitGesGtGKellarai.he.askrkekpfvavn 57
                                   k+++e++k+++k++   ++l  G  GtGK++ a+a+ h+   ++ ++ ++++n
  gi|118431491|ref|NP_147997.2| 25 KHVVERLKQFVKQRnmPHLLFAGPPGTGKTTAAHALaHDlFGENYRQYMLELN 77
                                   678888898887776568999*************9834433344444555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.46
                                    EEEEETGGGS-HHHHHHHHHHHH CS
                Sigma54_activat  96 tlfLDeigelplelQekLlrvlq 118
                                    +++LDe  +++ ++Q+ L r+++
  gi|118431491|ref|NP_147997.2| 107 IVLLDEADNMTSDAQQALRRLME 129
                                    578**************999887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00026     0.096      21      43 ..      43      65 ..      22     140 .. 0.68
   2 ?   -0.8   0.0       2.9   1.1e+03     160     185 ..     185     210 ..     181     217 .. 0.81
   3 ?    0.0   0.0       1.6   5.8e+02     138     179 ..     204     248 ..     192     261 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                         AAA_30 21 avltGpAGtGKttalkalreawe 43
                                    +  Gp+GtGKtta  al++ + 
  gi|118431491|ref|NP_147997.2| 43 LLFAGPPGTGKTTAAHALAHDLF 65
                                   4678**********999965443 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.9
                         AAA_30 160 seeraaalalregdaeealealadrg 185
                                    +e  +a  +++egd+++a++ l++ +
  gi|118431491|ref|NP_147997.2| 185 EEALDAIYEISEGDMRKAINVLQAAS 210
                                    56678999999****99999988876 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.6
                         AAA_30 138 rdlveaagigtaeLtevvRq....keseeraaalalregdaeeale 179
                                    + l++a+  g ++++ v+R     k  e r++     +gd+++a +
  gi|118431491|ref|NP_147997.2| 204 NVLQAASYLGKVTVDAVYRVvgmaKPREVREMLATALKGDFTAA-R 248
                                    45555566677888888887655334666666666667777744.3 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.5e-05     0.013      11      42 ..      32      65 ..      23     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.5e-05
                         AAA_11 11 ksalsese..itliqGPPGtgKTktivellsqll 42
                                   k+++++++    l+ GPPGtgKT++  +l + l 
  gi|118431491|ref|NP_147997.2| 32 KQFVKQRNmpHLLFAGPPGTGKTTAAHALAHDLF 65
                                   56666666556899************99999996 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 !   15.1   0.0   3.8e-05     0.014       3      71 ..      45     113 ..      43     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-05
                Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvks.tkgkililDEy 71 
                                     +G pG GK+t+   l+++ l    +r+    l+++ ++  n   + v++f  +++++   +ki++lDE+
  gi|118431491|ref|NP_147997.2|  45 FAGPPGTGKTTAAHALAHD-LFGENYRQYMLELNASDERGINVIREKVKEFARSRTPPeIPFKIVLLDEA 113
                                    5799*************99.77778888888888888999999999999**9999999999********8 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.05      40      75 ..      32      65 ..      19      88 .. 0.84
   2 ?   -2.3   0.0       5.1   1.9e+03     295     341 ..     209     255 ..     178     260 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 40 velikekklaGravLlaGpsgtGktalaiaiskelg 75
                                    +++k++++    +L+aGp+gtGkt  a a++++l 
  gi|118431491|ref|NP_147997.2| 32 KQFVKQRNMP--HLLFAGPPGTGKTTAAHALAHDLF 65
                                   5789999998..8*******************9984 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 295 fsylnraleselaPivilatnrgiakirGtdiisphGipvDlldrll 341
                                     syl ++  + +  +v +a  r + ++  t ++  +  ++ ll +++
  gi|118431491|ref|NP_147997.2| 209 ASYLGKVTVDAVYRVVGMAKPREVREMLATALKGDFTAARSLLRKIM 255
                                    35566666666666666666666666666666666666666665555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     0.001      0.37       2      28 ..      43      69 ..      42      71 .. 0.86
   2 ?    2.2   0.0       0.4   1.5e+02      72     147 ..      70     154 ..      66     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.001
                                   EEEE--TTSSHHHHHHHHHHHH...GG CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgv 28
                                   ++  GppG+GKtT  + +++ l  +++
  gi|118431491|ref|NP_147997.2| 43 LLFAGPPGTGKTTAAHALAHDLFGENY 69
                                   6789*************9999987776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.4
                                    TTEEE-HHHHHHHHHHHHHHHHHHH-...........EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHH CS
                       NTPase_1  72 gkyvvdvesfeelalealrkalsead...........viviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlal 140
                                     +y++++++ +e +++++r++++e             ++++DE  +m   +++  + + e+ +s + ++ +   +  +++
  gi|118431491|ref|NP_147997.2|  70 RQYMLELNASDERGINVIREKVKEFArsrtppeipfkIVLLDEADNMTSDAQQALRRLMELYSSVTRFILIANYP--SKI 147
                                    588999999999999999998854444556778888899999999999999988888888888888888777776..567 PP

                                    HHHHHT- CS
                       NTPase_1 141 veeirer 147
                                    ++ i++r
  gi|118431491|ref|NP_147997.2| 148 IDPIQSR 154
                                    8877777 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0003      0.11       5      37 ..      43      75 ..      40      83 .. 0.93
   2 ?   -1.6   0.0       5.9   2.2e+03      24      51 ..     248     275 ..     214     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0003
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLd 37
                                   ++++G  g+GK+t a+al++ L+ ++++ y+L+
  gi|118431491|ref|NP_147997.2| 43 LLFAGPPGTGKTTAAHALAHDLFGENYRQYMLE 75
                                   689*************************99996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.9
                                    HHHHHTT--EEEEEHHHHTTTTTTT--S CS
                     APS_kinase  24 kkLvekgisvylLdGdnvRhgLnkdLgf 51 
                                    ++L +k +  y + G+ v +++ ++L  
  gi|118431491|ref|NP_147997.2| 248 RSLLRKIMIEYGMSGEDVARQIHRELFS 275
                                    4444555555666666666666666643 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   0.00018     0.066       5      86 ..      43     125 ..      40     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                         AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlks.ldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                    +l  Gp+g+GKTt a  l        ++  ++ ++++  + +++++       e++++++ +    + ++k++ +D +d 
  gi|118431491|ref|NP_147997.2|  43 LLFAGPPGTGKTTAAHALahdlfgeNYRQYMLELNASDERgINVIR-------EKVKEFARSRTPPEIPFKIVLLDEADN 115
                                    5678*************97777777677777777775533133333.......445555555577777899999999999 PP

                         AAA_24  77 leelclaevi 86 
                                    + + + + ++
  gi|118431491|ref|NP_147997.2| 116 MTSDAQQALR 125
                                    9888877665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0014      0.54       7      52 ..      46      92 ..      42     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                        DUF2075  7 tGvaGtGKtvvllnllaeleddeeertavylsvN...hplvlvlreala 52
                                    G +GtGKt  + +l+++l    e++++ +l  N   ++ ++v+re+++
  gi|118431491|ref|NP_147997.2| 46 AGPPGTGKTTAAHALAHDL--FGENYRQYMLELNasdERGINVIREKVK 92
                                   699***************9..4444444444333111334556666554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00084      0.31      22     130 ..      43     153 ..      18     161 .. 0.86
   2 ?    0.2   0.1       1.1     4e+02     102     146 ..     189     238 ..     158     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00084
                         ATPase  22 vlitGepGtGKtifalqFlikgaekygepgvfvtveepa....edlrenakslGwdlekleeegklaiidasesaeesae 97 
                                     l +G pGtGKt+ a   +     + +++  +  ++ +     + +re++k++    +  e   k++++d + +++   +
  gi|118431491|ref|NP_147997.2|  43 LLFAGPPGTGKTTAAHALAHDLFGE-NYRQYMLELNASDergiNVIREKVKEFARSRTPPEIPFKIVLLDEADNMTS-DA 120
                                    5789*********999999888888.999999888777666788899****************9******9999887.55 PP

                         ATPase  98 ekdkedleelieelaeaikeikakrvviDsitg 130
                                    ++    l+el +++++ i   +    +iD+i++
  gi|118431491|ref|NP_147997.2| 121 QQALRRLMELYSSVTRFILIANYPSKIIDPIQS 153
                                    578888999999999999999999999999975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                         ATPase 102 edleel.ieelaeaikeika....krvviDsitglayeekeavaReilrq 146
                                    +++ e+   ++++ai+ ++a     +v +D +  +   +k+ ++Re l +
  gi|118431491|ref|NP_147997.2| 189 DAIYEIsEGDMRKAINVLQAasylGKVTVDAVYRVVGMAKPREVREMLAT 238
                                    33333314578888888888666678999999999999999999998876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00065      0.24       4      31 ..      44      71 ..      42     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00065
                                   EEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT  4 ilqGeaGsGKTtLlqklalawaegklpq 31
                                   +  G++G GKTt ++ la+++  +++ q
  gi|118431491|ref|NP_147997.2| 44 LFAGPPGTGKTTAAHALAHDLFGENYRQ 71
                                   678****************998888766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0011      0.42       7      36 ..      37      66 ..      32      99 .. 0.65
   2 ?    0.6   0.0       1.7   6.4e+02     102     126 ..     104     128 ..      58     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0011
                         AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallve 36
                                   + + ++ll  ++pGtGKT+  ++  + l  
  gi|118431491|ref|NP_147997.2| 37 QRNMPHLLFAGPPGTGKTTAAHALAHDLFG 66
                                   5566778888899*****987766655544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.7
                         AAA_19 102 eeellivDEfqdvdelqyrLlkall 126
                                      ++++ DE+ +++  +++ l++l+
  gi|118431491|ref|NP_147997.2| 104 PFKIVLLDEADNMTSDAQQALRRLM 128
                                    4458999**9999966655566555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00027       0.1       7      41 ..      30      65 ..      24      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                     Zeta_toxin  7 dkk.ypsq.erPklillgGqpGAGKselaellkdele 41
                                   + k +++q + P l l +G pG GK+++a++l+ +l 
  gi|118431491|ref|NP_147997.2| 30 RLKqFVKQrNMPHL-LFAGPPGTGKTTAAHALAHDLF 65
                                   44555555266655.67***************99986 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00076      0.28      12      44 ..      29      63 ..      24     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00076
                                   HHHHHHH..T-SS-EEEEEETT--HHHHHHCC--T CS
                Sigma54_activ_2 12 erLeqaa..qsklpvfltGekGsgkelvArlLhkn 44
                                   erL+q +  +++  ++ +G++G+gk++ A +L++ 
  gi|118431491|ref|NP_147997.2| 29 ERLKQFVkqRNMPHLLFAGPPGTGKTTAAHALAHD 63
                                   788886643455668899**************985 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.071        27      16      37 ..      42      63 ..      20      96 .. 0.79
   2 ?    5.3   0.0      0.04        15     123     148 ..     106     130 ..     102     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.071
                                   EEEEEESTTSSHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 16 dvlvaaeTGsGKTlaflipvlq 37
                                   ++l a++ G+GKT+a+   + +
  gi|118431491|ref|NP_147997.2| 42 HLLFAGPPGTGKTTAAHALAHD 63
                                   578999*********9876655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.04
                                    EEEEEETHHHHHHTTTHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 123 rflVlDEadrlldqgfsdfinrilnq 148
                                    +++ lDEad++ ++  ++ ++r+++ 
  gi|118431491|ref|NP_147997.2| 106 KIVLLDEADNMTSD-AQQALRRLMEL 130
                                    6899*********8.88888887765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.022       8.1       2      32 ..      46      76 ..      45      83 .. 0.78
   2 ?    3.8   0.0      0.11        42     189     225 ..     109     145 ..      83     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNL 32
                                   +Gp+G GKtt  +al+  l  ++++ +++ L
  gi|118431491|ref|NP_147997.2| 46 AGPPGTGKTTAAHALAHDLFGENYRQYMLEL 76
                                   8************998777666666666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.11
                     ATP_bind_1 189 llekeeekykklaeaiaelleefalvlrflplsseke 225
                                    ll++ ++ +++ ++a+++l+e+++ v+rf+ +++   
  gi|118431491|ref|NP_147997.2| 109 LLDEADNMTSDAQQALRRLMELYSSVTRFILIANYPS 145
                                    455666889999******************9997665 PP

>> DUF5613  Domain of unknown function (DUF5613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0006      0.22      48      96 ..      25      76 ..      17      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0006
                        DUF5613 48 kedeeylkefhkkkgqkhlkfifPe...neklseeleeylkkegyelgvleL 96
                                   k+ +e+lk+f k++++ hl f+ P    +++  ++l + l  e+y + +leL
  gi|118431491|ref|NP_147997.2| 25 KHVVERLKQFVKQRNMPHLLFAGPPgtgKTTAAHALAHDLFGENYRQYMLEL 76
                                   567899******************83335677889999999*********99 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0012      0.45      34      83 ..      24      70 ..      18      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHHT-SS-SS-EEEEEEE-TTSSHHHHHHHHHHHHSTTGGG CS
                         Torsin 34 kklvvksvkaylenekpkkpLvlsfhGwtGtGknfvaeiiaenlyrdGlr 83
                                   +k+vv+ +k ++++ +      l f G +GtGk   a+ +a++l+ +  r
  gi|118431491|ref|NP_147997.2| 24 QKHVVERLKQFVKQRNMPH---LLFAGPPGTGKTTAAHALAHDLFGENYR 70
                                   6899*******99876654...669*******************987665 PP

>> AraC_N  AraC-type transcriptional regulator N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.31   1.1e+02     101     120 ..     113     132 ..      68     142 .. 0.70
   2 ?    6.7   0.1     0.014       5.3     119     144 ..     278     303 ..     184     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.31
                         AraC_N 101 vskldeelldallRLlrlld 120
                                    +++++++ ++al RL++l  
  gi|118431491|ref|NP_147997.2| 113 ADNMTSDAQQALRRLMELYS 132
                                    388999**********9975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                         AraC_N 119 ldspedipvLaplivrEilyrlLqge 144
                                    l+ pe+ +vLa  ++ E++yrl  g 
  gi|118431491|ref|NP_147997.2| 278 LKMPEELRVLAADYLGEVHYRLVEGS 303
                                    5889******************9885 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   0.00085      0.32       4      32 ..      43      71 ..      41      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00085
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkv 32
                                   +l++G+ G+GKTt++  La+ l  e+++ 
  gi|118431491|ref|NP_147997.2| 43 LLFAGPPGTGKTTAAHALAHDLFGENYRQ 71
                                   699****************9987776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        48  (0.00267723); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              48  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.41
# Mc/sec: 2359.91
//
Query:       gi|118431492|ref|NP_147998.2|  [L=479]
Description: replication factor C large subunit [Aeropyrum pernix K1]
Scores for 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-17   63.3   0.0    8.2e-17   61.9   0.0    1.7  1  AAA             ATPase family associated with various cellula
    5.8e-08   32.6   0.0      1e-07   31.8   0.0    1.4  1  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
      7e-07   29.5   0.0    1.3e-06   28.6   0.0    1.4  1  AAA_2           AAA domain (Cdc48 subfamily)
    2.1e-06   27.1   0.0    1.2e-05   24.7   0.0    2.0  2  DUF815          Protein of unknown function (DUF815)
      4e-06   27.3   0.0    3.2e-05   24.4   0.0    2.4  1  AAA_16          AAA ATPase domain
    4.6e-06   26.6   0.0      2e-05   24.6   0.0    2.1  1  Bac_DnaA        Bacterial dnaA  protein
      7e-06   26.1   0.0    1.6e-05   25.0   0.0    1.6  1  AAA_5           AAA domain (dynein-related subfamily)
    5.1e-05   23.3   0.0    8.8e-05   22.5   0.0    1.4  1  Rad17           Rad17 P-loop domain
    9.9e-05   22.9   0.0    0.00032   21.2   0.0    1.9  1  AAA_18          AAA domain
    0.00014   22.1   0.1    0.00045   20.5   0.1    1.9  1  AAA_assoc_2     AAA C-terminal domain
    0.00022   21.1   0.0    0.00045   20.0   0.0    1.5  1  DNA_pol3_delta  DNA polymerase III, delta subunit
    0.00035   20.3   0.0    0.00074   19.3   0.0    1.5  1  IstB_IS21       IstB-like ATP binding protein
    0.00059   19.9   0.0     0.0011   19.0   0.0    1.4  1  AAA_14          AAA domain
    0.00068   19.9   0.0      0.013   15.8   0.0    2.7  1  AAA_22          AAA domain
     0.0025   18.2   0.0     0.0067   16.8   0.0    1.7  1  RNA_helicase    RNA helicase
     0.0048   16.2   0.0       0.01   15.1   0.0    1.5  1  Zeta_toxin      Zeta toxin
     0.0069   16.3   0.0       0.22   11.4   0.0    2.7  2  NACHT           NACHT domain
     0.0097   15.8   0.0      0.022   14.7   0.0    1.5  1  RsgA_GTPase     RsgA GTPase
  ------ inclusion threshold ------
      0.012   16.0   0.2      0.046   14.2   0.0    2.1  1  AAA_17          AAA domain
       0.02   14.5   0.0      0.072   12.7   0.0    2.0  2  AAA_25          AAA domain
      0.023   14.2   0.0      0.038   13.5   0.0    1.2  1  AAA_7           P-loop containing dynein motor region
      0.027   13.6   0.0      0.045   12.8   0.0    1.3  1  Parvo_NS1       Parvovirus non-structural protein NS1
      0.034   14.1   0.0       0.31   10.9   0.0    2.0  2  ATPase_2        ATPase domain predominantly from Archaea
      0.036   13.9   0.0      0.072   12.9   0.0    1.5  1  AAA_3           ATPase family associated with various cellula
      0.048   14.2   0.0       0.22   12.0   0.0    2.1  2  ABC_tran        ABC transporter
      0.066   13.0   0.0       0.22   11.3   0.0    1.8  2  AAA_11          AAA domain
      0.068   12.9   0.0       0.12   12.1   0.0    1.4  1  AAA_24          AAA domain
      0.084   12.6   0.0        0.2   11.4   0.0    1.6  1  AAA_29          P-loop containing region of AAA domain
       0.18   11.3   0.0        0.3   10.5   0.0    1.3  1  SMC_N           RecF/RecN/SMC N terminal 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 !   61.9   0.0   1.3e-19   8.2e-17       2     114 ..      53     151 ..      52     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.3e-19
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TS.EEEEEETGGGHHHHHTTC CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kp.silfiDEidalaksrsgs 77 
                                    llyGppG+GKT+l++a+a+e++ e++e+++s+ +      + ++i+ ++ +a++k+   k  +++++DE+d +++++   
  gi|118431492|ref|NP_147998.2|  53 LLYGPPGVGKTSLVEAIASEFNLEMIELNASDYR------RRSDIERIVGAASRKRsmfKRgVVILLDEVDGINPRE--- 123
                                    9*********************************......8999999999987777799555***********9999... PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                        +   +++Ll++++  ++      +++++n+p+k
  gi|118431492|ref|NP_147998.2| 124 ----DAGGIEALLSVIKTTEN-----PIVMTANDPWK 151
                                    ....8889***********99.....68999999764 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 !   31.8   0.0   1.7e-10     1e-07       2      88 ..      17     104 ..      16     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.7e-10
                         RuvB_N   2 rPksleeyigqekvkeklkifieaakk.reealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaallt 80 
                                    rPk++e+ + q++ k+ l    +a  + r+      llyGpPG+Gkt+l + ia+e++ ++    +    + +d+  ++ 
  gi|118431492|ref|NP_147998.2|  17 RPKRVEDVVNQDQAKKILVPWFKAWLEgRKPDKRAALLYGPPGVGKTSLVEAIASEFNLEMIELNASDYRRRSDIERIVG 96 
                                    9*****************999999754277778889************************99999999999999988876 PP

                         RuvB_N  81 nleekdvl 88 
                                      ++k  +
  gi|118431492|ref|NP_147998.2|  97 AASRKRSM 104
                                    54444333 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   2.1e-09   1.3e-06       6      84 ..      52     123 ..      48     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 2.1e-09
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG----- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKihpke 84 
                                     ll gp gvGkt l +a+a+  ++    ++i ++as++      ++ ++r +ga+    +  ++G ++llDE+d i p+e
  gi|118431492|ref|NP_147998.2|  52 ALLYGPPGVGKTSLVEAIASEFNL----EMIELNASDYRR----RSDIERIVGAASRKRSMFKRGvVILLDEVDGINPRE 123
                                    5789*******************8....************....999999999999999999999789*********952 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.9e-08   1.2e-05      20     105 ..      14      98 ..       5     116 .. 0.80
   2 ?   -0.8   0.0       1.1   6.9e+02     188     232 ..     162     201 ..     160     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                         DUF815  20 eevdevklddLvgidkqkealventeqfleglpan..nvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpk 97 
                                     ++++ +++d+v+ d+ k+ lv   +++leg++     +LL+G  G+GK slv a+ +e++   L +ie++ +d +  ++
  gi|118431492|ref|NP_147998.2|  14 IKYRPKRVEDVVNQDQAKKILVPWFKAWLEGRKPDkrAALLYGPPGVGKTSLVEAIASEFN---LEMIELNASDYRRRSD 90 
                                    566778999**********************98652269******************9996...7788888777776666 PP

                         DUF815  98 lvellrer 105
                                    + +++ ++
  gi|118431492|ref|NP_147998.2|  91 IERIVGAA 98 
                                    66665544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                         DUF815 188 lwlgFykldqeeYleiveklakklglelekeeleeeAlewalerg 232
                                    l++ F +l+ ++ +++++++++ +++e+e+     eAl++ +er+
  gi|118431492|ref|NP_147998.2| 162 LMVEFRPLTLTHIVAVLQRICEAERIECER-----EALRYIAERS 201
                                    677888888888888888888777777775.....5555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   5.2e-08   3.2e-05      21      63 ..      43      85 ..      32     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.2e-08
                         AAA_16 21 sgrp...elvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +gr    ++ ll+G++GvGK+slv++++ +++ +    ++ ++ ++
  gi|118431492|ref|NP_147998.2| 43 EGRKpdkRAALLYGPPGVGKTSLVEAIASEFNLE---MIELNASDY 85
                                   44444449********************998877...355444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   3.2e-08     2e-05      37     214 ..      52     214 ..      44     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.2e-08
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-HHHH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiqflagkektq 116
                                     ++yg+ G+Gkt L++ai+ e   +  el  +     + ++++v a   +k + fk+      v+l+D++  ++ +e+  
  gi|118431492|ref|NP_147998.2|  52 ALLYGPPGVGKTSLVEAIASEFNLEMIELNASDYRRRSDIERIVGAAS-RKRSMFKRG----VVILLDEVDGINPREDA- 125
                                    589****************99988887777766666666666666543.344556654....48899*********965. PP

                                    HHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHHHHHH CS
                       Bac_DnaA 117 eelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevpeevlefiae 196
                                      +  ++  +  +++ +v++++  P+     +d lr   e+ l+v+  p  l   +a+l++  eae++e  +e+l++iae
  gi|118431492|ref|NP_147998.2| 126 GGIEALLSVIKTTENPIVMTAND-PW-----KDFLRPLREVSLMVEFRPLTLTHIVAVLQRICEAERIECEREALRYIAE 199
                                    45667888888899999999875.55.....467888889**************************************** PP

                                    H--S-HHHHHHHHHHHHH CS
                       Bac_DnaA 197 rvtdnvRelegalnrlka 214
                                    r + ++R   +a+n l+a
  gi|118431492|ref|NP_147998.2| 200 RSEGDLR---SAINDLQA 214
                                    9998776...46666555 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 !   25.0   0.0   2.5e-08   1.6e-05       3      79 ..      53     121 ..      51     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 2.5e-08
                                    EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--H CS
                          AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraes 79 
                                    lL GppG+gK++l+e +a+ +n e+ + + +++ +++d+   +      +s++ s ++    +g +++lDEv+ +++
  gi|118431492|ref|NP_147998.2|  53 LLYGPPGVGKTSLVEAIASEFNLEMIELNASDYRRRSDIERIVGA----ASRKRSMFK----RGVVILLDEVDGINP 121
                                    8**************************************998884....555555555....9999******99884 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.4e-07   8.8e-05       6      81 ..       9      84 ..       4     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.4e-07
                          Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrk.kriLLisGPsGCgkstvvkvLskelgiklrewlnpvs 81
                                     +W+ ky+P+  e++    +  + +  w+ka    +++ kr  L+ GP+G gk+  v+ ++ e+  +++e ln+  
  gi|118431492|ref|NP_147998.2|  9 RVPWVIKYRPKRVEDVVNQDQAKKILVPWFKAWLEGRKPdKRAALLYGPPGVGKTSLVEAIASEFNLEMIE-LNASD 84
                                   568************97776666667889999766666535699*********************999998.45444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   5.2e-07   0.00032       2      76 ..      53     127 ..      53     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.2e-07
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                    ll G+pGvGKt+l ++++++ ++     n +d+ + ++++  v ++  ++++ + +  +  lld++++++  +e+++ 
  gi|118431492|ref|NP_147998.2|  53 LLYGPPGVGKTSLVEAIASEFNLemiELNASDYRRRSDIERIVGAA--SRKRSMFKRGVVILLDEVDGINP-REDAGG 127
                                    589****************987798999999999999999999999..9*********9*******99998.444444 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 !   20.5   0.1   7.3e-07   0.00045       3      50 ..     185     226 ..     183     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.3e-07
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                    AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitled 50 
                                    +++++e++al+++ae ++GD R+a+n L+++ae         ++tl  
  gi|118431492|ref|NP_147998.2| 185 ERIECEREALRYIAERSEGDLRSAINDLQAVAEGYG------RVTLTL 226
                                    6899*************************9998764......344444 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.3e-07   0.00045      78     171 ..     126     214 ..      70     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.3e-07
                                    THHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHH CS
                 DNA_pol3_delta  78 kllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealelLlel 157
                                      +++L +++++  +++ ++++a+   d  k  +  L + + +ve+ +l+   +   +q++++++ ++ e+eal +++e+
  gi|118431492|ref|NP_147998.2| 126 GGIEALLSVIKT--TENPIVMTAN---DPWKDFLRPLREVSLMVEFRPLTLTHIVAVLQRICEAERIECEREALRYIAER 200
                                    445555555555..5677777777...444567778888899************************************** PP

                                    HTT-HHHHHHHHHH CS
                 DNA_pol3_delta 158 vennlsaikqelek 171
                                    +e++l+ + + l+ 
  gi|118431492|ref|NP_147998.2| 201 SEGDLRSAINDLQA 214
                                    *********99986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06   0.00074      47     154 ..      49     153 ..      37     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
                      IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdl.gllpldqa 125
                                    k + +l Gp+GvGK+ l  a++ e    +l+++ + ++d  ++  ++r  g ++r+ + + +  +++lD++ g++p ++a
  gi|118431492|ref|NP_147998.2|  49 KRAALLYGPPGVGKTSLVEAIASE---FNLEMIELNASDYRRRSDIERIVGAASRKRSMFKRGVVILLDEVdGINPREDA 125
                                    556789***************876...567777789999999999*************************9788888877 PP

                      IstB_IS21 126 ea.ellfeviekryerrsiiitsnlpfaew 154
                                       e l+ vi+     ++i++t+n p +++
  gi|118431492|ref|NP_147998.2| 126 GGiEALLSVIKT--TENPIVMTANDPWKDF 153
                                    643889999986..5789******998877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-06    0.0011       3      76 ..      50     119 ..      48     159 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev 76 
                                    ++ ++ G+  vGKT l++ +++e      +++++n  d r ++  d e++  +  +k  + ++  +++lDE+  +
  gi|118431492|ref|NP_147998.2|  50 RAALLYGPPGVGKTSLVEAIASEFN---LEMIELNASDYRRRS--DIERIVGAASRKrSMFKRGVVILLDEVDGI 119
                                    78899***************98877...888888888877754..44456666555533336999******9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.1e-05     0.013       5      49 ..      49      84 ..      45     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                   ++  +++G++G+GKT l++ +++++         + e ++ +++ 
  gi|118431492|ref|NP_147998.2| 49 KRAALLYGPPGVGKTSLVEAIASEF---------NLEMIELNASD 84
                                   67899*****************999.........44444444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.1e-05    0.0067       2      86 ..      53     144 ..      52     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl......klkkkdsvys.rnpeddfwdgYtgqevvvidDfgqvkdeenpsdlaeli 74 
                                    +lyGp+g+GK++l++ +a+++  ++      ++ +++++    ++++   +++++  v++ d++  ++ +e+   ++ l+
  gi|118431492|ref|NP_147998.2|  53 LLYGPPGVGKTSLVEAIASEFNLEMielnasDYRRRSDIERiVGAASRKRSMFKRGVVILLDEVDGINPREDAGGIEALL 132
                                    69*******************97776777775555566655577888888888888888888888888775555777777 PP

                   RNA_helicase  75 rlvsstpyplnm 86 
                                     ++++t+ p+ m
  gi|118431492|ref|NP_147998.2| 133 SVIKTTENPIVM 144
                                    777777777766 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05      0.01      15      57 ..      48      88 ..      39     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                     Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                    + + ll G pG GK++l e+++ e+  + ++++l++ d+R++
  gi|118431492|ref|NP_147998.2| 48 DKRAALLYGPPGVGKTSLVEAIASEF--NLEMIELNASDYRRR 88
                                   5668999*******************..9************86 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00035      0.22       3      24 ..      52      73 ..      50      85 .. 0.86
   2 ?    1.8   0.0      0.32     2e+02      81     162 ..     107     181 ..      93     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                    +l G++G+GKT L++ +a++ 
  gi|118431492|ref|NP_147998.2| 52 ALLYGPPGVGKTSLVEAIASEF 73
                                   5899**************9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.32
                                    CCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHH.HCTTSSCE..EEEE--TCCHHHHHH CS
                          NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrd.leeqleeaivlevegfsesrrkqlv 159
                                    + ++++lD +D +    ++     ++ lL + i+    +e+++++t+    ++d l+ + e + ++e ++++  ++++++
  gi|118431492|ref|NP_147998.2| 107 RGVVILLDEVDGINPREDA---GGIEALL-SVIKT---TENPIVMTAND-PWKDfLRPLREVSLMVEFRPLTLTHIVAVL 178
                                    4466888888888885555...5555544.66666...89999988764.555625555555588888888877777777 PP

                                    HHC CS
                          NACHT 160 rky 162
                                     + 
  gi|118431492|ref|NP_147998.2| 179 QRI 181
                                    665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.6e-05     0.022      99     133 ..      49      83 ..      38      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.6e-05
                                    TSEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevsek 133
                                    ++ ++l G+ GvGK++L++a+++e +l++ e+ ++
  gi|118431492|ref|NP_147998.2|  49 KRAALLYGPPGVGKTSLVEAIASEFNLEMIELNAS 83 
                                    577899******************99998877665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.4e-05     0.046       1      29 [.      55      85 ..      55     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-05
                                   EE-TTSSHHHHHHHHHHHHTEEEE..EHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfthl..saGdl 29
                                   +G+PG+GK+ ++e ++ +++++++  +a+d+
  gi|118431492|ref|NP_147998.2| 55 YGPPGVGKTSLVEAIASEFNLEMIelNASDY 85
                                   7*******************99962256666 PP

>> AAA_25  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     0.072      25      52 ..      41      68 ..      17      73 .. 0.83
   2 ?   -3.2   0.0       8.7   5.4e+03     159     180 ..     199     220 ..     193     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                         AAA_25 25 lvkgllpagelallaGapgtGKttlald 52
                                   +++g  p +  all+G+pg+GKt l+  
  gi|118431492|ref|NP_147998.2| 41 WLEGRKPDKRAALLYGPPGVGKTSLVEA 68
                                   66788899***************99755 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.7
                         AAA_25 159 ensnsdvgalvealeriarrtg 180
                                    e s+ d ++++++l+ +a+ +g
  gi|118431492|ref|NP_147998.2| 199 ERSEGDLRSAINDLQAVAEGYG 220
                                    5667777788888888777777 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.1e-05     0.038      32      89 ..      48     102 ..      37     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                          AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekr 89 
                                     k+  ll+Gp G+GKt++++ + ++++   + ++ +n s +   +++ +i+ +   kr
  gi|118431492|ref|NP_147998.2|  48 DKRAALLYGPPGVGKTSLVEAIASEFN---LEMIELNASDYRRRSDIERIVGAASRKR 102
                                    57889******************9999...8888888888888888888877766666 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.2e-05     0.045     102     138 ..      37      73 ..      19      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                      Parvo_NS1 102 vllawlskqlgkrntvwfyGpantGktnlaeaIakav 138
                                    ++ awl+ ++  + + ++yGp+  Gkt l eaIa  +
  gi|118431492|ref|NP_147998.2|  37 WFKAWLEGRKPDKRAALLYGPPGVGKTSLVEAIASEF 73 
                                    667889999999*********************9876 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 ?   10.9   0.0    0.0005      0.31      22      44 ..      51      73 ..      39      93 .. 0.82
   2 ?    0.1   0.0         1   6.4e+02     113     148 ..     102     134 ..      75     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                       ATPase_2 22 iyfiYGpegsGKtaLlkeiienl 44
                                     ++YGp g+GKt+L+  i+++ 
  gi|118431492|ref|NP_147998.2| 51 AALLYGPPGVGKTSLVEAIASEF 73
                                   5689*************999886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                       ATPase_2 113 ikkkgkkiiiiiDelqklidlglngaellvkeLlnl 148
                                     +  ++ ++i++De+  +     ++++  +++Ll++
  gi|118431492|ref|NP_147998.2| 102 RSMFKRGVVILLDEVDGIN---PREDAGGIEALLSV 134
                                    3333344********8887...45555555555555 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 ?   12.9   0.0   0.00012     0.072       3      86 ..      53     131 ..      51     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                          AAA_3   3 llegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqsal 82 
                                    ll g PG++kt lv+a+a+ ++le+  +        sdi  + v  +++k+  fk+G v    +l de++  +p+ ++  
  gi|118431492|ref|NP_147998.2|  53 LLYGPPGVGKTSLVEAIASEFNLEMIELNASDYRRRSDIERI-VGAASRKRSMFKRGVV----ILLDEVDGINPREDAGG 127
                                    8999********************999998877888888644.4444555666888864....67788888888877766 PP

                          AAA_3  83 leam 86 
                                    +ea+
  gi|118431492|ref|NP_147998.2| 128 IEAL 131
                                    6654 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   0.00036      0.22      14      51 ..      52      87 ..      46     145 .. 0.75
   2 ?   -2.2   0.0       8.8   5.5e+03      24      51 ..     420     447 ..     415     460 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00036
                                   EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                     + G+ G GK++L++++a + + ++  i+l+  d ++
  gi|118431492|ref|NP_147998.2| 52 ALLYGPPGVGKTSLVEAIASEFNLEM--IELNASDYRR 87
                                   4578****************998644..4444444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.8
                                    HHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  24 KStLlkllagllkpteGeilldgkdlke 51 
                                    KS +lk++a   k   Ge  l+ ++ k 
  gi|118431492|ref|NP_147998.2| 420 KSEILKAMATVKKARLGEKPLEPQEAKA 447
                                    8999999999988888877666665555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00036      0.22       3      42 ..      26      74 ..      25     107 .. 0.66
   2 ?   -2.0   0.2       3.9   2.4e+03     122     122 ..     429     429 ..     340     469 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                         AAA_11  3 ndsqreai.....ksalsese....itliqGPPGtgKTktivellsqll 42
                                   n++q++ i     k  l+ ++     +l+ GPPG gKT+ + ++ s+ +
  gi|118431492|ref|NP_147998.2| 26 NQDQAKKIlvpwfKAWLEGRKpdkrAALLYGPPGVGKTSLVEAIASEFN 74
                                   555555555555555555555666689************9999999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                         AAA_11 122 k 122
                                    +
  gi|118431492|ref|NP_147998.2| 429 T 429
                                    1 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   0.00019      0.12       4      22 ..      51      69 ..      48     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                     l+yGp+g+GKT+l+  +
  gi|118431492|ref|NP_147998.2| 51 AALLYGPPGVGKTSLVEAI 69
                                   579***********99877 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   0.00032       0.2      24      43 ..      51      70 ..      37      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                         AAA_29 24 atlltGpsGsGKSTllDAiq 43
                                   a ll Gp G+GK++l+ Ai+
  gi|118431492|ref|NP_147998.2| 51 AALLYGPPGVGKTSLVEAIA 70
                                   69****************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 ?   10.5   0.0   0.00049       0.3       7      87 ..      35     117 ..      30     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                                    EESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHH..HHCTT....TTTTTTCHCCCCCC--BTTCSSTTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   7 ienFksyagktvilpfsksftaivGpNGSGKsnlldAil..FvLGer...sakklrseklsdlihkskekasvkkaevei 81 
                                    +  Fk +       + +k+   ++Gp G GK++l++Ai   F L      ++   r++++++++ + ++k+s+ k  v i
  gi|118431492|ref|NP_147998.2|  35 VPWFKAWL---EGRKPDKRAALLYGPPGVGKTSLVEAIAseFNLEMIelnASDYRRRSDIERIVGAASRKRSMFKRGVVI 111
                                    55566654...34456788999****************633555432111333445666777776644555544445555 PP

                                    EEEETT CS
                                    xxxxxx RF
                          SMC_N  82 tfdned 87 
                                    ++d+ d
  gi|118431492|ref|NP_147998.2| 112 LLDEVD 117
                                    555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3370.59
//
Query:       gi|14601461|ref|NP_147999.1|  [L=106]
Description: hypothetical protein APE_1525 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 853.11
//
Query:       gi|118431493|ref|NP_148000.2|  [L=194]
Description: CDP-alcohol phosphatidyltransferase [Aeropyrum pernix K1]
Scores for 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-10   39.2   1.0      9e-10   39.2   1.0    2.3  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 !   39.2   1.0     5e-14     9e-10       3      66 .]      30      92 ..      29      92 .. 0.91
   2 ?   -0.1   1.3     0.091   1.6e+03      16      27 ..     153     169 ..     105     189 .. 0.63

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 5e-14
                                   HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   Pn+ Tl++ +++ +a+ + + y   v+ +ll+ ++ l+Da+DG +AR ++ vs lG +lDs +D
  gi|118431493|ref|NP_148000.2| 30 PNIYTLASPVAAAAAL-PAWLYISPVASLLLIALSLLLDAVDGAVARFTGRVSPLGSFLDSSLD 92
                                   9*********866665.9988888899999999****************************988 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.091
                                    HHHHGGGS-H....... CS
                CDP-OH_P_transf  16 lailllltyyp.....l 27 
                                    lail + +y+      l
  gi|118431493|ref|NP_148000.2| 153 LAILAISIYNLqtalaL 169
                                    33333322322333321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1731.44
//
Query:       gi|118431494|ref|NP_148002.2|  [L=389]
Description: hypothetical protein APE_1528.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-07   30.4   0.0    1.2e-06   29.0   0.0    1.7  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-05   25.5   3.7    2.9e-05   24.5   0.6    2.6  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    6.3e-05   23.0   0.4    0.00042   20.3   0.1    2.2  2  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
       0.04   13.5   0.0       0.28   10.7   0.0    2.1  1  Glycos_transf_1  Glycosyl transferases group 1


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 ?   -3.3   0.0       2.5   1.1e+04      36      57 ..      95     118 ..      89     126 .. 0.59
   2 !   29.0   0.0   2.6e-10   1.2e-06       4     133 ..     205     341 ..     202     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                                    EES---....HHHHHHHT.T-T.TE CS
                Glyco_trans_1_4  36 ivGdgp..rpeeleelaa.gleerv 57 
                                    i+Gdgp    e+l e  + gl++ v
  gi|118431494|ref|NP_148002.2|  95 IYGDGPriV-EALLEIYKrGLASAV 118
                                    788887422.344434434666555 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 2.6e-10
                                    EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---.....HHHHHHHTT-T.TEEEE---...THHHHHHHH-SEEE CS
                Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp...rpeeleelaagleerveftGfv...edlaellaaadvfv 77 
                                    +++ G l ++ kg+d+l+ a++l+ + ++r+v++G +p    pee+      +  r+++  +    +++  l a +d  v
  gi|118431494|ref|NP_148002.2| 205 LVTPGFL-RPDKGLDVLASAAALVSDGKLRIVVAG-EPmgvAPEEIP----SMGGRIKVIEKYlstDEILMLAAMSDAIV 278
                                    5667777.556**************668*******.44343335554....33368998887778667************ PP

                                    E--..-....--SHHHHHHHHTT-EEEE-TGGGTTT--.TTSSEE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  78 aPs..e....gfglkllEamaaglpvVatdvggiaevv.gengllvppgdpealaeailrLle 133
                                    +P   +    +++ +l  +m + +pv  t+v+ + e+      l vpp++pe la++++ L +
  gi|118431494|ref|NP_148002.2| 279 LPYkdRpgkySVSGVLHLSMGSLKPVLGTRVPRLVELYeYSPMLTVPPRSPELLARRMEWLSS 341
                                    ***97355568********************999998854556899***********998876 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 !   24.5   0.6   6.5e-09   2.9e-05       2     160 .]      17     176 ..      16     176 .. 0.75
   2 ?    1.0   0.1      0.12   5.2e+02      47     100 ..     207     258 ..     180     359 .. 0.75
   3 ?   -1.1   0.1       0.5   2.3e+03      81     104 ..     347     369 ..     300     388 .. 0.48

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.5e-09
                Glyco_trans_4_4   2 GigryvaelaraLaar..GheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvha 79 
                                    G+g y+++la++L+     ++++v+ +++a+ ++ +  d + v  +p + r+    d ++   +r l   ++ + dvvh+
  gi|118431494|ref|NP_148002.2|  17 GVGEYTRMLASGLRTVlpSASIRVYSTGEAGWER-YYDDSLGVEVVPSYMRR----DTSYEGLVRNLE--DDGGADVVHL 89 
                                    99************843479******99999988.45556666667766554....345555556665..********** PP

                Glyco_trans_4_4  80 hs.pt.....aglaarla...rrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvp 150
                                    ++ +        ++ +l+   +r+    +v t+h+  + ++s+a++  + + +rr+  r  a+++ s  +  el+a+gv+
  gi|118431494|ref|NP_148002.2|  90 QHeYGiygdgPRIVEALLeiyKRGLASAVVATFHTVVH-KQSTASGE-RLETQRRAS-RLHAIITHSILMEFELQAQGVD 166
                                    99675666632344444444445778899******755.45555555.557788765.799******************* PP

                Glyco_trans_4_4 151 adrvvvvpng 160
                                    ++ +v +p g
  gi|118431494|ref|NP_148002.2| 167 PSVIVKIPHG 176
                                    *******987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                Glyco_trans_4_4  47 vprrpspladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplv 100
                                    +p   +p + l+ l+ +++l+   + +  +v+a +p++ ++ ++ +++ +i+++
  gi|118431494|ref|NP_148002.2| 207 TPGFLRPDKGLDVLASAAALV--SDGKLRIVVAGEPMGVAPEEIPSMGGRIKVI 258
                                    444455556677778888887..8888888888888888888888877777776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.5
                Glyco_trans_4_4  81 sptaglaarlarrrrgiplvvtlh 104
                                     + ++++   a+ ++ +p v + h
  gi|118431494|ref|NP_148002.2| 347 ASASAQLYSYAA-ATQWPMVASQH 369
                                    222334444444.44555555555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   9.4e-08   0.00042      59     165 ..      69     176 ..      17     179 .. 0.70
   2 ?    0.3   0.0      0.14   6.2e+02      56     108 ..     327     373 ..     293     389 .] 0.56

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 9.4e-08
                 Glyco_transf_4  59 aflrrlrrllkre.kpDvvHahspaalgaallalrr........rlgiplVltvHglyekrllkarlkplsrllralerr 129
                                    +++  l r l+   + DvvH ++++ ++  + ++           l   +V+t+H+  +        k  ++  ++le +
  gi|118431494|ref|NP_148002.2|  69 TSYEGLVRNLEDDgGADVVHLQHEYGIYGDGPRIVEalleiykrGLASAVVATFHTVVH--------KQSTASGERLETQ 140
                                    444444444444449********99997655555556667888889999*********3........3333444444433 PP

                 Glyco_transf_4 130 l.lrradrviavSeatadelrerygvppekitVipnG 165
                                      ++r +++i+ S  +  el++  gv+p+ i+ ip+G
  gi|118431494|ref|NP_148002.2| 141 RrASRLHAIITHSILMEFELQA-QGVDPSVIVKIPHG 176
                                    3369******************.************99 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                 Glyco_transf_4  56 rslaflrrlrrllkre..kpDvvHahspaalgaallalrrrlgiplVltvHglye 108
                                    rs+  l r +++      ++ +  + s+   +++++a+   ++ p+V++ H   +
  gi|118431494|ref|NP_148002.2| 327 RSPELLARRMEW---LssNYELAASASAQ--LYSYAAA---TQWPMVASQHIALY 373
                                    333333333333...13377777555533..3343333...58999999998775 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 ?   10.7   0.0   6.1e-05      0.28      15     162 ..     202     346 ..     195     355 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.1e-05
                                    -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCES CS
                Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellknad 94 
                                    + ++++ g l++ Kg+d+l  a+al+    + ++++v+aG+        +++ + + + +vi  +++s +++  l  ++d
  gi|118431494|ref|NP_148002.2| 202 ELLLVTPGFLRPDKGLDVLASAAALVS---DGKLRIVVAGEPMG--VAPEEIPSMGGRIKVIE-KYLSTDEILMLAAMSD 275
                                    5667788999**************994...89********3222..33333444444333332.3444556666666677 PP

                                    EEEEEESS....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                Glycos_transf_1  95 ifvlpsis....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                    ++vlp        +   vl  +m + +pv+ + ++ + e+ +     l v+p ++e la+++++l ++ el+
  gi|118431494|ref|NP_148002.2| 276 AIVLPYKDrpgkYSVSGVLHLSMGSLKPVLGTRVPRLVELYEYS-PMLTVPPRSPELLARRMEWLSSNYELA 346
                                    77777555666633333444466666677777666666655433.345555557777777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 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:                        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 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3280.37
//
Query:       gi|118431495|ref|NP_148003.2|  [L=108]
Description: hypothetical protein APE_1529.1 [Aeropyrum pernix K1]
Scores for 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   54.9   7.8    1.1e-14   54.6   7.8    1.1  1  FUN14     FUN14 family
  ------ inclusion threshold ------
      0.013   15.2   1.0      0.013   15.2   1.0    1.6  2  DUF3464   Photosynthesis affected mutant 68


Domain annotation for each model (and alignments):
>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   7.8   1.3e-18   1.1e-14       1      91 []      17     105 ..      17     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.3e-18
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FUN14   1 igiGaviGlvtGfalkkvgKlaaiavGggllllqilasqgyikvnwdkiekdveelldrnkdgklgtedeklltenlpfs 80 
                                    +g+G+++G+++G+alkk+ K+++++vG+  l l  la+ g+i+vnwdk+   ve++++  +++  + +  +++ +  pf+
  gi|118431495|ref|NP_148003.2|  17 LGGGGILGFAAGYALKKAIKILLLVVGVFTLGLMGLAYYGVISVNWDKLALLVERAISGGGAAAASLK--SYIIAATPFA 94 
                                    589***********************************************888875544444433333..999999**** PP

                                    xxxxxxxxxxx RF
                          FUN14  81 agFlaGfllGl 91 
                                    a+Fl Gf lG+
  gi|118431495|ref|NP_148003.2|  95 ASFLVGFSLGF 105
                                    **********8 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0   1.5e-06     0.013      97     123 ..      37      64 ..      18      67 .. 0.85
   2 ?   -1.8   0.2      0.26   2.4e+03     103     115 ..      95     108 .]      78     108 .] 0.53

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
                        DUF3464  97 vllvslvlFglgvlGls.YGvlSasWde 123
                                    +ll  +++F lg++Gl+ YGv+S  Wd+
  gi|118431495|ref|NP_148003.2|  37 ILLLVVGVFTLGLMGLAyYGVISVNWDK 64 
                                    5677789*********846*******96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.26
                        DUF3464 103 vlFglgv.lGlsYG 115
                                    + F +g+ lG+ YG
  gi|118431495|ref|NP_148003.2|  95 ASFLVGFsLGFKYG 108
                                    23444432666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.36u 0.19s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 958.37
//
Query:       gi|118431496|ref|NP_148004.2|  [L=450]
Description: MiaB-like protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-28  100.6   0.2    4.1e-28   98.9   0.1    2.0  2  Radical_SAM  Radical SAM superfamily
    1.5e-20   73.0   0.0    3.1e-20   72.0   0.0    1.5  1  UPF0004      Uncharacterized protein family UPF0004
    3.5e-13   49.3   0.0    7.2e-13   48.3   0.0    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 ?   -1.7   0.0      0.54   3.2e+03      80     101 ..      58      81 ..      37      91 .. 0.76
   2 !   98.9   0.1   6.8e-32   4.1e-28       3     167 .]     160     333 ..     158     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.54
                                    EEEEECSSCHG..HHHHHHHHHTT CS
                                    xxxxxxxxxxx..xxxxxxxxxxx RF
                    Radical_SAM  80 itvetngtlpd..eeklerllelg 101
                                    i v t+++++d   +++erl +l+
  gi|118431496|ref|NP_148004.2|  58 ILVNTCAVRLDteQRIAERLEKLR 81 
                                    557788888888877777777766 PP

  == domain 2  score: 98.9 bits;  conditional E-value: 6.8e-32
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.......TTHHHHHHHHHHTC. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx. RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.......pdfvellerlakla. 74 
                                    +++gC ++CsfC+++     ++ +rs s++ i+e v+e+ +ekg++e+ l+g ++ +y       p++++l++++ ++  
  gi|118431496|ref|NP_148004.2| 160 IQEGCLGDCSFCITKV---ARRQVRSYSPRVIVERVREA-VEKGAREIRLTGTDVAVYgvdlpgkPNLADLVAAILEKVe 235
                                    789************9...8*******************.9*********************998666666666666656 PP

                                    .CCTEEEEEEECSSCHG..HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEE CS
                                    .xxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxx RF
                    Radical_SAM  75 .vpgiritvetngtlpd..eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvd 147
                                     +  ir+ + t+  +    +  l+  ++ +   +++l+++++dde vlk+m+r++t++e+++  ++++++ +++    +d
  gi|118431496|ref|NP_148004.2| 236 gDYRIRVGMMTPDQVEPylDSLLDVYRDERvYKYFHLPVQSGDDE-VLKIMKRNYTVSEYKAIHRRIKSR-FPDamiATD 313
                                    667778888888887548888889998888***************.************************.********* PP

                                    EEEEBTTTSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 148 rivglpGendeeleellell 167
                                    +ivg+pGe++e ++++++l+
  gi|118431496|ref|NP_148004.2| 314 IIVGHPGETWEAFWNTVRLV 333
                                    ****************9986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   5.3e-24   3.1e-20       2      93 ..      20     110 ..      19     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 5.3e-24
                                    EEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS CS
                        UPF0004   2 vaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqr 81 
                                    +++e +GC+  e d+ ++as+L+++gy++v ++e+Adv+lvnTCavr ++e+++ ++l++l+ +  p++k vv+GC++++
  gi|118431496|ref|NP_148004.2|  20 YYLEVYGCSLSEFDALIMASRLEEAGYRRVARPEDADVILVNTCAVRLDTEQRIAERLEKLRLQL-PDRKYVVAGCLVKA 98 
                                    7899*********************************************************9998.9***********99 PP

                                    -HHHHHHH-TTS CS
                        UPF0004  82 ekeellkeepev 93 
                                    ++  +++  pe+
  gi|118431496|ref|NP_148004.2|  99 RPGLVARLVPEA 110
                                    988777777665 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.2e-16   7.2e-13       2      60 ..     386     444 ..     385     446 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.2e-16
                                    XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T...TEEEEEEEEEE-SSEEEEE CS
                           TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpg.IGdfVeVkItkvkrqyLrGe 60 
                                    syvG+ ++ lv+++s++eg ++Gr+dn+ ++++p+ +++ +G++V++++++++++ Lr++
  gi|118431496|ref|NP_148004.2| 386 SYVGRRVRALVTERSWREGSMTGRLDNYTPIILPY-EERaMGRWVYAEVEEATFFDLRSS 444
                                    8**********************************.6777*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3212.09
//
Query:       gi|118431497|ref|NP_148005.2|  [L=148]
Description: translation initiation factor IF-2 [Aeropyrum pernix K1]
Scores for 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-34  116.1   0.1    9.9e-34  115.7   0.1    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
    0.00033   21.0   0.7    0.00058   20.2   0.7    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0044   17.0   0.3     0.0079   16.2   0.3    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0079   16.3   0.0      0.011   15.8   0.0    1.2  1  BTB_3            BTB/POZ domain
  ------ inclusion threshold ------
       0.01   15.3   0.3      0.022   14.2   0.3    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.011   15.4   0.5      0.017   14.7   0.5    1.3  1  GATA             GATA zinc finger
      0.016   15.1   0.2      0.031   14.2   0.2    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.019   14.4   2.0       0.41   10.1   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.02   14.8   2.6       0.18   11.8   2.1    2.6  3  zinc_ribbon_4    zinc-ribbon domain
      0.024   14.8   0.3       0.68   10.2   0.0    2.5  2  zf-RING_7        C4-type zinc ribbon domain
      0.036   13.8   0.1       0.06   13.1   0.1    1.4  1  HTH_38           Helix-turn-helix domain
      0.037   14.1   0.6      0.062   13.4   0.6    1.3  1  Elf1             Transcription elongation factor Elf1 like
       0.06   13.3   1.5       0.13   12.3   0.2    2.2  2  YhfH             YhfH-like protein
      0.089   12.9   2.8        3.5    7.8   0.2    2.3  2  Zn-ribbon_8      Zinc ribbon domain
       0.14   11.9   1.5         12    5.7   0.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.15   12.0   0.6       0.39   10.6   0.6    1.8  1  DUF3797          Domain of unknown function (DUF3797)
       0.17   11.6   1.1         19    5.1   0.1    2.5  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        0.3   11.2   1.4         11    6.2   0.0    2.2  2  DUF678           Protein of unknown function (DUF678)
       0.58    9.9   3.6        2.7    7.7   3.6    1.9  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        1.1    9.3   3.7         32    4.6   0.6    2.2  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        1.1    9.3   5.4         19    5.2   5.4    2.4  1  DUF1451          Zinc-ribbon containing domain
        6.7    6.7   6.9          2    8.3   1.9    2.4  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit


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 !  115.7   0.1   1.2e-36   9.9e-34       8     116 ..      33     141 ..      28     142 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 1.2e-36
                                    SS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEES.ETTEEEESSSSSCCHHHHHHHHHHHH CS
                   eIF-5_eIF-2B   8 kerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsid.engrlilngkfeakkleklldkyiee 86 
                                    ++ y++p++q+ + g+ +tvi+Nf+eia+aL+rdp+ v++yl+kel+t++s++ e+g+liln k+++k +++ l+ ++++
  gi|118431497|ref|NP_148005.2|  33 TSEYRIPEPQIIRIGS-QTVIRNFREIAQALKRDPKLVARYLQKELATAASYEeESGQLILNVKVSRKVVNQFLQLFMKT 111
                                    46799***********.************************************99************************* PP

                                    HTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                   eIF-5_eIF-2B  87 yVlCkeCkspetelekeerllvlkCkaCga 116
                                    yV C++C+s +t+l ++er ++lkC+aCga
  gi|118431497|ref|NP_148005.2| 112 YVRCPTCGSIDTKLLRQERAYMLKCEACGA 141
                                    *****************************8 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 !   20.2   0.7   7.2e-07   0.00058       5      36 ..     114     141 ..     110     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.2e-07
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCga 36 
                                     CP Cg+ +++  +q +++    +  C+ Cga
  gi|118431497|ref|NP_148005.2| 114 RCPTCGSIDTKLLRQERAY----MLKCEACGA 141
                                    6******************....********* 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 !   16.2   0.3   9.7e-06    0.0079      17      45 ..     111     141 ..     103     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.7e-06
                  Zn_Tnp_IS1595  17 ngfvCPhCgsr..kayriktrglfqCkeCrk 45 
                                    + ++CP Cgs   k+ r +++  ++C++C++
  gi|118431497|ref|NP_148005.2| 111 TYVRCPTCGSIdtKLLRQERAYMLKCEACGA 141
                                    5578******9999999999*********96 PP

>> BTB_3  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05     0.011      18      80 ..      62     123 ..      49     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                          BTB_3  18 frahPdtllgrmfgsslesnltkpnekGeyevaegisaevfraildyykkGvikcPpgvsvke 80 
                                    +++ P+ l++r +   l++ +   +e+G+  ++ ++s +v +  l+ + k +++cP+  s++ 
  gi|118431497|ref|NP_148005.2|  62 LKRDPK-LVARYLQKELATAASYEEESGQLILNVKVSRKVVNQFLQLFMKTYVRCPTCGSIDT 123
                                    455554.77888888888888889********************************9888753 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   2.7e-05     0.022       2      27 ..     114     141 ..     113     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                    EETTTTC.EE.CHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgs.tn.lveDpergelvCtdCGl 27 
                                    +CP Cgs ++ l++ +    l C++CG+
  gi|118431497|ref|NP_148005.2| 114 RCPTCGSiDTkLLRQERAYMLKCEACGA 141
                                    7******97779999999999******6 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   2.1e-05     0.017       1      27 [.     115     140 ..     115     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                           GATA   1 CsnCgttkTplWRrg.pdgnksLCnaCG 27 
                                    C  Cg+++T+l R++   + k  C+aCG
  gi|118431497|ref|NP_148005.2| 115 CPTCGSIDTKLLRQErAYMLK--CEACG 140
                                    99*************667777..****9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   3.8e-05     0.031      29      55 ..     113     142 ..     105     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                 OrfB_Zn_ribbon  29 ktCseCgsknke...alsgrtfkCpnCgfe 55 
                                     +C+ Cgs++++   +     +kC++Cg+e
  gi|118431497|ref|NP_148005.2| 113 VRCPTCGSIDTKllrQERAYMLKCEACGAE 142
                                    68**********9766666688******86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00051      0.41       3      11 ..     113     121 ..     112     124 .. 0.84
   2 ?    3.6   0.2     0.056        46       3      11 ..     134     143 ..     133     147 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                    zf-ribbon_3   3 vrCPnCGap 11 
                                    vrCP CG++
  gi|118431497|ref|NP_148005.2| 113 VRCPTCGSI 121
                                    89*****97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.056
                    zf-ribbon_3   3 vrCPnCGa.p 11 
                                     +C +CGa +
  gi|118431497|ref|NP_148005.2| 134 LKCEACGAeQ 143
                                    5677888765 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.3   1.9e+03      10      19 ..      34      43 ..      33      49 .. 0.82
   2 ?    5.4   0.5     0.021        17      26      32 ..     113     119 ..     109     121 .. 0.75
   3 ?   11.8   2.1   0.00022      0.18       3      33 ..     113     141 ..     112     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.3
                  zinc_ribbon_4 10 akyeiddekl 19
                                   ++y+i++ ++
  gi|118431497|ref|NP_148005.2| 34 SEYRIPEPQI 43
                                   58****9775 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                  zinc_ribbon_4  26 vrCskCg 32 
                                    vrC+ Cg
  gi|118431497|ref|NP_148005.2| 113 VRCPTCG 119
                                    8888887 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00022
                  zinc_ribbon_4   3 itCpsCkakyeiddeklpakgv.kvrCskCgh 33 
                                    ++Cp C+   +id + l+++++ +++C +Cg+
  gi|118431497|ref|NP_148005.2| 113 VRCPTCG---SIDTKLLRQERAyMLKCEACGA 141
                                    6788887...69******77777*******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 ?   10.2   0.0   0.00084      0.68       8      32 ..      95     121 ..      93     121 .. 0.71
   2 ?    2.3   0.1      0.24   1.9e+02       1       6 [.     135     140 ..     130     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00084
                                    B--CCHHHHHCCS..TB-EE-TTT--E CS
                      zf-RING_7   8 elppqvlselrag..devvtCpeCGRI 32 
                                    +++  v+++  +   +  v+Cp CG I
  gi|118431497|ref|NP_148005.2|  95 KVSRKVVNQFLQLfmKTYVRCPTCGSI 121
                                    666666666666666668*******88 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.24
                                    EETTT- CS
                      zf-RING_7   1 tCgGCh 6  
                                    +C++C+
  gi|118431497|ref|NP_148005.2| 135 KCEACG 140
                                    677776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.4e-05      0.06      22      42 ..      54      74 ..      44      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-05
                         HTH_38 22 slreIArrLgrspsTIsRElk 42
                                   ++reIA+ L+r+p  ++R l+
  gi|118431497|ref|NP_148005.2| 54 NFREIAQALKRDPKLVARYLQ 74
                                   69***************9776 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   7.6e-05     0.062      18      54 ..     109     142 ..      94     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-05
                           Elf1  18 lptkFdCpfCnheksvevkldkkekiaevsCkvCges 54 
                                    ++t+ +Cp C++    + kl ++e+  +++C+ Cg++
  gi|118431497|ref|NP_148005.2| 109 MKTYVRCPTCGSI---DTKLLRQERAYMLKCEACGAE 142
                                    688999****965...99****************986 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       2.9   2.4e+03       7      15 ..      23      31 ..      21      33 .. 0.84
   2 ?   12.3   0.2   0.00016      0.13      15      37 .]     114     139 ..      99     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.9
                           YhfH  7 FfrnLPkKk 15
                                    +++ P+K 
  gi|118431497|ref|NP_148005.2| 23 LYKKVPPKS 31
                                   6999**995 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                           YhfH  15 kCteCGk...eieEqaecYgneCekC 37 
                                     C++CG+   ++  q+ +Y+ +Ce C
  gi|118431497|ref|NP_148005.2| 114 RCPTCGSidtKLLRQERAYMLKCEAC 139
                                    4*****7443699************* PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0043       3.5      27      36 ..     113     123 ..     102     126 .. 0.73
   2 ?    4.9   0.2     0.035        28       4      14 ..     132     142 ..     131     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0043
                    Zn-ribbon_8  27 taCPeCgs.ev 36 
                                    + CP+Cgs ++
  gi|118431497|ref|NP_148005.2| 113 VRCPTCGSiDT 123
                                    34*****9776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.035
                    Zn-ribbon_8   4 YeYrCeeCghe 14 
                                    Y  +Ce+Cg e
  gi|118431497|ref|NP_148005.2| 132 YMLKCEACGAE 142
                                    77789999965 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.015        12      16      25 ..     114     123 ..     111     123 .. 0.86
   2 ?    5.1   0.2     0.022        18       3      11 ..     136     144 ..     135     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                   Rubredoxin_2  16 rCpsCgsWnt 25 
                                    rCp Cgs +t
  gi|118431497|ref|NP_148005.2| 114 RCPTCGSIDT 123
                                    8*****9665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.022
                   Rubredoxin_2   3 CsqCGfesa 11 
                                    C++CG+e++
  gi|118431497|ref|NP_148005.2| 136 CEACGAEQP 144
                                    999*99986 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00048      0.39       5      22 ..     103     121 ..      98     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                        DUF3797   5 qivkLdek.YvqCPeCgNn 22 
                                    q ++L  k Yv CP Cg +
  gi|118431497|ref|NP_148005.2| 103 QFLQLFMKtYVRCPTCGSI 121
                                    556676667*******975 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 ?   -3.0   0.0       7.4   6.1e+03      14      22 ..      82      90 ..      81      91 .. 0.75
   2 ?    5.1   0.1     0.023        19       6      12 ..     114     120 ..     113     125 .. 0.83
   3 ?    4.7   0.1      0.03        24       3      12 ..     132     141 ..     130     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.4
                        zf-RRN7 14 sftlddGfy 22
                                   s+ ++ G+ 
  gi|118431497|ref|NP_148005.2| 82 SYEEESGQL 90
                                   577799986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                        zf-RRN7   6 pCgvCgc 12 
                                    +C++Cg+
  gi|118431497|ref|NP_148005.2| 114 RCPTCGS 120
                                    8*****9 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.03
                        zf-RRN7   3 kgppCgvCgc 12 
                                    ++  C++Cg+
  gi|118431497|ref|NP_148005.2| 132 YMLKCEACGA 141
                                    6789*****8 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.014        11      40      70 ..      95     124 ..      86     129 .. 0.73
   2 ?    4.3   0.3     0.052        43      56      67 ..     131     142 ..     122     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                         DUF678  40 dvskvslsklkvavgkgntlrCaACgSsLtl 70 
                                     vs+  ++++ +  +  + +rC  CgS  t+
  gi|118431497|ref|NP_148005.2|  95 KVSRKVVNQFLQL-FMKTYVRCPTCGSIDTK 124
                                    5666666666666.89999*******97555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.052
                         DUF678  56 gntlrCaACgSs 67 
                                       l+C ACg +
  gi|118431497|ref|NP_148005.2| 131 AYMLKCEACGAE 142
                                    5679******75 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 ?    7.7   3.6    0.0033       2.7       4      31 ..     113     143 ..     110     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0033
                  zf-NADH-PPase   4 rFCgrCGa...ptepaeggwarvCpaCgleh 31 
                                      C++CG+   +  ++e  +++ C+aCg+e+
  gi|118431497|ref|NP_148005.2| 113 VRCPTCGSidtKLLRQERAYMLKCEACGAEQ 143
                                    569****653377777777889******996 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.6      0.04        32       4      12 ..     135     143 ..     133     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.04
                 PhnA_Zn_Ribbon   4 kCplCaSey 12 
                                    kC+ C++e 
  gi|118431497|ref|NP_148005.2| 135 KCEACGAEQ 143
                                    8****9995 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   5.4     0.024        19      24      70 ..      54      99 ..      42     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.024
                        DUF1451 24 klseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldle 70
                                   + +e  ++ k + +lva+yl+++l+ aa++ ees++ l  + ++  +
  gi|118431497|ref|NP_148005.2| 54 NFREIAQALKRDPKLVARYLQKELATAASYEEESGQ-LILNVKVSRK 99
                                   55666677788899********************99.3333333333 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       5.8   4.8e+03      28      35 ..      82      89 ..      82      89 .. 0.81
   2 ?    8.3   1.9    0.0025         2       4      33 ..     115     145 ..     114     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.8
                                   S-EEESSC CS
                 RNA_POL_M_15KD 28 gYeepadq 35
                                   +Yee+++q
  gi|118431497|ref|NP_148005.2| 82 SYEEESGQ 89
                                   69**9876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0025
                                    ESTTTSBEEEEECSCCCE.EEESSSS-EEES CS
                 RNA_POL_M_15KD   4 CpkCgNlLlpkedkegkn.feCrqCgYeepa 33 
                                    Cp+Cg+       +e  + + C  Cg+e+p 
  gi|118431497|ref|NP_148005.2| 115 CPTCGSIDTKLLRQERAYmLKCEACGAEQPV 145
                                    899998755555566666789********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       124  (0.00691617); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1142.16
//
Query:       gi|14601468|ref|NP_148006.1|  [L=288]
Description: hypothetical protein APE_1534 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00064   19.9   1.6     0.0015   18.7   1.6    1.6  1  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.6   8.2e-08    0.0015      19     129 ..       2     109 ..       1     115 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.2e-08
                Acetyltransf_6  19 evrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglr....sgdrl 95 
                                   ev +r+  dp +le+++e +++ w+ r d+  +     +lr+l++       + ++ + ++gr v++ +g       g+ +
  gi|14601468|ref|NP_148006.1|   2 EVVVRRLSDPVELEEAVEVHARAWGSR-DYR-EVVAPHILRALVDNG-----GLVLGAFVGGRMVGASYGWFvgcgEGRYF 75 
                                   5778999********************.988.566677888888885.....679999********996654222245577 PP

                Acetyltransf_6  96 yywlggydpelaklspgllllweliedaaeeGlr 129
                                   y + +g+ + ++  ++g  l ++  e+  +eG++
  gi|14601468|ref|NP_148006.1|  76 YSHATGVEEGYKYRGVGFALKARQREEVLREGVS 109
                                   7799999999********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2418.97
//
Query:       gi|118431498|ref|NP_148007.2|  [L=365]
Description: PflX-like protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-10   41.0   0.0    4.5e-10   40.2   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
      3e-06   27.6   0.0    5.4e-06   26.7   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
     0.0003   20.9   0.0    0.00051   20.2   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   7.5e-14   4.5e-10       2     157 ..     147     295 ..     146     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 7.5e-14
                                    EEESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    +++ gCn+ C+fC+++   + + +++++++++++ e+ ++l ae g++++  +gg+p    + +++  ++a         
  gi|118431498|ref|NP_148007.2| 147 IFYGGCNFTCVFCQNWDVsQWKARDAHIVTPRRLGEIQDRL-AEAGARNINHVGGDPVPSLHVIVESMKYASH---LKPQ 222
                                    6889************999999*******************.899**************99999999999997...8999 PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGend 157
                                       +n ++   e l+ l++l  d    +l+ ++d+ +  ++   +  +e + +++ +++e+ ++  ++r++++pG  +
  gi|118431498|ref|NP_148007.2| 223 LWNSNMYMT-LEALDILVDLI-DIWLPDLKFGNDR-CAMRLSaVPRYWEVTTRNILLAAEH-GD-MIIRHLVMPGHVE 295
                                    999999998.*********99.*************.666666699****************.67.9*********866 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.1e-10   5.4e-06       9     100 ..     146     235 ..     139     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.1e-10
                        Fer4_12   9 slfvsgCnlsCkgCfn..ketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpek 86 
                                    ++f +gCn+ C +C n   + w+ +  + +t   l ei ++l++   + +  +GG+P+      +++e +k+    kp  
  gi|118431498|ref|NP_148007.2| 146 TIFYGGCNFTCVFCQNwdVSQWKARDAHIVTPRRLGEIQDRLAEAGARNINHVGGDPVP--SLHVIVESMKYASHLKP-- 221
                                    689************933456888899999****************************9..77777777777777776.. PP

                        Fer4_12  87 diwlytgytleels 100
                                    + w ++ y+  e +
  gi|118431498|ref|NP_148007.2| 222 QLWNSNMYMTLEAL 235
                                    68888888655443 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 !   20.2   0.0   8.5e-08   0.00051       2      69 ..     148     211 ..     147     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.5e-08
                        Fer4_14   2 fvrlsgCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellk 69 
                                    f   +gCn+ C++C   + ++wk +  ++ t + l +i + l +     +++  +GG+P    + +++++
  gi|118431498|ref|NP_148007.2| 148 FY--GGCNFTCVFCQnwDVSQWKARDAHIVTPRRLGEIQDRLAEAGA--RNINHVGGDPV--PSLHVIVE 211
                                    55..9*********977778999999999999999877755555555..5599******9..45666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3167.12
//
Query:       gi|118431499|ref|NP_148008.2|  [L=223]
Description: triosephosphate isomerase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-06   26.9   3.9    4.1e-06   26.3   3.7    1.6  1  ThiG          Thiazole biosynthesis protein ThiG
    6.1e-06   25.6   0.0    1.6e-05   24.2   0.0    1.6  1  IGPS          Indole-3-glycerol phosphate synthase
      3e-05   23.5   0.0    0.00012   21.6   0.0    1.8  2  TIM           Triosephosphate isomerase
     0.0024   16.9   2.2     0.0046   16.0   2.2    1.4  1  FMN_dh        FMN-dependent dehydrogenase
     0.0056   16.2   0.6       0.16   11.4   0.5    2.2  2  PcrB          PcrB family
     0.0092   15.5   0.1      0.017   14.6   0.1    1.4  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
       0.12   11.7   5.9       0.29   10.5   6.1    1.5  1  NMO           Nitronate monooxygenase


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 !   26.3   3.7   1.6e-09   4.1e-06     170     221 ..     165     221 ..     112     223 .] 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.6e-09
                                    HHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH....HHHHHHHH CS
                           ThiG 170 iieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdp....vamArafk 221
                                    + + a  v v+  AGi   +da  a+elGa++vl+++av +akdp     ++A+a++
  gi|118431499|ref|NP_148008.2| 165 VARVApGVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKAKDPhgkmLELAEAMA 221
                                    444455789999********************************9333234567765 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   6.2e-09   1.6e-05     142     251 ..      96     213 ..      88     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.2e-09
                                    S-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE..-CHHHHHHCHCC-......TTSEEE CS
                           IGPS 142 ledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlev..dlntteeLaklvp......kdvllv 213
                                    ++ ++l+++++ a+slglevL    + ee ++a  l  +++     +L    +  +  + e ++  v+        v + 
  gi|118431499|ref|NP_148008.2|  96 VTYRHLQAVVSKARSLGLEVLACADTPEEAAAAALLRPSMVALEPPELIGTGIpvSQAKPEVITRGVEavarvaPGVAVL 175
                                    5778999*****************************************7655400444444555444433344246999* PP

                                    EESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHH CS
                           IGPS 214 aeSGiktredveklkeegvnafLvGeslmrqedvekai 251
                                    a  Gi+  ed+++  e g++++Lv +++m+++d + ++
  gi|118431499|ref|NP_148008.2| 176 AGAGITAGEDARRAVELGAQGVLVASAVMKAKDPHGKM 213
                                    ********************************987665 PP

>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.7e-08   0.00012       2     122 ..       4     118 ..       3     129 .. 0.78
   2 ?   -0.0   0.0      0.18   4.6e+02     157     183 ..     133     159 ..     121     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.7e-08
                                    EEEEE-TBTS-H..HHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHH CS
                            TIM   2 liagNwKmnktl..eeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaeml 79 
                                    ++a N+K++ +   e a+ l++ ++   +e +v+v++++p+++ ++++ +       ++ q ++  + Ga+TG + +e  
  gi|118431499|ref|NP_148008.2|   4 VLAVNMKTYSSAfgEGARRLARDAARVAREVDVRVILVAPLINASSLAGVY----GDVYIQHADPVDLGAHTGYTPVEAA 79 
                                    577889988865325677777777777777888999999998888766665....58999******************** PP

                                    HHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEE CS
                            TIM  80 kdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilC 122
                                    +  g++ v++ HsE +  ++  +++v    ++a + gl+++ C
  gi|118431499|ref|NP_148008.2|  80 AAEGLRGVMVNHSEHKVTYRHLQAVV----SKARSLGLEVLAC 118
                                    ****************9998765554....4455666777666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.18
                                    CEEEEE--GGGSSSS----HHHHHHHH CS
                            TIM 157 nvviAYePvWAiGtgktatpeqaqevh 183
                                      ++A eP   iGtg ++++ + + + 
  gi|118431499|ref|NP_148008.2| 133 PSMVALEPPELIGTGIPVSQAKPEVIT 159
                                    568999999999999888776655444 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   2.2   1.8e-06    0.0046     263     306 ..     163     206 ..     150     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
                                    HHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
                         FMN_dh 263 eiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                                    e v++v+  + vl+  Gi+ G+D+ +A+ lGA++vl++ +++ +
  gi|118431499|ref|NP_148008.2| 163 EAVARVAPGVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKA 206
                                    5577777789***************************9888755 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.032        82      23      61 ..      76     115 ..      58     129 .. 0.85
   2 !   11.4   0.5   6.2e-05      0.16     170     216 ..     161     208 ..     146     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.032
                                    HHHHHCTT-SEEEEECST.CHHHHHHHHHHHHHCTSSS-E CS
                           PcrB  23 veiviesgtDavmigGsq.svtldntvrllkkvsriklPi 61 
                                    ve+++ +g  +vm+  s+ +vt+ + + +++k + ++l +
  gi|118431499|ref|NP_148008.2|  76 VEAAAAEGLRGVMVNHSEhKVTYRHLQAVVSKARSLGLEV 115
                                    7899999**********99************999888765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.2e-05
                                    HHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHH CS
                           PcrB 170 evialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekde 216
                                     v a+ ++  +  ++ G Gi  +E+A++ ve  A  ++v  +v + ++
  gi|118431499|ref|NP_148008.2| 161 GVEAVARVAPGVAVLAGAGITAGEDARRAVELgAQGVLVASAVMKAKD 208
                                    5678888899999******************99999988888876653 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   6.5e-06     0.017      63     113 ..     163     211 ..     148     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.5e-06
                                    HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHH CS
                   His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelik 113
                                    ++v+++a    + v  G GI   ed+++++e+ga+ v +++a++k ++   
  gi|118431499|ref|NP_148008.2| 163 EAVARVAPG--VAVLAGAGITAGEDARRAVELGAQGVLVASAVMKAKDPHG 211
                                    344444444..8899999999999999999999999999999998777555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.1   0.00011      0.29     184     232 ..     157     210 ..     101     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                            NMO 184 Lvpqvldavd.....iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesd 232
                                    ++ + ++av+     + v+A  Gi  +++   a  lGA+gv ++++ + +k+  
  gi|118431499|ref|NP_148008.2| 157 VITRGVEAVArvapgVAVLAGAGITAGEDARRAVELGAQGVLVASAVMKAKDPH 210
                                    55555666667777899*******************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 1944.38
//
Query:       gi|118431500|ref|NP_148009.2|  [L=439]
Description: hypothetical protein APE_1539.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 3361.96
//
Query:       gi|14601473|ref|NP_148011.1|  [L=716]
Description: hypothetical protein APE_1543 [Aeropyrum pernix K1]
Scores for complete 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  129.4   0.0      2e-37  128.8   0.0    1.3  1  Helicase_RecD    Helicase
    1.6e-18   67.0   0.4    3.1e-08   33.3   0.0    3.3  3  GNAT_acetyltr_2  GNAT acetyltransferase 2
    1.4e-09   38.2   0.1    2.3e-08   34.3   0.0    2.8  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.1e-09   36.1   0.0    2.5e-08   33.9   0.0    2.1  3  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.3e-07   31.9   0.0    3.3e-07   30.6   0.0    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0006   19.6   0.0     0.0011   18.7   0.0    1.4  1  AAA_30           AAA domain
     0.0037   17.2   0.0     0.0089   15.9   0.0    1.5  1  DUF1726          Domain of unknown function (DUF1726)
     0.0053   17.2   0.4       0.08   13.3   0.2    2.9  4  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.027   14.6   0.0       0.11   12.5   0.0    2.1  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.029   14.3   0.1      0.068   13.2   0.1    1.5  1  FR47             FR47-like protein
      0.095   12.8   0.0       0.23   11.6   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.0   1.2e-40     2e-37       2     176 ..     212     381 ..     211     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 1.2e-40
                 Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegk.snilvtapskenvktlfeflakglealglke..eekkkkaekaelrvrkqrieyi 79 
                                   + +dRGRGKS ++Glala ++ ++   + +++ p++ +v+++++ l +gl+ lglk     +++ +e ++++    ri y 
  gi|14601473|ref|NP_148011.1| 212 VRGDRGRGKSYVIGLALAYAAWRRLiGRAVLVGPTPLSVQSVMAGLLRGLDVLGLKGhrVVRTSGGEVIRVSGPWFRIAYE 292
                                   679****************999988899***************************9955556666777777777******* PP

                 Helicase_RecD  80 apdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelreleleepiRy 160
                                   +pd++  ++    l+vvDEAAa+ ++ +++l  +  + ++atT+hGYEG+Gr+f  ++l ++    ++ + elel+epiRy
  gi|14601473|ref|NP_148011.1| 293 QPDTAEPSP----LVVVDEAAAVGVARVRRLSWRSGKSLVATTIHGYEGSGRAF-ARLLPNI---LPKPFIELELREPIRY 365
                                   *****9976....9****************************************.6777775...5679************ PP

                 Helicase_RecD 161 aegdplEkwlndlLlL 176
                                    +gdplE+wl+++++L
  gi|14601473|ref|NP_148011.1| 366 LPGDPLEEWLYTVFML 381
                                   **************98 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   1.9e-11   3.1e-08       2      62 ..     414     467 ..     413     480 .. 0.81
   2 !   16.4   0.1   2.8e-06    0.0046      96     128 ..     488     520 ..     481     532 .. 0.85
   3 !   13.8   0.0   1.7e-05     0.028     192     225 ..     532     565 ..     528     567 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-11
               GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesv 62 
                                   + ++lv++HY+n+P+DL+ +  +P+h++++L a+        ++++v  v lEG   +e++
  gi|14601473|ref|NP_148011.1| 414 VYGILVQAHYRNTPDDLLAMLESPHHRIYALEADG-------TPVAVADVVLEGPDVEEEA 467
                                   5789***************************9955.......4788888888886544444 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.8e-06
               GNAT_acetyltr_2  96 aRivRiAvhpelqkmGYGsralellekyyegkl 128
                                    R+ RiAvh++lq++G Gsr l+++e+   ++ 
  gi|14601473|ref|NP_148011.1| 488 WRVSRIAVHEDLQRRGLGSRLLRHVEAQARESG 520
                                   69*********************9998877665 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 1.7e-05
               GNAT_acetyltr_2 192 eLlkFWkragfspvylrqtaneltGEhsaimlrs 225
                                   + + FW ++gf+p+y++   n +tGE  + + ++
  gi|14601473|ref|NP_148011.1| 532 DVIPFWLKNGFKPFYVSPRYNRVTGEKNVALAKP 565
                                   5678**********************98877666 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.47   7.7e+02      52      80 ..     207     240 ..     111     242 .. 0.45
   2 !   34.3   0.0   1.4e-11   2.3e-08       4     117 .]     414     542 ..     411     542 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.47
                                   EEET.....TSTTEEEEEEEEESGGGTTSSHHHH CS
                Acetyltransf_1  52 kipd.....ekggvayieslaVspeyrgkGlGsa 80 
                                   ++         +g+ y+++la + +++++ +G+a
  gi|14601473|ref|NP_148011.1| 207 WRSAlvrgdRGRGKSYVIGLALAYAAWRRLIGRA 240
                                   2222333334556666666666666666666665 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.4e-11
                                   HHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET..TSTTEEEEE.................. CS
                Acetyltransf_1   4 lvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipd..ekggvayie.................. 64 
                                   ++ +lv  +   n  +++ ++ es   ++ ++++ e dg++++ + +    +  e++ ++++e                  
  gi|14601473|ref|NP_148011.1| 414 VYGILVQAH-YRNTPDDLLAMLES---PHHRIYALEADGTPVAVADVVLEGPdvEEEARIALErllymagspgsgvvswrv 490
                                   566666553.33555555556777...88899999**********655555545333333333555555555555556667 PP

                                   .EEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  65 .slaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                    ++aV+++ +++GlGs+Ll+++e +are g+    +++  + +  i+++ k GF
  gi|14601473|ref|NP_148011.1| 491 sRIAVHEDLQRRGLGSRLLRHVEAQARESGASL--VTTMFSRHDVIPFWLKNGF 542
                                   7****************************9944..3577889999****99998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.5   5.7e+03      35      50 ..     303     318 ..     296     341 .. 0.66
   2 ?   -3.6   0.0       6.3     1e+04      20      47 ..     428     455 ..     423     460 .. 0.80
   3 !   33.9   0.0   1.5e-11   2.5e-08      52     109 ..     488     545 ..     475     553 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.5
               Acetyltransf_10  35 vaeeggkivGvielrd 50 
                                   v+ ++   vGv+++r+
  gi|14601473|ref|NP_148011.1| 303 VVVDEAAAVGVARVRR 318
                                   5566779999999954 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.3
               Acetyltransf_10  20 ealrerieegealllvaeeggkivGvie 47 
                                   + l +++e++++ ++++e +g++v v+ 
  gi|14601473|ref|NP_148011.1| 428 DDLLAMLESPHHRIYALEADGTPVAVAD 455
                                   5566677899999999999999998875 PP

  == domain 3  score: 33.9 bits;  conditional E-value: 1.5e-11
               Acetyltransf_10  52 shisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkav 109
                                   +++s+++V+++ +++G+g++Ll +ve++a++ g +l +t+ + +  +pf  k GFk+ 
  gi|14601473|ref|NP_148011.1| 488 WRVSRIAVHEDLQRRGLGSRLLRHVEAQARESGASLVTTMFSRHDVIPFWLKNGFKPF 545
                                   589**************************9999888999****************986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     2e-10   3.3e-07      25      76 .]     488     544 ..     437     544 .. 0.58

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2e-10
                                   TCTEEEEE-GGGTTSSHHHHHHHH...TT..SEEEEEEEEE.THHHHHHHHHHTTEEE CS
                Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLlea...ae..kgiileqlel.naekaikfYeklGFee 76 
                                       r+aV+++ +++G+G++Ll++   ++  +g  l+ +++ + +  i+f+ k+GF++
  gi|14601473|ref|NP_148011.1| 488 WRVSRIAVHEDLQRRGLGSRLLRHveaQAreSGASLV-TTMfSRHDVIPFWLKNGFKP 544
                                   34556******************85441145663223.23332226799*******85 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.9e-07    0.0011       4     108 ..     190     319 ..     188     328 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.9e-07
                        AAA_30   4 aeQaaaveall...tsgdrvavltGpAGtGKttalkal..reaweaa.ggrviglAptgkaAkvLa....eelgieastia 74 
                                   ++Qa+a+e+l+    ++ r a++ G  G GK+++++ +   +aw++  g r +++ pt    + +     ++l++ +   +
  gi|14601473|ref|NP_148011.1| 190 ESQARALESLArffRGRWRSALVRGDRGRGKSYVIGLAlaYAAWRRLiG-RAVLVGPTPLSVQSVMagllRGLDVLGLKGH 269
                                   677777776542216788999*************987655899999966.5555555555444433133335555555555 PP

                        AAA_30  75 kllkrlk................grarlepgtllivDEagmvdtkqlaal 108
                                   +++++ +                +  + ep+ l++vDEa+ v+ + +++l
  gi|14601473|ref|NP_148011.1| 270 RVVRTSGgevirvsgpwfriayeQPDTAEPSPLVVVDEAAAVGVARVRRL 319
                                   555444566699999999999*855678889************9999988 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.4e-06    0.0089       5      52 ..      69     116 ..      67     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.4e-06
                       DUF1726   5 ekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelk 52 
                                   e++LG +y ++++     l+P +++   etVr GG + ++++p ++++
  gi|14601473|ref|NP_148011.1|  69 ERILGGEYAAAIIAVPGLLRPSIIAGAGETVRSGGFLAIVADPPDRWD 116
                                   79***************************************9999996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       7.1   1.2e+04      71     106 ..       9      42 ..       4      61 .. 0.62
   2 !   13.3   0.2   4.9e-05      0.08       4      48 ..     187     231 ..     185     262 .. 0.81
   3 ?   -1.5   0.0       1.7   2.8e+03      22      37 ..     324     340 ..     317     446 .. 0.76
   4 ?   -1.1   0.0       1.3   2.2e+03      38     117 ..     506     594 ..     503     618 .. 0.48

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 7.1
                        AAA_16  71 alaqalareellrqlldeaesaeleawrekleeala 106
                                    ++q l r++ lr ll    + ++ aw+ekl + ++
  gi|14601473|ref|NP_148011.1|   9 GFIQRL-RHSRLRGLLVV-GTGDVKAWAEKLAGYAG 42 
                                   466666.55666666544.44467777777666655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 4.9e-05
                        AAA_16   4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellral 48 
                                   +R e +++ l+ l r  +gr ++ l++G++G GKs ++  +l ++
  gi|14601473|ref|NP_148011.1| 187 CRSESQARALESLARFFRGRWRSALVRGDRGRGKSYVIGLALAYA 231
                                   677777777777888999********************8888544 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.7
                        AAA_16  22 grp.elvllsGesGvGK 37 
                                   g +  ++ ++G+ G+G 
  gi|14601473|ref|NP_148011.1| 324 GKSlVATTIHGYEGSGR 340
                                   44445566677777764 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.3
                        AAA_16  38 sslvrellralekdggiflrgkcdqlesaipy......salaqalareellrqlldeaesaeleawrekleealaavpela 112
                                   s+l+r++  +++++g+ ++++ + ++   ip+       ++     r   ++ +++ a ++ l+ + ++++e ++ + +l+
  gi|14601473|ref|NP_148011.1| 506 SRLLRHVEAQARESGASLVTTMFSRH-DVIPFwlkngfKPFYVSP-RYNRVTGEKNVALAKPLDSAGAEILEKASKTLALK 584
                                   67777777777777766666666666.445554444433333333.33444444444444445555555555444333333 PP

                        AAA_16 113 gaea.....s 117
                                    a+a     +
  gi|14601473|ref|NP_148011.1| 585 LALAgssiyR 594
                                   3333444443 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       8.2   1.3e+04      36      60 ..     394     418 ..     377     421 .. 0.74
   2 ?   12.5   0.0     7e-05      0.11      76     113 ..     490     527 ..     480     544 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8.2
                                   HHHHTTSEEEEEEETTEEEEEEEEE CS
                Acetyltransf_9  36 rklleesrvlgaedngelvgqlall 60 
                                    +++e sr ++a+d + l +++++l
  gi|14601473|ref|NP_148011.1| 394 ARPVEVSREVLARDREVLRSVYGIL 418
                                   5667778889999999999998775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7e-05
                                   EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE- CS
                Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegqplsllf 113
                                   v+ +av+ + ++rg+ s+Ll+++ +++re g++l++ +
  gi|14601473|ref|NP_148011.1| 490 VSRIAVHEDLQRRGLGSRLLRHVEAQARESGASLVTTM 527
                                   7889*****************************99866 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.2e-05     0.068      25      57 ..     491     523 ..     488     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.2e-05
                                   EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-E CS
                          FR47  25 galqvlpehrrrGlgsrlvkalakeiaergktv 57 
                                   + + v+++ +rrGlgsrl + + ++ +e g  +
  gi|14601473|ref|NP_148011.1| 491 SRIAVHEDLQRRGLGSRLLRHVEAQARESGASL 523
                                   5689******************99999988765 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   0.00014      0.23      27      61 ..     490     524 ..     475     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
               Acetyltransf_CG  27 fthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                   +  + V+e l+++G++++L +++  +are g + v
  gi|14601473|ref|NP_148011.1| 490 VSRIAVHEDLQRRGLGSRLLRHVEAQARESGASLV 524
                                   66789*************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 5130.06
//
Query:       gi|118431501|ref|NP_148012.2|  [L=198]
Description: hypothetical protein APE_1545.1 [Aeropyrum pernix K1]
Scores for complete 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-34  117.7  20.2    4.4e-34  117.7  20.2    1.7  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 ?   -3.4   2.2      0.59   1.1e+04       1      13 [.      14      26 ..      14      28 .. 0.86
   2 !  117.7  20.2   2.5e-38   4.4e-34       1     135 []      31     166 ..      31     166 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.59
                         DUF996  1 lsivGliLvlval 13
                                   l+i+G  Lvl+++
  gi|118431501|ref|NP_148012.2| 14 LGIAGSALVLLGI 26
                                   6899999999998 PP

  == domain 2  score: 117.7 bits;  conditional E-value: 2.5e-38
                         DUF996   1 lsivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaas.lilllllvlii 79 
                                    ls++G++Lvlv+l+++sk++++e+if+na+i+++lsi++++v++++++++++a+a al++++l+  ++ +i+ ll+ ++i
  gi|118431501|ref|NP_148012.2|  31 LSLIGFVLVLVSLYMLSKQMGEESIFRNAVISVVLSIAGFIVFAFLTGASFFAMAGALGSGELTALTAaGIGSLLAGFVI 110
                                    689*************************************************************988889********** PP

                         DUF996  80 ayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                    +y+++++savf+++++e+l+ rtgv++F++agl y++G+i++ivlvG +illia++
  gi|118431501|ref|NP_148012.2| 111 LYIAMVASAVFFRRALEALAGRTGVDMFRHAGLAYLVGSITLIVLVGGLILLIAWV 166
                                    *******************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 1470.52
//
Query:       gi|14601475|ref|NP_148013.1|  [L=131]
Description: hypothetical protein APE_1546 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00031   21.1   7.5    0.00031   21.1   7.5    2.1  2  CopD      Copper resistance protein D
     0.0046   17.0   5.6     0.0046   17.0   5.6    2.1  2  DUF2269   Predicted integral membrane protein (DUF2269)
  ------ inclusion threshold ------
      0.098   12.9   3.1       0.95    9.7   0.0    2.2  2  UPF0093   Uncharacterised protein family (UPF0093)
       0.11   11.1   0.1       0.14   10.8   0.1    1.1  1  EMP70     Endomembrane protein 70


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 ?   -0.6   0.6      0.39   1.8e+03      49      66 ..      13      30 ..       2      44 .. 0.52
   2 !   21.1   7.5   6.9e-08   0.00031       5     103 ..      42     124 ..      38     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.39
                          CopD 49 alllvllalaalnrfrlv 66
                                  ++ ++l a a ln ++l+
  gi|14601475|ref|NP_148013.1| 13 VFAAILWAGAILNSLWLL 30
                                  333333333333444444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 6.9e-08
                          CopD   5 rrF.srlalaavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrl 84 
                                    rF ++ a++ v+v  ++G+++a+lr         +y  l +aK++l+++l+++++++++rl +         g++l+ ++
  gi|14601475|ref|NP_148013.1|  42 LRFtGWPATLGVVVAGASGLAMAHLR---------GYPPLAHAKIGLYALLFIIGGYAHYRLAKSR-------GEGLD-TV 105
                                   5664566888888888******9999.........4556778********************9999.......66666.66 PP

                          CopD  85 rrsaalelvlalvvlllaa 103
                                    r++   ++++ ++l++++
  gi|14601475|ref|NP_148013.1| 106 DRLLLFTAAVLTAALVVVG 124
                                   6777777777776666665 PP

>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   5.6     1e-06    0.0046       2      90 ..       7      88 ..       6     100 .. 0.81
   2 ?   -0.8   0.1      0.31   1.4e+03      83      99 ..     108     124 ..     104     128 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                       DUF2269  2 llkllHilsavlllgtgigiafyllrasrtrdaaviaevarlvvladwlftatavillpvtGlwlvhlagwpl.kqsWlllsl 83
                                  ll+l+H+++a+l  g+++ +     +  r rd +     +rlv+++  + ++++v++   +Gl+++hl g+p      + l  
  gi|14601475|ref|NP_148013.1|  7 LLQLIHVFAAILWAGAILNSLW---LLARGRDSD-----LRLVLRFTGWPATLGVVVAGASGLAMAHLRGYPPlAHAKIGLYA 81
                                  899**********999887654...556677754.....799999999999********************974666666666 PP

                       DUF2269 84 vLyllag 90
                                  +L+++ g
  gi|14601475|ref|NP_148013.1| 82 LLFIIGG 88
                                  6676665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.31
                       DUF2269  83 lvLyllagalwlpVvwl 99 
                                   l+L+++a++  ++Vv+ 
  gi|14601475|ref|NP_148013.1| 108 LLLFTAAVLTAALVVVG 124
                                   56777777777777654 PP

>> UPF0093  Uncharacterised protein family (UPF0093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.7     0.026   1.2e+02       3      24 ..       3      24 ..       1      32 [. 0.84
   2 ?    9.7   0.0   0.00021      0.95      53     113 ..      41      99 ..      34     128 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.026
                       UPF0093  3 elylwikalHiiavisWmAglf 24
                                    y  ++ +H++a i W  +++
  gi|14601475|ref|NP_148013.1|  3 LSYMLLQLIHVFAAILWAGAIL 24
                                  579999***********87765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                       UPF0093  53 LlkiimtpamiltlvlGllllalaeglvalssgWlhvKlllvllllayhlvlaklrkklaa 113
                                   +l++  +pa + ++v+G+  la+a+  +      +h+K+ l +ll+++ +++++ + k + 
  gi|14601475|ref|NP_148013.1|  41 VLRFTGWPATLGVVVAGASGLAMAH--LRGYPPLAHAKIGLYALLFIIGGYAHYRLAKSRG 99 
                                   478999***********99999987..4566799**************9999987766554 PP

>> EMP70  Endomembrane protein 70
   #    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     286     352 ..      58     128 ..      48     131 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                         EMP70 286 llgflspsnrg..slltvalllyvllgliaGYvsarlyktfgge..kwkkntlltalllpgllflvfflln 352
                                   + g+   + rg   l+++ + ly+ll +i+GY+  rl k+ g+    + + +l+ta +l++ l++v  +l 
  gi|14601475|ref|NP_148013.1|  58 ASGLAMAHLRGypPLAHAKIGLYALLFIIGGYAHYRLAKSRGEGldTVDRLLLFTAAVLTAALVVVGSMLR 128
                                   4555444444422478899**********************754436666677788888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1081.38
//
Query:       gi|118431502|ref|NP_148014.2|  [L=578]
Description: acylamino-acid-releasing enzyme [Aeropyrum pernix K1]
Scores for complete 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-41  142.0   0.0    1.8e-40  138.7   0.0    2.0  2  Peptidase_S9   Prolyl oligopeptidase family
    6.2e-12   45.7   0.2    4.6e-11   42.8   0.1    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
      9e-10   38.2   0.3    3.9e-09   36.1   0.1    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    3.6e-09   37.6   8.3    1.2e-07   32.5   1.9    3.6  3  Abhydrolase_6  Alpha/beta hydrolase family
      5e-07   29.6   0.3    1.6e-06   27.9   0.3    1.7  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    2.4e-06   27.3   0.0    3.9e-05   23.3   0.0    2.7  2  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.011   15.6   0.5      0.058   13.2   0.5    2.0  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.075   11.8   0.0       0.11   11.2   0.0    1.2  1  DUF5010        Domain of unknown function (DUF5010)
       0.09   12.1   1.6       0.11   11.7   0.3    1.8  2  LIP            Secretory lipase


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.15     3e+02      51      77 ..      17      43 ..      10      47 .. 0.83
   2 !  138.7   0.0   9.1e-44   1.8e-40       8     196 ..     379     562 ..     373     575 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                                   HHHHHHHTTS--GGGEEEEEETHHHHH CS
                   Peptidase_S9 51 aaealakegyvdserlaitGgSyGGyl 77
                                   a+e+   +g+vd ++l + G S G ++
  gi|118431502|ref|NP_148014.2| 17 AVEKYSLQGVVDGDKLLVVGFSEGSVN 43
                                   567777899*************99765 PP

  == domain 2  score: 138.7 bits;  conditional E-value: 9.1e-44
                                    HHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-GG CS
                   Peptidase_S9   8 qlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrpd 87 
                                    ++la++G+ vv++n+rGs+gyGe+++ ++ ++    e++D+ aaa+++ + g++  ++l+i+G SyGGy+t++al+++p 
  gi|118431502|ref|NP_148014.2| 379 ASLAAAGFHVVMPNYRGSTGYGEEWRLKIIGDPCGGELEDVSAAARWARESGLA--SELYIMGYSYGGYMTLCALTMKPG 456
                                    5788***********************************************998..89********************** PP

                                    G-SEEEEESE---CCCHHCSTTS.THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHH CS
                   Peptidase_S9  88 lFkaavaevpvvdvlrydsdtdl.lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealklv 166
                                    lFka+va+++vvd+  ++  +d+ +  ++ e+ +   ++e ++ +sp++++d+  ++ pl lih ++D+r+p++  l+l+
  gi|118431502|ref|NP_148014.2| 457 LFKAGVAGASVVDWEEMYELSDAaFR-NFIEQLTG-GSREIMRSRSPINHVDR--IKEPLALIHPQNDSRTPLKPLLRLM 532
                                    ********************999665.58888887.5666688**********..************************* PP

                                    HHHH--S-SEEEEEETTS-SSTTSSHHHHH CS
                   Peptidase_S9 167 aaLqkkgknvlllifpdegHgvgkprakve 196
                                     +L  +gk+++ +i pd+gH +++ ++ v+
  gi|118431502|ref|NP_148014.2| 533 GELLARGKTFEAHIIPDAGHAINTMEDAVK 562
                                    ********************9998877665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   2.3e-14   4.6e-11       1     118 [.     357     475 ..     357     491 .. 0.87
   2 ?    0.6   0.0      0.18   3.6e+02     206     252 ..     490     554 ..     474     558 .. 0.71

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.3e-14
                                    SEEEEE-STTT..CGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB....CHHSHHHHHHHHHHHHHHCTTSS CS
                  Abhydrolase_1   1 pvlvilhGlpg..ssdvwaerglapaLakdgfdvillDlrGv.gySspapacin...ddygtasvaddldrildalgddk 74 
                                    p++v++hG+p    sd+w    +a  La +gf+v++++ rG+ gy++ +  +i       ++ +v +  ++++++    +
  gi|118431502|ref|NP_148014.2| 357 PTVVLVHGGPFaeDSDSWDT--FAASLAAAGFHVVMPNYRGStGYGEEWRLKIIgdpCGGELEDVSAAARWARESGLASE 434
                                    78*******9888*******..*******************75899999988888884457888**************** PP

                                    EEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHH CS
                  Abhydrolase_1  75 ltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqr 118
                                    l+++G+S+GG + l ++ + p   ka v+ ++     +++e  +
  gi|118431502|ref|NP_148014.2| 435 LYIMGYSYGGYMTLCALTMKPGLFKAGVAGAS---VVDWEEMYE 475
                                    ****************************9999...555555444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                                    C..............THHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS...EEEEEEETCSSSH CS
                  Abhydrolase_1 206 e..............lknvlaptlvisgtsDplvpp.kaledlaqllpk...krlvvisdagHla 252
                                    +              ++ +++p  +i+ ++D  +p    l+ + +ll +    + ++i+dagH +
  gi|118431502|ref|NP_148014.2| 490 GgsreimrsrspinhVDRIKEPLALIHPQNDSRTPLkPLLRLMGELLARgktFEAHIIPDAGHAI 554
                                    355556666678888899999***************66666666665556544557899999976 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.61   1.2e+03      54      93 ..       4      47 ..       3      49 .. 0.70
   2 !   36.1   0.1     2e-12   3.9e-09       4     119 ..     356     476 ..     353     546 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.61
                    Hydrolase_4 54 sfddyvdDlaafvekvkeehpel....plfllGhSmGGlially 93
                                   +f+++v+D++ ++   k   ++     +l ++G S G++ a ly
  gi|118431502|ref|NP_148014.2|  4 EFSRIVRDVERLIAVEKYSLQGVvdgdKLLVVGFSEGSVNAYLY 47
                                   58899999999973333222222345699********9988766 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 2e-12
                    Hydrolase_4   4 kavvvlvHG..laehsgryaelaeaLaaqGfavyalDhrGhGrse...gkrghvpsfddyvdDlaafvekvkeehpelpl 78 
                                      +vvlvHG  +ae s+  + +a+ Laa+Gf+v++ ++rG    +     +   ++    ++D++a+ + ++e    ++l
  gi|118431502|ref|NP_148014.2| 356 GPTVVLVHGgpFAEDSDSWDTFAASLAAAGFHVVMPNYRGSTGYGeewRLKIIGDPCGGELEDVSAAARWARESGLASEL 435
                                    579******777***************************864443244666677889999************999999** PP

                    Hydrolase_4  79 fllGhSmGGliallyllrypdkvaglilsaPalkikaklka 119
                                    +++G S GG+++l +l+++p  +++ +  a+++++++++++
  gi|118431502|ref|NP_148014.2| 436 YIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEEMYEL 476
                                    ****************************9*99999988632 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.16   3.2e+02      62     104 ..      21      72 ..       1     333 [. 0.62
   2 !   32.5   1.9   6.2e-11   1.2e-07       1     119 [.     359     492 ..     359     521 .. 0.66
   3 ?    5.3   0.0     0.014        27     181     211 ..     521     556 ..     497     563 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.16
                                    ........TTSEEEEEETCHHHHHHHHHHCC........EE...EEES-..----TTT CS
                  Abhydrolase_6  62 a......gggpvvlvGHSlGGalalaaapla......lvvg...vlldppptalpagl 104
                                           +g++  +vG S G + a +   +       l++     +ldp    ++ g 
  gi|118431502|ref|NP_148014.2|  21 YslqgvvDGDKLLVVGFSEGSVNAYL---YDggetvkLNREpinSVLDP---HYGVGR 72 
                                    25556666677777777777777777...55555554222233344444...333332 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 6.2e-11
                                    EEEE--GC.......GCHHHH.HHHHCCTCEEEEE--TTS.T..........S-GGCS--HHHCHHHHHHHCCTT....T CS
                  Abhydrolase_6   1 vlllHGagss..assWlvapL.aallaagvhvlapDlpGh.G..........rsdpppldledladlaalldelaa..gg 64 
                                    v+l+HG+++   ++sW    + a l+aag+hv++p ++G  G          + dp   +l   +d++a+++  ++   +
  gi|118431502|ref|NP_148014.2| 359 VVLVHGGPFAedSDSWD--TFaASLAAAGFHVVMPNYRGStGygeewrlkiiG-DPCGGEL---EDVSAAARWAREsgLA 432
                                    8*****99888899996..6646667777*********887433333333321.2222444...4443333333222245 PP

                                    TSEEEEEETCHHHHHHHHHHCC........EEEEES-..----TTT.....S----TTHHHHHHTT CS
                  Abhydrolase_6  65 gpvvlvGHSlGGalalaaapla......lvvgvlldppptalpagl.....laaalelllallall 119
                                     + +++G+S+GG++ l    ++      + +gv+ ++   ++++ +      aa+++++++l++  
  gi|118431502|ref|NP_148014.2| 433 SELYIMGYSYGGYMTLC---ALtmkpglFKAGVAGAS---VVDWEEmyelsDAAFRNFIEQLTGGS 492
                                    556**********8888...33344777778899999...77777777777777777777776644 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.014
                                    C.....HHHHCHHCCCHSTTEEET.CE...SSS-HHH CS
                  Abhydrolase_6 181 p.....lvprllerllaqagarlp.vvlpgaGHlphl 211
                                           + rl+ +lla +g++++ +++p+aGH+++ 
  gi|118431502|ref|NP_148014.2| 521 SrtplkPLLRLMGELLA-RGKTFEaHIIPDAGHAINT 556
                                    23433333377889999.8888877********7765 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.3   8.2e-10   1.6e-06      22     153 ..     360     484 ..     338     530 .. 0.76
   2 ?    0.0   0.0      0.26   5.2e+02     208     242 ..     489     523 ..     475     552 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.2e-10
                                    EEEEEESS-CCT.CCCCHTTCHHCCHGGGHHHHHTT-EEEEEE-TTSTTS-S---TT.....TTTHHHHHHHHHHHHHHC CS
                  Peptidase_S15  22 vlltrtPYgkndelasdkalaleelelqdkvfvarGYavVvqdvrGtggSeGeftvg.....dsdeaedgadvidWlakq 96 
                                    vl++  P+ +++   +d           ++ ++a G++vV+ + rG+ g   e+           e ed++++ +W+++ 
  gi|118431502|ref|NP_148014.2| 360 VLVHGGPFAEDS-DSWDTF---------AASLAAAGFHVVMPNYRGSTGYGEEWRLKiigdpCGGELEDVSAAARWARES 429
                                    555555555322.222222.........2239****************99999*9999999999*************999 PP

                                    TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCSECTTEEBCCH CS
                  Peptidase_S15  97 pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyyregGlvrapg 153
                                      ++ +   +G SY+G++ l a++ ++   ka v+ a+++d+ + +y    +   ++
  gi|118431502|ref|NP_148014.2| 430 GLAS-ELYIMGYSYGGYMTLCALTMKPGLFKAGVAGASVVDWEE-MYELSDAAFRNF 484
                                    4444.46789*********************************9.554444444444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.26
                                    --SSSHHHHTT-HHHHHCT--S-EEEEEECCSSTT CS
                  Peptidase_S15 208 tgdydafWkdrnlsedadkvkapvllvgGwnDwnv 242
                                    tg  ++  ++r++ +++d++k p+ l++  nD   
  gi|118431502|ref|NP_148014.2| 489 TGGSREIMRSRSPINHVDRIKEPLALIHPQNDSRT 523
                                    566778899*******************9999655 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.27   5.3e+02      79     115 ..       9      47 ..       2      54 .. 0.75
   2 !   23.3   0.0   1.9e-08   3.9e-05       8     191 ..     349     556 ..     342     562 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.27
                            DLH  79 lddl..kaavaylksvpevstkkvgvvGfCmGGalalll 115
                                    ++d+    av+++  ++ v+ +k+ vvGf  G   a+l+
  gi|118431502|ref|NP_148014.2|   9 VRDVerLIAVEKYSLQGVVDGDKLLVVGFSEGSVNAYLY 47 
                                    5554212578888889999**********9998777765 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.9e-08
                            DLH   8 pkna..kkpvvvviqeifGvn..dnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlk 83 
                                    + +a  + p+vv ++     +  d  +  +++la +G+ +++P+ Y++     ++e   + +     ++      l+d++
  gi|118431502|ref|NP_148014.2| 349 SGRAptPGPTVVLVHGGPFAEdsDSWDTFAASLAAAGFHVVMPN-YRGST-GYGEEWRLKIIG----DPC--GGELEDVS 420
                                    4444467888888886544445788888999************9.66666.344444333333....333..33357888 PP

                            DLH  84 aavaylksvpevstkkvgvvGfCmGGalalllaaev.pevdaavafYG.............................lsp 133
                                    aa +++++ +    +++ ++G+  GG ++l   + +   ++a va                                ++ 
  gi|118431502|ref|NP_148014.2| 421 AAARWARESG--LASELYIMGYSYGGYMTLCALTMKpGLFKAGVAGASvvdweemyelsdaafrnfieqltggsreiMRS 498
                                    9999999999..779**************9877777588899988555899999**********************999* PP

                            DLH 134 ekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFan 191
                                     ++++++++ik p+  ++ ++D   p + + +l  +l a+++++e ++ p+agHa + 
  gi|118431502|ref|NP_148014.2| 499 RSPINHVDRIKEPLALIHPQNDSRTPLKPLLRLMGELLARGKTFEAHIIPDAGHAINT 556
                                    ******************************************************9765 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   2.9e-05     0.058       1      89 [.     359     451 ..     359     465 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                    EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TT....TS-TTH.......HHHHHHHHHHHHHHTHHHHTET CS
                  Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAP....ehpfPa.......avedalaalrwlaeqawelgad 69 
                                    +v +HGG f  +++d+ d+++++la+ +g  vv+++Yr +     e+++          +ed+ aa+rw++e+       
  gi|118431502|ref|NP_148014.2| 359 VVLVHGGPFA-EDSDSWDTFAASLAA-AGFHVVMPNYRGSTgygeEWRLKIigdpcggELEDVSAAARWARES-----GL 431
                                    6889***995.788999999999998.8**********88644446666541111111667777777777776.....89 PP

                                    TCEEEEEEETHHHHHHHHHH CS
                  Abhydrolase_3  70 psrivlaGdSaGGnlaaava 89 
                                    +s+++++G S GG +++ ++
  gi|118431502|ref|NP_148014.2| 432 ASELYIMGYSYGGYMTLCAL 451
                                    9*************998765 PP

>> DUF5010  Domain of unknown function (DUF5010)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.8e-05      0.11      40      69 ..     369     398 ..     362     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                        DUF5010  40 dedewWDnlveelayagldfvavnvRGllp 69 
                                    ++++ WD + + la ag  +v++n RG + 
  gi|118431502|ref|NP_148014.2| 369 EDSDSWDTFAASLAAAGFHVVMPNYRGSTG 398
                                    45678**********************765 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.7   5.4e+03      63      83 ..      22      42 ..      17      44 .. 0.80
   2 ?   11.7   0.3   5.7e-05      0.11      18      93 ..     377     455 ..     372     466 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.7
                            LIP 63 kvtgiksdakvalwGYSgGsl 83
                                   ++ g+ +  k  + G+S+Gs+
  gi|118431502|ref|NP_148014.2| 22 SLQGVVDGDKLLVVGFSEGSV 42
                                   5668888899999******97 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.7e-05
                            LIP  18 livplLkeGyyVvvpDyeGpks.....tftvgrqsgkavLdsiraalksekvtgiksdakvalwGYSgGslAsawAaelq 92 
                                    + ++l + G+ Vv+p y G  +        +  ++    L+ + aa +  + +g++s     ++GYS+G+  +  A +++
  gi|118431502|ref|NP_148014.2| 377 FAASLAAAGFHVVMPNYRGSTGygeewRLKIIGDPCGGELEDVSAAARWARESGLAS--ELYIMGYSYGGYMTLCALTMK 454
                                    55677789***********999888553344456667889**************765..67889**********999887 PP

                            LIP  93 p 93 
                                    p
  gi|118431502|ref|NP_148014.2| 455 P 455
                                    7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.38
# Mc/sec: 4566.63
//
Query:       gi|118431503|ref|NP_148015.2|  [L=300]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-27   94.7   0.0    8.8e-27   94.3   0.0    1.2  1  ABC_tran     ABC transporter
    2.2e-14   54.0   0.0    1.3e-08   35.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.1e-06   27.3   0.0      0.037   13.5   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00074   19.3   0.2     0.0032   17.2   0.2    1.9  1  AAA_30       AAA domain
     0.0018   18.0   0.1     0.0034   17.1   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0028   18.2   0.0     0.0041   17.6   0.0    1.1  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.049   13.5   0.0    1.9  2  NTPase_1     NTPase
      0.018   15.5   0.1      0.036   14.4   0.1    1.6  1  AAA_16       AAA ATPase domain
      0.029   14.0   0.0      0.039   13.6   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.054   13.2   0.0      0.083   12.6   0.0    1.3  1  AAA_24       AAA domain
      0.055   14.2   0.0       0.34   11.6   0.0    2.2  2  DUF4162      Domain of unknown function (DUF4162)
      0.077   13.0   0.2        1.5    8.8   0.1    2.7  3  AAA_5        AAA domain (dynein-related subfamily)
      0.078   12.9   0.0       0.14   12.1   0.0    1.4  1  NACHT        NACHT domain
       0.08   13.2   0.1       0.23   11.7   0.1    1.7  2  AAA_22       AAA domain
       0.08   10.4   0.0       0.11   10.1   0.0    1.0  1  DUF3584      Protein of unknown function (DUF3584)
      0.085   13.3   0.0       0.33   11.4   0.0    1.8  2  AAA          ATPase family associated with various cellular a
       0.12   12.7   0.0       0.89    9.8   0.0    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.14   11.9   0.0          8    6.2   0.0    2.1  2  IstB_IS21    IstB-like ATP binding protein
       0.15   11.8   0.2       0.21   11.3   0.2    1.2  1  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.18   12.0   0.0       0.59   10.4   0.0    1.8  2  AAA_28       AAA domain
       0.22   11.1   0.0       0.65    9.6   0.0    1.7  2  AAA_27       AAA domain
       0.24   11.0   0.1       0.39   10.3   0.1    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.0   1.1e-29   8.8e-27       3     135 ..      22     163 ..      20     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 1.1e-29
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                     vs+++  ge+  i+G+nG+GK+tLl++++g l+p  G++++ g d+  + ++++r  ig+ pq+p + +++t +e    
  gi|118431503|ref|NP_148015.2|  22 GVSFSVGDGERACIMGPNGSGKTTLLRMVSGVLRPSGGSVRVCGYDVWGDGWREARGLIGFAPQDPPMARRMTGAEYitv 101
                                    79**********************************************************************988889** PP

                                    ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                               +++e+ ++l+ lg +++  +vv    + LSgGq++ + +a al+++p++++lDEp
  gi|118431503|ref|NP_148015.2| 102 vggllglspgVARREARRVLEMLGFEDVLGRVV----ARLSGGQRRALGIALALASNPEVVVLDEP 163
                                    *********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 !   17.0   0.0   4.9e-06     0.004       3      24 ..      34      55 ..      33      87 .. 0.85
   2 !   35.0   0.0   1.6e-11   1.3e-08     232     299 ..     132     195 ..     106     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                   ++ GpNgsGK++LL+  +++ r
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMVSGVLR 55
                                   688************9988754 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 1.6e-11
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                    + ++ lS G++r+l++++al++ +    ++++DEp +gL+ ++ ++l+  l+++ + g  v++++H+p
  gi|118431503|ref|NP_148015.2| 132 RVVARLSGGQRRALGIALALASNP---EVVVLDEPGSGLDVRARESLWASLRKAFK-GRTVLFSSHDP 195
                                    556678****************99...9********************88855545.8*********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 !   11.8   0.1   0.00015      0.12      27      45 ..      33      51 ..      24      63 .. 0.83
   2 !   13.5   0.0   4.5e-05     0.037     136     205 ..     136     201 ..     110     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                   EEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlldAil 45
                                    +i+GpNGSGK+ ll  ++
  gi|118431503|ref|NP_148015.2| 33 ACIMGPNGSGKTTLLRMVS 51
                                   68**********9987766 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.5e-05
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                     LSgG++  + +aL +A +   p  +++lDe  + LD + ++ +   l+++ k   ++  s++ +  e  
  gi|118431503|ref|NP_148015.2| 136 RLSGGQRRALGIALALASN---P-EVVVLDEPGSGLDVRARESLWASLRKAFKGRTVLFSSHDPQEAEAE 201
                                    69******99999998864...3.4789*************************99999999998877665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   3.9e-06    0.0032      20     114 ..      32     181 ..      21     207 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.9e-06
                         AAA_30  20 vavltGpAGtGKttalkalreaweaag..................grviglAptg.kaAkvLa.............eelg 67 
                                     a++ Gp G+GKtt+l+ +  +++ +g                  + +ig+Ap+   +A++++              + g
  gi|118431503|ref|NP_148015.2|  32 RACIMGPNGSGKTTLLRMVSGVLRPSGgsvrvcgydvwgdgwreaRGLIGFAPQDpPMARRMTgaeyitvvggllgLSPG 111
                                    47899*********************857777777777777777766777777652356666644333333333331222 PP

                         AAA_30  68 ieastiakllkrlk......................grarlepg.tllivDEagm.vdtkqlaallkaaek 114
                                    ++ +   ++l+ l+                      +  +l+++ ++++ DE g  +d +  ++l ++++k
  gi|118431503|ref|NP_148015.2| 112 VARREARRVLEMLGfedvlgrvvarlsggqrralgiA-LALASNpEVVVLDEPGSgLDVRARESLWASLRK 181
                                    2222222222222233355555555555555777643.344444477777776542366666665555555 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 !   17.1   0.1   4.1e-06    0.0034      23      49 ..      30      57 ..      18      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.1e-06
                         AAA_29 23 g.atlltGpsGsGKSTllDAiqalLvpa 49
                                   g    ++Gp+GsGK+Tll  ++ +L p+
  gi|118431503|ref|NP_148015.2| 30 GeRACIMGPNGSGKTTLLRMVSGVLRPS 57
                                   34789*************8888888886 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.1e-06    0.0041      23      39 ..      34      50 ..      24      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.1e-06
                         AAA_23 23 lItGpNGaGKTTildAi 39
                                   +I GpNG+GKTT+l+ +
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMV 50
                                   8************9865 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.049       3      32 ..      34      65 ..      32      86 .. 0.76
   2 ?   -0.5   0.0       1.2     1e+03      75     105 ..     134     164 ..     125     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                                   EEE--TTSSHHHHHHHHHHHH...G..GGEEE CS
                       NTPase_1  3 fiTGppGvGKtTlvkkvlellkssg..vkvgG 32
                                   +i Gp G+GKtTl++ v+ +l+ sg  v+v+G
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMVSGVLRPSGgsVRVCG 65
                                   688******************99973356666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                    EE-HHHHHHHHHHHHHHHHHHH-EEEE---S CS
                       NTPase_1  75 vvdvesfeelalealrkalseadviviDEiG 105
                                    v ++   ++ al +     s+++v+v+DE G
  gi|118431503|ref|NP_148015.2| 134 VARLSGGQRRALGIALALASNPEVVVLDEPG 164
                                    55555555566655555568999*****977 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.5e-05     0.036      23      56 ..      29      62 ..      23     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekdggifl 56
                                   ++e   + G+ G+GK++l+r++   l+ +gg + 
  gi|118431503|ref|NP_148015.2| 29 DGERACIMGPNGSGKTTLLRMVSGVLRPSGGSVR 62
                                   4556679**************9977777765554 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 ?   13.6   0.0   4.8e-05     0.039       9      36 ..      25      52 ..      18     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                                   S-EBTT-EEEEEESTTSSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslsk 36
                                   f+++ G+r +i+g +g Gkt++++++s 
  gi|118431503|ref|NP_148015.2| 25 FSVGDGERACIMGPNGSGKTTLLRMVSG 52
                                   8999*******************99875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.083       4      22 ..      32      50 ..      29      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                   + +i+Gp+g+GKTtl+++ 
  gi|118431503|ref|NP_148015.2| 32 RACIMGPNGSGKTTLLRMV 50
                                   78*************9987 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.5     2e+03       5      31 ..     178     206 ..     177     212 .. 0.76
   2 ?   11.6   0.0   0.00042      0.34      47      80 ..     260     294 ..     217     295 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.5
                                    HHHTTS-SSEEEEE.-------..--.-E CS
                        DUF4162   5 eiKrsygknrieve.adaeelleepg.ve 31 
                                     ++++++++++  +  d+ e+++e++ v 
  gi|118431503|ref|NP_148015.2| 178 SLRKAFKGRTVLFSsHDPQEAEAESDrVL 206
                                    589***99999999877777777766565 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00042
                                    -----------.----EEEEEEEE---HHHHHHHH CS
                        DUF4162  47 eeaanellkal.tsgveirsFeeeePsLndIFiek 80 
                                      +  ++ +a   +g+ ++++e+ +PsL ++F  +
  gi|118431503|ref|NP_148015.2| 260 PGDVARIASAYsGAGILVERIEVLKPSLREVFFAV 294
                                    34677888888459999***************766 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 ?    8.8   0.1    0.0018       1.5       3      23 ..      34      54 ..      32      64 .. 0.84
   2 ?    0.6   0.0      0.63   5.1e+02      39      73 ..     127     162 ..     117     207 .. 0.84
   3 ?   -1.4   0.0       2.7   2.2e+03      38      57 ..     219     238 ..     217     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                   EEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  3 lLvGppGtgKselaerlaaal 23
                                   ++ Gp G+gK++l + ++ +l
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMVSGVL 54
                                   899***********9999877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.63
                                    HHHH--B--..........--------G-SEEEEES CS
                          AAA_5  39 edlkgrreik.ngttslvdsplvraaregeilvlDE 73 
                                    ed++gr+  + +g++++  +++   a ++e++vlDE
  gi|118431503|ref|NP_148015.2| 127 EDVLGRVVARlSGGQRRALGIALALASNPEVVVLDE 162
                                    567777776678888888888888888999999998 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.7
                                    HHHHH--B--.........- CS
                          AAA_5  38 eedlkgrreikngttslvds 57 
                                    +++l++r+ +k++ +++ d 
  gi|118431503|ref|NP_148015.2| 219 PRELIQRYAPKPRVRVWADR 238
                                    689***********999985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.14       3      20 ..      33      50 ..      31      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                   EEEEC-TTTCHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkl 20
                                    ++ G++GsGKTtLl+ +
  gi|118431503|ref|NP_148015.2| 33 ACIMGPNGSGKTTLLRMV 50
                                   5899***********976 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   0.00029      0.23       9      25 ..      34      50 ..      29      63 .. 0.91
   2 ?   -2.4   0.0       6.4   5.2e+03      39      99 ..     154     162 ..     132     188 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                         AAA_22  9 vvtGesGtGKTtllrrl 25
                                   +++G+ G+GKTtllr++
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMV 50
                                   79************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.4
                         AAA_22  39 rpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDE 99 
                                    +                                                    +e++++DE
  gi|118431503|ref|NP_148015.2| 154 N----------------------------------------------------PEVVVLDE 162
                                    2....................................................45666666 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00013      0.11      19      37 ..      32      50 ..      25      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                        DUF3584 19 htnieGtNaaGKTtLlrLi 37
                                   +  i G N++GKTtLlr++
  gi|118431503|ref|NP_148015.2| 32 RACIMGPNGSGKTTLLRMV 50
                                   67799************97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00041      0.33       2      22 ..      34      54 ..      33      88 .. 0.76
   2 ?   -0.8   0.0       2.3   1.9e+03      55      74 ..     150     170 ..     111     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00041
                                   EEESSTTSSHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakel 22
                                   +++Gp G GKT+l + v   l
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMVSGVL 54
                                   789*************98776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                                    HTS.TSEEEEEETGGGHHHHH CS
                            AAA  55 eka.kpsilfiDEidalaksr 74 
                                    + a +p ++++DE  +    r
  gi|118431503|ref|NP_148015.2| 150 ALAsNPEVVVLDEPGSGLDVR 170
                                    333458999999966655555 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 ?    9.8   0.0    0.0011      0.89      26      89 ..     130     180 ..     114     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    l r +++lSGG++  ++ +al      ++ s      ++++v+LDE  s+lD + +++l + l+
  gi|118431503|ref|NP_148015.2| 130 LGRVVARLSGGQR-RALGIAL------ALAS------NPEVVVLDEPGSGLDVRARESLWASLR 180
                                    5577888899988.2222333......3334......4789*************9999988776 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    0.0098         8      40      63 ..      22      46 ..       8      56 .. 0.84
   2 ?    3.6   0.0      0.06        49     102     150 ..     148     195 ..     130     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0098
                      IstB_IS21 40 tlsf.iekkenivllGpsGvGKshl 63
                                   + sf + + e  +++Gp G GK+ l
  gi|118431503|ref|NP_148015.2| 22 GVSFsVGDGERACIMGPNGSGKTTL 46
                                   555546788999**********987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.06
                      IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlp 150
                                    al+   ++++++lD+ g   ld  ++e l+  + k+++ r+++ +s  p
  gi|118431503|ref|NP_148015.2| 148 ALALASNPEVVVLDEPGS-GLDVRARESLWASLRKAFKGRTVLFSSHDP 195
                                    555667889*******95.79*********************9999876 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 ?   11.3   0.2   0.00026      0.21       1      29 [.      35      63 ..      35      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvav 29
                                   ++Gp GsGKtt+ + +s +l+ +g sv+v
  gi|118431503|ref|NP_148015.2| 35 IMGPNGSGKTTLLRMVSGVLRPSGGSVRV 63
                                   79***************999988888776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00072      0.59       2      19 ..      33      50 ..      32      75 .. 0.88
   2 ?   -2.2   0.0       5.1   4.2e+03      66      86 ..     196     216 ..     185     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00072
                         AAA_28  2 ivitGgestGKTtlleaL 19
                                    +i+G+ ++GKTtll+  
  gi|118431503|ref|NP_148015.2| 33 ACIMGPNGSGKTTLLRMV 50
                                   69************9976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                         AAA_28  66 eeaaaaankvlfcDrglldtl 86 
                                    +ea+a++++vl++ rg l+ +
  gi|118431503|ref|NP_148015.2| 196 QEAEAESDRVLIMHRGRLAAW 216
                                    567777788888777777665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0008      0.65      18      48 ..      22      52 ..      11      55 .. 0.78
   2 ?   -1.9   0.0       2.6   2.1e+03     137     173 ..     256     291 ..     253     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0008
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisd 48
                                    ++fs ++ +   i+GpN +GK+t+lr +s 
  gi|118431503|ref|NP_148015.2| 22 GVSFSVGDGERACIMGPNGSGKTTLLRMVSG 52
                                   5778888888889*************98875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.6
                         AAA_27 137 lleaegelgqlLfeasaGlaslrevleaLeaeadelf 173
                                    l+ea g++++ + +a +G   l e +e L+ + +e+f
  gi|118431503|ref|NP_148015.2| 256 LIEAPGDVAR-IASAYSGAGILVERIEVLKPSLREVF 291
                                    7889999988.58999999999999999988877776 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 ?   10.3   0.1   0.00048      0.39       4      20 ..      34      50 ..      32      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                                   EEEESTTCCHHHHHHHH CS
                           cobW  4 vltGflGsGKTtLlnhl 20
                                    + G+ GsGKTtLl+ +
  gi|118431503|ref|NP_148015.2| 34 CIMGPNGSGKTTLLRMV 50
                                   589***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2190.87
//
Query:       gi|118431504|ref|NP_148016.2|  [L=374]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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   44.2   7.1    4.8e-11   42.4   7.1    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00022   20.7   9.4    0.00046   19.7   5.9    2.1  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 !   42.4   7.1   5.3e-15   4.8e-11       2     344 ..      29     361 ..      28     362 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 5.3e-15
                ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdidg 81 
                                    s l++ + +P++l++++ +if  +      + ++v+ e +s+     +e le+   v+ v+e+ s+ e+ ++l  g i  
  gi|118431504|ref|NP_148016.2|  29 SVLLWYIGFPLLLLVIAKYIFLGGG---GAPVVGVYPE-GSPA----YEVLES-MGVK-VEEYGSLGELFEDLSRGFIVV 98 
                                    5788****************99877...5666775555.5555....677776.4466.67**************99998 PP

                ABC2_membrane_3  82 ilvipkgfskdllkgesatvtvlinssnlnss.......kailnalnsllqqlnasalv......lqseatstsaninve 148
                                    +++ ++g  + l+  +  ++++l ++    ++       +                  +       +++ +  +a ++ve
  gi|118431504|ref|NP_148016.2|  99 AVIEENGEARVLY--SGEEYSLLAQGVAEAVAasrlaggP------------------GagedlrALESLLFRAAGVHVE 158
                                    8877777776655..3444444555555444422333331..................1334444456677889999999 PP

                ABC2_membrane_3 149 stql.eeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill. 226
                                     +     +    a + v l+ + +++i ++  +v+++  ++ +++ l  +s+  p +++     + ++++l+++l il  
  gi|118431504|ref|NP_148016.2| 159 PFIDnAGPGRALAEYSVNLVGVESLYIALYGGMVMLIAMRREGMLDLVASSPGGPRSLLGFMTGMNLTASLVTTLAILTa 238
                                    977646666888999999***************************************99999999999999999988765 PP

                ABC2_membrane_3 227 .lafgl...gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifs 302
                                     +a+g    g++  ++++  +l+l+++ ++   +  ls l+k +eta +l++i  +ll++  g+ +p e lp+ l+ ++ 
  gi|118431504|ref|NP_148016.2| 239 sIALGAdysGVSPAGVVAGAFLILVGLETIFLASIPLSLLVKAEETAAALAGIAGFLLIFSTGLAVPREMLPGLLAEASL 318
                                    7788876666666677777788888888888889999*******************999999999*************** PP

                ABC2_membrane_3 303 iiPffapglgllrlitgd.plweillsliilalfavvylllal 344
                                    ++P++   ++ ++ i+   +++e+l+  + l+l+ ++ +l+++
  gi|118431504|ref|NP_148016.2| 319 YFPLTLAVELGKDAIFASaTPSEVLTEAWPLYLSLALAGLVGI 361
                                    ***************7666888888777777777777766655 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.01        91      14      41 ..      24      50 ..      19      67 .. 0.83
   2 !   19.7   5.9   5.2e-08   0.00046      69     204 ..     191     328 ..     147     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.01
                  ABC2_membrane 14 rwrdpslgllwrliqplllalvfgtvfg 41
                                     r+ps + lw + +plll+++  ++f 
  gi|118431504|ref|NP_148016.2| 24 LRRSPSVL-LWYIGFPLLLLVIAKYIFL 50
                                   56777777.9**************9998 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.2e-08
                  ABC2_membrane  69 tsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaass 146
                                    + v+++ +r++g+l+   +sp   + + +  ++ ++l+ sl+ +l++l+ ++ l g d+s  + + +++ ++l+++ + +
  gi|118431504|ref|NP_148016.2| 191 M-VMLIAMRREGMLDLVASSPG-GPRSLLGFMTGMNLTASLVTTLAILTASIAL-GADYSgvSPAGVVAGAFLILVGLET 267
                                    2.33555555566666666666.6666666666666777777777777777777.9999987444445555555555554 PP

                  ABC2_membrane 147 lgll...isalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavea 204
                                    ++l+   +s l++ +e+a+ la++  ++l++ +G  +p++++p+ l   + + Plt ave+
  gi|118431504|ref|NP_148016.2| 268 IFLAsipLSLLVKAEETAAALAGIAGFLLIFSTGLAVPREMLPGLLAEASLYFPLTLAVEL 328
                                    4444334999*************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2864.24
//
Query:       gi|14601479|ref|NP_148017.1|  [L=319]
Description: hypothetical protein APE_1552 [Aeropyrum pernix K1]
Scores for complete 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-21   76.9  15.7      2e-21   76.7  15.7    1.1  1  Voltage_CLC  Voltage gated chloride channel
    1.5e-12   47.7   0.7    3.8e-06   27.3   0.1    2.5  2  CBS          CBS domain


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7  15.7   2.2e-25     2e-21     219     353 ..       3     143 ..       1     144 [. 0.92

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 2.2e-25
                                   CSCC.CSSSSCCHHHHHCTT-S-.........HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHH CS
                   Voltage_CLC 219 llpasvlgggyeliasllegstl.........llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvl 290
                                   + p  v g+g + +a++l+g++          l+++++l+++ llk++at+l++gsg +gG+faP L+ GA+lG  + +++
  gi|14601479|ref|NP_148017.1|   3 AAPF-VAGSGRGVLAAVLSGEPVswipvgeagLWAFTVLATAGLLKIAATSLSIGSGGSGGVFAPGLLGGALLGLSFYALI 82 
                                   5566.8889999999999887668889999999999*****************************************9999 PP

                                   HHH-CTSSC...HHHHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHHC CS
                   Voltage_CLC 291 alllpgaassdpgafalvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkavad 353
                                   + +   +a+ + +a+a +Gm af+a+++++pl++ ++v E+ +++ l++p +la+++A+ v++
  gi|14601479|ref|NP_148017.1|  83 QEV--AQAPLPAAAYAYLGMSAFFAAAAKVPLATSIMVAEMGNNYLLIPPSLLASIVAREVSG 143
                                   999..4566788**********************************************99875 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   4.2e-10   3.8e-06      11      51 ..     191     230 ..     181     236 .. 0.87
   2 !   18.5   0.1   2.3e-07     0.002       9      56 ..     253     300 ..     239     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 4.2e-10
                                   EEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                           CBS  11 tvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                    v+ dt+ e +l+lm ekg   +PVVd+dg+++G++t   l
  gi|14601479|ref|NP_148017.1| 191 PVRHDTPAESVLKLM-EKGAPVVPVVDGDGRPIGVITPDSL 230
                                   6899***********.9887789999***********9876 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.3e-07
                                   CEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHHH CS
                           CBS   9 vvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllrall 56 
                                    ++v +d+ + + le+m  ++   ++ VVd dg++ G v  + ++ al+
  gi|14601479|ref|NP_148017.1| 253 APVVGEDEGVDDMLEKMLTYEsEAAI-VVDRDGRYKGTVLIEEVIAALA 300
                                   46899***********9865522366.9*****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2641.77
//
Query:       gi|118431505|ref|NP_148018.2|  [L=335]
Description: hypothetical protein APE_1555.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-48  163.4   4.1    8.4e-48  163.4   4.1    2.1  2  Voltage_CLC  Voltage gated chloride channel


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.5   1.2    0.0079   1.4e+02     161     179 ..      23      41 ..       3      49 .. 0.56
   2 !  163.4   4.1   4.7e-52   8.4e-48       2     212 ..      73     284 ..      72     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.0079
                                    GGGHHHHHHHHHHHHHHHH CS
                    Voltage_CLC 161 llelilfvllGilgGllga 179
                                      +l+++ llG+++Gl ++
  gi|118431505|ref|NP_148018.2|  23 AAALAFYWLLGVVAGLTAY 41 
                                    3344555555555555554 PP

  == domain 2  score: 163.4 bits;  conditional E-value: 4.7e-52
                                    HHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHHTT. CS
                    Voltage_CLC   2 ggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrllkl 81 
                                    g+l+++l+v+++ pea+g+G++   +a++++ +++++r+ +vk++as + vg+G+s G eGp+vqiGA++gs ++rll+l
  gi|118431505|ref|NP_148018.2|  73 GALVSSLIVYRFSPEAEGHGTDAAVKAFHRRAAQIPFRTGVVKAVASSILVGTGGSGGVEGPSVQIGASIGSTIARLLRL 152
                                    789****************************************************************************9 PP

                                    --SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T..---... CS
                    Voltage_CLC  82 srndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepafge..veslfa 158
                                    + +d +r  ++aG+++ ++A F++Plg ++fa E+ + r+++++al+p+fv+s++a+ ++ +  g+ep + +  v+   +
  gi|118431505|ref|NP_148018.2| 153 RIED-RRVALVAGMSGALSALFHSPLGSAFFAAEVlYKRDLEVQALVPAFVSSITAYTLATVA-GYEPPLPRlvVDGSDF 230
                                    8777.777***************************888*******************999998.7887766555666669 PP

                                    --GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHH CS
                    Voltage_CLC 159 lsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgll 212
                                    +s+++++ ++llG +++ +g+l++r+++ +er fr+le l ++  l+p+l+ l+
  gi|118431505|ref|NP_148018.2| 231 YSPQSIASYILLGAFLAPFGYLYARIFRESERGFRRLESLGLPRTLRPVLGRLA 284
                                    *************************************98888877799998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2517.99
//
Query:       gi|118431506|ref|NP_148020.2|  [L=312]
Description: alcohol dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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   67.1   0.7    3.6e-18   65.8   0.0    1.9  2  ADH_zinc_N      Zinc-binding dehydrogenase
    6.9e-11   42.0   0.1    2.2e-08   34.0   0.0    3.1  2  ADH_N           Alcohol dehydrogenase GroES-like domain
    9.5e-11   42.9   0.1    1.5e-10   42.3   0.1    1.4  1  ADH_zinc_N_2    Zinc-binding dehydrogenase
    6.3e-06   25.8   0.2    8.7e-06   25.4   0.2    1.1  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
     0.0011   18.4   0.1     0.0028   17.2   0.1    1.7  1  adh_short       short chain dehydrogenase
  ------ inclusion threshold ------
      0.022   14.7   0.2      0.042   13.7   0.2    1.5  1  NAD_binding_10  NAD(P)H-binding
       0.03   14.6   0.5       0.08   13.2   0.5    1.8  1  FAF             Fantastic Four meristem regulator
      0.037   13.3   0.7      0.054   12.8   0.7    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.094   12.2   0.1       0.14   11.6   0.1    1.3  1  Epimerase       NAD dependent epimerase/dehydratase family
        0.2   10.7   0.4        7.1    5.6   0.1    2.6  3  RmlD_sub_bind   RmlD substrate binding domain


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 ?   -1.5   0.1       1.3   2.3e+03      73      90 ..     136     153 ..     122     155 .. 0.78
   2 !   65.8   0.0     2e-21   3.6e-18       1     129 [.     156     276 ..     156     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                                    HHHHHCEEEEEEEEECSC CS
                     ADH_zinc_N  73 eaalkllkpgGrlvvvGg 90 
                                     a++++++pg r+ v G+
  gi|118431506|ref|NP_148020.2| 136 AASVASVRPGERVLVTGA 153
                                    578999999999999996 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 2e-21
                                    HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakk.lGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    gv l+++q++  lGaev+a  +s+ek++ +++ lG+++v      d+    +e      vdvv+e+vG   t+++++++l
  gi|118431506|ref|NP_148020.2| 156 GVALHGIQYLQLLGAEVVAYTRSREKARVLEEeLGVEAVTSL---DF---YRERG---RVDVVMETVG-APTINESMRAL 225
                                    8999**************************999******999...55...56667...9*********.*********** PP

                                    EEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdlla 129
                                    +p+Grlv++G  +ge +   +++ l+++e++i G+   + r+e+++a++ +a
  gi|118431506|ref|NP_148020.2| 226 RPRGRLVLIGNITGEPVtiKRPALLVMREITISGTAAFT-RKEWEAAIKTIA 276
                                    ***********666664444444477*************.*******99876 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 !   34.0   0.0   1.2e-11   2.2e-08       2     108 ..      29     114 ..      28     115 .. 0.89
   2 ?   -2.0   0.1       1.8   3.3e+03      48      62 ..     137     151 ..     128     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.2e-11
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                    g+v ++v+++g+Cg Dl ++kg   ++ k+pl+lGHE+ G           l+ G+ V v+p+i+   C++C        
  gi|118431506|ref|NP_148020.2|  29 GWVPVEVRSVGMCGRDLVVWKG-GFPNLKPPLVLGHEVFG-----------LHDGRPVSVYPAIAVPGCPDCP------- 89 
                                    7999******************.7**************99...........5679999999999999999995....... PP

                                    TTBEETTTSS-SSSBSEEEECGGGEEE CS
                          ADH_N  82 eeakllgvsldGgfaeyvvvpekklvk 108
                                       ++lg +l+Gg+ae+v+vp+++l++
  gi|118431506|ref|NP_148020.2|  90 --PSILGENLPGGYAERVYVPRENLIP 114
                                    ..5789999999999999999999887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                    TT-CS--TT-EEEE- CS
                          ADH_N  48 pevkklkvGdrVvve 62 
                                     +v +++ G+rV+v 
  gi|118431506|ref|NP_148020.2| 137 ASVASVRPGERVLVT 151
                                    568889999999986 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 !   42.3   0.1   8.2e-14   1.5e-10      13     133 .]     198     310 ..     168     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 8.2e-14
                                    THHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHH CS
                   ADH_zinc_N_2  13 dfeaatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsvkyeflfsmkasaqadile 91 
                                    df    +++ vDvv +tvg +++  +s+++l+++Grlv ig  +  + ++ +pa+    r ++++      a+ +++  e
  gi|118431506|ref|NP_148020.2| 198 DFY--RERGRVDVVMETVGAPTI-NESMRALRPRGRLVLIGnITGEPVTIKRPAL-LVMREITISGTA---AFTRKE-WE 269
                                    453..33566*********9998.*******888******944446666666666.444444444444...454556.** PP

                                    HHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  92 elaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                    +  + i++G ++p     + l++++ A++   +g+ +G+iV+
  gi|118431506|ref|NP_148020.2| 270 AAIKTIAKGGVKPFYK-AYRLDQINNALKEALQGARIGRIVI 310
                                    ***************7.9***********************7 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 !   25.4   0.2   4.9e-09   8.7e-06      25     176 ..     138     277 ..     126     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.9e-09
                    Glu_dehyd_C  25 safewep.esalvlGa.GslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemd 102
                                    s ++ +p e++lv+Ga G + L  +  l++   g e v v  +r+r++ ++ l eelG   v+s    +d    +   +d
  gi|118431506|ref|NP_148020.2| 138 SVASVRPgERVLVTGAsGGVALHGIQYLQL--LGAE-V-VAYTRSREKARV-LEEELGVEAVTS----LDFY-RERGRVD 207
                                    455555546889999757788888777776..4555.3.344566655555.7899**999976....7777.68899** PP

                    Glu_dehyd_C 103 lvvEaTGsakhafeaiealapnGvaaLlGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaa 176
                                    +v+E+ G++  + e+++al+p G  +L+G  +++ v ++  +l   lv++   + G+    r+++eaa++t+a+
  gi|118431506|ref|NP_148020.2| 208 VVMETVGAP-TINESMRALRPRGRLVLIGNITGEPVTIKRPAL---LVMREITISGTAAFTRKEWEAAIKTIAK 277
                                    *******65.689*************************99998...79999*******************9986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.5e-06    0.0028       2      47 ..     147     192 ..     146     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                                    EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT CS
                      adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee 47 
                                     vlvtGas+G+ +   + l   Ga+vv++ rs ek++ + +el+ e
  gi|118431506|ref|NP_148020.2| 147 RVLVTGASGGVALHGIQYLQLLGAEVVAYTRSREKARVLEEELGVE 192
                                    59**********************************9999998865 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 ?   13.7   0.2   2.4e-05     0.042       1      45 [.     152     195 ..     152     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevve 45 
                                    GA+G+v+ + ++ l    g ev+a++R+ ek+  le+e g+e+v+
  gi|118431506|ref|NP_148020.2| 152 GASGGVALHGIQYLQLL-GAEVVAYTRSREKARVLEEELGVEAVT 195
                                    9**************99.5*****************999999876 PP

>> FAF  Fantastic Four meristem regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   4.5e-05      0.08      16      52 ..     195     233 ..     176     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                            FAF  16 vllrshredGRL..vleevkvpsrheylraeRedGRLrL 52 
                                    + l  +re GR+  v+e v +p  +e +ra R +GRL+L
  gi|118431506|ref|NP_148020.2| 195 TSLDFYRERGRVdvVMETVGAPTINESMRALRPRGRLVL 233
                                    567789999995549**********************99 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7     3e-05     0.054      16      77 ..     132     196 ..     122     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                                    EEETTCEETCB---.EEEEEST.SHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE CS
                    AlaDh_PNT_C  16 kgtlaGgvpgvepa.kvlviGg.GvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev 77 
                                    +++ a+ v  v+p+ +vlv G+ G + l+ i+  + lga+V+++  + ++++ le+ lg + v+ 
  gi|118431506|ref|NP_148020.2| 132 TMMHAASVASVRPGeRVLVTGAsGGVALHGIQYLQLLGAEVVAYTRSREKARVLEEeLGVEAVTS 196
                                    455666777788885799***778899***********************999999888886665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     8e-05      0.14       1      79 [.     148     220 ..     148     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8e-05
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HHH CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggvaa 79 
                                    +lVtGa+G +  + +++l+  g ev++ +r +++ +  + e     el +   ++l+ + ++ ++d+v+   +  ++++
  gi|118431506|ref|NP_148020.2| 148 VLVTGASGGVALHGIQYLQLLGAEVVAYTRSREKARVLE-E-----ELGVEAVTSLDFYRERGRVDVVMETVGAPTINE 220
                                    79*****************************55555433.2.....566666666666666667777776666555555 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 ?    5.6   0.1     0.004       7.1       2      34 ..     147     181 ..     146     215 .. 0.79
   2 ?   -0.4   0.0      0.28     5e+02     165     187 ..     198     220 ..     187     226 .. 0.83
   3 ?    2.4   0.0     0.039        70     245     282 ..     239     276 ..     215     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.004
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..T CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..e 34 
                                    ++lvtGa+G ++ + ++ l+  g+ev+a tr+  +
  gi|118431506|ref|NP_148020.2| 147 RVLVTGASGGVALHGIQYLQLLGAEVVAYTRSreK 181
                                    79***************************998441 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.28
                                    HHHHH-SEEEEESS-EE--EEHH CS
                  RmlD_sub_bind 165 rlakereelkvvaDqlgsPTsar 187
                                    +  +er +++vv   +g+PT  +
  gi|118431506|ref|NP_148020.2| 198 DFYRERGRVDVVMETVGAPTINE 220
                                    5568999*************866 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.039
                                    CS--SS---SBE-B--HHHHHCCT----BHHHHHHHHH CS
                  RmlD_sub_bind 245 eyptpAkRPanSvLdtekleatfgiklrewrealkevl 282
                                      p   kRPa  v++   ++ t  ++ +ew++a+k++ 
  gi|118431506|ref|NP_148020.2| 239 GEPVTIKRPALLVMREITISGTAAFTRKEWEAAIKTIA 276
                                    568899****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2439.48
//
Query:       gi|14601483|ref|NP_148021.1|  [L=279]
Description: hypothetical protein APE_1558 [Aeropyrum pernix K1]
Scores for complete 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   40.3   0.9    8.4e-10   38.6   0.2    2.2  2  Mrr_N     Mrr N-terminal domain
    8.7e-06   25.8   0.1       0.08   12.9   0.1    2.8  3  HSDR_N    Type I restriction enzyme R protein N terminus (HSD
    7.3e-05   22.7   0.0    0.00014   21.8   0.0    1.5  1  HSDR_N_2  Type I restriction enzyme R protein N terminus (HSD
     0.0013   19.1   0.1     0.0032   17.8   0.1    1.7  1  HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
  ------ inclusion threshold ------
      0.051   13.5   0.6          5    7.1   0.0    3.2  3  MarR      MarR family
       0.15   12.0   0.5         16    5.5   0.1    2.6  2  HTH_12    Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.94   2.8e+03      55      76 ..     121     142 ..     108     146 .. 0.81
   2 !   38.6   0.2   2.8e-13   8.4e-10       8      76 ..     211     278 ..     206     279 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.94
                         Mrr_N  55 gWartyLkkagllespkrgvwk 76 
                                   +W   +L+++g +e+ +  +w+
  gi|14601483|ref|NP_148021.1| 121 SWIVYDLYREGNIEQKQILTWS 142
                                   6999999999999988766665 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 2.8e-13
                         Mrr_N   8 lLealad.gsehrlkeirervaerfglseeeraellpsgkqtrfknrvgWartyLkkagllespkrgvwk 76 
                                   +L +l++ ++  ++kei er++  f+ +ee+++ l ++g+  r++nr++W +++L k+gl+++ k gv+k
  gi|14601483|ref|NP_148021.1| 211 ILTILKSeKRPLSVKEIFERAQIMFEPTEEDKKVL-SNGE-VRWQNRIRWELSKLAKEGLIKRVKEGVYK 278
                                   78999888888999*****************9987.5885.5**************************97 PP

>> 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 !   10.2   0.0   0.00018      0.54       2      34 ..      34      66 ..      33      71 .. 0.89
   2 !   12.9   0.1   2.7e-05      0.08     123     191 ..      71     130 ..      64     133 .. 0.82
   3 ?   -1.2   0.0      0.57   1.7e+03      38      38 ..     194     194 ..     136     265 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                                  SSHHHHHH.HHHHHHHHTT-EE........... CS
                        HSDR_N  2 lsEaeleqelidellrelGyqvlskkdveiegr 34
                                   +Ea ++  lid++lr+ G++  ++k+v +e +
  gi|14601483|ref|NP_148021.1| 34 RNEALTRYVLIDPFLRSIGWDLGNPKEVIPEFS 66
                                  58999999*******************999876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2.7e-05
                                   -EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---SSSGGGGG-.....-EEEEE-SS-EEEEE--SS CS
                        HSDR_N 123 rpDivlfvnglplvviElKrpgtieeAinQikryrkeksdvsipqlfrYl.....qfgvisngketrfyaktkr 191
                                    pD+ l+++ +  ++iE+K+ g                +dv +     Y+     q++ i++g+ + +y+  ++
  gi|14601483|ref|NP_148021.1|  71 VPDYALLQDDKLFMFIEAKALG--------------KIKDVDQVKVVSYAvtkgvQYLTITDGDSWIVYDLYRE 130
                                   59******************65..............2334447777888888899**************98765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.57
                                   . CS
                        HSDR_N  38 v 38 
                                   +
  gi|14601483|ref|NP_148021.1| 194 L 194
                                   1 PP

>> HSDR_N_2  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 !   21.8   0.0   4.8e-08   0.00014      35     102 ..      68     132 ..      40     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.8e-08
                      HSDR_N_2  35 kkkraDivvykkdkkpllivecKapsvkiseevleqlksYlealkaeylvvtNglehivykvdkkkkk 102
                                   + + +D+++ ++d k ++++e+Ka    i++ +   + sY+ + +++yl +t+g++ ivy++ +++++
  gi|14601483|ref|NP_148021.1|  68 EVGVPDYALLQDD-KLFMFIEAKALGK-IKDVDQVKVVSYAVTKGVQYLTITDGDSWIVYDL-YREGN 132
                                   55678******88.*********9874.6666677788999999****************97.44444 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.1e-06    0.0032       3      30 ..     207     234 ..     205     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHHHHHH-S-EEHHHHHHHHHHH CS
                      HARE-HTH   3 lkeaAkqVLeeegrpltvkeIwekiqek 30 
                                     ++++++L++e+rpl+vkeI e++q +
  gi|14601483|ref|NP_148021.1| 207 ARDIILTILKSEKRPLSVKEIFERAQIM 234
                                   578999*******************965 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0017         5       8      41 ..     123     156 ..     116     161 .. 0.91
   2 ?   -0.9   0.0      0.53   1.6e+03       8      29 ..     211     233 ..     211     234 .. 0.72
   3 ?    2.5   0.1     0.046   1.4e+02      39      51 ..     261     273 ..     260     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0017
                                   HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHH CS
                          MarR   8 iLrilyeqgplsvseLakklgvskstvtrvldrL 41 
                                   i++ ly++g++ ++++   ++ s  +vt ++++L
  gi|14601483|ref|NP_148021.1| 123 IVYDLYREGNIEQKQILTWSMSSDDAVTIAIKAL 156
                                   7789************************999998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.53
                                   HHHHHHHSTT.EEHHHHHHHHTS CS
                          MarR   8 iLrilyeqgp.lsvseLakklgv 29 
                                   iL+il+++   lsv+e+ ++ ++
  gi|14601483|ref|NP_148021.1| 211 ILTILKSEKRpLSVKEIFERAQI 233
                                   677776554449****9998765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.046
                                   HHHHHTTSEEEEE CS
                          MarR  39 drLekkGlieRsk 51 
                                    +L k+Gli+R k
  gi|14601483|ref|NP_148021.1| 261 SKLAKEGLIKRVK 273
                                   59*********76 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 ?    5.5   0.1    0.0054        16       3      20 ..     211     228 ..     209     236 .. 0.90
   2 ?    4.1   0.0     0.015        46      34      52 ..     255     273 ..     239     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0054
                        HTH_12   3 ILkilaesdkpigakeia 20 
                                   IL il+ +++p++ kei 
  gi|14601483|ref|NP_148021.1| 211 ILTILKSEKRPLSVKEIF 228
                                   9***************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                        HTH_12  34 avRyrLrkleergltrrvg 52 
                                    +R  L kl ++gl++rv 
  gi|14601483|ref|NP_148021.1| 255 RIRWELSKLAKEGLIKRVK 273
                                   59***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2161.50
//
Query:       gi|118431507|ref|YP_874900.1|  [L=94]
Description: hypothetical protein APE_1558a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 755.15
//
Query:       gi|118431508|ref|YP_874901.1|  [L=94]
Description: hypothetical protein APE_1558b [Aeropyrum pernix K1]
Scores for 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-12   46.3   0.2    6.1e-12   46.0   0.2    1.1  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
    1.5e-10   40.9   0.0    1.9e-10   40.6   0.0    1.1  1  ParE-like_toxin  ParE-like toxin of type II bacterial toxin-a
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.023   14.8   0.0    1.1  1  Gp49             Phage derived protein Gp49-like (DUF891)
       0.12   12.6   0.0       0.19   11.9   0.0    1.3  1  HigB_toxin       HigB_toxin, RelE-like toxic component of a t


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 !   46.0   0.2   1.4e-15   6.1e-12       3      90 .]       6      86 ..       4      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.4e-15
                                   EEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE...CTSTCCTTEEEEEECTEEEEEEEETSTTEEEEE CS
                     ParE_toxin  3 ltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrp...rrelglkglrririgdyriiYriddeelvvvil 81
                                   +  +A++dlk++ +           +++ +  ++e+l+enp +g+    +  l+   ++++r+gdyr++Y +  + ++v+i+
  gi|118431508|ref|YP_874901.1|  6 IESSAKRDLKRLPK----------HIVQWVLNTVEELEENPFIGERlhlPASLHGLYCFKLRRGDYRLVYCYVPNRDTVYII 77
                                   6679********76..........569*******************554444446689999999*******988888999** PP

                                   EEEEHHHHC CS
                     ParE_toxin 82 rvlhrsedy 90
                                   +v+hr e+y
  gi|118431508|ref|YP_874901.1| 78 AVGHRGEIY 86
                                   *****9987 PP

>> ParE-like_toxin  ParE-like toxin of type II bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   4.1e-14   1.9e-10       1      85 [.       4      88 ..       4      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.1e-14
                ParE-like_toxin  1 vlqtrrfkkalkklkeklkadldkavkeiiedPelGeeKk..GDLsgvfvykfklnkqltllaYeldekkrvlvlllvGthe 80
                                   v+ ++++k+ lk+l ++  + + ++v+e+ e+P +Ge+      L g+++  fkl+   ++l Y++++++ ++++++vG + 
  gi|118431508|ref|YP_874901.1|  4 VYIESSAKRDLKRLPKHIVQWVLNTVEELEENPFIGERLHlpASLHGLYC--FKLRRGDYRLVYCYVPNRDTVYIIAVGHRG 83
                                   577899*******************************9872356777766..7788999*********************** PP

                ParE-like_toxin 81 NfYre 85
                                     Y++
  gi|118431508|ref|YP_874901.1| 84 EIYEK 88
                                   ***97 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 ?   14.8   0.0   5.1e-06     0.023       2      67 ..      13      76 ..      12      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                           Gp49  2 eldalpkkarakilaaldlleeggpdlgkplvkkle.dglwElrpksaggiiRvlyafdpgrkvilL 67
                                   +l++lpk + + +l +++ lee+ p +g+ l    + +gl+ ++ ++++  +R++y++ p+r  + +
  gi|118431508|ref|YP_874901.1| 13 DLKRLPKHIVQWVLNTVEELEEN-PFIGERLHLPASlHGLYCFKLRRGD--YRLVYCYVPNRDTVYI 76
                                   799*****************999.56777777666678*******7666..********99955443 PP

>> HigB_toxin  HigB_toxin, RelE-like toxic component of a toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.3e-05      0.19      35      66 ..      50      80 ..      45      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                                   STEEEEEETTTTEEEEEEEETTTTEEEEEEEE CS
                     HigB_toxin 35 nnrvvFnIkgNkyRLivaieyerkkvyirfil 66
                                   + +++F +++ +yRL+  +  +r +vyi  ++
  gi|118431508|ref|YP_874901.1| 50 G-LYCFKLRRGDYRLVYCYVPNRDTVYIIAVG 80
                                   4.89************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 784.52
//
Query:       gi|118431509|ref|YP_874902.1|  [L=57]
Description: hypothetical protein APE_1558c [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0006   19.5   1.9    0.00093   18.9   1.9    1.3  1  HTH_23    Homeodomain-like domain
     0.0046   17.0   0.0     0.0055   16.7   0.0    1.2  1  HTH_7     Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.9     1e-07   0.00093       2      38 ..      19      55 ..      18      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-07
                         HTH_23  2 asereRlrillllaeGlsvreIAreLgvsrrTvyrwl 38
                                   ++e+ R+ril+ + e++ ++++ ++ gvsr T++r l
  gi|118431509|ref|YP_874902.1| 19 LREDARYRILRRVVEKHGRKQVVELAGVSRVTLWRLL 55
                                   68999*****************************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 !   16.7   0.0   6.2e-07    0.0055      13      42 ..      26      55 ..      16      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.2e-07
                                   GGGSSTTTT--STTTSSSS---SSSS--SS CS
                          HTH_7 13 rvvkLleeGisiskIAkevnisRsTvYRyl 42
                                   r+++++ e++ ++++++  ++sR T+ R l
  gi|118431509|ref|YP_874902.1| 26 RILRRVVEKHGRKQVVELAGVSRVTLWRLL 55
                                   79999*********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 474.74
//
Query:       gi|118431510|ref|NP_148023.2|  [L=308]
Description: hypothetical protein APE_1559.1 [Aeropyrum pernix K1]
Scores for complete 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   50.4   0.6    7.5e-13   48.9   0.6    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
      2e-05   24.2   0.0    2.9e-05   23.7   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00042   20.2   0.0    0.00067   19.6   0.0    1.2  1  Lactamase_B_3  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 !   48.9   0.6   1.3e-16   7.5e-13       4     135 ..      16     145 ..      13     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-16
                                    CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                     ++n++l+e+ g  +L+DtG+++ +           +++ dvd v+ TH+H+DHi g + l+  + +++  ++ +a  l+
  gi|118431510|ref|NP_148023.2|  16 PFSNCVLVEDAGFKVLVDTGCEPWE-----------RGLVDVDVVVFTHFHPDHIRGFHRLRAGRVAAPEGEEPYAGRLE 84 
                                    579******************9855...........5556**************************************** PP

                                    CHHHHHHHHHCCHH.........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCE CS
                    Lactamase_B  84 meeaddaasrkgll.........lagvsadkpdvdeeeldgnaggrralyvtggpghghgh 135
                                    + ++ +a +r+  +         l+gv++++ ++ + e+  ++g +  +y+  g++ +h+ 
  gi|118431510|ref|NP_148023.2|  85 RLALRFAGERWREWismarlvmdLEGVPEPGEYFRPGEDLCFRGVCIKTYPARGHLQTHTL 145
                                    **********************************************************986 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   4.9e-09   2.9e-05      21      55 ..      38      70 ..      22     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.9e-09
                                   --SSS--..SEEEEE-SS--HHHHGGGGCCCCC-- CS
                  Lactamase_B_2 21 PvelrdelppidaVllthaHyDHlaglltlrelrp 55
                                   P e  + l ++d+V++th H DH+ g+  lr++r 
  gi|118431510|ref|NP_148023.2| 38 PWE--RGLVDVDVVVFTHFHPDHIRGFHRLRAGRV 70
                                   443..56789*********************9543 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 !   19.6   0.0   1.1e-07   0.00067       7      50 ..      18      59 ..      15      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-07
                  Lactamase_B_3  7 hnsflletagarilvDPfkanlgyeppaeeaDlvlisqaledHa 50
                                   +n++l+e+ag ++lvD +     +e+  +++D+v+ ++ ++dH 
  gi|118431510|ref|NP_148023.2| 18 SNCVLVEDAGFKVLVDTGC--EPWERGLVDVDVVVFTHFHPDHI 59
                                   69**************765..7888999***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2506.55
//
Query:       gi|14601485|ref|NP_148024.1|  [L=59]
Description: hypothetical protein APE_1559a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-13   50.5   2.0    3.1e-13   49.7   2.0    1.4  1  zf-CDGSH  Iron-binding zinc finger CDGSH type


Domain annotation for each model (and alignments):
>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   2.0   1.7e-17   3.1e-13       1      47 [.      11      42 ..       3      43 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.7e-17
                      zf-CDGSH  1 nGPllVeGdvelvdadgesvelregrevvaLCrCgrSknkPfCDgsH 47
                                  nGP+l+e                +g+  +aLCrCg+S+nkP+CDg+H
  gi|14601485|ref|NP_148024.1| 11 NGPYLLEV---------------DGKVQTALCRCGHSNNKPYCDGTH 42
                                  66666621...............222339****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 498.59
//
Query:       gi|14601486|ref|NP_148025.1|  [L=138]
Description: hypothetical protein APE_1561 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.2   0.0       0.13   11.9   0.0    1.2  1  DUF2201_N  Putative metallopeptidase domain


Domain annotation for each model (and alignments):
>> DUF2201_N  Putative metallopeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.1e-06      0.13      51      75 ..      71      95 ..      51     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-06
                     DUF2201_N 51 flesllleeqvgvlaHevlHvalrH 75
                                   ++ l+lee+v v++He+lH+ +  
  gi|14601486|ref|NP_148025.1| 71 KFDPLPLEEKVKVVIHELLHIPRTF 95
                                  3489*****************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1128.51
//
Query:       gi|118431511|ref|NP_148026.2|  [L=239]
Description: hypothetical protein APE_1563.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1977.95
//
Query:       gi|118431512|ref|NP_148027.2|  [L=214]
Description: hypothetical protein APE_1564.1 [Aeropyrum pernix K1]
Scores for complete 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  210.4   1.3    2.3e-62  210.1   1.3    1.0  1  PIN_5         PINc domain ribonuclease
  ------ inclusion threshold ------
       0.06   13.0   0.2       0.14   11.8   0.2    1.7  1  Nucleolin_bd  Nucleolin binding domain


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 !  210.1   1.3   2.5e-66   2.3e-62       2     201 ..      13     202 ..      12     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.1 bits;  conditional E-value: 2.5e-66
                          PIN_5   2 fvlDTsaltdpevreklgeeeleeavkklldliaearlklgiscyippsvykElkeflkreeveeeviakldtwlvkksp 81 
                                     v DT+++td+++re lg+++leea++ + +++a+a+ ++g+++yi+psv +E+++f+  ++v++++ia+l++w+ +k p
  gi|118431512|ref|NP_148027.2|  13 VVADTTMFTDAKLREVLGARSLEEAARIMARILARAS-RMGLTVYITPSVRAEIERFMLGNGVHPTTIARLMAWVRVKPP 91 
                                    589********************************97.899*************************************** PP

                          PIN_5  82 dryevkipaeilyeyveevrerinkGlrvaEeavreaaeeseklekeeeeeevgelikklRekYrealRkGilDsaeDld 161
                                    +++e+++pa++++ yve+vr+r++kGlrvaE++vr+a ++++         e g+++++lRekYre +RkG+lDs eD+d
  gi|118431512|ref|NP_148027.2|  92 TTHELRLPAAMFRRYVETVRARLDKGLRVAEDHVRRALRSRD---------EEGDIVRSLREKYREYTRKGMLDSVEDVD 162
                                    **************************************9976.........679************************** PP

                          PIN_5 162 vllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvl 201
                                     llLA EL aa+v+sDeG+++ ae+lGl+++++ ++ + +
  gi|118431512|ref|NP_148027.2| 163 TLLLALELGAAIVTSDEGLRRAAEDLGLTVLTPVELLEYI 202
                                    ********************************98877654 PP

>> Nucleolin_bd  Nucleolin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   1.6e-05      0.14      32      48 ..     136     152 ..     125     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.6e-05
                   Nucleolin_bd  32 damaaeLqrqYreYgRr 48 
                                    ++++++L+++YreY R+
  gi|118431512|ref|NP_148027.2| 136 GDIVRSLREKYREYTRK 152
                                    5799************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1602.46
//
Query:       gi|118431513|ref|NP_148028.2|  [L=385]
Description: hypothetical protein APE_1567.1 [Aeropyrum pernix K1]
Scores for complete 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-19   69.5   0.0    4.1e-19   68.8   0.0    1.3  1  Lig_C           Ligase Pab1020 C-terminal region
    1.1e-14   55.0   0.0    1.8e-14   54.4   0.0    1.3  1  RNA_ligase      RNA ligase
  ------ inclusion threshold ------
      0.079   12.6   0.0        1.8    8.1   0.0    2.2  2  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   6.9e-23   4.1e-19       3     114 ..     265     370 ..     263     380 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 6.9e-23
                                    CCSCCGS-STSCHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---EEEEEEE-SSHHHHHHHHH CS
                          Lig_C   3 fsylfelgrdFlfsRviReafqavefeeseeelrerakeLGesiLepmvetikkvkeeekvkeefrvrfkdeenieelle 82 
                                    ++y+fe gr+Flf R++Re f+ +e        r r+ eLGe+iL p +e++++v+++ ++ eef++ f +e ++ee ++
  gi|118431513|ref|NP_148028.2| 265 MRYPFEEGRSFLFPRILREIFREWETG------RRRYGELGEAILAPAIEAVEAVSRGGRLVEEFELVFANEVEAEEVIA 338
                                    69*****************99977754......5689******************************************* PP

                                    HHHCTT--EEEEEEE..TTEEEEE..EE-HHH CS
                          Lig_C  83 hLrrlgvkaeveekekedgelvvkfkkiaqst 114
                                    ++ +lgv++e+    +  + + v f+k  +s 
  gi|118431513|ref|NP_148028.2| 339 YFASLGVHLEIAGVARGVDGVRVAFRKPRKSE 370
                                    ***************99999999998876654 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   2.9e-18   1.8e-14       2     149 ..      93     245 ..      92     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 2.9e-18
                                    EEEEEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES...SS..... CS
                     RNA_ligase   2 evvvtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig..hsi...ky 74 
                                    +v v+EK++G+n+r+++  + v++a+R++ + p  +++ + ++ +  al+ k+ e+l+ e   + GE++g  +++   +y
  gi|118431513|ref|NP_148028.2|  93 TVLVEEKMNGYNVRVFTLGGmVYAATRGGLIcP--YTTRRLRRLYGGALQ-KILEDLGAEGSFIAGEVVGleNPYtryYY 169
                                    689**************9667**********54..555555555555555.45666666779********9755553233 PP

                                    TTSS....EEEEEEEEEEECTTBECE--HHHHHHHHHCCT..B..EEEEE.SS..HHHHHCCC..HHHHTC--EEEEEES CS
                     RNA_ligase  75 gglpk...efyvFdifdirdkeeqrylspdevealakglg..tvpvlyegkfl..aaeellell.lskgnkrEGlVikpe 146
                                    ++  +    ++ Fdif   +   +r l+p+    la ++g  tv +l e +++  + e l +++ + +++ rEG+++k++
  gi|118431513|ref|NP_148028.2| 170 EE--ApgfGYFIFDIF---K--GGRQLPPRVKFSLAPEYGlkTVNLLAEIPATasGVERLYTIVeDLEKRGREGVIVKDP 242
                                    33..244788888888...3..99********8888889999******9999976666666664337899********99 PP

                                    SSS CS
                     RNA_ligase 147 sel 149
                                    +++
  gi|118431513|ref|NP_148028.2| 243 EGR 245
                                    875 PP

>> 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 ?    1.9   0.0     0.025   1.5e+02      20      54 ..      92     126 ..      81     164 .. 0.73
   2 ?    8.1   0.0   0.00031       1.8     162     194 ..     217     249 ..     207     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.025
                                    SEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GG CS
                 DNA_ligase_A_M  20 kafivEiKyDGeRaqvhkegdkvklfSRrlkdita 54 
                                     +++vE+K++G+ ++v   g+ v+  +R +   ++
  gi|118431513|ref|NP_148028.2|  92 PTVLVEEKMNGYNVRVFTLGGMVYAATRGGLICPY 126
                                    57789***********9999999999998765555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00031
                                    SSHHHHHHHHHHHHHTTECEEEEEETT-CC-TT CS
                 DNA_ligase_A_M 162 kdveeleelleeaiseglEGlvvKnpdskYepg 194
                                    + ve l  ++e   + g EG++vK+p+++ ep 
  gi|118431513|ref|NP_148028.2| 217 SGVERLYTIVEDLEKRGREGVIVKDPEGRVEPL 249
                                    668888999999**************9987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2900.34
//
Query:       gi|118431514|ref|NP_148029.2|  [L=110]
Description: hypothetical protein APE_1568.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 800.64
//
Query:       gi|14601491|ref|NP_148030.1|  [L=157]
Description: hypothetical protein APE_1569 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       526  (0.0293379); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1221.32
//
Query:       gi|14601492|ref|NP_148031.1|  [L=284]
Description: prenyltransferase [Aeropyrum pernix K1]
Scores for complete 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  129.7  23.9    1.4e-37  129.4  23.9    1.0  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4  23.9   7.9e-42   1.4e-37       2     233 ..      13     249 ..      12     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 7.9e-42
                          UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgll 82 
                                   l++a+vg++l+ + +++l  ++l++++++ ++ a++a+N+++D +iD++++rt++RPlv G++s +ea++++++  ++ ++
  gi|14601492|ref|NP_148031.1|  13 LPFAYVGALLS-RYPFTLADAILMAAAVVGLRMAGMAYNNIADLDIDRLNPRTAKRPLVVGAVSLREAWALVAAGSAIYFA 92 
                                   77889999998.7778999************************************************************** PP

                          UbiA  83 llalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl........sllalllalavfll 155
                                    + +lln +++ll+ l+l++++ Y+    Kr ++l+++ +gi+ g ++++g++a++g+            ++l+ +av l+
  gi|14601492|ref|NP_148031.1|  93 SA-ALLNTYALLLSPLVLAIALTYP--HAKRLHPLPHLHLGIVLGSVVFGGAVAASGDEasslgevlRSVPWLYVAAVSLW 170
                                   **.**********************..9**************************888888999999988888888899*** PP

                          UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaaril...lalllavllla.llllllalllllylllalllaalallraar 232
                                   ++++++++++ d++ Dr  g+ ++p++lG+k a+     ++++ ++l++a + +++l++ +++ ++l+   a++++l++a+
  gi|14601492|ref|NP_148031.1| 171 VAGFDTIYSIMDIDFDRSHGLGSIPALLGPKGALAAslaMHAAAVALFIAgVEAYGLGAIATVSTALT---ALVIILVQAM 248
                                   ***********************************754333333333333422233333333333333...3333333222 PP

                          UbiA 233 l 233
                                    
  gi|14601492|ref|NP_148031.1| 249 A 249
                                   2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2214.33
//
Query:       gi|118431515|ref|NP_148032.2|  [L=487]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Aeropyrum pernix K1]
Scores for complete 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-129  431.4   0.0   3.6e-129  431.2   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.2   0.0    2e-133  3.6e-129       1     404 [.      11     427 ..      11     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 431.2 bits;  conditional E-value: 2e-133
                                    HHHCCCTTSEEEEESEB-TBTHHHHHHHHH.HHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHH CS
                           UbiD   1 lealekagelvrikeevdpelEiaeiarrv.leeggpallFenvkgkgskfpvltnlfgtrervalalglssleeilekl 79 
                                    le le++++l+r+++e +p lEi+ei+rr+ ++  g a+lFe+vkg+ ++f++++n+f + + v++alg++ le i+e+l
  gi|118431515|ref|NP_148032.2|  11 LEFLESKDMLRRVSVEASPILEIPEILRRImYRGSGYAVLFEKVKGH-EGFRIAGNIFCSLDVVRQALGVERLEVIGERL 89 
                                    578***************************999***********977.78****************************** PP

                                    HHHHHS..-..................---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-T CS
                           UbiD  80 aellepkpp..................ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdp 141
                                     e l+  pp                  + pk v +  a +  +v leg +++ + +P++++wp+DgG+y+t +lv +rdp
  gi|118431515|ref|NP_148032.2|  90 FEPLKGPPPlgiggklrslgevlslgkYMPKAVGR--AGFTANV-LEGREASFNLIPAFKVWPKDGGRYLTYALVHVRDP 166
                                    *****766699****************99****65..7788789.78********************************* PP

                                    TTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHT CS
                           UbiD 142 etgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrg 221
                                      g+ n+g+yR+++ ++++ ++hwqihk+g +  ++  +kg++++p+a++iG dP ++l++++p+P+ +++ +faG++rg
  gi|118431515|ref|NP_148032.2| 167 VRGVMNMGVYRVMIAGDKEGVVHWQIHKRGMQAQQDSVEKGERRIPAALVIGSDPGTLLTGAMPVPYPIDKHLFAGVVRG 246
                                    ******************************************************************************** PP

                                    S--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHH CS
                           UbiD 222 epvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeed 301
                                    e +++ + + ++++vpa+AEivleG+id +++++EGP+gdh+Gyy+++++ fp+f++++++hR++piy+  v+gkpp ed
  gi|118431515|ref|NP_148032.2| 247 EGLPVYRLP-NGIHVPANAEIVLEGYIDLEDLREEGPYGDHFGYYDKPSRLFPTFRLERVWHREEPIYYGSVTGKPPLED 325
                                    ******996.59*********************************************************555******** PP

                                    HCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTS CS
                           UbiD 302 allgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrd 381
                                    +++gk+ e++flp++++ +pev+d+ lp++g+f+ +a+vsi+krypgh kk++ al++l+q lsltK+++vvD+d++v+d
  gi|118431515|ref|NP_148032.2| 326 VVIGKFAERIFLPAIQTLLPEVVDIDLPPHGVFQGMAFVSIRKRYPGHGKKALLALMGLGQ-LSLTKIIVVVDHDINVHD 404
                                    ***********************************************************88.****************** PP

                                    HHHHHHHHHHC--CCCCEEEECC CS
                           UbiD 382 lkevlwaiatrvdpdrDlviieg 404
                                    +++v+wa++ +vdp+rD++++++
  gi|118431515|ref|NP_148032.2| 405 VNQVIWAVSSHVDPQRDVLVVPH 427
                                    ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.19s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3872.28
//
Query:       gi|14601494|ref|NP_148033.1|  [L=536]
Description: hypothetical protein APE_1573 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.4   0.1        0.1   12.5   0.0    1.9  2  PfaD_N    Fatty acid synthase subunit PfaD N-terminal domain


Domain annotation for each model (and alignments):
>> PfaD_N  Fatty acid synthase subunit PfaD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-06       0.1       5      27 ..     260     282 ..     258     284 .. 0.94
   2 ?   -2.4   0.0      0.26   4.6e+03      20      28 ..     428     436 ..     424     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-06
                                   TTS-B--HHHHHHHHT-TTS-EE CS
                        PfaD_N   5 ldsisfdeegIkqkLldldkpcY 27 
                                   +++i fd+++I +k ldldk++Y
  gi|14601494|ref|NP_148033.1| 260 PNTILFDPTTIDEKILDLDKHVY 282
                                   58999*****************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.26
                                   T-TTS-EEE CS
                        PfaD_N  20 ldldkpcYi 28 
                                   ++l kp+Y+
  gi|14601494|ref|NP_148033.1| 428 QALAKPVYV 436
                                   6799****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 4259.71
//
Query:       gi|118431516|ref|NP_148034.2|  [L=188]
Description: hypothetical protein APE_1574.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1389.81
//
Query:       gi|118431517|ref|YP_874903.1|  [L=93]
Description: hypothetical protein APE_1574a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.9   0.1       0.11   11.7   0.1    1.1  1  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     6e-06      0.11     115     175 ..       2      62 ..       1      68 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-06
                                    HHHHHHHHHHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHCCTTTTG CS
                   DHQ_synthase 115 aGlaEviKyalikdeelfelleenaeallkeeeeealeeliarsievkaevveeDekekgl 175
                                     GlaEv+K    + e++ ++l  ++e +++++++ ++++l+++ +++  +   ++e e+  
  gi|118431517|ref|YP_874903.1|   2 TGLAEVMKAVKTAVETFNNWLMGDMELVIDSIRDGTIKALVKQNCACSLDFSLKEEIENAF 62 
                                    69*********************************************99999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 715.82
//
Query:       gi|14601496|ref|NP_148035.1|  [L=377]
Description: peptide ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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-27   94.2   0.0    1.4e-26   93.6   0.0    1.3  1  ABC_tran     ABC transporter
    2.1e-17   63.4   0.2      4e-17   62.5   0.2    1.5  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    0.00019   21.4   1.8      0.041   13.7   0.3    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0012   18.6   0.0     0.0023   17.7   0.0    1.3  1  IstB_IS21    IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.013   15.3   0.2      0.028   14.1   0.0    1.5  2  AAA_30       AAA domain
      0.013   15.8   0.3      0.024   15.0   0.3    1.5  1  AAA_16       AAA ATPase domain
      0.027   14.9   0.1       0.06   13.8   0.1    1.6  1  AAA          ATPase family associated with various cellular a
      0.034   14.4   2.1       0.17   12.2   2.1    2.1  1  AAA_22       AAA domain
      0.052   13.2   0.0      0.063   12.9   0.0    1.2  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.053   12.9   0.0        1.2    8.5   0.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
       0.07   13.1   0.1       0.12   12.3   0.1    1.4  1  AAA_5        AAA domain (dynein-related subfamily)
      0.095   12.5   0.1       0.16   11.7   0.1    1.3  1  AAA_29       P-loop containing region of AAA domain
       0.11   12.8   0.2       0.29   11.4   0.2    1.7  1  AAA_19       AAA domain
       0.17   11.8   0.1       0.28   11.1   0.1    1.3  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
       0.19   11.8   0.1       0.31   11.1   0.1    1.3  1  TsaE         Threonylcarbamoyl adenosine biosynthesis 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 !   93.6   0.0   1.2e-29   1.4e-26       2     136 ..      51     223 ..      50     224 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.2e-29
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG......................B-HHHCCH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx......................xxxxxxxx RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke......................qeleslrk 59 
                                   + vs+++ +ge+  +vGe+G+GK+t  k++++l+k t G++ ++ +k++ e                      ++ + lr+
  gi|14601496|ref|NP_148035.1|  51 DGVSFSIARGEVFCLVGESGCGKTTTGKAILRLVKATGGRVFFKpKKEVLEelerrgvkslgdgfvdllavprRKFKPLRR 131
                                   78***************************************777766666667777777799999999999989999**** PP

                                   CEEEE-SS..--S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHH CS
                                   xxxxxxxx..xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  60 eigvlpqe..pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarall 124
                                   e++++ q+   +l+p+ t+++               e++e ++++l+ ++l+  + + +++ p++LSgGq+qrva+ara++
  gi|14601496|ref|NP_148035.1| 132 ELQIVYQDpyGSLNPRFTIKRIledpllihsignarEREEMVARMLEAVKLTP-ASDFMDRYPHQLSGGQRQRVAIARAFI 211
                                   ********8889******999999*********98777777*********999.899999********************* PP

                                   HTSSEEEEESTT CS
                                   xxxxxxxxxxxx RF
                      ABC_tran 125 kkpkllllDEpt 136
                                    +p+l+++DEp 
  gi|14601496|ref|NP_148035.1| 212 LNPSLVVADEPV 223
                                   ***********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 !   62.5   0.2   3.3e-20     4e-17       1      59 [.     275     336 ..     275     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.3e-20
                     oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCp 59 
                                   vE+g++++++++p HPYTkaL++++p++d+ ++   + + ikge ps+ +++ GC+F+pRC 
  gi|14601496|ref|NP_148035.1| 275 VETGDARRIIERPIHPYTKALVAAIPEPDPSNRkklREVPIKGEIPSAAAIPPGCRFHPRCV 336
                                   8*******************************9999999**********************5 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 !    6.9   0.0    0.0041       4.9       2      22 ..      63      83 ..      62     106 .. 0.85
   2 !   13.7   0.3   3.4e-05     0.041     231     300 ..     190     257 ..     137     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                        AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                   +l+G  g+GK++  +a+  l
  gi|14601496|ref|NP_148035.1| 63 FCLVGESGCGKTTTGKAILRL 83
                                  68****************877 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.4e-05
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsrngaQviltTHSpl 300
                                   ++ +++lS G+++  a++ a++  +   sl++ DEp + L+ ++ +++lell   +e+   g+ +++ TH+  
  gi|14601496|ref|NP_148035.1| 190 DRYPHQLSGGQRQRVAIARAFILNP---SLVVADEPVSMLDVSIRAEILELLlgfREK--LGTSLLFITHDLA 257
                                   567899******9988888888877...9***********************876333..4588******976 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 !   17.7   0.0   1.9e-06    0.0023      29      93 ..      41     106 ..      31     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                     IstB_IS21  29 sldkrkvkeLatlsf.iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkra 93 
                                   +  +r vk++ + sf i++ e ++l+G sG GK+    a+ +   ++g +v+f   ++++eel+r 
  gi|14601496|ref|NP_148035.1|  41 MKPQRFVKAVDGVSFsIARGEVFCLVGESGCGKTTTGKAILRLVKATGGRVFFKPKKEVLEELERR 106
                                   5678999999999998999*********************999999***************99975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05     0.028      19      50 ..      61      92 ..      53     111 .. 0.86
   2 ?   -2.8   0.0       3.7   4.4e+03      84     108 ..     209     234 ..     171     238 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                        AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                   v +l+G  G GKtt+ ka+ ++++a ggrv+
  gi|14601496|ref|NP_148035.1| 61 EVFCLVGESGCGKTTTGKAILRLVKATGGRVF 92
                                  4899***********************99996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                        AAA_30  84 arlepgtllivDE.agmvdtkqlaal 108
                                   a + + +l++ DE ++m+d +  a++
  gi|14601496|ref|NP_148035.1| 209 AFILNPSLVVADEpVSMLDVSIRAEI 234
                                   33334467777775567666655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.3     2e-05     0.024      23      56 ..      59      92 ..      48     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                        AAA_16 23 rpelvllsGesGvGKsslvrellralekdggifl 56
                                  r+e+  l+GesG+GK++  +++lr ++++gg ++
  gi|14601496|ref|NP_148035.1| 59 RGEVFCLVGESGCGKTTTGKAILRLVKATGGRVF 92
                                  447889*****************87777764442 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 ?   13.8   0.1     5e-05      0.06       2      23 ..      64      85 ..      63     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5e-05
                                  EEESSTTSSHHHHHHHHHHHHT CS
                           AAA  2 llyGppGtGKTllakavakelg 23
                                  +l+G  G+GKT++ ka+ + ++
  gi|14601496|ref|NP_148035.1| 64 CLVGESGCGKTTTGKAILRLVK 85
                                  89***************98765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.1   0.00014      0.17       7      29 ..      62      84 ..      58     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                        AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                  + +++GesG+GKTt+ + +l+  
  gi|14601496|ref|NP_148035.1| 62 VFCLVGESGCGKTTTGKAILRLV 84
                                  6789*************999876 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 ?   12.9   0.0   5.3e-05     0.063       3      38 ..      48      84 ..      47     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                                  HHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                                  xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ATP-synt_ab  3 rvlDal.fpivqGqrtlipgafgvGktvisqslskqs 38
                                  +++D + f+i++G+  +++g++g+Gkt+  +++++  
  gi|14601496|ref|NP_148035.1| 48 KAVDGVsFSIARGEVFCLVGESGCGKTTTGKAILRLV 84
                                  566654399*******************999988765 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 ?    8.5   0.0     0.001       1.2      96     184 ..     147     239 ..      48     270 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                                   CEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  96 evsisrrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDei 167
                                   +++i+r ++      + i + + +++ v+++le +++++          +LSgG+++ va+a  f ++     +l++ De 
  gi|14601496|ref|NP_148035.1| 147 RFTIKRILED-PLLIHSIGNAREREEMVARMLEAVKLTPAsdfmdryphQLSGGQRQRVAIARAFILN----PSLVVADEP 222
                                   4444443332.223555666677777788888888888878999999999999999999999887654....468888888 PP

                                   TTTS-HHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                         SMC_N 168 daaLDeknvkkvaellk 184
                                    + LD + ++++ ell 
  gi|14601496|ref|NP_148035.1| 223 VSMLDVSIRAEILELLL 239
                                   88888888887777765 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    0.0001      0.12       2      24 ..      63      88 ..      62     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                  EEEE--SSSSHHHHHHHGGGGB...S CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal...n 24
                                  ++LvG++G+gK++  + +++++   +
  gi|14601496|ref|NP_148035.1| 63 FCLVGESGCGKTTTGKAILRLVkatG 88
                                  69************999999984443 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   0.1   0.00014      0.16      13      46 ..      51      84 ..      48      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                  dg +++i + +++ l+G+sG GK+T   Ai  l 
  gi|14601496|ref|NP_148035.1| 51 DGVSFSIARGEVFCLVGESGCGKTTTGKAILRLV 84
                                  77889999777**************877776665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00025      0.29       9      41 ..      59      91 ..      53     252 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00025
                        AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvk 41
                                  + +v+++++  G+GKT++ k+i++l++++gg+ 
  gi|14601496|ref|NP_148035.1| 59 RGEVFCLVGESGCGKTTTGKAILRLVKATGGRV 91
                                  678999*******************99998763 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 ?   11.1   0.1   0.00023      0.28       1      30 [.      62      91 ..      62     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                          MobB  1 vlgivgksgsGKTtLleklipelkarglrv 30
                                  v+++vg sg+GKTt  + +++ +ka g rv
  gi|14601496|ref|NP_148035.1| 62 VFCLVGESGCGKTTTGKAILRLVKATGGRV 91
                                  689*********************999887 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   0.1   0.00026      0.31      14      44 ..      57      85 ..      42      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
                                  HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                          TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakalg 44
                                  +a+  g+v++L G+ G+GKTt  +++++ ++
  gi|14601496|ref|NP_148035.1| 57 IAR--GEVFCLVGESGCGKTTTGKAILRLVK 85
                                  333..889*****************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2757.85
//
Query:       gi|14601497|ref|NP_148036.1|  [L=324]
Description: peptide ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-29  103.7   0.0    1.5e-29  103.2   0.0    1.2  1  ABC_tran   ABC transporter
    2.9e-20   72.6   0.5    4.6e-20   71.9   0.5    1.3  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
    1.1e-06   28.2   0.4    7.3e-06   25.6   0.4    1.9  1  SMC_N      RecF/RecN/SMC N terminal domain
      1e-05   25.5   1.0    0.00012   22.0   0.1    2.1  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
     0.0016   18.1   0.0      0.003   17.3   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain
     0.0099   16.3   0.3      0.034   14.5   0.3    2.2  1  AAA_16     AAA ATPase domain
  ------ inclusion threshold ------
      0.021   15.1   1.2        2.8    8.2   0.1    2.3  2  AAA_22     AAA domain
      0.048   13.1   0.4       0.27   10.6   0.1    2.1  2  TniB       Bacterial TniB protein
       0.17   12.1   0.1        0.3   11.2   0.1    1.5  1  AAA_33     AAA domain
       0.17   11.6   0.0       0.24   11.1   0.0    1.3  1  PRK        Phosphoribulokinase / Uridine kinase family
       0.23   11.0   0.7        0.5    9.9   0.1    1.8  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 !  103.2   0.0   9.3e-33   1.5e-29       2     136 ..      26     182 ..      25     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 9.3e-33
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS..--S- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx..xxxx RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.....qeleslrkeigvlpqe..pqlf 71 
                                   + vs++l++ge+++i Ge+G+GKStL+  ++gl+ p      G+i +dg d+++      ++++  k++++++q   + l 
  gi|14601497|ref|NP_148036.1|  26 DGVSFTLRRGEVLGIAGESGSGKSTLAWSILGLVPPpgriVGGRIMIDGMDVTSmseaeLRRKVRWKKVSMVFQGamNVLT 106
                                   78*********************************999999999*******99999888788888899******999999* PP

                                   TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   xxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  72 peltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                   p +tv+++              e++++++++l+++gl+    +++++ p++LSgGqkqrv++a+al+ +p+++++DEpt
  gi|14601497|ref|NP_148036.1| 107 PVYTVGRQieevlqihrgvgrhEARQRVYELLESVGLHR---SIADRYPHELSGGQKQRVVIAMALALEPDIVIADEPT 182
                                   ****9999***********99999999999999999888...7778889*****************************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.5   2.8e-23   4.6e-20       2      65 .]     235     298 ..     234     298 .. 0.99

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.8e-23
                     oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                   E+gps+++f++p+HPYT+aLl+++p+l+ + d+l+ i+g++p+l++ + GC+F+pRCp a + C
  gi|14601497|ref|NP_148036.1| 235 EYGPSDAVFTKPQHPYTQALLKAIPKLRGPIDRLAYIPGSPPDLRNPPPGCRFHPRCPKAFDRC 298
                                   9*************************************************************99 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 !   25.6   0.4   4.5e-09   7.3e-06      28     212 ..      39     228 ..      28     234 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.5e-09
                                   EEEESTTSSHHHHHHHHHHHCTT...TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N  28 aivGpNGSGKsnlldAilFvLGer..sakklrseklsdlihk.....skekasvkkaeveitfdnedkklkiekeevsisr 101
                                    i G+ GSGKs l  +i   LG      + +  + + d +        + +++v   +v+++f+   +   + ++ +++ r
  gi|14601497|ref|NP_148036.1|  39 GIAGESGSGKSTLAWSI---LGLVppPGRIVGGRIMIDGMDVtsmseAELRRKVRWKKVSMVFQGAMN---VLTPVYTVGR 113
                                   68999999999999999...444311444444443333222222233355566666777777655444...4677788888 PP

                                   EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                   ++++  + +  + + +  ++ v elles+g++++       +LSgG+k+ v +a+ +A++      +++ De   aLD   
  gi|14601497|ref|NP_148036.1| 114 QIEEVLQIHRGVGR-HEARQRVYELLESVGLHRSiadryphELSGGQKQRVVIAMALALEP----DIVIADEPTTALDVVV 189
                                   88887775555554.55567899*********999999999***************99864....48999*********** PP

                                   HHHHHHHHHHH..CTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                   xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 176 vkkvaellkek..sknaQfivislreemlekadklvgvt 212
                                    +++ +llk+   +kn  +i i+++  ++++  ++v ++
  gi|14601497|ref|NP_148036.1| 190 QAQILNLLKKLawEKNLSIILITHDLSVIAELAETVMIM 228
                                   *********762268999******999988876666554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.071   1.2e+02       3      15 ..      39      51 ..      37      81 .. 0.88
   2 !   22.0   0.1   7.2e-08   0.00012     231     303 .]     149     219 ..     122     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.071
                        AAA_21  3 vliGpNgsGKSnL 15
                                  ++ G  gsGKS+L
  gi|14601497|ref|NP_148036.1| 39 GIAGESGSGKSTL 51
                                  689*********9 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.2e-08
                        AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpllld 303
                                   ++ ++elS G+k+   ++ a++ al++ ++++ DEp + L+  +++ +l ll k++ +++  +il TH+ ++++
  gi|14601497|ref|NP_148036.1| 149 DRYPHELSGGQKQR--VVIAMALALEP-DIVIADEPTTALDVVVQAQILNLLkKLAWEKNLSIILITHDLSVIA 219
                                   4568899*****98..55555555555.************************999999***********99885 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   0.0   1.8e-06     0.003      13      43 ..      26      56 ..      23      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiq 43
                                  dg ++++++ ++  ++G+sGsGKSTl  +i 
  gi|14601497|ref|NP_148036.1| 26 DGVSFTLRRGEVLGIAGESGSGKSTLAWSIL 56
                                  67778888666999***********965555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   2.1e-05     0.034      24      48 ..      35      59 ..      17     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
                        AAA_16 24 pelvllsGesGvGKsslvrellral 48
                                  +e++ + GesG+GKs+l++++l  +
  gi|14601497|ref|NP_148036.1| 35 GEVLGIAGESGSGKSTLAWSILGLV 59
                                  378889*************998544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0017       2.8       7      22 ..      37      52 ..      32      60 .. 0.83
   2 ?    5.6   0.1     0.011        19      81     128 ..     159     211 ..     119     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                        AAA_22  7 ilvvtGesGtGKTtll 22
                                  +l + GesG+GK+tl+
  gi|14601497|ref|NP_148036.1| 37 VLGIAGESGSGKSTLA 52
                                  56689*********97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                        AAA_22  81 aleqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                   + ++ + a a    + ++i DE    l+   ++++l+ L++l+   +k++++iL+
  gi|14601497|ref|NP_148036.1| 159 QKQRVVIAMALalePDIVIADEPTTaLDvvvQAQILNLLKKLAW--EKNLSIILI 211
                                   44444444444667789999**9998988878************..********8 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.36   5.8e+02      37      52 ..      37      52 ..      31      57 .. 0.83
   2 ?   10.6   0.1   0.00016      0.27      98     160 ..     151     211 ..     121     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                          TniB 37 nlllvGdsnnGKtmiv 52
                                   l ++G+s  GK++++
  gi|14601497|ref|NP_148036.1| 37 VLGIAGESGSGKSTLA 52
                                  56799********985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                          TniB  98 lkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                   +  + +  ++++ v+++  +l++ ++i DE   +l   +  q ++ln+lk+L  e +++i+l+
  gi|14601497|ref|NP_148036.1| 151 YPHELSGGQKQRVVIAMALALEPDIVIADEPTTAL--DVVVQAQILNLLKKLAWEKNLSIILI 211
                                   5555566789999999999*************999..7888999***************9987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00018       0.3       4      21 ..      40      57 ..      37     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                        AAA_33  4 lvGlpGsGKstlaerllk 21
                                  + G +GsGKstla+++l 
  gi|14601497|ref|NP_148036.1| 40 IAGESGSGKSTLAWSILG 57
                                  5799**********9864 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.24       1      22 [.      37      58 ..      37     140 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                           PRK  1 vIgvagsSGaGkttvarkleki 22
                                  v+g+ag+SG+Gk+t+a  +  +
  gi|14601497|ref|NP_148036.1| 37 VLGIAGESGSGKSTLAWSILGL 58
                                  68************99776554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0003       0.5      30      52 ..      32      54 ..       8      59 .. 0.89
   2 ?   -1.7   0.1       1.1   1.8e+03     166     188 ..     191     213 ..     117     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0003
                        AAA_25 30 lpagelallaGapgtGKttlald 52
                                  l++ge+  +aG +g+GK+tla +
  gi|14601497|ref|NP_148036.1| 32 LRRGEVLGIAGESGSGKSTLAWS 54
                                  789*****************976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                        AAA_25 166 galvealeriarrtgaavllvhH 188
                                   +++++ l+++a +++  ++l+ H
  gi|14601497|ref|NP_148036.1| 191 AQILNLLKKLAWEKNLSIILITH 213
                                   56666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2260.02
//
Query:       gi|118431518|ref|NP_148037.2|  [L=521]
Description: peptide ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-22   79.2  18.0    1.3e-21   77.2  16.4    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        0.3   11.1   0.0        0.3   11.1   0.0    3.7  3  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.036   3.3e+02     116     154 ..      26      64 ..      14      82 .. 0.80
   2 !   77.2  16.4   1.4e-25   1.3e-21       2     184 ..     336     520 ..     335     521 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.036
                   BPD_transp_1 116 lafggllggavlleflgswpGlgtllleailgydyseis 154
                                    + f++ll  av  e++g + ++ +++++++   dy+ + 
  gi|118431518|ref|NP_148037.2|  26 ILFVILLFMAVSFEIYGDQEAIRNWFTNTQYFEDYPKTV 64 
                                    456777778888888888888999999999999988765 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 1.4e-25
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslp 80 
                                     l Gi+++ + +++ d++++++ ++++slP + l+il+        i+g  i+  +++++++s++++++++r++a+++ +
  gi|118431518|ref|NP_148037.2| 336 SLYGIVSG-YLGGIADEVMLRFAQIIYSLPALPLLILFA------AIIGGNIWViIFLIVAFSWPGIAFVTRSMAFQIKS 408
                                    6789****.****************************99......9999888887999********************** PP

                   BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis...... 154
                                    + +veaa a Ga++ +i+  ++ P++lp+++++++l+++g++ + + l+fl     lg++ l +++g+ + e++      
  gi|118431518|ref|NP_148037.2| 409 EPYVEAAIASGAGTVRIVLLYLAPQVLPYMFASMALSVPGAVIAEASLSFLN----LGDPDL-VTWGKILFEAQdagaal 483
                                    ***************************************************9....776664.56666666666777778 PP

                   BPD_transp_1 155 .......nggvlalviavlllnlvadilqrlldprvr 184
                                           + + la++++ + ++++ ++l ++l+p+++
  gi|118431518|ref|NP_148037.2| 484 ngywwwvIPPGLAIAVVGMTFVFIGNALDAILNPKLK 520
                                    ***********************************97 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 ?   11.1   0.0   3.3e-05       0.3       6      32 ..      11      37 ..       8      65 .. 0.77
   2 ?   -4.0   7.1       1.8   1.6e+04      16      37 ..     374     396 ..     372     443 .. 0.78
   3 ?    0.1   0.1     0.088   7.9e+02      15      36 ..     497     519 ..     496     520 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.3e-05
                         OppC_N  6 awrrFkrNklAvvglvilllllliaif 32
                                   ++r  +r ++ +vgl+++++ll++a+ 
  gi|118431518|ref|NP_148037.2| 11 FFREYLRYPIGIVGLILFVILLFMAVS 37
                                   56778888999**************53 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.8
                         OppC_N  16 Avvglvilllllliaifa.Plia 37 
                                    A++g  i ++++li++f  P ia
  gi|118431518|ref|NP_148037.2| 374 AIIGGNIWVIIFLIVAFSwPGIA 396
                                    77777777777777766547665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.088
                         OppC_N  15 lAvvglvilll.llliaifaPli 36 
                                    +Avvg+ ++ +  +l ai++P +
  gi|118431518|ref|NP_148037.2| 497 IAVVGMTFVFIgNALDAILNPKL 519
                                    59999988777688889998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3614.33
//
Query:       gi|14601499|ref|NP_148038.1|  [L=363]
Description: peptide ABC transporter permease [Aeropyrum pernix K1]
Scores for 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  135.3  17.1      2e-39  135.3  17.1    2.2  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.17   11.5   0.0       0.26   10.9   0.0    1.2  1  AAA_12        AAA domain
       0.21   11.1   0.0       0.33   10.5   0.0    1.2  1  CLASP_N       CLASP N terminal
        1.5    8.5   5.8         20    5.0   0.1    2.8  2  Spore_YhaL    Sporulation protein YhaL


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   0.2      0.11   4.8e+02      52      88 ..      14      50 ..       4      57 .. 0.68
   2 ?   -3.1   0.2       1.2   5.5e+03     101     117 ..     124     140 ..     101     143 .. 0.50
   3 !  135.3  17.1   4.4e-43     2e-39       1     184 [.     144     359 ..     144     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                  BPD_transp_1 52 lilpviillllsaapyvrlirraalrslpkdlveaar 88
                                  +++ ++++lll +++++++++ +    l +++v a r
  gi|14601499|ref|NP_148038.1| 14 AAITLLVALLLISGIFAVYTVTELRGRLAEEYVLALR 50
                                  4455677777777777777777777777777776665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                  BPD_transp_1 101 vvlPnalppiitglila 117
                                    +++n+++ ++t  +++
  gi|14601499|ref|NP_148038.1| 124 LAMKNTAILFLTATLIT 140
                                   33344444444443333 PP

  == domain 3  score: 135.3 bits;  conditional E-value: 4.4e-43
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.................................vilsi 48 
                                   gi+lG+ +a+++++++d+ l+++  + +s+P+ ++ai+++l+f                                   + +
  gi|14601499|ref|NP_148038.1| 144 GIILGFQMARKPGSIFDRGLSVFGMISWSFPTWWVAIIMILIFsfylrlfpaqaqyvyfelsklppdlplfekiveQAKIW 224
                                   89*************************************************************************966668 PP

                  BPD_transp_1  49 lghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlle 129
                                   l+++ +pv++++l+s+++  +lir+ +l +l++d+v aara+G++++++++ +vl+ + ppi+t l+l+++g++gga+++e
  gi|14601499|ref|NP_148038.1| 225 LKYMTMPVMTIVLVSFGGASYLIRNIVLGILQEDFVTAARARGLPERRVIYGHVLRTSSPPIVTYLALSIVGAFGGAIITE 305
                                   99******************************************************************************* PP

                  BPD_transp_1 130 flgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                    +++wpG+g++ + ai+++d      +++++l+++++l +l++d+++ lldprvr
  gi|14601499|ref|NP_148038.1| 306 AVFGWPGMGLVYWIAIQQSDAKVLV-ASTWVLTVFFILTILILDFIYSLLDPRVR 359
                                   *************************.****************************8 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.8e-05      0.26       8      45 ..      40      77 ..      35     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.8e-05
                        AAA_12  8 rllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkd 45
                                  rl +++  +   L++qYR +pe+++  s+++Y++ ++ 
  gi|14601499|ref|NP_148038.1| 40 RLAEEYVLALRQLEVQYRNNPELLEEKSRQLYENLMER 77
                                  666667777889*********************98875 PP

>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   7.3e-05      0.33      61     128 ..      33     103 ..      10     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.3e-05
                       CLASP_N  61 alssLrttlsstgchllkelaiqlkeq...ldpmveillptLlkllgdtKkiisqnanqalaallsnasfs 128
                                   ++++Lr  l  + ++ l++l  q  ++   l++ +++l+++L+++ g t + +   a+ +++ + sn++f 
  gi|14601499|ref|NP_148038.1|  33 TVTELRGRLAEEYVLALRQLEVQYRNNpelLEEKSRQLYENLMERYGLTGNFVQDVATWTVKLIKSNITFD 103
                                   6889999999999999999987765443478899*********************************9975 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1    0.0045        20       7      25 ..      18      36 ..      16      40 .. 0.87
   2 ?    4.3   1.9     0.007        31       2      20 ..     174     192 ..     173     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0045
                    Spore_YhaL  7 lviagIlfSgymavktake 25
                                  l++a +l+Sg+ av+t  e
  gi|14601499|ref|NP_148038.1| 18 LLVALLLISGIFAVYTVTE 36
                                  6899***********9876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.007
                    Spore_YhaL   2 PwWvYlviagIlfSgymav 20 
                                   P W  ++i+ ++fS y+ +
  gi|14601499|ref|NP_148038.1| 174 PTWWVAIIMILIFSFYLRL 192
                                   767678999999**99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2588.77
//
Query:       gi|118431519|ref|NP_148039.2|  [L=915]
Description: peptide ABC transporter oligopeptide binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-17   62.1   0.4    1.4e-09   37.4   0.0    3.1  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.033   14.1   5.5      0.055   13.4   5.5    1.2  1  RIFIN      Rifin
      0.037   13.6   0.1       0.34   10.5   0.0    2.6  3  Kelch_1    Kelch motif
       0.42   10.1   1.0       0.74    9.3   1.0    1.4  1  Stevor     Subtelomeric Variable Open Reading frame
        5.5    7.0  13.3        0.2   11.7   3.9    2.2  2  DUF4366    Domain of unknown function (DUF4366)


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 !   37.4   0.0     4e-13   1.4e-09     168     288 ..     105     239 ..      34     272 .. 0.85
   2 !   21.5   0.0   2.7e-08   9.8e-05      29     144 ..     585     787 ..     584     806 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 4e-13
                                    HHHHTTSSSEEESTTCCTHCHHHHHTTEEE.....EEEEEEEEEEEEEETTT.....STGGGSHHHHHHHHHHS-HHHHH CS
                      SBP_bac_5 168 aalqsGeiddvaepppsdieqlkeakglkv.....lyespgggvtylafNtk.....kppfddkrvRqAlsyAiDreeiv 237
                                    ++ ++Gei +v    p+d e+++  +   +     l  + +++v   ++  +      +pf  k++RqAl++ +Dr  +v
  gi|118431519|ref|NP_148039.2| 105 DSTKQGEI-VVKVNGPGDYETIQGVQIPGLvyknsLDAFGSNWVDITQVDPNdrnieFNPFGVKKIRQALQLIVDRSFLV 183
                                    44588888.88888888888885555555555777777777777777777778888877********************* PP

                                    HHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.....SHHHHHHHHHHHTT-BCSS CS
                      SBP_bac_5 238 kavlegyatpansllppsspgadeeykpayka.....ydpekAkklLkeaGykdgd 288
                                    + +++g a p+ +++ +++p++    + +++       d++ A++l++ea ++ ++
  gi|118431519|ref|NP_148039.2| 184 NGIYQGSANPMLTAIRSGHPAYEWVADIPEELgvtsvADVATAQQLMEEAINELNQ 239
                                    **********************9988887655*******************99875 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.7e-08
                                    B-TTSSB-SHHHH....HHHHHHHHTGGGHCTTHHHHHC..........TCTEEEEEEEETTEEEEEESSETT....... CS
                      SBP_bac_5  29 kFsDGtpltAeDv....vfsferlldpdtasgyasllee..........dqdikkveavddytvrftlkkpna....... 87 
                                    k++DGt++t +D+    +f +e++ d  +  g  + +++           + i++++ vd+ t++++++  +        
  gi|118431519|ref|NP_148039.2| 585 KWHDGTDMTLADIlgvlAFYYEWAFDDSQITGQPDPYYDseidgavtgtLELIYGIKIVDEDTIEVYTPYLDVdpalias 664
                                    9***********833334689999999988888888877999*******99****************7777555543333 PP

                                    ...TTTTHCHHHHHHHGC.............................................................. CS
                      SBP_bac_5  88 ...lfltllaavpasiak.............................................................. 102
                                                +                                                                   
  gi|118431519|ref|NP_148039.2| 665 tidM--------WV---Wtplhmiialekavvedpggtnygwtdreatgeiavdllkhpdviaqmaselvgqpealkyvn 733
                                    3330........33...2233677777777888*********************************************** PP

                                    ...........CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTS CS
                      SBP_bac_5 103 ...........kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdY 144
                                               +    + ++ +++  ++v +GP+++++++p+   ++l+ ++dY
  gi|118431519|ref|NP_148039.2| 734 glnllsqsdmdARLQAYVNFINEKGHAVVFNGPFMVESYDPNAnVMELVFFEDY 787
                                    **********86666667777888888888***********9867889999999 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   5.5   1.5e-05     0.055     209     294 ..     822     903 ..     775     911 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                          RIFIN 209 kskaaltsakekekkeasskekikkkvekivekaekkaaaaaaeaaaeataeaekaetaaveattaslqtaiiasivaiv 288
                                    + ++++t++++++++e++ +e++  ++  i++++ek+ ++ ++e+ ++++ e+++++++a++++t+ ++t    +++a +
  gi|118431519|ref|NP_148039.2| 822 TPTETTTTETTTTETETTPTETTPAQTVVITKTVEKTVTQVQTETVTKTQVETQTETVTATTTVTTGVST----TVLAAI 897
                                    1112222222222233333333333333333333444444443444444444444444444444444444....455444 PP

                          RIFIN 289 vIvLim 294
                                    +I +i+
  gi|118431519|ref|NP_148039.2| 898 IILIIL 903
                                    444443 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.6e-05      0.34      26      42 ..     533     549 ..     528     551 .. 0.85
   2 ?   -1.1   0.0      0.41   1.5e+03      32      45 ..     579     592 ..     579     593 .. 0.90
   3 ?   -2.1   0.0      0.85     3e+03      29      37 ..     769     777 ..     767     778 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.6e-05
                                    EEEEEEEETTTTEEEEE CS
                        Kelch_1  26 lssvevyDpetntWrel 42 
                                     ++++vyDp++n+W  +
  gi|118431519|ref|NP_148039.2| 533 PDDAMVYDPVENKWITV 549
                                    5899**********765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.41
                                    EETTTTEEEEECCC CS
                        Kelch_1  32 yDpetntWrelpsM 45 
                                    +D++ ++W+  ++M
  gi|118431519|ref|NP_148039.2| 579 FDFVLGKWHDGTDM 592
                                    79999******999 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.85
                                    EEEEETTTT CS
                        Kelch_1  29 vevyDpetn 37 
                                    ve yDp  n
  gi|118431519|ref|NP_148039.2| 769 VESYDPNAN 777
                                    9*****866 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0   0.00021      0.74     177     261 ..     830     913 ..     807     915 .] 0.48

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
                         Stevor 177 aakvalsaealkklasslsilnlfsesslesalk.aavsaaaasdlagtaasaassafepygiaalvllilavvliiL.Y 254
                                    ++   +++e+ ++ ++++    ++ ++++e++++  ++ + + +++++++ +++ ++  + g++  vl  +++++i+   
  gi|118431519|ref|NP_148039.2| 830 ET---TTTETETTPTETTPAQTVVITKTVEKTVTqVQTETVTKTQVETQTETVTATTTVTTGVSTTVLAAIIILIILAaA 906
                                    22...222222233333334444445555555543444444445555555555555566677777776655443333222 PP

                         Stevor 255 iwlyrRR 261
                                     ++y RR
  gi|118431519|ref|NP_148039.2| 907 AFFYLRR 913
                                    3455555 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   4.5      0.36   1.3e+03      79     116 ..     801     838 ..     793     852 .. 0.54
   2 ?   11.7   3.9   5.7e-05       0.2      69     138 ..     843     911 ..     837     914 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.36
                        DUF4366  79 ctekcaagkvntdcpveepepekeaepeepeeepekks 116
                                    +t + + g+++t+ p +++e+++++++++++++ e+++
  gi|118431519|ref|NP_148039.2| 801 VTRNNVYGTIETAPPTTTTETTPTETTTTETTTTETET 838
                                    56667788999999986666555555444222222221 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.7e-05
                        DUF4366  69 aakeeeevcactekcaagkvntdcpveepepekeaepeepeeepekksnnglllvvlavaligggaayyf 138
                                    ++ +++ v + t +++  +v+t++ v++++ e+++e+ +++++ +++ ++++l +++++++++++a++y+
  gi|118431519|ref|NP_148039.2| 843 TTPAQTVVITKTVEKTVTQVQTET-VTKTQVETQTETVTATTTVTTGVSTTVLAAIIILIILAAAAFFYL 911
                                    4555677788899999999***99.666666666676677777777778888888888888898999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (915 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1502  (0.0837749); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.93u 0.32s 00:00:01.25 Elapsed: 00:00:00.46
# Mc/sec: 5968.13
//
Query:       gi|14601501|ref|NP_148040.1|  [L=146]
Description: hypothetical protein APE_1585 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   12.8   0.2      0.077   12.5   0.2    1.2  1  ComA      (2R)-phospho-3-sulfolactate synthase (ComA)
      0.066   13.8   0.4       0.13   12.9   0.4    1.6  1  RHH_6     Ribbon-helix-helix domain
       0.12   12.2   0.0       0.22   11.4   0.0    1.6  1  TusA      Sulfurtransferase TusA


Domain annotation for each model (and alignments):
>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.3e-05     0.077     145     208 ..      37      96 ..      20     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                                   CHHHHHHHHHHHHTECEEEE--TTT--SSTTB-TTS-B-HHHHHHHHTTS-GGGEEEE--SHHH CS
                          ComA 145 eklieeakrdleaGaekviiEaresGitegvydekgevrtdvvekiierlgleklifEApekkq 208
                                   +++++ ++++++ G+e +i+ +re+   +++   +++v++   ek +++l  e+ +fEA+ ++ 
  gi|14601501|ref|NP_148040.1|  37 ATVADAVEKCIKEGCEFIIVKGREGEFAVSI---SDAVKSYSREKTAAELR-EEALFEASGNAS 96 
                                   5678899*****************9999999...55666666666666654.456788876654 PP

>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   2.2e-05      0.13      27      68 ..      58     101 ..      38     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                         RHH_6  27 grkGdLSrfieeAVrayllelaveeakaa..nadvsedelsdli 68 
                                   gr+G+    i +AV++y +e++++e +++   +   ++ ++++i
  gi|14601501|ref|NP_148040.1|  58 GREGEFAVSISDAVKSYSREKTAAELREEalFEASGNASIQKVI 101
                                   89************************998776777777777777 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.22      31      68 ..      30      67 ..       6      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                  EEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEE CS
                          TusA 31 evladdpaatediprfakklghelveveeedgeyrivi 68
                                   v +d  a++ d  + + k+g+e++ v+ ++ge+ ++i
  gi|14601501|ref|NP_148040.1| 30 VVYVDSGATVADAVEKCIKEGCEFIIVKGREGEFAVSI 67
                                  4899***********************99*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1102.75
//
Query:       gi|14601502|ref|NP_148041.1|  [L=389]
Description: cysteine synthase [Aeropyrum pernix K1]
Scores for complete 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  165.4   0.1    3.1e-48  164.7   0.1    1.2  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 !  164.7   0.1   1.7e-52   3.1e-48       5     292 ..      94     367 ..      91     369 .. 0.88

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 1.7e-52
                                   SSS--EEEECCTCCCCCCEEEEEEGGGST.TSBTTHHHHHHHHHHHHTT.TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                          PALP   5 igpTPlvrlprlskelgvplflKlEslnp.tgSfKdRgaeyllarlkeg.tgaktvveassGNhgralAaaaallGlkvti 83 
                                    +pTPlvr+ rl+   gv+++lKlE+ np + S+KdR a+ +++rl +  +++  v+ a+s+N g+al+a+a+l+G+++++
  gi|14601502|ref|NP_148041.1|  94 GKPTPLVRS-RLQLPNGVRVWLKLEWYNPfSLSVKDRPAVEIISRLSRRvEKGSLVADATSSNFGVALSAVARLYGYRARV 173
                                   579*****9.678899999*********99***************8888899***************************** PP

                                   EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHH..HHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHH...HHTTTTE CS
                          PALP  84 vvpadaspekvallrllGaevvevggdydeavaa..aaelaaegegaylvsqfdnptvieg.ygtiglEil...eqlggkp 158
                                   ++p  a +  ++l rllGa+v++ ++ + +   +  +++  ++ eg+++v+qf n +++e+ +  ++ Ei    ++ g ++
  gi|14601502|ref|NP_148041.1| 174 YLPGAAEEFGKLLPRLLGAQVIVDPEAPSTVHLLprVMKDSKN-EGFVHVNQFYNDANFEAhMRGTAREIFvqsRRGGLAL 253
                                   **********************995544333333446677777.**************************97644455999 PP

                                   EEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEE CS
                          PALP 159 davvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvde 239
                                     v  ++G+ g +++ a++l++ +p++r + v+p++ d++ + +                     + + l + +ld + + 
  gi|14601502|ref|NP_148041.1| 254 RGVAGSLGTSGHMSAAAFYLQSVDPSIRAVLVQPAQGDSIPGIR-------------------RVETGMLWINMLDISYT- 314
                                   9**********************************888888888...................33355666666666666. PP

                                   EEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE CS
                          PALP 240 ivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvil 292
                                     +v+ eea+ea++++ar +g+v++ps++aa+ al k +  g+l++gd  vv++
  gi|14601502|ref|NP_148041.1| 315 LAEVTLEEAMEAVVEVARSDGLVIGPSGGAAVKALaKKAAEGDLEPGD-YVVVV 367
                                   9**********************************************5.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3022.34
//
Query:       gi|118431520|ref|YP_874904.1|  [L=48]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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   32.1   0.0    1.3e-07   32.0   0.0    1.0  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
     0.0001   22.6   0.0     0.0001   22.6   0.0    1.0  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 !   32.0   0.0   1.4e-11   1.3e-07      44      80 ..       4      40 ..       2      46 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.4e-11
                                   C-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1 44 gkplidhqlvreklaemaaeleaarllvyraaealda 80
                                   g+p +++q +++ +ae a eleaarllvy+aa+++d+
  gi|118431520|ref|YP_874904.1|  4 GRPTLSFQGISFPIAEAAMELEAARLLVYKAAWMADR 40
                                   89********************************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 !   22.6   0.0   1.1e-08    0.0001      31      67 ..       4      40 ..       1      47 [. 0.85

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-08
                                   -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2 31 gekladdpatqlalaeaaarldAAralleraaaraea 67
                                   g++   ++ + + +aeaa++l+AAr+l+++aa+ a +
  gi|118431520|ref|YP_874904.1|  4 GRPTLSFQGISFPIAEAAMELEAARLLVYKAAWMADR 40
                                   677778999***********************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 402.67
//
Query:       gi|118431521|ref|YP_874905.1|  [L=35]
Description: acyl-CoA dehydrogenase, partial [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0034   17.6   0.6     0.0036   17.5   0.6    1.0  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.6     2e-07    0.0036       1      27 [.       9      35 .]       9      35 .] 0.97

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-07
                                   TBHHHHHTTTT--S-----..-SHHHH CS
                  Acyl-CoA_dh_1  1 gkGfrvametlnheRlavaaaalglar 27
                                   ++Gf+vame++n   ++vaaa++g+ar
  gi|118431521|ref|YP_874905.1|  9 NRGFYVAMEGFNLAGILVAAANIGAAR 35
                                   89**********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.19s 00:00:00.50 Elapsed: 00:00:00.35
# Mc/sec: 303.08
//
Query:       gi|14601503|ref|NP_148042.1|  [L=132]
Description: hypothetical protein APE_1588 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-10   41.0   0.0    3.2e-10   40.6   0.0    1.1  1  PIN       PIN domain
     0.0081   16.9   0.1      0.014   16.2   0.1    1.2  1  PIN_3     PIN domain
  ------ inclusion threshold ------
      0.018   15.5   0.0      0.023   15.2   0.0    1.2  1  PIN_12    PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   5.3e-14   3.2e-10       3     116 ..       5     120 ..       4     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5.3e-14
                                   E-HHHHHHHH..TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                           PIN   3 lDTsvliall..rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaei 77 
                                   lDT++li+++  +  ek+e+a++ +e++     e ++s+ vlaE++y ++r k       + ++++ l + l+++  ++  
  gi|14601503|ref|NP_148042.1|   5 LDTNILIYAMdnKAGEKHEKAVEVIEQAlkhpTEYIVSSQVLAETIYAVKR-KYPAATPLAQTLAYTLTRTLRVVHYTHLE 84 
                                   8*********9977788899999999999999*******************.66666667777777777888888888888 PP

                                   HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                           PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedf 116
                                   +++a++   +y     D l+a t + +g++ i+t De+ 
  gi|14601503|ref|NP_148042.1|  85 VLQASQSPPRY---FWDRLLAYTYLNNGADRIITEDEKP 120
                                   88888888877...**********************985 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.3e-06     0.014       4     114 ..       5     117 ..       4     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                         PIN_3   4 lDtnvlldallfdsp....aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakva..lerkav 78 
                                   lDtn+l+ a+ ++       a  +++ + +++ + +vs ++l E  ++++r+  yp ++  a+ +a  l++    ++  + 
  gi|14601503|ref|NP_148042.1|   5 LDTNILIYAMDNKAGekheKAVEVIEQALKHPTEYIVSSQVLAETIYAVKRK--YPAATPLAQTLAYTLTRTLrvVHYTHL 83 
                                   8******887755546678999999999*********************999..*********999999998743222333 PP

                         PIN_3  79 apdaelrpllkcrDpdDqkvlelAlaaradvlVTkd 114
                                   +  ++ ++ +  r + D   + + l++ ad ++T+d
  gi|14601503|ref|NP_148042.1|  84 EVLQASQSPP--RYFWDRLLAYTYLNNGADRIITED 117
                                   3333333333..455666666666666677666666 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.8e-06     0.023       3      56 ..       5      60 ..       4      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-06
                        PIN_12  3 iDTnifl...deffrlseeealkklleliesgkiklivpdivldEflknrekkiees 56
                                  +DTni++   d++   ++e+a++ +++ +++   + iv+++vl E++  +++k+ ++
  gi|14601503|ref|NP_148042.1|  5 LDTNILIyamDNKAGEKHEKAVEVIEQALKH-PTEYIVSSQVLAETIYAVKRKYPAA 60
                                  8******444345555555688888666666.8**************9999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1005.33
//
Query:       gi|118431522|ref|YP_874906.1|  [L=77]
Description: phosphoenolpyruvate synthase [Aeropyrum pernix K1]
Scores for complete 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   96.8   0.4    1.5e-27   96.7   0.4    1.0  1  PPDK_N    Pyruvate phosphate dikinase, PEP/pyruvate binding d


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.4   8.5e-32   1.5e-27     100     173 ..       3      76 ..       1      77 [] 0.97

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 8.5e-32
                         PPDK_N 100 elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrkekgldheevalavvvqk 173
                                    + +vaV SSa+ EDlp+asfaGqq+ yLnv+g+eev+e +k+ +aSl+++rA++Yr + ++dhe v +av+vqk
  gi|118431522|ref|YP_874906.1|   3 NPRVAVGSSAMVEDLPEASFAGQQEAYLNVKGAEEVVEYVKKAWASLWTARAMSYRDSINIDHETVYMAVIVQK 76 
                                    689**********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 619.10
//
Query:       gi|118431523|ref|YP_874907.1|  [L=30]
Description: phosphoenolpyruvate synthase, partial [Aeropyrum pernix K1]
Scores for complete 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   23.7   0.0    2.7e-05   23.6   0.0    1.0  1  PPDK_N    Pyruvate phosphate dikinase, PEP/pyruvate binding d


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.5e-09   2.7e-05     185     210 ..       1      26 [.       1      28 [. 0.96

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.5e-09
                         PPDK_N 185 afsldpetGfkdevlinasyGlGeaV 210
                                    +f+++p tG+ d++++++ +GlGe +
  gi|118431523|ref|YP_874907.1|   1 MFTIHPVTGDTDKIMVESIWGLGEYI 26 
                                    9***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       144  (0.00803168); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); 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: 0.29u 0.22s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 268.07
//
Query:       gi|118431524|ref|NP_148044.2|  [L=101]
Description: acylphosphatase [Aeropyrum pernix K1]
Scores for 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-25   87.1   0.0      9e-25   86.9   0.0    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0     5e-29     9e-25       2      85 .]      15      99 ..      14      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5e-29
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdg.sVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkd 82
                                   r+lv+G VQgv+FR+ +r++A +lgl+G+vrNl+dg sVe+v+eg  ++ve+++ ++ +gpp+arv+e+ ve +++++ef++
  gi|118431524|ref|NP_148044.2| 15 RILVRGVVQGVFFRASMREEALRLGLSGWVRNLPDGeSVEAVVEGRGDAVERIICWCLRGPPAARVRELRVELEPYKGEFRG 96
                                   799******************************************************************************* PP

                Acylphosphatase 83 Fei 85
                                   Fei
  gi|118431524|ref|NP_148044.2| 97 FEI 99
                                   *98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 884.34
//
Query:       gi|118431525|ref|NP_148045.2|  [L=472]
Description: cysteinyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-124  413.6   0.0   5.8e-124  413.3   0.0    1.1  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    5.8e-16   58.2   0.5    1.8e-09   36.8   0.3    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
    6.4e-07   28.0   0.0    0.00076   17.8   0.0    2.3  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    0.00092   18.2   0.1      0.019   13.8   0.0    2.7  3  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d
     0.0051   17.3   0.0      0.024   15.1   0.0    2.1  2  DALR_2        DALR domain
  ------ inclusion threshold ------
      0.013   14.4   0.0       0.44    9.4   0.0    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)


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 !  413.3   0.0  1.9e-127  5.8e-124       4     298 ..      17     309 ..      14     312 .. 0.96

  Alignments for each domain:
  == domain 1  score: 413.3 bits;  conditional E-value: 1.9e-127
                                    -SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHH CS
                   tRNA-synt_1e   4 pleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieef 83 
                                    p +   v +YvCGptvyd++h+GhaR++ +fD ++r+l+ +gYdv +vqn+tDidDkii+raree++ ++e++ ++ +++
  gi|118431525|ref|NP_148045.2|  17 PYSPPLVGMYVCGPTVYDYTHIGHARTFTVFDAIKRYLRLRGYDVFHVQNITDIDDKIINRAREEGRDWREIVREYSRDY 96 
                                    55666799************************************************************************ PP

                                    HHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S-S CS
                   tRNA-synt_1e  84 kkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseekk 163
                                     + l +L+++  + +prv++++++ii+++e liekgyaY++++g vyf+v k++ Yg ls + ++e  +++e+ v +ekk
  gi|118431525|ref|NP_148045.2|  97 LEGLGSLGIQI-DHHPRVTDHISDIIRFIEGLIEKGYAYVAESGSVYFEVDKYPGYGMLSGHLSKEAWRQEED-VLHEKK 174
                                    *********98.99***********************************************988866555554.5689** PP

                                    STT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSSS--EEEEEE CS
                   tRNA-synt_1e 164 dkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafdkqlvkyflh 243
                                    ++ DfaLWka+k+gepsw+sPwg+GRPGWhieCsvm+s++lgs+idih+GG+DL+fPhhene aqse++f++++v+y+lh
  gi|118431525|ref|NP_148045.2| 175 SPYDFALWKAAKPGEPSWESPWGRGRPGWHIECSVMSSRYLGSRIDIHGGGVDLVFPHHENERAQSESYFGHRWVRYWLH 254
                                    ******************************************************************************** PP

                                    E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHH CS
                   tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeellee 298
                                    + +l+i+gekmsksL+n+i ++++l+++ p  lRl lls hyrs+ld++ee+l +
  gi|118431525|ref|NP_148045.2| 255 ASYLTIKGEKMSKSLGNIIPLREALREWGPGPLRLWLLSSHYRSNLDYSEEALGQ 309
                                    ***************************************************9976 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 !   36.8   0.3   6.1e-13   1.8e-09      12     126 ..      34     146 ..      25     148 .. 0.90
   2 !   19.6   0.0   1.1e-07   0.00032     317     369 ..     254     305 ..     229     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.1e-13
                                    S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEET CS
                   tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrt 91 
                                    + +H+Gh+++    D++ Ry rlrg++v++v        +i  +A++eg + +e+v+++++ + e + +l+i+ d++ r 
  gi|118431525|ref|NP_148045.2|  34 DYTHIGHARTFTVFDAIKRYLRLRGYDVFHVQNITDIDDKIINRAREEGRDWREIVREYSRDYLEGLGSLGIQIDHHPRV 113
                                    568*****************************999999****************************************99 PP

                                    TSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTT CS
                   tRNA-synt_1g  92 tseehkelvqeifkklkekgliyekeieqlycpkd 126
                                    t+  h +   ++++ l ekg+ y  e+  +y + d
  gi|118431525|ref|NP_148045.2| 114 TD--HISDIIRFIEGLIEKGYAYVAESGSVYFEVD 146
                                    86..55566789999******99999998887655 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.1e-07
                                    EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
                   tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswe 369
                                      +ylt++g+K+SkS g+++  +eal +  +  lR +l++++   ++ld+s+e
  gi|118431525|ref|NP_148045.2| 254 HASYLTIKGEKMSKSLGNIIPLREALREWGPGPLRLWLLSSH-YRSNLDYSEE 305
                                    578**********************************99854.4456677666 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 !    8.0   0.0   0.00025      0.73      31      65 ..      29      63 ..      15     134 .. 0.91
   2 !   17.8   0.0   2.5e-07   0.00076     559     599 ..     260     300 ..     248     303 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00025
                    tRNA-synt_1 31 PPyvtGslHiGhalaktlkdivirykrmkGkevly 65
                                    P v    HiGha + t+ d + ry r++G++v +
  gi|118431525|ref|NP_148045.2| 29 GPTVYDYTHIGHARTFTVFDAIKRYLRLRGYDVFH 63
                                   57777789***********************9965 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.5e-07
                    tRNA-synt_1 559 eeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdi 599
                                     +G KmSKslgN+i   + +++ g   lRl+l++s++ +++
  gi|118431525|ref|NP_148045.2| 260 IKGEKMSKSLGNIIPLREALREWGPGPLRLWLLSSHYRSNL 300
                                    58********************************9998776 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.094   2.8e+02      13      23 ..      35      45 ..      29      71 .. 0.89
   2 !   13.8   0.0   6.5e-06     0.019      49      98 ..      89     137 ..      78     147 .. 0.87
   3 ?   -0.6   0.0      0.16   4.9e+02     223     266 ..     244     287 ..     232     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.094
                                   S-BHHHHHHHH CS
                   tRNA-synt_1c 13 yLHiGhakaal 23
                                   y HiGha++  
  gi|118431525|ref|NP_148045.2| 35 YTHIGHARTFT 45
                                   88******965 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.5e-06
                                    -HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE- CS
                   tRNA-synt_1c  49 keeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvce 98 
                                    + e+    le l  lgi+ d+   + +d+   + +++e Li+kG+AYv+e
  gi|118431525|ref|NP_148045.2|  89 VREYSRDYLEGLGSLGIQIDH-HPRVTDHISDIIRFIEGLIEKGYAYVAE 137
                                    57899999***********77.558899********************97 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.16
                                    TT-S.-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTS CS
                   tRNA-synt_1c 223 lglevppfiheylrlnlekkklSKRklsllvdekqvkewddlre 266
                                    +g +  ++    + l+++++k+SK  ++++   ++++ew+  ++
  gi|118431525|ref|NP_148045.2| 244 FGHRWVRYWLHASYLTIKGEKMSKSLGNIIPLREALREWGPGPL 287
                                    5555556666778899**************99999999996655 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     8e-06     0.024       1      22 [.     354     375 ..     354     391 .. 0.90
   2 ?   -1.9   0.0       1.6   4.8e+03      19      30 ..     442     453 ..     440     463 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8e-06
                                    HHHHHHTBT--HHHHHHHHHHH CS
                         DALR_2   1 kFeeaMdDDFNTaeAiavlFel 22 
                                    ++ eaM DDFN  +A++ l e 
  gi|118431525|ref|NP_148045.2| 354 RWHEAMSDDFNMGKAMSSLWEF 375
                                    578****************986 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHH CS
                         DALR_2  19 lFelakeiNral 30 
                                    +++la ei+++l
  gi|118431525|ref|NP_148045.2| 442 MYDLADEIRSRL 453
                                    789999999844 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 ?    2.5   0.1     0.018        54      36      72 ..      35      71 ..      25      79 .. 0.89
   2 ?    9.4   0.0   0.00015      0.44     276     334 ..     260     316 ..     252     334 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.018
                   tRNA-synt_1f 36 liHiGnlrevltadlvaralrkrgeevrlilisDdmD 72
                                     HiG +r     d++ r lr rg +v ++  + d+D
  gi|118431525|ref|NP_148045.2| 35 YTHIGHARTFTVFDAIKRYLRLRGYDVFHVQNITDID 71
                                   58************************99998888887 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00015
                   tRNA-synt_1f 276 lkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdk 334
                                    +k gekms+S Gn++ l+++l+   p  lr+ +l+++ +++++ + +  + ++   Y++
  gi|118431525|ref|NP_148045.2| 260 IK-GEKMSKSLGNIIPLREALREWGPGPLRLWLLSSHYRSNLDYSEE-ALGQYRRLYER 316
                                    44.55*************************99999666665555544.44433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3727.32
//
Query:       gi|14601507|ref|NP_148046.1|  [L=267]
Description: ATP-dependent adenyltransferase [Aeropyrum pernix K1]
Scores for complete 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-62  209.5   0.0    5.7e-62  209.2   0.0    1.0  1  ThiF            ThiF family
    0.00062   19.8   0.1      0.002   18.2   0.1    1.8  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.033   13.9   0.1      0.049   13.3   0.1    1.3  1  ApbA            Ketopantoate reductase PanE/ApbA
      0.042   13.2   0.0      0.073   12.4   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.054   13.1   0.1        0.1   12.2   0.1    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.095   12.6   0.1       0.15   12.0   0.1    1.3  1  KR              KR domain


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 !  209.2   0.0   1.9e-65   5.7e-62       1     238 [.      23     246 ..      23     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: 209.2 bits;  conditional E-value: 1.9e-65
                                   THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaeal 81 
                                   ysrql llg  gq +L++skv++vG+GglG+ ++ +La+sGvg+l lvD D++e+sNlnRq+l+++ d+G++Ka +aae+l
  gi|14601507|ref|NP_148046.1|  23 YSRQLGLLGVRGQLRLSSSKVAVVGLGGLGNLAAAYLAASGVGRLILVDRDVVEPSNLNRQVLYGKGDVGRYKAVAAAERL 103
                                   89******************************************************************************* PP

                                   HHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  82 qeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeC 162
                                    e+np++e+e+v+e +++   +e+l +++D++vd+lDn+ ar++++ a  ++g+pl+++++++++gqv+++++g+++c+ C
  gi|14601507|ref|NP_148046.1| 104 GELNPEAEIEPVPEALDPAL-AEDLAREADVIVDGLDNWMARLWLDAASWRRGKPLVHGAAERMHGQVTTVERGRSSCLAC 183
                                   ****************9975.89************************************************99******** PP

                                   S-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 163 ldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerak 238
                                     p    +p e+  ++         +ia+t++vv++l +le++kll g  +   ++l  +dl ++r e ++l +  
  gi|14601507|ref|NP_148046.1| 184 IAP---SNP-ERAGCTT--------IIAPTVGVVSSLEVLEAIKLLTGVGEPLYNRLAVIDLTTPRIEVLRLAQ-M 246
                                   *98...444.4545555........6********************6666666666668999999988888833.3 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   6.8e-07     0.002       9      56 ..      37      84 ..      31     100 .. 0.89
   2 ?   -1.9   0.0         1   3.1e+03     104     115 ..     226     237 ..     205     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.8e-07
                                  ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                  Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56
                                  +l+++kv ++G G +++l+a +L+a+gv +++ + R++   ++l +++
  gi|14601507|ref|NP_148046.1| 37 RLSSSKVAVVGLGGLGNLAAAYLAASGVGRLILVDRDVVEPSNLNRQV 84
                                  5899********************************998877777665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                                   ..EEEEE--SS- CS
                  Shikimate_DH 104 kplllvDiavPR 115
                                   ++l ++D++ PR
  gi|14601507|ref|NP_148046.1| 226 NRLAVIDLTTPR 237
                                   456899999998 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.6e-05     0.049       1      41 [.      43      83 ..      43     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                                  EEEES-SHHHHHHHHHHHHHTHC.EEEE-SCHHHHHHHHHCE CS
                          ApbA  1 iailGaGaiGsllaakLakagad.vtlilrsrrlealkknGl 41
                                  +a++G+G++G l aa+La+ g    +l++r+  +e  + n  
  gi|14601507|ref|NP_148046.1| 43 VAVVGLGGLGNLAAAYLAASGVGrLILVDRDV-VEPSNLNRQ 83
                                  69*****************6655488888887.655554444 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   0.0   2.4e-05     0.073      32      70 ..      36      75 ..      12      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                  S-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHH CS
                  2-Hacid_dh_C 32 kelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskk 70
                                   +ls ++v+++GlG +G+ +a +l+a g+ ++i +dr   
  gi|14601507|ref|NP_148046.1| 36 LRLSSSKVAVVGLGGLGNLAAAYLAASGVgRLILVDRDVV 75
                                  4899************************989999998765 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 ?   12.2   0.1   3.4e-05       0.1       2      43 ..      42      84 ..      41     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                                  EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS CS
                UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgk 43
                                  k++v+GlG +G   aa la+ g   +i+vD d    ++ln++ 
  gi|14601507|ref|NP_148046.1| 42 KVAVVGLGGLGNLAAAYLAASGvGRLILVDRDVVEPSNLNRQV 84
                                  89********************779*******99888888765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     5e-05      0.15       8      35 ..      47      74 ..      41     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                                  TTSHHHHHHHHHHHHHHS-EEEEE-SS. CS
                            KR  8 GlGgLGlelarwlaekgarhlvllsRsa 35
                                  GlGgLG   a  la++g  +l+l+ R+ 
  gi|14601507|ref|NP_148046.1| 47 GLGGLGNLAAAYLAASGVGRLILVDRDV 74
                                  7************************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2011.76
//
Query:       gi|118431526|ref|YP_874908.1|  [L=101]
Description: hypothetical protein APE_1594a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 806.57
//
Query:       gi|14601508|ref|NP_148047.1|  [L=406]
Description: S-adenosylmethionine synthetase [Aeropyrum pernix K1]
Scores for 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-171  568.5   1.6   7.1e-171  568.4   1.6    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.032   14.0   0.6      0.058   13.2   0.6    1.3  1  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si


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 !  568.4   1.6  7.9e-175  7.1e-171       1     395 [.       3     401 ..       3     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 568.4 bits;  conditional E-value: 7.9e-175
                                   --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEEE CS
               AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevie 81 
                                   r+ivve++    ve+ +vE+vErKG+GHPD+i+D++aeavsr+lsk+yle+fg+ilhhn+Dkvllv+G+++p++gGGev++
  gi|14601508|ref|NP_148047.1|   3 RRIVVESYPYPRVEDLQVELVERKGLGHPDTICDAAAEAVSRELSKYYLERFGKILHHNVDKVLLVGGQAAPRLGGGEVLQ 83 
                                   689****************************************************************************** PP

                                   -EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESSSE CS
               AdoMet_Synthase  82 pieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaNDtS 158
                                   pi+il+sgr+t+ev    + e++pv+ i+l+a+k+y++en+r+ld+e++vivd+++g+gs dL+++fe+++k vplaNDtS
  gi|14601508|ref|NP_148047.1|  84 PIYILVSGRVTTEVrtggGVESVPVGPIILRAVKNYIRENFRFLDPEEHVIVDYRVGRGSVDLVGIFEAEDK-VPLANDTS 163
                                   **************88877899***********************************************766.9******* PP

                                   EEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHHHHH CS
               AdoMet_Synthase 159 fgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikeevee 239
                                   +g g+apls+le+lvleter+lns+e+k++lp+vGeD+Kvmg+R++k+i+lTva+a+v+++v ++++Yl+vkee ++ + +
  gi|14601508|ref|NP_148047.1| 164 IGSGHAPLSTLERLVLETERILNSRETKERLPAVGEDVKVMGVRDGKSITLTVAMAVVSSQVGSVSDYLAVKEEAESLILD 244
                                   ********************************************************************************* PP

                                   HHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HHHHHHHHH CS
               AdoMet_Synthase 240 lakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvGKiYnvla 320
                                   la++++ +++v+v++Nt D +e++++yltvtGtsaE+gDdG++GRGNRvnGlitp+rpms+EAaaGKNPv+HvGKiYnv+a
  gi|14601508|ref|NP_148047.1| 245 LASRIAPDYDVRVNINTGDIPEKKILYLTVTGTSAEHGDDGATGRGNRVNGLITPMRPMSMEAAAGKNPVNHVGKIYNVVA 325
                                   ********************************************************************************* PP

                                   HHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---.HHSHHHHHHHHHHHHT-HHHHHHHHTTT CS
               AdoMet_Synthase 321 neiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsl.eevekeveeiideelekieeiteelieg 395
                                   ne+a+ i++ev+gv+evyv+l+sqiGkpid+P++++v+v +e g ++ ++ ++e+e+i+++ l+ i+  te+l++g
  gi|14601508|ref|NP_148047.1| 326 NEMAALIHREVKGVEEVYVKLVSQIGKPIDRPRIVDVKVRMEGGREVtADAKREIEAIANSVLDGITGYTEKLVRG 401
                                   *****************************************9887752789***********************98 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 ?   13.2   0.6   6.4e-06     0.058      59     137 ..     306     387 ..     303     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-06
                                   HHHHTCCC.....CHHHHHHHHHHHHHHHHHHHHHHHHH.HHH..............HHHHHHHHHHHHHHHHHCCHHHHH CS
                     MCPsignal  59 EAARAGeq.....GrGFaVVAdEVrkLAersaqaakeie.aliieiqkeindsvesleetrqrveegselveetgealkei 133
                                   EAA AG++     G+ + VVA+E  +L +r  +  +e+  +l+ +i k i++    + +++ r+e g e +++++++++ i
  gi|14601508|ref|NP_148047.1| 306 EAA-AGKNpvnhvGKIYNVVANEMAALIHREVKGVEEVYvKLVSQIGKPIDRP--RIVDVKVRMEGGREVTADAKREIEAI 383
                                   555.6766666779******************999999637898999988875..57899********************* PP

                                   HHHH CS
                     MCPsignal 134 veav 137
                                   +++v
  gi|14601508|ref|NP_148047.1| 384 ANSV 387
                                   *987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2763.81
//
Query:       gi|118431527|ref|NP_148048.2|  [L=667]
Description: hypothetical protein APE_1599.1 [Aeropyrum pernix K1]
Scores for complete 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-44  149.6   0.0    1.1e-43  148.3   0.0    1.7  1  DUF460          Protein of unknown function (DUF460)
    8.4e-07   29.3   4.2    3.9e-06   27.2   0.2    3.1  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.8e-05   25.1   9.3    4.5e-05   23.8   9.3    1.6  1  ATG16           Autophagy protein 16 (ATG16)
    0.00019   22.3   9.6    0.00068   20.5   9.6    2.0  1  PRKG1_interact  cGMP-dependent protein kinase interacting dom
    0.00026   21.3   0.1     0.0008   19.7   0.1    1.8  1  Mur_ligase      Mur ligase family, catalytic domain
    0.00065   19.9  10.3    0.00065   19.9  10.3    2.0  2  Tropomyosin_1   Tropomyosin like
     0.0019   18.5   1.8     0.0056   17.0   1.8    1.8  1  OmpH            Outer membrane protein (OmpH-like)
     0.0019   18.2   5.0      0.002   18.2   3.3    1.9  1  Med9            RNA polymerase II transcription mediator comp
     0.0022   16.3   4.6      0.003   15.9   4.6    1.2  1  FPP             Filament-like plant protein, long coiled-coil
     0.0029   18.0  10.9       0.35   11.3   0.8    3.5  3  FlaC_arch       Flagella accessory protein C (FlaC)
      0.005   15.1   7.2     0.0068   14.6   7.2    1.1  1  HOOK            HOOK protein
      0.005   16.0   2.8     0.0095   15.1   2.8    1.4  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
     0.0061   15.7   6.0      0.011   14.9   6.0    1.3  1  CCDC144C        CCDC144C protein coiled-coil region
     0.0072   15.0   1.9      0.011   14.4   1.9    1.2  1  FapA            Flagellar Assembly Protein A
     0.0074   15.8   3.3      0.013   15.0   3.3    1.3  1  HMMR_N          Hyaluronan mediated motility receptor N-termi
  ------ inclusion threshold ------
      0.013   14.9   4.3       0.02   14.3   4.3    1.2  1  DUF2353         Uncharacterized coiled-coil protein (DUF2353)
      0.013   15.7   0.7      0.033   14.4   0.7    1.6  1  Fib_alpha       Fibrinogen alpha/beta chain family
      0.031   12.5   3.3      0.057   11.6   3.3    1.4  1  EzrA            Septation ring formation regulator, EzrA
      0.034   13.5  13.2      0.047   13.0  11.5    2.0  2  GAS             Growth-arrest specific micro-tubule binding
      0.034   13.0   7.6      0.067   12.1   7.6    1.5  1  Spc7            Spc7 kinetochore protein
      0.038   14.0  10.4       0.17   11.9   2.1    2.6  2  Sec2p           GDP/GTP exchange factor Sec2p
      0.045   12.8   2.0      0.065   12.3   2.0    1.1  1  AIP3            Actin interacting protein 3
      0.069   12.7   3.2      0.075   12.6   2.2    1.5  1  Exonuc_VII_L    Exonuclease VII, large subunit
       0.07   13.0   9.6       0.68    9.7   1.8    2.3  2  Spc29           Spindle Pole Component 29
      0.079   13.3   6.2       0.08   13.3   1.0    2.6  2  Csm1_N          Csm1 N-terminal domain
       0.15   10.0   4.2       0.21    9.5   4.2    1.1  1  V_ATPase_I      V-type ATPase 116kDa subunit family
       0.15   11.8   8.7      0.074   12.8   4.8    2.4  2  DivIC           Septum formation initiator
       0.16   12.1   4.6       0.25   11.4   4.6    1.2  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.16   12.4  12.6        2.5    8.6   4.0    2.7  2  ZapB            Cell division protein ZapB
       0.17   12.0   7.1       0.81    9.8   0.5    2.4  2  ADIP            Afadin- and alpha -actinin-Binding
        0.2   10.9   9.6       0.22   10.8   1.7    3.1  3  DUF3450         Protein of unknown function (DUF3450)
       0.29   10.9  12.6       0.78    9.5  12.5    1.7  1  KASH_CCD        Coiled-coil region of CCDC155 or KASH
       0.37    9.6   3.7       0.54    9.0   3.7    1.2  1  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
        0.4   10.0   4.8       0.64    9.4   4.8    1.2  1  NBP1            Fungal Nap binding protein NBP1
       0.48   10.6   2.7         52    4.1   0.0    3.9  3  DUF2703         Domain of unknown function (DUF2703)
       0.57   10.0   3.5        6.2    6.6   0.2    3.0  3  USP8_interact   USP8 interacting
        0.6   10.2   5.2        1.6    8.7   1.4    2.9  2  DUF1664         Protein of unknown function (DUF1664)
       0.65   10.6   5.6        1.6    9.3   0.7    2.5  2  BST2            Bone marrow stromal antigen 2
       0.65    9.5   7.7         13    5.2   7.3    2.4  2  Leu_zip         Leucine zipper
       0.71    9.0   2.5        1.1    8.3   2.5    1.2  1  dCache_2        Cache domain
       0.71    9.9  21.1        0.7    9.9   5.2    2.8  3  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        1.1    8.8  20.3        0.1   12.1   8.4    2.9  2  PspA_IM30       PspA/IM30 family
        1.1    7.5  15.6         41    2.3  15.3    2.2  2  MAD             Mitotic checkpoint protein
        1.1    9.3  11.0       0.72   10.0   8.8    1.8  1  BRE1            BRE1 E3 ubiquitin ligase
        1.3    9.1   6.6          3    7.9   6.6    1.5  1  DivIVA          DivIVA protein
        1.8    8.9  15.5       0.29   11.5   2.7    3.2  3  DUF641          Plant protein of unknown function (DUF641)
        1.9    8.7  12.0        6.8    6.8   2.0    3.0  2  TolA_bind_tri   TolA binding protein trimerisation
        2.4    8.3   8.1        4.3    7.5   7.6    1.7  1  End3            Actin cytoskeleton-regulatory complex protein
        2.7    8.8   7.7         26    5.6   3.8    3.0  2  Occludin_ELL    Occludin homology domain
        2.9    8.6  12.3         10    6.8  11.8    2.2  2  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        4.7    7.4   9.8         18    5.5   1.7    3.4  3  DUF2730         Protein of unknown function (DUF2730)
        4.9    7.2  12.3        4.9    7.2   8.5    2.5  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        5.3    7.4  11.4        2.3    8.6   8.2    2.0  1  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C
        5.6    5.7   9.9        9.7    4.9   9.1    1.7  2  PV-1            PV-1 protein (PLVAP)
          6    6.9   7.1         17    5.4   0.7    3.2  3  Serine_rich     Serine rich protein interaction domain
        6.8    6.4  13.4         11    5.7  12.2    1.9  1  DUF4201         Domain of unknown function (DUF4201)
        7.1    7.8  15.3        9.9    7.4  13.4    2.2  1  SOGA            Protein SOGA
        8.1    6.5   9.4        6.8    6.7   3.6    2.9  2  Laminin_II      Laminin Domain II
        8.3    5.2  12.9        6.9    5.4  11.1    1.5  2  DUF812          Protein of unknown function (DUF812)
        8.3    7.1   8.9      1e+02    3.6   1.0    2.4  2  YabA            Initiation control protein YabA
          9    6.6   6.3        2.4    8.4   1.4    2.3  2  HALZ            Homeobox associated leucine zipper
         10    6.7   7.0        7.9    7.0   0.8    2.9  2  UPF0449         Uncharacterised protein family UPF0449


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   0.0   3.8e-46   1.1e-43       3     141 .]     225     360 ..     223     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 3.8e-46
                         DUF460   3 kskdvkvevesvekdkiefeplkkkrkkklivGiDPGittgiavldldgevlalkssreldreevieliselGkpvivAt 82 
                                    ++ d++v++++v +++i   p++ +r++++ivGiDPGittg+avld++g++l+ +ss++ldr++v+e+++ lG+pvivA+
  gi|118431527|ref|NP_148048.2| 225 EGPDYTVRIKPVARSRILTLPDAPERSSPVIVGIDPGITTGLAVLDINGRLLHAESSKSLDRSRVTEIVYGLGRPVIVAV 304
                                    5789**************************************************************************** PP

                         DUF460  83 DvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                    Dv++ppet kkla++++a+ly+P  dl+++eK  la+++      +++d+H RDa aAA
  gi|118431527|ref|NP_148048.2| 305 DVADPPETAKKLAAQWGAMLYTPPADLTTSEKWGLARRVLG---SSVEDTHVRDAAAAA 360
                                    **************************************444...4469**********8 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   1.3e-08   3.9e-06      37      69 ..     156     188 ..     125     250 .. 0.76
   2 ?    1.9   0.6      0.87   2.5e+02      58      97 ..     549     588 ..     539     611 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.3e-08
                        acVLRF1  37 taaGGwSqqRfaRrrenqadalleavaeaaarl 69 
                                     + GGwSq+R++Rr+   + +++++++e ++r 
  gi|118431527|ref|NP_148048.2| 156 GSSGGWSQARYQRRVRAAISQAVSRIRESLDRA 188
                                    478***************************996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.87
                        acVLRF1  58 lleavaeaaarllaeesaevvlgGdrslvaevledarlap 97 
                                    +l++v+eaaa++ + +   v+ gGd  + ++v+e a+ + 
  gi|118431527|ref|NP_148048.2| 549 TLKTVREAAAAMRGGRLILVLRGGDTFTWDAVEELAKAGV 588
                                    4678888888887666666999****99999999866332 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   9.3   1.6e-07   4.5e-05      38     165 ..     401     529 ..     395     535 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-07
                          ATG16  38 naklekaaasakssksskksakekeasasq.....snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelq 112
                                    +++le+a++++  +  +++++ e+ a+++q     ++ +  +++++l + l +lr e + l ++ +e++  +  l+++l+
  gi|118431527|ref|NP_148048.2| 401 AEALERAIEEELGDGEPEAPRAERGARQHQeeaagDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLE 480
                                    45566666655553444444444444444422223455555555555555555555555555555555555555555555 PP

                          ATG16 113 kleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLql 165
                                    + ++++k+d    + +++e + ++++++++e +l+e + +v++l+ El+ L+ 
  gi|118431527|ref|NP_148048.2| 481 RARARAKSD----HGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELRR 529
                                    555555555....45889999999************************99975 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 !   20.5   9.6   2.4e-06   0.00068       3      82 ..     448     530 ..     446     537 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-06
                 PRKG1_interact   3 kkLYeeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkisel....eeelkelee 78 
                                    +++ e+ + en+ Lkr+Lee+e e+  lk++le+++  r +s +   + +e+ ++  r+ler++ e     ee   elee
  gi|118431527|ref|NP_148048.2| 448 REMLEALRIENSSLKRRLEEMEAEVMMLKAQLERAR-ARAKSDHGIRREAEMMRERVRKLERRLEESammvEELKGELEE 526
                                    7899******************************98.6677777778888999999999999988544443444446777 PP

                 PRKG1_interact  79 Lrae 82 
                                    Lr+ 
  gi|118431527|ref|NP_148048.2| 527 LRRA 530
                                    7765 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   2.8e-06    0.0008      10      78 ..     558     616 ..     553     619 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.8e-06
                                    CCHHHHHHHHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHH CS
                     Mur_ligase  10 rgmsagalflalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesrae 78 
                                    + m +g l+l l+G  +   d++e+l ++G++avv+++++           p   a k +++pv++ +e
  gi|118431527|ref|NP_148048.2| 558 AAMRGGRLILVLRGGDTFTWDAVEELAKAGVEAVVADHPS----------SPAANALKSRRVPVIPISE 616
                                    579*************************************..........7777777777777776655 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       6.3   1.8e+03      40      81 ..     367     407 ..     358     419 .. 0.66
   2 !   19.9  10.3   2.2e-06   0.00065      31     125 ..     452     546 ..     425     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 6.3
                  Tropomyosin_1  40 Ltkknqqleeevekleeklkeakekaeesekkktnnealtrk 81 
                                    L+ k++ +e  +ek+  ++   + k  +  + +t +eal+r 
  gi|118431527|ref|NP_148048.2| 367 LESKLRSVERTIEKMGIDVDVERVKI-DVIRGATLAEALERA 407
                                    77888888888888877765444433.344555666666664 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.2e-06
                  Tropomyosin_1  31 lekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLkettekLretdvka 110
                                    ++   e +sL+++++++e+ev  l+++l+ a++ a++ +  + ++e +  +++ LE  lees   ++e    L+e   + 
  gi|118431527|ref|NP_148048.2| 452 EALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAV 531
                                    55555778********************************************************************9999 PP

                  Tropomyosin_1 111 eelERkvkaLeqerd 125
                                    e l R ++ L  e d
  gi|118431527|ref|NP_148048.2| 532 ELLGRGTHLLAVEVD 546
                                    999999888776665 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.8   1.9e-05    0.0056       8      92 ..     438     529 ..     433     539 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-05
                                    HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS........-HHHHHHHHHHHHHHHHHHHHHH CS
                           OmpH   8 qkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e......keekeqelqkkeqelqqkqqqka 80 
                                     ++++e+ + +++ e l  + ++l+  le++e+e+  l+++l+++ + + +      +   ++ +++++++l++++++ a
  gi|118431527|ref|NP_148048.2| 438 GSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAkSdhgirrE---AEMMRERVRKLERRLEESA 514
                                    5799**************************************9877776448874332...2225555555555444444 PP

                                    ...HHHHHHHHHHHH CS
                           OmpH  81 ...qelqkkqqellk 92 
                                       +el+ + +el++
  gi|118431527|ref|NP_148048.2| 515 mmvEELKGELEELRR 529
                                    445888888877776 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 !   18.2   3.3     7e-06     0.002      13      77 ..     456     521 ..     445     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7e-06
                           Med9  13 iekdp.nlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                    ie+ + ++  +++e+++ +l+ +L++ar+  ++++gi r  e + +++++le +l+    + +++k
  gi|118431527|ref|NP_148048.2| 456 IENSSlKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELK 521
                                    45555789999********************************************99887777776 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 !   15.9   4.6     1e-05     0.003     688     788 ..     428     531 ..     364     559 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                            FPP 688 eenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslk...eskslaetqlkcmkesyesle 764
                                    ++++ +  +  ++  e + l   l+    ++ slk +l+e+E  +  lk++Le+++   +s   +  + + m e  ++le
  gi|118431527|ref|NP_148048.2| 428 QHQEEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARaraKSDHGIRREAEMMRERVRKLE 507
                                    44455555555666667777888888899999********************9987333566667777777777777777 PP

                            FPP 765 trateleaelnelkqkieaLeveL 788
                                     r++e    ++elk ++e+L   +
  gi|118431527|ref|NP_148048.2| 508 RRLEESAMMVEELKGELEELRRAV 531
                                    777777777777777777776544 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 ?    0.6   0.1       2.7   7.8e+02      12      30 ..     367     385 ..     365     396 .. 0.69
   2 !   10.7   0.7    0.0018      0.53       7      40 ..     442     475 ..     438     479 .. 0.92
   3 !   11.3   0.8    0.0012      0.35       1      32 [.     502     533 ..     502     536 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.7
                      FlaC_arch  12 lsteletvkkeneelsksv 30 
                                    l+++l +v++++e++  +v
  gi|118431527|ref|NP_148048.2| 367 LESKLRSVERTIEKMGIDV 385
                                    6778888888888765544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0018
                      FlaC_arch   7 nklsklsteletvkkeneelsksveelkenVkdl 40 
                                    +++s l  +le ++ en++l+  +ee++ +V +l
  gi|118431527|ref|NP_148048.2| 442 KEMSALREMLEALRIENSSLKRRLEEMEAEVMML 475
                                    799**************************99776 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0012
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksvee 32 
                                    r+ +lE +l++  +++e +k e+eel+  ve 
  gi|118431527|ref|NP_148048.2| 502 RVRKLERRLEESAMMVEELKGELEELRRAVEL 533
                                    899*************************9995 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   7.2   2.3e-05    0.0068     437     537 ..     432     529 ..     364     556 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                           HOOK 437 kssssgenlaaellpaevreklirLqhENKmLklkqegseeekltelqelledanrrk...neLetenrlanqrileLea 513
                                    + +  g ++ +e+  +++re+l  L+ EN  Lk + e+  e +++ l+++le a+ r    + ++ e  + ++r+ +Le+
  gi|118431527|ref|NP_148048.2| 432 EAAGDGGSVYKEM--SALREMLEALRIENSSLKRRLEEM-EAEVMMLKAQLERARARAksdHGIRREAEMMRERVRKLER 508
                                    3335566677776..468**************9999988.667777******9987651125799*************** PP

                           HOOK 514 qveelqkalqeqgskaedssllkk 537
                                    ++ee ++  +e +++ e+   l++
  gi|118431527|ref|NP_148048.2| 509 RLEESAMMVEELKGELEE---LRR 529
                                    ****99999988887776...444 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 !   15.1   2.8   3.3e-05    0.0095      24     111 ..     444     531 ..     434     559 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                          Atg14  24 lyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkk 103
                                    +  lre l  l++e+ slk+++e+++++    + + ++++ ++++   ++ + +  rer+++l+ +l++    +ee k +
  gi|118431527|ref|NP_148048.2| 444 MSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGE 523
                                    5678999999********************99999999999999999999999999***************999999999 PP

                          Atg14 104 laklsdkl 111
                                    l++l++++
  gi|118431527|ref|NP_148048.2| 524 LEELRRAV 531
                                    99999987 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   6.0   3.6e-05     0.011     214     283 ..     456     524 ..     438     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                       CCDC144C 214 akqesleerlaqlqsenmlLrqqLedaqnkadakekvvidiqdqfqdivkkLqaesekqvllleernkeL 283
                                     ++ sl+ rl +++ e m+L+ qLe a+ +a++   +  +++  +++ v+kL+   e+  +++ee + eL
  gi|118431527|ref|NP_148048.2| 456 IENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEM-MRERVRKLERRLEESAMMVEELKGEL 524
                                    567899***************************9977766655.89*******************88776 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.9   3.9e-05     0.011     335     412 ..     454     528 ..     431     559 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                           FapA 335 lkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskk 412
                                    l+ + + l+++lee+e+e+++lk+++++ ++   + + ++ ++ + ++++e   kl+++lee     +elk ele+ +
  gi|118431527|ref|NP_148048.2| 454 LRIENSSLKRRLEEMEAEVMMLKAQLERARA---RAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELR 528
                                    5556699******************999888...66778999999999999999999999999999999999999883 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 !   15.0   3.3   4.4e-05     0.013     191     275 ..     444     528 ..     429     546 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.4e-05
                         HMMR_N 191 lqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkss 270
                                    + ++ + Le+ + + + Lk +l ++e e +  k++ e+  +  +  + +++++e+ ++++++le  l+e +  +e+Lk +
  gi|118431527|ref|NP_148048.2| 444 MSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGE 523
                                    55666777788888888888999999998889999999988888888888888999999999999999999999999888 PP

                         HMMR_N 271 Leeke 275
                                    Lee  
  gi|118431527|ref|NP_148048.2| 524 LEELR 528
                                    88754 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   4.3   6.9e-05      0.02      65     151 ..     439     526 ..     385     549 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.9e-05
                        DUF2353  65 klsqlleesreenkalkleveeLrqklkeaqgDiklLReqlarqrlglkdedlletrhssaeereelv.kqlEklkekiq 143
                                    ++ + ++  re  +al+ e  +L+ +l+e++  + +L++ql+r r ++k ++ ++ + + ++er + + ++lE++    +
  gi|118431527|ref|NP_148048.2| 439 SVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLeRRLEESAMMVE 518
                                    45566677788888888888888888888888888888888888888877777777777766665544146777777777 PP

                        DUF2353 144 qlerdlka 151
                                    +l+ +l++
  gi|118431527|ref|NP_148048.2| 519 ELKGELEE 526
                                    77666654 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   0.00011     0.033      30     120 ..     444     533 ..     438     539 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 0.00011
                                    CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH CS
                      Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqn 109
                                     + +++ le l+ e ++++++ +e+e  v  +k +l+++ + +k +d+ i++ +++++e++ +l++++ +    +++L++
  gi|118431527|ref|NP_148048.2| 444 MSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAK-SDHGIRREAEMMRERVRKLERRLEESAMMVEELKG 522
                                    55667778888888889999999999999999999999998888.7********************************** PP

                                    HHHHHHHHHHH CS
                      Fib_alpha 110 vlesneqkiqk 120
                                     le++++ ++ 
  gi|118431527|ref|NP_148048.2| 523 ELEELRRAVEL 533
                                    **999988765 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.3    0.0002     0.057     391     491 ..     440     541 ..     426     546 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S-TTT.HHHHSTTTSTTTHHHHHHHT-TT--HHH CS
                           EzrA 391 ieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPgiPes.yleelkeasdeieelakeLekkpinike 469
                                    + ++   ++e+l++lr +++  +++l+e++ e+  +k ++e+ +    +++ +  e + +++++++l+++Le++ + ++e
  gi|118431527|ref|NP_148048.2| 440 VYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHgIRREAEMMRERVRKLERRLEESAMMVEE 519
                                    667888999***********************************999998736778888999****************** PP

                                    HHHHHHTTTTTSGGGTHHHHHH CS
                           EzrA 470 vnkrldeardlveklyektnel 491
                                    ++ +l+e r +ve l + t+ l
  gi|118431527|ref|NP_148048.2| 520 LKGELEELRRAVELLGRGTHLL 541
                                    ************9998888766 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 ?   -2.0   0.0       6.7   1.9e+03     143     161 ..     363     381 ..     346     395 .. 0.73
   2 ?   13.0  11.5   0.00016     0.047      44     128 ..     446     530 ..     436     539 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.7
                            GAS 143 knllLekklkalqeelEkk 161
                                      l Le kl +++ ++Ek 
  gi|118431527|ref|NP_148048.2| 363 AYLALESKLRSVERTIEKM 381
                                    5567888888888888875 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00016
                            GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerd 123
                                    + +  l+++  en++lk  L++ e+ev  L++ql++ +   +s   ++++ +++ + +++l+   e   + +e+++ e +
  gi|118431527|ref|NP_148048.2| 446 ALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGELE 525
                                    45566778889999999999999999999999999999999999999999999999999999999999999999999999 PP

                            GAS 124 elykk 128
                                    el++ 
  gi|118431527|ref|NP_148048.2| 526 ELRRA 530
                                    99875 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   7.6   0.00023     0.067     145     239 ..     441     534 ..     423     554 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                           Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelae 224
                                     +++++l+e  e L  +++ l++ l+e+e+e   l+++le+ +++a++ +   + e e +re++++l+  +ee   +++e
  gi|118431527|ref|NP_148048.2| 441 YKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKS-DHGIRREAEMMRERVRKLERRLEESAMMVEE 519
                                    344444555555555555555555555555555555555555554443.3333778899999999999999999999999 PP

                           Spc7 225 lqeqleeleekieel 239
                                    l+ +leel+ ++e l
  gi|118431527|ref|NP_148048.2| 520 LKGELEELRRAVELL 534
                                    999999999888866 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.5     0.041        12      42      75 ..     448     481 ..     442     488 .. 0.87
   2 ?   11.9   2.1   0.00057      0.17      42      81 ..     493     532 ..     484     536 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.041
                                    HHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSH CS
                          Sec2p  42 rkekealekkneklkeqLkeketlleslqeqLke 75 
                                    r+  eal+++n++lk++L+e e+ +  l++qL+ 
  gi|118431527|ref|NP_148048.2| 448 REMLEALRIENSSLKRRLEEMEAEVMMLKAQLER 481
                                    55568999************************85 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00057
                                    HHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTT CS
                          Sec2p  42 rkekealekkneklkeqLkeketlleslqeqLkeLkevle 81 
                                    r+e e ++++ +kl+++L+e+ +++e+l+ +L+eL++++e
  gi|118431527|ref|NP_148048.2| 493 RREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVE 532
                                    799********************************99765 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.0   0.00022     0.065      97     221 ..     406     531 ..     355     560 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                                    XXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXX CS
                           AIP3  97 ssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefks...eikeslselrekakkvk 173
                                    ++ie++    ++ + r e+ a+++++   a+ +  + +ke+++lr+ L++lr  +s+ k+   e+++++  l++++++ +
  gi|118431527|ref|NP_148048.2| 406 RAIEEELGDGEPEAPRAERGARQHQE--EAAGDGGSVYKEMSALREMLEALRIENSSLKRrleEMEAEVMMLKAQLERAR 483
                                    22344444444434444444444444..3346888899999999999999998888777511156677888888888888 PP

                                    XXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           AIP3 174 easlastkkssnrayiekgkkkLseesdklvtkvddLqDlvedlrkDV 221
                                    + + ++     + +++ +   kL+++ ++    v++L+  +e+lr  V
  gi|118431527|ref|NP_148048.2| 484 ARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAV 531
                                    555556666888899******************************877 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 ?   12.6   2.2   0.00026     0.075     155     269 ..     403     538 ..     354     574 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00026
                   Exonuc_VII_L 155 rlekaikrll..................eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerlee 216
                                     le+ai++ l                  ee++    ++ ++++  +e+le+ r + ++l++rle+ ++ ++   +++le+
  gi|118431527|ref|NP_148048.2| 403 ALERAIEEELgdgepeapraergarqhqEEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEE-MEAEVMMLKAQLER 481
                                    44444444445555554444433332221111222233344444555666666666666666666.66666666666666 PP

                   Exonuc_VII_L 217 lkerlk......ekleekkerlkklkerlelleekkerleeleeklealsp.lkvLkrGy 269
                                    +++r k      ++ e ++er++kl++rle   e+  ++eel+ +le l    ++L rG 
  gi|118431527|ref|NP_148048.2| 482 ARARAKsdhgirREAEMMRERVRKLERRLE---ESAMMVEELKGELEELRRaVELLGRGT 538
                                    665553354443444444444555544444...444444444444444433234444444 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.4    0.0096       2.8     132     166 ..     443     477 ..     439     494 .. 0.82
   2 ?    9.7   1.8    0.0024      0.68     109     164 ..     479     534 ..     476     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0096
                          Spc29 132 eIkeLkreleqqrtvnseLqekvaeleeevkrlaa 166
                                    e+ +L+  le  r  ns L+++++e+e ev +l+a
  gi|118431527|ref|NP_148048.2| 443 EMSALREMLEALRIENSSLKRRLEEMEAEVMMLKA 477
                                    5679**************************99975 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                          Spc29 109 ldsiyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrl 164
                                    l++ + + k+   + +  +  ++++++L+r le++ ++ +eL+  ++el + v+ l
  gi|118431527|ref|NP_148048.2| 479 LERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVELL 534
                                    66777777777778888888888899999999999999999999998888888544 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.0   0.00028      0.08      27      61 ..     456     490 ..     449     497 .. 0.87
   2 ?    1.4   0.4       1.4   4.1e+02      31      57 ..     505     531 ..     500     536 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00028
                         Csm1_N  27 hENsvLsqkletkdqeiesLkeqlaeleekvkele 61 
                                     ENs L+++le  + e+  Lk+ql+ ++++ k+ +
  gi|118431527|ref|NP_148048.2| 456 IENSSLKRRLEEMEAEVMMLKAQLERARARAKSDH 490
                                    5**************************99988765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.4
                         Csm1_N  31 vLsqkletkdqeiesLkeqlaeleekv 57 
                                     L+++le     +e+Lk +l+el+  v
  gi|118431527|ref|NP_148048.2| 505 KLERRLEESAMMVEELKGELEELRRAV 531
                                    588899999999999999999998776 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   4.2   0.00073      0.21      30     109 ..     463     541 ..     448     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00073
                     V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavl 109
                                    rr++eme ++ +l++++e+++    ++ +  +++++  ++++ +le++le+    ++el+ +le+l++ ++ l   +++l
  gi|118431527|ref|NP_148048.2| 463 RRLEEMEAEVMMLKAQLERARARAKSD-HGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVELLGRGTHLL 541
                                    89*****************55555444.4477777777888899999999999999999999999988877776666655 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.8   0.00026     0.074      16      74 ..     441     499 ..     437     505 .. 0.92
   2 ?   -0.5   0.1       3.8   1.1e+03      24      51 ..     501     528 ..     498     538 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00026
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXXXXXXXXXXXX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARselglvkpgEtv 74 
                                    +  +++l++ ++al  e+ +lk + ee+eaev  Lk + ++ ++rA+s++g  ++ E+ 
  gi|118431527|ref|NP_148048.2| 441 YKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMM 499
                                    6678999*****************************9***************9999976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.8
                                    HHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  24 qeiaalqaelaklkaeneeLeaevkdLk 51 
                                    + + +l++ l++     eeL+ e+++L+
  gi|118431527|ref|NP_148048.2| 501 ERVRKLERRLEESAMMVEELKGELEELR 528
                                    5566677777777777777777777775 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 ?   11.4   4.6   0.00087      0.25      81     172 ..     433     531 ..     398     548 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00087
                        UPF0242  81 d........eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellq 152
                                             ++++  +e le l+ e+  Lk++l+++e e+  lk + +  + +++   + + +    + e++++ + +l+
  gi|118431527|ref|NP_148048.2| 433 AagdggsvyKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKS-DHGIRREAEMMRERVRKLERRLE 511
                                    35555556667888999999999999999999999999999999988888876665.77899999999999999999999 PP

                        UPF0242 153 eyqetieeqrsvlekrqdqi 172
                                    e++ ++ee++ +le+    +
  gi|118431527|ref|NP_148048.2| 512 ESAMMVEELKGELEELRRAV 531
                                    99999999999999865555 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.0    0.0085       2.5      20      61 ..     444     485 ..     441     489 .. 0.85
   2 ?    7.9   1.4     0.014       4.1       4      51 ..     501     548 ..     496     562 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0085
                           ZapB  20 itlLqmeieeLkeeneelkeenreleeeneqlkeereawqer 61 
                                    +++L++ +e+L+ en++lk++ +e+e+e+  lk++ e  ++r
  gi|118431527|ref|NP_148048.2| 444 MSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARAR 485
                                    678999999999999999999999999999999999888877 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.014
                           ZapB   4 elLeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneql 51 
                                    e   +LE + ++   ++++L+ e+eeL++ +e l +    l  e+++l
  gi|118431527|ref|NP_148048.2| 501 ERVRKLERRLEESAMMVEELKGELEELRRAVELLGRGTHLLAVEVDRL 548
                                    677899999999999999999999999999998888777777776665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.8     0.078        22      61     106 ..     443     488 ..     427     494 .. 0.72
   2 ?    9.8   0.5    0.0028      0.81      65     124 ..     492     551 ..     486     561 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.078
                           ADIP  61 tirkleaeierlqskierlktqleqlerelalvqakerqlekklkt 106
                                    +++ l+  +e l+ + ++lk++le+ e e+  ++a++  ++++ k+
  gi|118431527|ref|NP_148048.2| 443 EMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKS 488
                                    5556666677777788888888888888888888887777777665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0028
                           ADIP  65 leaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                    ++ e e ++ ++++l+++le++++ ++ ++ ++ +l+++++ l + ++ ++ e+ rl  +
  gi|118431527|ref|NP_148048.2| 492 IRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVELLGRGTHLLAVEVDRLTLK 551
                                    5678888999*********************************99999999999998765 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.3   9.5e+02     127     153 ..      99     125 ..      97     128 .. 0.89
   2 ?   10.8   1.7   0.00077      0.22      33      92 ..     424     483 ..     399     488 .. 0.84
   3 ?    2.9   0.9       0.2        57      50      88 ..     493     531 ..     486     539 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.3
                        DUF3450 127 rlakLkelmdradvslaekyrrvleay 153
                                    rla+L+e+ +r+ + +++k+     ay
  gi|118431527|ref|NP_148048.2|  99 RLASLREVAERYGIRVEKKLTPTATAY 125
                                    99*****************98877777 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00077
                        DUF3450  33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                    + + + +++ + +  ++ +e+ al+e le+l+++n+ l+r ++++e+e+  l+ q+e+++
  gi|118431527|ref|NP_148048.2| 424 RGARQHQEEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERAR 483
                                    55556666666666677899************************************9876 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.2
                        DUF3450  50 laeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                     +e + ++e++ +le   e+ + +v++++ e+++l++  
  gi|118431527|ref|NP_148048.2| 493 RREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAV 531
                                    567778888889999999999999999999999988765 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 ?    9.5  12.5    0.0027      0.78      87     188 ..     427     531 ..     399     545 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0027
                       KASH_CCD  87 kaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleek....tkqiee 162
                                     ++++++  +  s  +++ +L e ++ l+ e++ lk++l+e+ +e   Lk ql  + +  a+ ++ +        +++ +
  gi|118431527|ref|NP_148048.2| 427 RQHQEEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARA-RAKSDHGIRREaemmRERVRK 505
                                    34555566677889999*************************9999999*99965555.444454443331111457889 PP

                       KASH_CCD 163 LkltieEyssiieeLraeksrLeeql 188
                                    L+ ++eE  +++eeL+ e + L   +
  gi|118431527|ref|NP_148048.2| 506 LERRLEESAMMVEELKGELEELRRAV 531
                                    9*****************99998766 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 ?    9.0   3.7    0.0019      0.54     170     241 ..     455     525 ..     444     559 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                     Fmp27_WPPW 170 rvqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkesee 241
                                    r+  + l++Rlee+e+++  l+ +le++  + ++ d+ +++e e +++ +++l+++le    ++e+lk + e
  gi|118431527|ref|NP_148048.2| 455 RIENSSLKRRLEEMEAEVMMLKAQLERARARAKS-DHGIRREAEMMRERVRKLERRLEESAMMVEELKGELE 525
                                    6778899*************************99.899******************9999999999988766 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.8    0.0022      0.64     141     217 ..     455     530 ..     441     546 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0022
                           NBP1 141 rilrseaFkkkllelkydkqmle.qLrrgrssnkserrvslrnnnleeDqvvlLqkkikklesklkdlekeLeitkkk 217
                                    ri+ s  +k++l+e++ +  ml+ qL r r + ks +    r+ ++   +v+ L++++++ +  +++l+ eLe ++++
  gi|118431527|ref|NP_148048.2| 455 RIENS-SLKRRLEEMEAEVMMLKaQLERARARAKSDHG-IRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRA 530
                                    66655.69**************7578887777777777.589999***************************988876 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0         2   5.8e+02      22      46 ..     171     195 ..     164     209 .. 0.86
   2 ?    4.1   0.0      0.18        52      22      51 ..     364     393 ..     350     408 .. 0.85
   3 ?    0.7   2.0       1.9   5.6e+02      22      57 ..     451     486 ..     439     556 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2
                        DUF2703  22 gktleeavkelkeaLealgievele 46 
                                     +++ +av++++e+L+++g++  l+
  gi|118431527|ref|NP_148048.2| 171 RAAISQAVSRIRESLDRAGLDYDLN 195
                                    56899**************988776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.18
                        DUF2703  22 gktleeavkelkeaLealgievelekvels 51 
                                      +le+ ++ +++ +e++gi+v +e v+++
  gi|118431527|ref|NP_148048.2| 364 YLALESKLRSVERTIEKMGIDVDVERVKID 393
                                    56799999*****************99987 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.9
                        DUF2703  22 gktleeavkelkeaLealgievelekvelseeelar 57 
                                     ++l+   + lk++Le+++ ev + k +l++++ + 
  gi|118431527|ref|NP_148048.2| 451 LEALRIENSSLKRRLEEMEAEVMMLKAQLERARARA 486
                                    556666667788888888888888888887776663 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.1   6.1e+02      76      97 ..     318     339 ..     312     359 .. 0.82
   2 ?    6.6   0.2     0.022       6.2      29      76 ..     439     485 ..     424     489 .. 0.81
   3 ?    1.7   0.1       0.7     2e+02       2      39 ..     499     536 ..     491     566 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.1
                  USP8_interact  76 trWGglistPDavlqavikraL 97 
                                     +WG+++ tP a l +  k +L
  gi|118431527|ref|NP_148048.2| 318 AQWGAMLYTPPADLTTSEKWGL 339
                                    58********998887666555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.022
                  USP8_interact  29 eqkrelellkeyiralrstnpvlraladqlerdevlrWveslklarvt 76 
                                    +  +e++ l+e++ alr+ n++l+   +++e  ev+   ++l++ar +
  gi|118431527|ref|NP_148048.2| 439 SVYKEMSALREMLEALRIENSSLKRRLEEMEA-EVMMLKAQLERARAR 485
                                    55689****************99999899875.788888899998865 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.7
                  USP8_interact   2 Lrelvqkqqqkiaelkkevaeqkqqlseqkrelellke 39 
                                    +re v+k +++++e   +v+e k +l+e +r +ell +
  gi|118431527|ref|NP_148048.2| 499 MRERVRKLERRLEESAMMVEELKGELEELRRAVELLGR 536
                                    45666666666666666666666666666666666543 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.93   2.7e+02      85     120 ..     440     475 ..     427     483 .. 0.66
   2 ?    8.7   1.4    0.0057       1.6      55     113 ..     490     548 ..     466     554 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.93
                        DUF1664  85 ikeevtevredlseigedvesvkeavegleskleri 120
                                    + +e++++re l++++ + +s+k+  e++e+++  +
  gi|118431527|ref|NP_148048.2| 440 VYKEMSALREMLEALRIENSSLKRRLEEMEAEVMML 475
                                    556666667777777777777777777776666554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0057
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                    + +++  + + +r+ +++++l+e++ + +e+k e++e+r+ ++ +g+  + +   v  l
  gi|118431527|ref|NP_148048.2| 490 HGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVELLGRGTHLLAVEVDRL 548
                                    4566777788999**************************99999988877777777666 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.7    0.0056       1.6      42      89 ..     439     486 ..     421     488 .. 0.82
   2 ?    3.0   0.4      0.54   1.6e+02      56      81 ..     505     530 ..     492     534 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0056
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                           BST2  42 tcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaev 89 
                                    +  + +  L++ Le  + ++   +++++e++ e+  L+ +L+ a+a  
  gi|118431527|ref|NP_148048.2| 439 SVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARA 486
                                    55566788999999999999999********************99876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.54
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  56 kekaqsqkqqakvqelqgeikkLnqk 81 
                                    k + + ++  + v+el+ge+++L   
  gi|118431527|ref|NP_148048.2| 505 KLERRLEESAMMVEELKGELEELRRA 530
                                    44455556667788888888888765 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.3     0.046        13     131     215 ..     447     528 ..     437     546 .. 0.72
   2 ?    1.2   0.0      0.76   2.2e+02       9      46 ..     549     592 ..     543     596 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.046
                        Leu_zip 131 LkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektlee 210
                                    L+  +e L+ en+ Lk rl+e+E++++ +     +le+a ++++++ g +++++   +++ kle++l+e  + +e+ + e
  gi|118431527|ref|NP_148048.2| 447 LREMLEALRIENSSLKRRLEEMEAEVMMLK---AQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGE 523
                                    67778999999*******999999988554...45555555555555555555556678888888888887777776666 PP

                        Leu_zip 211 ktasa 215
                                     ++  
  gi|118431527|ref|NP_148048.2| 524 LEELR 528
                                    55544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.76
                        Leu_zip   9 rlkavdacfqdlkdsRLv.....edtytvDEvtelld.glkavv 46 
                                     lk+v  +   ++  RL       dt+t D v+el + g++avv
  gi|118431527|ref|NP_148048.2| 549 TLKTVREAAAAMRGGRLIlvlrgGDTFTWDAVEELAKaGVEAVV 592
                                    677888888888888875334447**********9753566666 PP

>> dCache_2  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.5    0.0039       1.1       8      89 ..     452     532 ..     448     545 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0039
                       dCache_2   8 eiekleeetikerkellksevdsaielieyeknsleeslkesLksrveeaysiaeeiyekykn.elseeeakklikealr 86 
                                    e+ ++e++++k+r e++++ev +++ ++e  + +++++  + ++ ++e++++ + ++ ++ ++  +  ee+k ++ e+ r
  gi|118431527|ref|NP_148048.2| 452 EALRIENSSLKRRLEEMEAEVMMLKAQLE--RARARAKSDHGIRREAEMMRERVRKLERRLEEsAMMVEELKGELEELRR 529
                                    56799***********************8..77788888999*****************999989999999999988888 PP

                       dCache_2  87 sir 89 
                                    ++ 
  gi|118431527|ref|NP_148048.2| 530 AVE 532
                                    777 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 ?   -1.5   0.0       8.1   2.3e+03      28      53 ..     366     391 ..     362     415 .. 0.73
   2 ?    8.2  17.9    0.0083       2.4       6      89 ..     445     531 ..     441     533 .. 0.85
   3 ?    9.9   5.2    0.0024       0.7      15      74 ..     492     551 ..     490     556 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.1
                 CENP-F_leu_zip  28 nLerelemseenqekvileaEtskae 53 
                                    +Le+ l  +e+  ek+ ++++ ++ +
  gi|118431527|ref|NP_148048.2| 366 ALESKLRSVERTIEKMGIDVDVERVK 391
                                    67778888888888877777666654 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0083
                 CENP-F_leu_zip   6 lhvlekLKeserkadsLkdkvenLerelemseenqekvileaEts...kaevetlkeeieelaeelreleldLvalrsek 82 
                                      ++e L + + +++sLk + e++e+e+ m+++++e++   a +    + e+e ++e +++l+++l+e  + +++l+ e 
  gi|118431527|ref|NP_148048.2| 445 SALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDhgiRREAEMMRERVRKLERRLEESAMMVEELKGEL 524
                                    567788999999**************************999987544478999999999999999999999999999999 PP

                 CENP-F_leu_zip  83 eeLekel 89 
                                    eeL + +
  gi|118431527|ref|NP_148048.2| 525 EELRRAV 531
                                    9998765 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0024
                 CENP-F_leu_zip  15 serkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleld 74 
                                    ++r+a+ ++++v +Ler le+s    e+++ e E+ + +ve l    + la e  +l+l+
  gi|118431527|ref|NP_148048.2| 492 IRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVELLGRGTHLLAVEVDRLTLK 551
                                    589999999***********************9999999999999998888888888765 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   8.4   0.00036       0.1      63     150 ..     397     487 ..     367     494 .. 0.77
   2 ?    4.1   1.0       0.1        30      93     128 ..     496     531 ..     492     544 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                      PspA_IM30  63 qkeqakklekkAkaALtkgeeeLArealaeikslekqaea...letqlaqqrsaveqlrkqlealetkieelkakkellk 139
                                     +  a++le   ++ L  ge+e+ r+    ++  e+ a +     ++++ +r++ e lr + + l++++ee++a++ +lk
  gi|118431527|ref|NP_148048.2| 397 GATLAEALERAIEEELGDGEPEAPRAERGARQHQEEAAGDggsVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLK 476
                                    566677777777777777777766554444444444443311156889999***************************** PP

                      PspA_IM30 140 arekaakaqea 150
                                    a+++ a+a+++
  gi|118431527|ref|NP_148048.2| 477 AQLERARARAK 487
                                    ********986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                      PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealetki 128
                                    ++ + + +++le  l++++ +ve+l+++le+l + +
  gi|118431527|ref|NP_148048.2| 496 AEMMRERVRKLERRLEESAMMVEELKGELEELRRAV 531
                                    555667788888888888888888888888887665 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  15.3      0.14        41     428     521 ..     428     532 ..     404     534 .. 0.65
   2 ?    0.3   5.8      0.58   1.7e+02     507     550 ..     490     528 ..     475     558 .. 0.42

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.14
                            MAD 428 r.qqesladassskeevdslkkkleeLelerqrLreqkeelElele.......rreLqgdydlkktkVlhlseNPaakak 499
                                    + q+e++ d +s   e+++l+  le L++e+++L+++ ee+E+e++       r   + ++d    +   +    + k +
  gi|118431527|ref|NP_148048.2| 428 QhQEEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMmlkaqleRARARAKSDHGIRREAEMMRERVRKLE 507
                                    325666778888999**************************999885633333333334444444444444444443333 PP

                            MAD 500 ...qqkkeqlekLqaEierlkellk 521
                                       + ++ ++e+L+ E+e l++ ++
  gi|118431527|ref|NP_148048.2| 508 rrlEESAMMVEELKGELEELRRAVE 532
                                    1113445566777777777777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.58
                            MAD 507 ekLqaEierlkellkkleedkekkvaslpessltlafkevleLr 550
                                    + +++E e ++e+++kle   e+  a++ e+     + e+ eLr
  gi|118431527|ref|NP_148048.2| 490 HGIRREAEMMRERVRKLERRLEE-SAMMVEE----LKGELEELR 528
                                    33333333333333333333332.1111111....112222222 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   8.8    0.0025      0.72       2      89 ..     441     531 ..     440     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0025
                           BRE1   2 qkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfa...amrskdalenelkkLnkllsKsselieqL 78 
                                    +kE+  l +  e+l+ ++s+++  l+ +e +++ l+a+ ++a+   ++   ++r+ ++++  ++kL + l+ s+ ++e+L
  gi|118431527|ref|NP_148048.2| 441 YKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSdhgIRREAEMMRERVRKLERRLEESAMMVEEL 520
                                    799******************************9999999999888765669**************************** PP

                           BRE1  79 kelekefvrkl 89 
                                    k   +e++r +
  gi|118431527|ref|NP_148048.2| 521 KGELEELRRAV 531
                                    *9777777766 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.6      0.01         3      34     122 ..     437     530 ..     431     534 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXX CS
                         DivIVA  34 yeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekive......eaee 107
                                      +++ke ++l+e +++l+ + ++ k + e+++  +++ +   e+++a ak     i +eAe   e++ +      e++ 
  gi|118431527|ref|NP_148048.2| 437 GGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSD-HGIRREAEMMRERVRKlerrleESAM 515
                                    56889999999999999999999999999999998888888888888887643.34555555555554222222226666 PP

                                    XXXXXXXXXXXXXXX CS
                         DivIVA 108 eakkiaeeieelkrq 122
                                     +++++ e+eel+r 
  gi|118431527|ref|NP_148048.2| 516 MVEELKGELEELRRA 530
                                    666666666666665 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 ?   -0.5   0.1       5.2   1.5e+03      83     118 ..     367     403 ..     343     411 .. 0.73
   2 ?   11.5   2.7   0.00099      0.29      71     123 ..     435     487 ..     421     491 .. 0.84
   3 ?    3.9   2.4      0.22        64      85     123 ..     494     532 ..     485     536 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5.2
                         DUF641  83 qrsllktyeitvkkleaelkakdseieeLk.ekLeea 118
                                    + s+l++ e t++k+  +++  +++i+ ++ ++L+ea
  gi|118431527|ref|NP_148048.2| 367 LESKLRSVERTIEKMGIDVDVERVKIDVIRgATLAEA 403
                                    6788999999999999999999999998883345555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00099
                         DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnk 123
                                     +  ++ +e+  +r++l+++ i  ++l++ l++ ++e++ Lk++Le+a+++ k
  gi|118431527|ref|NP_148048.2| 435 GDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAK 487
                                    566677889999***********************************998876 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.22
                         DUF641  85 sllktyeitvkkleaelkakdseieeLkekLeeaeksnk 123
                                    +  + +  +v+kle+ l++  + +eeLk +Lee++++ +
  gi|118431527|ref|NP_148048.2| 494 REAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVE 532
                                    45566778899*********************9988765 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 ?    6.8   2.0     0.024       6.8       5      44 ..     443     482 ..     439     487 .. 0.82
   2 ?    5.6   2.3     0.058        17       3      35 ..     500     532 ..     498     539 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.024
                  TolA_bind_tri   5 rvarLErilearsqlllelqqqlealqqelreLRGqiEel 44 
                                     ++ L ++lea    +  l ++le++++e+  L+ q+E+ 
  gi|118431527|ref|NP_148048.2| 443 EMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERA 482
                                    5667778888888888999999999999999999999986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.058
                  TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelr 35 
                                     +rv +LEr le +  +  el  +le+l++ + 
  gi|118431527|ref|NP_148048.2| 500 RERVRKLERRLEESAMMVEELKGELEELRRAVE 532
                                    678899999998865555556666666655443 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.6     0.015       4.3      96     185 ..     455     535 ..     372     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                           End3  96 dweevrLkreLaeLeeklekveeeaekrkekereessksalvkreleqLLkYKeeqlreleegegkskeknlksvkedie 175
                                     +e+ +Lkr L+e+e++++ ++++ e+     r++ ++++ ++re+e + +    ++r+le   ++ +++ ++++k ++e
  gi|118431527|ref|NP_148048.2| 455 RIENSSLKRRLEEMEAEVMMLKAQLERA----RARAKSDHGIRREAEMMRE----RVRKLERRLEE-SAMMVEELKGELE 525
                                    57999*****************988843....333456789*****98844....44444444322.347899999**** PP

                           End3 176 tveeqVegLe 185
                                    +++  Ve L 
  gi|118431527|ref|NP_148048.2| 526 ELRRAVELLG 535
                                    **99999885 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.54   1.5e+02      19      45 ..     359     385 ..     354     411 .. 0.86
   2 ?    5.6   3.8      0.09        26      25      96 ..     459     531 ..     441     533 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.54
                   Occludin_ELL  19 keYkeYkelhaeleevskkfseLerel 45 
                                    + Yk Y +l+++l++v+++++++  ++
  gi|118431527|ref|NP_148048.2| 359 AAYKAYLALESKLRSVERTIEKMGIDV 385
                                    67******************9997655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.09
                   Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekkkrceyLkekLshiKkli 96 
                                    ++l+++lee+++++  L+++l++++ + k  + i +e     ++++k +++  e    +e+Lk +L+ +++ +
  gi|118431527|ref|NP_148048.2| 459 SSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKlERRLEESAMMVEELKGELEELRRAV 531
                                    57999**********************9988888888444445555557777788889999*****9999887 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 ?    6.4   2.0     0.048        14      18      79 ..     426     483 ..     421     492 .. 0.80
   2 ?    6.8  11.8     0.034        10      14      94 ..     450     529 ..     442     534 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.048
                 HIP1_clath_bdg  18 arqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesse 79 
                                    arq+qee +     + +e+ +l+e    +le  + e  +Lkr le+ +ae+  lk+ Le+  
  gi|118431527|ref|NP_148048.2| 426 ARQHQEEAAGDGGSVYKEMSALRE----MLEALRIENSSLKRRLEEMEAEVMMLKAQLERAR 483
                                    688888888888888888888765....6777788888999999999999999999998765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.034
                 HIP1_clath_bdg  14 qlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                    +l + r + ++++r  +e+e e+  lk++ er  +  k+    ++re e+ r+++ +l+  Le+s++  e+l+ +l++L+
  gi|118431527|ref|NP_148048.2| 450 MLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSD-HGIRREAEMMRERVRKLERRLEESAMMVEELKGELEELR 528
                                    778889999********************99987766665.56***********************************98 PP

                 HIP1_clath_bdg  94 a 94 
                                    +
  gi|118431527|ref|NP_148048.2| 529 R 529
                                    5 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.46   1.3e+02      46      74 ..     368     396 ..     357     410 .. 0.82
   2 ?    1.9   0.6       0.8   2.3e+02      65      96 ..     444     475 ..     440     483 .. 0.57
   3 ?    5.5   1.7     0.061        18      32      89 ..     493     548 ..     484     552 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.46
                        DUF2730  46 dkrlteletkvenLPtakdlekLklllad 74 
                                    +++l ++e ++e++   +d+e++k+++  
  gi|118431527|ref|NP_148048.2| 368 ESKLRSVERTIEKMGIDVDVERVKIDVIR 396
                                    789********************998754 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.8
                        DUF2730  65 lekLkllladlrgelkaleaevrqlshqvdLL 96 
                                    +++L+  l+ lr e + l++++++++  v +L
  gi|118431527|ref|NP_148048.2| 444 MSALREMLEALRIENSSLKRRLEEMEAEVMML 475
                                    55555555555555555555555555555443 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.061
                        DUF2730  32 redleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89 
                                    r + e + e v++ ++rl+e  + ve+L  + +le+L+  ++ l   ++ l+ ev++l
  gi|118431527|ref|NP_148048.2| 493 RREAEMMRERVRKLERRLEESAMMVEEL--KGELEELRRAVELLGRGTHLLAVEVDRL 548
                                    7788888899999999999999999998..6788888888887777777777777766 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.5     0.017       4.9      57     114 ..     449     512 ..     438     515 .. 0.65
   2 ?    2.4   2.0      0.54   1.6e+02      62     100 ..     492     530 ..     486     533 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                     TPR_MLP1_2  57 kelqalreelnelkaeiaelkaeaesakaeleeseeswe......eqkeelekelselekried 114
                                    + l+alr e ++lk +++e++ae+  +ka+le++++  +      ++ e++++++++le+r+e+
  gi|118431527|ref|NP_148048.2| 449 EMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKsdhgirREAEMMRERVRKLERRLEE 512
                                    5667777777777777777777777777777766666541111116777888888888888877 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.54
                     TPR_MLP1_2  62 lreelnelkaeiaelkaeaesakaeleeseesweeqkee 100
                                    +r e++ +++++++l+ ++e+    +ee + ++ee + +
  gi|118431527|ref|NP_148048.2| 492 IRREAEMMRERVRKLERRLEESAMMVEELKGELEELRRA 530
                                    567777777777777777777777777777777766654 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 ?    8.6   8.2    0.0081       2.3      11      85 ..     452     527 ..     442     532 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0081
                    Uso1_p115_C  11 aslkdeneklkaelqslskalesleqk.eakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDL 85 
                                    + l+ en++lk +l++++ ++  l+ + e   a ++ ++ ++ e++ +++++ kl+ +l+e++   +e + El++L
  gi|118431527|ref|NP_148048.2| 452 EALRIENSSLKRRLEEMEAEVMMLKAQlERARARAKSDHGIRREAEMMRERVRKLERRLEESAMMVEELKGELEEL 527
                                    4455555566666666666655555555555555666777777777777777777777777777776667777776 PP

>> PV-1  PV-1 protein (PLVAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.7   1.3e+03     254     276 ..     360     382 ..     353     431 .. 0.75
   2 ?    4.9   9.1     0.034       9.7     289     376 ..     446     535 ..     439     565 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.7
                           PV-1 254 synlyyplgselasirracdelP 276
                                    +y+ y  l+s+l s++r+ +++ 
  gi|118431527|ref|NP_148048.2| 360 AYKAYLALESKLRSVERTIEKMG 382
                                    67888888888888888888874 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.034
                           PV-1 289 slragiervarensdlqrqkleaeqslrasqeakekvekeaq.....areaklqaecarqtqlaleekaalrkerdnlak 363
                                     lr  +e +  ens l+r+ +e+e  +   +++ e++   a+      rea++  e +r+ +  lee a++ +   +l+ 
  gi|118431527|ref|NP_148048.2| 446 ALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKsdhgiRREAEMMRERVRKLERRLEESAMMVE---ELKG 522
                                    6899999999********99999887766665555555444421222699******************99976...5999 PP

                           PV-1 364 eleekkreveqlk 376
                                    elee +r ve l 
  gi|118431527|ref|NP_148048.2| 523 ELEELRRAVELLG 535
                                    *******999874 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.48   1.4e+02       4      57 ..     133     186 ..     130     188 .. 0.86
   2 ?    5.4   0.7     0.057        17      37     115 ..     460     536 ..     439     554 .. 0.65
   3 ?    0.6   0.2       1.8   5.1e+02      17      46 ..     628     657 ..     626     664 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.48
                    Serine_rich   4 dsAletlarlqqevesavskLlsfvsskWRskenleanlqeirlavdrlrtslr 57 
                                    + A + ++ l+++   +vs+  s  s +W +  ++++  ++i +av+r+r+sl 
  gi|118431527|ref|NP_148048.2| 133 EGAGTPVSVLEEKTLVTVSRARSGSSGGWSQARYQRRVRAAISQAVSRIRESLD 186
                                    556666777888888899999999999************************996 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.057
                    Serine_rich  37 nleanlqeirlavdrlrtslrefleFargalanaaklsdknlqtkLrkqlqkledsdqilqetsqeLdsceWslealas 115
                                    +l+++l+e+ + v  l++ l+     a++  +   + + + + ++ rk+ ++le+s+ +++e + eL++   ++e l +
  gi|118431527|ref|NP_148048.2| 460 SLKRRLEEMEAEVMMLKAQLERARARAKSDHGI--RREAEMMRERVRKLERRLEESAMMVEELKGELEELRRAVELLGR 536
                                    444444444444444444444443333333332..2344788999**********************998877777765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.8
                    Serine_rich  17 vesavskLlsfvsskWRskenleanlqeir 46 
                                    v+s v +L + +  +WR + + + +++ i 
  gi|118431527|ref|NP_148048.2| 628 VSSEVLRLAEEMRAEWRRRREASVDIMRIV 657
                                    78999999**********998888888775 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.2     0.039        11      77     171 ..     442     534 ..     438     539 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                        DUF4201  77 halthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekvee 156
                                    ++++ l+e l +l+ e+s lk +l+e+e++ + l+++l++++++ +  +  +++ +   +   v +L +  ++    vee
  gi|118431527|ref|NP_148048.2| 442 KEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRER--VRKLERRLEESAMMVEE 519
                                    5789999999999999999999999999999999999999998887777777666666665..66788999999999999 PP

                        DUF4201 157 krksvkkLrrkvkil 171
                                    ++ ++++Lrr v+ l
  gi|118431527|ref|NP_148048.2| 520 LKGELEELRRAVELL 534
                                    999999999999876 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  13.4     0.034       9.9       3      89 ..     445     528 ..     443     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.034
                           SOGA   3 aeLrrhLqfveeEaeLlrrslseleeenkqlteeLnkyksklgeeessleeeeeassdsskeaelkeeLklarlqineLs 82 
                                    + Lr+ L+    E + l+r+l e+e e   l+ +L++ +  ++++++  +e+e+     ++ ++l+ +L+ + + ++eL+
  gi|118431527|ref|NP_148048.2| 445 SALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMR---ERVRKLERRLEESAMMVEELK 521
                                    5689999999999999*******************************999955444...46789**************** PP

                           SOGA  83 gkvvkLq 89 
                                    g + +L 
  gi|118431527|ref|NP_148048.2| 522 GELEELR 528
                                    *999986 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.77   2.2e+02      82     102 ..     168     188 ..     162     189 .. 0.76
   2 ?    6.7   3.6     0.024       6.8       6      99 ..     431     531 ..     426     534 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.77
                                    HHH...HHHHHHHHHHHHHHH CS
                     Laminin_II  82 eeassslsdniseikelIaqA 102
                                    +  ++++s+ +s+i+e   +A
  gi|118431527|ref|NP_148048.2| 168 RRVRAAISQAVSRIRESLDRA 188
                                    344577*********977765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.024
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...X--TTTTTGGGHHHHHHHH CS
                     Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk...LeklapqLldklkelkqle 82 
                                    +ea     +v + + +l + le ++ + s+++r +ee++++v  ++ +++ Ar   k    + ++a+ + +++++l+ + 
  gi|118431527|ref|NP_148048.2| 431 EEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSdhgIRREAEMMRERVRKLERRL 510
                                    66667777888899999999999999999999999999999998888888887655533349999999999999999999 PP

                                    HH.......HHHHHHHHHHHH CS
                     Laminin_II  83 easss....lsdniseikelI 99 
                                    e+s+     l+ +++e++  +
  gi|118431527|ref|NP_148048.2| 511 EESAMmveeLKGELEELRRAV 531
                                    987667788888888888655 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.2   2.4e+03     550     576 ..     356     382 ..     349     392 .. 0.78
   2 ?    5.4  11.1     0.024       6.9     331     425 ..     436     530 ..     395     534 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.2
                         DUF812 550 svkkaYKylaalhenfeqLiktveetG 576
                                    ++  aYK + al ++   +  t+e+ G
  gi|118431527|ref|NP_148048.2| 356 AAAAAYKAYLALESKLRSVERTIEKMG 382
                                    444569999999999999999999887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                         DUF812 331 eleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasaq 410
                                    +  ++ +++++l++ +e+l+ e ++l+ +++++e e+  +k++ e+  +  k  + +   ++   e ++kL++ +e+sa 
  gi|118431527|ref|NP_148048.2| 436 DGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAKSDHGIRREAEMMRERVRKLERRLEESAM 515
                                    44567788888999999999999999999999999999999999999999999999999999999999999999999999 PP

                         DUF812 411 rlvelakqWekhRvp 425
                                     + el+ + e+ R++
  gi|118431527|ref|NP_148048.2| 516 MVEELKGELEELRRA 530
                                    999999999998865 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   8.5      0.86   2.5e+02       7      68 ..     441     501 ..     427     527 .. 0.54
   2 ?    3.6   1.0      0.36     1e+02       6      35 ..     499     528 ..     492     559 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.86
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXX CS
                           YabA   7 fdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelse 68 
                                    ++++++l e le+l  e ++lk++l+e+  e   L+++ e+ r r + +++  +++ + ++e
  gi|118431527|ref|NP_148048.2| 441 YKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQLERARARAK-SDHGIRREAEMMRE 501
                                    55555556666666666666666666666666666555555555552.22222222222233 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.36
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   6 lfdkleeleeqleelleeleelkeelaell 35 
                                    + +++++le++lee    +eelk el+el 
  gi|118431527|ref|NP_148048.2| 499 MRERVRKLERRLEESAMMVEELKGELEELR 528
                                    445677777777777777777777766654 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4    0.0084       2.4       8      42 ..     445     479 ..     442     480 .. 0.91
   2 ?   -0.4   0.2       4.8   1.4e+03      10      39 ..     520     549 ..     518     552 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0084
                           HALZ   8 dvLKasYdaLksdydsLkkenekLkaelqeLkekl 42 
                                     +L+   +aL+ ++ sLk+  e+ +ae++ Lk++l
  gi|118431527|ref|NP_148048.2| 445 SALREMLEALRIENSSLKRRLEEMEAEVMMLKAQL 479
                                    6899999*************************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 4.8
                           HALZ  10 LKasYdaLksdydsLkkenekLkaelqeLk 39 
                                    LK   + L+  ++ L +  + L  e+ +L+
  gi|118431527|ref|NP_148048.2| 520 LKGELEELRRAVELLGRGTHLLAVEVDRLT 549
                                    666667777777777777777777777776 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.8     0.027       7.9      48      98 ..     428     478 ..     407     481 .. 0.81
   2 ?    1.7   1.0       1.2   3.5e+02      45      95 ..     484     534 ..     472     540 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.027
                        UPF0449  48 seeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeee 98 
                                    +++e+   +  ++Y+++ ++ e+ e L+ ++++Lk+++ee+++    L+ +
  gi|118431527|ref|NP_148048.2| 428 QHQEEAAGDGGSVYKEMSALREMLEALRIENSSLKRRLEEMEAEVMMLKAQ 478
                                    345555666889******************************998888765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.2
                        UPF0449  45 assseeedleaeveelYeqvrtylelnerLeeak...eeLkqkceeLktageeL 95 
                                    a +++++ ++ e+e + e+vr++   ++rLee     eeLk ++eeL++a e L
  gi|118431527|ref|NP_148048.2| 484 ARAKSDHGIRREAEMMRERVRKL---ERRLEESAmmvEELKGELEELRRAVELL 534
                                    44445666666666666666654...4444443312267777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1441  (0.0803726); expected 358.6 (0.02)
Passed bias filter:                      897  (0.0500307); expected 358.6 (0.02)
Passed Vit filter:                       194  (0.0108205); 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):              62  [number of targets reported over threshold]
# CPU time: 1.09u 0.34s 00:00:01.43 Elapsed: 00:00:00.49
# Mc/sec: 4088.39
//
Query:       gi|118431528|ref|NP_148049.2|  [L=301]
Description: kinase [Aeropyrum pernix K1]
Scores for complete 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-53  181.5   0.0    1.5e-53  181.2   0.0    1.1  1  RIO1             RIO1 family
    4.2e-22   78.1   0.1    3.2e-21   75.3   0.1    2.2  2  Rio2_N           Rio2, N-terminal
    1.8e-07   31.4   1.2    0.00073   19.5   0.0    2.8  2  APH              Phosphotransferase enzyme family
    0.00089   18.1   0.0     0.0013   17.6   0.0    1.2  1  Pkinase_fungal   Fungal protein kinase
     0.0044   16.4   0.0      0.049   13.0   0.0    2.1  1  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0087   15.9   0.2      0.034   14.0   0.2    2.1  1  MarR_2           MarR family
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.051   12.9   0.0    1.8  1  Pkinase          Protein kinase domain
      0.032   13.4   0.0      0.044   13.0   0.0    1.2  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 !  181.2   0.0   6.9e-57   1.5e-53       1     183 [.     107     283 ..     107     288 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 6.9e-57
                                    EEEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEET CS
                           RIO1   1 nVyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkr 80 
                                    +Vy+avs  g+++++K+++ ++++F+k+++++s+  + +     t++++++k+ ae+Ef++L rlee+g+++P+p++++r
  gi|118431528|ref|NP_148049.2| 107 DVYVAVSPAGSKLTVKLHRAGRESFRKVRRHRSYALDLR----PTSWLDVSKALAEREFKILVRLEEEGARIPSPVAWNR 182
                                    69***********************************44....78*********************************** PP

                                    TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEETTSTT CS
                           RIO1  81 hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQaveldhpn 159
                                    h++v ++++  gv +++++ ++ +e a++++++vle++r++y+++g+vH+DLSeyNv+ +++ + v+ID++Q+v  d+p+
  gi|118431528|ref|NP_148049.2| 183 HAVVQRYVE--GVLLADVRVLD-TEAAASILRDVLETLRIAYTRVGVVHGDLSEYNVIATTEgRGVVIDWPQYVYRDEPH 259
                                    *********..***********.889999******************************9998***************** PP

                                    HHHHHHHHHHHHHHHHHTTC---- CS
                           RIO1 160 alefLerDveniikfFrrkgvekv 183
                                    ale+L+rDve+i k+Frr++  kv
  gi|118431528|ref|NP_148049.2| 260 ALELLRRDVEYILKYFRRRAGLKV 283
                                    ******************987655 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.1   1.4e-24   3.2e-21       2      82 .]      10      90 ..       9      90 .. 0.97
   2 ?    0.2   0.0      0.41   9.2e+02       3      17 ..     155     169 ..     153     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 1.4e-24
                         Rio2_N  2 ryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvkr 82
                                    +Ls +++rvL+a+E  mr++++Vp+el+e++srl  + +++++++l+  kl++r+  +  GY Lty G+D+LA+  l++r
  gi|118431528|ref|NP_148049.2| 10 TSLSGDELRVLRAIERWMRKYRYVPVELVERTSRLPPSRFSRAVKTLVTLKLVKRRLGSVSGYTLTYTGLDVLAIDNLRSR 90
                                   57999**********************************************************************999877 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                         Rio2_N   3 yLskedfrvLtavEm 17 
                                     L +++f++L  +E 
  gi|118431528|ref|NP_148049.2| 155 ALAEREFKILVRLEE 169
                                    7999******99985 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   1.4   8.9e-05       0.2       9     102 ..     129     217 ..      99     218 .. 0.73
   2 !   19.5   0.0   3.3e-07   0.00073     146     193 ..     204     249 ..     193     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-05
                                    SSCEEEEEEETT--EEEEEE-TT...S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS. CS
                            APH   9 asnrtylvttpagryvlrrnppa...raaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr. 84 
                                     s+r+++++   ++y+l + p++    +++ ++re+++l  L++ g+++P ++a+      ++ +++++ yv+g  l++ 
  gi|118431528|ref|NP_148049.2| 129 ESFRKVRRH---RSYALDLRPTSwldVSKALAEREFKILVRLEEEGARIPSPVAW------NR-HAVVQRYVEGVLLADv 198
                                    334444444...58999999999444455556799999999999999******93......44.6788888888888887 PP

                                    .HHHHHHHHHHHHHHHHHH CS
                            APH  85 .klsaaqlpellealgefl 102
                                      l+ + +  +l+++ e+l
  gi|118431528|ref|NP_148049.2| 199 rVLDTEAAASILRDVLETL 217
                                    7677777777777776666 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.3e-07
                                    HHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                            APH 146 eeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDf 193
                                    e++++ +l+ ++++l+    + +++HgDl+  N++ + ++  v  viD+
  gi|118431528|ref|NP_148049.2| 204 EAAAS-ILRDVLETLRIaYTRVGVVHGDLSEYNVIATTEGRGV--VIDW 249
                                    33333.6677777777688999***************888888..**** PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.8e-07    0.0013     309     356 ..     207     249 ..     196     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.8e-07
                 Pkinase_fungal 309 lealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDL 356
                                     + lrD+++++r  ++  g++H D Se+N++ t      e +g++iD 
  gi|118431528|ref|NP_148049.2| 207 ASILRDVLETLRIAYTRVGVVHGDLSEYNVIAT-----TEGRGVVIDW 249
                                    5679***************************99.....6788888885 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.2e-05     0.049      30      88 ..     129     187 ..     109     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                            Kdo  30 aalrkyyrggllgklskdlyrfklgrtravrEfrllkrLeeagvavpkpvaagavkvgl 88 
                                      +rk +r +  +   +   ++ ++++ a rEf++l rLee+g ++p pva +  +v  
  gi|118431528|ref|NP_148049.2| 129 ESFRKVRRHRSYALDLRPTSWLDVSKALAEREFKILVRLEEEGARIPSPVAWNRHAVVQ 187
                                    5677777777777777886777799999***********************98766544 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   1.5e-05     0.034       3      54 ..      12      65 ..      10      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   --HHHHHHHHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  3 ltpaqarvLaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   l++ ++rvL a+ r  ++   + v  ++r+ +l++s+ sr++k Lv   Lv rr
  gi|118431528|ref|NP_148049.2| 12 LSGDELRVLRAIERWMRKyrYVPVELVERTSRLPPSRFSRAVKTLVTLKLVKRR 65
                                   5667788888887776556556888889999*********************99 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.3e-05     0.051       5     140 ..      98     247 ..      95     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                                    EEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE............... CS
                        Pkinase   5 eklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee............... 69 
                                     k+G G+ G Vy av +  g +  vK  +  +++ +   kv+r  ++   l+    + + +++ e               
  gi|118431528|ref|NP_148049.2|  98 DKIGLGKEGDVYVAV-SPAGSKLTVKLHRAGRESFR---KVRRHRSYALDLRPTSWLDVSKALAErefkilvrleeegar 173
                                    678888888888888.57777777777666555443...34555555555555555555555544455555555555555 PP

                                    ......SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE- CS
                        Pkinase  70 ......kdelylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKit 140
                                           ++  +v+ yveg  lad+     +l+ e a +i++ +le l+  + + g++H Dl   N++  ++g   ++
  gi|118431528|ref|NP_148049.2| 174 ipspvaWNRHAVVQRYVEGVLLADVR----VLDTEAAASILRDVLETLRIAYtRVGVVHGDLSEYNVIATTEGRGVVI 247
                                    77777645556799999999888877....59********************6678***********99977765555 PP

>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.044     151     221 ..     187     258 ..     177     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                Fructosamin_kin 151 qRlgvqlelakekglefakieelvervaellskhqpkpsllHGdLWsgNaaltkdgepvifd.PaayygdrE 221
                                    qR    + la  + l+++ + +++  v e+l+    +  ++HGdL + N+ +t++g+ v++d P   y d+ 
  gi|118431528|ref|NP_148049.2| 187 QRYVEGVLLADVRVLDTEAAASILRDVLETLRIAYTRVGVVHGDLSEYNVIATTEGRGVVIDwPQYVYRDEP 258
                                    55555566777788888999999999***********************************98888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2245.02
//
Query:       gi|118431529|ref|YP_874909.1|  [L=87]
Description: ArsR family transcriptional regulator [Aeropyrum pernix K1]
Scores for 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-11   42.2   0.1    8.1e-11   41.6   0.1    1.3  1  HTH_5           Bacterial regulatory protein, arsR family
    5.1e-10   39.3   0.0    6.8e-10   38.9   0.0    1.1  1  HTH_20          Helix-turn-helix domain
    1.4e-06   27.7   0.7    2.3e-06   27.0   0.7    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.7e-05   24.0   0.0    3.6e-05   23.5   0.0    1.2  1  TrmB            Sugar-specific transcriptional regulator TrmB
    5.5e-05   23.0   0.0    8.3e-05   22.4   0.0    1.2  1  MarR            MarR family
      6e-05   22.9   0.1    7.5e-05   22.5   0.1    1.3  1  MarR_2          MarR family
    0.00053   20.4   0.0    0.00067   20.1   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
     0.0011   19.1   0.0     0.0013   18.9   0.0    1.3  1  HTH_34          Winged helix DNA-binding domain
     0.0031   17.4   0.2      0.006   16.5   0.2    1.5  1  HTH_11          HTH domain
     0.0054   16.8   0.1      0.008   16.3   0.1    1.2  1  DprA_WH         DprA winged helix domain
     0.0076   16.0   0.0      0.012   15.4   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0081   16.3   0.0      0.012   15.7   0.0    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
       0.01   15.8   0.1      0.013   15.4   0.1    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.012   15.8   0.1      0.021   14.9   0.0    1.5  2  HTH_28          Helix-turn-helix domain
      0.035   14.0   0.1      0.041   13.8   0.1    1.1  1  PAX             'Paired box' domain
      0.047   13.7   0.1      0.076   13.0   0.1    1.5  1  HTH_36          Helix-turn-helix domain
      0.079   12.8   0.0       0.13   12.1   0.0    1.5  1  Nuc_N           Nuclease N terminal


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 !   41.6   0.1   7.7e-14   8.1e-11       1      45 [.      16      60 ..      16      61 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 7.7e-14
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   ++tR +I+ lLa+g+++  el+e lg s++++S + +kL+e G+V
  gi|118431529|ref|YP_874909.1| 16 NETRTRIIELLASGPKTLDELSEVLGQSKANISSQIRKLEEIGIV 60
                                   68******************************************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 !   38.9   0.0   6.5e-13   6.8e-10       2      55 ..       9      61 ..       8      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 6.5e-13
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   ++a+ALa+++R ri  +L   ++ t+ el e l+ sk+++s ++r+Lee g+v 
  gi|118431529|ref|YP_874909.1|  9 KVAHALANETRTRIIELL-ASGPKTLDELSEVLGQSKANISSQIRKLEEIGIVV 61
                                   799***************.********************************995 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.7   2.2e-09   2.3e-06       2      47 ..      16      60 ..      16      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.2e-09
                         HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +et+ +I+elL   +  +  eL+e lg S+++++ ++++Lee G++
  gi|118431529|ref|YP_874909.1| 16 NETRTRIIELLAS-GPKTLDELSEVLGQSKANISSQIRKLEEIGIV 60
                                   789999***9999.999****************************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 !   23.5   0.0   3.4e-08   3.6e-05      16      55 ..      24      63 ..      22      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.4e-08
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                    Ll++gp+t de++e lg +++++ + +r+Le+ G+V  +
  gi|118431529|ref|YP_874909.1| 24 ELLASGPKTLDELSEVLGQSKANISSQIRKLEEIGIVVPR 63
                                   69**********************************9765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.9e-08   8.3e-05      11      56 ..      25      69 ..      16      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.9e-08
                                   HHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                           MarR 11 ilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56
                                   +   +gp ++ eL + lg sk++++ ++++Le+ G +  +  p+Dr
  gi|118431529|ref|YP_874909.1| 25 L-LASGPKTLDELSEVLGQSKANISSQIRKLEEIGIVVPRYQPGDR 69
                                   3.4579*****************************99777667765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   7.1e-08   7.5e-05       7      59 ..      19      68 ..      12      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.1e-08
                                   HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                         MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                     r++  L+ +p    t  el + lg sk+++s  +++L++ G v+ r  p+D
  gi|118431529|ref|YP_874909.1| 19 RTRIIELLASGPK---TLDELSEVLGQSKANISSQIRKLEEIGIVVPRYQPGD 68
                                   5677777777776...*****************************76633335 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.3e-07   0.00067      12      58 ..      26      70 ..      15      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.3e-07
                         HTH_27 12 irhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                   ++   ++k+l +l+++l  ++++is+ ++kL+e G v+    + dr+
  gi|118431529|ref|YP_874909.1| 26 LA--SGPKTLDELSEVLGQSKANISSQIRKLEEIGIVVPRYQPGDRG 70
                                   55..799****************************997776666665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.2e-06    0.0013       2      45 ..      19      61 ..      18      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                         HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   R  ++ +Las  + +  el+e l+ +++n+s++++kLe+ g ++
  gi|118431529|ref|YP_874909.1| 19 RTRIIELLASGPK-TLDELSEVLGQSKANISSQIRKLEEIGIVV 61
                                   6666776666554.6789*********************99765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   5.7e-06     0.006       2      45 ..      19      60 ..      18      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.7e-06
                         HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                   ++ i+elL  a gp + +eL+e L+ S++ +   I++Lee+g+ 
  gi|118431529|ref|YP_874909.1| 19 RTRIIELL--ASGPKTLDELSEVLGQSKANISSQIRKLEEIGIV 60
                                   57899999..55567***************************64 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   7.6e-06     0.008      10      50 ..      15      55 ..       8      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.6e-06
                        DprA_WH 10 lddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLE 50
                                   + +++ r+ ++L++ P ++D+L++ +g + a +s++   LE
  gi|118431529|ref|YP_874909.1| 15 ANETRTRIIELLASGPKTLDELSEVLGQSKANISSQIRKLE 55
                                   6799***********************99999999887777 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 !   15.4   0.0   1.2e-05     0.012       7      48 ..      21      60 ..      20      63 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                   +i+++la++p    l el++ +g +k++ +  ++ L+e G+v
  gi|118431529|ref|YP_874909.1| 21 RIIELLASGPKT--LDELSEVLGQSKANISSQIRKLEEIGIV 60
                                   799********6..**************************98 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05     0.012      26      53 ..      34      61 ..      22      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyve 53
                                    +l+e+L++s++ +s  ++kLe+ G v+
  gi|118431529|ref|YP_874909.1| 34 DELSEVLGQSKANISSQIRKLEEIGIVV 61
                                   68*********************99885 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 ?   15.4   0.1   1.2e-05     0.013       2      53 ..       9      63 ..       8      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHHHCTTTCEEEE....EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                      HTH_Crp_2  2 RlArfLlrlaeraggeiel....pltqeelAsmlGltretvsrilseLkreglis.r 53
                                   ++A+ L + +++ +  iel    p t +el++ lG +   +s  +++L++ g++  r
  gi|118431529|ref|YP_874909.1|  9 KVAHALANETRT-R-IIELlasgPKTLDELSEVLGQSKANISSQIRKLEEIGIVVpR 63
                                   678888664332.3.344455569999**************************9954 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       8.9   9.4e+03      14      19 ..       6      11 ..       2      15 .. 0.46
   2 ?   14.9   0.0     2e-05     0.021       2      41 ..      19      59 ..      18      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.9
                         HTH_28 14 svreaA 19
                                    ++ +A
  gi|118431529|ref|YP_874909.1|  6 HIAKVA 11
                                   344444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2e-05
                         HTH_28  2 RleiikllaaG.hsvreaArelgisrrtvyrWikryeegGi 41
                                   R +ii+lla+G ++ +e+++ lg s   +++ i+++ee+Gi
  gi|118431529|ref|YP_874909.1| 19 RTRIIELLASGpKTLDELSEVLGQSKANISSQIRKLEEIGI 59
                                   889********56***************************8 PP

>> PAX  'Paired box' 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     0.041      17      73 ..      13      70 ..       7      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                            PAX 17 plpdsirqkivelahsgvrpcv.isrqlrvshgcvskilgryqetgsirpgviggskp 73
                                    l +++r +i+el +sg +  + +s  l  s+  +s  + + +e g + p+   g + 
  gi|118431529|ref|YP_874909.1| 13 ALANETRTRIIELLASGPKTLDeLSEVLGQSKANISSQIRKLEEIGIVVPRYQPGDRG 70
                                   689**************9997549*************************998877665 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.2e-05     0.076      28      54 ..      33      59 ..      17      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                         HTH_36 28 qetlakrlglsknTvsraikeLeqlGy 54
                                    + l++ lg sk  +s+ i++Le+ G+
  gi|118431529|ref|YP_874909.1| 33 LDELSEVLGQSKANISSQIRKLEEIGI 59
                                   6889999*****************998 PP

>> Nuc_N  Nuclease N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.13      36      53 ..      42      59 ..      24      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                          Nuc_N 36 aSKAkiQsrIsklEkeGv 53
                                   +SKA+i s+I klE+ G+
  gi|118431529|ref|YP_874909.1| 42 QSKANISSQIRKLEEIGI 59
                                   7*************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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):              17  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 666.86
//
Query:       gi|14601511|ref|NP_148051.1|  [L=538]
Description: CTP synthetase [Aeropyrum pernix K1]
Scores for complete 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-119  397.4   0.1   3.8e-119  396.9   0.1    1.2  1  CTP_synth_N    CTP synthase N-terminus
    2.7e-47  161.0   0.0    4.2e-47  160.4   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    5.5e-12   45.9   0.0    1.1e-11   44.9   0.0    1.5  1  Peptidase_C26  Peptidase C26
    0.00025   21.1   0.0    0.00042   20.4   0.0    1.7  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain


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 !  396.9   0.1  8.5e-123  3.8e-119       1     263 [.       5     267 ..       5     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 396.9 bits;  conditional E-value: 8.5e-123
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT--- CS
                   CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikl 81 
                                   ky++vtGGv+S++GkG+++asl+ ll srg++v++ikiDPY+nvdagt++p+ hGEvfv++dG+etDlD+G+YeRfl+ +l
  gi|14601511|ref|NP_148051.1|   5 KYVIVTGGVLSSVGKGLTTASLALLLSSRGYSVEAIKIDPYINVDAGTMNPYMHGEVFVTEDGGETDLDIGHYERFLGKNL 85 
                                   8******************************************************************************** PP

                                   -GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHH CS
                   CTP_synth_N  82 tkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfleairqlkle 162
                                   ++++nittG+iy svi+ker+GdylG+tvqviph+tdeik+ri++v + + advviveigGtvgdie+lpflea rq++le
  gi|14601511|ref|NP_148051.1|  86 SRKHNITTGQIYFSVISKERSGDYLGQTVQVIPHITDEIKSRIKEVGDVSGADVVIVEIGGTVGDIEGLPFLEAARQMRLE 166
                                   ***********************************************9999****************************** PP

                                   H-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GGGEEEEE--S-G CS
                   CTP_synth_N 163 lgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvekeavisvkdvesi 243
                                    g +n+++ihv+l p+l ++ge+ktkp+qhs++elr++Giqpd +v+rs+++le+e  +kial++++++e+vi++ d+e+i
  gi|14601511|ref|NP_148051.1| 167 EGFDNTFFIHVALSPYLPTTGEQKTKPVQHSIQELRRIGIQPDAVVVRSHQPLEQEGLRKIALYATLPMENVINSYDIENI 247
                                   ********************************************************************************* PP

                                   GGHHHHHHHCTHHHHHHHHT CS
                   CTP_synth_N 244 yevpllleeqglaelilekl 263
                                   y++pllle+qgla+l+ ++l
  gi|14601511|ref|NP_148051.1| 248 YRLPLLLEKQGLARLVERRL 267
                                   **************999876 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.0   9.5e-51   4.2e-47       2     189 ..     304     531 ..     303     532 .. 0.92

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 9.5e-51
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHH....HH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeei....le.llknpdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                   l D+y s++e+l+ha++  gv+ e++++++++ e      +   +++dg +v +G+g +gvegkieai+++re k+P+LGI
  gi|14601511|ref|NP_148051.1| 304 LRDSYISIVEALKHASAYEGVRPELLWVESTDIERgvvdVDrVFEEADGAIVLPGFGVRGVEGKIEAIRRFREGKKPMLGI 384
                                   78***************************9988886655224589************************************ PP

                                   THHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEE CS
                        GATase  78 CLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknevierhr 127
                                   C+GmQl + e++r+v                        +++  +++ggtmrlg+++           lyg  +   erhr
  gi|14601511|ref|NP_148051.1| 385 CFGMQLSVVEYARNVLglkeahttevnpetphpvvdllpEQRGIDKLGGTMRLGARPVrivegtilWSLYGR-ELASERHR 464
                                   *************9999999999999999999999****77779***********999*****999899998.99****** PP

                                   EEEEEESG...CHHHTTEEEEEEEETTE.EEEEEEEETTT.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                        GATase 128 Hryevnpk...elepaglevtaksedde.elmeiiekknp.fvgvQFHPEststpegpellfnflik 189
                                   Hryevnp+   +l++agl+v+a+s+++  e +e++ ++ p f ++QFHPE++s+p +p+++f++++ 
  gi|14601511|ref|NP_148051.1| 465 HRYEVNPTyvdRLVEAGLVVSAWSQEGYvEAVELRPRDHPfFLATQFHPEFKSRPLNPAPVFKGFVT 531
                                   ************************999666677777777*************************986 PP

>> Peptidase_C26  Peptidase C26
   #    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      97     216 .]     370     514 ..     365     514 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.5e-15
                 Peptidase_C26  97 LiraalergvPilgiCrGlqllnvalGGtly..qdieeqsgltdhrehe...............q.....saashavkvek 155
                                    ir+  e ++P+lgiC G+ql  v +  ++   +++++++ + +    +               +        ++ v++++
  gi|14601511|ref|NP_148051.1| 370 AIRRFREGKKPMLGICFGMQLSVVEYARNVLglKEAHTTEVNPE----TphpvvdllpeqrgidKlggtmRLGARPVRIVE 446
                                   577788899************98887766541122332222222....13346888888766661555568889******* PP

                 Peptidase_C26 156 gsllaellgseeievnslHhqaike......laeelrveAvaeDgviEaieseeak.afvlgvQwHPE 216
                                   g++l +l+g+e ++    H+  ++       ++ +l v+A+++ g +Ea+e++ ++  f+l+ Q+HPE
  gi|14601511|ref|NP_148051.1| 447 GTILWSLYGRELASERHRHRYEVNPtyvdrlVEAGLVVSAWSQEGYVEAVELRPRDhPFFLATQFHPE 514
                                   *********999999999**999989999999*******************9887768*********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 !   20.4   0.0   9.4e-08   0.00042       8      55 ..      15     120 ..       8     432 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.4e-08
                                   TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                          CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                   + vGK  ++a+La +l+ rg+ V +++ Dp  n +a   g+ n                                      
  gi|14601511|ref|NP_148051.1|  15 SSVGKGLTTASLALLLSSRGYSVEAIKIDPYINVDA---GTMNPYMHgevfvtedggetdldighyerflgknlsrkhnit 92 
                                   78*****************************99988...333332224555555666666655555555555555555555 PP

                                   ...........................C CS
                                   ...........................x RF
                          CbiA  55 ...........................d 55 
                                                               
  gi|14601511|ref|NP_148051.1|  93 tgqiyfsviskersgdylgqtvqviphI 120
                                   5555555555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.40
# Mc/sec: 4056.64
//
Query:       gi|118431530|ref|NP_148052.2|  [L=267]
Description: phosphatase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-22   79.3   0.0    2.5e-21   75.7   0.0    2.1  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase
    2.4e-11   43.5   0.0    5.3e-11   42.4   0.0    1.6  1  Hydrolase_like  HAD-hyrolase-like
     0.0053   17.1   0.2     0.0087   16.4   0.2    1.4  1  Hydrolase       haloacid dehalogenase-like hydrolase


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 !   75.7   0.0   4.2e-25   2.5e-21       2      97 ..      14     108 ..      13     111 .. 0.95
   2 ?    1.2   0.0     0.066   3.9e+02      14      48 ..     165     200 ..     151     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 4.2e-25
                                    EEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHHSXXX CS
                    Hydrolase_6   2 lfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkrkadk 81 
                                    + D+dGv+w g+++i+    +l++l ++g ++v+lTNns++s++ ya+ le++g+di++ ++vtsa++aa +lkk+ + +
  gi|118431530|ref|NP_148052.2|  14 FADLDGVIWLGQEPIEDNLVVLRTLASEG-RLVVLTNNSTRSRRVYAAMLERVGLDIEPGRIVTSAYSAAVLLKKKLGPS 92 
                                    78***********************9987.7999********************************************** PP

                                    EEEEESXHHHHHHHHH CS
                    Hydrolase_6  82 kvlvigeeglreelke 97 
                                    + lv+geegl eel  
  gi|118431530|ref|NP_148052.2|  93 TALVVGEEGLVEELAV 108
                                    *************975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.066
                                    EE-TTHHHHHHHHHHT.T-EEEEEE---SS-HHHHH CS
                    Hydrolase_6  14 kaipgaaealnalraa.gkpvvllTNnsskseeeya 48 
                                     +ipga  ++  l++a g++ +++  + s+   e++
  gi|118431530|ref|NP_148052.2| 165 GLIPGAGSIVALLEKAtGVKPAIVAGKPSRGLAEVL 200
                                    567777777777766535555555544444444444 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   8.9e-15   5.3e-11       2      72 ..     189     260 ..     188     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 8.9e-15
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-T...TTHHHHHHHHT---SEE CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrp...edleepehkptyvaddl 72 
                                    +gKP++++ +     +  +p + l++GDr++tD+++A++ G++s+LVltG +r    e++++++ +   va +l
  gi|118431530|ref|NP_148052.2| 189 AGKPSRGLAEVLESLF--KPVRPLVVGDRIDTDVEFARAWGVDSLLVLTGLYRGvsiEEASRKAGEGVRVARSL 260
                                    6999999988776665..7789*******************************944434344445555555555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.5e-06    0.0087       2     209 ..      11     226 ..      10     227 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                                    SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg.............. 67 
                                    + v+ D+dG+++ g+  +ed +v + +                  + a ++r   lt++ t   r               
  gi|118431530|ref|NP_148052.2|  11 DIVFADLDGVIWLGQEPIEDNLVVL-R------------------TLASEGRLVVLTNNSTRSRRVyaamlervgldiep 71 
                                    78999**********8888866666.1..................34444444444444441111122222222222222 PP

                                    ......................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTTH CS
                                    ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 ......................ayaigkpewltaldippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpea 123
                                                          a+ +g++ ++++l               +g+ va    + +++av+   d +  + ++
  gi|118431530|ref|NP_148052.2|  72 grivtsaysaavllkkklgpstALVVGEEGLVEEL-------------AVEGHVVASSsdNIDVDAVVVGLDRNLTYGKL 138
                                    22233333333344444555556666666666666.............33333333334444699*************** PP

                                    HHHHHHHHHTTEEEEEEESSEHHHHH.HHHHH.TT.GGGE.SEEEEHHCES....STTTSHHHHHHHHHHHTSTGGGEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xx.xxxx.xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 124 aeavasLkaagievvlltgdnpetae.raanq.lG.ddyf.daviasdiet....vakpspegkvaaireLqgkpeevam 195
                                    a a  ++++ g  ++++t+ +++ +  r +   +G   ++ +   +    +    va+   +g+ ++++ L  kp + ++
  gi|118431530|ref|NP_148052.2| 139 ARAASAIHS-GS-LFVATNLDHALPTpRGLIPgAGsIVALlEKATG----VkpaiVAGKPSRGLAEVLESL-FKPVRPLV 211
                                    ******995.55.799999999888877777779932222122222....1356777777999********.9******* PP

                                    EESSHH.HHHHHHHT CS
                                    xxxxxx.xxxxxxxx RF
                      Hydrolase 196 VGDgvn.DaaalaaA 209
                                    VGD++  D+++++a 
  gi|118431530|ref|NP_148052.2| 212 VGDRIDtDVEFARAW 226
                                    **********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2175.21
//
Query:       gi|118431531|ref|YP_874910.1|  [L=79]
Description: hypothetical protein APE_1605a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 666.03
//
Query:       gi|118431532|ref|NP_148053.2|  [L=265]
Description: hypothetical protein APE_1609.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2022.83
//
Query:       gi|118431533|ref|NP_148054.2|  [L=229]
Description: hypothetical protein APE_1610.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1790.61
//
Query:       gi|14601515|ref|NP_148055.1|  [L=650]
Description: hypothetical protein APE_1611 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-34  117.7   0.0    7.6e-34  117.2   0.0    1.2  1  FbpA             Fibronectin-binding protein A N-terminus (Fb
    1.1e-21   77.5   0.0    7.2e-21   74.9   0.0    2.1  2  NFACT-R_1        NFACT protein RNA binding domain
  ------ inclusion threshold ------
        0.1   12.4   0.3       0.16   11.7   0.3    1.2  1  DUF724           Protein of unknown function (DUF724)
       0.16   10.6   3.1      0.096   11.4   0.5    1.7  2  DUF773           CDK5 regulatory subunit-associated protein 3
        4.5    6.8   4.8        8.6    5.9   4.8    1.5  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
        8.3    6.8  11.5        1.3    9.4   1.2    2.8  2  kleA_kleC        Uncharacterized KorC regulated protein A


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 !  117.2   0.0   2.5e-37   7.6e-34       3     412 ..       9     396 ..       7     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 2.5e-37
                                   HHHHHHHHHHHHHHTTXEEEEEEEE.ETTEEEEEEEETTEEEEEEEEXXTTTXEEEEXXX.XXXXXSSXXHHHHHHHHHHT CS
                          FbpA   3 lvlaavvaELqkellggridkiyqp.ekdelvltlranrgrhkLllsahpsyarihltek.pkenpkeppnFcmlLRkyLk 81 
                                   l+++    +L++ l g+r+d+iy p ek+ + ++++  +g+ ++  +      rih t++ +   +  p+ F+ +LRk+++
  gi|14601515|ref|NP_148055.1|   9 LDVHIAAIQLDNMLRGARLDNIYWPpEKKGVLMKFKGPTGTVNVIAEP---SVRIHATSRtAALREVVPTGFVAILRKRVR 86 
                                   677888889**************853788999****888887788887...89*****9977888999************* PP

                                   TXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSX CS
                          FbpA  82 garivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPp 162
                                   g+r++ ++qlgfdRivels+++          +L+vEim r + ++Lv++e+ +i+a   v +   r+R + p+ +Y +Pp
  gi|14601515|ref|NP_148055.1|  87 GSRLEGVRQLGFDRIVELSFSTG--------HRLYVEIMPR-GSLVLVNSEG-VIEATTVVAEF--RDRVLKPKTQYRPPP 155
                                   ***********************........9*********.******9886.55666666555..6**********8888 PP

                                   XXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTXXX CS
                          FbpA 163 sqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqelleele 243
                                     ++ nP+  e+  e++el s   +d v+ Lv+    + ++ aee+l r g+d  t+ +el   ++  ++ al+e+ +e  
  gi|14601515|ref|NP_148055.1| 156 L-QEENPFLKES-GELSELAS-RGADAVRGLVRGA-KVPGEAAEEALDRCGVDYSTRPSELGPGEWGCIARALNEIYKESL 232
                                   8.8899995555.45666644.369*********7.9*****************************************988 PP

                                   ....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          FbpA 244 eekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekklkklek 324
                                   +++   +     e+  e ++++ ++   l+ ++ ++++ alde ++    + ++  + ++l+k +e++++  e+ + +  +
  gi|14601515|ref|NP_148055.1| 233 QGRGYLCR---GERGLEADPFRRTR---LHCDEHSTFHSALDELFTPGGVEVEHP-EVARLRKSMEEAMKLAEE-YRRRAE 305
                                   65555444...44455555554433...556899***********9887766555.477899888887765555.455566 PP

                                   HHHCCGGH..HHHHCCHH-----------------------.--......---------------HHHHHHHHHHHHHHHH CS
                          FbpA 325 elekaeka..enyrligelltaylyaikkgmsevelenyydege......evtIpLdprkspsenAqkyfkkykKlkrave 397
                                   el ka++a    y+ ++e l        +g++e+ + ++   ++      +++++ +   ++ +   ++++++  l+ ++e
  gi|14601515|ref|NP_148055.1| 306 ELRKAAEAvaSAYQEVDEALRSAA----RGEKEAPVVEVRG-KTvlldlgGLRVAAQRGEDAGKLILRLYREAGELEAKAE 381
                                   777777777799*******99666....5555555554433.224444447899999999999999999999999999999 PP

                                   HHHHHHHHHHHHHHH CS
                          FbpA 398 aveeqieetkeeley 412
                                    +e++ +e++++le 
  gi|14601515|ref|NP_148055.1| 382 RAEKAFAEARSRLEE 396
                                   999999999998875 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 ?   -0.5   0.0      0.65     2e+03      37      51 ..     255     276 ..     248     321 .. 0.63
   2 !   74.9   0.0   2.4e-24   7.2e-21       1     109 []     420     530 ..     415     530 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                     NFACT-R_1  37 fhvdkessahvylr.......l 51 
                                   +h+d +s  h  l         
  gi|14601515|ref|NP_148055.1| 255 LHCDEHSTFHSALDelftpggV 276
                                   79*****999998866544441 PP

  == domain 2  score: 74.9 bits;  conditional E-value: 2.4e-24
                     NFACT-R_1   1 kvfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnk 80 
                                   k++w ++ +g+l i+G+D+ +ne ++k+yl ++d+++h+d+++++ ++l +++    +  ++ + +aa la+a+S+a ++ 
  gi|14601515|ref|NP_148055.1| 420 KYHWTITRNGFLAIGGRDAGQNESVVKRYLGDDDIFLHADIHGAPATVLLTRR-L--QPGDDDIYDAAVLAAAYSRAwKAG 497
                                   788999*****************************************999454.4..5778999***************** PP

                     NFACT-R_1  81 lssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                      v+v++v+ s++sk++p    l++G+++++g
  gi|14601515|ref|NP_148055.1| 498 AGGVSVYWVYGSQVSKSPPageyLARGAFMVYG 530
                                   ******************************986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   5.5e-05      0.16      86     185 ..     282     391 ..     255     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.5e-05
                        DUF724  86 dVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkl..eeeidelekkilelerqlallk........ekkeaa 156
                                   +V  l++ +++ ++l +e+++ +ee++k+ + ++ + +e  ++  ++   e+e  ++e++ + +ll         ++ e+a
  gi|14601515|ref|NP_148055.1| 282 EVARLRKSMEEAMKLAEEYRRRAEELRKAAEAVASAYQEVDEAlrSAARGEKEAPVVEVRGKTVLLDlgglrvaaQRGEDA 362
                                   588899999999***9999999999998888887766655544113445588999999999999998*******99999** PP

                        DUF724 157 dkeiarlkseaekleeeledveqeFeava 185
                                    k i rl  ea +le + e++e+ F +  
  gi|14601515|ref|NP_148055.1| 363 GKLILRLYREAGELEAKAERAEKAFAEAR 391
                                   *************************8865 PP

>> DUF773  CDK5 regulatory subunit-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   3.2e-05     0.096     123     162 ..     282     321 ..     280     326 .. 0.93
   2 ?   -1.3   0.1      0.22   6.6e+02     448     485 ..     365     402 ..     360     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.2e-05
                        DUF773 123 eiPalkkqiaklqqqleelerKeadlkrsaaeaaakyeea 162
                                   e+  l+k+++++ ++ ee++r+ ++l + a+++a++y+e 
  gi|14601515|ref|NP_148055.1| 282 EVARLRKSMEEAMKLAEEYRRRAEELRKAAEAVASAYQEV 321
                                   7899*********************************985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                        DUF773 448 qeeklkeklkdleekreelqeelselepkleklvkktr 485
                                    + +l +++ +le+k e ++++ +e +++le++v ++r
  gi|14601515|ref|NP_148055.1| 365 LILRLYREAGELEAKAERAEKAFAEARSRLEEAVRRAR 402
                                   56678888999999999999999999999999998775 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 ?    5.9   4.8    0.0029       8.6     157     210 ..     284     334 ..     278     405 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0029
                       HAUS6_N 157 rrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekk 210
                                    r+ + +++a+++ ++y+++a++l+k  +++++ ++e+++ l+   +aa+ ek+
  gi|14601515|ref|NP_148055.1| 284 ARLRKSMEEAMKLAEEYRRRAEELRKAAEAVASAYQEVDEALR---SAARGEKE 334
                                   5677788888888***************************998...44444433 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 ?    9.4   1.2   0.00042       1.3      18      53 ..     282     317 ..     266     327 .. 0.81
   2 ?    1.1   3.3      0.16   4.9e+02      28      59 ..     368     399 ..     353     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00042
                     kleA_kleC  18 dlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaa 53 
                                   ++   R  + + ++ Aee  r+aeeLR+ +    +a
  gi|14601515|ref|NP_148055.1| 282 EVARLRKSMEEAMKLAEEYRRRAEELRKAAEAVASA 317
                                   44455999999****************998776666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                     kleA_kleC  28 aklaeAeeLvrqaeeLRakvyeesaaLedrak 59 
                                    + +eA eL+ +ae+  +   e+++ Le+ ++
  gi|14601515|ref|NP_148055.1| 368 RLYREAGELEAKAERAEKAFAEARSRLEEAVR 399
                                   46799***********999999*****99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      792  (0.0441742); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 4453.66
//
Query:       gi|14601516|ref|NP_148056.1|  [L=160]
Description: hypothetical protein APE_1614 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.0   0.3       0.78   10.0   0.3    2.1  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


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 ?   10.0   0.3   4.4e-05      0.78       3      38 ..      65     102 ..      63     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.4e-05
                                   HHHHHHTT-B-TTTSSBCCCCT---EEEE-T..-EEEE CS
                FeS_assembly_P   3 avlaaLrtVtDPelgvdlvslglvreidieg..gkVsv 38 
                                   +v+++L++   P  ++dlv +g+v+ i+++   +k+++
  gi|14601516|ref|NP_148056.1|  65 KVEEVLASTEVPGFDIDLVTSGVVKRIRLSRdgSKAAI 102
                                   7999***********************99876544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1210.86
//
Query:       gi|14601517|ref|NP_148057.1|  [L=351]
Description: hypothetical protein APE_1615 [Aeropyrum pernix K1]
Scores for 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   54.9  20.6    1.1e-14   54.6  20.6    1.1  1  Cation_efflux  Cation efflux family


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6  20.6   6.1e-19   1.1e-14       2     199 .]      53     247 ..      52     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 6.1e-19
                 Cation_efflux   2 ilsllanlilalvelivgllt.nSlalladafhslsdlvsllllllalkls.rkppderfpfGygrlevlgalvsgllllg 80 
                                   ++s ++ +++a+++++++ll   S+++l++af +++++++++ l +a+ ++ +++  ++++f + r+e+l+al s+l+ ++
  gi|14601517|ref|NP_148057.1|  53 YASAIVSALMAAAGVTLYLLVfPSSVVLVEAFVWFVEAITFFSLAVAFNIAaSRTVYYKARFEILRIESLMALHSALVGVA 133
                                   5788899999999999997655*********************************************************** PP

                 Cation_efflux  81 lavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrkl..rsaalkaaalhvlgDaltslgvlvsalv 159
                                   ++vf++++a+   + +++ e  ++l++++ +vs +v++++ ++l ++ ++l  r  +lk +a + + D+l   + +  ++v
  gi|14601517|ref|NP_148057.1| 134 VVVFVMWKAL---F-SKGSEPTPILLALYPGVSGLVSYVIERYLFGKLKRLevRLVSLKFVAEKLRLDVLLEEAGAAVIIV 210
                                   ********99...4.899*****************************9999999****************44444444444 PP

                 Cation_efflux 160 illfnlksg.plaDpvaslligliilysalkllkeslseLl 199
                                   + l+    g ++++ v+ + +gl++ly   +++ ++l+ L+
  gi|14601517|ref|NP_148057.1| 211 TNLT----GlTVFETVIVVGVGLYLLYGLGSIALKNLLYLV 247
                                   4444....2256*************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2634.89
//
Query:       gi|118431534|ref|NP_148058.2|  [L=424]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Aeropyrum pernix K1]
Scores for 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-51  172.8   0.0    8.4e-51  172.2   0.0    1.3  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    1.4e-27   96.6   0.0    1.8e-27   96.3   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
  ------ inclusion threshold ------
       0.02   14.5   0.0       0.04   13.5   0.0    1.4  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 !  172.2   0.0   1.4e-54   8.4e-51       3     170 .]      36     223 ..      34     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 1.4e-54
                                    TSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGGG-.. CS
                   PhosphMutase   3 kGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrragri.s 81 
                                    ++++G+++tv++g+ap+Sd A+ls+lGy+p++yy+GRGplEA g+G+e++ gd+a+R+n++tvd+ + +iidrr gr  +
  gi|118431534|ref|NP_148058.2|  36 HAVCGMVYTVKPGVAPQSDYATLSLLGYNPDEYYPGRGPLEAFGAGIEMRRGDIALRANFATVDPGTLRIIDRRVGRSlT 115
                                    789**************************************************************9***********99* PP

                                    -TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE......--S-B--S--..SSTTS............------BS CS
                   PhosphMutase  82 teeakeLikalneel.e.egvevkfypgveyrhllvl......lsdkitdtdpphdkegk............eikellpl 141
                                    + ea+eL++a++++  e  + ++ f++++++r +lvl      lsd+i++tdp++++ g+            ++++ l+ 
  gi|118431534|ref|NP_148058.2| 116 SREARELASAVDGMElEdGEGTALFRATIGHRGVLVLrhrskpLSDAISNTDPAYERRGRfsvalekyepfiKLSNPLV- 194
                                    *************99966899***************************************9996666665443333333. PP

                                    .SGGGHHHHHHHHHHHHHHHHHHHHSHHH CS
                   PhosphMutase 142 kseeaketaellnelieksqeiLedhpvN 170
                                    ++e+a   a++lne+++k+ eiL++hpvN
  gi|118431534|ref|NP_148058.2| 195 EDEAAVLAARMLNEFTLKAVEILDSHPVN 223
                                    48888***********************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0     3e-31   1.8e-27       2     236 ..       2     408 ..       1     412 [. 0.95

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 3e-31
                                    EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                  Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.............. 67 
                                    k++ +vlDG +++p+++ + ++ A++P++d+L  +         +g+ ++++ +  + s+ + l+l              
  gi|118431534|ref|NP_148058.2|   2 KILYIVLDGAADSPTSPRKTLEEASKPNIDSLGSH-------AVCGMVYTVKPGVAPQSDYATLSLlgynpdeyypgrgp 74 
                                    7889****************************999.......78************************************ PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Metalloenzyme  68 ................................................................................ 67 
                                                                                                                    
  gi|118431534|ref|NP_148058.2|  75 leafgagiemrrgdialranfatvdpgtlriidrrvgrsltsrearelasavdgmeledgegtalfratighrgvlvlrh 154
                                    ******************************************************************************** PP

                                    ......................................................................HHHHTT---- CS
                                    ......................................................................xxxxxxxxxx RF
                  Metalloenzyme  68 ......................................................................lrisetvkfa 77 
                                                                                                           r +++  +a
  gi|118431534|ref|NP_148058.2| 155 rskplsdaisntdpayerrgrfsvalekyepfiklsnplvedeaavlaarmlneftlkaveildshpvnlAREKRGLLKA 234
                                    *********************************************************************99999****** PP

                                    -EEEEEEEE-S---SS..HHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEE CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme  78 hvtffwnggrsgyfnp..leereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlv 135
                                    + ++ +++g  ++ +p  ++er+++++++++++ +                    ++e  ++e a +a++a+  +++dlv
  gi|118431534|ref|NP_148058.2| 235 NAILSRDAGGLPEEKPpsFQERFGLRGASIVEMVVergisryiglddirveiegrAREEVYREEAARAVEAL--ETHDLV 312
                                    *****9977655444448***********************************99888888889999*****..669*** PP

                                    EEEE-HHHHHHHTT-HHHHHHHHHHHHH.HHHHHHTTS-TTT..EEEEEE-SSB--TTTSS........-----EEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 136 vvniknaDmvGHtgdleatiaaieaaDe.avkeildaieqvd..gilvvtADHgnaedmvkrdkqplTsHtlepVPiliv 212
                                    +v++k +D+ GH+g +e++i+a+e++D+   + +ld++++ +    +vvt+DH ++ d+          H+ +pVP++i 
  gi|118431534|ref|NP_148058.2| 313 YVHLKGPDEPGHDGSFEGKIRAVEDIDKhFFAPLLDRLSSAGlePAFVVTSDHATPWDVGA--------HSGDPVPLMIS 384
                                    ***************************97789******99872258*************99........*********** PP

                                    STT----S--SSHHHHTT-TTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 213 gkglapdkvkegakfrekggLanv 236
                                    +++++ +  k +++++ +g L+++
  gi|118431534|ref|NP_148058.2| 385 HQSIQGSIGKFSETVCLRGRLGTI 408
                                    ***998555559999999999987 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.96   5.7e+03       4      38 ..       6      43 ..       4      58 .. 0.66
   2 ?   13.5   0.0   6.7e-06      0.04     170     232 ..     299     365 ..     244     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.96
                                   EEETT-B......TTHHHHHGSTSHHHHHHHHHSEEESEEE CS
                   Phosphodiest  4 islDGlr......adlldrlaellpnlaaLakegvsapnlr 38
                                   i+lDG+        ++l++     pn+++L ++ v +  ++
  gi|118431534|ref|NP_148058.2|  6 IVLDGAAdsptspRKTLEE--ASKPNIDSLGSHAVCGM-VY 43
                                   8888888665555555555..59999999988555544.33 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.7e-06
                                    T.......SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHH.HHHHHHHHHHHTTGTTTEEEEEEES- CS
                   Phosphodiest 170 l.......ekpdlllvyleetDtvgHkfGpdspevedalrrvDk.aigdLlealderglsaetniilvSDH 232
                                            e+ dl++v+l ++D  gH    +      a++++Dk + + Ll+ l   gl  e +++++SDH
  gi|118431534|ref|NP_148058.2| 299 AaravealETHDLVYVHLKGPDEPGHDGSFE--GKIRAVEDIDKhFFAPLLDRLSSAGL--EPAFVVTSDH 365
                                    1333444599****************76433..35678999998347999999999999..999******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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:                         3  (0.000167327); expected 0.2 (1e-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: 3091.02
//
Query:       gi|14601519|ref|NP_148059.1|  [L=148]
Description: hypothetical protein APE_1617 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1125.92
//
Query:       gi|118431535|ref|NP_148060.2|  [L=903]
Description: aconitate hydratase [Aeropyrum pernix K1]
Scores for complete 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-177  591.3   0.0   1.9e-177  590.9   0.0    1.1  1  Aconitase    Aconitase family (aconitate hydratase)
    9.3e-39  132.8   0.0    1.5e-38  132.1   0.0    1.3  1  Aconitase_C  Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.027   14.9   0.0       0.31   11.5   0.0    2.6  2  NTS_2        N-terminal segments of P. falciparum erythrocyte


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 !  590.9   0.0  3.2e-181  1.9e-177       4     461 .]      73     566 ..      65     566 .. 0.92

  Alignments for each domain:
  == domain 1  score: 590.9 bits;  conditional E-value: 3.2e-181
                      Aconitase   4 wdahlveeegiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknled 78 
                                    w++ + +++ +++ p rv++qd+tgv+a+vdlaa+r+a+++ gg+++++++l+pvdl idhs+     g++ea++ nl++
  gi|118431535|ref|NP_148060.2|  73 WSEYAGRKD-VPFHPVRVVMQDFTGVPAVVDLAAMRDAMKQFGGDPSKVNPLIPVDLIIDHSIqvdyyGTAEAFRLNLKR 151
                                    444433444.999******************************************************************* PP

                      Aconitase  79 efernkeryefLksaakaf.girvvppgqGIvHqvnlEy...........g..lalpgktvvgtDSHTtmigglGvlaiG 144
                                    e+ern+ery+ Lk+a+kaf ++rvvppg+GI+HqvnlEy           g  +a p+ +++gtDSHTtmi+glGv+++G
  gi|118431535|ref|NP_148060.2| 152 EYERNRERYQLLKWAQKAFsNFRVVPPGKGIIHQVNLEYlarvvwlsrrnGtlYAHPD-SLLGTDSHTTMINGLGVFGWG 230
                                    **********************************************999846699***.********************* PP

                      Aconitase 145 vGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMa 224
                                    vGgieaeav+lgqp+++ +p+vvgv+l G+l+egvt +Dlvl++++klrkk+vvgk+vE+fGegv++Ls+ draTiaNMa
  gi|118431535|ref|NP_148060.2| 231 VGGIEAEAVILGQPYYMLLPEVVGVRLVGELREGVTTTDLVLYITEKLRKKNVVGKFVEYFGEGVKKLSVPDRATIANMA 310
                                    ******************************************************************************** PP

                      Aconitase 225 aEvGAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpl 303
                                    +E+GAt+g+fpvde+tleYL+ tgr+e  v lve+y+k+++l+   +d++++y++v+e+dls++eps++gp +P+d++pl
  gi|118431535|ref|NP_148060.2| 311 PEYGATMGFFPVDEATLEYLRGTGRPEWLVqLVERYTKETGLWYSLEDPEPRYSDVVEIDLSDVEPSISGPSHPEDRIPL 390
                                    *****************************99************8889********************************* PP

                      Aconitase 304 selvk..ke.fkeelekeaaekaley..klkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvk 377
                                    +e ++  ++ + e lek+ +  a+      +e+++l+dg+v++aa++SCTN+sn++v++aa+lla +av+kgl+++p+vk
  gi|118431535|ref|NP_148060.2| 391 REAKErvRKiIMEYLEKKGRGPAIVElkLGDEEVHLTDGSVVYAALTSCTNTSNPSVMIAAALLArNAVKKGLRTRPWVK 470
                                    8877633232333443443333332243234699********************************************** PP

                      Aconitase 378 tsvaPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrle........ege...aivsssNRNFegRqgpntra 446
                                    ts aPGS+vv +y ++ Gl+++Le++Gf+++g+gC+ Cigns++l+        e++   a+v+s+NRNF+gR++p +r 
  gi|118431535|ref|NP_148060.2| 471 TSNAPGSRVVPEYWNRLGLMPYLEALGFHITGYGCTVCIGNSGPLRpeieeairEHDlwvATVLSGNRNFSGRIHPLARG 550
                                    *********************************************9777666655559********************** PP

                      Aconitase 447 .yLaSPelvvaaAlaG 461
                                     +LaSP+lvva+AlaG
  gi|118431535|ref|NP_148060.2| 551 nFLASPPLVVAYALAG 566
                                    ***************9 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   0.0   2.5e-42   1.5e-38       3     129 ..     696     822 ..     694     824 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 2.5e-42
                                    CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--S CS
                    Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagk 82 
                                    ++l ++G+ + + +  ++++++++++++ t++n +++n+lv++ + + t+  ++ge + v+daa++y++ g +l+v+agk
  gi|118431535|ref|NP_148060.2| 696 QYLIEQGVPPSQLNTCGSRRGNHEVMMRCTFDNPRFRNKLVPDREGGWTIFWPTGEVMHVFDAAMKYREMGVPLIVLAGK 775
                                    689999************************************************************************** PP

                                    SBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                    Aconitase_C  83 nfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                    ++G GSSR++AAk+++llG+kaviaeS+erI+++nl+++g+Lplef 
  gi|118431535|ref|NP_148060.2| 776 QYGVGSSRDWAAKGPALLGVKAVIAESYERIHRSNLVGMGVLPLEFM 822
                                    *********************************************95 PP

>> NTS_2  N-terminal segments of P. falciparum erythrocyte membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.29   1.7e+03      11      19 ..     401     409 ..     395     418 .. 0.80
   2 ?   11.5   0.0   5.1e-05      0.31      17      46 ..     858     890 ..     850     896 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.29
                          NTS_2  11 iEaYLekks 19 
                                    i +YLekk 
  gi|118431535|ref|NP_148060.2| 401 IMEYLEKKG 409
                                    779****96 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.1e-05
                          NTS_2  17 kksDdSkieqsLKA...DPSevqYYrsGGDGdY 46 
                                    +ksD   ie  +KA    P ev+YY+ GG  +Y
  gi|118431535|ref|NP_148060.2| 858 RKSDGRVIEFKVKArldTPIEVEYYKHGGILQY 890
                                    79***********96644***********7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (903 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 6418.94
//
Query:       gi|118431536|ref|NP_148061.2|  [L=389]
Description: hypothetical protein APE_1622.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-07   29.6   0.2    0.00021   20.5   0.0    2.1  2  Lycopene_cycl  Lycopene cyclase protein
    4.5e-07   30.0   1.0    1.1e-05   25.5   0.2    2.7  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.2e-06   27.9   0.1    3.1e-06   26.6   0.1    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.7e-05   24.6   1.6      0.042   13.4   0.3    3.0  3  DAO            FAD dependent oxidoreductase
    7.3e-05   22.2   4.6      0.038   13.2   1.3    2.8  2  FAD_binding_3  FAD binding domain
    0.00044   20.8   0.2     0.0022   18.5   0.1    2.2  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00067   18.5   0.3     0.0018   17.0   0.1    1.7  2  HI0933_like    HI0933-like protein
     0.0056   15.8   0.1     0.0092   15.1   0.1    1.4  1  GIDA           Glucose inhibited division protein A
     0.0059   15.9   0.1       0.22   10.8   0.1    2.4  3  Amino_oxidase  Flavin containing amine oxidoreductase
     0.0066   15.6   1.7      0.013   14.6   0.2    2.2  3  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.054   13.5   1.6       0.99    9.4   0.1    2.9  3  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.3e-07   0.00021       2     152 ..       4     154 ..       3     190 .. 0.84
   2 !    7.3   0.1    0.0013       2.1     242     299 ..     226     281 ..     222     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-07
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga....leecvehsWsgtivylddgkkill 77 
                                    v+v+G+G Agl  A ++  a +gl+v l e    + +p   +    ++ +++      e +  s+  +++++ ++    l
  gi|118431536|ref|NP_148061.2|   4 VAVVGGGFAGLIFAREM--ASTGLRVDLYEEHGRVGMPEHCTGIVSERTVNTigreARETIIDSYDSLEIRFRGETLAVL 81 
                                    89***************..***********9999988887799988888887666877888899**********999888 PP

                  Lycopene_cycl  78 g.raYgrvsskrlkeellerlv.engvklleakvesveeeeageslvvleggrkirarlvvdarglaslk..karrlgl 152
                                    +  +  r+ + rl+e lle+l+  +g+  l  +v+sv  e       v +gg + r  +v+ a g a+++  + ++lg+
  gi|118431536|ref|NP_148061.2|  82 DvGTVYRLDRVRLEELLLESLMsLGGRAQLGKRVHSVGIEGS-----VKAGGSEARYDAVILADG-AHGElhRMLDLGY 154
                                    85455689**************66888889999999999888.....899999999999999999.4444236666666 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0013
                  Lycopene_cycl 242 viPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalressl 299
                                     iP   g++++rl    v+ +G a+glv+P  G  +    ++a+l as i + l+    
  gi|118431536|ref|NP_148061.2| 226 RIPA--GPPAERLRRGrVYVVGDAGGLVKPLSGGGLYPNAKAAKLAASLIKRGLDVG-E 281
                                    5777..88888887656****************999999999998888888877753.2 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2     7e-09   1.1e-05       1      32 [.       6      37 ..       6      51 .. 0.95
   2 ?    2.2   0.1      0.13   2.1e+02      13      40 ..      87     114 ..      84     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7e-09
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                   +vG+G++Gl +A+++a  g++v+l+e + r+G
  gi|118431536|ref|NP_148061.2|  6 VVGGGFAGLIFAREMASTGLRVDLYEEHGRVG 37
                                   8*****************************99 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                    HHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                  NAD_binding_8  13 ylLakagfdvlllekrdrlGGraasyev 40 
                                    y+L + +++ llle+  +lGGra+  ++
  gi|118431536|ref|NP_148061.2|  87 YRLDRVRLEELLLESLMSLGGRAQLGKR 114
                                    78888889999***********986544 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 !   26.6   0.1   1.9e-09   3.1e-06       2     112 ..       3     145 ..       2     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.9e-09
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve......legtclnggcllskallgvaedaeias.................. 57 
                                    +v+v+GgG+AGl +a+++a  g++v l+e        +  +  g++ s+  ++        +                  
  gi|118431536|ref|NP_148061.2|   3 RVAVVGGGFAGLIFAREMASTGLRVDLYEehgrvgMPE--HCTGIV-SERTVN--------Tigrearetiidsydslei 71 
                                    79**************************7644422111..222222.333333........2222333335677777766 PP

                                    ............................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E CS
                                    ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ............................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs 109
                                                                e + +l+   +l ++++ v+i   ++ vk        + +  yd+++lA G+
  gi|118431536|ref|NP_148061.2|  72 rfrgetlavldvgtvyrldrvrleelllESLMSLGGRAQLGKRVHSVGI---EGSVK------AGGSEARYDAVILADGA 142
                                    6777777777777777776666655555444444444444444444444...22344......566799**********9 PP

                                    EE- CS
                                    xxx RF
                    Pyr_redox_2 110 spr 112
                                    +  
  gi|118431536|ref|NP_148061.2| 143 HGE 145
                                    765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.3   2.6e-05     0.042       1      33 [.       3      37 ..       3      49 .. 0.86
   2 !    7.4   0.0    0.0018       2.9     152     210 ..      98     150 ..      84     175 .. 0.72
   3 ?    1.2   0.0      0.13   2.2e+02      73     163 ..     182     279 ..     155     338 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   +v+++GGG +Gl  A+e a  g  V l+e + ++g
  gi|118431536|ref|NP_148061.2|  3 RVAVVGGGFAGLIFAREMASTGlrVDLYEEHGRVG 37
                                   59****************9999*******997666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll 210
                                    l++ + +lG++  +g +v ++      + g   +++ g++ ++dav++a Ga+  +l ++l
  gi|118431536|ref|NP_148061.2|  98 LLESLMSLGGRAQLGKRVHSVG-----IEGS--VKAgGSEARYDAVILADGAHG-ELhRML 150
                                    7888999********9999992.....3333..344477745699*******94.332333 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.13
                                    HHHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHH...........HHTTTTEEEEEHHHHHHHSTTSTTTSEEEEETTE. CS
                            DAO  73 eelgididyrrtGllslaadeeelealdkllall...........leagldaelldaeevrelepalpgllgalfypdt. 140
                                    + l++ +d++  G++s+a     l+++++ ++ l            +ag++ae l++    +++    g +g+l+ p + 
  gi|118431536|ref|NP_148061.2| 182 RGLAFTWDVPTVGSVSVAGAMGTLAGVKRFFEVLkprafkvyggrIPAGPPAERLRRG---RVYV--VGDAGGLVKPLSg 256
                                    4456679999999999986434466676666666666666666666777777777775...3332..1335555555543 PP

                                    EEEEHHHHHHHHHHHHHHTT-EE CS
                            DAO 141 gqvdpakltaalaraaealGvei 163
                                    g + p + +a la+ + ++G ++
  gi|118431536|ref|NP_148061.2| 257 GGLYPNAKAAKLAASLIKRGLDV 279
                                    44455555555555555555554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.3   2.4e-05     0.038       2      50 ..       2      51 ..       1     158 [. 0.85
   2 !    9.1   0.1   0.00041      0.66     278     304 ..     233     259 ..     229     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.4e-05
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS.CCSSS--EEEHHHH CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrstt.vvlpradglnqrtm 50
                                   + V++VG+G aGl+ a+++++ G rv l e + +  +++   +++++rt+
  gi|118431536|ref|NP_148061.2|  2 VRVAVVGGGFAGLIFAREMASTGLRVDLYEEHGRVgMPEHCTGIVSERTV 51
                                   679**********************9998888643144445555566665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00041
                                    ESSSEETTEEE-GGGTEEE-STTSHHH CS
                  FAD_binding_3 278 aekyrkgrvflaGDAaHihpPtgGqGl 304
                                    ae++r+grv ++GDA   + P  G Gl
  gi|118431536|ref|NP_148061.2| 233 AERLRRGRVYVVGDAGGLVKPLSGGGL 259
                                    799*******************99997 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   1.4e-06    0.0022       1      48 [.       3      48 ..       3      74 .. 0.88
   2 ?   -0.8   0.0       1.5   2.4e+03      25      67 ..      83     119 ..      75     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHH CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqe 48
                                   +v+vvGgG+ gl +A ++a  g +V + e + ++   ++e +  i+ e
  gi|118431536|ref|NP_148061.2|  3 RVAVVGGGFAGLIFAREMASTGLRVDLYEEHGRVG--MPEHCTGIVSE 48
                                   79*****************************9999..66666655555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                    EEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE CS
                      Pyr_redox  25 VtvversdkllrllDeeaskilqeklekngievllntkveeie 67 
                                    V  v r d+++      ++++l e+l  +g +  l+++v ++ 
  gi|118431536|ref|NP_148061.2|  83 VGTVYRLDRVR------LEELLLESLMSLGGRAQLGKRVHSVG 119
                                    56678888888......89999999999888888888887775 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.1e-06    0.0018       2      36 ..       3      37 ..       2      45 .. 0.92
   2 ?   -1.7   0.0      0.56   9.1e+02     113     164 ..      96     142 ..      74     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +v+v+GgG AGl  A ++a++g rV l+e+  ++g
  gi|118431536|ref|NP_148061.2|  3 RVAVVGGGFAGLIFAREMASTGLRVDLYEEHGRVG 37
                                   699***************************99988 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                                    HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                    HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    ++ll+ l + g + +l ++v+sv    +g  +vk+ +++e + d+++lA G 
  gi|118431536|ref|NP_148061.2|  96 ELLLESLMSLGGRAQLGKRVHSVGI--EG--SVKA-GGSEARYDAVILADGA 142
                                    6788999999999999999999955..33..5788.8999999999999885 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.7e-06    0.0092       2      63 ..       4      62 ..       3     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.7e-06
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SH CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggli 63
                                   v V+GgG AG+  A ++a  G++v L+ ++    +   C   +    + ++ rE ++    i
  gi|118431536|ref|NP_148061.2|  4 VAVVGGGFAGLIFAREMASTGLRVDLYEEHGRVGMPEHCTGIVSERTVNTIGREARE---TI 62
                                   89*************************555444444444444444444444444444...44 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00014      0.22       1      27 [.      11      37 ..      11      37 .. 0.98
   2 ?    2.4   0.0     0.047        76     214     259 ..     100     139 ..      93     142 .. 0.79
   3 ?   -2.9   0.0       1.9   3.1e+03     132     191 ..     275     330 ..     262     356 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                   HHHHHHHHHHHHTTEEEEEEESSSSSB CS
                  Amino_oxidase  1 laGLaaArqLlsaGfdVtvlEardrvG 27
                                   +aGL+ Ar+++s G++V ++E  +rvG
  gi|118431536|ref|NP_148061.2| 11 FAGLIFAREMASTGLRVDLYEEHGRVG 37
                                   69************************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.047
                                    HHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE- CS
                  Amino_oxidase 214 ealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvT 259
                                    e+l +  +g++ +l++rV+++  eg  v+     g++ ++DaV+++
  gi|118431536|ref|NP_148061.2| 100 ESLMS--LGGRAQLGKRVHSVGIEG-SVKA---GGSEARYDAVILA 139
                                    55555..899*************33.3455...79999******97 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.9
                                    CHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCC CS
                  Amino_oxidase 132 ldldskslaesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpl 191
                                    + ld +  +e+ ++   +e+ ++ ++ rl++    + le  s++++g p  l ++l++++
  gi|118431536|ref|NP_148061.2| 275 RGLDVGEALEKSLSIVSHELRAQHAVARLVYG--TRVLETISRAVGGAP--LRLRLDYDT 330
                                    56677777777777777777777777788774..777777777777777..444444444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.2   7.9e-06     0.013       2      35 ..       4      37 ..       3      69 .. 0.87
   2 ?   -1.0   0.0      0.45   7.3e+02     159     204 ..      89     145 ..      48     155 .. 0.70
   3 ?   -2.4   0.0       1.2   1.9e+03     137     172 ..     273     308 ..     232     324 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefg 35
                                   v V+G+G+AGL  A e+a  Gl+v + e  +++g
  gi|118431536|ref|NP_148061.2|  4 VAVVGGGFAGLIFAREMASTGLRVDLYEEHGRVG 37
                                   89**********************9988877766 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.45
                                    EESEEEEEEEEC.....TT......EEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 159 qerteadeLive.....dg......rvtGavvenpesgrevrirakavvlatgGfgr 204
                                    ++r +++eL+ e     +g      rv+ + +e + + +  + r +av+la g+ g 
  gi|118431536|ref|NP_148061.2|  89 LDRVRLEELLLEslmslGGraqlgkRVHSVGIEGSVKAGGSEARYDAVILADGAHGE 145
                                    445555555555333333355566688888888776666667778899999999885 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                    ..HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT CS
                  FAD_binding_2 137 lvtghallarlvesarkagvdfqerteadeLivedg 172
                                    +  g  + ++l +s+    +++++++++++L++ ++
  gi|118431536|ref|NP_148061.2| 273 IKRGLDVGEALEKSLSIVSHELRAQHAVARLVYGTR 308
                                    444555556666666666688888888888887544 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 ?    9.4   0.1   0.00061      0.99       1      40 [.       5      38 ..       5      53 .. 0.89
   2 ?   -0.1   0.0      0.51   8.3e+02     138     154 ..     125     141 ..     114     143 .. 0.85
   3 ?    1.3   0.0      0.19   3.1e+02      82     119 ..     291     328 ..     273     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00061
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                   a+vG+G++Gl +++++++       l+++l+++++   g+
  gi|118431536|ref|NP_148061.2|  5 AVVGGGFAGLIFAREMAST-----GLRVDLYEEHGRV-GM 38
                                   89*************9998.....699***9999886.54 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.51
                  NAD_binding_9 138 ladgaslaadaVvLAlG 154
                                    +a+g++ ++daV+LA G
  gi|118431536|ref|NP_148061.2| 125 KAGGSEARYDAVILADG 141
                                    6789999********88 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                  NAD_binding_9  82 aeeldpddfvpRalyGrYlrdlfeellarlpegvtvev 119
                                     +el+ ++ v R +yG  + +++++++  +p ++++++
  gi|118431536|ref|NP_148061.2| 291 SHELRAQHAVARLVYGTRVLETISRAVGGAPLRLRLDY 328
                                    578999***********999999999999987666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 2983.59
//
Query:       gi|14601522|ref|NP_148062.1|  [L=548]
Description: cytochrome c oxidase (ba3-type) subunit I [Aeropyrum pernix K1]
Scores for complete 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-89  300.0  59.9    2.7e-89  300.0  59.9    1.8  2  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.0  59.9   1.5e-93   2.7e-89       3     432 .]      15     462 ..      13     462 .. 0.91
   2 ?   -0.5   0.2     0.024   4.3e+02      83     124 ..     463     523 ..     461     539 .. 0.38

  Alignments for each domain:
  == domain 1  score: 300.0 bits;  conditional E-value: 1.5e-93
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCT..CT-H...HCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS-S-HHH CS
                          COX1   3 gllylilalvlllvggllgllirlqla..fpdl...etynqlrtlHgnlmiflfatpfilgfgnylvplllgardlafprl 78 
                                   +++ +++a+++l +ggl+g+l+ ++++  fpd+    ty++++t Hg++++++f+t+fi+g++ ++v ++l  +  +++  
  gi|14601522|ref|NP_148062.1|  15 TKVTMLVAFLMLPLGGLFGILQLFKRTpnFPDPvsdSTYYTALTGHGVVLAIVFTTFFIMGISAFIVSREL--KTNFSRLA 93 
                                   577899*******************97334433555**********************************9..33455556 PP

                                   HHHHHHHHHHHHHHHHHHHH.CSS-STTTTTTTC.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHH CS
                          COX1  79 nalsfwlvvlgvvllllsll.gaattgwteYaplsevdlwllglllvvvssllgainfivtilkrrapgmtvaklplfvwa 158
                                    +ls+ l++lg+vl+++++l g+a++++t+Y+pl++ +l+++g +l++v+s+++++ +++ +lk r++++ ++ +p+++++
  gi|14601522|ref|NP_148062.1|  94 LNLSLGLALLGTVLAAVAILsGQAKVLYTFYPPLKANPLFYIGAALLIVGSWVFMFDLFRLVLKFRRENPDLK-VPVATYG 173
                                   789999********999999999*****************************************999999777.******* PP

                                   HHHHHHHHHHHCHHHHHHHHHCHHHHHCT-SSSC.E-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHH CS
                          COX1 159 vlatailillalpvlalalllllldrslgkffsp.gdplldqhlfWffgHpeVyililpalgivyyilpkfagrplfsykl 238
                                   +l++++++l+a+p +al++llll+++sl   f + +d ll+++lfW+fgHp+Vy+++lpa++++yy +p+++g plfs+++
  gi|14601522|ref|NP_148062.1| 174 ILTAWVIWLVATPPVALEVLLLLVPMSL---FGMeVDVLLARTLFWWFGHPLVYFWLLPAVALWYYAIPRILGVPLFSETM 251
                                   ***********************98887...6445********************************************** PP

                                   HHHHHHHHHHHCCCCGGGGTTTS.SS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCC..............TTS-CHC.HHH CS
                          COX1 239 svlafililflsflvwaHHlftt.glpewlkalgsvfslliavPsglkvfnwlatl..............wrgsirf.ktp 303
                                   + +a il+++ s++v++HH+f++ g+ +++k++++++++++a Ps+l+ fn+latl              w  ++ + + +
  gi|14601522|ref|NP_148062.1| 252 AKVAYILYMIASTPVGLHHQFVDpGIGPFFKLVHTLVTFVVATPSMLTAFNILATLeragrmrggrglvgWVFKLPWgSLA 332
                                   ***********************************************8888888888888888877777765555555666 PP

                                   HHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH.SB--HHHHHHHHHHHH CS
                          COX1 304 mlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpklt.grmlserlaklhfwll 383
                                   +  +++ ++lf  gG+tG+++a+ ++n vvhnt w+v+HfH+++ ga +++++aa+++l  +++ ++ +  +la ++f+++
  gi|14601522|ref|NP_148062.1| 333 FSGLMLPIILFANGGITGIINASFQLNTVVHNTTWIVGHFHTTVGGASALTFMAAMLLLAREMMkREVIAPWLAVAAFYMW 413
                                   66666689999*****************************************************666779999******** PP

                                   HHHHHHHHHHHHHHHHTTHBSSSST..--SCCCCHHHCHHHHHHHHHHHHH CS
                          COX1 384 fiGlvlmflpmhilGllgmprraad..yksfletvpelqplnvlrtiggvl 432
                                   ++G +l+++  +++G++g prr+ +  y       +e+ p+ +l +igg++
  gi|14601522|ref|NP_148062.1| 414 TVGQYLFSIGYYVAGVMGAPRRTSEllY--GGLAPTEWIPWLQLGAIGGMV 462
                                   ************************8445..556789************986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHHHH..CS....................S-STTTTTTTC.SHHHHHHHHHHH CS
                          COX1  83 fwlvvlgvvllllsll..ga....................attgwteYaplsevdlwllglllv 124
                                   fw++ + +v+l+++ l  g+                    +++g   Y  l+ev++w++  + +
  gi|14601522|ref|NP_148062.1| 463 FWIAGVILVGLIAATLlfGKkvsvpqgervlafdettpgrIENG--KYI-LEEVRFWIVVTIAL 523
                                   55333333332222222322333333344444444444334444..233.33566555433322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3929.89
//
Query:       gi|14601523|ref|NP_148063.1|  [L=109]
Description: hypothetical protein APE_1626 [Aeropyrum pernix K1]
Scores for 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  17.6      0.023   14.8  17.6    2.0  1  DUF5518      Family of unknown function (DUF5518)
  ------ inclusion threshold ------
       0.94    9.8  13.3         11    6.4  13.3    2.7  1  DUF4064      Protein of unknown function (DUF4064)
          5    7.5  21.9         14    6.1   3.4    3.0  2  DUF308       Short repeat of unknown function (DUF308)


Domain annotation for each model (and alignments):
>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  17.6   3.8e-06     0.023       5      75 ..      10     101 ..       7     109 .] 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-06
                       DUF5518   5 liGavvaivlslllg....................lllpsvgsllgl..lvgGlvaGylaggdskdgavaGalaGligaip 63 
                                    +G++ ai+ +l++                     ++++s++ llg+  ++gG+ a+y+a+++ ++ ++aG + Gl++ ++
  gi|14601523|ref|NP_148063.1|  10 YLGGIFAIIAGLVSLatavplgshlleaagvieepIISGSIVRLLGVvgIIGGVAAAYFAREENGQYVIAGGVLGLLAPCV 90 
                                   56666666666666666666667788888888889999999999998789******************************* PP

                       DUF5518  64 vlvlllvlllgl 75 
                                   + +l+++++  +
  gi|14601523|ref|NP_148063.1|  91 LSILAIIGGY-M 101
                                   *******996.3 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  13.3    0.0018        11       3      86 ..       3     106 ..       1     109 [] 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                       DUF4064   3 kaeiiLglIGgilgillglllllflfllssgefsqeltee...................qalsgedasavl.eflstlliv 63 
                                   ++ +iL+ +Ggi+ i++gl+ l +++ l+s   + +  +e                   +     +a++++ e  ++++i+
  gi|14601523|ref|NP_148063.1|   3 ETPKILAYLGGIFAIIAGLVSLATAVPLGSHLLEAAGVIEepiisgsivrllgvvgiigG----VAAAYFArEENGQYVIA 79 
                                   6889**********************9999999888888899999999999999965552....33333332222333333 PP

                       DUF4064  64 lgvi....aliaivlgivgalllkknk 86 
                                    gv+      ++++l i+g +++ k++
  gi|14601523|ref|NP_148063.1|  80 GGVLgllaPCVLSILAIIGGYMMLKKG 106
                                   333311114455666666666666665 PP

>> DUF308  Short repeat of unknown function (DUF308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.4    0.0023        14      23      44 ..       7      28 ..       3      42 .. 0.84
   2 ?    4.8  10.8    0.0061        37      23      72 ..      49     103 ..      40     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0023
                        DUF308 23 alvllfGilllvsGivqiiaaf 44
                                  +l++l Gi+++++G+v++++a+
  gi|14601523|ref|NP_148063.1|  7 ILAYLGGIFAIIAGLVSLATAV 28
                                  5789999999999999998876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0061
                        DUF308  23 alvllfGilllvsGivqiiaafaarkknrggrw....lgl....llGilyliaGllll 72 
                                    +v l+G++ +++G++  +  f ar++n+++ +    lgl    +l+il +i+G+++l
  gi|14601523|ref|NP_148063.1|  49 SIVRLLGVVGIIGGVAAAY--F-AREENGQYVIaggvLGLlapcVLSILAIIGGYMML 103
                                   578899*********9885..4.66666665554444444566778888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 845.65
//
Query:       gi|14601524|ref|NP_148064.1|  [L=233]
Description: hypothetical protein APE_1627 [Aeropyrum pernix K1]
Scores for complete 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-70  236.1   0.0      2e-70  235.8   0.0    1.0  1  DUF1122   Protein of unknown function (DUF1122)


Domain annotation for each model (and alignments):
>> DUF1122  Protein of unknown function (DUF1122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.8   0.0   1.1e-74     2e-70       1     175 [.      38     210 ..      38     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 235.8 bits;  conditional E-value: 1.1e-74
                                   EEEEEE.EEEE-SSTTEEEEEEEETT.....EEEEEEEEE--BTTB--EEEEES--G.......GGHHHHTTSHHHHHHHH CS
                       DUF1122   1 gelkleaevkqgrfkeevnlevyver.deakkellalkvFeGRdlyrpWiEifniswlreveldsltavffgskvEeelld 80 
                                   g+++l+a+++qgrf++e++l+v++er +e+ +el+++ vF+GR++yrpWiEifn+s++ +ve+d+ ta   gs+vE++lld
  gi|14601524|ref|NP_148064.1|  38 GSVRLSASISQGRFSGEFFLAVRLERaGEKLVELCNSLVFCGRGVYRPWIEIFNVSPSLPVETDMPTA---GSPVEAALLD 115
                                   6899**********************99************************************9999...********** PP

                                   HHTTT-S...EEEEE-TT-HHHHHHHHTT--GGGSHHHHHHHHTT--EEEEEES-TTTSSS-EEEEEE--SSHHHHHHHHH CS
                       DUF1122  81 llsevlgpgerlfveYvkDketlkelekgipaaltrLGfeLlkrGftwFkdWYfpEGfmEGspkiqaekPldeeeekrqle 161
                                   l++++lgp+e+l+veYv+D+etl+++++g+pa+++rLGfeL+krGf+wFk+WY+pEGfmEG++k+qaekPld+e+e+r ++
  gi|14601524|ref|NP_148064.1| 116 LAADALGPAEPLYVEYVWDRETLYQIQRGAPAPASRLGFELWKRGFRWFKTWYYPEGFMEGGEKLQAEKPLDREHESRLVA 196
                                   ********************************************************************************* PP

                                   HHHHHHHHHHHH-- CS
                       DUF1122 162 ellkeveefikkve 175
                                   e+++++e+fi ++e
  gi|14601524|ref|NP_148064.1| 197 EARRDLENFILAWE 210
                                   **********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1858.70
//
Query:       gi|14601525|ref|NP_148065.1|  [L=101]
Description: translation initiation factor Sui1 [Aeropyrum pernix K1]
Scores for complete 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   73.4   0.3    1.9e-20   73.2   0.3    1.1  1  SUI1      Translation initiation factor SUI1
    0.00065   19.9   0.4    0.00094   19.4   0.4    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 !   73.2   0.3   2.1e-24   1.9e-20       2      77 .]      22      93 ..      21      93 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 2.1e-24
                          SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77
                                  ++ i+irle+r+ ++ vT+++g+  ++++lkkla++lk+++a++g+  k+g   i++QGd+r++v+++L+e  g+p
  gi|14601525|ref|NP_148065.1| 22 EQIIKIRLEKRRFGREVTIIEGINEKEFNLKKLASTLKSRLATGGTA-KNG--RIELQGDHRHRVKKILVEL-GFP 93
                                  689*******************************************6.999..8*****************8.987 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 !   19.4   0.4   1.1e-07   0.00094      26      80 .]      37      92 ..      27      92 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                          Img2 26 kltvirkieG...DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                  ++t+i  i+    ++++l++ L++ l+  +  + ++g+ie++Gd++++vkk+L ++gF
  gi|14601525|ref|NP_148065.1| 37 EVTIIEGINEkefNLKKLASTLKSRLA--TGGTAKNGRIELQGDHRHRVKKILVELGF 92
                                  555555554311145566666777776..788899**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); 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:                         2  (0.000111551); expected 0.2 (1e-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: 740.69
//
Query:       gi|118431537|ref|NP_148066.2|  [L=73]
Description: hypothetical protein APE_1629a.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0038   16.8   1.4        1.4    8.6   0.2    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
     0.0052   16.4   3.7      0.073   12.8   3.7    2.1  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
  ------ inclusion threshold ------
      0.017   15.4   0.6       0.27   11.6   0.4    2.0  2  DUF3268         zinc-finger-containing domain
      0.019   14.7   1.2        1.9    8.3   0.1    2.2  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.027   14.4   4.2      0.042   13.8   1.9    2.3  3  zinc_ribbon_4   zinc-ribbon domain
       0.03   14.0   3.1       0.14   11.9   3.1    1.9  1  zf-CSL          CSL zinc finger
      0.063   13.5   0.3      0.093   12.9   0.3    1.2  1  zf-UBR          Putative zinc finger in N-recognin (UBR box)
      0.065   13.1   0.7        1.6    8.7   0.1    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.12   12.3   4.7       0.42   10.6   4.7    1.8  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.12   12.6   1.9        0.5   10.7   0.2    2.2  2  DUF2197         Uncharacterized protein conserved in bacteria
       0.13   12.2   0.8       0.48   10.4   0.7    1.8  1  DUF4428         Domain of unknown function (DUF4428)
       0.34   10.8   5.5        2.2    8.2   0.3    2.2  2  zf-CCHC_2       Zinc knuckle
       0.44   10.3   6.5        4.3    7.2   0.7    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.95    9.2   8.9        3.6    7.4   2.0    2.3  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


Domain annotation for each model (and alignments):
>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0028       3.6       3      17 ..      24      38 ..      23      40 .. 0.87
   2 !    8.6   0.2    0.0011       1.4       3      12 ..      45      54 ..      44      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0028
                         zf_UBZ  3 ylCerCgkeipesel 17
                                   y+C rCg++  ++el
  gi|118431537|ref|NP_148066.2| 24 YVCIRCGAQYTIDEL 38
                                   9*******9988876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                         zf_UBZ  3 ylCerCgkei 12
                                   y+C+rC ++i
  gi|118431537|ref|NP_148066.2| 45 YVCQRCSSRI 54
                                   9*****9988 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 !   12.8   3.7   5.7e-05     0.073       1      32 []      24      59 ..      24      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.7e-05
                                   -B-SSS--B----S....SS----SSS-----B--- CS
                 DNA_RNApol_7kD  1 YiCgeCgaevslkk....gdpiRCkeCGhRilYKkR 32
                                   Y C +Cga+ ++++    g    C+ C +Ri+ K+R
  gi|118431537|ref|NP_148066.2| 24 YVCIRCGAQYTIDEliqaGLGYVCQRCSSRIFIKPR 59
                                   99*****9998754111155556***********99 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00021      0.27      20      53 ..      13      46 ..       3      49 .. 0.77
   2 ?    4.8   0.1     0.026        34      28      45 ..      42      59 ..      33      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                        DUF3268 20 iYkerskgkllylCpkCdayvgvhkgtkiplGtl 53
                                   + +e +kg+++y+C +C+a   + +  +  lG +
  gi|118431537|ref|NP_148066.2| 13 VEEEPRKGQVVYVCIRCGAQYTIDELIQAGLGYV 46
                                   44556699***********999988888888876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.026
                        DUF3268 28 kllylCpkCdayvgvhkg 45
                                    l y+C++C + + ++++
  gi|118431537|ref|NP_148066.2| 42 GLGYVCQRCSSRIFIKPR 59
                                   567*******99988776 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0015       1.9      22      32 ..      24      34 ..      19      35 .. 0.83
   2 ?    5.5   0.1     0.011        14      21      29 ..      44      52 ..      37      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                  A2L_zn_ribbon 22 lvCieCgasfp 32
                                   +vCi Cga ++
  gi|118431537|ref|NP_148066.2| 24 YVCIRCGAQYT 34
                                   9******9765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                  A2L_zn_ribbon 21 ylvCieCga 29
                                   ++vC+ C++
  gi|118431537|ref|NP_148066.2| 44 GYVCQRCSS 52
                                   69*****85 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.4   5.6e+03      14      25 ..       8      19 ..       7      19 .. 0.76
   2 ?   13.8   1.9   3.3e-05     0.042       4      33 ..      25      52 ..      24      55 .. 0.74
   3 ?    2.0   0.6      0.16     2e+02       5      11 ..      47      53 ..      45      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.4
                  zinc_ribbon_4 14 iddeklpakgvk 25
                                   i++e + ++ +k
  gi|118431537|ref|NP_148066.2|  8 IEEELVEEEPRK 19
                                   789999887765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.3e-05
                  zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCgh 33
                                   +C +C+a+y+id+  + ++g    C +C+ 
  gi|118431537|ref|NP_148066.2| 25 VCIRCGAQYTIDE-LI-QAGLGYVCQRCSS 52
                                   6***********9.45.4455555888875 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.16
                  zinc_ribbon_4  5 CpsCkak 11
                                   C++C+++
  gi|118431537|ref|NP_148066.2| 47 CQRCSSR 53
                                   8888765 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.1   0.00011      0.14       8      54 ..      13      54 ..       5      59 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   SEEETTTTEEEEEE.TTSSEEEEEHHHHHTT....--EEEETTSSEEE CS
                         zf-CSL  8 fefdeeeesyyypC.RCgdeFelteedleegaegaevvvqCssCSLwi 54
                                   +e ++ ++  +y C RCg ++ + e  l +      +   C+ CS  i
  gi|118431537|ref|NP_148066.2| 13 VEEEPRKGQVVYVCiRCGAQYTIDE--LIQA----GLGYVCQRCSSRI 54
                                   45555666789**********8864..5555....4667788888666 PP

>> zf-UBR  Putative zinc finger in N-recognin (UBR box)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   7.3e-05     0.093       7      32 ..      18      52 ..      13      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                         zf-UBR  7 kkgevvyrCltCsld.........etsviCeeCfk 32
                                   +kg+vvy C  C+ +            ++C++C+ 
  gi|118431537|ref|NP_148066.2| 18 RKGQVVYVCIRCGAQytideliqaGLGYVCQRCSS 52
                                   689************99988876544599999986 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 ?    8.7   0.1    0.0012       1.6      27      39 .]      22      34 ..      15      34 .. 0.88
   2 ?    3.1   0.1     0.069        88      29      36 ..      45      52 ..      43      54 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                        TFIIS_C 27 vfykCtkCghrWr 39
                                   v y+C+ Cg +++
  gi|118431537|ref|NP_148066.2| 22 VVYVCIRCGAQYT 34
                                   78*******9985 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.069
                        TFIIS_C 29 ykCtkCgh 36
                                   y+C  C  
  gi|118431537|ref|NP_148066.2| 45 YVCQRCSS 52
                                   67777765 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 ?   10.6   4.7   0.00033      0.42       4      32 ..      23      52 ..      23      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                 Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhn.YrCrrCkg 32
                                   vY+C +Cg +yt    i+    Y C+rC +
  gi|118431537|ref|NP_148066.2| 23 VYVCIRCGAQYTIDELIQAGLgYVCQRCSS 52
                                   7************999977777******76 PP

>> DUF2197  Uncharacterized protein conserved in bacteria (DUF2197)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.33   4.2e+02      31      38 ..      23      30 ..      18      41 .. 0.66
   2 ?   10.7   0.2   0.00039       0.5      32      45 ..      45      58 ..      43      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.33
                        DUF2197 31 tYmCkeCe 38
                                   +Y+C  C 
  gi|118431537|ref|NP_148066.2| 23 VYVCIRCG 30
                                   56666664 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
                        DUF2197 32 YmCkeCeeRiaekt 45
                                   Y+C+ C++Ri  k+
  gi|118431537|ref|NP_148066.2| 45 YVCQRCSSRIFIKP 58
                                   9*********8876 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00038      0.48       5      30 ..      29      54 ..      25      66 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                        DUF4428  5 CgkKigllkrlkleDgyvCkdClkKl 30
                                   Cg   ++ + ++   gyvC+ C +++
  gi|118431537|ref|NP_148066.2| 29 CGAQYTIDELIQAGLGYVCQRCSSRI 54
                                   6666666665555558********99 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.017        21       4      11 ..      24      31 ..      24      32 .. 0.92
   2 ?    8.2   0.3    0.0017       2.2       3      10 ..      44      51 ..      43      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                      zf-CCHC_2  4 YvChiCgk 11
                                   YvC +Cg+
  gi|118431537|ref|NP_148066.2| 24 YVCIRCGA 31
                                   ******96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                      zf-CCHC_2  3 gYvChiCg 10
                                   gYvC +C 
  gi|118431537|ref|NP_148066.2| 44 GYVCQRCS 51
                                   8******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 ?    7.2   0.7    0.0033       4.3       1      10 [.      24      33 ..      24      34 .. 0.92
   2 ?    6.4   0.6    0.0058       7.4       1       8 [.      45      52 ..      45      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0033
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   YvC +CG+++
  gi|118431537|ref|NP_148066.2| 24 YVCIRCGAQY 33
                                   9*******97 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0058
                   Rubredoxin_2  1 YvCsqCGf 8 
                                   YvC++C++
  gi|118431537|ref|NP_148066.2| 45 YVCQRCSS 52
                                   9*****86 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 ?    7.4   2.0    0.0028       3.6      22      31 ..      24      33 ..      24      34 .. 0.91
   2 ?    6.0   0.7    0.0075       9.7      22      28 ..      45      51 ..      44      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                        zf-RRN7 22 yyCrrChtqe 31
                                   y+C rC+ q 
  gi|118431537|ref|NP_148066.2| 24 YVCIRCGAQY 33
                                   9******996 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0075
                        zf-RRN7 22 yyCrrCh 28
                                   y+C+rC 
  gi|118431537|ref|NP_148066.2| 45 YVCQRCS 51
                                   9*****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 572.18
//
Query:       gi|118431538|ref|NP_148067.2|  [L=477]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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-39  136.8   2.4    2.2e-39  136.3   2.4    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    2.4e-35  122.7   0.0    3.7e-35  122.1   0.0    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.2e-06   28.2   0.1      2e-05   24.1   0.1    2.2  2  SBP_bac_6   Bacterial extracellular solute-binding protein
    2.8e-06   27.2   0.0    3.1e-05   23.9   0.0    2.2  1  SBP_bac_11  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 !  136.3   2.4   4.9e-43   2.2e-39      10     314 ..      90     376 ..      82     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 4.9e-43
                                    HHHHHHHH....HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECT CS
                      SBP_bac_1  10 lqalvaka....fekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapg 85 
                                     q++v ++    f++ ++gikVe++  ++g+l   l+  +++G+  + +ia  ++ ++ +a++g+l++l+++ + +  + 
  gi|118431538|ref|NP_148067.2|  90 EQQFVKEEllppFTQ-ETGIKVEFIGMSYGDLNVRLQSEMESGKVTISLIADLHGGLDLYASKGWLEDLSKFGALEGREF 168
                                    577774448888999.8************************************************************999 PP

                                    TCCTEEEEHHHHTHHHHCEEEESEEEEE.EEEEEEETTTHH..CTTGGG........SHBHHHHHHHHHHHHHHCTCTHC CS
                      SBP_bac_1  86 vkdaadklsssvlpkildskvlyvPlya.argliYNkdlfe..kagldp........pwtWdelveaakklkekgkkpig 154
                                    ++  +d+   s l++i+++    vP+ + ++++++Nk  f+  ++gl++        +wt+d l+e+ak++ ++++ +  
  gi|118431538|ref|NP_148067.2| 169 PQVLEDY---SRLYGIKAY----VPWLTaTYVFVVNKEAFKylPPGLSEedvitgseKWTYDALLEWAKNIEAATGQK-- 239
                                    9988888...478888885....****77*******************9*****************************.. PP

                                    CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTS CS
                      SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGe 234
                                        g+ +g  ++f  +l + l + + ++ ++         +++  ++ +++ +l++ +  ++++++  +a++a + +Ge
  gi|118431538|ref|NP_148067.2| 240 --PLGFPAGPKGLFHRFLHGYLYPSFTGAQVK---------NFDSPEAVQMWSYLKELWNYVHPQSTVYEAMAAPLLNGE 308
                                    ..999999999999999999999888877776.........6666667778899999*********************** PP

                                    CSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                      SBP_bac_1 235 aamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                    + +a++ +               +++  ++++e+ v p Pag++g + il+  glaipk++++++aA+k++++l+ pe q
  gi|118431538|ref|NP_148067.2| 309 VLIAWDHTAR------------IKDAIVQKPDEFVVVPAPAGPKGRGYILVIVGLAIPKNAPHQDAAWKLIEYLTRPEVQ 376
                                    *******998............5666666666777888888888888888****************************98 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 !  122.1   0.0   8.2e-39   3.7e-35       4     270 ..     100     394 ..      97     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 8.2e-39
                                    HHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH..-HHHHHTT... CS
                      SBP_bac_8   4 kefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnldd..ltdalaav... 78 
                                      f+++tg+kv+++ ++++dl+  l++++++g++ +i ++   ++ l+ +a +g+l+dls++  l++  ++++l+++   
  gi|118431538|ref|NP_148067.2| 100 PPFTQETGIKVEFIGMSYGDLNVRLQSEMESGKV-TISLIADLHGGLDLYASKGWLEDLSKFGALEGreFPQVLEDYsrl 178
                                    57*******************************9.8************************99888888877777777543 PP

                                    .--TS.----EEEEEEE-EEEEEHHHHHH......S.......---BHHHHHHHHHHHHHH-.....SEGG---G.GGGG CS
                      SBP_bac_8  79 .gydgklygvPyasetpyvliynkdllek......a......edpktwdellaaakklkgkf.....glpdpasg.wlqa 139
                                     g++     vP+ + t yv+++nk++++       +      +  +t+d+ll++ak ++ ++     g+p+ + g ++++
  gi|118431538|ref|NP_148067.2| 179 yGIKA---YVPWLTAT-YVFVVNKEAFKYlppglsEedvitgSEKWTYDALLEWAKNIEAATgqkplGFPAGPKGlFHRF 254
                                    25555...7*****98.9*********765444431446667778********988776555444788899999988899 PP

                                    GTHHETTEE---H......HHH.HHHHHHHHHHHHTT-.EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTT.SEEEE CS
                      SBP_bac_8 140 allakdgksldddg....gkdglkealellkklkdngk.tydtgadavsefanGevaftingswdiaaaqkagk.klgai 213
                                    ++ + ++ s+++      ++++ ++++ +lk+l +++  +   ++++ + + nGev+++   +++i +a  +++ ++ ++
  gi|118431538|ref|NP_148067.2| 255 LHGY-LYPSFTGAQvknfDSPEAVQMWSYLKELWNYVHpQSTVYEAMAAPLLNGEVLIAWDHTARIKDAIVQKPdEFVVV 333
                                    9999.999998877788889999**********9998542233478889*********************7665277777 PP

                                    .--....S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT CS
                      SBP_bac_8 214 .vp....kqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaal 270
                                     +p      g+++ + gla+pkna+++d aA++++++lt pe q    ek g++p+  ++++
  gi|118431538|ref|NP_148067.2| 334 pAPagpkGRGYILVIVGLAIPKNAPHQD-AAWKLIEYLTRPEVQSLILEKVGFFPAVSGVSE 394
                                    4455543347******************.6**************************999885 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 ?    1.5   0.0     0.036   1.6e+02      49      72 ..     182     205 ..     138     208 .. 0.76
   2 !   24.1   0.1   4.5e-09     2e-05     116     230 ..     279     398 ..     262     408 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.036
                      SBP_bac_6  49 gkyypygvgplvlavnkdrlkgrp 72 
                                    + y+p+ + ++v++vnk+++k +p
  gi|118431538|ref|NP_148067.2| 182 KAYVPWLTATYVFVVNKEAFKYLP 205
                                    46889**************98764 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 4.5e-09
                      SBP_bac_6 116 vkkllrnlkanlhpaq..mvkaagslesgepavsvvpyffadilpekkkgk.....nlkvvwPed.Galvspifmlvkkg 187
                                    ++ +l++l + +hp     + +a++l  ge  v ++++  a+i  +  +         +   P+  G +++++ ++++k+
  gi|118431538|ref|NP_148067.2| 279 MWSYLKELWNYVHPQStvYEAMAAPLLNGE--VLIAWDHTARIKDAIVQKPdefvvVPAPAGPKGrGYILVIVGLAIPKN 356
                                    555666666666655555555566666666..555555555443333222221123223333677799************ PP

                      SBP_bac_6 188 .kkkelakafidfllspevqa.ilakaggvfPvvtnpavlnelpe 230
                                     ++++ a+++i++l+ pevq+ il+k g+ fP+v   +v ++lpe
  gi|118431538|ref|NP_148067.2| 357 aPHQDAAWKLIEYLTRPEVQSlILEKVGF-FPAV--SGVSEKLPE 398
                                    ********************934555665.**85..445555444 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 !   23.9   0.0   6.8e-09   3.1e-05      11     229 ..      93     385 ..      84     386 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.8e-09
                                    HHHHHHHHHHHHHH---EEEEESSHHHHHHHH.............HHH....-SEEEESSH.HHHHHHHHGGGGG..... CS
                     SBP_bac_11  11 aalrelaaaFeahtgvkvevsaggsgklarqi.............adga..rpDvwipassawlellaaaglvqa..... 70 
                                    ++ +el + F+++tg+kve+ + + g+l  ++             ++      D++++   +wle+l + g++       
  gi|118431538|ref|NP_148067.2|  93 FVKEELLPPFTQETGIKVEFIGMSYGDLNVRLqsemesgkvtislIADLhgGLDLYASK--GWLEDLSKFGALEGrefpq 170
                                    55678999999999966666666666666655555544444444455542345555555..6999999999999899999 PP

                                    ...........GG-EEEEEEEEEEEESTT-..........T...........T---SHHHHHHSS-..-.EEEE--T-TT CS
                     SBP_bac_11  71 ...........esavplassplviavpkgn..........p...........kkikgwadLlkpgl..k.lavadPttsp 115
                                               +++vp  +++ v++v+k++                      +    wa+ + + +  k l+++     p
  gi|118431538|ref|NP_148067.2| 171 vledysrlygiKAYVPWLTATYVFVVNKEAfkylppglseEdvitgsekwtyDALLEWAKNIEAATgqKpLGFPA---GP 247
                                    999999999999999999**********99887754443303333322222233333333333322221233332...33 PP

                                    TTH.......H.HHHHGGG--HHHHHHHHHTEEEEESSH...................HHHHHHHHT..TT-SEEEEEHH CS
                     SBP_bac_11 116 sGl.......aalalleaagaqellkalekkvvklgess...................rqlltavea..geadagivyes 167
                                     Gl       +            l+ ++ +  vk+ +s+                   +++++a++a   + +++i++ +
  gi|118431538|ref|NP_148067.2| 248 KGLfhrflhgY------------LYPSFTGAQVKNFDSPeavqmwsylkelwnyvhpqSTVYEAMAAplLNGEVLIAWDH 315
                                    33333322221............33333333332222222333333333333333333778888766335899******* PP

                                    HHH......HSTTSSEEEE--TTT....--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHH.HHTT- CS
                     SBP_bac_11 168 eakaa....engdkleavylpegl....nldpldypaavlkkaakreaAraFlafLrspeaqail.rkyGf 229
                                     a  +    +++d++++v+ p+g     ++  + +++a++k+a+++ aA +++++L+ pe+q ++ +k Gf
  gi|118431538|ref|NP_148067.2| 316 TARIKdaivQKPDEFVVVPAPAGPkgrgYI-LVIVGLAIPKNAPHQDAAWKLIEYLTRPEVQSLIlEKVGF 385
                                    **65556778999*****999887343333.68*****************************965366665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.58u 0.22s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3640.10
//
Query:       gi|14601528|ref|NP_148068.1|  [L=288]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0021   17.8  29.4      0.037   13.8  29.4    2.7  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 !   13.8  29.4   2.1e-06     0.037      43     172 ..      96     278 ..      15     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-06
                  BPD_transp_1  43 f...................................................vilsilghlilpviillllsaapyvrlir 72 
                                   f                                                   +     + ++l+v ++ ++ ++++v++i 
  gi|14601528|ref|NP_148068.1|  96 FrgrdaviyvlvmplalsdlaagliwysmltgkgflnklllnmglisdpiifFGYENRWLTFLAVYLAEVWRSTAIVFVIL 176
                                   0333333333333334444444444444448888888888888888888877666777889999***************** PP

                  BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG......lgtllleailg 147
                                    a+ + ++k+  eaa++ Gas    +r++++P+++p++ + l+++  +++  ++++ +l+   G       g    ++ + 
  gi|14601528|ref|NP_148068.1| 177 FAGAQLINKEVFEAAEVFGASFYVKLRHILIPMIKPSLQAALLIRTLFAFQVFAVVWILA---GrdipvlAGEAYYSIVEL 254
                                   ******************************************************999999...534456666666666666 PP

                  BPD_transp_1 148 ydyseisnggvlalviavlllnlva 172
                                     y+ ++  ++++++++ + + +v+
  gi|14601528|ref|NP_148068.1| 255 HKYDVAA-LYAIVIALLSASIGVVY 278
                                   6666555.66666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2139.38
//
Query:       gi|14601529|ref|NP_148069.1|  [L=270]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-14   52.6  22.7    4.5e-14   52.6  22.7    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 ?   -1.1   1.6     0.073   1.3e+03      53      66 ..      24      37 ..       4      86 .. 0.46
   2 !   52.6  22.7   2.5e-18   4.5e-14       1     173 [.      87     258 ..      87     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.073
                  BPD_transp_1 53 ilpviillllsaap 66
                                  il  +++++++a+ 
  gi|14601529|ref|NP_148069.1| 24 ILVPLAISIVYAFT 37
                                  22222222222222 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 2.5e-18
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpk 81 
                                   g+++G+ +a ++ +++++++   ii+++++P++v+ + l+   +++ +l ++ ++++++ + +a+p+v++i+ +++  +p+
  gi|14601529|ref|NP_148069.1|  87 GLPGGYALA-RYVFPGRDAVKLAIIATRMFPIIVISVSLL-KTFFNLGLNDTLIGLALAHTAMALPFVVIITGSIFGGIPR 165
                                   7999*****.999*********************999988.456666********************************** PP

                  BPD_transp_1  82 dlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis....nggv 158
                                   dl+ea  + G+s + +f +++lP+a+p + +  +++f +++++ ++++ l+    ++++l  +il++ ++  +    ++++
  gi|14601529|ref|NP_148069.1| 166 DLEEAGMIFGLSSIMVFLRITLPLAAPGLTAAGMFTFLLSWNEVFMASVLT---LVNRTLPAFILNSAFATPIepirFAAA 243
                                   **************************************************9...467777777777777755565555566 PP

                  BPD_transp_1 159 lalviavlllnlvad 173
                                   ++l++  l+++++a+
  gi|14601529|ref|NP_148069.1| 244 FMLILPALVFMFLAR 258
                                   666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      150  (0.00836633); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2039.41
//
Query:       gi|118431539|ref|NP_148070.2|  [L=352]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-33  114.7   0.0    8.4e-33  113.8   0.0    1.5  1  ABC_tran         ABC transporter
    6.3e-11   42.3   0.6    1.5e-10   41.1   0.1    1.9  2  TOBE_2           TOBE domain
    4.3e-07   30.1   0.0    1.6e-06   28.3   0.0    2.0  1  TOBE             TOBE domain
    8.1e-06   25.9   0.1       0.11   12.3   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.3e-05   25.9   3.9    4.7e-05   24.1   1.1    3.3  3  OB_MalK          MalK OB fold domain
      3e-05   24.5   2.9    5.1e-05   23.7   1.2    2.5  2  CysA_C_terminal  CysA C-terminal regulatory domain
     0.0012   19.2   0.0       0.02   15.3   0.0    2.2  2  AAA              ATPase family associated with various cellul
     0.0026   18.2   0.1      0.004   17.6   0.1    1.4  1  AAA_16           AAA ATPase domain
     0.0032   17.4   0.0     0.0056   16.6   0.0    1.3  1  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.021   15.1   0.5      0.063   13.5   0.5    1.9  1  AAA_22           AAA domain
      0.026   14.8   0.0      0.065   13.5   0.0    1.7  2  AAA_28           AAA domain
      0.032   13.9   0.0       0.11   12.2   0.0    1.8  2  AAA_30           AAA domain
      0.098   12.6   0.3       0.28   11.1   0.0    1.7  2  RsgA_GTPase      RsgA GTPase
       0.17   11.8   0.0       0.35   10.9   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.19   11.7   0.0       0.68   10.0   0.0    1.9  2  AAA_14           AAA domain
        0.2   11.4   0.1       0.47   10.2   0.1    1.6  1  AAA_29           P-loop containing region of 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 !  113.8   0.0   7.5e-36   8.4e-33       1     136 [.      19     161 ..      19     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 7.5e-36
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    lk ++l++k ge v+++G++G+GK+t l+++agl++p++G++ +dg+d++   l+  ++++++++q   l+p+++v +n 
  gi|118431539|ref|NP_148070.2|  19 LKGIDLEIKDGEAVVLLGPSGCGKTTTLRIVAGLERPDAGRVYFDGRDVTG--LPPKDRNVAMVFQSYALWPHMRVFDNi 96 
                                    7899***********************************************..9************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e  +++  a++ l++++l d+      ++LSgGq+qrva+ara++++p++ll+DEp 
  gi|118431539|ref|NP_148070.2|  97 afplkikklprdEIVRRVRWAAELLEIDHLLDRYP----HQLSGGQQQRVAVARAIVTEPEVLLMDEPL 161
                                    *******9988888888999999999999888887....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         8     9e+03      38      50 ..     133     145 ..     129     150 .. 0.68
   2 !   41.1   0.1   1.3e-13   1.5e-10       1      76 []     270     340 ..     270     340 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8
                         TOBE_2  38 elaggqlvvvrqp 50 
                                    +l ggq+++v+++
  gi|118431539|ref|NP_148070.2| 133 QLSGGQQQRVAVA 145
                                    5677777777665 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 1.3e-13
                         TOBE_2   1 laiRPEklrlaaaggan.glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                    +++RPE++ l   g ++ ++++ V+ ve lGs++++++++ +gq +v++ + ++   ++ pG++V  +++ ++++++
  gi|118431539|ref|NP_148070.2| 270 VGVRPEDVAL---GKGDlTFEAYVDFVEDLGSDSVVHLKTQSGQVIVAKLSGGE---PPSPGSRVIAGVSREKIHIF 340
                                    79********...88788******************************999999...******************98 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.4e-09   1.6e-06       6      64 .]     285     339 ..     283     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.4e-09
                           TOBE   6 qlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                    ++++ V+ ve+lgs+++V++ ++ g+ ++A++++   ++    pG++V a +  +k+h+
  gi|118431539|ref|NP_148070.2| 285 TFEAYVDFVEDLGSDSVVHLKTQSGQVIVAKLSGGEPPS----PGSRVIAGVSREKIHI 339
                                    68999**********************************....********99999996 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 !   11.5   0.0   0.00017      0.19       3      24 ..      33      54 ..      32      86 .. 0.78
   2 !   12.3   0.1   9.7e-05      0.11     220     299 ..     117     194 ..      87     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                         AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                   vl Gp g+GK++ L++  +l r
  gi|118431539|ref|NP_148070.2| 33 VLLGPSGCGKTTTLRIVAGLER 54
                                   9****************99954 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.7e-05
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       +le ++  ++ +++lS G+++  a++ a+   +    +ll DEp ++L+  l  +    +k+l+r  g+  i +TH+
  gi|118431539|ref|NP_148070.2| 117 AAELLEIDHLLDRYPHQLSGGQQQRVAVARAIVTEP---EVLLMDEPLSNLDAILRIKMRSEIKKLQRrLGVTMIYVTHD 193
                                    6778889999999************99999999988...9*************777777788877777788888999998 PP

                         AAA_21 299 p 299
                                     
  gi|118431539|ref|NP_148070.2| 194 Q 194
                                    5 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.9   4.4e+03      13      33 ..      11      33 ..       6      46 .. 0.59
   2 !   24.1   1.1   4.2e-08   4.7e-05       1      52 [.     235     276 ..     235     277 .. 0.73
   3 ?   -2.7   0.0       9.7   1.1e+04      35      48 ..     319     332 ..     297     332 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.9
                        OB_MalK 13 eedgvlvegggvtlplpeeq..k 33
                                   ++ g +v+ +g++l++++++  +
  gi|118431539|ref|NP_148070.2| 11 KRFGKTVALKGIDLEIKDGEavV 33
                                   55555566677777777666433 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 4.2e-08
                        OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                    GSP+MN++ ++v ++  l + gg  +   e+      +    ev++G+RPE+
  gi|118431539|ref|NP_148070.2| 235 GSPQMNLFSGKVAGGR-LEALGG-IV---EGV-----GLPDGEVLVGVRPED 276
                                    9************666.333333.22...233.....667899********9 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.7
                        OB_MalK  35 alklyagkevilGi 48 
                                     + +  g +vi G+
  gi|118431539|ref|NP_148070.2| 319 GEPPSPGSRVIAGV 332
                                    44566778888775 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 !   23.7   1.2   4.6e-08   5.1e-05       1      43 []     240     279 ..     240     279 .. 0.83
   2 ?   -2.3   0.0       6.3     7e+03      28      36 ..     324     332 ..     308     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.6e-08
                CysA_C_terminal   1 NlFhGrvedGklri.GglalpvPelagadgqevvayVRPhDlei 43 
                                    NlF G+v +G+l+  Gg+   v       ++ev ++VRP+D+ +
  gi|118431539|ref|NP_148070.2| 240 NLFSGKVAGGRLEAlGGIVEGVG----LPDGEVLVGVRPEDVAL 279
                                    9************9999644444....4467**********975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.3
                CysA_C_terminal  28 dgqevvayV 36 
                                     g++v+a+V
  gi|118431539|ref|NP_148070.2| 324 PGSRVIAGV 332
                                    588999998 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 !   15.3   0.0   1.8e-05      0.02       1      20 [.      32      51 ..      32      97 .. 0.81
   2 ?    1.7   0.0      0.28   3.2e+02      43      84 ..     135     178 ..     101     207 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                   EEEESSTTSSHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavak 20
                                   v+l Gp G+GKT++ + va 
  gi|118431539|ref|NP_148070.2| 32 VVLLGPSGCGKTTTLRIVAG 51
                                   6899**************97 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHHTS.TSEEEEEET....GGGHHHHHTTCCCHHHHH CS
                            AAA  43 ekkirelfkeakeka.kpsilfiDE....idalaksrsgseseeeer 84 
                                    +   ++ ++ a++   +p +l++DE    +da+ + +    ++e ++
  gi|118431539|ref|NP_148070.2| 135 SGGQQQRVAVARAIVtEPEVLLMDEplsnLDAILRIK---MRSEIKK 178
                                    4444555555554446699999999666677777777...3333333 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   0.1   3.5e-06     0.004      23      56 ..      28      60 ..      18     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.5e-06
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekdggifl 56
                                   ++e+v+l G+sG+GK++ +r ++  le+ ++  +
  gi|118431539|ref|NP_148070.2| 28 DGEAVVLLGPSGCGKTTTLRIVA-GLERPDAGRV 60
                                   5689***************9998.5666643333 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     5e-06    0.0056      35      66 ..      19      50 ..      15      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-06
                          Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                   lk   Le +  + +++ GPsGCgk+t++++++
  gi|118431539|ref|NP_148070.2| 19 LKGIDLEIKDGEAVVLLGPSGCGKTTTLRIVA 50
                                   55566777777778899************987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   5.6e-05     0.063       5      28 ..      29      52 ..      24     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                      +v+ G+sG+GKTt+lr ++  
  gi|118431539|ref|NP_148070.2| 29 GEAVVLLGPSGCGKTTTLRIVAGL 52
                                   56789*************988765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.8e-05     0.065       2      20 ..      32      50 ..      31      67 .. 0.82
   2 ?   -2.7   0.0       5.3   5.9e+03     133     155 ..     168     190 ..     129     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.8e-05
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   +v++G++++GKTt+l+  a
  gi|118431539|ref|NP_148070.2| 32 VVLLGPSGCGKTTTLRIVA 50
                                   9**************9887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                         AAA_28 133 ereaiderlrealrelgipviiv 155
                                     r ++   ++++ r+lg+ +i v
  gi|118431539|ref|NP_148070.2| 168 LRIKMRSEIKKLQRRLGVTMIYV 190
                                    45566666666666666666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.9e-05      0.11      19      54 ..      30      72 ..      20      91 .. 0.77
   2 ?   -1.5   0.0       1.5   1.7e+03     123     168 ..     136     182 ..     129     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g......grviglAp 54
                                     +vl Gp G GKtt+l+ ++ + + + g      ++v gl p
  gi|118431539|ref|NP_148070.2| 30 EAVVLLGPSGCGKTTTLRIVAGLERPDaGrvyfdgRDVTGLPP 72
                                   47899*************9998877774455555555555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                         AAA_30 123 GDerQlasVeaGgvlrdlveaagigtaeLtevvRqke.seeraaala 168
                                    G ++Q  +V +  v +  v   + +  +L+ + R+k  se++++ ++
  gi|118431539|ref|NP_148070.2| 136 GGQQQRVAVARAIVTEPEVLLMDEPLSNLDAILRIKMrSEIKKLQRR 182
                                    66677777776666654444456677788888888876777766665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.28      93     120 ..      22      50 ..       8      61 .. 0.80
   2 ?   -1.6   0.1         2   2.3e+03       8      49 ..     156     197 ..     149     207 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                    HHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinall 120
                                    +  ++kd + +vl+G+SG GK+t +  ++
  gi|118431539|ref|NP_148070.2|  22 IDLEIKDgEAVVLLGPSGCGKTTTLRIVA 50 
                                    5556777699*************887665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                                    ETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EE CS
                    RsgA_GTPase   8 lvrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiep 49 
                                    l++++ +N+d +l +   +e +  +++l   ++ + + ++e 
  gi|118431539|ref|NP_148070.2| 156 LMDEPLSNLDAILRIKMRSEIKKLQRRLGVTMIYVTHDQVEA 197
                                    555566666666555444444444445555555555555544 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 ?   10.9   0.0   0.00031      0.35       2      20 ..      32      50 ..      31      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                   EEEE--SSSSHHHHHHHGG CS
                          AAA_5  2 vlLvGppGtgKselaerla 20
                                   v+L+Gp+G+gK++  + +a
  gi|118431539|ref|NP_148070.2| 32 VVLLGPSGCGKTTTLRIVA 50
                                   89***********998776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       4.5   5.1e+03      11      20 ..      11      20 ..       7      22 .. 0.84
   2 ?   10.0   0.0   0.00061      0.68       3      38 ..      30      64 ..      28      99 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.5
                         AAA_14 11 RrvGKTtllk 20
                                   +r GKT+ lk
  gi|118431539|ref|NP_148070.2| 11 KRFGKTVALK 20
                                   899***9986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00061
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinl 38
                                   +++v+ G+  +GKTt l+ ++  +  ++   +y++ 
  gi|118431539|ref|NP_148070.2| 30 EAVVLLGPSGCGKTTTLRIVAGLER-PDAGRVYFDG 64
                                   789*************987775544.5555555554 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 ?   10.2   0.1   0.00042      0.47      16      39 ..      23      46 ..      17      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   ++ei+  +a++l GpsG GK+T l
  gi|118431539|ref|NP_148070.2| 23 DLEIKDGEAVVLLGPSGCGKTTTL 46
                                   567774459************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2463.33
//
Query:       gi|118431540|ref|NP_148071.2|  [L=312]
Description: agmatinase [Aeropyrum pernix K1]
Scores for 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  252.5   0.0    6.6e-75  252.2   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 !  252.2   0.0   3.7e-79   6.6e-75       4     278 ..      32     297 ..      30     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 252.2 bits;  conditional E-value: 3.7e-79
                                    EEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTESCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHTT CS
                       Arginase   4 allGvPfdaagsgrpGarfGPraireasarleealeynlelgvleelkivdlgdvavtpvdneevleqieeavaeilkag 83 
                                    +++GvP+d++ s+rpG rf+Pr+ir+as +le+  +y +e g+ ++++i+d gdva  p+++  +le++++ v++++++g
  gi|118431540|ref|NP_148071.2|  32 SVIGVPYDSTSSFRPGQRFAPREIRRASIELES-NGYYVE-GDIDRVPIADEGDVAAVPGSTLLTLERVARVVEDLAREG 109
                                    69*****************************96.455664.5599***********999999999*************** PP

                                    CEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STCSH CS
                       Arginase  84 klpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvdne 163
                                    k+p+vlGG+H ++lg+lr+la++ g + +v+ +DAH+Dlr+++  g+++sh+t+frr++ee  +   kl++iG+r+++++
  gi|118431540|ref|NP_148071.2| 110 KVPVVLGGEHLVTLGALRGLAAA-GVKPCVVVLDAHFDLRNDY-LGERFSHATVFRRVLEELGV---KLLYIGVRAYEAG 184
                                    *********************99.7789***************.8**************77666...5************ PP

                                    HHHHH.HHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHHHH CS
                       Arginase 164 eyela.kelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallrela 242
                                    e +la ++  i ++ mr +d  g++  v +++++ g +++++y+S+D+D+ Dpa+aPG+G pepgG ++re lal  +l 
  gi|118431540|ref|NP_148071.2| 185 EERLAvESGLIDYVPMRRMDIVGVDGAVLAARRFTG-DCEKIYISIDMDFYDPAYAPGVGNPEPGGASSREGLALASQLG 263
                                    998994555578***********************8.89****************************************9 PP

                                    CHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHHH CS
                       Arginase 243 eklnlvgaDvvEvnPaldteaeqtarlaarlvrell 278
                                    + ++++g+DvvEv+P++d+ ++ t++laa+ ++ell
  gi|118431540|ref|NP_148071.2| 264 D-RRVCGIDVVEVSPPYDP-GGATSLLAAKTLQELL 297
                                    9.9****************.56**********9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 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:                        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 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2249.78
//
Query:       gi|14601532|ref|NP_148072.1|  [L=583]
Description: glycyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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   88.6   0.1    4.7e-25   87.6   0.1    1.6  1  HGTP_anticodon  Anticodon binding domain
    0.00034   20.6   0.0    0.00077   19.5   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.077   12.8   1.1       0.46   10.4   0.1    2.3  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.18   11.7   0.1       0.18   11.7   0.1    1.9  2  zf-C2HC_2       zinc-finger of a C2HC-type
       0.46   10.4   2.0         12    5.9   0.0    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.47   10.6   2.0          5    7.3   2.0    2.4  1  Zn-ribbon_8     Zinc ribbon domain
        4.6    7.2   5.0        5.8    6.9   0.8    2.6  2  zinc_ribbon_4   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 !   87.6   0.1   1.8e-28   4.7e-25       1      92 [.     475     565 ..     475     567 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 1.8e-28
                                   SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEE CS
                HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqer 81 
                                   q+vv+pl e++e+l e a+ ++e L +ag+ v + d+++sig+++++ad++g+p av++++++le+gtvt+rdrdt +q+r
  gi|14601532|ref|NP_148072.1| 475 QAVVLPLVENDEKLVERARMVYETLVEAGFTVYY-DDSGSIGRRYARADEIGVPAAVTIDYQTLEDGTVTLRDRDTWRQVR 554
                                   89***************************95555.58******************************************** PP

                                   EETTHHHHHHH CS
                HGTP_anticodon  82 vsldelveklk 92 
                                   +  de+v+kl+
  gi|14601532|ref|NP_148072.1| 555 IGADEVVDKLR 565
                                   ********997 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 !   19.5   0.0     3e-07   0.00077      12      76 ..     162     227 ..     157     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3e-07
                                   EE-SSSHHHHHHHHHHHEE..EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGH CS
                                   xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  12 iLkPtneetfvelirdevl..rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasl 76 
                                   +L+P+  +++  +++      rs r+Pl ++q++++ R+E s  + L+R+reF+  + + f  +++ 
  gi|14601532|ref|NP_148072.1| 162 YLRPELAQGIFVAFKRVYEamRS-RIPLGIAQVGRVGRNEISPRQALVRLREFTIMEMEYFIDPEDQ 227
                                   79999999999999854322254.5****************9556***************9996644 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 ?    0.4   0.1      0.23   5.8e+02      25      35 ..      95     106 ..      91     109 .. 0.84
   2 ?   10.4   0.1   0.00018      0.46      18      31 ..     127     141 ..     120     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.23
                                   T--EE-HHH.HH CS
                 Rad50_zn_hook  25 CgReldeeh.rs 35 
                                   CgR++  +h  +
  gi|14601532|ref|NP_148072.1|  95 CGRTFRADHlVE 106
                                   ********9766 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                   -SE.E-TTT--EE-H CS
                 Rad50_zn_hook  18 akg.cCPlCgRelde 31 
                                   ++g +CP+C+ el++
  gi|14601532|ref|NP_148072.1| 127 ERGlRCPVCQGELGR 141
                                   45569*******986 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 ?   11.7   0.1   7.2e-05      0.18       3      17 ..      90     104 ..      88     106 .. 0.86
   2 ?   -4.3   0.9         7   1.8e+04       5       8 ..     132     135 ..     131     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.2e-05
                     zf-C2HC_2   3 vpCpkCgRsFnpdrl 17 
                                   v C  CgR+F +d l
  gi|14601532|ref|NP_148072.1|  90 VRCTSCGRTFRADHL 104
                                   78********99855 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 7
                     zf-C2HC_2   5 CpkC 8  
                                   Cp C
  gi|14601532|ref|NP_148072.1| 132 CPVC 135
                                   9999 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 ?    3.4   0.5     0.028        71       6      14 ..      91      99 ..      91     103 .. 0.83
   2 ?    5.9   0.0    0.0045        12      22      35 ..     126     140 ..     116     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.028
                Zn_ribbon_SprT  6 rCtgCgrey 14
                                  rCt+Cgr++
  gi|14601532|ref|NP_148072.1| 91 RCTSCGRTF 99
                                  8*****875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0045
                Zn_ribbon_SprT  22 rhn.YrCrrCkgtLr 35 
                                   r++  rC+ C+g+L+
  gi|14601532|ref|NP_148072.1| 126 RERgLRCPVCQGELG 140
                                   555789******995 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.0     0.002         5       7      39 ..      91     142 ..      89     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                   Zn-ribbon_8   7 rCeeCghefe...................vlqsisdapltaCPeCgsevrrv 39 
                                   rC++Cg++f                    +l +i ++    CP C++e+ rv
  gi|14601532|ref|NP_148072.1|  91 RCTSCGRTFRadhlveealginaeglsvsELDRIIRERGLRCPVCQGELGRV 142
                                   8********9999999999999988888888888877778899999988775 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.8    0.0023       5.8      26      36 .]      90     100 ..      89     100 .. 0.91
   2 ?    1.0   0.2      0.16     4e+02      26      32 ..     130     136 ..     125     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                 zinc_ribbon_4  26 vrCskCghvFr 36 
                                   vrC+ Cg +Fr
  gi|14601532|ref|NP_148072.1|  90 VRCTSCGRTFR 100
                                   9*******996 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.16
                 zinc_ribbon_4  26 vrCskCg 32 
                                   +rC+ C+
  gi|14601532|ref|NP_148072.1| 130 LRCPVCQ 136
                                   7999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.59u 0.22s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4169.59
//
Query:       gi|118431541|ref|YP_874911.1|  [L=141]
Description: hypothetical protein APE_1644.1 [Aeropyrum pernix K1]
Scores for complete 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-06   27.0   0.0      0.012   15.7   0.0    2.1  2  Molydop_binding  Molydopterin dinucleotide binding domain
  ------ inclusion threshold ------
       0.16   12.2   0.0        4.6    7.5   0.0    2.2  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0     3e-05      0.27      24      71 ..      57     103 ..      46     104 .. 0.79
   2 !   15.7   0.0   1.3e-06     0.012      27      64 ..     101     138 ..      95     141 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                                    HHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-T CS
                Molydop_binding  24 lakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrp 71 
                                    + + +pe ++i+p  A++lGi+d  +++v+ +r ++ ++a ++e+  p
  gi|118431541|ref|YP_874911.1|  57 DPRLKPEEARISPSLAKELGIEDFLEITVA-HRHRFAFKAIIDEEAEP 103
                                    444455889******************997.67789999999888765 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-06
                                    SSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEE CS
                Molydop_binding  27 pepevveinpedAaalGikdGdlVevesrrGsvevrak 64 
                                     ep++v++np+ +++ Gi+d+ + +v+  rG  ++ ++
  gi|118431541|ref|YP_874911.1| 101 AEPNRVYVNPDLMEEHGIADNSIATVRPYRGGEKLGVR 138
                                    45579**********************99998887776 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 ?    4.2   0.0    0.0054        48      17      52 ..      65     100 ..      61     105 .. 0.77
   2 ?    7.5   0.0   0.00052       4.6       7      34 ..      95     123 ..      92     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0054
                                    EEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBST CS
                        CDC48_N  17 vridpedmeelglepgdvveiegkrkTvaivwpaep 52 
                                    +ri+p+  +elg+e    +++  +++ + +++ +e+
  gi|118431541|ref|YP_874911.1|  65 ARISPSLAKELGIEDFLEITVAHRHRFAFKAIIDEE 100
                                    8************98888888776666666665554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00052
                                    CS.S-CSSTTEEEE-HHHHHHHTS-TTSE CS
                        CDC48_N   7 ap.qedvgrgivridpedmeelglepgdv 34 
                                    a  +e++  ++v+++p+ mee g+    +
  gi|118431541|ref|YP_874911.1|  95 AIiDEEAEPNRVYVNPDLMEEHGIADNSI 123
                                    455888899************99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1062.23
//
Query:       gi|118431542|ref|NP_148073.2|  [L=145]
Description: hypothetical protein APE_1645.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1135.57
//
Query:       gi|118431543|ref|NP_148074.2|  [L=186]
Description: tRNA-splicing endonuclease subunit alpha [Aeropyrum pernix K1]
Scores for 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-28   96.7   0.1    8.8e-28   96.2   0.1    1.2  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    2.9e-20   71.7   0.1    4.1e-20   71.2   0.1    1.2  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
  ------ inclusion threshold ------
      0.035   14.1   0.0      0.082   12.9   0.0    1.6  1  Rrp40_N          Exosome complex exonuclease Rrp40 N-terminal


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 !   96.2   0.1   1.5e-31   8.8e-28       1      85 []      95     178 ..      95     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.5e-31
                                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTT CS
                  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdae 80 
                                    f + y++yrdLre+G+vvrsGlkFG+dF+vY+ +p+ +h+ ++V+ +s ++++d+ ++++a+rl+hsv+Kk+++a++ + 
  gi|118431543|ref|NP_148074.2|  95 FSMLYNIYRDLRERGFVVRSGLKFGSDFAVYRLGPGIDHAPFIVHAYSPEDNIDPVEIVRAGRLSHSVRKKFVFAVT-RG 173
                                    56679***********************************************************************8.99 PP

                                    SCEEE CS
                  tRNA_int_endo  81 gdvty 85 
                                    gdv y
  gi|118431543|ref|NP_148074.2| 174 GDVSY 178
                                    99987 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 !   71.2   0.1   6.8e-24   4.1e-20       2      66 ..      11      85 ..      10      86 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 6.8e-24
                                   EEEEETTEEEESSHHHHHHHHHTTT-SEE.........CCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHH CS
                tRNA_int_endo_N  2 egeLsgdrvlvedeeaakrlyekgfYGkp.........lidepLqLslvEAlYLlekGklevv.kggeplsfeel 66
                                   +g+L gd+vlv d e+a++ly+ g+YG+p         + + pL+Lsl+E+lYL+ekG+lev   +g+++++e+l
  gi|118431543|ref|NP_148074.2| 11 SGVLIGDSVLVTDVEQARSLYSCGYYGQPldvekprgaDFEGPLRLSLIESLYLAEKGVLEVAkPDGSSVGVEDL 85
                                   799**********************************************************************98 PP

>> Rrp40_N  Exosome complex exonuclease Rrp40 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.082       9      37 ..     126     164 ..     123     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                        Rrp40_N   9 kLGPGLrhtP.......plst...liatraGiLhtkpkk 37 
                                    +LGPG+ h+P       p ++   +  +raG+L++  +k
  gi|118431543|ref|NP_148074.2| 126 RLGPGIDHAPfivhaysPEDNidpVEIVRAGRLSHSVRK 164
                                    8*********99998885455455556799999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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: 0.38u 0.20s 00:00:00.58 Elapsed: 00:00:00.35
# Mc/sec: 1610.42
//
Query:       gi|14601535|ref|NP_148075.1|  [L=197]
Description: aromatic acid decarboxylase [Aeropyrum pernix K1]
Scores for complete 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    4.1e-18   65.6   0.0    1.1  1  Flavoprotein  Flavoprotein


Domain annotation for each model (and alignments):
>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   2.3e-22   4.1e-18       3     125 ..       8     171 ..       6     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.3e-22
                                   EEEEE-SSCGGGCHHHHHHHHHHTTEEEE.EEESCHHHHCCHHG.GS....TCSSHHHHHHCT.................. CS
                  Flavoprotein   3 illgiTGsvaaikalellekLkkegievq.vvltkaAkkfiske.klklaaredpilhielrr.................. 63 
                                   + +++TGs+++  al+lle+Lk  ++e++ ++lt+ A+++++ e           i+  +lrr                  
  gi|14601535|ref|NP_148075.1|   8 VSIAVTGSSGVRVALRLLEALKG-EVEIRgIILTRGAEEVARYEeG---------IEPEDLRRllrsyaplymendmsspl 78 
                                   779*******************8.9999989***********8832.........33334444555566666666666666 PP

                                   .....TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTEEEEE.-- CS
                  Flavoprotein  64 .....wadllviaPasantlakianGiadnll..............................tlilratakkpiliaPamn 109
                                        + d++ i+Pas++t++ ia Gi  +l                               +l +   a+++ +++P   
  gi|14601535|ref|NP_148075.1|  79 asssnQPDAMAIVPASMKTVGLIARGIPSSLParaalavlrlgrrlvvapretplgvvelenMLAI---ARMGGIVVP-LT 155
                                   66666******************************************************8666555...99*******.** PP

                                   HHCCTCSTCHHHHHHH CS
                  Flavoprotein 110 pamyenpqtlknlekl 125
                                    ++y +p ++++l+++
  gi|14601535|ref|NP_148075.1| 156 LSFYIKPSSVEDLVDF 171
                                   ***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1421.09
//
Query:       gi|118431544|ref|NP_148076.2|  [L=189]
Description: hypothetical protein APE_1648.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-27   93.5   0.0    1.2e-26   93.0   0.0    1.2  1  Macro     Macro domain
  ------ inclusion threshold ------
      0.032   14.0   1.7        4.2    7.3   0.4    2.5  2  TetR_N    Bacterial regulatory proteins, tetR family


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 !   93.0   0.0   1.4e-30   1.2e-26       1     116 [.      27     136 ..      27     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 1.4e-30
                                    EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHHHHH CS
                          Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeellak 80 
                                    Vn+aNs + +ggg aga++ra+g+ ++ee+ +     +++++Geav+t++++lpa++vih+  p++++ + +    +  k
  gi|118431544|ref|NP_148076.2|  27 VNPANSLMIMGGGAAGALKRAGGSVIEEEAMRK----APVPVGEAVITSGGSLPARFVIHA--PTMEEPGMRIPLVNAFK 100
                                    9*****************************999....99**********************..****99*********** PP

                                    HHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHH CS
                          Macro  81 ayknalelaeekgiksvafPaistGifgvpweeaar 116
                                    a   al+la e gi+sva+Pa+++G++g+++ e+ar
  gi|118431544|ref|NP_148076.2| 101 ASYAALRLASEAGIESVAMPAMGAGVGGLSVAEVAR 136
                                    *********************************997 PP

>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.001         9       4      21 ..     104     121 ..     103     127 .. 0.88
   2 ?    7.3   0.4   0.00046       4.2      13      32 ..     125     144 ..     122     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.001
                                    HHHHHHHHHHTTT--HHH CS
                         TetR_N   4 aArelfaerGydattvre 21 
                                    aA++l +e G++++ +++
  gi|118431544|ref|NP_148076.2| 104 AALRLASEAGIESVAMPA 121
                                    8*************9987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00046
                                    HTTT--HHHHHHHHTSSHHH CS
                         TetR_N  13 GydattvreIAkrAGvskga 32 
                                    G  +++v+e+A++A ++++ 
  gi|118431544|ref|NP_148076.2| 125 GVGGLSVAEVAREAAMAASI 144
                                    8899***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1525.52
//
Query:       gi|118431545|ref|NP_148077.2|  [L=427]
Description: hypothetical protein APE_1649.1 [Aeropyrum pernix K1]
Scores for 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-29  100.7   0.0    1.2e-28  100.2   0.0    1.2  1  CLP1_P     mRNA cleavage and polyadenylation factor CLP1 P-lo
  ------ inclusion threshold ------
       0.18   11.5   0.0        0.4   10.4   0.0    1.5  1  PduV-EutP  Ethanolamine utilisation - propanediol utilisation


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 !  100.2   0.0   1.3e-32   1.2e-28       1     187 [.     104     279 ..     104     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 1.3e-32
                         CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnpsly 80 
                                    Gp+++GK++l+++L+N+ l +g  + ++D+DvGq +i+pPg++sl+l  + + + + +++ a    f+G+  p     ++
  gi|118431545|ref|NP_148077.2| 104 GPVEAGKTSLTAVLANRSLARGIPTGIIDADVGQADIGPPGFVSLSLPGSWVIWLRLLDPVA--LRFVGSIEPGPVAGRI 181
                                    89********************9999*********************999988865554443..79*******99999** PP

                         CLP1_P  81 lalvkelareveekleenkkakasgliIntpGwvkglga.ellleliealepdvvvvldqeellnelkrdlplskvkvvk 159
                                    + +v++l  +++         +a ++ ++t+Gwvkg ga e++ +l++ +++d+vvv+++ el+ +l+++l+ s+v +v+
  gi|118431545|ref|NP_148077.2| 182 VTAVASLRARAR-------GEGAAFVAVDTDGWVKGWGAlEYKIDLARGVNADAVVVVGDPELYGFLEKSLE-SNVYYVR 253
                                    ********9999.......3489**************955********************************.******* PP

                         CLP1_P 160 lpkspgvvqrsreerrelreerireYFy 187
                                    +p++++v  r   err+lr+e++ ++++
  gi|118431545|ref|NP_148077.2| 254 SPSVQAV--RGVDERRRLRSENYIRFLE 279
                                    *******..9************988776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   4.4e-05       0.4       5      26 ..     101     122 ..      98     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.4e-05
                      PduV-EutP   5 lliGkvgsGKttLtqalkgeel 26 
                                    +++G+v++GKt+Lt  l +++l
  gi|118431545|ref|NP_148077.2| 101 MVVGPVEAGKTSLTAVLANRSL 122
                                    99***************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2982.30
//
Query:       gi|14601538|ref|NP_148078.1|  [L=389]
Description: PqqE-like protein [Aeropyrum pernix K1]
Scores for complete 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-25   89.8   0.0    5.8e-25   88.6   0.0    1.7  1  Radical_SAM   Radical SAM superfamily
    9.4e-06   26.1   0.0    2.1e-05   25.0   0.0    1.5  1  SPASM         Iron-sulfur cluster-binding domain
      1e-05   25.8   0.0    1.8e-05   25.1   0.0    1.3  1  Fer4_12       4Fe-4S single cluster domain
     0.0018   18.4   0.0     0.0032   17.6   0.0    1.4  1  Fer4_14       4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.045   13.2   0.0    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
      0.099   12.5   0.0       0.32   10.9   0.0    1.8  1  DUF4224       Domain of unknown function (DUF4224)


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 !   88.6   0.0   1.9e-28   5.8e-25       2     153 ..      40     185 ..      39     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.9e-28
                                   EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                   ++tr+Cnl+C++C+++    +++ + +ls+ee l  +++l +e+gv  v+l+ggepl+++df  ++++l+    +  ++++
  gi|14601538|ref|NP_148078.1|  40 NITRACNLKCIHCYISAG--PHPLPGELSTEEALGVARQL-VEHGVPLVTLSGGEPLVRRDFWAIAKALSGH--DTPKLAL 115
                                   69**************96..********************.9******************************..7****** PP

                                   EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglp 153
                                   ++ngtl+++e ++rl++lg+ +v ++l+++d+  v+++++  ++ f++ +++ +++ e g++ v +r+++ +
  gi|14601538|ref|NP_148078.1| 116 SSNGTLITRETAARLRRLGFSYVGISLDSVDPG-VHDKFRgAPGAFKAAIRGARNALEEGLD-VGFRLTITK 185
                                   *********************************.9999988999****************99.777766554 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   6.9e-09   2.1e-05       1      68 []     284     346 ..     284     346 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 6.9e-09
                         SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIw..nseeyqefr...kskkfplielCrnCp 68 
                                   C  +++s+ I +dG+V pC     ++ ee+++G++r++ l eI+   ++ ++ f    +  + p    C  Cp
  gi|14601538|ref|NP_148078.1| 284 C--GRKSVSIYPDGTVRPC-----QFLEEVVIGDLRRQRLGEILsaDNPLLKPFIavdTMLRGP---KCGGCP 346
                                   5..78999***********.....35467***************54445666666443222333...377775 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 !   25.1   0.0   5.9e-09   1.8e-05      11      97 ..      39     123 ..      31     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.9e-09
                       Fer4_12  11 f..vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiw 89 
                                   +  +  Cnl+C  C+  +   +  g+  t+e+l  + ++l ++ ++ +tl+GGEPl+   ++++  ++k +  +   k  +
  gi|14601538|ref|NP_148078.1|  39 WniTRACNLKCIHCYISAGPHPLPGELSTEEALGVA-RQLVEHGVPLVTLSGGEPLV---RRDFWAIAKALSGHDTPKLAL 115
                                   255778***********************9999765.56669***************...899999999999998878899 PP

                       Fer4_12  90 lytgytle 97 
                                   +++g+ + 
  gi|14601538|ref|NP_148078.1| 116 SSNGTLIT 123
                                   99998765 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 !   17.6   0.0   1.1e-06    0.0032       5      90 ..      42     120 ..      38     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                       Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiwl 85 
                                   +  Cnl+C  C+ ++  +   g+ +tee l  + ++l ++ +    ++l+GGePL     +++  + k l  +  + k  l
  gi|14601538|ref|NP_148078.1|  42 TRACNLKCIHCYISAGPHPLPGELSTEEAL-GVARQLVEHGV--PLVTLSGGEPLVR---RDFWAIAKALSGHD-TPKLAL 115
                                   668************9**************.56657777777..559********54...66777766666555.455555 PP

                       Fer4_14  86 etngt 90 
                                    +ngt
  gi|14601538|ref|NP_148078.1| 116 SSNGT 120
                                   55555 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 ?   13.2   0.0   1.5e-05     0.045       2     153 ..     128     280 ..     127     285 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                   HHHHHCT-SEEEEECCTCSHHHHC........HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHH CS
                  AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel........sdeelrelrkaldelglriaslslftrfgypdederearreesvdalkr 74 
                                   a+++++Gf +v +++++ +p +++        +++++r  r+al e gl  ++++l++  ++             +d++ r
  gi|14601538|ref|NP_148078.1| 128 ARLRRLGFSYVGISLDSVDPGVHDkfrgapgaFKAAIRGARNAL-EEGLD-VGFRLTITKYN-------------LDDAPR 193
                                   57899*****************9999999995555555555555.55788.44444444444.............888889 PP

                                   HHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT..SEEEEE--TTTTSSSTC......HHHHHH CS
                  AP_endonuc_2  75 aielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekeg..vklalEtlagsgvelgd......eelarl 147
                                    i+la+++G+p + + + +   ++  + +   e l++++++++++  +++  v+++l   + +gv+l d      +e+++l
  gi|14601538|ref|NP_148078.1| 194 IIRLASDMGVPRVAIYVVDLLGRATPDLAPSPEDLRRAIDAILEESVRHQdrVEVLLVRANFAGVYLADrlaktrDEFLQL 274
                                   ****************99755555666667888888888888877666665544444444444444443446666666666 PP

                                   HHHHTT CS
                  AP_endonuc_2 148 ldavds 153
                                   l+ v+s
  gi|14601538|ref|NP_148078.1| 275 LSLVGS 280
                                   666665 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.32      20      43 ..      74      97 ..      73      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                       DUF4224 20 akwLranGipfvvradGrpiVlRa 43
                                  a++L ++G+p v+  +G p+V R+
  gi|14601538|ref|NP_148078.1| 74 ARQLVEHGVPLVTLSGGEPLVRRD 97
                                  789*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2993.09
//
Query:       gi|14601539|ref|NP_148079.1|  [L=403]
Description: PqqE-like protein [Aeropyrum pernix K1]
Scores for complete 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   71.0   0.0    2.8e-19   70.1   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    2.5e-05   24.6   0.0    4.5e-05   23.7   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    0.00015   22.2   0.0    0.00029   21.3   0.0    1.5  1  SPASM        Iron-sulfur cluster-binding domain
    0.00059   20.0   0.0     0.0011   19.1   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   6.3e-23   2.8e-19       3     166 ..      18     176 ..      16     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 6.3e-23
                                   EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritv 82 
                                    t++C l+C++C       +e+ + +ls++e l++v+++ +  +    ++++gg+pl+++df ++le ++     g+r++v
  gi|14601539|ref|NP_148079.1|  18 STKACLLACKHCRAEAL--TEPQPGELSTREALALVDQVVEFGRpYPILVITGGDPLMRRDFWRILEYAVSQ---GLRVAV 93 
                                   799************97..********************74444799************************8...888888 PP

                                   EECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHH CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  83 etngtlpd.eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendeele 161
                                     + t +  +e+++r++++gv r+s++++++ +e v++ ++  ++tf++ ++ ++ + +ag++ v +++++++   d+ l 
  gi|14601539|ref|NP_148079.1|  94 APSVTPLLtREVVRRMARMGVARISISIDSGLPE-VHDAIRgVPGTFKASVNIVREALAAGLP-VQINTTVMKPTVDS-LP 171
                                   777665555*************************.******999*******************.99999999855554.78 PP

                                   HHHHH CS
                                   xxxxx RF
                   Radical_SAM 162 ellel 166
                                   e+l+l
  gi|14601539|ref|NP_148079.1| 172 ETLKL 176
                                   88776 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 !   23.7   0.0     1e-08   4.5e-05      11      79 ..      16      84 ..       8      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1e-08
                       Fer4_12 11 f..vsgCnlsCkgCfnketwsfksgkeftkell...eeiiedlkkesiegltllGGEPllpenaeallelvkev 79
                                  +  ++ C l+Ck C ++++ +++ g+  t+e+l   ++++e    +  + l+++GG+Pl+   ++++ +++++ 
  gi|14601539|ref|NP_148079.1| 16 WesTKACLLACKHCRAEALTEPQPGELSTREALalvDQVVEFG--RPYPILVITGGDPLM---RRDFWRILEYA 84
                                  455789**********************966650004444433..6679***********...66666666655 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   6.5e-08   0.00029       6      68 .]     289     343 ..     285     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.5e-08
                         SPASM   6 rslfInsdGdVvpCcvdkktyveelklGnireesleeIwnse.eyqefrkskkfplielCrnCp 68 
                                     +f++++G V+p  +       ++ +G++r+ sl+eI++s+ e++ +r +  f+    C +C+
  gi|14601539|ref|NP_148079.1| 289 GVIFVSNKGLVYPSGFL------PYPVGDVRKSSLKEIYQSSpELEGLR-KAVFK--GRCGRCE 343
                                   6789**********333......6***************88879999**.33333..3599995 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.4e-07    0.0011       6      74 ..      20      84 ..      15     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.4e-07
                       Fer4_14  6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrl 74
                                    C l+Ck C  ++  + + g+ +t+e l + ++++ +       lv+tGG+PL+    +++ +++++ 
  gi|14601539|ref|NP_148079.1| 20 KACLLACKHCRAEALTEPQPGELSTREAL-ALVDQVVEFGRPYPILVITGGDPLMR---RDFWRILEYA 84
                                  67************************999.455444443333445*********65...5666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3097.64
//
Query:       gi|118431546|ref|NP_148080.2|  [L=199]
Description: aldolase class II protein [Aeropyrum pernix K1]
Scores for complete 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-38  132.4   0.2    1.9e-38  132.3   0.2    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.3   0.2   1.1e-42   1.9e-38       2     185 ..      16     189 ..      15     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 1.1e-42
                                    HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHH CS
                    Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiy 81 
                                    ++aea + l++rglv+++gGn+S+ ++  + ++  p+ v  ++l+  d++v++ld g+vv g     +psse+++H aiy
  gi|118431546|ref|NP_148080.2|  16 DVAEALKTLYERGLVQAMGGNVSALHN--GLVYLSPTRVFRGRLSWMDVAVMRLD-GSVVRG-----RPSSEWRMHIAIY 87 
                                    789*********************944..6666*********************9.****44.....8************ PP

                                    HH-TT-SEEEEE--HHHHHHHTCCSTSCHCC.SSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHH.HS-SEEEETTT CS
                    Aldolase_II  82 karpdaravvHtHspaavalsalagkeglpp.ltqeaaklllgdevpvipyaapgteelgealaealk.edakavllrnH 159
                                    ++   + avvH+H+pa++    + g + l p l  ea++ +  + v+ +p  +pgt el+ea+a al+   ++a++lrnH
  gi|118431546|ref|NP_148080.2|  88 RRLDGIAAVVHAHPPALLGADST-GLR-LNPsLLMEAEATV--GCVAGVPRVKPGTWELAEAVATALEaSGCRAAVLRNH 163
                                    *********************76.555.6663555555533..778888*******************879********* PP

                                    EEEEEESSHHHHHHHHHHHHHHHHHH CS
                    Aldolase_II 160 GlltvGetleeAvalaetleeaaeiq 185
                                    G+++vG++l eA+++ae++e +a+i 
  gi|118431546|ref|NP_148080.2| 164 GVVAVGRSLWEALDMAEAVEDLARIS 189
                                    ***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1748.15
//
Query:       gi|14601541|ref|NP_148081.1|  [L=335]
Description: oxidoreductase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-53  181.8   0.0    1.8e-53  181.7   0.0    1.0  1  Aldo_ket_red   Aldo/keto reductase family
  ------ inclusion threshold ------
      0.013   15.1   0.2      0.022   14.4   0.2    1.3  1  Abhydrolase_8  Alpha/beta hydrolase


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 !  181.7   0.0     2e-57   1.8e-53       2     292 ..      17     297 ..      16     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 2e-57
                                   EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTS CS
                  Aldo_ket_red   2 lglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeik 78 
                                   +glG+wq+gs+    ++ s +  ++ l  a+e+Gin++DtAevYg+g+se++lGealk+  + re+++i++Kv        
  gi|14601541|ref|NP_148081.1|  17 VGLGLWQFGSPmwggKALSADVLARGLSIAVEEGINLLDTAEVYGMGSSERMLGEALKR-LNAREDFVIVSKV------AG 90 
                                   89***********9999999999999*********************************.9************......** PP

                                   SSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--EE CS
                  Aldo_ket_red  79 sglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvkiv 158
                                   ++ ++ +i++  + +  rL  +  D++l H+p p +++++ v++ le+ v eG++ ++G+Sn+  + l  a + ++ +++v
  gi|14601541|ref|NP_148081.1|  91 FRSTAGDIVKGARGIAGRLS-SAPDVILHHWPPPVYSRLCSVVRGLEQAVNEGLASYYGFSNYGEDLLGDAlSCTRRLEPV 170
                                   ********************.9*************************************************9********* PP

                                   EEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHT CS
                  Aldo_ket_red 159 avqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakeh 239
                                   a q+ ynl  +  e+ l++l++++g+  ia+spl++G+l g + ++++ + ++p  +     +  +   + e l+++a+  
  gi|14601541|ref|NP_148081.1| 171 ADQILYNLAYRTPEQRLIPLLHQHGMTPIAWSPLAKGALAGFKGEPTRAQAGDPVFR-----TALEDTGLQEVLESVARRL 246
                                   **************************************************9999876.....345666777889999999* PP

                                   T--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                  Aldo_ket_red 240 gvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                   g s a +al+++   +++ ++i+g +++e++++ ++a  lklsee+va lde+
  gi|14601541|ref|NP_148081.1| 247 GASKASVALAWVA--YKGAVPIVGWRRPERVREAAAAARLKLSEEDVALLDEA 297
                                   *************..************************************97 PP

>> Abhydrolase_8  Alpha/beta hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   2.5e-06     0.022      42     118 ..     231     309 ..     214     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-06
                 Abhydrolase_8  42 earglraeaaaaeeaagkpesvAviAWlgYeaP.agaskevatddrAaagAaeLnallrdlrats.vpgqhlallgHSY 118
                                   e  gl++ +   +++ g +++  ++AW+ Y+     +++   +  r aa+Aa+L+   +d++    ++++ ++l g SY
  gi|14601541|ref|NP_148081.1| 231 EDTGLQEVLESVARRLGASKASVALAWVAYKGAvPIVGWRRPERVREAAAAARLKLSEEDVALLDeASKRYVTLWGSSY 309
                                   556788888899999*****9999******97634899***********************9998788999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 2939.75
//
Query:       gi|118431547|ref|NP_148082.2|  [L=148]
Description: hypothetical protein APE_1660.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-35  121.9   0.4    2.1e-35  121.7   0.4    1.0  1  CoA_binding_2  CoA binding domain
    2.6e-08   34.4   0.0    1.3e-07   32.2   0.0    1.8  2  CoA_binding    CoA binding domain
  ------ inclusion threshold ------
       0.04   14.7   0.2        1.2   10.0   0.2    2.3  1  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
       0.15   12.0   0.0        1.7    8.5   0.0    2.0  2  YjeF_N         YjeF-related protein N-terminus


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 !  121.7   0.4   4.8e-39   2.1e-35       1     115 [.      16     139 ..      16     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 121.7 bits;  conditional E-value: 4.8e-39
                                    --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T........T--EEEE-S-HHHHGGGHHHHH CS
                  CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslae.d...pepvdlvdvftppeatpeivkeal 76 
                                    r +aVvGas np+k +y+v++yl+++g++++pVnp ++eilgek+y+sl+e +     +vd+vdvf+pp ++++++++a+
  gi|118431547|ref|NP_148082.2|  16 RVVAVVGASRNPEKDAYRVPEYLKKAGYRIIPVNPSADEILGEKAYPSLDEiPdeiAREVDVVDVFRPPREAEAVAEQAI 95 
                                    679***********************************************97678999*********************9 PP

                                    HH.....--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHH CS
                  CoA_binding_2  77 al.....gakavwlqpgsedeeaaelaeeagirvvgdrCilveg 115
                                    +l     +  +vw+q g+ +eea++++ +ag++vv drC++ e+
  gi|118431547|ref|NP_148082.2|  96 RLarragRRIVVWFQKGTASEEAVKKLLDAGLDVVVDRCMMEEH 139
                                    99766644889*****************************9887 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   2.8e-11   1.3e-07       6      84 ..      18      96 ..      14     112 .. 0.91
   2 ?    0.2   0.0      0.28   1.2e+03      74      91 ..     114     131 ..      99     132 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.8e-11
                                   EEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC..TTTEEEEES-HHHHHHHHHHHHH CS
                    CoA_binding  6 viviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt..evdvavitvPaesaqeavdelve 84
                                   v+v+Ga+++  + +y++ e lk     +++vnp   ++e+lg ++y+s+de+++++  evdv  ++ P+++a+++++++++
  gi|118431547|ref|NP_148082.2| 18 VAVVGASRNPEKDAYRVPEYLKKAGYRIIPVNPS--ADEILGEKAYPSLDEIPDEIarEVDVVDVFRPPREAEAVAEQAIR 96
                                   9*********************9999********..********************75599999999********999986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHTT-SEEE CS
                    CoA_binding  74 saqeavdelveagikgiv 91 
                                    + +eav++l++ag  ++v
  gi|118431547|ref|NP_148082.2| 114 ASEEAVKKLLDAGLDVVV 131
                                    668999999999998886 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00027       1.2      46      91 ..      56     131 ..       8     148 .] 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                                    TTHEEESSHHHHHTCT..TESEEEE-S-G............................GGHHHHHHHHHHTT-EEEE CS
                   GFO_IDH_MocA  46 fgveaysdleelladp..eidavivatpn............................gtheelakaaleagkhvll 91 
                                    +g +ay +l+e++++   e+d+v v  p+                            +  ee +k++l ag +v++
  gi|118431547|ref|NP_148082.2|  56 LGEKAYPSLDEIPDEIarEVDVVDVFRPPreaeavaeqairlarragrrivvwfqkgTASEEAVKKLLDAGLDVVV 131
                                    5667899999999876889999999999955555555555555555555555554433355555555555555555 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.055   2.5e+02      27      91 ..      15      51 ..       5      66 .. 0.61
   2 ?    8.5   0.0   0.00039       1.7      54     107 ..      75     132 ..      70     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.055
                         YjeF_N 27 kkvlvlvGsgnnG.gdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvveekpe 91
                                   ++v+ +vG  +n   d++ +  +L ++g++++                               +p+
  gi|118431547|ref|NP_148082.2| 15 ARVVAVVGASRNPeKDAYRVPEYLKKAGYRIIP-----------------------------VNPS 51
                                   456666666644314666666666666666555.............................3333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00039
                         YjeF_N  54 ak.Vtvllleeeekldedaeralellkkaggkvveekpeedleekls.....apvdlviD 107
                                    ++ V+v  ++++++ +++ae+a++l+++ag ++v + ++  ++e++      a  d+v+D
  gi|118431547|ref|NP_148082.2|  75 VDvVDV--FRPPREAEAVAEQAIRLARRAGRRIVVWFQKGTASEEAVkklldAGLDVVVD 132
                                    333444..789999********************99888777666556677777788877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1290.76
//
Query:       gi|14601543|ref|NP_148083.1|  [L=124]
Description: peptidyl-tRNA hydrolase [Aeropyrum pernix K1]
Scores for complete 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-39  133.8   0.0    3.7e-39  133.6   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.064   13.1   0.0    1.2  1  BTHB      Basic tilted helix bundle domain
      0.046   13.5   1.5      0.062   13.1   0.1    1.7  2  HTH_ParB  HTH domain found in ParB protein
       0.12   12.4   0.0       0.16   12.1   0.0    1.1  1  DUF2396   Protein of unknown function (DUF2396)


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 !  133.6   0.0   8.3e-43   3.7e-39       1     117 []       6     124 .]       6     124 .] 0.96

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 8.3e-43
                                   EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CH..HHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEE CS
                          PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesne..kellkeWeeegqkkivlkveseeeLlelaakakalglpaa 79 
                                   +k+++vvr+DL+m++Gk aaq+ahA++++v  +l++ ++  +++l+ W+ +gq+k+vl+ves +eL+e+++ka ++glpa+
  gi|14601543|ref|NP_148083.1|   6 YKQAIVVRRDLGMGRGKAAAQAAHASCEAVFLILESGRPewRRWLEMWRLQGQAKVVLRVESLAELQEVYSKAVEEGLPAS 86 
                                   79*******************************9986446678************************************** PP

                                   EEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                          PTH2  80 lirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                    +rDag+tq+epgt+T+ a+gPap+++vd++tg Lkl+
  gi|14601543|ref|NP_148083.1|  87 FVRDAGKTQLEPGTPTAAAVGPAPSRLVDRITGGLKLF 124
                                   ************************************97 PP

>> BTHB  Basic tilted helix bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.064      32      65 ..      49      82 ..      46      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                          BTHB 32 FLkenkLlGniknVaKtankeqLieaYkklfesk 65
                                   L+ ++L+G++k V + ++  +L e+Y k +e++
  gi|14601543|ref|NP_148083.1| 49 WLEMWRLQGQAKVVLRVESLAELQEVYSKAVEEG 82
                                  7999*************************99986 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2      0.49   2.2e+03       5      19 ..       9      23 ..       7      31 .. 0.77
   2 ?   13.1   0.1   1.4e-05     0.062      15      41 ..      57      83 ..      56      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.49
                      HTH_ParB  5 eavsegkiseGHARa 19
                                    v ++ + +G ++a
  gi|14601543|ref|NP_148083.1|  9 AIVVRRDLGMGRGKA 23
                                  557888999999998 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.4e-05
                      HTH_ParB 15 GHARaLlslkdeelqlqlaekiieegL 41
                                  G+A++ l++++  + ++++ k++eegL
  gi|14601543|ref|NP_148083.1| 57 GQAKVVLRVESLAELQEVYSKAVEEGL 83
                                  9************************98 PP

>> DUF2396  Protein of unknown function (DUF2396)
   #    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      42      83 ..      36      78 ..      20      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                       DUF2396 42 lvhlqsgr.kwrlwegkwyrqhthpdgirfeihealdrlytqG 83
                                  ++ l+sgr +wr+w + w  q +    +r+e   +l+++y++ 
  gi|14601543|ref|NP_148083.1| 36 FLILESGRpEWRRWLEMWRLQGQAKVVLRVESLAELQEVYSKA 78
                                  3568999967**********************99999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1077.51
//
Query:       gi|118431548|ref|NP_148084.2|  [L=159]
Description: aspartate carbamoyltransferase regulatory subunit [Aeropyrum pernix K1]
Scores for 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   96.9   0.0    8.2e-28   96.5   0.0    1.2  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    1.3e-13   50.6   0.1    2.1e-13   49.9   0.1    1.4  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


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 !   96.5   0.0   9.1e-32   8.2e-28       2      93 ..       7      99 ..       6     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 9.1e-32
                                   -----SCEEEEEEEETT-HHHHHHHCT--T....TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEE CS
                           PyrI  2 kvkkienGiViDHIkagkalkvlklLkldkl.kseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniI 82
                                    v+ki++G+ViDHI+ g+a+++lk L+l      + ++a+++n++s+klg+Kdi+kieg + ++++l++l++iap at n+I
  gi|118431548|ref|NP_148084.2|  7 LVRKIRSGVVIDHIPPGRAFTMLKALGLLPPrGYRWRIAVVINAESSKLGRKDILKIEGYKPRQRDLEVLGIIAPGATFNVI 88
                                   699************************9765267789********************************************* PP

                                   ETTEEEEEE-- CS
                           PyrI 83 kdgevveKkkv 93
                                   +d++vveK k+
  gi|118431548|ref|NP_148084.2| 89 EDYKVVEKVKL 99
                                   ********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 !   49.9   0.1   2.4e-17   2.1e-13       3      48 .]     106     153 ..     104     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.4e-17
                                    ESSS--S-TTBGGGT..TS-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                         PyrI_C   3 egvlkCpNpnCItnn..epveskFkvedkekvklkCkYCekeiseeei 48 
                                    +gvl+CpNp+CIt++  e+  sk++++++++  ++C YC++++  +ei
  gi|118431548|ref|NP_148084.2| 106 QGVLRCPNPTCITRKerEKAVSKMVLVSQDPPAYRCVYCGTTVMGDEI 153
                                    79*************888*************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1187.10
//
Query:       gi|118431549|ref|NP_148085.2|  [L=308]
Description: aspartate carbamoyltransferase catalytic subunit [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-42  144.1   0.0    4.4e-42  143.6   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    1.3e-21   77.3   0.0    1.8e-21   76.8   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 !  143.6   0.0   4.9e-46   4.4e-42       1     147 [.       9     146 ..       9     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 4.9e-46
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTT CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqls 80 
                                    r+++s++d+++ ++e l+++a+ +++k      +k l+gk++al F+epStRTr+Sfe+A+krlGg++l +s +e     
  gi|118431549|ref|NP_148085.2|   9 RDVISITDFTRGDLELLFRQADVIESKA----GSKPLDGKVVALAFFEPSTRTRLSFETAVKRLGGSTLLISGEE---AI 81 
                                    799*********************9775....699*************************************663...45 PP

                                    TGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                       OTCace_N  81 svskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                    sv+kg  E+l+Dt+ +l++y+daiviRh+  ga  +   a+ a+ pviN+gdg ++HPtQa++Dl+t++
  gi|118431549|ref|NP_148085.2|  82 SVAKG--ENLADTITMLDSYADAIVIRHRyeGA--ALYAAEVAEKPVINGGDGRQHHPTQAMLDLYTVY 146
                                    57899..**********************7666..77899999************************86 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 !   76.8   0.0     2e-25   1.8e-21       1     156 [.     153     304 ..     153     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2e-25
                                    CC.EEEEESS.TTSHHHHHHHHHHHHCT-E.EEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                         OTCace   1 kglkiafvGd.kknnvanslikllarlgmd.vvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                    +gl++  +Gd  +++ a+s i +l+ ++   v+l++P++l+   evle ++k     g  +t  e l++++ + Dv+y +
  gi|118431549|ref|NP_148085.2| 153 DGLTYGVLGDlRYGRAASSFILGLSLFNPRhVYLISPPQLRARREVLEALEK----RGVPYTEVERLQDVLGELDVLYVT 228
                                    5899999*********************998***********99*9966655....69999999**************** PP

                                    -SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-T.T-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHH CS
                         OTCace  79 vwvsmgeekere...erlkklkd.yqvteellklakk.daivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAl 153
                                    +++     ker    +++++l++ y+vt +ll+   k  ++vlH+LP  r +E++ +V++s  +++f qa+ ++ +++Al
  gi|118431549|ref|NP_148085.2| 229 RIQ-----KERIpdpREYESLRGsYRVTLDLLESFAKeSLKVLHPLP--RVDEIDFSVDSSRYQAYFTQARLGVRVRMAL 301
                                    ***.....77777789****************9655549********..******************************* PP

                                    HHH CS
                         OTCace 154 lvl 156
                                    + l
  gi|118431549|ref|NP_148085.2| 302 MNL 304
                                    *76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2296.20
//
Query:       gi|14601546|ref|NP_148086.1|  [L=268]
Description: hypothetical protein APE_1666 [Aeropyrum pernix K1]
Scores for 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-09   35.6   0.0    2.2e-08   34.4   0.0    1.7  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.16   2.9e+03      65      91 ..      12      33 ..       7      72 .. 0.68
   2 !   34.4   0.0   1.2e-12   2.2e-08      21     121 ..      74     179 ..      39     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.16
                                  HHHHHHHHHHHHHHHHHHHHHHTTCCH CS
                            HD 65 eilrevekrlgldledvaklirehhes 91
                                  e+++e+e ++      +++li+e +e 
  gi|14601546|ref|NP_148086.1| 12 EKVKESEVLS-----SIYHLIEEDQEI 33
                                  5555555555.....666666665554 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.2e-12
                                   H................HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HD  21 e................eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledvakli 85 
                                   e                ee++ ++llaa lHDiG+ +++d             +He +ga + +++          + +++
  gi|14601546|ref|NP_148086.1|  74 EsgvtpstlsdgtledvEEAKAVVLLAAFLHDIGNSVHRD-------------NHELIGAVMSERI----------IDRIV 131
                                   2555555555566667789******************999.............7******666655..........999** PP

                                   HTTCCHHHHHHHH.......H.....HHHCCTSCHHHHHHHHHHHHHH CS
                            HD  86 rehheswegkkrp.......r.....glaerqlslearivklaDrlaa 121
                                   ++ + +w ++kr        +     + ++++l+ ea  vk+aD++++
  gi|14601546|ref|NP_148086.1| 132 SKVFPDWSTRKRVffrsevmHaiyatAPNVKALTVEAGTVKVADATDM 179
                                   ********999999987766156678*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1987.42
//
Query:       gi|14601547|ref|NP_148087.1|  [L=106]
Description: CutA-like protein [Aeropyrum pernix K1]
Scores for 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-34  115.4   0.0    9.4e-34  115.2   0.0    1.0  1  CutA1     CutA1 divalent ion tolerance protein


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 !  115.2   0.0   5.2e-38   9.4e-34       2      98 ..       6     101 ..       5     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 5.2e-38
                                   EEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEE CS
                         CutA1   2 lvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeiia 82 
                                   +vlvtap + + ++lar++ve++laACvn++ +i+S+Y+W+g i+ d+E ll+ikt+eek+++l k+vke+hpy+vpei+a
  gi|14601547|ref|NP_148087.1|   6 VVLVTAP-KGDGDRLAREIVEQRLAACVNVVRGIKSYYWWEGSINLDDEDLLIIKTSEEKLDSLIKAVKEMHPYSVPEILA 85 
                                   7899999.6779********************************************************************* PP

                                   EEESEEEHHHHHHHHH CS
                         CutA1  83 lpieagseaYlkWiee 98 
                                   l++++g+e+Y++W+ +
  gi|14601547|ref|NP_148087.1|  86 LDVSRGNESYVEWVVK 101
                                   *************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 857.76
//
Query:       gi|118431550|ref|NP_148088.2|  [L=464]
Description: dihydrolipoyl dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-62  211.2   3.8    2.4e-62  210.8   3.8    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.1e-33  114.3   0.3    7.5e-33  113.1   0.1    1.8  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    4.3e-22   78.5   7.9    3.7e-21   75.5   0.8    2.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    9.6e-17   61.2   0.4    3.7e-12   46.1   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-10   40.4   1.2    7.2e-06   25.3   0.6    2.7  3  GIDA            Glucose inhibited division protein A
    1.5e-09   37.8   9.7    7.4e-09   35.5   0.8    2.8  3  FAD_oxidored    FAD dependent oxidoreductase
      3e-08   33.8   1.4     0.0014   18.8   0.3    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    9.7e-07   27.8   9.2     0.0032   16.2   0.4    3.3  4  HI0933_like     HI0933-like protein
    5.9e-06   25.6   7.6    1.2e-05   24.6   0.3    2.8  3  FAD_binding_2   FAD binding domain
    6.3e-06   25.9   2.1    9.3e-05   22.1   0.1    2.6  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    9.5e-06   25.4  14.4      0.057   13.0   0.8    4.1  4  DAO             FAD dependent oxidoreductase
    0.00015   21.1   2.1     0.0074   15.6   0.2    3.0  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00052   19.9   2.4     0.0099   15.8   0.1    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.002   17.5   5.8      0.092   12.0   0.6    2.6  3  FAD_binding_3   FAD binding domain
     0.0038   17.7   1.3       0.37   11.2   0.2    2.8  2  NAD_binding_7   Putative NAD(P)-binding
     0.0063   15.6   9.5       0.17   10.9   0.2    3.1  3  Lycopene_cycl   Lycopene cyclase protein
     0.0081   15.4   3.5      0.026   13.8   0.0    2.8  3  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.025   13.5   2.4       0.45    9.3   0.1    2.3  2  Trp_halogenase  Tryptophan halogenase
       0.14   11.5   0.1       0.27   10.6   0.1    1.4  1  ThiF            ThiF family
       0.26   11.3   8.6        2.1    8.3   0.3    3.8  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 !  210.8   3.8   2.7e-65   2.4e-62       1     293 [.       4     314 ..       4     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 2.7e-65
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................... 57 
                                    +d+vv+GgGp+G+ aa ++aq g++v+lve   l+g+c n gc+++kall+ a+    ++                    
  gi|118431550|ref|NP_148088.2|   4 FDLVVVGGGPGGYPAAVRAAQEGLNVALVEmdsLGGECTNYGCIPTKALLHPAGLVASLArlkfvkgsvdvdfkglmewv 83 
                                    589**************************9999**************99998887766667******************* PP

                                    .HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 .evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaeal 136
                                      vvk +++g+ +ll+  +v++ +g++k+     + +   +i y klvlA G sp    ipG+ e  g++    ++   l
  gi|118431550|ref|NP_148088.2|  84 dSVVKGVSNGVSTLLKGYGVEVVKGRAKIRPGVVEVDGSGSIGYSKLVLALGTSPAS--IPGL-EPDGEV--VHNNRTIL 158
                                    *9999***********99********999885544466679***********88866..6999.666677..45566666 PP

                                    CCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 137 klkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekl 216
                                     l  +p r+++vGgGyiGvE+A a+a+lg+evt+ve +drll+++++++s+ +e++l++eGv+++++++v++++++++ +
  gi|118431550|ref|NP_148088.2| 159 GLRRKPGRMLIVGGGYIGVEYATAMARLGVEVTIVELLDRLLPNMQRDFSRVVERRLRAEGVKIHTKSKVEAVERRER-Y 237
                                    66666777******************************************************************9998.6 PP

                                    E.EEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTS.BESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 217 e.vvledgeeidadlvvvavGvrpstelle.eklglelderggivvdefl.rtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                      v+ +   ++++d ++vavG+rp+t  ++ eklg++ld++g+i+vd    +t vpg+ya GDv+   g p la+ A  q
  gi|118431550|ref|NP_148088.2| 238 AvVEVSGVGKMEYDAILVAVGRRPNTGDVGlEKLGVKLDKAGYIQVDGATlETGVPGVYASGDVT---GPPLLAHRAFLQ 314
                                    6588888999******************99*****************7554**************...888888888665 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 ?   -3.0   0.0       9.5   8.5e+03       7      21 ..     238     252 ..     214     254 .. 0.69
   2 !  113.1   0.1   8.4e-36   7.5e-33       1     109 [.     335     444 ..     335     445 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.5
                                    SSSEEEEEES-HHHH CS
                  Pyr_redox_dim   7 tdpevasvGlteeeA 21 
                                      +ev+ vG+ e +A
  gi|118431550|ref|NP_148088.2| 238 AVVEVSGVGKMEYDA 252
                                    445666666666555 PP

  == domain 2  score: 113.1 bits;  conditional E-value: 8.4e-36
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEECTTHHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivGpgageliqel 79 
                                    +p+vv+tdpe+a+vGlt eeA+aag++    ++p++++ r  a +  +++f+K+v+d++++ +lG+h+ +p+a+e+i+e+
  gi|118431550|ref|NP_148088.2| 335 VPAVVYTDPELATVGLTLEEARAAGVDAAETRLPLASLPRVGAIEGcRECFAKVVYDRSSRAILGFHVAAPHASEIIAEA 414
                                    79***************************************999999********************************* PP

                                    HHHHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                  Pyr_redox_dim  80 avaikagltvedladtihihPtlsealkea 109
                                    a+ai++g+t edla tih+hP++sealke 
  gi|118431550|ref|NP_148088.2| 415 ALAIEMGATLEDLALTIHPHPSVSEALKEV 444
                                    ***************************985 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.012        11       2      31 ..       6      35 ..       5      38 .. 0.94
   2 !   75.5   0.8   4.2e-24   3.7e-21       1      74 [.     166     240 ..     166     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                   +vvvGgG  g  +A  +a+ g +V +ve+ 
  gi|118431550|ref|NP_148088.2|  6 LVVVGGGPGGYPAAVRAAQEGLNVALVEMD 35
                                   79*************************986 PP

  == domain 2  score: 75.5 bits;  conditional E-value: 4.2e-24
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.ve 74 
                                    ++++vGgGyig+E+A+a+a+lg +Vt+ve  d+ll+++ +++s++++++l+++g+++++++kve++e  e+  v 
  gi|118431550|ref|NP_148088.2| 166 RMLIVGGGYIGVEYATAMARLGVEVTIVELLDRLLPNMQRDFSRVVERRLRAEGVKIHTKSKVEAVERRERYaVV 240
                                    689****************************************************************99986554 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3   4.3e-05     0.039       1      39 [.       7      44 ..       7      50 .. 0.93
   2 !   46.1   0.0   4.2e-15   3.7e-12     142     305 .]     140     299 ..     116     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyry 39
                                   +++G+GP G  aa+ + + gl ++  +E +++g   ++y
  gi|118431550|ref|NP_148088.2|  7 VVVGGGPGGYPAAVRAAQEGL-NVALVEMDSLGGECTNY 44
                                   79*******************.79*******99988888 PP

  == domain 2  score: 46.1 bits;  conditional E-value: 4.2e-15
                    Pyr_redox_3 142 nipGeeklvkhyskvkefhkya..gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrle 219
                                    +ipG e   ++ ++++ +  ++    +++++Gg+  +v++A+ ++r g eVt+v   + +     +++   + ++e rl+
  gi|118431550|ref|NP_148088.2| 140 SIPGLEPDGEVVHNNRTILGLRrkPGRMLIVGGGYIGVEYATAMARLGVEVTIVELLDRLLP---NMQRDFSRVVERRLR 216
                                    477777655555555555444411679***************************98775544...356666678888887 PP

                    Pyr_redox_3 220 elvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsf..lkkslfeldedgrpvlteeteetn 297
                                    +    e +k++++++v++++++e+ y v + +g    ++d +++a+G +p++    l+k +++ld+ g+++++ +t et 
  gi|118431550|ref|NP_148088.2| 217 A----EGVKIHTKSKVEAVERRER-YAVVEVSGVGKMEYDAILVAVGRRPNTGDvgLEKLGVKLDKAGYIQVDGATLETG 291
                                    6....459************9866.55555555555678999999******97646888********************* PP

                    Pyr_redox_3 298 vpglflaG 305
                                    vpg++  G
  gi|118431550|ref|NP_148088.2| 292 VPGVYASG 299
                                    *****988 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.6     8e-09   7.2e-06       1      55 [.       5      61 ..       5      72 .. 0.84
   2 !   12.6   0.0   6.1e-05     0.055       3      28 ..     168     193 ..     166     219 .. 0.86
   3 ?   -1.8   0.0       1.3   1.2e+03     349     366 ..     287     303 ..     280     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8e-09
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHH CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrE 55
                                   d++V+GgG  G+ AA+ aa+ G++v+L+      +++ + +C p+   +  + lv+ 
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRAAQEGLNVALVemDSLGGECTNYGCIPTKALLHPAGLVAS 61
                                   689*************************76667899********9988766555555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.1e-05
                                    EEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                                     ++GgG  G+e A a+arlG++v+++
  gi|118431550|ref|NP_148088.2| 168 LIVGGGYIGVEYATAMARLGVEVTIV 193
                                    79*********************998 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.3
                                    TSBBSSSBTEEE-CGGGT CS
                           GIDA 349 tLetkkvkgLflAGqinG 366
                                    tLet  v+g+++ G+++G
  gi|118431550|ref|NP_148088.2| 287 TLETG-VPGVYASGDVTG 303
                                    89997.***********9 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.8   8.3e-12   7.4e-09       1      43 [.       5      46 ..       5      73 .. 0.87
   2 !    7.5   0.4    0.0025       2.3       3      29 ..     168     194 ..     167     199 .. 0.92
   3 ?   -1.5   0.1       1.4   1.2e+03      90     125 ..     208     242 ..     204     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 8.3e-12
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv 43
                                   D+vVvGGgp+G+ AA+ Aa++G +v+Lve  + lGG  t+ + 
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRAAQEGLNVALVEM-DSLGGECTNYGC 46
                                   99**************************96.68*****99765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                   FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLve 29 
                                    ++vGGg  Gv  A a ar G +v +ve
  gi|118431550|ref|NP_148088.2| 168 LIVGGGYIGVEYATAMARLGVEVTIVE 194
                                    79************************9 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.4
                   FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtv 125
                                     +v+e  l+ +gv++ +++++++ve+++ r   v+v
  gi|118431550|ref|NP_148088.2| 208 SRVVERRLRAEGVKIHTKSKVEAVERRE-RYAVVEV 242
                                    57888889999**************986.7666666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   1.6e-06    0.0014       1      38 [.       8      44 ..       8      60 .. 0.93
   2 !   13.3   0.0   8.5e-05     0.076       1      31 [.     169     199 ..     169     206 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                   +vG+G +G  aA ++a++g++v l+e+ d+lGG ++ y
  gi|118431550|ref|NP_148088.2|  8 VVGGGPGGYPAAVRAAQEGLNVALVEM-DSLGGECTNY 44
                                   8**************************.69****9987 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.5e-05
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                    IvG+G  G  +A ++a+ g++v+++e  drl
  gi|118431550|ref|NP_148088.2| 169 IVGGGYIGVEYATAMARLGVEVTIVELLDRL 199
                                    9*************************88875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   3.5e-06    0.0032       2      32 ..       5      35 ..       4      40 .. 0.91
   2 ?   -2.7   0.0       1.9   1.7e+03     145     170 ..     117     144 ..     104     152 .. 0.75
   3 ?    1.3   0.2      0.12   1.1e+02       3      31 ..     167     195 ..     166     203 .. 0.90
   4 !   15.6   0.2   5.5e-06    0.0049      95     165 ..     193     260 ..     178     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                   d++v+GgG+ G  aA++aa++g +V+l+e  
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRAAQEGLNVALVEMD 35
                                   89**************************965 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                                    EEE.TTEEEEESEEEE----..SS-GGG CS
                    HI0933_like 145 vktkseeeleadklvlAtGG..lSiPkl 170
                                    v++++++++  +klvlA+G   +SiP l
  gi|118431550|ref|NP_148088.2| 117 VEVDGSGSIGYSKLVLALGTspASIPGL 144
                                    667788999999*****99733467765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.12
                                    EEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                    HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllek 31 
                                    ++++GgG  G+  A ++a+ g +V+++e 
  gi|118431550|ref|NP_148088.2| 167 MLIVGGGYIGVEYATAMARLGVEVTIVEL 195
                                    689***********************996 PP

  == domain 4  score: 15.6 bits;  conditional E-value: 5.5e-06
                                    E-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like  95 eedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    +e  +rl p+    +d  ++ +++l+++gvk++++++v++ve++e     v++++ +++e d++++A+G  
  gi|118431550|ref|NP_148088.2| 193 VELLDRLLPNM--QRDFSRVVERRLRAEGVKIHTKSKVEAVERRERY-AVVEVSGVGKMEYDAILVAVGRR 260
                                    55667777777..67888999********************886555.999999*************9964 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3   1.3e-08   1.2e-05       1      31 [.       5      35 ..       5      44 .. 0.91
   2 ?    4.8   0.3     0.014        12       2      30 ..     167     195 ..     166     199 .. 0.92
   3 ?   -3.9   0.1       6.2   5.6e+03     147     176 ..     211     244 ..     208     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                   D++V+G+G +G+ AA++aa++Gl+va+ve  
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRAAQEGLNVALVEMD 35
                                   89**************************965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.014
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvek 30 
                                     +++G+G  G   A+++a+ G +v++ve 
  gi|118431550|ref|NP_148088.2| 167 MLIVGGGYIGVEYATAMARLGVEVTIVEL 195
                                    59*************************96 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 6.2
                                    HHHHHHTCTEEEEESEEEEEEEECTT....EEEE CS
                  FAD_binding_2 147 lvesarkagvdfqerteadeLivedg....rvtG 176
                                    + +++r+ gv+++++ +++++ ++++    +v+G
  gi|118431550|ref|NP_148088.2| 211 VERRLRAEGVKIHTKSKVEAVERRERyavvEVSG 244
                                    4567777778888888888887765555555555 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 ?    3.0   0.1     0.073        66       4      33 ..       7      36 ..       4      50 .. 0.90
   2 !   22.1   0.1     1e-07   9.3e-05       3      63 ..     167     227 ..     165     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.073
                                   EEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                 UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDide 33
                                   +v+G G  G + a+  a+ g +v +v +d+
  gi|118431550|ref|NP_148088.2|  7 VVVGGGPGGYPAAVRAAQEGLNVALVEMDS 36
                                   79************************9996 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1e-07
                                    EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTT CS
                 UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgr 63 
                                    + ++G GY+G+  a+++a++g+ev++v   ++   +++++ + ++e+ L+    k +++++
  gi|118431550|ref|NP_148088.2| 167 MLIVGGGYIGVEYATAMARLGVEVTIVELLDRLLPNMQRDFSRVVERRLRAEGVKIHTKSK 227
                                    679********************************************99764444443444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.8   6.3e-05     0.057       1      37 [.       5      42 ..       5      46 .. 0.89
   2 ?   -0.4   0.0      0.78     7e+02     139     167 ..      49      85 ..      43     148 .. 0.48
   3 !    9.0   1.5    0.0011      0.95       3      27 ..     168     194 ..     166     197 .. 0.95
   4 !    9.5   0.2   0.00072      0.65     152     201 ..     211     258 ..     204     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37
                                   d+v++GGG  G  +A  +a++g  V+l+e++  +g +++
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRAAQEGlnVALVEMD-SLGGECT 42
                                   89*****************************.6664655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.78
                                    TEEEEEHHHHHHHHHHH.HHHTT-EEEES.......E CS
                            DAO 139 dtgqvdpakltaalara.aealGveileg.......t 167
                                    + + ++pa l+a+lar  + ++ v++ ++       +
  gi|118431550|ref|NP_148088.2|  49 TKALLHPAGLVASLARLkFVKGSVDVDFKglmewvdS 85 
                                    5566677777777776666666665544444444442 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0011
                                    EEECTSHHHHHHHHHHHHTT..EEEEE CS
                            DAO   3 viiGGGiiGlstAyeLarrg..Vtlle 27 
                                    +i+GGG+iG+  A + ar g  Vt++e
  gi|118431550|ref|NP_148088.2| 168 LIVGGGYIGVEYATAMARLGveVTIVE 194
                                    8***************999******98 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00072
                                    HHHHHHHTT-EEEESECEEEEEEEE.TCEEEEEEECTEEE.EEEEEEEE--G CS
                            DAO 152 laraaealGveilegtevtgleeed.gkvwgverttpgen.daadavVnaaG 201
                                    + r+++a Gv+i+++++v+++e+++   v++v   + g    ++da+ +a G
  gi|118431550|ref|NP_148088.2| 211 VERRLRAEGVKIHTKSKVEAVERRErYAVVEV---S-GVGkMEYDAILVAVG 258
                                    568899***************88653333333...2.333236799****99 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.043        39      31      60 ..       6      35 ..       1      41 [. 0.89
   2 !   15.6   0.2   8.3e-06    0.0074      24      69 ..     162     205 ..     150     247 .. 0.79
   3 ?   -1.2   0.0       1.1     1e+03     127     149 ..     416     438 ..     414     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.043
                                   EEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvr 60
                                    +v+GgG  G  A+  a++ g +V +++++
  gi|118431550|ref|NP_148088.2|  6 LVVVGGGPGGYPAAVRAAQEGLNVALVEMD 35
                                   79*******************999998875 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8.3e-06
                                    TCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                    AlaDh_PNT_C  24 pgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                    +  +p+++l++GgG  G++ + + ++lg +Vt++++  + l +++ 
  gi|118431550|ref|NP_148088.2| 162 R--KPGRMLIVGGGYIGVEYATAMARLGVEVTIVELLDRLLPNMQR 205
                                    4..79*****************************988777776666 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                                    TTGGGT-SBTT--TBBTTSEEEE CS
                    AlaDh_PNT_C 127 vAidqGGnvetsrltthgepvve 149
                                    +Ai+ G ++e+++lt h +p v+
  gi|118431550|ref|NP_148088.2| 416 LAIEMGATLEDLALTIHPHPSVS 438
                                    79*************99999876 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 ?    3.8   0.3     0.053        47       3      31 ..       7      35 ..       5      41 .. 0.92
   2 !   15.8   0.1   1.1e-05    0.0099       4      56 ..     169     221 ..     166     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.053
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                        3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdis 31
                                    v+G G  G   a  +a++gl+V lv+++
  gi|118431550|ref|NP_148088.2|  7 VVVGGGPGGYPAAVRAAQEGLNVALVEMD 35
                                   69************************986 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-05
                                    EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                        3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                                    ++G G +G + a+++a+ g+eV++v+  ++ l + ++  ++ +e+  +++ +k
  gi|118431550|ref|NP_148088.2| 169 IVGGGYIGVEYATAMARLGVEVTIVELLDRLLPNMQRDFSRVVERRLRAEGVK 221
                                    8**************************99999999988888888877766666 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2    0.0027       2.4       3      32 ..       5      34 ..       3      37 .. 0.91
   2 !   12.0   0.6    0.0001     0.092       5      39 ..     168     202 ..     166     211 .. 0.88
   3 ?   -1.2   0.0         1   9.3e+02     104     135 ..     204     235 ..     199     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0027
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                   d ++VG+Gp G  +a   ++ G +v lve 
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRAAQEGLNVALVEM 34
                                   678************************995 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                                    EEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39 
                                    lIVG+G  G+  a+ +++ Gv+v++ve  ++  ++
  gi|118431550|ref|NP_148088.2| 168 LIVGGGYIGVEYATAMARLGVEVTIVELLDRLLPN 202
                                    8*************************987776655 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHTEEETCSEEEECCEECC CS
                  FAD_binding_3 104 qteleriLvehaeerglqvrfktevesleqde 135
                                    q ++ r+++ +++++g++++ k +ve++e+ e
  gi|118431550|ref|NP_148088.2| 204 QRDFSRVVERRLRAEGVKIHTKSKVEAVERRE 235
                                    888999999999999*******9999998765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.049        44       7      40 ..       3      36 ..       1      93 [. 0.75
   2 !   11.2   0.2   0.00041      0.37       9      37 ..     166     194 ..     159     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.049
                  NAD_binding_7  7 gkkvlvvGgGevAarkvrklleagakvtvvapev 40
                                   +   +vvGgG+ ++  + + +++g +v +v  ++
  gi|118431550|ref|NP_148088.2|  3 RFDLVVVGGGPGGYPAAVRAAQEGLNVALVEMDS 36
                                   56789***********************998775 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00041
                  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvva 37 
                                    ++l+vGgG ++ + +  +++ g +vt+v 
  gi|118431550|ref|NP_148088.2| 166 RMLIVGGGYIGVEYATAMARLGVEVTIVE 194
                                    89*************************85 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00019      0.17       1      32 [.       5      34 ..       5      44 .. 0.93
   2 ?    3.6   0.2     0.031        28       3      36 ..     168     199 ..     167     205 .. 0.87
   3 !    5.9   0.5    0.0062       5.5      87     143 ..     205     259 ..     202     278 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                   D+vv+G+Gp g   A r   a+ gl+v l+e 
  gi|118431550|ref|NP_148088.2|  5 DLVVVGGGPGGYPAAVRA--AQEGLNVALVEM 34
                                   9*****************..**********85 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.031
                  Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                    +++G+G  g+  A  +  a+ g++v+++e  + l
  gi|118431550|ref|NP_148088.2| 168 LIVGGGYIGVEYATAM--ARLGVEVTIVELLDRL 199
                                    79**************..**********966555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0062
                  Lycopene_cycl  87 krlkeellerlvengvk.lleakvesveeeeageslvvleggrkirarlvvdarglas 143
                                    +++ +++++rl  +gvk  +++kve+ve  e    +v ++g  k++  ++++a g  +
  gi|118431550|ref|NP_148088.2| 205 RDFSRVVERRLRAEGVKiHTKSKVEAVERRER-YAVVEVSGVGKMEYDAILVAVG--R 259
                                    68999*******777761579********999.6666666666666666666666..3 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.9e-05     0.026      18      56 ..       4      40 ..       1      55 [. 0.86
   2 ?    0.8   0.3      0.27   2.4e+02      21      48 ..     168     194 ..     165     197 .. 0.93
   3 ?   -1.3   0.0       1.1     1e+03     101     135 ..     208     245 ..     205     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56
                                    D+v+vG+G+ G  aa   a++ +l+va++e   s+GG 
  gi|118431550|ref|NP_148088.2|  4 FDLVVVGGGPGGYPAAVRAAQE-GLNVALVEMD-SLGGE 40
                                   59********************.********86.66664 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                                    EEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4  21 vivGaGssGLtaayylakkpdlkvaile 48 
                                    +ivG+G  G+  a  +a+  +++v+i+e
  gi|118431550|ref|NP_148088.2| 168 LIVGGGYIGVEYATAMARL-GVEVTIVE 194
                                    79****************9.9***9998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                                    HHHHHHHHTSTTEEEEESEEEEEEEEET..B.TEEEEE CS
                           Thi4 101 stllskvlqlanvkllnavaveDlivre..g.egvaGv 135
                                    s+++ + l   +vk+ +   ve +  re    ++v+Gv
  gi|118431550|ref|NP_148088.2| 208 SRVVERRLRAEGVKIHTKSKVEAVERREryAvVEVSGV 245
                                    778889999999***99999999998885523566665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0005      0.45       2      37 ..       6      38 ..       5      49 .. 0.87
   2 ?    3.8   0.3     0.024        21       2      32 ..     167     194 ..     166     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0005
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                 Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                   +v+vGGG+ G+ aA   a+ +   l+v lve + +g
  gi|118431550|ref|NP_148088.2|  6 LVVVGGGPGGYPAAVRAAQEG---LNVALVEMDSLG 38
                                   79***********98777666...9******99886 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.024
                                    EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                 Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlve 32 
                                    ++ivGGG  G   A+a+a+ +   +evt+ve
  gi|118431550|ref|NP_148088.2| 167 MLIVGGGYIGVEYATAMARLG---VEVTIVE 194
                                    68******************9...8999998 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0003      0.27      19      43 ..     165     189 ..     155     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                                    SEEEEE--SHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  19 skvllvGaGglGsellknLalsGvg 43 
                                     ++l+vG G +G e ++++a++Gv+
  gi|118431550|ref|NP_148088.2| 165 GRMLIVGGGYIGVEYATAMARLGVE 189
                                    799********************96 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 ?    4.5   0.1     0.034        31       1      40 [.       7      40 ..       7      55 .. 0.85
   2 ?    0.3   0.0      0.68   6.1e+02     105     155 ..      84     136 ..      79     137 .. 0.68
   3 ?    0.2   0.2      0.73   6.6e+02       2      32 ..     169     194 ..     168     203 .. 0.80
   4 ?    8.3   0.3    0.0024       2.1     104     155 ..     207     259 ..     203     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.034
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                   ++vG+Gp G  ++ r +++      l++ l++ +++g g 
  gi|118431550|ref|NP_148088.2|  7 VVVGGGPGGYPAAVRAAQE-----GLNVALVEMDSLG-GE 40
                                   69************99998.....5999999999887.54 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.68
                  NAD_binding_9 105 eellarlpegvtvevhraevvdleeradgq..avlladgaslaadaVvLAlGh 155
                                    +++++ +++gv+  +    v+ ++ ra+ +   v  ++  s+ + ++vLAlG 
  gi|118431550|ref|NP_148088.2|  84 DSVVKGVSNGVSTLLKGYGVEVVKGRAKIRpgVVEVDGSGSIGYSKLVLALGT 136
                                    667777777777666666666666666665524555555899*********96 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.73
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfd 32 
                                    ivG+G  G+  ++++++       +e+t+++
  gi|118431550|ref|NP_148088.2| 169 IVGGGYIGVEYATAMARLG-----VEVTIVE 194
                                    9*********999999984.....5555554 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0024
                  NAD_binding_9 104 feellarlpegvtvevhra.evvdleeradgqavlladg.aslaadaVvLAlGh 155
                                    f+++++r  +   v++h++ +v+++e+r +++av++ +g  ++++da+ +A+G 
  gi|118431550|ref|NP_148088.2| 207 FSRVVERRLRAEGVKIHTKsKVEAVERR-ERYAVVEVSGvGKMEYDAILVAVGR 259
                                    6677776655567888865166666655.6666666666489**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 3571.52
//
Query:       gi|14601549|ref|NP_148089.1|  [L=412]
Description: branched-chain alpha-keto acid dehydrogenase E2 [Aeropyrum pernix K1]
Scores for 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-85  284.6   0.0    6.5e-85  284.3   0.0    1.1  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    2.6e-19   68.8   0.6    4.7e-19   68.0   0.6    1.4  1  Biotin_lipoyl    Biotin-requiring enzyme
    1.2e-13   51.2   5.8    2.1e-13   50.4   2.3    3.2  4  E3_binding       e3 binding domain
    4.4e-08   32.8   0.4     0.0001   22.1   0.0    2.5  2  Biotin_lipoyl_2  Biotin-lipoyl like
    0.00028   21.6   1.1      0.021   15.5   0.1    2.6  2  HlyD_3           HlyD family secretion protein
  ------ inclusion threshold ------
       0.18   11.3   2.5       0.25   10.8   2.5    1.2  1  DUF2868          Protein of unknown function (DUF2868)


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 !  284.3   0.0   2.2e-88   6.5e-85       2     232 ..     176     405 ..     175     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 284.3 bits;  conditional E-value: 2.2e-88
                                   XXXXXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG- CS
                  2-oxoacid_dh   2 keeervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelna 82 
                                   ++eer+p++gi++ +a++++ sk++iph+++ +evd+t+l +lr+ lk++++++  ++lt+l+f+ kava+A++++P +n+
  gi|14601549|ref|NP_148089.1| 176 EAEERIPVRGIKRSMAQSMSLSKSKIPHAYIAEEVDFTELSKLREALKRDAEEKG-VRLTYLPFVFKAVAKAIRKYPLVNS 255
                                   6799***********************************************8655.6************************ PP

                                   EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE--------- CS
                  2-oxoacid_dh  83 svdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGmlGvts 163
                                   ++dee+ eivvkk+vniG+Av+tp+GL+vPv+kn++kk+l  ia+e+++l+ kare +l+ e+++g+tfti+N+G++G+  
  gi|14601549|ref|NP_148089.1| 256 EFDEEKMEIVVKKAVNIGFAVDTPHGLVVPVVKNVEKKGLFAIAREIADLTAKAREMRLSLEEVSGATFTITNVGSIGSVI 336
                                   ********************************************************************************* PP

                                   ------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHXXXX CS
                  2-oxoacid_dh 164 ftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpeell 232
                                   + P+i pp+vaIlgv+r+ erpv+++gel++rk+  +sls+DHR+++Ga a rFl ++k+llenp++l+
  gi|14601549|ref|NP_148089.1| 337 GFPVIYPPNVAILGVHRLVERPVYVDGELKPRKIGFVSLSFDHRALEGAYATRFLMEVKRLLENPALLF 405
                                   *****************************************************************9987 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.6   1.6e-22   4.7e-19       2      73 .]       6      78 ..       5      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.6e-22
                                  EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                 Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                  ++k+P+iGe ++eg +ve+lv++G  Vk+  +l+ v + K+++ei++p +G+v+ +l+k Gd v vgd++++i
  gi|14601549|ref|NP_148089.1|  6 QVKLPDIGEGIAEGeIVEWLVEEGAVVKQFSPLVRVLTAKATVEIPSPYTGRVVRLLAKPGDVVRVGDPIIEI 78
                                  89********************************************************************997 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.6   4.8e+03       4      10 ..      36      42 ..      35      52 .. 0.77
   2 !   50.4   2.3   6.9e-17   2.1e-13       1      36 []     120     155 ..     120     155 .. 0.97
   3 ?   -2.1   0.0       1.7   5.2e+03      11      18 ..     226     233 ..     223     236 .. 0.81
   4 ?   -1.3   0.0      0.98   2.9e+03      11      23 ..     309     321 ..     309     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                                  -HHHHHH CS
                    E3_binding  4 sPaaRkl 10
                                  sP++R l
  gi|14601549|ref|NP_148089.1| 36 SPLVRVL 42
                                  9***976 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 6.9e-17
                                   SBE-HHHHHHHHHCT--TTTS---CTTTBE-HHHHC CS
                    E3_binding   1 vlAsPaaRklAkelGidLsdvkGtGpgGRItkeDVl 36 
                                   v+A P++R+lA++lG+dL+ v GtGp+G It++DV+
  gi|14601549|ref|NP_148089.1| 120 VRAPPRVRRLARQLGVDLARVRGTGPRGAITEDDVR 155
                                   789********************************6 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                                   HHHCT--T CS
                    E3_binding  11 AkelGidL 18 
                                   A+e+G+ L
  gi|14601549|ref|NP_148089.1| 226 AEEKGVRL 233
                                   99***976 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.98
                                   HHHCT--TTTS-- CS
                    E3_binding  11 AkelGidLsdvkG 23 
                                   A+e+ ++L++v+G
  gi|14601549|ref|NP_148089.1| 309 AREMRLSLEEVSG 321
                                   89*********76 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00068         2      10      26 ..      18      34 ..      14      34 .. 0.93
   2 !   22.1   0.0   3.4e-08    0.0001       2      37 ..      47      82 ..      45      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00068
               Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVka 26
                                   G +++++V++G +Vk+
  gi|14601549|ref|NP_148089.1| 18 EGEIVEWLVEEGAVVKQ 34
                                  599*************7 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 3.4e-08
               Biotin_lipoyl_2  2 vvsIaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                  +v+I +p  GrV++l+ k G++V  Gd ++e++ ++
  gi|14601549|ref|NP_148089.1| 47 TVEIPSPYTGRVVRLLAKPGDVVRVGDPIIEIEVEE 82
                                  589999**************************9765 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.014        41       8      42 ..      19      50 ..      17      52 .. 0.81
   2 !   15.5   0.1   6.9e-06     0.021       2      31 ..      50      79 ..      49      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                        HlyD_3  8 Gvvvelnveegevvqagdelleiippdtllveakv 42
                                  G++ve+ veeg vv +  +l++++   t+++++++
  gi|14601549|ref|NP_148089.1| 19 GEIVEWLVEEGAVVKQFSPLVRVL---TAKATVEI 50
                                  99*********************9...34444444 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.9e-06
                        HlyD_3  2 lrApvdGvvvelnveegevvqagdelleii 31
                                  + +p++G+vv l +++g+vv+ gd++ ei 
  gi|14601549|ref|NP_148089.1| 50 IPSPYTGRVVRLLAKPGDVVRVGDPIIEIE 79
                                  569************************995 PP

>> DUF2868  Protein of unknown function (DUF2868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.5   8.5e-05      0.25     144     275 ..      41     191 ..      37     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.5e-05
                       DUF2868 144 ralarlpldlslpgyqaLlarlqtpsletgvnda................aapePeaapepkaeaepepasep.advlele 207
                                     +a++++++  p++ ++++ l++p    +v d+                aa++P+a++ep ++ e+++++ + a ++ ++
  gi|14601549|ref|NP_148089.1|  41 VLTAKATVEIPSPYTGRVVRLLAKPGDVVRVGDPiieieveegeapkapeAAEKPSATVEPPKAEEAAAPPPQaAPAILVR 121
                                   455666666669**********999999999999*********96666666666666666555444444333344455555 PP

                       DUF2868 208 lderlaelelraglgvrvaasaadgGrld.drearsrvlaslaesaparvl..llvdas.qpPdretlrfLr 275
                                    + r   ++l+++lgv++a++   g r   ++++++r++a la +++ +    ++ +a+ + P+r++ r ++
  gi|14601549|ref|NP_148089.1| 122 APPRV--RRLARQLGVDLARVRGTGPRGAiTEDDVRRAAAMLATAPKPEAPppVAEEAEeRIPVRGIKRSMA 191
                                   55555..68888899999988888877766677677777777776443333337777752578888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3090.01
//
Query:       gi|14601550|ref|NP_148090.1|  [L=325]
Description: pyruvate dehydrogenase E1 subunit beta [Aeropyrum pernix K1]
Scores for complete 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  171.7   0.0    1.7e-50  171.1   0.0    1.1  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.7e-39  134.5   0.0    4.8e-39  133.1   0.0    1.7  2  Transketolase_C  Transketolase, C-terminal domain
     0.0051   17.1   0.0      0.011   16.0   0.0    1.6  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 !  171.1   0.0   2.9e-54   1.7e-50       3     176 ..       4     178 ..       3     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 2.9e-54
                                   EEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEE CS
                  Transket_pyr   3 iawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqF 81 
                                   +++ +a++ al e++++d++vv++g+Dv+  gg+f+v++gl +++ge+rvid++++E ++++fa+G+a+ g l++++e+qF
  gi|14601550|ref|NP_148090.1|   4 MNMVQALNTALREEMRRDKSVVVLGEDVGrrGGVFLVTEGLIDEFGEERVIDTPLTEMGIVAFAIGMAMYG-LRPVAEIQF 83 
                                   67899************************99****************************************.9******** PP

                                   HHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS CS
                  Transket_pyr  82 gdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairr 160
                                    dF+  A  qi++++a  + +++g+++v++v+r p+  g +G  h+s++ e ++ ++pgl+vv+Ps+p+++k+ll+  ir 
  gi|14601550|ref|NP_148090.1|  84 IDFIYEAfdQIVNNAAWYRFRSGGMYNVPLVIRGPCCGGIRGGMHHSQSNEPYFIHTPGLYVVMPSTPYDAKGLLKSSIR- 163
                                   ********************************************************************************. PP

                                   SS.SEEEEEE-SSEEC CS
                  Transket_pyr 161 edrkPvvlrlpksllr 176
                                    +++ v++++pks +r
  gi|14601550|ref|NP_148090.1| 164 -SDDAVIFLEPKSIYR 178
                                   .668*********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 ?   -1.9   0.0      0.49   2.9e+03      49      76 ..      10      37 ..       4      58 .. 0.75
   2 !  133.1   0.0     8e-43   4.8e-39       1     124 []     194     315 ..     194     315 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.49
                                  HHHHHHHHHHHHHSEEEEEEEEESTTSH CS
               Transketolase_C 49 lDketilesvkktgrlvvveeavkrgGi 76
                                  l +++ +e+ + +  +v+ e+  +rgG+
  gi|14601550|ref|NP_148090.1| 10 LNTALREEMRRDKSVVVLGEDVGRRGGV 37
                                  5555566666777777888888888886 PP

  == domain 2  score: 133.1 bits;  conditional E-value: 8e-43
                                   TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTT.TTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHH CS
               Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLeke.gisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsev 80 
                                   g+a++++eg+dvtlv++G+mv+ a eAae L+++ g+s+e++dlrt++p+Dk+++ +s++ktgrlv+v+ea+k+ G g+e+
  gi|14601550|ref|NP_148090.1| 194 GQARLVQEGSDVTLVTWGAMVHLAKEAAELLREKrGWSIEIIDLRTLQPWDKDMVVKSLEKTGRLVIVHEARKILGPGAEI 274
                                   899****************************9999********************************************** PP

                                   HHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
               Transketolase_C  81 aaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                   aa+++e+++d l +pvkrv+ +d+  p++  + ek+++++ +ki
  gi|14601550|ref|NP_148090.1| 275 AAYISENYIDLLRGPVKRVASYDT--PYP-LAHEKLYLPNLAKI 315
                                   ************************..666.66899999998876 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 !   16.0   0.0   1.8e-06     0.011       2      65 ..     204     268 ..     203     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
                                   SEEEEE-STHHHHHHHHHHHHHH.TT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT CS
                       PFOR_II   2 evvivamGsvagtaksavdelRe.egikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfg 65 
                                   +v +v+ G+++  ak+a++ lRe +g ++ ++ lrtl P  ++ + + l+k+ ++v +  + ++ 
  gi|14601550|ref|NP_148090.1| 204 DVTLVTWGAMVHLAKEAAELLREkRGWSIEIIDLRTLQPWDKDMVVKSLEKTGRLVIVHEARKIL 268
                                   899*******************736********************99999987766665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2579.01
//
Query:       gi|118431551|ref|NP_148091.2|  [L=377]
Description: pyruvate dehydrogenase E1 subunit alpha [Aeropyrum pernix K1]
Scores for 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-82  274.4   0.0    1.1e-81  274.0   0.0    1.1  1  E1_dh           Dehydrogenase E1 component
     0.0046   16.2   0.0      0.015   14.5   0.0    1.7  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
      0.024   14.4   0.8       0.48   10.2   0.5    2.6  2  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 !  274.0   0.0   1.9e-85   1.1e-81       2     296 ..      43     336 ..      42     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 274.0 bits;  conditional E-value: 1.9e-85
                                    HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TTTSS CS
                          E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvkgkg 81 
                                    + ++ +rv+d+   +++r +++ + +++ gqea++vg+a+ l ++D+++++YRe g  l+rg+s eeil     ++++ +
  gi|118431551|ref|NP_148091.2|  43 TYMVRARVIDSWLLKLQRMGKVALHAPNKGQEAVAVGAAKPLRRDDWVFPSYRELGAYLVRGMSEEEILDRALANADDPL 122
                                    568999*************************************************************************9 PP

                                    GTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEE CS
                          E1_dh  82 gsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNN 161
                                    ++     +++++ +++++  +vg q p+  G+a+a+k+ g ++v+++++GDgA++ Gd++++ln+a ++k+p+++v++NN
  gi|118431551|ref|NP_148091.2| 123 KGSDFAIFGNRKYNLVPAPVPVGNQIPISVGAAYAMKYLGRDTVTLTFFGDGATSRGDFHAGLNFAGVFKVPAVLVIQNN 202
                                    9999555599999******************************************************************* PP

                                    SEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSH CS
                          E1_dh 162 kygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrt 241
                                    +++is+++++++a+++la ++ ++g+pg+r+dgnD++ vy+ v  Aae ar+g gp+lie+vtYR+g+H++ Ddps+yr 
  gi|118431551|ref|NP_148091.2| 203 QWAISVPRARQTAAPSLAVKGLAYGVPGVRIDGNDVMVVYKIVSDAAEKARRGGGPTLIEAVTYRLGPHTTADDPSRYR- 281
                                    *******************************************************************************. PP

                                    HHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                          E1_dh 242 reeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskke 296
                                    + e e + +  +p+ r+++++ + g+++e+e   ie+e + +vee v+k+ +k+ 
  gi|118431551|ref|NP_148091.2| 282 TSEEERIMERYEPLRRMRKFMESMGILTEKEALSIEEEWNSKVEEIVRKVLAKPP 336
                                    66777777888**************************************998875 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 !   14.5   0.0   2.6e-06     0.015     116     176 ..     147     207 ..     144     214 .. 0.93
   2 ?   -1.5   0.0      0.19   1.1e+03     245     272 ..     233     264 ..     209     265 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-06
                 DXP_synthase_N 116 sisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsis 176
                                     i +++G a a ++ g+++ +++  GDga + G  + +ln +g  k   ++++ +N+++is
  gi|118431551|ref|NP_148091.2| 147 QIPISVGAAYAMKYLGRDTVTLTFFGDGATSRGDFHAGLNFAGVFKVPAVLVIQNNQWAIS 207
                                    577789*******************************************9999****9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.19
                 DXP_synthase_N 245 idGhdleelikvleevkkl....kgpvllhvv 272
                                    idG+d+  + k+++++ +      gp+l+  v
  gi|118431551|ref|NP_148091.2| 233 IDGNDVMVVYKIVSDAAEKarrgGGPTLIEAV 264
                                    99***999999887654431222667777766 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 ?   10.2   0.5     8e-05      0.48      29      90 ..     143     210 ..     128     263 .. 0.63
   2 ?   -2.3   0.0      0.56   3.4e+03     112     142 ..     297     331 ..     278     335 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8e-05
                                    -TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHH CS
                   TPP_enzyme_C  29 tmGyglpaAiGakla....kpdrevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtgg 90 
                                      G+++p+++Ga+ a     +d     + GDG++     +  l  a   ++p ++v+ nN++   + +
  gi|118431551|ref|NP_148091.2| 143 PVGNQIPISVGAAYAmkylGRDTVTLTFFGDGATSRGdfHAGLNFAGVFKVPAVLVIQNNQWAISVPR 210
                                    6799*********9643323466778999****87666467788888889999999999998755444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                                    -HHHHHHHTTSEEE....EESSH.HHHHHHHHHHH CS
                   TPP_enzyme_C 112 dfaklaealGakga....rvekadveeleealkea 142
                                    ++ k++e++G+       ++e++  +++ee++++ 
  gi|118431551|ref|NP_148091.2| 297 RMRKFMESMGILTEkealSIEEEWNSKVEEIVRKV 331
                                    67788888888754454555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2747.50
//
Query:       gi|118431552|ref|NP_148093.2|  [L=389]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-45  153.6   0.7    6.1e-45  153.1   0.7    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.6e-33  114.3   0.1    1.3e-32  112.8   0.1    1.8  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    8.5e-24   83.6   0.0    1.5e-23   82.8   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.5e-16   59.3   0.3    9.5e-16   58.3   0.1    1.7  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.12   12.0   0.0        1.2    8.8   0.0    2.2  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 !  153.1   0.7   1.7e-48   6.1e-45       1     147 [.     234     381 ..     234     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 1.7e-48
                                    TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                  Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                    g Gf+++m+tln +R+++ a  lg++++a++ al++a +r++ g+p+i+hq v+ ++aem ++le +rllvy+aa++ld+
  gi|118431552|ref|NP_148093.2| 234 GGGFKLVMHTLNEGRISTSASGLGVMQAAFDAALKHAGERESMGRPIIEHQMVSSMIAEMLVRLETSRLLVYTAAHKLDT 313
                                    67****************************************************************************** PP

                                    ----.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHH CS
                  Acyl-CoA_dh_1  81 gkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiar 147
                                    + pd  + as+aKl ++ + +++++ amq+lGg Gy++e  ver+yrd+++ +ig+Gt+e+qr+++ +
  gi|118431552|ref|NP_148093.2| 314 NSPDyIKYASLAKLHTATAGVDLVRMAMQVLGGIGYSRESDVERYYRDIKMIEIGDGTNEVQRMVLTK 381
                                    ****************************************************************9887 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 !  112.8   0.1   3.6e-36   1.3e-32       4     112 ..      15     123 ..      12     124 .. 0.96
   2 ?   -3.3   0.0         4   1.4e+04      97     112 ..     370     385 ..     368     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 3.6e-36
                                    HHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHH CS
                  Acyl-CoA_dh_N   4 qealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllg 83 
                                     +a+r++vrefae+++ap+a+e+d+++++p++l+++ ae+G++++ vpeeygG gl+ le+++++eel+ra++g++l+  
  gi|118431552|ref|NP_148093.2|  15 VRAVRESVREFAEKKVAPKAREIDATNTVPESLLREGAEMGFFALRVPEEYGGPGLSLLESVVAIEELSRASSGYGLIAV 94 
                                    689**********************9***************************************************888 PP

                                    HHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  84 vhsslvapailrfGteeqkrryLpklasg 112
                                    v+ s+v+++il+f++ee k++yL +la+g
  gi|118431552|ref|NP_148093.2|  95 VSGSMVVHPILKFASEEVKEKYLSRLAKG 123
                                    88888889*******************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                                    S-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  97 GteeqkrryLpklasg 112
                                    Gt e +r  L k+++g
  gi|118431552|ref|NP_148093.2| 370 GTNEVQRMVLTKFLQG 385
                                    8999999999999987 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 !   82.8   0.0   4.2e-27   1.5e-23       1      97 []     127     222 ..     127     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 4.2e-27
                                    EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE---- CS
                  Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvrrie 79 
                                    afalTEp  G+dvas+ +t+a+r+ggeyv++G+Ki+itn+a+a++++v art+k + r+rg+sl++v+r++  v+v+++ 
  gi|118431552|ref|NP_148093.2| 127 AFALTEPCCGTDVASLHMTTAKREGGEYVVSGQKIFITNSAYADFFIVAARTGKLEeRHRGISLLIVDRSDC-VEVSKL- 204
                                    79****************9********************************999999***********8776.9**9*9. PP

                                    -BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  80 eklGlrglptgelvfedv 97 
                                    e +G+rg  t+ ++f+d+
  gi|118431552|ref|NP_148093.2| 205 EMMGYRGSGTSIVYFNDC 222
                                    58**************97 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.9     1e+04      36      53 ..      22      39 ..      14      48 .. 0.55
   2 !   58.3   0.1   2.6e-19   9.5e-16       2     127 ..     250     366 ..     249     373 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.9
                                   --HHHHHHHHHHHHHHHH CS
                  Acyl-CoA_dh_2 36 ddpatqlalaeaaarldA 53
                                    ++ ++ ++a  a ++dA
  gi|118431552|ref|NP_148093.2| 22 VREFAEKKVAPKAREIDA 39
                                   344455555555555555 PP

  == domain 2  score: 58.3 bits;  conditional E-value: 2.6e-19
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH CS
                  Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedra 81 
                                    + +a  lG+ +aa+++++++a+er +   g+++ +++++   +ae+  rl++ r+l++ aa +     +++++   +  +
  gi|118431552|ref|NP_148093.2| 250 STSASGLGVMQAAFDAALKHAGERES--MGRPIIEHQMVSSMIAEMLVRLETSRLLVYTAAHK----LDTNSP---DYIK 320
                                    568999********************..9*********************************9....555554...889* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                  Acyl-CoA_dh_2  82 earraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                     a++a++++++  ++ v++++++ Gg ++  es ++R++RD+++++
  gi|118431552|ref|NP_148093.2| 321 YASLAKLHTATAGVDLVRMAMQVLGGIGYSRESDVERYYRDIKMIE 366
                                    ******************************************9986 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 ?    8.8   0.0   0.00033       1.2     179     208 ..     154     183 ..     137     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00033
                                    EEEEEEEEEEE-.--SSEEEE---SS-..T CS
                         HpaB_N 179 ivVrGakvlaTgaaladeilvlptramlke 208
                                     vV+G k+++T++a+ad ++v+    +l+e
  gi|118431552|ref|NP_148093.2| 154 YVVSGQKIFITNSAYADFFIVAARTGKLEE 183
                                    59******************9987444344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2922.45
//
Query:       gi|118431553|ref|NP_148094.2|  [L=322]
Description: transport system kinase [Aeropyrum pernix K1]
Scores for complete 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-117  390.0   2.0   4.6e-117  389.8   2.0    1.1  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    1.8e-07   30.9   0.4    7.8e-07   28.8   0.4    2.0  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    2.3e-05   24.3   0.2    7.5e-05   22.6   0.0    1.8  2  MobB             Molybdopterin guanine dinucleotide synthesis
      4e-05   23.7   0.0    0.00014   21.9   0.0    1.9  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00011   22.1   0.0    0.00025   20.9   0.0    1.6  2  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00023   20.9   0.2     0.0013   18.4   0.2    2.0  1  SRP54            SRP54-type protein, GTPase domain
    0.00034   20.6   0.1    0.00076   19.4   0.1    1.5  1  NTPase_1         NTPase
    0.00061   19.6   0.1     0.0014   18.4   0.1    1.5  1  AAA_30           AAA domain
     0.0029   18.1   0.2      0.012   16.1   0.2    2.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0051   16.9   0.0      0.016   15.3   0.0    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
      0.006   17.0   0.7      0.017   15.5   0.1    1.9  2  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.1   0.1       0.02   14.2   0.1    1.5  1  MipZ             ATPase MipZ
      0.013   15.8   0.0      0.029   14.7   0.0    1.5  1  AAA_22           AAA domain
      0.014   14.9   0.0       0.83    9.2   0.0    2.2  2  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.021   14.7   0.0      0.041   13.8   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
       0.03   13.5   0.0      0.055   12.7   0.0    1.4  1  NB-ARC           NB-ARC domain
       0.04   14.1   0.0       0.08   13.1   0.0    1.5  1  AAA_33           AAA domain
      0.041   13.2   0.0      0.075   12.4   0.0    1.4  1  ATPase           KaiC
      0.045   13.7   0.4       0.39   10.6   0.0    2.6  3  Ploopntkinase3   P-loop Nucleotide Kinase3
      0.045   14.3   0.0      0.082   13.4   0.0    1.4  1  ABC_tran         ABC transporter
      0.084   12.8   0.0        0.5   10.3   0.0    2.1  2  RsgA_GTPase      RsgA GTPase
        0.1   11.5   0.0       0.17   10.8   0.0    1.2  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.14   12.2   0.0       0.33   11.0   0.0    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.16   12.6   1.4       0.23   12.0   0.1    2.0  1  AAA_18           AAA domain
       0.19   12.0   0.9        2.3    8.4   0.1    2.4  2  AAA_28           AAA domain


Domain annotation for each model (and alignments):
>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.8   2.0  6.4e-120  4.6e-117       1     266 [.      19     286 ..      19     287 .. 0.98

  Alignments for each domain:
  == domain 1  score: 389.8 bits;  conditional E-value: 6.4e-120
                                    HHHHHHHHH--SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------------- CS
                           MeaB   1 LaraitlveserpeakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDk 80 
                                    L+r++tlve+  +ea ellerl+++aGraqv+G+tG+PGaGkstlv+++++ lrrrG+rvav+a+DP+spf+GGsi+GD+
  gi|118431553|ref|NP_148094.2|  19 LGRLLTLVENPGSEAVELLERLSSRAGRAQVIGFTGIPGAGKSTLVSRVITGLRRRGYRVAVVAIDPTSPFSGGSIMGDR 98 
                                    78****************************************************************************** PP

                                    ---HCCCTSTTEEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESSTTHHHHHHTT-SEEEEEEESSTTTTTTT CS
                           MeaB  81 lRleelavdegvfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGvGqsevdvaevvdtfvvlllpeaGDelqg 160
                                    lR++e+a+d+gvfiRs+p+rG++GGl++++++++++++a+G+D+++ietvGvGqsevd++++++t++v+++p+aGD++q+
  gi|118431553|ref|NP_148094.2|  99 LRMQEHAADPGVFIRSIPTRGIKGGLSMAALAMIEVFDAMGYDKIIIETVGVGQSEVDIINAAHTIIVVTMPGAGDDVQA 178
                                    ******************************************************************************** PP

                                    --CCCHHH-SEEEEE---HHHHHHHHHHHHHHHHHCSTT..BTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHH CS
                           MeaB 161 ikkGileiaDiivvnkaDkkeaekaarelraaleleeek..ekeWrpkvlktsavegeGidelvdaieehrevlkktGll 238
                                    +k+G++ei+Di+vvnk+Dk+ea+k+a++l++ale+e+    e++Wrpk++ktsav g+Gid lvdaieeh++++++tGl+
  gi|118431553|ref|NP_148094.2| 179 LKAGVMEIGDIYVVNKSDKPEANKTAAYLQFALEKEDIGrrESGWRPKLVKTSAVLGQGIDPLVDAIEEHWRFARNTGLH 258
                                    ***********************************99865599************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHC-H CS
                           MeaB 239 ekrrrerakeelrelvedellkrvkaae 266
                                    +++ ++r+   +++l+e+ l+++v+aa+
  gi|118431553|ref|NP_148094.2| 259 TEKVKARRLLLAKMLAESLLSSKVSAAM 286
                                    ***********************99987 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.4   1.1e-09   7.8e-07       2     158 ..      49     203 ..      48     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.1e-09
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCC....HCCCT.......EEEETTTTECCHCTT-H CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaell....retgve......ivelenGciCctlredl 69 
                                    v+++tG +G+GK+tL+++++   +r+g+++av+  +  +    ++++    r ++        i ++ + +i   l+  +
  gi|118431553|ref|NP_148094.2|  49 VIGFTGIPGAGKSTLVSRVItgLRRRGYRVAVVAIDPTSPFSGGSIMgdrlRMQEHAadpgvfIRSIPTRGIKGGLSMAA 128
                                    7899****************99999********99865433333333222233322245677788888888888888888 PP

                                    HHHHHHHHHHHTT-SEEEEEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE- CS
                           cobW  70 lkelealeereerldviliEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnK 149
                                    l+ +e + ++   +d i+iEt+G+ +              +++ +++ vv       ++++ + +    ++  d+ v+nK
  gi|118431553|ref|NP_148094.2| 129 LAMIEVFDAMG--YDKIIIETVGVGQSEVD---------IINAAHTIIVVTM---PGAGDDVQALKAGVMEIGDIYVVNK 194
                                    88888888887..9*********9998766.........6777777888877...4568888888899999********* PP

                                    HHHHCHC.. CS
                           cobW 150 tDlldeeal 158
                                     D  +++++
  gi|118431553|ref|NP_148094.2| 195 SDKPEANKT 203
                                    *98877755 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 !   22.6   0.0     1e-07   7.5e-05       1      33 [.      49      81 ..      49      87 .. 0.95
   2 ?   -2.0   0.0       4.2     3e+03      93     125 ..     129     161 ..     123     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1e-07
                           MobB  1 vlgivgksgsGKTtLleklipelkarglrvgti 33
                                   v+g++g  g+GK tL++++i+ l++rg+rv+++
  gi|118431553|ref|NP_148094.2| 49 VIGFTGIPGAGKSTLVSRVITGLRRRGYRVAVV 81
                                   799****************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.2
                           MobB  93 lvlvEGfkkealpkievlraelgkeellllede 125
                                    l ++E f +  ++ki +    +g++e+   +  
  gi|118431553|ref|NP_148094.2| 129 LAMIEVFDAMGYDKIIIETVGVGQSEVDIINAA 161
                                    567888888888888887777777665444444 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.9   2.8e+03      58     109 ..       3      50 ..       1      56 [. 0.67
   2 !   21.9   0.0   1.9e-07   0.00014       9      97 ..      57     183 ..      47     204 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.9
                                    CCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                           CbiA  58 rllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvl 109
                                    rl++lle+ + +   +l+ +g +l+ v+++    +  e le+l  r  + +v+
  gi|118431553|ref|NP_148094.2|   3 RLEKLLEMAYSG---NLRALGRLLTLVENP--GSEAVELLERLSSRAgRAQVI 50 
                                    566666666655...488899999999998..676677777776666555555 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.9e-07
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH................................C CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx................................x RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep................................d 55 
                                    G+GK+tl+   ++ l rrg+rV++v  Dp ++ +   ++g++ + ++                                d
  gi|118431553|ref|NP_148094.2|  57 GAGKSTLVSRVITGLRRRGYRVAVVAIDPTSPFSGGsIMGDRLRMQEhaadpgvfirsiptrgikgglsmaalamievfD 136
                                    9*****************************99987455555555555888889999999999888888887777777664 PP

                                    CHCCCHHH.HHHCHCHHHH......EEEEEEEEESS...-TTCHHHH CS
                                    xxxxxxxx.xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  56 lkrllell.ealgkkkall....lkiagvvlnrvdgeneetllkeal 97 
                                    +  + +++ e++g +++           +v+++++  +  ++lk ++
  gi|118431553|ref|NP_148094.2| 137 AMGYDKIIiETVGVGQSEVdiinAAHTIIVVTMPGAGDDVQALKAGV 183
                                    44444444333333333335544455555566666555555555555 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 !   20.9   0.0   3.5e-07   0.00025       2      35 ..      53      86 ..      52      90 .. 0.94
   2 ?   -3.3   0.0       8.6   6.2e+03     155     182 ..     184     212 ..     182     240 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.5e-07
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPA 35
                                   +G +G+GK+t+v++++  l+ rg++vavv +DP 
  gi|118431553|ref|NP_148094.2| 53 TGIPGAGKSTLVSRVITGLRRRGYRVAVVAIDPT 86
                                   79*******************************7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.6
                     ATP_bind_1 155 lelPhvvvlnkfDllkek.lekeleffed 182
                                    +e+  + v+nk D  + + +   l+f  +
  gi|118431553|ref|NP_148094.2| 184 MEIGDIYVVNKSDKPEANkTAAYLQFALE 212
                                    56667888888887554444444444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.8e-06    0.0013       2     112 ..      48     168 ..      47     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST...SSTTHH..H..HHHHHHHHTTEEEEE...SSTTSCHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt...fRaaAv..e..QLktlaeklgvpvik...kkeeadpaav 71 
                                    +vi + G+ GaGK t ++++   l+++g++v++va D    f  + +  +   ++++a   gv + +   +  +      
  gi|118431553|ref|NP_148094.2|  48 QVIGFTGIPGAGKSTLVSRVITGLRRRGYRVAVVAIDPtspFSGGSImgDrlRMQEHAADPGVFIRSiptRGIKGGLSMA 127
                                    578899*******************************6233555555333225677788877665555433333345556 PP

                                    HHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH CS
                          SRP54  72 akeavekakeekidvvlvDTaGrlqndkelmeelkkikkvv 112
                                    a + +e +++ ++d +++ T G  q++ ++++  ++i  v+
  gi|118431553|ref|NP_148094.2| 128 ALAMIEVFDAMGYDKIIIETVGVGQSEVDIINAAHTIIVVT 168
                                    66778999999999999999999999999999888887766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.1e-06   0.00076       2      31 ..      50      79 ..      49      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   +  TG pG GK+Tlv++v+  l+++g++v+
  gi|118431553|ref|NP_148094.2| 50 IGFTGIPGAGKSTLVSRVITGLRRRGYRVA 79
                                   567************************996 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.9e-06    0.0014      17      54 ..      46      83 ..      34      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrviglAp 54
                                   +++v   tG +G+GK+t+++ +   ++++g+rv+++A 
  gi|118431553|ref|NP_148094.2| 46 RAQVIGFTGIPGAGKSTLVSRVITGLRRRGYRVAVVAI 83
                                   4567788****************************995 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 !   16.1   0.2   1.7e-05     0.012       5      59 ..      62     129 ..      58     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                Glyco_trans_4_4   5 ryvaelaraLaarGheVtvltpapapg.............apeleedgvrvhrlpvprrpspladlaa 59 
                                    + v +++ +L++rG++V v++ +p+ +             ++++  +gv ++++p++   ++l ++a 
  gi|118431553|ref|NP_148094.2|  62 TLVSRVITGLRRRGYRVAVVAIDPTSPfsggsimgdrlrmQEHAADPGVFIRSIPTRGIKGGLSMAAL 129
                                    56788999*************55555557788888887666678899********9988877666442 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   2.2e-05     0.016       2      85 ..      50     169 ..      49     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke................................. 47 
                                    +++ G p +GKStL+++ +   + +  + + + +d++         +                                 
  gi|118431553|ref|NP_148094.2|  50 IGFTGIPGAGKSTLVSRVITGlRRRGYRVAVVAIDPTSPFSG---GSimgdrlrmqehaadpgvfirsiptrgikgglsm 126
                                    899**************9864344444444444444333111...11111123344455667777777778888888888 PP

                                    .....EEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEEEET CS
                       MMR_HSR1  48 .....ielvDtpGliegaseek.glgkaflaleeadlillvvda 85 
                                         ie+ D  G +++   e  g+g++  ++++a + ++vv +
  gi|118431553|ref|NP_148094.2| 127 aalamIEVFDAMG-YDKIIIETvGVGQSEVDIINAAHTIIVVTM 169
                                    8888888899999.654444445888888888887666666654 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   0.1   2.4e-05     0.017      18      55 ..      41      78 ..      31     106 .. 0.78
   2 ?   -0.9   0.1       2.6   1.8e+03      77     109 ..     269     301 ..     230     320 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                         AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggif 55
                                   + r+gr +++ ++G +G GKs+lv ++ + l+++g  +
  gi|118431553|ref|NP_148094.2| 41 SSRAGRAQVIGFTGIPGAGKSTLVSRVITGLRRRGYRV 78
                                   246677799******************99999995443 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.6
                         AAA_16  77 areellrqlldeaesaeleawrekleealaavp 109
                                     ++ l + ll+ + sa+ e +r+ leea+a+++
  gi|118431553|ref|NP_148094.2| 269 LAKMLAESLLSSKVSAAMEVHRTLLEEAAASGK 301
                                    333444555555566577777777777666333 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.8e-05      0.02      11      56 ..      57     103 ..      49     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                                    TSSHHHHHHHHHHHHHTTT--EEEEE--TTT-.HHHHHHHHHHHHHH CS
                           MipZ  11 GsGksttavhvavaLlkkGarvaaidldlrqr.tlarylenraatae 56 
                                    G+Gkst    v++ L ++G rva++ +d     +    +++r+ ++e
  gi|118431553|ref|NP_148094.2|  57 GAGKSTLVSRVITGLRRRGYRVAVVAIDPTSPfSGGSIMGDRLRMQE 103
                                    9**************************96543144555666665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     4e-05     0.029       4      58 ..      46      96 ..      42     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllr 58
                                   +a+++  tG +G+GK+tl+ r+   l ++      r+ vv ++++s+ s  +++ 
  gi|118431553|ref|NP_148094.2| 46 RAQVIGFTGIPGAGKSTLVSRVITGLRRRG----YRVAVVAIDPTSPFSGGSIMG 96
                                   5778889******************96554....599999999999988777765 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 ?    3.4   0.0     0.067        48       6      28 ..      50      72 ..      46      84 .. 0.81
   2 ?    9.2   0.0    0.0012      0.83     123     191 ..     186     248 ..     175     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.067
                                   EEEEESTTSSHHHHHHHHHHHTT CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLlyktg 28
                                   ig+ g   +GK+TL+ r+++ + 
  gi|118431553|ref|NP_148094.2| 50 IGFTGIPGAGKSTLVSRVITGLR 72
                                   677888899********998765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0012
                                    TEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 123 vpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                    +  i ++NK D+++a+       ++  l++++   ++ g +     ++v +Sa+ g+g+++l++a+ e+
  gi|118431553|ref|NP_148094.2| 186 IGDIYVVNKSDKPEANKTAAY--LQFALEKEDIGRRESGWR----PKLVKTSAVLGQGIDPLVDAIEEH 248
                                    44799******9965544333..333343333333334444....56*******************987 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.7e-05     0.041       2      36 ..      47      81 ..      46      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                     APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylL 36
                                   + v+ +tG+ g+GKst+  ++ + L+++g++v ++
  gi|118431553|ref|NP_148094.2| 47 AQVIGFTGIPGAGKSTLVSRVITGLRRRGYRVAVV 81
                                   56899************************998775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.6e-05     0.055       8      42 ..      36      69 ..      31      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                                   HHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC  8 viekLlekdelqslvvalvGmgGvGKttlakqiln 42
                                   + e+L+   +    v+++ G +G GK+tl++ ++ 
  gi|118431553|ref|NP_148094.2| 36 LLERLSSRAGRA-QVIGFTGIPGAGKSTLVSRVIT 69
                                   678888644444.6****************99976 PP

>> AAA_33  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      0.08       1      23 [.      49      71 ..      49      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                         AAA_33  1 lvllvGlpGsGKstlaerllkkl 23
                                   ++ + G pG+GKstl+ r++  l
  gi|118431553|ref|NP_148094.2| 49 VIGFTGIPGAGKSTLVSRVITGL 71
                                   56689*************96544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001     0.075      18      59 ..      46      86 ..      33     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                         ATPase 18 egrvvlitGepGtGKtifalqFlikgaekygepgvfvtveep 59
                                   +++v+  tG pG+GK++++ + +i+g+++ g+++  v+++ +
  gi|118431553|ref|NP_148094.2| 46 RAQVIGFTGIPGAGKSTLVSR-VITGLRRRGYRVAVVAIDPT 86
                                   6789999***********999.78999***********9865 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.4   2.4e+03       4      26 ..      21      43 ..      20      49 .. 0.82
   2 ?   10.6   0.0   0.00054      0.39       4      33 ..      48      77 ..      45     103 .. 0.81
   3 ?   -0.7   0.1       1.6   1.1e+03     134     157 ..     269     292 ..     245     315 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                 Ploopntkinase3  4 rliylvGqPGaGkstlmaeltkg 26
                                   rl+ lv +PG+   +l+  l++ 
  gi|118431553|ref|NP_148094.2| 21 RLLTLVENPGSEAVELLERLSSR 43
                                   8999*******999999888765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00054
                 Ploopntkinase3  4 rliylvGqPGaGkstlmaeltkgfdrskve 33
                                   ++i + G PGaGkstl++ + +g+ r  ++
  gi|118431553|ref|NP_148094.2| 48 QVIGFTGIPGAGKSTLVSRVITGLRRRGYR 77
                                   5677889**************999997665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
                 Ploopntkinase3 134 lgrvqneswvkgrlsasrkladal 157
                                    l ++ +es + +++sa+ ++  +l
  gi|118431553|ref|NP_148094.2| 269 LAKMLAESLLSSKVSAAMEVHRTL 292
                                    333333444444444443333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.082       4      34 ..      40      71 ..      37      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                                   EEEEEETTSEEEEEESTTSSHHHHH.HHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       ABC_tran  4 vslklkegekvaivGenGaGKStLl.kllagl 34
                                   +s    + ++++++G  GaGKStL+ ++++gl
  gi|118431553|ref|NP_148094.2| 40 LSSRAGRAQVIGFTGIPGAGKSTLVsRVITGL 71
                                   6666678899**************93456655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0007       0.5      89     122 ..      36      70 ..      10      81 .. 0.77
   2 ?   -0.7   0.0       1.6   1.1e+03      50      99 ..     189     247 ..     176     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0007
                                    THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                     le+l+++    +++ + G  G+GKStL+ +++  
  gi|118431553|ref|NP_148094.2|  36 LLERLSSRAGRaQVIGFTGIPGAGKSTLVSRVITG 70 
                                    4566666665558999*************988765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                    EEEEE-GGG--HHH.........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                    RsgA_GTPase  50 vivlnKiDlleeee.........eleelkeelealgyevllvsaktkegleelkellkd 99 
                                    + v+nK D  e ++         e e++  + + +  +++++sa  ++g++ l +++++
  gi|118431553|ref|NP_148094.2| 189 IYVVNKSDKPEANKtaaylqfalEKEDIGRRESGWRPKLVKTSAVLGQGIDPLVDAIEE 247
                                    56788888887777777776665666666667777777778888888888877777665 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 ?   10.8   0.0   0.00024      0.17      16      49 ..      48      81 ..      41      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                  TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrairargdraivl 49
                                   q i ++G  G+GK++ ++  ++++r+rg r+ v+
  gi|118431553|ref|NP_148094.2| 48 QVIGFTGIPGAGKSTLVSRVITGLRRRGYRVAVV 81
                                   668899**********************997553 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 ?   11.0   0.0   0.00047      0.33       8      80 ..      59     145 ..      55     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                Glyco_trans_4_2   8 lssvhtlrlakeLakrgyeVhvitpkkga...kdeleaegihvhrlkvd.........rkg.pleylk.afklkklikki 73 
                                     +s+ ++r++ +L+ rgy+V+v+  ++ +    +    ++++++++  d         ++g + ++ + a+++++++++ 
  gi|118431553|ref|NP_148094.2|  59 GKSTLVSRVITGLRRRGYRVAVVAIDPTSpfsGGSIMGDRLRMQEHAADpgvfirsipTRGiKGGLSMaALAMIEVFDAM 138
                                    568999*****************997665563445557888999995555666544444444666655356999999999 PP

                Glyco_trans_4_2  74 kPDvvha 80 
                                    ++D +++
  gi|118431553|ref|NP_148094.2| 139 GYDKIII 145
                                    9998865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00032      0.23       1      18 [.      50      67 ..      50      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
                         AAA_18  1 IlltGtpGvGKttlakeL 18
                                   I+ tG+pG+GK+tl  ++
  gi|118431553|ref|NP_148094.2| 50 IGFTGIPGAGKSTLVSRV 67
                                   899**********98776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0032       2.3       2      26 ..      50      78 ..      49      82 .. 0.74
   2 ?    1.6   0.1      0.41   2.9e+02      19      48 ..     273     306 ..     268     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0032
                         AAA_28  2 ivitGgestGKTtlleaLa....argypv 26
                                   i +tG +++GK+tl+++      +rgy+v
  gi|118431553|ref|NP_148094.2| 50 IGFTGIPGAGKSTLVSRVItglrRRGYRV 78
                                   568************76543443668776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.41
                         AAA_28  19 Laar....gypvvpEaareileeklakgedalpw 48 
                                    La+     +++   E++r++lee +a+g++  ++
  gi|118431553|ref|NP_148094.2| 273 LAESllssKVSAAMEVHRTLLEEAAASGKGLFRA 306
                                    44434433888999**********9998874444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 2482.50
//
Query:       gi|118431554|ref|NP_148095.2|  [L=161]
Description: coenzyme B12-dependent mutase [Aeropyrum pernix K1]
Scores for 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-22   77.7   0.1    8.5e-22   77.5   0.1    1.2  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
       0.12   13.3   0.1       0.98   10.4   0.1    2.2  1  LytR_C       LytR cell envelope-related transcriptional atten


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.1   9.5e-26   8.5e-22       2      95 ..      20     114 ..      19     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 9.5e-26
                    B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirp. 80 
                                    kvl+a+ g d h++G++v+a+alrdagfeV+++g+ +++e+++ a+ +e++dv+g+S+l +++l  +k+l+  l++ ++ 
  gi|118431554|ref|NP_148095.2|  20 KVLVAKMGLDGHDRGAKVVARALRDAGFEVVYTGLRQTPEQVAMAAVQEDVDVIGVSILNGAHLHLMKRLMAKLRELGAd 99 
                                    89***********************************************************************6666554 PP

                    B12-binding  81 rvkvvvGGahpsldp 95 
                                    +++vv+GG++p  d 
  gi|118431554|ref|NP_148095.2| 100 DIPVVLGGTIPIPDL 114
                                    9*******9985554 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 ?   10.4   0.1   0.00011      0.98      15      47 ..      34      63 ..      29     107 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                         LytR_C 15 lAarvadaLeerGftvgevgnagnadeettivy 47
                                    A+ va+aL+++Gf+v+ +g    ++++ ++  
  gi|118431554|ref|NP_148095.2| 34 GAKVVARALRDAGFEVVYTG---LRQTPEQVAM 63
                                   5899************9944...4444445543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1373.84
//
Query:       gi|14601556|ref|NP_148096.1|  [L=565]
Description: coenzyme B12-dependent mutase [Aeropyrum pernix K1]
Scores for complete 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-220  733.1   0.0   1.7e-220  733.0   0.0    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  733.0   0.0  9.4e-225  1.7e-220       1     513 []      39     557 ..      39     557 .. 0.98

  Alignments for each domain:
  == domain 1  score: 733.0 bits;  conditional E-value: 9.4e-225
                 MM_CoA_mutase   1 kTaegievkplYtaedl.eek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsvaf 79 
                                   +T ++i+v++lYt+ dl + +   +  +PGe+PftRG++atmyr + Wt+r++ g++ +eetn+r+k l+e+G tgls+af
  gi|14601556|ref|NP_148096.1|  39 TTLSDIPVRRLYTPLDLkDWDyLEKLGFPGEYPFTRGIHATMYRAKLWTMRMFSGYGGPEETNKRLKFLIEHGETGLSLAF 119
                                   5999*************73333445569***************************************************** PP

                 MM_CoA_mutase  80 dlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdleklsgtiqn 160
                                   d+ptl+g+D+d+p aeg+vG +Gv+++sl+dme+++dgid+ +v+++mtin +a+ ll+ y+a+ae+qgv+ +k+ gt qn
  gi|14601556|ref|NP_148096.1| 120 DEPTLVGIDPDDPLAEGHVGIEGVNVASLKDMEIIFDGIDMGRVTTNMTINPPAPVLLSYYVAVAEKQGVPYHKIGGTTQN 200
                                   ********************************************************************************* PP

                 MM_CoA_mutase 161 DiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvralleaGldvde 241
                                   D+Lke++a++ty++ppe +++++ d+ie+  k++pk+n+is+sgyhireaGatavqElAftladG+eYvr+ll++Gldvd+
  gi|14601556|ref|NP_148096.1| 201 DPLKEFIAQKTYVFPPEAAVKIAIDVIEWSVKNLPKWNPISISGYHIREAGATAVQELAFTLADGIEYVRQLLARGLDVDT 281
                                   ********************************************************************************* PP

                 MM_CoA_mutase 242 faprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNilRttlealaAvlgg 322
                                   faprlsFff+ + +ffeeiAk+RAaRr+Wa+i+ke fgak+++s++lr+h+qT+gvsl +q+py+Ni+Rt++ealaAvlgg
  gi|14601556|ref|NP_148096.1| 282 FAPRLSFFFDSHINFFEEIAKFRAARRMWAKIMKEWFGAKKKRSMWLRFHTQTAGVSLVVQEPYNNIVRTAIEALAAVLGG 362
                                   ********************************************************************************* PP

                 MM_CoA_mutase 323 tqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawklfqeieeaGGmlkaiesG 403
                                   tqslhtnsfDe +++P+ef+a+iA++tq+i+a+E+gva+++DPlgGSyyvE+LTde++e+awk++++ie++GGml+a++ G
  gi|14601556|ref|NP_148096.1| 363 TQSLHTNSFDEPFRVPSEFAAKIALRTQQIIAYETGVADTIDPLGGSYYVEWLTDEIEERAWKYIDKIEAMGGMLEAVKRG 443
                                   ********************************************************************************* PP

                 MM_CoA_mutase 404 lvqeeiaesaarrqkaiesrkevivGvNkfr..pneeekelevlkide.eveerqaerlealraerdeaavkaaLaalgea 481
                                   ++q+e+ esa++ q+++e++++ ivGvN fr  + +e +++++l++d+ e+eerq++r++++r+ r+++++++aL++l++a
  gi|14601556|ref|NP_148096.1| 444 YPQKEVTESAYKFQRDLEEGRKFIVGVNIFRseSIDEARNVPLLEFDQeEIEERQKRRVKEVRKMRNQERWRRALDNLRKA 524
                                   ******************************9543335679*******99******************************** PP

                 MM_CoA_mutase 482 arse.nllaraveaaralatlGeisdaleevfg 513
                                   a+++ n++++++eaara+atlGei+ +l+ev+g
  gi|14601556|ref|NP_148096.1| 525 AERGeNIMPYVLEAARAYATLGEIMGTLKEVYG 557
                                   *9889**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.36
# Mc/sec: 4642.39
//
Query:       gi|118431555|ref|NP_148097.2|  [L=274]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-21   74.7   0.0    1.1e-20   74.3   0.0    1.1  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 !   74.3   0.0   5.9e-25   1.1e-20       1     212 [.      25     223 ..      25     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 5.9e-25
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHHHHH CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedeellk 80 
                                    i+slsp++te+l++lG++d+++gv+ ++  p +a+    ++++vg++  +++  l +l PDl+++ +g   ++++ e l+
  gi|118431555|ref|NP_148097.2|  25 IVSLSPAITETLYMLGLEDRIAGVSVYDHKPPKAR----EKPKVGSYYKVNMKLLEQLNPDLILVTTGA--QRRILEDLS 98 
                                    9*********************************9....99****************************..********* PP

                                    HHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTT CS
                   Peripla_BP_2  81 sgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyi 160
                                      +p++  +    ++++ +q+ ++g ++g  +ea  l +e+ +k  +++ a + +      ++++ + gg+v ag  +yi
  gi|118431555|ref|NP_148097.2|  99 RRYPVYPIPLPVSVSGIIDQAVQVGIVTGALEEASRLETELLDKASKLRGAGRGL-----RIYYEVYLGGPVTAGAHTYI 173
                                    ***********999*****************************999988888877.....56666667888********* PP

                                    THHHHTS--EES.TTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HH CS
                   Peripla_BP_2 161 gdlldalgieni.aaeskkseyeeisaEqilasdpdvifvsgraeadnktgle 212
                                    +d ++++g+e    +e  +    + ++E+i+  +p+ i++  +  a + t +e
  gi|118431555|ref|NP_148097.2| 174 SDAFRIAGVETPfMSER-TTWIYQPPPERINRFKPQFILYEYS--AYAPTTAE 223
                                    ***********945555.66667899*************9988..55555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2120.52
//
Query:       gi|14601558|ref|NP_148098.1|  [L=163]
Description: hypothetical protein APE_1689 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1210.59
//
Query:       gi|118431556|ref|NP_148099.2|  [L=210]
Description: hypothetical protein APE_1690.1 [Aeropyrum pernix K1]
Scores for 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-08   32.3   1.1    9.3e-08   31.6   0.5    1.6  2  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.5   5.2e-12   9.3e-08       9      59 .]      96     144 ..      93     144 .. 0.90
   2 ?   -3.2   0.0       0.4   7.2e+03      20      27 ..     167     174 ..     166     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 5.2e-12
                         DUF309   9 negeffeaHEvlEelWkeageperkllqglIqlAvAlyhlrrgnvrgakrl 59 
                                     e +++eaHE+lE++  ++g  + + +++l+ +A+A  ++++g  +ga+rl
  gi|118431556|ref|NP_148099.2|  96 GEARYWEAHEALEDIYYRSG--RDERVRALLIAAAAAAKAQEGLIDGARRL 144
                                    5789************8887..57899*********************997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.4
                         DUF309  20 lEelWkea 27 
                                     E +W+e 
  gi|118431556|ref|NP_148099.2| 167 VESVWREG 174
                                    69999664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1567.25
//
Query:       gi|14601560|ref|NP_148100.1|  [L=269]
Description: zinc transporter [Aeropyrum pernix K1]
Scores for complete 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-15   56.0  30.0    1.3e-13   50.9  14.9    2.3  2  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   6.9   9.5e-06      0.17     243     300 ..      22      77 ..      10     103 .. 0.84
   2 !   50.9  14.9   7.2e-18   1.3e-13     185     332 ..     127     264 ..     107     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-06
                           Zip 243 kkav.llnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellp 300
                                   k a+ l+  +fa+t++ G l+  +     ++++ +++  + +++s+G+++  ++++ll 
  gi|14601560|ref|NP_148100.1|  22 KAAFlLSLYAFAMTSLGGFLVLAA---RTHGGRLDVLLDVGMGFSSGIMIVASFTSLLL 77 
                                   4555688889***********999...999**************************994 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 7.2e-18
                           Zip 185 raiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGiliG 263
                                   +a+++  ++i+H++++G+++G  +s   s+g+++ +A+    +pe+l++ ++++ a  s   a+l ++l++++ ++++ i 
  gi|14601560|ref|NP_148100.1| 127 AAWLVATAIIIHNLPEGMSIGaaASYAISEGLAVALAIGTQDFPEGLAVSLPVFAASGSLYLALLVAMLSGFSEVVAATIV 207
                                   69********************99**************************************************9988777 PP

                           Zip 264 ilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmlll 332
                                    +       +++  + +  la++aG ++ v   e lp E +++       ++ l+ +g+++Gf++ml l
  gi|14601560|ref|NP_148100.1| 208 AA-----LIGYSPGLLASALAFAAGAMVFVVSYEALP-ESHRSG------NEKLATVGFFAGFIIMLYL 264
                                   77.....5678888888889*****************.777777......799*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1878.32
//
Query:       gi|118431557|ref|NP_148101.2|  [L=176]
Description: inorganic pyrophosphatase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-54  183.8   0.0    2.1e-54  183.6   0.0    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase
  ------ inclusion threshold ------
       0.19   11.4   0.0        0.3   10.7   0.0    1.3  1  InPase           Inorganic Pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6   0.0   2.4e-58   2.1e-54       1     160 []      19     174 ..      19     174 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 2.4e-58
                                    EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEE CS
                Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGv 80 
                                    vv+Eip++s++Kye+dke   +++dr+l+ts+ yp+nYGfip Tle+     DgDP+Dvlv+++ep++pg+++e+ +++v
  gi|118431557|ref|NP_148101.2|  19 VVIEIPMNSSVKYEFDKEACIVKVDRFLYTSMVYPFNYGFIPGTLEE-----DGDPVDVLVISREPVAPGSLIEAVPVAV 93 
                                    79*********************************************.....**************************** PP

                                    EEEEETTEEEEEEEEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHHHHH CS
                Pyrophosphatase  81 lamiDegetDdKiiavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieeaher 158
                                    l m+De++ D K++avp+   dp + +++d+ d+p+ l+++i+hfFe+yk+le ++k+v+v++w+ +++A+++i++a+er
  gi|118431557|ref|NP_148101.2|  94 LDMEDEEGPDSKVVAVPKAklDPLFASYKDVGDIPDALKSKIKHFFEHYKELE-PGKWVRVTGWRPAADAKEIIRRAIER 172
                                    ******************999**88****************************.789*********************** PP

                                    HH CS
                Pyrophosphatase 159 yk 160
                                    yk
  gi|118431557|ref|NP_148101.2| 173 YK 174
                                    97 PP

>> InPase  Inorganic Pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.4e-05       0.3      50      72 ..      55      77 ..      47     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.4e-05
                         InPase 50 hYGyikgtkgaDgdhvDvflgdk 72
                                   +YG i gt   Dgd vDv + ++
  gi|118431557|ref|NP_148101.2| 55 NYGFIPGTLEEDGDPVDVLVISR 77
                                   8*****************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 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:                        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: 1303.83
//
Query:       gi|118431558|ref|NP_148102.2|  [L=252]
Description: hypothetical protein APE_1693.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 00:00:00.41
# Mc/sec: 1855.59
//
Query:       gi|118431559|ref|NP_148103.2|  [L=150]
Description: cytochrome AA3 controlling protein [Aeropyrum pernix K1]
Scores for 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-17   62.7  16.5      1e-09   37.9   0.5    2.0  2  COX15-CtaA       Cytochrome oxidase assembly protein
     0.0038   16.6  10.9     0.0053   16.2  10.9    1.2  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
  ------ inclusion threshold ------
      0.047   13.3   0.5      0.058   13.0   0.5    1.2  1  Pox_P21          Poxvirus P21 membrane protein
       0.22   11.6  10.1      0.026   14.6   5.4    1.8  2  SirB             Invasion gene expression up-regulator, SirB
       0.43    9.4   5.3       0.53    9.0   5.3    1.2  1  ALMT             Aluminium activated malate transporter
        1.1    9.7  14.0       0.27   11.7   7.8    2.2  2  MerC             MerC mercury resistance protein


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 !   37.9   0.5   3.4e-13     1e-09       3      46 ..      11      55 ..       9      59 .. 0.88
   2 !   29.6  10.0   1.2e-10   3.6e-07     246     323 ..      59     136 ..      54     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 3.4e-13
                     COX15-CtaA  3 wlllvlllvllvvvlGgltRltdsGlsi.tdWppctGalppltde 46
                                   ++++ ++l++l v +G++tR+ ++G+++ +dWp+c+G+++p t++
  gi|118431559|ref|NP_148103.2| 11 YAYAGVALLFLAVTIGAFTRAYGAGMGCgPDWPTCNGEIVPFTSD 55
                                   6678899*********************778*******8888776 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.2e-10
                     COX15-CtaA 246 tvqfaHRllAilvllvllllailllrkarspklarlavllaallllQvalGistvllavplslavaHqlgaallllal 323
                                    ++ ++HR++A l ++++ ++a+l+l++     ++  a++++++l++Q++lG + v+++++ +l ++H+++a++ ++++
  gi|118431559|ref|NP_148103.2|  59 LLEYFHRVAAGLGFVLVSYAAYLALKTPGDVSVRLWAMATVVVLVAQIILGAVVVWYHLNPPLSALHTTLAIVTVALA 136
                                    56899***************98888887779999999999*********************************99876 PP

>> Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  10.9   1.8e-06    0.0053     124     230 ..      17     140 ..       8     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.8e-06
                Cyt_bd_oxida_II 124 aalllGvalgnllqGvpf....dad..ey.g....flsdllnpfallvglllvalflllG.alylalktegelqerarrl 191
                                    a l+l v++g++ +          d  +  g    f+sd  ++  ++  +++ + f+l + a+ylalkt g++  r+ ++
  gi|118431559|ref|NP_148103.2|  17 ALLFLAVTIGAFTRAYGAgmgcGPDwpTCnGeivpFTSDTATLLEYFHRVAAGLGFVLVSyAAYLALKTPGDVSVRLWAM 96 
                                    556677777777773333112222255222245567777788888888887777777766589***************** PP

                Cyt_bd_oxida_II 192 alvlalvllvllvvvllwtll......lvllllavlalllavlll 230
                                    a+v++lv+ ++l +v++w  l      l    la+++++la  ++
  gi|118431559|ref|NP_148103.2|  97 ATVVVLVAQIILGAVVVWYHLnpplsaL-HTTLAIVTVALATGMA 140
                                    ****************998889998852.3344444444444332 PP

>> Pox_P21  Poxvirus P21 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   1.9e-05     0.058      69     137 ..      70     142 ..      38     150 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                        Pox_P21  69 lglilf....vlaltttpviavimiaiaslllPlpsLviaYCla.lqilnpsnantvgmsivcvllsivtivvn 137
                                    lg++l+     lal+t+  ++v + a+a++++ ++ ++++  ++  ++  p +a +++++iv v+l+   ++v+
  gi|118431559|ref|NP_148103.2|  70 LGFVLVsyaaYLALKTPGDVSVRLWAMATVVVLVAQIILGAVVVwYHLNPPLSALHTTLAIVTVALATG-MAVK 142
                                    5555542222489*******************999999976655167888899***********99872.3333 PP

>> SirB  Invasion gene expression up-regulator, SirB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.86   2.6e+03     104     111 ..      16      23 ..       5      34 .. 0.45
   2 ?   14.6   5.4   8.8e-06     0.026      48     116 ..      73     141 ..      49     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.86
                           SirB 104 Alvvflyi 111
                                      ++fl++
  gi|118431559|ref|NP_148103.2|  16 VALLFLAV 23 
                                    22222222 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.8e-06
                           SirB  48 lLllsgiaLlvllglspftkaWltaKlvllvvyivlgvvalkrakskklrllafvlAlvvflyivslAl 116
                                    +L+  + +L++ +   + +  W +a +v+lv+ i+lg+v++  + ++ l++l+  lA+v+++++  +A+
  gi|118431559|ref|NP_148103.2|  73 VLVSYAAYLALKTPGDVSVRLWAMATVVVLVAQIILGAVVVWYHLNPPLSALHTTLAIVTVALATGMAV 141
                                    566667777777766666656******************************************999997 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.3   0.00018      0.53      11      52 ..      62     103 ..      56     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                           ALMT  11 vvfslkvGlaltLvsllyflrplykelgknavWailTVvvvl 52 
                                    +++ ++ Gl   Lvs   +l     + ++  +Wa++TVvv+ 
  gi|118431559|ref|NP_148103.2|  62 YFHRVAAGLGFVLVSYAAYLALKTPGDVSVRLWAMATVVVLV 103
                                    6899**********************************9965 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4     0.093   2.8e+02      66      84 ..       8      26 ..       4      53 .. 0.70
   2 ?   11.7   7.8   9.2e-05      0.27      35     109 ..      60     134 ..      44     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.093
                           MerC 66 vlvlgalGllillvalflg 84
                                   v v + +G+++l++a+ +g
  gi|118431559|ref|NP_148103.2|  8 VHVYAYAGVALLFLAVTIG 26
                                   5566666666666666666 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.2e-05
                           MerC  35 sellhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflg...........teaeetllfgslwqvltvl 103
                                     e++h+v++ l+ ++  +a +++ ++  + sv +++++ +++l++  +lg                       ++  t+l
  gi|118431559|ref|NP_148103.2|  60 LEYFHRVAAGLGFVLVSYAAYLALKTPGDVSVRLWAMATVVVLVAQIILGavvvwyhlnppL-----------SALHTTL 128
                                    578**********************************************9544443332221...........2222333 PP

                           MerC 104 GaalLa 109
                                    +++ +a
  gi|118431559|ref|NP_148103.2| 129 AIVTVA 134
                                    333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1124.92
//
Query:       gi|118431560|ref|NP_148104.2|  [L=375]
Description: glycine cleavage system aminomethyltransferase T [Aeropyrum pernix K1]
Scores for 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-69  232.0   0.0    9.1e-69  231.7   0.0    1.1  1  GCV_T            Aminomethyltransferase folate-binding domain
    3.2e-17   62.2   0.1    7.2e-17   61.1   0.1    1.5  1  GCV_T_C          Glycine cleavage T-protein C-terminal barrel
  ------ inclusion threshold ------
      0.041   13.4   0.0      0.062   12.9   0.0    1.2  1  RNA_Me_trans     Predicted SAM-dependent RNA methyltransferas
       0.26   10.2   0.0       0.37    9.7   0.0    1.1  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase


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 !  231.7   0.0     2e-72   9.1e-69       1     246 [.       8     249 ..       8     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 2e-72
                          GCV_T   1 lydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgkat. 79 
                                    l+d+h+ lga+f+efagw++P++Y  e++ +eh avr++ag+fD+Shmg++ vsG++a++lL+r++t+++sk+k+g ++ 
  gi|118431560|ref|NP_148104.2|   8 LEDLHRSLGATFGEFAGWSVPMSY--EGTLKEHMAVRREAGIFDISHMGRMIVSGEGATELLERIYTKRVSKTKVGFMSg 85 
                                    6799********************..*************************************************99988 PP

                          GCV_T  80 ytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevlskllg 159
                                     tl+lne ++v+dD + +rl+e+e+l+v naa ++ +l+++++ a + +l+v+++d+ e++allalqGP a++v++++ g
  gi|118431560|ref|NP_148104.2|  86 PTLALNEYARVKDDEMPYRLGEEEWLIVPNAAVADAMLEYFSSIASSMGLNVSIRDLRERYALLALQGPGAARVMEEMGG 165
                                    9******************************************8888********************************* PP

                          GCV_T 160 adlselkffsfaevela.ggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRlEaglrl 238
                                     dl +lk  +f+e     g    +vsR+g+tGedGfei+ + e+a+++++a +eag+    kpaG++ArdtlR+Eag+ l
  gi|118431560|ref|NP_148104.2| 166 GDLLDLKPLQFRENAGIaGVTAYIVSRSGWTGEDGFEIIAEVEAAKRIFKAAVEAGA----KPAGIAARDTLRIEAGFVL 241
                                    ************8766635555******************************87776....******************* PP

                          GCV_T 239 yghdldee 246
                                     gh+  e+
  gi|118431560|ref|NP_148104.2| 242 GGHEYGED 249
                                    ****8876 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 !   61.1   0.1   1.6e-20   7.2e-17       4      78 ..     292     368 ..     291     369 .. 0.93

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.6e-20
                        GCV_T_C   4 vglelddg.apll.rggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkpf 78 
                                    vgl+++++ a+++ r g+ ++ d+  vG+vTSg++sp +g+ +a Ay+++ +a +g+++ev+vrgkr +a++ + p+
  gi|118431560|ref|NP_148104.2| 292 VGLVMKKKyARMIpRSGYRLYVDDVDVGWVTSGTFSPVIGRGVAQAYIDSRYAYIGDTIEVDVRGKRGEARLQEFPL 368
                                    9****966667777*********************************************************998886 PP

>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.062     120     177 ..      46     107 ..      36     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                   RNA_Me_trans 120 g.fegRrLGpvqmttDtAvrvtklvvedkvkleeieyvdepelkfnkkesv...empfrYvk 177
                                    g f   ++G + ++ ++A +  +++  ++v+  ++ ++  p+l +n+ ++v   emp+r   
  gi|118431560|ref|NP_148104.2|  46 GiFDISHMGRMIVSGEGATELLERIYTKRVSKTKVGFMSGPTLALNEYARVkddEMPYRLGE 107
                                    3577889****************************************66664448***9765 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 ?    9.7   0.0   8.2e-05      0.37     159     199 ..      90     131 ..      67     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.2e-05
                tRNA_U5-meth_tr 159 veeklevadrelvyrqven.sftqPnaavnekmleWalevtq 199
                                    ++e  +v+d e+ yr  e+  ++ Pnaav+  mle+   ++ 
  gi|118431560|ref|NP_148104.2|  90 LNEYARVKDDEMPYRLGEEeWLIVPNAAVADAMLEYFSSIAS 131
                                    678899*********976516799***********9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2757.33
//
Query:       gi|14601565|ref|NP_148105.1|  [L=116]
Description: hypothetical protein APE_1697 [Aeropyrum pernix K1]
Scores for 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   16.8   0.1     0.0082   16.2   0.1    1.4  1  DUF4192   Domain of unknown function (DUF4192)
  ------ inclusion threshold ------
       0.23   11.4   0.0       0.65   10.0   0.0    1.8  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> DUF4192  Domain of unknown function (DUF4192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.1e-07    0.0082     240     275 ..      64      99 ..      27     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.1e-07
                       DUF4192 240 alalalgeeaaaaerLwlalarrlpgplrAaalaLl 275
                                    l+ alge+ a ae+L+++l+rrlp+++ + +++Ll
  gi|14601565|ref|NP_148105.1|  64 SLEEALGESGAIAEDLLRWLSRRLPERIESSVICLL 99 
                                   5899*****************************997 PP

>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   7.3e-05      0.65      21      52 ..      25      56 ..      13     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.3e-05
                                  GGSTEEEEEEEEEEEEEC-STCTTBSS-HHHH CS
                          PTPS 21 crnlHGHnykvevtvegeeldetgmvvdfgel 52
                                    +lHGH  +v++  +g  ld + +v+ ++e+
  gi|14601565|ref|NP_148105.1| 25 YTRLHGHDITVTACYCGPPLDTEKIVAVLEEA 56
                                  579***************99999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 922.48
//
Query:       gi|118431561|ref|NP_148106.2|  [L=183]
Description: hypothetical protein APE_1698.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1373.96
//
Query:       gi|14601567|ref|NP_148107.1|  [L=167]
Description: hypothetical protein APE_1699 [Aeropyrum pernix K1]
Scores for complete 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-34  118.6   0.0    1.8e-34  118.4   0.0    1.0  1  DUF2299   Uncharacterized conserved protein (DUF2299)
  ------ inclusion threshold ------
       0.03   13.0   0.1      0.045   12.4   0.1    1.2  1  DUF3352   Protein of unknown function (DUF3352)


Domain annotation for each model (and alignments):
>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.0   2.1e-38   1.8e-34       1     137 [.      10     148 ..      10     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.1e-38
                                   HHHHHHHHTT-EEEE--...-TTEEEEEEEE-STT..-EEEEEEETT-SSEEEEEEEEE--HHHHHHHHHS-HHHHHHHHH CS
                       DUF2299   1 eikeWLkeeGlkveevp...danaefhilveppqpggvvvdvikpkgksdvvvvgmgvkvseehkkalsslkeeerkefls 78 
                                   +i  WL++e ++v+  +   +a+++++i++e+++p++v++ ++kp+g+ dvv+v++g+++s++h++als+l +  r+ef  
  gi|14601567|ref|NP_148107.1|  10 KILAWLADE-FNVSVKSlpkNAPLDWAIKAETQAPVKVALVIQKPRGR-DVVAVTIGIALSQKHREALSKLGPGAREEFAV 88 
                                   5889***99.6666555558***************************9.9******************************* PP

                                   HHHHHHTTTT-EEEEE-TTS--...-EEEEEEEEEGGG--HHHHHHHHHHHHHHHHHHHHH CS
                       DUF2299  79 elkrdLlrlcvdfqlipqdeel..pqsiqvskeiykdgltknelldavkrvrnakllviwl 137
                                   +l rdL++lc+++++i q++ +   q+i +s+e+y+d lt+++l+da  +++n++l+ +++
  gi|14601567|ref|NP_148107.1|  89 SLVRDLIALCPHCRVIAQPN-PrdLQTILISRELYSDSLTRQSLIDASVTLVNMFLVTVLK 148
                                   ****************9999.4488*******************************99876 PP

>> DUF3352  Protein of unknown function (DUF3352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     5e-06     0.045     350     390 ..       5      46 ..       3      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5e-06
                       DUF3352 350 ldldkdifsWmdGEfalallpss.nkgagwlfvaetsdrsaa 390
                                   ldl+++i++W+ +Ef +++   + n + +w++ aet+ + + 
  gi|14601567|ref|NP_148107.1|   5 LDLKNKILAWLADEFNVSVKSLPkNAPLDWAIKAETQAPVKV 46 
                                   8****************86555589***********988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1228.79
//
Query:       gi|118431562|ref|NP_148108.2|  [L=250]
Description: hypothetical protein APE_1701.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1948.90
//
Query:       gi|14601569|ref|NP_148109.1|  [L=253]
Description: ATPase involved in Fe-S cluster formation SufC [Aeropyrum pernix K1]
Scores for complete 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   81.0   0.0    1.5e-22   80.6   0.0    1.1  1  ABC_tran     ABC transporter
    4.1e-10   40.0   0.1    4.3e-06   26.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    3.1e-07   30.1   0.0      0.015   14.7   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0088   14.7   0.0       0.48    9.0   0.0    2.0  2  AAA_13       AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.024   14.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.054   13.4   0.1       0.11   12.4   0.1    1.5  1  DUF1979      Domain of unknown function (DUF1979)
       0.14   12.4   0.0       0.22   11.7   0.0    1.5  1  AAA_33       AAA domain
       0.17   11.4   0.0       0.31   10.6   0.0    1.4  1  AAA_27       AAA domain
       0.17   11.7   0.1       0.28   11.1   0.1    1.3  1  RsgA_GTPase  RsgA 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 !   80.6   0.0   7.5e-26   1.5e-22       1     136 [.      18     174 ..      18     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 7.5e-26
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                   l++v+++lk ge++a++G+nG+GKS+L  +++g +     eG+illdg+++ke  ++e++ k i + +q+p   p++++ +
  gi|14601569|ref|NP_148109.1|  18 LNKVDFDLKYGEVHAVMGPNGSGKSSLGYVIMGREIYevVEGDILLDGESIKElPPEERALKGIFMAQQDPPQIPGVRLSS 98 
                                   789******************************9877669*************999*********************8888 PP

                                   H....................HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   x....................xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  79 n....................esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                        +  ++++++++klgl+  + ++ v      +SgG+k+r +l +a++ +pk+++lDEp 
  gi|14601569|ref|NP_148109.1|  99 LiiafvnkrlgaqdlskpadpKIVKRMYEYATKLGLDReILNREV---NVGFSGGEKKRSELLQAMIFDPKIVILDEPD 174
                                   8**********9999998887777889999999998763444444...489**************************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 !   11.3   0.1   0.00011      0.22       3      19 ..      32      48 ..      30      55 .. 0.86
   2 !   26.8   0.0   2.1e-09   4.3e-06     220     303 .]     126     210 ..      62     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                        AAA_21  3 vliGpNgsGKSnLLdal 19
                                  ++ GpNgsGKS+L + +
  gi|14601569|ref|NP_148109.1| 32 AVMGPNGSGKSSLGYVI 48
                                  678*********98776 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 2.1e-09
                        AAA_21 220 gvvflengdgqelparel....SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                   + +  + g ++e+  re+    S G k+   ll a++ ++   +++++DEp++gL+   l+ ++e++k+l++ g  v+l T
  gi|14601569|ref|NP_148109.1| 126 YEYATKLGLDREILNREVnvgfSGGEKKRSELLQAMIFDP---KIVILDEPDSGLDIDGLKIVAEFIKQLRDSGRGVMLIT 203
                                   4455555666666666666666****************99...9************************************* PP

                        AAA_21 297 HSpllld 303
                                   H   ll+
  gi|14601569|ref|NP_148109.1| 204 HYARLLN 210
                                   *998886 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 !   14.7   0.0   7.6e-06     0.015      25      44 ..      29      48 ..      17      57 .. 0.84
   2 !   13.5   0.0   1.8e-05     0.036     137     204 ..     147     211 ..      90     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                                  SEEEEEESTTSSHHHHHHHH CS
                                  xxxxxxxxxxxxxxxxxxxx RF
                         SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                  ++ a++GpNGSGKs+l   i
  gi|14601569|ref|NP_148109.1| 29 EVHAVMGPNGSGKSSLGYVI 48
                                  4789***********97766 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.8e-05
                                   S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                         SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                   +SgGek+ + l  l A   ++p+ +++lDe d+ LD    k+vae++k+ +++   ++ i++ +++l+ 
  gi|14601569|ref|NP_148109.1| 147 FSGGEKKRSEL--LQA-MIFDPK-IVILDEPDSGLDIDGLKIVAEFIKQLRDSgRGVMLITHYARLLNF 211
                                   57777776654..222.224444.899**********************99885778899998877765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0098        20      18      37 ..      30      49 ..      20      61 .. 0.81
   2 !    9.0   0.0   0.00024      0.48     526     575 ..     164     210 ..     156     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0098
                        AAA_13 18 iNliYGwNGaGKTtLSrllr 37
                                  +  + G NG+GK++L  ++ 
  gi|14601569|ref|NP_148109.1| 30 VHAVMGPNGSGKSSLGYVIM 49
                                  55678**********98876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00024
                        AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffk 575
                                     kiv++D P S LD + l iv+ +ik+     ++ + +++ TH   +++
  gi|14601569|ref|NP_148109.1| 164 DPKIVILDEPDSGLDIDGLKIVAEFIKQLR---DSGRGVMLITHYARLLN 210
                                   679*************************97...99999999999877766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.024      15      38 ..      21      44 ..      16      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                        AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                   +++++  +++ ++Gp+GsGKS+l
  gi|14601569|ref|NP_148109.1| 21 VDFDLKYGEVHAVMGPNGSGKSSL 44
                                  5667776669************97 PP

>> DUF1979  Domain of unknown function (DUF1979)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.5e-05      0.11       2      35 ..      18      53 ..      17      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                       DUF1979  2 lsklifdivyGeGnvrfGqdGvDLse..fkmtsrGi 35
                                  l+k+ fd+ yGe    +G++G   s   ++++ r i
  gi|14601569|ref|NP_148109.1| 18 LNKVDFDLKYGEVHAVMGPNGSGKSSlgYVIMGREI 53
                                  89*******************988863367777766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.22       2      38 ..      31      82 ..      30     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                        AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdt...............lrrrlf 38
                                    + G++GsGKs l   ++ ++ +++++ d+               +++ +f
  gi|14601569|ref|NP_148109.1| 31 HAVMGPNGSGKSSLGYVIMGREIYEVVEGDIlldgesikelppeerALKGIF 82
                                  5689***************9999********666666666666444444444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.31      18      42 ..      20      44 ..      15      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                        AAA_27 18 sldfsaeeadlhliyGpNEAGKsta 42
                                  ++df+ +  ++h ++GpN +GKs++
  gi|14601569|ref|NP_148109.1| 20 KVDFDLKYGEVHAVMGPNGSGKSSL 44
                                  6788888999*************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00014      0.28      81     123 ..       9      52 ..       1      61 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                   E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                   + +  +k  l+++   lk  ++ +++G+ G GKS+L  ++++++
  gi|14601569|ref|NP_148109.1|   9 TAKIGEKVVLNKVDFDLKYgEVHAVMGPNGSGKSSLGYVIMGRE 52 
                                   455556667889999999889***************88888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1850.66
//
Query:       gi|14601570|ref|NP_148110.1|  [L=476]
Description: FeS assembly protein SufB [Aeropyrum pernix K1]
Scores for 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-65  218.3   0.1    1.3e-64  217.9   0.1    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.9   0.1   7.2e-69   1.3e-64       2     218 .]     220     445 ..     219     445 .. 0.97

  Alignments for each domain:
  == domain 1  score: 217.9 bits;  conditional E-value: 7.2e-69
                       UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakleltt 70 
                                   qfe+ liv++ega v+ i   +gc            g+ve ++++nA++k+++vqnws+d++nl++kra  ++ a++++++
  gi|14601570|ref|NP_148110.1| 220 QFEHSLIVADEGAYVEWI---EGCsaprltkfsfhdGMVEAYAHRNATIKIITVQNWSKDVINLNNKRAIAEEGARVDWVE 297
                                   89****************...666666666677777*********************************999999****** PP

                       UPF0051  71 vslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqkt 151
                                   +s+g+k+t  +ps+ lkg++++++   +++akg    d+++k++h g+nt+s++++k++++d++ +v+rg i++ kga ++
  gi|14601570|ref|NP_148110.1| 298 GSIGSKMTFVYPSTILKGDNSSSRSAVVTIAKGPYLKDSGSKMIHVGRNTRSQVINKTISADGGINVYRGIIRIVKGARNA 378
                                   ********************************************************************************* PP

                       UPF0051 152 dahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    a++e+++L+l+dk++a+t P+ ++d+  + ++H+At+G++ e qlfYL sRGl+eeeA++liv gf
  gi|14601570|ref|NP_148110.1| 379 VANVECESLILDDKSKAHTYPHNQVDEPTASVNHEATTGRLTEPQLFYLTSRGLTEEEAKSLIVLGF 445
                                   *****************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3308.33
//
Query:       gi|14601571|ref|NP_148111.1|  [L=391]
Description: FeS assembly protein SufD [Aeropyrum pernix K1]
Scores for complete 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  119.9   0.0    1.5e-34  119.6   0.0    1.1  1  UPF0051        Uncharacterized protein family (UPF0051)
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.23   11.4   0.0    1.5  1  BD_b_sandwich  Bdellovibrio Beta-sandwich


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 !  119.6   0.0   1.7e-38   1.5e-34       4     217 ..     149     369 ..     146     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 1.7e-38
                       UPF0051   4 ertlivveegaevtiieey........agcgvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggk 76 
                                   ++++i+v+ega+ +ii  y        +   vve  +g++A+++++ +  +++++ +++ +  e+  +a+le++++  gg+
  gi|14601571|ref|NP_148111.1| 149 HHVVIEVGEGAKGEII--YidysvspgLKTTVVEARMGRDAEVEVTNIVLHGSRSAVYTLRGFEVLDKASLEQYYLISGGR 227
                                   6899************..555677777555******************9999999999999999999************** PP

                       UPF0051  77 ltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqen 157
                                   +tr + +  l+g+ ++++    ++a+ +   d+ +   hngp++ +++ ++gv+ +++    rg  +  + a  + +++e+
  gi|14601571|ref|NP_148111.1| 228 MTRFQDDNLLDGRLSSLKALASTVARPNTASDVIISSLHNGPESDGEVRARGVVVGNGYLAQRGVAMLGETARLAASEVES 308
                                   ********************************************************************************* PP

                       UPF0051 158 rnLllsdkaradtiPeleidaddvk.asHgAtvGkideeqlfYLmsRGlseeeArrlivrg 217
                                      lls+k++ +++P lei++++++ a+H A+v +++e+ +fYL+sRGl+ ++   l+++g
  gi|14601571|ref|NP_148111.1| 309 YIFLLSEKGKGYAVPVLEIHTGEITrAGHSAAVASLAEDTIFYLKSRGLDDKDIVTLVMEG 369
                                   ************************99**************************999999988 PP

>> BD_b_sandwich  Bdellovibrio Beta-sandwich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.23       8      76 ..     145     213 ..     140     222 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                 BD_b_sandwich   8 qyeGvvrvgevsrkkgGelykvdlakalrLqslevkasaarvkivevtLvtakGdridvreysnaavle 76 
                                    y G   v ev   + Ge+  +d+  +  L+   v a+ +r   vevt ++ +G r+ v  ++   vl+
  gi|14601571|ref|NP_148111.1| 145 GYLGHHVVIEVGEGAKGEIIYIDYSVSPGLKTTVVEARMGRDAEVEVTNIVLHGSRSAVYTLRGFEVLD 213
                                   588999999**************************************************9999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2998.49
//
Query:       gi|14601572|ref|NP_148112.1|  [L=791]
Description: hypothetical protein APE_1708 [Aeropyrum pernix K1]
Scores for complete 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   33.8  53.1    2.5e-07   29.3  19.7    5.0  4  EzrA             Septation ring formation regulator, EzrA
  ------ inclusion threshold ------
       0.01   16.2   8.6       0.01   16.2   8.6    8.1  7  DUF1771          Domain of unknown function (DUF1771)
      0.036   14.1  51.3      0.092   12.8   0.0    8.4  7  PTS_IIA          PTS system, Lactose/Cellobiose specific IIA 
       0.15   12.7  64.0          3    8.5   3.6    9.1  9  DUF883           Bacterial protein of unknown function (DUF88
       0.33   11.1   4.7         13    6.0   0.5    4.5  4  Tape_meas_lam_C  Lambda phage tail tape-measure protein (Tape
        0.4   11.0  36.8        2.1    8.7   4.2    8.5  5  DUF948           Bacterial protein of unknown function (DUF94
        0.5   10.6  27.1       0.91    9.7   0.3    6.0  6  Fib_alpha        Fibrinogen alpha/beta chain family
        1.2    7.6  29.5       0.73    8.3   5.9    3.6  3  Zw10             Centromere/kinetochore Zw10
        2.2    8.4   5.2        4.7    7.4   0.0    4.0  4  Mustang          Musculoskeletal, temporally activated-embryo
        2.4    7.8  10.3        6.4    6.5   0.0    3.5  4  DUF713           Protein of unknown function (DUF713)
        2.5    7.9  16.0       0.75    9.6   0.8    4.5  4  Synaptobrevin    Synaptobrevin
        4.1    7.5  34.9      0.044   13.8   2.7    6.5  7  DUF1664          Protein of unknown function (DUF1664)
        4.2    8.0  29.9       0.47   11.1   1.0    6.0  5  ING              Inhibitor of growth proteins N-terminal hist
        4.7    6.2  47.6       0.51    9.4   5.9    6.3  6  APG17            Autophagy protein Apg17
        6.1    6.8  69.1       0.29   11.1   9.2    7.8  5  YfdX             YfdX protein
        6.2    6.7  40.5      0.054   13.4   0.6    5.6  5  TarH             Tar ligand binding domain homologue
        6.3    6.5  10.2        2.6    7.8   0.9    3.6  4  Baculo_p24       Baculovirus P24 capsid protein


Domain annotation for each model (and alignments):
>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.8     0.029        30     310     364 ..     268     319 ..     262     335 .. 0.46
   2 !   29.3  19.7   2.3e-10   2.5e-07      80     241 ..     449     611 ..     443     611 .. 0.96
   3 !   18.5  14.7   4.3e-07   0.00045     104     286 ..     578     755 ..     566     758 .. 0.71
   4 !    5.3   0.6    0.0043       4.5      76     124 ..     741     789 ..     730     791 .] 0.76

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.029
                                   SSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHH CS
                          EzrA 310 elkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeele 364
                                    ++ +l++le++++e+ ++++ +k +Y     el++  e +k l+e e+ + + +
  gi|14601572|ref|NP_148112.1| 268 IMEARLQKLEAIYQEVGAKIEAIKGEYGA---ELDQNPEAQKLLEEAEEALAKAR 319
                                   44444555555555555555555555543...33333333333333333333322 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 2.3e-10
                                   HHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--.TTTTHH CS
                          EzrA  80 ieellfeaeelldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkll.anrfsy 159
                                    ++ll ea  lld+ ++ +ak+k+a++e+ l+++++k+++  + l+ + e  e+ re+ie+++e   + + kl+ a + s 
  gi|14601572|ref|NP_148112.1| 449 ASSLLAEARSLLDEGRIAEAKEKIAQAEAALEKADSKLDTAEAILEVVEEYAERAREAIEEAEEALAKAEAKLQlAAQLSG 529
                                   56789******************************************************************9975788888 PP

                                   HHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTT CS
                          EzrA 160 gealeelekqleniekefsefeeltengdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegykemke 240
                                   +ea+ee  ++le+ ++++++ +e+ +ng y ea  + +++ +  +e +e+ e+  e  +e+ +e+ +q+eel + +k+++e
  gi|14601572|ref|NP_148112.1| 530 SEAVEEALNRLEEAKEKLEAAKEAYSNGRYGEAIVLAEEAASIAEEAKELAEKAIEAAQEAVSEVLNQVEELLDRVKDLQE 610
                                   99***************************************************************************9998 PP

                                   S CS
                          EzrA 241 e 241
                                   e
  gi|14601572|ref|NP_148112.1| 611 E 611
                                   6 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 4.3e-07
                                   HHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------- CS
                          EzrA 104 aeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeelt 184
                                   + +e+ ++ ++e + ++l++++el++  ++ +eeie++ ek re         ++ + a++e+  +l++  + ++e + l 
  gi|14601572|ref|NP_148112.1| 578 ELAEKAIEAAQEAVSEVLNQVEELLDRVKDLQEEIEDIAEKAREAGVLT----EEIQAAIDEVLGKLDQARSLLEEADSLA 654
                                   4566677777777777777777777777777777777777777665433....34566777777888999999******** PP

                                   -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHHH CS
                          EzrA 185 engdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegykemkeegYaleelniekeieelekkieeil 265
                                   ++gd + a++ l ++++ i+e  +++++i +++e   + + + ++el+  ++e+ e+  +l       e ++ +   +e+l
  gi|14601572|ref|NP_148112.1| 655 KEGDIDGARQKLGEARDVIEEAVSMVRDIRSMVE---QAIGDLIDELRRLIEELREKAAELNTEAAMLEAKARRMGDREAL 732
                                   *********9999999888887777777776655...56777788999999999998888887777777777777777777 PP

                                   HHHTT-..-HHHHHHHHHHHHHH CS
                          EzrA 266 erlkel..eledveeelktieee 286
                                    +++e   ++e++ e+l++ +++
  gi|14601572|ref|NP_148112.1| 733 RLIEEArsNIEEAIEKLQDATDK 755
                                   77776533666666666665554 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0043
                                   HTHHHHHT-GGGT--S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                          EzrA  76 klpeieellfeaeelldkykfkkakkklaeleeeldeveekikkileel 124
                                   +++e  e+l +a + l   k+ +a++++ ++e+ l+e+e k+++ ++ l
  gi|14601572|ref|NP_148112.1| 741 NIEEAIEKLQDATDKLGDGKLGEAREAIGQAEDLLNEAEMKLEEARQRL 789
                                   4555566777777777778999999999999999999999999888876 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.1       0.2   2.1e+02      15      50 ..     304     341 ..     299     345 .. 0.59
   2 ?    6.7   2.6     0.009       9.5       6      51 ..     440     485 ..     438     498 .. 0.88
   3 ?    0.8   4.8      0.64   6.7e+02      35      58 ..     497     520 ..     487     526 .. 0.82
   4 ?   16.2   8.6   9.9e-06      0.01       7      61 ..     535     596 ..     534     598 .. 0.82
   5 ?    2.1   0.0      0.25   2.6e+02      13      47 ..     641     675 ..     634     679 .. 0.85
   6 ?   -0.7   3.4       1.8   1.9e+03       4      42 ..     698     739 ..     696     755 .. 0.54
   7 ?    3.7   1.3     0.075        79       6      57 ..     736     787 ..     730     790 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                       DUF1771  15 rnelfekAaeAyrrGd..gaaAkelseqGkehgekmee 50 
                                    ++l+e+A eA ++      +A  l ++G + ge m+e
  gi|14601572|ref|NP_148112.1| 304 AQKLLEEAEEALAKARerLDRAYILLQEGAKVGEVMRE 341
                                   45566666666555544455666666666666666666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.009
                       DUF1771   6 aeAdeharkrnelfekAaeAyrrGdgaaAkelseqGkehgekmeea 51 
                                   +eA ++ ++ ++l+++A+    +G  a+Ake  +q+  + ek++  
  gi|14601572|ref|NP_148112.1| 440 DEAGALIDRASSLLAEARSLLDEGRIAEAKEKIAQAEAALEKADSK 485
                                   5899999***********************************9864 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.64
                       DUF1771  35 kelseqGkehgekmeeanreAaea 58 
                                    e++e+++e+ e++eea ++A ++
  gi|14601572|ref|NP_148112.1| 497 EEYAERAREAIEEAEEALAKAEAK 520
                                   588899999999999988888766 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 9.9e-06
                       DUF1771   7 eAdeharkrnelfekAaeAyrrGd.......gaaAkelseqGkehgekmeeanreAaeaIfe 61 
                                   eA    ++ +e +e+A+eAy++G         ++A+  +e++ke+ ek+ ea++eA  ++++
  gi|14601572|ref|NP_148112.1| 535 EALNRLEEAKEKLEAAKEAYSNGRygeaivlAEEAASIAEEAKELAEKAIEAAQEAVSEVLN 596
                                   677788899999************88888877788888888888888888888888877765 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.25
                       DUF1771  13 rkrnelfekAaeAyrrGdgaaAkelseqGkehgek 47 
                                   ++ ++l+e+A    ++Gd   A++   ++++  e+
  gi|14601572|ref|NP_148112.1| 641 DQARSLLEEADSLAKEGDIDGARQKLGEARDVIEE 675
                                   67899*************99999988888887665 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.8
                       DUF1771   4 lRaeAdeharkrnelfekAa....eAyrrGdgaaAkelseqGk 42 
                                   lR+   e+ +k +el  +Aa    +A+r Gd++ A  l e+++
  gi|14601572|ref|NP_148112.1| 698 LRRLIEELREKAAELNTEAAmleaKARRMGDRE-ALRLIEEAR 739
                                   555666666666666666632222555566543.555555555 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.075
                       DUF1771   6 aeAdeharkrnelfekAaeAyrrGdgaaAkelseqGkehgekmeeanreAae 57 
                                   +eA+   ++  e ++ A++    G+ ++A+e   q+ ++ +++e   +eA +
  gi|14601572|ref|NP_148112.1| 736 EEARSNIEEAIEKLQDATDKLGDGKLGEAREAIGQAEDLLNEAEMKLEEARQ 787
                                   6899999999999******************************999999876 PP

>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.9     0.066        70      26      48 ..     298     320 ..     284     365 .. 0.72
   2 ?    7.5   2.6     0.004       4.2      13      47 ..     449     483 ..     437     486 .. 0.92
   3 ?    5.5   5.3     0.017        18      13      48 ..     484     519 ..     483     537 .. 0.82
   4 ?    2.4   3.2      0.15   1.6e+02      20      49 ..     532     560 ..     519     573 .. 0.59
   5 ?   -1.7   7.4       2.8     3e+03      13      58 ..     543     588 ..     542     613 .. 0.81
   6 ?   12.8   0.0   8.7e-05     0.092      12      48 ..     642     678 ..     636     693 .. 0.92
   7 ?    6.5   0.7     0.008       8.5      12      49 ..     737     774 ..     732     788 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.066
                       PTS_IIA  26 egdfeeaeellkeAeeelkeAhk 48 
                                     +  ea++ll+eAee+l++A++
  gi|14601572|ref|NP_148112.1| 298 LDQNPEAQKLLEEAEEALAKARE 320
                                   5566789999******9999986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.004
                       PTS_IIA  13 ArslameAlkaakegdfeeaeellkeAeeelkeAh 47 
                                   A sl+ eA + + eg++ ea+e++++Ae +l++A 
  gi|14601572|ref|NP_148112.1| 449 ASSLLAEARSLLDEGRIAEAKEKIAQAEAALEKAD 483
                                   789999**************************996 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                       PTS_IIA  13 ArslameAlkaakegdfeeaeellkeAeeelkeAhk 48 
                                   ++  + eA+ ++ e+  e+a+e ++eAee+l++A  
  gi|14601572|ref|NP_148112.1| 484 SKLDTAEAILEVVEEYAERAREAIEEAEEALAKAEA 519
                                   677789***************************963 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.15
                       PTS_IIA  20 AlkaakegdfeeaeellkeAeeelkeAhka 49 
                                   A+++a  +++eea+e+l++A+e++++++  
  gi|14601572|ref|NP_148112.1| 532 AVEEAL-NRLEEAKEKLEAAKEAYSNGRYG 560
                                   444433.34566666666666666666555 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 2.8
                       PTS_IIA  13 ArslameAlkaakegdfeeaeellkeAeeelkeAhkaqteliqkea 58 
                                   A++++  A +a+++g++ ea  l +eA +  +eA+++  + i++ +
  gi|14601572|ref|NP_148112.1| 543 AKEKLEAAKEAYSNGRYGEAIVLAEEAASIAEEAKELAEKAIEAAQ 588
                                   7888888888888899999999999999998888888888887544 PP

  == domain 6  score: 12.8 bits;  conditional E-value: 8.7e-05
                       PTS_IIA  12 eArslameAlkaakegdfeeaeellkeAeeelkeAhk 48 
                                   +Arsl+ eA + akegd++ a+++l eA++ ++eA  
  gi|14601572|ref|NP_148112.1| 642 QARSLLEEADSLAKEGDIDGARQKLGEARDVIEEAVS 678
                                   69******************************99965 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.008
                       PTS_IIA  12 eArslameAlkaakegdfeeaeellkeAeeelkeAhka 49 
                                   eArs++ eA++++++   +  + +l eA+e++ +A ++
  gi|14601572|ref|NP_148112.1| 737 EARSNIEEAIEKLQDATDKLGDGKLGEAREAIGQAEDL 774
                                   68999999999999988888888888888888888764 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 ?   -0.4   0.1       1.7   1.8e+03       8      50 ..     204     246 ..     197     264 .. 0.81
   2 ?    8.0   0.9     0.004       4.2      22      59 ..     297     334 ..     274     374 .. 0.72
   3 ?    5.4   4.6     0.027        29       3      53 ..     409     459 ..     407     482 .. 0.74
   4 ?    2.8   7.2      0.17   1.7e+02       6      57 ..     467     517 ..     462     528 .. 0.70
   5 ?    0.3   1.0         1   1.1e+03      31      54 ..     531     554 ..     515     563 .. 0.70
   6 ?    8.2   6.9    0.0036       3.8       3      67 ..     565     628 ..     561     636 .. 0.81
   7 ?    5.5   0.7     0.025        27       6      54 ..     642     691 ..     639     704 .. 0.77
   8 ?    4.4   0.6     0.053        56      23      62 ..     674     713 ..     656     718 .. 0.67
   9 ?    8.5   3.6    0.0028         3       9      70 ..     714     776 ..     693     782 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                        DUF883   8 eslladleellkeaadeageeaeelRerleerlerarerlrda 50 
                                    ++ ++le l  e ++e g e+e++ + + + +  ar+ l+ +
  gi|14601572|ref|NP_148112.1| 204 GEVASKLETLKAEIEAEDGGEVEAALDSALSGILLARSILESV 246
                                   5788999999999999999999999888888887777777665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
                        DUF883  22 adeageeaeelRerleerlerarerlrdaeeavaerak 59 
                                   + + + ea++l e++ee+l++arerl++a+  ++e ak
  gi|14601572|ref|NP_148112.1| 297 ELDQNPEAQKLLEEAEEALAKARERLDRAYILLQEGAK 334
                                   3456789**********************998777665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.027
                        DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeea 53 
                                   +e e+ +l+++le l ++aa+  + e++e+ +++ + ++ra + l++a+  
  gi|14601572|ref|NP_148112.1| 409 VEIEIGELMEELETLQQKAASANQGEVQEILDEAGALIDRASSLLAEARSL 459
                                   666888999999999999999999999999999999988888888877654 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.17
                        DUF883   6 eleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaer 57 
                                   e ++ +a++e+ l e+ad+  ++ae++ e +ee++erare++++aeea+a+ 
  gi|14601572|ref|NP_148112.1| 467 EAKEKIAQAEAAL-EKADSKLDTAEAILEVVEEYAERAREAIEEAEEALAKA 517
                                   5566666666666.55566778888888888888888888888888876654 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 1
                        DUF883  31 elRerleerlerarerlrdaeeav 54 
                                   e+ e++ +rle+a+e+l++a+ea+
  gi|14601572|ref|NP_148112.1| 531 EAVEEALNRLEEAKEKLEAAKEAY 554
                                   444667778888888888777765 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0036
                        DUF883   3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                   l++e +s+ ++++el+++a + a+e ++e+ +++ee l+r+++  ++ e+ +ae+a+ea   +++
  gi|14601572|ref|NP_148112.1| 565 LAEEAASIAEEAKELAEKAIEAAQEAVSEVLNQVEELLDRVKDLQEEIED-IAEKAREAGVLTEE 628
                                   56788899999999999999999999999999999999999986665554.88888888766665 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.025
                        DUF883   6 eleslladleellkeaa.deageeaeelRerleerlerarerlrdaeeav 54 
                                     +sll+++++l+ke   d a++++ e+R+ +ee+++ +r+  + +e+a+
  gi|14601572|ref|NP_148112.1| 642 QARSLLEEADSLAKEGDiDGARQKLGEARDVIEEAVSMVRDIRSMVEQAI 691
                                   56899999999999876367889999999999999999998766666654 PP

  == domain 8  score: 4.4 bits;  conditional E-value: 0.053
                        DUF883  23 deageeaeelRerleerlerarerlrdaeeavaerakeaa 62 
                                   +ea + ++++R+ +e+++ ++ ++lr++ e+++e+a e  
  gi|14601572|ref|NP_148112.1| 674 EEAVSMVRDIRSMVEQAIGDLIDELRRLIEELREKAAELN 713
                                   4556666777777777777777777777777777776654 PP

  == domain 9  score: 8.5 bits;  conditional E-value: 0.0028
                        DUF883   9 slladleellkeaa.deageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVr 70 
                                   +  a le+ +++ + +ea + +ee+R+++ee++e+++++++++ +    +a+ea+ +a+d   
  gi|14601572|ref|NP_148112.1| 714 TEAAMLEAKARRMGdREALRLIEEARSNIEEAIEKLQDATDKLGDGKLGEAREAIGQAEDLLN 776
                                   444444443333330455667899**********************************99865 PP

>> Tape_meas_lam_C  Lambda phage tail tape-measure protein (Tape_meas_lam_C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.16   1.7e+02       7      32 ..     492     517 ..     487     524 .. 0.83
   2 ?    6.0   0.5     0.012        13      15      44 ..     566     595 ..     564     600 .. 0.89
   3 ?   -3.0   0.0       7.7   8.1e+03      12      27 ..     606     621 ..     594     623 .. 0.70
   4 ?   -0.9   0.0       1.7   1.8e+03      17      42 ..     668     693 ..     660     696 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
               Tape_meas_lam_C   7 vkrglaeYaesasnvagqvaeaatsa 32 
                                   + + ++eYae a+ + + ++ea+ +a
  gi|14601572|ref|NP_148112.1| 492 ILEVVEEYAERAREAIEEAEEALAKA 517
                                   5577899**********999998776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
               Tape_meas_lam_C  15 aesasnvagqvaeaatsafdsmedalaefv 44 
                                   ae+a+ +a+ ++e+a++a++ +++a++e +
  gi|14601572|ref|NP_148112.1| 566 AEEAASIAEEAKELAEKAIEAAQEAVSEVL 595
                                   689999999999999999999999999876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7.7
               Tape_meas_lam_C  12 aeYaesasnvagqvae 27 
                                   ++ +e+++++a++++e
  gi|14601572|ref|NP_148112.1| 606 KDLQEEIEDIAEKARE 621
                                   4556777777777766 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.7
               Tape_meas_lam_C  17 sasnvagqvaeaatsafdsmedalae 42 
                                   +a++v + + +++ ++ ++ e+a+ +
  gi|14601572|ref|NP_148112.1| 668 EARDVIEEAVSMVRDIRSMVEQAIGD 693
                                   78899999999999999999999876 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.1   9.5e+03      56      72 ..     199     215 ..     191     219 .. 0.67
   2 ?    5.7   0.1     0.016        17      21      87 ..     273     342 ..     263     345 .. 0.71
   3 ?    8.7   4.2     0.002       2.1      32      77 ..     581     629 ..     562     683 .. 0.66
   4 ?    6.3   0.6     0.011        12      23      59 ..     690     726 ..     666     758 .. 0.71
   5 ?    1.6   0.1      0.33   3.5e+02      27      69 ..     741     784 ..     731     789 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.1
                        DUF948  56 vnelledvneklekvdp 72 
                                   + e+l +v +kle++++
  gi|14601572|ref|NP_148112.1| 199 AIEILGEVASKLETLKA 215
                                   45667777777777765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                        DUF948  21 llklkktldeaaatieelekqvdpilk...evedllakvnelledvneklekvdplteavadlgesvsel 87 
                                   l kl+ + +e+ a ie ++ + ++ l+   e+++ll++++e l+  +e+l++   l ++ a++ge ++e+
  gi|14601572|ref|NP_148112.1| 273 LQKLEAIYQEVGAKIEAIKGEYGAELDqnpEAQKLLEEAEEALAKARERLDRAYILLQEGAKVGEVMREI 342
                                   6788999999999999999555555542224666666666666666668888888888888888877765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.002
                        DUF948  32 aatieelekqvdpilkevedllakvnelledvne...klekvdplteav 77 
                                   +++ie  ++ v ++l++ve+ll+ v++l+e++++   k  +   lte++
  gi|14601572|ref|NP_148112.1| 581 EKAIEAAQEAVSEVLNQVEELLDRVKDLQEEIEDiaeKAREAGVLTEEI 629
                                   4445555555555555555555555555444433222333333333333 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.011
                        DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnel 59 
                                    +++++de+++ ieel++++ ++ +e++ l ak++++
  gi|14601572|ref|NP_148112.1| 690 AIGDLIDELRRLIEELREKAAELNTEAAMLEAKARRM 726
                                   5678899999999999999999999999998888883 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.33
                        DUF948  27 tldeaaatieelekqv.dpilkevedllakvnelledvneklek 69 
                                    ++ea + +++ ++++ d+ l e+++++ ++++ll++ + kle+
  gi|14601572|ref|NP_148112.1| 741 NIEEAIEKLQDATDKLgDGKLGEAREAIGQAEDLLNEAEMKLEE 784
                                   33444444444443332344778888888888888888888876 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 ?   -2.3   0.1       4.4   4.6e+03      94     128 ..      72     106 ..      64     107 .. 0.73
   2 ?    5.7   0.0     0.015        16      39      95 ..     268     324 ..     259     351 .. 0.86
   3 ?    4.5   0.4     0.034        36      31     106 ..     407     481 ..     399     494 .. 0.86
   4 ?    2.8   4.5      0.12   1.2e+02      65     124 ..     559     618 ..     496     622 .. 0.69
   5 ?    9.7   0.3   0.00087      0.91      31     131 ..     627     722 ..     624     726 .. 0.82
   6 ?   -0.9   0.1       1.6   1.7e+03      26      47 ..     735     756 ..     728     787 .. 0.46

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.4
                                   HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  94 ketidaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                   +++i++++ +++  +++  s  +++++L  +i++k
  gi|14601572|ref|NP_148112.1|  72 EREIVEEIASLEDVRSLSPSEAERLAELGMAINEK 106
                                   56777788888888888888888888887777765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                                   CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                     Fib_alpha  39 kleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlke 95 
                                    +e +l++++  ++e+   +++ik  + ++  ++++ ++++++ ++ l +  +rl++
  gi|14601572|ref|NP_148112.1| 268 IMEARLQKLEAIYQEVGAKIEAIKGEYGAELDQNPEAQKLLEEAEEALAKARERLDR 324
                                   47899******************************9999999999999988887765 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.034
                                   CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.CCCHHHHHHHCCHHHHHH CS
                     Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee.eilrlketidaqesnirv 106
                                   ++v+ ++ +l +ele+++++  +a++   e++++l e+ +  +  ++++ + ++ l+e +i++ ke+i + e  +++
  gi|14601572|ref|NP_148112.1| 407 TEVEIEIGELMEELETLQQKAASANQG--EVQEILDEAGALIDRASSLLAEARSLLDEgRIAEAKEKIAQAEAALEK 481
                                   67888999************9999986..8999999999999999999*****999875899999999998877765 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha  65 lrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                                   + e+   +++  ++ ++ ++  e+ i+  +e +++  +++++L + +++++++i+++ ++
  gi|14601572|ref|NP_148112.1| 559 YGEAIVLAEEAASIAEEAKELAEKAIEAAQEAVSEVLNQVEELLDRVKDLQEEIEDIAEK 618
                                   333344444445666666777778888888888888899999999999999999988766 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00087
                                   CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHH CS
                     Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnv 110
                                   ++++  ++++  +l+++++  +ea++l ke +    ++qk  +    vi++  ++++    +++  + + +   i +L+ +
  gi|14601572|ref|NP_148112.1| 627 EEIQAAIDEVLGKLDQARSLLEEADSLAKEGDID-GARQKLGE-ARDVIEEAVSMVR----DIRSMVEQAIgDLIDELRRL 701
                                   5678889999999999999999999999886544.44455544.4789999999*99....7777788888899******* PP

                                   HHHHHHHHHHHHHHHHHHHHH CS
                     Fib_alpha 111 lesneqkiqkLeqdidqkerk 131
                                   +e++++k ++L+++ + +e+k
  gi|14601572|ref|NP_148112.1| 702 IEELREKAAELNTEAAMLEAK 722
                                   *************99999876 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 1.6
                                   CCCCCCCCCHHHCCCCCCCCCC CS
                     Fib_alpha  26 llkyekdvkkdlekleneleei 47 
                                   +++ ++++++ +ekl++  +++
  gi|14601572|ref|NP_148112.1| 735 IEEARSNIEEAIEKLQDATDKL 756
                                   3333444444444444444333 PP

>> Zw10  Centromere/kinetochore Zw10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.2    0.0095        10      14     139 ..     302     441 ..     296     465 .. 0.71
   2 ?    5.4   6.2    0.0052       5.4      48     136 ..     482     572 ..     464     583 .. 0.69
   3 ?    8.3   5.9   0.00069      0.73      39     171 ..     589     711 ..     572     732 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0095
                          Zw10  14 kkisklekkveeikeevskmivkkYs.........eflelsssaeellerveslskeidal.....kkkveneieqdlkaa 80 
                                     ++kl + +ee  ++ ++ ++  Y          e +     a+  l++ + l++ ++++     + + ++ +e + +  
  gi|14601572|ref|NP_148112.1| 302 PEAQKLLEEAEEALAKARERLDRAYIllqegakvgEVMREIARAQGYLSKAQALASAAEVIllsgpTTETGTAVETATETT 382
                                   566777777777777777777777774444443444477778888888888888888777522222356667788888888 PP

                          Zw10  81 veelaelkqqlkekevvlellealkkieealeelkealknkaflvaadlleelkslldl 139
                                    + ++  ++   e+++  e+l +l ++e  + el e l++ +  +a++  +e++++ld 
  gi|14601572|ref|NP_148112.1| 383 ITTITTTTTREAEETEAAEVLAELTEVEIEIGELMEELETLQQKAASANQGEVQEILDE 441
                                   88888777777777788899999999998888888888888888888888888888754 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0052
                          Zw10  48 aeellerveslskeidalkkkveneieqdlkaaveelae..lkqqlkekevvlellealkkieealeelkealknkaflva 126
                                   a+  l+  e + + ++   ++  + ie++++a ++  a+  l  ql   e+v e l++l++ +e+le  kea  n+++ +a
  gi|14601572|ref|NP_148112.1| 482 ADSKLDTAEAILEVVEEYAERAREAIEEAEEALAKAEAKlqLAAQLSGSEAVEEALNRLEEAKEKLEAAKEAYSNGRYGEA 562
                                   333344444444455555555555555555554444444224578889999****************************99 PP

                          Zw10 127 adlleelksl 136
                                     l ee+ s+
  gi|14601572|ref|NP_148112.1| 563 IVLAEEAASI 572
                                   9999998875 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00069
                          Zw10  39 seflelsssaeellerveslskeidalkkkveneieqdlkaaveelaelkqqlkekevvlellealkkieealeelkealk 119
                                   +  +e+ +  eell+rv+ l++ei+++ +k  +               l++++  + ++ e+l +l +  ++lee ++  k
  gi|14601572|ref|NP_148112.1| 589 EAVSEVLNQVEELLDRVKDLQEEIEDIAEKARE------------AGVLTEEI--QAAIDEVLGKLDQARSLLEEADSLAK 655
                                   222233333333333333333333333322222............22222222..23455677777777777777777777 PP

                          Zw10 120 nkaflvaadlleelksll..dlekvekafq..lkilkalrkelsvlsenlqykLge 171
                                   ++++  a + l+e++ ++  ++  v+ +     + +  l  el++l e+l++k +e
  gi|14601572|ref|NP_148112.1| 656 EGDIDGARQKLGEARDVIeeAVSMVRDIRSmvEQAIGDLIDELRRLIEELREKAAE 711
                                   77777777777777777764333333333332234556666777777777666554 PP

>> Mustang  Musculoskeletal, temporally activated-embryonic nuclear protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.4   1.5e+03      16      46 ..     308     338 ..     299     343 .. 0.83
   2 ?   -1.4   0.1       2.4   2.5e+03       9      29 ..     458     478 ..     452     491 .. 0.74
   3 ?   -2.7   0.1       6.3   6.6e+03      16      31 ..     540     555 ..     533     562 .. 0.78
   4 ?    7.4   0.0    0.0044       4.7      11      39 ..     654     682 ..     648     691 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                       Mustang  16 lkgArskLgskkevksktyqvlkecEqaGka 46 
                                   l++A + L++ +e   + y +l+e  ++G++
  gi|14601572|ref|NP_148112.1| 308 LEEAEEALAKARERLDRAYILLQEGAKVGEV 338
                                   7899999999999999999999999888875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                       Mustang   9 PvvkEedlkgArskLgskkev 29 
                                     + E+ + +A++k+++ ++ 
  gi|14601572|ref|NP_148112.1| 458 SLLDEGRIAEAKEKIAQAEAA 478
                                   557788899999998876654 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.3
                       Mustang  16 lkgArskLgskkevks 31 
                                   l++A++kL   ke  s
  gi|14601572|ref|NP_148112.1| 540 LEEAKEKLEAAKEAYS 555
                                   7899999977776655 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0044
                       Mustang  11 vkEedlkgArskLgskkevksktyqvlke 39 
                                    kE+d+ gAr+kLg+ ++v      ++++
  gi|14601572|ref|NP_148112.1| 654 AKEGDIDGARQKLGEARDVIEEAVSMVRD 682
                                   59************999887776666665 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       2.1   2.2e+03      72      86 ..     412     426 ..     382     438 .. 0.50
   2 ?   -0.9   0.0       1.1   1.2e+03      84     109 ..     530     555 ..     477     563 .. 0.68
   3 ?    5.0   1.9     0.017        18      69     127 ..     565     618 ..     530     656 .. 0.55
   4 ?    6.5   0.0    0.0061       6.4      30      99 ..     688     754 ..     685     759 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                        DUF713  72 dleelqselsnLakk 86 
                                   +  el++el+ L++k
  gi|14601572|ref|NP_148112.1| 412 EIGELMEELETLQQK 426
                                   223344444444444 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                        DUF713  84 akkvlsaynkLeeafeklkelsekfe 109
                                   ++ v +a n+Leea ekl+  +e ++
  gi|14601572|ref|NP_148112.1| 530 SEAVEEALNRLEEAKEKLEAAKEAYS 555
                                   45678888888888888887777765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.017
                        DUF713  69 ekedleelqselsnLakk.vlsaynkLeeafeklkelsekfedkiFlkvLqksisdvatk 127
                                     e+ + + +e+++La+k +  a+++++e  ++++el ++++d      Lq++i d+a+k
  gi|14601572|ref|NP_148112.1| 565 LAEEAASIAEEAKELAEKaIEAAQEAVSEVLNQVEELLDRVKD------LQEEIEDIAEK 618
                                   3455556666666665441344566666666666666665555......34444444333 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0061
                        DUF713  30 EqewsdwlkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeafe 99 
                                   Eq  +d++ +lr+ i +l ++ +++++e +  + + +++ +    e  + +++ ++ + +a +kL++a +
  gi|14601572|ref|NP_148112.1| 688 EQAIGDLIDELRRLIEELREKAAELNTEAAMLEAKARRMGD---REALRLIEEARSNIEEAIEKLQDATD 754
                                   8999*************************999988888877...33333344444555555555555555 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1         4   4.2e+03      31      43 ..     418     430 ..     406     453 .. 0.78
   2 ?    5.3   2.0     0.016        17       3      41 ..     582     620 ..     580     630 .. 0.93
   3 ?    9.6   0.8   0.00071      0.75       4      57 ..     672     726 ..     669     736 .. 0.86
   4 ?   -0.9   0.0       1.3   1.4e+03      30      44 ..     743     757 ..     735     760 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4
                                   CCHHHHCCCCHHH CS
                 Synaptobrevin  31 ekldeLvdktenL 43 
                                   e+l++L++k+   
  gi|14601572|ref|NP_148112.1| 418 EELETLQQKAASA 430
                                   6677777777654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                                   XHHHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCH CS
                 Synaptobrevin   3 dklakikaevdevkdimkeNidkvlergekldeLvdkte 41 
                                   + ++++++ v+ev + ++e +d+v + +e+++++ +k+ 
  gi|14601572|ref|NP_148112.1| 582 KAIEAAQEAVSEVLNQVEELLDRVKDLQEEIEDIAEKAR 620
                                   78999*******************************986 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00071
                                   HHHHHHHHHHCCCCHHCCHHHHCHCCCCC.HHHHCCCCHHHHHHHHHHHHHHHHH CS
                 Synaptobrevin   4 klakikaevdevkdimkeNidkvlergek.ldeLvdktenLqssaqqFkkqarkl 57 
                                    ++++ + v ++++++++ i ++++   + ++eL +k+ +L+++a   + +ar++
  gi|14601572|ref|NP_148112.1| 672 VIEEAVSMVRDIRSMVEQAIGDLIDELRRlIEELREKAAELNTEAAMLEAKARRM 726
                                   577777889999999*****99999877736*********************997 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.3
                                   CCCHHHHCCCCHHHH CS
                 Synaptobrevin  30 gekldeLvdktenLq 44 
                                   +e +++L+d t++L 
  gi|14601572|ref|NP_148112.1| 743 EEAIEKLQDATDKLG 757
                                   477888888888885 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.88   9.3e+02      50      77 ..     269     296 ..     259     343 .. 0.53
   2 ?   -0.7   0.2       1.3   1.4e+03      89     116 ..     399     426 ..     375     440 .. 0.54
   3 ?    5.2   1.3      0.02        21      42     122 ..     438     519 ..     430     523 .. 0.84
   4 ?    9.2   2.7    0.0011       1.2      40     123 ..     530     618 ..     521     619 .. 0.77
   5 ?   13.8   2.7   4.2e-05     0.044      37     104 ..     582     648 ..     577     656 .. 0.88
   6 ?    8.4   2.1     0.002       2.1      39     121 ..     629     713 ..     624     728 .. 0.85
   7 ?    1.1   0.2      0.37   3.9e+02      50     101 ..     735     787 ..     730     791 .] 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.88
                       DUF1664  50 leqvseslaatkrhLssridrvdkklde 77 
                                   +e   ++l+a  ++  ++i+ +  +  +
  gi|14601572|ref|NP_148112.1| 269 MEARLQKLEAIYQEVGAKIEAIKGEYGA 296
                                   3333333444444444444433333333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                       DUF1664  89 vtevredlseigedvesvkeaveglesk 116
                                    +ev  +l+e++ ++ ++ e  e+l++k
  gi|14601572|ref|NP_148112.1| 399 AAEVLAELTEVEIEIGELMEELETLQQK 426
                                   3333333333333333333333333333 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.02
                       DUF1664  42 avesvskqleqvseslaatkrhLss.ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    +++ +  +++ s+ la+++  L + ri++  +k+ + +++ ++ ++++++++  l+ ++e  e  +ea+e+ e+ l++ e
  gi|14601572|ref|NP_148112.1| 438 ILDEAGALIDRASSLLAEARSLLDEgRIAEAKEKIAQAEAALEKADSKLDTAEAILEVVEEYAERAREAIEEAEEALAKAE 518
                                   556667778899999999999996449999999999999999999999999999999999999999999999999888877 PP

                       DUF1664 122 e 122
                                   +
  gi|14601572|ref|NP_148112.1| 519 A 519
                                   6 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0011
                       DUF1664  40 sdavesvskqleqvseslaatkrhLss.....ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                   s+ave+  ++le+ +e+l+a+k+  s+      i   ++     +e+++  ++ +++++e +se+ ++ve++ + v++l++
  gi|14601572|ref|NP_148112.1| 530 SEAVEEALNRLEEAKEKLEAAKEAYSNgrygeAIVLAEEAASIAEEAKELAEKAIEAAQEAVSEVLNQVEELLDRVKDLQE 610
                                   67899999999999999999999887531111444444444555566666778899999********************** PP

                       DUF1664 116 klerieek 123
                                   ++e+i ek
  gi|14601572|ref|NP_148112.1| 611 EIEDIAEK 618
                                   **999876 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 4.2e-05
                       DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve 104
                                   + ++ a e vs+ l+qv e l ++k +L+++i+ + +k  e   +++ei++ ++ev ++l++ ++ +e
  gi|14601572|ref|NP_148112.1| 582 KAIEAAQEAVSEVLNQVEELLDRVK-DLQEEIEDIAEKAREAGVLTEEIQAAIDEVLGKLDQARSLLE 648
                                   67889999*********98888876.6*********************************99887665 PP

  == domain 6  score: 8.4 bits;  conditional E-value: 0.002
                       DUF1664  39 lsdavesvskqleqvseslaatkrhLss..ridrvdkkldeqkeiskeikeevtevredlse.igedvesvkeaveglesk 116
                                   ++ a+++v  +l+q  + l+++ + L++  +id   +kl e  ++++e  + v ++r+ +++ ig+ ++++++++e+l +k
  gi|14601572|ref|NP_148112.1| 629 IQAAIDEVLGKLDQARSLLEEA-DSLAKegDIDGARQKLGEARDVIEEAVSMVRDIRSMVEQaIGDLIDELRRLIEELREK 708
                                   6788999999999988777666.55654236****************************986488889************9 PP

                       DUF1664 117 lerie 121
                                    ++++
  gi|14601572|ref|NP_148112.1| 709 AAELN 713
                                   98886 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.37
                       DUF1664  50 leqvseslaatkrhLssridrv.dkkldeqkeiskeikeevtevredlseige 101
                                   +e+  ++++++ ++L++  d++ d kl e  e++ + ++ ++e++ +l+e ++
  gi|14601572|ref|NP_148112.1| 735 IEEARSNIEEAIEKLQDATDKLgDGKLGEAREAIGQAEDLLNEAEMKLEEARQ 787
                                   56666777777778888888774557888888888888888888887777665 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3      0.13   1.4e+02      22      74 ..     272     323 ..     263     342 .. 0.77
   2 ?    0.1   5.6       1.1   1.2e+03      53      97 ..     497     543 ..     396     547 .. 0.58
   3 ?   -0.6   0.1       1.9     2e+03      63      91 ..     556     584 ..     527     594 .. 0.58
   4 ?   11.1   1.0   0.00045      0.47       2      91 ..     598     691 ..     590     694 .. 0.81
   5 ?    7.2   1.6    0.0073       7.7       7      77 ..     689     761 ..     686     788 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHHHHHHTS..S-HHHHHHHHH.HHHHHHHHHHHHHH CS
                           ING  22 elreiDakvqellkeidskiekflkngslqknekeeels.riqeelkeaqelld 74 
                                   +l++++a +qe+ ++i+    ++    +l++n++ ++l  + +e+l +a e ld
  gi|14601572|ref|NP_148112.1| 272 RLQKLEAIYQEVGAKIEAIKGEYG--AELDQNPEAQKLLeEAEEALAKARERLD 323
                                   788999999999999988888887..5677777777766688888888877666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHC CS
                           ING  53 nekeeelsriqeelkeaqelldeKiqlaqqal..dlvdkhlrrLdqd 97 
                                   +e  e+ ++  ee +ea   ++ K+qla q+   + v++ l+rL+++
  gi|14601572|ref|NP_148112.1| 497 EEYAERAREAIEEAEEALAKAEAKLQLAAQLSgsEAVEEALNRLEEA 543
                                   33333444444455555555666666666663225666666666665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING  63 qeelkeaqelldeKiqlaqqaldlvdkhl 91 
                                   +  + ea+ l++e   +a++a +l +k +
  gi|14601572|ref|NP_148112.1| 556 NGRYGEAIVLAEEAASIAEEAKELAEKAI 584
                                   34455666666666666666666666655 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00045
                                   HHHHHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING   2 LedyldsvenLPlelqrnltelreiDakvqellkeidskiekfl....kngslqknekeeelsriqeelkeaqelldeKiq 78 
                                   +e++ld v+ L++e+++  ++ re  + ++e+++ id+ + k+       ++ ++  ke  +   +++l ea ++ +e + 
  gi|14601572|ref|NP_148112.1| 598 VEELLDRVKDLQEEIEDIAEKAREAGVLTEEIQAAIDEVLGKLDqarsLLEEADSLAKEGDIDGARQKLGEARDVIEEAVS 678
                                   6788888888888888888888888888888888887777777676664456788888889999***************** PP

                                   HHHHHHHHHHHHH CS
                           ING  79 laqqaldlvdkhl 91 
                                   ++ ++  +v++ +
  gi|14601572|ref|NP_148112.1| 679 MVRDIRSMVEQAI 691
                                   **99999999876 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0073
                                   TSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..TS..S-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           ING   7 dsvenLPlelqrnltelreiDakvqellkeidskiekfl..kngslqknekeeelsriqeelkeaqelldeKi 77 
                                   +++  L +el+r+++elre+ a++++  + ++ k++++   ++ +l ++ +++  + i++ ++++ +l+d K+
  gi|14601572|ref|NP_148112.1| 689 QAIGDLIDELRRLIEELREKAAELNTEAAMLEAKARRMGdrEALRLIEEARSNIEEAIEKLQDATDKLGDGKL 761
                                   6788899************************999999995433334444444444478888888888888887 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.0     0.052        54     247     305 ..     269     324 ..     262     357 .. 0.56
   2 ?    0.6   1.3      0.23   2.4e+02      19     102 ..     344     428 ..     336     435 .. 0.68
   3 ?    9.4   5.9   0.00049      0.51       7      90 ..     436     524 ..     433     548 .. 0.85
   4 ?    5.7   6.2    0.0065       6.8     238     321 ..     567     651 ..     565     656 .. 0.63
   5 ?    8.9   3.5    0.0007      0.74      20      96 ..     643     721 ..     639     761 .. 0.59
   6 ?    4.2   3.2     0.018        19     225     317 ..     697     789 ..     696     791 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.052
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH CS
                         APG17 247 lqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeefler 305
                                   +++rl+++e++++++ +k e+i+  + a  ++  e +++ ++ +e la   +++e l r
  gi|14601572|ref|NP_148112.1| 269 MEARLQKLEAIYQEVGAKIEAIKGEYGAELDQNPEAQKLLEEAEEALA---KARERLDR 324
                                   455555555555555555555555555555555555555555555555...44444433 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.23
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIII.IIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS CS
                         APG17  19 rAnelltsarqeleeavkllakteflrdglkqQlkllekirkslerkl.ekgkeefkdlikeldaanerLektlekLrktk 98 
                                   rA+ +l++a+ + + a+++l        g + + ++ ++i+    +++ e  ++e++++++el+++  ++ + +e+L++ +
  gi|14601572|ref|NP_148112.1| 344 RAQGYLSKAQALASAAEVILLSGPTTETGTAVETATETTITTITTTTTrEAEETEAAEVLAELTEVEIEIGELMEELETLQ 424
                                   666666666666666666666666666666666666666666555555688888888888888888888888888888776 PP

                                   -TTS CS
                         APG17  99 veps 102
                                    +++
  gi|14601572|ref|NP_148112.1| 425 QKAA 428
                                   6655 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00049
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHH CS
                         APG17   7 kksLseaqtlcqrAnelltsarqelee.....avkllakteflrdglkqQlkllekirkslerklekgkeefkdlikelda 82 
                                   ++ L ea  l  rA++ll++ar++l+e     a++++a++e   +  ++ l+++e+i + +e+  e+++e +++ +++l +
  gi|14601572|ref|NP_148112.1| 436 QEILDEAGALIDRASSLLAEARSLLDEgriaeAKEKIAQAEAALEKADSKLDTAEAILEVVEEYAERAREAIEEAEEALAK 516
                                   567999****************99875222226788999999999************************************ PP

                                   HHHHHHHH CS
                         APG17  83 anerLekt 90 
                                   a ++L+  
  gi|14601572|ref|NP_148112.1| 517 AEAKLQLA 524
                                   ****9865 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0065
                                   HHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHH CS
                         APG17 238 aeledVvkelqerleem.ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekl 317
                                   +e  ++ +e +e +e+  e+a++++se  +++e+ll+ +k++ ee+e++ +k +e   +++++++ + +   + ++  + l
  gi|14601572|ref|NP_148112.1| 567 EEAASIAEEAKELAEKAiEAAQEAVSEVLNQVEELLDRVKDLQEEIEDIAEKAREAGVLTEEIQAAIDEVLGKLDQARSLL 647
                                   556666666666666555777777777777777777777777777777766666666666777766666555555555555 PP

                                   HHHH CS
                         APG17 318 eele 321
                                   ee +
  gi|14601572|ref|NP_148112.1| 648 EEAD 651
                                   5555 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0007
                                   HHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHT CS
                         APG17  20 Anelltsarqeleea..vkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLrk 96 
                                   A++ll++a ++ +e   +   +k++  rd +++ + +++ ir+++e++  ++ +e+++li+el ++ ++L++  ++L++
  gi|14601572|ref|NP_148112.1| 643 ARSLLEEADSLAKEGdiDGARQKLGEARDVIEEAVSMVRDIRSMVEQAIGDLIDELRRLIEELREKAAELNTEAAMLEA 721
                                   5555555555555552233445566677777777777777777777777777777777777777777777776666654 PP

  == domain 6  score: 4.2 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHH CS
                         APG17 225 ereelleVlekDaaeledVvkelqerleem..ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeefl 303
                                   e + l+e l + aael    + l+++++ m   +a  l++e +++ie+++++l++a ++l +   kl e  + + ++e++l
  gi|14601572|ref|NP_148112.1| 697 ELRRLIEELREKAAELNTEAAMLEAKARRMgdREALRLIEEARSNIEEAIEKLQDATDKLGD--GKLGEAREAIGQAEDLL 775
                                   778899999999999999999**********99999*************************6..47777777777999999 PP

                                   HH...HHHHHHHHH CS
                         APG17 304 erweeekekieekl 317
                                   ++ e + e+  ++l
  gi|14601572|ref|NP_148112.1| 776 NEAEMKLEEARQRL 789
                                   99888888777766 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.2      0.88   9.3e+02       6      41 ..     152     187 ..     147     239 .. 0.54
   2 ?    1.8   9.6      0.19     2e+02      16     139 ..     300     449 ..     297     454 .. 0.69
   3 ?    2.0  20.5      0.17   1.8e+02       6     118 ..     454     548 ..     449     571 .. 0.59
   4 ?   11.1   9.2   0.00027      0.29      12     101 ..     572     673 ..     561     694 .. 0.75
   5 ?    6.6   0.6    0.0064       6.8       1      38 [.     745     782 ..     729     789 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.88
                                   HHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCC CS
                          YfdX   6 qkArlaldqgdtkeAkkllekAqgkleaaladdpkl 41 
                                    kA+ + ++gd+ +A++ l  ++++ e a a + + 
  gi|14601572|ref|NP_148112.1| 152 AKALREAARGDPGKAVDILVAVEAAVESAGAIEVAA 187
                                   555555666666666666666666666555555444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                                   -HHHHHHHHHHHHHHHTS-HHHHHCCB-.........................S--SSSS-EEEEEEEEEEE------HHH CS
                          YfdX  16 dtkeAkkllekAqgkleaaladdpklvk.........................kapasadalvPvdaevividdladtpek 71 
                                   ++ eA klle+A+++l++a+++  +  +                         +a asa++ + + +  +   + ++t + 
  gi|14601572|ref|NP_148112.1| 300 QNPEAQKLLEEAEEALAKARERLDRAYIllqegakvgevmreiaraqgylskaQALASAAEVILLSGPTTETGTAVETATE 380
                                   567999**************9999997788887778888777777766666443333444677777766666666666666 PP

                                   HHHHHHHHHHHHTT-HHHHHHHHHHT.T-EEEEEEEEEEHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                          YfdX  72 kaaikkanellkkgdtqaArelLkll.gseidittallPLatypaavkkAaelleegkyyeAkeaLkea 139
                                    ++ + + +  ++ +  +A+e+L++l ++ei i +    L+t +++ + A +   ++  +eA +++++a
  gi|14601572|ref|NP_148112.1| 381 TTITTITTTTTREAEETEAAEVLAELtEVEIEIGELMEELETLQQKAASANQGEVQEILDEAGALIDRA 449
                                   666666677777777777777776542567777777777777777777777666666666666666666 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.17
                                   HHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-............S--SSSS......-EEEEEEEEEEE------ CS
                          YfdX   6 qkArlaldqgdtkeAkkllekAqgkleaaladdpklvk............kapasad......alvPvdaevividdladt 68 
                                    +Ar+ ld+g ++eAk+ +++A+++le+a ++  +  +            ++    +      al  + a+++++  l  +
  gi|14601572|ref|NP_148112.1| 454 AEARSLLDEGRIAEAKEKIAQAEAALEKADSKLDTAEAilevveeyaeraRE----AieeaeeALAKAEAKLQLAAQLSGS 530
                                   68*****************************999995566666666554422....1333355444444444444443333 PP

                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHTT-EEEEEEEEEEHHHHHHHHH CS
                          YfdX  69 pekkaaikkanellkkgdtqaArelLkllgseidittallPLatypaavk 118
                                   +++++a+++++e                                 ++++ 
  gi|14601572|ref|NP_148112.1| 531 EAVEEALNRLEE--------------------------------AKEKLE 548
                                   333333333222................................222222 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00027
                                   HCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB-............S--SSSS-EEEEEEEEEEE------HHHHHHHHHHHH CS
                          YfdX  12 ldqgdtkeAkkllekAqgkleaaladdpklvk............kapasadalvPvdaevividdladtpekkaaikkane 80 
                                   ++++ ++ A k++e Aq++ +++l++  +l+              ++a ++  +    +  + ++l++++++ + +++a++
  gi|14601572|ref|NP_148112.1| 572 IAEEAKELAEKAIEAAQEAVSEVLNQVEELLDrvkdlqeeiediAEKAREAGVLTEEIQAAIDEVLGKLDQARSLLEEADS 652
                                   66667777777777777777777777777766655554465444444444466666666777778**************** PP

                                   HHHTT-HHHHHHHHHHTT-EE CS
                          YfdX  81 llkkgdtqaArelLkllgsei 101
                                   l k+gd ++Ar++L ++++ i
  gi|14601572|ref|NP_148112.1| 653 LAKEGDIDGARQKLGEARDVI 673
                                   **************9998654 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0064
                                   HHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHH CS
                          YfdX   1 AlrdiqkArlaldqgdtkeAkkllekAqgkleaaladd 38 
                                   A++++q A   l +g+  eA++++ +A+  l++a+ + 
  gi|14601572|ref|NP_148112.1| 745 AIEKLQDATDKLGDGKLGEAREAIGQAEDLLNEAEMKL 782
                                   56777777777777777777777777777777776655 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   5.1e-05     0.054      45      99 ..     300     354 ..     294     355 .. 0.84
   2 ?    8.2   3.0     0.002       2.2      49      99 ..     441     491 ..     422     495 .. 0.83
   3 ?   -1.0  12.0       1.4   1.5e+03      50     136 ..     503     591 ..     493     622 .. 0.73
   4 ?    1.6   0.1      0.22   2.3e+02      50      97 ..     629     676 ..     615     682 .. 0.83
   5 ?   -0.1   0.5      0.72   7.6e+02      52      93 ..     740     781 ..     705     788 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                                   HHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSS.SHHHHHHHHHHHHHHH CS
                          TarH  45 tnrlqqqaaLaearvsllqaRltLnragiaaladeaeda.kellaraeeslaqsee 99 
                                   +n  ++q  L ea+ +l++aR  L+ra i + +++  +   + +ara+ +l+++++
  gi|14601572|ref|NP_148112.1| 300 QNP-EAQKLLEEAEEALAKARERLDRAYILLQEGAKVGEvMREIARAQGYLSKAQA 354
                                   555.8999******************76666666666559************9986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.002
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHH CS
                          TarH  49 qqqaaLaearvsllqaRltLnragiaaladeaedakellaraeeslaqsee 99 
                                   ++ a ++ a++ l++aR  L+   ia ++ + ++a+++l++a++ l+ +e+
  gi|14601572|ref|NP_148112.1| 441 EAGALIDRASSLLAEARSLLDEGRIAEAKEKIAQAEAALEKADSKLDTAEA 491
                                   4667899***************99**********************99986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHHHHHHH..HHHTS---GGGHH.HHHHHHHHHHHH CS
                          TarH  50 qqaaLaearvsllqaRltLnragiaaladeaedakellaraeeslaqseeawk..aYlalprtaeeeealaaelkakykal 128
                                   +++a+ ea+ +l++a  +L  a+  +   + e+a  +l++a+e l++++ea+   +Y ++   aee +++a+e+k+  ++ 
  gi|14601572|ref|NP_148112.1| 503 AREAIEEAEEALAKAEAKLQLAAQLSGSEAVEEALNRLEEAKEKLEAAKEAYSngRYGEAIVLAEEAASIAEEAKELAEKA 583
                                   899******************666666666666699999*************74469999999966667777777666664 PP

                                   HHHHHHHH CS
                          TarH 129 qdglapli 136
                                    ++ ++++
  gi|14601572|ref|NP_148112.1| 584 IEAAQEAV 591
                                   45555544 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHHHHHH CS
                          TarH  50 qqaaLaearvsllqaRltLnragiaaladeaedakellaraeeslaqs 97 
                                    qaa++e+  +l qaR  L  a   a +++ ++a++ l +a++ ++++
  gi|14601572|ref|NP_148112.1| 629 IQAAIDEVLGKLDQARSLLEEADSLAKEGDIDGARQKLGEARDVIEEA 676
                                   578888888899999999999999999999999999999998877665 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.72
                                   HHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSSHHHHHHHHH CS
                          TarH  52 aaLaearvsllqaRltLnragiaaladeaedakellaraees 93 
                                   +++ ea  +l++a ++L   +   ++ +  +a++ll++ae+ 
  gi|14601572|ref|NP_148112.1| 740 SNIEEAIEKLQDATDKLGDGKLGEAREAIGQAEDLLNEAEMK 781
                                   344444444444444444422222222222334444444444 PP

>> Baculo_p24  Baculovirus P24 capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.6   1.7e+03     135     172 ..     380     417 ..     332     429 .. 0.51
   2 ?   -0.7   0.1      0.97     1e+03     165     165 ..     460     460 ..     398     529 .. 0.51
   3 ?    7.8   0.9    0.0025       2.6     104     177 ..     534     614 ..     521     619 .. 0.73
   4 ?    2.7   0.1     0.089        94     107     180 ..     630     710 ..     622     758 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                    Baculo_p24 135 tesssnenieslreilrseeasllsnlnsllesikslq 172
                                   +++ ++ ++++ re  ++e a++l++l+++   i +l+
  gi|14601572|ref|NP_148112.1| 380 ETTITTITTTTTREAEETEAAEVLAELTEVEIEIGELM 417
                                   22222233444444445555555555544444443333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.97
                    Baculo_p24 165 l 165
                                   l
  gi|14601572|ref|NP_148112.1| 460 L 460
                                   1 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0025
                    Baculo_p24 104 seavdplkdiktqlctlqecleesnvlvn....sttesssn...enieslreilrseeasllsnlnsllesikslqadltn 177
                                   +ea ++l++ k++l++ +e  +++ +  +    +++ s  +   e  e++ e  +++ +++l ++++ll+ +k+lq ++++
  gi|14601572|ref|NP_148112.1| 534 EEALNRLEEAKEKLEAAKEAYSNGRYGEAivlaEEAASIAEeakELAEKAIEAAQEAVSEVLNQVEELLDRVKDLQEEIED 614
                                   4577889999999999999999988766577763233333323366666667777777788999999********999876 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.089
                    Baculo_p24 107 vdplkdiktqlctlqecleesnvlvn.......sttesssn.....enieslreilrseeasllsnlnsllesikslqadl 175
                                      ++++  +l + ++ lee+++l++       + +    +     + ie++  ++r  ++ +   + +l++ ++ l+ +l
  gi|14601572|ref|NP_148112.1| 630 QAAIDEVLGKLDQARSLLEEADSLAKegdidgaR-Q----KlgearDVIEEAVSMVRDIRSMVEQAIGDLIDELRRLIEEL 705
                                   4556777777777777777777766666554421.2....12223467777777777777777777777777777777777 PP

                    Baculo_p24 176 tnkla 180
                                    +k a
  gi|14601572|ref|NP_148112.1| 706 REKAA 710
                                   76654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (791 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2736  (0.152602); expected 358.6 (0.02)
Passed bias filter:                      970  (0.0541023); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); expected 17.9 (0.001)
Passed Fwd filter:                       145  (0.00808746); 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: 2.65u 0.41s 00:00:03.06 Elapsed: 00:00:00.66
# Mc/sec: 3621.08
//
Query:       gi|14601575|ref|NP_148115.1|  [L=319]
Description: Lrp family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-09   36.7   0.0    4.4e-09   35.8   0.0    1.5  1  HTH_24         Winged helix-turn-helix DNA-binding
      2e-05   24.3   0.1    3.8e-05   23.4   0.1    1.4  1  HTH_IclR       IclR helix-turn-helix domain
    0.00074   19.4   0.0     0.0015   18.3   0.0    1.6  1  MarR_2         MarR family
     0.0013   18.6   0.0     0.0025   17.7   0.0    1.5  1  MarR           MarR family
     0.0031   17.3   0.1     0.0067   16.2   0.1    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0056   16.5   0.0      0.011   15.6   0.0    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.067   13.1   0.0    2.0  1  HTH_5          Bacterial regulatory protein, arsR family
      0.025   14.4   5.5       0.45   10.4   0.7    2.4  2  DUF4307        Domain of unknown function (DUF4307)
      0.045   13.8   0.0       0.08   13.0   0.0    1.4  1  HTH_20         Helix-turn-helix domain
       0.08   12.9   0.2       0.23   11.5   0.0    1.8  2  HTH_11         HTH domain
       0.12   12.9   0.0       0.23   12.0   0.0    1.5  1  HTH_27         Winged helix DNA-binding domain
       0.18   12.0   0.4          2    8.6   0.2    2.1  2  Sid-5          Sid-5 family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.9e-12   4.4e-09       1      48 []     249     297 ..     249     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.9e-12
                        HTH_24   1 ldetdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   ld td+ IL +L+  ++   q  L +++gl++st++rrl++Le +G+++
  gi|14601575|ref|NP_148115.1| 249 LDSTDKLILDTLKNAGGtSEQPALLKATGLPKSTLWRRLRKLEAMGYVR 297
                                   799***********999899***************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   2.5e-08   3.8e-05       8      49 ..     256     297 ..     255     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                   iLd l  a++      l ++tglpkSt  R L+ L+ +Gyv+
  gi|14601575|ref|NP_148115.1| 256 ILDTLKNAGGTSEQPALLKATGLPKSTLWRRLRKLEAMGYVR 297
                                   99***************************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     1e-06    0.0015       6      52 ..     252     297 ..     247     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                                   HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                        MarR_2   6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                   ++  +L  L +++g    + +l +++gl+ks++ r+l++L+a G+v+
  gi|14601575|ref|NP_148115.1| 252 TDKLILDTLKNAGGT-SEQPALLKATGLPKSTLWRRLRKLEAMGYVR 297
                                   566789999999996.499***************************8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0025       7      48 ..     255     297 ..     249     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                   HHHHHHHHSTTEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          MarR   7 viLrilyeqgplsvs.eLakklgvskstvtrvldrLekkGlie 48 
                                   +iL +l++ g+ s +  L k+ g+ kst+ r l++Le  G+++
  gi|14601575|ref|NP_148115.1| 255 LILDTLKNAGGTSEQpALLKATGLPKSTLWRRLRKLEAMGYVR 297
                                   79***************************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   4.5e-06    0.0067       1      42 []     249     291 ..     249     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                 HTH_AsnC-type   1 LDeiDrkILeaLqed.aRisyaeLAervGlSestvlrRvrrLe 42 
                                   LD +D+ IL+ L    +     +L +++Gl  st +rR+r+Le
  gi|14601575|ref|NP_148115.1| 249 LDSTDKLILDTLKNAgGTSEQPALLKATGLPKSTLWRRLRKLE 291
                                   8**************8899999********************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 !   15.6   0.0   7.3e-06     0.011      27      58 ..     271     302 ..     259     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.3e-06
                                   HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                          TrmB  27 eiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                    + +++g+p+s+  + Lr+Le +G+V+++k+ 
  gi|14601575|ref|NP_148115.1| 271 ALLKATGLPKSTLWRRLRKLEAMGYVRIIKKG 302
                                   57899***********************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 ?   13.1   0.0   4.5e-05     0.067      22      45 ..     273     296 ..     271     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                                   HHHHTS-HHHHHHHHHHHHHTTSE CS
                         HTH_5  22 aeelglsqstvShHLkkLreaGLV 45 
                                    +++gl++st+ + L+kL+ +G+V
  gi|14601575|ref|NP_148115.1| 273 LKATGLPKSTLWRRLRKLEAMGYV 296
                                   689********************9 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7    0.0003      0.45       5      52 ..      11      56 ..       7      64 .. 0.70
   2 ?    5.9   0.4    0.0071        11       6      41 ..     215     251 ..     208     256 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                       DUF4307  5 lvillvvlvvvalalvawigysqgsadvsaevvgfevvddstvevtfe 52
                                   +i+lv+l+v+a+++v+ ++++q  ++ s + v++++  d  +e++++
  gi|14601575|ref|NP_148115.1| 11 RAIVLVLLMVIAVLAVGQLALAQ--QEASINSVEVTIRGDGVAEARVQ 56
                                  57888999999999999999998..55555555556666666666655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0071
                       DUF4307   6 villvvlvvvalalvawigysq.gsadvsaevvgfev 41 
                                   +i+l++++++a+++v +++ ++ g + v+a v++ + 
  gi|14601575|ref|NP_148115.1| 215 AIILAAVIIIAGGAVLYMYRKKsGGNGVDAVVTSLDS 251
                                   3444444444444444444444677777777776665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.3e-05      0.08      16      60 ..     257     302 ..     250     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-05
                                   HHHHSTCTTB-HHH.HHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                        HTH_20  16 lraLaraegltase.laerldlskntlsyHLrvLeeagLvevvreg 60 
                                   l+ L+ a+g +  + l ++ +l+k+tl ++Lr+Le  g+v+  + g
  gi|14601575|ref|NP_148115.1| 257 LDTLKNAGGTSEQPaLLKATGLPKSTLWRRLRKLEAMGYVRIIKKG 302
                                   556655555555431555568*******************988876 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.4   6.6e+03      42      53 ..      48      62 ..      44      63 .. 0.74
   2 ?   11.5   0.0   0.00015      0.23       6      51 ..     257     303 ..     253     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.4
                        HTH_11 42 lg...vpIesepgrG 53
                                   g   +++++e+g+G
  gi|14601575|ref|NP_148115.1| 48 DGvaeARVQAEAGPG 62
                                  556668999999998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                        HTH_11   6 lelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIesepg 51 
                                   l  L++a g+     L + +++ ++t +r++++Le++g v+I+++ +
  gi|14601575|ref|NP_148115.1| 257 LDTLKNAGGTSEQPALLKATGLPKSTLWRRLRKLEAMGyVRIIKKGK 303
                                   5556556665666667777778889*************999998865 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 ?   12.0   0.0   0.00015      0.23       7      49 ..     255     297 ..     249     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                        HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49 
                                   l+L +++  ++++++ +l +++ + +s+    l+kL+++G+v 
  gi|14601575|ref|NP_148115.1| 255 LILDTLKNAGGTSEQPALLKATGLPKSTLWRRLRKLEAMGYVR 297
                                   67888887788888899*************************3 PP

>> Sid-5  Sid-5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2    0.0013         2      10      40 ..       5      35 ..       3      44 .. 0.88
   2 ?    0.9   0.0      0.35   5.2e+02      21      41 ..     216     236 ..     208     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                         Sid-5 10 kaaeencvilLaisilllllNilqvvffnRa 40
                                  k+a+  + i+L++++++ +l ++q++ ++ +
  gi|14601575|ref|NP_148115.1|  5 KKAQAGRAIVLVLLMVIAVLAVGQLALAQQE 35
                                  89**********************9987665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                         Sid-5  21 aisilllllNilqvvffnRak 41 
                                   +i+  ++++  + v++++R+k
  gi|14601575|ref|NP_148115.1| 216 IILAAVIIIAGGAVLYMYRKK 236
                                   4455567777899*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2221.40
//
Query:       gi|14601576|ref|NP_148116.1|  [L=394]
Description: citrate synthase [Aeropyrum pernix K1]
Scores for complete 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-107  359.1   0.0   2.9e-107  358.9   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 !  358.9   0.0  1.6e-111  2.9e-107       1     361 []      19     374 ..      19     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 358.9 bits;  conditional E-value: 1.6e-111
                                   GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTT.S--HHHHHHHHC CS
                  Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaear.klpekvlealea 80 
                                   gl +v++ et+is vd++ +  +YRGy+ie++  e++sf e+a+l+l+g+lP  eelke+k+++ ++r ++pek+++a+++
  gi|14601576|ref|NP_148116.1|  19 GLVNVIVDETRISGVDPKGEATIYRGYTIEDIG-EHASFYEAAHLILFGRLPCDEELKEIKSKIDKYRgQIPEKLFDAMKH 98 
                                   7889************88877**********88.8*******************************888************ PP

                                   SSTTS-HHHHHHHHHHHHHHHSTT..CTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHH CS
                  Citrate_synt  81 lpkdahpmavlraavsalsaddee..seakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflyml 159
                                   +p  +hpm   + ++++l++++           e+  +++al+l A+lp+i  + ++  ++++ l+pd+++++a  +l+m+
  gi|14601576|ref|NP_148116.1|  99 VP-VTHPMYYGIYGTALLGQYYAPewR--F--DEDFLYDHALRLTAQLPVIFTTGWNLAHHGTFLRPDPSKDHAWDVLRMI 174
                                   **.679***************975322..2..33444555555*****************98656***99*********** PP

                                   HSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG..... CS
                  Citrate_synt 160 rgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleeigsaev.... 236
                                     ++p++ ea++++  lvl++DH++naSTf++rv++Stl+dlysa+a+gi+alkGplhggane++++m+ ++ +++     
  gi|14601576|ref|NP_148116.1| 175 VMREPSDIEARAFESTLVLYMDHGFNASTFTTRVIGSTLSDLYSAVAGGIAALKGPLHGGANEKAMEMFLDAMKKAEekgv 255
                                   879*****************************************************************9988455447899 PP

                                   ....GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHGCT-EB- CS
                  Citrate_synt 237 ....eveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekeeknlypN 313
                                        +eey++++la+ ke+++GfGHr+yk +DpR+ +  +++ +l +    + ++k+++++eev+++     e k++ +N
  gi|14601576|ref|NP_148116.1| 256 plydYIEEYIKEKLAR-KEKIMGFGHRIYKLHDPRTDVAAKFVAKLKD---GEFWMKVLKKAEEVMWR-----E-KKIPAN 326
                                   ***************7.6*************************99855...788**************.....8.9***** PP

                                   THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                  Citrate_synt 314 vDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                   +D+y++vly++lgip +++t++fa++Rv+Gw+Ah++eq  +nk+iRP+
  gi|14601576|ref|NP_148116.1| 327 IDLYTAVLYYQLGIPIPMYTPIFAMGRVVGWSAHYIEQVLNNKLIRPT 374
                                   *************************************99********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2872.06
//
Query:       gi|118431563|ref|NP_148117.2|  [L=297]
Description: 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A synthase [Aeropyrum pernix K1]
Scores for complete 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-35  122.0   0.0    4.2e-35  121.8   0.0    1.0  1  CitG      ATP:dephospho-CoA triphosphoribosyl transferase
  ------ inclusion threshold ------
      0.073   12.3   0.0        0.1   11.8   0.0    1.1  1  DUF4928   Domain of unknown function (DUF4928)


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 !  121.8   0.0   4.7e-39   4.2e-35       4     277 ..      11     283 ..       8     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 4.7e-39
                                    XXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHHHH---- CS
                           CitG   4 avlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekamlaatggv 83 
                                    ++   +lE  ++pKPG V++++s    + +f +F+  a+ +++ ++ a+ ++++ +  +  ++s+ e+  +++    +g 
  gi|118431563|ref|NP_148117.2|  11 LSYGAVLEPYLHPKPGGVTPYASE--GGKSFGDFVLHATLSSRLLAWACLKAWK-NGPIGVIASVKERYLREVVPRFKG- 86 
                                    5667899*****************..***************************9.888888888888888888888888. PP

                                    --HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--H.HHHHHH.HHHHHH--.....---...HHHHHH.. CS
                           CitG  84 NThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltv.edavaf.rairlakv.....eel...kdelve.k 152
                                    N   G+++l+++la+a++++    +++++eelv +a++++  +t  ++++   + +r+ ++       +   +d   + +
  gi|118431563|ref|NP_148117.2|  87 NIAYGTFMLMAPLAVAIALS----KSSEPEELVTTARDTIYCCTGrRESLLHyKILRRLSPshlgrY-RgelPDVASGgE 161
                                    ******************77....67889***********999974566666899999999666550.154444444478 PP

                                    TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHHH CS
                           CitG 153 ksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallaelpDtnilrrgGaegaeevq 232
                                    +++  +  l +   +d++ +e+a+g+p+++e+   +l++  ++g++ ++al++all++lae+ Dt+i +++G  + + ++
  gi|118431563|ref|NP_148117.2| 162 RDIPPYPLLLKLNSWDMVHRELAKGYPITLEAYRHSLNRV-KEGRSVEEALLEALLKVLAEHGDTLIFQKYGGRAFKMAR 240
                                    99*****************************777777775.6889*********************************** PP

                                    HHHH..........H-.SHHHHHHHHHHHHHHT---HHHHHHHHHH CS
                           CitG 233 eeArallaaggvaaea.glealeeldrelvernisPGgsADllaat 277
                                    eeAr        ++++  ++a++ l+r ++ r+++PG + D++a++
  gi|118431563|ref|NP_148117.2| 241 EEARVAFHV---SERWgVRHAITWLERLWRGREWNPGAALDIVAVA 283
                                    ****55554...577779**************************98 PP

>> DUF4928  Domain of unknown function (DUF4928)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.1e-05       0.1      22      82 ..     178     243 ..     172     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                        DUF4928  22 vvlerlkegypldrday......laegrsqvrGasGatvanilkrhgedrdfakeGGrtsrgtkela 82 
                                    +v + l++gyp+  +ay      + egrs v  a   ++ ++l  hg++  f k GGr+ ++++e a
  gi|118431563|ref|NP_148117.2| 178 MVHRELAKGYPITLEAYrhslnrVKEGRS-VEEALLEALLKVLAEHGDTLIFQKYGGRAFKMAREEA 243
                                    688999*****998887333332345544.6667778999*******************99998744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2215.58
//
Query:       gi|14601578|ref|NP_148118.1|  [L=104]
Description: hypothetical protein APE_1716 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.01   16.9   0.0      0.012   16.8   0.0    1.1  1  SOGA         Protein SOGA
      0.064   13.6   0.0        0.1   12.9   0.0    1.4  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.8   0.0   1.3e-06     0.012       7      51 ..      17      61 ..      11      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                          SOGA  7 rhLqfveeEaeLlrrslseleeenkqlteeLnkyksklgeeessl 51
                                   hL+f++eE e+ +r + +++    q+ + L+ +  ++++  +  
  gi|14601578|ref|NP_148118.1| 17 AHLHFMKEEEEIVCRDIERIAGYLGQVSKALEELDADPEPLYHVW 61
                                  49*******************999999999998888877765554 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05       0.1       3      41 ..      23      69 ..      21      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                  HHHHHHHHHHHHHHHHHHTTCGC.S-.-T.T----S.......-EB- CS
                   Glu-tRNAGln  3 eeEleklakelnsildyveqLqe.vd.tt.gveplthp.....vlRe 41
                                   eE+e + +++++i +y  q+++ ++ ++ + epl+h+     + R+
  gi|14601578|ref|NP_148118.1| 23 KEEEEIVCRDIERIAGYLGQVSKaLEeLDaDPEPLYHVwesrsRIRD 69
                                  5899*************999886344444489******999764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 821.91
//
Query:       gi|118431564|ref|NP_148119.2|  [L=481]
Description: glutamyl-tRNA(Gln) amidotransferase subunit A [Aeropyrum pernix K1]
Scores for 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-120  401.3   0.0   6.4e-120  401.1   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.1   0.0  3.6e-124  6.4e-120       3     450 ..      25     462 ..      23     463 .. 0.95

  Alignments for each domain:
  == domain 1  score: 401.1 bits;  conditional E-value: 3.6e-124
                                    HHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS-- CS
                        Amidase   3 veaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDa 82 
                                    v+ +l+ + + + ++na++ +  ee l +Aa+  ++r r  e   L Gv++ vKDni++  +pttaGs++l +y+++++a
  gi|118431564|ref|NP_148119.2|  25 VSRVLDALRRWERDVNAFISLEAEEVLIDAAEEAARRWRRGEARRLEGVVVGVKDNISTSFLPTTAGSRMLDGYIPPFNA 104
                                    6778888999999********999999999999999999999************************************** PP

                                    HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHH CS
                        Amidase  83 tvverLkkaGavilgkTnmdefamgsstensvfgptrNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsf 162
                                    tvverL  +Ga+i+gkTn+defamgs++e s+fgptrNPwd+sr+pGGSS+Gs+A +A g +++a+G+DtGGS+R+PA++
  gi|118431564|ref|NP_148119.2| 105 TVVERLLMEGAIIIGKTNLDEFAMGSTGEFSAFGPTRNPWDLSRVPGGSSSGSGACLAYGACDAALGSDTGGSVRLPAAY 184
                                    ******************************************************************************** PP

                                    CTSEEEE--TTSC--TTB--SSTTT-EEEEEESSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEE CS
                        Amidase 163 cglvGlKPtygrvSragvvalessldvvGplarsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGv 242
                                    + +vGlKPtyg+vSr+g++++++sl+++ p+ars ed+ lll+vi+g d+ d ts ++  +  + + e++ ++++l   +
  gi|118431564|ref|NP_148119.2| 185 TATVGLKPTYGLVSRYGLIPYANSLEQISPMARSSEDVMLLLEVIAGGDEYDATSIYS--KPTTASREEGLKPEDLSLCI 262
                                    ********************************************************94..567777888889999***** PP

                                    EGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-C.CGGGHHHHHHHHHHHHHHHHTTT-SSSSS.---SS-SCCCCC CS
                        Amidase 243 vkedgvasldpevqravekalkaLeeaGhevvevelp.sleealslyylilvaeassnlarylgvry.erlsetkvlsel 320
                                    ++e+  +  +++v++a+ +++ +Le +G++++ v l  + ++al++yy+i++aea+snlary+g  y  r s  ++ ++ 
  gi|118431564|ref|NP_148119.2| 263 PEELV-EHSEEAVRKAFYNTVGKLEGLGARLEYVGLGgAEAYALPAYYTIALAEAASNLARYDGSLYpVRGSSGDY-WRQ 340
                                    ****9.79***************************8625678888**********************988888888.566 PP

                                    CCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHH CS
                        Amidase 321 lpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsyt 400
                                     ++ r  ++g evkrri +g y+ls++++++yyl a+k rr++r+++ k   ++ ++++P++p+++pr+ge+    d+++
  gi|118431564|ref|NP_148119.2| 341 AAEARGIGFGLEVKRRILMGVYVLSEGYKDEYYLAATKLRRVIRDAMLKTVGKC-LVATPASPIMPPRIGERV---DDPL 416
                                    66799***********************************************96.89**************97...89** PP

                                    HHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHH CS
                        Amidase 401 vlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetl 450
                                     ly+++++t   v++nl glpa+++p++    glPvG+q+ig+++ e+ l
  gi|118431564|ref|NP_148119.2| 417 KLYAMDVYT---VLANLSGLPAIALPIEIHG-GLPVGLQLIGPRLGERLL 462
                                    *********...****************987.*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 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:                        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 0.23s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3981.91
//
Query:       gi|14601580|ref|NP_148120.1|  [L=486]
Description: aspartyl/glutamyl-tRNA amidotransferase subunit B [Aeropyrum pernix K1]
Scores for complete 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-88  296.2   0.0    3.1e-88  295.7   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
    2.1e-28   99.1   0.0    3.4e-28   98.4   0.0    1.4  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.7   0.0   3.5e-92   3.1e-88       1     272 [.       8     294 ..       8     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 3.5e-92
                                   EEEEEEEEEEB--.SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TC CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N   1 lviGlEiHaqlkt.ksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfy 80 
                                   ++iGlEiH+ql++  sKlF+++ +e  g +pn++v++v+l+lPG+lPv++++ + lai+a++al+c++  ++ f+RK+yfy
  gi|14601580|ref|NP_148120.1|   8 VKIGLEIHVQLSNaGSKLFCGCDSEYRGYKPNTNVCPVCLGLPGALPVPSRRPIVLAIAASMALGCRVPGTVVFTRKHYFY 88 
                                   58*********8768********8778889*************************************************** PP

                                   TTCTTSEEEEESS....S.SEEEEEEEE.......TEEEEEEEEEEEE---EEEE....EETTEEEEETTSTT-EEEEEEE CS
                                   xxxxxxxxxxxxx....xxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N  81 pdlpkgyQitqke....eplakeGslel.......ekkvrierihlEeDaaksvh....eekeeslvdlnRaGvpLiEivt 146
                                   pdlpk+yQitq+e    +p++++G le         ++ ri+ri+lEeD +k+ +     ++++ lvd+nR+GvpL+Eivt
  gi|14601580|ref|NP_148120.1|  89 PDLPKNYQITQFEkaggAPVCMGGVLEYlntdswrWERARIRRINLEEDPGKTYYegsiLTSRYALVDYNRSGVPLLEIVT 169
                                   ***********99666679********888787777777***************9776636679***************** PP

                                   -STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 147 epdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrvEiKnlnslksiekaieyeierqie 227
                                   epd+ sp++ar +++ l  +l+++g+++ ++ eG +R+D+N+S++        g+rvE+Kn+ s++ +eka+++ei+rq  
  gi|14601580|ref|NP_148120.1| 170 EPDIPSPRHARMLIDYLLLTLEYIGATNPRL-EGVFRVDANISIEG-------GERVEVKNIGSTQDVEKALKFEISRQRL 242
                                   *******************************.7************4.......49*************************9 PP

                                   HH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHH CS
                                   xx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 228 ll.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseeli 272
                                   ++       +eTr++d+++g t+ lR kee++dY yfp+pdlpp+ei+e+++
  gi|14601580|ref|NP_148120.1| 243 IVerggkveRETRHWDAERGMTKPLRLKEEEADYLYFPDPDLPPVEITEDML 294
                                   99***********************************************986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   3.7e-32   3.4e-28       2     148 .]     334     478 ..     333     478 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 3.7e-32
                                   HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTC..SSTTHHHHHHHHHHHHTTSSGHHHHHHHH.HHHHHH.TXXHHH CS
                     GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleiee..lkltpeqlaellkliaegkIskkiakevl.eellee.gkspee 78 
                                   +f e+vk gad+++aa+ + ++l gel++ g+++ +  ++ +p+++a l +l+a+g+ + +++k ++ ++l+++ g+++++
  gi|14601580|ref|NP_148120.1| 334 LFLEAVKLGADPRIAARLVGVDLKGELKEMGKDLYSpnNWPPPQSIAILSNLVARGDYTYDSIKGLVvPKLAANpGSDVKS 414
                                   799*******************************998789999*********************8665999999******* PP

                                   HHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXS.XHHHHHHHHHHHS CS
                     GatB_Yqey  79 iieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGka.dpklvnellkekL 148
                                   ++ ek    ++d   +e+lveev+++++ av+dy +gk+kal++lvGqvM++ kG+a dp++++e+l ++L
  gi|14601580|ref|NP_148120.1| 415 LLPEK----VKD---IERLVEEVLNREKRAVQDYLAGKKKALNYLVGQVMRAAKGRAlDPRQAREILLRRL 478
                                   ****9....888...******************************************9*********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3218.01
//
Query:       gi|118431565|ref|NP_148121.2|  [L=190]
Description: hypothetical protein APE_1719.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.061   13.4   0.1      0.099   12.7   0.1    1.5  1  DUF4366          Domain of unknown function (DUF4366)
        0.1   13.0   0.0        0.2   12.0   0.0    1.5  1  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
       0.12   12.8   0.0       0.16   12.5   0.0    1.2  1  Thioredoxin_2    Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.7e-05     0.099      89     137 ..     135     187 ..      92     190 .] 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                        DUF4366  89 ntdcpveepepekeaepee.peeepekksn....nglllvvlavaligggaayy 137
                                    +t++  ++p++++e+++   +e+e+++         +++++l+v+li+++a+++
  gi|118431565|ref|NP_148121.2| 135 ETATGTTTPQETTEETTPMgTETEEAEA-GipfgLAAAIALLIVVLIAAAAYMF 187
                                    2333336665555544433444443333.2467555666666667777666554 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05       0.2       5      65 ..      34     118 ..      30     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                Cytochrome_CBB3   5 aGaalykk.nCasCHgkggag.............pslagrdwep..........dalvdiiknGkgaMpafgg.qlsdee 59 
                                    + +a++++  C+sCH  g ++             p++ g d ++          +  +++ ++ +  M+   g q +d +
  gi|118431565|ref|NP_148121.2|  34 EARATFESiGCVSCHN-GTVAvtwdeivdelkevPEKYGGDIDAyardvayfgqKGAFNTWNDLIATMAQNVGkQPNDPD 112
                                    5677888779*****8.666666998888888885555444443344555666688889999999999988777999999 PP

                Cytochrome_CBB3  60 lwalva 65 
                                    ++++ +
  gi|118431565|ref|NP_148121.2| 113 IQKINE 118
                                    998865 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.16      10      75 ..      37     122 ..      28     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                  Thioredoxin_2  10 vvftdpdCpyCkklkkelkelddvtvrvllfp..lkpsfepkavaiwcakekkkafkd....................ie 67 
                                    + f++ +C  C+   ++  ++d++ + +  +p  ++ +++++a+++ +  +k  af++                    i+
  gi|118431565|ref|NP_148121.2|  37 ATFESIGCVSCHN-GTVAVTWDEIVDELKEVPekYGGDIDAYARDVAYFGQKG-AFNTwndliatmaqnvgkqpndpdIQ 114
                                    78**********9.778999999****9***********************95.88887779888777777777777777 PP

                  Thioredoxin_2  68 envelark 75 
                                    + +e+  +
  gi|118431565|ref|NP_148121.2| 115 KINEFFLS 122
                                    77777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1487.29
//
Query:       gi|14601582|ref|NP_148122.1|  [L=196]
Description: cytochrome c oxidase (ba3-type) subunit II [Aeropyrum pernix K1]
Scores for complete 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-08   32.9   0.0    7.8e-08   32.2   0.0    1.4  1  COX2      Cytochrome C oxidase subunit II, periplasmic 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 !   32.2   0.0   4.3e-12   7.8e-08      46     114 ..      84     154 ..      55     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.3e-12
                          COX2  46 nrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsll..idreGvfyGqcselcGvnhssmp 114
                                   +++vl   +++ + v+++dv+h f +    v   ++pG +++ + +   + eG +   c e cGv h +m 
  gi|14601582|ref|NP_148122.1|  84 STIVLEDPKQVTFYVATSDVIHGFEIAGTNVNFMVIPGYIAKFTWYppKNAEGEYLILCNEYCGVGHQFMK 154
                                   678899999*********************************9987335779*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1473.01
//
Query:       gi|14601583|ref|NP_148123.1|  [L=254]
Description: SCO1 protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-07   30.4   0.0    1.5e-06   28.2   0.0    1.9  2  SCO1-SenC  SCO1/SenC


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 !   28.2   0.0   8.4e-11   1.5e-06      20      86 ..      75     143 ..      67     188 .. 0.86
   2 ?    0.0   0.0     0.042   7.5e+02     118     133 ..     204     219 ..     182     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.4e-11
                     SCO1-SenC  20 egkpslvffgFthCpdvCpttlanmaevldalgeea..ekvqplfiTvDPerDtpevlkeyleafdpri 86 
                                   eg + +v   + +CpdvC  + a m  ++ +l e++  +kv +++i v+P + t e+ k+y+e++  ++
  gi|14601583|ref|NP_148123.1|  75 EGVVNVVVPQYVNCPDVCHWESAIMIYLMGELVERGlqDKVVFVTIGVNPYYETIEDGKRYMESVAGDY 143
                                   7888899999*************************8668888888999**************9987665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.042
                     SCO1-SenC 118 tvdHsssvyLvdpdgr 133
                                    v+H++ +++vd dg 
  gi|14601583|ref|NP_148123.1| 204 GVNHTAGFIIVDGDGV 219
                                   589*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 1965.00
//
Query:       gi|14601584|ref|NP_148124.1|  [L=389]
Description: thioredoxin [Aeropyrum pernix K1]
Scores for complete 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   0.0    5.1e-08   32.8   0.0    1.5  1  Thioredoxin    Thioredoxin
    0.00044   20.7   0.0     0.0011   19.3   0.0    1.6  1  Thioredoxin_2  Thioredoxin-like domain
     0.0014   18.6   0.0     0.0036   17.3   0.0    1.6  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
      0.049   13.4   0.0      0.074   12.9   0.0    1.2  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.1e-11   5.1e-08      10      87 ..      59     142 ..      51     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.1e-11
                                   HHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT....TS...EEEEEETTTSHHHHHHTT-SSSSEEEEEETTE CS
                   Thioredoxin  10 FeeevakekklvlveFyApwCghCkalaPeleklaeelkd....kv...klakvdvdenedlakkyevegiPtlklfkngk 83 
                                   + + v++  ++vlv    + C  Ck+++P +e++a+e  +    kv   +l+kvd+++  dl ++++veg Ptl++++ng 
  gi|14601584|ref|NP_148124.1|  59 YWSVVKS-YDKVLVYVGQTGCLGCKKIEPAIERFATEQGEvkvvKVwldTLIKVDAESTFDLLARLGVEGTPTLIVYRNGV 138
                                   5555665.999**************************9988766333336799***************************9 PP

                                   EEEE CS
                   Thioredoxin  84 evkk 87 
                                   ev++
  gi|14601584|ref|NP_148124.1| 139 EVAR 142
                                   7765 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.5e-07    0.0011       7      95 ..      68     142 ..      63     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.5e-07
                 Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt.ivf 86 
                                   +vlv++ +++C  Ckk++  ++              +++ e k+v++w ++  k  + d e++++l+ ++gv+gtPt iv+
  gi|14601584|ref|NP_148124.1|  68 KVLVYVGQTGCLGCKKIEPAIERF-----------ATEQGEVKVVKVWLDTLIK--V-DAESTFDLLARLGVEGTPTlIVY 134
                                   7899999************99999...........6667789999999999876..3.3599***************6668 PP

                 Thioredoxin_2  87 ldgkeivar 95 
                                    +g  +var
  gi|14601584|ref|NP_148124.1| 135 RNGV-EVAR 142
                                   8887.5554 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     8e-07    0.0036       5      55 ..      71     133 ..      68     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8e-07
                                   E.E.SSSSTTCHHHHHHHHHHCHCCT.CEC.........EEECCTTHHHHHHCT-SSSSEEEC CS
                 Thioredoxin_3   5 v.l.gpgCakCpklekavkeaaaekg.ika.........evekvtdfeeiekygVmsvPalvi 55 
                                   v + ++gC  C+k+e a+++ a+e+g +k+         +v+  ++f+ +++ gV+ +P+l++
  gi|14601584|ref|NP_148124.1|  71 VyVgQTGCLGCKKIEPAIERFATEQGeVKVvkvwldtliKVDAESTFDLLARLGVEGTPTLIV 133
                                   4343678******************77*********77666666777777***********76 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05     0.074     132     201 ..      69     136 ..      64     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                          TraF 132 gLlfFyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdp 201
                                    L+++ + +c  c++  p +++fa +  + +v+ V +d  +   + + +   + +arlgv+ tP+l++ + 
  gi|14601584|ref|NP_148124.1|  69 VLVYVGQTGCLGCKKIEPAIERFATEQgEVKVVKVWLDTLIK--VDA-ESTFDLLARLGVEGTPTLIVYRN 136
                                   588888999***************999458888888888877..444.668899************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2871.73
//
Query:       gi|118431566|ref|YP_874912.1|  [L=158]
Description: hypothetical protein APE_1722a [Aeropyrum pernix K1]
Scores for 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-10   38.9   0.1    7.8e-10   38.5   0.1    1.2  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 !   38.5   0.1   4.4e-14   7.8e-10      14      90 ..      51     133 ..      28     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 4.4e-14
                                    SEEEEEEEEEECSSSEEEEEEEE-T..T..CCEEEEE.EETTTCEEEEEECS.SEEEETTEEEEE-..TTSCEEEEECES CS
                          PCuAC  14 kvsaaymtirNtgdeddkLvaassd..v..aasvelh.tvvedgvmkmrqveegieipaggqveLk..pggfhvMliglk 86 
                                    ++ ++y+ti+N++++   +v+a+    v     v +h tv+e+g   m +    i + +g+++e++  pg++hvM++g +
  gi|118431566|ref|YP_874912.1|  51 TSIGVYLTIKNNTNTTSCIVGADIAesVsgKVVVDIHkTVEEGGRVVMMPAG-PICLGPGETLEMRqgPGSYHVMIMGDR 129
                                    36688****************985422522445789*777779999999995.9***********84467*******977 PP

                                    S-B- CS
                          PCuAC  87 rdlk 90 
                                     +++
  gi|118431566|ref|YP_874912.1| 130 SAIE 133
                                    6654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1261.46
//
Query:       gi|118431567|ref|NP_148125.2|  [L=201]
Description: hypothetical protein APE_1723.1 [Aeropyrum pernix K1]
Scores for complete 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-08   33.3   0.0    3.5e-08   32.9   0.0    1.1  1  Methyltransf_3   O-methyltransferase
    7.9e-05   23.6   0.0    0.00011   23.1   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.024   14.6   0.0       0.03   14.3   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
      0.053   13.1   0.0      0.084   12.5   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.065   13.9   0.0       0.11   13.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      0.077   12.7   0.0      0.099   12.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.2e-11   3.5e-08      72     158 ..      75     164 ..      45     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.2e-11
                                    T-EEEEEES-HHHHHHHHHHHH..HTT-GGGEEEE..ES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTE CS
                 Methyltransf_3  72 DGkilaididreayeialkfiq..kagvaekieli..egdalkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLv 147
                                      ki+ai+ d e + i  + ++   a +  +ie+    gdal  + +l ++  +  fD++fvD +k +y++  e+l +L+
  gi|118431567|ref|NP_148125.2|  75 TCKIVAIEYDVELASILSRNLRevEAMFRGRIEFEvvSGDALDYFSRLEEKG-REVFDMAFVDIEKGDYPEALERLENLL 153
                                    369*********99987777662357889999875227999*9999998877.699************************ PP

                                    EEEEEEEEE-T CS
                 Methyltransf_3 148 kvGgliaiDnt 158
                                      Gg+ a+ n+
  gi|118431567|ref|NP_148125.2| 154 TAGGVAAFYNA 164
                                    *******9997 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   3.8e-08   0.00011       4     102 ..      53     160 ..      50     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.8e-08
                Methyltransf_24   4 GvysGvstlwllralrrnga...grlvavdhdpgaeeaaalare......aglddr..vrlikadseealasla...ags 69 
                                    G+  G+st+w+++ + ++ +    ++va++ d    e a ++ +      a ++ r  ++++++d+ +++++l+   ++ 
  gi|118431567|ref|NP_148125.2|  53 GAGIGYSTIWIAYGAYHRCTditCKIVAIEYDV---ELASILSRnlreveAMFRGRieFEVVSGDALDYFSRLEekgREV 129
                                    7778*********999998889999999***99...666666654433444444446699**************998888 PP

                Methyltransf_24  70 iDllfiDgghaaeavledleallprlapggvvl 102
                                    +D++f+D +  + ++ e+le l+++l+ ggv  
  gi|118431567|ref|NP_148125.2| 130 FDMAFVDIE--KGDYPEALERLENLLTAGGVAA 160
                                    *******86..7888888888888999998865 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05      0.03      28      87 ..      48     111 ..      36     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                Methyltransf_32  28 tvvDvGaGkgYLsfvlal...kek.eyklkvvgidakeelvekaekraeklgkkfnkrlsfael 87 
                                    + vD+GaG gY +  +a+   ++  +  +k+v+i+   el++  ++  ++++ +f  r++f+  
  gi|118431567|ref|NP_148125.2|  48 SYVDAGAGIGYSTIWIAYgayHRCtDITCKIVAIEYDVELASILSRNLREVEAMFRGRIEFEVV 111
                                    68****************987444369**************99999999999999999888765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05     0.084      66     148 ..      77     159 ..      74     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                    EEEEEES-HHHHHHHHHHHCCCT--T....TTEEEEES-HHHHCTS--SS.-EEEEEEE--SSSTTCH.HHHHHHHHHTT CS
                  Cons_hypoth95  66 kavlvekdkeavkilkenleelklee....etaelkedaleallklakkk.eefdivflDPPyakellieevlelleekk 140
                                    k+v++e d e ++il++nl+e+++      e++++  dal+ +++l +k+ e+fd+ f+D   +k++ + e+le le  +
  gi|118431567|ref|NP_148125.2|  77 KIVAIEYDVELASILSRNLREVEAMFrgriEFEVVSGDALDYFSRLEEKGrEVFDMAFVD--IEKGD-YPEALERLE--N 151
                                    5799*****************9976567899*************998775268*******..67887.588888888..6 PP

                                    -EEEEEEE CS
                  Cons_hypoth95 141 llkenalv 148
                                    ll+ +++ 
  gi|118431567|ref|NP_148125.2| 152 LLTAGGVA 159
                                    77766665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.8e-05      0.11       2      97 .]      50     157 ..      50     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                                    EEET-TTSHHHHHHHCTS....T..SSEEEEEESSHHHHHHHHHHHHHTTT....TEEE..EESBCCG.BSSSTTTEEEE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrl....g..kakvtgvDiseemleaareraeeegl....nvef..vqgdaed.lpfedgsfDlv 68 
                                    +d+G+G G  t+++a           +k+++++++ e+  +  ++++e ++    ++ef  v gda d ++  +++   v
  gi|118431567|ref|NP_148125.2|  50 VDAGAGIGYSTIWIAYGAyhrcTdiTCKIVAIEYDVELASILSRNLREVEAmfrgRIEFevVSGDALDyFSRLEEKGREV 129
                                    599*****9999998664443324789*******************9944447887777225566655333344444444 PP

                                    EEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  69 vssgalhhlsdedlekalkeiarvLkpgG 97 
                                    +  +a+  +++ d+++al+++ ++L+ gG
  gi|118431567|ref|NP_148125.2| 130 FD-MAFVDIEKGDYPEALERLENLLTAGG 157
                                    44.45556889999***********9998 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 ?   12.4   0.0   3.3e-05     0.099      78     132 ..      50     114 ..      43     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                    EEES-TTSHHHHHHHHHHCTTC.....EEEEEESBHHHHHHHHHHHHHCTTC.....SEEEEES- CS
                           PCMT  78 LevGsGsGyltavlarlvgekg.....rvvsierikelveeakrnlkkldle.....nvivvvgD 132
                                    ++ G+G Gy t  +a    +++     ++v+ie+  el++  +rnl++ +++     +  vv gD
  gi|118431567|ref|NP_148125.2|  50 VDAGAGIGYSTIWIAYGAYHRCtditcKIVAIEYDVELASILSRNLREVEAMfrgriEFEVVSGD 114
                                    689********9988665555555555*********************99988886666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1544.89
//
Query:       gi|118431568|ref|NP_148126.2|  [L=265]
Description: Rieske iron-sulfur protein [Aeropyrum pernix K1]
Scores for complete 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   46.2   0.0      6e-12   45.3   0.0    1.4  1  Rieske        Rieske [2Fe-2S] domain
     0.0044   17.0   0.3     0.0044   17.0   0.3    1.8  2  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
     0.0053   16.6   0.2      0.009   15.8   0.2    1.3  1  TAT_signal    TAT (twin-arginine translocation) pathway signa
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.18   12.1   0.0    1.4  1  zf-HC2        Putative zinc-finger


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 !   45.3   0.0   1.3e-15     6e-12      26      85 ..     133     212 ..     110     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.3e-15
                                    EEEEE-T...TS-EEEEESC-TTTT-BC.............GGSEEE...TT.EEE-TTT--EEE.TTSBEEE-.TTHHH CS
                         Rieske  26 lvvlrde...dgevyAlsdvCtHrgapl.............segkid...ekgvleCpcHgwayd.adGkvikg.Paprp 84 
                                    ++++      dg+++A++ +C+H+g+p              + +  +   ++gvl+C+cHg+ayd a+G+++ + P+ +p
  gi|118431568|ref|NP_148126.2| 133 FFIYPPGvgpDGNIVAYNLICQHLGCPYpalryyppgtpitT-NPPEvgaNGGVLHCMCHGSAYDpARGSIVLTpPTVKP 211
                                    6777733556*****************667799988888751.3332445899*******************99444455 PP

                                    E CS
                         Rieske  85 l 85 
                                    l
  gi|118431568|ref|NP_148126.2| 212 L 212
                                    5 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 !   17.0   0.3   9.9e-07    0.0044       6      38 ..       5      37 ..       4      38 .. 0.97
   2 ?   -3.6   0.4       2.8   1.2e+04      34      38 ..     134     138 ..     131     139 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.9e-07
                   CytB6-F_Fe-S  6 msrRqllNlllvGaialtaaaaLyPvvkFFiPP 38
                                   + rR +l l+ ++++a+ + + + P v + +PP
  gi|118431568|ref|NP_148126.2|  5 LRRRDFLKLVGAAGVAVSIIGVVPPIVRYTVPP 37
                                   67******************************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                   CytB6-F_Fe-S  34 FFiPP 38 
                                    F+ PP
  gi|118431568|ref|NP_148126.2| 134 FIYPP 138
                                    44466 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 !   15.8   0.2     2e-06     0.009       4      20 ..       7      21 ..       4      27 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-06
                     TAT_signal  4 RRdFLKgsAAaaAAaal 20
                                   RRdFLK  +++aA++a+
  gi|118431568|ref|NP_148126.2|  7 RRDFLK--LVGAAGVAV 21
                                   ******..777777776 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     4e-05      0.18       9      26 ..     109     126 ..     109     126 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                                    HHHHCCT-SCCCHCCCHH CS
                         zf-HC2   9 saYlDGeLspeerarvea 26 
                                    +a+lDG+Ls+ e  r+e+
  gi|118431568|ref|NP_148126.2| 109 PAWLDGDLSENEIKRLEE 126
                                    79**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2176.36
//
Query:       gi|14601587|ref|NP_148127.1|  [L=571]
Description: cytochrome b [Aeropyrum pernix K1]
Scores for complete 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-30  105.4   1.7    3.1e-30  105.4   1.7    3.3  3  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    1.3e-15   57.7   7.2    1.3e-15   57.7   7.2    2.1  2  Cytochrome_B     Cytochrome b/b6/petB
     0.0016   18.7   3.1     0.0016   18.7   3.1    3.1  4  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   1.7   5.1e-34   3.1e-30       2     159 ..      93     263 ..      92     282 .. 0.80
   2 ?   -2.5   0.2      0.75   4.5e+03      27      43 ..     346     362 ..     341     369 .. 0.76
   3 ?    0.4   0.0     0.096   5.7e+02     128     165 ..     474     512 ..     437     516 .. 0.62

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 5.1e-34
               Cytochrom_B_N_2   2 imiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiiss.vP.vvgtwlvellf 80 
                                   +m+i +++H +r++f+G Yk+pRel Wi+Gv   +l+l ++f+GysL++d ++ +a+++g+++  + ++  +g ++v++lf
  gi|14601587|ref|NP_148127.1|  93 FMLIGVFAHAFRNLFKGVYKRPRELVWIVGVATGFLALQTAFFGYSLVGDRIAKEAINIGSALNLRsLGeELGLYVVAILF 173
                                   8***********************************************************98855435525789******* PP

               Cytochrom_B_N_2  81 GgelpgeallsrlyalHilllpalllalivahlllvekkgqtpsrrkek....nvvg..........eplvpvnavkmlll 147
                                   G + ++ +   r+ alH+ ll+a + +l+++h+ l+e +g +p++ +e+    +              p++pvn+v  l++
  gi|14601587|ref|NP_148127.1| 174 GLDPTERY--FRITALHV-LLAATVFLLFLLHFGLFEVHGPAPKE-EETgwkaE--ParipqdrsdlAPWFPVNLVFILAV 248
                                   *8887555..6*******.************************86.33333330..13444444555*********99987 PP

               Cytochrom_B_N_2 148 flvl..valli.ala 159
                                   +l++  ++++  ++a
  gi|14601587|ref|NP_148127.1| 249 TLMTwgFIVFTaGMA 263
                                   777655555554443 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.75
               Cytochrom_B_N_2  27 nWiiGvllllltllegf 43 
                                    Wi+G+ ++llt  + +
  gi|14601587|ref|NP_148127.1| 346 PWITGLGIILLTGYMQL 362
                                   69**9999999976655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.096
               Cytochrom_B_N_2 128 eknvvgeplvpvnavkmlllflvl.vallialalinPvp 165
                                   +++    p++   ++   ++++++ +++l+a+a+i Pv 
  gi|14601587|ref|NP_148127.1| 474 QDPDSSIPWYLLLVALGEVGIASFsLIALAAIAFIDPVG 512
                                   345556888888777777788877788999999999986 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   7.2   2.2e-19   1.3e-15      16     184 ..      39     205 ..      29     210 .. 0.87
   2 ?   -2.1   0.3      0.49   2.9e+03      91     113 ..     340     362 ..     313     406 .. 0.65

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 2.2e-19
                  Cytochrome_B  16 lGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglkktrel 96 
                                   lG+++   +    ltG++l fyy+pt      s + i+ +  fG l+ + h ++a ++++ ++ h fr l+ g++k++rel
  gi|14601587|ref|NP_148127.1|  39 LGAIVASSFFWLALTGLLLLFYYRPTD--PLESSKAIIFERPFGALLLTSHLYAAHFMLIGVFAHAFRNLFKGVYKRPREL 117
                                   7888888888899***********975..56788999******************************************** PP

                  Cytochrome_B  97 vWviGvillllvivtafiGyvLpwdqmsyWavtvit..nllsaiPviGstlvellwgsvsvddatLtrffslhfllPflll 175
                                   vW++Gv   +l + taf Gy+L+ d+++  a+++ +  nl s    +G  +v +l+g    +     r+ +lh+ll   + 
  gi|14601587|ref|NP_148127.1| 118 VWIVGVATGFLALQTAFFGYSLVGDRIAKEAINIGSalNLRSLGEELGLYVVAILFGLDPTER--YFRITALHVLLAATVF 196
                                   ********************************9987224456667788888888888766554..57899*********** PP

                  Cytochrome_B 176 illllhlll 184
                                   +l llh+ l
  gi|14601587|ref|NP_148127.1| 197 LLFLLHFGL 205
                                   ******955 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.49
                  Cytochrome_B  91 kktrelvWviGvillllvivtaf 113
                                   +++ ++ W++G+ ++ll+  + +
  gi|14601587|ref|NP_148127.1| 340 TNPVDRPWITGLGIILLTGYMQL 362
                                   35666777777666666544444 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 ?   -4.1   0.2         3   1.8e+04      73      83 ..      44      54 ..      32      62 .. 0.50
   2 ?   -1.6   0.0      0.54   3.2e+03      59      88 ..     186     215 ..     166     223 .. 0.63
   3 !   18.7   3.1   2.6e-07    0.0016      12      87 ..     287     370 ..     284     383 .. 0.82
   4 ?   -2.5   0.0         1   6.2e+03      69      85 ..     445     461 ..     436     470 .. 0.72

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3
                                  HHHHHHHHHHH CS
                 Cytochrom_B_C 73 vvsfvvLgylG 83
                                  + sf++L++ G
  gi|14601587|ref|NP_148127.1| 44 ASSFFWLALTG 54
                                  23333333333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.54
                                   TT-.HHHHHHHHHHHHHHHHHHHHHTS-SS CS
                 Cytochrom_B_C  59 ryrkplakvllallvvsfvvLgylGvqppe 88 
                                   + +  la ++++l++++f +  + G  p+e
  gi|14601587|ref|NP_148127.1| 186 ALHVLLAATVFLLFLLHFGLFEVHGPAPKE 215
                                   444456666777777777777777766665 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.6e-07
                                   ---GGGHHHHHHHHCS.........SSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHH CS
                 Cytochrom_B_C  12 aPeWYflpfYaiLrai.........pakllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylG 83 
                                    P W+fl  Y i++++         p+ l  ++a++   +il+++p++dr+  ++   r p+ + l ++l++  + L++  
  gi|14601587|ref|NP_148127.1| 287 MPPWFFLYTYRIFQMTfltlslestPQLLQFIIALVLPPLILMIIPFVDRKVSTNPVDR-PWITGLGIILLTGYMQLTVWS 366
                                   599************7555555555788889999*****************99999999.888888999999999999888 PP

                                   TS-S CS
                 Cytochrom_B_C  84 vqpp 87 
                                   + +p
  gi|14601587|ref|NP_148127.1| 367 MIEP 370
                                   7665 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHHHHTS CS
                 Cytochrom_B_C  69 lallvvsfvvLgylGvq 85 
                                   ++ l+++ v+Lg+++++
  gi|14601587|ref|NP_148127.1| 445 FMGLAFATVILGWIAAK 461
                                   56677888889988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3976.72
//
Query:       gi|118431569|ref|NP_148128.2|  [L=147]
Description: hypothetical protein APE_1727.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-14   53.4   9.5    3.5e-14   53.1   9.5    1.1  1  VKOR      Vitamin K epoxide reductase family


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 !   53.1   9.5   1.9e-18   3.5e-14       4     121 ..      12     138 ..       9     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.9e-18
                                    HHHHHHHHHHHHHHHHHHH...HT---SS-SSSS.....HHHHHCSTTSEETT.EEHHHHHHHHHHHHHHHHHS-..... CS
                           VKOR   4 lvlalvGllvsiyltleklglktsssaalCdiss...vsCdkvlnSpyasilg.vplsllGllayalvlllalapl.... 75 
                                    l+  +vG+l+si  ++e  +    +   +C++++   ++C +    p+a i+g ++ls l+ ++++++l++a+++     
  gi|118431569|ref|NP_148128.2|  12 LAALAVGWLASIGGFIEFRRSLL-GGGFVCKADAkgwINCRSAYVIPQAFIAGrIHLSELAPIYFTATLATAVLGVlldi 90 
                                    56667788888755554443323.34457*655556***********************************999999999 PP

                                    ..HHHHHHHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHH CS
                           VKOR  76 ..lwlllllgslagvvfslyLiylslfvigalCpyClvsavlsllllv 121
                                      l+ l +l+++ g++ ++yL+yl++ v +a+C++C+++++ ++l+++
  gi|118431569|ref|NP_148128.2|  91 dlLAKLSYLLAAGGAASVPYLVYLEVRVAKAICLWCTIMHLSIILAVA 138
                                    998888999999*****************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1097.37
//
Query:       gi|14601589|ref|NP_148129.1|  [L=517]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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-28   99.3   3.5    1.4e-27   97.5   3.5    1.8  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    3.2e-21   76.4   0.1    5.2e-21   75.7   0.1    1.3  1  SBP_bac_8   Bacterial extracellular solute-binding protein
      2e-20   73.3   0.1    2.9e-20   72.7   0.1    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    7.8e-11   42.2   0.1    1.8e-10   41.0   0.1    1.5  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.086   13.0   0.0        7.9    6.7   0.0    2.5  2  Rhomboid_N  Cytoplasmic N-terminal domain of rhomboid serine 
       0.11   12.2   0.0       0.34   10.7   0.0    1.9  1  RHS         RHS 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 !   97.5   3.5   4.7e-31   1.4e-27      10     314 ..      99     356 ..      90     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 4.7e-31
                                   HHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCT CS
                     SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkda 89 
                                    ++++  ++ k+++ +++++ sv+  s++     ai++   ++Dv+++ +++ +++l +ag+l+pl+++++ ++a + +d 
  gi|14601589|ref|NP_148129.1|  99 KEEFLKSDLAKRYNIVDIKFYSVPPVSWIS----AIESRG-DIDVAWGgGPTLFDQLYQAGYLAPLTSDTALEAAAQIPDL 174
                                   33333333688899****************....777777.9*************************************** PP

                                   EEEEHHHHTHHHHCEEE.ES.EEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHH..HHHHHHHCTCTHCCHCCEEHHHHH CS
                     SBP_bac_1  90 adklsssvlpkildskv.ly.vPly.aargliYNkdlfekagldppwtWdelvea..akklkekgkkpiggarggsasgta 165
                                   ++ + ++ +++    ++ +y v    a+ g+ +N+d++ ++ l++p+ W +l+ +  a+ l+  g+   + ++  + s+ +
  gi|14601589|ref|NP_148129.1| 175 FAGAPMKRTDS----EGrIYwVAASvASFGFTVNHDVLNQYNLPVPKRWADLASPvyAEPLVLEGREV-IAIADPTRSTSN 250
                                   ****9999976....667999999955**************************862245555555555.555555555555 PP

                                   HHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHH CS
                     SBP_bac_1 166 yyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaal 246
                                      ++ +++ +g                  + + ++ l        +++ +   + ++a++++++ +G++a++i   ++ +
  gi|14601589|ref|NP_148129.1| 251 TRMYEIILQAYG------------------WEEGWRVLT-------GMAANALVEGGSAEVRDDVIQGRVAIGITIDFYGY 306
                                   555556666666..................555555555.......66777777777777777777777777777777777 PP

                                   HHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                     SBP_bac_1 247 aamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                   +amk++p+  ++++  +  +                  +++++a++++sk+peaA++F++++l+++++
  gi|14601589|ref|NP_148129.1| 307 TAMKANPATEYIIPEGETII------------------NGDPIALLTTSKHPEAAQAFIAWVLTEGQK 356
                                   77766666666666666655..................***************************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 !   75.7   0.1   1.7e-24   5.2e-21      38     273 ..     134     377 ..     126     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.7e-24
                                   -SEE.EEE-HHH.HHHHHHTTSB--GG...GSTTHHH-HHHHHTT.....--TS.----EEEEEEE-EEEEEHHHHHH.S. CS
                     SBP_bac_8  38 pdidvvwaneda.latlaeeglladls...dldnlddltdalaav.....gydgklygvPyasetpyvliynkdllek.a. 107
                                   +didv+w+ +   +++l ++g+la+l+    l+ +++++d +a++     + +g +y+v   + +  ++ +n d+l + + 
  gi|14601589|ref|NP_148129.1| 134 GDIDVAWGGGPTlFDQLYQAGYLAPLTsdtALEAAAQIPDLFAGApmkrtDSEGRIYWVAASVAS-FGFTVNHDVLNQyNl 213
                                   599****9977679*************9877799999***999999999777999*****88886.9**********9548 PP

                                   .---BHHHHHHHHHHH......HHH-..SEGG---GGGGGGTHH.ETTEE---H..HHH.HHHHHHHHHHHHTT-EE-S.. CS
                     SBP_bac_8 108 edpktwdellaaakkl......kgkf..glpdpasgwlqaalla.kdgksldddggkdglkealellkklkdngktydtga 179
                                    +pk w++l +  + +      +g+   +++dp+ ++  + ++   +           g++e ++ l+ + +n  + + +a
  gi|14601589|ref|NP_148129.1| 214 PVPKRWADLAS--PVYaeplvlEGREviAIADPTRSTSNTRMYEiIL----Q----AYGWEEGWRVLTGMAANALVEGGSA 284
                                   9********99..5554444663444336677776655444444102....2....2379***************99**** PP

                                   --SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHH.HH CS
                     SBP_bac_8 180 davsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpknaknedlaAldFlkwltspenqaalae.kt 259
                                   ++ +++ +G+va++i+ +    +a ka++  ++i+p   ++++g+++a ++ +k+++ aA++F+ w+++ e+q+ ++  ++
  gi|14601589|ref|NP_148129.1| 285 EVRDDVIQGRVAIGITIDFYGYTAMKANPATEYIIPEGETIINGDPIALLTTSKHPE-AAQAFIAWVLT-EGQKIWFReDI 363
                                   ************************************999******************.6********97.89*****99** PP

                                   ---BS-S-TTTHHH CS
                     SBP_bac_8 260 gyipvnksaalspe 273
                                   + +p+n++a + pe
  gi|14601589|ref|NP_148129.1| 364 NRLPSNPKAFELPE 377
                                   *******9977655 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 !   72.7   0.1   9.7e-24   2.9e-20       5     232 ..     137     379 ..     135     390 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 9.7e-24
                     SBP_bac_6   5 dlilsfdkdflekfieeglfqpld....panlpnvnkdfa..eeglkdpdgkyy..pygvgplvlavnkdrlkgrpv..Pk 75 
                                   d+ ++ ++ +++++ ++g+++pl+     + ++++++ fa    + +d++g++y  + +v  +++ vn+d+l++ ++  Pk
  gi|14601589|ref|NP_148129.1| 137 DVAWGGGPTLFDQLYQAGYLAPLTsdtaLEAAAQIPDLFAgaPMKRTDSEGRIYwvAASVASFGFTVNHDVLNQYNLpvPK 217
                                   8999999*****************77775555666666666656667777777766999999***********9888668* PP

                     SBP_bac_6  76 sWaDLldPeykgkvalpgnng........sdlfealllalykdfgedgvkkllrnlkanlhpaq.mvkaagslesgepavs 147
                                   +WaDL +P y++  +l g +         s++++ +  ++ + +g++++++ l  ++an      + +  + +++g+ a+ 
  gi|14601589|ref|NP_148129.1| 218 RWADLASPVYAEPLVLEGREViaiadptrSTSNTRMYEIILQAYGWEEGWRVLTGMAANALVEGgSAEVRDDVIQGRVAIG 298
                                   ************88888877788888888******************************9877799***********9999 PP

                     SBP_bac_6 148 vvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqail.akaggvfPvvtnpavln 226
                                   ++++f++ ++++ +    ++ ++Pe  ++++ + +++ +  k++e a+afi + l + +q+i+ +++ + +P++   +++ 
  gi|14601589|ref|NP_148129.1| 299 ITIDFYGYTAMKAN--PATEYIIPEGETIINGDPIALLTTsKHPEAAQAFIAWVLTE-GQKIWfREDINRLPSN---PKAF 373
                                   99999999988887..58999999999999988888888888*************98.6666515555588883...4444 PP

                     SBP_bac_6 227 elpega 232
                                   elpeg 
  gi|14601589|ref|NP_148129.1| 374 ELPEGR 379
                                   444444 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 !   41.0   0.1     6e-14   1.8e-10      22     224 ..     109     358 ..      95     362 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 6e-14
                                   HHH-.--EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGG...........GG-EEEEEEEEEEEESTT-T CS
                    SBP_bac_11  22 ahtg.vkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqa...........esavplassplviavpkgnp 90 
                                   ++++ v++++ ++++  ++++i++  + Dv + + ++  ++l +ag++++           + +  +a++p+         
  gi|14601589|ref|NP_148129.1| 109 KRYNiVDIKFYSVPPVSWISAIESRGDIDVAWGGGPTLFDQLYQAGYLAPltsdtaleaaaQIPDLFAGAPMKR------T 183
                                   3444699******************************************9999755544442222223333333......1 PP

                                   ..............................T---SHHHHHHS.........S-.-EEEE--T-TTTTHH.HHHHGGG.... CS
                    SBP_bac_11  91 ..............................kkikgwadLlkp.........gl.klavadPttspsGlaalalleaa.... 127
                                                                   +k wadL+ p         g   +a+adPt+s+s ++ ++++ +a    
  gi|14601589|ref|NP_148129.1| 184 dsegriywvaasvasfgftvnhdvlnqynlPVPKRWADLASPvyaeplvleGReVIAIADPTRSTSNTRMYEIILQAygwe 264
                                   23333344445555555555555555554346889*******9*99998864456*************9887777764554 PP

                                   --HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH...HSTTSSEEEE--TTT--...EEEEEEEE-TT--HH CS
                    SBP_bac_11 128 gaqellkalekkvvklgessrqlltaveageadagivyeseakaa.engdkleavylpeglnldpldypaavlkkaakrea 207
                                   ++ + l+ ++ ++ ++g+ s  + ++v +g++++gi+     ++a ++ + +e++ +  ++ +     p+a+l++++++ea
  gi|14601589|ref|NP_148129.1| 265 EGWRVLTGMAANALVEGG-SAEVRDDVIQGRVAIGITIDFYGYTAmKANPATEYIIPEGETII-N-GDPIALLTTSKHPEA 342
                                   22779999****996655.688***************98888777578889999988777776.3.4499*********** PP

                                   HHHHHHHTTSHHHHHHH CS
                    SBP_bac_11 208 AraFlafLrspeaqail 224
                                   A+aF+a+++  e+q+i+
  gi|14601589|ref|NP_148129.1| 343 AQAFIAWVL-TEGQKIW 358
                                   ********9.5677765 PP

>> Rhomboid_N  Cytoplasmic N-terminal domain of rhomboid serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.028        84       3      25 ..     333     355 ..     331     365 .. 0.81
   2 ?    6.7   0.0    0.0026       7.9      14      59 ..     445     486 ..     438     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.028
                    Rhomboid_N   3 lLlslenpraaqafidYlrsqgi 25 
                                   lL++++ p+aaqafi    ++g 
  gi|14601589|ref|NP_148129.1| 333 LLTTSKHPEAAQAFIAWVLTEGQ 355
                                   7999***********88776665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0026
                    Rhomboid_N  14 qafidYlrsqgiklelrseeegvq.lwle.deeqlaqveaeleeFlqn 59 
                                   q f dY++  g +l++    +g++ ++ e d ++ + v +e      n
  gi|14601589|ref|NP_148129.1| 445 QTFNDYMSMLGAPLKYVDPATGEEkVFTEeDAARVTSVLRE------N 486
                                   89********************999**99888888888777......4 PP

>> RHS  RHS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.34      10      36 ..     177     204 ..     175     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                           RHS  10 GtPeeLtDanGeivW.aaeydaWGnvte 36 
                                   G+P + tD++G+i W aa+  ++G +++
  gi|14601589|ref|NP_148129.1| 177 GAPMKRTDSEGRIYWvAASVASFGFTVN 204
                                   99*************6678888988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); 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: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3602.45
//
Query:       gi|118431570|ref|NP_148130.2|  [L=594]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-20   71.6  33.1    1.3e-12   47.8  10.7    3.7  4  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
       0.23   11.8   0.0       0.35   11.2   0.0    1.2  1  Sulfotransfer_3  Sulfotransferase 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 ?   -1.5   0.7      0.19   1.7e+03      47      78 ..       8      39 ..       5      51 .. 0.69
   2 !   38.2  14.3   1.3e-13   1.2e-09       3     177 ..     102     291 ..     100     293 .. 0.93
   3 ?    0.7   0.3     0.043   3.8e+02     108     171 ..     338     398 ..     321     412 .. 0.49
   4 !   47.8  10.7   1.5e-16   1.3e-12      10     173 ..     404     572 ..     388     587 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.19
                   BPD_transp_1 47 silghlilpviillllsaapyvrlirraalrs 78
                                   s+l ++++p+++ +ll +ap+++l+++  +  
  gi|118431570|ref|NP_148130.2|  8 SALLFTVFPLAFFGLLLIAPLALLLYKPLVTL 39
                                   55667777777777777777777776665555 PP

  == domain 2  score: 38.2 bits;  conditional E-value: 1.3e-13
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf..............vilsilghlilpviillllsaa 65 
                                    ++G  aa    ++ +++++++r+++ ++l   +fv a++++ +f              +  s+  ++  +vi++ +l++ 
  gi|118431570|ref|NP_148130.2| 102 VIGTAAAlltSSYYFPGRDVVRIVMMLPLLYTPFVNAFVVYNLFgkdngvlatitgslFGVSVYFQGLAGVILTQTLMFW 181
                                    677777787789999**************9999**9***99999*************98888888999999999999999 PP

                   BPD_transp_1  66 pyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleai 145
                                    p+v+++  a + +++ +l+e a+ lGa+  ++ r+v+lP+++p i +g++l+f++++ + +++  +  ++ +++++++ i
  gi|118431570|ref|NP_148130.2| 182 PIVYVNAFASMVQIDPSLKEQAENLGARGLRLHRTVTLPLSMPGITAGAALVFIFSMEDLAAPIAFRVDNVISRWIVNEI 261
                                    9999999999999******************************************************9999********* PP

                   BPD_transp_1 146 lgydyseisnggvlalviavlllnlvadilqr 177
                                    l+++  e +  +v +l++a++l+++++ ++++
  gi|118431570|ref|NP_148130.2| 262 LASPSVEEI--SVDTLILALILVSTASLWFVT 291
                                    ****99999..999999999999999999986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.043
                   BPD_transp_1 108 ppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlv 171
                                    +p +  l++af  ++ g++   f++    +  +l ++   + + +   +++l + ++ +++ + 
  gi|118431570|ref|NP_148130.2| 338 SPQLGVLVYAFSESWIGTTPQGFTLDH--MREVLSDSRVVNAFRNSV-TYALLASLISIVIAVT 398
                                    444444555555555555555555521..343443333333333333.3333333333333333 PP

  == domain 4  score: 47.8 bits;  conditional E-value: 1.5e-16
                   BPD_transp_1  10 lnrnkkldkllrpliivllslPsfvlaillvlvf.......vilsilghlilpviillllsaapyvrlirraalrslpkd 82 
                                     + + +l++ l++l  ++ +lP ++la+ ++ +f        +l+   + +l +++++ +   p++++   a+l+ l k+
  gi|118431570|ref|NP_148130.2| 404 ERLRTRLSEPLDVLATIPIALPGLALALGILIMFstsftrgTLLDPYEFPALFLVLAYSVRKSPFATRAAFAGLKHLHKS 483
                                    47788899999999999999999999999999999*****99999999******************************** PP

                   BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..nggvla 160
                                    l+eaa  lGa+r +++r +++P++ + ++ g++l+f++++++ +   ++g+ +   ++++ +  +ydy  +     g+++
  gi|118431570|ref|NP_148130.2| 484 LEEAAMNLGARRLRVIRDITVPLIGINLLGGVLLTFVYSVTEVSTSITIGGLNEDYSPITYI--IYDYVTGGygG-GAFV 560
                                    **************************************************665444444444..44444444332.3333 PP

                   BPD_transp_1 161 lviavlllnlvad 173
                                     ++a ++++l   
  gi|118431570|ref|NP_148130.2| 561 HLAASIVVILM-A 572
                                    22222222222.2 PP

>> Sulfotransfer_3  Sulfotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.35     108     161 ..     355     409 ..     282     419 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                                    EESSGGG-HHHHHHHBSSEEEEEEE--H..HHHHHHHHHTT----------..-.H CS
                Sulfotransfer_3 108 KsPshlfrldlllelfPdAkfihlvRdpv.dtvlssyvslfgkkresysedsld.e 161
                                     +P+  f ld++ e++ d +++   R+ v ++ l+s++s++ + ++sys ++l+ +
  gi|118431570|ref|NP_148130.2| 355 TTPQ-GFTLDHMREVLSDSRVVNAFRNSVtYALLASLISIVIAVTTSYSVERLRtR 409
                                    4555.578*******************664899999****9999999*96666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4216.94
//
Query:       gi|14601591|ref|NP_148131.1|  [L=358]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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  116.5   0.0    2.2e-33  115.7   0.0    1.4  1  ABC_tran      ABC transporter
    2.1e-11   43.9   1.1    3.9e-08   33.5   0.0    3.4  3  TOBE          TOBE domain
    5.8e-10   39.2   2.6    8.6e-10   38.7   0.0    2.6  4  TOBE_2        TOBE domain
    1.1e-06   28.7   0.3     0.0027   17.6   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0012   19.2   0.0     0.0031   17.9   0.0    1.7  1  RNA_helicase  RNA helicase
     0.0014   18.5   0.0     0.0022   17.9   0.0    1.2  1  Rad17         Rad17 P-loop domain
     0.0095   16.3   0.1      0.014   15.7   0.1    1.5  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.022   15.2   0.3      0.072   13.5   0.3    2.0  1  AAA           ATPase family associated with various cellular 
      0.048   13.5   0.4       0.41   10.5   0.2    2.4  2  eIF-1a        Translation initiation factor 1A / IF-1
      0.053   13.8   1.5       0.32   11.3   1.5    2.0  1  AAA_22        AAA domain
      0.081   12.6   0.0       0.16   11.6   0.0    1.4  1  AAA_30        AAA domain
        0.1   12.4   0.0       0.51   10.1   0.0    2.0  2  AAA_29        P-loop containing region of AAA domain
        0.1   12.5   0.0       0.23   11.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
       0.12   11.8   0.0       0.17   11.3   0.0    1.1  1  HSM3_N        DNA mismatch repair protein HSM3, N terminal do
       0.17   12.0   0.9        1.7    8.8   0.9    2.1  1  AAA_33        AAA domain
       0.23   12.0   0.2       0.36   11.3   0.2    1.2  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 !  115.7   0.0     2e-36   2.2e-33       1     136 [.      19     161 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2e-36
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                   l++vsl+++ ge+  ++G++G+GK+t l+++ag ++p+eG++ + ++d+++  l+ ++++ ++++q+  l+p+++v +n  
  gi|14601591|ref|NP_148131.1|  19 LDRVSLNISDGEIFTLLGPSGCGKTTTLRVIAGFETPDEGRVYIGSRDVTM--LKPYERNTAMVFQNYALWPHMRVFDNia 97 
                                   789************************************************..**************************** PP

                                   ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              e  +++  a++ l++++l d+      ++LSgGq+qrva+ara++++p++ll+DEp 
  gi|14601591|ref|NP_148131.1|  98 yglklrklprsEIVRRVRWAAELLEIDHLLDRYP----HQLSGGQQQRVAVARAIVTEPEVLLMDEPL 161
                                   *******998888888999999999999888887....*****************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   2.2e+03      34      59 ..     204     225 ..     184     227 .. 0.85
   2 !    6.4   0.8    0.0098        11       6      64 .]     239     289 ..     237     289 .. 0.84
   3 !   33.5   0.0   3.5e-11   3.9e-08       4      63 ..     296     350 ..     294     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                          TOBE  34 tArvtrrsaeeLgLapGeeVfalika 59 
                                   +A+++r ++e+    +G ++ +  k+
  gi|14601591|ref|NP_148131.1| 204 VAVMNRGRVEQ----VGTPMEVYEKP 225
                                   58889999999....99998888777 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0098
                          TOBE   6 qlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                   +l g+V++v   g   +Vrv+l+gg     ++ +   e  gL+ Ge+V ++i +++v++
  gi|14601591|ref|NP_148131.1| 239 VLDGRVSEVLGSG---MVRVALEGGL----SIVGTDMEG-GLRQGERVKVVIRPERVKV 289
                                   5778899998888...9*********....555777777.8999*********999975 PP

  == domain 3  score: 33.5 bits;  conditional E-value: 3.5e-11
                          TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                   +N+++g+V+   +lg+++++ v++gg++ +t   ++r+a+     pG++V++ i++++ +
  gi|14601591|ref|NP_148131.1| 296 ENVFEGKVSLAMFLGWRTQLKVEVGGQE-ITIYSDPRRAPL----PGQPVRFYIDPEEAK 350
                                   8***************************.************....***********9865 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       8.2   9.1e+03      38      50 ..     133     145 ..     129     150 .. 0.68
   2 ?   -3.0   0.0       7.9   8.9e+03      36      49 ..     189     202 ..     181     221 .. 0.54
   3 ?   -0.8   0.0       1.5   1.7e+03      21      66 ..     242     280 ..     234     281 .. 0.58
   4 !   38.7   0.0   7.7e-13   8.6e-10       1      73 [.     280     349 ..     280     351 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.2
                        TOBE_2  38 elaggqlvvvrqp 50 
                                   +l ggq+++v+++
  gi|14601591|ref|NP_148131.1| 133 QLSGGQQQRVAVA 145
                                   5677777777665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                        TOBE_2  36 vvelaggqlvvvrq 49 
                                   +v+ ++++ + ++ 
  gi|14601591|ref|NP_148131.1| 189 YVTHDQEEALSISH 202
                                   44444444444433 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.5
                        TOBE_2  21 GtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVel 66 
                                   G+V++v  lGs + ++v+l+gg   +v ++ +     l+ G++V +
  gi|14601591|ref|NP_148131.1| 242 GRVSEV--LGSGM-VRVALEGGLS-IVGTDMEG---GLRQGERVKV 280
                                   555554..44443.4677777755.55555555...6777777765 PP

  == domain 4  score: 38.7 bits;  conditional E-value: 7.7e-13
                        TOBE_2   1 laiRPEklrla.aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpdda 73 
                                   ++iRPE++++  +  g+n ++G+V+   +lG  t++ ve++g+++ +++ ++++   a+ pG+ V+  +dp+ a
  gi|14601591|ref|NP_148131.1| 280 VVIRPERVKVGhEYNGENVFEGKVSLAMFLGWRTQLKVEVGGQEI-TIYSDPRR---APLPGQPVRFYIDPEEA 349
                                   78********75444468**********************99977.99999999...9*************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 !    9.6   0.0   0.00065      0.73       2      22 ..      32      52 ..      31      86 .. 0.81
   2 !   17.6   0.1   2.4e-06    0.0027     220     298 ..     117     193 ..      60     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00065
                        AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    l Gp g+GK++ L+ + ++
  gi|14601591|ref|NP_148131.1| 32 FTLLGPSGCGKTTTLRVIAGF 52
                                  5799**************876 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.4e-06
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                      +le ++  ++ +++lS G+++  a++ a+   +    +ll DEp ++L+ +l  +  e + ++ +r g+ ++ +TH+
  gi|14601591|ref|NP_148131.1| 117 AAELLEIDHLLDRYPHQLSGGQQQRVAVARAIVTEP---EVLLMDEPLSNLDAHLRLKMREEIvRLQKRLGVTIVYVTHD 193
                                   6667888999999************99999999988...9*************99999995553777779*********8 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.7e-06    0.0031       3      58 ..      34      84 ..      32      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                  RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDf 58
                                  l Gpsg+GK+t+ +         ++++ +++vy+++ + ++++ Y++++++v++  
  gi|14601591|ref|NP_148131.1| 34 LLGPSGCGKTTTLRV-----IAGFETPDEGRVYIGSRDVTMLKPYERNTAMVFQNY 84
                                  78************9.....445679*************************99865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0022      34      66 ..      18      50 ..      11      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                         Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                  +l+  +L+    +i  + GPsGCgk+t+++v++
  gi|14601591|ref|NP_148131.1| 18 ALDRVSLNISDGEIFTLLGPSGCGKTTTLRVIA 50
                                  5667778888888999**************997 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   0.1   1.3e-05     0.014      20      55 ..      25      60 ..      16     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                        AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif 55
                                  + +++e+  l G+sG+GK++ +r ++   + d+g +
  gi|14601591|ref|NP_148131.1| 25 NISDGEIFTLLGPSGCGKTTTLRVIAGFETPDEGRV 60
                                  4455699****************9986555554444 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   0.3   6.5e-05     0.072       3      20 ..      34      51 ..      32     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.5e-05
                                  EESSTTSSHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavak 20
                                  l Gp G+GKT++ + +a 
  gi|14601591|ref|NP_148131.1| 34 LLGPSGCGKTTTLRVIAG 51
                                  89*************996 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.8     9e+02      27      41 ..     164     179 ..     153     203 .. 0.75
   2 ?   10.5   0.2   0.00037      0.41       4      45 ..     241     276 ..     239     295 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.8
                                   EEEEE-HHHH.CT--- CS
                        eIF-1a  27 vlaeipgkfR.nkiwi 41 
                                   + a+++ k+R   ++ 
  gi|14601591|ref|NP_148131.1| 164 LDAHLRLKMReEIVRL 179
                                   6799999999666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00037
                                   EEEEEEEETTTEEEEEE.SSSSBEE.EEE-HHHHCT----TT- CS
                        eIF-1a   4 igkViealgnnlfrVelpdngkevl.aeipgkfRnkiwikrGd 45 
                                    g+V+e+lg++++rV l+  g  ++   ++g +R      +G 
  gi|14601591|ref|NP_148131.1| 241 DGRVSEVLGSGMVRVALE-GGLSIVgTDMEGGLR------QGE 276
                                   69***************5.676544045666666......444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   0.00029      0.32       5      28 ..      29      52 ..      25     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                        AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                    i ++ G+sG+GKTt+lr ++  
  gi|14601591|ref|NP_148131.1| 29 GEIFTLLGPSGCGKTTTLRVIAGF 52
                                  5688999***********977655 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      18      49 ..      29      60 ..      21      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                        AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                    + +l Gp G GKtt+l++++   + ++grv
  gi|14601591|ref|NP_148131.1| 29 GEIFTLLGPSGCGKTTTLRVIAGFETPDEGRV 60
                                  4588999**************98777665444 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 ?   10.1   0.0   0.00045      0.51      13      39 ..      20      46 ..      14      56 .. 0.82
   2 ?   -1.1   0.0       1.5   1.6e+03      34      41 ..     235     242 ..     203     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00045
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                  d+ +++i+  +++ l GpsG GK+T l
  gi|14601591|ref|NP_148131.1| 20 DRVSLNISDGEIFTLLGPSGCGKTTTL 46
                                  55677787555999**********976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                        AAA_29  34 GKSTllDA 41 
                                   G ST+lD 
  gi|14601591|ref|NP_148131.1| 235 GRSTVLDG 242
                                   89999996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.23      89     121 ..      18      51 ..       2      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                   +l++++ +++d ++ +l+G+SG GK+t + ++++
  gi|14601591|ref|NP_148131.1|  18 ALDRVSLNISDgEIFTLLGPSGCGKTTTLRVIAG 51 
                                   5677777777779**************9999876 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.17      20     108 ..     122     210 ..     116     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                        HSM3_N  20 einellekcslnlstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalksei 100
                                   ei++ll++   +ls  ++ +  + r +++   +l+ +++ ++ld +l l++ +++v++ +   v  vy ++d ++al  + 
  gi|14601591|ref|NP_148131.1| 122 EIDHLLDRYPHQLSGGQQQRVAVARAIVTEPEVLLMDEPLSNLDAHLRLKMREEIVRLQKRLGVTIVYVTHDQEEALSISH 202
                                   7999*************************************************************************8776 PP

                        HSM3_N 101 dslvvaac 108
                                      v+   
  gi|14601591|ref|NP_148131.1| 203 RVAVMNRG 210
                                   66555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.9    0.0016       1.7       4     109 ..      34     195 ..      31     226 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                        AAA_33   4 lvGlpGsGKstlaerllkklg....avllssdt.............................lrrrlfgtdqqskt..... 46 
                                   l G++G+GK+t ++ ++  ++     v + s +                             +                  
  gi|14601591|ref|NP_148131.1|  34 LLGPSGCGKTTTLRVIAGFETpdegRVYIGSRDvtmlkpyerntamvfqnyalwphmrvfdnI------------Ayglkl 102
                                   67*********9998875555556634444433344444444444444444444333333330............033333 PP

                        AAA_33  47 ..........................dytr.vldrlyqilnelarkalsagrnvildat..nlsrrer....arflklarr 94 
                                                             +y++ ++    q++ ++ar   ++   ++ d +  nl+++ r    +++++l +r
  gi|14601591|ref|NP_148131.1| 103 rklprseivrrvrwaaelleidhlldRYPHqLSGGQQQRV-AVARAIVTEPEVLLMDEPlsNLDAHLRlkmrEEIVRLQKR 182
                                   3333334444444444444333333322221222233333.4444444555555556665544444444444677777777 PP

                        AAA_33  95 lgvpvrivvvetdee 109
                                   lgv   iv+v+ d+e
  gi|14601591|ref|NP_148131.1| 183 LGVT--IVYVTHDQE 195
                                   7744..444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00032      0.36      14      39 ..      23      49 ..      12      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                        AAA_23 14 eidFsk.gltlItGpNGaGKTTildAi 39
                                  +++ s+  ++ + Gp G+GKTT l+ i
  gi|14601591|ref|NP_148131.1| 23 SLNISDgEIFTLLGPSGCGKTTTLRVI 49
                                  55664426999***********99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2659.55
//
Query:       gi|118431571|ref|NP_148132.2|  [L=174]
Description: hypothetical protein APE_1734.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.0   0.0       0.07   12.8   0.0    1.2  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.9e-06      0.07      37      94 ..      26      78 ..       2     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-06
                                   HHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHHHHHHHHHHHHCHC CS
                Methyltrn_RNA_2 37 saalfvshgiRedvvvylvLegtpdpprtikieasevkkvspderniailikkalkav 94
                                   s +l +shg+R+ v  ++ L       + i +  sev++  pd+ ++ + +k++l+++
  gi|118431571|ref|NP_148132.2| 26 SSSLLLSHGVRQGVSAAVRLG-----GKWIVVRSSEVRRLYPDADSLEGWVKAVLRGR 78
                                   7899***********999888.....689**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1421.43
//
Query:       gi|14601593|ref|NP_148133.1|  [L=441]
Description: signal recognition 54 kDa protein [Aeropyrum pernix K1]
Scores for complete 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-64  215.7   0.0    6.2e-64  215.2   0.0    1.2  1  SRP54       SRP54-type protein, GTPase domain
    3.7e-29  101.3   0.7    9.5e-28   96.7   1.1    2.6  2  SRP_SPB     Signal peptide binding domain
    4.7e-15   55.6   0.0    1.4e-14   54.0   0.0    1.9  1  SRP54_N     SRP54-type protein, helical bundle domain
    5.9e-05   23.1   0.0    0.00012   22.1   0.0    1.6  1  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
    7.1e-05   23.2   0.0    0.00019   21.9   0.0    1.6  1  AAA_16      AAA ATPase domain
    0.00016   21.5   0.1    0.00053   19.8   0.0    1.8  2  AAA_30      AAA domain
    0.00053   19.9   0.0     0.0012   18.8   0.0    1.6  1  MobB        Molybdopterin guanine dinucleotide synthesis prot
    0.00053   20.2   0.0     0.0012   19.0   0.0    1.6  1  AAA_33      AAA domain
     0.0015   17.9   0.0     0.0027   17.0   0.0    1.4  1  Zeta_toxin  Zeta toxin
     0.0026   17.1   0.0     0.0078   15.6   0.0    1.8  1  ATPase      KaiC
     0.0033   17.5   0.0      0.017   15.2   0.0    2.2  2  MMR_HSR1    50S ribosome-binding GTPase
     0.0064   16.8   0.0      0.016   15.5   0.0    1.7  1  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.027   13.5   0.0    1.6  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.015   15.2   0.0      0.029   14.3   0.0    1.4  1  APS_kinase  Adenylylsulphate kinase
      0.017   15.1   0.1      0.061   13.3   0.0    2.0  1  AAA_5       AAA domain (dynein-related subfamily)
       0.03   14.9   0.0      0.075   13.6   0.0    1.9  1  AAA_18      AAA domain
      0.032   14.1   0.0       0.07   13.0   0.0    1.5  1  AAA_31      AAA domain
      0.033   14.6   0.0       0.21   12.0   0.0    2.5  2  AAA         ATPase family associated with various cellular ac
      0.033   13.6   0.0      0.057   12.8   0.0    1.3  1  ParA        NUBPL iron-transfer P-loop NTPase
      0.048   13.2   0.0       0.15   11.6   0.0    1.8  1  cobW        CobW/HypB/UreG, nucleotide-binding domain
      0.065   12.7   0.0       0.12   11.8   0.0    1.5  1  KTI12       Chromatin associated protein KTI12
      0.074   12.8   0.4        1.8    8.3   0.0    2.8  3  IstB_IS21   IstB-like ATP binding protein
      0.091   13.0   0.3       0.21   11.8   0.0    1.8  1  AAA_28      AAA domain
      0.092   12.5   0.0        1.8    8.3   0.0    2.4  2  CLP1_P      mRNA cleavage and polyadenylation factor CLP1 P-l
        0.1   12.9   0.0        1.6    9.1   0.0    2.5  2  PFOR_II     Pyruvate:ferredoxin oxidoreductase core domain II
       0.18   11.3   1.0        0.7    9.4   1.0    1.9  1  AAA_25      AAA domain
       0.25   11.5   1.3         16    5.7   0.2    4.1  5  HTH_20      Helix-turn-helix domain
       0.29   11.6   3.3       0.34   11.3   0.1    2.6  2  AAA_17      AAA 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 !  215.2   0.0   9.7e-67   6.2e-64       3     196 .]      98     292 ..      96     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 9.7e-67
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTT CS
                         SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeek 83 
                                   ++llvG+qG+GKTtt++KLa ++ ++g+kv lv+ Dt R++A+eQLk lae++g+ +++++ e dpa++a++++e   +++
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDTHRPGAYEQLKRLAEEAGAMFYGER-EGDPAEIARRGLEDLLSRG 177
                                   79****************************************************8877655.778**************** PP

                                   SSEEEEEE--SST..THHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHH CS
                         SRP54  84 idvvlvDTaGrlq..ndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsi 162
                                   +++v+vDTaGr+   ++++l++e+k+i++ v+pdev lv+da++gq+a+  a++F++++ i+++i+tk+Dg+a+gG+al++
  gi|14601593|ref|NP_148133.1| 178 AEIVIVDTAGRHGhgEEARLLDEMKAIASKVRPDEVALVIDASIGQKAMGLAERFHKSTPIGSIIVTKMDGTARGGGALTA 258
                                   ***********86226788************************************************************** PP

                                   HHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                         SRP54 163 aaelklPikfigvGekiedleefdperlvsrllg 196
                                   aa ++  ikfig+Ge++ +le+f p+r+v r+lg
  gi|14601593|ref|NP_148133.1| 259 AAVTGARIKFIGTGETLGELEPFAPRRFVARILG 292
                                   ********************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.94     6e+02      12      33 ..     288     309 ..     284     322 .. 0.71
   2 !   96.7   1.1   1.5e-30   9.5e-28       2      99 .]     324     424 ..     323     424 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.94
                                   HHHHCCCCCCHHHHCCC..... CS
                       SRP_SPB  12 qqikkmGplskllsmiPgmsae 33 
                                   ++i  mG+l++ll+ i  + + 
  gi|14601593|ref|NP_148133.1| 288 ARILGMGDLESLLERIKSLEEA 309
                                   678899*****99999875544 PP

  == domain 2  score: 96.7 bits;  conditional E-value: 1.5e-30
                                   SCTHHHHHHHHHHHCCCCCCHHHHCCC..........H.....CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHH CS
                       SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsae.....akae..eeaekklkrieaiidSMTkeErdspekllkesRkrRiA 75 
                                    t+r ++ ql+ ++k+Gpl k+l+m+Pg s +     +     + +e+k+kr++aii+SMT eE+d+pe +++++R+rRiA
  gi|14601593|ref|NP_148133.1| 324 ITMRTIYRQLRAMRKLGPLGKVLQMLPGAS-MlasidE--GalKLGEEKMKRWMAIIESMTYEELDRPE-IIDKRRMRRIA 400
                                   589*************************44.5566543..1558899**********************.999******** PP

                                   HHTTS-HHHHHHHHHHHHHHHHHT CS
                       SRP_SPB  76 rGsGtsvqevnellkqfeqmkkmm 99 
                                    GsGtsv++v+ell  ++++k+mm
  gi|14601593|ref|NP_148133.1| 401 IGSGTSVDDVRELLVYYKNLKTMM 424
                                   ***********************8 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 !   54.0   0.0   2.2e-17   1.4e-14       3      75 .]       3      78 ..       1      78 [. 0.94

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2.2e-17
                                  HHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                       SRP54_N  3 kklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                  +++++a++k+ +++ + e+++++++k+l++ L++aDV+vk+v +++ ++k++a++e+    +++++ ++kiv++eL
  gi|14601593|ref|NP_148133.1|  3 EGVRRAVAKFLRGGGVYEKAVDAFVKDLQRELIKADVNVKLVLNVTRRIKERALKEEPppgVTRRDWMIKIVYEEL 78
                                  678899999999999************************************9999666*****************8 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 !   22.1   0.0   1.9e-07   0.00012       9      87 ..     106     249 ..      98     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.9e-07
                                   TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                          CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................... 54 
                                   G+GKTt+a +La +  rrg++V lv  D+ ++ +   e+l+   e+                                   
  gi|14601593|ref|NP_148133.1| 106 GSGKTTTAGKLAYYYVRRGYKVGLVSSDTHRPGAY--EQLKRLAEEagamfygeregdpaeiarrgledllsrgaeivivd 184
                                   9*****************************99876..33333333377888888888889999999999999988888888 PP

                                   .....................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                   .....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  55 .....................................dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                                                        + ++  +l+e++ k+      i ++++++ dg 
  gi|14601593|ref|NP_148133.1| 185 tagrhghgeearlldemkaiaskvrpdevalvidasiG-QKAMGLAERFHKS----TPIGSIIVTKMDGT 249
                                   88888888888888888888888888888888877642.3445556666666....45666777776665 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   0.00019      25     142 ..      97     218 ..      89     220 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.9e-07
                        AAA_16  25 elvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysalaqalareellrqllde....aesaeleawre 99 
                                    +vll+G +G+GK++ + +l+ ++ ++g  +  ++ ++++           ++l + +l ++ +++     e + +e +r+
  gi|14601593|ref|NP_148133.1|  97 WIVLLVGVQGSGKTTTAGKLAYYYVRRGYKVglVSSDTHRP-------GAYEQL-K-RLAEEAGAMfygeREGDPAEIARR 168
                                   58*******************99999954442133333333.......355666.3.444444444555323334444444 PP

                        AAA_16 100 kleeala........avpelagaea......srllellkrllallsrderplvlvlD 142
                                    le+ l+        +++      +       rll+++k+++++ ++ ++ + lv+D
  gi|14601593|ref|NP_148133.1| 169 GLEDLLSrgaeivivDTAG-----RhghgeeARLLDEMKAIASKVRP-DE-VALVID 218
                                   4444444777776442222.....13345589**********99999.55.788888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   8.2e-07   0.00053      19     119 ..      97     208 ..      93     210 .. 0.70
   2 ?   -2.7   0.0       6.4   4.1e+03     145     157 ..     320     332 ..     289     371 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.2e-07
                        AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgk...aAkvLa...eelgi.........eastiakllkrlkgra 84 
                                   ++++l+G+ G+GKtt+ ++l+  + ++g++v ++++      a ++L+   ee+g+         +a+   + l+      
  gi|14601593|ref|NP_148133.1|  97 WIVLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDTHrpgAYEQLKrlaEEAGAmfygeregdPAEIARRGLED----- 172
                                   5889***************************999877652223333443334444333333322255555555533..... PP

                        AAA_30  85 rlepg.tllivDEagmvdtkqlaallkaaekagakv 119
                                    l++g +++ivD ag  +  + a+ll+++++   kv
  gi|14601593|ref|NP_148133.1| 173 LLSRGaEIVIVDTAGRHGHGEEARLLDEMKAIASKV 208
                                   344555********************9999876666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.4
                        AAA_30 145 gigtaeLtevvRq 157
                                     g +++++++Rq
  gi|14601593|ref|NP_148133.1| 320 LKGRITMRTIYRQ 332
                                   3445555555555 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   1.8e-06    0.0012       1      39 [.      98     136 ..      98     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                          MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhg 39 
                                   ++ +vg +gsGKTt   kl     +rg++vg++  ++h 
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDTHR 136
                                   6789*****************************999986 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   1.8e-06    0.0012       1      82 [.      98     189 ..      98     236 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                        AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdt....lrrrlfg.tdqqsktdytrvldrlyqilnelarkalsagr 71 
                                   +vllvG++GsGK+t a +l   + ++g  + l+ssdt    ++++l+   ++     y + + +  +i ++ +++ ls+g+
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLayyYVRRGykVGLVSSDThrpgAYEQLKRlAEEAGAMFYGEREGDPAEIARRGLEDLLSRGA 178
                                   599***************96664456667778*****55552222222322333336666666667788888899999999 PP

                        AAA_33  72 nvildatnlsr 82 
                                    +++  t  ++
  gi|14601593|ref|NP_148133.1| 179 EIVIVDTAGRH 189
                                   96666664443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.2e-06    0.0027      11      56 ..      91     137 ..      82     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-06
                    Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdelerqgnvv.rldpDdlRe 56 
                                    + ++P ++ll+G +G+GK+++a +l+ +  r+g  v  ++ D+ R+
  gi|14601593|ref|NP_148133.1|  91 DPPKTPWIVLLVGVQGSGKTTTAGKLAYYYVRRGYKVgLVSSDTHRP 137
                                   4559*******************999988775554441455666665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05    0.0078      21      68 ..      98     148 ..      94     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                        ATPase  21 vvlitGepGtGKtifalqFlikgaekygepgvfvtveepa....edlrenak 68 
                                   +vl++G+ G+GKt+ a + ++  +++ g+++ +v+ + +     e+l++ a+
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLAYYYVRR-GYKVGLVSSDTHRpgayEQLKRLAE 148
                                   79*********************999.***********99555555555554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.5   2.9e+03      17      42 ..      32      57 ..      29      76 .. 0.74
   2 !   15.2   0.0   2.7e-05     0.017       2      87 ..      99     223 ..      98     245 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.5
                                  HHHHTSTEEESSSTTSSSSEEEEEEE CS
                      MMR_HSR1 17 naltgekaivsdkpgtTrdinegrvk 42
                                  + l+++ + v+    +Tr i+e+ +k
  gi|14601593|ref|NP_148133.1| 32 RELIKADVNVKLVLNVTRRIKERALK 57
                                  56777778888888888888888776 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.7e-05
                                   EEEEESTTSSHHHHHHHHH....TSTEEESSSTTSSSSE.EEEEEE...ETTEE........................... CS
                      MMR_HSR1   2 vaivGrpNvGKStLinalt....gekaivsdkpgtTrdi.negrvk...lkgke........................... 47 
                                   v++vG   +GK+t   +l     ++  +v+     T  +  ++++k   +   e                           
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAyyyvRRGYKVGLVSSDTHRPgAYEQLKrlaE---Eagamfygeregdpaeiarrgledllsr 176
                                   67889999999998888872222345688888888888866666663321...1333444444455555555555555555 PP

                                   ...EEEEECGGCSSHHHHHH...HHHHHHHHHHCTSEEEEEEETT..T CS
                      MMR_HSR1  48 ...ielvDtpGliegaseek...glgkaflaleeadlillvvdas..e 87 
                                      i++vDt+G  +g+ ee    ++ ka++++ + d ++lv+das  +
  gi|14601593|ref|NP_148133.1| 177 gaeIVIVDTAG-RHGHGEEArllDEMKAIASKVRPDEVALVIDASigQ 223
                                   555********.76444444235666777777778********88542 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   2.4e-05     0.016       7     101 ..      98     187 ..      93     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                        AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka....erlsseelleale 83 
                                   i++++G  G+GKTt++ +l++ ++++ +    ++++v+ +   ++     +++l r  ++ +      ++++  e+ ++  
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLAYYYVRRGY----KVGLVSSDTHRPG----AYEQLKRLAEEAGAMfygeREGDPAEIARRGL 170
                                   789********************63322....4444444444444....34444444443333355565557777777777 PP

                        AAA_22  84 qalraravielliiDEaq 101
                                   + l +r++ e++i+D a 
  gi|14601593|ref|NP_148133.1| 171 EDLLSRGA-EIVIVDTAG 187
                                   77777777.799999775 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 ?   13.5   0.0   4.1e-05     0.027      33      66 ..     100     133 ..      95     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                                   EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                          MeaB  33 GltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                    l Gv G+Gk t+  +l+  ++rrG++v++++ D
  gi|14601593|ref|NP_148133.1| 100 LLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSD 133
                                   578***************************9877 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.5e-05     0.029       2      49 ..      96     143 ..      95     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
                                   -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                    APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                   + +v+l G+ gsGK+t a +l+ + v++g++v l+  d+ R g +++L
  gi|14601593|ref|NP_148133.1|  96 PWIVLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDTHRPGAYEQL 143
                                   5689**********************************9998887777 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   9.5e-05     0.061       2      36 ..      99     134 ..      98     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                                   EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT- CS
                         AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdt 36 
                                   vlLvG +G+gK++ a +la  + +r + + + ++dt
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAYYYvRRGYKVGLVSSDT 134
                                   89*****************99988888877777777 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00012     0.075       1      32 [.      99     135 ..      99     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                        AAA_18   1 IlltGtpGvGKttlakeL....skrlgf..gvnlrdva 32 
                                   +ll G++G+GKtt a  L     +r g+  g +++d++
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLayyyVRR-GYkvGLVSSDTH 135
                                   799***************6665444.334455555544 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011      0.07      12      40 ..     106     134 ..      98     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                        AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                   G GKTTt+ +la+   ++g+kv lv  D+
  gi|14601593|ref|NP_148133.1| 106 GSGKTTTAGKLAYYYVRRGYKVGLVSSDT 134
                                   99********************9999886 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   0.00033      0.21       1      70 [.      99     189 ..      99     291 .. 0.61
   2 ?   -2.5   0.0       9.9   6.3e+03     101     119 ..     396     414 ..     366     424 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00033
                                   EEEESSTTSSHHHHHHHHHHHH..............THEEEEEETTTCSSS.................STTHHHHHHHHHH CS
                           AAA   1 vllyGppGtGKTllakavakel..............gvefleisgsellsk.................yvgesekkirelf 50 
                                   vll+G  G GKT++a  +a                 +                               + ge+e + +e+ 
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAYYYvrrgykvglvssdtH-------------RpgayeqlkrlaeeagamFYGEREGDPAEIA 166
                                   79***************99985333222211211110.............0112222333333333336666666666666 PP

                                   HHHHHTS...TSEEEEEETGGGH CS
                           AAA  51 keakeka...kpsilfiDEidal 70 
                                   ++  e     +  i+++D + + 
  gi|14601593|ref|NP_148133.1| 167 RRGLEDLlsrGAEIVIVDTAGRH 189
                                   66433334544466666655555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.9
                                   STEEEEEEESSGGGSTHHH CS
                           AAA 101 skvivigatnrpdkldpal 119
                                    + i ig ++++d++ + l
  gi|14601593|ref|NP_148133.1| 396 MRRIAIGSGTSVDDVRELL 414
                                   2345666666666665555 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 ?   12.8   0.0     9e-05     0.057       6      45 ..      98     137 ..      95     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                          ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGp 45 
                                   i+ l g  G GK+t+a +lA+   ++g+kvgl+  D + p
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDTHRP 137
                                   5666777899***********************9998765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.15       3     151 ..      99     247 ..      97     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHHT CS
                          cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeeree 81 
                                   ++l+G  GsGKTt   +l     r+g+k+ ++  +    +  ++l r + +e+  +  G      +e + + le+l++r  
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAyyYVRRGYKVGLVSSDTHRPGAYEQLKRLA-EEAGAMFYGEREGDPAEIARRGLEDLLSRG- 177
                                   7899***********9999999999***********9766655554444.5678888888888888999999*****999. PP

                                   T-SEEEEEECT.TTTHHHH.HTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                          cobW  82 rldviliEttG.laePapv.aft.eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                     +++++ t G   +  +  ++   + ++s+++ d v  v+Da  + ++    +e +++     + ++++K+D
  gi|14601593|ref|NP_148133.1| 178 -AEIVIVDTAGrHGHGEEArLLDeMKAIASKVRPDEVALVIDA-SIGQKAMGLAERFHKSTPIGS-IIVTKMD 247
                                   .899*******9999988864446899999*************.444566666666666655544.5667777 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.12       4      41 ..      99     136 ..      97     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                         KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                   v+l G+  sGK+t a +La +   ++++v ++++++ +
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDTHR 136
                                   899******************************99876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0028       1.8      50      81 ..      99     130 ..      95     145 .. 0.92
   2 ?    0.7   0.0      0.61   3.9e+02      82     136 ..     325     379 ..     314     386 .. 0.85
   3 ?   -1.2   0.0       2.3   1.5e+03      75      95 ..     412     432 ..     399     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0028
                     IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfv 81 
                                   ++l+G  G GK+  a  l++  vr+g++v  v
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAYYYVRRGYKVGLV 130
                                   789*************************9766 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.61
                     IstB_IS21  82 rvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviek 136
                                   +++ + ++l++ r+ g l + l+ l  +++l   d g l+l +++ +  + +ie+
  gi|14601593|ref|NP_148133.1| 325 TMRTIYRQLRAMRKLGPLGKVLQMLPGASMLASIDEGALKLGEEKMKRWMAIIES 379
                                   7788999******************999888866678889999999998888875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.3
                     IstB_IS21  75 glsvlfvrvedLveelkrarr 95 
                                   +l v++  ++ ++++lkr++r
  gi|14601593|ref|NP_148133.1| 412 ELLVYYKNLKTMMKKLKRDKR 432
                                   566999999999999999876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.21       2      39 ..      99     143 ..      98     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                        AAA_28   2 ivitGgestGKTtlleaLa....argyp..vv.pEaareileekl 39 
                                   + ++G +++GKTt++ +La    +rgy+   v  +++r    e+l
  gi|14601593|ref|NP_148133.1|  99 VLLVGVQGSGKTTTAGKLAyyyvRRGYKvgLVsSDTHRPGAYEQL 143
                                   6799***************88877798844233666655555555 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 ?    8.3   0.0    0.0028       1.8       1      32 [.     103     134 ..     103     139 .. 0.91
   2 ?    1.3   0.0       0.4   2.6e+02     101     136 ..     176     215 ..     163     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0028
                        CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32 
                                   G + sGK+T a  L+ y +r+g+k+ +v  D 
  gi|14601593|ref|NP_148133.1| 103 GVQGSGKTTTAGKLAYYYVRRGYKVGLVSSDT 134
                                   5689***********************99985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.4
                        CLP1_P 101 akasgliIntpGwv.kglgaellle...liealepdvvvv 136
                                   ++a+++i++t G   +g+ a+ll e   +++ ++pd v++
  gi|14601593|ref|NP_148133.1| 176 RGAEIVIVDTAGRHgHGEEARLLDEmkaIASKVRPDEVAL 215
                                   5788999999997734677888855212466667765544 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0025       1.6      18      59 ..     116     157 ..     100     164 .. 0.80
   2 ?    0.4   0.0       1.2     8e+02      45      89 ..     170     216 ..     167     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                                   HHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE CS
                       PFOR_II  18 avdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvld 59 
                                    +  + ++g+kvGl+   t rP  +e+lk+l++++ +++  +
  gi|14601593|ref|NP_148133.1| 116 LAYYYVRRGYKVGLVSSDTHRPGAYEQLKRLAEEAGAMFYGE 157
                                   45556679***********************99887766555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                                   HHHHSTT-SEEEEEE-S--TT-G..-HHHHHHHHHTGGGTSEEEEEE CS
                       PFOR_II  45 lkellkkvkkvvvldrnisfgse..Gqlveevkaalkkskvkvvnfv 89 
                                   l++ll++ +++v +d +   g      l++e+ka  +k +++ v +v
  gi|14601593|ref|NP_148133.1| 170 LEDLLSRGAEIVIVDTAGRHGHGeeARLLDEMKAIASKVRPDEVALV 216
                                   56777888889999999888777679999999999988877666555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0    0.0011       0.7      35     139 ..      98     210 ..      95     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                        AAA_25  35 lallaGapgtGKttlaldlalava.tGkpwlg................pvapeqgkVlyvsaEdsedelrrRlravgealr 98 
                                   ++ll+G +g+GKtt a  la+ ++ +G ++ g                ++a e g+  y   E++ +e++rR  + +  + 
  gi|14601593|ref|NP_148133.1|  98 IVLLVGVQGSGKTTTAGKLAYYYVrRGYKV-GlvssdthrpgayeqlkRLAEEAGAMFYGEREGDPAEIARRGLEDLLSR- 176
                                   689********************9866655.5577777788899999888889999999999999999999866433332. PP

                        AAA_25  99 ddarllvldlagveslpLfakdrggtl.ltadvdaleaaiee 139
                                     a+  ++d ag+        ++g+++ l  +++a++ +++ 
  gi|14601593|ref|NP_148133.1| 177 -GAEIVIVDTAGR-------HGHGEEArLLDEMKAIASKVRP 210
                                   .466666665554.......3344444444445555555555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       7.7   4.9e+03      11      31 ..       5      24 ..       2      31 .. 0.82
   2 ?    0.0   0.0       1.4   9.1e+02      35      53 ..     133     152 ..     125     155 .. 0.84
   3 ?   -2.7   0.0       9.9   6.3e+03      12      23 ..     167     178 ..     166     207 .. 0.62
   4 ?    1.2   0.1       0.6   3.8e+02      34      52 ..     291     310 ..     287     317 .. 0.76
   5 ?    5.7   0.2     0.024        16      27      51 ..     309     339 ..     295     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.7
                                  HHHHHHHHHSTCTTB-HHHHH CS
                        HTH_20 11 vRrrilraLaraegltasela 31
                                  vRr++ + L r++g+  ++++
  gi|14601593|ref|NP_148133.1|  5 VRRAVAKFL-RGGGVYEKAVD 24
                                  899999999.99988887776 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.4
                                   TS-HHHHHHHHHHHHH.CTT CS
                        HTH_20  35 dlskntlsyHLrvLee.agL 53 
                                   d+++  ++ +L+ L+e ag+
  gi|14601593|ref|NP_148133.1| 133 DTHRPGAYEQLKRLAEeAGA 152
                                   5778889999****999986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 9.9
                                   HHHHHHHHSTCT CS
                        HTH_20  12 RrrilraLarae 23 
                                   Rr+++++L+r++
  gi|14601593|ref|NP_148133.1| 167 RRGLEDLLSRGA 178
                                   788888883332 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.6
                                   HT.S-HHHHHHHHHHHHHCT CS
                        HTH_20  34 ld.lskntlsyHLrvLeeag 52 
                                   l+ ++  +l  +++ Leeag
  gi|14601593|ref|NP_148133.1| 291 LGmGDLESLLERIKSLEEAG 310
                                   55466678999********9 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.024
                                   HHHHHHHH......TS-HHHHHHHHHHHHHC CS
                        HTH_20  27 aselaerl......dlskntlsyHLrvLeea 51 
                                   a+el+++       ++++ t++++Lr++++ 
  gi|14601593|ref|NP_148133.1| 309 AGELDRAAedvlkgRITMRTIYRQLRAMRKL 339
                                   567777775445556************9875 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00053      0.34       1     107 [.     102     215 ..     102     234 .. 0.62
   2 ?   -0.1   0.0       1.8   1.2e+03     103     132 ..     378     410 ..     343     432 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00053
                                   EE-TTSSHHHHHHHHHHHH...TEEE..EEHHHHHHHHHHTT..TSHSSHHHHCTS.HHHHHHHHHHHHHHHHHHHHHSSE CS
                        AAA_17   1 lGgPGsGKgtqceklveky...gfth..lsaGdllreeakrg..glakardemrkl.pleekkelqkeaaekiaeeakkkg 73 
                                   +G+ GsGK+t + kl+  y   g+++  +s +d  r  a ++   la++ ++m  +  + +  e+ ++  e++  + + + 
  gi|14601593|ref|NP_148133.1| 102 VGVQGSGKTTTAGKLAYYYvrrGYKVglVS-SDTHRPGAYEQlkRLAEEAGAMFYGeREGDPAEIARRGLEDLLSR-GAEI 180
                                   79*************955544444443055.888885554443345666666665413344556666666666654.6778 PP

                                   EEEEE-SEE..EETTEEEESSHHHHHHHH..SEEEE CS
                        AAA_17  74 vlvdghpri..keqagfldglpkevleelkpdaiil 107
                                   v+vd+  r    e+a++ld++++ +  ++ pd + l
  gi|14601593|ref|NP_148133.1| 181 VIVDTAGRHghGEEARLLDEMKA-IASKVRPDEVAL 215
                                   99998876411333444444443.456777766655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.8
                                   SEEEEEE--HHHHH.HHHHHH..TTST-TS-SH CS
                        AAA_17 103 daiilleadpeeil.errlkd..rtrgrdddne 132
                                   + +++ e d  ei+ +rr+++   ++g + d+ 
  gi|14601593|ref|NP_148133.1| 378 ESMTYEELDRPEIIdKRRMRRiaIGSGTSVDDV 410
                                   555555544333330444444322566655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3067.99
//
Query:       gi|118431572|ref|NP_148134.2|  [L=150]
Description: 30S ribosomal protein S13 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-43  147.3   0.1    3.3e-43  147.1   0.1    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0065   16.1   0.1      0.036   13.7   0.0    2.2  2  DUF5053        Domain of unknown function (DUF5053)
  ------ inclusion threshold ------
      0.019   15.3   0.1      0.046   14.1   0.0    1.7  2  Qn_am_d_aIII   Quinohemoprotein amine dehydrogenase, alpha su
      0.097   11.4   0.0       0.12   11.2   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.1   0.1   7.5e-47   3.3e-43       1     127 [.      12     139 ..      12     140 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.1 bits;  conditional E-value: 7.5e-47
                  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdG 79 
                                    Ri+g+didg+ k+ + l++ikGiG+++a+++++ +++d +k++g lteeei ++ e++   +q   p+w+ nr+kd+++G
  gi|118431572|ref|NP_148134.2|  12 RIAGVDIDGDLKLPYGLASIKGIGYTTAMAVIRMLGLDPEKKVGFLTEEEIRRLDEVLRDITQLGLPKWLyNRRKDYETG 91 
                                    9******************************************************************************* PP

                  Ribosomal_S13  80 kdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                    kd h++ ++l ++ r+dieR++ki+s+rG+RHk GlkvRGQrT+ttgR
  gi|118431572|ref|NP_148134.2|  92 KDLHLIGSELIFYARRDIEREMKIGSWRGIRHKYGLKVRGQRTRTTGR 139
                                    ***********************************************9 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     8e-06     0.036      27      56 ..      44      73 ..      42      75 .. 0.94
   2 ?   -1.1   0.0      0.33   1.5e+03      22      31 ..      79      88 ..      78      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8e-06
                        DUF5053 27 rlnGidvngkvatFteeeletLkeALqdls 56
                                   r+ G d ++kv+ +teee+ +L e L+d+ 
  gi|118431572|ref|NP_148134.2| 44 RMLGLDPEKKVGFLTEEEIRRLDEVLRDIT 73
                                   88999***********************97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.33
                        DUF5053 22 sWlyqrlnGi 31
                                    Wly+r   +
  gi|118431572|ref|NP_148134.2| 79 KWLYNRRKDY 88
                                   5***996655 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 ?   14.1   0.0     1e-05     0.046      20      53 ..      11      44 ..       2      53 .. 0.90
   2 ?   -2.8   0.0       1.9   8.4e+03      53      72 ..     128     147 ..     124     149 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                   Qn_am_d_aIII 20 lrlvGtaLaadvdlgkgvevvkvveaspnevvlr 53
                                   +r++G+ +++d++l+ g+  +k ++ +   +v+r
  gi|118431572|ref|NP_148134.2| 11 VRIAGVDIDGDLKLPYGLASIKGIGYTTAMAVIR 44
                                   8**********************99999888876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                   Qn_am_d_aIII  53 rvkvaadategvrevsvGsk 72 
                                    +v+ + + t+g   + +G +
  gi|118431572|ref|NP_148134.2| 128 KVRGQRTRTTGRLGMTIGVR 147
                                    45555555666666666655 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.6e-05      0.12     196     240 ..      30      74 ..      22      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.6e-05
                                    HBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHT CS
                           FbpA 196 afqGlspllaeelleragldketsakelseedlerlyealqelle 240
                                    +++G++ ++a  +++ +gld+e+++  l+ee+++rl e l+++ +
  gi|118431572|ref|NP_148134.2|  30 SIKGIGYTTAMAVIRMLGLDPEKKVGFLTEEEIRRLDEVLRDITQ 74 
                                    578**************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1119.03
//
Query:       gi|118431573|ref|NP_148135.2|  [L=171]
Description: 30S ribosomal protein S4 [Aeropyrum pernix K1]
Scores for 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-16   57.5   0.2    1.9e-15   56.3   0.2    1.7  1  S4            S4 domain
      1e-07   32.8   0.5    7.8e-07   29.9   0.2    2.0  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 !   56.3   0.2   2.1e-19   1.9e-15       1      46 [.     104     149 ..     104     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2.1e-19
                                    EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                             S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                    rRL+++++++gla+++ +Arql+ hG++ + G++v++p+y V+ ++
  gi|118431573|ref|NP_148135.2| 104 RRLQTIVYKKGLAKTIYQARQLVVHGHIAIAGRRVTSPGYLVSREE 149
                                    8*****************************************9876 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 !   29.9   0.2   8.7e-11   7.8e-07      36      80 ..      15      60 ..       3      79 .. 0.90
   2 ?    1.0   0.0     0.092   8.2e+02       8      39 ..     101     155 ..      96     167 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.7e-11
                                   --CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                   Ribosomal_S4 36 lseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                   + ++ k +l+++ +l++rYgl+ +k+++++ ++arr+r + ++ Ll 
  gi|118431573|ref|NP_148135.2| 15 KHPWIKeRLERERELMGRYGLRnKKELWKAETLARRFR-HRARSLLG 60
                                   5699999*******************************.*****996 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.092
                                    HHHCHCTS-STSSS......................S-S-SSTTTTS.-----CH CS
                   Ribosomal_S4   8 kllRrvgfklflkg......................reyppGqhgkr.rkklseY 39 
                                     l Rr+++ +++kg                      r + pG   +r ++kl +Y
  gi|118431573|ref|NP_148135.2| 101 VLERRLQTIVYKKGlaktiyqarqlvvhghiaiagrRVTSPGYLVSReEEKLIDY 155
                                    5678888888888888877777666666666666665566664433334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1369.88
//
Query:       gi|118431574|ref|NP_148136.2|  [L=133]
Description: 30S ribosomal protein S11 [Aeropyrum pernix K1]
Scores for 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-48  161.7   3.7    8.4e-48  161.4   3.7    1.1  1  Ribosomal_S11    Ribosomal protein S11
  ------ inclusion threshold ------
       0.08   12.9   0.3       0.14   12.1   0.3    1.4  1  M20_dimer        Peptidase dimerisation domain
      0.089   13.6   0.0       0.14   13.0   0.0    1.2  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma


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 !  161.4   3.7   1.4e-51   8.4e-48       1     110 []      11     129 ..      11     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.4e-51
                  Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........p 71 
                                    Gvahi++sfnnt ++itdl+Gae++++ +Gg++vka+r k+sPyaa+ aa++aa+k++++Gi a+++kv++        p
  gi|118431574|ref|NP_148136.2|  11 GVAHIYSSFNNTHVHITDLTGAETVARVTGGMVVKADReKPSPYAAMIAASRAAQKAMERGIAAIHIKVRApgghgpktP 90 
                                    9******************************************************************************* PP

                  Ribosomal_S11  72 GpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                    GpG++aa+ralaraG++igriedvtPiPhd++rrp++rr
  gi|118431574|ref|NP_148136.2|  91 GPGAQAAIRALARAGFIIGRIEDVTPIPHDTTRRPGGRR 129
                                    *************************************98 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   2.3e-05      0.14       3      35 ..      69     103 ..      67     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                    B-EEEEEEEEEE-B-EEGG.-TTTTB-.HHHHHHH CS
                      M20_dimer   3 hkGlaggkitvkgkagHsg.apgagaN.Aieklar 35 
                                    ++G+a  +i+v+  +gH+   pg ga  Ai++lar
  gi|118431574|ref|NP_148136.2|  69 ERGIAAIHIKVRAPGGHGPkTPGPGAQaAIRALAR 103
                                    79***********************9988888887 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05      0.14      29      80 ..      19      70 ..       7      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                                   .-EEEEEEE..EEEEEEEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                Ribosomal_S30AE 29 fieadVtls..kkkkvevtirlakgkviraeeesedlyaaidlavdklerqlrk 80
                                   f + +V+++      +e   r+++g v++a+ e ++ yaa+ +a+ ++++ +++
  gi|118431574|ref|NP_148136.2| 19 FNNTHVHITdlT--GAETVARVTGGMVVKADREKPSPYAAMIAASRAAQKAMER 70
                                   478899999553..5899998889999***9999************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1000.69
//
Query:       gi|118431575|ref|NP_148137.2|  [L=286]
Description: DNA-directed RNA polymerase subunit D [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-26   92.2   0.0    4.4e-26   91.4   0.0    1.4  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    4.5e-15   54.8   0.0    5.6e-15   54.5   0.0    1.1  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 !   91.4   0.0   4.9e-30   4.4e-26       2     112 .]      51     166 ..      50     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 4.9e-30
                                    EEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC......EEGGGCBESSSS CS
                  RNA_pol_A_bac   2 eieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge......vtagdlkledad 75 
                                    +i++nt++++DE+vaHrlgl+ l s++++e++   +e++  +e +ee++ ve++L+++   e      +tagdl ++d++
  gi|118431575|ref|NP_148137.2|  51 YIFDNTTAVYDEMVAHRLGLVVLDSNEAVEKYRRPEECA-GKEPSEEDCFVEVSLEAEVDAEgetgryITAGDLSISDPQ 129
                                    899***************************777777775.4799**************999999**************** PP

                                    CEESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                  RNA_pol_A_bac  76 veivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                    v++v+p+ +++ +++gq+++++a ++ G+Gkeh k+s
  gi|118431575|ref|NP_148137.2| 130 VKPVYPETPLIYVAPGQRIHVQAFARLGRGKEHTKWS 166
                                    ************************************8 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 !   54.5   0.0   6.2e-19   5.6e-15       3      68 ..      22     270 ..      20     271 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 6.2e-19
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                      RNA_pol_L   3 llrgvdhtlgNaLRrillsevpgvaiea.................................................... 30 
                                     +rg+ + + Na+Rr+ ls+vp++a++                                                     
  gi|118431575|ref|NP_148137.2|  22 RIRGYPVVFVNAIRRTVLSDVPTMAVDYayifdnttavydemvahrlglvvldsneavekyrrpeecagkepseedcfve 101
                                    689**********************************************9999999999999999999999999999999 PP

                                    ...........................................................................xx... RF
                      RNA_pol_L  31 ...........................................................................pv... 32 
                                                                                                               p+   
  gi|118431575|ref|NP_148137.2| 102 vsleaevdaegetgryitagdlsisdpqvkpvypetpliyvapgqrihvqafarlgrgkehtkwspaslsvlrytPIliy 181
                                    99999999999999999999888888888877766666666666666666666666666666666555555555511666 PP

                                    .....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  33 .....................................................vkvntdkdklilevetdgslkPeealk 59 
                                                                                         v+v+ d ++l leve++g+l+Pe++++
  gi|118431575|ref|NP_148137.2| 182 dsskagdecleclsaypqvvealksggkgslvleglrrtsglrycaetacrgaVEVRYDSSNLDLEVESTGALRPEKIVE 261
                                    666666666777777777777777777777777778777888888888888888************************** PP

                                    xxxxxxxxx RF
                      RNA_pol_L  60 eAlkiLkek 68 
                                     A++ L+ek
  gi|118431575|ref|NP_148137.2| 262 LAIRELEEK 270
                                    *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2102.57
//
Query:       gi|14601599|ref|NP_148139.1|  [L=120]
Description: 50S ribosomal protein L18 [Aeropyrum pernix K1]
Scores for complete 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   29.9   0.6    3.8e-07   29.7   0.6    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    0.00026   21.7   0.1    0.00041   21.0   0.1    1.4  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> 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 !   29.7   0.6   4.2e-11   3.8e-07      32     137 ..      19     118 ..       5     120 .] 0.89

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.2e-11
                 Ribosomal_L18  32 rfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetarari 112
                                   r  arR ++     v   L   r+ r+ + ls++ ++ +    ++++++v g+v+    l +  k++vaAL f+ +a  +i
  gi|14601599|ref|NP_148139.1|  19 RRAARRNSAPVWLRVAELLERPRRRRAEVNLSKINRHAR----DGEMVIVPGKVLGAGALEK--KVTVAALSFSLQALVKI 93 
                                   446899999999999999****************99988....46899999*****999986..9**************** PP

                 Ribosomal_L18 113 lkaGGeiltlDqLalraPtGkntvL 137
                                     +G   +tl++   ++P+G+ t +
  gi|14601599|ref|NP_148139.1|  94 RLSGSRAITLEEAVRENPRGSRTRI 118
                                   *********************9965 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 !   21.0   0.1   4.5e-08   0.00041      62     127 ..      38     101 ..      16     102 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.5e-08
                                   TTGTTS------EEEGGGTTTTSSS......SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                Ribosomal_L27A  62 deerleladeaeeidleelaeaglikk..kdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                   ++ r+    +++e++l+++  ++ ++      v  Kvlg g l+kk++v a +fS +A  kI   G +++
  gi|14601599|ref|NP_148139.1|  38 ERPRR----RRAEVNLSKI--NRHARDgeMVIVpgKVLGAGALEKKVTVAALSFSLQALVKIRLSGSRAI 101
                                   44443....4568999999..33333345444456***************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 890.90
//
Query:       gi|14601600|ref|NP_148140.1|  [L=155]
Description: 50S ribosomal protein L13 [Aeropyrum pernix K1]
Scores for 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-13   48.7   0.2    1.6e-10   41.3   0.2    2.1  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.2   8.7e-15   1.6e-10       4     114 ..      12     112 ..      10     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 8.7e-15
                                   EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHT.T-EEEEE-SSTTSEEEEEHHHHHCCS CS
                 Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkle.qkvyyrhtgypgglkevtakellekk 83 
                                   v+D +g+++grlas +ak+L             +G  v v+naek++l+g+     + y++    +++  + + +  + + 
  gi|14601600|ref|NP_148140.1|  12 VVDGSGMIMGRLASVVAKLLL------------AGWRVNVVNAEKIVLSGDPRMvVESYRTTVLGVKSHFSHKWRPKRPRT 80 
                                   789999999999999999886............577789***********9654045555555556666666777777889 PP

                                   HHHHHHHHHHCCS-SSHH.HHHHGCTEEEESS CS
                 Ribosomal_L13  84 peeilekaVkgmLpknkl.grrrlkrLkvyag 114
                                   p++++++aV+gmLpknk  grr l rL+vy g
  gi|14601600|ref|NP_148140.1|  81 PQRLFKHAVRGMLPKNKArGRRALARLRVYVG 112
                                   9**************996267777******88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1123.83
//
Query:       gi|14601601|ref|NP_148141.1|  [L=157]
Description: 30S ribosomal protein S9 [Aeropyrum pernix K1]
Scores for 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-32  110.2   0.0      1e-31  109.9   0.0    1.1  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9   0.0   5.8e-36     1e-31       1     121 []      17     157 .]      17     157 .] 0.87

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 5.8e-36
                                   EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS.S.EEEEEEEESS-HHHHHHHHHHHHHHHHH CS
                  Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllg.k.fdvfvkvkgGGlsgqaeAirlgiaraLv 79 
                                   G+rK+++Ar+ i++g+g++ +ng++le Y + e+ar k++epl ++g+   + +d++v+v+gGG++gqa+A+r++iar+Lv
  gi|14601601|ref|NP_148141.1|  17 GKRKRAIARAVIRPGRGRVWINGVPLEIY-PIEMARIKMMEPLLIAGEGVrSlVDIRVRVEGGGVMGQADAVRMAIARGLV 96 
                                   8***************************5.669*************9854436**************************** PP

                                   HHHH.............HHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                  Ribosomal_S9  80 alek.............eekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                   ++ +             ++ + L+      ++++l+ DpR++E+ K+ +  AR+++q+s+R
  gi|14601601|ref|NP_148141.1|  97 EFFRceesddelcrmmdKISRDLRtaflehDRTMLVGDPRRTEPEKYMRYSARRRWQKSYR 157
                                   **75554555555555333566667777788****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 00:00:00.40
# Mc/sec: 1183.74
//
Query:       gi|14601602|ref|NP_148142.1|  [L=77]
Description: DNA-directed RNA polymerase subunit N [Aeropyrum pernix K1]
Scores for 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-25   86.7   0.0    1.1e-24   86.5   0.0    1.1  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.017   15.3   0.0    1.3  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
       0.31   10.8   2.8        2.3    8.0   0.6    2.6  2  Ribosomal_S14   Ribosomal protein S14p/S29e


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 !   86.5   0.0   1.8e-28   1.1e-24       1      57 [.       1      57 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.8e-28
                                  ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THH CS
                     RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdlie 57
                                  M+ PVrCFtCG+++g++w +++el+  g++p++aLd+Lg++ryCCrr+l t v +ie
  gi|14601602|ref|NP_148142.1|  1 MLPPVRCFTCGRPLGHLWPRFRELVASGKTPGEALDELGVDRYCCRRTLFTSVTYIE 57
                                  9******************************************************98 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 ?   15.3   0.0   2.9e-06     0.017       2      48 ..       2      53 ..       1      64 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.9e-06
                Chordopox_RPO7  2 vfplvCstCGrDlsee..ryrLlvkk.kkLkdvlat..vkrkCCrlkLstqi 48
                                    p+ C tCGr l +   r+r lv   k+  + l++  v r CCr  L t +
  gi|14601602|ref|NP_148142.1|  2 LPPVRCFTCGRPLGHLwpRFRELVASgKTPGEALDElgVDRYCCRRTLFTSV 53
                                  55788*********9555**988865266678888633789****9997754 PP

>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.6   0.00039       2.3      17      49 ..       6      32 ..       5      34 .. 0.72
   2 ?   -1.4   0.1      0.34     2e+03      31      40 ..      38      47 ..      35      49 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00039
                                  --SSS--SSSEE-GGG-EHHHHHHHTTT...TT CS
                 Ribosomal_S14 17 rCrvtGrprGvirkfgLsRicfRelAlkgelpG 49
                                  rC  +Grp G +        +fRel+  g+ pG
  gi|14601602|ref|NP_148142.1|  6 RCFTCGRPLGHLW------PRFRELVASGKTPG 32
                                  99*****999874......35666666666665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.34
                                  GG-EHHHHHH CS
                 Ribosomal_S14 31 fgLsRicfRe 40
                                   g+ R+c R 
  gi|14601602|ref|NP_148142.1| 38 LGVDRYCCRR 47
                                  5778888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 618.93
//
Query:       gi|14601603|ref|NP_148143.1|  [L=205]
Description: 30S ribosomal protein S2 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-22   77.8   0.3    4.7e-17   62.0   0.4    2.0  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.2e-06     0.022      15      95 ..      27     106 ..      17     111 .. 0.84
   2 !   62.0   0.4   2.6e-21   4.7e-17     148     212 ..     114     178 ..     108     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-06
                  Ribosomal_S2  15 wnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrangyyvnerWlgGtLT 94 
                                    +  m+++++    +g++ +d  k+ + l  a+k+++ +  + +ki  v+ +   ++ v+ +++r++   ++ r ++Gt+T
  gi|14601603|ref|NP_148143.1|  27 CTRYMRQFVHRILpEGYYQLDYLKIDERLAMAAKFLSTF--EPEKIAVVSVRIYGQKPVRMMCERVGCKAITGRIIPGTFT 105
                                   566788888866547899999999999********9966..6678999999****************************** PP

                  Ribosomal_S2  95 N 95 
                                   N
  gi|14601603|ref|NP_148143.1| 106 N 106
                                   * PP

  == domain 2  score: 62.0 bits;  conditional E-value: 2.6e-21
                  Ribosomal_S2 148 lPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                                    Pd+vvv+dp+ ++ av Ea+k+gipv+a+vDt+ + +++d +IpaN+   rs+ li+ +l++ i
  gi|14601603|ref|NP_148143.1| 114 EPDVVVVTDPRMDRQAVVEASKVGIPVVALVDTDNSIENIDLVIPANNRGRRSLALIYWILTREI 178
                                   6************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1515.00
//
Query:       gi|14601604|ref|NP_148144.1|  [L=150]
Description: hypothetical protein APE_1751 [Aeropyrum pernix K1]
Scores for 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-20   71.4   0.1    1.1e-19   70.9   0.1    1.2  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.1   5.9e-24   1.1e-19       1     118 [.       9     122 ..       9     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 5.9e-24
                                   EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.....HHH CS
                   RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.....keL 76 
                                   +i+v+a+v++TEd+ekVl+a++n++++e+v++e+       g + +il +e ++   +++l++l++ lr e+i       +
  gi|14601604|ref|NP_148144.1|   9 RITVEAEVRPTEDREKVLKAVRNVVEPESVRFEKI------G-STEILVGESST---LASLSRLHSILRAERIldaarGAM 79 
                                   69**************************6444443......3.56677777777...****************95555555 PP

                                   HHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS.....EEEEEEE CS
                   RNA_binding  77 lkeleervdekgklylrldKQaaylgklslvegdd.....vIkvkik 118
                                   +k++++     ++++++l+KQaay+g+ls+v++d+     +I+++i+
  gi|14601604|ref|NP_148144.1|  80 KKGVQG----ADRMTIHLHKQAAYKGRLSFVSSDHespmgAIRITIE 122
                                   555555....99**********************9*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1177.33
//
Query:       gi|118431576|ref|NP_148145.2|  [L=187]
Description: hypothetical protein APE_1753.1 [Aeropyrum pernix K1]
Scores for complete 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-16   61.0   0.1    2.2e-16   60.5   0.1    1.2  1  AAA_17           AAA domain
    2.3e-11   44.3   0.1    3.2e-11   43.9   0.1    1.2  1  AAA_18           AAA domain
    1.9e-08   34.6   0.1    3.4e-08   33.8   0.1    1.4  1  AAA_33           AAA domain
    1.3e-06   27.9   0.0    1.7e-06   27.5   0.0    1.1  1  Zeta_toxin       Zeta toxin
    4.4e-05   23.2   0.0      0.068   12.8   0.0    2.3  2  CoaE             Dephospho-CoA kinase
    0.00028   21.2   0.0    0.00039   20.7   0.0    1.3  1  AAA_22           AAA domain
     0.0005   20.2   1.2       0.02   15.0   1.2    2.4  1  Cytidylate_kin2  Cytidylate kinase-like family
    0.00054   19.9   0.1     0.0014   18.5   0.1    1.8  1  APS_kinase       Adenylylsulphate kinase
    0.00057   19.7   0.1      0.025   14.3   0.0    2.1  2  Cytidylate_kin   Cytidylate kinase
    0.00065   20.1   0.1    0.00096   19.6   0.1    1.4  1  AAA_16           AAA ATPase domain
     0.0015   18.7   0.0     0.0019   18.3   0.0    1.3  1  ADK              Adenylate kinase
     0.0017   18.8   0.1     0.0037   17.7   0.0    1.7  1  AAA              ATPase family associated with various cellul
     0.0046   16.4   0.0     0.0065   15.9   0.0    1.1  1  KTI12            Chromatin associated protein KTI12
       0.01   15.8   0.3       0.02   14.8   0.2    1.6  1  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.033   13.9   0.0    1.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.022   14.8   0.1      0.038   14.0   0.1    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.033   13.4   0.0      0.068   12.3   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.042   13.6   0.3      0.087   12.5   0.3    1.9  1  AAA_30           AAA domain
      0.042   14.0   0.0       0.09   12.9   0.0    1.7  1  SKI              Shikimate kinase
      0.049   12.9   0.0      0.057   12.6   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.06   13.6   0.7       0.16   12.2   0.1    2.0  2  AAA_28           AAA domain
       0.08   13.0   0.0       0.12   12.5   0.0    1.3  1  Torsin           Torsin
      0.089   13.2   0.1       0.26   11.6   0.1    1.7  1  Radical_SAM      Radical SAM superfamily
       0.09   11.7   0.2       0.36    9.8   0.1    1.9  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.17   11.8   0.0       0.31   11.0   0.0    1.4  1  Arm-DNA-bind_2   Arm DNA-binding 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 !   60.5   0.1     3e-19   2.2e-16       1     128 [.      12     133 ..      12     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 3e-19
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea..kkkgvlvdg 78 
                                    +G+PGsGK+ +++ ++e++g+++  +Gd++ree  r+gl+++ ++++++    ++el + a +k+  e+    + +++dg
  gi|118431576|ref|NP_148145.2|  12 TGLPGSGKSVVARIVAEELGLEVKVMGDVVREETVRRGLEPTPENVERVARMLREELGRAAVAKLLAERlePGRSYVLDG 91 
                                    7********************************************************999999998887444466***** PP

                                    -SEEEETTEEEESSHHHHHHHH...SEEEEEE--HHHHHHHHHHHTTST-T CS
                         AAA_17  79 hprikeqagfldglpkevleelkp.daiilleadpeeilerrlkdrtrgrd 128
                                      +++e a+        vl+ +    +ii ++a+ ++ ler++++r +g +
  gi|118431576|ref|NP_148145.2|  92 LRSVEE-AE--------VLARAGWrVFIIGVYAPRKQRLERLMRRRRSGET 133
                                    **9854.33........3444444136777***************999975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.1   4.5e-14   3.2e-11       1     119 [.       9     133 ..       9     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.5e-14
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpe..aldeskrldedkldklldaleenss..aleegk 75 
                                    +++tG pG+GK+ +a+ ++++lg+ + + +dv++e+  + + +p    +++  r+ ++   +l +a  +     +le g 
  gi|118431576|ref|NP_148145.2|   9 VAVTGLPGSGKSVVARIVAEELGLeVKVMGDVVREETVRRGLEPTpeNVERVARMLRE---ELGRAAVAKLLaeRLEPGR 85 
                                    78********************999777788888888877777774433444444433...333333333333458**** PP

                         AAA_18  76 nlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeak 119
                                    ++v+dg+++  e e + +++     + ++a+ +++leRl +R+++   
  gi|118431576|ref|NP_148145.2|  86 SYVLDGLRSVEEAEVLARAGWrvfiIGVYAPRKQRLERLMRRRRSGET 133
                                    ************9988877779999***************99976555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   4.7e-11   3.4e-08       2     124 ..       9     133 ..       8     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.7e-11
                         AAA_33   2 vllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqsktdytr.vldr.lyqilnelarkalsagrnv 73 
                                    v + GlpGsGKs +a+ ++++lg      + ++++ t+rr l++t ++ ++  +r ++++  ++ +++l++++l+ gr++
  gi|118431576|ref|NP_148145.2|   9 VAVTGLPGSGKSVVARIVAEELGlevkvmGDVVREETVRRGLEPTPENVER-VARmLREElGRAAVAKLLAERLEPGRSY 87 
                                    7789*******************9999999999999999999998666554.344233332566999************* PP

                         AAA_33  74 ildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangdd 124
                                    +ld +++s +e +    ++ r+g +v i+ v +++++  eRl +R ++g++
  gi|118431576|ref|NP_148145.2|  88 VLD-GLRSVEEAE----VLARAGWRVFIIGVYAPRKQRLERLMRRRRSGET 133
                                    **9.566666654....3334578999999999999999999999998876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   2.3e-09   1.7e-06      18     145 ..       8     129 ..       2     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.3e-09
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelh.Peyeeilkadpkkaseltqkdase.lvekllqeaieng 95 
                                    ++ + G pG+GKs +a+ +++el   g  v++ +D +Re   ++  e   +++++++++ +++ ++  v+kll+e +e g
  gi|118431576|ref|NP_148145.2|   8 IVAVTGLPGSGKSVVARIVAEEL---GLEVKVMGDVVREETvRRGLEPTPENVERVARMLREELGRaAVAKLLAERLEPG 84 
                                    67899*****************9...889*********97614444444478999999999888662689********** PP

                     Zeta_toxin  96 yniivegtlrspdvvkklaealkkaGYevevvvvavkkelSrlgvldRye 145
                                    ++ +++g lrs ++++     l+ aG++v ++ v++++++  ++++ R +
  gi|118431576|ref|NP_148145.2|  85 RSYVLDG-LRSVEEAE----VLARAGWRVFIIGVYAPRKQRLERLMRRRR 129
                                    ******9.99999998....89999***************9999999876 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   9.5e-05     0.068       1      44 [.       7      52 ..       7      82 .. 0.79
   2 !    8.5   0.0    0.0021       1.5     124     178 ..     109     168 ..      98     169 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                                   EEEEEEESTTSSHHHHHHHHHH.TT-EE.EEHHHHHHHTTCCTHHH CS
                           CoaE  1 livgltGgiasGKstvanlfad.lgvpi.vDaDlvArqvvepgsea 44
                                   liv++tG  +sGKs+va++ a+ lg+++ v  D+v  + v  g e 
  gi|118431576|ref|NP_148145.2|  7 LIVAVTGLPGSGKSVVARIVAEeLGLEVkVMGDVVREETVRRGLEP 52
                                   69******************99999987688899988888877655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                                    EEEEEE--HHHHHHHHHHCC..TSTHHHH...HHHHHHS--HHHHHHH-SEEEE-.SSHH CS
                           CoaE 124 rvlvvdvelelqveRlvard..gvseeev...kaiiaaQlseeerlaladvvldNdssla 178
                                     ++ v ++ ++++eRl++r+  g +  ev   ++  +  l   e lal+d+++ N +sl+
  gi|118431576|ref|NP_148145.2| 109 FIIGVYAPRKQRLERLMRRRrsGETLWEVlelRDASNIELGVGEALALSDYLIVNTGSLE 168
                                    578899***********9983344444441003444455667899999999999998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   5.5e-07   0.00039       5      84 ..       6      90 ..       3     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.5e-07
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee..erpevv.fvtlpsstsskdllrellralglelka..erlsseellea 81
                                   + i++vtG +G+GK++++r ++e+l  e k      r e+v +   p +++ + ++r+l ++lg+ + a     ++e  +++
  gi|118431576|ref|NP_148145.2|  6 RLIVAVTGLPGSGKSVVARIVAEELGLEVKVMGdvVREETVrRGLEPTPENVERVARMLREELGRAAVAklLAERLEPGRSY 87
                                   6799*********************876666669956666657777777789999999999999888876533444444444 PP

                         AAA_22 82 leq 84
                                   + +
  gi|118431576|ref|NP_148145.2| 88 VLD 90
                                   444 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.2   2.8e-05      0.02       1     135 [.       8     128 ..       8     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-05
                Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekldd 79 
                                    i+++++  Gsg++++++ +Ae+Lgl++    ++++e   + gl++   e+v+   ++++++++l +a v      + l +
  gi|118431576|ref|NP_148145.2|   8 IVAVTGLPGSGKSVVARIVAEELGLEVKVMgDVVREETVRRGLEPT-PENVER--VARMLREELGRAAV-----AKLLAE 79 
                                    7899999*****************9873222444444444443322.123333..33444455444443.....456666 PP

                Cytidylate_kin2  80 elfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaere 135
                                    +l   ++ v+  l + e + ++ R+++       +v+ + ++ap+++r++r+++r+
  gi|118431576|ref|NP_148145.2|  80 RLEPGRSYVLDGLRSVEEAEVLARAGW-------RVFIIGVYAPRKQRLERLMRRR 128
                                    666666666666665456667777777.......5777777777777777777776 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     2e-06    0.0014       3      52 ..       7      53 ..       5      86 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                                   EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTT.TTT--SS CS
                     APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgL.nkdLgfs 52
                                   ++v +tGl gsGKs +a+ ++++L     +v++  Gd+vR++   ++L  +
  gi|118431576|ref|NP_148145.2|  7 LIVAVTGLPGSGKSVVARIVAEELG---LEVKV-MGDVVREETvRRGLEPT 53
                                   57899****************9885...44443.36666665303344333 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.5e-05     0.025       1      34 [.       9      42 ..       9      48 .. 0.86
   2 ?    3.6   0.0     0.066        47      98     195 ..      69     166 ..      40     172 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                                   EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHH CS
                 Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYR 34
                                   +a+ G  gsGKs var++ae+lgl++   g + R
  gi|118431576|ref|NP_148145.2|  9 VAVTGLPGSGKSVVARIVAEELGLEVKVMGDVVR 42
                                   6888999****************99877777766 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.066
                                    HHHHHHHHHHTT-B.SSBEEEEE.SSII.IIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHH CS
                 Cytidylate_kin  98 vRailvkklrelvk.karvvveG.RDig.tvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeikeRDklD 174
                                     Ra++ k+l e  +   ++v++G R +  + v+  a  ++f+      R +R l+ l ++    s e+l + ++ RD+  
  gi|118431576|ref|NP_148145.2|  69 GRAAVAKLLAERLEpGRSYVLDGlRSVEeAEVLARAGWRVFIIGVYAPRKQR-LERLMRR--RRSGETLWEVLELRDASN 145
                                    5777788877777767788888877764367999999999998766666544.4444444..355788888888999988 PP

                                    HCTSSS-S---TT-EEEETTT CS
                 Cytidylate_kin 175 kerevgpLklaedaliidtsk 195
                                     e  vg+  + +d li++t +
  gi|118431576|ref|NP_148145.2| 146 IELGVGEALALSDYLIVNTGS 166
                                    888888888888888888766 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   0.1   1.3e-06   0.00096      25     111 ..       7      98 ..       1     143 [. 0.61

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekd...ggiflrgkcdql.....esaipysalaqalareellrqlldeaesaelea 96 
                                     +v ++G +G+GKs ++r ++++l  +    g ++r+++++      ++++++  +a++l reel r+  +++ +  le+
  gi|118431576|ref|NP_148145.2|   7 LIVAVTGLPGSGKSVVARIVAEELGLEvkvMGDVVREETVRRgleptPENVER--VARML-REELGRAAVAKLLAERLEP 83 
                                    79*********************999954423335555555533222333333..66666.5566666666655556666 PP

                         AAA_16  97 wrekleealaavpel 111
                                     r   ++ l++v e+
  gi|118431576|ref|NP_148145.2|  84 GRSYVLDGLRSVEEA 98 
                                    666666666633333 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-06    0.0019       1      94 [.      11     103 ..      11     148 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                                    EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHH.HCT...-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaev.ksg...telGkeakevmdkgelvpdevvvklvkeelekedkkkg 76 
                                    + G Pg+GK  +a+ +++++gl     Gd++R+e+ ++g   t+   e  + m + el     v kl+ e+le     + 
  gi|118431576|ref|NP_148145.2|  11 VTGLPGSGKSVVARIVAEELGLEVKVMGDVVREETvRRGlepTPENVERVARMLREEL-GRAAVAKLLAERLE---PGRS 86 
                                    579*****************************99734442112222222223333343.45556777777776...4699 PP

                                    EEEESB-SSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                            ADK  77 fllDGfPRtveqaealee 94 
                                    ++lDG  R+ve+ae l +
  gi|118431576|ref|NP_148145.2|  87 YVLDGL-RSVEEAEVLAR 103
                                    *****7.99999998876 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 !   17.7   0.0   5.2e-06    0.0037       2      27 ..      10      35 ..       9      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.2e-06
                                   EEESSTTSSHHHHHHHHHHHHTHEEE CS
                            AAA  2 llyGppGtGKTllakavakelgvefl 27
                                    ++G pG GK+ +a+ va+elg e+ 
  gi|118431576|ref|NP_148145.2| 10 AVTGLPGSGKSVVARIVAEELGLEVK 35
                                   579*****************997643 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.1e-06    0.0065       4      72 ..       9      85 ..       7      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.1e-06
                                   EEEE--TTSSHHHHHHHHHHHHHH.TT--EEEE-THHHH........TTSSS--GGGHHHHHHHHHHHHHHHHTT.S CS
                          KTI12  4 vvltGlPssGKstrakeLakalee.ekrsvvviddeslg.......iekdsykdsakekalRsslrsavkrdLskek 72
                                   v +tGlP sGKs +a+ +a++l    k    v+++e+++        + + ++ + +e+  R+++ +  +++L+  +
  gi|118431576|ref|NP_148145.2|  9 VAVTGLPGSGKSVVARIVAEELGLeVKVMGDVVREETVRrgleptpENVERVARMLREELGRAAVAKLLAERLEPGR 85
                                   779*****************997625666789999999977444222222255555555555555555555555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   2.8e-05      0.02       2      41 ..       9      49 ..       8     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEE..E--- CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfytee..vreg 41
                                   v++TG pG+GK+ + + v+e+l   +vkv G +++e  vr+g
  gi|118431576|ref|NP_148145.2|  9 VAVTGLPGSGKSVVARIVAEEL-GLEVKVMGDVVREetVRRG 49
                                   78********************.7889999966544124554 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 ?   13.9   0.0   4.7e-05     0.033      36      64 ..       9      37 ..       5      47 .. 0.86
   2 ?   -3.3   0.0       8.9   6.4e+03      44      57 ..      68      81 ..      58      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvklkit 64
                                   v ++G PG Gk+ +a+i+a+elg ++k+ 
  gi|118431576|ref|NP_148145.2|  9 VAVTGLPGSGKSVVARIVAEELGLEVKVM 37
                                   55789********************9986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.9
                         RuvB_N 44 lGkttlakiiakel 57
                                   lG++++ak++a+ l
  gi|118431576|ref|NP_148145.2| 68 LGRAAVAKLLAERL 81
                                   78888888888766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.4e-05     0.038       4      82 ..      11     101 ..       8     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.4e-05
                                    EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.............G-SEEE CS
                          AAA_5   4 LvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.............egeilv 70 
                                    + G pG+gKs +a+ +a+ l+ e  ++ + +  +ee+++ ++e+++++ ++v   l ++                g+ +v
  gi|118431576|ref|NP_148145.2|  11 VTGLPGSGKSVVARIVAEELGLE--VKVMGDVVREETVRRGLEPTPENVERVARMLREELGraavakllaerlePGRSYV 88 
                                    689***************99865..5667889999999999999955555555555555444444899999999999999 PP

                                    EESGGG--.HHHH CS
                          AAA_5  71 lDEverae.sevl 82 
                                    lD++  +e  evl
  gi|118431576|ref|NP_148145.2|  89 LDGLRSVEeAEVL 101
                                    9999888766665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.5e-05     0.068      17      43 ..       3      29 ..       1      36 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.5e-05
                                   TSCSEEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlakqilnk 43
                                   ++++l+va+ G +G+GK+++a+ + ++
  gi|118431576|ref|NP_148145.2|  3 SPNRLIVAVTGLPGSGKSVVARIVAEE 29
                                   68899***************9987665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   0.00012     0.087      15      45 ..       3      33 ..       1     186 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                         AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaa 45
                                   + +++++++tG +G+GK+ + + ++e +  +
  gi|118431576|ref|NP_148145.2|  3 SPNRLIVAVTGLPGSGKSVVARIVAEELGLE 33
                                   55678999***********999988766544 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013      0.09       1      23 [.      15      37 ..      15      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                                   TTSSHHHHHHHHHHHHTSEEEEH CS
                            SKI  1 mGaGKstvGkllAkklglefiDl 23
                                   +G+GKs v++++A++lgle+  +
  gi|118431576|ref|NP_148145.2| 15 PGSGKSVVARIVAEELGLEVKVM 37
                                   69****************98755 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     8e-05     0.057       3      25 ..       8      30 ..       6      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-05
                        DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                   +v VtG +G+GK+vv+  ++ el
  gi|118431576|ref|NP_148145.2|  8 IVAVTGLPGSGKSVVARIVAEEL 30
                                   688************98888777 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   0.00023      0.16       2      39 ..       9      49 ..       8      91 .. 0.65
   2 ?   -1.1   0.0       2.7   1.9e+03     123     149 ..     116     142 ..      84     152 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                         AAA_28  2 ivitGgestGKTtlleaLaar...gypvvpEaareileekl 39
                                   +++tG +++GK+ +++  a++   +++v+ +++re +  ++
  gi|118431576|ref|NP_148145.2|  9 VAVTGLPGSGKSVVARIVAEElglEVKVMGDVVREETVRRG 49
                                   799****************9886656666777666443333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                         AAA_28 123 ddgeRredleereaiderlrealrelg 149
                                    + ++R e+l +r+++ e l e+l+ ++
  gi|118431576|ref|NP_148145.2| 116 PRKQRLERLMRRRRSGETLWEVLELRD 142
                                    446677777777777777777776555 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.12      53      88 ..       6      42 ..       2      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                   -EEEEEEE-TTSSHHHHHHHHHHHH.STTGGGSTTEE CS
                         Torsin 53 pLvlsfhGwtGtGknfvaeiiaenl.yrdGlrsdyvk 88
                                    L++++ G +G+Gk+ va+i+ae+l  +  ++ d+v+
  gi|118431576|ref|NP_148145.2|  6 RLIVAVTGLPGSGKSVVARIVAEELgLEVKVMGDVVR 42
                                   589999*****************98233345566665 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00037      0.26      85     140 ..      90     143 ..      54     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                                    CSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  85 ngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklrea 140
                                     g++   e +e l+++g+ ++ +g+ a+ + +  +lm+r+ + e ++e+le lr+a
  gi|118431576|ref|NP_148145.2|  90 DGLRS-VEEAEVLARAGWRVFIIGVYAPRKQRLERLMRRRRSGETLWEVLE-LRDA 143
                                    56665.99***********************99999999999999999998.5555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0005      0.36      30      53 ..       7      30 ..       2      42 .. 0.77
   2 ?   -0.7   0.0      0.79   5.7e+02     194     222 ..      97     125 ..      52     135 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0005
                                   EEEEEEE-TTSSHHHHHHHHHHHH CS
                           MeaB 30 qvvGltGvPGaGkstlvealglel 53
                                     v +tG+PG+Gks +   +++el
  gi|118431576|ref|NP_148145.2|  7 LIVAVTGLPGSGKSVVARIVAEEL 30
                                   6799**********9876666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.79
                                    HHCSTTBTTB--EEEEEBCCCTBSHHHHH CS
                           MeaB 194 eleeekekeWrpkvlktsavegeGidelv 222
                                    e e  ++++Wr  ++ + a +++ +++l+
  gi|118431576|ref|NP_148145.2|  97 EAEVLARAGWRVFIIGVYAPRKQRLERLM 125
                                    22333566777777777776666666665 PP

>> Arm-DNA-bind_2  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00043      0.31       6      44 ..      23      65 ..      18      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                 Arm-DNA-bind_2  6 ir.sggklridFrykGkrcresl...glpdtpanrKkaerlla 44
                                    r   + l +    +G  +re++   gl++tp+n ++++r+l 
  gi|118431576|ref|NP_148145.2| 23 ARiVAEELGLEVKVMGDVVREETvrrGLEPTPENVERVARMLR 65
                                   5555666777777899999***99988***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1281.49
//
Query:       gi|118431577|ref|NP_148146.2|  [L=391]
Description: aminotransferase [Aeropyrum pernix K1]
Scores for 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  123.4   0.0    2.4e-35  122.2   0.0    1.6  1  Aminotran_5      Aminotransferase class-V
    8.9e-08   31.7   0.0      2e-07   30.5   0.0    1.5  2  Aminotran_1_2    Aminotransferase class I and II
    3.9e-05   22.3   0.0      6e-05   21.7   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    8.3e-05   22.0   0.1    0.00014   21.3   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


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 !  122.2   0.0   5.4e-39   2.4e-35       1     371 []      20     382 ..      20     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 5.4e-39
                                    EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHH CS
                    Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvals 80 
                                    +yld a+  ++  +V da++ +++ +n+ +     +   ea + + e r  +a++++a+  ee+  + G t ++n+++ s
  gi|118431577|ref|NP_148146.2|  20 VYLDTAGAGPLTLDVKDAVEGFLELWNSEG-----EPWGEALDDILESRRLFAQMVGAKV-EEVAAVPGVTYGLNAFLSS 93 
                                    7***********************999988.....7788899999999***********8.******************* PP

                                    CCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHH CS
                    Aminotran_5  81 larslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpvee 160
                                    l  +l p+ ++vv+e++    + + +++a+r  ++ + i   ++g + ld +e l+++ t++v++ +vs +tG  +++  
  gi|118431577|ref|NP_148146.2|  94 L--KLPPDSNVVVSETNFPTGVYTFHAMARRGLIREVRIASASDGCVGLDGFERLIDDSTSIVYVDMVSWITGCREDLRT 171
                                    *..69************************9988888888899************************************** PP

                                    HHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEE CS
                    Aminotran_5 161 igklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleet 239
                                    +++la+ +gal++ D   a+g +pidvkklg+D ++ ++ K llg  G G+ yv++ell +lep+  g   +++  +e+ 
  gi|118431577|ref|NP_148146.2| 172 LAELAHSHGALMVSDVFHAAGVYPIDVKKLGLDAAFTGSYKwLLGLHGGGFAYVSEELLPSLEPMFSGWMAIDDSVMERM 251
                                    ****************************************************************9999999999999887 PP

                                    E................EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHH.HHHHHHHHHHHHHHHCTSTTEEEES. CS
                    Aminotran_5 240 t................faeapskfeaGTpnvagiiglgaaleyleeigleai.ekhekelaeyllerlkslpgvrlygp 302
                                                      a+    +e GT + +++++l+a l++l++ ++    ++h  +l ++l + l +++  ++   
  gi|118431577|ref|NP_148146.2| 252 ArgdplfsrpfnvrefrRASDAKVLEWGTWPAIAFVSLKASLKMLSAYDAPGLyASHTGRLVKRLIDSLTDMGVETV--- 328
                                    789*******999997634444559********************99999875155667888888888888777777... PP

                                    -B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                    Aminotran_5 303 dkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                      ++r  +   ++f+  h+e ++++L+++gI  +               +g+vR+S+++yn++e+v++l
  gi|118431577|ref|NP_148146.2| 329 --TPRGMAAGIVVFRHRHPERLGRFLESRGIVASV-------------RPGSVRVSIHFYNSREDVEAL 382
                                    ..355555555778899**************8653.............35889**************97 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   4.5e-11     2e-07      50     249 ..      63     239 ..      45     253 .. 0.82
   2 ?   -2.6   0.0      0.53   2.4e+03     286     362 ..     314     385 ..     307     386 .. 0.57

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.5e-11
                                    HHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-TH..HHHHHHHTTSEEEEEEBEETTT CS
                  Aminotran_1_2  50 eealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyas..yknilrlsggevvryplyseed 127
                                    +   a+ +g       k e +v   +G + +++a+   lkl+p+++++v++ +++   y+  + +++g ++++++ s+ d
  gi|118431577|ref|NP_148146.2|  63 RRLFAQMVG------AKVE-EVAAVPGVTYGLNAFLSSLKLPPDSNVVVSETNFPTgvYTFHAMARRGLIREVRIASASD 135
                                    555666666......5666.9*********************************964355555566666*********** PP

                                    TEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGS CS
                  Aminotran_1_2 128 fhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranv 207
                                      + l+++e+++++       t +++v  ++  tG    +e+l++l++la+++++l ++D  +a++v+        +   
  gi|118431577|ref|NP_148146.2| 136 GCVGLDGFERLIDD------STSIVYVDMVSWITGC---REDLRTLAELAHSHGALMVSDVFHAAGVYP-------IDVK 199
                                    **************......899************7...7788888888*******************8.......3333 PP

                                    TTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHH CS
                  Aminotran_1_2 208 eeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrp 249
                                    + + + + +gs+   +Gl G   G+++++++++  l+ + ++
  gi|118431577|ref|NP_148146.2| 200 KLGLDAAFTGSYKWLLGLHG--GGFAYVSEELLPSLEPMFSG 239
                                    44444577788888889998..88888888888777766555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.53
                                    HHHHHHHHHSTEEEECCS...CSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHHHHH CS
                  Aminotran_1_2 286 kelrdeLaelglkvlasq...sgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitv.Aglteeeleelve 361
                                    k+l d+L++ g++ +++    +g++++++  +e    l + L  +  v+ ++      pg++R+++    ++e++e l++
  gi|118431577|ref|NP_148146.2| 314 KRLIDSLTDMGVETVTPRgmaAGIVVFRHRHPE---RLGRFLESRGIVASVR------PGSVRVSIhFYNSREDVEALLR 384
                                    677777777766666665333556666555555...5555555553333333......7777777755556666666665 PP

                                    H CS
                  Aminotran_1_2 362 a 362
                                    a
  gi|118431577|ref|NP_148146.2| 385 A 385
                                    5 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 !   21.7   0.0   1.3e-08     6e-05      66     202 ..      76     216 ..      62     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-08
                                    T-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHHHHHHTHHHTTCE.EEEEST....TSHHHHHHHCCTTEE CS
                Cys_Met_Meta_PP  66 ggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqrllkkvlkklgie.vkfvdt....sdleelekaikentk 139
                                    +++a+  v+ G+ A    + +l l   +++vvs++ +      ++ ++++  i+ v++         l+ +e+ i++ t+
  gi|118431577|ref|NP_148146.2|  76 EVAAVPGVTYGLNAF---LSSLkLPPDSNVVVSETNFPTGVYTFHAMARRGLIReVRIASAsdgcVGLDGFERLIDDSTS 152
                                    444444445555555...2222023345677888888777778888887755541333333111245799********** PP

                                    EEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTTTC CS
                Cys_Met_Meta_PP 140 lvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKylgG 202
                                    +vy++ ++ ++    D++++a+la+++g+l+v D   a++ + +   klg D       K+l G
  gi|118431577|ref|NP_148146.2| 153 IVYVDMVSWITGCREDLRTLAELAHSHGALMVSDVFHAAGvYPIDVKKLGLDAAFTGSYKWLLG 216
                                    ***********************************99999555677789********99**988 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 !   21.3   0.1   3.2e-08   0.00014      31     151 ..      65     193 ..      55     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.2e-08
                                    HHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T...TTSSB-GGGCG CS
                DegT_DnrJ_EryC1  31 afaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp...dtynidpaaie 105
                                     fa+ +g  v+ + av   t +l   L+ l++ p+  V+v  ++F + + +   +  +    +v +    + ++  +  e
  gi|118431577|ref|NP_148146.2|  65 LFAQMVGakVEEVAAVPGVTYGLNAFLSSLKLPPDSNVVVSETNFPTGVYTFHAMARRGLIREVRIasaSDGCVGLDGFE 144
                                    5888888667899********************************997777766666666666654111679******** PP

                                    GG--TTEEEEEEB-GG....GB---HHHHHHHHHHCT-EEEEE-TT-TT- CS
                DegT_DnrJ_EryC1 106 aaitertkaIlpVhly....GqvadmdalkaiaakhglkvieDaAhAlGa 151
                                    ++i   t+ I+ V+++    G   d+  l ++a++hg  +++D  hA G 
  gi|118431577|ref|NP_148146.2| 145 RLIDDSTS-IVYVDMVswitGCREDLRTLAELAHSHGALMVSDVFHAAGV 193
                                    ****9996.666665511115666***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2839.51
//
Query:       gi|14601607|ref|NP_148147.1|  [L=644]
Description: arginyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for 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-33  113.7   0.0    7.3e-20   71.2   0.0    2.2  2  tRNA-synt_1d     tRNA synthetases class I (R)
    3.4e-28   98.2   0.0    6.5e-28   97.3   0.0    1.5  1  DALR_1           DALR anticodon binding domain
     0.0011   19.5   0.0     0.0038   17.8   0.0    2.0  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
      0.005   15.8   0.0       0.55    9.1   0.0    2.3  2  tRNA-synt_1f     tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.066   11.4   0.0       0.15   10.3   0.0    1.5  2  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
       0.17   10.6   0.0        0.8    8.4   0.0    2.0  2  tRNA-synt_1g     tRNA synthetases class I (M)


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   5.7e-14   1.7e-10      13      74 ..     113     174 ..     100     197 .. 0.86
   2 !   71.2   0.0   2.4e-23   7.3e-20     180     342 ..     348     507 ..     333     513 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.7e-14
                                   .---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHH CS
                  tRNA-synt_1d  13 qkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfG 74 
                                     +++  +++vv+++s n   ++h Gh r   +Gda++rlle+ G+ v r  +v D G+q  
  gi|14601607|ref|NP_148147.1| 113 TARTSRPETIVVEHTSANPIHPLHLGHARNSSLGDALARLLEARGHRVNRRFYVDDVGRQAV 174
                                   45667779***************************************************964 PP

  == domain 2  score: 71.2 bits;  conditional E-value: 2.4e-23
                                   TT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSST CS
                  tRNA-synt_1d 180 kglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvp 260
                                   + l+++ + a  + l++  +  ++++++sDG++lytt+D+a   ++ +   ad+v+ vi + q l   qi l+l  +gy  
  gi|14601607|ref|NP_148147.1| 348 EVLARDPEAASTIKLPRSLEIPPLILVRSDGTTLYTTRDLAYSVYKFRVTGADRVINVIGADQRLPQLQIRLALLGLGYRR 428
                                   457888888999999966666677********************************************************* PP

                                   TTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCCTS-T CS
                  tRNA-synt_1d 261 eskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvgaikyaDlsknr 341
                                   e+ ++ h  + +v    +++++ r+Ge v L++lL+ a  r+++ ++ +n+      d  e  ae ++vga+++a ++  r
  gi|14601607|ref|NP_148147.1| 429 EALNMMHYDYEIV-SLPGRRMSSRRGEYVTLDELLEMAKARSVREVESRNPG--ADRDWIESTAEKIAVGAVRFALVRPGR 506
                                   ************9.999**********************************9..99*****************99776666 PP

                                   T CS
                  tRNA-synt_1d 342 i 342
                                   +
  gi|14601607|ref|NP_148147.1| 507 L 507
                                   5 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   2.2e-31   6.5e-28       1     119 []     528     644 .]     528     644 .] 0.95

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 2.2e-31
                                   HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTS CS
                        DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkerv 81 
                                   +qy++aR++sil+k++e +  + +++ a+lee + +eL+ + ++fp v ++aa++l+p++la+yl  La+ f+++Y+k +v
  gi|14601607|ref|NP_148147.1| 528 LQYTYARASSILEKHGEID--YLKAHPASLEEGSRRELFVEALRFPLVSAKAADDLAPEDLASYLLRLADMFNSWYQKDSV 606
                                   6************999765..667777776788************************************************ PP

                                   TTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                        DALR_1  82 lkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                   ++ee e  ++a+ aLv +v++v+ +gL+lLG+e++ekm
  gi|14601607|ref|NP_148147.1| 607 IHEEWEGARHAKAALVLLVKSVIGEGLRLLGVEPLEKM 644
                                   *************************************9 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 !   17.8   0.0   1.3e-06    0.0038       4      84 ..      12      91 ..       9      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.3e-06
                                  HHHHHHHHHHHHSS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT.EEEEEEETT.EEEEE CS
               Arg_tRNA_synt_N  4 keaiaealkkaagadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei.iekvevagpGFiNff 84
                                  + +++  l+++ g d +++e  ++ p++++ GD+ +++ m++a+  + +   i e +  kl +++i  ++ +   +G++N+ 
  gi|14601607|ref|NP_148147.1| 12 HGILSSYLSEVLGVDRSVVERLLAPPPRKEYGDLGFPL-MRFARSSNASADSIVESLRGKLWERGItWASPTL-EAGYLNIV 91
                                  5677788888888899999999***************6.**************************96666666.669***96 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 !    4.1   0.0    0.0059        18      29      71 ..     127     169 ..     110     175 .. 0.82
   2 !    9.1   0.0   0.00018      0.55     268     305 ..     435     471 ..     431     484 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0059
                  tRNA-synt_1f  29 sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                   + + p  ++H+G +r+   +d++ar l++rg++v+  +++Dd+
  gi|14601607|ref|NP_148147.1| 127 TSANPIHPLHLGHARNSSLGDALARLLEARGHRVNRRFYVDDV 169
                                   566677789************************9999999997 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00018
                  tRNA-synt_1f 268 kvvYelillkggekmssSkGnvltledwlevaepevlr 305
                                   ++ Ye+++l g+  mss +G+++tl+++le+a+  ++r
  gi|14601607|ref|NP_148147.1| 435 HYDYEIVSLPGR-RMSSRRGEYVTLDELLEMAKARSVR 471
                                   567******999.9*******************99988 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 ?   10.3   0.0     5e-05      0.15      38     147 ..     135     246 ..     114     253 .. 0.69
   2 ?   -3.6   0.0       0.8   2.4e+03     561     591 ..     445     502 ..     441     513 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5e-05
                   tRNA-synt_1  38 lHiGhalaktlkdivirykrmkGkevlyvpGwDhaGl.aieakvekkl.gakekkerkklgreefrekvrewkaeyaeeir 116
                                   lH+Gha +++l d + r  + +G++v++++ +D  G  a+ a +  kl g + ++    +g++   +  + ++ +  +  +
  gi|14601607|ref|NP_148147.1| 135 LHLGHARNSSLGDALARLLEARGHRVNRRFYVDDVGRqAVVASLGFKLsGVTPRELASRMGVKVDHAVGWVYAVTHNALET 215
                                   8*******************************9988424555555554234444455555555555555555555555555 PP

                   tRNA-synt_1 117 kqvkrlGvsvDfdreylTldkeleeavkevf 147
                                    + ++ G +   d+   Tl    e   +evf
  gi|14601607|ref|NP_148147.1| 216 VTARKRGDTSKVDEALSTLARLKERGDREVF 246
                                   5555555555555555555555555555555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.8
                   tRNA-synt_1 561 GrKmSKslgNvidpldvik...........................kygadalRltli 591
                                   Gr+mS + g ++  +++++                           k ++ a+R++l+
  gi|14601607|ref|NP_148147.1| 445 GRRMSSRRGEYVTLDELLEmakarsvrevesrnpgadrdwiestaeKIAVGAVRFALV 502
                                   8999999999998888888777777777777777777777777777777777777776 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 ?    8.4   0.0   0.00027       0.8      13      80 ..     134     204 ..     126     249 .. 0.79
   2 ?   -1.4   0.0      0.25   7.6e+02     319     351 ..     439     471 ..     422     490 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00027
                                   ---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHH...HHTTS-HHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_1g  13 klHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkA...ekegvtpeelvekvheeikelfkk 80 
                                   +lHlGh+++   +D++aR   +rg+ v      D  G +  ++    + +gvtp+el++++  ++++   +
  gi|14601607|ref|NP_148147.1| 134 PLHLGHARNSSLGDALARLLEARGHRVNRRFYVDDVGRQAVVASlgfKLSGVTPRELASRMGVKVDHAVGW 204
                                   78******9999**************9988888999988877763337899*******9998888777666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.25
                                   --EEE--------------HHHHHHHH-HHHHH CS
                  tRNA-synt_1g 319 eyltvegkKlSkSrgvvvkakealerldadllR 351
                                   e + + g+++S+ rg  v+ +e+le  +a  +R
  gi|14601607|ref|NP_148147.1| 439 EIVSLPGRRMSSRRGEYVTLDELLEMAKARSVR 471
                                   5577889*****************998887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         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 0.25s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 4714.43
//
Query:       gi|118431578|ref|NP_148148.2|  [L=481]
Description: hypothetical protein APE_1758.1 [Aeropyrum pernix K1]
Scores for complete 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-166  554.0   0.0   2.8e-166  553.8   0.0    1.0  1  RtcB            tRNA-splicing ligase RtcB
  ------ inclusion threshold ------
      0.016   15.3   0.1      0.054   13.7   0.1    1.8  1  PGM_PMM_IV      Phosphoglucomutase/phosphomannomutase, C-term
      0.076   13.1   0.0       0.15   12.1   0.0    1.5  1  Complex1_LYR    Complex 1 protein (LYR family)
       0.11   12.0   0.0        7.7    6.0   0.0    2.4  2  Glycoamylase    Putative glucoamylase
       0.21   11.5   0.0       0.41   10.5   0.0    1.4  1  Glyco_hydro_45  Glycosyl hydrolase family 45


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 !  553.8   0.0  7.9e-170  2.8e-166       1     412 []      46     481 .]      46     481 .] 0.99

  Alignments for each domain:
  == domain 1  score: 553.8 bits;  conditional E-value: 7.9e-170
                                    HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-.....-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk.....gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkel 74 
                                    q++nva+l+gi+k++++mPD H+G+g+piG+V+a++     gvi+P++VG+DI CGvr+l+tnlt+ee+++klk+lv++l
  gi|118431578|ref|NP_148148.2|  46 QAANVACLQGIQKYSIVMPDGHQGYGFPIGGVAAMDieeenGVISPGGVGYDInCGVRVLRTNLTEEEVRPKLKDLVDTL 125
                                    89****************************************************************************** PP

                                    HHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB  75 ekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNH 154
                                     ++vp+glgs++kvkls +el++vl++g++wa+++g+g+ ed e+iee+g+++ ad++kvs++ak+r+++qlGtlGsGNH
  gi|118431578|ref|NP_148148.2| 126 YHNVPSGLGSTGKVKLSVQELDKVLDTGVEWAISRGYGWPEDKEHIEERGSWSLADSSKVSQTAKRRGAEQLGTLGSGNH 205
                                    ******************************************************************************** PP

                                    EEEEEEEEEES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 155 FiEvqlveeildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlk 234
                                    F+Evq+ve+++de++aka+gl egqvvvm+H+GSRglGhq+a+dyl i+++a++k+g+  pdr+La +p +s+e+q+Y++
  gi|118431578|ref|NP_148148.2| 206 FLEVQVVERVFDERIAKAYGLFEGQVVVMIHTGSRGLGHQVASDYLMIMERAMRKYGTIPPDRELASIPYNSPEAQNYVR 285
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-........ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx........ RF
                           RtcB 235 amqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA........ 302
                                    am+aaan+A++NRq+it+++re+++kv++++ ++l+le+v+dvaHNiak Ee+e d   +k+++hRKGAtrA        
  gi|118431578|ref|NP_148148.2| 286 AMAAAANFAWTNRQMITHWTRESFKKVFHQDPDKLGLEIVYDVAHNIAKIEEYEvDgkrKKLVIHRKGATRAfppghpei 365
                                    ******************************999*******************9996699********************* PP

                                    .....TT--EEEE--STTS-EEEEE--HHHH.SSSEE---S-----------------TTTTTCCCT-EEEE-------- CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 303 .....kvgqpviipGsmgtkSyivkGkgnae.sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvle 376
                                         +vgqpv+ipGsmgt+Syi++G  +   s+ ++ HGAGR msR++ak++ + ++v ++l+++gi+++a+++++v+e
  gi|118431578|ref|NP_148148.2| 366 pkdymDVGQPVLIPGSMGTGSYILAGVPEGVkSWYTAPHGAGRWMSRSRAKRTKTFNQVLEELAAKGIYIRASNRATVVE 445
                                    **************************998777************************************************ PP

                                    ----------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 377 EapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                    E+peaYKd+d+V++++++ g+ + var++p++v kg
  gi|118431578|ref|NP_148148.2| 446 EMPEAYKDVDRVAQVAHAVGIGRLVARMRPIGVTKG 481
                                    **********************************97 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 ?   13.7   0.1   1.5e-05     0.054      17      69 ..     415     464 ..     402     465 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                    CCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES.SHHHHHHHHHHH CS
                     PGM_PMM_IV  17 aallkvasikeglkilledGrrlavRpSGTepllrvyvEak.sdeelarlaeev 69 
                                    a+++k+  ++++l+ l+++G+ +  R+S+  +++  + Ea+ + +++a++a++v
  gi|118431578|ref|NP_148148.2| 415 AKRTKT--FNQVLEELAAKGIYI--RASNRATVVEEMPEAYkDVDRVAQVAHAV 464
                                    445555..***************..**************************986 PP

>> Complex1_LYR  Complex 1 protein (LYR family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05      0.15      11      46 ..     287     320 ..     283     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                   Complex1_LYR  11 LRearkfpdyntreyfrrriRdeFrknkhvtDpeki 46 
                                    + +a+ f ++n r+ + +++R++F+k  h +Dp+k+
  gi|118431578|ref|NP_148148.2| 287 MAAAANFAWTN-RQMITHWTRESFKKVFH-QDPDKL 320
                                    557899*****.**************999.999987 PP

>> Glycoamylase  Putative glucoamylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.013        47      91     125 ..      57      96 ..      36     103 .. 0.81
   2 ?    6.0   0.0    0.0021       7.7     121     168 ..     246     292 ..     222     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.013
                   Glycoamylase  91 reYaeenpkkfkgygedlWGltasdspeeekke.....gY 125
                                    ++Y + +p++++gyg  + G++a d +ee+  +     gY
  gi|118431578|ref|NP_148148.2|  57 QKYSIVMPDGHQGYGFPIGGVAAMDIEEENGVIspggvGY 96 
                                    68*********************99998655445555555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0021
                   Glycoamylase 121 kkegYaargapleeddGtisPtaalsslpfapeealaalrelykelkd 168
                                     +++Y   +  + ++ Gti P   l+s+p+   ea + +r +     +
  gi|118431578|ref|NP_148148.2| 246 VASDYLMIMERAMRKYGTIPPDRELASIPYNSPEAQNYVRAMA-AAAN 292
                                    4456777777777799****************99999999998.4444 PP

>> Glyco_hydro_45  Glycosyl hydrolase family 45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011      0.41      90     166 ..      23     100 ..      13     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                 Glyco_hydro_45  90 acyalefetdaqgkavkrkklivqvtnvggdlqdqnfdlqipggglgi.fdkgctaefgkeaalggdqyggvksasec 166
                                       a+ +  d   + +k++k ++q++nv    + q++ + +p g  g  f+ g  a +  e   g    ggv    +c
  gi|118431578|ref|NP_148148.2|  23 RVPAIVYADDFLIEKMKQDKTLLQAANVACLQGIQKYSIVMPDGHQGYgFPIGGVAAMDIEEENGVISPGGVGYDINC 100
                                    555666777788899*****************************9985599999998888877777777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3728.11
//
Query:       gi|118431579|ref|NP_148149.2|  [L=186]
Description: hypothetical protein APE_1761.1 [Aeropyrum pernix K1]
Scores for complete 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-27   95.9   2.2      3e-27   95.7   2.2    1.1  1  CYTH      CYTH domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   2.2   1.7e-31     3e-27       3     159 ..       6     155 ..       4     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.7e-31
                                    EEEEEEEE-HHHHHHHHHHHHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEEEETTTEEEEEEEEECSSST...EEE CS
                           CYTH   3 EvEvKflvsaaeyedlelrlaelrakeettveqrdtYydtpdrdlartdeaLRiRraegdgeeltlKgpgvdge...ree 79 
                                    EvE K++++ +e e +e  l++++ + e+ +   d+Yy +p+rd  ++deaLR+R  e++g  lt+Kgp ++g    ree
  gi|118431579|ref|NP_148149.2|   6 EVESKYRIECSEMEYIEAALRDAGLYLEGERLEVDIYYRHPCRDMLSRDEALRLRVYEDNGGRLTYKGPRMGGGfkaREE 85 
                                    9*******9777777666689***********************************9999999***************** PP

                                    EEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHH CS
                           CYTH  80 vegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedeeevkeaaek 159
                                    ve+e++          ++ea  ll++lg+e+  +v+k+R  y+ egv+v+lD ve l g++vE+E+e     e +e++ k
  gi|118431579|ref|NP_148149.2|  86 VEIELT---------RVEEARLLLARLGFEETLVVRKRRKYYRGEGVLVTLDNVESL-GCFVEVEAEDPGGIEMLESLLK 155
                                    ******.........8889999***********************************.*********9888876666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); 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: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1637.53
//
Query:       gi|14601611|ref|NP_148151.1|  [L=178]
Description: hypothetical protein APE_1763 [Aeropyrum pernix K1]
Scores for complete 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  177.3   1.7    2.1e-52  177.1   1.7    1.0  1  DUF2118   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.1   1.7   1.2e-56   2.1e-52       1     151 []      20     168 ..      20     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 1.2e-56
                       DUF2118   1 yklPrlYvEgkeseeevevileeeeevekfadkveekklkgkvvYeelldeivdvleekvtrdviivlp.derklillkkG 80 
                                   y++P+lY+Eg+ se   ++i+++eee ++++++ve+ k++g +vYe++++e++d++ ++v+r +++v+p +++++++l++G
  gi|14601611|ref|NP_148151.1|  20 YRFPELYLEGYVSE---RAIWVDEEEGKYYRRPVEGLKRYGLAVYEHAIKEAIDLVGSRVSRGFVVVIPwKGMRGLMLREG 97 
                                   89************...**************************************************************** PP

                       DUF2118  81 dklklipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVvfikeepagkrpnyiyyilpe 151
                                   +++kl++++gv+v++++ +G+rv e+++l++v+t+kge+r+lra vegvV++i +++++++p+yiy+i++e
  gi|14601611|ref|NP_148151.1|  98 TRVKLVEAAGVQVSHYSLEGTRVGERSVLSYVLTGKGETRTLRAGVEGVVAIILTDHNRQPPAYIYVIADE 168
                                   *********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1569.98
//
Query:       gi|118431580|ref|NP_148152.2|  [L=332]
Description: farnesylgeranyl diphosphate synthase [Aeropyrum pernix K1]
Scores for 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-68  228.6   0.0    7.6e-68  228.3   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 !  228.3   0.0   4.2e-72   7.6e-68       4     254 ..      32     280 ..      29     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 228.3 bits;  conditional E-value: 4.2e-72
                                    HHHHHHHHHHSSS--HHHHHHHHHHHHHS.CGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHH CS
                polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealk.eeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnkl 82 
                                    l+ a+ +l++agGKrlRpl++ll+a++l+   e    +a  la+ +e+ h++sL+hDDimD +e+RRG p+ h ++G + 
  gi|118431580|ref|NP_148152.2|  32 LSGASLHLIKAGGKRLRPLITLLTARMLGgL-E-AEARAIPLAASIETAHTFSLIHDDIMDRDEVRRGVPTTHVVYGDDW 109
                                    6778889**********************52.3.3388****************************************** PP

                                    HHHHHHHHHHHHHHHHHHHH.....STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCH CS
                polyprenyl_synt  83 Aindgdfllarafellaklf.....eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfa 156
                                    Ai++gd l a+af+++a+       +++  ++++++se+++q+ +Gq++d+  e++ d++   +++yl++v+ KT++l++
  gi|118431580|ref|NP_148152.2| 110 AILAGDTLHAAAFKMIADSRewgmsHEQaYRAFKVLSEAAIQISRGQAYDMLFEETWDVD---VADYLNMVRLKTGALIE 186
                                    *****************9988999844459*********************999999***...***************** PP

                                    HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHH CS
                polyprenyl_synt 157 lpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqrkvlk 236
                                    ++++++a++aga +e  + + ++g++ G+aFQi+DD+l + gdp+v+gKp+ +D++ gk tl++++a++   ++ r+++ 
  gi|118431580|ref|NP_148152.2| 187 AAARIGAVAAGAGSEIEKMMGEVGMNAGIAFQIRDDILGVIGDPKVTGKPVYNDLRRGKKTLLVIYAVK---KAGRREIV 263
                                    ************99999****************************************************...5556699* PP

                                    HHTTSSHHHHHHHHHHHH CS
                polyprenyl_synt 237 eilgkkaekeedvkeale 254
                                    +++g ka +e+d+k+a +
  gi|118431580|ref|NP_148152.2| 264 DLIGPKA-SEDDLKRAAS 280
                                    ****555.5777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2448.75
//
Query:       gi|118431581|ref|NP_148153.2|  [L=375]
Description: isopentenyl pyrophosphate isomerase [Aeropyrum pernix K1]
Scores for complete 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-16   59.5   2.8    2.5e-13   49.8   2.0    2.2  2  FMN_dh        FMN-dependent dehydrogenase
     0.0021   17.1   1.0     0.0051   15.9   0.2    1.9  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.003   16.7   0.4     0.0051   16.0   0.4    1.3  1  Glu_synthase  Conserved region in glutamate synthase


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 !    8.3   0.0   0.00018       1.1      31     102 ..      30     102 ..      14     125 .. 0.75
   2 !   49.8   2.0   4.1e-17   2.5e-13     207     341 ..     177     335 ..     159     341 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00018
                                    GGEEE---SSSS-S..S-B--EEETTEEESSSEEE--B..STGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HH CS
                         FMN_dh  31 erirlrprvlrdvs..kvdlsttllGqklslPvliaPv..glaklahpdgelalaraaakagipfvlstvastsle 102
                                    e +r++++   +v+  +v+l++++ G +l++P++i  +  g   + +   +++la  a+++gi ++++++ ++++e
  gi|118431581|ref|NP_148153.2|  30 EYVRIVHNPTPEVNlgDVSLEIDFCGGRLRAPLVITGMtgGHPDVEW--INRELASVAEELGIAIGVGSQ-RAAIE 102
                                    555565555555541167889999***********988544444444..6677999*******9999987.55555 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 4.1e-17
                                    HHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.......................TSSTT---HHHC CS
                         FMN_dh 207 dikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG.......................Rqldgapatidv 260
                                    +i++  e+  +p++vK+    l+ e + ++ ++Gv    v+  GG                         + g  +t  +
  gi|118431581|ref|NP_148153.2| 177 KIAEAAEAAGVPVIVKETgngLSREAVAQLRALGVRCFDVAGLGGtnwikievlrgrkagspleagplQDFWG-NPTAAA 255
                                    67788889999*****99999999********************************99999999998544444.556789 PP

                                    HHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHH CS
                         FMN_dh 261 LpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvae 340
                                    L e + a++ ++ ++++gG+r+G D+++A+alGAda +++ p++  l  gG++   ++l+ ++ +l+++  ++G ++v+ 
  gi|118431581|ref|NP_148153.2| 256 LMEARTAAP-DAYIIASGGVRNGLDAARAIALGADAAGVALPAIRSLLSGGRQATLKLLKAIEYQLKTAVYMVGETRVRG 334
                                    999999998.8***************************************************************999987 PP

                                    H CS
                         FMN_dh 341 l 341
                                    l
  gi|118431581|ref|NP_148153.2| 335 L 335
                                    6 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.16   9.4e+02     110     139 ..     180     209 ..     173     222 .. 0.67
   2 !   15.9   0.2   8.6e-07    0.0051     189     233 ..     249     291 ..     245     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.16
                                    HHHHHTT-SEEEEE-STSSSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 110 kalveagvdvlvvdsahghsekvleavkei 139
                                    +a  +agv v+v ++ +g s++ + +++++
  gi|118431581|ref|NP_148153.2| 180 EAAEAAGVPVIVKETGNGLSREAVAQLRAL 209
                                    455567777888888888777777766665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 8.6e-07
                                    ---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 189 GvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadav 233
                                    G p + A++e+ +aa   +  +ia GG+++  d ++A+a+Gada 
  gi|118431581|ref|NP_148153.2| 249 GNPTAAALMEARTAAP--DAYIIASGGVRNGLDAARAIALGADAA 291
                                    7888889998877765..6789********************985 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 !   16.0   0.4   8.5e-07    0.0051     249     306 ..     246     297 ..     204     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.5e-07
                                    HHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHH CS
                   Glu_synthase 249 khaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaa 306
                                    +  G P+ +al e+ ++           +ia+Gg++ g d + a+alGAda g++  a
  gi|118431581|ref|NP_148153.2| 246 DFWGNPTAAALMEARTA------APDAYIIASGGVRNGLDAARAIALGADAAGVALPA 297
                                    55566666666665554......445789**********************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2793.28
//
Query:       gi|118431582|ref|NP_148154.2|  [L=249]
Description: isopentenyl phosphate kinase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-26   92.3   0.3    4.7e-26   91.9   0.3    1.1  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 !   91.9   0.3   2.6e-30   4.7e-26       4     240 ..      14     228 ..      12     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2.6e-30
                                    EEEE-TTCCCCTCC......HHHHHHHHHHHHH.HHHTTEEEEEE--HHHHHHHHHH...TCCCCCHHHC....E..HHH CS
                      AA_kinase   4 VvKlGGssltdkee......aslrrlaeqiaal.kesgnklvvVhGggsftdgllal...ksglssgelaaglrstleea 73 
                                    VvKlGG ++t k++      a+l+r a q+aa+ k  g+  ++VhGggsf+++ +a+   + gl+++ +           
  gi|118431582|ref|NP_148154.2|  14 VVKLGGGLITFKDKpytidrAMLERTASQLAAYsKGTGRLAALVHGGGSFGHAAVAEaraQGGLTPRAAP---------- 83 
                                    9*********66666******************66667999****************8888888888887.......... PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                      AA_kinase  74 gevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                         + a+++l+ ++ a+ll++g++    +++ +++  +               e++++    g  p + g++ ++ +g
  gi|118431582|ref|NP_148154.2|  84 ---RVQLAMLKLAMEVAASLLKYGVEVSIHPPHTFCSGGECV------------LETLKRDYRLGLTPMTFGDA-VPADG 147
                                    ...3448999***************77777777777655555............9999999999********97.***** PP

                                    EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEE.EHHHCHHCSSS.TTTHHHHCHHHHHHHHHC CS
                      AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpei.svdeaeesaselatgGmkvkhpaalaaarr 232
                                    ++ ++s+D +a +lA++lg+++li++t V+GV  + +++v    +++ + +++++++   ++atgGm  k++aal+a rr
  gi|118431582|ref|NP_148154.2| 148 GVEIVSGDDLALWLAVELGVECLIYATRVPGVV-KGGRVV---PVIRGLgEFEDLGS---GDATGGMARKVKAALEASRR 220
                                    *9******************************9.557899...88888889999999...******************** PP

                                    TT-EEEEE CS
                      AA_kinase 233 ggipvvIt 240
                                    g+ +vvI+
  gi|118431582|ref|NP_148154.2| 221 GVSRVVIV 228
                                    ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1875.60
//
Query:       gi|118431583|ref|NP_148155.2|  [L=261]
Description: hypothetical protein APE_1769.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2085.42
//
Query:       gi|14601616|ref|NP_148156.1|  [L=281]
Description: hypothetical protein APE_1771 [Aeropyrum pernix K1]
Scores for 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-69  231.7   0.0    9.7e-69  231.5   0.0    1.0  1  Memo      Memo-like protein


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 !  231.5   0.0   5.4e-73   9.7e-69       2     269 ..       6     278 ..       5     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 231.5 bits;  conditional E-value: 5.4e-73
                          Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei........arviis..PHagyvysgevaakayaeles.skvervvilGp 71 
                                   +a+AG+fYp+  eel k +e+++ + +g+++         +++i+   PHagy+ysg++aa++y+ ++  +k++ vv+lGp
  gi|14601616|ref|NP_148156.1|   6 PAHAGTFYPATREELVKSIESSFTHPLGPGRLpqrgggsgEQAIAYipPHAGYMYSGPIAAHVYYDMSLgRKPDVVVLLGP 86 
                                   89****************************999999999844443356********************************* PP

                          Memo  72 sHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaqs 152
                                   +Ht+lg  +s+++ + ++TPlG+++vD+e+ + +v+++ i+++d+  + +EHSlEvqlpfL++l     f+ivPi+v +q+
  gi|14601616|ref|NP_148156.1|  87 NHTGLGLAASLWDEGVWRTPLGEVEVDSEAGRLVVEYSGIVAPDDEGHIYEHSLEVQLPFLQYLYGG-DFRIVPIVVLHQT 166
                                   *******************************************************************.5************ PP

                          Memo 153 eetakevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGekpi 231
                                    ++   +++a ++  ++    +++++ sDl+Hy+     p e+ +++ D  ++ka+ee + e++ +++e   ++ cG  pi
  gi|14601616|ref|NP_148156.1| 167 LDISIRIARAYHRLREENGvnAVLVATSDLNHYE-----PYEENKRK-DLLLLKAIEEGDPEAVFKTIEAHAISACGPSPI 241
                                   **********98887777698999**********.....88888888.********************************* PP

                          Memo 232 avilkalkklgakkakllkYaqssdvtsdtdsvVsyas 269
                                   a++++a + +g  k ++l+Ya+s+dvt+++  vV+y +
  gi|14601616|ref|NP_148156.1| 242 AAAVEAGRLAG-VKPRVLAYANSGDVTGEKAWVVGYPA 278
                                   ***********.99**********************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2094.64
//
Query:       gi|118431584|ref|NP_148157.2|  [L=442]
Description: MatE efflux family protein [Aeropyrum pernix K1]
Scores for complete 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-43  148.7  26.6    2.6e-22   79.2   6.1    2.4  2  MatE             MatE
    9.4e-09   35.5   6.1    9.4e-09   35.5   6.1    4.7  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
  ------ inclusion threshold ------
      0.039   13.9   3.4       0.18   11.7   3.4    2.1  1  TMEM239          Transmembrane protein 239 family


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3  12.6   7.1e-25   4.3e-21       1     161 []      18     176 ..      18     176 .. 0.96
   2 !   79.2   6.1   4.4e-26   2.6e-22       1     161 []     236     397 ..     236     397 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7.1e-25
                           MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                    P++++  + s+  ++dt++vg+lgs+++Aav++a  +++l++vf++ + +++ ++ gqa+G++n+  +++a+  gl l++
  gi|118431584|ref|NP_148157.2|  18 PLVVADSALSIAWIVDTYFVGGLGSESIAAVGAAGYLIWLYMVFSTLVYMGVLVILGQAIGSGNRGLVERAAGEGLTLSI 97 
                                    67777777888889****************************************************************** PP

                           MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                    lls+i+++++++ s+q+l ++   +ev +la +yl++ +l++ +  +++++++++r+ gkt+++ly s + +l n  l++
  gi|118431584|ref|NP_148157.2|  98 LLSIIVCAAAFAASKQLLVVL--APEVDQLAWEYLSVSLLTVALHYVTILYDAVFRALGKTMPILYSSGVFTLANTALDP 175
                                    *******************99..77788******************************************99***99987 PP

                           MatE 161 l 161
                                    +
  gi|118431584|ref|NP_148157.2| 176 I 176
                                    6 PP

  == domain 2  score: 79.2 bits;  conditional E-value: 4.4e-26
                           MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                    P+++e +++++ + +    v+r g++alAa++i+ +i sl f++l++++ta  ++vg ++Ga++  + k +    ++l+ 
  gi|118431584|ref|NP_148157.2| 236 PSMVERVVFVVGNVVYLGSVSRCGADALAAHTIGVRIESLAFLPLFSIATASGVMVGWEVGAGRIAESKSTGWELIKLSS 315
                                    99****************************************************************************** PP

                           MatE  81 llsliiallvllfseqils.lftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipl 158
                                    l++l++ ++ l++  +++  +ft d+ v+ la+ yl i++l++p+l++ +v+  i r ag+t++p+ ++l sl +l+++ 
  gi|118431584|ref|NP_148157.2| 316 LIGLVVGAA-LALGGWLVTpIFTGDPRVAWLAALYLVIAGLTEPLLGVVMVAGQIIRNAGDTRTPTLVNLGSLyILRVVP 394
                                    *********.66666655439*********************************************************** PP

                           MatE 159 nyl 161
                                    +yl
  gi|118431584|ref|NP_148157.2| 395 AYL 397
                                    997 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   3.9      0.37   2.2e+03     108     140 ..      32      72 ..      10      75 .. 0.46
   2 ?   -2.2   6.8      0.67     4e+03      91     135 ..      55     109 ..      45     115 .. 0.65
   3 !   35.5   6.1   1.6e-12   9.4e-09       1     104 [.     129     239 ..     129     260 .. 0.81
   4 ?    1.6   1.6     0.045   2.7e+02      79     137 ..     266     329 ..     262     335 .. 0.55
   5 ?    1.2   4.7     0.059   3.6e+02       2      69 ..     350     422 ..     349     440 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.37
                Polysacc_synt_C 108 llllllglllla........alalllavlvgalvYllllll 140
                                    +  +++g l ++        +  + l +++  lvY+++l++
  gi|118431584|ref|NP_148157.2|  32 VDTYFVGGLGSEsiaavgaaGYLIWLYMVFSTLVYMGVLVI 72 
                                    44444444433312222221124444444555555555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.67
                Polysacc_synt_C  91 llkpllaalvmgivvylllllllglllla..........alalllavlvgalvYl 135
                                    ++ +++++ ++++ v+ +l + +g  +            +l++ll+++v+a++++
  gi|118431584|ref|NP_148157.2|  55 IWLYMVFSTLVYMGVLVILGQAIGSGNRGlveraageglTLSILLSIIVCAAAFA 109
                                    4555555555555544444444444444467888888766688888888888876 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 1.6e-12
                Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavlnl 74 
                                    +L+++ l++ ++++++++ +++ +lg++  +l+++ +  l++ +l  +li      p +g+ Gaa+a+v+a l++++++ 
  gi|118431584|ref|NP_148157.2| 129 YLSVSLLTVALHYVTILYDAVFRALGKTMPILYSSGVFTLANTALDPILIygrlgaPALGVEGAAWASVAASLLGLLVL- 207
                                    589999********************************************999999999*****************987. PP

                Polysacc_synt_C  75 yalrrllgikl.ellrrll..kpllaalvmgiv 104
                                    ++l+r+l + l   lr +   + +la  + ++v
  gi|118431584|ref|NP_148157.2| 208 VYLSRYLDVGLrP-LRPTSvsRSILALGFPSMV 239
                                    7778888777742.3333224666665555555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.045
                Polysacc_synt_C  79 rllgikl..ellrrllkpllaalvmgiv.vylllllllglllla...alalllavlvgalvYlll 137
                                    +++g+++    +  l+ ++ a+ vm++  v    ++  + ++++    l+ l++++vga++ l+ 
  gi|118431584|ref|NP_148157.2| 266 HTIGVRIesLAFLPLFSIATASGVMVGWeVG-AGRIAESKSTGWeliKLSSLIGLVVGAALALGG 329
                                    5667777543355555777777777777422.222222222222333558888888888876665 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.059
                Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi.....vGaaiatvlallvv 69 
                                    L+i  l+ ++l++ +v ++i+   g +++++++++ ++ +  ++  +l+p +       +Ga +a+ +  +  
  gi|118431584|ref|NP_148157.2| 350 LVIAGLTEPLLGVVMVAGQIIRNAGDTRTPTLVNLGSLYILRVVPAYLLPGLMPtglcvLGAWLAMGIDIVGR 422
                                    7788888899**********************99999976666666666544321224466666666654443 PP

>> TMEM239  Transmembrane protein 239 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.4     3e-05      0.18      70     131 ..      95     156 ..      84     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                        TMEM239  70 lylllalglchalfttgshllrslwpvvaa.vwkhllpallllvlsalpallfaasfllllst 131
                                    l +ll++ +c a f++  +ll  l p v    w +l  +ll ++l  + ++l+ a f  l  t
  gi|118431584|ref|NP_148157.2|  95 LSILLSIIVCAAAFAASKQLLVVLAPEVDQlAWEYLSVSLLTVALHYV-TILYDAVFRALGKT 156
                                    789***********************8875269999999999999765.67788888766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3156.07
//
Query:       gi|118431585|ref|NP_148158.2|  [L=500]
Description: carboxypeptidase [Aeropyrum pernix K1]
Scores for complete 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-158  528.6   0.0   1.7e-158  528.4   0.0    1.0  1  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.4   0.0  9.7e-163  1.7e-158       3     488 .]      14     497 ..      12     497 .. 0.98

  Alignments for each domain:
  == domain 1  score: 528.4 bits;  conditional E-value: 9.7e-163
                  Peptidase_M32   3 kellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavveelkr 82 
                                     e ++ v+++++a +l+ wD+et+mpk+g  +ra + a L  l+++ll +ee+ +lle++e+++  l+e e+ vv+ lkr
  gi|118431585|ref|NP_148158.2|  14 VEAYRPVWSVSHALSLMGWDSETYMPKGGVGERALARADLFVLRRRLLLREELLRLLERAESQEG-LNEYEAGVVRVLKR 92 
                                    567888999***************************************************97766.7789********** PP

                  Peptidase_M32  83 eykkakkvpaelvealakasakaeaaWreareandfalfepsLeevielkreiaelledlkkspYdaLldeyepgltvek 162
                                    e + a+++p+e+v ++ak+ ++a++aWr+are++df lf+p+Le+++e++r++a++l + + +pY+aLld +e+gltv +
  gi|118431585|ref|NP_148158.2|  93 EVRIARSLPEEFVFEFAKLREEATHAWRTARERDDFGLFKPYLERIVEYARRMADYL-GWEGHPYNALLDLHEEGLTVGD 171
                                    *********************************************************.********************** PP

                  Peptidase_M32 163 idalFeelkealvpllkkikeskekekkdksflereipeekqrelsrellkalgfdfdrgrldeseHPFttsfsrkDvRi 242
                                    +d++F+++  +l+  l+++ +     ++ +s+ + e+++  +++++re+l+ lgf +drgrld+s HPFt+s++  DvRi
  gi|118431585|ref|NP_148158.2| 172 VDRIFDSIVPTLRRALDRVLSTGSY-PRSHSLESVEYEQGVMEAVNREVLDLLGFPWDRGRLDVSPHPFTISMGIGDVRI 250
                                    **********************985.56678************************************************* PP

                  Peptidase_M32 243 ttryeednllsslfsvlHEaGHalYeqnlpeelsktplgggvslgihEsqSrlyEniigrskeFwevllpklkeafpeql 322
                                    ttrye +++ ++lf+v+HE+GHalYe++++e+l+  pl++g+slg+hEsqSr++En++ rs++F+  + p+l+++ p  l
  gi|118431585|ref|NP_148158.2| 251 TTRYEGRDFRHTLFAVIHEFGHALYELQIDERLKASPLAEGASLGVHESQSRFWENVVARSRSFIPLVTPILRKRLPF-L 329
                                    ***************************************************************************887.7 PP

                  Peptidase_M32 323 ddvsleefyeavnkvepsliRveADEltYslHillRyelEkeliegklsvkdlpeaWnekykeyLgidppddaeGvLQDv 402
                                    +d+s +++y ++n v+p+liRveADEltY++Hi+lRy+lEk lieg+++v+dlpe+Wn+ ++++Lg++p++ ++GvLQD+
  gi|118431585|ref|NP_148158.2| 330 KDYSDDDVYLYFNIVRPGLIRVEADELTYNFHIYLRYTLEKGLIEGSIKVDDLPELWNSMMEDLLGVRPKSYRDGVLQDI 409
                                    77****************************************************************************** PP

                  Peptidase_M32 403 HWssgafGYFPtYalGniyaaqlfeamekdlpel..eiakgefseikkWLkenihqkGslysseellkkatgeslnaeyy 480
                                    HWs+g++GYFPtY+lG++++aq+  a++ +l +l   +++ge++ ++++L+enih++Gs+y ++el+++  ge+ln+eyy
  gi|118431585|ref|NP_148158.2| 410 HWSHGSIGYFPTYTLGTVLSAQIKAAIDGSLGGLyrLVENGELDRVRTFLRENIHRYGSTYAPKELVERGLGEPLNPEYY 489
                                    *******************************8889999****************************************** PP

                  Peptidase_M32 481 idyLkeky 488
                                     +y++ek+
  gi|118431585|ref|NP_148158.2| 490 NQYITEKF 497
                                    *******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3534.98
//
Query:       gi|118431586|ref|YP_874913.1|  [L=385]
Description: hypothetical protein APE_1777 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.7   0.0      0.077   12.8   0.0    1.4  1  HTH_IclR  IclR helix-turn-helix domain
        0.1   12.5   0.0       0.23   11.4   0.0    1.6  1  MarR_2    MarR family
       0.12   12.4   0.0       0.21   11.6   0.0    1.4  1  HTH_29    Winged helix-turn helix
       0.13   11.8   0.1        1.3    8.7   0.0    2.6  3  HTH_24    Winged helix-turn-helix DNA-binding


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 ?   12.8   0.0   1.7e-05     0.077       6      46 ..      23      63 ..      22      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTT CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelG 46
                                   l++Lda+     +  +  lAr tgl  S v+R +  L + G
  gi|118431586|ref|YP_874913.1| 23 LELLDAIQYSHNPPEIGHLARMTGLDVSYVRRVVENLRNTG 63
                                   789*****999999*********************999887 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.2e-05      0.23      16      49 ..      33      63 ..      23      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                                   CTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTT CS
                         MarR_2 16 rrpgrdltvgelarrlglsksavsrilkrLvaaG 49
                                   ++p+    +g lar +gl+ s+v r+++ L   G
  gi|118431586|ref|YP_874913.1| 33 HNPP---EIGHLARMTGLDVSYVRRVVENLRNTG 63
                                   3443...89*******************998765 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.7e-05      0.21      18      43 ..      41      66 ..      19      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                         HTH_29 18 iAkllglsrrtvyrwlkrfeegGlaa 43
                                   +A+++gl+ ++v+r+++  +++G++a
  gi|118431586|ref|YP_874913.1| 41 LARMTGLDVSYVRRVVENLRNTGVRA 66
                                   7*********************9877 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 ?    8.7   0.0   0.00028       1.3      23      46 ..      41      64 ..      38      64 .. 0.95
   2 ?   -1.3   0.0      0.38   1.7e+03      22      38 ..     138     154 ..     134     156 .. 0.83
   3 ?   -3.1   0.0       1.3     6e+03       9      21 ..     166     178 ..     166     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00028
                         HTH_24 23 LAerlglSpstvnrrlkrLeeeGl 46
                                   LA+++gl +s v+r +++L + G+
  gi|118431586|ref|YP_874913.1| 41 LARMTGLDVSYVRRVVENLRNTGV 64
                                   9*******************9996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.38
                         HTH_24  22 eLAerlglSpstvnrrl 38 
                                     LA ++ lS++  +++ 
  gi|118431586|ref|YP_874913.1| 138 LLANEVLLSKPSFTYYF 154
                                    5999999**99999885 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.3
                         HTH_24   9 LelLqknprisqr 21 
                                    LelL  +p+i++ 
  gi|118431586|ref|YP_874913.1| 166 LELLDNHPKIPII 178
                                    899999**99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3002.29
//
Query:       gi|118431587|ref|NP_148160.2|  [L=145]
Description: hypothetical protein APE_1779.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.9   0.0     0.0093   16.5   0.0    1.3  1  ASCH      ASCH domain


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 !   16.5   0.0   5.2e-07    0.0093       1      58 [.       1      58 [.       1     108 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.2e-07
                                   EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEE CS
                           ASCH  1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevk 58
                                   +s+++ +a +i++G+K+ e r      p  +g + i++a+   + ++g+++ ++v   
  gi|118431587|ref|NP_148160.2|  1 MSIRPQYARAIMAGRKKYELRRIHGVPPIEEGSIIIVYASGNVKSIIGEFQAKRVIQA 58
                                   78999**************886555445566999999999999999999999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        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 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1183.60
//
Query:       gi|118431588|ref|NP_148161.2|  [L=245]
Description: NAD-dependent deacetylase [Aeropyrum pernix K1]
Scores for complete 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-56  189.7   0.0    4.9e-56  189.5   0.0    1.1  1  SIR2            Sir2 family
     0.0028   17.7   1.0     0.0051   16.9   1.0    1.3  1  Zn-ribbon_8     Zinc ribbon domain
     0.0081   16.2   0.0      0.014   15.4   0.0    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
       0.11   12.6   0.4       0.18   11.9   0.4    1.3  1  DZR             Double zinc ribbon
       0.23   11.2   2.5          1    9.1   2.5    2.0  1  zinc_ribbon_2   zinc-ribbon domain
       0.34   10.4   2.2        2.7    7.5   0.3    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.38   10.7   2.0        4.7    7.2   0.2    2.4  2  Nudix_N_2       Nudix N-terminal
       0.73    9.4   3.2        8.7    6.0   0.1    2.1  1  TF_Zn_Ribbon    TFIIB zinc-binding
          2    8.4   4.5         19    5.2   4.5    2.1  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.5   0.0   2.4e-59   4.9e-56       1     177 []      22     193 ..      22     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.5 bits;  conditional E-value: 2.4e-59
                                    -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHHHHHHHHHHHHCCTSS--HHHHHHHHHHHTTCEEEEEE CS
                           SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllveevfyniarellaeeaepnaaHkalkklekkgkllrliT 80 
                                    GAGiS+esGip+fR+k+Gl++++++++la+pea++++++lv+e +y+++ e +   a+pn+aH++l+ le++g l+++iT
  gi|118431588|ref|NP_148161.2|  22 GAGISAESGIPTFRGKDGLWSRFDPRDLATPEAFNRDPRLVWE-WYSWRIERVL-AAKPNKAHRLLARLEDSGVLKAVIT 99 
                                    9******************************************.*****99999.6************************ PP

                                    S-SSSHHHHTT-SSEEETTEEEEEEEETTTSBEEECCGGHCHHHCCTT.B-TTTCCBEEEEE--CTSB-S.HHHHHHHHH CS
                           SIR2  81 QNiDgLekkaGskkvvelHGslakakcvkcekkldkeelqeeieaekvpecekcgkllkpdvvfFGealp.dklkkliek 159
                                    QN+DgL+++aGs++v+elHG++++a+c++c+ kl++    e+ ++  +p+c++cg++l+pdvv+FGe l+ + l++++  
  gi|118431588|ref|NP_148161.2| 100 QNVDGLHRRAGSRRVLELHGNVLRARCTRCGSKLEWR---EKPSNL-PPSCPRCGGVLRPDVVWFGEPLDtSLLEEAFGL 175
                                    ********************************99994...444443.788********************999999**** PP

                                    HHH-SEEEEES--STSTT CS
                           SIR2 160 veeadlllviGtSlkVap 177
                                    +++ d++++iGtS +V p
  gi|118431588|ref|NP_148161.2| 176 ARRSDVMIIIGTSGAVDP 193
                                    ***************987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0   2.6e-06    0.0051       7      34 ..     125     151 ..     124     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                    Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs 34 
                                    rC++Cg++ e + + s   l++ CP+Cg+
  gi|118431588|ref|NP_148161.2| 125 RCTRCGSKLEWREKPSN--LPPsCPRCGG 151
                                    8*********7776664..6666*****8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.1e-06     0.014      60      94 ..     113     151 ..      89     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                                    -EEEEEEE--EEEETTTS-EEECHHH..HH..S-TTTSS CS
                           HypA  60 aeLeieevpvkvrCreCgkefeleek..al..rCpkCgs 94 
                                     +Le++   +++rC++Cg++ e +ek  +l  +Cp+Cg+
  gi|118431588|ref|NP_148161.2| 113 RVLELHGNVLRARCTRCGSKLEWREKpsNLppSCPRCGG 151
                                    5788999999************7664332266*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   8.9e-05      0.18      15      40 ..     126     155 ..     120     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.9e-05
                            DZR  15 CseCgtklkavaa....edrCpsCgekvdp 40 
                                    C +Cg+kl+  ++    +  Cp+Cg  + p
  gi|118431588|ref|NP_148161.2| 126 CTRCGSKLEWREKpsnlPPSCPRCGGVLRP 155
                                    *******9866669999*******987665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.5   0.00052         1       1      20 [.     125     150 ..     125     153 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00052
                  zinc_ribbon_2   1 fCpnCGaelqdnakF......CpyCG 20 
                                    +C++CG +l+ ++k       Cp+CG
  gi|118431588|ref|NP_148161.2| 125 RCTRCGSKLEWREKPsnlppsCPRCG 150
                                    6*********99999999*******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 ?    2.2   0.1     0.064   1.3e+02       5      26 .]     126     133 ..     124     134 .. 0.53
   2 ?    7.5   0.3    0.0014       2.7       4      16 ..     145     157 ..     144     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.064
                    zf-ribbon_3   5 CPnCGaplssddnvCpyCGtkl 26 
                                    C +CG              +kl
  gi|118431588|ref|NP_148161.2| 126 CTRCG--------------SKL 133
                                    55555..............544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                    zf-ribbon_3   4 rCPnCGaplssdd 16 
                                    +CP+CG +l++d+
  gi|118431588|ref|NP_148161.2| 145 SCPRCGGVLRPDV 157
                                    6999998878875 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0024       4.7      21      29 ..     122     130 ..     112     139 .. 0.68
   2 ?    2.5   0.1     0.069   1.4e+02       3      10 ..     146     153 ..     145     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                                    -EEEETTTT CS
                      Nudix_N_2  21 eRlvCpaCg 29 
                                     R++C++Cg
  gi|118431588|ref|NP_148161.2| 122 LRARCTRCG 130
                                    566666665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.069
                                    -TTT--B- CS
                      Nudix_N_2   3 CsqCGtpv 10 
                                    C+ CG+ +
  gi|118431588|ref|NP_148161.2| 146 CPRCGGVL 153
                                    77777765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1    0.0044       8.7      21      30 ..     125     134 ..     123     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0044
                                    EESSSSBEEE CS
                   TF_Zn_Ribbon  21 vCtdCGlVle 30 
                                    +Ct+CG+ le
  gi|118431588|ref|NP_148161.2| 125 RCTRCGSKLE 134
                                    7******998 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 ?    5.2   0.8      0.01        20       5      33 ..     124     132 ..     110     137 .. 0.74
   2 ?    5.2   4.5    0.0097        19       5      35 ..     124     154 ..     123     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.01
                 Zn_ribbon_SprT   5 YrCtgCgreythhlsirrhnYrCrrCkgt 33 
                                    +rCt+Cg                    ++
  gi|118431588|ref|NP_148161.2| 124 ARCTRCG--------------------SK 132
                                    4555555....................44 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0097
                 Zn_ribbon_SprT   5 YrCtgCgreythhlsirrhn..YrCrrCkgtLr 35 
                                    +rCt+Cg+  + + + ++ n    C+rC+g+Lr
  gi|118431588|ref|NP_148161.2| 124 ARCTRCGS--KLEWREKPSNlpPSCPRCGGVLR 154
                                    7999**95..55555566666688999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1973.73
//
Query:       gi|118431589|ref|NP_148162.2|  [L=99]
Description: hypothetical protein APE_1783.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       370  (0.020637); 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:                         0  (0); expected 0.2 (1e-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 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 748.97
//
Query:       gi|118431590|ref|NP_148164.2|  [L=151]
Description: hypothetical protein APE_1785.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.8   0.0       0.19   11.9   0.0    1.7  1  SelB-wing_2  Elongation factor SelB, winged helix
       0.15   12.5   0.0        0.2   12.1   0.0    1.3  1  FUN14        FUN14 family


Domain annotation for each model (and alignments):
>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.1e-05      0.19      30      56 ..      38      64 ..       6      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                   S-HCCHHHHHHHHHHTTSEEE-SSEEE CS
                    SelB-wing_2 30 lpaklfqallealvargilavegdwvh 56
                                   l+++ +++lle+l+++g +++++d + 
  gi|118431590|ref|NP_148164.2| 38 LDDEEIDSLLESLAKKGYIKLNRDKIE 64
                                   78999*****************99876 PP

>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.2e-05       0.2      32      68 ..      46      76 ..      45     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          FUN14 32 llqilasqgyikvnwdkiekdveelldrnkdgklgte 68
                                   ll+ la++gyik n dkie      l++++++ ++  
  gi|118431590|ref|NP_148164.2| 46 LLESLAKKGYIKLNRDKIE------LSEQGEKAVAAG 76
                                   6899***************......222233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1145.08
//
Query:       gi|118431591|ref|NP_148165.2|  [L=510]
Description: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase [Aeropyrum pernix K1]
Scores for 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-120  402.5   0.0   2.2e-120  402.3   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
      4e-06   26.1   0.0    8.1e-05   21.8   0.0    2.3  1  LuxC      Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
      0.032   13.7   0.0          5    6.5   0.0    2.2  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 !  402.3   0.0  3.8e-124  2.2e-120       9     462 .]      42     497 ..      35     497 .. 0.95

  Alignments for each domain:
  == domain 1  score: 402.3 bits;  conditional E-value: 3.8e-124
                                    EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHH.HHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHHHH CS
                         Aldedh   9 ievinPatgeviakvpaataedvdaavaaAke.afkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplaear 87 
                                      v +P++g++iakv++ +a+ +++ v+   +   ++ +++p e+R +iL ++adlle+++ ++ e++t ++Gk+ ++a+
  gi|118431591|ref|NP_148165.2|  42 AVVRSPIDGSIIAKVSRLDAAAIEEGVDVVYRlGRRRIRDVPGEKRLNILSRIADLLEKNAGDFEEVLTVNAGKTRKQAA 121
                                    56889*************************997777******************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHSEEEEEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE- CS
                         Aldedh  88 aeveeaidvlryyaelaeklegevlpss.....egklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKPa 162
                                    +eve +id lr +a  ++kl+ge +p +      +++ +vrreP+Gvv+aI+P+N+Pl+ ++ k++   + GN++++KP 
  gi|118431591|ref|NP_148165.2| 122 GEVEASIDRLRKAALDLRKLQGEYVPGDwdrhtLESEGIVRREPYGVVLAIIPFNYPLFDTVNKFVYSTIPGNAFIVKPP 201
                                    ***************************856665566779***************************************** PP

                                    TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEE CS
                         Aldedh 163 eetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknpl 242
                                    +  pl ++++a+l+ eag+P++ l + t +gse+ e lv+++++ ++s+tGs+e+g k++++a+  +k++++ElGG +p+
  gi|118431591|ref|NP_148165.2| 202 SADPLPVIMFARLAIEAGFPPESLMIATLRGSEA-EKLVADRRISVISLTGSSETGVKVMRSAG--IKQLIMELGGGDPA 278
                                    ****************************999986.568899***********************..9************* PP

                                    EE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHHHHHHHHH CS
                         Aldedh 243 ivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPliseaqlekvek 322
                                    ivl+daDl++a+++i++g+++++GQ+C a++ +lv+e +y+e+ + lve+++k+kvgdp++++t++GPli++++++ + +
  gi|118431591|ref|NP_148165.2| 279 IVLADADLKSAASKIATGITSYSGQRCDAIKLVLVEEPVYNEMKKLLVEELSKIKVGDPRNDSTTMGPLIDKEAVDAMVE 358
                                    ******************************************************************************** PP

                                    HHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEE....S-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHSSSEESE CS
                         Aldedh 323 yveeakeegaklllGgereeaglekgyfvePtvla....nvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNdteyGLa 398
                                     +eea+++gakll+Gge     +  + +++P +++    nv ++ +++++E+F+PV+++++f++++eaie+aN  +yGL 
  gi|118431591|ref|NP_148165.2| 359 AIEEAVSRGAKLLYGGE-----RIGDTYITPALVEvedkNVLRELKLYKDEVFAPVAVITSFSTLDEAIELANGRRYGLD 433
                                    ****************3.....346699***99963334799999*********************************** PP

                                    EEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                         Aldedh 399 agvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                    a++f+++++r++++++ le+G +yiN++ ++ +   pfgG k+Sg+Greg  +++e +t +kt+
  gi|118431591|ref|NP_148165.2| 434 AAIFGESMARIRKLIRFLEVGAIYINEYPRHGIGYYPFGGRKDSGIGREGIGYSIEYVTALKTI 497
                                    ************************************************************9986 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-08   8.1e-05       4     269 ..      82     334 ..      79     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-08
                           LuxC   4 lsleeildlleeaaklladdeyskraierlakitgyeealleilkalaallkreeLk.kvleseLgqpeiLdeflktkek 82 
                                    ++ e+ l++l ++a+ll+ +  ++  + ++++ +  ++a+ e ++a+++ l++ +L  ++l+ e   p   d+   + e 
  gi|118431591|ref|NP_148165.2|  82 VPGEKRLNILSRIADLLEKNAGDFEEVLTVNAGKTRKQAAGE-VEASIDRLRKAALDlRKLQGEYV-PGDWDRHTLESE- 158
                                    566777899999999998885555555555554444444444.79999999999986245555542.233355545555. PP

                           LuxC  83 syekaqprglvlhvlsgNvpll.pvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfksgdt 161
                                    +  ++ p g+vl +++ N pl   v   + + + +n+ ++k++s dp  ++ +++  ++     +    ++ +   +g++
  gi|118431591|ref|NP_148165.2| 159 GIVRREPYGVVLAIIPFNYPLFdTVNKFVYSTIPGNAFIVKPPSADPLPVIMFARLAIEAGFP-PESLMIATL---RGSE 234
                                    999******************9346789********************999999976666553.444456666...3333 PP

                           LuxC 162 kleeeiv.qnaDvvvawGgeeaikaiseklkpgkqlikfGakvSfavvdkealeeealdkaaeraAkDiivfdQqAClsp 240
                                    + e+ +      v++  G++e+   +   +  +  +++ G     a+v  +a    +l++aa ++A+ i ++  q C + 
  gi|118431591|ref|NP_148165.2| 235 A-EKLVAdRRISVISLTGSSETGVKVMRSAGIKQLIMELGGGDP-AIVLADA----DLKSAASKIATGITSYSGQRCDAI 308
                                    2.22222256889999*****99999988888777777877654.4554555....8*********************** PP

                           LuxC 241 qvvfvekddkieidefaeaLaaaLekrar 269
                                    + v+ve   +  ++e++++L ++L k+  
  gi|118431591|ref|NP_148165.2| 309 KLVLVE---EPVYNEMKKLLVEELSKIKV 334
                                    ******...679************99875 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0   0.00084         5       9      61 ..     279     333 ..     277     336 .. 0.87
   2 ?    4.8   0.0    0.0027        16     114     167 ..     409     459 ..     399     499 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00084
                        DUF1487   9 vifedgDlnsalealveslke..Pfaegavatvlveesirdefvervrsklkpls 61 
                                    ++++d+Dl+sa+ +++  +       ++a+  vlvee + +e+ +++ ++l +++
  gi|118431591|ref|NP_148165.2| 279 IVLADADLKSAASKIATGITSysGQRCDAIKLVLVEEPVYNEMKKLLVEELSKIK 333
                                    7999*************998711456899*****************999998775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0027
                        DUF1487 114 tgvvTlhtFrnakEvvkllakeslkfasvsvwneklaavyelvarlnvdvftiN 167
                                     +v  +  F++  E+++l++  +  +++ ++++e +a + +l+  l+v  ++iN
  gi|118431591|ref|NP_148165.2| 409 VAV--ITSFSTLDEAIELANGRRYGLDA-AIFGESMARIRKLIRFLEVGAIYIN 459
                                    444..458************99999987.89******************99999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3729.46
//
Query:       gi|118431592|ref|NP_148166.2|  [L=120]
Description: hypothetical protein APE_1789.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.7   0.3        5.8    7.6   0.3    2.1  1  Trm112p   Trm112p-like protein
       0.24   11.0   1.4         15    5.3   0.1    2.3  2  zf_UBZ    Ubiquitin-Binding Zinc Finger
        2.3    8.7   6.1    3.1e+02    1.9   0.0    3.0  2  zf-IS66   zinc-finger binding domain of transposase IS66


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 ?    7.6   0.3   0.00097       5.8       9      42 ..      53      92 ..      11     104 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00097
                                   B-TTTHHC--HHHHHHHHH.TT---.S-SS----S..........C CS
                        Trm112p  9 aCpackgpLdwealvevaa.lglne.lpkekpedy..........e 42
                                   +Cp c  pL       va+ ++++   ++e  e+y          +
  gi|118431592|ref|NP_148166.2| 53 QCPRCEAPL------SVARpRKIEImTRDEFEEEYvvtkfevlrrT 92
                                   588888888......7777777776666666666666666555443 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0041        25       2      11 ..      12      21 ..      12      23 .. 0.81
   2 ?    5.3   0.1    0.0025        15       4      14 ..      53      63 ..      50      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0041
                         zf_UBZ  2 tylCerCgke 11
                                   t +C++C+ +
  gi|118431592|ref|NP_148166.2| 12 TLVCSKCNFK 21
                                   579****965 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0025
                         zf_UBZ  4 lCerCgkeipe 14
                                   +C+rC +++++
  gi|118431592|ref|NP_148166.2| 53 QCPRCEAPLSV 63
                                   7****998876 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 ?    1.9   0.0     0.052   3.1e+02       3      20 ..      14      33 ..      12      43 .. 0.67
   2 ?    1.1   6.5     0.092   5.5e+02       3      37 ..      53     100 ..      51     104 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.052
                        zf-IS66  3 tCpcCGg.l.lkpigedrvr 20
                                   +C++C+  l    ig+++ r
  gi|118431592|ref|NP_148166.2| 14 VCSKCNFkLyWYVIGDKSNR 33
                                   69999985566666666555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.092
                        zf-IS66   3 tCpcCGg.l....lkpigedrvr.............eeldipPakfrViehir 37 
                                    +Cp C + l          +++               ++++   +  V ehir
  gi|118431592|ref|NP_148166.2|  53 QCPRCEApLsvarP-----RKIEimtrdefeeeyvvTKFEVLRRTTLVEEHIR 100
                                    78888884444442.....3333333333222222266666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 894.72
//
Query:       gi|118431593|ref|NP_148167.2|  [L=215]
Description: hypothetical protein APE_1790.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1706.61
//
Query:       gi|118431594|ref|NP_148168.2|  [L=465]
Description: tRNA CCA-pyrophosphorylase [Aeropyrum pernix K1]
Scores for 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-39  132.4   0.0    1.1e-38  131.9   0.0    1.2  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    2.5e-19   69.3   0.0    3.9e-19   68.7   0.0    1.3  1  NTP_transf_2     Nucleotidyltransferase domain


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 !  131.9   0.0   1.2e-42   1.1e-38       1     112 [.     165     281 ..     165     282 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 1.2e-42
                                    HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE..........EEE...-SS-EEE CS
                tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekea....llkkf.deplvvi 75 
                                    d++ l+K+flkgigvYG+e++v GfsGYlaE+l++++g+fee+++aa++w+p+v++d+++ +a    l++++ d+p++v 
  gi|118431594|ref|NP_148168.2| 165 DDILLFKSFLKGIGVYGAETRVGGFSGYLAEVLIIHHGGFEETVKAASSWRPPVMVDTTSGKAdldmLARRYpDSPIIVP 244
                                    79*******************************************************877776788777777899***** PP

                                    ETTEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                tRNA_NucTransf2  76 DPvDpkRNvaaalsleklaefilaareflkkpseeff 112
                                    DPvDp+RN+aa+++ ++lae+++aa+ fl+kps +ff
  gi|118431594|ref|NP_148168.2| 245 DPVDPSRNTAASVTPKRLAELVHAANIFLRKPSPTFF 281
                                    ************************************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   4.3e-23   3.9e-19       2      95 .]      40     163 ..      39     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 4.3e-23
                                    HHHHHHHHHHTT...TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH..................HHHEHHHHHHHH CS
                   NTP_transf_2   2 kklleelkelep...vakvvlfGSyarGtalkg.SDiDllvvlpeevsre..................kkeegleklaei 59 
                                    +++lee+++l++   +++v l+GS+a+Gt+l++ +++D++++l+++  re                  +++   +k++e+
  gi|118431594|ref|NP_148168.2|  40 ARALEECEDLRLsipSYRVELVGSAAKGTLLRDkWEVDVFLLLDAP--REevrrlgesllrsclggrlPYY---FKYSEH 114
                                    789*******************************************..7779*************665555...****** PP

                                    CCCEEECTTEEEEEE..............CEEECCCCTEEEEEECEEEHH CS
                   NTP_transf_2  60 ikfleellglevdlv..............trekledpllvksileerpll 95 
                                    ++++++l+g+++d+v              +r++++ +++v+s+leerp+l
  gi|118431594|ref|NP_148168.2| 115 PYATVSLMGMQADVVpaplavdprdavgvERTPFH-TRYVRSRLEERPWL 163
                                    ***********************************.************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3845.09
//
Query:       gi|14601629|ref|NP_148169.1|  [L=176]
Description: 2'-5' RNA ligase [Aeropyrum pernix K1]
Scores for 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  113.0   0.1    1.3e-16   60.6   0.1    2.0  2  LigT_PEase       LigT like Phosphoesterase
    1.1e-13   51.3   0.0    1.4e-13   51.0   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.8e-08   34.5   0.0    4.4e-08   33.3   0.0    1.6  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.016   14.7   0.0    1.2  1  HVSL             Uncharacterised conserved protein
       0.13   12.5   0.7        2.8    8.2   0.1    2.6  2  FeoA             FeoA 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 !   60.6   0.1   3.5e-20   1.3e-16      10      87 .]       4      77 ..       2      77 .. 0.95
   2 !   50.7   0.0   4.2e-17   1.5e-13       7      87 .]      83     162 ..      78     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3.5e-20
                                  HHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCEEE CS
                    LigT_PEase 10 elarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprviy 87
                                  +larl++ ++  + +   k v+++n+HiTL+f+gev+e+ ++e+ e+la+i  ++e+f+++++g+g+fp + rprv++
  gi|14601629|ref|NP_148169.1|  4 RLARLRDSIA--HTGVPMKTVEDENFHITLRFIGEVSEPVAAEIGERLASI--RFERFRIELRGLGAFPRPDRPRVVW 77
                                  7999999999..889999999******************************..7889********************9 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 4.2e-17
                                   HHHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECC.SCC CS
                    LigT_PEase   7 iaeelarlaaeleralaklglkpv.rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvglfpsrl.rpr 84 
                                    a el+r+++e+er l ++g++p+ ++f+pH+TLa+++  +  +++ +ll+++++++ g     ++v+ + l +s l r++
  gi|14601629|ref|NP_148169.1|  83 GAGELRRIRDEVERILTSMGFSPEkQEFHPHVTLARIKGARnLPALVKLLREMGDVEVGS----VEVSSIRLKQSILtRQG 159
                                   5789**********************************8776788888999***997774....***************** PP

                                   EEE CS
                    LigT_PEase  85 viy 87 
                                   +iy
  gi|14601629|ref|NP_148169.1| 160 PIY 162
                                   **9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   3.9e-17   1.4e-13      19     137 ..      20     139 ..       4     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3.9e-17
               2_5_RNA_ligase2  19 kayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh..kksvvylsv.sdsealqalraalleal 95 
                                   k +++   HitL + ++ +e   a++ e+l+ +  ++e f+++l g+g F++  + +vv++ v  +  +l+++r+++++ l
  gi|14601629|ref|NP_148169.1|  20 KTVEDENFHITLRFIGEVSEPVaAEIGERLASI--RFERFRIELRGLGAFPRpdRPRVVWVGVgGGAGELRRIRDEVERIL 98 
                                   55778889***********96555666666555..8****************95555************************ PP

               2_5_RNA_ligase2  96 peagdkedsgeftPHlTiaqsadstsaaelleklaqalpple 137
                                      g   +++ef+PH+T+a+ + ++   +l++ l ++  ++e
  gi|14601629|ref|NP_148169.1|  99 TSMGFSPEKQEFHPHVTLARIKGARNLPALVKLL-REMGDVE 139
                                   ****99999***********99999988877777.4444444 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 !   33.3   0.0   1.2e-11   4.4e-08      40     205 ..      24     168 ..       4     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.2e-11
                                   TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTT.S--EEEEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHH CS
                     AKAP7_NLS  40 peklHlTllvlkLknkeeiaaakevLkevkeeikdaldn.kplslrlkGletfnddpakarVlYakveeesneekLqelad 119
                                    e++H+Tl  +   ++   a+  e       ++ ++    ++++++l+Gl+ f   p + rV++++v   +  ++L++++d
  gi|14601629|ref|NP_148169.1|  24 DENFHITLRFIGEVSEPVAAEIGE-------RLASI--RfERFRIELRGLGAF-PRPDRPRVVWVGVG--GGAGELRRIRD 92 
                                   555555554443323333333333.......33333..13899**********.799**********9..569******** PP

                                   HHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S--GG.GGGGGTT-EEEEEE--EEEEEESSS---TTS--E CS
                     AKAP7_NLS 120 riikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfdareilkqfkdfefgeekineihLsqlesddesdgyYk 200
                                    + + + + g++ ek++  +++H+Tl+ ++ +++  a  k       +l++++d e g++++++i L q   +++    Yk
  gi|14601629|ref|NP_148169.1|  93 EVERILTSMGFSPEKQE--FHPHVTLARIKGARNLPALVK-------LLREMGDVEVGSVEVSSIRLKQSILTRQ-GPIYK 163
                                   ************99985..6*********98887777666.......*********************9999988.88888 PP

                                   EEEEE CS
                     AKAP7_NLS 201 viasv 205
                                   ++ +v
  gi|14601629|ref|NP_148169.1| 164 TLYEV 168
                                   87766 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.4e-06     0.016     104     190 ..      38     122 ..       8     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-06
                          HVSL 104 kdsfldslkkelkssakrrFevsfsglkwvsndektRsFlvlrvkspendeLkklleavnkvleefglpplykdeaFHiSi 184
                                    +++ +++ ++l+s + +rF+++++gl  ++ +++ R+ +v  v   +  eL+++ ++v+++l+++g  p  ++ ++H+ +
  gi|14601629|ref|NP_148169.1|  38 SEPVAAEIGERLASIRFERFRIELRGLGAFPRPDRPRVVWVG-V-GGGAGELRRIRDEVERILTSMGFSPEKQEFHPHVTL 116
                                   567777888888888889*******************98888.5.55669******************************* PP

                          HVSL 185 awslge 190
                                   a   g 
  gi|14601629|ref|NP_148169.1| 117 ARIKGA 122
                                   987764 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00079       2.8       9      38 ..      82     108 ..      81     108 .. 0.87
   2 ?    1.9   0.0     0.078   2.8e+02      12      35 ..     117     139 ..     111     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00079
                                   T-EEEEEEE-TT.SSHHHHHHHHT--TT-E CS
                          FeoA   9 GergeiarisdedpellrrLremGlvpGar 38 
                                   G +ge +ri+de   ++r L +mG+ p ++
  gi|14601629|ref|NP_148169.1|  82 GGAGELRRIRDE---VERILTSMGFSPEKQ 108
                                   7899*****975...88*********9875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.078
                                   EEEEEE-TT.SSHHHHHHHHT--T CS
                          FeoA  12 geiarisdedpellrrLremGlvp 35 
                                   ++i++ +   p+l + LremG v+
  gi|14601629|ref|NP_148169.1| 117 ARIKGARNL-PALVKLLREMGDVE 139
                                   567777666.99999999999555 PP



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:                      276  (0.0153941); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1444.00
//
Query:       gi|14601630|ref|NP_148170.1|  [L=673]
Description: DNA topoisomerase I [Aeropyrum pernix K1]
Scores for complete 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-103  345.8   0.0   4.1e-103  345.6   0.0    1.1  1  Topoisom_bac  DNA topoisomerase
    2.3e-08   34.2   0.0    5.5e-08   33.0   0.0    1.7  1  Toprim        Toprim domain
  ------ inclusion threshold ------
      0.042   13.3   0.5      0.086   12.3   0.5    1.5  1  CHZ           Histone chaperone domain CHZ


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 !  345.6   0.0  6.9e-107  4.1e-103       3     413 .]     149     558 ..     147     558 .. 0.93

  Alignments for each domain:
  == domain 1  score: 345.6 bits;  conditional E-value: 6.9e-107
                  Topoisom_bac   3 nenlvdaaeaRrelDwliGinlsrlltk...klkg.kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekke 79 
                                   + ++++a++aR+e+Dwl+Gin+sr+l++   ++ g   +lsaGRVq+ptL   ++R rei+ +vp+    v++t +k+++ 
  gi|14601630|ref|NP_148170.1| 149 DVEMIEAGMARSEMDWLWGINVSRALMEaarRAAGrRVILSAGRVQSPTLVEAYRRWREINLHVPKASVAVKITAEKGGGV 229
                                   7789************************765333368999**********************************9999999 PP

                  Topoisom_bac  80 kekkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYekag 159
                                   ++  ++ + ++ ++ e a++i ++l+k+  + ve+v+++++  +pp  f++ +Lqkea+r+lgl + +t+sia++LY +  
  gi|14601630|ref|NP_148170.1| 230 FD--ARPHGWKPQSLETARSIKSELRKNpWLAVEEVRSERSILRPPPAFNLGDLQKEANRILGLPPLRTQSIAEELYLE-A 307
                                   85..8888888889999********9988************997777*******************************7.* PP

                  Topoisom_bac 160 litYpRTdstrlseeaelkailealakkygkeylefaekllkktkkks..vvknkkveaHeAIrPteelpklkelsddekk 238
                                   li+YpRT+s++l+++ + +ail++la+   + + + a++llk+t +    v+++k++ aH+AI+Pt+e p+ ++ls+++  
  gi|14601630|ref|NP_148170.1| 308 LISYPRTNSQKLPPSINYRAILDKLAHG--P-LGREARELLKETGGVLrpVQGSKDDPAHPAIHPTGEKPS-QRLSKEHMA 384
                                   ***************669********95..6.7777888888887766877777777***********996.89******* PP

                  Topoisom_bac 239 lYelIvrrflaslmkdakyeettvklev.eeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkeveleek 318
                                   +YelIvrrfla+++++a++++ +v l+  +++ ++a+g ++ + G++k+y+++   e++  +p+l +g++ +v  v+++ +
  gi|14601630|ref|NP_148170.1| 385 VYELIVRRFLAAFSREAIVSKSSVLLRDfQGRVWRAEGLRVEDLGWLKYYHYSTPGEKP--MPPLDRGDKARVVRVDVRVE 463
                                   **************************555************************999886..******************** PP

                  Topoisom_bac 319 kTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaeleekL 398
                                   + + p r+ +asL+++me+ +iGt+ Tra iie+l++rgY+e  +++  +t+lG+a++ +++++ ++l +p+lT+++e+++
  gi|14601630|ref|NP_148170.1| 464 WSQTPVRLDKASLLRWMESVNIGTEGTRARIIETLYKRGYLEG-SRKSEVTPLGEAVAVIIQTLfPELSKPDLTRRFESMI 543
                                   *******************************************.6689*************6666**************** PP

                  Topoisom_bac 399 deIaegkadakevld 413
                                   ++I++g+++++ev+d
  gi|14601630|ref|NP_148170.1| 544 EDIRSGRRTRQEVID 558
                                   ************985 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   9.3e-12   5.5e-08       3     102 ..       1     132 [.       1     133 [. 0.95

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 9.3e-12
                                   EEESSHHHHHHHHHTHT.....................STEEEEEEESSSSEEEHS..........TTEEEEE...ECTTT CS
                        Toprim   3 vivEgpsdaktiakalg.....................sgfqavtaslGhildlet..........efkpvye...eiedk 49 
                                   +++E+p++a++ia al+                     +   +v +s Gh++   t          e+ p++e      + 
  gi|14601630|ref|NP_148170.1|   1 MVAEKPKAAAKIAYALSdgrgvlrcseygvpywivrrdGAAIVVAPSAGHLFGPHTdsrgfpvfdfEWRPIFEfdrGAGYL 81 
                                   79***********************************99999*******************************88888888 PP

                                   HHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                        Toprim  50 kkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefse 102
                                    k   +l +++  a+  + a+D D eG+ i+++++e++++ +++  +r++fs 
  gi|14601630|ref|NP_148170.1|  82 SKFYRMLSRILPGASLYVNACDYDIEGSVIGFKIIEAFGDVNRA--RRMKFST 132
                                   88888899999****************************99999..***9985 PP

>> CHZ  Histone chaperone domain CHZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   1.4e-05     0.086      15      30 ..     546     561 ..     546     563 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                           CHZ  15 IsgGRRTRgktiDfak 30 
                                   I +GRRTR  +iD +k
  gi|14601630|ref|NP_148170.1| 546 IRSGRRTRQEVIDMSK 561
                                   789**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 4633.15
//
Query:       gi|118431595|ref|NP_148171.2|  [L=147]
Description: signal peptidase [Aeropyrum pernix K1]
Scores for 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-09   35.6   0.6    1.1e-08   34.9   0.6    1.4  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 !   34.9   0.6   6.1e-13   1.1e-08       2      48 ..      26      70 ..      25      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 6.1e-13
                                   XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEE CS
                  Peptidase_S24  2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrvig 48
                                   v+G SMep l++Gdl+++    ++  Gdivv r  +   ++i+r+i 
  gi|118431595|ref|NP_148171.2| 26 VQGRSMEPILHSGDLVVIIDKGDYSVGDIVVYRKGDR--LIIHRIIA 70
                                   99******************************99888..9*****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1120.86
//
Query:       gi|14601632|ref|NP_148172.1|  [L=229]
Description: hypothetical protein APE_1797 [Aeropyrum pernix K1]
Scores for complete 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  106.2   0.0    3.6e-30  104.9   0.0    1.5  2  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 ?   -1.8   0.0      0.12   2.2e+03       5      30 ..      19      43 ..      17      47 .. 0.85
   2 !  104.9   0.0     2e-34   3.6e-30       2     150 ..      66     216 ..      65     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.12
                                  EEEEEEES--.-----HHHHHHHHHT CS
                          B3_4  5 yaarvlrgvkktapspewlqrrLrra 30
                                   + rv +gv+ +++sp  l + Lr++
  gi|14601632|ref|NP_148172.1| 19 LVYRVFDGVS-VGESPGELVEILRSV 43
                                  6789999999.9****9999999876 PP

  == domain 2  score: 104.9 bits;  conditional E-value: 2e-34
                                   SSEEEEEEEES--.-----HHHHHHHHHTT---.--HHHHHHHHHHHHHT--EEEEEGGGTBTEEEEEE--TTEEEEBTTS CS
                          B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirp.innvVDitNyvmlelgqPlhafDldkiqgdivvrlakegeklvtldg 81 
                                   ++r+++r++ +++k++ps+e+l rr+ r    p innvVD  N  +l++ +P++ +Dld+++++++++l+++ge + +++g
  gi|14601632|ref|NP_148172.1|  66 YRRFLWRLGIDPTKVRPSSEALARRVLRGSSIPlINNVVDAGNIASLKTLVPIGLYDLDTVKPPLKLALSRGGEVFEPIGG 146
                                   79******************************************************************************* PP

                                   -EEEE-TTSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHHTT---HHHHHHH CS
                          B3_4  82 kereldeedlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirktarrlglrseaskrfe 150
                                   k+  l +++++ +ds++ v ++++++++  s+++ +T++v+  aa+++ v      r++++ se  +rf 
  gi|14601632|ref|NP_148172.1| 147 KHQSLPQGYPILVDSRGLVmHIYPHRDSRVSMITSSTRRVLAVAAGVEGVGMDDLRRAIEMLSELLERFA 216
                                   *****************999******************************99999999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1792.18
//
Query:       gi|118431596|ref|NP_148173.2|  [L=267]
Description: fructose-1,6-bisphosphatase [Aeropyrum pernix K1]
Scores for complete 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  134.9   0.3    4.2e-39  134.7   0.3    1.0  1  Inositol_P  Inositol monophosphatase family
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.23   10.9   0.0    1.4  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.3   4.6e-43   4.2e-39       3     251 ..       5     243 ..       3     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 4.6e-43
                                    HHHHHHHHHHHH.HHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.S CS
                     Inositol_P   3 eevtkaavelaa.kagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgeksel 81 
                                    e++ +++v++ +  ag + + ++s ++l ++ ++        t ad+++e++il+ l++++ + ++++ee+++ ++   +
  gi|118431596|ref|NP_148173.2|   5 EQLRRVSVKVSSeTAGLLRDLACS-EDLGRVVSG------ETTVADKRAEDYILDLLRRELGQVQVISEEAGGVAS---K 74 
                                    566666777777455555555555.677766666......5789********************************...7 PP

                                    SSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE..TTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTE CS
                     Inositol_P  82 tedgltwivDPiDGTknFvrgipqvaVsigllv..egkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseal 159
                                    t+d+++ +vDP+DG +n+++ i ++ Vs+++++   g++++G +a +++g  +s a+gkG++  g  l++++ + i++++
  gi|118431596|ref|NP_148173.2|  75 TSDAPIALVDPLDGSTNYLSCITWCSVSVAFADprSGEILAGSVAPVYAGMPVSFARGKGCYHGG--LKVEDPS-IRGSI 151
                                    8888*************************************************************..9999988.88887 PP

                                    EEEEESSSSSSHHHHCHHHHHHHCCCCCH.EEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTEEEE CS
                     Inositol_P 160 lvtlfavssrkdtseasllekvesavsae.gvrsvgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGGvvt 237
                                    +  ++ v++   ++  +   + ++ v++  +vrs+gs+al+la++a G ++++ + + r+   D+AA++  ++e+GGvvt
  gi|118431596|ref|NP_148173.2| 152 I--SVYVDEPGAIESVAGAIGRLKGVRRDfKVRSLGSAALELAYTAIGYIAVFADLRaRLRNIDVAAAVGAVRECGGVVT 229
                                    7..6899******99999999999999999**************************99********************** PP

                                    ESSSCSSSTTSSEE CS
                     Inositol_P 238 dakgegrlllargi 251
                                    da+g+++ +  +++
  gi|118431596|ref|NP_148173.2| 230 DAHGQPLRIGVWRV 243
                                    *****554444333 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 ?   10.9   0.0   2.6e-05      0.23      63     116 ..      41      91 ..       6     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                         FBPase  63 klDvladeiliealkaseevkvlvSEEeeelivlerekegkyvvafDPlDGSSn 116
                                      D +a++ + + l+ +     ++SEE   +     +++++++ ++DPlDGS n
  gi|118431596|ref|NP_148173.2|  41 VADKRAEDYILDLLRRELGQVQVISEEAGGVASK--TSDAPIA-LVDPLDGSTN 91 
                                    458899999*****9999889999**99987655..7788776.68******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2203.87
//
Query:       gi|118431597|ref|NP_148174.2|  [L=286]
Description: hypothetical protein APE_1799.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.8  11.8        1.8    8.6   6.0    2.3  2  DZR            Double zinc ribbon
       0.49   10.2  14.3      0.051   13.3   6.9    2.7  3  zinc_ribbon_2  zinc-ribbon 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 ?    6.4   0.3     0.001       9.3      13      36 ..       8      36 ..       2      42 .. 0.79
   2 ?    8.6   6.0    0.0002       1.8       1      20 [.     264     283 ..     263     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.001
                            DZR 13 r.fCseCgtklkavaa....edrCpsCge 36
                                   r +Cs Cg ++    +    ++ C++C +
  gi|118431597|ref|NP_148174.2|  8 RpMCSVCGVRPAVFYRrfsgHRLCSRCMR 36
                                   448*****999766668999999999976 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0002
                            DZR   1 CpqCgeelppdarfCseCgt 20 
                                    C  Cg+++p ++++C++C t
  gi|118431597|ref|NP_148174.2| 264 CRACGAPVPCGSKYCEDCHT 283
                                    88999999999999999976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2     0.091   8.2e+02      16      20 ..      11      15 ..       5      16 .. 0.72
   2 ?   -0.5   0.0      0.13   1.1e+03      14      19 ..      29      34 ..      26      39 .. 0.70
   3 ?   13.3   6.9   5.7e-06     0.051       1      21 [.     263     283 ..     263     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.091
                  zinc_ribbon_2 16 CpyCG 20
                                   C+ CG
  gi|118431597|ref|NP_148174.2| 11 CSVCG 15
                                   77777 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.13
                  zinc_ribbon_2 14 kFCpyC 19
                                   + C++C
  gi|118431597|ref|NP_148174.2| 29 RLCSRC 34
                                   568888 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 5.7e-06
                  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                    +C  CGa+++ ++k+C+ C t
  gi|118431597|ref|NP_148174.2| 263 KCRACGAPVPCGSKYCEDCHT 283
                                    8******************65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2384.64
//
Query:       gi|118431598|ref|YP_874914.1|  [L=79]
Description: hypothetical protein APE_1799a [Aeropyrum pernix K1]
Scores for complete 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   0.1    1.8e-10   40.7   0.1    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0027   17.7   0.1     0.0035   17.4   0.1    1.2  1  NapD            NapD protein
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.015   15.2   0.0    1.1  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 !   40.7   0.1     3e-14   1.8e-10       1      72 [.       9      78 ..       9      79 .] 0.84

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3e-14
                                   EEEEE-GGGTTHHHHHHHHHHT..STTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                 AsnC_trans_reg  1 vlvslepghpeqleefeealae..lpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72
                                   vl++++ g+    +e+ e++ +    +V+e+ ++ Gd+d++++  + +++ l++++   ++s+pgv rt+t+i+
  gi|118431598|ref|YP_874914.1|  9 VLINVDVGK---EKEVLEEILKryGRNVTEARVTYGDFDLIVRLEAGNMRLLDKIVTG-IRSIPGVLRTTTLIA 78
                                   678888888...444444444434579****************************999.************996 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   5.8e-07    0.0035       6      68 ..       9      74 ..       5      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.8e-07
                           NapD  6 lvVqarperlaavkaalaalpgvEvhasdee...gklVvviEaesedeladtieaiealpgVlsas 68
                                   ++++++ ++ ++v++++ +  g  v  +        l+v +Ea + + l ++++ i+++pgVl ++
  gi|118431598|ref|YP_874914.1|  9 VLINVDVGKEKEVLEEILKRYGRNVTEARVTygdFDLIVRLEAGNMRLLDKIVTGIRSIPGVLRTT 74
                                   689999999999999999999988877776664478***************************986 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.5e-06     0.015      21      79 ..      17      76 ..      11      79 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                            GYD 21 rreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaa.sGtvrtetl 79
                                   +++e+ e++ ++ G ++ +  +t G++D++v +Ea   +   ++   +++  G +rt+tl
  gi|118431598|ref|YP_874914.1| 17 KEKEVLEEILKRYGRNVTEARVTYGDFDLIVRLEAGNMRLLDKIVTGIRSiPGVLRTTTL 76
                                   5789999999*************************9988888888877773466666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 620.43
//
Query:       gi|118431599|ref|NP_148176.2|  [L=356]
Description: pelota-like protein [Aeropyrum pernix K1]
Scores for 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-22   77.6   0.0    2.3e-21   76.4   0.0    1.6  1  eRF1_3       eRF1 domain 3
      9e-18   64.5   0.0    1.5e-17   63.8   0.0    1.3  1  eRF1_1       eRF1 domain 1
    1.6e-05   25.2   0.0    3.5e-05   24.1   0.0    1.6  1  eRF1_2       eRF1 domain 2
  ------ inclusion threshold ------
      0.054   14.2   5.9      0.037   14.7   2.1    2.5  3  MDMPI_N      Mycothiol maleylpyruvate isomerase N-terminal do
      0.079   13.4   1.1         14    6.2   0.2    3.2  3  GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain


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 !   76.4   0.0   6.3e-25   2.3e-21       2     113 .]     251     349 ..     250     349 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 6.3e-25
                                    HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS-HHH-HHHHHHHHHHHHHHHHH CS
                         eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekvketgeelelvelieelvenvee 80 
                                    ++ + +leefl+++ak  ++++Y+  evl++++mgAv+t+L++++l +s d+ ++e+             ++e ++ ve+
  gi|118431599|ref|NP_148176.2| 251 VEAEGVLEEFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVLLVDTLLHSPDDaVREA-------------VDEALRLVES 317
                                    788899*******************************************99978777.............9********* PP

                                    TT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                         eRF1_3  81 sgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                    +g++v+ii+ +s++Ge+l  +fgG++a+LRy+v
  gi|118431599|ref|NP_148176.2| 318 MGGRVIIIPGDSPAGERL-VSFGGVIALLRYPV 349
                                    ******************.9***********97 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   4.1e-21   1.5e-17      10     126 ..       7     121 ..       1     123 [. 0.93

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 4.1e-21
                                    TTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSSEEEEEEEEEE CS
                         eRF1_1  10 kdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdagvlrisGkvie 89 
                                     +++  v+L+pe++edlw l   ++pgd vr  t+r v      gs  +erv ++L+i+  +++f++ +g lrisG v+e
  gi|118431599|ref|NP_148176.2|   7 DNKRRIVRLRPESEEDLWLLRITLRPGDVVRIRTSRDVPV----GSGRKERVVMTLRIRLDSIEFQPFTGKLRISGIVVE 82 
                                    578899********************************77....78888******************************* PP

                                    GGGG.--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHH CS
                         eRF1_1  90 eneh.vklgafhtldlelkrpftiikee.wdsfalerLk 126
                                    + ++   +g+ h+  + ++  + +++++ w++  lerL 
  gi|118431599|ref|NP_148176.2|  83 GPDEfGVKGRRHSTAVSIGTWLVVERDKgWSEQELERLA 121
                                    99886789******************777********96 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   9.9e-09   3.5e-05       7     128 ..     134     242 ..     128     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.9e-09
                                    EETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEEEEESS CS
                         eRF1_2   7 ldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgiilagpg 86 
                                    +d +e  +++l g+ +++l+  +  +P+K    + +++      e+ +++  k+++e+a ++            ++agpg
  gi|118431599|ref|NP_148176.2| 134 VDYDEFALAVLAGHGMKILEDTSARLPGKDDP-SREQE-----VEKYVDRAAKRIVEEAARH-------RSPIAVIAGPG 200
                                    6778888999********************85.22222.....3555666666666666665.......5566799**** PP

                                    THHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC..CH CS
                         eRF1_2  87 fvkeefldkdlldaelkkkviklvdvsyggesglnevlek..aa 128
                                    + k+   +k   +    + ++ +vd+s gg +g++e+l+   + 
  gi|118431599|ref|NP_148176.2| 201 QLKTSVAEKV--QRAMPSLKVATVDTSMGGVAGVREALRResVT 242
                                    *****98874..5556667889****************975555 PP

>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.1     1e-05     0.037      20     128 ..     130     238 ..     113     266 .. 0.86
   2 ?   -0.2   0.2      0.43   1.5e+03      95     136 ..     265     298 ..     233     303 .. 0.52
   3 ?   -0.4   0.1      0.49   1.8e+03     125     136 ..     287     298 ..     257     334 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                        MDMPI_N  20 waapspcpGWtvadlvaHlarsaralaaalaaegaesalardaaaalvtaadaeavdlaaslapeallaafraavtrlaa 99 
                                    + a +  ++  +a l++H     + ++a l+++ +++++++++  ++ +aa++  +++a+ ++p a++a   +  t++a+
  gi|118431599|ref|NP_148176.2| 130 VIAAVDYDEFALAVLAGHGMKILEDTSARLPGK-DDPSREQEVEKYVDRAAKRIVEEAARHRSPIAVIAGPGQLKTSVAE 208
                                    55666677788889999999999********97.777778888888899998**************************** PP

                        MDMPI_N 100 alaalppdaiadrl.gipggprslgeflrt 128
                                    ++ ++ p   ++++ +  gg++ + e+lr+
  gi|118431599|ref|NP_148176.2| 209 KVQRAMPSLKVATVdTSMGGVAGVREALRR 238
                                    **************7777777777667776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.43
                        MDMPI_N  95 trlaaalaalppdaiadrlgipggprslgeflrtrlvEavvH 136
                                    ++ ++ +a +         g  + +++ g++ ++ lv++ +H
  gi|118431599|ref|NP_148176.2| 265 AKSRDTVAYT--------PGEVLAVARMGAVDTVLLVDTLLH 298
                                    2222222222........233333333444445555555555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.49
                        MDMPI_N 125 flrtrlvEavvH 136
                                    + ++ lv++ +H
  gi|118431599|ref|NP_148176.2| 287 VDTVLLVDTLLH 298
                                    333333333333 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.041   1.5e+02      41      73 ..     152     186 ..     146     189 .. 0.74
   2 ?    6.2   0.2    0.0039        14       5      67 ..     205     266 ..     201     268 .. 0.86
   3 ?    0.7   0.0      0.21   7.4e+02      65      88 ..     292     315 ..     289     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.041
                                    HHHHHS-S...-------.-TTHHHHHHHHHHHHH CS
                    GlutR_dimer  41 leralkkla.ldgedree.lekltrslvnkllhep 73 
                                    le + ++l+  d+  re+ +ek +++  ++++ e 
  gi|118431599|ref|NP_148176.2| 152 LEDTSARLPgKDDPSREQeVEKYVDRAAKRIVEEA 186
                                    67777888875666666669999999999888765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHH CS
                    GlutR_dimer   5 iIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedreelekltrslvn 67 
                                     ++e+v++ +  lk   v+  +  +    e++r+e ++r+l++l+   e + +le+++r++ +
  gi|118431599|ref|NP_148176.2| 205 SVAEKVQRAMPSLKVATVDTSMGGVAGVREALRRESVTRILRELS-IVEAEGVLEEFLRRIAK 266
                                    68899999999999999999999999999***************8.55666669999999876 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHHHHHSS-TTTTHHH CS
                    GlutR_dimer  65 lvnkllheptarLkeaedeeeell 88 
                                    lv+ llh p  +++ea de+ +l+
  gi|118431599|ref|NP_148176.2| 292 LVDTLLHSPDDAVREAVDEALRLV 315
                                    7899***********955554544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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:                         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: 00:00:00.39
# Mc/sec: 2709.87
//
Query:       gi|14601637|ref|NP_148178.1|  [L=418]
Description: hypothetical protein APE_1804 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2932.44
//
Query:       gi|118431600|ref|NP_148179.2|  [L=823]
Description: valyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-111  373.6   0.0   2.2e-110  369.7   0.0    2.0  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
      8e-23   81.1   0.1    1.5e-22   80.2   0.1    1.5  1  Anticodon_1     Anticodon-binding domain of tRNA
    1.1e-22   80.3   0.0    2.6e-12   46.2   0.0    4.1  3  tRNA-synt_1g    tRNA synthetases class I (M)
     0.0021   18.0   1.8       0.21   11.7   0.3    3.1  3  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.01   15.3   0.0       0.24   10.9   0.0    2.2  2  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
       0.11   11.9   0.0        9.5    5.5   0.0    2.6  3  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
       0.41   11.1   5.0         73    3.9   0.0    3.8  3  zf-IS66         zinc-finger binding domain of transposase IS6
        1.5    8.2   7.3        8.7    5.8   0.1    3.9  4  zf-TFIIB        Transcription factor zinc-finger
        2.1    8.2   4.9        5.4    6.9   0.1    3.1  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
        3.7    7.7   5.9         45    4.3   2.9    3.2  3  Zn-ribbon_8     Zinc ribbon domain
        4.9    6.7  10.5        9.5    5.8   0.4    4.1  4  zf-ribbon_3     zinc-ribbon domain
        5.6    7.7  10.3        6.8    7.4   0.1    3.9  4  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        9.1    6.0   6.0         17    5.2   0.5    3.1  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon 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 !  369.7   0.0  1.6e-113  2.2e-110       2     601 ..      22     583 ..      21     584 .. 0.93

  Alignments for each domain:
  == domain 1  score: 369.7 bits;  conditional E-value: 1.6e-113
                    tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakve 81 
                                    l++ W++ed++k++l+ ++ ++  ++  +PPy  G+ H+G a + t  d++ ry r+kG++v   +  D  Gl++e +ve
  gi|118431600|ref|NP_148179.2|  22 LLSLWDAEDLHKSTLDPDDPREIVVIDTPPPYPSGKWHVGGAAHYTQIDMIARYFRLKGYNVVAPFYADRNGLPVEVQVE 101
                                    6889**************************************************************************** PP

                    tRNA-synt_1  82 kklgak.ekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgk 160
                                    k++g   ++  r+  gre+f + + e+ ++  +ei + ++rlG  +D+ re  T ++ +   ++ +f  l  +gliy+++
  gi|118431600|ref|NP_148179.2| 102 KTYGVVaHEMARTTEGRERFLALCSEFLDKVESEIVQLWRRLGCGFDYWREG-TDSPRYRSMTQATFIDLWRRGLIYEAE 180
                                    ***975155689999**********************************996.889************************ PP

                    tRNA-synt_1 161 klvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeall 240
                                    ++v w++++kt+l+e+E+e+k+ +d +++v++ l+++ +  lv+aTT+Pe l g  a+a +pe                 
  gi|118431600|ref|NP_148179.2| 181 RPVRWCPRCKTTLAEAEIEHKEDEDFIYYVKYRLEEDGR-DLVVATTRPELLAGCAALAYHPE----------------- 242
                                    ***********************************9999.9**********************................. PP

                    tRNA-synt_1 241 kslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinilded 320
                                                  der+k L gk+++ pl + +++i++   v+k++GtG+  i  + de+D ++  + +l++ + +de+
  gi|118431600|ref|NP_148179.2| 243 --------------DERYKGLAGKTAIAPLYGHRVKIVEHPAVKKDFGTGLMMICSYGDEEDVRLFLELDLKPKVLIDEN 308
                                    ..............9***************************************************************** PP

                    tRNA-synt_1 321 gtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqf 400
                                    g+++e+a+  +gl v++ar+ + e l+ +gll+k+e+i hsvp+c+r k+p+        f r+ +++da+ +a  k+ f
  gi|118431600|ref|NP_148179.2| 309 GVMNENAGPIAGLPVKEARRRIAEILEREGLLVKKERIVHSVPVCWRCKTPLQIIHRRELFLRQLDFKDAVKQAAAKMDF 388
                                    ******************************************************************************** PP

                    tRNA-synt_1 401 vpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekge 479
                                    +p++++k+ ++w+  i+ dW iSR+r++G+ ipl+  ++ +   v e   ++        ae+  ++  +  + +  +  
  gi|118431600|ref|NP_148179.2| 389 KPEMHRKKLYDWIDSIKmDWPISRERFYGTEIPLWTCEKCGAKLVPEPGRYYR-----PWAEEPPWD--SCPRCGAPRRY 461
                                    ***************966*********************99777633222222.....223333333..33345788999 PP

                    tRNA-synt_1 480 lekdedvlDvWFsSgswpfstlgypeedteelkkffpadmll.eGlDiirgWvarlillslaltgsePfkevlvhglvrd 558
                                    l+ ++ v+D+WF+S+ +p  +  +     + + ++   ++l  +G Diir W++ +il  l+ltg+  f+ v ++gl +d
  gi|118431600|ref|NP_148179.2| 462 LKGETRVFDTWFDSSISPLYVTRWMWD--KRFYERASRNVLRpQGQDIIRTWLYYSILRVLQLTGKPAFRWVRITGLGLD 539
                                    ************************988..666667777777549************************************ PP

                    tRNA-synt_1 559 eeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                     +Gr m KslgNvidp+ +i kyg da R++ +  ++ g d ++
  gi|118431600|ref|NP_148179.2| 540 PKGRPMHKSLGNVIDPEPIIAKYGGDAFRFWAAiAAKLGYDYRF 583
                                    *******************************9988888888776 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 !   80.2   0.1   1.1e-25   1.5e-22       1     150 [.     623     772 ..     623     775 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 1.1e-25
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk...ra.aqevllevletllrl 76 
                                    d+ +l+  +++++ +++ay e++ ++ a+ +ye+ w+ ++++y+elvk+r y++s+      ++ a ++l+e+l+ +l  
  gi|118431600|ref|NP_148179.2| 623 DKAFLALADEYLEAADKAYGELDVYEPANLIYELAWDIFASHYVELVKERSYNRSGLFTreeQEaAWATLHELLRRILVA 702
                                    8999***************************************************988888866688************* PP

                    Anticodon_1  77 laPfmPfitEelwqreeeelgkkesimlaewpekaeelekel..e.eeevellkeivkairklrselkikpsselkv 150
                                    l+P+mPf+t+ +     ++  + +s++++ wp ++ + ++e+  e   +  l+ +++ka+ +l+ +++ k  ++l+ 
  gi|118431600|ref|NP_148179.2| 703 LSPIMPFVTDAIH----RR-LYGSSVHRQRWP-DPLF-TPEErrElAGKARLIVSVNKAVWNLKRSMGKKLYEPLDT 772
                                    *************....44.45689*******.5533.333322357888999999**********99998888665 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 !   46.2   0.0   1.9e-15   2.6e-12       2     136 ..      46     199 ..      45     202 .. 0.82
   2 !   13.0   0.0   2.4e-05     0.033     167     238 ..     351     421 ..     323     431 .. 0.85
   3 !   13.1   0.0   2.1e-05     0.029     323     385 ..     540     600 ..     465     605 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.9e-15
                                    EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HH................ CS
                   tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpe................ 64 
                                    ++ t+ pY++gk H+G ++++ + D++aRy rl+g++v+     D  G p+e++ ek  gv ++                
  gi|118431600|ref|NP_148179.2|  46 VIDTPPPYPSGKWHVGGAAHYTQIDMIARYFRLKGYNVVAPFYADRNGLPVEVQVEKTyGVVAHemarttegrerflalc 125
                                    78999***********************************99*********99977643333330111111111222222 PP

                                    .HHHHHHHHHHHHHHHHTT---SEEEE.TTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                   tRNA-synt_1g  65 .elvekvheeikelfkklnisfdkygr.ttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                     e+ +kv++ei +l+++l+  fd++ + t+s + ++++q+ f  l ++gliye e  + +cp+++++l++ ++e
  gi|118431600|ref|NP_148179.2| 126 sEFLDKVESEIVQLWRRLGCGFDYWREgTDSPRYRSMTQATFIDLWRRGLIYEAERPVRWCPRCKTTLAEAEIE 199
                                    2677899999***************8648889999***********************************9997 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.4e-05
                                    ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                   tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                    p++  +++  ++ ++++lf++  +f++++k+  ++ +  ++e  +k++ +w+++   d+ isr+  +G ++P
  gi|118431600|ref|NP_148179.2| 351 PVCWRCKTPLQIIHRRELFLRQLDFKDAVKQAAAKMD-FKPEMHRKKLYDWIDSIKMDWPISRERFYGTEIP 421
                                    78999999999999*****************995555.57888888999*****999**************9 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 2.1e-05
                                    E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHH CS
                   tRNA-synt_1g 323 vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgn 385
                                     +g+ + kS g+v++++ ++ ++  d++R++ a +a+   D  f ++++    N   a kl n
  gi|118431600|ref|NP_148179.2| 540 PKGRPMHKSLGNVIDPEPIIAKYGGDAFRFWAAIAAKLGYDYRFDENKVKTGRN--FATKLWN 600
                                    57899************************************9999998865544..4555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.11   1.5e+02      13      24 ..     184     195 ..     177     209 .. 0.79
   2 ?    0.7   0.0      0.41   5.7e+02      30      39 ..     352     361 ..     336     366 .. 0.69
   3 !   11.7   0.3   0.00015      0.21      14      37 ..     424     458 ..     422     462 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                            DZR  13 rfCseCgtklka 24 
                                    r C++C+t+l +
  gi|118431600|ref|NP_148179.2| 184 RWCPRCKTTLAE 195
                                    678888888864 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.41
                            DZR  30 rCpsCgekvd 39 
                                    +C++C+++++
  gi|118431600|ref|NP_148179.2| 352 VCWRCKTPLQ 361
                                    4555555544 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00015
                            DZR  14 fCseCgtklkavaa...........edrCpsCgek 37 
                                    +C++Cg+kl +++             d Cp+Cg++
  gi|118431600|ref|NP_148179.2| 424 TCEKCGAKLVPEPGryyrpwaeeppWDSCPRCGAP 458
                                    6*******9988889*********99******986 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 ?    2.1   0.0     0.088   1.2e+02      12      43 ..     210     241 ..     208     245 .. 0.85
   2 ?   10.9   0.0   0.00017      0.24      85     144 ..     250     309 ..     238     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.088
                  tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalap 43 
                                    +++++ee+ ++l v ttrp+ l G   +a  p
  gi|118431600|ref|NP_148179.2| 210 VKYRLEEDGRDLVVATTRPELLAGCAALAYHP 241
                                    7899999999**************98777655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00017
                  tRNA-synt_1_2  85 tglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikped 144
                                     g +ai P+ g+++ i     v  ++gtg +m +   d++D +   + +l+ k  i +++
  gi|118431600|ref|NP_148179.2| 250 AGKTAIAPLYGHRVKIVEHPAVKKDFGTGLMMICSYGDEEDVRLFLELDLKPKVLIDENG 309
                                    5889***********************************************999998665 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 ?    5.5   0.0    0.0069       9.5      22      48 ..      57      83 ..      53      87 .. 0.93
   2 ?    3.0   0.0     0.038        52     251     281 ..     542     572 ..     528     592 .. 0.81
   3 ?   -2.5   0.0       1.9   2.6e+03      62      96 ..     616     650 ..     604     653 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0069
                                   --BHHHHHHHHHHHHHHHHHHHTT-EE CS
                   tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdv 48
                                   + h+G a  +  +D+++r+++ +gY+v
  gi|118431600|ref|NP_148179.2| 57 KWHVGGAAHYTQIDMIARYFRLKGYNV 83
                                   57************************9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                                    TBE--TTTT---BHHHHHTTS-HHHHHHHHH CS
                   tRNA-synt_1e 251 gekmsksLknfitikdvlkkfdprqlRllll 281
                                    g+ m ksL+n+i  + ++ k+ + ++R+  +
  gi|118431600|ref|NP_148179.2| 542 GRPMHKSLGNVIDPEPIIAKYGGDAFRFWAA 572
                                    677***********************98644 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.9
                                    HHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----S CS
                   tRNA-synt_1e  62 ikrareeeksvkelaekfieefkkdleaLnvlkpt 96 
                                    +++a+e +k + +la+++ e+  k++ +L+v +p 
  gi|118431600|ref|NP_148179.2| 616 LEKATEVDKAFLALADEYLEAADKAYGELDVYEPA 650
                                    578999999999******************99875 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.2      0.08   1.1e+02      35      46 .]     179     190 ..     176     190 .. 0.84
   2 ?    2.5   0.0      0.15     2e+02       3      16 ..     424     437 ..     423     443 .. 0.79
   3 ?    3.9   0.0     0.053        73       3      17 ..     451     465 ..     450     474 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.08
                        zf-IS66  35 hirpkyaCpcCe 46 
                                      rp+++Cp+C+
  gi|118431600|ref|NP_148179.2| 179 AERPVRWCPRCK 190
                                    579********5 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                        zf-IS66   3 tCpcCGgllkpige 16 
                                    tC +CG++l+p ++
  gi|118431600|ref|NP_148179.2| 424 TCEKCGAKLVPEPG 437
                                    7******7777655 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.053
                        zf-IS66   3 tCpcCGgllkpiged 17 
                                    +Cp CG++ + ++++
  gi|118431600|ref|NP_148179.2| 451 SCPRCGAPRRYLKGE 465
                                    7*****976777666 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0063       8.7       2      14 ..     186     198 ..     185     203 .. 0.86
   2 ?   -0.7   0.0      0.66   9.1e+02       4      16 ..     355     367 ..     352     371 .. 0.81
   3 ?    2.1   0.0     0.089   1.2e+02      15      26 ..     418     429 ..     410     429 .. 0.83
   4 ?    0.6   0.6      0.26   3.6e+02       2       6 ..     452     456 ..     448     460 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0063
                       zf-TFIIB   2 CPkCqdeleeser 14 
                                    CP+C+++l e+e 
  gi|118431600|ref|NP_148179.2| 186 CPRCKTTLAEAEI 198
                                    ********98775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.66
                       zf-TFIIB   4 kCqdeleesergg 16 
                                    +C+++l+++ r++
  gi|118431600|ref|NP_148179.2| 355 RCKTPLQIIHRRE 367
                                    8******988865 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.089
                       zf-TFIIB  15 ggveidyCpqCr 26 
                                     ++++++C++C+
  gi|118431600|ref|NP_148179.2| 418 TEIPLWTCEKCG 429
                                    589********7 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.26
                       zf-TFIIB   2 CPkCq 6  
                                    CP+C+
  gi|118431600|ref|NP_148179.2| 452 CPRCG 456
                                    66665 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 ?   -0.2   0.1      0.62   8.6e+02       3      11 ..     185     193 ..     183     195 .. 0.73
   2 ?    6.9   0.1    0.0039       5.4       3      17 ..     424     438 ..     423     440 .. 0.83
   3 ?    1.1   0.2      0.26   3.5e+02       3      10 ..     451     458 ..     450     464 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.62
                                    E-SSS--EE CS
                 zf-C4_Topoisom   3 kCPkCggdL 11 
                                     CP C+  L
  gi|118431600|ref|NP_148179.2| 185 WCPRCKTTL 193
                                    699998766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0039
                                    E-SSS--EEEEEE-S CS
                 zf-C4_Topoisom   3 kCPkCggdLvlkrgk 17 
                                    +C+kCg++Lv   g+
  gi|118431600|ref|NP_148179.2| 424 TCEKCGAKLVPEPGR 438
                                    7********976665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.26
                                    E-SSS--E CS
                 zf-C4_Topoisom   3 kCPkCggd 10 
                                     CP Cg++
  gi|118431600|ref|NP_148179.2| 451 SCPRCGAP 458
                                    6*****75 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.18   2.5e+02      25      36 ..     182     193 ..     175     196 .. 0.69
   2 ?    1.1   0.2      0.32   4.4e+02      26      35 ..     422     431 ..     415     435 .. 0.73
   3 ?    4.3   2.9     0.032        45       8      34 ..     425     457 ..     423     461 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                    Zn-ribbon_8  25 plta.CPeCgsev 36 
                                    p +  CP+C+ ++
  gi|118431600|ref|NP_148179.2| 182 P-VRwCPRCKTTL 193
                                    4.445****8754 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.32
                    Zn-ribbon_8  26 ltaCPeCgse 35 
                                    l +C +Cg++
  gi|118431600|ref|NP_148179.2| 422 LWTCEKCGAK 431
                                    5568888885 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.032
                    Zn-ribbon_8   8 CeeCghefe.....vlqsisdaplta.CPeCgs 34 
                                    Ce+Cg +         ++ +++p+ + CP+Cg+
  gi|118431600|ref|NP_148179.2| 425 CEKCGAKLVpepgrYYRPWAEEPPWDsCPRCGA 457
                                    888888777777775555566666666****98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.17   2.4e+02       5      11 ..     186     193 ..     184     197 .. 0.78
   2 ?    1.2   0.1      0.19   2.6e+02       5      13 ..     353     361 ..     352     362 .. 0.85
   3 ?    1.8   0.2      0.12   1.7e+02      19      26 .]     425     432 ..     424     435 .. 0.69
   4 ?    5.8   0.4    0.0069       9.5       4      11 ..     451     458 ..     450     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                    zf-ribbon_3   5 CPnCGa.p 11 
                                    CP+C++ +
  gi|118431600|ref|NP_148179.2| 186 CPRCKTtL 193
                                    99999866 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                    zf-ribbon_3   5 CPnCGapls 13 
                                    C++C++pl+
  gi|118431600|ref|NP_148179.2| 353 CWRCKTPLQ 361
                                    *****9876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                    zf-ribbon_3  19 CpyCGtkl 26 
                                    C +CG+kl
  gi|118431600|ref|NP_148179.2| 425 CEKCGAKL 432
                                    77777765 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0069
                    zf-ribbon_3   4 rCPnCGap 11 
                                    +CP+CGap
  gi|118431600|ref|NP_148179.2| 451 SCPRCGAP 458
                                    7*****97 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 ?    3.1   0.1      0.11   1.6e+02       2      11 ..     183     192 ..     182     205 .. 0.81
   2 ?   -3.0   0.3       9.1   1.3e+04       3       8 ..     351     356 ..     342     366 .. 0.57
   3 ?    2.0   0.1      0.25   3.4e+02       3      13 ..     423     433 ..     421     447 .. 0.71
   4 ?    7.4   0.1     0.005       6.8       4      23 ..     451     468 ..     450     471 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.11
                        zf-ISL3   2 phrCPnCgsk 11 
                                    +++CP+C+ +
  gi|118431600|ref|NP_148179.2| 183 VRWCPRCKTT 192
                                    689****987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.1
                        zf-ISL3   3 hrCPnC 8  
                                    ++C +C
  gi|118431600|ref|NP_148179.2| 351 PVCWRC 356
                                    344444 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.25
                        zf-ISL3   3 hrCPnCgsktv 13 
                                    ++C +Cg+k v
  gi|118431600|ref|NP_148179.2| 423 WTCEKCGAKLV 433
                                    89*****9955 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.005
                        zf-ISL3   4 rCPnCgsktvvkhgkkerrv 23 
                                     CP+Cg++ ++ +g  e+rv
  gi|118431600|ref|NP_148179.2| 451 SCPRCGAPRRYLKG--ETRV 468
                                    5************9..7776 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 ?    1.0   0.0      0.25   3.4e+02       4       9 ..     184     189 ..     183     198 .. 0.84
   2 ?    0.5   0.1      0.37     5e+02       8      18 ..     427     437 ..     425     439 .. 0.84
   3 ?    5.2   0.5     0.012        17       6      12 ..     452     458 ..     452     466 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                  zf-NADH-PPase   4 rFCgrC 9  
                                    r+C+rC
  gi|118431600|ref|NP_148179.2| 184 RWCPRC 189
                                    899999 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                  zf-NADH-PPase   8 rCGaptepaeg 18 
                                    +CGa+ +p++g
  gi|118431600|ref|NP_148179.2| 427 KCGAKLVPEPG 437
                                    79999999886 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.012
                  zf-NADH-PPase   6 CgrCGap 12 
                                    C+rCGap
  gi|118431600|ref|NP_148179.2| 452 CPRCGAP 458
                                    ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (823 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 5011.17
//
Query:       gi|14601639|ref|NP_148180.1|  [L=176]
Description: hypothetical protein APE_1807 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1296.74
//
Query:       gi|14601640|ref|NP_148181.1|  [L=163]
Description: hypothetical protein APE_1808 [Aeropyrum pernix K1]
Scores for complete 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   55.5   7.1    1.6e-14   53.6   7.1    1.7  1  YdjM          LexA-binding, inner membrane-associated putativ
  ------ inclusion threshold ------
       0.49   10.4   5.3       0.26   11.4   1.5    2.3  2  COPI_assoc    COPI associated protein


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   7.1   1.7e-18   1.6e-14       1     167 [.       1     151 [.       1     157 [. 0.75

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.7e-18
                          YdjM   1 MdgltHallGaalglalaallgaake.avllavavlg.AllPDiDhpsstlgrklgllskklaklvgHRgftHSllflall 79 
                                   M    H+ +++a+++++ + l  +     ++ ++++g ++lPD+D     l+ ++    +       HR  tH l + +++
  gi|14601640|ref|NP_148181.1|   1 MNRDGHFGMAMAIVFGAYSVLDIKSTeSLIIGFLIVGlSTLPDVD-----LALEI----A-------HRKYTHNLAASIVA 65 
                                   66679****************99877555555555669*******.....55454....3.......************** PP

                          YdjM  80 alvlllllrlfgrsalrlgll..lllg...vlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltllsrrglvale 155
                                   +l+l ++l   g +   lg++  +++g   v++H+l+Dllt + ++ +wP+s +kv+l+l+   +    +   +r ++ l 
  gi|14601640|ref|NP_148181.1|  66 GLLLGAVLEMGGFK--GLGFIegFVAGftaVWIHILGDLLTYMEFQPFWPISRRKVALKLFKSSNRT--V---NRAMATLG 139
                                   *********99999..55555557777878999******************9655555555553333..2...23444366 PP

                          YdjM 156 lvllvlylviil 167
                                    ++++ y++  +
  gi|14601640|ref|NP_148181.1| 140 SAIMIYYFITHF 151
                                   666665555444 PP

>> COPI_assoc  COPI associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2     0.085   7.6e+02      94     112 ..      27      45 ..       5      63 .. 0.56
   2 ?   11.4   1.5   2.9e-05      0.26      10      59 ..      68     116 ..      58     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.085
                    COPI_assoc  94 llflvGLvyillhlvpsie 112
                                     +++G++ ++l  +p+++
  gi|14601640|ref|NP_148181.1|  27 ESLIIGFLIVGLSTLPDVD 45 
                                   3455555555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.9e-05
                    COPI_assoc  10 vvgglaillgisqliilfsnflsfilsiYiillgivlillEfrvpfeiyk 59 
                                     g+++ ++g+  l  +++ f + +++++i +lg +l ++Ef+ ++ i +
  gi|14601640|ref|NP_148181.1|  68 LLGAVLEMGGFKGL-GFIEGFVAGFTAVWIHILGDLLTYMEFQPFWPISR 116
                                   33444444444443.448**************************998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1284.39
//
Query:       gi|14601641|ref|NP_148182.1|  [L=558]
Description: hypothetical protein APE_1810 [Aeropyrum pernix K1]
Scores for 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-151  504.8   0.0   2.6e-151  504.4   0.0    1.1  1  ABC_ATPase  Predicted ATPase of the ABC class
     0.0034   17.9   0.0     0.0064   17.0   0.0    1.4  1  AAA_23      AAA domain
  ------ inclusion threshold ------
      0.089   11.9   0.1       0.17   10.9   0.1    1.4  1  Parvo_NS1   Parvovirus non-structural protein NS1


Domain annotation for each model (and alignments):
>> 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 !  504.4   0.0  4.4e-155  2.6e-151       3     435 ..       6     432 ..       4     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 504.4 bits;  conditional E-value: 4.4e-155
                                   HHHHHHHHTTTSBGGGGGGGTT-.EESSSEEEEES---SSTTSS-EEEEEEEE--S-HHSSSSGS-HHHHHHHHHHHHHHH CS
                    ABC_ATPase   3 elektlksldgkgykaYkelkge.ydlsdltllidrvqsdpfappSkvrvsvpaavakleeellkskerrvaledfllrkl 82 
                                   ++e++l+++dg+gykaYk+l+g+  dl++l+++++rvq+dpfappS v+v v++           + ++ v ++d+++r l
  gi|14601641|ref|NP_148182.1|   6 SIESVLRRIDGRGYKAYKDLTGAsEDLGRLEIRVTRVQGDPFAPPSVVEVYVRGVSP-------PAGAHPVPYADYVHRLL 79 
                                   6899*******************9*****************************9766.......68899************ PP

                                   HHCC....CTT-SSS--S-EE-----SEE--BSSEEE..--EEE...EEEEEE---EETTSE-HHHHHHHHHTTHHHHHHH CS
                    ABC_ATPase  83 kaelekltsksagsgksgalaidkksqevlersavel..sdeki...elrlrvgLPaegrrilgkeaiellleelpkivek 158
                                   ++ l +++++ +g+g sg+l+++++s+ ++ rsave+  +++++    lr++vgLP++grr+lg++a+ellle+lpk+v +
  gi|14601641|ref|NP_148182.1|  80 SRVLPRYSMRGVGEGGSGKLSVPTPSPIIIPRSAVEAqpRGDGVwslLLRVWVGLPSRGRRVLGRAARELLLERLPKAVLT 160
                                   *************************************775555555599******************************** PP

                                   HTTT-..-HHHHHHHHHHHHHHHHHHCTTTTTT-SEEEETT---SBSSTTS-SB-TS-------GGGEEEEEETTTEEEEE CS
                    ABC_ATPase 159 vllaekldeealeehvelvedqealrkqLeelglvaFvadgsilpResgesdkPlkeavpFesPesleveielpngkkvsG 239
                                   vl+    +   +e+h+++++dqe++r++Le++gl+aFv+dgsilpR++g +++Pl++avpFesP+s++veielp+gk vsG
  gi|14601641|ref|NP_148182.1| 161 VLEGL--KGGGVEQHITVWKDQEHIRSRLEDMGLYAFVGDGSILPRKCGGCWEPLEDAVPFESPPSMRVEIELPSGKVVSG 239
                                   *8866..9************************************************************************* PP

                                   EEE-SSEEEEEE-TTSSHHHHHHHHHHCCSEE-TTSS-TTEEE-TT-EEE---TT--EEEE--TTTB---CCC--STTEEE CS
                    ABC_ATPase 240 mgipkGvtlIvGggfhGKsTLLeAlekGvynhvpgDGRefvvtdktavkiraEdgrsvkgvDispFinnLPegkdttkfst 320
                                   mg+p+Gvt+I+G++fhGK+TL eA+++Gv+nh+pgDGRe+vv+d++++++++E+gr+v++vD spFi++LP g+dt++f+t
  gi|14601641|ref|NP_148182.1| 240 MGLPRGVTTITGPAFHGKTTLAEAIAQGVWNHIPGDGRELVVSDHMLAYVESENGRWVSCVDASPFIEALPGGADTRCFTT 320
                                   ********************************************************************************* PP

                                   SS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCC CS
                    ABC_ATPase 321 edASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdy 401
                                    dASG+ts Aa+i+e++eaga+ +L+DED++AtN+++rD +++e++   k++++pl+d++ ++ kk+g+s+i v++g++ +
  gi|14601641|ref|NP_148182.1| 321 PDASGATSIAASIQEYVEAGASGVLFDEDQTATNIIHRDVWAEEIT--GKRTVNPLSDMAPSM-KKAGLSMIAVASGAMPL 398
                                   **********************************************..9999**********9.***************** PP

                                   TTT-SEEEEEETTEEEE-HHHHHHHHHCHT---- CS
                    ABC_ATPase 402 ldvAdtvilmeeykpkdvtekakeiaeelatkrk 435
                                   l+++d++++m+e++++d+tek  e ++ l +  +
  gi|14601641|ref|NP_148182.1| 399 LESSDRIVVMDEFRARDATEKRMEASRVLREMGY 432
                                   *******************995555444433333 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   1.1e-06    0.0064      19      53 ..     244     278 ..     226     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                        AAA_23  19 kgltlItGpNGaGKTTildAiklaLygetprlsrk 53 
                                   +g+t ItGp   GKTT+ +Ai  + +++ p+ +r+
  gi|14601641|ref|NP_148182.1| 244 RGVTTITGPAFHGKTTLAEAIAQGVWNHIPGDGRE 278
                                   79*************************99987764 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 ?   10.9   0.1   2.9e-05      0.17     109     138 ..     239     268 ..     233     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.9e-05
                     Parvo_NS1 109 kqlgkrntvwfyGpantGktnlaeaIakav 138
                                     + +r+   ++Gpa  Gkt laeaIa++v
  gi|14601641|ref|NP_148182.1| 239 GMGLPRGVTTITGPAFHGKTTLAEAIAQGV 268
                                   556799999******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3977.42
//
Query:       gi|118431601|ref|NP_148183.2|  [L=156]
Description: hypothetical protein APE_1813.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   20.9   8.7    0.00098   18.5   8.7    2.1  1  YdjM      LexA-binding, inner membrane-associated putative hy
     0.0024   18.1   0.3     0.0048   17.1   0.1    1.7  2  DUF1286   Protein of unknown function (DUF1286)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   8.7   1.1e-07   0.00098       1     141 [.       1     132 [.       1     156 [] 0.62

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-07
                           YdjM   1 MdgltHallGaalglalaallgaake...avllavavlg..AllPDiDhpsstlgrklgllskklaklvgHR.gftHSll 74 
                                    M++ tH+++G+ +++++aa  ++         l+ +vl+  ++   iD    +l++++  +++        R  + HS+ 
  gi|118431601|ref|NP_148183.2|   1 MKTETHIVFGLGVAILAAAAAAEIGLgrsC--LVPLVLAsaGIHVAID----RLSHETVQAFS-------LRtRILHSVE 67 
                                    999*******99999988888875557542..3333333224555577....33333333333.......343799**99 PP

                           YdjM  75 flallalvlllllrlfgrsa....lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidp 141
                                     l  l++++ l++  +        l  + ++l++ lsHl+lD+l++ Gv ll       +r+s+++ ++d+
  gi|118431601|ref|NP_148183.2|  68 TLTPLSAAAGLVAGYVAGGSleceLGGAAVFLASGLSHLFLDALNPTGVWLL------GRRISIPMGRWDD 132
                                    9888888888888777766644333333447777***************876......5666666665555 PP

>> DUF1286  Protein of unknown function (DUF1286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   5.4e-07    0.0048       1      68 [.       1      66 [.       1      87 [. 0.76
   2 ?   -2.8   0.0      0.82   7.4e+03     105     112 .]     101     108 ..      93     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-07
                        DUF1286  1 mrlrthyvfsiGlltliesvlvs.nflealilsgi.vsvlgnsliDrlGhkeiktrrGkipvrtPlthtl 68
                                   m+ +th vf +G+  l  ++  +  + ++ ++  +  s  + + iDrl h+ ++     +  rt   h +
  gi|118431601|ref|NP_148183.2|  1 MKTETHIVFGLGVAILAAAAAAEiGLGRSCLVPLVlASAGIHVAIDRLSHETVQ----AFSLRTRILHSV 66
                                   899************99999888555555555555056666788*******777....567777777765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.82
                        DUF1286 105 vGpshmlL 112
                                    +G sh++L
  gi|118431601|ref|NP_148183.2| 101 SGLSHLFL 108
                                    56777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1197.10
//
Query:       gi|118431602|ref|NP_148184.2|  [L=301]
Description: hypothetical protein APE_1814.1 [Aeropyrum pernix K1]
Scores for complete 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   38.0  25.7    1.2e-05   25.3   7.5    2.4  2  VIT1             VIT family
    1.5e-06   28.6   9.6    9.9e-06   26.0   9.2    2.1  1  Rubrerythrin     Rubrerythrin
    7.2e-05   22.6   0.1    7.2e-05   22.6   0.1    2.1  2  COQ7             Ubiquinone biosynthesis protein COQ7
    0.00054   20.2   0.7       0.26   11.5   0.0    2.9  2  Ferritin_2       Ferritin-like domain
  ------ inclusion threshold ------
      0.031   13.1   0.0      0.043   12.6   0.0    1.2  1  FA_desaturase_2  Fatty acid desaturase
      0.076   11.3   0.2        0.1   10.9   0.2    1.2  1  TcdA_TcdB_pore   TcdA/TcdB pore forming domain
       0.64   10.0   3.0       0.49   10.3   0.8    1.8  2  Ferritin         Ferritin-like domain
       0.98    9.2   7.0        1.1    9.1   1.0    2.5  2  RPAP1_N          RPAP1-like, N-terminal
        2.1    7.6   3.9        3.6    6.8   3.9    1.4  1  HlyE             Haemolysin E (HlyE)


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 !   21.0   9.3   1.3e-07   0.00025       6      62 ..     146     201 ..     143     203 .. 0.82
   2 !   25.3   7.5   5.9e-09   1.2e-05     131     214 ..     201     284 ..     196     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                           VIT1   6 lGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdl 62 
                                    lG++D +v ++++ aG  +a++ ++ +  +aGl   l+ aiSM++ +Yl +k e+++
  gi|118431602|ref|NP_148184.2| 146 LGLADAIVEITGVHAGFLGATA-TTLVAGVAGLIVGLSAAISMAAAAYLQAKHESST 201
                                    8*****************7774.5555556666666799*************99875 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 5.9e-09
                           VIT1 131 lasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaa 210
                                    ++ pl +A+++++++++  +   lpy++++s++la+v+s++++++ + +f + ++++ ++s +++++++l + +++aaaa
  gi|118431602|ref|NP_148184.2| 201 TTAPLPSAIATGIAYFFAVVTLALPYFITHSNILAFVASVMLAVALISIFVFYSSVINETSFRREIVENLGVLFGTAAAA 280
                                    46899**********************************999999999******************************** PP

                           VIT1 211 ylig 214
                                    y++g
  gi|118431602|ref|NP_148184.2| 281 YIFG 284
                                    *987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   9.2     5e-09   9.9e-06       9     132 ..      15     128 ..      11     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5e-09
                                    HHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS-------TTGGHHHHHHH CS
                   Rubrerythrin   9 gEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakpkflttaknLee 87 
                                     E+ ++ +Y +l++      ++ +++++e+Ae+E +H ++ ++l+++ + + +   ++  v +++ +   +++t k Le 
  gi|118431602|ref|NP_148184.2|  15 DEYIDYVVYSYLSSIEG--DEENRRILREMAEQEYRHYEFWKELVGS-DCKVNvSRIRLAVLGFMRRIMGVTFTVKFLE- 90 
                                    57778888998888755..89999*********************98.4444447888888888888888888888888. PP

                                    HHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  88 aiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeer 132
                                       + ++e +e+y+ + e++e    e +++++++++e+E +He+ 
  gi|118431602|ref|NP_148184.2|  91 ---RHEKEVIESYKRFLEHLE---GE-TRRRLEEIIEDEISHENY 128
                                    ...445555555555555555...44.9**************986 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   3.6e-08   7.2e-05      29     139 ..      30     128 ..      16     146 .. 0.85
   2 ?   -1.2   0.9      0.76   1.5e+03      64      89 ..     166     191 ..     158     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.6e-08
                           COQ7  29 kkdpelkpllkemleqEkeHlatfeellkerrvrpslllplwkvagfalGaltallGkeaamacteavEtvigeHYneql 108
                                    + d+e +++l+em+eqE +H+++++el+ +      +   + ++   +lG++  ++G    + + e  E+++ e Y++ l
  gi|118431602|ref|NP_148184.2|  30 EGDEENRRILREMAEQEYRHYEFWKELVGSD-----CKVNVSRIRLAVLGFMRRIMGVTFTVKFLERHEKEVIESYKRFL 104
                                    5677789*********************998.....566788888899******************************** PP

                           COQ7 109 releeleeeedkelleiikqfrddEleHldt 139
                                    ++le        e +  ++++ +dE+ H++ 
  gi|118431602|ref|NP_148184.2| 105 EHLE-------GETRRRLEEIIEDEISHENY 128
                                    ***9.......56777888888899999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.76
                           COQ7  64 slllplwkvagfalGaltallGkeaa 89 
                                    ++ + +  vag+++G+ +a+    aa
  gi|118431602|ref|NP_148184.2| 166 TATTLVAGVAGLIVGLSAAISMAAAA 191
                                    67788889999999999887655555 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00013      0.26      33      65 ..      29      60 ..      11     104 .. 0.77
   2 !    5.8   0.7    0.0074        15      33      65 ..     105     136 ..      83     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                     Ferritin_2 33 alldaevrevaeeiakheeaHveflkaaleGaa 65
                                      d+e r++++e+a++e  H+ef+k+ + G+ 
  gi|118431602|ref|NP_148184.2| 29 IEGDEENRRILREMAEQEYRHYEFWKELV-GSD 60
                                   5557889**********************.554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0074
                     Ferritin_2  33 alldaevrevaeeiakheeaHveflkaaleGaa 65 
                                    + l+ e+r+ +eei ++e++H ++l + +  ++
  gi|118431602|ref|NP_148184.2| 105 EHLEGETRRRLEEIIEDEISHENYLISRI-NES 136
                                    578999******************99988.455 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.2e-05     0.043     179     262 ..      30     114 ..      23     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                FA_desaturase_2 179 agdellakicgaiaadEkrHeaaYtrvvekllevdpdeavlaladmmrkk..itmPaallrdgkdeelFeefsavaqrlg 256
                                    +gde   +i++ +a+ E rH+ +++++v    +v+ +++ la+   mr+   +t   ++l + +++e  e+++   ++l+
  gi|118431602|ref|NP_148184.2|  30 EGDEENRRILREMAEQEYRHYEFWKELVGSDCKVNVSRIRLAVLGFMRRImgVTFTVKFL-ERHEKEVIESYKRFLEHLE 108
                                    6899999****************************************9831123333334.4455555666665555555 PP

                FA_desaturase_2 257 vYtard 262
                                      t r 
  gi|118431602|ref|NP_148184.2| 109 GETRRR 114
                                    555555 PP

>> TcdA_TcdB_pore  TcdA/TcdB pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2     5e-05       0.1     215     268 ..     144     196 ..      82     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5e-05
                 TcdA_TcdB_pore 215 lafdsaalvtsavGigaglvGasivaavlsillvplaGlsvGftaLaeafgava 268
                                    +a+  a  +  + G+ ag++Ga+ ++ v++ +++++ Gls+ ++  a a++  +
  gi|118431602|ref|NP_148184.2| 144 IALGLADAIVEITGVHAGFLGATATTLVAGVAGLIV-GLSAAISMAAAAYLQAK 196
                                    57777888999************9999999998875.89999988888777654 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.3   2.5e+03     118     127 ..      26      35 ..       7      58 .. 0.52
   2 ?   10.3   0.8   0.00025      0.49      90     132 ..      91     129 ..      82     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                    HHHHHHHHHH CS
                       Ferritin 118 ledfleeqee 127
                                    l  +  ++e 
  gi|118431602|ref|NP_148184.2|  26 LSSIEGDEEN 35 
                                    4444444322 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00025
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  90 ehekkvteslrelielaeeegDpatadfledfleeqeehewel 132
                                     hek+v+es+++  e+ e e    t+  le+++e++  he+ l
  gi|118431602|ref|NP_148184.2|  91 RHEKEVIESYKRFLEHLEGE----TRRRLEEIIEDEISHENYL 129
                                    79*****************9....9999999999999999877 PP

>> RPAP1_N  RPAP1-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.0   0.00056       1.1       4      18 ..      32      46 ..      32      49 .. 0.95
   2 ?    2.8   0.6      0.05     1e+02       5      34 ..     109     137 ..     105     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00056
                        RPAP1_N  4 deENrarLasMspeE 18
                                   deENr++L++M ++E
  gi|118431602|ref|NP_148184.2| 32 DEENRRILREMAEQE 46
                                   89***********99 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.05
                        RPAP1_N   5 eENrarLasMspeEIeeereeLlesLdPkl 34 
                                     E r+rL++  ++EI +e + L ++++ ++
  gi|118431602|ref|NP_148184.2| 109 GETRRRLEEIIEDEISHE-NYLISRINESI 137
                                    599************999.45666666665 PP

>> HlyE  Haemolysin E (HlyE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.9    0.0018       3.6     179     222 ..     156     200 ..     146     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0018
                                    GGG............SS-HHHHHHHHHHH.....HHHHHHTHHHH CS
                           HlyE 179 vGv.igliftaitafvaGPiGlilalaiafppaiaavvkGkliae 222
                                    +Gv  g++ ++ t++vaG  Gli+ l+ a+  a aa ++ k  + 
  gi|118431602|ref|NP_148184.2| 156 TGVhAGFLGATATTLVAGVAGLIVGLSAAISMAAAAYLQAKHESS 200
                                    444224555677899****************99999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1450  (0.0808746); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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):               9  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 2131.06
//
Query:       gi|118431603|ref|NP_148185.2|  [L=444]
Description: fumarate hydratase [Aeropyrum pernix K1]
Scores for 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-86  288.7   0.1    7.5e-86  288.3   0.1    1.1  1  Lyase_1        Lyase
    1.6e-08   34.8   3.9    1.8e-08   34.6   0.3    3.1  4  FumaraseC_C    Fumarase C C-terminus
  ------ inclusion threshold ------
      0.055   13.0   0.1       0.12   12.0   0.0    1.6  2  Lant_dehydr_C  Lantibiotic biosynthesis dehydratase C-term
       0.26   11.3   1.7         11    6.2   0.1    3.3  3  DUF2148        Uncharacterized protein containing a ferredoxi
       0.41   10.6   2.0         10    6.1   0.8    2.9  3  RadC           RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.3   0.1   2.1e-89   7.5e-86      13     308 ..      14     311 ..       2     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 288.3 bits;  conditional E-value: 2.1e-89
                                    HHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHH CS
                        Lyase_1  13 iftersrenfrlseedikalaalkkaaakanvdl....keeaaaiikaldevleegklddqfvlkviqegsgtavnmnln 88 
                                    ++ +r++e++ +        +++k +aakan++l    ++ a+ai++a+ ev+e gk+ d++v++v+q+gsgt +nmn+n
  gi|118431603|ref|NP_148185.2|  14 NTGTRFPERIVWA------IGMVKYSAAKANMELglldEKRASAIMQAALEVAE-GKHSDKIVVDVFQTGSGTGLNMNVN 86 
                                    5555555555555......89999999999999999******************.************************* PP

                                    HHHH....HHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEE CS
                        Lyase_1  89 evig....ellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAt 164
                                    evi+    e+ g  v+pnd+v+++qSsnD++pTa+rla+++a+  +L+p le++i++l     +++ vvk+GrThl+dA 
  gi|118431603|ref|NP_148185.2|  87 EVIAerasEIAGVDVHPNDHVNMSQSSNDVIPTAIRLAAASAVLSELVPSLETIINSLGSAEAKYARVVKPGRTHLRDAL 166
                                    ****99999999******************************************************************** PP

                                    EEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST.EESSSHHHHHHC-H CS
                        Lyase_1 165 Pvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp.vkapnsfeavsdrD 243
                                    Pvt+gqe+ a+ +a+ +d+ +++e+l + ++e+  ggtavgtg+na+pe+ ++ ++ la+ tg+p  +a+ +f+a++  +
  gi|118431603|ref|NP_148185.2| 167 PVTFGQEMGAFKDAFSKDLAMVREAL-EAVLEVPLGGTAVGTGINAHPEYPRRAVSILAEKTGIPvKPAASRFRAMRLVT 245
                                    **************************.9999999999******************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHH CS
                        Lyase_1 244 avvellgalkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlElltgvag 308
                                    ++++l +a++ +a++L ++++Dlrl+ sg+ +g+ e++++++ pGSS+MPgKvNPv+lE+  ++a+
  gi|118431603|ref|NP_148185.2| 246 DLAMLTAAVRSVAIDLWRLSQDLRLMYSGPfTGIAEVEIPQEVPGSSMMPGKVNPVTLEAAMQAAS 311
                                    ************************************************************888775 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.94   3.4e+03      33      48 ..      39      54 ..      34      58 .. 0.72
   2 ?   -3.3   0.0       3.7   1.3e+04      21      34 ..     224     237 ..     223     242 .. 0.78
   3 ?   -2.8   0.0       2.4   8.7e+03      12      33 ..     304     325 ..     304     329 .. 0.83
   4 !   34.6   0.3   5.2e-12   1.8e-08       1      53 [.     381     431 ..     381     432 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.94
                                   HHTT-.-HHHHHHHT- CS
                    FumaraseC_C 33 lelgllteeeldelld 48
                                   +elgll+e++  ++++
  gi|118431603|ref|NP_148185.2| 39 MELGLLDEKRASAIMQ 54
                                   6888888887776654 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.7
                                    HHHHT--HHHHHHH CS
                    FumaraseC_C  21 Alkegktlreavle 34 
                                    A k+g++++ a+ +
  gi|118431603|ref|NP_148185.2| 224 AEKTGIPVKPAASR 237
                                    67999999988865 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.4
                                    HHHHHHHHHHHHHT--HHHHHH CS
                    FumaraseC_C  12 ekAakIAkeAlkegktlreavl 33 
                                    e+A + A  A++ + +l +a l
  gi|118431603|ref|NP_148185.2| 304 EAAMQAASYAIALDSSLVQASL 325
                                    5788899999999999998876 PP

  == domain 4  score: 34.6 bits;  conditional E-value: 5.2e-12
                                    GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHHH CS
                    FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekMt 53 
                                    L+T  +p+IGYekAa++ +  + eg+++rea  + gl  +e +++lld ek++
  gi|118431603|ref|NP_148185.2| 381 LITLVAPIIGYEKAAEVSRMLY-EGRSIREALKAVGL-GDEAIEKLLDLEKLV 431
                                    79**************987666.5************7.8999*********98 PP

>> Lant_dehydr_C  Lantibiotic biosynthesis dehydratase 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      0.12     162     234 ..     121     193 ..     105     252 .. 0.83
   2 ?   -2.8   0.0         1   3.6e+03     245     262 ..     364     381 ..     342     402 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHSSSS-HHHHH..HHHHHHHHHHHHTSTTHHH.HHHHHHHHHHHTHHHHHHHHHHHHHHHH-SSS CS
                  Lant_dehydr_C 162 lalqlvdvllstfgldleekvdlleryaeaflaefsdtkkalrealdrkyraqrealearlravlaaaaepes 234
                                    + l++++++ls + ++le+ +++l ++++++++ ++++ + lr+al   + +++ a+++++++ la+++e+ +
  gi|118431603|ref|NP_148185.2| 121 IRLAAASAVLSELVPSLETIINSLGSAEAKYARVVKPGRTHLRDALPVTFGQEMGAFKDAFSKDLAMVREALE 193
                                    334445777**********************************************************997644 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHH CS
                  Lant_dehydr_C 245 laewaerlrelrrrleal 262
                                    +++ +er+rel +r++al
  gi|118431603|ref|NP_148185.2| 364 VEPRVERMRELAERSQAL 381
                                    445567777777777777 PP

>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.003        11      32      60 ..      30      60 ..      23      64 .. 0.87
   2 ?    2.3   0.0     0.047   1.7e+02      11      35 ..     249     273 ..     241     281 .. 0.85
   3 ?   -1.4   0.0      0.69   2.5e+03       8      26 ..     308     326 ..     304     338 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.003
                        DUF2148 32 vmysvGaaAkslgllke..asvvlgiplsvs 60
                                   v ys+++a ++lgll+e  as ++  +l+v+
  gi|118431603|ref|NP_148185.2| 30 VKYSAAKANMELGLLDEkrASAIMQAALEVA 60
                                   78**************988888888888775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.047
                        DUF2148  11 DlGiAlgsavkvaadlrvDnRvmys 35 
                                     l  A+ s++   ++l+ D R mys
  gi|118431603|ref|NP_148185.2| 249 MLTAAVRSVAIDLWRLSQDLRLMYS 273
                                    4678999999999***********9 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.69
                        DUF2148   8 kaiDlGiAlgsavkvaadl 26 
                                    +a   +iAl+s   +a+ l
  gi|118431603|ref|NP_148185.2| 308 QAASYAIALDSSLVQASLL 326
                                    5555666666666665543 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.8    0.0029        10      56      87 ..      85     116 ..      68     131 .. 0.78
   2 ?    0.4   0.0      0.17   5.9e+02      53      75 ..     114     136 ..     111     143 .. 0.87
   3 ?    1.8   0.0     0.063   2.3e+02      34      68 ..     325     361 ..     302     365 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0029
                                    HHHHHHTT-SEEEEEEE-TTS--S--HHHHHH CS
                           RadC  56 fkealklnAaavilaHnhPsgdlepSeeDiel 87 
                                    ++e+++++A+++  ++ hP+ +++ S++  ++
  gi|118431603|ref|NP_148185.2|  85 VNEVIAERASEIAGVDVHPNDHVNMSQSSNDV 116
                                    4577888*************988888765444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                                    HHHHHHHHHTT-SEEEEEEE-TT CS
                           RadC  53 revfkealklnAaavilaHnhPs 75 
                                    ++v+ +a++l Aa+ +l    Ps
  gi|118431603|ref|NP_148185.2| 114 NDVIPTAIRLAAASAVLSELVPS 136
                                    578999*************9999 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.063
                                    EEEEEEEEESTT-..GGGCSHHHHHHHHHHTT-SEEE CS
                           RadC  34 liadeelseGtln..stlvdprevfkealklnAaavi 68 
                                    l+++ els G      ++v + e+++eal++ A  vi
  gi|118431603|ref|NP_148185.2| 325 LLGEFELSMGLPLagYAAVRQAEIVAEALRKTAGLVI 361
                                    5566666666533226789999*********998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3292.55
//
Query:       gi|118431604|ref|NP_148186.2|  [L=142]
Description: hypothetical protein APE_1817.1 [Aeropyrum pernix K1]
Scores for complete 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-42  143.3   0.1    4.3e-42  143.1   0.1    1.0  1  DUF2286   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2286  Uncharacterized protein conserved in archaea (DUF2286)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.1   0.1   2.4e-46   4.3e-42       1     134 [.       2     136 ..       2     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 2.4e-46
                        DUF2286   1 kvlvikaeegkiaskeivegdleevvkevakealkeWnpeesDfivlrdklelelklplkpelydklkelsl.sregnea 79 
                                    kv vi+ae+g+++++ ++e++leevvk++a++al+eW+p +sDf+v+rd++e+++  ++++++++ l+  +  + eg e+
  gi|118431604|ref|NP_148186.2|   2 KVAVIRAEHGRVEESLVFEARLEEVVKDMARHALEEWDPGSSDFLVIRDDIEVTVVGDVEEDVLKELEAQGRvEGEGGET 81 
                                    799**********************************************************999999888778******* PP

                        DUF2286  80 ivklPvyvisfdnewidedtyvdkkvyvvapyiddeakkeleeeaaevtkeekee 134
                                    +v +P+y+isfdne+id+++y+dk+++v+ap++++ +k+ele++aa++t++++  
  gi|118431604|ref|NP_148186.2|  82 RVLVPIYYISFDNEMIDDENYIDKRILVIAPLVYKGFKDELEAHAASMTAPPQRP 136
                                    **************************************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1070.76
//
Query:       gi|14601646|ref|NP_148187.1|  [L=127]
Description: 50S ribosomal protein L7 [Aeropyrum pernix K1]
Scores for 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-33  112.0   0.3      1e-32  111.7   0.3    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    3.9e-05   23.5   0.4    8.5e-05   22.4   0.2    1.7  2  PELOTA_1        PELOTA RNA binding domain
  ------ inclusion threshold ------
      0.066   13.3   0.0      0.069   13.2   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 !  111.7   0.3   1.7e-36     1e-32       2      94 ..      18     110 ..      17     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 1.7e-36
                                   HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSE CS
                Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsa 82 
                                   +++e++k a+++g++++G++e+tka+erg aklv++Aedv+p+e++ +l+ lc ek++pyv+v+skk+LGe++g ++++++
  gi|14601646|ref|NP_148187.1|  18 KAYEAVKRARETGRIKKGTNETTKAVERGLAKLVVIAEDVDPPEIVMHLPLLCDEKKIPYVYVPSKKRLGEAAGIEVAAAS 98 
                                   789****************************************************************************** PP

                                   EEEEESTTTHHH CS
                Ribosomal_L7Ae  83 laikdegdskdl 94 
                                   +ai+++gd++ l
  gi|14601646|ref|NP_148187.1|  99 VAIIEPGDAETL 110
                                   ********9987 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.2   1.4e-08   8.5e-05      16      71 ..      26      83 ..      14      94 .. 0.87
   2 ?   -1.4   0.0      0.36   2.2e+03      17      29 ..      97     109 ..      86     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-08
                      PELOTA_1 16 iedinliKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                   +++ +iK g  E+T+++ R   + v+++++ +  + + hl lL++ek++p++ vp++
  gi|14601646|ref|NP_148187.1| 26 ARETGRIKKGTNETTKAVERGLAKLVVIAEDVDppEIVMHLPLLCDEKKIPYVYVPSK 83
                                  567889**********************99888655689*************999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                      PELOTA_1  17 edinliKPgigEa 29 
                                    ++  i Pg +E+
  gi|14601646|ref|NP_148187.1|  97 ASVAIIEPGDAET 109
                                   5677788888876 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 ?   13.2   0.0   1.2e-05     0.069      51     111 ..      27      83 ..       7     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                  RNase_P_pop3  51 neeseltvglneivelLecsesddvvllvcnkDtPsvLlsqlpllvavanltvklvqlpks 111
                                    e   +  g ne  +  e  + ++ v+++ + D P  ++ +lpll+  ++  ++ v +p +
  gi|14601646|ref|NP_148187.1|  27 RETGRIKKGTNETTKAVE-RGLAKLVVIAEDVD-PPEIVMHLPLLCDEKK--IPYVYVPSK 83 
                                   344568889999999999.77777788888777.888899*******999..666666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 896.13
//
Query:       gi|14601647|ref|NP_148188.1|  [L=363]
Description: tRNA pseudouridine synthase D [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.3   0.0    2.4e-11   43.1   0.0    3.2  3  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   1.3e-15   2.4e-11      25     178 ..      37     172 ..      33     192 .. 0.80
   2 !   14.3   0.0   7.7e-07     0.014     255     299 ..     220     266 ..     175     298 .. 0.80
   3 !    6.7   0.0   0.00015       2.8     372     412 ..     305     346 ..     283     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.3e-15
                          TruD  25 FiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisirkvepeelealei 105
                                   F+V E  +++    +++  ++++ v+kr   t ++++ l+r lg   +  ++aG+KD+ +v+ Q++s+++++ +   +++ 
  gi|14601647|ref|NP_148188.1|  37 FRVVES-RVDW---EERRGWVLYLVRKRLLSTPTAASVLSRLLGC--RLYSYAGLKDACSVSWQHVSLYRCRRRPA-RVKA 110
                                   777776.3333...2456789999********************9..6789*******************887774.4666 PP

                          TruD 106 kdvele.vvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileeleekggvPNyfGvQRFGsrrpvthl 178
                                    + ++e ++ + +  +  G ++GN F ir++               +++    g +P  +G QRFG  rp++h+
  gi|14601647|ref|NP_148188.1| 111 YNGRMEaWLLKRGVYVYPGGHKGNMFSIRLETR---G------GCRASR---LGWIPAHYGPQRFGVFRPNSHI 172
                                   6666651566778899**************992...2......233333...456******************7 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.7e-07
                          TruD 255 lpknLqrlFvhAyqSylFNrvlseRlerglpldep..veGDvvifae 299
                                   l ++L ++  +A +Sy+FNr+l + +e g ++ +    e D+v+ ++
  gi|14601647|ref|NP_148188.1| 220 LGQRLDSIIAEALRSYIFNRALTRAIELGASFWSLaeFEADTVCGSK 266
                                   778999999********************998764115678888765 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.00015
                          TruD 372 lsskGtrRaillrvedlelsaeede.ltleFsLpkGsYATvv 412
                                   l s+G +R++l +v + +++  +d+ l ++  Lp+G +AT+ 
  gi|14601647|ref|NP_148188.1| 305 LPSRGGWRPLLYPVCRYRCRRVGDSeLSIHLHLPPGAFATIA 346
                                   4589***********88888776655**************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2813.82
//
Query:       gi|14601648|ref|NP_148189.1|  [L=470]
Description: oxidoreductase [Aeropyrum pernix K1]
Scores for 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   0.1    9.7e-10   38.4   0.1    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    2.4e-07   30.7   6.1    1.8e-06   27.8   6.0    2.1  1  DAO             FAD dependent oxidoreductase
    2.5e-07   30.8   1.7    2.5e-07   30.8   1.7    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.5e-07   29.3   2.9    4.3e-06   26.1   3.0    2.1  2  FAD_binding_2   FAD binding domain
    1.4e-05   24.6   1.5    2.2e-05   23.9   1.5    1.3  1  FAD_binding_3   FAD binding domain
    1.9e-05   24.0   1.4    3.3e-05   23.1   1.4    1.4  1  GIDA            Glucose inhibited division protein A
      2e-05   24.0   1.5    2.1e-05   23.9   0.3    1.6  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00023   20.5   0.4    0.00038   19.8   0.4    1.2  1  Thi4            Thi4 family
    0.00029   21.4   2.3     0.0019   18.7   0.9    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00037   19.3   0.6    0.00053   18.8   0.6    1.2  1  HI0933_like     HI0933-like protein
     0.0018   17.7   1.6     0.0036   16.6   1.6    1.4  1  Amino_oxidase   Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.059   12.4   1.5        0.1   11.6   1.5    1.3  1  Lycopene_cycl   Lycopene cyclase protein
        1.8    7.4   6.1       0.15   10.9   0.9    1.7  2  Trp_halogenase  Tryptophan halogenase


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 !   38.4   0.1     7e-13   9.7e-10       1      47 [.       5      51 ..       5     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 7e-13
                  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdi 47
                                  DvvVvGGg  G++AA++ a +G +v+Lve r+ lGGl++ gl   + 
  gi|14601648|ref|NP_148189.1|  5 DVVVVGGGHNGLVAALTLALHGIRVALVEARDQLGGLSSDGLSLGVR 51
                                  9***************************************9976555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   6.0   1.3e-09   1.8e-06       1     183 [.       5     253 ..       5     278 .. 0.45

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-09
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGGSSEEEEESSSSTHHSTH....................... CS
                           DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSgrnsgllhsglrylpeas....................... 55 
                                   dvv++GGG  Gl +A+ La +g  V+l+e++d++g   + g + g+ ++ ++                             
  gi|14601648|ref|NP_148189.1|   5 DVVVVGGGHNGLVAALTLALHGirVALVEARDQLGGlSSDGLSLGVRYPRVA-----Yalglfpedlarflgidlknytvl 80 
                                   9**********************************32333333344444333.....133345666677777777777777 PP

                                   .........................................HHHHHHHHHHHHHHHHHHH...........HSSTTSEEEE CS
                           DAO  56 .........................................elarlslealeelreleee...........lgididyrrt 84 
                                                                                    +le +r+ ++e           ++    +rr+
  gi|14601648|ref|NP_148189.1|  81 tdpswvvvdslsgetvfrwwlsrdalrrefvekglpeseagM----FVGLLESWRRCSGEiifsirppsleEA-SERLRRC 156
                                   777776655555554443333333333333333322221110....111111111111111111111110000.0112333 PP

                                   EEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.ST...TTSEEEE..ETTEEEEEHHHHHHHHHHHHHHT CS
                           DAO  85 Gllslaadeeelealdkllallleagldaelldaeevrelepa.lp...gllgalf..ypdtgqvdpakltaalaraaeal 159
                                   G  +la+  +  e++dk l++ll+  l   ll+     e ep+ ++    + g+++   p  g+   a l+  l ++a+++
  gi|14601648|ref|NP_148189.1| 157 GGEQLAS--AFYERFDKTLGRLLPRELWG-LLTYP-GYESEPGaTSllhLWNGGVWmqLPR-GW---APLLLDLEEKAREH 229
                                   3333321..12333333333332111110.11111.1122222211232334443322333.44...44455577777777 PP

                                   T-EEEESECEEEEEEEETCEEEEE CS
                           DAO 160 Gveilegtevtgleeedgkvwgve 183
                                   Gv++++g     ++ + g+v+gve
  gi|14601648|ref|NP_148189.1| 230 GVDVFRGLGPAVIRVKAGRVQGVE 253
                                   777777733333333445666663 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 !   30.8   1.7   1.8e-10   2.5e-07       1      38 [.       8      45 ..       8      62 .. 0.89
   2 ?   -3.3   0.0       7.9   1.1e+04      28      37 ..     436     445 ..     435     455 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.8e-10
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                  +vG+G  GlvaA +La +g++v l+e+rd+lGG +++ 
  gi|14601648|ref|NP_148189.1|  8 VVGGGHNGLVAALTLALHGIRVALVEARDQLGGLSSDG 45
                                  8********************************98875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.9
                                   SSSSSGGG-E CS
                 NAD_binding_8  28 rdrlGGraas 37 
                                   ++++GG+++ 
  gi|14601648|ref|NP_148189.1| 436 SSHPGGQVSG 445
                                   5799999875 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   3.0   3.1e-09   4.3e-06       1      36 [.       5      40 ..       5      49 .. 0.93
   2 ?    0.8   0.0      0.14     2e+02     141     182 ..     216     257 ..     145     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.1e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  Dv+V+G+G  GL+AAl++a +G +va+ve  ++ gg
  gi|14601648|ref|NP_148189.1|  5 DVVVVGGGHNGLVAALTLALHGIRVALVEARDQLGG 40
                                  9*****************************999988 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET CS
                 FAD_binding_2 141 hallarlvesarkagvdfqerteadeLivedgrvtGavvenp 182
                                     ll  l e+ar++gvd++  +  + + v+ grv G++v  +
  gi|14601648|ref|NP_148189.1| 216 APLLLDLEEKAREHGVDVFRGLGPAVIRVKAGRVQGVEVGGK 257
                                   4577889999***********9999999999*****999754 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   1.5   1.6e-08   2.2e-05       2      35 ..       4      37 ..       3      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.6e-08
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                  +dV++VG+G  Gl++al L+ +G+rv lve r++
  gi|14601648|ref|NP_148189.1|  4 YDVVVVGGGHNGLVAALTLALHGIRVALVEARDQ 37
                                  79****************************9875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   1.4   2.4e-08   3.3e-05       1      39 [.       5      42 ..       5      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.4e-08
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--S CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaels 39
                                  dv+V+GgGh G+ AAl++a  G++v+L+ +  d+++ ls
  gi|14601648|ref|NP_148189.1|  5 DVVVVGGGHNGLVAALTLALHGIRVALV-EARDQLGGLS 42
                                  79*************************9.7778887765 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 !   23.9   0.3   1.5e-08   2.1e-05       1      33 [.       4      36 ..       4      54 .. 0.89
   2 ?   -3.1   0.0       2.5   3.5e+03     190     233 ..     223     266 ..     222     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.5e-08
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                  +dvvv+GgG+ Gl aaltla +g++v+lve+++
  gi|14601648|ref|NP_148189.1|  4 YDVVVVGGGHNGLVAALTLALHGIRVALVEARD 36
                                  69***************************7544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                   HHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 190 eealekeGvevklgtsvkeidgngeklevvledgeeidadlvvv 233
                                   ee+ +++Gv+v  g  +  i+ +  +++ v+  g++++a  vv+
  gi|14601648|ref|NP_148189.1| 223 EEKAREHGVDVFRGLGPAVIRVKAGRVQGVEVGGKVLEAGRVVY 266
                                   78889999999888888666666667777777777788877776 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4   2.8e-07   0.00038      18      57 ..       4      42 ..       2      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.8e-07
                                  EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                          Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                   Dvv+vG+G  GL aa +la + +++va++e++  +GG +
  gi|14601648|ref|NP_148189.1|  4 YDVVVVGGGHNGLVAALTLALH-GIRVALVEARDQLGGLS 42
                                  59********************.**********9999955 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.9   1.4e-06    0.0019       2      35 ..       6      39 ..       5      46 .. 0.93
   2 ?    1.0   0.0      0.47   6.5e+02      46      78 ..     222     254 ..     221     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  vvvvGgG  gl +A +la +g +V +ve++d+l 
  gi|14601648|ref|NP_148189.1|  6 VVVVGGGHNGLVAALTLALHGIRVALVEARDQLG 39
                                  8*******************************97 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                                   HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                     Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvkl 78 
                                   l+ek +++g++v  +  ++ i+ ++  v++v++
  gi|14601648|ref|NP_148189.1| 222 LEEKAREHGVDVFRGLGPAVIRVKAGRVQGVEV 254
                                   6899**********9999999988877998876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.6   3.8e-07   0.00053       1      36 [.       4      39 ..       4      40 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-07
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                  +dv+v+GgG  Gl aA+++a +g rV+l+e+ ++lg
  gi|14601648|ref|NP_148189.1|  4 YDVVVVGGGHNGLVAALTLALHGIRVALVEARDQLG 39
                                  59*****************************99987 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.6   2.6e-06    0.0036       3      28 ..      15      40 ..      15      46 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                                  HHHHHHHHHHTTEEEEEEESSSSSBT CS
                 Amino_oxidase  3 GLaaArqLlsaGfdVtvlEardrvGG 28
                                  GL+aA +L+ +G +V ++Eard++GG
  gi|14601648|ref|NP_148189.1| 15 GLVAALTLALHGIRVALVEARDQLGG 40
                                  9************************* PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.5   7.4e-05       0.1       1      36 [.       5      38 ..       5      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.4e-05
                 Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                  Dvvv+G+G  gl  A  l  a  g++v l+ea ++l
  gi|14601648|ref|NP_148189.1|  5 DVVVVGGGHNGLVAALTL--ALHGIRVALVEARDQL 38
                                  9*****************..***********98875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   0.00011      0.15       1      34 [.       5      35 ..       5      40 .. 0.91
   2 ?   -2.0   0.4      0.87   1.2e+03     160     200 ..     222     261 ..     221     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                  ++v+vGGG  G +aA +la ++   ++v lve+ 
  gi|14601648|ref|NP_148189.1|  5 DVVVVGGGHNGLVAALTLALHG---IRVALVEAR 35
                                  69****************9988...99****985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.87
                                   HHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE- CS
                Trp_halogenase 160 LrrvaearGvtrvegkvvevqldedgrveslrledgrevea 200
                                   L++ a ++Gv++ +g    v   + grv+++++  g+++ea
  gi|14601648|ref|NP_148189.1| 222 LEEKAREHGVDVFRGLGPAVIRVKAGRVQGVEV-GGKVLEA 261
                                   6788999*********99999999*******99.7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3449.41
//
Query:       gi|14601649|ref|NP_148190.1|  [L=102]
Description: DNA/RNA-binding protein albA [Aeropyrum pernix K1]
Scores for 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   67.2   0.7    1.1e-18   66.8   0.7    1.1  1  Alba      Alba
  ------ inclusion threshold ------
      0.013   15.4   2.9       0.28   11.1   2.9    2.1  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 !   66.8   0.7   1.2e-22   1.1e-18       2      66 ..       8      70 ..       7      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.2e-22
                                  EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                          Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                  e+++++ +p+m+yv+++l+ L ++++++Vv+ka+Gr+I++Av+ +ei+++rf  + +++++++++
  gi|14601649|ref|NP_148190.1|  8 EVRIGR-KPVMNYVLAILTTLMEQGTNQVVVKARGRNINRAVDAVEIVRKRFA-KNIEIKDIKID 70
                                  79****.**************9******************************6.67*****9986 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 ?   11.1   2.9   3.2e-05      0.28      59     136 ..      30      93 ..      24      94 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.2e-05
                         Rpp20  59 lkkeeVfvkatGrAiekalsvgrwfqekeeykvrvetgsVevvDdivedeeekankaaededeeepetrtRwvsmvev 136
                                   +  ++V+vka Gr i++a+   +  +++  ++ ++e + ++       d++e       + ++ e +trtR vs++e+
  gi|14601649|ref|NP_148190.1|  30 QGTNQVVVKARGRNINRAVDAVEIVRKR--FAKNIEIKDIK------IDSQE------IEVQTPEGQTRTRRVSSIEI 93 
                                   56789**************988888776..55555555444......33322......23467888999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 825.18
//
Query:       gi|14601650|ref|NP_148191.1|  [L=385]
Description: hypothetical protein APE_1824 [Aeropyrum pernix K1]
Scores for complete 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-103  345.4   0.0   3.2e-103  345.2   0.0    1.0  1  DUF763           Protein of unknown function (DUF763)
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.21   11.0   0.0    1.4  1  Methyltransf_19  S-adenosyl methyltransferase
       0.16   10.6   0.1       0.21   10.3   0.1    1.1  1  Glt_symporter    Sodium/glutamate symporter


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 !  345.2   0.0  5.4e-107  3.2e-103       1     311 [.       3     342 ..       3     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 345.2 bits;  conditional E-value: 5.4e-107
                        DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkealkse 81 
                                   G+adLpLh+gkvP+w+l+ m++L++ i+++ive +g++ +++ l+dP+wFq+++n++GmdWdsSGsTtv+l++l+++  se
  gi|14601650|ref|NP_148191.1|   3 GVADLPLHSGKVPPWMLKVMERLARSIARAIVEIHGPDAVVRGLADPYWFQAFNNAIGMDWDSSGSTTVLLAVLRKVSLSE 83 
                                   89******************************************************************************* PP

                        DUF763  82 elgilvaGGkGkksrktpeeleklaeklgldeeklvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviqQGmneeer 162
                                   +lg++v+GGkG+++r +++e+e+la+++g+d++kl  +s+ + +v n++lqdgy+ Y+ha++ se+g ++ +qQGmn e  
  gi|14601650|ref|NP_148191.1|  84 DLGFIVVGGKGRRMRGIDSEVEALADRVGIDASKLLGFSQAAGRVSNVLLQDGYSPYIHAVVASETGLMVAVQQGMNVEAG 164
                                   ********************************************************************************* PP

                        DUF763 163 lARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekkl...... 237
                                   l+RRYh      ++ veep +g++g  +++ vln v++es+eark+++dl++e+++++++ + e++++++g+ +l      
  gi|14601650|ref|NP_148191.1| 165 LSRRYHV----DRESVEEPFRGVSGILSHSGVLNAVASESKEARKLYVDLAREGASRIERMVLEASRMVSGAPTLldymdr 241
                                   ******4....6899*********************************************************999999999 PP

                        DUF763 238 ...............klpakhev.....lekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPv.. 296
                                                  + p  + v     ++k le ++++ p d ++ll+++g++pk +raLalva++iyg ++s++DPv  
  gi|14601650|ref|NP_148191.1| 242 hpgashrnasggprsSKPYYKPVpidsrTRKYLEMLADNPPVDEQDLLTAPGLTPKVVRALALVADIIYGVPTSHRDPVst 322
                                   99988888888888733444444777789**************************************************** PP

                        DUF763 297 .....kysfavGgKdgvPyp 311
                                         y+++vGgKdgvPy+
  gi|14601650|ref|NP_148191.1| 323 plnpfVYAYSVGGKDGVPYR 342
                                   *******************7 PP

>> Methyltransf_19  S-adenosyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.5e-05      0.21      13      64 ..     323     376 ..     314     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.5e-05
               Methyltransf_19  13 phsaRvydylLGGkdn..ypvDreaaeallkalpelvkvaranRaflrRavrvl 64 
                                   p    vy y +GGkd   y  Dr+ ae++  al e+v+ ar  R+   Ra r l
  gi|14601650|ref|NP_148191.1| 323 PLNPFVYAYSVGGKDGvpYRFDRRTAERVVLALEEAVELARLGRDEKLRALRRL 376
                                   566679*********644999***********************9999998876 PP

>> Glt_symporter  Sodium/glutamate symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   3.5e-05      0.21      29     128 ..      33     129 ..      18     159 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.5e-05
                 Glt_symporter  29 LkkfniPepvvgGlivallllllkkisglelefdaslqdvlmlaffttiGLsanlkllkkGGkvllvfllvvailiviqnl 109
                                   + +++ P++vv Gl     + +++  + + +++d+s  ++++la    + Ls +l  +  GGk   +  +  + +  + + 
  gi|14601650|ref|NP_148191.1|  33 IVEIHGPDAVVRGLADPYWFQAFN--NAIGMDWDSSGSTTVLLAVLRKVSLSEDLGFIVVGGKGRRMRGI-DSEVEALADR 110
                                   566788*********999999999..6788999******************************9887654.5667788899 PP

                 Glt_symporter 110 vGvslasllgldpllGlla 128
                                   vG+  ++llg + + G ++
  gi|14601650|ref|NP_148191.1| 111 VGIDASKLLGFSQAAGRVS 129
                                   9********9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); 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:                         3  (0.000167327); expected 0.2 (1e-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: 2921.45
//
Query:       gi|118431605|ref|NP_148192.2|  [L=376]
Description: hypothetical protein APE_1825.1 [Aeropyrum pernix K1]
Scores for 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-47  160.1   0.0    7.3e-47  160.0   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
    8.4e-06   25.4   0.1    2.6e-05   23.8   0.1    1.9  2  DAGK_cat    Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.0   0.0   8.1e-51   7.3e-47       2     292 .]       6     375 ..       5     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: 160.0 bits;  conditional E-value: 8.1e-51
                                    EEEEESSC.........................GGTCSHHHHHHHHHHHCT.-.....EEEEECCGGCCSSSTT--HHHH CS
                     NAD_kinase   2 vgivvnpi.........................kkeaieraeevarwLlda.ls...rvlevtveeklgeslaeaaefrs 52 
                                    +g++vnp                          +  a  ra+  ++ L d  +s   +v  +++ + +ges+a++a++  
  gi|118431605|ref|NP_148192.2|   6 IGLIVNPLagvggrlgfkgsdgaygiralmmgaDLVAPRRARAFLESLDDElASkgiQVKLLLPPGRMGESVAREAGRLR 85 
                                    78999999999999999999999999999877766677777777777777754466666667999********9988766 PP

                                    TTTT--.................EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SE..E CS
                     NAD_kinase  53 evisvl.kkvkttd.........dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltef..e 120
                                     v+ +  + v   d         dt++ +++  +++vdl++++GGDGTa+d+  +++  + Pvlg++ Gvk+++++f  +
  gi|118431605|ref|NP_148192.2|  86 AVKVETvPCV---DpriwpttahDTIRCARTI-ENEVDLLVFAGGDGTARDILNAVDM-RLPVLGIPSGVKVYSGVFavN 160
                                    6554330333...2346998888998888877.9***********************5.********************* PP

                                    GGGHHHHHHHHHHT-SEEEEEEEEE...............................EEEEETTE......EEEEEEESSE CS
                     NAD_kinase 121 peaaaellekllegeirvekrevld...............................avimrskgeediadiviensvlne 169
                                    p+ aa++ +++leg++r+e+r v+d                                ++  ++g edia + +e+  ++ 
  gi|118431605|ref|NP_148192.2| 161 PRSAARVVTAFLEGRARLEERPVVDvdeeefrrdrlvlrtfgkllvpvaegvvespKTLAGGEGVEDIARFFAEELYRDC 240
                                    ******************************************999999999998888888888888************** PP

                                    EEEEESSSSS-EE..EEEEETTEEEEEEEESEE.......................EEE-TGGGGTHHHHTT--EE-TT- CS
                     NAD_kinase 170 vviirgpgstlie..lelyvdtelleadqldgl.......................ivstPtGstayslsaGgplisPgv 224
                                     ++i+gpg t++     l+v ++ll++d + ++                       iv++P+G++++ l++G+++isP+v
  gi|118431605|ref|NP_148192.2| 241 TLYILGPGRTVARiaEYLGVRKTLLGVDAVHNKrlvgkdldeeaiieliekhprtvIVLSPIGGQGFILGRGNQQISPRV 320
                                    *************9788*************************************************************** PP

                                    --EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE. CS
                     NAD_kinase 225 lailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfklirl 292
                                     +        ++ ++ ++Vvs+++klr         l++++G+++++   ++++rv  ++ k k++r+
  gi|118431605|ref|NP_148192.2| 321 VR--------KVGKEGIVVVSDPEKLR-----SLGRLRVDTGDDDVDRMMRGYIRVLIGYGKWKMVRV 375
                                    **........*****************.....99******************************9986 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   2.9e-09   2.6e-05      40      91 ..     103     149 ..      45     152 .. 0.88
   2 ?   -4.1   0.0       1.3   1.1e+04       5      24 ..     158     176 ..     154     190 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.9e-09
                                    STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-S CS
                       DAGK_cat  40 epgdakelakeakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlG 91 
                                     ++d  ++a+++++ +vdl+v aGGDGt++ +ln++      ++p+  iP G
  gi|118431605|ref|NP_148192.2| 103 TAHDTIRCARTIEN-EVDLLVFAGGDGTARDILNAVDM----RLPVLGIPSG 149
                                    37788999999999.7********************99....5555556666 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.3
                                    EE-TTCTTTTHHHHHHHCHH CS
                       DAGK_cat   5 ivNpksGkgkgekllrkvre 24 
                                     vNp+s  + +  +l + r 
  gi|118431605|ref|NP_148192.2| 158 AVNPRSAARVVTAFL-EGRA 176
                                    578888755444444.3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2719.21
//
Query:       gi|118431606|ref|NP_148194.2|  [L=274]
Description: hypothetical protein APE_1827.1 [Aeropyrum pernix K1]
Scores for complete 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-08   33.3  21.5    3.2e-08   33.3  21.5    1.6  2  ABC2_membrane  ABC-2 type transporter


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 !   33.3  21.5   1.8e-12   3.2e-08       1     208 [.      12     224 ..      12     226 .. 0.83
   2 ?   -2.0   0.3      0.11   1.9e+03     136     142 ..     244     250 ..     231     261 .. 0.42

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.8e-12
                  ABC2_membrane   1 tqikallkreflqrwrdpslgllwrliqp..lllalvfgtvfgnlgnsedglnrpgllffsvlflafsa....ltsvapv 74 
                                    tq+ ++++   +++wr ++ ++ w +i    ll++++ g++f       d+++ + +lffsv+++++++     ++  + 
  gi|118431606|ref|NP_148194.2|  12 TQFTVMVWAHSKRAWRMRYNLVNWAIIDAlwLLIFVFAGLAFT---PPGDYVEVVPVLFFSVVMWSLMStpvwSIGNWIK 88 
                                    69****************8888888888843444444555555...4667776666666666665532212112344578 PP

                  ABC2_membrane  75 ferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldlsrf.....flflllllltalaasslgl 149
                                    f +  g++++  +s   s+  +++ +++ +l++sll +l + ++ y  +g+++  f      l+ l ll++al+++ ++l
  gi|118431606|ref|NP_148194.2|  89 FYVAIGLMDEVEASSA-SHTLFLATRAIPSLAISLLSSLGVGIMLYSSTGVNI--FsvrspPLLALSLLILALMSTLYAL 165
                                    9999999*99999999.************************************..4445578889999************ PP

                  ABC2_membrane 150 lisalapsfedasqlaslvllpllllsGffipidsm.pkwlqwiaylnPltyavealrsn 208
                                     ++ +  ++++ +    ++ l +++ +G+ + ++++    l+ +a l P+++  e++r++
  gi|118431606|ref|NP_148194.2| 166 GLAFIGLKLKVPAPSLDVMNLAMFFIGGVAVDVETLiW-PLRLVAVLTPYSHPAEIMRYA 224
                                    ************************************85.79*****************86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.11
                  ABC2_membrane 136 lllltal 142
                                    +l l++l
  gi|118431606|ref|NP_148194.2| 244 FLALLTL 250
                                    1111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2014.05
//
Query:       gi|118431607|ref|NP_148195.2|  [L=281]
Description: hypothetical protein APE_1828.1 [Aeropyrum pernix K1]
Scores for complete 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   40.9  19.7    1.4e-10   40.9  19.7    1.6  1  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
      0.048   13.4   0.1       0.18   11.6   0.1    2.0  1  PDR_assoc        Plant PDR ABC transporter associated
        5.1    6.1  27.9         13    4.8  27.9    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9  19.7   2.4e-14   1.4e-10      13     204 ..      29     230 ..      20     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.4e-14
                  ABC2_membrane  13 qrwrdpslgll...wrliqplllalvfgtvfgnlg..nsedglnr.......pgllffsvlflafsaltsvapvfererg 80 
                                       r+++++++   w+ ++ +l + ++gt +g+++      g++        + +++f+++ +     ts ++++ r  g
  gi|118431607|ref|NP_148195.2|  29 ELRRNKQYTIItlsWPYLM-MLSIYILGTSYGSIDyyRHVTGVEDpliflavASAVAFTAVGII--DYTSNSLLWHRWLG 105
                                    5678888885522233322.34455779999976654333333226666644666666666666..999999******** PP

                  ABC2_membrane  81 vl.erelvsplyslsayvlakvlvelpvsllqalifll.ivyflvgldlsrf..flflllllltala.asslgllisala 155
                                    +l +  l+sp     +y+la+ ++  ++s+++  + ++ ++++l gld   f  ++++++++l++++ +++++++ s l+
  gi|118431607|ref|NP_148195.2| 106 TLpYVILASPR--FTVYLLASGTALTVFSVAINYVSIVpLILVLGGLDS--FfrLMVIVAIVLLGMIpLMGIAIVASLLS 181
                                    **999999999..666666666666666666666666646666669999..55755555555555443899********* PP

                  ABC2_membrane 156 psfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavea 204
                                      ++  +++ +++  +llllsG+f+p++ +p+ l w +++ P+ty+ve+
  gi|118431607|ref|NP_148195.2| 182 IVAREEGNVLGFLNPLLLLLSGVFYPVELLPRILEWASKIIPVTYVVES 230
                                    ***********************************************97 PP

>> PDR_assoc  Plant PDR ABC transporter associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     3e-05      0.18      36      62 ..     251     277 ..     242     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                      PDR_assoc  36 allgftiLFNilftlaLtYLnplgksq 62 
                                    a    ++L+N+  +laL+YL+ + +++
  gi|118431607|ref|NP_148195.2| 251 AFALMSLLYNVGGVLALEYLEKVAQRR 277
                                    5556689*************9988766 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 ?    4.8  27.9    0.0021        13     170     338 ..      77     258 ..      33     267 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0021
                ABC2_membrane_3 170 ilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.l.afgl.........gipfgnl 238
                                    +++   ++f+av+i+   ++ ++   ++  +    +   +++ ++l++ + l ++ + + ++++           +f+ l
  gi|118431607|ref|NP_148195.2|  77 LAVASAVAFTAVGIIDYTSNSLLWHRWLGTLPYVILASPRFTVYLLASGTALTVFSVaInYVSIvplilvlggLDSFFRL 156
                                    45555555556666655555554333333344444444455555555555554433222322223333333335555677 PP

                ABC2_membrane_3 239 glllllfllfgl..ayialgyllsslfkns.etaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllr 315
                                    ++++  +ll+++  + ia+++ l s++ ++ +++ +++ +   ll++++g+++p+e lp +l w++ iiP +++ ++ + 
  gi|118431607|ref|NP_148195.2| 157 MVIVAIVLLGMIplMGIAIVASLLSIVAREeGNVLGFLNP---LLLLLSGVFYPVELLPRILEWASKIIPVTYVVESAKL 233
                                    7766444444432266666666666666552555555555...5667888888888999******************988 PP

                ABC2_membrane_3 316 li.tgdplweil.lsliilalfavv 338
                                    ++ + +p++ ++ + l + al++++
  gi|118431607|ref|NP_148195.2| 234 VSgFDAPGVKVIyIVLYAFALMSLL 258
                                    8644445555443333333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2006.46
//
Query:       gi|14601655|ref|NP_148196.1|  [L=345]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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   95.5   0.0    5.1e-27   95.1   0.0    1.2  1  ABC_tran  ABC transporter
    1.7e-16   60.9   0.1    9.4e-12   45.3   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0002   21.2   0.0       0.43   10.2   0.0    2.1  2  AAA_15    AAA ATPase domain
  ------ inclusion threshold ------
       0.01   14.5   0.0        1.5    7.4   0.0    2.1  2  AAA_13    AAA domain
      0.029   14.1   0.0      0.052   13.3   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.036   14.8   0.0      0.098   13.4   0.0    1.8  1  DUF4162   Domain of unknown function (DUF4162)
      0.052   13.2   0.0      0.084   12.5   0.0    1.2  1  SRP54     SRP54-type protein, GTPase domain
      0.053   14.0   0.0      0.091   13.3   0.0    1.3  1  AAA_23    AAA domain
       0.12   12.3   0.0       0.21   11.5   0.0    1.3  1  Rad17     Rad17 P-loop 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 !   95.1   0.0   2.5e-30   5.1e-27       1     136 [.      28     174 ..      28     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2.5e-30
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren. 79 
                                   lk vs++++ege++ ++G+nGaGK+t +++l+ ll+p+ Ge ++ g d+ + e+ ++rk+igv+      +  +lt ren 
  gi|14601655|ref|NP_148196.1|  28 LKGVSFSVYEGEIYSFLGPNGAGKTTTVRILSTLLDPDGGEARVAGFDVVK-ERWEVRKRIGVMLSVeRGFYWKLTGRENl 107
                                   799**********************************************99.88899999998877736777788899*** PP

                                   ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e +++i+++l+ +gl++l    +++  +++S G+k r+ lar+llk+p++l+lDEpt
  gi|14601655|ref|NP_148196.1| 108 yyfgriygipqgELKSRIKEVLDLVGLTDLGG--ADKPFEEMSLGMKARLGLARVLLKDPEVLILDEPT 174
                                   *****************************543..33455*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   1.9e-05     0.037       4      24 ..      43      63 ..      40      91 .. 0.76
   2 !   45.3   0.0   4.7e-15   9.4e-12     220     300 ..     130     207 ..      76     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                        AAA_21  4 liGpNgsGKSnLLdaldllar 24
                                  + GpNg+GK++  ++l+ l +
  gi|14601655|ref|NP_148196.1| 43 FLGPNGAGKTTTVRILSTLLD 63
                                  68**************99975 PP

  == domain 2  score: 45.3 bits;  conditional E-value: 4.7e-15
                        AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                   ++v l + +g + p+ e+S G+k  l+l+  ll ++    +l++DEp +gL+P+  r++ +++++l+++g  +++tTH+ +
  gi|14601655|ref|NP_148196.1| 130 DLVGLTDLGGADKPFEEMSLGMKARLGLARVLLKDP---EVLILDEPTLGLDPASARTIRGVIRSLASEGRTIFITTHNMV 207
                                   66666667788889***********9*******999...9***********************999999*********976 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0005         1      25      49 ..      40      64 ..      30      86 .. 0.86
   2 !   10.2   0.0   0.00022      0.43     315     365 ..     163     205 ..     109     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0005
                        AAA_15 25 ltvliGkNnsGKSsilealdlFlnn 49
                                  +  + G+N++GK++ +++l  +l+ 
  gi|14601655|ref|NP_148196.1| 40 IYSFLGPNGAGKTTTVRILSTLLDP 64
                                  56799***************99985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00022
                        AAA_15 315 ekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                   +       ++ +l+++EP + L p   + +   +++la++++  ++itTH+
  gi|14601655|ref|NP_148196.1| 163 K-------DPEVLILDEPTLGLDPASARTIRGVIRSLASEGR-TIFITTHN 205
                                   3.......4589*****************************9.9******8 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00074       1.5      22      39 ..      44      61 ..      38      79 .. 0.88
   2 ?    5.1   0.0    0.0037       7.3     527     571 ..     165     206 ..     158     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00074
                        AAA_13 22 YGwNGaGKTtLSrllrsl 39
                                   G NGaGKTt  r+l+ l
  gi|14601655|ref|NP_148196.1| 44 LGPNGAGKTTTVRILSTL 61
                                  59************9987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0037
                        AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                    ++ ++D P   LD  s   + + i+s +   ++ + +fi THn+
  gi|14601655|ref|NP_148196.1| 165 PEVLILDEPTLGLDPASARTIRGVIRSLA---SEGRTIFITTHNM 206
                                   67999***********************9...9***********7 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.6e-05     0.052      16      50 ..      32      66 ..      26      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                        AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                  ++++ + +++ + Gp+G+GK+T +  +++lL p+ 
  gi|14601655|ref|NP_148196.1| 32 SFSVYEGEIYSFLGPNGAGKTTTVRILSTLLDPDG 66
                                  55565444999*************99999999875 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.9e-05     0.098       1      79 [.     228     326 ..     228     328 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-05
                                   E-HHHHHTTS.-SSEEEEE......-------.........---EEE...E-TTS-EEEEE-..----------------E CS
                       DUF4162   1 GtleeiKrsy.gknrieve......adaeellee.......pgveev...eeeggelelkle..deeaanellkaltsgve 62 
                                   Gt++e+Kr+   + ++e +      a    +++         g ++v   +  +g l+++++   +e a+ +++++t+ ++
  gi|14601655|ref|NP_148196.1| 228 GTPDELKRRVfSSINLEFRvkasghA----AKKFfydvkgeYGNRIVggvTFSDGILTFRVSvnRDEPAEPIIDRITRLAY 304
                                   88999999987888888665444320....222233334434555554424334555555555269999999999954333 PP

                                   .....EEEEEEE---HHHHHHH CS
                       DUF4162  63 .....irsFeeeePsLndIFie 79 
                                        i +++  ePsL+d+F+ 
  gi|14601655|ref|NP_148196.1| 305 qyrfkILEIKALEPSLEDVFVA 326
                                   3567799999**********96 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.2e-05     0.084       4      39 ..      41      76 ..      39      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                                  EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                         SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                  + ++G++GaGKTtt+  L+ ll  +g ++ ++  D+
  gi|14601655|ref|NP_148196.1| 41 YSFLGPNGAGKTTTVRILSTLLDPDGGEARVAGFDV 76
                                  5699**************999998888888777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.6e-05     0.091      20      40 ..      39      59 ..      27      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                        AAA_23 20 gltlItGpNGaGKTTildAik 40
                                   ++ + GpNGaGKTT ++ + 
  gi|14601655|ref|NP_148196.1| 39 EIYSFLGPNGAGKTTTVRILS 59
                                  577899*********988776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.21      32      69 ..      25      62 ..      19      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                         Rad17 32 kewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                   e+lk  +    + +i    GP G gk+t+v++Ls  l
  gi|14601655|ref|NP_148196.1| 25 VEALKGVSFSVYEGEIYSFLGPNGAGKTTTVRILSTLL 62
                                  56666666666666788889**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 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:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2511.95
//
Query:       gi|118431608|ref|NP_148197.2|  [L=335]
Description: glyoxylate reductase [Aeropyrum pernix K1]
Scores for 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-68  227.9   0.0    7.1e-68  227.5   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      2e-39  134.3   0.0    2.3e-39  134.1   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00034   20.8   0.0     0.0011   19.1   0.0    1.8  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0031   17.1   0.0     0.0072   15.9   0.0    1.6  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
       0.04   14.0   0.0       0.12   12.5   0.0    1.7  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
       0.16   12.6   0.1       0.82   10.3   0.0    2.1  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.5   0.0   2.4e-71   7.1e-68       2     178 .]     111     292 ..     110     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.5 bits;  conditional E-value: 2.4e-71
                                    HHHHHHHTTHHHHHHHHHTTCC......HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCH CS
                   2-Hacid_dh_C   2 alllallrrlaeadeevregew......ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeee 75 
                                    al+la++rr+ ead+ vr gew      + +  +lg el+gkt+Gi+G+GrIG++va++ kafgm++i+++rs+k+e  e
  gi|118431608|ref|NP_148197.2| 111 ALILAAARRVVEADHFVRWGEWwrlrtgWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHSRSRKREI-E 189
                                    79********************9999999999*****************************************99777.9 PP

                                    HHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                   2-Hacid_dh_C  76 eelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                    +elg+e+ sle+ll+esDi+s+hlplt+etrhli+++el++mkk+ail+Nt+RG++vd+ aL++aL++g+ia+aalDvfe
  gi|118431608|ref|NP_148197.2| 190 KELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAALDVFE 269
                                    ******************************************************************************** PP

                                    SSSSGTCHHHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 156 eeplpedspllelpnviltPHia 178
                                    eepl++++pl+ ++nv+l PH a
  gi|118431608|ref|NP_148197.2| 270 EEPLNPNHPLTAFKNVVLAPHAA 292
                                    *********************87 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.1   0.0   7.7e-43   2.3e-39       1     134 []       6     324 ..       6     324 .. 0.99

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 7.7e-43
                                    EEEEST.CHHHHHHHHHTTE.EEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB- CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh   1 vlileplreeelellkeegv.evevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvD 76 
                                    v++++++ +e+lell++  + +vev+d   +++ e+ll+ka++adal +  +++++ ++l+++p+L+++a+++vG+Dn+D
  gi|118431608|ref|NP_148197.2|   6 VFVTREVFPEALELLSK--YyDVEVWDkyqPPPYETLLSKAREADALYTLLTDRIDCDLLSQAPRLRIVAQMAVGFDNID 83 
                                    67899999*********..55********9999*********************************************** PP

                                    HHHHHHTT-EEEE-TTTTHHHHHHHH...................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                     2-Hacid_dh  77 ldaakerGilVtnvpgystesvAElt...................................................... 102
                                    ++ a+++Gi Vtn+pg+ te++AE+t                                                      
  gi|118431608|ref|NP_148197.2|  84 VECATRLGIYVTNTPGVLTEATAEFTwalilaaarrvveadhfvrwgewwrlrtgwhpmmmlgvelrgktlgilgmgrig 163
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|118431608|ref|NP_148197.2| 164 srvaeigkafgmriiyhsrsrkreiekelgaeyrsledllresdilsihlpltdetrhligeselklmkktailvntgrg 243
                                    ******************************************************************************** PP

                                    .................................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                    .................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 .................................................aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                                                     +aT+e++ ++a++aaenlvaf++g+ p+n v
  gi|118431608|ref|NP_148197.2| 244 aivdtgalvkalregwiaaaaldvfeeeplnpnhpltafknvvlaphaaSATRETRLRMAMMAAENLVAFAQGKVPPNLV 323
                                    *******************************************************************************9 PP

                                    S CS
                                    x RF
                     2-Hacid_dh 134 n 134
                                    n
  gi|118431608|ref|NP_148197.2| 324 N 324
                                    8 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   3.3e+03      15      40 ..      16      42 ..      15      58 .. 0.67
   2 !   19.1   0.0   3.7e-07    0.0011       2     106 ..     154     257 ..     153     266 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                   HHHHHHTT-EEEEE-SSH.HHHHHHHH CS
                  NAD_binding_2 15 alnllkagykvavynrtk.ekveelva 40
                                   al+ll++ y+v v++  +    e+l++
  gi|118431608|ref|NP_148197.2| 16 ALELLSKYYDVEVWDKYQpPPYETLLS 42
                                   5678999999***99654144444444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.7e-07
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC- CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.lleal 80 
                                    +g++G+G +Gs  a+  ++ g++++ + r+++  +e+ +e    + s+e+l+++ d+  + ++ +++++++i +  l+ +
  gi|118431608|ref|NP_148197.2| 154 LGILGMGRIGSRVAEIGKAFGMRIIYHSRSRK--REIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGEsELKLM 231
                                    79**********************99998844..566666677899**************************9988999* PP

                                    -TT-EEEE-S---HHHHHHHHHHHHH CS
                  NAD_binding_2  81 kkgdilidgstsspedtrelakelke 106
                                    kk +il++++  ++ dt  l k+l+e
  gi|118431608|ref|NP_148197.2| 232 KKTAILVNTGRGAIVDTGALVKALRE 257
                                    ***************99999999876 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   5.6e+03      58      79 ..      44      65 ..      40      79 .. 0.75
   2 !   15.9   0.0   2.4e-06    0.0072       2      91 ..     149     237 ..     148     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                                   HHT-SEEEE-S-HHHHHHHHHH CS
                           IlvN 58 vkkadvvmiliPDelqkevyee 79
                                   +++ad + +l+ D++  +++++
  gi|118431608|ref|NP_148197.2| 44 AREADALYTLLTDRIDCDLLSQ 65
                                   6789999999999988877765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.4e-06
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-..HHHHHHHHHH CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP..Delqkevyee 79 
                                    l+gk++ ++G+G  G   a+  +  g+ +++  r+ ++ ++  ke g e  +++++ +++d++ i +P  De+++ + e+
  gi|118431608|ref|NP_148197.2| 149 LRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHSRSRKREIE--KELGAEYRSLEDLLRESDILSIHLPltDETRHLIGES 226
                                    789****************************9999886665..68899999***********999999767777777766 PP

                                    HTGGG--TT-EE CS
                           IlvN  80 eiepnlkegkal 91 
                                    e++  +k+ ++l
  gi|118431608|ref|NP_148197.2| 227 ELK-LMKKTAIL 237
                                    664.44554444 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 ?   -2.9   0.0       2.1   6.2e+03      93     132 ..      59      98 ..      51     122 .. 0.58
   2 ?   12.5   0.0   3.9e-05      0.12      21     111 ..     149     242 ..     143     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.1
                                    -HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEE CS
                  AdoHcyase_NAD  93 tlehlkkmkddaivcniGhfdseidvaaleanalkkeevk 132
                                      + l++     iv+ +     +idv+  ++ ++ +++  
  gi|118431608|ref|NP_148197.2|  59 DCDLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTP 98 
                                    5555666666667777766666677776666666555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.9e-05
                                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE....-SSSSSSB-HHH CS
                  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvt....ttGnkdiitleh 96 
                                    l Gk+  + G G +G   a+  k++G r+i         +   + G e + le++++++di+      t  ++ +i   +
  gi|118431608|ref|NP_148197.2| 149 LRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHSRSRKREIEKEL-GAEYRSLEDLLRESDILSIhlplTDETRHLIGESE 227
                                    789***************************99999999888776.8999***********98542232567899****** PP

                                    HCCS-TTEEEEE-SS CS
                  AdoHcyase_NAD  97 lkkmkddaivcniGh 111
                                    lk mk++ai+ n G 
  gi|118431608|ref|NP_148197.2| 228 LKLMKKTAILVNTGR 242
                                    ************997 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 ?   10.3   0.0   0.00027      0.82       2      69 ..     154     213 ..     153     237 .. 0.80
   2 ?   -0.8   0.1      0.79   2.4e+03       3      21 ..     244     262 ..     242     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlav 69 
                                    +gi+G+G++g+ +a+   a g     i+   sr+ +  +e+++elg++  +   e++++e+d++ + +
  gi|118431608|ref|NP_148197.2| 154 LGILGMGRIGSRVAEIGKAFG---MRII-YHSRSRK--REIEKELGAEYRS--LEDLLRESDILSIHL 213
                                    89*************888889...7777.4466666..7899999955555..999999999875555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.79
                                    EEETTSHHHHHHHHHHHHT CS
                  F420_oxidored   3 giiGaGnmgealasgllaa 21 
                                    +i+ +G + +al +g++aa
  gi|118431608|ref|NP_148197.2| 244 AIVDTGALVKALREGWIAA 262
                                    67789***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2608.80
//
Query:       gi|14601657|ref|NP_148198.1|  [L=659]
Description: acylamino-acid-releasing enzyme [Aeropyrum pernix K1]
Scores for complete 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-55  186.5   0.0    5.9e-55  186.0   0.0    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    4.3e-08   33.1   0.0    2.8e-05   23.9   0.2    2.3  2  Abhydrolase_1  alpha/beta hydrolase fold
      1e-06   28.5   8.8    6.5e-06   25.9   0.0    5.0  6  PD40           WD40-like Beta Propeller Repeat
    3.9e-06   26.7   0.0     0.0016   18.0   0.0    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
      1e-05   24.9   0.0        0.1   11.8   0.1    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    9.4e-05   21.2   0.0     0.0041   15.8   0.0    2.2  1  AXE1           Acetyl xylan esterase (AXE1)
    0.00077   19.1   0.0      0.002   17.7   0.0    1.7  1  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.011   15.0   0.0       0.65    9.1   0.0    2.1  2  DUF2920        Protein of unknown function (DUF2920)
      0.016   14.7   0.0      0.029   13.9   0.0    1.3  1  Esterase_phd   Esterase PHB depolymerase
        0.2   11.6   0.0        3.4    7.5   0.0    2.1  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   0.0   3.3e-58   5.9e-55       3     211 ..     444     655 ..     442     656 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 3.3e-58
                                   --HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHHHHHHH CS
                  Peptidase_S9   3 fsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakeg.yvdserlaitGgSyGGyltgaal 82 
                                   f +e+q+la++G++v++ n+rGs+gy+e+f+d +++++g  +++ ++++++++ + + + d++r ++tGgSyGGy+t++++
  gi|14601657|ref|NP_148198.1| 444 FIHEFQMLASQGFAVIYSNPRGSDGYSEEFAD-LRGRYGVDDYSELMKVVDEALSDFpQLDPQRGGVTGGSYGGYMTNVIV 523
                                   779*****************************.************************************************ PP

                                   HH-GGG-SEEEEESE---CCCHHCSTTS...THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-TH CS
                  Peptidase_S9  83 nqrpdlFkaavaevpvvdvlrydsdtdl...lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppa 160
                                   + ++++Fkaav +++++++++++ ++d+   +++e    ++p+++ e+y ++sp+  ++n  +++plL+ih+++D r+p++
  gi|14601657|ref|NP_148198.1| 524 T-KTRRFKAAVTQRSCSNWISFYGESDIgwyFAPELISAQEPWRDLEKYVDFSPLFSVEN--IETPLLIIHSTEDFRCPLS 601
                                   *.****************************8888**************************..******************* PP

                                   HHHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHCT- CS
                  Peptidase_S9 161 ealklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkealgk 211
                                    a++l++aL+ kg++++ll+fp+e+H   ++g+p+++v++l+ +++++ke+lg+
  gi|14601657|ref|NP_148198.1| 602 GAIQLFTALKLKGVETRLLVFPGENHnlsRSGTPKRRVARLRAIASWFKEHLGS 655
                                   **************************999999*******************986 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   1.6e-08   2.8e-05       1     104 [.     427     535 ..     427     548 .. 0.72
   2 !    7.6   0.0    0.0015       2.7     194     251 ..     535     628 ..     522     631 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.6e-08
                                   SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH......HHHCTTSSE CS
                 Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri......ldalgddkl 75 
                                   p+++++hG+p++s+ +a    ++ La +gf vi  ++rG++  s   a    +yg +++ + ++ +        +l+ ++ 
  gi|14601657|ref|NP_148198.1| 427 PWILYIHGGPKTSYGYAFIHEFQMLASQGFAVIYSNPRGSDGYSEEFADLRGRYGVDDYSELMKVVdealsdFPQLDPQRG 507
                                   79*********888855555********************66555555555888888888888866211244445566667 PP

                                   EEEEETHHHHHHHHHHHHHGGGEEEEEEE CS
                 Abhydrolase_1  76 tlvGhSmGGmialayaaeyperVkalvll 104
                                    + G+S+GG +      +   r ka v+ 
  gi|14601657|ref|NP_148198.1| 508 GVTGGSYGGYMTNVIVTK-TRRFKAAVTQ 535
                                   799999999886665554.5556655555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0015
                                   HCCHHHHHHHHHC................................THHHHSEEEEEEETTCSSSCH.HHHHHHHHC.HTS. CS
                 Abhydrolase_1 194 ttdsaklllrlre................................lknvlaptlvisgtsDplvpp.kaledlaql.lpk. 239
                                   ++ +++++ +++e                                + n+  p l+i++t+D   p  +a+  +++l l++ 
  gi|14601657|ref|NP_148198.1| 535 QRSCSNWISFYGEsdigwyfapelisaqepwrdlekyvdfsplfsVENIETPLLIIHSTEDFRCPLsGAIQLFTALkLKGv 615
                                   5556666666666666777777788888888888888889999999********************999999999965559 PP

                                   .EEEEEEETCSSS CS
                 Abhydrolase_1 240 .krlvvisdagHl 251
                                     rl+v++++ H+
  gi|14601657|ref|NP_148198.1| 616 eTRLLVFPGENHN 628
                                   99*******9997 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.073   1.3e+02      13      30 ..      21      38 ..      11      51 .. 0.79
   2 !   25.9   0.0   3.6e-09   6.5e-06       4      30 ..      59      85 ..      58      96 .. 0.84
   3 ?   -2.6   0.2       3.3   5.9e+03      12      30 ..     115     133 ..     112     136 .. 0.78
   4 ?    0.1   0.0      0.46   8.3e+02      16      26 ..     195     205 ..     187     208 .. 0.86
   5 ?   -0.7   0.0      0.85   1.5e+03      14      24 ..     240     250 ..     236     250 .. 0.87
   6 ?   -1.9   0.1         2   3.6e+03      20      38 .]     353     371 ..     346     372 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.073
                                  EEEE-TTSSEEEEEEECT CS
                          PD40 13 aPsfSPDGkrlaFsSdRg 30
                                  +Ps+SP G + a+  ++ 
  gi|14601657|ref|NP_148198.1| 21 NPSVSPEGDKVAYLATKA 38
                                  799999999999988776 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 3.6e-09
                                  --SSSS.EEEEEE-TTSSEEEEEEECT CS
                          PD40  4 ltntpgnegaPsfSPDGkrlaFsSdRg 30
                                  ++++  ++ +P++SPDG  +aFs++ +
  gi|14601657|ref|NP_148198.1| 59 PLTGGPYDRCPAWSPDGEIIAFSRTVN 85
                                  5566668*****************977 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.3
                                   EEEEE-TTSSEEEEEEECT CS
                          PD40  12 gaPsfSPDGkrlaFsSdRg 30 
                                   +++ +S  G+++ + S+++
  gi|14601657|ref|NP_148198.1| 115 TSIKWSSQGSMIGYLSRKP 133
                                   6788999999998888765 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.46
                                   E-TTSSEEEEE CS
                          PD40  16 fSPDGkrlaFs 26 
                                   f PD ++++++
  gi|14601657|ref|NP_148198.1| 195 FAPDDNTIVYA 205
                                   99*******97 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.85
                                   EEE-TTSSEEE CS
                          PD40  14 PsfSPDGkrla 24 
                                    +f+P G+++a
  gi|14601657|ref|NP_148198.1| 240 VAFDPRGRYIA 250
                                   58*******97 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 2
                                   SSEEEEEEECT.TCEE.EEE CS
                          PD40  20 GkrlaFsSdRgsGkpd.Iyv 38 
                                   G ++a++  ++  +p  Iy+
  gi|14601657|ref|NP_148198.1| 353 GDTIAYVKMGP-TSPPdIYI 371
                                   88999998888.44444775 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.2e-07    0.0016      52     140 ..     434     543 ..     374     553 .. 0.73
   2 !    6.3   0.0    0.0035       6.2     223     265 ..     579     624 ..     555     627 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.2e-07
                                   H................HHHTT-EEEEEE-TTS.TTS-S---TT...TTTHHHHHHHHHHHHHHC..TTEEEEEEEEEECH CS
                 Peptidase_S15  52 v................fvarGYavVvqdvrGt.ggSeGeftvg...dsdeaedgadvidWlakq..pwsnGkVgmtGiSY 110
                                                    ++++G+av++++ rG+ g+Se + +     + d+ +   +v+d +     +    + g+tG SY
  gi|14601657|ref|NP_148198.1| 434 GgpktsygyafihefqmLASQGFAVIYSNPRGSdGYSEEFADLRgryGVDDYSELMKVVDEALSDfpQLDPQRGGVTGGSY 514
                                   0555555555555566699*************7467888888886777777777777787777766355678889****** PP

                                   HHHHHHHHCTT--TTEEEEEEECE-S-TCC CS
                 Peptidase_S15 111 lGttqllaaatgvpalkaivpeaaisdlyd 140
                                   +G++ +++ + ++++ ka+v + + s++  
  gi|14601657|ref|NP_148198.1| 515 GGYMTNVIVT-KTRRFKAAVTQRSCSNWIS 543
                                   ******9999.99***********999987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0035
                                   HHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEECE CS
                 Peptidase_S15 223 dadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgpw 265
                                    ++++++p+l++++  D      gai+l+ alk +gv  +l++ p+
  gi|14601657|ref|NP_148198.1| 579 SVENIETPLLIIHSTEDFRCPlSGAIQLFTALKLKGVetRLLVFPG 624
                                   4599*************99999*************99999988777 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   5.8e-05       0.1       7     105 ..     429     533 ..     427     538 .. 0.84
   2 !   10.7   0.0   0.00013      0.23     187     234 ..     580     629 ..     577     631 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.8e-05
                   Hydrolase_4   7 vvlvHGlaehsgrya..elaeaLaaqGfavyalDhrGh.Grse.....gkrghvpsfddyvdDlaafvekvkeehpelplf 79 
                                   ++ +HG   +s  ya  + ++ La qGfav+  + rG  G se       r  v++++++++ ++++++ + +  p++   
  gi|14601657|ref|NP_148198.1| 429 ILYIHGGPKTSYGYAfiHEFQMLASQGFAVIYSNPRGSdGYSEefadlRGRYGVDDYSELMKVVDEALSDFPQLDPQR-GG 508
                                   5678888887777762257899***************769999***9955555*************999999999988.58 PP

                   Hydrolase_4  80 llGhSmGGliallyllrypdkvagli 105
                                   + G S GG+++  ++++ ++ +++++
  gi|14601657|ref|NP_148198.1| 509 VTGGSYGGYMTNVIVTKTRR-FKAAV 533
                                   99********9999988888.77766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                   Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHel 234
                                   +++i++Pll++h+++D  ++ +++ +l+ +l+ k  + +l ++pg  H l
  gi|14601657|ref|NP_148198.1| 580 VENIETPLLIIHSTEDFRCPLSGAIQLFTALKLKgvETRLLVFPGENHNL 629
                                   57899***************************997677788888888876 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.3e-06    0.0041      57     203 ..     397     534 ..     376     538 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-06
                                   EEEEEEEGGGEEEEEEEEEES.S...SSSEEEEEEEE-TT--...GGGHHHHHHHHHTT-EEEEEE-TTTS..SSB-SSCC CS
                          AXE1  57 ydltfegvrgarikaklvlPkek...eeklPavvefhGYegs...rgeihdllnyaaaGyavvvmdvRGqggesedkvgsk 131
                                    +l  ++  g  i a+++lP ++   ++ lP ++  hG  ++      ih+    a++G+av+  + RG +g+se+     
  gi|14601657|ref|NP_148198.1| 397 VRLQVQSPLGGSIDAWILLPPDAgecSGCLPWILYIHGGPKTsygYAFIHEFQMLASQGFAVIYSNPRGSDGYSEEFADLR 477
                                   567777888899*****9997542226789*****999766522256799999********************99977766 PP

                                   SS-SSSSTTTTTTSTTT-HHHHHHHHHHHHH.HHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEE CS
                          AXE1 132 gnkakGfiirGlldkeklyyrrvflDavrlv.eivaslpevDeeRvavlGasqGGalalavaalekrikavva 203
                                   g         G++d  +l         +++v e+++++p+ D++R +v+G+s GG ++ ++ +  +r ka+v+
  gi|14601657|ref|NP_148198.1| 478 GR-------YGVDDYSEL---------MKVVdEALSDFPQLDPQRGGVTGGSYGGYMTNVIVTKTRRFKAAVT 534
                                   32.......488885554.........3333168999********************9999888888888775 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06     0.002      88     195 ..     495     635 ..     449     653 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                           DLH  88 ylksvpevstkkvgvvGfCmGGalalllaaevpevdaav.........afYG........................lspek 135
                                   +l  +p+ ++++ gv+G   GG ++ ++ ++  +++aav         +fYG                            +
  gi|14601657|ref|NP_148198.1| 495 ALSDFPQLDPQRGGVTGGSYGGYMTNVIVTKTRRFKAAVtqrscsnwiSFYGesdigwyfapelisaqepwrdlekYVDFS 575
                                   566778888999999999999999999999998899886333333333799999999999999999999999888755668 PP

                           DLH 136 eleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                   +l  +++i++p+l+++ +eD   p + + +l  alk ++v+ +l v+pg  H   +   +
  gi|14601657|ref|NP_148198.1| 576 PLFSVENIETPLLIIHSTEDFRCPLSGAIQLFTALKLKGVETRLLVFPGENHNLSRSGTP 635
                                   9999************************************************76655444 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00036      0.65     155     199 ..     480     524 ..     477     544 .. 0.79
   2 ?    3.6   0.0     0.017        31     280     325 ..     579     625 ..     571     628 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00036
                       DUF2920 155 fGimaAlDiinalkdlvkrfpkeadlpviliGgsyGGYlalLiaK 199
                                   +G+    +++ ++++++  fp+   +   + GgsyGGY++++i  
  gi|14601657|ref|NP_148198.1| 480 YGVDDYSELMKVVDEALSDFPQLDPQRGGVTGGSYGGYMTNVIVT 524
                                   566666778899999999999999899999*********998743 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                       DUF2920 280 sqknkntiyvsyHsekDklapaeeKiqlakilkklgfdveleli.de 325
                                   s +n +t  +++Hs++D   p+   iql ++lk +g + +l ++  e
  gi|14601657|ref|NP_148198.1| 579 SVENIETPLLIIHSTEDFRCPLSGAIQLFTALKLKGVETRLLVFpGE 625
                                   667777999*****************************999988545 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.6e-05     0.029       6     129 ..     414     537 ..     411     548 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                  Esterase_phd   6 ylpp..GarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwyk.dtdraGrGeaavvva 83 
                                    lpp  G   g++p ++ +hG  ++   +a    +++la  +G++v+y +   r   ++  + +   + r G  + + ++ 
  gi|14601657|ref|NP_148198.1| 414 LLPPdaGECSGCLPWILYIHGGPKTSYGYAFIHEFQMLAS-QGFAVIYSNP--RGS-DGYSEEFAdLRGRYGVDDYSELMK 490
                                   5799889999****************************97.6******764..444.444444541567788888777777 PP

                  Esterase_phd  84 lvd.alvdehrvdaarvyvaGlsaGaaladllalhypdvfaavalhs 129
                                   +vd al d  ++d+ r  v+G s G+ +++++  +     aav+  s
  gi|14601657|ref|NP_148198.1| 491 VVDeALSDFPQLDPQRGGVTGGSYGGYMTNVIVTKTRRFKAAVTQRS 537
                                   7653899999*********************9988877778887766 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 ?    7.5   0.0    0.0019       3.4      86     171 ..     555     637 ..     494     648 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                                   TTS-EE-TT-B--TTTGGGCCCB--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S---ST CS
                        BAAT_C  86 knglldivdvlallkeklaekalipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGHliepP 166
                                   +++l+ + + +++l++  +   l+ ve++++p+l++ +++D   p +  + ++   Lk +g +  ++ll +p+  H++   
  gi|14601657|ref|NP_148198.1| 555 APELISAQEPWRDLEKYVDFSPLFSVENIETPLLIIHSTEDFRCPLSGAI-QLFTALKLKGVE--TRLLVFPGENHNLSRS 632
                                   5566666666777777777778999****************988877665.677778877766..7888888888888777 PP

                                   T---- CS
                        BAAT_C 167 yfplc 171
                                    +p  
  gi|14601657|ref|NP_148198.1| 633 GTPKR 637
                                   77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (659 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.25s 00:00:00.87 Elapsed: 00:00:00.39
# Mc/sec: 5127.49
//
Query:       gi|118431609|ref|NP_148199.2|  [L=94]
Description: DNA/RNA-binding protein albA [Aeropyrum pernix K1]
Scores for complete 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-18   64.8   0.5    7.4e-18   64.1   0.5    1.3  1  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 !   64.1   0.5   4.1e-22   7.4e-18       1      65 [.       9      71 ..       9      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 4.1e-22
                                   CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEE CS
                           Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlts 65
                                   n+i V++ +p  +yv +alklL +++++eVv+ka+Gr+I++Av+++e+lk+ f+k+   ++++ +
  gi|118431609|ref|NP_148199.2|  9 NTILVGR-KPTINYVMAALKLLNEEGAPEVVIKARGRNICNAVDTVEMLKNLFIKN-LVIKKVNI 71
                                   89*****.**************9999***************************977.66766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 833.64
//
Query:       gi|118431610|ref|NP_148200.2|  [L=309]
Description: ribose-phosphate pyrophosphokinase [Aeropyrum pernix K1]
Scores for 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-18   65.1   0.0    9.4e-18   64.3   0.0    1.4  1  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    8.4e-14   51.4   0.1    1.8e-13   50.3   0.1    1.5  2  Pribosyltran    Phosphoribosyl transferase domain
    5.6e-10   39.5   0.0    1.2e-08   35.3   0.0    2.1  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
     0.0065   15.9   0.0      0.011   15.3   0.0    1.3  1  UPRTase         Uracil phosphoribosyltransferase


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 !   64.3   0.0   2.1e-21   9.4e-18       6     116 .]      14     126 ..      10     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.1e-21
                 Pribosyltran_N   6 gssskeLaekiakrlgvelgkakvsrfadgEikveieesvrg.kdvfiiqslskpvndnlmelllmidalrrasakrita 84 
                                    gs+s e++e +++++g++l+k+  + f+d+E +v+ie ++ g +  +++qs+ +p++ +l+  ll++dal++a + ri++
  gi|118431610|ref|NP_148200.2|  14 GSASAEFSEGLSRNMGLKLVKPVFKLFPDEEEYVRIEGDISGfTGAIVVQSFERPASRSLVYSLLIADALKEAGVGRIVL 93 
                                    78999************************************9466999******************************** PP

                 Pribosyltran_N  85 ViPylgysrqdrk.ksrepisaklvaklLeaaG 116
                                      Py+gy rqdr   + ep+s + v++ L ++G
  gi|118431610|ref|NP_148200.2|  94 MAPYMGYTRQDRVfLPGEPVSVRAVMRALASSG 126
                                    *****************************9988 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       1.9   8.4e+03     107     124 ..      80      97 ..      78     107 .. 0.66
   2 !   50.3   0.1   4.1e-17   1.8e-13      29     124 ..     167     256 ..     159     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.9
                                    HHHHHCC-BSEEEEEEEE CS
                   Pribosyltran 107 lelLkekgpeevriavlv 124
                                    +++Lke+g+ ++ +++++
  gi|118431610|ref|NP_148200.2|  80 ADALKEAGVGRIVLMAPY 97 
                                    578888888777666655 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 4.1e-17
                                    GGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHH CS
                   Pribosyltran  29 kpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaal 107
                                     ++++v++++g++p++ +la+e +++ + y+ k++ r  g    a+        + dp+gk  ++VDDi++tGgT+  a 
  gi|118431610|ref|NP_148200.2| 167 DNTIIVAPDKGSLPRVERLARETGCRsYGYLVKERDRITGEVRLAK-------STVDPRGKNAIVVDDIISTGGTIALAS 239
                                    6899**********************77788888888888888776.......6679*********************** PP

                                    HHHHCC-BSEEEEEEEE CS
                   Pribosyltran 108 elLkekgpeevriavlv 124
                                    ++L e g+ +v + + +
  gi|118431610|ref|NP_148200.2| 240 QWLLENGANSVFVLAAH 256
                                    ********988666555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.044     2e+02      58     120 ..      30      97 ..      16     118 .. 0.71
   2 !   35.3   0.0   2.6e-12   1.2e-08      80     151 ..     216     287 ..     209     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.044
                                    -------------------EES--TTSE.EEEEEEEE-S-.HHHHH...HHHHHHHTT--EEEEEEEE CS
                 Pribosyl_synth  58 vekslelpellakekppltvvGdvgGri.aiivddliddv.esfva...aaevlkerGaykiyvlath 120
                                    ++ ++ + +l + e   + + Gd++G   ai+v  +   + +s+v     a+ lke G  +i+ +a +
  gi|118431610|ref|NP_148200.2|  30 LKLVKPVFKLFPDEEEYVRIEGDISGFTgAIVVQSFERPAsRSLVYsllIADALKEAGVGRIVLMAPY 97 
                                    55556666777888888899999999653777777655431456542226999*****9999999976 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 2.6e-12
                                    --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHH CS
                 Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqk 151
                                    d  G+ ai+vdd+i    ++  a++ l e+Ga  ++vla+h l   +a +++ ++ +  vv  nt+p++  k
  gi|118431610|ref|NP_148200.2| 216 DPRGKNAIVVDDIISTGGTIALASQWLLENGANSVFVLAAHYLGIGNAEEKMMKAGVSRVVTGNTLPRKPSK 287
                                    6689***************************************************************98754 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.3e-06     0.011     118     156 ..     216     254 ..     193     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                        UPRTase 118 kiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlv 156
                                    +++ ++++++D +i+TGg++a a q L+e+g+++  +l 
  gi|118431610|ref|NP_148200.2| 216 DPRGKNAIVVDDIISTGGTIALASQWLLENGANSVFVLA 254
                                    456788***********************9987544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 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:                        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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2302.79
//
Query:       gi|14601660|ref|NP_148201.1|  [L=350]
Description: methyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-48  163.2   0.0      2e-47  161.4   0.0    1.8  1  UPF0020        Putative RNA methylase family UPF0020
      0.001   18.7   0.0     0.0021   17.7   0.0    1.5  1  Cons_hypoth95  Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.025   14.1   0.0    1.2  1  MTS            Methyltransferase small domain
      0.026   14.2   0.0          6    6.5   0.0    2.1  2  N6_N4_Mtase    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 !  161.4   0.0   4.5e-51     2e-47       1     196 [.     170     343 ..     170     344 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 4.5e-51
                                   -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEE CS
                       UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklyg 81 
                                   +g+R+f++p+pL+++L++a+v+l+++++g +++DP+CG+G+++IEa+llga+++                         ++
  gi|14601660|ref|NP_148201.1| 170 PGRRPFFKPGPLSPRLSRAFVNLSRLQRGGSFADPFCGTGGFAIEACLLGASRI-------------------------AC 225
                                   699**************************************************9.........................6* PP

                                   EES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHHH-TT..- CS
                       UPF0020  82 sDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkrvlrgggr 161
                                    Dld+++v+g+  N+++++  +++ +s+++aakL+l++++vd+i+t+pPYG+++++ ++   +L+++fl+++ +vlr++g+
  gi|14601660|ref|NP_148201.1| 226 GDLDWAMVRGGPLNLSRYCPPGIWFYSAWNAAKLPLSSNSVDSIATDPPYGRSTTTGRMGyLSLTRAFLNTAVEVLRSEGW 306
                                   ***********************************9999********************99******************** PP

                                   EEEEEESSHHHHHCC---..ESEEEEEEETTEEEEEE CS
                       UPF0020 162 lvlltsenkalekaleer..alrkvkeknvklglllk 196
                                   +v++ +++++ e+++e++  ++ kv e++v+++l+++
  gi|14601660|ref|NP_148201.1| 307 IVYAGPTRMSPETLAEDAglRVVKVIEMFVHGSLTRS 343
                                   ******************7777888899999999875 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-07    0.0021      37     130 ..     193     281 ..     180     322 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-07
                                   CCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEE CS
                 Cons_hypoth95  37 aaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdiv 117
                                   +   +g ++ D f+G+G+ ++EA   ga+++ + + d ++v+    nl++    + +  +   ++ +l   +  ++++d +
  gi|14601660|ref|NP_148201.1| 193 SRLQRGGSFADPFCGTGGFAIEACLLGASRIACGDLDWAMVRGGPLNLSRYCPPG-IWFYSAWNAAKL---PLSSNSVDSI 269
                                   4556778899****************************************99887.333433333333...3445689*** PP

                                   EE--SSSTTCH.H CS
                 Cons_hypoth95 118 flDPPyakellie 130
                                     DPPy ++ +  
  gi|14601660|ref|NP_148201.1| 270 ATDPPYGRSTT-T 281
                                   ******99976.3 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.7e-06     0.025      31     136 ..     197     308 ..     186     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTTSTTS-EEEEEE---ST CS
                           MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle...vevvasdvleeveekkfdlivsNPPfh 108
                                   + g+ +D  cG+G  ++++     + ++ + d d++ ++    nl++           ++ +   ++ +++d i + PP+ 
  gi|14601660|ref|NP_148201.1| 197 RGGSFADPFCGTGGFAIEACLLGAS-RIACGDLDWAMVRGGPLNLSRYCPPgiwFYSAWNAAKLPLSSNSVDSIATDPPYG 276
                                   467789999*******999887766.8*******************9998875455567777777889************8 PP

                                   TTCHCH....HHHHHHHHHHHHHHEEEEEEEE CS
                           MTS 109 agkate....lavaeeliaeAkeaLkegGeLl 136
                                   +++ t     l+++++++++A e+L+++G ++
  gi|14601660|ref|NP_148201.1| 277 RSTTTGrmgyLSLTRAFLNTAVEVLRSEGWIV 308
                                   8776642222689****************544 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0013         6     189     214 ..     195     220 ..     161     231 .. 0.78
   2 ?    5.7   0.0    0.0023        11       1      60 [.     266     315 ..     266     343 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0013
                                   S-TT-EEEETT-TTTHHHHHHHHTT- CS
                   N6_N4_Mtase 189 tkkgdivlDpFaGSGtTavaakelgr 214
                                   ++ g++ +DpF+G+G  a++a  lg 
  gi|14601660|ref|NP_148201.1| 195 LQRGGSFADPFCGTGGFAIEACLLGA 220
                                   5779***********99999988876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0023
                                   EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCC CS
                   N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddse 60 
                                   vd i tdpPY+ +                +yl++ + +l+ + +vL   g i+     ++
  gi|14601660|ref|NP_148201.1| 266 VDSIATDPPYGRSTT----------TGRMGYLSLTRAFLNTAVEVLRSEGWIVYAGPTRM 315
                                   68899******9999..........77889999999999999999999999987755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2651.58
//
Query:       gi|118431611|ref|NP_148202.2|  [L=310]
Description: ribonuclease Z [Aeropyrum pernix K1]
Scores for complete 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   50.6   0.1    4.1e-12   46.0   0.1    2.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.7e-07   30.0   0.2    2.3e-06   27.8   0.1    2.0  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.066   12.5   0.0       0.24   10.7   0.0    1.8  2  YcaO           YcaO cyclodehydratase, ATP-ad Mg2+-binding


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 !   46.0   0.1   6.8e-16   4.1e-12       2     200 ..      34     273 ..      33     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 6.8e-16
                                    EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE..EEEEEE.......HHHHHH CS
                  Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk..lplyap.......kgvlav 69 
                                     +L+Dag ++    lr+        ++++id++ +th H DH++g+  l     l+ ++  l+++ +        ++l+ 
  gi|118431611|ref|NP_148202.2|  34 TVLLDAGEGVQIR-LRKV-----GVSPSSIDVLAITHPHGDHINGVAGLLMtmsLQSRRkpLTIISTseslefiSETLEA 107
                                    69*******6433.5555.....567889**************8888887777744444469999773555444555556 PP

                                    CCTTCGHHHCHTT...........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C...................TCC CS
                  Lactamase_B_2  70 leanfvylaleee...........pavnvheldwgesfelgdggleitatparhksgr...................rld 119
                                     ++n+ ++++ ++           p  ++ +++w                 a h+ +                    rld
  gi|118431611|ref|NP_148202.2| 108 TRENLGFEVMLVDaresgvldvgrPSGDRLTIEW---------------ERACHNIESlafklvwtlrpridarileRLD 172
                                    6666666665555444333333333333333333...............3333333333333333334456677999999 PP

                                    E-TTTSEEEEEECTTEE....................EEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT- CS
                  Lactamase_B_2 120 rnagdtlGlriegggkr....................vyyigDtgyipeeigerlggadllllditayeddemir.hmgH 178
                                     +ag+++  +ie+g+ +                    v+y+gDt  ++ ++++ l+g d+l++d t+ ++   ++ + gH
  gi|118431611|ref|NP_148202.2| 173 LKAGPWIRELIEKGRAHvegrivtlkdisasgerkysVAYTGDTSPCT-RVAKFLHGSDILIHDSTLDSSLAREAaERGH 251
                                    9999********666668999999************************.5567*************9999887669**** PP

                                    --STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 179 ltpeeaveaaadlgakrlvliH 200
                                    +t  +a++ a   gak l+l+H
  gi|118431611|ref|NP_148202.2| 252 STSLDAARNALTSGAKLLILFH 273
                                    ********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   3.8e-10   2.3e-06      15      64 ..      32      76 ..      23      94 .. 0.90
   2 ?   -0.3   0.0      0.15   9.2e+02     145     153 ..     210     218 ..     204     273 .. 0.43

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.8e-10
                                   TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGC CS
                    Lactamase_B 15 ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglggl 64
                                   g ++L D+G + +  + +     +g+ p  +d + +TH+H DHi g++gl
  gi|118431611|ref|NP_148202.2| 32 GNTVLLDAGEGVQIRLRK-----VGVSPSSIDVLAITHPHGDHINGVAGL 76
                                   678999999999999975.....*************************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.15
                                    EEEECTTTS CS
                    Lactamase_B 145 vlftGDall 153
                                    v++tGD+++
  gi|118431611|ref|NP_148202.2| 210 VAYTGDTSP 218
                                    667777766 PP

>> YcaO  YcaO cyclodehydratase, ATP-ad Mg2+-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.14   8.2e+02     160     182 ..      99     122 ..      77     131 .. 0.68
   2 ?   10.7   0.0   3.9e-05      0.24     136     186 ..     148     205 ..     145     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.14
                           YcaO 160 peirellerlre.agievrlldat 182
                                    + i e le+ re  g+ev+l da+
  gi|118431611|ref|NP_148202.2|  99 EFISETLEATREnLGFEVMLVDAR 122
                                    667788888888889999999886 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.9e-05
                           YcaO 136 iERdafalawyer.....lplpridlasdpeirellerlre..agievrlldatldlg 186
                                    iE  af l+w+ r       l r+dl++ p+irel+e+ r+  +g+ v l+d+++ ++
  gi|118431611|ref|NP_148202.2| 148 IESLAFKLVWTLRpridaRILERLDLKAGPWIRELIEKGRAhvEGRIVTLKDISASGE 205
                                    56668899998885533222334557777**********9999**********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2374.27
//
Query:       gi|118431612|ref|NP_148203.2|  [L=135]
Description: hypothetical protein APE_1838.1 [Aeropyrum pernix K1]
Scores for complete 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   99.4   1.6      6e-16   58.6   0.2    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 !   40.3   0.1   1.8e-14   3.1e-10       8      55 ..      13      60 ..       7      62 .. 0.86
   2 !   58.6   0.2   3.4e-20     6e-16       1      56 [.      70     125 ..      70     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.8e-14
                                   SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   +++t+ p+t+++e++++m   g s+  VVd d++++Gi+t+rD++r++
  gi|118431612|ref|NP_148203.2| 13 KPLTAAPQTPVREVVKMMYTQGKSAAVVVDQDNRPIGIFTERDVVRVV 60
                                   789***************76664566589****************987 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 3.4e-20
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    V+++mtr++v v+ +++l +al lm+e++v++lPVVd +gklvGi+t + + ++l+
  gi|118431612|ref|NP_148203.2|  70 VEEYMTRNPVAVRDNESLTKALALMIEHRVRHLPVVDQEGKLVGIITASSITEVLK 125
                                    789************************************************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1052.25
//
Query:       gi|118431613|ref|NP_148205.2|  [L=373]
Description: hypothetical protein APE_1840.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); 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: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2751.27
//
Query:       gi|14601665|ref|NP_148206.1|  [L=104]
Description: 30S ribosomal protein S10 [Aeropyrum pernix K1]
Scores for complete 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   92.9   0.0    1.2e-26   92.8   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
  ------ inclusion threshold ------
       0.11   12.3   0.1        0.2   11.4   0.1    1.5  1  NETI           NETI protein


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 !   92.8   0.0   1.3e-30   1.2e-26       1      98 []       6     100 ..       6     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 1.3e-30
                                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHHH CS
                 Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketidt 80 
                                   ri l S++ ++Le++v++i ++a+++gi+++gpvplP kr++v+v + ph++ +k +e++e+++hkRlid+ +a+++++++
  gi|14601665|ref|NP_148206.1|   6 RIWLWSTNVRSLENVVEQIRNIANKTGIRMRGPVPLPVKRLEVPVFRLPHGEgSKYWEHWEMKVHKRLIDL-EADERVLRH 85 
                                   789********************************************************************.6******** PP

                                   HS-...S---SS-EEEEE CS
                 Ribosomal_S10  81 llkllqlnlpegVsvevk 98 
                                   l++   +++pe V +e+k
  gi|14601665|ref|NP_148206.1|  86 LMR---IKVPEDVYIEIK 100
                                   ***...*********996 PP

>> NETI  NETI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.2e-05       0.2      23      45 ..      41      63 ..      33      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.2e-05
                          NETI 23 mPvrRiEkPvFkevkkngkkeie 45
                                  +Pv+R E PvF+  + +g+k  e
  gi|14601665|ref|NP_148206.1| 41 LPVKRLEVPVFRLPHGEGSKYWE 63
                                  69**********98777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 789.67
//
Query:       gi|14601666|ref|NP_148207.1|  [L=437]
Description: elongation factor 1-alpha [Aeropyrum pernix K1]
Scores for complete 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-57  193.5   0.0    3.7e-57  193.0   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.2e-35  121.3   0.2    7.4e-35  119.6   0.1    1.9  2  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    2.5e-16   59.8   1.2    8.3e-16   58.1   1.2    2.0  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.2e-05   25.3   0.1      8e-05   22.7   0.1    2.2  1  MMR_HSR1     50S ribosome-binding GTPase
    0.00011   22.0   0.7    0.00038   20.3   0.7    1.8  1  GTP_EFTU_D4  Elongation factor Tu domain 4
     0.0011   19.7   0.7      0.004   17.8   0.1    1.9  2  Amelogenin   Amelogenin
      0.008   15.9   0.0      0.013   15.2   0.0    1.2  1  MRP-S22      Mitochondrial 28S ribosomal protein S22
  ------ inclusion threshold ------
      0.012   15.7   0.1        3.2    7.8   0.0    2.5  2  Dynamin_N    Dynamin family
      0.022   14.1   0.0      0.055   12.7   0.0    1.6  1  Septin       Septin
      0.061   12.9   0.3       0.66    9.6   0.1    2.2  2  Ras          Ras family
       0.11   12.6   0.0       0.22   11.6   0.0    1.4  1  TetR_C_2     MAATS-type transcriptional repressor, C-terminal
       0.13   11.7   0.2       0.68    9.4   0.0    2.0  2  Arf          ADP-ribosylation factor family
       0.14   12.4   0.3        6.9    6.9   0.1    2.4  2  Roc          Ras of Complex, Roc, domain of DAPkinase


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 !  193.0   0.0   2.7e-60   3.7e-57       1     191 [.       4     222 ..       4     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 2.7e-60
                                   TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHST............HCHSHHHHHHTSCSSCEEEEEETTCS CS
                      GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeerv............lDtlkeErergiTiksaaisleketk 68 
                                   k+++n+++ighvDhGK+TL+++Lly++g i++k+ k+ ee++             lD++keErergiTi+ + +++e  tk
  gi|14601666|ref|NP_148207.1|   4 KPHMNLVVIGHVDHGKSTLVGHLLYRLGYIEEKKLKElEEQAKsrgkesfkfawiLDKMKEERERGITIDLTFMKFE--TK 82 
                                   579*****************************999997333335789999***************************..** PP

                                   SEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESCGSTHHHHHH CS
                      GTP_EFTU  69 kylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKmDrlkaelke 141
                                   ky +++iD+PGH+dF+k++i+g++++D a+lvv+a++G        e qt+e+l la+++g++ iiv++NKmD ++ ++++
  gi|14601666|ref|NP_148207.1|  83 KYVFTIIDAPGHRDFVKNMITGASQADAAILVVSARKGefeagmsTEGQTREHLLLARTMGIEqIIVAVNKMDAPDVNYDQ 163
                                   ***************************************************************************555554 PP

                                   HHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHHHH CS
                      GTP_EFTU 142 iveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealvel 191
                                      e   ++   ++ ++  g++ + ++p++++Sa+kg+++             tl+eal++l
  gi|14601666|ref|NP_148207.1| 164 KRYEFVVSV--LKKFMKGLGYQVD-KIPFIPVSAWKGDNLIerspnmpwyngpTLVEALDQL 222
                                   444433222..2444888899985.*************877677777777777899888876 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 ?   -2.1   0.0       3.5   4.8e+03       6      28 ..     106     127 ..     102     170 .. 0.67
   2 !  119.6   0.1   5.4e-38   7.4e-35       3     111 ..     321     427 ..     319     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.5
                                   CCEEEEEEESSS..SS-BSTT-E CS
                   GTP_EFTU_D3   6 tkfeAqvyilekerhtpitagYr 28 
                                   ++ +A +++++  r++++ ag +
  gi|14601666|ref|NP_148207.1| 106 SQADAAILVVSA-RKGEFEAGMS 127
                                   556677777777.7877777654 PP

  == domain 2  score: 119.6 bits;  conditional E-value: 5.4e-38
                                   EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE- CS
                   GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpiale 83 
                                   + +++feA++ ++ +  +++it gY+pv++++ta+v+ +++e+++kld+kt++v+e++p+f+k Gd++iv+ ++ kp+++e
  gi|14601666|ref|NP_148207.1| 321 TVAEEFEARIFVIWH--PSAITVGYTPVIHVHTASVSSRIIEIKAKLDPKTGQVVEQNPQFLKAGDAAIVRFKPVKPLVVE 399
                                   6789***********..**************************************************************** PP

                                   -TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                   GTP_EFTU_D3  84 kgseypqlGrFaiReggrTvaaGvvtei 111
                                   k+se+pqlGrFa+R+++rTv++G+vt++
  gi|14601666|ref|NP_148207.1| 400 KFSEIPQLGRFAMRDMNRTVGIGIVTDV 427
                                   **************************98 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 !   58.1   1.2   6.1e-19   8.3e-16       1      72 [.     247     312 ..     247     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 6.1e-19
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                   Gtv  grv++G+l++Gd+v++++         v++++s+e++ +++++a++g+n+G+ v+++  +d i++Gd+
  gi|14601666|ref|NP_148207.1| 247 GTVPVGRVETGVLRVGDKVVFMPpG------VVGEVRSIEMHYQQLQQAEPGDNIGFAVRGVSKSD-IKRGDV 312
                                   99*******************8833......46*********************************.*****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 !   22.7   0.1   5.8e-08     8e-05       2      94 ..       9     126 ..       8     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.8e-08
                                   EEEEESTTSSHHHHHHHHH...............T................STEEESSSTTSSSSEEEEEEEETTEEEEEE CS
                      MMR_HSR1   2 vaivGrpNvGKStLinalt...............g................ekaivsdkpgtTrdinegrvklkgkeielv 51 
                                    +++G+   GKStL+  l+               +                +k + +++ g T+d ++ ++++k+  ++++
  gi|14601666|ref|NP_148207.1|   9 LVVIGHVDHGKSTLVGHLLyrlgyieekklkeleEqaksrgkesfkfawilDKMKEERERGITIDLTFMKFETKKYVFTII 89 
                                   689***************977777766666555505555666777676665689999999************9999***** PP

                                   ECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHH CS
                      MMR_HSR1  52 DtpGliegaseekglgkaflaleeadlillvvdaseeklkpld 94 
                                   D pG  +    +  +++ +    +ad+++lvv+a+++++++  
  gi|14601666|ref|NP_148207.1|  90 DAPG--H----RDFVKNMITGASQADAAILVVSARKGEFEAGM 126
                                   ****..3....23466666667789*******99844443322 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.7   2.8e-07   0.00038      21      84 ..     251     312 ..     243     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.8e-07
                                   EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT-E CS
                   GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegdi 84 
                                   vG +v +Gv+++g k++      vGe+++i+ + ++l++a+ G++++ +++g     +ik gd+
  gi|14601666|ref|NP_148207.1| 251 VG-RVETGVLRVGDKVVFMPPGVVGEVRSIEMHYQQLQQAEPGDNIGFAVRGVS-KSDIKRGDV 312
                                   88.9***********9987777****************************9965.667888775 PP

>> Amelogenin  Amelogenin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.9e-06     0.004      13      94 ..     166     249 ..     158     257 .. 0.87
   2 ?   -0.4   0.0       1.1   1.6e+03      63     106 ..     356     398 ..     332     432 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.9e-06
                    Amelogenin  13 ye.vltplkwyqslikhqypsyGyepmgGwlhhavvpvlsqltfqqhpsvhsllhhvvp.klpalqpflvpqqplvpvpgq 91 
                                   ye v++ lk +   ++ q  +  + p++ w  ++++   + ++  + p+    l++++p   p  +p  +p q + ++pg 
  gi|14601666|ref|NP_148207.1| 166 YEfVVSVLKKFMKGLGYQVDKIPFIPVSAWKGDNLIERSPNMPWYNGPTLVEALDQLQPpAKPVDKPLRIPVQNVYSIPGA 246
                                   664678999999999**********************************988887776516899***************98 PP

                    Amelogenin  92 hsl 94 
                                    ++
  gi|14601666|ref|NP_148207.1| 247 GTV 249
                                   765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                    Amelogenin  63 sllhhvvpklpalqpflvpqqplvpvpgqhslipqfqpalggpi 106
                                   s   ++  kl ++   +v q+p     g+ +++  f+p ++  +
  gi|14601666|ref|NP_148207.1| 356 SRIIEIKAKLDPKTGQVVEQNPQFLKAGDAAIVR-FKPVKPLVV 398
                                   3334445555555555666666665555555443.666555444 PP

>> MRP-S22  Mitochondrial 28S ribosomal protein S22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.6e-06     0.013      40      96 ..      33      90 ..      25     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-06
                       MRP-S22 40 ltdeeleeaqekaeekakklLqmpPvlkerkeieev.lsedkelkgldtskyvftDit 96
                                  + +++l+e +e+a+++ k+  ++  +l++ ke +e  ++ d ++ +++t+kyvft i 
  gi|14601666|ref|NP_148207.1| 33 IEEKKLKELEEQAKSRGKESFKFAWILDKMKEERERgITIDLTFMKFETKKYVFTIID 90
                                  6789***********************9999666555******************876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0023       3.2       1      19 [.       9      27 ..       9      31 .. 0.90
   2 ?    5.6   0.0     0.011        15      50     138 ..      40     118 ..      28     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                                  EEEEEBTTTTHHHHHHHHH CS
                     Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                  ++v+G++ +GKS+++ +Ll
  gi|14601666|ref|NP_148207.1|  9 LVVIGHVDHGKSTLVGHLL 27
                                  69************99987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                                   ...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTE CS
                     Dynamin_N  50 avkeelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkad 130
                                   + +e+ k++ k+  +f  + +++++e+e+         ++ +++ +++ ++   t++D PG  +  k   ++++ + +  +
  gi|14601666|ref|NP_148207.1|  40 ELEEQAKSRGKESFKFAWILDKMKEERERGI-------TIDLTFMKFETKKYVFTIIDAPGHRDFVK---NMITGASQADA 110
                                   4555556667777777777777777766655.......23455666677777889******988433...47777777777 PP

                                   EEEEEEET CS
                     Dynamin_N 131 iilavtsa 138
                                   +il+v++ 
  gi|14601666|ref|NP_148207.1| 111 AILVVSAR 118
                                   77776654 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     4e-05     0.055       4      78 ..       6     100 ..       3     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
                                   EEEEEEEEBTTSSCCCCCCTTSSSS----......................--------------S-EEEEEEEEETTCEE CS
                        Septin   4 eftlmvvGesglGkttlintlfetdliee......................ekleeasekkkktveikkkkvvieedgvkl 62 
                                   +++l+v+G+   Gk+tl+  l+ +  + e                        l++ +e+ ++ ++i+ + ++ e +  k 
  gi|14601666|ref|NP_148207.1|   6 HMNLVVIGHVDHGKSTLVGHLLYRLGYIEekklkeleeqaksrgkesfkfaWILDKMKEERERGITIDLTFMKFETK--KY 84 
                                   589***************99987655444478888888888888888776544455555666666666666665555..78 PP

                                   EEEEEE---BSSSSSH CS
                        Septin  63 nltviDtpgfGdavdn 78 
                                    +t+iD pg+ d+v n
  gi|14601666|ref|NP_148207.1|  85 VFTIIDAPGHRDFVKN 100
                                   8899999999999988 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.2   2.8e+02       2      17 ..       9      24 ..       8      36 .. 0.89
   2 ?    9.6   0.1   0.00048      0.66      10     147 ..      48     198 ..      45     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.2
                                  EEEEESTTSSHHHHHH CS
                           Ras  2 lvlvGdsavGKtslll 17
                                  lv++G    GK++l+ 
  gi|14601666|ref|NP_148207.1|  9 LVVIGHVDHGKSTLVG 24
                                  89***********985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                                   SSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTH CS
                           Ras  10 vGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenv 90 
                                    GK s+ + ++ dk kee e  i +d +   ++++ k++ ++i D  G  +f +   +  ++a++++lv +  +   fe  
  gi|14601666|ref|NP_148207.1|  48 RGKESFKFAWILDKMKEERERGITIDLTF--MKFETKKYVFTIIDAPGHRDFVKNMITGASQADAAILVVSARK-GEFEAG 125
                                   69*******************99777665..566788999************999999999*****99988655.446655 PP

                                   HHHHHHHHHHST....TTSEEEEEE.ETTTGGG..........G-SS-HHHHHHHHHHHT.SEEEEEBTTTTC CS
                           Ras  91 kkwveeikrvae....envpivLvG.nKvDlee..........kravsteegeelakelg.lkfletSAktne 147
                                    +   + +++        ++ ++v+ nK+D  +             v ++  + l  +++ ++f+ +SA +  
  gi|14601666|ref|NP_148207.1| 126 MSTEGQTREHLLlartMGIEQIIVAvNKMDAPDvnydqkryefVVSVLKKFMKGLGYQVDkIPFIPVSAWKGD 198
                                   5555555555444444445544443388888776666666544344444445555555555666666666555 PP

>> TetR_C_2  MAATS-type transcriptional repressor, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.22      23      77 ..     109     163 ..      98     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                      TetR_C_2  23 qralleilfhKCEFvgemsavleirkelllaeysrleevlqeciekgllpanldl 77 
                                     a+l +   K EF  +ms++ + r++llla+   +e+++ +  +++    n d 
  gi|14601666|ref|NP_148207.1| 109 DAAILVVSARKGEFEAGMSTEGQTREHLLLARTMGIEQIIVAVNKMDAPDVNYDQ 163
                                   5678899999****************************99988777665555555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.52   7.1e+02      12      34 ..       4      26 ..       1      31 [. 0.84
   2 ?    9.4   0.0   0.00049      0.68      31     138 ..      59     167 ..      55     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.52
                                  TTEEEEEEEESTTSSHHHHHHHH CS
                           Arf 12 kkelrilllGLDnaGKtTilkkl 34
                                  k ++ ++++G    GK+T++ +l
  gi|14601666|ref|NP_148207.1|  4 KPHMNLVVIGHVDHGKSTLVGHL 26
                                  568999****999*****99776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                                   HHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT-CT...THHHHHHHHHHHC CS
                           Arf  31 lkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvDsadre...RleeakeeLkall 108
                                   l k+k+e+      Ti  +  + e+k++ ft+ D  G++   +   +  ++ da i vv + + e    +++  +  ++ll
  gi|14601666|ref|NP_148207.1|  59 LDKMKEERER--GITIDLTFMKFETKKYVFTIIDAPGHRDFVKNMITGASQADAAILVVSARKGEfeaGMSTEGQTREHLL 137
                                   5555555444..4489999999******************99999999***********99876544478888889999** PP

                                   TSGCCTTSEEEEEEE-TTSTTSS-HHHHHH CS
                           Arf 109 eeeelkevallvlaNKqDlpealseeelre 138
                                     +++   +++v  NK+D+p+   +++  e
  gi|14601666|ref|NP_148207.1| 138 LARTMGIEQIIVAVNKMDAPDVNYDQKRYE 167
                                   ******99***********98766655544 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.063        87       2      20 ..       9      27 ..       8      40 .. 0.88
   2 ?    6.9   0.1     0.005       6.9      10     119 ..      48     155 ..      45     156 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.063
                                  EEEESSTTSSHHHHHHCHC CS
                           Roc  2 vvlvGdsgvGKtsllkrfv 20
                                  +v++G    GK++l+ +++
  gi|14601666|ref|NP_148207.1|  9 LVVIGHVDHGKSTLVGHLL 27
                                  799************9886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.005
                                   SSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEEGH CS
                           Roc  10 vGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalailvydsr 90 
                                    GK s+   ++ dk++e+++  i +d++  ++   +       +kk+ + i D  G+ +f + +    ++a++ailv+ +r
  gi|14601666|ref|NP_148207.1|  48 RGKESFKFAWILDKMKEERERGITIDLTFMKF---E-------TKKYVFTIIDAPGHRDFVKNMITGASQADAAILVVSAR 118
                                   68888888899999999998888888865443...2.......35689*************99999999999999999866 PP

                                   H..H......HCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                           Roc  91 s..s......enlkeWlkelkkvagkspvilvgnkiD 119
                                   +  +      e   +    l + +g +++i+ +nk+D
  gi|14601666|ref|NP_148207.1| 119 KgeFeagmstEGQTREHLLLARTMGIEQIIVAVNKMD 155
                                   4112212111112223333455566677888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3091.96
//
Query:       gi|118431614|ref|NP_148208.2|  [L=205]
Description: 30S ribosomal protein S7 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-41  141.4   0.0      2e-41  141.1   0.0    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e
  ------ inclusion threshold ------
      0.098   13.1   0.0       0.16   12.4   0.0    1.4  1  Spa1_C        Lantibiotic immunity protein Spa1 C-terminal do


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 !  141.1   0.0   2.2e-45     2e-41      17     149 .]      64     205 .]      54     205 .] 0.95

  Alignments for each domain:
  == domain 1  score: 141.1 bits;  conditional E-value: 2.2e-45
                                    STTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE- CS
                   Ribosomal_S7  17 kynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevr 92 
                                    k++ ++ve+l+nklm+     Gkk+lA++iv++a+dii  +t+++p++vl++A+en++Pr++++++ +GG+ty+v+v+v+
  gi|118431614|ref|NP_148208.2|  64 KAEVPIVERLMNKLMRpgrnGGKKHLAYNIVKTAFDIIYFETGENPIQVLVKAIENSAPREDTTKITYGGITYRVSVDVA 143
                                    47899*************999*********************************************************** PP

                                    HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                   Ribosomal_S7  93 pkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                    p+Rr+++Al++i+++a   ++++ k+++e+LaeEli Aa+g+  ++a++++ee++r+A ++r
  gi|118431614|ref|NP_148208.2| 144 PQRRVDQALKFIADGArqcAFNNPKPIEECLAEELILAARGDprSYAIRQKEEIERIALSSR 205
                                    ****************888899*******************999**************9876 PP

>> Spa1_C  Lantibiotic immunity protein Spa1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.7e-05      0.16       4      38 ..     124     158 ..     122     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.7e-05
                         Spa1_C   4 edvteitykgkvYeiledtVseeelgeylgviael 38 
                                    ed t+ity+g +Y+++ d  ++ ++++ l +ia+ 
  gi|118431614|ref|NP_148208.2| 124 EDTTKITYGGITYRVSVDVAPQRRVDQALKFIADG 158
                                    899**************************999853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 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:                        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 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1539.41
//
Query:       gi|118431615|ref|NP_148210.2|  [L=156]
Description: hypothetical protein APE_1848.1 [Aeropyrum pernix K1]
Scores for complete 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   34.7   0.1    1.5e-08   34.4   0.1    1.1  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.1   8.2e-13   1.5e-08      28     125 ..      50     151 ..      32     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 8.2e-13
                                    EEE--HHHHHHHHHHHCT---SS--HHHHHHH.HHHHTTEE.EEEEEEEEEET..TEEEEEEEEEET---EEEEE-HHHH CS
                    DNase-RNase  28 pIwigaaeaqaialalegeeppRPlthDLlas.llealgak.vervvItdled..gtfyAelvlrkeeeeleidaRpSDa 103
                                     I ++  ea +++ +  +++ ++ l   L+ s +++   ++ v++vvI+++++  g + A+lvl+++  +l++   pS a
  gi|118431615|ref|NP_148210.2|  50 NIPVEIVEAVNVMKNNIDTPRRQSLFIFLMNSeVFKDAAVNfVKEVVIDEIDQntGLYTATLVLEEDGFKLKLKMIPSHA 129
                                    47777888888888888888888888888864255555444399*******994456********97444********** PP

                                    HHHHHHHT--EEEEHHHHHHH- CS
                    DNase-RNase 104 iaLAlrtgapIyveeevleeas 125
                                    + LAl +g pIyv e++++e+ 
  gi|118431615|ref|NP_148210.2| 130 VYLALIAGRPIYVLEKLVHESY 151
                                    *****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1239.83
//
Query:       gi|14601670|ref|NP_148211.1|  [L=147]
Description: 30S ribosomal protein S12 [Aeropyrum pernix K1]
Scores for 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-47  157.6   0.3      1e-46  157.2   0.3    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 !  157.2   0.3   5.8e-51     1e-46       4     114 .]      35     146 ..      32     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 5.8e-51
                                   -----S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--...... CS
               Ribosom_S12_S23   4 lrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk.gka 83 
                                   l +k k d+legap++rG+vlekv+vea++PnsAlRk+vrv+L kn+k vtaf+p +g + ++dEhdev+++Gi+++ g++
  gi|14601670|ref|NP_148211.1|  35 LDLKRKYDPLEGAPMARGIVLEKVGVEARQPNSALRKCVRVQLVKNKKVVTAFVPRDGGILYVDEHDEVIIEGIGGPrGRS 115
                                   567999**********************************************************************99*** PP

                                   BTTSTTEEEEBETS---TSSSTTTTT----T CS
               Ribosom_S12_S23  84 vkDlpGvrykvvkvagvslkalskykkekpk 114
                                   ++D+pGvry+vv v+gvslkal+ +kk+kp+
  gi|14601670|ref|NP_148211.1| 116 MGDIPGVRYRVVMVNGVSLKALWEGKKQKPR 146
                                   *****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1286.33
//
Query:       gi|14601671|ref|NP_148212.1|  [L=144]
Description: transcription elongation factor NusA-like protein [Aeropyrum pernix K1]
Scores for complete 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-22   78.3   4.1    6.8e-15   54.7   0.1    2.1  2  KH_2      KH domain
      6e-13   48.7   4.9      3e-11   43.2   0.2    2.2  2  KH_5      NusA-like KH domain
    6.7e-09   35.5   1.9    0.00015   21.5   0.2    2.2  2  KH_4      KH domain
    1.4e-07   31.2   1.0     0.0014   18.4   0.1    2.4  2  KH_1      KH domain
  ------ inclusion threshold ------
      0.061   11.8   0.0      0.078   11.5   0.0    1.1  1  Aldedh    Aldehyde dehydrogenase family
       0.12   11.8   0.1       0.22   11.0   0.1    1.4  1  DsbC_N    Disulfide bond isomerase protein N-terminus


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.1   2.3e-18   6.8e-15       3      75 ..      14      98 ..      12     101 .. 0.96
   2 !   25.0   1.5   4.1e-09   1.2e-05      25      59 ..     103     137 ..      98     144 .] 0.87

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.3e-18
                                  HHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC............EEEEEEEE CS
                          KH_2  3 peslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk............VklnivkV 73
                                  ++s++++i++ ++ ++++++++nr+i+ + e++ g++IG+gG+ ik ++++l+k+ie++e++             Vk+++++V
  gi|14601671|ref|NP_148212.1| 14 YISVFHSITGVTAYRCIVDEENNRLIFLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEYSSdlerivknlfpgVKIESINV 96
                                  789****************************************************************************9999 PP

                                  TT CS
                          KH_2 74 kk 75
                                  ++
  gi|14601671|ref|NP_148212.1| 97 RE 98
                                  98 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 4.1e-09
                                   CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                          KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                   ++v+i + e  +g +IGkgG+n+k+ +  l k ++
  gi|14601671|ref|NP_148212.1| 103 KQVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLFG 137
                                   899***************************99996 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.2     1e-14     3e-11       2      69 .]      35      96 ..      34      96 .. 0.96
   2 !    7.5   0.9    0.0014       4.3       5      32 ..     105     127 ..     101     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 1e-14
                          KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                  ++r ++ V +++     +G ++g++G+ ik + + L g++i+vve+s+Dl++ ++n++  ++++s+++
  gi|14601671|ref|NP_148212.1| 35 NNRLIFLVSEGE-----AGRAIGRGGRLIKLLREAL-GKNIEVVEYSSDLERIVKNLFPGVKIESINV 96
                                  589999999999.....*******************.***************************9986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                          KH_5   5 tkvaVkshnpnvdpvGaivgkkGsrika 32 
                                   +++ V +++      Ga++gk+G+++k 
  gi|14601671|ref|NP_148212.1| 105 VVIKVSEDD-----KGAAIGKGGKNVKR 127
                                   445555555.....**********9985 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   1.6e-05     0.048      23      55 ..      30      62 ..      20      65 .. 0.87
   2 !   21.5   0.2   5.1e-08   0.00015       4      52 ..      78     126 ..      75     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                          KH_4 23 eeeeeeveielnvegedlGrvIGkrGrtldAlq 55
                                    +ee++++   v++ + Gr IG+ Gr ++ l+
  gi|14601671|ref|NP_148212.1| 30 IVDEENNRLIFLVSEGEAGRAIGRGGRLIKLLR 62
                                  56788999*******************998665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.1e-08
                          KH_4   4 vedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                                   +e i+k+l+   +  +++++e +  +++ ++v+++d+G  IGk G++++
  gi|14601671|ref|NP_148212.1|  78 LERIVKNLFPGVKIESINVRERNGVKQVVIKVSEDDKGAAIGKGGKNVK 126
                                   67777777754443344444457789********************997 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.6e-07    0.0014       4      48 ..      40      82 ..      37      84 .. 0.84
   2 !   11.3   0.1     8e-05      0.24       3      24 ..     106     127 ..     103     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.6e-07
                                  EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT...T.-EE CS
                          KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedegsderev 48
                                  +lv    +gr IG+gG+ Ik +re  g +I v++ s+d    er+v
  gi|14601671|ref|NP_148212.1| 40 FLVSEGEAGRAIGRGGRLIKLLREALGKNIEVVEySSD---LERIV 82
                                  6899999*****************66******987776...36655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 8e-05
                                   EEEEGGGHHHHHHTGGGHHHHH CS
                          KH_1   3 rilvPsslvgriIGkgGsnIke 24 
                                   +i+v  +  g+ IGkgG+n+k+
  gi|14601671|ref|NP_148212.1| 106 VIKVSEDDKGAAIGKGGKNVKR 127
                                   68999999************97 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05     0.078     185     260 ..      17      88 ..      15      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                                   SEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHH CS
                        Aldedh 185 vlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGGknplivledaDldkaveaivkg 260
                                   v++ +tg   ++ + +v++++ +++ ++ + e gr i +   ++l +++ E  Gkn  +v  + Dl++ v+++  g
  gi|14601671|ref|NP_148212.1|  17 VFHSITG--VTAYRCIVDEENNRLIFLVSEGEAGRAIGRG--GRLIKLLREALGKNIEVVEYSSDLERIVKNLFPG 88 
                                   6666666..778999***********************95..56**************************998766 PP

>> DsbC_N  Disulfide bond isomerase protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.2e-05      0.22       4      30 ..      82     108 ..      79     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.2e-05
                                   HHTTT..--S----B-SSTTEE--EET CS
                        DsbC_N   4 LekllpnlkvesvspspipGLyEVvig 30 
                                   +++l+p++k+es++  + +G+++Vvi+
  gi|14601671|ref|NP_148212.1|  82 VKNLFPGVKIESINVRERNGVKQVVIK 108
                                   6899*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1123.53
//
Query:       gi|118431616|ref|NP_148213.2|  [L=100]
Description: 50S ribosomal protein L30 [Aeropyrum pernix K1]
Scores for complete 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-20   72.2   0.0    2.4e-20   72.0   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.093   12.3   0.0       0.12   11.9   0.0    1.3  1  Peripla_BP_4    Periplasmic binding protein domain


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   2.7e-24   2.4e-20       2      94 ..       2      94 ..       1      95 [. 0.91

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2.7e-24
                                   HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEE..EEESCHHHHHHHTTSSSECS CS
                 Ribosomal_L7Ae  2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpy..vkvkskkeLGelvgkkrpvs 81
                                   ++e++lk  +k+g +++G k+++ka++ geak +++Ae+++pe  +k le+++k  ++p+  ++++   ++G ++g+++ vs
  gi|118431616|ref|NP_148213.2|  2 SVEKALKDLVKTGVYAMGFKQSLKAVKAGEAKAIVIAENTPPELRRK-LEYYAKLAGIPIivYRGTR-MDMGLVMGRRHGVS 81
                                   689********************************************.******7777764155555.************** PP

                                   EEEEEESTTTHHH CS
                 Ribosomal_L7Ae 82 alaikdegdskdl 94
                                   +la++deg s++l
  gi|118431616|ref|NP_148213.2| 82 VLAVIDEGSSRIL 94
                                   **********987 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 ?   11.9   0.0   1.3e-05      0.12      46      86 ..      22      63 ..       2      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHTT-SEEEE--SSHHHHHHHHHH.HHHTT-EEEEE CS
                   Peripla_BP_4 46 aqiedaiakgvdgiivapvdstalapalkk.akaaGIpVvaf 86
                                   + + ++ a  +++i++a + +++l+  l+  ak aGIp++++
  gi|118431616|ref|NP_148213.2| 22 QSLKAVKAGEAKAIVIAENTPPELRRKLEYyAKLAGIPIIVY 63
                                   5566666777***************999999*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 810.68
//
Query:       gi|118431617|ref|NP_148214.2|  [L=407]
Description: DNA-directed RNA polymerase subunit A'' [Aeropyrum pernix K1]
Scores for 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-57  192.8   0.1      1e-56  192.4   0.1    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.099   13.0   0.0       0.18   12.2   0.0    1.3  1  FhuF            Ferric iron reductase FhuF-like transporter


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.4   0.1   1.1e-60     1e-56      56     260 ..      25     347 ..      17     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 1.1e-60
                                    -EEESSGGGTS....................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHH CS
                                    xxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  56 eivqflygedg....................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeil 115
                                    e+v+ ++ edg                    l +pGeavG++aaQSiGePgTQ+tl+TFH+aG+ +  vtlG+prl ei+
  gi|118431617|ref|NP_148214.2|  25 ELVETVEKEDGlseedkisvvketirtylrsLAQPGEAVGTVAAQSIGEPGTQMTLRTFHYAGIMEFDVTLGLPRLIEIV 104
                                    56677777777888888888888888888889************************************************ PP

                                    TT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE............................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                 RNA_pol_Rpb1_5 116 nvskniksksltvllvdeeakelekakkvkkaiek............................................. 150
                                    +++++ +++ ++++l de+ak+lekak+++++ie+                                             
  gi|118431617|ref|NP_148214.2| 105 DAKQTPSQPLMYIYLKDEYAKDLEKAKEAARKIEYttlekiidniewdlgdrvvaivinaeymedkgvtvdmvlealdks 184
                                    **********************************9********************************************* PP

                                    ........................................................CBTTEEEEEEEEEEEEEEETEEEE CS
                                    ........................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 151 ........................................................gikkikrilvkeaekgkeeekelv 174
                                                                                            gik+i+++ v+++e ++++  e++
  gi|118431617|ref|NP_148214.2| 185 klgkvvedgvrevseggvkkvivyfeisdkqlpdeelfnsnayhkvleklkntyikGIKGIRKVTVRREEGEDSY--EYM 262
                                    *******************************************************************88877777..799 PP

                                    EEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 175 letegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivav 254
                                    l +eg nl+evl  +e vd ++ +sndi+ei+++lgieaar+a+++ei+ v++  g++v+ rHl+li+d+mt  g++ ++
  gi|118431617|ref|NP_148214.2| 263 LIVEGSNLREVLMLPE-VDHRRSISNDIQEIAQVLGIEAARTAIIEEIKRVLEDSGLDVDIRHLMLIADLMTWPGYVRQI 341
                                    ****************.*************************************************************** PP

                                    STTCHC CS
                                    xxxxxx RF
                 RNA_pol_Rpb1_5 255 nrsGin 260
                                    +r G+ 
  gi|118431617|ref|NP_148214.2| 342 GRLGVV 347
                                    **9986 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 ?   12.2   0.0     2e-05      0.18      85     133 ..      14      62 ..       4      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2e-05
                                    HHIIIIIIIHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHSGGGHHH CS
                           FhuF  85 vfyglfvnhlapliealaaagglsekllWsnvaellewylaelpelaer 133
                                      y l  ++  +l+e++++++glse++  s v+e ++ yl++l+++ e+
  gi|118431617|ref|NP_148214.2|  14 ARYILPESLYKELVETVEKEDGLSEEDKISVVKETIRTYLRSLAQPGEA 62 
                                    456777777889*******************************887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); 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: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 3231.77
//
Query:       gi|118431618|ref|NP_148215.2|  [L=891]
Description: DNA-directed RNA polymerase subunit A' [Aeropyrum pernix K1]
Scores for 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-78  262.3   0.0    8.5e-78  261.8   0.0    1.2  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    8.7e-70  234.2   0.0      3e-69  232.5   0.0    1.8  2  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    1.7e-38  132.0   0.0    3.7e-38  130.9   0.0    1.6  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    1.6e-30  105.2   0.0    3.5e-30  104.1   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    8.3e-27   94.3   0.1    1.5e-26   93.4   0.1    1.4  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
       0.13   12.4   4.6        0.7   10.1   0.1    3.1  3  Zn-ribbon_8     Zinc ribbon domain
        2.6    8.1   4.1         12    5.9   0.0    3.4  4  CpXC            CpXC protein
          5    7.5   5.1        2.2    8.6   0.0    3.2  4  zf-HC2          Putative zinc-finger
        7.9    6.1  10.4        1.5    8.3   0.4    2.7  3  zf-ribbon_3     zinc-ribbon domain


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 !  261.8   0.0   4.3e-81   8.5e-78       4     312 .]      14     320 ..      11     320 .. 0.93

  Alignments for each domain:
  == domain 1  score: 261.8 bits;  conditional E-value: 4.3e-81
                                    --EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   4 ikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfhi 83 
                                    +++i fg++sp eir++++v v + +++e +  +P +gGl D++ g+i+   +C +Cg++++eC+ghfG ieLa+Pv+  
  gi|118431618|ref|NP_148215.2|  14 LDKILFGVLSPHEIRQLAKVTVVRGDLYEADG-TPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIP 92 
                                    57999************************995.*********************************************** PP

                                    HHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC...CCHHHHHHHHCCS-BE-SSSSB-EEEEEETTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1  84 gffklilkilecvckecskllldeekkkllsklkkrekleelk...krlkaieelckkinlcekCgavqpkleeegeklk 160
                                     ++++++kil+ +c+ c+++ l eek k +  + +r + +  +   + ++++ +   + ++c +Cg  +p+++   ++  
  gi|118431618|ref|NP_148215.2|  93 HYTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLRGKWPQlakTFATMVVKEAAQATQCPHCG--KPQYKVVYIRPF 170
                                    *************************8765544433332222223337788999999999*******..9**********9 PP

                                    EEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 161 aalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrd 240
                                    +  +k+ e  + kl+++++++ l++   +++e+lg+++++srPew++ tvl VpP  +RPs++l++g rsedDlt+ l++
  gi|118431618|ref|NP_148215.2| 171 HFYEKKPE-GDVKLTPSEIRERLEKTG-SEIEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAE 248
                                    99999999.99**************99.9*************************************************** PP

                                    HHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 241 iikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                    i+++N++L++ + ++ape +iee++ +LQe va+++dne +g ++ t++ kr lk+l qrLkGK Gr+RgnL
  gi|118431618|ref|NP_148215.2| 249 IVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRGNL 320
                                    ***********************************************************************9 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   2.8e+03      35      70 ..     264     300 ..     258     316 .. 0.69
   2 !  232.5   0.0   1.5e-72     3e-69       1     166 []     322     490 ..     322     490 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                                    EEEE-STTTHHHHHHHHHH.TTTSSSSEEEEESTTSS CS
                 RNA_pol_Rpb1_2  35 vpeivtelnikklrklven.gpevyPgasyvkredgs 70 
                                     pe++ e n   l+++v+   +++ Pga+++++++++
  gi|118431618|ref|NP_148215.2| 264 APETLIEENWMVLQEMVAAyIDNELPGARRLTHRRKR 300
                                    5777788888888888875257899***999655443 PP

  == domain 2  score: 232.5 bits;  conditional E-value: 1.5e-72
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEE.ESTTSSEEETTTT-S CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyv.kredgsekklkakkr 79 
                                    Gkrv+ysaR+vispdp ++++evgvP ++ak+lt++ +vt++n ++ r++v ngp+++Pga  v k ++ ++ +l+  k+
  gi|118431618|ref|NP_148215.2| 322 GKRVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRYVLNGPDKWPGALFVyKASERKKYDLRFFKD 401
                                    9**************************************************************97778889999*98877 PP

                                    ..CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHH CS
                 RNA_pol_Rpb1_2  80 ..klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseear 157
                                      kla++le gd+verh+++gd+vl+NRqPsLh++sim+h v+v+++kt+rlnl+v+ +yNaDFDGDemnlh+p+ eea+
  gi|118431618|ref|NP_148215.2| 402 yeKLAESLEPGDVVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQ 481
                                    657***************************************************************************** PP

                                    HHHHHCSBT CS
                 RNA_pol_Rpb1_2 158 aEaeelllv 166
                                    aEa+e++lv
  gi|118431618|ref|NP_148215.2| 482 AEAREIMLV 490
                                    ******986 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 !  130.9   0.0   1.8e-41   3.7e-38       1     157 []     493     659 ..     493     659 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 1.8e-41
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHCCCC CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpnein 80 
                                    +il+p+ g P+ig  QD ++G+yllT +  ++++ee+++ll+    +    ++++pailkp++lwtgkq++s +lp+++ 
  gi|118431618|ref|NP_148215.2| 493 HILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSVAGYK---GDLPEPAILKPEPLWTGKQLASIFLPEDLS 569
                                    79******************************************776...789*************************** PP

                                    EEEE.SSSS.............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_3  81 yerk.neek.............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyll 146
                                     ++k +  +             d++++i ng l++Gv+dkk++g+++ ++l+h++a+eyg  +++++lds+ r+++++l 
  gi|118431618|ref|NP_148215.2| 570 FKGKsK-TNagdlacsdelclhDSYIVITNGKLLEGVLDKKAIGAEEPNNLLHIIALEYGNSKARQLLDSFYRMFIRMLE 648
                                    ***852.2257799999*************************************************************** PP

                                    HHCEB-TGGGG CS
                 RNA_pol_Rpb1_3 147 qsgftigigDt 157
                                     +g+ti++ D+
  gi|118431618|ref|NP_148215.2| 649 LRGLTISLHDI 659
                                    ********997 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 !  104.1   0.0   1.8e-33   3.5e-30       1     108 []     684     790 ..     684     790 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 1.8e-33
                                    HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCST.TTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBT CS
                 RNA_pol_Rpb1_4   1 ieeaerygkledlpgksleelfeakinkilnkardkagkiasksla.asNsiliMvksGaKGsiinisqiagclGqqnve 79 
                                    iee+++ g le++pg+slee++e ki+++l++ r++++++as++l+ + N +++M+++Ga+Gs +nisq+a++lGqq+v+
  gi|118431618|ref|NP_148215.2| 684 IEEYRK-GTLEPIPGRSLEESLEIKIMEVLDELRKRVQEVASNNLDpF-NDVFVMARTGARGSDVNISQMAAMLGQQAVR 761
                                    678888.***************************************88.******************************* PP

                                    TBSS--SSTSCSSTTSSSSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  80 gkripkgfsgrtlphfkkidespesrGFv 108
                                    g+ri +g ++r+l hfk++d +pe+ GFv
  gi|118431618|ref|NP_148215.2| 762 GRRIRRGLRNRVLAHFKENDIEPEAWGFV 790
                                    ****************************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 !   93.4   0.1   7.5e-30   1.5e-26       1      66 [.     797     862 ..     797     885 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 7.5e-30
                                    B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                    GL ++e ffh+ +gReGL+DtAvkT++sGY+qRrl++al+d+vv+yd+tvr+  g+++q++ygedg
  gi|118431618|ref|NP_148215.2| 797 GLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQLKYGEDG 862
                                    9****************************************************************8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.089   1.8e+02      24      34 ..      61      71 ..      56      75 .. 0.75
   2 ?   -0.8   0.1      0.89   1.8e+03      27      34 ..     104     111 ..      97     116 .. 0.55
   3 ?   10.1   0.1   0.00035       0.7      15      35 ..     140     160 ..     137     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.089
                    Zn-ribbon_8 24 apltaCPeCgs 34
                                   +p + CP Cg 
  gi|118431618|ref|NP_148215.2| 61 EPGERCPVCGN 71
                                   45677****96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.89
                    Zn-ribbon_8  27 taCPeCgs 34 
                                     +C  Cg 
  gi|118431618|ref|NP_148215.2| 104 ATCRVCGR 111
                                    23555554 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00035
                    Zn-ribbon_8  15 fevlqsisdaplta.CPeCgse 35 
                                    f  ++ +++a++ + CP+Cg++
  gi|118431618|ref|NP_148215.2| 140 FATMV-VKEAAQATqCPHCGKP 160
                                    66666.667777777*****95 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       3.5     7e+03      40      46 ..      66      72 ..      65      74 .. 0.61
   2 ?    0.6   0.0      0.28   5.7e+02      35      56 ..     101     122 ..      98     125 .. 0.85
   3 ?    5.9   0.0    0.0062        12      27      55 ..     141     166 ..     134     182 .. 0.77
   4 ?   -0.3   0.0      0.54   1.1e+03      82     101 ..     389     408 ..     357     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.5
                           CpXC 40 CpkCgat 46
                                   Cp Cg++
  gi|118431618|ref|NP_148215.2| 66 CPVCGNS 72
                                   7777765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                           CpXC  35 lfeatCpkCgatakleapllyh 56 
                                    +++atC  Cg+ + +e ++ y 
  gi|118431618|ref|NP_148215.2| 101 ILQATCRVCGRITLPEEKIKYY 122
                                    6789*******99999988875 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0062
                           CpXC  27 keklldgslfeatCpkCgatakleaplly 55 
                                    +  ++++  + ++Cp+Cg+    +++++y
  gi|118431618|ref|NP_148215.2| 141 ATMVVKEAAQATQCPHCGKP---QYKVVY 166
                                    56678889999******974...455555 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.54
                           CpXC  82 eekegytlRlvidmaelaEk 101
                                    +e ++y lR+++d+++laE 
  gi|118431618|ref|NP_148215.2| 389 SERKKYDLRFFKDYEKLAES 408
                                    34489************995 PP

>> zf-HC2  Putative zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.4   4.8e+03       8      24 ..      14      30 ..      12      31 .. 0.80
   2 ?   -3.9   0.6         9   1.8e+04      30      34 ..     153     157 ..     152     157 .. 0.89
   3 ?    8.6   0.0    0.0011       2.2       5      21 ..     277     293 ..     275     294 .. 0.91
   4 ?   -3.5   0.1       6.6   1.3e+04      18      29 ..     484     495 ..     482     496 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.4
                                   HHHHHCCT-SCCCHCCC CS
                         zf-HC2  8 LsaYlDGeLspeerarv 24
                                   L+  l G Lsp e +++
  gi|118431618|ref|NP_148215.2| 14 LDKILFGVLSPHEIRQL 30
                                   5666889******9987 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9
                                    HTCHH CS
                         zf-HC2  30 eCpdC 34 
                                     Cp+C
  gi|118431618|ref|NP_148215.2| 153 QCPHC 157
                                    6**** PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0011
                                    HHHHHHHHCCT-SCCCH CS
                         zf-HC2   5 relLsaYlDGeLspeer 21 
                                    +e++ aY+D+eL+++ r
  gi|118431618|ref|NP_148215.2| 277 QEMVAAYIDNELPGARR 293
                                    89***********9987 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6.6
                                    CCCHCCCHHHHC CS
                         zf-HC2  18 peerarveaHLa 29 
                                    ++e   ve H+ 
  gi|118431618|ref|NP_148215.2| 484 AREIMLVEKHIL 495
                                    6788999***85 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5     0.013        26       3      11 ..      64      72 ..      62      75 .. 0.82
   2 ?   -4.2   0.2       6.8   1.3e+04      18      23 ..     105     110 ..     103     110 .. 0.69
   3 ?    8.3   0.4   0.00077       1.5      16      25 ..     151     160 ..     148     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                    zf-ribbon_3  3 vrCPnCGap 11
                                    rCP CG+ 
  gi|118431618|ref|NP_148215.2| 64 ERCPVCGNS 72
                                   59*****85 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 6.8
                    zf-ribbon_3  18 vCpyCG 23 
                                    +C  CG
  gi|118431618|ref|NP_148215.2| 105 TCRVCG 110
                                    688787 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00077
                    zf-ribbon_3  16 dnvCpyCGtk 25 
                                    ++ Cp+CG++
  gi|118431618|ref|NP_148215.2| 151 ATQCPHCGKP 160
                                    5556666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (891 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.71u 0.25s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 6177.90
//
Query:       gi|14601675|ref|NP_148216.1|  [L=1169]
Description: DNA-directed RNA polymerase subunit B [Aeropyrum pernix K1]
Scores for complete 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-125  418.1   0.0   5.2e-125  417.5   0.0    1.2  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    3.7e-45  153.9   0.0      6e-45  153.3   0.0    1.3  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    1.8e-31  108.3   0.5    5.8e-31  106.7   0.0    2.1  2  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.5e-29  103.0   0.0    2.3e-29  102.4   0.0    1.3  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    5.8e-26   90.5   0.0    1.3e-25   89.3   0.0    1.7  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    1.6e-18   66.8   1.0    4.6e-18   65.3   0.1    2.3  2  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    8.7e-07   29.4   0.1    2.1e-06   28.2   0.1    1.7  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.5   0.0    2e-128  5.2e-125       2     390 .]     689    1061 ..     688    1061 .. 0.96

  Alignments for each domain:
  == domain 1  score: 417.5 bits;  conditional E-value: 2e-128
                                    HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEE CS
                RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqn 80  
                                    a+ +++ eh+qspr+++qaam+kqalg+y+ln+  r+++++yll+++q P+v+t+  +++++        ++e ++Gqn
  gi|14601675|ref|NP_148216.1|  689 AATIGYLEHNQSPRNTYQAAMAKQALGVYALNYRIRLDSHSYLLQYPQVPIVQTR-MLDIMG--------YNERPAGQN 758 
                                    7899***************************************************.999999........********* PP

                                    EEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-.--.-S--..-.....-SS-GGGS-TTSB-- CS
                RNA_pol_Rpb2_6   81 avVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge.eeitrdipnv.....seealkkLdedGivr 153 
                                    +vVA+msy+GYniEDa+i+n+ ++d +++++++++ y+   +++++ge ++it  +p++     + +a++kL+ dGiv 
  gi|14601675|ref|NP_148216.1|  759 MVVAIMSYTGYNIEDALIFNKGSIDMGLARAYFFRVYTGIENEYPGGErDRITLPKPDEvydyrGAAAYAKLEADGIVA 837 
                                    ************************************99999****999899999888889**9999************* PP

                                    SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT--EEEEE CS
                RNA_pol_Rpb2_6  154 vgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvnklvkv 232 
                                    +++ev+ g+il+g+v  ++ ++  e ++++  +    r  +dts+ ++ ge+gvVd v +       +++ + nklvkv
  gi|14601675|ref|NP_148216.1|  838 PETEVEGGEILIGRV--SPPRFLGEGRVISMAT---VR-RRDTSIPMRLGEKGVVDMVVI-------STTVERNKLVKV 903 
                                    **************9..8999997776654433...33.689******************.......788999****** PP

                                    EEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B-- CS
                RNA_pol_Rpb2_6  233 yvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaalegkkvdat 311 
                                    +v++ R +++GDKfasrhGqKGv+++i+p+ DmP++e+Gi +D++lNP+++PSRmt+gqllE ++gk +a++g++vdat
  gi|14601675|ref|NP_148216.1|  904 RVRNLRIPEIGDKFASRHGQKGVIGMIFPRYDMPYTEEGIEPDVILNPHAIPSRMTVGQLLEEIAGKLGAIKGRFVDAT 982 
                                    ******************************************************************************* PP

                                    TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                RNA_pol_Rpb2_6  312 vFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390 
                                    +F +++ + ++ +L ++g++ +++ev+ydGrtG+ +ea+i++Gv Yy++L+h+v+dKihaR+tG+++llt+QP++Gka+
  gi|14601675|ref|NP_148216.1|  983 PFFKEDIDGLRIELLKEGYDPNAREVMYDGRTGQIIEAPITIGVAYYQRLYHMVADKIHARATGRVHLLTRQPTEGKAR 1061
                                    ***8888**********************************************************************96 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 !  153.3   0.0   2.3e-48     6e-45       1     202 [.      30     423 ..      30     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 2.3e-48
                                   CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSC................EEEEEEEEEEESCSSEC.TTSCEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxx.xxxxxxx RF
                RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgee................lelkfvsirlgkPvvde.sdasere 64 
                                   gL++q+ldSFn +v q+++kii+   +++ + +i     +                +++ f++ r ++P+ +e ++  +r+
  gi|14601675|ref|NP_148216.1|  30 GLARQHLDSFNRLVTQEIQKIIDSIREVRPQWRIYAGR-RryrrgrfeeheihlpdVKIVFGKARFKEPMAREvIESFDRR 109
                                   589*********************99999999885443.2588999**************************9899***** PP

                                   S.HHHHHHCTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1  65 iyPkearlrnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinG 145
                                   ++P e+r+r++tYsapl+v+++ v     ++  +k +ev+i + P+M++s  + ls+ +ee ++e++E+p d+GGyFiinG
  gi|14601675|ref|NP_148216.1| 110 VTPFECRVRGITYSAPLMVEMTIVQ----DNMIEKTREVKIADFPVMVKSVLDPLSKYDEETVIEMGEDPGDPGGYFIING 186
                                   ************************9....8999999********************************************* PP

                                   CEEEEXEEEE....................................................................... CS
                                   xxxxxxxxxx....................................................................... RF
                RNA_pol_Rpb2_1 146 tekvivaqek....................................................................... 155
                                   +ekvivaqe+                                                                       
  gi|14601675|ref|NP_148216.1| 187 SEKVIVAQEDlavnriivnkstaatarithtakavstvlglrrqaivdrmsdgtleaslsrlryriplvvllralglekdm 267
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                RNA_pol_Rpb2_1 156 ................................................................................. 155
                                                                                                                    
  gi|14601675|ref|NP_148216.1| 268 eimlavsadpdvqremlpslekgralaptkedalkylgnriapgqpldvrirraeefldtqllphlgnrpedrikkayfla 348
                                   ********************************************************************************* PP

                                   ............................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                   ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                RNA_pol_Rpb2_1 156 ............................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                               laG+L+a+lfr+ l+ l++ + ++l+ +l + +++ l+ lv+   i+
  gi|14601675|ref|NP_148216.1| 349 emanrvlqlylgkrgeddkdflgnkrlrLAGDLIAELFRESLEALANTMAQKLEEQLAERRQIRLDFLVRPTIIS 423
                                   ********************************************************************9988886 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 ?   -1.8   0.1       1.7   4.4e+03       1      13 [.       6      18 ..       6      21 .. 0.86
   2 !  106.7   0.0   2.3e-34   5.8e-31       1      85 [.    1063    1153 ..    1063    1155 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
                                  BBEEEEHHHHHHH CS
                RNA_pol_Rpb2_7  1 GGlrfGEMErdal 13
                                  GG+r GE  +d l
  gi|14601675|ref|NP_148216.1|  6 GGQRSGEIGVDEL 18
                                  9******988865 PP

  == domain 2  score: 106.7 bits;  conditional E-value: 2.3e-34
                                    BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHHH CS
                RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLlq 73  
                                    GGlrfGEMErd+l+++Ga++lL++r++++SDa+ ++vc++c+++a+ n      eC+i+ +e +i++v++p+afklLlq
  gi|14601675|ref|NP_148216.1| 1063 GGLRFGEMERDCLVGHGASMLLRDRMLDNSDAYVMYVCNTCGNIAWFNrrkkvlECPIHGEEGDIRPVKVPYAFKLLLQ 1141
                                    9****************************************************************************** PP

                                    HHHHTTBEEEEE CS
                RNA_pol_Rpb2_7   74 eLqslgialkll 85  
                                    e++s++i+++l+
  gi|14601675|ref|NP_148216.1| 1142 EITSMMIKPELK 1153
                                    *********986 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 !  102.4   0.0   9.1e-33   2.3e-29       3     190 .]     200     376 ..     198     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 9.1e-33
                                   SCEEEEE-SSSSSE...SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTH CS
                RNA_pol_Rpb2_2   3 ngiyvekekdknki...satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydseds 80 
                                   n+i+v+k ++ + +    a+ +s+    r + ++ +++++tl +++   +++ip+v++l+Algl +d eI+ +++   +d+
  gi|14601675|ref|NP_148216.1| 200 NRIIVNKSTAATARithTAKAVSTVLGLRRQAIVDRMSDGTLEASLSRLRYRIPLVVLLRALGLEKDMEIMLAVS---ADP 277
                                   8888888888887778877777777788888999999**************************************...79* PP

                                   HHHHHHHHHHHHHCTS.SSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH...HHH CS
                RNA_pol_Rpb2_2  81 qlleelleeleekeei.qtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkr.lkaq 159
                                    ++ e+l++le+   + +t+e+al+y+g+++a +++  +r+++a+e+l         + + l+ hlg   +   +r +ka+
  gi|14601675|ref|NP_148216.1| 278 DVQREMLPSLEKGRALaPTKEDALKYLGNRIAPGQPLDVRIRRAEEFL---------DTQLLP-HLGNRPE---DRiKKAY 345
                                   *********999876527*****************************9.........466666.***9999...4558*** PP

                                   HHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                RNA_pol_Rpb2_2 160 dilymidrLlslklgrrevDDiDhlgnkRvr 190
                                   ++++m++r+l+l lg+r +DD+D lgnkR+r
  gi|14601675|ref|NP_148216.1| 346 FLAEMANRVLQLYLGKRGEDDKDFLGNKRLR 376
                                   *****************************97 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 !   89.3   0.0   5.1e-29   1.3e-25       1      68 []     444     508 ..     444     508 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 5.1e-29
                RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                   q ldr+n++s lshlrrv s+   ls+ ++++e+Rdlh shwGr Cp+eTPEG ncGlvk+Lal+a++
  gi|14601675|ref|NP_148216.1| 444 QQLDRTNWISLLSHLRRVISP---LSRGQAHFEARDLHGSHWGRYCPFETPEGINCGLVKNLALSAYI 508
                                   679******************...*****************************************987 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 ?   -1.7   0.1       1.4   3.7e+03      11      30 ..      44      63 ..      43      90 .. 0.74
   2 !   65.3   0.1   1.8e-21   4.6e-18       1      62 []     553     620 ..     553     620 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                  -S-HCCHHHHHHHHCCTTSS CS
                RNA_pol_Rpb2_4 11 trdpkklvetlRelRRkgki 30
                                  t++ +k+++++Re+R + +i
  gi|14601675|ref|NP_148216.1| 44 TQEIQKIIDSIREVRPQWRI 63
                                  67778899999999875444 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 1.8e-21
                                   EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-....TT-EEEE-TT..T--EEEE-SSEEB-EEEEE-S CS
                RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkis....eevsivlnek..qkevkiatDgGRvcRPliiVe 62 
                                   Vf+NGr lG++ ++++l++++RelRR+ k++     evs+++ ++   +e++++tD+GR++RP+++Ve
  gi|14601675|ref|NP_148216.1| 553 VFINGRPLGYHPNGAELARKIRELRRSDKLEverpWEVSVYHLREgeIDELYVNTDSGRLMRPVVVVE 620
                                   9*************************9999888889*****99888899******************7 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 !   28.2   0.1   8.2e-10   2.1e-06       1      33 [.     641     673 ..     641     705 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 8.2e-10
                                   HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST CS
                RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks 33 
                                   + dL+++gvvE+lD eEE++a+Ia  p +++k+
  gi|14601675|ref|NP_148216.1| 641 FWDLVKQGVVEMLDPEEEQNALIAELPWEVTKE 673
                                   669**********************99888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.82u 0.27s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 7716.74
//
Query:       gi|14601676|ref|NP_148217.1|  [L=90]
Description: DNA-directed RNA polymerase subunit H [Aeropyrum pernix K1]
Scores for complete 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-28   98.5   0.1    1.8e-28   98.2   0.1    1.1  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
  ------ inclusion threshold ------
      0.028   14.2   0.0        4.5    7.1   0.0    2.0  2  FAS_meander     Fatty acid synthase meander beta sheet 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 !   98.2   0.1     2e-32   1.8e-28       3      73 .]      12      82 ..      11      82 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 2e-32
                                  -TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                RNA_pol_Rpb5_C  3 itkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                  i++He+vP+h++ls ee+ ++lk l+ik++qLPkis +Dp+ar l++k+Gd+++Itr+s tagea +YR+V
  gi|14601676|ref|NP_148217.1| 12 ILEHEYVPEHRLLSIEEAVQVLKMLGIKPWQLPKISVNDPIARLLKAKPGDIIEITRRSYTAGEAKYYRFV 82
                                  89*******************************************************************98 PP

>> FAS_meander  Fatty acid synthase meander beta sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0014        13     103     129 ..       5      31 ..       1      35 [. 0.84
   2 ?    7.1   0.0    0.0005       4.5      38      60 ..      48      70 ..      42      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0014
                   FAS_meander 103 egesvpLeleFeYkpetglapIhEvme 129
                                   +++s  + le eY pe +l +I E ++
  gi|14601676|ref|NP_148217.1|   5 TRKSSRVILEHEYVPEHRLLSIEEAVQ 31 
                                   467788899***************876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0005
                   FAS_meander 38 veNPlrrllaprkgqlveieead 60
                                  v+ P+ rll++++g ++ei++ +
  gi|14601676|ref|NP_148217.1| 48 VNDPIARLLKAKPGDIIEITRRS 70
                                  788****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 667.02
//
Query:       gi|118431619|ref|NP_148218.2|  [L=250]
Description: hypothetical protein APE_1861.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-08   34.0   0.7    1.3e-06   29.1   0.0    2.1  2  Metallophos    Calcineurin-like phosphoesterase
    0.00012   22.3   0.0    0.00022   21.4   0.0    1.4  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 !   29.1   0.0   1.4e-10   1.3e-06       3      86 ..      25     125 ..      23     150 .. 0.70
   2 ?    3.2   1.0     0.012   1.1e+02     189     203 ..     148     162 ..     131     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.4e-10
                                    EEEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHH.TS CS
                    Metallophos   3 ilvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaalvky.pi 65 
                                     ++++DlHl            l   ql++++ +ld++    kp   +++GD+ +       +   e+++ll++l ++  +
  gi|118431619|ref|NP_148218.2|  25 TILFSDLHLgyeqamaeagvFLPRVQLRRAILTLDRVVMGLKPKKAVIVGDIKHAFdrllkQEALETAKLLEWLSSRgVD 104
                                    5789********9999999977778888888888888555555555555**66665566887777778888888888778 PP

                                    EEEEEC-TTSCHHH.HHHHHHH CS
                    Metallophos  66 pvylllGNHegfee.ellnkyg 86 
                                    +v++++GNH+  ++ ++  k g
  gi|118431619|ref|NP_148218.2| 105 KVIVIRGNHD-NYIpGVVTKSG 125
                                    99********.44435555543 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
                                    HHTTESEEEEESSSS CS
                    Metallophos 189 kkygvdlvisGHtHv 203
                                     ++++d++i GH+H+
  gi|118431619|ref|NP_148218.2| 148 AEFDADIIIIGHEHP 162
                                    46889*********7 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 !   21.4   0.0   2.5e-08   0.00022       4     130 ..      26     163 ..      24     193 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.5e-08
                  Metallophos_2   4 aiiSDlH.................snldaleavlealkevgvdaiihaGD.......leeeep........evleellel 51 
                                    +++SDlH                 + ++a+ ++ + + + ++ + + +GD       l    +        + le+l ++
  gi|118431619|ref|NP_148218.2|  26 ILFSDLHlgyeqamaeagvflprvQLRRAILTLDRVVMGLKPKKAVIVGDikhafdrL----LkqealetaKLLEWLSSR 101
                                    689999999999999988888766333333333445555667799999**55554441....033333333577777777 PP

                  Metallophos_2  52 a..pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHv 129
                                       +v+++rGN+D +++   v ++  e+ +d+    +++ +g  +  +Hg+        +++ ++    +d+++ GH H 
  gi|118431619|ref|NP_148218.2| 102 GvdKVIVIRGNHD-NYIPGVVTKSGGEFVEDY---LDVD-KG--IVAVHGH--------KKAEFD----ADIIIIGHEHP 162
                                    7************.445555555555555554...3444.33..6666666........222222....24445555544 PP

                  Metallophos_2 130 p 130
                                    +
  gi|118431619|ref|NP_148218.2| 163 A 163
                                    3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1895.92
//
Query:       gi|118431620|ref|NP_148219.2|  [L=203]
Description: transcription factor [Aeropyrum pernix K1]
Scores for complete 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-60  200.9   0.8    1.6e-31  108.1   0.1    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.6e-08   33.4   0.0     0.0076   16.4   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)


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 !   91.7   0.1   2.3e-30   2.1e-26       2      82 ..      23     101 ..      22     103 .. 0.96
   2 !  108.1   0.1   1.8e-35   1.6e-31       2      84 ..     114     194 ..     113     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 2.3e-30
                                    EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                            TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81 
                                    +ki+N+va++ l+ +ldL+ +++k   +++ Y+p++fpglvyrl++p+vt+liF+sGk+vitGaks ++l  ++kk+++ 
  gi|118431620|ref|NP_148219.2|  23 VKIENIVATVILENQLDLNLIETKI--QDVDYNPDQFPGLVYRLESPRVTVLIFKSGKMVITGAKSINQLIHVVKKLLKA 100
                                    79*******************9998..*************************************************9987 PP

                                    H CS
                            TBP  82 l 82 
                                    +
  gi|118431620|ref|NP_148219.2| 101 F 101
                                    6 PP

  == domain 2  score: 108.1 bits;  conditional E-value: 1.8e-35
                                    EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                            TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81 
                                    ++iqN+vasanl++ +dLek al+   +n+ Yepe+fpgl+yr++ep+v++liFssGk+vitGak e+e+++a+kk+a++
  gi|118431620|ref|NP_148219.2| 114 IQIQNIVASANLKVYIDLEKAALEF--ENSLYEPEQFPGLIYRMDEPRVVMLIFSSGKMVITGAKMENEVYDAVKKVARK 191
                                    89*******************9887..***************************************************** PP

                                    HHH CS
                            TBP  82 lkk 84 
                                    lk+
  gi|118431620|ref|NP_148219.2| 192 LKE 194
                                    *97 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.4e-07    0.0076      22      55 ..      52      85 ..      30      89 .. 0.80
   2 !   15.0   0.0   2.3e-06      0.02      22      60 ..     143     181 ..     125     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.4e-07
                        DUF3378 22 lrskkppyavfaakkndttItaYtSgKVlFQGkn 55
                                    +  + p+ v++ +++ +t+ +++SgK ++ G++
  gi|118431620|ref|NP_148219.2| 52 YNPDQFPGLVYRLESPRVTVLIFKSGKMVITGAK 85
                                   456789************************9976 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-06
                        DUF3378  22 lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeA 60 
                                     + ++ p+ +++ +++ ++  ++ SgK ++ G++ e e 
  gi|118431620|ref|NP_148219.2| 143 YEPEQFPGLIYRMDEPRVVMLIFSSGKMVITGAKMENEV 181
                                    466789***************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 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:                        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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1601.61
//
Query:       gi|118431621|ref|NP_148220.2|  [L=157]
Description: hypothetical protein APE_1864.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       418  (0.0233142); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1303.42
//
Query:       gi|118431622|ref|NP_148221.2|  [L=366]
Description: PflA-like protein [Aeropyrum pernix K1]
Scores for complete 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   74.0   0.0    4.6e-20   72.6   0.0    1.6  2  Radical_SAM     Radical SAM superfamily
    0.00024   20.6   4.1      0.057   12.9   0.1    2.9  3  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0023   18.2   0.0     0.0047   17.2   0.0    1.5  1  Fer4_12         4Fe-4S single cluster domain
     0.0031   17.0   2.2        1.5    8.4   0.3    2.4  2  zf_C2H2_10      C2H2 type zinc-finger
     0.0084   15.8  10.4      0.028   14.1   0.1    2.9  3  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.015   15.2   0.4      0.054   13.4   0.4    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.016   15.2   0.0      0.016   15.2   0.0    2.6  3  DZR             Double zinc ribbon
       0.16   12.0   2.5         13    5.8   0.1    2.6  2  DUF1610         Domain of unknown function (DUF1610)
       0.21   11.7   5.2       0.36   10.9   0.8    3.0  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.24   11.0   0.7        2.3    7.8   0.1    2.3  2  DpnI            Dam-replacing family
       0.24   11.6   0.1       0.24   11.6   0.1    1.9  3  IBR             IBR domain, a half RING-finger domain
       0.28   10.6   7.0        1.2    8.6   0.1    2.8  3  zf-ribbon_3     zinc-ribbon domain
       0.29   11.2   9.5       0.84    9.7   0.4    3.1  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.43   10.6   1.4         27    4.8   0.1    2.6  2  CpXC            CpXC protein
       0.86    9.6   6.7        1.7    8.6   0.1    3.0  3  zinc-ribbons_6  zinc-ribbons
       0.95    9.5   3.7        4.6    7.3   0.1    2.9  3  HypA            Hydrogenase/urease nickel incorporation, meta
        3.3    7.5   8.4         15    5.3   0.1    3.4  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


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 !   72.6   0.0   4.4e-23   4.6e-20       3     167 .]      92     253 ..      90     253 .. 0.94
   2 ?   -2.1   0.0       4.1   4.3e+03     127     144 ..     282     299 ..     258     311 .. 0.48

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 4.4e-23
                                    EESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                    xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                     t gCn+ C fC++ e      +++ +g ++++ee+++++  +     +++++ +  ep+   + v +++++ak+   g+
  gi|118431622|ref|NP_148221.2|  92 STVGCNFFCQFCQNFEIsqsrLEKGLYGVYRTPEEVVRLALVYG----ADGITYTYNEPTIFFETVYDVAKEAKK--HGL 165
                                    689******************999****************9998....***************************..7** PP

                                    EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                    Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGend 157
                                     +t++tng++  +e +++l  l  d  +++ + + d ++ ++++  +++e ++ea+ +++++g+   +++ +v + G   
  gi|118431622|ref|NP_148221.2| 166 FNTMVTNGYMT-PEAVDELGSLI-DAATVDFKGGGDPEFYRKIMFVPDPEPIYEAILAMKDKGWWIeITNLVVPILGDKP 243
                                    **********8.*********99.********976664666666*******************99999999999999999 PP

                                    HHHHHHHHHH CS
                                    xxxxxxxxxx RF
                    Radical_SAM 158 eeleellell 167
                                    e ++ +++++
  gi|118431622|ref|NP_148221.2| 244 EYVRRMARWI 253
                                    9999999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                    HHHHHHHHHHHHHTTSET CS
                                    xxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 127 feevlealeklreagikr 144
                                    ++ + ++ +++ e g+k 
  gi|118431622|ref|NP_148221.2| 282 VKTLEKLARIAMEEGLKH 299
                                    222222333333333332 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       4.7     5e+03      19      25 ..      97     103 ..      97     104 .. 0.85
   2 !   12.9   0.1   5.4e-05     0.057      19      41 ..     312     334 ..     306     335 .. 0.94
   3 !    8.2   0.0    0.0017       1.7      18      30 ..     337     349 ..     336     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.7
                                    CEEESSS CS
                   TF_Zn_Ribbon  19 elvCtdC 25 
                                    +++C +C
  gi|118431622|ref|NP_148221.2|  97 NFFCQFC 103
                                    6899999 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.4e-05
                                    CEEESSSSBEEEECCCCCCCHHH CS
                   TF_Zn_Ribbon  19 elvCtdCGlVlednsidegpewr 41 
                                    +++C++CG+ + d+     +ewr
  gi|118431622|ref|NP_148221.2| 312 DTYCPKCGYKVVDREGFAIVEWR 334
                                    89********************8 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0017
                                    TCEEESSSSBEEE CS
                   TF_Zn_Ribbon  18 gelvCtdCGlVle 30 
                                     +++C++CG+ l 
  gi|118431622|ref|NP_148221.2| 337 SDFRCPRCGYKLN 349
                                    69*******9986 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 !   17.2   0.0   4.5e-06    0.0047       6     100 ..      87     180 ..      83     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-06
                        Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeek 83 
                                    ++ls+ + gCn+ C++C n e+ + + +k       + ee+++ +  +  +g+t++  EP      e++++++ke k+++
  gi|118431622|ref|NP_148221.2|  87 TVLSISTVGCNFFCQFCQNFEISQSRLEKGLYgvYRTPEEVVRLALVYGADGITYTYNEPTI--FFETVYDVAKEAKKHG 164
                                    55677889*************99888776664358888888988889***************..99************** PP

                        Fer4_12  84 pekdiwlytgytleels 100
                                    +  + ++++gy+  e  
  gi|118431622|ref|NP_148221.2| 165 L-FNTMVTNGYMTPEAV 180
                                    9.589******987765 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 !    8.4   0.3    0.0014       1.5       5      12 ..     315     322 ..     312     326 .. 0.86
   2 !    8.0   0.1    0.0019         2       2      12 ..     338     348 ..     337     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                     zf_C2H2_10   5 CPKCqekl 12 
                                    CPKC++k+
  gi|118431622|ref|NP_148221.2| 315 CPKCGYKV 322
                                    ******97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0019
                     zf_C2H2_10   2 efsCPKCqekl 12 
                                    +f CP+C++kl
  gi|118431622|ref|NP_148221.2| 338 DFRCPRCGYKL 348
                                    699******97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.5       7.5   7.9e+03      15      19 ..      99     103 ..      99     105 .. 0.47
   2 !   14.1   0.1   2.6e-05     0.028       1      12 [.     314     325 ..     308     328 .. 0.67
   3 !    8.4   0.2    0.0017       1.8       2       9 ..     341     348 ..     336     349 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.5
                  zinc_ribbon_2  15 FCpyC 19 
                                    FC  C
  gi|118431622|ref|NP_148221.2|  99 FCQFC 103
                                    44444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.6e-05
                  zinc_ribbon_2   1 fCpnCGaelqdn 12 
                                    +Cp+CG+++ d+
  gi|118431622|ref|NP_148221.2| 314 YCPKCGYKVVDR 325
                                    567777666666 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0017
                  zinc_ribbon_2   2 CpnCGael 9  
                                    Cp+CG++l
  gi|118431622|ref|NP_148221.2| 341 CPRCGYKL 348
                                    66666665 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 ?   13.4   0.4   5.1e-05     0.054      30      57 ..     314     349 ..     283     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-05
                 OrfB_Zn_ribbon  30 tCseCgsknke........alsgrtfkCpnCgfead 57 
                                     C++Cg+k+ +         + +  f+Cp+Cg++++
  gi|118431622|ref|NP_148221.2| 314 YCPKCGYKVVDregfaiveWRLTSDFRCPRCGYKLN 349
                                    7********9999**9888788899*******9976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.4   1.5e+03      29      37 ..      29      37 ..      14      49 .. 0.73
   2 ?   -2.4   1.0       4.8   5.1e+03      14      19 ..      99     104 ..      93     109 .. 0.70
   3 ?   15.2   0.0   1.5e-05     0.016       9      40 ..     309     350 ..     305     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                            DZR 29 drCpsCgek 37
                                    rC+ C++ 
  gi|118431622|ref|NP_148221.2| 29 VRCDLCQRR 37
                                   467777766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                            DZR  14 fCseCg 19 
                                    fC+ C+
  gi|118431622|ref|NP_148221.2|  99 FCQFCQ 104
                                    555554 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.5e-05
                            DZR   9 ppdarfCseCgtklkavaa..........edrCpsCgekvdp 40 
                                    p ++ +C++Cg k+   +             rCp+Cg+k++ 
  gi|118431622|ref|NP_148221.2| 309 PLEDTYCPKCGYKVVDREGfaivewrltsDFRCPRCGYKLNF 350
                                    56789********97655599******99999*****99865 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5      0.02        21      18      23 ..     314     319 ..     313     320 .. 0.94
   2 ?    5.8   0.1     0.013        13      15      23 ..     337     345 ..     335     346 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                        DUF1610  18 pCPNCG 23 
                                    +CP+CG
  gi|118431622|ref|NP_148221.2| 314 YCPKCG 319
                                    7****9 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                        DUF1610  15 vvFpCPNCG 23 
                                    + F CP CG
  gi|118431622|ref|NP_148221.2| 337 SDFRCPRCG 345
                                    579*****9 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       3.7   3.9e+03       9      18 ..     120     129 ..     120     129 .. 0.82
   2 ?   10.9   0.8   0.00034      0.36       2      21 ..     315     342 ..     314     343 .. 0.78
   3 ?    3.1   0.3     0.094        99       1       9 [.     340     348 ..     340     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
                 DNA_ligase_ZBD   9 vvReegeaiy 18 
                                    v R+++e+++
  gi|118431622|ref|NP_148221.2| 120 VYRTPEEVVR 129
                                    5799***985 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00034
                 DNA_ligase_ZBD   2 CPvCGsavvReeg........eaiyRCt 21 
                                    CP CG +vv  eg         ++ RC+
  gi|118431622|ref|NP_148221.2| 315 CPKCGYKVVDREGfaivewrlTSDFRCP 342
                                    *********8887666666777777777 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.094
                 DNA_ligase_ZBD   1 hCPvCGsav 9  
                                    +CP CG ++
  gi|118431622|ref|NP_148221.2| 340 RCPRCGYKL 348
                                    5*****776 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.28   2.9e+02      28      45 ..      94     111 ..      86     126 .. 0.68
   2 ?    7.8   0.1    0.0022       2.3      30      62 ..     311     347 ..     299     360 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.28
                                    HHHH---TTT--SS-EE- CS
                           DpnI  28 vaknlyCpkCgskklsef 45 
                                    v  n++C  C++ ++s+ 
  gi|118431622|ref|NP_148221.2|  94 VGCNFFCQFCQNFEISQS 111
                                    555677777777666654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                                    HH---TTT--SS-EE..--..------EEE-TTT--E CS
                           DpnI  30 knlyCpkCgskklse..fe..nnkpvaDfyCesckee 62 
                                    +++yCpkCg k++++  f+    +  +Df C +c  +
  gi|118431622|ref|NP_148221.2| 311 EDTYCPKCGYKVVDRegFAivEWRLTSDFRCPRCGYK 347
                                    689********99753344225678899999999755 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 ?   -2.9   0.2       7.7   8.1e+03      39      45 ..      29      35 ..      14      54 .. 0.66
   2 ?   -2.8   0.1       7.2   7.6e+03      48      52 ..      99     103 ..      66     106 .. 0.70
   3 ?   11.6   0.1   0.00023      0.24      19      50 ..     313     350 ..     310     353 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.7
                            IBR 39 vtCskCg 45
                                   v+C  C+
  gi|118431622|ref|NP_148221.2| 29 VRCDLCQ 35
                                   4555554 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.2
                            IBR  48 fCfnC 52 
                                    fC  C
  gi|118431622|ref|NP_148221.2|  99 FCQFC 103
                                    33333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00023
                            IBR  19 kwCprpdCeaiiekseg........cksvtCskCgfefCf 50 
                                    ++Cp  +C++ + + eg        +++ +C++Cg++  f
  gi|118431622|ref|NP_148221.2| 313 TYCP--KCGYKVVDREGfaivewrlTSDFRCPRCGYKLNF 350
                                    79**..******999997777666666699******9877 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.3       5.4   5.6e+03      18      24 ..      99     105 ..      99     106 .. 0.74
   2 ?    8.6   0.1    0.0012       1.2      16      25 ..     312     321 ..     309     325 .. 0.73
   3 ?    5.5   0.2     0.011        12       5      24 ..     341     346 ..     337     348 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.4
                    zf-ribbon_3  18 vCpyCGt 24 
                                    +C  C+ 
  gi|118431622|ref|NP_148221.2|  99 FCQFCQN 105
                                    6989975 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0012
                    zf-ribbon_3  16 dnvCpyCGtk 25 
                                    d+ Cp+CG+k
  gi|118431622|ref|NP_148221.2| 312 DTYCPKCGYK 321
                                    5667777765 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.011
                    zf-ribbon_3   5 CPnCGaplssddnvCpyCGt 24 
                                    CP+CG              +
  gi|118431622|ref|NP_148221.2| 341 CPRCG--------------Y 346
                                    55555..............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 ?   -2.1   0.2       3.7   3.9e+03      19      27 ..      98     106 ..      95     118 .. 0.69
   2 ?    6.5   0.3     0.008       8.4      14      27 ..     305     321 ..     302     329 .. 0.81
   3 ?    9.7   0.4   0.00079      0.84      12      27 ..     332     347 ..     328     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.7
                  Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                    f C +C++ 
  gi|118431622|ref|NP_148221.2|  98 FFCQFCQNF 106
                                    669999875 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.008
                  Zn_Tnp_IS1595  14 rWpng...fvCPhCgsr 27 
                                    +W++      CP+Cg++
  gi|118431622|ref|NP_148221.2| 305 VWGHPledTYCPKCGYK 321
                                    7888888666*****86 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00079
                  Zn_Tnp_IS1595  12 alrWpngfvCPhCgsr 27 
                                    ++r  + f+CP+Cg++
  gi|118431622|ref|NP_148221.2| 332 EWRLTSDFRCPRCGYK 347
                                    6788889*******76 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.04        42      35      47 ..     310     322 ..     301     335 .. 0.82
   2 ?    4.8   0.1     0.026        27      37      49 ..     338     350 ..     329     355 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.04
                           CpXC  35 lfeatCpkCgata 47 
                                    l ++ CpkCg+++
  gi|118431622|ref|NP_148221.2| 310 LEDTYCPKCGYKV 322
                                    67899*****986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.026
                           CpXC  37 eatCpkCgatakl 49 
                                    +++Cp+Cg++  +
  gi|118431622|ref|NP_148221.2| 338 DFRCPRCGYKLNF 350
                                    799*****98765 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2       1.3   1.4e+03      17      26 ..      29      38 ..      20      49 .. 0.73
   2 ?    3.1   0.3     0.086        91      49      63 ..      97     112 ..      87     115 .. 0.70
   3 ?    8.6   0.1    0.0017       1.7       2      26 ..     314     348 ..     313     354 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                   EE-TTT--EE CS
                 zinc-ribbons_6 17 yhCeaCqedl 26
                                   ++C+ Cq+++
  gi|118431622|ref|NP_148221.2| 29 VRCDLCQRRC 38
                                   5777787754 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.086
                                    EE--TTTT--.--TTS CS
                 zinc-ribbons_6  49 dyfCnkcneL.iSkkr 63 
                                    ++fC+ c+++ iS++r
  gi|118431622|ref|NP_148221.2|  97 NFFCQFCQNFeISQSR 112
                                    8899988876456655 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0017
                                    --SSS-S--EE-S..........SEEE-TTT--EE CS
                 zinc-ribbons_6   2 kCpeCqqelekrg..........eqyhCeaCqedl 26 
                                    +Cp+C  +++ r+          + ++C  C  +l
  gi|118431622|ref|NP_148221.2| 314 YCPKCGYKVVDREgfaivewrltSDFRCPRCGYKL 348
                                    7*********7777999999998899999997765 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 ?   -1.0   0.1       1.6   1.7e+03      68      84 ..      26      42 ..       7      57 .. 0.70
   2 ?    1.7   0.0      0.25   2.6e+02      60      82 ..      87     108 ..      80     117 .. 0.81
   3 ?    7.3   0.1    0.0044       4.6      71      94 ..     313     346 ..     307     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                                   --EEEETTTS-EEECHH CS
                           HypA 68 pvkvrCreCgkefelee 84
                                   +  vrC+ C+++  ++ 
  gi|118431622|ref|NP_148221.2| 26 EGWVRCDLCQRRCVIAP 42
                                   45678998988877654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.25
                                    -EEEEEEE--EEEETTTS-EEEC CS
                           HypA  60 aeLeieevpvkvrCreCgkefel 82 
                                    ++L+i++v  ++ C+ C+ +fe+
  gi|118431622|ref|NP_148221.2|  87 TVLSISTVGCNFFCQFCQ-NFEI 108
                                    57999************9.5654 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0044
                                    EEETTTS-EEECHHH.HH.........S-TTTSS CS
                           HypA  71 vrCreCgkefeleek.al.........rCpkCgs 94 
                                    ++C +Cg+++  +e  a+         rCp+Cg 
  gi|118431622|ref|NP_148221.2| 313 TYCPKCGYKVVDREGfAIvewrltsdfRCPRCGY 346
                                    68*****99986653233678888999*****96 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.9      0.74   7.8e+02      13      26 ..      24      37 ..      19      40 .. 0.73
   2 ?    4.7   0.1     0.024        25      20      28 ..     315     323 ..     311     325 .. 0.91
   3 ?    5.3   0.1     0.014        15      19      27 ..     340     348 ..     332     351 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.74
                                   -SSS----SSS--- CS
                 DNA_RNApol_7kD 13 kkgdpiRCkeCGhR 26
                                    k+  +RC  C  R
  gi|118431622|ref|NP_148221.2| 24 GKEGWVRCDLCQRR 37
                                   566689**999776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                                    -SSS----- CS
                 DNA_RNApol_7kD  20 CkeCGhRil 28 
                                    C +CG++++
  gi|118431622|ref|NP_148221.2| 315 CPKCGYKVV 323
                                    9******97 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.014
                                    --SSS---- CS
                 DNA_RNApol_7kD  19 RCkeCGhRi 27 
                                    RC  CG+++
  gi|118431622|ref|NP_148221.2| 340 RCPRCGYKL 348
                                    9******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2538.72
//
Query:       gi|118431623|ref|NP_148222.2|  [L=234]
Description: hypothetical protein APE_1866.1 [Aeropyrum pernix K1]
Scores for complete 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-31  107.5   1.0    2.8e-31  107.5   1.0    1.9  2  DUF2258   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2258  Uncharacterized protein conserved in archaea (DUF2258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   1.0   1.5e-35   2.8e-31       1      77 [.       4      80 ..       4      81 .. 0.98
   2 ?   -1.4   0.0      0.14   2.6e+03      54      66 ..     197     209 ..     180     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.5e-35
                                   EEEECEEGGGHHHHHHHHHHHHTCCCCHTTSS.HHHHHHHHHHHHHHHHHHHHCCTT--TTSEEEEEEEEEEETTEE CS
                        DUF2258  1 lsTGlviaaaYAdKlRrvlfaalsklvkkkkeekkeiaraiaeLNkklYevlveklkidKldvvrirveyeveekkl 77
                                   l+TGlviaa+YAdK+Rrvlfa+l++++k+ + ++k +a a+++LN++l+e+lv+klk+dKldvvri+++yev+++++
  gi|118431623|ref|NP_148222.2|  4 LRTGLVIAAGYADKVRRVLFAQLRDAIKSGELSNKDVAMAAGNLNRVLFELLVNKLKADKLDVVRIQIDYEVRDSQI 80
                                   79************************************************************************987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.14
                                    CCTT--TTSEEEE CS
                        DUF2258  54 eklkidKldvvri 66 
                                    e  +++K + vr+
  gi|118431623|ref|NP_148222.2| 197 EAQNVEKREAVRV 209
                                    5567888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1845.92
//
Query:       gi|118431624|ref|NP_148223.2|  [L=286]
Description: small conductance mechanosensitive channel MscS [Aeropyrum pernix K1]
Scores for 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-41  140.0   0.4    7.2e-41  140.0   0.4    1.5  2  MS_channel   Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.098   12.1   0.0       0.23   10.9   0.0    1.6  1  PP_kinase_C  Polyphosphate kinase C-terminal domain 2
       0.11   12.6   0.1       0.74    9.9   0.0    2.1  2  DUF1938      Domain of unknown function (DUF1938)
       0.15   12.0   8.2       0.19   11.7   7.3    1.6  1  Trep_Strep   Hypothetical bacterial integral membrane protein
       0.61    9.8   8.5       0.97    9.1   8.5    1.2  1  FtsK_4TM     4TM region of DNA translocase FtsK/SpoIIIE


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.4       1.1     4e+03      23      38 ..      24      39 ..       9      40 .. 0.73
   2 !  140.0   0.4     2e-44   7.2e-41       2     205 ..      62     258 ..      61     259 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                   -SCCHHHHHHHHHHHH CS
                     MS_channel 23 nvsallavlGalglal 38
                                    +++l+ ++Ga+++ l
  gi|118431624|ref|NP_148223.2| 24 LTAILILSVGAVAALL 39
                                   3677777888877765 PP

  == domain 2  score: 140.0 bits;  conditional E-value: 2e-44
                                    .HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                     MS_channel   2 kilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                     il ++i++++ +++l +lg+++s +l++ G++g+alg+a++++ snl+aG++l++e+pfk+GD v +g i G V di++
  gi|118431624|ref|NP_148223.2|  62 RILFYTILFLTGVAALAQLGIDISVFLVAGGIVGIALGIASQTVASNLIAGVFLYLERPFKVGDPVIVGSIGGVVYDISI 141
                                    58999*************************************************************************** PP

                                    SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEE CS
                     MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvld 161
                                    ++ ki ++dg +  iPn++l++sn+  l++ s +rr++++i v+ +sd    +k++e+ ++a++e+p  l ++e++v++d
  gi|118431624|ref|NP_148223.2| 142 LSSKILKWDGVMARIPNEALFKSNVDVLNK-SLARRVEYRIPVKETSD---YSKAAEIALNAIQEEPLALAEPEPQVFVD 217
                                    ******************************.*****************...***************************** PP

                                    EE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT-- CS
                     MS_channel 162 efgdsslnfevrvfvktvvpeeylsvqseinlrikkileeegie 205
                                    +++ ++ ++ vr+++++   +++++ + +    i k l  +g+e
  gi|118431624|ref|NP_148223.2| 218 NISERGAELVVRFWAPS---DQWFNAKIKMLSIIVKRLLDAGVE 258
                                    *****************...9**999988888887777777776 PP

>> PP_kinase_C  Polyphosphate kinase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.5e-05      0.23     101     138 ..     158     195 ..     152     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.5e-05
                    PP_kinase_C 101 eeevyisSaDlmtRnldrRvevlvpvedeklkkelkei 138
                                    +e ++ s  D+++++l rRve  +pv++++  ++  ei
  gi|118431624|ref|NP_148223.2| 158 NEALFKSNVDVLNKSLARRVEYRIPVKETSDYSKAAEI 195
                                    7899**********************998766655554 PP

>> DUF1938  Domain of unknown function (DUF1938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.38   1.4e+03      20      50 ..      89     119 ..      84     131 .. 0.80
   2 ?    9.9   0.0   0.00021      0.74      14      67 ..     136     191 ..     127     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.38
                                    ESSSEEEEEEESSHHHHHH.HHHHHHHHHHH CS
                        DUF1938  20 sedkvfGiifaidegelikhripdlieflek 50 
                                      + + Gi++ i   ++  + i  +  +le+
  gi|118431624|ref|NP_148223.2|  89 VAGGIVGIALGIASQTVASNLIAGVFLYLER 119
                                    5678999999999999988888877777775 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00021
                                    EEEEEEESSSE...EEEEEESSHHHHHH.HHHHHHHHHHHT------B--..-SHHH CS
                        DUF1938  14 vyiGvlsedkv...fGiifaidegelikhripdlieflekrlskklevkegnsdyse 67 
                                    vy   + + k+    G++  i +  l+k  +  l + l +r++ ++ vke  sdys+
  gi|118431624|ref|NP_148223.2| 136 VYDISILSSKIlkwDGVMARIPNEALFKSNVDVLNKSLARRVEYRIPVKE-TSDYSK 191
                                    5533444444422259999999****************************.9***97 PP

>> Trep_Strep  Hypothetical bacterial integral membrane protein (Trep_Strep)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.3   5.4e-05      0.19      29      91 ..      26      90 ..      16     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.4e-05
                     Trep_Strep 29 pvlmll.lpaivallagivymllvakvpkfgailimglllgllllltGhgwlvlllaii.gglia 91
                                    +l+l   ++ + l+ g vy++l+++  +  a++i+ +l+  +l+ltG  +l+ l++ i + l+a
  gi|118431624|ref|NP_148223.2| 26 AILILSvGAVAALLVRGRVYIYLSKRTSRDIAVAISRILFYTILFLTGVAALAQLGIDIsVFLVA 90
                                   4444441556666788********************************95554443322133333 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.5   0.00027      0.97      54     139 ..      24     107 ..      23     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                       FtsK_4TM  54 ladlllslfGlsawllvvlllawglrllrrkslerrllrllgalllll.asaalfalrlasledelpggaGGvlGrllaa 132
                                    l ++l+  +G +a+llv   +++ l+  ++++++ ++ r+l+ ++l+l  +aal++l ++   +++   aGG++G  l+ 
  gi|118431624|ref|NP_148223.2|  24 LTAILILSVGAVAALLVRGRVYIYLSKRTSRDIAVAISRILFYTILFLtGVAALAQLGID---ISVFLVAGGIVGIALGI 100
                                    56789999**************************99999876555544277888887777...566789*********** PP

                       FtsK_4TM 133 alstllg 139
                                    a++t+  
  gi|118431624|ref|NP_148223.2| 101 ASQTVAS 107
                                    *999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2346.77
//
Query:       gi|118431625|ref|NP_148224.2|  [L=251]
Description: hypothetical protein APE_1868.1 [Aeropyrum pernix K1]
Scores for 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-21   74.4   0.0    1.6e-20   73.5   0.0    1.4  1  DUF432    Protein of unknown function (DUF432)


Domain annotation for each model (and alignments):
>> DUF432  Protein of unknown function (DUF432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   8.9e-25   1.6e-20      10     123 .]      79     186 ..      71     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 8.9e-25
                         DUF432  10 kyllveleeplvvepkseveiyvkvpveigvfikskkeveliDvfsl..skkkYaLYGspesGviaryvksevyseppel 87 
                                    ++l+++l++p+vv+p+++ +i +kvp++i+v+++sk +++liD+f+     +k a+YGs  +G ++r+++ e        
  gi|118431625|ref|NP_148224.2|  79 NCLYMRLRSPVVVPPGDSFSIELKVPFDIAVIASSKGRHTLIDFFPPggVVPKMAVYGSNVEGLLCRFWRDEWRGP---- 154
                                    79*********************************************8889*******************988765.... PP

                         DUF432  88 dpleeavveleikNetdevvevskivfdalglklyy 123
                                         a ++l+i+N++d  ++vs++v++  gl+++y
  gi|118431625|ref|NP_148224.2| 155 ----AASARLTIVNNADVQATVSRVVLPRRGLSMFY 186
                                    ....5899***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1923.32
//
Query:       gi|14601684|ref|NP_148225.1|  [L=421]
Description: 3-hydroxy-3-methylglutaryl-coenzyme A reductase [Aeropyrum pernix K1]
Scores for complete 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-132  440.4   0.1   5.5e-132  440.2   0.1    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


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 !  440.2   0.1  3.1e-136  5.5e-132       4     367 .]      42     415 ..      39     415 .. 0.98

  Alignments for each domain:
  == domain 1  score: 440.2 bits;  conditional E-value: 3.1e-136
                                   HHHHHHHHS-HHHHHHHTT----.HHHHHHHSSS---------EEEEEEEETTE....EEEEEE---STTHHHHHHHHHHH CS
                   HMG-CoA_red   4 eRrklleelteeeleelkeesld.eevadkmiEnviGyvqlPlGvagpllingk....eylvPmAteEgslvAsasrgaka 79 
                                    Rr +le+lt+++l++++++ ld +e ++++iEn iG+vq+P+Gvagpl+ing+    ++++P+At+Eg+lvAs++rgaka
  gi|14601684|ref|NP_148225.1|  42 VRRLYLERLTGASLSSVASTILDfQELYGRNIENPIGAVQVPVGVAGPLRINGDyargDFYIPLATTEGALVASVNRGAKA 122
                                   6999***************************************************************************** PP

                                   HHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEEEE-SSEEEEEEEEE-TT CS
                   HMG-CoA_red  80 inesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdievvlagrlvvlrlkvdtgD 160
                                   i+ sgG++++v+kdgmtra++++++sv +a++l  w+  ++++e+l++ +  ++r+g+l++i +++ g+lv+lrl+++tgD
  gi|14601684|ref|NP_148225.1| 123 ITLSGGARAKVIKDGMTRAPLLWTPSVYEAHRLAMWV--EDRIEDLRSVVAGVTRHGRLQHIYPYIIGNLVWLRLSFSTGD 201
                                   *************************************..****************************************** PP

                                   C--HHHHHHHHHHHHHHHHHHHTS.EEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHHHHHHHH-HHH CS
                   HMG-CoA_red 161 AmGaNmvnkateaaaelieeefge.eellsilsNlctdkkasainaiegrgksvvaeatigeevvekilkasaealvdlnr 240
                                   AmG+Nmv++  ++++++iee++++ ++++++++N+ctdkk++ain i grgk vvaea+i+ evv+++lk++++++  +n+
  gi|14601684|ref|NP_148225.1| 202 AMGMNMVTISSDRICRYIEENYDGdAKCIALSGNMCTDKKPAAINKILGRGKYVVAEAVIKGEVVKNVLKTTPQNINLVNV 282
                                   *********************98779******************************************************* PP

                                   H....HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.----SBSHHHHH-HHHHH CS
                   HMG-CoA_red 241 a.n.igtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsleVGtvGGgtklppqael 319
                                   + n +g+a++G+ +fnah+aN+iaA+f+AtGqD+a+v+ess++++++e   ++dly+svtlPsleVGtvGGgt+lp+q+el
  gi|14601684|ref|NP_148225.1| 283 TkNlLGSAAAGSHSFNAHFANIIAAIFIATGQDAAQVVESSMGYTWTEVR-GEDLYISVTLPSLEVGTVGGGTRLPTQREL 362
                                   **********************************************9999.666*************************** PP

                                   HHHTT---HH........HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                   HMG-CoA_red 320 lkllgvkgak.....nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                   l llgv+g +     na +Laeiia+++LA+el +l+A+aa++l+++H+ l+r
  gi|14601684|ref|NP_148225.1| 363 LALLGVAGGGnppgsNALKLAEIIASAVLAGELNLLSAIAAGQLARAHELLGR 415
                                   ************************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3101.19
//
Query:       gi|118431626|ref|NP_148226.2|  [L=133]
Description: hypothetical protein APE_1871.1 [Aeropyrum pernix K1]
Scores for complete 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   47.6   5.9    1.9e-12   46.8   5.9    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    6.8e-11   42.0   2.1      1e-10   41.5   2.1    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
     0.0018   18.3   0.2     0.0026   17.7   0.2    1.2  1  DZR            Double zinc ribbon
     0.0054   16.4   4.6     0.0089   15.7   4.6    1.4  1  zinc_ribbon_2  zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.7   0.2      0.022   14.8   0.2    1.4  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.033   13.6   5.0      0.064   12.7   5.0    1.5  1  zf-ribbon_3    zinc-ribbon domain
      0.057   13.5   4.1       0.17   12.0   4.1    1.8  1  Zn-ribbon_8    Zinc ribbon domain
       0.17   11.6   0.1       0.24   11.1   0.1    1.1  1  TackOD1        Thaumarchaeal output domain 1
       0.18   11.9   0.0        6.6    6.8   0.0    2.2  2  CpXC           CpXC protein
       0.19   12.2   2.8        1.3    9.6   0.4    2.3  2  zf-C2H2        Zinc finger, C2H2 type
       0.23   11.0   3.1        1.3    8.6   0.1    2.7  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.28   11.2   1.3        3.2    7.8   0.2    2.2  2  YhfH           YhfH-like protein
        2.8    7.9   4.5         34    4.5   0.1    2.4  2  zf-C2HC_2      zinc-finger of a C2HC-type


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 !   46.8   5.9   1.4e-15   1.9e-12       5      36 ..      15      46 ..      11      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.4e-15
                        DUF35_N  5 aegrLvgqrCpdCGtvqfPPravCphCgsddl 36
                                    ++rL+g+rC+dCG+ ++PP  +Cp+Cgs+++
  gi|118431626|ref|NP_148226.2| 15 PRYRLLGGRCSDCGRSFYPPAKACPYCGSRNV 46
                                   79***************************996 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 !   41.5   2.1   7.2e-14     1e-10       2      65 .]      49     112 ..      48     112 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 7.2e-14
                                    EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES...TT-B-EEE-S CS
                  OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpde.vriGmrVravfr 65 
                                    +el++ G+++++tv +    g++++ P+v+g+V+L    ++++++v+v ++e ++ G  V+avfr
  gi|118431626|ref|NP_148226.2|  49 TELPRVGRLEAYTVLYSVESGARDRSPVVIGLVDLGV-AKVVSEIVDVSDPEsLERGVQVEAVFR 112
                                    799********************************99.88********85555***********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   1.9e-06    0.0026      30      49 .]      23      42 ..       9      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.9e-06
                            DZR 30 rCpsCgekvdpearfCpeCG 49
                                   rC+ Cg++  p a+ Cp+CG
  gi|118431626|ref|NP_148226.2| 23 RCSDCGRSFYPPAKACPYCG 42
                                   56666666666666666665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.6   6.4e-06    0.0089       1      21 [.      23      43 ..      23      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.4e-06
                  zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                   +C+ CG+   + ak CpyCG+
  gi|118431626|ref|NP_148226.2| 23 RCSDCGRSFYPPAKACPYCGS 43
                                   6*******************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 ?   14.8   0.2   1.6e-05     0.022      71      98 ..      22      47 ..      14      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                   EEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA 71 vrCreCgkefeleekalrCpkCgsadve 98
                                    rC++Cg++f   +k   Cp Cgs++v 
  gi|118431626|ref|NP_148226.2| 22 GRCSDCGRSFYPPAK--ACPYCGSRNVA 47
                                   68********97744..8******9875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.0   4.6e-05     0.064       4      25 ..      23      44 ..      22      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                    zf-ribbon_3  4 rCPnCGa.plssddnvCpyCGtk 25
                                   rC+ CG     + +++CpyCG++
  gi|118431626|ref|NP_148226.2| 23 RCSDCGRsF-YPPAKACPYCGSR 44
                                   8******77.***********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 ?   12.0   4.1   0.00012      0.17       7      36 ..      23      46 ..      15      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                    Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.ev 36
                                   rC +Cg+ f        +p +aCP Cgs +v
  gi|118431626|ref|NP_148226.2| 23 RCSDCGRSFY-------PPAKACPYCGSrNV 46
                                   6*****8888.......66788******887 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00017      0.24      75     102 ..      23      50 ..      18      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                        TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqe 102
                                     C+ C  +     ++Cp C+S ++ e+e
  gi|118431626|ref|NP_148226.2|  23 RCSDCGRSFYPPAKACPYCGSRNVAETE 50 
                                    5**********************99876 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.039        54      28      51 ..      12      35 ..       5      37 .. 0.77
   2 ?    6.8   0.0    0.0048       6.6      39      75 ..      37      73 ..      35     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                           CpXC 28 eklldgslfeatCpkCgataklea 51
                                    ++   +l+  +C +Cg++++++a
  gi|118431626|ref|NP_148226.2| 12 TRVPRYRLLGGRCSDCGRSFYPPA 35
                                   556666788889******998876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0048
                           CpXC 39 tCpkCgatakleapllyhdpekellillvpesersee 75
                                    Cp+Cg ++ +e +l  + + + + +l+  es +++ 
  gi|118431626|ref|NP_148226.2| 37 ACPYCGSRNVAETELPRVGRLEAYTVLYSVESGARDR 73
                                   6********9999998777777777777777666555 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00095       1.3       2      11 ..      23      32 ..      23      35 .. 0.88
   2 ?    2.3   0.1       0.2   2.8e+02       3       7 ..      38      42 ..      37      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                                   EETTTTEEES CS
                        zf-C2H2  2 kCpdCgksFk 11
                                   +C+dCg+sF 
  gi|118431626|ref|NP_148226.2| 23 RCSDCGRSFY 32
                                   7********5 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                                   ETTTT CS
                        zf-C2H2  3 CpdCg 7 
                                   Cp+Cg
  gi|118431626|ref|NP_148226.2| 38 CPYCG 42
                                   ****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4      0.12   1.7e+02      21      26 ..      23      28 ..      22      31 .. 0.79
   2 ?    8.6   0.1   0.00097       1.3       3      11 ..      38      46 ..      37      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.12
                                   EESSSS CS
                   TF_Zn_Ribbon 21 vCtdCG 26
                                   +C+dCG
  gi|118431626|ref|NP_148226.2| 23 RCSDCG 28
                                   588888 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00097
                                   ETTTTCEEC CS
                   TF_Zn_Ribbon  3 CPnCgstnl 11
                                   CP+Cgs+n+
  gi|118431626|ref|NP_148226.2| 38 CPYCGSRNV 46
                                   ******994 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.12   1.7e+02      16      22 ..      24      30 ..      19      32 .. 0.85
   2 ?    7.8   0.2    0.0023       3.2      12      21 ..      34      43 ..      33      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                           YhfH 16 CteCGke 22
                                   C++CG  
  gi|118431626|ref|NP_148226.2| 24 CSDCGRS 30
                                   *****75 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0023
                           YhfH 12 PkKkCteCGk 21
                                   P+K C+ CG+
  gi|118431626|ref|NP_148226.2| 34 PAKACPYCGS 43
                                   99*******7 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.1     0.029        40       5      12 ..      24      31 ..      23      34 .. 0.83
   2 ?    4.5   0.1     0.025        34       4       9 ..      37      42 ..      36      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.029
                      zf-C2HC_2  5 CpkCgRsF 12
                                   C  CgRsF
  gi|118431626|ref|NP_148226.2| 24 CSDCGRSF 31
                                   777***** PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.025
                      zf-C2HC_2  4 pCpkCg 9 
                                    Cp+Cg
  gi|118431626|ref|NP_148226.2| 37 ACPYCG 42
                                   6****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1052.57
//
Query:       gi|118431627|ref|NP_148227.2|  [L=377]
Description: 3-ketoacyl-CoA thiolase [Aeropyrum pernix K1]
Scores for complete 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-10   39.2   1.0    5.9e-10   38.9   0.1    1.6  2  Thiolase_N   Thiolase, N-terminal domain
    0.00062   19.4   0.2    0.00062   19.4   0.2    1.9  2  Thiolase_C   Thiolase, C-terminal domain
  ------ inclusion threshold ------
        1.8    8.5   6.9        2.1    8.2   0.8    2.8  3  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   9.9e-14   5.9e-10      18     191 ..      17     179 ..       4     195 .. 0.82
   2 ?   -3.7   0.1         1     6e+03     248     256 ..     208     216 ..     203     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 9.9e-14
                                    TTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHH CS
                     Thiolase_N  18 lkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipeevpavtvnkvcsSglkavala 95 
                                    + +  +eeL++eal+++l++ag   ++vd v+v+  +    +gq+ ia  ++  +g+   ++a+tv+   +Sgl+a ++a
  gi|118431627|ref|NP_148227.2|  17 HFSSGVEELAKEALESALSDAGW--ASVDAVVVSSFVYPrLSGQAdIASYIVSSLGF-GGATAITVEAGEASGLAAAVTA 93 
                                    5566789**************95..568888888766555*****************.99******************** PP

                                    HHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHH CS
                     Thiolase_N  96 aqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqde 175
                                    a+  a g+   vv+ Gv +ms+ap +   ++ +g+          + +dg+  +++    Gl a+++  +y+++R+ +  
  gi|118431627|ref|NP_148227.2|  94 ARLAAEGKK--VVLLGVDKMSDAPSSRVYSILKGVYN--------IDWDGVYPISHAAIHGLLADMYMSRYGVDRDTLSY 163
                                    **9998875..7889*********9987554433322........234566667889999******************** PP

                                    HHHHHHHHHHHHHHTT CS
                     Thiolase_N 176 fAvkshqkaaaaqkag 191
                                    + +  h++a++++ a 
  gi|118431627|ref|NP_148227.2| 164 WPALMHSNAKENPYAM 179
                                    ************9886 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1
                                    EEEEEEEEE CS
                     Thiolase_N 248 sDGaaavll 256
                                     DGaaav l
  gi|118431627|ref|NP_148227.2| 208 GDGAAAVTL 216
                                    69****977 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.1   6.5e+03      73      84 ..      72      83 ..      62     107 .. 0.53
   2 !   19.4   0.2     1e-07   0.00062      26      98 ..     248     341 ..     223     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.1
                                   --HHHH-B-TTT CS
                     Thiolase_C 73 GGaialGHPlGa 84
                                   GGa a+    G 
  gi|118431627|ref|NP_148227.2| 72 GGATAITVEAGE 83
                                   455554444442 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1e-07
                                    HHHHHHHHHHT.--.GGGESEEEE--SBHHHHHHHHHHHT--G...................GGBSTT--HHHH-B-TTT CS
                     Thiolase_C  26 yaikkvlkkag.lt.vedidlfEinEAFaaqaLavakaldldl...................ekvNvnGGaialGHPlGa 84 
                                    +a+k++ +ka  l  v++id++E+++ ++   +  +++l+l++                     vN  GG  a GH  Ga
  gi|118431627|ref|NP_148227.2| 248 PAVKEAWDKARsLAgVNNIDVLEVHDSYTITGIIILESLGLAEkgtaakrvaegyftpsgegPTVNASGGLKARGHSGGA 327
                                    67777777764233499*******************************************999***************** PP

                                    HHHHHHHHHHHHHH CS
                     Thiolase_C  85 sGaRivvtllselk 98 
                                    +G+ ++  ++ +l 
  gi|118431627|ref|NP_148227.2| 328 TGVYMLGEIAMQLA 341
                                    ***99999988775 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 ?    0.3   0.4       0.1   6.2e+02      55      68 ..      73      86 ..      41     100 .. 0.73
   2 ?    2.4   0.3     0.024   1.4e+02       9      39 ..      85     113 ..      78     118 .. 0.82
   3 ?    8.2   0.8   0.00035       2.1      50      74 ..     205     228 ..     201     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                                   EEEEEEEEEESSSS CS
                    ACP_syn_III 55 GAgAvvleaseeeg 68
                                   GA+A+ +ea+e +g
  gi|118431627|ref|NP_148227.2| 73 GATAITVEAGEASG 86
                                   99999999997665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                                    HHHHHHHHHHHHHHTTS-SEEEEEEEEEGGG CS
                    ACP_syn_III   9 gfvyalsvAdaliesgaakrvLvigaetlsk 39 
                                    + ++a  +A++l + g  k+v++ g +++s+
  gi|118431627|ref|NP_148227.2|  85 SGLAAAVTAARLAAEG--KKVVLLGVDKMSD 113
                                    5567778888999999..***********97 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00035
                                    TTB-EEEEEEEEEEESSSSCEEEEE CS
                    ACP_syn_III  50 vlfGDGAgAvvleaseeegarilds 74 
                                    + +GDGA+Av l+++ + g  +l++
  gi|118431627|ref|NP_148227.2| 205 FAMGDGAAAVTLSRG-DGGLAVLKA 228
                                    578***********7.466566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 3109.94
//
Query:       gi|118431628|ref|NP_148228.2|  [L=361]
Description: hypothetical protein APE_1873.1 [Aeropyrum pernix K1]
Scores for complete 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   41.6   0.0    2.2e-10   40.5   0.0    1.5  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    0.00013   21.7   0.0       0.01   15.5   0.0    2.1  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    0.00062   19.2   0.2     0.0017   17.8   0.5    1.5  2  Thiolase_N      Thiolase, N-terminal domain
  ------ inclusion threshold ------
      0.019   14.8   3.1      0.021   14.7   1.6    1.9  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha


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 !   40.5   0.0     5e-14   2.2e-10       2      81 ..     232     311 ..     231     320 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 5e-14
                                    HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEET CS
                  ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvgfGa 79 
                                    ek+gl+p d+d+ ++hq n ++  +vakklg+++e+v   l    +Gnt  as +l L + ++    kpgd++l++ fG 
  gi|118431628|ref|NP_148228.2| 232 EKTGLSPGDFDYAIFHQPNGKFPVKVAKKLGFTMEQVKPGLvtPFIGNTYNASALLGLVKVLD--VAKPGDRILVAPFGS 309
                                    799********************************88776644789*****************..99*********9999 PP

                                    TT CS
                  ACP_syn_III_C  80 Gl 81 
                                    G 
  gi|118431628|ref|NP_148228.2| 310 GA 311
                                    96 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 !    5.6   0.0    0.0023        10      62      92 ..     233     263 ..     217     270 .. 0.70
   2 !   15.5   0.0   2.3e-06      0.01     139     211 ..     263     330 ..     251     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0023
                                    -----GGG-SEEEE--SSHHHHHHHHHHHHH CS
                 HMG_CoA_synt_C  62 dkeftlddfdyvifhsPfcklvqkslarlly 92 
                                    ++  +  dfdy ifh P  k+  k   +l +
  gi|118431628|ref|NP_148228.2| 233 KTGLSPGDFDYAIFHQPNGKFPVKVAKKLGF 263
                                    45556679***********987776666655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-06
                                    HHHHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHH CS
                 HMG_CoA_synt_C 139 lfkkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsil 211
                                    ++ ++vkp l+ p  +Gn Y as+   l+ +l         g ri++  +GsG  +  +sl v++  +e ++l
  gi|118431628|ref|NP_148228.2| 263 FTMEQVKPGLVTP-FIGNTYNASALLGLVKVLDV----AKPGDRILVAPFGSGAGSDAYSLIVTDAIEEAKPL 330
                                    5678999998877.69*******99999999933....34699*********************999886554 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5   3.7e-07    0.0017      23     113 ..      62     152 ..      53     168 .. 0.93
   2 ?   -3.1   0.0      0.86   3.8e+03      29      50 ..     225     246 ..     223     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.7e-07
                                    HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTT CS
                     Thiolase_N  23 aeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaag 102
                                    ++ ++ ea+++++++a vdp+++  v++G   +  + +  a  +a ++gi   ++a+ ++ +c  + +++ + ++ +a+g
  gi|118431628|ref|NP_148228.2|  62 STTMGVEAARNAIARARVDPASIGAVFFGSESKPYAVKPSATIIAEALGITPVTMASDLEFACRAASEGMRASIGLVASG 141
                                    678999************************************************************************** PP

                                    SHSEEEEEEEE CS
                     Thiolase_N 103 eadvvvagGvE 113
                                     +  ++++G  
  gi|118431628|ref|NP_148228.2| 142 VVGYTLVVGSD 152
                                    *********76 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.86
                                    HHHHHHHHHHTS-GGGCCEEEE CS
                     Thiolase_N  29 ealkallekagvdpeevdeviv 50 
                                    +a+k+l ek+g++p + d+ i+
  gi|118431628|ref|NP_148228.2| 225 SAVKGLFEKTGLSPGDFDYAIF 246
                                    689999**********999886 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 ?   14.7   1.6   4.7e-06     0.021       2      73 ..     119     186 ..     118     191 .. 0.80
   2 ?   -3.6   0.0       2.3     1e+04      45      57 ..     300     312 ..     290     313 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-06
                                    EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEESSSSCEEEE CS
                    ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleaseeegarild 73 
                                    Dl+ aC ++  ++    +l++sg + + Lv+g++t      +      +  + GA+A+v+++s+     +++
  gi|118431628|ref|NP_148228.2| 119 DLEFACRAASEGMRASIGLVASGVVGYTLVVGSDTAQA--SP-GDVLEFSASSGAAAFVIGPSKGAA-AVFE 186
                                    8999*******************************665..22.344566778899999999985333.4555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.3
                                    THHHHTTB-EEEE CS
                    ACP_syn_III  45 drstavlfGDGAg 57 
                                    dr  +  fG GAg
  gi|118431628|ref|NP_148228.2| 300 DRILVAPFGSGAG 312
                                    5777778999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.35
# Mc/sec: 3085.63
//
Query:       gi|118431629|ref|NP_148229.2|  [L=356]
Description: hypothetical protein APE_1874.1 [Aeropyrum pernix K1]
Scores for 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-25   88.7   0.0    8.9e-25   88.0   0.0    1.4  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0     5e-29   8.9e-25       3     166 ..      48     215 ..      46     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 5e-29
                                    EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpgi 78 
                                    ++  C ++C+fC++     +rr++ ++++ +e+++  v++++ ++ g  + +i g gepl +p++++++++l+ l+ +  
  gi|118431629|ref|NP_148229.2|  48 PSTLCFHNCIFCSVDAGpsSRRRRSEYTVEWEQLVVWVEKVArVKGGgLEALIDGVGEPLTHPHITRIIKALKGLD-AIE 126
                                    5678***********99**999*******************9999999***************************7.*** PP

                                    EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGend 157
                                    r+++et g+ +++  +++l ++g+dr++l+++aad++  + l++ + +++++vl++ e + ++   +vv + v+lpG+n+
  gi|118431629|ref|NP_148229.2| 127 RVALETHGGSLSKSLARALEKAGLDRINLSVDAADPRLARSLVGvDWYGVDRVLKTAEWIIANTSIDVVLTPVVLPGVNE 206
                                    *************************************6666666888888************99888************* PP

                                    HHHHHHHHH CS
                                    xxxxxxxxx RF
                    Radical_SAM 158 eeleellel 166
                                    +e+  l+++
  gi|118431629|ref|NP_148229.2| 207 KEMATLVHW 215
                                    **9888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.19s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 3106.61
//
Query:       gi|14601689|ref|NP_148230.1|  [L=245]
Description: hypothetical protein APE_1876 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.5   0.0       0.31   11.3   0.0    2.0  2  DUF1598   Protein of unknown function (DUF1598)


Domain annotation for each model (and alignments):
>> DUF1598  Protein of unknown function (DUF1598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.1   1.8e+03      11      37 ..      88     114 ..      80     124 .. 0.71
   2 ?   11.3   0.0   1.7e-05      0.31      34      72 ..     182     218 ..     159     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.1
                       DUF1598  11 kklqqllksvkqrlspgeveklveglk 37 
                                   ++l++++++v  r sp++  +lve+l+
  gi|14601689|ref|NP_148230.1|  88 QNLSATVRRVLYRSSPEDSVSLVESLE 114
                                   455566666666789999999999886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 1.7e-05
                       DUF1598  34 eglkkaLGrQdvtvtGipadsrvArvlveaDyrmKligi 72 
                                   +++++ L    ++++G++a    Ar lveaD+r++  g 
  gi|14601689|ref|NP_148230.1| 182 ASIASYL--EAMKLVGVEAPALNARELVEADRRLRSQGF 218
                                   6666655..457899******************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2156.19
//
Query:       gi|118431630|ref|NP_148231.2|  [L=253]
Description: subfamily S26B peptidase [Aeropyrum pernix K1]
Scores for 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-38  131.2  18.6      3e-38  131.2  18.6    1.6  2  Rhomboid  Rhomboid family
     0.0064   17.0   1.6     0.0071   16.9   0.2    1.9  2  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   0.1      0.35   3.1e+03     132     145 ..      27      40 ..      14      45 .. 0.61
   2 !  131.2  18.6   3.3e-42     3e-38       4     148 ..      64     237 ..      61     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHHHHH CS
                       Rhomboid 132 lgGllaGlllglll 145
                                    ++ +++Gl++ +++
  gi|118431630|ref|NP_148231.2|  27 FAAFIVGLTAPWVI 40 
                                    45566666666665 PP

  == domain 2  score: 131.2 bits;  conditional E-value: 3.3e-42
                                    CC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S................ CS
                       Rhomboid   4 rgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses............. 70 
                                     ++l++++tsmflH++w+H+l+Nml+l++fG ++e++lG++r+++ly+ sgl++++++++  a + s             
  gi|118431630|ref|NP_148231.2|  64 GERLYTVFTSMFLHGSWAHILGNMLYLYIFGDNIESILGRARYIILYIGSGLGAVVFHIASIAFMPSealinaalssanp 143
                                    6899*************************************************99999998888877999********** PP

                                    ...-EESSHHHHHHHHHHHHHHHHCCCCGS----HC............CCCCCCCCCCHHHCTSS....STTTHHHHHHH CS
                       Rhomboid  71 ...plvGaSGaifgllgallvlvprnrkllrkliia.........llllllfillnlvlgllpra....ggvsnlAHlgG 134
                                       p+vGaSGai+g+lga+++l+p++r ++ +++++          ++++++++++lv+gl ++     +g++++AH+gG
  gi|118431630|ref|NP_148231.2| 144 wmiPAVGASGAISGVLGAYALLIPFSRVRMLTFWGWfplvlsvpaSIFIGFWFVYQLVMGLATSVsgvsAGIAFWAHVGG 223
                                    ****************************************************************9*************** PP

                                    HHHHHHHHHHHCCH CS
                       Rhomboid 135 llaGlllgllllrr 148
                                    +l+G++l+ ll+ +
  gi|118431630|ref|NP_148231.2| 224 FLTGVALAPLLVDK 237
                                    *******9998765 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   7.9e-07    0.0071       3      75 ..      60     140 ..      58     163 .. 0.63
   2 ?   -2.6   0.1      0.94   8.4e+03      56      56 ..     200     200 ..     181     220 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.9e-07
                        DUF1751   3 allp..ypwtlltasfveqnvwkvlvslltlllggkylErlWg.skEllkFi.....lvvnvitnllvvlltlllylvtk 74 
                                    +++     +t++t++f   ++ ++l ++l l+++g  +E++ g ++ ++ +i     +vv  i+++  +    l++++ +
  gi|118431630|ref|NP_148231.2|  60 YVVAgeRLYTVFTSMFLHGSWAHILGNMLYLYIFGDNIESILGrARYIILYIgsglgAVVFHIASIAFMPSEALINAALS 139
                                    555555789**********************************4444444443333334444444444444444444433 PP

                        DUF1751  75 s 75 
                                    s
  gi|118431630|ref|NP_148231.2| 140 S 140
                                    3 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.94
                        DUF1751  56 v 56 
                                    +
  gi|118431630|ref|NP_148231.2| 200 L 200
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1891.67
//
Query:       gi|14601691|ref|NP_148232.1|  [L=305]
Description: protoheme IX farnesyltransferase [Aeropyrum pernix K1]
Scores for complete 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-46  157.7  24.2    4.2e-46  157.3  24.2    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 !  157.3  24.2   2.3e-50   4.2e-46       2     249 ..      34     280 ..      33     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 2.3e-50
                          UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgll 82 
                                   l+ ++ g+ +a+ggs+d+++l+ll++ ++  ++++ a+N+yfDr+iDa+m rt++RPl+sG ++p eal+ +++l+i+g+l
  gi|14601691|ref|NP_148232.1|  34 LMLTMYGAYFAGGGSLDPRMLALLTIMGFTSIGGVTAFNMYFDRDIDAIMGRTRRRPLPSGVLNPYEALAGSLALVIAGVL 114
                                   7889999999*********************************************************************** PP

                          UbiA  83 llalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaiala 162
                                    + + +n ++al+++++l +  ++Yt+  +Kr+t+l +++g+ia+ +p+l+gwaa++gs++   +l+al+vfl++  + ++
  gi|14601691|ref|NP_148232.1| 115 SA-AAINTYVALTVIAGLYFDiIAYTQ-LTKRFTPLSIIFGSIAGSMPALGGWAAAAGSITTGGVLMALIVFLWQPMHVWF 193
                                   **.*****************99****7.********************************999999999999999999999 PP

                          UbiA 163 ndlrdregDrkagiktlpvvlGrkaaril....lalllavlllallllllalllllylllalllaalallraarlvrrrda 239
                                     +  +e++  a i+ lp    ++ +  l    la l+av++++   +l+++++ l+++++++laala+ r   + r+ ++
  gi|14601691|ref|NP_148232.1| 194 LGYYFKEEYSVARIPILPSNGNPRLVSSLiavsLAGLIAVAWAF---ALYYGYGFLTAVITTVLAALAISRIGGFARTGER 271
                                   9889***************9987777776555556666666665...************************9999999999 PP

                          UbiA 240 kkaakfflfl 249
                                   ++a k+f ++
  gi|14601691|ref|NP_148232.1| 272 REALKLF-KF 280
                                   9988888.43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); 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:                         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 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2394.82
//
Query:       gi|118431631|ref|NP_148233.2|  [L=259]
Description: hypothetical protein APE_1880.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2086.86
//
Query:       gi|118431632|ref|NP_148235.2|  [L=812]
Description: hypothetical protein APE_1882.1 [Aeropyrum pernix K1]
Scores for complete 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   34.3   0.0     0.0005   19.4   0.0    3.2  3  BNR_2           BNR repeat-like domain
    3.2e-05   23.9   0.4    0.00014   21.8   0.0    1.8  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
    0.00031   20.3  10.4        1.4    9.2   0.2    4.8  4  BNR             BNR/Asp-box repeat
     0.0005   20.5   0.7     0.0013   19.1   0.7    1.8  1  NPV_P10         Nucleopolyhedrovirus P10 protein
     0.0027   17.7   1.5      0.007   16.4   1.0    1.7  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
  ------ inclusion threshold ------
      0.013   13.7   1.3      0.018   13.2   1.3    1.0  1  HOOK            HOOK protein
       0.02   13.8   0.3      0.028   13.3   0.3    1.2  1  DUF812          Protein of unknown function (DUF812)
      0.034   13.4   0.2      0.062   12.5   0.2    1.3  1  TMPIT           TMPIT-like protein
      0.035   12.3   0.8       0.05   11.8   0.8    1.1  1  EzrA            Septation ring formation regulator, EzrA
      0.069   13.2   2.2       0.15   12.1   0.4    2.1  2  DUF1664         Protein of unknown function (DUF1664)
      0.075   11.6   0.4        0.1   11.1   0.4    1.1  1  CCDC154         Coiled-coil domain-containing protein 154
       0.11   11.9   1.7       0.35   10.2   1.4    1.8  2  SF-assemblin    SF-assemblin/beta giardin
       0.13   12.4   0.8       0.52   10.4   0.3    1.9  2  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
       0.19   12.0   0.4         21    5.4   0.1    2.5  2  DUF948          Bacterial protein of unknown function (DUF948
       0.21   11.1   1.6       0.31   10.6   1.6    1.1  1  Filament        Intermediate filament protein
       0.23   11.5   0.9       0.38   10.8   0.9    1.3  1  GldM_N          GldM N-terminal domain
       0.23   12.1   0.0       0.52   11.0   0.0    1.5  1  SlyX            SlyX
       0.26   10.6   0.7        0.4    9.9   0.7    1.2  1  CorA            CorA-like Mg2+ transporter protein
       0.32   11.0   4.4        1.1    9.3   0.3    2.3  2  Phasin          Poly(hydroxyalcanoate) granule associated pro


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 !    6.5   0.0    0.0048       4.5     125     202 ..     118     212 ..      80     233 .. 0.56
   2 !   19.4   0.0   5.3e-07    0.0005      81     158 ..     274     378 ..     255     399 .. 0.69
   3 ?    4.7   0.0     0.016        15       1      65 [.     393     450 ..     393     469 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                                    EEEEE...SS--.EEEEEEEESSTTSS-EE----S.....SSEEEEEEEE.EEETTEEEEEEEE..............EE CS
                          BNR_2 125 ilPsshe.lagk.wrallelsddggktWkkgrvve.....qisgeiqpsilvekdgslvalaRs...rka........ai 186
                                    +++s+he lag   ++ +++s dgg tW    v       +i +   p++    dg  ++ + s   r+          i
  gi|118431632|ref|NP_148235.2| 118 VVASHHErLAGLpNAIGVYYSMDGGATWAGPLVMPlaqegDI-YHSDPALASTGDGVFYLAYMSigpRETpggyylsaSI 196
                                    445555542222134445556666666554333334455444.5555555555555444444333221113345555556 PP

                                    EEEEESSTTSS-EEE- CS
                          BNR_2 187 leseSedgGetWskve 202
                                    ++++S dgG++Ws  +
  gi|118431632|ref|NP_148235.2| 197 VVAKSVDGGASWSIIH 212
                                    6666666666665433 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 5.3e-07
                                    ---EEEESSTTSS----E....HHHGG....EEEEEE-SS--..EE--T--EEEEEE.......SS--EEEEEEEESSTT CS
                          BNR_2  81 kitrvtSkDdGktWsapr....rlpks....pflnisgpvknkpiqladGrlilPsshe.....lagkwrallelsddgg 147
                                    +it+v S D+G tW  p     ++ +s        i+ +   +p +  dG++ ++++       l+gk ++++ +s+d g
  gi|118431632|ref|NP_148235.2| 274 RITAVVSPDGGSTWIGPStvaeAVNTSegmrFGGGIQVLQGSNPAVSPDGSIYVAYYDSlsdgyLEGKAAIMVSVSQDLG 353
                                    35569************9555444444444323334444445677777*******888888888999************* PP

                                    SS-EE----S..............S CS
                          BNR_2 148 ktWkkgrvve..............q 158
                                    +tW+k +  +              +
  gi|118431632|ref|NP_148235.2| 354 QTWSKPEQAAvieremdyyspsgfR 378
                                    ***9977665555555555555553 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.016
                                    XTEEEEEESSSSGGGEEEEEEEEEETTEEE.EEEEEE-TTS-...BTTEEEEEEEEEEETTTEEE CS
                          BNR_2   1 gtLlaawfggsregapdvaiwvsvsdkgsneWsapqvvadreqsrearkklgNPvlfqdpsgtli 65 
                                    gt+++a+ ++ +++  dv + ++  +++s+ W +p +++ +e     +     P l +d+sg+++
  gi|118431632|ref|NP_148235.2| 393 GTIYVAYASAGQDDPGDVFLVYK--TPESQVWEEPLMISRGE-----GSLQFFPWLDVDESGRVH 450
                                    789999*****************..*************9999.....555555555555555555 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.2   1.2e+03     124     157 ..     644     677 ..     637     686 .. 0.53
   2 !   21.8   0.0   1.5e-07   0.00014       2      89 ..     689     776 ..     688     787 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHH-----..-----SSSHHH CS
                 Apolipoprotein 124 eelrqklaerleelkeslaphaeeveerlssrve 157
                                    +  rq++ e++ e   s   ++e++e+r++s  e
  gi|118431632|ref|NP_148235.2| 644 DASRQEILESVRETAMSTGSALESLETRMASLEE 677
                                    4455555555555555555555555555544333 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.5e-07
                                    HHHCCCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHH CS
                 Apolipoprotein   2 leesldelkayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapytee 81 
                                    ++ sld+++a +++l+++l+++  ++  ++ +++e++++++r+e e  r+ + + + e++  +++++ ++   ++ +   
  gi|118431632|ref|NP_148235.2| 689 IKGSLDDVSASVDTLSSRLGDIESSINSKIDAASEDIKNEVRSEGEKTRSTVNSMLGEIESLINEKTSGIMGAIEDLGTS 768
                                    5679******************99*************************************************9999999 PP

                                    HHHHHHHC CS
                 Apolipoprotein  82 lrerlaad 89 
                                    +++ ++++
  gi|118431632|ref|NP_148235.2| 769 IQKGVEEA 776
                                    99988765 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0064         6       1      10 [.     136     145 ..     136     146 .. 0.94
   2 ?    5.3   0.2     0.028        27       3      11 ..     201     209 ..     200     209 .. 0.93
   3 ?    2.1   0.1      0.33   3.1e+02       3      10 ..     280     287 ..     278     287 .. 0.85
   4 !    9.2   0.2    0.0015       1.4       2      12 .]     348     358 ..     347     358 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0064
                                    EEESSTTSS- CS
                            BNR   1 yyStDgGktW 10 
                                    yyS DgG tW
  gi|118431632|ref|NP_148235.2| 136 YYSMDGGATW 145
                                    8********* PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.028
                                    ESSTTSS-E CS
                            BNR   3 StDgGktWs 11 
                                    S DgG +Ws
  gi|118431632|ref|NP_148235.2| 201 SVDGGASWS 209
                                    89******8 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.33
                                    ESSTTSS- CS
                            BNR   3 StDgGktW 10 
                                    S DgG tW
  gi|118431632|ref|NP_148235.2| 280 SPDGGSTW 287
                                    66****** PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0015
                                    EESSTTSS-EE CS
                            BNR   2 yStDgGktWsk 12 
                                    +S+D G+tWsk
  gi|118431632|ref|NP_148235.2| 348 VSQDLGQTWSK 358
                                    7********97 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   1.4e-06    0.0013       2      67 ..     646     716 ..     645     753 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                        NPV_P10   2 S.qniLlvIradikavddkVdalqqqvddv....qenlpdvtelnekLdaqsaqLaeletkvenIqdiLnp 67 
                                    S q iL  +r+    + + +++l+++++++    ++n++d+ e++  Ld+ sa++++l++ + +I++  n+
  gi|118431632|ref|NP_148235.2| 646 SrQEILESVRETAMSTGSALESLETRMASLeeiaRQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINS 716
                                    669999999999999999******999666222257******************************99884 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 !   16.4   1.0   7.4e-06     0.007      32     138 ..     639     744 ..     627     747 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.4e-06
                   Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNinstL 108
                                    +l+++ +  ++i +++ + + +  s+l++l+tr+++l +   +     +    +++  L+ + + + +L s ++ i+s++
  gi|118431632|ref|NP_148235.2| 639 VLGAVDASRQEILESVRETAMSTGSALESLETRMASLEEIARQN----SqdiGEIKGSLDDVSASVDTLSSRLGDIESSI 714
                                    23444444444444444444444444444444444433333333....244458999*********************** PP

                   Baculo_PEP_C 109 nnllqalnnldlgalsqeledaldtveeil 138
                                    n+ + a    +++++ +e+e++ +tv+++l
  gi|118431632|ref|NP_148235.2| 715 NSKIDAASEDIKNEVRSEGEKTRSTVNSML 744
                                    *******9999**********999999887 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   1.9e-05     0.018     475     573 ..     653     754 ..     646     768 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                           HOOK 475 seeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed.ssllkkkleehleklk.evqee 552
                                    s +e  +++ + le  + r+ +Le+  r++ q i e++  ++++  + ++  s+  d  s+ ++k+++  e +k ev +e
  gi|118431632|ref|NP_148235.2| 653 SVRETAMSTGSALESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDiESSINSKIDAASEDIKnEVRSE 732
                                    556777888899******************************************99988999******999996489*** PP

                           HOOK 553 lqkkkeqleelepklssnk.qk 573
                                     +k + +++++  +++s   +k
  gi|118431632|ref|NP_148235.2| 733 GEKTRSTVNSMLGEIESLInEK 754
                                    ***9999998877766655455 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3     3e-05     0.028     313     391 ..     667     744 ..     598     775 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                         DUF812 313 elakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlell 391
                                    +l++++ + ee+  ++++++ e++  ++++++++++l++ + ++essi+   +++ e + +ne + +  k++  + ++l
  gi|118431632|ref|NP_148235.2| 667 SLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINSKIDAASE-DIKNEVRSEGEKTRSTVNSML 744
                                    2347899***************************************99876555544.444555555555555555555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   6.6e-05     0.062       4      94 ..     665     757 ..     663     763 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                          TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.eeeeeeveelkeelkerkkvl 82 
                                    +e+le+++ +lee a++  q++ e++ + +++s ++++ + rl +++ss+++   +++ + ++e  +e +++ ++ +++l
  gi|118431632|ref|NP_148235.2| 665 LESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINSKIDAASeDIKNEVRSEGEKTRSTVNSML 744
                                    6899**********************************************876555441445555556666666677777 PP

                          TMPIT  83 kevesllpkk.ng 94 
                                     e+esl+ +k +g
  gi|118431632|ref|NP_148235.2| 745 GEIESLINEKtSG 757
                                    7999998888444 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   5.3e-05      0.05     102     205 ..     650     753 ..     644     782 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.3e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH-------- CS
                           EzrA 102 klaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefe 181
                                     l++++e+  ++ + ++++ + ++ l e  ++n++ i ++k   ++++ ++ + +  +g++++++++++++  +++++ +
  gi|118431632|ref|NP_148235.2| 650 ILESVRETAMSTGSALESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINSKIDAASEDIKNEV 729
                                    56777888888889999**********************************************************99988 PP

                                    --------HHHHHHHHHHHHHHHH CS
                           EzrA 182 eltengdyveakeilkkleeeide 205
                                        ++  ++++ +l ++e+ i+e
  gi|118431632|ref|NP_148235.2| 730 RSEGEKTRSTVNSMLGEIESLINE 753
                                    888888888888888888877764 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00016      0.15      51     119 ..     648     716 ..     636     720 .. 0.91
   2 ?    8.9   0.2    0.0016       1.5      43     118 ..     693     770 ..     689     777 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                        DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                    +++ es+++t     s ++++++++ + +ei+++ ++++ e+++ l++++  v+++++   ++es++++
  gi|118431632|ref|NP_148235.2| 648 QEILESVRETAMSTGSALESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINS 716
                                    678899999999999************************************************999975 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                        DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqk.eiskeikeevtevredlse.igedvesvkeavegleskle 118
                                    +++vs +++++s+ l +    ++s+id   + +++      +++++ v+++ +++++ i+e+ + +  a+e+l+++++
  gi|118431632|ref|NP_148235.2| 693 LDDVSASVDTLSSRLGDIESSINSKIDAASEDIKNEVrSEGEKTRSTVNSMLGEIESlINEKTSGIMGAIEDLGTSIQ 770
                                    578999999999999999999999999999988765504567899999999999976367778889999999999886 PP

>> CCDC154  Coiled-coil domain-containing protein 154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   0.00011       0.1     317     419 ..     650     749 ..     623     786 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                        CCDC154 317 lqesleavqlatdlarrEtesalellqEKsqaleesvaelatqlkDLsDhvlalsWrldLqeqtLslklseakeewekae 396
                                    + es+ ++ ++t  a    e+ ++ l+E      +++ e++  l D+s  v +ls rl   e  ++ k+++a e+++++ 
  gi|118431632|ref|NP_148235.2| 650 ILESVRETAMSTGSALESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINSKIDAASEDIKNEV 729
                                    44566666688899999999999*****999999************************9999**********99988776 PP

                        CCDC154 397 rrsleklvqwekeveahLrevqe 419
                                    r   ek    + +v+  L e++ 
  gi|118431632|ref|NP_148235.2| 730 RSEGEKT---RSTVNSMLGEIES 749
                                    6666665...6666666666654 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.52   4.9e+02      72     123 ..     643     693 ..     636     708 .. 0.68
   2 ?   10.2   1.4   0.00037      0.35      62     134 ..     708     777 ..     666     788 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.52
                   SF-assemblin  72 ikklqekikeevddlalelkkaveelnekinnveanvenekakrrdaiekla 123
                                    ++   ++i+e v + a+   +a+e+l+ ++  +e   + +  + + +i+   
  gi|118431632|ref|NP_148235.2| 643 VDASRQEILESVRETAMSTGSALESLETRMASLEEIAR-QNSQDIGEIKGSL 693
                                    55566788999999999999999999999999986544.4444455555544 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00037
                   SF-assemblin  62 kdiqeefkkeikklqekikeevddlalelkkaveelnekinnveanvenekakrrdaieklakelvkelnele 134
                                     di + ++++i+   e ik+ev     + +++v+++   + ++e++++++      aie l +++ k + e +
  gi|118431632|ref|NP_148235.2| 708 GDIESSINSKIDAASEDIKNEVRSEGEKTRSTVNSM---LGEIESLINEKTSGIMGAIEDLGTSIQKGVEEAK 777
                                    58999******************9999999988776...8899****9999999************9998865 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 ?   -0.2   0.0       1.1   9.9e+02      21      67 ..     648     686 ..     638     707 .. 0.48
   2 ?   10.4   0.3   0.00055      0.52      36     106 ..     712     783 ..     677     789 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                      ApoLp-III  21 eevvetiKe...nsenlvdqlkqvikslqeelkkksdeleealkevkkki 67 
                                    +e++e ++e   ++ +++++l++ ++sl+e + ++s+            i
  gi|118431632|ref|NP_148235.2| 648 QEILESVREtamSTGSALESLETRMASLEEIARQNSQD-----------I 686
                                    44444444311134445555555555555544443332...........2 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00055
                      ApoLp-III  36 dqlkqvikslqeelkk.ksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqkl 106
                                    +++++ i+ ++e++k+   +e e++ + v++++ e+   ++e+ +++  ++++l +++Q+gv++   +++++
  gi|118431632|ref|NP_148235.2| 712 SSINSKIDAASEDIKNeVRSEGEKTRSTVNSMLGEIESLINEKTSGIMGAIEDLGTSIQKGVEEAKGDAETA 783
                                    578888888888888866778899999999999999999999*******************99766555555 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 ?    5.4   0.1     0.023        21      23      61 ..     674     712 ..     633     723 .. 0.48
   2 ?    5.1   0.0     0.028        27      34      86 ..     717     771 ..     705     772 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.023
                         DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelle 61 
                                    +l+++++++++ i e++  +d ++  v++l +   ++ +
  gi|118431632|ref|NP_148235.2| 674 SLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIES 712
                                    233333333333333333333333333333333333333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
                         DUF948  34 tieelekqvd.pilkevedllakvnelledvne.klekvdplteavadlgesvse 86 
                                     i+   ++++ ++  e e++ ++vn +l ++++   ek   ++ a++dlg+s+++
  gi|118431632|ref|NP_148235.2| 717 KIDAASEDIKnEVRSEGEKTRSTVNSMLGEIESlINEKTSGIMGAIEDLGTSIQK 771
                                    555555555414556788999999999999999455899************9985 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.6   0.00033      0.31     191     271 ..     666     747 ..     643     757 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                                    XXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 191 ewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkq.kasleaqlaeleerleaeleklqeklselee 269
                                    e  +++++ l+e a++ns+++ + k  + ++  ++++l++ l +++++ ++++ a+ +++++++ +e ek++++++++  
  gi|118431632|ref|NP_148235.2| 666 ESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSiNSKIDAASEDIKNEVRSEGEKTRSTVNSMLG 745
                                    556899999*******************************9999987625556666777777777777777777665544 PP

                                    HH CS
                       Filament 270 el 271
                                    e+
  gi|118431632|ref|NP_148235.2| 746 EI 747
                                    44 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00041      0.38      17     131 ..     661     780 ..     652     791 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                         GldM_N  17 nenasekNaalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkded.vgeikak.dnldaas 94 
                                    + +a e+ ++ +asle+ a++n +  +e++   ++v++  d l + + ++   i  +++   ed ++e++++ +++  + 
  gi|118431632|ref|NP_148235.2| 661 TGSALESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINSKIDAASEDiKNEVRSEgEKTRSTV 740
                                    556667778999***********************************************998887666666655777777 PP

                         GldM_N  95 elmlaeg...ksgkGkeLkkkineyreellklvndlakda 131
                                    + ml e     ++k   ++ +i++  + ++k v++ + da
  gi|118431632|ref|NP_148235.2| 741 NSMLGEIeslINEKTSGIMGAIEDLGTSIQKGVEEAKGDA 780
                                    7788444679999999999999999999999999844444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00055      0.52       4      56 ..     664     716 ..     662     725 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                           SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                     le LE+++a +e+   + ++ + e    +d   + ++ l  rl ++e+s ++
  gi|118431632|ref|NP_148235.2| 664 ALESLETRMASLEEIARQNSQDIGEIKGSLDDVSASVDTLSSRLGDIESSINS 716
                                    5899******************************************9998664 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.7   0.00042       0.4     117     234 ..     648     759 ..     634     762 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00042
                           CorA 117 deivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeyl 194
                                    +ei+++++e+     + l+ le+++   +++ ++  ++       +++++ +l +  + + + l+ ++ + +++  +  +
  gi|118431632|ref|NP_148235.2| 648 QEILESVRETAMSTGSALESLETRMasLEEIARQNSQD-------IGEIKGSLDDVSASV-DTLS-SRLGDIESSINSKI 718
                                    67777788888888888888888884444444444444.......666666666666666.4444.35555555555668 PP

                           CorA 195 rdlldeler.llemlealrerleslqdtyssllserlNrvm 234
                                    +  ++++++ +  + e +r+ ++s+  ++ sl++e++  +m
  gi|118431632|ref|NP_148235.2| 719 DAASEDIKNeVRSEGEKTRSTVNSMLGEIESLINEKTSGIM 759
                                    999999998899999999****************9998777 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 ?    3.3   0.5     0.082        78      54     124 ..     635     703 ..     619     705 .. 0.81
   2 ?    9.3   0.3    0.0012       1.1      46     108 ..     709     774 ..     700     781 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.082
                         Phasin  54 vaeekleevresvkskveevkekaeeqwdklekafdervakaLsrlgvpsredveaLsarvdeLtkelekl 124
                                     ++  l +v  s ++ +e+v+e a ++ + le+ +++r+a +L+++  ++++d+ +++  +d ++++++ l
  gi|118431632|ref|NP_148235.2| 635 YIDVVLGAVDASRQEILESVRETAMSTGSALES-LETRMA-SLEEIARQNSQDIGEIKGSLDDVSASVDTL 703
                                    556667778888888899999999999999987.578875.79*******************999999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                         Phasin  46 klekktkkvaeekleevresvkskveevkekaeeqwdklekafderva...kaLsrlgvpsredve 108
                                    ++e++ +++++++ e+++++v+s+ e+ ++ +++ + ++e++++e+ +    a++ lg + ++ ve
  gi|118431632|ref|NP_148235.2| 709 DIESSINSKIDAASEDIKNEVRSEGEKTRSTVNSMLGEIESLINEKTSgimGAIEDLGTSIQKGVE 774
                                    6788899999**********************************9976111566777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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):              19  [number of targets reported over threshold]
# CPU time: 0.85u 0.29s 00:00:01.13 Elapsed: 00:00:00.44
# Mc/sec: 5580.33
//
Query:       gi|118431633|ref|YP_874915.1|  [L=41]
Description: hypothetical protein APE_1882a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       118  (0.00658152); expected 358.6 (0.02)
Passed bias filter:                       97  (0.00541023); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 314.01
//
Query:       gi|14601697|ref|NP_148238.1|  [L=275]
Description: 5'-methylthioadenosine phosphorylase [Aeropyrum pernix K1]
Scores for complete 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-48  163.5   0.0    5.4e-48  163.3   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
       0.16   11.8   0.0       0.55   10.1   0.0    1.7  2  NinB       NinB protein


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 !  163.3   0.0     6e-52   5.4e-48       2     233 ..      14     252 ..      13     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 6e-52
                                   EEEEESSH....HHHHHHHHHEEEEEEEEEE.TTEEEEEEEE.TTEEEEEEE--....SSHHHHHHHHHHHHHHHC--SEE CS
                     PNP_UDP_1   2 iaiivgsp....gevellaespleetpfgregrgfkfvtGtl.kgkpvvivstG....iGkpnaavvaeirllkefgvkai 73 
                                   +++i+gs+    g ve+  e    +tp+g++  + ++v+G + + k+ ++ ++G    i ++ ++++a+i++lk++gvk +
  gi|14601697|ref|NP_148238.1|  14 VGVIGGSGlydpGIVENPVEV-KVSTPYGNP--SDFIVVGDVaGVKVAFLPRHGrghrIPPHAINYRANIWALKALGVKWV 91 
                                   689999997666666666666.99*******..*********5556669********99999999**************** PP

                                   EEEEEEEESSTTT-TT-EEEEEEEEESSSCCG.CCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEEEEES CS
                     PNP_UDP_1  74 iriGtaGglnpdlkvGDvvipddainfdgrsp.lygpkeegqyfpdsydapadpelrallkeaaealgikvhr.Gvvatad 152
                                   i+++++G+l++d+++GD+v+pd++i+++  ++ +++++ +   ++ ++d+ ++++lr++l  + ++lg++vh+ G++++ +
  gi|14601697|ref|NP_148238.1|  92 ISVSAVGSLREDYRPGDFVVPDQFIDMTKNRRhYTFYDGPVTVHVSMADP-FCEDLRQRLIDSGRRLGYTVHErGTYVCIE 171
                                   **************************666555266666668888888888.*********************99******* PP

                                   ESS-CHHHHHH.HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHHH CS
                     PNP_UDP_1 153 gfyaeteaelr.llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaalllal 232
                                   g++++t+ae+r +   + ad+++M+ +++  lA e+++++a++++v+d ++ +ad++ t eeve ++  ++++a + l  +
  gi|14601697|ref|NP_148238.1| 172 GPRFSTRAESRvWKDVFKADIIGMTLVPEINLACEAQLCYATLAMVTD-YDVWADRPVTAEEVERVMISNVERARRMLYDV 251
                                   ***********7777777******************************.899**********************9998776 PP

                                   H CS
                     PNP_UDP_1 233 l 233
                                   +
  gi|14601697|ref|NP_148238.1| 252 I 252
                                   6 PP

>> NinB  NinB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.19   1.7e+03      66      79 ..     179     192 ..     176     206 .. 0.79
   2 ?   10.1   0.0   6.1e-05      0.55      47      96 ..     209     258 ..     201     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.19
                          NinB  66 ldaeeWKdlltaal 79 
                                    ++  WKd++ a +
  gi|14601697|ref|NP_148238.1| 179 AESRVWKDVFKADI 192
                                   56778****99865 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.1e-05
                          NinB  47 llwallkdiarqvewagekldaeeWKdlltaalkqatgeeqevvpgleGg 96 
                                   l +a+l+ +     wa++  +aee  +++++ + +a++   +v+p l G+
  gi|14601697|ref|NP_148238.1| 209 LCYATLAMVTDYDVWADRPVTAEEVERVMISNVERARRMLYDVIPKLAGE 258
                                   5589999999999************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2175.39
//
Query:       gi|118431634|ref|NP_148239.2|  [L=285]
Description: hypothetical protein APE_1886.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2040.52
//
Query:       gi|118431635|ref|NP_148240.2|  [L=429]
Description: hypothetical protein APE_1887.1 [Aeropyrum pernix K1]
Scores for 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   15.5   0.0       0.02   14.0   0.0    1.6  2  Phosphatase  Phosphatase
  ------ inclusion threshold ------
       0.08   13.0   0.0       0.17   11.9   0.0    1.5  1  SIS_2        SIS domain


Domain annotation for each model (and alignments):
>> Phosphatase  Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.21   1.9e+03      78     129 ..     135     186 ..     128     200 .. 0.81
   2 !   14.0   0.0   2.2e-06      0.02      83     154 ..     199     271 ..     187     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.21
                    Phosphatase  78 tvdaldrlaerlakaaerrervllatGHPakLlgvyaaladalraaGcevlt 129
                                    ++ +l++  + l +a + r + + a G P+  l   +a+ + l + G e+++
  gi|118431635|ref|NP_148240.2| 135 ALRTLEQGVRGLWAASRVRGSRIAAIGPPSPWLVSSRAWHEDLARLGVELVE 186
                                    4667777788888899999999999999999999999999999999988874 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.2e-06
                    Phosphatase  83 drlaerlakaaerrervl.latGHPakLlgvyaaladalraaGcevltpaagrsveietelgarereiryveg 154
                                    + + e l++ + rr +vl la G P+k l vy+a++++ +++G + ++pa  + ++ + ++    +++   eg
  gi|118431635|ref|NP_148240.2| 199 ESVPESLGEEVLRRGEVLdLADGEPKKSLRVYRAIKRMWKSRGLDAVSPACWWFYKEAGANACLAHSLLNDEG 271
                                    66778888888889999879*********************************99998888777777666555 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.9e-05      0.17     105     133 ..      66      94 ..      58      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                                    -EEEEE-SS--SHHHHHHHHHHHHHT-EE CS
                          SIS_2 105 DvLlviSnsGnnavvveaaeaakergmkv 133
                                     +Llv+ ++G +av++ea+e+ake g++v
  gi|118431635|ref|NP_148240.2|  66 SLLLVLATGGTEAVALEAVEKAKEEGVPV 94 
                                    689************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3038.14
//
Query:       gi|14601700|ref|NP_148241.1|  [L=224]
Description: hypothetical protein APE_1889 [Aeropyrum pernix K1]
Scores for 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-11   43.0   0.0    1.2e-10   41.9   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    1.5e-05   25.6   0.0    3.6e-05   24.4   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
    0.00066   19.5   0.0     0.0021   17.9   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
     0.0071   17.1   0.0        4.8    8.0   0.0    2.3  2  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
       0.02   14.2   0.0      0.065   12.6   0.0    1.9  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   3.4e-14   1.2e-10       1      95 [.      51     136 ..      51     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 3.4e-14
                                   EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHH CS
               Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekal 81 
                                   L+vG+GtG +a  +   +    g+D+s  ml++a+e++ +       v +  e++pf++  f   ++  +l++ +dp+++l
  gi|14601700|ref|NP_148241.1|  51 LEVGVGTGFFASIVGADA----GLDPSLGMLRRARERGIPLL-----VAGVGERMPFRSRVFGSALIVVTLCFADDPQELL 122
                                   89*************555....9***********99998886.....9999999*************************** PP

                                   HHHHHHEEEEEEEE CS
               Methyltransf_11  82 keiaRvLkpgGllv 95 
                                   +e++RvL  gG+lv
  gi|14601700|ref|NP_148241.1| 123 REVWRVLAWGGVLV 136
                                   ***********997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0     1e-08   3.6e-05       2      97 .]      51     133 ..      50     133 .. 0.87
   2 ?   -2.6   0.0       2.7   9.7e+03      23      37 ..     165     179 ..     152     193 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1e-08
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEEESTGGGSSHHH CS
               Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvssgalhhlsded 81 
                                   L++G GtG ++  + +        g+D+s +ml++arer       + ++++ + e++pf ++ f   +++ +l++ +  d
  gi|14601700|ref|NP_148241.1|  51 LEVGVGTGFFASIVGADA------GLDPSLGMLRRARERG------IPLLVAGVgERMPFRSRVFGSALIVVTLCFAD--D 117
                                   89******9999998875......9**************9......77777666599**********99986688766..6 PP

                                   HHHHHHHHHHHEEEEE CS
               Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    +++l+e++rvL  gG
  gi|14601700|ref|NP_148241.1| 118 PQELLREVWRVLAWGG 133
                                   679*********9998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                                   EEEEEESSHHHHHHH CS
               Methyltransf_25  23 kvtgvDiseemleaa 37 
                                   +++  ++ ++ml++a
  gi|14601700|ref|NP_148241.1| 165 RFITNEMHHTMLKNA 179
                                   444444444455444 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.8e-07    0.0021      14     162 ..      40     183 ..      17     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.8e-07
               Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......kakkaqkdqfdeqeaaepqgkfdlIv 87 
                                    r+l  + ++  +L++G GtG ++++  +     +g D+s  +  +a+                   +  ++ ++ f  + 
  gi|14601700|ref|NP_148241.1|  40 SRAL--EGSPRPLLEVGVGTGFFASIVGAD----AGLDPSLGMLRRARergipllV-----AGVG--ERMPFRSRVFGSAL 107
                                   3333..4566699********999977555....8999999999999988544432.....3333..34455888999999 PP

               Methyltransf_23  88 lrevlehvpdppellrqiatllkpgGylllseplaslkedrllldw.lylvpagrhisffsarslkelleeaGlev 162
                                      +l+  +dp ellr +++ l+ gG+l+ + + +++++ + ++   ++  p   + +f++ +   ++l++aG+++
  gi|14601700|ref|NP_148241.1| 108 IVVTLCFADDPQELLREVWRVLAWGGVLVSCIVPRDSSWGEYYEAKgRAGHPFYSKARFITNEMHHTMLKNAGFSL 183
                                   999*****************************99999999998887567777778889999888899999999976 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0013       4.8       1      39 [.      51      83 ..      51      88 .. 0.94
   2 !    6.8   0.0    0.0031        11      75      99 .]     111     135 ..      98     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0013
               Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakek 39
                                  Le+G GtG +++ + ++       g+D+s  ++ +a+e+
  gi|14601700|ref|NP_148241.1| 51 LEVGVGTGFFASIVGAD------AGLDPSLGMLRRARER 83
                                  8****************......**********999987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0031
               Methyltransf_12  75 vlhhlkdirevldnirklLkpgGrl 99 
                                   +l+  +d++e+l+++ ++L+ gG+l
  gi|14601700|ref|NP_148241.1| 111 TLCFADDPQELLREVWRVLAWGGVL 135
                                   56667******************87 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05     0.065     102     150 ..      88     136 ..      11     143 .. 0.90
   2 ?   -1.3   0.0      0.31   1.1e+03     197     215 ..     165     183 ..     161     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                   EEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
               Ubie_methyltran 102 flqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                   ++ + +e++pf    f +  +   l    D ++ L+e++rvl  GG lv
  gi|14601700|ref|NP_148241.1|  88 LVAGVGERMPFRSRVFGSALIVVTLCFADDPQELLREVWRVLAWGGVLV 136
                                   467889****************************************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.31
                                   HS--HHHHHHHHHHTTEEE CS
               Ubie_methyltran 197 afPdqetlkeliedaGfks 215
                                   +f  +e  ++++++aGf+ 
  gi|14601700|ref|NP_148241.1| 165 RFITNEMHHTMLKNAGFSL 183
                                   56677888999*****974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1538.47
//
Query:       gi|118431636|ref|YP_874916.1|  [L=84]
Description: hypothetical protein APE_1889a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 629.46
//
Query:       gi|118431637|ref|NP_148242.2|  [L=248]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for 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  130.7   0.0    6.8e-38  130.3   0.0    1.2  1  ABC_tran      ABC transporter
    1.1e-10   41.8   0.1    5.9e-05   23.0   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.6e-07   30.3   0.1     0.0044   16.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    5.2e-06   26.1   0.0    9.5e-06   25.3   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
    5.5e-06   26.9   0.1    9.8e-06   26.1   0.1    1.4  1  AAA_16        AAA ATPase domain
    0.00059   20.1   0.1     0.0021   18.3   0.1    1.8  1  AAA_22        AAA domain
     0.0011   18.9   0.1     0.0045   16.9   0.1    1.8  2  RsgA_GTPase   RsgA GTPase
     0.0012   17.8   0.2        1.1    8.0   0.0    2.3  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.003   17.3   0.0     0.0055   16.5   0.0    1.4  1  AAA_24        AAA domain
     0.0031   17.9   0.0      0.019   15.4   0.0    2.0  1  AAA           ATPase family associated with various cellular 
     0.0037   17.5   0.4      0.044   14.0   0.5    2.3  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0053   16.5   0.0      0.011   15.5   0.0    1.8  1  AAA_30        AAA domain
     0.0057   16.4   0.0       0.24   11.1   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
     0.0059   16.0   0.0      0.016   14.6   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0075   16.8   0.0      0.012   16.1   0.0    1.2  1  AAA_23        AAA domain
     0.0075   16.2   0.0       0.12   12.2   0.0    2.2  2  NACHT         NACHT domain
     0.0083   16.3   0.3      0.058   13.6   0.3    2.0  1  AAA_33        AAA domain
  ------ inclusion threshold ------
      0.012   14.7   0.1      0.041   13.0   0.0    1.8  2  T2SSE         Type II/IV secretion system protein
      0.015   15.0   0.0       0.38   10.4   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.065   12.4   0.0      0.093   11.9   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.066   13.8   0.0       0.12   12.9   0.0    1.5  1  AAA_18        AAA domain
      0.068   11.9   0.0      0.095   11.5   0.0    1.1  1  Adeno_IVa2    Adenovirus IVa2 protein
      0.075   12.9   0.0       0.13   12.2   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
       0.11   12.4   0.1       0.61   10.0   0.0    2.0  2  NTPase_1      NTPase
       0.11   12.8   0.1       0.25   11.6   0.0    1.6  1  AAA_28        AAA domain
       0.11   11.6   0.0       0.18   10.9   0.0    1.3  1  DUF815        Protein of unknown function (DUF815)
       0.14   12.5   0.0       0.21   12.0   0.0    1.4  1  RNA_helicase  RNA helicase
       0.17   12.0   0.0       0.34   11.0   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
       0.17   11.5   0.0       0.35   10.4   0.0    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.0   1.1e-40   6.8e-38       1     137 []      20     169 ..      20     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 1.1e-40
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvr 77 
                                    lk v+++l+ gek++i+G++G+GKStLlk++ +l++p++G+i ++g d+++    +l+ +r++ig+lpq  +lfp++tv 
  gi|118431637|ref|NP_148242.2|  20 LKGVDVSLSYGEKLVIMGPSGSGKSTLLKAIPRLVEPDSGSIVFRGVDVTRlsgSQLRMVRRKIGYLPQSYSLFPHMTVL 99 
                                    789*************************************************99************************** PP

                                    HH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +n              +++e++ k+ls lg+++l++++     + LSgGq+qr alaral+ +p++lllDEpt+
  gi|118431637|ref|NP_148242.2| 100 RNityplekalglsrrDAEERAVKYLSMLGIEDLAHRHP----ARLSGGQQQRAALARALAMEPDILLLDEPTS 169
                                    *************99988999************999998....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0     5e-06    0.0031       3      67 ..      34      99 ..      33     126 .. 0.62
   2 !   23.0   0.0   9.5e-08   5.9e-05     234     297 ..     138     198 ..      86     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl....drdvegltdelsggggirkipslldlydpeipfefeieefls 67
                                   v+ Gp gsGKS+LL+a+  l  +     + v+++ d+ + +g+   + ++  +y p + + f    +++
  gi|118431637|ref|NP_148242.2| 34 VIMGPSGSGKSTLLKAIPRL--VepdsGSIVFRGVDVTRLSGSQLRMVRRKIGYLPQSYSLFPHM-TVL 99
                                   899**************666..2335555555555555555555555555555555555555555.555 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 9.5e-08
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTH 297
                                    ++ lS G+++ +al+ al+  +   ++ll+DEp + L+P+  + +le l + ++  g   i++TH
  gi|118431637|ref|NP_148242.2| 138 PARLSGGQQQRAALARALAMEP---DILLLDEPTSALDPESRADVLEALfRVATL-GKAMIVVTH 198
                                    566899*****99999999988...9********************888677777.555699998 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 !   12.2   0.0   0.00014     0.088      27      44 ..      33      50 ..      11      61 .. 0.82
   2 !   16.5   0.0   7.2e-06    0.0044     136     205 ..     140     206 ..      68     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                   EEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlldAi 44
                                    +i+Gp GSGKs ll Ai
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAI 50
                                   589**************9 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 7.2e-06
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH.HHCTTSEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk.eksknaQfivislreemleka 205
                                     LSgG+++ +ala  +A++   p  + llDe  +aLD + ++ v e l   ++    +iv+++++++  k+
  gi|118431637|ref|NP_148242.2| 140 RLSGGQQQRAALARALAME---P-DILLLDEPTSALDPESRADVLEALFrVATLGKAMIVVTHEADFAVKV 206
                                    7************999975...4.4889***********9999988776145556899*****99876544 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 !   25.3   0.0   1.5e-08   9.5e-06      14      50 ..      22      58 ..      17      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   g +++++  +  +++GpsGsGKSTll Ai  l  p++
  gi|118431637|ref|NP_148242.2| 22 GVDVSLSYGEKLVIMGPSGSGKSTLLKAIPRLVEPDS 58
                                   5667777666999****************99998876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   1.6e-08   9.8e-06      25     167 ..      31     193 ..      19     201 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.6e-08
                         AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdql.........esaipysa.laqalareellrqlldeaesae 93 
                                    e +++ G+sG+GKs+l+++++r +e d g i++rg  +           +++i y++   +++   ++lr +  ++e+a+
  gi|118431637|ref|NP_148242.2|  31 EKLVIMGPSGSGKSTLLKAIPRLVEPDsGSIVFRGVDVTRlsgsqlrmvRRKIGYLPqSYSLFPHMTVLRNITYPLEKAL 110
                                    5689*****************99999873455444444443322223344447777778888888888888888877777 PP

                         AAA_16  94 leawrekleeala........avpelagaea......srllellkrllallsrderplvlvlDdlq.wadeaslql.laa 157
                                        r++ e+a++        +   la  ++      ++ +++l+r+l  + +   p +l+lD+    +d++s++  l+a
  gi|118431637|ref|NP_148242.2| 111 GLSRRDAEERAVKylsmlgieD---LAHRHParlsggQQQRAALARAL--AME---PDILLLDEPTsALDPESRADvLEA 182
                                    7777777777777888885552...33333322112233333333333..222...457777765545666666655777 PP

                         AAA_16 158 Llrllesk.pl 167
                                    L+r ++ +  +
  gi|118431637|ref|NP_148242.2| 183 LFRVATLGkAM 193
                                    77777664344 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   3.4e-06    0.0021       8     112 ..      33     183 ..      28     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee......................erpevv...fvtlpsstsskdllrellr 62 
                                    lv++G+sG+GK+tll+ + +  + +                           ++ +++   +   p+ t ++++   l +
  gi|118431637|ref|NP_148242.2|  33 LVIMGPSGSGKSTLLKAIPRLVEPD----SgsivfrgvdvtrlsgsqlrmvrRKIGYLpqsYSLFPHMTVLRNITYPLEK 108
                                    79***************99988533....133457777777777777775544444446645555555566666666777 PP

                         AAA_22  63 alglelka....................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeL 112
                                    algl++ +                          +l   + ++a+ ara    + +l++DE    l+   ++++le L
  gi|118431637|ref|NP_148242.2| 109 ALGLSRRDaeeravkylsmlgiedlahrH---PARLSgGQQQRAALARALamePDILLLDEPTSaLDpesRADVLEAL 183
                                    77766666777777777777777664331...3333333333333333334455577777766656554335555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   7.2e-06    0.0045      81     119 ..      11      50 ..       2      64 .. 0.77
   2 ?   -0.8   0.0       2.1   1.3e+03      13      38 ..     186     210 ..     165     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.2e-06
                                    E--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  81 lvsaktkegleelkellkd.ktsvlvGqSGvGKStLinal 119
                                    +vs + ++ l+ +   l+  +  v++G+SG GKStL++a+
  gi|118431637|ref|NP_148242.2|  11 VVSYSGEKVLKGVDVSLSYgEKLVIMGPSGSGKSTLLKAI 50 
                                    55555566666677777666889**************987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                    EES--EEEEEEESTTTT--HHHHHHH CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrf 38 
                                    va + +++ivv+ +  ++ ++  dr+
  gi|118431637|ref|NP_148242.2| 186 VATLGKAMIVVTHE-ADFAVKVADRM 210
                                    88889999999988.99999999986 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 !    8.0   0.0    0.0017       1.1     247     266 ..      33      52 ..      12      56 .. 0.87
   2 !    7.7   0.0    0.0021       1.3     324     353 ..     142     171 ..     138     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0017
                                    EEEEE-TTSSHHHHHHHHHH CS
                     ABC_ATPase 247 tlIvGggfhGKsTLLeAlek 266
                                     +I+G+   GKsTLL+A+ +
  gi|118431637|ref|NP_148242.2|  33 LVIMGPSGSGKSTLLKAIPR 52 
                                    589**************965 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-H CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAt 353
                                    SG   q a++++al ++ ++lL+DE tsA 
  gi|118431637|ref|NP_148242.2| 142 SGGQQQRAALARALAMEPDILLLDEPTSAL 171
                                    99999***********************95 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.9e-06    0.0055       4      27 ..      32      54 ..      30      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.9e-06
                         AAA_24  4 kiliyGpsgiGKTtlakelgpkpl 27
                                   k++i+Gpsg+GK+tl+k + p+ +
  gi|118431637|ref|NP_148242.2| 32 KLVIMGPSGSGKSTLLKAI-PRLV 54
                                   89****************9.6655 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 !   15.4   0.0     3e-05     0.019       2      72 ..      34     172 ..      33     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3e-05
                                    EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS.................................. CS
                            AAA   2 llyGppGtGKTllakavakel..........gvefleisgsellsk.................................. 37 
                                    +++Gp G GK++l ka+ + +          gv++ ++sgs+l+ +                                  
  gi|118431637|ref|NP_148242.2|  34 VIMGPSGSGKSTLLKAIPRLVepdsgsivfrGVDVTRLSGSQLR-Mvrrkigylpqsyslfphmtvlrnityplekalgl 112
                                    689****************9766655555666999999999999.44788999999999999999999999999999999 PP

                                    ..........................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                            AAA  38 ..........................yvgesekkirelfkeakekakpsilfiDEidalak 72 
                                                                  + ++ r+ +++a +++ p il++DE  +   
  gi|118431637|ref|NP_148242.2| 113 srrdaeeravkylsmlgiedlahrhpARLSGGQQQRAALARALAME-PDILLLDEPTSALD 172
                                    9999999999999999888888887766666666777776666665.89999998666555 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 !   14.0   0.5   7.2e-05     0.044      28      88 ..     136     183 ..     129     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.2e-05
                        SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    r+ ++lSGG++         aala ++         +++++LDE  s lD+es+a +le+l
  gi|118431637|ref|NP_148242.2| 136 RHPARLSGGQQ-------QRAALARALAM------EPDILLLDEPTSALDPESRADVLEAL 183
                                    55567788888.......34666666666......489********************986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-05     0.011      21      49 ..      33      61 ..      23     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrv 49
                                    v+ Gp G+GK+t+lka+ +++e + g++
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAIPRLVEPDSGSI 61
                                   6899**************99999884443 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 !   11.1   0.0   0.00039      0.24      47      80 ..      30      63 ..      22      99 .. 0.78
   2 ?    3.5   0.0     0.084        52      98     151 ..     148     202 ..     106     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                      IstB_IS21 47 kenivllGpsGvGKshlaialgveavraglsvlf 80
                                    e +v++GpsG GKs l  a+ +    +  s++f
  gi|118431637|ref|NP_148242.2| 30 GEKLVIMGPSGSGKSTLLKAIPRLVEPDSGSIVF 63
                                   5889*************99997654445555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.084
                      IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfevie..kryerrsiiitsnlpf 151
                                    ++a a +  +++d+l+lD+  +  ld +++++++e +   +  +++ i++t +  f
  gi|118431637|ref|NP_148242.2| 148 RAALARALAMEPDILLLDEP-TSALDPESRADVLEALFrvATLGKAMIVVTHEADF 202
                                    2222222334569*****96.56788888888877764114678888888877666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.6e-05     0.016      13      50 ..      21      58 ..      14      82 .. 0.82
   2 ?   -2.0   0.0       3.1   1.9e+03       9     115 ..     145     167 ..     138     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                   Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllppls 50
                                   + ++++ + g +l+++Gp+GsGK+ l k++p l+ p s
  gi|118431637|ref|NP_148242.2| 21 KGVDVSLSYGEKLVIMGPSGSGKSTLLKAIPRLVEPDS 58
                                   567788888899*******************9987655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.1
                   Mg_chelatase   9 eeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaska 88 
                                    ++++ al  a a + +                                                                
  gi|118431637|ref|NP_148242.2| 145 QQQRAALARALAMEPD---------------------------------------------------------------- 160
                                    4444444444444444................................................................ PP

                   Mg_chelatase  89 alvGggskpkpGeislahnGvLfLDEl 115
                                                        +L+LDE 
  gi|118431637|ref|NP_148242.2| 161 --------------------ILLLDEP 167
                                    ....................4444442 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     2e-05     0.012      23      39 ..      34      50 ..      18      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                         AAA_23 23 lItGpNGaGKTTildAi 39
                                   +I Gp G+GK+T+l Ai
  gi|118431637|ref|NP_148242.2| 34 VIMGPSGSGKSTLLKAI 50
                                   8***************9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0    0.0002      0.12       3      21 ..      33      51 ..      31      59 .. 0.88
   2 ?    1.7   0.0      0.34   2.1e+02      91     129 ..     165     200 ..     135     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   +++ G++GsGK+tLl+ + 
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAIP 51
                                   7899***********9985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                                    TT-SS-TCH.........HHHHHCTTTTT--EEEEEEEC CS
                          NACHT  91 DelvtdlgqkekqpvrtlLselirkkllpeasllltvrp 129
                                    De  + l++   ++  ++L+ l+r + l +a++++t   
  gi|118431637|ref|NP_148242.2| 165 DEPTSALDP---ESRADVLEALFRVATLGKAMIVVTHEA 200
                                    566665555...788899****************99765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.3   9.4e-05     0.058       3      20 ..      34      51 ..      33     222 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.4e-05
                         AAA_33  3 llvGlpGsGKstlaerll 20
                                   ++ G++GsGKstl++ + 
  gi|118431637|ref|NP_148242.2| 34 VIMGPSGSGKSTLLKAIP 51
                                   678**********99763 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   6.6e-05     0.041     127     161 ..      28      62 ..       5      64 .. 0.81
   2 ?   -1.6   0.0       1.8   1.1e+03     187     205 ..     146     164 ..      99     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-05
                          T2SSE 127 rerglilvsGgTgsGKttllyallkeinksderiv 161
                                    +    +++ G+ gsGK+tll a+   ++ ++  iv
  gi|118431637|ref|NP_148242.2|  28 SYGEKLVIMGPSGSGKSTLLKAIPRLVEPDSGSIV 62 
                                    45567899**************9999988877665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                          T2SSE 187 tfadllraaLRlrPDrimv 205
                                    + +++l  aL ++PD++++
  gi|118431637|ref|NP_148242.2| 146 QQRAALARALAMEPDILLL 164
                                    4567788888899998877 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   0.00062      0.38      20      48 ..      26      55 ..      18      80 .. 0.80
   2 ?    2.8   0.0      0.12        77     323     365 ..     158     199 ..     145     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00062
                         AAA_15 20 dlsee.ltvliGkNnsGKSsilealdlFln 48
                                   +ls     v+ G+ +sGKS++l+a+  + +
  gi|118431637|ref|NP_148242.2| 26 SLSYGeKLVIMGPSGSGKSTLLKAIPRLVE 55
                                   444334889****************77665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    +++ill++EP   L p+    + ++l ++a  +k   i+ TH 
  gi|118431637|ref|NP_148242.2| 158 EPDILLLDEPTSALDPESRADVLEALFRVATLGK-AMIVVTHE 199
                                    579******************************9.99999996 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015     0.093      25      49 ..      32      56 ..      17      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                   EEEEEESTTSSHHHHHHHHHHHCS- CS
                        G-alpha 25 kllllGqseSGKsTilkqlkllykk 49
                                   kl+++G s+SGKsT+lk + +l ++
  gi|118431637|ref|NP_148242.2| 32 KLVIMGPSGSGKSTLLKAIPRLVEP 56
                                   899***************9988766 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    0.0002      0.12       2      21 ..      34      53 ..      33      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                         AAA_18  2 lltGtpGvGKttlakeLskr 21
                                   +++G++G+GK+tl k++ ++
  gi|118431637|ref|NP_148242.2| 34 VIMGPSGSGKSTLLKAIPRL 53
                                   699************99554 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015     0.095      91     129 ..      34      70 ..      17      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                     Adeno_IVa2  91 viyGPtGsGksqllrnlissklisPiPetvifitPekdm 129
                                    vi GP GsGks ll+++   +l++P    ++f   ++  
  gi|118431637|ref|NP_148242.2|  34 VIMGPSGSGKSTLLKAI--PRLVEPDSGSIVFRGVDVTR 70 
                                    79*************97..68999988888886666555 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 ?   12.2   0.0    0.0002      0.13      23      44 ..      33      54 ..      23      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                       ATPase_2 23 yfiYGpegsGKtaLlkeiienl 44
                                   ++i Gp gsGK++Llk i    
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAIPRLV 54
                                   79**************886555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00098      0.61       2      24 ..      33      55 ..      32      85 .. 0.80
   2 ?   -0.0   0.0       1.2   7.2e+02      94     143 ..     157     209 ..     144     221 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00098
                                   EEEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellk 24
                                   ++i Gp+G+GK+Tl+k + +l++
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAIPRLVE 55
                                   7899***********99988775 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.2
                                    HHH-EEEE--.-STTGGG-H.HHHHHHHHHHTTTSEEEEE--SS-.-SHHHHH CS
                       NTPase_1  94 seadviviDE.iGkmElksk.kfkeaveevLksekpvlavihrrk.dlalvee 143
                                     e+d++++DE    +  +s+  + ea+ +v + +k +++v h+++   ++ ++
  gi|118431637|ref|NP_148242.2| 157 MEPDILLLDEpTSALDPESRaDVLEALFRVATLGKAMIVVTHEADfAVKVADR 209
                                    56777777773334554443146677777777888888888887655455554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0004      0.25       2      19 ..      33      50 ..      32      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                         AAA_28  2 ivitGgestGKTtlleaL 19
                                    vi+G++++GK+tll+a+
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAI 50
                                   79*************986 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    0.0003      0.18      55     112 ..      32      93 ..      25      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                         DUF815  55 nvLLwGarGtGKSslvkallneyaeeg....Lrlievekedlkelpklvellrerperfilf 112
                                    +++++G  G+GKS+l+ka+ + ++ ++     r ++v++ + ++l ++ +++   p+ + lf
  gi|118431637|ref|NP_148242.2|  32 KLVIMGPSGSGKSTLLKAIPRLVEPDSgsivFRGVDVTRLSGSQLRMVRRKIGYLPQSYSLF 93 
                                    67899**************9999988778888999999999999999999998888877666 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   0.00034      0.21       2      39 ..      34      66 ..      33     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39
                                   ++ Gpsg GKStl k + + +     ++ ++s+++r++
  gi|118431637|ref|NP_148242.2| 34 VIMGPSGSGKSTLLKAIPRLV-----EPDSGSIVFRGV 66
                                   799************954433.....455566666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00055      0.34       2      20 ..      33      51 ..      32      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                                   EEEEESTTSSHHHHHHHHH CS
                       MMR_HSR1  2 vaivGrpNvGKStLinalt 20
                                    +i+G + +GKStL++a+ 
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAIP 51
                                   689*************985 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00057      0.35       3      20 ..      33      50 ..      31      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00057
                                   EEEEESTTCCHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhl 20
                                   +v+ G+ GsGK+tLl+++
  gi|118431637|ref|NP_148242.2| 33 LVIMGPSGSGKSTLLKAI 50
                                   699************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 1857.79
//
Query:       gi|14601702|ref|NP_148243.1|  [L=220]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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   64.4  11.2    1.1e-17   64.4  11.2    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.7      0.03   5.4e+02     149     170 ..      17      38 ..       6      45 .. 0.46
   2 !   64.4  11.2   6.2e-22   1.1e-17       7     182 ..      38     210 ..      30     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.03
                  BPD_transp_1 149 dyseisnggvlalviavlllnl 170
                                   +y++++ +++l +++ + l+++
  gi|14601702|ref|NP_148243.1|  17 MYTLAITIISLSMGFTISLILT 38 
                                   2222222333333333333333 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 6.2e-22
                  BPD_transp_1   7 laa.lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlvea 86 
                                    aa +   k+l+ +   +i++++++P +v ++++++ +  l++  +++ +++i++ l +++y   i r a++ +p++++ +
  gi|14601702|ref|NP_148243.1|  38 TAArFLGFKPLRMAAEAYINFFRGTPLLVQILMVFFGLPSLGVNLSAFYSAVIAIGLNSGAYQAEILRVAIKGIPEEQMLV 118
                                   3447777899*******************888888777777777777788******************************* PP

                  BPD_transp_1  87 aralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavll 167
                                   ar lG+s+++i++ vv+P+a++ +i+gl +  ++ll++++l++ +g    +  l+   + +   ++ +  ++l +++++l+
  gi|14601702|ref|NP_148243.1| 119 ARSLGLSEIEIMKGVVIPQAVRNAIPGLTNETVILLKESSLASVIG----VMELTRVGEYMVSATFRALEAYLLIALIYLA 195
                                   **********************************************....7766666666666666669************ PP

                  BPD_transp_1 168 lnlvadilqrlldpr 182
                                   l+ +a+ + +  ++ 
  gi|14601702|ref|NP_148243.1| 196 LSMIAFRMLKRAEKS 210
                                   *****9999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1803.51
//
Query:       gi|118431638|ref|NP_148244.2|  [L=283]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for 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-52  175.9   0.2    9.8e-52  175.6   0.2    1.1  1  SBP_bac_3        Bacterial extracellular solute-binding prote
    5.7e-06   26.5   0.1    6.6e-05   23.1   0.1    2.3  1  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine
     0.0026   17.3   0.5       0.81    9.2   0.1    2.2  2  YhfZ_C           YhfZ C-terminal domain
     0.0034   17.4   1.5       0.39   10.6   0.1    2.2  2  NMT1             NMT1/THI5 like
  ------ inclusion threshold ------
      0.029   13.9   0.3        0.4   10.2   0.3    2.4  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
      0.076   13.1   1.5       0.13   12.3   1.5    1.4  1  DUF2613          Protein of unknown function (DUF2613)


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 !  175.6   0.2   3.3e-55   9.8e-52       1     221 [.      57     274 ..      57     282 .. 0.92

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 3.3e-55
                                    EEEEE-S-BTTTBEE-TTS-EESHHHHHHHHHHHHCT-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3   1 lrvgvdadypPfsykdengeltGfdvdlakaiakrlgvkvefvpvswdelipalksgkvDiaiaaititpeReekvdFsq 80 
                                    l+vg++ad+pP++y+d++g ++G+d++lak+ia+ lgv++e+v++++++l++a++sgkvDi+ia++++ peR e vdF+ 
  gi|118431638|ref|NP_148244.2|  57 LKVGTSADWPPYEYIDPQGGYAGIDIELAKKIADGLGVQLEIVDMKFAALFQAVQSGKVDIVIADVAMKPERLEAVDFTI 136
                                    79****************************************************************************** PP

                                    ESE.EEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHCTSEEEEE.SSHHHHHHHHHTTSSSEEEE CS
                                    xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3  81 pyf.sagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkkgaeivef.dtleealqaLkngrvdavva 158
                                    py  ++g +++v+++da   s++++++ L+gkk+gvq +++ eel+++++ ++aeiv++   ++e++ aLk+g++da+va
  gi|118431638|ref|NP_148244.2| 137 PYRcETGKAIIVKAEDA---SGYTGFDWLAGKKIGVQSATVEEELANKYFGDKAEIVTYdRVYPEMTIALKTGKIDAMVA 213
                                    **725699999997655...6888888*********************9999******94568999************** PP

                                    EHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 159 dspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelkadgtlakisek 221
                                       v++ +v+ ++++ +v   +  +     ++v+    eL+k++ +++ +l+++g+l+ki ++
  gi|118431638|ref|NP_148244.2| 214 APDVARLIVTAEEGLVIVD--QIPYFGCSTVVVPHCAFELKKEVSSIIWDLIQSGELQKIIDQ 274
                                    *********9999999998..88888888999****************************762 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   2.2e-08   6.6e-05      69     113 ..     105     150 ..      57     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.2e-08
                                    HHHHHHHTTS-SEE-SS-B--HHHHTTSEEESES.EEE-EEEEEES CS
                Lig_chan-Glu_bd  69 GmigellekkadlavapltitaeReevvdFtkpf.melgisilikk 113
                                     + + + ++k+d+++a++ +++eR e+vdFt p+ +e+g +i++k 
  gi|118431638|ref|NP_148244.2| 105 ALFQAVQSGKVDIVIADVAMKPERLEAVDFTIPYrCETGKAIIVKA 150
                                    566788899*************************445688888876 PP

>> YhfZ_C  YhfZ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0014       4.3     138     166 ..      95     123 ..      83     157 .. 0.73
   2 !    9.2   0.1   0.00027      0.81     114     166 ..     164     216 ..     143     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0014
                         YhfZ_C 138 dvelveisynqllelllkgkiDavvWnld 166
                                    + e+v+++++ l++++ +gk+D v+  + 
  gi|118431638|ref|NP_148244.2|  95 QLEIVDMKFAALFQAVQSGKVDIVIADVA 123
                                    789*********************98777 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00027
                         YhfZ_C 114 glrvgvDsnSlDqkilteaifegk.dvelveisynqllelllkgkiDavvWnld 166
                                    g ++gv s++     l++++f +k ++   +  y ++  +l+ gkiDa+v   d
  gi|118431638|ref|NP_148244.2| 164 GKKIGVQSATVEE-ELANKYFGDKaEIVTYDRVYPEMTIALKTGKIDAMVAAPD 216
                                    6788888877765.4899999988788888899****************97776 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0038        11     121     148 ..      95     121 ..      77     140 .. 0.83
   2 !   10.6   0.1   0.00013      0.39      84     147 ..     155     214 ..     141     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0038
                                    G-EEEE-.TT-HHHHHHCTSSSEEECEE CS
                           NMT1 121 dvtlvnvggtslakalltgkvDaaiggy 148
                                    ++++v++++  l++a+ +gkvD +i + 
  gi|118431638|ref|NP_148244.2|  95 QLEIVDMKFAALFQAVQSGKVDIVI-AD 121
                                    789********************99.44 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00013
                                    --SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECE CS
                           NMT1  84 gikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaigg 147
                                    g + +  L+Gk+ig++ + +e+ l ++     g +++ vt  +v + +++ al tgk+Da++++
  gi|118431638|ref|NP_148244.2| 155 GYTGFDWLAGKKIGVQSATVEEELANKY---FGDKAEIVTYDRV-YPEMTIALKTGKIDAMVAA 214
                                    46777779*********87777666543...3445556677667.999999*********9854 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 ?   10.2   0.3   0.00013       0.4      19     220 ..      84     265 ..      82     281 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEEEETT--SEEEEEEEEETTS..S CS
                 Phosphonate-bd  19 ladyLseelGvevelvvatdyaavvealragqvDiaflgplayvqardqagveplatrvrsdGsasyrsviivrads..d 96 
                                    la+ + + lGv+ e+v +  +aa+ +a+++g+vDi+ ++     +     +++ + ++ r     +   +iiv+a++  +
  gi|118431638|ref|NP_148244.2|  84 LAKKIADGLGVQLEIVDM-KFAALFQAVQSGKVDIVIADVAMKPERL---EAVDFTIPYR----CETGKAIIVKAEDasG 155
                                    788899999******999.5****************98744333322...3333444444....3444555555554225 PP

                                    --SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEE.EE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH- CS
                 Phosphonate-bd  97 iqsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsev.fsgshdaavlavlsgdadaaavsadaledlvaeg 175
                                    ++ ++ L+gk+i++ s++        + +L    ++  +d  + v +   ++++  a+  g++da++   d+++  v ++
  gi|118431638|ref|NP_148244.2| 156 YTGFDWLAGKKIGVQSATV-------EEELA---NKYFGDKAEIVtYDRVYPEMTIALKTGKIDAMVAAPDVARLIVTAE 225
                                    8888888888888766553.......33442...2222333344434445566666666666666666666555555432 PP

                                    HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHHHH---S CS
                 Phosphonate-bd 176 pedkdelrviassppipndpvvvrkelseelkekiqdallslaet 220
                                        + l+++ ++p + +   vv ++   elk+++++++ +l ++
  gi|118431638|ref|NP_148244.2| 226 ----EGLVIVDQIPYF-GCSTVVVPHCAFELKKEVSSIIWDLIQS 265
                                    ....455555555544.5555555666666666666666665555 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.5   4.5e-05      0.13       3      28 ..       2      30 ..       1      43 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                        DUF2613  3 lgPaaaSaVaGivlGvva...vfgvtavv 28
                                   l +a+++ V+G++lGv+a   vf  +++v
  gi|118431638|ref|NP_148244.2|  2 LAAALVALVVGLALGVAAyqaVFSGGQTV 30
                                   789*************9722255544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2272.54
//
Query:       gi|14601704|ref|NP_148245.1|  [L=239]
Description: hypothetical protein APE_1894 [Aeropyrum pernix K1]
Scores for 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   1.5    1.8e-09   37.3   0.2    2.6  2  ACT_7        ACT domain
      0.002   17.0   0.1     0.0054   15.6   0.0    1.7  1  DUF2791      P-loop Domain of unknown function (DUF2791)
     0.0022   17.7   4.0      0.021   14.6   0.1    3.3  3  ACT          ACT domain
     0.0095   16.2   0.1      0.045   14.0   0.1    2.1  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
      0.047   13.4   0.4       0.64    9.8   0.2    2.2  2  DUF3509      Protein of unknown function (DUF3509)
      0.093   12.5   0.1        9.1    6.0   0.0    2.2  2  DUF4922      Domain of unknown function (DUF4922)


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00028      0.84      20      64 ..      97     141 ..      86     142 .. 0.89
   2 !   37.3   0.2     6e-13   1.8e-09       2      65 .]     146     210 ..     145     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00028
                                   S--HHHHHHHHHHTTT---EEEE-SS-EEEEEEGGGHHHHHHHHH CS
                         ACT_7  20 vtGivaklaspLaeagIsifqiStyrtdyiLVpeedlekAveaLh 64 
                                   ++ ++ k++s L e+   i ++ + rt  i+V +ed+ek +e L+
  gi|14601704|ref|NP_148245.1|  97 SITRALKIVSQLGENSRFIQFVQSLRTATIIVASEDKEKILERLQ 141
                                   566899*********************************999887 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 6e-13
                                   EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHHH CS
                         ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLhe 65 
                                   + d+ +++ +v+++  + ++G+va +++ La+ gI+i+q+  +y + +++ ++e++ kA+  Lh+
  gi|14601704|ref|NP_148245.1| 146 VIDRQSAVILVSPRSIVTTPGVVAYITGFLARSGINITQVIsCYVDTILVLNSEEASKAYTLLHR 210
                                   568999999****99999*********************997999999999************96 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.8e-06    0.0054     285     373 ..      12     106 ..       3     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                       DUF2791 285 lltGTpeflederrGvysyeaLrsRlaedrfakeaglkdlrapvirLkplteeellvlleklrdiyaeg......yeeev. 358
                                   +++G p  le  r+G+ +y+aL++Rlaed  +++ + +++ a+ + L +l e+   + + ++++i a+       y   + 
  gi|14601704|ref|NP_148245.1|  12 YVAGDPVLLECLRKGIVNYSALARRLAEDLEKATGEKHSVVAVKMALVRLAEKLESEPIGEIERIIAASalavqdY---Is 89 
                                   578889999999*****************77777788899999999998888777777777777776654433222...13 PP

                       DUF2791 359 ..lvsdeelkafleevt 373
                                     +v+ e++++ l+ v+
  gi|14601704|ref|NP_148245.1|  90 viTVPRESITRALKIVS 106
                                   34777777777666554 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.62   1.8e+03      43      65 ..      86     108 ..      72     110 .. 0.71
   2 ?    2.7   0.1     0.035   1.1e+02      43      66 ..     121     144 ..     113     145 .. 0.86
   3 !   14.6   0.1   7.2e-06     0.021      10      33 ..     164     187 ..     160     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.62
                                   EEEEEEEEEHHHHHHHHHHHHTT CS
                           ACT  43 ivfvvivvdeedleevlealkkl 65 
                                    +++vi+v  e++  +l+ + +l
  gi|14601704|ref|NP_148245.1|  86 DYISVITVPRESITRALKIVSQL 108
                                   57788888888888888887776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.035
                                   EEEEEEEEEHHHHHHHHHHHHTTC CS
                           ACT  43 ivfvvivvdeedleevlealkkle 66 
                                   + + +i+v  ed e++le+l++++
  gi|14601704|ref|NP_148245.1| 121 LRTATIIVASEDKEKILERLQNVI 144
                                   56779999************9986 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 7.2e-06
                                   STTHHHHHHHHHHHTTSEEEEEEE CS
                           ACT  10 rPGlLarvfgaladrgiNidsieq 33 
                                    PG+ a ++g la+ giNi+ + +
  gi|14601704|ref|NP_148245.1| 164 TPGVVAYITGFLARSGINITQVIS 187
                                   6*******************9876 PP

>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.5e-05     0.045       4      71 ..     123     218 ..     120     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                   EEEEE-TTC-HHHHHHHHHTTSTTS.............................E---EEEEEE-CCC-EEEEEEEEESSH CS
                   RNA_binding   4 vrafvhaTEdeekVlealsnllpee.............................eveieeeeaeGhygnpitileaelekk 55 
                                     +++ a+Ed+ek+le l+n+++ +                             ++ i+++++ ++y + i++l+ e  + 
  gi|14601704|ref|NP_148245.1| 123 TATIIVASEDKEKILERLQNVIEVIdrqsavilvsprsivttpgvvayitgflaRSGINITQVISCYVDTILVLNSEEAS- 202
                                   568899****************988999**********************999977899999999**9999999988777. PP

                                   HHHHHHHHHHHHHCCC CS
                   RNA_binding  56 kakkvlkkllellree 71 
                                   ka  +l++l+++lr++
  gi|14601704|ref|NP_148245.1| 203 KAYTLLHRLIDALRRK 218
                                   5699999999999875 PP

>> DUF3509  Protein of unknown function (DUF3509)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00021      0.64      45      82 ..     106     143 ..      91     147 .. 0.88
   2 ?    1.3   0.0     0.099     3e+02      51      68 ..     206     223 ..     198     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00021
                       DUF3509  45 aQlndkrqLedvvdairrdLaieaGelpvdviaaLqsq 82 
                                    Ql ++ ++ ++v+++r    i a+e + +++++Lq+ 
  gi|14601704|ref|NP_148245.1| 106 SQLGENSRFIQFVQSLRTATIIVASEDKEKILERLQNV 143
                                   7***********************************86 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.099
                       DUF3509  51 rqLedvvdairrdLaiea 68 
                                     L++++da+rr   +++
  gi|14601704|ref|NP_148245.1| 206 TLLHRLIDALRRKYSVAE 223
                                   57999******9877776 PP

>> DUF4922  Domain of unknown function (DUF4922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0096        29      67     107 ..     110     150 ..      80     159 .. 0.77
   2 ?    6.0   0.0    0.0031       9.1      73     113 ..     184     224 ..     169     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0096
                       DUF4922  67 keeeelsllkeylrpvlvieskekeeaaelfeklyealpve 107
                                   +++  ++ ++++ ++++++ s++ke++ e +++++e+++ +
  gi|14601704|ref|NP_148245.1| 110 ENSRFIQFVQSLRTATIIVASEDKEKILERLQNVIEVIDRQ 150
                                   333447889999999999**************999998765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0031
                       DUF4922  73 sllkeylrpvlvieskekeeaaelfeklyealpveegeeEp 113
                                   ++++ y+ ++lv++s+e+++a +l+++l++al+ +++  E+
  gi|14601704|ref|NP_148245.1| 184 QVISCYVDTILVLNSEEASKAYTLLHRLIDALRRKYSVAEA 224
                                   457789999************************99988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1807.34
//
Query:       gi|118431639|ref|NP_148246.2|  [L=551]
Description: flagellar protein J-like protein [Aeropyrum pernix K1]
Scores for complete 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-20   72.1   8.4    6.9e-12   45.4   0.1    3.2  3  T2SSF         Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.047   13.5   4.0       0.11   12.3   2.6    2.4  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


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 !   31.2   0.1   1.9e-11   1.7e-07       4     122 ..      75     199 ..      72     202 .. 0.91
   2 ?   -3.3   1.7       0.9   8.1e+03     108     122 ..     220     234 ..     212     237 .. 0.45
   3 !   45.4   0.1   7.7e-16   6.9e-12       1     124 [.     321     450 ..     321     451 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.9e-11
                                    HHHHHHHTT--HHHHHHHHHHHHS.SHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-H CS
                          T2SSF   4 qlatllsaGvplveaLellaeeae.ngplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnL 77 
                                    ++ +  s+  p+ ++++++a+  + +g +++ +++i++  +++g s+++a++    + + + +++ +++l+ +   g ++
  gi|118431639|ref|NP_148246.2|  75 HMRLVASGKPPVGRIFRAIADFPQvYGGYSRLFRSIYDLGKEWGySFPKAVSiiadSVEGEILRNILQRLSGVLAVGEDV 154
                                    5666667777999***************************9988899*****99986666777***************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                          T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillai 122
                                    +e++er  ++l +e+e+ + +  +++ +ll ++v++l +l++l+ 
  gi|118431639|ref|NP_148246.2| 155 EEFFEREYRTLLAEYENVYTRTMNSARVLLGIYVTMLGSLVFLVS 199
                                    ****************************************99975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.9
                                    XXXXXXXXXXXXXXX CS
                          T2SSF 108 llvvallvllillai 122
                                     +v+++++ll ll++
  gi|118431639|ref|NP_148246.2| 220 AAVTVGAILLGLLVF 234
                                    333344444444443 PP

  == domain 3  score: 45.4 bits;  conditional E-value: 7.7e-16
                                    HHHHHHHHHHTT--HHHHHH.HHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT CS
                          T2SSF   1 flrqlatllsaGvplveaLe.llaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageegg 75 
                                    f+r+ +++ls+  ++v+aLe ll ++   + ++++ kr+++rl++ ++++ a++    +t+s+  ++ ++ ++ ++e+gg
  gi|118431639|ref|NP_148246.2| 321 FIRSYGSHLSTVGNMVKALEpLLISNL-GILMGPI-KRLYTRLKNSINPNVAWDlfsaETGSEMARRGIIIFTDTVEAGG 398
                                    89******************6666666.6666665.*********************99998666*************** PP

                                    -HHHHHHHHHHHHHHHHHHH...HHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                          T2SSF  76 nLaevLerlaeyleeerelr...rkllaallepllllvvallvllillaill 124
                                    n + +   ++++++++++lr   +++++ + ++l++++ a++++l++++ ll
  gi|118431639|ref|NP_148246.2| 399 NPDLAGALISDHHNDMNRLRklrYQVASTFSSTLFIMHGAAIIILLIMSKLL 450
                                    ************99998888888*************************9876 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 ?   -2.0   0.0      0.29   2.6e+03     114     136 ..     181     203 ..     127     207 .. 0.65
   2 ?   12.3   2.6   1.2e-05      0.11      43      93 ..     257     307 ..     253     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.29
                   Trp_oprn_chp 114 eltawpvlalaggvllllagvll 136
                                    ++  + +++++g ++ l+   ++
  gi|118431639|ref|NP_148246.2| 181 RVLLGIYVTMLGSLVFLVSTFMV 203
                                    22236666666666666665555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.2e-05
                   Trp_oprn_chp  43 paltalAlvllAaavAvlavrglgrrvvgvllalagagaavaalslltdpa 93 
                                     a+  lA++l Aa+ A ++  + g+   g++la a+ag+++ ++ +++  +
  gi|118431639|ref|NP_148246.2| 257 KAAGGLAIALGAAVGAGIIYMRGGLDFTGLVLAYAAAGLLLLPVGVIARME 307
                                    57889***************************************9988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3852.96
//
Query:       gi|118431640|ref|NP_148247.2|  [L=576]
Description: flagellar protein I-like protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-47  161.5   0.0    2.9e-47  161.0   0.0    1.1  1  T2SSE     Type II/IV secretion system protein
    2.6e-05   23.9   0.0    5.1e-05   22.9   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0011   19.5   0.0     0.0047   17.4   0.0    2.0  2  ABC_tran  ABC transporter
  ------ inclusion threshold ------
      0.065   13.5   0.0       0.19   12.0   0.0    1.8  1  AAA_22    AAA domain
      0.075   13.5   0.2       0.18   12.3   0.2    1.5  1  AAA_23    AAA domain
      0.094   12.4   0.0       0.16   11.7   0.0    1.2  1  AAA_15    AAA ATPase domain
        0.1   12.4   0.0       0.17   11.7   0.0    1.3  1  DEAD      DEAD/DEAH box helicase


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 !  161.0   0.0   1.1e-50   2.9e-47       4     262 ..     188     450 ..     185     459 .. 0.92

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 1.1e-50
                          T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrv 82 
                                    +le++l+d+   di  +  +  ++v++   +   + v++ ++ +l  +i ++    ++ is+ rp++da+lp +g r+++
  gi|118431640|ref|NP_148247.2| 188 PLEPFLRDPYLEDISCNGVGPvYVVHKMFRS-LESSVRFETEGELDDFILKLGEKIGKPISHARPVVDATLP-DGSRINI 265
                                    78999****************7777655555.88899999999*****************************.******* PP

                          T2SSE  83 vllP.vvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                    v+   v+ +  +++iRk s+  +++ +l++ ++++++ia+ +   ++e +++ + G T sGKtt+l+a+  +i  +  +i
  gi|118431640|ref|NP_148247.2| 266 VFGSdVSLKgSNFTIRKVSKIPISVTQLIKWGTFDARIAAYMWMMLEEGMSVFICGETASGKTTSLNAISVFIRPD-AKI 344
                                    997624444699**************************************************************99.*** PP

                          T2SSE 161 vtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHans 235
                                    vt+ED++E+ l ++n ++  ++     +++vt+ dllraaLR+rP  i+vGEiR++e   + +A++TGH++ ++T Ha +
  gi|118431640|ref|NP_148247.2| 345 VTIEDTAEVVLPHPNWTRELTRntgkpETSVTMFDLLRAALRQRPNYIIVGEIRGAEGNIAFQAMQTGHPV-MATFHAAN 423
                                    *****************9888889**********************************999**********.******** PP

                          T2SSE 236 aagalerLeqlgaeveaaelkssilav 262
                                        l+rL +   +v+++++ s  +a 
  gi|118431640|ref|NP_148247.2| 424 LSRLLQRLTNHPINVPKTNIDSLNIAW 450
                                    *********999999999998876655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0     2e-08   5.1e-05       4      51 ..     291     343 ..     288     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2e-08
                         AAA_29   4 lqlvNWgtfdght....ieidlkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                     ql+ Wgtfd +     +++ ++g ++++ G++ sGK+T l Ai++ + p+ k
  gi|118431640|ref|NP_148247.2| 291 TQLIKWGTFDARIaaymWMMLEEGmSVFICGETASGKTTSLNAISVFIRPDAK 343
                                    699*******8642222666778899*******************99999875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0047       7      48 ..     310     351 ..     306     388 .. 0.84
   2 ?   -2.3   0.0       2.2   5.7e+03      30      72 ..     392     435 ..     390     467 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkd 48 
                                     l+eg  v i Ge+ +GK+t l++++   +p++  ++++++ 
  gi|118431640|ref|NP_148247.2| 310 MLEEGMSVFICGETASGKTTSLNAISVFIRPDAKIVTIEDTA 351
                                    6899******************************99999543 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                    HHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  30 llagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfp 72 
                                    ++ g+ + +eG+i ++  ++ +    ++  ++++ l q  +  p
  gi|118431640|ref|NP_148247.2| 392 IIVGEIRGAEGNIAFQAMQTGHpVMATFHAANLSRLLQRLTNHP 435
                                    68888899999998874444443555555666666666644444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.5e-05      0.19       6      99 ..     315     396 ..     310     400 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                     +++++Ge+ +GKTt+l+ +             rp+   vt+    +      +  r+l++++ + + +s  ++++l+ a
  gi|118431640|ref|NP_148247.2| 315 MSVFICGETASGKTTSLNAISVFI---------RPDAKIVTIEDTAEVVLPHPNWTRELTRNTGK-PETSVTMFDLLRAA 384
                                    6789**************999887.........55555444444444444455555555544445.67778888888888 PP

                         AAA_22  86 lraravielliiDE 99 
                                    lr+r     +i+ E
  gi|118431640|ref|NP_148247.2| 385 LRQRPN--YIIVGE 396
                                    888777..666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   6.9e-05      0.18      23      40 ..     318     335 ..     313     338 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                         AAA_23  23 lItGpNGaGKTTildAik 40 
                                     I+G++ +GKTT l+Ai 
  gi|118431640|ref|NP_148247.2| 318 FICGETASGKTTSLNAIS 335
                                    7***************96 PP

>> AAA_15  AAA ATPase domain
   #    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      26      50 ..     317     341 ..     308     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                         AAA_15  26 tvliGkNnsGKSsilealdlFlnnk 50 
                                     +++G+ +sGK++ l+a+ +F+  +
  gi|118431640|ref|NP_148247.2| 317 VFICGETASGKTTSLNAISVFIRPD 341
                                    4799*****************9977 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.5e-05      0.17       4      40 ..     304     338 ..     301     387 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.5e-05
                                    HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivy 40 
                                     a ++  + +g +v++++eT+sGKT+   + +++ ++
  gi|118431640|ref|NP_148247.2| 304 AAYMWMMLEEGMSVFICGETASGKTTS--LNAISVFI 338
                                    566667777999*************97..44444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3835.50
//
Query:       gi|14601707|ref|NP_148248.1|  [L=245]
Description: flagellar accessory protein FlaH [Aeropyrum pernix K1]
Scores for complete 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   54.0   0.0    1.7e-14   53.7   0.0    1.0  1  ATPase    KaiC
    0.00094   18.5   0.0     0.0014   17.9   0.0    1.3  1  Rad51     Rad51
     0.0012   19.1   0.2     0.0037   17.5   0.2    1.7  1  AAA_22    AAA domain
     0.0026   17.5   0.0     0.0041   16.8   0.0    1.2  1  DUF835    Protein of unknown function (DUF835)
     0.0038   17.8   0.1     0.0078   16.8   0.1    1.5  1  AAA_18    AAA domain
      0.004   17.6   0.2     0.0085   16.5   0.1    1.7  1  AAA_16    AAA ATPase domain
      0.004   16.3   0.3       0.23   10.6   0.1    2.0  2  PAXNEB    PAXNEB protein
     0.0094   15.4   0.1      0.017   14.6   0.1    1.4  1  RecA      recA bacterial DNA recombination protein
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.055   13.2   0.0    1.6  1  AAA_24    AAA domain
      0.075   13.2   0.0       0.14   12.3   0.0    1.5  1  AAA_33    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 !   53.7   0.0   9.6e-18   1.7e-14       1     226 [.      16     237 ..      16     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 9.6e-18
                        ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                   v+tg e++D  l gG+p  +   i G  GtGKt +++ Fl kga ++g +g+ v +e++ +  + + ++ G+ l++   +g
  gi|14601707|ref|NP_148248.1|  16 VPTGNEEFDIKLGGGVPFPSLLIIEGPHGTGKTALSQLFL-KGALDMGLRGLAVVTESTIRGYILKSEAAGISLTEHFLRG 95 
                                   79***********************************998.788999*********************************9 PP

                        ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkklgvTail 160
                                   +l +  +  ++++     ++ ++  l++ + + +++     + +++Ds++ +a ++++      +++ vr ++++g   +l
  gi|14601707|ref|NP_148248.1|  96 RLDVYSTQFEGSRW----GRRSATVLLDLISRFLESESRryEVLLVDSLSHIAIYSSPIR-VLNFFNTVRLIADRGKLVVL 171
                                   99988777776664....45555555555555554433333789********43333333.34688999************ PP

                        ATPase 161 vsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskk.ehpfeIte.egikv 226
                                   +    +  e  ++ + +   +dg ++L l + ++++v++l+ivk+ g++ + + +++f++++  gik 
  gi|14601707|ref|NP_148248.1| 172 TLHEGVLREDLTTRARAT--CDGYMKLSLASLAGKTVKVLKIVKLKGARSQFDpTITFDVDPsFGIKL 237
                                   **9888777777776666..**************************9998865256677777667766 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.9e-07    0.0014      19     141 ..      16     140 ..       8     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.9e-07
                                   E--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHH......H CS
                         Rad51  19 lttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveia......e 93 
                                   + tG++++D  LgGG++  s+  i G +++Gkt l+ +l +   l++ l G       + te+t+r   l + a      e
  gi|14601707|ref|NP_148248.1|  16 VPTGNEEFDIKLGGGVPFPSLLIIEGPHGTGKTALS-QLFLKGALDMGLRGL-----AVVTESTIRGYILKSEAagisltE 90 
                                   67********************************97.688888888766654.....356888888777766554555555 PP

                                   HTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS..-EEEEEEETT CS
                         Rad51  94 rykldkeevlenvayaRaytiehqeellqqaaallaed..kfallivDsv 141
                                   ++   + +v +       +   + + ll+ ++  l ++  ++ +l+vDs+
  gi|14601707|ref|NP_148248.1|  91 HFLRGRLDVYSTQFEGSRWGRRSATVLLDLISRFLESEsrRYEVLLVDSL 140
                                   55555555555544444455556666666555555332225667777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.1e-06    0.0037       6     124 ..      35     169 ..      34     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.1e-06
                        AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.................erpevvfvtlpsstsskdllrellralglelk 69 
                                   ++l++ G+ GtGKT l + +l+ +       +                  ++e + + l++   ++  l     +++ ++ 
  gi|14601707|ref|NP_148248.1|  35 SLLIIEGPHGTGKTALSQLFLKGALD-----MglrglavvtestirgyiLKSEAAGISLTEHF-LRGRLDVYSTQFEGSRW 109
                                   5799*******************953.....34455699755555555555555555555555.44444444444444444 PP

                        AAA_22  70 aerlsseellealeqalrarav.ielliiDEaqhlr...s....eealeeLrsllnlsrkgvq 124
                                   + r s   ll+++ + l++ ++  e+l++D   h+    s     + ++++r +++  r ++ 
  gi|14601707|ref|NP_148248.1| 110 G-RRSATVLLDLISRFLESESRrYEVLLVDSLSHIAiysSpirvLNFFNTVRLIAD--RGKLV 169
                                   4.78888888999999999999999*********9888537778999999999999..55443 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.3e-06    0.0041      61     126 ..     114     180 ..     105     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.3e-06
                        DUF835  61 lekltetivkflkeaekg..vvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealee 126
                                    ++l++ i++fl+++++   v l+D+l  + ++++  +vl f+ t++  ++ ++++++l++ + +l e
  gi|14601707|ref|NP_148248.1| 114 ATVLLDLISRFLESESRRyeVLLVDSLSHIAIYSSPIRVLNFFNTVR-LIADRGKLVVLTLHEGVLRE 180
                                   5789**********999889**************************9.77888999999888877765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   4.3e-06    0.0078       2     114 ..      38     186 ..      37     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-06
                        AAA_18   2 lltGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpe...aldeskrldedkldklldaleenss......... 69 
                                   ++ G++G+GKt l++   k    +g +   v++e+ ++ +  +     ++ ++ + +++ld+ ++++e+++          
  gi|14601707|ref|NP_148248.1|  38 IIEGPHGTGKTALSQLFLKGAlDMGLRGLAVVTESTIRGYILKSeaaGISLTEHFLRGRLDVYSTQFEGSRWgrrsatvll 118
                                   799************997764466444444444444444444433344566666666666666666666543334444444 PP

                        AAA_18  70 .........aleegknlvidghlaeleseaakdikk..............vvLtaspeelleRlekRg 114
                                             ++  ++l++d++    ++ + ++                 vvLt+++ +l+e l +R 
  gi|14601707|ref|NP_148248.1| 119 dlisrflesESRRYEVLLVDSLSHIAIYSSPIRVLNffntvrliadrgklVVLTLHEGVLREDLTTRA 186
                                   44444444455677777777766666655555433378999999999999999999999998887775 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   4.7e-06    0.0085      24      63 ..      34      70 ..      26     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
                        AAA_16 24 pelvllsGesGvGKsslvrellralekd...ggiflrgkcdql 63
                                  p+l+++ G+ G+GK++l + +l+ + +    g       ++  
  gi|14601707|ref|NP_148248.1| 34 PSLLIIEGPHGTGKTALSQLFLKGALDMglrG------LAVVT 70
                                  58999*****************9777774432......22222 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00013      0.23      18      44 ..      15      41 ..       8      59 .. 0.80
   2 ?    4.1   0.0     0.012        21     188     288 ..     118     205 ..      99     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                        PAXNEB 18 ltStGtpsLDklLgGGLplGsillieE 44
                                  ++ tG++++D  LgGG+p  s+l+ie 
  gi|14601707|ref|NP_148248.1| 15 IVPTGNEEFDIKLGGGVPFPSLLIIEG 41
                                  788**********************94 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                        PAXNEB 188 lnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslv 268
                                   l+ i+++l++es+  +       +++ sL + ++       s+p ++l+F+ ++r ++ + +lv+l tl   ++  ++ l+
  gi|14601707|ref|NP_148248.1| 118 LDLISRFLESESRRYE------VLLVDSLSHIAI------YSSPIRVLNFFNTVRLIADRGKLVVL-TLHEGVL--REDLT 183
                                   5555555555222222......257889999999......36899**********99999999875.8888888..899** PP

                        PAXNEB 269 rkieqlvDtvieL..esfagse 288
                                   ++ +  +D+ ++L  +s+ag++
  gi|14601707|ref|NP_148248.1| 184 TRARATCDGYMKLslASLAGKT 205
                                   ********98765115776654 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   9.4e-06     0.017      28      71 ..      10      52 ..       3      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.4e-06
                                  -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHH CS
                          RecA 28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlal 71
                                  + kve +++G+  +di lG GG+p   ++ i Gp  +Gkt+l+ 
  gi|14601707|ref|NP_148248.1| 10 EGKVEIVPTGNEEFDIKLG-GGVPFPSLLIIEGPHGTGKTALSQ 52
                                  5689***************.********************9974 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.1e-05     0.055       6      77 ..      38     143 ..      35     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                        AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.....................................sw 49 
                                   +i Gp g+GKT l   +    l   +++Gl+ l +    +i+                                     s 
  gi|14601707|ref|NP_148248.1|  38 IIEGPHGTGKTALSQLF----LKGALDMGLRGLAVVTESTIRgyilkseaagisltehflrgrldvystqfegsrwgrrSA 114
                                   577*********99999....777889999999999999999999998888888888888877777777777777888777 PP

                        AAA_24  50 edfldevvel.aaeladyktlviDtidel 77 
                                   + +ld +  + + e ++y++l +D+++++
  gi|14601707|ref|NP_148248.1| 115 TVLLDLISRFlESESRRYEVLLVDSLSHI 143
                                   78888777768***************997 PP

>> AAA_33  AAA 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       1     122 [.      36     189 ..      36     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                        AAA_33   1 lvllvGlpGsGKstlaerllkklg......avllssdt...................lrrrlfg..tdqqsktdytrvldr 54 
                                   l+++ G+ G+GK+ l++  lk           ++++ t                   lr rl +  t+ +  ++  r ++ 
  gi|14601707|ref|NP_148248.1|  36 LLIIEGPHGTGKTALSQLFLKGALdmglrgLAVVTESTirgyilkseaagisltehfLRGRLDVysTQFEGSRWGRRSATV 116
                                   6899*************9864322466676888888886777777777777777776555555544666666666667777 PP

                        AAA_33  55 lyqilnelarkalsagrnvildat......nlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                   l + ++++++   s+++ v+l         + s+ +  +f++ +r +  + ++vv++  e +l+e l  Ra+++
  gi|14601707|ref|NP_148248.1| 117 LLDLISRFLE-SESRRYEVLLVDSlshiaiYSSPIRVLNFFNTVRLIADRGKLVVLTLHEGVLREDLTTRARAT 189
                                   8888877774.577777777766645555455566667777777777767788888888888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1847.22
//
Query:       gi|14601708|ref|NP_148249.1|  [L=182]
Description: hypothetical protein APE_1899 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       467  (0.0260472); 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:                         0  (0); expected 0.2 (1e-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: 1336.13
//
Query:       gi|14601709|ref|NP_148250.1|  [L=161]
Description: hypothetical protein APE_1901 [Aeropyrum pernix K1]
Scores for complete 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   74.4   0.4    1.4e-20   74.1   0.4    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 !   74.1   0.4   8.1e-25   1.4e-20       3     162 ..       5     156 ..       2     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 8.1e-25
                                   -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-.-E CS
                Arch_flagellin   3 vgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGss.pi 82 
                                   ++i+++ + I++V +A+++ag++i +++ + ++ qs +++++++++++++++ +v+d+a+n     + +y+k n+G +  +
  gi|14601709|ref|NP_148250.1|   5 TVIAHALLTIVAVTMASIFAGIAIFSSYEIGNSLQSIYKSISDKMRTEVTLVYIVYDEANNL----YRVYLK-NTGLTpMT 80 
                                   67******************************************************999987....******.*****889 PP

                                   EGGG-EEEEEESS--EE--E.........................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SS CS
                Arch_flagellin  83 dlnkttisvtddgqetlltadefgivvisdtdgsltng.......devlekgekvelevnvneddgitagdevsvevvpen 156
                                   +++++++++   g        e++++++++t g+ t++       d v+e ge++el++n     +   ++ v++ +v+++
  gi|14601709|ref|NP_148250.1|  81 NIENMEVFLGPYG-------GELDYYTYNTTGGQGTWSyveygtqDGVWEVGELIELVLNP----PSAYSNPVKLILVTPT 150
                                   ********99999.......89999***********************************7....799************* PP

                                   S--EEE CS
                Arch_flagellin 157 Gastti 162
                                   Ga++++
  gi|14601709|ref|NP_148250.1| 151 GAKMSF 156
                                   **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1204.94
//
Query:       gi|118431641|ref|YP_874917.1|  [L=259]
Description: hypothetical protein APE_1902.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00096   18.9   0.5     0.0058   16.4   0.0    2.1  2  SinI      Anti-repressor SinI
  ------ inclusion threshold ------
      0.047   13.8   0.1       0.14   12.3   0.1    1.9  1  DUF3420   Domain of unknown function (DUF3420)


Domain annotation for each model (and alignments):
>> SinI  Anti-repressor SinI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.4e-07    0.0058       6      21 ..     204     219 ..     204     219 .. 0.97
   2 ?    0.2   0.1     0.076   6.8e+02      12      23 ..     228     239 ..     228     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-07
                                    HHHHHHHHHHT--SHH CS
                           SinI   6 veLikEAkesGlskeE 21 
                                    +eL+ EA++ Gl++eE
  gi|118431641|ref|YP_874917.1| 204 IELMREARKLGLTPEE 219
                                    79*************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.076
                                    HHHHT--SHHHH CS
                           SinI  12 AkesGlskeEfR 23 
                                    A+  G+  eEf+
  gi|118431641|ref|YP_874917.1| 228 ARSLGIRDEEFE 239
                                    899*******98 PP

>> DUF3420  Domain of unknown function (DUF3420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.6e-05      0.14      10      28 ..     173     191 ..     168     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                        DUF3420  10 eLPievlakIkelRlkssl 28 
                                    ++P+ev++kI++l ++s++
  gi|118431641|ref|YP_874917.1| 173 SMPPEVFEKIIDLLEASGQ 191
                                    79***********988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2037.85
//
Query:       gi|14601712|ref|NP_148253.1|  [L=203]
Description: flagellin-like protein [Aeropyrum pernix K1]
Scores for 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-37  127.5   0.9    6.4e-37  127.3   0.9    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 !  127.3   0.9   3.6e-41   6.4e-37       1     164 []       6     188 ..       6     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 3.6e-41
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                   G vgi+++Iv+IA+V+VAA++a v++n++ f++qk++++++++ e+++s+le++g+v+++ t+g+++ i+i +k+++G + 
  gi|14601712|ref|NP_148253.1|   6 GIVGIEAAIVLIAFVIVAAALAFVALNMGLFTTQKSKEVMQRGLEEATSALEVDGSVIANVTSGSVDAIAIPIKVSPGREG 86 
                                   779*****************************************************************************9 PP

                                   EEGGG-EEE..EEESS.--EE--E....................................T-EE-TT-EEEEEEE--TTT- CS
                Arch_flagellin  82 idlnkttis..vtddg.qetlltad........efgivvisdtdgsltng..........devlekgekvelevnvneddg 141
                                   +d++ ++++  v+ +  + ++ ++         ++++++i+++ +++t +          d+vle gek+ l++++   ++
  gi|14601712|ref|NP_148253.1|  87 VDMSVDKTTvrVMLPSkFYENAYCGvfdgsslsDSKLSTITSSIACTTGWaylvifngdgDNVLELGEKGLLVLELP--TP 165
                                   99876665544788887888888878999988888888888888888888**************************7..9* PP

                                   --TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 142 itagdevsvevvpenGasttief 164
                                   ++ ++e++vev+p +Ga++t+e+
  gi|14601712|ref|NP_148253.1| 166 LNSYEEFKVEVRPVQGAALTVER 188
                                   ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1558.99
//
Query:       gi|14601713|ref|NP_148254.1|  [L=246]
Description: flagellin-like protein [Aeropyrum pernix K1]
Scores for 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  104.8   0.2    6.6e-30  104.5   0.2    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.038   14.0   0.3      0.061   13.3   0.3    1.2  1  CcmE            CcmE


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 !  104.5   0.2   7.3e-34   6.6e-30       1     164 []       6     216 ..       6     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 7.3e-34
                                   X--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEE.........EEE-SSSSSE.... CS
                Arch_flagellin   1 GfvgigtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvg.........dsatngtine.... 68 
                                   G vgi+++Iv+IA+V+VAA++a v++n++ f++qk++++++++ e+++s+le++g+v+         +++      +    
  gi|14601713|ref|NP_148254.1|   6 GIVGIEAAIVLIAFVIVAAALAFVALNMGLFTTQKSKEVMQRGLEEATSALEVDGSVIaraidadttTGS------Ynivv 80 
                                   779*******************************************************998663333333......24466 PP

                                   ..EEEEEE--TTS--EEGGG-EEE...EEESS--EE--E.......................................... CS
                Arch_flagellin  69 ..itiyvklnaGsspidlnkttis...vtddgqetlltad..........................efgivvisdtdgslt 118
                                     +++ +k ++G + idl+ ++++   ++ +g+ +++++                           + g +v +d+  ++ 
  gi|14601713|ref|NP_148254.1|  81 daLAVPLKISPGREGIDLDPSKLTvrlLLPNGFYENVYCGyasgsagedfeavlsnaptgcepyttSPGPFVATDAYVYVI 161
                                   77*********************9884455559999999899******999999999999999998889999999999999 PP

                                   ....T-EE-TT-EEEEEEE--.......TTT---TT-EEEEEEE-SSS--EEEEE CS
                Arch_flagellin 119 ng..devlekgekvelevnvn.......eddgitagdevsvevvpenGasttief 164
                                   ng  d vle gek+ l + ++       + d + ++d++ +e+++ +Gas+t+e+
  gi|14601713|ref|NP_148254.1| 162 NGdgDSVLELGEKGLLIIRLDsdttatiDVDYLEPYDKIMIELRAVSGASLTLER 216
                                   989*************************9999*******************9985 PP

>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.9e-06     0.061       9      75 ..      13      80 ..       3      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-06
                                  XXXXXXXXXXXXXXXXXXXXXSSSXXBXTTTTTS--S-.TTSEEEEEEEE-TTT-EE-TTSSEEEEEE CS
                          CcmE  9 ivllllvlaavvvlvlsalqenlvyfltpsevlekkae.egrrlrvgGlVkegsvkrdpesleveFvv 75
                                  +++l+++++++++l++ al+  l    + +ev++++ e +++ l v G V++  ++ d+++ +++ vv
  gi|14601713|ref|NP_148254.1| 13 AIVLIAFVIVAAALAFVALNMGLFTTQKSKEVMQRGLEeATSALEVDGSVIARAIDADTTTGSYNIVV 80
                                  45667778888899999999999999999******8877****************9887666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1962.10
//
Query:       gi|118431642|ref|NP_148255.2|  [L=189]
Description: hypothetical protein APE_1908.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1566.81
//
Query:       gi|118431643|ref|NP_148256.2|  [L=246]
Description: hypothetical protein APE_1909.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy 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:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1981.34
//
Query:       gi|118431644|ref|NP_148257.2|  [L=294]
Description: hypothetical protein APE_1911.1 [Aeropyrum pernix K1]
Scores for complete 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-25   89.0   0.0    5.3e-25   88.5   0.0    1.2  1  ABC_tran  ABC transporter
    2.2e-10   40.8   0.5    0.00036   20.4   0.4    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00021   20.4   0.2    0.00033   19.7   0.2    1.2  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00064   20.0   0.0     0.0018   18.6   0.0    1.7  1  AAA_22    AAA domain
     0.0082   16.5   1.2      0.019   15.3   1.2    1.9  1  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.12   12.5   0.1    2.2  1  AAA_33    AAA domain
      0.016   14.9   0.0      0.037   13.7   0.0    1.5  1  AAA_30    AAA domain
       0.02   14.6   0.0      0.052   13.3   0.0    1.6  2  AAA_29    P-loop containing region of AAA domain
      0.024   15.1   0.0      0.035   14.6   0.0    1.2  1  AAA_23    AAA domain
      0.025   14.2   0.0      0.041   13.5   0.0    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.051   13.2   0.1       0.28   10.7   0.0    2.1  2  AAA_25    AAA domain
      0.074   12.6   0.3       0.11   12.0   0.3    1.2  1  cobW      CobW/HypB/UreG, nucleotide-binding domain
        0.2   11.1   0.0          2    7.8   0.0    2.0  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 !   88.5   0.0   3.8e-28   5.3e-25       1     137 []      20     159 ..      20     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 3.8e-28
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++v+l++ +ge v++vG+nGaGK+tL+k+ +gl + + G++ll+g d  +  ++++r+ +gv+++ p+l + + v e  
  gi|118431644|ref|NP_148257.2|  20 LDRVDLEVGRGEAVGLVGPNGAGKTTLIKVSLGLARRDGGRVLLNGLDPWR--EPRAREGVGVVFERPNLPSSMPVVEFl 97 
                                    789******************************************777666..89********************99999 PP

                                    ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             s ++++ a++  gl++ + ++      +LS G kqr a+a all +p++l++DEpt+
  gi|118431644|ref|NP_148257.2|  98 esaaaiigSSPSRVDWAIRAAGLEGHEWKTF----PQLSAGLKQRAAIAHALLGEPRFLVADEPTS 159
                                    9999999999999***********9887877....9****************************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 !   18.5   0.0     1e-06    0.0014       3      25 ..      34      56 ..      33      98 .. 0.71
   2 !   20.4   0.4   2.6e-07   0.00036     234     297 ..     128     189 ..     121     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                   +l+GpNg+GK++L++   +lar 
  gi|118431644|ref|NP_148257.2| 34 GLVGPNGAGKTTLIKVSLGLARR 56
                                   69*************99999874 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.6e-07
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                    + +lS G k+ +a++ all  +   ++l+ DEp ++L+P   r++l+ll +l+r +g  +++++H
  gi|118431644|ref|NP_148257.2| 128 FPQLSAGLKQRAAIAHALLGEP---RFLVADEPTSNLDPLERREVLRLLARLNReHGLSLLVSSH 189
                                    6789999999977777777766...************************66666699******** 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 !   19.7   0.2   2.4e-07   0.00033      14      67 ..      15      68 ..       3      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.4e-07
                                   HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB 14 eakellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                   + + +l+r+  + Gr + vGl G  GaGk tl++      rr G rv +  +DP
  gi|118431644|ref|NP_148257.2| 15 RGQPVLDRVDLEVGRGEAVGLVGPNGAGKTTLIKVSLGLARRDGGRVLLNGLDP 68
                                   67899****************************877777788899*99999988 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   1.3e-06    0.0018      10     127 ..      35     186 ..      28     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.................erpevv..fvtlpsstsskdllrellralglelka 70 
                                    ++G+ G+GKTtl++  l  + ++                      e+++vv  + +lpss+   ++l+  + ++g++ ++
  gi|118431644|ref|NP_148257.2|  35 LVGPNGAGKTTLIKVSLGLARRD----GgrvllngldpwreprarEGVGVVfeRPNLPSSMPVVEFLESAAAIIGSSPSR 110
                                    79************998887432....24577999*******9999999999999************************* PP

                         AAA_22  71 .............erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliL 127
                                                 e+++  +l   + ++a+ a+a    +++l+ DE    l+   + e+l+ L +l    ++g++l++
  gi|118431644|ref|NP_148257.2| 111 vdwairaagleghEWKTFPQLSaGLKQRAAIAHALlgePRFLVADEPTSnLDpleRREVLRLLARLNR--EHGLSLLV 186
                                    *********9888666666666444444444444488889******9988987766999999988888..99999875 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   1.2   1.4e-05     0.019      22      63 ..      28      69 ..      18     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   gr+e+v l+G+ G GK++l++  l  +++dgg +l    d  
  gi|118431644|ref|NP_148257.2| 28 GRGEAVGLVGPNGAGKTTLIKVSLGLARRDGGRVLLNGLDPW 69
                                   77899****************999999999888876666655 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   8.9e-05      0.12       4      97 ..      35     178 ..      33     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                         AAA_33   4 lvGlpGsGKstlaer...llkklg.avllssdt.............................................lr 34 
                                    lvG++G+GK+tl++    l+++ g  vll+  +                                             + 
  gi|118431644|ref|NP_148257.2|  35 LVGPNGAGKTTLIKVslgLARRDGgRVLLNGLDpwrepraregvgvvferpnlpssmpvveflesaaaiigsspsrvdWA 114
                                    79**********99622246666666666655566666666666666666666666666666665555555555555533 PP

                         AAA_33  35 rrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflklarrlgv 97 
                                     r +g + +  +  ++++  l+q+  ++a+  l + r +++d +  nl++ er+++l+l+ rl+ 
  gi|118431644|ref|NP_148257.2| 115 IRAAGLEGHEWKTFPQLSAGLKQRA-AIAHALLGEPRFLVADEPtsNLDPLERREVLRLLARLNR 178
                                    3333333333334455555666665.777777777777777777777778888887777777774 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.7e-05     0.037      20      51 ..      32      63 ..      24      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvig 51
                                    + l+Gp G+GKtt++k+   +++++ggrv++
  gi|118431644|ref|NP_148257.2| 32 AVGLVGPNGAGKTTLIKVSLGLARRDGGRVLL 63
                                   5779*********************9999975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.052      15      39 ..      23      47 ..      19      51 .. 0.81
   2 ?   -3.4   0.0       6.4   8.8e+03       8      20 ..     124     136 ..     120     147 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    ++e+ + +a+ l+Gp+G+GK+Tl+
  gi|118431644|ref|NP_148257.2| 23 VDLEVGRGEAVGLVGPNGAGKTTLI 47
                                   556666555889************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.4
                         AAA_29   8 NWgtfdghtieid 20 
                                    +W tf + ++ ++
  gi|118431644|ref|NP_148257.2| 124 EWKTFPQLSAGLK 136
                                    6999877555554 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   2.5e-05     0.035      23      36 ..      34      47 ..      14      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                         AAA_23 23 lItGpNGaGKTTil 36
                                    ++GpNGaGKTT++
  gi|118431644|ref|NP_148257.2| 34 GLVGPNGAGKTTLI 47
                                   589**********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 ?   13.5   0.0     3e-05     0.041       6      41 ..      35      70 ..      31      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                                   EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                          SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                   lvG++GaGKTt +     l +++g +vll  +D +R
  gi|118431644|ref|NP_148257.2| 35 LVGPNGAGKTTLIKVSLGLARRDGGRVLLNGLDPWR 70
                                   8*********9986555566666**********999 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   0.00021      0.28      30      82 ..      27      85 ..      11      94 .. 0.71
   2 ?   -0.7   0.0      0.65     9e+02     162     189 ..     160     190 ..     126     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                         AAA_25 30 lpagelallaGapgtGKttla.ldlalava.tGkpwlg...pvap.eqgkVlyvsaEds 82
                                   + +ge + l+G+ g+GKttl  ++l+la    G+ +l    p++  + +  + v++E +
  gi|118431644|ref|NP_148257.2| 27 VGRGEAVGLVGPNGAGKTTLIkVSLGLARRdGGRVLLNgldPWREpRAREGVGVVFERP 85
                                   46899999***********8536666666644444444788554446666666666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.65
                         AAA_25 162 nsd..v.galvealeriarrtgaavllvhHv 189
                                    n d  + ++++  l+r+ r++g  +l+  Hv
  gi|118431644|ref|NP_148257.2| 160 NLDplErREVLRLLARLNREHGLSLLVSSHV 190
                                    4333334778888888888999888888886 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   8.2e-05      0.11       2      26 ..      32      58 ..      31      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.2e-05
                                   EEEEEESTTCCHHHHHHHHH..CT--S CS
                           cobW  2 vtvltGflGsGKTtLlnhll..enrag 26
                                   +++l+G+ G+GKTtL++  l  ++r+g
  gi|118431644|ref|NP_148257.2| 32 AVGLVGPNGAGKTTLIKVSLglARRDG 58
                                   5789************99886544444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0015         2      27      41 ..      33      47 ..      11      55 .. 0.82
   2 ?    1.1   0.0      0.17   2.3e+02     160     196 ..     150     188 ..     127     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                                   EEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnll 41
                                     +vGpNG+GK+ l+
  gi|118431644|ref|NP_148257.2| 33 VGLVGPNGAGKTTLI 47
                                   569*********997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                                    SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          SMC_N 160 plyllDeidaaLDeknvkkvaellkekskn..aQfivis 196
                                     + + De  ++LD  ++++v +ll + + +    ++v s
  gi|118431644|ref|NP_148257.2| 150 RFLVADEPTSNLDPLERREVLRLLARLNREhgLSLLVSS 188
                                    48899***************9999865544225555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2322.05
//
Query:       gi|118431645|ref|NP_148258.2|  [L=394]
Description: MFS transporter [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-23   82.7  59.3    2.7e-19   69.3  45.7    2.2  2  MFS_1       Major Facilitator Superfamily
    1.4e-06   27.4  18.0    5.9e-05   22.1   6.0    2.3  2  MFS_1_like  MFS_1 like family
    4.7e-05   22.0  27.2      0.026   12.9   0.2    3.2  3  MFS_3       Transmembrane secretion effector
     0.0034   16.3   0.8     0.0034   16.3   0.8    3.2  3  Sugar_tr    Sugar (and other) transporter
     0.0056   15.5   0.7      0.031   13.1   0.0    2.1  3  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 !   69.3  45.7   7.4e-23   2.7e-19       1     324 [.      14     325 ..      14     327 .. 0.82
   2 !   18.9  33.6   1.6e-07   0.00057      29     168 ..     243     381 ..     207     388 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 7.4e-23
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l+la+f   ++ ++l+ ++  a+ae+lg+s++e+g++++ly+ +a+ as+ +G ++d++Gr++ l++gl++  l+++l +
  gi|118431645|ref|NP_148258.2|  14 LALAGFAGLMDTAFLLGVVA-AYAEHLGASKAEAGFIAGLYSMAAIPASIAAGIVVDKVGRKKALIAGLAWDTLAVTLYT 92 
                                    57899999999999999999.9*****************************************************44444 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                     ++s +  l++ r l ++g+++++pa  +++ d + +   g a g + a +++G++lg ++gg  ++ lg++ +  +l +
  gi|118431645|ref|NP_148258.2|  93 -TASTPgELALYRGLHAIGGSLVYPAFFSIVGDTSRRGGEGYAAGRYLAVIGAGVALGSAAGGRAVEMLGFQNALRLLSL 171
                                    .388898************************************************************************* PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllplylqevl 238
                                    +++++     + +  ++++++  + +      ++  +++ +k l +       +++l+l+f ++ g l+t l+     v 
  gi|118431645|ref|NP_148258.2| 172 ILAIGTA---AAVALPYRDSGIARRAGV----ARGLMASRLKVLGAAA----TMASLYLGFGILVGgLSTALTGE-GVVE 239
                                    *****88...555566666666655555....4455555344454444....66666666555555677777773.5555 PP

                          MFS_1 239 gls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgf 316
                                    g   +  lagl ++++++++++++ll+grl+d    r +l la ++++++a + al+  +s++ +l+++ +   + g+g+
  gi|118431645|ref|NP_148258.2| 240 GEEeASALAGLSIGVASIASLPAFLLSGRLIDA--GRGALALAAASASALAGAAALAQSPSHPGVLVFAALYGPLiGAGM 317
                                    55585599999*********************8..578888888888888888888888867777666555555557777 PP

                          MFS_1 317 vfpsllal 324
                                    + +++la+
  gi|118431645|ref|NP_148258.2| 318 TLSTYLAI 325
                                    77777665 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-07
                          MFS_1  29 ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa..sslwlllvlrvlqGlgagalfpag 106
                                     + + +gl +++ +++++ a l+ Grl+d  Gr  + l+++ ++al+++++l a  +s++ +lv+ +l G   ga+++++
  gi|118431645|ref|NP_148258.2| 243 EASALAGLSIGVASIASLPAFLLSGRLIDA-GRGALALAAASASALAGAAAL-AqsPSHPGVLVFAALYGPLIGAGMTLS 320
                                    344558999999*****************8.9***99999999999955555.445888899999999999999***999 PP

                          MFS_1 107 aaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlf 168
                                     +l+   +p+  rg  i++ ++++ lG+++g++lgg+l+ + g +++ + +a+ +ll++ l 
  gi|118431645|ref|NP_148258.2| 321 TYLAIT-VPPWSRGTSIAIQQVSNILGVAVGAPLGGVLSGAMGLEGIALGIAGSTLLLAALS 381
                                    776666.7778**********************************************98864 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 !   22.1   6.0   1.6e-08   5.9e-05     248     375 ..      32     158 ..      11     168 .. 0.90
   2 !   11.0   4.1   3.9e-05      0.14     259     374 ..     245     358 ..     239     364 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-08
                     MFS_1_like 248 lflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisf 327
                                    +  Y ++lgas+  +G +  l  +a ip  + a  +++k+G  k li++l   +l   ly + + +  + +   Lh+i  
  gi|118431645|ref|NP_148258.2|  32 VAAYAEHLGASKAEAGFIAGLYSMAAIPASIAAGIVVDKVGRKKALIAGLAWDTLAVTLYTTASTPGELALYRGLHAIGG 111
                                    67899*************************************************************************** PP

                     MFS_1_like 328 gllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwd 375
                                     l++ a  + v +   ++ e+   g + ++ +g+G alGs +GG   +
  gi|118431645|ref|NP_148258.2| 112 SLVYPAFFSIVGDTSRRGGEGYAAGRYLAV-IGAGVALGSAAGGRAVE 158
                                    ***********************9999877.9************7655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 3.9e-05
                     MFS_1_like 259 ntllGslvalgvvaeiplfffaeklleklGhvklliiallayi.lrfllyaiienawlvlpievLhgisfgllwaaavey 337
                                    + l+G  + +  +a++p f+++ +l++  G   l ++a +a + +    +a   +   vl++ +L+g  +g+  +++ +y
  gi|118431645|ref|NP_148258.2| 245 SALAGLSIGVASIASLPAFLLSGRLIDA-GRGALALAAASASAlAGAAALAQSPSHPGVLVFAALYGPLIGAG-MTLSTY 322
                                    5789**********************96.5555555554444403444455557777899999****999998.89**** PP

                     MFS_1_like 338 vskiapksleatgqgllsglyfglGralGsliGGllw 374
                                     ++ +p+  ++t +++ +  +  lG a+G+ +GG+l 
  gi|118431645|ref|NP_148258.2| 323 LAITVPPWSRGTSIAIQQV-SNILGVAVGAPLGGVLS 358
                                    ***************9765.56799999999999875 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   7.3e-06     0.026      58     133 ..      57     127 ..      27     130 .. 0.80
   2 !    8.3   1.5   0.00018      0.66     348     397 ..     138     187 ..     131     206 .. 0.89
   3 !    9.6  13.2   7.6e-05      0.27     286     395 ..     277     387 ..     230     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-06
                          MFS_3  58 ifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvk 133
                                     +  si aG++ D++ r+k l+a+ ++  l+ +l     ++   +p  l  +  l +iG +l  Pa+  +vg+  +
  gi|118431645|ref|NP_148258.2|  57 AIPASIAAGIVVDKVGRKKALIAGLAWDTLAVTL-----YTTASTPGELALYRGLHAIGGSLVYPAFFSIVGDTSR 127
                                    45569*******************9998665554.....44556778888889999****************9755 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00018
                          MFS_3 348 YltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklpe 397
                                    Yl+v+  g+a+Gs++ G  +e l+ ++aL + ++ l +++a+ + l+ ++
  gi|118431645|ref|NP_148258.2| 138 YLAVIGAGVALGSAAGGRAVEMLGFQNALRLLSLILAIGTAAAVALPYRD 187
                                    9999*********************************9999998887665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 7.6e-05
                          MFS_3 286 lvllaavalAlvllslalas.slwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWG 364
                                    l l aa a A  + ++ala+ +    vlv++ + +  i a  tl +   ++vP W +g ++a+ ++    g+a G+ l G
  gi|118431645|ref|NP_148258.2| 277 LALAAASASA-LAGAAALAQsPSHPGVLVFAALYGPLIGAGMTLSTYLAITVPPWSRGTSIAIQQVSNILGVAVGAPLGG 355
                                    3333333333.33334444313455677888888899******************************************* PP

                          MFS_3 365 avaealsvt.laLlaaaaalllaaaillllkl 395
                                    +++ a++++ +aL +a+ +lllaa+ +l lk+
  gi|118431645|ref|NP_148258.2| 356 VLSGAMGLEgIALGIAGSTLLLAALSILSLKM 387
                                    ********8469**********9998887765 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8   9.6e-07    0.0034      42     115 ..      40     110 ..      13     129 .. 0.72
   2 ?    1.9   4.0     0.022        79      49      96 ..     136     183 ..     109     220 .. 0.86
   3 ?   -0.2   9.0     0.099   3.6e+02      41     160 ..     241     356 ..     208     385 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.6e-07
                                    HH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHH CS
                       Sugar_tr  42 eessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGig 115
                                     +s+   g+i+++++  ai  s+ ag+++d++GRkk+l+++ +    +  l  +a    +   l++ R l  ig
  gi|118431645|ref|NP_148258.2|  40 GASKAEAGFIAGLYSMAAIPASIAAGIVVDKVGRKKALIAGLAWDTLAVTLYTTAS---TPGELALYRGLHAIG 110
                                    33556678888888888888888888888888888888888877777766666666...567777777666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.022
                                    HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-T CS
                       Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaa 96 
                                    g  +++  +G ++Gs  +g +++++G +++l   ++++ ig++  +a 
  gi|118431645|ref|NP_148258.2| 136 GRYLAVIGAGVALGSAAGGRAVEMLGFQNALRLLSLILAIGTAAAVAL 183
                                    66778888999******************************9887765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.099
                                    HHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                       Sugar_tr  41 keessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                    +ee+s l gl+ +++++ ++   l++g l+d      +l++a++ +++ga+  a ++   s+  ++v   l G  +G+  
  gi|118431645|ref|NP_148258.2| 241 EEEASALAGLSIGVASIASLPAFLLSGRLIDAGRGALALAAASASALAGAAALAQSP---SHPGVLVFAALYGPLIGAGM 317
                                    334577999*********************985555666778899999999999999...7777778889***9999886 PP

                                    HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglg 160
                                    +  ++y++   p+  Rg+ + ++q++ ++G  v+a +g +
  gi|118431645|ref|NP_148258.2| 318 T-LSTYLAITVPPWSRGTSIAIQQVSNILGVAVGAPLGGV 356
                                    5.567888899********************999877655 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   8.6e-06     0.031      34      80 ..      35      81 ..      19      93 .. 0.87
   2 !    8.0   0.1    0.0003       1.1     282     390 ..      67     174 ..      66     183 .. 0.81
   3 ?   -3.6   0.1      0.99   3.5e+03     368     400 ..     353     385 ..     339     389 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-06
                      LacY_symp 34 lkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvi 80
                                    +e+lg sk+e G +    s+ +i      G++ dk+G kk l+  +
  gi|118431645|ref|NP_148258.2| 35 YAEHLGASKAEAGFIAGLYSMAAIPASIAAGIVVDKVGRKKALIAGL 81
                                   47999**************************************9655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0003
                      LacY_symp 282 ivnriGaknalliagvimsvrilgsafattalevvilkllhalevplllvgvfkyitsafdkrlsatifligfqlskqla 361
                                    +v+++G k al+ + +  ++ ++  + a t+ e+ + + lha+   l +  +f  i++   +r     +  g  l+   a
  gi|118431645|ref|NP_148258.2|  67 VVDKVGRKKALIAGLAWDTLAVTLYTTASTPGELALYRGLHAIGGSL-VYPAFFSIVGDTSRR-GGEGYAAGRYLAVIGA 144
                                    799********999999999999999*****************9775.566777788887666.5566888877776666 PP

                      LacY_symp 362 ivll.stlaGklydkvGfqtaylvlgiivl 390
                                     v l s+  G+  + +Gfq+a  +l++i  
  gi|118431645|ref|NP_148258.2| 145 GVALgSAAGGRAVEMLGFQNALRLLSLILA 174
                                    55552788899**********999999865 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 0.99
                      LacY_symp 368 laGklydkvGfqtaylvlgiivlsltlisvftl 400
                                    l G l   +G + + l ++  +l+l  +s++ l
  gi|118431645|ref|NP_148258.2| 353 LGGVLSGAMGLEGIALGIAGSTLLLAALSILSL 385
                                    444444455555555555544554444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.20s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3128.42
//
Query:       gi|14601719|ref|NP_148260.1|  [L=441]
Description: peptidase [Aeropyrum pernix K1]
Scores for complete 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  112.5   0.0    3.1e-32  112.0   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
  ------ inclusion threshold ------
      0.044   13.5   0.0       0.36   10.5   0.0    2.0  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.0   3.5e-36   3.1e-32       1     206 [.      69     437 ..      69     438 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 3.5e-36
                                   EEEEES-BSSTTCGGGSSS..TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THH CS
                                   xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                 Peptidase_M20   1 llgsHlDvVpeeetdgwtt..pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGa 78 
                                   l+++H DvVp+++   w+   pf++ ++ G+lyGrGa+d+k  v+a+  al  ++      +gt+ ++f++dEE+g+ +Ga
  gi|14601719|ref|NP_148260.1|  69 LFMAHFDVVPPGPG--WRVtePFKPVVKGGRLYGRGAADDKSNVAAISLALSGFEPG----RGTVIIAFTGDEEIGGeRGA 143
                                   79********7766..9999*******************************998776....89***********8778*** PP

                                   HHHHHHHH.TTTCESEEEEEEEESSSBTCHSTETEEEE........................................... CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
                 Peptidase_M20  79 kallegle.erekvdavfelhieepgileagklaigvv........................................... 115
                                   ++l++ l+ e+  +d+v+    +++++         ++                                           
  gi|14601719|ref|NP_148260.1| 144 GWLAGRLRsEGLWPDYVV---NGDGSMGA------VITrrrnvfnaivrvraeradaegvsrrvmrlglevrgrptrhaay 215
                                   *****9999999999966...88888877......2335666779999********************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                 Peptidase_M20 116 ................................................................................. 115
                                                                                                                    
  gi|14601719|ref|NP_148260.1| 216 fipgvdshplltaaalvreagllasslsgewvksnvlpasvelealepgggghgvydpgltallksliplsritpgrllys 296
                                   ********************************************************************************* PP

                                   ....................................................EEEEEEEEEESHEEECCHHHHHHHHHHHH CS
                                   ....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 116 ....................................................kvevelleggapvtlndsplvkalaeaae 144
                                                                                       +++v+  +gg+ +t ++++lvk++ ++ +
  gi|14601719|ref|NP_148260.1| 297 dygvtatpnvyrlaegwhevivdvramtgdpaavdeavarsleeslgsrvewEYRVT-GGGGYLYTPSSAELVKLALRVNQ 376
                                   ***********************************************9765555555.47777777779**********99 PP

                                   HHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEESSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 Peptidase_M20 145 elfgekvelivsgpggtdarff..agiptvmifgpgsglaHspnEyvdledlekgikvlarlle 206
                                   +l g+  e+   + g++d+r+f   g  +++ +gp +g++H+p+Eyv++++le++++++ r++e
  gi|14601719|ref|NP_148260.1| 377 SL-GLPGEPREAA-GASDSRYFspRGS-QAIDYGPLGGNVHGPDEYVEIRQLEAAVEFYRRVAE 437
                                   98.9887777777.9*******66666.66559*777***********************9976 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     4e-05      0.36      13      74 ..      66     139 ..      56     165 .. 0.76
   2 ?    0.4   0.0     0.049   4.4e+02     121     163 ..     365     406 ..     354     437 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4e-05
                                   EEEEEEEE--B-TTT..............TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCS.SEEEEEEEESSCSG.S CS
                 Peptidase_M28  13 evlllgAHyDsvgvg..............rgp..ifvGAdDnAsgvaalLelarvlaasgsrp.krgvrflffdaEEa.g 74 
                                    v l++AH+D v+ g                      GA D+ s vaa+   +  ++     p + +v+++f++ EE  g
  gi|14601719|ref|NP_148260.1|  66 PVTLFMAHFDVVPPGpgwrvtepfkpvvkG-GrlYGRGAADDKSNVAAISLALSGFE-----PgRGTVIIAFTGDEEIgG 139
                                   47799********999***99998877752.245567**********9987777776.....425677777777777652 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.049
                                   HHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEE CS
                 Peptidase_M28 121 kelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldl 163
                                   +el +la +v+++    p ++r+ +g sD + f  +g +++d+
  gi|14601719|ref|NP_148260.1| 365 AELVKLALRVNQS-LGLPGEPREAAGASDSRYFSPRGSQAIDY 406
                                   5566677777765.4689999999*************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3361.36
//
Query:       gi|118431646|ref|YP_874918.1|  [L=167]
Description: homing endonuclease I-ApeII [Aeropyrum pernix K1]
Scores for complete 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   35.3   0.0    3.9e-08   34.2   0.0    1.5  2  LAGLIDADG_1    LAGLIDADG endonuclease
  ------ inclusion threshold ------
       0.16   11.4   0.0       0.24   10.8   0.0    1.3  1  Flagellar_rod  Paraflagellar rod protein


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 !   34.2   0.0   4.4e-12   3.9e-08       2      92 ..      11     100 ..      10     109 .. 0.89
   2 ?   -2.2   0.0      0.94   8.4e+03      35      43 ..     140     148 ..     126     157 .. 0.52

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4.4e-12
                                    HHHHHHHEEEEEEEEETTTTTTSEEEEEEEEEEEEGGGHHHHHHHHHHHTECEEEEETTTE.EEEEEE-SHHHHHHTHHH CS
                    LAGLIDADG_1   2 aGFiDgdGsfsitvtkskskktslkvqlefqielkkkdesllekikeylglgsikkrkkdk.yvsyiisnsskslkilip 80 
                                    aG iD+++s s++++ ++  +  ++v + f+i+++    ++l+ +k+y+g+g +  +  ++  + y++ + +  ++ lip
  gi|118431646|ref|YP_874918.1|  11 AGIIDAEASLSVSIKIQEDLRCRVRVDPVFSITQD--SKDVLNVVKNYFGCGRLMPKPGQEhLTLYVVDRLEALADCLIP 88 
                                    89****************9999999**********..6779*****************9997888888889999****** PP

                                    HHHHST-SSTHH CS
                    LAGLIDADG_1  81 yfdkypllssKy 92 
                                     +d+ pl+ +K 
  gi|118431646|ref|YP_874918.1|  89 KLDRLPLIVKKR 100
                                    *******98774 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.94
                                    EEGGGHHHH CS
                    LAGLIDADG_1  35 lkkkdesll 43 
                                     k+k+   l
  gi|118431646|ref|YP_874918.1| 140 KKSKRKRSL 148
                                    223333333 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.7e-05      0.24     135     184 ..      70     119 ..      39     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.7e-05
                  Flagellar_rod 135 elVkegvkklkakqdklqnalselllevrkefleafralyltlgeltykK 184
                                     l    v++l+a  d l  +l+ l l v+k  +e fr+ +ltl +++y++
  gi|118431646|ref|YP_874918.1|  70 HLTLYVVDRLEALADCLIPKLDRLPLIVKKRGFEMFREIVLTLTRMKYRR 119
                                    45555678888888**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1291.19
//
Query:       gi|118431647|ref|NP_148261.2|  [L=222]
Description: homing endonuclease I-ApeI [Aeropyrum pernix K1]
Scores for complete 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-12   47.0   2.1    2.1e-09   37.6   0.0    2.2  2  LAGLIDADG_3  LAGLIDADG-like domain
  ------ inclusion threshold ------
        0.1   13.0   0.6        3.6    8.0   0.2    2.4  2  SPOR         Sporulation related domain
       0.13   12.4   0.0       0.24   11.6   0.0    1.5  1  Sld7_C       Sld7 C-terminal domain
       0.14   13.2   1.3         36    5.4   0.0    3.0  3  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 !    9.0   0.5   0.00039       1.7      14      76 ..      15      74 ..      14      80 .. 0.69
   2 !   37.6   0.0   4.7e-13   2.1e-09       3      83 .]     107     183 ..     105     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00039
                                   CCECCECSTTTTSEEEEES-HHHHHHHHHH.HHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTC CS
                    LAGLIDADG_3 14 DGsvskskkkgvsisltssskelledvqrl.LlrlGIestiyekkkakgrgvyrlliisgenlk 76
                                   DGsv   +++  ++  +ss+k++le v    L  lG ++  +    + +rg yr++i+s++ ++
  gi|118431647|ref|NP_148261.2| 15 DGSVYRYSRN-YYVIWYSSNKDYLERVIVSkLRILGFHNV-RVY--QYKRGAYRVRISSKQLFH 74
                                   9******976.55777777777777765540556666553.333..479999999888887665 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 4.7e-13
                                    HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGTTT CS
                    LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFleki 82 
                                    + ++ +G+ da+Gsv ks+k+ v++ +++   e l+ ++++L++ G++ t       + +gv+rl+i s  +l+rF+ +i
  gi|118431647|ref|NP_148261.2| 107 QIEYVKGFVDAEGSVIKSSKG-VQVDVSQQIMEPLKFLAQVLEKVGVKVTGIYL---GSDGVWRLRIASLASLRRFAHYI 182
                                    67899**************76.66***********************9886666...6*********************9 PP

                                    X CS
                    LAGLIDADG_3  83 g 83 
                                    g
  gi|118431647|ref|NP_148261.2| 183 G 183
                                    8 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2    0.0008       3.6      22      48 ..      42      67 ..      22      72 .. 0.89
   2 ?    2.8   0.0     0.034   1.5e+02      20      53 ..     142     174 ..     135     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0008
                                   HHHCCHHT--...EEECCSSSCEEEEE CS
                           SPOR 22 aakLrakgfaaavavvsgggglyrVrv 48
                                   ++kLr  gf+++  v++ ++g yrVr+
  gi|118431647|ref|NP_148261.2| 42 VSKLRILGFHNV-RVYQYKRGAYRVRI 67
                                   799*******98.*************9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.034
                                    HHHHHCCHHT--...EEECCSSSCEEEEESSBCT CS
                           SPOR  20 rlaakLrakgfaaavavvsgggglyrVrvGpfas 53 
                                     la+ L + g +++   + g +g++r+r+   as
  gi|118431647|ref|NP_148261.2| 142 FLAQVLEKVGVKVT-GIYLGSDGVWRLRIASLAS 174
                                    56777777788877.8888999999999976555 PP

>> Sld7_C  Sld7 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.24       2      24 ..      31      53 ..      30      89 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                         Sld7_C  2 eqnkealsklilagLRlrGlsqs 24
                                   ++nk+ l+++i++ LR+ G+++ 
  gi|118431647|ref|NP_148261.2| 31 SSNKDYLERVIVSKLRILGFHNV 53
                                   579*****************987 PP

>> LAGLIDADG_1  LAGLIDADG endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.14   6.2e+02      51      79 ..      15      41 ..       3      46 .. 0.71
   2 ?    4.1   0.2      0.02        88      49      89 ..      47      87 ..      34      92 .. 0.74
   3 ?    5.4   0.0    0.0079        36       3      36 ..     113     139 ..     111     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                                   TECEEEEETTTEEEEEEE-SHHHHHHTHH CS
                    LAGLIDADG_1 51 glgsikkrkkdkyvsyiisnsskslkili 79
                                   + gs+++++++ yv+++ sn ++ l+ +i
  gi|118431647|ref|NP_148261.2| 15 D-GSVYRYSRNYYVIWYSSN-KDYLERVI 41
                                   4.999999998899999999.55554444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.02
                                   HHTECEEEEETTTE.EEEEEE-SHHHHHHTHHHHHHHST-SS CS
                    LAGLIDADG_1 49 ylglgsikkrkkdk.yvsyiisnsskslkilipyfdkyplls 89
                                   +lg+ +++ ++ ++ +++++is+ ++   il++ f++    s
  gi|118431647|ref|NP_148261.2| 47 ILGFHNVRVYQYKRgAYRVRISS-KQLFHILVNQFEHPLSTS 87
                                   4555566655555559******9.***********9865544 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0079
                                    HHHHHHEEEEEEEEETTTTTTSEEEEEEEEEEEE CS
                    LAGLIDADG_1   3 GFiDgdGsfsitvtkskskktslkvqlefqielk 36 
                                    GF+D++Gs   + ++       ++v ++ qi+  
  gi|118431647|ref|NP_148261.2| 113 GFVDAEGSVIKSSKG-------VQVDVSQQIMEP 139
                                    *******96433333.......345555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); 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: 00:00:00.38
# Mc/sec: 1764.85
//
Query:       gi|14601723|ref|NP_148264.1|  [L=252]
Description: hypothetical protein APE_1930 [Aeropyrum pernix K1]
Scores for complete 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-06   27.3   8.8    4.1e-06   27.3   8.8    2.3  2  SNARE_assoc      SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.78   10.2   4.4        1.8    9.0   0.2    2.4  2  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
        1.7    6.8  11.2        2.1    6.5  11.2    1.1  1  DUF2070          Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   8.8   6.9e-10   4.1e-06      13     119 ..      43     154 ..      28     155 .. 0.78
   2 ?    2.3   0.2     0.038   2.3e+02      15      42 ..     175     202 ..     162     239 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 6.9e-10
                   SNARE_assoc  13 lf.....glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlver.ygflallllrllpivPrdlvny 87 
                                   ++     ++l + l++ lga +G++  ++++ y+++k +r + +++  +k  e+   +   ++a++++ llpi P+d++ +
  gi|14601723|ref|NP_148264.1|  43 AAvsensHWLATALYAGLGAGIGKVALFAASLYAFSKTGRGRRVKQYSAKLMESRRAKvSLAIAIFFIALLPI-PDDIIYI 122
                                   22346668888************************66666666666555554443333144578********6.8****** PP

                   SNARE_assoc  88 vaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                   ++++t +++  F +a + G+++ ++++  +G+
  gi|14601723|ref|NP_148264.1| 123 PLAATFYNLLYFSIAVVTGKLVLVTLFYGVGR 154
                                   ***************************99996 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.038
                   SNARE_assoc  15 glllgtlvtslgallGaslayllgrylg 42 
                                   g+ lg ++++++++lG sla +++  + 
  gi|14601723|ref|NP_148264.1| 175 GYPLGAVLALVAVSLGFSLAIAAVVLAI 202
                                   5556666666666666666655554444 PP

>> 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 ?    9.0   0.2    0.0003       1.8      45      80 ..      37      72 ..      25      84 .. 0.86
   2 ?    2.4   0.6     0.034   2.1e+02      37      66 ..     172     201 ..     136     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0003
               Phage_holin_5_1 45 ailgalatsldgsgslatmiwagalagaggtglfeq 80
                                  +++ a a++ + s  lat ++ag  ag g   lf  
  gi|14601723|ref|NP_148264.1| 37 TVISAYAAVSENSHWLATALYAGLGAGIGKVALFAA 72
                                  5788999999***********************975 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.034
               Phage_holin_5_1  37 ptvsilvgailgalatsldgsgslatmiwa 66 
                                   pt    +ga+l  +a sl  s ++a+++ a
  gi|14601723|ref|NP_148264.1| 172 PTAGYPLGAVLALVAVSLGFSLAIAAVVLA 201
                                   78888899***999*999999999988876 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  11.2   0.00035       2.1      40     177 ..      68     204 ..      28     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00035
                       DUF2070  40 gillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall.qalvllalvlslalvfalrllvl 119
                                   ++++  l a+  +    +v +++ + ++++r+  ++l++++++++++ ++  + ++  +a +++ l +s+a+v++  +lv+
  gi|14601723|ref|NP_148264.1|  68 ALFAASLYAFSKTGRGRRVKQYSAKLMESRRA-KVSLAIAIFFIALLPIPDDIIYIPlAATFYNLLYFSIAVVTGKLVLVT 147
                                   33333333333344444444444444666665.5555555555555566666665556899******************** PP

                       DUF2070 120 vavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdr 177
                                   ++++  + +k ++ a++  ll  + +  y +   +l l+++sl f la+++++  +d 
  gi|14601723|ref|NP_148264.1| 148 LFYGVGRASKGLISAVLDYLLPEAPTAGY-PLGAVLALVAVSLGFSLAIAAVVLAIDW 204
                                   **********9999999888887777777.6788889999999999999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1834.84
//
Query:       gi|118431648|ref|NP_148265.2|  [L=406]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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   70.4  12.8    3.1e-19   69.3  12.8    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein
    7.1e-19   68.2  12.7    1.2e-18   67.4  12.7    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
    3.2e-10   39.8  11.5    3.2e-10   39.8  11.5    2.2  3  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
      0.013   15.5   6.0      0.013   15.5   6.0    2.6  3  ABC2_membrane_4  ABC-2 family transporter protein
       0.08   12.5   3.5       0.15   11.7   3.5    1.4  1  DUF1182          Protein of unknown function (DUF1182)


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 !   69.3  12.8   8.6e-23   3.1e-19       2     344 ..      22     394 ..      21     395 .. 0.71

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 8.6e-23
                ABC2_membrane_3   2 sfliitlllPiilvlllglifsnsveddentpiavvdednsslsqqlv....ealea.spsvelvyevdseeeakkalkn 76 
                                    ++l ++++lP++ + +l+++ s +  +++++ +++vded+s+ s+ ++    e+le+  p v    +v+ ++   + ++ 
  gi|118431648|ref|NP_148265.2|  22 KTLAYVVVLPLVALPGLAIF-SGGLYSAQSMDVYIVDEDGSEISSLFAeglaEYLESgLPGVA--VNVEILSGV-EGFDT 97 
                                    688899********986666.556668*************66666666222266666566666..666666655.57888 PP

                ABC2_membrane_3  77 gdidgilvipkgfskdll..kgesatvtvlinssnlnss.........kailna.lns.llqqlnasalv......lqse 137
                                       + ++vip+gfs+ l+  +g+ +   v++ +s l  +         +++++a ++s +++       +         e
  gi|118431648|ref|NP_148265.2|  98 PFGSIAVVIPEGFSRGLEdlDGRVSIRLVVTPGSPLAGQvaslvegyaSLFEEAvVESrVSRL------AeaagveVDVE 171
                                    888999***********9985566666666666666544443444444334444233322222......02223355666 PP

                ABC2_membrane_3 138 atstsaninvestqleeelsnvasf.......lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlski 210
                                     + ++ +++ e +     + ++          +v++ l++++   ++f++ siv E+e+r++e +l++g s+l+++++k+
  gi|118431648|ref|NP_148265.2| 172 RLLDPLEVEREYIGFGGGAAGARGEavamsarVVAFSLFFVVNPAIVFVSDSIVGERERRTLEKLLLTGASRLEILVGKV 251
                                    6666666666666664444444443332222233344444444447778889**************************** PP

                ABC2_membrane_3 211 lgdflvyllqlll.illl..afgl.gipfgnlglll....llfllfglayialgyllsslfknsetaqilifivilllsg 282
                                     + ++++l  ++   l+l  +f l g++   + ll+      + l  ++++ +++++s+ + + ++aq+  fiv++++++
  gi|118431648|ref|NP_148265.2| 252 AAAAALGLAAAAAdSLALvaFFTLsGFSLLLSPLLVaswaASSALLVILTAGITAFISARSETIRSAQSGSFIVLMVALA 331
                                    ***********86555553233313333333333444677888888999999999999999999************9888 PP

                ABC2_membrane_3 283 ffgglfp..ledlpsalkwifsiiPffapglgllrlitgdplweillsliilalfavvylllal 344
                                    +++   +   + lp +l++++  iPf++ +l+ ++ + gd l+ + +++++l +f+++++++a+
  gi|118431648|ref|NP_148265.2| 332 IYFSALVvdYSRLPAWLSILLQAIPFTHASLAVIKASVGD-LAATTIHMAVLTGFTALFIAAAA 394
                                    777665538888****************************.88999**************9997 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 !   67.4  12.7   3.5e-22   1.2e-18       2     283 ..       8     397 ..       7     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.5e-22
                ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli.dvalaylkdlgsslqseakaikeatla.leyveaasasdeaedtdqdlkv... 76 
                                    ai++kE+ dl r+ ++l+ +v+lpl+    la+++    s qs  + i++ + + ++++ a    +++e           
  gi|118431648|ref|NP_148265.2|   8 AILWKELLDLSRDYKTLAYVVVLPLVaLPGLAIFSGGLYSAQSMDVYIVDEDGSeISSLFAEGLAEYLE-------Sglp 80 
                                    79************************6334445554444555555554444444033333333333333.......2334 PP

                ABC2_membrane_2  77 ................................................................................ 76 
                                                                                                                    
  gi|118431648|ref|NP_148265.2|  81 gvavnveilsgvegfdtpfgsiavvipegfsrgledldgrvsirlvvtpgsplagqvaslvegyaslfeeavvesrvsrl 160
                                    555588899999999999999999999999999999******************************************** PP

                ABC2_membrane_2  77 ...........................................vstimavlipviaalfgadaiagEkergTlkllLskP 113
                                                                               v+++  ++++  a++f +d+i+gE+er+Tl+ lL + 
  gi|118431648|ref|NP_148265.2| 161 aeaagvevdverlldplevereyigfgggaagargeavamsarVVAFSLFFVVNPAIVFVSDSIVGERERRTLEKLLLTG 240
                                    *************************************999998888888888888************************* PP

                ABC2_membrane_2 114 vsRdeillgKfigglaiglaiavallatvll..alaiilalgivlaledllllvvasvlllllvvflalglllSsvarss 191
                                    +sR eil+gK+ + +a+gla   a+ a  l+  a++   +++  l+   +   +++s ll++l   +++++++S+ + + 
  gi|118431648|ref|NP_148265.2| 241 ASRLEILVGKVAAAAALGLA---AAAADSLAlvAFFTLSGFSLLLSPLLVASWAASSALLVIL--TAGITAFISARSETI 315
                                    *****************665...4444444400455555555555555555555555555553..49********99987 PP

                ABC2_membrane_2 192 reaaala.lglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlnalgstatnllilll 270
                                    r+a   + ++l+v+lai ++ ++ + + l+a  ++       l+   p+ +  +++   + g+    l++t+ ++++l +
  gi|118431648|ref|NP_148265.2| 316 RSAQSGSfIVLMVALAIYFSALVVDYSRLPAWLSI-------LLQAIPFTHASLAVIKASVGD----LAATTIHMAVLTG 384
                                    77776662456677888888888888888885555.......777777777777777777777....79*********** PP

                ABC2_membrane_2 271 llavllvlgyvlF 283
                                     +a +++ ++  F
  gi|118431648|ref|NP_148265.2| 385 FTALFIAAAAREF 397
                                    *******998766 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.16   5.9e+02       3      33 ..       6      35 ..       5      56 .. 0.63
   2 !   39.8  11.5     9e-14   3.2e-10      53     202 ..     205     361 ..     183     368 .. 0.80
   3 ?   -3.8   0.3       1.9   6.9e+03     141     155 ..     380     394 ..     373     399 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
                  ABC2_membrane  3 ikallkreflqrwrdpslgllwrliqpllla 33
                                   +ka+l++e+l   rd  ++ +  ++ pl+ +
  gi|118431648|ref|NP_148265.2|  6 VKAILWKELLDLSRDYKTL-AYVVVLPLVAL 35
                                   5677888888777777666.55555555543 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 9e-14
                  ABC2_membrane  53 pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifll.ivyflv..gldls. 128
                                    + +  f+v++ a + + s ++v erer++le++l ++  s+ +++++kv++ ++++l++a++ +l +v f++  g+ l  
  gi|118431648|ref|NP_148265.2| 205 VAFSLFFVVNPA-IVFVSDSIVGERERRTLEKLLLTGA-SRLEILVGKVAAAAALGLAAAAADSLaLVAFFTlsGFSLLl 282
                                    666677777777.6667777******************.*****************999998666555554446888877 PP

                  ABC2_membrane 129 rf...flflllllltalaasslgllisalapsfedasqlaslvllp..llllsGffipidsmpkwlqwiaylnPltyav 202
                                    +    +   +   l+++++ ++  +isa +++++ a+  +++vl++   +++s  ++ ++++p wl  + ++ P+t+a 
  gi|118431648|ref|NP_148265.2| 283 SPllvASWAASSALLVILTAGITAFISARSETIRSAQSGSFIVLMValAIYFSALVVDYSRLPAWLSILLQAIPFTHAS 361
                                    334556667778888999999***************99888877762267*************9*************96 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 1.9
                  ABC2_membrane 141 alaasslgllisala 155
                                    a+++ + +l+i+a a
  gi|118431648|ref|NP_148265.2| 380 AVLTGFTALFIAAAA 394
                                    333333444444444 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 ?   -2.2   0.0      0.95   3.4e+03       4      32 ..      12      40 ..       9      54 .. 0.50
   2 ?   15.5   6.0   3.5e-06     0.013      51     153 ..     204     305 ..     188     336 .. 0.69
   3 ?   -3.2   7.8       1.9   6.9e+03      29     121 ..     295     390 ..     285     405 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.95
                ABC2_membrane_4  4 tEflKlkrskivwllvlaallvpllally 32
                                    E+l l r    ++ v+++ lv+l++l++
  gi|118431648|ref|NP_148265.2| 12 KELLDLSRDYKTLAYVVVLPLVALPGLAI 40
                                   55555555433344444444444443333 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.5e-06
                ABC2_membrane_4  51 vfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfs 130
                                    v+ f+l++++    +++ s +i  E++  tl +Ll+   sr ++l++K+++ + l ++   +  l+ v+f  lsgf+ + 
  gi|118431648|ref|NP_148265.2| 204 VVAFSLFFVVNP-AIVFVSDSIVGERERRTLEKLLLTGASRLEILVGKVAAAAALGLAAAAADSLALVAFFTLSGFSLLL 282
                                    455554433333.3368999999****************************************************99765 PP

                ABC2_membrane_4 131 vklvlellkkclelgllvffavl 153
                                    + l++ +   +  l +++++ ++
  gi|118431648|ref|NP_148265.2| 283 SPLLVASWAASSALLVILTAGIT 305
                                    44433333322222222222222 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.9
                ABC2_membrane_4  29 allyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLl..tiPvsrtklllaKlivlllls 106
                                    all++ ++g t++  a   +  + + + +++l++ l+i+ s l+ +      + ++l   iP + ++l + K +v  l +
  gi|118431648|ref|NP_148265.2| 295 ALLVILTAGITAFISARSETIRSAQSGSFIVLMVALAIYFSALVVDYSRLPAWLSILlqAIPFTHASLAVIKASVGDLAA 374
                                    44444445555544444444444444445555555555544444444444445444436899999999999999975544 PP

                ABC2_membrane_4 107 v.llmlvtflitvlfa 121
                                      + m v++ +t+lf 
  gi|118431648|ref|NP_148265.2| 375 TtIHMAVLTGFTALFI 390
                                    3256666666666663 PP

>> DUF1182  Protein of unknown function (DUF1182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.5   4.1e-05      0.15      61     145 ..     270     355 ..     259     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                        DUF1182  61 ivfvtlgsfllslplillqayl.vvflqalvepvytvavcsllknitssttsaaqvlplavalyryrivvlkkkmsswfv 139
                                    + f tl  f l l  +l+  +     l        t ++ +   +i s+ + ++ vl +a+a+y   +vv   + ++w+ 
  gi|118431648|ref|NP_148265.2| 270 VAFFTLSGFSLLLSPLLVASWAaSSALLVILTAGITAFISARSETIRSAQSGSFIVLMVALAIYFSALVVDYSRLPAWLS 349
                                    67899999988876666666651567888889999********************************************9 PP

                        DUF1182 140 vvvhii 145
                                    + + +i
  gi|118431648|ref|NP_148265.2| 350 ILLQAI 355
                                    988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2945.35
//
Query:       gi|118431649|ref|NP_148266.2|  [L=255]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   80.8   0.0    1.8e-22   80.4   0.0    1.2  1  ABC_tran  ABC transporter
    5.9e-13   49.3   0.0    2.7e-08   34.0   0.0    2.0  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0012   18.6   0.0     0.0021   17.8   0.0    1.5  1  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.016   13.9   0.0        1.7    7.2   0.0    2.0  2  AAA_13    AAA domain
      0.042   13.3   0.0          3    7.2   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.046   13.3   0.0      0.069   12.8   0.0    1.2  1  SRP54     SRP54-type protein, GTPase domain
       0.11   12.1   0.0        1.2    8.7   0.0    1.9  2  AAA_15    AAA ATPase domain
       0.13   11.9   0.1       0.23   11.0   0.1    1.4  1  AAA_27    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.0   7.9e-26   1.8e-22       1     137 []      30     175 ..      30     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 7.9e-26
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vsl++k ge++++ G nGaGK+t l++l gll+ ++Ge ++ g d      e+++ e+g+lp+++++ ++lt  en 
  gi|118431649|ref|NP_148266.2|  30 LRGVSLSVKFGEIHVLAGLNGAGKTTSLRVLVGLLSRDSGEARVLGVDPWGGGFERVKGEVGYLPEDASVYERLTGMENi 109
                                    678******************************************9999999***********************99999 PP

                                    .........HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                             ++d+e  +e+a+   g   l  + + +++  +S+G+k+r+ l  +l++kp+l++lDEpt+
  gi|118431649|ref|NP_148266.2| 110 lfyarlysgWRDVEelVENAVFYSG---LSREDLARRAGGYSKGMKRRLLLGITLMSKPRLVVLDEPTS 175
                                    *****98663333233333333333...33444446669****************************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 !   16.7   0.0   2.2e-06     0.005       1      83 [.      42     122 ..      42     138 .. 0.91
   2 !   34.0   0.0   1.2e-11   2.7e-08     177     301 ..     104     208 ..     101     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrler 80 
                                    + vl G Ng+GK++ L+ l +l + ++++e +    ++ gg  +  +   +y pe ++++e   ++++++ +  +l  ++
  gi|118431649|ref|NP_148266.2|  42 IHVLAGLNGAGKTTSLRVLVGLLS-RDSGEARVLGVDPWGGGFERVKGEVGYLPEDASVYERL-TGMENILFYARLYSGW 119
                                    679********************9.999999999999999*999**************99999.9999999999999999 PP

                         AAA_21  81 sqv 83 
                                    ++v
  gi|118431649|ref|NP_148266.2| 120 RDV 122
                                    999 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 1.2e-11
                         AAA_21 177 gfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralk 256
                                    ++++++ +  rl++++++ve  +++                   ++      +  + a   S G+kr   ll + l   +
  gi|118431649|ref|NP_148266.2| 104 TGMENILFYARLYSGWRDVEELVENA-----------------VFYSGLSREDLARRAGGYSKGMKRR-LLLGITLMSKP 165
                                    67788888999999999999999999.................99999999999999***********.66666665554 PP

                         AAA_21 257 kgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                      +l+++DEp +g +P +  r+ ++l+ lsr+g  +++tTH+  l
  gi|118431649|ref|NP_148266.2| 166 --RLVVLDEPTSGVDPIASNRIKKILRGLSREGRAILVTTHDLAL 208
                                    ..**************888888888888899999********887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.1e-07    0.0021      20      82 ..      42     158 ..      34     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.1e-07
                         AAA_30  20 vavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelgi...eastiakllkrlk............. 81 
                                    ++vl G  G+GKtt+l++l+ ++ ++ g  rv+g+ p g   ++++ e+g    +as  ++l+   +             
  gi|118431649|ref|NP_148266.2|  42 IHVLAGLNGAGKTTSLRVLVGLLSRDsGeARVLGVDPWGGGFERVKGEVGYlpeDASVYERLTGMENilfyarlysgwrd 121
                                    789*******************9999766999999999999999999999767677777777766657777666666666 PP

                         AAA_30  82 ....................................g 82 
                                                                        g
  gi|118431649|ref|NP_148266.2| 122 veelvenavfysglsredlarraggyskgmkrrlllG 158
                                    6666666666666655555555555555555555554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00076       1.7      14      39 ..      38      63 ..      31      75 .. 0.83
   2 ?    4.7   0.0    0.0044       9.9     524     580 ..     162     215 ..     157     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00076
                         AAA_13 14 dfkriNliYGwNGaGKTtLSrllrsl 39
                                   +f++i ++ G NGaGKTt  r+l  l
  gi|118431649|ref|NP_148266.2| 38 KFGEIHVLAGLNGAGKTTSLRVLVGL 63
                                   6999999***********88887665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0044
                         AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                    ++k + vv+D P S  D  +++ +   ++       + + +++ TH l +  e+ ++
  gi|118431649|ref|NP_148266.2| 162 MSKPRLVVLDEPTSGVDPIASNRIKKILRGLS---REGRAILVTTHDLALAEEIADR 215
                                    56999************977777777776665...999**********999998776 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 ?    4.1   0.0     0.012        27      23      42 ..      40      58 ..      29      73 .. 0.75
   2 ?    7.2   0.0    0.0013         3     147     207 ..     153     214 ..     123     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                   TSSEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 23 sksftaivGpNGSGKsnlld 42
                                    + + ++ G NG+GK+  l 
  gi|118431649|ref|NP_148266.2| 40 GE-IHVLAGLNGAGKTTSLR 58
                                   44.7899********97665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                                    HHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                          SMC_N 147 laLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadk 207
                                      Ll+ i  +++  l++lDe  +  D    +++ ++l+  s +   ++v++++  + e+   
  gi|118431649|ref|NP_148266.2| 153 RRLLLGITLMSKPRLVVLDEPTSGVDPIASNRIKKILRGLSREgRAILVTTHDLALAEEIAD 214
                                    57899999999999************************888773667777887777766544 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   0.0   3.1e-05     0.069       3      31 ..      42      70 ..      40      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkk 31
                                   + +l+Gl+GaGKTt+l  L  ll+++  +
  gi|118431649|ref|NP_148266.2| 42 IHVLAGLNGAGKTTSLRVLVGLLSRDSGE 70
                                   6799************9998888877544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00055       1.2      18      50 ..      36      67 ..      31     109 .. 0.87
   2 ?    1.5   0.0     0.086   1.9e+02     323     366 ..     164     206 ..     147     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00055
                         AAA_15 18 eidlseeltvliGkNnsGKSsilealdlFlnnk 50
                                   ++++ e + vl G N++GK++ l++l  +l+++
  gi|118431649|ref|NP_148266.2| 36 SVKFGE-IHVLAGLNGAGKTTSLRVLVGLLSRD 67
                                   688999.*******************9998865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.086
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                    k+ +++++EP     p a + + k l+ l+++++  +++tTH  
  gi|118431649|ref|NP_148266.2| 164 KPRLVVLDEPTSGVDPIASNRIKKILRGLSREGR-AILVTTHDL 206
                                    34569999999999999999999**********9.9******86 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0001      0.23      22      50 ..      36      64 ..      30      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                         AAA_27 22 saeeadlhliyGpNEAGKstalrAisdll 50
                                   s +  ++h++ G N AGK+t+lr +  ll
  gi|118431649|ref|NP_148266.2| 36 SVKFGEIHVLAGLNGAGKTTSLRVLVGLL 64
                                   4455689***************9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1839.11
//
Query:       gi|118431650|ref|YP_874919.1|  [L=212]
Description: hypothetical protein APE_1936.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1674.31
//
Query:       gi|118431651|ref|NP_148267.2|  [L=262]
Description: hypothetical protein APE_1937.1 [Aeropyrum pernix K1]
Scores for complete 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-66  223.3   0.0    1.8e-66  223.1   0.0    1.1  1  PPS_PS    Phosphopantothenate/pantothenate synthetase


Domain annotation for each model (and alignments):
>> PPS_PS  Phosphopantothenate/pantothenate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.1   0.0   9.9e-71   1.8e-66       1     176 []      69     247 ..      69     247 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.1 bits;  conditional E-value: 9.9e-71
                         PPS_PS   1 lllakkpvisvNGNtaaLvaeeiveLaealg..aklevNlfyrteeRvekiaellkeagaeevlgleeda.ripeleseR 77 
                                    lll+k+pvisvNGN+aaL+a ei++L+ealg  a +evN+fyrteeRv++i+e+l +ag++ +l  + ++ r+p+les R
  gi|118431651|ref|NP_148267.2|  69 LLLSKRPVISVNGNYAALAAGEIARLSEALGgrAVVEVNIFYRTEERVRRIHEVLASAGVKGLLPPDCEKtRVPGLESPR 148
                                    799**************************975578*******************************99998********* PP

                         PPS_PS  78 akvskeGiysaDvvlvplEDGDRaeaLvkmgKkviaiDLNPlsRtartatitivdnvvRalpnlteavkelkkkskeele 157
                                    ++v+ eGi saD+vl+++EDGDR+eaLvk+gK+v aiDLNP+sRta++a++tivd+ vRa++n+t++v+el+ +s+eel+
  gi|118431651|ref|NP_148267.2| 149 GIVCVEGIASADFVLLAIEDGDRTEALVKWGKRVAAIDLNPFSRTAQKASVTIVDEAVRATRNITRFVDELSGASEEELR 228
                                    ******************************************************************************** PP

                         PPS_PS 158 eivkefdnkkvlkealkei 176
                                    +iv+ ++n+++l++a+k+i
  gi|118431651|ref|NP_148267.2| 229 SIVAGYSNRETLSRAFKAI 247
                                    **************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1932.33
//
Query:       gi|118431652|ref|NP_148268.2|  [L=279]
Description: hypothetical protein APE_1939.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.15   12.3   5.6       0.57   10.5   5.2    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 ?   10.5   5.2   3.2e-05      0.57       8      65 ..      76     131 ..      74     132 .. 0.76
   2 ?    4.1   0.1    0.0031        56       7      28 ..     115     136 ..     109     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.2e-05
                                    SHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HHHHHHHHHHHHHHHHHHHSHHHHHHHHS CS
                 GHMP_kinases_N   8 iPvgaGLGSSAAlavalvaAllallglsl.eeaklaleaerlaqggngsggDvaasvyG 65 
                                    +P+g+G + SAA a  +++A++   g  + + ++ a e e   ++ +++ gDva +++G
  gi|118431652|ref|NP_148268.2|  76 LPPGRGYAVSAASAILGALAAAMERGAGVfRAYRAAHEVE---VRRSTGLGDVASIACG 131
                                    8*************99999987777755423344444444...456799****998887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0031
                                    SSHTTSSSCHHHHHHHHHHHHH CS
                 GHMP_kinases_N   7 eiPvgaGLGSSAAlavalvaAl 28 
                                    e+  ++GLG  A++a+++ + l
  gi|118431652|ref|NP_148268.2| 115 EVRRSTGLGDVASIACGVGLVL 136
                                    677899********99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2194.31
//
Query:       gi|118431653|ref|NP_148269.2|  [L=212]
Description: 6-phospho 3-hexuloisomerase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-18   66.2   0.0    4.4e-18   65.4   0.0    1.4  1  SIS       SIS domain
    8.7e-10   38.8   1.5    3.1e-07   30.5   0.7    2.3  2  SIS_2     SIS domain
  ------ inclusion threshold ------
       0.24   11.2   3.0        4.2    7.2   0.2    2.2  2  PRMT5     PRMT5 arginine-N-methyltransferase


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   7.4e-22   4.4e-18       3     109 ..      51     151 ..      49     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 7.4e-22
                                    CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                            SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                    +++++++v+GaG+s+ ++k +a+ l ++g++ ++  ++       ++ ++e+dlv++is sg+tk  v aae ak+ ga+
  gi|118431653|ref|NP_148269.2|  51 REKRKVLVMGAGRSGLVGKAFAMRLLHLGFNSYVLGETI------VPSVREGDLVVAISGSGRTKVIVTAAETAKQVGAT 124
                                    6789*********************99999888776554......588******************************** PP

                                    EEEEESSTTSHHHHHSSEEEEEEEECH CS
                            SIS  83 iiaITdskgsplareadlalyinaepe 109
                                    + aIT  ++spl r +d++++++   +
  gi|118431653|ref|NP_148269.2| 125 VAAITTYPDSPLGRLSDIVVRVPGRTK 151
                                    ********************9987665 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00079       4.7      10      60 ..      28      78 ..      24      91 .. 0.80
   2 !   30.5   0.7   5.2e-11   3.1e-07      94     137 ..      88     129 ..      81     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00079
                                   HHHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-B CS
                          SIS_2 10 lerivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaraggl 60
                                   +++i e +  ++++ +  +    ++++kvlv+G+G S +  + +a r+  l
  gi|118431653|ref|NP_148269.2| 28 INSINEIDVGQVDRFVGELERVYREKRKVLVMGAGRSGLVGKAFAMRLLHL 78
                                   666777777888888888889999****************99999998764 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 5.2e-11
                                    HHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2  94 qilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                    +i  +  +++gD+ + iS sG+ +v+v aae ak++g++v A+t
  gi|118431653|ref|NP_148269.2|  88 TIVPS--VREGDLVVAISGSGRTKVIVTAAETAKQVGATVAAIT 129
                                    55555..89**********************************9 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2   0.00071       4.2      64      84 ..      52      72 ..      38      84 .. 0.82
   2 ?    4.4   0.3    0.0049        29      63      92 ..      95     124 ..      81     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00071
                                   -EEEEEEES-TTSHHHHHHHH CS
                          PRMT5 64 kklvilvvGaGRGplvdralk 84
                                   +k  +lv+GaGR +lv +a+ 
  gi|118431653|ref|NP_148269.2| 52 EKRKVLVMGAGRSGLVGKAFA 72
                                   56789***********99886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0049
                                    .-EEEEEEES-TTSHHHHHHHHHHHHHCCC CS
                          PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvt 92 
                                    e +lv+++ G+GR  ++ +a +++++ + t
  gi|118431653|ref|NP_148269.2|  95 EGDLVVAISGSGRTKVIVTAAETAKQVGAT 124
                                    5789**********9999988888887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1586.46
//
Query:       gi|14601729|ref|NP_148270.1|  [L=286]
Description: hypothetical protein APE_1941 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2194.33
//
Query:       gi|118431654|ref|NP_148272.2|  [L=310]
Description: hypothetical protein APE_1943.1 [Aeropyrum pernix K1]
Scores for 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   20.0   0.0     0.0011   19.2   0.0    1.4  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0     6e-08    0.0011       4      39 ..     123     161 ..     120     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6e-08
                                    HHHHHHHHTT..TSEEEEEHHHHCTTSCTT.SSEEEEEE CS
                   NTP_transf_2   4 lleelkelep..vakvvlfGSyarGtalkg.SDiDllvv 39 
                                    l ++ ++le+  +  + l+GS a+ t+++  SDiD++v+
  gi|118431654|ref|NP_148272.2| 123 LYKIARSLEKlpIRGLGLTGSLATLTYNPLySDIDVVVF 161
                                    5555566666669*************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2321.08
//
Query:       gi|118431655|ref|NP_148275.2|  [L=115]
Description: hypothetical protein APE_1946.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 869.38
//
Query:       gi|14601735|ref|NP_148276.1|  [L=153]
Description: hypothetical protein APE_1947 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1199.12
//
Query:       gi|14601736|ref|NP_148277.1|  [L=115]
Description: hypothetical protein APE_1948 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0099   14.2   1.3     0.0097   14.2   1.3    1.0  1  Spc7_N    N-terminus of kinetochore NMS complex subunit Spc7
  ------ inclusion threshold ------
       0.24   10.8  11.6       0.33   10.3  11.6    1.2  1  SelP_N    Selenoprotein P, N terminal region
       0.99    8.7   4.4        1.1    8.6   4.4    1.1  1  FAM76     FAM76 protein


Domain annotation for each model (and alignments):
>> Spc7_N  N-terminus of kinetochore NMS complex subunit Spc7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.3   1.6e-06    0.0097     813     869 ..      13      69 ..       3     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-06
                        Spc7_N 813 edpskleeevdrereeeekresgiieaeqleerdatlnLkdlIssLtPKknklkgRK 869
                                   ed+ k+ eev+re+++e+++++ + ++e+ + + a + L dl++sL+ + + l +R 
  gi|14601736|ref|NP_148277.1|  13 EDIEKIVEEVEREHHHEHEHHHHHHHHEESDLEIAVKVLEDLVDSLSARARVLESRL 69 
                                   8999**************999998888755556678889********9999998884 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  11.6   5.5e-05      0.33     180     207 ..      16      41 ..       3      58 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.5e-05
                        SelP_N 180 ektehehahshkqghkhhekhghhHkek 207
                                   ek  +e + +h+  h+h+++h+hhH+e+
  gi|14601736|ref|NP_148277.1|  16 EKIVEEVEREHH--HEHEHHHHHHHHEE 41 
                                   222222222222..33333333333332 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.4   0.00018       1.1     155     241 ..      12      96 ..       2     113 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                         FAM76 155 kskkskkskeksk.ekkaskkkskkhkkrssrlevskleeeklaeekesnetskksldsnssdhlvavtqLkeeiaslkkq 234
                                   k++ +k  +e ++ +++++++++++h++++s le++      l +   s +++++ l+s+   h +a+  L   +a+l   
  gi|14601736|ref|NP_148277.1|  12 KEDIEKIVEEVEReHHHEHEHHHHHHHHEESDLEIAVK---VLEDLVDSLSARARVLESRLDSHSIAIGTLYRVVAHLVEA 89 
                                   33323322222220222222222233333333333322...2344455555666789999999999999999999999999 PP

                         FAM76 235 leqkdqe 241
                                   +++ d+e
  gi|14601736|ref|NP_148277.1|  90 IATDDEE 96 
                                   9887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2122  (0.118356); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 997.36
//
Query:       gi|118431656|ref|NP_148278.2|  [L=211]
Description: hypothetical protein APE_1949.1 [Aeropyrum pernix K1]
Scores for 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-33  116.5   0.0    1.5e-33  115.9   0.0    1.3  1  zf-ZPR1          ZPR1 zinc-finger domain
     0.0069   16.5   0.8          1    9.5   0.1    2.8  3  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.038   14.4   1.5      0.076   13.4   0.1    2.1  3  Lar_restr_allev  Restriction alleviation protein Lar
      0.047   13.8   0.9        1.5    9.0   0.0    2.5  2  UPF0547          Uncharacterised protein family UPF0547
      0.066   13.3   1.0        0.1   12.7   0.1    1.7  2  DZR              Double zinc ribbon
      0.068   12.9   2.0        1.9    8.3   0.3    2.4  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.15   12.5   0.0       0.25   11.8   0.0    1.4  1  REV1_C           DNA repair protein REV1 C-terminal domain
       0.19   11.2   4.3        1.4    8.4   0.1    2.8  3  zf-ribbon_3      zinc-ribbon domain
       0.28   10.1   0.1       0.36    9.7   0.1    1.1  1  eIF-3_zeta       Eukaryotic translation initiation factor 3 s
       0.36   10.5   5.2        3.3    7.5   0.3    2.8  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
       0.76    9.8   3.2         20    5.3   3.4    2.5  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.0   9.5e-37   1.5e-33       2     158 ..      32     186 ..      31     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 9.5e-37
                        zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveip 81 
                                     Cp+Cg++ ++   +l ++Pyf++++i+  eC++Cgy+ ++v+ a++ e+  k+i++ v+ e++l+  + kS  ++v ip
  gi|118431656|ref|NP_148278.2|  32 VCPACGARAMKLSEYLYSVPYFNNIVISVGECRNCGYRYRDVRLAEATEP--KKIVVAVRGEKQLRYLLAKSPLSAVYIP 109
                                    6****988888888888*********************************..**************************** PP

                        zf-ZPR1  82 eleleippg.tlegrlttvEGlLeqikeeleke.egdqaeredeekekieeflekleeliegeepftlildDpagnSfi 158
                                    e++le+ pg ++ g++ttvEG+L++++e  + + ++d    e+e+ ek++++++ lee+ieg+++ftli+ D  g S +
  gi|118431656|ref|NP_148278.2| 110 EMDLEMVPGvASVGFITTVEGILHRFHEVAQVAcKEDVV--EAEDLEKCRSVIRWLEEAIEGRRAFTLIICDFDGLSRV 186
                                    *********9******************99522133333..3467******************************9987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00062         1      22      38 ..      26      42 ..      17      43 .. 0.72
   2 ?    4.2   0.0     0.029        47       7      19 ..      62      74 ..      61      84 .. 0.70
   3 ?   -2.6   0.0       3.8   6.3e+03      18      30 ..     132     144 ..     128     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00062
                    Zn-ribbon_8 22 sdapltaCPeCgsevrr 38
                                   ++ ++ +CP+Cg+++ +
  gi|118431656|ref|NP_148278.2| 26 AEVDNAVCPACGARAMK 42
                                   4445667*****97655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
                    Zn-ribbon_8  7 rCeeCghefevlq 19
                                   +C++Cg ++  ++
  gi|118431656|ref|NP_148278.2| 62 ECRNCGYRYRDVR 74
                                   6*****9998555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.8
                    Zn-ribbon_8  18 lqsisdapltaCP 30 
                                    l+++++ +++aC+
  gi|118431656|ref|NP_148278.2| 132 LHRFHEVAQVACK 144
                                    6667777777786 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 ?   13.4   0.1   4.7e-05     0.076       5      42 ..      32      74 ..      29      86 .. 0.78
   2 ?   -3.3   0.0       7.6   1.2e+04      29      32 ..     141     144 ..     129     157 .. 0.62
   3 ?   -1.5   0.0       2.1   3.3e+03       6      24 ..     178     196 ..     174     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigq.....cvyCadCgastpwfk 42
                                    CP Cg ra +  +++ +  +       + +C +Cg+   +++
  gi|118431656|ref|NP_148278.2| 32 VCPACGARAMKLSEYLYSVPYFNnivisVGECRNCGYRYRDVR 74
                                   6*************99998666699999999*****9444443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.6
                Lar_restr_allev  29 vyCa 32 
                                    v+C+
  gi|118431656|ref|NP_148278.2| 141 VACK 144
                                    3333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.1
                Lar_restr_allev   6 CPfCggravlersqrvvae 24 
                                    C+f g   v++++++v++e
  gi|118431656|ref|NP_148278.2| 178 CDFDGLSRVIGEHPYVAEE 196
                                    8888888888888888775 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.087   1.4e+02      16      21 ..      32      37 ..      28      39 .. 0.68
   2 ?    9.0   0.0   0.00092       1.5      12      23 ..      58      69 ..      55      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.087
                        UPF0547 16 fCphCG 21
                                   +Cp CG
  gi|118431656|ref|NP_148278.2| 32 VCPACG 37
                                   466665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00092
                        UPF0547 12 vaaqfCphCGyv 23
                                   +++ +C+ CGy+
  gi|118431656|ref|NP_148278.2| 58 ISVGECRNCGYR 69
                                   7899*******8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.2e-05       0.1      11      37 ..      29      69 ..      24      74 .. 0.85
   2 ?   -2.9   0.1       4.5   7.4e+03      18      31 ..     143     156 ..     141     158 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.2e-05
                            DZR 11 darfCseCgtklkavaa..............edrCpsCgek 37
                                   d+ +C++Cg++  + ++                 C +Cg+ 
  gi|118431656|ref|NP_148278.2| 29 DNAVCPACGARAMKLSEylysvpyfnnivisVGECRNCGYR 69
                                   7889*******76666678899****************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                            DZR  18 CgtklkavaaedrC 31 
                                    C++++ ++++ ++C
  gi|118431656|ref|NP_148278.2| 143 CKEDVVEAEDLEKC 156
                                    55555444444444 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.028        46      17      22 ..      33      38 ..      32      43 .. 0.65
   2 ?    8.3   0.3    0.0012       1.9       2      11 ..      62      71 ..      62      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.028
                   Rubredoxin_2 17 CpsCgs 22
                                   Cp+Cg+
  gi|118431656|ref|NP_148278.2| 33 CPACGA 38
                                   666664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                   Rubredoxin_2  2 vCsqCGfesa 11
                                   +C++CG++++
  gi|118431656|ref|NP_148278.2| 62 ECRNCGYRYR 71
                                   6******997 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 ?   11.8   0.0   0.00015      0.25      32      57 ..     146     170 ..     139     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                         REV1_C  32 kvveeerdlekavavlkwlrvlleee 57 
                                    +vv e +dlek+++v++wl+  +e +
  gi|118431656|ref|NP_148278.2| 146 DVV-EAEDLEKCRSVIRWLEEAIEGR 170
                                    567.889*************999866 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00086       1.4      14      24 ..      28      38 ..      25      39 .. 0.72
   2 ?    3.2   0.5     0.038        63      19      25 ..      63      69 ..      62      69 .. 0.89
   3 ?   -2.1   0.0       1.7   2.8e+03       7      16 ..     142     152 ..     141     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00086
                    zf-ribbon_3 14 sddnvCpyCGt 24
                                    d  vCp CG+
  gi|118431656|ref|NP_148278.2| 28 VDNAVCPACGA 38
                                   57778888886 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.038
                    zf-ribbon_3 19 CpyCGtk 25
                                   C +CG++
  gi|118431656|ref|NP_148278.2| 63 CRNCGYR 69
                                   9****85 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                    zf-ribbon_3   7 nCGa.plssdd 16 
                                    +C++ +++++d
  gi|118431656|ref|NP_148278.2| 142 ACKEdVVEAED 152
                                    69999988776 PP

>> eIF-3_zeta  Eukaryotic translation initiation factor 3 subunit 7 (eIF-3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00022      0.36     346     374 ..      61      91 ..      41     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00022
                                    .CB-SEEEEEEEEE-STT.....-EEEEEEE CS
                     eIF-3_zeta 346 eelasvaYrYrkfdLsde..eekielvvRte 374
                                     e+ +++YrYr ++L +    +ki + vR e
  gi|118431656|ref|NP_148278.2|  61 GECRNCGYRYRDVRLAEAtePKKIVVAVRGE 91 
                                    57899***********975688999999998 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.015        25      10      28 ..      23      41 ..      20      42 .. 0.77
   2 ?    7.5   0.3     0.002       3.3      20      26 ..      63      69 ..      57      70 .. 0.92
   3 ?   -2.8   0.1       3.2   5.3e+03       6      10 ..     143     147 ..     139     157 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.015
                                   ----SSS----SSS----- CS
                 DNA_RNApol_7kD 10 vslkkgdpiRCkeCGhRil 28
                                    ++ + d   C  CG R +
  gi|118431656|ref|NP_148278.2| 23 LRIAEVDNAVCPACGARAM 41
                                   5677777778******976 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                                   -SSS--- CS
                 DNA_RNApol_7kD 20 CkeCGhR 26
                                   C++CG+R
  gi|118431656|ref|NP_148278.2| 63 CRNCGYR 69
                                   ******9 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.2
                                    S--B- CS
                 DNA_RNApol_7kD   6 Cgaev 10 
                                    C+++v
  gi|118431656|ref|NP_148278.2| 143 CKEDV 147
                                    44444 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.4     0.012        20      18      43 ..      30      66 ..      28      69 .. 0.58
   2 ?    2.7   0.2     0.077   1.3e+02      20      28 ..      62      71 ..      44      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.012
                  Zn_Tnp_IS1595 18 gfvCPhCgsrkayrikt............rglfqCkeC 43
                                   + vCP+Cg ++a +++               + +C+ C
  gi|118431656|ref|NP_148278.2| 30 NAVCPACG-ARAMKLSEylysvpyfnnivISVGECRNC 66
                                   579*****.55555554444555555555555555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.077
                  Zn_Tnp_IS1595 20 vCPhCgsr.k 28
                                    C +Cg+r +
  gi|118431656|ref|NP_148278.2| 62 ECRNCGYRyR 71
                                   5999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 00:00:00.40
# Mc/sec: 1598.98
//
Query:       gi|118431657|ref|NP_148279.2|  [L=176]
Description: small heat shock protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-12   46.5   0.0    2.9e-12   46.0   0.0    1.3  1  ArsA_HSP20   HSP20-like domain found in ArsA
    1.3e-10   41.4   2.8    4.7e-09   36.3   2.8    2.2  1  HSP20        Hsp20/alpha crystallin family
    9.3e-06   26.6   0.8    1.4e-05   26.0   0.8    1.2  1  CS           CS domain
      0.003   17.9   0.1     0.0046   17.3   0.1    1.3  1  PIH1_CS      PIH1 CS-like domain
  ------ inclusion threshold ------
      0.021   14.9   0.2       0.06   13.4   0.2    1.7  1  bZIP_1       bZIP transcription factor
      0.025   13.9   0.1      0.025   13.9   0.1    1.4  2  DPCD         DPCD protein family
      0.027   14.6   0.0      0.032   14.3   0.0    1.3  1  GvpH         GvpH
      0.041   14.6   0.3      0.062   14.0   0.3    1.3  1  HlyD_3       HlyD family secretion protein
      0.053   13.8   0.3       0.11   12.7   0.0    1.6  2  DUF3014      Protein of unknown function (DUF3014)
      0.059   13.8   0.4       0.75   10.3   0.1    2.2  2  Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57


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 !   46.0   0.0   1.6e-15   2.9e-12       1      63 []      97     161 ..      97     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.6e-15
                     ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig...nfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                    dde+ +++d+P+++k++i+++ ++d  +Ik++   ++ +++ LP +++ k + +A++++gvLeI++
  gi|118431657|ref|NP_148279.2|  97 DDEVWIVADIPGANKDKIKVRATEDKVVIKAEngkKYYKEVELPAKVDPKSA-KASYRNGVLEIKL 161
                                    6788899*************************66667778**********77.***********86 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   2.8   2.6e-12   4.7e-09       1      97 [.      92     173 ..      92     176 .] 0.88

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 2.6e-12
                                    E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTE CS
                          HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGv 80 
                                    d++e ++e  + +d+pg +k+ +kv  ++++v++k+e+                +k+ ++++LP  vd+++ kas+++Gv
  gi|118431657|ref|NP_148279.2|  92 DVIERDDEVWIVADIPGANKDKIKVRATEDKVVIKAENG---------------KKYYKEVELPAKVDPKSAKASYRNGV 156
                                    57789999999999************9999999999999...............678889******************** PP

                                    EEEEEEBSS--..---- CS
                          HSP20  81 Ltvtvpkkepekkkker 97 
                                    L+++++k +p+++ +e 
  gi|118431657|ref|NP_148279.2| 157 LEIKLKKIKPAEEGTEV 173
                                    *********99764443 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.8   7.8e-09   1.4e-05       7      76 .]      95     163 ..      91     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 7.8e-09
                                    EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                             CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvkigk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                    +++deV +   ++++  +k+++kv+ +e+++ +k ++ +k ++e eL +++dp++++ +  +  +ei+LkK
  gi|118431657|ref|NP_148279.2|  95 ERDDEVWIVADIPGA--NKDKIKVRATEDKVVIKAENgKKYYKEVELPAKVDPKSAKASYRNGVLEIKLKK 163
                                    6799**********9..*************9999944479999999************************9 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.6e-06    0.0046      35      87 ..     102     154 ..      90     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                        PIH1_CS  35 ieielPllksikevklrvgerrleleskk.akyfLslkLpYpvdedkveAkFvk 87 
                                    i  ++P+     ++k+r +e+++++++++ +ky  +++Lp +vd ++++A + +
  gi|118431657|ref|NP_148279.2| 102 IVADIPGA-NKDKIKVRATEDKVVIKAENgKKYYKEVELPAKVDPKSAKASYRN 154
                                    56667776.5678*************99999********************975 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.4e-05      0.06      20      57 ..       4      41 ..       2      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 20 sRqRKqaeieeLerrvkaLekeNksLkseleelkkeve 57
                                   +R+R++   + Le+ + ++e+e  +L +e e+l+  v+
  gi|118431657|ref|NP_148279.2|  4 FRRRRKSFFDLLEDIFREFEEEFRELEEEFEKLASRVQ 41
                                   8********************************99988 PP

>> DPCD  DPCD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1         4   7.2e+03      29      43 ..      27      41 ..      18      44 .. 0.60
   2 ?   13.9   0.1   1.4e-05     0.025     112     139 ..     113     141 ..      88     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4
                           DPCD 29 kemvEEYdvktdell 43
                                   +e+ EE++  ++ ++
  gi|118431657|ref|NP_148279.2| 27 RELEEEFEKLASRVQ 41
                                   566677766555555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.4e-05
                           DPCD 112 svtvdeeereivvrTtN.kKYyKklsipd 139
                                    +++v ++e ++v++ +N kKYyK++++p 
  gi|118431657|ref|NP_148279.2| 113 KIKVRATEDKVVIKAENgKKYYKEVELPA 141
                                    6888899999*****9989******9983 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.8e-05     0.032      99     173 ..      96     171 ..      24     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                           GvpH  99 dsdelvvvadlpGvtdedvdvaletdeqaltlrvdddvverlvld.dpdvaitdltlrnqvlelrlarsedsdgae 173
                                      de+ +vad+pG   +++ v    d+  +  + +    + + l  + d   ++ + rn vle++l + ++++ ++
  gi|118431657|ref|NP_148279.2|  96 RDDEVWIVADIPGANKDKIKVRATEDKVVIKAENGKKYYKEVELPaKVDPKSAKASYRNGVLEIKLKKIKPAEEGT 171
                                    569999*************99888799999999999998888885245666677889**********999998776 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   3.4e-05     0.062      25      89 ..      88     159 ..      78     176 .] 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                         HlyD_3  25 delleiipp.dtllveakvpaadlgsik..kkgqkvtlkldqgsdy....tlkgkierisptvdaktgaykv 89 
                                    ++l+ +i   d++++ a +p a+ ++ik   +++kv +k+++g++y    +l++k++  s+++  ++g++++
  gi|118431657|ref|NP_148279.2|  88 EPLVDVIERdDEVWIVADIPGANKDKIKvrATEDKVVIKAENGKKYykevELPAKVDPKSAKASYRNGVLEI 159
                                    67777777549******************************8877765446677766555555445554444 PP

>> DUF3014  Protein of unknown function (DUF3014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.1   3.8e+03      76      96 ..      15      35 ..       9      47 .. 0.54
   2 ?   12.7   0.0   6.3e-05      0.11      28      71 ..     111     154 ..      91     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.1
                        DUF3014 76 lqeayeeLGypkasFndrlva 96
                                   l+++++e+ ++ +++++ + +
  gi|118431657|ref|NP_148279.2| 15 LEDIFREFEEEFRELEEEFEK 35
                                   555555555544444444433 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.3e-05
                        DUF3014  28 eekftveeaeeklviaeanaaRYdayvnllesvdkdklvalYrr 71 
                                    ++k++v+++e+k+vi+++n + Y + v+l ++vd++++ a Yr+
  gi|118431657|ref|NP_148279.2| 111 KDKIKVRATEDKVVIKAENGKKYYKEVELPAKVDPKSAKASYRN 154
                                    67899*************************************85 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 ?   10.3   0.1   0.00042      0.75      12      41 ..      14      43 ..       5      49 .. 0.85
   2 ?    1.4   0.0      0.25   4.5e+02      48      66 ..      78      96 ..      75     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                    Cep57_MT_bd 12 aLaevlkeLedEfehlklelqelaaqynal 41
                                    L+++ +e e+Ef++l  e+++la++ ++ 
  gi|118431657|ref|NP_148279.2| 14 LLEDIFREFEEEFRELEEEFEKLASRVQSR 43
                                   689999*******************99875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
                    Cep57_MT_bd 48 rkRkdLaeeleelvkrlEa 66
                                   r R ++ ee+e lv+ +E+
  gi|118431657|ref|NP_148279.2| 78 RGRPQIREEMEPLVDVIER 96
                                   5688999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1300.70
//
Query:       gi|118431658|ref|NP_148281.2|  [L=463]
Description: hypothetical protein APE_1952.1 [Aeropyrum pernix K1]
Scores for complete 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-08   33.6   1.8    3.3e-05   23.7   0.0    2.5  3  DAO             FAD dependent oxidoreductase
    2.6e-06   26.9   0.1     0.0066   15.7   0.0    3.0  3  FAD_binding_3   FAD binding domain
    5.6e-05   22.4   0.1       0.22   10.6   0.0    2.7  3  FAD_binding_2   FAD binding domain
     0.0023   17.2   0.0     0.0053   16.0   0.0    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0024   16.8   0.0      0.073   11.9   0.0    2.4  2  Trp_halogenase  Tryptophan halogenase
     0.0038   16.5   0.5      0.035   13.3   0.2    2.4  3  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.032   13.3   0.7      0.081   12.0   0.2    1.8  2  Lycopene_cycl   Lycopene cyclase protein
       0.04   14.1   0.3       0.26   11.6   0.1    2.4  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.069   12.2   0.0       0.11   11.6   0.0    1.3  1  GIDA            Glucose inhibited division protein A
        0.1   11.9   0.5        1.1    8.5   0.0    2.1  2  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0005      0.89       1      27 [.       8      36 ..       8      46 .. 0.85
   2 !   23.7   0.0   1.8e-08   3.3e-05     129     302 ..      84     280 ..      53     321 .. 0.63
   3 ?   -3.2   0.0       2.7   4.9e+03      86     121 ..     414     450 ..     382     460 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0005
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEE CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtlle 27
                                   dvvi+G G +G+s Ay L   g  V+ l+
  gi|118431658|ref|NP_148281.2|  8 DVVIVGLGPAGSSLAYLLKDTGlkVAGLD 36
                                   9*****************65577777665 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.8e-08
                                    TTTSEEEEETTEEEE.EHHHHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEE...EECTEEE.E......EEEEE CS
                            DAO 129 pgllgalfypdtgqv.dpakltaalaraaealGveilegtevtg.leeedgkvwgve...rttpgen.d......aadav 196
                                    ++++  l +p++g + d  k+   l+++a++ Gv+++++t + + +  e+g+++gv+   +   ge  d      + + +
  gi|118431658|ref|NP_148281.2|  84 EEVKIRLSEPEGGFMiDRNKYGLQLLEEAQKSGVDVYLKTHALSpI-IENGRLVGVYakrH---GEDgDvnvkfyS-KII 158
                                    3667778899998888****************************66.6689*****76532...544333445433.44* PP

                                    EE--GGGHHHH.HTT.CTTTSEEEEEEEEEEEEEECCTHSTGSG.CSEEEEE........EEETTTTEEEEEETTSEEE. CS
                            DAO 197 VnaaGawsdll.gll.keldlpispvrgqvlvlkplseklvspa.ailpvpe........tdddgrgvyvtprkdgrvl. 264
                                    V a+G +   + ++l     + ++p++ +  +++ ++   +  +    p  +         + +g++  ++p  + r+  
  gi|118431658|ref|NP_148281.2| 159 VDATGSGG-AIkRKLpSSW-PVVEPLKPTDSAVAYRKI-VELDYdIEEP--DviriyinaDIAPGGYWWLFPK-GRRIAn 232
                                    *****773.4444443222.344666655555533322.1122212222..1235555556666666666664.233333 PP

                                    EEESSE...........EETTCSSTSCSHHHHHHHHHHHHHHSGGGCGE CS
                            DAO 265 vGgtad...........eesgdddpevdeedidellealrklfPqlgdv 302
                                    +G   +           +e+  d  ++d  ++ +ll+++ +l+P+ ++ 
  gi|118431658|ref|NP_148281.2| 233 IGIGVQrgrgyphprhlYEKYLDK-RPDTGRVVRLLNEAGALLPTRRPA 280
                                    344333567777777766666666.888888989999999999886443 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.7
                                    EEEEESSHHHHHHHHHHHHHH..HHTTTTEEEEEHHHH CS
                            DAO  86 llslaadeeelealdkllall..leagldaelldaeev 121
                                    l+ l + +e + +++kl+ +   ++ gl+ +++d+ e+
  gi|118431658|ref|NP_148281.2| 414 LMELLTVAEYMSKVKKLYYEYpeRPDGLP-RWVDRVET 450
                                    33333333456666555555456666665.68887334 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.7e-06    0.0066       2      28 ..       7      33 ..       6      41 .. 0.91
   2 ?    2.6   0.0     0.035        63      93     175 ..      90     175 ..      55     199 .. 0.71
   3 !    4.8   0.1    0.0076        14     285     318 ..     287     320 ..     268     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.7e-06
                                   EEEEEE--SHHHHHHHHHHHHTTHHEE CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvv 28
                                   +dV+IVG GpaG +la lL+  G +v 
  gi|118431658|ref|NP_148281.2|  7 YDVVIVGLGPAGSSLAYLLKDTGLKVA 33
                                   79*********************9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.035
                                    HHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEEC.CEECCC..CCCCEEEECCTTEEEEEEEEEEEE--GTT-HHH CS
                  FAD_binding_3  93 esspervtvypqteleriLvehaeerglqvrfkteves.leqdee..gvtaevrdketgeeetvrakYlvGaDGgrStvr 169
                                    +s+pe   ++  ++    L+e+a++ g++v+ kt  +s + +++   gv a+  +++ + + ++ +k +v a G  +++ 
  gi|118431658|ref|NP_148281.2|  90 LSEPEGGFMIDRNKYGLQLLEEAQKSGVDVYLKTHALSpIIENGRlvGVYAKRHGEDGDVNVKFYSKIIVDATGSGGAIK 169
                                    4667777777777777789999************9777244444422555555566666677778888999999999998 PP

                                    HHHTGG CS
                  FAD_binding_3 170 ktlgie 175
                                    ++l+ +
  gi|118431658|ref|NP_148281.2| 170 RKLPSS 175
                                    888866 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0076
                                    TEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHH CS
                  FAD_binding_3 285 rvflaGDAaHihpPtgGqGlNtaiqDavnLawkL 318
                                    +   +GD a ++ P++G G+  a+  a++ a+ +
  gi|118431658|ref|NP_148281.2| 287 NFVSIGDNAYTVNPVHGGGMGYAMTAAMYAARGI 320
                                    55669********************999988766 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2   0.00046      0.82       1      26 [.       8      33 ..       8      43 .. 0.94
   2 !   10.6   0.0   0.00012      0.22     146     204 ..     107     167 ..      90     194 .. 0.80
   3 ?   -2.0   0.0      0.78   1.4e+03     273     298 ..     217     253 ..     213     325 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00046
                                   SEEEE--SHHHHHHHHHHHHTTT-EE CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkva 26
                                   Dv+++G G AG + A+ +++ Glkva
  gi|118431658|ref|NP_148281.2|  8 DVVIVGLGPAGSSLAYLLKDTGLKVA 33
                                   9***********************98 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00012
                                    HHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET..TTTCEEEEEESEEEE-----GG CS
                  FAD_binding_2 146 rlvesarkagvdfqerteadeLivedgrvtGavvenp..esgrevrirakavvlatgGfgr 204
                                     l+e+a+k gvd++ +t a++ i+e+gr +G++++    ++  +v++ +k +v+atg  g+
  gi|118431658|ref|NP_148281.2| 107 QLLEEAQKSGVDVYLKTHALSPIIENGRLVGVYAKRHgeDGDVNVKFYSKIIVDATGSGGA 167
                                    58999******************************88544444457888888888887775 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.78
                                    TT-EEE-.TTSSBTH..........GGGS-HHHHHHH CS
                  FAD_binding_2 273 eGgilvd.kdGrrFm..........nelasrdvvsra 298
                                    +Gg+++   +Grr            +  ++r+ + + 
  gi|118431658|ref|NP_148281.2| 217 PGGYWWLfPKGRRIAnigigvqrgrGYPHPRHLYEKY 253
                                    5666666666666555555555555444444444333 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   0.0     3e-06    0.0053       1      93 [.       7     146 ..       7     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-06
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE................TTHCHHHCSHHHHC..HHHHHHHHHHHHH..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxx..xxxxxxxxxxxxx..... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve................legtclnggcllsk..allgvaedaeias..... 57 
                                    +dvv++G GpAG ++a  l+  g+kv+ ++                 +g++l  g +l+k  a+ +v  + +i s     
  gi|118431658|ref|NP_148281.2|   7 YDVVIVGLGPAGSSLAYLLKDTGLKVAGLDiadfnrvwgkpcgdaiGKGHFLETGLPLPKgeAMMQVVNAVDIYSpseev 86 
                                    69************************999666566666677777765666666666665545666666666666688788 PP

                                    .......................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC...T CS
                                    .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                    Pyr_redox_2  58 .......................evvkklnqgielllgeevvkidpgkkkvklekkke...g 93 
                                                           e+   +++g++++l++++++ + ++++++    k+   +
  gi|118431658|ref|NP_148281.2|  87 kirlsepeggfmidrnkyglqllEE--AQKSGVDVYLKTHALSPIIENGRLVGVYAKRhgeD 146
                                    8888888888888888888754422..23445777777777666666655555444434442 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.037        67       1      22 [.       8      29 ..       8      43 .. 0.84
   2 !   11.9   0.0   4.1e-05     0.073     146     350 ..      94     324 ..      68     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.037
                                   EEEEE--SHHHHHHHHHHHHHT CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakal 22
                                   ++vivG G+aG+  A +l+ ++
  gi|118431658|ref|NP_148281.2|  8 DVVIVGLGPAGSSLAYLLKDTG 29
                                   69*************9999776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.1e-05
                                    --EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.......S-EEE-SEEEE-SGGG-IIIIIIT CS
                 Trp_halogenase 146 syAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled.......greveadlfiDcsGfrgllieqaL 218
                                    + ++ +d+++y   L + a++ Gv++   + +   + e+gr  ++  +          ++   +++D++G  g +  + L
  gi|118431658|ref|NP_148281.2|  94 EGGFMIDRNKYGLQLLEEAQKSGVDVYLKTHALSPIIENGRLVGVYAKRhgedgdvNVKFYSKIIVDATGSGGAIKRK-L 172
                                    55799************************999999999**9999988766665433334555668*****99987777.9 PP

                                    ---EEE-TTT----EEEEEEEE--H........---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHH CS
                 Trp_halogenase 219 ktgfedwsdvLltdrAlavqvesee........lvepytrataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaell 289
                                     + +  +    +td+A+a     e         +++ y +a     G  W  P  +r+ n G+ + + +    +  +  +
  gi|118431658|ref|NP_148281.2| 173 PSSWPVVEPLKPTDSAVAYRKIVELdydieepdVIRIYINADIAPGGYWWLFPKGRRIANiGIGVQRGRG-YPHPRHLYE 251
                                    ******************7533222245555669999*********************999998877766.334444455 PP

                                    HHCT--TTTS-.EEEE---EE........ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT- CS
                 Trp_halogenase 290 aeldgkleaep.rkirfttGr........rkqawvknvvalGlasgfvePlestsihliqa....alrrLlall 350
                                    + ld+++++    ++  ++G         ++ +w  n+v++G+ +  v+P+ + ++  +++    a+r + + +
  gi|118431658|ref|NP_148281.2| 252 KYLDKRPDTGRvVRLLNEAGAllptrrpaNTIVW-DNFVSIGDNAYTVNPVHGGGMGYAMTaamyAARGIEKAF 324
                                    5566666655433333345557888777455555.799999999999999999988776663333555555555 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.2     2e-05     0.035      17      45 ..       6      33 ..       1      39 [. 0.88
   2 ?    0.4   0.0      0.18   3.3e+02     157     178 ..     153     170 ..     117     208 .. 0.67
   3 ?   -2.8   0.0       1.6   2.9e+03      39      59 ..     203     223 ..     198     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EE CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkva 45
                                   + DvvivG G++G + ay l    +lkva
  gi|118431658|ref|NP_148281.2|  6 KYDVVIVGLGPAGSSLAYLLKDT-GLKVA 33
                                   57****************99888.***98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.18
                                    EEEEEEEE--GSSSTTTTHHHH CS
                           Thi4 157 irakvvvdatGhdgeivavvvk 178
                                      +k++vdatG  g i     +
  gi|118431658|ref|NP_148281.2| 153 FYSKIIVDATGSGGAIK----R 170
                                    4589*******988764....3 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.6
                                    CTTS-EEEEESSSS--TTTTT CS
                           Thi4  39 kpdlkvailersvspGGGawl 59 
                                    +pd+  + +++ ++pGG  wl
  gi|118431658|ref|NP_148281.2| 203 EPDVIRIYINADIAPGGYWWL 223
                                    5788888899******99996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   4.5e-05     0.081       1      31 [.       8      36 ..       8      52 .. 0.87
   2 ?   -1.5   0.0      0.57     1e+03     256     293 ..     286     323 ..     259     343 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlie 31
                                   Dvv++G GpAg slA  l  + +glkv  ++
  gi|118431658|ref|NP_148281.2|  8 DVVIVGLGPAGSSLAYLL--KDTGLKVAGLD 36
                                   9*****************..999***99885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.57
                  Lycopene_cycl 256 qkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaa 293
                                     + + iG +a  v P  G  +  ++ +a   a  i +a
  gi|118431658|ref|NP_148281.2| 286 DNFVSIGDNAYTVNPVHGGGMGYAMTAAMYAARGIEKA 323
                                    34688999999999987655555555555444455544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00014      0.26       1      28 [.      11      38 ..      11      40 .. 0.91
   2 ?   -1.3   0.0       1.5   2.7e+03       3      18 ..     303     318 ..     274     331 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                   IvG G +G+++AylL++ g++v  l+ +
  gi|118431658|ref|NP_148281.2| 11 IVGLGPAGSSLAYLLKDTGLKVAGLDIA 38
                                   9********************9888765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                    --SHHHHHHHHHHHCC CS
                  NAD_binding_8   3 GaGlsGlvaAylLaka 18 
                                    G+G++ + +A+ +a +
  gi|118431658|ref|NP_148281.2| 303 GGGMGYAMTAAMYAAR 318
                                    6666544444444444 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.9e-05      0.11       1      48 [.       8      65 ..       8     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.9e-05
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGGTT--SSSSEEE-T.........T CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldtiaelsCnpsiggi.........a 48
                                   dv+++G G AG+  A+ ++  G+kv+ +   +++++   +C ++ig            
  gi|118431658|ref|NP_148281.2|  8 DVVIVGLGPAGSSLAYLLKDTGLKVAGLdIADFNRVWGKPCGDAIGKGhfletglplP 65
                                   79***********************977689999999999999997543444444443 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3       0.1   1.8e+02       1      25 [.       8      32 ..       8      38 .. 0.89
   2 ?    8.5   0.0   0.00064       1.1      97     146 ..     109     165 ..      69     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakv 25
                                   Dvv+vG gpaG   A+  +  G kv
  gi|118431658|ref|NP_148281.2|  8 DVVIVGLGPAGSSLAYLLKDTGLKV 32
                                   9**********99998888888877 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00064
                   FAD_oxidored  97 l...aeagvtvllntrlvevekegkriesvtveske..g..rktirAkvfiDATgdG 146
                                    l   +++gv+v+l+t + +++ e++r+ +v ++++   g  + ++ +k+++DATg G
  gi|118431658|ref|NP_148281.2| 109 LeeaQKSGVDVYLKTHALSPIIENGRLVGVYAKRHGedGdvNVKFYSKIIVDATGSG 165
                                    2333778***************999*****9988775446778899*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3189.09
//
Query:       gi|14601741|ref|NP_148282.1|  [L=191]
Description: N-terminal acetyltransferase [Aeropyrum pernix K1]
Scores for complete 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-21   75.4   0.0    6.3e-21   74.8   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.3e-13   51.2   0.1    1.3e-12   47.9   0.1    2.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.4e-11   44.2   0.0    2.4e-11   43.4   0.0    1.3  1  FR47             FR47-like protein
    4.5e-11   42.8   0.0      1e-08   35.1   0.0    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
      1e-08   35.0   0.1    2.4e-08   33.8   0.0    1.5  2  Acetyltransf_8   Acetyltransferase (GNAT) domain
    6.5e-07   29.6   0.0    9.2e-05   22.6   0.0    2.4  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.1e-05   25.5   0.1    0.00015   21.9   0.1    2.3  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
    5.9e-05   22.6   0.0    7.3e-05   22.3   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase
    0.00034   21.3   0.0    0.00054   20.6   0.0    1.4  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0088   15.8   0.1      0.012   15.3   0.1    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.027   14.6   0.0      0.063   13.4   0.0    1.6  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 !   74.8   0.0   3.9e-24   6.3e-21      21     117 .]      37     167 ..      18     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 3.9e-24
                                   HHH.HHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET...............................TSTTEEEEEEEEE CS
                Acetyltransf_1  21 eee.feesfsleae.gllvaeedgeliGfisllkipd...............................ekggvayieslaV 68 
                                   +++ f+++  ++ +  +lvae +ge++G+++ +  +                                e+++v+++ s+aV
  gi|14601741|ref|NP_148282.1|  37 YWYgFYKYILDNWGeAFLVAEVGGEIVGYAMSRVEQTsdpvllgmkdelegdksvidkildairnqlsEERPVGHLVSIAV 117
                                   3336666656655547888***********666666666666666666666666667777777788899999********* PP

                                   SGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                Acetyltransf_1  69 speyrgkGlGsaLlealeeraree.gikkivlaveedndaairlYeklGF 117
                                   +p +rg+G+Gs+Ll a ++ +++   +++i+l+v+++n +airlYek+GF
  gi|14601741|ref|NP_148282.1| 118 RPGFRGRGIGSKLLSATVRVMKNVyRVDAIFLEVRVSNMPAIRLYEKFGF 167
                                   *************************************************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1     8e-16   1.3e-12       3      76 .]      51     169 ..      49     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 8e-16
                                   EEEEEEEETTEEEEEEEEEEES.....................................TCTEEEEE-GGGTTSSHHHHHH CS
                Acetyltransf_7   3 gevfVaeddgkivGfialslld.....................................aeitrlaVdpeyrgkGiGraLl 46 
                                   + ++Vae +g+ivG++   +++                                     +++  +aV+p +rg+GiG++Ll
  gi|14601741|ref|NP_148282.1|  51 EAFLVAEVGGEIVGYAMSRVEQtsdpvllgmkdelegdksvidkildairnqlseerpvGHLVSIAVRPGFRGRGIGSKLL 131
                                   5689999999999887766666888888888888888888888888887777666655555555***************** PP

                                   HH.....TTSEEE....EE.EEEETHHHHHHHHHHTTEEE CS
                Acetyltransf_7  47 ea.....aekgii....le.qlelnaekaikfYeklGFee 76 
                                    a     +  ++     ++ ++++++ +ai++Yek+GF++
  gi|14601741|ref|NP_148282.1| 132 SAtvrvmK--NVYrvdaIFlEVRVSNMPAIRLYEKFGFRK 169
                                   98555431..322333333345555559**********85 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.5e-14   2.4e-11      18      80 ..     106     170 ..     101     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.5e-14
                                   E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH..S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                          FR47  18 rkdggelgalqvlpehrrrGlgsrlvkalakeiae..rgktvllvvvasNtpsirlyeklGfeki 80 
                                   ++++g l ++ v+p +r+rG gs+l +a  + + +  r + ++l v+ sN p+irlyek Gf+k 
  gi|14601741|ref|NP_148282.1| 106 ERPVGHLVSIAVRPGFRGRGIGSKLLSATVRVMKNvyRVDAIFLEVRVSNMPAIRLYEKFGFRKV 170
                                   6899************************99999888899************************97 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0067        11      27      48 ..      47      70 ..      25      87 .. 0.79
   2 !   35.1   0.0   6.4e-12     1e-08      52     112 ..     110     173 ..      91     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0067
               Acetyltransf_10 27 eegealllvaeeggkivGvi..el 48
                                  ++    +lvae+gg+ivG++  ++
  gi|14601741|ref|NP_148282.1| 47 DNWGEAFLVAEVGGEIVGYAmsRV 70
                                  5556779************94333 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 6.4e-12
               Acetyltransf_10  52 shisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnasp.yavpfYeklGFkavgee 112
                                   +h+  ++V+p +rg+Gig++Ll a  + +++        l+v+ s+  a+++Yek+GF++v + 
  gi|14601741|ref|NP_148282.1| 110 GHLVSIAVRPGFRGRGIGSKLLSATVRVMKNVYRVDaiFLEVRVSNmPAIRLYEKFGFRKVRRI 173
                                   39999********************9998666444368999*******************9654 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   3.2e+03      35      59 ..      42      66 ..      24      77 .. 0.69
   2 !   33.8   0.0   1.4e-11   2.4e-08      86     143 ..     115     173 ..      96     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                                  HHHHC.STTEEEEE.EEETTEEEEEE CS
                Acetyltransf_8 35 lakldadphsepli.glldgepvgyf 59
                                  ++++  d++ e+++ +++ ge vgy+
  gi|14601741|ref|NP_148282.1| 42 YKYIL-DNWGEAFLvAEVGGEIVGYA 66
                                  55555.44444444157888888885 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 1.4e-11
                                   ES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEEEE CS
                Acetyltransf_8  86 ig.eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekekev 143
                                   i+  + +rg+g++++ll+a v+ + +  r++ + +E +v+N  airl+ek Gf+k++++
  gi|14601741|ref|NP_148282.1| 115 IAvRPGFRGRGIGSKLLSATVRVMKNVYRVDAIFLEVRVSNMPAIRLYEKFGFRKVRRI 173
                                   5546889************************************************9987 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.013        22      51     107 ..      52     104 ..      14     119 .. 0.82
   2 !   22.6   0.0   5.7e-08   9.2e-05      91     150 ..     123     183 ..     112     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                Acetyltransf_4  51 vflvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlk 107
                                    flvae  ++ivGya  + +++   +  ++l +  ++++  +++++ +++da+ + l+
  gi|14601741|ref|NP_148282.1|  52 AFLVAEvGGEIVGYAMSR-VEQ--TSDPVLLGM--KDELEGDKSVIDKILDAIRNQLS 104
                                   5999999*******9988.555..455555543..56788888888888888888774 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 5.7e-08
                Acetyltransf_4  91 keglgrelidaleqvl.keqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrw 150
                                    +g+g++l+ a + v+   + +  ++ e+ ++n ++i +++++GF++v++ k+++ ++   
  gi|14601741|ref|NP_148282.1| 123 GRGIGSKLLSATVRVMkNVYRVDAIFLEVRVSNMPAIRLYEKFGFRKVRRIKGYYRDGEDA 183
                                   5799************8889*********************************99887665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.12     2e+02       2      56 ..      14      65 ..      13      69 .. 0.74
   2 !   21.9   0.1     9e-08   0.00015      69     127 ..     105     169 ..      40     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.12
                                  EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT..SEEEEEEETTEEEEE CS
                Acetyltransf_9  2 irelteedldevlellkyaFqdeespleeireyfrkllee..srvlgaedngelvgq 56
                                  ir+++ +d++ v+e+  ++  ++  +      +++++l++  + +l+ae +ge+vg 
  gi|14601741|ref|NP_148282.1| 14 IRKARAQDIPIVMEINLESLPENYWYG-----FYKYILDNwgEAFLVAEVGGEIVGY 65
                                  788888888888888888777777764.....4577888655678888889999986 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 9e-08
                                   EEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--.....SSHHHHHTTT-EE CS
                Acetyltransf_9  69 ktlkaagvtgVavapehrgrgvlskLlaraleemree.gqplsllfP.....ssipiYrrfGyei 127
                                   ++ +++ ++++av p  rgrg+ skLl ++++ m+   ++  ++l        +i++Y++fG+++
  gi|14601741|ref|NP_148282.1| 105 EERPVGHLVSIAVRPGFRGRGIGSKLLSATVRVMKNVyRVDAIFLEVrvsnmPAIRLYEKFGFRK 169
                                   6889*******************************877888888866654333379******986 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   4.5e-08   7.3e-05      65     139 ..     102     170 ..      36     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.5e-08
               Acetyltransf_15  65 silieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkg 139
                                     ++e+ v  + ++ v + +rg+G+  klL  +++ +k+ Y vd    + L +      M+ + +lY + gFrk+
  gi|14601741|ref|NP_148282.1| 102 QLSEERPVGHLVSIAVRPGFRGRGIGSKLLSATVRVMKNVYRVDA---IFLEV--RVSNMP-AIRLYEKFGFRKV 170
                                   555666666778999*****************************3...33333..334565.7889999999886 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.3e-07   0.00054      83     138 .]     113     168 ..      85     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.3e-07
                Acetyltransf_3  83 lgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                   +++ ++p f+g+G+++  ++a ++++ +  +++ ++ ++  +N   ir++ek Gf+
  gi|14601741|ref|NP_148282.1| 113 VSIAVRPGFRGRGIGSKLLSATVRVMKNVYRVDAIFLEVRVSNMPAIRLYEKFGFR 168
                                   56888999******************9999*************************6 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   7.6e-06     0.012      47      95 ..      93     143 ..      91     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.6e-06
                          PanZ  47 dRlLgAvkveledk..eaelsdlcVRevTRrRGVgsyLleearrqaPevks 95 
                                   d+ L A++ +l+++  +++l ++ VR   R RG+gs+Ll  + r + +v +
  gi|14601741|ref|NP_148282.1|  93 DKILDAIRNQLSEErpVGHLVSIAVRPGFRGRGIGSKLLSATVRVMKNVYR 143
                                   567888887777665699*********************999988766654 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 ?   13.4   0.0   3.9e-05     0.063      26      52 ..     111     137 ..      98     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
               Acetyltransf_CG  26 dfthTeVpeelrGkGiAkkLvkaaldd 52 
                                   ++  + V + +rG+Gi++kL  a +  
  gi|14601741|ref|NP_148282.1| 111 HLVSIAVRPGFRGRGIGSKLLSATVRV 137
                                   567789***************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 00:00:00.41
# Mc/sec: 1414.41
//
Query:       gi|118431659|ref|NP_148283.2|  [L=115]
Description: hypothetical protein APE_1955.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 934.82
//
Query:       gi|14601743|ref|NP_148284.1|  [L=400]
Description: hypothetical protein APE_1956 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.7   1.9        3.5    7.9   0.0    3.0  3  HTH_52    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_52  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00019       3.5      29      46 ..     251     268 ..     235     273 .. 0.89
   2 ?    1.3   0.1     0.022   3.9e+02      23      49 ..     346     372 ..     340     381 .. 0.83
   3 ?   -1.0   0.1      0.11     2e+03      31      47 ..     382     398 ..     380     400 .] 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00019
                        HTH_52  29 svDLevlleyLveKgiie 46 
                                   svD e ++e LveK+++e
  gi|14601743|ref|NP_148284.1| 251 SVDVESIIEVLVEKRLVE 268
                                   89**************98 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.022
                        HTH_52  23 peledYsvDLevlleyLveKgiievvk 49 
                                    e++  ++++++l++ Lv+K++ ev++
  gi|14601743|ref|NP_148284.1| 346 REVKGRTIEITILVDGLVKKRLAEVEE 372
                                   67777789999**********999987 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.11
                        HTH_52  31 DLevlleyLveKgiiev 47 
                                   D+  ++e+  +K+ iev
  gi|14601743|ref|NP_148284.1| 382 DIDKIIEHILKKRDIEV 398
                                   788899*****999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2925.66
//
Query:       gi|118431660|ref|NP_148286.2|  [L=66]
Description: hypothetical protein APE_1956a.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00028   21.5   0.0    0.00042   20.9   0.0    1.3  1  zf-C2H2_4    C2H2-type zinc finger
     0.0014   19.0   0.0      0.002   18.5   0.0    1.3  1  zf-C2H2      Zinc finger, C2H2 type
     0.0099   16.1   0.0      0.014   15.7   0.0    1.2  1  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
  ------ inclusion threshold ------
      0.035   14.6   0.1      0.057   13.9   0.1    1.4  1  Zn-C2H2_12   Autophagy receptor zinc finger-C2H2 domain


Domain annotation for each model (and alignments):
>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   9.4e-08   0.00042       2      24 .]      35      57 ..      34      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.4e-08
                      zf-C2H2_4  2 kCpiCgksFsskkaLlrHlkthH 24
                                   kCp+C + Fs++++L  H+++ H
  gi|118431660|ref|NP_148286.2| 35 KCPLCEAIFSTPRDLEYHIAAYH 57
                                   8******************9988 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.4e-07     0.002       2      23 .]      35      57 ..      34      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.4e-07
                                   EETTTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2  2 kCpdCgksFkrksnLkrHirt.H 23
                                   kCp C   F+++ +L+ Hi   H
  gi|118431660|ref|NP_148286.2| 35 KCPLCEAIFSTPRDLEYHIAAyH 57
                                   8******************8777 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 !   15.7   0.0     3e-06     0.014       3      21 ..      35      53 ..      33      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3e-06
                                   BBTTTTBBBSSHHHHHCCT CS
                    zf-C2H2_jaz  3 YCvlCdKyFksenaldnHl 21
                                    C+lC+  F++ ++l+ H+
  gi|118431660|ref|NP_148286.2| 35 KCPLCEAIFSTPRDLEYHI 53
                                   7*****************8 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.3e-05     0.057       2      12 ..      35      45 ..      35      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                     Zn-C2H2_12  2 eCPlCseqFpk 12
                                   +CPlC+ +F++
  gi|118431660|ref|NP_148286.2| 35 KCPLCEAIFST 45
                                   7********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.35u 0.20s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 554.04
//
Query:       gi|118431661|ref|NP_148287.2|  [L=286]
Description: NAD synthetase [Aeropyrum pernix K1]
Scores for 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-74  248.2   0.0      7e-74  248.0   0.0    1.0  1  NAD_synthase   NAD synthase
    0.00091   18.1   0.0      0.016   14.0   0.0    2.1  2  tRNA_Me_trans  tRNA methyl transferase
     0.0031   17.1   0.0      0.018   14.5   0.0    1.9  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.053   13.2   0.0      0.055   13.1   0.0    1.2  1  Asn_synthase   Asparagine synthase


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 !  248.0   0.0   1.6e-77     7e-74       3     242 .]      22     267 ..      20     267 .. 0.97

  Alignments for each domain:
  == domain 1  score: 248.0 bits;  conditional E-value: 1.6e-77
                                    HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--.SSSTTHHHHHHHHHHHHHHTSEEEE--- CS
                   NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllP.ssvsseedvedalalaenlgievktidi 81 
                                    +++++fl++y++ +ga+g vlG+SGGvDSsl+ alav+a+g+ +v+al++P  +v++e+dvedal l+ ++g+e  +idi
  gi|118431661|ref|NP_148287.2|  22 QAITQFLRKYLEASGASGYVLGVSGGVDSSLALALAVDAVGSGRVTALIMPdREVTPERDVEDALRLVRSFGVEHAVIDI 101
                                    6899***********************************************999************************** PP

                                    HHHHHHHHH...HHHHHH.-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HH CS
                   NAD_synthase  82 kpivrafeq...elkeak.edlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKt 157
                                    +piv ++ +    +++++ + +  gNl+aRiR++ily++ankl++lvlgTg++sE+++GyfTkyGD a+d+ap++ l+K+
  gi|118431661|ref|NP_148287.2| 102 SPIVMVYISalpIFEDEEkDRVPVGNLRARIRANILYYYANKLGKLVLGTGDRSEYLIGYFTKYGDAACDVAPLTVLYKS 181
                                    *******9977756666658899********************************************************* PP

                                    HHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTG CS
                   NAD_synthase 158 evkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekieklvkkse 236
                                    +v++La+ ++vP+ +  kp s +L++g   e+eLg++Y+e+D iL   ++ k   eei + ++l++ +ve++  l + s 
  gi|118431661|ref|NP_148287.2| 182 QVRRLAELIGVPRDIAYKPSSPRLWKGHEAEAELGLSYNEIDVILYsRFDLKIPWEEIPRATGLERAKVERVRLLHEASS 261
                                    *********************************************999******************************** PP

                                    GGGSSS CS
                   NAD_synthase 237 hKrklp 242
                                    hKr++p
  gi|118431661|ref|NP_148287.2| 262 HKRSPP 267
                                    ***987 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   3.5e-06     0.016       5      70 ..      42     101 ..      40     109 .. 0.78
   2 ?    1.7   0.0      0.02        91     166     193 ..     173     202 ..     167     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-06
                  tRNA_Me_trans   5 valSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70 
                                     ++SgGVDSs+a+al  ++  + + v+  ++ +     +e + e+d++da r  + +g+++ v+d+
  gi|118431661|ref|NP_148287.2|  42 LGVSGGVDSSLALALAVDAVGSGR-VTALIMPD-----REVTPERDVEDALRLVRSFGVEHAVIDI 101
                                    689*********999888765543.33333333.....3567789****************99987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.02
                  tRNA_Me_trans 166 fPlgeltKeevrkiAkeagla..vaekkdS 193
                                     Pl  l K++vr++A+ +g++  +a k+ S
  gi|118431661|ref|NP_148287.2| 173 APLTVLYKSQVRRLAELIGVPrdIAYKPSS 202
                                    59999***********99998777777766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     4e-06     0.018       3      72 ..      41     112 ..      39     136 .. 0.84
   2 ?   -0.0   0.0      0.12   5.2e+02     155     178 ..     172     195 ..     166     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
                                    EEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-T.TSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG CS
                           QueC   3 vvllSGGlDSttvlalakkeg..kevealtfdYgqr.hkkeleaakkiakelgveehkildldllkelggsaL 72 
                                    v+ +SGG+DS+ +lala +++   +v+al +   +   ++++e a ++++++gv eh ++d++ +  +  saL
  gi|118431661|ref|NP_148287.2|  41 VLGVSGGVDSSLALALAVDAVgsGRVTALIMPDREVtPERDVEDALRLVRSFGV-EHAVIDISPIVMVYISAL 112
                                    6679*************99874468888887655555999**************.*******98877777776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.12
                                    E-TTTT--HHHHHHHHHHTTHHHH CS
                           QueC 155 eaPlidlsKaeivklgkelgvple 178
                                    +aPl+ l K+++ +l++ +gvp++
  gi|118431661|ref|NP_148287.2| 172 VAPLTVLYKSQVRRLAELIGVPRD 195
                                    58***************9999876 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.055       3      81 ..      21     103 ..      19     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                   Asn_synthase   3 relLedaVkrrlradvpvGalL..SGGlDSSliaalaarqsksplktFsigf.ee.kgsdeakyakevaehlgtehtelv 78 
                                    r+++++  ++ l+a    G +L  SGG+DSSl  ala     s   t  i    e     +++ a ++++ +g+eh  + 
  gi|118431661|ref|NP_148287.2|  21 RQAITQFLRKYLEASGASGYVLgvSGGVDSSLALALAVDAVGSGRVTALIMPdREvTPERDVEDALRLVRSFGVEHAVID 100
                                    555555566666666666666555*************999974444444444422688999999************9998 PP

                   Asn_synthase  79 lte 81 
                                    +++
  gi|118431661|ref|NP_148287.2| 101 ISP 103
                                    876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2358.63
//
Query:       gi|118431662|ref|NP_148288.2|  [L=412]
Description: coenzyme A biosynthesis bifunctional protein CoaBC [Aeropyrum pernix K1]
Scores for complete 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-49  167.1   0.0    1.3e-47  162.1   0.0    2.3  2  DFP           DNA / pantothenate metabolism flavoprotein
    1.3e-33  116.0   0.7    6.7e-33  113.7   0.2    2.0  2  Flavoprotein  Flavoprotein
  ------ inclusion threshold ------
      0.027   14.4   0.0        6.1    6.7   0.0    2.4  2  YjeF_N        YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.018   1.1e+02      34      55 ..      40      61 ..      37      73 .. 0.78
   2 !  162.1   0.0   2.2e-51   1.3e-47       1     180 [.     196     375 ..     196     381 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.018
                                   HHHHHHHHTT-EEEEEE-S-SS CS
                            DFP 34 alAeaaaarGaeVtlvsgpvsl 55
                                    lA+ +++rGa+V  v  p + 
  gi|118431662|ref|NP_148288.2| 40 DLARWLLRRGARVITVMTPEAA 61
                                   699*************999543 PP

  == domain 2  score: 162.1 bits;  conditional E-value: 2.2e-51
                                    TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHHHHH CS
                            DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleaveeal 80 
                                    leg + lvt G+TrE iD VRfisN+SSG mG++ A +++arGaeV +v+g +s+e p+ +++vk e++e+m++avee +
  gi|118431662|ref|NP_148288.2| 196 LEGIRALVTLGSTREWIDRVRFISNPSSGVMGLEAALELYARGAEVDVVAGYTSVEIPHLFNTVKTETTEDMAAAVEELT 275
                                    68999************************************************************************999 PP

                                    TT-..SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-S.S...-HHHHHHH CS
                            DFP  81 kea..divimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaet.e...ellenare 154
                                    ++   d+v++aAA  D+rp+ a e+Ki+    +++l lele++p++l+ +a   ++ ++lv+Faae  +   +l + a e
  gi|118431662|ref|NP_148288.2| 276 SKReyDAVVAAAAPVDFRPAGAFEGKIRS---GQRLVLELEPTPKVLEGIA---RRPKVLVAFAAEYvDnldSLRDPALE 349
                                    66566**********************95...568***************4...4557********754577999***** PP

                                    HHHHTT-SEEEEEEGGGTTGGG-SS- CS
                            DFP 155 klerkgldlivaNdvskeeagfgsde 180
                                    k+e+ ++dl+vaN+v+ e+ gf+s  
  gi|118431662|ref|NP_148288.2| 350 KMEKYDADLVVANRVGVEGVGFASPL 375
                                    ******************99999865 PP

>> Flavoprotein  Flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.2   1.1e-36   6.7e-33       1     149 [.      23     180 ..      23     190 .. 0.91
   2 ?    0.2   0.0     0.095   5.7e+02      20      71 ..     231     286 ..     219     291 .. 0.67

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 1.1e-36
                                    EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHHCTTESEEEEEEE CS
                   Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhielrrwadllviaPa 73 
                                    k i+lg+T sva +  l+l + L ++g++v  v+t++A+k++s+e +++a+        ++ ++hi+++r+a ++v+aPa
  gi|118431662|ref|NP_148288.2|  23 KTIVLGVTASVALYRSLDLARWLLRRGARVITVMTPEAAKLVSPEMFHWASggpvytgFTGGVEHISIARAASAMVVAPA 102
                                    679******************************************88887799*************************** PP

                                    EHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................GHHHHH CS
                   Flavoprotein  74 santlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgkmaeiee 149
                                    +  tlakia+G+ dn++ l + +  +  kp++ +Pam+ +mye+pq  + +++l ++gv v++P+  + g +k++++++
  gi|118431662|ref|NP_148288.2| 103 TLSTLAKIAHGVVDNPVALAAVSimGYGKPVIAVPAMHGNMYESPQAREVVDRLrSQGVLVVDPK-IEGGVAKYPDTHA 180
                                    *****************77774456889**************************66*********.5667777776554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.095
                                    HHHHHHTTEEEEEEESCHHHHCCHHGGS........TCSSHHHHHHCTTESEEEEE CS
                   Flavoprotein  20 lekLkkegievqvvltkaAkkfiskeklklaa....redpilhielrrwadllvia 71 
                                      +L  +g+ev+vv+  ++ ++ + ++  +++    +   +++   +r++d++v a
  gi|118431662|ref|NP_148288.2| 231 ALELYARGAEVDVVAGYTSVEIPHLFNTVKTEttedMAAAVEELTSKREYDAVVAA 286
                                    45677789999999999998887766333333444445555555568888888866 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.003        18      41      67 ..      37      63 ..      12      73 .. 0.79
   2 ?    6.7   0.0     0.001       6.1      33      63 ..     218     248 ..     199     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.003
                         YjeF_N 41 dglaaArhLaqegakVtvllleeeekl 67
                                   + l +Ar+L+++ga+V+++++ e +kl
  gi|118431662|ref|NP_148288.2| 37 RSLDLARWLLRRGARVITVMTPEAAKL 63
                                   56789**********999877666665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.001
                         YjeF_N  33 vGsgnnGgdglaaArhLaqegakVtvlllee 63 
                                    +++  +G  gl aA +L+ +ga+V+v+    
  gi|118431662|ref|NP_148288.2| 218 ISNPSSGVMGLEAALELYARGAEVDVVAGYT 248
                                    666778999*****************54433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3472.77
//
Query:       gi|14601748|ref|NP_148289.1|  [L=272]
Description: oxidoreductase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-55  188.9   0.0    1.6e-53  181.8   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.053   13.2   0.0      0.059   13.0   0.0    1.2  1  Peripla_BP_6  Periplasmic binding protein


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 !  181.8   0.0   1.8e-57   1.6e-53       2     292 ..      24     271 ..      23     272 .] 0.96

  Alignments for each domain:
  == domain 1  score: 181.8 bits;  conditional E-value: 1.8e-57
                                   EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSSSS- CS
                  Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiksgls 82 
                                   +glGtw++ +      ++ale   +a+e+Gin++DtAe+Yg g++e+++G++l +  + r+ v ++tK+      ++++++
  gi|14601748|ref|NP_148289.1|  24 VGLGTWAIRD-----YSSALESYVYAIERGINHIDTAEMYGAGEAERFVGKVLRS--VGRDRVYVVTKL------YPFRFR 91 
                                   89******95.....8***************************************..************......777776 PP

                                   .HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--EEEEE CS
                  Aldo_ket_red  83 .keniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvkivavq 161
                                    +++ +++ ++s +r+g++yvD++l+H+pdp++p i ++++ le   ++G++r+iGvSnfs eqle+a  ++kk++iv++q
  gi|14601748|ref|NP_148289.1|  92 dPDEAVKAARASAERMGVSYVDIILIHWPDPQTP-IKDQVKSLEAIAEAGLARYIGVSNFSKEQLEEAlTATKKHEIVVNQ 171
                                   2569******************************.*********************************999********** PP

                                   -B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHHTT-- CS
                  Aldo_ket_red 162 veynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselakehgvs 242
                                   v+y++l ++ +e+l++l+ +k + l ayspl +G                                 ++ l ++++++g++
  gi|14601748|ref|NP_148289.1| 172 VKYSVL-DRRAEELIPLAVEKSILLEAYSPLERGHVA-----------------------------EVRLLAKIGRQYGKT 222
                                   ******.*************************99988.............................6789*********** PP

                                   HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                  Aldo_ket_red 243 laqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                   + q+al++++ + ++ i+ip+a + e+++++l++l ++l++e+++ ++e+
  gi|14601748|ref|NP_148289.1| 223 PVQVALNFIV-SRPNFIAIPKAERREHVDEILGSLGWRLKPEDIELIEEK 271
                                   **********.6899*******************************9985 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.6e-06     0.059     121     188 ..      62     135 ..      50     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-06
                                   HHHHHHHHHHHHTTSCEEEEEEESSHH....HHHHHHHHHHHHHCCTEEEEEEEEE..-TTHHHHHHHHHHHHT CS
                  Peripla_BP_6 121 qasalveylakelggkkvalvyadyaf....gregiaalkaaakaaGgevvgeepv..plgttdfsaqvlqika 188
                                   +a+++v+ +++++g+ +v++v+  y+f    ++e+++a++a+a++ G+  v+ + +  p ++t  + qv  ++a
  gi|14601748|ref|NP_148289.1|  62 EAERFVGKVLRSVGRDRVYVVTKLYPFrfrdPDEAVKAARASAERMGVSYVDIILIhwPDPQTPIKDQVKSLEA 135
                                   78999*********************94444588999************8888655005555666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2297.31
//
Query:       gi|118431663|ref|NP_148290.2|  [L=439]
Description: serine hydroxymethyltransferase [Aeropyrum pernix K1]
Scores for complete 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-65  220.1   0.0    5.4e-65  219.5   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase
      1e-07   31.5   0.0    4.8e-07   29.3   0.0    2.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.6e-07   30.9   0.0      4e-07   29.6   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00093   18.6   0.1     0.0018   17.7   0.1    1.5  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.28   11.3   0.0    1.5  1  EcoEI_R_C        EcoEI R protein C-terminal


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 !  219.5   0.0   1.5e-68   5.4e-65      13     399 .]      22     390 ..      12     390 .. 0.93

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 1.5e-68
                                    HHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE--- CS
                           SHMT  13 kkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnvqp 92 
                                    ++++ r +e+i+liasen++s ++l+a  s +  +yaeG P kryy G+ ++de+e l+ +    + +++     v+++p
  gi|118431663|ref|NP_148290.2|  22 RHNVWRLRESINLIASENVMSLTALKAYLSDFMFRYAEGKPFKRYYQGTRYIDELEVLTGELMGSMMGTN----LVELRP 97 
                                    5667799*****************************************************9999999999....****** PP

                                    SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH--SE CS
                           SHMT  93 lsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefkPkl 172
                                     sG+ an++v+  l epgd+ +   + +G h++h        + a ++   s++y   +e+  +d d+  k  +e+kP++
  gi|118431663|ref|NP_148290.2|  98 VSGTIANASVFRVLAEPGDKAVIAPVQAGAHVSHTKFG---TLGALGIEQVSMPYD--EENMNVDVDKAVKLIEEVKPRF 172
                                    **********************************7554...469999999999996..56999***************** PP

                                    EEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEEEC-SEEEE CS
                           SHMT 173 ivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglillrkgvksv 251
                                     v G s y      + + e  ++vg  l+ d ah+ Gl+ +g  p+P+e  ad vt  thkt+ Gp+gg +++r      
  gi|118431663|ref|NP_148290.2| 173 AVLGGSVYIFPHPTREIAEAIHSVGGKLIYDAAHVLGLIMGGAWPNPLERgADAVTGSTHKTFPGPQGGAVFFR------ 246
                                    **********999999999999**************************9659**********************...... PP

                                    ETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EEGGG...S- CS
                           SHMT 252 dktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgyklvsg...Gt 328
                                           +e+l+kk+ +++fP      + h i a+a++  e ++   + y++qv +na++laeal  +g k++ +    t
  gi|118431663|ref|NP_148290.2| 247 -------DEQLYKKVSKTIFPWWVSNHHLHRIPATAITAVE-MKLYGRDYASQVTSNARKLAEALAAEGLKVIGEhlgYT 318
                                    .......699*************************998654.677789*************************8533269 PP

                                    SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHHTT--HHHHHHHHHHH CS
                           SHMT 329 dnhlvlvdlrekgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpaltsrgfkeedlekvakfi 399
                                     +h v+vd+r+ g  G+++ ++le+ ni +nkn +P d  +    +sG+r+G   +t+ g+k+ ++e++ak+i
  gi|118431663|ref|NP_148290.2| 319 RSHQVVVDVRDLG-GGAKCASLLEESNIIVNKNLLPWDppEAVKDPSGIRIGVQEVTRLGMKHGEMEEIAKLI 390
                                    ***********98.699999******************94444569************************986 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 !   29.3   0.0   1.3e-10   4.8e-07      40     334 ..      67     349 ..      28     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.3e-10
                                    T-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEE.E..ESS-THHHHH..HHHTT CS
                  Aminotran_1_2  40 ygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilv.p..dptyasykni..lrlsg 114
                                    y+ ++  +ele  + +++g    + ++   ++   sG+ a+++++  l++  pgd+ ++ p  +  + s+++   l + g
  gi|118431663|ref|NP_148290.2|  67 YQGTRYIDELEVLTGELMG--SMMGTNLV-ELRPVSGTIANASVFRVLAE--PGDKAVIaPvqAGAHVSHTKFgtLGALG 141
                                    6788889999999999999..33334444.66667********9999996..7777665142245799998752267789 PP

                                    SEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCB CS
                  Aminotran_1_2 115 gevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfv 194
                                    +e v++p y+ee++++d+++  ++++e +    ++  +l  s++     ++++++ +++++ +++ +  l+ D a+  + 
  gi|118431663|ref|NP_148290.2| 142 IEQVSMP-YDEENMNVDVDKAVKLIEEVK----PRFAVLGGSVY-----IFPHPT-REIAEAIHSVGGKLIYDAAHVLGL 210
                                    9999999.77*****************65....45568888886.....777775.889999**************9776 PP

                                    SSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEE.EHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHH CS
                  Aminotran_1_2 195 fgsldavatranveeepnllivgslsKaf.GlaGeRvGyilg.naavvsqlrklsrpfls.ssllqaavaaalsdallkq 271
                                        +a   ++n  e+ +++++gs  K f G  G   G+++  ++ + + + k   p+++   +l ++ a+a+ ++++k 
  gi|118431663|ref|NP_148290.2| 211 IMG-GA---WPNPLERGADAVTGSTHKTFpGPQG---GAVFFrDEQLYKKVSKTIFPWWVsNHHLHRIPATAITAVEMKL 283
                                    653.44...55544445559*********99***...*****999***************888999*********99765 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSS....EEEEEETHHCHHHHHHHHHHTCTEEEEE CS
                  Aminotran_1_2 272 seleemrqrlqkrrkelrdeLaelglkvlasqsgm....flltdlsaetakelskkLleevgvyvtp 334
                                     +  + ++++ +++++l ++La+ glkv++++ g+     +++d++ +   + + +Llee +++v +
  gi|118431663|ref|NP_148290.2| 284 -YGRDYASQVTSNARKLAEALAAEGLKVIGEHLGYtrshQVVVDVRDLGGGAKCASLLEESNIIVNK 349
                                    .********************9999999998766622223455555556666777777777777654 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.1e-10     4e-07      53     284 ..      97     404 ..      64     416 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.1e-10
                                    ES-HHHHHHHHHHHH--TTEEEEEETT...-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEE CS
                Beta_elim_lyase  53 vpqGtaAnsillkillqrgeevivtep...ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekik 129
                                     ++Gt An+  +++l+++g++ ++      ah+  +  g + +l+  ++   + +e+ ++d++k  ++i+e      k++
  gi|118431663|ref|NP_148290.2|  97 PVSGTIANASVFRVLAEPGDKAVIAPVqagAHVSHTKFGTLGALGIEQVSMPYDEENMNVDVDKAVKLIEE-----VKPR 171
                                    579****************99886554567555555556666665555555555555889***********.....3455 PP

                                    EEEEESSBTTTTTB---.HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEE CS
                Beta_elim_lyase 130 lisltvTnntagGqvvs.leelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvl 208
                                    + +        gG v+  +   re+a+  ++ g +l++D+A ++      g+ +  + +++D vt s  K    + Gg +
  gi|118431663|ref|NP_148290.2| 172 FAV-------LGGSVYIfPHPTREIAEAIHSVGGKLIYDAAHVLGLI-MGGAWPNPLERGADAVTGSTHKTFPGPQGGAV 243
                                    544.......478888615669********************99766.9999**************************** PP

                                    EE-HH.......................................HHHHHHHHHHHHT---SSTHHHHH............ CS
                Beta_elim_lyase 209 afrddel...................................edylaerveqrkylggglrqagvlaa............ 241
                                    +frd++l                                    dy ++ +  +++l++ l   g+++             
  gi|118431663|ref|NP_148290.2| 244 FFRDEQLykkvsktifpwwvsnhhlhripataitavemklygRDYASQVTSNARKLAEALAAEGLKVIgehlgytrshqv 323
                                    *****99**************************************9999999************9998888888888888 PP

                                    ........................................HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--EEECCGT CS
                Beta_elim_lyase 242 ......................................leagiraleeglaslerdhktaeqlaeklelvrlaiprrvyt 283
                                                                             gir   +++ +l+ +h   e+ a+ +++v + +++++++
  gi|118431663|ref|NP_148290.2| 324 vvdvrdlgggakcaslleesniivnknllpwdppeavkDPSGIRIGVQEVTRLGMKHGEMEEIAKLIRKVLIDKEDPKKV 403
                                    88888888888888888888888888888888888887666777777777777777777777777766666666555555 PP

                                    T CS
                Beta_elim_lyase 284 q 284
                                     
  gi|118431663|ref|NP_148290.2| 404 A 404
                                    4 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     5e-07    0.0018      81     195 ..     138     255 ..      92     312 .. 0.81
   2 ?   -3.9   0.0       1.7   6.2e+03     100     120 ..     399     419 ..     398     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5e-07
                                    HHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT... CS
                DegT_DnrJ_EryC1  81 lelgakpvfvDvdpdtynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg... 155
                                      lg + v +  d++ +n+d++++ ++i+e     a+l   +y  +    ++ +  ++ g k+i DaAh lG  + g   
  gi|118431663|ref|NP_148290.2| 138 GALGIEQVSMPYDEENMNVDVDKAVKLIEEVKprFAVLGGSVYIFPHPTREIAEAIHSVGGKLIYDAAHVLGLIMGGawp 217
                                    467888999999*****************987768******************************************999 PP

                                    EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHH CS
                DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekar 195
                                     ++   +da + S +  K++    GGav+++de+l +k++
  gi|118431663|ref|NP_148290.2| 218 NPLERGADAVTGSTH--KTFPGPQGGAVFFRDEQLYKKVS 255
                                    888888899999976..8999****************997 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.7
                                    -GGGCGGG--TTEEEEEEB-G CS
                DegT_DnrJ_EryC1 100 dpaaieaaitertkaIlpVhl 120
                                    dp+++++ + e +k  + +h+
  gi|118431663|ref|NP_148290.2| 399 DPKKVAEQVKEFRKQFMKIHY 419
                                    789999999999999999997 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.8e-05      0.28      68     104 ..     380     418 ..     362     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.8e-05
                      EcoEI_R_C  68 q..ltdlidlirkiagldeeletrserverafkrwikek 104
                                    +  +  +  lirk+++++e +++ +e+v++++k+++k +
  gi|118431663|ref|NP_148290.2| 380 HgeMEEIAKLIRKVLIDKEDPKKVAEQVKEFRKQFMKIH 418
                                    34577999**************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); 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):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.36
# Mc/sec: 3652.14
//
Query:       gi|118431664|ref|NP_148291.2|  [L=390]
Description: alcohol dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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-100  335.4   0.8   3.7e-100  335.3   0.8    1.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
      2e-24   86.7   4.5    5.7e-14   52.4   1.8    2.1  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
     0.0025   17.0   3.5       0.48    9.5   0.3    2.5  2  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.3   0.8  6.2e-104  3.7e-100       1     364 []       7     382 ..       7     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 335.3 bits;  conditional E-value: 6.2e-104
                                    -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT CS
                         Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalaree 80 
                                    P+riv+ +   + l++ll + g+k++l+vtd++++ +++++++++e++++ g+ev +fdgv+p+p+ +  +++a+ ar  
  gi|118431664|ref|NP_148291.2|   7 PRRIVYNESLPRALETLLGDKGVKHVLVVTDGKVA-AMSWFKEAVEHVASLGVEVCIFDGVTPEPEFDVGDAIASEARRC 85 
                                    899999999999*********************88.888***************************************** PP

                                    .--EEEEEESHHHHHHHHHHHHHTT........................--EEEEESS-S-S-TT-SEEEEE.-TTS..E CS
                         Fe-ADH  81 gadvviavGGGsviDtAKaialllanpe.....vedyl.gegkakkkkalpliaiPTtaGtGsevtplavitdeeeg..e 152
                                    +a++++avGGGsviD+AKa  +   +p+     +      +    +++++ l+a+PTt+GtGs ++   v+t+  +g  e
  gi|118431664|ref|NP_148291.2|  86 RAEAIVAVGGGSVIDAAKAGFVKFVRPDadlegL---ApFNYLGLEDSGIVLVAVPTTSGTGSDASYGIVLTKRVNGgrE 162
                                    ************************9985564442...332222445678***********************9888678* PP

                                    EEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHH CS
                         Fe-ADH 153 klsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedlea 232
                                    k++++++e++P+++i+Dp +tl++P r+t+ t++Dalah +Ea +s++anplsdala +a++++++ l+++v+d+++++a
  gi|118431664|ref|NP_148291.2| 163 KIAVGSYEVVPYASILDPSITLGMPERLTVGTAVDALAHSVEAIASTNANPLSDALAAKAAEIVFRRLPEVVNDPGNYDA 242
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..............HHHHHHT.......T- CS
                         Fe-ADH 233 reqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfna...eaap.erlaqlaralggesdeea 308
                                    r++m++a+t+ag+af+n+glg++Ha+ah+lga++g++hg++++++lp+v+rfn    +  + +++ +l   l      e+
  gi|118431664|ref|NP_148291.2| 243 RAEMHIAATMAGMAFTNSGLGLAHAIAHPLGARLGTHHGATVGMVLPHVVRFNEsrsDY-ArRKYWELKLLLESLLGLEE 321
                                    ******************************************************65333.34999999999755566677 PP

                                    -HHHHHHHHHHHHHTT---SHHHHT.-TT-HH....HHHHHHHT-TSGGGGSSS---HHHH CS
                         Fe-ADH 309 aeeliealrellkelglptsLselg.vdeedl....dklaeaalkdrslannpreltaedv 364
                                      +l+++++el++++g pt+++el  +++e++    d++aeaa++d+ la np+ +t edv
  gi|118431664|ref|NP_148291.2| 322 RGSLADHIEELYARVGQPTRVRELAgIERERYltlaDEVAEAAFRDPELAFNPVMPTMEDV 382
                                    888********************977***9666778*********************9997 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   2.1e-12   1.3e-08       7      93 ..      17     104 ..      11     111 .. 0.92
   2 !   52.4   1.8   9.5e-18   5.7e-14      99     250 .]     131     285 ..     128     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.1e-12
                       Fe-ADH_2   7 leklgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgG 85 
                                     + l+ ll ++++k+vl+v+d ++ ++   ++  e++++ g++v +++ v++e++++   ++++++r  +++++vavGgG
  gi|118431664|ref|NP_148291.2|  17 PRALETLLGDKGVKHVLVVTDGKVAAMsWFKEAVEHVASLGVEVCIFDGVTPEPEFDVGDAIASEARRCRAEAIVAVGGG 96 
                                    5678999****************99986789999999******************************************* PP

                       Fe-ADH_2  86 tiiDiaky 93 
                                    ++iD+ak 
  gi|118431664|ref|NP_148291.2|  97 SVIDAAKA 104
                                    ******95 PP

  == domain 2  score: 52.4 bits;  conditional E-value: 9.5e-18
                       Fe-ADH_2  99 nvpyvsvpTaaSvDGfaspgaslvvd....gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwkl 173
                                    ++ +v+vpT+    + as+g+ l+++     +k+ v     +P+a i+D ++    P+rl+     D+l+ ++    +  
  gi|118431664|ref|NP_148291.2| 131 GIVLVAVPTTSGTGSDASYGIVLTKRvnggREKIAVgSYEVVPYASILDPSITLGMPERLTVGTAVDALAHSVEAIASTN 210
                                    6779*******************998776567888887889*************************************** PP

                       Fe-ADH_2 174 anevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalHGeqVG 250
                                    an +s+ la ++a++v+  + ++v+d+++  a +e+  a +++g+++++++ G  H i+H l ++    + HG+ VG
  gi|118431664|ref|NP_148291.2| 211 ANPLSDALAAKAAEIVFRRLPEVVNDPGNYDARAEMHIAATMAGMAFTNSGLGLAHAIAHPLGARL--GTHHGATVG 285
                                    *****************************************************************9..999****98 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.2   0.00025       1.5      25      49 ..      81     107 ..      73     110 .. 0.79
   2 !    9.5   0.3     8e-05      0.48      56     218 ..     131     298 ..     115     358 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00025
                                    HTT--TT-EEEEEESHHHHHHH..HHH CS
                   DHQ_synthase  25 eakleRksllialGGGvvgDla..Gfv 49 
                                    ea+  R ++++a+GGG v D a  Gfv
  gi|118431664|ref|NP_148291.2|  81 EARRCRAEAIVAVGGGSVIDAAkaGFV 107
                                    5667899*************8533665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 8e-05
                                    --EEEEEE-SHHHHHTTTSSS..EEEEEETTEEEEEEEE-.--SEEEEEGGGGGGS-HHHHHHHHHHHHHHHH..HT-HH CS
                   DHQ_synthase  56 GvrfvqvPttllaqvDssvGg..KtainlplgKNliGafa.qPkavlidlevLktLperelraGlaEviKyal..ikdee 130
                                    G+ +v vPtt     D+s G      +n  + K  +G++   P a ++d+++   +per +     +++ +++  i+ ++
  gi|118431664|ref|NP_148291.2| 131 GIVLVAVPTTSGTGSDASYGIvlTKRVNGGREKIAVGSYEvVPYASILDPSITLGMPERLTVGTAVDALAHSVeaIASTN 210
                                    999***************996324569************637**********9999999877777777766542133333 PP

                                    HHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHH....HHHHHCCTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHH CS
                   DHQ_synthase 131 lfelleenaeallkeeeeealeeliarsievka....evveeDekekglralLnlGHtigHaiEallgyekllHGeaVai 206
                                      + l++  +a+++e+  + l e+++   ++ a    ++ ++      + + L l H i+H + a lg+   +HG  V +
  gi|118431664|ref|NP_148291.2| 211 A-NPLSDALAAKAAEIVFRRLPEVVNDPGNYDAraemHIAATMAGMAFTNSGLGLAHAIAHPLGARLGT---HHGATVGM 286
                                    3.5555555555556677777777765544444100033333333333444566777777777777777...89988866 PP

                                    HHHHHHHHHHHT CS
                   DHQ_synthase 207 Gmvlaaelsekl 218
                                     +   +++ e+ 
  gi|118431664|ref|NP_148291.2| 287 VLPHVVRFNESR 298
                                    555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2942.22
//
Query:       gi|118431665|ref|NP_148292.2|  [L=133]
Description: hypothetical protein APE_1964.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-18   66.3   0.0    3.3e-18   66.0   0.0    1.1  1  SCP2      SCP-2 sterol transfer family


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   1.8e-22   3.3e-18       2      99 ..      13     116 ..      12     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.8e-22
                                    HHHHHHHHHH.HHHHHHCCH-EEEEEEECTC.TEEEEEETTS.TEEESSCTT.BS-S..EEEEEEHHHHHHHHCTSS-HH CS
                           SCP2   2 nqllerlkdp.ekkealkklagvlrfdltdlkgsltldlkeg.qldvaakde.gkad..vtlslsledllelaegklnpq 76 
                                    ++++++l+++ ++++a+k + + + f+++d+++ ++ldlk+g +l v++ d+ ++ad  v++s++l+d+l++++gk+np 
  gi|118431665|ref|NP_148292.2|  13 EEFCKTLDSSeKYRSAAKGWVHPILFKISDGGQGFILDLKDGrCLGVQWFDDtSRADapVIISGRLSDWLDVINGKVNPL 92 
                                    68999996666*****************************8878999888888888888********************* PP

                                    HHHHTTSSEEE.C-HHHHHHHHHH CS
                           SCP2  77 kafmqgkLkie.GDielaqkleal 99 
                                    +a+++++L+ie GD+ l ++++a+
  gi|118431665|ref|NP_148292.2|  93 TALLTRRLRIEkGDLSLILRYSAA 116
                                    **********747*****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1001.03
//
Query:       gi|118431666|ref|NP_148293.2|  [L=120]
Description: hypothetical protein APE_1965.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.5   0.0        0.2   11.4   0.0    1.1  1  Baculo_gp41  Structural glycoprotein p40/gp41 conserved regio


Domain annotation for each model (and alignments):
>> Baculo_gp41  Structural glycoprotein p40/gp41 conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.1e-05       0.2       7      63 ..      19      74 ..      14      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.1e-05
                    Baculo_gp41  7 elieyyarLekklgaavklskdksifdksfvvskilkayadkfykdklaeaakqLse 63
                                   ++i  ++rL+++lg++ + + dk if   ++ +  lk+ a+k  + +l  a+++  e
  gi|118431666|ref|NP_148293.2| 19 DVIIKLERLKRRLGSQYSEQVDKWIFTFAYIREG-LKSIAEKLEEGRLISASNEACE 74
                                   6677899**********************99887.********99999888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 972.08
//
Query:       gi|14601753|ref|NP_148294.1|  [L=109]
Description: hypothetical protein APE_1966 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 945.87
//
Query:       gi|118431667|ref|NP_148295.2|  [L=198]
Description: hypothetical protein APE_1967.1 [Aeropyrum pernix K1]
Scores for complete 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   44.0   9.3      1e-05   24.9   0.1    2.5  2  Peptidase_M50  Peptidase family M50


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 !   20.7   6.0   1.1e-08    0.0002       4     107 ..      52     138 ..      50     141 .. 0.86
   2 !   24.9   0.1   5.7e-10     1e-05     178     224 ..     137     183 ..     134     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-08
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkveefsigfGpkl.lsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkk 82 
                                    +++++  v+HE +H lvA ++g+k e   i +Gp l ++f  g +++ i l p  GyV+   +                +
  gi|118431667|ref|NP_148295.2|  52 VAVFLGFVLHEAAHKLVAIRMGMKSEF--IAYGPGLlITFLSGLVPFIIVLAP--GYVRSIHTG--------------WA 113
                                    566777889***************976..888886516888************..****99988..............56 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  83 spwqrllivlAGplanfilailvfv 107
                                    +p   l  v+AGp++n+ la++++v
  gi|118431667|ref|NP_148295.2| 114 HPKGFLYSVAAGPAVNIALALAAAV 138
                                    78999999***********998876 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 5.7e-10
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 178 qlaseaaeaglssflqllalisvnLgilNLlPipvLDGghllfalle 224
                                    ++a + a a+l ++l  ++ ++  ++++NLlP+p+LDG ++++a+ +
  gi|118431667|ref|NP_148295.2| 137 AVALQFAPATLVAYLRAVVDVNAWFAFFNLLPVPPLDGSKIFRATPT 183
                                    56677888899999999999**********************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1535.47
//
Query:       gi|14601755|ref|NP_148296.1|  [L=316]
Description: carbamate kinase [Aeropyrum pernix K1]
Scores for complete 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-27   95.3   0.0    5.7e-27   94.9   0.0    1.2  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 !   94.9   0.0   3.2e-31   5.7e-27       2     240 ..       6     296 ..       5     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 3.2e-31
                                   EEEEEE-TTCCC.CTCC........HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC.......... CS
                     AA_kinase   2 rvVvKlGGsslt.dkee........aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa......... 64 
                                   + V++lGG++++ ++          a+++r+  +ia+   +g + v+ hG+g+++  l+++   l++++ ++         
  gi|14601755|ref|NP_148296.1|   6 LAVIALGGNAIAgPG-MdvsvesqtAAVKRASSIIADVLADGWRSVITHGNGPQVGYLSEAFEALPPERPRQplyiatamt 85 
                                   67**********554.45*******************************************77777777777889977877 PP

                                   .......E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.........................H CS
                     AA_kinase  65 ....glrstleeagevatrdalaslgerlvaallaaglpavglsaaaldateagr.......................deg 118
                                       gl++++  + e+ +r + + +   +++ l++   p+++ ++++++++ ++                         ++
  gi|14601755|ref|NP_148296.1|  86 qawiGLLLKHSLEEELRRRGLNVLVPVVISRVLVDVSDPSFNNPSKPVGPIYGREeaeelsrrygwvfkrdprggfrrVVP 166
                                   8888777777777777887777777777777777777777777777777777777777*********************** PP

                                   HHTTTCEEECCHHHHHHHTT.-EEEEESEE..EEETTTE.....EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTT CS
                     AA_kinase 119 sdgnvesvdaeaieelleag.vvpvltgfi..gldeege.....lgrgssDtiaallAealgAdkliiltdVdGVydadpk 191
                                   s+++v+ vd++ i+e  ++   v+ l+g++  ++ ++g+      +++++D +++llA  l+Ad l+iltdV+GV  + ++
  gi|14601755|ref|NP_148296.1| 167 SPRPVSIVDRDLIAEASAESpAVVALGGGGvpVVERPGGvlepvEAVVDKDLASSLLATQLNADLLVILTDVPGVAVNYGR 247
                                   *****************88736666666555566666669999988**********************************9 PP

                                   TCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                     AA_kinase 192 kvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvIt 240
                                   +    r l++ +++e+++   ++++  g+m +k++aa+ +++r g p+vI 
  gi|14601755|ref|NP_148296.1| 248 EG--ERWLRRAAASELKKylREGHFPPGSMGPKVEAAISFVERTGKPAVIG 296
                                   98..599************************************99***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2384.78
//
Query:       gi|118431668|ref|NP_148297.2|  [L=450]
Description: hypothetical protein APE_1971.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-06   25.9   0.0    2.4e-05   24.0   0.0    1.8  2  cobW        CobW/HypB/UreG, nucleotide-binding domain
    0.00016   21.8   0.1      0.001   19.2   0.0    2.1  2  CbiA        CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.012   15.4   0.5      0.075   12.8   0.1    2.1  2  AAA_26      AAA domain
      0.027   14.2   0.1      0.052   13.3   0.1    1.4  1  AAA_30      AAA domain
      0.043   13.3   0.3      0.085   12.3   0.3    1.5  1  ParA        NUBPL iron-transfer P-loop NTPase
       0.11   11.8   0.0       0.21   10.8   0.0    1.4  1  Zeta_toxin  Zeta toxin
       0.13   12.0   0.0       0.29   10.8   0.0    1.7  2  PRK         Phosphoribulokinase / Uridine kinase family
       0.17   11.7   0.0       0.42   10.5   0.0    1.6  2  AAA_31      AAA domain


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 ?   -1.0   0.0      0.52   1.2e+03       9      27 ..     132     150 ..     123     155 .. 0.67
   2 !   24.0   0.0   1.1e-08   2.4e-05     111     175 ..     237     298 ..     224     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.52
                                    TTCCHHHHHHHHHCT--SS CS
                           cobW   9 lGsGKTtLlnhllenragl 27 
                                     G+GK+t+ +++ +  +g+
  gi|118431668|ref|NP_148297.2| 132 TGAGKSTVSRAIARIMRGK 150
                                    6******988887555544 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.1e-08
                                    CECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-E CS
                           cobW 111 tldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakv 175
                                    + d++++v Da  l   +e  +  +e  +  ad +++nK+D ++ee +++++ee +r++np+a +
  gi|118431668|ref|NP_148297.2| 237 KPDFMITVADA--LRPGQEVGSFPGEVNVRLADAVIINKVDRAPEE-NVRRIEENVRSINPKALI 298
                                    66999******..4456666777788899*****************.56************9865 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 !   19.2   0.0   4.5e-07     0.001       1      33 [.     125     157 ..     125     161 .. 0.96
   2 ?   -0.0   0.0      0.38   8.4e+02      78     101 ..     268     289 ..     168     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.5e-07
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllv 33 
                                    ia+++   G+GK+t++ ++ar++  +g+rV++v
  gi|118431668|ref|NP_148297.2| 125 IAVTAVRTGAGKSTVSRAIARIMRGKGYRVVPV 157
                                    7999999***********************997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.38
                                    EEEEEEESS...-TTCHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  78 gvvlnrvdgeneetllkealeelk 101
                                     v++n+vd     ++    +ee  
  gi|118431668|ref|NP_148297.2| 268 AVIINKVDRA--PEENVRRIEENV 289
                                    5889999876..444444444443 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.3e-05     0.075       3      32 ..     125     154 ..     124     163 .. 0.93
   2 ?    0.1   0.0      0.26   5.9e+02     161     179 ..     268     288 ..     237     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                         AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkv 32 
                                    i vt+++tg+GK++vs +++r+++ kg++v
  gi|118431668|ref|NP_148297.2| 125 IAVTAVRTGAGKSTVSRAIARIMRGKGYRV 154
                                    779************************997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.26
                         AAA_26 161 GvilNkv.rnp.envetlekk 179
                                    +vi+Nkv r+p env+ +e++
  gi|118431668|ref|NP_148297.2| 268 AVIINKVdRAPeENVRRIEEN 288
                                    69****843445688877765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.3e-05     0.052      13      51 ..     118     156 ..     115     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.3e-05
                         AAA_30  13 lltsgdrvavltGpAGtGKttalkalreaweaaggrvig 51 
                                    llts+  +av   + G+GK+t+ +a++++++ +g+rv+ 
  gi|118431668|ref|NP_148297.2| 118 LLTSKPVIAVTAVRTGAGKSTVSRAIARIMRGKGYRVVP 156
                                    677887788888899*********************985 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 ?   12.3   0.3   3.8e-05     0.085       3      35 ..     122     154 ..     120     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                           ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkv 35 
                                    k viav++ + G GKStv+  +A  ++ kg++v
  gi|118431668|ref|NP_148297.2| 122 KPVIAVTAVRTGAGKSTVSRAIARIMRGKGYRV 154
                                    679***************************998 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   9.5e-05      0.21      14      43 ..     121     151 ..     113     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdele.rq 43 
                                    ++P++ + +  +GAGKs++++++++ ++ ++
  gi|118431668|ref|NP_148297.2| 121 SKPVIAVTAVRTGAGKSTVSRAIARIMRgKG 151
                                    79**********************9996333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.29       1      33 [.     124     157 ..     124     197 .. 0.71
   2 ?   -3.1   0.0       2.4   5.3e+03     101     116 ..     305     322 ..     281     322 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                            PRK   1 vIgvag.sSGaGkttvarklekifgrekvkaaei 33 
                                    vI+v++   GaGk+tv+r++  i+++++ + + +
  gi|118431668|ref|NP_148297.2| 124 VIAVTAvRTGAGKSTVSRAIARIMRGKGYRVVPV 157
                                    799988469***************9887665444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                            PRK 101 p..dkeeliegadvlviE 116
                                       d++e+i+g+ v+v+E
  gi|118431668|ref|NP_148297.2| 305 VevDNPEMISGKRVVVVE 322
                                    133678888888888876 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00019      0.42       3      34 ..     124     155 ..     122     160 .. 0.94
   2 ?   -3.9   0.0         5   1.1e+04     110     124 ..     213     227 ..     210     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                         AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvL 34 
                                    vIa++  + G GK+T s ++a  +  +g++v 
  gi|118431668|ref|NP_148297.2| 124 VIAVTAVRTGAGKSTVSRAIARIMRGKGYRVV 155
                                    8*****************************97 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5
                         AAA_31 110 llekvkdeYDyiiiD 124
                                    +l++v++e D+i+ D
  gi|118431668|ref|NP_148297.2| 213 VLREVEKESDIILWD 227
                                    789999*****9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 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:                        80  (0.00446204); 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 0.22s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 3543.06
//
Query:       gi|118431669|ref|NP_148298.2|  [L=703]
Description: hypothetical protein APE_1973.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.22s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 5541.12
//
Query:       gi|118431670|ref|NP_148299.2|  [L=166]
Description: hypothetical protein APE_1975.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   13.1   0.2       0.11   12.6   0.2    1.2  1  SAM_KSR1  SAM like domain present in kinase suppressor RAS 1
      0.082   13.0   0.0       0.55   10.4   0.0    2.3  2  SpoIIID   Stage III sporulation protein D


Domain annotation for each model (and alignments):
>> SAM_KSR1  SAM like domain present in kinase suppressor RAS 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   1.3e-05      0.11      53     126 ..      40     114 ..      26     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                       SAM_KSR1  53 klaereranelqky.pelkqWLrvvglsqetleailnkklsleelLkmseeelkqllsevqaeeeelrRllaAmk 126
                                    ++ e+e a+ l +  + +   L+ vgl+ et+ a+ +   ++e+l+k+  e +kq  ++ q    +++ ll+A++
  gi|118431670|ref|NP_148299.2|  40 HMLESEDAERLASRlEYIDYILEAVGLRLETILALQPSIEAVEDLMKLPYELVKQAAKQAQDLPPDITSLLTALE 114
                                    4567888999988856677789*********************************99999988888888888875 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.1e-05      0.55      14      39 ..      17      42 ..       8      72 .. 0.77
   2 ?   -0.5   0.0      0.16   1.4e+03      39      55 ..     105     121 ..      91     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.1e-05
                        SpoIIID 14 yiveskatvRkaakvfgvskstvhkD 39
                                    ive  atvR+a  ++ v ks +h  
  gi|118431670|ref|NP_148299.2| 17 EIVEALATVRQARFKLKVYKSRLHML 42
                                   599*********************63 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.16
                        SpoIIID  39 DvterLkkinkklakqv 55 
                                    D+t  L+ ++++la+ +
  gi|118431670|ref|NP_148299.2| 105 DITSLLTALEQSLASAI 121
                                    99999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1350.03
//
Query:       gi|118431671|ref|NP_148300.2|  [L=460]
Description: seryl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.8e-35  120.3   0.0    1.5e-34  119.6   0.0    1.3  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    3.6e-20   72.2   5.4    7.9e-20   71.1   5.4    1.6  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
      0.021   15.3   4.8      0.044   14.3   4.8    1.4  1  APG6_N        Apg6 coiled-coil region
       0.71    9.7   6.1         42    4.0   0.0    3.5  3  DivIC         Septum formation initiator


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 !  119.6   0.0   3.2e-38   1.5e-34       8     178 ..     247     423 ..     239     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 3.2e-38
                                    SEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                    +++++L++t+e+++++l+ +  + +++LPlkl+ +++++R+E+     d++G++Rv++Fh+ +++v+++++++    ++l
  gi|118431671|ref|NP_148300.2| 247 GEDLYLIATAEHPLAALYYNSEIYDEDLPLKLVGVSPCFRKEAGagnrDLKGIFRVHQFHKVEQFVYSLPEESSKLHEEL 326
                                    589*****************99*********************778899*********************99******** PP

                                    HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.SEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                   tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.reksvimi 162
                                    i  +++if+ l ++fr++    ++  a + +k+++ea+++ ++k++e+++++++ + ++ rlg++ +++++ ++  v+++
  gi|118431671|ref|NP_148300.2| 327 ISNAKEIFKGLEIPFRVVNIASGDLGACAVKKYDLEAWMPAQGKYREMVSASNCTDWQAYRLGIRLVRRKGmERGYVHTL 406
                                    ****************99999999****************************************999999967779**** PP

                                    EEE.EEHHHHHHHHHHH CS
                                    xxx.xxxxxxxxxxxxx RF
                   tRNA-synt_2b 163 caa.igveRllsaileq 178
                                    +a+ ++ +R++ aile+
  gi|118431671|ref|NP_148300.2| 407 NATaVASTRTITAILEN 423
                                    **99***********98 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   5.4   1.8e-23   7.9e-20       5     108 .]       8     110 ..       7     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.8e-23
                                    HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHH CS
                   Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelk 84 
                                     l+r+npea+ke+++kR  d+a vd+ + ld ++r+l + ++e+++++Ne+++ I+ka  + e++e+liae+k l  e +
  gi|118431671|ref|NP_148300.2|   8 ELLRSNPEALKEHVRKRLMDPAIVDRAYRLDVEWRRLLTMVNEVRRRHNEITRMIAKAGSR-EERERLIAEAKRLLRERE 86 
                                    79********************************************************987.7***************** PP

                                    HHHHHHHHHHHHHHHHHCTS---- CS
                   Seryl_tRNA_N  85 aleaelkeleaeleklllaiPNip 108
                                    +le++lk++e e e++ll +PNi+
  gi|118431671|ref|NP_148300.2|  87 DLEEKLKKVEREREEALLGLPNIV 110
                                    **********************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 ?   14.3   4.8   9.9e-06     0.044      28      79 ..      44     101 ..      32     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.9e-06
                         APG6_N  28 Yeeflkklkkekkeeek......qdeeleeleeeleklekeeeelleeLkelekeree 79 
                                    +++  ++++++++e ++      ++ee+e+l  e ++l +e+e+l+e+Lk++e+eree
  gi|118431671|ref|NP_148300.2|  44 LLTMVNEVRRRHNEITRmiakagSREERERLIAEAKRLLREREDLEEKLKKVEREREE 101
                                    5555556665555544467777778899999999999999999999999999999986 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.053   2.4e+02      48      65 ..       8      25 ..       6      26 .. 0.92
   2 ?    3.0   2.5     0.019        86      23      52 ..      68      97 ..      58     103 .. 0.80
   3 ?    4.0   0.0    0.0093        42      46      72 ..     231     257 ..     227     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.053
                                   CC-XXXXXXXXXXXXXXX CS
                          DivIC 48 kdLksdedyieerARsel 65
                                   ++L+s++++++e  R++l
  gi|118431671|ref|NP_148300.2|  8 ELLRSNPEALKEHVRKRL 25
                                   789************998 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.019
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                          DivIC 23 kqeiaalqaelaklkaeneeLeaevkdLks 52
                                   ++e+++l ae ++l  e+e+Le+++k+ + 
  gi|118431671|ref|NP_148300.2| 68 REERERLIAEAKRLLREREDLEEKLKKVER 97
                                   678888899999999999999999888754 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0093
                                    HHCC-XXXXXXXXXXXXXXXXXXXXXX CS
                          DivIC  46 evkdLksdedyieerARselglvkpgE 72 
                                    +v dL+  +d+i e+A ++l+l+   E
  gi|118431671|ref|NP_148300.2| 231 RVIDLETFKDAIYEIAGEDLYLIATAE 257
                                    78889889***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3402.63
//
Query:       gi|118431672|ref|NP_148301.2|  [L=107]
Description: hypothetical protein APE_1977.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   0.0      0.026   14.2   0.0    1.4  1  Get5_C    Get5 C-terminal domain


Domain annotation for each model (and alignments):
>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-06     0.026      13      37 ..      22      46 ..      19      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-06
                         Get5_C 13 LknkfkndaearavleRLqKGWelt 37
                                   Lk+ f  d++++a+leRL   We++
  gi|118431672|ref|NP_148301.2| 22 LKAAFYGDPKVSAILERLFEAWESA 46
                                   9******************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 804.86
//
Query:       gi|118431673|ref|NP_148302.2|  [L=138]
Description: hypothetical protein APE_1979.1 [Aeropyrum pernix K1]
Scores for complete 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-21   75.1   1.2    5.3e-21   74.6   1.2    1.3  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.031   14.4   0.0    1.5  2  NifU            NifU-like 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 !   74.6   1.2     6e-25   5.3e-21       2      74 .]      20      97 ..      19      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 6e-25
                                   HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T....-EEEEEE--SSTT-TTHHHHHHHHHHHHC..STT--EEEEEE CS
                 FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg....gkVsvditltypacslaeairadaeaalr.alpgvevveVev 74
                                   +++ +aL++V+DPe++v++++lgl++e+++eg     +++v+++lt ++c++  a+ a +e+a+r a+p++e+veVev
  gi|118431673|ref|NP_148302.2| 20 DRIVEALKEVYDPEIPVNVYDLGLIYEVRVEGprekPRIKVKMSLTAIGCPVSVALPAYVEDAIReAVPEAEDVEVEV 97
                                   789*************************************************************************98 PP

>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.88   7.9e+03      51      63 ..      21      33 ..      17      37 .. 0.60
   2 ?   14.4   0.0   3.5e-06     0.031      28      67 .]      55      94 ..      40      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.88
                                   HHHHHHHHH-TT- CS
                           NifU 51 giekaLkeevpev 63
                                    i +aLke  +++
  gi|118431673|ref|NP_148302.2| 21 RIVEALKEVYDPE 33
                                   4566677766554 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.5e-06
                                   T.EEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                           NifU 28 g.vVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                   + ++kv+++    gCp s   l + +e a++e+vpe + Ve
  gi|118431673|ref|NP_148302.2| 55 KpRIKVKMSLTAIGCPVSV-ALPAYVEDAIREAVPEAEDVE 94
                                   2699************985.677*************99996 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:                        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 0.22s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 995.72
//
Query:       gi|118431674|ref|YP_874920.1|  [L=72]
Description: hypothetical protein APE_1979a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    9.4   5.6          2    8.9   5.6    1.3  1  DUF202    Domain of unknown function (DUF202)
        2.2    8.6   8.4        2.7    8.3   8.0    1.5  1  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.6   0.00023         2      19      67 ..      19      67 ..      14      68 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00023
                         DUF202 19 alialglallrffltgepsalgkilglilivlgiltllv.glvrylrrqr 67
                                   a++++gla++ +  + +  +l +++gl+ i+l+ ++ l  ++ r++r +r
  gi|118431674|ref|YP_874920.1| 19 AIVVAGLAIVLVADSRGSLPL-MVVGLVVIALAPFLSLAvVVARFRRAVR 67
                                   788888999888555555553.9999999999877666615556665554 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.0    0.0003       2.7      36      81 ..       5      50 ..       1      61 [. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0003
                        DUF3040 36 arrrslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvmlag 81
                                   ++rr + + ++l ++++vaGl+++++  +  ++ l vvG+vv++++
  gi|118431674|ref|YP_874920.1|  5 SPRRIVAEKLLLTAAIVVAGLAIVLVADSRGSLPLMVVGLVVIALA 50
                                   4566667779999999999****9999555557*******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 550.85
//
Query:       gi|118431675|ref|NP_148303.2|  [L=268]
Description: competence damage-inducible protein A [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-37  126.9   0.0    5.8e-37  126.5   0.0    1.2  1  MoCF_biosynth   Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.044   14.0   0.6       0.23   11.7   0.6    2.1  1  CinA_KH         Damage-inducible protein CinA KH domain
      0.055   13.9   0.1       0.11   12.9   0.1    1.5  1  Arm-DNA-bind_3  Arm DNA-binding domain
      0.062   12.9   0.1       0.14   11.7   0.1    1.6  2  LDcluster4      SLOG cluster4 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 !  126.5   0.0   1.3e-40   5.8e-37       2     143 ..       9     173 ..       8     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1.3e-40
                                    EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHH CS
                  MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealakl 81 
                                    +i+vG+ell g++ +tn+++l ++l+ lg+ev+++ +vpD  e+i+e++ +al +a+v+ittGG+Gpt dDvt + +a +
  gi|118431675|ref|NP_148303.2|   9 IISVGNELLIGRTINTNAAWLGSRLTLLGFEVERVVTVPDRVEDIAEEVGRALGRARVVITTGGLGPTYDDVTLQGVAMA 88 
                                    9************************************************7777999************************ PP

                                    HSEE-HHHHHHHHHHHHHHCC........................TTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHH CS
                  MoCF_biosynth  82 fekelegfeeafrrvslkpgk........................pvgvapgailsravgktiigLPGspkavkealeei 137
                                    +++ l++++ a+++v++++ k                        pvg apga+++ + g+ +  LPG+p+++++++e+ 
  gi|118431675|ref|NP_148303.2|  89 LGRGLKLHPGALEMVRRFYSKrglgltedrvkmamlpdgaeplenPVGAAPGAVVEAR-GSLVASLPGVPSEMEAMFEKA 167
                                    *******************************************************954.55588**************** PP

                                    HHGGHH CS
                  MoCF_biosynth 138 llpale 143
                                    l+p le
  gi|118431675|ref|NP_148303.2| 168 LRPLLE 173
                                    **9997 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6     5e-05      0.23       6      66 ..     188     254 ..     186     258 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                                    E-S--HHHHHHHHGGGS-BSSS.EEEEEEETTE.....EEEEEE...EEHHHHHHHHH....HHHHH CS
                        CinA_KH   6 tfGigESavaekladlidrenp.tlAiyakege.....vtvRltakaaneeeaealiapveeeirer 66 
                                    ++G+ ES++a  +++  + +    +   ++ +e     v+vR+ a+a++ eea+a + ++ e++r+ 
  gi|118431675|ref|NP_148303.2| 188 VVGVPESSLAPYIKEASRVSPRvYVKSHPQGSEigkplVRVRVLARASTLEEARAEALKALEKVRRG 254
                                    567777777777777666533335555555543222228****************999999999985 PP

>> Arm-DNA-bind_3  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.5e-05      0.11      44      65 ..     234     255 ..     199     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                 Arm-DNA-bind_3  44 avslaeARkkarelraliaqGi 65 
                                    a +l+eAR++a ++++++++G+
  gi|118431675|ref|NP_148303.2| 234 ASTLEEARAEALKALEKVRRGV 255
                                    35******************96 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.2e-05      0.14      17      57 ..      49      90 ..      34     102 .. 0.77
   2 ?   -3.7   0.0       1.8   8.1e+03      27      46 ..     173     193 ..     164     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                     LDcluster4 17 ealelaeelGrliAkegavlltGgrt.GvmeaaskGakeagG 57
                                   +++++aee+Gr++ ++++v+ tGg +  + ++  +G+  a G
  gi|118431675|ref|NP_148303.2| 49 RVEDIAEEVGRALGRARVVITTGGLGpTYDDVTLQGVAMALG 90
                                   4567********************965666666666666555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.8
                     LDcluster4  27 rliAkegavlltGgrt.Gvme 46 
                                    ++iA  gav+ +G    Gv+e
  gi|118431675|ref|NP_148303.2| 173 EEIAPPGAVVECGIAVvGVPE 193
                                    577778888877755447776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1990.20
//
Query:       gi|118431676|ref|NP_148306.2|  [L=194]
Description: hypothetical protein APE_1984.1 [Aeropyrum pernix K1]
Scores for complete 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   37.6   0.1    2.5e-09   36.9   0.1    1.4  1  FR47             FR47-like protein
    4.9e-09   36.5   0.7    8.8e-09   35.6   0.7    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.4e-07   31.1   1.1    3.3e-07   30.6   0.5    1.6  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.5e-05   24.2   0.1    3.7e-05   23.6   0.1    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0031   18.2   0.2     0.0071   17.0   0.0    1.7  2  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.055   13.6   0.0    1.7  2  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   8.5e-13   2.5e-09      18      82 ..      62     125 ..      39     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 8.5e-13
                                    E-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                           FR47  18 rkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfekiee 82 
                                    r + g ++ + vlp +r+rGlg+ lv++  +++ +  +  ++ +   Nt+s r++++lG++++  
  gi|118431676|ref|NP_148306.2|  62 RVELGVIYYVVVLPRARGRGLGKMLVSSCEERLGAL-HFYVATIELRNTASARMFQSLGYRVMAD 125
                                    445699**************************9876.678899******************9854 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.7   2.9e-12   8.8e-09      34     117 .]      40     120 ..      14     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.9e-12
                                    EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHH CS
                 Acetyltransf_1  34 gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYe 113
                                     +lva+  ge +G i ++     + + ++i+ ++V p +rg+GlG++L+  +eer+    +   v+++e  n+a+ r+++
  gi|118431676|ref|NP_148306.2|  40 VGLVARLAGEEAGAIICYRAGS-RVELGVIYYVVVLPRARGRGLGKMLVSSCEERLGALHF--YVATIELRNTASARMFQ 116
                                    5667777788888887777777.7888***************************9999966..34455556********8 PP

                                    HTTE CS
                 Acetyltransf_1 114 klGF 117
                                     lG+
  gi|118431676|ref|NP_148306.2| 117 SLGY 120
                                    8*98 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.5   1.1e-10   3.3e-07       6      75 ..      42     121 ..      23     122 .. 0.73
   2 ?   -2.8   0.0         3   8.9e+03      29      34 ..     150     156 ..     127     169 .. 0.50

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.1e-10
                                    EEEEETTEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHH.HTT.SEEE..EE.EEEETHHHHHHHHHHTTEE CS
                 Acetyltransf_7   6 fVaeddgkivGfialslld.....aeitrlaVdpeyrgkGiGraLle.aae.kgii..le.qlelnaekaikfYeklGFe 75 
                                    +Va+  g++ G i++++ +     + i +++V+p +rg+G+G+ L+  ++e  g     + + el+++++++++++lG++
  gi|118431676|ref|NP_148306.2|  42 LVARLAGEEAGAIICYRAGsrvelGVIYYVVVLPRARGRGLGKMLVSsCEErLGALhfYVaTIELRNTASARMFQSLGYR 121
                                    5777778888988888877887766666799***************94333455212322333454447899*******8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                                    E.EEE-G CS
                 Acetyltransf_7  29 r.laVdp 34 
                                      +a+++
  gi|118431676|ref|NP_148306.2| 150 DlIAIKE 156
                                    1355544 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   1.2e-08   3.7e-05      34     109 ..      42     123 ..      13     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                Acetyltransf_10  34 lvaeeggkivGviel.rdgs.....hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYeklGF 106
                                    lva   g+ +G+i   r gs      i+ ++V p +rg+G+gk+L+  +ee++   +  + +++++ +  a +++++lG+
  gi|118431676|ref|NP_148306.2|  42 LVARLAGEEAGAIICyRAGSrvelgVIYYVVVLPRARGRGLGKMLVSSCEERLGALHFYVaTIELRNTASA-RMFQSLGY 120
                                    55666666677774435555777889999***********************9777777556666666555.678***** PP

                Acetyltransf_10 107 kav 109
                                    +++
  gi|118431676|ref|NP_148306.2| 121 RVM 123
                                    987 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.4e-06    0.0071      54     137 ..      40     120 ..       2     121 .. 0.73
   2 ?   -1.6   0.0       1.4   4.1e+03      66      77 ..     161     172 ..     126     191 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                 Acetyltransf_3  54 ygwaivlkdtgviGsvglrdleeedeeaelgymla.psfwgkGyateavralleyafeelglerlvavidkeNeaSirvl 132
                                    +g++ +l ++ + G + ++++  + e + + y++  p ++g+G+++  v+++ e +     l+  va+i+ +N+aS+r +
  gi|118431676|ref|NP_148306.2|  40 VGLVARLAGE-EAGAIICYRAGSRVELGVIYYVVVlPRARGRGLGKMLVSSCEERL---GALHFYVATIELRNTASARMF 115
                                    3333322333.588888888888766677778887688*************99999...55789**************** PP

                 Acetyltransf_3 133 eklGf 137
                                    ++lG+
  gi|118431676|ref|NP_148306.2| 116 QSLGY 120
                                    ****8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                 Acetyltransf_3  66 iGsvglrdleee 77 
                                    +G   l ++e++
  gi|118431676|ref|NP_148306.2| 161 VGLEILSEAEPD 172
                                    444444444444 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 ?   13.6   0.0   1.8e-05     0.055      13      49 ..      53      90 ..      43     101 .. 0.76
   2 ?   -2.8   0.0       2.4   7.2e+03      62      69 ..     143     150 ..     140     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                Acetyltransf_CG 13 afleYevrkegvl.dfthTeVpeelrGkGiAkkLvkaa 49
                                   a++ Y++    +l +++ ++V ++ rG+G++k Lv ++
  gi|118431676|ref|NP_148306.2| 53 AIICYRAGSRVELgVIYYVVVLPRARGRGLGKMLVSSC 90
                                   6667763333333389*******************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                Acetyltransf_CG  62 ptCsyvaa 69 
                                    +tCsy ++
  gi|118431676|ref|NP_148306.2| 143 ATCSYEED 150
                                    57888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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:                         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 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1534.42
//
Query:       gi|118431677|ref|YP_874921.1|  [L=79]
Description: hypothetical protein APE_1984a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 657.34
//
Query:       gi|118431678|ref|NP_148307.2|  [L=115]
Description: hypothetical protein APE_1985.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.0       0.07   13.1   0.0    1.2  1  Mrr_cat   Restriction endonuclease


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 ?   13.1   0.0   3.9e-06      0.07      13      80 ..      23      83 ..      19     111 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-06
                                   HHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SE CS
                        Mrr_cat 13 vaellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgadk 80
                                   va  ++  Gy+ ve++++s +  +++ a +++   e ++v++  ++++v v +V+el++a  +    k
  gi|118431678|ref|NP_148307.2| 23 VAAGYRMAGYE-VEVVDGSPEATANFKAWRRG---ESLVVRVYMKSGRVPVSVVEELASASGGS---K 83
                                   56678999**9.****************9976...89********************9997665...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 889.14
//
Query:       gi|118431679|ref|NP_148308.2|  [L=172]
Description: nicotinamide-nucleotide adenylyltransferase [Aeropyrum pernix K1]
Scores for 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-10   41.0   0.0    2.3e-10   40.8   0.0    1.4  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.3e-14   2.3e-10       2      58 ..       5      60 ..       4     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.3e-14
                                   EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH CS
                CTP_transf_like  2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela 58
                                   + G+F+p+H+GHl ++++a++ +  +l+ +v  + ++    +++++a eR+em++l 
  gi|118431679|ref|NP_148308.2|  5 IFGRFQPFHKGHLSIVKWAFERGYSELVFLVGMASENYTP-RNPFTAGERIEMIRLS 60
                                   68***********************977777777777766.99***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1412.24
//
Query:       gi|118431680|ref|NP_148309.2|  [L=373]
Description: peptide chain release factor 1 [Aeropyrum pernix K1]
Scores for complete 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-45  153.2   0.3      8e-45  152.4   0.3    1.4  1  eRF1_2          eRF1 domain 2
    2.9e-24   85.7   2.7    2.5e-23   82.7   0.5    3.0  3  eRF1_3          eRF1 domain 3
    1.2e-17   64.4   0.0    5.7e-17   62.2   0.0    2.1  3  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    1.9e-10   41.1   0.0    7.3e-10   39.2   0.0    1.9  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    3.3e-05   24.1   0.1    0.00083   19.6   0.1    2.7  2  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
     0.0011   19.0   0.0      0.002   18.1   0.0    1.5  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
      0.059   13.6   0.0       0.17   12.1   0.0    1.9  1  Clr5            Clr5 domain
      0.078   13.3   0.1         14    6.1   0.0    2.6  2  ATP-synt_F      ATP synthase (F/14-kDa) subunit


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 !  152.4   0.3   3.6e-48     8e-45       2     131 ..     143     274 ..     142     276 .. 0.98

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 3.6e-48
                                    EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH.HCHTTTESEE CS
                         eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafl.lvdkdklkgi 80 
                                    +g+i++++++Atigllkg+r evlk++e+ vP+Khk+Ggqs+rr+eR++e++++ef+kkv+e+a++ ++ l++k++lkg+
  gi|118431680|ref|NP_148309.2| 143 IGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKKVGEEASNLLVpLAEKGVLKGV 222
                                    79****************************************************************************** PP

                                    EEEESSTHHHHHHHHHHHHHHHHTCCEE.EEE-S-TSCHHHHHHHHCCHHHH CS
                         eRF1_2  81 ilagpgfvkeefldkdlldaelkkkvik.lvdvsyggesglnevlekaaevl 131
                                    i+agpg +k+ef+++++ld++lkk  +  lvdv+y+g +gl+e+++ka++v+
  gi|118431680|ref|NP_148309.2| 223 IVAGPGLAKQEFVEGNYLDYRLKKILAPeLVDVAYQGLQGLKEAVMKAEKVV 274
                                    ************************99888*******************9987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.7   3.9e+03       3      20 ..     124     141 ..     122     145 .. 0.81
   2 ?   -3.3   0.0       5.4   1.2e+04       6      16 ..     193     203 ..     178     208 .. 0.71
   3 !   82.7   0.5   1.1e-26   2.5e-23       4     113 .]     282     370 ..     279     370 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHHCTCS CS
                         eRF1_3   3 qekklleefleelakdtg 20 
                                     +k+ +++fle + +d++
  gi|118431680|ref|NP_148309.2| 124 TDKRFITDFLEDMVEDNN 141
                                    57899999***9999965 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.4
                                    HHHHHHHHHHH CS
                         eRF1_3   6 klleefleela 16 
                                    ++++ef++++ 
  gi|118431680|ref|NP_148309.2| 193 QMVDEFFKKVG 203
                                    56677776665 PP

  == domain 3  score: 82.7 bits;  conditional E-value: 1.1e-26
                                    HHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT- CS
                         eRF1_3   4 ekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesga 83 
                                     ++++eef  +lak+tg++vYG+++v++alemgAv+tLL++e+ e+                     +ee+ve++++sga
  gi|118431680|ref|NP_148309.2| 282 AVNAMEEFKLHLAKGTGMIVYGEKDVEAALEMGAVKTLLIHESRED---------------------LEEWVEKAKSSGA 340
                                    6799**************************************9887.....................579********** PP

                                    EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                         eRF1_3  84 kveiisseseeGeqlvkafgGiaaiLRykv 113
                                    +v++++++ +e+e+++k+fgG+a+iLR+++
  gi|118431680|ref|NP_148309.2| 341 QVIVVPESLAEAEWFLKTFGGLAGILRFRI 370
                                    ****************************96 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.8   6.3e+03      53      68 ..      69      84 ..      60     104 .. 0.56
   2 !   62.2   0.0   2.5e-20   5.7e-17       3     127 ..     143     273 ..     141     276 .. 0.91
   3 ?   -1.0   0.0      0.87     2e+03      51     104 ..     274     326 ..     271     338 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                        acVLRF1 53 nqadalleavaeaaar 68
                                   + ++++l+a+ ++++ 
  gi|118431680|ref|NP_148309.2| 69 QAVKRALSAAMDRLQM 84
                                   3445555555555553 PP

  == domain 2  score: 62.2 bits;  conditional E-value: 2.5e-20
                        acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae.....v 77 
                                    +g+++v r+  ++g+++g +l+  k+ +  v g+++ GG+Sq+R++R +e+ +d+ +++v e+a +ll + +++     v
  gi|118431680|ref|NP_148309.2| 143 IGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKKVGEEASNLLVPLAEKgvlkgV 222
                                    7999****************************************************************65555566788* PP

                        acVLRF1  78 vlgGdrslvaevledar.laplatlareelldvpdprravLedavrrarav 127
                                    +++G+  + +e+ e +  + +l++   +el+dv+    + L++av +a++v
  gi|118431680|ref|NP_148309.2| 223 IVAGPGLAKQEFVEGNYlDYRLKKILAPELVDVAYQGLQGLKEAVMKAEKV 273
                                    ***************7635669999999******999*******9998876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.87
                        acVLRF1  51 renqadalleavaeaaarllaeesaevvlgGdrslvaevledarlaplatlare 104
                                    +e q+ + + ++ e+ + +l ++   +++ G++ + a+++  a ++ l +  re
  gi|118431680|ref|NP_148309.2| 274 VEAQMYRDAVNAMEEFKLHL-AKGTGMIVYGEKDVEAALEMGAVKTLLIHESRE 326
                                    56666666666666666666.444447788888888888777665555555555 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 ?   -3.0   0.0       3.6     8e+03      64     101 ..      66     103 ..      64     107 .. 0.63
   2 !   39.2   0.0   3.2e-13   7.3e-10       6     105 ..     133     235 ..     128     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                 baeRF_family10  64 reeeqaerhlkevAellaklleergverlvlgGdeeet 101
                                    r ++ ++r+l ++ + l+ l ++ +   ++ +G +  t
  gi|118431680|ref|NP_148309.2|  66 RTRQAVKRALSAAMDRLQMLTSTPPNGLVLFCGEDMST 103
                                    56666777777777777777777666666666666555 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 3.2e-13
                 baeRF_family10   6 LlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklle 85 
                                    L + ++++  +g+++v+r++a +    + +le  +e+eg vpg++k gg+ sq+r++r  e+++++++k+v+e + +ll 
  gi|118431680|ref|NP_148309.2| 133 LEDMVEDNNAIGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQ-SQRRYERIIEQMVDEFFKKVGEEASNLLV 211
                                    55677889999***************************************.***********************999864 PP

                 baeRF_family10  86 erg....verlvlgGdeeetaall 105
                                    +      ++ ++++G+  ++++++
  gi|118431680|ref|NP_148309.2| 212 PLAekgvLKGVIVAGPGLAKQEFV 235
                                    333333699999999988877776 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.22   4.9e+02      49      70 ..      77      97 ..      61     100 .. 0.79
   2 !   19.6   0.1   3.7e-07   0.00083       1      51 [.     300     347 ..     300     351 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                  SpoU_sub_bind 49 vdkekLdklsgtanHQGvvaev 70
                                   +  ++L+ l+ + +++G+v+ +
  gi|118431680|ref|NP_148309.2| 77 AAMDRLQMLT-STPPNGLVLFC 97
                                   5677888899.7778***9987 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3.7e-07
                  SpoU_sub_bind   1 liyGlhaVleaLksgrriekllvtegradkrleellklakkrgikvelvdk 51 
                                    ++yG + V++aL+ g  +++ll++e+r+d +  e++++ak+ g +v+ v++
  gi|118431680|ref|NP_148309.2| 300 IVYGEKDVEAALEMGA-VKTLLIHESREDLE--EWVEKAKSSGAQVIVVPE 347
                                    69************96.*********77777..****************97 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.8e-07     0.002      10     128 ..      29     136 ..      18     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.8e-07
                                    TTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT...SSEEEEEEE CS
                         eRF1_1  10 kdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd...agvlrisGk 86 
                                       + +++L++++   l++++ l+++++s+  +++ k +r         + vk +L   + ++++ ++   +g++ ++G+
  gi|118431680|ref|NP_148309.2|  29 APATVLLSLYIPPGRPLSDVMTLLRQEYSITDNIKLKRTR---------QAVKRALSAAMDRLQMLTStppNGLVLFCGE 99 
                                    5567789******************************999.........99999*****999999999788899999995 PP

                                    EEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                         eRF1_1  87 vieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                          ++ +g+f  + + +++p++++ ++ +++f ++ L+++
  gi|118431680|ref|NP_148309.2| 100 ------DMSTGKFECFMFSPPEPIRVFYYRtDKRFITDFLEDM 136
                                    ......345789****************998999999999987 PP

>> Clr5  Clr5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.7e-05      0.17       5      37 ..      27      59 ..      22      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                           Clr5  5 WeahkatIrrLYleenrsLkdvmeiMeeehgFk 37
                                   W a   ++ +LY+  +r+L+dvm+ +++e++ +
  gi|118431680|ref|NP_148309.2| 27 WSAPATVLLSLYIPPGRPLSDVMTLLRQEYSIT 59
                                   7777778899********************987 PP

>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0063        14      23      50 ..     123     151 ..     105     158 .. 0.87
   2 ?    4.3   0.0     0.022        50       3      53 ..     301     351 ..     296     353 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0063
                                    CSSHHHHHHHHHHHHH.HTTEEEEEEEHH CS
                     ATP-synt_F  23 vtdeeeieealkelle.redigiilitek 50 
                                     td+  i + l++++e ++ igii+++ +
  gi|118431680|ref|NP_148309.2| 123 RTDKRFITDFLEDMVEdNNAIGIIIVERD 151
                                    78888999*******98999*****9876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.022
                                    EEESHHHHHHHHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHC CS
                     ATP-synt_F   3 vIGdedtvtgfrlaGvgeve.vtdeeeieealkelleredigiilitekiae 53 
                                    v G++d+   + +  v++    +++e++ee ++++  +++ ++i++ e +ae
  gi|118431680|ref|NP_148309.2| 301 VYGEKDVEAALEMGAVKTLLiHESREDLEEWVEKAK-SSGAQVIVVPESLAE 351
                                    445666666666666666655667999******997.999********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 2777.81
//
Query:       gi|14601769|ref|NP_148310.1|  [L=111]
Description: hypothetical protein APE_1990 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00024   21.1   0.2    0.00035   20.5   0.2    1.2  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
      0.029   14.7   0.0      0.038   14.3   0.0    1.2  1  ArsD           Arsenical resistance operon trans-acting repre
      0.066   12.9   0.1       0.24   11.1   0.0    1.8  2  PEP-utilizers  PEP-utilising enzyme, mobile 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 !   20.5   0.2   5.9e-08   0.00035      16      72 ..      21      77 ..      17      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.9e-08
                                  HHHHHHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHH CS
                 Thioredoxin_3 16 lekavkeaaaekgikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeir 72
                                  +++a++ +a e g+ +ev  v+ +++  + + +  P l++dg vv++G+vps ee+ 
  gi|14601769|ref|NP_148310.1| 21 VREAAAILAREYGVPLEVSVVEIPSDSRESESRGLPVLMVDGIVVAEGRVPSIEEVV 77
                                  566777778888****99999999999999999*********************985 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    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      68      95 ..      50      77 ..      39      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                          ArsD 68 kgaeaLPlvlvdgeivktgrYptreela 95
                                  + +  LP+++vdg +v +gr p+ ee+ 
  gi|14601769|ref|NP_148310.1| 50 SESRGLPVLMVDGIVVAEGRVPSIEEVV 77
                                  45678******************99986 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 ?   11.1   0.0     4e-05      0.24      38      57 ..      25      47 ..      21      63 .. 0.62
   2 ?    0.6   0.0     0.079   4.7e+02      18      32 ..      52      68 ..      44      77 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                  HHHHHHHTT--E...EE--SSHH CS
                 PEP-utilizers 38 aAivArelgiPa...Vvgvgeat 57
                                  aAi+Are+g+P    Vv +++ +
  gi|14601769|ref|NP_148310.1| 25 AAILAREYGVPLevsVVEIPSDS 47
                                  8**********943444444433 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.079
                                  HTTS-..GEEEEEES-- CS
                 PEP-utilizers 18 iagld..kaaGivterG 32
                                    gl+   + Giv+++G
  gi|14601769|ref|NP_148310.1| 52 SRGLPvlMVDGIVVAEG 68
                                  55666667899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 851.55
//
Query:       gi|118431681|ref|NP_148311.2|  [L=314]
Description: ornithine carbamoyltransferase [Aeropyrum pernix K1]
Scores for complete 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-57  192.7   0.0    8.7e-57  191.6   0.0    1.5  2  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    8.1e-48  162.2   0.0    1.4e-47  161.5   0.0    1.4  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 ?   -2.3   0.0      0.46   4.1e+03      14      40 ..      61      87 ..      56     119 .. 0.76
   2 !  191.6   0.0   9.7e-61   8.7e-57       1     156 [.     156     311 ..     156     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.46
                                   HHHHHHHHHHHHCT-EEEEES-TTSSH CS
                         OTCace 14 nvanslikllarlgmdvvlvaPkglep 40
                                   ++  sl  ++a+lg + v+++P +++ 
  gi|118431681|ref|NP_148311.2| 61 RTRISLEVAVAQLGGHTVYMTPSETQL 87
                                   566677888899999999999988543 PP

  == domain 2  score: 191.6 bits;  conditional E-value: 9.7e-61
                                    CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--S CS
                         OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvw 80 
                                    +g+k+afvGd+  nv++sl+ + ++lg+++++++P++++pd+ +l+ a k a++sggs++i +d+ eav gaDvvytdvw
  gi|118431681|ref|NP_148311.2| 156 EGVKLAFVGDGADNVLHSLLLAGSKLGLHITVATPPQIRPDERILSIALKAAEESGGSVEIVSDPYEAVRGADVVYTDVW 235
                                    699*******99******************************************************************** PP

                                    SETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                         OTCace  81 vsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                    vsmg+e+  ee+++ lk+yqv+++l++++  +ai++HcLPakrg+EvtdeV+d+p s+v++qaeNrlh++kA+l l
  gi|118431681|ref|NP_148311.2| 236 VSMGQESMAEEKVQLLKPYQVNAKLMEATGGRAIFMHCLPAKRGQEVTDEVIDGPWSAVWDQAENRLHAHKAVLSL 311
                                    **************************************************************************87 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 !  161.5   0.0   1.5e-51   1.4e-47       1     148 []       9     150 ..       9     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 1.5e-51
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT.TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCT CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk.ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediql 79 
                                    rhll l+d++ eei+++++l  e+k++  + e+  + l+g++++llFe+pStRTr+S evA+++lGg++++++ ++++ql
  gi|118431681|ref|NP_148311.2|   9 RHLLWLADYTGEEIRHMVELTLEMKRRYYAgERVIPVLRGRSVGLLFEKPSTRTRISLEVAVAQLGGHTVYMT-PSETQL 87 
                                    8************************999888888999************************************.879999 PP

                                    TTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                       OTCace_N  80 ssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                    +     r+E+++Dtarvlsry daiv+R++++++lee+a++as+pviN++ +d  HP+Qa+aD+ ti e
  gi|118431681|ref|NP_148311.2|  88 G-----RGETVADTARVLSRYLDAIVARVRSHKTLEEMARHASIPVINGL-SDLTHPLQAIADMATILE 150
                                    9.....78******************************************.***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2306.48
//
Query:       gi|118431682|ref|NP_148312.2|  [L=193]
Description: hypothetical protein APE_1995.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.7   0.0    1.3  1  HTH_45        Winged helix-turn-helix
       0.02   14.7   1.8      0.052   13.4   1.8    1.7  1  HTH_IclR      IclR helix-turn-helix domain
      0.021   14.9   0.5      0.032   14.3   0.5    1.3  1  HemN_C        HemN C-terminal domain
       0.19   10.7   0.0       0.23   10.4   0.0    1.1  1  Topoisom_bac  DNA topoisomerase


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 ?   14.7   0.0   4.9e-06     0.022      29      75 ..      41      87 ..      23      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-06
                         HTH_45 29 anLsykllnkYLdmLvekglikkskekYvlTekGlelleklkeleel 75
                                     L    ++  L+++ e gl++k +  ++ T +G+el ++l +++++
  gi|118431682|ref|NP_148312.2| 41 LGLGEASTRTLLEIMGELGLVEKAGRGFQPTSRGRELAKTLSRVIRV 87
                                   56677788999*******************************99986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.8   1.2e-05     0.052      14      50 ..      29      63 ..      19      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                   TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      ++l+ + lAr +gl  ++++ lL  + elG+ve+
  gi|118431682|ref|NP_148312.2| 29 G--ERLGRQRLARSLGLGEASTRTLLEIMGELGLVEK 63
                                   3..4466899*************************97 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   7.2e-06     0.032      37      65 ..      47      75 ..      27      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-06
                         HemN_C 37 llaaaleklqeqGLLeldggrlrltprGr 65
                                   + +  le + e GL+e +g+++++t rGr
  gi|118431682|ref|NP_148312.2| 47 STRTLLEIMGELGLVEKAGRGFQPTSRGR 75
                                   348899**********************8 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   5.2e-05      0.23     326     382 ..      18      84 ..       3      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.2e-05
                   Topoisom_bac 326 yteasLikameka...........giGtpaTraeiieklvergYverkkkslvptelGkalvellekf 382
                                    y  a+ ++++e +           g+G  +Tr + +e + e g ve+ ++ ++pt+ G++l+++l+++
  gi|118431682|ref|NP_148312.2|  18 YHAARALNLLEGErlgrqrlarslGLGEASTR-TLLEIMGELGLVEKAGRGFQPTSRGRELAKTLSRV 84 
                                    5555556666666666666666679**99998.799***********88***************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1515.18
//
Query:       gi|118431683|ref|NP_148313.2|  [L=255]
Description: hypothetical protein APE_1996.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0033   17.4   0.2      0.048   13.7   0.0    2.9  4  HTH_45     Winged helix-turn-helix
     0.0098   15.8   0.2        1.6    8.7   0.0    3.2  3  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.077   12.9   0.0    2.2  2  MarR_2     MarR family
      0.025   14.6   0.0       0.12   12.4   0.0    2.1  2  KorB       KorB domain
      0.056   13.7   0.1       0.23   11.7   0.1    2.0  2  DUF4096    Putative transposase of IS4/5 family (DUF4096)
      0.082   12.9   0.3       0.24   11.4   0.3    1.7  1  Med31      SOH1
      0.094   12.7   0.1        0.4   10.7   0.0    2.1  4  HTH_Crp_2  Crp-like helix-turn-helix domain
       0.14   11.9   0.1       0.26   11.1   0.1    1.4  1  GAD-like   GAD-like 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 !   13.7   0.0   2.1e-05     0.048      31      69 ..      57      95 ..      30     102 .. 0.80
   2 ?   -2.9   0.0       3.2   7.2e+03      36      52 ..     111     127 ..     108     130 .. 0.68
   3 ?   -1.2   0.0      0.91     2e+03      16      45 ..     173     202 ..     165     205 .. 0.73
   4 ?   -1.2   0.0      0.93   2.1e+03      32      49 ..     207     224 ..     201     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                         HTH_45 31 LsykllnkYLdmLvekglikkskekYvlTekGlellekl 69
                                    s + +++YL++   +g+++ +++ ++lT  G+e+ +++
  gi|118431683|ref|NP_148313.2| 57 YSTRYISSYLSYWKTRGYVEYESGLWYLTTLGEEYAREV 95
                                   5667889***************************98875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                         HTH_45  36 lnkYLdmLvekglikks 52 
                                    +++ L+ L +k  i+ +
  gi|118431683|ref|NP_148313.2| 111 AQRILNSLPDKTAINSK 127
                                    66778888888777654 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.91
                         HTH_45  16 segeakkTkimykanLsykllnkYLdmLve 45 
                                    +e+ea+  + +++ + ++ ++  YLd+L+e
  gi|118431683|ref|NP_148313.2| 173 DEEEAEIMRFLLDHYAKWGTTYIYLDQLQE 202
                                    466666667777777788899999999976 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.93
                         HTH_45  32 sykllnkYLdmLvekgli 49 
                                    +++ l k L  L+ kg+i
  gi|118431683|ref|NP_148313.2| 207 DFQWLVKNLRSLQTKGFI 224
                                    67888999999**99998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0007       1.6      15      56 ..      38      79 ..      34      87 .. 0.90
   2 ?    1.1   0.0      0.17   3.7e+02      38      57 ..     110     129 ..      81     139 .. 0.72
   3 ?    1.9   0.0     0.093   2.1e+02      42      55 ..     214     227 ..     211     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0007
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   l++l  +p++a eia +lg +   + ++L+  + +G+Ve e 
  gi|118431683|ref|NP_148313.2| 38 LVMLLAKPMRAAEIAGILGYSTRYISSYLSYWKTRGYVEYES 79
                                   5677899*******************************9886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                                    CHHHHHHHHHHCTSEEEESS CS
                           TrmB  38 kvYevLrsLedkGlVerekg 57 
                                     ++++L+sL dk  ++ +++
  gi|118431683|ref|NP_148313.2| 110 VAQRILNSLPDKTAINSKRE 129
                                    58999****99998887765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.093
                                    HHHHHHHCTSEEEE CS
                           TrmB  42 vLrsLedkGlVere 55 
                                     LrsL  kG++++ 
  gi|118431683|ref|NP_148313.2| 214 NLRSLQTKGFIYIY 227
                                    59*********976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.4e-05     0.077      11      56 ..      38      80 ..      25      81 .. 0.84
   2 ?   -1.5   0.0       1.1   2.4e+03      40      56 ..     213     229 ..     209     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                                   HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   L  L + p   ++++e+a  lg+s  ++s  l     +G+ve+++g
  gi|118431683|ref|NP_148313.2| 38 LVMLLAKP---MRAAEIAGILGYSTRYISSYLSYWKTRGYVEYESG 80
                                   44455555...9******************************9976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                                    HHHHHHHHTTSEEEEES CS
                         MarR_2  40 rilkrLvaaGLverrpg 56 
                                    + l+ L+ +G++   ++
  gi|118431683|ref|NP_148313.2| 213 KNLRSLQTKGFIYIYRD 229
                                    57999*****9976655 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.5e-05      0.12       4      33 ..      46      75 ..      43      81 .. 0.88
   2 ?   -1.4   0.0       1.1   2.5e+03      57      81 ..     174     202 ..     167     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                           KorB  4 vkqadIAkaLGksksfvslylklldvpdyl 33
                                   +  a+IA +LG s  ++s yl++ +   y+
  gi|118431683|ref|NP_148313.2| 46 MRAAEIAGILGYSTRYISSYLSYWKTRGYV 75
                                   6789*******************9987776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                           KorB  57 khpaevrafv....aengeagltrsavrr 81 
                                    +++ae+ +f+    a++g   +++++ ++
  gi|118431683|ref|NP_148313.2| 174 EEEAEIMRFLldhyAKWGTTYIYLDQLQE 202
                                    55666666666666666666666666554 PP

>> DUF4096  Putative transposase of IS4/5 family (DUF4096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0001      0.23       1      39 [.       1      41 [.       1      45 [. 0.84
   2 ?   -2.0   0.0       1.9   4.3e+03      51      66 ..     186     201 ..     181     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                        DUF4096  1 LtDeqWellepllpepkkrr..GrprkvdlrevlngIlyvl 39
                                   ++D++W+ ++++l+++++++   r r+ ++ +++++Il +l
  gi|118431683|ref|NP_148313.2|  1 MSDDLWRAVREYLEQHEEAKakARGRRGPRSRLVDAILVML 41
                                   69***********99998889955555578999****9887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                        DUF4096  51 dfgswstvyrrfrrWs 66 
                                    ++ +w t y ++ + +
  gi|118431683|ref|NP_148313.2| 186 HYAKWGTTYIYLDQLQ 201
                                    6899999999988766 PP

>> Med31  SOH1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00011      0.24      39      77 ..      64      99 ..      57     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                   HGGGGGSTTCCCTT--CHHHHHHHHHHSSTTCCCCTCTC CS
                          Med31 39 kYLeywkepeYakfltyPqcLkaLellqeeefrkelkkp 77
                                   +YL+ywk++ Y+   +y + L +L+ l ee  r+ l ++
  gi|118431683|ref|NP_148313.2| 64 SYLSYWKTRGYV---EYESGLWYLTTLGEEYAREVLDRE 99
                                   6*******9986...577899999999988887766554 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018       0.4      21      53 ..      45      77 ..      16      87 .. 0.85
   2 ?   -3.7   0.0       5.7   1.3e+04      40      52 ..     113     125 ..     111     130 .. 0.72
   3 ?   -3.5   0.0         5   1.1e+04       4      13 ..     180     189 ..     179     200 .. 0.68
   4 ?   -3.1   0.0       3.5   7.9e+03      40      52 ..     213     225 ..     209     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr 53
                                   p+  +e+A +lG +   +s  ls +k +g+++ 
  gi|118431683|ref|NP_148313.2| 45 PMRAAEIAGILGYSTRYISSYLSYWKTRGYVEY 77
                                   89999*************************994 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.7
                                    HHHHHHHHTTSEE CS
                      HTH_Crp_2  40 rilseLkreglis 52 
                                    ril+ L ++  i 
  gi|118431683|ref|NP_148313.2| 113 RILNSLPDKTAIN 125
                                    8888888887776 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5
                                    HHHHHHHHCT CS
                      HTH_Crp_2   4 ArfLlrlaer 13 
                                     rfLl+++++
  gi|118431683|ref|NP_148313.2| 180 MRFLLDHYAK 189
                                    6899988554 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 3.5
                                    HHHHHHHHTTSEE CS
                      HTH_Crp_2  40 rilseLkreglis 52 
                                    + l+ L+ +g i 
  gi|118431683|ref|NP_148313.2| 213 KNLRSLQTKGFIY 225
                                    5688899988886 PP

>> GAD-like  GAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00011      0.26      27      55 ..      57      85 ..      42      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                       GAD-like 27 ykgklPeklleywrekGfcgygdglfwlv 55
                                   y  +   ++l+yw+++G+  y  gl +l+
  gi|118431683|ref|NP_148313.2| 57 YSTRYISSYLSYWKTRGYVEYESGLWYLT 85
                                   666666789***************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1894.74
//
Query:       gi|14601773|ref|NP_148314.1|  [L=410]
Description: hypothetical protein APE_1998 [Aeropyrum pernix K1]
Scores for complete 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-91  306.2   0.0    3.2e-91  305.9   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    7.5e-24   83.8   0.0    1.4e-23   82.9   0.0    1.5  1  Nre_C     Archaeal Nre, C-terminal
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.26   11.1   0.0    1.4  1  HrpE      HrpE/YscL/FliH and V-type ATPase subunit E


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 !  305.9   0.0   5.3e-95   3.2e-91       1     270 []      18     291 ..      18     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 305.9 bits;  conditional E-value: 5.3e-95
                         Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg..dasvldspekwl..glsledi 76 
                                   Lcgl++cpil++lr+++++++++  s+e++Gs+pPs++VG++gYP V+++++vpp +   +a+ +++p  w   +++l  i
  gi|14601773|ref|NP_148314.1|  18 LCGLPSCPILDRLRSQARSLERArWSREVQGSTPPSILVGERGYPGVRLYYMVPPGVAgpEAQRYEDPLGWRssRTPLGSI 98 
                                   8********************9999******************************9999*************999****** PP

                         Nre_N  77 iklrlslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprk 157
                                   ++lr++lv g  +++ ++++e  + +ei  +alse+pvd+ +el++ p ++++fd++++PvGp+a++++++v++np+++++
  gi|14601773|ref|NP_148314.1|  99 VRLRSELVAGVLRADARRPHELLYQREIGPAALSERPVDSFLELARLPVPRVSFDGYTKPVGPTAPARRVEVEGNPRLEKP 179
                                   *******************9666679******************************************************* PP

                         Nre_N 158 veklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfs 238
                                   ve+++++ d kAe   +eL+++gv+vy+iqr+LS+G+LG+ + rrlVPTrW+ITAvd++++++l++ +k++pei  vev+ 
  gi|14601773|ref|NP_148314.1| 180 VERAIWE-DEKAEVMAWELFNRGVNVYTIQRALSIGFLGRLRARRLVPTRWAITAVDEMLSRRLRRLLKTAPEIGGVEVYF 259
                                   *******.************************************************************************* PP

                         Nre_N 239 geylgNrflviLaPgkwsfelvEawapgslwn 270
                                   +eyl+Nrfl+iL Pg+  +e++E+w+p+++w+
  gi|14601773|ref|NP_148314.1| 260 SEYLHNRFLIILKPGPGWMEWIEIWHPHTVWT 291
                                   *******************************6 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   2.3e-27   1.4e-23       5     110 .]     308     408 ..     304     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 2.3e-27
                         Nre_C   5 grkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevseklk 85 
                                   grk++ +  G++ aa+l+vle+L++++r+a+vi++re+ p+Y+aPvG+W++Re+v++al++kp   +     l+++++kl 
  gi|14601773|ref|NP_148314.1| 308 GRKNMED--GGFSAAKLPVLEHLYSRGRRADVIIVREVLPQYYAPVGNWHIRETVKHALAQKPLAKNPQPGELDALASKLI 386
                                   5666666..******************************************************777777777777777776 PP

                         Nre_C  86 lplkkllkkskllkelkkqktLddF 110
                                       ++  ++++ + +k +ktL+++
  gi|14601773|ref|NP_148314.1| 387 G---EWGLAKRISQLMKPRKTLESY 408
                                   4...677777777777777888766 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.4e-05      0.26      76     111 ..     215     250 ..     210     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.4e-05
                          HrpE  76 lLrglqqeRealeeqlltaveqLLsdalarlLdetp 111
                                   +L+ l+  R    ++++tav+++Ls  l+rlL+  p
  gi|14601773|ref|NP_148314.1| 215 FLGRLRARRLVPTRWAITAVDEMLSRRLRRLLKTAP 250
                                   788999999999********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3185.57
//
Query:       gi|14601774|ref|NP_148315.1|  [L=382]
Description: hypothetical protein APE_1999 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-10   40.1   1.0    8.7e-05   22.3   0.2    2.5  2  TrkA_C    TrkA-C domain
    9.1e-06   26.0   1.5       0.03   14.8   0.1    2.4  2  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   9.7e-09   8.7e-05      29      69 ..     137     177 ..     123     178 .. 0.84
   2 !   16.1   0.0   8.2e-07    0.0073      15      68 ..     311     365 ..     310     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.7e-09
                                   EEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHHH CS
                        TrkA_C  29 vvairRggeliipsgdtvLeeGDvllvvgspsdlaelrell 69 
                                   v+ +rRgg+ ++ ++d+ ++eGDvl+v gs ++l e++e l
  gi|14601774|ref|NP_148315.1| 137 VLILRRGGRALLSPEDFSIREGDVLIVRGSLEALLEAAESL 177
                                   4444999**************************99988876 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.2e-07
                                   SBHHHHTHHHHS-EEEEEE-T.-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                        TrkA_C  15 ktlkelnlrargvlvvairRg.geliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                   ++l+el+l ++g  +va + g +++i   +d ++  GD++l    + + ++l+el
  gi|14601774|ref|NP_148315.1| 311 RRLSELGLDEEGLVIVAAKVGgKWIIPFLEDPEISRGDTVLAKIYSGQADTLKEL 365
                                   689***************766588888888************9999999999987 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   8.5e-05      0.76       3      88 ..      17      98 ..      15      99 .. 0.81
   2 !   14.8   0.1   3.3e-06      0.03       7      86 ..     206     278 ..     200     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.5e-05
                                  HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU  3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavni 85
                                  +  ++++ m+d+++ +++ +d+ +a e + ++d++d++ +e    l  a+  r p       + +++++a    R +D a ++
  gi|14601774|ref|NP_148315.1| 17 EARRLTSIMIDLSIYSVAFGDRLAALETLMLEDDVDEIIREAVGLLSLAV--RGPGH--TGLAKGIVELAAAFDRASDAAGDL 95
                                  66788999*************8888*************998888866666..33332..2345679999***********999 PP

                                  HHH CS
                          PhoU 86 aer 88
                                  a+ 
  gi|14601774|ref|NP_148315.1| 96 AQL 98
                                  986 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.3e-06
                                   HHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          PhoU   7 iveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavnia 86 
                                   +++  +d +l +l  +d  lar v+++++ +d+    + ++++ a +   p+       l+l+   r+lE  +D a++ a
  gi|14601774|ref|NP_148315.1| 206 LARAGFDASLYSLLAGDAGLARTVLDMEEMLDNDILSLMEDIV-AQGLTGPE------TLTLILFLRSLEDFSDAAARAA 278
                                   6667789999**********************99777777744.33333343......457999**********998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 3271.89
//
Query:       gi|118431684|ref|NP_148317.2|  [L=156]
Description: hypothetical protein APE_2001.1 [Aeropyrum pernix K1]
Scores for complete 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  111.4   0.0    3.4e-32  111.0   0.0    1.1  1  DUF2122   RecB-family nuclease (DUF2122)


Domain annotation for each model (and alignments):
>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.0   0.0   1.9e-36   3.4e-32       1     105 [.      40     145 ..      40     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 1.9e-36
                        DUF2122   1 GaAAqsGipevlklalklgksllvlpdlkDalellkpekvlllskeegeelleeeel.eekgrvllvfsgadegfskkel 79 
                                    G AAqsG+pe+++lalklgksl+vlp+l+Da++ll+p++vl+++++++e+l+    l   +grvl+vfsg++++++++e+
  gi|118431684|ref|NP_148317.2|  40 GGAAQSGVPEAMRLALKLGKSLVVLPELRDAVNLLSPTHVLAVTPSRAERLVGPGGLeGLEGRVLVVFSGGEPELDPSEA 119
                                    78***************************************************9998789******************** PP

                        DUF2122  80 elgetvkvegveadvgelaelavvly 105
                                      +  v++egve +vg++ae+a++ly
  gi|118431684|ref|NP_148317.2| 120 AGAIRVYIEGVEGKVGPIAEAALILY 145
                                    *************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1183.80
//
Query:       gi|14601777|ref|NP_148318.1|  [L=327]
Description: cytosine-specific DNA methylase [Aeropyrum pernix K1]
Scores for 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-44  150.2   0.0    4.5e-28   98.6   0.0    2.0  2  DNA_methylase    C-5 cytosine-specific DNA methylase
  ------ inclusion threshold ------
       0.23   11.0   0.0        0.4   10.2   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0     5e-32   4.5e-28       2     158 ..       6     176 ..       5     183 .. 0.87
   2 !   49.6   0.0   3.9e-17   3.5e-13     273     332 ..     257     316 ..     216     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 5e-32
                                   EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-......GS--..-SEEEE---GGG CS
                 DNA_methylase   2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..kvsigDitkidkk......klpe.diDlLvgGfPCqp 73 
                                   +  d faG GGf+ g+e+agf++ +a+++ + aa tY+anf+    +  D++++  +       l+  ++D++++++PC p
  gi|14601777|ref|NP_148318.1|   6 TAADVFAGGGGFSRGFEEAGFRVRVAIDNYPPAARTYKANFPhtAFIADDVKEVGLEeissvsGLSPgEVDVVIASPPCEP 86 
                                   5689**************************************997788888888777677888565559************ PP

                                   TECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEE.EEEEEEEGGG CS
                 DNA_methylase  74 fSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYe.vsykllnasd 146
                                   f  a          +   d+ g+Lf   ir+i   kP +f++ENV+g+ +++ ++++     +l+++GY+ v+++ll+a++
  gi|14601777|ref|NP_148318.1|  87 FTGANPrrmerplDRLYRDPAGQLFLHAIRLIGLLKPRFFVIENVPGIAHPEIERAV---RMELSKAGYRrVYFNLLRAEE 164
                                   **99984444444444578999*****************************776655...5799*****5499******** PP

                                   TT-SB--EEEEE CS
                 DNA_methylase 147 yGvpQnReRvfi 158
                                    G+p +R Rvf+
  gi|14601777|ref|NP_148318.1| 165 HGTPSRRLRVFV 176
                                   ***********7 PP

  == domain 2  score: 49.6 bits;  conditional E-value: 3.9e-17
                                   TEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHH CS
                 DNA_methylase 273 nkerfkpviekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiake 332
                                   +++ ++++i++ + R Lt+rE arl+GfPd  +f +++ a+y ++G++Vp+p+++aia+ 
  gi|14601777|ref|NP_148318.1| 257 TVMGSRRFIHPWQDRLLTVREQARLMGFPDYHIFLGSRDAQYNMVGEAVPPPLAKAIAEY 316
                                   45556669*************************************************986 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 ?   10.2   0.0   4.5e-05       0.4       5      81 ..       8      84 ..       5      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.5e-05
               Methyltransf_15  5 lDlfsGaGGnviqfalv.fekviaieinleklacaqhNa..evYgvsdkitlvlgdvfellaklklekikvdlvflSpPw 81
                                   D+f+G+GG +  f +  f+  +ai+  +      + N    ++ ++d ++ v  +  + ++ l   ++  d+v++SpP+
  gi|14601777|ref|NP_148318.1|  8 ADVFAGGGGFSRGFEEAgFRVRVAIDNYPPAARTYKANFphTAF-IADDVKEVGLEEISSVSGLSPGEV--DVVIASPPC 84
                                  59*************995666689**999988888888621344.899999999999999**9999999..*******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2409.38
//
Query:       gi|118431685|ref|NP_148319.2|  [L=189]
Description: transcription factor E [Aeropyrum pernix K1]
Scores for 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-09   35.1   0.9    1.2e-08   34.3   0.9    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    1.2e-08   34.8   0.0    2.2e-08   33.9   0.0    1.5  1  TFIIE_alpha     TFIIE alpha subunit
    2.6e-05   23.7   1.9       0.12   11.9   0.2    2.3  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
    0.00017   20.9   0.3       0.51    9.8   0.0    2.3  2  zf-ribbon_3     zinc-ribbon domain
    0.00091   19.1   2.3     0.0045   16.9   2.3    2.0  1  zinc_ribbon_4   zinc-ribbon domain
     0.0014   18.6   0.0      0.011   15.7   0.1    1.9  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0046   16.8   0.8        2.2    8.2   0.1    2.4  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
     0.0098   16.0   2.8       0.55   10.4   2.1    2.5  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
  ------ inclusion threshold ------
       0.01   15.8   1.0        5.3    7.1   0.0    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.012   15.7   0.0      0.029   14.4   0.0    1.7  1  DUF1451         Zinc-ribbon containing domain
      0.014   14.9   2.2       0.34   10.5   0.0    2.4  2  zf_C2H2_10      C2H2 type zinc-finger
      0.014   15.7   0.2        5.7    7.3   0.0    2.5  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
       0.02   14.8   2.0      0.074   13.0   2.0    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.025   14.6   2.3      0.089   12.8   2.7    1.4  1  DZR             Double zinc ribbon
      0.039   13.9   0.3        2.1    8.4   0.1    2.4  2  YhfH            YhfH-like protein
      0.045   13.7   0.1      0.078   13.0   0.1    1.3  1  zinc-ribbons_6  zinc-ribbons
      0.047   13.6   5.6       0.91    9.4   2.6    2.2  2  zf-HIT          HIT zinc finger
      0.049   14.0   0.0       0.16   12.3   0.0    1.8  2  Rrf2            Transcriptional regulator
      0.051   13.6   0.5       0.35   11.0   0.5    2.2  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
      0.056   13.3   0.7        8.7    6.3   0.2    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.059   13.4   0.0       0.09   12.8   0.0    1.3  1  Zn_Tnp_IS91     Transposase zinc-binding domain
      0.061   13.6   0.7        5.1    7.5   0.1    2.4  2  zinc_ribbon_9   zinc-ribbon
      0.064   13.9   0.9         15    6.3   0.1    2.5  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
      0.066   13.0   5.0        0.4   10.5   4.6    2.1  3  zinc_ribbon_2   zinc-ribbon domain
      0.077   13.1   0.6        3.9    7.6   0.0    2.6  3  Mut7-C          Mut7-C RNAse domain
      0.094   12.4   1.3        6.6    6.5   0.1    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.096   12.0   1.4        3.2    7.2   0.1    2.4  2  zf-TFIIB        Transcription factor zinc-finger
       0.11   12.3   0.4       0.11   12.3   0.4    2.2  2  zf-CSL          CSL zinc finger
       0.17   12.0   4.2        1.7    8.8   4.1    2.2  3  Zn-ribbon_8     Zinc ribbon domain
       0.23   11.4   5.6        1.4    9.0   0.3    2.6  2  DUF1610         Domain of unknown function (DUF1610)
       0.27   10.7   5.4        1.2    8.6   0.2    2.4  2  Mu-like_Com     Mu-like prophage protein Com
       0.28   11.2   5.7        4.5    7.3   0.3    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.32   11.1   4.9        3.7    7.7   0.1    2.7  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.37   10.9   2.9        8.2    6.5   0.1    2.5  2  CpXC            CpXC protein
       0.42   10.4   1.8         17    5.2   0.1    2.3  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.44   10.6   2.0        7.1    6.8   0.1    2.3  2  Elf1            Transcription elongation factor Elf1 like
       0.52   10.8   1.8         11    6.5   0.1    2.2  2  DUF983          Protein of unknown function (DUF983)
       0.56   10.1   5.2        6.8    6.6   0.5    2.3  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.58   10.1   5.4         10    6.1   5.4    2.3  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.9   2.6e-11   1.2e-08       1      39 [.     128     166 ..     128     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.6e-11
                                    EEETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCH CS
                   TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdCGlVlednsidegpe 39 
                                    y+CP Cgs++   ++ + +++C++CG+Vle+ +  eg e
  gi|118431685|ref|NP_148319.2| 128 YTCPRCGSKYSFDEAFTLDFTCPRCGEVLEEADSREGLE 166
                                    79*******95555889*************988666655 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   4.8e-11   2.2e-08      25      96 ..      44     115 ..      23     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.8e-11
                                    TTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHHH CS
                    TFIIE_alpha  25 kgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkkL 96 
                                    +g ++++dl+ +++ ++  +r++L  L ++r++  ++ r + k+  +y+wri+ +++   +   +++v+ kL
  gi|118431685|ref|NP_148319.2|  44 NGGISDDDLESLTGYKQSDIRRILRLLGDKRIIVSRKGRHPRKEATRYFWRIDSDTINVSLLTLKKKVLEKL 115
                                    7899****************************************************9877766666666666 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1    0.0005      0.23       2      15 ..     127     140 ..     126     142 .. 0.82
   2 !   11.9   0.2   0.00027      0.12       3      17 ..     147     161 ..     146     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0005
                         zf_UBZ   2 tylCerCgkeipes 15 
                                    +y+C+rCg++ + +
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCGSKYSFD 140
                                    7*******998765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00027
                         zf_UBZ   3 ylCerCgkeipesel 17 
                                    ++C+rCg+ ++e++ 
  gi|118431685|ref|NP_148319.2| 147 FTCPRCGEVLEEADS 161
                                    9*********99875 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   0.0    0.0018      0.81       2      11 ..     127     136 ..     126     143 .. 0.75
   2 !    9.8   0.0    0.0011      0.51       4      14 ..     148     158 ..     147     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                    zf-ribbon_3   2 tvrCPnCGap 11 
                                    +++CP+CG++
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCGSK 136
                                    689*****95 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0011
                    zf-ribbon_3   4 rCPnCGaplss 14 
                                    +CP+CG++l++
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEVLEE 158
                                    6*****98887 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.3   9.7e-06    0.0045       4      34 ..     129     155 ..     128     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.7e-06
                  zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCghv 34 
                                    tCp+C++ky++d+    a +   +C++Cg+v
  gi|118431685|ref|NP_148319.2| 129 TCPRCGSKYSFDE----AFTLDFTCPRCGEV 155
                                    8************....68999*******87 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 ?    0.7   0.0       1.1   5.1e+02      32      56 ..      19      43 ..       3      64 .. 0.75
   2 !   15.7   0.1   2.5e-05     0.011      64      95 ..     121     155 ..      85     167 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.1
                                   EEETTCT--HHHHHHHHHHHHCC.T CS
                           HypA 32 evGelsgvepeaLefafellaegtv 56
                                   ++ + +g++pe+ + +f+l+ e+t+
  gi|118431685|ref|NP_148319.2| 19 KLAQANGIKPEMAAHIFHLIYEETP 43
                                   3566778999999999999998886 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.5e-05
                                    EEEE--EEEETTTS-EEECHH..H.HHS-TTTSSS CS
                           HypA  64 ieevpvkvrCreCgkefelee..k.alrCpkCgsa 95 
                                     ++ +  ++C +Cg++++ +e  + +++Cp+Cg+ 
  gi|118431685|ref|NP_148319.2| 121 HDSGNSYYTCPRCGSKYSFDEafTlDFTCPRCGEV 155
                                    344556789*********877443788******86 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 !    8.2   0.1    0.0049       2.2      15      27 ..     120     133 ..     114     134 .. 0.79
   2 ?    6.7   0.1     0.014       6.4       4      12 ..     149     157 ..     146     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0049
                                    EC.TTEEEEE-TTT CS
                   zf-FPG_IleRS  15 gq.agrstyfCprC 27 
                                     + +g+s y CprC
  gi|118431685|ref|NP_148319.2| 120 AHdSGNSYYTCPRC 133
                                    5558999999***9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.014
                                    -TTT--BBE CS
                   zf-FPG_IleRS   4 CpRCwryie 12 
                                    CpRC+ ++e
  gi|118431685|ref|NP_148319.2| 149 CPRCGEVLE 157
                                    999998776 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 ?    7.3   0.4     0.011       4.9      11      27 ..     122     138 ..     113     144 .. 0.76
   2 !   10.4   2.1    0.0012      0.55       2      54 ..     130     183 ..     129     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                       zf-Mss51  11 apkhvdfeCpdCGipty 27 
                                    ++ +  ++Cp+CG  + 
  gi|118431685|ref|NP_148319.2| 122 DSGNSYYTCPRCGSKYS 138
                                    567889*******8665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0012
                       zf-Mss51   2 CPvpkhkqt..apkhvdfeCpdCGiptycseehwedDyeahleicdtLrq.vnede 54 
                                    CP + +k +  +    df+Cp+CG +    e+  ++  e+ ++ +d+Lr+ + +de
  gi|118431685|ref|NP_148319.2| 130 CPRCGSKYSfdEAFTLDFTCPRCGEVL--EEADSREGLERLRRTIDALREeIARDE 183
                                    9999999888788899********775..566667777766668888887777665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3     0.012       5.7       1       8 [.     129     136 ..     129     137 .. 0.91
   2 ?    7.1   0.0     0.012       5.3       1      11 [.     148     158 ..     148     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.012
                 DNA_ligase_ZBD   1 hCPvCGsa 8  
                                    +CP CGs+
  gi|118431685|ref|NP_148319.2| 129 TCPRCGSK 136
                                    7******7 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                 DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                    +CP CG  ++ 
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEVLEE 158
                                    7*****99985 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   6.2e-05     0.029      24     140 ..      40     154 ..      20     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.2e-05
                        DUF1451  24 klseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealasi.aDktqvelaelaedlehag 102
                                    ++   + +++++le ++ y + D++ + r l +++       s + +  +++++  + +i +D  +v l  l++++ ++ 
  gi|118431685|ref|NP_148319.2|  40 EETPNGGISDDDLESLTGYKQSDIRRILRLLGDKRI----IVSRKGRHPRKEATRYFWRIdSDTINVSLLTLKKKVLEKL 115
                                    556667788999999999999999999999999888....566666677777788888885688899*********9999 PP

                        DUF1451 103 vyqsGevvglGtlvCekCgkelalkkteeip.pCpkCga 140
                                    v +     g   ++C +Cg + +++++ ++  +Cp+Cg+
  gi|118431685|ref|NP_148319.2| 116 VVKEAHDSGNSYYTCPRCGSKYSFDEAFTLDfTCPRCGE 154
                                    99999999**********************868****96 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.5      0.11        52       3      10 ..     128     135 ..     127     137 .. 0.82
   2 ?   10.5   0.0   0.00073      0.34       2      16 ..     146     160 ..     146     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.11
                     zf_C2H2_10   3 fsCPKCqe 10 
                                    + CP+C+ 
  gi|118431685|ref|NP_148319.2| 128 YTCPRCGS 135
                                    78****86 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00073
                     zf_C2H2_10   2 efsCPKCqeklPDiD 16 
                                    +f CP+C+e+l   D
  gi|118431685|ref|NP_148319.2| 146 DFTCPRCGEVLEEAD 160
                                    69*******986555 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 ?    7.3   0.0     0.012       5.7      21      42 ..     117     138 ..     108     144 .. 0.76
   2 ?    6.0   0.0     0.033        15       2      14 ..     146     158 ..     145     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                        zf-Di19  21 vedeHrveskevvCPvCaekvt 42 
                                    v++ H + + ++ CP C +k +
  gi|118431685|ref|NP_148319.2| 117 VKEAHDSGNSYYTCPRCGSKYS 138
                                    5677888888888888876654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.033
                        zf-Di19   2 sftCPyCgkeltv 14 
                                    +ftCP Cg+ l++
  gi|118431685|ref|NP_148319.2| 146 DFTCPRCGEVLEE 158
                                    69******97765 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 ?   13.0   2.0   0.00016     0.074      27      56 ..     126     157 ..     106     162 .. 0.75
   2 ?    7.6   0.1    0.0077       3.5      30      44 ..     148     162 ..     140     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                 OrfB_Zn_ribbon  27 TSktCseCgsknke.alsgrtfkCpnCgfe.a 56 
                                    +  tC++Cgsk +  +  +  f+Cp+Cg +  
  gi|118431685|ref|NP_148319.2| 126 SYYTCPRCGSKYSFdEAFTLDFTCPRCGEVlE 157
                                    4469*******9998888999*******9844 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0077
                 OrfB_Zn_ribbon  30 tCseCgsknkealsg 44 
                                    tC++Cg++++ea+s+
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEVLEEADSR 162
                                    899999999995554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.7   0.00019     0.089      28      49 .]     127     153 ..     106     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00019
                            DZR  28 edrCpsCgekvdpearf.....CpeCG 49 
                                     ++Cp+Cg+k + +++f     Cp CG
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCGSKYSFDEAFtldftCPRCG 153
                                    789**************99*******9 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.18        82      15      22 ..     129     136 ..     127     142 .. 0.84
   2 ?    8.4   0.1    0.0045       2.1      15      26 ..     148     159 ..     147     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                           YhfH  15 kCteCGke 22 
                                    +C+ CG++
  gi|118431685|ref|NP_148319.2| 129 TCPRCGSK 136
                                    7*****87 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0045
                           YhfH  15 kCteCGkeieEq 26 
                                    +C+ CG+++eE 
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEVLEEA 159
                                    7*********95 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00017     0.078      13      41 ..     124     158 ..     112     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00017
                                    -SSEEE-TTT--......EEEEEEE-SSS-S---E CS
                 zinc-ribbons_6  13 rgeqyhCeaCqe......dlkkealCpeCeqelev 41 
                                     ++ y+C  C +       ++   +Cp+C++ le 
  gi|118431685|ref|NP_148319.2| 124 GNSYYTCPRCGSkysfdeAFTLDFTCPRCGEVLEE 158
                                    45779999999988888788899999999999986 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.6     0.002      0.91      13      23 ..     127     137 ..     123     137 .. 0.88
   2 ?    5.0   0.1     0.049        23      15      21 ..     148     154 ..     144     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                                    SEE-TTT--EE CS
                         zf-HIT  13 kYkCpkCntry 23 
                                     Y+Cp+C+ +y
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCGSKY 137
                                    5*******998 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.049
                                    E-TTT-- CS
                         zf-HIT  15 kCpkCnt 21 
                                    +Cp+C++
  gi|118431685|ref|NP_148319.2| 148 TCPRCGE 154
                                    9****96 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.82   3.8e+02      27      47 ..      16      36 ..      11      49 .. 0.87
   2 ?   12.3   0.0   0.00035      0.16       8      62 ..      29      83 ..      26      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.82
                                   -HHHHHHHHTS-HHHHHHHHH CS
                           Rrf2 27 sseeiaerqnispsylekila 47
                                    ++++a+  +i+p+++++i++
  gi|118431685|ref|NP_148319.2| 16 YVRKLAQANGIKPEMAAHIFH 36
                                   57899**********999987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00035
                                   HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                           Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                   e+a h+   + +e  ++ +s +++ + ++ ++s +++il+ L  + ++ s++G++
  gi|118431685|ref|NP_148319.2| 29 EMAAHIFHLIYEETPNGGISDDDLESLTGYKQSDIRRILRLLGDKRIIVSRKGRH 83
                                   789999999999999999***********************************85 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 ?   11.0   0.5   0.00075      0.35       8      30 ..     130     159 ..     127     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00075
                                    -TTT-.......-EESSSB-TTT-SB-B-S CS
                         Nop10p   8 cgkcr.......vYTLkkvcpecggptksa 30 
                                    c++c+         TL  +cp+cg+ ++ a
  gi|118431685|ref|NP_148319.2| 130 CPRCGskysfdeAFTLDFTCPRCGEVLEEA 159
                                    66666667777799***********98876 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 ?    6.3   0.2     0.019       8.7      16      35 ..     122     141 ..     115     142 .. 0.74
   2 ?    5.4   0.0     0.036        17       4      19 ..     149     164 ..     145     166 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.019
                                    CSCCCEEEESSSS-EEESSC CS
                 RNA_POL_M_15KD  16 dkegknfeCrqCgYeepadq 35 
                                    d  ++++ C  Cg+++ +d+
  gi|118431685|ref|NP_148319.2| 122 DSGNSYYTCPRCGSKYSFDE 141
                                    344555*********98875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.036
                                    ESTTTSBEEEEECSCC CS
                 RNA_POL_M_15KD   4 CpkCgNlLlpkedkeg 19 
                                    Cp Cg  L+ ++ +eg
  gi|118431685|ref|NP_148319.2| 149 CPRCGEVLEEADSREG 164
                                    ********99988876 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0002      0.09      18      69 ..     106     158 ..      90     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0002
                    Zn_Tnp_IS91  18 psqrkavekilrCrtaalGfaryeCeeCghekivyfsCksrh.CpsCqkkate 69 
                                    +  +k++ek+   + ++ G + y C+ Cg++  +       + Cp+C++  +e
  gi|118431685|ref|NP_148319.2| 106 TLKKKVLEKLVVKEAHDSGNSYYTCPRCGSKYSFDEAFTLDFtCPRCGEVLEE 158
                                    556788888888888999***********99999999988888****987655 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.011       5.1      18      29 ..     124     135 ..     116     137 .. 0.65
   2 ?    4.1   0.1      0.12        55      23      28 ..     148     153 ..     140     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
                  zinc_ribbon_9  18 edsdvlCPhCgg 29 
                                     +s  +CP+Cg+
  gi|118431685|ref|NP_148319.2| 124 GNSYYTCPRCGS 135
                                    333349****98 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.12
                  zinc_ribbon_9  23 lCPhCg 28 
                                    +CP+Cg
  gi|118431685|ref|NP_148319.2| 148 TCPRCG 153
                                    7****8 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 ?    6.3   0.1     0.033        15       4      11 ..     129     136 ..     127     139 .. 0.89
   2 ?    5.6   0.1     0.054        25       4      11 ..     148     155 ..     146     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.033
                        zf-ISL3   4 rCPnCgsk 11 
                                    +CP+Cgsk
  gi|118431685|ref|NP_148319.2| 129 TCPRCGSK 136
                                    8*****97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.054
                        zf-ISL3   4 rCPnCgsk 11 
                                    +CP+Cg++
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEV 155
                                    8*****86 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5     0.012       5.4      16      21 ..     130     135 ..     121     137 .. 0.66
   2 ?   10.5   4.6   0.00087       0.4       2      22 ..     130     155 ..     129     156 .. 0.92
   3 ?    7.3   0.2    0.0083       3.8       2      10 ..     149     157 ..     148     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                  zinc_ribbon_2  16 CpyCGt 21 
                                    Cp+CG+
  gi|118431685|ref|NP_148319.2| 130 CPRCGS 135
                                    666665 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00087
                  zinc_ribbon_2   2 CpnCGaelqdnakF.....CpyCGtp 22 
                                    Cp+CG + + ++ F     Cp+CG+ 
  gi|118431685|ref|NP_148319.2| 130 CPRCGSKYSFDEAFtldftCPRCGEV 155
                                    *********999999*********85 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0083
                  zinc_ribbon_2   2 CpnCGaelq 10 
                                    Cp+CG+ l+
  gi|118431685|ref|NP_148319.2| 149 CPRCGEVLE 157
                                    888887666 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.5   1.6e+03      40      65 ..      71      96 ..      58     109 .. 0.61
   2 ?    7.6   0.0    0.0086       3.9      97     133 ..     101     137 ..      97     139 .. 0.91
   3 ?    3.4   0.0      0.17        77      92     121 ..     148     177 ..     135     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.5
                         Mut7-C 40 kekrillTrdreLlkraklkkgvllt 65
                                    +kri+++r+ +  +++ ++   +++
  gi|118431685|ref|NP_148319.2| 71 GDKRIIVSRKGRHPRKEATRYFWRID 96
                                   57788888876666555555444445 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0086
                         Mut7-C  97 ngeleevekeevkervpekvyeeadeftrCekCrkvf 133
                                    n  l +++k+  ++ v +++ ++ +++++C++C+  +
  gi|118431685|ref|NP_148319.2| 101 NVSLLTLKKKVLEKLVVKEAHDSGNSYYTCPRCGSKY 137
                                    888999999999999******************9766 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.17
                         Mut7-C  92 rCvaCngeleevekeevkervpekvyeead 121
                                     C +C ++lee+++ e  er+ + +    +
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEVLEEADSREGLERLRRTIDALRE 177
                                    59**********999999988777665555 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     0.014       6.6       6      12 ..     130     136 ..     130     142 .. 0.85
   2 ?    4.7   0.1     0.051        23       6      12 ..     149     155 ..     148     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.014
                  zf-NADH-PPase   6 CgrCGap 12 
                                    C+rCG++
  gi|118431685|ref|NP_148319.2| 130 CPRCGSK 136
                                    *****98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.051
                  zf-NADH-PPase   6 CgrCGap 12 
                                    C+rCG  
  gi|118431685|ref|NP_148319.2| 149 CPRCGEV 155
                                    9999975 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.097        45       2       6 ..     130     134 ..     121     138 .. 0.77
   2 ?    7.2   0.1     0.007       3.2       2      15 ..     149     162 ..     148     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.097
                       zf-TFIIB   2 CPkCq 6  
                                    CP+C+
  gi|118431685|ref|NP_148319.2| 130 CPRCG 134
                                    66666 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.007
                       zf-TFIIB   2 CPkCqdeleeserg 15 
                                    CP+C+  lee++++
  gi|118431685|ref|NP_148319.2| 149 CPRCGEVLEEADSR 162
                                    *********99874 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   0.00023      0.11      17      32 ..     126     142 ..     111     146 .. 0.76
   2 ?    1.2   0.6      0.65     3e+02      19      26 ..     147     155 ..     140     169 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                    EEEEE.TTSSEEEEEHH CS
                         zf-CSL  17 yyypC.RCgdeFeltee 32 
                                     yy+C RCg+++++ e+
  gi|118431685|ref|NP_148319.2| 126 SYYTCpRCGSKYSFDEA 142
                                    69**********99885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.65
                                    EEE.TTSSE CS
                         zf-CSL  19 ypC.RCgde 26 
                                     +C RCg+ 
  gi|118431685|ref|NP_148319.2| 147 FTCpRCGEV 155
                                    5799**985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4     0.025        11      28      35 ..     129     136 ..     112     140 .. 0.79
   2 ?    8.8   4.1    0.0036       1.7       6      34 ..     128     154 ..     126     159 .. 0.74
   3 ?    6.7   0.3     0.017       7.9       5      17 ..     146     158 ..     144     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.025
                    Zn-ribbon_8  28 aCPeCgse 35 
                                    +CP+Cgs+
  gi|118431685|ref|NP_148319.2| 129 TCPRCGSK 136
                                    49999985 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                    Zn-ribbon_8   6 YrCeeCghefevlqsis.dapltaCPeCgs 34 
                                    Y C +Cg+++    +++ d    +CP+Cg+
  gi|118431685|ref|NP_148319.2| 128 YTCPRCGSKYSFDEAFTlD---FTCPRCGE 154
                                    99*****999955555522...44****97 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.017
                    Zn-ribbon_8   5 eYrCeeCghefev 17 
                                    ++ C +Cg++ e+
  gi|118431685|ref|NP_148319.2| 146 DFTCPRCGEVLEE 158
                                    6888888887775 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.062        28      16      23 ..     127     134 ..     121     135 .. 0.81
   2 ?    9.0   0.3     0.003       1.4      17      24 .]     147     154 ..     146     154 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.062
                        DUF1610  16 vFpCPNCG 23 
                                     + CP CG
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCG 134
                                    578****9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.003
                        DUF1610  17 FpCPNCGE 24 
                                    F CP CGE
  gi|118431685|ref|NP_148319.2| 147 FTCPRCGE 154
                                    99*****9 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.1     0.094        43      26      32 ..     129     135 ..     119     139 .. 0.89
   2 ?    8.6   0.2    0.0027       1.2      18      32 ..     141     154 ..     137     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.094
                    Mu-like_Com  26 KCPRCGt 32 
                                     CPRCG 
  gi|118431685|ref|NP_148319.2| 129 TCPRCGS 135
                                    5*****5 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0027
                    Mu-like_Com  18 eAlDeltiKCPRCGt 32 
                                    eA+  l   CPRCG 
  gi|118431685|ref|NP_148319.2| 141 EAFT-LDFTCPRCGE 154
                                    7888.999******5 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   0.3    0.0097       4.5      19      27 ..     128     136 ..     110     145 .. 0.81
   2 ?    6.5   0.5     0.018       8.5      19      26 ..     147     154 ..     140     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0097
                  Zn_Tnp_IS1595  19 fvCPhCgsr 27 
                                     +CP+Cgs+
  gi|118431685|ref|NP_148319.2| 128 YTCPRCGSK 136
                                    58*****87 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                  Zn_Tnp_IS1595  19 fvCPhCgs 26 
                                    f+CP+Cg 
  gi|118431685|ref|NP_148319.2| 147 FTCPRCGE 154
                                    89****95 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.052        24      19      26 .]     126     133 ..     125     135 .. 0.76
   2 ?    7.7   0.1    0.0081       3.7       3      11 ..     148     156 ..     147     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.052
                         zf-ACC  19 nlyVCPkC 26 
                                    ++y+CP C
  gi|118431685|ref|NP_148319.2| 126 SYYTCPRC 133
                                    67888888 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0081
                         zf-ACC   3 KCpsCgeml 11 
                                     Cp+Cge+l
  gi|118431685|ref|NP_148319.2| 148 TCPRCGEVL 156
                                    6******98 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.018       8.2      37      52 ..     127     142 ..      97     146 .. 0.83
   2 ?    5.0   0.3     0.052        24      37      46 ..     146     155 ..     140     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.018
                           CpXC  37 eatCpkCgatakleap 52 
                                     +tCp+Cg + +++  
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCGSKYSFDEA 142
                                    5899999999887765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.052
                           CpXC  37 eatCpkCgat 46 
                                    ++tCp+Cg+ 
  gi|118431685|ref|NP_148319.2| 146 DFTCPRCGEV 155
                                    799****986 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 ?    4.3   0.3     0.071        33      42      53 ..     125     136 ..     116     137 .. 0.79
   2 ?    5.2   0.1     0.037        17      39      53 ..     141     155 ..     136     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.071
                 zinc_ribbon_10  42 evkyrCpkCgal 53 
                                    +  y Cp Cg++
  gi|118431685|ref|NP_148319.2| 125 NSYYTCPRCGSK 136
                                    5679******86 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.037
                 zinc_ribbon_10  39 eleevkyrCpkCgal 53 
                                    e+ ++ + Cp Cg++
  gi|118431685|ref|NP_148319.2| 141 EAFTLDFTCPRCGEV 155
                                    666789******985 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.015       7.1      11      32 ..     116     138 ..     107     144 .. 0.66
   2 ?    3.1   0.3      0.22     1e+02      21      29 ..     146     154 ..     141     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                           Elf1  11 kkkkkkk.lptkFdCpfCnheks 32 
                                      k+++   +++++Cp+C+++ s
  gi|118431685|ref|NP_148319.2| 116 VVKEAHDsGNSYYTCPRCGSKYS 138
                                    34444444788999999998855 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.22
                           Elf1  21 kFdCpfCnh 29 
                                     F+Cp+C++
  gi|118431685|ref|NP_148319.2| 146 DFTCPRCGE 154
                                    6******86 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.046        21      10      24 ..     129     143 ..     126     147 .. 0.88
   2 ?    6.5   0.1     0.023        11       1      24 [.     139     162 ..     139     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.046
                         DUF983  10 aCeaCgldlsharad 24 
                                    +C++Cg ++s+ +a+
  gi|118431685|ref|NP_148319.2| 129 TCPRCGSKYSFDEAF 143
                                    7*********99886 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                         DUF983   1 FkgfLkvadaCeaCgldlsharad 24 
                                    F++ +++  +C++Cg+ l+ a++ 
  gi|118431685|ref|NP_148319.2| 139 FDEAFTLDFTCPRCGEVLEEADSR 162
                                    677788999*********999876 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.029        13      28      38 ..     127     137 ..     119     138 .. 0.75
   2 ?    6.6   0.5     0.015       6.8      21      36 ..     139     154 ..     137     156 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                        TFIIS_C  28 fykCtkCghrW 38 
                                    +y+C  Cg ++
  gi|118431685|ref|NP_148319.2| 127 YYTCPRCGSKY 137
                                    67777777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                        TFIIS_C  21 aDEpmtvfykCtkCgh 36 
                                     DE  t+ ++C  Cg+
  gi|118431685|ref|NP_148319.2| 139 FDEAFTLDFTCPRCGE 154
                                    5999999999999996 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 ?    6.1   5.4     0.022        10       5      34 ..     128     156 ..     126     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                 Zn_ribbon_SprT   5 YrCtgCgreythhlsirrhnYrCrrCkgtL 34 
                                    Y+C++Cg++y +   +      C+rC+++L
  gi|118431685|ref|NP_148319.2| 128 YTCPRCGSKYSFDEAFTLDF-TCPRCGEVL 156
                                    9******9998765555544.677777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1298.50
//
Query:       gi|118431686|ref|NP_148320.2|  [L=183]
Description: tRNA ribose 2'-O-methylase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-44  149.3   0.0    5.1e-44  149.0   0.0    1.1  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.0   2.8e-48   5.1e-44       1     118 [.      62     179 ..      62     180 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 2.8e-48
                                    H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS--- CS
                          Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkekdllvvvGaekvprevyeladynvsvgnqPhs 80 
                                    wGg+f+ve+ +s +++++ +++ gg+vvhltmyG+n+++v   i ++ ++ lvvvGaekv+r +ye ad+nvsvg+qPhs
  gi|118431686|ref|NP_148320.2|  62 WGGPFTVECGVSGRRYVRMWREGGGEVVHLTMYGVNVDDVAPVIAASPRRKLVVVGAEKVERFYYEEADWNVSVGTQPHS 141
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                          Trm56  81 evaalaifldrllegkelekefedaklkviPsergkkv 118
                                    evaala+fldrl++g+    +++++ l+v+ s+rgk+v
  gi|118431686|ref|NP_148320.2| 142 EVAALALFLDRLFRGEWRFIDYSGGFLRVMESQRGKRV 179
                                    ************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1342.50
//
Query:       gi|14601780|ref|NP_148321.1|  [L=372]
Description: GTP-binding protein HflX [Aeropyrum pernix K1]
Scores for complete 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   0.0    2.7e-16   59.7   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
    2.1e-13   50.6   1.6    4.4e-13   49.6   1.6    1.6  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    9.3e-12   45.5   0.0    2.5e-11   44.1   0.0    1.8  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    2.6e-08   33.6   0.0    5.2e-08   32.6   0.0    1.5  1  FeoB_N        Ferrous iron transport protein B
    0.00012   21.7   0.0     0.0034   16.9   0.0    2.7  3  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0014   18.7   0.0      0.011   15.8   0.0    2.1  2  Dynamin_N     Dynamin family
      0.002   17.6   0.0      0.046   13.2   0.0    2.4  2  Arf           ADP-ribosylation factor family
     0.0022   17.5   0.0      0.009   15.5   0.0    1.9  1  SRPRB         Signal recognition particle receptor beta subun
     0.0084   16.1   0.0      0.015   15.3   0.0    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
  ------ inclusion threshold ------
      0.052   13.4   0.0        3.1    7.7   0.0    2.4  2  RsgA_GTPase   RsgA GTPase
      0.092   13.0   0.0        1.1    9.5   0.0    2.1  1  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.093   13.2   0.0       0.18   12.3   0.0    1.4  1  ABC_tran      ABC transporter
       0.13   11.8   0.1        5.7    6.5   0.0    2.5  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.14   12.4   0.0       0.29   11.4   0.0    1.6  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   2.1e-19   2.7e-16       1     114 []     185     306 ..     185     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.1e-19
                                   EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHH..HHHHHHHHHHCTSE CS
                      MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseek..glgkaflaleeadl 78 
                                   +v ivG+  +GK++L+n ltge   v+ + +tT+++++ r++++g + +  +Dt+G+i +   e    +  ++++++ +d+
  gi|14601780|ref|NP_148321.1| 185 QVSIVGYASAGKTSLFNLLTGEDRPVGPEYFTTLQPKHSRITWGGvEGVLAADTVGFIRDVPPEIveAFHATLAEVKHSDA 265
                                   589*****************************************9999********88621112222455555557779** PP

                                   EEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                      MMR_HSR1  79 illvvdaseeklkpldeeleellee......akkplilvlnk 114
                                   i++v+da+ e  ++++e+l++ ++          p+++++nk
  gi|14601780|ref|NP_148321.1| 266 IVFVIDAA-EPPSDIEEKLHAGIDTlarigaLSAPMVIAANK 306
                                   ******88.545555555554443344455578888888887 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 !   49.6   1.6   3.4e-16   4.4e-13       1      79 []     101     178 ..     101     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.4e-16
                                   H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.....T CS
                     GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrkkR 79 
                                   +A+++ea lQ+e A++k+++p  +    + s++g   g+ GpG +  + + r++r+r  k+++eL+k++++re + ++R
  gi|14601780|ref|NP_148321.1| 101 HASSREALLQIEAARIKHEIPLAR-EFVRRSKMGEYPGFLGPGMYAADQYLRHLRRRLVKIRRELDKMRSTRESRLSSR 178
                                   9********************993.33333444222459**********************************998877 PP

>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   1.9e-14   2.5e-11       2      89 .]      17      99 ..      16      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.9e-14
                     GTP-bdg_N  2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqLI 84
                                  ++l+E+ +La+tag++v+     +     +  +i kG ++ ik+ +++  a+++i   +L+ps + ++ +e++++V+DR +LI
  gi|14601780|ref|NP_148321.1| 17 RHLDEALALAETAGYDVARLWRNR-----HPRIIKKGLLDAIKDEARSSGAEALIYYGDLQPSSKFTVMRETGLNVVDRVMLI 94
                                  689*************98554444.....34579************************************************* PP

                     GTP-bdg_N 85 LdIFA 89
                                  L+IFA
  gi|14601780|ref|NP_148321.1| 95 LEIFA 99
                                  ****8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   4.1e-11   5.2e-08       2     156 .]     185     353 ..     184     353 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4.1e-11
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSE CS
                        FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardflleeepdv 81 
                                   +v +vG   +Gkt+lfn ltg +  vg    +t + k+ ++++ g + v   D  G     +  + e    ++   ++ d+
  gi|14601780|ref|NP_148321.1| 185 QVSIVGYASAGKTSLFNLLTGEDRPVGPEYFTTLQPKHSRITWGGvEGVLAADTVGFIRDVPPEIVEAFHATLAEVKHSDA 265
                                   6899***********************9999************996778889****9888888888888888888999*** PP

                                   EEEEEEGGG....HHHHHHH....HHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS.....-EEEEBTTTTBTH CS
                        FeoB_N  82 vvnvvdatn....lernLyL....tlqllelgvpvvlalnmideaekkgieidlkkLsekLgv.....pvvktsakkkegi 149
                                   +v v+da++    +e +L+     ++++  l++p+v+a n+id+++  +i   ++ ++++  +     pv+++sak++ g+
  gi|14601780|ref|NP_148321.1| 266 IVFVIDAAEppsdIEEKLHAgidtLARIGALSAPMVIAANKIDALQPPEIGERIALIEREASIlphspPVIPISAKTGYGV 346
                                   *******7433337888876111145666899**************98887777777766554444559************ PP

                                   HHHHHHH CS
                        FeoB_N 150 eellkai 156
                                   ++l+++i
  gi|14601780|ref|NP_148321.1| 347 DRLVRSI 353
                                   **99875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.81     1e+03      82     124 ..      76     117 ..      70     122 .. 0.78
   2 ?    0.6   0.0      0.28   3.6e+02       5      24 ..     185     204 ..     182     213 .. 0.85
   3 !   16.9   0.0   2.7e-06    0.0034      91     191 ..     260     356 ..     253     358 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.81
                                   GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE CS
                      GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp 124
                                   +F+   ++gl+v+D ++l++++     + ++e l ++ + +++
  gi|14601780|ref|NP_148321.1|  76 KFTVMRETGLNVVDRVMLILEIF-ALHASSREALLQIEAARIK 117
                                   788999999*****999999876.5667777777777766665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                   EEEEEESTTSSHHHHHHHHH CS
                      GTP_EFTU   5 nigiighvDhGKtTLtdrLl 24 
                                   +++i+g   +GKt+L   L+
  gi|14601780|ref|NP_148321.1| 185 QVSIVGYASAGKTSLFNLLT 204
                                   6899***********98876 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 2.7e-06
                                   HHT-SEEEEEEETTTB......STHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      GTP_EFTU  91 lrvlDgavlvvdaveG......vepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekg 164
                                   ++  D  v+v+da+e         +     l  + ++  p++++ NK+D l   e+ e +  ++++        +  +   
  gi|14601780|ref|NP_148321.1| 260 VKHSDAIVFVIDAAEPpsdieeKLHAGIDTLARIGALSAPMVIAANKIDALqPPEIGERIALIEREA-------SILPH-- 331
                                   677899999***9966433222334444445556677888***********7445555555555444.......22233.. PP

                                   TTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                      GTP_EFTU 165 ekevpvvfgSalkgegvktllealvel 191
                                       pv+++Sa++g gv+ l++ +++ 
  gi|14601780|ref|NP_148321.1| 332 --SPPVIPISAKTGYGVDRLVRSIIKI 356
                                   ..469****************999986 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   8.7e-06     0.011       1      32 [.     186     216 ..     186     221 .. 0.90
   2 ?    0.3   0.0      0.49   6.3e+02     121     142 ..     255     276 ..     230     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                     Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptT 32 
                                   + +vG  S+GK+S+ n L+ged  p+gp+  T
  gi|14601780|ref|NP_148321.1| 186 VSIVGYASAGKTSLFNLLTGED-RPVGPEYFT 216
                                   679*******************.999999776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.49
                                   HHHHHHSTTEEEEEEEETTS-C CS
                     Dynamin_N 121 lvkeyikkadiilavtsanhdl 142
                                    +   +k++d+i++v +a    
  gi|14601780|ref|NP_148321.1| 255 ATLAEVKHSDAIVFVIDAAEPP 276
                                   5666689*********998755 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   1.4e+02      16      38 ..     185     207 ..     171     230 .. 0.82
   2 !   13.2   0.0   3.6e-05     0.046      81     168 ..     262     350 ..     258     357 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                                   EEEEEESTTSSHHHHHHHHHHSS CS
                           Arf  16 rilllGLDnaGKtTilkklklee 38 
                                   ++ ++G  +aGKt + + l+ e+
  gi|14601780|ref|NP_148321.1| 185 QVSIVGYASAGKTSLFNLLTGED 207
                                   46689*********999887665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.6e-05
                                   TESEEEEEEETT-C.TTHHHH.HHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGG.SSSSSSEEEEEEBT CS
                           Arf  81 ktdavifvvDsadr.eRleea.keeLkalleeeelkevallvlaNKqDlpealseeelrellglee.lkgkrkleiqkcsa 158
                                   + da++fv+D+a+  + +ee  ++ +++l +   l ++++++ aNK+D+ +  +  e  +l++ e  +   ++  ++  sa
  gi|14601780|ref|NP_148321.1| 262 HSDAIVFVIDAAEPpSDIEEKlHAGIDTLARIGAL-SAPMVIAANKIDALQPPEIGERIALIEREAsIL-PHSPPVIPISA 340
                                   679********986246666514556666666555.79**********766555444444443333343.45556666777 PP

                                   TTTBTHHHHH CS
                           Arf 159 vkgeglkegl 168
                                    +g g++  +
  gi|14601780|ref|NP_148321.1| 341 KTGYGVDRLV 350
                                   7777666655 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 !   15.5   0.0     7e-06     0.009       5      95 ..     185     282 ..     181     312 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7e-06
                                   EEEEE-STTSSHHHHHHHHHHS......S---B---SS-EEETTG......GGTT-SEEEETT-GCCSHHHHHHHHHHGGE CS
                         SRPRB   5 avllvGlsdsGKTslftrLttd......svkktvtSqessaalkv...ksekgskltliDfPGheklrqklleklkakssl 76 
                                   +v +vG   +GKTslf++Lt +      ++ +t    +s ++          ++   + D+P +  +   +  +l + ++ 
  gi|14601780|ref|NP_148321.1| 185 QVSIVGYASAGKTSLFNLLTGEdrpvgpEYFTTLQPKHSRITWGGvegVLAADTVGFIRDVPPE--IVEAFHATLAEVKHS 263
                                   6889****************98787666444444444444443323222345555567788864..566666777777788 PP

                                   EEEEEEEETTS-HHHHHHH CS
                         SRPRB  77 kglvfvvDStidpkevkev 95 
                                    ++vfv+D++  p +++e 
  gi|14601780|ref|NP_148321.1| 264 DAIVFVIDAAEPPSDIEEK 282
                                   8999999999888888775 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.2e-05     0.015      56     102 ..     298     355 ..     253     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleelde.lare..........pnsvviSaekelnldeLkekiwe 102
                                    p++++ NKiD+++  e+ e +a            p +++iSa++++++d+L+  i +
  gi|14601780|ref|NP_148321.1| 298 APMVIAANKIDALQPPEIGErIALIereasilphsPPVIPISAKTGYGVDRLVRSIIK 355
                                   6899********77655533122213347788777899***************99865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0024       3.1      96     123 ..     178     207 ..     143     221 .. 0.77
   2 ?    3.3   0.0     0.054        69      39      96 ..     290     352 ..     258     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                                   HCTT..SEEEEECSTTSSHHHHHHHHCTT- CS
                   RsgA_GTPase  96 llkd..ktsvlvGqSGvGKStLinallpel 123
                                   + k+  k + +vG   +GK++L n l++e+
  gi|14601780|ref|NP_148321.1| 178 RAKSglKQVSIVGYASAGKTSLFNLLTGED 207
                                   44443467889***************9984 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.054
                                   HHHHHHTT-EEEEEEE-GGG--HHH.....HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                   RsgA_GTPase  39 LvlaeekgiepvivlnKiDlleeee.....eleelkeelealgyevllvsaktkegleelkel 96 
                                   L+ + +  +++vi+ nKiD l+  e     +l e ++ +     +v+ +sakt+ g+++l + 
  gi|14601780|ref|NP_148321.1| 290 LARIGALSAPMVIAANKIDALQPPEigeriALIEREASILPHSPPVIPISAKTGYGVDRLVRS 352
                                   55666777899***********99988766555555666666788999999999999888765 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 ?    9.5   0.0   0.00085       1.1       2     119 ..     186     308 ..     185     309 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00085
                                   EEEESSTTSSHHHHHHCHCT-CCC..-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG..GCTTTT-HHHHC CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfs..ekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq..erfrslhplylr 78 
                                   v +vG +++GKtsl++ ++ ++    +++ +t++ + ++ ++  ++gv      ++v + i D+  +  e f+++    ++
  gi|14601780|ref|NP_148321.1| 186 VSIVGYASAGKTSLFNLLTGEDRPvgPEYFTTLQPKHSRITWGGVEGVLA---ADTVGF-IRDVPPEivEAFHATLAE-VK 261
                                   7799***********99998776422666666666665555444444433...333443.667765333555554433.35 PP

                                   TSCEEEEEEE.....GHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                           Roc  79 eaalailvyd.....srssenlkeWlkelkkvag.kspvilvgnkiD 119
                                   +++++++v+d     s+ +e+l+  ++ l + +  ++p+++ +nkiD
  gi|14601780|ref|NP_148321.1| 262 HSDAIVFVIDaaeppSDIEEKLHAGIDTLARIGAlSAPMVIAANKID 308
                                   55666667764443333456777777787777663568888888887 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014      0.18      12      37 ..     184     209 ..     174     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                   SEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  12 ekvaivGenGaGKStLlkllagllkp 37 
                                   + v ivG   aGK++L++ll+g+ +p
  gi|14601780|ref|NP_148321.1| 184 KQVSIVGYASAGKTSLFNLLTGEDRP 209
                                   5689******************9988 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 ?    2.6   0.0     0.071        91       4      21 ..     187     204 ..     184     210 .. 0.83
   2 ?    6.5   0.0    0.0045       5.7     100     155 ..     251     312 ..     233     333 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.071
                                   EEEESTTCCHHHHHHHHH CS
                          cobW   4 vltGflGsGKTtLlnhll 21 
                                    ++G+  +GKT+L n l+
  gi|14601780|ref|NP_148321.1| 187 SIVGYASAGKTSLFNLLT 204
                                   699**********99776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0045
                                   HTTSHHHHHCCCECEEEEEEETTTH......CCHCCHHHHHHHHHHTSSEEE.EE-HHHHCH CS
                          cobW 100 afteeelksdltldavvavvDaknl.....eaeeekieekaedqlaaadllv.lnKtDllde 155
                                      + +l++    da+v+v+Da++      e+ +  i ++a+ +   a +++  nK+D l+ 
  gi|14601780|ref|NP_148321.1| 251 EAFHATLAEVKHSDAIVFVIDAAEPpsdieEKLHAGIDTLARIGALSAPMVIaANKIDALQP 312
                                   3337888999999*********7776665544445555555555556666553589998765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.29       2      38 ..     186     222 ..     185     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                        AAA_28   2 ivitGgestGKTtlleaLaargypvvpEaareileek 38 
                                   + i+G  s+GKT+l + L+ ++ pv pE+++++  ++
  gi|14601780|ref|NP_148321.1| 186 VSIVGYASAGKTSLFNLLTGEDRPVGPEYFTTLQPKH 222
                                   679999***********************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2680.57
//
Query:       gi|118431687|ref|NP_148322.2|  [L=171]
Description: HTH-type transcriptional regulator [Aeropyrum pernix K1]
Scores for complete 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-12   45.9   1.0    6.4e-12   45.4   1.0    1.3  1  HTH_3     Helix-turn-helix
    2.4e-09   37.4   0.4    2.4e-09   37.4   0.4    2.0  2  HTH_31    Helix-turn-helix domain
    5.9e-08   32.5   0.5    5.9e-08   32.5   0.5    1.7  2  HTH_25    Helix-turn-helix domain
    5.3e-07   29.6   0.3      1e-06   28.7   0.3    1.4  1  HTH_19    Helix-turn-helix domain
  ------ inclusion threshold ------
      0.027   14.4   0.0       0.05   13.6   0.0    1.3  1  zf-FCS    MYM-type Zinc finger with FCS sequence motif
      0.038   14.4   0.5       0.08   13.4   0.5    1.6  1  HTH_26    Cro/C1-type HTH DNA-binding domain
      0.038   14.0   0.2      0.053   13.6   0.2    1.2  1  DZR       Double zinc ribbon
      0.072   13.0   0.2       0.15   12.1   0.1    1.5  2  HTH_37    Helix-turn-helix domain
       0.17   11.7   0.1       0.25   11.2   0.1    1.3  1  ZZ        Zinc finger, ZZ type


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 !   45.4   1.0   3.2e-15   6.4e-12       1      53 [.      87     139 ..      87     140 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 3.2e-15
                                    HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                          HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsld 53 
                                    ++e+R+++g+s + LA+kl +s + ++riE+G+ +Psl+ +k+++k Lgv+l 
  gi|118431687|ref|NP_148322.2|  87 IREAREARGWSTAVLAQKLRISETMLRRIESGKLKPSLDLAKRMEKMLGVKLL 139
                                    8*************************************************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 ?   -2.9   1.0       4.5   9.1e+03       4      10 ..      46      52 ..      44      63 .. 0.64
   2 !   37.4   0.4   1.2e-12   2.4e-09       4      57 ..      85     137 ..      83     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4.5
                         HTH_31  4 alLralR 10
                                   +lLr++R
  gi|118431687|ref|NP_148322.2| 46 QLLREAR 52
                                   5666666 PP

  == domain 2  score: 37.4 bits;  conditional E-value: 1.2e-12
                         HTH_31   4 alLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57 
                                    ++ r++Re++G+s + +A+ l++se+ l+r+E+G+   ps++   ++   lg+ 
  gi|118431687|ref|NP_148322.2|  85 ERIREAREARGWSTAVLAQKLRISETMLRRIESGKL-KPSLDLAKRMEKMLGVK 137
                                    588*********************************.6******9999999985 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       4.1   8.1e+03       2       9 ..      48      55 ..      47      56 .. 0.77
   2 !   32.5   0.5     3e-11   5.9e-08       1      35 [.      86     120 ..      86     123 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.1
                                   HHHHHHTT CS
                         HTH_25  2 LraaRear 9 
                                   Lr+aR +r
  gi|118431687|ref|NP_148322.2| 48 LREARPSR 55
                                   99999766 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 3e-11
                                    HHHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                         HTH_25   1 rLraaRearglsleevaketkIrkdylealEeddf 35 
                                    r r+aRearg+s   +a++++I++ +l+++E++++
  gi|118431687|ref|NP_148322.2|  86 RIREAREARGWSTAVLAQKLRISETMLRRIESGKL 120
                                    579*****************************986 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.3     5e-10     1e-06       2      48 ..      85     130 ..      85     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5e-10
                         HTH_19   2 erLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48 
                                    er++eaRe +g++ + la++l+is ++++ iE+gk  +ps +l ++ 
  gi|118431687|ref|NP_148322.2|  85 ERIREAREARGWSTAVLAQKLRISETMLRRIESGKL-KPSLDLAKRM 130
                                    8*********************************88.8887776655 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-05      0.05       4      33 ..       6      32 ..       5      32 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                         zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFC 33
                                   + C+ C+ +i g p+    ++ +gv+ + C
  gi|118431687|ref|NP_148322.2|  6 AYCELCGAEIRGRPY---RVSVEGVEMDLC 32
                                   67************9...**********99 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 ?   13.4   0.5     4e-05      0.08       1      40 [.      86     124 ..      86     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4e-05
                         HTH_26   1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsl 40 
                                    ++re+  +rg +++ La+++ is++ l r+ +gk   +sl
  gi|118431687|ref|NP_148322.2|  86 RIREAREARGWSTAVLAQKLRISETMLRRIESGKL-KPSL 124
                                    7999*****************************97.4444 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   2.7e-05     0.053      10      38 ..       3      39 ..       1      45 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                            DZR 10 pdarfCseCgtklkavaa........edrCpsCgekv 38
                                   + + +C+ Cg++++  +         +d C sC  k+
  gi|118431687|ref|NP_148322.2|  3 QASAYCELCGAEIRGRPYrvsvegveMDLCLSCYMKL 39
                                   6789*********9777799*************7665 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.4   8.8e+03      33      46 ..      40      53 ..      37      57 .. 0.57
   2 ?   12.1   0.1   7.3e-05      0.15      22      56 ..      86     120 ..      79     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.4
                                   -HHHHHHHHT--HH CS
                         HTH_37 33 sqseaaqllgiaqP 46
                                   + s  aqll  a+P
  gi|118431687|ref|NP_148322.2| 40 ARSGRAQLLREARP 53
                                   44445666666655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.3e-05
                                    HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                         HTH_37  22 aiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56 
                                    +i+e +e+r++s++ +aq+l i++  + r++ gkl
  gi|118431687|ref|NP_148322.2|  86 RIREAREARGWSTAVLAQKLRISETMLRRIESGKL 120
                                    599****************************9998 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00013      0.25       5      37 ..       6      38 ..       2      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                   EE-TTT-S..EESSEEE.ESSSSS-EE-HHHHHH CS
                             ZZ  5 ytCdgCseapligvRyh.clrcsdYDLCqsCfst 37
                                   + C+ C++ ++ g  y+ ++   + DLC sC+ +
  gi|118431687|ref|NP_148322.2|  6 AYCELCGA-EIRGRPYRvSVEGVEMDLCLSCYMK 38
                                   67999**9.88888898678999********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1303.84
//
Query:       gi|14601782|ref|NP_148323.1|  [L=409]
Description: proteasome-activating nucleotidase [Aeropyrum pernix K1]
Scores for complete 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-44  152.1   0.0    2.3e-44  151.0   0.0    1.6  1  AAA              ATPase family associated with various cellul
      5e-18   64.6   0.2    1.1e-17   63.5   0.2    1.6  1  AAA_lid_3        AAA+ lid domain
    1.9e-11   43.7   0.7    4.9e-11   42.4   0.7    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    4.1e-07   30.3   0.0    2.5e-06   27.7   0.0    2.1  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.4e-06   28.1   1.1     0.0012   19.2   0.1    2.7  2  AAA_16           AAA ATPase domain
    9.2e-06   25.5   0.0    2.3e-05   24.2   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.2e-05   24.9   2.4    3.3e-05   23.4   1.0    2.4  2  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
    5.6e-05   23.2   0.5    0.00068   19.6   0.5    2.6  1  AAA_5            AAA domain (dynein-related subfamily)
    6.6e-05   23.2   1.1       0.02   15.2   0.1    2.7  2  AAA_22           AAA domain
     0.0013   18.9   0.0     0.0025   18.0   0.0    1.5  1  AAA_33           AAA domain
     0.0022   17.3   0.0     0.0039   16.5   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0031   17.3   0.1      0.018   14.8   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
     0.0051   16.9   0.4      0.011   15.8   0.4    1.5  1  bZIP_1           bZIP transcription factor
     0.0082   16.0   0.0      0.051   13.4   0.0    2.2  2  AAA_3            ATPase family associated with various cellul
     0.0092   15.2   0.0      0.016   14.4   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.028   14.7   0.0    1.6  1  AAA_28           AAA domain
      0.014   14.8   0.1      0.035   13.5   0.1    1.6  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.027   14.5   0.0      0.057   13.5   0.0    1.5  1  AAA_14           AAA domain
      0.049   14.1   0.0       0.18   12.3   0.0    2.0  1  ABC_tran         ABC transporter
      0.052   13.9   0.0       0.16   12.4   0.0    1.8  1  RNA_helicase     RNA helicase
      0.053   14.1   0.0       0.14   12.7   0.0    1.8  1  AAA_18           AAA domain
      0.056   13.2   0.0       0.12   12.1   0.0    1.5  1  AAA_30           AAA domain
      0.063   13.0   1.2       0.36   10.5   0.0    2.7  3  Sigma54_activat  Sigma-54 interaction domain
      0.089   12.9   0.0        0.2   11.8   0.0    1.5  1  Torsin           Torsin
      0.095   12.6   0.5       0.59   10.0   0.1    2.1  2  NACHT            NACHT domain
       0.12   11.6   0.0       0.28   10.4   0.0    1.6  1  Zeta_toxin       Zeta toxin
       0.12   12.1   0.1       0.27   11.0   0.0    1.6  1  AAA_11           AAA domain
       0.14   11.6   0.0       0.28   10.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.18   11.8   0.0        0.3   11.1   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


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 !  151.0   0.0   3.8e-47   2.3e-44       1     132 []     176     309 ..     176     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 3.8e-47
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCC CS
                           AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgse 78 
                                   vll+GppGtGKTllakava e++++f+++ gsel++k++ge+++ +re+f+ a+eka psilfiDEida+a++r    +s 
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETEATFIRVVGSELVNKFIGEGARLVREIFRLAREKA-PSILFIDEIDAIASKRvdiGTSG 255
                                   79******************************************************9.*****************998889 PP

                                   CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                           AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                   ++e +r++ qLl+eldg++  ++ v vi+atnr d +dpa+lr gRfdr+ie++l
  gi|14601782|ref|NP_148323.1| 256 DREVQRTMLQLLAELDGFDPLDN-VKVIAATNRLDLIDPAVLRpGRFDRIIEVPL 309
                                   999*****************755.****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.2   1.8e-20   1.1e-17       1      45 []     331     375 ..     331     375 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.8e-20
                     AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                   dvdl+++A++TeG+SGADl+a++ eA+ +A+rrg   itm+d+++
  gi|14601782|ref|NP_148323.1| 331 DVDLEAIAKLTEGFSGADLKAVVVEAGYNAIRRGSRVITMDDMIK 375
                                   9*****************************************975 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 !   42.4   0.7   7.9e-14   4.9e-11       4      57 .]      66     118 ..      64     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 7.9e-14
                                   EEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                Prot_ATP_ID_OB   4 VsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                   V Ev+dd +r++Vk+s++ + +v++a+ v++  L+pg+ Va++++   i+++LP
  gi|14601782|ref|NP_148323.1|  66 VLEVIDD-NRVVVKSSTGPNLIVNVAAGVDARSLKPGAIVALNNRGSTIVDVLP 118
                                   89*****.*********************************************9 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     4e-09   2.5e-06       6     103 ..     176     267 ..     171     271 .. 0.84
   2 ?   -0.4   0.0       1.8   1.1e+03      22      70 ..     356     401 ..     341     409 .] 0.75

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 4e-09
                                   EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG----- CS
                         AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpke 84 
                                   +ll gp g+Gkt+laka+a   ++    ++ir+  sel      + + +     ++    a e+   i+++DEid i++k+
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETEA----TFIRVVGSELVN----KFIGEGARLVREIFRLAREKApsILFIDEIDAIASKR 248
                                   6899***************99985....************....77777788888888888888888************64 PP

                                   --------HHHHHHHHHHH CS
                         AAA_2  85 ssgadvSregVqrdLLqil 103
                                            +Vqr +Lq+l
  gi|14601782|ref|NP_148323.1| 249 VDIGTSGDREVQRTMLQLL 267
                                   3333444569*******98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                   HHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS CS
                         AAA_2  22 alaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG 70 
                                   a  + ++ + ++ +++ d+ +  e  +v+  +++  g  p++ +++++G
  gi|14601782|ref|NP_148323.1| 356 AGYNAIR-RGSRVITMDDMIKAVE--KVKAALDKRGGGDPFIRAQQKSG 401
                                   4455555.6677788889999998..99999999999998888888777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     2e-06    0.0012      22      47 ..     171     196 ..     162     212 .. 0.77
   2 ?    6.6   0.0     0.015         9     121     146 ..     219     254 ..     215     282 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-06
                        AAA_16  22 grpelvllsGesGvGKsslvrellra 47 
                                   + p  vll+G++G+GK+ l+++++ +
  gi|14601782|ref|NP_148323.1| 171 DPPKGVLLHGPPGTGKTLLAKAVAGE 196
                                   45689***************999854 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                        AAA_16 121 ellkrllallsrderplvlvlDdlq...........w 146
                                   +l++++++l+++ + p +l++D+++            
  gi|14601782|ref|NP_148323.1| 219 RLVREIFRLARE-KAPSILFIDEIDaiaskrvdigtS 254
                                   566778899998.778*********444444444441 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 !   24.2   0.0   3.7e-08   2.3e-05      35      98 ..     175     246 ..     144     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.7e-08
                        RuvB_N  35 hvllyGpPGlGkttlakiiakelgvkl.kitsgPvleka.gdlaalltnl......eekdvlfideihrlsr 98 
                                    vll+GpPG Gkt lak +a e ++++ ++  +  ++k  g+ a l+ ++      ++  +lfidei  +++
  gi|14601782|ref|NP_148323.1| 175 GVLLHGPPGTGKTLLAKAVAGETEATFiRVVGSELVNKFiGEGARLVREIfrlareKAPSILFIDEIDAIAS 246
                                   69*********************9986166655666663344444443332222224558*******98765 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.0   5.4e-08   3.3e-05       3      55 ..      64     117 ..      63     121 .. 0.89
   2 ?   -1.8   0.0       4.2   2.6e+03      31      41 ..     290     300 ..     289     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.4e-08
                 Prot_ATP_OB_N   3 GtflavnsqdgtadVlvggrrmrVavsPlvdaeeLrpGqeVlLnE.alvvVeal 55 
                                   +++l+v ++ + +  ++ g  + V+v++ vda +L+pG+ V Ln  ++++V++l
  gi|14601782|ref|NP_148323.1|  64 AVVLEVIDDNRVVVKSSTGPNLIVNVAAGVDARSLKPGAIVALNNrGSTIVDVL 117
                                   7999999889999999***************************97358888877 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.2
                 Prot_ATP_OB_N  31 lvdaeeLrpGq 41 
                                   l+d++ LrpG+
  gi|14601782|ref|NP_148323.1| 290 LIDPAVLRPGR 300
                                   599*******6 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 !   19.6   0.5   1.1e-06   0.00068       1     124 [.     175     289 ..     175     299 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                         AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                   +vlL GppGtgK+ la+ +a  +++++  v +++  ++    g r +          ++ r ar   ++il++DE++ + s
  gi|14601782|ref|NP_148323.1| 175 GVLLHGPPGTGKTLLAKAVAGETEATFIRVVGSELVNKFIGEGARLV---------REIFRLARekAPSILFIDEIDAIAS 246
                                   59************************999999985544444444443.........4555566656789999999999998 PP

                                   HHHHHHHHH.HHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                         AAA_5  80 evlnsLlsl.leerrllleeggelvkaknddllerfrviatanpld 124
                                   + +++  s   e +r +l  + el ++++   l ++ via++n+ld
  gi|14601782|ref|NP_148323.1| 247 KRVDIGTSGdREVQRTMLQLLAELDGFDP---LDNVKVIAATNRLD 289
                                   77776544302333333333344444443...44588888888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   3.2e-05      0.02       8      29 ..     176     197 ..     171     207 .. 0.85
   2 ?    6.5   0.1     0.016       9.8      74     121 ..     216     277 ..     194     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.2e-05
                        AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                   ++++G++GtGKT+l++ ++ + 
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGET 197
                                   689*************998765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                        AAA_22  74 sseellealeqalraravielliiDEaqhlr....s..........eealeeLrsllnl.srk 121
                                   +  +l++ + + +r++a  ++l iDE++ +                 ++l+ L +l  +   +
  gi|14601782|ref|NP_148323.1| 216 EGARLVREIFRLAREKAP-SILFIDEIDAIAskrvDigtsgdrevqRTMLQLLAELDGFdPLD 277
                                   667888999999999999.**********9866440445566667677777776665544455 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     4e-06    0.0025       2      28 ..     176     204 ..     176     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-06
                        AAA_33   2 vllvGlpGsGKstlaerllkklg..avll 28 
                                   vll+G+pG+GK+ la+ ++ ++   ++++
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETEatFIRV 204
                                   799****************9999444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.3e-06    0.0039      51      92 ..     174     213 ..     163     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                   ++vLl Gp+gtGkt la a++ e      f+ ++gse+    
  gi|14601782|ref|NP_148323.1| 174 KGVLLHGPPGTGKTLLAKAVAGETE--ATFIRVVGSELVNKF 213
                                   89*******************9965..88*******997655 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   2.9e-05     0.018      47      71 ..     173     197 ..     164     245 .. 0.78
   2 ?   -0.6   0.0       1.5   9.5e+02      67      94 ..     356     381 ..     343     387 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                     IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                    ++++l Gp+G+GK+ la a++ e+
  gi|14601782|ref|NP_148323.1| 173 PKGVLLHGPPGTGKTLLAKAVAGET 197
                                   57899**************998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                     IstB_IS21  67 lgveavraglsvlfvrvedLveelkrar 94 
                                    g++a+r+g +v  ++++d+++ +++ +
  gi|14601782|ref|NP_148323.1| 356 AGYNAIRRGSRV--ITMDDMIKAVEKVK 381
                                   5899*****999..58999998887655 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.8e-05     0.011      27      61 ..      24      58 ..      21      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekLks 61
                                  ei  L+++v  L+ke  sL++ele +k+e+ kL+s
  gi|14601782|ref|NP_148323.1| 24 EIRILKDKVRSLTKEKISLQKELEYYKNEITKLLS 58
                                  6778*****************************97 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.1   1.3e+03      74      97 ..      58      81 ..      38      87 .. 0.86
   2 !   13.4   0.0   8.2e-05     0.051       2      30 ..     176     204 ..     175     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.1
                         AAA_3 74 appktqsalleameerqvtveget 97
                                  +pp +++ +le++++++v v+++t
  gi|14601782|ref|NP_148323.1| 58 SPPYIEAVVLEVIDDNRVVVKSST 81
                                  578899999********9998876 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.2e-05
                         AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                   vll+g PG++ktll+ka+a   +++f r+
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETEATFIRV 204
                                   89************************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 !   14.4   0.0   2.6e-05     0.016      52     116 ..     172     241 ..     126     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-05
                        DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDDL 116
                                   p + vLL G  GtGK  l ka+  e++++ +r++  e+ ++ + e  +lv+++    +++   ilf+D +
  gi|14601782|ref|NP_148323.1| 172 PPKGVLLHGPPGTGKTLLAKAVAGETEATFIRVVgsELVNKFIGEGARLVREIFrlaREKAPSILFIDEI 241
                                   6678*****************************9777888889888888887642225666789999975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   4.5e-05     0.028       2      40 ..     176     219 ..     175     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-05
                        AAA_28   2 ivitGgestGKTtlleaLa....argypvv.pEaareileekla 40 
                                   + + G+++tGKT l++a a    a+ ++vv  E + +++ e+++
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAgeteATFIRVVgSELVNKFIGEGAR 219
                                   6799***************8654448889989988888877765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.7e-05     0.035      25      43 ..     176     194 ..     172     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                  Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                   +ll GppG+GKt+lak+++
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVA 194
                                   79*************9875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.2e-05     0.057       5      76 ..     176     244 ..     173     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.2e-05
                        AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                   +++ G+  +GKT l+k ++ e       ++ +   +  +k + + ++l ++i+++++e+  ++lf+DEi  +
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETE---ATFIRVVGSELVNKFIGEGARLVREIFRLAREKAPSILFIDEIDAI 244
                                   7899**************98888...777777777666655555557888888886667899*******877 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00029      0.18       7      37 ..     169     199 ..     166     243 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00029
                                   EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkp 37 
                                    + + + v + G+ G+GK+ L+k++ag+++ 
  gi|14601782|ref|NP_148323.1| 169 GIDPPKGVLLHGPPGTGKTLLAKAVAGETEA 199
                                   566777899******************9976 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   0.00026      0.16       1      52 [.     176     218 ..     176     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqev 52 
                                   ++l+Gp+g+GK++lak +a +         ++ +++r + ++ ++++ g+ +
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGE---------TEATFIRVVGSELVNKFIGEGA 218
                                   689*************94443.........3444455555555555555555 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   0.00022      0.14       1      35 [.     176     231 ..     176     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00022
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvaken 35 
                                   +ll G+pG+GKt lak+++ +++                      ++++  +a+e+
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETEAtfirvvgselvnkfigegarlVREIFRLAREK 231
                                   7899**************76653335655554444444555555555555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.12      21      51 ..     176     206 ..     163     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                        AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                   ++l+Gp+GtGKt + ka++   ea   rv+g
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAGETEATFIRVVG 206
                                   789***************9988888777775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.9     3e+03     123     148 ..      13      38 ..       9      54 .. 0.71
   2 ?   10.5   0.0   0.00058      0.36      23      46 ..     174     197 ..     166     214 .. 0.81
   3 ?   -0.5   0.1       1.4   8.5e+02      96     107 ..     235     246 ..     226     305 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.9
                                   ESBTSSSEEE--EEEEEEESS-HHHH CS
               Sigma54_activat 123 ervGsskeikvdvriiaatnedleea 148
                                   ++ G+++e++v++ri+    ++l+++
  gi|14601782|ref|NP_148323.1|  13 RHNGGHSERDVEIRILKDKVRSLTKE 38 
                                   56699999999999998877777654 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00058
                                   S-EEEECSTTSSHHHHHHHHHHHS CS
               Sigma54_activat  23 lsvlitGesGtGKellaraiheas 46 
                                     vl++G  GtGK+lla+a+  ++
  gi|14601782|ref|NP_148323.1| 174 KGVLLHGPPGTGKTLLAKAVAGET 197
                                   569***************986554 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.4
                                   EEEEETGGGS-H CS
               Sigma54_activat  96 tlfLDeigelpl 107
                                   +lf+Dei  +  
  gi|14601782|ref|NP_148323.1| 235 ILFIDEIDAIAS 246
                                   566666665543 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00032       0.2      56      92 ..     176     215 ..     150     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                                   EEEEE-TTSSHHHHHHHHH...HHHSTTGGGSTTEEEEEH CS
                        Torsin  56 lsfhGwtGtGknfvaeiia...enlyrdGlrsdyvkkfva 92 
                                   + +hG +GtGk  +a+ +a   e+++ + + s+ v+kf++
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVAgetEATFIRVVGSELVNKFIG 215
                                   569***************8444678999999*****9997 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00096      0.59       3      21 ..     176     194 ..     174     201 .. 0.89
   2 ?    0.4   0.0      0.89   5.5e+02      68     114 ..     220     268 ..     205     279 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00096
                                   EEEEC-TTTCHHHHHHHHH CS
                         NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                   v+l+G++G GKT L++ +a
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLLAKAVA 194
                                   79*************9987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.89
                                   SS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                         NACHT  68 pvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                    v+e++ +  e + ++L+ +D +D ++++      ++ ++v++ + +l+ 
  gi|14601782|ref|NP_148323.1| 220 LVREIFRLAREKAPSILF-IDEIDAIASKRVDigtSGDREVQRTMLQLLA 268
                                   566655555556666666.5888888876555777777777777777765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00046      0.28      15      50 ..     172     205 ..     165     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00046
                    Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    Pk +ll G pG GK+ la++++ e+  +  ++r+ 
  gi|14601782|ref|NP_148323.1| 172 PPKGVLLHGPPGTGKTLLAKAVAGET--EATFIRVV 205
                                   5999********************98..66677665 PP

>> AAA_11  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      0.27      20      33 ..     176     189 ..     161     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                        AAA_11  20 tliqGPPGtgKTkt 33 
                                   +l++GPPGtgKT  
  gi|14601782|ref|NP_148323.1| 176 VLLHGPPGTGKTLL 189
                                   79**********43 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   0.00045      0.28      32      58 ..     172     198 ..     160     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                         AAA_7  32 nkkpvllvGptGtGKtviikdllkkld 58 
                                     k vll Gp GtGKt+++k +  + +
  gi|14601782|ref|NP_148323.1| 172 PPKGVLLHGPPGTGKTLLAKAVAGETE 198
                                   5688**************998776655 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   0.0   0.00049       0.3      20      46 ..     174     200 ..     145     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00049
                                   EEEEEEESTTSSHHHHHHHHHHHTT-- CS
                          TsaE  20 dvilLeGdLGaGKTtlvrglakalgve 46 
                                   + +lL+G+ G+GKT l++++a + + +
  gi|14601782|ref|NP_148323.1| 174 KGVLLHGPPGTGKTLLAKAVAGETEAT 200
                                   349*****************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 2811.75
//
Query:       gi|118431688|ref|NP_148324.2|  [L=121]
Description: hypothetical protein APE_2015.1 [Aeropyrum pernix K1]
Scores for 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-24   83.8   0.2    1.1e-23   83.5   0.2    1.0  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.2   6.2e-28   1.1e-23       5     118 ..       6     110 ..       3     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 6.2e-28
                   RNA_pol_RpbG   5 eckvksieksklkdlkivkikcqneeielDiiselnifkeedkveviisrekPeyldgkdFcghGylvtekeeenkiitl 84 
                                     +k++s+e++kl++  i+ +k+++ ++ +D+i++l  ++e+d++ +++ +ekP+ ld + FcghGy v +++   + +++
  gi|118431688|ref|NP_148324.2|   6 DLKIESMEPGKLQGQLIATAKSKKATVMFDVIKDLVPLSEGDRIVIEVLEEKPKSLDKYVFCGHGYKVPSEK---SGVDI 82 
                                    689****************************************************************99998...79*** PP

                   RNA_pol_RpbG  85 iSlfGllvkisskkdllnelglkvmdkvYlcvrk 118
                                    +S++G+l+       ++++ +l+ ++k+Y+c+ k
  gi|118431688|ref|NP_148324.2|  83 LSVWGILFV------FEPQIELELDKKYYVCISK 110
                                    *********......9****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 942.44
//
Query:       gi|14601784|ref|NP_148325.1|  [L=512]
Description: 7-cyano-7-deazaguanine tRNA-ribosyltransferase [Aeropyrum pernix K1]
Scores for complete 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-70  238.1   0.0      2e-70  237.7   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.18   11.2   0.0    1.2  1  BtpA      BtpA family


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 !  237.7   0.0   2.2e-74     2e-70       3     349 ..      11     333 ..       8     334 .. 0.93

  Alignments for each domain:
  == domain 1  score: 237.7 bits;  conditional E-value: 2.2e-74
                                   EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-S CS
                           TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsg 83 
                                   +R+G++ ++hg++etPaf+pv      ++++ de++ ++g   +++n+y l++r g e +  ++g+h++lg+++ ++tdsg
  gi|14601784|ref|NP_148325.1|  11 GRIGRIYTQHGVVETPAFFPV-IDVYRQEVSVDEVR-AAGFGQVITNAYLLWKRFGWEAA--EKGVHRILGFPGVVMTDSG 87 
                                   8********************.7778899******5.88******************995..67***************** PP

                                   HHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH.. CS
                           TGT  84 gfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah.. 162
                                   ++q+++              + G  v+l+  e++e+q++lgsDi+++ld  ++ +  + ++e+sv++T+r++ ++      
  gi|14601784|ref|NP_148325.1|  88 AYQILE--------------Y-GG-VELSQGEVVEYQKRLGSDIAVILDI-PTGDVGRREAEESVRETIRRALEARVMIeg 151
                                   ***886..............4.99.9***********************8.777899**************9999855577 PP

                                   ..SEEEEEE--TT-HHHHHHHHHHHHHH--.SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHH CS
                           TGT 163 ..qalfgivqGglyedlreesaeelakrdf.dgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedlle 237
                                      +++ +vqGg y dl eesa+   +++f  +y ig+   + e   ++ ++e v +++++lp  +p++l+G+g+P  +  
  gi|14601784|ref|NP_148325.1| 152 deRIWVYPVQGGRYFDLVEESARVGGRLGFyRMYGIGSpTVFLEryMYHVVVEAVYRAKKHLPWGRPVHLFGAGHPLIFPY 232
                                   7566***********************9985799****65567756778999999************************** PP

                                   HHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHH CS
                           TGT 238 avalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNl 318
                                   avalGvD fd++ ++++ar+gr++t++g +++++  y     p    CsC++C++yt+++l+++ + ++   ++Ll++HNl
  gi|14601784|ref|NP_148325.1| 233 AVALGVDTFDSASYILYAREGRYITEYGVYRIEDLDYL----P----CSCPVCSRYTPQELREMDRVER---TRLLALHNL 302
                                   *********************************88887....9....******99***********999...********* PP

                                   HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                           TGT 319 hyylelfkriReaIkegtfeefveefarkye 349
                                   +++   ++r+++aI+eg+++e+ ee  rk++
  gi|14601784|ref|NP_148325.1| 303 YVISASMRRVKQAIREGRLWELLEETSRKHP 333
                                   ****************************997 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.1e-05      0.18     121     180 ..      95     151 ..      78     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.1e-05
                          BtpA 121 GilegkaaellrykkllesrvkiladvavkhavplverdlesavkdtvergladavilsG 180
                                   G +e   +e++ y+k+l+s+++++ d+       ++ r+ e++v++t+ r+l + v++ G
  gi|14601784|ref|NP_148325.1|  95 GGVELSQGEVVEYQKRLGSDIAVILDIPTG---DVGRREAEESVRETIRRALEARVMIEG 151
                                   55677889*******************865...6789999****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); 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: 0.59u 0.22s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3697.44
//
Query:       gi|118431689|ref|NP_148326.2|  [L=244]
Description: hypothetical protein APE_2018.1 [Aeropyrum pernix K1]
Scores for 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-30  104.2   0.0    1.1e-29  104.1   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 !  104.1   0.0   5.9e-34   1.1e-29       2     210 ..      22     225 ..      21     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 5.9e-34
                                    EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE..E-HSC CS
                           PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg..repil 79 
                                    ++Gf g G+Vg+l+ ++L+ sl+  k g+i s+  +p     pvv+ve++++  p+ +y+++ g+r l++++   +e ++
  gi|118431689|ref|NP_148326.2|  22 VTGFRGFGLVGYLVSKHLALSLGSSKRGYILSPI-MP-----PVVIVEDDGPGYPFDIYYSE-GKRVLTIVHRanPEREV 94 
                                    79********************************.**.....****************9885.24555555558888888 PP

                                    HHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES...TTS-.EEEEEESSHHHHHHHHCT...-CEEEEHHHHHHHHHHH CS
                           PAC2  80 qyeefakalldwaeelgvkevvvLggldageradv.phtrpekvtgaatdeelleelees...eyggivgitglLlsaak 155
                                    q e +  +l  w++e+gv +v+++ggl      +  p ++++++ + a++ +   +le+     + g+vg+ +lL++ ++
  gi|118431689|ref|NP_148326.2|  95 QDE-YLHTLSLWLREMGVGRVILVGGLNM----EFmPREEKHGYRWLANRHYKGPKLEAPtmeAGLGVVGPLALLYMYLD 169
                                    888.***********************94....444789999***************73345688999************ PP

                                    HTT-EEEEEEEEEECCC--HHHHHHHHHHH.HHHHT---HCHHHHHHHHHHHHHHH CS
                           PAC2 156 ergipavgllaevphylpdPkaaaallefl.skllglevdtedLeedaeeleeqle 210
                                      g+pa+++l+++  + +d +aa++ l+++   ++g+e++t++ e++a + +e le
  gi|118431689|ref|NP_148326.2| 170 YLGVPAAMVLPYSVAERVDYEAAIRGLKVIgGSIIGVEIPTDEIEKMASMQREILE 225
                                    ******************************77778***************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1833.48
//
Query:       gi|14601786|ref|NP_148327.1|  [L=146]
Description: hypothetical protein APE_2020 [Aeropyrum pernix K1]
Scores for complete 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   44.6   0.0    1.7e-11   44.0   0.0    1.3  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    2.2e-05   24.3   0.3    3.9e-05   23.5   0.3    1.4  1  PUA       PUA domain
     0.0081   16.4   0.2      0.016   15.4   0.0    1.5  2  UPF0113   UPF0113 PUA domain
  ------ inclusion threshold ------
       0.12   12.2   0.3       0.36   10.7   0.2    1.8  2  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 !   44.0   0.0   3.9e-15   1.7e-11       8      71 .]      14      78 ..      12      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 3.9e-15
                        TGT_C2  8 dYqFGagagdaLfped.vtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71
                                  + qF  +a+daL   + +++   a gr+rqv ++ge ++tlra dg ++Ls  +++ l +s++ P
  gi|14601786|ref|NP_148327.1| 14 ALQFSPEAADALLSVEgLEVSFGAGGRVRQVWAGGEPYLTLRAGDGYFSLSTRAGEFLRRSIAKP 78
                                  57***********5434888877************************************999887 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   8.6e-09   3.9e-05      18      69 ..      93     144 ..      87     146 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.6e-09
                                   EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEE CS
                           PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksve 69 
                                   s++a+ vv+ ++ +++gd+  +vde+++l++vG+++   + ++  ++g +v+
  gi|14601786|ref|NP_148327.1|  93 SVFAKQVVGGDEGLRPGDEAIVVDEEDRLLGVGRVRIPLAFIRGLDRGEVVR 144
                                   89*********************************98777777777777665 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.5   1.1e+04      71      76 .]      68      73 ..      67      73 .. 0.85
   2 !   15.4   0.0   3.7e-06     0.016      18      53 ..      94     129 ..      92     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                       UPF0113 71 GeYlRr 76
                                  Ge+lRr
  gi|14601786|ref|NP_148327.1| 68 GEFLRR 73
                                  9****7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.7e-06
                       UPF0113  18 vlkesilkitesvkenqvvvVlnengeplGiGkirk 53 
                                   v+ ++++  +e+++ ++ ++V++e++++lG+G++r+
  gi|14601786|ref|NP_148327.1|  94 VFAKQVVGGDEGLRPGDEAIVVDEEDRLLGVGRVRI 129
                                   8999999999***********************987 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   8.1e-05      0.36      18      49 ..      94     125 ..      93     128 .. 0.92
   2 ?   -1.9   0.0      0.67     3e+03      26      38 ..     134     145 ..     131     146 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.1e-05
                         PUA_3  18 vfsneiasvegeledGdvVdvfsekgkflGtG 49 
                                   vf++ +   ++ l++Gd + v++e+++ lG+G
  gi|14601786|ref|NP_148327.1|  94 VFAKQVVGGDEGLRPGDEAIVVDEEDRLLGVG 125
                                   788889888999******************99 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.67
                         PUA_3  26 vegeledGdvVdv 38 
                                   ++  l  G+vV++
  gi|14601786|ref|NP_148327.1| 134 IR-GLDRGEVVRL 145
                                   55.4789999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1072.14
//
Query:       gi|118431690|ref|NP_148328.2|  [L=139]
Description: FUR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-20   73.3   0.2      2e-20   73.1   0.2    1.1  1  FUR              Ferric uptake regulator family
    1.8e-06   27.5   0.0    2.5e-06   27.0   0.0    1.2  1  RepL             Firmicute plasmid replication protein (RepL)
    0.00081   19.3   0.0      0.027   14.4   0.0    2.2  2  PadR             Transcriptional regulator PadR-like family
    0.00086   19.1   0.3      0.014   15.2   0.0    2.8  3  TrmB             Sugar-specific transcriptional regulator Trm
     0.0023   17.8   0.0     0.0069   16.2   0.0    1.8  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0036   17.3   0.0     0.0059   16.6   0.0    1.4  1  HTH_20           Helix-turn-helix domain
     0.0042   16.8   0.1      0.041   13.7   0.0    2.4  3  HTH_23           Homeodomain-like domain
     0.0045   16.5   0.0      0.021   14.4   0.0    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.033   14.1   0.0    1.8  2  HTH_36           Helix-turn-helix domain
      0.011   16.0   0.3      0.029   14.7   0.1    1.7  2  DUF2513          Hypothetical protein (DUF2513)
      0.021   14.7   0.0      0.061   13.2   0.0    1.7  1  HxlR             HxlR-like helix-turn-helix
      0.026   14.3   0.1      0.078   12.8   0.0    1.8  2  HTH_IclR         IclR helix-turn-helix domain
      0.029   14.3   0.0       0.52   10.3   0.0    2.4  2  HTH_11           HTH domain
       0.05   13.9   0.2       0.11   12.8   0.1    1.7  2  HTH_WhiA         WhiA C-terminal HTH domain
      0.054   14.1   0.1      0.087   13.5   0.1    1.4  1  HTH_32           Homeodomain-like domain
      0.084   13.2   0.0       0.14   12.6   0.0    1.3  1  Penicillinase_R  Penicillinase repressor
       0.12   12.6   0.0       0.21   11.8   0.0    1.5  1  YjcQ             YjcQ protein


Domain annotation for each model (and alignments):
>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.2   1.9e-23     2e-20       1     116 [.      15     126 ..      15     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.9e-23
                                    HTTHCHHHHHHHHHHH.HHHHSSSBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESSSSSEE CS
                            FUR   1 eaglklTkqRekilev.lekseehlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelakkehhd 79 
                                    ++g++lT+qR +++++ l + e+h s  e+++++ +e p is++TVY tLk+lee+g++k++e++ g+ +  +   + h 
  gi|118431690|ref|NP_148328.2|  15 KRGMRLTPQRVALVKYvLVNVEKHESLREIHEKISREMPGISVSTVYHTLKMLEELGFIKTFEIN-GKIH--IDRPHFHI 91 
                                    589***********963677788*****************************************9.5555..55569*** PP

                                    EEEETTT--EEEE--HHHHHHHHHHHHHTT-EEEEEE CS
                            FUR  80 hlicekCgkviefkddeiekiqeeiaekegfklvshr 116
                                    +l c ++gk+++++ d +  i+e+  +  g+k+ ++ 
  gi|118431690|ref|NP_148328.2|  92 NLHCLDTGKITDVDVD-LGGIAEKLGR-SGLKIRNII 126
                                    ************9766.6666666554.677776665 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   2.4e-09   2.5e-06      55     108 ..      22      76 ..       6      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.4e-09
                           RepL  55 nkktrlvyylidnlnsnntliatnRelaeet.gislktvsetlkileeanilkkk 108
                                     ++  lv+y++ n++++  l   + ++++e  gis+ tv +tlk+lee +++k  
  gi|118431690|ref|NP_148328.2|  22 PQRVALVKYVLVNVEKHESLREIHEKISREMpGISVSTVYHTLKMLEELGFIKTF 76 
                                    6999***********************98744********************974 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.1   1.1e+02      30      45 ..       2      17 ..       1      23 [. 0.87
   2 !   14.4   0.0   2.6e-05     0.027      14      51 ..      43      77 ..      31      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                                   THHHHHHHHHHHHHTT CS
                           PadR 30 seGslYpaLkrLekeg 45
                                    +G+lY++L+  +k g
  gi|118431690|ref|NP_148328.2|  2 DDGQLYQVLSMIRKRG 17
                                   57********999987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEE CS
                           PadR 14 eiikeleelsegllelseGslYpaLkrLekeglvesew 51
                                   ei +++++ + g   +s +++Y +Lk Le+ g++++ +
  gi|118431690|ref|NP_148328.2| 43 EIHEKISREMPG---ISVSTVYHTLKMLEELGFIKTFE 77
                                   788889999888...89*****************9865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.1   1.2e+03      38      51 ..       5      18 ..       2      36 .. 0.74
   2 !   15.2   0.0   1.4e-05     0.014      31      58 ..      52      79 ..      25      89 .. 0.78
   3 ?    0.1   0.0       0.7   7.4e+02      28      50 ..     111     133 ..     106     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                   CHHHHHHHHHHCTS CS
                           TrmB 38 kvYevLrsLedkGl 51
                                   + Y+vL+   ++G+
  gi|118431690|ref|NP_148328.2|  5 QLYQVLSMIRKRGM 18
                                   57999999999987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                                   CTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 31 elgvprskvYevLrsLedkGlVerekgr 58
                                   + g++ s+vY +L+ Le+ G++++ + +
  gi|118431690|ref|NP_148328.2| 52 MPGISVSTVYHTLKMLEELGFIKTFEIN 79
                                   348899****************987765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.7
                                    HCCCTTSSCHCHHHHHHHHHHCT CS
                           TrmB  28 iaeelgvprskvYevLrsLedkG 50 
                                    iae+lg++  k+ +++ + e++G
  gi|118431690|ref|NP_148328.2| 111 IAEKLGRSGLKIRNIIVEVENCG 133
                                    99*****9999999888877777 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.1   5.4e+03       2      11 ..      22      31 ..      21      35 .. 0.81
   2 !   16.2   0.0   6.6e-06    0.0069      26      46 ..      54      74 ..      47      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.1
                                   HHHHHHHHHH CS
                          HTH_5  2 ptRlkILklL 11
                                   p+R+ ++k++
  gi|118431690|ref|NP_148328.2| 22 PQRVALVKYV 31
                                   8999999886 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.6e-06
                                   TS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 26 glsqstvShHLkkLreaGLVe 46
                                   g+s stv h Lk+L+e+G+++
  gi|118431690|ref|NP_148328.2| 54 GISVSTVYHTLKMLEELGFIK 74
                                   89*****************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.6e-06    0.0059      25      56 ..      39      75 ..       8      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-06
                                   B-HHHHHHHH.....TS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20 25 ltaselaerl.....dlskntlsyHLrvLeeagLvev 56
                                    ++ e++e +     ++s +t+++ L+ Lee g++++
  gi|118431690|ref|NP_148328.2| 39 ESLREIHEKIsrempGISVSTVYHTLKMLEELGFIKT 75
                                   5677888888555566******************985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.1   3.3e+03       8      24 ..       7      26 ..       7      26 .. 0.70
   2 !   13.7   0.0   3.9e-05     0.041      20      45 ..      45      71 ..      31      75 .. 0.85
   3 ?   -0.4   0.0       1.1   1.1e+03      23      30 ..     111     118 ..     110     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                         HTH_23  8 lrillllae...GlsvreIA 24
                                   +++l + ++   +l+++++A
  gi|118431690|ref|NP_148328.2|  7 YQVLSMIRKrgmRLTPQRVA 26
                                   57888999886666666665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.9e-05
                         HTH_23 20 vreIAreL.gvsrrTvyrwlkryreeG 45
                                    ++I+re+ g+s +Tvy+ lk  +e G
  gi|118431690|ref|NP_148328.2| 45 HEKISREMpGISVSTVYHTLKMLEELG 71
                                   689*****************9887666 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.1
                         HTH_23  23 IAreLgvs 30 
                                    IA++Lg+s
  gi|118431690|ref|NP_148328.2| 111 IAEKLGRS 118
                                    99****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 !   14.4   0.0     2e-05     0.021      28      48 .]      54      74 ..      53      74 .. 0.98
   2 ?   -1.5   0.0       1.9     2e+03      23      30 ..     111     118 ..     110     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                         HTH_24 28 glSpstvnrrlkrLeeeGlIk 48
                                   g+S+stv   lk Lee G+Ik
  gi|118431690|ref|NP_148328.2| 54 GISVSTVYHTLKMLEELGFIK 74
                                   8*******************7 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                         HTH_24  23 LAerlglS 30 
                                    +Ae+lg S
  gi|118431690|ref|NP_148328.2| 111 IAEKLGRS 118
                                    89999977 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   3.1e-05     0.033      31      55 .]      48      73 ..      40      73 .. 0.87
   2 ?   -1.4   0.0       2.2   2.3e+03      31      53 ..     111     133 ..     109     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                         HTH_36 31 lakrl.glsknTvsraikeLeqlGyi 55
                                   +++ + g+s++Tv+  +k+Le+lG+i
  gi|118431690|ref|NP_148328.2| 48 ISREMpGISVSTVYHTLKMLEELGFI 73
                                   5555579*****************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                         HTH_36  31 lakrlglsknTvsraikeLeqlG 53 
                                    +a++lg s  +++++i e e +G
  gi|118431690|ref|NP_148328.2| 111 IAEKLGRSGLKIRNIIVEVENCG 133
                                    78888888777777777666655 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.7e-05     0.029       6      60 ..      27      78 ..      25      95 .. 0.86
   2 ?   -1.6   0.0       3.3   3.4e+03       7      19 ..     122     134 ..     121     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                        DUF2513  6 lvRdiLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekk 60
                                   lv+ +L ++e++e+ +e  +     + +++g s  +++ +lk+l+e g+i++ + 
  gi|118431690|ref|NP_148328.2| 27 LVKYVLVNVEKHESLREIHEK---ISREMPGISVSTVYHTLKMLEELGFIKTFEI 78
                                   899**********99998544...4459**********************98655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.3
                        DUF2513   7 vRdiLltleelet 19 
                                    +R+i+ ++e++ +
  gi|118431690|ref|NP_148328.2| 122 IRNIIVEVENCGK 134
                                    89******99765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.8e-05     0.061      22      51 ..      46      75 ..      29      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                                   HHHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
                           HxlR 22 selkralpkisqkmLaqrLreLeqdglier 51
                                   ++++r++p+is ++  ++L++Le+ g+i+ 
  gi|118431690|ref|NP_148328.2| 46 EKISREMPGISVSTVYHTLKMLEELGFIKT 75
                                   6799**********************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.4   6.7e+03       8      21 ..       9      22 ..       8      26 .. 0.57
   2 ?   12.8   0.0   7.4e-05     0.078      29      49 ..      54      74 ..      36      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.4
                                   HHCT-CTTBSS-BH CS
                       HTH_IclR  8 iLdalaeapqeltl 21
                                   +L ++++++ +lt 
  gi|118431690|ref|NP_148328.2|  9 VLSMIRKRGMRLTP 22
                                   66666666655555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.4e-05
                                   TS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 29 glpkStvhRlLqtLvelGyve 49
                                   g++ Stv++ L+ L+elG+++
  gi|118431690|ref|NP_148328.2| 54 GISVSTVYHTLKMLEELGFIK 74
                                   8999***************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0005      0.52      26      46 ..      54      78 ..      39      82 .. 0.86
   2 ?    1.3   0.0      0.31   3.3e+02      21      38 ..     111     128 ..     103     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0005
                         HTH_11 26 nvSrrtvrrdIkaLeelg....vpI 46
                                   ++S +tv+  +k Leelg    ++I
  gi|118431690|ref|NP_148328.2| 54 GISVSTVYHTLKMLEELGfiktFEI 78
                                   79****************6666666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.31
                         HTH_11  21 LAeeLnvSrrtvrrdIka 38 
                                    +Ae+L++S   +r+ I +
  gi|118431690|ref|NP_148328.2| 111 IAEKLGRSGLKIRNIIVE 128
                                    8******98777776655 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00011      0.11      52      83 ..      36      70 ..       4      71 .. 0.75
   2 ?   -1.9   0.0         4   4.2e+03      66      76 ..     113     123 ..     107     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                   -TTS-HHHHHHTT.....T--HHHHHHHHHHHHHH CS
                       HTH_WhiA 52 npdaSLkeLgell...eppisKSgvnhrlrklkel 83
                                   +++ SL+e+ e +    p is S+v+h l+ l+el
  gi|118431690|ref|NP_148328.2| 36 EKHESLREIHEKIsreMPGISVSTVYHTLKMLEEL 70
                                   3567*********9999***************996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4
                                    .T--HHHHHHH CS
                       HTH_WhiA  66 ppisKSgvnhr 76 
                                    +++++Sg++ r
  gi|118431690|ref|NP_148328.2| 113 EKLGRSGLKIR 123
                                    57788887655 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.2e-05     0.087      25      73 .]      14      64 ..       3      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.2e-05
                         HTH_32 25 rpr..klsdevrariiallre.eprWsprqlaarlaeregvkvShstvyriL 73
                                   r+r  +l+++ +a ++ +l + e + s+r++++++  re   +S stvy  L
  gi|118431690|ref|NP_148328.2| 14 RKRgmRLTPQRVALVKYVLVNvEKHESLREIHEKI-SREMPGISVSTVYHTL 64
                                   45556899999999999997656799*********.666577*******876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.14      18      56 ..      39      78 ..      27      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                   EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEE CS
                Penicillinase_R 18 atvkevveeleee.kelaysTVktllrrLvkKgllsreke 56
                                    + +e++e++++e    + sTV  +l+ L++ g++++ + 
  gi|118431690|ref|NP_148328.2| 39 ESLREIHEKISREmPGISVSTVYHTLKMLEELGFIKTFEI 78
                                   6789*********5567******************99776 PP

>> YjcQ  YjcQ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.21      18      57 ..      44      83 ..      27     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                   .-S---HHHHTS-HHHHHHHHHHHHHHTSEE--EESSS.. CS
                           YjcQ 18 dnkelsaekldisesrfndiiemlveegyikGvkvkktkk 57
                                     +++s e  +is s  +++++ml+e g+ik ++++ +++
  gi|118431690|ref|NP_148328.2| 44 IHEKISREMPGISVSTVYHTLKMLEELGFIKTFEINGKIH 83
                                   46899**************************999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1017.87
//
Query:       gi|118431691|ref|YP_874922.1|  [L=92]
Description: hypothetical protein APE_2021a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 736.09
//
Query:       gi|14601788|ref|NP_148329.1|  [L=394]
Description: hypothetical protein APE_2022 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 2912.33
//
Query:       gi|118431692|ref|YP_874923.1|  [L=115]
Description: hypothetical protein APE_2022a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 921.37
//
Query:       gi|14601789|ref|NP_148330.1|  [L=411]
Description: cysteine desulfurase [Aeropyrum pernix K1]
Scores for complete 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-131  437.3   0.0   4.7e-131  437.1   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    9.6e-06   25.1   0.1    1.7e-05   24.3   0.1    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00044   18.9   0.0     0.0008   18.0   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0064   15.5   0.0      0.012   14.6   0.0    1.5  1  SelA             L-seryl-tRNA selenium transferase
     0.0085   15.3   0.0      0.013   14.7   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.1   0.0  1.3e-134  4.7e-131       1     371 []      21     399 ..      21     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 437.1 bits;  conditional E-value: 1.3e-134
                                   EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHC CS
                   Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalsl 81 
                                   +yld+aA+t kp++V++a++e++++++anvhr+vh+l++ea+ka+e+a+e va+l++ ++ +e++ft++ttea++l+al+l
  gi|14601789|ref|NP_148330.1|  21 VYLDNAASTLKPRRVVEAMREFSYRSYANVHRGVHRLSMEASKAYEDAHEVVARLVGGSW-DEVVFTRNTTEAMQLAALTL 100
                                   7**********************************************************9.******************** PP

                                   CCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHH CS
                   Aminotran_5  82 ars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveei 161
                                   a++ l +g e++vt+a+hh++l+pw+++a+  g + +++pld +g  ++d le++++e+t++va+ hvsnvtG++ pve+i
  gi|14601789|ref|NP_148330.1| 101 AYNgLLRGGEVLVTAADHHSTLLPWVRAARLGGGRARILPLDGRGVPRWDLLEDYITEDTRAVAVGHVSNVTGVVAPVEDI 181
                                   ********************************************************************************* PP

                                   HHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEE.. CS
                   Aminotran_5 162 gklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsleett.. 240
                                   +k+akk+galv++D+aq+v+h p+d++++gvD++afsghK+lgPtGiGvl++r++lle+lep l+gg++v++v+l++ +  
  gi|14601789|ref|NP_148330.1| 182 VKAAKKVGALVVLDSAQGVPHLPVDFRRMGVDMAAFSGHKMLGPTGIGVLWARRDLLEELEPPLGGGGTVSRVRLQGGSve 262
                                   ***************************************************************************877668 PP

                                   ..EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTST...TEEEES.-B-CTCBSEEEEEE CS
                   Aminotran_5 241 ..faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslp...gvrlygpdkaerrasivsfnf 316
                                     ++e+p+kfeaGTp++++++gl++a+++l+eig+e++++he+el++++++ l+ l     +r +gpdk  +r++ivs+++
  gi|14601789|ref|NP_148330.1| 263 ieWEEPPWKFEAGTPPIIEAVGLAEAANMLMEIGMEHVARHEDELTSHTMKLLEPLYsegLIRYVGPDKPGERHGIVSITT 343
                                   88************************************************9999875111567789*************** PP

                                   TTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S.-EEEEE--TTS-HHHHHHH CS
                   Aminotran_5 317 kgvhaedvatlLdeegIavrsGhhcaqplmkrlale.gtvRaSlyiynteeevdrl 371
                                   +  ++++++ lLd++gIavr+G hca++l+++++ + g+v+aS+yiyn++e+ +rl
  gi|14601789|ref|NP_148330.1| 344 HLKSPDELGLLLDRRGIAVRTGLHCAHILHDHVDASmGSVWASFYIYNCKEDAERL 399
                                   **********************************999***************9997 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 !   24.3   0.1   4.9e-09   1.7e-05      38     150 ..      80     201 ..      43     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.9e-09
                                   -SEEEEESSHHHHHHHHHHH...TTTTTT-EEEEESSS-THH....HHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TT CS
               DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLra...lgvgpgdeVIvpsltFvat....anavlelgakpvfvDvdpdtynidpaaieaaiter 111
                                    + ++ + + t+A++la       g+ +g eV+v+++   +t    + a++  g ++  +  d     +  + +e  ite 
  gi|14601789|ref|NP_148330.1|  80 WDEVVFTRNTTEAMQLAALTlayNGLLRGGEVLVTAADHHSTllpwVRAARLGGGRARILPLD-GRGVPRWDLLEDYITED 159
                                   46789999******9976552335666***************333234455556666666666.67899************ PP

                                   EEEEEEB-G...GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
               DegT_DnrJ_EryC1 112 tkaIlpVhl...yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                   t+a+ + h+    G va ++ + + a+k g  v+ D+A+++ 
  gi|14601789|ref|NP_148330.1| 160 TRAVAVGHVsnvTGVVAPVEDIVKAAKKVGALVVLDSAQGVP 201
                                   ****998853337**************************986 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 !   18.0   0.0   2.2e-07    0.0008     130     201 ..     152     224 ..     142     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.2e-07
                                   HHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTT.S-GGGGT-SEEEEETTTTTT CS
               Cys_Met_Meta_PP 130 lekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspll.qrplklgaDivvhSaTKylg 201
                                   le  i+e t++v +  ++n +  v+ +e+i+k+akk+g+lvv+D +   p l +   ++g+D+   S+ K lg
  gi|14601789|ref|NP_148330.1| 152 LEDYITEDTRAVAVGHVSNVTGVVAPVEDIVKAAKKVGALVVLDSAQGVPHLpVDFRRMGVDMAAFSGHKMLG 224
                                   78899*****************************************999966144446899999999988775 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.3e-06     0.012     198     234 ..     206     242 ..     153     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                                   HHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                          SelA 198 ealaeGvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                   +  + Gvd+ +fsG k+lG    G++  +++l+e+l+
  gi|14601789|ref|NP_148330.1| 206 DFRRMGVDMAAFSGHKMLGPTGIGVLWARRDLLEELE 242
                                   45578****************************9985 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 !   14.7   0.0   3.7e-06     0.013      48     189 ..      67     197 ..      21     201 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-06
                                   HHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH...HTTT-EEEEEESS-THH....HHHHHHTTSEEEEEE CS
                 Aminotran_1_2  48 eleealakflgrseklklkreaavvvgsGagaliealifllk...lnpgdeilvpdptyasy....knilrlsggevvryp 121
                                   ++ e +a+++g          ++vv++  ++++ ++++  l    l +g e+lv +  + s      +++rl gg  +  p
  gi|14601789|ref|NP_148330.1|  67 DAHEVVARLVG-------GSWDEVVFTRNTTEAMQLAALTLAyngLLRGGEVLVTAADHHSTllpwVRAARLGGGRARILP 140
                                   55555666666.......444566666666666666665555344345555555555554431111456666666666666 PP

                                   BEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                 Aminotran_1_2 122 lyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                                   l+        ++ le+ ++e       t+ ++v  ++N tG+va+ e+++k    akk ++l+++D a
  gi|14601789|ref|NP_148330.1| 141 LD--GRGVPRWDLLEDYITE------DTRAVAVGHVSNVTGVVAPVEDIVKA---AKKVGALVVLDSA 197
                                   55..5555667778888888......889***********************...***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); 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:                         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 0.22s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2916.48
//
Query:       gi|118431693|ref|NP_148334.2|  [L=360]
Description: hypothetical protein APE_2029.1 [Aeropyrum pernix K1]
Scores for complete 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   46.2   0.6    5.4e-12   45.6   0.6    1.1  1  DBI_PRT   Phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> DBI_PRT  Phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.6     3e-16   5.4e-12      89     256 ..      88     258 ..      83     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3e-16
                                    HHHHHHCTEEEEEEEEE.-S..--TEE-.-SSSSB--TTTS-SS-HHHHHHHHHHHHHHHHHHHCTTECEEEEEEE-TTC CS
                        DBI_PRT  89 nvlarqagaelrvvDvg.va..dlevdr.kvrrgtaniakepAmtreeaeaaleaGieladeladagadllalGemGigN 164
                                     ++ar++++ l +vD+g  +  +++  +   r   ++i++ep +   + e+ ++ +  l  +l ++g+d +a+Ge   g 
  gi|118431693|ref|NP_148334.2|  88 RAVARAFNIPLLPVDAGsWTeaRVPHAKlPSRVTGGRIDVEPGLPSGASERLFREAYMLGSSL-ARGLDWIAVGESIPGG 166
                                    5789*************5443443344445777889*********************999997.67************** PP

                                    HHHHHHHHHHHHT--HHHH---TTT--HHHHHHHHHHHHHHHHCH...-TT.HHHHHHHHS-HHHHHHHHHHHHHHHTT- CS
                        DBI_PRT 165 ttaaaallaallglepeevvGrGtglddeglarKiavieqalarh...aekdplevLakvGGleiaalaGailgAaarri 241
                                    tt aaa++ al  + ++ v   G   +d+  + K +v++qal+r     ++d le++ +vG    + +aG+ +gA++++ 
  gi|118431693|ref|NP_148334.2| 167 TTVAAAVMEALGYRAADLVSSSG---KDNPRELKKRVVAQALSRLrecGARDVLEIVDCVGDPVHVSIAGLAVGAREAGA 243
                                    **********9888887777666...57888999***********643245***************************** PP

                                    -EEE-SHHHHHHHHH CS
                        DBI_PRT 242 pvvlDGfistaAalv 256
                                     v+l G   + A+l+
  gi|118431693|ref|NP_148334.2| 244 FVILAGGTQMGAVLA 258
                                    ****99888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2618.87
//
Query:       gi|118431694|ref|NP_148335.2|  [L=357]
Description: hypothetical protein APE_2032.1 [Aeropyrum pernix K1]
Scores for 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-33  114.0   0.0    1.5e-32  113.3   0.0    1.3  1  CbiZ      Adenosylcobinamide amidohydrolase
  ------ inclusion threshold ------
      0.069   13.2   0.7        0.7    9.9   0.7    2.3  1  PgpA      Phosphatidylglycerophosphatase A
        7.1    7.3   9.0         20    5.8   0.4    4.5  5  LRV       Leucine rich repeat variant


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   2.4e-36   1.5e-32       2     191 ..      18     194 ..      17     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 2.4e-36
                           CbiZ   2 feeprrvlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedlevt 81 
                                    +++p rv+++ ++++G   + ++++ +vpe++++++ +++++++ +++gl  +++v++lTaa++++  ++  +  + e +
  gi|118431694|ref|NP_148335.2|  18 LSTPLRVVTTLPHQPGR--TGYIVFKKVPESFRCDSIASFYRRVRRSMGL--REAVVFLTAAEVDRPLHEVID--EPETH 91 
                                    67899********9997..789****************************..8*************9999988..99*** PP

                           CbiZ  82 avvTaGvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsrysegatGTgTDaiav 161
                                    +++T+G+ + +++ g  +  a++pGTINi+v+++a L+ a  +++l +++EAK+aa  ++ +++ ++  atGT+TDaiav
  gi|118431694|ref|NP_148335.2|  92 IIATVGL-KPPACPGG-TAGAPRPGTINIAVATSAGLSRAGAIDLLRVVAEAKAAAAAEALLPCLHR--ATGTATDAIAV 167
                                    *******.99999998.5799******************************************9888..9********** PP

                           CbiZ 162 aadkegeeeltyaGkhtklGeliaraVyeA 191
                                    +++  g    +++G  t+lG l++r  y A
  gi|118431694|ref|NP_148335.2| 168 LHT-PGA--TDFSGFYTRLGGLVGRSLYFA 194
                                    **9.444..58**************98866 PP

>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.7   0.00012       0.7      65     141 ..     286     350 ..     257     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                                    HHT-TT--HHHHTTHHHHH........TTHHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHHHH CS
                           PgpA  65 ekDpgeiviDEvvgqwiallllpatllalllafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvlal 141
                                    + D ++iv DE+++ ++a +l+ +     lla+i        K    g +d     gl +++DD+++++++ lv++l
  gi|118431694|ref|NP_148335.2| 286 KGDSKAIVADELLAAALAEYLAGF---KGLLATIW-----VEKLKSMGLADA----GLPMFMDDMVSAVVGSLVSRL 350
                                    67999***********99966655...33444443.....566777788887....7999********999999876 PP

>> LRV  Leucine rich repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.88   5.3e+03       5      16 ..     164     173 ..     164     174 .. 0.82
   2 ?    5.8   0.4    0.0034        20       5      22 ..     198     213 ..     196     214 .. 0.92
   3 ?    3.8   0.0     0.015        92      16      25 ..     247     256 ..     245     257 .. 0.88
   4 ?   -2.0   0.0       1.1   6.5e+03       5      15 ..     262     272 ..     261     274 .. 0.80
   5 ?   -3.2   0.0       2.6   1.6e+04       8      17 ..     347     354 ..     345     356 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.88
                            LRV   5 aaVArrPdlPpe 16 
                                    a+++++  +P++
  gi|118431694|ref|NP_148335.2| 164 AIAVLH--TPGA 173
                                    689999..**97 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0034
                            LRV   5 aaVArrPdlPpeaLerLa 22 
                                    aaVArr   P   L++L 
  gi|118431694|ref|NP_148335.2| 198 AAVARR--GPDSLLRALT 213
                                    79****..*******996 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.015
                            LRV  16 eaLerLahDP 25 
                                     +Ler+++DP
  gi|118431694|ref|NP_148335.2| 247 RMLERMMRDP 256
                                    69*******9 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.1
                            LRV   5 aaVArrPdlPp 15 
                                    +++Ar  dl++
  gi|118431694|ref|NP_148335.2| 262 LIAARELDLHG 272
                                    68999988876 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 2.6
                            LRV   8 ArrPdlPpea 17 
                                    ++r  l+ e+
  gi|118431694|ref|NP_148335.2| 347 VSR--LHDEV 354
                                    566..66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 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:                        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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2580.74
//
Query:       gi|118431695|ref|NP_148336.2|  [L=183]
Description: nucleoside triphosphate:adenosylcobinamide-phosphate guanylyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   74.7   0.1    1.2e-20   74.5   0.1    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0029   17.4   0.0     0.0031   17.3   0.0    1.1  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
        0.2   11.2   0.0       0.36   10.4   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.1   1.9e-24   1.2e-20       1     127 [.       4     130 ..       4     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 1.9e-24
                                    EEEEEESS-TTTT.TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                   NTP_transf_3   1 aviLAGGrSsRmg.gdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplasla 77 
                                    ++++AGG++ Rmg ++K+ll ++g+p+l rvl alr a ++++ +v  +  + v++ + +  +  ve  +     ++ l+
  gi|118431695|ref|NP_148336.2|   4 CLVMAGGQGARMGfREKPLLSVCGQPMLLRVLSALRMA-CRRIAIVYSRhtPGVKRLCLSGALGAVECIEGPGSYVKDLR 82 
                                    589**********66*********************99.*******655356788888888888999988889999**** PP

                                    HHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
                   NTP_transf_3  78 aalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                                     + +++  ++++lv+++DmP+l+p++++ ++++a a+ga++v ++ +g+ 
  gi|118431695|ref|NP_148336.2|  83 LGFSHI--STPLLVAPADMPFLNPHHLNLFIDRALADGASIVNLSLRGRG 130
                                    *****9..7******************************99988888775 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.2e-07    0.0031       3      74 ..       4      74 ..       2     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-07
                                   EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG...CCEEEEE-- CS
                           IspD  3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld...ksiqlvaGG 74
                                    ++ A G+G Rm+  ++K +l++ gq++l + ++al    a+ +i +v s++  + ++ l l+     ++ ++G 
  gi|118431695|ref|NP_148336.2|  4 CLVMAGGQGARMGF-REKPLLSVCGQPMLLRVLSALRM--ACRRIAIVYSRHT-PGVKRLCLSgalGAVECIEGP 74
                                   5799********98.6899****************988..9******999887.777777665556567777775 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     6e-05      0.36       3      68 ..       5      63 ..       4      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6e-05
                                   EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTS CS
                NTP_transferase  3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkeg 68
                                   +++aGG+G R+      + k+l+ v g+ +++  +ls+l    +++ i ++ ++h + v++   +g
  gi|118431695|ref|NP_148336.2|  5 LVMAGGQGARMG----FREKPLLSVCGQ-PMLLRVLSALR-MACRR-IAIVYSRHTPGVKRLCLSG 63
                                   69********94....799*********.**********9.58999.7777778888888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1376.10
//
Query:       gi|118431696|ref|NP_148337.2|  [L=354]
Description: threonine-phosphate decarboxylase [Aeropyrum pernix K1]
Scores for complete 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  123.4   0.0    1.4e-35  123.1   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0     8e-40   1.4e-35       6     362 ..      13     346 ..       9     347 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 8e-40
                                    SSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHH CS
                  Aminotran_1_2   6 LgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagalieali 85 
                                    L+s  ++ +    ++p+v     e a + g  ++y++++ +  ++ea+a f++      ++ e +v+ ++Ga +++ +++
  gi|118431696|ref|NP_148337.2|  13 LSSPSNPLG----PPPRVDNIILE-AVERGVHTRYPDYE-YLGFREAVAGFYR------IDLE-RVIPLNGAAEILPLAA 79 
                                    555555555....66666666666.78889999******.*************......9999.**************** PP

                                    HHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET.TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B CS
                  Aminotran_1_2  86 fllklnpgdeilvpdptyasyknilrlsggevvryplyse.edfhldlealeealkeapegnkktkvilvesphNPtGtv 164
                                    ++l+    + i+v +p+++ ++  +  +g++++++ l+++ + f+l   a++ + ++  eg+     i++ +p+NPtG++
  gi|118431696|ref|NP_148337.2|  80 AALR---PRSIVVVEPNFGDHTILALSAGIPCHSVQLREAgDRFSLEPGAVCSLPRSVVEGSL----IVLSNPNNPTGSA 152
                                    ***6...678999*************************99999*********98888665555....************* PP

                                    --HHHHHHHHHHHHHT.TEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEE.EHHHHH CS
                  Aminotran_1_2 165 atleeleklldlakky.nlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilg.naavvs 241
                                    a + +l++l++ a+ +  l ++vDe +a++   +       + +   p+ +++++sl K ++l G+R+G+++  +aa++ 
  gi|118431696|ref|NP_148337.2| 153 AARGDLRELAACATLRgALAVVVDESFADLSRVE-------SVLGSVPEgVIVARSLTKTLALQGLRIGFAYTdDAALAA 225
                                    *************9995566899*********83.......3344444458**********************888999* PP

                                    HHHHHHHHHTSSHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHH CS
                  Aminotran_1_2 242 qlrklsrpflsssllqaavaaalsdallkqs.eleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakel 320
                                     l  + +p+++ s+++ +v   l d   + + ++  + + ++ +  +l+++  +lg k ++sq+ ++l+++ ++     +
  gi|118431696|ref|NP_148337.2| 226 RLDMARQPWNVNSIAALLVERLLGDMASEVKgHIARAIEAIEGLKPRLYSAVSALGAKPYSSQAPFILVRHRRRN--PLF 303
                                    *************************9988888999999**************999**************999988..889 PP

                                    HHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHHH CS
                  Aminotran_1_2 321 skkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelvea 362
                                    ++ Lle  gvy++  +sf+   p + Ri+v +   e le+l ea
  gi|118431696|ref|NP_148337.2| 304 ARCLLEAAGVYIRDASSFRHltPYHSRISV-APGVERLERLQEA 346
                                    999****************999999*****.6666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2765.73
//
Query:       gi|118431697|ref|NP_148338.2|  [L=261]
Description: cobalamin synthase [Aeropyrum pernix K1]
Scores for 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-31  108.4  14.5    6.4e-31  108.1  14.5    1.0  1  CobS       Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1  14.5   3.6e-35   6.4e-31       3     203 ..      11     249 ..       9     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 3.6e-35
                           CobS   3 sflTrlPvp.....elaralaffPlvGlllGlll.llallllllll..llaallavaalvlltgglHlDGlaDtaDglgs 74 
                                    s+lT lP+      e ar+++++Pl  l +G++   + +l+  ++   ++ ++++++a +lltgg+H+DGlaD+ D lgs
  gi|118431697|ref|NP_148338.2|  11 SLLTALPLGggsldEAARSFYLVPLLALAVGAASaSPSALAVEAGVgyIAGGAVYTLAYILLTGGIHMDGLADYSDVLGS 90 
                                    789*****877665558899999**********9999999998888854455555778899******************* PP

                           CobS  75 grdrerrleImkDsrvGafGvlalvlvlllkvaa...laala........lllapvlsRlaallaiallpyae.eglgal 142
                                    + +  ++l+I+kD+r Gaf++lal l+++l +++   ++ l+        ++ ++  + +++ +++a++p+ +  g++++
  gi|118431697|ref|NP_148338.2|  91 RASGGEALRILKDPRKGAFAALALSLAIALSIVFpgeVLRLSspgafiilAASSHSGAAASMYMLLAAGPPEPyRGMARA 170
                                    **********************************76633333667743322233555555566666666655469***** PP

                           CobS 143 faeaqkk.....lvllal.............avlllllall............laallvalllrrlarrklggvtGDvlG 192
                                    f+ +++      +    +             a        l            l  l++ +++ r ar +lg v+GDv+G
  gi|118431697|ref|NP_148338.2| 171 FSLEARGrvalfA----AtstasatassaalA--------LygypwwlvplqwLSSLATGVWVLRSARSTLGYVNGDVAG 238
                                    9874444343330....233444344333220........123333445555556666777888999999********** PP

                           CobS 193 avieltellvl 203
                                    ++ e ++++ +
  gi|118431697|ref|NP_148338.2| 239 FCFEASRIASI 249
                                    ******99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.47u 0.19s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2005.38
//
Query:       gi|118431698|ref|NP_148340.2|  [L=320]
Description: cobalamin biosynthesis protein [Aeropyrum pernix K1]
Scores for complete 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-60  203.9   5.4    3.3e-60  203.6   5.4    1.1  1  CobD_Cbib  CobD/Cbib protein


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.6   5.4   1.9e-64   3.3e-60       1     249 [.      20     280 ..      20     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 203.6 bits;  conditional E-value: 1.9e-64
                      CobD_Cbib   1 lllAlllDlllgdprrl...lhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla..laallglv 75 
                                    l+++l+lDl++ ++r l   lhPv+    ++ +l +    + + r++G++++ll++   ++v++ ll+++  ++++l ++
  gi|118431698|ref|NP_148340.2|  20 LAVGLMLDLAYPEHRGLalkLHPVHTSYIMALRLVR----PGAGRAWGAAIWLLTISSHMMVYASLLAASylVHPALHTL 95 
                                    6799**********999999******9999999977....345688***************9999999665322234668 PP

                      CobD_Cbib  76 lealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaPlfyflll 154
                                    + ++++kl++ lr Ll+++ k  +   +g +e+ R+ v+ iV+Rd s      +++A++Es+aE+l+Dg+++Pl y++ll
  gi|118431698|ref|NP_148340.2|  96 AVGVIVKLSMPLRLLLDTCIKASRMAaAGRVECSRRLVQGIVRRDLSGEPLGRVLSACIESTAESLVDGYTSPLTYYILL 175
                                    88*******************999995599************************************************** PP

                      CobD_Cbib 155 glpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllala.........aalriarrdarkhpSpN 225
                                    g++gal++++ nTlD  vG+k++ + + Gw++A++D+lln+iPARlta+++ala          +lr+++r ar  +S N
  gi|118431698|ref|NP_148340.2| 176 GPLGALLQRLSNTLDGAVGFKTPLLYRQGWFSAKADTLLNFIPARLTAVMVALAaplagastlGSLRCIARCARLLESVN 255
                                    *****************************************************766666555555*************** PP

                      CobD_Cbib 226 sgwpeaalAgalgvrLggpnvY.lg 249
                                    +g+p++a+Agal+vrL++++ Y  +
  gi|118431698|ref|NP_148340.2| 256 AGYPISAFAGALDVRLEKKGFYiVN 280
                                    **********************644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2545.38
//
Query:       gi|118431699|ref|NP_148341.2|  [L=318]
Description: asparagine synthetase [Aeropyrum pernix K1]
Scores for 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-25   88.2   0.2    2.2e-21   76.9   0.1    2.1  2  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.046   13.6   0.3      0.084   12.7   0.3    1.3  1  Rad50_zn_hook  Rad50 zinc hook motif
      0.047   13.7   0.7      0.089   12.8   0.7    1.4  1  DZR            Double zinc ribbon
       0.14   12.8   0.2       0.25   12.0   0.2    1.3  1  PLATZ          PLATZ transcription factor


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 !   76.9   0.1   4.9e-25   2.2e-21      21     149 ..      26     151 ..      12     171 .. 0.86
   2 !    9.3   0.0   0.00017      0.78     234     303 ..     172     238 ..     166     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 4.9e-25
                   Asn_synthase  21 GalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgte.htelvlteeelldalpdviyhlee.. 97 
                                    ++ LSGG+D S +aa+  + +   l++F++++   g ++++ya+ +ae+lg++ h+ +    +++ +a++ v++ +e   
  gi|118431699|ref|NP_148341.2|  26 CITLSGGIDTSFVAAVHPKRR--VLRAFTVDL---GGSDVRYARLAAERLGLKdHIIVNPGLDDFSKAVDWVLRSMEVid 100
                                    468***************988..8********...9****************98888888999**************99* PP

                   Asn_synthase  98 pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsref 149
                                    p+  +++   y++  +a  +g+ +vLsG+G+DElf GY+ f  ++++   e+
  gi|118431699|ref|NP_148341.2| 101 PVEVAASSIHYIALSAAAGEGCGCVLSGDGGDELFLGYS-FLLDKSIGYLEE 151
                                    999999999999999999*********************.887776654444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00017
                   Asn_synthase 234 glEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpKegfsapvgewklkgelre 303
                                    g+++  P+  ++  ++al+ p e  ++g+++K++ R +l+ +  +ei+ R K ++  ++g+    ++l+ 
  gi|118431699|ref|NP_148341.2| 172 GVDVIAPLYSRESRRLALETPLECLVKGRWGKWMIRMLLDELGLREIAFRDKAPVTEGSGSL---AALKS 238
                                    7888889999999999**************************************99988876...34554 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 ?   12.7   0.3   1.9e-05     0.084      16      30 ..     281     295 ..     278     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
                                    TT-SEE-TTT--EE- CS
                  Rad50_zn_hook  16 keakgcCPlCgReld 30 
                                    +++k  CP+CgRel 
  gi|118431699|ref|NP_148341.2| 281 SQEKRACPVCGRELR 295
                                    566779*******96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7     2e-05     0.089       9      41 ..     281     309 ..     277     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                            DZR   9 ppdarfCseCgtklkavaaedrCpsCgekvdpe 41 
                                    ++++r C+ Cg +l+       C  Cg+ v+p+
  gi|118431699|ref|NP_148341.2| 281 SQEKRACPVCGRELR----RGWCRFCGATVSPQ 309
                                    578899********9....8*******999885 PP

>> PLATZ  PLATZ transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   5.6e-05      0.25      53      77 ..     279     303 ..     262     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                          PLATZ  53 skkssseaCetCareLqdeefrfCS 77 
                                    +++++++aC +C+reL+   +rfC 
  gi|118431699|ref|NP_148341.2| 279 KASQEKRACPVCGRELRRGWCRFCG 303
                                    3334568*****************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2348.85
//
Query:       gi|118431700|ref|NP_148342.2|  [L=232]
Description: hypothetical protein APE_2042.1 [Aeropyrum pernix K1]
Scores for 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-22   78.2   0.0    7.2e-22   78.0   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
     0.0024   16.7   0.0      0.003   16.4   0.0    1.1  1  tRNA_Me_trans    tRNA methyl transferase


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 !   78.0   0.0     8e-26   7.2e-22       2     200 ..       4     204 ..       3     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 8e-26
                Diphthami_syn_2   2 kvavlysGGkDsilaLykalke.seve.sLvsvisenkesymfhvvnvhlvellaesvGiplikletaGe...eekeved 76 
                                    k++v +sGGkDs l +y   +  ++ve  Lv+v s  k     h v ++ ve++a + G++l      G+   ee +   
  gi|118431700|ref|NP_148342.2|   4 KTVVSWSGGKDSSLTIYSLYRMgFDVEgVLVTVDSTSKR-VTGHRVPLEAVEAQARAAGLELHIAWLPGDlpsEEVYRSI 82 
                                    999***************99988***9467888887777.899********************99999964325555566 PP

                Diphthami_syn_2  77 Lkgtlkkldvea...vviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLG 153
                                    + +tl++l++ +   +  G++ +    ++  r+ ++ Gl +v PL +  ++ ++e +   +fe++vv+v    l   l  
  gi|118431700|ref|NP_148342.2|  83 VLETLRELRMKGyryIGHGDVFLWDMIEYKRRLAEKAGLEAVYPLVGFGSRGVVEAFFTLGFEALVVSVDTARLPGWLAC 162
                                    7899999996542227789***999999999*****************************************99655557 PP

                Diphthami_syn_2 154 rridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevke 200
                                     r+ ++++++l +      +d age Ge++tlv +aP+f+  l+   
  gi|118431700|ref|NP_148342.2| 163 SRFSREFVENLPST-----VDVAGEYGEFHTLVYNAPFFQEPLRPSV 204
                                    9**********998.....********************98776555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.3e-07     0.003       3      65 ..       5      68 ..       3      94 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-07
                  tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg.keccaeedlkdaervaeklgipl 65
                                    vv  SgG DSs++ + l + g++v+gv + + +++++ + ++ + e+  ++a+++  +l i  
  gi|118431700|ref|NP_148342.2|  5 TVVSWSGGKDSSLTIYSLYRMGFDVEGVLVTVDSTSKRVTgHRVPLEAVEAQARAAGLELHIAW 68
                                   68999***********************999888766655344555444445555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1837.06
//
Query:       gi|118431701|ref|NP_148343.2|  [L=345]
Description: hydrogenase expression/formation protein HypE [Aeropyrum pernix K1]
Scores for complete 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-20   74.0   2.6    1.4e-20   74.0   2.6    1.7  2  AIRS_C    AIR synthase related protein, C-terminal domain
    1.5e-14   54.4   0.9    3.6e-14   53.2   0.9    1.7  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 ?   -2.2   0.0      0.45     4e+03     115     144 ..      90     119 ..      88     128 .. 0.59
   2 !   74.0   2.6   1.6e-24   1.4e-20       1     149 [.     157     311 ..     157     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.45
                                    EEEEEEHGGHHHHHHHHHHTTCCCEEEEEE CS
                         AIRS_C 115 llvavppeeadavlaileeeglpeaavIGe 144
                                    l v+ pp +++  la l    +  a++IG 
  gi|118431701|ref|NP_148343.2|  90 LAVLMPPGSSEDSLASLLGDAVRAAEEIGV 119
                                    556677777744444444444557888886 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 1.6e-24
                                    STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTHHHHHHHH CS
                         AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGGLlgalae 78 
                                    +pGd+++ +++  + g ++ + +  +   ++   +  ++ ++++  ++  ++++++l   g v+a+hD T+GG+lg l e
  gi|118431701|ref|NP_148343.2| 157 RPGDLVLQVKPAAIEGTAIIATDFADMLRSRGVGEDAIAGARMLASRVSIVEEAIELaeAGVVRAMHDPTEGGVLGGLVE 236
                                    79*********9999988888877766666554444455555555555555555555556******************** PP

                                    HHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                         AIRS_C  79 mapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                    ma as+  +e+++dk+ + + ++     +++++l+  +sG ll +vpp++a +++ +lee g+ e++ IG+v a+ 
  gi|118431701|ref|NP_148343.2| 237 MALASRTVIEVEEDKIIVGEATRivasaLGIDPLRLISSGTLLATVPPDKAGEARYVLEELGV-EYSFIGRVAARS 311
                                    **************55555555555556***********************************.8*******9986 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 !   53.2   0.9     4e-18   3.6e-14       2      93 ..      41     144 ..      40     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 4e-18
                                    SSEEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT- CS
                           AIRS   2 Daavvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgv 71 
                                    Daa +v+       + ++p++     +G++av+v+++D+a++GArP++ +l++ +p       l+ ++ +  +aaee+gv
  gi|118431701|ref|NP_148343.2|  41 DAA-IVSLGPIDLVMHLDPITEagalAGWLAVHVAANDIAVTGARPRWEMLAVLMPpgssedSLASLLGDAVRAAEEIGV 119
                                    777.33333233334444444455567********************9999999999*********************** PP

                                    EEEEEEEEEESS...EEEEEEEEEE CS
                           AIRS  72 plvgGdtsfsne...ptisvtavGl 93 
                                    ++vgG+t+  ++   p+i+++a G+
  gi|118431701|ref|NP_148343.2| 120 EIVGGHTEAAPGvprPIIVAAAAGI 144
                                    ********99888899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2589.30
//
Query:       gi|14601803|ref|NP_148344.1|  [L=332]
Description: methionine synthase [Aeropyrum pernix K1]
Scores for 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-69  232.9   0.0    6.5e-69  232.7   0.0    1.0  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
    2.1e-14   53.8   0.0    1.6e-11   44.3   0.0    2.1  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
  ------ inclusion threshold ------
      0.017   14.3   0.0      0.029   13.5   0.0    1.2  1  URO-D        Uroporphyrinogen decarboxylase (URO-D)
       0.12   12.2   0.6       0.12   12.2   0.6    2.1  2  SHOCT        Short C-terminal domain


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 !  232.7   0.0   1.4e-72   6.5e-69       1     323 [.      11     326 ..      11     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 232.7 bits;  conditional E-value: 1.4e-72
                                   S-BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS CS
                   Meth_synt_2   1 lpTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkn 81 
                                   +pTt++GS+P+     ea +++++ge+seee ++ +re i+ vv++   +gvD++++ge  R dmv yf+e+l+g+   + 
  gi|14601803|ref|NP_148344.1|  11 FPTTVVGSYPKIGPASEAIKKRRAGEISEEEFHRIARESIRMVVEDYIWAGVDIISDGEQTREDMVVYFAERLEGYR--EG 89 
                                   8**************************************************************************95..57 PP

                                   --EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-S.S-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHH CS
                   Meth_synt_2  82 gwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltd.kpvkglltGpvtilnwsfvrddvdraeaaaqialalrdevk 161
                                   +wv  + + + r pi+ g v   ++m ++   +a s+   +pvk ++tGp t+l+wsf     dr+e ++++a a+r e+ 
  gi|14601803|ref|NP_148344.1|  90 DWVRVFDNVYFRKPIVAGRVRWVRPMIIEDWEYARSISAgRPVKFIITGPYTMLEWSFDLHYGDRRELIFDLARAIRREID 170
                                   8****************************9999999875378*************************************** PP

                                   HHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--SEEEESBS CS
                   Meth_synt_2 162 dLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvDvitieas 242
                                   +  a G++ iQ+Depal++ +p k+  +a+ l++a     ld i  ++ ++  +H+Cy el+ il+ i +  vD  ++e+ 
  gi|14601803|ref|NP_148344.1| 171 EALARGAEYIQVDEPALST-RPFKE--EAELLKEA-----LDIIFKGVGAKRIVHICYGELERILPYILDYPVDQFDLEMK 243
                                   888889***********98.55555..57888876.....45555556666678*************************** PP

                                   SS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCT..S-STSB-BB-SS-STTS-HHHHHHHHHHHHHH CS
                   Meth_synt_2 243 rsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldv..apkerlwvnPdCGLktrkreearaalknmvda 321
                                   +s+  ll +l+e +y++++g Gv+d+hs +v+s+ e++++i + +++  +  e+++v+PdCGLk+++r+ ara+lknmv+a
  gi|14601803|ref|NP_148344.1| 244 NSNFRLLPYLKEYGYDKEIGYGVIDVHSFQVESVGEVKEAIDRLMKMdiVGPEKVYVDPDCGLKRLPRDVARAKLKNMVEA 324
                                   *******************************************999888889***************************** PP

                                   HH CS
                   Meth_synt_2 322 Ak 323
                                   A+
  gi|14601803|ref|NP_148344.1| 325 AR 326
                                   96 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 !    7.5   0.0   0.00059       2.6       4      68 ..      16      77 ..      13      86 .. 0.86
   2 !   44.3   0.0   3.6e-15   1.6e-11     139     292 ..     121     271 ..     108     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00059
                                  -S---SSTTTTHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHCTT-SBEEES---SS-HHH CS
                   Meth_synt_1  4 ilGfPriGekRelkkalesywkgkiseeeLektakeLrakhwkkqkeagidlipvndfslYDhvL 68
                                  + ++P+iG+  e   a+++  +g+iseee+++ a+e  +  ++ +  ag+d+i+ ++ +  D v 
  gi|14601803|ref|NP_148344.1| 16 VGSYPKIGPASE---AIKKRRAGEISEEEFHRIARESIRMVVEDYIWAGVDIISDGEQTREDMVV 77
                                  457******987...6667779********************************99998888776 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 3.6e-15
                                   HHHHHHHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE-GGGGSSGCHHHHHHHH CS
                   Meth_synt_1 139 evkeakalgieakpvllGpltflkLskakeekveklellekLlpvYkelleeLkeagvewvqidEPalvldlekeelealk 219
                                   e+ +  ++g  +k ++ Gp+t l  s   +   ++ el+ +L  + ++ ++e  ++g+e++q+dEPal++   kee+e+lk
  gi|14601803|ref|NP_148344.1| 121 EYARSISAGRPVKFIITGPYTMLEWSFDLHYG-DRRELIFDLARAIRREIDEALARGAEYIQVDEPALSTRPFKEEAELLK 200
                                   45566789999***************999888.99********************************************** PP

                                   HHHHHHTCCTTTSEEEEE--SS-.CCHHHHHTTSSTSEEEEETSSHCHHHHHHHHCTT.TTSEEEEEEE-SSS CS
                   Meth_synt_1 220 eaYeelakekkelklllatyFdsvaealellaelpveglglDlvraeenlealkkaglpedkvLsaGvidGrn 292
                                   ea + +  +  ++k +++  ++++++ l  ++++pv+ + l++ +++ +l    k ++  dk +  Gvid + 
  gi|14601803|ref|NP_148344.1| 201 EALDII-FKGVGAKRIVHICYGELERILPYILDYPVDQFDLEMKNSNFRLLPYLK-EYGYDKEIGYGVIDVHS 271
                                   ******.588999999***************************996666666665.6778*********9665 PP

>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.4e-06     0.029     178     344 ..     157     326 ..     150     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-06
                                   HHHHHHHHHHHHHHHHHHTT-SEEEEEETTGGGS-HHHHH...HHTHHHHHHHHHHHHH.H--S-EEEEESSHH.H.HHHH CS
                         URO-D 178 lldkltdvvieylkaqieagAdaiqifDswagllspedfe...efvlpylkrivdevkaegpkvpvilfikgagae.iled 254
                                   l+  l++++ + +++ ++ gA+ iq+ +     ls + f+   e+  ++l  i+++v a     + i++i+    e il++
  gi|14601803|ref|NP_148344.1| 157 LIFDLARAIRREIDEALARGAEYIQVDEPA---LSTRPFKeeaELLKEALDIIFKGVGA-----KRIVHICYGELErILPY 229
                                   6666788888999999999******99965...45555541115666777777777777.....89****9775555**** PP

                                   HTTS--SEEE--TTS-HHHHHH......SS.....EEE--B-G.GGGGS-HHHHHHHHHHHHT.T---SSSEEB-BSS-.. CS
                         URO-D 255 laelgadvlsldwtvdlkeaar......evg.dkvalqGnldPialLlgspeeiekevkeilekgaggkkgyilnlGhg.. 326
                                   + + ++d + l+ +++ +   r      e g dk +  G +d +++ ++s  e++++++++++ ++ g+++  + + +g  
  gi|14601803|ref|NP_148344.1| 230 ILDYPVDQFDLEMKNSNF---RllpylkEYGyDKEIGYGVIDVHSFQVESVGEVKEAIDRLMKMDIVGPEKVYVDPDCGlk 307
                                   ********9999999542...2223555888899999******99999***************88999***********88 PP

                                   .--TTS-HHHHHHHHHHHH CS
                         URO-D 327 .ippetppenvkalveavk 344
                                    +p ++  +++k +vea++
  gi|14601803|ref|NP_148344.1| 308 rLPRDVARAKLKNMVEAAR 326
                                   8899***********9986 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   2.6e-05      0.12      10      22 ..      32      44 ..      29      48 .. 0.86
   2 ?   -2.6   0.1       1.2   5.4e+03       6      14 ..     169     177 ..     167     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                         SHOCT 10 yarGeIteEEFea 22
                                  + +GeI+eEEF +
  gi|14601803|ref|NP_148344.1| 32 RRAGEISEEEFHR 44
                                  679********98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                         SHOCT   6 LkeLyarGe 14 
                                    +e +arG+
  gi|14601803|ref|NP_148344.1| 169 IDEALARGA 177
                                   578899995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2429.51
//
Query:       gi|118431702|ref|NP_148345.2|  [L=336]
Description: methylcobalamin:homocysteine methyltransferase [Aeropyrum pernix K1]
Scores for complete 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-21   76.3   0.0    3.1e-20   72.9   0.0    2.1  2  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    4.2e-19   69.0   0.0    6.5e-19   68.4   0.0    1.1  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 !   72.9   0.0   3.5e-24   3.1e-20     101     311 ..      76     286 ..      62     288 .. 0.83
   2 ?    0.7   0.0     0.033     3e+02      67      86 ..     293     312 ..     291     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 3.5e-24
                                    TTCT--EEEESTTSS-EEEE-BE-SS.----S..-THHHHHHHHHHHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHH CS
                    Meth_synt_1 101 kdvaalemtkwFntnYHYlvPelekdtefkla..seklleevkeakalgieakpvllGpltflkLskakeekveklelle 178
                                    ++v+++ + ++F+ n+ Y  P ++ + e +      ++l+    + a   + k v+ Gp+tf  +s+++++  + +el e
  gi|118431702|ref|NP_148345.2|  76 RNVTPTGLLRYFDNNFFYRIPLFTGEPEPTDPvlAPRVLSYS--QVAEPAKLKVVVPGPVTFTLMSRNESGI-SDEELAE 152
                                    567889999**************9875554331133333333..3445668999*************99987.8999*** PP

                                    HHHHHHHHHHHHHHHTT-SEEEEE-GGGGSSGCHHHHHHHHHHHH.HHTCCTTTSEEEEE--SS-.C.CHHHHHTTSSTS CS
                    Meth_synt_1 179 kLlpvYkelleeLkeagvewvqidEPalvldlekeelealkeaYe.elakekkelklllatyFdsva.ealellaelpve 256
                                    ++ ++ ++ +e+  +ag+ +vq+dEP+l+   ++++ ++l +  +  +a+++ +++ +l+ yF   + e +e+l+e  v+
  gi|118431702|ref|NP_148345.2| 153 AIANLLADEVEKAVKAGAGFVQVDEPILSEPKATRDHALLAAELAgVIASRSGSAETMLSVYFYPPKpEVYEALLEARVD 232
                                    *****************************99988888877766651567888999*******988552789********* PP

                                    EEEEETSS.HCHHHHHHHHCTT.TTSEEEEEEE-SSS-B---HHHHHHHHHHHHHC CS
                    Meth_synt_1 257 glglDlvr.aeenlealkkaglpedkvLsaGvidGrniWradlekalelleelaek 311
                                     l +Dlv+ +++ le ++     +++ L++Gvid r i+   lek+ + ++++ e+
  gi|118431702|ref|NP_148345.2| 233 YLMVDLVAaGSKGLEVITG--KGAGEGLALGVIDARSIYSESLEKVEAPVRRIVES 286
                                    ********66777777765..67899*******************99988888765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.033
                                    HHHHHHHTT---GGGTT.SS CS
                    Meth_synt_1  67 vLdtavllgaiPerfkleek 86 
                                    +L+t++ l+ iP r++l+++
  gi|118431702|ref|NP_148345.2| 293 ILTTSTWLDLIPYRYALRKT 312
                                    799************97443 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 !   68.4   0.0   7.2e-23   6.5e-19       5     295 ..       7     292 ..       4     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 7.2e-23
                                    --SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS--E CS
                    Meth_synt_2   5 tiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkngwv 84 
                                    ++G +P +  vr+a +++++ge+s+ e    ++++  +v++ q   g   +v+g  +  d    f+ea   +  t +g +
  gi|118431702|ref|NP_148345.2|   7 VLGGYPRSRYVRRALRRLEQGEISAVELMGVLNQASSAVIGAQVSQGFPYVVDGMLDWHDIFRPFAEAWRNV--TPTGLL 84 
                                    589****************************************************************98776..566677 PP

                                    EEETTE.EE---EE-SS---SS-.SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHHH CS
                    Meth_synt_2  85 qsygsr.cvrppiivgdvsrpaa.mtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalrdevkd 162
                                      + +  ++r p+  g+ + + + ++ ++  + q+ + +++k ++ Gpvt +  s+ +  ++ +e a  ia  l dev++
  gi|118431702|ref|NP_148345.2|  85 RYFDNNfFYRIPLFTGEPEPTDPvLAPRVLSYSQVAEPAKLKVVVPGPVTFTLMSRNESGISDEELAEAIANLLADEVEK 164
                                    66655426899*9999988877735678899999**99****************************************** PP

                                    HHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--SEEEESBS CS
                    Meth_synt_2 163 LeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvDvitieas 242
                                      +aG+  +Q+Dep l+e   ++     + l  a  a  +++ + +++t +++ + y+  +++ +a+ +  vD + ++  
  gi|118431702|ref|NP_148345.2| 165 AVKAGAGFVQVDEPILSEPKATRD----HALLAAELAGVIASRSGSAETMLSVYF-YPPKPEVYEALLEARVDYLMVDLV 239
                                    ******************887776....566677778889999999999999987.66677777***9999997766655 PP

                                    SS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB CS
                    Meth_synt_2 243 rsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldvapkerl 295
                                       ++ le++  ++ g+g+ lGv+d  s   +s e+++a +++++++++ e++
  gi|118431702|ref|NP_148345.2| 240 AAGSKGLEVITGKGAGEGLALGVIDARSIYSESLEKVEAPVRRIVESVKPEKI 292
                                    55555*****************************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 2688.67
//
Query:       gi|118431703|ref|NP_148347.2|  [L=389]
Description: GTP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-23   81.1   0.2    7.5e-23   80.4   0.2    1.4  1  TGS            TGS domain
    2.7e-17   62.9   0.0    6.4e-17   61.7   0.0    1.6  1  MMR_HSR1       50S ribosome-binding GTPase
    9.3e-14   51.3   0.0    1.5e-13   50.7   0.0    1.3  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    1.1e-08   34.8   0.0    2.9e-08   33.4   0.0    1.7  2  FeoB_N         Ferrous iron transport protein B
    8.2e-05   22.6   0.0       0.48   10.3   0.0    3.3  3  RsgA_GTPase    RsgA GTPase
     0.0011   19.1   0.3       0.15   12.3   0.3    2.5  1  YchF-GTPase_C  Protein of unknown function (DUF933)
  ------ inclusion threshold ------
      0.011   15.5   0.0       0.24   11.2   0.0    2.4  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
      0.018   14.7   0.0       0.06   13.0   0.0    1.8  2  Ras            Ras family
      0.063   13.1   0.0       0.14   11.9   0.0    1.5  1  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
      0.069   12.9   0.0       0.14   11.9   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
      0.083   12.6   0.0       0.15   11.8   0.0    1.3  1  AAA_15         AAA ATPase domain
       0.16   12.2   0.0       0.37   11.1   0.0    1.6  1  AAA_22         AAA domain
       0.47   10.9   1.2        5.7    7.4   0.0    2.3  3  AAA_23         AAA 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 !   80.4   0.2   5.4e-26   7.5e-23       1      59 [.     316     387 ..     316     388 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 5.4e-26
                                    EEEEE.TTSSEEE.....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                            TGS   1 irvyt.PdGkvpd.....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                    +rvyt  + k+pd     l+rg+tv+D+A++Ih++l+++f+yA+V+G       qrvg +hv+edgd+veI 
  gi|118431703|ref|NP_148347.2| 316 VRVYTkQPNKEPDkdplvLHRGSTVMDVAKHIHKDLVRRFKYARVWGksvkypgQRVGPEHVVEDGDIVEIH 387
                                    79********************************************************************96 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   4.7e-20   6.4e-17       2     100 ..      84     182 ..      83     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 4.7e-20
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlil 80 
                                    ++++G pN+GKS+++ alt++k +v+d+p+tTr ++ g + +++ ++++vDtp l+    ++ ++++++l l + ad+i+
  gi|118431703|ref|NP_148347.2|  84 AVLIGPPNSGKSSILAALTNAKPEVADYPFTTRMPRAGMLPYEDIQFQIVDTPPLLP--GSGSSVNNRVLGLARnADAII 161
                                    689**************************************99***********997..45668889999877769**** PP

                                    EEEETT....TTCSHHHHHHHHHH CS
                       MMR_HSR1  81 lvvdas....eeklkpldeeleel 100
                                    lv+++         + +d  + e+
  gi|118431703|ref|NP_148347.2| 162 LVFSLDdpnlV---ETIDAVVREV 182
                                    **987653332...3333333333 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 !   50.7   0.0   1.1e-16   1.5e-13       3     105 ..     206     314 ..     204     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.1e-16
                   MMR_HSR1_Xtn   3 GikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDl.....isleeldela 77 
                                    G++i++  +lt+ +e++v+++l++y+i+na v+i++dv++Dd+  ++  n v +p+l +lNK+Dl     + +  +++l 
  gi|118431703|ref|NP_148347.2| 206 GVRIEGPGRLTDATEDDVRRLLSQYRIYNAIVYIEGDVSLDDVESAVYINLVRKPALAILNKADLpgareAAEPAVKRLG 285
                                    999999999********************************************************764433444444444 PP

                   MMR_HSR1_Xtn  78 re.pnsvviSaekelnldeLkekiweeLn 105
                                    +   +++v Sa ++ +l e+  ++++ L+
  gi|118431703|ref|NP_148347.2| 286 EIgIDTIVASALRGDGLGEIAPRLFRMLD 314
                                    43569*****************9999987 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 !   33.4   0.0   2.1e-11   2.9e-08       3      57 ..      84     138 ..      82     176 .. 0.87
   2 ?   -2.2   0.0         2   2.7e+03     107     152 ..     260     305 ..     252     307 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.1e-11
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE---- CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi 57 
                                     +l+G pn+Gk++++ alt+ak +v+ +p +t   + g l +++ +++ivD P  
  gi|118431703|ref|NP_148347.2|  84 AVLIGPPNSGKSSILAALTNAKPEVADYPFTTRMPRAGMLPYEDIQFQIVDTPPL 138
                                    689************************************************9965 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                    SEEEEEETHHHHHHTTE.EE-HHHHHHHHTS-EEEEBTTTTBTHHHH CS
                         FeoB_N 107 pvvlalnmideaekkgi.eidlkkLsekLgvpvvktsakkkegieel 152
                                    p + +ln+ d   +++  e  +k+L  ++g++ + +sa +++g+ e+
  gi|118431703|ref|NP_148347.2| 260 PALAILNKADLPGAREAaEPAVKRL-GEIGIDTIVASALRGDGLGEI 305
                                    5566666666655444303344444.457888888888888887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.044        61     101     122 ..      83     104 ..      73     116 .. 0.85
   2 ?    4.7   0.0     0.018        25      13      46 ..     154     186 ..     126     190 .. 0.78
   3 !   10.3   0.0   0.00035      0.48      50      97 ..     262     309 ..     250     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.044
                                    EEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe 122
                                     +vl+G+   GKS+++ al++ 
  gi|118431703|ref|NP_148347.2|  83 QAVLIGPPNSGKSSILAALTNA 104
                                    579**************99875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.018
                                    EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekg 46 
                                    + N d +++v+sl++p+l  +++d ++ ++e++g
  gi|118431703|ref|NP_148347.2| 154 ARNADAIILVFSLDDPNLV-ETIDAVVREVEDRG 186
                                    679***********99874.56666666666655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00035
                                    EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                    RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                    + +lnK+Dl   +e++e   ++l ++g+++++ sa +++gl e++++l
  gi|118431703|ref|NP_148347.2| 262 LAILNKADLPGAREAAEPAVKRLGEIGIDTIVASALRGDGLGEIAPRL 309
                                    5689**************************************999887 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.3   0.00011      0.15      17      45 ..     334     362 ..     332     389 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                  YchF-GTPase_C  17 ikkgttapqaAgviHsDfekgFiraevik 45 
                                    +++g+t+ + A+ iH+D+ + F  a+v  
  gi|118431703|ref|NP_148347.2| 334 LHRGSTVMDVAKHIHKDLVRRFKYARVWG 362
                                    57899******************999864 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.13   1.8e+02       4      24 ..      84     104 ..      81     175 .. 0.82
   2 ?   11.2   0.0   0.00017      0.24      79     138 ..     248     306 ..     208     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.13
                      PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                     +liG+ +sGK ++  al++ 
  gi|118431703|ref|NP_148347.2|  84 AVLIGPPNSGKSSILAALTNA 104
                                    579999999999999999874 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                      PduV-EutP  79 vfppgfasvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieell 138
                                    v ++ + ++++k+ + i+ k+dl+  +e+ e + ++L + G+++i   sa++ +g+ e+ 
  gi|118431703|ref|NP_148347.2| 248 VESAVYINLVRKPALAILNKADLPGAREAAEPAVKRLGEIGIDTIV-ASALRGDGLGEIA 306
                                    556778899**********************************997.5999999999886 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   4.3e-05      0.06       2      99 ..      84     184 ..      83     189 .. 0.80
   2 ?   -2.7   0.0       2.8   3.8e+03     106     144 ..     260     297 ..     215     311 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                    EEEEESTTSSHHHHHHHHHHSSCS.SSCTTTSSEEEEEEEEEETTEEEEEEEEEE....TTSG.GGHHHHHHHHTTESEE CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFk.eeyesTigvdfytkeievdgkevkleiwDT....AGqe.efkslrelyyrdaegi 75 
                                     vl+G  + GK+s+l   ++ k +  +y  T     + +  ++  ++++++i DT     G     ++      r+a++i
  gi|118431703|ref|NP_148347.2|  84 AVLIGPPNSGKSSILAALTNAKPEvADYPFTT---RMPRAGMLPYEDIQFQIVDTppllPGSGsSVNNRVLGLARNADAI 160
                                    59****************99886514455555...888999999***********5555254414444455678****** PP

                                    EEEEETTBHHHHHTHHHHHHHHHH CS
                            Ras  76 llvyditsresfenvkkwveeikr 99 
                                    +lv+++++ +  e+++  v+e+++
  gi|118431703|ref|NP_148347.2| 161 ILVFSLDDPNLVETIDAVVREVED 184
                                    *****************9999976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.8
                                    EEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTT CS
                            Ras 106 pivLvGnKvDleekravsteegeelakelglkfletSAk 144
                                    p + + nK+Dl   r+  +  +++l  e+g+  + +SA 
  gi|118431703|ref|NP_148347.2| 260 PALAILNKADLPGAREAAEPAVKRL-GEIGIDTIVASAL 297
                                    4455668888887777665555544.3455555555555 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 ?   11.9   0.0    0.0001      0.14       2      22 ..      84     104 ..      84     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                         AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                    +vliGp +sGKS++L al  +
  gi|118431703|ref|NP_148347.2|  84 AVLIGPPNSGKSSILAALTNA 104
                                    59****************655 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 ?   11.9   0.0    0.0001      0.14      22      43 ..      81     102 ..      73     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                         AAA_29  22 kgatlltGpsGsGKSTllDAiq 43 
                                    +g  +l+Gp  sGKS++l A++
  gi|118431703|ref|NP_148347.2|  81 AGQAVLIGPPNSGKSSILAALT 102
                                    45789*************8886 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   0.00011      0.15      27      43 ..      85     101 ..      79     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                         AAA_15  27 vliGkNnsGKSsileal 43 
                                    vliG+ nsGKSsil al
  gi|118431703|ref|NP_148347.2|  85 VLIGPPNSGKSSILAAL 101
                                    8***************9 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   0.00027      0.37       3      34 ..      79     110 ..      76     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                         AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeak 34 
                                    ++ag  v++G++ +GK+  l+ l++ ++e+a+
  gi|118431703|ref|NP_148347.2|  79 SGAGQAVLIGPPNSGKSSILAALTNAKPEVAD 110
                                    578889*******************9988764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.0      0.72   9.9e+02     149     189 ..      23      64 ..       7      67 .. 0.44
   2 ?    7.4   0.0    0.0041       5.7      22      40 ..      84     102 ..      74     132 .. 0.91
   3 ?   -2.8   0.0       5.6   7.7e+03     115     140 ..     217     241 ..     155     266 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.72
                         AAA_23 149 kdkkerleelekeleeledekkllekl.eqekekekeleele 189
                                    ++k ++lee++ +  + + +++ll +   ++ e ++elee++
  gi|118431703|ref|NP_148347.2|  23 EEKIQALEEFISAVPKHKGTENLLLWArRRLAELREELEEKR 64 
                                    344444444444444444433333333334444444444444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0041
                         AAA_23  22 tlItGpNGaGKTTildAik 40 
                                     +++Gp  +GK++il A++
  gi|118431703|ref|NP_148347.2|  84 AVLIGPPNSGKSSILAALT 102
                                    58899************98 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.6
                         AAA_23 115 deleqfisellgskkiilnlilflgq 140
                                    d++e+ +++ l s+++i n i+++  
  gi|118431703|ref|NP_148347.2| 217 DATEDDVRR-LLSQYRIYNAIVYIEG 241
                                    556666665.4567777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2859.48
//
Query:       gi|118431704|ref|NP_148348.2|  [L=225]
Description: hypothetical protein APE_2054.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1786.59
//
Query:       gi|118431705|ref|NP_148349.2|  [L=299]
Description: carbon-nitrogen hydrolase [Aeropyrum pernix K1]
Scores for complete 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-19   69.6   0.0    8.1e-19   68.0   0.0    1.8  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 !   68.0   0.0   4.5e-23   8.1e-19       1     260 [.       6     257 ..       6     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 4.5e-23
                                    EEEEEEBB-..STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEE CS
                   CN_hydrolase   1 rvAvvQlpq..kaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiav 78 
                                    rvAvvQ+++     +  +n  k++ l+++A r + d++v+PE+f +        +         + +++ ++ ++ g++v
  gi|118431705|ref|NP_148349.2|   6 RVAVVQPAPvnNDPSHPGNPLKAAGLVTRASRLDPDIVVFPEYFPF--------H---------ESRGFLDAVADSGVYV 68 
                                    79*******554445568**************************98........2.........46778889999***** PP

                                    EEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS....-SSS-EEEETTEEEEEEEGG CS
                   CN_hydrolase  79 vigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfep....gdgipvfdtpvgkiGaaiCy 154
                                    v+g+++r  ++g+l  ynta++ +++g  + ++rK+          +++er l++     gd + v+d  ++k+G+a+C 
  gi|118431705|ref|NP_148349.2|  69 VAGIAYR--EGGRL--YNTATIYSPEGYPLYRQRKRY--------VGRLERRLWGFdrwsGD-YGVVDIGGVKLGVAVCA 135
                                    *******..9****..*********************........8**********999877.9**************** PP

                                    GGG.SHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHH..HHHHHHTSEEEEEEBEEE................. CS
                   CN_hydrolase 155 eig.fpellralalkgaeilvnlserapvpksmgppqwellgr..aralengcfviaanqvgg................. 214
                                    + + fpe+++ l l ga++ +n s       +m     +++    +ral+   +v+ +  +                   
  gi|118431705|ref|NP_148349.2| 136 DFWsFPEAALELFLGGADLFINPS-------YMFSMEGHWIKAnlSRALDFYTPVVGVDMASFplstkrytfrggglshv 208
                                    *6659*****************55.......4555555555550055555555555555544488888888888888888 PP

                                    ......HCETTEEEE--EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                   CN_hydrolase 215 ......yeqlilwpvghSaiidpdGrilaglgeeeegvliaeidladvratr 260
                                            + ++w v +++ +d ++r+  g ge+     + +id + v+++r
  gi|118431705|ref|NP_148349.2| 209 ivppstGDEANRWWVSGASTADGWVRLKLGSGEDM---GVYTIDVQGVYSWR 257
                                    88888877777777777778888888876655555...44455555777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2165.32
//
Query:       gi|118431706|ref|NP_148350.2|  [L=151]
Description: NUDIX hydrolase [Aeropyrum pernix K1]
Scores for 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   60.2   0.3    2.3e-16   60.0   0.3    1.1  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.099   12.1   0.0        2.4    7.6   0.0    2.2  1  DUF4916   Domain of unknown function (DUF4916)


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 !   60.0   0.3   2.6e-20   2.3e-16       4     123 ..      10     120 ..       7     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.6e-20
                                    EEEEEEEEETTSEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHS..EEE.EEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   4 ravgvvllnekgevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtG..lea.ellellgrlhylapydgpygd 80 
                                    + + +++ +e+g++L+++    ++ ++ +PgG+ve+ E++  +++RE++EE+G  +e+ +ll ++++l++       + +
  gi|118431706|ref|NP_148350.2|  10 VRARCIIEREDGRLLVQWDP--KKEAYVFPGGRVEYSESIPLCLVREMKEEAGiiVEPdKLLYIVEVLET-------DQP 80 
                                    67899************988..444468**********888************54477666666664433.......333 PP

                                    EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCT CS
                          NUDIX  81 eheilyvfleevegelepndenevsevrwvpleellkeklaae 123
                                     heil++f+++ +g+++ +    + +++w ++ee+  ekl+++
  gi|118431706|ref|NP_148350.2|  81 FHEILFYFTCNYKGNPRSR--SKFVQLEWRRPEEF-IEKLWPR 120
                                    789************8887..99************.4444443 PP

>> DUF4916  Domain of unknown function (DUF4916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00027       2.4      56      84 ..      37      65 ..      16     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00027
                                   EEEE--TT--HHHHHHHHHHHHH-TT--B CS
                        DUF4916 56 vsGrvlyhetvreallrhiekdlGelalp 84
                                     Grv y e++   l+r+++++ G ++ p
  gi|118431706|ref|NP_148350.2| 37 PGGRVEYSESIPLCLVREMKEEAGIIVEP 65
                                   57899999999999999998888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1195.20
//
Query:       gi|118431707|ref|NP_148351.2|  [L=107]
Description: hypothetical protein APE_2057.1 [Aeropyrum pernix K1]
Scores for 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   18.8   0.0     0.0014   18.7   0.0    1.0  1  Replic_Relax  Replication-relaxation
  ------ inclusion threshold ------
      0.027   14.8   0.1       0.44   10.9   0.0    2.2  2  Sterol_MT_C   Sterol methyltransferase C-terminal
      0.066   13.1   0.0       0.13   12.2   0.0    1.5  1  MarR_2        MarR family


Domain annotation for each model (and alignments):
>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.4e-07    0.0014       1      88 [.       9      92 ..       9     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-07
                   Replic_Relax  1 LrlLaehrvlTtrqiarllfashratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqra....epep 78
                                   L+ + e +vlT     rl  a + + +  + + L+elgl ++++ r      gs + v+aLt +G+++l a+++    +   
  gi|118431707|ref|NP_148351.2|  9 LKAIGENGVLTPGDAVRLVSAPRYR-VLAAFQVLEELGLAETIYSR------GS-HKVFALTSLGRKVLLAVENgltiRGLL 82
                                   78899999**********9999999.****************8888......33.78************6665556553333 PP

                   Replic_Relax 79 rskrdrrere 88
                                   + + +r+  +
  gi|118431707|ref|NP_148351.2| 83 EEGVERASPT 92
                                   4444444444 PP

>> Sterol_MT_C  Sterol methyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.054   3.2e+02       5      28 ..      25      48 ..      22      53 .. 0.82
   2 ?   10.9   0.0   7.4e-05      0.44       3      48 ..      58     105 ..      56     107 .] 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.054
                    Sterol_MT_C  5 rmtkvGrfithnlvkvleflglap 28
                                   r+ +  r+ + ++ +vle lgla 
  gi|118431707|ref|NP_148351.2| 25 RLVSAPRYRVLAAFQVLEELGLAE 48
                                   55566788888999*******996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7.4e-05
                    Sterol_MT_C   3 vfrmtkvGrfithnlvkvleflglapkGtqkvaefLekA..adsLvaG 48 
                                    vf +t++Gr +  ++ + l + gl  +G+ + + +L++A  ad+++ +
  gi|118431707|ref|NP_148351.2|  58 VFALTSLGRKVLLAVENGLTIRGLLEEGVERASPTLSEAssADQVISS 105
                                    899**********************************99333466655 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05      0.13       4      54 ..       2      50 ..       1      57 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   ++ ++ vL a+g ++   lt+g+ +r    ++ +v  + + L++ GL e+ 
  gi|118431707|ref|NP_148351.2|  2 EGLIYAVLKAIGENGV--LTPGDAVRLVSAPRYRVLAAFQVLEELGLAETI 50
                                   667899********97..9*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 836.99
//
Query:       gi|118431708|ref|YP_874924.1|  [L=126]
Description: hypothetical protein APE_2058 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 904.05
//
Query:       gi|118431709|ref|NP_148352.2|  [L=211]
Description: hypothetical protein APE_2059.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   0.1       0.34   10.4   0.1    1.6  2  Exo5      Exonuclease V - a 5' deoxyribonuclease


Domain annotation for each model (and alignments):
>> Exo5  Exonuclease V - a 5' deoxyribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.11   1.9e+03      19      35 ..      16      32 ..      12      38 .. 0.82
   2 ?   10.4   0.1   1.9e-05      0.34     334     366 ..     175     205 ..     163     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.11
                           Exo5 19 LvspaWCElqyeYtLtk 35
                                   + s+++CE + + +L +
  gi|118431709|ref|NP_148352.2| 16 VASQLYCEYKVHLDLGR 32
                                   57899*****9999977 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 1.9e-05
                           Exo5 334 eelawWrgeReaegVeieeafkCrsCeFaeeCe 366
                                    + l++WrgeR++e+ +  +  +C +C ++  Ce
  gi|118431709|ref|NP_148352.2| 175 RLLQYWRGERPPEPRPSPS--RCAKCRYKGLCE 205
                                    6799*********977655..566666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1688.08
//
Query:       gi|118431710|ref|NP_148353.2|  [L=391]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.1e-34  117.5   0.0    8.9e-34  116.9   0.0    1.2  1  ABC_tran     ABC transporter
    1.1e-09   38.5   0.5    0.00055   19.8   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00044   19.7   0.0        0.6    9.5   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0023   17.6   0.0     0.0045   16.7   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0084   16.9   0.1      0.032   15.1   0.0    2.0  1  OB_MalK      MalK OB fold domain
  ------ inclusion threshold ------
      0.013   16.0   0.3      0.029   14.9   0.0    1.6  2  AAA_23       AAA domain
      0.017   15.4   0.0      0.033   14.5   0.0    1.5  1  TOBE         TOBE domain
      0.018   15.4   0.0      0.059   13.8   0.0    1.7  2  AAA_16       AAA ATPase domain
      0.037   13.1   0.0      0.081   12.0   0.0    1.5  1  T2SSE        Type II/IV secretion system protein
      0.063   13.7   0.0       0.19   12.1   0.0    1.8  1  AAA          ATPase family associated with various cellular a
      0.067   13.5   0.1       0.19   12.0   0.1    1.8  1  AAA_22       AAA domain
      0.091   12.5   0.0       0.21   11.3   0.0    1.5  1  AAA_30       AAA domain
       0.11   12.4   0.0        0.2   11.5   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
       0.14   11.5   0.0         12    5.1   0.0    2.2  2  ATPase       KaiC
       0.15   11.9   0.0       0.34   10.8   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
       0.16   12.0   0.0       0.45   10.6   0.0    1.8  1  AAA_14       AAA domain
        0.2   11.4   0.0       0.42   10.3   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein
        0.2   10.8   0.0       0.38    9.9   0.0    1.4  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 !  116.9   0.0   8.9e-37   8.9e-34       2     136 ..      20     161 ..      19     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.9 bits;  conditional E-value: 8.9e-37
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++v+l ++  e v i+G++G+GK+tLl l+ag +kp  G+i +++ d+++  l+  +++ig ++q+  l p++tv+en  
  gi|118431710|ref|NP_148353.2|  20 RDVNLYIEDKEFVSILGPSGSGKTTLLYLIAGIYKPSRGRIYFNDVDVTD--LPPNKRNIGLVFQNYALYPHMTVYENia 97 
                                    699*****************************************999999..**************************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               + +e++  +++ lg+++l d+      ++LSgGq+qrvalaral+k+p++lllDEp 
  gi|118431710|ref|NP_148353.2|  98 fplrlrnfgepAIKEKVLSVAKLLGIEGLLDRYP----AQLSGGQQQRVALARALVKEPEVLLLDEPL 161
                                    **********999999************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   3.7e-06    0.0037       3      74 ..      33      95 ..      31     114 .. 0.83
   2 !   19.8   0.1   5.5e-07   0.00055     230     299 ..     127     194 ..      99     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryry 74
                                    + Gp gsGK++LL+++ ++          +++++++  ++++   l+++  +i  +f+ + +  ++++y+ 
  gi|118431710|ref|NP_148353.2| 33 SILGPSGSGKTTLLYLIAGI---------YKPSRGRIYFNDVDVTDLPPNKRNIGLVFQNYALYPHMTVYEN 95
                                   699***************99.........5788888888888888888888888888888888777777765 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.5e-07
                         AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                     ++ +++lS G+++  al+ al   +    +ll+DEp ++L+  l  ++   lk+l++  g+  i +TH+ 
  gi|118431710|ref|NP_148353.2| 127 LDRYPAQLSGGQQQRVALARALVKEP---EVLLLDEPLSNLDALLRIKIRSELKKLQKeLGITAIYVTHDQ 194
                                    56678999***999999999999888...9********************999888888**********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 !    8.2   0.0    0.0015       1.5      23      42 ..      28      47 ..      19      52 .. 0.87
   2 !    9.5   0.0   0.00061       0.6     134     207 ..     131     203 ..      69     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                                   TSSEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 23 sksftaivGpNGSGKsnlld 42
                                   +k+f +i+Gp GSGK+ ll 
  gi|118431710|ref|NP_148353.2| 28 DKEFVSILGPSGSGKTTLLY 47
                                   5789************9986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00061
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHH.HCCC-SC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislree.mlekadk 207
                                    + +LSgG+++ vala       vk   + llDe  ++LD+  + k+ + lk+ +k+     i +++++   l+ ad+
  gi|118431710|ref|NP_148353.2| 131 PAQLSGGQQQRVALARA----LVKEPEVLLLDEPLSNLDALLRIKIRSELKKLQKElgITAIYVTHDQSeALAMADR 203
                                    449******99988754....455666789***********************999444445555554303333344 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   4.5e-06    0.0045      18      55 ..      25      63 ..      13      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                         AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                    i+ k+++ + GpsGsGK+Tll  i+ +  p++ ++ fN
  gi|118431710|ref|NP_148353.2| 25 YIEDKEFVSILGPSGSGKTTLLYLIAGIYKPSRgRIYFN 63
                                   566667899************987777777777777777 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.2e-05     0.032       1      51 [.     235     286 ..     235     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.2e-05
                        OB_MalK   1 GSPaMNflpatveedg.vlvegggvtlplpeeqklalklyagkevilGiRPE 51 
                                    G+P+ N++ + ++ +   l++ gg +   p++ + +l++ +   vilG+RPE
  gi|118431710|ref|NP_148353.2| 235 GTPPANLVSVPLDSSRrCLLLPGGGRYCPPRRIAEKLAAVKTNSVILGFRPE 286
                                    99***********888955555554555466655699999***********9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0     3e-05     0.029      12      39 ..      21      49 ..       4      53 .. 0.80
   2 ?   -2.6   0.2       6.7   6.6e+03     180     192 ..     171     183 ..     139     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                         AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAi 39
                                   d+++   +k ++ I Gp G+GKTT+l  i
  gi|118431710|ref|NP_148353.2| 21 DVNLYIeDKEFVSILGPSGSGKTTLLYLI 49
                                   4555556788999************9776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.7
                         AAA_23 180 ekekeleeleeel 192
                                    + + el++l++el
  gi|118431710|ref|NP_148353.2| 171 KIRSELKKLQKEL 183
                                    3444555555543 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.3e-05     0.033       8      63 ..     302     352 ..     300     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                           TOBE   8 pgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                    +++V+ ve+lg e  V++ ++g + + + v++   ++    pG+++f+ i   kv+
  gi|118431710|ref|NP_148353.2| 302 EAEVYTVETLGRENIVTLLVNGSQ-VKVIVPPVVEPR----PGSRIFINIEEDKVM 352
                                    799*********************.************....*******99999986 PP

>> AAA_16  AAA ATPase 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     0.059      25      51 ..      30      56 ..      19      88 .. 0.80
   2 ?   -1.6   0.0       3.1   3.1e+03      71     106 ..     143     177 ..     119     217 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekd 51
                                   e v + G+sG+GK++l+  ++  ++ +
  gi|118431710|ref|NP_148353.2| 30 EFVSILGPSGSGKTTLLYLIAGIYKPS 56
                                   7899*************8888666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.1
                         AAA_16  71 alaqalareellrqlldeaesaeleawrekleeala 106
                                    ala+al + e    llde+ s++ +  r k++++l+
  gi|118431710|ref|NP_148353.2| 143 ALARALVK-EPEVLLLDEPLSNLDALLRIKIRSELK 177
                                    45555544.333444444455555555555555555 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   8.2e-05     0.081     128     160 ..      28      60 ..      20      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.2e-05
                          T2SSE 128 erglilvsGgTgsGKttllyallkeinksderi 160
                                     +  + + G+ gsGKttlly +  + + s  ri
  gi|118431710|ref|NP_148353.2|  28 DKEFVSILGPSGSGKTTLLYLIAGIYKPSRGRI 60 
                                    55666688************9998888776666 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   0.0   0.00019      0.19       3      66 ..      34     159 ..      32     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                    EESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCS.SS....................................... CS
                            AAA   3 lyGppGtGKTllakavakelg.....vefleisgsell.sk....................................... 37 
                                    + Gp G GKT+l   +a   +     ++f  +++++l  +k                                       
  gi|118431710|ref|NP_148353.2|  34 ILGPSGSGKTTLLYLIAGIYKpsrgrIYFNDVDVTDLPpNKrniglvfqnyalyphmtvyeniafplrlrnfgepaikek 113
                                    68****************98655555778888888888555777777777777777777777777777777777777777 PP

                                    ................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                    y  + +   ++ ++ a++   +p +l++DE
  gi|118431710|ref|NP_148353.2| 114 vlsvakllgieglldrYPAQLSGGQQQRVALARALVkEPEVLLLDE 159
                                    7777777777777777444444444444444444434477777777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00019      0.19       4      25 ..      28      49 ..      25     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                         AAA_22  4 tagilvvtGesGtGKTtllrrl 25
                                   ++ ++ + G+sG+GKTtll  +
  gi|118431710|ref|NP_148353.2| 28 DKEFVSILGPSGSGKTTLLYLI 49
                                   678999***********98665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.21      18      47 ..      29      58 ..      21      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaagg 47
                                   + ++ + Gp G+GKtt+l  ++ +++ + g
  gi|118431710|ref|NP_148353.2| 29 KEFVSILGPSGSGKTTLLYLIAGIYKPSRG 58
                                   4578899**************999987744 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    0.0002       0.2      16      57 ..      27      65 ..      16      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                   e   +e++ i Gp gsGKt+Ll  i+   +  +  +iy++++
  gi|118431710|ref|NP_148353.2| 27 E--DKEFVSILGPSGSGKTTLLYLIAGIYKP-SRGRIYFNDV 65
                                   3..488999************9887776644.5577887776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.012        12      18      46 ..      28      54 ..      25      91 .. 0.79
   2 ?    4.0   0.0     0.027        27     138     185 ..     166     212 ..     155     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
                         ATPase 18 egrvvlitGepGtGKtifalqFlikgaek 46
                                   +++ v i G +G+GKt++   +li g+ k
  gi|118431710|ref|NP_148353.2| 28 DKEFVSILGPSGSGKTTL--LYLIAGIYK 54
                                   678899**********97..467777655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.027
                         ATPase 138 avaReilrqlvrvl.kklgvTailvsekssseeaaggygveefivdgvi 185
                                    a++R  +r  ++ l k+lg+Tai v+   +se  a   +++  i++gvi
  gi|118431710|ref|NP_148353.2| 166 ALLRIKIRSELKKLqKELGITAIYVTHD-QSEALAMADRIAI-IASGVI 212
                                    5667777766666769*********994.5556666677777.777777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00034      0.34      92     121 ..      21      51 ..      11      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                                    HHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +++ +++d +++ ++G+SG GK+tL+  +++
  gi|118431710|ref|NP_148353.2|  21 DVNLYIEDkEFVSILGPSGSGKTTLLYLIAG 51 
                                    5666777768899************988765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00045      0.45       3      40 ..      30      66 ..      28      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00045
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldd 40
                                   + + i G+  +GKTtll+ ++  +  +++  +y+n  d
  gi|118431710|ref|NP_148353.2| 30 EFVSILGPSGSGKTTLLYLIAGIYK-PSRGRIYFNDVD 66
                                   6789*************99987666.777777776444 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 ?   10.3   0.0   0.00042      0.42      43      64 ..      25      46 ..      15      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                      IstB_IS21 43 fiekkenivllGpsGvGKshla 64
                                   +ie+ke + +lGpsG GK+ l 
  gi|118431710|ref|NP_148353.2| 25 YIEDKEFVSILGPSGSGKTTLL 46
                                   89*****************885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00038      0.38      17      38 ..      28      47 ..      19      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00038
                                   TSCSEEEEEEESTTSSHHHHHH CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlak 38
                                   + +  +v++ G  G+GKttl+ 
  gi|118431710|ref|NP_148353.2| 28 DKE--FVSILGPSGSGKTTLLY 47
                                   444..9*************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 3132.03
//
Query:       gi|118431711|ref|NP_148354.2|  [L=979]
Description: ribonucleotide reductase, B12-dependent [Aeropyrum pernix K1]
Scores for 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-126  422.6   0.0    3.2e-92  309.7   0.0    2.5  2  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    5.2e-14   52.0   0.4    1.3e-13   50.8   0.4    1.6  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
       0.24   11.6   1.9       0.67   10.2   0.1    2.9  2  DUF2795          Protein of unknown function (DUF2795)


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 !  110.2   0.0   1.6e-35   9.7e-32       1      92 [.     144     235 ..     144     236 .. 0.99
   2 !  309.7   0.0   5.4e-96   3.2e-92      93     524 .]     297     899 ..     290     899 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.6e-35
                                    EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAa 80 
                                    s+C+v+ v d+++sI+++++ +a+++k+ggG G+++s+lR++ ++v+gt+g +sGp+sfm+l+d+v++ vkqgGkRrGA+
  gi|118431711|ref|NP_148354.2| 144 SACYVTPVYDDMDSIMDAATVQAKTFKWGGGQGFSFSELRPRWDVVRGTSGYSSGPMSFMRLYDTVTELVKQGGKRRGAN 223
                                    79****************************************************************************** PP

                                    XXXXXXXXXXXX CS
                                    xxxxxxxxxxxx RF
                Ribonuc_red_lgC  81 mvylevwHpDie 92 
                                    m++++vwHpDi 
  gi|118431711|ref|NP_148354.2| 224 MGIMHVWHPDIY 235
                                    **********96 PP

  == domain 2  score: 309.7 bits;  conditional E-value: 5.4e-96
                                    XXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...........XXX................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx............. RF
                Ribonuc_red_lgC  93 kfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrt...........vvkleklyg............. 148
                                     fi+aK+      + +l+n+nisvg +d Fm+av e++dw +++Pr                                  
  gi|118431711|ref|NP_148354.2| 297 GFIQAKKPPLQ--DANLTNFNISVGANDAFMQAVVEGGDWWMVNPRYtasdragiykiH-------Ysiskatglgrlgt 367
                                    59****77666..9********************************8666666666652.......04444444666666 PP

                                    .....................................................XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    ......................xxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 149 ......................eefeeeyeeleekakik............kkevkakeLfeeiaesawetgePgvlfkD 194
                                                          e++ +++e lee+a+ +                +a+e+++ei+e+aw  g+Pg++++D
  gi|118431711|ref|NP_148354.2| 368 liekhpwllenpyinlfedvisEALPKALEMLEEQARKTgmpadprqknvhAWVAPAREIWREIVEAAWGGGDPGLVYFD 447
                                    66666666655555555555546677777777777555568899986555333559************************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 195 tiNrrnvlekakggkIratNlCgEiplleyesvavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvn 274
                                    + N+++++ +   g+++atN+C+E++l++ e    CnL+s+ + k+v        +fd++++++ ++ +++a+d+vid+n
  gi|118431711|ref|NP_148354.2| 448 NHNKWSPTPW--LGAVNATNPCSEQTLYPFEP---CNLGSLSVDKYV-----AGGRFDLERFANDVEFLTEAMDAVIDLN 517
                                    ********54..58******************...************.....578************************* PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 275 kyplpeiekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskg 354
                                    + p +++++++k tR+iGlG+mgladala lg+pydseea++f+  ++  l + ++k+S e+  + g  p fe   +   
  gi|118431711|ref|NP_148354.2| 518 RHPDERQDTANKFTRKIGLGIMGLADALAGLGYPYDSEEAVAFTTILMAGLEVFSWKRSWEMGARLGHAPAFECRMFDWR 597
                                    ************************************************************************87665555 PP

                                    XXXXXXX..X...................................................................... CS
                                    xxxxxxx..xxxx................................................................... RF
                Ribonuc_red_lgC 355 ilpvdef..eeke................................................................... 365
                                     l+++e   +  e                                                                   
  gi|118431711|ref|NP_148354.2| 598 SLECREKgsP--Eelaelhtpalvkagmvarlegewlkvryhsidlngpaaevlekafgerferdgsvrlvrrdaldava 675
                                    5555555332..12456777888899999999999999999*************************************** PP

                                    .......................................XXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    ....................................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 366 ....................................kedweeLreeikkyGl...rnamvtalaPTgsiSliagtssgie 406
                                                                         e w+ Lre  ++ G    rn+++t++aPTg+iS++agtssgie
  gi|118431711|ref|NP_148354.2| 676 rrvfgisedmalealnmgpaavesprhllalavykpMEAWRLLREYGRRLGAkapRNTVTTTIAPTGTISILAGTSSGIE 755
                                    ************************************9********99988865559************************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXX.......................XXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.......................xxxxxxxxxx RF
                Ribonuc_red_lgC 407 PifalvykksvtvgeflevnpvfeeeLkklglwse...ellkkiles.......................vqgleeipee 460
                                    P+falvyk++v+vg flev   f e+L k   ++    ++l+ ++e+                        +g  e   +
  gi|118431711|ref|NP_148354.2| 756 PYFALVYKRQVAVGTFLEVVSRFREDLLKAAEKHGvgrDVLEIVYEEvrrhkgslrwslnvlaekldgrvDDGFLEELAR 835
                                    **************************9877665431114444445556677889999*****999999965566666788 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                Ribonuc_red_lgC 461 ikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                    + r + t++d     h+ +q a+q ++dq+iSkt+nlp +at +dv++ yl Aw  GlKg+t+Y
  gi|118431711|ref|NP_148354.2| 836 LARKYATSMDFPLWYHLAHQIAAQLYVDQAISKTVNLPRTATPDDVEASYLAAWLGGLKGFTVY 899
                                    999************************************************************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 !   50.8   0.4   2.1e-17   1.3e-13       3      78 ..      70     134 ..      68     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.1e-17
                Ribonuc_red_lgN   3 ltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmna 78 
                                    +tyna++vl++rY+ kde g+ +E+p  +++RvAl++ +           + + +++y+l+++++f+ +sPtl+n+
  gi|118431711|ref|NP_148354.2|  70 FTYNAVRVLMARYMVKDEMGRFLETPSMVMRRVALGFRE-----------RVDPDRLYRLLVERRFMFNSPTLFNM 134
                                    9************************************76...........77889********************7 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00011      0.67      10      30 ..     779     799 ..     779     801 .. 0.94
   2 ?   -4.3   0.2         3   1.8e+04      10      20 ..     919     929 ..     919     930 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                        DUF2795  10 KdeLveyArrngApdevleaL 30 
                                    +++L+++A+++g++ +vle++
  gi|118431711|ref|NP_148354.2| 779 REDLLKAAEKHGVGRDVLEIV 799
                                    89****************986 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 3
                        DUF2795  10 KdeLveyArrn 20 
                                    ++ L+++Ar++
  gi|118431711|ref|NP_148354.2| 919 RGRLLRRARKA 929
                                    6789****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (979 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.72u 0.23s 00:00:00.95 Elapsed: 00:00:00.39
# Mc/sec: 7591.22
//
Query:       gi|118431712|ref|NP_148355.2|  [L=325]
Description: thymidylate synthase [Aeropyrum pernix K1]
Scores for 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-58  195.1   0.0    3.2e-57  193.4   0.0    1.7  1  Thy1      Thymidylate synthase complementing protein


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.4   0.0   1.8e-61   3.2e-57       1     187 [.      15     258 ..      15     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 193.4 bits;  conditional E-value: 1.8e-61
                                    EEEEEE.CHHHHHHHHHHHHHTTCSSHHHH..S.GCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTS CS
                           Thy1   1 kLldyt.dpeklvaaaarvcygsseeaeele.e.eekkeklikkllkhghgsplehasftfeiegvSravlrqlvrHRia 77 
                                    +Ll+yt d e++va a +v+ + ++ ae+l    e++ e++i + ++++h sp+eh+++tf +eg+Sr++++qlvrHR+a
  gi|118431712|ref|NP_148355.2|  15 RLLEYTgDGERIVAVASKVSLS-RSPAERLLaIgEDEVETWILETFRRQHFSPWEHSVYTFMVEGLSRVASHQLVRHRVA 93 
                                    69*******************5.5677777765689999***************************************** PP

                                    EEEE--TTTSGCCCTC......................................................BS--GGGCC. CS
                           Thy1  78 sfsqqSqRYvesskea......................................................fvippeieqk 103
                                    s++q S RY+e   ++                                                      fvipp+i ++
  gi|118431712|ref|NP_148355.2|  94 SYTQLSHRYSEGYLREaalkacesigldcpskpaeteggrkaayrlysqaleraardfgaserfaiaakaFVIPPTILAR 173
                                    **************555*************************************************************64 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHHH.HHHHHSSTTS-HHHHHHHHHHHHHH CS
                           Thy1 104 eeleelyeeamekaleaykelleagvarEdaryvLPlatktklvvtmNlrsLlh.flelracsrAqwEirelaeemleel 182
                                     +  + + ea+ ++ + y+ ll++g  rEdary+LP+a++t++vvtmN+r+L++ f+ lr+c+rAqwEir++a+ +++el
  gi|118431712|ref|NP_148355.2| 174 GDGGDGVVEAYLRSAAIYYSLLSRGARREDARYILPDALRTRIVVTMNARELIQvFFPLRMCTRAQWEIRHIAWLLWREL 253
                                    33445566788888888999************************************************************ PP

                                    HHHSH CS
                           Thy1 183 kkvaP 187
                                    ++v+P
  gi|118431712|ref|NP_148355.2| 254 SRVHP 258
                                    ***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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 0.20s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 2773.68
//
Query:       gi|118431713|ref|NP_148356.2|  [L=84]
Description: hypothetical protein APE_2065.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 740.75
//
Query:       gi|118431714|ref|NP_148357.2|  [L=385]
Description: glycosyl transferase, group 1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-44  150.2   0.0    1.4e-43  148.4   0.0    1.9  3  Glycos_transf_1  Glycosyl transferases group 1
    3.8e-32  111.5   0.0    1.4e-31  109.6   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-24   86.9   0.2    2.4e-24   86.2   0.2    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
    4.4e-14   53.2   0.2    1.5e-13   51.5   0.0    2.0  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.1e-13   51.4   0.0      3e-13   50.0   0.0    1.7  2  Glyco_trans_1_2  Glycosyl transferases group 1
    3.3e-05   23.9   0.0    8.6e-05   22.6   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.028   13.1   0.0      0.048   12.4   0.0    1.3  1  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
      0.033   13.9   0.1        1.5    8.5   0.0    2.3  2  Glyco_transf_5   Starch synthase catalytic domain
      0.038   14.6   0.0      0.078   13.6   0.0    1.5  1  PIGA             PIGA (GPI anchor biosynthesis)
      0.049   12.6   0.0      0.091   11.7   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.18   12.2   0.0        0.4   11.1   0.0    1.5  1  EnY2             Transcription factor e(y)2
       0.19   11.4   0.1         21    4.8   0.0    2.2  2  DUF3492          Domain of unknown function (DUF3492)


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 ?   -3.4   0.0       4.1   6.1e+03     115     126 ..     120     131 ..     117     134 .. 0.81
   2 ?   -0.8   0.0      0.65   9.8e+02     117     148 ..     160     193 ..     156     200 .. 0.84
   3 !  148.4   0.0   9.2e-47   1.4e-43       6     171 ..     193     358 ..     188     359 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.1
                                    TT--EEEETTTT CS
                Glycos_transf_1 115 aglpviasnagg 126
                                    +glp ia+n++ 
  gi|118431714|ref|NP_148357.2| 120 LGLPRIATNHSI 131
                                    79*******875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.65
                                    --EEEET.TTTHCHHCHTTTSEEEE-TT.-HHHH CS
                Glycos_transf_1 117 lpviasn.aggpaevvkdgetGllvkpn.naeal 148
                                    ++ ++++  +++  +v d ++ ++++++ ++e +
  gi|118431714|ref|NP_148357.2| 160 VISVSTAaDKMVEGIVGDSVDRYIIPNGvDVERF 193
                                    56677887899999************99898876 PP

  == domain 3  score: 148.4 bits;  conditional E-value: 9.2e-47
                                    HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsred 85 
                                    +k +  + + +++l++grl+ +Kg ++l++af+++ ++   ++kl i G+ge e  +k l++ ++l++nv++lg v++++
  gi|118431714|ref|NP_148357.2| 193 FKPSTPKADYPLVLFLGRLVWRKGAHVLVRAFRHVVDE-IRDAKLYIGGKGEFEPIIKLLIARYGLENNVKMLGVVPESE 271
                                    3444445899*************************997.***************************************** PP

                                    HHHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHH CS
                Glycos_transf_1  86 leellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrer 164
                                    +++l+++a ++++psi  E+fGiv+lE++++g+pv+as  gg+++vvk+g+tGllvkp++ ++la+a++ ll+d+ lr+r
  gi|118431714|ref|NP_148357.2| 272 KPSLYSSAWVTAVPSIVnESFGIVALESLSSGTPVVASRQGGLKDVVKHGKTGLLVKPGSSKELAKALITLLQDSGLRKR 351
                                    ******************************************************************************** PP

                                    HHHHHHH CS
                Glycos_transf_1 165 lgenark 171
                                    ++e+ark
  gi|118431714|ref|NP_148357.2| 352 MSEEARK 358
                                    *****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 ?   -1.4   0.0         2     3e+03      15      39 ..      27      52 ..      13     131 .. 0.55
   2 !  109.6   0.0   9.7e-35   1.4e-31       2     134 .]     203     345 ..     202     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2
                                   GTHHHHHHHHHHHH.H.HEEEEEES- CS
                Glyco_trans_1_4 15 kgvdllleavpllrkk.dvrlvivGd 39
                                    gv+  ++ + +l+++  + +viv +
  gi|118431714|ref|NP_148357.2| 27 GGVQSHVRDLTRLLQDfGYDVVIVSR 52
                                   55555555554444332244444442 PP

  == domain 2  score: 109.6 bits;  conditional E-value: 9.7e-35
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                    p +lf+Grl  ++kg+++l++a+ ++ ++  d++l+i G+g+ +p  ++ l+a  gle++v+++G v  +++++l+++a+
  gi|118431714|ref|NP_148357.2| 203 PLVLFLGRL-VWRKGAHVLVRAFRHVVDEirDAKLYIGGKGEfEP-IIKLLIAryGLENNVKMLGVVpeSEKPSLYSSAW 280
                                    679******.567**********999978755*********9887.666555569************8666********* PP

                                    EEEE--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  75 vfvaPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    v+ +Ps   e+fg+++lE++++g+pvVa++ gg+++vv  g++gllv+pg++++la+a+++Ll+d
  gi|118431714|ref|NP_148357.2| 281 VTAVPSivnESFGIVALESLSSGTPVVASRQGGLKDVVkhGKTGLLVKPGSSKELAKALITLLQD 345
                                    ********99*****************************************************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 !   86.2   0.2   1.6e-27   2.4e-24       1     170 []      26     192 ..      26     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 1.6e-27
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                    vGGv+ hv++L+r L++ G++V++v+++ ++   +       +  v ++++    + ++ +++lrr ++  kpDvvH+h+
  gi|118431714|ref|NP_148357.2|  26 VGGVQSHVRDLTRLLQDFGYDVVIVSRALGKGDVKD-LEAEGHYIVKPLFPLEIIFVPPDPSDLRREIESLKPDVVHSHH 104
                                    7************************88877777766.34445555556678889999*********************** PP

                 Glyco_transf_4  81 paalgaallalrr..rlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppek 158
                                     ++l  +llal++   lg+p ++t H+ +   + k  l++   ++    r+ll +a++vi vS a+ + ++   g ++ +
  gi|118431714|ref|NP_148357.2| 105 IYTLT-SLLALKAarDLGLPRIATNHSIF-LAYDKVALWRIASIVLP-TRYLLPNAQAVISVSTAADKMVEGIVG-DSVD 180
                                    88873.3333333347*************.55556666666666665.67789*******************888.5555 PP

                 Glyco_transf_4 159 itVipnGvDler 170
                                     ++ipnGvD+er
  gi|118431714|ref|NP_148357.2| 181 RYIIPNGVDVER 192
                                    5*********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 !   51.5   0.0     1e-16   1.5e-13       1     160 []      27     187 ..      27     187 .. 0.80
   2 ?   -1.9   0.1       2.8   4.2e+03      77     106 ..     198     226 ..     189     236 .. 0.60
   3 ?   -3.1   0.0       6.4   9.6e+03      71      95 ..     289     312 ..     264     349 .. 0.55

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1e-16
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape.leedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvha 79 
                                    gG++ +v++l r L++ G++V+++ +a   g+   le++g +++  p+ + +     +  + +lrr +  ++ +pdvvh+
  gi|118431714|ref|NP_148357.2|  27 GGVQSHVRDLTRLLQDFGYDVVIVSRALGKGDVKdLEAEG-HYIVKPLFPLE-IIFVPPDPSDLRREI--ESLKPDVVHS 102
                                    8************************886666443155555.45555888886.556666778899999..9********* PP

                Glyco_trans_4_4  80 hs.pt.aglaarlarrrrgiplvvtlhg..lllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvpadrvv 155
                                    h+ +t ++l+a+ a+r  g+p + t h+  l++++ + ++ + +    r+ll +a av++vs+a  + ++   ++  +  
  gi|118431714|ref|NP_148357.2| 103 HHiYTlTSLLALKAARDLGLPRIATNHSifLAYDKVALWRIASIVLPTRYLLPNAQAVISVSTAADKMVEGIVGDSVDRY 182
                                    **6557556666666599*********95566666688887777888****************98777777889989999 PP

                Glyco_trans_4_4 156 vvpng 160
                                    ++png
  gi|118431714|ref|NP_148357.2| 183 IIPNG 187
                                    99998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                Glyco_trans_4_4  77 vhahsptaglaarlarrrrgiplvvtlhgl 106
                                      a +p+  +++rl   r+g+ ++v ++ +
  gi|118431714|ref|NP_148357.2| 198 PKADYPLVLFLGRLVW-RKGAHVLVRAFRH 226
                                    5555566666666666.6666666655544 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.4
                Glyco_trans_4_4  71 rerpdvvhahsptaglaarlarrrr 95 
                                     e + +v ++s+ +g ++++ r + 
  gi|118431714|ref|NP_148357.2| 289 NESFGIVALESLSSGTPVVASR-QG 312
                                    4555555555554444444444.33 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 ?   -2.4   0.0       4.5   6.7e+03      42      59 ..      77      95 ..      47      97 .. 0.74
   2 !   50.0   0.0     2e-16     3e-13       9      91 ..     290     374 ..     270     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
                Glyco_trans_1_2 42 evilfe.dleelaekiryl 59
                                   e+i++  d+ +l + i+ l
  gi|118431714|ref|NP_148357.2| 77 EIIFVPpDPSDLRREIESL 95
                                   7888888999999988765 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 2e-16
                Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                                    es+  + +E + +G+++++++  gl + ++ gk+++l++  + +ela+++  ll++ ++r++++e+ar+ vl+++++++ 
  gi|118431714|ref|NP_148357.2| 290 ESFGIVALESLSSGTPVVASRQGGLKDVVKHGKTGLLVKpgSSKELAKALITLLQDSGLRKRMSEEARKIVLERYDWRKV 369
                                    789999************************************************************************** PP

                Glyco_trans_1_2  87 aeqll 91 
                                    + q+l
  gi|118431714|ref|NP_148357.2| 370 VPQIL 374
                                    99998 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 !   22.6   0.0   5.8e-08   8.6e-05      12     137 ..      32     162 ..      23     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.8e-08
                Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkga..kdeleaegihvhrlkvdrkgpleylka....fklkklikkikPDvvhahyakp 85 
                                    h++ l + L++ gy+V+++++  g+   ++leaeg ++ +      +ple + +      l++ i+ +kPDvvh h +  
  gi|118431714|ref|NP_148357.2|  32 HVRDLTRLLQDFGYDVVIVSRALGKgdVKDLEAEGHYIVKPL----FPLEIIFVppdpSDLRREIESLKPDVVHSHHIYT 107
                                    88888999*************665433666666666555544....6888886556659******************966 PP

                Glyco_trans_4_2  86 y.gllgslaarlsgvipvvlsvwGldvlkfpkksklkkl.....llklalkkatkvis 137
                                    +  ll+  aar +g  p +++ +  +++   +k +l ++       +++l +a++vis
  gi|118431714|ref|NP_148357.2| 108 LtSLLALKAARDLG-LPRIATNH--SIFLAYDKVALWRIasivlPTRYLLPNAQAVIS 162
                                    6688999999*999.66667777..454444444433333445556777778888877 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 ?   12.4   0.0   3.2e-05     0.048     281     349 ..      30     103 ..      25     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                                    SHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.......SEEEES.CHHHHHHHHHHHT-SEEEE- CS
                 Oxidored_nitro 281 pdrvvalarllkelGmevvaagtetahrddeerlkaeleeg......epeviddadleeleelikelkpdlllgg 349
                                    +++v  l+rll++ G +vv ++   ++ d++ +l+ae +         + +++ +d  +l++ i+ lkpd++ ++
  gi|118431714|ref|NP_148357.2|  30 QSHVRDLTRLLQDFGYDVVIVSRALGKGDVK-DLEAEGHYIvkplfpLEIIFVPPDPSDLRREIESLKPDVVHSH 103
                                    589999****************999988877.7888766669999*94489999*****************9776 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 ?    8.5   0.0   0.00099       1.5       8      43 ..      20      54 ..      14      74 .. 0.82
   2 ?    3.0   0.0     0.045        68     131     176 ..      95     137 ..      87     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00099
                 Glyco_transf_5  8 EvaplaktGGLadvvgaLpkaLaklghdvrvilPry 43
                                    ++p + +GG+  +v++L + L+  g+dv +++ + 
  gi|118431714|ref|NP_148357.2| 20 DFHP-SSVGGVQSHVRDLTRLLQDFGYDVVIVSRAL 54
                                   5567.89************************99877 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.045
                 Glyco_transf_5 131 wkpdvihahDWhtalvpallkelykerglfkkiktvftiHNlayqg 176
                                     kpdv+h h  +t    + lk+++  +  + +i+t ++i  lay++
  gi|118431714|ref|NP_148357.2|  95 LKPDVVHSHHIYTLTSLLALKAAR--DLGLPRIATNHSIF-LAYDK 137
                                    38***********99999999975..23344466666665.77765 PP

>> PIGA  PIGA (GPI anchor biosynthesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.2e-05     0.078      52      86 ..      98     132 ..      87     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                           PIGA  52 divhghqalstlaheailhaktlGlktvftDhsLf 86 
                                    d+vh+h+  +  +  a+  a+ lGl  + t+hs+f
  gi|118431714|ref|NP_148357.2|  98 DVVHSHHIYTLTSLLALKAARDLGLPRIATNHSIF 132
                                    89******999999999*****************9 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 ?   11.7   0.0   6.1e-05     0.091     102     128 ..      25      51 ..      21      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                                    -HHHHHHHHHHHHHHHHHTT-SEEEEE CS
                           MeaB 102 alGGlaaktrevvllleaaGfDvvlie 128
                                     +GG+  + r++ +ll+ +G+Dvv++ 
  gi|118431714|ref|NP_148357.2|  25 SVGGVQSHVRDLTRLLQDFGYDVVIVS 51 
                                    57***********************96 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027       0.4       8      44 ..     326     362 ..     323     376 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                    HHHTTHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                           EnY2   8 LvesGererlkelLrerLeesGWrdevkelckeiire 44 
                                    Lv+ G  ++l+++L + L++sG r++++e++++i+ e
  gi|118431714|ref|NP_148357.2| 326 LVKPGSSKELAKALITLLQDSGLRKRMSEEARKIVLE 362
                                    8899*****************************9986 PP

>> DUF3492  Domain of unknown function (DUF3492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.014        21      11      40 ..      22      51 ..      14      58 .. 0.90
   2 ?    4.4   0.0     0.018        27     174     213 ..      98     138 ..      90     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                        DUF3492 11 YPyvsGGVSsWvhqlitklpeveFavlfig 40
                                    P + GGV s v +l + l ++ ++v+++ 
  gi|118431714|ref|NP_148357.2| 22 HPSSVGGVQSHVRDLTRLLQDFGYDVVIVS 51
                                   5999**********************9986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.018
                        DUF3492 174 dvyHav.stGyAgllgallkerkgtpllltEHGiYtrErki 213
                                    dv+H++    + +ll++ ++++ g p + t H i++   k+
  gi|118431714|ref|NP_148357.2|  98 DVVHSHhIYTLTSLLALKAARDLGLPRIATNHSIFLAYDKV 138
                                    5666541345899*********************9865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3245.96
//
Query:       gi|118431715|ref|NP_148358.2|  [L=313]
Description: homoserine kinase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-12   46.7   0.3    7.5e-12   45.5   0.3    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
    8.9e-12   45.1   5.5    1.5e-11   44.4   3.5    2.3  2  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 !   45.5   0.3   8.4e-16   7.5e-12       2      83 ..     215     292 ..     214     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 8.4e-16
                 GHMP_kinases_C   2 lealergdlellgellnlsqrs....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                    ++a+ +gdl+++g l+     s    e+  ++++  p  +++ +a++++Galg++lsGa  Gp+ +al+++ ++a ++a 
  gi|118431715|ref|NP_148358.2| 215 VAAAVNGDLKSMGALMM----SdeivEP--RRRSYVPCYTQVRKAALQAGALGFSLSGA--GPSMIALAPSSEAAREIAA 286
                                    57889************....66778**..*****************************..******************* PP

                 GHMP_kinases_C  78 alreef 83 
                                    a+ e +
  gi|118431715|ref|NP_148358.2| 287 AMEESC 292
                                    **8876 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 ?   -0.8   0.0       0.2   1.8e+03      23      33 ..      23      33 ..      12      57 .. 0.77
   2 !   44.4   3.5   1.6e-15   1.5e-11       2      66 .]      85     151 ..      84     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                                   HHHHHHHHHTT CS
                 GHMP_kinases_N 23 alvaAllallg 33
                                   al++Al a+++
  gi|118431715|ref|NP_148358.2| 23 ALAVALDAYYD 33
                                   67888888884 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 1.6e-15
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                    i++++ +P+g+GLGSS+A a+a+vaA+ ++l l++  +  +  a  +er+a+ g ++ +++aas++Gg
  gi|118431715|ref|NP_148358.2|  85 IRVYKGVPPGRGLGSSGASAAAAVAAVSHALALEVpvDRlVFYAGLGERAAA-GQPHFDNAAASILGG 151
                                    7899*************************99766433335999******999.**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 2731.04
//
Query:       gi|14601818|ref|NP_148359.1|  [L=389]
Description: cystathionine gamma-synthase [Aeropyrum pernix K1]
Scores for complete 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-98  329.2   0.0    2.9e-98  328.9   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.9   0.0  1.6e-102   2.9e-98      10     381 ..      15     386 ..       5     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 328.9 bits;  conditional E-value: 1.6e-102
                                   TCHTTTTBSS--B---SBBBESSHHHH.CTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS- CS
               Cys_Met_Meta_PP  10 ekdeqtgavavpiyltstykfkdvdea.fageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallk 89 
                                   +kd+  + v++p+  ++ y++     +    +  + +Y+R +npt+  lee+++ Le++  +la++sGmaA+++ +l+ ++
  gi|14601818|ref|NP_148359.1|  15 SKDPVREPVVPPVNVSAIYVHPPGSFErEYPRVGDLKYGRENNPTVLGLEEALTSLEEARWTLAFNSGMAALSTLVLHEVS 95 
                                   456688999************95444434445555********************************************** PP

                                   TTEE.EEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-E CS
               Cys_Met_Meta_PP  90 aGde.ivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvl 169
                                    G + +++++  Yg+t++ll+ + + +giev+   +  ++ l  ++    +l+ +E+++np+l+v+ +  i + a + gv 
  gi|14601818|ref|NP_148359.1|  96 RGAKkVLLERLTYGSTRSLLEMLSSITGIEVRLAGPPWEDLLDLVC--WADLIIVESMANPTLRVPPLSGIYREAGSCGVR 174
                                   *97647788889**********************997777777666..5789***************************** PP

                                   EEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHHHHHHHTTHH CS
               Cys_Met_Meta_PP 170 vvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawlllrGlkTLs 250
                                   vvvDntfa+p+  rpl+ ga  +++S TKy++Gh+dvv+G +     ee  + l ++ + lG +++p da+l  rG+kTL+
  gi|14601818|ref|NP_148359.1| 175 VVVDNTFATPIAYRPLERGAHYSLESLTKYIAGHNDVVGGSLSGRV-EEDLEPLWNMRKILGTIMQPIDAYLAWRGMKTLK 254
                                   *******************************************888.66666688899*********************** PP

                                   HHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-S.EEEEEESSHHHHHHHHHHC-SSSEECSS-SS CS
               Cys_Met_Meta_PP 251 lRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgagg.vlsFelkseeekakkfvdnlklfslaeslGg 330
                                    R e++++ A++vAe+Le+h kv+kvyYpgl+shp+hela+++l+g  g v+sFe+++++e++ k++++lkl++ + s+Gg
  gi|14601818|ref|NP_148359.1| 255 ARFEAQSRAAVEVAEWLESHRKVKKVYYPGLSSHPDHELARRELNGLYGaVVSFEIEGGREEVFKLLSRLKLVTPSPSFGG 335
                                   **********************************************8667******************************* PP

                                   SS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
               Cys_Met_Meta_PP 331 veslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                   ve++i++pa+ +h ++++ er + gvtd+l+RlsvG+Edv D+i+Dl+qal
  gi|14601818|ref|NP_148359.1| 336 VETIISYPAISSHSNLDPLERSELGVTDGLLRLSVGLEDVSDIIDDLSQAL 386
                                   **************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 3382.09
//
Query:       gi|118431716|ref|NP_148360.2|  [L=110]
Description: hypothetical protein APE_2069.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 861.76
//
Query:       gi|14601820|ref|NP_148361.1|  [L=140]
Description: hypothetical protein APE_2070 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1129.17
//
Query:       gi|118431717|ref|NP_148362.2|  [L=178]
Description: purine phosphoribosyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-27   93.8   0.1    9.4e-27   93.5   0.1    1.0  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.044   13.2   0.0      0.057   12.8   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase


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 !   93.5   0.1     1e-30   9.4e-27       7     153 ..      23     163 ..      20     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1e-30
                                    T---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----T CS
                   Pribosyltran   7 enpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpa 86 
                                    +++ i+dav++ a +i+ + +++pdv+vgi+rgG+++a  lad+L+v+   v + k +++++   +r +  ++ l ++++
  gi|118431717|ref|NP_148362.2|  23 SWRDIEDAVRDVADKIVGS-GFEPDVIVGILRGGIVPALLLADALGVKNIGVMEIKLYTSVGVRKPRPFLRQP-LVIEVK 100
                                    5678888************.****************************9999999999999999999998876.****** PP

                                    TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE- CS
                   Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvg 153
                                    ++ Vl+VDD+ d+G Tl++a+e++  + p++v++a+l+ kp t + +d++ k+++    +++v++++
  gi|118431717|ref|NP_148362.2| 101 DRNVLVVDDVSDSGLTLQHAIEAVDLYLPAQVKTATLYIKPWTNLVPDYYSKSLD----KWIVFPWE 163
                                    *******************************************************....66666654 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.4e-06     0.057      70     144 ..      47     124 ..      29     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-06
                        UPRTase  70 alVpilRaGegmeealrel..lpearvghlglqreeetlepveyynk.LPkkiaertvlllDpviaTGgsaaaaiqlL 144
                                    ++V ilR+G   +  l ++  ++++ v++++l+++    +p+ ++ + L  ++++r+vl++D v  +G ++++ai+ +
  gi|118431717|ref|NP_148362.2|  47 VIVGILRGGIVPALLLADAlgVKNIGVMEIKLYTSVGVRKPRPFLRQpLVIEVKDRNVLVVDDVSDSGLTLQHAIEAV 124
                                    689******988888888734689999*********99999976643266666**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1357.68
//
Query:       gi|14601822|ref|NP_148363.1|  [L=74]
Description: 30S ribosomal protein S17 [Aeropyrum pernix K1]
Scores for complete 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-19   69.6   0.7    2.3e-19   69.5   0.7    1.0  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 !   69.5   0.7   1.3e-23   2.3e-19       1      66 [.       1      67 [.       1      74 [] 0.90

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.3e-23
                                  XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHH.TTSS-- CS
                Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkr.iqkgpv 66
                                  mg+vr + vK++ar+++eky   +t dF++nk+v+++    +skklrn+iaGy+thl++   +++++
  gi|14601822|ref|NP_148363.1|  1 MGKVRIRLVKRTARKLLEKYPDLFTGDFEHNKRVVSQLIEYRSKKLRNQIAGYITHLVNMaSKRKKA 67
                                  9********************************************************9873444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 573.12
//
Query:       gi|118431718|ref|NP_148364.2|  [L=548]
Description: thermosome beta subunit [Aeropyrum pernix K1]
Scores for 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-184  613.8   8.3   2.3e-184  613.6   8.3    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.076   12.9   1.9        1.9    8.3   0.0    2.5  2  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 !  613.6   8.3  2.6e-188  2.3e-184       1     490 [.      42     533 ..      42     534 .. 0.98

  Alignments for each domain:
  == domain 1  score: 613.6 bits;  conditional E-value: 2.6e-188
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    +a+i+ktt+GPkGmdKmlv++ g++++Tn Gatil ++++ hPaak+lv++++ q++e+GDGT t+vi+ageLl+eaekl
  gi|118431718|ref|NP_148364.2|  42 IAQILKTTYGPKGMDKMLVDSLGDITITNNGATILDKMDVAHPAAKMLVQISKGQEDEAGDGTKTTVIFAGELLKEAEKL 121
                                    799***************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS... CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene... 157
                                    ++ ++hpt i+egy++al ka e +++ia+ +s   +d e+L+ +a+tsl+sk +++ ++++++l+v+Av+++ e++   
  gi|118431718|ref|NP_148364.2| 122 LDINIHPTIIVEGYKEALRKASEVIESIAEPVS--YDDVEKLKLIAKTSLNSKAVAEARDYFAELAVEAVRTVAERRgdr 199
                                    ****************************66665..569********************************7777777799 PP

                                    EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHH CS
                     Cpn60_TCP1 158 keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekae 237
                                      +dl++i++vk++ggsl+d++lv+G+vldk+v++pdmp+++ena+++lld++Leiek+e++ ++ ++++e++++l +++
  gi|118431718|ref|NP_148364.2| 200 WYVDLNNIQIVKKHGGSLRDTRLVRGIVLDKEVVHPDMPRRVENARIALLDTPLEIEKPEIDLEISITSPEQIKALYEKQ 279
                                    99****************************************************************************** PP

                                    HHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEE CS
                     Cpn60_TCP1 238 ekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkvee 317
                                    e++l+e++eki+++g+nvv++qkgidd+a+hflak+gila+rrvk++d+e++a+atGa++v+++edl pe+lG+a+ vee
  gi|118431718|ref|NP_148364.2| 280 ERILQEKIEKIAATGANVVITQKGIDDVAQHFLAKKGILAVRRVKRSDIEKIARATGARIVTDIEDLRPEDLGYAELVEE 359
                                    ******************************************************************************** PP

                                    CCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCC CS
                     Cpn60_TCP1 318 ekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsge 397
                                    +k+g++k+++ie+ k++k++tillrg  +  +de+er+++dAl+vv+ ai d+k+v+GGGa+e e+ak l eya++++g+
  gi|118431718|ref|NP_148364.2| 360 RKVGEDKMVFIEGAKNPKSVTILLRGGFERLVDEAERSLHDALSVVADAIMDGKIVAGGGAVEAEVAKVLYEYASKLPGK 439
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTX.TTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 398 eqlaieafakALevipktLaeNaGldpievlaklraahnkge.kelgidvesgeiidlveagvvDplkvkrqalksAtea 476
                                     qla+eafa+A e++p++La+NaG+dpievl klr+ah+k e k++g+d+++gei+d++++gv++p++vk +alk+Ate+
  gi|118431718|ref|NP_148364.2| 440 TQLAVEAFARAVEALPQALAHNAGHDPIEVLVKLRSAHEKPEnKWYGVDLDTGEIVDMWSRGVLEPMRVKLNALKAATEV 519
                                    **************************************887769************************************ PP

                                    HHHHHCEEEEEXXX CS
                     Cpn60_TCP1 477 astiLrideiikak 490
                                    as+iLrid++i a+
  gi|118431718|ref|NP_148364.2| 520 ASLILRIDDVIAAR 533
                                    ***********987 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4    0.0078        70      19     133 ..      76     192 ..      64     197 .. 0.69
   2 ?    8.3   0.0   0.00022       1.9      12      93 ..     384     465 ..     381     469 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0078
                                    HHHHHC---SSHHHHHHHHHHHHHHH--.ST.HHHHHHHHHHHHHHHC........TT---HHHHHHHHHHHHHHHH--- CS
                           Dak2  19 lkaleeleeaslaevlkalakallsgag.Gt.sGvlysqflralakalkekee...ldaedlaaalkaaleaiqavgkar 93 
                                    l++++    + +a++l +++k+ +++ag Gt   v+++  l++ a++l + +    + +e  ++al++a+e i+++  a+
  gi|118431718|ref|NP_148364.2|  76 LDKMDV--AHPAAKMLVQISKGQEDEAGdGTkTTVIFAGELLKEAEKLLDINIhptIIVEGYKEALRKASEVIESI--AE 151
                                    444443..47788999999999999886555256788777777777776633334588999***************..99 PP

                                    TTSSSTHHHHHHHHHHHHT............T---HHHHHH CS
                           Dak2  94 pgdkTmlDvlrpavealekakd.gedlkealekaakaaekg 133
                                    p+    +  l+ ++++  ++k+  e  + ++e a++a +  
  gi|118431718|ref|NP_148364.2| 152 PVSYDDVEKLKLIAKTSLNSKAvAEARDYFAELAVEAVRTV 192
                                    99888888888888887777774444444455555555554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHC---SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.....TT---HHHHHHHHHHHHHHHH- CS
                           Dak2  12 argaeavlkaleeleeaslaevlkalakallsgagGtsGvlysqflralakalkekeeldaedlaaalkaaleaiqavgk 91 
                                    + g+e +++++e+   + l+ v++a+ ++ + + gG+  +  + +l + a++l +k++l +e++a+a++a  +a+ + ++
  gi|118431718|ref|NP_148364.2| 384 RGGFERLVDEAERSLHDALSVVADAIMDGKIVAGGGAVEAEVAKVLYEYASKLPGKTQLAVEAFARAVEALPQALAHNAG 463
                                    56999999999999999999*************************************************99898887665 PP

                                    -- CS
                           Dak2  92 ar 93 
                                     +
  gi|118431718|ref|NP_148364.2| 464 HD 465
                                    55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3787.33
//
Query:       gi|118431719|ref|NP_148365.2|  [L=361]
Description: tyrosyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for 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-46  158.7   0.0    2.5e-44  151.8   0.0    2.0  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 !  151.8   0.0   1.4e-48   2.5e-44       4     291 ..      31     334 ..      28     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 1.4e-48
                                    S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                   tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                     +++ y G +P+g  H+G+lv + k+ +l +ag++  +l a +hA+i+d+   ++  +r++++ +  +   + a+g+++e
  gi|118431719|ref|NP_148365.2|  31 ARIKGYIGYEPSGVAHIGWLVWMYKVKDLVEAGVDFSVLEATWHAYINDKLGGDMDLIRAAARIVRRV---MEAAGVPVE 107
                                    57889**********************************************99***************...********* PP

                                    TEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHH CS
                   tRNA-synt_1b  84 kaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqn 163
                                    ++++v   e  + ++++ l+ +++k  sl+r+ ++ +++ r +e+ ++ ++ ++Ypl+q  Di++++ d+ +gG+DQ++ 
  gi|118431719|ref|NP_148365.2| 108 RVRFVDAEELASDKDYWGLVIRVAKRASLARVRRALTIMGRRAEEAEVDASKLIYPLMQVSDIFYMDLDIALGGMDQRKA 187
                                    *************************************9999999789********************************* PP

                                    HHHHHHHHHHHHHHSTTSS-EEEEET................-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHC CS
                   tRNA-synt_1b 164 ielgrdlarrfnkkevfkkpegltvp................lltgldGekKmSKSagnsaIfLddekesvkkkiqkavt 227
                                      l+rd+a+++++k    kp+++ +p                 ++++  e KmSKS++++a+f  d+ ++++ ki+ka++
  gi|118431719|ref|NP_148365.2| 188 HMLARDVAEKLGRK----KPVAIHTPiisslqgpgrmeasqgEIDDVLAEVKMSKSKPETAVFVVDSDDDIRRKIRKAYC 263
                                    **************....888888887777888885555555333333456***************************** PP

                                    STTC..SHHHHHHHHHTHHH.....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 228 dsde..evekllklktelsn.....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealnel 291
                                      ++  ++  l+  ++ l+        ++r  +++g  +++++eel+ ++ ++++h+ dlk+a+ae+l+e+
  gi|118431719|ref|NP_148365.2| 264 PAKQvqGNPVLEIARYILFArdgftLRVDRPAKYGGPVEYTSYEELERDYTDGRLHPLDLKNAVAESLIEV 334
                                    ***99966666666666665555546899*******999***************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2673.37
//
Query:       gi|14601825|ref|NP_148366.1|  [L=464]
Description: hypothetical protein APE_2075 [Aeropyrum pernix K1]
Scores for 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-32  111.0   0.0      1e-31  110.3   0.0    1.4  1  PAPS_reduct      Phosphoadenosine phosphosulfate reductase fa
    0.00033   19.8   0.0    0.00054   19.1   0.0    1.2  1  NAD_synthase     NAD synthase
    0.00064   19.3   0.0     0.0011   18.5   0.0    1.4  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.024   14.1   0.0    1.2  1  QueC             Queuosine biosynthesis protein QueC
      0.046   13.5   0.0      0.086   12.6   0.0    1.4  1  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   2.9e-35     1e-31       2     171 ..     241     411 ..     240     414 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 2.9e-35
                                   EEEE--SSCTCHHHHHHHHHHCTT..HEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHHC CS
                   PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkp..vpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslyee 80 
                                   ++v +sgGkds++ l La++af    v+ v+vdtg  f e  e+v+++++ +g++l +++ + +  e++  e+ +  + e 
  gi|14601825|ref|NP_148366.1| 241 VIVPWSGGKDSTAALLLAVEAFGRdaVKAVYVDTGIDFIENAEYVEKVASTLGVDLVYARADVD--EGLLIEGMPMPDPEY 319
                                   6899******************995569***************************777666655..666666665555555 PP

                                   HHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-.CCCT--HHHHHHHHHHCT--B-CC CS
                   PAPS_reduct  81 aaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvf.PllnWteedvwqyilrenipynpL 158
                                   ++++ +K+e+l++a + +  ++++++tG R  es++r k p ++ de+    + v  Pl  W+  +v+ yil+++ip+npL
  gi|14601825|ref|NP_148366.1| 320 RWCTGRKLEALRQAFRTVsrGKTVVVTGDRDGESEKRGKRPPLRYDEKLG--YPVVsPLKLWSGGHVQLYILSKGIPLNPL 398
                                   55**************9977789*************************77..55555************************ PP

                                   CCTT-SS--BCTT CS
                   PAPS_reduct 159 ydqgfrsiGcvpc 171
                                   y++gf +iGc+ c
  gi|14601825|ref|NP_148366.1| 399 YEAGFYRIGCYLC 411
                                   ***********99 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-07   0.00054      18      75 ..     238     295 ..     223     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
                                   TSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSE CS
                  NAD_synthase  18 akgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgie 75 
                                    + v++  SGG DS+ +  lav+a+g++ v+a+++ +     e++e   ++a  lg++
  gi|14601825|ref|NP_148366.1| 238 VDTVIVPWSGGKDSTAALLLAVEAFGRDAVKAVYVDTGIDFIENAEYVEKVASTLGVD 295
                                   5789999****************************99999999999999999998875 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.2e-07    0.0011       3      67 ..     241     302 ..     239     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.2e-07
               Diphthami_syn_2   3 vavlysGGkDsilaLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikleta 67 
                                   v+v +sGGkDs+ aL  a++ +  + + +v  +        + n++ ve +a ++G++l+  ++ 
  gi|14601825|ref|NP_148366.1| 241 VIVPWSGGKDSTAALLLAVEAFGRDAVKAVYVDTGI---DFIENAEYVEKVASTLGVDLVYARAD 302
                                   7899*******************9999999887655...5789****************998876 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.7e-06     0.024       2      53 ..     241     294 ..     240     309 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.7e-06
                                   EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT-- CS
                          QueC   2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgv 53 
                                   ++v  SGG DSt++l+la +++  ++v+a+ +d g    ++ e+++k+a++lgv
  gi|14601825|ref|NP_148366.1| 241 VIVPWSGGKDSTAALLLAVEAFgrDAVKAVYVDTGIDFIENAEYVEKVASTLGV 294
                                   57889***************997789***********999***********999 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05     0.086       2      70 ..     241     305 ..     240     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--HHH CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdvak 70 
                                   v+v  SgG DS+a lll+++   +    + a++vd g+     e+ae+v++++++l+++l+++++dv++
  gi|14601825|ref|NP_148366.1| 241 VIVPWSGGKDSTAALLLAVEAFGR--DAVKAVYVDTGID--FIENAEYVEKVASTLGVDLVYARADVDE 305
                                   68999*******988888888553..3789999**9996..567889***************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3285.80
//
Query:       gi|118431720|ref|NP_148368.2|  [L=241]
Description: hypothetical protein APE_2077.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1806.66
//
Query:       gi|14601828|ref|NP_148369.1|  [L=437]
Description: hypothetical protein APE_2078 [Aeropyrum pernix K1]
Scores for complete 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-78  263.2   0.3    4.4e-78  262.9   0.3    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase
  ------ inclusion threshold ------
       0.19   11.8   0.1       0.45   10.6   0.0    1.6  2  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


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 !  262.9   0.3     5e-82   4.4e-78      11     405 ..      16     386 ..       9     387 .. 0.93

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 5e-82
                                   EEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS..---- CS
                          UbiD  11 vrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellepkppipp 91 
                                   + +++ ++ e+E+a ++ ++   g+  +l  +++g   + pv++n++ tre++ +alg++   e ++k+ + +    p + 
  gi|14601828|ref|NP_148369.1|  16 RVVDRTLSREYEVARLIAETQ--GCGPPLLARIEG--VRQPVAVNVVDTREKLYKALGVTGDSEAYAKIVDSTMR--PGRL 90 
                                   6789999************97..777788889963..478*******************8889999999988665..4777 PP

                                   EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHH CS
                          UbiD  92 kvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhwqihkgga 172
                                   + v+  k+p   e+         + LP+ ++++g++G y+++g+vi+    +g+ n++i+R+ +l+++++++++++++ ++
  gi|14601828|ref|NP_148369.1|  91 EYVD--KPPLD-EM-----PEGFEGLPAARFYEGEAGLYLSSGIVIAC--YEGVCNASIHRLLILGRERAAIRIVPRHLWH 161
                                   8884..47777.55.....236899**********************8..48***********************998877 PP

                                   HHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEE CS
                          UbiD 173 ehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivleGeidpget 253
                                     +rka+++g e+lp++v++G +Pa++laA+++ P g+ El +a+++ g ++++ +++ ++ +vp  A +v + +i+  e+
  gi|14601828|ref|NP_148369.1| 162 L-YRKARERG-EDLPATVVVGLHPAVLLAAATSPPLGVFELGLAAGMLGGSMKVYRSPVHGNPVPLGAAMVADVWITG-EQ 239
                                   7.********.9*****************************************************************8.67 PP

                                   EECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTT CS
                          UbiD 254 apEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggf 334
                                   ++EGP++d + +y++vr+ +pv++++a + ++  + +t+  g   e+ +l+g+++ea++++++++++p+v++v+l++++g+
  gi|14601828|ref|NP_148369.1| 240 VEEGPYVDALLTYDRVRR-QPVVRLEAAYIKEGEYTHTI-MGGSLEHVNLMGFPREASIWEAVRRALPRVRAVRLTPASGG 318
                                   ****************99.5******************9.55555************************************ PP

                                   TCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                          UbiD 335 hllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                   +l+av++++k+++g+ k +++a++a+++  sl K+v+vvD dvdv+d+ +v+waiatr+++d+Dlvii+++
  gi|14601828|ref|NP_148369.1| 319 WLHAVIAVEKQHEGDGKTAIMAAFAAHP--SL-KHVVVVDSDVDVDDPMQVEWAIATRFQADKDLVIIPRA 386
                                   ****************************..99.***********************************986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.75   6.8e+03      91     123 ..       4      33 ..       2      36 .. 0.73
   2 ?   10.6   0.0     5e-05      0.45       1      39 [.     324     360 ..     324     392 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.75
                                   TTCHHHHHHHHHHCTS-EEE.EEE--CCHCCCCH CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                          CbiA  91 tllkealeelkqrygvpvlg.viprdeavaeapa 123
                                   ++lk++le++    g +v++  ++r  +va+++a
  gi|14601828|ref|NP_148369.1|   4 ASLKSFLEKV----GYRVVDrTLSREYEVARLIA 33 
                                   5677777777....88888888888888887766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5e-05
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqa 39 
                                   ia++ +  G GKT + a++a+  +   ++V++vD D++ 
  gi|14601828|ref|NP_148369.1| 324 IAVEKQHEGDGKTAIMAAFAAHPSL--KHVVVVDSDVDV 360
                                   78999999*************9999..99*****99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3189.82
//
Query:       gi|118431721|ref|NP_148370.2|  [L=156]
Description: ADP-ribose pyrophosphatase [Aeropyrum pernix K1]
Scores for 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   78.0   0.0    7.3e-22   77.8   0.0    1.0  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.027   14.5   0.1    1.4  1  SH3_18    CarS bacterial SH3 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 !   77.8   0.0   8.2e-26   7.3e-22       4     123 ..      11     128 ..       8     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 8.2e-26
                                    EEEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   4 ravgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygde 81 
                                    ++vg++++++  ++Llv+r+  p     W++PgG+v+ gEt+ee A+REleEEtG++ + l +++ +++  ++d++  + 
  gi|118431721|ref|NP_148370.2|  11 VGVGCLVFRGG-RILLVKRKYPPG-RgkWSIPGGHVRLGETLEEVAARELEEETGIKGRPLGVVN-VDDAITVDDKGVRY 87 
                                    79********9.6*******4444.36*****************************999999998.99999999999998 PP

                                    EEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCT CS
                          NUDIX  82 heilyvfl.eevegelepndenevsevrwvpleellkeklaae 123
                                    h++l+++l e++ ge++ +d++e  e+ +++l+e+lk +l+++
  gi|118431721|ref|NP_148370.2|  88 HYVLITVLlEDLGGEPRGGDDAE--EAGFYTLDEALKLNLTPS 128
                                    99887777799999999998888..6667******77777665 PP

>> SH3_18  CarS bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     3e-06     0.027      14      73 ..      40     101 ..      36     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                         SH3_18  14 eGaPvriGekvkivst...seddsidkrflGraGivvalvfddPelqyPrdPlikvrveglGe 73 
                                     G  vr+Ge+++ v +   +e+  i+ r lG + +  a+  dd  ++y +  li v +e+lG 
  gi|118431721|ref|NP_148370.2|  40 PGGHVRLGETLEEVAArelEEETGIKGRPLGVVNVDDAITVDDKGVRY-HYVLITVLLEDLGG 101
                                    6889****9987664412267889************************.679*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       233  (0.0129957); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1228.95
//
Query:       gi|118431722|ref|NP_148371.2|  [L=372]
Description: aminopeptidase [Aeropyrum pernix K1]
Scores for 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-97  324.4   0.0      1e-96  324.2   0.0    1.0  1  Peptidase_M29  Thermophilic metalloprotease (M29)


Domain annotation for each model (and alignments):
>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.2   0.0  5.7e-101     1e-96       6     406 .]       9     367 ..       4     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 324.2 bits;  conditional E-value: 5.7e-101
                                    HHHHHHHHHTTT---TT-EEEEEEETT-HHHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT---HHHHHHH CS
                  Peptidase_M29   6 ekyAellvkvglnlqkgqevvinaevealelarlvaeeaykagakkvvvewsdeeltkerlknaseeqleevpeweaekl 85 
                                     + A+l+v+++++  +g++v +++ + a+++ar+va e++++ga ++   ++de + +++++ a+ee l+++++++    
  gi|118431722|ref|NP_148371.2|   9 GEAARLIVDYCISASRGDDVAVSFGLPAIDFARAVALEVLSRGAYPLLN-LRDEYVAEAMYRLAPEELLDYISPID---- 83 
                                    567*******************************************987.**************************.... PP

                                    HHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHHHHHHHHHHTTSS-B-BEE---TTTHHHH---S-HHHHHH CS
                  Peptidase_M29  86 eelveegaarlsilae.dpkllkgvdpekiaaaqkarskalkeyreriasgklrWcvvavPteawAkkvfpdleaeeale 164
                                     +++e+ +a +si+++ ++k l+++dp k+a++++a++++++ +++r  +g+lrW+v+a+P +++A+      ea++ l 
  gi|118431722|ref|NP_148371.2|  84 MYMLEKVDASISIISPlHTKPLATADPGKVARRSRASRPLTELFMKRDGEGSLRWTVTAYPAPSLAQ------EAGMGLL 157
                                    *******************************************************************......******* PP

                                    HHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHTT-SEEEEE.ETTEEEEEEE-TTB--EESS---SSS----SBS CS
                  Peptidase_M29 165 klwdaifkavrldeedpvaaWeehnaelekrakyLnelkfkeLhyksspgtdLtvglaeghiWiggaektkkgiefvaNi 244
                                    +++d++++a+ l+e+dpvaaW+++ + +ek+a+ L++   +eL++ ss gtd+t ++ eg+iWi+ ++k+        N+
  gi|118431722|ref|NP_148371.2| 158 EFEDFVVRALKLHEDDPVAAWKRQAEWQEKVAALLSK--ASELRVVSS-GTDITFRV-EGRIWINDDGKK--------NM 225
                                    *************************************..*******77.********.***********9........** PP

                                    S---EEE-EEEEEEEEEEE-SS-EEETTEEEBS-EEEEETTEEEEEE-SB-HHHHHHHTTSSSGGGSEEEEE---TTSHH CS
                  Peptidase_M29 245 PteevftaPdkrgvnGvvratkPlsysGnliegirltFedGkvveakAekGeevLkklletDegarrLGEvALvpndspi 324
                                    P +evftaP+++gv+Gvv++++P++++G ++eg+rl+F+ G+vv+a+A+kGee L+++letDega+rLGE+A++ n+  i
  gi|118431722|ref|NP_148371.2| 226 PGGEVFTAPHEDGVEGVVTFDFPAVWRGLEVEGVRLEFRGGQVVKASASKGEEHLRRILETDEGAKRLGELAFGLNY-DI 304
                                    *****************************************************************************.9* PP

                                    HHHT-----HHHHHT..TS-EEEEE---GGGB--..-----SHHHHT----S-EEEEE---TT-EEEEE-TTS-EEEEEE CS
                  Peptidase_M29 325 sqsgilfyntLfDen..ascHlAlGaaypecleggeelteeelkaaglNdSlihvDfmigsedldidgitedgkevpifr 402
                                    ++    ++n+LfDe+  +++H+AlGaayp++              +g N+S+ih+D m+++ + +   + +dg   +if+
  gi|118431722|ref|NP_148371.2| 305 QR---HIKNILFDEKigGTMHMALGAAYPST--------------GGRNQSAIHWD-MVKDLRRE-SRVYADGD--LIFE 363
                                    **...**************************..............9**********.****9984.34445665..9999 PP

                                    TTEE CS
                  Peptidase_M29 403 nGef 406
                                    nG+f
  gi|118431722|ref|NP_148371.2| 364 NGRF 367
                                    9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2966.53
//
Query:       gi|118431723|ref|NP_148372.2|  [L=346]
Description: hypothetical protein APE_2084.1 [Aeropyrum pernix K1]
Scores for 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   55.2   2.6    2.3e-13   50.4   0.4    2.5  2  PhoU            PhoU domain
    6.2e-10   38.8   0.0    1.6e-09   37.5   0.0    1.8  1  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 !   50.4   0.4   2.6e-17   2.3e-13       1      85 [.     147     235 ..     147     239 .. 0.89
   2 !    4.4   0.1    0.0057        51       9      88 ..     261     330 ..     253     335 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.6e-17
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriardlE 76 
                                    l+rma+i+ em++d+ + le++d+ l++ v erd+ +d+l+  + r+   a + r pl         e+++l  +++++E
  gi|118431723|ref|NP_148372.2| 147 LSRMARIAAEMIRDVARGLENGDRGLLDLVAERDQLVDKLYLYMARQMTMASSGRLPLKDlgvySPAEIVHLFLAVKSIE 226
                                    68*********************************************55555667788778889778889********** PP

                                    HHHHHHHHH CS
                           PhoU  77 RigDhavni 85 
                                    R++Dha+ +
  gi|118431723|ref|NP_148372.2| 227 RVADHATIL 235
                                    ******976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0057
                                    HHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   9 eemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlERigDhavniae 87 
                                     e +++++eal + d  la  +      + +++ ++e    ++  + + +l   lr+l     ++ ++ Ri  ++ +iae
  gi|118431723|ref|NP_148372.2| 261 AEGFSKSVEALIKADAGLAASI---APVLSEYRSRLESMTAQEFLRgGGSL---LRYL-----VIDSMRRITGYSLDIAE 329
                                    5668899999999999999999...67777777777555555553324443...6664.....78888888888888887 PP

                                    H CS
                           PhoU  88 r 88 
                                     
  gi|118431723|ref|NP_148372.2| 330 A 330
                                    5 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 !   37.5   0.0   1.8e-13   1.6e-09       2      45 ..      14      58 ..      13      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.8e-13
                                   EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHHSX CS
                 MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplkslp 45
                                   ++ ++++v++Pke+++ + + +G+ev+lev++d ++ ++p +s++
  gi|118431723|ref|NP_148372.2| 14 TGRSTYIVSLPKEWVETWRLGRGSEVTLEVMPDgSLKIAPSASER 58
                                   56799*********************************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2589.96
//
Query:       gi|118431724|ref|NP_148373.2|  [L=139]
Description: translation initiation factor IF-5A [Aeropyrum pernix K1]
Scores for complete 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-12   45.9   0.1      7e-12   45.3   0.1    1.3  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    8.8e-06   25.7   0.0    3.3e-05   23.8   0.0    2.0  2  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.018   15.0   1.2      0.033   14.2   1.2    1.6  1  EFP       Elongation factor P (EF-P) OB domain
      0.022   14.9   0.0        0.3   11.3   0.0    2.3  2  UPF0180   Uncharacterised protein family (UPF0180)


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   1.6e-15     7e-12       1      69 []      69     135 ..      69     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.6e-15
                                    --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG...GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
                         eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklp.egelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                                    +++++  q+++ ++D ++++md ++++t+e ++ p  +e ++q+ +k+++g +  V+++ +mG+ kii+++
  gi|118431724|ref|NP_148373.2|  69 VIEKRLGQVLADMGD-MVQIMDlETYDTFE-VEKPgGNEEEEQLAAKLQPGVT--VEYWLIMGKPKIIRIR 135
                                    68999**********.**************.****555***************..*************997 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   7.4e-09   3.3e-05       3      32 ..       9      38 ..       7      41 .. 0.93
   2 ?   -3.1   0.0       1.9   8.5e+03       3      13 ..     112     122 ..     111     122 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.4e-09
                                   GG--TT-EEEETTEEEEEEEEEEEEETTS- CS
                          EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGq 32
                                    +lkkG  i idg++++++e    k Gk +
  gi|118431724|ref|NP_148373.2|  9 GDLKKGSYIVIDGEPCRIVEMSRAKTGKHG 38
                                   69*************************987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.9
                                    GG--TT-EEEE CS
                          EFP_N   3 selkkGlviei 13 
                                      l +G ++e+
  gi|118431724|ref|NP_148373.2| 112 AKLQPGVTVEY 122
                                    67889999986 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.2   7.4e-06     0.033       9      28 ..      81     100 ..      75     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.4e-06
                                    ETTEEEEEETTT--EEEEEH CS
                            EFP   9 dgdeyvFMdnetYeqielpk 28 
                                     gd++  Md etY+ +e++k
  gi|118431724|ref|NP_148373.2|  81 MGDMVQIMDLETYDTFEVEK 100
                                    59****************98 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.038   1.7e+02      32      55 ..      11      34 ..       3      37 .. 0.80
   2 ?   11.3   0.0   6.6e-05       0.3      29      61 ..      39      71 ..      24      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.038
                        UPF0180 32 aqsvdaiVvtGqdtnvmgiedtet 55
                                    ++ + iV++G+ +++++++ ++t
  gi|118431724|ref|NP_148373.2| 11 LKKGSYIVIDGEPCRIVEMSRAKT 34
                                   6667789**********9998776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.6e-05
                        UPF0180 29 eedaqsvdaiVvtGqdtnvmgiedtetkapvIn 61
                                   +++a+ v ++V +Gq++ +++  dt  ++pvI+
  gi|118431724|ref|NP_148373.2| 39 SAKAHVVAICVFSGQKKSLVAPVDTRVQIPVIE 71
                                   566788889999********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1060.55
//
Query:       gi|14601833|ref|NP_148374.1|  [L=331]
Description: hypothetical protein APE_2086 [Aeropyrum pernix K1]
Scores for 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-11   42.1   0.0    1.5e-10   41.2   0.0    1.5  1  ATP_bind_3      PP-loop family
    0.00013   20.8   0.0     0.0002   20.3   0.0    1.2  1  tRNA_Me_trans   tRNA methyl transferase
    0.00042   19.8   5.2     0.0035   16.9   0.5    3.2  3  RecR            RecR protein
  ------ inclusion threshold ------
      0.048   13.3   0.1      0.065   12.9   0.1    1.2  1  Asn_synthase    Asparagine synthase
      0.093   12.8   0.0        0.2   11.7   0.0    1.6  2  PAPS_reduct     Phosphoadenosine phosphosulfate reductase fam
       0.12   12.7   0.0        9.5    6.6   0.0    2.4  2  DUF3243         Protein of unknown function (DUF3243)
       0.55    9.7   0.0       0.55    9.7   0.0    2.3  3  QueC            Queuosine biosynthesis protein QueC
        2.2    8.1   6.2        4.8    7.0   0.4    3.2  3  Rubredoxin_2    Rubredoxin metal binding domain
          3    7.7   6.7          5    7.0   0.0    3.2  3  zf-C2H2_3       zinc-finger of acetyl-transferase ESCO
        8.6    6.1   7.7        2.7    7.7   0.1    2.8  3  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        8.9    6.3   6.5         28    4.7   0.0    3.5  4  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


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 !   41.2   0.0     9e-14   1.5e-10       2     150 ..      51     210 ..      50     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9e-14
                                   EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H..........HHCT CS
                    ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv..........akkk 72 
                                   vl+AvSgG DS +Ll +l +l+++ g+++va++++ g+ e s++ +e+  +l+++l+++l++ +++           +++k
  gi|14601833|ref|NP_148374.1|  51 VLAAVSGGKDSSTLLAVLSRLSRRIGFHVVALYIHLGIYEYSEKSREASIRLASQLDVPLIVFDLNEvlgagipelaKASK 131
                                   799**************************************************************9888888887743333 PP

                                   TSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHC.CT--CCHHH-S-SEEEETT..CCEE-CCCT--HH CS
                    ATP_bind_3  73 gknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrla.rgsglaglagikeaseias..irlvRPlLkvske 150
                                             +RY v++ a+ + g++ ++l+h+adD a   l ++  ++ +  + +g+k++s i +  +  vRPl+ v+ +
  gi|14601833|ref|NP_148374.1| 132 RPPCSVCGMVKRY-VINAAAVELGVDAVALGHNADDIAVYNLKSFLnQDLEAISKLGVKTES-IPGvaVGRVRPLYYVYEK 210
                                   4445555556677.78999999**************98766655440444556667777766.433135668999987655 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   1.2e-07    0.0002       2     127 ..      50     165 ..      49     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                 tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeq....gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                   +v++a+SgG DSs  +a+l +     g++v++++++l       +    +e+  +   r a++l++pl v+d++     +v
  gi|14601833|ref|NP_148374.1|  50 RVLAAVSGGKDSSTLLAVLSRLsrriGFHVVALYIHLGIY----E---YSEKSREASIRLASQLDVPLIVFDLN-----EV 118
                                   89***********998888764111145555555554444....2...44555566779*************95.....69 PP

                 tRNA_Me_trans  79 feefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYar 127
                                   +   + e+++ +   P+ +C   +K   +  +a+e lg+da+a GH a 
  gi|14601833|ref|NP_148374.1| 119 LGAGIPELAKASKRPPCSVCG-MVKRYVINAAAVE-LGVDAVALGHNAD 165
                                   9999*******9999*****7.6998888888887.**********885 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.23   3.8e+02      18      23 ..       3       8 ..       1      12 [. 0.80
   2 ?    2.3   0.1     0.075   1.2e+02      18      24 ..     134     140 ..     128     143 .. 0.67
   3 !   16.9   0.5   2.2e-06    0.0035      15      39 ..     275     299 ..     271     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
                                  E-TTT- CS
                          RecR 18 hCsrCg 23
                                  +Cs+Cg
  gi|14601833|ref|NP_148374.1|  3 RCSVCG 8 
                                  799998 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.075
                                   E-TTT-- CS
                          RecR  18 hCsrCgn 24 
                                   +Cs+Cg 
  gi|14601833|ref|NP_148374.1| 134 PCSVCGM 140
                                   5777765 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 2.2e-06
                                   H-EE-TTT--EESSSS-CCCCSTTS CS
                          RecR  15 kvrhCsrCgnlteedlCaICsdprR 39 
                                   ++++C+ Cg l+    C++C+ +rR
  gi|14601833|ref|NP_148374.1| 275 SIGRCPSCGLLSSGGECSFCRVTRR 299
                                   799******************9999 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-05     0.065      19     131 ..      50     167 ..      31     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                  Asn_synthase  19 pvGalLSGGlDSSliaalaarqsk...splktFsigf......eekgsdeakyakevaehlgtehtelvlteeellda.lp 89 
                                   +v a  SGG DSS++ a+++r s+      + ++  +       e + + +++  ++a +l ++   +v++ +e+l a +p
  gi|14601833|ref|NP_148374.1|  50 RVLAAVSGGKDSSTLLAVLSRLSRrigF--HVVA--LyihlgiYEYSEKSREASIRLASQLDVP--LIVFDLNEVLGAgIP 124
                                   677889****************984321..3332..2444444445555566677889999999..577777778877799 PP

                  Asn_synthase  90 dviyhleepfadrsaiplyllsrla.krkgvkvvLsGeGaDEl 131
                                   +++++  +p ++   + + ++ ++a  + gv  v  G+ aD +
  gi|14601833|ref|NP_148374.1| 125 ELAKASKRPPCSVCGMVKRYVINAAaVELGVDAVALGHNADDI 167
                                   9999999988888888888888888348888888888888865 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012       0.2       3     126 ..      52     181 ..      50     226 .. 0.73
   2 ?   -1.8   0.0       1.7   2.8e+03      30      59 ..     230     260 ..     204     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   EEE--SSCTCHHHHHHHHHHCTTH......EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-TH CS
                   PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv......pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssl 77 
                                     +vsgGkds+ ll  +++  + +        +++   +  ++  e   +l++++++ l+v++ +e   ++i +  + s+ 
  gi|14601833|ref|NP_148374.1|  52 LAAVSGGKDSSTLLAVLSRLSRRIgfhvvaLYIHLGIYEYSEKSREASIRLASQLDVPLIVFDLNEVLGAGIPELAKASKR 132
                                   5689***********9999999964555433444444455555566677888888999*******9999999999977777 PP

                                   HHCHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTT CS
                   PAPS_reduct  78 yeeaaeriaKveplkkaLekldedalltGaRrdesksraklpiveided 126
                                       ++ ++K + ++ a  +l+ da+  G  +d+ +    +++++ d +
  gi|14601833|ref|NP_148374.1| 133 PPCSVCGMVKRYVINAAAVELGVDAVALGHNADDIAVYNLKSFLNQDLE 181
                                   66699***********999999999999999988877777777766654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                                   EEE-STB-HHHHHHHHHHHHHT.T-EEEEEE CS
                   PAPS_reduct  30 fvdtghefpetiefvdeleery.glrlkvye 59 
                                   fv+ ++   e+ e+v++le++  gl+l++++
  gi|14601833|ref|NP_148374.1| 230 FVERRQMEVELKETVNQLEDKRpGLKLQMVS 260
                                   6777777778888888888888788877665 PP

>> DUF3243  Protein of unknown function (DUF3243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0058       9.5       9      34 ..     172     197 ..     169     200 .. 0.91
   2 ?    3.4   0.0     0.061        99      13      40 ..     240     269 ..     234     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0058
                                   HHHHHHHHHHHHHHHHHHTT----HH CS
                       DUF3243   9 wkkfLgdrveqaeklGlseetieklA 34 
                                    k+fL++ +e+  klG+++e i  +A
  gi|14601833|ref|NP_148374.1| 172 LKSFLNQDLEAISKLGVKTESIPGVA 197
                                   699*******************9888 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.061
                                   HHHHHHHHH..HHHHHTT----HHHHHHHH CS
                       DUF3243  13 Lgdrveqae..klGlseetieklAyevGdy 40 
                                   L++ v+q e  + Gl+ ++++klA++v dy
  gi|14601833|ref|NP_148374.1| 240 LKETVNQLEdkRPGLKLQMVSKLAKRVEDY 269
                                   7777877651167**************998 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00034      0.55       2      62 ..      51     116 ..      50     131 .. 0.69
   2 ?   -0.9   0.0      0.58   9.5e+02     108     129 ..     149     170 ..     144     199 .. 0.77
   3 ?   -4.0   0.9       5.4   8.8e+03     194     201 ..     277     284 ..     271     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00034
                                   EEEE--SSHHHHHHHHHHHHH-....SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-G CS
                          QueC   2 avvllSGGlDSttvlalakkeg....kevealtfdYgqr..hkkeleaakkiakelgveehkildld 62 
                                   ++  +SGG DS+t+la+ ++       +v al ++ g     +k  ea  ++a++l+v    ++dl+
  gi|14601833|ref|NP_148374.1|  51 VLAAVSGGKDSSTLLAVLSRLSrrigFHVVALYIHLGIYeySEKSREASIRLASQLDV-PLIVFDLN 116
                                   56789**********9987654111166777777777652344555666677777777.66666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                                   HHHHHT-SEEEE---S-STT-- CS
                          QueC 108 yaealgaeaiiiGvneedfsgY 129
                                    a +lg++a+++G n+ d++ Y
  gi|14601833|ref|NP_148374.1| 149 AAVELGVDAVALGHNADDIAVY 170
                                   577899999******9999998 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5.4
                                   SSSHHHHH CS
                          QueC 194 geCdaCal 201
                                   g+C++C l
  gi|14601833|ref|NP_148374.1| 277 GRCPSCGL 284
                                   78999976 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.089   1.4e+02       2       8 ..       3       9 ..       3      15 .. 0.77
   2 ?   -0.6   0.1       0.7   1.1e+03       3       8 ..     135     140 ..     134     143 .. 0.81
   3 ?    7.0   0.4    0.0029       4.8      15      21 ..     277     283 ..     275     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.089
                  Rubredoxin_2 2 vCsqCGf 8
                                 +Cs CG+
  gi|14601833|ref|NP_148374.1| 3 RCSVCGA 9
                                 7999997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.7
                  Rubredoxin_2   3 CsqCGf 8  
                                   Cs CG 
  gi|14601833|ref|NP_148374.1| 135 CSVCGM 140
                                   999996 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0029
                  Rubredoxin_2  15 GrCpsCg 21 
                                   GrCpsCg
  gi|14601833|ref|NP_148374.1| 277 GRCPSCG 283
                                   9*****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 ?   -0.3   0.2      0.61   9.9e+02      15      20 ..       3       8 ..       1       9 [. 0.86
   2 ?    7.0   0.0    0.0031         5      14      22 ..     130     141 ..     118     147 .. 0.75
   3 ?    1.9   1.0      0.12     2e+02      14      22 ..     277     285 ..     270     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.61
                     zf-C2H2_3 15 qCkeCg 20
                                  +C++Cg
  gi|14601833|ref|NP_148374.1|  3 RCSVCG 8 
                                  7****9 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0031
                     zf-C2H2_3  14 sq...CkeCgMv 22 
                                   s+   C++CgMv
  gi|14601833|ref|NP_148374.1| 130 SKrppCSVCGMV 141
                                   33467******7 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.12
                     zf-C2H2_3  14 sqCkeCgMv 22 
                                    +C+ Cg++
  gi|14601833|ref|NP_148374.1| 277 GRCPSCGLL 285
                                   35*****85 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 ?    2.5   0.2     0.072   1.2e+02       6      12 ..       3       9 ..       2      16 .. 0.82
   2 ?    7.7   0.1    0.0017       2.7       3      11 ..     131     139 ..     129     148 .. 0.80
   3 ?   -2.6   0.5       2.9   4.7e+03       6      11 ..     278     283 ..     277     284 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.072
                       zf-RRN7  6 pCgvCgc 12
                                  +C vCg+
  gi|14601833|ref|NP_148374.1|  3 RCSVCGA 9 
                                  7*****8 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                       zf-RRN7   3 kgppCgvCg 11 
                                   k+ppC vCg
  gi|14601833|ref|NP_148374.1| 131 KRPPCSVCG 139
                                   89******9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.9
                       zf-RRN7   6 pCgvCg 11 
                                   +C+ Cg
  gi|14601833|ref|NP_148374.1| 278 RCPSCG 283
                                   677776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1     0.098   1.6e+02      30      50 ..       3      24 ..       2      30 .. 0.82
   2 ?    4.7   0.0     0.017        28      31      66 ..     135     172 ..     127     174 .. 0.82
   3 ?    0.3   0.2      0.42   6.9e+02      42      53 ..     272     283 ..     260     287 .. 0.69
   4 ?   -0.5   0.9      0.76   1.2e+03      48      53 ..     278     283 ..     268     314 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.098
                OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCp 50
                                  +Cs+Cg+      + +r++ C+
  gi|14601833|ref|NP_148374.1|  3 RCSVCGAPAVAyIRYQRRYLCR 24
                                  6*****9988887888888886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                OrfB_Zn_ribbon  31 CseCgsknke..alsgrtfkCpnCgfeadrDvnAaiNi 66 
                                   Cs+Cg ++++  + +  ++  ++  + +++D  A++N+
  gi|14601833|ref|NP_148374.1| 135 CSVCGMVKRYviNAAAVELGVDAVALGHNADDIAVYNL 172
                                   *******9999966666666666889999999999998 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.42
                OrfB_Zn_ribbon  42 lsgrtfkCpnCg 53 
                                   ++g   +Cp+Cg
  gi|14601833|ref|NP_148374.1| 272 PKGSIGRCPSCG 283
                                   555566777777 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.76
                OrfB_Zn_ribbon  48 kCpnCg 53 
                                   +Cp+Cg
  gi|14601833|ref|NP_148374.1| 278 RCPSCG 283
                                   455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2345.60
//
Query:       gi|118431725|ref|YP_874925.1|  [L=74]
Description: hypothetical protein APE_2086a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   16.2   0.3      0.015   15.9   0.3    1.1  1  ThiS      ThiS family
       0.13   12.1   0.2       0.67    9.8   0.1    2.0  2  Ub-Mut7C  Mut7-C ubiquitin


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 ?   15.9   0.3   1.7e-06     0.015      12      77 .]      17      74 .]      10      74 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-06
                                   T.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS 12 g.eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   g e++++ + + + +ell+ Lg +       ++ +v+++g+ + +   +  +++g +v+++ + +GG
  gi|118431725|ref|YP_874925.1| 17 GgERVIQAERPLKAGELLRMLGMNE------EVAVVLRDGKPLLP---EDLVSPGETVDVVRVLSGG 74
                                   268899999999**********999......**************...******************9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.05   4.5e+02      67      71 ..      17      21 ..       2      41 .. 0.53
   2 ?    9.8   0.1   7.5e-05      0.67      48      74 ..      42      68 ..      31      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.05
                       Ub-Mut7C 67 dGdrv 71
                                    G+rv
  gi|118431725|ref|YP_874925.1| 17 GGERV 21
                                   44443 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 7.5e-05
                       Ub-Mut7C 48 EVelilvnGesvgfshiledGdrvavy 74
                                   EV ++l +G++  ++ ++++G+ v v 
  gi|118431725|ref|YP_874925.1| 42 EVAVVLRDGKPLLPEDLVSPGETVDVV 68
                                   9***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 558.43
//
Query:       gi|118431726|ref|NP_148375.2|  [L=402]
Description: aconitase, subunit [Aeropyrum pernix K1]
Scores for complete 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-126  422.1   0.0   2.2e-126  421.8   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.8   0.0  1.2e-130  2.2e-126       1     398 [.       1     396 [.       1     398 [. 0.95

  Alignments for each domain:
  == domain 1  score: 421.8 bits;  conditional E-value: 1.2e-130
                         DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvpttlnp 80 
                                    m+Lt+eee++l+GeeGea +ka+e++v++Ge++gAerL+p+++ahvsg+sy+tigdagl+fl +lae+ga+++vptt+np
  gi|118431726|ref|NP_148375.2|   1 MYLTREEERILAGEEGEARAKALEVIVKVGEAVGAERLIPIKHAHVSGASYMTIGDAGLRFLARLAESGARFSVPTTVNP 80 
                                    9******************************************************************************* PP

                         DUF521  81 igvdlerweel...gvdeefaekqeriieayeklGveltftCtpyllgnapk.....kGehlawsESsavvyaNSvlGar 152
                                    +++d e+  ++   ++++++++ q++i++a+e++G++l +tCtpy++ ++p+     +G+++aw+ESsav+yaNSvlG++
  gi|118431726|ref|NP_148375.2|  81 VSYDVEEPGAIpmtRLSPRIVKAQSEILKALEAMGADLILTCTPYYT-EVPRrvglrEGDSVAWGESSAVAYANSVLGIH 159
                                    ****8776665223799*****************************8.8888788989********************** PP

                         DUF521 153 TnreggpsalaaAitGrtpeyGlhldenRkptvlveveae.sedeadygalGylvGkkvgeriPvlkglekpsedelKal 231
                                    Tnreggp+al+a+i+Grt+ yG h  e Rkp+v +++e+    de + g+lG +++++++++ P l   +   e +lK++
  gi|118431726|ref|NP_148375.2| 160 TNREGGPLALMAGIAGRTYFYGAHDPEWRKPRVAYRLETPkVLDETEAGVLGEVIATQHRDEHPPLLDAPLGGEAALKEF 239
                                    *************************************998899*****************6655555456559******* PP

                         DUF521 232 gAalaasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElrelae 311
                                    +Aa++++g+ a++hi gvTP      +   +   +e +t++  dl++ +e+l  a+  ++d+ ++GcPh+s+eElr+l++
  gi|118431726|ref|NP_148375.2| 240 SAAVGSAGSLAMVHITGVTPG-----D--PGDMIEEVVTMDYGDLARRMEDL--APGFEPDILYVGCPHASIEELRRLYR 310
                                    *********************.....2..2456699****************..9999********************** PP

                         DUF521 312 llkgkkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpgltgvkv 391
                                    +l++ +++ +++++v +sr+++ +a r+glvekl+  Gv++++d+C++vsp+++ +++ +vatnS+Ka++Yl++++ v+v
  gi|118431726|ref|NP_148375.2| 311 ALSKAGERAGRRTVVSISRSLYLQALREGLVEKLKGLGVRFVRDSCLIVSPFSSGARGVRVATNSYKAYFYLSKKG-VEV 389
                                    ******************************************************99*****************996.999 PP

                         DUF521 392 algslee 398
                                     l+ +e+
  gi|118431726|ref|NP_148375.2| 390 GLAPIEA 396
                                    9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3007.45
//
Query:       gi|14601835|ref|NP_148376.1|  [L=132]
Description: aconitase, subunit [Aeropyrum pernix K1]
Scores for complete 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   84.9   0.1    3.3e-24   84.5   0.1    1.2  1  DUF126    Aconitase X swivel domain
  ------ inclusion threshold ------
      0.096   13.3   0.1       0.16   12.6   0.1    1.3  1  MBG_2     MBG domain (YGX type)


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.1   3.7e-28   3.3e-24       1      79 [.      26      98 ..      26      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 3.7e-28
                                  --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--E CS
                        DUF126  1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPl 79
                                  lSf+g+vdpetG+ +       g+ +ag++ ++++++GStvgsyv+++l++ng+aP A+++++a+pi+++G+++a+iPl
  gi|14601835|ref|NP_148376.1| 26 LSFYGEVDPETGVTSG------GKPLAGRVAAIRRSRGSTVGSYVIYALKENGVAPLAILMERAEPIVIAGCVLAGIPL 98
                                  8************997......9999****************************************************8 PP

>> MBG_2  MBG domain (YGX type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.8e-05      0.16      10      54 ..      27      67 ..      21      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                         MBG_2 10 kvyGdadPeltytvsGlvngDtlssltgtlsrtagenvGtYaita 54
                                   +yG+ dPe  +t  G      ++    ++ r  g++vG+Y i a
  gi|14601835|ref|NP_148376.1| 27 SFYGEVDPETGVTSGGKPLAGRVA----AIRRSRGSTVGSYVIYA 67
                                  68*******999977766655555....789**********8864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 964.38
//
Query:       gi|14601836|ref|NP_148377.1|  [L=208]
Description: thymidylate kinase [Aeropyrum pernix K1]
Scores for 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-35  120.4   0.0    8.2e-35  120.2   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    5.9e-07   29.5   0.0    1.2e-06   28.6   0.0    1.5  2  dNK              Deoxynucleoside kinase
    0.00021   21.8   0.0    0.00036   21.1   0.0    1.4  1  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.038   14.1   0.0      0.056   13.6   0.0    1.2  1  SKI              Shikimate kinase
      0.049   13.2   0.0      0.068   12.7   0.0    1.3  1  Ploopntkinase1   P-loop Nucleotide Kinase1
       0.13   12.5   0.1        0.2   11.9   0.1    1.2  1  ApbA_C           Ketopantoate reductase PanE/ApbA C terminal
        0.2   11.8   1.9        1.6    8.9   0.3    2.3  2  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0   3.2e-38   8.2e-35       1     166 [.       6     168 ..       6     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 3.2e-38
                                   EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTH.HHHHHHHHTT CS
               Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehle.ekikpalkqg 80 
                                   +EG+DG+G +t+++ll +rl  +g k +l +ep+++++G++ir+ l  +e +++  +allfaadr + l+  ++++   + 
  gi|14601836|ref|NP_148377.1|   6 LEGIDGSGVSTHSRLLHARLAGAGVKSCLWKEPTEGPVGRLIRGFLRSTEGVDSDLMALLFAADRLWGLRlGVVERCGGSP 86 
                                   6*********************************************************************66677777889 PP

                                   -EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHH CS
               Thymidylate_kin  81 ktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvreryle 161
                                   ++++vdRy +SslaYqg+++  +l++v  +n++++ + ++ +++dv+ eval+R+++r+   +e++e  +fl++v+  y e
  gi|14601836|ref|NP_148377.1|  87 EVLVVDRYKYSSLAYQGVGS--GLEWVDAVNRKAP-EAEILVYIDVPTEVALRRITARER--REVFETPEFLERVKSMYEE 162
                                   9*****************99..7***********9.************************..9**************9999 PP

                                   HHH.TT CS
               Thymidylate_kin 162 lak.ed 166
                                   +++ ++
  gi|14601836|ref|NP_148377.1| 163 VLRlAR 168
                                   987544 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   3.8e+03       2      22 ..       5      25 ..       4      29 .. 0.85
   2 !   28.6   0.0   4.5e-10   1.2e-06     111     182 ..     109     179 ..      78     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                                  EEEESTTSSHHHHHHHHHCCS CS
                           dNK  2 vveGnIgaGKstlvklLskkl 22
                                  ++eG  g+G st   lL+ +l
  gi|14601836|ref|NP_148377.1|  5 ALEGIDGSGVSTHSRLLHARL 25
                                  689999******999998765 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 4.5e-10
                                   HHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS CS
                           dNK 111 elldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevpvlvidvee 182
                                   e+ d++++++++ ++l+Y+++++e+ l+ri  R+r e  +++ ++le++++ yee l+   +  v vi+ve 
  gi|14601836|ref|NP_148377.1| 109 EWVDAVNRKAPEAEILVYIDVPTEVALRRITARERREVFETP-EFLERVKSMYEEVLRLARARGVKVIRVEG 179
                                   7999999****************************9966665.8**************99999999999885 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.4e-07   0.00036       1     117 [.       4     145 ..       4     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                        AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenss...........a 70 
                                   ++l G+ G+G +t ++ L  rl  g  +++ ++++ ++ +v    ++ ++r  e+++  l+ +l ++++            
  gi|14601836|ref|NP_148377.1|   4 VALEGIDGSGVSTHSRLLHARL-AGAGVKSCLWKEPTEGPVGRL-IRGFLRSTEGVDSDLMALLFAADRlwglrlgvverC 82 
                                   6899**************7775.499999999999999999999.99*******************999888888888884 PP

                        AAA_18  71 leegknlvidghlaeleseaakdikk................vvLtaspeelleRlekRgyee 117
                                    +++++lv+d      + ++ +  +                 v++++++e+ l+R+ +R+++e
  gi|14601836|ref|NP_148377.1|  83 GGSPEVLVVDRYKYSSLAYQGVGSGLewvdavnrkapeaeilVYIDVPTEVALRRITARERRE 145
                                   444444455544444444444433336666666666999999*****************9876 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.2e-05     0.056      78     119 ..     115     155 ..     105     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHH CS
                           SKI  78 nrellkekgiviyLdvsleellerlkadkeRPllqekskeee 119
                                   nr++ +  +i++y+dv+ e+ l+r++a+++R ++++++  e+
  gi|14601836|ref|NP_148377.1| 115 NRKAPE-AEILVYIDVPTEVALRRITARERREVFETPEFLER 155
                                   455544.899*********************99988876333 PP

>> Ploopntkinase1  P-loop Nucleotide Kinase1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05     0.068     116     165 ..     109     159 ..      93     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                Ploopntkinase1 116 twieklnrparrl.vvlfldtpletclsrvdsrnggedfnedlvvekfkrv 165
                                    w++ +nr a +  + +++d p e+ l r+ +r+  e f++   +e+ k +
  gi|14601836|ref|NP_148377.1| 109 EWVDAVNRKAPEAeILVYIDVPTEVALRRITARERREVFETPEFLERVKSM 159
                                   5*******8876527789*****************9999987777666554 PP

>> ApbA_C  Ketopantoate reductase PanE/ApbA C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.6e-05       0.2      22      73 ..     138     190 ..     133     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                        ApbA_C  22 lldckngellespelralvrallkEalavaeaegve.lseerleeaveavlek 73 
                                   ++    +e++e+pe+ + v+++ +E+l++a+a+gv+ ++ e ++  ve+ +e 
  gi|14601836|ref|NP_148377.1| 138 ITARERREVFETPEFLERVKSMYEEVLRLARARGVKvIRVEGVRGGVERGIED 190
                                   566677899***************************99999887777777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.072   1.8e+02       2      26 ..       4      28 ..       3      52 .. 0.87
   2 ?    8.9   0.3   0.00061       1.6      98     124 ..     121     146 ..     106     166 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.072
                        AAA_33  2 vllvGlpGsGKstlaerllkklgav 26
                                  v l G  GsG st ++ l+++l++ 
  gi|14601836|ref|NP_148377.1|  4 VALEGIDGSGVSTHSRLLHARLAGA 28
                                  7899**************9998854 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00061
                        AAA_33  98 pvrivvvetdeetlkeRlakRaangdd 124
                                   ++ +v+++++ e++ +R+ +R++++ +
  gi|14601836|ref|NP_148377.1| 121 AEILVYIDVPTEVALRRITARERRE-V 146
                                   2456*******************74.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1467.22
//
Query:       gi|118431727|ref|NP_148378.2|  [L=320]
Description: ATP-dependent glucokinase [Aeropyrum pernix K1]
Scores for complete 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  162.6   0.1    1.6e-47  162.4   0.1    1.0  1  ROK       ROK family


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 !  162.4   0.1     9e-52   1.6e-47       2     292 ..       5     311 ..       4     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 9e-52
                                    EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSGGCG CS
                            ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivstpni 81 
                                    +++d+G+t +++a+v   g + +  k  + ++ tee+l+ +++ l + +    + + +vg +s G+++  +g+iv  pni
  gi|118431727|ref|NP_148378.2|   5 VAVDVGATWVRMAIVR--GGVIEAIKR-ERNPGTEEGLERVLQGLAEGLGIDRGRVEKVGAASIGPLDLRRGYIVGSPNI 81 
                                    79***********998..555555555.356788999*9999999999988888888*********************** PP

                                    CCCCTTHHHHHHHHH.TS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GGGSBS CS
                            ROK  82 twenfdlvekleerl.nvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvagelGHiql 160
                                    + + + l + l+  + +  v ++nD+ aaa++E+ +g  +++ ++ y+t++tGvG+G++++g+l+ G++G+a e+GHi +
  gi|118431727|ref|NP_148378.2|  82 KSHIVRLSTILKRLFpKSKVAIANDAVAAAWGEYLLGRLAGTPDLGYITMSTGVGGGFVVGGRLLLGSRGNAHEVGHIVV 161
                                    *************996679************************************************************9 PP

                                    -..TTS-B-TTS-BSBHHHCCSHHHHHHCHTC.................CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHH CS
                            ROK 161 d..pegekcgCGnqgClEtlasgralekraqq.................kgekleakeiiklaekgdevaeevverlaey 221
                                    d   eg +cgCG +g +E++a gr + +  +                  +g+  +a+e++++a  gd  a +v++++a++
  gi|118431727|ref|NP_148378.2| 162 DmgWEGGRCGCGGTGHWEAIAGGRWIPRTSSVlargwrgpetslyraalEGRVGSAREVFEAAAVGDDFALHVIDYIARA 241
                                    9888999********************9999999**************999***************************** PP

                                    HHHHHHHHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-.EEEE-S-STTHHHHHHHHHHC CS
                            ROK 222 lakaiadlinlfdpqaivlgGgvseadklleairklvkkylnkklevpvv.eivaaklgdkagllGaaaLak 292
                                     a++ia +++++d +a+++gG+v   ++ +  +r l++++l+ +++ +   e+v a++gd++g++Ga a+a 
  gi|118431727|ref|NP_148378.2| 242 SAAGIASVKAAYDVDAVIIGGSVYLNNRRM--LRPLIERHLAAYAPFSSRiEVVDASFGDNEGVMGAYAIAY 311
                                    ***********************9776655..699999999998887665599***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2506.20
//
Query:       gi|14601838|ref|NP_148379.1|  [L=514]
Description: hypothetical protein APE_2093 [Aeropyrum pernix K1]
Scores for complete 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   55.1   0.0    1.7e-14   54.5   0.0    1.2  1  DUF87          Helicase HerA, central domain
    7.9e-08   31.3   0.0    2.1e-05   23.3   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    2.1e-05   24.0   0.0    4.2e-05   23.0   0.0    1.4  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
    2.4e-05   23.5   0.0    0.00014   20.9   0.0    1.9  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00014   22.1   0.1       0.78   10.0   0.3    2.4  2  AAA_22         AAA domain
     0.0037   17.3   0.1     0.0086   16.1   0.1    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.071   12.5   0.4       0.16   11.4   0.4    1.5  1  IPT            Isopentenyl transferase
       0.11   12.1   0.2       0.18   11.4   0.2    1.3  1  SRP54          SRP54-type protein, GTPase domain
       0.14   12.2   0.0         15    5.6   0.1    2.2  2  ResIII         Type III restriction enzyme, res subunit
       0.15   11.1   0.0       0.24   10.4   0.0    1.2  1  T2SSE          Type II/IV secretion system protein
        0.2   11.3   0.4        0.6    9.8   0.4    1.7  2  AAA_30         AAA domain
       0.23   11.1   0.0       0.46   10.1   0.0    1.4  1  Zot            Zonular occludens toxin (Zot)
       0.25   11.8   0.3       0.74   10.3   0.5    1.7  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 !   54.5   0.0   1.2e-17   1.7e-14      14     144 ..     205     328 ..     195     356 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.2e-17
                         DUF87  14 vyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsakdkelkinp 94 
                                   +yl   + ++ H++++gsTGsGK++t a +   ++ + g+++++ D+HGEY ++   ++  + +vi+p ++ + ++l++  
  gi|14601838|ref|NP_148379.1| 205 LYLEQ-SDIEGHIGVFGSTGSGKTTTLATIACGAA-EAGLPVVVADWHGEYQRLV-GGGGCRPRVIDPGREGGVNPLSLGW 282
                                   55555.67899************************.******************9.8888889999999999999999975 PP

                         DUF87  95 wsldpee..lldlleeddkpaaavqrsvleealdqakakeekeklssdepve 144
                                   +  +++   l++ l+     +++ q+ +l ++l++++ + ++e  s  e ve
  gi|14601838|ref|NP_148379.1| 283 D-YSVKTalLASALG-----LTEPQHYMLLKLLEEHEPRSLIELHSMVEDVE 328
                                   4.3333300334444.....48888888888888886544444444444444 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 !   23.3   0.0   1.5e-08   2.1e-05      12      69 ..     204     261 ..     196     279 .. 0.84
   2 !    5.7   0.0    0.0033       4.5     260     333 ..     407     474 ..     402     509 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-08
                        DUF853  12 elalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaGe 69 
                                   +l+l+ +    h  + G+tG Gkt tL ++a + +eaG pv++ad  G+   ++  G 
  gi|14601838|ref|NP_148379.1| 204 PLYLEQSDIEGHIGVFGSTGSGKTTTLATIACGAAEAGLPVVVADWHGEYQRLVGGGG 261
                                   6667777777788899********************************9888776665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0033
                        DUF853 260 vfffdeahLLfndapkallekveqvvrLirskGvGvy..fvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavk 333
                                    +  deah +f++   ++       + +  s+  G+y  + tqnP  lP   ++   +++ h+lr +   d +++ 
  gi|14601838|ref|NP_148379.1| 407 LLVVDEAHNMFDGEE-SFP-----SIMMAESRKFGLYiaLATQNPHLLPLRAVSNTNTKIVHSLRWWR--DLESIA 474
                                   566788888887643.332.....34455666666662268************************885..444443 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     3e-08   4.2e-05      23      64 ..     196     238 ..     187     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3e-08
                                   EEET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHH CS
                  FtsK_SpoIIIE  23 gkei.sgnplvldlkkmashllvaGatgsGKStalntLilSla 64 
                                   + +  + +pl+l+++  ++h+ v G+tgsGK+t+l t+ +++a
  gi|14601838|ref|NP_148379.1| 196 RLDTpTPEPLYLEQSDIEGHIGVFGSTGSGKTTTLATIACGAA 238
                                   556667799*******************************998 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 !   20.9   0.0     1e-07   0.00014      10      56 ..     208     254 ..     203     261 .. 0.91
   2 ?   -0.3   0.0      0.28   3.8e+02     264     285 ..     427     448 ..     406     463 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1e-07
                 TrwB_AAD_bind  10 pkeretqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                   ++++ + hi ++G+tGsGKt++l  +  ++ + g  ++v+D +G++ 
  gi|14601838|ref|NP_148379.1| 208 EQSDIEGHIGVFGSTGSGKTTTLATIACGAAEAGLPVVVADWHGEYQ 254
                                   6667789*************************************985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.28
                 TrwB_AAD_bind 264 llaegRkfGgavvlglqsiaql 285
                                   ++ae+RkfG  + l+ q+ + l
  gi|14601838|ref|NP_148379.1| 427 MMAESRKFGLYIALATQNPHLL 448
                                   5799*************98765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.3   0.00056      0.78       6      26 ..     214     234 ..     211     245 .. 0.87
   2 !    9.4   0.0   0.00085       1.2      75     108 ..     386     422 ..     339     448 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                        AAA_22   6 gilvvtGesGtGKTtllrrll 26 
                                   g++ v+G +G+GKTt+l++++
  gi|14601838|ref|NP_148379.1| 214 GHIGVFGSTGSGKTTTLATIA 234
                                   7889************99875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00085
                        AAA_22  75 seell.ealeqalrarav.ielliiDEaqhlr.seea 108
                                    + ll ++l+  + +r   + ll++DEa++++  ee 
  gi|14601838|ref|NP_148379.1| 386 YSILLaAYLQYKAYSRELgPLLLVVDEAHNMFdGEES 422
                                   45555455555555555578**********8654444 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 !   16.1   0.1   6.2e-06    0.0086       6      34 ..     220     248 ..     218     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.2e-06
                                   SSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA   6 tkGGvGKTtlaanLaralarrglrVllvD 34 
                                   ++ G+GKTt++a++a+  a++gl V++ D
  gi|14601838|ref|NP_148379.1| 220 GSTGSGKTTTLATIACGAAEAGLPVVVAD 248
                                   678************************99 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   0.00011      0.16       6      46 ..     218     261 ..     215     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                           IPT   6 ifGatttGKtaeaikl...aketgapvivlDRvqcyselavgsG 46 
                                   +fG+t++GKt +   +   a e g+pv+v+D    y+ l  g+G
  gi|14601838|ref|NP_148379.1| 218 VFGSTGSGKTTTLATIacgAAEAGLPVVVADWHGEYQRLVGGGG 261
                                   79********9988773345799********9999999888777 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   0.2   0.00013      0.18       6      34 ..     218     246 ..     214     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                   EEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                         SRP54   6 lvGlqGaGKTttlaKLaallkkegkkvll 34 
                                   ++G +G+GKTttla +a    + g  v++
  gi|14601838|ref|NP_148379.1| 218 VFGSTGSGKTTTLATIACGAAEAGLPVVV 246
                                   78***************988887777665 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 ?    5.6   0.1     0.011        15      31      45 ..     220     234 ..     207     246 .. 0.82
   2 ?    4.2   0.0     0.028        38     132     159 ..     404     432 ..     374     442 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                                   ESTTSTHHHHHHHHH CS
                        ResIII  31 maTGtGKTlvaakli 45 
                                     TG+GKT ++a ++
  gi|14601838|ref|NP_148379.1| 220 GSTGSGKTTTLATIA 234
                                   57*********9987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.028
                                   T-SEEEEETGGGTTS..TTTHHHHHT--- CS
                        ResIII 132 rfdviiiDEaHrlgak.kswreilekfke 159
                                     +++++DEaH++ +  +s+ +i+ + ++
  gi|14601838|ref|NP_148379.1| 404 GPLLLVVDEAHNMFDGeESFPSIMMAESR 432
                                   33499******998873466666555555 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 ?   10.4   0.0   0.00017      0.24     129     149 ..     213     233 ..     204     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                         T2SSE 129 rglilvsGgTgsGKttllyal 149
                                   +g i v G TgsGKtt+l ++
  gi|14601838|ref|NP_148379.1| 213 EGHIGVFGSTGSGKTTTLATI 233
                                   6778899**********9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00043       0.6      23      52 ..     218     247 ..     213     258 .. 0.89
   2 ?   -3.9   0.0       6.8   9.4e+03      91      97 ..     407     413 ..     397     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00043
                        AAA_30  23 ltGpAGtGKttalkalreaweaaggrvigl 52 
                                   + G  G+GKtt+l++++  +++ag +v+++
  gi|14601838|ref|NP_148379.1| 218 VFGSTGSGKTTTLATIACGAAEAGLPVVVA 247
                                   56999****************9**999975 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.8
                        AAA_30  91 llivDEa 97 
                                   ll+vDEa
  gi|14601838|ref|NP_148379.1| 407 LLVVDEA 413
                                   89****9 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   0.0   0.00034      0.46      83     130 ..     407     448 ..     391     463 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                           Zot  83 llviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdiski 130
                                   llv+DE++++f  +  +    p +    +e R++g  i l tq++  +
  gi|14601838|ref|NP_148379.1| 407 LLVVDEAHNMFDGEESF----PSI--MMAESRKFGLYIALATQNPHLL 448
                                   79***********9998....444..4689**************9766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00054      0.74      14      32 ..     216     234 ..     211     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                                   EEEEESTTSSHHHHHHHHT CS
                                   xxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  14 vaivGenGaGKStLlklla 32 
                                   ++++G++G+GK+t l+++a
  gi|14601838|ref|NP_148379.1| 216 IGVFGSTGSGKTTTLATIA 234
                                   799************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3742.93
//
Query:       gi|118431728|ref|NP_148380.2|  [L=197]
Description: hypothetical protein APE_2094.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-11   44.3   0.0    2.6e-10   40.9   0.0    2.4  2  AAA_18           AAA domain
    6.9e-06   26.3   0.0    8.5e-05   22.7   0.0    2.2  1  SKI              Shikimate kinase
    1.6e-05   25.4   0.1    2.8e-05   24.6   0.1    1.4  1  AAA              ATPase family associated with various cellul
    0.00015   22.0   0.0     0.0011   19.1   0.0    2.2  1  AAA_33           AAA domain
     0.0012   18.7   0.1       0.15   11.8   0.0    2.3  2  Cytidylate_kin   Cytidylate kinase
  ------ inclusion threshold ------
      0.022   15.0   0.1      0.048   13.9   0.1    1.6  1  AAA_28           AAA domain
      0.024   15.1   0.3      0.058   13.8   0.3    1.6  1  AAA_16           AAA ATPase domain
      0.024   14.4   0.2      0.054   13.2   0.1    1.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.031   14.6   0.1      0.091   13.0   0.1    1.7  2  AAA_22           AAA domain
      0.048   12.9   0.1       0.06   12.6   0.1    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.07   13.1   0.1       0.16   12.0   0.1    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
       0.11   12.6   0.0       0.38   10.9   0.0    1.8  2  Cytidylate_kin2  Cytidylate kinase-like family
       0.12   12.7   0.0       0.18   12.1   0.0    1.4  1  AAA_19           AAA domain
       0.12   12.8   0.0       0.33   11.4   0.1    1.7  2  AAA_17           AAA domain


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 !   40.9   0.0   2.1e-13   2.6e-10       2     129 ..       4     124 ..       3     125 .. 0.86
   2 ?    0.1   0.0      0.87   1.1e+03      45      81 ..     142     172 ..     127     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.1e-13
                         AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidg 81 
                                    l+tGtpG+GKt++++ +++++g+ ++ ++++ e    +++dp    +   ++e+   +++d l+  +      + +v++ 
  gi|118431728|ref|NP_148380.2|   4 LVTGTPGTGKTSVGRLIAEETGCRFVESSLLLEALGATSRDPT--GRATLVVEWS--AAVDRLRSLDM-----GCWVVST 74 
                                    79*****************************************..5555555555..78888888765.....7779999 PP

                         AAA_18  82 hlaeleseaakdikk..vvLtaspeelleRlekRgyeeakikeneeaeil 129
                                    +   l  ea    +   v L+++p +l eRl+ Rg+ e k  en  ae++
  gi|118431728|ref|NP_148380.2|  75 VTPSLWLEAVGLEVAlaVLLRTNPIVLEERLKGRGWPEGKVVENVLAEAF 124
                                    98877777776655579***********************9999999876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.87
                         AAA_18  45 aldeskrldedkldklldaleenssaleegknlvidg 81 
                                    ++d s r  ++++d+++d++e+++        + id+
  gi|118431728|ref|NP_148380.2| 142 EVDTSTRSPREVVDEVFDKVERWDT------GVRIDW 172
                                    3577788888888888888888864......223444 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   6.7e-08   8.5e-05       1     156 [.       9     160 ..       9     162 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.7e-08
                                    TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHCCCS..SEEEEE-TTGGGSHHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeifeeegeegFrelEsevlkelleee..glViatGGGavlseen 78 
                                    +G+GK++vG+l+A++ g++f+++  l+e   g++ ++     g +    ++s+++++l + +    V++t   +  s   
  gi|118431728|ref|NP_148380.2|   9 PGTGKTSVGRLIAEETGCRFVESSLLLEA-LGATSRDPT---GRATLVVEWSAAVDRLRSLDmgCWVVST---VTPSLWL 81 
                                    69********************9877775.555555544...6667777777777776655554567777...3333334 PP

                                    HHHHHHHSEEEEEE--HHHHHHHHHHTTS.SGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHHH CS
                            SKI  79 rellkekgiviyLdvsleellerlkadke.RPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeilea 156
                                     ++  e ++ ++L++++ +l erlk +      + e+  +e+  e  +e  +   ea+++ vd+s++s++ev++e++++
  gi|118431728|ref|NP_148380.2|  82 EAVGLEVALAVLLRTNPIVLEERLKGRGWpEGKVVENVLAEAFGEIGWELVEQGFEASTIEVDTSTRSPREVVDEVFDK 160
                                    4444466777777777777777777777643344444445555666664444445567777777777777777777665 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 !   24.6   0.1   2.2e-08   2.8e-05       1      31 [.       3      33 ..       3      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.2e-08
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEET CS
                            AAA  1 vllyGppGtGKTllakavakelgvefleisg 31
                                   +l++G+pGtGKT++ + +a+e+g +f+e s+
  gi|118431728|ref|NP_148380.2|  3 LLVTGTPGTGKTSVGRLIAEETGCRFVESSL 33
                                   699***********************99775 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.8e-07    0.0011       1     122 [.       2     112 ..       2     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.8e-07
                         AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnl 80 
                                    l+l+ G pG+GK+ + + +++++g+ +++s  l+++l +t ++++      ++ + ++  + +++ +s   ++ + +t +
  gi|118431728|ref|NP_148380.2|   2 LLLVTGTPGTGKTSVGRLIAEETGCRFVESSLLLEALGATSRDPTG----RATLVVEWS-AAVDRLRSLDMGCWVVSTVT 76 
                                    68999********************************998776543....333444554.45555566666666666643 PP

                         AAA_33  81 srrerarflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                     ++ + + + l        ++v ++t + +l+eRl+ R  ++
  gi|118431728|ref|NP_148380.2|  77 -PSLWLEAVGLEV-----ALAVLLRTNPIVLEERLKGRGWPE 112
                                    .344433333332.....256777777777777777776655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00012      0.15       5      33 ..       7      35 ..       4      62 .. 0.89
   2 ?    4.7   0.0     0.017        22     188     210 ..     140     162 ..     135     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                   -STTSSHHHHHHHHHHHHT-EEEEHHHHH CS
                 Cytidylate_kin  5 GPagsGKssvaralaeklglkyldtgalY 33
                                   G  g+GK sv+r++ae+ g+++++++ l 
  gi|118431728|ref|NP_148380.2|  7 GTPGTGKTSVGRLIAEETGCRFVESSLLL 35
                                   7789********************99875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                                    -EEEETTTS-HHHHHHHHHHHHH CS
                 Cytidylate_kin 188 aliidtskltieevvekilelik 210
                                     + +dts+ + +evv+++ ++++
  gi|118431728|ref|NP_148380.2| 140 TIEVDTSTRSPREVVDEVFDKVE 162
                                    589***************99886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.7e-05     0.048       3      28 ..       4      30 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                         AAA_28  3 vitGgestGKTtlleaLaar.gypvvp 28
                                    +tG+++tGKT++ + +a++ g + v+
  gi|118431728|ref|NP_148380.2|  4 LVTGTPGTGKTSVGRLIAEEtGCRFVE 30
                                   58****************766888774 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   4.6e-05     0.058      26      46 ..       2      22 ..       1      40 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                         AAA_16 26 lvllsGesGvGKsslvrellr 46
                                   l+l++G +G+GK+s+ r +++
  gi|118431728|ref|NP_148380.2|  2 LLLVTGTPGTGKTSVGRLIAE 22
                                   68*************999986 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 ?   13.2   0.1   4.3e-05     0.054      36      63 ..       3      30 ..       2      39 .. 0.87
   2 ?   -3.0   0.0       4.3   5.5e+03      99     129 ..     115     144 ..     113     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvklki 63
                                   +l++G PG Gkt++ ++ia+e g ++  
  gi|118431728|ref|NP_148380.2|  3 LLVTGTPGTGKTSVGRLIAEETGCRFVE 30
                                   5899*****************9988755 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.3
                         RuvB_N  99 aveevlysamedfrldivigkGpsarsikld 129
                                    +ve+vl  a+ ++  ++ +++G  a +i++d
  gi|118431728|ref|NP_148380.2| 115 VVENVLAEAFGEIGWEL-VEQGFEASTIEVD 144
                                    67788888887777775.6888888888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.1e-05     0.091       7      29 ..       2      24 ..       1      50 [. 0.86
   2 ?   -1.4   0.0         2   2.5e+03      44      66 ..     140     163 ..     118     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                   +l+vtG +GtGKT + r ++e+ 
  gi|118431728|ref|NP_148380.2|  2 LLLVTGTPGTGKTSVGRLIAEET 24
                                   689*************9999876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                         AAA_22  44 fvtlpsst.sskdllrellralgl 66 
                                    ++++  st s++++  e++ ++++
  gi|118431728|ref|NP_148380.2| 140 TIEVDTSTrSPREVVDEVFDKVER 163
                                    444444555688888888877765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.7e-05      0.06       3      25 ..       2      24 ..       1      53 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.7e-05
                        DUF2075  3 vvlVtGvaGtGKtvvllnllael 25
                                   ++lVtG +GtGKt v+  ++ e 
  gi|118431728|ref|NP_148380.2|  2 LLLVTGTPGTGKTSVGRLIAEET 24
                                   689************98887765 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   0.1   0.00013      0.16       2      28 ..       3      29 ..       2      38 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   EEEE--SSSSHHHHHHHGGGGBS--EE CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnreve 28
                                   +l+ G pGtgK+++ + +a+ ++++++
  gi|118431728|ref|NP_148380.2|  3 LLVTGTPGTGKTSVGRLIAEETGCRFV 29
                                   6889****************9977765 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.38       5      40 ..       6      41 ..       5      74 .. 0.85
   2 ?   -1.5   0.0       1.8   2.3e+03      14      28 ..     177     191 ..     175     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                Cytidylate_kin2  5 sreyGsgGetigeaLAekLglpfydreiieevakel 40
                                   +++ G+g++ +g+ +Ae+ g +f++  ++ e+   +
  gi|118431728|ref|NP_148380.2|  6 TGTPGTGKTSVGRLIAEETGCRFVESSLLLEALGAT 41
                                   5789**********************9999987765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.8
                Cytidylate_kin2  14 tigeaLAekLglpfy 28 
                                    ++++++Ae Lg +++
  gi|118431728|ref|NP_148380.2| 177 EVARRVAELLGRDYL 191
                                    799*****9997775 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   0.00014      0.18      13      32 ..       3      22 ..       1      67 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         AAA_19 13 llvtaGpGtGKTrvlkhiva 32
                                   llvt+ pGtGKT v + i +
  gi|118431728|ref|NP_148380.2|  3 LLVTGTPGTGKTSVGRLIAE 22
                                   79**********98766655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00026      0.33       1      32 [.       6      36 ..       6      50 .. 0.84
   2 ?   -2.5   0.0       4.9   6.3e+03     103     123 ..      89     108 ..      84     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                                   EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllre 32
                                   +G PG GK+ + + ++e+ g  +++ ++ll e
  gi|118431728|ref|NP_148380.2|  6 TGTPGTGKTSVGRLIAEETGCRFVE-SSLLLE 36
                                   69**********************9.555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                                    SEEEEEE--HHHHHHHHHHHT CS
                         AAA_17 103 daiilleadpeeilerrlkdr 123
                                     + +ll ++p  +le+rlk r
  gi|118431728|ref|NP_148380.2|  89 ALAVLLRTNP-IVLEERLKGR 108
                                    5667788877.5777777643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1442.90
//
Query:       gi|118431729|ref|NP_148382.2|  [L=419]
Description: DNA primase [Aeropyrum pernix K1]
Scores for complete 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   33.4   1.4    7.9e-08   32.7   0.1    2.1  2  Toprim_4  Toprim domain
      1e-06   28.9   0.1    3.7e-06   27.1   0.0    2.0  2  Toprim    Toprim domain
    9.4e-06   26.0   0.0    5.2e-05   23.6   0.0    2.3  2  Toprim_2  Toprim-like
  ------ inclusion threshold ------
       0.01   15.8   0.9      0.025   14.6   0.9    1.6  1  CARD      Caspase recruitment 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 ?   -2.3   0.1       1.4   6.5e+03      33      58 ..     108     134 ..      94     134 .. 0.50
   2 !   32.7   0.1   1.8e-11   7.9e-08       1      72 [.     168     228 ..     168     240 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                       Toprim_4  33 pldgirpeklktenlve....aekkvkevi 58 
                                     l++i+   ++     +    +e  ++e+i
  gi|118431729|ref|NP_148382.2| 108 RLEKIKQRARELL---RlmkeKEPDIREII 134
                                    3344442222222...13335666777766 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.8e-11
                       Toprim_4   1 seiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeatae 72 
                                    ++ii+VEg+ Dv  l ++g++nv+a  g + + ++ i+  +l +          k+vil++dgD  Ge   +
  gi|118431729|ref|NP_148382.2| 168 DTIIVVEGRSDVNTLLRYGYTNVIALGGAREKVPETIK--RLAE---------QKKVILFVDGDRGGELILK 228
                                    58***********************5555555555565..5555.........49**********9997655 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3     6e+03      51      51 ..     107     107 ..      56     138 .. 0.61
   2 !   27.1   0.0   8.2e-10   3.7e-06       2      85 ..     170     232 ..     169     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                    H CS
                         Toprim  51 k 51 
                                    +
  gi|118431729|ref|NP_148382.2| 107 E 107
                                    1 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 8.2e-10
                                    EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHH CS
                         Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiaw 81 
                                    +++vEg sd+ t+ ++   g+++v+a+ G   ++++                 ++k+la + +++il  D+Dr Ge i +
  gi|118431729|ref|NP_148382.2| 170 IIVVEGRSDVNTLLRY---GYTNVIALGGAREKVPE-----------------TIKRLA-EQKKVILFVDGDRGGELILK 228
                                    89**************...9**********999999.................677777.899***************99 PP

                                    HHHH CS
                         Toprim  82 elle 85 
                                     +l 
  gi|118431729|ref|NP_148382.2| 229 NVLP 232
                                    9884 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-08   5.2e-05       1      69 [.     171     235 ..     171     251 .. 0.86
   2 ?   -1.8   0.1      0.98   4.4e+03      57      84 ..     282     314 ..     274     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                       Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGt.alteaalkllerypekkvvlalDnDkaGrkaakrlaellr 69 
                                    +v+Eg  D+  l+++g +   nv+algG  +  ++ +k l+++  kkv+l +D D+ G+   k++  +++
  gi|118431729|ref|NP_148382.2| 171 IVVEGRSDVNTLLRYGYT---NVIALGGArEKVPETIKRLAEQ--KKVILFVDGDRGGELILKNVLPQMK 235
                                    69***************7...********98889999999999..99************99887766664 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.98
                       Toprim_2  57 Grkaakrlaellreag.....vrekirelpegk 84 
                                     ++a+kr  e + ea+     v+ek++++pe+k
  gi|118431729|ref|NP_148382.2| 282 AEEAVKREEEAAAEAKppapaVQEKAAKPPEEK 314
                                    456666666666666677777888888888766 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.9   5.5e-06     0.025      32      77 ..      97     144 ..      95     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                                    -HHHHHHHHT..SSSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHSHH CS
                           CARD  32 teeeeekika..kttrlskareLldlvqkkgekacqaflealkegqpd 77 
                                    t ee+ + +   + + +++areLl+l+++k +   ++++e+l+e+q++
  gi|118431729|ref|NP_148382.2|  97 TIEEIRDLRLerLEKIKQRARELLRLMKEKEPDIREIIREVLQEEQAK 144
                                    666666666666888999**************************7764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      947  (0.0528195); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 2967.70
//
Query:       gi|118431730|ref|NP_148383.2|  [L=803]
Description: DNA polymerase II [Aeropyrum pernix K1]
Scores for 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-68  230.2   0.0    5.7e-68  229.7   0.0    1.2  1  DNA_pol_B       DNA polymerase family B
    7.6e-35  120.6   0.0    9.8e-33  113.7   0.0    2.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    2.8e-07   30.7   0.0    5.6e-07   29.7   0.0    1.6  1  RNase_H_2       RNase_H superfamily
    1.7e-05   24.6   0.0    3.1e-05   23.8   0.0    1.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
  ------ inclusion threshold ------
      0.044   12.6   0.0       0.19   10.5   0.0    1.9  1  DNA_pol_B_2     DNA polymerase type B, organellar and viral


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 !  229.7   0.0   1.6e-71   5.7e-68       4     457 ..     384     777 ..     381     779 .. 0.88

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 1.6e-71
                                    HHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTT CS
                      DNA_pol_B   4 srvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcytt 83 
                                     +v++ +  +r e  L+r+a + g  +p+r e  ++ +  Y+Ga Vl Pk g++++ ++vlDFaS+YP+i++++N+ + t
  gi|118431730|ref|NP_148383.2| 384 DQVMAASVGFRLEWRLIREAAKLGELVPNRVER-SEGR--YAGAIVLRPKPGVHED-IAVLDFASMYPNIMVKYNVGPDT 459
                                    5666677778889999************55555.5666..*************986.99********************* PP

                                    CE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHH.CS--HHHHHHHHHHHHHHHHH CS
                      DNA_pol_B  84 lvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelk.eekdefekalldkqQlalKvt 162
                                    lv+  ee  e  +e+ y   ev+    +f   ++  g + k+L+++l+ R++i++e+k +  d+ e +lld++Q+a+K++
  gi|118431730|ref|NP_148383.2| 460 LVRPGEEYGE--EEV-YTAPEVGH---KF--RKSPPGFFKKILERFLSWRRQIRSEMKkHPPDSPEYKLLDERQKAIKLL 531
                                    ****999664..323.43333333...34..77889**********************44455569************** PP

                                    HHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSH CS
                      DNA_pol_B 163 aNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdv 242
                                    aN+ YG++G  + r +c + A+ vT+ GR ++ ++ +   +                  +l+viYGDTDS+f++ + ++v
  gi|118431730|ref|NP_148383.2| 532 ANASYGYMGWPHARWYCRECAEAVTAWGRSIIRTAIRKAGEL-----------------GLEVIYGDTDSLFVKNDPEKV 594
                                    ********************************8876666644.................9**************999999 PP

                                    HHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHH CS
                      DNA_pol_B 243 eellkigkelaeevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRrdncklvkevikkv 321
                                    e+l+++       v+e+l ++   ++++kvy ++ ++ +KK+Y+gl+v+     +k+++ G + vR d+++l+ke+  kv
  gi|118431730|ref|NP_148383.2| 595 ERLIRF-------VEEELGFD---IKVDKVYRRVFFTeAKKRYVGLTVD-----GKIDVVGFEAVRGDWSELAKETQFKV 659
                                    988876.......55556666...999********9846**********.....************************** PP

                                    HHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TT CS
                      DNA_pol_B 322 lelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneeapevg 401
                                     e +lk+     s++e+++++++i+    e+l+ ++v+++k+v+ k+l+++p+ y++++ ph+++a  ++ r + ++e+g
  gi|118431730|ref|NP_148383.2| 660 AEIVLKT----GSVDEAVDYVRNII----EKLRRGQVDMRKLVIWKTLTRPPSMYEARQ-PHVTAALLME-RAGIKVEPG 729
                                    *******....**************....9*************************9999.****998665.5589***** PP

                                    CEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHHT CS
                      DNA_pol_B 402 drisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarlle 457
                                     +i Yv+++ +          + ra  + y  +++ ++d+eyY++ q+++++ r+l+
  gi|118431730|ref|NP_148383.2| 730 AKIGYVVTKGS-------GPLYTRA--KPYFMASKEEVDVEYYVDkQVVPAALRILQ 777
                                    ********996.......4788776..568889999******************997 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 !  113.7   0.0   2.7e-36   9.8e-33       4     337 .]      35     317 ..      33     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.7e-36
                                    TTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHH CS
                 DNA_pol_B_exo1   4 egksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelk 83 
                                    +g +v+v   +f+pyfY+ +  +  l+++++ +++l++  s  +    +ve  ++++++g e +    lkv++  p  ++
  gi|118431730|ref|NP_148383.2|  35 DGSRVVVFYGEFRPYFYVLPDGSVGLDQLAAMIRRLSRPSSPIL----SVE-RVRRRFIGREVE---ALKVTTLVPASVR 106
                                    67888999999**********999*9999999998886666544....577.788*********...8************ PP

                                    HHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C.-.SEEEEEETTTSCEETTTCC.S-EEE CS
                 DNA_pol_B_exo1  84 kirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkis.ncdveidcdvddliakpkese.pplrv 161
                                    + r+ +++l  + dv e+d+++  rf+id ++ +++wy  ++++v + + +s    + ++ d +++++  +e+    lrv
  gi|118431730|ref|NP_148383.2| 107 EYREAVRRLGGVRDVLEADIPFALRFIIDFNLYPMRWYVAEVREVAVPHGYSvDRAYTLSGDIREDETRIQEDPlKGLRV 186
                                    **************************************999555544444431445555555566666555555899*** PP

                                    EEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHH CS
                 DNA_pol_B_exo1 162 lsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsEkel 241
                                    ++FDIe++sk +  pd+++  dp+i+I +   g           + + e                       e +s+k++
  gi|118431730|ref|NP_148383.2| 187 MAFDIEVYSKMR-TPDPKK--DPVIMIGLQQAGGE---------IEILEA----------------------EDRSDKKV 232
                                    **********99.******..*******8766644.........222222......................34799*** PP

                                    HHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHH CS
                 DNA_pol_B_exo1 242 LqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqarekvkisgrihlDlyr 321
                                    + +f+e +k++dPdvi+gYN + FD+pY+ +Ra+ l +       +l  g rs   ++g      +++++sgr+++Dl++
  gi|118431730|ref|NP_148383.2| 233 IAGFVERVKSIDPDVIVGYNQNRFDWPYLVERARVLGV-------KLAVGRRSVEPQPGLY----GHYSVSGRLNVDLLD 301
                                    **********************************4444.......4435666666666666....*************** PP

                                    HHHHHSSSSG-SHHHH CS
                 DNA_pol_B_exo1 322 vvkrklklpsYkLnav 337
                                    ++ +    +  +L++v
  gi|118431730|ref|NP_148383.2| 302 FAEELHEVKVKTLEEV 317
                                    *999877776666665 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.6e-10   5.6e-07       3     164 ..     189     367 ..     187     369 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.6e-10
                      RNase_H_2   3 fDiEttGl....spkknliyliGvldvdekeiekltqllaeepeeekailelf.lellekkkalvtfngksFDvpflkrl 77 
                                    fDiE +      +pkk+ +++iG+ +  + eie +  l ae+++++k i  ++   +  + + +v +n ++FD+p+l ++
  gi|118431730|ref|NP_148383.2| 189 FDIEVYSKmrtpDPKKDPVIMIGLQQ-AGGEIE-I--LEAEDRSDKKVIAGFVeRVKSIDPDVIVGYNQNRFDWPYLVER 264
                                    777776434444789999*****996.667777.4..45899999999999774445556688***************** PP

                      RNase_H_2  78 f.........kkyklde...............eefrhiDLlkelrk.kklesysLksvekelgierreedlsGsqavkly 132
                                    +                                 +  +DLl  +++ ++++   L++v+ +lg+         + + +++
  gi|118431730|ref|NP_148383.2| 265 ArvlgvklavG-----RrsvepqpglyghysvSGRLNVDLLDFAEElHEVKVKTLEEVADYLGVVKI----GERVTLEWW 335
                                    *7777655552.....144444778888887755577777777755334444458889999998876....567789999 PP

                      RNase_H_2 133 q..eylrtgdeellekilaYNedDvralatlyek 164
                                    q  ey    d+++ e + +Y +dDvr++  l ek
  gi|118431730|ref|NP_148383.2| 336 QigEYW--DDPSKREILRKYLRDDVRSTMGLAEK 367
                                    855554..89******************999886 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   8.7e-09   3.1e-05      26     167 ..     218     362 ..     206     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.7e-09
                 DNA_pol_B_exo2  26 kvkslgeeessekelikkffegvekkkpq.lVsfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystr 104
                                    ++  l++e+ s+k++i+ f e v++  p  +V++n + fD p l  ra + gv+ +    + +  +   +  y    s r
  gi|118431730|ref|NP_148383.2| 218 EIEILEAEDRSDKKVIAGFVERVKSIDPDvIVGYNQNRFDWPYLVERARVLGVKLAVGRRSVE-PQPGLYGHYSV--SGR 294
                                    6777899999*****************97479*********************9987666666.57888888864..344 PP

                 DNA_pol_B_exo2 105 .hlDLmdllseygaranakLdelakllgl...PGKlgvdGskVaelyqegklkei.reYcetDvlnTY 167
                                      +DL+d   e +  + + L+e+a  lg+     ++ ++  ++ e++++ + +ei r+Y + Dv +T 
  gi|118431730|ref|NP_148383.2| 295 lNVDLLDFAEELHEVKVKTLEEVADYLGVvkiGERVTLEWWQIGEYWDDPSKREIlRKYLRDDVRSTM 362
                                    48999999999988899999999999886221446677778888999887666654889999988876 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.4e-05      0.19     213     246 ..     421     453 ..     325     458 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.4e-05
                    DNA_pol_B_2 213 yrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthy 246
                                    y G ++ +p+  g + e+i v D+ S+YP++m++y
  gi|118431730|ref|NP_148383.2| 421 YAGAIVlRPK-PG-VHEDIAVLDFASMYPNIMVKY 453
                                    6788887555.33.569***************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (803 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 5580.52
//
Query:       gi|14601843|ref|NP_148384.1|  [L=108]
Description: hypothetical protein APE_2102 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.085   12.6   0.0       0.12   12.2   0.0    1.2  1  FTCD_N    Formiminotransferase domain, N-terminal subdomain


Domain annotation for each model (and alignments):
>> FTCD_N  Formiminotransferase domain, N-terminal subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.5e-06      0.12      85     128 ..       9      52 ..       8      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-06
                        FTCD_N  85 vDvipfiPlkevtleecaelAkelaeelgeelgvpvylygaaaq 128
                                   +D +p +Pl+++ le + +lAkel+ el  + +  v+  ++ ++
  gi|14601843|ref|NP_148384.1|   9 LDDLPHHPLHKMWLELAEKLAKELGVELEVKKEDYVFAMEHGDT 52 
                                   699************************99988888888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 854.82
//
Query:       gi|118431731|ref|NP_148385.2|  [L=280]
Description: endonuclease IV [Aeropyrum pernix K1]
Scores for complete 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-23   83.1   0.0    2.1e-23   82.9   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
    6.4e-05   22.3   0.0    8.5e-05   21.9   0.0    1.3  1  UvdE          UV-endonuclease UvdE


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 !   82.9   0.0   2.4e-27   2.1e-23       2     200 ..      24     228 ..      23     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 2.4e-27
                                    HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaa 81 
                                    ++++++G d+ E+    +v +se   +++r+l +a++e+g+ ++++ +++ + ++++d   ++ e+s+++l + + +++ 
  gi|118431731|ref|NP_148385.2|  24 EFLRSIGLDALEYEAVRGVRISE---AKARRLGEAARENGVILSMHAPYYVNLSSPDD---SVVERSIKRLYDSMIASEW 97 
                                    5799*****************95...8***************************9984...447899************* PP

                                    HTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHH..HHTSEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEE CS
                   AP_endonuc_2  82 LGapllvlhpGtagagpkgseeeawerlaeslneladyae..kegvklalEtlagsgvelgdeelarlldavdspnvgvc 159
                                    +G   +v+hpG   + + +s+eea++r++e+ln+l++ +    +  ++a Et+ ++ +    ee+++++  +++  ++ c
  gi|118431731|ref|NP_148385.2|  98 MGSYAVVVHPG--YYKGLKSREEAVKRVIEALNRLIESLPswVKTPWIAPETMGKQSQVGSLEETVEICLNTPR--CRPC 173
                                    ***********..89************************877888************98888***********8..**** PP

                                    EEHHHHHHH........TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSST CS
                   AP_endonuc_2 160 lDtgHllia........eedvddalraladr.......ikhvHikDakgdlgagrd 200
                                     D++Hl+++         ++v +a++ +++          h H++ ++   ++g+ 
  gi|118431731|ref|NP_148385.2| 174 VDWAHLYARaegkfvtsVDQVVKAIEYIESNlgreavdPLHTHFSKIEYG-KGGER 228
                                    **********8888777777777777777778888866666666666663.33333 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   9.5e-09   8.5e-05      88     175 ..      48     129 ..      35     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 9.5e-09
                           UvdE  88 eleevGelakelglRltfHPeqftllnSdrkevtesairdlayHdklldalklaeqq.davliiHvGGkfgdkeaalerf 166
                                    + +  Ge+a+e g+ l++H   ++ l+S+ ++v+e++i+ l   d ++      e      +++H G  +++ +++ e  
  gi|118431731|ref|NP_148385.2|  48 KARRLGEAARENGVILSMHAPYYVNLSSPDDSVVERSIKRLY--DSMI----ASEWMgSYAVVVHPG-YYKGLKSREEAV 120
                                    56789*********************************9873..3333....333332346788988.666655555555 PP

                           UvdE 167 kenikrlpd 175
                                    k+ i+ l +
  gi|118431731|ref|NP_148385.2| 121 KRVIEALNR 129
                                    544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2425.81
//
Query:       gi|118431732|ref|NP_148386.2|  [L=282]
Description: uridine phosphorylase [Aeropyrum pernix K1]
Scores for 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-45  153.4   2.7    7.4e-45  153.0   2.7    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 !  153.0   2.7   4.1e-49   7.4e-45       1     226 [.      31     256 ..      31     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 4.1e-49
                                    CEEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEE CS
                      PNP_UDP_1   1 kiaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaG 80 
                                    +++++ g+p++ +l+a+   +e +   ++r+++++tG +kg+ ++++stGiG p++a +a+ +ll  + ++++ir+Gt G
  gi|118431732|ref|NP_148386.2|  31 RYVLLPGDPERTDLIARL-WDEARLVAHHREYRTWTGFYKGTSISVTSTGIGSPSTA-IAVEELLRVG-AETFIRVGTMG 107
                                    5799**************.**************************************.********66.*********** PP

                                    ESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CH.. CS
                      PNP_UDP_1  81 glnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaet.. 158
                                    g+++dl++G++vi ++a++++g+s+        qy+p  ++a a+ + +a+l+eaaealg+++++Gvva++d+fy  +  
  gi|118431732|ref|NP_148386.2| 108 GIREDLRPGTLVIGSAAVRMEGTSG--------QYAPRGFPAAASYDVVAALVEAAEALGVRYEVGVVASTDSFYLGQgr 179
                                    *************************........*********************************************** PP

                                    ........HHHHH...HHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH..HCCCHHHHHHHHHHH CS
                      PNP_UDP_1 159 ........eaelr...llrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeath.eeveefaqeaaknaa 226
                                            +++++   llr+ g+   eME++a+++l++++g++++++++v     ++ ++e  + + ve++a+ a++++a
  gi|118431732|ref|NP_148386.2| 180 pgyggymtPEASEvipLLRSAGVLGFEMEASALFTLSQLYGARAGCVCAVVA---NRVSGEFVVnAGVEDAARVASEAVA 256
                                    *******966666789*****************************9999943...3333433332333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2495.90
//
Query:       gi|118431733|ref|NP_148387.2|  [L=306]
Description: ATP-dependent 6-phosphofructokinase [Aeropyrum pernix K1]
Scores for 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  121.0   0.0    5.6e-34  117.8   0.0    1.9  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 !  117.8   0.0   3.1e-38   5.6e-34       5     300 ..       5     285 ..       1     287 [. 0.87

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 3.1e-38
                                    EEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTE CS
                           PfkB   5 vviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyv 82 
                                     ++G ++ d+++ +++l  ++e+v +++ + + GGa+ N A a+a+lg++ +++ + G       + ++l+ +gvd+++v
  gi|118431733|ref|NP_148387.2|   5 IAVGNINLDISLSVDRLpgPEEVVFARDAWIGVGGAATNYAIAVAQLGQKPVLVAVAGREMERLGVVDTLRRRGVDVSRV 84 
                                    689***************888888******************************************************** PP

                                    EEESSSEEEEEEEEETTT.SEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTEE CS
                           PfkB  83 kidedtrtglalivvded.gertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggtf 161
                                    k + d + g+ +++v +    r++v  rga+++l k   ee++d ++   +++++++ +++l  a    + +    g   
  gi|118431733|ref|NP_148387.2|  85 K-TVDRPSGVVVVMVVASdSHRSMVSMRGANEELLKYIEEEPLDGVSGECHVHMASVPPQALDFAPGGCTLSYDPGGE-- 161
                                    *.6666****99999999999***************766688888888888888885554444444444444444444.. PP

                                    EEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEE CS
                           PfkB 162 dpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgel 241
                                         + + +   + l + l+ +d+++ n  El+ ++g+   d + a ++l+     g k +v ++G  Ga vve++  +
  gi|118431733|ref|NP_148387.2| 162 -----AFKRP---KSLWSRLPRVDWMFINTPELKGMSGSG--DLAAAYRLLES----GLKRLVLKHGRGGATVVERGFCV 227
                                    .....22222...334456899******************..88888888765....*********************** PP

                                    EEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSC CS
                           PfkB 242 kvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslp 300
                                      ++ p  ++vD+tGAGD+f ++f  a  +g+s+eealr+a+a++++ v ++g+++ +p
  gi|118431733|ref|NP_148387.2| 228 TLDRTPVLEPVDVTGAGDAFDAAFNIAVKAGWSVEEALRLAVAAGSAKVLRRGSSN-MP 285
                                    *****************************************************997.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.19s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2648.89
//
Query:       gi|14601847|ref|NP_148388.1|  [L=402]
Description: acetyl-CoA acetyltransferase [Aeropyrum pernix K1]
Scores for complete 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-65  221.3   0.0    1.7e-65  221.0   0.0    1.1  1  Thiolase_N     Thiolase, N-terminal domain
    2.5e-41  140.2   0.0    7.9e-41  138.6   0.0    1.9  2  Thiolase_C     Thiolase, C-terminal domain
  ------ inclusion threshold ------
      0.032   13.8   2.4       0.38   10.3   1.8    2.5  3  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 !  221.0   0.0   2.8e-69   1.7e-65       1     259 [.      13     271 ..      13     272 .. 0.97

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 2.8e-69
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v+iv+++rt igkfg slkd++a++L+a ++++lle+agvdp+ ++  + G v+ ag   n a+qaalkag+  +     v
  gi|14601847|ref|NP_148388.1|  13 VYIVDGVRTTIGKFGRSLKDFKAVDLAALTIRELLERAGVDPNYIELAVYGHVIRAGTHMNTAKQAALKAGLRSDLEGFNV 93 
                                   89******************************************************************************* PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSS...SSEEEEEHHHHHHTEETTTTSEHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglkl...gdekakdllipdgladafneehmGlta 159
                                   ++vc+Sg+++v++a   i ag ++ ++agG+Esmsnap  ++ ++r+g++l   g+ ++kd ++ dgl d  n+  mG  a
  gi|14601847|ref|NP_148388.1|  94 DMVCASGMASVVKASLLIDAGMYSLALAGGMESMSNAPFIAPPSIRWGVRLlyqGALEMKDAMVSDGLYDPLNQLVMGQEA 174
                                   **********************************************887752227889*********************** PP

                                   HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-B CS
                    Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvt 240
                                   +++a +y+++Ree+d  A +s  +aa a++ g+ ++  +Pvk  g     ++d+de+ir+++t+e+L+kl p+F  +G  t
  gi|14601847|ref|NP_148388.1| 175 DETAWEYGAQREELDWIAYESNMRAARAWERGHMQKYTIPVKAGGAV---VLDYDEGIRPDTTVERLSKLPPVFTPKGPHT 252
                                   *****************************************988755...******************************* PP

                                   TTSB--BEEEEEEEEEEEH CS
                    Thiolase_N 241 AgnasqisDGaaavllmse 259
                                   Agn+sqisDGa  +l++ e
  gi|14601847|ref|NP_148388.1| 253 AGNSSQISDGAVSLLVAGE 271
                                   **************99876 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.39   2.3e+03      27      44 ..      42      59 ..      25     100 .. 0.78
   2 !  138.6   0.0   1.3e-44   7.9e-41       1     123 []     279     401 ..     279     401 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.39
                                  HHHHHHHHHT--GGGESE CS
                    Thiolase_C 27 aikkvlkkagltvedidl 44
                                   i+++l++ag++ + i+l
  gi|14601847|ref|NP_148388.1| 42 TIRELLERAGVDPNYIEL 59
                                  567777777777766655 PP

  == domain 2  score: 138.6 bits;  conditional E-value: 1.3e-44
                                   ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B- CS
                    Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHP 81 
                                   lkp+a+i+ + ++gvdp+ + ++P+ a++++lkk g++ved+d++E nEAFa+  L ++++l++ +e++Nv GG+ia+GHP
  gi|14601847|ref|NP_148388.1| 279 LKPKARIVGWGYAGVDPRRFPVAPVHAVRALLKKLGWRVEDVDYWENNEAFAVNSLIMNRELGVPYERLNVVGGSIAVGHP 359
                                   589****************************************************************************** PP

                                   TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                    Thiolase_C  82 lGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                   lG +GaR++ +l+++l+++g++ gva++C g g ++a+ ie+
  gi|14601847|ref|NP_148388.1| 360 LGSTGARLILQLVYTLEENGARRGVASICHGLGGAAAVAIER 401
                                   **************************************9985 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 ?    0.0   0.0     0.087   5.2e+02      91     122 ..      38      69 ..      33      91 .. 0.68
   2 ?   10.3   1.8   6.3e-05      0.38     170     207 ..      92     129 ..      84     134 .. 0.86
   3 ?   -1.3   0.0      0.21   1.3e+03      84     108 ..     258     282 ..     233     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.087
                                   HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEES CS
                 ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvg 122
                                   l+  + +e le+ag++p+ ++    g +i +g
  gi|14601847|ref|NP_148388.1|  38 LAALTIRELLERAGVDPNYIELAVYGHVIRAG 69 
                                   56678899*********888766655544333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.3e-05
                                   EEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                 ketoacyl-synt 170 tvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                    vd  C+S+ + v  a   + +g  ++alaGG+e + +
  gi|14601847|ref|NP_148388.1|  92 NVDMVCASGMASVVKASLLIDAGMYSLALAGGMESMSN 129
                                   57889****77777777*****************8865 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.21
                                   TS-HHHHHHHHHHHHHHHHHTS-HH CS
                 ketoacyl-synt  84 amdpqqrllleaawealedagltpe 108
                                   +++  +  ll+a +ea+++ gl+p+
  gi|14601847|ref|NP_148388.1| 258 QISDGAVSLLVAGEEAVREMGLKPK 282
                                   5666677789999999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3410.40
//
Query:       gi|14601848|ref|NP_148389.1|  [L=447]
Description: hypothetical protein APE_2109 [Aeropyrum pernix K1]
Scores for complete 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-24   86.5   0.0    1.9e-23   83.7   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
    7.7e-12   45.3   1.0    1.9e-11   44.0   1.0    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 ?    0.6   0.0     0.075   6.7e+02      29      74 ..      29      73 ..      17     156 .. 0.70
   2 !   83.7   0.0   2.1e-27   1.9e-23       1     165 [.     160     333 ..     160     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.075
                                  HHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 29 lsveeileevkelkaekgvkevilgggepllypdfvellerlakla 74
                                  +  e+    v+el +++g ++v++ g    +  +++ ++ r ++la
  gi|14601848|ref|NP_148389.1| 29 MVEESPDPVVREL-VRRGRRVVVMYGVSSPAFLELAGEISRVSRLA 73
                                  5555666677888.78888888888877777777777777777766 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 2.1e-27
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.........SSTGGGSTTHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.........ggepllypdfvellerlak 72 
                                   ++++rgC++rC fC++p+       +r++sve++++ +  + +  g+ e+ ++          +  + +p  ve+l+ +++
  gi|14601848|ref|NP_148389.1| 160 IEIMRGCSYRCMFCQVPWE--FKSQVRFRSVESVAAAAADY-VAAGKSEIRFVapigfaygsEDLRTPNPAAVEELLSRVR 237
                                   689***************5..********************.999********9999997665556666777777777777 PP

                                   TCCCTEEEEEEECSSCHG...HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEE CS
                                   xxxxxxxxxxxxxxxxxx...xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  73 lavpgiritvetngtlpd...eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdri 149
                                       +  +    ++t+p+   +e+l+  ++l    r+s+gl++++d   l++++rgh++ee ++a  ++ e+g+ +vvd+i
  gi|14601848|ref|NP_148389.1| 238 AVGGKPYLGSFPSETRPEfvtPEILRVVRRLAyNRRISIGLQSGSDM-LLERVGRGHGVEEAVRAAGLAIEYGFTPVVDII 317
                                   75333333334444444466677778888877789***********8.********************************* PP

                                   EEBTTTSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                   Radical_SAM 150 vglpGendeeleelle 165
                                   +g+pGe+ e+++e+++
  gi|14601848|ref|NP_148389.1| 318 FGMPGESYEDVVETVN 333
                                   *************986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   1.0   2.1e-15   1.9e-11      20     120 ..      14     109 ..       8     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 2.1e-15
                   B12-binding  20 laaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvellkrirprvkvvvGGahpsldpeetle 100
                                   +a al  +g++V++  ++ +++ +v+++ ++  +vv++   ++ + +a+ el+ ++ r+++ +++vvGG+h++ +++++l+
  gi|14601848|ref|NP_148389.1|  14 VASALAGSGVDVRIEMVEESPDPVVRELVRRGRRVVVM---YGVSSPAFLELAGEISRVSRLAPTVVGGPHATGAYWQVLR 91 
                                   89************************************...99*************************************9 PP

                   B12-binding 101 aklgiddvvvgegedaleal 120
                                     lg++ +vvg+ge a+ ++
  gi|14601848|ref|NP_148389.1|  92 --LGAAAAVVGDGEIAAVEI 109
                                   ..9***********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.18s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 3884.09
//
Query:       gi|14601849|ref|NP_148390.1|  [L=247]
Description: hypothetical protein APE_2110 [Aeropyrum pernix K1]
Scores for 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-52  176.2  10.5    5.1e-52  176.2  10.5    1.6  2  Vut_1     Putative vitamin uptake transporter


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.17     3e+03      27      52 ..       8      33 ..       2      42 .. 0.68
   2 !  176.2  10.5   2.9e-56   5.1e-52       1     149 [.      49     221 ..      49     222 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.17
                         Vut_1 27 rkvvllgflanllalillllalllpa 52
                                   + v+  +la++++ + l+ a +l a
  gi|14601849|ref|NP_148390.1|  8 DRSVWPLVLAAAVFSVALVSANYLSA 33
                                  56677777777777777777766655 PP

  == domain 2  score: 176.2 bits;  conditional E-value: 2.9e-56
                         Vut_1   1 taGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa........ealesvfgltprivlasliay 73 
                                   +aGv+++++tf++td++sevyG++aa  vv +gf+++++al+l+ +a++ p+        e++++v+   ++i++asl+ay
  gi|14601849|ref|NP_148390.1|  49 PAGVVAYSVTFIVTDVVSEVYGRRAAGAVVAAGFASQIVALFLTAVAIASPPapfslvqqEEYAKVVMAGFNIIVASLVAY 129
                                   69*************************************************99999999999******************* PP

                         Vut_1  74 lvsqlldvyvfhrlkkltkgkklwlrnigStlvsqlvdtlifvtiaflg................eqlleiilsqylikll 138
                                   +vsq++dv++fh++kk+t++++lwlrn++St+vsql+dt++f+++af++                ++l+++i sqy+ikl 
  gi|14601849|ref|NP_148390.1| 130 IVSQYHDVWAFHFWKKMTGSRWLWLRNNLSTWVSQLIDTVVFLSLAFYIipllspeasrvepvslSTLWAMIYSQYIIKLG 210
                                   ***********************************************88******************************** PP

                         Vut_1 139 ialldtplvyl 149
                                   ia+ldtp+vyl
  gi|14601849|ref|NP_148390.1| 211 IAVLDTPVVYL 221
                                   **********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 00:00:00.40
# Mc/sec: 1860.38
//
Query:       gi|118431734|ref|NP_148391.2|  [L=132]
Description: hypothetical protein APE_2112.1 [Aeropyrum pernix K1]
Scores for 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  109.9   0.0    8.9e-32  109.7   0.0    1.0  1  CTP-dep_RFKase  Domain of unknown function DUF120


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 !  109.7   0.0     5e-36   8.9e-32       1     119 [.      10     127 ..      10     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 5e-36
                                    EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEEC.C CS
                 CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypakie.k 79 
                                    V+sGlg+G++yvs+  y++++++ lg++pypGTLN+++ ++ ++l  ++e+++g++ie    +++++ +v ++p++ie +
  gi|118431734|ref|NP_148391.2|  10 VFSGLGHGSFYVSI--YARNLRRALGYTPYPGTLNLRVGDAAERLAGCIERARGVRIEPPPIPGERLASVLAFPVEIEgG 87 
                                    89************..*************************************************************989 PP

                                    EEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEE CS
                 CTP-dep_RFKase  80 ikaavvvperthyeedvlEiiapekLReklelkdgdevev 119
                                    +++++v+pe t y+ dv+Ei+a++ LR+ l+++dgd+v+ 
  gi|118431734|ref|NP_148391.2|  88 VRGHIVRPEITVYKGDVVEIVADVYLRDVLKISDGDKVRF 127
                                    9*************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1022.46
//
Query:       gi|14601851|ref|NP_148392.1|  [L=144]
Description: hypothetical protein APE_2113 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1157.91
//
Query:       gi|118431735|ref|NP_148394.2|  [L=391]
Description: hypothetical protein APE_2115.1 [Aeropyrum pernix K1]
Scores for complete 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   27.5   0.0    4.9e-06   26.1   0.0    1.6  1  Amidohydro_1  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 !   26.1   0.0   2.7e-10   4.9e-06       1     297 [.      32     298 ..      32     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.7e-10
                                    EEEE-EEEEEEECETTECSSS.........GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHS CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.........tledwl.............vppetaaealesgiktalksGtttvadmgat 58 
                                    +++PG+ D H H +   +++a            +wl              + + ++  ++ ++++ l  G+t va++g  
  gi|118431735|ref|NP_148394.2|  32 VIVPGFSDGHMHTQ---VVDAglepsrvwsNSYEWLetrrlrvdeaavrSDLDLSSRLAAAAFSRSLLEGVTLVAATGRL 108
                                    689*********96...67778898866665556669******************************************5 PP

                                    STHHHHHHHHHHHTSSSEEEEEEESSEGGS......GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH CS
                   Amidohydro_1  59 tstgiealleaaeelplglrilggkvsldr......gsaetskasreklkagaaetikgkadgvvkvalapheapafsde 132
                                       +++  l  +++    +r+++  +++dr      +          +++ ++++++    dg+ k+++  h+  ++++e
  gi|118431735|ref|NP_148394.2| 109 S-ANVRGWLSLTSR----PRAIFLPTVMDRagwpsiR----------EVEVEIERLEGLLRDGLAKIGVFVHSLGTAKPE 173
                                    3.377777777777....99***99***966553333..........33333344445557888889999********** PP

                                    HHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HHHHHHHHHHH CS
                   Amidohydro_1 133 elkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt..pteaellkerl 210
                                     ++ al+ a++r   + +H++e   e              g +++v++    + +++++++h++ ++  pt         
  gi|118431735|ref|NP_148394.2| 174 SVRRALQTAARRRSIMGMHLSEGLPEA-------------GRLVDVLGR--GPYPARIVAVHCMEVEdlPT--------- 229
                                    ********************6654443.............224555444..34456899********8888......... PP

                                    HHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHT CS
                   Amidohydro_1 211 keagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaT 290
                                     +++ ++cp+sn+il   +++  + +d     g+g+D    + ++      r++ ++ +        +  +l e+l++aT
  gi|118431735|ref|NP_148394.2| 230 -GVRCVSCPASNQILYRRTRPTLEGVD-----GFGSDWPLLIGTI-----ARHLPLINK-------LYPGRLQEILYKAT 291
                                    .88899*********999999999999.....7999966555555.....233332222.......35689999999999 PP

                                    HHHHHHT CS
                   Amidohydro_1 291 ingAkal 297
                                    i+g +a+
  gi|118431735|ref|NP_148394.2| 292 IGGYRAY 298
                                    9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.35
# Mc/sec: 3335.90
//
Query:       gi|118431736|ref|NP_148397.2|  [L=108]
Description: hypothetical protein APE_2118.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 845.87
//
Query:       gi|118431737|ref|NP_148398.2|  [L=482]
Description: hypothetical protein APE_2119.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3799.22
//
Query:       gi|118431738|ref|NP_148400.2|  [L=520]
Description: glycine dehydrogenase subunit 2 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00018   20.6   0.1    0.00035   19.6   0.0    1.4  2  Aminotran_5      Aminotransferase class-V
    0.00047   19.1   0.0    0.00086   18.2   0.0    1.4  1  GDC-P            Glycine cleavage system P-protein
     0.0065   15.7   0.0      0.011   14.9   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.02   14.3   0.7       0.16   11.4   0.1    2.1  2  Bac_luciferase   Luciferase-like monooxygenase
       0.06   12.6   0.1       0.15   11.3   0.0    1.6  2  Beta_elim_lyase  Beta-eliminating lyase


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 !   19.6   0.0   9.8e-08   0.00035      85     203 ..     166     282 ..     154     288 .. 0.77
   2 ?   -3.9   0.1       1.4   4.8e+03     262     289 ..     443     470 ..     433     471 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.8e-08
                                    -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHH CS
                    Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveeigk 163
                                    l++++ i+v ++  h++  p+ +++   g++v+ +p  ++g++d+++l++++  +t+ ++it  s+ +G   + + ei +
  gi|118431738|ref|NP_148400.2| 166 LDKRRVIIVPDS-AHGTN-PASAAM--GGFQVVEVPTGDDGNVDMEALKAAVGGDTAGLMITNPST-LGLfEENILEISR 240
                                    555555555555.55555.577665..8*********************************98877.6775899****** PP

                                    HHHHTT-EEEEE-TTTTTTS.---HHHHTESEEEEETTT.TT CS
                    Aminotran_5 164 lakkkgalvlvDaaqavghi.pidvkklgvDflafsghK.ll 203
                                    l++++g l+  D+a   g i +    +++ D++ +  hK + 
  gi|118431738|ref|NP_148400.2| 241 LVHEAGGLLYYDGANLNGIIgRARPGDMEFDIAHVNLHKtFS 282
                                    *************98665432556667777777777777444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.4
                                    HHHHHHHHCHHHHHHHHHHHHHHHHHHH CS
                    Aminotran_5 262 gaaleyleeigleaiekhekelaeylle 289
                                    ++ +e+ e+   e+ie+++++l+e ++e
  gi|118431738|ref|NP_148400.2| 443 ALMIEFTESETKENIEAYAARLKEIAEE 470
                                    5678888889999999999999988765 PP

>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.4e-07   0.00086      99     277 ..     108     298 ..      38     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-07
                                    -SS.GGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS....--E.EEEETTS-HHHHHHHH CS
                          GDC-P  99 PYq.aEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkk....akk.vvvdkkvhpqtlevlk 172
                                    P q  E  qG Lea+   q  +  +tG+d        ++      vl+++r +  +    +++ ++v  + h  +     
  gi|118431738|ref|NP_148400.2| 108 PLQdDETVQGVLEAIYMVQEWLRHITGMDACTVHPAAGSQGELAGVLMIKRFHEMRgdldKRRvIIVPDSAHGTN----P 183
                                    55525899*********************8776555554444445666666554442222223033333333333....3 PP

                                    HHHGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEEEE-TTGGGT.B- CS
                          GDC-P 173 trakglgieivevdlteekvtd.......kekevagvlvqypnteGried.lkelvekakkkkslvvvaadllaLtl.lk 243
                                      a   g+++vev++ +++  d       +  ++ag+++  p+t G  e+ + e++  +++   l+      l   +  +
  gi|118431738|ref|NP_148400.2| 184 ASAAMGGFQVVEVPTGDDGNVDmealkaaVGGDTAGLMITNPSTLGLFEEnILEISRLVHEAGGLLYYDGANLNGIIgRA 263
                                    45667788888888887777777778787889**************9986599********9998887665555555156 PP

                                    -HHHHT-SEE.EEE-TTTT---GGG----EEEEE- CS
                          GDC-P 244 pPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvk 277
                                     Pg++  Di+ v   + f vP g GGP  g + vk
  gi|118431738|ref|NP_148400.2| 264 RPGDMEFDIAhVNLHKTFSVPHGGGGPGSGPVCVK 298
                                    7********95666889**********98877665 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 !   14.9   0.0   3.1e-06     0.011      90     158 ..     166     226 ..     116     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-06
                                    HTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS- CS
                  Aminotran_1_2  90 lnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesph 158
                                    l++ ++i+vpd  ++     + + g++vv++p+   +d ++d+eal++a+         t ++ +++p+
  gi|118431738|ref|NP_148400.2| 166 LDKRRVIIVPDSAHGTNPASAAMGGFQVVEVPTG--DDGNVDMEALKAAVGG------DTAGLMITNPS 226
                                    78999***************************66..**************99......77899988775 PP

>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.074   2.7e+02     170     185 ..     355     370 ..     352     374 .. 0.90
   2 ?   11.4   0.1   4.5e-05      0.16     190     234 ..     448     492 ..     437     506 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.074
                 Bac_luciferase 170 yvaaaspaglelaarh 185
                                    y+ a++p+gl+la+++
  gi|118431738|ref|NP_148400.2| 355 YILAMGPQGLRLAGEV 370
                                    899***********98 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.5e-05
                 Bac_luciferase 190 llageppeeaaelierlragaaeagrdpadirvgisltvivadte 234
                                    ++ +e+ e ++++++rl++ a+ea rdp+++r +++ t++++ ++
  gi|118431738|ref|NP_148400.2| 448 FTESETKENIEAYAARLKEIAEEARRDPSTPRKWPRNTTSARVDN 492
                                    344599****************************99998887655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.1e-05      0.15      34     169 ..     122     254 ..     108     258 .. 0.65
   2 ?   -2.6   0.0      0.74   2.6e+03     229     277 ..     420     492 ..     410     501 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                                    HHHHHHHHHHHTT-SEEEEES.-HHHHHHHHH.........HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-E CS
                Beta_elim_lyase  34 vnrLedavaelfgkeaalfvp.qGtaAnsill.........killqrgeevivtepahihfdetgaiaelagvklrdlkn 103
                                    ++ +++ +++++g++a    p  G +++   +         +  l +   +iv + ah+   ++ a a+++g +++++++
  gi|118431738|ref|NP_148400.2| 122 IYMVQEWLRHITGMDACTVHPaAGSQGELAGVlmikrfhemRGDLDKRRVIIVPDSAHG---TNPASAAMGGFQVVEVPT 198
                                    55666666667777654432213444444333222322222111222233444444555...56778889********** PP

                                    BTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
                Beta_elim_lyase 104 keaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                                     ++G++d+e+l+aa+    +    ++ +++t+      G  +  e++ e++ ++++ g  l +DgA
  gi|118431738|ref|NP_148400.2| 199 GDDGNVDMEALKAAVGG--D----TAGLMITNPSTL--G--LFEENILEISRLVHEAGGLLYYDGA 254
                                    **************998..3....455566665554..4..6789999999999999999999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.74
                                    HT---SSTHHHHH..........................HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT--E CS
                Beta_elim_lyase 229 lggglrqagvlaa........................leagiraleeglaslerdhktaeqlaeklelvrlai 277
                                    +++gl +ag+ a                          ea    l+e +++++rd+ t+++  ++    r+  
  gi|118431738|ref|NP_148400.2| 420 VAKGLLDAGLYAPtiyfpliveealmieftesetkenIEAYAARLKEIAEEARRDPSTPRKWPRNTTSARVDN 492
                                    5566666665555666666666666666666666666556666677777888888888888777776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3634.48
//
Query:       gi|118431739|ref|NP_148401.2|  [L=465]
Description: glycine dehydrogenase subunit 1 [Aeropyrum pernix K1]
Scores for 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-108  363.0   0.0   2.2e-108  362.8   0.0    1.0  1  GDC-P     Glycine cleavage system P-protein


Domain annotation for each model (and alignments):
>> GDC-P  Glycine cleavage system P-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.8   0.0  1.2e-112  2.2e-108      11     429 ..      14     458 ..       3     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 362.8 bits;  conditional E-value: 1.2e-112
                                    HHHHHHHHT-SSHHHHHHHHS-GGGB--S-------......--HHHHHHHHHHHHTTB---EE...--BTTB------H CS
                          GDC-P  11 qkemLetlGlkslddliekavPkeiklkkelkleap......ksEeellaelekiasknkvvks...fiGaGyydtilPa 81 
                                      emLe++G++s+ddl  +++P++i l+ e+  + p       sE+e+la+++ i s+nk+++    f+G G++ +++P+
  gi|118431739|ref|NP_148401.2|  14 LDEMLEAIGVSSVDDLY-RDIPPTILLSPEEWDSLPigegrpLSEAEVLARINDILSRNKYFTDpppFVGGGVWPRYVPS 92 
                                    479**************.999999987765544444456677*******************764455************* PP

                                    HHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEET CS
                          GDC-P  82 viqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdk 161
                                    v++  ++ ++e++taYtPYqaEisqG ++al+++q+lva+l  +++ nasl+D ++A++EA+l+a r+++++  +v+v +
  gi|118431739|ref|NP_148401.2|  93 VVKA-LITRGEFLTAYTPYQAEISQGLMQALFEYQSLVAELLEMEVVNASLYDWSSAVGEAMLMARRVTRRN--RVLVPE 169
                                    **99.****************************************************************999..****** PP

                                    TS-HHHHHHHHHHHGGGT-EEEEE-GG.G--S-...........S-EEEEEEEES-T.TSB---.-HHHHHHHHHTT-EE CS
                          GDC-P 162 kvhpqtlevlktrakglgieivevdlt.eekvtd........kekevagvlvqypnt.eGried.lkelvekakkkkslv 230
                                    +++p  le+  t+a g gi +++v +  e+++ d        ++ ++a++ + yp+  +G i + +++  e+++k   l+
  gi|118431739|ref|NP_148401.2| 170 TMNPLHLETATTYAYGGGIRVEKVRVDrETGFIDledlesrlSQGDTAALYMEYPSSyTGVIDEnVEAAGEAVHKAGGLF 249
                                    *********************9988651455666899*999999***********862677765588999********** PP

                                    EEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GG..GGGG--S-EEEEEEBTTS-EEEEEE-CCG CS
                          GDC-P 231 vvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkek..lkRkiPGRlvGvskDaegkralrlalqtR 308
                                    ++ ++++++++lkpPg lgaDi+vG++q +G+ l yGGP+ g fAv+ +  l+R++PGRl+G++ Daeg+ra+ + lqtR
  gi|118431739|ref|NP_148401.2| 250 ILGVEPVSMAILKPPGRLGADIAVGDGQPLGLGLNYGGPYLGVFAVRWDgrLVRQMPGRLIGMTVDAEGRRAFAMILQTR 329
                                    **********************************************97667***************************** PP

                                    SHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT...T-E.E--SSBSSEEEEE--T CS
                          GDC-P 309 EqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk..leee.lkkkkffdtllievee 385
                                    EqHirR kAtsni t+ aL+A++aa+y  ++G++gl+e+a+ ++  ++++ak l +   +e   l+++   d+ ++   +
  gi|118431739|ref|NP_148401.2| 330 EQHIRRAKATSNITTNEALMAIAAAVYLSLLGPQGLREVAEASWYMSHYAAKRLSELrgVEAPlLEGEFIMDFTVRLPMD 409
                                    ****************************************************9998755555525556667876665444 PP

                                    ..TTHHHHHHHHHHTT..E.E-EEESTTEEEEE--TT--HHHHHHHHHH CS
                          GDC-P 386 ..kaaekvlkkaekeg..l.nlrkvelktvgialdEtvtkedieallkv 429
                                       a +++l+k+  +g  l ++   ++++++++++E+ t+++++ l+++
  gi|118431739|ref|NP_148401.2| 410 agVARRRLLEKGVLAGipLgGFSFFSDNDMLLTVTEAHTRRHVDLLVNL 458
                                    3578888********9442245667888***************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3253.52
//
Query:       gi|118431740|ref|NP_148402.2|  [L=161]
Description: thiol peroxidase [Aeropyrum pernix K1]
Scores for 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-38  129.1   0.0    9.8e-38  128.9   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    5.5e-23   81.3   0.0    6.2e-23   81.1   0.0    1.0  1  Redoxin        Redoxin
    0.00031   20.8   0.0     0.0027   17.8   0.0    2.0  2  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
      0.041   14.2   0.2      0.076   13.4   0.2    1.5  1  Thioredoxin_8  Thioredoxin-like
      0.083   12.4   0.0        0.1   12.1   0.0    1.1  1  DUF899         Bacterial protein of unknown function (DUF899)
       0.14   12.1   0.0       0.21   11.5   0.0    1.5  1  SCO1-SenC      SCO1/SenC


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.9   0.0   3.3e-41   9.8e-38       2     123 ..       5     132 ..       4     133 .. 0.99

  Alignments for each domain:
  == domain 1  score: 128.9 bits;  conditional E-value: 3.3e-41
                                    TSB----EEESTTCEEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH CS
                       AhpC-TSA   2 gdkapdfelknadgetvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiek 79 
                                    g+kapdf+l+n+d+e+v+l ++  +g+p+vl f+p++++pvCt+el+ +++++ +++++++ev+++svdsp  +kkf+++
  gi|118431740|ref|NP_148402.2|   5 GEKAPDFTLPNQDFEPVNLYEVlkRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDE 84 
                                    99********************9999****************************************************** PP

                                    -H.SSEEEE-TTSHHHHHTT-EETT....TTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  80 eslnfpllsDeegkvakaygvlkee....kglalratfvidkegkiry 123
                                    ++l f+llsD +++v+k y+v++e+    k++a ra+f+++++g+++y
  gi|118431740|ref|NP_148402.2|  85 NRLAFNLLSDYNREVIKLYNVYHEDlkglKMVAKRAVFIVKPDGTVAY 132
                                    **********************************************99 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0   2.1e-26   6.2e-23       3     146 ..       5     148 ..       3     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 2.1e-26
                                    TSBB---ECCEETTCEEEEEHHH..HTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHHHH CS
                        Redoxin   3 gdkaPdftlplaatdgnsvslse..fkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvkef 79 
                                    g+kaPdftlp+  +d ++v+l e   +g+++v++f+p+af+P+C++e++ + +k a+l ++ + +v+a+++d+    k+f
  gi|118431740|ref|NP_148402.2|   5 GEKAPDFTLPN--QDFEPVNLYEvlKRGRPAVLIFFPAAFSPVCTKELCtFRDKMAQL-EKANAEVLAISVDSPWCLKKF 81 
                                    99******977..***********888999*******************888899999.99999999999999999**** PP

                                    HHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSCHTSTTSHHHH CS
                        Redoxin  80 wgkeglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepepeteesnaeav 146
                                     +++ l f +lsD + ++ k ++++ e  ++   ++ ++++++  dg v y+ v ++p + e+++++v
  gi|118431740|ref|NP_148402.2|  82 KDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKmVAKRAVFIVKPDGTVAYKWVTDNPLN-EPDYDEV 148
                                    *************************998888886777777788889**********9987.9999987 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 !   17.8   0.0   9.2e-07    0.0027       3      61 ..      54     113 ..      52     122 .. 0.85
   2 ?    1.3   0.0      0.12   3.7e+02      95     111 ..     120     136 ..     114     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.2e-07
                     AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkrglklkl 61 
                                    +++ ++l++a+ ++ ai++++p  +kkF +++   f+l+ D ++++ ++ +++    ++l
  gi|118431740|ref|NP_148402.2|  54 RDKMAQLEKANAEVLAISVDSPwCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGL 113
                                    45579*****************66**********************99999986554444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                     AhpC-TSA_2  95 Gtflfdkqgelvyehrd 111
                                    ++f+++++g ++y++  
  gi|118431740|ref|NP_148402.2| 120 AVFIVKPDGTVAYKWVT 136
                                    68************975 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.5e-05     0.076       4      82 ..      34     107 ..      31     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                                    EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT CS
                  Thioredoxin_8   4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynvka 82 
                                    vl++f a ++p c++ + +  + + +l+ k + e++++s+d+    + k +k+   + l++   ++ + +++k ynv +
  gi|118431740|ref|NP_148402.2|  34 VLIFFPAAFSPVCTKELCTFRDKMAQLE-KANAEVLAISVDSP--WCLKKFKDE--NRLAFNLLSDYNREVIKLYNVYH 107
                                    8999*********999999999999997.8***********96..678888888..78888887788888888888865 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 ?   12.1   0.0   3.5e-05       0.1      86     178 ..      44     137 ..      33     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                         DUF899  86 pgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpglsvfl 165
                                    p C+  +  +  ++a+Le+++  + ++s      l+++k++    +++ s+++ ++ + +nv  e+ +  + +   +vf+
  gi|118431740|ref|NP_148402.2|  44 PVCTKELCTFRDKMAQLEKANAEVLAISVDSPWCLKKFKDENRLAFNLLSDYNREVIKLYNVYHEDLKGLKMVAKRAVFI 123
                                    68999999999*****************99999*****************************999999999999999998 PP

                         DUF899 166 rdd.grvfhtYsty 178
                                     +  g+v   ++t+
  gi|118431740|ref|NP_148402.2| 124 VKPdGTVAYKWVTD 137
                                    77669999999886 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.1e-05      0.21       3      93 ..      10      96 ..       8     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
                      SCO1-SenC  3 pFelvdqdgeavteedl..egkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleaf 82
                                   +F+l +qd e+v+  ++  +g+p ++ f+ +    vC+++l + ++ +++l+++  + ++l i+vD    +p  lk++ ++ 
  gi|118431740|ref|NP_148402.2| 10 DFTLPNQDFEPVNLYEVlkRGRPAVLIFFPAAFSPVCTKELCTFRDKMAQLEKA--NAEVLAISVD----SPWCLKKFKDEN 85
                                   8999999999999887644799999999999999******************99..7778888886....555666665555 PP

                      SCO1-SenC 83 dpriigltGsk 93
                                      +  l++ +
  gi|118431740|ref|NP_148402.2| 86 RLAFNLLSDYN 96
                                   55555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1248.99
//
Query:       gi|118431741|ref|NP_148403.2|  [L=639]
Description: 2-oxoacid:ferredoxin oxidoreductase alpha subunit [Aeropyrum pernix K1]
Scores for complete 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-60  204.5   0.0    2.7e-60  204.0   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    8.5e-36  123.7   0.0    1.6e-35  122.8   0.0    1.4  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    4.5e-09   36.5   0.1    5.6e-08   33.0   0.0    2.6  3  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    4.9e-06   26.4   0.0    4.4e-05   23.4   0.0    2.3  2  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.026   14.2   0.0    1.5  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.0   0.0   7.6e-64   2.7e-60       3     227 ..     255     492 ..     253     496 .. 0.88

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 7.6e-64
                                    HHHCTEEEEEE--BTTTCC...HHHHHCHCCCCCTT.EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                          POR_N   3 aiaagvdviaaYPITPsse...iaeelaellakgev.gdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                    ++ +gv+ +a+YPITP+s+   ++ee++ l  +ge  g + ++q+e+Ei+a+s viGAa++Gara TaTSg+G++Lm+e+
  gi|118431741|ref|NP_148403.2| 255 KVVGGVRYQAYYPITPASDesvLLEEFEGLKIDGESlGSIAILQTEDEIAAVSSVIGAALTGARASTATSGPGFSLMVEA 334
                                    566899************988888888888888887899***************************************** PP

                                    HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEE CS
                          POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlf 153
                                    lg+a+ + +P+vi++++R++pstgl++r++qsDl++ +     +++ i+l+s+++ eaf +a++A+nlAe++++Pvi+l+
  gi|118431741|ref|NP_148403.2| 335 LGWAGKNDVPMVITYYQRGGPSTGLPTRGSQSDLLFSLfashgEFPRIILSSGDHLEAFYDAIEAYNLAERFQMPVIHLL 414
                                    ******************************************************************************** PP

                                    EHHHH.HEEEEEEC-SGG..G....S-----SBXXXXXXXX....SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHH CS
                          POR_N 154 Dgfllshevekvelpdee.de....lklikekleeyerkey....aldpekpiargtaanpdtglehrekgneaedaaek 224
                                    D+fl+ ++v +v++pd +  +    + l+k +  + +        +   ++p+   +a +++tg+e +e+g+++ed   +
  gi|118431741|ref|NP_148403.2| 415 DKFLA-NMVASVPFPDWKaIKidrgKTLFKAPTGPFK---RfprdQPLADRPVLGSGAITWYTGDENDEYGHIDED-PVN 489
                                    *****.*********9884221111234444444444...255567778**************************9.444 PP

                                    HHH CS
                          POR_N 225 vve 227
                                    +  
  gi|118431741|ref|NP_148403.2| 490 RLV 492
                                    444 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.0   4.4e-39   1.6e-35       2     173 ..      14     216 ..      11     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 4.4e-39
                                    TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                            POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                    G G++t+ ++la a+a+ Gy v+anrey s+i G+hsy+h+r+s++ + +++  ++ad+l a+daet+++h+d++ +g +
  gi|118431741|ref|NP_148403.2|  14 GSGLETTMQVLAPAYASLGYGVLANREYFSNIVGRHSYIHIRVSSSGEARPLY-YPADFLGAMDAETVFTHWDDIGEGAF 92 
                                    99********************************************8888888.************************** PP

                                    EEEECTCGTT-CCHHHCTS-HHHHHHH.........................T-EEEEE-HHHHHH........HCCC.. CS
                            POR  82 iiynseelkpdelkkakeeerelkerl.........................gvrvygvdatkiak........eiggn. 127
                                    ++y+ + ++   l++  ++e++l++rl                         +vrv+g+++t++++              
  gi|118431741|ref|NP_148403.2|  93 LLYDLG-TARMRLQQIASMEPDLRSRLmqqyreagiepftvekvveylerekRVRVIGLSFTALFDvlikkhglS---Ra 168
                                    *****6.6888888889999***9999*************************************99988866653...04 PP

                                    ..CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHH CS
                            POR 128 ..eraaNtvmlGalaallglplealeeaikkrfpkkkeviekNlkafr 173
                                      +r+++ +++Ga+a+l++l++eal+ ++++rf+ + +v+e N + + 
  gi|118431741|ref|NP_148403.2| 169 qaQRFRSSILIGAIAGLTSLDREALDLGLQRRFGSRPKVLEINRDFIA 216
                                    44*********************************99******99876 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.33   1.2e+03      38      63 ..     128     153 ..     123     176 .. 0.87
   2 ?   -2.7   0.0         2   7.2e+03      26      39 ..     254     267 ..     250     284 .. 0.71
   3 !   33.0   0.0   1.6e-11   5.6e-08       1      70 [.     522     592 ..     522     618 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                    BS--HHHHHHHSTT-SEEEEEE-S-- CS
                        PFOR_II  38 rPFPeeelkellkkvkkvvvldrnis 63 
                                     PF  e++ e+l++ k+v v+ ++++
  gi|118431741|ref|NP_148403.2| 128 EPFTVEKVVEYLEREKRVRVIGLSFT 153
                                    59999*************99988874 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                    T--EEEEEES--BS CS
                        PFOR_II  26 gikvGllrlrtlrP 39 
                                    g  vG +r ++++P
  gi|118431741|ref|NP_148403.2| 254 GKVVGGVRYQAYYP 267
                                    56677777777777 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 1.6e-11
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-S..EEEEEE-S--TT-G-HH CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvk..kvvvldrnisfgseGql 70 
                                    Aev++v+ Gsv   a +a+++lRe g+++ +l lr+l P P+++++e+l++++  +v+ ++ n+ +g+++ +
  gi|118431741|ref|NP_148403.2| 522 AEVLLVGWGSVKIPALEAIERLREMGVNAAYLHLRMLSPLPKRRVSEVLSRFDadRVIAVEANY-LGQASKI 592
                                    9************************************************987611688888888.5555433 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.28     1e+03      19      50 ..     127     157 ..     125     166 .. 0.79
   2 !   23.4   0.0   1.2e-08   4.4e-05       8      81 ..     520     593 ..     516     615 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.28
                                    THHHHHHHHHHHHHTTTTCEEEEE-SEEESHH CS
                Transketolase_C  19 smveealeAaeeLekegisaeVvdlrtvkplD 50 
                                     + +++ +++e Le+e  +++V+ l ++  +D
  gi|118431741|ref|NP_148403.2| 127 IEPFTVEKVVEYLERE-KRVRVIGLSFTALFD 157
                                    5556788899999877.899****99999999 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.2e-08
                                    TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHH..HSEEEEEEEEESTTSHHHHHH CS
                Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkk..tgrlvvveeavkrgGigseva 81 
                                    e  +v+lv++Gs    aleA+e+L++ g++a  + lr ++pl k+ ++e++ +   +r++ ve ++   G +s+++
  gi|118431741|ref|NP_148403.2| 520 EDAEVLLVGWGSVKIPALEAIERLREMGVNAAYLHLRMLSPLPKRRVSEVLSRfdADRVIAVEANYL--GQASKIV 593
                                    5789********************************************9887622567777777665..6666655 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 ?   14.2   0.0   7.2e-06     0.026      39     147 ..     293     400 ..     268     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                                    TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH..S..TC--T-C CS
                   TPP_enzyme_N  39 girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg..qgvlqqeldq 116
                                    +i ++++ +E +a+    g a       +  +tsgpG+  ++ al  A ++ +P+++   +r+  ++g  + + q     
  gi|118431741|ref|NP_148403.2| 293 SIAILQTEDEIAAVSSVIGAALTG--ARASTATSGPGFSLMVEALGWAGKNDVPMVITYYQRGGPSTGlpTRGSQ-SDLL 369
                                    577777888888887777776664..4567789*****************************9999996655555.4457 PP

                                    CHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                   TPP_enzyme_N 117 lalfrpvtkyaervtspeelpealrrAirta 147
                                     +lf+++ ++ + + s+ +  ea+ +Ai++ 
  gi|118431741|ref|NP_148403.2| 370 FSLFASHGEFPRIILSSGDHLEAFYDAIEAY 400
                                    7889999999999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.39
# Mc/sec: 4945.75
//
Query:       gi|14601863|ref|NP_148404.1|  [L=318]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Aeropyrum pernix K1]
Scores for complete 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  109.2   0.1    2.6e-31  108.5   0.1    1.3  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.8e-22   79.2   0.3    3.9e-22   78.1   0.3    1.6  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.1   2.8e-35   2.6e-31       2     153 .]      50     197 ..      49     197 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 2.8e-35
                                   SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEE CS
                  TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvvl 80 
                                   iGc++            +++++ +g+++ +G+g+++A+G+kla+p+ +v++  GDG++l i + +++   rrnl++tv+++
  gi|14601863|ref|NP_148404.1|  50 IGCSSK----------TPHFINvNGVHTIHGRGIAFATGIKLANPQLKVIVNGGDGDLLGIgVAHFVALGRRNLDVTVLIH 120
                                   777777..........889***9********************************************************** PP

                                   E-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  81 nNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                   nN++yg+t+gq   + ++g+k ks p ++ ++ v++ +la a G + +ar  +  v++l+e+lk+a+++kg+a+i+v
  gi|14601863|ref|NP_148404.1| 121 NNKVYGLTKGQaspTLRRGEKVKSLPVPNLQDAVNPIALAIASGYTfVARAYSLWVDHLKEILKAAINHKGSAVIDV 197
                                   ***********998889999999999999*****************99999999*********************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 !   78.1   0.3   4.4e-26   3.9e-22       1      63 [.     201     274 ..     201     276 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 4.4e-26
                                   XTTTXSSSXSXXXXX-EEEGGGS.T---EE.........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT CS
                    PFO_beta_C   1 CvtFNkvnTfdwYkervykleed.gyDpsd.........lekAlekalewgdkiplGifYk.eekptyeerlee 63 
                                   Cvt+N+++T ++Yk+r+ykle+d ++Dp +         +++A++ka+ewg +ip+G+fY    k tyeerl++
  gi|14601863|ref|NP_148404.1| 201 CVTYNDIYTAEFYKDRLYKLEDDpSWDPIVrdpsedeekKAAAIKKAEEWGTRIPVGVFYVnPLKDTYEERLAQ 274
                                   ***********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 2766.93
//
Query:       gi|118431742|ref|NP_148405.2|  [L=155]
Description: hypothetical protein APE_2129.1 [Aeropyrum pernix K1]
Scores for 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-07   29.9   0.0      7e-07   29.5   0.0    1.2  1  DUF1850   Domain of unknown function (DUF1850)
  ------ inclusion threshold ------
       0.08   12.8   0.0       0.18   11.6   0.0    1.6  1  SH3_19    Myosin X N-terminal SH3 domain


Domain annotation for each model (and alignments):
>> DUF1850  Domain of unknown function (DUF1850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   7.8e-11     7e-07       2      77 ..      53     127 ..      52     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.8e-11
                        DUF1850   2 tlswtHSVektpveEdyrvegggLvleetrfksfGaGlpspaeagervedgwfvlr.inrpleelrlrvggiadhrl 77 
                                    ++s+ HSV+k   +++ +v+++g++l e+r+ ++GaG+p++ e+      g ++++     ++ l++ +g+   ++l
  gi|118431742|ref|NP_148405.2|  53 EISFLHSVHKEVETDVMSVDNRGFWLREVRLPETGAGTPYNLEDLG--GSGSVYFDqGVLVFTDLNVYRGRSIVYNL 127
                                    79**************************************998888..45555566466668888887777655555 PP

>> SH3_19  Myosin X N-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.18      22      52 .]      28      58 ..      15      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                         SH3_19 22 ddgsvvlttdYGevitlkqeelsrekVtpMh 52
                                    d ++v + dYG v + + e+++  ++  +h
  gi|118431742|ref|NP_148405.2| 28 TDYNIVVRCDYGDVSKAWSESVETLEISFLH 58
                                   6889*****************9988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.33
# Mc/sec: 1425.77
//
Query:       gi|118431743|ref|NP_148406.2|  [L=430]
Description: glutamate-1-semialdehyde aminotransferase [Aeropyrum pernix K1]
Scores for 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  202.3   0.0    1.3e-59  201.9   0.0    1.1  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 !  201.9   0.0   7.4e-64   1.3e-59      11     397 ..      35     414 ..      27     423 .. 0.88

  Alignments for each domain:
  == domain 1  score: 201.9 bits;  conditional E-value: 7.4e-64
                                    EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEE CS
                    Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkv 90 
                                    l+++ a+G+++ d  g++y+D+  ++ +v+lGh++ +v++ v+eq++ l++   ga  ++  +++a+ l++ +p  +dkv
  gi|118431743|ref|NP_148406.2|  35 LIVSWAKGSRIRDYRGREYIDFHMAFGAVALGHNDDDVAARVSEQLNRLVL--HGAGVSDAEIEFAKMLIRKFPM-YDKV 111
                                    78889********************************************44..4688889999************.**** PP

                                    EEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB- CS
                    Aminotran_3  91 flansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlke 170
                                    ++ nsGseAv+ A++lar+      +t +  +++f+g++HG   +++   ++  + +++    + +v+++ ++  evl++
  gi|118431743|ref|NP_148406.2| 112 LFTNSGSEAVMMAMRLARA------YTGRDVVVKFDGNYHGWHDYSIYNIKN--PASKGKTVESKGVPSATASTVEVLPY 183
                                    *******************......9***************99998877766..8888888999**************** PP

                                    HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGC CS
                    Aminotran_3 171 neeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAleha 250
                                    n+        +le++ ++  d vaA i+Ep+   +Gv++a+++f+++lr+lc+ h+ lli+DE+ t + r  +    +++
  gi|118431743|ref|NP_148406.2| 184 ND------VDALEDYAERFGDRVAAYILEPVAHSMGVIPAEKGFVERLRKLCDTHGSLLIFDEIITFI-RASDRGMQDYF 256
                                    **......88899999**************************************************66.44445567888 PP

                                    TS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS.B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH CS
                    Aminotran_3 251 gvspDlmtlaKaltgGlplsavlataevmqalapgs.hgsTfgGnplacavalavleiieeekllenaqelgaalkegLe 329
                                    gv +Dl+t++Ka+++G+p++avl+ ++vm+ la g   ++T++G pl +a+ +a+le +e+  l +  +   +al   L+
  gi|118431743|ref|NP_148406.2| 257 GVRADLTTVGKAIANGMPVAAVLGGDNVMELLARGVvSSGTYSGHPLSMAAGVATLEKAEDVGLTRALRSRAEALAGILR 336
                                    ********************************99998999**************************************** PP

                                    HHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHH CS
                    Aminotran_3 330 elqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGvlilsaGdnvirllppliitdeeide 397
                                    +++++  v + v + G  ++i +  +++ k+            + ++ +++  G+l+ +    + r+  ++  ++ee+++
  gi|118431743|ref|NP_148406.2| 337 DISEDLGVEAAVSQFGGSVSIYFGIDRRPKNleealrangdayRVFAREMRRRGILVTPNP--LKRMHLAYSHSEEELEA 414
                                    ***9998888999999888887776666555666777777776666677777787766543..55555566666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 3650.04
//
Query:       gi|14601866|ref|NP_148407.1|  [L=731]
Description: hypothetical protein APE_2133 [Aeropyrum pernix K1]
Scores for 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-77  258.6  58.4    2.9e-53  181.2  19.8    3.4  3  DctM      Tripartite ATP-independent periplasmic transporter,


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.1   0.1    0.0078   1.4e+02     275     310 ..      23      58 ..      14      92 .. 0.81
   2 !  181.2  19.8   1.6e-57   2.9e-53       3     259 ..     151     425 ..     147     435 .. 0.87
   3 !   83.2  27.1   9.3e-28   1.7e-23     237     412 ..     455     650 ..     425     653 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.0078
                          DctM 275 taavlfilaaagifaglltltgvplklselllslsg 310
                                   +a +++++aa  +f  ++++ +++l l ++l s++ 
  gi|14601866|ref|NP_148407.1|  23 AAKIVLAVAAFMAFLEVFYVMQFGLVLYRFLESMGL 58 
                                   68899********************99999999876 PP

  == domain 2  score: 181.2 bits;  conditional E-value: 1.6e-57
                          DctM   3 sllvllalgvpvaislalasl.....lllallgelllgvpleqilaqrvve...........glssfallaipfFvlaGiv 67 
                                   ++++ +a++++++i l ++ +      +++ ++  + gv+ +q++   v +           +l++ + +++  F+++ ++
  gi|14601866|ref|NP_148407.1| 151 LVALAEATRRSLGILLPAIMAvfvayGFIYAYTHPPFGVEGLQVFRRLVTAfisqnqgflgvPLTVMVYYVFI-FLFFSSF 230
                                   56677999***99999887773443334444444455554444444444445556777887778888888887.******* PP

                          DctM  68 lersGlakrlidlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaaviaasstlgqi 148
                                   l++ G++k + dl++al+Gr +GG+akv+vv+sa++g+iSGs+vAn++++G++tipamkr+G+++e a+a++  +st+gq+
  gi|14601866|ref|NP_148407.1| 231 LDKLGVGKYITDLMTALFGRKPGGPAKVAVVSSAMMGTISGSSVANTLTTGTFTIPAMKRAGFPPEVAGAIEPVASTGGQL 311
                                   ********************************************************************************* PP

                          DctM 149 iPPslglivfama.vlgvsigdlfaaaiipglllavglllavaiaakkenlrsktkaelkrlgqalkeaipalllpliili 228
                                   +PP++g+++f+ma ++g+++g +++aa++p++l++  + + v+ ++kk+ l++ ++ el+ l+ +l++    l +pli+++
  gi|14601866|ref|NP_148407.1| 312 MPPIMGAAAFIMAeFVGIPYGMVVIAALLPAILYFYSIYVFVDKESKKRRLKGLPDSELPPLRPLLVRLYYLLPIPLILIG 392
                                   **********************************************************************9999999**** PP

                          DctM 229 gillgiftpteagavavvyalviallv..yrrl 259
                                    + l    +  ag  a+v+++vi +++  +r+ 
  gi|14601866|ref|NP_148407.1| 393 LLRLAPHHAVMAGILATVAVYVIDTILygSRSA 425
                                   999*********************999444444 PP

  == domain 3  score: 83.2 bits;  conditional E-value: 9.3e-28
                          DctM 237 pteagavavvyalviallvyrrltleevaaa....llstakttaavlfilaaagifaglltltgvplklselllslsggk. 312
                                      ag++++v alv +ll     +l+++aaa    ++s+ + ++ v+++ a+a+++  ++t+t+++ +l+++ll+ls g  
  gi|14601866|ref|NP_148407.1| 455 LFFAGGASIVVALVAGLLS---GNLRDLAAAtvkaVESSFRNSIPVFLAAATASVIQSMITFTNLHKTLGDMLLTLSMGIl 532
                                   3458899999999999994...344444444112267777778**********************************9998 PP

                          DctM 313 llfLilvnllvlvlGmfldttaaiiilvpilaPaaaklgidp.........ihfgvvivlnlsiglitPPvGlalfvassi 384
                                   +l+Li++++++++lGm+++tta++ii+++ila  +a    +          ++ ++++++++ +++itPPv+la+fv++  
  gi|14601866|ref|NP_148407.1| 533 ILLLIATAVFSIILGMGVPTTANYIITATILAGTLAGYLKENlgyaeleatLASHMFVLYYGILADITPPVALAAFVGAVL 613
                                   889999*************************9887654444457788999999**************************** PP

                          DctM 385 a.........kvsveeivkalvPflvvlvvalvlitl 412
                                   a         ++++ +  k+++Pf++v ++a++++t+
  gi|14601866|ref|NP_148407.1| 614 AgadfwrtaiNATIYGFAKYILPFVFVYSPAILIVTV 650
                                   *********************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.37
# Mc/sec: 5873.17
//
Query:       gi|118431744|ref|NP_148408.2|  [L=326]
Description: TRAP transporter solute-binding component [Aeropyrum pernix K1]
Scores for complete 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-82  276.6   0.2    2.7e-82  276.4   0.2    1.0  1  NMT1_3          NMT1-like family
    1.7e-08   34.7   0.1    2.7e-08   34.0   0.1    1.3  1  NMT1            NMT1/THI5 like
    6.3e-05   22.7   0.4    0.00016   21.3   0.4    1.9  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.4   0.2   4.6e-86   2.7e-82       1     289 []      37     323 ..      37     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: 276.4 bits;  conditional E-value: 4.6e-86
                         NMT1_3   1 igTastgGtyYpvGvaiatliseklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGeg..efegkkp 78 
                                    +gT+s gG y p+G +ia+++s+    ++kv+++aq+s++sv N + +k+g+ +la++qsdva+ Ay+G+    feg +p
  gi|118431744|ref|NP_148408.2|  37 MGTGSPGGIYNPLGFKIAEVVSKY---SDKVEIEAQESGASVANAKGIKAGDYQLAMMQSDVAFFAYNGKLlkDFEG-NP 112
                                    79*****************99744...468***************************************95449**9.8* PP

                         NMT1_3  79 lknlraitmlyaevfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkd 158
                                    +++lra+++ly+e++q+v+++ +gi++i dl+gkrv+vG++gsG  ++a +il+algl + ++++  e g++e+ +a+k+
  gi|118431744|ref|NP_148408.2| 113 VEDLRALAALYPEPIQIVARAGAGIETIWDLEGKRVAVGNPGSGLYATAYTILSALGLWD-KIDK-VEFGFAEASSAMKQ 190
                                    *********************************************************975.5565.466*********** PP

                         NMT1_3 159 gqldgaalvaGvPvsavtqlaasedikliplddeqldkllkeyp..vftkyvipagtyp.qdedikTiavpnflvvradl 235
                                    g +d+ ++vaGvP+  + ++a+++d+ l+++ d+ ++kl+++     + ky+ipag y+ q+ed++T+ v+++lv  +d+
  gi|118431744|ref|NP_148408.2| 191 GTVDVLFIVAGVPTPKIEEIATQVDVVLVKVPDDAIQKLKDAGLgnLYLKYTIPAGSYDfQKEDVTTLTVTALLVIDKDV 270
                                    ***************************************98864227***********9679****************** PP

                         NMT1_3 236 deelvYeitkaifenldelnsihkaakeislekalaglpvplHpGAerYYkEqG 289
                                    +e+ +Yei+k++fe+lde++++h+ a++isl+ka   +p+plHpGAe+YYkEqG
  gi|118431744|ref|NP_148408.2| 271 PEDIAYEIVKTMFEHLDEIKTVHARAQDISLDKA-PIVPIPLHPGAEKYYKEQG 323
                                    ********************************98.579***************9 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   4.5e-12   2.7e-08      42     164 ..      92     215 ..      74     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.5e-12
                                    S-SEEEE-HHHHHHHHHTT--EE...EEEEEE-S--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT- CS
                           NMT1  42 kadfgvsyqesllaarakglpvv...svaallqeplsglivlkdsgikspkDLkGkrigyvg.spfekallkallakdgg 117
                                    + d+++ + +  l++  +g pv    ++aal+  ++ ++++++++gi+++ DL+Gkr+++ + ++   a+  ++l++ g+
  gi|118431744|ref|NP_148408.2|  92 QSDVAFFAYNGKLLKDFEGNPVEdlrALAALY-PEPIQIVARAGAGIETIWDLEGKRVAVGNpGSGLYATAYTILSALGL 170
                                    56777777777777777787775111556666.5678999*******************655377788999999999999 PP

                                    -GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT--EE CS
                           NMT1 118 dpsdvtlvnvggtslakalltgkvDaaiggyenwegvelesegkelr 164
                                      +++  v+ g+ ++++a+ +g+vD+ + ++ ++ + ++e+ + +++
  gi|118431744|ref|NP_148408.2| 171 -WDKIDKVEFGFAEASSAMKQGTVDVLF-IVAGVPTPKIEEIATQVD 215
                                    .999999999*****************9.888888777775555444 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 !   21.3   0.4   2.7e-08   0.00016      88     173 ..     128     208 ..      52     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.7e-08
                                    EEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEE.EE--HHHHHHHHHTTSSSEEEEEHH CS
                 Phosphonate-bd  88 viivradsdiqsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsev.fsgshdaavlavlsgdadaaavsad 166
                                    +i++ra+++i+++ dL+gk++a++ p S  G ++ a+++++  gl   d +++v f+    +++    +g++d+ ++ a+
  gi|118431744|ref|NP_148408.2| 128 QIVARAGAGIETIWDLEGKRVAVGNPGS--GLYATAYTILSALGLW--DKIDKVeFGFAEASSAM--KQGTVDVLFIVAG 201
                                    79************************96..99*******9888876..55677756654444444..4799999997766 PP

                                    HHHHHHH CS
                 Phosphonate-bd 167 aledlva 173
                                    + +  ++
  gi|118431744|ref|NP_148408.2| 202 VPTPKIE 208
                                    6555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2671.83
//
Query:       gi|14601868|ref|NP_148409.1|  [L=122]
Description: hypothetical protein APE_2138 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0004   20.8   0.1    0.00065   20.1   0.1    1.3  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 !   20.1   0.1   3.6e-08   0.00065      11      95 ..      37     113 ..      30     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.6e-08
                                   HHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHHHHHHSHHHHHH CS
                          OsmC  11 lllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkllekaekrCpvsntl 91 
                                   ++l+ l++C++  ++ +a   ++++ ++e+ v +++  eg ++i++i ++++  ++        ++++ k  ++Cpv +++
  gi|14601868|ref|NP_148409.1|  37 FMLSMLSACIGKKVAENAGVDKVSV-SIEAYVNVDKLLEGKEEIEHIVVRIRAPAS--------EEAVLKGVENCPVFKLI 108
                                   6889999***999999999998888.888888888888887789999988888433........3566667789*****99 PP

                                   .CT-S CS
                          OsmC  92 .kngv 95 
                                    k+ v
  gi|14601868|ref|NP_148409.1| 109 dKSRV 113
                                   66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 972.38
//
Query:       gi|118431745|ref|NP_148410.2|  [L=223]
Description: hypothetical protein APE_2139.1 [Aeropyrum pernix K1]
Scores for complete 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  155.5   0.1    1.7e-45  155.3   0.1    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 !  155.3   0.1   9.6e-50   1.7e-45       6     201 .]      10     206 ..       5     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 155.3 bits;  conditional E-value: 9.6e-50
                                    SSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE....--------.------EEEEEEES.SS-EEEEE--SSSEEEEE CS
                          AIM24   6 epssllsvtLspgeelyaerGalvamsgkvemet....gllkalkr.lltgeslfllkftakissgtvllapklpgtivt 80 
                                      +++l+v+L++ge++++e+G+ +  +g++e++t    g+ ++l r + +geslf++ +ta+ s+ +v++ap++ g+i+ 
  gi|118431745|ref|NP_148410.2|  10 PAFTILKVELNEGESIWVESGSYMLNKGDIEVKTtmggGIVRGLLRaVAGGESLFFNIITAR-SKSEVWIAPPVTGDIAA 88 
                                    4789******************************99999999999999************86.88*************** PP

                                    EEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EEEEEEEGGGEE CS
                          AIM24  81 lelgggdwlivqkdafLAatgnveldikfqkglkglfggeglflqkltGrGlvalsgyGaiyeielkageelvvdpghlv 160
                                    +el gg+++++q++++LA+ g+ve+++ ++ g+kgl++  +l++ k +GrG+v+++++Ga+  i++++ge++++d+gh v
  gi|118431745|ref|NP_148410.2|  89 VEL-GGEEVYIQDSSYLAHIGDVEVGVGWR-GFKGLIAEGELVWVKAKGRGTVFINSFGALEHIRVGPGEKITIDNGHFV 166
                                    ***.6669**********************.7888986656*************************************** PP

                                    EEETTEEEEEEEETT---STTTTS-EEEEEEEEEEEEEESS CS
                          AIM24 161 afsgslkfdiervgglkrrligGeglflkltGpgtvllqsr 201
                                    a++g+ k +i++ gg+k+ ++gGeg+++ ++Gp  +++q+r
  gi|118431745|ref|NP_148410.2| 167 AIKGG-KWNIRKFGGWKTFFLGGEGVVVDVEGPADLWVQTR 206
                                    ***76.*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1677.54
//
Query:       gi|118431746|ref|YP_874926.1|  [L=71]
Description: twin arginine-targeting protein translocase [Aeropyrum pernix K1]
Scores for complete 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   55.9   0.3    2.3e-15   55.7   0.3    1.2  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
      0.012   16.6   0.0      0.013   16.4   0.0    1.0  1  DUF4834      Domain of unknown function (DUF4834)


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 !   55.7   0.3   2.5e-19   2.3e-15       1      48 [.       8      55 ..       8      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.5e-19
                                   S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH--- CS
                    MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleeene 48
                                   lg+pel++Il++ l++FGp+k+PE+ar+LG + +e ++ ++++ e  +
  gi|118431746|ref|YP_874926.1|  8 LGVPELVLILLILLIIFGPSKIPEIARNLGLAVKELRNSISGEGEAAS 55
                                   699*************************************99877633 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4   0.0   1.5e-06     0.013       7      64 ..      14      68 ..      10      71 .] 0.65

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                        DUF4834  7 ilifiiailviglsilsvilrtvfglgsrkkssksaqkqfgnstnsnqqksqsrsetk 64
                                   +li++i+++++g s +  i r++ gl  ++  +    +++g++ +++q+k++s se++
  gi|118431746|ref|YP_874926.1| 14 VLILLILLIIFGPSKIPEIARNL-GLAVKELRN--SISGEGEAASTQQSKKSSGSEKE 68
                                   48999******************.866655543..44444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 540.33
//
Query:       gi|118431747|ref|NP_148412.2|  [L=458]
Description: glutamine synthetase [Aeropyrum pernix K1]
Scores for complete 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-118  395.9   0.0   1.6e-118  395.7   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    2.4e-14   52.8   0.0    4.7e-14   51.9   0.0    1.5  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 !  395.7   0.0  1.8e-122  1.6e-118       2     345 .]      98     455 ..      97     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 395.7 bits;  conditional E-value: 1.8e-122
                                    T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCE...SSEEEEEEE.T......B...B.TSS-TTBHCCCCCTC CS
                     Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedke...asksllevdse......ekgrpaekggyfsvapvdeae 72 
                                    rdPR  +++a++ ++++G++v +g+E+EFf+fdk   +    a++  + v+s+      ++   + k++y   +p d+  
  gi|118431747|ref|NP_148412.2|  98 RDPRLAAETAEKIMSSMGYRVKAGAEIEFFIFDKIGVDVlnpARGLGYIVESReqpggqDGIFGQVKKSYHMPEPPDSLL 177
                                    79********************************99887655555666666658899987778899************** PP

                                    CHHHHHHHHHHHTT--EECCEEECCCTEEEEEE.--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEE CS
                     Gln-synt_C  73 dlrreivealealgieveashhEvatgQvEinl.kfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmH 151
                                    d+r  ++e+l++++++v  shhEva +QvE+++ + +++ +  D+++t+K+v k +Ar+ g  atFmpKp++gdnGsgmH
  gi|118431747|ref|NP_148412.2| 178 DYRLMLTETLQRFKVDVAVSHHEVAVSQVEVSIgSRTSLARLGDDIMTVKWVSKVLARMDGRVATFMPKPIFGDNGSGMH 257
                                    *********************************88888999*************************************** PP

                                    EEEEEEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE- CS
                     Gln-synt_C 152 vhlSlwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa 231
                                    +hlSlw+  g+nlfa+++d  +lse+a+hfi+G+l+ha++l+a+++pt+nSY+Rlv+gyeaPv++awg rNRsa++Ripa
  gi|118431747|ref|NP_148412.2| 258 IHLSLWSPGGENLFAGHGD-SDLSETALHFIAGILEHARSLSAILSPTTNSYRRLVAGYEAPVYVAWGWRNRSAMIRIPA 336
                                    *****************95.69********************************************************** PP

                                    ..TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCS CS
                     Gln-synt_C 232 ..skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeed 307
                                      ++ +a r+E+R+pd++aNPYLalAal++AgldG+++kl p++p+e++ly++spee   kgi++lP++l+eAl++le+d
  gi|118431747|ref|NP_148412.2| 337 saGNIDAVRIEVRSPDPTANPYLALAALFMAGLDGVKKKLAPPDPYEGNLYKISPEELreKGIKTLPRNLDEALDELESD 416
                                    98999***************************************************9999******************** PP

                                    .HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                     Gln-synt_C 308 .ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                     ++lk ++++e++e+y+++kr+E e+ + +++++e+ +y
  gi|118431747|ref|NP_148412.2| 417 nDYLKPAFTREMLESYIEVKRKESEDTRLYPHPIEVYKY 455
                                    ***********************************9887 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0   5.3e-18   4.7e-14       5      82 ..      18      90 ..      16      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 5.3e-18
                                   EEEEEE-SSS-EEEEEEEHHHHHHHTTTT-E.EEETTSSTTT------EEEEEEEGGGEEE-SS-SS-.EEEEEEEEE- CS
                     Gln-synt_N  5 vdlqFtDikgklkhvtipadelsedaleegv.sFDGSsiegfaeieeSDmlLkPdlstavidPfreekktarvicdvyd 82
                                   v + +tDi g l++v++p +++ e+ +   v sFDGSs+ gf+++e+SD+lLk +++t+v +P+r+     rvi+ vy+
  gi|118431747|ref|NP_148412.2| 18 VLVHYTDIAGYLRQVEVPLRNV-EKEF---VaSFDGSSVYGFTPVEDSDLLLKHVPETLVSVPWRSG--LWRVIATVYN 90
                                   6678**************8777.4433...339********************************74..69******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3470.10
//
Query:       gi|118431748|ref|NP_148413.2|  [L=901]
Description: ATP-dependent helicase [Aeropyrum pernix K1]
Scores for complete 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-55  186.7   0.0    9.6e-55  185.3   0.0    1.8  2  DEAD_assoc       DEAD/H associated
    2.8e-28   98.8   0.0    4.5e-27   94.9   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
      2e-17   63.5   0.5    4.7e-17   62.3   0.5    1.6  1  Helicase_C       Helicase conserved C-terminal domain
    3.5e-08   33.6   0.0      1e-07   32.1   0.0    1.8  2  ResIII           Type III restriction enzyme, res subunit
     0.0014   18.7   0.2      0.011   15.8   0.0    2.5  2  Ubiq_cyt_C_chap  Ubiquinol-cytochrome C chaperone
     0.0035   16.1   0.0     0.0061   15.3   0.0    1.3  1  SNF2_N           SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.056   13.6   0.0       0.25   11.5   0.0    2.2  2  TetR_C_8         Transcriptional regulator C-terminal region
      0.087   12.3   0.0       0.19   11.2   0.0    1.5  1  PhoH             PhoH-like protein
       0.15   12.4   0.9        5.9    7.2   0.3    2.8  2  AAA_19           AAA domain
        0.2   11.9   1.6         12    6.2   0.9    3.5  2  AAA_22           AAA domain
       0.25   10.8   1.7         13    5.2   1.0    2.4  2  UvrD-helicase    UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         4   6.5e+03      34      92 ..     161     211 ..     159     212 .. 0.65
   2 !  185.3   0.0   5.9e-58   9.6e-55       1     191 []     654     846 ..     654     846 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4
                     DEAD_assoc  34 alalllaarlsrrfgidvqvaanDdgivlll.pleerlpllldellellspdeleedlea 92 
                                     la++laa   r++ ++v+ ++ D+  +l + +   r       +  ++s ++lee++++
  gi|118431748|ref|NP_148413.2| 161 SLAAALAAPKFRERLSTVKWVVLDEIHELASnK---R------GAHLMVSVERLEELVRE 211
                                    678888888888888888888888888885532...2......12234556666666655 PP

  == domain 2  score: 185.3 bits;  conditional E-value: 5.9e-58
                     DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll....pleerlp..lll 74 
                                    +P+d+ +l+E f  e  +w +v+h++fGrrvn+al++++a  lsrr g++v+va++D+g++l++    +     p   ll
  gi|118431748|ref|NP_148413.2| 654 VPSDKLVLIEYFPYED-GWGIVFHTLFGRRVNDALSRAYAVALSRRIGLPVRVAVTDNGFMLTVseagK-----PdaSLL 727
                                    8***********5544.78*******************************************9976542.....223568 PP

                     DEAD_assoc  75 dellellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldv.areypdfpllleavr 153
                                    ++l++ ++p++++ +le+a+ ++el+krrF +vAar+++++rry+gk++++++ +l++++Ll+v ++e++d p ++e++r
  gi|118431748|ref|NP_148413.2| 728 EKLIRDVTPENIRGILEEAISRTELMKRRFKHVAARMFIVLRRYKGKEVSPERLQLNSQKLLEVfLEEMKDSPPIRETFR 807
                                    99**************************************************************445666********** PP

                     DEAD_assoc 154 evledqlDlerlaellrriaageirvveve.tprpSpfA 191
                                    e+led++D+ ++ ++l++i++gei++v    +p pSp+A
  gi|118431748|ref|NP_148413.2| 808 EILEDYMDIGAAGKVLEWIRKGEIEIVIKGpLPYPSPMA 846
                                    ***************************9889*******8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   2.8e-30   4.5e-27       1     170 [.      39     227 ..      39     233 .. 0.85
   2 ?    1.3   0.0      0.15   2.5e+02      43      94 ..     289     347 ..     278     409 .. 0.72

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 2.8e-30
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid. 75 
                                    t+ Q++aipl+ +g++vl+  +TG+GKTla+++ v+++++       +++g  a++v+P+r+L +++ +nl++ +  i+ 
  gi|118431748|ref|NP_148413.2|  39 TEPQRQAIPLVKQGKSVLITSPTGTGKTLAAFLGVIDEILFLmenrWEEKGILAVYVSPLRALNNDIRRNLEEPLRGIEe 118
                                    678*********************************998766787669999*************************8888 PP

                                    ...........SEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ...........lrvlliiggvaardqlskldng.vdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdf 141
                                               ++v + +++++  ++++ + ++ ++i+++tp+ l+  l   k++  ls v+++VlDE+++l +++++ +
  gi|118431748|ref|NP_148413.2| 119 karemglepprVKVAVRTSDTTPYEKQKMV-KDpPHILITTPESLAAALAAPKFRerLSTVKWVVLDEIHELASNKRGAH 197
                                    888888889555555444444444555555.445*************9966665556*********************** PP

                                    HHHHHHHSHHHCTTST.TTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                           DEAD 142 inrilnqlpqitcdgk.lqrqvivlSATlp 170
                                    +   +++l++   +   +  + i lSAT+ 
  gi|118431748|ref|NP_148413.2| 198 LMVSVERLEELVREAGgKPLRRIGLSATIA 227
                                    ********9999998878888*******97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                                    TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST......SEEE.EEETTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxx.xxxxxxxxxxxxxxx RF
                           DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyid......lrvl.liiggvaardqlskl 94 
                                      k++  +li + tr+ +e ++++lk+++ + +      ++++ + ++ + + d  ++l
  gi|118431748|ref|NP_148413.2| 289 LVKQHRTTLIFTNTRSATERVVHKLKQILVKEGiasedqIEAHhSSLSRNLRLDVEERL 347
                                    457777899****************9998753322333333322333444444444444 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 !   62.3   0.5   2.9e-20   4.7e-17       6     108 ..     282     393 ..     276     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.9e-20
                                    HHHHH.HHTTTTSEEEEEESSHHHHHH....HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                     Helicase_C   6 llell.kleeeggkilifvntidrlek....vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                    +++ + +l ++++++lif+nt++  e+    +k +l k+    + ++ ++h++l+ n r+++ e+ ++ge +v+++++ +
  gi|118431748|ref|NP_148413.2| 282 IYRKIaELVKQHRTTLIFTNTRSATERvvhkLKQILVKEgiasEDQIEAHHSSLSRNLRLDVEERLKRGELKVVVSSTSL 361
                                    444445778999***********66555344444444556777789999******************************* PP

                                    TSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                     Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                    e Gidi  ++lVi ++ p++v+++ qr+GR+g
  gi|118431748|ref|NP_148413.2| 362 ELGIDIGYIDLVILLSSPKSVSRLLQRVGRAG 393
                                    *******************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   6.3e-11     1e-07       4     169 ..      23     226 ..      20     228 .. 0.71
   2 ?   -2.9   0.1       3.5   5.8e+03      49      80 ..     290     319 ..     282     347 .. 0.61

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.3e-11
                                    E-HHHHHHHHHHT...............TTSEEEEEESTTSTHHHHH.HHHHHH...H-S........-EEEEESSHHHH CS
                         ResIII   4 lreyQeeaienlleklks.........krdkrglikmaTGtGKTlva.aklier...llkkgkee...kflflvprksll 67 
                                    lr+y +e  +++  ++++         k+ k +li  +TGtGKTl a + +i++   l+++++ee    ++ + p ++l 
  gi|118431748|ref|NP_148413.2|  23 LRPYVAEWFRSTYGSFTEpqrqaiplvKQGKSVLITSPTGTGKTLAAfLGVIDEilfLMENRWEEkgiLAVYVSPLRALN 102
                                    6777777777777777777777888889999***************9888887722245777777766677788888999 PP

                                    HHHHHHGGGGTGG...................GEEEESSS-B--...............-SEEEEEHHHHHHTH...... CS
                         ResIII  68 eqtleefkkflseayke...............igkkvsgdkkka........kekdstnkkilvttiqsldadseeeeee 124
                                    +  ++++++ l    ++                                   ++  ++  +il+tt +sl a++      
  gi|118431748|ref|NP_148413.2| 103 NDIRRNLEEPLRGIEEKaremglepprvkvavR----------TsdttpyekQKMVKDPPHILITTPESLAAAL---AAP 169
                                    999988866655544443445555554322221..........02223445455778999**************...566 PP

                                    ..HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT-.....--SEEEEEESS- CS
                         ResIII 125 seellrdrfdviiiDEaHrlgakk.......swreilekf.....keavllglTATp 169
                                    + + + ++ + ++ DE H l+++k       s++++ e +     k+  ++gl+AT+
  gi|118431748|ref|NP_148413.2| 170 KFRERLSTVKWVVLDEIHELASNKrgahlmvSVERLEELVreaggKPLRRIGLSATI 226
                                    66666677779***********9666777776666655553334566*********7 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                                    -S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                         ResIII  49 lkkgkeekflflvprkslleqtleefkkflse 80 
                                     k+++   +l++ +++s +e+  +++k++l +
  gi|118431748|ref|NP_148413.2| 290 VKQHR--TTLIFTNTRSATERVVHKLKQILVK 319
                                    44333..5666666666666666666655543 PP

>> Ubiq_cyt_C_chap  Ubiquinol-cytochrome C chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0         1   1.6e+03     109     134 ..     634     659 ..     605     661 .. 0.75
   2 !   15.8   0.0   6.9e-06     0.011       7      51 ..     751     798 ..     746     804 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                Ubiq_cyt_C_chap 109 leklaglvgyvraqlatlsalageal 134
                                     +++a +v+y+++ql  +  +++++l
  gi|118431748|ref|NP_148413.2| 634 ERAAATIVEYILEQLGYIGVVPSDKL 659
                                    45999**********99999998877 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.9e-06
                Ubiq_cyt_C_chap   7 dtfagrfqllvlhtwlllrRlkaeg..peg.reieqelldkffedvde 51 
                                    + ++ rf+++ + ++++lrR k++   pe  +  +q+ll+ f+e++ +
  gi|118431748|ref|NP_148413.2| 751 ELMKRRFKHVAARMFIVLRRYKGKEvsPERlQLNSQKLLEVFLEEMKD 798
                                    56889********************974446999***********987 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.7e-06    0.0061     123     201 ..     129     201 ..      84     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                                    -EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 123 alrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavs 201
                                    +++v v +++++      + ++ +    +++itt + l+   + +k r+ l+ v+w  vvlDE h l ++++ a+ +vs
  gi|118431748|ref|NP_148413.2| 129 RVKVAVRTSDTTPY----EKQKMVKDPPHILITTPESLAAALAAPKFRERLSTVKW--VVLDEIHELASNKRGAHLMVS 201
                                    55555555554222....22344445579**************************9..9************99999987 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.8   9.5e+03       6      40 ..     282     316 ..     280     327 .. 0.64
   2 ?   11.5   0.0   0.00015      0.25      20      86 ..     764     830 ..     726     833 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.8
                                    HHHHHHHHHHHTHHHHHHHHHH-.THHHHHHHHHH CS
                       TetR_C_8   6 gllklfeyikenkdfyknllssngresfekylkel 40 
                                    ++ k+ e +k++++ +  +      e + ++lk++
  gi|118431748|ref|NP_148413.2| 282 IYRKIAELVKQHRTTLIFTNTRSATERVVHKLKQI 316
                                    56677777777777666665555555555555555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                                    HHHHHHHH-.THHHHHHHHHHHHHHHHHHHHHH-TT--S-HHHHHHHHHHHHHHHHHHHHHHHHTTS CS
                       TetR_C_8  20 fyknllssngresfekylkelikelilkvieelsegkelseedkefiadfysygfvgvildWlengm 86 
                                    ++ +l + +g+e   ++l+   ++l++  +ee++++ +++e  +e++ d++  g  g +l+W+++g 
  gi|118431748|ref|NP_148413.2| 764 MFIVLRRYKGKEVSPERLQLNSQKLLEVFLEEMKDSPPIRETFREILEDYMDIGAAGKVLEWIRKGE 830
                                    6777778888888889998889999999999999999***************************996 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.19       6      40 ..      39      73 ..      36      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                   SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHH CS
                           PhoH  6 tkeQkeylealkkndivfaiGpaGtGKtylavala 40
                                   t+ Q++++  +k+ + v ++ p+GtGKt+ a    
  gi|118431748|ref|NP_148413.2| 39 TEPQRQAIPLVKQGKSVLITSPTGTGKTLAAFLGV 73
                                   6789************************9887655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0036       5.9       1      25 [.      42      67 ..      42     208 .. 0.73
   2 ?    2.6   0.0     0.095   1.5e+02      29      73 ..     284     332 ..     278     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0036
                         AAA_19  1 qreave.alkekvllvtaGpGtGKTr 25
                                   qr+a+    + k +l+t + GtGKT 
  gi|118431748|ref|NP_148413.2| 42 QRQAIPlVKQGKSVLITSPTGTGKTL 67
                                   89999878899999***********6 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.095
                         AAA_19  29 hivallvelggvkpeeillvaftgrAakelrerlaalgae........atTiH 73 
                                     ++a+lv+++    ++ l+ + t+ A++++  +l++++++        ++  H
  gi|118431748|ref|NP_148413.2| 284 RKIAELVKQH----RTTLIFTNTRSATERVVHKLKQILVKegiasedqIEAHH 332
                                    4556666666....889***************999888777777777655555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.9    0.0074        12       4     104 ..      51     190 ..      48     220 .. 0.56
   2 ?    0.5   0.0      0.41   6.8e+02      48      98 ..     331     408 ..     309     431 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0074
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelka........... 70 
                                    + +++++t ++GtGKT+ +  l   +++    e+  e+++++ v+++ +     l +++ r+l+++l +           
  gi|118431748|ref|NP_148413.2|  51 QGKSVLITSPTGTGKTLAA-FLGVIDEILFLMENrwEEKGILAVYVSPLR---ALNNDIRRNLEEPLRGieekaremgle 126
                                    6789999********9765.333333444444445566666666666655...555556666666655555556666666 PP

                         AAA_22  71 ............................erlsseell.ealeqalrarav.ielliiDEaqhlr 104
                                                                   + e l  ++ +  +r+r   ++ +++DE++ l 
  gi|118431748|ref|NP_148413.2| 127 pprvkvavrtsdttpyekqkmvkdpphiLITTPESLAaALAAPKFRERLStVKWVVLDEIHELA 190
                                    6666666666666666666665554444222333333233333333333356667777777765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.41
                         AAA_22  48 psstsskdllrellralglelka........................erlsseellealeqalrarav...ielliiD 98 
                                     +s+ s++l+ ++ + l+++  +                        +++s ++ll+++ +a ++ ++    +l+++D
  gi|118431748|ref|NP_148413.2| 331 HHSSLSRNLRLDVEERLKRGELKvvvsstslelgidigyidlvillsSPKSVSRLLQRVGRAGHRIRDvskGRLIVVD 408
                                    5555566666666666666666677777777777778888888888889999***********999999988888888 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 ?    3.5   0.0     0.025        41       4      28 ..      41      67 ..      38      93 .. 0.78
   2 ?    5.2   1.0    0.0077        13      30      82 ..     282     328 ..     278     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
                                   HHHHHHHS..-SSEEEEEE-TTSSHHH CS
                  UvrD-helicase  4 eqreaias..lggpilveAsAGsGKTf 28
                                    qr+ai     g+++l+ +  G+GKT 
  gi|118431748|ref|NP_148413.2| 41 PQRQAIPLvkQGKSVLITSPTGTGKTL 67
                                   566666665488999999********6 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0077
                                    HHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHH CS
                  UvrD-helicase  30 laerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderl 82 
                                    +  +i++l+k++    +  l++T T+ A+e   ++++++l k+   s d+  +
  gi|118431748|ref|NP_148413.2| 282 IYRKIAELVKQH----RTTLIFTNTRSATERVVHKLKQILVKEGIASEDQ--I 328
                                    344555555555....679*******************999887554433..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (901 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.72u 0.26s 00:00:00.98 Elapsed: 00:00:00.43
# Mc/sec: 6224.67
//
Query:       gi|118431749|ref|NP_148414.2|  [L=403]
Description: hypothetical protein APE_2146.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0029   17.3   0.2     0.0062   16.3   0.2    1.6  1  DivIC           Septum formation initiator
     0.0038   17.8   0.1     0.0061   17.1   0.1    1.3  1  BST2            Bone marrow stromal antigen 2
     0.0047   17.3   1.8     0.0082   16.6   1.8    1.3  1  ZapB            Cell division protein ZapB
     0.0049   16.9   0.3     0.0097   16.0   0.3    1.4  1  TolA_bind_tri   TolA binding protein trimerisation
     0.0052   16.4   0.6     0.0078   15.8   0.6    1.2  1  Filament        Intermediate filament protein
     0.0096   16.2   0.4      0.025   14.8   0.4    1.6  1  Spc24           Spc24 subunit of Ndc80
  ------ inclusion threshold ------
      0.012   16.1   0.6      0.018   15.5   0.6    1.2  1  APG6_N          Apg6 coiled-coil region
      0.014   15.8   1.1      0.014   15.8   1.1    2.2  2  FlaC_arch       Flagella accessory protein C (FlaC)
      0.015   14.2   1.5      0.022   13.7   1.5    1.2  1  Spc7            Spc7 kinetochore protein
      0.016   13.9   0.2      0.022   13.5   0.2    1.1  1  WEMBL           Weak chloroplast movement under blue light
      0.016   15.4   1.5      0.035   14.3   1.5    1.5  1  HALZ            Homeobox associated leucine zipper
      0.018   15.4   0.1      0.035   14.5   0.1    1.4  1  HCMV_UL139      Human Cytomegalovirus UL139 protein
       0.02   14.9   1.9      0.036   14.1   1.9    1.4  1  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
      0.022   14.9   2.3       0.05   13.8   2.3    1.6  1  JIP_LZII        JNK-interacting protein  leucine zipper II
      0.024   14.7   1.5      0.047   13.8   1.5    1.4  1  bZIP_1          bZIP transcription factor
      0.025   14.6   2.5      0.054   13.5   2.4    1.5  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.026   14.6   1.0      0.037   14.1   1.0    1.2  1  ADIP            Afadin- and alpha -actinin-Binding
      0.027   14.6   0.4      0.043   14.0   0.4    1.3  1  Herpes_BLRF2    Herpesvirus BLRF2 protein
      0.028   14.0   0.2      0.042   13.4   0.2    1.2  1  PspA_IM30       PspA/IM30 family
      0.032   13.9   1.1       0.05   13.3   1.1    1.2  1  SHE3            SWI5-dependent HO expression protein 3
      0.033   12.6   0.2      0.044   12.2   0.2    1.1  1  BicD            Microtubule-associated protein Bicaudal-D
      0.055   12.6   1.2       0.08   12.0   1.2    1.1  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.062   13.1   0.1      0.094   12.5   0.1    1.2  1  Spc29           Spindle Pole Component 29
      0.072   13.0   1.6        0.1   12.5   0.6    1.7  1  Prefoldin_2     Prefoldin subunit
      0.075   13.0   0.3       0.25   11.3   0.1    1.9  1  Prefoldin       Prefoldin subunit
       0.12   11.5   0.4       0.17   11.0   0.4    1.1  1  Taxilin         Myosin-like coiled-coil protein
       0.15   11.5   0.6       0.25   10.7   0.6    1.3  1  DUF4618         Domain of unknown function (DUF4618)
       0.15   11.6   0.6       0.51    9.9   0.9    1.6  2  NRBF2           Nuclear receptor-binding factor 2, autophagy 
        0.2   12.3   1.0       0.34   11.5   1.0    1.3  1  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
       0.48   10.5   3.1       0.74    9.9   3.1    1.2  1  DHR10           Designed helical repeat protein 10 domain
        1.9    9.2   3.2        2.8    8.6   0.6    1.9  2  SlyX            SlyX


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.1e-05    0.0062      18      56 ..     319     357 ..     310     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                          DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56 
                                    ++ +l++ +++l + l++l+ eneeL++++++L+  +dy
  gi|118431749|ref|NP_148414.2| 319 RIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDY 357
                                    577899***************************877777 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.1e-05    0.0061      37      90 ..     317     370 ..     314     371 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                           BST2  37 eaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                    e+ +a  n+ v+tL++sL+  ++++++ ++k+ elqg     n k+ + e+e++
  gi|118431749|ref|NP_148414.2| 317 EKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQ 370
                                    566778899****************************************99986 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.8   1.4e-05    0.0082      10      55 ..     317     369 ..     316     381 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
                           ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenrele.......eeneqlkeer 55 
                                    E++i  +  ++++L++ ++ L+ eneelk++ +el+       +++ +l+ee 
  gi|118431749|ref|NP_148414.2| 317 EKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQgrddywnAKITELEEEL 369
                                    77888888888899999999999999999999998888887776666666554 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 !   16.0   0.3   1.7e-05    0.0097      20      54 ..     320     354 ..     316     357 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                  TolA_bind_tri  20 llelqqqlealqqelreLRGqiEelqyqleqleer 54 
                                    + +l +++e+l++ l++LR ++Eel+ +l++l+ r
  gi|118431749|ref|NP_148414.2| 320 IADLNSRVETLRNSLDSLRSENEELKRKLDELQGR 354
                                    6799***************************9977 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   1.4e-05    0.0078     216     278 ..     318     376 ..     315     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 216 eeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireem 278
                                    + i++l+ ++++l+  l+sl+++++ l+++l el+ r +      ++k++eleeel+  + + 
  gi|118431749|ref|NP_148414.2| 318 KRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDD----YWNAKITELEEELQFYKIRS 376
                                    6799*****************************998865....57788999999998766555 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4   4.2e-05     0.025       7      44 ..     314     354 ..     312     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                          Spc24   7 friakelsdleselesleselaelkeeleeleeesee...k 44 
                                    f + k + dl+s +e l+++l++l++e eel+++  e   +
  gi|118431749|ref|NP_148414.2| 314 FGFEKRIADLNSRVETLRNSLDSLRSENEELKRKLDElqgR 354
                                    56788999999999999999999999999999999886542 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.6   3.2e-05     0.018      46      92 ..     324     370 ..     307     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.2e-05
                         APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                    ++ +e l+++l+ l++e eel ++L+el+  ++  +a++ +leeel+
  gi|118431749|ref|NP_148414.2| 324 NSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQ 370
                                    467899***************************************98 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 ?   15.8   1.1   2.4e-05     0.014       1      34 [.     319     352 ..     317     354 .. 0.91
   2 ?   -0.5   0.1         3   1.7e+03       1      10 [.     361     370 ..     361     377 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-05
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelk 34 
                                    ri +l ++++ l  +l+++++eneel+ +++el+
  gi|118431749|ref|NP_148414.2| 319 RIADLNSRVETLRNSLDSLRSENEELKRKLDELQ 352
                                    7899999999999999999999999999999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3
                      FlaC_arch   1 ridelEnkls 10 
                                    +i elE++l+
  gi|118431749|ref|NP_148414.2| 361 KITELEEELQ 370
                                    899****997 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.5   3.8e-05     0.022     198     244 ..     324     370 ..     316     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                           Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqks 244
                                    + ++e+lr++l++l +e ee+k++l+elq + +  ++ki+el+e+ +
  gi|118431749|ref|NP_148414.2| 324 NSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQ 370
                                    45789999999999999999999999999999999999999999877 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 ?   13.5   0.2   3.7e-05     0.022     308     360 ..     319     371 ..     315     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                          WEMBL 308 niekakdevklLkvaaasLrseLekekaeLaslrqregmasiavssLeaelsr 360
                                     i   ++ v++L++   sLrse e+ k +L++l+ r+    + ++ Le+el+ 
  gi|118431749|ref|NP_148414.2| 319 RIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQF 371
                                    57777899*******************************************85 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   6.1e-05     0.035      12      40 ..     325     353 ..     320     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.1e-05
                           HALZ  12 asYdaLksdydsLkkenekLkaelqeLke 40 
                                    ++ + L+ + dsL+ ene+Lk +l eL +
  gi|118431749|ref|NP_148414.2| 325 SRVETLRNSLDSLRSENEELKRKLDELQG 353
                                    5668899999****************986 PP

>> HCMV_UL139  Human Cytomegalovirus UL139 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.1e-05     0.035      34      76 ..     315     357 ..     302     378 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-05
                     HCMV_UL139  34 lLerkiadlnsrilslrseidaldakyvaisrdlrslkgevee 76 
                                      e++iadlnsr+ +lr  +d+l++  +   r+l +l+g ++ 
  gi|118431749|ref|NP_148414.2| 315 GFEKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDY 357
                                    56899************99999999999999999888887654 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 ?   14.1   1.9   6.2e-05     0.036      24      70 ..     323     369 ..     318     372 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-05
                     TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                    L +    l+n++++Lr++n+el  +++el+ + +  + +++elee+l
  gi|118431749|ref|NP_148414.2| 323 LNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEEL 369
                                    566667899*********************99999999999999987 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 ?   13.8   2.3   8.6e-05      0.05      33      71 .]     332     370 ..     318     370 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-05
                       JIP_LZII  33 arvdeLtsereiLreEleslqkakerlesrikelEeelk 71 
                                    + +d L se+e L+  l++lq   +  + +i+elEeel+
  gi|118431749|ref|NP_148414.2| 332 NSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQ 370
                                    457888888888888888888888888999999999996 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.5   8.2e-05     0.047      26      60 ..     318     352 ..     317     355 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLk 60 
                                    ++i+ L +rv++L +   sL+se+eelk + ++L+
  gi|118431749|ref|NP_148414.2| 318 KRIADLNSRVETLRNSLDSLRSENEELKRKLDELQ 352
                                    78999***********************9998875 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 ?   13.5   2.4   9.3e-05     0.054      57      95 ..     316     354 ..     305     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-05
                 CENP-F_leu_zip  57 lkeeieelaeelreleldLvalrsekeeLekelqkkqer 95 
                                    +++ i  l+++ + l+  L++lrse+eeL+++l + q r
  gi|118431749|ref|NP_148414.2| 316 FEKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGR 354
                                    7889999999999******************99998865 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.0   6.4e-05     0.037      60     111 ..     318     369 ..     315     379 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-05
                           ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqkl 111
                                    ++i +l++  e l+++ ++l  ++e+l+r+l+ +q ++   ++k+++le+ l
  gi|118431749|ref|NP_148414.2| 318 KRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEEL 369
                                    5666666666666666666666666666666666666666666666666655 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   7.4e-05     0.043       3      43 ..     326     369 ..     324     377 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.4e-05
                   Herpes_BLRF2   3 tvEdlaaelakLkvENkaLkkklkssvspkd...eeLTaaekea 43 
                                     vE l + l  L++EN++Lk+kl +  + +d    ++T+ e e+
  gi|118431749|ref|NP_148414.2| 326 RVETLRNSLDSLRSENEELKRKLDELQGRDDywnAKITELEEEL 369
                                    69*********************988875541224666666665 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   7.3e-05     0.042      92     143 ..     319     377 ..     316     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.3e-05
                      PspA_IM30  92 eikslekqaealetqlaqqrsaveqlrkqleale.......tkieelkakkellkarek 143
                                    +i++l + +e l+ +l+ +rs  e+l+++l++l        +ki+el+++ + +k+r++
  gi|118431749|ref|NP_148414.2| 319 RIADLNSRVETLRNSLDSLRSENEELKRKLDELQgrddywnAKITELEEELQFYKIRSE 377
                                    89999**************************9963333333799999999999999986 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 ?   13.3   1.1   8.6e-05      0.05      65     114 ..     317     366 ..     316     372 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.6e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH CS
                           SHE3  65 errlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlk 114
                                    e+r+ dl++ ++ l++s ++l+ e+++lk +l++++ ++   ++++ +l+
  gi|118431749|ref|NP_148414.2| 317 EKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELE 366
                                    79**********************************99999888888776 PP

>> BicD  Microtubule-associated protein Bicaudal-D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   7.6e-05     0.044      32      94 ..     316     378 ..     306     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                           BicD  32 leqkilelqnelkqaravlenvqaeneRlaslsqelkeekelvelerarlrdelkeykvrear 94 
                                    +e++i +l++ +  +r++l++ ++ene l+    el+ + +  +++ ++l +el+ yk+r  r
  gi|118431749|ref|NP_148414.2| 316 FEKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQFYKIRSER 378
                                    6899*******************************************************9876 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 ?   12.0   1.2   0.00014      0.08      74     122 ..     318     366 ..     316     379 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                          Atg14  74 sliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslq 122
                                    ++iadl++r+++l+ +l++l++e+ee k+kl +l+    + ++++  l+
  gi|118431749|ref|NP_148414.2| 318 KRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELE 366
                                    6899***************************998765555555555555 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016     0.094     121     160 ..     315     354 ..     292     379 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                          Spc29 121 elekklddqkleIkeLkreleqqrtvnseLqekvaeleee 160
                                      ek + d + ++++L++ l+  r  n+eL++k++el+ +
  gi|118431749|ref|NP_148414.2| 315 GFEKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGR 354
                                    4577888888888888888888888888888888888754 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   0.00018       0.1      68     104 ..     317     353 ..     316     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                    Prefoldin_2  68 eerketlekeiktlekqleklekeleelkeelqkklq 104
                                    e+r+++l+ +++tl ++l++l+ e eelk +l ++++
  gi|118431749|ref|NP_148414.2| 317 EKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQG 353
                                    79999***************************99886 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00043      0.25      65     111 ..     306     352 ..     289     354 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                                    EETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  65 lGagyyveksleeAiellkkkleelekqlekleeeleklkdqittle 111
                                    + a++   + +e+ i+ l+ ++e+l+++l++l  e e+lk+++++l+
  gi|118431749|ref|NP_148414.2| 306 IKASVPTGFGFEKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQ 352
                                    55555555666777889999999999999999999999999999886 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4    0.0003      0.17     108     171 ..     316     375 ..     314     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                        Taxilin 108 fqakLkdiqaqieekserneklreenaelteKlkslieqyelreehfekllktkelelqlaeaK 171
                                    f++ ++d+++++e  +++ ++lr en+el+ Kl++l    + r+ +++  + + e elq+ + +
  gi|118431749|ref|NP_148414.2| 316 FEKRIADLNSRVETLRNSLDSLRSENEELKRKLDEL----QGRDDYWNAKITELEEELQFYKIR 375
                                    8999*****************************987....567777777777777777776655 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   0.00043      0.25      63     106 ..     328     371 ..     316     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                        DUF4618  63 kqleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnv 106
                                    + l ++ + L + +e++++kl +L+   ++ nak+++l+eel++
  gi|118431749|ref|NP_148414.2| 328 ETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQF 371
                                    345555566777889999************************99 PP

>> NRBF2  Nuclear receptor-binding factor 2, autophagy regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.5   2.6e+03     116     139 ..     133     156 ..     130     167 .. 0.83
   2 ?    9.9   0.9   0.00089      0.51      87     120 ..     319     352 ..     316     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.5
                          NRBF2 116 kaRLqkeplekeldvdaDfvekse 139
                                    +aRL   + + ++d+d D ++  e
  gi|118431749|ref|NP_148414.2| 133 EARLTFYAYKPQIDIDIDIINEGE 156
                                    589999999999******997665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00089
                          NRBF2  87 kiadLkrlvelLlaenerLrkenkqLkaekaRLq 120
                                    +iadL+  ve+L +  + Lr+en++Lk     Lq
  gi|118431749|ref|NP_148414.2| 319 RIADLNSRVETLRNSLDSLRSENEELKRKLDELQ 352
                                    79************************98766655 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 ?   11.5   1.0   0.00059      0.34      49      95 ..     322     368 ..     316     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00059
                 HIP1_clath_bdg  49 eqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaE 95 
                                    + ++ +e+L++ l + r e ++lk  L++ +  ++ +++++++L++E
  gi|118431749|ref|NP_148414.2| 322 DLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEE 368
                                    556789***************************************99 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 ?    9.9   3.1    0.0013      0.74      54     102 ..     322     370 ..     318     379 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                          DHR10  54 eakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                    + +++++ lr+ l++++ e +el+rk + lq + + ++ k++ l+e+ +
  gi|118431749|ref|NP_148414.2| 322 DLNSRVETLRNSLDSLRSENEELKRKLDELQGRDDYWNAKITELEEELQ 370
                                    56789999*********************************99998765 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6    0.0048       2.8      16      53 ..     317     354 ..     316     360 .. 0.87
   2 ?   -0.2   0.1       2.7   1.6e+03       3      14 ..     360     371 ..     358     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0048
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                           SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                    e+ i +Ln  v   +  +d l+ + ++l+++l el+ +
  gi|118431749|ref|NP_148414.2| 317 EKRIADLNSRVETLRNSLDSLRSENEELKRKLDELQGR 354
                                    67899999999999999999999999999999999876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHH CS
                           SlyX   3 erleeLEiklaf 14 
                                    ++++eLE++l f
  gi|118431749|ref|NP_148414.2| 360 AKITELEEELQF 371
                                    689999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      948  (0.0528752); expected 358.6 (0.02)
Passed Vit filter:                       268  (0.0149478); 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):              31  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 2812.42
//
Query:       gi|118431750|ref|NP_148415.2|  [L=458]
Description: 2-methylcitrate dehydratase [Aeropyrum pernix K1]
Scores for complete 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  468.6   0.0   1.8e-140  468.4   0.0    1.0  1  MmgE_PrpD  MmgE/PrpD family
  ------ inclusion threshold ------
      0.013   15.2   0.5      0.068   12.8   0.8    1.9  2  SDH_alpha  Serine dehydratase alpha chain


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 !  468.4   0.0    2e-144  1.8e-140       2     438 ..       7     442 ..       6     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: 468.4 bits;  conditional E-value: 2e-144
                                    HHHHHHHHH-----H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT.-EE-TTSS-EE-HHHHHHHHHH CS
                      MmgE_PrpD   2 eqlaefvaelryddlpeevverakrlilDtlGvalaglrepavkkaleavkgtggpg.gatvigtgerlspvkAAfvnGa 80 
                                    +++a++v++lr++d+p+evve++k++++Dt+Gva+++ +e++v++ +++++gt+g++ ++ ++gt   +s+ +AAf nG+
  gi|118431750|ref|NP_148415.2|   7 KAMARWVHSLRFSDIPSEVVEEVKKRVVDTAGVAVGAFNEEPVRISRSIALGTTGSRiSSLIWGTLSYASADQAAFTNGC 86 
                                    579*********************************************999999988789999***************** PP

                                    HHHCTS-S-BEESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHHHHHHHHH CS
                      MmgE_PrpD  81 aihalDfdDthlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgtfgaaaaa 160
                                    a++++Df+Dt+l++e  hpsd++pa++A+Ae ++a+gk l+++iv++yE+++rl+++ s++++g +d++++ ++++aa+a
  gi|118431750|ref|NP_148415.2|  87 AARYFDFNDTYLSKEALHPSDTIPALVAAAEIVDADGKSLIEGIVAAYEIAARLADSYSVRSRG-WDHTVYIGIASAAGA 165
                                    ****************************************************************.*************** PP

                                    HHHTT--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHHHHHSTT- CS
                      MmgE_PrpD 161 akLlgLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGflavlsggk 240
                                    ak+lgLd++ i++A+ ia+t++ +lrq+r+++ +++k +aa++AarnG+++allA +G+tGps+++eg+ Gf++v + g+
  gi|118431750|ref|NP_148415.2| 166 AKILGLDEDGIEHAINIAVTTGLALRQTRAGELSMWKGCAAAHAARNGLFSALLAWKGMTGPSPVFEGKFGFFKVALCGD 245
                                    ******************************************************************************** PP

                                    ----S.S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCT.CCCEEEEEEEE-HHHHHHC---S...---SH CS
                      MmgE_PrpD 241 dlelevkplgegesweienvlfKpypaerhthaaidaalklraelklk.pddIesieirtseaalriigkkg...ppenr 316
                                    ++el+  plg +  ++++++++K +p+e+h+ +a++aalklr++ ++  pddIes+e++t+ + ++ii +++   +p++r
  gi|118431750|ref|NP_148415.2| 246 KFELA--PLG-EGGYKVMQTSIKYWPVEYHSMSAVEAALKLREKAGDIkPDDIESVEVETFTVSYKIIVEDPekwDPKTR 322
                                    *****..666.579******************************99878*********************999******* PP

                                    HHHCT-CCHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHHTTT---EEEEETTS-B---EEESS-T CS
                      MmgE_PrpD 317 adadhSlqyvvAvalldgrvtledfederladpevqaLrekvevvedpeltadypekrsivvvvlkdggrtleerveypk 396
                                    ++adhSl+y+vA+alldg+v le f++er   ++v+++++k++++++p++++ ype    +v+v +++grtlee+  yp 
  gi|118431750|ref|NP_148415.2| 323 ETADHSLPYIVAAALLDGKVWLETFKPERFLADDVRKVMKKMSIRVNPKYDEIYPEGIGNKVIVRLRDGRTLEEESIYPP 402
                                    *****************************9999*********************************************** PP

                                    TSGGHHHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHSHH CS
                      MmgE_PrpD 397 GhprnplsreeleeKfrrlaegvlseeeaereeileevlele 438
                                    Gh++npl+r  +e+Kf+rl+eg ++  e++r+e l+++++le
  gi|118431750|ref|NP_148415.2| 403 GHFKNPLDRSGVEAKFTRLLEGLVT--EERRREFLKDAWNLE 442
                                    *************************..999999999999986 PP

>> SDH_alpha  Serine dehydratase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   7.6e-06     0.068     106     186 ..     109     186 ..     106     191 .. 0.90
   2 ?   -1.6   0.0      0.19   1.7e+03     229     257 ..     351     378 ..     333     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-06
                      SDH_alpha 106 lPavlvalleelkas.eellraLllaaligilikrnasisgAecGcqaevGvacamAAaglaallggspeqienAaeial 184
                                    +Pa+++a +e ++a+ ++l++ +++a  i+  ++ + s+ +     ++ +G+a   +Aag a++lg + + ie+A++ia+
  gi|118431750|ref|NP_148415.2| 109 IPALVAA-AEIVDADgKSLIEGIVAAYEIAARLADSYSVRSRGWDHTVYIGIA---SAAGAAKILGLDEDGIEHAINIAV 184
                                    7888887.666777799************************************...**********************98 PP

                      SDH_alpha 185 eh 186
                                     +
  gi|118431750|ref|NP_148415.2| 185 TT 186
                                    65 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.19
                      SDH_alpha 229 givsldevietmrntgkdmsekyketseg 257
                                     +   d+v + m+++   ++ ky e   +
  gi|118431750|ref|NP_148415.2| 351 RFLA-DDVRKVMKKMSIRVNPKYDEIYPE 378
                                    5555.999*********999999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3333.42
//
Query:       gi|118431751|ref|NP_148416.2|  [L=270]
Description: ribulose-1,5-biphosphate synthetase [Aeropyrum pernix K1]
Scores for complete 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-62  210.2   0.2    3.5e-62  209.7   0.0    1.3  2  Thi4            Thi4 family
    4.7e-14   52.3   3.7    1.8e-09   37.2   1.3    2.1  2  FAD_binding_2   FAD binding domain
    4.9e-14   52.5   0.3      8e-14   51.8   0.3    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    1.3e-09   38.1   0.2    1.3e-09   38.1   0.2    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.4e-09   36.7   5.3      2e-06   27.7   1.9    2.2  2  DAO             FAD dependent oxidoreductase
    8.9e-09   35.0   0.9    1.6e-07   30.9   0.5    2.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.2e-08   32.7   0.0    4.1e-08   32.3   0.0    1.2  1  HI0933_like     HI0933-like protein
    5.9e-08   32.3   0.2    2.5e-07   30.3   0.1    1.8  2  FAD_binding_3   FAD binding domain
    1.4e-06   27.6   1.2    2.8e-06   26.7   1.2    1.4  1  GIDA            Glucose inhibited division protein A
    9.1e-06   25.0   2.7    0.00022   20.4   0.3    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    3.4e-05   23.2   0.2    6.4e-05   22.3   0.2    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    7.3e-05   22.2   0.2    0.00014   21.3   0.2    1.4  1  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0023   18.0   1.3     0.0056   16.7   0.2    2.0  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0026   17.1   0.1      0.007   15.7   0.1    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.012   16.2   1.0      0.029   14.9   0.3    2.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.017   14.0   0.5      0.084   11.7   0.4    1.9  2  Trp_halogenase  Tryptophan halogenase
      0.038   14.4   0.0        0.1   13.1   0.0    1.7  1  NAD_binding_7   Putative NAD(P)-binding
      0.078   13.2   0.0       0.14   12.5   0.0    1.4  1  OKR_DC_1_N      Orn/Lys/Arg decarboxylase, N-terminal domain
       0.09   12.4   0.4       0.22   11.2   0.4    1.6  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.7   0.0   3.7e-65   3.5e-62       2     235 .]      13     238 ..      12     238 .. 0.95
   2 ?   -3.9   0.1         7   6.6e+03      28      46 ..     244     262 ..     244     264 .. 0.82

  Alignments for each domain:
  == domain 1  score: 209.7 bits;  conditional E-value: 3.7e-65
                                    HHHHHHHHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHHHHTT CS
                           Thi4   2 raiveryfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelLdelg 81 
                                     ai+   ++ l k+  sDv++vGaG++GLtaa  la++ + +v+i+e++  +GGG wlGG   + + +r pa+ +Ldel+
  gi|118431751|ref|NP_148416.2|  13 EAILDGFYSSLKKHLRSDVIVVGAGPAGLTAAWRLAEA-GARVLIVEQNNYLGGGLWLGGYFMNPVTIRAPAQRILDELE 91 
                                    68999999******************************.***************************************** PP

                                    ---EEESSEEEESEHHHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEE CS
                           Thi4  82 ikyedegdyvvvkdaalftstllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakv 161
                                    ++ye  + +++  +  l+ ++l++++l+ a++ +ln ++++D+iv + ++vaGvv+nw+ v+    + +cvDP  +ra+ 
  gi|118431751|ref|NP_148416.2|  92 VPYEAVKPGLYRTKGPLLAAKLAARALE-AGAEVLNLTMLDDVIVEN-SRVAGVVVNWSPVQGLPRQITCVDPVGLRAEY 169
                                    ****************************.*****************9.***************99899************ PP

                                    EEE--GSSSTTTTHHHHHHHHCTTTS-----ECB-HHHHHHHHHHHECEEETTEEE-THHHHHHHT-EB--SB- CS
                           Thi4 162 vvdatGhdgeivavvvkkikleakiekvkgeksldaekaedaivkktrevvpnlyvaGmevaevdganRmGpif 235
                                    vvdatGhd+ +   ++ +   ea     +   ++++e++ed +v+kt ev+p+l+vaG++vaev+g++RmGp+f
  gi|118431751|ref|NP_148416.2| 170 VVDATGHDAVVTRKLAERGMVEA-----SKLGPMWVERSEDLVVEKTGEVYPGLVVAGIAVAEVYGLPRMGPTF 238
                                    ********976655555544444.....456699***************************************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7
                                    HHHHHHHHHHHCTTS-EEE CS
                           Thi4  28 sGLtaayylakkpdlkvai 46 
                                    sG  aa  +++k +lkv +
  gi|118431751|ref|NP_148416.2| 244 SGEKAAALIGEKLGLKVKV 262
                                    5778999999999999976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   1.3   1.9e-12   1.8e-09       1      36 [.      30      65 ..      30      77 .. 0.94
   2 !   15.5   0.0   7.6e-06    0.0072     138     200 ..     104     175 ..      89     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.9e-12
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   DviV+G+G AGL+AA ++aeaG++v++ve+ ++ gg
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAGARVLIVEQNNYLGG 65
                                   9******************************99887 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.6e-06
                                    .HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET.........TTTCEEEEEESEEEE--- CS
                  FAD_binding_2 138 vtghallarlvesarkagvdfqerteadeLivedgrvtGavvenp.........esgrevrirakavvlatg 200
                                    + g+ l+a l+++a++ag ++++ t +d++ive+ rv G+vv+ +         +    v +ra  vv+atg
  gi|118431751|ref|NP_148416.2| 104 TKGPLLAAKLAARALEAGAEVLNLTMLDDVIVENSRVAGVVVNWSpvqglprqiTCVDPVGLRAEYVVDATG 175
                                    589999************************************977777666665555555777777777777 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.3   8.5e-17     8e-14       1     144 [.      30     175 ..      30     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 8.5e-17
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlk..kr 78 
                                    Dv+VvG+gpaG++AA   a+aGa+vl+ve++++lGG l  g+   ++++      ++  a+++l++l+    +  +  k+
  gi|118431751|ref|NP_148416.2|  30 DVIVVGAGPAGLTAAWRLAEAGARVLIVEQNNYLGGGLWLGG--YFMNPV----TIRAPAQRILDELEV--PY--EavKP 99 
                                    9**********************************9987555..666655....678888888888855..33..11122 PP

                   FAD_oxidored  79 skwntfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.g..........rktirAkvfiDATg 144
                                       +t  p  a++++   l+  g +vl  t+l++v++e+ r+ +v+v+ +  +             +rA++++DATg
  gi|118431751|ref|NP_148416.2| 100 GLYRTKGPLLAAKLAARALEA-GAEVLNLTMLDDVIVENSRVAGVVVNWSPvQglprqitcvdPVGLRAEYVVDATG 175
                                    222467899999999999966.9*********999999977777776543332131000001144568888888887 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 !   38.1   0.2   1.4e-12   1.3e-09       1      33 [.      33      65 ..      33      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.4e-12
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                   +vGaG +Gl+aA++La+ag++vl++e++++lGG
  gi|118431751|ref|NP_148416.2| 33 VVGAGPAGLTAAWRLAEAGARVLIVEQNNYLGG 65
                                   8*******************************9 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   1.9   2.1e-09     2e-06       1      34 [.      30      65 ..      30      72 .. 0.94
   2 !   10.2   0.1   0.00041      0.39     147     210 ..     108     184 ..      87     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.1e-09
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags 34
                                   dv+++G+G +Gl++A+ La++g  V+++e+++ +g 
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAGarVLIVEQNNYLGG 65
                                   9******************************99883 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00041
                                    HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..............EECT.EEEEEEEEEEE--GGGHHHHHTT CS
                            DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgve..............rttp.gendaadavVnaaGawsdllgll 210
                                     l+a la++a ++G+e+l+ t   ++  e+ +v+gv                + p g +  a++vV a+G+ +  +++l
  gi|118431751|ref|NP_148416.2| 108 LLAAKLAARALEAGAEVLNLTMLDDVIVENSRVAGVVvnwspvqglprqitCVDPvGLR--AEYVVDATGHDAVVTRKL 184
                                    578999**************555555444555555555444433222222212233554..799******997444333 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 !   30.9   0.5   1.7e-10   1.6e-07       2      42 ..      30      69 ..      29      85 .. 0.85
   2 ?    2.8   0.0     0.062        59     166     239 ..      90     178 ..      70     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.7e-10
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll 42
                                   dv+v+G+GpAGl+aa +la+aga+v++v ++++ l+gg +l
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAGARVLIV-EQNNYLGGGLWL 69
                                   8***************************.777777777665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.062
                                    -EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE..EEETTSCE.............EEESE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.............xxxxx RF
                    Pyr_redox_2 166 kevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle..vvledgee.............idadl 230
                                     ev++    + l+r+ ++ l+a l+++  + G ev   t+  +++ +++++   vv+ +  +             + a++
  gi|118431751|ref|NP_148416.2|  90 LEVPYEAVKPGLYRTKGPLLAAKLAARALEAGAEVLNLTMLDDVIVENSRVAgvVVNWSPVQglprqitcvdpvgLRAEY 169
                                    489999999*********************************99999995544322222222455556666666677777 PP

                                    EEE-S-EEE CS
                                    xxxxxxxxx RF
                    Pyr_redox_2 231 vvvavGvrp 239
                                    vv a+G  +
  gi|118431751|ref|NP_148416.2| 170 VVDATGHDA 178
                                    777777665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   4.4e-11   4.1e-08       2      43 ..      30      71 ..      29     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.4e-11
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                   dviv+G+G+AGl aA ++a++g+rVl++e+++ lg  + + G
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAGARVLIVEQNNYLGGGLWLGG 71
                                   8*******************************9998776655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.1   2.6e-10   2.5e-07       2      33 ..      29      60 ..      28      63 .. 0.94
   2 ?   -0.5   0.0      0.62   5.8e+02     153     175 ..     165     187 ..     154     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.6e-10
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                    dV++VGaGpaGl++a  L+eaG rv++ve+ 
  gi|118431751|ref|NP_148416.2| 29 SDVIVVGAGPAGLTAAWRLAEAGARVLIVEQN 60
                                   69****************************86 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.62
                                    EEEEEEEE--GTT-HHHHHHTGG CS
                  FAD_binding_3 153 vrakYlvGaDGgrStvrktlgie 175
                                    +ra+Y+v a G    v ++l  +
  gi|118431751|ref|NP_148416.2| 165 LRAEYVVDATGHDAVVTRKLAER 187
                                    799********999999888655 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   1.2   2.9e-09   2.8e-06       1      31 [.      30      60 ..      30      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.9e-09
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithk 31
                                   dviV+G+G AG+ AA+ +a++Ga+vl++ ++
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAGARVLIVEQN 60
                                   8************************999665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   2.3e-07   0.00022       1      33 [.      30      60 ..      30      72 .. 0.92
   2 ?    4.8   0.1     0.013        12      97     142 ..     128     176 ..     108     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieas 33
                                   Dv+v+GaGpAgl  A rl  a++g +v+++e  
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRL--AEAGARVLIVEQN 60
                                   9*****************..99999****9875 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.013
                  Lycopene_cycl  97 lvengvklleakvesve....eeeageslvvleggrkirarlvvdargla 142
                                     + + v+  +++v+ v+    +++   +++++ + + +ra  vvda+g  
  gi|118431751|ref|NP_148416.2| 128 TMLDDVIVENSRVAGVVvnwsPVQGLPRQITCVDPVGLRAEYVVDATG-H 176
                                    33466666777776655111144446789*******************.3 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   6.8e-08   6.4e-05       1      31 [.      32      61 ..      32      64 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.8e-08
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                   i++GaGPaGl+aa  l +ag  ++li+E++n
  gi|118431751|ref|NP_148416.2| 32 IVVGAGPAGLTAAWRLAEAGA-RVLIVEQNN 61
                                   89*******************.8*****987 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   1.5e-07   0.00014       2      28 ..      39      65 ..      38      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-07
                                   HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                  Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                   aGL+aA++L++aG +V+++E ++ +GG
  gi|118431751|ref|NP_148416.2| 39 AGLTAAWRLAEAGARVLIVEQNNYLGG 65
                                   9*************************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 !   16.7   0.2     6e-06    0.0056       2      42 ..      33      68 ..      32      86 .. 0.88
   2 ?   -0.7   0.0       1.3   1.3e+03     125     155 ..     145     176 ..     128     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsep.gagrvw 42
                                   +vGaGp+Gl+++ rL++        ++ +++++++ g g+ w
  gi|118431751|ref|NP_148416.2| 33 VVGAGPAGLTAAWRLAEA-----GARVLIVEQNNYlG-GGLW 68
                                   8***************99.....59*******88856.9999 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                  NAD_binding_9 125 vdleeradg.qavlladgaslaadaVvLAlGh 155
                                    v+ ++ ++  ++++  d   l+a++Vv A+Gh
  gi|118431751|ref|NP_148416.2| 145 VNWSPVQGLpRQITCVDPVGLRAEYVVDATGH 176
                                    55555443324566667777888888888888 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 !   15.7   0.1   7.4e-06     0.007      28      60 ..      28      60 ..       9      63 .. 0.90
   2 ?   -3.0   0.0       3.9   3.6e+03      97     113 ..     239     255 ..     238     256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.4e-06
                                   --EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C 28 pakvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                   ++ v+v+G+G aGl A++  ++ ga+V +++ +
  gi|118431751|ref|NP_148416.2| 28 RSDVIVVGAGPAGLTAAWRLAEAGARVLIVEQN 60
                                   678*************************99987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.9
                                    E---BTTSS---SC-HH CS
                    AlaDh_PNT_C  97 gtvlipGkkaPkLvtee 113
                                    g++l+ G+ka+ L+ e+
  gi|118431751|ref|NP_148416.2| 239 GAMLLSGEKAAALIGEK 255
                                    789999******99775 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3   3.1e-05     0.029       2      35 ..      31      64 ..      30      72 .. 0.93
   2 ?   -2.5   0.0       8.3   7.8e+03      50      75 ..     117     142 ..     103     146 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   v+vvG+G  gl +A  lae g++V +ve ++ l 
  gi|118431751|ref|NP_148416.2| 31 VIVVGAGPAGLTAAWRLAEAGARVLIVEQNNYLG 64
                                   89**************************998876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.3
                                    HHHTTEEEECSEEEEEEEEETTSEEE CS
                      Pyr_redox  50 lekngievllntkveeiegsedgves 75 
                                      + g evl  t +  +  +++ v +
  gi|118431751|ref|NP_148416.2| 117 ALEAGAEVLNLTMLDDVIVENSRVAG 142
                                    33444455544444444444444444 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   8.9e-05     0.084       1      34 [.      30      60 ..      30      64 .. 0.92
   2 ?    0.1   0.0      0.29   2.8e+02     195     223 ..     162     190 ..     109     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                   ++++vG+G+aG +aA  la+a+   ++v++ve++
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAG---ARVLIVEQN 60
                                   699*******************...899999986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                                    S-EEE-SEEEE-SGGG-IIIIIIT---EE CS
                 Trp_halogenase 195 greveadlfiDcsGfrgllieqaLktgfe 223
                                       + a+ ++D++G+ + +  +  + g+ 
  gi|118431751|ref|NP_148416.2| 162 PVGLRAEYVVDATGHDAVVTRKLAERGMV 190
                                    455789999*****999888876666655 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 ?   13.1   0.0   0.00011       0.1       9      39 ..      30      60 ..      25      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvape 39
                                    v+vvG+G+ +++ + +l+eaga+v +v ++
  gi|118431751|ref|NP_148416.2| 30 DVIVVGAGPAGLTAAWRLAEAGARVLIVEQN 60
                                   699************************9876 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.14       9      47 ..     114     148 ..     109     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                     OKR_DC_1_N   9 laealekegfevvgvtstdDllsvieqnsriaavvlsvd 47 
                                     a+ale  g ev+++t  d    vi +nsr+a+vv++++
  gi|118431751|ref|NP_148416.2| 114 AARALE-AGAEVLNLTMLD---DVIVENSRVAGVVVNWS 148
                                    678899.************...899*************8 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00023      0.22       1      31 [.      31      61 ..      31      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                   + ++GaG  G + a++La+aga v ++ +++
  gi|118431751|ref|NP_148416.2| 31 VIVVGAGPAGLTAAWRLAEAGARVLIVEQNN 61
                                   579*********************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2073.94
//
Query:       gi|118431752|ref|NP_148417.2|  [L=503]
Description: serine protease [Aeropyrum pernix K1]
Scores for 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-12   45.7   1.2    2.8e-11   43.6   1.2    2.2  1  NfeD          NfeD-like C-terminal, partner-binding
     0.0014   17.7   0.2     0.0023   17.0   0.2    1.2  1  SDH_sah       Serine dehydrogenase proteinase
      0.002   18.0   0.4      0.004   17.0   0.4    1.5  1  CLP_protease  Clp protease
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.073   12.7   0.0    1.4  1  STAS          STAS domain
        3.9    7.7   5.9        9.2    6.5   0.4    3.3  3  DUF2613       Protein of unknown function (DUF2613)


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 !   43.6   1.2   7.8e-15   2.8e-11       5      84 .]     412     490 ..     408     490 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 7.8e-15
                                    XXXXXXXXXXXXS---SSS--S.S---.GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSSE CS
                           NfeD   5 vsvlllvllrplllkklkkkekktnae.aliGkegvvledi..g.tGrvkvdGeeWsarsegeiekgerVrVveveGltl 80 
                                    ++ l+ ++++++++ k+       ++  +l G++g++++di  g tG + v+Ge+W+a++  ++++g++V+Vv+ eG  l
  gi|118431752|ref|NP_148417.2| 412 MGGLTAFVVYKVVKAKR-A----PQTLwKLKGAVGEAVDDIpeGgTGFILVEGEYWKAKAITPVARGDKVVVVDKEGPYL 486
                                    55677788888888876.2....333457*************9459**************999***************** PP

                                    EEEE CS
                           NfeD  81 iVep 84 
                                    +V++
  gi|118431752|ref|NP_148417.2| 487 VVKK 490
                                    **98 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   6.3e-07    0.0023      96     161 ..     122     188 ..      97     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-07
                        SDH_sah  96 liihtpGGlvlaatqiakalkehkakt.rvivphyamsGGtlialaadeiildenavlGpvdpqlgq 161
                                    + + tpGG+v aat++  ++ + + ++   +v ++a s Gt+i +++    +++ +++G v+p   +
  gi|118431752|ref|NP_148417.2| 122 VELNTPGGFVDAATEMVVSISKARIPVvGYVVEKWAESAGTMILMSTHIAAMQPGTIIGSVQPIAYD 188
                                    3368************99999888775157999****************************996555 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   1.1e-06     0.004      18     180 ..      91     250 ..      79     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                                    EEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE.EEEETHHHHHHHTS CS
                   CLP_protease  18 iiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticl.GlaaSmgslllaag 96 
                                    ii + + id+++ + + + +  +  e+++  + + +n+pGG v+a++++   +   + +v+ +++  +a S+g+++l++ 
  gi|118431752|ref|NP_148417.2|  91 IIRIEGTIDNAMMDYLKQSIERA--EEENAVLIVELNTPGGFVDAATEMVVSISKARIPVVGYVVeKWAESAGTMILMST 168
                                    67777777777776666666555..4555568888*************99999999887777776589***********9 PP

                                    -TTGEEEETTEEEEES-TEEE..EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTS CS
                   CLP_protease  97 ekgkRfalpnarimihqPlgg..aqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGL 174
                                    +    ++ p + i   qP     ++g+ + +  + + ++ i ++l e  a +  +++  ++  l +d++  aeeA+e G 
  gi|118431752|ref|NP_148417.2| 169 HIA--AMQPGTIIGSVQPIAYdpTTGSYQPV-LDSKIINPIVKTLCEHGATRGRNPEALVRFVLYNDNY-GAEEALEKGV 244
                                    999..78899999999997652145544444.5678899999999999999988888888888888886.7999999999 PP

                                    SSEE-S CS
                   CLP_protease 175 idevie 180
                                    id + +
  gi|118431752|ref|NP_148417.2| 245 IDLIAR 250
                                    998865 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.073       8      39 ..      87     118 ..      76     229 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                    TTEEEEEEEEEESHHHHHHHHHHHHHHHHCCC CS
                           STAS   8 egililrldgpidfanaesfkeklkravgeep 39 
                                    +  li+r++g id a  +++k++++ra++e++
  gi|118431752|ref|NP_148417.2|  87 PKALIIRIEGTIDNAMMDYLKQSIERAEEENA 118
                                    4459*************************995 PP

>> DUF2613  Protein of unknown function (DUF2613)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.4    0.0026       9.2      12      37 ..      19      44 ..      17      52 .. 0.76
   2 ?   -1.6   0.4      0.83     3e+03      13      24 ..     323     335 ..     315     342 .. 0.73
   3 ?    2.1   0.0     0.058   2.1e+02      12      36 ..     408     432 ..     406     437 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0026
                        DUF2613 12 aGivlGvvavfgvtavvqqdsrPstd 37
                                   aG++l+++++f +t +  q+++ +t+
  gi|118431752|ref|NP_148417.2| 19 AGLLLALALAFAATYAKAQETVETTT 44
                                   8**********888887777765555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                        DUF2613  13 GivlGvv.avfgv 24 
                                    Gi+lG+  +v+g+
  gi|118431752|ref|NP_148417.2| 323 GIALGGFlLVLGL 335
                                    9999875156655 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.058
                        DUF2613  12 aGivlGvvavfgvtavvqqdsrPst 36 
                                     G++ G+ ++f v  vv+++  P+t
  gi|118431752|ref|NP_148417.2| 408 LGATMGGLTAFVVYKVVKAKRAPQT 432
                                    699****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 3912.34
//
Query:       gi|118431753|ref|NP_148418.2|  [L=271]
Description: erythrocyte band 7 integral membrane protein [Aeropyrum pernix K1]
Scores for complete 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-38  132.5   2.9    2.3e-38  132.0   2.9    1.2  1  Band_7    SPFH domain / Band 7 family
    1.2e-05   25.1   0.6    0.00011   22.1   0.3    2.2  2  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
      0.054   13.1   0.4      0.087   12.5   0.4    1.3  1  LEDGF     Lens epithelium-derived growth factor (LEDGF)


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 !  132.0   2.9   3.8e-42   2.3e-38       2     178 .]      34     204 ..      33     204 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 3.8e-42
                         Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaa 81 
                                    i++e e++v++r G+l +v++pGl +i+Pf++++++v++r++t+d++  + ++tkD++ v++d++v+y+v  d+ k+v +
  gi|118431753|ref|NP_148418.2|  34 IVREYERAVIFRLGRLIGVKGPGLFLIIPFVDTLVKVDLRIVTVDIPE-QRTITKDNVTVGVDAVVYYKV-FDPEKAVVR 111
                                    799*********************************************.*********************.********* PP

                         Band_7  82 veresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakq 161
                                    +    +n+   +  +++ +lr vi++ +l++ll +ree++++l++ l +  + +G+ v+ v+i+++++p+   +a+a+ +
  gi|118431753|ref|NP_148418.2| 112 I----ENYHYAVVMLAQTTLRDVIGQVELDDLLTKREEINKKLQEILDQLTDPWGIKVTAVTIKEVKLPESMLRAMAKQA 187
                                    *....*************************************************************************** PP

                         Band_7 162 aaeaeaqaeiaraeaea 178
                                    +ae+ ++a+i +ae+e+
  gi|118431753|ref|NP_148418.2| 188 EAERWRRARIIEAEGER 204
                                    **************995 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 ?    0.7   0.0     0.062   3.7e+02      18      43 ..      34      59 ..      29      72 .. 0.89
   2 !   22.1   0.3   1.8e-08   0.00011     145     209 ..     127     189 ..     108     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.062
                       Band_7_1 18 ivregqeavfvneGqiaDvfapGtyt 43
                                   ivre  +av  + G++  v +pG + 
  gi|118431753|ref|NP_148418.2| 34 IVREYERAVIFRLGRLIGVKGPGLFL 59
                                   8********************99875 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.8e-08
                       Band_7_1 145 lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                    l dv++  ++ + dl +k ee+ +kl+e l++  +  G+++++++i+++ lpe++ +a+ k+a++
  gi|118431753|ref|NP_148418.2| 127 LRDVIG--QVELDDLLTKREEINKKLQEILDQLTDPWGIKVTAVTIKEVKLPESMLRAMAKQAEA 189
                                    555554..4667899**********************************************9976 PP

>> LEDGF  Lens epithelium-derived growth factor (LEDGF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   1.4e-05     0.087      28     109 ..     153     235 ..     137     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                          LEDGF  28 aLdelks...lqvtplmLkKnpeivetikklrrYkgnleewklteeekvefkekakeirkkAeeiYnkfkslflvpeges 104
                                    +Ld+l +   ++vt + +k + ++ e + +    ++++e+w   +  ++e +++a++i+ +A e Y+k    +   e + 
  gi|118431753|ref|NP_148418.2| 153 ILDQLTDpwgIKVTAVTIK-EVKLPESMLRAMAKQAEAERWRRARIIEAEGERQAAKIMAEAAEFYEKHPAALRLRELQ- 230
                                    5555543333677777664.45555555555556788899****************************99999988888. PP

                          LEDGF 105 nfwek 109
                                    +  e 
  gi|118431753|ref|NP_148418.2| 231 TLIEV 235
                                    44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2205.72
//
Query:       gi|118431754|ref|NP_148419.2|  [L=285]
Description: twin-arginine translocation protein, TatC [Aeropyrum pernix K1]
Scores for complete 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-38  131.8  17.1    3.3e-38  131.6  17.1    1.1  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.6  17.1   1.9e-42   3.3e-38       2     207 .]      25     256 ..      24     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 1.9e-42
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCCHHHHC..C.....................TTS-EE--SSS-HHHH CS
                           TatC   2 hLeeLrkrlirallavaiafiitfvfaeeliafllepleea.e.....................eevelivlspleafll 59 
                                    h++eL +rl ++++a+a+a+ii+      li + ++p+    +                      ev+li +sp++++ l
  gi|118431754|ref|NP_148419.2|  25 HVQELIMRLRKVAIAFAVASIIVP-----LIPVSIAPYVPLlTvftkyfinsvvpstidvlgyhVEVRLIQTSPFAGLSL 99 
                                    99*********************4.....444444444332223344444445566667777654699************ PP

                                    HHHHHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT.......TTTSS CS
                           TatC  60 klkvslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll.......seeve 132
                                     +k++l++gl+++sP+++y+l+af++p+Ly+he r+v+++ ++++ lf++Ga++a+ v+lpl + + +       ++++ 
  gi|118431754|ref|NP_148419.2| 100 LIKTALLMGLLVVSPLLAYELYAFIKPALYPHEDRFVRTLGPIAVGLFMFGALIAFKVILPLGYAISFvtsvvlvGDKLV 179
                                    *************************************************************9998666556666655667 PP

                                    TTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHH.TTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
                           TatC 133 pllslseylsfvlllllafgiaFelPlvlvllarlglvsaetlr.kkrryaivvilvvaavltP.pdvisqlllavP 207
                                    +  +++++l++ +l+++++g+++e+P++l+ ++r+glvs+++l+ +k r++++++l ++av++P  + + +l+l++P
  gi|118431754|ref|NP_148419.2| 180 AFADVNNILQTSILVIVGVGLLYETPVLLYGAVRAGLVSPNILSgDKGRMVLLGLLALGAVISPdGTGLGMLVLTLP 256
                                    78*****************************************97899**************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.20s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2328.02
//
Query:       gi|118431755|ref|YP_874927.1|  [L=59]
Description: twin arginine-targeting protein translocase [Aeropyrum pernix K1]
Scores for complete 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   65.5   0.2    2.1e-18   65.4   0.2    1.0  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
      0.076   13.2   0.0      0.085   13.1   0.0    1.1  1  Nterm_IS4    Insertion element 4 transposase N-terminal
      0.089   13.8   0.1        0.1   13.6   0.1    1.1  1  DUF4834      Domain of unknown function (DUF4834)


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 !   65.4   0.2   3.5e-22   2.1e-18       1      49 [.       7      55 ..       7      59 .] 0.94

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 3.5e-22
                                   S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH---X CS
                    MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleeenek 49
                                   +g++el+iI+v+al++FGp++L E+ar+LG + +eF+ a++e+ ee ++
  gi|118431755|ref|YP_874927.1|  7 VGLTELIIIFVIALIVFGPERLTEIARNLGTAVKEFRRAMSEASEERKR 55
                                   799****************************************998765 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 ?   13.1   0.0   1.4e-05     0.085      36      78 ..      11      51 ..       9      59 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                      Nterm_IS4 36 evvvylvlalaLfrdesyeevvrrLtagleeeaewelpaksai 78
                                   e+++ +v+al  f  e ++e++r+L ++ +e +  +++++++ 
  gi|118431755|ref|YP_874927.1| 11 ELIIIFVIALIVFGPERLTEIARNLGTAVKEFR--RAMSEASE 51
                                   68999********************99999986..45555544 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.7e-05       0.1       6      44 ..      12      47 ..       7      58 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                        DUF4834  6 filifiiailviglsilsvilrtvfglgsrkkssksaqk 44
                                    i+if+ia++v+g   l  i r++ g+  ++   ++a +
  gi|118431755|ref|YP_874927.1| 12 LIIIFVIALIVFGPERLTEIARNL-GTAVKEF--RRAMS 47
                                   689*********************.6332221..11111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1047  (0.058397); expected 358.6 (0.02)
Passed bias filter:                      816  (0.0455129); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 517.72
//
Query:       gi|118431756|ref|YP_874928.1|  [L=77]
Description: hypothetical protein APE_2154b, partial [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   10.9   0.0       0.26   10.7   0.0    1.1  1  SMC_N     RecF/RecN/SMC N terminal 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 ?   10.7   0.0   1.4e-05      0.26     162     215 ..       2      53 ..       1      58 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.4e-05
                                    EEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-.SCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          SMC_N 162 yllDeidaaLDeknvkkvaellkeksknaQfivislreemleka.dklvgvtkve 215
                                     llDe    LD +  + v   + e s ++ +iv +++ +++ ++ d+++ v   +
  gi|118431756|ref|YP_874928.1|   2 TLLDEPTTGLDREAYESVRAAILELSLDSAVIVATHDVRLVGDVaDRVYMV---R 53 
                                    689*********************************999886542554444...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 601.75
//
Query:       gi|118431757|ref|NP_148422.2|  [L=243]
Description: hypothetical protein APE_2155.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-10   38.9  11.1    1.1e-09   38.3  11.1    1.3  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
      0.073   13.3   0.1        3.2    8.0   0.0    2.7  2  BC10      Bladder cancer-related protein BC10
      0.098   12.7   0.5      0.098   12.7   0.5    2.6  3  TPPK_C    Thiamine pyrophosphokinase C terminal


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 !   38.3  11.1   1.8e-13   1.1e-09      40     211 ..      35     213 ..       4     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.8e-13
                                    HHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE.................EECTTEEE...E-TTHHHHHHHHHHHHHH CS
                           CbiQ  40 lllllllvilprvlaqalilpllflllgllillf..........qlittegefvfagggqisitseGllrglllalRilt 109
                                    ll+++l+ ++p + + ++++++l+ll+ l ++ +           l + +g +v  ++  ++i +  + + +++alR+++
  gi|118431757|ref|NP_148422.2|  35 LLATFLITGVPGFVLGFARYRFLVLLIPLTVIGTflnalaiyytGLAREPGDVVARIWV-VEIPEFAVETTAVIALRVFS 113
                                    68999999*****************999999988899******9667889999999999.9999999************9 PP

                                    HHHHHHHHHHHS-HH.HHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHH CS
                           CbiQ 110 llslllllalTTppe.eltsslerlgvPlelalillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaa 188
                                    +  + lll+   +p   l s  e+lg P+ la+ l+ a+R+++l+   + + +  ++lR+ ++   i  s + +   ia+
  gi|118431757|ref|NP_148422.2| 114 FAGAGLLLVSLVSPRdALRSLTEELGLPKGLAFSLAFALRLFPLIRRDLGEVMAVRRLRGYRT---IPLSPSDYMSIIAP 190
                                    998888866555555056666799**************************************9...9999********** PP

                                    HHHHHHHHHHHHHHHHHTTS-SS CS
                           CbiQ 189 lflralkraervalAmeaRGYtg 211
                                    l+  +l+ra  v  + e RG++ 
  gi|118431757|ref|NP_148422.2| 191 LLNVSLERAVWVGVSAELRGFRL 213
                                    *********************98 PP

>> BC10  Bladder cancer-related protein BC10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00054       3.2      34      57 ..       3      26 ..       3      32 .. 0.91
   2 ?    2.2   0.0     0.037   2.2e+02      37      62 ..     176     201 ..     174     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00054
                           BC10 34 igftvelkPcvycsiilgllikai 57
                                   ++++v+lkP+++++++ g+l++ i
  gi|118431757|ref|NP_148422.2|  3 LSAVVRLKPRPWALFVYGILVTII 26
                                   689*****************9886 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.037
                           BC10  37 tvelkPcvycsiilgllikaicrpnl 62 
                                    t++l+P+ y+sii  ll    +r ++
  gi|118431757|ref|NP_148422.2| 176 TIPLSPSDYMSIIAPLLNVSLERAVW 201
                                    7999*********9888887777777 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   1.6e-05     0.098       9      32 ..       7      30 ..       6      42 .. 0.87
   2 ?   -2.6   0.1      0.98   5.9e+03      23      30 ..      59      66 ..      56      78 .. 0.62
   3 ?   -2.6   1.2      0.97   5.8e+03      19      27 ..     230     238 ..     222     243 .] 0.50

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                         TPPK_C  9 srisggallllvlAaLvAvavall 32
                                   +r++++ ++l v ++Lv +++++ 
  gi|118431757|ref|NP_148422.2|  7 VRLKPRPWALFVYGILVTIIAIVG 30
                                   699****************99985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.98
                         TPPK_C 23 aLvAvava 30
                                    L+++ v+
  gi|118431757|ref|NP_148422.2| 59 LLIPLTVI 66
                                   46666666 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.97
                         TPPK_C  19 lvlAaLvAv 27 
                                    ++l ++ A+
  gi|118431757|ref|NP_148422.2| 230 AILLIIQAA 238
                                    233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1753.45
//
Query:       gi|118431758|ref|NP_148423.2|  [L=304]
Description: hypothetical protein APE_2156.1 [Aeropyrum pernix K1]
Scores for 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   1.2      1e-27   97.5   1.2    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0066   16.0   0.1      0.011   15.3   0.1    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   1.2   1.1e-31     1e-27       5     197 .]      18     217 ..      14     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 1.1e-31
                                    SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHC CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfm 84 
                                    +++ +li  dg++ +iD+G  t+++r ++    l   + ++++vilTH HlDH++++g +v+  d + +++ +   a  m
  gi|118431758|ref|NP_148423.2|  18 MGSYILIAPDGDAAMIDSGPKTSWERVRE---ELQSMGVRLRYVILTHIHLDHASAAGSIVRSLDTVEAVYVHPRGARHM 94 
                                    678899*********************96...9999999**************************998888888888888 PP

                                    HHHHHHHHHCCHH..........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSS CS
                    Lactamase_B  85 eeaddaasrkgll..........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDalla 154
                                      +++ +++ +            +++v++ k +v+e+++ ++++g++ l+v+++pgh ++h++++++ ++v ftGD   +
  gi|118431758|ref|NP_148423.2|  95 ADPERLWQASKQFlgdyadffgkPEPVPEGKIVVPEDGEVLELPGGVKLHVIYTPGHASHHMSFYLPQEGVMFTGDSAGV 174
                                    888777777777788****************************************************************9 PP

                                    HHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 155 getgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        +++    ++++++p    +y++sl+ +a+ k+e+l+++H
  gi|118431758|ref|NP_148423.2| 175 SLKDDDGTLVEFPTTPPPFKPVEYINSLDAMARFKPEKLAFAH 217
                                    99999999999******************************99 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.2e-06     0.011      29      75 ..      53      99 ..      31     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-06
                                   .SEEEEE-SS--HHHHGGGGCCCCC--EEEE.EEEEHHHHHHCCTTCG CS
                  Lactamase_B_2 29 ppidaVllthaHyDHlaglltlrelrpkklp.lyapkgvlavleanfv 75
                                    ++  V+lth H DH   + ++ +  ++ ++ +y++++ ++++++   
  gi|118431758|ref|NP_148423.2| 53 VRLRYVILTHIHLDHASAAGSIVRSLDT-VEaVYVHPRGARHMADPER 99
                                   58999***********888888884443.44399**999999887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 00:00:00.38
# Mc/sec: 2374.89
//
Query:       gi|118431759|ref|NP_148424.2|  [L=248]
Description: hypothetical protein APE_2157.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2058.73
//
Query:       gi|118431760|ref|NP_148425.2|  [L=399]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-48  163.0   2.6    7.7e-48  162.5   2.6    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    8.7e-34  116.6   0.6    1.6e-33  115.7   0.1    1.8  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.7e-23   82.0   0.0      5e-23   81.1   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    3.9e-19   69.2   1.0    6.4e-19   68.6   1.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.063   12.9   0.0    1.8  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 !  162.5   2.6   2.1e-51   7.7e-48       2     149 ..     242     390 ..     241     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 162.5 bits;  conditional E-value: 2.1e-51
                                    BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH----- CS
                  Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdag 81 
                                    +Gf+v+ +t +++R+++aa+a+g+a++ +e al+ya +r+ fg+pli++q + +kla+m+ +leaarll+y aa ++d+g
  gi|118431760|ref|NP_148425.2| 242 EGFKVIVSTYDYTRIGIAAQAVGIAQASFEKALNYALQREVFGQPLIQFQMIIDKLANMYMKLEAARLLTYWAATLADKG 321
                                    8******************************************************************************* PP

                                    ---.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                  Acyl-CoA_dh_1  82 kpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                    k +  ++as+aK+fa+e+a+++a++a+q++Gg+G+  e++ver++rda +++i+eGt+eiqr++i r+l
  gi|118431760|ref|NP_148425.2| 322 KREfIVAASLAKAFATEAAEWIARQAIQIHGGYGVDPETGVERYLRDAIITTIYEGTNEIQRLTIVRQL 390
                                    *****************************************************************9986 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 !  115.7   0.1   4.5e-37   1.6e-33       1     112 [.      16     126 ..      16     127 .. 0.96
   2 ?   -3.6   0.0       4.8   1.7e+04      16      29 ..     332     345 ..     327     352 .. 0.52

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 4.5e-37
                                    THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                  Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80 
                                    tee+e +r+++ref+e ++ p+ +e++e++++p++++k++a+lG++g+ +peeygG+g++ l +a+++ee+ara  +l++
  gi|118431760|ref|NP_148425.2|  16 TEEHELFRKSIREFVESKVMPRWREIEETNRIPEDILKEAADLGIFGVGIPEEYGGQGGGHLMTALLTEEIARAVPALGV 95 
                                    89*************************999************************************************** PP

                                    HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                  Acyl-CoA_dh_N  81 llgvhsslvapailrfGteeqkrryLpklasg 112
                                    ++gv++   a +il fGteeqkr+y+ ++a+g
  gi|118431760|ref|NP_148425.2|  96 TIGVNHL-FAVPILLFGTEEQKRKYVTPIAQG 126
                                    ****765.5569******************99 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                                    HHHTHHHHHHHHHH CS
                  Acyl-CoA_dh_N  16 eeelaphaaewdee 29 
                                    ++  a  aaew ++
  gi|118431760|ref|NP_148425.2| 332 AKAFATEAAEWIAR 345
                                    44444445555433 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 !   81.1   0.0   1.4e-26     5e-23       3      97 .]     133     229 ..     131     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1.4e-26
                                    E---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS---...----EEEEEEE..GGGEEE--- CS
                  Acyl-CoA_dh_M   3 alTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpd...rarglslflvprdapgvsvrri 78 
                                    a TEp++Gsdva+++t +a++ +++yv+nG+K++i++a++a++++v ar +  p+   r  g+s+f+v++d+pg+++++ 
  gi|118431760|ref|NP_148425.2| 133 ANTEPTGGSDVAGIRT-TARKVNDHYVINGRKVFISGARDADYLVVSARtN-PPRedkRWWGISVFIVEKDMPGLKIGQQ 210
                                    78**************.77788889************************62.333467899****************999 PP

                                    --BSS-TTS-EEEEEEE.. CS
                  Acyl-CoA_dh_M  79 eeklGlrglptgelvfedv 97 
                                     + lG+rg + +e+ +edv
  gi|118431760|ref|NP_148425.2| 211 FKVLGMRGEQPYEVILEDV 229
                                    9*************99997 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 !   68.6   1.0   1.8e-22   6.4e-19       1     133 [.     256     379 ..     256     380 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.8e-22
                                    .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHH CS
                  Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedr 80 
                                    +giaa+a+G+A+a +++++ +a +r    +g++l +++++  +la++ ++l+AAr+l++ aa+     a++gk+   e  
  gi|118431760|ref|NP_148425.2| 256 IGIAAQAVGIAQASFEKALNYALQREV--FGQPLIQFQMIIDKLANMYMKLEAARLLTYWAATL----ADKGKR---EFI 326
                                    589************************..***********************************....777766...569 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                  Acyl-CoA_dh_2  81 aearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                      a++a+a+a+e a  +++++++++Gg++++ e  ++R++RDa ++++++++n
  gi|118431760|ref|NP_148425.2| 327 VAASLAKAFATEAAEWIARQAIQIHGGYGVDPETGVERYLRDAIITTIYEGTN 379
                                    9*************************************************998 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 ?   12.9   0.0   1.7e-05     0.063     180     269 ..     158     235 ..     111     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                                    EEEEEEEEEE-.--SSEEEE---SS-..TTSGGG..-EEEEEETT-TTEEEEE-------S..-TTT-TTTTT----EEE CS
                         HpaB_N 180 vVrGakvlaTgaaladeilvlptramlkeedkdy..avafavpvdapGlklicresfedkleesefdyplssrfdendal 257
                                    v++G kv+++ga  ad+++v    ++   edk++    +f+v+ d pGlk+  +++f+          ++    +e+   
  gi|118431760|ref|NP_148425.2| 158 VINGRKVFISGARDADYLVVSARTNP-PREDKRWwgISVFIVEKDMPGLKI--GQQFKV--------LGMR---GEQPYE 223
                                    9********************99888.555555533468***********8..455554........1222...566666 PP

                                    EEEEEEEEEGGG CS
                         HpaB_N 258 vvfDdVfVPwer 269
                                    v+++dV VP e+
  gi|118431760|ref|NP_148425.2| 224 VILEDVKVPAEN 235
                                    888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2988.83
//
Query:       gi|14601882|ref|NP_148426.1|  [L=489]
Description: hypothetical protein APE_2161 [Aeropyrum pernix K1]
Scores for 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  197.6   0.0    7.6e-58  197.1   0.0    1.0  1  Amidohydro_3  Amidohydrolase family
     0.0033   16.8   0.0       0.16   11.3   0.0    2.4  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 !  197.1   0.0   8.5e-62   7.6e-58       9     452 ..      52     472 ..      50     483 .. 0.87

  Alignments for each domain:
  == domain 1  score: 197.1 bits;  conditional E-value: 8.5e-62
                  Amidohydro_3   9 lvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwi.vgeGwdeaqfaeerfpyalaeldevle 88 
                                   ++lP++vD+H+H+ + g+ +r ++l +  ++s e+v +++++          i vg+Gw+e  f   +    +  ld  l 
  gi|14601882|ref|NP_148426.1|  52 FLLPPLVDAHLHMRSLGASFRIVNLKG--ASSPEEVAKRLAAANSP------IaVGRGWNEEEFRPGSRL-DRRILDSYLG 123
                                   789************************..**********9998887......99*************998.9********* PP

                  Amidohydro_3  89 dapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllreg.afhlvldlapl.areaeaaavaaala 167
                                   + p l+ ++++H+av+nsa +++ g ++  p+     +     +    gll e+    +v+ ++++ + e++++ +a ala
  gi|14601882|ref|NP_148426.1| 124 EKPALAVRICGHVAVANSAFIRESGVDKLFPN-----L----VDR-ERGLLLEDaVSYAVSVAMKTyNNEELLRDAASALA 194
                                   **********************9555544444.....3....333.46677777344444444466699999888888888 PP

                  Amidohydro_3 168 alasyGitsveagggnvsslddleplfeltaeeklplrvi...ikelldaaerlglplspgseeltigavklfadgvlgsr 245
                                     + +G+ s+       +s++++ +l  + ++  l +rv+     ++  +++r g       ++  i +vklfadg+lg+r
  gi|14601882|ref|NP_148426.1| 195 SVGVFGVSSM------ACSEEEVRALSLIGDA--LEVRVAcylRRGVEPPPKRAG-------ARWSIVGVKLFADGSLGGR 260
                                   8888888888......8888888888888888..678888775333334444444.......556699************* PP

                  Amidohydro_3 246 talltepyf.......tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrr.rlehaegvt 318
                                   ta+l +py        +g + +++ ++ae +  + +rgl  a+haigdaa+d+vl++f +a    g++    r+eha+   
  gi|14601882|ref|NP_148426.1| 261 TAYLRRPYIsgenegwRGLKLLSSRDIAEEAVSNSHRGLATAVHAIGDAALDEVLEGFSNA-ISRGVEPGMlRVEHASLAW 340
                                   *************8888888888999********************************888.4444444345********* PP

                  Amidohydro_3 319 esqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg 399
                                   ++qi+r+a+l+v   vqp f+  d++l+sr+g  + ++ +p++++l+agvk+al++Dapv+++dp+ ++ aav +      
  gi|14601882|ref|NP_148426.1| 341 PNQIDRLASLRVWTVVQPLFRVSDWWLESRVGSDMLQAAYPFASMLRAGVKLALSTDAPVETYDPAETFKAAVGLCSS--- 418
                                   **************************************************************************9998... PP

                  Amidohydro_3 400 evlrpdeelsleealalyTrgpAkalgledrk.GtLevGadADlvvldadpldv 452
                                   +++r++e l+ +e l+lyT ++A a g +    G+L+ Ga+A ++v + d l  
  gi|14601882|ref|NP_148426.1| 419 RLCRESESLTPRETLKLYTLNSALASGGPVAWlGRLRRGAPALFAVANVDVLNS 472
                                   9*****************************878*************99887765 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.0    0.0064        58       1      18 [.      52      66 ..      52      95 .. 0.73
   2 !   11.3   0.0   1.7e-05      0.16     231     317 ..     381     465 ..     377     485 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0064
                                  EEEE-EEEEEEECETTEC CS
                  Amidohydro_1  1 ivlPGlIDaHvHleqsll 18
                                  ++lP l+DaH+H +   +
  gi|14601882|ref|NP_148426.1| 52 FLLPPLVDAHLHMR---S 66
                                  689*********97...2 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT...TTHCHCHHHHHHHHHTHHHHHHTT-T.TTSSSS- CS
                  Amidohydro_1 231 alrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye...deegglslkealrmaTingAkalgld.dkvGsie 307
                                   +++ +l++Gvk +l+tD       +   e+ + a+    gl  +   +e   l++ e l+++T+n A a g +   +G++ 
  gi|14601882|ref|NP_148426.1| 381 PFASMLRAGVKLALSTDAPVETYDP--AETFKAAV----GLCSSrlcRESESLTPRETLKLYTLNSALASGGPvAWLGRLR 455
                                   578899***********66666666..67777777....3333347788999***************98885423578888 PP

                                   TTSB--EEEE CS
                  Amidohydro_1 308 vGkdADlvvv 317
                                    G +A ++v 
  gi|14601882|ref|NP_148426.1| 456 RGAPALFAVA 465
                                   8888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3842.65
//
Query:       gi|118431761|ref|YP_874929.1|  [L=73]
Description: hypothetical protein APE_2161a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   15.4   0.0      0.012   15.1   0.0    1.2  1  PRP4      pre-mRNA processing factor 4 (PRP4) like
  ------ inclusion threshold ------
       0.13   12.3   0.2       0.17   12.0   0.2    1.1  1  DUF962    Protein of unknown function (DUF962)
        0.2   11.4   2.8       0.44   10.3   2.8    1.5  1  DUF2157   Predicted membrane protein (DUF2157)
        2.9    8.4   8.7        1.5    9.3   1.9    2.1  2  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> PRP4  pre-mRNA processing factor 4 (PRP4) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.8e-06     0.012      11      24 ..      56      69 ..      53      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-06
                           PRP4 11 PitLFGEthadRre 24
                                   P+ LFGEt+a+ r+
  gi|118431761|ref|YP_874929.1| 56 PALLFGETPAAVRK 69
                                   9**********996 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.7e-05      0.17      24      75 ..      12      69 ..       4      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                         DUF962 24 Hfigvplilltvlllllrak......lklllalfvvgyifafvGHfvfEkrkPAlfkn 75
                                    ++gv lil+++   +++ +      ++  +a+++vg+++  +G +++ ++ PA +++
  gi|118431761|ref|YP_874929.1| 12 TVVGVLLILYAIYSGFVNETigstekFSADAAAMIVGWFAVLIGPALLFGETPAAVRK 69
                                   578888888888888877778888889999***********************99875 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   9.9e-05      0.44      40      97 ..       6      70 ..       1      72 [. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.9e-05
                        DUF2157 40 vlGalllglGlilfvAanW.....qglsrlvkfllllvll...llslllg.avlwrdrrvpprlgea 97
                                   + Gall ++G++l+ +a +     ++++ ++kf   ++++   ++++l+g a+l    + p+++++a
  gi|118431761|ref|YP_874929.1|  6 AAGALLTVVGVLLILYAIYsgfvnETIGSTEKFSADAAAMivgWFAVLIGpALLFG--ETPAAVRKA 70
                                   56888888888888888887777777888888865444441114555666566665..556666665 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.9   0.00033       1.5      41      63 ..       5      27 ..       2      32 .. 0.85
   2 ?    3.8   0.7     0.017        77      36      56 ..      40      60 ..      26      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00033
                         DUF202 41 kilglilivlgiltllvglvryl 63
                                   +++g++l v+g+l++l+++++ +
  gi|118431761|ref|YP_874929.1|  5 QAAGALLTVVGVLLILYAIYSGF 27
                                   689****************9866 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.017
                         DUF202 36 psalgkilglilivlgiltll 56
                                     a+++i+g++++++g ++l+
  gi|118431761|ref|YP_874929.1| 40 ADAAAMIVGWFAVLIGPALLF 60
                                   33456999**99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 639.23
//
Query:       gi|118431762|ref|NP_148427.2|  [L=602]
Description: carbon starvation protein A [Aeropyrum pernix K1]
Scores for 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-101  340.6  22.4     1e-101  340.6  22.4    1.6  2  CstA      Carbon starvation protein CstA
    2.4e-26   92.4   9.1    2.4e-26   92.4   9.1    3.2  4  CstA_5TM  5TM C-terminal transporter carbon starvation CstA
  ------ inclusion threshold ------
       0.09   12.6   0.6       0.56   10.0   0.6    2.4  1  Lig_chan  Ligand-gated ion channel


Domain annotation for each model (and alignments):
>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.6  22.4  1.7e-105    1e-101       4     350 ..       4     361 ..       1     376 [. 0.93
   2 ?   -3.4   0.5      0.58   3.5e+03     133     166 ..     532     571 ..     524     593 .. 0.49

  Alignments for each domain:
  == domain 1  score: 340.6 bits;  conditional E-value: 1.7e-105
                           CstA   4 vllvvvavvvfviayrfYgkfi.akkvlklddkraTPaerledgkdyvptnklvlfghhFasiagagPlvGpvlAaqfGy 82 
                                    +llv+v ++++++ay fYg+ i ++kv+++ ++r+TPa +  dg+dyvp++++vlfghhFasiagagP+vGp++A+ +G+
  gi|118431762|ref|NP_148427.2|   4 LLLVAVILAIYAVAYLFYGRNIlQEKVVRASPERETPAIAKFDGVDYVPAHRFVLFGHHFASIAGAGPIVGPAIAMAYGW 83 
                                    678888999**********975389******************************************************* PP

                           CstA  83 lPgllWilvGavfagavhDfvvlvasvrrkgkslgelakkelgkvakllallaillililvlavlalvvvkalaespaav 162
                                    l  l+W+l+G+vf+gavhD+++l+asvr  g s+ ++ ++ +g++a+ l+l+ +l++lilv a++a + ++ +a+ p  +
  gi|118431762|ref|NP_148427.2|  84 LLPLVWVLFGNVFMGAVHDYLSLMASVRYGGISIVSVGENLMGRKARYLFLIYVLFTLILVYAAFASIAASLFARDPRVA 163
                                    ******************************************************************************** PP

                           CstA 163 fsviltipialllGvllrklrkgvleasvigvvllllavvvgseveealaell..........tlsketlaivlivYvfv 232
                                    + +il++p+alllG++++++  g+  ++vi+vvl+++a+v++ +    +  ++           ++ + ++i+l +Y ++
  gi|118431762|ref|NP_148427.2| 164 TLSILFMPLALLLGIMMYRMGLGMGPSTVITVVLVIAAFVYSYNH-GIVIGTFdpslppgeggWVAYHRWVIILGLYALL 242
                                    ***************************************998876.223333355678999989999************* PP

                           CstA 233 AsvlPvwlllaPrdYlstflligtivllal.gilvvapelklpavtefvdgegpvfagslfPllfitiACGaiSGFHslv 311
                                    A+ lPvw ll+PrdYl++++l +++ l+a+ +il+ + +lk pa+t+f         ++++P + + iACG++SGFHslv
  gi|118431762|ref|NP_148427.2| 243 AASLPVWYLLQPRDYLNAYILWTGLGLAAIaAILLGTQSLKGPAYTSFQPNIIAGQPTPFWPAIPLIIACGSLSGFHSLV 322
                                    ************************98887736888999**********66555556678********************* PP

                           CstA 312 ssgttskllekesdarlvgygamllEslvailalvaaav 350
                                    +sgttsk+l+ e da +vgygamllE+ ++ la+++ ++
  gi|118431762|ref|NP_148427.2| 323 ASGTTSKQLASELDALFVGYGAMLLEGALSGLAVIIPIS 361
                                    *****************************9999987655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.58
                           CstA 133 llaillililvlavlalvvvkal......aespaavfsvi 166
                                    ll +l++ + v+a l++  +  l      ++ +a++++++
  gi|118431762|ref|NP_148427.2| 532 LLPSLFLWVTVTAGLTWWLMVILpvlpaiQQFGAGSMILF 571
                                    5555555566666655544433333332233333333333 PP

>> CstA_5TM  5TM C-terminal transporter carbon starvation CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.61   3.6e+03      55      74 ..      80      93 ..      21      95 .. 0.67
   2 ?   -2.5   0.3       1.1   6.5e+03      86      93 ..     149     156 ..     117     182 .. 0.57
   3 ?   -2.7   1.3       1.3   7.5e+03     114     114 ..     180     180 ..     134     210 .. 0.58
   4 !   92.4   9.1   3.9e-30   2.4e-26       2     114 ..     412     543 ..     411     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.61
                       CstA_5TM 55 alavllllwggintlWplFG 74
                                   a +     w  +  +W lFG
  gi|118431762|ref|NP_148427.2| 80 AYG-----W-LLPLVWVLFG 93
                                   222.....2.2567888888 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                       CstA_5TM  86 lvvtvwll 93 
                                    + +++ l+
  gi|118431762|ref|NP_148427.2| 149 ASIAASLF 156
                                    22333333 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.3
                       CstA_5TM 114 l 114
                                    +
  gi|118431762|ref|NP_148427.2| 180 M 180
                                    1 PP

  == domain 4  score: 92.4 bits;  conditional E-value: 3.9e-30
                       CstA_5TM   2 avaytfailfvalfalTtlDtatRlaRyilqellgelk......kkaltnkyvatliavalavll......llwg..... 64 
                                    ++ + fa l++++++lTtlDt+tRlaR+++qel+++l+      ++ +tnk+v++l++v+++ +l      +  g     
  gi|118431762|ref|NP_148427.2| 412 SFFTLFASLMLSMYVLTTLDTGTRLARFAWQELFDWLAnvdknlYSIVTNKWVSSLAVVIIGSALaypvleI--Gagyka 489
                                    57899*******************************998755544449*****************5555440..156677 PP

                       CstA_5TM  65 gintlWplFGaaNQlLAalaLlvvtvwll.ktgr...kalvtliPmvfmlvvtl 114
                                    ++n++Wp+F+ aNQ+LAa+aLl+ ++w++   +      l++l+P +f++v+++
  gi|118431762|ref|NP_148427.2| 490 AYNVVWPAFAGANQMLAAIALLTSALWVYgVLNVrggTGLLILLPSLFLWVTVT 543
                                    9***************************976555677999999*******9875 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   9.5e-05      0.56      64      99 ..     122     157 ..      99     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lig_chan  64 esprsvsgRivvavWwffvlillssYtAnLaafltv 99 
                                    e+     +R + +++++f+lil+ +  A++aa l  
  gi|118431762|ref|NP_148427.2| 122 ENLMGRKARYLFLIYVLFTLILVYAAFASIAASLFA 157
                                    66677789************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.36
# Mc/sec: 4944.80
//
Query:       gi|14601884|ref|NP_148428.1|  [L=107]
Description: hypothetical protein APE_2163 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 845.42
//
Query:       gi|118431763|ref|NP_148429.2|  [L=123]
Description: arsenical pump-driving ATPase, partial [Aeropyrum pernix K1]
Scores for complete 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   52.7   0.0    3.9e-14   52.5   0.0    1.1  1  ArsA_ATPase   Anion-transporting ATPase
      5e-07   29.8   0.2    8.2e-07   29.1   0.2    1.5  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    2.6e-06   27.5   0.0      3e-06   27.3   0.0    1.2  1  AAA_31        AAA domain
    0.00074   19.0   0.6      0.001   18.6   0.6    1.2  1  ParA          NUBPL iron-transfer P-loop NTPase
     0.0017   17.6   0.0     0.0026   17.1   0.0    1.2  1  Zeta_toxin    Zeta toxin
     0.0045   16.9   0.0     0.0058   16.5   0.0    1.1  1  APS_kinase    Adenylylsulphate kinase
  ------ inclusion threshold ------
      0.015   15.9   0.7      0.016   15.7   0.7    1.3  1  AAA_18        AAA domain
      0.032   13.6   0.0      0.045   13.1   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.047   14.1   1.7      0.077   13.4   1.7    1.4  1  AAA_16        AAA ATPase domain
      0.053   12.8   0.1      0.068   12.4   0.1    1.2  1  MipZ          ATPase MipZ
      0.065   12.4   0.7      0.094   11.9   0.7    1.3  1  NB-ARC        NB-ARC domain
      0.073   13.0   0.1        0.1   12.5   0.1    1.4  1  NTPase_1      NTPase
      0.075   13.1   0.1       0.18   11.9   0.1    1.7  1  AAA_14        AAA domain
      0.095   12.4   0.1       0.12   12.1   0.1    1.3  1  AAA_24        AAA domain
        0.1   11.6   0.4       0.13   11.2   0.4    1.2  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.18   11.3   0.0       0.18   11.3   0.0    1.2  1  CBP_BcsQ      Cellulose biosynthesis protein BcsQ


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   3.5e-17   3.9e-14       3      88 ..      13      97 ..      11     114 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 3.5e-17
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHCCHHGGG CS
                    ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakqevqkee 84
                                   v++v+GKGGVGKttvs  +++ ls+ g+ +l+is+D A  l   +d +  + +  v+  L+a+  d+  ++++  +e +  +
  gi|118431763|ref|NP_148429.2| 13 VVFVTGKGGVGKTTVSILLGTLLSRVGE-TLVISLDQAKHLKEYLDLEDVNRVYNVRGGLYAMQFDTGRDIDRLSSEYMMLM 93
                                   89************************96.89*******************************************99999988 PP

                                   SCCH CS
                    ArsA_ATPase 85 eall 88
                                   ++++
  gi|118431763|ref|NP_148429.2| 94 KRIM 97
                                   8876 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 !   29.1   0.2   7.3e-10   8.2e-07       1      55 [.      13      81 ..      13     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.3e-10
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................C CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................x RF
                           CbiA  1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................d 55
                                   ++++ +kGGvGKTt+++ L+++l+r   ++l++ +D    + ++   + +d+++                 d
  gi|118431763|ref|NP_148429.2| 13 VVFVTGKGGVGKTTVSILLGTLLSR-VGETLVISLDQAKHLKEY--LDLEDVNRvynvrgglyamqfdtgrD 81
                                   57899********************.778899999988777764..33333333345666666666666663 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.7e-09     3e-06       4      54 ..      13      62 ..      11     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.7e-09
                         AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne 54
                                   ++++  KGGvGKTT s+ l+  l++ g+ +L++ lD  + +  +l++e  +
  gi|118431763|ref|NP_148429.2| 13 VVFVTGKGGVGKTTVSILLGTLLSRVGE-TLVISLDQAKHLKEYLDLEDVN 62
                                   678899*******************997.79*****988888877775444 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 !   18.6   0.6   9.2e-07     0.001       6      35 ..      13      42 ..      10      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.2e-07
                           ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkv 35
                                   ++ + gKGGVGK+tv++ l + L++ g + 
  gi|118431763|ref|NP_148429.2| 13 VVFVTGKGGVGKTTVSILLGTLLSRVGETL 42
                                   45578******************9988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.3e-06    0.0026      13      61 ..       8      55 ..       3      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                     Zeta_toxin 13 qerPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPey 61
                                   +  P ++++ G  G GK++++ ll + l r g+ ++++ D+ + l  ey
  gi|118431763|ref|NP_148429.2|  8 GAGPHVVFVTGKGGVGKTTVSILLGTLLSRVGETLVISLDQAKHLK-EY 55
                                   477**************************************99875.55 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.2e-06    0.0058       3      61 ..      12      68 ..      10      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.2e-06
                                   EEEEEESSTTSSHHHHHHHHHHHHHHTT.--EEEEEHHHHTTTTTTT--SSHHHHHHHHH CS
                     APS_kinase  3 vvvwltGlsgsGKstianalekkLvekg.isvylLdGdnvRhgLnkdLgfseedRkenir 61
                                    vv++tG  g GK+t++  l + L + g + v+ Ld     ++L++ L  ++ +R  n+r
  gi|118431763|ref|NP_148429.2| 12 HVVFVTGKGGVGKTTVSILLGTLLSRVGeTLVISLDQ--A-KHLKEYLDLEDVNRVYNVR 68
                                   79*******************9999999445555654..3.5688888888888888887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.7   1.4e-05     0.016       1      25 [.      14      49 ..      14     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.4e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf..........g 25
                                   +++tG+ GvGKtt++  L  +l  +           
  gi|118431763|ref|NP_148429.2| 14 VFVTGKGGVGKTTVSILLGTLLsRVgetlvisldqA 49
                                   79**************99776622254443333331 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     4e-05     0.045      19      60 ..       8      49 ..       4      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                   Mg_chelatase 19 aaGgHnlllvGppGsGKtmlakrlpsllpplseeealevaki 60
                                    aG H ++++G  G GKt +   l +ll+++ e+ ++   + 
  gi|118431763|ref|NP_148429.2|  8 GAGPHVVFVTGKGGVGKTTVSILLGTLLSRVGETLVISLDQA 49
                                   59**************************99988777666555 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   1.7   6.8e-05     0.077      21      41 ..       7      28 ..       2      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                         AAA_16 21 sgrp.elvllsGesGvGKsslv 41
                                   sg + ++v+++G  GvGK+++ 
  gi|118431763|ref|NP_148429.2|  7 SGAGpHVVFVTGKGGVGKTTVS 28
                                   555569**************86 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.1e-05     0.068       3      39 ..      13      48 ..      11      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.1e-05
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--T CS
                           MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldl 39
                                   +v+   kGG Gk+t+++ + + L++ G    +i ld 
  gi|118431763|ref|NP_148429.2| 13 VVFVTGKGGVGKTTVSILLGTLLSRVGETL-VISLDQ 48
                                   899999*******************99875.566765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   8.4e-05     0.094      20      36 ..      11      27 ..       4      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                                   SEEEEEEESTTSSHHHH CS
                         NB-ARC 20 slvvalvGmgGvGKttl 36
                                     vv++ G+gGvGKtt+
  gi|118431763|ref|NP_148429.2| 11 PHVVFVTGKGGVGKTTV 27
                                   459*************7 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.2e-05       0.1       2      17 ..      14      29 ..      13      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.2e-05
                                   EEEE--TTSSHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvk 17
                                   vf+TG+ GvGKtT+  
  gi|118431763|ref|NP_148429.2| 14 VFVTGKGGVGKTTVSI 29
                                   8************865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00016      0.18       3      56 ..      12      65 ..      10     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk.ladpeklleli 56
                                   +++++tG   vGKTt+   l  +ll +  ++l i+ld+ +  k + d e++++++
  gi|118431763|ref|NP_148429.2| 12 HVVFVTGKGGVGKTTVSILLG-TLLSRVGETLVISLDQAKHLKeYLDLEDVNRVY 65
                                   6899***********976665.666577899******988854155666666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00011      0.12       4      40 ..      13      55 ..      11     117 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                         AAA_24  4 kiliyGpsgiGKTtlakel......gpkplfidtekGlkslda 40
                                    ++++G+ g+GKTt+   l        ++l+i +++  +  + 
  gi|118431763|ref|NP_148429.2| 13 VVFVTGKGGVGKTTVSILLgtllsrVGETLVISLDQAKHLKEY 55
                                   5789**********99888888888899999966653333333 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 ?   11.2   0.4   0.00012      0.13      27      65 ..      10      46 ..       1      55 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                   S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE CS
                           MeaB 27 GraqvvGltGvPGaGkstlvealglelrrrGkrvavlav 65
                                   G  +vv +tG  G+Gk t+   lg+ l r G+   v+++
  gi|118431763|ref|NP_148429.2| 10 G-PHVVFVTGKGGVGKTTVSILLGTLLSRVGETL-VISL 46
                                   3.58999***********9999999999999875.5555 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.18      10      41 ..      19      49 ..      11      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                       CBP_BcsQ 10 RGGvGttsllaaLawalhelgesvlviDlspd 41
                                   +GGvG+t+++  L++ l ++ge  lvi l  +
  gi|118431763|ref|NP_148429.2| 19 KGGVGKTTVSILLGTLLSRVGET-LVISLDQA 49
                                   8********************97.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 998.34
//
Query:       gi|14601886|ref|NP_148430.1|  [L=197]
Description: arsenical pump-driving ATPase, partial [Aeropyrum pernix K1]
Scores for 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-27   94.5   0.0    7.2e-27   94.4   0.0    1.0  1  ArsA_ATPase  Anion-transporting ATPase
  ------ inclusion threshold ------
       0.17   11.3   0.1        1.2    8.5   0.0    2.0  2  ParA         NUBPL iron-transfer P-loop NTPase


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0     8e-31   7.2e-27     113     288 ..       3     176 ..       1     190 [. 0.87

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 8e-31
                                   HHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHH CS
                   ArsA_ATPase 113 feellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsplakqlvkllglggvsieealeeleetkee 193
                                   + ++l++++++ + +vv+Dt+PTG tlr+lslp+    +le l+ ++e + +l   + + +g      + +l++l+e+ ++
  gi|14601886|ref|NP_148430.1|   3 LRKILELYRDSRFKYVVVDTPPTGLTLRILSLPRLYTFWLESLIGIRERIVSLRYVIARSIGREPEMDDPVLDKLREMQDR 83 
                                   67889999*************************************************9988777777779*********** PP

                                   HHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHH CS
                   ArsA_ATPase 194 ikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeqenCeflearkkiqkkylkeieel 274
                                   + k+++ l + ertsf++V +pE l+++E ++ ++ L+++g k   ++vN++lp+e ++         ++q+k l+e++  
  gi|14601886|ref|NP_148430.1|  84 YAKLSNDLVERERTSFAIVATPEPLPVYEARKTVEFLESMGAKPSIIVVNRILPAEIASRLG----VLEVQSKALNELRTR 160
                                   *********************************************************97444....456777777777665 PP

                                   T..TTSEEEEEE--SS CS
                   ArsA_ATPase 275 f..edlevvklpllee 288
                                      ++ ++v++p++e+
  gi|14601886|ref|NP_148430.1| 161 VcrKPCVLVEIPMVET 176
                                   4225667777787765 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 ?    0.9   0.0     0.029   2.6e+02     110     122 ..      13      25 ..       1      33 [. 0.72
   2 ?    8.5   0.0   0.00013       1.2     137     173 ..      97     133 ..      82     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.029
                          ParA 110 gelDyLiiDlPPG 122
                                   +   y+++D+PP 
  gi|14601886|ref|NP_148430.1|  13 SRFKYVVVDTPPT 25 
                                   45569*******4 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00013
                          ParA 137 agaviVttpqevaladvkkaiemfkkvkvkvlGvveN 173
                                   +   iV+tp+ + + +++k++e+++++ +k   +v N
  gi|14601886|ref|NP_148430.1|  97 TSFAIVATPEPLPVYEARKTVEFLESMGAKPSIIVVN 133
                                   56789**********************9988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1691.10
//
Query:       gi|14601887|ref|NP_148431.1|  [L=900]
Description: alanyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-114  383.6   0.0   1.9e-114  383.2   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.5e-21   77.3   4.1    3.5e-21   76.1   4.1    1.7  1  DHHA1         DHHA1 domain
    2.3e-15   56.4   0.2    4.8e-15   55.4   0.2    1.6  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
  ------ inclusion threshold ------
       0.09   12.0   0.0       0.17   11.1   0.0    1.3  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit


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 !  383.2   0.0  4.3e-118  1.9e-114       1     552 []      48     579 ..      48     579 .. 0.94

  Alignments for each domain:
  == domain 1  score: 383.2 bits;  conditional E-value: 4.3e-118
                                   HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTS.S CS
                  tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGkt.a 80 
                                   e re+Fl+fFek+gHt+v+  +vv++++++l++++A+++ f+p ++++   p+++++v+sQ++iR++    D++nVG+t +
  gi|14601887|ref|NP_148431.1|  48 EAREAFLSFFEKHGHTRVPPRPVVARWREDLYLTIASIVVFQPHVTSGLVPPPANPLVISQPSIRLE----DIDNVGITiG 124
                                   569****************************************************************....*******978 PP

                                   S--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHH CS
                  tRNA-synt_2c  81 rHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekd 154
                                   rH+T FeM+++++f+      Y+kee++ +a+e++t++lg+++e ++++++++++  +a++ +e  vg+ e ++l+f   +
  gi|14601887|ref|NP_148431.1| 125 RHLTSFEMAAHHAFNypdrqVYWKEETVRLAFEFFTQVLGIPPELIVFKESWWEGggNAGPSFEVAVGGLELATLVF---M 202
                                   ******************************************************999********************...* PP

                                   HEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHH CS
                  tRNA-synt_2c 155 nfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavL 235
                                   +++ +   ++++p +++++++g e+ ++  +++++a  +++  +++   ++ ++e + +++ + +  +++G  + +  + L
  gi|14601887|ref|NP_148431.1| 203 KYRVVDGRYEEIPLKIVDTGYGVERLAWFTQKTPTAFHAIYGSLVDDFRRMLGVE-KPDENVMWAAFRVAGFLDPEDPESL 282
                                   *****************************************************99.88999999***************** PP

                                   TTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHHHHHTT CS
                  tRNA-synt_2c 236 qevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrhakkLg 316
                                   ++  + +++  +  v+   + ++          + +l+ + DH++++a +l+dG+vpsn+g+gY++R+++Rra+r ++ L+
  gi|14601887|ref|NP_148431.1| 283 RNYYQTVASLAGGDVETVRSILTR---------EARLYSVLDHTKTIALMLGDGIVPSNSGEGYLARLVVRRALRQLSLLN 354
                                   ********9999999888888877.........789********************************************* PP

                                   -SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHHHHHCHXXX CS
                  tRNA-synt_2c 317 lkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafkLydtyGfP 397
                                   ++ + l +lv+ ++++    +p+lke+ +++ ++++ EeerF+  l++ ++++e+++k+   kk l  +d+++Lyd+ G+P
  gi|14601887|ref|NP_148431.1| 355 AEVP-LVDLVERQARFWMRDFPQLKENLDYILDAVSLEEERFRDVLRKARSIVERELKR---KKRLGVDDLIRLYDSMGVP 431
                                   ****.99*************************************************997...889**************** PP

                                   HHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEE CS
                  tRNA-synt_2c 398 vdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdkefvee 478
                                   +++ +eia+++g+ v+++ ++++++++r+r  ++ ++ +   +++   +++++    +g ++      + +    k  +++
  gi|14601887|ref|NP_148431.1| 432 PEIAAEIAASRGAPVEVPHNFYSLVAARHRGPEKIRGYG--FDETGLPRDVEEWARRFGETR----RVFHEDPYAKAWKAR 506
                                   *******************************98888877..233333344444433333333....33333466789999* PP

                                   EEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHHH CS
                  tRNA-synt_2c 479 veegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdeer 552
                                   v  ++  ++v d+T fY+++GGqi D+G+i+ ++++ r+ dvqk++  ++h+++ e    + gd+v++e+d+er
  gi|14601887|ref|NP_148431.1| 507 VLGVKGRYLVADSTIFYPTGGGQIHDTGVIRVNNQQYRIIDVQKVGDAIVHVAERE-IAAEPGDEVWMEIDWER 579
                                   *******************************************************8.9*************986 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   4.1   7.9e-25   3.5e-21       2     137 ..     758     898 ..     757     899 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 7.9e-25
                                   HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECT. CS
                         DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegd. 81 
                                   + l + +++++++l+++++ + k  +e+++++a++v+gvkvl++e+  e+d+++++++  kl s++++ ++++v+++eg+ 
  gi|14601887|ref|NP_148431.1| 758 KGLIASLEQAREDLKRYRDYWVKTIEEAYISRARRVNGVKVLAVES-LEKDRRTVQEILRKLTSRHEDLIAALVVENEGNt 837
                                   6688999***************************************.********************************** PP

                                   EEEEEEEESSH.SS-HHHHHHHHHHHTTCCEEEE.TCEEE...EEEEHCHHHHHHHHHHHH CS
                         DHHA1  82 kvkvsarskkd.gvdagelakeaaaklgggGGGH.dlAaG...agipaekleealealeea 137
                                   +v + a+ k++ +vd+g+l+k +++k+gg+GGG+   A+    ++++a+k+ee+l+++ e 
  gi|14601887|ref|NP_148431.1| 838 QVEIAAGPKAAeKVDLGALVKIVIKKVGGRGGGRgSYASLrveGRLSADKVEELLADALEN 898
                                   *********99***********************8888777778888*********99875 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 !   55.4   0.2   1.1e-18   4.8e-15       1      44 []     678     721 ..     678     721 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.1e-18
                                   EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                      tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                   +r+v+++d++ve+C GtHv+nTgeIg fki+s ++i++g+ R++
  gi|14601887|ref|NP_148431.1| 678 LRLVFVEDWDVEACFGTHVRNTGEIGGFKIISYSRIQDGVVRLE 721
                                   69****************************************86 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 ?   11.1   0.0   3.8e-05      0.17     107     177 ..     171     243 ..     154     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                                   EEEEEEEEEGGGTEEEEEEEEEETTCEEEEEEEEE.EETTEE-SS--EEE...EEEHHHHHHHHCT-SSGGG-EC CS
                  tRNA-synt_2e 107 rfveDdWesptlGawGlGwevwldGmeitqftYfq.qvgglelkpvsvei...tyGleRlamylqevdnvydlew 177
                                    f e  We    G  G  +ev + G+e++ + +++ +v     ++++  i    yG+eRla + q++ + +   +
  gi|14601887|ref|NP_148431.1| 171 VFKESWWEG--GGNAGPSFEVAVGGLELATLVFMKyRVVDGRYEEIPLKIvdtGYGVERLAWFTQKTPTAFHAIY 243
                                   566666664..5899**************9999874465555666654442227***********9987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (900 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.38
# Mc/sec: 7026.76
//
Query:       gi|14601888|ref|NP_148432.1|  [L=111]
Description: 50S ribosomal protein L12 [Aeropyrum pernix K1]
Scores for complete 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   57.1  22.4    2.5e-15   56.8  22.4    1.1  1  Ribosomal_60s    60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.016   14.2   0.0      0.018   14.1   0.0    1.1  1  DEC-1_N          DEC-1 protein, N-terminal region
      0.017   15.0   0.1      0.025   14.4   0.1    1.4  1  EF-hand_8        EF-hand domain pair
       0.03   14.6   1.9      0.043   14.1   1.9    1.3  1  Imm5             Immunity protein Imm5
      0.031   14.3   8.5       0.87    9.6   0.2    2.2  2  PepSY_2          Peptidase propeptide and YPEB domain
      0.037   14.9   2.0      0.061   14.2   2.0    1.3  1  WRNPLPNID        Putative WW-binding domain and destruction b
      0.099   12.6   7.6       0.12   12.3   7.6    1.2  1  Spore_coat_CotO  Spore coat protein CotO
       0.11   12.8   0.0       0.18   12.1   0.0    1.4  1  DUF1376          Protein of unknown function (DUF1376)
       0.21   11.6   6.2       0.26   11.3   6.2    1.2  1  Band_7           SPFH domain / Band 7 family
       0.29    9.7   2.3       0.31    9.6   2.3    1.0  1  AMP-binding      AMP-binding enzyme
       0.35   11.1   3.1       0.45   10.7   3.1    1.2  1  Flavodoxin_1     Flavodoxin
       0.57   10.8   5.7       0.84   10.3   5.7    1.2  1  DUF3824          Domain of unknwon function (DUF3824)
        4.2    5.7   5.7        4.7    5.6   5.7    1.1  1  Cytomega_UL84    Cytomegalovirus UL84 protein


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8  22.4   1.8e-18   2.5e-15       2      88 .]      22     109 ..      21     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.8e-18
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--S. CS
                 Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedd. 81 
                                   +++e++kk  +a g +v++a++k lv++le++++ee+l+++ a+   aaaaaa+aaa+aa+++a+eekk+eeee+ ee+  
  gi|14601888|ref|NP_148432.1|  22 IDEETLKKAAEAIGMQVDEAKIKMLVASLEEVNLEEVLKQAVAA-PVAAAAAAPAAAPAAEEKAEEEKKEEEEEKKEEEVd 101
                                   899**************************************988.344455555555555555555555555555455551 PP

                                   S--.STTT CS
                 Ribosomal_60s  82 dmG.fgLF 88 
                                     G  g+F
  gi|14601888|ref|NP_148432.1| 102 LSGlSGMF 109
                                   55666666 PP

>> DEC-1_N  DEC-1 protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.018      91     138 ..      33      84 ..      19     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                       DEC-1_N  91 dlgpqvGaalqsl....lplqsldgllGaaapapalaaapppapapvpddpa 138
                                    +g qv +a  ++    l   +l+++l +a  ap+ aaa  pa ap++++ a
  gi|14601888|ref|NP_148432.1|  33 AIGMQVDEAKIKMlvasLEEVNLEEVLKQAVAAPVAAAAAAPAAAPAAEEKA 84 
                                   555555544333323223445789***********************98876 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.8e-05     0.025       2      32 ..      19      47 ..      18      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                     EF-hand_8  2 kgkItreelrrilrilglkkglseeevdilf 32
                                  +gkI+ e+l++++ ++g++  + e ++ +l+
  gi|14601888|ref|NP_148432.1| 19 GGKIDEETLKKAAEAIGMQ--VDEAKIKMLV 47
                                  8************666***..9999988876 PP

>> Imm5  Immunity protein Imm5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.9   3.1e-05     0.043      73     144 ..      37     105 ..      11     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-05
                          Imm5  73 ktdkeeiekeadklsndlendsgeeaeetvalaglaAlkvivtliysietdaesil.eeddyldeddfDpesw 144
                                   ++d+ +    ++ l   le+ + ee  +++++a++aA+ ++  ++ ++e +ae+   ee+++++e+++D   +
  gi|14601888|ref|NP_148432.1|  37 QVDEAK----IKMLVASLEEVNLEEVLKQAVAAPVAAAAAAPAAAPAAEEKAEEEKkEEEEEKKEEEVDLSGL 105
                                   444444....4445557778779999999999*************999**99999988899999999998765 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 ?    9.6   0.2   0.00063      0.87      30      51 ..      22      43 ..      17      46 .. 0.90
   2 ?    7.3   3.5    0.0033       4.5       5      30 ..      65      92 ..      61     103 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00063
                       PepSY_2 30 lpreklvakleaqGykvkkiev 51
                                  +++e+l++ +ea G++v+++++
  gi|14601888|ref|NP_148432.1| 22 IDEETLKKAAEAIGMQVDEAKI 43
                                  689*****************98 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0033
                       PepSY_2  5 alalallaaaAlA..grrdtdspkadwl 30
                                  a ++a++aa+A A  ++++ +++k+++ 
  gi|14601888|ref|NP_148432.1| 65 APVAAAAAAPAAApaAEEKAEEEKKEEE 92
                                  3344444455555324444444444433 PP

>> WRNPLPNID  Putative WW-binding domain and destruction box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.0   4.4e-05     0.061      14      60 ..      48      99 ..      45     108 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                     WRNPLPNID 14 Peidl.eLeeLllldse...aeessege.svdedeeaeeeeeeeeeeedeed 60
                                  +++++  Lee l++      a  + ++      +e+aeee++eeeee++ee+
  gi|14601888|ref|NP_148432.1| 48 ASLEEvNLEEVLKQAVAapvAAAAAAPAaAPAAEEKAEEEKKEEEEEKKEEE 99
                                  5789999999998766688733333333333333333333333333333332 PP

>> Spore_coat_CotO  Spore coat protein CotO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   7.6   8.4e-05      0.12      49      99 ..      51     101 ..      21     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
               Spore_coat_CotO  49 eekkpekaveeeveqekkkeaaePaeqeeeekaeeeekkeeeeqkeeeeek 99 
                                   ee + e+ +++ v  + ++ aa Pa +   e++ eeekkeeee+k+eee +
  gi|14601888|ref|NP_148432.1|  51 EEVNLEEVLKQAVAAPVAAAAAAPAAAPAAEEKAEEEKKEEEEEKKEEEVD 101
                                   455556667777888888888999988888888888888888888888766 PP

>> DUF1376  Protein of unknown function (DUF1376)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.18      19      59 ..       2      43 ..       1      67 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                       DUF1376 19 aeehgaYllLldlyyategpip.dDdkklarlagasteewra 59
                                  a+e +aY+ L  ++y  +g i+ +  kk+a ++g++++e + 
  gi|14601888|ref|NP_148432.1|  2 AQEGKAYIHLALAIYYAGGKIDeETLKKAAEAIGMQVDEAKI 43
                                  68999*****************5556999*******877642 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.2   0.00019      0.26     118     177 ..      24      87 ..      11      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                        Band_7 118 eelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaeaea.........qaeiaraeae 177
                                   ee  +++++++  q+++  + +l ++++++++++ ++qa+aa  aa a a         +     ae+e
  gi|14601888|ref|NP_148432.1|  24 EETLKKAAEAIGMQVDEAKIKMLVASLEEVNLEEVLKQAVAAPVAAAAAApaaapaaeeK-----AEEE 87 
                                   556678888899999********************************9999988665432.....2222 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.3   0.00022      0.31      59     152 ..       7      96 ..       1     106 [. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCH CS
                   AMP-binding  59 ewvvallailkaGavvvplnptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelke 139
                                    ++ ++lai +aG+ +     +  ae++ ++++++++k+l+a  ++ +le++l++a + ++ ++     a+++++e +++e
  gi|14601888|ref|NP_148432.1|   7 AYIHLALAIYYAGGKIDEETLKKAAEAIGMQVDEAKIKMLVASLEEVNLEEVLKQAVAAPVAAAAAAPAAAPAAEE-KAEE 86 
                                   678889999999999999999999*****************42233335666665554433333333333232222.2222 PP

                                   CCCCSCTTS-TSC CS
                   AMP-binding 140 eeeseekaekpee 152
                                   e+++ee+   +++
  gi|14601888|ref|NP_148432.1|  87 EKKEEEE---EKK 96 
                                   2222211...112 PP

>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.1   0.00032      0.45      11      95 ..      28     111 .]      23     111 .] 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                                   HHHHHHHHHHHHHTTTEEEEEEEEGTTSC..GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHHHCHHGCCSTTTTEE CS
                  Flavodoxin_1  11 eklAkqlaeelgehgfnadvvslsdydes..lseieeealllvvtsTfgnGdppengesffqdllelkgdeledgdlsgvr 89 
                                   +k A++++ +++e++++  v sl++++ +  l++  +  +++  ++++    ++e++e+++ +++e+  +++e++dlsg++
  gi|14601888|ref|NP_148432.1|  28 KKAAEAIGMQVDEAKIKMLVASLEEVNLEevLKQAVAAPVAAAAAAPAAAPAAEEKAEEEKKEEEEE--KKEEEVDLSGLS 106
                                   689************************6555555555555555555566556666666333333333..3478899**997 PP

                                   EEEEEE CS
                  Flavodoxin_1  90 favfgl 95 
                                     +fg+
  gi|14601888|ref|NP_148432.1| 107 -GMFGF 111
                                   .57775 PP

>> DUF3824  Domain of unknwon function (DUF3824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.7   0.00061      0.84      10      45 ..      64      99 ..      59     105 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00061
                       DUF3824 10 AeaalaaggaglAaheyakrrerkkaerererrree 45
                                  A+  +aa++a  Aa  ++++ e+ k+e+e+e+++ee
  gi|14601888|ref|NP_148432.1| 64 AAPVAAAAAAPAAAPAAEEKAEEEKKEEEEEKKEEE 99
                                  443344444444444444444444445555544333 PP

>> Cytomega_UL84  Cytomegalovirus UL84 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.7    0.0034       4.7     143     173 ..      71      99 ..      37     104 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0034
                 Cytomega_UL84 143 qtapatsqeeetaashepekkkekeekkeee 173
                                    +apa++   e     e ekk e eekkeee
  gi|14601888|ref|NP_148432.1|  71 AAAPAAAPAAEE--KAEEEKKEEEEEKKEEE 99 
                                   223333322222..23455666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2064  (0.115121); expected 358.6 (0.02)
Passed bias filter:                      965  (0.0538234); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 875.82
//
Query:       gi|118431764|ref|NP_148433.2|  [L=341]
Description: acidic ribosomal protein P0 [Aeropyrum pernix K1]
Scores for complete 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   70.0   0.9    5.8e-19   68.1   0.1    2.3  3  Ribosomal_L10  Ribosomal protein L10
    6.7e-16   58.1   0.0    1.8e-15   56.7   0.0    1.8  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
     0.0048   17.5  17.0      0.015   15.8  17.0    1.9  1  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.1   9.7e-23   5.8e-19       3      97 ..      15     111 ..      13     113 .. 0.95
   2 ?   -1.3   0.0      0.41   2.4e+03      39      60 ..     149     170 ..     144     171 .. 0.78
   3 ?   -2.5   0.0         1     6e+03      51      64 ..     249     262 ..     244     288 .. 0.56

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 9.7e-23
                                    CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S...SCGCCSSSE CS
                  Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek...lkellkgpv 79 
                                    +e+K+ +++el+el++k+++v+++d++g ++  +q +Rkkl ++ + ++v+K++++ rA++ +g e +   l++l++g++
  gi|118431764|ref|NP_148433.2|  15 PEWKTLMLRELEELFSKHRVVLFADLTGTPTFVVQRVRKKLWKK-YPMMVAKKRIILRAMKAAGLELDdnlLDDLVRGQM 93 
                                    79****************************************99.********************7446899******** PP

                                    EEEEESS-TCHHHHCCCC CS
                  Ribosomal_L10  80 alvftnedpvalakvlee 97 
                                    +lvf +++p++++k +e+
  gi|118431764|ref|NP_148433.2|  94 LLVFADGNPFKIVKEVEK 111
                                    **************9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.41
                                    CCCHHHHHGCEEEEESCCCCCC CS
                  Ribosomal_L10  39 lRkklrengaelkvvKntlmrr 60 
                                    lR + +  g+++ ++K t++ +
  gi|118431764|ref|NP_148433.2| 149 LRIQYQVRGGKIYIAKETVVAK 170
                                    56666666899*******9875 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1
                                    EEESCCCCCCCCHC CS
                  Ribosomal_L10  51 kvvKntlmrrAlee 64 
                                     +vK  l+  Al+ 
  gi|118431764|ref|NP_148433.2| 249 AIVKAALAASALAA 262
                                    56666666666654 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 !   56.7   0.0     3e-19   1.8e-15       2      71 .]     119     188 ..     118     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 3e-19
                   RL10P_insert   2 raGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                    ++G++A+ +++ip+g ++l+Pg+i + + kl+++ +++ Gki + ++++v+k G++++ + a lL  Lgi
  gi|118431764|ref|NP_148433.2| 119 KPGDKAETEIRIPEGMTNLTPGPILSVFGKLRIQYQVRGGKIYIAKETVVAKPGDVISEDLAGLLMALGI 188
                                    89******************************************************************98 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  17.0   2.6e-06     0.015       7      80 ..     246     329 ..     240     339 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..............XXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Ribosomal_60s   7 ikkvlkaagveveaarvkllvkalegkdieellangaakla..............aaaaaaaaaaaaaaaaaaaeekkke 72 
                                    +++ + +a     a++++++  +++  ++e+++ ++ a  a                   aa+aaa+aa+++a+eekk+e
  gi|118431764|ref|NP_148433.2| 246 VESAIVKAAL--AASALAAETGFIAPGTVEDVVRKAIAEEAavvallgdkarelgI--EEAAPAAAPAAEEKAEEEKKEE 321
                                    5555555544..6778888888888888888888776665567889*999999641..3344444444444444444444 PP

                                    XXX.XX-- CS
                  Ribosomal_60s  73 eeeeEeed 80 
                                    eee+ e+ 
  gi|118431764|ref|NP_148433.2| 322 EEEKKEDQ 329
                                    44432222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 2693.72
//
Query:       gi|118431765|ref|NP_148435.2|  [L=217]
Description: 50S ribosomal protein L1 [Aeropyrum pernix K1]
Scores for 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-35  120.6   0.0    8.8e-35  120.3   0.0    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   4.9e-39   8.8e-35       7     204 .]      24     209 ..      12     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 4.9e-39
                                    SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHH CS
                   Ribosomal_L1   7 kkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfea 86 
                                    k+f++svei++ l++++ k+++ r+++++ Lp+   ke+k+c+++ ++ +    +akeag   +v+  ++l++  +++++
  gi|118431765|ref|NP_148435.2|  24 KRFKQSVEIIVALKDIDLKSPQARIRETVFLPNRPPKEAKVCVVAHGDMEL---QAKEAG--VEVLNRQDLQNLSQNKRE 98 
                                    579************************************************...******..****************** PP

                                    HHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTS CS
                   Ribosomal_L1  87 krkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsf 166
                                     +kl+  + ++l+  ++m l +++LG+ +g+r+k P+pv      ++++k  +e++++ +v+vr++++  +++++G+ ++
  gi|118431765|ref|NP_148435.2|  99 VKKLARRCYWVLVRADLMGLAGRILGPALGPRGKAPVPV--P--PNANIKDLIERYKA-AVWVRIRNQPQVMARIGTEDM 173
                                    ***************************************..4..2579**********.********************* PP

                                    SHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS- CS
                   Ribosomal_L1 167 taeelaeNieavvkalvekvpkkwkniksiylkttmsp 204
                                    ++ elaeN+ av++ ++++   +  +i  iy+k tm+p
  gi|118431765|ref|NP_148435.2| 174 SPRELAENALAVLQVIENR--LGRGKISRIYVKKTMGP 209
                                    *******************..66779**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1880.44
//
Query:       gi|14601892|ref|NP_148436.1|  [L=108]
Description: 50S ribosomal protein L11 [Aeropyrum pernix K1]
Scores for 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-18   65.3   0.6    6.5e-18   65.0   0.6    1.1  1  Ribosomal_L11  Ribosomal protein L11, RNA binding 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 !   65.0   0.6   3.6e-22   6.5e-18       2      70 .]       8      75 ..       7      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3.6e-22
                                  --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                 Ribosomal_L11  2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70
                                   P+t+ lL+ka+ ++  sg p ++++G++ +++++eIA  Kk+dl a+ +l+aavk+ilg+Ars+G++V
  gi|14601892|ref|NP_148436.1|  8 KPSTTELLLKAVSAKAPSGDPIHQKIGDLPFEKIVEIAIEKKPDLLAK-TLKAAVKTILGSARSIGVTV 75
                                  6*********************************************99.******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 950.26
//
Query:       gi|118431766|ref|NP_148437.2|  [L=151]
Description: transcription antitermination protein NusG [Aeropyrum pernix K1]
Scores for 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-20   70.3   0.0    1.6e-19   69.5   0.0    1.4  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    1.5e-07   31.1   0.9    3.8e-07   29.8   0.9    1.7  1  KOW       KOW motif
  ------ inclusion threshold ------
       0.73    9.3   4.0       0.27   10.7   0.6    1.9  2  ProQ_C    ProQ C-terminal domain


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 !   69.5   0.0   2.7e-23   1.6e-19       1      83 [.       8      86 ..       8      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 2.7e-23
                       Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEved 82
                                   +++a+ +t+g E +va+ ++++    a+  +l+I+S+++p+ +kGy+++EA+++ +v +a +g+++v+++ + +++++Ev++
  gi|118431766|ref|NP_148437.2|  8 RFYAILVTSGAEVNVATIIAER----ARALGLDIRSIIVPPRIKGYVILEAHDPGDVYDATRGLRHVKRRRPLILKFEEVMK 85
                                   58*******************9....77779*************************************************99 PP

                       Spt5-NGN 83 l 83
                                   l
  gi|118431766|ref|NP_148437.2| 86 L 86
                                   7 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.9   6.4e-11   3.8e-07       1      31 [.      98     128 ..      98     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6.4e-11
                                    TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                            KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31 
                                    pG++V++v+G +kG +++V +v+q k  V+v
  gi|118431766|ref|NP_148437.2|  98 PGQVVEIVAGAFKGMKARVIDVNQSKGQVTV 128
                                    8*************************88887 PP

>> ProQ_C  ProQ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.23   1.4e+03      11      25 ..      12      26 ..      11      27 .. 0.72
   2 ?   10.7   0.6   4.5e-05      0.27       3      34 ..      94     128 ..      92     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.23
                                   B---SSSS---EEEE CS
                         ProQ_C 11 VkVklGkspmpAtil 25
                                   + V  G     Ati+
  gi|118431766|ref|NP_148437.2| 12 ILVTSGAEVNVATII 26
                                   567778888888875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.5e-05
                                    SSS-TT--B---SSS.S---EEEEEE-..SSSEEE CS
                         ProQ_C   3 aeLkvGqqVkVklGk.spmpAtileia..KddVrV 34 
                                      Lk Gq V + +G  + m+A +++++  K  V+V
  gi|118431766|ref|NP_148437.2|  94 PALKPGQVVEIVAGAfKGMKARVIDVNqsKGQVTV 128
                                    579***********9678********833445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 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:                        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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1177.10
//
Query:       gi|118431767|ref|YP_874930.1|  [L=60]
Description: preprotein translocase subunit SecE [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0066   16.4   0.0     0.0078   16.1   0.0    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.4e-07    0.0078       2      47 ..       9      54 ..       8      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.4e-07
                                   HCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SecE  2 kFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvf 47
                                   +++  +++ l    +P+ +E+    +  l++++++g +++l+ l+ 
  gi|118431767|ref|YP_874930.1|  9 EYIVAWRRILTLARKPDEEEYSLLLKLNLLGFALVGGIGYLIHLGY 54
                                   6788889999999*****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 489.07
//
Query:       gi|118431768|ref|NP_148439.2|  [L=171]
Description: hypothetical protein APE_2177.1 [Aeropyrum pernix K1]
Scores for complete 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  171.2   0.1    1.6e-50  171.0   0.1    1.0  1  Mut7-C          Mut7-C RNAse domain
    1.4e-05   24.7   0.0    2.3e-05   24.0   0.0    1.4  1  DUF5615         Domain of unknown function (DUF5615)
     0.0084   16.0   1.0        1.9    8.4   0.0    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.044   13.7   0.3      0.079   12.9   0.3    1.4  1  zf_CopZ         Zinc binding domain
      0.045   14.1   0.0      0.078   13.3   0.0    1.4  1  PIN_9           PIN like domain
        0.3   10.7   1.0        1.5    8.5   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
        2.6    7.8   8.4        4.3    7.1   2.6    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        4.2    7.0   6.4         76    2.9   6.4    2.4  1  TF_Zn_Ribbon    TFIIB zinc-binding


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 !  171.0   0.1   7.3e-54   1.6e-50       2     146 .]      13     159 ..      12     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 7.3e-54
                         Mut7-C   2 rfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlreviar 79 
                                    rf++D mlg+lak+LRl+Gyd+ly+++++d ++l++a++ +ri++Trdr L+++a++     ++++s ++ee+l+e+ a+
  gi|118431768|ref|NP_148439.2|  13 RFIVDSMLGSLAKWLRLMGYDTLYSRTYSDWQILRIAKSSGRIIVTRDRWLHSKARKMGLksIYIESLSTEERLAELSAK 92 
                                    9****************************************************999986688****************** PP

                         Mut7-C  80 lglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveell 146
                                    +gl+l+l+pe srC  Cng+le v+ke v++rvpe +y++ d+f+ C++C+kv+W+G+hw++++++l
  gi|118431768|ref|NP_148439.2|  93 AGLDLRLEPERSRCPICNGVLEPVDKEAVRDRVPEATYRVVDKFYVCTRCGKVYWEGAHWRNMRKTL 159
                                    ***************************************************************9975 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     1e-08   2.3e-05       2      56 ..      13      61 ..      12      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                        DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDk 56
                                   ++++D  l  +l+++lr  g+d+l+      +  sD +il++Ak+ +riivT+D+
  gi|118431768|ref|NP_148439.2| 13 RFIVDSMLG-SLAKWLRLMGYDTLYS-----RTYSDWQILRIAKSSGRIIVTRDR 61
                                   788888888.9***********9999.....4578*******************6 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 !    8.4   0.0   0.00086       1.9      19      36 ..      98     115 ..      94     117 .. 0.83
   2 !    5.2   1.1     0.009        20       5      11 ..     137     143 ..     136     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00086
                 Zn_ribbon_SprT  19 sirrhnYrCrrCkgtLrg 36 
                                    +  +++ rC++C g+L++
  gi|118431768|ref|NP_148439.2|  98 RLEPERSRCPICNGVLEP 115
                                    56678899*******987 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.009
                 Zn_ribbon_SprT   5 YrCtgCg 11 
                                    Y+Ct+Cg
  gi|118431768|ref|NP_148439.2| 137 YVCTRCG 143
                                    99****9 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.5e-05     0.079       2      48 ..     104     146 ..     103     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.5e-05
                                    -B-TTT--B-EEE-HHHHHHHB-GGGGGG--S-EE.E---TT-SEEE CS
                        zf_CopZ   2 kkCPvCgkkGkkVkliTvkhllkpellekvkeedYylCknedCdVvY 48 
                                    ++CP C+   ++V+++ v+  + +        +++y+C+   C  vY
  gi|118431768|ref|NP_148439.2| 104 SRCPICNGVLEPVDKEAVRDRVPEATYR--VVDKFYVCTR--CGKVY 146
                                    68********************995554..456799**74..55555 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.5e-05     0.078      73     113 ..      38      77 ..      16      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                          PIN_9  73 eekaDdailelakeldaavlvTnDreLkkrllekgipvilL 113
                                    + + D +il++ak+ +  ++vT+Dr L  ++++ g++ i++
  gi|118431768|ref|NP_148439.2|  38 RTYSDWQILRIAKSSG-RIIVTRDRWLHSKARKMGLKSIYI 77 
                                    368999********99.6666***************99986 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.24   5.3e+02       5      14 ..     106     115 ..     103     119 .. 0.75
   2 ?    8.5   0.1   0.00067       1.5       3      12 ..     137     146 ..     135     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.24
                         zf_UBZ   5 CerCgkeipe 14 
                                    C+ C+  +++
  gi|118431768|ref|NP_148439.2| 106 CPICNGVLEP 115
                                    ****977665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00067
                         zf_UBZ   3 ylCerCgkei 12 
                                    y+C rCgk  
  gi|118431768|ref|NP_148439.2| 137 YVCTRCGKVY 146
                                    9******986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.018        41       6      13 ..     105     112 ..     100     113 .. 0.83
   2 ?    7.1   2.6    0.0019       4.3      21      30 ..     136     145 ..     136     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.018
                        zf-RRN7   6 pCgvCgcr 13 
                                    +C++C+++
  gi|118431768|ref|NP_148439.2| 105 RCPICNGV 112
                                    8*****86 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0019
                        zf-RRN7  21 fyyCrrChtq 30 
                                    fy+C+rC+ +
  gi|118431768|ref|NP_148439.2| 136 FYVCTRCGKV 145
                                    8******965 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   6.4     0.034        76       3      28 ..     106     145 ..     104     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.034
                                    ETTTTCEEC...............HEETSTTCEEESSSSBE CS
                   TF_Zn_Ribbon   3 CPnCgstnl...............veDpergelvCtdCGlV 28 
                                    CP+C++  l               ++      +vCt+CG V
  gi|118431768|ref|NP_148439.2| 106 CPICNGV-LepvdkeavrdrvpeaTYRVVDKFYVCTRCGKV 145
                                    7777775.3345677766666666333334679******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1438.77
//
Query:       gi|118431769|ref|NP_148440.2|  [L=280]
Description: hypothetical protein APE_2178.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-29  101.6   6.6    7.3e-08   32.7   0.0    4.1  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.038   13.9   0.0       0.14   12.1   0.0    2.0  3  DeoRC     DeoR C terminal sensor 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 !   25.1   0.0     2e-09   1.8e-05       1      56 [.      13      67 ..       6      68 .. 0.88
   2 !   16.6   0.0     9e-07    0.0081       3      56 ..      83     136 ..      81     137 .. 0.85
   3 !   27.9   0.9   2.7e-10   2.4e-06       1      55 [.     146     199 ..     146     201 .. 0.93
   4 !   32.7   0.0   8.1e-12   7.3e-08       5      45 ..     227     264 ..     221     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2e-09
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                   V+++  ++v++++ d +l+e+l+  ++++++r + ++  + + G++t rD+l++++
  gi|118431769|ref|NP_148440.2| 13 VEEVAGKEVPVLDKDFSLAEILKAVEKAKIDRAFLTE-GNSIRGVLTFRDILDKIA 67
                                   677778899****************7666****9*94.55599*********9985 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 9e-07
                                    HHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEE.EEEEHHHHHHHHH CS
                            CBS   3 dimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklv.GivtlrDllrall 56 
                                    ++m+++v +v     ++ ale+m  +g ++++PVV + g +v G +t+  l+r+++
  gi|118431769|ref|NP_148440.2|  83 SFMNEPVKYVEVGREVSHALETM-ANGmFTSVPVV-GAGGVVeGGITRFELARLVK 136
                                    6899*9999999999********.666899*****.5665666*****99999875 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 2.7e-10
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    V+d+m++ +v+v+ +t +  + +l+ e+++s +PV+ ++g++vG+v l  l+  +
  gi|118431769|ref|NP_148440.2| 146 VRDVMRTFLVSVNLQTRILHVRQLLYEYDISVIPVM-DEGRFVGVVGLDELMAII 199
                                    89**********************99999*999***.6********999998765 PP

  == domain 4  score: 32.7 bits;  conditional E-value: 8.1e-12
                                    SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEE CS
                            CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGi 45 
                                    m  ++++v+pd++l+ea+e+m ek+++++ VVd ++k+vG 
  gi|118431769|ref|NP_148440.2| 227 M--RPPVVTPDASLAEAAEKMLEKRYRAVVVVD-SEKPVGF 264
                                    4..678***********************7785.777**95 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.1   9.9e+03      86      98 ..      35      47 ..      25      61 .. 0.69
   2 ?   -2.7   0.0      0.54   4.8e+03      90     114 ..     108     131 ..      98     139 .. 0.62
   3 ?   12.1   0.0   1.6e-05      0.14      96     138 ..     218     260 ..     205     273 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.1
                          DeoRC 86 ealrqfnvdkafl 98
                                   +a+++ ++d afl
  gi|118431769|ref|NP_148440.2| 35 KAVEKAKIDRAFL 47
                                   5666777777776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.54
                          DeoRC  90 qfnvdkaflgangidaegglttsde 114
                                     +  ++ ++ga g+ + gg+t +++
  gi|118431769|ref|NP_148440.2| 108 GMFTSVPVVGAGGVVE-GGITRFEL 131
                                    4555556677777764.67776665 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 1.6e-05
                          DeoRC  96 aflgangidaegglttsdeeeaevkralieaarrvillaDssK 138
                                     ++ a++i  +  ++t+d   ae++++++e+  r ++++Ds+K
  gi|118431769|ref|NP_148440.2| 218 YVIVADAIRMRPPVVTPDASLAEAAEKMLEKRYRAVVVVDSEK 260
                                    6788999999999****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.19s 00:00:00.61 Elapsed: 00:00:00.34
# Mc/sec: 2435.31
//
Query:       gi|118431770|ref|NP_148442.2|  [L=250]
Description: hypothetical protein APE_2180.1 [Aeropyrum pernix K1]
Scores for complete 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-31  108.6   0.1      6e-31  108.3   0.1    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 !  108.3   0.1   3.3e-35     6e-31      16     216 ..      19     241 ..      12     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 3.3e-35
                                    CT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCC.......S................G-SCHHHHHHHH CS
                          DUF72  16 rhfntVEinstFYalpspetvakwaaqtpedFrFavKapraith.......e.........r......nedaeealerfl 73 
                                    + +++VE+++tFY +p ++++ +w++++pedF+F+vKa+  +th       +         r      +  ++e l+++ 
  gi|118431770|ref|NP_148442.2|  19 KLLDAVEVQQTFYDPPPRSRLDSWRSEAPEDFEFTVKAWMLVTHgynprlwRrlkrrvagdRsayggfK-LTRENLWAWS 97 
                                    4589****************************************7766555145555554414444332.4667777666 PP

                                    HH.CHHH.CT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-...S.EEEE--BGGGH..H.HHHHHHHTT-EEEEE--SS CS
                          DUF72  74 esalepL.geklgpllfQlppsfkfdeenlerLeaflaalp...l.lavEvRhrswf..e.llellrehgvavvldepkk 145
                                     + le+  + k+ ++++Q p+sf+ + en er+ +f+++ +     +a+E R + w   + l e  r+ g+++  d    
  gi|118431770|ref|NP_148442.2|  98 VT-LEAAeALKARIIVVQTPASFEASIENSERIVEFFNKAErggFiIAWEPRGAWWEnpNlLAETARKAGLVIAGD-VLR 175
                                    65.66664468889*********99977********9988789955*******99988667899999999777777.688 PP

                                    C--------SSTEEEEEE--S...HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHHH CS
                          DUF72 146 pklpledvttadfvyvRlhgr...eeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraLa 216
                                    ++lp+++     + y Rlhg    e +y+y+Y++++l+++a +i   +    e+yv+fnn    ++ ++a +++
  gi|118431770|ref|NP_148442.2| 176 GRLPPDEQE---LLYARLHGLgggEVNYKYKYTDDDLKRLATTICGGLW--SEAYVMFNNV---YSFDDALRFK 241
                                    999997665...9*********97589******************9665..689*****95...4566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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 0.20s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 2183.10
//
Query:       gi|118431771|ref|YP_874931.1|  [L=78]
Description: hypothetical protein APE_2180a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 585.05
//
Query:       gi|14601898|ref|NP_148443.1|  [L=251]
Description: DNA polymerase sliding clamp B1 [Aeropyrum pernix K1]
Scores for 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-06   26.0   0.0    1.1e-05   25.1   0.0    1.5  1  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    0.00011   22.4   0.3     0.0045   17.2   0.1    3.0  3  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma


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 !   25.1   0.0   1.3e-09   1.1e-05       1     103 [.       1     103 [.       1     114 [. 0.91

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.3e-09
                                   CEEEEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTT CS
                        PCNA_N   1 mlearleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkc 81 
                                   m+ + ++ +s +k + +++  + +e  f+ + +G+++  +   + +L  le+ s +fe+y  + ++ + +    l+ki k 
  gi|14601898|ref|NP_148443.1|   1 MFRLVYTASSKFKYIAQTLAKINDEGVFEFSLDGLRAWIMSPDKTSLAILEMPSLSFEEYMVEEEMRVVLRTDELNKISKR 81 
                                   67777888999********************************************************************** PP

                                   STTTSEEEEEEETTSSEEEEEE CS
                        PCNA_N  82 annedsvtlkaedeadtlalvf 103
                                   a  +d ++++ + e+++l + +
  gi|14601898|ref|NP_148443.1|  82 ATRNDDIIFQWNAEEQALEVEL 103
                                   ***9999998887777776554 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.021   1.8e+02      13      42 ..       7      36 ..       3     118 .. 0.75
   2 ?   -0.5   0.0      0.15   1.3e+03      66      66 ..     124     124 ..      68     170 .. 0.67
   3 !   17.2   0.1     5e-07    0.0045      66     127 ..     186     247 ..     129     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.021
                                  EEHHHHHHHHHHHTTT-SEEEEEEETTEEE CS
                        PCNA_C 13 lpssefaricrdlsqlsdsvvisvtkegvk 42
                                   +ss f+ i++ l++++d+ v   + +g++
  gi|14601898|ref|NP_148443.1|  7 TASSKFKYIAQTLAKINDEGVFEFSLDGLR 36
                                  568888888888888888877777777765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.15
                                   G CS
                        PCNA_C  66 e 66 
                                   e
  gi|14601898|ref|NP_148443.1| 124 E 124
                                   3 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 5e-07
                                   GGCBEEEESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                        PCNA_C  66 eeavklelkepvtltfalkYlaeftkatsLservtlslssevPlvveykikdvgllayllak 127
                                   +    le++e  +  ++ + l   tk    +e v++s++s+ P+++ey+  ++  +  ++a+
  gi|14601898|ref|NP_148443.1| 186 DVLLSLEVEEDAKSIYSRQVLEIATKPVGAAESVKVSFASDYPMKIEYTFPNGERMELYMAP 247
                                   345689999*******************************************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1835.82
//
Query:       gi|118431772|ref|NP_148444.2|  [L=131]
Description: hypothetical protein APE_2184.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.2   0.4      0.045   13.5   0.4    1.5  1  DUF592    Protein of unknown function (DUF592)
       0.12   12.7   0.1       0.98    9.8   0.1    2.2  1  B5        tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> DUF592  Protein of unknown function (DUF592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4     5e-06     0.045      63     123 ..      32      98 ..      13     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-06
                         DUF592  63 elIklLGFelkdkellnaiskvve..veadseekvek....eeleDpLekkeivrlikdLqkainkv 123
                                    e+ ++LGFe +d + +  i ++++   ++ +++  ++    ++++D + +k iv+ +k +++  +++
  gi|118431772|ref|NP_148444.2|  32 EVTRRLGFESQDASETYRIIRNFDafYDMAKKKFKDYivpsKSMNDMILGKVIVDKVKLVKEGDKRI 98 
                                    57789**********999****9976555555555558888*************9999988766665 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00011      0.98      14      32 ..     105     123 ..      13     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                                    S---HHHHHHHHHHTT-E. CS
                                    xxxxxxxxxxxxxxxxxxx RF
                             B5  14 idlseeeiikiLkrlgcer 32 
                                      +se++ ++iLk++g+++
  gi|118431772|ref|NP_148444.2| 105 RRISEDTLAEILKNMGYQV 123
                                    35799***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 986.29
//
Query:       gi|118431773|ref|NP_148445.2|  [L=145]
Description: hypothetical protein APE_2185.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        1.5    7.0   5.7        1.5    6.9   5.7    1.0  1  SSP160      Special lobe-specific silk protein SSP160


Domain annotation for each model (and alignments):
>> SSP160  Special lobe-specific silk protein SSP160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.7   8.4e-05       1.5     337     419 ..      63     141 ..      35     145 .] 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 8.4e-05
                         SSP160 337 qslqalllqeatcapalaanakksgvrelspckaaktasscaks.gekkvkrkarlekmraksrravgnrlkgsmkkrvr 415
                                    ++l+a+   eat++ ala  +   g+ e+   ++ k     aks  +kk k+ka  +k ++ks++a g + k   k    
  gi|118431773|ref|NP_148445.2|  63 DTLEAVARGEATVSEALAFLS-TEGIEEVLL-QTRKPVKKRAKSrAKKKEKKKAVAQKTKSKSKKASGGKSKSKSK---S 137
                                    568888889999999998755.568887642.33334455566624678899****************99554333...3 PP

                         SSP160 416 srak 419
                                    s++k
  gi|118431773|ref|NP_148445.2| 138 SKSK 141
                                    4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2715  (0.151431); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1051.53
//
Query:       gi|118431774|ref|NP_148446.2|  [L=281]
Description: hypothetical protein APE_2187.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2196.61
//
Query:       gi|118431775|ref|NP_148447.2|  [L=948]
Description: ATP-dependent helicase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-29  102.9   0.0    3.4e-29  101.8   0.0    1.6  1  DEAD            DEAD/DEAH box helicase
    4.5e-20   72.0   0.0    2.7e-18   66.3   0.0    2.5  2  Helicase_C      Helicase conserved C-terminal domain
    1.4e-14   54.3   0.7    3.6e-14   53.0   0.2    2.0  2  DEAD_assoc      DEAD/H associated
    6.7e-07   29.5   0.0    1.4e-06   28.4   0.0    1.5  1  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.026   14.5   0.0        0.1   12.6   0.0    2.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.054   13.8   0.4       0.85    9.9   0.2    3.0  2  AAA_22          AAA domain
       0.12   12.1   0.2         21    4.7   0.0    2.7  2  AAA_30          AAA domain
       0.16   12.3   0.1       0.96    9.8   0.0    2.4  2  AAA_19          AAA domain
       0.37   10.6   1.0          1    9.1   0.7    2.0  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
        1.7    9.0   6.1       0.27   11.5   0.8    2.5  3  HalOD1          Halobacterial output domain 1


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.0   1.9e-32   3.4e-29       2     171 ..      24     194 ..      23     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.9e-32
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                    +iQ++a+p+i++g + lv a+TGsGKT+a+l p+l+++ +    +  g k+++v+P+r+L ++   +++++    +++v+
  gi|118431775|ref|NP_148447.2|  24 PIQEKAFPIIYRGLNALVVAPTGSGKTEAALAPLLARLRNGrvASGGGVKVVYVTPLRALNRDLEGRVERLAGLFGYTVQ 103
                                    8*************************************777888999**************************9999999 PP

                                    EEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH..HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  80 liiggvaardqlskldngvdivvgtpgrlddll..stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                    +  g++ +++ ++ l++ +div++tp+ l+ ll  ++ k  l+q r +V+DE+++l++++++ +++  l++l+   +  +
  gi|118431775|ref|NP_148447.2| 104 VRHGDTVQSSRRRFLERPPDIVITTPESLALLLtvKRAKEVLKQARAVVVDEIHELMESKRGVELSLNLEKLE-LMAGRR 182
                                    999999999999999777*************9866666667*******************************4.444444 PP

                                    TTSEEEEEESSBSH CS
                                    xxxxxxxxxxxxxx RF
                           DEAD 158 lqrqvivlSATlpk 171
                                    lq   i lSAT+++
  gi|118431775|ref|NP_148447.2| 183 LQ--RIGLSATVSR 194
                                    66..*******983 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 ?    3.0   0.0     0.073   1.3e+02      31      63 ..      89     122 ..      58     177 .. 0.80
   2 !   66.3   0.0   1.5e-21   2.7e-18       4     108 ..     240     343 ..     237     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.073
                                    H.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH CS
                     Helicase_C  31 k.vklllekkgikvavlhgelpqnereeileqfn 63 
                                      v+ l   +g++v v hg++ q++r++ le+  
  gi|118431775|ref|NP_148447.2|  89 GrVERLAGLFGYTVQVRHGDTVQSSRRRFLERPP 122
                                    2456666778******************999874 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 1.5e-21
                                    HHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                     Helicase_C   4 eallellkleeeggkilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                    +a+ el+  + egg +lif+nt++++e + + l+++ g +v ++hg+l+   re++ ++f++g+++ ++at+ +e Gid+
  gi|118431775|ref|NP_148447.2| 240 KAIAELV--KGEGGSVLIFANTRSTVETLAFALSRElGEEVPAHHGSLSRHVRERVERDFKEGRVKAIVATSSLELGIDV 317
                                    5566666..799**************986666777789****************************************** PP

                                    TTESEEEESSSSSSHHHHHHHHTTSS CS
                     Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtg 108
                                     +v lV++f  pr+vt ++qr+GR g
  gi|118431775|ref|NP_148447.2| 318 GRVALVVQFLSPRQVTAMVQRAGRSG 343
                                    ************************87 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   4.3e+03      32     100 ..     282     346 ..     265     353 .. 0.65
   2 !   53.0   0.2     2e-17   3.6e-14       8     191 .]     607     772 ..     602     772 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                     DEAD_assoc  32 nealalllaarlsrrfg.idvqvaanDdgivlllpleerlpllldellellspdeleedleaalnaself 100
                                    +  l++ +++r++r f+   v++ ++   ++l ++  ++       ++++lsp+++ +++++a  + + f
  gi|118431775|ref|NP_148447.2| 282 HGSLSRHVRERVERDFKeGRVKAIVATSSLELGIDVGRV-----ALVVQFLSPRQVTAMVQRAGRSGHRF 346
                                    556677777777776642466677777777774443333.....23567888888888887776655555 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 2e-17
                     DEAD_assoc   8 lvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlp....llldellellsp 83 
                                    +vE+ +        ++++++G+r n al+lll++ ++ +  + v++   +++iv  +p+++ l     +   ++l++l+p
  gi|118431775|ref|NP_148447.2| 607 VVEEAEG-----LAILYACLGSRGNFALSLLLSKLMEGS--VAVEFHYIPYAIVFKSPASRGLGrlvaH-SLKTLAKLEP 678
                                    6666644.....479*********************876..56677788******99776666677753.3458999*** PP

                     DEAD_assoc  84 deleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlDle 163
                                    +e   +l +a+ +s  +  rF +vA+r++++  +           +l+ + + ++a  ++++p+  e+v+e ++++lD++
  gi|118431775|ref|NP_148447.2| 679 AERLGMLYDAVRRSRAYLVRFYQVAKRMGVVDPD----------ATLSLDIIRKMADAMQGTPVDIETVKELVHEKLDID 748
                                    *******************************877..........5779999999999999******************** PP

                     DEAD_assoc 164 rlaellrriaageirvvevetprpSpfA 191
                                    +l ++l+++++  + vve  ++r Sp+A
  gi|118431775|ref|NP_148447.2| 749 ALNRFLDDVSD--VAVVE--LQRLSPLA 772
                                    **********8..88888..******98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   7.8e-10   1.4e-06      25     170 ..      37     193 ..      14     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.8e-10
                                    SEEEEEESTTSTHHHHH.HHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--... CS
                         ResIII  25 krglikmaTGtGKTlva.aklierllkkgkee....kflflvprkslleqtleefkkflseaykeigkkvsgdkkka..k 97 
                                     ++l++++TG+GKT  a a l +rl++ +  +    k++ + p ++l   ++ ++++++      + ++ +gd+ ++  +
  gi|118431775|ref|NP_148447.2|  37 LNALVVAPTGSGKTEAAlAPLLARLRNGRVASgggvKVVYVTPLRALNRDLEGRVERLAGLFGY-TVQVRHGDTVQSsrR 115
                                    47899************7778888888766669*******************888777664322.444444444444322 PP

                                    ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHH.HHT---SEEEEEESS- CS
                         ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swrei.lekfkeavllglTATp 169
                                    +  +   +i++tt +sl   +   + ++ +   ++   +++DE H l ++k       + +++ l + ++  ++gl+AT 
  gi|118431775|ref|NP_148447.2| 116 RFLERPPDIVITTPESLALLL---TVKRAKEVLKQARAVVVDEIHELMESKrgvelslNLEKLeLMAGRRLQRIGLSATV 192
                                    33788899*************...8899999999999************86444444455554333336699*******8 PP

                                    S CS
                         ResIII 170 e 170
                                     
  gi|118431775|ref|NP_148447.2| 193 S 193
                                    6 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 ?   12.6   0.0   5.7e-05       0.1      53      96 ..     794     843 ..     735     852 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                                    CC.TTTT-EEEEEEE--EEEETTTS-EEECHH....H..HHS-TTTSSS- CS
                           HypA  53 egtvlegaeLeieevpvkvrCreCgkefelee....k..alrCpkCgsad 96 
                                     ++++e ++ +++e+++++ C +C+k+ e++     +  a+rCp Cgs  
  gi|118431775|ref|NP_148447.2| 794 LDKIIEAKKRRLSEKRIVFLCISCDKRHEKKVaelpRgtAYRCPYCGSLA 843
                                    555666666779999************99775334324455******976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.2   0.00047      0.85       8     106 ..      39     169 ..      34     229 .. 0.61
   2 ?   -1.4   0.0       1.5   2.7e+03      52      96 ..     262     306 ..     243     360 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                         AAA_22   8 lvvtGesGtGKTtllrr.lleqldeeakaee.......................erpevvfvtlpsstsskdllrellra 63 
                                     +v++++G+GKT  +   ll +l +   a                         +                     l+  
  gi|118431775|ref|NP_148447.2|  39 ALVVAPTGSGKTEAALApLLARLRNGRVASGggvkvvyvtplralnrdlegrveR---------------------LAGL 97 
                                    6899********8776515555544444444444444444444444444432221.....................2222 PP

                         AAA_22  64 lglelka..........................erlsseell.ealeqalraravielliiDEaqhlr.s......e 106
                                    +g    +                           + s+  ll  + ++ + ++a+  ++++DE++ l+ s       
  gi|118431775|ref|NP_148447.2|  98 FG---YTvqvrhgdtvqssrrrflerppdivitTPESLALLLtVKRAKEVLKQAR--AVVVDEIHELMeSkrgvelS 169
                                    22...12334555566666666666666666644444444444344444444444..9********98743444443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                         AAA_22  52 sskdllrellralglelka.erlsseellealeqalraravielli 96 
                                    + ++l+ +l r+lg+e  a  +  s++++e++e+ +++ +v ++++
  gi|118431775|ref|NP_148447.2| 262 TVETLAFALSRELGEEVPAhHGSLSRHVRERVERDFKEGRV-KAIV 306
                                    56666666666777666663333344444666666666666.4444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.012        21      20      97 ..      38     156 ..      22     168 .. 0.61
   2 ?    4.1   0.1     0.018        33      33      66 ..     237     270 ..     219     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                         AAA_30  20 vavltGpAGtGKtta.....lkalreaweaag..grviglAptgkaAkvLaeelg....i........eastiakllkrl 80 
                                     a++++p G+GKt a     l+ lr+   a+g   +v+ ++p  +  ++L+  ++    +        +++t+++     
  gi|118431775|ref|NP_148447.2|  38 NALVVAPTGSGKTEAalaplLARLRNGRVASGggVKVVYVTPLRALNRDLEGRVErlagLfgytvqvrHGDTVQSSR--- 114
                                    47899********8532222444444433332569999999999988888843332112222222223444444333... PP

                         AAA_30  81 k.........................grarlepgtllivDEa 97 
                                    +                         +++ l++++ ++vDE+
  gi|118431775|ref|NP_148447.2| 115 RrflerppdivittpeslallltvkrAKEVLKQARAVVVDEI 156
                                    134466777777777777777777765455666688888886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                         AAA_30  33 talkalreaweaaggrviglAptgkaAkvLaeel 66 
                                     ++ka++e+++ +gg+v+++A t    ++La +l
  gi|118431775|ref|NP_148447.2| 237 NSVKAIAELVKGEGGSVLIFANTRSTVETLAFAL 270
                                    5789**********************99998543 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00054      0.96       8     115 ..      34     160 ..      26     174 .. 0.65
   2 ?   -1.6   0.0       1.7   3.1e+03      52      92 ..     721     755 ..     695     826 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00054
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp...eeillvaftgrAakelrerlaalgae.........atTiHrl 75 
                                     +  + lv+a+ G+GKT+   + +   +++g+v+     +++ v++ +   + l+ r++ l +                 
  gi|118431775|ref|NP_148447.2|  34 YRGLNALVVAPTGSGKTEAALAPLLARLRNGRVASgggVKVVYVTPLRALNRDLEGRVERLAGLfgytvqvrhG------ 107
                                    5566789**********998888888888887876777899999999988889998886655545444333332...... PP

                         AAA_19  76 al................ldfddlltealelle..........eaeeekklqeee.llivDEfqdvd 115
                                                      +                          ++ k++ +++ +++vDE+ ++ 
  gi|118431775|ref|NP_148447.2| 108 -DtvqssrrrflerppdiV-------------IttpeslalllTVKRAKEVLKQArAVVVDEIHELM 160
                                    .122444445555555431.............033333333343444444446666******98876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.7
                         AAA_19  52 grAakelrerlaalgaeatTiHrlalldfddlltealelle 92 
                                    +    ++++++++  ++++T+ +l  ++ + +++    +l+
  gi|118431775|ref|NP_148447.2| 721 R----KMADAMQGTPVDIETVKEL--VHEKLDIDALNRFLD 755
                                    3....4555555555778888777..333333323333333 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 ?   -2.9   0.0       3.4     6e+03       2       9 ..     583     590 ..     582     594 .. 0.85
   2 ?    9.1   0.7   0.00058         1      16      53 ..     805     842 ..     794     843 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.4
                 zinc_ribbon_10   2 fDrvldvL 9  
                                    ++rvldvL
  gi|118431775|ref|NP_148447.2| 583 MERVLDVL 590
                                    89*****9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00058
                 zinc_ribbon_10  16 saknryalICskChshnGlapkeeleevkyrCpkCgal 53 
                                    + ++r    C  C +       e ++ + yrCp+Cg+l
  gi|118431775|ref|NP_148447.2| 805 LSEKRIVFLCISCDKRHEKKVAELPRGTAYRCPYCGSL 842
                                    5577888889999877766668999999********87 PP

>> HalOD1  Halobacterial output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       8.1   1.5e+04      60      71 ..      99     110 ..      99     111 .. 0.87
   2 ?   -3.0   0.0       5.3   9.5e+03      49      64 ..     638     653 ..     632     656 .. 0.81
   3 ?   11.5   0.8   0.00015      0.27       3      42 ..     713     756 ..     711     766 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.1
                         HalOD1  60 gyeVtVrsdgei 71 
                                    gy+V Vr+  ++
  gi|118431775|ref|NP_148447.2|  99 GYTVQVRHGDTV 110
                                    89*****99888 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.3
                         HalOD1  49 radgsvsFtyegyeVt 64 
                                    ++++ v+F y  y ++
  gi|118431775|ref|NP_148447.2| 638 EGSVAVEFHYIPYAIV 653
                                    56799*****999886 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00015
                         HalOD1   3 espstaVveavaavegvdptelep....LydaiDpdALdaLfas 42 
                                     ++s  +++  a+++   p+++e+     ++  D dAL++++++
  gi|118431775|ref|NP_148447.2| 713 ATLSLDIIRKMADAMQGTPVDIETvkelVHEKLDIDALNRFLDD 756
                                    6899******************9999999************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (948 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 5736.19
//
Query:       gi|14601903|ref|NP_148448.1|  [L=354]
Description: hypothetical protein APE_2190 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.2   0.0      0.065   13.5   0.0    1.4  1  DHH       DHH family
      0.075   13.0   0.0       0.15   12.0   0.0    1.4  1  CHAD      CHAD domain
       0.18   12.2   1.2       0.28   11.6   0.3    1.7  2  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 ?   13.5   0.0   1.1e-05     0.065       2      56 ..      10     107 ..       9     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                   EEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCH..... CS
                                   xxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxx..... RF
                           DHH   2 ilivghknpDtDsigSaialan.......................................llvDhneksqavege..... 38 
                                   +++  + + D+D+++Sa  +++                                       +++D   +++ ++g      
  gi|14601903|ref|NP_148448.1|  10 VVV--VADWDADGVVSAAEIYYsqkyreafphkgkavvemepsgprgfqdkagslscgdivVILDIPYTDEVKAGLktyvd 88 
                                   555..99*********77777768999999999999999888888888888888888888778888888887777789999 PP

                                   .HCCCSEEEEEEE-S---S CS
                                   .xxxxxxxxxxxxxxxxxx RF
                           DHH  39 .akeeaedviiiDHHrlge 56 
                                    ++e+ e ++  DHH +  
  gi|14601903|ref|NP_148448.1|  89 gCRERIESILYFDHHDSTL 107
                                   9**************9964 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.15      60     156 ..     178     276 ..     169     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHHHHHH...HHHTHHHHH.HTS-TTTCGGGHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHT--S- CS
                          CHAD  60 wlaraLGeaRDldV...llerllsrleerlpaaeqealerllkrlekerkrararvlaaLdsaryqalldaldallaaerl 137
                                    ++++L++ RD dV   ++e l++ l + +p++   + e + ++  +e ++a ++v +  ++   +++++ +  +++a+ +
  gi|14601903|ref|NP_148448.1| 178 SISKTLNRRRDPDVwrrYVEWLANPL-PFEPTKLPGTGETIVEASLEESREADEEVKRVATDLAMSSVKLGIVSFVDARGK 257
                                   68899*********776666777777.888888888899999998899999999*9*********************9999 PP

                                   -TSBHHHHHHHHHHHHHHH CS
                          CHAD 138 eaepaaaalekrlrkayrk 156
                                   +++p a al+  ++k +++
  gi|14601903|ref|NP_148448.1| 258 WKRPGASALASFVHKIVKT 276
                                   9************999987 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.1   1.3e+04      46      62 ..      12      27 ..       9      34 .. 0.71
   2 ?   11.6   0.3   4.7e-05      0.28       6     128 ..     223     334 ..     217     343 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.1
                                  ECHCCHHHHHHHHHHHH CS
                         DHHA1 46 evgeewdagalgiaadk 62
                                   v ++wda+ + +aa+ 
  gi|14601903|ref|NP_148448.1| 12 VV-ADWDADGVVSAAEI 27
                                  45.78999888888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEE CS
                         DHHA1   6 eerkelekeleelkealaklkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvkv 85 
                                   ee +e+ +e+          k+ +       vk g   +v +   +w++     +a+ +++  k pv++++  ++g    +
  gi|14601903|ref|NP_148448.1| 223 EESREADEEV----------KRVATDLAMSSVKlGIVSFVDAR-GKWKRPGASALASFVHKIVKTPVALLFERDDG-VRVL 291
                                   3444444444..........33222222233334777777777.89999999999999999556688888888888.8888 PP

                                   EEEESSHSS-HHHHHHHHHHHTTCCE..EEETCEEEEEEEHCH.HH CS
                         DHHA1  86 sarskkdgvdagelakeaaaklgggG..GGHdlAaGagipaek.le 128
                                   ++rs+     a  lake  ++lg+    GGH++ a a++ ++  le
  gi|14601903|ref|NP_148448.1| 292 VLRSS--AGEAKMLAKE-LEELGLVEdlGGHENVATARLREDTtLE 334
                                   88999..5677777777.777777544499*777777775444344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2669.13
//
Query:       gi|118431776|ref|NP_148450.2|  [L=442]
Description: aspartyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-84  283.1   0.0      3e-84  282.8   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.5e-13   50.5   0.2    2.4e-13   49.8   0.2    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0018   17.8   0.2        1.4    8.3   0.0    2.2  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 !  282.8   0.0   4.9e-88     3e-84       4     313 ..     121     436 ..     118     437 .. 0.94

  Alignments for each domain:
  == domain 1  score: 282.8 bits;  conditional E-value: 4.9e-88
                                    HHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx RF
                    tRNA-synt_2   4 lrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqsp 79 
                                    +rlk+r+ld+r++ vs++++l + v+k +r+y+ ++gf+ei tP ++ + te+ga+ F v        +f    +L+qsp
  gi|118431776|ref|NP_148450.2| 121 TRLKYRWLDIRNPMVSAIFELEAMVAKVFRDYYWSQGFVEIFTPKIVAAGTESGAEVFPV-------VYFdktaFLAQSP 193
                                    79**********************************************************.......34444447***** PP

                                    HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHH.HHHHHHHHHHHHHHHHHHCSCCCCCHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeed.imqvleelikslvkevlessakdiefvir 158
                                    q+y+++ ++ag++rvf+i+++FRaE ++t+rhl+E+ ++++e+ fie  + +m+++e++++ +v+ + e+ ++ +e    
  gi|118431776|ref|NP_148450.2| 194 QFYKQFAVIAGLERVFEIGPVFRAEPHHTSRHLNEYHSLDIEVGFIESYNdVMNYVEGFMRAIVRMLEEDGRRVLELYGV 273
                                    **********************************************98777****************7777666666666 PP

                                    TTSEE-SSS-EEEEHHHHHHHHHTS.......-SS--HHHHHHHHH....HS--SEEEEEEEBGGGSTTCBBBSTTSTTB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 159 rnskdlkkpfkrltykeaieklnei.......gkdldkaderalvk....keknepvfvtdfPaelkpFyarkeeddkkl 227
                                    +  + +++ +++++ ++a e+l+e+       g+dld++ er++      + ++++vf++++P++++pFy+ +++d++  
  gi|118431776|ref|NP_148450.2| 274 ELPRIPASGIPKIPLRKAYEILEEKygkkveyGEDLDSEGERLMGAyageELDSDFVFIVEYPWKVRPFYTMRKDDEPSW 353
                                    666555555*************999*****************998766668999************************** PP

                                    BSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 228 tesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdv 307
                                    t s+Dll++g+E+v+G +R++++++l e+l++kgld    e+f++yl+ ++ GapphgG g+Gl+R+vm  l++e+Ir++
  gi|118431776|ref|NP_148450.2| 354 TYSFDLLYRGLEIVTGGQREHRYHRLLENLRDKGLD---AESFQFYLDFFKHGAPPHGGAGMGLERIVMQTLKLENIREA 430
                                    ************************************...***************************************** PP

                                    SSS-XX CS
                                    xxxxxx RF
                    tRNA-synt_2 308 iaFPkl 313
                                     + P+ 
  gi|118431776|ref|NP_148450.2| 431 RMLPRD 436
                                    ****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 !   49.8   0.2   4.1e-17   2.4e-13       1      76 []      22     100 ..      22     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 4.1e-17
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTS.SEEEEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpgg.elelkveeiel 75 
                                    V+v+G+  +i  r+ g++ fi +rD++g iq+++ r    e+a + ae+lk ++vv v+G+++  p++  +e+kve++e+
  gi|118431776|ref|NP_148450.2|  22 VRVCGWAYRI--RDLGRLKFILVRDRSGVIQATVKRgespEDALRAAEDLKLESVVCVEGELRQAPTReGVEVKVERLEV 99 
                                    89********..*****************************************************66655********98 PP

                                    E CS
                tRNA_anti-codon  76 l 76 
                                    l
  gi|118431776|ref|NP_148450.2| 100 L 100
                                    6 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 !    7.1   0.0   0.00055       3.3     103     148 ..     207     256 ..     201     268 .. 0.68
   2 !    8.3   0.0   0.00024       1.4     214     233 ..     410     429 ..     405     438 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00055
                                    EEEEEEEEEBSST.-SSSB-SEEEEEE...EEEEETT--HHHHHHHHHHH CS
                   tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqve...glvvdenvsladlkgvleel 148
                                    +++ ig vfR +    ++hl e+h+++   g++   n  ++ + g+++++
  gi|118431776|ref|NP_148450.2| 207 RVFEIGPVFRAEPhHTSRHLNEYHSLDievGFIESYNDVMNYVEGFMRAI 256
                                    899*********978899******98822222223333444444444444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00024
                                    EEEEHHHHHHHHHT-SSGHH CS
                   tRNA-synt_2d 214 fGlGveRlamlkygieDiRe 233
                                     G+G+eR+ m ++++e+iRe
  gi|118431776|ref|NP_148450.2| 410 AGMGLERIVMQTLKLENIRE 429
                                    6******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3071.63
//
Query:       gi|14601906|ref|NP_148451.1|  [L=141]
Description: hypothetical protein APE_2195 [Aeropyrum pernix K1]
Scores for complete 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   60.3   0.0    2.2e-16   60.0   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 !   60.0   0.0   1.2e-20   2.2e-16       7     123 ..      18     135 ..      14     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 1.2e-20
                                   HHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSS.SE..EEEES-H CS
                         DUF61   7 eiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpel.gesvylvrgka 86 
                                   + k++ +++P+e++tL e+ ++   ti + +g+ h +dkee+e++ e +p ++w+  ++PI+l+++++  g   y+v+g+ 
  gi|14601906|ref|NP_148451.1|  18 TAKRLAQNIPRETVTLYEASRGR-LTITLHSGEAHTLDKEEVERILEAAPPYFWKLARIPIVLRYEKTPsGVARYVVQGDS 97 
                                   678999************97765.55566*************************************99867778******* PP

                                   H.HHHHHHHHT--...-SSEEEHH.HHHHHHHH-ST.. CS
                         DUF61  87 e.vkvvskilgkereeedelviykpevrelrrklptat 123
                                   +  ++v++i+  +   ++ + ++ ++ +++  +++++ 
  gi|14601906|ref|NP_148451.1|  98 WqRRLVEIIVRGDYTPQGLHELTVSQFQRIAARYRSIF 135
                                   *************9999999999999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1118.16
//
Query:       gi|14601907|ref|NP_148452.1|  [L=233]
Description: fibrillarin [Aeropyrum pernix K1]
Scores for complete 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-102  340.6   0.0   3.1e-102  340.5   0.0    1.0  1  Fibrillarin  Fibrillarin
    0.00042   20.1   0.0    0.00066   19.5   0.0    1.5  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran
  ------ inclusion threshold ------
      0.016   14.9   0.0      0.029   14.1   0.0    1.5  1  GCD14        tRNA methyltransferase complex GCD14 subunit


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 !  340.5   0.0  5.3e-106  3.1e-102       1     225 [.       7     232 ..       7     233 .] 0.99

  Alignments for each domain:
  == domain 1  score: 340.5 bits;  conditional E-value: 5.3e-106
                                   EEEECSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTT CS
                   Fibrillarin   1 veeheklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaa 80 
                                   v+eh++++gvy+v+ e+g+ r+atknlvpg++vYgE+++++++eEyR+Wn++rsKlaaa+lkgl elp+k+g+++LYlG+a
  gi|14601907|ref|NP_148452.1|   7 VREHDRWRGVYVVElEDGSLRIATKNLVPGQRVYGERIFRYNGEEYREWNAYRSKLAAALLKGLIELPVKEGDRILYLGIA 87 
                                   6799***************************************************************************** PP

                                   TSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHH CS
                   Fibrillarin  81 sGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilakna 161
                                   sGtt+sH+sDi+g++g++y+vef+prv+r+l++v+++R+ni+Pil+DAr+PekYr+lve vD ++aDvaqp+qa i+++na
  gi|14601907|ref|NP_148452.1|  88 SGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVVRDRRNIFPILGDARFPEKYRHLVEGVDGLYADVAQPEQAAIVVRNA 168
                                   ********************************************************************************* PP

                                   HHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEEE CS
                   Fibrillarin 162 klflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgkyk 225
                                   ++fl++ggy+l++ikarsidvt+ep+ev+k+e+++l + gl+++++v+l+p+++dha+++++++
  gi|14601907|ref|NP_148452.1| 169 RFFLRDGGYMLMAIKARSIDVTTEPSEVYKREIKTLMDGGLEIKDVVHLDPFDRDHAMIYAVMR 232
                                   ************************************************************9876 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   1.1e-07   0.00066      63     118 ..      65     122 ..      54     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-07
                                   HHHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHH CS
                          PCMT  63 alalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnl 118
                                   al+  l+e  +k+g+r+L +G  sG  +  ++ ++g++gr+ ++e  ++++++    +
  gi|14601907|ref|NP_148452.1|  65 ALLKGLIElpVKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVMRDLLTVV 122
                                   44445566669***********************************999988765555 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.8e-06     0.029      35      78 ..      72     115 ..      64     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.8e-06
                         GCD14  35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqra 78 
                                   +L +k+G +++  G  sg+ ++ ++  ++P+G+++ +ef  + +
  gi|14601907|ref|NP_148452.1|  72 ELPVKEGDRILYLGIASGTTASHMSDIIGPRGRIYGVEFAPRVM 115
                                   6889***********************************76544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1777.77
//
Query:       gi|118431777|ref|NP_148453.2|  [L=419]
Description: C/D box methylation guide ribonucleoprotein complex aNOP56 subunit [Aeropyrum pernix K1]
Scores for complete 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  247.1   0.0    1.9e-73  246.8   0.0    1.1  1  Nop             snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
       0.02   15.4   0.1      0.073   13.5   0.1    1.9  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
       0.02   14.8   0.1       0.19   11.7   0.0    2.7  3  UBA             UBA/TS-N domain
      0.044   13.7   0.0       0.11   12.4   0.0    1.7  1  DUF3173         Domain of unknown function (DUF3173)
       0.23   10.1   0.1        1.6    7.3   0.0    2.0  2  Tweety          Tweety
       0.27   11.1   2.7       0.92    9.4   1.3    2.4  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
       0.51   10.8   3.1       0.58   10.7   0.1    2.7  3  RuvA_C          RuvA, C-terminal domain


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 !  246.8   0.0   7.3e-77   1.9e-73       2     229 ..     153     378 ..     152     379 .. 0.92

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 7.3e-77
                                    HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.......HHHHHHHHHHHHCHHHH- CS
                            Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkee......deelakevimaakvtasts 75 
                                    +d+idk++n ++ r+rewYs hFpEL++lv+++ +Y+k+v+++g +r++++ + +      +ee+a+++ +a    a++s
  gi|118431777|ref|NP_148453.2| 153 IDDIDKTVNLFVARLREWYSIHFPELNDLVREHEDYVKIVSAVG-HRDNITVE-RlvdlgfSEEKARRIAEA----AKQS 226
                                    79******************************************.88999555.346344433344444444....556* PP

                                    SSS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT- CS
                            Nop  76 mgaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGa 155
                                     ga+lse d++ ++ l++ + el++lr++l+eY+e+ m+++APN++aLvG+ ++arLis aGgL +La+mPastiq+lGa
  gi|118431777|ref|NP_148453.2| 227 IGADLSEIDIQAVQTLARITSELYQLRRRLTEYIEQVMNEVAPNITALVGPLLGARLISLAGGLDKLARMPASTIQVLGA 306
                                    ******************************************************************************** PP

                                    HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                            Nop 156 ekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                    ekalfral+ +++ pk+G+i++ + ++++ p+++++kiaR+laaK+a+aa++Daf  +   +G+klree+ +++ 
  gi|118431777|ref|NP_148453.2| 307 EKALFRALRtGGKPPKHGIIFQYPDIHRS-PKWQRGKIARALAAKLAIAAKVDAF--TGRFIGDKLREELRRRIA 378
                                    *********777***************99.*************************..7899***********996 PP

>> 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 ?   13.5   0.1   2.8e-05     0.073      14     100 ..     160     262 ..     156     270 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHHHS..HCSHHHHHHSHHHHHHHHHTT..............STTHHHHHHHHHHHHHHHH.......S-SS CS
                                    xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxx.......xxxx RF
                        HhH-GPD  14 anriierlferfg..fptpedladadeekLrelire..............lGfyrrKakyikelArilv.......gkpd 70 
                                    +n  ++rl+e +   fp+++dl +  e+ ++   ++              lGf++ Ka++i e+A++ +       +   
  gi|118431777|ref|NP_148453.2| 160 VNLFVARLREWYSihFPELNDLVREHEDYVKIV-SAvghrdnitverlvdLGFSEEKARRIAEAAKQSIgadlseiD--- 235
                                    555555555555555555555555554444433.33455666666666666***************99955442220... PP

                                    S--TTSHHHHHHHHHHTTSSSSTTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  71 vlivvDvhvrrilkrlrsikekktkkkvek 100
                                      i +   ++ri + l++++++  ++ +e+
  gi|118431777|ref|NP_148453.2| 236 --IQAVQTLARITSELYQLRRR-LTEYIEQ 262
                                    ..11223466666666666664.5555555 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.9   4.8e+03      16      24 ..      36      44 ..      36      44 .. 0.86
   2 ?   -1.7   0.0       1.2     3e+03      27      37 .]     113     123 ..     111     123 .. 0.90
   3 ?   11.7   0.0   7.5e-05      0.19       5      21 ..     202     218 ..     198     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                   HHHHHHHHH CS
                            UBA 16 reevveALr 24
                                   +e+v eALr
  gi|118431777|ref|NP_148453.2| 36 DEAVTEALR 44
                                   5899****8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                    TTSHHHHHHHH CS
                            UBA  27 gnNeErAveyL 37 
                                    +++e+ A+ +L
  gi|118431777|ref|NP_148453.2| 113 FGSEDDALSWL 123
                                    6899******9 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 7.5e-05
                                    HHHHHHHTTS-HHHHHH CS
                            UBA   5 aiqrLveMGFdreevve 21 
                                    +++rLv++GF++e +++
  gi|118431777|ref|NP_148453.2| 202 TVERLVDLGFSEEKARR 218
                                    79***********9997 PP

>> DUF3173  Domain of unknown function (DUF3173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.2e-05      0.11       3      27 ..     201     225 ..     199     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                        DUF3173   3 vtkkdLiklGfkehtArdiIrqaKk 27 
                                    +t + L++lGf+e  Ar+i   aK+
  gi|118431777|ref|NP_148453.2| 201 ITVERLVDLGFSEEKARRIAEAAKQ 225
                                    67889***************99997 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00062       1.6     103     177 ..     151     225 ..     142     231 .. 0.89
   2 ?   -0.2   0.0      0.12   3.1e+02     297     335 ..     237     275 ..     229     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00062
                         Tweety 103 htlagikklvseteesleekleeeLtkleeifakrtdlletlrlvqeqveevvqqlselpflkkkdvsltelaeq 177
                                    +++  i+k+v+   ++l+e  + +  +l++++ +++d+++++ +v +  +  v+ l +l f ++k   ++e a+q
  gi|118431777|ref|NP_148453.2| 151 RAIDDIDKTVNLFVARLREWYSIHFPELNDLVREHEDYVKIVSAVGHRDNITVERLVDLGFSEEKARRIAEAAKQ 225
                                    67788999999*************************************************999998888877766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
                         Tweety 297 eqveellriavelfptaekkLlaiqellnsternlhqLt 335
                                    ++v++l ri+ el++   +  + i++++n    n++ L+
  gi|118431777|ref|NP_148453.2| 237 QAVQTLARITSELYQLRRRLTEYIEQVMNEVAPNITALV 275
                                    458999999999999998888999999999888888776 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.3   0.00036      0.92     112     178 ..     192     271 ..     127     276 .. 0.55
   2 ?   -1.3   0.0      0.68   1.7e+03      81      93 ..     368     380 ..     348     386 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00036
                                    HHHHHHHHCHHHHHHH......HHHHHHHHHHHH-----..---.......--SSSHHHHHHHTS-TTSHHHHHS--XXX CS
                 Apolipoprotein 112 vealkarlapyveelr......qklaerleelkeslaphaeeve.......erlssrveelrekleeqaeelrerleanl 178
                                    v+a+  r    ve+l+      +k ++ +e+ k+s+ + + e+        +r++s++ +lr++l+e++e++ +++ +n+
  gi|118431777|ref|NP_148453.2| 192 VSAVGHRDNITVERLVdlgfseEKARRIAEAAKQSIGADLSEIDiqavqtlARITSELYQLRRRLTEYIEQVMNEVAPNI 271
                                    55555555555555555555545666666666666666666555444445555666666666666666666655555554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.68
                                    HHHHHHHHCHHCC CS
                 Apolipoprotein  81 elrerlaadaeel 93 
                                    +lre l++++ e+
  gi|118431777|ref|NP_148453.2| 368 KLREELRRRIAEI 380
                                    3333333333333 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.5   8.9e+03      34      45 ..      34      45 ..      33      45 .. 0.76
   2 ?   -2.1   0.1       2.2   5.5e+03      20      28 ..     146     154 ..     137     161 .. 0.71
   3 ?   10.7   0.1   0.00023      0.58      10      37 ..     206     233 ..     203     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.5
                                   -HHHHHHHHHCC CS
                         RuvA_C 34 sveelIraALkl 45
                                   sv+e++ +AL+l
  gi|118431777|ref|NP_148453.2| 34 SVDEAVTEALRL 45
                                   688888888875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                    HHHHHHHHH CS
                         RuvA_C  20 aekAvakvl 28 
                                    a++A+++++
  gi|118431777|ref|NP_148453.2| 146 AAQAIRAID 154
                                    677777776 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00023
                                    HHHCTS-HHHHHHHHHHHHC-TTS-HHH CS
                         RuvA_C  10 LlaLGYkekeaekAvakvlanpgasvee 37 
                                    L+ LG++e+ a+++ +++++  ga+ +e
  gi|118431777|ref|NP_148453.2| 206 LVDLGFSEEKARRIAEAAKQSIGADLSE 233
                                    899****************988877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.40
# Mc/sec: 3121.19
//
Query:       gi|14601909|ref|NP_148454.1|  [L=50]
Description: 30S ribosomal protein S30 [Aeropyrum pernix K1]
Scores for complete 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-12   46.9   4.2    2.4e-12   46.8   4.2    1.0  1  Ribosomal_S30  Ribosomal protein S30
  ------ inclusion threshold ------
      0.034   14.6   4.4      0.053   14.0   4.2    1.5  2  Sas10          Sas10 C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   4.2   2.7e-16   2.4e-12       2      47 ..       3      47 ..       2      50 .] 0.87

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 2.7e-16
                                  TBX-STTTTHHHHHS-------------THHHHHHHHHHHTTSSS- CS
                 Ribosomal_S30  2 vhGsLarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvnvvv 47
                                   hGsL++AGKVr+qTP+   + +kK+   R k Rl+Y+ R ++v++
  gi|14601909|ref|NP_148454.1|  3 THGSLTKAGKVRKQTPRLPAK-QKKNYPPRLKNRLKYQVRIEKVAS 47
                                  5****************6555.49999**************99654 PP

>> Sas10  Sas10 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.8      0.06   5.3e+02      17      35 ..       7      25 ..       4      28 .. 0.67
   2 ?   14.0   4.2     6e-06     0.053      19      47 ..      21      49 ..      12      50 .] 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.06
                         Sas10 17 LtpkRkkenrnpRvkkrkk 35
                                  Lt+  k ++++pR+  ++k
  gi|14601909|ref|NP_148454.1|  7 LTKAGKVRKQTPRLPAKQK 25
                                  6666677778888766555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6e-06
                         Sas10 19 pkRkkenrnpRvkkrkkYekakkklksqv 47
                                  p ++k+n  pR+k+r kY+   +k++s +
  gi|14601909|ref|NP_148454.1| 21 PAKQKKNYPPRLKNRLKYQVRIEKVASAR 49
                                  78999999****************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 403.26
//
Query:       gi|14601910|ref|NP_148455.1|  [L=427]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Aeropyrum pernix K1]
Scores for complete 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-61  207.5   0.0    2.6e-61  206.5   0.0    1.5  1  Asparaginase     Asparaginase, N-terminal
    1.2e-33  115.7   0.1      3e-32  111.2   0.0    2.4  2  Asparaginase_C   Glutaminase/Asparaginase C-terminal domain
    9.2e-14   50.5   0.1    1.9e-13   49.5   0.1    1.6  1  GatD_N           GatD N-terminal domain
  ------ inclusion threshold ------
      0.022   13.2   0.0      0.031   12.7   0.0    1.2  1  Gly_reductase    Glycine/sarcosine/betaine reductase componen
      0.028   14.0   0.0       0.25   10.9   0.0    2.0  2  Peripla_BP_4     Periplasmic binding protein domain
       0.17   11.1   0.0       0.25   10.6   0.0    1.2  1  Calmodulin_bind  Calmodulin binding protein-like


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 !  206.5   0.0   8.6e-65   2.6e-61       1     185 [.      75     269 ..      75     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 206.5 bits;  conditional E-value: 8.6e-65
                                   EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT.-SEEE CS
                  Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealee.ydgfV 80 
                                   +v+++++GGTias++d+++ga++p l+a+el +++pel+++a++e+eql++i S++m+p+ w+ ++++ ++ le  ydg+V
  gi|14601910|ref|NP_148455.1|  75 RVYIIGAGGTIASRVDYETGAVKPYLDASELATTIPELQRYASIEAEQLFSILSEDMKPSMWEAIVDRAARVLEAgYDGVV 155
                                   79***********************************************************************666***** PP

                                   EE--STTHHHHHHHHHHHE.ES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......EEET CS
                  Asparaginase  81 vlhGTDTlaytAsaLslml.knldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......llra 153
                                   v+hGTDT+a+tAsaLs+++ k+l+ pv+ltGsqr++++++sD++ Nl++++l+a+   ++a+v+vv++g+        +r+
  gi|14601910|ref|NP_148455.1| 156 VAHGTDTMAFTASALSFAFhKGLPSPVILTGSQRSSDRPSSDAAFNLTASVLAASRA-PFAEVAVVMHGEtgdtyalAHRG 235
                                   ******************978899*******************************99.*********************** PP

                                   TTEEE-BSSSSS-EEETTT--SEEE..ETTEEEE CS
                  Asparaginase 154 nrvtKvhtssldaFespnlgplaev..egskvkv 185
                                    rv+K+h+s++daF+s+n +pla++   +++v++
  gi|14601910|ref|NP_148455.1| 236 VRVKKMHSSRRDAFQSVNDKPLARIypFEGRVEM 269
                                   ***********************99555556655 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 ?    2.0   0.0     0.078   2.3e+02      18      32 ..     145     159 ..     118     177 .. 0.77
   2 !  111.2   0.0     1e-35     3e-32       1     114 []     291     404 ..     291     404 .. 1.00

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.078
                                   HHHHTT--EEEEEEB CS
                Asparaginase_C  18 allkkgakGvvlegt 32 
                                    +l++g++Gvv++ +
  gi|14601910|ref|NP_148455.1| 145 RVLEAGYDGVVVAHG 159
                                   355999*****9965 PP

  == domain 2  score: 111.2 bits;  conditional E-value: 1e-35
                                   -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHHT CS
                Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerlg 81 
                                   rV+++k +pg+  +v++all++g kG+v+egtG G+++s+ ++ +++a+++g+++v+t+q+++g+v+ ++y++g+++ ++g
  gi|14601910|ref|NP_148455.1| 291 RVALVKHFPGLISEVIDALLDRGFKGIVVEGTGFGHVSSDAIKSIERARDQGVPIVITTQTVFGRVNLNVYSTGRKMLAAG 371
                                   8******************************************************************************** PP

                                   EEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                Asparaginase_C  82 visaddmtpeaarikLmlllgkgldpaevrklf 114
                                   +i a+dmt eaa++kL ++l+++++ + vrk+f
  gi|14601910|ref|NP_148455.1| 372 AIPAGDMTSEAAYAKLSWILARTRELEVVRKMF 404
                                   ********************************9 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.1   6.3e-17   1.9e-13       9      52 ..       3      47 ..       1      49 [. 0.88

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.3e-17
                                  EE-SS.-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.-- CS
                        GatD_N  9 vekkg.reyeGilmPrselsdddiivlKLdnGYNiGikieeieki 52
                                  v++++ ++++G+lmP++e+s +d++v+KL nGYNiG+ + e ++i
  gi|14601910|ref|NP_148455.1|  3 VRRGDgSVFRGVLMPKHETSHPDTVVIKLGNGYNIGVLVGEGDDI 47
                                  6666669******************************99887666 PP

>> Gly_reductase  Glycine/sarcosine/betaine reductase component B subunits
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05     0.031     303     348 ..     313     358 ..     302     408 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                 Gly_reductase 303 gadgvivseeGyGnpdtdlimnikklekaGiktvlitdelaGrdga 348
                                   g++g++v   G+G+ ++d i  i+++ ++G+  v+ t+ + Gr + 
  gi|14601910|ref|NP_148455.1| 313 GFKGIVVEGTGFGHVSSDAIKSIERARDQGVPIVITTQTVFGRVNL 358
                                   6789************************************999765 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 ?    0.6   0.0      0.11   3.3e+02      51     152 ..     146     261 ..     133     278 .. 0.70
   2 ?   10.9   0.0   8.4e-05      0.25      46      85 ..     304     347 ..     303     366 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                                   HHHTT-SEEEE--.SSHHHHH.HHHHHHHHTT-..EEEEESTT...GCTTT-CEEEEEC-HHHHHHHHHHHHHHHCTTH.E CS
                  Peripla_BP_4  51 aiakgvdgiivap.vdstala.palkkakaaGI..pVvafdsd...dapsgerlayvgfdneaaGelqaeylaeklggkkg 124
                                   ++++g+dg++va  +d+ a + +al  a  +G   pV+   s+   d ps++ + + ++   aa ++    +a  + g++g
  gi|14601910|ref|NP_148455.1| 146 VLEAGYDGVVVAHgTDTMAFTaSALSFAFHKGLpsPVILTGSQrssDRPSSDAAFNLTASVLAASRAPFAEVAVVMHGETG 226
                                   567888888876514556666688888888888555888888877777777777777777777777777777777777745 PP

                                   EEEEE..TSCCCHHHHHHHHHHHHHHHHH.....- CS
                  Peripla_BP_4 125 kvvil..aGspgdpnaeeriegfrkvlke.....y 152
                                   + ++l  +G+   + +  r ++f +v ++     y
  gi|14601910|ref|NP_148455.1| 227 DTYALahRGVRVKKMHSSRRDAFQSVNDKplariY 261
                                   55555568888888888888888888666444454 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.4e-05
                                   HHHHHHHHTT-SEEEE--SSH....HHHHHHHHHHHHTT-EEEE CS
                  Peripla_BP_4  46 aqiedaiakgvdgiivapvds....talapalkkakaaGIpVva 85 
                                   ++i++++++g++gi+v  +      + + + +++a+++G+p+v 
  gi|14601910|ref|NP_148455.1| 304 EVIDALLDRGFKGIVVEGTGFghvsSDAIKSIERARDQGVPIVI 347
                                   689************8876543333444458999*******886 PP

>> Calmodulin_bind  Calmodulin binding protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   8.3e-05      0.25     186     225 ..     106     145 ..      91     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-05
               Calmodulin_bind 186 IktVqdflkllvkdeekLrkilgkgmsdkmWektveHAkt 225
                                    +t+ ++ +   +++e+L +il ++m+  mWe++v+ A +
  gi|14601910|ref|NP_148455.1| 106 ATTIPELQRYASIEAEQLFSILSEDMKPSMWEAIVDRAAR 145
                                   36788999999*************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3351.85
//
Query:       gi|14601911|ref|NP_148456.1|  [L=642]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Aeropyrum pernix K1]
Scores for complete 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-72  243.5   0.0    3.3e-72  243.2   0.0    1.1  1  GatB_N       GatB/GatE catalytic domain
    2.7e-22   79.3   0.1    4.8e-22   78.4   0.1    1.4  1  GatB_Yqey    GatB domain
    5.7e-22   77.8   0.0    1.5e-21   76.4   0.0    1.8  1  GAD          GAD domain
    3.5e-07   30.4   0.2    7.5e-07   29.3   0.2    1.5  1  YqeY         Yqey-like protein
  ------ inclusion threshold ------
      0.026   15.0   0.9       0.11   12.9   0.2    2.4  2  FumaraseC_C  Fumarase C C-terminus


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 !  243.2   0.0   9.2e-76   3.3e-72       2     272 ..      12     449 ..      11     450 .. 0.96

  Alignments for each domain:
  == domain 1  score: 243.2 bits;  conditional E-value: 9.2e-76
                                   EEEEEEEEEB--SB-SSSSSBSS...SSCE........S.TTSS--TTTTTS...........................TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxx...xxxx........x.xxxxxxxxxxxx...........................xx RF
                        GatB_N   2 viGlEiHaqlktksKlFssaste...eege........e.pnsevsevdlal...........................PG 43 
                                   ++GlEiH+ql+t++KlF+s+++e   e  e        + ++se++ vd a+                           P 
  gi|14601911|ref|NP_148456.1|  12 KVGLEIHQQLDTREKLFCSCPAElgeE--EhdefvrqlRpTRSELGDVDPAAlfewrkgrlyiyqaplnhsclveadeeP- 89 
                                   89*******************876541..13457888844899999999999************************9998. PP

                                   ..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE---EE CS
                                   xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                        GatB_N  44 tlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDaaks 122
                                     P+ +n+eav +a+++a+al++ i +e++++RK+++++++++g+Q+t+    +a +Gs+++ +k+v ie+i +EeDaa++
  gi|14601911|ref|NP_148456.1|  90 --PHpINREAVAVAVAVAKALGSAIVDEVHVMRKTVIDGSNTSGFQRTA---IVALGGSIRVgSKEVPIETIVIEEDAARK 165
                                   ..999********************************************...5669*****9999**************** PP

                                   EEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTSSS.--E CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 123 vheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekgeeegtrv 203
                                   v e+ ++++++l+R+G+pLiEi+t+p ++sp ear+v+ +++++lr +g++++++  G++R+D+NvS+r        g+++
  gi|14601911|ref|NP_148456.1| 166 VGEKGRYVVYRLDRLGIPLIEIATAPVIESPGEAREVALAIGTMLRLTGKVKRGL--GTIRQDLNVSIRG-------GAKT 237
                                   *******************************************************..************4.......59** PP

                                   EEEEE-SHHHHHHHHHHHHHHHHHHH....................................................... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                        GatB_N 204 EiKnlnslksiekaieyeierqiell....................................................... 229
                                   EiK++++l+ i ++ieye+ rq++ll                                                       
  gi|14601911|ref|NP_148456.1| 238 EIKGVQRLELIPRVIEYEVLRQLSLLrirdmlrergvsreelenvepvdvssllagsksrvikkvlssggkviavklprmk 318
                                   ********************************************************************************* PP

                                   ................................................................................. CS
                                   ................................................................................. RF
                        GatB_N 230 ................................................................................. 229
                                                                                                                    
  gi|14601911|ref|NP_148456.1| 319 giigmeimpgrrfgteladyarfwggvggiihsdelpgygitgdevekiyeavggdpgvdafalvadkpsnalraaravle 399
                                   ********************************************************************************* PP

                                   ..........-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHH CS
                                   ..........xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                        GatB_N 230 ..........qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseeli 272
                                             +eTr++ ed g+t++lR+++ +a   r++pe+d+ppl+i+e+++
  gi|14601911|ref|NP_148456.1| 400 rvaaalegvpEETRAALED-GTTRYLRPRPgSA---RMYPETDIPPLRIDENIL 449
                                   *******************.**********555...**************9876 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.1   1.3e-25   4.8e-22      18     148 .]     507     632 ..     493     632 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.3e-25
                                   HHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHHHH CS
                     GatB_Yqey  18 nwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeeiieekgLkqisdeeelekl 97 
                                   + +++ +l+ l+ eg+e+ +  + ++ l+++l+++a+g+I+ ++a e+++ l+++ g+++ee++e+ gL+ +s  ee+e++
  gi|14601911|ref|NP_148456.1| 507 AGFFVVVLRGLEGEGVEVWK--VDDAILEKILDMVAQGEIAREAAAELVKYLANNpGSTVEEAVEKLGLRRLSR-EEVERI 584
                                   556788999***********..9**************************************************8.****** PP

                                   HHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                     GatB_Yqey  98 veeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                   v+e++       e++ ++ eka+++ +G+ M k++G+ad++lv+e++ +k+
  gi|14601911|ref|NP_148456.1| 585 VDEIVGGL---REEILKRGEKAVGLVMGRAMAKLRGRADGRLVSEIVSRKI 632
                                   ********...9**********************************99876 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   4.2e-25   1.5e-21       1      94 [.     299     393 ..     299     394 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 4.2e-25
                                   HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TT.E CS
                           GAD   1 fsealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeeg.D 79 
                                   ++++l+sgg+v a+++p+ +++++++ei+++++f++el++++++w +v+g  ++++++ + +t++ev+k++eavg ++g D
  gi|14601911|ref|NP_148456.1| 299 IKKVLSSGGKVIAVKLPR-MKGIIGMEIMPGRRFGTELADYARFWGGVGGIIHSDELPGYgITGDEVEKIYEAVGGDPGvD 378
                                   6899**************.8************************************************************* PP

                                   EEEEEEEEHHHHHHH CS
                           GAD  80 illfvAdkkktvnka 94 
                                   ++ +vAdk +++ +a
  gi|14601911|ref|NP_148456.1| 379 AFALVADKPSNALRA 393
                                   ********9999887 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.2   2.1e-10   7.5e-07      90     142 ..     575     631 ..     568     632 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.1e-10
                                   ---HHHHHHHHHHHHHHTT--....BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH CS
                          YqeY  90 qlseeeiealvkeaiaevgae....smkdmGkvmkalkpkvkGkaDgkkvsalvkek 142
                                   +ls+ee+e++v+e++  + +e    + k++G vm+ +++k++G+aDg+ vs++v +k
  gi|14601911|ref|NP_148456.1| 575 RLSREEVERIVDEIVGGLREEilkrGEKAVGLVMGRAMAKLRGRADGRLVSEIVSRK 631
                                   79*************76655544459****************************876 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.2   4.4e+03      28      45 ..     265     281 ..     263     285 .. 0.82
   2 ?   12.9   0.2   3.1e-05      0.11      12      48 ..     547     586 ..     547     587 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                   HHHHHHHTT-.-HHHHHH CS
                   FumaraseC_C  28 lreavlelgllteeelde 45 
                                   +r++  e+g+ ++eel+ 
  gi|14601911|ref|NP_148456.1| 265 IRDMLRERGV-SREELEN 281
                                   8999999996.9999875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHH.HT--HHHHHHHTT-...-HHHHHHHT- CS
                   FumaraseC_C  12 ekAakIAkeAlk.egktlreavlelgl..lteeeldelld 48 
                                   e+Aa+++k   +  g t+ eav +lgl  l++ee+++++d
  gi|14601911|ref|NP_148456.1| 547 EAAAELVKYLANnPGSTVEEAVEKLGLrrLSREEVERIVD 586
                                   67899998755527************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4669.31
//
Query:       gi|118431778|ref|NP_148457.2|  [L=284]
Description: hypothetical protein APE_2206.1 [Aeropyrum pernix K1]
Scores for complete 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   52.8   0.4    3.6e-14   52.8   0.4    2.2  2  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.082   13.4   8.7      0.077   13.5   6.6    2.0  2  RexB      Membrane-anchored ion channel, Abi component
        0.9    9.1  10.5        2.5    7.7   0.1    2.6  2  DUF417    Protein of unknown function, DUF417


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 !   52.8   0.4     6e-18   3.6e-14       1     124 [.      75     201 ..      75     202 .. 0.94
   2 ?   -2.1   1.6      0.57   3.4e+03     106     118 ..     264     276 ..     253     282 .. 0.51

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 6e-18
                                    HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHCT-TT....TS.-HHHHHHHHHHHHHT- CS
                          T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslsealertps...sef.pelvvqlirageeggn 76 
                                    flr +a   ++G+++++++ +l++ + +gpl+++++ria+ l+ G+sl+++++r+ +   ++   + ++ l+ +++ gg 
  gi|118431778|ref|NP_148457.2|  75 FLRDIAETRKTGLSPEQSIISLSARD-YGPLTKVVRRIATSLQLGMSLEDSVRRSVRrikDWAsLSALRFLVDSISVGGG 153
                                    89999*********************.**************************4444444799899************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                          T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                     +evL++la+y      ++ + ++++  ++++ +++++++++  +++l
  gi|118431778|ref|NP_148457.2| 154 SPEVLDALARYTYGLVSIQDEFRKRTRIYIIMPYLGAIIVAASTLVML 201
                                    ****************************************99988887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.57
                                    XXXXXXXXXXXXX CS
                          T2SSF 106 llllvvallvlli 118
                                    ++l+v++l+++ +
  gi|118431778|ref|NP_148457.2| 264 IILIVITLAIVTL 276
                                    4444444444333 PP

>> RexB  Membrane-anchored ion channel, Abi component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.54   3.3e+03      69      84 ..      97     112 ..      42     119 .. 0.66
   2 ?   13.5   6.6   1.3e-05     0.077      49     129 ..     189     268 ..     179     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.54
                           RexB  69 kireygymtsvvivya 84 
                                      r+yg +t vv   a
  gi|118431778|ref|NP_148457.2|  97 SARDYGPLTKVVRRIA 112
                                    3467777777775555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.3e-05
                           RexB  49 iailiaaltfligsrtrrlakireygymtsvvivyalsfvelgalffcgllllssisgymiptiaigiasasfihicilv 128
                                     ai++aa t+++   t +  ++ + g  tsvv v    +  +g ++  g++l s + g m   i  g   a fih  il+
  gi|118431778|ref|NP_148457.2| 189 GAIIVAASTLVMLGYTIKTLQVVNPGGETSVVAVPEN-IGVVGLILAIGVMLNSWMMGLMAGKIREGTIGAGFIHSIILI 267
                                    4899*****999889999999999999****999754.455799999****************************98886 PP

                           RexB 129 f 129
                                    +
  gi|118431778|ref|NP_148457.2| 268 V 268
                                    5 PP

>> DUF417  Protein of unknown function, DUF417
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00041       2.5      75     112 ..     173     210 ..     160     219 .. 0.88
   2 ?    2.9   6.4     0.012        73      82     116 ..     218     250 ..     214     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00041
                         DUF417  75 kewhkengvykvsnllGiievivgilvliglrnakvgl 112
                                     e++k  ++y +   lG+i+v +  lv++g   +++ +
  gi|118431778|ref|NP_148457.2| 173 DEFRKRTRIYIIMPYLGAIIVAASTLVMLGYTIKTLQV 210
                                    58999*************************98887765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.012
                         DUF417  82 gvykvsnllGiievivgilvliglrnakvgllggl 116
                                     v +v + +G++ +i++i+v+++ ++  +gl++g 
  gi|118431778|ref|NP_148457.2| 218 SVVAVPENIGVVGLILAIGVMLNSWM--MGLMAGK 250
                                    6778999****************997..4555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2311.47
//
Query:       gi|118431779|ref|NP_148458.2|  [L=332]
Description: hypothetical protein APE_2207.1 [Aeropyrum pernix K1]
Scores for complete 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-14   53.3   0.4    2.6e-14   53.3   0.4    2.5  3  T2SSF            Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.66   10.2  13.4       0.14   12.4   3.7    2.2  2  EI24             Etoposide-induced protein 2.4 (EI24)
        2.1    7.0  10.2        1.9    7.2   0.2    2.1  2  DUF2207          Predicted membrane protein (DUF2207)
        4.6    7.0   6.8         24    4.6   0.1    2.2  2  FA_desaturase    Fatty acid desaturase


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 ?   -1.0   0.3      0.36   1.6e+03      84     124 ..      47      87 ..      41      89 .. 0.65
   2 ?   -4.7   2.5         4   1.8e+04     106     120 ..     105     119 ..      96     122 .. 0.53
   3 !   53.3   0.4   5.7e-18   2.6e-14       1     123 [.     145     272 ..     145     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.36
                                    HHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                          T2SSF  84 laeyleeerelrrkllaallepllllvvallvllillaill 124
                                    la  l + +el+r+l+ a +++  ++++  l+ll   ++ll
  gi|118431779|ref|NP_148458.2|  47 LAVRLVKTFELERNLKIAGIQVYPVMYMSRLLLLSTAVFLL 87 
                                    66667777777777777777777777776666666666654 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 4
                                    XXXXXXXXXXXXXXX CS
                          T2SSF 106 llllvvallvllill 120
                                    ++++v+++l +++++
  gi|118431779|ref|NP_148458.2| 105 KAIVVLIALSAPFMV 119
                                    444444444444444 PP

  == domain 3  score: 53.3 bits;  conditional E-value: 5.7e-18
                                    HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT CS
                          T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageegg 75 
                                    f+ +l+++ ++Gvp+  +++++a+ + +++l+ee + i++++r  g ++ +ale     +pss+f++++  +++a++ g+
  gi|118431779|ref|NP_148458.2| 145 FAAYLSIMGRGGVPVSLVIDRVASLKIFKALREEAEMIRTKIRLLGkNPLDALEehvlDSPSSVFRDFILGYTTAVKVGS 224
                                    7889***************************************9887888999988889999****************** PP

                                    -HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                          T2SSF  76 nLaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                    ++ ++Le   ++l e+r + ++lla+++   l+++++++v++ +++++
  gi|118431779|ref|NP_148458.2| 225 DVIHYLEIRTQDLFERRLNDIRLLAERMTLYLEIYLVVAVIATIVFYI 272
                                    ******************************************999987 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 ?   12.4   3.7   3.2e-05      0.14      18      74 ..      73     130 ..      66     190 .. 0.74
   2 ?    3.4   2.1     0.018        81      44     108 ..     259     316 ..     206     322 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHHHHHHHHHHHH-.TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EI24  18 llllplllnlllfllllvlllw.vllasllvllllllplwlfplvalllaapfyglla 74 
                                    ++   lll+ ++fll++++ +w  l  + +++ ++++++ l+  + ++ a+++y+ l 
  gi|118431779|ref|NP_148458.2|  73 YMSRLLLLSTAVFLLGVYFSFWtLLSGFSIIVKAIVVLIALSAPFMVFAAGLMYPSLK 130
                                    566789****************744445555555555555555666666666666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHCCTTSHHHHHHHHHHHHHHHHHHHHH CS
                           EI24  44 sllvllllllplwlfplvalllaapfygllaekvekrhlglvkslaeslkslllllllllvllpl 108
                                     l+v  ++++++++f +++ ++ + + g+ +++ ++            l+s+l+l ++++++l+l
  gi|118431779|ref|NP_148458.2| 259 YLVVAVIATIVFYIFFTISSVFHGNLGGVASAQYASTTQ-------LILYSFLVLPTINVIMLLL 316
                                    344444445555555566666666666666666654333.......5566666666666666655 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.0    0.0081        36     379     431 ..      73     122 ..      66     140 .. 0.67
   2 ?    7.2   0.2   0.00042       1.9     377     433 ..     250     320 ..     170     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0081
                        DUF2207 379 klkklsalglgliilglilillallllvlllvfllilllillliaiivlllfs 431
                                    ++ +l +l++++++lg+++++++ll+ ++++v + ++l++l   ++++   ++
  gi|118431779|ref|NP_148458.2|  73 YMSRLLLLSTAVFLLGVYFSFWTLLSGFSIIVKAIVVLIALSAPFMVF---AA 122
                                    67899999999*********9999987654444444444443333333...33 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00042
                        DUF2207 377 kkklkklsalglgliilglilillallllvll..............lvfllilllillliaiivlllfsrl 433
                                    ++ + +l +++++++i+ +++ +++ ++ v++                ++l+ +l+l+ i++i+lll  r 
  gi|118431779|ref|NP_148458.2| 250 ERMTLYLEIYLVVAVIATIVFYIFFTISSVFHgnlggvasaqyastTQLILYSFLVLPTINVIMLLLVDRA 320
                                    445556667777777777777777777777778889********998888888999999999999887665 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.2    0.0087        39     128     171 ..      63     113 ..       9     130 .. 0.64
   2 ?    4.6   0.1    0.0054        24      88     159 ..     205     275 ..     189     312 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0087
                  FA_desaturase 128 sksrrrkwrllawlllllawlglwlalllllglall.......lwlvplll 171
                                    +++++ + ++++ +llll+ ++++l++++ ++ +l+       +++v ++l
  gi|118431779|ref|NP_148458.2|  63 IAGIQVYPVMYMSRLLLLSTAVFLLGVYFSFWTLLSgfsiivkAIVVLIAL 113
                                    233333377888888888888888888888877777654333322222222 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0054
                  FA_desaturase  88 rfeglfryllrlllgllvlgwllalvlglwlrrlarrrapsksrrrkwrllawlllllawlglwlalllllg 159
                                    + + ++ ++l+++  + v + ++ ++++ +   + rr  +++  + + +l++   l++a+ ++ ++++ ++ 
  gi|118431779|ref|NP_148458.2| 205 PSSVFRDFILGYTTAVKVGSDVIHYLEIRTQDLFERRLNDIRLLAERMTLYLEIYLVVAV-IATIVFYIFFT 275
                                    555566677788888888887777777778888888888888888773333333333332.22222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2668.54
//
Query:       gi|118431780|ref|NP_148459.2|  [L=580]
Description: protein kinase [Aeropyrum pernix K1]
Scores for complete 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-47  160.5   0.0    8.9e-47  159.4   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
    0.00024   20.8   0.1    0.00099   18.8   0.1    2.1  2  AAA_29           P-loop containing region of AAA domain
     0.0011   19.5   0.0     0.0029   18.1   0.0    1.6  1  ABC_tran         ABC transporter
      0.008   16.5   0.0      0.022   15.1   0.0    1.7  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.032   14.0   0.1       0.13   12.0   0.0    1.9  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.039   13.3   0.0      0.097   12.0   0.0    1.6  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.043   13.4   0.1      0.082   12.5   0.1    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.063   13.8   0.7       0.13   12.7   0.7    1.5  1  AAA_23           AAA domain
      0.098   13.0   0.0       0.31   11.4   0.0    1.8  2  AAA_16           AAA ATPase domain
       0.11   12.1   0.4       0.24   11.1   0.1    1.7  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   0.0     5e-50   8.9e-47       4     245 ..     188     438 ..     186     458 .. 0.94

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 5e-50
                          T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrv 82 
                                    +++ l++de   di     +r v v  +  +   +++ + ++++l  +i  +a+ a+++is   p++da lp +g+r+ +
  gi|118431780|ref|NP_148459.2| 188 PIDVLMKDEYLEDISCDGVGRpVYVWHQEYESIKSNIVFEDERQLDHMILLLAHRAGKHISVAFPVLDAVLP-EGHRVAA 266
                                    56778999999***********99977777778999************************************.9****99 PP

                          T2SSE  83 vllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                     +   v +   +++iRk +a  l++ dl++ ++ +++ia+ l    + r+  ++ G TgsGKtt+l+a+ + +  +  +i
  gi|118431780|ref|NP_148459.2| 267 TFRREVSTqgSTFTIRKFKATPLSIVDLIIGGTISPDIAAYLWLMAEYRMPGIIMGVTGSGKTTTLNAIATLLRPN-VKI 345
                                    998776665699********************************99999999*********************999.*** PP

                          T2SSE 161 vtvEDpvEiqleganqvqlnak.........kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTl 231
                                    vt+ED+ Ei+l ++n vql+++         ++++ + dl+r +LR rPD+i+vGE+R++e++ + +A+ TGH g l+T+
  gi|118431780|ref|NP_148459.2| 346 VTIEDTPEIKLPHENWVQLVSRpsfsvtgesRGEISLYDLVRVSLRYRPDVIIVGEVRGEEAYVLFQALATGHGG-LTTI 424
                                    *************************************************************************99.**** PP

                          T2SSE 232 HansaagalerLeq 245
                                    H+++    ++rL  
  gi|118431780|ref|NP_148459.2| 425 HSETIEAMIRRLTS 438
                                    ***********986 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   0.1   5.5e-07   0.00099      26      51 ..     319     344 ..     310     347 .. 0.87
   2 ?   -2.3   0.0       2.2   3.9e+03       3      19 ..     491     508 ..     490     515 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.5e-07
                         AAA_29  26 lltGpsGsGKSTllDAiqalLvpakk 51 
                                    +++G +GsGK+T l Ai++lL p+ k
  gi|118431780|ref|NP_148459.2| 319 IIMGVTGSGKTTTLNAIATLLRPNVK 344
                                    89********************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                         AAA_29   3 rlqlvNWgtfdg.htiei 19 
                                     ++++ W  f++ h++ +
  gi|118431780|ref|NP_148459.2| 491 AIEVARWNPFTKeHEHFM 508
                                    589999****99665544 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-06    0.0029      16      48 ..     320     352 ..     317     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                                    EEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  16 ivGenGaGKStLlkllagllkpteGeilldgkd 48 
                                    i+G +G+GK+t l+++a ll+p+   +++++++
  gi|118431780|ref|NP_148459.2| 320 IMGVTGSGKTTTLNAIATLLRPNVKIVTIEDTP 352
                                    99********************99999998654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.022       5      98 ..     315     400 ..     312     403 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...erlsseellea 81 
                                    +  ++++G +G+GKTt+l+ ++  l         rp v  vt+    + k   ++ ++ + ++  +   e   +  l+++
  gi|118431780|ref|NP_148459.2| 315 RMPGIIMGVTGSGKTTTLNAIATLL---------RPNVKIVTIEDTPEIKLPHENWVQLVSRPSFSvtgESRGEISLYDL 385
                                    56799******************99.........7776666666655555555555555555555554333344444444 PP

                         AAA_22  82 leqalraravielliiD 98 
                                    ++  lr r +  ++i+ 
  gi|118431780|ref|NP_148459.2| 386 VRVSLRYRPD--VIIVG 400
                                    4444444444..66665 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 ?   -1.5   0.0      0.95   1.7e+03      61      94 ..     220     251 ..     211     252 .. 0.75
   2 ?   12.0   0.0   7.2e-05      0.13       2      41 ..     319     353 ..     318     377 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.95
                Viral_helicase1  61 tkgkililDEylllhaGyilllaalskaklvilf 94 
                                     k++i++ DE +l h  +illla++++ ++ ++f
  gi|118431780|ref|NP_148459.2| 220 IKSNIVFEDERQLDH--MILLLAHRAGKHISVAF 251
                                    457888889999999..78888888887776665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.2e-05
                Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk.pk 41 
                                    ++ Gv G+GK+t +  ++         rp+++++t    p+
  gi|118431780|ref|NP_148459.2| 319 IIMGVTGSGKTTTLNAIATL------LRPNVKIVTIEDtPE 353
                                    799*********99999988......555555555444433 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.4e-05     0.097      38      59 ..     316     335 ..     302     341 .. 0.88
   2 ?   -3.8   0.0       3.5   6.4e+03     102     129 ..     518     548 ..     510     555 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                                    S-.SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE  38 mashllvaGatgsGKStalntL 59 
                                    m+  ++++G tgsGK+t+ln++
  gi|118431780|ref|NP_148459.2| 316 MP--GIIMGVTGSGKTTTLNAI 335
                                    55..89**************96 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.5
                                    HHHHHHHHHHHHHHHHHHH...HHHHHTT-S CS
                   FtsK_SpoIIIE 102 peralraleeLvkemeery...alfreagvr 129
                                     + +  + +e+++e+e+r+     ++++g+r
  gi|118431780|ref|NP_148459.2| 518 GKLVGLTKDEVLAEIERRKlvlLWMAKSGIR 548
                                    5555566788999999999533334444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.6e-05     0.082       5      31 ..     319     345 ..     317     350 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.6e-05
                                    EEEESTTSSHHHHHHHHHHHHHHTTS- CS
                          SRP54   5 llvGlqGaGKTttlaKLaallkkegkk 31 
                                    +++G++G+GKTttl  +a ll+ + k 
  gi|118431780|ref|NP_148459.2| 319 IIMGVTGSGKTTTLNAIATLLRPNVKI 345
                                    589***************999877554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   7.4e-05      0.13      23      43 ..     319     339 ..     318     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.4e-05
                         AAA_23  23 lItGpNGaGKTTildAiklaL 43 
                                    +I G +G+GKTT l+Ai   L
  gi|118431780|ref|NP_148459.2| 319 IIMGVTGSGKTTTLNAIATLL 339
                                    699**************8765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.5   9.9e+03     103     127 ..      42      67 ..      15      74 .. 0.67
   2 ?   11.4   0.0   0.00018      0.31      28      77 ..     319     366 ..     312     419 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.5
                         AAA_16 103 eala.avpelagaeasrllellkrll 127
                                    e+++ + ++l++a++ +l ++l rl 
  gi|118431780|ref|NP_148459.2|  42 EVIRrEEKALRPAIEASLDAKLLRLS 67 
                                    22224556777888888888887765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                         AAA_16  28 llsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqala 77 
                                    ++ G  G+GK++ ++++++ l+ +  +++++ + +     +p   ++q+ +
  gi|118431780|ref|NP_148459.2| 319 IIMGVTGSGKTTTLNAIATLLRPNVkIVTIEDTPEIK---LPHENWVQLVS 366
                                    689***************9888883244455555444...55555666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         5   8.9e+03     149     167 ..      38      56 ..      34      62 .. 0.77
   2 ?   11.1   0.1   0.00013      0.24      21      43 ..     318     340 ..     305     349 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 5
                         AAA_30 149 aeLtevvRqkeseeraaal 167
                                     +L+ev+R +e++ r a +
  gi|118431780|ref|NP_148459.2|  38 ETLDEVIRREEKALRPAIE 56 
                                    6899999998888877765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                         AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                     ++ G+ G+GKtt+l+a++ +++
  gi|118431780|ref|NP_148459.2| 318 GIIMGVTGSGKTTTLNAIATLLR 340
                                    5899**************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 4164.75
//
Query:       gi|118431781|ref|NP_148460.2|  [L=144]
Description: hypothetical protein APE_2211.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-12   46.0   0.0      8e-12   45.5   0.0    1.2  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 !   45.5   0.0   4.5e-16     8e-12       1      98 [.      45     138 ..      44     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.5e-16
                                    TTXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHH CS
                           OsmC   1 gdgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkllek 80 
                                    g+++g +P  ll+a+lasC  +  r v ++ g++  d++v v+a+ +   a+g+ ++ +++ +k  +    ++++ ++ k
  gi|118431781|ref|NP_148460.2|  45 GPERGLTPLGLLAASLASCEVLMSRLVGRMLGYNGFDVRVAVTADVQV--AEGLRSLSIRYVFKGVD-I--DTANLIVSK 119
                                    56679**************************77766777776666554..467999*****997443.4..89******* PP

                                    HHHHSHHHHHH.CT-SSSE CS
                           OsmC  81 aekrCpvsntl.kngvkve 98 
                                    +++ Cpv+n+l +ngv+ve
  gi|118431781|ref|NP_148460.2| 120 VKELCPVYNSLvRNGVSVE 138
                                    ****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1095.32
//
Query:       gi|118431782|ref|NP_148461.2|  [L=292]
Description: hypothetical protein APE_2212.1 [Aeropyrum pernix K1]
Scores for 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-116  386.3   0.0   7.3e-116  386.2   0.0    1.0  1  SDH_sah        Serine dehydrogenase proteinase
    2.6e-06   27.5   0.0    9.2e-06   25.7   0.0    1.8  2  CLP_protease   Clp protease
     0.0099   15.8   0.0      0.019   14.9   0.0    1.5  1  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.36   11.0   0.0    1.4  1  Ku_PK_bind     Ku C terminal domain like


Domain annotation for each model (and alignments):
>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.2   0.0  1.6e-119  7.3e-116       8     278 ..       6     281 ..       1     289 [. 0.95

  Alignments for each domain:
  == domain 1  score: 386.2 bits;  conditional E-value: 1.6e-119
                        SDH_sah   8 sslssllwfllflylllapqlkrkqlllarlkvlrkleekrksrvitmihrqesigflGipiykfitiedseevlrairl 87 
                                    +sl+ ll++ll+l  +l+p l  ++l++arl+++r +e+k + rvitmihr+e ++f+Gip+ +fi+i+dse v+rair+
  gi|118431782|ref|NP_148461.2|   6 TSLVWLLFWLLILASMLNPVLAVRRLQAARLELIRSMEKKYGWRVITMIHREERVSFFGIPLRRFIDIDDSEAVIRAIRS 85 
                                    6789999************************************************************************* PP

                        SDH_sah  88 tpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlg......q 161
                                    tp +kpi li+htpGGlvlaa qia+alk h+ +  vivphyamsGGtlialaadei +d+navlGp+dpql+       
  gi|118431782|ref|NP_148461.2|  86 TPPEKPIALILHTPGGLVLAASQIARALKRHRGRKIVIVPHYAMSGGTLIALAADEIRMDPNAVLGPLDPQLSagptgpA 165
                                    ************************************************************************83333334 PP

                        SDH_sah 162 ypaasilkvvekkeakdiddktliladiakkaikqveefvyellkdkydeekakeiakklteGrwthdypltveelkelG 241
                                    +pa+s++kv   k+ kd++d tlilad+a+kai++++e++ ellkdk++ eka+e a  lteGrwthdyp+t e+++e+G
  gi|118431782|ref|NP_148461.2| 166 VPAPSVVKVARMKG-KDAQDTTLILADVAEKAIEEMREVITELLKDKMGVEKARETAVLLTEGRWTHDYPITFEKAREIG 244
                                    89**********99.9**************************************************************** PP

                        SDH_sah 242 levntnvpeevyellelyeqplgqrpsveyipvpvkk 278
                                    l+v+ +vp evy+l+ely+q   +rp vey+p p+  
  gi|118431782|ref|NP_148461.2| 245 LPVSDEVPPEVYQLMELYPQAPANRPGVEYLPQPIPY 281
                                    ********************************99865 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   2.1e-09   9.2e-06      39     101 ..      82     143 ..      52     150 .. 0.88
   2 ?   -1.0   0.0      0.32   1.4e+03     129     153 ..     194     218 ..     181     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.1e-09
                                    HHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS-TTGE CS
                   CLP_protease  39 lLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaagekgkR 101
                                    ++ ++ p+k+i l++++pGG v a+  I+ +++ ++ + ++i+   a+S g+l+++a+++  R
  gi|118431782|ref|NP_148461.2|  82 AIRSTPPEKPIALILHTPGGLVLAASQIARALKRHRGRKIVIVPHYAMSGGTLIALAADEI-R 143
                                    5567789**************************************************9976.4 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHHHHHHHTS-HHH CS
                   CLP_protease 129 aeellkikerlneilakhtgqslek 153
                                     + +++++e ++e+l+++ g +  +
  gi|118431782|ref|NP_148461.2| 194 EKAIEEMREVITELLKDKMGVEKAR 218
                                    4678899999999998888766554 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.3e-06     0.019      10      40 ..     121     151 ..     113     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                                    EEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                  Peptidase_S49  10 vasaenvaaSggYylasaadkivanpstivg 40 
                                    ++++  +a Sgg ++a aad+i ++p+++ g
  gi|118431782|ref|NP_148461.2| 121 IVIVPHYAMSGGTLIALAADEIRMDPNAVLG 151
                                    467889**********************987 PP

>> Ku_PK_bind  Ku C terminal domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     8e-05      0.36      17      51 ..     191     225 ..     182     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8e-05
                     Ku_PK_bind  17 dlvekavkqlksvIeqlvedslgdssydkaveclk 51 
                                    d  eka++++ +vI++l++d++g ++ ++ +  l+
  gi|118431782|ref|NP_148461.2| 191 DVAEKAIEEMREVITELLKDKMGVEKARETAVLLT 225
                                    66899*****************9977666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 2360.09
//
Query:       gi|14601917|ref|NP_148462.1|  [L=163]
Description: aldehyde dehydrogenase, small subunit [Aeropyrum pernix K1]
Scores for complete 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-31  107.0   0.0    3.6e-31  107.0   0.0    2.3  3  Fer2_2    [2Fe-2S] binding domain
    3.1e-06   27.0   0.2    3.1e-06   27.0   0.2    2.2  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
     0.0003   20.7   0.1    0.00049   20.1   0.1    1.5  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.088   12.6   0.3        1.6    8.5   0.0    2.7  3  DUF348    G5-linked-Ubiquitin-like domain
       0.48   10.5   3.7         11    6.1   2.6    2.7  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 ?   -0.2   0.8      0.29   1.1e+03      21      31 ..      46      56 ..      40      65 .. 0.85
   2 ?   -1.9   0.0      0.96   3.4e+03      65      75 ..      67      77 ..      58      78 .. 0.82
   3 !  107.0   0.0   9.9e-35   3.6e-31       1      74 [.      81     152 ..      81     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.29
                        Fer2_2 21 eegasqCGyCt 31
                                   ++ s CG Ct
  gi|14601917|ref|NP_148462.1| 46 GCDTSNCGACT 56
                                  578899****9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.96
                        Fer2_2 65 CtgYrpivdAv 75
                                  Ct Y+ +vd +
  gi|14601917|ref|NP_148462.1| 67 CTVYTFMVDGA 77
                                  99999988865 PP

  == domain 3  score: 107.0 bits;  conditional E-value: 9.9e-35
                        Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdA 74 
                                   T+egl+++  +lhp+qeaf e++++qCG+CtpG++m+++++l++n ++pte+e+r+a++gnlCRCtgY +iv+ 
  gi|14601917|ref|NP_148462.1|  81 TIEGLEQN-GKLHPIQEAFWENHGLQCGFCTPGMIMTLHDFLSRN-KSPTESEVRRAIEGNLCRCTGYVNIVRS 152
                                   9****988.78**********************************.88888********************986 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 !   27.0   0.2   8.6e-10   3.1e-06       2      55 ..      14      67 ..      13      91 .. 0.84
   2 ?   -0.1   0.5      0.26   9.5e+02      38      44 ..     103     110 ..     100     148 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.6e-10
                                  ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTT CS
                          Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegevqsd 55
                                  +++gk+++  v++    l  ++++  g ++++++C  ++Cg+C+v v+ + v+s+
  gi|14601917|ref|NP_148462.1| 14 KVNGKTYTHHVPPRML-LVHFLRDvLGLTGTHVGCDTSNCGACTVLVNGKAVKSC 67
                                  789**99999866665.*******9*********************997766544 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                                   SS.SSTTE CS
                          Fer2  38 gg.CgtCl 44 
                                   g  Cg C+
  gi|14601917|ref|NP_148462.1| 103 GLqCGFCT 110
                                   55699997 PP

>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.4e-07   0.00049      50      90 ..      45      84 ..      13      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                        Fer2_3 50 asCregiCGscavainGkptlaCtatikdlakqkseielep 90
                                    C    CG+c+v +nGk    Ct  +  ++  +  +++e 
  gi|14601917|ref|NP_148462.1| 45 VGCDTSNCGACTVLVNGKAVKSCTVYTFMVDGAE-ITTIEG 84
                                  57*********************98766555443.345555 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0   0.00045       1.6       1      12 [.      11      22 ..      11      26 .. 0.89
   2 ?   -0.1   0.0      0.22   7.9e+02       2      11 ..      56      65 ..      56      68 .. 0.86
   3 ?   -0.4   0.0      0.27   9.6e+02       2      11 ..      71      80 ..      71      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00045
                                  EEEEETTEEEEE CS
                        DUF348  1 VtltvDGktvtv 12
                                  Vtl+v+Gkt+t 
  gi|14601917|ref|NP_148462.1| 11 VTLKVNGKTYTH 22
                                  9*********96 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                                  EEEETTEEEE CS
                        DUF348  2 tltvDGktvt 11
                                  t+ v+Gk v+
  gi|14601917|ref|NP_148462.1| 56 TVLVNGKAVK 65
                                  899****875 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.27
                                  EEEETTEEEE CS
                        DUF348  2 tltvDGktvt 11
                                  t  vDG ++t
  gi|14601917|ref|NP_148462.1| 71 TFMVDGAEIT 80
                                  678***9887 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 ?    2.2   0.0     0.051   1.8e+02       3      14 ..      10      21 ..       9      25 .. 0.88
   2 ?    6.1   2.6    0.0031        11      46      79 ..      47      81 ..      41      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.051
                        Fer2_4  3 pvtltfDGkevt 14
                                  +vtl+++Gk++t
  gi|14601917|ref|NP_148462.1| 10 RVTLKVNGKTYT 21
                                  59********98 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0031
                        Fer2_4 46 caggeCrnClVevegepnvracstp..vedGlkvet 79
                                  c  ++C  C V v+g+  v++c++   + dG +++t
  gi|14601917|ref|NP_148462.1| 47 CDTSNCGACTVLVNGKA-VKSCTVYtfMVDGAEITT 81
                                  8899***********99.9***97522567777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1205.37
//
Query:       gi|118431783|ref|NP_148464.2|  [L=785]
Description: aldehyde dehydrogenase, large subunit [Aeropyrum pernix K1]
Scores for complete 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-189  630.3   0.0     3e-189  630.0   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    4.3e-30  104.3   0.2    1.2e-29  102.9   0.1    1.9  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
      0.011   15.5   2.6      0.011   15.4   0.1    2.2  2  DUF865         Herpesvirus-7 repeat of unknown function (DUF8
       0.13   12.2   0.1        0.3   11.0   0.1    1.6  1  DUF3659        Protein of unknown function (DUF3659)


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 !  630.0   0.0  6.7e-193    3e-189       1     550 []     154     716 ..     154     716 .. 0.96

  Alignments for each domain:
  == domain 1  score: 630.0 bits;  conditional E-value: 6.7e-193
                                    STTT-STTEEEEEEE..E-.HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHH CS
                  Ald_Xan_dh_C2   1 vheeapdnvlakiek..Gd.veaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvae 77 
                                    +h+eap n+++k+++  G+ ++++ ++ad+v+++++ ++r  + ++Et++a+a +++  +elt+++++q+ph +r +++ 
  gi|118431783|ref|NP_148464.2| 154 LHDEAPGNIAFKWRFsgGEsFDKVAEKADVVIKQRMVNQRLIPSAMETRGAVASFNRGLEELTLWVTSQNPHVHRLVLSG 233
                                    6999*******7775447647*********************************************************** PP

                                    HHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEE CS
                  Ald_Xan_dh_C2  78 vlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkital 157
                                    vlglpe+k+rvi+p+vGGGFG+K+ ++p ev++  +A+ +g pVk+v++R+e+++ t +++++  +++++a++dG+++++
  gi|118431783|ref|NP_148464.2| 234 VLGLPEHKIRVIAPDVGGGFGSKIPVYPGEVIVSRLAMDLGVPVKWVETRRENFVGTIHGRDHVEYVEAAATRDGRLLGV 313
                                    ******************************************************************************** PP

                                    EEEEEEEESST.HHHCHCCHCCTTGGGT.TTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT-- CS
                  Ald_Xan_dh_C2 158 dvdlladaGay.adlspavleralshld.gpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgld 235
                                    +v++la++Gay ++++p+v++  ++ +  gpYki++v+ve+ +v tNt+p++a+RG+G+p+a+++lEr+md +A++lgld
  gi|118431783|ref|NP_148464.2| 314 RVKTLANMGAYlSTAAPGVPTILFGLMLqGPYKIESVDVEVLGVLTNTTPVDAYRGAGRPEATYILERVMDLVARKLGLD 393
                                    ***********7799******99999877*************************************************** PP

                                    HHHHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.... CS
                  Ald_Xan_dh_C2 236 plelRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgf...t 309
                                    p+e+RrrNli++  +t+       vydsg+++e+++k+++ ++ye++r+eq +++++++ +Gig++ ++e +gl++    
  gi|118431783|ref|NP_148464.2| 394 PAEVRRRNLIEEAPYTT---VtglVYDSGRYKEVFEKALQIAEYEKWREEQMKARQEGRLIGIGISSYIEMCGLAPsriA 470
                                    **********8765544...34459******************************88899****************6431 PP

                                    EETTEE.......EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HH CS
                  Ald_Xan_dh_C2 310 akflnq.......egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrst 382
                                         +       e++++rv+++G+v+v+tg++++GqG et++aqi+aeeLgvp+edv++++gdtd +p+g+gt++Sr+t
  gi|118431783|ref|NP_148464.2| 471 ---RATgfglglyESVTIRVHPTGKVSVYTGSHPHGQGEETSFAQIVAEELGVPVEDVEIIHGDTDETPFGLGTYGSRTT 547
                                    ...3335677788******************************************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH.......TTSSEEEEEEE. CS
                  Ald_Xan_dh_C2 383 dlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl.......ervslsatgfyk 452
                                     ++g+Av+ Aa+++re+++kiaa+lle+++ed+ +++gk++vk   eksvs++e+a +ayl        +++l+at+fy 
  gi|118431783|ref|NP_148464.2| 548 PVGGGAVALAARRIREKARKIAAALLEAREEDVVFSEGKFHVKghpEKSVSFQEVALEAYLadklpegLEPGLEATTFY- 626
                                    *************************************************************9999999999********. PP

                                    ..EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTE CS
                  Ald_Xan_dh_C2 453 tldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGq 532
                                            +p++++f+yg++v+ VevD++t + k+lr+v+v+D+G +iNp+++egQ++GG+vqGi++al+E  vyde+G+
  gi|118431783|ref|NP_148464.2| 627 --------DPENFVFPYGTHVCIVEVDRDTWKPKILRYVAVDDAGVIINPMLAEGQVHGGVVQGIAQALFEYAVYDESGN 698
                                    ........9*********************************************************************** PP

                                    ESS-STTTS----GGGS- CS
                  Ald_Xan_dh_C2 533 lltasladYkiPtaadiP 550
                                    llta++ dY iPta+d+P
  gi|118431783|ref|NP_148464.2| 699 LLTAGFNDYMIPTAKDLP 716
                                    ****************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 !  102.9   0.1   2.7e-33   1.2e-29       1     110 []      22     138 ..      22     138 .. 0.88
   2 ?   -3.5   0.0       2.9   1.3e+04      63      82 ..     573     592 ..     555     593 .. 0.65

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 2.7e-33
                                    TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT..TSSS-EE.....EESS- CS
                   Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig..siledee.....dalla 73 
                                    tG++ YvdDi++pg++y+af+r ++ahA+i+sid+s+a+++pGVv v+t++  +++       ++l++ +       + a
  gi|118431783|ref|NP_148464.2|  22 TGRGLYVDDIKLPGMVYAAFLRASYAHARIKSIDTSKAEKMPGVVGVYTGEYFKDKVAPLTtaWALANADlkpvfWPVVA 101
                                    8************************************************998888776665553333333335665688* PP

                                    SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                   Ald_Xan_dh_C  74 edkvrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                    +dkvr+ g++va+vvAed +tA +A+++++veYe+lp
  gi|118431783|ref|NP_148464.2| 102 HDKVRFTGDIVAVVVAEDPYTAYDALEAIDVEYEPLP 138
                                    **********************************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.9
                                    SSS-EEEESS-SSEESSTT- CS
                   Ald_Xan_dh_C  63 iledeedallaedkvrsvgq 82 
                                      ++eed ++ e k +++g+
  gi|118431783|ref|NP_148464.2| 573 LEAREEDVVFSEGKFHVKGH 592
                                    34455678999999988887 PP

>> DUF865  Herpesvirus-7 repeat of unknown function (DUF865)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       0.6   2.7e+03       2       8 ..     498     504 ..     497     507 .. 0.84
   2 ?   15.4   0.1   2.6e-06     0.011       9      27 ..     724     742 ..     721     748 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.6
                         DUF865   2 GSHPFRQ 8  
                                    GSHP  Q
  gi|118431783|ref|NP_148464.2| 498 GSHPHGQ 504
                                    9***877 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.6e-06
                         DUF865   9 ErPrPHNPLTFKPVKTTGT 27 
                                    E+P PHNPL  K +  TGT
  gi|118431783|ref|NP_148464.2| 724 ETPSPHNPLGAKGIGETGT 742
                                    9*****************9 PP

>> DUF3659  Protein of unknown function (DUF3659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.6e-05       0.3       7      45 ..     658     700 ..     652     703 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.6e-05
                        DUF3659   7 kvnkaGevvd...eeGnvvGrvveGdlkkLaGkkv.dedGniv 45 
                                     v++aG +++   +eG+v G vv+G ++ L    v de Gn++
  gi|118431783|ref|NP_148464.2| 658 AVDDAGVIINpmlAEGQVHGGVVQGIAQALFEYAVyDESGNLL 700
                                    58889999987778*****************999989*9*987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5649.17
//
Query:       gi|14601920|ref|NP_148465.1|  [L=292]
Description: aldehyde dehydrogenase, middle subunit [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-55  187.6   0.0      2e-55  187.1   0.0    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    2.1e-26   92.1   0.7    2.1e-26   92.1   0.7    1.6  2  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 !  187.1   0.0   2.3e-59     2e-55       2     170 ..       5     174 ..       4     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 2.3e-59
                                   EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHHH CS
                 FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaaea 81 
                                   +fe+l p+sl+eal++l++ +++ak++aGg++l+++m++++++p  +i+i++ip l++i+e++g+++iGA++t++e+ +++
  gi|14601920|ref|NP_148465.1|   5 SFEVLIPKSLDEALDMLEKyGDNAKVLAGGHSLIPMMRLRLVKPTYVIYIGRIPGLSYIREEGGEIRIGALTTHNEIEESS 85 
                                   6899***************999*********************************************************** PP

                                   HHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS-TT-E CS
                 FAD_binding_5  82 lvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgktalepgel 162
                                   l++e+ p lse+++ki++ q+Rn++TiGG+la+a+p++D+++aL+al+A+v+lrs++ger v+le+f+ gp+ t+l+p+el
  gi|14601920|ref|NP_148465.1|  86 LLKEKNPLLSETASKIGDLQVRNMGTIGGSLAHADPAADYPAALAALEASVVLRSKAGERVVKLEDFIIGPYITDLQPSEL 166
                                   ********************************************************************************* PP

                                   EEEEEEE- CS
                 FAD_binding_5 163 itaveiPa 170
                                   +++v++P+
  gi|14601920|ref|NP_148465.1| 167 LVEVRVPS 174
                                   *******6 PP

>> CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.4   1.3e+04      12      28 ..     128     144 ..     126     154 .. 0.60
   2 !   92.1   0.7   2.3e-30   2.1e-26       2     102 ..     182     282 ..     181     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.4
                                   S-ESEEEEEEEEEETTC CS
                 CO_deh_flav_C  12 diaivnaAfrveleedg 28 
                                   ++a++ a + ++ ++++
  gi|14601920|ref|NP_148465.1| 128 ALAALEASVVLRSKAGE 144
                                   45555555555555554 PP

  == domain 2  score: 92.1 bits;  conditional E-value: 2.3e-30
                                   EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHTCT CS
                 CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspasdp 81 
                                   ay kl  r++ d+aiv++A++v+l++dg+ e++r++++gv ++pvra+ +e+ L Gk+lse+l+++aa++++e ++p +d+
  gi|14601920|ref|NP_148465.1| 182 AYeKLVFRAS-DFAIVGVAALVQLSGDGTAEKVRVGLTGVDEKPVRARGVEEELEGKRLSEDLIARAAERASEGINPPTDI 261
                                   7989999999.********************************************************************** PP

                                   TC-HHHHHHHHHHHHHHHHHH CS
                 CO_deh_flav_C  82 rasaeYRrslavsllfrflle 102
                                   rasaeYR+++a++l++r+l++
  gi|14601920|ref|NP_148465.1| 262 RASAEYRKRMARALTKRALTR 282
                                   ******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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 0.19s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2341.32
//
Query:       gi|118431784|ref|NP_148466.2|  [L=298]
Description: CoxD-like protein [Aeropyrum pernix K1]
Scores for 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   45.5   0.0    1.2e-10   41.6   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
      3e-10   40.6   0.0    7.7e-10   39.3   0.0    1.7  1  AAA              ATPase family associated with various cellul
    2.1e-09   37.4   0.0     0.0018   18.2   0.0    2.2  2  AAA_3            ATPase family associated with various cellul
    1.5e-06   28.7   0.2    2.1e-05   24.9   0.2    2.4  1  AAA_16           AAA ATPase domain
    1.4e-05   25.4   0.0    6.4e-05   23.2   0.0    2.0  1  AAA_22           AAA domain
    0.00013   21.8   0.1      0.048   13.4   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.001   18.1   0.0     0.0015   17.5   0.0    1.2  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0021   18.0   0.1      0.013   15.4   0.1    2.2  1  NACHT            NACHT domain
     0.0039   17.3   0.0     0.0087   16.2   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0097   15.6   0.0        2.3    7.9   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.014   15.9   0.1      0.088   13.4   0.1    2.4  1  AAA_18           AAA domain
      0.022   14.9   0.1      0.047   13.9   0.1    1.7  1  AAA_33           AAA domain
       0.03   14.7   0.0      0.083   13.3   0.0    1.9  1  RNA_helicase     RNA helicase
       0.04   13.9   0.0       0.08   13.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.047   12.9   0.2       0.12   11.6   0.0    1.8  2  TIP49            TIP49 P-loop domain
      0.099   12.0   0.0       0.16   11.3   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI


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 !   41.6   0.0     1e-13   1.2e-10       2     137 ..      47     198 ..      46     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 1e-13
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...............................--- CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik......................ngttslvdspl 59 
                                    +l+ G+pG gK+ela+ la+al++e+   q+++++ +++ ++ +++                        +++ lv++pl
  gi|118431784|ref|NP_148466.2|  47 LLVEGEPGNGKTELAKVLAEALGTELIRLQCYEGIDASQALYDWNYPkqllairmlersgdvesiereiYSEKYLVKGPL 126
                                    7999******************************************9999999999999999999888888999999999 PP

                                    -----....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  60 vraar....egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                     ra++    ++ +l++DE++ra+ e  + Ll  l e ++ ++e g+   +++        v+ t+n+ +    e+ + lr
  gi|118431784|ref|NP_148466.2| 127 LRAVThrgpKPPVLLIDEIDRADEEFEAFLLEFLAEFQVTVPEIGTFRAERR------PIVVITSNRTR----EVGEGLR 196
                                    99999**************************************999998888......47888888887....5555666 PP

                                    TT CS
                          AAA_5 136 sR 137
                                    +R
  gi|118431784|ref|NP_148466.2| 197 RR 198
                                    66 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 !   39.3   0.0   6.9e-13   7.7e-10       1     124 [.      47     199 ..      47     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.9e-13
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS..............................STTHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk..............................yvgesekkirelf 50 
                                    +l+ G pG GKT lak +a+ lg+e++++++ e ++                                +   +  +++ +
  gi|118431784|ref|NP_148466.2|  47 LLVEGEPGNGKTELAKVLAEALGTELIRLQCYEGIDAsqalydwnypkqllairmlersgdvesierEIYSEKYLVKGPL 126
                                    5899*****************************996679**************666666666665553333334444444 PP

                                    HHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.........SSTEEEEEEESSGGGSTHHH CS
                            AAA  51 keakeka..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.........eskvivigatnrpdkldpal 119
                                     +a +++  kp +l+iDEid+  ++             + Ll++l +++           e++ iv++++nr +++ + l
  gi|118431784|ref|NP_148466.2| 127 LRAVTHRgpKPPVLLIDEIDRADEE-----------FEAFLLEFLAEFQVTvpeigtfraERRPIVVITSNRTREVGEGL 195
                                    44444448999**********9444...........5999*********999********8889**************** PP

                                    HSTTS CS
                            AAA 120 lrgRf 124
                                    + +R+
  gi|118431784|ref|NP_148466.2| 196 R-RRC 199
                                    *.687 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 !   17.0   0.0   3.6e-06     0.004       2      32 ..      47      77 ..      46      87 .. 0.93
   2 !   18.2   0.0   1.6e-06    0.0018      64     114 ..     138     189 ..     117     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                          AAA_3  2 vllegvPGlaktllvkalakaldlefkriqf 32
                                   +l+eg PG +kt l+k la+al++e+ r+q+
  gi|118431784|ref|NP_148466.2| 47 LLVEGEPGNGKTELAKVLAEALGTELIRLQC 77
                                   699**************************98 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.6e-06
                          AAA_3  64 nllladeinrappktqsalleameerqvtveg.ethklpepflvlatqnPie 114
                                     +ll dei+ra    ++ lle ++e qvtv +  t++ ++  +v+ t n   
  gi|118431784|ref|NP_148466.2| 138 PVLLIDEIDRADEEFEAFLLEFLAEFQVTVPEiGTFRAERRPIVVITSNRTR 189
                                    589**************************97625888888888999988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   1.9e-08   2.1e-05      18     160 ..      40     162 ..      30     183 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.9e-08
                         AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                    +++ g    +l+ Ge+G GK+ l++ l++al ++   ++r +c +       +   qal    + +qll+     e++ +
  gi|118431784|ref|NP_148466.2|  40 ALKLG--KPLLVEGEPGNGKTELAKVLAEALGTE---LIRLQCYEG------IDASQALYDWNYPKQLLAIRML-ERSGD 107
                                    55555..459**********************99...789999888......2244444333333333333222.33333 PP

                         AAA_16  98 rekleealaavpelagaeasrllellkrll.allsrderplvlvlDdlqwadeaslql.laaLlr 160
                                     e +e+++           s  + +   ll a ++r+ +p vl++D++++ade+  ++ l++L++
  gi|118431784|ref|NP_148466.2| 108 VESIEREIY----------SEKYLVKGPLLrAVTHRGPKPPVLLIDEIDRADEEFEAFlLEFLAE 162
                                    444444444..........333333344444668888899*****************95665554 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   5.7e-08   6.4e-05       7     121 ..      46     163 ..      42     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.7e-08
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.....erpevvfvtlpsstsskdllrellralglelka.......erls 74 
                                     l+v Ge+G GKT l++ l+e l  e           ++++++++ + ++ +    r+l r       +       e  s
  gi|118431784|ref|NP_148466.2|  46 PLLVEGEPGNGKTELAKVLAEALGTELIR-LqcyegIDASQALYDWNYPKQLLA-IRMLERS------GdvesierEIYS 117
                                    58999******************322222.124433333333444444442222.2333333......144555688889 PP

                         AAA_22  75 seell.ealeqalrarav.ielliiDEaqhlr...seealeeLrsllnlsrk 121
                                    ++ l+   l +a+ +r+  +++l+iDE+++ +   ++ +le+L +      +
  gi|118431784|ref|NP_148466.2| 118 EKYLVkGPLLRAVTHRGPkPPVLLIDEIDRADeefEAFLLEFLAE------F 163
                                    9999999999999999999***********954333555555543......3 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 !   13.4   0.0   4.3e-05     0.048      36      61 ..      47      72 ..      32      84 .. 0.91
   2 !    6.1   0.0    0.0075       8.5      84     115 ..     136     167 ..     103     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvkl 61
                                   +l+ G PG Gkt lak++a+ lg++l
  gi|118431784|ref|NP_148466.2| 47 LLVEGEPGNGKTELAKVLAEALGTEL 72
                                   6899******************9876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0075
                         RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldi 115
                                    +  vl+idei r +++ e +l   + +f++ +
  gi|118431784|ref|NP_148466.2| 136 KPPVLLIDEIDRADEEFEAFLLEFLAEFQVTV 167
                                    5569******************9999999876 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 !   17.5   0.0   1.4e-06    0.0015      23      72 ..      35      84 ..      30      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                          AAA_6 23 ltltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyk 72
                                   ++l  Alkl     ++G  g GKtE  k La+al++ ++ ++c +++d++
  gi|118431784|ref|NP_148466.2| 35 MALYLALKLGKPLLVEGEPGNGKTELAKVLAEALGTELIRLQCYEGIDAS 84
                                   677788888888999********************************986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.1e-05     0.013       2      99 ..      46     154 ..      45     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.......... CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse.......... 71 
                                    +++++Ge+G GKT L++ la+a+ ++    +  ++     +++l +      +++ll+  ++e +++v+           
  gi|118431784|ref|NP_148466.2|  46 PLLVEGEPGNGKTELAKVLAEALGTELIRLQ--CYEGIDASQALYD---WNYPKQLLAIRMLERSGDVESiereiyseky 120
                                    689*******************998764442..2222222222222...2456666666666666666665556555555 PP

                                    ......CHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                          NACHT  72 ......vwavllelperlLlilDglDelvtdlgq 99 
                                           +av  + p+  +l++D +D++ +++++
  gi|118431784|ref|NP_148466.2| 121 lvkgplLRAVTHRGPKPPVLLIDEIDRADEEFEA 154
                                    5555555555556666666777777777766655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.8e-06    0.0087       7      82 ..      48     150 ..      45     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.8e-06
                                    EEE--TTSSHHHHHHHHHHHTT-........................-EEEEEGGG---.----THHH..HHHHHHTTT- CS
                          AAA_2   7 lllgptgvGktelakalaellfv....................kkekkliradaselle.eeevehlv..srligappgy 63 
                                    l+ g+ g Gktelak lae l                      +  k+l  + + e     e +e+ +  ++ +++ p  
  gi|118431784|ref|NP_148466.2|  48 LVEGEPGNGKTELAKVLAEALGTelirlqcyegidasqalydwNYPKQLLAIRMLERSGdVESIEREIysEKYLVKGPLL 127
                                    788999***************98776666666666666666664444444444444433222222222113444555555 PP

                                    HHHHTTS....EEEEETGGG--- CS
                          AAA_2  64 vgaeegG....ivllDEidKihp 82 
                                     ++  +G    ++l+DEid++ +
  gi|118431784|ref|NP_148466.2| 128 RAVTHRGpkppVLLIDEIDRADE 150
                                    5566666*************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 !    7.9   0.0    0.0021       2.3      19      44 ..      41      66 ..      30      84 .. 0.81
   2 ?    5.5   0.0     0.011        13      96     155 ..     139     197 ..     134     206 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                                   CTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat 19 aktdlsvlitGesGtGKellaraihe 44
                                    k   ++l++Ge G GK+ la+ + e
  gi|118431784|ref|NP_148466.2| 41 LKLGKPLLVEGEPGNGKTELAKVLAE 66
                                   5566789**************99876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                                    EEEEETGGGS-HHHHHHHHHHHHHSEEE..SBTSSSEEE--EEEEEEESS-HHHHHHTTSS- CS
                Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegeve..rvGsskeikvdvriiaatnedleeaveegkfr 155
                                    +l++Dei + + e+ + Ll++l e +v+   +G+ +  +  + +i+   ++ +++v eg  r
  gi|118431784|ref|NP_148466.2| 139 VLLIDEIDRADEEFEAFLLEFLAEFQVTvpEIGTFRAERRPIVVIT---SNRTREVGEGLRR 197
                                    699*******************998765226776655554444443...3334455555444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.9e-05     0.088       2      25 ..      48      80 ..      47     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.9e-05
                         AAA_18  2 lltGtpGvGKttlakeLskrlgf.........g 25
                                   l+ G pG GKt+lak L++ lg          g
  gi|118431784|ref|NP_148466.2| 48 LVEGEPGNGKTELAKVLAEALGTelirlqcyeG 80
                                   689*****************9555454444441 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.2e-05     0.047       3      33 ..      48     126 ..      47     245 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt................................................l 33 
                                    l+ G pG GK+ la+ l+++lg++l++                                                   l
  gi|118431784|ref|NP_148466.2|  48 LVEGEPGNGKTELAKVLAEALGTELIRLQCyegidasqalydwnypkqllairmlersgdvesiereiysekylvkgpL 126
                                    789*******************888876554455555555555555555555555555555555555555555555555 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   7.4e-05     0.083       2      26 ..      48      72 ..      47     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.4e-05
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                   ++ G++g GK+ lak La+al ++l
  gi|118431784|ref|NP_148466.2| 48 LVEGEPGNGKTELAKVLAEALGTEL 72
                                   689******************9887 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.1e-05      0.08      15      46 ..      40      71 ..      29      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                                   HHCHTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE 15 akalgdvilLeGdLGaGKTtlvrglakalgve 46
                                   a +lg+ +l eG+ G GKT l++ la+alg e
  gi|118431784|ref|NP_148466.2| 40 ALKLGKPLLVEGEPGNGKTELAKVLAEALGTE 71
                                   334467899********************986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.12      50      78 ..      44      72 ..      32     118 .. 0.80
   2 ?   -2.0   0.2       1.4   1.5e+03     281     301 ..     139     159 ..     137     191 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 50 GravLlaGpsgtGktalaiaiskelgedv 78
                                   G+ +L+ G++g Gkt la  ++++lg+++
  gi|118431784|ref|NP_148466.2| 44 GKPLLVEGEPGNGKTELAKVLAEALGTEL 72
                                   79***********************9664 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                    XXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 281 vlfiDevhmlDiecfsylnra 301
                                    vl iDe+   D e  ++l   
  gi|118431784|ref|NP_148466.2| 139 VLLIDEIDRADEEFEAFLLEF 159
                                    666666666666655555433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.16      14      47 ..      36      69 ..      30     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                   Mg_chelatase 14 aleiaaaGgHnlllvGppGsGKtmlakrlpsllp 47
                                   al +a   g  ll+ G pG GKt lak l++ l 
  gi|118431784|ref|NP_148466.2| 36 ALYLALKLGKPLLVEGEPGNGKTELAKVLAEALG 69
                                   667777778889***************9987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 00:00:00.43
# Mc/sec: 2099.41
//
Query:       gi|118431785|ref|NP_148467.2|  [L=361]
Description: CoxE-like protein [Aeropyrum pernix K1]
Scores for complete 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-65  220.1   2.1    3.5e-65  219.5   2.1    1.2  1  VWA_CoxE  VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.052   13.5   0.0       0.39   10.6   0.0    2.0  2  VWA_3     von Willebrand factor type A 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 !  219.5   2.1   3.9e-69   3.5e-65       4     221 ..     132     347 ..     129     349 .. 0.94

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 3.9e-69
                       VWA_CoxE   4 klaalllglarrrrrrkrrrrgrriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaiflallhA 83 
                                    +la l+++l  +  rr+  rr++riD++r++r++lr++ge+v+lvr++ r+r+++++++l+DvS+Sm++y+ ++l +l+A
  gi|118431785|ref|NP_148467.2| 132 SLALLRRRLGLEEGRRRVPRRRGRIDFKRSMRRSLRTFGETVRLVRAS-RKRSKTDILVLLDVSNSMKDYWPWILGILNA 210
                                    555555555444445789999***************************.999999************************* PP

                       VWA_CoxE  84 llqqlp.rtevfaFdtrlvdlTralrerDpaeaLarvsaaved.lgGgTrigaalaeflelvtrpaLsrravvvlvsDgl 161
                                    l++  p ++e+f+F+trlv+ T++++++  ae L+r+ ++ve+ +g+gTri+++++e+le++t paL+r+a+v+++sDg+
  gi|118431785|ref|NP_148467.2| 211 LRRLPPgSYEAFLFSTRLVRATPMVEAAGGAEDLRRLLSRVEGlWGSGTRISQSVEELLESHT-PALHRGAAVLVFSDGW 289
                                    *************************************99************************.**************** PP

                       VWA_CoxE 162 ergdreellaelarlvrrarrlvwlnplsdagtpgydpearalrailphvdelrpleqla 221
                                    + gd  +l+++la+l+rra  lvw++p+s+++++g++p+  ++r+i++h+d +++le+l 
  gi|118431785|ref|NP_148467.2| 290 DLGDLGRLASALAELRRRAGFLVWVTPESPRRDAGGEPS--TMRIIRRHADLTIDLETLL 347
                                    **************************************9..9**************9985 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.065   5.9e+02      18      45 ..      45      72 ..      31      94 .. 0.70
   2 ?   10.6   0.0   4.4e-05      0.39       2     108 ..     186     290 ..     185     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.065
                          VWA_3 18 klvkdaLsvalrqLptndkiavllfgtk 45
                                   + +k+aL++al ++p + +++  lf+++
  gi|118431785|ref|NP_148467.2| 45 ERLKQALRAALAKDPGRHRLFDYLFDVY 72
                                   5567777777777777777766666666 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.4e-05
                          VWA_3   2 evvivvDvsssmsaenklvkdaLsvalrqLptndkiavllfgtkprplfpgsrav.saaelqealqkikelelslgasnl 80 
                                    ++ +++Dvs sm++ + + + ++ +alr Lp++ ++  +lf t+ ++ +p   a+  a++l+++l  ++ l    ++++ 
  gi|118431785|ref|NP_148467.2| 186 DILVLLDVSNSMKD-YWPWILGILNALRRLPPG-SYEAFLFSTRLVRATPMVEAAgGAEDLRRLLSRVEGLWG--SGTRI 261
                                    7999*********8.599999***********9.68888999988899998665526899**********888..89999 PP

                          VWA_3  81 egaLkealrqp.akpgevrsvilltDgss 108
                                     ++ +e l++  +   +  +v++++Dg +
  gi|118431785|ref|NP_148467.2| 262 SQSVEELLESHtPALHRGAAVLVFSDGWD 290
                                    99999999976433355667888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2760.79
//
Query:       gi|14601923|ref|NP_148468.1|  [L=205]
Description: PucB-like protein [Aeropyrum pernix K1]
Scores for 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-29  100.9   1.4    1.2e-28  100.5   1.4    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0016   18.2   0.0     0.0037   17.0   0.0    1.6  2  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr


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 !  100.5   1.4   1.3e-32   1.2e-28       4     157 ..       2     163 ..       1     167 [. 0.88

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.3e-32
                                   EEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTC......T.S-EEE-TTSS-SHHHHH CS
                  NTP_transf_3   4 LAGGrSsRmggdKallplggkpllervldalraa.gvdevvvvggdeevlaalarl......g.vrvvededpgkgplasl 76 
                                   LA+G S+Rmg +K+l+pl+gk++l++vl+ +++  gv e  vv+ + ev++ l+r       g  rvv+++++ +g ++s+
  gi|14601923|ref|NP_148468.1|   2 LAAGMSRRMGFNKLLAPLCGKRVLWHVLELVARFeGVLEGAVVVTSGEVADVLRRErppgrrGlFRVVVNREQWRGLSHSI 82 
                                   9********************************966755555555556777665443333333699*************** PP

                                   HHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHCHHHH CS
                  NTP_transf_3  77 aaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrllrrl 157
                                   + +++a+++a a+l++ +D P++++++v+r+la + a++  +++p + g    p++  +rl+ +l++l+gd+g r+l+ ++
  gi|14601923|ref|NP_148468.1|  83 RLGVEASPGARAYLFFNGDRPFVSKHTVARVLALYMARRPLIAAPMAGGAIAPPVVVDSRLRGELLRLSGDTGVRSLFGKY 163
                                   ************************************99*********99999999**********************9876 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.2e-07    0.0037       6     119 ..       2     119 ..       1     134 [. 0.76
   2 ?   -3.7   0.0      0.92   8.3e+03     202     215 ..     177     190 ..     166     193 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-07
                                   ECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG..........CCEEEEE--SS CS
                          IspD   6 pAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld..........ksiqlvaGGde 76 
                                    AAG+ +Rm  g +K++  l g+ +l h ++ ++  + v +  vvv+  ++  +                +  ++v+  + 
  gi|14601923|ref|NP_148468.1|   2 LAAGMSRRM--GFNKLLAPLCGKRVLWHVLELVARFEGVLEGAVVVTSGEVADVLR---RerppgrrglfR--VVVNREQW 75 
                                   59******9..689*****************9999988877777777766333322...223356654322..45555555 PP

                                   H..HHHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHT CS
                          IspD  77 R..aesVlnglkalegeakfVLvHDaARpllkaadiaellaaaeq 119
                                   R  ++s+  g++a ++ a+  L  ++ Rp+++++++a++la    
  gi|14601923|ref|NP_148468.1|  76 RglSHSIRLGVEA-SPGARAYLFFNGDRPFVSKHTVARVLALYMA 119
                                   55589********.7888999*******************98775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.92
                                   TG----SHHHHHHH CS
                          IspD 202 dnlKittpeDlalA 215
                                     l + tpeDl +A
  gi|14601923|ref|NP_148468.1| 177 LHLDVDTPEDLERA 190
                                   45778899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1557.52
//
Query:       gi|118431786|ref|NP_148470.2|  [L=147]
Description: CoxG-like protein [Aeropyrum pernix K1]
Scores for complete 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-46  157.8   0.0    1.5e-46  157.6   0.0    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
    3.4e-14   53.3   0.0    3.8e-14   53.2   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    2.5e-05   24.5   0.0    6.2e-05   23.2   0.0    1.6  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    0.00014   22.1   0.0    0.00017   21.8   0.0    1.1  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.025   14.8   0.0    1.4  2  DUF3211          Protein of unknown function (DUF3211)


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 !  157.6   0.0   4.2e-50   1.5e-46       1     140 []       7     145 ..       7     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 4.2e-50
                                    EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEEE-S CS
                           COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsfkarvelselekensttieikGkGrga 80 
                                    G+f+v++++e+v+efL+dp++++r++PG+ksve+e+++++++++l++Gpl+g++++r+++++lek++++t  +kG+Grga
  gi|118431786|ref|NP_148470.2|   7 GSFEVSKTPEEVFEFLTDPKRFSRAFPGFKSVEVEDGSFTIELRLSLGPLRGDARVRASFEDLEKPSKAT--VKGSGRGA 84 
                                    99******************************************************************87..******** PP

                                    SEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHHT CS
                           COXG  81 gvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfecissklg 140
                                    g++ df+l+++ve++gg +r+sw++++nvggl+as+G+r++ds+ar++in++++ ++++lg
  gi|118431786|ref|NP_148470.2|  85 GSTLDFTLRFAVEPSGGgSRVSWVFEGNVGGLAASMGGRVLDSLARRMINDVISGVKRELG 145
                                    ********************************************************99985 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 !   53.2   0.0     1e-17   3.8e-14       3     142 ..       4     144 ..       2     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 1e-17
                                    EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS...SEEEEEEEEEE.TTTTEEEEE CS
                Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr...gtvreelvevd.pegrllsyr 78 
                                    + + s ++  +pe+V+++++d++ ++r  p+ ++ve+e+ g+    +e +++ g +   ++vr  +++++ p++ +++  
  gi|118431786|ref|NP_148470.2|   4 RYEGSFEVSKTPEEVFEFLTDPKRFSRAFPGFKSVEVED-GSF--TIELRLSLGPLrgdARVRASFEDLEkPSKATVKGS 80 
                                    567789999*****************************6.444..4445555555588888*********5555555555 PP

                                    EE.SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHH CS
                Polyketide_cyc2  79 ivkpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarl 142
                                    +++  ++ +++ +++v+p ggg+rv+w +e  +g+l++ + + +++++ ++ + + + + k++l
  gi|118431786|ref|NP_148470.2|  81 GRGAGSTLDFTLRFAVEPSGGGSRVSWVFEGNVGGLAASMGGRVLDSLARRMINDVISGVKREL 144
                                    547888999********************99999999999999999999999999999999887 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 !   23.2   0.0   1.7e-08   6.2e-05       1     128 [.      11     135 ..      11     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.7e-08
                                    ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE....EEEECSTTSSCEEEEEEEEEEETTT.......EEECTTCC CS
                 Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaes.glsadlevgfggltesftarvtldppee.......itfklveg 72 
                                    v+  +++v+++++d  ++++ +p+ +svev + + + +l+ +l   +g  + + + +++++p+                g
  gi|118431786|ref|NP_148470.2|  11 VSKTPEEVFEFLTDPKRFSRAFPGFKSVEVEDGSFTiELRLSLGPLRGDARVRASFEDLEKPSKAtvkgsgrG-----AG 85 
                                    5789**************************9999975333333333333333333333333333333222221.....34 PP

                                    CCCEEEEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHH CS
                 Polyketide_cyc  73 dfkslegkWtieslppnsggtrtkvalevdfkfaspllgalvgqvaervldellaa 128
                                       ++  +  +e+++    g+r+ +++e ++   ++l + + g v+++ +++++++
  gi|118431786|ref|NP_148470.2|  86 STLDFTLRFAVEPSGG---GSRVSWVFEGNV---GGLAASMGGRVLDSLARRMIND 135
                                    4445666778888887...999999999888...9999999999999999999986 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 !   21.8   0.0   4.8e-08   0.00017       3     106 ..      14     119 ..      12     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.8e-08
                                    -HHHHHHHHH-HHHHHH.HEEEEEEEE--STTE.EEEE..EETTTSEEEEEEEEEEEEETTTEEEEEEEEETSETEEEEE CS
                          AHSA1   3 pperVfraltdpellkr.WftlteaemdlrpGg.kfrl..rdspdgkefgnegeylevvpperlvytwrledepeeeest 78 
                                    +pe+Vf+ ltdp+++ r +  +   +++++ G+ +++l    +p  ++   +++++++++p +   + + ++ +++ ++t
  gi|118431786|ref|NP_148470.2|  14 TPEEVFEFLTDPKRFSRaF--PGFKSVEVEDGSfTIELrlSLGPLRGDARVRASFEDLEKPSKATVKGSGRGAGSTLDFT 91 
                                    79***************77..88888888777655555877889999********************8888888899*** PP

                                    EEEEEEEETTEEEEEEEEEEEEHCHHHH CS
                          AHSA1  79 vtieleeegggTrltlthtglprkqkee 106
                                    +++  e+ ggg r+  + +g   + ++ 
  gi|118431786|ref|NP_148470.2|  92 LRFAVEPSGGGSRVSWVFEGNVGGLAAS 119
                                    *************998887766655555 PP

>> DUF3211  Protein of unknown function (DUF3211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     7e-06     0.025       4      64 ..       6      65 ..       1     101 [. 0.82
   2 ?   -2.5   0.0       1.6   5.7e+03     105     123 ..     126     144 ..     103     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7e-06
                                   EEEEE-SS-HHHHHHHHT-HHHHHHHHSTTEEEEEEECTTEEEEEEETTEEEEEEEEEEEE CS
                        DUF3211  4 eieiktkheieavlkiLSDpkFvlpkllpaikivkveeksFevegefllveieikgtvyvs 64
                                   e +++ ++++e v++ L Dpk  + + +p  k+v+ve+ sF++e +++l ++    +v  s
  gi|118431786|ref|NP_148470.2|  6 EGSFEVSKTPEEVFEFLTDPKR-FSRAFPGFKSVEVEDGSFTIELRLSLGPLRGDARVRAS 65
                                   56799999*************5.68889999*************99998887766666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHHHHHHHH CS
                        DUF3211 105 ekliskllskrikkfeknl 123
                                    ++l++++++  i+ ++++l
  gi|118431786|ref|NP_148470.2| 126 DSLARRMINDVISGVKREL 144
                                    3444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1102.22
//
Query:       gi|14601927|ref|NP_148472.1|  [L=298]
Description: CoxF-like protein [Aeropyrum pernix K1]
Scores for 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-25   87.5   0.0    1.6e-24   86.8   0.0    1.3  1  XdhC_C     XdhC Rossmann domain
    4.5e-16   58.8   1.4    9.7e-16   57.7   0.4    2.1  2  XdhC_CoxI  XdhC and CoxI family
  ------ inclusion threshold ------
       0.17   12.1   3.7       0.34   11.2   1.2    2.5  3  TetR_C_16  Tetracyclin repressor-like, C-terminal domain


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 !   86.8   0.0   2.7e-28   1.6e-24       3     125 .]     128     262 ..     126     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 2.7e-28
                                   EE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE..............-EEEE--S-H.HHHHHHHHHHSSS- CS
                        XdhC_C   3 ifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade..............tavvvlthdh.klDaealeaalrkk 68 
                                   ifG ++v++al rla+ lgf+vtv+dp +    +e++p+a+               t+ v++t +  + D e+l ++l+k+
  gi|14601927|ref|NP_148472.1| 128 IFGNNEVTKALSRLAQLLGFKVTVIDPSAG---PEDYPGAKVlasledggvrldrhTYPVLATMGRtDVDVEVLLRILDKP 205
                                   9**************************996...899999988999***********9999999987699*********999 PP

                                   -SEEEESS-HHHHHHHCTTS.--.......TTEESS-S--S---SHHHHHHHHHHHH CS
                        XdhC_C  69 aayigllGSrkkaarrlerlraaglseeelarlhaPiGldigaktpeeIAvsilAei 125
                                   +a + l++S ++a+++l+rl+++g++++ l+++ +P+G+d+ga tpee A+s+lA i
  gi|14601927|ref|NP_148472.1| 206 VARVFLVASVNRAEEVLRRLARKGVPPDLLEKIESPAGIDLGAATPEELALSVLAGI 262
                                   *******************************************************76 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.4   1.6e-19   9.7e-16       3      66 ..      24      87 ..      22      88 .. 0.96
   2 ?   -2.5   0.0      0.99   5.9e+03      11      30 ..     149     168 ..     149     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.6e-19
                                  HCT..EEEEEEEEEECSSSSGTT-EEEEETTS-EEE-SSSSCHHHHHHHHHHHHHHCT--EEEE CS
                     XdhC_CoxI  3 aagrpvalaTVvdteGsaprplGakmlvrpdgrviGsvgggclEaavideArallaagrtalvr 66
                                  ++ r++++aTVv+++Gsa +++G+k ++ pdg+v G++gg c E a++  A+ +l++gr++lv+
  gi|14601927|ref|NP_148472.1| 24 EEEREFVIATVVSVKGSAAARVGSKGVILPDGTVRGWLGGWCSENALLTVALSALKEGRPKLVK 87
                                  789*********************************************************9985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.99
                                   EEEEEEECSSSS.GTT-EEEE CS
                     XdhC_CoxI  11 aTVvdteGsapr.plGakmlv 30 
                                   +TV+d    +p   +Gak l 
  gi|14601927|ref|NP_148472.1| 149 VTVID-PSAGPEdYPGAKVLA 168
                                   68888.446777788888765 PP

>> TetR_C_16  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.1   6.5e+03       6      30 ..      14      37 ..       9      45 .. 0.53
   2 ?   -0.0   0.0      0.17     1e+03       7      54 ..      56     100 ..      52     103 .. 0.77
   3 ?   11.2   1.2   5.7e-05      0.34      23      99 ..     206     286 ..     195     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                  HHHHHHHHHHHHHT-HHHHHHHHH- CS
                     TetR_C_16  6 rlvravlevwepearepllallrsa 30
                                  ++v  v +++e e+re   a+++s+
  gi|14601927|ref|NP_148472.1| 14 EFVDMVRGLME-EEREFVIATVVSV 37
                                  45555555555.5666666666666 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHT-HHHHHHHHH--------HHHHHHHHHHHHHHCTT CS
                     TetR_C_16   7 lvravlevwepearepllallrsalsseeaaellrefleeqvlaplaa 54 
                                    vr  l+ w   ++ +ll++  sa  +e   +l++ +++ + l+++++
  gi|14601927|ref|NP_148472.1|  56 TVRGWLGGWC--SENALLTVALSA-LKEGRPKLVKLVMSGETLKQVSE 100
                                   5788888899..888999999999.56668888888888888877766 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 5.7e-05
                                   HHHHHHH--------HHHHHHHHHHHHHHCTTTS-ST.....THHHHHHHHHHHHHHHHHHHHTS--TTCCCS-HHHHHHH CS
                     TetR_C_16  23 llallrsalsseeaaellrefleeqvlaplaarlggp.....daelRaalvasqllGlalaRyvlrleplasasreelval 98 
                                    + ++  a s ++a+e+lr++ ++ v + l ++++ p      a++  +l++s+l+G++ aR+     p+ +a  + +++ 
  gi|14601927|ref|NP_148472.1| 206 VARVFLVA-SVNRAEEVLRRLARKGVPPDLLEKIESPagidlGAATPEELALSVLAGIVAARRGGSGRPMREARGDPVAKV 285
                                   44455555.778899999999999999999999999887767789999***************999999999999999887 PP

                                   H CS
                     TetR_C_16  99 v 99 
                                   v
  gi|14601927|ref|NP_148472.1| 286 V 286
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2198.00
//
Query:       gi|118431787|ref|NP_148473.2|  [L=633]
Description: DNA polymerase II [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-14   53.3   0.0    1.3e-13   50.5   0.0    2.2  1  DNA_pol_B  DNA polymerase family B
  ------ inclusion threshold ------
        4.6    7.6   5.3        4.3    7.7   1.2    2.4  2  Htr2       Htr2 transmembrane 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 !   50.5   0.0   1.4e-17   1.3e-13      52     371 ..     293     565 ..     283     576 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.4e-17
                                    ---EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHH CS
                      DNA_pol_B  52 PkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdlla 131
                                    P+ g+y   v+ lD++SLYP +i  +N++ +t+++   ++   ++         ++  +++    +r+gl+p++L +l++
  gi|118431787|ref|NP_148473.2| 293 PEPGVYW-GVVQLDYSSLYPRLIAMYNISAETVDTPCGNTL--DPAP-----GYGG--HRV--CMDRRGLVPEVLGRLVD 360
                                    6666665.4789*********************99988854..4433.....1233..233..45899************ PP

                                    HHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGG CS
                      DNA_pol_B 132 kRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskl 211
                                     R++++++ + e+           Q a+K +  s +G++G++ns++ ++a  ++vT+  R++L +++e   ++       
  gi|118431787|ref|NP_148473.2| 361 LREEARRRGAGEE-----------QEAIKWILVSGFGYLGFRNSLFGSIAAYETVTAAARRALAAAEEAAVEM------- 422
                                    ****998755444...........77****************************************9999988....... PP

                                    GT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEE..EEEEEEEEEET...TEEEE CS
                      DNA_pol_B 212 lalpeeaeeeklkviYGDTDSvfielkvkdveellkigkelaeevseklfkkplklefe..kvykkllLisK...KkYag 286
                                              +++vi    DSvfi+  v+      ++++e+++++       p+k+e+e    y +  L       kY+g
  gi|118431787|ref|NP_148473.2| 423 ----------GYRVIHSLVDSVFIQP-VEPRGPPGEVAREIERRTGV-----PVKIEAEykWLYIPPTLRGHgavNKYYG 486
                                    ..........9*************85.34444444555555554443.....4555555216899999986533379999 PP

                                    EEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EE CS
                      DNA_pol_B 287 lkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvls 366
                                       +     + +  KG+  vRrd  ++v+e   + + +l ++ ++  + + ++e   ++++  ++ l+e++ p+ek+v+ 
  gi|118431787|ref|NP_148473.2| 487 ALES-----GGVKLKGIAAVRRDTPEIVREAQASAIARLAEA-RHPGEWPGAVERAWKVVDGYMRLLREGEPPVEKLVIE 560
                                    9888.....6689**************************999.788899999********9999***************9 PP

                                    EEESS CS
                      DNA_pol_B 367 kelsk 371
                                    k++ +
  gi|118431787|ref|NP_148473.2| 561 KRVDP 565
                                    99876 PP

>> Htr2  Htr2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.2   0.00048       4.3      13      39 ..     394     420 ..     385     427 .. 0.81
   2 ?    0.8   0.2     0.066   5.9e+02      15      43 ..     491     518 ..     480     521 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00048
                           Htr2  13 aFGga.aYlevtaalasGDaaavgeaav 39 
                                    +FG++ aY  vtaa+     aa +eaav
  gi|118431787|ref|NP_148473.2| 394 LFGSIaAYETVTAAARR-ALAAAEEAAV 420
                                    69986268889999888.7788899998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.066
                           Htr2  15 GgaaYlevtaalasGDaaavgeaavsaiL 43 
                                    Gg+    ++a   +  + +v ea  sai 
  gi|118431787|ref|NP_148473.2| 491 GGVKLKGIAAVRRD-TPEIVREAQASAIA 518
                                    55555555555555.899*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4538.17
//
Query:       gi|14601932|ref|NP_148477.1|  [L=216]
Description: hypothetical protein APE_2235 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1709.76
//
Query:       gi|14601933|ref|NP_148478.1|  [L=244]
Description: hypothetical protein APE_2236 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1846.14
//
Query:       gi|118431788|ref|NP_148479.2|  [L=196]
Description: hypothetical protein APE_2238.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1548.29
//
Query:       gi|118431789|ref|NP_148480.2|  [L=344]
Description: NAD-dependent alcohol dehydrogenase [Aeropyrum pernix K1]
Scores for complete 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  105.1   0.1    2.8e-30  104.4   0.1    1.3  1  ADH_N            Alcohol dehydrogenase GroES-like domain
      5e-27   94.4   0.7    7.6e-27   93.9   0.1    1.6  2  ADH_zinc_N       Zinc-binding dehydrogenase
    1.2e-12   49.1   1.0    2.7e-12   47.9   0.2    2.1  3  ADH_zinc_N_2     Zinc-binding dehydrogenase
    0.00076   19.0   0.1     0.0012   18.4   0.1    1.2  1  Glu_dehyd_C      Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
      0.039   13.3   0.9      0.067   12.5   0.9    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.078   12.8   0.0        0.2   11.4   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
       0.08   12.8   0.1       0.16   11.8   0.1    1.5  1  UPF0146          Uncharacterised protein family (UPF0146)


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.1   1.1e-33   2.8e-30       3     109 .]      28     136 ..      26     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 1.1e-33
                                    EEEEEEEEEEE-HHHHHHHTTS..TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG CS
                          ADH_N   3 evlikvkaagiCgsDlhilkgg..kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenl 80 
                                    +v+++++ ag+C++Dlh+++g+  + l+ klp +lGHE vG +eev ++v++l++Gd V+++p++++g+C aC+ ge+ +
  gi|118431789|ref|NP_148480.2|  28 DVIVRIAGAGVCHTDLHLVQGMwhELLQPKLPYTLGHENVGYIEEVAEGVEGLEKGDPVILHPAVTDGTCLACRAGEDMH 107
                                    79*******************98888999*************************************************** PP

                                    -TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                          ADH_N  81 CeeakllgvsldGgfaeyvvvpekklvkl 109
                                    Ce+ ++ g+++dGgfae + +++++++kl
  gi|118431789|ref|NP_148480.2| 108 CENLEFPGLNIDGGFAEFMRTSHRSVIKL 136
                                    ************************99986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.1   5.3e+03      70      90 ..     160     180 ..     156     181 .. 0.81
   2 !   93.9   0.1     3e-30   7.6e-27       1     126 [.     182     305 ..     182     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.1
                                    HHHHHHHHCEEEEEEEEECSC CS
                     ADH_zinc_N  70 atleaalkllkpgGrlvvvGg 90 
                                    ++++ a + l pg  +++vG+
  gi|118431789|ref|NP_148480.2| 160 RAVKKAARTLYPGAYVAIVGV 180
                                    578889999999999999996 PP

  == domain 2  score: 93.9 bits;  conditional E-value: 3e-30
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                    g+G++avql+k +   +via d++eekl+la++lGad+v+++++ d+v+++ elt+g+gv+v++++vGs+at++    ll
  gi|118431789|ref|NP_148480.2| 182 GLGHIAVQLLKVMTPaTVIALDVKEEKLKLAERLGADHVVDARR-DPVKQVMELTRGRGVNVAMDFVGSQATVDYTPYLL 260
                                    89*********77655**************************88.*********************************** PP

                                    EEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHH CS
                     ADH_zinc_N  80 kpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkeald 126
                                     + Grl +vG g++   f++ +++  e+s+ Gsl+g+   e+ e++ 
  gi|118431789|ref|NP_148480.2| 261 GRMGRLIIVGYGGEL-RFPTIRVISSEVSFEGSLVGN-YVELHELVT 305
                                    **********75555.5********************.566666665 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         7   1.8e+04      20      33 ..      25      37 ..      17      48 .. 0.64
   2 ?   -1.7   0.0       2.3   5.8e+03      88     101 ..     143     156 ..     117     200 .. 0.71
   3 !   47.9   0.2   1.1e-15   2.7e-12       1     133 []     215     342 ..     215     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7
                                   TT-EEEEEES-HHH CS
                   ADH_zinc_N_2 20 gegvDvvldtvgge 33
                                   g+ +Dv++  +g  
  gi|118431789|ref|NP_148480.2| 25 GR-FDVIVRIAGAG 37
                                   44.99999887743 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHHHH CS
                   ADH_zinc_N_2  88 dileelaalieeGk 101
                                    + l e+a l ++G 
  gi|118431789|ref|NP_148480.2| 143 EKLVEMAPLADAGI 156
                                    33677777777664 PP

  == domain 3  score: 47.9 bits;  conditional E-value: 1.1e-15
                                    TT-SEEEETTSTTHH...HHH-TT-EEEEEES-HHHHH.HHHHHHE.EEEEEEEE--.--.S-EEE-CHHHCTTT-EEEE CS
                   ADH_zinc_N_2   1 lGAdevidyrtedfe...aatggegvDvvldtvggealleaslkvl.pggGrlvsig.gpplsaallkpakkrkgrsvky 75 
                                    lGAd+v+d r++ ++   + t+g+gv+v+ d vg++a+++ +  +l +  Grl+ +g g     +l+ p+ +  +  v++
  gi|118431789|ref|NP_148480.2| 215 LGADHVVDARRDPVKqvmELTRGRGVNVAMDFVGSQATVDYTPYLLgRM-GRLIIVGyG----GELRFPTIRVISSEVSF 289
                                    8*********99999999****************999967776555555.***999977....35555555454455555 PP

                                    --GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                   ADH_zinc_N_2  76 eflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                    e  + +  +   + l el++l  +Gk+r+ vd   +l+e+++ +++le+g + G+ Vl
  gi|118431789|ref|NP_148480.2| 290 EGSL-V-GN-YVE-LHELVTLALQGKVRVEVD-IHKLDEINDVLERLEKGEVLGRAVL 342
                                    5555.3.44.688.******************.9********************9997 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.6e-07    0.0012      15      99 ..     154     236 ..     144     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.6e-07
                    Glu_dehyd_C  15 Kaielaeasrsafe..wepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatY.vdsretpv 91 
                                     +i   +a+++a++  +  + + ++G G lG +a+ ll+++  +  +v  l+    ++ +++l e+lGa   vd r++pv
  gi|118431789|ref|NP_148480.2| 154 AGITAYRAVKKAARtlYPGAYVAIVGVGGLGHIAVQLLKVM--TPATVIALDV---KEEKLKLAERLGADHvVDARRDPV 228
                                    55555555555544336667899***************985..3455667765...556999*******873699***** PP

                    Glu_dehyd_C  92 deipease 99 
                                    +++ e ++
  gi|118431789|ref|NP_148480.2| 229 KQVMELTR 236
                                    **987653 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   2.6e-05     0.067      28      75 ..     172     220 ..     155     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                    --EEEEESTSHHHHHHHHHHHHTT.-EEEEEESSHHHHHHHHHTTTCEC CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglg.akVtvlDvrparleqleslgakfv 75 
                                     a v ++G+G  G  A++  k +  a+V +lDv++++l+  e lga  v
  gi|118431789|ref|NP_148480.2| 172 GAYVAIVGVGGLGHIAVQLLKVMTpATVIALDVKEEKLKLAERLGADHV 220
                                    5889*****************996599****************999844 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.7     7e+03      71      80 ..      24      32 ..      13      45 .. 0.70
   2 ?   11.4   0.0   7.8e-05       0.2      13      51 ..     182     219 ..     179     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.7
                Methyltransf_31 71 edekfDlils 80
                                   e  +fD+i+ 
  gi|118431789|ref|NP_148480.2| 24 E-GRFDVIVR 32
                                   3.89999986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.8e-05
                Methyltransf_31  13 GtGeltfelaeelgpkaevvGiDiseeaielArenaqkl 51 
                                    G G+++ +l  ++ + a+v+ +D +ee ++lA+   +++
  gi|118431789|ref|NP_148480.2| 182 GLGHIAVQLL-KVMTPATVIALDVKEEKLKLAERLGADH 219
                                    6799999999.99999****************9865555 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.2e-05      0.16       6      65 ..     163     225 ..     159     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.2e-05
                                    HHHHHHS-SS.EEEEET-TT--HHHHHHHHHS..-EEEEE-SS-S....STTEE---SSS--H CS
                        UPF0146   6 kkiaeenarg.kvvEvGiGrkldvaealakrg..vdlvatDikekkakegvrivrDDvtdPnl 65 
                                    kk+a++ ++g  v+ vG+G   ++a +l k      ++a D+ke+k k+  r+  D v+d ++
  gi|118431789|ref|NP_148480.2| 163 KKAARTLYPGaYVAIVGVGGLGHIAVQLLKVMtpATVIALDVKEEKLKLAERLGADHVVDARR 225
                                    677888888878999**********99998765789************999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2794.17
//
Query:       gi|14601936|ref|NP_148481.1|  [L=324]
Description: amidohydrolase [Aeropyrum pernix K1]
Scores for complete 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-40  140.2   0.9    1.3e-40  140.0   0.9    1.0  1  Amidohydro_2  Amidohydrolase


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.9   7.5e-45   1.3e-40       2     291 .]       6     295 ..       5     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 7.5e-45
                                   EEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHHHHHHHHHHHHHHHHCT CS
                  Amidohydro_2   2 DvHaHllppeaairddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaalcrgannrvlaeaakrpd 82 
                                   D+H  l p             ++ +++++f++  + +  ++ +++  v  a ++ a+ +++ ++++g +n++  +a+k+p 
  gi|14601936|ref|NP_148481.1|   6 DYHKSLSP------------DEYVWDYEEFLYYGSDKFIKDVFVDGGVDIALSQPAYLQFFFREPFGNTNEFGTMALKYPY 74 
                                   56666544............6788999****************************************************** PP

                                   TCBECEEECTSSHCHHHHHHHHHHHHTTECE.....EEEESST.........TTCCTTTCGGHHHHHHHHHHHT-EEE.EE CS
                  Amidohydro_2  83 rfvggaavvpldpedaaaeleraveelgfkG.....vrlnphv.........ggddllgdrldrpifealeelglpvd.ih 148
                                   rf+ g  ++p+++e+  ++le+ v ++++k      v+l+++          +g +l+++    +++e  +elg+ ++  h
  gi|14601936|ref|NP_148481.1|  75 RFIIGTRWDPREGEEGKRQLEEDVRKYRVKPwqmrhVKLYTAEwkevnggisRGWRLDSPQA-FEFLEFNRELGIDIQvPH 154
                                   *********************************99999999994444333322444444444.6**************779 PP

                                   ....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHHC CS
                  Amidohydro_2 149 tGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrpnvyvklsglytellyfdsplad 229
                                    G      ++ ++   +a++ ++++ +a  fP+l++v+ H G p  r  ++ ++  + +nvy+ l   +t  +++  p+++
  gi|14601936|ref|NP_148481.1| 155 KG------PTVWPLSKDAFDVHDVDTAASSFPELRFVVTHVGLP--RIDDFSWIGVQDKNVYAGLAV-ATA-FIRKRPKYF 225
                                   77......************************************..****************88855.454.9******** PP

                                   HHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH........SSHHHHHHHHTHHHHHHCTB CS
                  Amidohydro_2 230 ppalarlieavgpdrilfGsDyPhptleaepealalldlval........lsdeerekilggNAarlygl 291
                                   ++++a+l++++gpdri+fGsDy ++++++  e++ +++l+ +        l+ e ++kilg+NAarl+g+
  gi|14601936|ref|NP_148481.1| 226 AEIMAELLFWLGPDRIIFGSDYAIWHPKWIIEDFIKFELPRDleseygveLTLENKKKILGENAARLWGI 295
                                   ****************************************99**************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2480.75
//
Query:       gi|118431790|ref|NP_148482.2|  [L=279]
Description: hypothetical protein APE_2242.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-12   46.6   0.1    1.2e-11   44.6   0.1    1.9  2  FeS_assembly_P   Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.049   13.7   0.0      0.098   12.8   0.0    1.5  1  TSNR_N           Thiostrepton-resistance methylase, N terminu
      0.053   13.3   0.1      0.092   12.5   0.1    1.4  1  Phage_integrase  Phage integrase family


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 !   44.6   0.1   1.9e-15   1.2e-11       1      73 [.       4      77 ..       4      78 .. 0.91
   2 ?   -1.2   0.0      0.39   2.3e+03      26      38 ..     149     161 ..     138     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.9e-15
                                   HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-T..THHHHHHHHHHHHC.STT--EEEEE CS
                 FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacs..laeairadaeaalralpgvevveVe 73
                                   k ++ +aL+ V+DPel++++++lgl+ +i+     +V v+i++++  cs  + ++i +da++al++l g   ++V+
  gi|118431790|ref|NP_148482.2|  4 KSDIVRALEAVRDPELDIPITELGLIDSITTGSgEVVEVTIRMPTYWCSpnFTYMIVEDARKALEKLVG--PARVK 77
                                   579*************************99866699******************************999..55554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.39
                                    --EEEE-T-EEEE CS
                 FeS_assembly_P  26 vreidieggkVsv 38 
                                    ++++++++g+V++
  gi|118431790|ref|NP_148482.2| 149 LEDLEVSQGSVTI 161
                                    5679999999987 PP

>> TSNR_N  Thiostrepton-resistance methylase, N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.6e-05     0.098      32      69 ..      84     121 ..      62     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                         TSNR_N  32 eDleplvqairaGvevieiYilegrdvsakleelaekr 69 
                                     D e +++++++G+ + e Y  e+ +  ++l +  +++
  gi|118431790|ref|NP_148482.2|  84 HDGERITKCVNSGLRFEECYPEEAGEGLEGLRARMREK 121
                                    599********************999998887776665 PP

>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.5e-05     0.092      21     119 ..     125     217 ..     110     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHCCTTTSBSSBE CS
                Phage_integrase  21 irdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellskaleeaeksellfas 100
                                    +r   l+++l++ Gl  +El +Lr++dl++ +g +++       + +  ++l +  +  + e+++   e+   +  l+ +
  gi|118431790|ref|NP_148482.2| 125 ARLHGLIRILLRKGLTLGELERLRLEDLEVSQGSVTI-------RGAKRITLESMEADRIVEYIGMLREAGVTRGPLL-R 196
                                    455567*******************************.......3344566666666666666666633333333333.3 PP

                                    T..TSSB--HHHHHHHHHHHH CS
                Phage_integrase 101 k..rgkplsrqtvrkafkrav 119
                                    +  rg+pl +++++  f+ra+
  gi|118431790|ref|NP_148482.2| 197 RnlRGEPLGKEKMELLFSRAR 217
                                    336777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2002.58
//
Query:       gi|118431791|ref|YP_874932.1|  [L=101]
Description: hypothetical protein APE_2242a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 802.95
//
Query:       gi|118431792|ref|YP_874933.1|  [L=56]
Description: hypothetical protein APE_2242b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.19s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 490.67
//
Query:       gi|118431793|ref|NP_148485.2|  [L=178]
Description: hypothetical protein APE_2246.1 [Aeropyrum pernix K1]
Scores for 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  104.2   0.0    7.8e-30  104.0   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 !  104.0   0.0   4.4e-34   7.8e-30       4     122 .]      17     144 ..      14     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 4.4e-34
                         DUF488   4 rvydllkkdgvrvlvDVRlwPrSr.npgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdpr......weefferY 76 
                                    ++ dl ++ g rv+vDVR+wPrSr +p  s+++l+ +l+ +g+aY++l++lg+ r   ++++ + r      ++e f++Y
  gi|118431793|ref|NP_148485.2|  17 EIGDLVESVGSRVVVDVRRWPRSRrHPWASRDTLEGFLRGRGVAYIHLPALGGYRSFGRDVDPSLRalfscfESEGFNAY 96 
                                    677899999*****************************************************66655999*99******* PP

                         DUF488  77 aaeleskeaakealeelkelakkg..vaLlcaekdperchrvvlaeyl 122
                                    aa+l+s++aa ++le ++ la+ g   +++c+e+ p+rchr+v+a++l
  gi|118431793|ref|NP_148485.2|  97 AAYLASSPAAWRGLEVIAYLAEAGarPVVMCSERLPWRCHRKVVADWL 144
                                    ******88999**********9999*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1370.87
//
Query:       gi|14601941|ref|NP_148486.1|  [L=194]
Description: 3-methyladenine DNA glycosylase [Aeropyrum pernix K1]
Scores for complete 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-41  141.0   0.0    3.4e-41  140.6   0.0    1.2  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 !  140.6   0.0   1.9e-45   3.4e-41       1     175 []       8     180 ..       8     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 1.9e-45
                 Pur_DNA_glyco   1 effdrdalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgrternavmFgppgtlYvYliygihhclnvv 81 
                                   +f+ r+++ vA+eLLGk+lv  ++   ++++++E EAY ge DpAs+a rgr +  ++++g+pg++ vY ++  +++ln+v
  gi|14601941|ref|NP_148486.1|   8 SFYYRQPDVVARELLGKILVSCASGACMRCMVTEAEAYFGECDPASRARRGRGRIWRALYGEPGRALVYGMHR-QWLLNIV 87 
                                   599*******************9988***********************************************.******* PP

                 Pur_DNA_glyco  82 teeegeasaVLiRalevveglelmrarrglanGPgkLcqaLgidkelngadlle.seelvle..keeaeeeeivagpRiGi 159
                                   +++eg a+aVL+R+++++e  +      +   GPg+L++aL+id+ ++ga++ e +++l+l    e++e  +++ + R+G+
  gi|14601941|ref|NP_148486.1|  88 AHSEGMAGAVLLRSCQPLEPPR---LDPP-PIGPGRLARALSIDRGVDGAPVYErGSPLTLWenPEAVEGFRVACSGRVGV 164
                                   *****************76654...3333.67********************9998898888667789999********** PP

                 Pur_DNA_glyco 160 skaaelpwRfyikgnp 175
                                   s++ elp+Rfyi+gnp
  gi|14601941|ref|NP_148486.1| 165 SEDLELPLRFYIAGNP 180
                                   **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1513.40
//
Query:       gi|118431794|ref|NP_148487.2|  [L=405]
Description: aspartate aminotransferase [Aeropyrum pernix K1]
Scores for complete 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-72  243.9   0.0    3.1e-72  243.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.4e-12   47.6   0.0    2.3e-12   46.9   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.1e-06   25.4   0.0      1e-05   24.7   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    0.00011   21.6   0.0    0.00018   20.9   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00016   20.3   0.0    0.00027   19.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  243.7   0.0   8.7e-76   3.1e-72       2     361 ..      38     393 ..      37     395 .. 0.96

  Alignments for each domain:
  == domain 1  score: 243.7 bits;  conditional E-value: 8.7e-76
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                     vi +g++++++     t++++++a+k+  +  ++++ y+ + g pel+ea+a +l+++++ ++ +e +v+ ++Ga+ +i
  gi|118431794|ref|NP_148487.2|  38 RVISFGIGQPDFP----TPHHIREAAKK--ALDEGFTGYTETAGIPELREAIAWYLNSRYGADVSPE-EVIATTGAKTAI 110
                                    6899********9....**********9..88999********************************.************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET..TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-T CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyse..edfhldlealeealkeapegnkktkvilvesphN 159
                                     + ++l  l pgde+++pdp+y  y ++++l g+  v++p++ e   +f+ d+e++e+a++e      kt++i+v++phN
  gi|118431794|ref|NP_148487.2| 111 FLGMALY-LRPGDEVIIPDPSYYAYAQVAKLFGARPVYVPMKFEpgLGFRFDIEGIERAVSE------KTRMIVVNNPHN 183
                                    *******.*******************************998886789**************......************ PP

                                    TT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHH CS
                  Aminotran_1_2 160 PtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaav 239
                                    PtG+v++++++e++ d+a++++l+++ De+Y  f ++++ + +t+++ + + nl+ v+++sK f+++G+R+Gy++   +v
  gi|118431794|ref|NP_148487.2| 184 PTGSVFPPDQVEAIHDIARRRGLIILADEIYDNFLYTEKPFKSTLSLPDWRENLVYVNGFSKTFSMTGWRLGYVVLRREV 263
                                    ********************************************99999999**************************** PP

                                    HHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH. CS
                  Aminotran_1_2 240 vsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae. 315
                                    +  + +l+ +++s  +s++q+a +aal+ +      + em++++ +r++ l+d L ++ g++ + ++++++++ ++  + 
  gi|118431794|ref|NP_148487.2| 264 IPKALDLAVTIYScpPSIAQKAGVAALRGDWG---PVREMVEEFRSRARILYDILSQAeGIEPYLPEGAFYMFPRVAGLl 340
                                    *****************************997...8*******************999********************** PP

                                    .....CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHH CS
                  Aminotran_1_2 316 .....takelskkLleevgvyvtpgtsftv...pgrlRitvAglteeeleelve 361
                                         + ++l++kLl  +gv+v+pgtsf     ++++R+++ ++ +++++e +e
  gi|118431794|ref|NP_148487.2| 341 rktglSVEQLAEKLLYSYGVLVLPGTSFPEsvgREHVRLSF-ATATSDVKEGAE 393
                                    *****************************999*99******.666666666665 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 !   46.9   0.0   6.3e-16   2.3e-12      39     144 ..      98     211 ..      54     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 6.3e-16
                                    SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TT...TSSB-GGGCGGG--TTEEEE CS
                DegT_DnrJ_EryC1  39 khaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpd...tynidpaaieaaitertkaI 115
                                    + +ia++ + +A+ l++ al + pgdeVI+p  ++ a a+++   ga+pv+v ++ +    +  d + ie+a+ e+t+ I
  gi|118431794|ref|NP_148487.2|  98 EEVIATTGAKTAIFLGM-ALYLRPGDEVIIPDPSYYAYAQVAKLFGARPVYVPMKFEpglGFRFDIEGIERAVSEKTRMI 176
                                    67899999999999997.7899********************************987333589***************** PP

                                    EEB...-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 116 lpV...hlyGqva...dmdalkaiaakhglkvieD 144
                                    ++    +  G v+   +++a+ +ia++ gl+++ D
  gi|118431794|ref|NP_148487.2| 177 VVNnphNPTGSVFppdQVEAIHDIARRRGLIILAD 211
                                    976221467888777789**************998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.9e-09     1e-05      45     175 ..      76     211 ..      68     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.9e-09
                                    HHHHHHHHHHHHT-S.....TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE CS
                    Aminotran_5  45 veearekvaelinae.....seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvi 119
                                    + e re +a+ +n +     s ee+i t G+ +ai l +  +   l+pgde+++ +  + a      ++ak  ga+ +++
  gi|118431794|ref|NP_148487.2|  76 IPELREAIAWYLNSRygadvSPEEVIATTGAKTAIFLGMALY---LRPGDEVIIPDPSYYAYA----QVAKLFGARPVYV 148
                                    56778888888876533333579****************999...**********99888877....8888888888887 PP

                                    EBETT....SCBEGGGHHHH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                    Aminotran_5 120 pldee....geldldelekllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                    p++ e     + d++ +e +++ekt+++ ++   n tG ++p   ve+i ++a+++g ++l+D
  gi|118431794|ref|NP_148487.2| 149 PMKFEpglgFRFDIEGIERAVSEKTRMIVVNNPHNPTGSVFPpdqVEAIHDIARRRGLIILAD 211
                                    7764311115788**************************987556899999**********99 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.1e-08   0.00018      67     167 ..     117     211 ..      55     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.1e-08
                                    H--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT....TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTT CS
                Beta_elim_lyase  67 llqrgeevivtepahihfdetgaiaelagvklrdlknkea....GkmdlekleaaikevgaheekiklisltvTnntagG 142
                                     l++g+evi+ +p+ +      ++a l g++++ ++ k +      +d+e +e+a+ e      k+++i++ + +n   G
  gi|118431794|ref|NP_148487.2| 117 YLRPGDEVIIPDPSYYAY---AQVAKLFGARPVYVPMKFEpglgFRFDIEGIERAVSE------KTRMIVVNNPHNP-TG 186
                                    347777777777775443...344455566566555555565655899******9999......699*********5.9* PP

                                    B---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 143 qvvsleelrevaaiakkygiplhlD 167
                                     v ++++++++++ia+++g+ ++ D
  gi|118431794|ref|NP_148487.2| 187 SVFPPDQVEAIHDIARRRGLIILAD 211
                                    *******************988877 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.4e-08   0.00027      69     176 ..      99     214 ..      89     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.4e-08
                                    EEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST....TSHHHHHHHCCTTEEEEEE CS
                Cys_Met_Meta_PP  69 aalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt....sdleelekaikentklvyl 143
                                    +++a++   +Ai++ +   l+ Gde+++ d  Y    ++ k +  + + + +kf        d+e +e+a++e+t+++ +
  gi|118431794|ref|NP_148487.2|  99 EVIATTGAKTAIFLGMALYLRPGDEVIIPDPSYYAYAQVAKLFGARpVYVPMKFEPGlgfrFDIEGIERAVSEKTRMIVV 178
                                    6677888889999999999***********9999888888877777577777777766666799**************** PP

                                    ESS-TTTT---..-.HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 144 Etptnpllkvv..D.iekiaklakkagvlvvvDntf 176
                                      p np+ +v   D +e+i ++a+ +g++++ D  +
  gi|118431794|ref|NP_148487.2| 179 NNPHNPTGSVFppDqVEAIHDIARRRGLIILADEIY 214
                                    *********96444499**********999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3209.72
//
Query:       gi|118431795|ref|NP_148488.2|  [L=185]
Description: hypothetical protein APE_2249.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1546.48
//
Query:       gi|118431796|ref|NP_148490.2|  [L=302]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-09   37.3  20.6    2.2e-09   37.3  20.6    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   2.5     0.029   5.3e+02     108     182 ..      27     115 ..      15     117 .. 0.52
   2 !   37.3  20.6   1.2e-13   2.2e-09       3     177 ..     104     289 ..     102     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.029
                   BPD_transp_1 108 ppiitglilafggllggavlleflgswpGlgtllleailgydyseis...............nggvlalviavlllnlva 172
                                      + + +il+ g+l+  ++ + +++ +p l+++  +  ++ ++  ++                 ++l++++ v+l  +++
  gi|118431796|ref|NP_148490.2|  27 LLAGSPIILTYGLLILSSFSTNMVT-DPLLTDFQPTLDNWIMFLRGQityatgglernvvemTLVTLTVAVGVALTATLV 105
                                    3333334444444444444444444.333455555555555555455667777777777776566666666666666666 PP

                   BPD_transp_1 173 dilqrlldpr 182
                                     +l+++   r
  gi|118431796|ref|NP_148490.2| 106 SLLAAYSISR 115
                                    6666666555 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1.2e-13
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf.......vilsilghlilp.viillllsaapyvrli 71 
                                    l+++laa    ++ +k++ +++   i+l ++P ++l+i ++++f        +l+   +++++ +i++ +   +p+++++
  gi|118431796|ref|NP_148490.2| 104 LVSLLAAysiSRMEFKGRGVFTAGLIMLHAFPGVALIIGVYMIFriigdvlGVLGEE-FYAIAyIILARAALEVPMAIWL 182
                                    67788888889999*********************999999999****664444444.555555**************** PP

                   BPD_transp_1  72 rraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydys 151
                                    ++++++ +p +l+  a+++Gasr ++ + +++P+++p i++ li++f + + +++  + ++   G+ +l + ++++   +
  gi|118431796|ref|NP_148490.2| 183 FKGFFDKIPWELEWSALVDGASRVRVWWSILVPLVKPGIAAVLIFTFLAGWEEFIYFYVFLKPFGIDSLPTFIEEIVAAA 262
                                    *************************************************************9999666555555555555 PP

                   BPD_transp_1 152 eis.nggvlalviavlllnlvadilqr 177
                                    e++  ++++a++ ++ll ++v+++l++
  gi|118431796|ref|NP_148490.2| 263 ENYqLTIIAAAGTFYLLPTIVFFVLTQ 289
                                    555533444444444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2519.39
//
Query:       gi|118431797|ref|NP_148491.2|  [L=314]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-09   36.8  23.4    3.1e-09   36.8  23.4    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        2.1    8.5   4.0        4.6    7.4   4.0    1.5  1  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t
        9.3    6.7  11.9       0.21   11.9   2.2    2.9  3  ASFV_L11L     African swine fever virus (ASFV) L11L protein


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   8.4      0.71   4.3e+03     110     174 ..       9      93 ..       6     108 .. 0.66
   2 !   36.8  23.4   5.2e-13   3.1e-09       3     172 ..      90     297 ..      88     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.71
                   BPD_transp_1 110 iitglilafggllggavlleflgswpGlgtllleailgydyseis........................nggvlalviav 165
                                    ++ +l+ a+ ++++ ++l+++l+    + t +++  +++  ++                           ++++++v+++
  gi|118431797|ref|NP_148491.2|   9 LAFFLGPALLIVITFFFLPLLLT----VYTSFTNMRNWNVDAYLFdivglynykvlvhfakydpmfrnaLITTVVFVAVT 84 
                                    45566666677777777777777....66666666666666655577788888888899999998888866666666666 PP

                   BPD_transp_1 166 lllnlvadi 174
                                    l++n++  +
  gi|118431797|ref|NP_148491.2|  85 LVVNVLGGL 93 
                                    666666544 PP

  == domain 2  score: 36.8 bits;  conditional E-value: 5.2e-13
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf.........................vilsilghlil 54 
                                    l+G+ +a   ++   +++   r l  +++++P+ v  +l++++f                         + +  lg +++
  gi|118431797|ref|NP_148491.2|  90 LGGLTLAiltFFLEERISIHYRLLWLLPRMTPVAVYSLLWYYFFhsdaigtlnrilllagvidkpinwgSYMLPLG-TWW 168
                                    6777777777788888888899999999*******999999999******************99998544443444.333 PP

                   BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw 134
                                     +i++  l  + + ++++++a+rs+p +++ aar++Gas   i+r++++P++   ++   ++++ +ll+ ++++ +l  w
  gi|118431797|ref|NP_148491.2| 169 ILIFVNGLVGVSFGMIVFYSAIRSIPWEYIAAARVDGASNLVIIRRIIVPMIRWHLLFVTVWQMLSLLTTYTHIFLLYEW 248
                                    36666667778899****************************************************************** PP

                   BPD_transp_1 135 pGlgtllleailgydyseis...........nggvlalviavlllnlva 172
                                    + + +++ ++ +   ++++            ++++ +lv++ ++l lv+
  gi|118431797|ref|NP_148491.2| 249 GVVDRTWGQTWSLLVFNLAFlpvgelrqglaAAAATVLVVIGAILGLVT 297
                                    75666666665556666555*******8776333333333333333333 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.0   0.00076       4.6       2      22 ..      19      39 ..      17      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00076
                      TM_PBP2_N  2 lLlvfqvfpvlyTistafTNy 22
                                   +++ f  +p+l T++t+fTN+
  gi|118431797|ref|NP_148491.2| 19 IVITFFFLPLLLTVYTSFTNM 39
                                   56789999************7 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 ?   11.9   2.2   3.5e-05      0.21      25      62 ..       2      39 ..       1      52 [. 0.87
   2 ?   -3.3   0.1       2.1   1.2e+04       8      22 ..     119     133 ..     115     149 .. 0.61
   3 ?    0.3   0.4      0.15   9.2e+02      16      63 ..     184     232 ..     171     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                      ASFV_L11L 25 klhklitialflgclffilrdfcfppmlwtilqnitlt 62
                                   +l +l t+a+flg  ++i+  f f p+l t+    t  
  gi|118431797|ref|NP_148491.2|  2 RLDRLFTLAFFLGPALLIVITFFFLPLLLTVYTSFTNM 39
                                   7899************************9998887765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.1
                      ASFV_L11L   8 mapiplvliflysyf 22 
                                    m+p+ +  ++ y +f
  gi|118431797|ref|NP_148491.2| 119 MTPVAVYSLLWYYFF 133
                                    566665555555554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                      ASFV_L11L  16 iflysyfkiklhklitialflgc.lffilrdfcfppmlwtilqnitltl 63 
                                    i +ys ++      i+ a   g   + i+r +  p + w+ l  +   +
  gi|118431797|ref|NP_148491.2| 184 IVFYSAIRSIPWEYIAAARVDGAsNLVIIRRIIVPMIRWHLLFVTVWQM 232
                                    5566666666666666666666514678899999999999887666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 2584.03
//
Query:       gi|118431798|ref|NP_148492.2|  [L=575]
Description: ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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-54  186.2   5.7    1.8e-54  185.8   5.7    1.2  1  SBP_bac_1  Bacterial extracellular solute-binding protein
    6.7e-07   29.4   4.8    1.3e-06   28.5   4.8    1.4  1  SBP_bac_8  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.039   14.3   0.0      0.098   13.0   0.0    1.7  1  GST_N      Glutathione S-transferase, N-terminal domain
        1.2    9.2   3.7        9.1    6.4   3.7    2.5  1  TFIIB      Transcription factor TFIIB repeat


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 !  185.8   5.7   4.1e-58   1.8e-54      17     314 ..     107     481 ..      91     482 .. 0.92

  Alignments for each domain:
  == domain 1  score: 185.8 bits;  conditional E-value: 4.1e-58
                                    H........HHHHHTTEEEEEEEECHHHHHHHHHHHHHTTS...SSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECT CS
                      SBP_bac_1  17 a........fekehpgikVeiesvgsgslaqkltlaiaaGd...gpaDviavdndwiarlakaglllpldpyvkaylapg 85 
                                    +        +e+e+ + k++ie++ +++ a++ +++++++    ++aD+iav+++wi+++ak+g+ll++++y++ay++ +
  gi|118431798|ref|NP_148492.2| 107 EaaarlnkiLEEEGVNFKIVIEDIKFSANADEPAKVFQQSFplkQEADIIAVSYRWISTFAKEGYLLDITDYANAYMGSE 186
                                    3344566677999*******************************999********************************* PP

                                    TCCTEEEEHHHHTHHHHCEEE.ES.EEEEE.EEEEEEETTTHH.....CTTGGG.....SHBHHHHHHHHHHHHHHCTCT CS
                      SBP_bac_1  86 vkdaadklsssvlpkildskv.ly.vPlya.argliYNkdlfe.....kagldp.....pwtWdelveaakklkekgkkp 152
                                     +d++d+l+ssv++k     + +y +P+++ ar+l++ k+++e      +++++     ++tW+++++ ak++++kg+++
  gi|118431798|ref|NP_148492.2| 187 LEDYYDSLWSSVTYK-----GrIYaLPQDTeARPLYILKPVMEclgydAWDIAAkidsgEYTWKDVMRIAKEAVDKGCSE 261
                                    ************974.....46799****77************999995555556666********************** PP

                                    ....................HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT......................HHCS CS
                      SBP_bac_1 153 ....................iggarggsasgtayyfalalakslggkvfdkdgg......................gldn 190
                                                        +gg ++gs+ +++y++++al+k+l+++++ +++g                      ++++
  gi|118431798|ref|NP_148492.2| 262 wgvihrkgsahpdlvqfyyaFGGEFTGSDPDKLYLNLEALYKWLAVEYALARNGltpenmlewdwakqihptivsaKTAF 341
                                    ****************************************************************************7788 PP

                                    HHHHS..HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTE CS
                      SBP_bac_1 191 pegvt..aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeel 268
                                    ++g t  ++++++k+y+++ +t e++g ++e++++++a++lf aGe +   v+l++++++m++a++++++++++++ke +
  gi|118431798|ref|NP_148492.2| 342 DIGGTwyWTEWQTKKYYTDPQTGEQRGLTPEEVKERFAYSLFPAGEPGKSPVTLSQPFVWMISANAGKLNPKYDDLKEAY 421
                                    8888888************************************************************************* PP

                                    EEECEEBETTTTSEE......EEEEEEEEBTTCST....HHH....HHHHHHHHTSHHHH CS
                      SBP_bac_1 269 gvaplPagkggkpgi......lgayglaipkgskn....pea....AkkFldfllspeaq 314
                                    + +++ ++ ++++++      +++ ++ i  +++     +e     A+  ld++ s+ea 
  gi|118431798|ref|NP_148492.2| 422 HRIAFLLILKANDPDlvaihsIVSAHIPIREKAALlmddQEFvgklAQGNLDMFVSDEAR 481
                                    ***************899998888889999999888754333888899999999999986 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 !   28.5   4.8   2.9e-10   1.3e-06      40     234 ..     153     409 ..     116     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.9e-10
                                    EE.EEE-HHHHHHHHHTTSB--GGGSTTHHH...-HHHHHTT....--TS.----EEEEEEE-EEEEEHHHHHH...... CS
                      SBP_bac_8  40 idvvwanedalatlaeeglladlsdldnldd...ltdalaav....gydgklygvPyasetpyvliynkdllek...... 106
                                    +d++  +  +++t+a+eg+l d++d+ n+     l+d++++     +y+g +y++P ++e    l+  k ++e       
  gi|118431798|ref|NP_148492.2| 153 ADIIAVSYRWISTFAKEGYLLDITDYANAYMgseLEDYYDSLwssvTYKGRIYALPQDTEA-RPLYILKPVMEClgydaw 231
                                    567777779***************8644444577455444445555**************8.787777777765555533 PP

                                    ..S.....---BHHHHHHHHHHH..HHH-..........SEGG---GGGGGGTHHETTEE---H...HHH.HHHHHHHHH CS
                      SBP_bac_8 107 ..a....edpktwdellaaakkl..kgkf..........glpdpasgwlqaallakdgksldddg.gkdglkealellkk 167
                                      a    +   tw+++  +ak++  kg+           ++pd   +++ ++  +  g ++d+ + + ++l ++l+    
  gi|118431798|ref|NP_148492.2| 232 diAakidSGEYTWKDVMRIAKEAvdKGCSewgvihrkgsAHPDLVQFYYAFGGEF-TGSDPDKLYlNLEALYKWLAVEYA 310
                                    3314674445799999998888867666666654444444455556688889999.999999998888888888777778 PP

                                    HHHTT-EE.....-S..--SS.TTTTTSBSEEEE-TTHHHHHH...................-TTTSEEEE.--...S-- CS
                      SBP_bac_8 168 lkdngkty.....dtgadavs.efanGevaftingswdiaaaq...................kagkklgai.vp...kqg 218
                                    l  ng t+     +++a++++  + + + af i+g+w ++ +q                   + ++++++  +p   + g
  gi|118431798|ref|NP_148492.2| 311 LARNGLTPenmleWDWAKQIHpTIVSAKTAFDIGGTWYWTEWQtkkyytdpqtgeqrgltpeEVKERFAYSlFPageP-G 389
                                    88999988999999**999998999**************************999999999855588999997776641.2 PP

                                    ....EEEEEEEEEEBTTS-H CS
                      SBP_bac_8 219 ....sfaggkglavpknakn 234
                                        ++++   +++++na++
  gi|118431798|ref|NP_148492.2| 390 kspvTLSQPFVWMISANAGK 409
                                    34324444445889999876 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.098       3      53 ..     100     151 ..      98     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                                    EEEESSSTSHTHHHHHHHHHHTT-EEEE..EEECSTTTCGGC.HHHHHHCTTS- CS
                          GST_N   3 ltlysirgsprahrirlllaakgveyev..vpldfeageeks.pellklnplgk 53 
                                    +++y+i++   a r+   l++ gv++++   +++f+a+++++ + + +++pl++
  gi|118431798|ref|NP_148492.2| 100 MRVYGIVE--AAARLNKILEEEGVNFKIviEDIKFSANADEPaKVFQQSFPLKQ 151
                                    689*****..******************66788888888888888999999876 PP

>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.7     0.002       9.1      38      51 ..      20      33 ..       5      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                                   HHHTTHHHHHHTTT CS
                          TFIIB 38 giaAAclyiAcrke 51
                                   +i+AA+lyiA+r++
  gi|118431798|ref|NP_148492.2| 20 AIIAAALYIATRQA 33
                                   79**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 4112.44
//
Query:       gi|118431799|ref|NP_148493.2|  [L=306]
Description: hypothetical protein APE_2256.1 [Aeropyrum pernix K1]
Scores for complete 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  129.0   0.0    2.2e-37  128.0   0.0    1.5  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)


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 !  128.0   0.0   1.2e-41   2.2e-37       3     135 ..      89     225 ..      87     226 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 1.2e-41
                    Cas_APE2256   3 asAElnallkllekkkkeqke....elvllssdTaaGklvaeilkeyleeegaevevveieklsdlg.reeFreglrnLv 77 
                                    +sAElna+  ++++++k+++     e++l+++dT+aG+++aei+k +le+  ++v++++ ++++ lg  +++ egl+nLv
  gi|118431799|ref|NP_148493.2|  89 YSAELNAMKYFISQSTKDCSVtmldEAILYHTDTHAGRVSAEIVKGFLER-LCHVKTYS-KQVTGLGvFDRLFEGLSNLV 166
                                    7*****************999999**************************.******99.89*****8999********* PP

                    Cas_APE2256  78 eklarevknkkregekvlinaTgGfKpeiavltlvall.ladevyYihEsfsevvelPk 135
                                    +++ +++k +  +g+ vl+n+TgGfKpe+++l+l+++l +a+++yYihE++++ v +P+
  gi|118431799|ref|NP_148493.2| 167 REAYCDIKVRIGRGNVVLLNLTGGFKPESGALLLAGSLaGASAAYYIHEAARKPVFIPI 225
                                    **********************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 2402.14
//
Query:       gi|14601949|ref|NP_148494.1|  [L=515]
Description: dipeptide ABC transporter dipeptide-binding protein DppA [Aeropyrum pernix K1]
Scores for 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-89  300.2   0.2    2.4e-89  299.9   0.2    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
        1.3    9.4   3.9         36    4.7   0.6    3.0  3  Wzz        Chain length determinant protein


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 !  299.9   0.2   2.7e-93   2.4e-89       2     376 ..      77     437 ..      76     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 299.9 bits;  conditional E-value: 2.7e-93
                                   EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEE CS
                     SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftl 82 
                                   +vp LAe+ we  + gk+++f+LR+++kF DGtp  A+ vv s++r++   + +++  + +    +++vea+d  tv+ftl
  gi|14601949|ref|NP_148494.1|  77 IVPYLAER-WESQEGGKVWIFYLRQDAKFPDGTPCDADVVVRSIKRVMTIQGDPSWLVTEF----VENVEALDQWTVKFTL 152
                                   89******.7**********************************************99985....**************** PP

                                   SSETTTTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-B.SSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEEEEEE-.S CS
                     SBP_bac_5  83 kkpnalfltllaavpasiakkaaekeddkdkdtnekpvg.tGPYklkefkpgqkivlernpdYwgggkpkldriefkvipd 162
                                   k+p+ +fl+++a +p+ +++   +++ + d + ++++ g  GPY+++ef+++q+++l+ np+++ g++pk d +++++++ 
  gi|14601949|ref|NP_148494.1| 153 KQPTGYFLAVVATPPYYPVH---PNYPE-DQPAPDATWGgCGPYMIDEFVRDQYLRLKPNPNFF-GEEPKNDGVIIRFYEG 228
                                   *******************4...44445.55555555555***********************9.**************99 PP

                                   HHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHHHHHCTT CS
                     SBP_bac_5 163 sdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtkkppfddkrvRqAlsyAiDreeivkavle 242
                                   s++ + al++Geid++   ++psd+e    +kg+++ +e pg+ + yl++  ++pp+d+++vRqAl+ AiDr++iv++v++
  gi|14601949|ref|NP_148494.1| 229 SEDLRSALEAGEIDVAwRTLNPSDLED-LRSKGYNI-KEVPGLFIRYLVLRVSQPPLDNVAVRQALAAAIDRQDIVDRVFR 307
                                   99999999*****88844555555555.56777777.8******************************************* PP

                                   TSSEEESSSSTTTSTTCCSCHCCCSHH.SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHH CS
                     SBP_bac_5 243 gyatpansllppsspgadeeykpayka.ydpekAkklLkeaGykdgdggglrekklkltlllasgspaekaiaeliqqqlk 322
                                   g+ +p +s++p++++g+++ +k++y +  +++ A++lL +aGy  +++  +     +l ++   ++ +e a+a++i++q++
  gi|14601949|ref|NP_148494.1| 308 GTMEPLYSMVPSGMWGHYPAFKEKYGEgPNIDLARQLLSQAGYSESNKLQV-----ELWYTPEHYGDTEAALAAVIKEQWE 383
                                   ***********************999899******************9876.....78888888888888*********** PP

                                   HTT.EEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCTT CS
                     SBP_bac_5 323 kiG.ikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssgag 376
                                   + G i ve+k+ +w  ty ++ ++g++ ++llgw++dy dpdnfl pfl s++++
  gi|14601949|ref|NP_148494.1| 384 ATGmISVEIKSSEW-GTYVDQLSSGQMMISLLGWYPDYLDPDNFLTPFLLSTANS 437
                                   **************.**********************************999876 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.004        36      12      40 ..       3      31 ..       1      66 [. 0.78
   2 ?    4.4   0.0    0.0053        48      32      55 ..     373     396 ..     371     427 .. 0.76
   3 ?   -2.1   0.1      0.57   5.1e+03      58      79 ..     454     475 ..     444     478 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.004
                                  XXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                           Wzz 12 LwkrkklIilvtllfallaviyaflatpk 40
                                  L   ++++++++++ +++a++y ++++++
  gi|14601949|ref|NP_148494.1|  3 LANTRVILAAIIVILVIAAGFYILFSRQQ 31
                                  55667888888888888999998888775 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0053
                                   XXXXXXXX-EEEEEEEES--CHHH CS
                           Wzz  32 iyaflatpkYtataqilvpekkqv 55 
                                   ++a + +++++at +i v+ k++ 
  gi|14601949|ref|NP_148494.1| 373 ALAAVIKEQWEATGMISVEIKSSE 396
                                   678999************998873 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.57
                                   HHHHCCHHHHHHHHHHHHHHHH CS
                           Wzz  58 ssltaqdvqanlqlasteieil 79 
                                   + +t +d+++  ql++  +eil
  gi|14601949|ref|NP_148494.1| 454 KAMTSSDMNERAQLYKQVQEIL 475
                                   4566679999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 3977.86
//
Query:       gi|14601950|ref|NP_148495.1|  [L=339]
Description: dipeptide ABC transporter permease DppB [Aeropyrum pernix K1]
Scores for 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-42  142.8  11.4    9.4e-42  142.8  11.4    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 ?   -0.9   0.5     0.063   1.1e+03     159     175 ..      16      32 ..       3      49 .. 0.50
   2 !  142.8  11.4   5.2e-46   9.4e-42       1     185 []     121     339 .]     117     339 .] 0.98

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.063
                  BPD_transp_1 159 lalviavlllnlvadil 175
                                   la+v  vl+l +v++i+
  gi|14601950|ref|NP_148495.1|  16 LAIVPTVLILYTVVFIV 32 
                                   33333333333333333 PP

  == domain 2  score: 142.8 bits;  conditional E-value: 5.2e-46
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....................................v 44 
                                   g++ G++aa +r++ +d+llr+ +iv ++l + +l+++l +vf                                     +
  gi|14601950|ref|NP_148495.1| 121 GVGSGVVAA-FRGGLVDRLLRTSSIVAYTLFIPWLGLMLKYVFsiklgilptggridprvnldvvtglyvldsiitanpaA 200
                                   688899999.*********************************************************************** PP

                  BPD_transp_1  45 ilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllgga 125
                                   + s++ hlilp ++l+++ ++ y+rl+r  + ++l ++   a+ra+G+++ +i + ++l+ +l+p+it ++l+f++llgga
  gi|14601950|ref|NP_148495.1| 201 LVSAVEHLILPSLTLGIVLSGVYTRLVRIHVAEALRSEVAVAYRARGLRESRIAV-HMLRISLIPTITMMGLQFAILLGGA 280
                                   ****************************************************666.************************* PP

                  BPD_transp_1 126 vlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                   vl+e ++swpGlg+ll+e i+++dys i+ g++++++++v l++l++di++++++prvr+
  gi|14601950|ref|NP_148495.1| 281 VLTEATFSWPGLGSLLVERISYRDYSTIQ-GVTVFFAFMVGLVSLIVDIIYAIVNPRVRY 339
                                   *****************************.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2552.09
//
Query:       gi|14601951|ref|NP_148496.1|  [L=280]
Description: dipeptide ABC transporter permease DppC [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-26   92.1  13.0    3.4e-26   92.1  13.0    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
    5.6e-05   23.0   0.3    5.6e-05   23.0   0.3    3.9  3  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
        1.3    9.7   4.3          3    8.5   3.4    2.0  2  DUF4690       Small Novel Rich in Cartilage


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 ?    0.7   0.5     0.065   3.9e+02     156     181 ..      13      38 ..       2      39 .. 0.78
   2 !   92.1  13.0   5.7e-30   3.4e-26       1     184 [.      96     276 ..      96     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.065
                  BPD_transp_1 156 ggvlalviavlllnlvadilqrlldp 181
                                    g++a+++a++++ lv+ + + +++p
  gi|14601951|ref|NP_148496.1|  13 SGFIAAGLAIVAFYLVVALAAPYIAP 38 
                                   47888888888888888888777765 PP

  == domain 2  score: 92.1 bits;  conditional E-value: 5.7e-30
                  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrslp 80 
                                   g++lG++++ ++++++d++l+++++ l+++P +vlai +       s+lg ++l  +i+l++++ ++y+r++r++++++  
  gi|14601951|ref|NP_148496.1|  96 GVPLGLVSG-YFGGPVDRVLSVVMDSLYAFPGIVLAIAIA------SVLGPSVLNaAIALMVVYVPAYFRMTRARVIEIKT 169
                                   89*******.******************************......****9999999************************ PP

                  BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis....... 154
                                   +d++ a r+lGa++ +i++++vlP ++p+++   +la++ ++   + l+f+g    l  +   + +g d+s+++       
  gi|14601951|ref|NP_148496.1| 170 QDYIVALRVLGAPHSRIMFRHVLPGVMPTVLVVYGLASADAILTEAGLSFFG----LVVTYPAPDWGLDISYGIkqflsgs 246
                                   ****************************************************....************************* PP

                  BPD_transp_1 155 nggvlalviavlllnlvadilqrlldprvr 184
                                   ++++l+ ++a+l l l +  + + l+ r+r
  gi|14601951|ref|NP_148496.1| 247 WWLTLFPGLAILTLALGFAMIGEGLAERFR 276
                                   999999999999999988888877777765 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 !   23.0   0.3   9.3e-09   5.6e-05      18      44 ..      18      48 ..      17      58 .. 0.84
   2 ?   -0.9   2.9      0.28   1.7e+03      22      36 ..     127     141 ..     126     175 .. 0.79
   3 ?    2.1   0.0     0.033     2e+02      19      37 ..     254     272 ..     253     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.3e-09
                        OppC_N 18 vglvilllllliaifaPliaPydp....qdl 44
                                  +gl+i+++ l++a+ aP+iaPy+p    +d+
  gi|14601951|ref|NP_148496.1| 18 AGLAIVAFYLVVALAAPYIAPYSPhskvSDV 48
                                  69*********************98666554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
                        OppC_N  22 illlllliaifaPli 36 
                                   i+l+++++++++P +
  gi|14601951|ref|NP_148496.1| 127 IVLAIAIASVLGPSV 141
                                   677788888888876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.033
                        OppC_N  19 glvilllllliaifaPlia 37 
                                   gl+il l l +a +++ +a
  gi|14601951|ref|NP_148496.1| 254 GLAILTLALGFAMIGEGLA 272
                                   89************99886 PP

>> DUF4690  Small Novel Rich in Cartilage
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.86   5.1e+03      76      86 ..      75      85 ..      41      95 .. 0.65
   2 ?    8.5   3.4    0.0005         3      65      88 ..     125     151 ..     116     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                       DUF4690 76 lLgasvllaLv 86
                                  +Lg+ ++l +v
  gi|14601951|ref|NP_148496.1| 75 VLGTRIVLKVV 85
                                  44444444433 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0005
                       DUF4690  65 PGaiaaiviaalLgasvl...laLvvi 88 
                                   PG + ai ia++Lg svl   +aL+v+
  gi|14601951|ref|NP_148496.1| 125 PGIVLAIAIASVLGPSVLnaaIALMVV 151
                                   9****************9444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.20s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2227.22
//
Query:       gi|118431800|ref|NP_148497.2|  [L=316]
Description: dipeptide ABC transporter ATP-binding protein DppD [Aeropyrum pernix K1]
Scores for complete 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  100.2   0.0    1.8e-28   99.8   0.0    1.2  1  ABC_tran    ABC transporter
    1.6e-19   70.1   0.1    2.8e-19   69.4   0.1    1.4  1  oligo_HPY   Oligopeptide/dipeptide transporter, C-terminal re
    1.5e-08   34.8   0.2      7e-07   29.3   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    8.7e-05   22.1   0.5      0.025   14.0   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
    0.00027   20.6   0.0    0.00047   19.8   0.0    1.4  1  AAA_29      P-loop containing region of AAA domain
     0.0039   17.6   0.1     0.0069   16.8   0.1    1.6  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.012   14.8   0.1      0.095   11.9   0.0    1.9  2  NB-ARC      NB-ARC domain
      0.023   14.2   0.1       0.44   10.1   0.0    2.1  2  AAA_25      AAA domain
      0.026   14.8   0.1       0.33   11.2   0.0    2.1  2  AAA_22      AAA domain
      0.041   13.6   0.6       0.13   12.0   0.0    1.8  2  AAA_24      AAA domain
       0.19   10.5   0.3          4    6.1   0.0    2.2  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 !   99.8   0.0   1.1e-31   1.8e-28       2     136 ..      24     180 ..      23     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 1.1e-31
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..pqlf 71 
                                    + vsl++++ge + ivGe+G+GKStL+  + +l  p      G+il+ g dl +    + ++   +eig+++q+  + l+
  gi|118431800|ref|NP_148497.2|  24 DGVSLSVNKGEWISIVGESGSGKSTLALSIPRLIMPpgriVGGRILYSGVDLLSlageELRRYRGREIGMVFQDptAYLD 103
                                    78**********************************999999999******9999995556666789*******877899 PP

                                    TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  72 peltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    p  tv+++               e+++ + +al+ +g++    ++++  p++LSgGq+qrva+a+a++ +pk+l++DEpt
  gi|118431800|ref|NP_148497.2| 104 PYRTVGSQiaesllehglassgsEAESMAGDALELVGIPR---DRASVYPHQLSGGQRQRVAIAAAVALEPKILIADEPT 180
                                    9999**************9655444444666666666555...666677******************************9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.1   1.7e-22   2.8e-19       1      65 []     232     295 ..     232     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.7e-22
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE+gp+++++++p HPYT++L++svp++ + ++ ++ i+g++p+l++ + GC+F+pRCp +++ C
  gi|118431800|ref|NP_148497.2| 232 VEIGPAEDVVSNPIHPYTEMLIKSVPDPWEDRE-VKPIPGSPPDLRNPPPGCRFHPRCPLRQPLC 295
                                    8***************************77777.****************************999 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.028        46       4      15 ..      38      49 ..      36      73 .. 0.93
   2 !   29.3   0.0   4.3e-10     7e-07     227     301 ..     143     215 ..     101     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.028
                         AAA_21  4 liGpNgsGKSnL 15
                                   ++G  gsGKS+L
  gi|118431800|ref|NP_148497.2| 38 IVGESGSGKSTL 49
                                   8**********9 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 4.3e-10
                         AAA_21 227 gdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                     d+  + +++lS G+++  a+++a++  +   ++l+ DEp + L+  +++++++l+k+l++ +g  v+l+TH+  l
  gi|118431800|ref|NP_148497.2| 143 RDRASVYPHQLSGGQRQRVAIAAAVALEP---KILIADEPTTALDVVVQAKIMDLMKKLQEeRGLTVMLVTHDIGL 215
                                    57778999**********9****999999...9***********************888888**********9766 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   0.2    0.0034       5.5      26      44 ..      35      53 ..      25      56 .. 0.84
   2 !   14.0   0.0   1.5e-05     0.025     130     204 ..     146     218 ..      97     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0034
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                     +ivG+ GSGKs l  +i
  gi|118431800|ref|NP_148497.2| 35 WISIVGESGSGKSTLALSI 53
                                   568**********997666 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.5e-05
                                    TT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                          SMC_N 130 agiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlek 204
                                    a +++++LSgG+++ va+a  +A++   p+ + + De   aLD    +k+ +l+k+ +++    ++ ++++ ++ ++
  gi|118431800|ref|NP_148497.2| 146 ASVYPHQLSGGQRQRVAIAAAVALE---PK-ILIADEPTTALDVVVQAKIMDLMKKLQEErgLTVMLVTHDIGLAAE 218
                                    4455669************888875...44.6789********************9998834555556665555544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.9e-07   0.00047      13      50 ..      24      61 ..      21      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.9e-07
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   dg +++++  + + ++G+sGsGKSTl  +i  l++p+ 
  gi|118431800|ref|NP_148497.2| 24 DGVSLSVNKGEWISIVGESGSGKSTLALSIPRLIMPPG 61
                                   66778888555999************999999999986 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   0.1   4.2e-06    0.0069      20      52 ..      31      65 ..      16     209 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-06
                         AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd....g 52
                                   ++g  e + ++GesG+GKs+l+ +++r +       g
  gi|118431800|ref|NP_148497.2| 31 NKG--EWISIVGESGSGKSTLALSIPRLIMPPgrivG 65
                                   444..7899*****************98877733331 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.8e-05     0.095      21      40 ..      34      53 ..      20      57 .. 0.85
   2 ?    0.5   0.0      0.17   2.8e+02     109     150 ..     183     222 ..     173     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.8e-05
                                   EEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                    ++++vG  G+GK+tla +i
  gi|118431800|ref|NP_148497.2| 34 EWISIVGESGSGKSTLALSI 53
                                   49**************9877 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                                    EEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S- CS
                         NB-ARC 109 lDDVweeedwdkigvvlparenrlrvllTTRdeevanavsat 150
                                    lD V++ + +d ++  l+ +e++l v+l T d  +a + s++
  gi|118431800|ref|NP_148497.2| 183 LDVVVQAKIMD-LMKKLQ-EERGLTVMLVTHDIGLAAEYSDR 222
                                    56666766664.444455.799999***99999999888876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00027      0.44      31      53 ..      31      53 ..      25      68 .. 0.91
   2 ?    1.9   0.0     0.091   1.5e+02     166     188 ..     189     211 ..     174     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                         AAA_25 31 pagelallaGapgtGKttlaldl 53
                                    +ge + ++G +g+GK+tlal++
  gi|118431800|ref|NP_148497.2| 31 NKGEWISIVGESGSGKSTLALSI 53
                                   6899999*************985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.091
                         AAA_25 166 galvealeriarrtgaavllvhH 188
                                    +++++ +++++++ g +v+lv H
  gi|118431800|ref|NP_148497.2| 189 AKIMDLMKKLQEERGLTVMLVTH 211
                                    5667778999************9 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    0.0002      0.33       8      23 ..      36      51 ..      30      56 .. 0.85
   2 ?    1.3   0.0      0.23   3.8e+02      52     128 ..     127     209 ..     105     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                         AAA_22  8 lvvtGesGtGKTtllr 23
                                   + ++GesG+GK+tl+ 
  gi|118431800|ref|NP_148497.2| 36 ISIVGESGSGKSTLAL 51
                                   789**********985 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.23
                         AAA_22  52 sskdllrellralglelka...erlsseellealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnlsrk 121
                                    + ++++ + l+ +g ++++   ++++++      ++ + a+av   +++li DE    l+   +++++   ++l++  + 
  gi|118431800|ref|NP_148497.2| 127 EAESMAGDALELVGIPRDRasvYPHQLSGGQ--RQRVAIAAAValePKILIADEPTTaLDvvvQAKIMDLMKKLQE--ER 202
                                    5666667777777776666444333333333..2222222222456899999998888877766888888888888..88 PP

                         AAA_22 122 gvqliLv 128
                                    g+++ Lv
  gi|118431800|ref|NP_148497.2| 203 GLTVMLV 209
                                    8888887 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     8e-05      0.13       5      27 ..      36      57 ..      32      61 .. 0.88
   2 ?   -0.8   0.1      0.64     1e+03     107     130 ..     187     211 ..     185     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8e-05
                         AAA_24  5 iliyGpsgiGKTtlakelgpkpl 27
                                   i i+G+sg+GK+tla+++ p+ +
  gi|118431800|ref|NP_148497.2| 36 ISIVGESGSGKSTLALSI-PRLI 57
                                   679**************9.8876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.64
                         AAA_24 107 laeefrrllkklqelrk.nvifiah 130
                                    +++++++l+kklqe r+ +v ++ h
  gi|118431800|ref|NP_148497.2| 187 VQAKIMDLMKKLQEERGlTVMLVTH 211
                                    6789999*******99999999988 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 ?    2.2   0.1     0.037        60     240     264 ..      28      53 ..      14      59 .. 0.80
   2 ?    6.1   0.0    0.0025         4     322     366 ..     152     196 ..     142     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.037
                                    EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                                    + + kG  + IvG    GKsTL  ++
  gi|118431800|ref|NP_148497.2|  28 LSVNKGeWISIVGESGSGKSTLALSI 53 
                                    4567887889************8666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0025
                                    S--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS CS
                     ABC_ATPase 322 dASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelv 366
                                    + SG   q ++i+ a+ ++ k+l+ DE t+A   +++ + m+ + 
  gi|118431800|ref|NP_148497.2| 152 QLSGGQRQRVAIAAAVALEPKILIADEPTTALDVVVQAKIMDLMK 196
                                    569999999***********************9999877776433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2238.15
//
Query:       gi|118431801|ref|NP_148498.2|  [L=341]
Description: dipeptide ABC transporter ATP-binding protein DppF [Aeropyrum pernix K1]
Scores for complete 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  106.0   0.0    2.8e-30  105.6   0.0    1.2  1  ABC_tran     ABC transporter
    1.9e-17   63.5   0.3    3.3e-17   62.8   0.3    1.4  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    7.4e-06   26.0   0.4      0.018   14.9   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0024   18.1   0.5     0.0099   16.2   0.5    1.9  1  AAA_22       AAA domain
     0.0051   16.2   0.1     0.0099   15.2   0.1    1.4  1  ATPase       KaiC
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.026   14.8   0.0    1.4  1  AAA_19       AAA domain
       0.04   13.6   0.3       0.26   11.0   0.2    2.0  1  AAA_30       AAA domain
      0.043   14.2   0.4      0.069   13.5   0.3    1.6  1  AAA_16       AAA ATPase domain
      0.047   12.4   0.0       0.67    8.5   0.0    2.0  2  AAA_13       AAA domain
      0.048   13.1   0.0        3.1    7.2   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.064   12.8   1.4        0.4   10.2   0.0    2.4  2  AAA_25       AAA domain
      0.064   13.2   0.0       0.12   12.3   0.0    1.5  1  NACHT        NACHT domain
      0.067   12.4   0.7        0.1   11.8   0.1    1.4  2  NB-ARC       NB-ARC domain
      0.074   12.8   0.0       0.13   12.1   0.0    1.3  1  AAA_29       P-loop containing region of AAA domain
      0.089   12.7   0.2       0.42   10.5   0.0    2.0  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
       0.14   12.1   0.0       0.23   11.3   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.15   11.7   0.0       0.22   11.1   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
       0.16   10.7   2.0       0.37    9.5   0.3    2.0  2  ABC_ATPase   Predicted ATPase of the ABC class
       0.19   11.5   0.0       0.37   10.5   0.0    1.4  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.22   12.0   0.3        0.3   11.6   0.3    1.1  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 !  105.6   0.0   3.2e-33   2.8e-30       2     136 ..      39     191 ..      38     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 3.2e-33
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltv 76 
                                    + v+l ++ege++aivGe+G+GK+tL k++ g ++p  G i ++g+ l+     + ++lr+++++++q+  ++l+p + v
  gi|118431801|ref|NP_148498.2|  39 DGVDLGIREGEVLAIVGESGCGKTTLGKAIVGIEEPSDGAIYYRGELLTPhrlARDRRLRRKLQMVFQDpyKSLDPLMPV 118
                                    789****************************************99999998898999************9999******* PP

                                    HHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +++              e+++++ ++l+++gl+  ++  + ++p++LSgGq+qrva+ar+l+ +p+++++DEp 
  gi|118431801|ref|NP_148498.2| 119 GDQvaeplvihglargeEARRRAVEMLETVGLTPGREFYW-RKPHQLSGGQRQRVAIARTLVLEPEVIVADEPV 191
                                    ****************999999************777776.999*****************************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 !   62.8   0.3   3.7e-20   3.3e-17       1      65 []     243     307 ..     243     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 3.7e-20
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE g+ + ++++p+HPYT+aL+ s+p++ r++ +   i ge+ps+ +++ GC+F+pRCp a++ C
  gi|118431801|ref|NP_148498.2| 243 VEVGEPRSVIENPRHPYTAALVTSTPSISRRRPPRFPISGEVPSAVAIPPGCRFHPRCPLASSLC 307
                                    8************************************************************9988 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 !    9.6   0.1   0.00081      0.72       3      22 ..      52      71 ..      50      86 .. 0.86
   2 !   14.9   0.0     2e-05     0.018     229     299 ..     156     224 ..      92     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00081
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +++G  g+GK++L +a+ ++
  gi|118431801|ref|NP_148498.2| 52 AIVGESGCGKTTLGKAIVGI 71
                                   89***************776 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2e-05
                         AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                     +++ +++lS G+++  a++  l   +    +++ DEp + ++ ++ +++l+l+ ++++r+ga ++l TH+ 
  gi|118431801|ref|NP_148498.2| 156 FYWRKPHQLSGGQRQRVAIARTLVLEP---EVIVADEPVSMIDVSMRASILDLImDYHRRTGATIVLITHDI 224
                                    567788999999999977777777777...9********************999788888**********96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   1.1e-05    0.0099       5      43 ..      48      79 ..      45     226 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                                     +l+++GesG+GKTtl + ++   +       ++++ +
  gi|118431801|ref|NP_148498.2| 48 GEVLAIVGESGCGKTTLGKAIVGIEE-------PSDGAI 79
                                   6789*************999887653.......244444 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.1e-05    0.0099      15      37 ..      44      66 ..      32      78 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                         ATPase 15 GipegrvvlitGepGtGKtifal 37
                                   Gi eg+v  i+Ge+G+GKt++++
  gi|118431801|ref|NP_148498.2| 44 GIREGEVLAIVGESGCGKTTLGK 66
                                   9********************97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     3e-05     0.026      10     126 ..      48     207 ..      42     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAak.elrerlaalgae.................atT 71 
                                     +vl++++  G+GKT++ k+iv + +   g    +  l+++ + A + +lr +l+++ ++                    
  gi|118431801|ref|NP_148498.2|  48 GEVLAIVGESGCGKTTLGKAIVGIEEPSDGAIYYRGELLTPHRLARDrRLRRKLQMVFQDpyksldplmpvgdqvaePLV 127
                                    67999***********************99999************86379999*9999999**************88789 PP

                         AAA_19  72 iHrlalldfddlltealelle..........................eaeeekklqeeellivDE.fqdvd.elqyrLlk 123
                                    iH+la    ++    a+e+le                            + ++ + e e+++ DE ++++d  +  ++l+
  gi|118431801|ref|NP_148498.2| 128 IHGLAR--GEEARRRAVEMLEtvgltpgrefywrkphqlsggqrqrvAIA-RTLVLEPEVIVADEpVSMIDvSMRASILD 204
                                    999955..444444566777777777777777777777777777654323.34455888******88****888888888 PP

                         AAA_19 124 all 126
                                     ++
  gi|118431801|ref|NP_148498.2| 205 LIM 207
                                    776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00029      0.26      19      68 ..      49     103 ..      41     223 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g...grviglAptgkaAkv.Laeelgi 68 
                                     v +++G  G GKtt+ ka++ + e + g   +r  +l+p   a ++ L+++l++
  gi|118431801|ref|NP_148498.2|  49 EVLAIVGESGCGKTTLGKAIVGIEEPSdGaiyYRGELLTPHRLARDRrLRRKLQM 103
                                    5899*****************9999885577755556666555555445554443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   7.7e-05     0.069      23      45 ..      47      69 ..      32     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.7e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                   ++e++ ++GesG+GK++l +++ 
  gi|118431801|ref|NP_148498.2| 47 EGEVLAIVGESGCGKTTLGKAIV 69
                                   44899************987765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.084        76      21      46 ..      53      78 ..      49     110 .. 0.79
   2 ?    8.5   0.0   0.00075      0.67     525     580 ..     180     233 ..     171     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.084
                         AAA_13 21 iYGwNGaGKTtLSrllrslelgetep 46
                                   i G  G GKTtL +++  +e+ +   
  gi|118431801|ref|NP_148498.2| 53 IVGESGCGKTTLGKAIVGIEEPSDGA 78
                                   56899***********9998766555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00075
                         AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                     + +++v D PvS  D  +  ++  li ++   +   + + + TH +   + v ++
  gi|118431801|ref|NP_148498.2| 180 LEPEVIVADEPVSMIDVSMRASILDLIMDYH--RRTGATIVLITHDIAVARAVADR 233
                                    5889**************************8..4555668888***9999888776 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 ?    7.2   0.0    0.0035       3.1      26      44 ..      50      68 ..      43      74 .. 0.89
   2 ?    4.0   0.0     0.033        29     135     201 ..     153     226 ..      89     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0035
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                   + aivG+ G+GK+ l  Ai
  gi|118431801|ref|NP_148498.2| 50 VLAIVGESGCGKTTLGKAI 68
                                   679**************99 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.033
                                    T.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHH CS
                                    x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                          SMC_N 135 e.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreem 201
                                              +LSgG+++ va+a  + +   +p+ + + De  + +D + ++ + +l+   ++++ a ++ i+++  +
  gi|118431801|ref|NP_148498.2| 153 GrefywrkphQLSGGQRQRVAIARTLVL---EPE-VIVADEPVSMIDVSMRASILDLIMdyHRRTGATIVLITHDIAV 226
                                    45555555559**********9977544...444.4466888888888888888887773333344556666665555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00045       0.4      30      49 ..      45      64 ..      26      69 .. 0.89
   2 ?    1.2   0.4      0.25   2.3e+02     169     188 ..     203     222 ..      94     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                         AAA_25 30 lpagelallaGapgtGKttl 49
                                   +++ge+ +++G +g+GKttl
  gi|118431801|ref|NP_148498.2| 45 IREGEVLAIVGESGCGKTTL 64
                                   579****************8 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.25
                         AAA_25 169 vealeriarrtgaavllvhH 188
                                    ++ + +  rrtga+++l+ H
  gi|118431801|ref|NP_148498.2| 203 LDLIMDYHRRTGATIVLITH 222
                                    44455567899999999998 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   0.00013      0.12       2      21 ..      50      69 ..      49     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   ++++ Ge+G+GKTtL + ++
  gi|118431801|ref|NP_148498.2| 50 VLAIVGESGCGKTTLGKAIV 69
                                   789************88876 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   0.1   0.00011       0.1      21      41 ..      49      69 ..      38      75 .. 0.88
   2 ?   -3.5   0.0       5.1   4.5e+03     128     150 ..     211     233 ..     196     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EEEEEEESTTSSHHHHHHHHC CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqil 41
                                    v+a+vG  G+GKttl k i+
  gi|118431801|ref|NP_148498.2| 49 EVLAIVGESGCGKTTLGKAIV 69
                                   499*************99886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.1
                                    CHTTSEEEEEESBCCCCCCS-S- CS
                         NB-ARC 128 renrlrvllTTRdeevanavsat 150
                                    r  +  ++l T d +va av+++
  gi|118431801|ref|NP_148498.2| 211 RRTGATIVLITHDIAVARAVADR 233
                                    67788899999999999998875 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 ?   12.1   0.0   0.00014      0.13      13      41 ..      39      67 ..      36      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDA 41
                                   dg ++ i++ ++  ++G+sG GK+Tl  A
  gi|118431801|ref|NP_148498.2| 39 DGVDLGIREGEVLAIVGESGCGKTTLGKA 67
                                   5666777755699************9655 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 ?   10.5   0.0   0.00047      0.42       1      20 [.      50      69 ..      50      76 .. 0.88
   2 ?   -0.7   0.0       1.4   1.3e+03      52      70 ..     210     228 ..     208     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00047
                           MobB  1 vlgivgksgsGKTtLlekli 20
                                   vl+ivg sg+GKTtL + ++
  gi|118431801|ref|NP_148498.2| 50 VLAIVGESGCGKTTLGKAIV 69
                                   799************88776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                           MobB  52 hrkAGAkevlvaskerlal 70 
                                    hr+ GA+ vl++++  +a 
  gi|118431801|ref|NP_148498.2| 210 HRRTGATIVLITHDIAVAR 228
                                    8999**9999998876664 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   0.00026      0.23      99     121 ..      48      70 ..      36      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                    TSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                    +++ ++vG+SG GK+tL +a+++
  gi|118431801|ref|NP_148498.2|  48 GEVLAIVGESGCGKTTLGKAIVG 70 
                                    58999************999887 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.22       9      46 ..      43      81 ..      35     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                   S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                    ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiy 46
                                   + i +G+ ++i+g++g+Gkt++ ++++   + +d ai y
  gi|118431801|ref|NP_148498.2| 43 LGIREGEVLAIVGESGCGKTTLGKAIVGIEEPSDgAIYY 81
                                   56789999***************9999876665634444 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 ?    9.5   0.3   0.00041      0.37     240     264 ..      43      68 ..      33      73 .. 0.88
   2 ?    0.4   0.1      0.24   2.2e+02     375     420 ..     201     246 ..     163     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00041
                                    EEE-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAl 264
                                    +gi++G v +IvG    GK+TL +A+
  gi|118431801|ref|NP_148498.2|  43 LGIREGeVLAIVGESGCGKTTLGKAI 68 
                                    7***********************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.24
                                    -HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE-H CS
                     ABC_ATPase 375 plvdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdvt 420
                                    +++d++++ ++++g +++l++  +    +vAd++ +m   k+ +v 
  gi|118431801|ref|NP_148498.2| 201 SILDLIMDYHRRTGATIVLITHDIAVARAVADRIAVMYLGKIVEVG 246
                                    6788999999999999999999999999999999999766666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00041      0.37       6      23 ..      53      70 ..      49      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                      PduV-EutP  6 liGkvgsGKttLtqalkg 23
                                   ++G++g+GKttL +a+ g
  gi|118431801|ref|NP_148498.2| 53 IVGESGCGKTTLGKAIVG 70
                                   79************9976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00033       0.3      21      39 ..      50      68 ..      39      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                         AAA_23 21 ltlItGpNGaGKTTildAi 39
                                   + +I+G+ G+GKTT+  Ai
  gi|118431801|ref|NP_148498.2| 50 VLAIVGESGCGKTTLGKAI 68
                                   668************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2350.72
//
Query:       gi|118431802|ref|NP_148499.2|  [L=292]
Description: hypothetical protein APE_2265.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-09   36.0   1.1    7.6e-08   32.6   1.1    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0036   16.9   0.0      0.072   12.6   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   1.1   8.5e-12   7.6e-08       7     197 .]      18     200 ..      13     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.5e-12
                                    EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                    Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                    ++ +  ++ +++++D+G +  +a++ +   ++  k+      i+TH+H+DH + l      ++  ++  + ++ a+  + 
  gi|118431802|ref|NP_148499.2|  18 STLFYKHGRTLFIVDPGHGRKRAKQIS---KAAEKLGGEAVAIITHFHSDHLSTLYQ---GFQPSTALAPVKDLAMVQDR 91 
                                    556677*******************75...5566666666678********998754...33333333333333333333 PP

                                    HHHHHHHCCHH...TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC. CS
                    Lactamase_B  87 addaasrkgll...lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridlt 163
                                    +++    +g +   ++ +  +k + ++++++++a  ++ l  ++ pgh++g+  ve ++g vl++ D ++ +  + +   
  gi|118431802|ref|NP_148499.2|  92 VMRLHYTFGYPftgAEDYLLFKAEDVDNVEPLEAERIKPLRLVPLPGHTPGQTGVETPDG-VLYAADSIFGERVLQTYA- 169
                                    3322222222244577899999************************************86.899999999888777777. PP

                                    TTCEEE-SHCHHHHHHHHHHHHHHH..CHSEEEESS CS
                    Lactamase_B 164 lrgaevrdpsdaekyldsllklagl..kaevlvpgH 197
                                         v+++s   ++l++l++l++   + ev+vp+H
  gi|118431802|ref|NP_148499.2| 170 -----VPYHSNPCQALETLTRLRDRvnRLEVIVPSH 200
                                    .....5555555555555555544300445566666 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 !   12.6   0.0     8e-06     0.072       3      55 ..      29      75 ..      27     136 .. 0.70
   2 !    2.5   0.0    0.0099        89     125     193 ..      98     188 ..      81     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8e-06
                                   EEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCC.C-- CS
                  Lactamase_B_2  3 iLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlre.lrp 55
                                   +++D+g + r+ a++     + + ++l   ++ ++th H DHl    tl + ++p
  gi|118431802|ref|NP_148499.2| 29 FIVDPGHG-RKRAKQI----SkAAEKLGGEAVAIITHFHSDHLS---TLYQgFQP 75
                                   68999999.3332222....2255667777888**********5...45554444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0099
                                    SEEEEEECTTEEEEE.ESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.....................HHT---ST CS
                  Lactamase_B_2 125 tlGlriegggkrvyy.igDtgyipeeigerlggadllllditayeddemir.....................hmgHltpe 182
                                    t+G+ ++g++  +++ + D+  +++  +er++++ l+ l++    +   +                       ++H++p 
  gi|118431802|ref|NP_148499.2|  98 TFGYPFTGAEDYLLFkAEDVDNVEPLEAERIKPLRLVPLPGHTPGQTGVETpdgvlyaadsifgervlqtyaVPYHSNPC 177
                                    56666665544433326677788877788888888888887655555544466677777777777777778889999999 PP

                                    SHHHHCTTSSS CS
                  Lactamase_B_2 183 eaveaaadlga 193
                                    +a+e +++l+ 
  gi|118431802|ref|NP_148499.2| 178 QALETLTRLRD 188
                                    99999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2220.77
//
Query:       gi|118431803|ref|YP_874934.1|  [L=36]
Description: hypothetical protein APE_2265a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.20s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 314.48
//
Query:       gi|118431804|ref|NP_148500.2|  [L=459]
Description: pyridoxal-dependent decarboxylase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-18   66.0   0.0      4e-18   65.3   0.0    1.2  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    7.9e-08   31.6   0.0    3.2e-07   29.7   0.0    1.9  1  Aminotran_5      Aminotransferase class-V
    0.00018   20.8   0.0    0.00076   18.8   0.0    1.8  2  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.014   15.4   0.5      0.036   14.2   0.5    1.7  1  PT-VENN          Pre-toxin domain with VENN motif
      0.035   13.4   0.0      0.052   12.9   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.045   12.5   0.0      0.063   12.0   0.0    1.1  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
       0.17   10.4   0.0       0.31    9.5   0.0    1.4  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   1.5e-21     4e-18     102     345 ..      84     311 ..      70     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.5e-21
                                    T.-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB CS
                  Pyridoxal_deC 102 e.gggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqahssvekaalvlgvklrvipldengkl 180
                                    e  +g+++ g++es++la +Aar+ + + +  +           ++ +++ + +h sv+kaa++lg++l   p+d+ g  
  gi|118431804|ref|NP_148500.2|  84 EgVVGTVTYGGTESIILAAMAARE-WYRSLGGSR----------TPGIVAPQTVHPSVRKAARYLGMRLSIAPVDP-G-S 150
                                    43689*****************96.666665444..........678****************************9.7.4 PP

                                    -HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGGGGGGSGGGGG.......GGTT CS
                  Pyridoxal_deC 181 rgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaGsaficpeirh.......llkg 253
                                       +   ++  ++++  +  +vv+ +    +g  dd++ ++++++   +wlHvDA  +G  fi p++r+       + + 
  gi|118431804|ref|NP_148500.2| 151 KRVDIDSLVSLVDDR--TA-MVVVSAPNYPYGTVDDVRSVAEALSSQRVWLHVDACVGG--FILPFMRElglysgaFAFD 225
                                    556788888888888..66.7888889999*****************************..********99999999999 PP

                                    GGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEECCCGSSSSSGHHT.HHHHHHHHHHHHH CS
                  Pyridoxal_deC 254 ieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaadlgtkaiplsrrvr.ilklwfvlralGv 332
                                    +e + S+++  hK++  + ++s+l+++d +  ++    +  + +       + + + ++  sr+v   +  w v   lG+
  gi|118431804|ref|NP_148500.2| 226 VEGVYSVSMDLHKYGYSPKGASVLLFRDGSLKKHSIFADLRWPG-------YPFINTTVLSSRSVApLAAAWAVTNYLGR 298
                                    ***************************98765555544444444.......56667777777765515567888888888 PP

                                    HHHHHHHHHHHHH CS
                  Pyridoxal_deC 333 eglqnqirksvel 345
                                    +g+ +  rk ve 
  gi|118431804|ref|NP_148500.2| 299 RGYLELARKAVEA 311
                                    8888887777765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.2e-10   3.2e-07      67     179 ..      91     205 ..      89     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.2e-10
                                    ESSHHHHHHHHHHHCCCC...-TTTSE..EEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT.SCBEGGGHHHH--TTE CS
                    Aminotran_5  67 tsGtteainlvalslars...lkpgde..ivvteaehhanlvpwqelakrtgakvkvipldee.geldldelekllnekt 140
                                    t G+te+i l+a++++++   l   ++  iv  ++ h + +    ++a+  g+++ ++p+d++ +++d+d l +l++++t
  gi|118431804|ref|NP_148500.2|  91 TYGGTESIILAAMAAREWyrsLGGSRTpgIVAPQTVHPSVR----KAARYLGMRLSIAPVDPGsKRVDIDSLVSLVDDRT 166
                                    88******999999988876544443344999999999999....888999**********9636799************ PP

                                    EEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTT CS
                    Aminotran_5 141 klvaithvsnvtGtiqpveeigklakkkgalvlvDaaqa 179
                                    ++v +++ +   Gt+++v ++++++  + ++++vDa+ +
  gi|118431804|ref|NP_148500.2| 167 AMVVVSAPNYPYGTVDDVRSVAEALSSQRVWLHVDACVG 205
                                    ************************************865 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     3e-07   0.00076      70     187 ..      88     201 ..      31     213 .. 0.79
   2 ?   -0.5   0.0      0.21   5.4e+02     248     310 ..     275     338 ..     272     355 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3e-07
                                    GEEEESHHHHHHHHHHHHHH......HTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHH CS
                  Aminotran_1_2  70 avvvgsGagaliealifllk......lnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeap 143
                                      v+ +G+ ++i a++++ +        +   i++p+ +++s+ +++r+ g+ +   p+ ++ + ++d+++l  ++++  
  gi|118431804|ref|NP_148500.2|  88 GTVTYGGTESIILAAMAAREwyrslgGSRTPGIVAPQTVHPSVRKAARYLGMRLSIAPV-DPGSKRVDIDSLVSLVDD-- 164
                                    55666777777777777665777655455556**************************5.59999*************.. PP

                                    CTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                  Aminotran_1_2 144 egnkktkvilvesphNPtGtvatleeleklldlakkynlllfvD 187
                                        +t +++v  p+ P Gtv   ++++ +++   +++++l vD
  gi|118431804|ref|NP_148500.2| 165 ----RTAMVVVSAPNYPYGTV---DDVRSVAEALSSQRVWLHVD 201
                                    ....9**************98...55555555578888888888 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.21
                                    HHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEE CS
                  Aminotran_1_2 248 rpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmfllt 310
                                    +++lss ++++++aa++ +  l ++   e +++  + r+e+  +L+++g+  la+  s+++++ 
  gi|118431804|ref|NP_148500.2| 275 TTVLSSRSVAPLAAAWAVTNYLGRRGYLELARKAVEARDEIMRGLESIGFRSLAPIeSTILSVA 338
                                    6778888888888887777776666555555555666778888899999887777546666655 PP

>> PT-VENN  Pre-toxin domain with VENN motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   1.4e-05     0.036       8      42 ..      69     106 ..      68     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                        PT-VENN   8 EKqtvsalstlaaGl...aGgvvggtladavaGaeage 42 
                                    E+++vs +s+la+G+   +G v+ g + + +++a a++
  gi|118431804|ref|NP_148500.2|  69 ERELVSFASSLAGGVegvVGTVTYGGTESIILAAMAAR 106
                                    9************86222666666**********9996 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 ?   12.9   0.0     2e-05     0.052      24     146 ..      71     203 ..      54     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                    HHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH.......TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTT CS
                DegT_DnrJ_EryC1  24 eveeFEkafaaylgvkhaiavssGtaAlhlaLra.......lgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdt 96 
                                    e  +F++ +a  ++      +  Gt+++ la +a       lg ++   ++ p++   +  +a+++lg++   + vdp +
  gi|118431804|ref|NP_148500.2|  71 ELVSFASSLAGGVEGVVGTVTYGGTESIILAAMAarewyrsLGGSRTPGIVAPQTVHPSVRKAARYLGMRLSIAPVDPGS 150
                                    55677888888777777777888999999988887888866666688889999999************************ PP

                                    SSB-GGGCGGG--TTEEEEEEB-...GGGB---HHHHHHHHHHCT-EEEEE-T CS
                DegT_DnrJ_EryC1  97 ynidpaaieaaitertkaIlpVh...lyGqvadmdalkaiaakhglkvieDaA 146
                                      +d +++ +++  rt+ +++      yG v d+ ++ +  +++ +++  Da+
  gi|118431804|ref|NP_148500.2| 151 KRVDIDSLVSLVDDRTAMVVVSApnyPYGTVDDVRSVAEALSSQRVWLHVDAC 203
                                    ****************8887653222599999999999999999999999998 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05     0.063     170     323 ..     167     324 ..     146     349 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                    SEEEEESS-T.TSEEE-HHHHHHHHTTSESEEEEE-TT-TTGGGSGGGTTSSSSSSS.-BTTBEEE.EEEEHCCCCS--T CS
                       OKR_DC_1 170 rlavitnsTY.dGvlynakeivdkleklsdrilfDeAwvgyeqfiplyadaskllae.nendpgil.vtqSvHKllaals 246
                                     ++v+  + Y +G++ +++++ + l +  + +++D   +g++   p++ +    ++    + +g++ v    HK   +  
  gi|118431804|ref|NP_148500.2| 167 AMVVVSAPNYpYGTVDDVRSVAEALSSQRVWLHVDACVGGFIL--PFMRELGLYSGAfAFDVEGVYsVSMDLHKYGYSPK 244
                                    578999999989***********************99999863..555555444444444455666255689******** PP

                                    T-EEEEEES-BT--HHHHHHH....HHHTS-SS--HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHSSS-- CS
                       OKR_DC_1 247 qaSlihvkeelivneerlnea....fmmhattSpsYpllAsldvaakmlegesgrrlleevveraielrkeikrldnael 322
                                     aS++  +++   +++ +++     +   +tt  s   +A l  a +++ +  grr   e  ++a+e+r+ei r  ++  
  gi|118431804|ref|NP_148500.2| 245 GASVLLFRDGSLKKHSIFADLrwpgYPFINTTVLSSRSVAPLAAAWAVT-NYLGRRGYLELARKAVEARDEIMRGLESIG 323
                                    **********998888888754455889999999999999998887776.889999999999999999999988444333 PP

                                    - CS
                       OKR_DC_1 323 i 323
                                    +
  gi|118431804|ref|NP_148500.2| 324 F 324
                                    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 ?   -3.9   0.0       1.4   3.7e+03      93     108 ..      84      99 ..      75     108 .. 0.60
   2 ?    9.5   0.0   0.00012      0.31     125     176 ..     153     204 ..     116     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.4
                                    EEEEESTSSHHHHHHH CS
                Cys_Met_Meta_PP  93 eivvsddlYggtqrll 108
                                    e vv +  Yggt++++
  gi|118431804|ref|NP_148500.2|  84 EGVVGTVTYGGTESII 99 
                                    4555566666666554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00012
                                    TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
                Cys_Met_Meta_PP 125 sdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                     d+++l + ++++t +v + +p  p   v D++++a++  ++ v + vD+++
  gi|118431804|ref|NP_148500.2| 153 VDIDSLVSLVDDRTAMVVVSAPNYPYGTVDDVRSVAEALSSQRVWLHVDACV 204
                                    4678889999***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3843.30
//
Query:       gi|118431805|ref|NP_148501.2|  [L=382]
Description: MFS transporter [Aeropyrum pernix K1]
Scores for 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-22   78.3  33.3    5.1e-22   78.3  33.3    1.9  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 !   78.3  33.3   2.9e-26   5.1e-22       1     347 [.      10     341 ..       7     347 .. 0.80
   2 !   10.3  19.2   1.3e-05      0.23      34     170 ..     242     377 ..     237     381 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 2.9e-26
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l+l++f s + + +++p+ + ++aedl +s+ e+gll+ +y ++++++++p G+l dr   r +l +g+ll++++++l l
  gi|118431805|ref|NP_148501.2|  10 LALSVFSSQAIWVTYSPVTS-LVAEDLDVSKEEVGLLAIVYPAAFLALTIPSGVLLDRA-FRTWLTVGVLLTGAAGVLRL 87 
                                    57888888899999999999.99***********************************4.599************77777 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                    + + ++ +ll++ vl++lg+ +l+ + a +++ + p+ +r  +++lls ++ lG+i + + g ++++ lg +++ + +a+
  gi|118431805|ref|NP_148501.2|  88 LDPLSYeWLLACQVLAALGQPLLLNSFAPAASTIRPE-RRDTVVSLLSFAMYLGIIYALGTGYYIYTRLGLQWLNIPIAA 166
                                    53335559***********977777777777776666.****************************************** PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqev 237
                                    vs+ +++    l+++  p+ + +++  +    g + +v+ +++l  ++ lw  l++l+l+  +  +  ++++l   + + 
  gi|118431805|ref|NP_148501.2| 167 VSAASVI----LYVAGLPALPQQAGSGL----GFKDVVSEFRLLAGRRDLW--LLGLILGLGVALFdnMSIWLEA-ALSP 235
                                    ****955....66677777777777777....55556666********996..4444444333333568888888.5888 PP

                          MFS_1 238 lglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfv 317
                                     gl+   +ag  +al+ l+g+++  ++   + r+g  r +++  ++ll+a+l lal+  t s +++  ++ l+G+ +  +
  gi|118431805|ref|NP_148501.2| 236 KGLG--DIAGSSVALALLAGLVGVAVIPPRVVRVG-LRSWYIRAAALLVAVLYLALALET-SRLAVQTLIPLAGLVMLPA 311
                                    8888..34444455555555555557777777777.588888889999999999988888.44444446777899***** PP

                          MFS_1 318 fpsllalasdlappeeagtasglfntagsl 347
                                    +p ++ ++s ++ ++ +g+a+g++++++ +
  gi|118431805|ref|NP_148501.2| 312 YPVIMEWISTYYDKRLQGKAAGAIGFVSRI 341
                                    *************************99886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 1.3e-05
                          MFS_1  34 igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslw.lllvlrvlqGlgagalfpagaalia 111
                                    +g  ++l  l+ +v++ ++ + + r+G r++++ +++l+++  l+l++a  ++  ++  l  l+Gl +  ++p+++ +i+
  gi|118431805|ref|NP_148501.2| 242 AGSSVALALLAGLVGVAVIPPRVVRVGLRSWYIRAAALLVAV-LYLALAlETSRlAVQTLIPLAGLVMLPAYPVIMEWIS 320
                                    66778889999999999999999****999666666666666.3444344777768999999****************** PP

                          MFS_1 112 dwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                     ++ k+ +g+a g ++  + + ++  + ++ l++ss   +a f +la++s +af ++ll
  gi|118431805|ref|NP_148501.2| 321 TYYDKRLQGKAAGAIGFVSRILTVSLASAATLFLSS--PSAYFTFLAVLSTIAFAIALL 377
                                    *****************9999998888888877755..567788999999999876443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); 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:                         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: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.35
# Mc/sec: 3284.64
//
Query:       gi|118431806|ref|NP_148502.2|  [L=547]
Description: hypothetical protein APE_2271.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   13.6   0.0       0.07   12.7   0.0    1.4  1  STAR_dimer  Homodimerisation region of STAR domain protein


Domain annotation for each model (and alignments):
>> STAR_dimer  Homodimerisation region of STAR domain protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.9e-06      0.07      23      38 ..     262     277 ..     257     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-06
                     STAR_dimer  23 pnvftHlerLLdeEIs 38 
                                    p+v+tHl+rL+++EIs
  gi|118431806|ref|NP_148502.2| 262 PKVMTHLKRLIEKEIS 277
                                    89*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.36
# Mc/sec: 4520.69
//
Query:       gi|118431807|ref|NP_148503.2|  [L=657]
Description: hypothetical protein APE_2272.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-16   61.0   0.0    4.4e-16   59.6   0.0    1.7  1  ABC_tran         ABC transporter
    1.1e-11   45.2   0.6    5.2e-08   33.1   0.0    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.2e-06   26.8   0.0    1.5e-05   25.3   0.0    1.8  1  AAA_22           AAA domain
    2.1e-05   24.7   0.0    7.6e-05   22.9   0.0    2.0  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00038   20.8   0.0      0.001   19.5   0.0    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00049   19.6   0.0      0.063   12.7   0.0    2.0  2  SMC_N            RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.012   15.4   2.0      0.014   15.1   0.3    2.0  2  AAA_30           AAA domain
      0.012   15.3   0.0      0.024   14.4   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.013   15.1   0.3      0.063   12.8   0.3    2.2  1  AAA_25           AAA domain
      0.023   14.6   0.0      0.048   13.6   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
      0.024   14.6   0.0      0.056   13.4   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      0.084   13.3   2.2        0.1   12.9   0.6    2.0  1  AAA_16           AAA ATPase domain
      0.088   13.2   0.0       0.39   11.1   0.0    2.0  1  AAA              ATPase family associated with various cellul
      0.098   12.8   0.9       0.35   11.0   0.2    2.4  2  AAA_33           AAA domain
       0.13   12.3   0.1       0.28   11.3   0.1    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
       0.15   12.6   0.0       0.28   11.7   0.0    1.3  1  AAA_23           AAA domain
       0.18   12.1   0.1       0.47   10.8   0.1    1.7  1  AAA_19           AAA domain
       0.22   10.9   0.0       0.33   10.3   0.0    1.3  1  GNAT_acetyltr_2  GNAT acetyltransferase 2
       0.23   11.0   0.7       0.37   10.3   0.7    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.98    9.3   2.4       0.88    9.5   0.6    1.8  2  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   4.9e-19   4.4e-16       1     135 [.     456     592 ..     456     594 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4.9e-19
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    lk+v++++++g++ a+vG +GaGK+tLl++++g+     Ge    +  + +  ++   k  + lp e +  f + t+ e+
  gi|118431807|ref|NP_148503.2| 456 LKDVNITVNPGSVAAVVGASGAGKTTLLRMILGKALGIGGEGYRPDSGVVK--IPTNTKAAALLPGElEPSFGGETLLEH 533
                                    79********************************99988887333444444..777777788888776555666667777 PP

                                    .....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                          +   + ++ls++gl +  +   + s  +LS Gqk+r +la +l+++p+ll++DE 
  gi|118431807|ref|NP_148503.2| 534 vasklGDPGAAVEVLSSVGLGD--AIFFRASFGELSTGQKERAKLASLLAERPNLLVIDEF 592
                                    6554455555999999999999..55566688****************************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 !   10.2   0.2   0.00051      0.46       1      20 [.     468     487 ..     468     511 .. 0.80
   2 !   33.1   0.0   5.8e-11   5.2e-08     233     303 .]     562     630 ..     558     630 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00051
                         AAA_21   1 lnvliGpNgsGKSnLLdald 20 
                                    +++++G+ g+GK++LL+ + 
  gi|118431807|ref|NP_148503.2| 468 VAAVVGASGAGKTTLLRMIL 487
                                    5799*************983 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 5.8e-11
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpllld 303
                                    ++ elS G+k+ ++l+++l++++    ll+iDE+ ++L+P   rr+++ l k+++++g+ +i++T  p++ld
  gi|118431807|ref|NP_148503.2| 562 SFGELSTGQKERAKLASLLAERP---NLLVIDEFMAHLDPLTARRIARKLgKLARSKGITLIVSTNRPEILD 630
                                    6889****************999...89*******************888577777************9997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.7e-08   1.5e-05       6     131 ..     467     625 ..     463     632 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-08
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglelka. 70 
                                    ++ +v+G sG+GKTtllr++l ++   +  e               + + ++  +l  s + ++ll++++++lg+++ a 
  gi|118431807|ref|NP_148503.2| 467 SVAAVVGASGAGKTTLLRMILGKAL-GIGGEGyrpdsgvvkiptntKAAALLPGELEPSFGGETLLEHVASKLGDPGAAv 545
                                    6789******************984.34444489888888887665555555888888889******************* PP

                         AAA_22  71 ...................erlsseellealeqalraravielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqliL 127
                                                       e  + +  +++l+  l +r    ll+iDE+   l+  +  ++ ++L +l+   +kg++li+
  gi|118431807|ref|NP_148503.2| 546 evlssvglgdaiffrasfgELSTGQKERAKLASLLAERPN--LLVIDEFMAhLDplTaRRIARKLGKLAR--SKGITLIV 621
                                    ***************9997666666667777777777777..******7555975524777777777777..99999998 PP

                         AAA_22 128 vGtp 131
                                       +
  gi|118431807|ref|NP_148503.2| 622 STNR 625
                                    7655 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   8.5e-08   7.6e-05      57     117 .]     293     358 ..     166     358 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.5e-08
                                    STTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE.EE.EEETT.EHHH..HHHHHHTTE CS
                 Acetyltransf_1  57 kggvayieslaVspeyrgkGlGsaLlealeerareegikki.vl.aveed.ndaa..irlYeklGF 117
                                    ++  a i +++V+p+yrg GlG a +  ++e+ re+ i ++  + +v e+  + a   +++e+ GF
  gi|118431807|ref|NP_148503.2| 293 NTAAARIARVVVHPDYRGDGLGVASVSLALEWIRERRIPEMrRAkHVVETiAQMAryNPFFERAGF 358
                                    45667889****************************998876775443332222245778888887 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06     0.001      24      75 ..     289     359 ..     267     360 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
                                    S.......TCTEEEEE-GGGTTSSHHHHHHHH........TTSEEE......EEEEEE.THH..HHHHHHHHTTEE CS
                 Acetyltransf_7  24 d.......aeitrlaVdpeyrgkGiGraLlea........aekgii......leqlel.nae..kaikfYeklGFe 75 
                                            a i r++V+p+yrg G+G a + +        +    i       +++e+ + +  + ++f+e+ GF+
  gi|118431807|ref|NP_148503.2| 289 LrrantaaARIARVVVHPDYRGDGLGVASVSLalewirerR----IpemrraKHVVETiA-QmaRYNPFFERAGFK 359
                                    1334455667888***************9995455554331....123323211222221.1334456*******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 ?    4.1   0.1     0.029        26      25      44 ..     467     486 ..     453     494 .. 0.77
   2 !   12.7   0.0     7e-05     0.063     136     203 ..     565     630 ..     543     641 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.029
                                    SEEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAi 44 
                                    s+ a+vG+ G+GK+ ll  i
  gi|118431807|ref|NP_148503.2| 467 SVAAVVGASGAGKTTLLRMI 486
                                    5789***********99877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7e-05
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemle 203
                                    +LS G+k  + la l+A    ++  l ++De+ a+LD    +++a+ l   ++sk   +iv + r e+l 
  gi|118431807|ref|NP_148503.2| 565 ELSTGQKERAKLASLLA----ERPNLLVIDEFMAHLDPLTARRIARKLGklARSKGITLIVSTNRPEILD 630
                                    69999999999998877....556799*********************9444566788888888887765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.2     2e+03      35      77 ..     260     303 ..     258     330 .. 0.75
   2 ?   15.1   0.3   1.5e-05     0.014      14     109 ..     462     605 ..     459     622 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                         AAA_30  35 lkalreaweaag.grviglAptgkaAkvLaeelgieastiakll 77 
                                    l+  re+++  g +r++ +A  ++ A++  + ++++a++ia+++
  gi|118431807|ref|NP_148503.2| 260 LARFRELAKLYGsRRIARAAVGEEIADEALRRANTAAARIARVV 303
                                    55666666666447888888888888886667788888888876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.5e-05
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkal.reaweaag......grviglAptgkaAkvLaeelg..ieastiakllkrlk... 81 
                                    + ++  va+++G+ G+GKtt+l+ +  +a+   g        v+ +  + kaA+ L  el+  + ++t+ + + +     
  gi|118431807|ref|NP_148503.2| 462 TVNPGSVAAVVGASGAGKTTLLRMIlGKALGIGGegyrpdSGVVKIPTNTKAAALLPGELEpsFGGETLLEHVASKLgdp 541
                                    5667789****************995555555557888886777777777777777765553344555444442222466 PP

                         AAA_30  82 ...................................grarlepgtllivDEa.gmvdtkqlaall 109
                                                                       +    e+ +ll++DE  + +d  ++++++
  gi|118431807|ref|NP_148503.2| 542 gaavevlssvglgdaiffrasfgelstgqkeraklASLLAERPNLLVIDEFmAHLDPLTARRIA 605
                                    6666677777778888888888888888888877633333444888888851444555555544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05     0.024       5      39 ..     449     483 ..     446     487 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                         AAA_29   5 qlvNWgtfdghtieidlkgatlltGpsGsGKSTll 39 
                                    ++v+ + +++  i++++ ++  ++G+sG+GK+Tll
  gi|118431807|ref|NP_148503.2| 449 RVVERYVLKDVNITVNPGSVAAVVGASGAGKTTLL 483
                                    5677778888999999999***************8 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   7.1e-05     0.063      30     153 ..     463     594 ..     433     621 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                         AAA_25  30 lpagelallaGapgtGKttlaldlalava..tGkpwlg..........pvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                    +  g++a+++Ga+g+GKttl+  +  + +   G+   g          p  ++ ++ l   +E s  + +  l+ v  +l
  gi|118431807|ref|NP_148503.2| 463 VNPGSVAAVVGASGAGKTTLLRMILGKALgiGGE---GyrpdsgvvkiPTNTKAAALLPGELEPSF-GGETLLEHVASKL 538
                                    5679***************986665555555444...32224445544333344444444444443.4444444455555 PP

                         AAA_25  98 .rddarllvldlagveslpLfakdrggtll.tadvdaleaaieevegvrlvviDplsr 153
                                     ++ a + vl+ +g ++   f + +g+  + + + ++l+  + + e++ l+viD + +
  gi|118431807|ref|NP_148503.2| 539 gDPGAAVEVLSSVGLGDAIFFRASFGELSTgQKERAKLASLL-A-ERPNLLVIDEFMA 594
                                    555666777777666555566666666664144444444444.4.4578888887765 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   5.4e-05     0.048      91     122 ..     457     489 ..     430     503 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    ++++  ++  +++++vG SG+GK+tL+ ++l++
  gi|118431807|ref|NP_148503.2| 457 KDVNITVNPgSVAAVVGASGAGKTTLLRMILGK 489
                                    55555555558999**************99986 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-05     0.056      52     108 ..     294     360 ..     271     374 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                Acetyltransf_10  52 s...hisllfVdpeyrgqGigkaLleaveee.....aekdgikl.eltvnasp.yavpfYeklGFka 108
                                        +i++++V+p+yrg G+g a +  ++e      + +++ ++  ++  a+     pf+e+ GFk 
  gi|118431807|ref|NP_148503.2| 294 TaaaRIARVVVHPDYRGDGLGVASVSLALEWirerrIPEMRRAKhVVETIAQMaRYNPFFERAGFKY 360
                                    14559****************8755544443000134455566678888888889999999999985 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   0.6   0.00012       0.1      25      47 ..     467     489 ..     454     593 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                         AAA_16  25 elvllsGesGvGKsslvrellra 47 
                                    ++  ++G+sG GK++l+r++l  
  gi|118431807|ref|NP_148503.2| 467 SVAAVVGASGAGKTTLLRMILGK 489
                                    6788**************99854 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 ?   11.1   0.0   0.00044      0.39       3     117 ..     471     631 ..     469     637 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                                    EESSTTSSHHHHHHHHHHHH........THE..................EEEEETTTCSSS................... CS
                            AAA   3 lyGppGtGKTllakavakel........gve..................fleisgsellsk................... 37 
                                    ++G  G GKT+l + +  ++          +                             +                   
  gi|118431807|ref|NP_148503.2| 471 VVGASGAGKTTLLRMILGKAlgiggegyR-PdsgvvkiptntkaaallpG----------Elepsfggetllehvasklg 539
                                    7899**************97666555430.13343344333333344440..........25555555555555555555 PP

                                    ......................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHH CS
                            AAA  38 ......................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteld 94 
                                                           +ge +   +e  k a+  a +p  l+iDE+ a            ++r++ +L     
  gi|118431807|ref|NP_148503.2| 540 dpgaavevlssvglgdaiffraSFGELSTGQKERAKLASLLAeRPNLLVIDEFMAHLDPL------TARRIARKL----G 609
                                    5688888888888888888888778877888888877777777899******98887777......444455554....4 PP

                                    HTTTSSSTEEEEEEESSGGGSTH CS
                            AAA  95 gvkkkeskvivigatnrpdkldp 117
                                    ++ ++++ +++i+ tnrp+ ld 
  gi|118431807|ref|NP_148503.2| 610 KLARSKG-ITLIVSTNRPEILDA 631
                                    4444434.899999999998875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.8e+03      52      84 ..     262     294 ..     203     349 .. 0.59
   2 ?   11.0   0.2   0.00039      0.35       3      22 ..     470     489 ..     468     627 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                         AAA_33  52 ldrlyqilnelarkalsagrnvildatnlsrre 84 
                                    ++r  + l +  r+a++a +  i+d  ++++++
  gi|118431807|ref|NP_148503.2| 262 RFRELAKLYGSRRIARAAVGEEIADEALRRANT 294
                                    333333333444444444444455555555433 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00039
                         AAA_33   3 llvGlpGsGKstlaerllkk 22 
                                     +vG++G+GK+tl++ +l k
  gi|118431807|ref|NP_148503.2| 470 AVVGASGAGKTTLLRMILGK 489
                                    68************987644 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00032      0.28       2      22 ..     469     489 ..     468     517 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                    EEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                    +a+vG + +GK+tL++ ++g+
  gi|118431807|ref|NP_148503.2| 469 AAVVGASGAGKTTLLRMILGK 489
                                    58****************986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00031      0.28      11      39 ..     457     486 ..     452     499 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                         AAA_23  11 rdqeidFskg.ltlItGpNGaGKTTildAi 39 
                                    +d++i  ++g + +++G  GaGKTT+l+ i
  gi|118431807|ref|NP_148503.2| 457 KDVNITVNPGsVAAVVGASGAGKTTLLRMI 486
                                    67788888853779*************987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00053      0.47       9     111 ..     465     592 ..     459     620 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp...eeillvaftgrAakelrerlaa.lgaeatTiHrlal....... 77 
                                    + +v +v++  G GKT++l++i+  ++ +gg+       ++ +  + +Aa  l  +l+  +g+e+   H           
  gi|118431807|ref|NP_148503.2| 465 PGSVAAVVGASGAGKTTLLRMILGKALGIGGEGYrpdSGVVKIPTNTKAAALLPGELEPsFGGETLLEHVA-Sklgdpga 543
                                    567899****************9998887765432334455555555777666665532023332222222.22344444 PP

                         AAA_19  78 .................ldfddlltealelle........eaeeekklqeee.llivDEf 111
                                                       f                    +a+  + l e+  ll++DEf
  gi|118431807|ref|NP_148503.2| 544 avevlssvglgdaiffrASF-----------GelstgqkeRAKLASLLAERPnLLVIDEF 592
                                    44444443333333333111...........02333332222223334344346777776 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00037      0.33      91     128 ..     292     329 ..     275     382 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                GNAT_acetyltr_2  91 aslsGaRivRiAvhpelqkmGYGsralellekyyegkl 128
                                    a+ + aRi R+ vhp++++ G G + ++l  +++ ++ 
  gi|118431807|ref|NP_148503.2| 292 ANTAAARIARVVVHPDYRGDGLGVASVSLALEWIRERR 329
                                    556789******************99998666554433 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 ?   10.3   0.7   0.00042      0.37       2      23 ..     468     489 ..     467     494 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                                    EEEEEESTTCCHHHHHHHHHCT CS
                           cobW   2 vtvltGflGsGKTtLlnhllen 23 
                                    v  ++G  G+GKTtLl+ +l +
  gi|118431807|ref|NP_148503.2| 468 VAAVVGASGAGKTTLLRMILGK 489
                                    56799************99854 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.6   0.00098      0.88       2      21 ..     468     487 ..     467     492 .. 0.87
   2 ?   -3.0   0.0       6.5   5.9e+03      84     115 ..     586     614 ..     566     633 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00098
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    + ++ G++G GKTtLl+ + 
  gi|118431807|ref|NP_148503.2| 468 VAAVVGASGAGKTTLLRMIL 487
                                    56899***********9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.5
                                    EEEEE-STT-SS-TCH.........HHHHHCT CS
                          NACHT  84 LlilDglDelvtdlgqkekqpvrtlLselirk 115
                                    Ll++D    + ++l++ +++++ + L++l r 
  gi|118431807|ref|NP_148503.2| 586 LLVIDE---FMAHLDPLTARRIARKLGKLARS 614
                                    455554...44444443345555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.71u 0.27s 00:00:00.98 Elapsed: 00:00:00.42
# Mc/sec: 4660.98
//
Query:       gi|118431808|ref|NP_148504.2|  [L=394]
Description: thioredoxin [Aeropyrum pernix K1]
Scores for complete 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   50.8   0.0    1.8e-13   50.3   0.0    1.2  1  Thioredoxin    Thioredoxin
    1.5e-05   25.4   0.3    0.00029   21.2   0.2    2.4  2  Thioredoxin_2  Thioredoxin-like domain
     0.0031   17.5   0.0      0.006   16.6   0.0    1.4  1  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
       0.15   12.2   0.7        9.9    6.3   0.0    2.2  2  Thioredoxin_4  Thioredoxin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   4.1e-17   1.8e-13      15     101 ..      62     149 ..      50     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4.1e-17
                                    TTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHH..CTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS CS
                    Thioredoxin  15 akekklvlveFyApwCghCkalaPeleklaee..lkd.kvklakvdvdenedlakkyevegiPtlklfkngkevkkyega 91 
                                     +++  + v F ++ C+ Ck ++P++++l+e   +k+ ++ ++k+d+d+ +    k +v+g Pt++lf+ngke ++y+ga
  gi|118431808|ref|NP_148504.2|  62 VEASGRIAVMFSSETCPTCKVIEPVWTELCESggYKGvRLAVIKLDNDTADAFL-KNNVTGTPTFILFENGKELSRYVGA 140
                                    34488999*********************99744777999********996555.56**********************9 PP

                                    -HHHHHHHHH CS
                    Thioredoxin  92 rekeklaafl 101
                                     +  ++++ +
  gi|118431808|ref|NP_148504.2| 141 FK-GDIEDGI 149
                                    77.4555444 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   6.5e-08   0.00029       6     100 ..      66     141 ..      62     146 .. 0.73
   2 ?   -2.7   0.0       1.7   7.8e+03      81     107 ..     346     373 ..     345     374 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.5e-08
                  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                     +++v+f++++Cp Ck ++ +  el     +      +  ++ +  a+ + ++            +   k +v+gtPt++
  gi|118431808|ref|NP_148504.2|  66 GRIAVMFSSETCPTCKVIEPVWTEL-----C-----ESGGYKGVRLAVIKLDNDT---------ADAFLKNNVTGTPTFI 126
                                    6899****************99999.....3.....3444455555555544443.........2444455*******66 PP

                  Thioredoxin_2  86 .fldgkeivarlpGyv 100
                                     f +gk ++ r++G+ 
  gi|118431808|ref|NP_148504.2| 127 lFENGK-ELSRYVGAF 141
                                    488888.999**9986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.7
                  Thioredoxin_2  81 tPtivfldgk.eivarlpGyvpaeelea 107
                                    +P  +   +  + +ar+pG + +++l++
  gi|118431808|ref|NP_148504.2| 346 MPVAIAVAAVrTGIARVPGILGSARLLK 373
                                    6787766677789999999998877765 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06     0.006       3      55 ..      68     127 ..      67     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                                    EEE.ESSS.STTCHHHHHHHHHHCHCCTCEC...EEECC.TTHHHH.HHCT-SSSSEEEC CS
                  Thioredoxin_3   3 ikv.lgpg.CakCpklekavkeaaaekgika...evekv.tdfeei.ekygVmsvPalvi 55 
                                    i v +++  C++C+ +e +++e+ ++ g k     v+k  +d+ +   k++V+ +P+ ++
  gi|118431808|ref|NP_148504.2|  68 IAVmFSSEtCPTCKVIEPVWTELCESGGYKGvrlAVIKLdNDTADAfLKNNVTGTPTFIL 127
                                    677554445****************9876655558888879999999*********9865 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3      0.01        45      18      38 ..      70      90 ..      63     106 .. 0.82
   2 ?    6.3   0.0    0.0022       9.9     131     152 ..     111     135 ..     102     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.01
                                   EEEE-TT-HHHHHHHHHHHHH CS
                  Thioredoxin_4 18 ieyedlrCphCakfeeevekl 38
                                   + +++ +Cp+C+  e    +l
  gi|118431808|ref|NP_148504.2| 70 VMFSSETCPTCKVIEPVWTEL 90
                                   78**********988766665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0022
                                    HHH.HHHT--SS-EEEE..TTEEE- CS
                  Thioredoxin_4 131 kea.kkagiestPtfii..ngekve 152
                                    ++a  k+++++tPtfi+  ng+ ++
  gi|118431808|ref|NP_148504.2| 111 ADAfLKNNVTGTPTFILfeNGKELS 135
                                    5565799**********99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3061.39
//
Query:       gi|14601960|ref|NP_148505.1|  [L=999]
Description: cytochrome C-type biogenesis protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-14   52.0  16.2    7.7e-14   52.0  16.2    4.0  4  Cytochrom_C_asm  Cytochrome C assembly protein


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.5      0.49   8.7e+03      27      47 ..      34      54 ..      12      66 .. 0.40
   2 !   52.0  16.2   4.3e-18   7.7e-14       7     203 ..      92     266 ..      86     279 .. 0.71
   3 ?   -1.3   0.2     0.088   1.6e+03      30      52 ..     283     317 ..     255     364 .. 0.52
   4 ?   -4.4   4.0      0.75   1.3e+04       3       3 ..     455     455 ..     384     521 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.49
               Cytochrom_C_asm 27 rklnlsllaavaliaalillg 47
                                        + a++++i++ ++ +
  gi|14601960|ref|NP_148505.1| 34 GAARKTFTASLLMIVLGWIPY 54
                                  222223333333344444433 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 4.3e-18
               Cytochrom_C_asm   7 sllllawilsllgllleylarkln...lsllaavaliaalillgfalflllaelqesadlnpalqspilmiHvplallsYa 84 
                                   sl+l +  lsl  ll   l+++ln   + ++  ++l++++ ++++ +f      + +  +np+l++++++ H+++ +l+Y+
  gi|14601960|ref|NP_148505.1|  92 SLYLFSAFLSLAILLQMLLNKGLNrraMAVFTLLVLTSMTSATLMGAFGTGPGERGGLGINPVLKNYWVVPHPTTTFLGYS 172
                                   55555555554444444445555500055555566666666666666688888899999********************** PP

               Cytochrom_C_asm  85 tliigallsialliierqlkkkkklklsanlkllkqldrlsyriiliGfvlltigiilGsvWa..eeaWGsywsWDpketa 163
                                   + ++g+++ ++                           r    i l+G  +lt+g+++G +W     +WG+yw WDp+et+
  gi|14601960|ref|NP_148505.1| 173 FILVGSVALVLGY--------------------Y----RTGLPIQLLGLAFLTFGLVFGGMWSyeTFGWGGYWAWDPVETS 229
                                   *****99888888....................1....22456788*****************76779************* PP

               Cytochrom_C_asm 164 slitWlvfaallhsri.ekgwrgkkaailailgflllllay 203
                                    l +Wl   a +h++   ++++   aa+     +  + la 
  gi|14601960|ref|NP_148505.1| 230 QLAVWLATVASIHMIGpLRSLNRGFAAYA----ASSVFLAL 266
                                   *************9843323333333333....33333444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.088
               Cytochrom_C_asm  30 nlsllaavaliaalillgfalf............l 52 
                                    +s +  +++ +++++l ++lf             
  gi|14601960|ref|NP_148505.1| 283 SFSAVLLLSASLVMLALSMLLFsegvgetlekwkS 317
                                   34444445555555555555555554444444442 PP

  == domain 4  score: -4.4 bits;  conditional E-value: 0.75
               Cytochrom_C_asm   3 n 3  
                                    
  gi|14601960|ref|NP_148505.1| 455 S 455
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (999 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.23s 00:00:00.96 Elapsed: 00:00:00.38
# Mc/sec: 7951.48
//
Query:       gi|14601961|ref|NP_148506.1|  [L=745]
Description: hypothetical protein APE_2275 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   15.4   0.5      0.079   12.8   0.0    2.3  2  PA14      PA14 domain


Domain annotation for each model (and alignments):
>> PA14  PA14 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2     0.056     1e+03       8      56 ..     440     496 ..     435     499 .. 0.68
   2 ?   12.8   0.0   4.4e-06     0.079      57     120 ..     596     654 ..     577     679 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.056
                                   ECCTCTTSSSEEEE.........EESSSCTSBEGCCCTTT-GCGCCSCEEEEEEEEEB CS
                          PA14   8 iyfknakfsgdpvl.........edtdkdiafawdtevpgegeaadnfsarwtGylkp 56 
                                   +y++++++sg +v+         +   ++ ++   t+ ++ g+  ++ +  + G+++p
  gi|14601961|ref|NP_148506.1| 440 VYDNPTTLSGLYVVlapkdegggT-DTSTTTTTTITTITITGTRTTTTYTTFPGTVTP 496
                                   7999999***99999999999953.444444445555566666666666666666555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 4.4e-06
                                   SSSEEEEEEETTCCCEEEEETTCCCEETT-TTS--TT----S-EEEEEEE-TT-EEEEEEEEEE CS
                          PA14  57 pesGtYtFkvasddgvrlsidgelvidnngqqekksnadasteesatlyltaGkkYpirieyfh 120
                                   p +G  +   ++dd+ +l+idg lv  ++gq++     + +t++ +t  l+++ + +ir+  +h
  gi|14601961|ref|NP_148506.1| 596 PAPGQLVMEWSADDSGELFIDGTLVQTHSGQNA-----FQTTTSYQTSLLQGNHTIEIRVMDEH 654
                                   67788888889******************9999.....55666666666666666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (745 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5471.72
//
Query:       gi|118431809|ref|NP_148508.2|  [L=268]
Description: hydrolase [Aeropyrum pernix K1]
Scores for complete 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-35  123.0   0.0    1.5e-35  122.8   0.0    1.0  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 !  122.8   0.0   8.6e-40   1.5e-35       2     261 .]       3     248 ..       2     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 8.6e-40
                                    EEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTT..TTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEE CS
                   CN_hydrolase   2 vAvvQlpqkaadleanlqklleliaeAarkgadLivlPElf..itgykeeahfleaAeaglgetlallaalarkngiavv 79 
                                    +Av Q ++ + +++anl+ +++l+++ +++  d+++ PE+   ++ +  ++ +++aAe ++g   + l+++a+  g  + 
  gi|118431809|ref|NP_148508.2|   3 IAVLQVAS-TREKDANLESVKRLASR-VKNSPDIVLTPEYLmlDPTGLGRDAIYDAAEDLEGRWSRELSKIAESLGSCLL 80 
                                    89******.79***************.99**********8622566679******************************* PP

                                    EEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEGGGGGS CS
                   CN_hydrolase  80 igliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiCyeigf 158
                                    ++l+ +   +g++   n+avl ++dg ++g yrK+hLf    +  ++ve++  epgd+ +++ +  ++ iG+aiCye +f
  gi|118431809|ref|NP_148508.2|  81 GHLFLKT-PSGRV--ANAAVLYSRDGGIIGVYRKTHLF----DAYGYVESSFTEPGDElWEPRKACGASIGVAICYELRF 153
                                    *****95.89999..9*********************9....479************88888888888************ PP

                                    HHHHHH.HHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEE CS
                   CN_hydrolase 159 pellra.lalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrila 237
                                    pe+ r+     g++i +     a++ +   ++ +++l+rara+en  +v+ a+++g+       +vg S+ii p G  la
  gi|118431809|ref|NP_148508.2| 154 PEIFRTqSLVGGVDIFLV--PAAWYRGPGKEEALSVLSRARAQENTSYVAVASNAGA------NFVGRSMIIHPLGYTLA 225
                                    ******555589******..789**********************************......***************** PP

                                    ECCSSSTEEEEEEEEHHHHHHHHH CS
                   CN_hydrolase 238 glgeeeegvliaeidladvratrr 261
                                    +++ +e  vl  eidl +++++r+
  gi|118431809|ref|NP_148508.2| 226 QAPPWEW-VLEHEIDLREIERARK 248
                                    ******5.***********99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2139.24
//
Query:       gi|14601964|ref|NP_148509.1|  [L=250]
Description: thioredoxin peroxidase [Aeropyrum pernix K1]
Scores for 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-31  108.5   0.0    3.3e-31  107.8   0.0    1.3  1  AhpC-TSA        AhpC/TSA family
    1.8e-13   50.5   0.0    2.3e-13   50.1   0.0    1.2  1  Redoxin         Redoxin
    4.5e-10   39.2   0.0    8.8e-10   38.3   0.0    1.5  1  1-cysPrx_C      C-terminal domain of 1-Cys peroxiredoxin
    0.00048   20.2   0.0     0.0006   19.9   0.0    1.4  1  AhpC-TSA_2      AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
        0.1   13.3   0.1       0.34   11.7   0.1    1.9  1  Sel1            Sel1 repeat


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 !  107.8   0.0   9.2e-35   3.3e-31       1     123 [.       8     139 ..       8     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.8 bits;  conditional E-value: 9.2e-35
                                   TTSB----EEESTTCEEEECHHH...TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                      AhpC-TSA   1 vgdkapdfelknadgetvslsdy...kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                   +g+++p++e+++ + + ++l d    +gk+ vlf +p+d++pvCtte  ++a++ye+f+ +gv++ig+svds++sh k++e
  gi|14601964|ref|NP_148509.1|   8 IGERFPEMEVTTDH-GVIKLPDHyvsQGKWFVLFSHPADFTPVCTTEFVSFARRYEDFQRLGVDLIGLSVDSVFSHIKWKE 87 
                                   799*******9776.899996666999****************************************************** PP

                                   H-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                      AhpC-TSA  79 kes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                    ++      ++fp+++D++g+va+++g+l+ e ++ ++r++f++d++g+ir 
  gi|14601964|ref|NP_148509.1|  88 WIErhigvrIPFPIIADPQGTVARRLGLLHAEsATHTVRGVFIVDARGVIRT 139
                                   *****************************9999999**************96 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   6.5e-17   2.3e-13       3     135 ..       9     145 ..       7     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 6.5e-17
                                   TSBB---ECCEETTCEEEEEHHH...HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...HH CS
                       Redoxin   3 gdkaPdftlplaatdgnsvslse...fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...vk 77 
                                   g+++P+ +   ++td   ++l +    +gk  v+++ p+ f+P+C++e + ++  +e +   gvd +++++d+       k
  gi|14601964|ref|NP_148509.1|   9 GERFPEME---VTTDHGVIKLPDhyvSQGKWFVLFSHPADFTPVCTTEFVSFARRYEDFQRLGVDLIGLSVDSVFShikWK 86 
                                   67788877...55888888888887668999*******************888887888**********999987778888 PP

                                   HHHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSS CS
                       Redoxin  78 efwgk...eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepe 135
                                   e++++     ++fp+++D+++ +++ lGl  +e  s++   + ++++d+ g+++ + + p+
  gi|14601964|ref|NP_148509.1|  87 EWIERhigVRIPFPIIADPQGTVARRLGLLHAE--SATHTVRGVFIVDARGVIRTMLYYPM 145
                                   88888999888*****************66555..55558*************98766655 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   2.5e-13   8.8e-10       1      40 []     160     203 ..     160     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2.5e-13
                                   HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHHHHT CS
                    1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkryleg 40 
                                   AL+l d+ + a PA+W p     G+  ivpPp+te++a++r+++g
  gi|14601964|ref|NP_148509.1| 160 ALKLGDSLKRAVPADW-PnneiiGEGLIVPPPTTEDQARARMESG 203
                                   9***************.99***********************987 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 !   19.9   0.0   1.7e-07    0.0006       3      55 ..      58     134 ..      56     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                    AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.s...akkFvkl...tgfpfelyvDpsaklyqalglk.................r 55 
                                   +r+ +++++ gv+l++ +++++ s    k+++++   + +pf++++Dp++++ ++lgl                  r
  gi|14601964|ref|NP_148509.1|  58 ARRYEDFQRLGVDLIGLSVDSVfShikWKEWIERhigVRIPFPIIADPQGTVARRLGLLhaesathtvrgvfivdaR 134
                                   577899***************99987789***98888999*****************98666666666666666663 PP

>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.4e-05      0.34      21      36 ..     220     236 ..     214     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-05
                          Sel1  21 k.DpekAiewyekAAeq 36 
                                   + D+e+A++++++AAe+
  gi|14601964|ref|NP_148509.1| 220 RdDVEEARRYLRRAAEK 236
                                   3689***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2031.05
//
Query:       gi|118431810|ref|NP_148510.2|  [L=634]
Description: hypothetical protein APE_2279.1 [Aeropyrum pernix K1]
Scores for complete 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-10   39.4   0.0      1e-09   38.2   0.0    1.5  1  Lon_C     Lon protease (S16) C-terminal proteolytic domain


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   5.8e-14     1e-09     108     174 ..     110     176 ..      97     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.8e-14
                                    GGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGG CS
                          Lon_C 108 dGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenek 174
                                     GPsaG+++a a +sllt  +     a tG i     v p+GGlkekl aa  +g k  ++P+  ek
  gi|118431810|ref|NP_148510.2| 110 GGPSAGLAMALATYSLLTTGSCLDGYAATGMILPDTSVGPVGGLKEKLEAAASSGAKVFLIPHGQEK 176
                                    6*************************************************************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4336.97
//
Query:       gi|118431811|ref|NP_148511.2|  [L=246]
Description: cytidylyltransferase [Aeropyrum pernix K1]
Scores for complete 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   66.7   2.2    2.5e-18   65.9   2.2    1.4  1  DUF357           Protein of unknown function (DUF357)
    2.9e-11   43.7   0.0    4.5e-11   43.1   0.0    1.3  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   2.2   2.8e-22   2.5e-18       1      73 []      14      89 ..      14      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.8e-22
                                   HHHHHHHHHHHHHH........TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                         DUF357  1 rYirlleealekvk..iap.deesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                   +Yir++++a+e++k  + + +++ +++ + e++++ ae+Y+ Da+y+ +kgd+ +Al++ sYaeG++D++++lg+l
  gi|118431811|ref|NP_148511.2| 14 KYIRNAKTAVERLKsrLGQeNDRRSISIDIESLIDAAERYVGDAEYYAAKGDYATALSAASYAEGLIDSLKYLGVL 89
                                   8*************6633337788888888********************************************96 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0     5e-15   4.5e-11       2      96 ..     105     196 ..     104     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5e-15
                                    EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHH CS
                CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrevlkk 79 
                                    +gGtF ++H GH +ll+ a +l+++  +v ++ d ++ k k  kp+  ++ Rl+ + + ++v +++  ++ +   + ++k
  gi|118431811|ref|NP_148511.2| 105 VGGTFEILHPGHVELLRYASSLGKL--YVVIARDSTVEKIKgrKPILGEKSRLKVVSAVRYVYNAFLGSEKDFL-DSVEK 181
                                    79*********************98..5567888888877558*******************************.599** PP

                                    TTTTEEEEEEEHHHHHH CS
                CTP_transf_like  80 lkpdklylvigadvled 96 
                                     kpd  ++v+g d+  d
  gi|118431811|ref|NP_148511.2| 182 VKPD--IIVLGPDQGFD 196
                                    ****..******97544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1861.23
//
Query:       gi|118431812|ref|NP_148512.2|  [L=206]
Description: hypothetical protein APE_2283.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-17   63.7   0.1    3.4e-17   63.1   0.1    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    1.8e-10   40.6   0.0    3.2e-10   39.8   0.0    1.4  1  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    1.2e-06   29.2   0.0    1.3e-05   25.8   0.0    2.0  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 !   63.1   0.1   5.6e-21   3.4e-17       3     153 ..       6     191 ..       5     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 5.6e-21
                  Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellela.pvlaVrGNnDeevveedvlreaaelgt 79 
                                    ++++SD+H +l++le +++ l    + ++  +GD+  e+++  ++e+ ++   p++aV GN D  + +++vlr+a  l++
  gi|118431812|ref|NP_148512.2|   6 ILHVSDIHCSLRRLEDIISSLPVK-PSTVAATGDFecEKAAVAIVEWSRREGvPLVAVTGNLD-HAGVRRVLRSAGVLMD 83 
                                    79******************7666.**********76666666777666666***********.4444444444444444 PP

                  Metallophos_2  80 dl................p.eeaelelagek.......vlliHgdpl........gvkdalaellkeaeegsd.vvvcGH 126
                                                      p ++ e+ l+  +       vll+H+ p+        gv+++l++l++  ++ +    ++GH
  gi|118431812|ref|NP_148512.2|  84 GRvdrvgglvfggvggmdPrTSMEMLLRSLEssgltvdVLLTHHPPHgvldttfaGVRAGLHDLRSLVDSLKPrAHLFGH 163
                                    33477888888888888744555555544444455578******999********8888887777775544445****** PP

                  Metallophos_2 127 tHvp.evekeggvlvvnPGsvgeprdgd 153
                                    +H+  ++e +gg+++vnPG + e+r++ 
  gi|118431812|ref|NP_148512.2| 164 IHESpGIESIGGTVFVNPGPAYEGRYAL 191
                                    **977*****************998875 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   5.4e-14   3.2e-10     157     253 ..     102     200 ..      83     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.4e-14
                                    EHHHHHHHGGGGGGS---EEEEEESS--S-SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE- CS
                  Metallophos_3 157 PaweveyrLkvlkelkdrrkvlllatpPigelvadkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlvvnP 234
                                    P+  +e  L+ l+       vll + pP g l++      +g + +  lv +l+P+  + gh + +   e +g t+ vnP
  gi|118431812|ref|NP_148512.2| 102 PRTSMEMLLRSLESSGLTVDVLLTHHPPHGVLDTTFAGVRAGLHDLRSLVDSLKPRAHLFGHIHESPgiESIGGTVFVNP 181
                                    78888999999999988999*************7777799***********************998899*********** PP

                                    -BGGGTEEEEEETTTTEEE CS
                  Metallophos_3 235 GaleeGdfavvdleekkve 253
                                    G   eG++a+v + +  v+
  gi|118431812|ref|NP_148512.2| 182 GPAYEGRYALVRILGSVVK 200
                                    ***********99887776 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.2e-09   1.3e-05       3     203 ..       6     166 ..       4     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.2e-09
                                    EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCHHH.HH CS
                    Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegfee.el 81 
                                    il+++D+H      +l++l+++++ l +  kp  v  +GD +++     +++e+     ++++p++++ GN +   + ++
  gi|118431812|ref|NP_148512.2|   6 ILHVSDIH-----CSLRRLEDIISSL-PV-KPSTVAATGD-FECEKAAVAIVEW---SRREGVPLVAVTGNLD---HaGV 71 
                                    9*******.....**********999.44.79********.6665444445555...444456**********...2122 PP

                                    HHHHHHHHHHHHHHEHHHCEEETSEEEE.EETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTC CS
                    Metallophos  82 lnkygylgifsepwrsdaevfnnlplas.lgsgslkvlllhGgspellvsldklgslnleleapepgdewlkdlekreka 160
                                     +                     l +a+ l++g  +v  + G        +  +g+ + ++      + +l+   + ++ 
  gi|118431812|ref|NP_148512.2|  72 RR--------------------VLRSAGvLMDG--RVDRVGGL------VFGGVGGMDPRTSM----EMLLRS-LESSGL 118
                                    22....................23333334445..33333333......12222333333222....444444.777888 PP

                                    SEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 161 dwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHv 203
                                     ++++l+H+p++     + +g   g + l+ l +  ++ + ++GH+H+
  gi|118431812|ref|NP_148512.2| 119 TVDVLLTHHPPHgvldtTFAGVRAGLHDLRSLVDSLKPRAHLFGHIHE 166
                                    888*********999999999999999999*****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1491.00
//
Query:       gi|118431813|ref|NP_148513.2|  [L=550]
Description: long-chain-fatty-acid--CoA ligase [Aeropyrum pernix K1]
Scores for 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-106  355.1   0.0     5e-106  354.8   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    5.3e-19   69.0   1.9    1.7e-18   67.3   1.9    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 !  354.8   0.0  5.6e-110    5e-106      31     422 ..      48     447 ..      43     448 .. 0.86

  Alignments for each domain:
  == domain 1  score: 354.8 bits;  conditional E-value: 5.6e-110
                                    HHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE..ETCTCCCHH CS
                    AMP-binding  31 rvnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvli..atvdselle 108
                                      +++A +Lrs+Gv+kgd+V+++lpnsp++ +a++++l aGa+v+p+n  ++++e++++l+d +a+vl+  +     +  
  gi|118431813|ref|NP_148513.2|  48 LLSKFAGYLRSRGVGKGDVVGLFLPNSPQFAIAFYGALIAGAIVSPMNVLYSPREIRHQLSDNKARVLValD---MFKDR 124
                                    5689******99*********************************************************331...22233 PP

                                    HHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.................-TSCCCS-BTTSEEEEEEE--SS CS
                    AMP-binding 109 klleaaakleavklvivldadellkeeelkeeeeseekae.................kpeeeeelkpddlayiiYTSGTT 171
                                     l+   +++e+v ++ + d  + lk+  l++  +++ + +                 +  ++e +  +d+a ++YT+GTT
  gi|118431813|ref|NP_148513.2| 125 VLAGLPSSVEEVLWTGIQDYLPGLKA-LLYKLFKKPPSPPkggihkkftdalkhepiDS-KPEINPHEDVAALMYTGGTT 202
                                    34444445556677777776666655.45555545544424667788889999998644.5557888************* PP

                                    SS-EEEEEEHHHHHHHHHHHH.HHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHH CS
                    AMP-binding 172 GkPKGVmlshrnlvanvaslk.letrfklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelie 250
                                    G+PKG+ml+hrnl+anv +++ +   ++++ +dv++  lp +hi+gl++ l+  + + at++++ + +    + ++++ie
  gi|118431813|ref|NP_148513.2| 203 GTPKGAMLTHRNLLANVLQIDaW-FKRGVRGKDVFVGALPWFHIYGLTAVLNSGVQKAATIIVYARPNI---EEIMRDIE 278
                                    *******************9852.23556679*******************************996654...5578**** PP

                                    HHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCT CS
                    AMP-binding 251 klkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlple 330
                                    ++k+tv++gvP+++++++++++ +    + +l sl+++++g+epl+++++++f +++g ++ egYGlTEt++v++v+p +
  gi|118431813|ref|NP_148513.2| 279 RYKATVFHGVPTLYRMIINHPKVE----KFNLRSLEVCISGAEPLPKAVAERFMEITGAKLREGYGLTETSPVTHVNPIM 354
                                    *******************98887....34899*****************************************855545 PP

                                    TTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEE..TCCEEEEEEEEEEETTS CS
                    AMP-binding 331 edkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafds..egrwlrTGDlgrldedG 408
                                    ++ ++ gs+G p+p + ++++D+e    +++g++Gel+v+gp+vmkgY+++pe+++++f++  + rwlrTGD++r+dedG
  gi|118431813|ref|NP_148513.2| 355 GE-ARYGSIGIPVPSTVAAVADPESPAILEPGQVGELVVSGPQVMKGYYNRPEENEKVFFEccGLRWLRTGDMARMDEDG 433
                                    55.789******************************************************754346************** PP

                                    EEEEEEECCCEEEE CS
                    AMP-binding 409 yleivgRkkdlikl 422
                                    y++iv+Rkkd+ik 
  gi|118431813|ref|NP_148513.2| 434 YFYIVDRKKDIIKY 447
                                    ************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   1.9   1.9e-22   1.7e-18       1      76 []     456     533 ..     456     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.9e-22
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+E++l +h+ V+eaaV+Gvp++   e+++afV l+d+   +   +e++++++rk+l+py+vpk+v++ ++lpk   GK
  gi|118431813|ref|NP_148513.2| 456 EIEEVLYRHECVREAAVIGVPHPEYNEVPKAFVALRDEckgK-VKPEDIIEFARKHLAPYKVPKEVEIREDLPKSGVGK 533
                                    8**********************999*********8756332.357******************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.21s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4136.06
//
Query:       gi|118431814|ref|YP_874935.1|  [L=78]
Description: hypothetical protein APE_2284a [Aeropyrum pernix K1]
Scores for complete 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-19   68.3   1.8    4.3e-19   68.3   1.8    1.5  2  YHS              YHS domain
    1.2e-05   25.6   1.6    1.9e-05   24.9   1.6    1.3  1  Arc_trans_TRASH  Archaeal TRASH domain
     0.0015   18.5   1.4      0.002   18.0   0.6    1.7  2  zf-FCS           MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.018   14.6   0.0    1.1  1  FAP206           Domain of unknown function
      0.066   12.6   5.3      0.066   12.6   5.3    1.1  1  SelP_N           Selenoprotein P, N terminal region


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 !   68.3   1.8   1.2e-22   4.3e-19       2      47 ..       5      50 ..       4      51 .. 0.97
   2 ?   -2.9   0.3       2.1   7.6e+03      16      24 ..      61      69 ..      58      70 .. 0.67

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.2e-22
                            YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYata 47
                                    dPvcgm v+   a +k+ YkGk YyFcS++Ck +Fe++Pe Y+t+
  gi|118431814|ref|YP_874935.1|  5 VDPVCGMEVETSSAMYKTVYKGKIYYFCSPQCKTAFEKNPEYYLTH 50
                                   7*******************************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                            YHS 16 eekseYkGk 24
                                   +e  e++G+
  gi|118431814|ref|YP_874935.1| 61 HEHHEHHGH 69
                                   566678886 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.6   5.2e-09   1.9e-05       4      35 ..       9      42 ..       8      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.2e-09
                Arc_trans_TRASH  4 CGkeivgePivyk..lknkvYyvCCktCkselkk 35
                                   CG e+   + +yk  +k k+Yy+C + Ck+ + k
  gi|118431814|ref|YP_874935.1|  9 CGMEVETSSAMYKtvYKGKIYYFCSPQCKTAFEK 42
                                   ************966699**************98 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6   5.7e-07     0.002      23      41 .]      22      40 ..       9      40 .. 0.86
   2 !    5.2   0.2    0.0058        21       8      26 ..      35      51 ..      35      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.7e-07
                         zf-FCS 23 lendgvvgqFCStsCldsY 41
                                   + ++g++++FCS +C++ +
  gi|118431814|ref|YP_874935.1| 22 TVYKGKIYYFCSPQCKTAF 40
                                   6789************988 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0058
                         zf-FCS  8 fCkkyikgkpeftyvlend 26
                                   +Ck+ ++  pe  y+l+++
  gi|118431814|ref|YP_874935.1| 35 QCKTAFEKNPE--YYLTHG 51
                                   6*****99999..888887 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.9e-06     0.018     227     254 ..      23      50 ..      15      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-06
                         FAP206 227 kykdkyyaFsseeaareFaadpdrfiea 254
                                     yk+k y F s+++  +F+++p++++++
  gi|118431814|ref|YP_874935.1|  23 VYKGKIYYFCSPQCKTAFEKNPEYYLTH 50 
                                    599**********************987 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   5.3   1.8e-05     0.066     163     204 ..      31      74 ..       9      77 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                         SelP_N 163 eckevtkaaeekpaeaeekteheha..hshkqghkhhekhghhH 204
                                    +c+ + k a ek  e   +++ + +  h+h++ h+hh +hgh H
  gi|118431814|ref|YP_874935.1|  31 FCSPQCKTAFEKNPEYYLTHGPQGMpgHEHHEHHEHHGHHGHGH 74 
                                    45555555555555543444333332344445566666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); 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:                         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: 00:00:00.40
# Mc/sec: 589.50
//
Query:       gi|14601969|ref|NP_148514.1|  [L=393]
Description: threonine synthase [Aeropyrum pernix K1]
Scores for complete 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-81  273.4   3.7    2.9e-81  273.1   3.7    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
     0.0096   14.7   0.0      0.032   13.0   0.0    1.7  2  CdhD      CO dehydrogenase/acetyl-CoA synthase delta subunit
  ------ inclusion threshold ------
       0.05   13.5   0.6        0.1   12.5   0.6    1.5  1  DUF1936   Domain of unknown function (DUF1936)
      0.065   12.0   0.0      0.083   11.6   0.0    1.1  1  HAUS5     HAUS augmin-like complex subunit 5


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 !  273.1   3.7   6.5e-85   2.9e-81       1     294 []      52     353 ..      52     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 273.1 bits;  conditional E-value: 6.5e-85
                                   GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                          PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkv 81 
                                   +t+g+g TPlv+l++ls++ gv+++ KlE+lnptgSfKdRg++  ++ +    + + vv+as+GN+++++Aa+a+++Gl  
  gi|14601969|ref|NP_148514.1|  52 VTMGEGSTPLVKLENLSRAMGVEVYGKLEFLNPTGSFKDRGMTVGVSIASSF-SYRLVVAASTGNTAASMAAYARRAGLNP 131
                                   5789*******************************************99999.**************************** PP

                                   EEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEE CS
                          PALP  82 tivvpadas.pekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdav 161
                                   +i++p++   ++k+ ++ +lGa v ev+g++d+a++aa+++a++ + ay +++  np++ eg++ti++Eile+++ ++d+v
  gi|14601969|ref|NP_148514.1| 132 VILIPKGGIaSGKLSQIAALGAWVLEVEGSFDDALDAARAAAEK-GLAYSLNSI-NPYRLEGQKTIAFEILEDVD-RVDHV 209
                                   *****999945**************************9888888.888888888.9******************5.***** PP

                                   EEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCC..S..S.SS..B.SSS.CCSTCS..CGTTCCHHH CS
                          PALP 162 vvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarsl..ragrrvtvpvsdtiadglavg..spselafel 232
                                   vvpvG++g+i++i++g+ke    + p+  +r++gv++eg+++l+r++  +  ++++v  ++tia+++++g  +++++a+++
  gi|14601969|ref|NP_148514.1| 210 VVPVGNAGNISAIWKGFKEagllGLPSmrPRMVGVQAEGASPLYRAWveKMDSVERVRNPSTIASAIRIGnpVNAAKALAA 290
                                   *******************9988777799******************6666666666666**********98899999999 PP

                                   HSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                          PALP 233 ldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                   ++++ + i++vsd+e+l+a+ +la++eg++vep+saa+la+l klr++g ++ g++vv+iltg
  gi|14601969|ref|NP_148514.1| 291 VRESDGLIISVSDAEILKAAATLAENEGMLVEPASAASLAGLiKLRNQGIIASGSSVVLILTG 353
                                   9*************************************************************8 PP

>> CdhD  CO dehydrogenase/acetyl-CoA synthase delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.16   7.3e+02     143     183 ..     103     143 ..      97     149 .. 0.75
   2 !   13.0   0.0   7.1e-06     0.032      77     140 ..     276     336 ..     249     373 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.16
                                   TT--EEEE-.SSHHHHHHHHHHHHCTT---EEEE---.SH.. CS
                          CdhD 143 ykvpvvllsindleelkelarkllkagvkdivldPtt.aalG 183
                                   +   +v+ +    ++++++a++ ++ag++ ++l P+  +a+G
  gi|14601969|ref|NP_148514.1| 103 FSYRLVVAA-STGNTAASMAAYARRAGLNPVILIPKGgIASG 143
                                   555555555.45689999************999997656666 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.1e-06
                                   --SSST.HHHHHHHHHHHCC--SEEEEE-SSHHHHHHHHTTTCCC--EEEEE-TTTHHHHHHHH CS
                          CdhD  77 listdPakkfakavekvakavkvplvlggsdpevlkaalevvederpllyaAtkddykeiaela 140
                                    + ++P  ++aka+++v +     l++  sd+e+lkaa+  +e+e +l+  A+ + ++ +++l 
  gi|14601969|ref|NP_148514.1| 276 IRIGNP-VNAAKALAAVRE--SDGLIISVSDAEILKAAATLAENEGMLVEPASAASLAGLIKLR 336
                                   455788.899999****98..66799***********************999999888888764 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   2.3e-05       0.1       2      18 ..      16      31 ..      15      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                                  -TTTSSSBEEEEE-TTS CS
                       DUF1936  2 CPKCnvGkLEPVYNekG 18
                                  CPKC+ G LEP Y + G
  gi|14601969|ref|NP_148514.1| 16 CPKCG-GLLEPFYIDGG 31
                                  ****9.*******9977 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 ?   11.6   0.0   1.9e-05     0.083     491     546 ..     254     314 ..     209     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.9e-05
                         HAUS5 491 rrllegm.....ardPsailSihRlsaalqyeaslasvlesLefplkkapeslledlakai 546
                                   r+ +e m      r Ps i+S  R+  +++++++la+v es ++ + ++++++l+ +a+++
  gi|14601969|ref|NP_148514.1| 254 RAWVEKMdsverVRNPSTIASAIRIGNPVNAAKALAAVRESDGLIISVSDAEILKAAATLA 314
                                   555555577777899****************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3014.94
//
Query:       gi|14601970|ref|NP_148515.1|  [L=188]
Description: hypothetical protein APE_2288 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0029   17.6   1.6      0.018   15.0   0.1    2.4  2  DUF1488         Protein of unknown function (DUF1488)
  ------ inclusion threshold ------
      0.017   13.7   0.1      0.024   13.2   0.1    1.2  1  Proteasom_PSMB  Proteasome non-ATPase 26S subunit
      0.022   15.1   0.3      0.041   14.2   0.3    1.4  1  E2F_CC-MB       E2F transcription factor CC-MB domain
      0.059   13.1   4.8        1.1    9.0   0.2    2.2  2  Hira            TUP1-like enhancer of split


Domain annotation for each model (and alignments):
>> DUF1488  Protein of unknown function (DUF1488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.083   3.7e+02      34      54 ..      16      37 ..      10      56 .. 0.78
   2 !   15.0   0.1     4e-06     0.018      42      77 ..     153     186 ..     137     188 .] 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.083
                                  HHH....HTS---.HHHHHHHH CS
                       DUF1488 34 eaLedhfgaeslr.eedllaaF 54
                                  e+Le+++++esl+ +e++l+ F
  gi|14601970|ref|NP_148515.1| 16 EVLEEIYWQESLEeAEKRLEEF 37
                                  8999999999999777777776 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4e-06
                                   TS---HHHHHHHHHHTHHHHHHHHHHHHHTT---TT CS
                       DUF1488  42 aeslreedllaaFeahRfdieeaaerlieaeggded 77 
                                   a     +++l + e+ R++ie +aerl+e+ g  ++
  gi|14601970|ref|NP_148515.1| 153 ALA--RAEMLGLVEEMREHIEMMAERLFEESGSPHS 186
                                   433..789********************99987655 PP

>> Proteasom_PSMB  Proteasome non-ATPase 26S subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.4e-06     0.024      60     127 ..       7      74 ..       2      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-06
                Proteasom_PSMB  60 vtlcvellklilkalavdelaedlkvvlleglshanpnvkalvLaeleRiveekegalellkneelll 127
                                   v+   +  k +l+++  +e +e+ ++ l+e++ + ++++++l L + +    + e+++++l  e ll+
  gi|14601970|ref|NP_148515.1|   7 VDPVSQAFKEVLEEIYWQESLEEAEKRLEEFIASMDEDLRELLLEKRREYCSNPEAVVSILSLEALLS 74 
                                   5556677899********************************999888899**********9999986 PP

>> E2F_CC-MB  E2F transcription factor CC-MB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   9.1e-06     0.041       6      58 ..      25      91 ..      23     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.1e-06
                     E2F_CC-MB  6 esleeeeqkLDelieklteqlknl.tedeknq.............laYvtyedirsiasfkeqtvia 58
                                  eslee e++L+e i+++ e+l++l  e+ ++               a +++ed++ +++  +q +ia
  gi|14601970|ref|NP_148515.1| 25 ESLEEAEKRLEEFIASMDEDLRELlLEKRREYcsnpeavvsilslEALLSSEDLKDVEQEYKQAMIA 91
                                  79********************996554444345666666666655558899999988777776665 PP

>> Hira  TUP1-like enhancer of split
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.8    0.0022       9.7     163     201 ..      53      91 ..      10      94 .. 0.79
   2 ?    9.0   0.2   0.00024       1.1     173     210 ..     144     181 ..     125     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0022
                          Hira 163 ekegfenleesvtlahlEnrlaaallLgsadEfkkwlla 201
                                    +e  +n e++v++  lE+ l++  l + ++E+k++++a
  gi|14601970|ref|NP_148515.1|  53 RREYCSNPEAVVSILSLEALLSSEDLKDVEQEYKQAMIA 91 
                                   356678999************99999999******9986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00024
                          Hira 173 svtlahlEnrlaaallLgsadEfkkwllaYakrLaeeg 210
                                      l++lE  la a++Lg  +E ++++ + a+rL ee+
  gi|14601970|ref|NP_148515.1| 144 NHALEMLEIALARAEMLGLVEEMREHIEMMAERLFEES 181
                                   567899****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1387.58
//
Query:       gi|118431815|ref|NP_148516.2|  [L=162]
Description: hypothetical protein APE_2289.1 [Aeropyrum pernix K1]
Scores for complete 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  245.7   0.1    1.7e-73  245.5   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 !  245.5   0.1   9.5e-78   1.7e-73       1     154 []       8     161 ..       8     161 .. 1.00

  Alignments for each domain:
  == domain 1  score: 245.5 bits;  conditional E-value: 9.5e-78
                                    EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEEEEE CS
                  Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvfvil 80 
                                    v+ie+pe++nvi+g+shfiktvedlyealvts+p++kfg+afcEasgkrLvr++gnde+l++ a++++++igaghvfv++
  gi|118431815|ref|NP_148516.2|   8 VDIEIPEGANVIIGRSHFIKTVEDLYEALVTSCPSLKFGIAFCEASGKRLVRHDGNDEDLRKKAIEACMKIGAGHVFVVY 87 
                                    79****************************************************************************** PP

                                    EEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                  Adenosine_kin  81 lknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                    ++n++Pinvlnaiksv+evv+i aAtanp++v+va+  ++r++lgv DGf+p+gve e+d++erke+lrkigYk
  gi|118431815|ref|NP_148516.2|  88 IRNGWPINVLNAIKSVQEVVSIDAATANPVKVVVADLGEQRALLGVADGFKPLGVEGEDDIRERKEFLRKIGYK 161
                                    *************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1207.73
//
Query:       gi|118431816|ref|NP_148517.2|  [L=639]
Description: acylamino-acid-releasing enzyme [Aeropyrum pernix K1]
Scores for complete 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  175.0   0.2      2e-51  174.5   0.2    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    4.9e-11   42.7   1.8    4.3e-08   33.1   0.9    2.3  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    8.9e-06   25.5   0.3    2.6e-05   24.0   0.3    1.9  1  PD40           WD40-like Beta Propeller Repeat
    9.5e-06   24.5   1.2     0.0008   18.2   1.2    2.3  1  AXE1           Acetyl xylan esterase (AXE1)
    1.3e-05   25.0   0.1    4.8e-05   23.1   0.1    1.7  2  Abhydrolase_1  alpha/beta hydrolase fold
     0.0028   17.2   0.0     0.0062   16.1   0.0    1.5  1  DLH            Dienelactone hydrolase family
     0.0029   17.1   0.0     0.0083   15.6   0.0    1.7  1  Esterase_phd   Esterase PHB depolymerase
  ------ inclusion threshold ------
       0.12   12.3   0.1        0.8    9.6   0.0    2.1  2  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
       0.23   10.5   0.0       0.37    9.8   0.0    1.2  1  DUF2048        Abhydrolase domain containing 18


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.5   0.2     1e-54     2e-51       3     210 ..     412     620 ..     410     622 .. 0.96

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 1e-54
                                    --HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHH CS
                   Peptidase_S9   3 fsselqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaal 82 
                                    f  e+ql+a++G+ v++an+rGs+gy e+f+d +++++g+ +++++++ ++a+++ + vd+ ++a+tG SyGGy+t++++
  gi|118431816|ref|NP_148517.2| 412 FYGEMQLFASEGFTVAYANPRGSDGYEEEFAD-IRGRYGDTDYKQLMKFLDAVVEGSDVDEGKMAVTGISYGGYMTNVIV 490
                                    66799***************************.*********************************************** PP

                                    HH-GGG-SEEEEESE---CCCHHCSTTS...THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-T CS
                   Peptidase_S9  83 nqrpdlFkaavaevpvvdvlrydsdtdl...lteeymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvpp 159
                                    + ++++F+aav+e++++d++++    d+   + +   + g+p +n e+y ++sp+ +++n  +++p++lih+++D+r+ +
  gi|118431816|ref|NP_148517.2| 491 T-KTSRFRAAVSENGIADWIADFWAADIgywFDPDQIG-GTPLDNLEEYVKRSPAFHAKN--VNTPVMLIHSMEDYRCFI 566
                                    *.***************************988887777.89999****************..****************** PP

                                    HHHHHHHHHHH--S-SEEEEEETTS-S...STTSSHHHHHHHHHHHHHHHHHCT CS
                   Peptidase_S9 160 aealklvaaLqkkgknvlllifpdegH...gvgkprakveelarllaFlkealg 210
                                     +al + +aL+ +gk++ l++f++  H    +++pr+++++l+  l+++ke+lg
  gi|118431816|ref|NP_148517.2| 567 DQALAMHTALKVNGKESFLVVFTKGSHghsILASPRHRRKRLELKLKWIKEKLG 620
                                    ************************999888899******************997 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.9   2.2e-11   4.3e-08      52     169 ..     414     540 ..     361     546 .. 0.80
   2 !    9.7   0.0   0.00029      0.59     217     268 ..     539     594 ..     532     595 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.2e-11
                                    H....HHHTT-EEEEEE-TTSTTS-S---TT.TTTHHHHHHHHHHHHHH....CTTEEEEEEEEEECHHHHHHHHHCTT- CS
                  Peptidase_S15  52 v....fvarGYavVvqdvrGtggSeGeftvg.dsdeaedgadvidWlak....qpwsnGkVgmtGiSYlGttqllaaatg 122
                                         f+++G++v +++ rG+ g e ef    ++   +d+++  + l +     +  +Gk ++tGiSY+G++ +++ + +
  gi|118431816|ref|NP_148517.2| 414 GemqlFASEGFTVAYANPRGSDGYEEEFADIrGRYGDTDYKQLMKFLDAvvegSDVDEGKMAVTGISYGGYMTNVIVT-K 492
                                    04445***************9887777766665666666666666666666556********************9999.9 PP

                                    -TTEEEEEEECE-S-TCCC.CSECTTEEBCCHHHHHHHHHCCCCHHTS CS
                  Peptidase_S15 123 vpalkaivpeaaisdlydd.yyregGlvrapgglswedldllaealts 169
                                    + + +a+v+e +i+d+  d ++ + G    p+   +++ld l e +++
  gi|118431816|ref|NP_148517.2| 493 TSRFRAAVSENGIADWIADfWAADIGYWFDPDQIGGTPLDNLEEYVKR 540
                                    9******************99999999999999999888888776665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
                                    TT-HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-...EEEEECECTT CS
                  Peptidase_S15 217 drnlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv...klilgpwtHv 268
                                    +r++  +a++v++pv+l++++ D     ++a++++ alk +g+    +++++++H+
  gi|118431816|ref|NP_148517.2| 539 KRSPAFHAKNVNTPVMLIHSMEDYRCFiDQALAMHTALKVNGKesfLVVFTKGSHG 594
                                    56666689***************88778**************99888888899986 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.3   1.3e-08   2.6e-05       9      35 ..      65      90 ..      62      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.3e-08
                                   S.EEEEEE-TTSSEEEEEEECT.TCEE CS
                           PD40  9 gnegaPsfSPDGkrlaFsSdRgsGkpd 35
                                   g + +Ps+SPD ++laF+S+RgsGk +
  gi|118431816|ref|NP_148517.2| 65 G-DSMPSWSPDASKLAFASRRGSGKGE 90
                                   5.899*****************87755 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.2     4e-07    0.0008      65     203 ..     377     501 ..     360     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4e-07
                                    GGEEEEEEEEEES.SSSSEEEEEEEE-TT--...GGGHHHHHHHHHTT-EEEEEE-TTTS..SSB-SSCCSS-SSSSTTT CS
                           AXE1  65 rgarikaklvlPkekeeklPavvefhGYegs...rgeihdllnyaaaGyavvvmdvRGqggesedkvgskgnkakGfiir 141
                                    +g+ ++++++ P+  e++ P+++  hG  ++    g   ++  +a++G++v+  + RG +g++e+              r
  gi|118431816|ref|NP_148517.2| 377 EGEVVEGWYIEPE-GEGRKPLILFIHGGPKGmygYGFYGEMQLFASEGFTVAYANPRGSDGYEEEFADI----------R 445
                                    57889********.9***********9765533478999*********************998876544..........4 PP

                                    TTTSTTT-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEE CS
                           AXE1 142 GlldkeklyyrrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavva 203
                                    G     +  y++     ++ +++v + + vDe ++av+G s GG ++ ++ +  +r +a+v+
  gi|118431816|ref|NP_148517.2| 446 GRYGDTD--YKQ----LMKFLDAVVEGSDVDEGKMAVTGISYGGYMTNVIVTKTSRFRAAVS 501
                                    5444333..333....3566667788889999999999999999998777777777666665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   2.4e-08   4.8e-05       1     139 [.     395     537 ..     395     557 .. 0.76
   2 ?    1.6   0.0     0.088   1.7e+02     186     227 ..     506     566 ..     498     594 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.4e-08
                                    SEEEEE-STTTCGGG..GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB......CHHSHHHHHHHHHHHHHHCTTS CS
                  Abhydrolase_1   1 pvlvilhGlpgssdv..waerglapaLakdgfdvillDlrGvgySspapacin.....ddygtasvaddldrildalgdd 73 
                                    p+++++hG+p++ +   +++   ++ +a +gf+v   ++rG++  +   a i      +dy    + ++ld++++  ++d
  gi|118431816|ref|NP_148517.2| 395 PLILFIHGGPKGMYGygFYG--EMQLFASEGFTVAYANPRGSDGYEEEFADIRgrygdTDYKQ--LMKFLDAVVEGSDVD 470
                                    789********665555999..********************999999999996676666666..677777887777666 PP

                                    ..SEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHH CS
                  Abhydrolase_1  74 ..kltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnp 139
                                      k ++ G S+GG +      +  +r +a v+ ++i+++++   a++   + +pd+  g+  d+ +  
  gi|118431816|ref|NP_148517.2| 471 egKMAVTGISYGGYMTNVIVTK-TSRFRAAVSENGIADWIADFWAADIGYWFDPDQIGGTPLDNLEEY 537
                                    22677*********98888887.999******999776666666666666666666666666655555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.088
                                    HHHHHHHHHCCHHHHHHHHHC...................THHHHSEEEEEEETTCSSSCH CS
                  Abhydrolase_1 186 lksieqwpttdsaklllrlre...................lknvlaptlvisgtsDplvpp 227
                                    + +i  + + d +++++ +++                    knv+ p+++i++++D    +
  gi|118431816|ref|NP_148517.2| 506 ADWIADFWAADIGYWFDPDQIggtpldnleeyvkrspafhAKNVNTPVMLIHSMEDYRCFI 566
                                    56778888888888888888899999999999999999999************99965555 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.1e-06    0.0062      87     190 ..     461     596 ..     416     619 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-06
                            DLH  87 aylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG................................lspe 134
                                    +++ + ++v+++k++v+G   GG ++ ++ ++  ++ aav+  G                                    
  gi|118431816|ref|NP_148517.2| 461 DAVVEGSDVDEGKMAVTGISYGGYMTNVIVTKTSRFRAAVSENGiadwiadfwaadigywfdpdqiggtpldnleeYVKR 540
                                    44445566889*************************************************************99987788 PP

                            DLH 135 keleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFa 190
                                    ++  +a+++++p++ ++  eD     d++  ++ alk ++++  l+v+    H+  
  gi|118431816|ref|NP_148517.2| 541 SPAFHAKNVNTPVMLIHSMEDYRCFIDQALAMHTALKVNGKESFLVVFTKGSHGHS 596
                                    99999********************************************9999865 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.1e-06    0.0083       5     125 ..     384     500 ..     380     513 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-06
                   Esterase_phd   5 lylpp.GarrgamplvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwyk.dtdraGrGeaavvv 82 
                                     y+ p G  r   pl++++hG  + +  +     m+l+a + G++v y +   r  +++  + +   + r G  + + ++
  gi|118431816|ref|NP_148517.2| 384 WYIEPeGEGR--KPLILFIHGGPKGMYGYGFYGEMQLFASE-GFTVAYANP--RG-SDGYEEEFAdIRGRYGDTDYKQLM 457
                                    5777757777..8******************9****99986.9****9764..33.3444445552567888899999** PP

                   Esterase_phd  83 alvdalvdehrvdaarvyvaGlsaGaaladllalhypdvfaav 125
                                     + da+v+   vd  ++ v+G+s G+ +++++  +     aav
  gi|118431816|ref|NP_148517.2| 458 KFLDAVVEGSDVDEGKMAVTGISYGGYMTNVIVTKTSRFRAAV 500
                                    *******************************987765555555 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 ?    9.6   0.0    0.0004       0.8      17      54 ..     467     504 ..     457     511 .. 0.90
   2 ?   -0.5   0.0      0.48   9.5e+02     108     159 ..     543     591 ..     531     606 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0004
                                    TTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES- CS
                         BAAT_C  17 pkvkkdkigllGiSkGgelalllasflkkisavvling 54 
                                    + v + k+++ GiS Gg +++++ ++ +  +a+v+ ng
  gi|118431816|ref|NP_148517.2| 467 SDVDEGKMAVTGISYGGYMTNVIVTKTSRFRAAVSENG 504
                                    568899*****************************999 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                                    B--GGG--SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB CS
                         BAAT_C 108 lipvekakgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpka 159
                                     + + + ++p++l+ +++D     ++    +   Lk +gk+ +  ++ + k+
  gi|118431816|ref|NP_148517.2| 543 AFHAKNVNTPVMLIHSMEDYRCFIDQAL-AMHTALKVNGKE-SFLVV-FTKG 591
                                    56677889********999765544433.577788888888.33333.5444 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00018      0.37     176     199 ..     472     495 ..     456     502 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00018
                        DUF2048 176 GplgltGlSmGGhmaslaasnwpk 199
                                    G++++tG+S GG m+++ +++  +
  gi|118431816|ref|NP_148517.2| 472 GKMAVTGISYGGYMTNVIVTKTSR 495
                                    9***************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4251.21
//
Query:       gi|14601973|ref|NP_148518.1|  [L=239]
Description: sugar-phosphate nucleotidyl transferase [Aeropyrum pernix K1]
Scores for complete 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-35  121.4   0.0      5e-35  121.3   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    1.8e-12   47.9   0.0    2.1e-12   47.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00027   20.8   0.0    0.00038   20.2   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.3   0.0   8.3e-39     5e-35       2     246 ..       3     228 ..       2     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 8.3e-39
                                   EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
               NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                   a+ILaGG+G+RL+PLt   +k+l+ v+gk +++ ++++ l   g+ee  v l  + ++++ e++++g+kfgv++++++e++
  gi|14601973|ref|NP_148518.1|   3 ALILAGGYGKRLRPLTEHKPKPLLEVAGK-PVLVHQIEWLRYYGVEE-FVLLVGYLKERIIEEMGSGAKFGVKITYVVEDK 81 
                                   89***************************.*****************.8888899999*********************** PP

                                   --BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEE CS
               NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfv 163
                                   + gtA+A+  a+ ++e+e+   lvlv++gD++++ +   +v+  +e++a    + gi  v   + yG+ e d+ g+v+ f 
  gi|14601973|ref|NP_148518.1|  82 PLGTAGALWNARHIIEKEN---LVLVVNGDIVTNIDPDPLVRLVREREA----VAGIAAVPLRSPYGILELDD-GNVTGFR 154
                                   ****************999...7*************************9....889999999**********9.8****** PP

                                   CS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHH CS
               NTP_transferase 164 EKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldslleanek 244
                                   EKP   +  ++++ G+Y   +e++++l       +++ d  + ++p++ ++gk  +a  +    yW+ + t++++ ea+++
  gi|14601973|ref|NP_148518.1| 155 EKPFIYD--YWINGGLYAVSKEIVKYL-------PQQGDIEKTTFPQLASDGKLVAARYEIPPFYWRSIDTFKDIEEASKE 226
                                   *****99..***************999.......667788888899999998887765555555**************998 PP

                                   HH CS
               NTP_transferase 245 la 246
                                   ++
  gi|14601973|ref|NP_148518.1| 227 IE 228
                                   86 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 !   47.7   0.0   3.5e-16   2.1e-12       1     121 [.       3     135 ..       3     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.5e-16
                                   EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-E..EE-TTSS CS
                  NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrv..vededpg 69 
                                   a+iLAGG ++R+    +  +K+ll+++gkp+l ++++ lr  gv+e v+ +g+  e + +++   a++gv++  v+++ + 
  gi|14601973|ref|NP_148518.1|   3 ALILAGGYGKRLRpltEhkPKPLLEVAGKPVLVHQIEWLRYYGVEEFVLLVGYlkERIIEEMgsgAKFGVKItyVVED-KP 82 
                                   79**********6544245********************************998655555443336667665215554.46 PP

                                   -SHHHHHHHHHHHH.SSSCEEEEETT-TT.--HHHHHHHHHCHHHHTSSEEEE CS
                  NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPl.ltpelverllaaaaasgadvvvp 121
                                    g++++l  a + ++++  vlv+ +D++  ++p+ + rl+++ +a  + ++vp
  gi|14601973|ref|NP_148518.1|  83 LGTAGALWNARHIIEKENLVLVVNGDIVTnIDPDPLVRLVREREAVAGIAAVP 135
                                   9**********99*************876699999999999987555444444 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 !   20.2   0.0   6.4e-08   0.00038       1     131 [.       1     137 [.       1     160 [. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.4e-08
                                   EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG....CCEEEEE-- CS
                          IspD   1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld....ksiqlvaGG 74 
                                   + ++i A G GkR++   + +pK +le++g+++l h ++ l  +++ + +++v   ++   +e++ +      +i+ v+  
  gi|14601973|ref|NP_148518.1|   1 MLALILAGGYGKRLRpltEHKPKPLLEVAGKPVLVHQIEWLRYYGVEEFVLLVGYLKE-RIIEEMGSGakfgVKITYVVED 80 
                                   5789*********75333899******************9998887777777766666.6777777666766455554433 PP

                                   S..SHHHHHHHHHHTTSSTTSEEEE--TT.-TT--HHHHHHHHHHHHTTCSEEEEEEE-S CS
                          IspD  75 d..eRaesVlnglkalegeakfVLvHDaA.Rpllkaadiaellaaaeqstqgailalpvk 131
                                   +    a +  n+ +++e+e ++VLv ++   + + ++ + +l+ + e    + i+a+p++
  gi|14601973|ref|NP_148518.1|  81 KplGTAGALWNARHIIEKE-NLVLVVNGDiVTNIDPDPLVRLVRERE--AVAGIAAVPLR 137
                                   3113455666777776666.677777665144567777777777777..47888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1686.13
//
Query:       gi|118431817|ref|YP_874936.1|  [L=528]
Description: hypothetical protein APE_2292.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3766.85
//
Query:       gi|118431818|ref|NP_148520.2|  [L=326]
Description: hypothetical protein APE_2295.1 [Aeropyrum pernix K1]
Scores for complete 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   36.4   0.1      1e-08   35.0   0.0    1.6  2  Lactamase_B_2  Beta-lactamase superfamily domain
    9.2e-05   22.3   0.3    0.00096   19.0   0.0    2.3  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
     0.0038   17.4   0.0      0.014   15.6   0.0    1.9  2  DRMBL          DNA repair metallo-beta-lactamase
  ------ inclusion threshold ------
      0.067   13.2   1.9       0.35   10.8   1.9    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
       0.16   12.3   0.0       0.31   11.3   0.0    1.5  1  Pec_lyase_N    Pectate lyase, N terminus


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 !   35.0   0.0   2.8e-12     1e-08      35     173 ..      32     148 ..      21     165 .. 0.84
   2 ?   -2.2   0.0       0.7   2.5e+03     167     197 ..     266     298 ..     263     299 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.8e-12
                                    E-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE- CS
                  Lactamase_B_2  35 llthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatparhks 114
                                    ++thaH DH++gl    +   ++l ++a++ + + le  +++      p+++++el  g s++++++  ++t++ arh +
  gi|118431818|ref|NP_148520.2|  32 IVTHAHEDHMKGLSRSVR---ESLLIIATPYTFRFLEVLGKRV-----PPERRVELPYGASLDFDGE--RVTLVKARHIA 101
                                    89**********875444...247799************7532.....46799***********843..7********** PP

                                    -CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHH CS
                  Lactamase_B_2 115 grrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemi 173
                                    g          + +++e+g+ r+ y+ D + +p+     l+++d+l++d+t+ +++  +
  gi|118431818|ref|NP_148520.2| 102 GS---------AQVLVETGHGRFGYTSDFK-MPGT--PPLQDLDILVVDATYGSPRLQR 148
                                    *9.........99*****************.7767..579***********98887644 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.7
                                    SSTTHHHH..HHT---STSHHHHCTTSSSSEEE CS
                  Lactamase_B_2 167 yeddemir..hmgHltpeeaveaaadlgakrlv 197
                                    ++ d+mi+     H+t +e ++ ++++++kr++
  gi|118431818|ref|NP_148520.2| 266 WSGDRMINvsFSDHATFREIIDYVREARPKRVI 298
                                    666666666555699999999999999999987 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 ?    0.5   0.1      0.17   6.1e+02      35      51 ..      32      48 ..      26      57 .. 0.80
   2 !   19.0   0.0   2.7e-07   0.00096       8      36 ..     271     299 ..     269     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                          RMMBL 35 ilvHGeeeatsalarll 51
                                   i+ H +e++++ l r  
  gi|118431818|ref|NP_148520.2| 32 IVTHAHEDHMKGLSRSV 48
                                   667*********99977 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.7e-07
                          RMMBL   8 ieeidfSgHadknellelirklkprnvil 36 
                                    + +++fS Ha ++e+++++r  +p++vi+
  gi|118431818|ref|NP_148520.2| 271 MINVSFSDHATFREIIDYVREARPKRVIV 299
                                    6789**********************985 PP

>> DRMBL  DNA repair metallo-beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   3.7e+03      27      54 ..      35      62 ..      30      69 .. 0.80
   2 !   15.6   0.0   3.9e-06     0.014      46     103 ..     253     298 ..     238     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                          DRMBL 27 eklekylkalkekfdsvlafrPtGWtkk 54
                                   ++ e+++k l+++  + l +++t +t++
  gi|118431818|ref|NP_148520.2| 35 HAHEDHMKGLSRSVRESLLIIATPYTFR 62
                                   5667888888888999999999999987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.9e-06
                          DRMBL  46 frPtGWtkkekkkkdlekikessksrekisiyrvpYSeHSSfrELkefvkslkpkkii 103
                                    +r tGW+ ++++ ++ +             + +v +S+H  frE+ + v+  +pk++i
  gi|118431818|ref|NP_148520.2| 253 VRLTGWEMRAPAAWSGD------------RMINVSFSDHATFREIIDYVREARPKRVI 298
                                    67788888887544444............589*************************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 ?   10.8   1.9   9.8e-05      0.35      49     185 ..      32     162 ..      30     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.8e-05
                                    E-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECT CS
                    Lactamase_B  49 ilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtgg 128
                                    i+TH+H DH+ gl   v++    ++  +   +      +             v++   ++ + +  ++ +g r + v   
  gi|118431818|ref|NP_148520.2|  32 IVTHAHEDHMKGLSRSVRESLLIIATPYTFRFLEVLGKR-------------VPPERRVELPYGASLDFDGERVTLVKAR 98 
                                    89***********99999988887777777766666666.............6666667999999999999999999999 PP

                                    TSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........TTCEEE-SHCHHHHHHHHHHHH CS
                    Lactamase_B 129 pghghghgvveygggkvlftGDallagetgridl.......tlrgaevrdpsdaekyldsllkl 185
                                    +  g+ ++ ve g g++ +t D+  +g  ++ dl       t++ +    +++ ++++++l+++
  gi|118431818|ref|NP_148520.2|  99 HIAGSAQVLVETGHGRFGYTSDFKMPGTPPLQDLdilvvdaTYGSPRLQRRWSEWDAIAALIEI 162
                                    9999999999999999999999999888888888878888877777777777777777777766 PP

>> Pec_lyase_N  Pectate lyase, N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.5e-05      0.31      19      44 ..      20      45 ..      18      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.5e-05
                    Pec_lyase_N 19 aaleaYepnPleVtdhFneevneale 44
                                   +a +aY+  P+ +++h +e + + l 
  gi|118431818|ref|NP_148520.2| 20 FAADAYHRRPVRIVTHAHEDHMKGLS 45
                                   6899****************998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 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:                        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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2351.19
//
Query:       gi|14601976|ref|NP_148521.1|  [L=416]
Description: glutamyl-tRNA reductase [Aeropyrum pernix K1]
Scores for 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-32  110.6   0.0    1.1e-31  109.6   0.0    1.5  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    2.8e-25   89.0   0.0    4.6e-25   88.3   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    4.4e-07   30.3   0.9    1.2e-06   28.9   0.9    1.7  1  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
  ------ inclusion threshold ------
      0.026   14.1   0.9       0.38   10.3   0.3    2.2  2  DAO              FAD dependent oxidoreductase
      0.037   14.0   0.9      0.055   13.4   0.2    1.7  2  CHAD             CHAD domain
      0.041   13.9   0.6        1.5    8.9   0.1    3.2  4  TetR_C_7         AefR-like transcriptional repressor, C-termi
      0.042   14.7   0.0        0.1   13.5   0.0    1.7  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.093   13.0   0.9         22    5.4   0.0    2.6  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
       0.34   10.3   0.6       0.59    9.5   0.6    1.4  1  ParA             NUBPL iron-transfer P-loop NTPase


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   5.4e-35   1.1e-31       1     145 [.       8     143 ..       8     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 5.4e-35
                       GlutR_N   1 iginhktapvelreklafseeelkellkelee.kvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyv 80 
                                   ig+n kta+   re++a  e+e ++ l+++   +++++vi++TCNR+E+yl + +  +  e+l++ +     +   e l  
  gi|14601976|ref|NP_148521.1|   8 IGVNVKTAS---REHVARLEKEWEKHLDTI-GyASRGTVIIATCNRFEVYLDSPS--RLVEDLASSI----ASPGGEGLVR 78 
                                   577777775...888888889999999999.33778**************74433..3444444433....444558999* PP

                       GlutR_N  81 legeeavrHlfrVasGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrte 145
                                   l+g +a+rHlfrVasGL+S+++G++++lgQv++a+ +++e+g++++ L+++f++a+k++ rvr+e
  gi|14601976|ref|NP_148521.1|  79 LQGIDAARHLFRVASGLESQIIGDHEVLGQVRRAWLKSREKGFTTPLLDEVFHRALKTGARVRSE 143
                                   ***************************************************************98 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.0   2.3e-28   4.6e-25       2     132 ..     160     283 ..     159     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 2.3e-28
                                   HHHHHHS...TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEE CS
                  Shikimate_DH   2 lakkkle.slkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvi 80 
                                   la + l+  l++++v ++GaG+ a  +a++L+++ + + v+v+NRt er +e+a +++g+e+ +l+l+el +l++e d ++
  gi|14601976|ref|NP_148521.1| 160 LAASLLGgGLDGARVGIVGAGMAAVGIARALCTRwRPRVVAVFNRTPERGWEVAGKCRGVESLVLPLDELAKLINELDALF 240
                                   56666666899*********************99899******************************************** PP

                                   E-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEH CS
                  Shikimate_DH  81 sataseepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytv 132
                                   +a+a +++ile+++ve+ +++    +++vDi++P  v+p+va     r++++
  gi|14601976|ref|NP_148521.1| 241 VAIAGSTNILERGRVERGVSP----RVIVDISNP-PVTPKVAG----RVFHM 283
                                   ******************966....7********.99999986....45555 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.9   5.9e-10   1.2e-06       2      85 ..     304     387 ..     303     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.9e-10
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..-------.-TTHHHHHHHHHHHHHHHHHHSS- CS
                   GlutR_dimer   2 AeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedree.lekltrslvnkllheptarLkeae 81 
                                   AeaiIeee+e++++ l ++++ +  +++ + ++ ++e+e er+l+ l+ +g d++e +e  ++s ++k+  +  + L ea+
  gi|14601976|ref|NP_148521.1| 304 AEAIIEEELEALLDALSRRRARESSRSVMRALSILAEREYERTLAGLR-NGVDPREaVELALNSYTKKVGGALRRLLEEAS 383
                                   9***********************************************.**999888***********9888888888885 PP

                                   TTTT CS
                   GlutR_dimer  82 deee 85 
                                   d+++
  gi|14601976|ref|NP_148521.1| 384 DRGQ 387
                                   5555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.061   1.2e+02      61     106 ..      20      71 ..       9     159 .. 0.54
   2 ?   10.3   0.3   0.00019      0.38       2      75 ..     174     247 ..     173     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.061
                                   HHHHHHHHHHHHHHHSSTTSEEEEEEEEEES.S.........HHHHHHHHHHHHHH CS
                           DAO  61 slealeelreleeelgididyrrtGllslaa.d.........eeelealdkllall 106
                                   ++++ +e++++ ++    i+y  +G++++a+ +         ++  e+l+ ++a++
  gi|14601976|ref|NP_148521.1|  20 VARLEKEWEKHLDT----IGYASRGTVIIATcNrfevyldspSRLVEDLASSIASP 71 
                                   45555666555555....89*********964222233333312222233333332 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                                   EEEECTSHHHHHHHHHHHHT..T..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                           DAO   2 vviiGGGiiGlstAyeLarr..g..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                   v i+G+G++ +++A++L +r  +  V+++ + ++ g++  g+  g+ +  l   p   ela+l  e+ +++ ++++++
  gi|14601976|ref|NP_148521.1| 174 VGIVGAGMAAVGIARALCTRwrPrvVAVFNRTPERGWEVAGKCRGVESLVL---PLD-ELAKLINELDALFVAIAGST 247
                                   78***************8765558********9999999888877765533...322.55666666655555555555 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   3.5e+03     134     134 ..      93      93 ..      12     145 .. 0.52
   2 ?   13.4   0.2   2.8e-05     0.055      84     161 ..     302     390 ..     222     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                   - CS
                          CHAD 134 a 134
                                    
  gi|14601976|ref|NP_148521.1|  93 S 93 
                                   0 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.8e-05
                                   HTS-TTTCGGGHHHHHHHHHHHHHHHHHHH....HHHTSHHHHHHHHHHHHHHT--S--........TSBHHHHHHHHHHH CS
                          CHAD  84 erlpaaeqealerllkrlekerkrararvl....aaLdsaryqalldaldallaaerle........aepaaaalekrlrk 152
                                   ++++a  +e+le+ll++l+++r+r+ +r +    + L++++y++ l+ l++ ++ +r++        ++++  al+++l++
  gi|14601976|ref|NP_148521.1| 302 PAAEAIIEEELEALLDALSRRRARESSRSVmralSILAEREYERTLAGLRNGVD-PREAvelalnsyTKKVGGALRRLLEE 381
                                   5666777799*************998887778889******************4.33334666777777777777777777 PP

                                   HHHHH.HHH CS
                          CHAD 153 ayrklekra 161
                                   a  +++   
  gi|14601976|ref|NP_148521.1| 382 ASDRGQLSL 390
                                   777765555 PP

>> TetR_C_7  AefR-like transcriptional repressor, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.35   6.9e+02      37      77 ..      50      89 ..      42      94 .. 0.84
   2 ?   -2.4   0.0       2.4   4.8e+03      26      40 ..     198     212 ..     189     228 .. 0.75
   3 ?   -1.4   0.0       1.1   2.3e+03       3      26 ..     312     335 ..     306     358 .. 0.58
   4 ?    8.9   0.1   0.00076       1.5      40      71 ..     363     394 ..     356     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.35
                                  HCCHHHT.T----HHHHHHHHHHHHTTSB-SS-HHHHHHHH CS
                      TetR_C_7 37 arafyeagpgrveealaayLeaavaaGrLridDpelAAeqf 77
                                   + ++++ p+r++e+la+ +++   +G +r + ++ A + f
  gi|14601976|ref|NP_148521.1| 50 FEVYLDS-PSRLVEDLASSIASPGGEGLVRLQGIDAARHLF 89
                                  5667777.99************999**99999999888877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                                   HHHHHHT-HHHHCCH CS
                      TetR_C_7  26 viaeaerfPelaraf 40 
                                   v+a + r+Pe + ++
  gi|14601976|ref|NP_148521.1| 198 VVAVFNRTPERGWEV 212
                                   788888888887554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHT-HHHHHHHHHH CS
                      TetR_C_7   3 LtalgrallalllspevlalaRlv 26 
                                   L+al+ al +  +++++++++R +
  gi|14601976|ref|NP_148521.1| 312 LEALLDALSRRRARESSRSVMRAL 335
                                   444555555555555555555544 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00076
                                   HHHT.T----HHHHHHHHHHHHTTSB-SS-HH CS
                      TetR_C_7  40 fyeagpgrveealaayLeaavaaGrLridDpe 71 
                                    +++  ++v  al+++Le+a+++G+L  +D+e
  gi|14601976|ref|NP_148521.1| 363 ALNSYTKKVGGALRRLLEEASDRGQLSLEDIE 394
                                   55666789999*******************98 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     5e-05       0.1       2      74 ..     173     247 ..     172     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH......HHHTTHE....EESSHHHHHTCTTESEEEE-S-G CS
                  GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav......aesfgve....aysdleelladpeidavivatpn 72 
                                   rv+i+GaG+++   +r+l  +  + +vva++++ +er  +v            e      ++l++l +  e da++va+  
  gi|14601976|ref|NP_148521.1| 173 RVGIVGAGMAAVGIARALCTR-WRPRVVAVFNRTPERGWEVagkcrgV-----EslvlPLDELAKLIN--ELDALFVAIAG 245
                                   89*****99888877666665.788*************9996444433.....454444778888888..9******9976 PP

                                   GG CS
                  GFO_IDH_MocA  73 gt 74 
                                   +t
  gi|14601976|ref|NP_148521.1| 246 ST 247
                                   54 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 ?    5.2   0.5     0.013        26      35      73 ..     296     338 ..     288     340 .. 0.78
   2 ?    5.4   0.0     0.011        22      25      63 ..     374     412 ..     363     416 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                                   H...TS--TTT--HHHHHHHHHS-----..-----HHHHHHHH CS
               Phage_int_SAM_1  35 e..rgkesleqlttedvraflaeleeeg..lsatslarrlsal 73 
                                   e  r ++++e++ +e++ a l++l +++   s++s+ r+ls l
  gi|14601976|ref|NP_148521.1| 296 ErlRWIPAAEAIIEEELEALLDALSRRRarESSRSVMRALSIL 338
                                   4445588999999**********99999778888888888865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHH.TS--TTT--HHHHHHHHHS-------- CS
               Phage_int_SAM_1  25 dLrrflkflaergkesleqlttedvraflaeleeeglsa 63 
                                   +Lrr+l+ +++rg+ sle +++  v++f +  e++g++ 
  gi|14601976|ref|NP_148521.1| 374 ALRRLLEEASDRGQLSLEDIEAILVSEFARIAENSGFKN 412
                                   699**************************9999988554 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 ?    9.5   0.6    0.0003      0.59      12      46 ..     148     185 ..     139     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0003
                          ParA  12 KGGVGKStvavnlAlaLa...kkglkvgllDaDiyGps 46 
                                    GGVG S+ av+lA++L      g++vg++ a +    
  gi|14601976|ref|NP_148521.1| 148 SGGVGYSSAAVSLAASLLgggLDGARVGIVGAGMAAVG 185
                                   49***************866678999*99987666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2984.48
//
Query:       gi|118431819|ref|NP_148522.2|  [L=307]
Description: hydroxymethylbilane synthase [Aeropyrum pernix K1]
Scores for complete 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-56  189.7   0.0    5.4e-56  189.3   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    2.7e-10   40.5   0.0    4.3e-10   39.8   0.0    1.3  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
  ------ inclusion threshold ------
      0.059   13.3   0.0       0.16   11.9   0.0    1.7  1  PD40             WD40-like Beta Propeller Repeat


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.3   0.0     9e-60   5.4e-56       1     198 [.       3     207 ..       3     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 189.3 bits;  conditional E-value: 9e-60
                 Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke....eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKD 76 
                                    +r+++R+S+L+l+q+e+  e+L++    + + e+v +k+ GD  +d+pL++ig  g+Ft+e+++a+++g +d+aVhSlKD
  gi|118431819|ref|NP_148522.2|   3 VRVAARGSRLSLLQVEQALEELSRyagvSMHWEVVRVKSAGDVWSDRPLESIGVVGVFTREVDRAVASGAADIAVHSLKD 82 
                                    69********************6555434446************************************************ PP

                 Porphobil_deam  77 lptelpe.glelaavlkredprDvlvvks...sleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldeg 152
                                    +pt+     l+++ + +r ++rD+l+ ++   ++e+l++g+++gTsS RR+a   ++ p+++v++lRGn+dtRlrkl+eg
  gi|118431819|ref|NP_148522.2|  83 MPTSGYGgPLKIVYIASRPSARDALISRQgpgRVEDLEPGSTLGTSSARRRALSLHYNPRIRVENLRGNLDTRLRKLREG 162
                                    ***9875269****************7558889*********************************************** PP

                 Porphobil_deam 153 eydaiiLAaAGLkRlgleerisevlspeellpavgQGalavevrke 198
                                     ydaii ++AGL Rlg++ + +  l+p+ + pa+gQG +av +r +
  gi|118431819|ref|NP_148522.2| 163 LYDAIIASEAGLIRLGVDVEYTP-LDPSYFPPAPGQGFVAVVARVG 207
                                    ****************7777766.******************9976 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   7.2e-14   4.3e-10       4      73 ..     226     293 ..     223     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 7.2e-14
                                    HHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHH CS
                Porphobil_deamC   4 vlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakgeleeaeelGkklaeel 73 
                                    + aER +l+   +GC +P+++yae  + + ++ +++ ls+dg+++   +ae+++  eea+ +G +l+eel
  gi|118431819|ref|NP_148522.2| 226 AWAERGVLEGARAGCRTPVAAYAEPLGRSMVRVTAAALSPDGSRAYWARAEGRI--EEARRIGVSLGEEL 293
                                    579*********************996666**************9999999999..8***********98 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05      0.16      12      27 ..     259     274 ..     258     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                                    EEEEE-TTSSEEEEEE CS
                           PD40  12 gaPsfSPDGkrlaFsS 27 
                                    +a ++SPDG+r ++++
  gi|118431819|ref|NP_148522.2| 259 TAAALSPDGSRAYWAR 274
                                    5789**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2408.28
//
Query:       gi|118431820|ref|NP_148523.2|  [L=429]
Description: glutamate-1-semialdehyde aminotransferase [Aeropyrum pernix K1]
Scores for complete 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-68  231.2   0.0    2.1e-68  230.9   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
    3.6e-05   23.1   0.0    4.9e-05   22.7   0.0    1.2  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 !  230.9   0.0   2.3e-72   2.1e-68       7     377 ..      31     396 ..      26     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: 230.9 bits;  conditional E-value: 2.3e-72
                                    --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                    Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                    ++ ++ ++++eG+yl+ vdg r++Dlv ++ +++lGh+hP+v++av+e++a  ++    a +++++l ++++l  +  + 
  gi|118431820|ref|NP_148523.2|  31 KPYPFYVKRGEGAYLYTVDGARIVDLVLAYGPLILGHKHPRVLEAVEEALARGWLYG--APGEAEVLLAEKILGYVKRG- 107
                                    556699***********************************************8765..99999999888888888877. PP

                                    .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGG CS
                    Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdee 166
                                      ++ ++nsG+eA++tA++lar       +t +  i++f+g++HG   + l ++gs    ++   p++++v+ + + ++ 
  gi|118431820|ref|NP_148523.2| 108 -GMIRFVNSGTEATMTAIRLARG------YTGRDLILKFDGCYHGSHDAVLVAAGS--AAAHYGVPTSAGVPEAVARLTL 178
                                    .89********************......9*************************9..55556668899*********** PP

                                    GTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT..TTTSSS CS
                    Aminotran_3 167 vlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf..GrTGkl 244
                                    v+++n+       e+le++ ++  d +a+vivEp+ +++Gv+++  efla+l+ l ++ ++lli DEv tGf  G  G  
  gi|118431820|ref|NP_148523.2| 179 VTPYND------VEALERVFAEYGDRIAGVIVEPVIANAGVIPPRREFLAALQRLSRESGALLILDEVVTGFrlGLEG-- 250
                                    ******......89999999****************************************************777777.. PP

                                    SGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                    Aminotran_3 245 fAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeekllenaqelg 321
                                     A  +++++ D+++l+K ++gG+p+ av++ +evm+ l+p++    ++Tf + p+ +a+ la+l+++eee +    +e+ 
  gi|118431820|ref|NP_148523.2| 251 -AQGYFNIEGDIIVLGKIIGGGFPVGAVAGSREVMSLLTPQGkvfNAGTFNAHPITMAAGLATLKALEEEPVYSVSREAA 329
                                    .99999**********************************999999***********************99887666666 PP

                                    HHHHH....HHHHHCTT-TTEEEEEEE.TTEEEEEEBCCCETTC.......HHHHHHHHHCTEE-EEE CS
                    Aminotran_3 322 aalke....gLeelqkkyevikevRgk.Glmiaielkeeaevke.......keilkkakekGvlilsa 377
                                    +al+e     L +    y  i++v ++  l+i++e +++a + +        ++ ++++  Gv i ++
  gi|118431820|ref|NP_148523.2| 330 KALEEaaseVLDRTGLPY-TINRVESMmQLFIGVEEVSNAAQARkadkkfyVKLHEEMLRRGVFIAPS 396
                                    666551000555555555.888888877899***9999888655789666656667777778888776 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 !   22.7   0.0   5.4e-09   4.9e-05      73     327 ..     112     385 ..      70     407 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.4e-09
                                    EESHHHHHHHHHHHHHHHTTT-E.EE.EEESS-THHHHHHHHTTSEEEEEEBEET............TTTEE-HHHHHHH CS
                  Aminotran_1_2  73 vgsGagaliealifllklnpgde.il.vpdptyasyknilrlsggevvryplyse............edfhldlealeea 138
                                    + +  +++  ++i+l++  +g++ il  +  +++s++ +l ++g++   y +  +             +  +d+eale+ 
  gi|118431820|ref|NP_148523.2| 112 FVNSGTEATMTAIRLARGYTGRDlILkFDGCYHGSHDAVLVAAGSAAAHYGVPTSagvpeavarltlVTPYNDVEALERV 191
                                    556666677777777775555551443466788888888888888877776555567888888888878889*******9 PP

                                    HTTHHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEE CS
                  Aminotran_1_2 139 lkeapegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivg 217
                                     +e  +g+ ++ +++ve +  + G+++++ e l +l +l ++ ++ll++De+  gf +g ++a+  ++n+e    ++iv 
  gi|118431820|ref|NP_148523.2| 192 FAE--YGD-RIAGVIVEPVIANAGVIPPRREfLAALQRLSRESGALLILDEVVTGFRLGLEGAQG-YFNIEG---DIIV- 263
                                    998..333.478***************9877256666778888****************445444.666666...4666. PP

                                    ESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHH CS
                  Aminotran_1_2 218 slsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdallkqs...eleemrqrlqkrrkelrdeLa 293
                                     l+K  G  G+ vG+++g+ +v s l+     f+  +  + ++++aa  ++l+  +     + +r+  +++ +   + L+
  gi|118431820|ref|NP_148523.2| 264 -LGKIIG-GGFPVGAVAGSREVMSLLTPQGKVFNAgTFNAHPITMAAGLATLKALEeepVYSVSREAAKALEEAASEVLD 341
                                    .79***9.59999*******999999988888888744444444444444443333355788888888888888889998 PP

                                    HSTEEEECCS..CSSEEEEEETHH........CHHHHHHHHHHT CS
                  Aminotran_1_2 294 elglkvlasq..sgmflltdlsae........takelskkLlee 327
                                    + gl+++++   s m l+ ++++         ++k+++ kL ee
  gi|118431820|ref|NP_148523.2| 342 RTGLPYTINRveSMMQLFIGVEEVsnaaqarkADKKFYVKLHEE 385
                                    89999999988677888888887777777776666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.20s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3521.92
//
Query:       gi|118431821|ref|NP_148524.2|  [L=353]
Description: delta-aminolevulinic acid dehydratase [Aeropyrum pernix K1]
Scores for 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-130  432.7   0.0   8.5e-130  432.6   0.0    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.6   0.0  4.7e-134  8.5e-130       2     316 ..      22     344 ..      21     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 432.6 bits;  conditional E-value: 4.7e-134
                                    --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEG..GGHHHHHHHHHHTT--EEEEEEE-S CS
                           ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsv..delvkeveelvklgikavllFgvpe 79 
                                     r rrlr ++ +r+lv+etrl++s++ilplfv++g +++++++ +pg+++++    elv+ v++++ lg++++l+Fg p+
  gi|118431821|ref|NP_148524.2|  22 VRARRLRLHPGVRSLVAETRLDPSMFILPLFVEDGLKTPKPLRGLPGHFKYPPesRELVELVSRALYLGVRSFLVFGTPS 101
                                    599************************************************9733579********************** PP

                                    S-BSS-GGGGSTTSHHHHHHHHHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.....EEHHHHHHHHHHHHHHHHHCT CS
                           ALAD  80 ekdeegsealnedglvqrairaikeev.pelvvitDvclceytshGhcgileeke....vdndetlellakvavsqaeaG 154
                                     k+ eg ea++++g+vqrai+ +++e+  + v+++Dvclc yt+hGhcg  +e+     ++nd+++e++ k++vs aeaG
  gi|118431821|ref|NP_148524.2| 102 MKSFEGAEAWSPRGPVQRAIKFVRAELgWRPVIMADVCLCGYTDHGHCGYPRETPrgvlIENDKSIEAYGKISVSLAEAG 181
                                    **************************9889*********************77667899********************* PP

                                    -SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHH CS
                           ALAD 155 adivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealreveldl 234
                                    ad+vapS+mmDg+vaair+aLd+ag++ev i+sYsaKyaS fYgPFrd+++sap+fgdr++Yqmdp+n+ ea++ev ld 
  gi|118431821|ref|NP_148524.2| 182 ADFVAPSGMMDGQVAAIRSALDNAGYTEVGIMSYSAKYASGFYGPFRDVMDSAPRFGDRRSYQMDPRNRFEAVKEVLLDA 261
                                    ******************************************************************************** PP

                                    HTT-SBEEEES-TTGHHHHHHHHTT-.SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEETTHHH CS
                           ALAD 235 eeGADivmvKPalaylDiirevkeef.dlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltYfake 313
                                    +eGADivmvKPal+ylD+i+evk+++  lp+aay+vSGEY m+kaaae+g++d ++v+lE l+si RAGad+++tY+a e
  gi|118431821|ref|NP_148524.2| 262 AEGADIVMVKPALSYLDVISEVKRSVpWLPLAAYNVSGEYLMLKAAAEKGLVDYETVMLEILTSIARAGADAVITYHALE 341
                                    **************************88***************************************************9 PP

                                    HHH CS
                           ALAD 314 vak 316
                                    +a+
  gi|118431821|ref|NP_148524.2| 342 AAE 344
                                    986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2542.69
//
Query:       gi|118431822|ref|NP_148525.2|  [L=488]
Description: phenylalanyl-tRNA synthetase subunit alpha [Aeropyrum pernix K1]
Scores for complete 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-82  275.6   0.0    4.5e-82  275.2   0.0    1.1  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.6e-06   26.6   0.0    0.00028   20.4   0.0    2.6  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    0.00026   20.4   0.8        0.8    8.9   0.0    3.2  3  tRNA-synt_His    Histidyl-tRNA synthetase
     0.0038   16.4   0.0        4.3    6.3   0.0    3.2  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0079   16.1   6.7      0.047   13.6   0.1    4.1  4  MarR_2           MarR family
  ------ inclusion threshold ------
      0.069   12.6   0.0       0.11   12.0   0.0    1.2  1  NQRA             Na(+)-translocating NADH-quinone reductase s
        0.2   11.5   0.9       0.73    9.8   0.3    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm


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 !  275.2   0.0   1.7e-85   4.5e-82       2     244 ..     219     482 ..     218     483 .. 0.98

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 1.7e-85
                                    .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-..... CS
                   tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka..... 76 
                                    ++v+++ +r+ ++++h l++++e++++i++elgf+ev+gp ve e++nfd+L++ qdhpaR+++d++++k+p++      
  gi|118431822|ref|NP_148525.2| 219 YNVKAEPPRVLPARRHFLAEFIERLRDILRELGFREVRGPLVELELFNFDVLFQAQDHPAREIHDSLWIKSPRRGdlsgy 298
                                    8**********************************************************************9999***** PP

                                    ......................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEE CS
                   tRNA-synt_2d  77 ......................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqveglvvd 133
                                                          v+++++LR++ttav++r l ++++pp++++++g+vfR+dav  t+l+eFhq++g+  d
  gi|118431822|ref|NP_148525.2| 299 sdlvervasvhergwkyrwspeVASRYILRSQTTAVSARILaTRPNPPARFFTVGKVFRSDAVGPTRLPEFHQLDGIEGD 378
                                    **********************999****************99999********************************** PP

                                    TT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEE CS
                   tRNA-synt_2d 134 envsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfa 213
                                    e+++++dl+g l+e+++ l g +  ++f+p+yfpftePs+e  v l   +++wlEl+gaGm+rpevleavg+  ++++ a
  gi|118431822|ref|NP_148525.2| 379 EGYTFRDLLGRLDEIASML-GLK--LKFKPAYFPFTEPSVEGYVKL--PNGRWLELFGAGMFRPEVLEAVGV--DYPVGA 451
                                    ******************9.877..********************9..9***********************..****** PP

                                    EEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                   tRNA-synt_2d 214 fGlGveRlamlkygieDiRelvendlrflrq 244
                                    +G+G+eRlam  yg++DiR+l++++++ +r+
  gi|118431822|ref|NP_148525.2| 452 WGFGIERLAMAFYGVSDIRKLYTRNVDEVRE 482
                                    *************************998876 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 ?    3.0   0.0     0.023        60      15      37 ..     233     255 ..     223     280 .. 0.85
   2 !   20.4   0.0   1.1e-07   0.00028      92     207 ..     342     449 ..     339     454 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.023
                tRNA_synthFbeta  15 lnkeqklrrklrdllagaGlnEv 37 
                                    ++   ++ ++lrd+l ++G+ Ev
  gi|118431822|ref|NP_148525.2| 233 RHFLAEFIERLRDILRELGFREV 255
                                    556678999*************8 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.1e-07
                tRNA_synthFbeta  92 rgnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehp 170
                                    r n+  r+F +gkvf++d  + ++  e ++l ++   +            + f dl g ++++++ lg+ k++f+pa  p
  gi|118431822|ref|NP_148525.2| 342 RPNPPARFFTVGKVFRSDaVGPTRLPEFHQLDGIEGDEG-----------YTFRDLLGRLDEIASMLGL-KLKFKPAYFP 409
                                    78999*************866777889999998877777...........*******************.********** PP

                tRNA_synthFbeta 171 alhpgrsAeikvdgk...evGvlGelhpevleafdlkqrv 207
                                    + +p     +k+ +    e+  +G + pevlea +++++v
  gi|118431822|ref|NP_148525.2| 410 FTEPSVEGYVKLPNGrwlELFGAGMFRPEVLEAVGVDYPV 449
                                    ************55447877789************99987 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.017        43     163     222 ..      32     102 ..      22     136 .. 0.66
   2 !    4.9   0.0    0.0052        13       5      40 ..     228     263 ..     227     280 .. 0.88
   3 !    8.9   0.0   0.00031       0.8      67     114 ..     327     372 ..     322     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.017
                                    HTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTH............HHCCHCC...HCCHCCCHHHHCHCCH CS
                  tRNA-synt_His 163 aaglsesleeallaalarkdlaelkelaaeaglk............ealrellkalelygdaevleealeal 222
                                     +g+++s  + l ++la+k ++e++e ++e+++             ++  +l+  l  +g++ ++ee ++al
  gi|118431822|ref|NP_148525.2|  32 ILGVDKSSLASLSNLLAEKGVVEVEERVEEHYVLtergrdalerglPE-EKLVLFLAGRGGEASVEEVRRAL 102
                                    57999999**********************997744555555444322.22222223444555555555544 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0052
                                    EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEH CS
                  tRNA-synt_His   5 llpeeaekieelrrrlldlfeswGYelVspPllEyl 40 
                                    +lp++ +  +e  +rl d++++ G+++V+ Pl+E +
  gi|118431822|ref|NP_148525.2| 228 VLPARRHFLAEFIERLRDILRELGFREVRGPLVELE 263
                                    57777777888999*******************975 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00031
                                    E-SSSHHHHHHHHHHHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEE CS
                  tRNA-synt_His  67 lRaDiTpqvaRiaahrlnrerplRlcYaGsvlrtrpdglgrsreplQv 114
                                    lR+ +T+  aRi a+r   + p+R+   G+v+r  + g +r  e+ Q+
  gi|118431822|ref|NP_148525.2| 327 LRSQTTAVSARILATRP--NPPARFFTVGKVFRSDAVGPTRLPEFHQL 372
                                    8999***********95..789****************9999999997 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 ?   -1.3   0.0      0.35   8.9e+02      27      49 ..     238     260 ..     233     263 .. 0.87
   2 !    5.7   0.0    0.0025       6.5      93     119 ..     348     373 ..     345     376 .. 0.94
   3 !    6.3   0.0    0.0017       4.3     282     307 ..     447     472 ..     438     474 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHHHTT-EE----SE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  27 tvtkavrkyleengfieietPiL 49 
                                    + ++ +r++l e gf e+  P++
  gi|118431822|ref|NP_148525.2| 238 EFIERLRDILRELGFREVRGPLV 260
                                    567889*************9975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
                                    EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                    r f+++++FR   +  +r + EF q++
  gi|118431822|ref|NP_148525.2| 348 RFFTVGKVFRSDAVGPTRLP-EFHQLD 373
                                    89******************.****98 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0017
                                    -SEEEEEEEHHHHHHHHCT-SSGGGC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 282 pphgGlglGldRlvmlllgsesIrdv 307
                                     p g +g+G++Rl m + g ++Ir++
  gi|118431822|ref|NP_148525.2| 447 YPVGAWGFGIERLAMAFYGVSDIRKL 472
                                    48899*******************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.8e-05     0.047       4      54 ..       6      56 ..       3      62 .. 0.87
   2 ?    0.2   0.0      0.28   7.3e+02       9      32 ..      82     103 ..      76     105 .. 0.75
   3 ?    2.6   0.2      0.05   1.3e+02      41      59 ..     161     175 ..     154     178 .. 0.85
   4 ?   -3.1   0.0       2.9   7.4e+03      23      32 ..     242     251 ..     220     253 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +  ++r+L   + r+ r+ t  e  + lg++ks++  + + L ++G ve +
  gi|118431822|ref|NP_148525.2|  6 SQGEYRLLKLMAERGFREGTLEEASKILGVDKSSLASLSNLLAEKGVVEVE 56
                                   6678999999999997756*****************************987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.28
                                    HHHHHHHCTTTSEEEHHHHHHHHT CS
                         MarR_2   9 rvLaaLgrrpgrdltvgelarrlg 32 
                                     vL+  gr+++   +v e+ r+lg
  gi|118431822|ref|NP_148525.2|  82 LVLFLAGRGGE--ASVEEVRRALG 103
                                    56666666666..8******9997 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.05
                                    HHHHHHHTTSEEEEESSSS CS
                         MarR_2  41 ilkrLvaaGLverrpgpeD 59 
                                    +l+++ ++GL++r+    +
  gi|118431822|ref|NP_148525.2| 161 LLREALSRGLIRRE----A 175
                                    7999********99....4 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.9
                                    EHHHHHHHHT CS
                         MarR_2  23 tvgelarrlg 32 
                                    + +++ r+lg
  gi|118431822|ref|NP_148525.2| 242 RLRDILRELG 251
                                    6677777776 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.11     107     142 ..     190     225 ..     166     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                           NQRA 107 kkelaslsreevkeqLlksGlwtalrtrPfskvaap 142
                                    +   a+++++ +++ +lksG w  lr +P++  a+p
  gi|118431822|ref|NP_148525.2| 190 ALARARVEAAVLTRDMLKSGEWRRLRFKPYNVKAEP 225
                                    445577889999*******************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.3   0.00028      0.73      22      60 ..      23      61 ..       3      67 .. 0.80
   2 ?   -2.5   0.0       1.9   4.7e+03      43      58 ..     162     177 ..     156     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                                   CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                           TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                   + t +e +++lgv++s+  +  + L +kG+Ve+e++   
  gi|118431822|ref|NP_148525.2| 23 EGTLEEASKILGVDKSSLASLSNLLAEKGVVEVEERVEE 61
                                   6688999**************************987544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                    HHHHHHCTSEEEESST CS
                           TrmB  43 LrsLedkGlVerekgr 58 
                                    Lr+ +++Gl++re +r
  gi|118431822|ref|NP_148525.2| 162 LREALSRGLIRREARR 177
                                    6666789999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.20s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 3930.62
//
Query:       gi|14601981|ref|NP_148526.1|  [L=548]
Description: phenylalanyl-tRNA synthetase subunit beta [Aeropyrum pernix K1]
Scores for 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-44  150.3   0.1      7e-44  149.8   0.1    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    3.6e-20   72.0   0.0    1.1e-13   51.2   0.0    2.6  2  B5               tRNA synthetase B5 domain
    3.8e-06   26.7   0.0    8.4e-06   25.6   0.0    1.5  1  B3_4             B3/4 domain
  ------ inclusion threshold ------
      0.017   15.3   0.1       0.34   11.2   0.0    3.0  3  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.1   1.6e-47     7e-44      18     214 .]     360     538 ..     349     538 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 1.6e-47
               tRNA_synthFbeta  18 eqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlargnedvr 98 
                                   e  + r+++dll+g+G++Ev+   ++s+  ++++      + ave++nP+++++svlR++Ll +lL++l++N++r+++ v+
  gi|14601981|ref|NP_148526.1| 360 ETHVYRAVKDLLVGLGFTEVLQLVLTSPRLVEAA---GFSSMAVEVLNPVQQEYSVLRPTLLITLLQTLRENQHRRKP-VK 436
                                   567789****************************...8899*************************************.** PP

               tRNA_synthFbeta  99 lFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepaehpalhpgrsAe 179
                                   +FE g+ +  +  + +p+ e++la+++  ++           ++f+d+ + + a+l+ +g+ ++e+e+a+hp++  gr+A 
  gi|14601981|ref|NP_148526.1| 437 VFEAGNAVYLE--DGEPRDEEKLALGVLDEE-----------AGFEDVQAPLYAVLRIMGV-DFEVEEASHPMFMEGRTAA 503
                                   ********999..99****************...........*******************.******************* PP

               tRNA_synthFbeta 180 ikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                   +kv+g+++G++Ge++pevleaf+l+++v+++E++l
  gi|14601981|ref|NP_148526.1| 504 VKVGGERLGYIGEVKPEVLEAFGLEYPVAAAEISL 538
                                   *********************************87 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.4e-07    0.0024       1      52 [.       4      53 ..       4      60 .. 0.91
   2 !   51.2   0.0   2.6e-17   1.1e-13       3      67 .]     278     341 ..     276     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.4e-07
                                  EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT-- CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5  1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDle 52
                                  +++r e++++l+G  ls  e +++L rl+ce++e ++ +l+V+v + R+D+ 
  gi|14601981|ref|NP_148526.1|  4 IRVRRERLESLTG--LSIGELEELLFRLKCEVEEPEEGVLEVEVNPDRPDMY 53
                                  578999*******..78899******************************85 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 2.6e-17
                                   EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                   l+ + ++k lG+dl++ee + +L+r+ +++ +  + l++V vP++R+D++ e+Dl+E++a+ +GY
  gi|14601981|ref|NP_148526.1| 278 LDPGTVSKALGVDLTPEEAALHLRRMRHNA-SPAGGLVNVRVPPFRVDILGEVDLVEDIAISIGY 341
                                   78899***********************96.*********************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.9e-09   8.4e-06      36     135 ..     111     237 ..      91     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.9e-09
                                   -HHHHHHHHHHHHHT-.....-EEEEEGGGTBT.EEEEEE--TTEEEEBTTS-EEEE-TTSEEEETE.............. CS
                          B3_4  36 nnvVDitNyvmlelgq.....PlhafDldkiqg.divvrlakegeklvtldgkereldeedlviads.............. 96 
                                   + ++  +++++ +lg+     +++ +Dl+k+   +++ rl + + ++ +l+    e++ ++ + ad+              
  gi|14601981|ref|NP_148526.1| 111 EELIQFQEKLHDSLGRrrakiAIGFHDLAKLPSaSVEYRLMTLDTRMKPLGYGGSEMSFREFLLADEkgslygglatkdns 191
                                   668889999999*******************977999**********9997666777775555555444444444444455 PP

                                   .......EEEEEETTTEEBTTTB--TT--EEEEEEEE--HHHHHHH CS
                          B3_4  97 .......ekpvslagvmggeeskvsedTknvfleaaafdpvsirkt 135
                                           ++++ ++v+++e ++v+  T++ f+ +++ + + ++kt
  gi|14601981|ref|NP_148526.1| 192 hpfllsgGEVIAAPPVINSEITRVEPGTRDLFIDVTGTSAELVAKT 237
                                   55555426666**************************999999987 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.6e-05      0.34       1      78 [.       1      63 [.       1      67 [. 0.86
   2 ?   -2.2   0.0       1.1   5.2e+03      31      43 ..     101     113 ..      98     126 .. 0.74
   3 ?   -1.4   0.0      0.64   2.8e+03      55      79 ..     313     337 ..     288     340 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.6e-05
                     PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralk 78
                                  MP+i v++e+L +++g ++   ele+llf++  E+ e     e         e ++ +++   r+D+   eg+ara+k
  gi|14601981|ref|NP_148526.1|  1 MPVIRVRRERLESLTGLSIG--ELEELLFRLKCEVEE----PE---------EGVLEVEVNPDRPDMYIGEGIARAVK 63
                                  9**************98875..799*****9998754....33.........56899999999999999999999986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                     PhetRS_B1  31 fGlElDeiveeee 43 
                                   +G+ +De   ee 
  gi|14601981|ref|NP_148526.1| 101 YGVNVDELFLEEL 113
                                   9999999887765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.64
                     PhetRS_B1  55 iykidipAnryDLLcleglaralkv 79 
                                   ++ + +p  r D+L    l++ +++
  gi|14601981|ref|NP_148526.1| 313 LVNVRVPPFRVDILGEVDLVEDIAI 337
                                   67899999*****998888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 4144.36
//
Query:       gi|14601982|ref|NP_148527.1|  [L=283]
Description: hypothetical protein APE_2308 [Aeropyrum pernix K1]
Scores for 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-56  190.4   0.0    4.6e-56  190.2   0.0    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
    0.00011   22.7   0.0    0.00045   20.7   0.0    1.9  2  FolB      Dihydroneopterin aldolase


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 !  190.2   0.0   5.1e-60   4.6e-56       3     259 .]       2     266 ..       1     266 [. 0.91

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 5.1e-60
                                   XXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHHHS-SSEEG...GGHHH. CS
                        GCHY-1   3 DvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevleeaeeelee...kslee. 79 
                                   Dvq+ k+  ++ l+rVG +gv+    ++++e+   tl  e+d+fvdL+++k+G+h+SR++e++e   ++++e   +s+e  
  gi|14601982|ref|NP_148527.1|   2 DVQDLKPPKPLYLERVGFRGVRRRALLETPEGP-VTLDLELDVFVDLDRSKRGVHLSRNIEAVE---AVVSErraRSIEGl 78 
                                   9****************************9976.5*****************************...55555222444446 PP

                                   ...HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE..TTEEEEEEEEEEEEEEE-HHHHHHS... CS
                        GCHY-1  80 ...ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaelerkeevkltvgvevpvttlCPCskeisrel 157
                                      i++ell+++ yae+a+v+ +++y+i+ +a   g++g e ++v+++++l+r+   ++ v v+v+++t+CP++++++ e+
  gi|14601982|ref|NP_148527.1|  79 lrsIAKELLSRHGYAEKATVRARTRYYIDLEAA--GVKGREPVDVAVTVSLTRSGGERWRVAVSVKGMTVCPSAQSTIAEA 157
                                   667**************************9995..778*************996579*********************888 PP

                                   .......SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHHHHHTS---HHHHHHHHHHH CS
                        GCHY-1 158 l......eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavtekayenpkFvEDvvRevaaa 232
                                   +      +a++H+Q+  ++ +v++   +  v+iedl +++ +s+s+++++llK+++E+ ++ +a+++p+FvEDvvRe+a +
  gi|14601982|ref|NP_148527.1| 158 EgisdpsRAPSHSQKVLLKGTVDT--GKVMVRIEDLARALLQSFSAPTFTLLKKPQEARLILEAFTRPMFVEDVVREAAWR 236
                                   8**********************4..6789*************************************************** PP

                                   HHS-TTEEEE...EEEEEEE-TTTSSEEEE CS
                        GCHY-1 233 leeeerveef...sveveneESiHnHnavA 259
                                   + + + +      +ve+ + ESiH+H+ vA
  gi|14601982|ref|NP_148527.1| 237 IAAIPYIPGEallQVEAVSLESIHPHDLVA 266
                                   *777666544778**************998 PP

>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     5e-08   0.00045      24     108 ..      34     113 ..      30     116 .. 0.83
   2 ?   -1.8   0.0      0.51   4.5e+03      47      61 ..     178     192 ..     162     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5e-08
                                   EEEEEEEEEE-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHHHCHST.ESEEEEEEEETTSSSTCE CS
                          FolB  24 rvvvdleleldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaealleefp.vekvevrveKpnapigaa 103
                                   +v++dlel++        d+ ++ v+  + ++av+++v++++ +++E l ++ia++ll+++  +ek++vr +    +  ++
  gi|14601982|ref|NP_148527.1|  34 PVTLDLELDVF----VDLDRSKRGVHLSRNIEAVEAVVSERRARSIEGLLRSIAKELLSRHGyAEKATVRARTRYYI--DL 108
                                   67778888663....456778888***************99******************9999*******9988764..45 PP

                                   SEEEE CS
                          FolB 104 davgv 108
                                   +a+gv
  gi|14601982|ref|NP_148527.1| 109 EAAGV 113
                                   55555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.51
                                   SS-HHHHHHHHHHHH CS
                          FolB  47 tvdYaelakavkelv 61 
                                   tvd +++  ++++l+
  gi|14601982|ref|NP_148527.1| 178 TVDTGKVMVRIEDLA 192
                                   444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2146.24
//
Query:       gi|118431823|ref|NP_148528.2|  [L=383]
Description: hypothetical protein APE_2310.1 [Aeropyrum pernix K1]
Scores for 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-10   41.0   1.8    3.4e-10   40.3   1.8    1.4  1  APH       Phosphotransferase enzyme family


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 !   40.3   1.8   1.9e-14   3.4e-10      13     211 ..      54     279 ..      46     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.9e-14
                                    EEEEEETT.--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEETTE.EEEEEE----EE-SS..... CS
                            APH  13 tylvttpa.gryvlrrnpparaaeeirrevallrlLakagv.pvPevlagdtddeeigl.lfalieyvpgrsllr..... 84 
                                    +y++ +   g ++ ++++ +   + + re  llr+La++ +  vP++l     +  +g+ +++++eyv+g ++++     
  gi|118431823|ref|NP_148528.2|  54 SYRLLSRPyGLLAAKVYRRP---PPVDREWLLLRFLAASSLpLVPRPLC---RASLEGRtYMVVHEYVEGVPAATlfiea 127
                                    57777777777777777777...88999999******999977999999...33333333799999999999999999** PP

                                    .....HHHHHHHHHHHHHHHHHHCCHHCH.............-STTTB-SHHCHTCCHHHHHHCHHHCCCGCCTCC...H CS
                            APH  85 .....klsaaqlpellealgeflaalhqv............dpaalpladflaqdlellrqlesatarllaselld...l 144
                                         k   a  p  ++alg + aa+h++            +p++++++++  + l+  +   +  ar+l+++      +
  gi|118431823|ref|NP_148528.2| 128 akqslKTGVATVPSEAGALGVAVAAIHSAlascreswcmpeEPTEAMVERWMSR-LAIRASMIEDLARGLPADEARivyD 206
                                    *****5556666666666666666666664444444444432444444444433.4444444444444455444445444 PP

                                    HHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---.........TT-EEEECCHHHHCCHHH CS
                            APH 145 leeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDf.........edaglgpplyDlavllrs 211
                                    ++ + +q+ ++ ++ l+  + +  +HgDlh+  +lv  + gr+  v Df         + +   +p  Dla llrs
  gi|118431823|ref|NP_148528.2| 207 AASALRQLHQREWRGLL-GGVAMQTHGDLHLYQVLVS-RSGRI-VVTDFegepsrqpaGAMEKEHPERDLAALLRS 279
                                    55555555555555555.5888889************.88888.68899777777666666677777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3005.94
//
Query:       gi|118431824|ref|NP_148529.2|  [L=299]
Description: hypothetical protein APE_2311.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-06   28.4   0.0    1.8e-06   28.0   0.0    1.2  1  DUF2797   Protein of unknown function (DUF2797)


Domain annotation for each model (and alignments):
>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     1e-10   1.8e-06      69     134 ..     136     205 ..      96     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-10
                        DUF2797  69 lqphvVYLa....nssevKVGiTrkeqvptRwidQGAvqaiplaevanRrlaglvevalketvaDktnwr 134
                                      ++ VYL      s+ vKVG+Tr+ ++ +R  +Q    a+++a +++ ++a+l+e ++ ++   + + r
  gi|118431824|ref|NP_148529.2| 136 SMEYAVYLTafysPSAPVKVGVTRRFRLLERVAEQPHIAATAVAFLDSAYKARLLEIEIGRRGIARQSTR 205
                                    5689****988866788*****************************************998744444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.20s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2569.10
//
Query:       gi|118431825|ref|YP_874937.1|  [L=80]
Description: hypothetical protein APE_2311a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   16.6   0.0     0.0077   15.9   0.0    1.4  1  DUF3989   Protein of unknown function (DUF3989)
  ------ inclusion threshold ------
        0.1   12.0   1.0       0.12   11.8   1.0    1.1  1  DUF373    Domain of unknown function (DUF373)
       0.12   12.3   0.0       0.16   11.9   0.0    1.3  1  DUF4492   Domain of unknown function (DUF4492)
       0.16   12.5   0.1        0.2   12.2   0.1    1.1  1  DUF1240   Protein of unknown function (DUF1240)
        1.3    9.5   7.0        3.4    8.2   7.2    1.6  1  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF3989  Protein of unknown function (DUF3989)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-06    0.0077      29      54 ..      12      37 ..       2      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                        DUF3989 29 ivvllllllfallslYmtvssiydig 54
                                   iv + l++lfa lslY+++ +++ i 
  gi|118431825|ref|YP_874937.1| 12 IVAIGLAMLFAALSLYFFGNALSLIT 37
                                   78899****************99876 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.0   3.4e-05      0.12     159     203 ..      13      67 ..       9      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                         DUF373 159 vplGlllliyallll..........lglpelalaiillllGlylllrGfgldell 203
                                    v +Gl++l+ al+l           l+ p++a++++++l+Gl+ll   ++l ++l
  gi|118431825|ref|YP_874937.1|  13 VAIGLAMLFAALSLYffgnalslitLEEPRVAASLLAALIGLALLSASVSLARSL 67 
                                    77899999999988899999999999999******************99998865 PP

>> DUF4492  Domain of unknown function (DUF4492)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.16      22      45 ..      11      34 ..       4      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                        DUF4492 22 liiliKLfiifvvLklfffpdvLk 45
                                    i+ i L  +f+ L l+ff ++L+
  gi|118431825|ref|YP_874937.1| 11 EIVAIGLAMLFAALSLYFFGNALS 34
                                   69*******************997 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.5e-05       0.2       9      70 ..      15      75 ..      12      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-05
                        DUF1240  9 vvlllfssPlllYfsvlvvlvaitnklakvndklvkllaiiailsfvlslflslYvdyklks 70
                                   ++l+++ + l lYf     l+ it + ++v  +l  +l  +a+ls+ +sl  sl ++  l+ 
  gi|118431825|ref|YP_874937.1| 15 IGLAMLFAALSLYFFG-NALSLITLEEPRVAASLLAALIGLALLSASVSLARSLVLSRALER 75
                                   6778888888899875.5567899999**************************999888775 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   7.2   0.00095       3.4      22      67 ..      21      71 ..      12      72 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00095
                         DUF202 22 alglallrffl.....tgepsalgkilglilivlgiltllvglvrylrrqr 67
                                   +++l l+ f +     t e+ ++++ l ++li+l++l+++v+l r+l + r
  gi|118431825|ref|YP_874937.1| 21 FAALSLYFFGNalsliTLEEPRVAASLLAALIGLALLSASVSLARSLVLSR 71
                                   444444432224455555555556777779**************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 616.76
//
Query:       gi|14601986|ref|NP_148531.1|  [L=146]
Description: hypothetical protein APE_2314 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0066   16.0   0.5      0.012   15.1   0.5    1.4  1  Shal-type  Shal-type voltage-gated potassium channels, N-term


Domain annotation for each model (and alignments):
>> Shal-type  Shal-type voltage-gated potassium channels, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.5   6.6e-07     0.012       5      21 ..       8      25 ..       5      29 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.6e-07
                     Shal-type  5 aW.LPFaRAAAIGWvPvA 21
                                   W L FaRAAAIG + +A
  gi|14601986|ref|NP_148531.1|  8 GWlLRFARAAAIGLLDLA 25
                                  59899********88777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1112.81
//
Query:       gi|14601987|ref|NP_148532.1|  [L=123]
Description: hypothetical protein APE_2315 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 955.26
//
Query:       gi|118431826|ref|YP_874938.1|  [L=93]
Description: hypothetical protein APE_2315a [Aeropyrum pernix K1]
Scores for complete sequence (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    9.4   8.4       0.21   11.7   1.9    2.1  2  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 ?   11.7   1.9   1.2e-05      0.21      47      69 ..      12      34 ..       2      35 .. 0.90
   2 ?    1.6   0.6     0.016   2.9e+02       8      22 ..      64      78 ..      61      83 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.2e-05
                        DUF1206 47 vllglvglgllgyglwqlveAvt 69
                                   +ll+++gl+++g++++ ++ A++
  gi|118431826|ref|YP_874938.1| 12 ALLIILGLAMVGFVFYTAYDAYR 34
                                   79*******************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.016
                        DUF1206  8 vvylllgllalqaal 22
                                   v++l+++l a +++l
  gi|118431826|ref|YP_874938.1| 64 VAFLAIALAAGSVVL 78
                                   456666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 748.45
//
Query:       gi|14601988|ref|NP_148533.1|  [L=449]
Description: tryptophan synthase subunit beta [Aeropyrum pernix K1]
Scores for complete 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-42  145.4   0.4    2.9e-42  145.1   0.4    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 !  145.1   0.4   1.6e-46   2.9e-42       2     290 ..      78     413 ..      77     419 .. 0.79

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 1.6e-46
                                   GGCSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                          PALP   2 tlgigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallGl 79 
                                   + + +pTPl+r+ +l+++l++p  +++K+E+ +ptgS+K+++a    ++   eg   + v+e+++G++g al+aa+a +G+
  gi|14601988|ref|NP_148533.1|  78 SFARRPTPLLRAVNLERALNTPaeIYYKYEGVTPTGSHKINTALAQAYYnKLEG-VERLVTETGAGQWGSALSAAGAYFGV 157
                                   67899***************************************9999967777.8999999999**************** PP

                                   EEEEEEETTS-...HHHHHHHHHTT-EEEEE............CCHHHHHHHHHHHHHHH..................... CS
                          PALP  80 kvtivvpadas...pekvallrllGaevvev............ggdydeavaaaaelaae..................... 124
                                   kv++++ + +    p+++ l++l+Gaev  +                            e                     
  gi|14601988|ref|NP_148533.1| 158 KVRVYMVRVSYlqkPYRRTLMELYGAEVYPSpsdktefgrkllA---------------Enpnhpgslgiaiseaiedvin 223
                                   *****7666655669****************4443333333331...............3233333333333333333444 PP

                                   .STTCEE--TTTSHHHHHHHHTHHHHHH...HHTTTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTT CS
                          PALP 125 .gegaylvsqfdnptviegygtiglEil...eqlggkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegs 195
                                    g++a +   +   +v + ++ iglE     ++ g  pd ++ +vGgG+++aG+  ++      +  +  +r+i+vep+ s
  gi|14601988|ref|NP_148533.1| 224 sGGNAKYSLGSVLNHVLLHQTVIGLEAEkqfREAGVYPDIMIGAVGGGSNFAGFTYPFIRhrlkG--SssTRFIAVEPKAS 302
                                   4555555555557778888********74556667***********************9966543..146*********** PP

                                   CGGTTCC...S..S.SS..B.................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHH CS
                          PALP 196 dalarsl...ragrrvtvpvs................dtiadglavgspselafelldrlvdeivtvsdeealeamrllar 257
                                   ++++r++   + g+                       +  a gl+ + +++    ll+  + e+ +  + e+++a+  +a+
  gi|14601988|ref|NP_148533.1| 303 PSMTRGVytyDYGDTAG---LtpllkmhtlghtyqvpPIHAGGLRYHGVAPTLSVLLKHGIVEARAYHQREVFRAAHMFAK 380
                                   *******5553333333...25558888999999998**********888888889999999******************* PP

                                   HHSB-B-HHHHHHHHHH..HHHHHHCCTTCEEEEE CS
                          PALP 258 regivvepssaaalaal..klreagelkegdrvvv 290
                                   +egiv+ p sa+a+ a+  ++ +a++ ++   vv+
  gi|14601988|ref|NP_148533.1| 381 AEGIVPAPESAHAVKAAidEAIKARDEGRR--VVI 413
                                   *****************8655555555555..443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3334.78
//
Query:       gi|118431827|ref|NP_148534.2|  [L=574]
Description: glutamyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-70  237.6   0.0    2.1e-70  237.1   0.0    1.2  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    4.9e-21   75.4   0.0    7.9e-21   74.7   0.0    1.4  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.1   0.0   2.3e-74   2.1e-70       2     313 ..     103     412 ..     102     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.1 bits;  conditional E-value: 2.3e-74
                                    -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--H..HHHHHHHHHHHHTT---SSEEEEGGGGHH CS
                   tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdpereke..eaeesiledlkwlgikwdekptyqsdrfd 79 
                                    V+ RfaP+P    H+G+a+ a++n+ +A+ ++G+++lR+eDTdp  +++  ea + i +dlkwlg++w ++ + qs r++
  gi|118431827|ref|NP_148534.2| 103 VKLRFAPNPDFVIHMGNARPAIVNHEYARMYKGRMVLRFEDTDPRTKTPlrEAYDLIRQDLKWLGVSW-DEEYIQSLRME 181
                                    899*****************************************99986559999*************.55899****** PP

                                    HHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGG CS
                   tRNA-synt_1c  80 elkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vef 158
                                     ++++a + i++G AYv++c  e  e + +      +++rd   e+nl+lf e+m +g++ +++avvR+k d +++   +
  gi|118431827|ref|NP_148534.2| 182 VFYSVARRAIERGCAYVDNCGREGKELLSR---GEYCPTRDLGPEDNLELF-EKMLEGEFYEGEAVVRMKTDPRHPnPSL 257
                                    *********************998665543...45789*************.9**********************99*** PP

                                    SSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EE CS
                   tRNA-synt_1c 159 rDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrln 238
                                    rD v+ ri  ++++ h+lv++++ + PtY+fav +dD+++eithvlr++e++ nt+k++++++ +g++ pp+   + rl 
  gi|118431827|ref|NP_148534.2| 258 RDWVAMRIIDTEKHPHPLVGSRYLVWPTYNFAVSVDDHMMEITHVLRGKEHQLNTEKQLAVYRCMGWR-PPYFIHFGRLK 336
                                    ************9*******************************************************.7777789**** PP

                                    ETTSB-SHHHHHHHHHT..TSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHHH CS
                   tRNA-synt_1c 239 lekkklSKRklsllvde..kqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkLe 313
                                    le+  lSK k+  l +e   ++ + dd+r+ ++ +lrr+G+ +e++r+++ + ++   +  ++++ +l+a++rk L+
  gi|118431827|ref|NP_148534.2| 337 LEGFILSKSKIRKLLEErpGEFMGYDDPRFGTIAGLRRRGVLAEAIRQIILEVGVKPTD-ATISWANLAAANRKLLD 412
                                    **********9999876235899********************************9998.*************9887 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 !   74.7   0.0   8.8e-25   7.9e-21       1     174 []     415     560 ..     415     560 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 8.8e-25
                 tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfs.keiyiereDakrlkpgeevrLkelynikveevek 79 
                                    A+R+m+V+dpv++++e l + +   +e+p+hp++p+++ r    + +++++ reDa    +g+++rL++l n++v++   
  gi|118431827|ref|NP_148534.2| 415 ADRIMYVEDPVEMEVE-LAQVECRAAEIPFHPSRPQRKRRITLCTgDKVLLTREDA---VEGRQLRLMGLSNFTVSQG-- 488
                                    89**************.776799*************98776555547********5...6789************765.. PP

                 tRNA-synt_1c_C  80 desgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvl.eeglaepalanl 157
                                               e+d+ sle ar+ k  i++Wv++  ++++                ++l+p +l+   ++g+ae a++ +
  gi|118431827|ref|NP_148534.2| 489 ----IL----REVDP-SLEYARRMKLpIVQWVKKGGEASV----------------EVLEPVELELRrHQGYAEDAIRGY 543
                                    ....33....35787.9999999***********999999................99*****986689*********** PP

                 tRNA-synt_1c_C 158 kkgdivQfeRiGyfrvd 174
                                     +++++Qf R+G++rvd
  gi|118431827|ref|NP_148534.2| 544 GVDSRLQFVRYGFVRVD 560
                                    ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 4442.45
//
Query:       gi|118431828|ref|NP_148536.2|  [L=199]
Description: hypothetical protein APE_2322.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.4   0.0      0.049   13.4   0.0    1.5  1  DUF447    Protein of unknown function (DUF447)


Domain annotation for each model (and alignments):
>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.7e-06     0.049      15     142 ..      24     150 ..      15     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.7e-06
                                    EEEEEEEESSSEEEEEEETTSHHHHHHHHHSE....EEEEE---HHHHHHHHHS---GGGEEEETTTCTT..EETT-SEE CS
                         DUF447  15 aaPiGvivkgdkvvlrlfkgsrTleNllenge....lvinvtdDpllfakaalgdleesdfdsetkpakia.vlksaeaw 89 
                                      P+Gv+ +g  + +rl++g   l  ++e++     l +    Dpl ++++ l++lee+   +   p   +  l s +a+
  gi|118431828|ref|NP_148536.2|  24 TMPLGVMGSGGAWRFRLYPG-VGLLSIAESRGwrldLRLLTPLDPLAYMESYLHRLEERLSYRGGCPE-PDpALGSWYAC 101
                                    5799**99999*******99.7777787777512224456678***********99999554444333.33477777776 PP

                                    EEEEEEEECTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC CS
                         DUF447  90 veveveevegdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi 142
                                     +v+      ++ a+ ++++ ++    +   +p+ R+ ++++E++++at    
  gi|118431828|ref|NP_148536.2| 102 PAVKEGV---EDGAVWFRCKSLRPLASA-PQHPYYRAYGCFVELLIAATKARA 150
                                    6666553...344444444444444444.445*****************7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1641.76
//
Query:       gi|14601992|ref|NP_148537.1|  [L=222]
Description: hypothetical protein APE_2323 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.0   0.0       0.19   11.4   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 ?   11.4   0.0     1e-05      0.19      94     163 ..     100     166 ..      79     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1e-05
                    MAF_flag10  94 diplvfasgvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliG 163
                                    +++++ +g+n ++   ++   ++ +  s q+ +     + +    G +++++a  lA+ l++++I++ G
  gi|14601992|ref|NP_148537.1| 100 RVYILHLHGDNWWVTTPWRIAGFM-RAYSSQVRPAA--PNPVLAPLGYTDGDRAAVLAMALEAESIVFQG 166
                                   689999999999999999999886.44445554444..23335689**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1834.35
//
Query:       gi|118431829|ref|NP_148538.2|  [L=94]
Description: 50S ribosomal protein L35 [Aeropyrum pernix K1]
Scores for complete 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   0.4    1.5e-09   37.9   0.4    1.9  1  Ribosomal_L35Ae  Ribosomal protein L35Ae


Domain annotation for each model (and alignments):
>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.4   8.5e-14   1.5e-09       3      94 ..       4      87 ..       3      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 8.5e-14
                                   EEEEEEEEE--SSSSS-EEEEEEESS--SHHHHHCCTT-EE..EEE-......TTT-EEEEEEEEECTTT.TEEEEEETT-- CS
                Ribosomal_L35Ae  3 vkavflgykrgkrnqrentaLlkiegvkskeeaefylGkrvayvykakkkkkgskvrviwGkvtrahGns.gvvrakFkknL 83
                                   +++v+lgy+rg ++q++++aL+k+   ++  +a  y+   +a++ +           v++G+v r hG++ gvv +kF+  L
  gi|118431829|ref|NP_148538.2|  4 ARGVVLGYRRGTNTQYPQHALVKLL-LDDPRKAGLYVSG-IAFY-RD------RYGNVYKGRVLRLHGRRgGVVVVKFNPPL 76
                                   589********************97.6677777788764.5543.43......467899*********9735899******* PP

                                   SSS-TT-EEEE CS
                Ribosomal_L35Ae 84 ppkaigarvrv 94
                                   p++a g  v+v
  gi|118431829|ref|NP_148538.2| 77 PGQATGGVVEV 87
                                   *******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 720.78
//
Query:       gi|14601994|ref|NP_148539.1|  [L=157]
Description: phospholipase A2/esterase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-42  144.1   0.4    1.7e-42  143.7   0.1    1.3  2  PriX      Primase X
  ------ inclusion threshold ------
       0.18   12.1   0.0       0.35   11.2   0.0    1.4  1  SepF      Cell division protein SepF


Domain annotation for each model (and alignments):
>> PriX  Primase X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8   1.6e+04      44      56 ..      27      40 ..      20      44 .. 0.67
   2 !  143.7   0.1   1.9e-46   1.7e-42       1      98 [.      53     151 ..      53     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                                  HHHH.....TTSSS CS
                          PriX 44 kefl.ksckkkknl 56
                                  ++fl ++c++   +
  gi|14601994|ref|NP_148539.1| 27 QRFLeEACREAGTC 40
                                  67777778777666 PP

  == domain 2  score: 143.7 bits;  conditional E-value: 1.9e-46
                                   -HHHHHHHHH--SSTHHHHHHHTHHHHHHHTS---HHHHHHHHHHHH.....TTSSSS---HHHHHHHHHHHHHHT----- CS
                          PriX   1 yeWiekvlekglpDgRkrlilyvisrYLvnvkklseeealkklkefl.ksckkkknlskiyeswirsvikgvkekglkpis 80 
                                   y W+e+++++g+pDgR+rlilyvisrYLvnvk+l+  ea + ++efl ++c+k+ n++kiy+swir+v+++v+e+g++p++
  gi|14601994|ref|NP_148539.1|  53 YVWVESIIRSGVPDGRSRLILYVISRYLVNVKGLEPGEAEAVIDEFLrVCCEKHGNCRKIYKSWIRNVLRRVREGGWRPWT 133
                                   78*********************************************99******************************** PP

                                   HHHHHHH-HHHHHHHHHH CS
                          PriX  81 lkklkekdkelyeviekv 98 
                                   l++++++d+ely++ie++
  gi|14601994|ref|NP_148539.1| 134 LERIRSEDPELYRIIEPI 151
                                   ***************987 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.9e-05      0.35      26      61 ..      80     115 ..      79     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.9e-05
                                   EEE-CCCTCHHHHHHHHHHHHHHHHCT-EEEEECTT CS
                          SepF  26 ilnledldkeeakrivdflsgvvyaldGdiqkvgkk 61 
                                   ++n+++l++ ea+ ++d+   v+ + +G+ +k+ k+
  gi|14601994|ref|NP_148539.1|  80 LVNVKGLEPGEAEAVIDEFLRVCCEKHGNCRKIYKS 115
                                   69*****************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1252.87
//
Query:       gi|118431830|ref|NP_148540.2|  [L=102]
Description: V-type ATP synthase subunit K [Aeropyrum pernix K1]
Scores for 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-18   64.4  15.1    8.6e-18   64.4  15.1    1.8  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.12   2.1e+03      48      55 ..       7      14 ..       3      26 .. 0.64
   2 !   64.4  15.1   4.8e-22   8.6e-18       1      60 []      39      98 ..      39      98 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.12
                                   HHHHHHHH CS
                     ATP-synt_C 48 aialygLi 55
                                   ++ l+gL+
  gi|118431830|ref|NP_148540.2|  7 TLMLLGLV 14
                                   44555554 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 4.8e-22
                                   HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                   +gaglavGl+++g G+++G+ag+a+ +++ ++p++f++sl+++++ e ia+ygL++al+l
  gi|118431830|ref|NP_148540.2| 39 IGAGLAVGLAGIGGGYAVGVAGAAATSSITEKPEMFGRSLLFVVLGEGIAIYGLLIALLL 98
                                   7*********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 808.83
//
Query:       gi|14601997|ref|NP_148542.1|  [L=485]
Description: prolyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for complete 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-23   82.4   0.1    5.3e-23   81.9   0.1    1.2  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.5e-21   76.3   0.1    2.5e-21   75.6   0.1    1.4  1  HGTP_anticodon  Anticodon binding domain
    5.1e-13   49.0   0.1    9.9e-13   48.1   0.1    1.5  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
       0.36   10.7   1.6          1    9.3   1.6    1.8  1  Rad50_zn_hook   Rad50 zinc hook motif


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 !   81.9   0.1   1.2e-26   5.3e-23       5     177 ..     102     274 ..      94     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.2e-26
                                   ETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTSTBCTTTB-SEEEE.EEEEEEES.GGGHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxx RF
                  tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEksdsrGLlRvreFhq.kdgyvfha.easlddslrd 82 
                                   ++ d +++L+Pt+e+ ++ +   + ++s+r LP k+yq+ +++R+E++++r+++R+re +  k+++ +h   ++++ ++ +
  gi|14601997|ref|NP_148542.1| 102 EELDVKLALRPTSETSITYMETFW-IKSYRqLPKKYYQVVSIFRYETKATRPMIRLREVTTfKEAHTVHEsFEDAERQVLE 181
                                   4558899*************9977.***777***************************97549*******6699******* PP

                                   HHHHHHHHHHHTT.SCEEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b  83 likaisriferlglefraiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvim 161
                                    i++++ if rl+++ ++i +   +++  a + ++  f+ +++  +++++igt++ lg+++ ++++ ++  +++r  ++  
  gi|14601997|ref|NP_148542.1| 182 AIEVYKAIFDRLLIP-YVISKRpeWDK-FAGALYTIAFDTIMP-DGRALQIGTVHHLGQSFTRAFDFRIQMRDERLDHPWQ 259
                                   ***************.77888887775.49999**********.9************************99********** PP

                                   EEEEEEHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                  tRNA-synt_2b 162 icaaigveRllsaile 177
                                   + ++++  R+++ +++
  gi|14601997|ref|NP_148542.1| 260 TSYGVS-DRVVASLIA 274
                                   ****99.999998776 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.1   5.7e-25   2.5e-21       1      93 [.     292     389 ..     292     390 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.7e-25
                                   SEEEEESSSS....HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                HGTP_anticodon   1 qvvviplnek....aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                   qvvvip++ +    + ++++y  k ae+L++ag+rv++dd + e++g k+ +++ +g+p++v++G +e+e++t+t+ +rdt
  gi|14601997|ref|NP_148542.1| 292 QVVVIPITPGdeekRGKVLTYTAKAAEALEKAGLRVHVDDrEWERPGAKFYYWEAKGVPIRVEIGLREAEQDTLTIARRDT 372
                                   8*********888877888************************************************************** PP

                                   CEEEEEETTHHHHHHHH CS
                HGTP_anticodon  77 reqervsldelveklke 93 
                                    e+ +v+l e+ + ++e
  gi|14601997|ref|NP_148542.1| 373 LEKTEVPLGEAGNRIRE 389
                                   ***********999998 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 !   48.1   0.1   2.2e-16   9.9e-13       2      69 .]     417     485 .]     416     485 .] 0.92

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.2e-16
                                   HHHHHHHHTT-.EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                     ProRS-C_1   2 eefkealekkg.fvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                   ee  + +e ++ ++ +pWcg+e c  +++e+++ k+l+ p+ +ep eeg++C +cg+pa  w+  +++Y
  gi|14601997|ref|NP_148542.1| 417 EEARDWVEGRRgIAEIPWCGRESCGLEMEERVNGKVLGTPWPEEPVEEGKRCPLCGRPAVAWIRLAKTY 485
                                   566666766666*****************************9999**********************99 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.6   0.00022         1      17      28 ..     464     474 ..     460     474 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00022
                                   T-SEE-TTT--E CS
                 Rad50_zn_hook  17 eakgcCPlCgRe 28 
                                   e + +CPlCgR+
  gi|14601997|ref|NP_148542.1| 464 E-GKRCPLCGRP 474
                                   3.33*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3557.69
//
Query:       gi|118431831|ref|YP_874939.1|  [L=95]
Description: 30S ribosomal protein S26 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-22   78.2   2.4    6.9e-22   77.9   2.4    1.1  1  Ribosomal_S26e  Ribosomal protein S26e
     0.0055   16.9   0.3       0.08   13.1   0.2    2.4  2  zf-RING_7       C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.046   13.9   0.1      0.046   13.9   0.1    2.1  2  Tat             Transactivating regulatory protein (Tat)
       0.14   12.3   0.8       0.14   12.3   0.8    2.3  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


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 !   77.9   2.4   1.5e-25   6.9e-22       1      95 [.       1      91 [.       1      94 [. 0.95

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.5e-25
                                   X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHHHTT CS
                 Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscaihsk 82
                                   m+kKR ++gr k  +g+  +v+C+nc+r+vp dKai  + +++ v+ + +++l+++      ++ ++ ++++ycvsca+h  
  gi|118431831|ref|YP_874939.1|  1 MPKKRESRGRRKGAKGKAGTVQCDNCGRVVPADKAICVTRMYSPVDPQLAEELEKK----GAIIMRYPVTKCYCVSCAVHYG 78
                                   9*****************************************************98....667778888999********** PP

                                   SS----TTTTS-- CS
                 Ribosomal_S26e 83 vvrvRsredrknr 95
                                   +v+ R +e+rk +
  gi|118431831|ref|YP_874939.1| 79 IVKIRPEEQRKPK 91
                                   **********976 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   1.8e-05      0.08      23      32 ..      20      29 ..       5      30 .. 0.74
   2 ?    1.3   0.0     0.092   4.1e+02       9      23 ..      45      59 ..      45      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                   -EE-TTT--E CS
                      zf-RING_7 23 vvtCpeCGRI 32
                                    v+C++CGR 
  gi|118431831|ref|YP_874939.1| 20 TVQCDNCGRV 29
                                   59*******6 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.092
                                   --CCHHHHHCCSTB- CS
                      zf-RING_7  9 lppqvlselragdev 23
                                   ++pq+  el +++ +
  gi|118431831|ref|YP_874939.1| 45 VDPQLAEELEKKGAI 59
                                   69*******999765 PP

>> Tat  Transactivating regulatory protein (Tat)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.6      0.76   3.4e+03      49      56 ..       6      12 ..       2      20 .. 0.46
   2 ?   13.9   0.1     1e-05     0.046       2      35 ..      44      79 ..      43      84 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.76
                                   XXXXXXXX CS
                            Tat 49 kkrrqrrr 56
                                     r  rr+
  gi|118431831|ref|YP_874939.1|  6 ESR-GRRK 12
                                   223.2332 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1e-05
                                   ---TTS.-GGGS-B-.S-SS---S--SCCHHTSSHH CS
                            Tat  2 PvdPrl.epwkhpgs.qpktactncyckkcsfhcqv 35
                                   PvdP+l e  ++ g+   +   t cyc  c+ h  +
  gi|118431831|ref|YP_874939.1| 44 PVDPQLaEELEKKGAiIMRYPVTKCYCVSCAVHYGI 79
                                   9999985445555541678899**********9755 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 ?    2.1   0.6      0.05   2.2e+02      17      37 ..      22      38 ..      19      39 .. 0.64
   2 ?   12.3   0.8   3.2e-05      0.14      22      39 ..      57      73 ..      57      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.05
                  Auto_anti-p27 17 tCpvCgvPLmrdrkggkvyCv 37
                                    C++Cg +   d    k +Cv
  gi|118431831|ref|YP_874939.1| 22 QCDNCGRVVPAD----KAICV 38
                                   599997665553....23565 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.2e-05
                  Auto_anti-p27 22 gvPLmrdrkggkvyCvaC 39
                                   g+++mr++  +k+yCv+C
  gi|118431831|ref|YP_874939.1| 57 GAIIMRYPV-TKCYCVSC 73
                                   6799***93.69****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 703.52
//
Query:       gi|14601998|ref|NP_148543.1|  [L=160]
Description: hypothetical protein APE_2330 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1164.83
//
Query:       gi|118431832|ref|NP_148546.2|  [L=213]
Description: hypothetical protein APE_2333.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-05   25.6   0.0    2.9e-05   24.2   0.0    1.8  1  UPF0102        Uncharacterised protein family UPF0102
    2.1e-05   24.3   1.0      6e-05   22.9   0.4    2.0  2  HTH_1          Bacterial regulatory helix-turn-helix protein,
    8.4e-05   22.6   0.1    0.00019   21.5   0.1    1.6  1  Mrr_cat        Restriction endonuclease
      0.002   17.7   0.4          3    7.5   0.0    3.3  3  HTH_50         Helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   14.9   0.1       0.13   12.3   0.0    2.3  2  Dimerisation   Dimerisation domain
      0.029   13.7   0.2      0.048   13.0   0.2    1.4  1  NucS           Endonuclease NucS
      0.071   13.3   0.0       0.13   12.4   0.0    1.4  1  COG5           Golgi transport complex subunit 5
      0.079   13.0   0.1       0.18   11.8   0.1    1.7  1  Hjc            Archaeal holliday junction resolvase (hjc)
       0.11   12.3   4.9       0.38   10.6   0.3    3.2  3  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.4e-08   2.9e-05       2      44 ..      11      60 ..      10      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.4e-08
                                   HHHHHHHHHHTT-EEEEEEEEETT.....EEEEEEE..TTEEEEEEEEE- CS
                        UPF0102  2 EelaaeyLekkgyeilernwrcra.....gEiDiia..tevlvfvEVKtR 44
                                   Ee+aa++Lek g+++l+  +  +      gEiDi+a  +     vEVK+ 
  gi|118431832|ref|NP_148546.2| 11 EEIAARILEKSGFRVLDFHVPIEDggvevGEIDIVAekGGSRYSVEVKAG 60
                                   9****************9998844445559********77899*****85 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 ?   -1.3   0.0       1.1   2.3e+03      35      47 ..      93     105 ..      89     111 .. 0.80
   2 !   22.9   0.4     3e-08     6e-05       2      38 ..     145     181 ..     144     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                                    HHHHHHHTS-SEE CS
                          HTH_1  35 krLEeelgvpLfe 47 
                                    ++L e lgv+L++
  gi|118431832|ref|NP_148546.2|  93 RKLAEKLGVELIV 105
                                    5788888888875 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3e-08
                                    HHHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHH CS
                          HTH_1   2 rqlrlfvavaeegsftrAAeeLglsqpavsrqikrLE 38 
                                    ++l++++a+a+++sf++AA +Lg++   + +++ rL 
  gi|118431832|ref|NP_148546.2| 145 EDLEVLEAIAKAKSFREAASKLGTAVEELAARVDRLK 181
                                    68***************************99999996 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   9.4e-08   0.00019       6     106 ..       7     104 ..       4     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.4e-08
                                    TTCHHHHHHHHHHHHSSS....EEE---B.-TTSSB--EEEETTEEEEEEEEEEE--T...S-B-HHHHHHHHHHCTTS. CS
                        Mrr_cat   6 pkeFeklvaellealGyk....eveltgr.sgDggiDliakkdplgserilvqaKryk...nkvgvkeVqeligalkkrg 77 
                                    ++  e+++a++le+ G++    +v + ++  + g iD++a+k   g  r+ v++K      n+v +  V++li+ +k   
  gi|118431832|ref|NP_148546.2|   7 WRNSEEIAARILEKSGFRvldfHVPIEDGgVEVGEIDIVAEK---GGSRYSVEVKAGMadiNAVRQAYVNSLISGMKPM- 82 
                                    67779*************665544333330334457878876...459********94458999999*******99976. PP

                                    .SEEEEEESS-B-HHHHHHHHTT--EEEE CS
                        Mrr_cat  78 adkgifvttsdftkaAreeaeelnkieLl 106
                                          +++ +  +aAr+ ae+  ++eL+
  gi|118431832|ref|NP_148546.2|  83 ------IVARGADEAARKLAEK-LGVELI 104
                                    ......7777788888888888.566666 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0086        17      26      35 ..      92     101 ..      90     102 .. 0.91
   2 ?    1.3   0.0      0.13   2.6e+02       3      21 ..     116     134 ..     114     135 .. 0.82
   3 !    7.5   0.0    0.0015         3      18      36 ..     151     169 ..     140     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0086
                         HTH_50  26 tRklAkrLGv 35 
                                    +RklA++LGv
  gi|118431832|ref|NP_148546.2|  92 ARKLAEKLGV 101
                                    7********8 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                         HTH_50   3 sLkeyveefErelikkaye 21 
                                    +Lke+vee   ++i +++e
  gi|118431832|ref|NP_148546.2| 116 DLKEIVEEAVDQAILSLLE 134
                                    89*****988888888775 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0015
                         HTH_50  18 kayekYpStRklAkrLGvS 36 
                                    +a++k +S+R +A +LG+ 
  gi|118431832|ref|NP_148546.2| 151 EAIAKAKSFREAASKLGTA 169
                                    5677889**********85 PP

>> Dimerisation  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.97   1.9e+03       7      24 ..      37      54 ..      36      56 .. 0.79
   2 ?   12.3   0.0   6.3e-05      0.13       8      46 ..     146     180 ..     145     183 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.97
                   Dimerisation  7 iELglldiiakaggkpls 24
                                   +E g +di a++gg+  s
  gi|118431832|ref|NP_148546.2| 37 VEVGEIDIVAEKGGSRYS 54
                                   577889******997665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.3e-05
                   Dimerisation   8 ELglldiiakaggkplspsEiaskLptknpeapvlldRl 46 
                                    +L++l++iaka     s  E askL t   e ++ +dRl
  gi|118431832|ref|NP_148546.2| 146 DLEVLEAIAKAK----SFREAASKLGTAVEELAARVDRL 180
                                    69*********8....***********9999999****8 PP

>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.4e-05     0.048     134     209 ..      37     104 ..      14     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                           NucS 134 vaiGivdiLgkdeegklvivelkrrkaevdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefk 209
                                    v +G +di++ ++ g+   ve+k   a+++av+q   yv+ l      ++++ ++va+   + a+kl+++ g+e+ 
  gi|118431832|ref|NP_148546.2|  37 VEVGEIDIVA-EKGGSRYSVEVKAGMADINAVRQ--AYVNSLI-----SGMKPMIVARGADEAARKLAEKLGVELI 104
                                    6789999986.6889999***************9..5998764.....57889999*999999***9999999875 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.5e-05      0.13      56     119 ..     145     208 ..     125     211 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHHHH CS
                           COG5  56 nhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtldLl 119
                                    + le+le + k ks ++  s+l + +e+L a ++rlk+  + p  + +  ++a+  +   ++Ll
  gi|118431832|ref|NP_148546.2| 145 EDLEVLEAIAKAKSFREAASKLGTAVEELAARVDRLKRAGVLPRSSYKRMRAAAIIVLAGCRLL 208
                                    67899*********************************99999999999999988888888887 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.3e-05      0.18       8      66 ..      16      77 ..      10     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.3e-05
                                   HHHHHTT-EEE..EBSCSSSSSS.SS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHH CS
                            Hjc  8 kiLrergfavv..RsagSggatk.plpDviAirgdvvlviEvKsskkeriylkkeqveklle 66
                                   +iL++ gf v+   ++   g+++    D++A +g+  + +EvK    +   +++  v++l++
  gi|118431832|ref|NP_148546.2| 16 RILEKSGFRVLdfHVPIEDGGVEvGEIDIVAEKGGSRYSVEVKAGMADINAVRQAYVNSLIS 77
                                   688888988863356777777676889*****************999988899999998875 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 ?    0.9   0.1      0.21   4.1e+02      16      29 ..      88     101 ..      83     102 .. 0.80
   2 ?    0.8   0.1      0.23   4.5e+02       3      12 ..     124     133 ..     123     134 .. 0.87
   3 ?   10.6   0.3   0.00019      0.38      18      42 .]     157     181 ..     147     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                  HTH_AsnC-type  16 aRisyaeLAervGl 29 
                                    a    ++LAe++G+
  gi|118431832|ref|NP_148546.2|  88 ADEAARKLAEKLGV 101
                                    5667899******8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.23
                  HTH_AsnC-type   3 eiDrkILeaL 12 
                                    ++D++IL++L
  gi|118431832|ref|NP_148546.2| 124 AVDQAILSLL 133
                                    58******99 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00019
                  HTH_AsnC-type  18 isyaeLAervGlSestvlrRvrrLe 42 
                                     s++e A ++G + ++ ++Rv+rL+
  gi|118431832|ref|NP_148546.2| 157 KSFREAASKLGTAVEELAARVDRLK 181
                                    59*********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1588.20
//
Query:       gi|118431833|ref|YP_874940.1|  [L=58]
Description: hypothetical protein APE_2333a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 455.31
//
Query:       gi|118431834|ref|NP_148547.2|  [L=239]
Description: hypothetical protein APE_2334.1 [Aeropyrum pernix K1]
Scores for 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  120.9   0.0    6.8e-35  120.7   0.0    1.0  1  NMD3          NMD3 family
  ------ inclusion threshold ------
        4.1    7.2   5.5        6.8    6.5   1.1    2.8  2  Rubredoxin_2  Rubredoxin metal binding domain
        5.6    7.2   6.2        9.8    6.4   1.4    2.9  3  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   1.1e-38   6.8e-35       1     243 []       7     230 ..       7     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 1.1e-38
                           NMD3   1 CcrCGkeieelinglCedCllkevditegiek.ievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseev 79 
                                    C  CG+ +e l +glC++C+ +++ ++eg +  + v+vC +Cgr++ ++kW++     ee + ++l ++   +Lk  + v
  gi|118431834|ref|NP_148547.2|   7 CASCGRGSEVLLRGLCPECFDRRYGVVEGLPWeLVVDVCTSCGRVRIGHKWLEY-ATAEEAVGLMLSSM---SLKPVHPV 82 
                                    9*******99*9***************************************886.67888888999988...77777778 PP

                           NMD3  80 eevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqkrelte 159
                                    e+v++e +  e   t     r++v++++++++r+   t ++ + ++ ++++ ++Cp C  + +g+y+ +vQvR+      
  gi|118431834|ref|NP_148547.2|  83 ERVELEDWALE---TRL-DWRTRVRLRFRANYRD---TLFRVSRVIVLRLNPSTCPLCIVRRSGEYDTLVQVRGY----- 150
                                    88887744444...666.8999999999999955...899***********************************..... PP

                           NMD3 160 eehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvke.seklvsedkksgkevyrlt 238
                                        r+ e +e+++++ d ++  +++  v+ G+D+yf ++ aA+++v++l s+  ++v+  +++ v++ ++ g+++ r t
  gi|118431834|ref|NP_148547.2| 151 ----RAGEAVEKTLNSLDPREAPIDVVPVRGGVDVYFHHRGAAARFVSRLASTARVRVSRvEHEHVGT-SSLGRRRSRKT 225
                                    ....99999999999999***************************************96616678888.556******** PP

                           NMD3 239 ysvrl 243
                                    ++vrl
  gi|118431834|ref|NP_148547.2| 226 ILVRL 230
                                    ***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 ?    6.5   1.1    0.0011       6.8       3      20 ..       7      25 ..       6      27 .. 0.85
   2 ?    1.9   0.2     0.032   1.9e+02       2       9 ..      44      51 ..      44      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0011
                   Rubredoxin_2  3 CsqCGfesakwf.GrCpsC 20
                                   C +CG  s  ++ G Cp+C
  gi|118431834|ref|NP_148547.2|  7 CASCGRGSEVLLrGLCPEC 25
                                   99***99987644****** PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.032
                   Rubredoxin_2  2 vCsqCGfe 9 
                                   vC +CG +
  gi|118431834|ref|NP_148547.2| 44 VCTSCGRV 51
                                   79999976 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   1.4    0.0016       9.8       8      32 ..       7      25 ..       5      29 .. 0.84
   2 ?    1.2   0.0     0.067     4e+02       8      13 ..      45      50 ..      40      53 .. 0.72
   3 ?   -0.9   0.0      0.31   1.8e+03      26      32 ..     127     133 ..     116     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                    Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeC 32
                                   C +Cg+  evl +        CPeC
  gi|118431834|ref|NP_148547.2|  7 CASCGRGSEVLLRG------LCPEC 25
                                   *********99743......39999 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.067
                    Zn-ribbon_8  8 CeeCgh 13
                                   C++Cg+
  gi|118431834|ref|NP_148547.2| 45 CTSCGR 50
                                   777774 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.31
                    Zn-ribbon_8  26 ltaCPeC 32 
                                    + +CP C
  gi|118431834|ref|NP_148547.2| 127 PSTCPLC 133
                                    456**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1892.88
//
Query:       gi|118431835|ref|NP_148548.2|  [L=165]
Description: hypothetical protein APE_2335.1 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   12.8   0.5         12    6.5   0.0    2.3  2  DUF902    Domain of Unknown Function (DUF902)


Domain annotation for each model (and alignments):
>> DUF902  Domain of Unknown Function (DUF902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0029        52      19      30 ..      23      34 ..      20      38 .. 0.87
   2 ?    6.5   0.0   0.00065        12       9      26 ..     141     158 ..     137     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0029
                         DUF902 19 vLyCygkqlCtI 30
                                    L C ++++Ct 
  gi|118431835|ref|NP_148548.2| 23 LLACRSAAVCTL 34
                                   599********7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.00065
                         DUF902   9 CgrklsFspqvLyCygkq 26 
                                    Cgr +   pq+L C g +
  gi|118431835|ref|NP_148548.2| 141 CGRLWRRLPQTLPCGGDP 158
                                    9*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1344.36
//
Query:       gi|118431836|ref|NP_148549.2|  [L=471]
Description: RNA-loop binding protein FAU-1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.4e-13   50.8   0.1    2.6e-13   50.0   0.1    1.5  1  DUF402     Protein of unknown function (DUF402)
    0.00065   19.2   0.0    0.00096   18.6   0.0    1.2  1  RNase_E_G  Ribonuclease E/G family


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   2.9e-17   2.6e-13       2      68 .]     372     438 ..     371     438 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.9e-17
                                    -EEEEE-TT-SEEEEEEEETTTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE......-HHHH CS
                         DUF402   2 lelwllplglwynvfhfldgdgrlqglYvDiatppevgegawktiDlyLDlvvspdgevevlDedEL 68 
                                    + +++++ g w ++++++d++grl+g+Y +i+tppevg + +k+ Dl +D+v  p +e e +D+ EL
  gi|118431836|ref|NP_148549.2| 372 RGVTHVYMGDWLTIHEYYDKSGRLLGVYANINTPPEVGFQGLKYLDLLVDVVKRPGEEPETIDQGEL 438
                                    6789999******************************9855***********99**********998 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-07   0.00096       9     103 ..     158     252 ..     151     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-07
                      RNase_E_G   9 llpegkkvgvSkkiedeeererlkell.eelkpeevGlIvRtaaegaseeelekdleelkkkweeilekakkrkapslly 87 
                                    ++  g+ v +S+ +++e+  ++lk++  + +  +++++ +R+ a  ase ++ +++++l+++ e++ ++     +p++l 
  gi|118431836|ref|NP_148549.2| 158 VMHPGSGVRISRHLTSEDAAKALKAVEaSGIDLNQFSVHIRSGARLASEGDISDEIRRLAREAERLWREGP-GGEPAVLS 236
                                    444566689***************99857788899*******************************99997.77888888 PP

                      RNase_E_G  88 eeedlllrvlrdllne 103
                                    + e l l +l  ++++
  gi|118431836|ref|NP_148549.2| 237 RGEYLSLVYLPSTAKH 252
                                    8777766666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3497.81
//
Query:       gi|14602005|ref|NP_148550.1|  [L=91]
Description: hypothetical protein APE_2336a [Aeropyrum pernix K1]
Scores for complete 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-34  116.4   0.4    4.9e-34  116.2   0.4    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
     0.0087   16.4   0.2      0.017   15.5   0.2    1.5  1  HEAT_2    HEAT repeats
  ------ inclusion threshold ------
       0.01   16.4   0.7      0.024   15.3   0.7    1.7  1  HEAT_PBS  PBS lyase HEAT-like repeat
      0.037   14.3   0.0          1    9.7   0.0    2.2  2  UPF0253   Uncharacterised protein family (UPF0253)


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 !  116.2   0.4   1.1e-37   4.9e-34       2      81 .]      10      89 ..       9      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 1.1e-37
                                  HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                       UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                  e kik ++++L +ii+dt vPrniRraa +a+++L+d + s+avraa+ais+L+e+s+DpnmP++aRt+iw+v++ LEt+
  gi|14602005|ref|NP_148550.1| 10 EGKIKLAMSILVTIINDTGVPRNIRRAAANALTHLRDPRLSPAVRAANAISALEEVSQDPNMPFYARTRIWQVITILETV 89
                                  7799**************************************************************************97 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   3.7e-06     0.017      33      75 ..      17      70 ..      11      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.7e-06
                        HEAT_2 33 lpaLvelleded..pavRraaaeaLgaigdpe.........alpaLkelldddd 75
                                  + +Lv +++d+   +++Rraaa+aL  ++dp+         a++aL+e  +d++
  gi|14602005|ref|NP_148550.1| 17 MSILVTIINDTGvpRNIRRAAANALTHLRDPRlspavraanAISALEEVSQDPN 70
                                  566777776654435899999999998887665554555557777777777766 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 ?   15.3   0.7   5.4e-06     0.024       1      27 []      33      68 ..      33      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                                  HHHHHHHHHHHCTS.........GGGHHHHHHHCTC CS
                      HEAT_PBS  1 vRraAakaLgqlgd.........eeaipaLleaLqd 27
                                  +RraAa aL  l+d           ai aL e+ qd
  gi|14602005|ref|NP_148550.1| 33 IRRAAANALTHLRDprlspavraANAISALEEVSQD 68
                                  6*******************************9997 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00023         1      27      55 ..      13      41 ..       9      45 .. 0.89
   2 ?    2.6   0.0     0.036   1.6e+02      29      44 ..      57      72 ..      48      78 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
                       UPF0253 27 iscalktLdevaanealpeevrekAAyAA 55
                                  i+ a+  L ++ ++  +p+++r  AA A 
  gi|14602005|ref|NP_148550.1| 13 IKLAMSILVTIINDTGVPRNIRRAAANAL 41
                                  78899********************9885 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.036
                       UPF0253 29 calktLdevaanealp 44
                                   a+ +L+ev ++ ++p
  gi|14602005|ref|NP_148550.1| 57 NAISALEEVSQDPNMP 72
                                  3577777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 741.07
//
Query:       gi|14602006|ref|NP_148551.1|  [L=316]
Description: hypothetical protein APE_2338 [Aeropyrum pernix K1]
Scores for complete 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-75  252.5   0.0    3.9e-75  252.3   0.0    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 !  252.3   0.0   2.2e-79   3.9e-75       2     234 ..       9     280 ..       8     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 252.3 bits;  conditional E-value: 2.2e-79
                                   EEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EEEEEET CS
               SAM_adeno_trans   2 tLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterralvveak 82 
                                    L++DFG ++py+g+m++vi+si+++++i+Di H+ip+f++ ++a+++a++++++pkg+v++avVDpgvgt+r al+ve++
  gi|14602006|ref|NP_148551.1|   9 GLISDFG-DSPYTGIMRAVIKSISRELQIIDIDHSIPSFSPLAGAYVVAHTYQWLPKGSVIVAVVDPGVGTSRYALAVETE 88 
                                   699****.9************************************************************************ PP

                                   TSEEEEESSSTTHHHH...SEEEEEEGSSCC....................--TS-HHHHTHHHHHHHHHCT.--GGGCSE CS
               SAM_adeno_trans  83 ggyfvgPDNGlltlal...lleeaveieeee....................ssatFhgrDvFapvaarlaag.vsleelge 139
                                   +++f+gPDNG+l +a+   +++++++++e++                     s+tFhgrDvFap++a +aag  sleelg+
  gi|14602006|ref|NP_148551.1|  89 NYVFIGPDNGVLYPAAasdGIKRVYALREKDvnslarmktsstagtvkpwsISRTFHGRDVFAPAGALIAAGhASLEELGD 169
                                   ****************9987789999988778888999999999999999988*******************999****** PP

                                   EESGGGS-SSS.....E..CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTC....EE........EEEEESSGGGSTTT CS
               SAM_adeno_trans 140 eldpeelvrle.....e..derlegevlyvDrFGNvitniskelleelekerk....va........klkkvetyaevaeg 201
                                   e++pe++ r +     +   ++++++v+y+D+FGNv ++i+    ++l+ + +    v+        +++  +t++++++g
  gi|14602006|ref|NP_148551.1| 170 EIEPERMKRASidhveKlgPSTFRATVVYIDKFGNVALSIR---PKKLGINLSlyksVVlgthttsnTIRMGKTFGDANPG 247
                                   ****99988877666424456778*****************...6666666555555116777888655555********* PP

                                   SEEEEE-TTSEEEEEETTC-HHHHHT--TT-EE CS
               SAM_adeno_trans 202 ellalvnssglleiavnkgsaaellglkvgdev 234
                                   el+a+ ns g+leiavn+g+aa++lgl+ +++v
  gi|14602006|ref|NP_148551.1| 248 ELVAYENSFGHLEIAVNRGNAAKKLGLELEARV 280
                                   ****************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2204.55
//
Query:       gi|118431837|ref|NP_148552.2|  [L=127]
Description: hypothetical protein APE_2340.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   12.7   3.7       0.13   12.0   3.7    1.3  1  DUF1678   Protein of unknown function (DUF1678)
       0.18   12.0   0.0       0.23   11.6   0.0    1.2  1  DRMBL     DNA repair metallo-beta-lactamase


Domain annotation for each model (and alignments):
>> DUF1678  Protein of unknown function (DUF1678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.7   1.4e-05      0.13      27      69 ..      37      81 ..      30      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                        DUF1678 27 kpslevtyrtvnG..kvyGpyyvarwkrdskfkrGrtlylGkeen 69
                                   kp  +v yrt  G  kvy  y    w+ + ++ r r +y+G+e+ 
  gi|118431837|ref|NP_148552.2| 37 KPVHKVYYRTTGGrsKVYEYYGRYWWRIEGQGSRRRLIYVGREKP 81
                                   79999******994346666666779****************975 PP

>> DRMBL  DNA repair metallo-beta-lactamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.6e-05      0.23      27      67 ..       9      50 ..       3      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                          DRMBL 27 eklekylkalkek.fdsvlafrPtGWtkkekkkkdlekikes 67
                                   +++++yl++lk+  ++   ++rPtG+  k+  k  + +++  
  gi|118431837|ref|NP_148552.2|  9 SRIRDYLDSLKPAlYSYNSMIRPTGYYLKPVHKVYYRTTGGR 50
                                   6899*******9989999********9999877777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1002.80
//
Query:       gi|14602008|ref|NP_148553.1|  [L=264]
Description: lipoate-protein ligase [Aeropyrum pernix K1]
Scores for 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   29.4   0.0    1.1e-06   28.6   0.0    1.4  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 !   28.6   0.0   5.9e-11   1.1e-06      15     131 .]      52     154 ..      42     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.9e-11
                                   .GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH......HHTT-TTEEE CS
                 BPL_LplA_LipB  15 slnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrdskpgiegipvfi 95 
                                   ++n+++  ++g+ vvrr +gG +v+h+  g+ + s+ +  +      +++  +v+ ++l++l+ l       gieg + + 
  gi|14602008|ref|NP_148553.1|  52 EVNIEQARAEGVPVVRRISGGGAVFHD-LGNMNVSVYIPRRL---GVDEAYALVTSIILKTLHRL-------GIEGRVEN- 120
                                   689999*********************.***********775...43355555************.......77777666. PP

                                   ETTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                 BPL_LplA_LipB  96 kwpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                      nD+ v+  K++G+a   + ++tl h ++++ ++
  gi|14602008|ref|NP_148553.1| 121 --GNDVAVGPWKVSGSAAAIRARATLAHATLLLTTD 154
                                   ..9**************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1926.70
//
Query:       gi|118431838|ref|NP_148554.2|  [L=264]
Description: lipoate-protein ligase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-25   88.7   0.0      4e-25   88.2   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 !   88.2   0.0   2.2e-29     4e-25       2     131 .]      45     177 ..      44     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 2.2e-29
                                    EEEES-HHHHHH..GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH CS
                  BPL_LplA_LipB   2 gevikstntllkeslnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavleal 79 
                                    g++++       e++n++e e++g+v+vrr+tgG +++h +++e+tysl+l++++++++ +v+e    +   v  +le+l
  gi|118431838|ref|NP_148554.2|  45 GRRQSV------EDVNLAEAEKRGYVLVRRPTGGAALLHPWEREITYSLVLDSRHPYYSLDVAESAatIAGGVALALEEL 118
                                    556666......689****************************************************9************ PP

                                    .............HHTT-TTEEEE.TTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                  BPL_LplA_LipB  80 g...yrd....skpgiegipvfik.wpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                    g   +      + pg  g  ++++ +++D++v grK++G+a++++ g+ l+h++++++++
  gi|118431838|ref|NP_148554.2| 119 GiatR-VggytPPPGVIGGLCYVRpGSSDVVVAGRKVSGSAQRRIGGRLLQHGTLLLRFD 177
                                    98742.134569*******************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2105.38
//
Query:       gi|118431839|ref|NP_148555.2|  [L=293]
Description: lipoyl synthase [Aeropyrum pernix K1]
Scores for complete 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   51.8   0.0    2.4e-13   50.8   0.0    1.5  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   1.4e-17   2.4e-13       4     166 ..      55     213 ..      52     214 .. 0.92
   2 ?   -2.7   0.0      0.37   6.7e+03      37      54 ..     245     262 ..     231     284 .. 0.54

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.4e-17
                                    ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                    +  C+++C+fC++++     g+++ l++ e  + + ++    g ++v+l++ + ++ pd     +++  +a + +r   +
  gi|118431839|ref|NP_148555.2|  55 GDTCTRGCRFCYVKK-----GVPEPLDPLEPYKVALAV-DALGLDYVTLTSVDRDDLPDGGASHFAATVRAIKRLRPDTI 128
                                    678***********6.....899999999999999999.6889***************************9888888888 PP

                                    ECSSCHG....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                    xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  84 tngtlpd....eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGende 158
                                    + ++ pd    ee++++ +  g+ ++++++e++       l++ r+ ++ + l++le+++e g+  +++ i+++ Ge ++
  gi|118431839|ref|NP_148555.2| 129 VEALIPDfqgvEEHVRLVAASGLEVLAHNIETVER--LTPLVRdRRAGYRQSLRVLEIAKEEGVV-TKSSILLGLGEDKS 205
                                    8888888***************************9..688888899*******************.************** PP

                                    HHHHHHHH CS
                                    xxxxxxxx RF
                    Radical_SAM 159 eleellel 166
                                    e+ e +++
  gi|118431839|ref|NP_148555.2| 206 EVIEAMRD 213
                                    **999886 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.37
                                    HHHHHHHHTT.SEEEEEES CS
                                    xxxxxxxxxx.xxxxxxxx RF
                    Radical_SAM  37 evkelkaekg.vkevilgg 54 
                                    e++el aekg   ++  + 
  gi|118431839|ref|NP_148555.2| 245 EFREL-AEKGlRMGFAYVV 262
                                    33333.3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2087.11
//
Query:       gi|118431840|ref|NP_148556.2|  [L=92]
Description: hypothetical protein APE_2347.1 [Aeropyrum pernix K1]
Scores for 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-13   49.9   2.6    2.9e-13   49.4   2.6    1.2  1  Biotin_lipoyl    Biotin-requiring enzyme
    5.5e-06   26.1   1.2    0.00045   20.0   0.1    2.2  2  Biotin_lipoyl_2  Biotin-lipoyl like
    6.5e-05   22.8   0.3    8.3e-05   22.5   0.3    1.2  1  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0016   18.3   1.4     0.0022   17.9   1.0    1.4  1  GCV_H            Glycine cleavage H-protein
     0.0047   17.0   0.6        1.6    8.8   0.1    2.1  2  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
  ------ inclusion threshold ------
      0.016   15.1   0.2      0.019   14.8   0.2    1.1  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
       0.02   14.1   0.7       0.35   10.0   0.1    2.0  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
      0.022   15.4   0.5       0.04   14.6   0.4    1.5  1  HlyD_3           HlyD family secretion protein
      0.032   13.9   0.1      0.056   13.1   0.1    1.4  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
      0.035   13.7   0.4       0.94    9.1   0.1    2.1  2  T2SSB            Type II secretion system protein B
      0.043   13.6   0.3        1.4    8.7   0.0    2.3  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.077   12.4   0.5      0.088   12.2   0.5    1.0  1  NQRA             Na(+)-translocating NADH-quinone reductase s


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 !   49.4   2.6   1.9e-16   2.9e-13      15      72 ..      22      79 ..      18      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.9e-16
                                   ..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
                  Biotin_lipoyl 15 g.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72
                                   g vv+v++k+Gd V++g+vlae+e  K+  e+e+p++G+v +i+ + G++v+  +++a+
  gi|118431840|ref|NP_148556.2| 22 GkVVRVYKKPGDLVEKGEVLAEIEIEKAILEVESPVSGRVRSIVGE-GEEVTPESVVAV 79
                                   55788**************************************999.****99998876 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1     3e-07   0.00045      11      34 ..      22      45 ..      20      51 .. 0.94
   2 ?    5.3   0.1     0.011        17       4      16 ..      52      64 ..      47      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3e-07
                Biotin_lipoyl_2 11 GrVaqlnVkdGqrVkaGdvLaelD 34
                                   G+V++++ k G+ V++G vLae++
  gi|118431840|ref|NP_148556.2| 22 GKVVRVYKKPGDLVEKGEVLAEIE 45
                                   9*********************97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.011
                Biotin_lipoyl_2  4 sIaapvsGrVaql 16
                                   ++ +pvsGrV ++
  gi|118431840|ref|NP_148556.2| 52 EVESPVSGRVRSI 64
                                   689*******987 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 !   22.5   0.3   5.6e-08   8.3e-05      39      81 ..      22      65 ..      17      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.6e-08
                         RnfC_N 39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81
                                   G+  ++  k gd V+kG+++ae e     ++v ++vsG+V +i 
  gi|118431840|ref|NP_148556.2| 22 GKVVRVYKKPGDLVEKGEVLAEIEIeKAILEVESPVSGRVRSIV 65
                                   5556677899************9855679************985 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.0   1.5e-06    0.0022      33      73 ..      24      63 ..      20      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                                   EEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                          GCV_H 33 vvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73
                                   vv v  ++ g+ v+kge la +E  Ka+ ev +pvsG v  
  gi|118431840|ref|NP_148556.2| 24 VVRV-YKKPGDLVEKGEVLAEIEIEKAILEVESPVSGRVRS 63
                                   5555.4788****************************9965 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 !    8.8   0.1    0.0011       1.6      48      69 ..      25      46 ..      16      57 .. 0.83
   2 !    7.1   0.1    0.0037       5.5      47      70 ..      60      83 ..      48      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                   EEESS-TT-EEETTEEEEEEEE CS
                      QRPTase_N 48 vellvkDGervekgdvlleieG 69
                                   v +++k G+ vekg+vl+eie 
  gi|118431840|ref|NP_148556.2| 25 VRVYKKPGDLVEKGEVLAEIEI 46
                                   78999**************985 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0037
                                   EEEESS-TT-EEETTEEEEEEEEE CS
                      QRPTase_N 47 evellvkDGervekgdvlleieGn 70
                                   +v   v +Ge+v+++ v++ +eG 
  gi|118431840|ref|NP_148556.2| 60 RVRSIVGEGEEVTPESVVAVVEGH 83
                                   5777899***************95 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 ?   14.8   0.2   1.3e-05     0.019      39      96 ..      28      83 ..      14      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                   SS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE--EEE.E-TTSECEEECET CS
                ATP-synt_ab_Xtn 39 kvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiaeege.ytvedtiaevete 96
                                     k gd v++g++l++++ +++i   + v   v+g+v +i+ ege  t e ++a+ve +
  gi|118431840|ref|NP_148556.2| 28 YKKPGDLVEKGEVLAEIEIEKAI---LEVESPVSGRVRSIVGEGEeVTPESVVAVVEGH 83
                                   5689************9976665...2356668***********758889999999855 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 ?   10.0   0.1   0.00024      0.35      27      54 ..      21      47 ..      14      50 .. 0.89
   2 ?    3.2   0.1     0.029        44     109     139 ..      51      80 ..      47      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 27 eGwveklyvnatgdkVkkGqpLaelysp 54
                                    G v ++y +  gd V+kG+ Lae++ +
  gi|118431840|ref|NP_148556.2| 21 RGKVVRVYKK-PGDLVEKGEVLAEIEIE 47
                                   5889****99.*************9865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.029
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 109 vtvkapisGvVteknvreGqyvqpgdtlfti 139
                                    ++v++p+sG V +  v eG+ v+p+++++ +
  gi|118431840|ref|NP_148556.2|  51 LEVESPVSGRVRSI-VGEGEEVTPESVVAVV 80 
                                    67888899988765.8888888888887766 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   2.7e-05      0.04       7      58 ..      21      72 ..      17      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                         HlyD_3  7 dGvvvelnveegevvqagdelleiippdtll.veakvpaadlgsikkkgqkvt 58
                                    G+vv +  ++g+ v++g++l+ei  ++ +l ve  v+ + ++ + ++g +vt
  gi|118431840|ref|NP_148556.2| 21 RGKVVRVYKKPGDLVEKGEVLAEIEIEKAILeVESPVSGRVRSIV-GEGEEVT 72
                                   599*********************988544449999988888877.5888887 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 ?   13.1   0.1   3.8e-05     0.056      35      53 ..      26      44 ..      25      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                   EES--TT-EEBTTSEEEEE CS
                         PYNP_C 35 elhkklGdkVkkGeplati 53
                                   ++ kk+Gd V+kGe+la i
  gi|118431840|ref|NP_148556.2| 26 RVYKKPGDLVEKGEVLAEI 44
                                   678**************98 PP

>> T2SSB  Type II secretion system protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00063      0.94      28      52 ..      30      54 ..      23      56 .. 0.91
   2 ?    2.9   0.0     0.056        84      40      54 ..      69      83 ..      67      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00063
                                   -TT--SBTTEEEEEE-SSEEEEEET CS
                          T2SSB 28 reGdeiapgltleeIepdgvvlrfk 52
                                   + Gd +++g +l eIe ++++l+++
  gi|118431840|ref|NP_148556.2| 30 KPGDLVEKGEVLAEIEIEKAILEVE 54
                                   68********************986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.056
                                   EEE-SSEEEEEETTE CS
                          T2SSB 40 eeIepdgvvlrfkgq 54
                                   ee++p++vv  ++g+
  gi|118431840|ref|NP_148556.2| 69 EEVTPESVVAVVEGH 83
                                   79********99995 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 ?    8.7   0.0   0.00093       1.4      80     107 ..      21      48 ..       3      58 .. 0.85
   2 ?    3.2   0.1     0.047        70      25      46 ..      63      82 ..      51      84 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00093
                                    TTTTEEES----SEE-SEEEEEEE-HHH CS
                     PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdlea 107
                                    +g++ +++ k gd V++g+ l+e+++e+
  gi|118431840|ref|NP_148556.2|  21 RGKVVRVYKKPGDLVEKGEVLAEIEIEK 48 
                                    6899999*****************9986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.047
                                   -TTSEEEEEEE-SSEEEES--E CS
                     PTS_EIIA_1 25 kmlGdGvaiepsegkvvapvdG 46
                                    ++G+G  ++p+   vva v+G
  gi|118431840|ref|NP_148556.2| 63 SIVGEGEEVTPE--SVVAVVEG 82
                                   467777777773..47777666 PP

>> NQRA  Na(+)-translocating NADH-quinone reductase subunit A (NQRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   5.9e-05     0.088      44      91 ..      28      77 ..      20      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.9e-05
                           NQRA 44 kvkegdkVkkGqvlfedKknpgvl.ftspasGevvein.rGekRvlqsvv 91
                                     k gd V+kG+vl+e   ++ +l + sp+sG+v++i   Ge  + +svv
  gi|118431840|ref|NP_148556.2| 28 YKKPGDLVEKGEVLAEIEIEKAILeVESPVSGRVRSIVgEGEEVTPESVV 77
                                   5689***********988777765267********985256665555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 753.16
//
Query:       gi|14602012|ref|NP_148557.1|  [L=244]
Description: orotidine 5'-phosphate decarboxylase [Aeropyrum pernix K1]
Scores for complete 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-27   95.4   0.0    4.5e-27   95.1   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
  ------ inclusion threshold ------
       0.14   11.8   0.5       0.32   10.7   0.0    1.8  2  DUF3693    Phage related protein


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 !   95.1   0.0     5e-31   4.5e-27       2     223 ..      12     220 ..      11     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 5e-31
                                   EEEEEE-SSSH...HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHST CS
                     OMPdecase   2 nLclalDvata...relleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatag 79 
                                   ++++alD+a +   ++ll++a+ v    + +K+++++++  g+e ++a++a+l +    l ++D+K+aDIG++++++a+  
  gi|14602012|ref|NP_148557.1|  12 RVIVALDPARRgdvDRLLDMARLVCGVGAGIKVGLPMLALGGSE-ALAEAARLCKGG-GLRVLDLKLADIGYIMRLAAE-- 88 
                                   799******99999**************************9955.666666666555.5999****************8.. PP

                                   CHHHHTTESEEEEEGTGH.HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEECCC CS
                     OMPdecase  80 sarikewadivtvhavaG.kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfvaqe 159
                                       + + d+ ++ha++G ++ + +l+++++  g + l++++ ms++g+ ++ +      c++++ + +++ + +G+va +
  gi|14602012|ref|NP_148557.1|  89 --SLSRGFDAAIAHAFVGyEGGLVELKKTLDGLG-ARLVLVVSMSHPGSREVLD-----PCLDKLLAVARRVEPWGVVAPA 161
                                   ..478*************999************8.9*************88888.....9*********999********* PP

                                   HTH....HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
                     OMPdecase 160 tln....ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                                   t++    + + +  ++ ++l pg+g+         q  +p ++i   gad+ ivGR + +++dpv++++
  gi|14602012|ref|NP_148557.1| 162 TRPevvaRVR-EtLPTTVILSPGVGA---------QGGKPGDAICLGGADYEIVGRMVAGSPDPVSALR 220
                                   *996653223.246677777777776.........444566778889******************9987 PP

>> DUF3693  Phage related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.37   3.3e+03      30      46 ..      40      52 ..      32      63 .. 0.45
   2 ?   10.7   0.0   3.6e-05      0.32      25      52 ..     116     143 ..     111     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.37
                       DUF3693 30 avLvlgvgmalpgraqa 46
                                  a+  +g    lp++a +
  gi|14602012|ref|NP_148557.1| 40 AGIKVG----LPMLALG 52
                                  332223....3333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.6e-05
                       DUF3693  25 LnalaavLvlgvgmalpgraqalsipse 52 
                                   L +l+a Lvl+v+m++pg  ++l+ + +
  gi|14602012|ref|NP_148557.1| 116 LDGLGARLVLVVSMSHPGSREVLDPCLD 143
                                   5589**************8887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1847.09
//
Query:       gi|118431841|ref|NP_148558.2|  [L=186]
Description: orotate phosphoribosyltransferase [Aeropyrum pernix K1]
Scores for complete 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   0.2    2.4e-16   59.7   0.1    1.5  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0046   16.4   0.0     0.0058   16.1   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.19   11.2   0.0       0.31   10.5   0.0    1.4  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 !   59.7   0.1     4e-20   2.4e-16      32     131 ..      69     158 ..      51     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 4e-20
                                    EEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHH CS
                   Pribosyltran  32 vvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLk 111
                                    +v+g+a+gG+p+a  la +L  pl yvr +++ +++ +++          ++dp + +V++VDD+ +tG+++ + +e L+
  gi|118431841|ref|NP_148558.2|  69 AVIGVATGGLPWAAMLALRLSKPLGYVRPERKGHGTLSQV----------EGDPPKGRVVVVDDVATTGTSIAKSIEVLR 138
                                    8***********************************9999..........58**************************** PP

                                    CC-BSEEEEEEEEE-HHHHH CS
                   Pribosyltran 112 ekgpeevriavlvdkpatee 131
                                    + g ++  + vlvd+++++ 
  gi|118431841|ref|NP_148558.2| 139 SNGYTVGTALVLVDRGEGAG 158
                                    ****8666667779998876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.7e-07    0.0058     112     156 ..     105     149 ..      83     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.7e-07
                        UPRTase 112 ynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlv 156
                                    ++++  ++ + +v+++D v  TG s+a+ i++L+++g ++   lv
  gi|118431841|ref|NP_148558.2| 105 LSQVEGDPPKGRVVVVDDVATTGTSIAKSIEVLRSNGYTVGTALV 149
                                    556677888899***********************9998775444 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.2e-05      0.31     122     148 ..     115     141 ..     105     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.2e-05
                       PRTase_2 122 kelvLvDDEistGktalnliralqekl 148
                                    +++v+vDD ++tG+++++ i+ l+++ 
  gi|118431841|ref|NP_148558.2| 115 GRVVVVDDVATTGTSIAKSIEVLRSNG 141
                                    689***************999998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1405.45
//
Query:       gi|118431842|ref|NP_148559.2|  [L=207]
Description: hydrolase [Aeropyrum pernix K1]
Scores for 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-43  146.8   0.0    8.7e-43  146.5   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 !  146.5   0.0   4.8e-47   8.7e-43       1     164 [.      26     187 ..      26     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 4.8e-47
                Isochorismatase   1 talvviDmqndfv.eegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgaelv 79 
                                    ta+vv+Dmqndfv ++g   +++++a++e i++ll++ar ag++v++t+d+h     +gd++ + + +h++ gt+g+++v
  gi|118431842|ref|NP_148559.2|  26 TAVVVVDMQNDFVkPQGKLFVPTAPATIEPIRRLLEKARSAGVRVFYTQDTHY----EGDPEFEIWGEHVRYGTWGWRIV 101
                                    79***********9999999*********************************....*********************** PP

                Isochorismatase  80 pelaple.gdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelhda 158
                                    +el+p+e  d+vv Ktr+++f+gt ld++L+  g+k++v++G  +++CV++ta +a+ + y+vvv+ D+++al+  ++ a
  gi|118431842|ref|NP_148559.2| 102 EELKPVEgRDIVVMKTRYDGFYGTMLDDLLRVYGVKNLVIVGTVANICVLHTAGSAALRWYKVVVPLDGISALNDFDYHA 181
                                    *******99*****************************************************************999*** PP

                Isochorismatase 159 alkrlk 164
                                    al++++
  gi|118431842|ref|NP_148559.2| 182 ALRQIS 187
                                    **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1608.55
//
Query:       gi|118431843|ref|NP_148560.2|  [L=317]
Description: hypothetical protein APE_2352.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-10   39.8   0.0    3.7e-08   33.5   0.0    2.2  2  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0028        49      42      79 ..     130     167 ..     105     172 .. 0.81
   2 !   33.5   0.0   2.1e-12   3.7e-08       2      84 ..     210     292 ..     209     293 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0028
                            CCG  42 Gagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                    Ga  + +g e  +e+  +r ++ ++e+g++ ivt++p+
  gi|118431843|ref|NP_148560.2| 130 GAILYENGLESSFERHINRVYRRLREAGVERIVTIDPH 167
                                    77777888888999999999**************9997 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 2.1e-12
                            CCG   2 ayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacp 78 
                                    +++d+C+++r +    e+r++ ++  +  + e ++  +  +CCG +     +  la+++a+ +++++e +  ++iv+acp
  gi|118431843|ref|NP_148560.2| 210 VIHDPCYYARFEgvIGEPRRIAERA-GLRLKEPPRSgRMTYCCGGPVE-GLMPSLAKRIARARLQELEGV-SRKIVVACP 286
                                    68*****99999*9******99999.*******************998.555559**************8.899****** PP

                            CCG  79 gCllql 84 
                                     C ++l
  gi|118431843|ref|NP_148560.2| 287 ICMINL 292
                                    **9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2673.78
//
Query:       gi|14602016|ref|NP_148561.1|  [L=405]
Description: acyl-CoA dehydrogenase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-32  111.0   2.8      9e-32  110.4   2.8    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.7e-16   60.9   0.1    4.1e-16   59.6   0.1    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.1e-16   59.9   2.3    4.5e-16   59.3   2.3    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    3.3e-14   52.8   0.0    5.4e-14   52.2   0.0    1.3  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 !  110.4   2.8     2e-35     9e-32       1     149 [.     240     397 ..     240     398 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2e-35
                                   TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC.-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                 Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafg.kplidhqlvreklaemaaeleaarllvyraaealda 80 
                                   g+Gf+vame++   R++vaaa++g+ar ale+a+e++r+r+ fg +p++++q v++ +ae  a leaarllvyraa+++d+
  gi|14602016|ref|NP_148561.1| 240 GRGFYVAMEGFPLARILVAAANVGAARWALERAVEWSRERRLFGgRPIASFQGVSFSIAEAFAGLEAARLLVYRAAWTADR 320
                                   79******************************************9********************************8887 PP

                                   ----.......HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSS.S-HHHHHHHHHHHH CS
                 Acyl-CoA_dh_1  81 gkpd.......raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrige.Gtseiqrniiarrl 149
                                                 ++ aKl+a ++a  + ++ m+++Gg ++++e  v+r +  ++++ +g+ G+++i++ iiar l
  gi|14602016|ref|NP_148561.1| 321 YVRGeaareelNLYSASAKLKAVDTAFSIFQETMKIVGGISFTKEVDVHRGLLGTLSYLVGAeGAQNIMKYIIARDL 397
                                   66555668888899999*******************************************988***********976 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   9.2e-20   4.1e-16       3     113 .]       8     120 ..       6     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 9.2e-20
                                   HHHHHHHHHHHHHHHHT.HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH.H CS
                 Acyl-CoA_dh_N   3 eqealrdtvrefaeeel.aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal.l 81 
                                   + e +r+++r+ +e+ l   + ae+de+g  p e+++ l++lG+l++  pee gG+g+++leaai+aee++++d ++++ +
  gi|14602016|ref|NP_148561.1|   8 DLELFRESLRRGLEKLLgGGRWAEIDEAGVLPAETIRGLGALGVLALVCPEELGGQGGGWLEAAIAAEEIGYHDPSMSTaV 88 
                                   6789***********9977799*****************************************************999966 PP

                                   HHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                 Acyl-CoA_dh_N  82 lgvhsslvapailrfGteeqkrryLpklasge 113
                                   + + ++    ++ r+G++e     + k+a+ge
  gi|14602016|ref|NP_148561.1|  89 YTLLNNAWPFILSRHGSPEVAGGIVEKVAKGE 120
                                   666555554589*****************998 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   2.3     1e-19   4.5e-16       2     118 ..     256     370 ..     255     372 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 1e-19
                                   HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHH CS
                 Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtvedrae 82 
                                   ++aa+ +GaAr al+ +ve+ rer    +g+++a ++ + + +aea a l+AAr+l++raa++a +   +g++  +e+ + 
  gi|14602016|ref|NP_148561.1| 256 LVAAANVGAARWALERAVEWSRERRL-FGGRPIASFQGVSFSIAEAFAGLEAARLLVYRAAWTADR-YVRGEAAREELNLY 334
                                   79**********************99.9***********************************666.5566666899**** PP

                                   HHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHH CS
                 Acyl-CoA_dh_2  83 arraaalavelaiaavdalfeaaGgsalrkesplqR 118
                                   ++ a++ av++a ++ ++ ++++Gg + +ke  + R
  gi|14602016|ref|NP_148561.1| 335 SASAKLKAVDTAFSIFQETMKIVGGISFTKEVDVHR 370
                                   ****************************99998887 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 !   52.2   0.0   1.2e-17   5.4e-14       1      95 [.     124     226 ..     124     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.2e-17
                                   EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT.-SEE.....EEEEETS-------EEEEEEE..GG.... CS
                 Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaai.atla.....lvlartekpdrarglslflvprdap.... 71 
                                   ++a+TEp++Gsdva++kt  aer+g+ y+++GeKi i+++++  +++     l+lart+++  +rgls f+ + ++     
  gi|14602016|ref|NP_148561.1| 124 GIASTEPGGGSDVAGIKT-RAERSGDYYRVYGEKILISGVREaLETLdyggwLLLARTGGEG-HRGLSAFAFTGKWDgsla 202
                                   589***************.77777778***************6233356677*****88888.**********99995555 PP

                                   .GEEE-----BSS-TTS-EEEEEEE CS
                 Acyl-CoA_dh_M  72 .gvsvrrieeklGlrglptgelvfe 95 
                                    g++ + + +++G++g++tg l+++
  gi|14602016|ref|NP_148561.1| 203 sGLEYSIL-DTIGRHGISTGILRLD 226
                                   55555544.89**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3053.33
//
Query:       gi|118431844|ref|NP_148562.2|  [L=130]
Description: hypothetical protein APE_2356.1 [Aeropyrum pernix K1]
Scores for complete 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   31.9   3.0    1.9e-07   31.3   3.0    1.3  1  NfeD      NfeD-like C-terminal, partner-binding


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 !   31.3   3.0   1.1e-11   1.9e-07       2      84 .]      41     127 ..      40     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.1e-11
                                    XXXXXXXXXXXXXXXS---S..SS--S..S---GGTTSEEEEEE-B.S-EE..EEETTEEEEEE-.SS.B-TT-EEEEEE CS
                           NfeD   2 favvsvlllvllrplllkkl..kkkek.ktnaealiGkegvvledi.gtGr..vkvdGeeWsarsege.iekgerVrVve 74 
                                    +++vs ++l+l +  ++      +  k + + +al G +g+v+e   g Gr  v+++Ge W+ +   + + +g+ V+V +
  gi|118431844|ref|NP_148562.2|  41 AVMVSPIALFLAVAAAKAVEamGR--KpSVGPDALEGLKGRVVEVReG-GRvvVEIEGELWRGVLLRGsVRPGDVVVVRG 117
                                    566676777766644333221122..2348899***********5565.66336688*****9985445*********** PP

                                    E-SSSEEEEE CS
                           NfeD  75 veGltliVep 84 
                                     +Gl l Vep
  gi|118431844|ref|NP_148562.2| 118 SRGLLLLVEP 127
                                    *********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1053.49
//
Query:       gi|118431845|ref|NP_148563.2|  [L=227]
Description: hypothetical protein APE_2357.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1902.82
//
Query:       gi|118431846|ref|NP_148564.2|  [L=185]
Description: hypothetical protein APE_2359.1 [Aeropyrum pernix K1]
Scores for 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   51.7   0.0    1.2e-13   51.3   0.0    1.1  1  HD_3      HD domain
    1.3e-08   34.8   0.0    2.2e-08   34.0   0.0    1.4  1  HD_2      HD containing hydrolase-like enzyme
    5.6e-06   26.6   0.1    1.3e-05   25.4   0.1    1.7  1  HD        HD domain
  ------ inclusion threshold ------
       0.18   12.1   1.0        2.5    8.5   0.0    2.8  2  Nif11     Nif11 domain


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   2.6e-17   1.2e-13       4     125 ..      11     130 ..       8     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 2.6e-17
                           HD_3   4 LKfqkRqgwlqtg..rvreesvaeHmwrvalmalllseelk...ekvdiarvikmfLiHDlvEiltgDiispdelakeek 78 
                                    L +  R+gw+  g  ++ +e+vaeH +  a++a  ++  +     ++  ++++  +L HD++E++ gDi   +       
  gi|118431846|ref|NP_148564.2|  11 LSSLSRTGWMLRGvpHQLAETVAEHLFASAVIAGEIAWRARssgLQASPEKAVAIALYHDMAESVIGDISKRA-----GL 85 
                                    6667899**9988334567*************977765554222689**********************6655.....44 PP

                           HD_3  79 eeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDkl 125
                                    ++ ++ea+ r ++ lp +  e +++l+ EFee++++ea++a+  + l
  gi|118431846|ref|NP_148564.2|  86 SRAKREAEARAFASLPLS--EGVKNLFREFEEASSPEARIARVAELL 130
                                    556677777889999988..99******************8766655 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 !   34.0   0.0     5e-12   2.2e-08      21      98 ..      27      98 ..       5     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 5e-12
                           HD_2 21 treenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeireaykevEeeaee 98
                                      e+vaeH +  a+ia  +a  ++   g +  +e+++++alyHD++E ++GD+          +++a +e E++a  
  gi|118431846|ref|NP_148564.2| 27 QLAETVAEHLFASAVIAGEIAWRARSS-GLQASPEKAVAIALYHDMAESVIGDISK-----RAGLSRAKREAEARAFA 98
                                   45799***************9977766.78************************74.....34555555555555544 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   2.9e-09   1.3e-05       1     117 [.      32     128 ..      32     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.9e-09
                                    HHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                             HD   1 rleHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                    ++eH ++ a +a+++a +      ++ +e+++++aL+HD+++ ++gd                  g + ++++ + + ++
  gi|118431846|ref|NP_148564.2|  32 VAEHLFASAVIAGEIAWRARSsglQASPEKAVAIALYHDMAESVIGDI-------------SKRAGLSRAKREAEARAFA 98 
                                    579*************99988*************************93.............3445555555555555444 PP

                                    HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHH CS
                             HD  78 ledvaklirehheswegkkrprglaerqlslearivklaD 117
                                       +++ +++ ++  e          ++ s+eari+++a 
  gi|118431846|ref|NP_148564.2|  99 SLPLSEGVKNLFREFE----------EASSPEARIARVAE 128
                                    4446666666666665..........56677777777775 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.11   4.9e+02      18      34 ..     108     124 ..      60     129 .. 0.71
   2 ?    8.5   0.0   0.00055       2.5      28      42 ..     153     167 ..     146     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.11
                          Nif11  18 alreqlkacsdheevva 34 
                                    +l  ++  +s++e+++a
  gi|118431846|ref|NP_148564.2| 108 NLFREFEEASSPEARIA 124
                                    45567777888888776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00055
                          Nif11  28 dheevvalAkeaGye 42 
                                    + ee +alA+e+G e
  gi|118431846|ref|NP_148564.2| 153 SLEEALALAREWGLE 167
                                    789**********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1491.07
//
Query:       gi|118431847|ref|YP_874941.1|  [L=198]
Description: hypothetical protein APE_2360.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1515.97
//
Query:       gi|118431848|ref|NP_148565.2|  [L=279]
Description: hydrolase [Aeropyrum pernix K1]
Scores for 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-24   87.4   7.5    2.6e-24   87.1   7.5    1.1  1  Abhydrolase_6   Alpha/beta hydrolase family
    3.3e-18   66.3   0.0    2.8e-15   56.7   0.1    2.1  2  Abhydrolase_1   alpha/beta hydrolase fold
    1.3e-16   60.7   0.2    1.8e-16   60.1   0.2    1.2  1  Hydrolase_4     Serine aminopeptidase, S33
     0.0073   16.1   0.1        2.8    7.7   0.0    2.2  2  Abhydrolase_2   Phospholipase/Carboxylesterase
  ------ inclusion threshold ------
        0.1   12.2   0.0       0.18   11.4   0.0    1.3  1  Abhydro_lipase  Partial alpha/beta-hydrolase lipase region


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 !   87.1   7.5   7.2e-28   2.6e-24       1     219 [.      32     264 ..      32     265 .. 0.68

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 7.2e-28
                                    EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH...CHHHHHHHCCTT..TTSEEEEEETCHH CS
                  Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldled...ladlaalldelaagggpvvlvGHSlGG 76 
                                    +l+lHG+g ++++Wl  a+Laa l+a++  + pDl+GhG+s p   +++    + dl+al+ +++   g+v+l+G SlGG
  gi|118431848|ref|NP_148565.2|  32 ILMLHGLGENSRVWLhIARLAAGLGARI--VLPDLRGHGGSRPGQGGVSLeamAKDLEALVKREG--QGRVHLMGFSLGG 107
                                    79************6699*********9..9*******856666655544336788888888885..999********** PP

                                    HHHHHHHHCC.............EEEEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHC CS
                  Abhydrolase_6  77 alalaaapla...........lvvgvlldppptalpagllaaalelllallallrllawlsreplprlfladedadaawr 145
                                    +++l+a++             ++vg l  p   a+p g++a+a+   ++    +++ a  +        ++++ +  a++
  gi|118431848|ref|NP_148565.2| 108 FVVLEAVDKDilepgggfesaILVGALHRP---ADPEGMRARARLARERGVEEAAR-AIAA------AVYRGVNMNLAYQ 177
                                    *****6666688777775555555555555...77777766666666655554444.2322......5555555556666 PP

                                    HCCCGHHHHCCHHC............HTTCCHHTT-TTGCEEECTT-CHHHHCHHCCCH..STTEEETCE...SSS-HHH CS
                  Abhydrolase_6 146 arlarlaallaglg............llpaaawadlpvpllvlggeDplvprllerlla..qagarlpvvlpgaGHlphl 211
                                    a+l  l++  ++++            +++ +++++  ++++v+g++Dpl + lle++ +   ++ r+ vv++gaGHl+hl
  gi|118431848|ref|NP_148565.2| 178 AALKLLQRIGPHVYasiveelagrdyTRAFQRLTAEAPTTVVVGSRDPLAAGLLEEARRilGPRGRI-VVIEGAGHLVHL 256
                                    6666666555533322222111111122344555555555788*****99988777777777*****.************ PP

                                    HSHHHHHH CS
                  Abhydrolase_6 212 eepdevae 219
                                    e++ +++e
  gi|118431848|ref|NP_148565.2| 257 EAASRLIE 264
                                    77777665 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.1   7.8e-19   2.8e-15       2     107 ..      31     134 ..      30     171 .. 0.87
   2 !    7.9   0.0    0.0006       2.1     205     256 ..     208     258 ..     173     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 7.8e-19
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEET CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhS 81 
                                    ++++lhGl+++s vw    +a+  a  g++++l+DlrG+g S+p+        ++ ++a+dl++++ + g+++++l+G+S
  gi|118431848|ref|NP_148565.2|  31 TILMLHGLGENSRVWLH--IARLAAGLGARIVLPDLRGHGGSRPGQG----GVSLEAMAKDLEALVKREGQGRVHLMGFS 104
                                    69***************..***99999*******************5....689999*********************** PP

                                    HHHHHHHHHHHHH....GGGEEEEEEESEC CS
                  Abhydrolase_1  82 mGGmialayaaey....perVkalvllgai 107
                                    +GG+++l++  +          + +l+ga+
  gi|118431848|ref|NP_148565.2| 105 LGGFVVLEAVDKDilepGGGFESAILVGAL 134
                                    *******99887766666666666666664 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0006
                                    HCTHHHHS..EEEEEEETTCSSSCHHHHHHHHHC.HTSEEEEEEETCSSSHHHHS CS
                  Abhydrolase_1 205 relknvla..ptlvisgtsDplvppkaledlaql.lpkkrlvvisdagHlafleg 256
                                    ++    +a  pt v+ g+ Dpl+  + le+ ++   p+ r vvi++agHl++le 
  gi|118431848|ref|NP_148565.2| 208 QR---LTAeaPTTVVVGSRDPLAA-GLLEEARRIlGPRGRIVVIEGAGHLVHLEA 258
                                    22...22233*************6.88888888774446*************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.2     5e-20   1.8e-16       6     237 ..      31     257 ..      29     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 5e-20
                    Hydrolase_4   6 vvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSm 85 
                                    +++++HGl+e s+   ++a+  a  G  ++  D rGhG s + +g v s++ + +Dl+a+v    +++++ ++ l+G S+
  gi|118431848|ref|NP_148565.2|  31 TILMLHGLGENSRVWLHIARLAAGLGARIVLPDLRGHGGSRPGQGGV-SLEAMAKDLEALV----KREGQGRVHLMGFSL 105
                                    799**************************************888855.89*******9996....7788889******** PP

                    Hydrolase_4  86 GGliallyl....lrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayead 161
                                    GG+++l+++    l+    ++ +il++++ +++     p+ +++ ++l+ +   +    ++  a+ + r   +  ay+a 
  gi|118431848|ref|NP_148565.2| 106 GGFVVLEAVdkdiLEPGGGFESAILVGALHRPA----DPEGMRARARLARERGVEE--AARAIAAAVYRGVNMNLAYQAA 179
                                    *********9887777779***********999....4677777555555544443..4477888899999999999999 PP

                    Hydrolase_4 162 plvhgkitvrlllelld..amkrleeraakit..lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnE 237
                                      + ++i  ++++++++  a+ + ++  +++t  +P+ ++ G++D++   +  +e+ + lg  + ++ +++g+ H ++ E
  gi|118431848|ref|NP_148565.2| 180 LKLLQRIGPHVYASIVEelAGRDYTRAFQRLTaeAPTTVVVGSRDPLAA-GLLEEARRILG-PRGRIVVIEGAGHLVHLE 257
                                    9999999999999999755788999999999999*************99.44555555555.69***********99998 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00077       2.8      15      36 ..      30      51 ..      20      63 .. 0.81
   2 !    6.2   0.0    0.0022       7.7     104     123 ..      95     114 ..      79     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00077
                                   EEEEEE--TT--SHHHHHHHH. CS
                  Abhydrolase_2 15 avviflHGlGdsghawaeaakt 36
                                    ++++lHGlG++   w  +a+ 
  gi|118431848|ref|NP_148565.2| 30 DTILMLHGLGENSRVWLHIARL 51
                                   69************99998874 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0022
                                    GGGEEEEEETHHHHHHHHHH CS
                  Abhydrolase_2 104 ssriiigGFSqGaalalyla 123
                                    + r+ ++GFS G+ ++l+++
  gi|118431848|ref|NP_148565.2|  95 QGRVHLMGFSLGGFVVLEAV 114
                                    57999************986 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.1e-05      0.18      42      61 ..      27      46 ..       5      48 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.1e-05
                 Abhydro_lipase 42 ekkpvVlLqHGLlasSevwv 61
                                    ++  +l+ HGL ++S vw+
  gi|118431848|ref|NP_148565.2| 27 WGGDTILMLHGLGENSRVWL 46
                                   467789*************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.61
# Mc/sec: 1380.96
//
Query:       gi|118431849|ref|NP_148566.2|  [L=499]
Description: hypothetical protein APE_2362.1 [Aeropyrum pernix K1]
Scores for complete 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-41  141.3   0.1    6.5e-41  140.4   0.1    1.4  1  Carb_kinase  Carbohydrate kinase
    4.1e-38  130.9   1.9    7.2e-38  130.1   1.9    1.4  1  YjeF_N       YjeF-related protein N-terminus


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 !  140.4   0.1   7.2e-45   6.5e-41       1     242 [.     254     490 ..     254     492 .. 0.90

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 7.2e-45
                                    EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SSS CS
                    Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgrd 80 
                                    vlv+gGs++y GA++laalaa ++g++lv  a      a+l  + pe++   ++e+++       er++avv GpG+g +
  gi|118431849|ref|NP_148566.2| 254 VLVVGGSSEYVGAPILAALAAYAAGVDLVYLASPFSREAAL--ARPEIVPRRMEEASR-----VVERVHAVVAGPGMGGE 326
                                    79******************************977766665..456666665554444.....599***********976 PP

                                    ..HCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEE CS
                    Carb_kinase  81 ..ekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavv 158
                                      +  +++l+ ++++ +p v+DAdgL+ la      +  +  +LTPh +E k Ll+  +      l +are+a++++a+ 
  gi|118431849|ref|NP_148566.2| 327 geDLLWEVLDAARKRGVPAVVDADGLKALARRG--DRLWGGAVLTPHRGEAKLLLGGED---LPPLRAAREIAARYGATT 401
                                    214456688888999999*************95..9999***************99888...77899************* PP

                                    EEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTS......SHHHHHHHHHHHHHHHHHHHCCCT-TS CS
                    Carb_kinase 159 llkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqne......asyeaaiaaawlhgaasdeaaekkgvg 232
                                    ++k  +d + speg +   + g + + +GG+GDvLaG+++++La  +      ++++ a+aa + +g+a++++a ++g+ 
  gi|118431849|ref|NP_148566.2| 402 IVKAPVDAVCSPEGRCRESPWGAPEMSVGGTGDVLAGVLAGFLARRRalgldpDPLNTAAAALYTVGKAGEDLATEEGL- 480
                                    ******************************************************************************9. PP

                                    -HCHHHHHHH CS
                    Carb_kinase 233 mlatelskii 242
                                    + + +l +++
  gi|118431849|ref|NP_148566.2| 481 VSPLRLVEAV 490
                                    8888887765 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   1.9   8.1e-42   7.2e-38       3     171 .]      37     202 ..      35     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 8.1e-42
                         YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralellkka 81 
                                     Lmenag ava vl+ ll +  +++kv vl+G+g nGgdg+aaAr La +ga+V++ l++++    +  a+++l+ +++ 
  gi|118431849|ref|NP_148566.2|  37 LLMENAGNAVAGVLECLL-GGLQGAKVAVLAGKGGNGGDGIAAARRLAARGARVEIHLTHPRGeVKHPAARTMLKGVEAS 115
                                    59****************.79***********************************66666553888899999******* PP

                         YjeF_N  82 ggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkadv 161
                                    +++v+e   +  l+      vd v+DAllGig++g lr+++++++e  n+++ + ++vD+P G+d+dtG+  + av++d+
  gi|118431849|ref|NP_148566.2| 116 RVEVLEPGAPGWLDL---GGVDAVVDALLGIGVKGGLRGSVKAAAEAYNKAGGLKISVDVPTGVDPDTGDAVEGAVRSDY 192
                                    *****8887776653...58************************************************************ PP

                         YjeF_N 162 tvtfgapkrg 171
                                    tv+++ pk+g
  gi|118431849|ref|NP_148566.2| 193 TVSMHKPKKG 202
                                    ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3611.80
//
Query:       gi|118431850|ref|NP_148567.2|  [L=147]
Description: hypothetical protein APE_2365.1 [Aeropyrum pernix K1]
Scores for 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-14   51.7   0.2    1.2e-13   51.3   0.2    1.1  1  PIN_9          PIN like domain
    2.3e-08   34.4   0.0      3e-08   34.0   0.0    1.2  1  Fcf1           Fcf1
    2.2e-05   24.5   0.0    2.9e-05   24.1   0.0    1.2  1  NYN_YacP       YacP-like NYN domain
     0.0001   22.2   0.0    0.00016   21.6   0.0    1.4  1  5_3_exonuc_N   5'-3' exonuclease, N-terminal resolvase-like d
     0.0017   18.9   0.1     0.0023   18.4   0.1    1.3  1  PIN            PIN domain
  ------ inclusion threshold ------
      0.039   14.3   0.1       0.28   11.5   0.0    2.1  2  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
       0.07   13.4   0.1       0.57   10.5   0.1    2.1  1  PIN_4          PIN domain
      0.084   13.1   0.1        1.1    9.5   0.1    2.0  1  Hydrolase      haloacid dehalogenase-like hydrolase


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 !   51.3   0.2   5.5e-17   1.2e-13       1     115 [.      13     134 ..      13     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 5.5e-17
                          PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgk.ertaakvalsLaer..ceiveaeeekaD 77 
                                    v+lD+n L++ +   +     le +  s +  + ++v++EL+ la+  + +   + a+ al+L ++  +e++e+e+++aD
  gi|118431850|ref|NP_148567.2|  13 VLLDSNTLILMASGRIAPSMILEAINSSFKPATTSTVVAELRGLAEIHRTRlLGRRAQTALRLLQQmgVEVIETESRDAD 92 
                                    789***********99999999999999****************887777525689999**998776899********** PP

                          PIN_9  78 dailelakeld....aavlvTnDreLkkrllekgipvilLRq 115
                                    d + e a++l+      +++T+Dr L++rl+++g+p+i+ R 
  gi|118431850|ref|NP_148567.2|  93 DSLEEAAEKLKvegaKVYVATSDRSLRRRLRRRGVPTIYYRS 134
                                    ********998333235889*******************995 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.3e-11     3e-08       3      98 ..      37     140 ..      35     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.3e-11
                                    CTS-EEEEEEHHHHHHHHHCT...........-HHHHHHHTTSEEE----SS---HHHHHHHHH-B.TB-TT-EEEE-S- CS
                           Fcf1   3 LqakvkpliTqCviaeleklg.........kklkealkiaktferlkCnhkkptsaddClvsvvkk.kknkkryivAtqD 72 
                                    +++++kp +T+ v+ael+ l          ++ ++al++++++ +   +  ++ +add l++  +k k +  + +vAt D
  gi|118431850|ref|NP_148567.2|  37 INSSFKPATTSTVVAELRGLAeihrtrllgRRAQTALRLLQQMGVEVIET-ESRDADDSLEEAAEKlKVEGAKVYVATSD 115
                                    56789**************9966554444444889999999755555555.779***********8545678888***** PP

                                    HHHHHHHHTSTT--EEEEE--EEEE- CS
                           Fcf1  73 kdlrrrlrkipgvPilyikrsvmvlE 98 
                                    ++lrrrlr+  gvP +y+++s   lE
  gi|118431850|ref|NP_148567.2| 116 RSLRRRLRR-RGVPTIYYRSSEARLE 140
                                    ********7.6********9999888 PP

>> NYN_YacP  YacP-like NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.3e-08   2.9e-05      66     116 ..      79     128 ..      66     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.3e-08
                                    .T-EEEE--TT--HHHHHHHHHHHC--TT--EEEE---CSSCTGGGGCTEE CS
                       NYN_YacP  66 eglevvytkegetADsvIeklvaelrkekeevvVvTSDraeqlvvfgkGAl 116
                                     g+ev+ t++ ++AD+  e+ +++l+ e  +v+V+TSDr  ++  +++G+ 
  gi|118431850|ref|NP_148567.2|  79 MGVEVIETES-RDADDSLEEAAEKLKVEGAKVYVATSDRSLRRRLRRRGVP 128
                                    4889998988.9******************************999999975 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   7.2e-08   0.00016      83     134 ..      69     122 ..      60     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.2e-08
                   5_3_exonuc_N  83 lplikevlealgikvlevegyEADDvigtlakrae.e.egvvivsgDkDllQlv 134
                                     +   ++l+++g++v+e e  +ADD +   a++ + e ++v++ ++D+ l   +
  gi|118431850|ref|NP_148567.2|  69 AQTALRLLQQMGVEVIETESRDADDSLEEAAEKLKvEgAKVYVATSDRSLRRRL 122
                                    5667789**************************7756456********986655 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1     1e-06    0.0023       1      85 [.      13      98 ..      13     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-06
                                   EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHH CS
                            PIN  1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaeea 81
                                   ++lD++ li + +g+     +++++++  + +t++ v+aEl+  ++  +++ + +++ ++l+ll   +++++++ +++a+  
  gi|118431850|ref|NP_148567.2| 13 VLLDSNTLILMASGRIAPSMILEAINSSFKPATTSTVVAELRGLAEIHRTRLLGRRAQTALRLLqQMGVEVIETESRDADDS 94
                                   689******999******************************999997788888888888888889*******777777665 PP

                                   HHHH CS
                            PIN 82 aeia 85
                                   +e a
  gi|118431850|ref|NP_148567.2| 95 LEEA 98
                                   5433 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.28      65      93 ..      70      98 ..      63     100 .. 0.89
   2 ?    2.2   0.0       0.1   2.3e+02      66      86 ..      97     118 ..      95     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                   HHHHHHHCTTTSEEEES-SSBHHHHHHHH CS
                  Nitro_FeMo-Co 65 pralakleaagievykgaggtveealkev 93
                                   + al+ l++ g+ev+++++++ ++ l+e 
  gi|118431850|ref|NP_148567.2| 70 QTALRLLQQMGVEVIETESRDADDSLEEA 98
                                   68999*******************99986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
                                    HHHHHHCTTTSEEEES.-SSBH CS
                  Nitro_FeMo-Co  66 ralakleaagievykg.aggtv 86 
                                    +a++kl+ +g +vy++ +++++
  gi|118431850|ref|NP_148567.2|  97 EAAEKLKVEGAKVYVAtSDRSL 118
                                    799***********98666665 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00026      0.57      27      98 ..      46     102 ..      13     133 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00026
                          PIN_4  27 PitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsaeelpeeeseseknDnrIlavalel 98 
                                      tV+ EL++l + +++r l+r+a+ a+rll+++  +             ++  e  s+ +D++  ++a +l
  gi|118431850|ref|NP_148567.2|  46 TSTVVAELRGLAEIHRTRLLGRRAQTALRLLQQMGVEV------------IET-E--SRDADDSLEEAAEKL 102
                                    56888888888888888888888888888887763332............111.1..112333333333333 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00048       1.1     103     143 ..      66     115 ..       8     135 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00048
                                    H..........TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESS CS
                                    x..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 103 l..........qaralavftiadplkvkpeaaeavasLkaagievvlltgd 143
                                               q+  ++v++ +      + ++ea ++Lk  g +v+++t+d
  gi|118431850|ref|NP_148567.2|  66 GrraqtalrllQQMGVEVIETESR-DADDSLEEAAEKLKVEGAKVYVATSD 115
                                    022222222222222222222211.23344445555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1059.25
//
Query:       gi|118431851|ref|NP_148568.2|  [L=414]
Description: translation initiation factor IF-2 [Aeropyrum pernix K1]
Scores for complete 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  108.4   1.0    4.2e-31  107.0   1.0    1.8  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
    4.6e-30  104.6   0.0    2.7e-29  102.1   0.0    1.9  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    2.6e-08   34.1   3.4      8e-08   32.6   2.3    2.3  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    7.1e-05   22.8   0.1     0.0015   18.4   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
    0.00023   21.2   0.0    0.00053   20.0   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0037   17.0   0.1       0.88    9.3   0.0    2.5  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
  ------ inclusion threshold ------
      0.027   13.4   0.2       0.36    9.8   0.0    2.1  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.045   13.3   1.5        4.2    6.9   0.1    2.6  2  FeoB_N        Ferrous iron transport protein B
       0.12   12.4   0.0       0.23   11.5   0.0    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.18   11.9   0.0       0.26   11.3   0.0    1.5  1  Dynamin_N     Dynamin family


Domain annotation for each model (and alignments):
>> 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 !  107.0   1.0   2.3e-34   4.2e-31       2      86 .]     329     413 ..     328     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 2.3e-34
                                    EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEE CS
                         eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLi 81 
                                    +l+ie +lle++vg+kee +ve+++++E+Lml++G+a t gvvt++ kde++v+L++Pv+++ ++++alsRr+ +rWrLi
  gi|118431851|ref|NP_148568.2| 329 TLRIEHHLLEKVVGMKEEARVEPIRRGEMLMLSVGTAITLGVVTRAGKDEIEVQLRRPVVTWPKARVALSRRIMGRWRLI 408
                                    699***************************************************************************** PP

                                    EEEEE CS
                         eIF2_C  82 GwGei 86 
                                    GwG i
  gi|118431851|ref|NP_148568.2| 409 GWGLI 413
                                    ***76 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 !  102.1   0.0   1.5e-32   2.7e-29       4     193 ..      11     203 ..       8     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.5e-32
                                    EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................... CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................... 64 
                                    +nig++ghvDhGKtTL+ +L+    +               +++eE +rg+Tik   +  e                   
  gi|118431851|ref|NP_148568.2|  11 VNIGVVGHVDHGKTTLVQALTGVWTM---------------RHSEEIRRGMTIKLGYADGEvwecegcgfperfspepvc 75 
                                    8*******************944444...............345899********99999999999************** PP

                                    ......TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST. CS
                       GTP_EFTU  65 ......ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl. 135
                                          + + +++++ +D+PGH+  + ++  g++ +Dga+lvv+a+e  ++pqt+e+l  +   g++ i+++ NK+D + 
  gi|118431851|ref|NP_148568.2|  76 ecdpqaSASLRRRVSYVDAPGHEILMATMLSGAALMDGALLVVAANEPcPQPQTKEHLVALEIIGIKnIVIVQNKVDVVs 155
                                    **998659999***********************************9879*****************999999******8 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                    +++ ke+ +e+  ++      ++   ++g+   p++++Salk  +++++l a+ +++p
  gi|118431851|ref|NP_148568.2| 156 RERAKESYQEIL-NF------IKGTIAEGS---PIIPVSALKRANIDAVLAAIEKFIP 203
                                    888999999999.67......677777776...********************99998 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 ?   -0.9   0.0       1.2   2.2e+03      13      21 ..      42      50 ..      38      57 .. 0.74
   2 !   32.6   2.3   4.4e-11     8e-08       1      65 [.     235     307 ..     235     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                                   EETTEEEEE CS
                    GTP_EFTU_D2 13 lkkGdevri 21
                                   +++G+++++
  gi|118431851|ref|NP_148568.2| 42 IRRGMTIKL 50
                                   788888887 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 4.4e-11
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEE........EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke........ivtrissletfhededeavaganaGvivaikgled 65 
                                    G+v++g++++G++++Gde++i + + + +k+         +t+i+sl     +++ea++g+ + +++ +++  +
  gi|118431851|ref|NP_148568.2| 235 GGVVGGSIIQGVFRVGDEIEISPgVAV-RKPggrveyvrLHTTITSLRFGSIEVEEARPGGLVAIGTQLDPSVT 307
                                    89*********************8888.7778*********************************999887655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.1   1.8e+02     104     126 ..      15      37 ..       9      47 .. 0.74
   2 !   18.4   0.0   8.5e-07    0.0015      13      97 ..     108     198 ..      83     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.1
                                    EECSTTSSHHHHHHHHCTT---- CS
                    RsgA_GTPase 104 lvGqSGvGKStLinallpelelk 126
                                    +vG+   GK+tL+ al++  +++
  gi|118431851|ref|NP_148568.2|  15 VVGHVDHGKTTLVQALTGVWTMR 37 
                                    5788889*********9964443 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 8.5e-07
                                    EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TT CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsak 85 
                                    +a +d +l+vv+++ep  +++  +  Lv++e  gi ++viv nK+D++++e+      e+ ++ + + a g +++ vsa 
  gi|118431851|ref|NP_148568.2| 108 AALMDGALLVVAANEPCPQPQ-TKEHLVALEIIGIkNIVIVQNKVDVVSRERakesyqEILNFIKGTIAEGSPIIPVSAL 186
                                    8889**********7777776.57789********7789999********996664444444444555667788888888 PP

                                    THTTHHHHHHHC CS
                    RsgA_GTPase  86 tkegleelkell 97 
                                    ++++++++ +++
  gi|118431851|ref|NP_148568.2| 187 KRANIDAVLAAI 198
                                    888887776665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     3e-07   0.00053       1      96 [.      12     131 ..      12     150 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3e-07
                                    EEEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEE.ET..........................TEEEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvk.lk..........................gkeiel 50 
                                    ++++vG+   GK+tL++altg    +   + + g T++  ++  + ++                          ++++  
  gi|118431851|ref|NP_148568.2|  12 NIGVVGHVDHGKTTLVQALTGVwtmRHSEEIRRGMTIKLGYADGEvWEcegcgfperfspepvcecdpqasaslRRRVSY 91 
                                    599******************76334444555688888887776642233444444444444444444444444445*** PP

                                    EECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT....TTCSHHHHHH CS
                       MMR_HSR1  51 vDtpGliegaseekglgkaflalee.adlillvvdas....eeklkpldee 96 
                                    vD pG  e       l  ++l+    +d +llvv a+    +    p+ +e
  gi|118431851|ref|NP_148568.2|  92 VDAPG-HE------ILMATMLSGAAlMDGALLVVAANepcpQ----PQTKE 131
                                    *****.44......6888888766658999999997743331....22222 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00049      0.88       4      23 ..      13      32 ..      11      44 .. 0.87
   2 !    5.1   0.1    0.0096        17      67     142 ..     114     199 ..      83     200 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00049
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   i ++G+v+ GKttL qal+g
  gi|118431851|ref|NP_148568.2| 13 IGVVGHVDHGKTTLVQALTG 32
                                   5589**************87 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0096
                      PduV-EutP  67 ialvqdateeesvfppgfasvfnkeviGi......itkidlaedeenieaveelLks.....aGaekifevsavekegie 135
                                      lv++a +e +  p++  ++++ e+iGi        k+d+++ e + e  +e L+      a  + i+ vsa+++ +i+
  gi|118431851|ref|NP_148568.2| 114 ALLVVAA-NEPCPQPQTKEHLVALEIIGIknivivQNKVDVVSRERAKESYQEILNFikgtiAEGSPIIPVSALKRANID 192
                                    3344333.344556666666666677775332211469999977777777777776421111445679************ PP

                      PduV-EutP 136 ellkyle 142
                                     +l+ +e
  gi|118431851|ref|NP_148568.2| 193 AVLAAIE 199
                                    9999887 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 ?    1.1   0.0     0.087   1.6e+02      31      51 ..      12      32 ..       8      40 .. 0.86
   2 ?    9.8   0.0    0.0002      0.36     165     229 ..     138     202 ..     127     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.087
                                   EEEEEE-TTSSHHHHHHHHHH CS
                           MeaB 31 vvGltGvPGaGkstlvealgl 51
                                    +G+ G    Gk tlv+al+ 
  gi|118431851|ref|NP_148568.2| 12 NIGVVGHVDHGKTTLVQALTG 32
                                   59****************985 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                                    CHHH-SEEEE.E---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHH CS
                           MeaB 165 ileiaDiivv.nkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehr 229
                                    i+ i +i++v nk D    e+a++ ++ +l+  + + +e  ++++ +sa++   id +++aie++ 
  gi|118431851|ref|NP_148568.2| 138 IIGIKNIVIVqNKVDVVSRERAKESYQEILNFIKGTIAEG-SPIIPVSALKRANIDAVLAAIEKFI 202
                                    556666655549********************99987775.56999*****************985 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 ?    6.9   0.1    0.0023       4.2       2      23 ..      12      33 ..      11      36 .. 0.91
   2 ?    4.8   0.2      0.01        18     106     156 .]     142     198 ..     128     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                                   EEEEEESTTSSHHHHHHHHHTT CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                   ++ +vG  + Gkttl+ altg+
  gi|118431851|ref|NP_148568.2| 12 NIGVVGHVDHGKTTLVQALTGV 33
                                   6889****************96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                                    SSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHHHH CS
                         FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellkai 156
                                    +++v++ n++d++++++ +   +++ + +      g p++++sa k+ +i+++l+ai
  gi|118431851|ref|NP_148568.2| 142 KNIVIVQNKVDVVSRERAKESYQEILNFIkgtiaeGSPIIPVSALKRANIDAVLAAI 198
                                    5788999******9999998888877665433444789*************998875 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 ?   11.5   0.0   0.00013      0.23      58     100 ..     144     198 ..     140     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                   MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                     ++v NK+D +s e  +e ++e            + ++++Sa k+ n+d+++ +i
  gi|118431851|ref|NP_148568.2| 144 IVIVQNKVDVVSRERAKESYQEilnfikgtiaegSPIIPVSALKRANIDAVLAAI 198
                                    68899***********9999978899999999877999***********998876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.26       1      30 [.      13      42 ..      13     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnp 30
                                   i vvG++ +GK++++ aL+g   +  ++++
  gi|118431851|ref|NP_148568.2| 13 IGVVGHVDHGKTTLVQALTGVWTMRHSEEI 42
                                   79******************8766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3163.78
//
Query:       gi|118431852|ref|NP_148569.2|  [L=235]
Description: 30S ribosomal protein S6 [Aeropyrum pernix K1]
Scores for 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-24   84.5   0.0    1.5e-23   83.1   0.0    1.7  1  Ribosomal_S6e  Ribosomal protein S6e
  ------ inclusion threshold ------
      0.012   15.3   0.1      0.029   14.1   0.1    1.6  1  DUF2922        Protein of unknown function (DUF2922)


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 !   83.1   0.0   1.7e-27   1.5e-23      12     103 ..     123     211 ..     117     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1.7e-27
                                    EEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTSSSS-SSSSS-E CS
                  Ribosomal_S6e  12 kqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskggvgyrprrkGer 91 
                                    k+ +i v +    +l g +ig+ +dg+++G  ++g ++ki gg+d +G+pm++gv+++gr ++Ll++  +g++pr++Ger
  gi|118431852|ref|NP_148569.2| 123 KSWQIAVPDDVHVKLAGLEIGDVFDGGLIG--MPGLKFKIRGGTDATGIPMHPGVPGSGRYKVLLAG-PPGFHPRERGER 199
                                    556677766777899***************..**********************************9.************ PP

                                    EEEEEE-SB--S CS
                  Ribosomal_S6e  92 krksvrGcivsa 103
                                    +rksvrG+++ +
  gi|118431852|ref|NP_148569.2| 200 RRKSVRGRMIPD 211
                                    ********9953 PP

>> DUF2922  Protein of unknown function (DUF2922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.3e-06     0.029       3      38 ..      70     106 ..      69     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-06
                        DUF2922   3 LeLtFkteegktvtlsip.npkedlteaeVkaaMdlI 38 
                                    L+L+F+t +gk+v++  + ++ke+l +  V+  M+l+
  gi|118431852|ref|NP_148569.2|  70 LTLRFTTPDGKKVKVPFKaEVKEGLEDNVVEVNMELL 106
                                    9***************9658**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1782.47
//
Query:       gi|14602026|ref|NP_148571.1|  [L=617]
Description: translation initiation factor IF-2 [Aeropyrum pernix K1]
Scores for 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-37  124.8   0.2    2.6e-36  123.4   0.2    1.8  1  GTP_EFTU_D4  Elongation factor Tu domain 4
    3.2e-31  108.4   0.0    1.4e-30  106.3   0.0    1.9  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.9e-21   76.1   0.0    4.1e-21   75.1   0.0    1.5  1  IF-2         Translation-initiation factor 2
    3.4e-13   49.8   2.8    8.3e-13   48.5   0.3    2.6  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.7e-07   31.3   0.0    4.8e-07   29.9   0.0    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.022   15.0   0.0    1.5  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.085   12.6   0.0       0.42   10.3   0.0    2.2  2  ATP_bind_1   Conserved hypothetical ATP binding protein
        0.1   12.2   0.0       0.44   10.2   0.0    2.1  1  STAS         STAS domain
       0.18   11.4   0.0        1.2    8.7   0.0    2.4  2  Ras          Ras family


Domain annotation for each model (and alignments):
>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.2   1.3e-39   2.6e-36       1      86 []     475     561 ..     475     561 .. 0.99

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1.3e-39
                                   S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-.TTTS-- CS
                   GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki.vGrqik 80 
                                   rPgk++ilpg+vfrrsdpaivGvevlgGvi+pg+++++++Gre+G+i++i+d++++leea+ G+ va+si+g+i +Gr+++
  gi|14602026|ref|NP_148571.1| 475 RPGKFRILPGYVFRRSDPAIVGVEVLGGVIRPGYPVMDSQGRELGRIMAIKDRDRSLEEARLGAAVAVSIQGRIlIGRHAN 555
                                   7******************************************************************************** PP

                                   TT-EEE CS
                   GTP_EFTU_D4  81 egdily 86 
                                   egdily
  gi|14602026|ref|NP_148571.1| 556 EGDILY 561
                                   *****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 !  106.3   0.0   7.2e-34   1.4e-30       5     190 ..      18     225 ..      15     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 7.2e-34
                                   EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHH CS
                      GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFsk 85 
                                    ++++ghvDhGKtTL+d++  ++ a +++g  ++ +      +++    i    + +    +     + +iDtPGH+ Fs+
  gi|14602026|ref|NP_148571.1|  18 IVVVLGHVDHGKTTLLDKIRRTAVAAKEAGGITQ-HIGASIVPADVIEKIAEPLKKVIPV-KLVIPGLLFIDTPGHELFSN 96 
                                   589*****************99999888777664.5567777777777777666655544.477999************** PP

                                   HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHHHH.. CS
                      GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqklsrk.. 153
                                      rg +v+D+a+lvvd++eG +pqt e l+l+++++vp+ ++ NK+Dr+           +++++++  +v++ l+++  
  gi|14602026|ref|NP_148571.1|  97 LRRRGGSVADFAILVVDIMEGFKPQTYEALELLKERRVPFLIAANKIDRIpgwkpnpdapfIETIRRQDPKVREILEQRvy 177
                                   ****************************************************99999888855555555555555544432 PP

                                   ..HHHHHHHHHTTT.............TTEEEEEEBTTTTBTHHHHHHHHHH CS
                      GTP_EFTU 154 ..eeklekygekge.............kevpvvfgSalkgegvktllealve 190
                                      +k+ ++                  +++ +v++Sa +geg+ +ll +l  
  gi|14602026|ref|NP_148571.1| 178 eiVGKMYEA----GlpaelftrikdfrRKIAIVPVSARTGEGIPELLAVLAG 225
                                   222333333....2455588888888899******************98875 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   2.1e-24   4.1e-21       4     105 .]     353     455 ..     347     455 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.1e-24
                                   HHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST......EEEEEESSSCTH CS
                          IF-2   4 lfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn......aiiigFnvkvsk 78 
                                   ++ee+  ++++++v++kaD+ G+leAl eaL++ +     v+v  +++G++++sDv  a++++      +++++Fnvkv +
  gi|14602026|ref|NP_148571.1| 353 EIEELRFRTENIGVVVKADTLGTLEALVEALRRRG-----VPVRLADIGPVSRSDVLDAAVTRkidpylGVVLAFNVKVLP 428
                                   44444545599**********************84.....9******************9965588999************ PP

                                   HHHHCCCCCTSEEEEESSHHHHHHHHH CS
                          IF-2  79 kakklaekegvkirlynvIYkliddvk 105
                                   +a+++a++ gvki+  ++IYkli+d++
  gi|14602026|ref|NP_148571.1| 429 EAEEEASRAGVKIFRESMIYKLIEDYE 455
                                   ************************985 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.3   4.2e-16   8.3e-13       1      74 []     256     335 ..     256     335 .. 0.92
   2 ?    0.6   0.2      0.38   7.6e+02       3      59 ..     494     545 ..     493     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 4.2e-16
                                   EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCSGSSTT CS
                   GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea..........vaganaGvivaikgledaiivG 70 
                                   Gtv+++++y+G+lkk d ++++g  +    +ivtr+++l+++ + +d+           ++ a+aGv +a++gl+d +i+G
  gi|14602026|ref|NP_148571.1| 256 GTVVDAVIYDGVLKKEDIIVVGGrEG----PIVTRVRALLMPAPLQDIRsrearfvqvdRVYAAAGVRIAAPGLDD-VIAG 331
                                   9********************77544....8***********6666666***************************.**** PP

                                   CEEE CS
                   GTP_EFTU_D2  71 dtlt 74 
                                   ++++
  gi|14602026|ref|NP_148571.1| 332 SPIY 335
                                   9986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.38
                                   EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEE CS
                   GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGviva 59 
                                   ++++ v  G++++G  v+   +   +  +++ri ++      ++ea+ ga++ v + 
  gi|14602026|ref|NP_148571.1| 494 IVGVEVLGGVIRPGYPVMD--S---QGRELGRIMAIKDRDRSLEEARLGAAVAVSIQ 545
                                   6788899999999998887..4...33468999888888888888888888877765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.4e-10   4.8e-07       2     114 .]      19     142 ..      18     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.4e-10
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE..................EEEEECGGCSSHHHHHH CS
                      MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke..................ielvDtpGliegaseek 64 
                                   v+++G+   GK+tL+ ++ ++++ +++  g T++i    v  +  e                  + ++DtpG  e      
  gi|14602026|ref|NP_148571.1|  19 VVVLGHVDHGKTTLLDKIRRTAVAAKEAGGITQHIGASIVPADVIEkiaeplkkvipvklvipgLLFIDTPG-HE-----L 93 
                                   899*****************99999**********99988733222455677778888888888********.44.....2 PP

                                   HHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                      MMR_HSR1  65 glgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    +++  ++  + ad ++lvvd+  e++kp+  e  ell+e++ p+++++nk
  gi|14602026|ref|NP_148571.1|  94 -FSNLRRRGGSvADFAILVVDIM-EGFKPQTYEALELLKERRVPFLIAANK 142
                                   .222222222348********99.78**********************998 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 ?   15.0   0.0   1.1e-05     0.022       2     119 ..      19     144 ..      18     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                   EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSGGCT.TBTTTTCEEE.....EEEEE-SGGCTTTT CS
                           Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkikgve.ndkkvkkvkl.....niWDtaGqerfrsl 72 
                                   vv++G    GKt+ll+++ +  +  ke    ++ ig++++  +v   +++    kkv  vkl      + Dt G+e f++l
  gi|14602026|ref|NP_148571.1|  19 VVVLGHVDHGKTTLLDKIRRTAVAAKEaggiTQHIGASIVPADVI--EKIAePLKKVIPVKLvipglLFIDTPGHELFSNL 97 
                                   799****************99998876333368999999988874..33330233444455422332679*********** PP

                                   -HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                           Roc  73 hplylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                   ++   + a+ ailv+d  +  +  + ++ l+   + + p+++ +nkiD
  gi|14602026|ref|NP_148571.1|  98 RRRGGSVADFAILVVDIMEGFKP-QTYEALELLKErRVPFLIAANKID 144
                                   ****************7654443.33455555554146899999*999 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 ?   -1.9   0.0       1.2   2.4e+03       1      20 [.      21      40 ..      21      46 .. 0.80
   2 ?   10.3   0.0   0.00021      0.42      93     236 ..      83     224 ..      44     229 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                    ATP_bind_1  1 vvGpaGsGKttfvgalseil 20
                                  v+G++  GKtt+  ++  ++
  gi|14602026|ref|NP_148571.1| 21 VLGHVDHGKTTLLDKIRRTA 40
                                  7899999*****99887665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                    ATP_bind_1  93 yllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek. 172
                                   +l +DtPG   + +++  +         ++a  ++ +vD     +p     ++  al  + + ++P++++ nk+D +    
  gi|14602026|ref|NP_148571.1|  83 LLFIDTPGHELFSNLRRRGG--------SVADFAILVVDIMEGFKP-----QTYEALELLKERRVPFLIAANKIDRIPGWk 150
                                   55566666544444455555........333333333443333333.....333456777889************876434 PP

                    ATP_bind_1 173 ....lek.eleffedvealslllekee........ekykklaeaiaelleefalvlrflplssekeesiedllslid 236
                                       + + e  + +d++  + l+   +         + + l++++   +++f + + ++p+s++++e+i +ll+++ 
  gi|14602026|ref|NP_148571.1| 151 pnpdAPFiETIRRQDPKVREILE---QrvyeivgkMYEAGLPAELFTRIKDFRRKIAIVPVSARTGEGIPELLAVLA 224
                                   33432221222334444444444...14469999778889********************************99876 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00022      0.44      17      93 ..     332     400 ..     328     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                   EEESHHHHHHHHHHHHHHHHCCC........-SEEEEEEEEEEEE-HHHHHHHHHHHHHHHHTT-EEEEES--HHHH CS
                          STAS  17 gpidfanaesfkeklkravgeepervekkeslkslildlsavsfiDssGvraLkeilkelkrigvevvlvnikpevr 93 
                                   +pi++a +e+  +kl +av+ e       e+l++   +++ v   D   +++L+ +++ l+r+gv v l+ i p  r
  gi|14602026|ref|NP_148571.1| 332 SPIYAAESEEEARKLMEAVQREI------EELRFRTENIGVVVKAD--TLGTLEALVEALRRRGVPVRLADIGPVSR 400
                                   89******************994......44555555555556666..5779******************9998655 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00061       1.2      49     115 ..      82     144 ..      18     179 .. 0.70
   2 ?   -3.5   0.0       3.6   7.1e+03     131     158 ..     554     581 ..     552     582 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00061
                                   EEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTT CS
                           Ras  49 kleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvD 115
                                    l   DT G e f++lr+   + a+ ++lv di +   f+   + +e ++  +e++vp+++ +nK+D
  gi|14602026|ref|NP_148571.1|  82 GLLFIDTPGHELFSNLRRRGGSVADFAILVVDIME--GFKP--QTYEALELLKERRVPFLIAANKID 144
                                   35568***************************975..4553..455556666666688888899888 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.6
                                   HHHHTSEEEEEBTTTTCTHHHHHHHHHH CS
                           Ras 131 akelglkfletSAktnenveeafeellr 158
                                   a+e ++ ++++ A++++++ + f++l++
  gi|14602026|ref|NP_148571.1| 554 ANEGDILYTNVPAQHAYKILTEFKDLVS 581
                                   5666799999999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 4348.21
//
Query:       gi|14602027|ref|NP_148572.1|  [L=141]
Description: nucleoside diphosphate kinase [Aeropyrum pernix K1]
Scores for complete 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-57  192.3   0.0    3.5e-57  192.2   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2   0.0     2e-61   3.5e-57       1     135 []       4     138 ..       4     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 2e-61
                                   EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHH CS
                           NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaie 81 
                                   +rtl+++KPd+v+rglige++sr+e+kglkiva+km+rlt+e+aee+Y+ h++kpff elvef+tsgpvva+v+eg++a++
  gi|14602027|ref|NP_148572.1|   4 QRTLLVVKPDGVERGLIGEVVSRVERKGLKIVAMKMMRLTREKAEEFYSVHRDKPFFGELVEFITSGPVVAMVVEGDEAVS 84 
                                   79******************************************************************************* PP

                                   HHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                           NDK  82 kvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                   +vr +iG+t+ ++aapgtiR+df++++ +N+vH+Sds+es ere +++F+e+ei
  gi|14602027|ref|NP_148572.1|  85 VVRLMIGSTDGRKAAPGTIRGDFSLDIMKNIVHASDSPESFEREFRVLFSESEI 138
                                   **************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1026.75
//
Query:       gi|14602028|ref|NP_148573.1|  [L=221]
Description: hypothetical protein APE_2379 [Aeropyrum pernix K1]
Scores for 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-21   74.6  12.1    7.8e-21   74.4  12.1    1.0  1  LysE      LysE type translocator


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4  12.1   4.3e-25   7.8e-21       2     191 ..      21     210 ..      20     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 4.3e-25
                          LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlalrdak 82 
                                   s++lspGp  l  +  g+  g+ gg++valg++  ++ ++ll+l   + + +    + + l+++  ++ +++ +l + +a+
  gi|14602028|ref|NP_148573.1|  21 SGALSPGPLSLSAIVAGAYLGWIGGVFVALGHMAFELPFVLLLLKASSSIERHIKKLYRPLTTAISLFIIYFSLLSFDAAL 101
                                   689****************************************************************************** PP

                          LysE  83 ekkveaeksve...aslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfsllaflaar 160
                                   +  +   ++     as+++ f+ g++l+  N +++l+w+sv+  l++ a+  +  g  i++a++v+ +++w++lla ++++
  gi|14602028|ref|NP_148573.1| 102 KGPEAGGNAIPlepASYSSAFIIGVVLTGFNAHFLLWWVSVGFPLITGAARNPPLGPAIMYASHVWMDFVWLALLAGMGDV 182
                                   *99755555549999********************************889999**************************** PP

                          LysE 161 lsrrlsskkvlriinvvvgvlligfavklll 191
                                    s+   ++k   +++++vg++l++fa++l+ 
  gi|14602028|ref|NP_148573.1| 183 ASQFAPAYK---ALMALVGLMLLLFALDLMA 210
                                   *****9997...89***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); 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 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1716.00
//
Query:       gi|14602029|ref|NP_148574.1|  [L=63]
Description: 50S ribosomal protein L24 [Aeropyrum pernix K1]
Scores for 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   67.6   1.0    9.6e-19   67.4   1.0    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    2.2e-05   24.3   2.0    3.1e-05   23.8   2.0    1.3  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
    0.00052   19.9   1.0      0.051   13.6   0.1    2.1  2  DUF2116         Uncharacterized protein containing a Zn-ribbo
     0.0011   19.0   0.1     0.0015   18.6   0.1    1.2  1  YHS             YHS domain
     0.0062   16.8   0.0     0.0062   16.8   0.0    1.1  1  Ta0938          Ta0938
  ------ inclusion threshold ------
       0.19   12.1   0.0        0.2   12.0   0.0    1.1  1  NosL            NosL
       0.43   10.5   5.2        8.4    6.3   5.2    2.1  1  VATC            Vms1-associating treble clef domain


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 !   67.4   1.0   3.8e-22   9.6e-19       2      57 ..       3      59 ..       2      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.8e-22
                                  XX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-X CS
                Ribosomal_L24e  2 ktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRr 57
                                  k ++CsF+g +i+PG+G ++v + g+++ F+ssKc ++++k +r+P kl+W +++++
  gi|14602029|ref|NP_148574.1|  3 KSRTCSFCGGSIEPGTGLMYVLRNGQILWFCSSKCyKNFVKLRRKPDKLEWVRKVKK 59
                                  679********************************88999***********998876 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 !   23.8   2.0   1.2e-08   3.1e-05       2      40 ..       3      40 ..       2      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                        zf-FCS  2 vkkrCwfCkkyikgkpeftyvlendgvvgqFCStsClds 40
                                  ++++C+fC+  i+ ++    ++ ++g++  FCS+ C + 
  gi|14602029|ref|NP_148574.1|  3 KSRTCSFCGGSIEPGT-GLMYVLRNGQILWFCSSKCYKN 40
                                  689*************.689999*************775 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 !    5.5   0.1    0.0066        17       4      16 ..       5      17 ..       2      20 .. 0.84
   2 !   13.6   0.1     2e-05     0.051      19      40 ..      32      53 ..      27      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0066
                       DUF2116  4 kHCivCGkaIpld 16
                                  + C  CG +I+++
  gi|14602029|ref|NP_148574.1|  5 RTCSFCGGSIEPG 17
                                  77********986 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                       DUF2116 19 fCsekCqeeyekkrkkvarsqq 40
                                  fCs kC +++ k r+k  ++ +
  gi|14602029|ref|NP_148574.1| 32 FCSSKCYKNFVKLRRKPDKLEW 53
                                  9***************888776 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   5.7e-07    0.0015       6      37 ..      10      41 ..       9      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.7e-07
                           YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCkdkF 37
                                  cg ++++++   ++ ++G+   FcS +C+  F
  gi|14602029|ref|NP_148574.1| 10 CGGSIEPGTGLMYVLRNGQILWFCSSKCYKNF 41
                                  9999**************************99 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.4e-06    0.0062      13      63 ..       3      57 ..       1      63 [] 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.4e-06
                                  GGGS-SS---S-....--SS-B-TT--BSSS--SSSS-TTS-THHHHHHHHHHHS CS
                        Ta0938 13 kekgcalcgatw....gdyyeevdgeklffccdicakefvnllnevkkrtglski 63
                                  k++ c++cg++     g  y   +g+ l+fc   c k+fv l ++  k   + k+
  gi|14602029|ref|NP_148574.1|  3 KSRTCSFCGGSIepgtGLMYVLRNGQILWFCSSKCYKNFVKLRRKPDKLEWVRKV 57
                                  8899*****97434337899999*****************997776665555555 PP

>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     8e-05       0.2       6      55 ..       3      49 ..       1      58 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8e-05
                          NosL  6 aeaecdvCgMliaehpgpkgqifyededepakFcstrdlfafllepeerk 55
                                  ++++c++Cg  i+   g  g +++ ++++ ++Fcs+++  +f+  ++++ 
  gi|14602029|ref|NP_148574.1|  3 KSRTCSFCGGSIEP--G-TGLMYVLRNGQILWFCSSKCYKNFVKLRRKPD 49
                                  56789999988874..4.4556666679***********99998877755 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.2    0.0033       8.4       3      32 ..       4      38 ..       2      41 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0033
                          VATC  3 vlrCsiCgeslegkv...yFekfdf..rYCstkCl 32
                                   ++Cs+Cg s+e+ +   y  +      +Cs kC 
  gi|14602029|ref|NP_148574.1|  4 SRTCSFCGGSIEPGTglmYVLRNGQilWFCSSKCY 38
                                  589*********84433255444331158888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 478.78
//
Query:       gi|118431853|ref|NP_148575.2|  [L=82]
Description: 30S ribosomal protein S28 [Aeropyrum pernix K1]
Scores for complete 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-31  108.5   2.8    1.4e-31  108.2   2.8    1.1  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 !  108.2   2.8   7.9e-36   1.4e-31       4      64 .]      18      78 ..      15      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 7.9e-36
                                   EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                 Ribosomal_S28e  4 klAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                    +AeVi+++grtG++GevtqVrv++leg+dkgri++RnV GPvr GDiL+L+EterEAr+L
  gi|118431853|ref|NP_148575.2| 18 FPAEVIQIIGRTGVTGEVTQVRVRILEGRDKGRILTRNVIGPVRIGDILILRETEREARKL 78
                                   58**********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 633.42
//
Query:       gi|118431854|ref|NP_148576.2|  [L=79]
Description: hypothetical protein APE_2380.1 [Aeropyrum pernix K1]
Scores for 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-26   91.4   0.4    7.2e-26   91.2   0.4    1.0  1  SCFA_trans  Short chain fatty acid transporter


Domain annotation for each model (and alignments):
>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.4     4e-30   7.2e-26     382     453 .]       6      77 ..       3      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 4e-30
                     SCFA_trans 382 pilipaaqalGvdlGksvlaiayGdawtnliqPfwalPalaiaGlgardilGycitalilaglilviglvll 453
                                     il++a+  lGv++Gk+++a+++Gd+wtnl+qPfwa+P+l i+ ++ard++Gy+i+ +il + + +++l+l+
  gi|118431854|ref|NP_148576.2|   6 RILVRAGHELGVPIGKTIIAYGFGDSWTNLLQPFWAIPLLDITRTRARDVFGYTIALMILIAPVAAVTLTLI 77 
                                    699**************************************************************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 626.57
//
Query:       gi|118431855|ref|YP_874942.1|  [L=409]
Description: hypothetical protein APE_2381.1 [Aeropyrum pernix K1]
Scores for 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-114  381.8   9.4   5.7e-114  381.6   9.4    1.0  1  SCFA_trans  Short chain fatty acid transporter
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.072   12.9   0.0    1.7  1  DUF5596     Domain of unknown function (DUF5596)


Domain annotation for each model (and alignments):
>> SCFA_trans  Short chain fatty acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.6   9.4  6.3e-118  5.7e-114       3     382 ..      11     408 ..       9     409 .] 0.93

  Alignments for each domain:
  == domain 1  score: 381.6 bits;  conditional E-value: 6.3e-118
                     SCFA_trans   3 erlsaalvalvskylPdplifallltlvtfvlvlvltkqtavs.........lvdvwgnGfwnllsfamqmalilvtGqa 73 
                                    e +++al + v  ++Pdp+ifa+llt+++ vl l+l+ +             + + w+ Gfw+ll+f+mqm+lilvtG+ 
  gi|118431855|ref|YP_874942.1|  11 EAFGEALERRVRGVMPDPFIFAILLTFIAIVLDLILLRPIQHVglggtvkflVYSAWYGGFWKLLTFSMQMTLILVTGYV 90 
                                    6677888899999*******************999988765556899999977899************************ PP

                     SCFA_trans  74 lassklvkkllkkiaslakdtksavvlvtllaliaavinwGlGlvvgailakevar....rvkgldyalliaaayigl.l 148
                                    +a+++lv+++l++ia l++dtk+a+vl + +a+  +++ wGl l+ gaila+e+ r    r++ ++y++++ aay+gl l
  gi|118431855|ref|YP_874942.1|  91 IAYHPLVYRVLSRIAGLPRDTKQAAVLAAAVAIALSYLSWGLSLIGGAILAREIGRqaafRGRKIHYPVVVVAAYSGLgL 170
                                    ****************************************************9988333346899*************** PP

                     SCFA_trans 149 twhgGlsgsiPllvatpneplkkiavelvgreiiPvsetlfssynliilailivvlplitamlaPkkeevksidk...kl 225
                                    twh+Gl++s+Pll++tp+++l++++ el+g e+iP+s+t+f++y++i+ + +  +   i+ ++ P ++ v++i++   + 
  gi|118431855|ref|YP_874942.1| 171 TWHWGLTASAPLLMNTPGHFLANVVKELYGVETIPLSQTIFHPYTIINFLLITLAALAIYWLISPSRGPVRGIEEfdpDA 250
                                    **************************************************99999999**********998875444499 PP

                     SCFA_trans 226 lkeekeeekklkskkdatiaekleeskllallisilGiaylgvyfyekGfn..ltlnsvnlifllvGlllhktPlaymra 303
                                    lkee+    + +  +  t+a++le+s+ la+l +ilG++ +++ +y +G    l+ln++n+ifl++Glll+ +P++y ra
  gi|118431855|ref|YP_874942.1| 251 LKEEAAPAGEKP--RIETLADRLENSRTLAILTVILGFTAVAIELYTRGISraLNLNTMNFIFLMTGLLLYANPMSYARA 328
                                    999998887777..789********************************9888*************************** PP

                     SCFA_trans 304 itraarsvaGilvqfPfyaGimgmmessa.lGGpslatliaeafinvankktfplltlfsaalinifiPsGGGewaiqgp 382
                                      r+  s aG+++qf fyaGi g+++      G+s a++iae +++v++++ +p++++++a+++n+fiPsGGGewa+ g+
  gi|118431855|ref|YP_874942.1| 329 FYRSVSSAAGVILQFHFYAGIFGLLNTPFePLGKSSAQIIAEGLADVSTPFIWPVVAFLTAGIVNLFIPSGGGEWAAIGE 408
                                    *************************9865444669*****************************************9997 PP

>> DUF5596  Domain of unknown function (DUF5596)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.1e-06     0.072       6      54 ..     263     310 ..     259     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-06
                        DUF5596   6 awpqlpeklgedeelfllyallaaapdvleayrkrGIseeifwaTladl 54 
                                     +++l ++l++   l +l+++l +++ ++e y  rGIs +  + T+ ++
  gi|118431855|ref|YP_874942.1| 263 RIETLADRLENSRTLAILTVILGFTAVAIELY-TRGISRALNLNTMNFI 310
                                    6789999*************************.9************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); 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: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 3410.38
//
Query:       gi|118431856|ref|NP_148577.2|  [L=385]
Description: acetyl-CoA acetyltransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); 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:                         0  (0); expected 0.2 (1e-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 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2898.49
//
Query:       gi|14602032|ref|NP_148578.1|  [L=394]
Description: acetyl-CoA acetyltransferase [Aeropyrum pernix K1]
Scores for complete 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-09   36.1   0.1    7.1e-05   22.3   0.0    2.8  2  Thiolase_N   Thiolase, N-terminal domain
      0.003   17.2   0.0        4.1    7.1   0.0    2.7  2  Thiolase_C   Thiolase, C-terminal domain
  ------ inclusion threshold ------
       0.14   12.0   0.0        7.5    6.5   0.0    2.4  2  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.2e-08   7.1e-05       1     191 [.      13     190 ..      13     205 .. 0.78
   2 !   10.1   0.1   6.4e-05      0.38     243     259 ..     214     230 ..     209     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-08
                                   EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEE CS
                    Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtv 81 
                                   v++v+a  t + +        + +eL+ ea++++l++ag++  ++d v++G    a++g  ++ +   +       p+v+v
  gi|14602032|ref|NP_148578.1|  13 VAVVGAGITLFRR----RMLETPRELAWEAARQALDSAGLTLRDIDCVVIGSAPDAFDGVHMKGEYLADGSGGLFKPTVRV 89 
                                   6777777777777....5556789*************************************98887777666678999999 PP

                                   EHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHH CS
                    Thiolase_N  82 nkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenl 162
                                       + g+   ++a+  +a+g +  v+a+  E+ms+a    +  v   + + d  ++  l p+ l+        +l  +++
  gi|14602032|ref|NP_148578.1|  90 YVGGGTGVFVPIAAWWHVASGLCRTVLAVAEEKMSHARPHPQ-GVF--AYIWDPVLERPLGPNLLW------IFALEMRRY 161
                                   99999999999*************************865554.232..223333444444444233......347777888 PP

                                   HHHHT--HHHHHHHHHHHHHHHHHHHHTT CS
                    Thiolase_N 163 akkykisReeqdefAvkshqkaaaaqkag 191
                                    +k ++s+e  + + vk++++a + ++a+
  gi|14602032|ref|NP_148578.1| 162 MHKCNVSKETIALVSVKNKRNALDHPAAQ 190
                                   88888888888888888888887766666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.4e-05
                                   SB--BEEEEEEEEEEEH CS
                    Thiolase_N 243 nasqisDGaaavllmse 259
                                   ++s++sDGaaa++l+se
  gi|14602032|ref|NP_148578.1| 214 DVSPVSDGAAALVLASE 230
                                   78*************98 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00069       4.1      26      48 ..      37      59 ..      26      74 .. 0.82
   2 !    6.9   0.0   0.00077       4.6      26     102 ..     268     364 ..     263     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00069
                                  HHHHHHHHHHT--GGGESEEEE- CS
                    Thiolase_C 26 yaikkvlkkagltvedidlfEin 48
                                   a++++l+ aglt++did++ i 
  gi|14602032|ref|NP_148578.1| 37 EAARQALDSAGLTLRDIDCVVIG 59
                                  58899*************98764 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00077
                                   HHHHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TTTHH CS
                    Thiolase_C  26 yaikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlGasG 86 
                                   ya++++ k ag++   +did+ E  + F  + L  ++ l l+                     +   GG + +G P+ a+G
  gi|14602032|ref|NP_148578.1| 268 YAARMAYKMAGIErpWRDIDFAEPYDPFDYKELHHIEGLMLARpceapklleegwfdrsgeLPTSPSGGLLGVGNPIAAAG 348
                                   7888999999998667899999999999999999999999888899999999999999986668899************** PP

                                   HHHHHHHHHHHHHCTT CS
                    Thiolase_C  87 aRivvtllselkkegg 102
                                      ++ l  +l+ e g
  gi|14602032|ref|NP_148578.1| 349 LMKAAELFWQLRYEAG 364
                                   9999999988887665 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 ?    2.8   0.0     0.018   1.1e+02      21      39 ..     107     125 ..     101     128 .. 0.90
   2 ?    6.5   0.0    0.0013       7.5      51      72 ..     217     237 ..     192     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.018
                                   HHTTS-SEEEEEEEEEGGG CS
                   ACP_syn_III  21 iesgaakrvLvigaetlsk 39 
                                   ++sg +++vL ++ e++s+
  gi|14602032|ref|NP_148578.1| 107 VASGLCRTVLAVAEEKMSH 125
                                   899**************96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0013
                                   TB-EEEEEEEEEEESSSSCEEE CS
                   ACP_syn_III  51 lfGDGAgAvvleaseeegaril 72 
                                    ++DGA+A+vl  ++e + r+ 
  gi|14602032|ref|NP_148578.1| 217 PVSDGAAALVLASENEAR-RVT 237
                                   579********9975443.455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.49
# Mc/sec: 2396.36
//
Query:       gi|14602033|ref|NP_148579.1|  [L=181]
Description: hypothetical protein APE_2389 [Aeropyrum pernix K1]
Scores for 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   45.4   0.4    9.6e-12   44.7   0.4    1.4  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    4.1e-11   42.5   2.9    9.2e-11   41.4   2.9    1.6  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.031   14.3   0.1      0.057   13.5   0.1    1.4  1  DZR            Double zinc ribbon
      0.032   13.9   3.5       0.07   12.9   3.5    1.6  1  zinc_ribbon_2  zinc-ribbon domain
      0.056   13.7   0.0      0.092   13.0   0.0    1.3  1  DUF3809        Protein of unknown function (DUF3809)


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 !   44.7   0.4   2.7e-15   9.6e-12       1      65 []      82     161 ..      82     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2.7e-15
                                   EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT..............-EE-EEEEEEES......TT-B-EEE-S CS
                 OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvr...........imarlvgvdpdevr....iGmrVravfr 65 
                                   wve+sg+G+v +++v + + ++++ e+P +++vV+L  ++            +++ l+gv +++v+    iGmrV+  +r
  gi|14602033|ref|NP_148579.1|  82 WVEVSGEGEVHTAVVSYISTFRERMEKPEIIAVVRLYAPGYtgkrdeyefpgMFHKLCGVSEEDVKtgrvIGMRVKPKWR 161
                                   **************************************5555778*******************888888******9986 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 !   41.4   2.9   2.6e-14   9.2e-11       2      34 ..      46      78 ..      45      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.6e-14
                       DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphCgsd 34
                                  ++++eg+++g +Cp CG+v++PPr +C +C++ 
  gi|14602033|ref|NP_148579.1| 46 QGLREGKILGVKCPRCGRVYVPPRSYCEYCFAP 78
                                  79****************************986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.6e-05     0.057      31      48 ..      58      75 ..      26      84 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                           DZR 31 CpsCgekvdpearfCpeC 48
                                  Cp+Cg+   p  ++C +C
  gi|14602033|ref|NP_148579.1| 58 CPRCGRVYVPPRSYCEYC 75
                                  666666655555666666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.5   1.9e-05      0.07       1      19 [.      57      75 ..      57      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                 zinc_ribbon_2  1 fCpnCGaelqdnakFCpyC 19
                                  +Cp+CG+   +   +C+yC
  gi|14602033|ref|NP_148579.1| 57 KCPRCGRVYVPPRSYCEYC 75
                                  8****************** PP

>> DUF3809  Protein of unknown function (DUF3809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.092      78     111 ..      78     110 ..      66     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                   TTB-EEEEEEEEEE-GGGEEEEEEEEEEE-B--- CS
                       DUF3809  78 eerawaevsGraeveeggelayelelrvhlslPe 111
                                   +   w+evsG++ev+  + + y  ++r +++ Pe
  gi|14602033|ref|NP_148579.1|  78 PTGEWVEVSGEGEVH-TAVVSYISTFRERMEKPE 110
                                   5567***********.999*********999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1332.72
//
Query:       gi|118431857|ref|NP_148580.2|  [L=154]
Description: hypothetical protein APE_2390.1 [Aeropyrum pernix K1]
Scores for 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   0.7    5.4e-10   39.1   0.7    1.4  1  OB_aCoA_assoc    DUF35 OB-fold domain, acyl-CoA-associated
    5.9e-07   29.2   0.0    8.6e-07   28.7   0.0    1.3  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
       0.25   10.5   0.0       0.35   10.0   0.0    1.1  1  Polysacc_deac_2  Divergent polysaccharide deacetylase


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 !   39.1   0.7     9e-14   5.4e-10      10      65 .]      78     133 ..      77     133 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 9e-14
                                    EEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                  OB_aCoA_assoc  10 vysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                    ++s+t+v+++ +g++ e+P+v++v+  ++    +++ v++dpdev iGm+V+ vf+
  gi|118431857|ref|NP_148580.2|  78 IESYTIVYESLDGKPLEKPVVIAVIAPEDAEGALVHYVDADPDEVYIGMPVEPVFK 133
                                    89***************************777888888899*************96 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 !   28.7   0.0   1.4e-10   8.6e-07       2      31 ..      37      64 ..      36      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.4e-10
                        DUF35_N  2 daaaegrLvgqrCpdCGtvqfPPravCphC 31
                                   +a++egr+vg++C d  tv++PP+ +Cp  
  gi|118431857|ref|NP_148580.2| 37 KALKEGRIVGTKCGD--TVYVPPTTFCPDM 64
                                   79************8..***********86 PP

>> Polysacc_deac_2  Divergent polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   5.9e-05      0.35      19      61 ..      93     135 ..      89     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5.9e-05
                                    SSTTCEEEEETTSTTHHHHHHHHHHCT-EEEEEEEE--TTTTT CS
                Polysacc_deac_2  19 lpapvtlAilPyaphskelaeaaraaghevllhlPmepksypk 61 
                                    l++pv +A++   ++  +l++ ++a   ev + +P+ep  +p 
  gi|118431857|ref|NP_148580.2|  93 LEKPVVIAVIAPEDAEGALVHYVDADPDEVYIGMPVEPVFKPP 135
                                    889**********************************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1220.59
//
Query:       gi|118431858|ref|NP_148582.2|  [L=815]
Description: hypothetical protein APE_2392.1 [Aeropyrum pernix K1]
Scores for complete 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-56  189.6   0.0    1.2e-55  188.1   0.0    1.8  2  Helicase_RecD    Helicase
    8.3e-41  139.9   0.0    2.8e-29  102.1   0.0    2.8  3  GNAT_acetyltr_2  GNAT acetyltransferase 2
    2.1e-30  104.5   0.0    4.9e-30  103.3   0.0    1.7  1  DUF1726          Domain of unknown function (DUF1726)
    7.3e-09   35.7   0.0    1.4e-08   34.7   0.0    1.4  1  tRNA_bind_2      Possible tRNA binding domain
    4.7e-06   26.9   0.1    2.6e-05   24.5   0.1    2.3  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.9e-05   24.3   0.1    8.7e-05   22.7   0.1    1.9  1  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0012   18.6   0.0     0.0056   16.4   0.0    2.0  2  AAA_30           AAA domain
     0.0017   18.0   0.2     0.0052   16.4   0.2    1.9  1  Sigma70_r4_2     Sigma-70, region 4
  ------ inclusion threshold ------
      0.053   13.6   0.0       0.22   11.6   0.0    2.0  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.066   13.1   0.0       0.14   12.1   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
       0.13   12.3   0.0       0.41   10.6   0.0    1.8  1  FR47             FR47-like protein
       0.15   11.8   0.0       0.56   10.0   0.0    1.9  1  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   0.0   8.3e-59   1.2e-55       1     177 []     250     429 ..     250     429 .. 0.97
   2 ?   -2.9   0.0       3.5   5.3e+03     130     153 ..     649     668 ..     648     674 .. 0.72

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 8.3e-59
                  Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk.....snilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqr 75 
                                    v+tAdRGRGKS+alG+ l al++e       ++i+vtaps++nv++l+e ++k+ e+lgl+ ++ ++ ++ +e++ rk +
  gi|118431858|ref|NP_148582.2| 250 VITADRGRGKSSALGIGLVALAHELGkvkhrVRIIVTAPSPSNVQSLMELAIKTAETLGLEPKPVRRGGRIIEVQGRKFS 329
                                    79**************9999988766688889************************************************ PP

                  Helicase_RecD  76 ieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelrelele 155
                                    +ey++p ++++l+   d++ vDEA+ i++pll+k++++++r+v++ T+hGYEG+Grgf+++fl+++kk+ ++ +re+++e
  gi|118431858|ref|NP_148582.2| 330 LEYWEPATVVRLQG--DIVAVDEASGIHVPLLHKIWRAHRRLVFSATIHGYEGAGRGFNVRFLSAVKKSGDTIIREFKME 407
                                    ***********975..**************************************************************** PP

                  Helicase_RecD 156 epiRyaegdplEkwlndlLlLd 177
                                    epiRya+gdp+E+wl+++LlL+
  gi|118431858|ref|NP_148582.2| 408 EPIRYAPGDPIERWLYNTLLLN 429
                                    ********************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.5
                  Helicase_RecD 130 Grgfslkflkqlkkekkrelrele 153
                                     r f+lk+l+ l+++    +r++e
  gi|118431858|ref|NP_148582.2| 649 AREFKLKLLNSLHDT----YRDME 668
                                    799********9754....44444 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.84   1.3e+03     152     187 ..      68     103 ..      31     112 .. 0.74
   2 !  102.1   0.0   1.9e-32   2.8e-29       2     123 ..     470     585 ..     469     590 .. 0.93
   3 !   35.1   0.0     6e-12   8.9e-09     179     226 ..     590     637 ..     583     638 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.84
                GNAT_acetyltr_2 152 lsleeeklkprkelpplllklseekpekldylgvsf 187
                                       +e   +  ke  ++l +++ +  e+  ylg++f
  gi|118431858|ref|NP_148582.2|  68 RLRKEIVKRAVKEKGSMLEQVTARYEESDRYLGTTF 103
                                    344455556667778888888889999999999998 PP

  == domain 2  score: 102.1 bits;  conditional E-value: 1.9e-32
                GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipwtl 81 
                                    l++++v +HY+n+P+DL +l+DaP+h++ +  +  k      +++++ qva EG + +e +++ l rg++ +G++ip+ +
  gi|118431858|ref|NP_148582.2| 470 LFGIYVLAHYRNEPDDLGMLADAPHHSIRAVRTAGK-----GKIVSAAQVAEEGGLGEELIDRLL-RGEKIAGNIIPDRM 543
                                    899**************************9998665.....79****************887766.666*********** PP

                GNAT_acetyltr_2  82 sqqfqdeefaslsGaRivRiAvhpelqkmGYGsralelleky 123
                                     ++ + +ef++++G RivRiA+hpe+q++G Gs  le+l ++
  gi|118431858|ref|NP_148582.2| 544 LKHARIREFGRMVGWRIVRIATHPEVQGRGIGSWLLERLYEE 585
                                    **************************************9875 PP

  == domain 3  score: 35.1 bits;  conditional E-value: 6e-12
                GNAT_acetyltr_2 179 kldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                      d+lg +fG+ ++Ll+FW r+gf  ++l+  +n ++GE++ ++++++
  gi|118431858|ref|NP_148582.2| 590 GYDWLGSGFGINEQLLRFWLRNGFLVLHLSPDRNPVSGEYTSLVMKPI 637
                                    579****************************************99986 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   3.3e-33   4.9e-30       1      93 []      92     184 ..      92     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 3.3e-33
                        DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplteevkkrfnkrfi 80 
                                    y+es+++LG+t+++lvldl+++l+Pn++grlve+V+GGGliil +p++e++++  t f+k+l+v+ + ee ++ f+++f+
  gi|118431858|ref|NP_148582.2|  92 YEESDRYLGTTFQALVLDLTNDLKPNDVGRLVEVVEGGGLIILQAPSWERWDTALTLFKKNLLVPGH-EEPRHIFISWFK 170
                                    99*****************************************************************.5*********** PP

                        DUF1726  81 rklkeh.egilivd 93 
                                    rkl eh +gi+++d
  gi|118431858|ref|NP_148582.2| 171 RKLLEHnRGIIVYD 184
                                    *****956677665 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   9.4e-12   1.4e-08      59     156 ..     690     787 ..     649     807 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 9.4e-12
                                    ---HHHHHHHHHHHHS---HHHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHHHT--SSHHHHH CS
                    tRNA_bind_2  59 llspfDlkRLesYannllDYhvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlekeLnlpsnQvlal 138
                                     l+   l RL  Y    + Y+  +D++ +la  y++ + +++ +L  +++ +L+a  LQ ks  ++++eL++ ++ v+  
  gi|118431858|ref|NP_148582.2| 690 RLTRIQLDRLWIYNYGPMTYEAATDVIHELAMAYWKMEPEARPRLGDLERRVLVAKVLQAKSWGEVAQELGVREHKVMTT 769
                                    57888999************************************************************************ PP

                                    HHHHHHHHHHHH-HHHHH CS
                    tRNA_bind_2 139 Fvkiirkvskalreilek 156
                                    + +++r++s  l  ++e+
  gi|118431858|ref|NP_148582.2| 770 LKEAVRRMSRELFGLAED 787
                                    *********988777664 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.4   6.6e+03      26      38 ..     469     481 ..     449     482 .. 0.74
   2 !   24.5   0.1   1.8e-08   2.6e-05      25      74 ..     558     613 ..     513     614 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.4
                                    CTEEEEE-GGGTT CS
                 Acetyltransf_7  26 eitrlaVdpeyrg 38 
                                    ++ +++V+ +yr+
  gi|118431858|ref|NP_148582.2| 469 QLFGIYVLAHYRN 481
                                    33449******97 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.8e-08
                                    TCTEEEEE-GGGTTSSHHHHHHH..HTT...SEEEEEEEEE......THHHHHHHHHHTTE CS
                 Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLle..aae...kgiileqlel......naekaikfYeklGF 74 
                                      i r+a++pe +g+GiG+ Lle  ++e   +g+     +l      n+ + ++f+ ++GF
  gi|118431858|ref|NP_148582.2| 558 WRIVRIATHPEVQGRGIGSWLLErlYEEsveRGY----DWLgsgfgiNE-QLLRFWLRNGF 613
                                    45778*****************964322344332....23322222111.3488****999 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   5.9e-08   8.7e-05      60     117 .]     557     613 ..     511     613 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5.9e-08
                                    EEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT.EHHHHHHHHHTTE CS
                 Acetyltransf_1  60 vayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed.ndaairlYeklGF 117
                                     + i ++a +pe +g+G+Gs Lle l e+  e+g++  +l      n++  r++ + GF
  gi|118431858|ref|NP_148582.2| 557 GWRIVRIATHPEVQGRGIGSWLLERLYEESVERGYD--WLGSGFGiNEQLLRFWLRNGF 613
                                    466789***************************983..444444446666666666655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.8e-06    0.0056      17     112 ..     245     366 ..     223     376 .. 0.79
   2 ?   -1.4   0.0       1.1   1.7e+03      34      64 ..     766     796 ..     764     803 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                         AAA_30  17 gdrvavltGpAGtGKttalkal.reaweaag.....grviglAptgkaAkvLaeelgieastiakllkrlk......... 81 
                                    ++++ v+t+  G GK+ al+   ++++++ g      r+i+ Ap+    + L e +  +a+t+    k  +         
  gi|118431858|ref|NP_148582.2| 245 RKKMIVITADRGRGKSSALGIGlVALAHELGkvkhrVRIIVTAPSPSNVQSLMELAIKTAETLGLEPKPVRrggriievq 324
                                    56799**************9762666666689**999***************9543345556555554444788888899 PP

                         AAA_30  82 ...........grarlepg.tllivDEagmvdtkqlaallkaa 112
                                               + + ++ + +++ vDEa+ +    l+++ +a 
  gi|118431858|ref|NP_148582.2| 325 grkfsleywepA-TVVRLQgDIVAVDEASGIHVPLLHKIWRAH 366
                                    999999999963.4455555**********9999999988765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                         AAA_30  34 alkalreaweaaggrviglAptgkaAkvLae 64 
                                    ++++l+ea+++  ++++glA  +++  +L e
  gi|118431858|ref|NP_148582.2| 766 VMTTLKEAVRRMSRELFGLAEDSRVGVELHE 796
                                    78999999999999*******9999988874 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   3.5e-06    0.0052      14      54 .]     737     777 ..     731     777 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                                    HHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  14 rqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                     +r++++ + l+ +s  E+A++lg+ e  V + l+ A +++
  gi|118431858|ref|NP_148582.2| 737 LERRVLVAKVLQAKSWGEVAQELGVREHKVMTTLKEAVRRM 777
                                    69**********************************99986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       4.3   6.4e+03      32      51 ..     167     186 ..     141     189 .. 0.71
   2 ?   11.6   0.0   0.00015      0.22      76     107 ..     560     591 ..     549     606 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.3
                                    HHHHHHHHTTSEEEEEEETT CS
                 Acetyltransf_9  32 reyfrklleesrvlgaedng 51 
                                      ++rklle++r ++++d +
  gi|118431858|ref|NP_148582.2| 167 SWFKRKLLEHNRGIIVYDAD 186
                                    34578999999999999865 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                                    EEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT- CS
                 Acetyltransf_9  76 vtgVavapehrgrgvlskLlaraleemreegq 107
                                    ++ +a++pe +grg+ s Ll+r++ee  e+g+
  gi|118431858|ref|NP_148582.2| 560 IVRIATHPEVQGRGIGSWLLERLYEESVERGY 591
                                    7899**********************999986 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.5e-05      0.14      52      83 ..     553     589 ..     505     614 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-05
                Acetyltransf_10  52 s.....hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                    +     +i +++ +pe +g+Gig+ Lle++ ee  ++
  gi|118431858|ref|NP_148582.2| 553 GrmvgwRIVRIATHPEVQGRGIGSWLLERLYEESVER 589
                                    344455999********************98886555 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.41      24      56 ..     560     592 ..     548     602 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                    EEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S- CS
                           FR47  24 lgalqvlpehrrrGlgsrlvkalakeiaergkt 56 
                                    +  + ++pe+++rG gs l + l +e +erg++
  gi|118431858|ref|NP_148582.2| 560 IVRIATHPEVQGRGIGSWLLERLYEESVERGYD 592
                                    66799*********************9999987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00037      0.56      13      76 ..     245     309 ..     224     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                                    TTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                    +++ +++ a+ G GK+ a  i +++   e  k k++ ++++ +P+ + ++  ++ + k  ++++l
  gi|118431858|ref|NP_148582.2| 245 RKKMIVITADRGRGKSSALGIGLVALAHELgKVKHRVRIIVTAPSPSNVQSLMELAIKTAETLGL 309
                                    457899******************77766699************988777777777666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 5891.28
//
Query:       gi|14602037|ref|NP_148583.1|  [L=367]
Description: translation factor [Aeropyrum pernix K1]
Scores for 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  201.0   0.0      2e-59  200.1   0.0    1.5  2  Sua5_yciO_yrdC  Telomere recombination
    3.8e-26   92.2   0.0      6e-26   91.6   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin


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 !  200.1   0.0   2.3e-63     2e-59       1     179 []      31     206 ..      31     206 .. 0.98
   2 ?   -3.6   0.0      0.77   6.9e+03      41      60 ..     249     268 ..     243     280 .. 0.61

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 2.3e-63
                                   HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                   e+lr+Gg+va+ptetvYgL++da n++a +r++e+Kgrp d+pl+v+v+sle+++++ae  ++ +al+l+e++wPGp+tl+
  gi|14602037|ref|NP_148583.1|  31 EVLRRGGLVAFPTETVYGLGADALNPRAAARIFEVKGRPPDNPLIVHVSSLEMARTVAE--IPGKALRLVEKLWPGPLTLV 109
                                   689*******************************************************7..******************** PP

                                   EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS-- CS
                Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvd 162
                                   l+r+   +p+ v++gl+tv+vr+P++++a++L++a+g+p++a+San sg+ps+t+ e+v ++l+  vd+ild+ge+  gv+
  gi|14602037|ref|NP_148583.1| 110 LPRKPV-VPDIVTAGLETVAVRMPAHKVALELVKAAGRPVAAPSANPSGRPSPTSGEHVIRDLDCMVDVILDAGETYFGVE 189
                                   **7444.************************************************************************** PP

                                   -EEEETTSSTSSECEXX CS
                Sua5_yciO_yrdC 163 stVvdltegkpkilRrG 179
                                   st++dlt  +p +lR+G
  gi|14602037|ref|NP_148583.1| 190 STIIDLTRTPPVLLRPG 206
                                   ********9******98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.77
                                   CC--EEEESSCCCCCCCC-T CS
                Sua5_yciO_yrdC  41 dkplavlvasledlkklaes 60 
                                   d pl+++ +s   +++++e 
  gi|14602037|ref|NP_148583.1| 249 DTPLILVDTSPGAVERIVEA 268
                                   55666666666666666652 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   6.6e-30     6e-26       4     134 .]     211     362 ..     208     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 6.6e-30
                                   HHHHHHS-..-...-.........-------------S-SSEEEEE--GGGHHHH.......HHHHHTTS-EEEEEEGGGT CS
                          SUA5   4 eeleevld..a...vek.....keekpraPGmkyrHYaPkapvvlveaeeeeeaake..ekleekkksgkkvgvlatsesk 72 
                                   e le++l+  +     +     + ++p aPGmkyrHYaP++p++lv+++  + ++    +  e ++++g +v+++  +e  
  gi|14602037|ref|NP_148583.1| 211 EVLERLLEekIlvpP-EarglrAADRPLAPGMKYRHYAPDTPLILVDTSPGAVERIVeaAVREVARARGLRVALVGPDELV 290
                                   566666632212221.1345667899*******************999988777655778888999999999999966666 PP

                                   GG......TSEEEEE...........E-TT-HHHHHHHHHHHHHHHHH.S--SEEEEE----STTHHHHHHHHHHHTT CS
                          SUA5  73 ea......assvlsls.........lgsrsdleeaarnLFaaLrelDe.egvdlilvegvpeeglglAvmnRLrkAAg 134
                                   +              +         lg+ +d++ aar+LF++Lr++De  ++d+ +v  +pe+g+glAvmnRLrkAA+
  gi|14602037|ref|NP_148583.1| 291 DVvalllrL------RgvepaaifrLGPLADTTVAARRLFKTLRRIDElGNIDVAIVLPFPERGIGLAVMNRLRKAAS 362
                                   555555440......14555666679*********************73477******9******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2877.16
//
Query:       gi|118431859|ref|NP_148584.2|  [L=460]
Description: phosphomethylpyrimidine kinase [Aeropyrum pernix K1]
Scores for 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-96  319.9   3.3    1.2e-95  319.5   3.3    1.1  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    7.6e-60  201.3   0.2    2.3e-58  196.4   0.1    2.3  2  ThiP_synth    Thiamine-phosphate synthase
    2.2e-11   43.6   0.6    4.3e-11   42.7   0.4    1.4  1  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.041   14.0   0.0    1.5  1  Smoa_sbd      Styrene monooxygenase A putative substrate bind
       0.04   14.0   0.3       0.61   10.3   0.0    2.7  2  4PPT_N        4'-phosphopantetheinyl transferase N-terminal d


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 !  319.5   3.3   3.5e-99   1.2e-95       1     246 []      19     263 ..      19     263 .. 0.99

  Alignments for each domain:
  == domain 1  score: 319.5 bits;  conditional E-value: 3.5e-99
                                    ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHH CS
                   Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvae 80 
                                    Ds+GGAGiqADlktf+ +gv+g+s+it++taqnt +v+++h++p+++v+aq+eav++d++vda+K+Gml+++ ii++vae
  gi|118431859|ref|NP_148584.2|  19 DSGGGAGIQADLKTFAVMGVHGASAITSITAQNTMEVRAIHDVPPDVVKAQVEAVADDLGVDAAKTGMLSNTGIIKAVAE 98 
                                    9******************************************************************************* PP

                                    HHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH.TT-SEE CS
                   Phos_pyr_kin  81 klkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk.lgakaV 159
                                    ++++y++p+V+DPVmvaksg++ll++ea ealk+ ++p+at++tPN pEae+L+g k+ ++++++eaa+ +++ lga+a 
  gi|118431859|ref|NP_148584.2|  99 VVDEYGFPLVVDPVMVAKSGARLLKPEAEEALKKLVIPRATIVTPNAPEAEVLTGVKVVDLDTAREAARIIVEeLGAEAA 178
                                    *************************************************************************9****** PP

                                    EEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BST CS
                   Phos_pyr_kin 160 likGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealelg 239
                                    ++kGghl+g  ++v+dvly+++e++ ++++rie+ +thGtGC++s+aiaa lakg+s+eeAv+ Ak+++t a+ ++le+g
  gi|118431859|ref|NP_148584.2| 179 VVKGGHLRG--EYVVDVLYHRGEYRLFKERRIEKATTHGTGCAFSAAIAAGLAKGRSVEEAVDVAKKFITVAVDYGLEIG 256
                                    ******955..6677***************************************************************** PP

                                    SSS-B-- CS
                   Phos_pyr_kin 240 kgagpvn 246
                                     g+gpvn
  gi|118431859|ref|NP_148584.2| 257 GGHGPVN 263
                                    *****97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.029     1e+02     100     143 ..     152     200 ..     142     204 .. 0.75
   2 !  196.4   0.1   6.5e-62   2.3e-58       1     163 [.     280     450 ..     280     452 .. 0.98

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.029
                                    TTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC......S-ECEEEE--BC CS
                     ThiP_synth 100 lglkvvefdreeepeevgstmewgvaeaieel......evpdviydeGgv 143
                                     g+kvv+ d  +e   +    e g+++a+ +        v dv+y++G++
  gi|118431859|ref|NP_148584.2| 152 TGVKVVDLDTAREAARI-IVEELGAEAAVVKGghlrgeYVVDVLYHRGEY 200
                                    57899999999999996.4444466666655555654349********87 PP

  == domain 2  score: 196.4 bits;  conditional E-value: 6.5e-62
                                    HHHHHHHHHHCC--..GCC--TT-B-EEEE-S..T--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC CS
                     ThiP_synth   1 eleralelleeeee.fakliPevgsNiayalp..dAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkf 77 
                                    +le+a e+l ++e+ +++l+Pev +Nia+a+p  +A+++ Dvaa+pGRI +++gr+++ g+pefgas+h+ar++laam++
  gi|118431859|ref|NP_148584.2| 280 NLEKAGETLRQAEDvVHTLVPEVLMNIAMAIPypYARTPLDVAAFPGRIGVHMGRLVFKGKPEFGASRHMARLVLAAMSV 359
                                    5899********9999****************99********************************************** PP

                                    -TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEE CS
                     ThiP_synth  78 dpevraainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpmiyvl 152
                                    +p++raa ni+y++++++a+e+lgl ++  dr++ep++v    g+t++w+ ++a+e+l ++pdviydeG+vGkEpm+++l
  gi|118431859|ref|NP_148584.2| 360 NPDIRAAGNIKYSKDVVRAAEDLGLLTYRGDRRAEPPDVkareGGTLPWMLRSAYESLgRLPDVIYDEGEVGKEPMVRIL 439
                                    **********************************************************99******************** PP

                                    ESSHHHHHHHH CS
                     ThiP_synth 153 gkdaeevvekv 163
                                    g++a++v++ +
  gi|118431859|ref|NP_148584.2| 440 GRTAVDVARVI 450
                                    ********977 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.4   1.2e-14   4.3e-11     161     284 ..     109     243 ..      88     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.2e-14
                                    EEEEECESSSHH.....HHHHHHHHH.CTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTS.SEEEEEEGG.GEE CS
                           PfkB 161 fdpnlldplgaq.....fkeallell.aladllkpneeElealtgekledieealaalhklkakga.ktvvvtlGk.eGa 232
                                    +dp++++++ga      + eal++l+ + a++++pn+ E+e ltg k +d + a +a+  ++++   +  vv+ G  +G 
  gi|118431859|ref|NP_148584.2| 109 VDPVMVAKSGARllkpeAEEALKKLViPRATIVTPNAPEAEVLTGVKVVDLDTAREAARIIVEELGaEAAVVKGGHlRGE 188
                                    6888888888888888899*****999*********************99999999999988877669999999975799 PP

                                    EEEE...TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                           PfkB 233 lvve...kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfana 284
                                    +vv+   + ge++  + + ++   t G+G +f ++++a+l++g s+eea+  a +
  gi|118431859|ref|NP_148584.2| 189 YVVDvlyHRGEYRLFKERRIEKATTHGTGCAFSAAIAAGLAKGRSVEEAVDVAKK 243
                                    9999***77777777778899999**************************99976 PP

>> Smoa_sbd  Styrene monooxygenase A putative substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.1e-05     0.041      62     105 ..     259     302 ..     252     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                       Smoa_sbd  62 sGpceillleavpggpldawkdvktpeehlerllellrefaPwe 105
                                    +Gp++ + ++a+p g ++++++ +++ e l+++++++++ +P++
  gi|118431859|ref|NP_148584.2| 259 HGPVNPVAWQAIPAGRWEVLENLEKAGETLRQAEDVVHTLVPEV 302
                                    79****************************************86 PP

>> 4PPT_N  4'-phosphopantetheinyl transferase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.24   8.4e+02      20      42 ..     162     184 ..     161     188 .. 0.85
   2 ?   10.3   0.0   0.00017      0.61      12      35 ..     338     361 ..     331     371 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.24
                         4PPT_N  20 GRicAraalarlgleavpllsge 42 
                                    +R +Ar + ++lg+ea+ +  g+
  gi|118431859|ref|NP_148584.2| 162 AREAARIIVEELGAEAAVVKGGH 184
                                    799***********999888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                         4PPT_N  12 kRkaeFlaGRicAraalarlglea 35 
                                    k k eF a+R++Ar  la+++ ++
  gi|118431859|ref|NP_148584.2| 338 KGKPEFGASRHMARLVLAAMSVNP 361
                                    7799***************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3514.63
//
Query:       gi|118431860|ref|NP_148585.2|  [L=211]
Description: hypothetical protein APE_2403.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1770.61
//
Query:       gi|118431861|ref|NP_148587.2|  [L=226]
Description: hypothetical protein APE_2406.1 [Aeropyrum pernix K1]
Scores for complete 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   53.9   0.0      7e-13   49.3   0.0    2.6  2  ABC_tran         ABC transporter
      6e-09   36.1   0.6    0.00014   21.8   0.2    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.9e-05   23.9   0.0    7.2e-05   23.4   0.0    1.1  1  AAA_23           AAA domain
    8.2e-05   22.3   0.3    0.00018   21.2   0.0    1.7  2  AAA_29           P-loop containing region of AAA domain
    0.00048   20.6   0.3     0.0016   18.8   0.2    1.8  2  AAA_16           AAA ATPase domain
     0.0011   18.5   0.0      0.011   15.2   0.0    1.9  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0013   18.5   0.1     0.0022   17.8   0.1    1.5  1  AAA_30           AAA domain
     0.0037   16.1   0.1     0.0059   15.5   0.1    1.2  1  ABC_ATPase       Predicted ATPase of the ABC class
     0.0048   17.2   0.0      0.011   16.0   0.0    1.7  1  AAA_22           AAA domain
     0.0055   16.5   0.0     0.0071   16.1   0.0    1.1  1  AAA_15           AAA ATPase domain
     0.0071   13.9   0.2     0.0088   13.6   0.2    1.0  1  DUF3584          Protein of unknown function (DUF3584)
  ------ inclusion threshold ------
      0.013   14.8   0.3      0.047   13.0   0.0    1.8  2  AAA_8            P-loop containing dynein motor region D4
      0.027   15.0   0.1       0.55   10.8   0.1    2.2  2  AAA_18           AAA domain
      0.027   14.5   0.4        1.4    8.9   0.1    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
      0.031   14.2   0.3      0.076   12.9   0.1    1.7  2  NACHT            NACHT domain
      0.052   13.7   0.4        1.6    8.9   0.1    2.5  3  AAA_33           AAA domain
      0.054   13.6   0.0      0.077   13.1   0.0    1.2  1  DUF3520          Domain of unknown function (DUF3520)
      0.085   12.5   0.3       0.21   11.2   0.1    1.7  2  SRP54            SRP54-type protein, GTPase domain
       0.11   13.0   0.0        6.5    7.2   0.0    2.3  2  AAA_17           AAA domain
       0.13   12.6   0.1       0.24   11.7   0.1    1.4  1  AAA_19           AAA domain
       0.14   11.9   0.0       0.22   11.3   0.0    1.2  1  MukB             MukB N-terminal
       0.16   12.2   0.7       0.42   10.8   0.1    2.0  2  AAA_28           AAA domain
       0.17   11.8   0.0       0.28   11.1   0.0    1.4  1  NTPase_1         NTPase
       0.19   11.5   0.0        1.8    8.3   0.0    2.0  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.24   10.0   0.0       0.63    8.6   0.0    1.6  2  AAA_13           AAA domain
       0.26   10.9   0.1        5.7    6.6   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
       0.37   10.8   0.8       0.85    9.7   0.1    1.9  2  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 !   49.3   0.0     1e-15     7e-13       1     137 []       7     131 ..       7     131 .. 0.83
   2 ?   -0.5   0.0       2.5   1.7e+03      18      35 ..     132     149 ..     132     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1e-15
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    l++v+l++ +g ++ai+G nG+GK+tLlkl a+llkp+ G++             +  +++g   q+    f + tv+e 
  gi|118431861|ref|NP_148587.2|   7 LRDVTLSIPRG-VTAILGANGSGKTTLLKLAARLLKPDRGSV-------------EGPRRVGAALQNpYLGFLGPTVAED 72 
                                    67899999998.78****************************.............5667778888884333556667777 PP

                                    .....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           + e+ k+l++ gl++  ++      ++LS G+ + +++ +a+   p+ +++DEpt+
  gi|118431861|ref|NP_148587.2|  73 lartaGGRGEALKLLREAGLEYASERSP----YTLSMGEARILSVLMAISWGPEAVVIDEPTS 131
                                    6654455666889999999998777776....*****************************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.5
                                    ESTTSSHHHHHHHHTTSS CS
                                    xxxxxxxxxxxxxxxxxx RF
                       ABC_tran  18 GenGaGKStLlkllagll 35 
                                    G  G+GK  L++l+a+l 
  gi|118431861|ref|NP_148587.2| 132 GLDGSGKRWLASLIARLG 149
                                    678**********99975 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 !   21.8   0.2   2.1e-07   0.00014       1      23 [.      18      40 ..      18      68 .. 0.81
   2 !   12.7   0.0   0.00012      0.08     231     276 ..      97     142 ..      80     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-07
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   ++++ G+NgsGK++LL++   l 
  gi|118431861|ref|NP_148587.2| 18 VTAILGANGSGKTTLLKLAARLL 40
                                   699**************998884 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00012
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllr 276
                                    e++++ lS+G  r+l +l a+   +     ++iDEp +gL+    ++l+
  gi|118431861|ref|NP_148587.2|  97 ERSPYTLSMGEARILSVLMAISWGP---EAVVIDEPTSGLDGsgkRWLA 142
                                    78899****************9988...77**********965555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.1e-07   7.2e-05      11      36 ..       8      33 ..       5      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.1e-07
                         AAA_23 11 rdqeidFskgltlItGpNGaGKTTil 36
                                   rd+++   +g+t+I G NG+GKTT+l
  gi|118431861|ref|NP_148587.2|  8 RDVTLSIPRGVTAILGANGSGKTTLL 33
                                   788888999****************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 !   21.2   0.0   2.7e-07   0.00018      14      50 ..       9      44 ..       4      48 .. 0.81
   2 ?   -3.1   0.1        10   6.6e+03      29      35 ..     132     138 ..     131     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.7e-07
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   + t++i  +g+t + G++GsGK+Tll   + lL p++
  gi|118431861|ref|NP_148587.2|  9 DVTLSIP-RGVTAILGANGSGKTTLLKLAARLLKPDR 44
                                   5667775.889***************88888887765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 10
                         AAA_29  29 GpsGsGK 35 
                                    G  GsGK
  gi|118431861|ref|NP_148587.2| 132 GLDGSGK 138
                                    7789**9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   2.5e-06    0.0016      20      99 ..      11      89 ..       2     154 .. 0.64
   2 ?    0.6   0.0      0.97   6.5e+02      30      88 ..     131     183 ..     109     218 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-06
                         AAA_16 20 rsgrp.elvllsGesGvGKsslvrellralekdggif....lrgkcdqlesaipysa.laqalareellrqlldeaesaele 95
                                     + p +++ + G+ G+GK++l++ ++r l+ d+g +      g + q     py+  l  +  +e+l r  + + e+  l 
  gi|118431861|ref|NP_148587.2| 11 TLSIPrGVTAILGANGSGKTTLLKLAARLLKPDRGSVegprRVGAALQ----NPYLGfLGPTV-AEDLARTAGGRGEA--LK 85
                                   4455557899*****************999999776655444444444....48888444444.66777777777444..33 PP

                         AAA_16 96 awre 99
                                     re
  gi|118431861|ref|NP_148587.2| 86 LLRE 89
                                   3333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.97
                         AAA_16  30 sGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                    sG  G+GK  l+  ++ +l     ++++g+  ++  a++ + +a +l r++ +r  +d+
  gi|118431861|ref|NP_148587.2| 131 SGLDGSGKRWLASLIA-RLGVP--VLVAGHDIDF--AAAVAGWAVIL-RDGRVRVSGDM 183
                                    5788999999998888.45544..5577777777..33344466666.66666655555 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 !   15.2   0.0   1.6e-05     0.011      18      41 ..      10      33 ..       6      37 .. 0.88
   2 ?    1.1   0.0      0.34   2.3e+02     136     185 ..     102     147 ..      74     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                                   EEEETTSSEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 18 vilpfsksftaivGpNGSGKsnll 41
                                   v+l + +++tai+G+NGSGK+ ll
  gi|118431861|ref|NP_148587.2| 10 VTLSIPRGVTAILGANGSGKTTLL 33
                                   6788999**************986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.34
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke 185
                                    +LS Ge  ++  ++l+Ai    p++ +++De  + LD +  + +a+l+ +
  gi|118431861|ref|NP_148587.2| 102 TLSMGEARIL--SVLMAIS-WGPEA-VVIDEPTSGLDGSGKRWLASLIAR 147
                                    6778887764..4566765.44544.578999999999999999999876 PP

>> AAA_30  AAA 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    0.0022      17     124 ..      15     157 ..       7     188 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk............... 81 
                                    ++ v+++ G+ G+GKtt+lk ++++++ + g+v g    g+a ++    lg+ + t+a+ l r++               
  gi|118431861|ref|NP_148587.2|  15 PRGVTAILGANGSGKTTLLKLAARLLKPDRGSVEGPRRVGAALQN--PYLGFLGPTVAEDLARTAggrgealkllreagl 92 
                                    67899*********************9996566554333333332..223444444444443333333344444444456 PP

                         AAA_30  82 ....................grarlepg.tllivDE.agmvdtkqlaallkaaekagakvilvGD 124
                                                          ++++ g + +++DE ++ +d +  + l++ +++ g+ v+++G 
  gi|118431861|ref|NP_148587.2|  93 eyaserspytlsmgearilsVLMAISWGpEAVVIDEpTSGLDGSGKRWLASLIARLGVPVLVAGH 157
                                    77777777777777777777333444444777777744555666666666666666666666665 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 !   15.5   0.1   8.9e-06    0.0059     240     262 ..      12      34 ..       7      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.9e-06
                                    EEE-SSEEEEEE-TTSSHHHHHH CS
                     ABC_ATPase 240 mgipkGvtlIvGggfhGKsTLLe 262
                                    + ip+Gvt+I G +  GK+TLL+
  gi|118431861|ref|NP_148587.2|  12 LSIPRGVTAILGANGSGKTTLLK 34 
                                    78*******************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05     0.011       5      71 ..      16      93 ..      14     164 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsst...sskdllrellralglelka.........e 71
                                   +g++++ G  G+GKTtll+  ++ l+ +    +   e+p+ v   l+++       +++++l+r  g +++a         e
  gi|118431861|ref|NP_148587.2| 16 RGVTAILGANGSGKTTLLKLAARLLKPD----RgsvEGPRRVGAALQNPYlgfLGPTVAEDLARTAGGRGEAlkllreaglE 93
                                   7899*****************9999532....24453444442222222221333344455555555444443333333331 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05    0.0071      13      44 ..       6      37 ..       5      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                         AAA_15 13 slkdveidlseeltvliGkNnsGKSsileald 44
                                   +l+dv++++   +t + G+N+sGK+++l++  
  gi|118431861|ref|NP_148587.2|  6 RLRDVTLSIPRGVTAILGANGSGKTTLLKLAA 37
                                   689999999999****************9755 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   1.3e-05    0.0088      16      36 ..      15      35 ..       3      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                        DUF3584 16 ldghtnieGtNaaGKTtLlrL 36
                                   ++g t i G+N++GKTtLl+L
  gi|118431861|ref|NP_148587.2| 15 PRGVTAILGANGSGKTTLLKL 35
                                   5899***************98 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     7e-05     0.047      20      49 ..      12      41 ..       9      52 .. 0.91
   2 ?   -0.8   0.1       1.1   7.6e+02      31      45 ..     132     146 ..     130     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                          AAA_8 20 lrqprghaLlvGvgGsGrqsltkLAafiae 49
                                   l++prg + ++G +GsG+ +l kLAa +++
  gi|118431861|ref|NP_148587.2| 12 LSIPRGVTAILGANGSGKTTLLKLAARLLK 41
                                   789***********************9876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                          AAA_8  31 GvgGsGrqsltkLAa 45 
                                    G+ GsG++ l++L a
  gi|118431861|ref|NP_148587.2| 132 GLDGSGKRWLASLIA 146
                                    899******999866 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00082      0.55       3      22 ..      21      40 ..      20      99 .. 0.87
   2 ?    2.3   0.0      0.35   2.3e+02       4      25 ..     131     156 ..     130     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00082
                         AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                   + G+ G+GKttl k  +++l
  gi|118431861|ref|NP_148587.2| 21 ILGANGSGKTTLLKLAARLL 40
                                   89************999986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.35
                         AAA_18   4 tGtpGvGKttlakeLskrlgf.....g 25 
                                    +G  G+GK  la  ++++ g+     g
  gi|118431861|ref|NP_148587.2| 131 SGLDGSGKRWLASLIARL-GVpvlvaG 156
                                    5999***********998.44445554 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 ?    8.9   0.1    0.0022       1.4       4      24 ..      21      42 ..      19      52 .. 0.84
   2 ?    3.4   0.0      0.11        72       6      22 ..     132     148 ..     131     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0022
                                   EE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  4 LvGppGtgKselaerlaaal.n 24
                                   ++G+ G+gK++l +  a++l  
  gi|118431861|ref|NP_148587.2| 21 ILGANGSGKTTLLKLAARLLkP 42
                                   68****************9951 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                                    --SSSSHHHHHHHGGGG CS
                          AAA_5   6 GppGtgKselaerlaaa 22 
                                    G  G+gK++la  +a++
  gi|118431861|ref|NP_148587.2| 132 GLDGSGKRWLASLIARL 148
                                    778*********99986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00011     0.076       3      25 ..      19      41 ..      17      47 .. 0.82
   2 ?   -2.0   0.0       4.4   2.9e+03       8      21 ..     133     146 ..     127     154 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                    ++ G++GsGKTtLl+  a++++
  gi|118431861|ref|NP_148587.2| 19 TAILGANGSGKTTLLKLAARLLK 41
                                   689************97766665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.4
                                    -TTTCHHHHHHHHH CS
                          NACHT   8 eaGsGKTtLlqkla 21 
                                      GsGK  L+  +a
  gi|118431861|ref|NP_148587.2| 133 LDGSGKRWLASLIA 146
                                    55666655555444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0024       1.6       3      20 ..      20      37 ..      18      47 .. 0.78
   2 ?    1.9   0.0      0.35   2.3e+02       5      30 ..     131     156 ..     130     177 .. 0.75
   3 ?   -1.3   0.0       3.4   2.3e+03      67      93 ..     164     191 ..     159     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0024
                         AAA_33  3 llvGlpGsGKstlaerll 20
                                    + G++GsGK+tl++  +
  gi|118431861|ref|NP_148587.2| 20 AILGANGSGKTTLLKLAA 37
                                   578*********987544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.35
                         AAA_33   5 vGlpGsGKstlaerllkklg.avllss 30 
                                     Gl GsGK  ++ +l+++lg  vl++ 
  gi|118431861|ref|NP_148587.2| 131 SGLDGSGKR-WLASLIARLGvPVLVAG 156
                                    599*****5.55556668886666655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.4
                         AAA_33  67 lsagrnvildatnlsr.rerarflklar 93 
                                    + ag++vil+ + ++   +++r+l++++
  gi|118431861|ref|NP_148587.2| 164 AVAGWAVILRDGRVRVsGDMERVLRMLP 191
                                    5689999999998887678888888765 PP

>> DUF3520  Domain of unknown function (DUF3520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012     0.077     122     157 ..     155     190 ..     136     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                        DUF3520 122 asedfrfaaavaafgqllrdseykgkasldkviela 157
                                    a +d+ faaava ++ +lrd ++  + ++++v+++ 
  gi|118431861|ref|NP_148587.2| 155 AGHDIDFAAAVAGWAVILRDGRVRVSGDMERVLRML 190
                                    6789********************999999998765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00032      0.21       3      27 ..      18      41 ..      16      47 .. 0.80
   2 ?   -1.7   0.0       2.8   1.9e+03       8      45 ..     132     165 ..     131     182 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00032
                                   EEEEEESTTSSHHHHHHHHHHHHHH CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkk 27
                                   v++++G +G+GKTt l KLaa+l k
  gi|118431861|ref|NP_148587.2| 18 VTAILGANGSGKTTLL-KLAARLLK 41
                                   6789********9976.78877655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                                    ESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHH CS
                          SRP54   8 GlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAv 45 
                                    Gl G+GK      La l+ + g  vl++  D+  aaAv
  gi|118431861|ref|NP_148587.2| 132 GLDGSGKRW----LASLIARLGVPVLVAGHDIDFAAAV 165
                                    677777743....5555566666677777776666665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0098       6.5       1      17 [.      22      37 ..      22      43 .. 0.81
   2 ?    3.7   0.0      0.11        75       2      27 ..     132     156 ..     131     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0098
                                   EE-TTSSHHHHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklve 17
                                   lG  GsGK+t++ kl+ 
  gi|118431861|ref|NP_148587.2| 22 LGANGSGKTTLL-KLAA 37
                                   699*********.5543 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                    E-TTSSHHHHHHHHHHHHTEEEEEHH CS
                         AAA_17   2 GgPGsGKgtqceklvekygfthlsaG 27 
                                    G+ GsGK  ++  l  ++g+++l aG
  gi|118431861|ref|NP_148587.2| 132 GLDGSGKRWLA-SLIARLGVPVLVAG 156
                                    899*****888.99999******999 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00037      0.24       7      35 ..      13      41 ..       8      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00037
                         AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallv 35
                                    ++++v ++++  G+GKT++lk + +ll+
  gi|118431861|ref|NP_148587.2| 13 SIPRGVTAILGANGSGKTTLLKLAARLLK 41
                                   678999***************99988876 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.22      22      54 ..      12      44 ..       7      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                   E-HHHHHHHHHS--SHHHHHHHHHHHHHHS--T CS
                           MukB 22 fdldelvttlsGgnGaGksttmaafvtaliPdl 54
                                     + + vt++ G+nG+Gk+t +  +   l Pd 
  gi|118431861|ref|NP_148587.2| 12 LSIPRGVTAILGANGSGKTTLLKLAARLLKPDR 44
                                   567789**************9998888888986 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   0.00064      0.42       3      17 ..      20      34 ..      18      48 .. 0.85
   2 ?   -1.8   0.0       4.9   3.3e+03       8      27 ..     134     153 ..     131     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                         AAA_28  3 vitGgestGKTtlle 17
                                   +i+G+ ++GKTtll+
  gi|118431861|ref|NP_148587.2| 20 AILGANGSGKTTLLK 34
                                   79***********97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                         AAA_28   8 estGKTtlleaLaargypvv 27 
                                     ++GK +l++ +a+ g+pv+
  gi|118431861|ref|NP_148587.2| 134 DGSGKRWLASLIARLGVPVL 153
                                    68999999999999888874 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00041      0.28       4      32 ..      21      49 ..      18      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                                   EE--TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkvgG 32
                                   i G  G+GKtTl+k +++llk +  +v+G
  gi|118431861|ref|NP_148587.2| 21 ILGANGSGKTTLLKLAARLLKPDRGSVEG 49
                                   6799****************998888887 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 ?    8.3   0.0    0.0027       1.8       3      25 ..      21      40 ..      19      60 .. 0.80
   2 ?    1.1   0.0      0.42   2.8e+02      32      73 ..      92     131 ..      73     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                Viral_helicase1  3 vhGvpGcGKStlirkllrtslil 25
                                   + G+ G+GK+tl++ ++r    l
  gi|118431861|ref|NP_148587.2| 21 ILGANGSGKTTLLKLAARL---L 40
                                   8899********9988877...4 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.42
                Viral_helicase1  32 aelltegkpklpnlsvrtvdsflmalvkstkgkililDEyll 73 
                                     e ++e++p++ +    ++ s+lma +++   + +++DE ++
  gi|118431861|ref|NP_148587.2|  92 LEYASERSPYTLSMGEARILSVLMAISWG--PEAVVIDEPTS 131
                                    566788889999999999*********98..89******776 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00094      0.63      21      38 ..      21      38 ..       8      50 .. 0.83
   2 ?   -1.9   0.0       1.4   9.3e+02     529     541 ..     123     135 ..     120     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00094
                         AAA_13 21 iYGwNGaGKTtLSrllrs 38
                                   i G+NG+GKTtL +l + 
  gi|118431861|ref|NP_148587.2| 21 ILGANGSGKTTLLKLAAR 38
                                   88**********877665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                         AAA_13 529 ivviDDPvSSLDs 541
                                     vviD P S LD 
  gi|118431861|ref|NP_148587.2| 123 AVVIDEPTSGLDG 135
                                    5999***999995 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0086       5.7       3      22 ..      23      42 ..      21      48 .. 0.87
   2 ?    1.9   0.0      0.23   1.5e+02       3      18 ..     132     147 ..     131     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0086
                                   ESTTSSHHHHHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlke 22
                                   G +G+GKtt ++l ++ lk 
  gi|118431861|ref|NP_148587.2| 23 GANGSGKTTLLKLAARLLKP 42
                                   89**********99998875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.23
                                    ESTTSSHHHHHHHHHH CS
                Thymidylate_kin   3 GlDGaGKttqaellke 18 
                                    GlDG+GK   a l+++
  gi|118431861|ref|NP_148587.2| 132 GLDGSGKRWLASLIAR 147
                                    9******988888765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0013      0.85       3      24 ..      17      38 ..      15      48 .. 0.80
   2 ?   -1.3   0.1       3.1   2.1e+03       7      14 ..      47      54 ..      41      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                         AAA_14  3 kilvitGaRrvGKTtllkqlik 24
                                    + +i Ga  +GKTtllk  ++
  gi|118431861|ref|NP_148587.2| 17 GVTAILGANGSGKTTLLKLAAR 38
                                   5789************987664 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.1
                         AAA_14  7 itGaRrvG 14
                                   ++G+RrvG
  gi|118431861|ref|NP_148587.2| 47 VEGPRRVG 54
                                   89*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1680.28
//
Query:       gi|118431862|ref|NP_148588.2|  [L=237]
Description: hypothetical protein APE_2408.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-17   64.4   0.0    2.2e-17   63.9   0.0    1.3  1  ABC_tran    ABC transporter
     0.0009   19.1   1.5      0.064   13.0   0.1    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
     0.0011   18.6   0.1     0.0021   17.7   0.1    1.4  1  AAA_29      P-loop containing region of AAA domain
     0.0016   19.0   0.0     0.0024   18.4   0.0    1.1  1  AAA_23      AAA domain
     0.0057   17.0   0.2     0.0082   16.5   0.2    1.3  1  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.036   13.1   0.3      0.055   12.5   0.3    1.2  1  T2SSE       Type II/IV secretion system protein
      0.082   12.8   0.0       0.11   12.4   0.0    1.1  1  Rad17       Rad17 P-loop domain
       0.14   11.8   1.8       0.31   10.7   1.8    1.7  1  AAA_30      AAA domain
       0.15   11.6   0.1       0.31   10.6   0.1    1.5  1  AAA_25      AAA domain
       0.17   11.5   0.0       0.27   10.8   0.0    1.3  1  CDPS        Cyclodipeptide synthase
       0.18   10.6   1.2        2.2    7.0   0.5    2.0  2  ABC_ATPase  Predicted ATPase of the ABC class
       0.25   10.2   0.0       0.45    9.4   0.0    1.3  1  AAA_PrkA    PrkA 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 !   63.9   0.0   1.4e-20   2.2e-17       4     136 ..      23     156 ..      20     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.4e-20
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx... RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren... 79 
                                    vsl+  +g ++ + G++G GKSt+l++ agl +   G        l  + + ++r +   +pq+ + +   lt re+   
  gi|118431862|ref|NP_148588.2|  23 VSLEAPRG-ITLLAGPTGGGKSTILRVAAGLATRIYGGY------L--RGEVEARGKPVLVPQDyDLFILSLTPREEley 93 
                                    56665555.6789*******************9977665......2..24678899999999995555567778888999 PP

                                    ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              e+++e+ +++++lg+++l d++v    s+LS G++qrva+a al+  +++ll+DEp 
  gi|118431862|ref|NP_148588.2|  94 cyeasglppwEARREAVRLAEELGIEDLLDRRV----SKLSAGERQRVAIASALALGAEVLLMDEPL 156
                                    999999999999999******************....*****************************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 !   13.0   0.1   4.3e-05     0.064       1      25 [.      31      55 ..      31      97 .. 0.77
   2 ?    5.3   0.2      0.01        15     228     283 ..     120     172 ..     102     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                   +++l Gp g GKS++L+   +la  
  gi|118431862|ref|NP_148588.2| 31 ITLLAGPTGGGKSTILRVAAGLATR 55
                                   799*****************99753 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellk 283
                                    d  ++ +++lS G ++  a+++al+  +    +ll DEp +  +P  +++l++ll+
  gi|118431862|ref|NP_148588.2| 120 DLLDRRVSKLSAGERQRVAIASALALGA---EVLLMDEPLAYQDPLGVESLIRLLR 172
                                    55566778899***99999999999988...9*******99988877777777775 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   0.1   1.4e-06    0.0021      21      39 ..      28      46 ..      19      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-06
                         AAA_29 21 lkgatlltGpsGsGKSTll 39
                                   ++g+tll+Gp+G GKST+l
  gi|118431862|ref|NP_148588.2| 28 PRGITLLAGPTGGGKSTIL 46
                                   5889*************98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0024      15      37 ..      25      47 ..      18      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                         AAA_23 15 idFskgltlItGpNGaGKTTild 37
                                   ++  +g+tl+ Gp+G GK+Til+
  gi|118431862|ref|NP_148588.2| 25 LEAPRGITLLAGPTGGGKSTILR 47
                                   55668****************96 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   0.2   5.5e-06    0.0082      22     116 ..      26     134 ..      19     181 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                         AAA_16  22 grp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesa....ipysalaqalareellrqlldeaesaelea 96 
                                      p +++ll G+ G GKs+++r ++  +++ +g +lrg+ +  ++       y+ ++  l+ +e l+   +++    +ea
  gi|118431862|ref|NP_148588.2|  26 EAPrGITLLAGPTGGGKSTILRVAAGLATRIYGGYLRGEVEARGKPvlvpQDYDLFILSLTPREELEYCYEASGLPPWEA 105
                                    445589****************9997666666666666666652222322335555555555566666666644434443 PP

                         AAA_16  97 wrekleeala.........avpelagaea 116
                                     re+ + a +          v++l++ e+
  gi|118431862|ref|NP_148588.2| 106 RREAVRLAEElgiedlldrRVSKLSAGER 134
                                    33332222224355555554444444433 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 ?   12.5   0.3   3.7e-05     0.055     122     149 ..      25      49 ..      21      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                          T2SSE 122 lrkavrerglilvsGgTgsGKttllyal 149
                                    l+++   rg+ l++G+Tg GK+t+l ++
  gi|118431862|ref|NP_148588.2|  25 LEAP---RGITLLAGPTGGGKSTILRVA 49 
                                    5566...99***************9766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.5e-05      0.11      39      66 ..      24      50 ..      17      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-05
                          Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLs 66
                                   +Le +++ i L++GP+G gkst+++v +
  gi|118431862|ref|NP_148588.2| 24 SLE-APRGITLLAGPTGGGKSTILRVAA 50
                                   454.4588****************9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.8   0.00021      0.31      16      46 ..      27      58 ..      23     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa.g 46
                                    ++ +++l Gp G GK+t+l++++ ++++  g
  gi|118431862|ref|NP_148588.2| 27 APRGITLLAGPTGGGKSTILRVAAGLATRIyG 58
                                   567899*****************998887655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0002      0.31      32      52 ..      28      48 ..      12      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                         AAA_25 32 agelallaGapgtGKttlald 52
                                     +++llaG++g GK+t++  
  gi|118431862|ref|NP_148588.2| 28 PRGITLLAGPTGGGKSTILRV 48
                                   46899************8643 PP

>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.27      54      96 ..      86     130 ..      82     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                    E--TTHHHHHHHTT--HHHHHHHHHHHHHHH..HHHHHHHHHHHT CS
                           CDPS  54 vadtevaellealGyspeeArrkaarelrav..rarieraleeag 96 
                                     + +e++  +ea+G +p+eArr a+r  +++     ++r ++++ 
  gi|118431862|ref|NP_148588.2|  86 TPREELEYCYEASGLPPWEARREAVRLAEELgiEDLLDRRVSKLS 130
                                    67789999******************8776411455666666665 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 ?    7.0   0.5    0.0015       2.2     242     262 ..      27      47 ..      13      58 .. 0.85
   2 ?    2.3   0.0     0.039        58     329     348 ..     135     154 ..     127     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0015
                                    E-SSEEEEEE-TTSSHHHHHH CS
                     ABC_ATPase 242 ipkGvtlIvGggfhGKsTLLe 262
                                     p+G+tl++G+   GKsT+L+
  gi|118431862|ref|NP_148588.2|  27 APRGITLLAGPTGGGKSTILR 47 
                                    59*****************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.039
                                    HHHHHHHHHHTT-SEEEEEG CS
                     ABC_ATPase 329 qAanimealeagakllLiDE 348
                                    q ++i+ al +ga++lL+DE
  gi|118431862|ref|NP_148588.2| 135 QRVAIASALALGAEVLLMDE 154
                                    66789**************9 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0003      0.45      84     188 ..      25     140 ..      21     144 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0003
                       AAA_PrkA  84 leerkqilyllGPvggGksslverlkklleaa..piyal.....egsPv.feePlhlipeelrkkleeeygirlegllsP 155
                                    le  + i +l GP ggGks++       l ++    y        g Pv   + + l+  +l+   e ey  +  + l P
  gi|118431862|ref|NP_148588.2|  25 LEAPRGITLLAGPTGGGKSTILRV-AAGLATRiyGGYLRgeveaRGKPVlVPQDYDLFILSLTPREELEYCYEA-SGLPP 102
                                    7888999*************9754.4444443233333344444444442334444554444433333443333.34667 PP

                       AAA_PrkA 156 lat....krleeefg.Gdiekfkvekilfsilkrigia 188
                                    + +     rl ee+g  d+ + +v+k+   +++r +ia
  gi|118431862|ref|NP_148588.2| 103 WEArreaVRLAEELGiEDLLDRRVSKLSAGERQRVAIA 140
                                    65411115677887734577778888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1867.15
//
Query:       gi|14602043|ref|NP_148589.1|  [L=169]
Description: hypothetical protein APE_2409 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   18.9   0.0     0.0012   18.9   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.1       0.04   13.9   0.1    1.7  2  AAA_5     AAA domain (dynein-related subfamily)
      0.047   14.1   0.2      0.064   13.6   0.2    1.5  1  AAA_16    AAA ATPase domain
       0.12   12.3   0.2       0.18   11.7   0.2    1.3  1  NACHT     NACHT domain
        0.2   11.1   0.1        1.2    8.6   0.0    2.0  2  DUF3343   Protein of unknown function (DUF3343)


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.4e-07    0.0012       9      38 ..      14      43 ..       7     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.4e-07
                                  TSSHHHHHHHHHHHHHHTT--EEEEEEEES CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          CbiA  9 GvGKTtlaanLaralarrglrVllvDaDpq 38
                                  G GKT l+ ++a +la  gl++++vD+ p+
  gi|14602043|ref|NP_148589.1| 14 GRGKTRLTWHIASLLAGLGLEIVAVDLAPD 43
                                  89**************************99 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 ?   13.9   0.1   1.1e-05      0.04       2      30 ..       7      36 ..       6      44 .. 0.83
   2 ?   -1.2   0.0      0.53   1.9e+03      45      74 ..      80     110 ..      74     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                  EEEE--SSSSHHHHHHHGGGGB.S--EEEE CS
                         AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyv 30
                                  +l+vG++G gK++l+ ++a++l +  +e+v
  gi|14602043|ref|NP_148589.1|  7 LLIVGEQGRGKTRLTWHIASLLaGLGLEIV 36
                                  89*******************986555555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.53
                                   B--.........--------.G-SEEEEESG CS
                         AAA_5  45 reikngttslvdsplvraar.egeilvlDEv 74 
                                   +e++  +++ +  +l raa   g++lv+++ 
  gi|14602043|ref|NP_148589.1|  80 WELARHNAEQTSRVLERAAVePGDVLVVNDA 110
                                   6666666777777777776557888888775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.8e-05     0.064      25      49 ..       5      29 ..       3     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                        AAA_16 25 elvllsGesGvGKsslvrellrale 49
                                  + +l++Ge+G GK++l ++++  l 
  gi|14602043|ref|NP_148589.1|  5 SGLLIVGEQGRGKTRLTWHIASLLA 29
                                  579****************995444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   4.9e-05      0.18       3      27 ..       7      31 ..       5      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.9e-05
                                  EEEEC-TTTCHHHHHHHHHHHHCTS CS
                         NACHT  3 vilqGeaGsGKTtLlqklalawaeg 27
                                  +++ Ge+G GKT L  ++a+++a  
  gi|14602043|ref|NP_148589.1|  7 LLIVGEQGRGKTRLTWHIASLLAGL 31
                                  689*****************99965 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00034       1.2      35      65 ..      71     102 ..      63     105 .. 0.84
   2 ?   -0.1   0.0      0.18   6.6e+02      35      44 ..     142     151 ..     124     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00034
                       DUF3343  35 is.agCGlalrvneedieeasrllseaeipye 65 
                                    s  +C la+++   + e+ sr+l++a +++ 
  gi|14602043|ref|NP_148589.1|  71 ESrGDCRLAWELARHNAEQTSRVLERAAVEPG 102
                                   44489**********************99876 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.18
                       DUF3343  35 isagCGlalr 44 
                                   +  gCG+a r
  gi|14602043|ref|NP_148589.1| 142 LGLGCGIAAR 151
                                   5669**9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1234.37
//
Query:       gi|118431863|ref|NP_148591.2|  [L=184]
Description: hypothetical protein APE_2411.1 [Aeropyrum pernix K1]
Scores for complete 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-45  153.9  16.4    3.7e-45  153.7  16.4    1.0  1  ThiW          Thiamine-precursor transporter protein (ThiW)
  ------ inclusion threshold ------
       0.19   11.8  14.1       0.31   11.1  14.1    1.3  1  ECF_trnsprt   ECF transporter, substrate-specific component
        0.8    9.2  17.8          2    7.9  17.8    1.7  1  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 !  153.7  16.4   6.2e-49   3.7e-45       1     149 [.      12     167 ..      12     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 6.2e-49
                           ThiW   1 lallavlialgvvlssllsipvgvakvaPvqhvvNvvaavllGPwyalavalvisliRnllgtgtllalpGsiiGallag 80 
                                    lal+a+l +l+v+ls + +i+vg++k++P+qh+vNvva+v+lGPw+a ++al+++l+R++lg+gt++++pG+i+Gall+g
  gi|118431863|ref|NP_148591.2|  12 LALAAILGGLAVALSVI-RIDVGPTKALPWQHMVNVVAGVTLGPWWASGLALAVGLVRMALGIGTVYSIPGGIPGALLVG 90 
                                    789**************.************************************************************** PP

                           ThiW  81 l....lyrltrklllaalgEvlGtgiiGal.laypvaklllgkeaal...lvlvisFilstliGsviallvlkalek 149
                                    l    l+rl+r+ l a l E+lGt++iG+l + y++a+l+ + ea+    +v+++ +++stliG++++l++l+ale+
  gi|118431863|ref|NP_148591.2|  91 LgavaLLRLGRSPLPAGLLEPLGTAVIGFLlALYVFAPLMGDVEAWRsalTVIWLGWLSSTLIGTTLGLAALVALER 167
                                    *999999***********************788999999999998877789************************97 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 ?   11.1  14.1   5.1e-05      0.31       1     158 [.      10     152 ..      10     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                                    HHHHHHHHHHHHHHHHHHHHEEE.STSE.EESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHHH CS
                    ECF_trnsprt   1 kklvitglliAisivlsllgyiplpnik.itiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiafls 79 
                                    +kl+++++l ++++ ls    i +++ k +   h+  +++g+ +Gp+++  l++   ++++ l g +++ s+  p+ ++ 
  gi|118431863|ref|NP_148591.2|  10 RKLALAAILGGLAVALS-VIRIDVGPTKaLPWQHMVNVVAGVTLGPWWASGLALAVGLVRMAL-GIGTVYSI--PGGIPG 85 
                                    689**************.3334444444488889999999***********************.55556666..****** PP

                                    HHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC.HHHHS.............--HHHHHHHHHCCTT CS
                    ECF_trnsprt  80 riligliagllykkgkkknlkeivvsfilagvlgtivatllvllii.lplylklktakaiaiagkallaailgpiivkgl 158
                                    ++l+gl a+ l + g++ +        +l+  lgt v  +l++l++  pl++ +      a +   +l++i+++ +  +l
  gi|118431863|ref|NP_148591.2|  86 ALLVGLGAVALLRLGRSPLP------AGLLEPLGTAVIGFLLALYVfAPLMGDVE-----AWR--SALTVIWLGWLSSTL 152
                                    *********99988888755......55555555555544444333367775222.....222..334444443333333 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 ?    7.9  17.8   0.00033         2      16     161 ..       9     157 ..       2     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00033
                   5TM-5TMR_LYT  16 ksklllglifglfsilgtytgieie.gaiantRaigvvvaGllgGplvGliagliaglhRyl..lgGftalacgistila 92 
                                     +kl+l +i+g++++ +    i +         +++ vvaG+  Gp+++ + +l +gl+R++  +g + +++ gi   l 
  gi|118431863|ref|NP_148591.2|   9 ERKLALAAILGGLAVALSVIRIDVGpTKALPWQHMVNVVAGVTLGPWWASGLALAVGLVRMAlgIGTVYSIPGGIPGALL 88 
                                    67999999999999999999999975477889999***************************555669999999999999 PP

                   5TM-5TMR_LYT  93 gllaGlihrklkrrr...kkltvlvalligllveilqmllilllakpfdqalalvktialPmilvnslgtal 161
                                      l++++  +l r+      l++l +++ig+l+ +    ++  l+ + ++  + + +i+l  +  +++gt+l
  gi|118431863|ref|NP_148591.2|  89 VGLGAVALLRLGRSPlpaGLLEPLGTAVIGFLLAL---YVFAPLMGDVEAWRSALTVIWLGWLSSTLIGTTL 157
                                    99999999999987788888888888888888664...4444444444444455566666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1332.77
//
Query:       gi|14602047|ref|NP_148593.1|  [L=116]
Description: hypothetical protein APE_2413 [Aeropyrum pernix K1]
Scores for 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   35.0   0.1    1.8e-08   34.1   0.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    5.6e-06   25.8   0.2    9.5e-06   25.1   0.2    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00011   22.0   0.1    0.00018   21.4   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00015   21.5   0.0    0.00023   20.8   0.0    1.3  1  LexA_DNA_bind   LexA DNA binding domain
    0.00032   20.5   0.2      0.012   15.4   0.2    2.2  1  DUF1495         Winged helix DNA-binding domain (DUF1495)
    0.00046   20.5   0.1    0.00066   20.0   0.1    1.3  1  Rrf2            Transcriptional regulator
    0.00088   19.3   0.0     0.0013   18.7   0.0    1.2  1  HTH_20          Helix-turn-helix domain
     0.0011   18.7   0.0     0.0018   18.1   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
     0.0036   17.4   0.2     0.0052   16.9   0.2    1.3  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0059   16.8   0.1      0.011   15.9   0.1    1.5  1  HTH_34          Winged helix DNA-binding domain
      0.009   16.0   0.0      0.013   15.4   0.0    1.3  1  HTH_1           Bacterial regulatory helix-turn-helix protein
     0.0098   15.8   0.0      0.021   14.8   0.0    1.6  1  HTH_36          Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.014   15.9   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
      0.029   14.3   0.0       0.04   13.9   0.0    1.1  1  Dimerisation2   Dimerisation domain
      0.062   13.3   0.1       0.16   11.9   0.1    1.7  1  HTH_11          HTH domain
       0.08   13.1   0.1       0.15   12.2   0.1    1.5  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
      0.092   12.5   0.0       0.16   11.7   0.0    1.5  1  PheRS_DBD1      PheRS DNA binding domain 1
      0.097   12.7   0.0       0.15   12.1   0.0    1.3  1  HTH_29          Winged helix-turn helix
        0.1   12.5   0.0       0.15   12.0   0.0    1.3  1  MarR_2          MarR family
       0.12   12.1   0.0       0.28   11.0   0.0    1.6  2  Imm27           Immunity protein 27
       0.14   11.8   0.1        0.2   11.3   0.1    1.4  1  RP-C            Replication protein C N-terminal 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 !   34.1   0.1   2.1e-11   1.8e-08       4      46 ..      33      77 ..      31      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.1e-11
                                  HHHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                         HTH_5  4 RlkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                  ++kIL +La+  ++ ++  +++ +g+s  +v  HLk+L++ GLVe
  gi|14602047|ref|NP_148593.1| 33 KIKILLYLADlaEPSSIRRISRNVGMSHKNVIKHLKALENIGLVE 77
                                  689********999******************************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 !   25.1   0.2   1.1e-08   9.5e-06       6      48 .]      34      77 ..      30      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                        HTH_24  6 rkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                  +kIL +L +     s+r +++ +g+S  +v ++lk Le+ Gl++
  gi|14602047|ref|NP_148593.1| 34 IKILLYLADlAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVE 77
                                  799*9****7778*****************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.1e-07   0.00018      12      63 ..      35      89 ..      30      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.1e-07
                                  CHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEE CS
                          TrmB 12 kvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYr 63
                                  k+ l+L    +p++++ i++++g ++ +v + L+ Le+ GlVe+  ++   +lY+
  gi|14602047|ref|NP_148593.1| 35 KILLYLAdLAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVEVAYKQsnLTLYK 89
                                  66677777789********************************987554466776 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 !   20.8   0.0   2.7e-07   0.00023      25      59 ..      46      79 ..      36      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.7e-07
                                  ---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                 LexA_DNA_bind 25 pPsireiaralglkSpsaveehLkaLerKGyierd 59
                                  p sir i+r++g++  + v +hLkaLe+ G++e+ 
  gi|14602047|ref|NP_148593.1| 46 PSSIRRISRNVGMS-HKNVIKHLKALENIGLVEVA 79
                                  789*********97.888999***********986 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 !   15.4   0.2   1.4e-05     0.012      12      82 ..      34      93 ..      24      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                       DUF1495 12 kkvllyLysiypeksnlqeisrrvrskpsnvkGaleGmgkrynsessLielGLveeeeeseglklYkltee 82
                                   k+llyL++  +  s +  isr+v+++ +nv+  l+          +L + GLve   ++++l+lYkl+e+
  gi|14602047|ref|NP_148593.1| 34 IKILLYLADLAE-PSSIRRISRNVGMSHKNVIKHLK----------ALENIGLVEVAYKQSNLTLYKLSEH 93
                                  59******7665.99****************97765..........6667899998889999999998875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   7.8e-07   0.00066      11      57 ..      34      78 ..      30      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.8e-07
                                  HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                  +++llyLa  +e  p s++ i++++++s++ + k l+ L++ glv++
  gi|14602047|ref|NP_148593.1| 34 IKILLYLADLAE--PSSIRRISRNVGMSHKNVIKHLKALENIGLVEV 78
                                  689*******99..78*****************************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 !   18.7   0.0   1.6e-06    0.0013      15      56 ..      36      78 ..      33      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-06
                                  HHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20 15 ilraL.araegltaselaerldlskntlsyHLrvLeeagLvev 56
                                  il +L   ae+ +   + + +++s +++ +HL++Le  gLvev
  gi|14602047|ref|NP_148593.1| 36 ILLYLaDLAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVEV 78
                                  666777779999******************************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 !   18.1   0.0     2e-06    0.0018       7      49 ..      35      77 ..      34      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                                  HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                      HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   iL +la  +++ +++ ++r+ g++  +v  +L+ L++ G+ve
  gi|14602047|ref|NP_148593.1| 35 KILLYLADLAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVE 77
                                  79****************************************8 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 !   16.9   0.2     6e-06    0.0052       6      54 ..      30      78 ..      25      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6e-06
                       DUF2250  6 edelalkvl.khlkkanvdYaksiakeleipleevrellkkLeelGLler 54
                                  +d+ ++k+l + ++ a++   + i++++ ++ ++v + lk+Le++GL+e 
  gi|14602047|ref|NP_148593.1| 30 RDP-KIKILlYLADLAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVEV 78
                                  444.55555055567899999***************************95 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.2e-05     0.011       3      51 ..      34      83 ..      33     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                        HTH_34  3 lavlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefk 51
                                  +++l yLa+ ++  + ++++  ++++  n  +hlk+Le+ g +ev  + +
  gi|14602047|ref|NP_148593.1| 34 IKILLYLADlAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVEVAYKQS 83
                                  68999***99999******************************9976544 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.5e-05     0.013       4      39 ..      37      72 ..      34      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                                  HHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_1  4 lrlfvavaeegsftrAAeeLglsqpavsrqikrLEe 39
                                  l ++  +ae  s++r  + +g+s++ v +++k+LE+
  gi|14602047|ref|NP_148593.1| 37 LLYLADLAEPSSIRRISRNVGMSHKNVIKHLKALEN 72
                                  6689999****************************8 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.5e-05     0.021      10      55 .]      36      76 ..      32      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                        HTH_36 10 llgslasfanknggcfp.sqetlakrlglsknTvsraikeLeqlGyi 55
                                  +l++la++a    +  p s ++++++ g+s + v++++k Le  G++
  gi|14602047|ref|NP_148593.1| 36 ILLYLADLA----E--PsSIRRISRNVGMSHKNVIKHLKALENIGLV 76
                                  566666666....2..33789**********************9985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   1.6e-05     0.014      15      49 ..      43      77 ..      31      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                        HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLve 49
                                    ++++++++++ + ++  ++++ lk+L++ GLve
  gi|14602047|ref|NP_148593.1| 43 LAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVE 77
                                  6689999***************************5 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.7e-05      0.04      26      83 ..      39      97 ..      32     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.7e-05
                 Dimerisation2 26 lLke.eeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsntelasty 83
                                   L++  ep s + +++++g+s+k +   l+a+  +gL e+  k+++ +lY+ +e ++ +
  gi|14602047|ref|NP_148593.1| 39 YLADlAEPSSIRRISRNVGMSHKNVIKHLKALENIGLVEVAYKQSNLTLYKLSEHSRLW 97
                                  6777789**********************************8888789***99998765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00019      0.16       4      45 ..      35      77 ..      33      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                        HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vp 45
                                  +il  L +  +p s+ ++++  ++S + v +++kaLe +g v+
  gi|14602047|ref|NP_148593.1| 35 KILLYLADLAEPSSIRRISRNVGMSHKNVIKHLKALENIGlVE 77
                                  7888899999999**************************9655 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00018      0.15      25      49 ..      53      77 ..      49     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                B-block_TFIIIC 25 akeskqdprslfyrlksLekkgLIv 49
                                  ++ ++++ +++ ++lk+Le++gL++
  gi|14602047|ref|NP_148593.1| 53 SRNVGMSHKNVIKHLKALENIGLVE 77
                                  56789******************96 PP

>> PheRS_DBD1  PheRS DNA binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.16       8      55 ..      35      82 ..      28      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                    PheRS_DBD1  8 qlLqrLekkgevdsl.elAaelgvdHqkvVGavKSLqalgelIkaeqrs 55
                                  ++L +L++  e  s+  +++++g++H +v+   K L+ +g l++++ ++
  gi|14602047|ref|NP_148593.1| 35 KILLYLADLAEPSSIrRISRNVGMSHKNVIKHLKALENIG-LVEVAYKQ 82
                                  688888886666665269**********************.**998665 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   0.0   0.00017      0.15       6      58 ..      41      91 ..      34      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                        HTH_29  6 lllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprn.rls 58
                                  + lae   ++++i +++g+s + v ++lk+ e+ G   l +  + + ++   +ls
  gi|14602047|ref|NP_148593.1| 41 ADLAEPS-SIRRISRNVGMSHKNVIKHLKALENIG---LVEvAYKQSNLTLyKLS 91
                                  4555655.5**************************...55555666665555555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.15      10      53 ..      36      78 ..      24      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                  HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                        MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                  +L++L++  ++  +++ + r  g+s+ +v ++lk L+  GLve 
  gi|14602047|ref|NP_148593.1| 36 ILLYLADLAEP-SSIRRISRNVGMSHKNVIKHLKALENIGLVEV 78
                                  67777777776.4*****************************96 PP

>> Imm27  Immunity protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.1   4.4e+03       7      20 ..      13      26 ..       9      31 .. 0.70
   2 ?   11.0   0.0   0.00033      0.28       6      50 ..      58     101 ..      53     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.1
                         Imm27  7 ikddalarikslik 20
                                  +kd+ +++ + li 
  gi|14602047|ref|NP_148593.1| 13 CKDEFMQFLNKLIT 26
                                  67777777777764 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00033
                         Imm27   6 vikddalariksliknkLkelksdedgwetlYkdpndgrlWeLaY 50 
                                   +   ++++  k l +  L e++ ++ +  tlYk ++  rlW L++
  gi|14602047|ref|NP_148593.1|  58 MSHKNVIKHLKALENIGLVEVAYKQ-SNLTLYKLSEHSRLWTLQF 101
                                   6677778888888889999998765.789**************99 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 ?   11.3   0.1   0.00023       0.2      72     101 ..      47      76 ..       2      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                          RP-C  72 psNaqLsralglsestlrrhlaaLveaGli 101
                                    s +++sr++g+s++ + +hl+aL + Gl+
  gi|14602047|ref|NP_148593.1|  47 SSIRRISRNVGMSHKNVIKHLKALENIGLV 76 
                                   4668899**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 856.44
//
Query:       gi|118431864|ref|NP_148594.2|  [L=475]
Description: MatE efflux family protein [Aeropyrum pernix K1]
Scores for complete 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-44  151.1  45.2      8e-25   87.4  20.0    2.7  3  MatE             MatE
    6.3e-07   28.4  13.0    6.3e-07   28.4  13.0    2.2  2  MurJ             Lipid II flippase MurJ
    0.00033   20.8  49.6     0.0012   18.9  23.6    4.5  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6  10.6   5.5e-25   3.3e-21       1     161 []      28     188 ..      28     188 .. 0.98
   2 ?   -3.1   0.5      0.88   5.2e+03      47      59 ..     201     213 ..     190     224 .. 0.54
   3 !   87.4  20.0   1.3e-28     8e-25       1     161 []     251     412 ..     251     412 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 5.5e-25
                           MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                    Pi+ + ll  +   +d +++gr+++++lAa ++a+++l+l+  +++g++t l++lv+qa+Ga+++  a++++ + l ++l
  gi|118431864|ref|NP_148594.2|  28 PIVAARLLAATQESVDAIFLGRVSTEDLAAPAAASPLLWLFAGLGIGINTTLSALVSQAIGARDYASAQRYASKLLGATL 107
                                    899999999999******************************************************************** PP

                           MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislllniplny 160
                                     l+++ al+++l +e  + l +     le+a  y ++ ++g+p+++ ++ +++++ + g+t++p+ +s++s++ln++l++
  gi|118431864|ref|NP_148594.2| 108 MLGAASALAIILTAETVFILQGFQGRSLEVALAYTLVEAVGMPFMLALFYFNAVMAASGDTRTPFKVSALSSILNVILDP 187
                                    ***************99999999999****************************************************98 PP

                           MatE 161 l 161
                                    +
  gi|118431864|ref|NP_148594.2| 188 I 188
                                    6 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.88
                           MatE  47 glstalttlvgqa 59 
                                    ++++a++t+ ++a
  gi|118431864|ref|NP_148594.2| 201 AVGAAVATVLARA 213
                                    3555555555544 PP

  == domain 3  score: 87.4 bits;  conditional E-value: 1.3e-28
                           MatE   1 PialenllesllslidtllvgrlgskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqglilll 80 
                                    P+ l+ l++s+ +l+++ +v+rlg+  +Aa++++l i+ ++ +  +g+++a++t+vgq+lGa n  ra +a+++g+ l++
  gi|118431864|ref|NP_148594.2| 251 PVSLQRLVVSMGFLVMMGIVARLGAPVVAAYNVSLVIIHIVQSATFGFNIATATVVGQNLGASNISRAVRAAYTGVALVF 330
                                    899***************************************************************************** PP

                           MatE  81 llsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisl.llnipln 159
                                    +l  i a++++  +  ++slft+ eev  +a+r+++i++lg+p+l+ ++++ g+ rg g+t ++ ++ +++l ll+ip +
  gi|118431864|ref|NP_148594.2| 331 GLLSIGAVAIVGGRSMLVSLFTSIEEVQFYAERMISIVALGMPFLGAFFTAMGVARGSGRTAFISALGIARLwLLRIPAA 410
                                    ******************************************************************************99 PP

                           MatE 160 yl 161
                                    y+
  gi|118431864|ref|NP_148594.2| 411 YT 412
                                    96 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4  13.0   1.1e-10   6.3e-07     237     404 ..      59     227 ..       2     236 .. 0.76
   2 ?   -4.8   5.2       1.2   7.4e+03     295     395 ..     338     438 ..     308     453 .. 0.61

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.1e-10
                           MurJ 237 ayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFsee 316
                                    a a+ +l l  g +g+ i t+l + +S++  ++d  ++++  s+ +  tl+l   ++  +++ ++ +  l      F+  
  gi|118431864|ref|NP_148594.2|  59 AAASPLLWLFAG-LGIGINTTLSALVSQAIGARDYASAQRYASKLLGATLMLGAASALAIILTAETVFILQ----GFQGR 133
                                    555555555555.599999999999***********99999999999999999987777777776544433....45555 PP

                           MurJ 317 dveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnills......llllpplgvvglalatslsal 390
                                    ++e + +   + a+g+++++    + +v  A++dt+tP+k+s +s++ln++l+      l+llpplg+vg a+at+l+  
  gi|118431864|ref|NP_148594.2| 134 SLEVALAYTLVEAVGMPFMLALFYFNAVMAASGDTRTPFKVSALSSILNVILDpilifgLILLPPLGAVGAAVATVLARA 213
                                    5554444445679*****99999999****************************************************** PP

                           MurJ 391 iglvllyvllrkrl 404
                                    + + ++++ll + +
  gi|118431864|ref|NP_148594.2| 214 AAVSIAFYLLLRGA 227
                                    ********998865 PP

  == domain 2  score: -4.8 bits;  conditional E-value: 1.2
                           MurJ 295 gllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnills..... 369
                                    + +v ++ ++  lf    + ee   ++ +++++ alg++++    +++++  Ar+  +t+++ +l ++ l +l       
  gi|118431864|ref|NP_148594.2| 338 VAIVGGRSMLVSLF---TSIEEVQFYAERMISIVALGMPFLG--AFFTAMGVARGSGRTAFISALGIARLWLLRIpaayt 412
                                    34566777777777...4444455566778888888888755..456667778888888777665444332222233344 PP

                           MurJ 370 llllpplgvvglalatslsaliglvl 395
                                    l+ + +lg +g  la +ls++i  +l
  gi|118431864|ref|NP_148594.2| 413 LVYIYSLGDMGVWLAMTLSNIIAGTL 438
                                    66666777777777777777665443 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   4.6     0.044   2.6e+02      48     124 ..      63     138 ..      58     148 .. 0.62
   2 !   18.9  23.6     2e-07    0.0012       6      98 ..     146     248 ..     141     354 .. 0.77
   3 !    8.9   6.1   0.00024       1.4       2      89 ..     365     454 ..     364     461 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.044
                Polysacc_synt_C  48 lliplfgivGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllgllllaalall 124
                                    +l+ lf  +G+ i t+l+ lv+ ++  +      ++  +ll  +  +l aa +++i++++ + ++l+ +++ +l+++
  gi|118431864|ref|NP_148594.2|  63 PLLWLFAGLGIGINTTLSALVSQAIGARDYASAQRYASKLLGAT-LMLGAASALAIILTAETVFILQGFQGRSLEVA 138
                                    678888889*************9999777776666666434444.34555555555544444444444444434333 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 2e-07
                Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigalvklilnllli......plfgivGaaiatvlallvvavlnlyalrr 79 
                                    a++++f+     +++++ + g +++++k+++++ ++++il  +li      p +g+vGaa+atvla +++  + +y+l r
  gi|118431864|ref|NP_148594.2| 146 AVGMPFMLALFYFNAVMAASGDTRTPFKVSALSSILNVILDPILIfglillPPLGAVGAAVATVLARAAAVSIAFYLLLR 225
                                    7899999999***********************************998888899****************9999888877 PP

                Polysacc_synt_C  80 .llgikl...ellrrllkpllaa 98 
                                       g+++   +  r+l+ ++l  
  gi|118431864|ref|NP_148594.2| 226 gAPGFRVkpsMPDRQLIGHILRI 248
                                    46666666663333333333222 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00024
                Polysacc_synt_C   2 LailalsiiflslstvlssiLqglgrqkialkalvigal.vklilnllli..plfgivGaaiatvlallvvavlnlyalr 78 
                                    ++i+al+++fl+ + +  ++  g gr+ ++    ++ +  + +   + l+  +++g +G+ +a++l+ +++  l + ++ 
  gi|118431864|ref|NP_148594.2| 365 ISIVALGMPFLGAFFTAMGVARGSGRTAFISALGIARLWlLRIPAAYTLVyiYSLGDMGVWLAMTLSNIIAGTLAIAWVA 444
                                    789***********************9988777777664499999999994355577*****************999999 PP

                Polysacc_synt_C  79 rllgiklellr 89 
                                     ++  k+ +++
  gi|118431864|ref|NP_148594.2| 445 GRTWAKP-IVK 454
                                    8888887.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3312.47
//
Query:       gi|118431865|ref|NP_148595.2|  [L=144]
Description: hypothetical protein APE_2417.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1177.14
//
Query:       gi|118431866|ref|NP_148596.2|  [L=280]
Description: electron transfer flavoprotein beta-subunit [Aeropyrum pernix K1]
Scores for complete 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-42  144.0   0.0    5.6e-42  143.7   0.0    1.1  1  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 !  143.7   0.0   3.1e-46   5.6e-42       1     171 [.      24     198 ..      24     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.7 bits;  conditional E-value: 3.1e-46
                                    EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHH CS
                            ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeataka 80 
                                    +++l+++gv++++np dl a+e A+rl+++ ggev+av++Gpp a + l++ +  mG+d  ++++d+a+ag+d++at+++
  gi|118431866|ref|NP_148596.2|  24 TGTLIRQGVPSIINPPDLAAVELALRLRDEYGGEVIAVTMGPPPALKGLEHLIG-MGVDYGYMFSDRAFAGADTLATSYV 102
                                    5799**************************99****************999999.************************* PP

                                    HHHHHHHC.....--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSE CS
                            ETF  81 laalikke.....dpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpa 152
                                    l++ ik +      +dl l+g+++i    +++++++A++L++p+i +v +  v+ggkl+++R +e+   + e+ e++lpa
  gi|118431866|ref|NP_148596.2| 103 LSEGIKYIerergRVDLALFGQETIdSstAHIGAQVASWLQWPYIYYVRKAAVDGGKLVAERIVEN--YV-ETYELPLPA 179
                                    ********777766***********55***************************************..88.********* PP

                                    EEEE-TTSS----S-TT-- CS
                            ETF 153 vltvrpgafepaaimaakk 171
                                    v++v+ +af+p+++  ++k
  gi|118431866|ref|NP_148596.2| 180 VASVAIRAFKPREVTLSGK 198
                                    ***********77655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 2318.08
//
Query:       gi|14602051|ref|NP_148597.1|  [L=372]
Description: electron transfer flavoprotein alpha-subunit [Aeropyrum pernix K1]
Scores for complete 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-38  132.3   0.0    2.4e-38  131.8   0.0    1.2  1  ETF        Electron transfer flavoprotein domain
    3.2e-33  113.6   0.7    6.6e-33  112.6   0.7    1.6  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
  ------ inclusion threshold ------
      0.064   11.3   0.0      0.088   10.8   0.0    1.1  1  FRQ        Frequency clock protein


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 !  131.8   0.0   4.1e-42   2.4e-38       1     180 [.      24     204 ..      24     206 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.8 bits;  conditional E-value: 4.1e-42
                                   EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHH CS
                           ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakal 81 
                                   v+v+ae + +  +++++l++l+ Arr+++k+g++v++v++Gpp + ++l+ ++ ++Gad+vi+v++++l +y ++ + +++
  gi|14602051|ref|NP_148597.1|  24 VWVVAELD-EQGVSEASLQMLTPARRIADKLGESVVGVIAGPPGS-SQLAVEMVERGADEVIVVEHERLSEYYPDVVGSVI 102
                                   79*****7.99*******************99**********666.667999999************************** PP

                                   HHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCC..EEEEEECCCCTEEEEEE-T.SSSEEEEE-TT CS
                           ETF  82 aalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggk..ltvtRpieggnglaevvea.dlpavltvrpg 159
                                   ++l  k++p+++l++ata g+++ap +A  L++++++d+t+++v+ ++  + ++Rp ++   la ++++ ++p++ t rp+
  gi|14602051|ref|NP_148597.1| 103 VELSLKYKPSVILFAATARGREMAPYVANTLKTGITADCTDFDVDPKTrdVLLIRPPFSAIMLAYIRTPfRRPQIGTARPN 183
                                   *********************************************777********************************* PP

                                   SS----S-TT---EEEE--HH CS
                           ETF 160 afepaaimaakkkeveeveva 180
                                   +f+ +++++ +++ +++ ev+
  gi|14602051|ref|NP_148597.1| 184 VFPLPERQPGRQGRIVREEVE 204
                                   ***************998876 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 !  112.6   0.7   1.1e-36   6.6e-33       2      84 .]     224     306 ..     223     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.1e-36
                                   -TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHHGGGT CS
                     ETF_alpha   2 dLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhlaGmk 82 
                                    +e+a+v+vsgGrGl+++e++++leela+ lg+ ++ sR++vdagwip erqvGqtGk+v+P lyiavGisG+ qh++G++
  gi|14602051|ref|NP_148597.1| 224 PIEKAEVIVSGGRGLGTPEGFRVLEELASLLGGVIAGSRKAVDAGWIPPERQVGQTGKSVKPILYIAVGISGSAQHMVGVR 304
                                   689*****************************************************************************9 PP

                                   T- CS
                     ETF_alpha  83 es 84 
                                   e+
  gi|14602051|ref|NP_148597.1| 305 EA 306
                                   85 PP

>> FRQ  Frequency clock protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.5e-05     0.088     119     161 ..     320     364 ..     304     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.5e-05
                           FRQ 119 klsaarsssadDYrsviDDLtveikkLkeeLkrykqk..Gpdllr 161
                                      +a  s   DYr vi  L  e ++Lkee  ry ++  Gp+ lr
  gi|14602051|ref|NP_148597.1| 320 IIRQADYSLIADYREVIPALIEELRRLKEERSRYLEEllGPEALR 364
                                   55667778889***********************87555999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2657.09
//
Query:       gi|14602052|ref|NP_148598.1|  [L=436]
Description: FixC protein [Aeropyrum pernix K1]
Scores for 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-18   65.0   7.4    4.4e-10   39.7   0.5    2.2  2  DAO             FAD dependent oxidoreductase
    1.5e-09   37.5   3.9    3.3e-08   33.1   0.6    2.4  2  Thi4            Thi4 family
    3.7e-09   36.2   7.0    1.3e-06   27.7   2.7    2.4  2  FAD_binding_2   FAD binding domain
    7.2e-09   35.5   3.5    1.7e-08   34.3   3.5    1.6  1  FAD_oxidored    FAD dependent oxidoreductase
    3.3e-08   33.6   1.3    7.9e-08   32.4   1.3    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.5e-08   32.6   1.3    2.4e-07   29.8   1.0    2.1  2  HI0933_like     HI0933-like protein
    1.5e-07   31.0   3.0    5.1e-07   29.2   0.3    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.5e-07   30.3   3.6    6.4e-07   28.9   0.8    2.6  3  FAD_binding_3   FAD binding domain
    2.9e-06   26.4   2.6      0.038   12.9   0.1    2.9  3  Trp_halogenase  Tryptophan halogenase
    4.9e-05   22.7   0.6    8.1e-05   22.0   0.6    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0001   21.5   6.1    0.00029   20.0   3.9    2.4  2  Lycopene_cycl   Lycopene cyclase protein
    0.00016   22.2   1.4     0.0045   17.5   0.9    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0007   18.8   1.4     0.0007   18.8   1.4    2.0  2  GIDA            Glucose inhibited division protein A
     0.0013   18.1   0.4     0.0025   17.2   0.1    1.7  2  Amino_oxidase   Flavin containing amine oxidoreductase
      0.008   14.7   0.1          1    7.8   0.1    2.2  2  GDI             GDP dissociation inhibitor
  ------ inclusion threshold ------
      0.044   13.8   1.1       0.13   12.2   1.1    1.9  1  NAD_binding_9   FAD-NAD(P)-binding
       0.18   11.7   1.3       0.63    9.9   0.4    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.19   11.0   1.9        0.3   10.3   1.2    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.9   4.3e-10   4.3e-07       1      48 [.      11      59 ..      11      93 .. 0.78
   2 !   39.7   0.5   4.5e-13   4.4e-10     140     351 ..     101     335 ..      58     336 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.3e-10
                                  EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS CS
                           DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl 48
                                  dvv++GGG  Gl++A  Lar+g  V++le+g+++g + S   +++ ++ l
  gi|14602052|ref|NP_148598.1| 11 DVVVVGGGPGGLAAATVLARAGfkVLVLERGREPG-AKSLFGGKVYAQPL 59
                                  9******************************9999.66655555555444 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 4.5e-13
                                   EEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTT...... CS
                           DAO 140 tgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgllkel...... 213
                                   + +    +l++++a +ae++G+ ++ +  v ++  +dg v+gv   + g +++a+ vV a G+  + ll   ++l      
  gi|14602052|ref|NP_148598.1| 101 AFTTYLPELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGV--RSGGDEVRAKVVVDAEGVN-RmLL---ERLglvdpp 175
                                   555566789******************99999*9999******..33355534577******99.4366...333334223 PP

                                   .TSEEEEEEEEEEEEEECCTHSTGS...GCSEEEEE...........EEETTTTEEEEEETTSEEEEEESSEEETTCSSTS CS
                           DAO 214 .dlpispvrgqvlvlkplseklvsp...aailpvpe...........tdddgrgvyvtprkdgrvlvGgtadeesgdddpe 279
                                    + ++     +v++lkp + +  +    +      e           +  +g+g +v+ + +++v vG       +  + +
  gi|14602052|ref|NP_148598.1| 176 dPSRLALGVKEVIRLKPDEIEARFGldkK------EglawliagditNWIPGGG-FVYTM-NDSVSVGIV----LRVSS-A 243
                                   23555557788999977543222223322......1445344666644444444.55554.466888874....56666.8 PP

                                   CSHHHHHHHHHHHHHHSGGG.CG..EEEEEEE.................EEE..E.TTSSEEEEEEETEEEEEEEEECTTT CS
                           DAO 280 vdeedidellealrklfPql.gd..vlrkwaG.................lrp..l.pdglpligetpgvkglylatGhsgh 337
                                   v++++   ++e++++++ +l  +  ++r w+G                 ++p  l ++gl ++g      gl+l+tG+  +
  gi|14602052|ref|NP_148598.1| 244 VEAAEKGVIREHVSRMVERLrLHpyFKRFWTGgdiaeyggrlaiegglgYMPrkLaTNGLVVVGD---AAGLLLNTGYTIR 321
                                   88888888888888888774322234455554454444445555555558885434688999988...48*********** PP

                                   HHHHHHHHHHHHHH CS
                           DAO 338 GltlapatGkllae 351
                                   G+ +a+ +Gkl+ae
  gi|14602052|ref|NP_148598.1| 322 GVDFAAYSGKLAAE 335
                                   ************98 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.6   3.3e-11   3.3e-08      16      65 ..       8      56 ..       2      60 .. 0.93
   2 ?    5.0   0.1     0.013        13     106     135 ..     116     143 ..     105     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.3e-11
                                  TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBS CS
                          Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfs 65
                                  a  Dvv+vG+G+ GL+aa +la++ ++kv++ler   pG  +  GG+++ 
  gi|14602052|ref|NP_148598.1|  8 ASYDVVVVGGGPGGLAAATVLARA-GFKVLVLERGREPGAKSLFGGKVYA 56
                                  567*********************.*********************9886 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                                   HHHTSTTEEEEESEEEEEEEEETBTEEEEE CS
                          Thi4 106 kvlqlanvkllnavaveDlivregegvaGv 135
                                   k  + a++ +++ v+v+D++v++  +v Gv
  gi|14602052|ref|NP_148598.1| 116 K-AEEAGALVIDEVVVDDIVVKD-GSVVGV 143
                                   4.4459999**************.556665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   2.7   1.4e-09   1.3e-06       1      36 [.      11      46 ..      11      60 .. 0.90
   2 !   10.1   0.1   0.00031      0.31     141     207 ..     107     165 ..      68     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.4e-09
                                  SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                 FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                  Dv+V+G+G +GLaAA+ +a+aG kv+v+e + e g 
  gi|14602052|ref|NP_148598.1| 11 DVVVVGGGPGGLAAATVLARAGFKVLVLERGREPGA 46
                                  9****************************9987555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG... CS
                 FAD_binding_2 141 hallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrall 207
                                   ++l++ ++ +a++ag  + ++  +d+++v+dg v+G+  +  ++g evr  a +vv+ ++G++r +l
  gi|14602052|ref|NP_148598.1| 107 PELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGV--R--SGGDEVR--A-KVVVDAEGVNR-ML 165
                                   789999******************************7..5..5577665..4.56666667775.33 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   3.5   1.7e-11   1.7e-08       1     142 [.      11     158 ..      11     162 .. 0.65

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.7e-11
                  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee............qvvtgiareflerlrq 69 
                                   DvvVvGGgp+G+aAA   araG kvl++e+ +  G  +  g+       +  +              v+++     +r++ 
  gi|14602052|ref|NP_148598.1|  11 DVVVVGGGPGGLAAATVLARAGFKVLVLERGREPGAKSLFGGKVYAQPLRDVWpdldkkapihrwVRVERFSLTSGDRVAT 91 
                                   9****************************9887665544444333333222222233333344333333333333333322 PP

                  FAD_oxidored  70 rggarlkkrskwntfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                                     ++rl+++ +++t+ pe +k ++ +  +eag  v+ + ++++++++++ + +v+     g+ ++rAkv++DA
  gi|14602052|ref|NP_148598.1|  92 -IEYRLGRPVAFTTYLPELVKWMAGKA-EEAGALVIDEVVVDDIVVKDGSVVGVRS----GGDEVRAKVVVDA 158
                                   .22233444444567777777766665.6779999999999999999877777776....79**********9 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 !   32.4   1.3   7.9e-11   7.9e-08       1      35 [.      14      48 ..      14      53 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 7.9e-11
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                  +vG+G +Gl+aA  La+agf+vl+le+++ +G ++
  gi|14602052|ref|NP_148598.1| 14 VVGGGPGGLAAATVLARAGFKVLVLERGREPGAKS 48
                                  8*******************************875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   1.0   2.4e-10   2.4e-07       1      43 [.      10      52 ..      10      54 .. 0.95
   2 ?    0.3   0.0      0.22   2.1e+02      83     163 ..      81     160 ..      67     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.4e-10
                                  -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                   HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                  +dv+v+GgG+ Gl aA  +a++g +Vl+le+++++g K l  G
  gi|14602052|ref|NP_148598.1| 10 YDVVVVGGGPGGLAAATVLARAGFKVLVLERGREPGAKSLFGG 52
                                  59************************************99887 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.22
                                   HHHHHHTT--EEE-STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                   HI0933_like  83 ialveelgvelkeedsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                    +l +  +v++ e + gr    ++   ++v+ +  +++eag  +  e  v ++  ++++++ v+  +++e++a+ +v A G
  gi|14602052|ref|NP_148598.1|  81 FSLTSGDRVATIEYRLGRPVAFTTYLPELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGVRS-GGDEVRAKVVVDAEG 160
                                   56666777777777777776666677899999***************************999999.9*******9998877 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 !   29.2   0.3   5.1e-10   5.1e-07       1      33 [.      10      42 ..      10      61 .. 0.85
   2 ?    1.6   0.1      0.13   1.3e+02     167     238 ..      88     162 ..      80     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 5.1e-10
                                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33
                                  +dvvv+GgGp+Glaaa+ la+ag+kv+++e+++
  gi|14602052|ref|NP_148598.1| 10 YDVVVVGGGPGGLAAATVLARAGFKVLVLERGR 42
                                  69***************************7443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                                   E.EEEEESSSSSS..TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EE CS
                                   x.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 167 e.vtlveardrll..raldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvr 238
                                   + +t+ +++ r++   ++ +el ++++ + e+ G  v  + +v +i  ++ ++  v + g+e+ a+ vv a Gv 
  gi|14602052|ref|NP_148598.1|  88 RvATIEYRLGRPVafTTYLPELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGVRSGGDEVRAKVVVDAEGVN 162
                                   54788899999988889999*****************9999999999999988899*************999975 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.8   6.4e-10   6.4e-07       2      35 ..      10      43 ..       9      49 .. 0.92
   2 ?    0.4   0.0      0.31   3.1e+02     138     173 ..     136     170 ..      77     184 .. 0.73
   3 ?   -1.3   0.0         1     1e+03     317     337 ..     337     357 ..     294     363 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.4e-10
                                  EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                 FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                  +dV++VG+Gp Gl +a++L++aG +v+++e+ ++
  gi|14602052|ref|NP_148598.1| 10 YDVVVVGGGPGGLAAATVLARAGFKVLVLERGRE 43
                                  69****************************9776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.31
                                   CCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHT CS
                 FAD_binding_3 138 vtaevrdketgeeetvrakYlvGaDGgrStvrktlg 173
                                    +  v + ++g + +vrak +v a+G++    ++lg
  gi|14602052|ref|NP_148598.1| 136 KDGSVVGVRSGGD-EVRAKVVVDAEGVNRMLLERLG 170
                                   4556667777777.8999999999999877777776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                                   HHHHHHTTSS-GGGGHHHHHH CS
                 FAD_binding_3 317 kLaavlkGeAkeelLdtYeee 337
                                    + a  kG+ +e+ L tYee+
  gi|14602052|ref|NP_148598.1| 337 IIQALSKGDTSEATLRTYEEK 357
                                   344556889999999999887 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4   0.00012      0.12       1      32 [.      11      39 ..      11      45 .. 0.90
   2 !   12.9   0.1   3.8e-05     0.038     157     216 ..     110     168 ..      66     173 .. 0.91
   3 ?    0.8   0.0      0.18   1.8e+02     309     370 ..     276     361 ..     227     369 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                  EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                  ++v+vGGG+ G  aA++la+a+   ++v+++e
  gi|14602052|ref|NP_148598.1| 11 DVVVVGGGPGGLAAATVLARAG---FKVLVLE 39
                                  69*******************9...7888887 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.8e-05
                                   HHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIII CS
                Trp_halogenase 157 akfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieq 216
                                    k++   ae++G  +++  vv+  + +dg+v ++r   g ev a  ++D+ G +++l+e+
  gi|14602052|ref|NP_148598.1| 110 VKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGVRS-GGDEVRAKVVVDAEGVNRMLLER 168
                                   5778889****************************9.9999***************9986 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.18
                                   E..................ES-SEETTEEE-CCCTEE--CCCS-..HHHHHHH....HHHHHHHT--BTT--HHHHHHHHH CS
                Trp_halogenase 309 r..................rkqawvknvvalGlasgfvePlest..sihliqa....alrrLlallpdksdepaaiaefnr 365
                                                       ++   +++v +G+a+g +     t  ++ ++ +    a++++++ l ++  ++a++  +++
  gi|14602052|ref|NP_148598.1| 276 GdiaeyggrlaiegglgymPRKLATNGLVVVGDAAGLLLNTGYTirGVDFAAYsgklAAETIIQALSKGDTSEATLRTYEE 356
                                   455555555555555555556677889999999999986544333377777778888999999999999999999999999 PP

                                   HHHHH CS
                Trp_halogenase 366 evare 370
                                   ++++ 
  gi|14602052|ref|NP_148598.1| 357 KLKAS 361
                                   88765 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 !   22.0   0.6   8.1e-08   8.1e-05       1      31 [.      13      42 ..      13      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.1e-08
                   Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                  +++G+GP Glaaa+ l +ag+ ++l+lE+g+
  gi|14602052|ref|NP_148598.1| 13 VVVGGGPGGLAAATVLARAGF-KVLVLERGR 42
                                  79*******************.7******94 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   3.9   2.9e-07   0.00029       1     142 [.      11     162 ..      11     174 .. 0.67
   2 ?   -0.8   0.0       0.6     6e+02     258     305 ..     303     351 ..     290     376 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.9e-07
                 Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlie....aspsllfpnny...vWsdefedlgaleecvehsWsgtivylddgkk 74 
                                   Dvvv+G+Gp gl+ A  l  a++g kv+++e    +++++lf+++       d   dl+  +++  h+W +++        
  gi|14602052|ref|NP_148598.1|  11 DVVVVGGGPGGLAAATVL--ARAGFKVLVLErgrePGAKSLFGGKVyaqPLRDVWPDLD--KKAPIHRWVRVERFSLTSGD 87 
                                   9***************99..**********64333788889988743112233334444..66778999877655444444 PP

                 Lycopene_cycl  75 illgraYgr...vss....krlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdargla 142
                                   +  + +Y+    v       +l + ++ +  e+g+   +  v     +++g ++ v +gg ++ra++vvda g+ 
  gi|14602052|ref|NP_148598.1|  88 RVATIEYRLgrpVAFttylPELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGVRSGGDEVRAKVVVDAEGVN 162
                                   444445543111222101135666777787788887776655444445556899999****************65 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.6
                 Lycopene_cycl 258 vlaiGaaaglvhPaTGYsv..arslaeapll.asaiaaalresslsarawa 305
                                    + +G aagl    TGY++  ++  a + +l a+ i +al +     +a+ 
  gi|14602052|ref|NP_148598.1| 303 LVVVGDAAGLLL-NTGYTIrgVDFAAYSGKLaAETIIQALSKG-DTSEATL 351
                                   567899999886.79**99333444555544167888888853.3333333 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   4.5e-06    0.0045       2      35 ..      12      45 ..      11      54 .. 0.91
   2 ?    2.0   0.0      0.32   3.1e+02      40      77 ..     107     144 ..      86     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                                  EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  vvvvGgG  gl +A++la+ g kV v+er+ ++ 
  gi|14602052|ref|NP_148598.1| 12 VVVVGGGPGGLAAATVLARAGFKVLVLERGREPG 45
                                  8****************************99987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                     Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                   +e+ k+++ k e+ g  v+ + +v  i+ ++  v +v+
  gi|14602052|ref|NP_148598.1| 107 PELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGVR 144
                                   6889************************8887687775 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.4   7.1e-07    0.0007       1      28 [.      11      38 ..      11      52 .. 0.91
   2 ?    0.4   0.1      0.28   2.8e+02     102     149 ..     114     160 ..     108     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.1e-07
                                  CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                          GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                  dv+V+GgG  G++AA  +ar+G+kvl +
  gi|14602052|ref|NP_148598.1| 11 DVVVVGGGPGGLAAATVLARAGFKVLVL 38
                                  79***********************987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.28
                                   HHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                          GIDA 102 teklenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                     k e+   l i e  v++++v++++v gv+ + g +++ak+vv a G
  gi|14602052|ref|NP_148598.1| 114 AGKAEEAGALVIDEVVVDDIVVKDGSVVGVR-SGGDEVRAKVVVDAEG 160
                                   55556667788888999************97.5788899999998877 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.5e-06    0.0025       2      27 ..      20      45 ..      19      66 .. 0.82
   2 ?   -2.6   0.0       2.4   2.4e+03     206     218 ..     288     300 ..     272     338 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                                  HHHHHHHHHHHTTEEEEEEESSSSSB CS
                 Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvG 27
                                   GLaaA+ L++aGf+V+vlE    +G
  gi|14602052|ref|NP_148598.1| 20 GGLAAATVLARAGFKVLVLERGREPG 45
                                  5*******************876665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                                   TTHTHHHHHHHHH CS
                 Amino_oxidase 206 rgGlsqlpealae 218
                                   +gGl+ +p+ la 
  gi|14602052|ref|NP_148598.1| 288 EGGLGYMPRKLAT 300
                                   5555555555554 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0098       9.7       3      42 ..       8      47 ..       6      63 .. 0.90
   2 !    7.8   0.1     0.001         1     245     281 ..     120     156 ..     104     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0098
                                  XEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGG CS
                           GDI  3 eeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGge 42
                                    ydv+v+G G      + +l+  g kvl+l+r    G++
  gi|14602052|ref|NP_148598.1|  8 ASYDVVVVGGGPGGLAAATVLARAGFKVLVLERGREPGAK 47
                                  57******************************98877765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                                   T-EEETS--ECEEEE-TTS-EEEEEETTEEEEECEEE CS
                           GDI 245 GGtymlnkpvdevvldedgkvvGvkseeevakakkvi 281
                                    G+ ++++ v++ ++ +dg vvGv+s+++ ++ak v+
  gi|14602052|ref|NP_148598.1| 120 AGALVIDEVVVDDIVVKDGSVVGVRSGGDEVRAKVVV 156
                                   57778888776666669************99998776 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   0.00013      0.13       1     154 [.      13     160 ..      13     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                 NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqseelllNvpasemslftddpptfaeWlrerga.. 78 
                                   ++vG+Gp Gla+++ L++       +++ + ++ +epga++ +  +         p +++ +  d++   ++W+r ++   
  gi|14602052|ref|NP_148598.1|  13 VVVGGGPGGLAAATVLARA-----GFKVLVLERgREPGAKSLFGGKVY-----AQPLRDVWPDLDKKAPIHRWVRVERFsl 83 
                                   69************99999.....6********9999*9999888844.....4588888999999999999999988654 PP

                 NAD_binding_9  79 lee..aeeldpddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                   + +    ++ +++  +   +  Yl +l++ ++ +++e   + + +  v d+  +++++  + ++g++++a+ Vv A G
  gi|14602052|ref|NP_148598.1|  84 T-SgdRVATIEYRLGRPVAFTTYLPELVKWMAGKAEEAGALVIDEVVVDDIVVKDGSVVGVRSGGDEVRAKVVVDAEG 160
                                   1.2333444466666667789999999999998887765444444444467777777666677888889988887665 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 ?    9.9   0.4   0.00063      0.63       2      31 ..      12      41 ..      11      49 .. 0.90
   2 ?   -0.9   0.0       1.3   1.3e+03      15      70 ..     310     361 ..     304     377 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00063
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                  v v+G G  G   a+v+a+ag++V ++++ 
  gi|14602052|ref|NP_148598.1| 12 VVVVGGGPGGLAAATVLARAGFKVLVLERG 41
                                  89************************9975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                   HHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEE CS
                       3HCDH_N  15 aavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisft 70 
                                   a +++++g++++ vd ++ + + a+e+i + l    +kg ++e++ +++ ++++++
  gi|14602052|ref|NP_148598.1| 310 AGLLLNTGYTIRGVDFAAYSGKLAAETIIQAL----SKGDTSEATLRTYEEKLKAS 361
                                   66778888888888888888888887777644....44555555555555555554 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 ?   10.3   1.2    0.0003       0.3      30      59 ..      11      40 ..       2      56 .. 0.86
   2 ?   -3.7   0.0         6     6e+03     188     211 ..     118     140 ..     101     141 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDv 59
                                   v+v+GgG  Gl+A+ + ++ g kV vl+ 
  gi|14602052|ref|NP_148598.1| 11 DVVVVGGGPGGLAAATVLARAGFKVLVLER 40
                                  69***********************99986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6
                                   HTCCHHHCTSHHHHCCEEEETTEE CS
                   AlaDh_PNT_C 188 kglkkalkedealrkglvvkkGkv 211
                                   ++   al  de++   +vvk+G+v
  gi|14602052|ref|NP_148598.1| 118 EEA-GALVIDEVVVDDIVVKDGSV 140
                                   333.56666777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2973.80
//
Query:       gi|14602053|ref|NP_148599.1|  [L=382]
Description: aspartate aminotransferase [Aeropyrum pernix K1]
Scores for complete 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  115.8   0.0    2.7e-33  115.5   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.026   13.0   0.0       0.04   12.5   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


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 !  115.5   0.0     3e-37   2.7e-33       2     338 ..       4     323 ..       3     338 .. 0.94

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 3e-37
                                   EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHC CS
                   Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalsl 81 
                                   +l+ +++t++ +eVl a++             ++h + ++ ++  e+ + +++l+ ++   ++  + G+++ +++ +++s+
  gi|14602053|ref|NP_148599.1|   4 LLMIPGPTPVDPEVLLAMARP----------VISHTSPDFDEIHGETVSMLQKLFRTSG--KVFLLPGSGSlGMEFAVRSV 72 
                                   58999*************999..........599***********************96..999999*9999********* PP

                                   CCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--..TTEEEEEEESBETTTTEB--HHH CS
                   Aminotran_5  82 arslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln..ektklvaithvsnvtGtiqpvee 160
                                        +g +++v +a++ +     +++ +  ga v+v++   +   +  ++e++l+   ++++v+++hv+++t + +pv e
  gi|14602053|ref|NP_148599.1|  73 ---AGRGSRALVLKAGYFGGY--FERILRSLGASVTVVESPVGRGFTGADVEEALDraGDVDVVFVQHVETSTSVANPVRE 148
                                   ...89****************..9*******************************65589********************* PP

                                   HHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEE CS
                   Aminotran_5 161 igklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsleett 240
                                   i+ ++kk+ga ++vD+ ++vg + + ++++gvD++  +++K l  P+G+ ++ +++e+ ++le+ +++g +++  sl +  
  gi|14602053|ref|NP_148599.1| 149 IAGVVKKNGARLVVDGIASVGGMDLRLDEWGVDVALTGSQKaLSTPPGLAIVAFSSEYSVELEKREPSGIYFDFLSLSREM 229
                                   *****************************************999*********************************7766 PP

                                   EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEE.TTCS CS
                   Aminotran_5 241 faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnf.kgvh 320
                                     e+ + ++  Tp v+ + +l+a l+ +   gle+  ++++ la + + ++++l+   +  +++  r  +++++ + +g++
  gi|14602053|ref|NP_148599.1| 230 --ESTRNYHI-TPAVNLVFALNASLKRILGEGLENRFERHRVLARAFTRAMEALGLRLV--AEEPFRAWTVTAVYLpQGID 305
                                   ..56777786.*********************************************999..34567778888888899*** PP

                                   HHHHHHHHHHTTEEEEEE CS
                   Aminotran_5 321 aedvatlLdeegIavrsG 338
                                   ++ + ++++++g++v +G
  gi|14602053|ref|NP_148599.1| 306 WSRFYSVMRKRGVEVAGG 323
                                   ***************998 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.4e-06      0.04      67     196 ..      52     187 ..      36     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-06
                                   -SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.....TSHHHHHHHCCT..TEEE CS
               Cys_Met_Meta_PP  67 geaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.....sdleelekaike..ntkl 140
                                   g+  l+  sG   ++ a+++++  G++ +v +  Y g   +++++l+ lg +v++v+         +++e+a++    +++
  gi|14602053|ref|NP_148599.1|  52 GKVFLLPGSGSLGMEFAVRSVAGRGSRALVLKAGYFGG--YFERILRSLGASVTVVESpvgrgFTGADVEEALDRagDVDV 130
                                   5556677899999999*********9988888777775..5899999999999999985555567889999999877899* PP

                                   EEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEET CS
               Cys_Met_Meta_PP 141 vylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSa 196
                                   v++  +   +     +++ia ++kk+g+ +vvD   + + +  r  ++g+D+ +   
  gi|14602053|ref|NP_148599.1| 131 VFVQHVETSTSVANPVREIAGVVKKNGARLVVDGIASVGgMDLRLDEWGVDVALTGS 187
                                   **999999999999999****************998777466666679999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2810.95
//
Query:       gi|14602054|ref|NP_148600.1|  [L=220]
Description: haloacid dehalogenase superfamily protein [Aeropyrum pernix K1]
Scores for complete 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-07   30.3   0.0    9.4e-07   29.0   0.0    1.7  2  Translin  Translin family


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.057     1e+03       3      33 ..      32      62 ..      30     105 .. 0.67
   2 !   29.0   0.0   5.3e-11   9.4e-07     113     191 ..     100     191 ..      57     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.057
                                  HHHHHHHHHHHHHHHHHHHHHHHTTGSSTTT CS
                      Translin  3 reriikasrditaaskkiifllhrvrsekte 33
                                  re+ i++ rd+ ++s  +++++h+   e++e
  gi|14602054|ref|NP_148600.1| 32 REEAIRLARDVVRYSGWAVTAVHKGSLEEAE 62
                                  8999999999999998888888875544433 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 5.3e-11
                                   S..............SSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHHHHHHHHHHTS----HH... CS
                      Translin 113 n..............eedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkflrelragfellnlkndsakd 179
                                   +              + d++ +++  Y+ Gl dL+gEL R++   v +g+++ k+ + l+ +++++ ++++l+ +      
  gi|14602054|ref|NP_148600.1| 100 EarlfidiitgrglsSPDELRVPIVPYIQGLGDLVGELRRLSLELVRRGEFR-KAWSLLDIMEAIYLELRSLDYPEALLPG 179
                                   044555555555666789999******************************9.********************99655668 PP

                                   HHHHHTTHHHHH CS
                      Translin 180 lrkKldvlkqsv 191
                                   +r+K dv +  v
  gi|14602054|ref|NP_148600.1| 180 VRHKADVARRLV 191
                                   999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1723.22
//
Query:       gi|14602055|ref|NP_148601.1|  [L=326]
Description: hypothetical protein APE_2425 [Aeropyrum pernix K1]
Scores for complete 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-06   28.8   0.1    2.6e-06   27.7   0.1    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
     0.0003   21.0   0.2    0.00068   19.8   0.2    1.6  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 !   27.7   0.1   2.9e-10   2.6e-06       3      82 ..     221     302 ..     219     305 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.9e-10
                GHMP_kinases_C   3 ealergdlellgellnlsqrs.....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvara 78 
                                   +++ +g++++ ++ + +++r        ++    ++ e+ee+++a+ ++G  + +  ++++Gptv++l+    +a+ v++a
  gi|14602055|ref|NP_148601.1| 221 ANAAEGRWGEAARWMGEFNRRlgeywAGEQGGIYCCSEVEEIVRAMVDAG--AWSGLQSSWGPTVYGLT-PARRAASVLEA 298
                                   6778899999******99999*****55559*******************..****************9.99999*99999 PP

                GHMP_kinases_C  79 lree 82 
                                    r++
  gi|14602055|ref|NP_148601.1| 299 ARRA 302
                                   9776 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 !   19.8   0.2   7.6e-08   0.00068       1      46 [.      83     129 ..      83     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.6e-08
                                   EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH.HHHHHHHHHHH CS
                GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallgls.leeaklaleae 46 
                                   +i+i+ eiP + GLGS +Ala+++   +++ +gl+ l++ +la++a 
  gi|14602055|ref|NP_148601.1|  83 KIRIYEEIPAHVGLGSTTALALSIGSSIYRICGLEpLDLRELAVTAG 129
                                   5899*****************************99877777877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2640.89
//
Query:       gi|118431867|ref|NP_148602.2|  [L=363]
Description: Na(+)/H(+) antiporter [Aeropyrum pernix K1]
Scores for complete 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-50  172.3  58.1    1.9e-50  171.8  58.1    1.2  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.8  58.1   1.1e-54   1.9e-50       2     369 ..      12     354 ..       9     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 1.1e-54
                                    HHHHHHHHHHHH.HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHH CS
                 Na_H_Exchanger   2 vllillallvgl.larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksil 80 
                                    ++l++ ++l+ + +a+ ++lp+ v++ii+G +l+ +g++   ++ e+l++l+ +g  lllF aG e+dl+ lr+ l +++
  gi|118431867|ref|NP_148602.2|  12 IVLVAFYILAATrIAHVIGLPPGVVEIIMGAMLAFWGVK---ST-EVLTLLAAIGANLLLFMAGSEIDLALLRSILPQAV 87 
                                    23333344444466************************9...66.*********************************** PP

                                    HHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCH CS
                 Na_H_Exchanger  81 llallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvlla 160
                                    ++al++ l++++l + ll++   lg++l+ +l++ a lsat++++++ +l+ +++v++rlg+l+l+ ++l D++++++l+
  gi|118431867|ref|NP_148602.2|  88 IVALVSALAPLAL-TALLHV--YLGLSLTSSLVILASLSATSVALTYLLLSSYRLVRSRLGQLALASAMLLDLSGMIMLN 164
                                    *************.888887..589******************************************************* PP

                                    HHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHH CS
                 Na_H_Exchanger 161 vllalakeeaggetslllllliflvvavgglllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilg 240
                                    ++ a +             + ++++ +v++l++ l+ ++l+rl  +      e e++l+ ++++++ +l++ +gv+++l 
  gi|118431867|ref|NP_148602.2| 165 IATASI-------------SPSLAFYIVILLAALLLYPLLPRLGGAP----FEAEIRLITMTVIILGFLSDFVGVHSVLT 227
                                    *77665.............778999999999***********99997....6**************************** PP

                                    HHHHHHHHH.HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXS CS
                 Na_H_Exchanger 241 aflaGlvls.eyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilavflllrllg 319
                                    +f++G++ s +++++ +l+ekles+++g+f p+fF+ +G+s+d+ +    l+ ++l+l+  va+ l+r+ +v+++ rl+g
  gi|118431867|ref|NP_148602.2| 228 SFILGVIASeTVRTRVQLREKLESLATGFFTPFFFIASGMSIDPGIP---LHYVALALAGGVALALARTYTVYFYFRLTG 304
                                    *********88899999**************************9999...9***************************** PP

                                    SXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHH CS
                 Na_H_Exchanger 320 lslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvl 369
                                     s+r++li++ + ++ ++v++++a++g +lgll++ +y++l+++v+ t+l
  gi|118431867|ref|NP_148602.2| 305 SSRRSSLIAASSTAMLLTVTIIAASVGFQLGLLDSLMYSVLVWIVVGTIL 354
                                    ************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2845.16
//
Query:       gi|118431868|ref|NP_148604.2|  [L=159]
Description: thioredoxin [Aeropyrum pernix K1]
Scores for 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-17   61.4   0.0    9.2e-17   60.9   0.0    1.2  1  Thioredoxin    Thioredoxin
      5e-07   30.2   0.0    9.3e-06   26.1   0.0    2.5  2  Thioredoxin_2  Thioredoxin-like domain
    0.00013   21.8   0.0     0.0002   21.2   0.0    1.4  1  DIM1           Mitosis protein DIM1
    0.00031   20.2   0.0    0.00034   20.1   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0013   18.6   0.0     0.0018   18.2   0.0    1.2  1  TraF           F plasmid transfer operon protein
     0.0056   16.8   0.0       0.01   16.0   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
     0.0076   16.2   0.1      0.024   14.6   0.1    1.8  1  HyaE           Hydrogenase-1 expression protein HyaE
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.024   14.4   0.0    1.4  1  Thioredoxin_9  Thioredoxin
      0.073   13.5   0.0       0.13   12.7   0.0    1.5  1  DUF836         Glutaredoxin-like domain (DUF836)
      0.081   13.3   0.0        3.1    8.2   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
      0.096   12.6   0.0       0.15   12.0   0.0    1.2  1  DFF-C          DNA Fragmentation factor 45kDa, C terminal dom
        0.1   12.6   0.0       0.17   11.9   0.0    1.4  1  Thioredoxin_3  Thioredoxin domain
       0.32   11.1   2.5        1.9    8.6   0.1    2.9  3  Lambda_CIII    Lambda Phage CIII


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 !   60.9   0.0   6.7e-20   9.2e-17       7     102 ..      46     141 ..      40     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 6.7e-20
                                    HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEE CS
                    Thioredoxin   7 kenFeeevakekklvlveFyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlklfkngkev 85 
                                    +en  + +++ ++  ++ F+A+wCg C  ++  l+++a++l   ++++ +vdvd   +la++y+v+ iPt +++ +g+ v
  gi|118431868|ref|NP_148604.2|  46 NENLPKVLSQ-HRVAVILFTAEWCGRCILMQDILTRIASRLFRdDIVFGRVDVDRAFSLAERYGVQHIPTTLIIVEGRVV 124
                                    5666666677.9**************************997666************************************ PP

                                    EEEESS-HHHHHHHHHH CS
                    Thioredoxin  86 kkyegarekeklaaflk 102
                                    + ++g+ ++ekl + ++
  gi|118431868|ref|NP_148604.2| 125 DALVGSVSEEKLLERIN 141
                                    ***********998876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   2.8e+03      22      58 ..      21      49 ..      17      55 .. 0.71
   2 !   26.1   0.0   6.7e-09   9.3e-06       3     107 ..      54     138 ..      51     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                  Thioredoxin_2 22 klkkelkelddvtvrvllfplkpsfepkavaiwcake 58
                                    lk+el ++ d+        +++ ++++ v+i+ ++ 
  gi|118431868|ref|NP_148604.2| 21 TLKDELLKIGDI--------ISRRSSQILVDIDNENL 49
                                   566677777555........78888899999888765 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 6.7e-09
                  Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtP 82 
                                    ++++  +++ft+++C+ C ++++ l  +    +r     +++++++  v++++a +             la++ygv+  P
  gi|118431868|ref|NP_148604.2|  54 SQHRVAVILFTAEWCGRCILMQDILTRI---ASR----LFRDDIVFGRVDVDRAFS-------------LAERYGVQHIP 113
                                    5788999*************99877777...444....155664444444444444.............78********* PP

                  Thioredoxin_2  83 t.ivfldgkeivarlpGyvpaeelea 107
                                    t +++ +g+ +v+ l+G v++e+l++
  gi|118431868|ref|NP_148604.2| 114 TtLIIVEGR-VVDALVGSVSEEKLLE 138
                                    *888*****.************9987 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.4e-07    0.0002      19     105 ..      55     142 ..      43     159 .] 0.84

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.4e-07
                                    SSSEEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEE.EEETTT--TTSCCCTT-.SSSEEEEEETTEEEEEE-SSS-- CS
                           DIM1  19 eerlvviRFGrdedaeClklDelLakiaeklknfaviy.lvdidevpdfnkmyele.dpvtilffyrnkhmkvDfgtgdn 96 
                                    ++r+ vi F  ++   C+ + ++L++ia++l +  +++  vd+d+   + + y ++  p+t+++  +++ +   +g+  +
  gi|118431868|ref|NP_148604.2|  55 QHRVAVILFTAEWCGRCILMQDILTRIASRLFRDDIVFgRVDVDRAFSLAERYGVQhIPTTLIIV-EGRVVDALVGSVSE 133
                                    789***************************9877655438****************667666666.99999999999999 PP

                                    SSB-S---- CS
                           DIM1  97 nKlnfvled 105
                                    +Kl   ++ 
  gi|118431868|ref|NP_148604.2| 134 EKLLERINR 142
                                    999877664 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 !   20.1   0.0   2.5e-07   0.00034      10     102 ..      37     118 ..      31     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.5e-07
                      OST3_OST6  10 s.ngviklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvF 88 
                                    s + ++++++en+ ++l++ r    v+l+Ta+     C  C  +++ ++ +a+  ++d      +++F++vd+d++ ++ 
  gi|118431868|ref|NP_148604.2|  37 SsQILVDIDNENLPKVLSQHR--VAVILFTAE----WCGRCILMQDILTRIASRLFRD------DIVFGRVDVDRAFSLA 104
                                    2357899*********98666..6899****9....7*********************......6*************** PP

                      OST3_OST6  89 qklglnsaPhlllf 102
                                    +++g++++P  l++
  gi|118431868|ref|NP_148604.2| 105 ERYGVQHIPTTLII 118
                                    *********99887 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.3e-06    0.0018     111     223 ..      40     140 ..      33     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                           TraF 111 vlndarkeekeaalkklakeygLlfFyrgkcpyceaqapilqafadky...glevraVsvdgrplpelpnarvdkgqaar 187
                                    +l d ++e+  ++l++  ++++ ++F ++ c+ c  +++il ++a +     +    V+vd+ ++  l++         r
  gi|118431868|ref|NP_148604.2|  40 ILVDIDNENLPKVLSQ--HRVAVILFTAEWCGRCILMQDILTRIASRLfrdDIVFGRVDVDRAFS--LAE---------R 106
                                    5555666666666665..5799***********************987665899999******99..777.........* PP

                           TraF 188 lgvkrtPalvlvdpksqkvvpvaaGllsldeleeri 223
                                    +gv+++P+++++ +   +vv   +G +s+++l+eri
  gi|118431868|ref|NP_148604.2| 107 YGVQHIPTTLIIVEG--RVVDALVGSVSEEKLLERI 140
                                    *************99..88888899**********9 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.6e-06      0.01      10      65 ..      49     102 ..      42     119 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.6e-06
                                    HHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                  Thioredoxin_7  10 lakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65 
                                    l k  ++++   + f+a+wc+ C  +++  l++    +++++++v+ rvdv++   
  gi|118431868|ref|NP_148604.2|  49 LPKVLSQHRVAVILFTAEWCGRCILMQD-ILTR-IASRLFRDDIVFGRVDVDRAFS 102
                                    5566778888889**********98875.5555.46666************87655 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.7e-05     0.024      14     100 ..      44     128 ..      32     133 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                                    E-CCCHHHHHHHHSEEEEEESS-.SS-SSSSS-HCHHHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEET CS
                           HyaE  14 vdadtlddflkaagdavlllagD.pkrfpEvsDvaVvlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrd 92 
                                    +d+++l++ l+++  av+l++++   r   ++D    ++   + F +      v d ++   laer+gv++ P++l++ +
  gi|118431868|ref|NP_148604.2|  44 IDNENLPKVLSQHRVAVILFTAEwCGRCILMQDILTRIA--SRLFRDDIVFGRV-DVDRAFSLAERYGVQHIPTTLIIVE 120
                                    667777777777777666665432445555555333332..2444444444444.4778889****************** PP

                                    TEEEEEEE CS
                           HyaE  93 geylgvla 100
                                    g+++ +l 
  gi|118431868|ref|NP_148604.2| 121 GRVVDALV 128
                                    **998775 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.7e-05     0.024      39     107 ..      54     121 ..      33     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                    --S-EEEEEE--TT-HHHHHHHHHHHHHHHH..-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
                  Thioredoxin_9  39 iekklkilvltedwCgDaavnvPvlakiael..npnievkillrdenlelmdqyltngaraiPtliildee 107
                                     + ++ ++ +t++wCg ++ +  +l +ia+    ++i +  +  d+   l ++y   g + iPt +i+ e+
  gi|118431868|ref|NP_148604.2|  54 SQHRVAVILFTAEWCGRCILMQDILTRIASRlfRDDIVFGRVDVDRAFSLAERY---GVQHIPTTLIIVEG 121
                                    456689999********************8622566777777777777777777...88999999998765 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.6e-05      0.13       2      51 ..      60     113 ..      59     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-05
                                    EEEEE-TT-HHHHHHHHHHHH...HCCCTTEEEEEEETTT-CCCHCCCCTT.TT CS
                         DUF836   2 ltLyskpgChlCeqakekLke...lkleegleleviDIakdeeleakYgle.ip 51 
                                    ++L++ + C+ C  ++++L +      ++++   ++D+++  +l ++Yg++ ip
  gi|118431868|ref|NP_148604.2|  60 VILFTAEWCGRCILMQDILTRiasRLFRDDIVFGRVDVDRAFSLAERYGVQhIP 113
                                    89*****************984333345559999*****9999*****975355 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.069        95       3      30 ..      58      85 ..      56     101 .. 0.75
   2 ?    8.2   0.0    0.0023       3.1      69      90 ..      98     119 ..      86     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.069
                                   EEEEEE--SSSHHHHHHHHHHHHHHHHH CS
                  Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyekl 30
                                   v ++ f a+wc  c  +   l+++ ++l
  gi|118431868|ref|NP_148604.2| 58 VAVILFTAEWCGRCILMQDILTRIASRL 85
                                   67899*********77777777766555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                                    T-HHHHTT-S--TT-SEEEEE- CS
                  Thioredoxin_8  69 kkrnklkkkynvkaiPtlvvld 90 
                                    ++   l+++y+v++iPt++++ 
  gi|118431868|ref|NP_148604.2|  98 DRAFSLAERYGVQHIPTTLIIV 119
                                    445589***********99985 PP

>> DFF-C  DNA Fragmentation factor 45kDa, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.15      27      69 ..      15      58 ..       3      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                          DFF-C 27 WknlarqLkedlssii.llseedLqvLidvpcsdLaselgqsek 69
                                     ++ar Lk++l +i  ++s    q+L+d+  ++L + l+q++ 
  gi|118431868|ref|NP_148604.2| 15 LYQVARTLKDELLKIGdIISRRSSQILVDIDNENLPKVLSQHRV 58
                                   5789**********95489********************99876 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.17       7      72 ..      64     138 ..      56     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                    SSS.STTCHHHHHHHHHHCHCC.TCEC..EEECC.TTHHHHHHCT-SSSSEE..ECTTCEE..EESS---CCHHH CS
                  Thioredoxin_3   7 gpg.CakCpklekavkeaaaek.gika..evekv.tdfeeiekygVmsvPal..vidgkvv..vsGkvpseeeir 72 
                                    +   C +C  ++ +++++a ++ + ++    ++v   f+  e+ygV+ +P++  +++g+vv   +G+v +e+ ++
  gi|118431868|ref|NP_148604.2|  64 TAEwCGRCILMQDILTRIASRLfRDDIvfGRVDVdRAFSLAERYGVQHIPTTliIVEGRVVdaLVGSVSEEKLLE 138
                                    44559999988888888888876433322334442566666**********977788999655788776666555 PP

>> Lambda_CIII  Lambda Phage CIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.35   4.8e+02      10      36 ..       7      33 ..       3      35 .. 0.76
   2 ?   -1.0   0.1       1.4     2e+03      17      25 ..      77      85 ..      73      88 .. 0.83
   3 ?    8.6   0.1    0.0014       1.9      12      33 ..     131     155 ..     125     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                    Lambda_CIII 10 aGvpqESlLdRitrklRegwkrlidiL 36
                                   +G      L  ++r l++   ++ di+
  gi|118431868|ref|NP_148604.2|  7 MGETVSGSLYQVARTLKDELLKIGDII 33
                                   555544568889*****9999999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                    Lambda_CIII 17 lLdRitrkl 25
                                    L Ri+ +l
  gi|118431868|ref|NP_148604.2| 77 ILTRIASRL 85
                                   5899*9997 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0014
                    Lambda_CIII  12 vpqESlLdRitrklRe...gwkrli 33 
                                    v++E lL+Ri r l +   g kr++
  gi|118431868|ref|NP_148604.2| 131 VSEEKLLERINRELTDiekGGKRIA 155
                                    788*********9876333666776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1216.49
//
Query:       gi|118431869|ref|YP_874943.1|  [L=194]
Description: hypothetical protein APE_2431.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.8   0.4    1.4e-18   67.3   0.4    1.1  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.4     8e-23   1.4e-18       6     135 ..      28     162 ..      23     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 8e-23
                                    HHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST..........TECEEEEEEEEEESSHHHHHHHHHHHH CS
                          THUMP   6 llkegkvnverveagkgrivvelkgekpeedeellkealekar..........giqrvipvcevceadledileaakeiv 75 
                                    + + ++v+ve+ ++  g++++  ++++++ +++ ++++le  r           + rvipv+++++a++ed+++a++++ 
  gi|118431869|ref|YP_874943.1|  28 YREYKDVAVEDLRYALGEVYIIATRMNVIFARASYEDPLELRRrlerrlpedtPVLRVIPVMRIVPAEVEDVKKAVHSLL 107
                                    567899************************************************************************** PP

                                    HHHHHHCT-EEEEEEEESSSTS..SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEET CS
                          THUMP  76 kkkfeeeketFaVrvkrrgkhf..eftsreinrevGkaivektglkVdlenPdivvrveiik 135
                                     +++ +   +Fa+r ++r  ++  e+ ++e  +++++ +++    +Vdl +Pdi+v++++++
  gi|118431869|ref|YP_874943.1| 108 ATQKPG---SFAIRLEARLLREgrEIPRMEAVKIIAEGVNR----SVDLGRPDILVLIKPFR 162
                                    ***987...*********999999*****************....9************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1566.78
//
Query:       gi|118431870|ref|NP_148606.2|  [L=489]
Description: phospho-sugar mutase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-37  127.6   0.0    5.8e-37  126.5   0.0    1.6  2  PGM_PMM_I       Phosphoglucomutase/phosphomannomutase, alpha/
    3.1e-16   59.8   0.0    6.6e-16   58.8   0.0    1.5  1  PGM_PMM_II      Phosphoglucomutase/phosphomannomutase, alpha/
    1.1e-08   35.1   1.3    1.7e-08   34.5   0.1    1.9  2  PGM_PMM_IV      Phosphoglucomutase/phosphomannomutase, C-term
    6.8e-05   23.0   0.1    0.00025   21.2   0.0    2.0  2  PGM_PMM_III     Phosphoglucomutase/phosphomannomutase, alpha/
  ------ inclusion threshold ------
       0.16   12.3   0.0        7.7    7.0   0.0    2.5  2  FCSD-flav_bind  Flavocytochrome c sulphide dehydrogenase, fla


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 !  126.5   0.0   1.6e-40   5.8e-37       2     133 ..       6     133 ..       5     137 .. 0.97
   2 ?   -3.4   0.0       2.1   7.5e+03      29      49 ..     266     286 ..     262     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1.6e-40
                                    GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHH CS
                      PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPa 81 
                                    ++fgt+G+Rg++   ++tp l++++g a+a y+ +   ++++vv++D R++s+ la+ +a+g++a Gv++il+g +p Pa
  gi|118431870|ref|NP_148606.2|   6 RLFGTAGIRGRYL-RKVTPLLAYQVGLALAGYVGS---GGSIVVAHDVRTTSPLLASMAASGVMAGGVDAILVGQVPLPA 81 
                                    68***********.559*****************9...8***************************************** PP

                                    HHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCC CS
                      PGM_PMM_I  82 vsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiek 133
                                    +s+++ + + ++gim+taSHnpp +ngiK+++s+G+++++++ee++e+iie 
  gi|118431870|ref|NP_148606.2|  82 ASYSVVRSGSKSGIMVTASHNPPWDNGIKIVDSRGMELTRSEEEELESIIED 133
                                    ************************************************9986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                                    HHHHHCHHCSTS-EEEEEE-S CS
                      PGM_PMM_I  29 aiaeylkaeakkkkvvvGrDt 49 
                                    a+ ++ k +++k++vvv+ D 
  gi|118431870|ref|NP_148606.2| 266 ALLSWWKLRERKGSVVVSVDV 286
                                    566666767789999999986 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 !   58.8   0.0   1.8e-19   6.6e-16       3      97 ..     158     250 ..     156     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 1.8e-19
                                    HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-.EEEES-----TT-TTSS----TT-TTTTHHHHGGGG CS
                     PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgv.dvvelnaepdpdfptkapnpeekealkllielvkke 81 
                                    Y+e+++++   +   +++l++++d+++Ga++++++ +l+++gv +v++ n++pd+ fp+++p+p++ ++l+ +i+  +  
  gi|118431870|ref|NP_148606.2| 158 YMEDIVART--AVDGETSLSMAVDCANGAASGVTPIVLRSIGVrRVYTFNCHPDGYFPGRHPEPRP-DVLEPFIKSSSIL 234
                                    666665554..35677899************************99999******************.************* PP

                                    G-SEEEEE-TTS-BEE CS
                     PGM_PMM_II  82 gadlglafDgDaDRlg 97 
                                    g ++ +a+DgDaDR +
  gi|118431870|ref|NP_148606.2| 235 GVQAFIAHDGDADRTA 250
                                    **************87 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 ?   -2.5   0.2       1.6   5.9e+03      25      42 ..     287     303 ..     274     304 .. 0.79
   2 !   34.5   0.1   4.7e-12   1.7e-08      25      66 ..     406     447 ..     381     453 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                                    CCCCCCCCGCCEEEE.EE CS
                     PGM_PMM_IV  25 ikeglkilledGrrlavR 42 
                                     +e+++++ e G r+ vR
  gi|118431870|ref|NP_148606.2| 287 GIEVEEVVEELGGRI-VR 303
                                    468899999999999.88 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 4.7e-12
                                    CCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHH CS
                     PGM_PMM_IV  25 ikeglkilledGrrlavRpSGTepllrvyvEaksdeelarla 66 
                                    +++g++i++ed ++l  R SGTep+lrvy+ a+++e+l +l 
  gi|118431870|ref|NP_148606.2| 406 PIDGVRIDYEDRSWLLFRKSGTEPKLRVYAQAREKERLVELL 447
                                    6789999999999999*****************888887765 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 ?   -2.1   0.0       1.2   4.2e+03      10      42 ..      34      63 ..      27      68 .. 0.51
   2 !   21.2   0.0     7e-08   0.00025       5     109 ..     264     363 ..     260     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                                   HHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT CS
                    PGM_PMM_III 10 akylleeklkpgagvvktvmtslalervakklg 42
                                   a y+ +    ++ +v+++v t++ l   +++ g
  gi|118431870|ref|NP_148606.2| 34 AGYVGS---GGSIVVAHDVRTTSPLLASMAASG 63
                                   444422...233356666666665555444444 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 7e-08
                                    HHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS-- CS
                    PGM_PMM_III   5 llallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattkD 84 
                                    ++all+   l+  +++g  vv +v     +e+v+++lg+++v+++ G  +  ++++e +avl+ E    +i +d   + D
  gi|118431870|ref|NP_148606.2| 264 VIALLSWWKLR--ERKGS-VVVSVDVGIEVEEVVEELGGRIVRSRLGKIH-EKLLQEANAVLAAEP-WKLIDPDWGLWVD 338
                                    55555554444..34555.****************************754.334566689***997.78*********** PP

                                    HHHHHHHHHHHHHHHTS-HHHHHHH CS
                    PGM_PMM_III  85 Gilaallvleilaetgkslsellee 109
                                    G++ a+l+++i   tgk++ ell+ 
  gi|118431870|ref|NP_148606.2| 339 GVYQAALLAHISLATGKTPRELLDM 363
                                    **********************954 PP

>> FCSD-flav_bind  Flavocytochrome c sulphide dehydrogenase, flavin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.055     2e+02      10      39 ..      84     116 ..      82     130 .. 0.73
   2 ?    7.0   0.0    0.0021       7.7      11      27 ..     327     343 ..     319     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.055
                 FCSD-flav_bind  10 YSlva..pdyaisVagvYry.kdgkivevegsg 39 
                                    YS+v   ++ +i V++ +++  d++i+ v+  g
  gi|118431870|ref|NP_148606.2|  84 YSVVRsgSKSGIMVTASHNPpWDNGIKIVDSRG 116
                                    8888766899**********9777777775433 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                 FCSD-flav_bind  11 SlvapdyaisVagvYry 27 
                                     l++pd++ +V gvY++
  gi|118431870|ref|NP_148606.2| 327 KLIDPDWGLWVDGVYQA 343
                                    59*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 4005.87
//
Query:       gi|14602061|ref|NP_148607.1|  [L=255]
Description: hypothetical protein APE_2435 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-74  250.2   5.1      2e-74  250.1   5.1    1.0  1  DUF2208   Predicted membrane protein (DUF2208)
  ------ inclusion threshold ------
        4.4    7.0   9.5       0.84    9.3   5.2    2.0  2  YjcZ_2    Family of unknown function


Domain annotation for each model (and alignments):
>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.1   5.1   2.3e-78     2e-74       2     231 .]       9     243 ..       8     243 .. 0.98

  Alignments for each domain:
  == domain 1  score: 250.1 bits;  conditional E-value: 2.3e-78
                       DUF2208   2 milisqvsiilfalvlafl...pqylflviilYiivimvimsvltsrsllrerkkleevesgktLfeEknalkliekDeel 79 
                                   +il+sq++iil++l++++l   ++++ ++iil+i++++v++ + +++  l ++++++++es+++L+eEk a++l++kDe l
  gi|14602061|ref|NP_148607.1|   9 RILMSQAFIILYSLLASILgrsWKTFAVIIILFIVLSIVMSRRSKGP--LGVKASPADIESARRLYEEKGARELQMKDEGL 87 
                                   79*******************99***************999999999..599***************************** PP

                       DUF2208  80 qkelkeqlkasmitllllliviilffllyryiiplassllgev.leeklarflaflalFealflismflrllarrvlkklv 159
                                    ++l+eq+ka+m++ l++++++++f+l++r+i pl+++++ +v ++e la+flafla+Fe++f++++++ +++++++++++
  gi|14602061|ref|NP_148607.1|  88 ASDLQEQSKALMSMNLIMIVGLAYFILFWRFIDPLYEFVAANVtSNELLAHFLAFLAYFEGYFVVNTVSAYVVSKRSGPMI 168
                                   ******************************************9999*********************************** PP

                       DUF2208 160 mlimatsykvtekGivlk...krtgikfplkenieiklneerkfVElrstkqklktriRLYtkdpeklyeilerl 231
                                   +++m+t+y+v ekGiv+k   ++t+i+fpl+e+++++lne+rkfVE+r+ ++k+++r+RLY+++p++ly+i+er+
  gi|14602061|ref|NP_148607.1| 169 TINMPTEYTVSEKGIVYKgliSKTAIPFPLPEGVRVSLNERRKFVEIRKVNTKTDFRLRLYARNPKRLYTIIERY 243
                                   *************************************************************************97 PP

>> YjcZ_2  Family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.2   9.3e-05      0.84       5      19 ..      33      47 ..      32      47 .. 0.92
   2 ?   -1.6   0.1      0.24   2.2e+03      18      24 .]     106     112 ..     103     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 9.3e-05
                        YjcZ_2  5 GFALIVVLFILLIIv 19
                                  +FA I++LFI+L Iv
  gi|14602061|ref|NP_148607.1| 33 TFAVIIILFIVLSIV 47
                                  7***********887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.24
                        YjcZ_2  18 IvGaawi 24 
                                   IvG a++
  gi|14602061|ref|NP_148607.1| 106 IVGLAYF 112
                                   9**9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1934.05
//
Query:       gi|14602062|ref|NP_148608.1|  [L=375]
Description: hydrolase [Aeropyrum pernix K1]
Scores for 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   43.8   0.0    1.1e-10   41.4   0.0    2.1  2  Amidohydro_1  Amidohydrolase family
    0.00019   21.0   0.0    0.00035   20.2   0.0    1.4  1  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 ?   -0.9   0.0     0.091   8.1e+02       3      35 ..      52      88 ..      50     102 .. 0.65
   2 !   41.4   0.0   1.2e-14   1.1e-10     140     273 ..     179     292 ..     175     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.091
                                  EE-EEEEEEECETTECSSS......GHHHHHSTTHHHHH CS
                  Amidohydro_1  3 lPGlIDaHvHleqsllrga......tledwlvppetaae 35
                                  +P  ++aH+H ++     +       le++++pp+ +++
  gi|14602062|ref|NP_148608.1| 52 VPPSVNAHIHSSDVQW--PevgndlSLEELVAPPRGLKH 88
                                  67779*****864422..134666777777766665555 PP

  == domain 2  score: 41.4 bits;  conditional E-value: 1.2e-14
                                   HHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHH CS
                  Amidohydro_1 140 eakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpf 220
                                   + kk ++ +++H++et++       +++        le a ++g+ +     + hg+hl+ +++ell+e+  ++ +++ p+
  gi|14602062|ref|NP_148608.1| 179 LLKKSGMRIHAHVAETREMR----LEGD--------LEAALDIGVDT-----VIHGTHLSREDLELLREH--GVTLVLSPR 240
                                   66777888888886655443....1122........22222222222.....467777777777777777..777777799 PP

                                   HHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCT CS
                  Amidohydro_1 221 snsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrglly 273
                                   sn+  + g++++++a + Gvk+++gtD +a+ n l+ ++e r+a++++r++  
  gi|14602062|ref|NP_148608.1| 241 SNMWHGVGLPPVAEAYRVGVKIAFGTD-NAAWNMLDPWDEARQAMLVARLQGV 292
                                   ***************************.9999*************99996554 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.9e-08   0.00035     269     390 ..     177     283 ..     144     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.9e-08
                  Amidohydro_3 269 vaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnfedelldsrl 349
                                   ++++++ g++++ h+ ++   +     +e   e+  + ++ +++h++ ++ +++e +++ +v+  ++p++n          
  gi|14602062|ref|NP_148608.1| 177 MRLLKKSGMRIHAHVAETREMR-----LEGDLEAALDIGVDTVIHGTHLSREDLELLREHGVTLVLSPRSNM--------- 243
                                   5666666666666666555555.....555555555555559*************************99988......... PP

                  Amidohydro_3 350 gperargs..tpvkellnagvkvalgsD.apvgpfdpwprigaa 390
                                       ++g+  +pv+e  + gvk+a+g+D a  +++dpw + + a
  gi|14602062|ref|NP_148608.1| 244 ----WHGVglPPVAEAYRVGVKIAFGTDnAAWNMLDPWDEARQA 283
                                   ....555555****************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2672.26
//
Query:       gi|118431871|ref|YP_874944.1|  [L=114]
Description: hypothetical protein APE_2436a [Aeropyrum pernix K1]
Scores for complete 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-18   66.1   0.1    3.7e-18   65.9   0.1    1.0  1  SCP2            SCP-2 sterol transfer family
    2.8e-05   24.4   0.0    3.7e-05   24.0   0.0    1.2  1  Alkyl_sulf_C    Alkyl sulfatase C-terminal
  ------ inclusion threshold ------
      0.034   13.8   0.0      0.049   13.3   0.0    1.4  1  YkyA            Putative cell-wall binding lipoprotein
      0.042   12.1   0.1      0.049   11.9   0.1    1.0  1  Pox_VERT_large  Poxvirus early transcription factor (VETF), l
      0.084   13.3   0.0       0.13   12.7   0.0    1.2  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 !   65.9   0.1     1e-21   3.7e-18       2     100 ..      12     107 ..       8     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1e-21
                                    HHHHHHHHHHHHHHHHCCH-EEEEEEECTC.TEEEEEETTSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHT CS
                           SCP2   2 nqllerlkdpekkealkklagvlrfdltdlkgsltldlkegqldvaakdegkadvtlslsledllelaegklnpqkafmq 81 
                                    ++l  +   +e  +++++++ v+++ l+d  g++++++++g+l++a++   ++ +tl+l++++l+e++eg+++++kafm+
  gi|118431871|ref|YP_874944.1|  12 EELFGK--AKESLPEIQSWNKVYQIVLEDD-GEFYIEISGGELKIADGRHPSPIATLTLTSDTLKEILEGQTDAMKAFMM 88 
                                    344444..56999*****************.78************988889***************************** PP

                                    TSSEEEC-HHHHHHHHHHH CS
                           SCP2  82 gkLkieGDielaqkleall 100
                                    +kLki G++   ++l++++
  gi|118431871|ref|YP_874944.1|  89 RKLKITGNVLDTMNLKRII 107
                                    *********9999999886 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 !   24.0   0.0     1e-08   3.7e-05      37     115 ..      33     108 ..      22     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                                    EEEETTTTEEEEEEEETTEEEE.ECT---TTSSEEEEE-HHHHHHHHTTSS-HHHHHHTTTEEEEE-TCHHHHHHCTB- CS
                   Alkyl_sulf_C  37 nlvvtDvdekyllrlsngvLthtrkaaqaddadltvtltreqLvalllgkatlgkevaagklkieGdaealakllslld 115
                                    ++v++D   ++ +++s g L    ++++ +++ +t+tlt ++L ++l g++ + k++   klki+G++     l  ++d
  gi|118431871|ref|YP_874944.1|  33 QIVLEDD-GEFYIEISGGELKI-ADGRH-PSPIATLTLTSDTLKEILEGQTDAMKAFMMRKLKITGNVLDTMNLKRIID 108
                                    6677885.58999*******99.55555.9**************************************99999988887 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.049      97     146 ..       5      54 ..       2      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                           YkyA  97 eelkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltle 146
                                    e+lkk++eel  + +e    +++ +k Y+ +le d e+Y +++  el++ 
  gi|118431871|ref|YP_874944.1|   5 EDLKKKFEELFGKAKESLPEIQSWNKVYQIVLEDDGEFYIEISGGELKIA 54 
                                    689***************************************99999886 PP

>> Pox_VERT_large  Poxvirus early transcription factor (VETF), large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.4e-05     0.049     171     263 ..       7     105 ..       3     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                 Pox_VERT_large 171 veskfnnifrtnlkatglkniikkkkdkkllllksdeyfikltGnkfvlld.......eklnlsiwdqdeslaissdg.d 242
                                    +++kf+++f     +  l +i   +k ++++l    e++i+++G ++ + d        +l l+    +e+l+  +d  +
  gi|118431871|ref|YP_874944.1|   7 LKKKFEELFG--KAKESLPEIQSWNKVYQIVLEDDGEFYIEISGGELKIADgrhpspiATLTLTSDTLKEILEGQTDAmK 84 
                                    6789999998..3456799********************************66665444444444445556655555425 PP

                 Pox_VERT_large 243 tivvndvklftdllkdedvkm 263
                                    + ++ ++k+  ++l+ +++k 
  gi|118431871|ref|YP_874944.1|  85 AFMMRKLKITGNVLDTMNLKR 105
                                    666777777777777666664 PP

>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.6e-05      0.13      29      92 ..      37     101 ..      33     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                                    GGSEEEEEEEETTSEE.EECSCE-SCE..EEEEHHHHHHHHTTSS-HHHHHHTTSSBSSHHHHHHH CS
                         SCP2_2  29 wnngrfrltiedgkge.evgkeeeada.dltldiqtLaqlllGyrsaseLarlgriegaeealatl 92 
                                    + +g f ++i++g+ +  +g+++ ++  +ltl+ +tL ++l G  +a ++  + +++ + ++l+t+
  gi|118431871|ref|YP_874944.1|  37 EDDGEFYIEISGGELKiADGRHP-SPIaTLTLTSDTLKEILEGQTDAMKAFMMRKLKITGNVLDTM 101
                                    678999********997777776.56669************************9999666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 905.43
//
Query:       gi|118431872|ref|NP_148609.2|  [L=235]
Description: deoxyribose-phosphate aldolase [Aeropyrum pernix K1]
Scores for 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   32.8   0.0    1.1e-07   31.7   0.0    1.5  1  DeoC      DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.023   13.7   4.7       0.18   10.8   2.0    2.5  3  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 !   31.7   0.0   1.3e-11   1.1e-07      21     205 ..      33     202 ..      20     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.3e-11
                                    SHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCT...TSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEE CS
                           DeoC  21 neqledlkalvkealtpgasavlldpgviasaskeyak...diallvkldkgtyllkskqrdvdevasveeakalGAdav 97 
                                     +  ed+++lv+ea   g  + +l+p +  + s   +k   +   +++++ g+  l+ k      + +++ ++++GA+++
  gi|118431872|ref|NP_148609.2|  33 RATEEDVRNLVREASDYGFRCAVLTPVYTVKISGLAEKlgvKLCSVIGFPLGQAPLEVK------LVEAQTVLEAGATEL 106
                                    35558***********************9998877777777999******999999999......99************* PP

                                    EEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHT..EEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSC CS
                           DeoC  98 kvvvyyradgseeeqqklaeikrvkeacheeg..lplilelylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpke 175
                                    +vv  + ++g+e+   +++e++ + + ++++g   ++ile+ l d++                 s+ +GaDi+K++++  
  gi|118431872|ref|NP_148609.2| 107 DVVPHL-SLGPEA---VYREVSGIVKLAKSYGavVKVILEAPLWDDK---------TLSLLVDSSRRAGADIVKTSTG-- 171
                                    *99888.888886...6777777777777766336789997777777.........57788888999***********.. PP

                                    C.B.HHHHHHHHHHHHHCHSSTE.EEEETTS CS
                           DeoC 176 vvnateedaevfkdvikaapvpg.vvlsGGv 205
                                    v  ++ + ++vf+ +  a p+ + v+ sGG+
  gi|118431872|ref|NP_148609.2| 172 VYTKGGDPVTVFRLASLAKPLGMgVKASGGI 202
                                    556666678899999999988878******9 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.19   1.7e+03     120     143 ..      34      57 ..      25      61 .. 0.83
   2 ?    2.8   0.0    0.0054        49     270     289 ..     149     168 ..      93     172 .. 0.75
   3 ?   10.8   2.0     2e-05      0.18     261     298 ..     185     220 ..     175     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.19
                                    SSHHHHHHHHHHHHHCTESEEEEE CS
                         FMN_dh 120 kdrelteellkraeaagykalvlt 143
                                      +e +++l+++a + g++  vlt
  gi|118431872|ref|NP_148609.2|  34 ATEEDVRNLVREASDYGFRCAVLT 57 
                                    567889999999999999999887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0054
                                    .SS-EEEESS--SHHHHHHH CS
                         FMN_dh 270 grievlvDgGirrGsDvlkA 289
                                    + + +lvD+  r G+D++k 
  gi|118431872|ref|NP_148609.2| 149 KTLSLLVDSSRRAGADIVKT 168
                                    46999*************96 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 2e-05
                                    HHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEE CS
                         FMN_dh 261 LpeiveavggrievlvDgGirrGsDvlkAlalGAdavl 298
                                    L ++++ +g  + v ++gGir+G D++ A+  GAd+++
  gi|118431872|ref|NP_148609.2| 185 LASLAKPLG--MGVKASGGIRSGIDAVLAVGAGADIIG 220
                                    555556665..88999*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1772.78
//
Query:       gi|14602064|ref|NP_148610.1|  [L=515]
Description: hypothetical protein APE_2438 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-08   33.2   0.0    6.6e-05   22.9   0.0    2.5  2  DUF4346   Domain of unknown function (DUF4346)


Domain annotation for each model (and alignments):
>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00019       3.3      12      36 ..     421     445 ..     418     449 .. 0.93
   2 !   22.9   0.0   3.7e-09   6.6e-05      93     118 .]     474     499 ..     451     499 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00019
                       DUF4346  12 elDpaGYflikvdreaklivakhys 36 
                                   ++D +GY  i+vd+e++ i++++y 
  gi|14602064|ref|NP_148610.1| 421 SMDRTGYAHIQVDHERGVIMLTFYP 445
                                   59*********************95 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.7e-09
                       DUF4346  93 dhaaYlGRelqraeaaLlsgkeYiqD 118
                                   +ha Y+G el +ae+aL+ gk+Y+qD
  gi|14602064|ref|NP_148610.1| 474 EHAGYIGYELAKAEIALALGKTYVQD 499
                                   7************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3932.99
//
Query:       gi|14602065|ref|NP_148611.1|  [L=324]
Description: mevalonate kinase [Aeropyrum pernix K1]
Scores for 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-16   58.6   1.4    2.3e-15   56.7   1.0    2.0  2  GHMP_kinases_C   GHMP kinases C terminal
    1.5e-14   54.0   1.2    3.4e-14   52.8   1.2    1.7  1  GHMP_kinases_N   GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.092   12.3   0.1       0.18   11.4   0.1    1.5  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 ?   -1.3   0.0      0.49   2.9e+03      24      49 ..      64      87 ..      51      91 .. 0.69
   2 !   56.7   1.0   3.9e-19   2.3e-15       1      79 [.     227     302 ..     225     307 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.49
                GHMP_kinases_C 24 elkavvgilppeleellealselGal 49
                                  +    +++++p+le  +  l++l a 
  gi|14602065|ref|NP_148611.1| 64 QG--AAAKVSPVLEPYIAVLRSLAAR 87
                                  55..7788889999999888877655 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 3.9e-19
                GHMP_kinases_C   1 llealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaral 79 
                                   +l a+e+gd+e+lg ++n  q   l+  +g ++ e+e+l+  ++++Galgakl+GaG+G++v++lf ++ e+e+ ++++
  gi|14602065|ref|NP_148611.1| 227 ALHAIEKGDAERLGLIMNAAQG--LLSSLGASSLEIETLVYRMRSAGALGAKLTGAGWGGCVIGLF-KEGEVERGLESV 302
                                   5789999***************..899***************************************.999999988877 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 !   52.8   1.2   5.6e-18   3.4e-14       2      66 .]      96     162 ..      95     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 5.6e-18
                                   EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                   i ++s iP+ aGLGSSAA  va ++   a+ g +l  e+ +  a e+e++a+ g++sg+Dv+ +v Gg
  gi|14602065|ref|NP_148611.1|  96 ILVESGIPPRAGLGSSAASMVAYALSYSAMHGDPLsaEDlYSVAMEGEKIAH-GKPSGVDVTIAVRGG 162
                                   889*****************************99965558************.*************98 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 ?   11.4   0.1     3e-05      0.18      14      47 ..       7      40 ..       2      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                                  EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEE CS
               GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyiav 47
                                  asAPG v + GEH    g   + +Ai ++  + v
  gi|14602065|ref|NP_148611.1|  7 ASAPGKVIIVGEHFVVRGSLAIVAAIGRRLRVTV 40
                                  89***********999999999999888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2445.73
//
Query:       gi|118431873|ref|NP_148612.2|  [L=595]
Description: acylamino-acid-releasing enzyme [Aeropyrum pernix K1]
Scores for complete 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-45  154.8   0.0    2.8e-45  154.4   0.0    1.2  1  Peptidase_S9   Prolyl oligopeptidase family
    1.6e-12   47.6   0.0      6e-05   22.8   0.0    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.9e-10   39.4   0.0    2.1e-05   23.9   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    8.8e-07   28.7   0.0    2.6e-06   27.2   0.0    1.7  1  DLH            Dienelactone hydrolase family
    6.5e-06   25.9   6.0    0.00061   19.7   0.1    4.2  4  PD40           WD40-like Beta Propeller Repeat
    2.5e-05   23.1   0.1     0.0014   17.4   0.1    2.1  1  AXE1           Acetyl xylan esterase (AXE1)
    4.4e-05   24.2   0.8     0.0018   18.9   0.3    2.3  2  Abhydrolase_6  Alpha/beta hydrolase family
    0.00017   21.5   0.0       0.06   13.1   0.0    2.3  2  Abhydrolase_2  Phospholipase/Carboxylesterase
     0.0002   21.3   0.6     0.0098   15.8   0.6    2.4  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.006   15.8   0.0       0.38    9.9   0.0    2.2  2  DUF2920        Protein of unknown function (DUF2920)
     0.0074   15.6   0.1        1.8    7.8   0.0    2.1  2  LIP            Secretory lipase
      0.009   15.6   0.0        2.4    7.7   0.0    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.034   14.2   0.0    1.4  1  Abhydrolase_4  TAP-like protein
      0.031   13.8   0.0        3.8    6.9   0.0    2.2  2  Esterase_phd   Esterase PHB depolymerase
      0.048   12.4   0.0       0.95    8.1   0.0    2.1  2  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
      0.098   12.4   0.0       0.19   11.5   0.0    1.5  1  HET-S          N-terminal small S protein of HET, non-prionic


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0   2.5e-48   2.8e-45       7     210 ..     390     593 ..     384     595 .] 0.96

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 2.5e-48
                                    HHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH-G CS
                   Peptidase_S9   7 lqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnqrp 86 
                                    +q la+ G++ +++n+rGs+gyG+ f +  + ++    ++D+  a++a+++ g+vd +rl+++GgSyGGylt++ l+  p
  gi|118431873|ref|NP_148612.2| 390 PQALAAIGIATIAPNYRGSTGYGRRFVHLDDVEKRMDAVRDVYYAVKAAVEAGLVDGSRLCVMGGSYGGYLTLMSLAIYP 469
                                    688999**********************9999************************************************ PP

                                    GG-SEEEEESE---CCCHHCSTTSTHH..HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-THHHHH CS
                   Peptidase_S9  87 dlFkaavaevpvvdvlrydsdtdllte..eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvppaealk 164
                                    dl+k++v  v++v+++++  +t+ + +  +  e+g+p+   e + +lsp+++++n   ++pl++ihG +D rvp++ea++
  gi|118431873|ref|NP_148612.2| 470 DLWKCGVEIVGIVNLVTFIRNTSPYRRryRIAEYGDPDVHGEIMLKLSPITYVEN--MKAPLMVIHGAKDPRVPVSEAEQ 547
                                    *********************99965537889*****99***9************..99********************* PP

                                    HHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHCT CS
                   Peptidase_S9 165 lvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkealg 210
                                    lv+aL ++g+ v+++   degHg+ k ++k + +++ l+F+ e+l 
  gi|118431873|ref|NP_148612.2| 548 LVEALSSRGVRVRYVRLEDEGHGIVKLENKLRVYREALEFIYENLA 593
                                    *****************************************99886 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   6.2e-08     7e-05       1      97 [.     369     471 ..     369     481 .. 0.81
   2 !   22.8   0.0   5.4e-08     6e-05     203     253 ..     497     572 ..     480     576 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 6.2e-08
                                    SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTS.TTSSSTTTGB.CHHSHHHHHHHHHHH....HHHCTTSSE CS
                  Abhydrolase_1   1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGv.gySspapacinddygtasvaddldri....ldalgddkl 75 
                                    p++v+lhG+p+s +  + + +++aLa  g  +i+++ rG+ gy+++     +++ ++++v+d+++++     + l d++ 
  gi|118431873|ref|NP_148612.2| 369 PAVVYLHGGPESQERVRFNVFPQALAAIGIATIAPNYRGStGYGRRFVHLDDVEKRMDAVRDVYYAVkaavEAGLVDGSR 448
                                    79*********999999999******99**********974566655554336668888888888443344666777777 PP

                                    E.EEEETHHHHHHHHHHHHHGGG CS
                  Abhydrolase_1  76 t.lvGhSmGGmialayaaeyper 97 
                                      ++G+S+GG + l+ +a yp+ 
  gi|118431873|ref|NP_148612.2| 449 LcVMGGSYGGYLTLMSLAIYPDL 471
                                    77******************996 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 5.4e-08
                                    HHHC.....................THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS....EEEEEEETCSSSHH CS
                  Abhydrolase_1 203 rlre.....................lknvlaptlvisgtsDplvppkaledlaqllpk....krlvvisdagHlaf 253
                                    r+r+                     + n++ap +vi+g++Dp vp ++ e+l ++l++    +r+v+++d+gH ++
  gi|118431873|ref|NP_148612.2| 497 RYRIaeygdpdvhgeimlklspityVENMKAPLMVIHGAKDPRVPVSEAEQLVEALSSrgvrVRYVRLEDEGHGIV 572
                                    23333344466699999999999999*****************************99889*************876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.9e-08   2.1e-05       5     103 ..     369     475 ..     366     489 .. 0.78
   2 !   13.2   0.0   3.5e-05     0.039     188     226 ..     523     561 ..     519     572 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.9e-08
                    Hydrolase_4   5 avvvlvHGlaehsgryae..laeaLaaqGfavyalDhrGhGrsegkrghvpsfd...dyvdDlaafvekvkeehpel..p 77 
                                     +vv +HG  e+ +r+    + +aLaa G+a++a ++rG    + + +h+++++   d v+D+  +v++++e       +
  gi|118431873|ref|NP_148612.2| 369 PAVVYLHGGPESQERVRFnvFPQALAAIGIATIAPNYRGSTGYGRRFVHLDDVEkrmDAVRDVYYAVKAAVEAGLVDgsR 448
                                    57999******99875543399****************98777655566655551117788888888888866544466* PP

                    Hydrolase_4  78 lfllGhSmGGliallyllrypdkva.g 103
                                    l ++G S GG+++l  l+ ypd ++ g
  gi|118431873|ref|NP_148612.2| 449 LCVMGGSYGGYLTLMSLAIYPDLWKcG 475
                                    **************9999999977644 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.5e-05
                    Hydrolase_4 188 akitlPllllhGeaDkvvdpeasrelyerlgskdktlkl 226
                                    +++++Pl+++hG++D+ v+ +++++l+e+l+s+ +++++
  gi|118431873|ref|NP_148612.2| 523 ENMKAPLMVIHGAKDPRVPVSEAEQLVEALSSRGVRVRY 561
                                    6789****************************9888765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   2.3e-09   2.6e-06      71     195 ..     422     577 ..     353     590 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.3e-09
                            DLH  71 skvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalall.laaevpevdaavafYG................... 130
                                    +k+   + ++d+  av+++ + + v+ +++ v+G   GG l+l  la + +  ++ v   G                   
  gi|118431873|ref|NP_148612.2| 422 EKR--MDAVRDVYYAVKAAVEAGLVDGSRLCVMGGSYGGYLTLMsLAIYPDLWKCGVEIVGivnlvtfirntspyrrryr 499
                                    233..4566677799999999999999*************9975156666999*************************** PP

                            DLH 131 .............lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                                 +   +++++++++kap+++++g +D+ +p +e+e+l eal+ ++v ++ +  ++ gH+ ++ +++
  gi|118431873|ref|NP_148612.2| 500 iaeygdpdvhgeiMLKLSPITYVENMKAPLMVIHGAKDPRVPVSEAEQLVEALSSRGVRVRYVRLEDEGHGIVKLENK 577
                                    *********999877889****************************************************98776655 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.67   7.5e+02      13      37 ..      18      42 ..      14      43 .. 0.74
   2 ?    4.7   0.1     0.026        30      17      38 .]      65      86 ..      64      86 .. 0.91
   3 !   19.7   0.1   5.5e-07   0.00061      16      38 .]     109     132 ..     109     132 .. 0.84
   4 ?    0.6   0.0      0.54     6e+02      20      37 ..     247     263 ..     246     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.67
                                   EEEE-TTSSEEEEEEECT.TCEEEE CS
                           PD40 13 aPsfSPDGkrlaFsSdRgsGkpdIy 37
                                    P+++P    +++ Sd  s +p I+
  gi|118431873|ref|NP_148612.2| 18 TPRIDPSTGCIYYLSDSASSQPVIW 42
                                   56666666669*****558888899 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                                   -TTSSEEEEEEECT..TCEEEEE CS
                           PD40 17 SPDGkrlaFsSdRg.sGkpdIyv 38
                                    PDG   aFs d++ + ++ Iy+
  gi|118431873|ref|NP_148612.2| 65 APDG-LVAFSTDKDgDERWSIYI 86
                                   69**.*********999999997 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 5.5e-07
                                    E-TTSSEEEEEEECT..TCEEEEE CS
                           PD40  16 fSPDGkrlaFsSdRg.sGkpdIyv 38 
                                    +SPDG+ laF+S++    ++d+yv
  gi|118431873|ref|NP_148612.2| 109 WSPDGRLLAFTSNKRnGVDFDLYV 132
                                    *************98665666876 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.54
                                    SSEEEEEEECT.TCEEEE CS
                           PD40  20 GkrlaFsSdRgsGkpdIy 37 
                                    Gk+ ++s + + G +++y
  gi|118431873|ref|NP_148612.2| 247 GKTVVYSLNVD-GESRVY 263
                                    9*********9.999888 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.2e-06    0.0014      58     198 ..     342     471 ..     333     522 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
                                    EEEEEEGGGEEEEEEEEEES.S.SSSEEEEEEEE-TT--GGGHHHHH...HHHHTT-EEEEEE-TTTS..SSB-SSCCSS CS
                           AXE1  58 dltfegvrgarikaklvlPkek.eeklPavvefhGYegsrgeihdll...nyaaaGyavvvmdvRGqggesedkvgskgn 133
                                    +  +e++ g +++a l +P++    + Pavv  hG  +s+  +  ++     aa G+a+++ + RG  g+ +  v   + 
  gi|118431873|ref|NP_148612.2| 342 HFSYESFDGIKVRALLYKPDKPlYTPPPAVVYLHGGPESQERVRFNVfpqALAAIGIATIAPNYRGSTGYGRRFVHLDD- 420
                                    6778888888888888888864245678888888888877776666522236778888888888888877666544442. PP

                                    -SSSSTTTTTTSTTT-HHHHHHHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS- CS
                           AXE1 134 kakGfiirGlldkeklyyrrvflDavrlveivaslpevDeeRvavlGasqGGalalavaalekri 198
                                              ++k+    r    D++ +v+++ +   vD +R+ v+G+s GG l+l   a+ +++
  gi|118431873|ref|NP_148612.2| 421 ----------VEKRMDAVR----DVYYAVKAAVEAGLVDGSRLCVMGGSYGGYLTLMSLAIYPDL 471
                                    ..........222222333....4445788888899********************999998776 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   1.6e-06    0.0018       1      84 [.     371     467 ..     371     492 .. 0.66
   2 ?    3.2   0.0       0.1   1.1e+02     160     208 ..     516     571 ..     485     583 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                                    EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTS...TS-GGCS--HHH....CHHH.HHHHCCTT.....TTSEE CS
                  Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGh...Grsdpppldled....ladl.aalldelaa...gggpvv 68 
                                    v+ lHG++ s++  ++  + +al+a g++++ap ++G    Gr+  + +d+e     ++d+  a+ +++ a   +g + +
  gi|118431873|ref|NP_148612.2| 371 VVYLHGGPESQERVRFNVFpQALAAIGIATIAPNYRGStgyGRRFVHLDDVEKrmdaVRDVyYAVKAAVEAglvDGSRLC 450
                                    688999997766664456645555555999******8873354433333333344446777755555555577699999* PP

                                    EEEETCHHHHHHH.HHH CS
                  Abhydrolase_6  69 lvGHSlGGalala.aap 84 
                                    ++G S+GG+l l+ +a 
  gi|118431873|ref|NP_148612.2| 451 VMGGSYGGYLTLMsLAI 467
                                    *********99984444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                                    HTTCCHHTT-TTGCEEE.CTT-C.....HHH.HCHHCCCHSTTEEET.CE...SSS.- CS
                  Abhydrolase_6 160 llpaaawadlpvpllvl.ggeDp.....lvp.rllerllaqagarlp.vvlpgaGH.l 208
                                    l p + ++ + +pl+v+ g++Dp       + +l+e+l   +g+r+  v l++ GH  
  gi|118431873|ref|NP_148612.2| 516 LSPITYVENMKAPLMVIhGAKDPrvpvsE-AeQLVEALSS-RGVRVRyVRLEDEGHgI 571
                                    44555666777888888679999555432.1244444444.44444459999****44 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0096        11      84     138 ..     425     480 ..     415     494 .. 0.81
   2 !   13.1   0.0   5.4e-05      0.06     155     203 ..     525     573 ..     514     588 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0096
                                    HHHHHHHHHHHHHHHHTT.--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES- CS
                  Abhydrolase_2  84 kksaekleelidaelkkg.ipssriiigGFSqGaalalylaltlpkklggivafsg 138
                                    +++++ +   ++a +++g ++ sr  ++G S G+ l+l +  ++p   ++ v + g
  gi|118431873|ref|NP_148612.2| 425 MDAVRDVYYAVKAAVEAGlVDGSRLCVMGGSYGGYLTLMSLAIYPDLWKCGVEIVG 480
                                    56677777789999999999*********************999987766555544 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.4e-05
                                    GG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--H CS
                  Abhydrolase_2 155 kklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHside 203
                                     k p + iHg +Dp vp++ ++++ e+l++   +v  + +e+ +H i++
  gi|118431873|ref|NP_148612.2| 525 MKAPLMVIHGAKDPRVPVSEAEQLVEALSSRGVRVRYVRLEDEGHGIVK 573
                                    578999***************************************9875 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.6   8.8e-06    0.0098      48     210 ..     427     572 ..     371     573 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.8e-06
                                    HHHHHHHHHHHHHHTHHHHT.ETTCEEEEEEETHHHHHHHHHHHHHHHTT---..EEEEEEESE-SSTSSTTSHHHHHCH CS
                  Abhydrolase_3  48 avedalaalrwlaeqawelg.adpsrivlaGdSaGGnlaaavalrardegepk..vagqvliyPvtdlertesesikkae 124
                                    av d++ a++ ++    e+g +d sr++++G S GG l++  +    d  + +  ++g+v +       r++s+ + +  
  gi|118431873|ref|NP_148612.2| 427 AVRDVYYAVKAAV----EAGlVDGSRLCVMGGSYGGYLTLMSLAIYPDLWKCGveIVGIVNLVTFI---RNTSPYR-RR- 497
                                    3333333333333....33449*****************998887777654443366666666654...4434444.22. PP

                                    HTTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC.S-SST---EEEEEETT-TT..HHHHHHHHHHHHHTT--EEEEE CS
                  Abhydrolase_3 125 eladgplltraaldlfwrlylpeadrddplasplla.edlsglpptlvvvaefDpl..rdegeayaerlraagvevelie 201
                                        + + +  + d   +++l         +sp+   e+++  +p +v+ + +Dp    +e+e++ e+l + gv+v++++
  gi|118431873|ref|NP_148612.2| 498 ----YRIAEYGDPDVHGEIML--------KLSPITYvENMK--APLMVIHGAKDPRvpVSEAEQLVEALSSRGVRVRYVR 563
                                    ....34555667777777777........466775534555..8999*******872258999***************** PP

                                    ETTEETTGG CS
                  Abhydrolase_3 202 yegmvHgfa 210
                                     e++ Hg++
  gi|118431873|ref|NP_148612.2| 564 LEDEGHGIV 572
                                    ******975 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00034      0.38     162     203 ..     430     470 ..     423     477 .. 0.72
   2 ?    3.6   0.0     0.028        31     287     323 ..     528     564 ..     518     575 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                        DUF2920 162 DiinalkdlvkrfpkeadlpviliGgsyGGYlalLiaKiaPw 203
                                    D+  a+k +v+ ++   +  + ++GgsyGGYl+l+   i P 
  gi|118431873|ref|NP_148612.2| 430 DVYYAVKAAVE-AGLVDGSRLCVMGGSYGGYLTLMSLAIYPD 470
                                    45555555555.34444688999**********998888776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.028
                        DUF2920 287 iyvsyHsekDklapaeeKiqlakilkklgfdveleli 323
                                      +++H  kD+ +p+ e +ql+++l  +g  v+   +
  gi|118431873|ref|NP_148612.2| 528 PLMVIHGAKDPRVPVSEAEQLVEALSSRGVRVRYVRL 564
                                    56899************************99976655 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.2    0.0079       8.8      24     103 ..     395     480 ..     387     492 .. 0.78
   2 !    7.8   0.0    0.0016       1.8     215     259 ..     526     569 ..     519     588 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0079
                            LIP  24 keGyyVvvpDyeGpks...tftvgrqsgkavLdsira...alksekvtgiksdakvalwGYSgGslAsawAaelqpe.YA 96 
                                    + G + + p y G  +    f v  ++ ++ +d++r    a+k+   +g+ + ++  ++G S+G+  +    ++ p+ + 
  gi|118431873|ref|NP_148612.2| 395 AIGIATIAPNYRGSTGygrRF-VHLDDVEKRMDAVRDvyyAVKAAVEAGLVDGSRLCVMGGSYGGYLTLMSLAIYPDlWK 473
                                    56999999***9998877778.99999999999999722245677778******************99999888876334 PP

                            LIP  97 PelelvG 103
                                      +e+vG
  gi|118431873|ref|NP_148612.2| 474 CGVEIVG 480
                                    5555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0016
                            LIP 215 qiPvlvyhgvidelipikdakklaknwcdkgiaslefaedlssgH 259
                                    + P++v+hg  d  +p+++a++l +   ++g+ ++ +++   +gH
  gi|118431873|ref|NP_148612.2| 526 KAPLMVIHGAKDPRVPVSEAEQLVEALSSRGV-RVRYVRLEDEGH 569
                                    57*****************************6.9****9998888 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0083       9.3     101     143 ..     447     488 ..     349     496 .. 0.74
   2 !    7.7   0.0    0.0021       2.4     219     260 ..     517     562 ..     509     571 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0083
                                    EEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCS CS
                  Peptidase_S15 101 GkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyy 143
                                     + +++G SY+G++ l+ +a  ++  k+ v +++i++l++  +
  gi|118431873|ref|NP_148612.2| 447 SRLCVMGGSYGGYLTLMSLAIYPDLWKCGVEIVGIVNLVT-FI 488
                                    4789****************999999*****999999987.55 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                                    -HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-...EE CS
                  Peptidase_S15 219 nlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv...kl 260
                                    ++ + ++++kap+++++G  D  v   +a +l eal+++gv   ++
  gi|118431873|ref|NP_148612.2| 517 SPITYVENMKAPLMVIHGAKDPRVPvSEAEQLVEALSSRGVrvrYV 562
                                    5566789**************99999************99866544 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.1e-05     0.034      33      79 ..     525     575 ..     515     579 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                  Abhydrolase_4  33 gaapvLllqnerDpaTPyegakklakalgg.a...vlvtvegeGHgalaag 79 
                                     +ap +++ +  Dp +P + a++l +al + +   + v  e+eGHg ++ +
  gi|118431873|ref|NP_148612.2| 525 MKAPLMVIHGAKDPRVPVSEAEQLVEALSSrGvrvRYVRLEDEGHGIVKLE 575
                                    3589*************************87666667788999**998754 PP

>> Esterase_phd  Esterase PHB depolymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0034       3.8      17     122 ..     369     472 ..     356     485 .. 0.74
   2 ?    4.4   0.0      0.02        23     170     197 ..     527     554 ..     517     560 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0034
                   Esterase_phd  17 plvvmlhGctqsveefaaGtrmnlladklGvvvlypeqslranaqkcwnwykdtdraGrGeaavvvalvdalvdehrvda 96 
                                    p vv lhG  +s e        ++la   G++ + p+    +   + +   +d +++     +v    v+a v++  vd 
  gi|118431873|ref|NP_148612.2| 369 PAVVYLHGGPESQERVRFNVFPQALAA-IGIATIAPNYRGSTGYGRRFVHLDDVEKRMDAVRDV-YYAVKAAVEAGLVDG 446
                                    778888888888777766666666664.688888887666555555555666666665554444.455789999****** PP

                   Esterase_phd  97 arvyvaGlsaGaaladllalhypdvf 122
                                    +r+ v G s G+ l+ +    ypd +
  gi|118431873|ref|NP_148612.2| 447 SRLCVMGGSYGGYLTLMSLAIYPDLW 472
                                    **************99988999*976 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                   Esterase_phd 170 lpalvvqGdadtvvavknaeslvvalrr 197
                                     p +v++G  d  v v +ae+lv al +
  gi|118431873|ref|NP_148612.2| 527 APLMVIHGAKDPRVPVSEAEQLVEALSS 554
                                    5899*******************99976 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.041        45     108     125 ..     109     126 ..      97     128 .. 0.84
   2 ?    8.1   0.0   0.00085      0.95     159     297 ..     129     251 ..     109     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.041
                                    E-TTSSEEEEEEEECTTS CS
                        DPPIV_N 108 WspdgsrlaylrfdeseV 125
                                    Wspdg+ la+++   ++V
  gi|118431873|ref|NP_148612.2| 109 WSPDGRLLAFTSNKRNGV 126
                                    999999999998877666 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00085
                                    EEEEEECTTSCEEECS-HHHHCTTCEEEEEEEECTTSCCEEEEEEETTST.EEEEEEEETTTCCEEEEEEEESSS-SSS- CS
                        DPPIV_N 159 elkvvdlasgktvevqlpdslsekdeyitrvkWtsdeksllvqwlnRsqn.rlkvvlvdaetgravvkleetsdgWvelh 237
                                    +l+v d ++g+   v+++    e + +i+  +W++ ++   +  ++R++n  +++ +v++ +g+a+v ++   +   el+
  gi|118431873|ref|NP_148612.2| 129 DLYVFDREKGS---VSIV---VEGEGIIAASSWIDGSR---LLAVKRNSNlDSDILAVNVYKGEAKVLTRHRGE---ELN 196
                                    44444444443...2333...56788888888888887...445566666356777777777777777765555...688 PP

                                    S-EEE-TTTSSEEEEEEE.TTSSEEEEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEE CS
                        DPPIV_N 238 devhflkrdesgflwise.kdGfkHLylfdldgkseikqlTsGeweVtsilavdekrdlvy 297
                                    ++++++   + + l+is+  + f  ++l+dl+++   + + + +w+V + l v+   ++v 
  gi|118431873|ref|NP_148612.2| 197 TSPRPI--GGGKALFISNmDSEFTGIALIDLQTGD-RRLVFREQWDV-EALEVSG--KTVV 251
                                    888888..78999999999999************9.99999*****9.4444443..3444 PP

>> HET-S  N-terminal small S protein of HET, non-prionic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.19       4      15 ..     251     262 ..     249     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                          HET-S   4 VqSLnASGsSRV 15 
                                    V SLn++G+SRV
  gi|118431873|ref|NP_148612.2| 251 VYSLNVDGESRV 262
                                    67*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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 0.31s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 4211.43
//
Query:       gi|118431874|ref|NP_148613.2|  [L=322]
Description: transcription initiation factor IIB [Aeropyrum pernix K1]
Scores for complete 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  117.1   0.4    3.2e-16   59.1   0.0    2.4  2  TFIIB            Transcription factor TFIIB repeat
    0.00016   21.5   0.1       0.77    9.7   0.1    2.6  2  SCAB-ABD         Actin-binding domain of plant-specific actin
     0.0012   18.3   2.0      0.011   15.2   0.3    2.9  3  Sigma70_r4       Sigma-70, region 4
     0.0022   17.8   0.0      0.013   15.3   0.0    2.3  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0058   16.3   2.6       0.13   11.9   0.4    3.3  3  Sigma70_r4_2     Sigma-70, region 4
  ------ inclusion threshold ------
      0.019   14.7   0.4       0.43   10.4   0.4    2.8  1  HTH_23           Homeodomain-like domain
      0.022   14.8   0.0      0.044   13.8   0.0    1.4  1  RB_B             Retinoblastoma-associated protein B domain
      0.049   13.7   0.5       0.15   12.1   0.1    2.0  3  DUF2089          Protein of unknown function (DUF2089)
      0.056   13.5   0.0       0.33   11.1   0.0    2.0  2  Cyclin_C         Cyclin, C-terminal domain
      0.086   12.9   0.9        1.4    9.0   0.1    3.0  3  Phage_terminase  Phage terminase small subunit
       0.17   11.7   0.0       0.52   10.0   0.0    1.7  2  Cyclin_N         Cyclin, N-terminal domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.1     2e-18   3.2e-15       1      63 [.     127     189 ..     127     195 .. 0.96
   2 !   59.1   0.0     2e-19   3.2e-16       4      71 .]     229     296 ..     226     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2e-18
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHH CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissv 63 
                                    i+++a+++++pe+V ++A +++++a+e++++ Grs ++i+AA+ly A+r  ++ +++++i + 
  gi|118431874|ref|NP_148613.2| 127 INEVASRMGMPEIVVEDASKIYREAMEKGLTRGRSIESIVAASLYAASRIHGLPHSLTDIIKA 189
                                    7899********************************************************865 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 2e-19
                                    HHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   4 fadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    + +al+Lpe Va +A ++++l+ ++++++G+ p g+a+A++y+A++k + ++tqkei+ v+ V+e+ti
  gi|118431874|ref|NP_148613.2| 229 IISALGLPEHVAIEAIKIIDLSRKKGLTAGKDPGGLAGAAVYLAALKHGIRKTQKEIAHVVGVTEVTI 296
                                    6689**************************************************************98 PP

>> SCAB-ABD  Actin-binding domain of plant-specific actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00075       1.2      17      42 ..     106     130 ..      99     131 .. 0.89
   2 !    9.7   0.1   0.00047      0.77       2      27 ..     191     216 ..     190     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00075
                       SCAB-ABD  17 kRLSVRDLasKFekglaAAakLseea 42 
                                     RLS R L s  +k+l +A +L +e+
  gi|118431874|ref|NP_148613.2| 106 PRLSARPLTS-VDKNLQTALSLINEV 130
                                    59******98.7************96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
                       SCAB-ABD   2 kevvakEtadLvdqhkRLSVRDLasK 27 
                                    k  v+ Et + v++  RL VRDL  K
  gi|118431874|ref|NP_148613.2| 191 KGNVDAETRRDVARSYRLLVRDLNIK 216
                                    667999*****************987 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.2   3.2e+02      25      47 ..     129     154 ..     127     154 .. 0.72
   2 !   15.2   0.3     7e-06     0.011      21      48 ..     280     307 ..     274     308 .. 0.90
   3 ?    2.0   0.0      0.09   1.5e+02      23      34 ..     300     311 ..     299     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                                    HHHHHHTS-H...HHHHHHHHHHHHH CS
                     Sigma70_r4  25 EIgerlgiSr...erVrqiekrAlrk 47 
                                    E++ r+g+++   e ++ i ++A++k
  gi|118431874|ref|NP_148613.2| 129 EVASRMGMPEivvEDASKIYREAMEK 154
                                    99999999974446667777777776 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7e-06
                                    --HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4  21 lTleEIgerlgiSrerVrqiekrAlrkL 48 
                                     T++EI+ + g+++ ++r + k+  + L
  gi|118431874|ref|NP_148613.2| 280 KTQKEIAHVVGVTEVTIRNRYKEIAQAL 307
                                    6*******************99987665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.09
                                    HHHHHHHHTS-H CS
                     Sigma70_r4  23 leEIgerlgiSr 34 
                                    ++EI++ lgi +
  gi|118431874|ref|NP_148613.2| 300 YKEIAQALGIEE 311
                                    79*******966 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 !   15.3   0.0   7.9e-06     0.013       9      39 ..     271     301 ..     271     303 .. 0.93
   2 ?    2.1   0.0      0.11   1.8e+02      20      31 ..     300     311 ..     297     312 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.9e-06
                  HTH_AsnC-type   9 LeaLqedaRisyaeLAervGlSestvlrRvr 39 
                                    L+aL +  R + +e+A  vG++e t+++R++
  gi|118431874|ref|NP_148613.2| 271 LAALKHGIRKTQKEIAHVVGVTEVTIRNRYK 301
                                    78899999*********************98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                  HTH_AsnC-type  20 yaeLAervGlSe 31 
                                    y+e+A+++G+ e
  gi|118431874|ref|NP_148613.2| 300 YKEIAQALGIEE 311
                                    99*******865 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 ?   -0.4   0.0      0.57   9.3e+02      31      40 ..     129     138 ..     127     142 .. 0.86
   2 !   11.9   0.4   8.1e-05      0.13      28      48 ..     281     301 ..     279     307 .. 0.90
   3 ?    5.1   0.1     0.011        18      29      39 ..     300     310 ..     299     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.57
                                    HHHHHHT--H CS
                   Sigma70_r4_2  31 EIAellgise 40 
                                    E+A+++g++e
  gi|118431874|ref|NP_148613.2| 129 EVASRMGMPE 138
                                    99******98 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8.1e-05
                                    -HHHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2  28 sykEIAellgisegtVksrls 48 
                                    ++kEIA + g++e+t+++r++
  gi|118431874|ref|NP_148613.2| 281 TQKEIAHVVGVTEVTIRNRYK 301
                                    89*****************97 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.011
                                    HHHHHHHHT-- CS
                   Sigma70_r4_2  29 ykEIAellgis 39 
                                    ykEIA+ lgi 
  gi|118431874|ref|NP_148613.2| 300 YKEIAQALGIE 310
                                    9********96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.4   0.00026      0.43      14      39 ..     272     301 ..     267     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00026
                         HTH_23  14 lae....GlsvreIAreLgvsrrTvyrwlk 39 
                                    +a     +++++eIA   gv++ T+++  k
  gi|118431874|ref|NP_148613.2| 272 AALkhgiRKTQKEIAHVVGVTEVTIRNRYK 301
                                    332256699****************95443 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.7e-05     0.044      10      95 ..     120     205 ..     115     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                           RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrk..qpq 87 
                                    +++a + ++++ +r+ + + + e + ++ ++++  e+ l + R ++ i+ +++Y+  +++   +s+++iika +    ++
  gi|118431874|ref|NP_148613.2| 120 LQTALSLINEVASRMGMPEIVVEDASKIYREAM--EKGLTRGRSIESIVAASLYAASRIHGLPHSLTDIIKAMKGnvDAE 197
                                    566777777777777777766666555555544..67899*******************************999633455 PP

                           RB_B  88 asskvyrs 95 
                                    ++++v rs
  gi|118431874|ref|NP_148613.2| 198 TRRDVARS 205
                                    55556665 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.6   5.9e+03      68      84 ..     125     141 ..     118     159 .. 0.62
   2 ?   -3.8   0.0       7.7   1.3e+04      70      84 ..     183     197 ..     181     209 .. 0.68
   3 ?   12.1   0.1   9.3e-05      0.15      53      86 ..     283     316 ..     277     321 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.6
                        DUF2089  68 nrldeileaLgyeeeee 84 
                                    + ++e+++++g+ e   
  gi|118431874|ref|NP_148613.2| 125 SLINEVASRMGMPEIVV 141
                                    55677777777766544 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.7
                        DUF2089  70 ldeileaLgyeeeee 84 
                                    l +i++a++ + ++e
  gi|118431874|ref|NP_148613.2| 183 LTDIIKAMKGNVDAE 197
                                    678888888777755 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 9.3e-05
                        DUF2089  53 kevekelgisYpTvrnrldeileaLgyeeeeeee 86 
                                    ke+++ +g++  T+rnr +ei++aLg+eee ee+
  gi|118431874|ref|NP_148613.2| 283 KEIAHVVGVTEVTIRNRYKEIAQALGIEEELEEK 316
                                    789999**********************997744 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.75   1.2e+03      46      63 ..     165     181 ..     162     209 .. 0.66
   2 ?   11.1   0.0    0.0002      0.33      44      90 ..     261     307 ..     245     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.75
                                    HHHHHHHHHCCHHHHS-- CS
                       Cyclin_C  46 liAaaalllarstlnspe 63 
                                    ++A a+l++a+++ + p+
  gi|118431874|ref|NP_148613.2| 165 IVA-ASLYAASRIHGLPH 181
                                    455.55566655555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                                    HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                       Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                    p  +A aa++la    +  + ++++ h+ g+++  +++ ++ i+++l
  gi|118431874|ref|NP_148613.2| 261 PGGLAGAAVYLAALKHGIRKTQKEIAHVVGVTEVTIRNRYKEIAQAL 307
                                    66699***************************************988 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.64     1e+03      18      28 ..      14      24 ..      13      27 .. 0.88
   2 ?    9.0   0.1   0.00084       1.4      18      41 ..     275     298 ..     269     303 .. 0.90
   3 ?   -0.3   0.0      0.67   1.1e+03      25      36 ..     300     311 ..     298     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.64
                Phage_terminase 18 EsggtlklkdI 28
                                   E +g +k+k+I
  gi|118431874|ref|NP_148613.2| 14 EESGEIKCKNI 24
                                   889******99 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00084
                Phage_terminase  18 EsggtlklkdIAkvLdvsestvrk 41 
                                     +g  +  k+IA+v +v e t+r+
  gi|118431874|ref|NP_148613.2| 275 KHGIRKTQKEIAHVVGVTEVTIRN 298
                                    58888999**************98 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.67
                Phage_terminase  25 lkdIAkvLdvse 36 
                                     k+IA+ L++ e
  gi|118431874|ref|NP_148613.2| 300 YKEIAQALGIEE 311
                                    69*******987 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00032      0.52      28     126 ..     116     217 ..      95     218 .. 0.84
   2 ?   -1.4   0.0       1.1   1.8e+03      72      88 ..     260     276 ..     224     307 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                                    H.HHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTT.. CS
                       Cyclin_N  28 p.emRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitde.. 104
                                      +  +++++ + eva+++ + + ++  a +++   ++k  ++ + ++ ++a++L+ A++++   p +l d++ ++++  
  gi|118431874|ref|NP_148613.2| 116 VdKNLQTALSLINEVASRMGMPEIVVEDASKIYREAMEKGLTRGRSIESIVAASLYAASRIHGL-PHSLTDIIKAMKGnv 194
                                    4466778899999*******99999999**********9999999****************998.99******9997767 PP

                                    .SS-HHHHHHHHHHHHHHTTT-- CS
                       Cyclin_N 105 .afteeeilemErliLetLnfdl 126
                                     a t++++ +  rl+++ Ln ++
  gi|118431874|ref|NP_148613.2| 195 dAETRRDVARSYRLLVRDLNIKI 217
                                    78899999999999999998765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                    CHHHHHHHHHHHHHHHH CS
                       Cyclin_N  72 klqlvgatcLllAaKve 88 
                                    +   ++ ++++lAa  +
  gi|118431874|ref|NP_148613.2| 260 DPGGLAGAAVYLAALKH 276
                                    55555556666665333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2352.21
//
Query:       gi|14602068|ref|NP_148614.1|  [L=356]
Description: hypothetical protein APE_2444 [Aeropyrum pernix K1]
Scores for complete sequence (score 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   14.8   0.0      0.059   13.1   0.0    1.8  1  LexA_DNA_bind  LexA DNA binding domain
      0.034   14.3   0.2       0.17   12.1   0.0    2.3  2  HTH_28         Helix-turn-helix domain
       0.17   12.3   0.1        4.2    7.8   0.0    2.5  2  HTH_Tnp_1      Transposase


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 ?   13.1   0.0   9.9e-06     0.059       9      38 ..      26      55 ..      22      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-06
                                  HHHHHHHHHHHHHHSS---HHHHHHHHTS- CS
                 LexA_DNA_bind  9 revldlikasieetgypPsireiaralglk 38
                                  +++++ + ++ +e+g pPsi+  a++lgl+
  gi|14602068|ref|NP_148614.1| 26 AQIIEALTRYSTEEGLPPSIKSYAQKLGLA 55
                                  6899************************97 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.8e-05      0.17      14      41 ..      44      71 ..      26      74 .. 0.82
   2 ?   -1.7   0.0      0.56   3.3e+03      13      30 ..     209     230 ..     196     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                        HTH_28 14 svreaArelgisrrtvyrWikryeegGi 41
                                  s++  A++lg+ +r +y++++r ++ G+
  gi|14602068|ref|NP_148614.1| 44 SIKSYAQKLGLAERNLYKLVQRARAAGF 71
                                  78888********************997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
                        HTH_28  13 hsvreaArelgi....srrtvy 30 
                                   +sv+  Ar +g+    ++r  y
  gi|14602068|ref|NP_148614.1| 209 RSVASMARTYGLslikTQRKYY 230
                                   4667777777774444455555 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0007       4.2      20      52 ..      37      71 ..      23      88 .. 0.76
   2 ?    1.6   0.0     0.059   3.5e+02      20      46 ..     205     236 ..     188     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0007
                     HTH_Tnp_1 20 lepg..ksvsevArrhgvspnqLykWrrqyregee 52
                                   e+g   s+++ A+++g+ +  Lyk ++ +r+   
  gi|14602068|ref|NP_148614.1| 37 TEEGlpPSIKSYAQKLGLAERNLYKLVQRARAAGF 71
                                  5555224799********************96655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.059
                     HTH_Tnp_1  20 lepgksvsevArrhgvs.....pnqLykWrrq 46 
                                    ++ +sv++ Ar +g+s     ++ ++ W+r+
  gi|14602068|ref|NP_148614.1| 205 IDALRSVASMARTYGLSliktqRKYYRLWKRK 236
                                   5677899999**99997333334556667766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2628.40
//
Query:       gi|14602070|ref|NP_148616.1|  [L=365]
Description: hypothetical protein APE_2446 [Aeropyrum pernix K1]
Scores for complete 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   0.1    1.6e-23   83.2   0.1    2.0  1  DUF711    Uncharacterised ACR (DUF711)


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.1   9.2e-28   1.6e-23     182     403 ..     146     352 ..       1     355 [. 0.72

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 9.2e-28
                        DUF711 182 pednPFfpgAfhgvgeaeavinvGvsgpgvvkkaleeakkeasleelaeaikktafkitrlgelvarevakrlgvefggiD 262
                                   +  +P+fp A++    ++ +++v++  p  + + +++      l+ + + + ++a    +l  +++++vak  + +f+g+D
  gi|14602070|ref|NP_148616.1| 146 HILTPYFPLATSP--GEQRTVTVALLYPRYLLESFRKG-G---LQAVIDSMVDAA----QLSGEYGKAVAKDVEGSFAGVD 216
                                   5568999999997..67888999999999988888887.4...455555554444....45556666667779******** PP

                        DUF711 263 lSlaPtpavgdSvaeileelglesfGapGtlaalalltdavkkGGvmasskvgGlsGlflpvsEDaglaeaaeegaltiek 343
                                   lS++P   +++S  +++ee+g  ++ +pG    l l+++a+    + ++ + +G++ + lpv ED++l  +++e + + ++
  gi|14602070|ref|NP_148616.1| 217 LSISPW--MEESSLALVEEVGGVRLPEPGFAYGLRLVNEAIAA-AASKTGYAVGFNEVQLPVAEDSKLKVRVAELETSARD 294
                                   ******..456666789**************************.78888999***************************** PP

                        DUF711 344 LlamsaVCsvGLDmvpipgdtsaetiaaliaDeaalavrlnKtlavRliPvpgkkaGdkv 403
                                   Ll +s VC  GLDm  ip     + +a+l+++  a + +    ++vRliP  g ++Gd+v
  gi|14602070|ref|NP_148616.1| 295 LLRLSGVCLAGLDMAVIPAS--LDGVAGLLLEARAYSRAKGSIVGVRLIPLDGVEPGDEV 352
                                   ******************75..579*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 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:                        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: 00:00:00.40
# Mc/sec: 2743.23
//
Query:       gi|14602071|ref|NP_148617.1|  [L=142]
Description: hypothetical protein APE_2447 [Aeropyrum pernix K1]
Scores for complete 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   49.8   5.3    3.7e-13   49.8   5.3    1.5  2  CopD      Copper resistance protein D
     0.0072   16.0   2.0      0.017   14.7   1.8    1.6  2  DUF4153   Domain of unknown function (DUF4153)
  ------ inclusion threshold ------
       0.04   14.0   0.3      0.059   13.5   0.1    1.5  1  DUF212    Divergent PAP2 family
       0.65   10.4   5.3       0.64   10.4   4.4    1.4  1  DUF2628   Protein of unknown function (DUF2628)
       0.97    9.5  11.1        4.1    7.4  11.1    2.1  1  DUF2269   Predicted integral membrane protein (DUF2269)


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 ?   -2.3   0.1       1.7     6e+03      94      99 ..      20      25 ..       6      38 .. 0.51
   2 !   49.8   5.3     1e-16   3.7e-13       5     104 ..      48     138 ..      40     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                          CopD 94 lalvvl 99
                                  ++  ++
  gi|14602071|ref|NP_148617.1| 20 IGGHIV 25
                                  222222 PP

  == domain 2  score: 49.8 bits;  conditional E-value: 1e-16
                          CopD   5 rrFsrlalaavavvlvtGvvnallrvgl.agllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrl 84 
                                   + +++++++++++ +vtG+++ ++++g+ +g+++    +l+ +K+all+++++la+ +r+r+++r+    ++gg+  + ++
  gi|14602071|ref|NP_148617.1|  48 SVYEKIGMPSLVIAAVTGLYM-AVKLGWpEGAVA----SLVNLKIALLVATILLAVDARLRIIRRY----RRGGSISTVDM 119
                                   4579*****************.588895599998....89**************************....779999999** PP

                          CopD  85 rrsaalelvlalvvlllaaa 104
                                   +++++++++++++ ++++++
  gi|14602071|ref|NP_148617.1| 120 AAHIIAVTLISIL-FAVVGW 138
                                   ***********99.888777 PP

>> DUF4153  Domain of unknown function (DUF4153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.8   4.8e-06     0.017      27     130 ..      13     114 ..       5     135 .. 0.80
   2 ?    0.1   0.1      0.15   5.4e+02       7      23 ..     123     139 ..     116     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-06
                       DUF4153  27 ylflfvallfglvffLsllpee..laeeeqskrfkvLlkfillplviiYlliLylYlikilflaelPkGlvallvllylal 105
                                    l++ v++  ++v++L+ lp    + + ++ ++f+   + i +p ++i +++  lY++   ++  +P+G va lv l +al
  gi|14602071|ref|NP_148617.1|  13 ILAASVWIGGHIVIVLGYLPRFiaTGDFRHLEQFESVYEKIGMPSLVI-AAVTGLYMA---VKLGWPEGAVASLVNLKIAL 89 
                                   4557777777889999999975435789999*****************.9**999986...7889**************** PP

                       DUF4153 106 lllilllllrsekkwlklflrvfpl 130
                                   l++ +ll+++   ++++++ r + +
  gi|14602071|ref|NP_148617.1|  90 LVATILLAVDARLRIIRRYRRGGSI 114
                                   *999999999999999998776643 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                       DUF4153   7 aivllaidkLfvkvsir 23 
                                   +i++++i++Lf  v+++
  gi|14602071|ref|NP_148617.1| 123 IIAVTLISILFAVVGWE 139
                                   57788888888777776 PP

>> DUF212  Divergent PAP2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.6e-05     0.059      32      82 ..      45     100 ..      12     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                        DUF212  32 dlkllvstGgmPSsHsalvtalatavgl..eegldsslf..alalvfalivm.yDA 82 
                                   +++ ++++ gmPS   a+vt+l +av l   eg+  sl+   +al++a+i++  DA
  gi|14602071|ref|NP_148617.1|  45 QFESVYEKIGMPSLVIAAVTGLYMAVKLgwPEGAVASLVnlKIALLVATILLaVDA 100
                                   489999****************9998775566666555411567777777641454 PP

>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.4   0.00018      0.64      10      89 ..      44     142 .]      33     142 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                       DUF2628  10 erfafvedgkirlsfnvwAfffgfiwLlyrklwlkalvllviavavsvvlavl.....................gfsdavr 69 
                                   e+f+ v ++ i +   v+A++ g ++++++  w +++v  ++++ +++ +a +                     ++++a++
  gi|14602071|ref|NP_148617.1|  44 EQFESVYEK-IGMPSLVIAAVTG-LYMAVKLGWPEGAVASLVNLKIALLVATIllavdarlriirryrrggsisTVDMAAH 122
                                   444444444.5666667777665.79**********999998888777777777799999999****************** PP

                       DUF2628  70 lllalliaillgleanslyy 89 
                                   ++   li+il+++ + +++y
  gi|14602071|ref|NP_148617.1| 123 IIAVTLISILFAVVGWEIRY 142
                                   ***********998766665 PP

>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  11.1    0.0012       4.1       3      94 ..       8      96 ..       6     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                       DUF2269  3 lkllHilsavlllgtgigiaf.yllrasrtrdaaviaevarlvvladwlftatavillpvtGlwlvhlagwplkqsWlllslv 84
                                   +l+Hil+a + +g+ i+i + yl r   t+d + + +  +     +  + ++++++  vtGl++++  gwp +    l+ l 
  gi|14602071|ref|NP_148617.1|  8 AQLIHILAASVWIGGHIVIVLgYLPRFIATGDFRHLEQFES----VYEKIGMPSLVIAAVTGLYMAVKLGWPEGAVASLVNLK 86
                                  679**************999834445556666665555444....34457899*******************87655555555 PP

                       DUF2269 85 Lyllagalwl 94
                                  + ll++ + l
  gi|14602071|ref|NP_148617.1| 87 IALLVATILL 96
                                  4444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); 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:                         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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1145.14
//
Query:       gi|14602072|ref|NP_148618.1|  [L=287]
Description: BtpA-like protein [Aeropyrum pernix K1]
Scores for complete 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-112  375.5   0.0   1.4e-112  375.3   0.0    1.0  1  BtpA            BtpA family
    0.00043   20.5   0.2       0.72   10.1   0.0    2.2  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
  ------ inclusion threshold ------
       0.15   10.9   0.1       0.25   10.1   0.1    1.3  1  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 !  375.3   0.0  2.3e-116  1.4e-112       1     253 [.       6     278 ..       6     279 .. 0.99

  Alignments for each domain:
  == domain 1  score: 375.3 bits;  conditional E-value: 2.3e-116
                          BtpA   1 kekpvigvvHLkpLPgsaeyka...........nleevidkAvkeakaleegGvDavilenygdaPflkevdpetvaamtv 70 
                                   ++kp++gvvHL+pLPgs+ yka           +lee+i++Av+ea+++e++G+D+vilenygd+P++k+++p++v+amt+
  gi|14602072|ref|NP_148618.1|   6 RCKPLLGVVHLPPLPGSTGYKArrypprlgkvwSLEEIIEYAVSEASVYEDAGFDGVILENYGDTPYPKTPGPLQVSAMTR 86 
                                   69******************************************************************************* PP

                          BtpA  71 ivkevksdvsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkll....esrvkiladv 147
                                   iv+ev+s+v+ip+Gvn+Lrn++v+ala+A+++g++FiRvn+l++++ls+eGile++aa+l+++ +ll    e+r++iladv
  gi|14602072|ref|NP_148618.1|  87 IVREVSSAVGIPVGVNMLRNGSVEALASAYSGGGSFIRVNSLCETRLSPEGILEPDAARLAKSLALLgileERRIEILADV 167
                                   *******************************************************************9998999******* PP

                          BtpA 148 avkhavplverdlesavkdtver..gladavilsGkatGgevdleelklaketvk...vkvlvgsGvseenlekllsiadG 223
                                   +vkh++plve++++++v+d++er  +++++v+l+G+atGg++d++e+++a++t++   vk++vgsGvs+ nl+k+++iadG
  gi|14602072|ref|NP_148618.1| 168 DVKHSQPLVETSIAQTVRDCIERsgVPIAGVVLTGHATGGAPDADEVVAAARTASeyeVKTVVGSGVSQLNLSKYWHIADG 248
                                   ***********************9889***************************9999*********************** PP

                          BtpA 224 vivgtsikkdGkianaiDkervrkivelae 253
                                   +i+g+sik +Gk++n+iDke++r i++lae
  gi|14602072|ref|NP_148618.1| 249 FIIGSSIKLGGKPWNPIDKEKARLIASLAE 278
                                   **************************9997 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 !   10.1   0.0   0.00012      0.72      21      96 ..      56     147 ..      39     162 .. 0.70
   2 !    8.4   0.1    0.0004       2.4      23      62 ..     194     235 ..     167     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                   HTT--EEEEEEBTTTB--H........HHHHHHHHHHTT.T-EE.EEEESSSBS-----H.............HHHHHTEE CS
                Asparaginase_C  21 kkgakGvvlegtGvGnlps........allealkeakar.givv.vatsqcpsgsvsnseye........agkelerlgvi 83 
                                   ++g +Gv+le +G +  p+        a+ + ++e+ ++ gi+v v+  +  +gsv++   +          + l++ ++ 
  gi|14602072|ref|NP_148618.1|  56 DAGFDGVILENYGDTPYPKtpgplqvsAMTRIVREVSSAvGIPVgVNMLR--NGSVEALASAysgggsfiRVNSLCETRLS 134
                                   6799**************88888999999999999995537777344444..44444443334478888777777777777 PP

                                   E-TT--HHHHHHH CS
                Asparaginase_C  84 saddmtpeaarik 96 
                                     + + p aar+ 
  gi|14602072|ref|NP_148618.1| 135 PEGILEPDAARLA 147
                                   7777777777765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0004
                                   T--EEEEEEBTTTB--H..HHHHHHHHHHTTT-EEEEEESSS CS
                Asparaginase_C  23 gakGvvlegtGvGnlps..allealkeakargivvvatsqcp 62 
                                    + Gvvl g  +G++p+  +++ a++ a + ++  v+ s ++
  gi|14602072|ref|NP_148618.1| 194 PIAGVVLTGHATGGAPDadEVVAAARTASEYEVKTVVGSGVS 235
                                   368*************9889********99998888877655 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   4.2e-05      0.25     176     229 ..     201     255 ..     192     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.2e-05
                                   SSTTSSB-TTHHHHHHHHHHCT..SS-EEEESSS-SHHHHHHHHTT-SEEEE-HHH CS
                     Trp_syntA 176 Tgaenavaaevdelverlkklt..avPvavGFGistkeqvkqvakvadGvivGSal 229
                                   Tg  +  a + de+v++ ++++  +v + vG G+s+ +  ++  ++adG i+GS +
  gi|14602072|ref|NP_148618.1| 201 TGHATGGAPDADEVVAAARTASeyEVKTVVGSGVSQLNL-SKYWHIADGFIIGSSI 255
                                   88888888889999998888875578899******9975.55667*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2244.97
//
Query:       gi|118431875|ref|NP_148619.2|  [L=492]
Description: leucine aminopeptidase [Aeropyrum pernix K1]
Scores for complete 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-100  337.0   0.0   1.3e-100  336.7   0.0    1.1  1  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
    2.7e-08   33.7   0.5    2.3e-07   30.7   0.0    2.7  3  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.7   0.0  1.4e-104  1.3e-100       2     311 .]     168     481 ..     167     481 .. 0.93

  Alignments for each domain:
  == domain 1  score: 336.7 bits;  conditional E-value: 1.4e-104
                                    HHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SSTTSEEEE CS
                  Peptidase_M17   2 lardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgakekekkla 81 
                                    lard++n+p+++l p+kla+++e+l ++ ++v+vev++ ++l e+g+g++++Vg gS ee+prl+ ++y+g   + +++a
  gi|118431875|ref|NP_148619.2| 168 LARDIANAPPHRLPPAKLAAAVEDLFSKFDNVDVEVFSYDRLLEEGFGGIVSVGMGS-EEKPRLIIIKYRGG--AGEPIA 244
                                    79*********************98778888**************************.66***********9..6***** PP

                                    EEEEEEEEEE-TTSS--HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEEEE-TTS-EE CS
                  Peptidase_M17  82 lVGKGitfDtGGlslKpsasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdvitamnGktv 161
                                    lVGK+++fD+GG++lKps++m+ m+aD++G+Aav+ga+ ++a+l++++ +++++p++ N++sg+++ p+dvi++ +G+ v
  gi|118431875|ref|NP_148619.2| 245 LVGKAVVFDSGGINLKPSQGMTLMRADKAGGAAVVGAMWTAARLGIKASIIGLIPAVINVPSGSSYLPSDVIRMWDGTMV 324
                                    ******************************************************************************** PP

                                    EES-TTGCHHHHHHHHHHHHHGCT--SEEEEEE---THHHHHHTTTSEEEEES-HHHHHHHHHHHHHHS-EEEE----HH CS
                  Peptidase_M17 162 evlnTDaEGRLvLADalayaeekekpdlivdvATLTgavvvalGkkaaglfsnddelaeelekageeagervwrlpleee 241
                                    e++nTDaEGRL+LADa++ya+++ ++++++d+ATLTga+vvalG  +aglf+++d la+++e+a++++ge++wr+p+e+e
  gi|118431875|ref|NP_148619.2| 325 EITNTDAEGRLILADAISYAAKQLGAKTVIDLATLTGAIVVALGPLIAGLFTRSDGLARAFEEASRTTGEKIWRMPMEDE 404
                                    ********************9899******************************************************** PP

                                    HGGGG--SS..SSEESS-SSSSTHHHHHHHHHHTTSSECGEEEEE-TTTTE..S.BTTB.S......EE--TTHHHHH CS
                  Peptidase_M17 242 ykkqlkskv..aDlknvgkkrragaitAalFLkefvketpWaHlDiagtal..kekealkke....kgatGvgvrtLv 311
                                    y k+l+++    ++ n ++ r +gai  alFL++fv+ +++aHlDiag+ +  ++ +  + +      a G+gvr+L+
  gi|118431875|ref|NP_148619.2| 405 YAKSLTQPAqaGEIVNAAQ-RYGGAIFGALFLERFVHGKEFAHLDIAGPGIafEAGSLAPPYwpekGMAPGYGVRLLI 481
                                    *****97774467888887.788*************6699*********7644433333333666467789***9985 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   2.5e-11   2.3e-07       1     124 [.      25     138 ..      25     140 .. 0.89
   2 ?   -1.2   0.0      0.19   1.7e+03     103     115 ..     157     169 ..     146     170 .. 0.80
   3 ?   -1.9   0.1      0.31   2.7e+03      52      65 ..     214     227 ..     207     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.5e-11
                Peptidase_M17_N   1 vvgvfeggklspaaekldealagllsellkegdftGkagevlvlralsgekakrvllVGLGkeeeltaealrkaagaaar 80 
                                    v++vf++g + ++ e l ++l+ ll+e  +++ +++++g+v++l+  +g     v++ G+G++++   e +r+ ++aa r
  gi|118431875|ref|NP_148619.2|  25 VIPVFKEGDSIKLPEGLPQDLESLLKESYNSKAVSPEPGSVAKLPYRGGL----VVTAGCGAPGD--LEGVRRGFAAASR 98 
                                    89**********************************************98....**********6..9************ PP

                Peptidase_M17_N  81 alkgakvttiavalp.legknsd.ekaeaaaegallglYrfdryks 124
                                     + + + +++ ++l  l     d  +  +a+ gallg+Yr +++k 
  gi|118431875|ref|NP_148619.2|  99 QVVD-SFEEAQLYLVgL-----DtVSSTEAVIGALLGAYRLEEFKN 138
                                    ****.555555555522.....33566789**************97 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.19
                Peptidase_M17_N 103 ekaeaaaegallg 115
                                    ++a+a+aeg+ l+
  gi|118431875|ref|NP_148619.2| 157 DYAQAVAEGVYLA 169
                                    89*******9986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.31
                Peptidase_M17_N  52 akrvllVGLGkeee 65 
                                    +  ++ VG G+ee+
  gi|118431875|ref|NP_148619.2| 214 FGGIVSVGMGSEEK 227
                                    667999*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3689.49
//
Query:       gi|14602074|ref|NP_148620.1|  [L=512]
Description: GMP synthase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-37  126.9   0.0      4e-37  126.2   0.0    1.4  1  GMP_synt_C     GMP synthase C terminal domain
    1.5e-31  109.6   0.0    2.3e-31  109.1   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    2.2e-10   40.1   0.1    7.3e-06   25.3   0.0    2.2  2  NAD_synthase   NAD synthase
    5.8e-10   39.3   0.2    4.6e-08   33.1   0.1    3.1  2  Peptidase_C26  Peptidase C26
    9.5e-06   25.3   0.0     0.0039   16.7   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.016   14.9   0.0    1.4  1  ATP_bind_3     PP-loop family
      0.046   13.3   0.0      0.074   12.6   0.0    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
      0.048   13.7   0.0       0.09   12.8   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
      0.055   12.3   0.1       0.21   10.4   0.1    1.7  2  tRNA_Me_trans  tRNA methyl transferase
       0.27   10.8   0.6       0.62    9.7   0.2    1.7  2  Asn_synthase   Asparagine synthase


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   2.2e-40     4e-37       1      92 []     420     511 ..     420     511 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 2.2e-40
                                   CCCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE CS
                    GMP_synt_C   1 eelkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyd 81 
                                   ee+++agl  k+wQ+favl+   ++Gv+gd+R+y+yvva+Raves Damta+ aelp+ +Le+i++ri++e+++v rvvyd
  gi|14602074|ref|NP_148620.1| 420 EEVEAAGLGGKLWQYFAVLTASMATGVRGDSRSYGYVVAVRAVESVDAMTAKPAELPWWLLERIARRITSEIPEVVRVVYD 500
                                   7999***************************************************************************** PP

                                   ---TTTS-S-- CS
                    GMP_synt_C  82 itskPpatiEw 92 
                                   itskPp+tiEw
  gi|14602074|ref|NP_148620.1| 501 ITSKPPSTIEW 511
                                   *********** PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.0   1.3e-34   2.3e-31       2     186 ..      12     189 ..      11     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 1.3e-34
                                   EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHH CS
                        GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQ 82 
                                   ++D++ ++ + ++++++elgv+ e+vp ++  +   e+l  + g+++sgGpgs+    + ea+  +++ ++P+LGIC+G+Q
  gi|14602074|ref|NP_148620.1|  12 VVDFGGQYAHLIARRIRELGVYSEIVPATS-LDALGEALPRAAGVVLSGGPGSVWGSRHDEAAAMVLQLGKPVLGICYGHQ 91 
                                   89*************************986.333434699***************99999********************* PP

                                   HHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTT CS
                        GATase  83 llaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknp 163
                                   lla+ +g++v +    e    + ++ d    ll+gl+++++++++H ++v +    p + +v+a++  + + ++++e+  +
  gi|14602074|ref|NP_148620.1|  92 LLAKVLGGEVGRSPLPEFGPTEVEVLD-YGILLNGLPSRFKVWMSHYDAVLR---PPGEAKVLART-PG-SPVAAMELWGR 166
                                   **************5555555566666.559********************9...9999***9999.66.79********* PP

                                   EEEESSBTTSTTSTTHHHHHHHH CS
                        GATase 164 fvgvQFHPEststpegpellfnf 186
                                   ++gvQ+HPE+++t+ g e+l n 
  gi|14602074|ref|NP_148620.1| 167 VFGVQWHPEVRHTQYGREVLDNW 189
                                   *******************9986 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   4.1e-09   7.3e-06       5      89 ..     208     288 ..     203     317 .. 0.80
   2 !   12.7   0.0   2.9e-05     0.051     148     177 ..     360     389 ..     354     395 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4.1e-09
                                   HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH CS
                  NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv 85 
                                   lv+++k+   + g   +v  +SGGvDS+++a +a+ka+g  +   + + +  ++e +ve  ++l  +lg+e   +d  +  
  gi|14602074|ref|NP_148620.1| 208 LVESVKK---EVGDALAVAAVSGGVDSTVAALIAKKAIG-SRLYPVFIDHGLHPEGEVERVVKLLSRLGLEPVMVDAGEEF 284
                                   3333333...34456678899*****************5.68999*************************99999987665 PP

                                   HHHH CS
                  NAD_synthase  86 rafe 89 
                                    a  
  gi|14602074|ref|NP_148620.1| 285 LAAL 288
                                   5554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.9e-05
                                   BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                  NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                   ++p+   +K ev+ La++l+vP++++ k+P
  gi|14602074|ref|NP_148620.1| 360 VEPLRYFYKDEVRLLAEKLGVPRELIWKQP 389
                                   5799*************************9 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.11   1.9e+02      31      70 ..      25      64 ..      12      75 .. 0.80
   2 !   33.1   0.1   2.6e-11   4.6e-08     101     216 .]      76     175 ..      68     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                 Peptidase_C26 31 eavekagglpvllpieedeedvkaildkldgllltGgq.dv 70
                                  + +++ g+ + ++p++ + + + ++l +  g++l+Gg+  v
  gi|14602074|ref|NP_148620.1| 25 RRIRELGVYSEIVPAT-SLDALGEALPRAAGVVLSGGPgSV 64
                                  5778888888899999.99999***************9666 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 2.6e-11
                 Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikel 181
                                   +l+ g+P+lgiC G+qll+ +lGG++ ++               ++   +v+v   ++l + l  ++++v   H  a+ + 
  gi|14602074|ref|NP_148620.1|  76 VLQLGKPVLGICYGHQLLAKVLGGEVGRSPL------------PEFGPTEVEVLDYGILLNGLP-SRFKVWMSHYDAVLRP 143
                                   57889*******************9876544............234566888888888888887.8*************** PP

                 Peptidase_C26 182 aeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                     e +v A+++   + a+e+      v+gvQwHPE
  gi|14602074|ref|NP_148620.1| 144 PGEAKVLARTPGSPVAAMELWG---RVFGVQWHPE 175
                                   ********************99...69*******9 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.2e-06    0.0039       2      59 ..     221     278 ..     220     291 .. 0.87
   2 !    6.4   0.0    0.0032       5.7     125     180 ..     323     385 ..     300     387 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                                   EEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEE CS
                          QueC   2 avvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkil 59 
                                   av  +SGG+DSt+++++akk++  +++ + +d g + + e+e + k+ ++lg+ e  ++
  gi|14602074|ref|NP_148620.1| 221 AVAAVSGGVDSTVAALIAKKAIgSRLYPVFIDHGLHPEGEVERVVKLLSRLGL-EPVMV 278
                                   7899**************9985499***********************99999.55555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0032
                                   STT--GGGSHHHHHHHHHHHHHH.......HTS--EEE-TTTT--HHHHHHHHHHTTHHHHH- CS
                          QueC 125 dfsgYPDcrdefvkalnkalnlg.......edkkieieaPlidlsKaeivklgkelgvpleet 180
                                   + + YPD  +   +    ++++        +d +++++ Pl  + K e+  l+++lgvp+e+ 
  gi|14602074|ref|NP_148620.1| 323 QGTIYPDVIESGARPGADTIKTHhnvgglpKDMRLKLVEPLRYFYKDEVRLLAEKLGVPRELI 385
                                   556677765544332222222222222555999*************************99875 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.1e-06     0.016       3      46 ..     222     262 ..     220     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.1e-06
                                   EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHH CS
                    ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskee 46 
                                   ++AvSgG+DS++  l+++k     g++l  + +dhgl++e + e
  gi|14602074|ref|NP_148620.1| 222 VAAVSGGVDSTVAALIAKKA---IGSRLYPVFIDHGLHPEGEVE 262
                                   78*********988877777...6789**********9987644 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.1e-05     0.074       6     116 ..     221     325 ..     216     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                          ThiI   6 vlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekv.. 83 
                                   ++a +SgG+DS Vaa ++ k  G r   v+++    ++ + ++ ve++++ll++ +    ++ v+vd  e     le v  
  gi|14602074|ref|NP_148620.1| 221 AVAAVSGGVDSTVAALIAKKAiGSRLYPVFID----HGLHPEGEVERVVKLLSRLG----LEPVMVDAGEEFLAALEGVgd 293
                                   57889**********99887559999999996....77788889999999999988....577777777766666666654 PP

                          ThiI  84 kekltivllkrkmlriAekvaeeegakalvtGe 116
                                   +e+ + v+  r    + e+ a+  ga+ lv+G 
  gi|14602074|ref|NP_148620.1| 294 PEEKRRVVG-RVYAEVLERAARDIGAEYLVQGT 325
                                   555555544.45677777788888888888775 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-05      0.09       3      77 ..     222     297 ..     221     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                                   EEE--SSCTCHHHHHHHHHHCTTH.EEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-TH CS
                   PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpv.pvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgssl 77 
                                   v +vsgG ds+V   +a ka   +   vf+d g + +  +e v +l +r+gl+  +++  ee+ ++++  + ++++
  gi|14602074|ref|NP_148620.1| 222 VAAVSGGVDSTVAALIAKKAIGSRlYPVFIDHGLHPEGEVERVVKLLSRLGLEPVMVDAGEEFLAALEGVGDPEEK 297
                                   6799******************97459*************************988888888888877777777665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00012      0.21       4      23 ..     222     241 ..     220     259 .. 0.85
   2 ?   -1.2   0.0      0.38   6.9e+02     163     185 ..     358     380 ..     351     384 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00012
                 tRNA_Me_trans   4 vvalSgGVDSsvaaallkeq 23 
                                   v+a+SgGVDS+vaa++ k++
  gi|14602074|ref|NP_148620.1| 222 VAAVSGGVDSTVAALIAKKA 241
                                   689***********999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
                 tRNA_Me_trans 163 kllfPlgeltKeevrkiAkeagl 185
                                   kl+ Pl  + K+evr +A++ g+
  gi|14602074|ref|NP_148620.1| 358 KLVEPLRYFYKDEVRLLAEKLGV 380
                                   5677999***********99876 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00035      0.62       5      41 ..     207     242 ..     204     291 .. 0.75
   2 ?   -1.9   0.0       1.2   2.1e+03      90     116 ..     460     486 ..     457     489 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                  Asn_synthase   5 lLedaVkrrlradvpvGalLSGGlDSSliaalaarqs 41 
                                    L ++Vk+ + +d    a  SGG+DS++ a +a++  
  gi|14602074|ref|NP_148620.1| 207 ELVESVKKEV-GDALAVAAVSGGVDSTVAALIAKKAI 242
                                   5889999766.777888889******99998888765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                  Asn_synthase  90 dviyhleepfadrsaiplyllsrlakr 116
                                   ++++ ++ ++a ++++p++ll r a+r
  gi|14602074|ref|NP_148620.1| 460 RAVESVDAMTAKPAELPWWLLERIARR 486
                                   57788899*************999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3881.36
//
Query:       gi|118431876|ref|YP_874945.1|  [L=98]
Description: hypothetical protein APE_2454.1 [Aeropyrum pernix K1]
Scores for 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-05   22.4   2.8     0.0017   18.4   0.1    2.2  2  UPF0547          Uncharacterised protein family UPF0547
  ------ inclusion threshold ------
       0.01   15.5   0.2        2.7    7.8   0.0    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.014   15.0   2.9        1.2    8.9   0.1    2.3  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.019   15.4   0.2      0.033   14.5   0.2    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.023   14.8   0.6       0.79    9.9   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.023   14.7   0.1       0.05   13.6   0.1    1.6  1  DZR              Double zinc ribbon
      0.041   14.2   1.5        0.2   12.0   0.0    2.1  2  DUF4379          Probable Zinc-ribbon domain
       0.06   13.4   0.2        6.6    6.8   0.0    2.1  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.066   12.9   3.5          3    7.7   0.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.067   13.2   1.3       0.25   11.3   1.3    1.9  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.08   13.0   0.2       0.31   11.1   0.2    1.9  1  Elf1             Transcription elongation factor Elf1 like
      0.093   12.6   1.5        3.9    7.4   0.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.11   12.6   0.3          6    7.1   0.0    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.11   12.2   1.3        2.4    8.0   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.12   12.9   0.3        1.5    9.4   0.1    2.1  2  zf-H2C2_2        Zinc-finger double domain
       0.21   12.1   0.9       0.53   10.8   0.1    1.8  2  Ribosomal_L44    Ribosomal protein L44
       0.24   10.9   2.9        1.5    8.4   0.5    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.32   10.7   0.7       0.76    9.5   0.7    1.7  1  DUF2225          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.049        49       2       7 ..      12      17 ..      12      19 .. 0.69
   2 !   18.4   0.1   1.7e-06    0.0017      13      26 .]      46      59 ..      44      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.049
                        UPF0547  2 vCPeCe 7 
                                   vCP C 
  gi|118431876|ref|YP_874945.1| 12 VCPSCG 17
                                   588886 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.7e-06
                        UPF0547 13 aaqfCphCGyvFqa 26
                                   a+ +C++CGy+++a
  gi|118431876|ref|YP_874945.1| 46 AVLSCRECGYSWKA 59
                                   8899********97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0027       2.7      19      29 ..       8      18 ..       6      20 .. 0.85
   2 ?    5.7   0.1     0.012        12      22      30 ..      48      56 ..      45      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                  A2L_zn_ribbon 19 qgylvCieCga 29
                                   ++ +vC+ Cga
  gi|118431876|ref|YP_874945.1|  8 RDPYVCPSCGA 18
                                   6789******8 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.012
                  A2L_zn_ribbon 22 lvCieCgas 30
                                   l+C eCg+s
  gi|118431876|ref|YP_874945.1| 48 LSCRECGYS 56
                                   79*****98 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 ?    6.1   0.7    0.0088       8.8      13      26 ..       6      19 ..       3      20 .. 0.85
   2 ?    8.9   0.1    0.0012       1.2      11      25 ..      41      55 ..      38      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0088
                                   -SSS----SSS--- CS
                 DNA_RNApol_7kD 13 kkgdpiRCkeCGhR 26
                                   k++dp  C  CG R
  gi|118431876|ref|YP_874945.1|  6 KQRDPYVCPSCGAR 19
                                   78899999999998 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                                   ---SSS----SSS-- CS
                 DNA_RNApol_7kD 11 slkkgdpiRCkeCGh 25
                                   ++   +++ C+eCG+
  gi|118431876|ref|YP_874945.1| 41 TITVMAVLSCRECGY 55
                                   577778999*****8 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.4e-05     0.033       4      49 ..      11      72 ..       8      76 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                Lar_restr_allev  4 kpCPfCggravlers.qrvvaeigq..............cvyCadCga....stpwfkiaedeae 49
                                   + CP Cg ra  ++     v+   +              + +C +Cg+      +++k+ +de++
  gi|118431876|ref|YP_874945.1| 11 YVCPSCGARAGEVEKtWTLVS---PlpdkygrititvmaVLSCRECGYswkaPIKKMKTGGDEEA 72
                                   67*****99855444044443...3448999*****************76664455555555555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00079      0.79      25      36 ..       8      20 ..       1      24 [. 0.67
   2 ?    3.4   0.0     0.087        86       8      21 ..      50      64 ..      47      73 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                    Zn-ribbon_8 25 plta.CPeCgsev 36
                                    ++  CP+Cg+++
  gi|118431876|ref|YP_874945.1|  8 RDPYvCPSCGARA 20
                                   34555*****965 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.087
                    Zn-ribbon_8  8 CeeCghefe.vlqsi 21
                                   C+eCg     ++ ++
  gi|118431876|ref|YP_874945.1| 50 CRECGYSWKaPIKKM 64
                                   999997766555554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     5e-05      0.05       9      38 ..       7      57 ..       3      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-05
                            DZR  9 ppdarfCseCgtklkavaa.....................edrCpsCgekv 38
                                   + d  +C+ Cg++  +v++                        C +Cg++ 
  gi|118431876|ref|YP_874945.1|  7 QRDPYVCPSCGARAGEVEKtwtlvsplpdkygrititvmaVLSCRECGYSW 57
                                   667889*******8877778999999999*********99999****9985 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.53   5.3e+02      47      56 .]       5      16 ..       1      17 [. 0.61
   2 ?   12.0   0.0    0.0002       0.2      31      47 ..      49      65 ..      40      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.53
                        DUF4379 47 tkgssk...CpkC 56
                                     ++++   Cp C
  gi|118431876|ref|YP_874945.1|  5 K-KQRDpyvCPSC 16
                                   2.33336889999 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                        DUF4379 31 kCakCgheWeasvsnrt 47
                                    C++Cg++W+a +++  
  gi|118431876|ref|YP_874945.1| 49 SCRECGYSWKAPIKKMK 65
                                   6************9875 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 ?    5.0   0.0     0.025        25      85     100 ..       9      24 ..       2      30 .. 0.70
   2 ?    6.8   0.0    0.0066       6.6      66      83 ..      43      60 ..      36      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                                    HHHS-TTTSSS-EEEE CS
                           HypA  85 kalrCpkCgsadveiv 100
                                    + + Cp+Cg++  e+ 
  gi|118431876|ref|YP_874945.1|   9 DPYVCPSCGARAGEVE 24 
                                    3568*****9987776 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0066
                                   EE--EEEETTTS-EEECH CS
                           HypA 66 evpvkvrCreCgkefele 83
                                   +v +++ CreCg++++  
  gi|118431876|ref|YP_874945.1| 43 TVMAVLSCRECGYSWKAP 60
                                   5678899******99854 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2     0.003         3       1      10 [.      11      20 ..      11      23 .. 0.79
   2 ?    6.2   0.3    0.0085       8.5       3       9 ..      50      56 ..      49      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.003
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   YvC +CG+++
  gi|118431876|ref|YP_874945.1| 11 YVCPSCGARA 20
                                   8899999876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0085
                   Rubredoxin_2  3 CsqCGfe 9 
                                   C++CG++
  gi|118431876|ref|YP_874945.1| 50 CRECGYS 56
                                   *****97 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 ?   11.3   1.3   0.00025      0.25      18      45 ..      10      55 ..       3      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                  Zn_Tnp_IS1595 18 gfvCPhCgsr..kayrikt................rglfqCkeCrk 45
                                     vCP Cg r  ++ +++t                  ++ C+eC++
  gi|118431876|ref|YP_874945.1| 10 PYVCPSCGARagEVEKTWTlvsplpdkygrititvMAVLSCRECGY 55
                                   479*****88887777777999999999999999999999999987 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00031      0.31      19      63 ..       8      65 ..       1      69 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                           Elf1 19 ptkFdCpfCnheksvevkldkkek................iaevsCkvCgesfetkvnals 63
                                      + Cp C++  + ev+ +                    +a++sC+ Cg s +  +++++
  gi|118431876|ref|YP_874945.1|  8 RDPYVCPSCGAR-AGEVEKTW--TlvsplpdkygrititvMAVLSCRECGYSWKAPIKKMK 65
                                   455778888776.32332222..222446666777888889***********999998875 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.041        41       2       8 ..      12      18 ..      10      20 .. 0.53
   2 ?    7.4   0.1    0.0039       3.9      30      39 .]      49      58 ..      44      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                        TFIIS_C  2 kCpkCgs 8 
                                    Cp+Cg 
  gi|118431876|ref|YP_874945.1| 12 VCPSCGA 18
                                   3555554 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0039
                        TFIIS_C 30 kCtkCghrWr 39
                                    C +Cg+ W+
  gi|118431876|ref|YP_874945.1| 49 SCRECGYSWK 58
                                   7********7 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 ?    7.1   0.0     0.006         6      12      33 ..       6      27 ..       2      29 .. 0.74
   2 ?    3.9   0.0     0.057        57      17      32 ..      48      63 ..      43      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.006
                       zf-Mss51 12 pkhvdfeCpdCGiptycseehw 33
                                   +++  + Cp CG      e+ w
  gi|118431876|ref|YP_874945.1|  6 KQRDPYVCPSCGARAGEVEKTW 27
                                   56778*******8766666665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.057
                       zf-Mss51 17 feCpdCGiptycseeh 32
                                   + C +CG++     ++
  gi|118431876|ref|YP_874945.1| 48 LSCRECGYSWKAPIKK 63
                                   58*****987665555 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0024       2.4       2       7 ..      13      18 ..       7      25 .. 0.78
   2 ?    3.1   0.1     0.081        81      16      21 ..      50      55 ..      47      56 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                  zinc_ribbon_2  2 CpnCGa 7 
                                   Cp+CGa
  gi|118431876|ref|YP_874945.1| 13 CPSCGA 18
                                   777776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.081
                  zinc_ribbon_2 16 CpyCGt 21
                                   C +CG+
  gi|118431876|ref|YP_874945.1| 50 CRECGY 55
                                   556665 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 ?    9.4   0.1    0.0015       1.5      11      22 ..       7      18 ..       2      21 .. 0.77
   2 ?    1.3   0.0      0.52   5.2e+02      16      23 ..      49      56 ..      41      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                      zf-H2C2_2 11 gekpyeCplCdk 22
                                   +  py Cp+C+ 
  gi|118431876|ref|YP_874945.1|  7 QRDPYVCPSCGA 18
                                   4469******85 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.52
                      zf-H2C2_2 16 eCplCdka 23
                                    C +C+++
  gi|118431876|ref|YP_874945.1| 49 SCRECGYS 56
                                   59***996 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.5   1.5e+03      48      61 ..       5      18 ..       2      25 .. 0.78
   2 ?   10.8   0.1   0.00053      0.53      37      71 ..      31      65 ..      25      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.5
                                   BB--EEEEETTT-- CS
                  Ribosomal_L44 48 KKivlrleCteCkk 61
                                   KK    + C  C+ 
  gi|118431876|ref|YP_874945.1|  5 KKQRDPYVCPSCGA 18
                                   67777789999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00053
                                   GS----.--SSBB--EEEEETTT--EEE----BBS CS
                  Ribosomal_L44 37 kpvfkkkaKttKKivlrleCteCkkkrlkalkRak 71
                                   +p + k  + t  +   l C eC+++   ++k++k
  gi|118431876|ref|YP_874945.1| 31 SPLPDKYGRITITVMAVLSCRECGYSWKAPIKKMK 65
                                   67888888888999999***************999 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0015       1.5       5      10 ..      13      18 ..      10      20 .. 0.61
   2 ?    2.5   0.1       0.1     1e+02      19      24 ..      50      55 ..      47      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                    zf-ribbon_3  5 CPnCGa 10
                                   CP+CGa
  gi|118431876|ref|YP_874945.1| 13 CPSCGA 18
                                   555554 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                    zf-ribbon_3 19 CpyCGt 24
                                   C  CG+
  gi|118431876|ref|YP_874945.1| 50 CRECGY 55
                                   999*97 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 ?    9.5   0.7   0.00077      0.76      36      58 ..      35      57 ..       8      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00077
                        DUF2225 36 akYeevnplfYevvvCpkCgYaa 58
                                   +kY+++  ++  v  C +CgY+ 
  gi|118431876|ref|YP_874945.1| 35 DKYGRITITVMAVLSCRECGYSW 57
                                   79*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 841.71
//
Query:       gi|118431877|ref|YP_874946.1|  [L=286]
Description: hypothetical protein APE_2455.1 [Aeropyrum pernix K1]
Scores for 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-08   32.3   0.7      1e-07   31.7   0.7    1.2  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
       0.57   10.7   5.5        1.3    9.6   5.5    1.6  1  DUF2061     Predicted membrane protein (DUF2061)


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 !   31.7   0.7   1.1e-11     1e-07       8     204 ..      72     265 ..      70     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.1e-11
                                    HHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS.SEEEEEEEE-SSEEEE CS
                     MS_channel   8 iivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig.dieGtVediglrttki 86 
                                    +iv++++++ +++      ++ + ++l +a+ la  dl++n++a   +++++ ++ ++++ ++ +++G V+di  +++ +
  gi|118431877|ref|YP_874946.1|  72 LIVLITVMIAFYIVTGSRFIIILIAVLLAAILLATWDLLMNMAAYYAIIITRIVSRDEYIIMPnGVRGWVRDIRPLFVIV 151
                                    5889999999999999999*******************************************999*************** PP

                                    EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SS CS
                     MS_channel  87 rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgds 166
                                    +t  g +  +Pns+++   +   +++s +r  +++ g++ ++ +++++++l+++ + l+ + e        v++de++ +
  gi|118431877|ref|YP_874946.1| 152 ETKYG-VYHVPNSMMLRLGVLTKRERSYYRLTVRVWGLPSQQLIDNVRDALDNVVNTLLPEDERSA-VMKRVIIDEISED 229
                                    *****.788*******76665555556666666666777777766666666665555555554443.3344555555555 PP

                                    SEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHHT- CS
                     MS_channel 167 slnfevrvfvktvvpeeylsvqseinlrikkileeegi 204
                                    s ++++ v ++    e + +  +++++r  + l+e+gi
  gi|118431877|ref|YP_874946.1| 230 SATVRIIVGMPH--TEPKPERLADFVERLSRRLQEHGI 265
                                    555555555544..666666777777777777777777 PP

>> DUF2061  Predicted membrane protein (DUF2061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.5   0.00015       1.3      10      45 ..      73     117 ..      68     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                        DUF2061  10 ihtvvtflvaylltgs.........lalAgaialvEpvvktvlYy 45 
                                    i ++++++  y++tgs         l +A+ +a+ + ++++++Yy
  gi|118431877|ref|YP_874946.1|  73 IVLITVMIAFYIVTGSrfiiiliavLLAAILLATWDLLMNMAAYY 117
                                    66788889999*************999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2139.73
//
Query:       gi|14602214|ref|NP_148621.1|  [L=220]
Description: Trk system potassium uptake protein TrkA [Aeropyrum pernix K1]
Scores for complete 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   86.4   1.0    2.2e-24   85.9   0.4    1.5  1  TrkA_N           TrkA-N domain
    3.3e-09   37.1   0.1      8e-09   35.9   0.1    1.6  2  NAD_binding_7    Putative NAD(P)-binding
    5.3e-06   26.2   1.2    1.8e-05   24.5   0.2    2.2  2  TrkA_C           TrkA-C domain
    1.1e-05   25.7   0.1    1.8e-05   25.0   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    1.8e-05   24.7   0.0      3e-05   24.0   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    2.1e-05   24.2   0.0    3.3e-05   23.6   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
    3.3e-05   23.4   0.3     0.0014   18.1   0.1    2.1  2  ThiF             ThiF family
    3.4e-05   24.3   0.5    0.00013   22.5   0.1    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    3.9e-05   24.1   0.0    6.3e-05   23.5   0.0    1.5  1  XdhC_C           XdhC Rossmann domain
    5.4e-05   22.7   0.2    9.9e-05   21.9   0.0    1.5  1  adh_short        short chain dehydrogenase
    8.1e-05   23.1   0.1    0.00023   21.6   0.1    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    9.3e-05   22.1   0.0    0.00017   21.2   0.0    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
    0.00011   21.6   0.2    0.00025   20.4   0.1    1.6  2  FAD_binding_3    FAD binding domain
    0.00012   21.5   0.1    0.00024   20.5   0.0    1.6  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00013   22.1   0.0    0.00028   20.9   0.0    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00026   20.9   0.0    0.00051   20.0   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding
    0.00063   19.3   0.0     0.0011   18.5   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00064   19.1   0.2    0.00095   18.5   0.2    1.5  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0018   18.5   0.0     0.0024   18.0   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.003   17.7   0.1     0.0074   16.4   0.1    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0045   17.7   0.0     0.0074   17.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0055   16.9   0.1      0.012   15.9   0.1    1.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      0.007   15.7   0.3      0.009   15.3   0.3    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0097   14.9   0.7      0.013   14.5   0.2    1.4  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
  ------ inclusion threshold ------
       0.02   15.7   0.0      0.037   14.9   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
      0.032   13.8   0.0      0.051   13.1   0.0    1.2  1  MTS              Methyltransferase small domain
      0.033   13.3   0.0       0.05   12.7   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
      0.035   13.7   0.0      0.052   13.1   0.0    1.3  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      0.041   14.2   0.0      0.079   13.2   0.0    1.5  1  OKR_DC_1_N       Orn/Lys/Arg decarboxylase, N-terminal domain
      0.044   13.0   1.1        1.5    8.0   0.1    2.1  2  Thi4             Thi4 family
       0.05   13.2   0.1      0.092   12.3   0.1    1.4  1  DAO              FAD dependent oxidoreductase
      0.059   13.3   0.0       0.12   12.2   0.0    1.5  1  LpxI_N           LpxI N-terminal domain
      0.088   13.2   0.1       0.28   11.5   0.1    1.9  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
       0.12   12.2   0.0       0.27   11.1   0.0    1.7  1  Rossmann-like    Rossmann-like domain
       0.19   11.6   1.4         21    5.0   0.1    3.0  3  Transketolase_C  Transketolase, C-terminal domain
       0.19   10.8   0.0       0.28   10.2   0.0    1.3  1  FAD_binding_2    FAD binding domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.4   4.5e-27   2.2e-24       1     114 [.       3     117 ..       3     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 4.5e-27
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                        TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddeanila 79 
                                   i+i+G+GrvGr+la++Ls+ g+ +v+++dkd e++e ++ e  +e ++ d+td+ +  e++i ++d+++aat++de+n+++
  gi|14602214|ref|NP_148621.1|   3 ILIVGAGRVGRELAKRLSQaGY-SVTIVDKDGEKLEIAQSEAdVEGLQIDVTDPRFYSEIDIPSYDVLVAATDKDEVNLFL 82 
                                   79*****************777.5**************98888************************************** PP

                                   HHHHHHHTSSSEEEEEESSGGGHHHHHHHTT.SEEE CS
                        TrkA_N  80 vllakelnpkkkiiaraqdpehaellkklga.dvvi 114
                                   v++a    +  ki++r++ +e++++l +lg+ d ++
  gi|14602214|ref|NP_148621.1|  83 VAMAMA-YGMEKIYVRVRMKETVRILTTLGVyDMIV 117
                                   ****85.77799******************966665 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 !   35.9   0.1   1.6e-11     8e-09       9      85 ..       2      89 ..       1     102 [. 0.77
   2 ?   -1.9   0.0       9.2   4.6e+03      72      72 ..     187     187 ..     146     216 .. 0.47

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.6e-11
                 NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele..........elvklaeeel..ekdlegadlviaatddrelneria 79
                                  ++l+vG+G+v+ + +++l +ag  vt+v+++  e+le           ++++++  +  e d+  +d+++aatd++e+n  ++
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAGYSVTIVDKDG-EKLEiaqseadvegLQIDVTDPRFysEIDIPSYDVLVAATDKDEVNLFLV 83
                                  79*****************************5.33334444455544334444433435678999**************9988 PP

                 NAD_binding_7 80 eaakar 85
                                  ++a a+
  gi|14602214|ref|NP_148621.1| 84 AMAMAY 89
                                  888665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9.2
                 NAD_binding_7  72 r 72 
                                   +
  gi|14602214|ref|NP_148621.1| 187 N 187
                                   2 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.5   1.2e+03      50      65 ..      66      81 ..      59      85 .. 0.76
   2 !   24.5   0.2   3.6e-08   1.8e-05       2      68 ..     150     219 ..     149     220 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.5
                                  T-EEEEEEEHHHHHHH CS
                        TrkA_C 50 GDvllvvgspsdlael 65
                                   Dvl+ ++++++++ +
  gi|14602214|ref|NP_148621.1| 66 YDVLVAATDKDEVNLF 81
                                  5888888888888876 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.6e-08
                                   EEEEEE--GGGTTSBHHH.HTHHHH..S-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHHHH CS
                        TrkA_C   2 vevtvpagsplvGktlke.lnlrar..gvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelrel 68 
                                   +  tv++ sp+ G++l++ l+ r+   +v v+a+  g+e+  p +  ++eeG +++ +++++ l+e+++l
  gi|14602214|ref|NP_148621.1| 150 AAATVTKQSPVRGQRLRDvLRSRDLegRVKVLAVFDGNEIREPEEVVTIEEGHTIIALVDREYLEEFAKL 219
                                   6789**************9999999******************************************987 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 !   25.0   0.1   3.6e-08   1.8e-05       1      76 [.       3      72 ..       3     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.6e-08
                                  EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSEEEE- CS
               Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdlvvnl 76
                                  +li+GaG+vG+ +a+ l++ + +   +t++d++ ekle +    ++ ++e  ++d+ +++   +++ + ++d++v +
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAG-Y--SVTIVDKDGEKLEIAQ---SEADVEGLQIDVTDPRF-YSEIdIPSYDVLVAA 72
                                  89*****************98.5..7**********75554...78899999999999887.555557777777755 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 !   24.0   0.0   6.1e-08     3e-05       2      42 ..       3      43 ..       2      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.1e-08
                                  EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHH CS
                       3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekaleki 42
                                  + ++GaG +G+++a+ + +ag++V++vd + e+le a++++
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSEA 43
                                  679*******************************9998776 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   6.7e-08   3.3e-05       1      64 [.       3      73 ..       3      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.7e-08
                                  EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT...CEEEEEECEEECCH....SCC CS
                          ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg...geeilrppealsae....eks 64
                                  i+i+GaG +G+ la +L++ag+ vt+++++  +le + +   ++++ +   ++ +++ +  +++     +  
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAGYSVTIVDKDGeKLE-IAQSEADVEGLQidvTDPRFYSEIDIPSYdvlvAAT 73
                                  89*****************************7776.677766666666334444444444444444444444 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.7e-06    0.0014      19      51 ..       1      32 [.       1      39 [. 0.93
   2 ?    3.4   0.0     0.081        40      85     138 ..      40      94 ..      33     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-06
                                  SEEEEE--SHHHHHHHHHHHHHTTTEEEEEESS CS
                                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF 19 skvllvGaGglGsellknLalsGvgkltlvDnD 51
                                  +++l+vGaG +G el+k L  +G  ++t+vD D
  gi|14602214|ref|NP_148621.1|  1 MRILIVGAGRVGRELAKRLSQAGY-SVTIVDKD 32
                                  59*********************8.59999998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.081
                                   -TTSEEEEEES-CCGCC.S-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEE CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ThiF  85 npdveveavteritdet.vleellesvDlVvdalDniearrlvnracvkkgipli 138
                                    ++++ve ++ ++td   ++e  + s+D+ v a+D+ e+ + +  ++  +g+  i
  gi|14602214|ref|NP_148621.1|  40 QSEADVEGLQIDVTDPRfYSEIDIPSYDVLVAATDKDEVNLFLVAMAMAYGMEKI 94 
                                   5778999999999997634555599***********9999999999888776555 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 !   22.5   0.1   2.6e-07   0.00013       1      48 [.       2      45 ..       2      76 .. 0.89
   2 ?   -0.7   0.0       4.4   2.2e+03      33      78 ..     171     217 ..     150     220 .] 0.58

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.6e-07
                                  EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC- CS
                 F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgv 48
                                  +i i+GaG++g+ la++l++ag   ++++++ +++ ek+e +++e+ v
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAG---YSVTIV-DKDGEKLEIAQSEADV 45
                                  57899*****************...****88.*******998888774 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.4
                                   ESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHHHH CS
                 F420_oxidored  33 srnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedveevl 78 
                                   sr+ e + +  + +  + +  + ee+++  e   ++  v  e++ee++
  gi|14602214|ref|NP_148621.1| 171 SRDLEGRVKVLAVFDGNEIR-EPEEVVTieEGHTIIALVDREYLEEFA 217
                                   55555555555555422222.444444433777777777777777766 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.3e-07   6.3e-05       2      65 ..       4      87 ..       3     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.3e-07
                                  EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.....................-EEEE--S-HHHHHHHHHH CS
                        XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade.....................tavvvlthdhklDaealea 63
                                  +i+Gag v+++la+ ++++g++vt+vd++ e  + ++ ++                        +++v++t + +    +++ 
  gi|14602214|ref|NP_148621.1|  4 LIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSEAD-VeglqidvtdprfyseidipsyDVLVAATDKDEVNLFLVAM 85
                                  89****************************75544444422.24677777777777788889777777777666666666655 PP

                                  HS CS
                        XdhC_C 64 al 65
                                  a+
  gi|14602214|ref|NP_148621.1| 86 AM 87
                                  55 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     2e-07   9.9e-05       3      63 ..       3      57 ..       1      61 [. 0.85

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-07
                                  EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHH CS
                     adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdree 63
                                  +l++Ga++ +Gr++ak+l ++G++v++vd+  ekle + +e     a++  +q+Dvtd + 
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGR-VGRELAKRLSQAGYSVTIVDKDGEKLEIAQSE-----ADVEGLQIDVTDPRF 57
                                  79999996.9*************************544444.....45999*****99865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   4.7e-07   0.00023       1      35 [.       2      36 ..       2      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.7e-07
                                  EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                     Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                  ++++vG+G +g ElA+ l++ g +Vt+v+   + l
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKL 36
                                  79**************************9877665 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 !   21.2   0.0   3.4e-07   0.00017       1      39 [.       1      39 [.       1      49 [. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.4e-07
                                  SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                  m+i ++G+G vG   a  l+++g  v++vD+d ek +  
  gi|14602214|ref|NP_148621.1|  1 MRILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIA 39
                                  89*******************************998754 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1     5e-07   0.00025       3      40 ..       2      39 ..       1      45 [. 0.89
   2 ?   -2.4   0.0       4.2   2.1e+03      48      64 ..     102     118 ..      98     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5e-07
                                  EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS CS
                 FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp 40
                                   +lIVGaG +G  la+ Ls+aG +v++v+k  ++ +  
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIA 39
                                  589***************************99987655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                                   HHHHHHHHTT-HHHHHH CS
                 FAD_binding_3  48 rtmellrqlGledrila 64 
                                   +t+++l +lG+ d i +
  gi|14602214|ref|NP_148621.1| 102 ETVRILTTLGVYDMIVE 118
                                   78899999999887765 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 !   20.5   0.0   4.8e-07   0.00024      38      79 ..       2      42 ..       1      63 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.8e-07
                                  EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelg 79
                                  ++ i+G+Gr+G+++akrl++ g  v+++d+  +k e  ++ +
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLE-IAQSE 42
                                  689**************************9988666.33333 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.7e-07   0.00028      14      87 ..       2      77 ..       1      96 [. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.7e-07
                                  EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCGHHHH.HHT-SEEEE-SSSSS CS
                  Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealkleelkel.laeadvvisatasee 87
                                  ++l++GaG++++++ak L+++g+  v+++  + e+ +   +e   +g +i +++   ++e+ + ++dv+++at   e
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAGYS-VTIVDKDGEKLEIAQSEAdvEGLQIDVTDPRFYSEIdIPSYDVLVAATDKDE 77
                                  79*********************9.*********9876665551133344443333233323888899988887665 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 !   20.0   0.0     1e-06   0.00051       3      53 ..       8      57 ..       7     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1e-06
                                  TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCH CS
                NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdved 53
                                   G+vGr+l+k+l ++ g++vt++  + ekl+  ++e+ +e +++dvtd+  
  gi|14602214|ref|NP_148621.1|  8 AGRVGRELAKRLSQA-GYSVTIVDKDGEKLEIAQSEADVEGLQIDVTDPRF 57
                                  7**************.5*************9767889***********965 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.2e-06    0.0011       1      54 [.       3      56 ..       3      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                                  EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.EEEE--TT-HH CS
                     Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.elveldltdrs 54
                                  il++Ga G +G+ l+k+l ++gy v+ +d++ ++ + a+ e   e  ++d+td+ 
  gi|14602214|ref|NP_148621.1|  3 ILIVGA-GRVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSEADvEGLQIDVTDPR 56
                                  789998.************************887776665544689999999876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.9e-06   0.00095     144     175 ..       2      33 ..       1      93 [. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                                   EEEEES-SHHHHHHHHHHHHHT-EEEEEESSS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveard 175
                                   ri++vG+G +G ElA  l+++g+ vt+v+   
  gi|14602214|ref|NP_148621.1|   2 RILIVGAGRVGRELAKRLSQAGYSVTIVDKDG 33 
                                   56677777777777777777777777666544 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 !   18.0   0.0   4.9e-06    0.0024       2      42 ..       3      43 ..       2     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.9e-06
                                  EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT CS
                 NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg 42
                                  i ++G G  G+++a++l +agy+v++++ + ek+e + +e 
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSEA 43
                                  6689**************************99998776654 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.5e-05    0.0074       1      91 [.       1      90 [.       1      95 [. 0.60

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-05
                                  EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH...-SEEEE-S-HHHH CS
                        DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek...advliDFTtpeav 80
                                  +++++vGa Gr+G+e++k +++ +++ ++  vd+++++le  +  + ++++ l++ vtd       +    dvl+  T  + v
  gi|14602214|ref|NP_148621.1|  1 MRILIVGA-GRVGRELAKRLSQ-AGYSVTI-VDKDGEKLEIAQ--SEADVEGLQIDVTDPRFYSEIDipsYDVLVAATDKDEV 78
                                  89*****9.***********99.6666554.455554444332..23455555555554333332223458899998866554 PP

                                  .HHHHHHHHHTT CS
                        DapB_N 81 .lenlklalekg 91
                                   l ++++a+++g
  gi|14602214|ref|NP_148621.1| 79 nLFLVAMAMAYG 90
                                  144555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.5e-05    0.0074       6      70 ..       6      71 ..       4     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-05
                                  -TTSHHHHHHHCTS..TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTT....TEEEEEE CS
               Methyltransf_25  6 cGtGrltlalakrl..gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedg....sfDlvvs 70
                                   G Gr+ ++lakrl    ++vt vD + e le+a+++a+     ve +q d++d  f ++    s+D+ v+
  gi|14602214|ref|NP_148621.1|  6 VGAGRVGRELAKRLsqAGYSVTIVDKDGEKLEIAQSEAD-----VEGLQIDVTDPRFYSEidipSYDVLVA 71
                                  599**********97526********************5.....555555555544422212226777666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.3e-05     0.012       1      28 [.       5      32 ..       5      36 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-05
                                  EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                 NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                  IvGaG  G  +A +L++ag++v++++k 
  gi|14602214|ref|NP_148621.1|  5 IVGAGRVGRELAKRLSQAGYSVTIVDKD 32
                                  9*************************95 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   0.3   1.8e-05     0.009      30      98 ..       2      72 ..       1     144 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.8e-05
                                  EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHH.HHHH-SEEEE- CS
                   AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksqeellae.avkeadvvigt 98
                                  ++l++G+G +G + ++  ++ g +Vt++D++ ++le  +s    + +++   + + ++e  + + dv++ +
  gi|14602214|ref|NP_148621.1|  2 RILIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSeADVEGLQIDVTDPRFYSEiDIPSYDVLVAA 72
                                  799********************************999988444445554444443333145555555554 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 !   14.5   0.2   2.6e-05     0.013       3     100 ..       5     107 ..       3     117 .. 0.77
   2 ?   -3.0   0.0       5.6   2.8e+03       8      31 ..     143     168 ..     142     205 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                     3Beta_HSD   3 tGgaGFlGralvkeLvrleelkevrvlD.....lrespelleels..kvnvkk...viegDvtdkdkleealegvdvvihl 73 
                                   + gaG +Gr+l k+L +++    v ++D     l++ +    +++  +++v++   + e D+ + d l +a+++ +v+++l
  gi|14602214|ref|NP_148621.1|   5 IVGAGRVGRELAKRLSQAGY--SVTIVDkdgekLEIAQ-SEADVEglQIDVTDprfYSEIDIPSYDVLVAATDKDEVNLFL 82 
                                   45889**************5..8888885566522222.22334400444555999************************* PP

                     3Beta_HSD  74 aslvdvagkltedeimkvnvkGTrnvl 100
                                    ++ +  g   e+ + +v +k T  +l
  gi|14602214|ref|NP_148621.1|  83 VAMAMAYG--MEKIYVRVRMKETVRIL 107
                                   99999999..56678899999888877 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                     3Beta_HSD   8 FlGralvkeLvrlee..lkevrvlDl 31 
                                   F+Gr++v +   +++  ++  r  D+
  gi|14602214|ref|NP_148621.1| 143 FVGRYVVAAATVTKQspVRGQRLRDV 168
                                   56666665433333212222233333 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 ?   14.9   0.0   7.4e-05     0.037       1      54 [.       1      66 [.       1      94 [. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.4e-05
                                  EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE....EESS...........H CS
                  GFO_IDH_MocA  1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve....aysd...........l 54
                                  +r++i+GaG++g++ ++ l ++  ++  v ++d+d e+ e +  + +ve     ++d           +
  gi|14602214|ref|NP_148621.1|  1 MRILIVGAGRVGRELAKRLSQA--GY-SVTIVDKDGEKLEIAQSEADVEglqiDVTDprfyseidipsY 66
                                  69*************9777777..55.555************888888865553333444333444441 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.051      40     102 ..       6      70 ..       4      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                   -TTSHHHHHHHHHTTC.E..EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
                           MTS  40 cGaGvlgaalakespeae..vtlvdvdarAlesakenleanklevevvasdvleeveekkfdliv 102
                                    GaG +g +lak+ ++a   vt+vd+d + le+a+  +  ++l+++v+    ++e++  ++d++v
  gi|14602214|ref|NP_148621.1|   6 VGAGRVGRELAKRLSQAGysVTIVDKDGEKLEIAQSEADVEGLQIDVTDPRFYSEIDIPSYDVLV 70 
                                   59***********9998666*************************************99999987 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 ?   12.7   0.0    0.0001      0.05       1      41 [.       1      42 [.       1      63 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                  EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..T--TTSHH CS
                 RmlD_sub_bind  1 mkilvtGanGqlGseLakqlaeeglevlaltre..eldltdae 41
                                  m+il++Ga G +G+eLak+l+++g++v+ ++++  +l+++++e
  gi|14602214|ref|NP_148621.1|  1 MRILIVGA-GRVGRELAKRLSQAGYSVTIVDKDgeKLEIAQSE 42
                                  89****97.9******************998876644444443 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.052       6      54 ..      11      56 ..       8     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHH CS
                  adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdee 54
                                  +Gr++Ak+l ++G++v ++d + e+   +e +++e + e l++DVtd+ 
  gi|14602214|ref|NP_148621.1| 11 VGRELAKRLSQAGYSVTIVDKDGEK---LEIAQSEADVEGLQIDVTDPR 56
                                  699*******************999...555555555666******986 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00016     0.079       4      48 ..      10      54 ..       8      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                    OKR_DC_1_N  4 aairelaealekegfevvgvtstdDllsvieqnsriaavvlsvdd 48
                                  ++ rela++l++ g++v+ v++ ++ l+++++++++ ++ ++v d
  gi|14602214|ref|NP_148621.1| 10 RVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSEADVEGLQIDVTD 54
                                  6679*********************************99998874 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.059        30      20      49 ..       3      31 ..       1      35 [. 0.90
   2 ?    8.0   0.1     0.003       1.5      85     136 ..      75     126 ..      61     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.059
                                  EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                          Thi4 20 vvivGaGssGLtaayylakkpdlkvailer 49
                                  ++ivGaG  G   a+ l+++ +  v+i+++
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQA-GYSVTIVDK 31
                                  89*****************9.999999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                                   EEESSEEEESEH.HHHHHHHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEE CS
                          Thi4  85 edegdyvvvkda.alftstllskvlqlanvkllnavaveDlivregegvaGvv 136
                                   +de + ++v+ a a  + ++ ++v  +  v++l+++ v D+iv + + +aG+ 
  gi|14602214|ref|NP_148621.1|  75 KDEVNLFLVAMAmAYGMEKIYVRVRMKETVRILTTLGVYDMIVEP-DIIAGLL 126
                                   456677888887245689******999******************.8999975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018     0.092       2      29 ..       3      32 ..       2      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                  EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                           DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                  ++i+G+G +G   A  L+++g  Vt+++k+
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAGysVTIVDKD 32
                                  99***************************8 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00024      0.12       4      43 ..       4      43 ..       2      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                        LpxI_N  4 liAGsGrlPllvaeaakaagrevvvvalegeadeelekiv 43
                                  li G+Gr   ++a+++ +ag++v +v   ge  e  ++++
  gi|14602214|ref|NP_148621.1|  4 LIVGAGRVGRELAKRLSQAGYSVTIVDKDGEKLEIAQSEA 43
                                  9*************************99997666555554 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 ?   11.5   0.1   0.00057      0.28       1      30 [.       1      31 [.       1      81 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00057
                                  CEEEEESTSHHHHHHHHHHHHHT.TCEEEEE CS
                       Gp_dh_N  1 vkvainGfGRIGrlvlralleek.elevvai 30
                                  +++ i G GR+Gr +++ l +   ++++v  
  gi|14602214|ref|NP_148621.1|  1 MRILIVGAGRVGRELAKRLSQAGySVTIVDK 31
                                  79**************999966557777653 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   0.0   0.00053      0.27      13      39 ..       3      29 ..       1      55 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                 Rossmann-like 13 vGiisaGrvGtalgaaleraghvvvgi 39
                                  + i++aGrvG  l++ l +ag+ v+ +
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAGYSVTIV 29
                                  569*******************99866 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0       0.1        51      26      42 ..      14      30 ..       2      32 .. 0.78
   2 ?    5.0   0.1     0.042        21      30      62 ..      42      74 ..      34      78 .. 0.82
   3 ?   -0.4   0.0       1.9   9.7e+02      49      74 ..     184     205 ..     178     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                                  HHHHHHHTTTTCEEEEE CS
               Transketolase_C 26 eAaeeLekegisaeVvd 42
                                  e a++L++ g+s+++vd
  gi|14602214|ref|NP_148621.1| 14 ELAKRLSQAGYSVTIVD 30
                                  6799************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.042
                                  HHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHS CS
               Transketolase_C 30 eLekegisaeVvdlrtvkplDketilesvkktg 62
                                  e+  eg++++V d+r+ + +D    + +v+ t+
  gi|14602214|ref|NP_148621.1| 42 EADVEGLQIDVTDPRFYSEIDIPSYDVLVAATD 74
                                  45567****************999998888776 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.9
                                   HHHHHHHHHHHHHSEEEEEEEEESTT CS
               Transketolase_C  49 lDketilesvkktgrlvvveeavkrg 74 
                                   +D + i+    + +++v++ee+ ++ 
  gi|14602214|ref|NP_148621.1| 184 FDGNEIR----EPEEVVTIEEGHTII 205
                                   5555555....8899******98876 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00057      0.28       2      43 ..       3      41 ..       2      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                                  EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                 FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                  ++++G+G  G   A ++++aG +v++v+k +e    + ++q 
  gi|14602214|ref|NP_148621.1|  3 ILIVGAGRVGRELAKRLSQAGYSVTIVDKDGE---KLEIAQS 41
                                  79***************************999...5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1595.24
//
Query:       gi|14602076|ref|NP_148623.1|  [L=432]
Description: enolase [Aeropyrum pernix K1]
Scores for complete 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-106  354.9   0.0   4.1e-106  354.5   0.0    1.1  1  Enolase_C     Enolase, C-terminal TIM barrel domain
    8.1e-45  152.2   0.0    1.4e-44  151.5   0.0    1.4  1  Enolase_N     Enolase, N-terminal domain
    1.2e-08   34.9   0.1    1.8e-08   34.3   0.1    1.2  1  MR_MLE_C      Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.023   13.9   0.0       0.04   13.1   0.0    1.3  1  MAAL_C        Methylaspartate ammonia-lyase C-terminus
      0.055   13.0   0.2        0.2   11.2   0.0    1.8  2  Peripla_BP_4  Periplasmic binding protein domain


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 !  354.5   0.0  1.1e-109  4.1e-106       4     291 ..     145     424 ..     142     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 354.5 bits;  conditional E-value: 1.1e-109
                                   E-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHHHH CS
                     Enolase_C   4 lPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkeald 84 
                                   lP+P+lnvinGG hagn+l++qefmi+P g +sf+ea+r  +e+y +lks+lk++yg sa nvGdeGGfaP ++s++eal+
  gi|14602076|ref|NP_148623.1| 145 LPIPLLNVINGGVHAGNELDFQEFMIIPYGFESFTEAMRAAVETYGELKSLLKDRYGASAVNVGDEGGFAPPMRSAEEALK 225
                                   9******************************************************************************** PP

                                   HHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-H CS
                     Enolase_C  85 liveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldeddw 163
                                   ++v+a+ekaGy++  ++ +++d+a+s++y  ++++y +++k+        l+ e+l  ly+ lv++yPiv +edp+ edd+
  gi|14602076|ref|NP_148623.1| 226 TLVDAVEKAGYQPgsEIALGIDAAASQLY--SNGRYSVEGKS--------LSREELLSLYQRLVEQYPIVYLEDPFSEDDY 296
                                   ************9899*************..778***99998........9****************************** PP

                                   HHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--H CS
                     Enolase_C 164 eawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGetedtt 244
                                   e++k  ++ l  +  ivGddl+vtnp+r+kea   ka   ll+kvnq+G+lte+lea++ a++ g   +vshrsG+tedt+
  gi|14602076|ref|NP_148623.1| 297 EGFKAAVDALSTETIIVGDDLLVTNPQRVKEASALKAVTGLLVKVNQVGTLTEALEAIQAARDRGIVHIVSHRSGDTEDTF 377
                                   ********************************************************************************* PP

                                   HHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGG CS
                     Enolase_C 245 iadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkk 291
                                   iadlav+++a  iktGapar er +kyn+ll ie+ lg +a+yaG +
  gi|14602076|ref|NP_148623.1| 378 IADLAVATEALMIKTGAPARGERTSKYNRLLEIENILGYSAEYAGPE 424
                                   *********************************************76 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.0   3.8e-48   1.4e-44       1     131 []       8     137 ..       8     137 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 3.8e-48
                                   EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBT CS
                     Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldv 81 
                                   I++v + ++ldSrGnpTv++ v+++ g+lg  ++psGaS ge+ea+elrDg   ++ gkgv++av+  n+++ap+l g+d+
  gi|14602076|ref|NP_148623.1|   8 IERVWGLQVLDSRGNPTVKAYVKLAGGSLGWGIAPSGASRGEREAVELRDG-GGKWRGKGVSRAVSLLNTVVAPRLEGVDA 87 
                                   899***********************************************9.899************************** PP

                                   T-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                     Enolase_N  82 tdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                   ++q++iD+llielDgt+nks+lG+N+++a+S+Av +aaA++++l+l++yl
  gi|14602076|ref|NP_148623.1|  88 RRQAQIDRLLIELDGTPNKSRLGGNTTTALSIAVSRAAAAQARLELFQYL 137
                                   *************************************************7 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 !   34.3   0.1   4.9e-12   1.8e-08      33     154 ..     227     366 ..     182     403 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 4.9e-12
                                   HHHHHHHH.HTTTSTSEEEEE-TTTS..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHHHH.. CS
                      MR_MLE_C  33 rvravrea.vgpgddvdlmvDanqaw..............dlatAirvarelee.ldllwlEEPvppeddleglaelra.. 95 
                                    v av +a  +pg ++ l +Da ++               ++++ + + ++l e + + +lE+P++  dd+eg ++  +  
  gi|14602076|ref|NP_148623.1| 227 LVDAVEKAgYQPGSEIALGIDAAASQlysngrysvegkslSREELLSLYQRLVEqYPIVYLEDPFSE-DDYEGFKAAVDal 306
                                   4555555535679999999999988455777778888888************555***********9.7899999888766 PP

                                   HHSSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEE CS
                      MR_MLE_C  96 rasipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvap 154
                                    +++ i+++  l + +++++e+ + +av+ + ++v++vg +tea++ ++ a+ +g+  ++
  gi|14602076|ref|NP_148623.1| 307 STETIIVGDDLLVTnPQRVKEASALKAVTGLLVKVNQVGTLTEALEAIQAARDRGIVHIV 366
                                   325556666665555****************************************86333 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 ?   13.1   0.0   1.1e-05      0.04     129     219 ..     299     388 ..     270     395 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        MAAL_C 129 lreklkekgikvelvaDeWcnt.ledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarv 208
                                   +++++++ +++  +v D+   t  + ++e  + +a+  + +k+  +G++++++ea++ ++++g+   +   + +t+     
  gi|14602076|ref|NP_148623.1| 299 FKAAVDALSTETIIVGDDLLVTnPQRVKEASALKAVTGLLVKVNQVGTLTEALEAIQAARDRGIVHIVSHRSGDTED--TF 377
                                   57788888999999999976551688**************************************9998777766664..56 PP

                        MAAL_C 209 svhvalatrpa 219
                                   ++++a+at++ 
  gi|14602076|ref|NP_148623.1| 378 IADLAVATEAL 388
                                   77788887764 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 ?   -1.3   0.0      0.36   1.3e+03     197     220 ..     226     250 ..     174     255 .. 0.57
   2 ?   11.2   0.0   5.5e-05       0.2       8      84 ..     287     365 ..     283     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.36
                                   CHHHHHHHTTT.TSTEEEEEES-HH CS
                  Peripla_BP_4 197 galealeaagl.agkvvvtgqDatp 220
                                     ++a+e+ag+  g  +  g+Da  
  gi|14602076|ref|NP_148623.1| 226 TLVDAVEKAGYqPGSEIALGIDAAA 250
                                   4666777777733334466666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.5e-05
                                   SSTCHHHHHHHHHHHHHHHTTCEEEEEECSTT-HHHHHHHHHHHHHTT-SEEEE--SSH...HHHHHHHHHHHHTT-EEE CS
                  Peripla_BP_4   8 ksnpffsaaregleeaakelgaevtvvgdaendaaeQvaqiedaiakgvdgiivapvds...talapalkkakaaGIpVv 84 
                                    ++pf + + eg+++a+++l  e+++v  ++  ++  + + e+   k v g++v ++++   t++ +a+++a+++GI+ +
  gi|14602076|ref|NP_148623.1| 287 LEDPFSEDDYEGFKAAVDALSTETIIV-GDDLLVTNPQRVKEASALKAVTGLLVKVNQVgtlTEALEAIQAARDRGIVHI 365
                                   57889999******************8.55555566666666666699***********444444456677888888644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 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:                        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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3304.65
//
Query:       gi|118431878|ref|YP_874947.1|  [L=112]
Description: hypothetical protein APE_2458a [Aeropyrum pernix K1]
Scores for complete sequence (score 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      0.021   14.5   0.0    1.0  1  PBP_like_2  PBP superfamily domain
       0.02   14.0   0.0      0.026   13.7   0.0    1.1  1  Ldh_2       Malate/L-lactate dehydrogenase
       0.04   13.3   0.0      0.048   13.1   0.0    1.1  1  DUF4504     Domain of unknown function (DUF4504)
       0.16   11.8   0.0       0.85    9.5   0.0    1.9  2  TusA        Sulfurtransferase TusA


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 ?   14.5   0.0   4.7e-06     0.021     126     216 ..      16     104 ..       1     110 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.7e-06
                     PBP_like_2 126 vlglpadgpIkvvhrsdgsgttflfstalaeqgpwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtn 204
                                    + g++    I  v+++d+      + ++la +g+ + ++i+as  ++v +a+ s +g+i +v+ ++ +  k++ +++ + 
  gi|118431878|ref|YP_874947.1|  16 GRGGL-SRVIVAVAPKDDEEALPRILRWLAAKGLRPDETIEASSKDEVIQALdSLKGMIVVVTTSSMA--KNLEEWAKSR 92 
                                    56666.78899999999999999999*************************9677**********998..78******** PP

                     PBP_like_2 205 gagkfvlptaat 216
                                    g+g++v+    +
  gi|118431878|ref|YP_874947.1|  93 GQGVVVIDVDSN 104
                                    ***999887444 PP

>> Ldh_2  Malate/L-lactate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-06     0.026      47     110 ..      36     100 ..      34     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-06
                                    HHHHHHHHHTTSSBSS---EEEEEETTEEEEEETTE-HHHHHHHHHHHHHHH.HHHHSEEEEEEE CS
                          Ldh_2  47 lpryverlkkgkinpkaepevvketpavavvDgdnglGqvvakkamelaiek.akehGigivavr 110
                                    lpr++++l+++ ++p++++e  ++ +++  +D  +g+  vv++ +m++ +e  ak+ G g+v++ 
  gi|118431878|ref|YP_874947.1|  36 LPRILRWLAAKGLRPDETIEASSKDEVIQALDSLKGMIVVVTTSSMAKNLEEwAKSRGQGVVVID 100
                                    899****************************************99988776439999****9985 PP

>> DUF4504  Domain of unknown function (DUF4504)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.048      71     110 ..      68     108 ..      53     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        DUF4504  71 viedmiylinveklkehlekllssele.lafvDveasdekp 110
                                    ++++mi+++ +++++++le+ ++s+ + ++++Dv+++ + +
  gi|118431878|ref|YP_874947.1|  68 SLKGMIVVVTTSSMAKNLEEWAKSRGQgVVVIDVDSNAPGM 108
                                    479*******************9987669******998866 PP

>> TusA  Sulfurtransferase TusA
   #    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      35      53 ..      31      49 ..      30      65 .. 0.80
   2 ?    9.5   0.0   0.00019      0.85      30      57 ..      73      99 ..      43     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                                   SSCHHHHHHHHHHHHHTEE CS
                           TusA 35 ddpaatediprfakklghe 53
                                   dd++a   i r++  +g++
  gi|118431878|ref|YP_874947.1| 31 DDEEALPRILRWLAAKGLR 49
                                   7889999999999998874 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00019
                                   EEEEESSCHHHHHHHHHHHHHTEEEEEE CS
                           TusA 30 levladdpaatediprfakklghelvev 57
                                   + v+++  +  ++++++ak++g  +v +
  gi|118431878|ref|YP_874947.1| 73 I-VVVTTSSMAKNLEEWAKSRGQGVVVI 99
                                   3.6666666779**********998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 889.85
//
Query:       gi|118431879|ref|NP_148624.2|  [L=92]
Description: FixX protein [Aeropyrum pernix K1]
Scores for complete 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-05   23.7   0.1    5.3e-05   23.3   0.1    1.3  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu


Domain annotation for each model (and alignments):
>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.9e-09   5.3e-05      46     103 ..      38      89 ..      14      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-09
                                    HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---STT-C--- CS
                         ETF_QO  46 eqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeGggGPky 103
                                     +  CPa+ y  + de      l  + + Cv C  C + +p+++i+w     g G +y
  gi|118431879|ref|NP_148624.2|  38 LALLCPAACYTEMGDE------LLFSYEGCVECALCRVITPKEKISWRYLRSGRGIQY 89 
                                    5568****99877555......89999**********************999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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 0.22s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 693.71
//
Query:       gi|118431880|ref|NP_148625.2|  [L=372]
Description: tryptophanyl-tRNA synthetase [Aeropyrum pernix K1]
Scores for 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-41  140.8   0.0    7.5e-41  140.3   0.0    1.2  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.037   14.6   0.0      0.095   13.3   0.0    1.7  1  PKS_DE        Polyketide synthase dimerisation element domain


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 !  140.3   0.0   8.4e-45   7.5e-41       4     292 ..      69     349 ..      65     350 .. 0.93

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 8.4e-45
                                    S--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                   tRNA-synt_1b   4 rplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                    ++++v++G++P+gk+H G+ + + +l++lqk+g +vf+ iaD++A+ ++     e+ +r ++e++ +    ++a gldp+
  gi|118431880|ref|NP_148625.2|  69 ERVAVLTGFMPSGKFHFGHKLTVDQLIYLQKNGFKVFVAIADAEAFAVRRI-GREEAVRIAVEEYIAN---MIALGLDPK 144
                                    7899***********************************************.77**************...********* PP

                                    TEEEEETHHHHTTH.HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHH CS
                   tRNA-synt_1b  84 kaevvlqsewlehl.elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkq 162
                                    ++e+++q++       l++l++  ++  +++ ++   +  k +++    +++++++ +L+++  +  +  +vp+G DQ+ 
  gi|118431880|ref|NP_148625.2| 145 DTEFYFQTNRGTPYfRLIQLFSGKVTAAEMEAIYGELTPAKMMAS--LTQAADILHVQLDEYGGY--RHVVVPVGADQDP 220
                                    ********9887766999999999999999999999998888888..358999999999999987..889********** PP

                                    HHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHH CS
                   tRNA-synt_1b 163 nielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklk 240
                                    +++l+rdla+r+     ++ p +++++l +gldG  KmS+S + s+IfL+d +e ++ k  +a+t  ++  e ++ l + 
  gi|118431880|ref|NP_148625.2| 221 HLRLTRDLADRMAGVVELERPASTYHKLQPGLDGR-KMSSSRPDSTIFLTDPPEVARNKLFRALTGGRAtaEEQRRLGGV 299
                                    *************99999*****************.*******************************9999999****** PP

                                    HTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 241 telsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                    +e++  ++    +++  ++  e+++++ +++ +++ +g++k+ + e+l+++l
  gi|118431880|ref|NP_148625.2| 300 PEVCS-VYHMDLYHLMPDD-GEVKHIYTSCRLGKILCGECKQIAWEKLERFL 349
                                    *****.7777777666666.8***********************99999988 PP

>> PKS_DE  Polyketide synthase dimerisation element domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.1e-05     0.095       5      35 ..       9      36 ..       8      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                         PKS_DE  5 WaaVereDlaaLaatLgldadasLsavLPaL 35
                                   W aVe +D + L +t g++   ++s+vLP L
  gi|118431880|ref|NP_148625.2|  9 WGAVEIKDYDRLLRTFGIR---PFSEVLPLL 36
                                   ******************7...5******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2718.66
//
Query:       gi|118431881|ref|NP_148627.2|  [L=145]
Description: hypothetical protein APE_2462.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-19   69.4  18.9    3.4e-19   69.2  18.9    1.0  1  VKOR      Vitamin K epoxide reductase family


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 !   69.2  18.9   1.9e-23   3.4e-19       3     123 ..       8     135 ..       6     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 1.9e-23
                                    HHHHHHHHHHHHHHHHHHHH...HT---SS-SSSS.......HHHHHCSTTSEETT.EEHHHHHHHHHHHHHHHHHS-.. CS
                           VKOR   3 llvlalvGllvsiyltleklglktsssaalCdiss.....vsCdkvlnSpyasilg.vplsllGllayalvlllalapl. 75 
                                    ll++ lvG ++si  ++e++     s + +C+i++     v+C++v + p a ++g v+ls+l+ ++++l+ l+ala + 
  gi|118431881|ref|NP_148627.2|   8 LLAVTLVGYAASIAGYFEYV-----SGSGVCEIGDvgfavVNCSSVYDIPEAVVFGvVHLSVLAPVYFTLLSLVALAYWi 82 
                                    7899****************.....34457*988889999****************99******************999* PP

                                    .....HHHHHHHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHHHH CS
                           VKOR  76 .....lwlllllgslagvvfslyLiylslfvigalCpyClvsavlsllllvla 123
                                         + ++  ++sl+gvv ++yL+yl+lfv ga+C++C+v+++ +ll+++la
  gi|118431881|ref|NP_148627.2|  83 rrsriFLIASSFLSLVGVVTVPYLVYLELFVAGAVCLWCTVMHISILLAFALA 135
                                    **76655666777779**********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1163.67
//
Query:       gi|118431882|ref|NP_148628.2|  [L=105]
Description: hypothetical protein APE_2463.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       201  (0.0112109); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 786.51
//
Query:       gi|118431883|ref|NP_148629.2|  [L=387]
Description: hypothetical protein APE_2464.1 [Aeropyrum pernix K1]
Scores for 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-47  160.0   0.0    7.9e-47  159.4   0.0    1.3  1  PhoH      PhoH-like protein
      6e-12   45.2   4.3    5.9e-08   32.4   0.8    2.5  2  KH_2      KH domain
    8.8e-07   28.7   2.8    0.00021   21.0   0.5    2.7  2  KH_1      KH domain
    5.8e-06   26.3   0.4     0.0002   21.4   0.1    2.4  2  KH_5      NusA-like KH domain
    0.00041   20.1   0.0     0.0011   18.8   0.0    1.7  1  AAA_30    AAA domain
     0.0072   16.7   0.0      0.023   15.0   0.0    1.8  1  AAA_19    AAA domain
     0.0073   16.6   0.3      0.044   14.0   0.3    2.2  1  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.026   14.1   0.0      0.058   13.0   0.0    1.7  1  AAA_25    AAA domain
      0.055   13.4   0.3         15    5.5   0.0    2.6  2  KH_4      KH domain


Domain annotation for each model (and alignments):
>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   0.0   3.9e-50   7.9e-47       2     202 ..      14     216 ..      13     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 3.9e-50
                                    ----SHHHHHHHHHHH.H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T..T----SS---------T CS
                           PhoH   2 ikpktkeQkeylealk.kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea..geelGflpgdleekvdp 78 
                                    ++pk+++Q+e+ eal  + d+v ++Gp+GtGK++++++++v+++ +++++r++l+rp++++  g+el+++ +d + + + 
  gi|118431883|ref|NP_148629.2|  14 LEPKSEGQRELKEALLsDVDLVGVFGPTGTGKSLFSIVYGVSMTAEGRFRRVVLARPVIDVvtGRELTVM-TDAQSYRRL 92 
                                    689***********99899****************************************9889*****76.679****** PP

                                    TTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE----- CS
                           PhoH  79 ylrplydaLkdllgaekvekllekgkievaplaymRGrTlndafvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqi 158
                                      ++l+d L+ +lg+e+v+++l+++ + +++ +++RGrT++++++i+D++Q++ +e + +++tRlG +sk++v Gd+ ++
  gi|118431883|ref|NP_148629.2|  93 AAEYLMDILSGFLGEERVREILSSDSLVLVDPHFLRGRTFDNSVIIVDDSQSMPPEAIVEIITRLGTGSKLIVIGDPVFQ 172
                                    ******************************************************************************** PP

                                    ---------THHHHHHTTT-TTEEEEE--GGG----HHHHHHHH CS
                           PhoH 159 dlpkgkksGlaealevlknvegieivelkkkdvvRhplvkkivk 202
                                     + +   +G + a+e+l+n+ ++e+v+l  kd+vR ++ + +  
  gi|118431883|ref|NP_148629.2| 173 RTSEPGLDGASMAREILSNEPTAEVVDLGLKDIVRPGAKRGVKM 216
                                    ***999*****************************999887665 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.8     3e-11   5.9e-08      15      65 ..     257     308 ..     246     331 .. 0.81
   2 !   13.6   0.1   2.2e-05     0.044      25      74 ..     335     378 ..     324     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3e-11
                                    EEEEEEECCS.CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
                           KH_2  15 vskveIerta.nrviiviresqpgivIGkgGsnikkigkelrkdieklegkk 65 
                                    ++k  Ie  +  +v +v++e++ g+ IG+gG++i+ki+ e + +i+++e++ 
  gi|118431883|ref|NP_148629.2| 257 KRKWGIESDHvPDVLVVVKEGHLGRFIGRGGERIEKIEGETGLRIRAIEHTL 308
                                    567778886669***********************************99975 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.2e-05
                                    CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEET CS
                           KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVk 74 
                                     +++i + ++++g  +G++G+ i+ + + +rk +    g  V+  +++V+
  gi|118431883|ref|NP_148629.2| 335 PQLKIKVSKEHMGPMLGQKGAHIRFLDEIVRKLL----GVGVF--VEEVE 378
                                    67899*****************************....55555..55665 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.5   1.1e-07   0.00021       5      36 ..     273     304 ..     270     314 .. 0.87
   2 !    6.9   0.1    0.0028       5.6       2      25 ..     337     360 ..     336     381 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                    EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEE CS
                           KH_1   5 lvPsslvgriIGkgGsnIkeIreetgakIkvp 36 
                                     v+  + gr IG+gG++I +I+ etg +I+ +
  gi|118431883|ref|NP_148629.2| 273 VVKEGHLGRFIGRGGERIEKIEGETGLRIRAI 304
                                    6788899****************9*****976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                    EEEEEGGGHHHHHHTGGGHHHHHH CS
                           KH_1   2 lrilvPsslvgriIGkgGsnIkeI 25 
                                    l+i+v ++++g ++G +G++I+ +
  gi|118431883|ref|NP_148629.2| 337 LKIKVSKEHMGPMLGQKGAHIRFL 360
                                    5799*****************987 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1     1e-07    0.0002       5      62 ..     270     320 ..     268     324 .. 0.91
   2 ?    2.7   0.0     0.069   1.4e+02       2      32 ..     334     359 ..     333     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1e-07
                           KH_5   5 tkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPa 62 
                                    + v+Vk+++     +G ++g++G+ri++++ e  g +i+ +e + Dl+e + +a++P+
  gi|118431883|ref|NP_148629.2| 270 VLVVVKEGH-----LGRFIGRGGERIEKIEGET-GLRIRAIEHTLDLKEIV-RAIHPV 320
                                    6899*****.....******************9.**************965.677775 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.069
                           KH_5   2 GertkvaVkshnpnvdpvGaivgkkGsrika 32 
                                    G + k+ V +++     +G ++g+kG+ i+ 
  gi|118431883|ref|NP_148629.2| 334 GPQLKIKVSKEH-----MGPMLGQKGAHIRF 359
                                    667899999999.....9*********9984 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.4e-07    0.0011       3     125 ..      18     169 ..      16     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.4e-07
                         AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag..grviglAptgkaAkvLaeelgieastiakllkrl 80 
                                    +++Q+++ eall++ d ++ + Gp GtGK+    ++   ++a+g  +rv+++ p   +    +  + ++a++  +l    
  gi|118431883|ref|NP_148629.2|  18 SEGQRELKEALLSDVD-LVGVFGPTGTGKSLFSIVYGVSMTAEGrfRRVVLARPVIDVVTGRELTVMTDAQSYRRL---- 92 
                                    689*********9998.999**********9999998888888666666666665555444333333344444444.... PP

                         AAA_30  81 k...................................grarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDe 125
                                    +                                   g  r  +++++ivD +  +  + + ++++++ + g k+i++GD+
  gi|118431883|ref|NP_148629.2|  93 AaeylmdilsgflgeervreilssdslvlvdphflrG--RTFDNSVIIVDDSQSMPPEAIVEIITRLGT-GSKLIVIGDP 169
                                    33344778888889999999999999******99642..566779**********************99.*********8 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05     0.023      11     138 ..      33     169 ..      24     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                         AAA_19  11 kvllvtaGpGtGKTrv.lkhivallvelggvkp..eeillvaftgrAakelrerlaalgaeatTiHrlal.......... 77 
                                    +++ v ++ GtGK+   ++  v++  e + + +  ++ ++  +tgr    ++++          + rla           
  gi|118431883|ref|NP_148629.2|  33 DLVGVFGPTGTGKSLFsIVYGVSMTAEGRFRRVvlARPVIDVVTGRELTVMTDAQ--------SYRRLAAeylmdilsgf 104
                                    6778899999999864255555555544433222244444455666666665555........44444444444444566 PP

                         AAA_19  78 .........ldfddlltealelleeaeeekklqeeellivDEfqdvd.elqyrLlkallgekkklllvGDp 138
                                             l  d+l+    ++l+     +++ ++ ++ivD +q +  e +++++ +l  ++ kl+++GDp
  gi|118431883|ref|NP_148629.2| 105 lgeervreiLSSDSLVLVDPHFLRG----RTF-DNSVIIVDDSQSMPpEAIVEIITRLG-TGSKLIVIGDP 169
                                    6666666666777777666667664....344.6667**********99*********9.7777******7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3   2.2e-05     0.044      10     131 ..      37     169 ..      31     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.....erpevv.fvtlpsst...sskdllrellralglelka.......erl 73 
                                    v+G++GtGK++    +  + ++e   ++     +   v+  vt  ++t   + ++ +r  ++ l + l++       ++ 
  gi|118431883|ref|NP_148629.2|  37 VFGPTGTGKSLFSIVYGVSMTAEGRFRRvvlarP---VIdVVTGRELTvmtDAQSYRRLAAEYLMDILSGflgeervREI 113
                                    89********998888887765555555895443...4444444444443133333333333333333335555555466 PP

                         AAA_22  74 sseellealeqalrarav..ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp 131
                                     s++ l ++  ++ + ++   +++i+D+ q + ++ea+ e+ ++l    +g +li++G p
  gi|118431883|ref|NP_148629.2| 114 LSSDSLVLVDPHFLRGRTfdNSVIIVDDSQSM-PPEAIVEIITRLG---TGSKLIVIGDP 169
                                    6666666777777777779*************.*999999988888...89999999988 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   2.9e-05     0.058      15      74 ..      14      71 ..       6     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
                         AAA_25 15 laapppprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkV 74
                                   l+ + + +r l + ll   +l+ ++G++gtGK+ + +  +++++ +G+ +   +++  ++V
  gi|118431883|ref|NP_148629.2| 14 LEPKSEGQRELKEALLSDVDLVGVFGPTGTGKSLFSIVYGVSMTaEGR-FR--RVVLARPV 71
                                   55566667777788888889999*********************6766.42..34444444 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0086        17      30      51 ..     269     290 ..     253     293 .. 0.83
   2 ?    5.5   0.0    0.0077        15      29      51 ..     335     357 ..     313     368 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0086
                           KH_4  30 eielnvegedlGrvIGkrGrtl 51 
                                     + + v++ +lGr IG+ G+ +
  gi|118431883|ref|NP_148629.2| 269 DVLVVVKEGHLGRFIGRGGERI 290
                                    5667789999*********976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0077
                           KH_4  29 veielnvegedlGrvIGkrGrtl 51 
                                     +++++v++e++G   G +G  +
  gi|118431883|ref|NP_148629.2| 335 PQLKIKVSKEHMGPMLGQKGAHI 357
                                    689*****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2651.35
//
Query:       gi|118431884|ref|NP_148630.2|  [L=451]
Description: RNA (cytosine-C(5)-)-methyltransferase [Aeropyrum pernix K1]
Scores for 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-50  169.4   0.0    1.1e-49  168.8   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    4.5e-05   23.3   0.0    7.1e-05   22.6   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    0.00011   22.3   0.0    0.00021   21.5   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    0.00086   20.0   0.0      0.003   18.2   0.0    2.1  1  Methyltransf_25  Methyltransferase domain
     0.0037   17.7   0.0     0.0087   16.5   0.0    1.7  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.035   13.8   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020


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 !  168.8   0.0   3.6e-53   1.1e-49       3     200 .]     253     448 ..     251     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 3.6e-53
                                    HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EE CS
                Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfD 81 
                                    lL+p+++e +lD+caaPGgKTth+ael + +++++  d+   Rl+r+++ ++    +  + v++aDa + +k+lg   +D
  gi|118431884|ref|NP_148630.2| 253 LLQPRPGEIVLDMCAAPGGKTTHLAELSRLQARILGFDIYWDRLRRMKTLVEATASEaAVAVVKADAANAPKILGRGSVD 332
                                    79***********************************************999998885789******************* PP

                                    EEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEE CS
                Methyltr_RsmB-F  82 riLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredve 161
                                    +iLlD PCs+tg ++++ d+++r + + i++l++lqk ll+aa++++k+gG ++Y+ Cs+l eE e v+ +aL+k  + e
  gi|118431884|ref|NP_148630.2| 333 KILLDPPCSTTGGLHKNVDARWRLTRRKIMELQELQKTLLDAAVETVKPGGLILYTVCSILAEEGEDVVLHALEKWGNLE 412
                                    ****************************************************************************9999 PP

                                    EESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEEE CS
                Methyltr_RsmB-F 162 lvetelsepkglklgeeagtlrllPhtenkdgffiaklk 200
                                    +v++  ++p   +     gt+r +Ph++ + gff+a l+
  gi|118431884|ref|NP_148630.2| 413 IVPL--NGPYDESP-ILPGTMRAWPHRHGVTGFFYALLR 448
                                    9999..44333333.334589***************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.4e-08   7.1e-05       4     117 ..     259     395 ..     256     420 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.4e-08
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn. 81 
                                    g  vlD  ++ G +t  lae+ + +a++ G+Di  + ++++++  +   ++  v + ++d+ +++k l + ++D il + 
  gi|118431884|ref|NP_148630.2| 259 GEIVLDMCAAPGGKTTHLAELSRLQARILGFDIYWDRLRRMKTLVEATASEaAVAVVKADAANAPKILGRGSVDKILLDp 338
                                    5679***************98888*******************999999998999999*******88999*********8 PP

                Methyltransf_31  82 ....................evlnaladpdkile.eiervlkpggilliedprllae 117
                                                          ++ l +++k+l   + + +kpgg +l + +++lae
  gi|118431884|ref|NP_148630.2| 339 pcsttgglhknvdarwrltrRKIMELQELQKTLLdAAVETVKPGGLILYTVCSILAE 395
                                    88888888887777777777444666666665543888999****999999995554 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.9e-08   0.00021      21     137 ..     258     391 ..     231     414 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.9e-08
                                    TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEE.......CS-CCCSSHHHHHCHCHHHSSEEEEEE CS
                           FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvtti.......qgditdpetiekikealserkvdlvvs 93 
                                    pg+ v+D +aaPGg +  l++    +++++++D+   +++   t++          + + +++++  + l++  vd ++ 
  gi|118431884|ref|NP_148630.2| 258 PGEIVLDMCAAPGGKTTHLAELSRLQARILGFDIYWDRLRRMKTLVeataseaAVAVVKADAANAP-KILGRGSVDKILL 336
                                    7788***************99876689*******98744433333333344433444444444443.4677899****** PP

                                    --S-SS-CH..HHHHHHHH.........CCCCHHHHCCHCCCCECCCEEEECCCH CS
                           FtsJ  94 Dgapdvsgv..hdldeylq.........sqLllaalelalkllkpggtfvlkifr 137
                                    D   +++g   +++d+  +          +L +  l  a++++kpgg ++  ++ 
  gi|118431884|ref|NP_148630.2| 337 DPPCSTTGGlhKNVDARWRltrrkimelQELQKTLLDAAVETVKPGGLILYTVCS 391
                                    *8766666323556665558999999977999999************96654444 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     1e-06     0.003       1      70 [.     262     336 ..     262     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1e-06
                                    EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHH..TTTTEEEEESBCCGBS..SSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraee..eglnvefvqgdaedlp..fedgsfDlvvs 70 
                                    vLd+++ +G  t +la+    +a+++g+Di  + l+++++ +e+  +++ v +v++da + p  +  gs+D +++
  gi|118431884|ref|NP_148630.2| 262 VLDMCAAPGGKTTHLAELSRlQARILGFDIYWDRLRRMKTLVEAtaSEAAVAVVKADAANAPkiLGRGSVDKILL 336
                                    9***************997579*****************99988555569**********995457889998875 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 !   16.5   0.0   2.9e-06    0.0087      15      48 ..     170     204 ..     160     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                    G.GHHHHHHHHH-----EEE--TTS..TTHHHHHH CS
                Methyltr_RsmF_N  15 e.eaeaflaaleeprkkglRvNtlKisveelekls 48 
                                    + e+e++l+a+++p+ +++RvNtlK+s +e+ k+ 
  gi|118431884|ref|NP_148630.2| 170 DdELEKLLDAINRPPVNSVRVNTLKASFDEVYKAI 204
                                    459**********************9988776544 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.2e-05     0.035      71     136 ..     278     345 ..     249     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.2e-05
                                    HHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--..STTS---EEEE--------- CS
                        UPF0020  71 eearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLr..lkegevdvivtnpPYGerlg 136
                                    e  r ++++ g+D+ +  +++ ++  e++  +  +++++adaa+ +  l +g+vd i+ +pP     g
  gi|118431884|ref|NP_148630.2| 278 ELSRLQARILGFDIYWDRLRRMKTLVEATASEAAVAVVKADAANAPkiLGRGSVDKILLDPPCSTTGG 345
                                    34445667**************************************99999***********765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3447.99
//
Query:       gi|14602084|ref|NP_148631.1|  [L=395]
Description: MFS transporter [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-30  106.7  57.8    5.6e-23   81.4  36.2    2.0  2  MFS_1       Major Facilitator Superfamily
    8.3e-08   31.5   9.6     0.0011   17.9   3.2    2.4  2  MFS_1_like  MFS_1 like family
     0.0041   15.6  12.9     0.0084   14.6   4.0    2.3  2  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
       0.46    9.2  10.0      0.076   11.8   0.7    3.0  3  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 !   81.4  36.2   1.3e-26   5.6e-23       6     353 .]       8     337 ..       3     337 .. 0.81
   2 !   39.1  13.6   9.6e-14   4.3e-10      12     182 ..     215     381 ..     204     393 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.3e-26
                         MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.... 82 
                                   ++ ++a + +++++p +++++lg+s   ig ++++ +l++a+  + +G+ +dr+G+r +++l+ +l ++g+++l+ +    
  gi|14602084|ref|NP_148631.1|   8 VFRGFAVGGYMALFP-MYMRSLGYSMENIGGVIAVSSLVSALVLPAVGVYIDRMGPRTWVILTGVLQFAGIAILI-Pdpsi 86 
                                   67789999*******.788***************************************66666666666636666.33223 PP

                         MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                   ++l+    l +l +++  a+ p+ ++++a+    +  g  +g+ s+ fs++ ++gp++gg+++++lg++++f +la+ sl+
  gi|14602084|ref|NP_148631.1|  87 AGLT-SSYLLFLLSFM--AGQPSRMSFLARSIDVSSLGYIVGVTSSVFSASRLVGPAAGGYISEALGFQGAFEVLAASSLV 164
                                   3322.33444444554..478************************************************************ PP

                         MFS_1 164 afvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllf.ffgfsglltllplylqevlglsgl 243
                                   +++   l+   +   r r+ +        p+++++a+k+ll++ + +  +++++++  + +s+ +++l+      +g+s  
  gi|14602084|ref|NP_148631.1| 165 GLM---LFTILSTGVRLREVD-------RPRSVLEAYKSLLNPDPGFGRFLVFIGVdRLSWSLWFQMLTAH-LYNHGFS-E 233
                                   *66...455455555544443.......4557777799999999776677777777766899999999997.9******.9 PP

                         MFS_1 244 llaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllal 324
                                   ++agl++ ++++v  ++ +lagrl+drlg+ + l+ + +l+++aa++l+       ++ ++ ++vl+G+  +  +ps++ +
  gi|14602084|ref|NP_148631.1| 234 FQAGLAVTVSGVVQTGGLPLAGRLVDRLGAVIGLIASEALGAMAAILLMDPT----PLRVYPAMVLMGLSIAYWVPSYNKM 310
                                   ***************************9984444444444444444444333....5577779****************** PP

                         MFS_1 325 asdlappeeagtasglfntagslggalgp 353
                                   ++ l    e gt +  +nt++s++ga gp
  gi|14602084|ref|NP_148631.1| 311 VALLR--GEGGTGYTQVNTVRSIAGAPGP 337
                                   *****..9*****************9887 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 9.6e-14
                         MFS_1  12 rsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvl 91 
                                   +s+ + +l+ a   ++g+s+ ++gl++t+ ++++  + +++Grl+dr+G+   l+++ +l a + ++ll+  + +  ++ +
  gi|14602084|ref|NP_148631.1| 215 WSLWFQMLT-AHLYNHGFSEFQAGLAVTVSGVVQTGGLPLAGRLVDRLGAVIGLIASEALGAMA-AILLM-DPTPlRVYPA 292
                                   444444444.3346789***********************************************.77777.777866**** PP

                         MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                    vl+Gl   a++  ++  ++++  + e g ++  +++  s++ + gp lggll+++++  a+f +  i++l +++l+  l+
  gi|14602084|ref|NP_148631.1| 293 MVLMGLSI-AYWVPSYNKMVALLRG-EGGTGYTQVNTVRSIAGAPGPYLGGLLYDAISPMAPFAVSSILLLSLAILGKKLM 371
                                   *******7.7777777777777777.9*************************************************99999 PP

                         MFS_1 173 peepperkrk 182
                                    +e+ e++ +
  gi|14602084|ref|NP_148631.1| 372 IVERAEEEAV 381
                                   8888877665 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 !   17.0   0.3   4.8e-07    0.0022      15      74 ..      14      73 ..       6      87 .. 0.86
   2 !   17.9   3.2   2.5e-07    0.0011     177     383 ..     149     353 ..     112     355 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-07
                    MFS_1_like 15 lgsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslll 74
                                  +g+ +  + +y++s g+++++ig + ++  l+s l  p +gv  Dr+g r+ v++ ++l 
  gi|14602084|ref|NP_148631.1| 14 VGGYMALFPMYMRSLGYSMENIGGVIAVSSLVSALVLPAVGVYIDRMGPRTWVILTGVLQ 73
                                  5556666789*******************************************9988764 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.5e-07
                    MFS_1_like 177 lpysallyvlaallvisllvvlilnetekesklkvtk.slqvllnilk.npeviifllvalilgmswgiienFlflYLkel 255
                                   l+++ ++ vlaa  ++ l+++ il  +   ++++    +l++ + +l+ +p    fl+++ +   sw++  + l+ +L ++
  gi|14602084|ref|NP_148631.1| 149 LGFQGAFEVLAASSLVGLMLFTILSTGVRLREVDRPRsVLEAYKSLLNpDPGFGRFLVFIGVDRLSWSLWFQMLTAHLYNH 229
                                   3367778888888888888877777777666655544044555555543566778999999999***************** PP

                    MFS_1_like 256 gasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.enawlvlpievLhgisfgllwaaav 335
                                   g+s++ +G +v++  v +   + +a +l+++lG+v  li++  + ++  +l+  +   +  v p+ vL g+s++  w+   
  gi|14602084|ref|NP_148631.1| 230 GFSEFQAGLAVTVSGVVQTGGLPLAGRLVDRLGAVIGLIASEALGAMAAILL--MdPTPLRVYPAMVLMGLSIAY-WVPSY 307
                                   *********************************9877766655554443332..236778889999******985.66555 PP

                    MFS_1_like 336 eyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflF 383
                                   + +  +   +  +tg   +++   ++ +a G ++GGll+d  s++  F
  gi|14602084|ref|NP_148631.1| 308 NKMVALLRGE-GGTGYTQVNT-VRSIAGAPGPYLGGLLYDAISPMAPF 353
                                   5555444333.3344443444.46889999*********999988776 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   4.0   1.9e-06    0.0084      46     191 ..      34     174 ..      22     192 .. 0.78
   2 !    6.2   1.6   0.00065       2.9     148     182 ..     325     363 ..     253     391 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-06
                         MFS_3  46 mvAlvqaaatLPifllsilaGalaDnfd.rRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWq 125
                                   ++  v a ++L   l+   +G+  D +  r +v+l++ l  a  ++l+   ++ gl+s +ll  l++++g      +P+  
  gi|14602084|ref|NP_148631.1|  34 NIGGVIAVSSLVSALVLPAVGVYIDRMGpRTWVILTGVLQFAGIAILIPDPSIAGLTSSYLLFLLSFMAG------QPSRM 108
                                   555555666666555555679999988725578888888889999999999****************998......68888 PP

                         MFS_3 126 AsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkr 191
                                     +   ++ + +   v ++s  +  +R vGPA gG +  a+G   af v a s l+ ++ ++    
  gi|14602084|ref|NP_148631.1| 109 SFLARSIDVSSLGYIVGVTSSVFSASRLVGPAAGGYISEALGFQGAFEVLAASSLVGLMLFTILST 174
                                   88888999999999**********************************999999876655444433 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00065
                         MFS_3 148 iniaRsv....GPAlgGvlvaavGaalafavnalsylal 182
                                   +n++Rs+    GP lgG+l  a+ +++ fav ++  l l
  gi|14602084|ref|NP_148631.1| 325 VNTVRSIagapGPYLGGLLYDAISPMAPFAVSSILLLSL 363
                                   455555444449*******************99876654 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   1.7e-05     0.076      17      89 ..       8      76 ..       1     114 [. 0.81
   2 ?    0.7   0.2     0.039   1.8e+02     350     396 ..     122     170 ..     113     181 .. 0.63
   3 ?    1.4   0.2     0.025   1.1e+02      12      79 ..     204     270 ..     198     305 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.7e-05
                     LacY_symp 17 ffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfap 89
                                  +f  f ++ y++lfp++++  lg s  ++G v +v sl+s l  p  G+  d++G +    wvi + ++ fa 
  gi|14602084|ref|NP_148631.1|  8 VFRGFAVGGYMALFPMYMRS-LGYSMENIGGVIAVSSLVSALVLPAVGVYIDRMGPRT---WVILTGVLQFAG 76
                                  566788999********985.799*******************************886...555444444554 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.039
                     LacY_symp 350 fligfqlskqlaivll.stlaGklydkvGfqtaylvlgiivls.ltlis 396
                                   +++g + s   a+ l+  +  G + + +Gfq a+ vl++  l+ l+l++
  gi|14602084|ref|NP_148631.1| 122 YIVGVTSSVFSASRLVgPAAGGYISEALGFQGAFEVLAASSLVgLMLFT 170
                                   666665554444444414556788999*******999875543133443 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.025
                     LacY_symp  12 falffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwv 79 
                                   f +f  +  + +s++f +++  l ++ g+s+ + G+  +v  ++     pl G + d+lG    l+ +
  gi|14602084|ref|NP_148631.1| 204 FLVFIGVDRLSWSLWFQMLTAHLYNH-GFSEFQAGLAVTVSGVVQTGGLPLAGRLVDRLGAVIGLIAS 270
                                   55555555567999****99999986.899999**99999999999999*********9977666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 3173.97
//
Query:       gi|14602085|ref|NP_148632.1|  [L=116]
Description: hypothetical protein APE_2467 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      154  (0.00858944); 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: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.34
# Mc/sec: 1024.85
//
Query:       gi|118431885|ref|NP_148633.2|  [L=554]
Description: propionate CoA-transferase [Aeropyrum pernix K1]
Scores for 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-55  185.9   0.1    2.7e-52  177.3   0.0    2.8  3  CoA_trans        Coenzyme A transferase
  ------ inclusion threshold ------
      0.063   11.6   0.0       0.12   10.7   0.0    1.4  1  Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, trans
       0.16   11.6   0.0       0.24   11.0   0.0    1.2  1  DUF4038          Protein of unknown function (DUF4038)


Domain annotation for each model (and alignments):
>> CoA_trans  Coenzyme A transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.0   4.5e-56   2.7e-52       2     217 .]      15     262 ..      14     262 .. 0.98
   2 ?   -0.7   0.0      0.13   7.8e+02      18      58 ..     324     360 ..     322     366 .. 0.73
   3 !    5.2   0.0    0.0021        12      95     148 ..     384     430 ..     372     509 .. 0.89

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 4.5e-56
                                    CHHHHHHCTT--TTEEEEE-SBTTBTHHHHHHHHHHHHT....TTSEEEEESTT..TE..ECCHHHHHTTTEEEEEESCT CS
                      CoA_trans   2 etaaeavakeikdGmtvavGGFgligiPealiaalarsg....vkdltviisea..gv..lglgplllngsvkkviasyg 73 
                                     ta+ea++ +i+dG++va++GF+++++Pe+li++l+r++    + ++ +iis++  gv  +gl+++++++++k ++  ++
  gi|118431885|ref|NP_148633.2|  15 VTAEEALS-NIRDGSVVAISGFNMAMTPEYLIEELYRLYlktgHPRDLFIISDTfpGVpgRGLDRIAMDMYEKGEEE-FI 92 
                                    689*****.******************************9999***********776699****************9.** PP

                                    TBBC.....EHHHHHHHHTTSS.EEEEHHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTT................ES CS
                      CoA_trans  74 getv.....nprfgkqflsgel.efellpqgtlaerlraGgaglpelgfltntgigtlvapk................lk 131
                                    + ++     ++r+ ++++ +e+ e+++++ g++a+++r  g+g p  g+l+++g++t+++p+                + 
  gi|118431885|ref|NP_148633.2|  93 SGMLlpfygWSRTLQRMIIEEWfEAYTWSIGIMAYWFREVGSGRP--GVLSRVGVETFLDPRrggcslnekarkagrvRG 170
                                    **99*****************************************..*******************************99 PP

                                    EEEEETTEEEEEEESSSEEEEEEECCEEETTCSEESSGGGHTTHSHHHHH......HEEEEEEEEEEEECTTSSECCCES CS
                      CoA_trans 132 kvpgfgGaeyilepalkadvalikaskadeegnlvfeksagnfnkpaiae......aakvtileveeivekgkldpekvl 205
                                    ++ +++G+eyil++a+k+dv l++ s+ade+gn+++e++  +++ ++ia+      ++++++++v+++ ++g+++ ++v+
  gi|118431885|ref|NP_148633.2| 171 RILEIDGREYILYQAPKPDVGLLRGSTADEKGNVSIEDEGIQGTILNIAQavkarpKRGFNVVQVLRVARFGNIRAKNVT 250
                                    ******************************************************************************** PP

                                    BTGGGHSEEEET CS
                      CoA_trans 206 iPgvlvdavvea 217
                                    +Pg l+d vv+a
  gi|118431885|ref|NP_148633.2| 251 VPGPLIDFVVVA 262
                                    **********85 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                                    EEE-SBTTBTHHHHHHHHHH.HHTTTSEEEEESTTTEECCHH CS
                      CoA_trans  18 vavGGFgligiPealiaala.rsgvkdltviiseagvlglgp 58 
                                    v++G    +giP +l+a +a + +v+d + i+ e+g +g  p
  gi|118431885|ref|NP_148633.2| 324 VNLG----VGIP-SLVAHVAvEEDVSDFMEITIESGPWGGIP 360
                                    8999....****.77776651555888888888888877555 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0021
                                    HHHHHHHHHHHHHHHTEETTEEEESTTTTSHGGTTESEEEEETTEEEEEEESSS CS
                      CoA_trans  95 lpqgtlaerlraGgaglpelgfltntgigtlvapklkkvpgfgGaeyilepalk 148
                                    + +g++++ + +G ++++++g++++++++       +++pg gG  +i+ ++++
  gi|118431885|ref|NP_148633.2| 384 IYEGGILDAASLGFLQVDREGNVNSSILP-------DRLPGPGGFSVIAAGSPN 430
                                    5689************************9.......478888888888877765 PP

>> Mal_decarbox_Al  Malonate decarboxylase, alpha subunit, transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     2e-05      0.12     136     207 ..     186     265 ..     158     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2e-05
                Mal_decarbox_Al 136 liPnvalvaaekadreGnlytGantedtPaiveataf....kdgiviaqvneivd....klprvdiPadwvdfvveadkp 207
                                      P+v l+ +++ad++Gn+ +  +  +   +  a a     k g  ++qv ++      + + v +P+  +dfvv a++ 
  gi|118431885|ref|NP_148633.2| 186 PKPDVGLLRGSTADEKGNVSIEDEGIQGTILNIAQAVkarpKRGFNVVQVLRVARfgniRAKNVTVPGPLIDFVVVAPRD 265
                                    3699***************998887766655545444112268********999888778899**************986 PP

>> DUF4038  Protein of unknown function (DUF4038)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     4e-05      0.24      37     104 ..     221     288 ..     207     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                                    HHHHHHHTT--EEEEES-...SSSS-B-TTS-BS-SST....-S-THHHHHHHHHHHHHHTT-EEEEE CS
                        DUF4038  37 YlddRaeqGFnviqavvlaeldglkapnaygekplidndltkpneaYfdhvdkivelaaekgllialv 104
                                     ++ R ++GFnv+q+  +a   +++a+n++   plid  +  p ++ ++ +   +++  + +++  l+
  gi|118431885|ref|NP_148633.2| 221 AVKARPKRGFNVVQVLRVARFGNIRAKNVTVPGPLIDFVVVAPRDKHWQGASMDMDRRVSGEIITPLA 288
                                    5789********************************999999*999**98877666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 4242.96
//
Query:       gi|14602087|ref|NP_148634.1|  [L=103]
Description: 30S ribosomal protein S25 [Aeropyrum pernix K1]
Scores for complete 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   44.3   1.0    2.4e-11   43.7   1.0    1.3  1  Ribosomal_S25  S25 ribosomal protein
    0.00058   19.5   1.6     0.0014   18.3   1.6    1.7  1  GntR           Bacterial regulatory proteins, gntR family
    0.00087   18.9   0.3    0.00095   18.8   0.3    1.0  1  HTH_42         Winged helix DNA-binding domain
     0.0014   17.9   0.1     0.0016   17.7   0.1    1.1  1  EAP30          EAP30/Vps36 family
     0.0044   16.9   0.1     0.0064   16.4   0.1    1.2  1  HTH_11         HTH domain
     0.0082   16.0   0.0      0.012   15.5   0.0    1.3  1  MarR           MarR family
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.14   12.2   0.0    1.2  1  Replic_Relax   Replication-relaxation


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 !   43.7   1.0   9.5e-15   2.4e-11      18      98 ..       5      89 ..       1      92 [. 0.80

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 9.5e-15
                 Ribosomal_S25 18 kakkKKwskgkvkdkln..navl..fdketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvskhraqv 96
                                    +kKK  + k  +k +  + ++  + ++++++  kev + + +tp  +++++ +++s+Arr+Lr lee+g++ l  ++r++ 
  gi|14602087|ref|NP_148634.1|  5 DMAKKKAPSAKEGEKQQgfKEIIpeVTEKLVEQARKEVARERWVTPHKLAQKMGVKVSIARRVLRILEEEGVLVLFTRNRRSP 87
                                  4447777666666666522233223678999999**********************************************998 PP

                 Ribosomal_S25 97 iY 98
                                   Y
  gi|14602087|ref|NP_148634.1| 88 LY 89
                                  88 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.6   5.4e-07    0.0014      29      59 ..      52      82 ..      29      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.4e-07
                                  HHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                          GntR 29 eLaaefgVsrttvReALrrLeaeglverrqg 59
                                  +La+++gV+ +  R++Lr Le+eg+++   +
  gi|14602087|ref|NP_148634.1| 52 KLAQKMGVKVSIARRVLRILEEEGVLVLFTR 82
                                  89***********************988766 PP

>> HTH_42  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   3.7e-07   0.00095      64     157 ..       9      95 ..       4     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.7e-07
                        HTH_42  64 amapalaaelara..kgldareaaalaaavlerlaaegpltarelgealarrgwwgwkkpgkaskralellrlegelvvar 142
                                    +ap  +++ +++  k++  +  ++l++++++++a+e+ +t+  l++++  +     +     ++r+l++l+ eg lv  +
  gi|14602087|ref|NP_148634.1|   9 KKAPSAKEGEKQQgfKEIIPEVTEKLVEQARKEVARERWVTPHKLAQKMGVK----VS----IARRVLRILEEEGVLVLFT 81 
                                   55555555534446999*******************************9998....66....99***************** PP

                        HTH_42 143 rergfekvydlaerv 157
                                   r+r   ++y +  +v
  gi|14602087|ref|NP_148634.1|  82 RNRR-SPLYLPKKKV 95 
                                   9965.5888776666 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   6.4e-07    0.0016     180     233 ..      26      78 ..       8      79 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.4e-07
                         EAP30 180 vl.evakrlvsllaekssg.ggvtaselaeeeenlgwsvarakeaLeelereGllw 233
                                   ++ ev ++lv+ ++++ ++ + vt  +la++   +g++v++a+++L+ le+eG+l+
  gi|14602087|ref|NP_148634.1|  26 IIpEVTEKLVEQARKEVAReRWVTPHKLAQK---MGVKVSIARRVLRILEEEGVLV 78 
                                   4456666665555544443578******999...*******************997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.5e-06    0.0064      12      51 ..      43      83 ..      32      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.5e-06
                        HTH_11 12 argp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                  ar+  ++  +LA++++v  +  rr +++Lee gv +  +++
  gi|14602087|ref|NP_148634.1| 43 ARERwVTPHKLAQKMGVKVSIARRVLRILEEEGVLVLFTRN 83
                                  57788999*************************98877666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.7e-06     0.012      19      46 ..      49      76 ..      42      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                                  EHHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                          MarR 19 svseLakklgvskstvtrvldrLekkGl 46
                                  + ++La k+gv+ s + rvl+ Le++G 
  gi|14602087|ref|NP_148634.1| 49 TPHKLAQKMGVKVSIARRVLRILEEEGV 76
                                  778***********************95 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.3e-05      0.14       5      46 ..      43      83 ..      40      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.3e-05
                  Replic_Relax  5 aehrvlTtrqiarllfashratarrrLarLrelgllsrlrkr 46
                                  a+ r  T + +a+ +  +++  arr+L++L+e+g+l  ++++
  gi|14602087|ref|NP_148634.1| 43 ARERWVTPHKLAQKMGVKVSI-ARRVLRILEEEGVLVLFTRN 83
                                  678999999************.****************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      796  (0.0443973); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 00:00:00.36
# Mc/sec: 850.84
//
Query:       gi|118431886|ref|NP_148635.2|  [L=291]
Description: hypothetical protein APE_2472.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00079   19.3   0.0     0.0015   18.4   0.0    1.4  1  AAA_26    AAA domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   8.2e-08    0.0015       3      42 ..       7      46 ..       6      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.2e-08
                         AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgi 42
                                   ++vtg ++++GKT++++gL++++++ g++++ fKP ++ +
  gi|118431886|ref|NP_148635.2|  7 VLVTGLGEDSGKTSLTTGLLASFRSLGIEARGFKPAGATN 46
                                   68*********************************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2341.32
//
Query:       gi|118431887|ref|NP_148636.2|  [L=237]
Description: hypothetical protein APE_2473.1 [Aeropyrum pernix K1]
Scores for complete 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-09   37.4   0.0    5.6e-09   36.8   0.0    1.2  1  Metallophos  Calcineurin-like phosphoesterase


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 !   36.8   0.0   3.1e-13   5.6e-09       3     203 ..       4     199 ..       3     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 3.1e-13
                                    EEEEESBTBTTCCTHHHHHHHHHHHH...HHHTTESEEEEESTSSSSS...HHHHHHHHHHHHHHHHTSEE.EEEC-TTS CS
                    Metallophos   3 ilvigDlHlalgggqlddllkllddl...lreekpdlvllaGDlvdrg...dlekellellaalvkypipv.ylllGNHe 75 
                                    ++ +gD+H      + ++l+ l+  +   + + +p +vllaGDlv+ g    ++    +ll+++++    v + + GN +
  gi|118431887|ref|NP_148636.2|   4 VAATGDIH------SPRYLNLLIAAAgswRGD-EPCMVLLAGDLVEKGraeAFSP-AFKLLREKFS--GSVfVGVFGNED 73 
                                    789*****......444444444333443666.9999999********5555555.4444455555..455599****** PP

                                    CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEE..THHHHHHHHHHHSCHHHHCC..... CS
                    Metallophos  76 gfee.ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspel..lvsldklgslnleleapepg..... 147
                                     +    +  +y+       +w +d    + +   +  sg   ++ + G       l+ l+++ ++n+++ ++  +     
  gi|118431887|ref|NP_148636.2|  74 -WNReAMVKLYP-----EVVWLDD----SVFTGDC--SG--GTVAVVGS---TgaLDRLTPWQRRNMPWLVDVFKrrpri 136
                                    .77744444444.....4455554....2222222..22..23333333...1225777777778888777777777666 PP

                                    .HHHHHHHHHHTTCSEEEEEESSESS........CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 148 .dewlkdlekrekadwvivlgHsply........rgsgylfgdealedllkkygvdlvisGHtHv 203
                                     + +l++  +r++ad+v++l+H ++          +++++  +  +e+   + ++d+ +++H H 
  gi|118431887|ref|NP_148636.2| 137 lEGLLRE--ARREADYVVLLTHYGVAratimgedPRIHPYLYSSGMERMIARARPDVAVHAHAHN 199
                                    6777777..*****************9999999999999999999999999999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1928.08
//
Query:       gi|118431888|ref|YP_874948.1|  [L=83]
Description: hypothetical protein APE_2473a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.0   0.4      0.076   13.0   0.2    1.9  2  Cdc6_C    CDC6, C terminal winged helix domain
      0.095   12.7   0.0       0.16   12.0   0.0    1.6  1  HTH_36    Helix-turn-helix 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 ?    1.0   0.0     0.048   4.3e+02      23      43 ..      16      38 ..       2      46 .. 0.66
   2 ?   13.0   0.2   8.5e-06     0.076      37      64 ..      48      73 ..      21      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.048
                                   HHHHHHHHHT..T-----HHHHH CS
                         Cdc6_C 23 evYkslCese..gvdpltqrevs 43
                                    vY+++ +++  g +p+t++  +
  gi|118431888|ref|YP_874948.1| 16 LVYETIVKRTknGQTPITESDLM 38
                                   56777777775566777776665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.5e-06
                                   --HHHHHHHHHHHHHTTSEEEEEEE-CC CS
                         Cdc6_C 37 ltqrevsdllseLemlgileleksskGr 64
                                    ++re++++l eLe+ g +++++s  G+
  gi|118431888|ref|YP_874948.1| 48 ASRREIVNILMELETHGYVRVKSS--GE 73
                                   589******************998..43 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.16      35      55 .]      41      66 ..       6      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                         HTH_36 35 l.....glsknTvsraikeLeqlGyi 55
                                   l     + s++ +++++ eLe++Gy+
  gi|118431888|ref|YP_874948.1| 41 LeneglKASRREIVNILMELETHGYV 66
                                   46665599*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 681.34
//
Query:       gi|118431889|ref|NP_148637.2|  [L=737]
Description: cell division protein CDC48 [Aeropyrum pernix K1]
Scores for complete 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-100  331.6   0.0    6.1e-51  172.3   0.0    2.4  2  AAA              ATPase family associated with various cellul
      1e-36  124.4   5.6    1.1e-19   69.9   1.4    2.9  2  AAA_lid_3        AAA+ lid domain
    9.1e-34  115.5   2.9    4.2e-33  113.4   2.5    2.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    2.9e-16   59.6   0.1    1.6e-07   31.2   0.0    3.4  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.6e-14   53.9   0.6    2.4e-06   28.0   0.0    3.9  3  AAA_16           AAA ATPase domain
    3.5e-14   53.3   0.0    3.9e-07   30.3   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.3e-13   50.5   3.3    1.3e-13   50.5   3.3    2.1  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    3.7e-11   43.4   0.6    0.00044   20.5   0.0    4.3  3  AAA_22           AAA domain
    8.9e-11   42.1   0.0    0.00027   21.1   0.0    2.9  2  AAA_33           AAA domain
    4.5e-10   39.7   2.6      0.001   19.1   0.1    4.1  2  AAA_5            AAA domain (dynein-related subfamily)
    1.2e-09   37.8   2.2    0.00099   18.4   0.0    3.1  4  TIP49            TIP49 P-loop domain
    1.9e-09   37.7   0.0    0.00031   20.8   0.0    2.4  2  AAA_14           AAA domain
    4.4e-09   36.2   0.5    9.3e-05   22.4   0.0    3.3  2  Vps4_C           Vps4 C terminal oligomerisation domain
    4.3e-08   33.1   0.0      0.011   15.5   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.7e-07   31.8   0.0      0.012   16.2   0.0    2.7  2  AAA_18           AAA domain
    2.6e-07   30.6   0.0      0.003   17.3   0.0    2.8  2  AAA_24           AAA domain
    4.6e-07   30.2   0.0      0.038   14.2   0.0    2.6  2  AAA_28           AAA domain
    7.8e-07   28.7   0.6      0.041   13.3   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    8.1e-07   28.9   0.1      0.083   12.6   0.0    3.8  3  Sigma54_activat  Sigma-54 interaction domain
    1.5e-06   27.7   0.5       0.18   11.1   0.0    3.5  3  ATPase           KaiC
    1.7e-06   27.6   0.1    1.1e-05   25.0   0.1    2.1  2  UFD1             Ubiquitin fusion degradation protein UFD1
    3.7e-06   27.3   0.0      0.063   13.7   0.0    2.5  2  RNA_helicase     RNA helicase
      9e-06   25.8   0.1      0.025   14.5   0.1    3.7  3  ATPase_2         ATPase domain predominantly from Archaea
    1.3e-05   24.8   0.0       0.12   11.9   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    2.2e-05   24.5   0.0       0.28   11.2   0.0    2.7  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.5e-05   23.4   0.4        0.2   11.1   0.1    2.7  2  PhoH             PhoH-like protein
    7.4e-05   22.0   0.0       0.24   10.5   0.0    2.6  2  DUF815           Protein of unknown function (DUF815)
     0.0001   22.9   0.0       0.56   10.7   0.0    2.5  2  ABC_tran         ABC transporter
    0.00016   20.8   0.1       0.19   10.8   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    0.00017   20.9   0.0       0.47    9.7   0.0    2.7  2  Zeta_toxin       Zeta toxin
    0.00018   21.4   0.0       0.63    9.9   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
    0.00018   21.5   0.2        1.4    8.8   0.0    3.4  3  NACHT            NACHT domain
    0.00025   20.4   0.0      0.093   12.0   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00075   19.1   8.7       0.32   10.5   1.0    3.9  3  AAA_25           AAA domain
     0.0013   18.5   0.3        2.3    7.9   0.0    2.8  2  AAA_30           AAA domain
     0.0021   18.4   1.6        4.8    7.5   0.0    3.3  3  AAA_19           AAA domain
     0.0025   17.0   0.0       0.91    8.7   0.0    2.8  3  NB-ARC           NB-ARC domain
     0.0029   17.5   0.0        2.1    8.0   0.0    2.3  2  AAA_11           AAA domain
     0.0035   17.8   0.0          3    8.3   0.0    2.9  2  AAA_17           AAA domain
     0.0056   16.6   0.6         12    5.7   0.0    4.0  3  NTPase_1         NTPase
     0.0074   16.4   0.0        3.9    7.6   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   15.7   0.0        1.1    9.1   0.0    2.8  2  Bac_DnaA         Bacterial dnaA  protein
      0.011   15.4   0.2         55    3.4   0.0    4.0  4  Guanylate_kin    Guanylate kinase
      0.018   14.5   0.1        2.2    7.6   0.0    2.4  2  IPT              Isopentenyl transferase
      0.022   13.6   0.0        2.8    6.7   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.034   13.9   0.8         13    5.4   0.0    3.1  3  Cytidylate_kin   Cytidylate kinase
       0.06   13.3   0.0         10    6.0   0.0    2.7  2  Rad17            Rad17 P-loop domain
      0.066   12.9   0.0        3.8    7.2   0.0    2.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.083   12.6   0.0         14    5.5   0.0    2.3  2  AAA_29           P-loop containing region of AAA domain
      0.083   12.6   0.0         11    5.8   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili


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 !  172.3   0.0   1.7e-53   6.1e-51       1     132 []     225     355 ..     225     355 .. 0.98
   2 !  157.0   0.0   9.1e-49   3.3e-46       1     131 [.     498     628 ..     498     629 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 1.7e-53
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +llyGppGtGKTllakava+e++++f++i+g+e++sky gese+++re+f+eak++a psi+fiDEida+a++r++   e
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYFISINGPEIMSKYYGESEQRLREIFEEAKKNA-PSIIFIDEIDAIAPKRDEVVGE 303
                                    69******************************************************9.********************** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                    +e+rvv+qLl+ +dg++ + ++vivi+atnrp+ +dpal+r gRfdr+ie++l
  gi|118431889|ref|NP_148637.2| 304 VERRVVAQLLALMDGLEAR-GNVIVIAATNRPNAIDPALRRpGRFDREIEVPL 355
                                    ******************7.66****************************985 PP

  == domain 2  score: 157.0 bits;  conditional E-value: 9.1e-49
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    vll+GppGtGKTllakava+e+g++f+ + g+e+lsk+vgese+ ire+f++a+++a p ++f+DEida+a+ r ++  +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESERAIREIFAKARQHA-PAVVFFDEIDAIAPVRgTDVGT 576
                                    79******************************************************9.****************8889** PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +++er+v+qLlte+dgv++  ++v+vi+atnrpd++dpal+r gR+++ i+++
  gi|118431889|ref|NP_148637.2| 577 RVTERIVSQLLTEIDGVSDL-HDVVVIAATNRPDMVDPALMRpGRLEKMIYVP 628
                                    *******************6.77***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.2   9.5e-18   3.4e-15       1      43 [.     377     436 ..     377     438 .. 0.74
   2 !   69.9   1.4   3.2e-22   1.1e-19       1      44 [.     651     696 ..     651     697 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 9.5e-18
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr................gike.itmedf 43 
                                    d dl++LAe+T+G++GADlaal reAa+ Alrr                 +k  +tmedf
  gi|118431889|ref|NP_148637.2| 377 DMDLEKLAEMTKGFTGADLAALAREAAMYALRRylpeidldqesipvevLEKMvVTMEDF 436
                                    569******************************555555555544444223334666666 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 3.2e-22
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfe 44 
                                    dvdl+e+A+rTeGy+GAD++al+reA+l+Alr++i   e++m++fe
  gi|118431889|ref|NP_148637.2| 651 DVDLAEIARRTEGYTGADIEALVREASLAALREDINaaEVSMRHFE 696
                                    9***********************************766******8 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 !  113.4   2.5   1.2e-35   4.2e-33       2      84 ..      17      99 ..      16     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 1.2e-35
                                   EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                        CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                   LrVaea+++d+gr++vrid + m+elg+epgdvveiegk+kTvaiv+pa+ped g +iIrmdg++R+na+v+iG+kV+Vrk+
  gi|118431889|ref|NP_148637.2| 17 LRVAEAKPRDSGRKRVRIDIDIMKELGVEPGDVVEIEGKKKTVAIVMPAYPEDMGLDIIRMDGILRRNADVNIGEKVIVRKT 98
                                   9*******************************************************************************98 PP

                                   - CS
                        CDC48_N 84 e 84
                                   +
  gi|118431889|ref|NP_148637.2| 99 S 99
                                   6 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 ?   -1.1   0.0       3.9   1.4e+03      97     139 ..      56      98 ..      44     108 .. 0.74
   2 !   31.2   0.0   4.5e-10   1.6e-07      34     104 ..     223     301 ..     198     343 .. 0.84
   3 !   24.0   0.0   7.6e-08   2.7e-05      35      97 ..     497     567 ..     459     577 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.9
                         RuvB_N  97 sraveevlysamedfrldivigkGpsarsikldlpkftlvgat 139
                                    +++v  v+ +  ed+ ldi+  +G   r+  +++ +  +v  t
  gi|118431889|ref|NP_148637.2|  56 KKTVAIVMPAYPEDMGLDIIRMDGILRRNADVNIGEKVIVRKT 98 
                                    5555555555569*******99999999999998877777665 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 4.5e-10
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevl 104
                                      +llyGpPG Gkt lak +a+e ++ + +  gP +      e ++ l  ++ + +++   ++fidei  ++++ +ev+
  gi|118431889|ref|NP_148637.2| 223 KGILLYGPPGTGKTLLAKAVANEADAYFISINGPEImskyygESEQRLREIFEEAKKNapSIIFIDEIDAIAPKRDEVV 301
                                    679*******************************984433333456789999888776347************999987 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 7.6e-08
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrls 97 
                                     vll+GpPG Gkt lak +a+e g+++ +  gP +      e ++ +  ++++ +++   v+f dei  ++
  gi|118431889|ref|NP_148637.2| 497 GVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEIlskwvgESERAIREIFAKARQHapAVVFFDEIDAIA 567
                                    69*******************************87443333445667777777665523588888887665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.7e-09   2.4e-06      23     139 ..     221     327 ..     209     329 .. 0.72
   2 !   17.7   0.1   9.9e-06    0.0036      24      57 ..     495     527 ..     485     539 .. 0.79
   3 ?    2.8   0.0      0.39   1.4e+02     122     147 ..     542     566 ..     538     576 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.7e-09
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleawrekl 101
                                     p  +ll+G++G+GK+ l++++++   +++++f++ +  +  ++  y          + lr++ +e +++a    + +++
  gi|118431889|ref|NP_148637.2| 221 PPKGILLYGPPGTGKTLLAKAVAN---EADAYFISINGPEI-MSKYYGESE------QRLREIFEEaKKNAPSIIFIDEI 290
                                    4689*******************7...44499*********.332222233......44444444413345556666667 PP

                         AAA_16 102 eealaavpelagaeasrllellkrllallsrderplvl 139
                                    ++ +   +e+ g+ ++r+ ++l +l++ l+ ++  +++
  gi|118431889|ref|NP_148637.2| 291 DAIAPKRDEVVGEVERRVVAQLLALMDGLEARGN-VIV 327
                                    777778999999999***********99998676.443 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 9.9e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflr 57 
                                    p+ vll G++G+GK+ l+++++++  ++ +i++r
  gi|118431889|ref|NP_148637.2| 495 PRGVLLFGPPGTGKTLLAKAVATESGAN-FIAVR 527
                                    599*******************876666.44444 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.39
                         AAA_16 122 llkrllallsrderplvlvlDdlqwa 147
                                    ++++++a++++ + p v+++D+++ +
  gi|118431889|ref|NP_148637.2| 542 AIREIFAKARQ-HAPAVVFFDEIDAI 566
                                    67889999999.778********965 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   1.1e-09   3.9e-07       6     106 ..     225     319 ..     220     337 .. 0.88
   2 !   20.5   0.0   1.2e-06   0.00041       6      93 ..     498     577 ..     493     606 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.1e-09
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a+  ++     +i ++  e++     + + ++++  ++   +a+++   i+++DEid i+pk
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADA----YFISINGPEIMS----KYYGESEQRLREIFEEAKKNApsIIFIDEIDAIAPK 296
                                    8999******************96....************....99999999999999999999899************9 PP

                                    .---------HHHHHHHHHHHH-- CS
                          AAA_2  84 .essgadvSregVqrdLLqilegg 106
                                     ++   +v r  V+  LL +++g 
  gi|118431889|ref|NP_148637.2| 297 rDEVVGEVERR-VVAQLLALMDGL 319
                                    77777777775.777789999985 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.2e-06
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +ll gp g+Gkt+laka+a    +    ++i +   e+l     + + +++   ++   +a ++   +v++DEid i+p 
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGA----NFIAVRGPEILS----KWVGESERAIREIFAKARQHApaVVFFDEIDAIAP- 568
                                    6788****************9996....9***********....77777777778888888888888************. PP

                                    ---------H CS
                          AAA_2  84 essgadvSre 93 
                                       g dv   
  gi|118431889|ref|NP_148637.2| 569 -VRGTDVGTR 577
                                    .666666543 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 !   50.5   3.3   3.7e-16   1.3e-13       3      63 ..     118     178 ..     116     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.7e-16
                                    SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                        CDC48_2   3 dgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                    d+++  y+k++++g p+t+Gd+vv+++ gq+++l Vv+  Pkg+v+++e+T++++ +kpv 
  gi|118431889|ref|NP_148637.2| 118 DEGFKRYVKKKLQGVPITEGDVVVVPVIGQAVQLQVVDARPKGAVIVSEETIVDVLEKPVA 178
                                    677445*****************************************************95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.2e-06   0.00044       8      59 ..     225     276 ..     219     280 .. 0.74
   2 ?    4.7   0.0     0.095        34      73     111 ..     265     303 ..     254     332 .. 0.66
   3 !   14.6   0.1   8.3e-05      0.03       8      29 ..     498     519 ..     493     602 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                    ++++G++GtGKT+l++ +++++d++     ++pe++ +++  s+  ++++++e
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYFISI-NGPEIMsKYYGESEQRLREIFEE 276
                                    89*******************98654333.46666666666666666666665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.095
                         AAA_22  73 lsseellealeqalraravielliiDEaqhlr..seealee 111
                                     s+++l+e +e+a +++    ++ iDE++ +   ++e++ e
  gi|118431889|ref|NP_148637.2| 265 ESEQRLREIFEEAKKNAPS--IIFIDEIDAIApkRDEVVGE 303
                                    5667777777777666666..*********97653443333 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 8.3e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++GtGKT+l++ ++ + 
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATES 519
                                    689**************99876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   7.5e-07   0.00027       2      80 ..     225     333 ..     225     353 .. 0.74
   2 !   17.8   0.0   7.8e-06    0.0028       2      44 ..     498     542 ..     498     606 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.5e-07
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    +ll G+pG+GK+ la+ ++++ +  ++ ++ ++++++++g+ +q+++                               +v
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADayFISINGPEIMSKYYGESEQRLReifeeakknapsiifideidaiapkrdeVVGEV 304
                                    6789***************99999778899**********9888888777777777777778877777777554422335 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvildatnl 80 
                                    + r+ ++l +l +   ++g+ +++ atn+
  gi|118431889|ref|NP_148637.2| 305 ERRVVAQLLALMDGLEARGNVIVIAATNR 333
                                    55566666666654444444455566654 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.8e-06
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqs 44 
                                    vll G+pG+GK+ la+ ++ + g  ++ ++ ++++++ +g+ ++ 
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGanFIAVRGPEILSKWVGESERA 542
                                    7899*******************9999999999777777754443 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   2.2e-05     0.008       2     135 ..     225     342 ..     224     344 .. 0.65
   2 !   19.1   0.1   2.9e-06     0.001       1     134 [.     497     615 ..     497     618 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                    +lL GppGtgK+ la+ +a    + +  +++++ +++     +          +  ++ ++a+   ++i+++DE++ +  
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYFISINGPEIMSKYYGESE---------QRLREIFEEAKknAPSIIFIDEIDAIAp 295
                                    89*****************999998888888887765433333.........3335666666667788999999998762 PP

                                    ..HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  79 ..sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                      +ev++++ +    + l l++g e  +         + via++n+++     ++palr
  gi|118431889|ref|NP_148637.2| 296 krDEVVGEVERRVVAQLLALMDGLEARGN--------VIVIAATNRPN----AIDPALR 342
                                    22345555544444444444444444322........77888887777....7777776 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.9e-06
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae 78 
                                    +vlL GppGtgK+ la+ +a   ++++  v +++      ++ ++    g+ ++   ++  +ar   ++++++DE++ + 
  gi|118431889|ref|NP_148637.2| 497 GVLLFGPPGTGKTLLAKAVATESGANFIAVRGPE------ILSKWV---GESERAIREIFAKARqhAPAVVFFDEIDAIA 567
                                    59****************************9998......666666...3333333444444554789999999999999 PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                    +     + +   er ++  ++ ++++  +d  l ++ via++n++d     ++pal
  gi|118431889|ref|NP_148637.2| 568 PVRGTDVGTRVTERIVS--QLLTEIDGVSD--LHDVVVIAATNRPD----MVDPAL 615
                                    88877787777777777..44444444343..44588999999888....455555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       7.8   2.8e+03     111     184 ..      38      57 ..      27      75 .. 0.62
   2 ?   -3.1   0.2       9.7   3.5e+03     160     180 ..     123     143 ..      85     182 .. 0.62
   3 !   18.4   0.0   2.8e-06   0.00099      51      97 ..     223     267 ..     215     291 .. 0.87
   4 !   17.8   0.0   4.3e-06    0.0015      51     102 ..     496     546 ..     489     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.8
                                    XXX-S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT--TT-EEEEETTT- CS
                          TIP49 111 ikeekevleGevveleveeaenplskekkikevkitlktakeekklklgskiaeellkekvkegDviviekesG 184
                                    i                                                        +  v+ gDv+ ie ++ 
  gi|118431889|ref|NP_148637.2|  38 IMK------------------------------------------------------ELGVEPGDVVEIEGKKK 57 
                                    222......................................................23566677776665544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.7
                                    HHHHHHHHHHT--TT-EEEEE CS
                          TIP49 160 skiaeellkekvkegDvivie 180
                                      + ++l+   ++egDv+v+ 
  gi|118431889|ref|NP_148637.2| 123 RYVKKKLQGVPITEGDVVVVP 143
                                    344555555566666666554 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 2.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                    +++Ll Gp+gtGkt la a+++e   d  f++++g e+ s     +e
  gi|118431889|ref|NP_148637.2| 223 KGILLYGPPGTGKTLLAKAVANEA--DAYFISINGPEIMSKYYGESE 267
                                    89********************95..699*********998766655 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 4.3e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqa 102
                                    r+vLl Gp+gtGkt la a++ e g    f+a+ g e+ s  v  +e ++ + 
  gi|118431889|ref|NP_148637.2| 496 RGVLLFGPPGTGKTLLAKAVATESG--ANFIAVRGPEILSKWVGESErAIREI 546
                                    89********************988..78***********9998888344444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   8.6e-07   0.00031       5      77 ..     225     294 ..     222     332 .. 0.78
   2 !   14.4   0.0   8.4e-05      0.03       5      76 ..     498     566 ..     495     604 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 8.6e-07
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp 77 
                                    +++ G+  +GKT l+k +++e       ++ in  +   k + ++e+ l++i+e++k++  +++f+DEi  + 
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEAD---AYFISINGPEIMSKYYGESEQRLREIFEEAKKNAPSIIFIDEIDAIA 294
                                    7899**************98888...89999999998888888777666666666666799********9884 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.4e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT l+k ++ e+     +++ +   +   k   ++e+ +++i++k++++   ++f+DEi  +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESG---ANFIAVRGPEILSKWVGESERAIREIFAKARQHAPAVVFFDEIDAI 566
                                    6899***************9999...999999999998888888777777777776667999*******877 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 !   10.2   0.0    0.0016      0.58      19      44 ..     421     446 ..     413     447 .. 0.79
   2 !   22.4   0.0   2.6e-07   9.3e-05      22      58 ..     683     719 ..     670     721 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                         Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                    ip + l +  vt++Dflkal++  p+
  gi|118431889|ref|NP_148637.2| 421 IPVEVLEKMVVTMEDFLKALREITPS 446
                                    6655566669***********99887 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 2.6e-07
                         Vps4_C  22 dkllePpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                    +++ + +v++++f+ alkk++p+V+++ +e ++++ +
  gi|118431889|ref|NP_148637.2| 683 EDINAAEVSMRHFEVALKKVKPSVTPQMVEYYKRWLE 719
                                    6677889****************************76 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.1e-05     0.011      47      71 ..     222     246 ..     214     289 .. 0.92
   2 !   15.0   0.0   4.3e-05     0.015      48      71 ..     496     519 ..     488     534 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                     ++i+l Gp+G+GK+ la a++ ea
  gi|118431889|ref|NP_148637.2| 222 PKGILLYGPPGTGKTLLAKAVANEA 246
                                    5789*****************9987 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.3e-05
                      IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                     +++l+Gp+G+GK+ la a+++e 
  gi|118431889|ref|NP_148637.2| 496 RGVLLFGPPGTGKTLLAKAVATES 519
                                    5799****************9886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.3e-05     0.012       1      36 [.     225     281 ..     225     335 .. 0.60
   2 !   12.9   0.0   0.00033      0.12       1      26 [.     498     521 ..     498     605 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakeng 36 
                                    Ill G+pG+GKt lak+++++  ++                     +++ + ak+n 
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEAdAYfisingpeimskyygeseqrLREIFEEAKKNA 281
                                    99****************999877788777776666666666555333333333333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00033
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgv 26 
                                    +ll G+pG+GKt lak+++ +   g 
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATES--GA 521
                                    799***************8775..22 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.4e-06     0.003       5      77 ..     225     293 ..     222     339 .. 0.83
   2 !   10.3   0.0    0.0012      0.41       5      35 ..     498     521 ..     495     575 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.4e-06
                         AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                    il+yGp+g+GKT lak    + ++ fi +++   ++  + +   es + +++ ++e +++ +  ++++iD id +
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVanEADAYFISING--PEIMSKYYG--ESEQRLREIFEEAKKNAP--SIIFIDEIDAI 293
                                    89****************9999999999998..333333333..477888888888877777..89999999987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                         AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGl 35 
                                    +l++Gp+g+GKT lak          te G+
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAV-------ATESGA 521
                                    79*************988.......444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   0.00011     0.038       2      48 ..     225     276 ..     224     314 .. 0.78
   2 !   13.4   0.0    0.0002     0.071       2      37 ..     498     534 ..     497     568 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00011
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileeklakgedalpw 48 
                                    i + G+++tGKT l++a a++     +++  pE++ +++ e  ++ +++ ++
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEadayFISINgPEIMSKYYGESEQRLREIFEE 276
                                    7899***************765543444448888888887776666655554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.0002
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareilee 37 
                                    + ++G+++tGKT l++a a + g + ++  + eil++
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATEsGANFIAVRGPEILSK 534
                                    6799***************655444443333333322 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00011     0.041      25      42 ..     225     242 ..     222     245 .. 0.90
   2 !   13.0   0.1   0.00014     0.049      25      43 ..     498     516 ..     494     518 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKt+lak++
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAV 242
                                    89*************987 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00014
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+lak+++
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVA 516
                                    79*************9875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00023     0.083      23      62 ..     223     259 ..     212     340 .. 0.68
   2 !   10.1   0.0    0.0013      0.48      23      52 ..     496     522 ..     481     540 .. 0.81
   3 ?   -1.2   0.0       4.1   1.5e+03      95     143 ..     556     607 ..     544     618 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00023
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaip 62 
                                      +l+ G  GtGK+lla+a+ ++   +++ f+++n  +i 
  gi|118431889|ref|NP_148637.2| 223 KGILLYGPPGTGKTLLAKAVANE---ADAYFISINGPEIM 259
                                    569***************99765...56899999977653 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0013
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekp 52 
                                      vl+ G  GtGK+lla+a+ ++s    ++
  gi|118431889|ref|NP_148637.2| 496 RGVLLFGPPGTGKTLLAKAVATESG---AN 522
                                    579****************987765...44 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.1
                                    SEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSS...SEEE--EEEEEEESS CS
                Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegevervGss...keikvdvriiaatne 143
                                     ++f+Dei  + +   + + + + e+ v+++ ++    +   dv +iaatn+
  gi|118431889|ref|NP_148637.2| 556 AVVFFDEIDAIAPVRGTDVGTRVTERIVSQLLTEidgVSDLHDVVVIAATNR 607
                                    5678888888877766666666666666665543111344568889999987 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0011      0.41      14      37 ..     217     240 ..     192     246 .. 0.87
   2 ?    2.3   0.1      0.25        88     108     155 ..     267     320 ..     250     336 .. 0.70
   3 !   11.1   0.0    0.0005      0.18      13      40 ..     489     516 ..     463     526 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                         ATPase  14 gGipegrvvlitGepGtGKtifal 37 
                                     Gi   + +l++G pGtGKt++a+
  gi|118431889|ref|NP_148637.2| 217 LGIEPPKGILLYGPPGTGKTLLAK 240
                                    578888899*************97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                         ATPase 108 ieelaeaikeika...krvviDsitglayeekeav...aReilrqlvrvlkklg 155
                                     ++l+e+ +e k    + + iD i+++a + +e v    R+ + ql+  + +l+
  gi|118431889|ref|NP_148637.2| 267 EQRLREIFEEAKKnapSIIFIDEIDAIAPKRDEVVgevERRVVAQLLALMDGLE 320
                                    45566666655544458899*******544444332226888999988887665 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0005
                         ATPase  13 kgGipegrvvlitGepGtGKtifalqFl 40 
                                      Gi   r vl+ G pGtGKt++a+  +
  gi|118431889|ref|NP_148637.2| 489 RMGIRPPRGVLLFGPPGTGKTLLAKAVA 516
                                    579999999**************98755 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.5   5.5e+02      76      95 ..      37      56 ..      27      70 .. 0.82
   2 !   25.0   0.1     3e-08   1.1e-05      73     165 ..      77     168 ..      55     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.5
                           UFD1 76 wmmenlgleegdlveiesvs 95
                                    +m++lg+e gd+veie  +
  gi|118431889|ref|NP_148637.2| 37 DIMKELGVEPGDVVEIEGKK 56
                                   589************99654 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3e-08
                           UFD1  73 lPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvyelkvle 152
                                    +   + +n +++ g+ v ++++s+ +++ vkl p s ++   +  k   +k+L+    +t+gdv+ + +  + ++l+v++
  gi|118431889|ref|NP_148637.2|  77 MDGILRRNADVNIGEKVIVRKTSVRTATKVKLAPVSYTMTVDEGFKRYVKKKLQGV-PITEGDVVVVPVIGQAVQLQVVD 155
                                    44557889999*************************99999999*********985.68********************* PP

                           UFD1 153 vkpesavsiietd 165
                                     +p+ av + e  
  gi|118431889|ref|NP_148637.2| 156 ARPKGAVIVSEET 168
                                    *******998754 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00017     0.063       1      26 [.     225     250 ..     225     296 .. 0.72
   2 !   11.1   0.0    0.0011      0.39       1      26 [.     498     523 ..     498     568 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00017
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    i+lyGp+g+GK++lak +a++    +
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYF 250
                                    789**************777655443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    ++l+Gp+g+GK++lak +a++   ++
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGANF 523
                                    679**************888766554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1     7e-05     0.025      13     122 ..     215     328 ..     211     338 .. 0.63
   2 ?    3.9   0.0      0.12        43      23      43 ..     498     518 ..     488     526 .. 0.85
   3 ?    2.0   0.0      0.45   1.6e+02      99     207 ..     536     645 ..     520     667 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7e-05
                       ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal.......... 82 
                                    + l  ep + +++YGp g GKt L k ++++ +      +  i+  e+ ++++ e+  e++ ++ +e+a+          
  gi|118431889|ref|NP_148637.2| 215 KRLGIEPPKGILLYGPPGTGKTLLAKAVANEADA----YFISINGPEIMSKYYGES--EQRLREIFEEAKknapsiifid 288
                                    566678888899************9999999833....222345555666666666..3333333333334554455666 PP

                       ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                     i+    + +e++ e  + v +++ +l++ ++ +g  i+i
  gi|118431889|ref|NP_148637.2| 289 EIDAIAPKRDEVVGEVERRVVAQLLALMDGLEARGNVIVI 328
                                    4444444455566677777777777777777777776655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                       ATPase_2  23 yfiYGpegsGKtaLlkeiien 43 
                                    ++++Gp g GKt L k ++++
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATE 518
                                    689***********9998876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.45
                       ATPase_2  99 sklvfkaielllekikkkgkkiiiiiDelqkli.....dlglngaellvkeLlnliesltkekhlcvviclsSeglfier 173
                                      + ++ai ++++k ++ +   ++++De+  +      d+g +  e  v++Ll+ i+   ++ h +vvi+++    + + 
  gi|118431889|ref|NP_148637.2| 536 VGESERAIREIFAKARQHAP-AVVFFDEIDAIApvrgtDVGTRVTERIVSQLLTEIDG-VSDLHDVVVIAATNRPDMVD- 612
                                    55556666666666665533.78999**999863333366777999999999999998.88899999999987655555. PP

                       ATPase_2 174 vyneselegrhky.ilvddldketalnflkegfke 207
                                         ++ gr +  i+v + d+ + l++l+   ++
  gi|118431889|ref|NP_148637.2| 613 --PALMRPGRLEKmIYVPPPDFSSRLEILRIHTRK 645
                                    ..444555555444555555556666655555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00033      0.12      33      61 ..     222     249 ..     212     299 .. 0.83
   2 !    9.8   0.0    0.0014      0.51      30      56 ..     492     518 ..     484     527 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldkek 61 
                                     k +ll+Gp GtGKt+++k + ++ d   
  gi|118431889|ref|NP_148637.2| 222 PKGILLYGPPGTGKTLLAKAVANEAD-AY 249
                                    5789****************999988.33 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkk 56 
                                    ++  + vll Gp GtGKt+++k + ++
  gi|118431889|ref|NP_148637.2| 492 IRPPRGVLLFGPPGTGKTLLAKAVATE 518
                                    5556789*************9986654 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   0.00077      0.28      19      51 ..     222     256 ..     194     271 .. 0.74
   2 ?   -2.0   0.0       9.7   3.5e+03      85     104 ..     465     484 ..     458     495 .. 0.66
   3 !   10.1   0.1    0.0017      0.61      21      51 ..     497     529 ..     466     532 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00077
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                     + ilL+G+ G+GKT l++++a++ +    +++ P
  gi|118431889|ref|NP_148637.2| 222 PKGILLYGPPGTGKTLLAKAVANEADAYfiSINGP 256
                                    3459******************9987655556655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9.7
                                    TCCCCSTSCEEEEETGGGGC CS
                           TsaE  85 leeyleeeavvlvEWpekle 104
                                      e +++e   +vEWp k  
  gi|118431889|ref|NP_148637.2| 465 GLEDVKQELREVVEWPLKHP 484
                                    444444556789***98854 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0017
                                    EEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                     +lL G+ G+GKT l++++a + g +  +v+ P
  gi|118431889|ref|NP_148637.2| 497 GVLLFGPPGTGKTLLAKAVATESGANfiAVRGP 529
                                    399******************999887677665 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     0.002       0.7      23      41 ..     226     244 ..     219     248 .. 0.86
   2 !   11.1   0.1   0.00055       0.2      22      42 ..     498     518 ..     490     526 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                                    EEE--TTSSTTHHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavalav 41 
                                       Gp GtGKt+la a+a 
  gi|118431889|ref|NP_148637.2| 226 LLYGPPGTGKTLLAKAVAN 244
                                    578***********99986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00055
                                    EEEE--TTSSTTHHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalave 42 
                                    v  +Gp GtGKt+la a+a e
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATE 518
                                    6789*************9976 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00066      0.24      52     116 ..     221     290 ..     182     344 .. 0.66
   2 !    8.8   0.0    0.0022      0.79      24      82 ..     457     524 ..     441     564 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                         DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrl..ievekedl....kelpklvellrerperfilfvDDL 116
                                    p + +LL+G  GtGK  l ka+ ne+ +  + +   e+  +      + l +++e+ + ++   i+f+D +
  gi|118431889|ref|NP_148637.2| 221 PPKGILLYGPPGTGKTLLAKAVANEADAYFISIngPEIMSKYYgeseQRLREIFEEAK-KNAPSIIFIDEI 290
                                    56789********************998875542235555444100033444444433.334467777765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                         DUF815  24 evklddLvgidkqkealvente.......qfleg..lpannvLLwGarGtGKSslvkallneyaeegL 82 
                                    ev+++d+ g+++ k++l e +e       +f +   +p + vLL+G  GtGK  l ka+ +e  ++ +
  gi|118431889|ref|NP_148637.2| 457 EVRWSDIGGLEDVKQELREVVEwplkhpeAFTRMgiRPPRGVLLFGPPGTGKTLLAKAVATESGANFI 524
                                    56666666666666666555441111111333211256688******************999877764 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0016      0.56       7      67 ..     218     276 ..     216     333 .. 0.76
   2 !    9.5   0.0    0.0037       1.3       8      62 ..     492     544 ..     488     601 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0016
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                     +++ + + + G+ G+GK+ L+k++a++ +     i ++g ++ ++   +++++++ +++e
  gi|118431889|ref|NP_148637.2| 218 GIEPPKGILLYGPPGTGKTLLAKAVANEADA--YFISINGPEIMSKYYGESEQRLREIFEE 276
                                    6777788899****************99875..4555577777776666666666666666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0037
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeig 62 
                                    +++ + v ++G+ G+GK+ L+k++a ++   +  i ++g ++ ++   ++++ i+
  gi|118431889|ref|NP_148637.2| 492 IRPPRGVLLFGPPGTGKTLLAKAVATESG--ANFIAVRGPEILSKWVGESERAIR 544
                                    56667789****************99875..455555666665555555555555 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 !   10.8   0.0   0.00052      0.19     117     141 ..     225     249 ..     219     254 .. 0.88
   2 !    7.7   0.0    0.0047       1.7     117     136 ..     498     517 ..     490     522 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                    +++yGp+ tGkt la+a a+  + y
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAY 249
                                    89****************9977655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                      Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                    v+++Gp+ tGkt la+a a+
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVAT 517
                                    8899*************987 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0013      0.47      14      49 ..     220     253 ..     211     268 .. 0.85
   2 !    8.1   0.0    0.0041       1.5      16      49 ..     495     526 ..     485     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                    e Pk ill G pG GK+ la+++++e   +  ++ +
  gi|118431889|ref|NP_148637.2| 220 EPPKGILLYGPPGTGKTLLAKAVANEA--DAYFISI 253
                                    6799********************998..4555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0041
                     Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                    P  +ll G pG GK+ la+++++e   + n++ +
  gi|118431889|ref|NP_148637.2| 495 PRGVLLFGPPGTGKTLLAKAVATES--GANFIAV 526
                                    77899*******************8..7777766 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0017      0.63       2      31 ..     225     254 ..     224     334 .. 0.78
   2 !    8.7   0.0    0.0042       1.5       2      30 ..     498     526 ..     497     608 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    +ll g PG++ktll+ka+a+  d+ f  i 
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYFISIN 254
                                    7999*****************999987775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0042
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    vll g PG++ktll+ka+a+  +++f  +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGANFIAV 526
                                    7999****************999998766 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0038       1.4       3      24 ..     225     246 ..     223     249 .. 0.89
   2 ?   -0.4   0.0       2.7   9.6e+02      62     129 ..     263     332 ..     257     353 .. 0.67
   3 !    7.9   0.1    0.0073       2.6       3      23 ..     498     518 ..     496     522 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0038
                                    EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                    ++l G++G GKT L++ +a ++
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEA 246
                                    7899************999875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.7
                                    CTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHCTTTTT--EEEEEEEC CS
                          NACHT  62 lpepaapvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselirkkllpeasllltvrp 129
                                    + e++++ +e++++  +++ ++ + +D +D ++ + ++   + +++v   L  l+ +   +++ +++++++
  gi|118431889|ref|NP_148637.2| 263 YGESEQRLREIFEEAKKNAPSIIF-IDEIDAIAPKRDEvvgEVERRVVAQLLALMDGLEARGNVIVIAATN 332
                                    566677777766666666667666.5999999988888888445555555557888866666666665544 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0073
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    v+l G++G GKT L++ +a++
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATE 518
                                    7899************99976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00026     0.093       4      63 ..     225     277 ..     222     302 .. 0.70
   2 ?    6.0   0.0     0.017         6       6      25 ..     500     519 ..     496     551 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkea 63 
                                    +l  G +GtGKt+++ ++++e+        a ++s N+p+++ +++ + +++  ++ ++ea
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEA-------DAYFISINGPEIMsKYYGESEQRL-REIFEEA 277
                                    6789****************99.......788888998887635555554444.4443333 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                        DUF2075   6 VtGvaGtGKtvvllnllael 25 
                                      G +GtGKt+++ ++++e 
  gi|118431889|ref|NP_148637.2| 500 LFGPPGTGKTLLAKAVATES 519
                                    5699*********9999886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.2    0.0042       1.5      36      52 ..     225     241 ..     220     246 .. 0.87
   2 ?    2.4   0.1      0.29     1e+02     128     177 ..     268     317 ..     240     334 .. 0.73
   3 !   10.5   1.0   0.00089      0.32      36     147 ..     498     601 ..     477     603 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                         AAA_25  36 allaGapgtGKttlald 52 
                                    +ll+G+pgtGKt la  
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKA 241
                                    69***********9965 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.29
                         AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                    + ++++ +++++ + +  + iD ++++ +   +   +v +++v++l  + +
  gi|118431889|ref|NP_148637.2| 268 QRLREIFEEAKK-NAPSIIFIDEIDAIAPKRDEVVGEVeRRVVAQLLALMD 317
                                    556788899999.77************999555555555888888877765 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00089
                         AAA_25  36 allaGapgtGKttlaldlalavatGkpwlgpvapeqgkVly.vsaEdsedelrrRlravgealrddarllvldlagvesl 114
                                    +ll+G+pgtGKt la   a+a+ +G ++     ++    l  +++E  +  +r+ ++++++++  +a +++  ++    +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAK--AVATESGANFIA---VRGPEILSkWVGESER-AIREIFAKARQHA--PAVVFFDEIDA---I 566
                                    689*********9875..445557777744...3444444325556666.7888888888887..67777777633...4 PP

                         AAA_25 115 pLfakdrggtl.ltadvdaleaaieeveg.vrlvv 147
                                      +  ++ gt+ +++ v +l  +i+ v +  ++vv
  gi|118431889|ref|NP_148637.2| 567 APVRGTDVGTRvTERIVSQLLTEIDGVSDlHDVVV 601
                                    44444555666345557777777777777444555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0063       2.3      22      41 ..     226     245 ..     216     255 .. 0.85
   2 !    7.5   0.1    0.0087       3.1      21      40 ..     498     517 ..     485     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0063
                         AAA_30  22 vltGpAGtGKttalkalrea 41 
                                    +l Gp+GtGKt + ka+++ 
  gi|118431889|ref|NP_148637.2| 226 LLYGPPGTGKTLLAKAVANE 245
                                    688***********999765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0087
                         AAA_30  21 avltGpAGtGKttalkalre 40 
                                    ++l Gp+GtGKt + ka++ 
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVAT 517
                                    6789*********9999864 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.014         5      11      31 ..     223     243 ..     219     254 .. 0.82
   2 ?   -0.3   0.0       3.3   1.2e+03      97     133 ..     276     313 ..     258     318 .. 0.70
   3 ?    7.5   0.0     0.013       4.8      12      30 ..     497     515 ..     490     549 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                         AAA_19  11 kvllvtaGpGtGKTrvlkhiv 31 
                                    k +l+ ++pGtGKT + k++ 
  gi|118431889|ref|NP_148637.2| 223 KGILLYGPPGTGKTLLAKAVA 243
                                    56899*********9877765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.3
                         AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkallgek.kkll 133
                                    e k ++  ++++DE+  + +   +++ ++  +  ++ll
  gi|118431889|ref|NP_148637.2| 276 EAKKNAPSIIFIDEIDAIAPKRDEVVGEVERRVvAQLL 313
                                    333335569*******9999988888888765555555 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.013
                         AAA_19  12 vllvtaGpGtGKTrvlkhi 30 
                                     +l+ ++pGtGKT + k++
  gi|118431889|ref|NP_148637.2| 497 GVLLFGPPGTGKTLLAKAV 515
                                    5899*********877665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0025      0.91      23      44 ..     225     246 ..     212     251 .. 0.84
   2 ?   -2.7   0.0       7.5   2.7e+03     120     148 ..     350     379 ..     347     387 .. 0.80
   3 ?    4.9   0.0     0.036        13      23      43 ..     498     518 ..     494     527 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0025
                                    EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                    + l+G +G GKt lak + n+ 
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEA 246
                                    789***************9985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                                    ....HHHHCHTTSEEE.EEESBCCCCCCS- CS
                         NB-ARC 120 kigvvlparenrlrvl.lTTRdeevanavs 148
                                    +i v+lp+++ rl++l + TR + +a+ + 
  gi|118431889|ref|NP_148637.2| 350 EIEVPLPDKHGRLEILqIHTRHMPLAEDMD 379
                                    789999999999999867899998888775 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.036
                                    EEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                    v l G +G GKt lak +  +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATE 518
                                    6689************99876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0     0.006       2.1      20      41 ..     225     246 ..     210     284 .. 0.78
   2 ?    7.0   0.0     0.013       4.5      20      40 ..     498     518 ..     481     556 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.006
                         AAA_11  20 tliqGPPGtgKTktivellsql 41 
                                     l+ GPPGtgKT    ++ +++
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEA 246
                                    5899********7766666655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                         AAA_11  20 tliqGPPGtgKTktivellsq 40 
                                    +l+ GPPGtgKT    ++  +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATE 518
                                    6899********666555554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0083         3       1      26 [.     228     253 ..     228     305 .. 0.74
   2 ?    6.5   0.0      0.03        11       1      24 [.     501     524 ..     501     553 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0083
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                    +G+PG GK+ +++ ++ + +  ++s 
  gi|118431889|ref|NP_148637.2| 228 YGPPGTGKTLLAKAVANEADAYFISI 253
                                    7**************99987666654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.03
                                    EE-TTSSHHHHHHHHHHHHTEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                    +G+PG GK+ +++ ++ + g  ++
  gi|118431889|ref|NP_148637.2| 501 FGPPGTGKTLLAKAVATESGANFI 524
                                    6***********999998876655 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     0.034        12       2      25 ..     225     248 ..     224     258 .. 0.82
   2 ?    1.0   0.1      0.99   3.6e+02      81     107 ..     266     293 ..     259     316 .. 0.73
   3 ?    4.7   0.0      0.07        25       2      23 ..     498     519 ..     497     550 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.034
                                    EEEE--TTSSHHHHHHHHHHHH.. CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                    +++ GppG+GKt l k v+++ + 
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADA 248
                                    6788************99998765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.99
                                    HHHHHHHHHHHHH.HHH-EEEE---STT CS
                       NTPase_1  81 feelalealrkal.seadviviDEiGkm 107
                                     e+   e++++a  + + +i iDEi  +
  gi|118431889|ref|NP_148637.2| 266 SEQRLREIFEEAKkNAPSIIFIDEIDAI 293
                                    567777888888745666******9665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.07
                                    EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                    v++ GppG+GKt l k v+ + 
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATES 519
                                    6788********9999998765 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 ?    6.0   0.0     0.033        12      24      47 ..     225     248 ..     220     299 .. 0.62
   2 ?    7.6   0.0     0.011       3.9      24      48 ..     498     522 ..     493     573 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.033
                                    EEEEEETT--HHHHHHCC--TTS- CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                    ++l G++G+gk+l A++ ++++  
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADA 248
                                    799*************99987543 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                                    EEEEEETT--HHHHHHCC--TTS-E CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                    v+l G++G+gk+l A++ + +sg +
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGAN 522
                                    9****************99988874 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     0.003       1.1      37     145 ..     225     338 ..     220     383 .. 0.59
   2 ?    3.2   0.0      0.19        66      37      61 ..     498     522 ..     493     534 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.003
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-H.. CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagke.. 113
                                    +++yg+ G Gkt L ka++ne+ + +       +++ e +++     +++  e f e  +++  ++ iD+i  +a k   
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYFI-----SINGPEIMSKYYGESEQRLREIFEEAKKNApSIIFIDEIDAIAPKRde 299
                                    79****************998866543.....455555555555555555555555555533156667777777766421 PP

                                    .......HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-S CS
                       Bac_DnaA 114 .......ktqeelfhtfnalleegkqvvlssDrsPkele 145
                                           ++  +l+ +++ l   g+ +v+++   P++++
  gi|118431889|ref|NP_148637.2| 300 vvgeverRVVAQLLALMDGLEARGNVIVIAATNRPNAID 338
                                    111111122334444555555556666666666666654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                                    EEEE-SSSSSHHHHHHHHHHHHHHH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlen 61 
                                    ++++g+ G Gkt L ka++ e  +n
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVATESGAN 522
                                    799***************9887666 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.21        76       4      30 ..     224     250 ..     222     257 .. 0.86
   2 ?    3.4   0.0      0.15        55      75      96 ..     259     283 ..     253     297 .. 0.78
   3 ?    3.1   0.0      0.18        65       3      30 ..     496     523 ..     494     531 .. 0.87
   4 ?    0.0   0.0       1.6   5.9e+02      77     107 ..     534     568 ..     527     578 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                                    EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                     + l gp g+Gk  l ka+ +e   +f
  gi|118431889|ref|NP_148637.2| 224 GILLYGPPGTGKTLLAKAVANEADAYF 250
                                    6899**************999988877 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.15
                                    TTEEEEEEHHHHHHHHHTTSE...E CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgki...v 96 
                                     +++yg+s +  +e++e++k+    
  gi|118431889|ref|NP_148637.2| 259 MSKYYGESEQRLREIFEEAKKnapS 283
                                    679***************9985552 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.18
                                    SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                    r v l gp g+Gk  l ka+ +e   +f
  gi|118431889|ref|NP_148637.2| 496 RGVLLFGPPGTGKTLLAKAVATESGANF 523
                                    6789***************999988777 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.6
                                    EEEEEEHHHHHHHHHTTSE.....EEEE--CHHHHH CS
                  Guanylate_kin  77 nlygtsveaieevlekgki.....viLDvdiqavkq 107
                                    +  g+s  ai+e+++k+++     v+ D +i+a++ 
  gi|118431889|ref|NP_148637.2| 534 KWVGESERAIREIFAKARQhapavVFFD-EIDAIAP 568
                                    56799***********998777533333.3555555 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.067        24       5      31 ..     226     252 ..     223     255 .. 0.87
   2 ?    7.6   0.0    0.0063       2.2       5      32 ..     499     526 ..     496     542 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.067
                            IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                    l++G+ +tGKt  a ++a+e  a  i+
  gi|118431889|ref|NP_148637.2| 226 LLYGPPGTGKTLLAKAVANEADAYFIS 252
                                    89****************998877666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0063
                            IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                    l+fG+ +tGKt  a ++a e ga  i++
  gi|118431889|ref|NP_148637.2| 499 LLFGPPGTGKTLLAKAVATESGANFIAV 526
                                    89********************999875 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0079       2.8      55      81 ..     215     241 ..     187     334 .. 0.87
   2 ?    4.5   0.0     0.038        14      59      79 ..     492     512 ..     469     518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0079
                    AFG1_ATPase  55 krksvepvrglYlwGgvGrGKtylmdl 81 
                                    kr   ep++g+ l+G+ G GKt l   
  gi|118431889|ref|NP_148637.2| 215 KRLGIEPPKGILLYGPPGTGKTLLAKA 241
                                    345679****************99655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                    AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                     +p+rg+ l G+ G GKt l 
  gi|118431889|ref|NP_148637.2| 492 IRPPRGVLLFGPPGTGKTLLA 512
                                    579***************985 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.039        14       3      27 ..     227     251 ..     225     255 .. 0.88
   2 ?    5.4   0.0     0.037        13       5      27 ..     502     524 ..     498     527 .. 0.90
   3 ?   -1.4   0.0       4.6   1.7e+03      25      86 ..     665     729 ..     654     735 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.039
                                    EE-STTSSHHHHHHHHHHHHT-EEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                    + GP g+GK  +a+a+a++ ++ ++
  gi|118431889|ref|NP_148637.2| 227 LYGPPGTGKTLLAKAVANEADAYFI 251
                                    67****************9998877 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.037
                                    -STTSSHHHHHHHHHHHHT-EEE CS
                 Cytidylate_kin   5 GPagsGKssvaralaeklglkyl 27 
                                    GP g+GK  +a+a+a++ g++++
  gi|118431889|ref|NP_148637.2| 502 GPPGTGKTLLAKAVATESGANFI 524
                                    9****************999987 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.6
                                    EEEEHHHHHHHHHHHHHHTT--TT-HH..HHHHHHHT--EEEEEEEEEETTEE-TTG.GGSHHHH CS
                 Cytidylate_kin  25 kyldtgalYRalalaalrrkvdlldea..alvelakevelsfeaekvllngedveee.lrsdeve 86 
                                    +  d  al R  +laalr++++ ++++  +++  +k+v+ s++ + v + ++ +e+   r++ev+
  gi|118431889|ref|NP_148637.2| 665 TGADIEALVREASLAALREDINAAEVSmrHFEVALKKVKPSVTPQMVEYYKRWLETVkQRQEEVK 729
                                    55566678899999999998887665411455566777777777755444444333225555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.13        45      48      79 ..     225     255 ..     214     290 .. 0.74
   2 ?    6.0   0.0     0.028        10      45      82 ..     495     532 ..     470     570 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                    +L+ GP+G gk+   k ++ e    ++  +n+
  gi|118431889|ref|NP_148637.2| 225 ILLYGPPGTGKTLLAKAVANEADAYFI-SING 255
                                    6789********999999988765444.3444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.028
                          Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklrewlnpvsl 82 
                                     r +L+ GP+G gk+   k ++ e g +++    p  l
  gi|118431889|ref|NP_148637.2| 495 PRGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEIL 532
                                    4557899*****************99998877766554 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 ?    2.9   0.0      0.22        78       4      71 ..     228     290 ..     225     295 .. 0.64
   2 ?    7.2   0.0     0.011       3.8       4      71 ..     501     563 ..     498     568 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pG GK+ l + ++++   + + +++   e+ ++   +++++  + ++++ +++       i+++DE+
  gi|118431889|ref|NP_148637.2| 228 YGPPGTGKTLLAKAVANEAdaYFI-SING-PEIMSKYYGESEQRLREIFEEAKKNA-----PSIIFIDEI 290
                                    588**************9884444.4433.36666655555555555555444443.....358888886 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.011
                Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pG GK+ l + ++ +s  ++ ++r   e+l++++ ++++   + + ++ +++ +     ++++DE+
  gi|118431889|ref|NP_148637.2| 501 FGPPGTGKTLLAKAVATESgANFIAVRG-PEILSKWVGESERAIREIFAKARQHAPA-----VVFFDEI 563
                                    588*************999*88888888.9*******99999989999988888764.....8999997 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     0.077        28      21      39 ..     222     239 ..     213     244 .. 0.77
   2 ?    5.5   0.0      0.04        14      21      42 ..     495     515 ..     474     517 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.077
                         AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                    +kg +ll Gp G+GK+ l 
  gi|118431889|ref|NP_148637.2| 222 PKG-ILLYGPPGTGKTLLA 239
                                    356.9**********8765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.04
                         AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                    ++g +ll Gp G+GK+ l  A+
  gi|118431889|ref|NP_148637.2| 495 PRG-VLLFGPPGTGKTLLAKAV 515
                                    355.9**********8776555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.03        11       2      26 ..     223     247 ..     222     252 .. 0.88
   2 ?    4.2   0.0     0.095        34       4      23 ..     498     517 ..     495     520 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkgeel 26 
                                    k ill G+ g+GKt L++a+ +e+ 
  gi|118431889|ref|NP_148637.2| 223 KGILLYGPPGTGKTLLAKAVANEAD 247
                                    6699****************99875 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.095
                      PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                    +ll+G+ g+GKt L++a+  
  gi|118431889|ref|NP_148637.2| 498 VLLFGPPGTGKTLLAKAVAT 517
                                    89**************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.85u 0.29s 00:00:01.13 Elapsed: 00:00:00.46
# Mc/sec: 4845.97
//
Query:       gi|118431890|ref|NP_148638.2|  [L=90]
Description: elongation factor 1-beta [Aeropyrum pernix K1]
Scores for complete 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   0.7    2.1e-18   66.3   0.7    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 !   66.3   0.7   1.2e-22   2.1e-18       2      90 .]       6      89 ..       5      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.2e-22
                                   EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEES.SS-GGGGHHHHHHTTS-S.....SEE CS
                        EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvie.ddkvstdeleekieeiegeledlVqs 81
                                   vv++v P+d+  d + l++++ks kl+  +++  a  +epiafGlk+L++ ++++ d++++t+e+e+ +++ieg     Vq+
  gi|118431890|ref|NP_148638.2|  6 VVVKVYPDDVSIDPKTLAERIKS-KLPSgYEVL-AEGEEPIAFGLKALKLVIAMNeDTEGGTEEVEQLLKNIEG-----VQE 80
                                   89*********************.99999***9.69******************88999***************.....*** PP

                                   EEEEEEEE- CS
                        EF1_GNE 82 veivsfnkl 90
                                   ve+++++++
  gi|118431890|ref|NP_148638.2| 81 VEVENVSRM 89
                                   ******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 687.44
//
Query:       gi|118431891|ref|YP_874949.1|  [L=68]
Description: hypothetical protein APE_2480a [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-10   39.6  12.9    1.3e-07   31.5   7.3    2.3  2  DUF1610          Domain of unknown function (DUF1610)
    8.7e-05   22.1  18.0    0.00063   19.4   2.7    3.0  2  zinc_ribbon_2    zinc-ribbon domain
    0.00067   19.7   2.2    0.00067   19.7   2.2    2.8  2  Zn-ribbon_8      Zinc ribbon domain
     0.0012   18.7  11.5      0.016   15.1   1.2    2.4  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0015   18.5  12.9     0.0085   16.1   1.4    2.3  2  DZR              Double zinc ribbon
     0.0022   17.3  15.9       0.32   10.5   0.5    3.9  4  zf-ribbon_3      zinc-ribbon domain
     0.0024   18.2   2.3     0.0024   18.2   2.3    2.1  2  DUF2072          Zn-ribbon containing protein
     0.0036   17.4   6.8      0.071   13.2   0.2    2.2  2  zf-MYND          MYND finger
     0.0077   16.7   7.6       0.13   12.8   8.0    2.0  2  zf-CHY           CHY zinc finger
  ------ inclusion threshold ------
      0.016   15.2  10.8      0.036   14.1   0.4    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.035   14.2   2.8      0.035   14.2   2.8    2.4  2  Elf1             Transcription elongation factor Elf1 like
      0.039   13.8   2.9      0.039   13.8   2.9    3.2  3  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
      0.049   13.2  12.8        1.7    8.3   0.1    3.9  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.08   13.3  10.6       0.99    9.8   7.2    2.2  2  C1_2             C1 domain
       0.11   10.4   3.2       0.11   10.3   3.2    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
       0.13   12.2  14.9       0.35   10.8   3.3    3.7  3  Nudix_N_2        Nudix N-terminal
       0.13   12.5   0.5       0.13   12.5   0.5    2.7  2  zinc_ribbon_9    zinc-ribbon
       0.14   12.4  19.0       0.24   11.6   0.2    3.6  3  zf-RING_7        C4-type zinc ribbon domain
       0.14   12.2   9.3       0.21   11.6   2.5    2.3  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
       0.15   12.2  10.0      0.049   13.8   3.5    2.1  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.21   11.1  19.0        1.6    8.3   0.2    3.5  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.28   10.8  10.0       0.46   10.2   0.0    3.7  4  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.49   10.4  22.1         10    6.2   0.2    3.5  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.52    9.0  10.0        1.1    8.0   3.0    2.0  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct
       0.53   10.4  13.2         23    5.1  13.2    2.8  1  DUF1272          Protein of unknown function (DUF1272)
       0.56   10.3   0.2       0.56   10.3   0.2    2.7  3  DUF2752          Protein of unknown function (DUF2752)
        0.6    9.9  19.5        1.4    8.7   0.2    4.0  3  Rubredoxin_2     Rubredoxin metal binding domain
       0.67   10.0   9.9          1    9.4   0.6    2.1  2  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.67    9.7  15.9        3.1    7.6   0.4    3.8  4  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.74    9.8  18.5        2.6    8.0   0.5    4.0  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        1.5    8.8  18.8        0.3   11.0   6.8    3.1  2  zf-HIT           HIT zinc finger
          2    8.6  10.7        1.2    9.3   1.9    3.0  3  Ribosomal_L37ae  Ribosomal L37ae protein family
        2.2    8.3  17.8         15    5.6   0.3    4.1  4  zinc_ribbon_4    zinc-ribbon domain
        2.4    8.0  10.3         10    6.1   1.4    3.6  4  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
          3    7.2  15.4         31    4.0   0.1    3.6  3  zf-TFIIB         Transcription factor zinc-finger
        3.4    7.5  13.7        2.2    8.1   3.2    3.6  2  A2L_zn_ribbon    A2L zinc ribbon domain
        4.5    7.3  11.0         20    5.3   0.1    3.8  4  ADK_lid          Adenylate kinase, active site lid
        6.8    6.9  14.9         21    5.3   0.4    3.9  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        7.1    6.8  13.6        3.6    7.8   2.0    2.7  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        7.8    7.1  15.1        5.4    7.6   0.4    3.8  4  zf-H2C2_2        Zinc-finger double domain
        8.3    6.4  18.2         11    6.0   0.6    4.0  4  HalOD2           Halobacterial output domain 2
        9.5    6.5  10.4        1.4    9.1   1.7    2.6  2  zf-B_box         B-box zinc finger


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   7.3     3e-10   1.3e-07       1      24 []      19      42 ..      19      42 .. 0.99
   2 !   11.5   0.3   0.00052      0.22      16      23 ..      57      64 ..      52      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3e-10
                        DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                   CtSCG+   p+  a+ FpCPNCGE
  gi|118431891|ref|YP_874949.1| 19 CTSCGRIVEPGSTATRFPCPNCGE 42
                                   ***********************9 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00052
                        DUF1610 16 vFpCPNCG 23
                                    + CPNCG
  gi|118431891|ref|YP_874949.1| 57 TYTCPNCG 64
                                   578****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 !   19.4   2.7   1.5e-06   0.00063       1      21 [.      18      42 ..      18      43 .. 0.96
   2 ?    7.1   7.5     0.011       4.6       1      21 [.      47      65 ..      47      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.5e-06
                  zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGt 21
                                   +C++CG+ ++++++     Cp+CG+
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVEPGSTAtrfpCPNCGE 42
                                   6***********************7 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                  zinc_ribbon_2  1 fCpnCGaelqdnakF.CpyCGt 21
                                   +C++C ++   +a++ Cp+CG+
  gi|118431891|ref|YP_874949.1| 47 RCSRCRKQ---GATYtCPNCGF 65
                                   69999998...**********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 !   19.7   2.2   1.6e-06   0.00067       3      35 ..      10      44 ..      10      47 .. 0.82
   2 ?    5.4  11.9     0.048        20       6      33 ..      35      64 ..      34      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                    Zn-ribbon_8  3 iYeYr....CeeCghefevlqsisdapltaCPeCgs.e 35
                                   +Y+Y     C++Cg+  e+  ++++ p   CP+Cg+ e
  gi|118431891|ref|YP_874949.1| 10 VYDYVhpprCTSCGRIVEPGSTATRFP---CPNCGEvE 44
                                   699999999*********888766555...****9855 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.048
                    Zn-ribbon_8  6 YrCeeCghefevlqsis..dap.lta.CPeCg 33
                                   + C +Cg e e+++ +   +    t  CP+Cg
  gi|118431891|ref|YP_874949.1| 35 FPCPNCG-EVEIWRCSRcrK-QgATYtCPNCG 64
                                   67*****.***888666633.347778****9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.2   3.8e-05     0.016      30      55 ..      18      43 ..      17      47 .. 0.93
   2 !    8.5   3.1    0.0045       1.9      32      55 ..      49      66 ..      45      67 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-05
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                   +C  Cg+++++  +  +f CpnCg +
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVEPGSTATRFPCPNCGEV 43
                                   6**********9************86 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0045
                 OrfB_Zn_ribbon 32 seCgsknkealsgrtfkCpnCgfe 55
                                   s+C      +++g t++CpnCgf+
  gi|118431891|ref|YP_874949.1| 49 SRC------RKQGATYTCPNCGFT 66
                                   444......346788*******96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.4     2e-05    0.0085      26      49 .]      14      41 ..       3      41 .. 0.84
   2 ?    5.9  10.3      0.03        13       1      35 [.      37      64 ..      37      67 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2e-05
                            DZR 26 aaedrCpsCgekvdpearf....CpeCG 49
                                    ++ rC sCg+ v+p+++     Cp+CG
  gi|118431891|ref|YP_874949.1| 14 VHPPRCTSCGRIVEPGSTAtrfpCPNCG 41
                                   4589*********999887788*****9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.03
                            DZR  1 CpqCgeelppdarfCseCgtklkavaaedrCpsCg 35
                                   Cp+Cge    +   Cs+C+++       ++Cp+Cg
  gi|118431891|ref|YP_874949.1| 37 CPNCGEV---EIWRCSRCRKQGA----TYTCPNCG 64
                                   6777766...5556777777766....67777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1      0.02       8.6       4      17 ..      18      31 ..      18      32 .. 0.82
   2 !   10.2   0.3   0.00089      0.38       5      11 ..      37      43 ..      34      45 .. 0.77
   3 ?   -0.0   0.6       1.5   6.4e+02       4       8 ..      47      51 ..      47      53 .. 0.90
   4 !   10.5   0.5   0.00074      0.32       2       9 ..      57      64 ..      56      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                    zf-ribbon_3  4 rCPnCGaplssddn 17
                                   rC +CG +++++ +
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVEPGST 31
                                   79999998899876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00089
                    zf-ribbon_3  5 CPnCGap 11
                                   CPnCG++
  gi|118431891|ref|YP_874949.1| 37 CPNCGEV 43
                                   8888875 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.5
                    zf-ribbon_3  4 rCPnC 8 
                                   rC++C
  gi|118431891|ref|YP_874949.1| 47 RCSRC 51
                                   7*999 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00074
                    zf-ribbon_3  2 tvrCPnCG 9 
                                   t++CPnCG
  gi|118431891|ref|YP_874949.1| 57 TYTCPNCG 64
                                   78899998 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.3   5.5e-06    0.0024       1      27 [.      16      42 ..      16      46 .. 0.94
   2 ?    1.3   3.3      0.92   3.9e+02       6      27 ..      47      65 ..      44      67 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.5e-06
                        DUF2072  1 PHkCtkCekvfedgskeilkGCpsCGg 27
                                   P +Ct+C+++ e gs+  +  Cp+CG 
  gi|118431891|ref|YP_874949.1| 16 PPRCTSCGRIVEPGSTATRFPCPNCGE 42
                                   779***********************5 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.92
                        DUF2072  6 kCekvfedgskeilkGCpsCGg 27
                                   +C +  ++g++     Cp+CG 
  gi|118431891|ref|YP_874949.1| 47 RCSRCRKQGAT---YTCPNCGF 65
                                   45555566777...78*****6 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   0.00017     0.071       1      23 [.      19      49 ..      19      50 .. 0.82
   2 ?    6.9   3.7     0.016       6.9       1      17 [.      48      64 ..      48      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                                   -TTT--......B-SC.E-TTTS-S..EESS CS
                        zf-MYND  1 CavCgk.....aealk.kCagCksv..fYCs 23
                                   C +Cg+     + a++ +C++C  v  + Cs
  gi|118431891|ref|YP_874949.1| 19 CTSCGRivepgSTATRfPCPNCGEVeiWRCS 49
                                   9*******998888889*****865336676 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.016
                                   -TTT--.B-SCE-TTTS CS
                        zf-MYND  1 CavCgkaealkkCagCk 17
                                   C+ C+k+ a+  C++C 
  gi|118431891|ref|YP_874949.1| 48 CSRCRKQGATYTCPNCG 64
                                   9*****66666*****5 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2     0.012       5.3      56      73 ..      18      41 ..       7      43 .. 0.86
   2 !   12.8   8.0    0.0003      0.13      38      74 ..      31      65 ..      18      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.012
                         zf-CHY 56 lCkkCkk......efaeyfCpiCk 73
                                    C++C++      +++++ Cp+C 
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRivepgsTATRFPCPNCG 41
                                   699**99999998899999****6 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0003
                         zf-CHY 38 evkevlcllCeteqekavlCkkCkkefaeyfCpiCkl 74
                                   +++++ c +C ++  +   C++C+k+ a+y+Cp+C +
  gi|118431891|ref|YP_874949.1| 31 TATRFPCPNCGEV--EIWRCSRCRKQGATYTCPNCGF 65
                                   4567889999997..7889****************75 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   0.4   8.4e-05     0.036      72      96 ..      18      44 ..       3      46 .. 0.80
   2 ?    6.2   4.1     0.023       9.9      71      93 ..      46      64 ..      44      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
                                   EETTTS-EEECHH.H.HHS-TTTSSS- CS
                           HypA 72 rCreCgkefelee.k.alrCpkCgsad 96
                                   rC++Cg+ +e  + + ++ Cp+Cg+ +
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVEPGStAtRFPCPNCGEVE 44
                                   8*********66633689******865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.023
                                   EEETTTS-EEECHHHHHS-TTTS CS
                           HypA 71 vrCreCgkefeleekalrCpkCg 93
                                    rC++C+k++ +    ++Cp+Cg
  gi|118431891|ref|YP_874949.1| 46 WRCSRCRKQGAT----YTCPNCG 64
                                   58*****99985....48****8 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   1.6       4.3   1.9e+03      47      52 ..      18      23 ..       7      32 .. 0.69
   2 ?   14.2   2.8   8.2e-05     0.035      18      52 ..      31      64 ..      23      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.3
                           Elf1 47 sCkvCg 52
                                   +C++Cg
  gi|118431891|ref|YP_874949.1| 18 RCTSCG 23
                                   566666 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 8.2e-05
                           Elf1 18 lptkFdCpfCnheksvevkldkkekiaevsCkvCg 52
                                     t+F Cp+C++ +  +++  +k + a+ +C +Cg
  gi|118431891|ref|YP_874949.1| 31 TATRFPCPNCGEVEIWRCSRCRK-QGATYTCPNCG 64
                                   689**********9999998888.66999*****8 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 ?   13.8   2.9   9.1e-05     0.039       1      23 [.      17      40 ..      17      41 .. 0.86
   2 ?    2.8   2.0      0.25   1.1e+02      20      24 ..      48      52 ..      41      54 .. 0.87
   3 ?    1.7   0.5      0.55   2.4e+02       3       7 ..      60      64 ..      58      67 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.1e-05
                                   -B-SSS--B--SS-S---B.-TTT CS
                     HscB_4_cys  1 PrCWnCGgpgapgrgdefF.CpqC 23
                                   PrC +CG+  +pg  +  F Cp C
  gi|118431891|ref|YP_874949.1| 17 PRCTSCGRIVEPGSTATRFpCPNC 40
                                   9***********98765444**** PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.25
                                   -TTT- CS
                     HscB_4_cys 20 CpqCR 24
                                   C++CR
  gi|118431891|ref|YP_874949.1| 48 CSRCR 52
                                   ****9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.55
                                   -SSS- CS
                     HscB_4_cys  3 CWnCG 7 
                                   C nCG
  gi|118431891|ref|YP_874949.1| 60 CPNCG 64
                                   66777 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.95   4.1e+02       5      13 ..      19      27 ..      18      30 .. 0.81
   2 ?    6.0   0.2      0.02       8.7       2      10 ..      34      42 ..      33      43 .. 0.85
   3 ?    5.2   0.4     0.037        16       3      11 ..      46      54 ..      44      54 .. 0.84
   4 ?    8.3   0.1    0.0039       1.7       2      10 ..      57      65 ..      56      68 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.95
                         zf_UBZ  5 CerCgkeip 13
                                   C  Cg+ ++
  gi|118431891|ref|YP_874949.1| 19 CTSCGRIVE 27
                                   999*99776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                         zf_UBZ  2 tylCerCgk 10
                                    ++C+ Cg+
  gi|118431891|ref|YP_874949.1| 34 RFPCPNCGE 42
                                   69*****97 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.037
                         zf_UBZ  3 ylCerCgke 11
                                   + C+rC k+
  gi|118431891|ref|YP_874949.1| 46 WRCSRCRKQ 54
                                   78****985 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0039
                         zf_UBZ  2 tylCerCgk 10
                                   ty+C+ Cg 
  gi|118431891|ref|YP_874949.1| 57 TYTCPNCGF 65
                                   9******95 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.8     0.097        41      20      38 ..      18      40 ..      12      43 .. 0.78
   2 ?    9.8   7.2    0.0023      0.99      17      41 ..      44      66 ..      30      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.097
                           C1_2 20 nCsaCgrk....idgffYsCseC 38
                                   +C  Cgr     ++ +++ C+ C
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIvepgSTATRFPCPNC 40
                                   69999999766555555999988 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0023
                           C1_2 17 esfnCsaCgrkidgffYsCseCdfs 41
                                   e ++Cs C+++  g  Y+C+ C f+
  gi|118431891|ref|YP_874949.1| 44 EIWRCSRCRKQ--GATYTCPNCGFT 66
                                   5689******9..677******995 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.2   0.00026      0.11     619     662 ..      17      64 ..       2      67 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                       PolC_DP2 619 rkCkkCgk......etlearCeeCgekteeklvCkkceeeveeekcekce 662
                                     +C++Cg+      +++++ C++Cge     ++C++c+++  + +c++c+
  gi|118431891|ref|YP_874949.1|  17 PRCTSCGRivepgsTATRFPCPNCGEVEI--WRCSRCRKQGATYTCPNCG 64 
                                    56777764222221456777888887654..4888888888888888886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.3   0.00081      0.35       3      31 ..      19      43 ..      19      44 .. 0.85
   2 ?   -1.0   0.4       4.1   1.8e+03      25      28 ..      48      51 ..      47      53 .. 0.62
   3 ?    5.5   0.2     0.037        16      24      30 ..      59      65 ..      58      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00081
                                   -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                   C++CG      +++g + +R+ Cp+Cg +
  gi|118431891|ref|YP_874949.1| 19 CTSCGRI----VEPGSTATRFPCPNCGEV 43
                                   8888876....56788***********88 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.1
                                   ETTT CS
                      Nudix_N_2 25 CpaC 28
                                   C++C
  gi|118431891|ref|YP_874949.1| 48 CSRC 51
                                   6666 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.037
                                   EETTTTE CS
                      Nudix_N_2 24 vCpaCgt 30
                                   +Cp+Cg+
  gi|118431891|ref|YP_874949.1| 59 TCPNCGF 65
                                   7999997 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   0.00031      0.13       5      28 ..      19      41 ..      18      44 .. 0.92
   2 ?    3.4   3.8      0.22        96      19      28 ..      54      64 ..      43      67 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00031
                  zinc_ribbon_9  5 ChqCdrfVsvspdedsdvlCPhCg 28
                                   C +C r V++ ++ ++ + CP+Cg
  gi|118431891|ref|YP_874949.1| 19 CTSCGRIVEPGSTATRFP-CPNCG 41
                                   668***************.****8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.22
                  zinc_ribbon_9 19 dsdv.lCPhCg 28
                                   + ++ +CP+Cg
  gi|118431891|ref|YP_874949.1| 54 QGATyTCPNCG 64
                                   344448****7 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 ?   11.6   0.2   0.00057      0.24      24      33 .]      17      26 ..       9      26 .. 0.91
   2 ?    4.5   1.2     0.097        41      25      30 ..      36      41 ..      34      41 .. 0.88
   3 ?    4.1   5.8      0.13        55      18      30 ..      52      64 ..      44      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00057
                                   EE-TTT--EE CS
                      zf-RING_7 24 vtCpeCGRIL 33
                                   ++C +CGRI+
  gi|118431891|ref|YP_874949.1| 17 PRCTSCGRIV 26
                                   79*******7 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.097
                                   E-TTT- CS
                      zf-RING_7 25 tCpeCG 30
                                    Cp+CG
  gi|118431891|ref|YP_874949.1| 36 PCPNCG 41
                                   5****9 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.13
                                   CCSTB-EE-TTT- CS
                      zf-RING_7 18 ragdevvtCpeCG 30
                                   r+++   tCp+CG
  gi|118431891|ref|YP_874949.1| 52 RKQGATYTCPNCG 64
                                   5556678*****9 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.5   0.00049      0.21      18      42 ..      17      42 ..       9      50 .. 0.83
   2 ?    4.4   5.0     0.085        36      20      41 ..      37      64 ..      31      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00049
                       zf-C2HC5 18 pnClnCGkiiCakegls.kpCsfCgs 42
                                   p C++CG i+      +  pC+ Cg+
  gi|118431891|ref|YP_874949.1| 17 PRCTSCGRIVEPGSTATrFPCPNCGE 42
                                   99********776666669*****95 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.085
                       zf-C2HC5 20 ClnCGki......iCakeglskpCsfCg 41
                                   C nCG +       C k+g + +C+ Cg
  gi|118431891|ref|YP_874949.1| 37 CPNCGEVeiwrcsRCRKQGATYTCPNCG 64
                                   999999854444449999999******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 ?   13.8   3.5   0.00011     0.049      10      38 ..      18      49 ..      11      57 .. 0.82
   2 ?    2.1   3.6      0.52   2.2e+02      10      30 ..      47      64 ..      45      66 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                   NOB1_Zn_bind 10 rChaCfkvt...kdmtkkFCpkCGnktLkrva 38
                                   rC++C +++   ++ t+  Cp+CG+  + r++
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVepgSTATRFPCPNCGEVEIWRCS 49
                                   9********6655577777******9999987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.52
                   NOB1_Zn_bind 10 rChaCfkvtkdmtkkFCpkCG 30
                                   rC  C    k+     Cp+CG
  gi|118431891|ref|YP_874949.1| 47 RCSRC---RKQGATYTCPNCG 64
                                   55555...45677778****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 ?    8.3   0.2    0.0037       1.6      21      32 ..      18      29 ..      17      35 .. 0.86
   2 ?    7.9   0.6     0.005       2.1       3       9 ..      37      43 ..      31      45 .. 0.65
   3 ?    3.1  13.4      0.16        69       2      26 ..      36      64 ..      35      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0037
                                   EESSSSBEEEEC CS
                   TF_Zn_Ribbon 21 vCtdCGlVledn 32
                                   +Ct+CG ++e  
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVEPG 29
                                   6********965 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.005
                                   ETTTTCE CS
                   TF_Zn_Ribbon  3 CPnCgst 9 
                                   CPnCg  
  gi|118431891|ref|YP_874949.1| 37 CPNCGEV 43
                                   6666654 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.16
                                   EETTTTCEEC....HEETSTTCEEESSSS CS
                   TF_Zn_Ribbon  2 kCPnCgstnl....veDpergelvCtdCG 26
                                    CPnCg  ++          ++++C++CG
  gi|118431891|ref|YP_874949.1| 36 PCPNCGEVEIwrcsRCRKQGATYTCPNCG 64
                                   6********87765445777888*****9 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0011      0.46       8      17 ..      18      27 ..       5      28 .. 0.79
   2 ?    1.2   0.2      0.66   2.8e+02       7      15 ..      35      43 ..      30      45 .. 0.80
   3 ?    1.6   1.5      0.51   2.2e+02       3      12 ..      42      51 ..      40      54 .. 0.87
   4 ?    2.2   0.3      0.32   1.4e+02       4      13 ..      55      64 ..      52      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                                   E-TTT--EEE CS
                Desulfoferrod_N  8 kCevCGniVe 17
                                   +C+ CG iVe
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVE 27
                                   9********8 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.66
                                   EE-TTT--E CS
                Desulfoferrod_N  7 YkCevCGni 15
                                   + C  CG++
  gi|118431891|ref|YP_874949.1| 35 FPCPNCGEV 43
                                   67999*975 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.51
                                   TT-EEE-TTT CS
                Desulfoferrod_N  3 klevYkCevC 12
                                   + e+++C  C
  gi|118431891|ref|YP_874949.1| 42 EVEIWRCSRC 51
                                   5799***999 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.32
                                   T-EEE-TTT- CS
                Desulfoferrod_N  4 levYkCevCG 13
                                   +  Y C  CG
  gi|118431891|ref|YP_874949.1| 55 GATYTCPNCG 64
                                   668******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 ?    3.7  16.6      0.14        61      18      46 .]      16      54 ..      13      54 .. 0.88
   2 ?    6.2   0.2     0.024        10      19      25 ..      58      64 ..      55      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.14
                  Zn_Tnp_IS1595 18 gfvCPhCgsr.kayrikt.........rglfqCkeCrkq 46
                                    ++C  Cg   ++ +++t          + ++C++Crkq
  gi|118431891|ref|YP_874949.1| 16 PPRCTSCGRIvEPGSTATrfpcpncgeVEIWRCSRCRKQ 54
                                   58899999889999999999999999999********98 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.024
                  Zn_Tnp_IS1595 19 fvCPhCg 25
                                    +CP+Cg
  gi|118431891|ref|YP_874949.1| 58 YTCPNCG 64
                                   68****9 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4    0.0034       1.4     509     535 ..      18      47 ..      14      47 .. 0.76
   2 ?    8.0   3.0    0.0025       1.1     507     526 ..      45      64 ..      43      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0034
                                    EETT.--...EESS...SB-TTT--BE.EEEEE CS
                           NRDD 509 vCnecgy...kgei...ekCpkCgseeevevir 535
                                    +C +cg+    g +   + Cp+Cg  e ve++r
  gi|118431891|ref|YP_874949.1|  18 RCTSCGRivePGSTatrFPCPNCG--E-VEIWR 47 
                                    79****9876333366789*****..5.88775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0025
                                    EEEETT.--EESSSB-TTT- CS
                           NRDD 507 idvCnecgykgeiekCpkCg 526
                                    i +C +c ++g +++Cp+Cg
  gi|118431891|ref|YP_874949.1|  45 IWRCSRCRKQGATYTCPNCG 64 
                                    568****************9 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  13.2     0.055        23       6      48 ..      17      64 ..      14      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.055
                        DUF1272  6 pnCecCdkdlppdseearicsyEct.....FCaeCaeevlenvCPncg 48
                                   p+C  C + ++p s+++r     c       C++C ++  + +CPncg
  gi|118431891|ref|YP_874949.1| 17 PRCTSCGRIVEPGSTATRFPCPNCGeveiwRCSRCRKQGATYTCPNCG 64
                                   79*********99988887554443222227****************8 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       7.2   3.1e+03      11      15 ..      19      23 ..      18      24 .. 0.88
   2 ?   10.3   0.2    0.0013      0.56       5      15 ..      31      41 ..      28      47 .. 0.89
   3 ?    6.0   1.1     0.029        13       9      17 ..      58      66 ..      53      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.2
                        DUF2752 11 CPGCG 15
                                   C  CG
  gi|118431891|ref|YP_874949.1| 19 CTSCG 23
                                   99**9 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0013
                        DUF2752  5 altGipCPGCG 15
                                   + t +pCP CG
  gi|118431891|ref|YP_874949.1| 31 TATRFPCPNCG 41
                                   689*******9 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.029
                        DUF2752  9 ipCPGCGlt 17
                                   + CP CG t
  gi|118431891|ref|YP_874949.1| 58 YTCPNCGFT 66
                                   78*****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 ?    3.1   0.4      0.19        80       2       7 ..      18      23 ..      18      25 .. 0.64
   2 ?    1.9   7.8      0.43   1.9e+02       3      21 ..      37      52 ..      35      56 .. 0.77
   3 ?    8.7   0.2    0.0033       1.4       1      10 [.      58      67 ..      58      68 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.19
                   Rubredoxin_2  2 vCsqCG 7 
                                   +C +CG
  gi|118431891|ref|YP_874949.1| 18 RCTSCG 23
                                   566666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.43
                   Rubredoxin_2  3 CsqCGfesakwfGrCpsCg 21
                                   C +CG +     +rC  C+
  gi|118431891|ref|YP_874949.1| 37 CPNCGEVE---IWRCSRCR 52
                                   88888877...59999997 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0033
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   Y C +CGf+ 
  gi|118431891|ref|YP_874949.1| 58 YTCPNCGFTG 67
                                   99*****986 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6    0.0024         1      41      66 ..      18      43 ..      12      46 .. 0.79
   2 ?    6.3   2.4     0.023       9.8      27      47 ..      45      65 ..      43      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0024
                    Zn_Tnp_IS91 41 eCeeCghekivyfsCksrh.CpsCqkk 66
                                   +C++Cg   + + s   r+ Cp+C++ 
  gi|118431891|ref|YP_874949.1| 18 RCTSCGR-IVEPGSTATRFpCPNCGEV 43
                                   8****97.566778888888****986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                    Zn_Tnp_IS91 27 ilrCrtaalGfaryeCeeCgh 47
                                   i rC++ +  +a+y C++Cg 
  gi|118431891|ref|YP_874949.1| 45 IWRCSRCRKQGATYTCPNCGF 65
                                   667888888999*******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 ?    1.0   0.3      0.81   3.5e+02      46      52 ..      18      24 ..      10      26 .. 0.84
   2 ?    6.5   2.3     0.015       6.6      40      52 ..      30      42 ..      19      44 .. 0.74
   3 ?    3.9   0.5       0.1        45      44      52 ..      45      53 ..      42      55 .. 0.81
   4 ?    7.6   0.4    0.0073       3.1      43      52 ..      56      65 ..      52      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.81
                 zinc_ribbon_10 46 rCpkCga 52
                                   rC +Cg 
  gi|118431891|ref|YP_874949.1| 18 RCTSCGR 24
                                   7999996 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                 zinc_ribbon_10 40 leevkyrCpkCga 52
                                   ++ +++ Cp+Cg+
  gi|118431891|ref|YP_874949.1| 30 STATRFPCPNCGE 42
                                   56789******98 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.1
                 zinc_ribbon_10 44 kyrCpkCga 52
                                    +rC+ C+ 
  gi|118431891|ref|YP_874949.1| 45 IWRCSRCRK 53
                                   69*****86 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0073
                 zinc_ribbon_10 43 vkyrCpkCga 52
                                    +y Cp+Cg+
  gi|118431891|ref|YP_874949.1| 56 ATYTCPNCGF 65
                                   58******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 ?    1.9   5.2      0.49   2.1e+02       6      30 ..      18      40 ..      18      43 .. 0.62
   2 ?    5.6   0.5     0.035        15       5      12 ..      46      53 ..      45      56 .. 0.74
   3 ?    8.0   0.5    0.0062       2.6       4      11 ..      57      64 ..      57      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.49
                 Zn_ribbon_SprT  6 rCtgCgreythhlsirrhnYrCrrC 30
                                   rCt+Cgr ++  ++  r    C+ C
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIVEPGSTATR--FPCPNC 40
                                   79999976665555555..335555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.035
                 Zn_ribbon_SprT  5 YrCtgCgr 12
                                   +rC +C++
  gi|118431891|ref|YP_874949.1| 46 WRCSRCRK 53
                                   88888874 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0062
                 Zn_ribbon_SprT  4 vYrCtgCg 11
                                   +Y+C++Cg
  gi|118431891|ref|YP_874949.1| 57 TYTCPNCG 64
                                   7******9 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   6.9       3.2   1.4e+03      12      21 ..      33      42 ..      15      49 .. 0.66
   2 ?   11.0   6.8    0.0007       0.3       4      20 ..      47      64 ..      46      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.2
                                   -SEE-TTT-- CS
                         zf-HIT 12 akYkCpkCnt 21
                                    +  Cp+C++
  gi|118431891|ref|YP_874949.1| 33 TRFPCPNCGE 42
                                   5667999986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0007
                                   B-TTT-S.B-SEE-TTT- CS
                         zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                    C+ C +  a Y+Cp+C+
  gi|118431891|ref|YP_874949.1| 47 RCSRCRKqGATYTCPNCG 64
                                   5****************7 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.6   1.1e+03      53      61 ..      18      26 ..      14      36 .. 0.72
   2 ?    9.3   1.9    0.0028       1.2      34      62 ..      35      56 ..      25      57 .. 0.78
   3 ?    6.8   0.3     0.017       7.1      29      41 ..      53      65 ..      52      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.6
                                   EETTTTEEE CS
                Ribosomal_L37ae 53 kCkkcgktv 61
                                   +C++cg+ v
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIV 26
                                   477776655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0028
                                   BEESSSSSSEEEEEETTEEEETTTTEEEE CS
                Ribosomal_L37ae 34 ytCpfcgktkvkRkavgiwkCkkcgktva 62
                                   + Cp+cg        v+iw+C++c+k+ a
  gi|118431891|ref|YP_874949.1| 35 FPCPNCG-------EVEIWRCSRCRKQGA 56
                                   5666666.......489*******99876 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                                   HHHS-BEESSSSS CS
                Ribosomal_L37ae 29 sqhakytCpfcgk 41
                                   +q a+ytCp+cg 
  gi|118431891|ref|YP_874949.1| 53 KQGATYTCPNCGF 65
                                   6899*******96 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3      0.13        55      27      33 ..      18      24 ..      17      26 .. 0.83
   2 ?    5.2   0.1     0.046        20      28      33 ..      37      42 ..      29      43 .. 0.66
   3 ?    2.9   2.3      0.24     1e+02      27      33 ..      47      53 ..      45      54 .. 0.78
   4 ?    5.6   0.3     0.036        15       4      10 ..      59      65 ..      57      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                  zinc_ribbon_4 27 rCskCgh 33
                                   rC+ Cg 
  gi|118431891|ref|YP_874949.1| 18 RCTSCGR 24
                                   8999986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.046
                  zinc_ribbon_4 28 CskCgh 33
                                   C++Cg+
  gi|118431891|ref|YP_874949.1| 37 CPNCGE 42
                                   666665 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.24
                  zinc_ribbon_4 27 rCskCgh 33
                                   rCs+C++
  gi|118431891|ref|YP_874949.1| 47 RCSRCRK 53
                                   7888875 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.036
                  zinc_ribbon_4  4 tCpsCka 10
                                   tCp+C++
  gi|118431891|ref|YP_874949.1| 59 TCPNCGF 65
                                   6888875 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 ?    2.6   0.0      0.28   1.2e+02      14      20 ..      17      23 ..       8      25 .. 0.82
   2 ?    3.4   0.1      0.16        69      13      20 ..      32      41 ..      27      43 .. 0.75
   3 ?    0.1   0.4       1.7   7.4e+02      14      19 ..      46      51 ..      41      54 .. 0.78
   4 ?    6.1   1.4     0.024        10      11      22 ..      54      66 ..      49      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.28
                      zf-C2H2_3 14 sqCkeCg 20
                                   ++C+ Cg
  gi|118431891|ref|YP_874949.1| 17 PRCTSCG 23
                                   78****8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.16
                      zf-C2H2_3 13 asq..CkeCg 20
                                   a++  C++Cg
  gi|118431891|ref|YP_874949.1| 32 ATRfpCPNCG 41
                                   34588****8 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.7
                      zf-C2H2_3 14 sqCkeC 19
                                    +C+ C
  gi|118431891|ref|YP_874949.1| 46 WRCSRC 51
                                   57***9 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.024
                      zf-C2H2_3 11 fga.sqCkeCgMv 22
                                    ga  +C++Cg +
  gi|118431891|ref|YP_874949.1| 54 QGAtYTCPNCGFT 66
                                   455477*****75 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3       0.7     3e+02      21      26 ..      18      23 ..       4      25 .. 0.75
   2 ?    3.1  10.7      0.14        61       2      26 ..      19      52 ..      17      52 .. 0.72
   3 ?    4.0   0.1     0.072        31      21      26 ..      59      64 ..      54      65 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.7
                       zf-TFIIB 21 yCpqCr 26
                                   +C++C+
  gi|118431891|ref|YP_874949.1| 18 RCTSCG 23
                                   677775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.14
                       zf-TFIIB  2 CPkCqdele...eser......ggveidyCpqCr 26
                                   C +C+   e   ++ r      g+vei++C +Cr
  gi|118431891|ref|YP_874949.1| 19 CTSCGRIVEpgsTATRfpcpncGEVEIWRCSRCR 52
                                   88887544433444446999999**********8 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.072
                       zf-TFIIB 21 yCpqCr 26
                                   +Cp+C+
  gi|118431891|ref|YP_874949.1| 59 TCPNCG 64
                                   677775 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 ?    1.4   2.8      0.64   2.7e+02      24      28 ..      37      41 ..      18      44 .. 0.65
   2 ?    8.1   3.2    0.0052       2.2       3      30 ..      45      66 ..      43      68 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.64
                  A2L_zn_ribbon 24 CieCg 28
                                   C++Cg
  gi|118431891|ref|YP_874949.1| 37 CPNCG 41
                                   99998 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0052
                  A2L_zn_ribbon  3 lkvCsvCggngilnseqgylvCieCgas 30
                                   ++ Cs C+++g        + C++Cg++
  gi|118431891|ref|YP_874949.1| 45 IWRCSRCRKQGAT------YTCPNCGFT 66
                                   5778888888888......99*****98 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 ?    3.2   0.1       0.2        86       4      10 ..      19      25 ..      10      25 .. 0.88
   2 ?    5.3   0.1     0.046        20       1      10 [.      34      43 ..      34      43 .. 0.80
   3 ?   -0.4   0.1       2.8   1.2e+03       4      11 ..      51      58 ..      46      59 .. 0.70
   4 ?    4.3   0.7     0.094        40       3       8 ..      59      64 ..      58      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.2
                                   -TTT--E CS
                        ADK_lid  4 CpkCGrs 10
                                   C +CGr+
  gi|118431891|ref|YP_874949.1| 19 CTSCGRI 25
                                   8899986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.046
                                   EEE-TTT--E CS
                        ADK_lid  1 RrvCpkCGrs 10
                                   R  Cp+CG++
  gi|118431891|ref|YP_874949.1| 34 RFPCPNCGEV 43
                                   667****985 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.8
                                   -TTT--EE CS
                        ADK_lid  4 CpkCGrsY 11
                                   C+k G++Y
  gi|118431891|ref|YP_874949.1| 51 CRKQGATY 58
                                   66667777 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.094
                                   E-TTT- CS
                        ADK_lid  3 vCpkCG 8 
                                   +Cp+CG
  gi|118431891|ref|YP_874949.1| 59 TCPNCG 64
                                   8****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 ?    5.0   0.1     0.063        27       3      11 ..      18      26 ..      18      26 .. 0.83
   2 ?    5.1   0.3     0.055        24       4      10 ..      37      43 ..      35      43 .. 0.83
   3 ?    0.1   0.4         2   8.7e+02       3       8 ..      47      52 ..      46      54 .. 0.76
   4 ?    5.3   0.4     0.049        21      21      26 .]      58      63 ..      57      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.063
                         zf-ACC  3 KCpsCgeml 11
                                   +C+sCg ++
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIV 26
                                   6*****876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.055
                         zf-ACC  4 CpsCgem 10
                                   Cp Cge+
  gi|118431891|ref|YP_874949.1| 37 CPNCGEV 43
                                   9999985 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 2
                         zf-ACC  3 KCpsCg 8 
                                   +C +C 
  gi|118431891|ref|YP_874949.1| 47 RCSRCR 52
                                   799995 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.049
                         zf-ACC 21 yVCPkC 26
                                   y+CP+C
  gi|118431891|ref|YP_874949.1| 58 YTCPNC 63
                                   789999 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 ?   -0.9   0.2       4.3   1.8e+03      18      23 ..      18      23 ..      14      28 .. 0.84
   2 ?    3.9   3.9      0.13        57      13      23 ..      31      41 ..      18      46 .. 0.80
   3 ?    7.8   2.0    0.0084       3.6      12      24 ..      53      65 ..      44      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.3
                       zf-Mss51 18 eCpdCG 23
                                    C  CG
  gi|118431891|ref|YP_874949.1| 18 RCTSCG 23
                                   599999 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                       zf-Mss51 13 khvdfeCpdCG 23
                                      +f Cp+CG
  gi|118431891|ref|YP_874949.1| 31 TATRFPCPNCG 41
                                   5679******9 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0084
                       zf-Mss51 12 pkhvdfeCpdCGi 24
                                   ++  +++Cp+CG+
  gi|118431891|ref|YP_874949.1| 53 KQGATYTCPNCGF 65
                                   56689*******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 ?    0.2   0.1       2.8   1.2e+03      16      21 ..      18      23 ..       7      24 .. 0.81
   2 ?    5.7   0.8     0.052        22      13      21 ..      33      41 ..      27      43 .. 0.84
   3 ?    2.9   0.1       0.4   1.7e+02      15      24 ..      46      55 ..      42      57 .. 0.80
   4 ?    7.6   0.4     0.013       5.4      15      23 ..      58      66 ..      53      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.8
                      zf-H2C2_2 16 eCplCd 21
                                    C +C+
  gi|118431891|ref|YP_874949.1| 18 RCTSCG 23
                                   699997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.052
                      zf-H2C2_2 13 kpyeCplCd 21
                                   +++ Cp C+
  gi|118431891|ref|YP_874949.1| 33 TRFPCPNCG 41
                                   579*****8 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.4
                      zf-H2C2_2 15 yeCplCdkaF 24
                                   + C+ C+k  
  gi|118431891|ref|YP_874949.1| 46 WRCSRCRKQG 55
                                   78*****975 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.013
                      zf-H2C2_2 15 yeCplCdka 23
                                   y+Cp C+ +
  gi|118431891|ref|YP_874949.1| 58 YTCPNCGFT 66
                                   9*****975 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.027        11      33      41 ..      18      26 ..      14      35 .. 0.72
   2 ?    4.3   0.1     0.091        39      33      40 ..      36      43 ..      29      45 .. 0.80
   3 ?    5.4   1.6     0.039        17      31      38 ..      45      52 ..      43      59 .. 0.78
   4 ?    2.8   0.3      0.26   1.1e+02       4      10 ..      59      65 ..      56      67 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.027
                         HalOD2 33 kCtrCGevq 41
                                   +Ct CG + 
  gi|118431891|ref|YP_874949.1| 18 RCTSCGRIV 26
                                   688888765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.091
                         HalOD2 33 kCtrCGev 40
                                    C +CGev
  gi|118431891|ref|YP_874949.1| 36 PCPNCGEV 43
                                   6999*998 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.039
                         HalOD2 31 vWkCtrCG 38
                                   +W+C+rC 
  gi|118431891|ref|YP_874949.1| 45 IWRCSRCR 52
                                   8******5 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.26
                         HalOD2  4 kCseCsl 10
                                    C++C++
  gi|118431891|ref|YP_874949.1| 59 TCPNCGF 65
                                   3555554 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       1.3   5.6e+02      18      23 ..      19      24 ..      17      26 .. 0.68
   2 ?    9.1   1.7    0.0033       1.4       3      22 ..      45      64 ..      43      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.3
                       zf-B_box 18 CedCqq 23
                                   C++C+ 
  gi|118431891|ref|YP_874949.1| 19 CTSCGR 24
                                   777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0033
                       zf-B_box  3 etkCpeHknkpatlfCedCq 22
                                    ++C ++ ++ at+ C +C+
  gi|118431891|ref|YP_874949.1| 45 IWRCSRCRKQGATYTCPNCG 64
                                   589****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 445.62
//
Query:       gi|118431892|ref|NP_148640.2|  [L=389]
Description: hypothetical protein APE_2481.1 [Aeropyrum pernix K1]
Scores for complete 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-125  418.2   0.0   2.4e-125  418.0   0.0    1.0  1  DUF1464   Protein of unknown function (DUF1464)
  ------ inclusion threshold ------
       0.21   12.0   0.0       0.38   11.1   0.0    1.4  1  PBD       P21-Rho-binding domain


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 !  418.0   0.0  2.7e-129  2.4e-125       1     325 [.       6     366 ..       6     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 418.0 bits;  conditional E-value: 2.7e-129
                        DUF1464   1 GiDPGtksydvvvvdd.lgkvvlekeiptdevekdpsvlvkaieea.....radivalpSGyGlPlkriselaereilll 74 
                                    GiDPGt+s+dv+++dd +++v+le++ip+dev++dps++++++eea     ++d+v++pSGyG+Plkr+se+a+ +i+++
  gi|118431892|ref|NP_148640.2|   6 GIDPGTGSMDVLGFDDeSNNVFLEESIPRDEVTRDPSLPLRIVEEAsakvgGLDAVVAPSGYGMPLKRASETAPGDICEA 85 
                                    9*************9989****************************9999999*************************** PP

                        DUF1464  75 tlaeeseegl....vGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavlavadeaeee..eyre 148
                                    t++++s+e+l    vGLr+l++ +as++l+a+++PgVi+LptvP+wRKv++iDmGtADKl+++++a+++e+e++  e+++
  gi|118431892|ref|NP_148640.2|  86 TFIHSSDEVLglriVGLRRLMALFASSDLPAWFTPGVIHLPTVPAWRKVGRIDMGTADKLYTVAAALRTEVEYHgvEPEA 165
                                    *********999*9****************************************************************** PP

                        DUF1464 149 lsFilvEvGsgfnaviaVknGkivDGlGgti.lpGflsaGalDgEvAyllgkva.kiekslifsgGvasiagea...ele 223
                                    ++Fi+vE+G++++a++aV++Gk+vDG+Ggt+ ++Gf++ Ga+DgE+Ay+l++va +++ksl+f+gG++++ag++   ele
  gi|118431892|ref|NP_148640.2| 166 ARFIAVEAGMAYTAAVAVVGGKVVDGVGGTSgFHGFMGGGAMDGEAAYALAAVApRFSKSLLFKGGAGWVAGVSspvELE 245
                                    ******************************************************9******************99***** PP

                        DUF1464 224 kklsee....aferlke.vvksvaellsskyklee....iivSGrlkrikelgkklesrleev...........kllela 283
                                    +k+se     a+e+l e vvksva+ll+s  ++e+    ++vSGrl+++ +lg++l+srl+++           ++++l 
  gi|118431892|ref|NP_148640.2| 246 EKASEGggleALEMLGEgVVKSVATLLPSL-RPEGgevrVYVSGRLFSLGRLGSELRSRLRDFissigltprvlTIERLG 324
                                    *****999*********************9.77777888***************************************** PP

                        DUF1464 284 skaKeaaqGaAiianalaGgryrelvdhleiekssgtvldyv 325
                                    sk+Ke+a+GaA++a++laGgry++lvdhle+e+ssg+++d++
  gi|118431892|ref|NP_148640.2| 325 SKTKEGASGAALVASGLAGGRYKWLVDHLELERSSGSIFDHL 366
                                    ****************************************96 PP

>> PBD  P21-Rho-binding 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      0.38      14      49 ..       5      42 ..       5      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                                   EEEETTTTEEE..S--CCHCCCHHHT.TTSXXXBEXXX CS
                            PBD 14 VGwdgdsgnft..glPpewkkllkssgItedelkenpk 49
                                   VG+d+++g     g+++e ++++ +++I +de  ++p+
  gi|118431892|ref|NP_148640.2|  5 VGIDPGTGSMDvlGFDDESNNVFLEESIPRDEVTRDPS 42
                                   9*******98789*********************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2796.02
//
Query:       gi|118431893|ref|NP_148641.2|  [L=155]
Description: phosphohistidine phosphatase [Aeropyrum pernix K1]
Scores for 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-12   45.3   0.0    1.2e-11   44.7   0.0    1.2  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   6.8e-16   1.2e-11       1      75 [.       4      76 ..       4      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 6.8e-16
                                   EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-G CS
                     His_Phos_1  1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpvelde 75
                                   +++ RHG+ e +  g         LteeG + +e +a+ l+g+++ +i++Sp++Ra+qTae++a++l+l++ + e
  gi|118431893|ref|NP_148641.2|  4 IVFFRHGKAEPKMPG--VDDRERRLTEEGAADVECAARLLRGRGVVRILTSPYRRAIQTAEILARTLDLEYSVVE 76
                                   7899*******8885..5666777********************************************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1181.37
//
Query:       gi|118431894|ref|NP_148642.2|  [L=184]
Description: hypothetical protein APE_2485.1 [Aeropyrum pernix K1]
Scores for complete 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  16.4    3.6e-22   79.1  16.4    1.3  1  SpoIIM     Stage II sporulation protein M
  ------ inclusion threshold ------
        2.6    7.8   6.4       0.71    9.7   1.8    1.8  2  Arteri_Gl  Arterivirus GL envelope glycoprotein


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 !   79.1  16.4     4e-26   3.6e-22       4     156 .]      22     174 ..       8     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 4e-26
                         SpoIIM   4 lflvgillgallaasnfa.eqis...seskensalslflaifanNlrvalllfllGllllgiptilvllinGfvlG.ava 78 
                                    +fl+g l+g++  + +   e++s   +     ++l   l if+nN+  a l+++l + +l ip i v+++nG+++G av 
  gi|118431894|ref|NP_148642.2|  22 VFLAGSLAGYIKPNYS-LlENVSekaGLIMRLPPLLRPLGIFLNNIVAATLTYILTI-VLIIPGISVIALNGYIVGsAVR 99 
                                    6777777777777733.246666766666788899999******************8.999***************6666 PP

                         SpoIIM  79 alvaef.gglllflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakrellklllllvpllliAaliEafvtp 156
                                    + v e   +ll++llli+Phgile+pa++ a+++g+r   +     +  ++ +++ l +  +++pllliAa+iE fvtp
  gi|118431894|ref|NP_148642.2| 100 YAVEEGgLSLLTALLLIIPHGILEIPAFLAAVGFGMRCLAYC----RGVRRVIENTLSMYAVTAPLLLIAAFIEIFVTP 174
                                    66666676699***************************5555....57789***************************8 PP

>> Arteri_Gl  Arterivirus GL envelope glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.8     0.028   2.5e+02      46      87 ..      61     102 ..      57     118 .. 0.64
   2 ?    9.7   1.8   7.9e-05      0.71      43     105 ..     108     170 ..      93     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.028
                      Arteri_Gl  46 plltkllslkllttahl.llflnvaalsytgyvhvryvlssay 87 
                                    + l  +++ +l +++++ l+  +++++++ gy +v ++++ a 
  gi|118431894|ref|NP_148642.2|  61 IFLNNIVAATLTYILTIvLIIPGISVIALNGY-IVGSAVRYAV 102
                                    67778899999999987355667888899999.5555555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 7.9e-05
                      Arteri_Gl  43 vllplltkllslkllttahlllflnvaalsytgyvhvryvlssayaalalvAlvlgvysfvvr 105
                                     ll +l+ ++ +++l + ++l ++++++  ++   +vr+v++  +++ a+ A +l++  f++ 
  gi|118431894|ref|NP_148642.2| 108 SLLTALLLIIPHGILEIPAFLAAVGFGMRCLAYCRGVRRVIENTLSMYAVTAPLLLIAAFIEI 170
                                    46677889999*****************655555579***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1371.93
//
Query:       gi|118431895|ref|NP_148643.2|  [L=253]
Description: tRNA (m1A) methyltransferase [Aeropyrum pernix K1]
Scores for complete 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-21   75.8   0.0    5.2e-21   75.5   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    4.9e-08   33.0   0.0    7.3e-08   32.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.9e-06   26.7   0.0      5e-06   26.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.4e-05   23.6   0.0    3.5e-05   23.1   0.0    1.2  1  Methyltransf_3   O-methyltransferase
    3.9e-05   24.3   0.0    5.7e-05   23.7   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
     0.0012   19.4   0.0      0.002   18.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0073   17.3   0.0      0.012   16.6   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
  ------ inclusion threshold ------
      0.031   14.0   0.0      0.088   12.5   0.0    1.6  1  UPF0020          Putative RNA methylase family UPF0020
      0.083   12.5   0.0       0.12   12.1   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.087   13.6   0.0       0.13   13.0   0.0    1.3  1  Methyltransf_12  Methyltransferase domain


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 !   75.5   0.0   2.9e-24   5.2e-21      11     159 ..      60     206 ..      49     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.9e-24
                          GCD14  11 eLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehel 90 
                                    eL     + rtq++y +D  +i + +  +pG++ +e+G Gsg +++ +a  + PtG+l  +e   +  e+ar +++  +l
  gi|118431895|ref|NP_148643.2|  60 ELMEGFYERRTQVIYPKDSGMIAVLVGARPGARLLEAGVGSGFMTTVLAMGLCPTGRLIGLEVRSENLETARRNLEAAGL 139
                                    666666789*********************************************************************** PP

                          GCD14  91 sqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaL 159
                                     + v ++  Dv +    e++ g  D v LD+P Pw a+++++  + k +++   f P   q+ + + ++
  gi|118431895|ref|NP_148643.2| 140 LDCVDLRLGDVRNPASVEGL-GPFDGVVLDMPDPWRALESISGEV-KPSAVAVVFVPTSTQLEKLITNM 206
                                    ************99998998.99**********************.77888899999999988877665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   4.1e-11   7.3e-08      63     145 ..      79     164 ..      68     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 4.1e-11
                                    HHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGG..TTGG CS
                           PCMT  63 alalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrk..Gyee 139
                                    +++  l+  ++gar Le G GsG+ t vla+ + ++gr++++e   e  e+a+rnl++ +l   v ++ gD r+   +e 
  gi|118431895|ref|NP_148643.2|  79 GMIAVLVGARPGARLLEAGVGSGFMTTVLAMGLCPTGRLIGLEVRSENLETARRNLEAAGLLdCVDLRLGDVRNpaSVEG 158
                                    5666677899************************************************9975489999999875224566 PP

                                    G-SEEE CS
                           PCMT 140 kaPYda 145
                                      P+d 
  gi|118431895|ref|NP_148643.2| 159 LGPFDG 164
                                    667765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.8e-09     5e-06       4     109 ..      90     191 ..      87     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.8e-09
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklled.ekfDlils 80 
                                    g r+l++G G+G+ t +la  l+p ++++G++   e +e Ar n++  gl   v ++ gd+ + ++  +e   +fD ++ 
  gi|118431895|ref|NP_148643.2|  90 GARLLEAGVGSGFMTTVLAMGLCPTGRLIGLEVRSENLETARRNLEAAGLLdCVDLRLGDVRNpAS--VEGlGPFDGVVL 167
                                    6799********************************************986599*********666..444489**9988 PP

                Methyltransf_31  81 nevlnaladpdkileeiervlkpggilli 109
                                         +++dp  +le+i+  +kp  + ++
  gi|118431895|ref|NP_148643.2| 168 -----DMPDPWRALESISGEVKPSAVAVV 191
                                    .....589999999888887777766655 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     2e-08   3.5e-05      32     109 ..      75     151 ..      52     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2e-08
                                    -HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HH CS
                 Methyltransf_3  32 svdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdal 109
                                    ++d + ++ +Lv      r le Gv  G+    +a++l + G+++ +++  e+ e a++ ++ ag+ + ++l+ gd +
  gi|118431895|ref|NP_148643.2|  75 PKD-SGMIAVLVGARPGARLLEAGVGSGFMTTVLAMGLCPTGRLIGLEVRSENLETARRNLEAAGLLDCVDLRLGDVR 151
                                    444.445677888888889******************************************************99976 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.2e-08   5.7e-05       2      70 ..      94     167 ..      93     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.2e-08
                                    EEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS..SSTTTEEEEEE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp..fedgsfDlvvs 70 
                                    L++G G+G +t  la  l + ++++g+++ +e le+ar+++e++gl   v+++ gd+++    +  g fD vv+
  gi|118431895|ref|NP_148643.2|  94 LEAGVGSGFMTTVLAMGLcPTGRLIGLEVRSENLETARRNLEAAGLldCVDLRLGDVRNPAsvEGLGPFDGVVL 167
                                    89*************988779************************************99662346679999987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.1e-06     0.002       1      85 [.      94     180 ..      94     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                                    EEET-TTSHHHHHHH.HTT..SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCT.SS-T.T-EEEEEEES-CCC CS
                Methyltransf_11   1 LdvGcGtGrlaeala.krg..arvvgvDlskemlklakekaseegl..kvefvvadaekl.pfed.nsfDlvvssevlhh 73 
                                    L++G+G+G ++  la   +  +r++g+++  e l++a+++ + +gl   v+++ +d+++   +e  + fD vv+      
  gi|118431895|ref|NP_148643.2|  94 LEAGVGSGFMTTVLAmGLCptGRLIGLEVRSENLETARRNLEAAGLldCVDLRLGDVRNPaSVEGlGPFDGVVLD----- 168
                                    799************5333889***********************987777788888873234444566666654..... PP

                                    -CCHHHHHHHHH CS
                Methyltransf_11  74 vedpekalkeia 85 
                                    ++dp +al+ i 
  gi|118431895|ref|NP_148643.2| 169 MPDPWRALESIS 180
                                    355555555555 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.9e-06     0.012       1      78 [.      94     170 ..      94     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.9e-06
                Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDgg 78 
                                    +E Gv sG+ t +l+  l+ +g+  l+ ++   +  e+a+++++ agl d v+l+ +d ++ ++    g++D +++D++
  gi|118431895|ref|NP_148643.2|  94 LEAGVGSGFMTTVLAMGLCPTGR--LIGLEVRSEnLETARRNLEAAGLLDCVDLRLGDVRNPASVEGLGPFDGVVLDMP 170
                                    799******************95..99999977546678888999**************88755333589*****9987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.9e-05     0.088      78     130 ..     116     170 ..     105     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                                    -EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--..STTS---EEEE--- CS
                        UPF0020  78 klygsDldrrvvqgareNaekagvgdliefsqadaakLr..lkegevdvivtnpP 130
                                    +l+g++  ++ +++ar+N+e+ag+ d ++++  d+++    +  g +d +v ++P
  gi|118431895|ref|NP_148643.2| 116 RLIGLEVRSENLETARRNLEAAGLLDCVDLRLGDVRNPAsvEGLGPFDGVVLDMP 170
                                    48999******************************98775556679999999999 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.4e-05      0.12       7      88 ..      88     170 ..      82     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                                    -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EEEEEE CS
                Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfDriLl 85 
                                    +++ ++l++  + G  Tt +a  + ++g+++ +++ +e l+   +nl+  g+   + +  +D+r++ +v g   fD + l
  gi|118431895|ref|NP_148643.2|  88 RPGARLLEAGVGSGFMTTVLAMGLCPTGRLIGLEVRSENLETARRNLEAAGLLdCVDLRLGDVRNPASVEGLGPFDGVVL 167
                                    5677889999999999***99999***************************984567889******9999999******* PP

                                    EE- CS
                Methyltr_RsmB-F  86 DaP 88 
                                    D P
  gi|118431895|ref|NP_148643.2| 168 DMP 170
                                    *99 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.1e-05      0.13       1      71 [.      94     166 ..      94     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvv 71 
                                    Le G G+G ++ +l+  l p+ +++g+++ ++ +e a++ l + + +++  ++l +     + +g + fD vv
  gi|118431895|ref|NP_148643.2|  94 LEAGVGSGFMTTVLAMGLcPTGRLIGLEVRSENLETARRNLEAAGLLDCVDLRLGDVRNPASVEGlGPFDGVV 166
                                    89*******************************************9998877775544333333358888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1843.10
//
Query:       gi|118431896|ref|NP_148644.2|  [L=148]
Description: hypothetical protein APE_2489.1 [Aeropyrum pernix K1]
Scores for complete 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  111.7   9.8    3.8e-17   62.5   0.7    2.1  2  CBS       CBS domain
     0.0092   16.2   0.0        1.2    9.5   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 !   53.7   2.8   2.3e-18   2.1e-14       1      55 [.      15      69 ..      15      71 .. 0.91
   2 !   62.5   0.7   4.2e-21   3.8e-17       3      56 ..      82     135 ..      80     136 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.3e-18
                                   HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55
                                   ++dim ++vvtv+pd+++  a++lm+e + +++++VVd++g+l Givt+rD++ ++
  gi|118431896|ref|NP_148644.2| 15 ASDIMITEVVTVKPDDPVTRAAKLMVE-NlIGSVLVVDDEGRLRGIVTERDIVYVV 69
                                   58***********************55.55**********************8765 PP

  == domain 2  score: 62.5 bits;  conditional E-value: 4.2e-21
                                    HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    +imt+++++v+pd++l  ++++m e++v++lPVVde g +vGi++ rD+l++l+
  gi|118431896|ref|NP_148644.2|  82 EIMTENPIVVRPDDDLLTVVRKMSETNVRHLPVVDEKGAPVGIISFRDVLDFLM 135
                                    89**************************************************97 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 !    4.4   0.0    0.0052        47       9      33 ..      46      70 ..      43      92 .. 0.86
   2 !    9.5   0.0   0.00013       1.2       7      31 ..     109     133 ..     105     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0052
                                   EEEEE-SSS-EEEEEEHHHHHHHHH CS
                          IF3_N  9 evrlvdedGeqlGvistreAlrlae 33
                                    v +vd++G   G+++ r+++    
  gi|118431896|ref|NP_148644.2| 46 SVLVVDDEGRLRGIVTERDIVYVVS 70
                                   589*******99****999987655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00013
                                    SSEEEEE-SSS-EEEEEEHHHHHHH CS
                          IF3_N   7 arevrlvdedGeqlGvistreAlrl 31 
                                    +r+  +vde+G  +G+is r++l+ 
  gi|118431896|ref|NP_148644.2| 109 VRHLPVVDEKGAPVGIISFRDVLDF 133
                                    78889****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1158.97
//
Query:       gi|118431897|ref|NP_148645.2|  [L=276]
Description: FTR1 family protein [Aeropyrum pernix K1]
Scores for complete 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  218.3  20.6    1.5e-64  218.1  20.6    1.0  1  FTR1         Iron permease FTR1 family
  ------ inclusion threshold ------
      0.057   13.7   0.0       0.72   10.2   0.0    2.1  2  PFOR_II      Pyruvate:ferredoxin oxidoreductase core domain I
       0.09   11.5   0.0       0.12   11.1   0.0    1.2  1  Pneumo_ncap  Pneumovirus nucleocapsid protein


Domain annotation for each model (and alignments):
>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1  20.6   2.5e-68   1.5e-64       2     305 ..       5     267 ..       4     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 2.5e-68
                           FTR1   2 faiflvvlregleaslivsvllallkqtqretdklqvwagialavllalaigqafasitaalqkdkalieeellegvlsl 81 
                                    +a++lv +re++ea l+ +++++llk+++++ + + v+++++l+v+l++a+g+++++i+++++      e+el+e+++s+
  gi|118431897|ref|NP_148645.2|   5 LATGLVAFREAFEAILLSTIIIMLLKKMGEHGKIKIVYTTAILSVVLGVALGAGIYTIFRGFP------EKELVEAGMSY 78 
                                    7899***********************************************************......8********** PP

                           FTR1  82 iavvviswmilwmrrvgkklkeeveqklakavaeiknrekaaqkgekgsekwalfilsFlivlREGlEavLfvaaivayt 161
                                    +a++vi ++i+w+ r+g k+k+e+e kla++++                  +a+++++F++v+RE++E+vL+ a++++++
  gi|118431897|ref|NP_148645.2|  79 LAAMVIGTVIVWGVRHGPKIKGEIEAKLASSLS-----------------AKAVAVVTFIFVFREVFETVLITAPFLVSN 141
                                    ********************************8.................89**************************** PP

                           FTR1 162 vkrvsalilgvvlGaliavvlglliyrglvklslqsffilegflLllvaagLfsvgtlellekaeacngkdyiefkksks 241
                                    +   s+ ilgv++G+l a++lg+++y+++++++l++ff+ +++lL++va+gL+++gt+elle+ e+ +g + + ++k+ +
  gi|118431897|ref|NP_148645.2| 142 P---SSNILGVSGGTLGALALGVAVYWLGMRINLRTFFLGTSILLAFVASGLVGYGTHELLEWFEE-EGIKLGVLGKKIQ 217
                                    *...**************************************************************.************* PP

                           FTR1 242 lskisllslllvaflaveregleivlaliGwantgplglivyaavwlvvlillgllliklgvrl 305
                                    l+++ ++sll++   +++++g  ++++++G++++         +++++++++ ++ll+ l++++
  gi|118431897|ref|NP_148645.2| 218 LLNVGENSLLHP---KNAIGG--LLSVMVGYYHY---------MEIARIILQGSTLLLLLAYII 267
                                    ************...******..***********.........***************999986 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 ?   10.2   0.0   0.00012      0.72      30      89 ..      56     118 ..      50     122 .. 0.80
   2 ?    0.9   0.0     0.096   5.7e+02       4      32 ..     184     212 ..     183     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                                    EEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G..-HHHHHHHHHTGGG.TSEEEEEE CS
                        PFOR_II  30 GllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse..Gqlveevkaalkks.kvkvvnfv 89 
                                    G    +++r FPe+el e+  ++ + +v+   i  g++    +  e++a+l +s + k+v +v
  gi|118431897|ref|NP_148645.2|  56 GAGIYTIFRGFPEKELVEAGMSYLAAMVIGTVIVWGVRhgPKIKGEIEAKLASSlSAKAVAVV 118
                                    5555679*****************************999556777999999888755555444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.096
                                    EEEE-STHHHHHHHHHHHHHHTT--EEEE CS
                        PFOR_II   4 vivamGsvagtaksavdelReegikvGll 32 
                                    ++va G v   +++  + + eegik+G+l
  gi|118431897|ref|NP_148645.2| 184 AFVASGLVGYGTHELLEWFEEEGIKLGVL 212
                                    5788888888899999999********98 PP

>> Pneumo_ncap  Pneumovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.1e-05      0.12     320     364 ..      45      88 ..      26     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                    Pneumo_ncap 320 nfasvvlGnaaGlGiiGeyrGrvrntelydaakayakslkesnki 364
                                       svvlG a G Gi   +rG + ++el +a  +y   +    +i
  gi|118431897|ref|NP_148645.2|  45 AILSVVLGVALGAGIYTIFRGFP-EKELVEAGMSYLAAMVIGTVI 88 
                                    5679*****************75.789*******98777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); 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:                         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: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2334.32
//
Query:       gi|118431898|ref|NP_148646.2|  [L=277]
Description: hypothetical protein APE_2491.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2315.72
//
Query:       gi|118431899|ref|NP_148647.2|  [L=543]
Description: hypothetical protein APE_2493.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-15   57.7   0.0    2.8e-15   57.1   0.0    1.3  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   1.5e-19   2.8e-15       2     166 ..     193     390 ..     192     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.5e-19
                                    EEESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.......SSTGGGS........TT CS
                                    xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxx........xx RF
                    Radical_SAM   2 vvtrgCnlr....CsfCarpetvrregrgrslsveeileevkelkaekgvkevilg.......ggeplly........pd 62 
                                    +++rgC++     CsfC  p     +gr+  + +e i++ev++l ++ gv ++ lg        g p l+        p+
  gi|118431899|ref|NP_148647.2| 193 ETYRGCARWvsggCSFCVEP----LRGRPIQRRPEAIAREVEAL-YRAGVLHFRLGrqadilvYGSPALDseewpppnPR 267
                                    5667776555555*******....7*******************.8**********988888844444446666644488 PP

                                    HHHHHHHHHHTC...CCTEEEEEEECSSCHG.....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHH CS
                                    xxxxxxxxxxxx...xxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  63 fvellerlakla...vpgiritvetngtlpd.....eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevle 132
                                    + e+l+  ++ a    + ++i  + +gt ++     e+ l+ +++l+   d+ ++gle+ad++ v +++n +  +e+vle
  gi|118431899|ref|NP_148647.2| 268 ELEKLFTGVRSAapgLRVLHIDNVNPGTIVRypvasEKALKVIVKLHtpGDVAAMGLETADPK-VARINNLNTHPEDVLE 346
                                    8888888888889**999999999999999999999***************************.******99******** PP

                                    HHHHHHHTTSET..........EEEEEEEBTTTSHHHHHHHHHH CS
                                    xxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 133 aleklreagikr..........vvdrivglpGendeeleellel 166
                                    a+++ +++g  r           +++i+glpGe  e+++  +e+
  gi|118431899|ref|NP_148647.2| 347 AVRIVNRVGAARgwngmphllpGINFILGLPGERSETYRLNREF 390
                                    *********4445555555666***********98887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 4108.30
//
Query:       gi|118431900|ref|NP_148648.2|  [L=149]
Description: HIT family protein [Aeropyrum pernix K1]
Scores for 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-22   77.8   0.0    2.3e-21   76.3   0.0    1.6  2  HIT       HIT domain
    7.6e-12   45.7   0.0    1.3e-11   45.0   0.0    1.3  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
     0.0038   17.1   0.0     0.0053   16.6   0.0    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


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 !   76.3   0.0   3.9e-25   2.3e-21       2      95 ..      11     104 ..      10     106 .. 0.98
   2 ?   -1.0   0.0      0.49     3e+03      40      64 ..     115     139 ..     107     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 3.9e-25
                                    GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGG CS
                            HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngaha 81 
                                    +e+++  vy+ + v++fld  p ++ghlLv+p +h++ +h +++   ak++ a+  +a++ ++k  + +++v++n g+ a
  gi|118431900|ref|NP_148648.2|  11 GEAEAYTVYKGNGVTVFLDRYPASKGHLLVVPDEHYESIHTAPPRVAAKVWLAASAIARYYREKAGAPAVNVLTNSGRYA 90 
                                    7899999************************************************************************* PP

                                    T-SSSS-EEEEEEC CS
                            HIT  82 gqsvahlHiHvipr 95 
                                    gq ++h H+Hvipr
  gi|118431900|ref|NP_148648.2|  91 GQIIFHFHVHVIPR 104
                                    ************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.49
                                    GGGCCHHHHHHHHHHHHHHHHHHHT CS
                            HIT  40 lhdlteeelakllsavkkvakalqk 64 
                                     h++t+ee +++l + + v k +++
  gi|118431900|ref|NP_148648.2| 115 RHEITPEEAGEVLDTLRGVEKLIEE 139
                                    6889999999999988887776665 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 !   45.0   0.0   2.1e-15   1.3e-11       1     100 [.       2     102 ..       2     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.1e-15
                                    T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.-EE CS
                         DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.vda 79 
                                    +++f++++kg+ ++  vy+ ++++v+ D +p++k hllv+p ++ +s++   +     +      +    +ek  +    
  gi|118431900|ref|NP_148648.2|   2 ECIFCRIVKGEAEAYTVYKGNGVTVFLDRYPASKGHLLVVPDEHYESIHTAPPRVAAKVWLAASAIARYYREKAGApAVN 81 
                                    69*************************************************99999999999999999999988667555 PP

                                    EEE--SCCCT--S-S--EEEE CS
                         DcpS_C  80 eelrvgvhyqPsvyhlHlHvi 100
                                       + g  + + ++h+H+Hvi
  gi|118431900|ref|NP_148648.2|  82 VLTNSGRYAGQIIFHFHVHVI 102
                                    56899***************9 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 !   16.6   0.0   8.8e-07    0.0053      13     108 ..       2     103 ..       1     104 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.8e-07
                                    H-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHHHHHT.T--EE. CS
                       CwfJ_C_1  13 sClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkmykkq.dkdav. 90 
                                    +C fC   +  +++  v  gn v + l + p s+gH+l++p eH ++  +++  v   +    +a+++ y ++ +  av 
  gi|118431900|ref|NP_148648.2|   2 ECIFCRIVKGEAEAYTVYKGNGVTVFLDRYPASKGHLLVVPDEHYESIHTAPPRVAAKVWLAASAIARYYREKaGAPAVn 81 
                                    699999999999999999999999*********************************99999999999996541444441 PP

                                    EEEE-....SSS-----EEEEE CS
                       CwfJ_C_1  91 vfEis....sersvHlaiqvip 108
                                    v+ +s     +   H++++vip
  gi|118431900|ref|NP_148648.2|  82 VLTNSgryaGQIIFHFHVHVIP 103
                                    3444355444555688888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 1086.80
//
Query:       gi|118431901|ref|NP_148649.2|  [L=143]
Description: thioredoxin [Aeropyrum pernix K1]
Scores for 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-14   51.5   0.0    1.2e-13   50.9   0.0    1.3  1  Thioredoxin    Thioredoxin
      6e-10   39.6   0.2    3.5e-09   37.1   0.2    2.0  1  Thioredoxin_2  Thioredoxin-like domain
     0.0002   21.4   0.0    0.00042   20.3   0.0    1.6  2  Thioredoxin_3  Thioredoxin domain
     0.0046   17.1   0.1      0.013   15.7   0.0    1.9  2  Glutaredoxin   Glutaredoxin
     0.0047   16.8   0.0      0.006   16.4   0.0    1.1  1  TraF           F plasmid transfer operon protein
     0.0064   16.3   0.3       0.23   11.2   0.1    2.0  2  DSBA           DSBA-like thioredoxin domain
     0.0095   15.7   0.0      0.012   15.3   0.0    1.1  1  Redoxin        Redoxin
  ------ inclusion threshold ------
       0.06   13.5   0.5        2.5    8.2   0.4    2.1  2  Thioredoxin_4  Thioredoxin
       0.12   12.5   0.0       0.27   11.4   0.0    1.6  1  Thioredoxin_7  Thioredoxin-like


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 !   50.9   0.0     6e-17   1.2e-13      11     102 ..      44     134 ..      34     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 6e-17
                                    HHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEES CS
                    Thioredoxin  11 eeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyeg 90 
                                    +e + +  + v+  Fy p C+ C++l+P++e++a+ +++k  +a v+    + + + +++ g Pt++ f  g+e+ +++g
  gi|118431901|ref|NP_148649.2|  44 REMLDN-CRVVIAFFYTPTCPYCRMLKPVFEEAARFYRGKALFAAVNLARFPFMSDALGIMGTPTIIAFVRGREAGRLVG 122
                                    555555.77788889***************************************************************** PP

                                    S-HHHHHHHHHH CS
                    Thioredoxin  91 arekeklaaflk 102
                                      + e+l+af++
  gi|118431901|ref|NP_148649.2| 123 LMPPERLEAFVE 134
                                    *******99987 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2   1.8e-12   3.5e-09       6     108 ..      51     132 ..      47     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.8e-12
                  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                    + v+++f++p+CpyC+ lk +++e  ++        ++ +  + ++a+  a+ +             ++++g+ gtPti+
  gi|118431901|ref|NP_148649.2|  51 RVVIAFFYTPTCPYCRMLKPVFEEAARF--------YRGK--ALFAAVNLARFPF-----------MSDALGIMGTPTII 109
                                    568999*******************555........7888..5555555566652...........3477********88 PP

                  Thioredoxin_2  86 .fldgkeivarlpGyvpaeeleal 108
                                     f  g+ ++ rl+G++p+e+lea 
  gi|118431901|ref|NP_148649.2| 110 aFVRGR-EAGRLVGLMPPERLEAF 132
                                    799999.999***********985 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.9   5.7e+03      28      41 ..      27      42 ..      13      47 .. 0.49
   2 !   20.3   0.0   2.1e-07   0.00042       7      54 ..      59     109 ..      50     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
                                   TCEC..EEECCTTHHH CS
                  Thioredoxin_3 28 gika..evekvtdfee 41
                                   +i++   v +v d++e
  gi|118431901|ref|NP_148649.2| 27 RIDYegPVAEVLDPRE 42
                                   4444223445555544 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.1e-07
                                    SSSSTTCHHHHHHHHHHCHCCTCEC..EEECCTTHHHH.HHCT-SSSSEEE CS
                  Thioredoxin_3   7 gpgCakCpklekavkeaaaekgika..evekvtdfeei.ekygVmsvPalv 54 
                                    +p+C++C+ l+ +++eaa   + ka    ++   f+ + +  g+m +P+++
  gi|118431901|ref|NP_148649.2|  59 TPTCPYCRMLKPVFEEAARFYRGKAlfAAVNLARFPFMsDALGIMGTPTII 109
                                    89*******************88886677777999***9**********94 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   4.5e+03      34      44 ..       4      14 ..       2      21 .. 0.63
   2 !   15.7   0.0   6.7e-06     0.013       3      41 ..      56     100 ..      52     115 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                   SHHHHHHHHHH CS
                   Glutaredoxin 34 deeireelkel 44
                                   d+e+re l+++
  gi|118431901|ref|NP_148649.2|  4 DPELREILRKK 14
                                   56666666655 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.7e-06
                                    EEESTSSHHHHHHHHHHHHTT......GGEEEEEGCCSHHHHHHH CS
                   Glutaredoxin   3 lftkptCpyCkkakrlLkelg......vkfeeidvdkdeeireel 41 
                                     f +ptCpyC++ k +++e        + f+ +++   + + ++l
  gi|118431901|ref|NP_148649.2|  56 FFYTPTCPYCRMLKPVFEEAArfyrgkALFAAVNLARFPFMSDAL 100
                                    5778**********9998876554443446666666666666655 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06     0.006     131     202 ..      52     114 ..      42     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                           TraF 131 ygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpk 202
                                    + + fFy ++cpyc+++ p+ ++ a+ y  + ++ +v+   +p +++         +lg+  tP+++++ + 
  gi|118431901|ref|NP_148649.2|  52 VVIAFFYTPTCPYCRMLKPVFEEAARFYRGKALFAAVNLARFPFMSD---------ALGIMGTPTIIAFVRG 114
                                    6788************************9999988888888886888.........9999999999988776 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00012      0.23       2      39 ..      54      95 ..      53      99 .. 0.75
   2 ?    3.7   0.0     0.023        46     162     189 ..      99     130 ..      96     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                   EEEEEBTTBHHHHHHHHHHHHHHHHC....CTEEEEEEE-SS CS
                           DSBA  2 vdeffDvlCPyCylgkerleklaars....pdvkvvlrpfel 39
                                   + +f+   CPyC + k+++e++a+ +      + v l  f++
  gi|118431901|ref|NP_148649.2| 54 IAFFYTPTCPYCRMLKPVFEEAARFYrgkaLFAAVNLARFPF 95
                                   889999****************99886643225555555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.023
                                    HTT-SSSSEEEE..TTC..EEEESSSSHHHHH CS
                           DSBA 162 slgvtGvPtvvv..dgk..rmvfGadrldtla 189
                                    +lg+ G+Pt+++   g+    ++G  +++ l+
  gi|118431901|ref|NP_148649.2|  99 ALGIMGTPTIIAfvRGReaGRLVGLMPPERLE 130
                                    79*******99887665575677766666665 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     6e-06     0.012      23      97 ..      43     117 ..      35     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                                    HHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHH CS
                        Redoxin  23 lse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaf 97 
                                    l+e + + +vv+ f+ + +cP+C+   p +e+ a++++ k   + av+ +  +f+++++g  g + +++  ++ + 
  gi|118431901|ref|NP_148649.2|  43 LREmLDNCRVVIAFFYTPTCPYCRMLKPVFEEAARFYRGK-ALFAAVNLARFPFMSDALGIMGTPTIIAFVRGREA 117
                                    6677778899**999999*******999********7777.6788*********9999998777776666555555 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4    0.0013       2.5      14      49 ..      51      84 ..      48      93 .. 0.79
   2 ?    3.8   0.0     0.029        58     132     146 ..      96     110 ..      86     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                                   SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEE CS
                  Thioredoxin_4 14 pvtvieyedlrCphCakfeeeveklleeyidtGkvk 49
                                    v++  +   +Cp+C+ ++   e+  + y   Gk  
  gi|118431901|ref|NP_148649.2| 51 RVVIAFFYTPTCPYCRMLKPVFEEAARFY--RGKAL 84
                                   68999999********9988877777666..66655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                                    HHHHHT--SS-EEEE CS
                  Thioredoxin_4 132 eakkagiestPtfii 146
                                    + +++gi +tPt+i 
  gi|118431901|ref|NP_148649.2|  96 MSDALGIMGTPTIIA 110
                                    56899********96 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.27       9      50 ..      42      80 ..      37      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                   HHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HH CS
                  Thioredoxin_7  9 alakaaergkpvlvffgaswcftCqalerdflsdeevkaala 50
                                    l+++  + + v+ ff   +c++C+ l+ +f+++ ++   ++
  gi|118431901|ref|NP_148649.2| 42 ELREMLDNCRVVIAFFYTPTCPYCRMLKPVFEEAARF---YR 80
                                   67788888899999*****************998766...44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1072.83
//
Query:       gi|14602102|ref|NP_148650.1|  [L=199]
Description: small neutral amino acid transporter [Aeropyrum pernix K1]
Scores for complete 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-32  111.1  14.1      6e-32  110.7  14.1    1.2  1  MarC             MarC family integral membrane protein
  ------ inclusion threshold ------
        5.2    6.7   8.2       0.48   10.1   1.1    2.2  2  Kinocilin        Kinocilin 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 !  110.7  14.1   6.7e-36     6e-32       4     202 ..       7     193 ..       4     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 6.7e-36
                          MarC   4 iikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillflia 84 
                                   +++++++L+++++p+g  p + s++ + ++ er+ri+++a+ +a +il++f l+G  +l+++g+s+d +k+a g+ll++ a
  gi|14602102|ref|NP_148650.1|   7 VVSSIILLFIVLDPVGVSPYVASIVARRPEGERERIVRTALASAGAILVAFTLIGVAVLDILGVSMDEFKVAAGLLLLIYA 87 
                                   68899**********************************************************************999988 PP

                          MarC  85 idmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllilllss 165
                                      l+  +       se +     de+a++PLA+Pl+aGPg+i+tv+ ++ +       ++ ++ail+ +++++ il+ s 
  gi|14602102|ref|NP_148650.1|  88 TADLFEIKI----GYSEPS----GDEVAIFPLATPLLAGPGSIATVMYIMGSSGI----AVALIAILVNLVLAYPILHASL 156
                                   765554333....356666....79***********************9988776....688999**************** PP

                          MarC 166 lilrllgktginaleRlmGllLvalavqlivdGikei 202
                                    ++rllg+ g  ++++ +++l+v  av +i+dG+++i
  gi|14602102|ref|NP_148650.1| 157 KLVRLLGRHGSLLVAKFTAFLMVGFAVSIIFDGLRGI 193
                                   ***********************************98 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.0     0.053   4.8e+02      23      56 ..      54      87 ..      39      96 .. 0.56
   2 ?   10.1   1.1   5.4e-05      0.48      42      78 ..     133     170 ..     105     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.053
                     Kinocilin 23 lagsiiigvsvskaaaavggifigaaglglllla 56
                                  l    +igv+v          f  aagl ll++a
  gi|14602102|ref|NP_148650.1| 54 LVAFTLIGVAVLDILGVSMDEFKVAAGLLLLIYA 87
                                  2233345555555555444555566666555554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.4e-05
                     Kinocilin  42 gifig.aaglgllllaypflkarfnldrilpaignlri 78 
                                   gi +   a l  l+layp+l+a + l r+l   g+l +
  gi|14602102|ref|NP_148650.1| 133 GIAVAlIAILVNLVLAYPILHASLKLVRLLGRHGSLLV 170
                                   33332134566789*****************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1393.36
//
Query:       gi|118431902|ref|NP_148651.2|  [L=134]
Description: hypothetical protein APE_2499.1 [Aeropyrum pernix K1]
Scores for complete 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   0.1    2.5e-06   27.8   0.1    1.2  1  4HBT      Thioesterase superfamily


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 !   27.8   0.1   1.4e-10   2.5e-06       8      77 ..      40     109 ..      33     110 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.4e-10
                                    HHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCE CS
                           4HBT   8 vylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrl 77 
                                    ++l + +++a ++l  +  +g + v+ve  +++l+p+ +g+++++ear++ + ++ +++ ++v++ dg+l
  gi|118431902|ref|NP_148651.2|  40 YMLLYGEVTARECLDQHLPAGMASVGVEALVRHLAPIPVGSRVMIEARIISVDGKGVSIVIRVKRHDGTL 109
                                    56667777888888888888*********************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1000.21
//
Query:       gi|118431903|ref|NP_148652.2|  [L=1180]
Description: hypothetical protein APE_2500.1 [Aeropyrum pernix K1]
Scores for complete 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  180.8  30.6    6.3e-28   97.7  11.7    2.4  2  MMPL       MMPL family
  ------ inclusion threshold ------
       0.13   12.0   0.1       0.13   12.0   0.1    3.1  3  MotA_ExbB  MotA/TolQ/ExbB proton channel family


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7  11.7     7e-32   6.3e-28      90     307 ..     612     830 ..     534     854 .. 0.87
   2 !   88.4  10.8   4.5e-29     4e-25      84     320 ..     944    1164 ..     921    1174 .. 0.88

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 7e-32
                           MMPL  90 alvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlva 169
                                    +l+ + g  g + a+++++++r+ v+ea  + +++v ++G  a+ ++l++a+ +dl+   +++ +++++iL+ v + ++ 
  gi|118431903|ref|NP_148652.2| 612 FLIAYLGGGGYEGAKAAAEDVRRLVNEAL-DGDARVMLAGEEALRKELQEAVVEDLRRSDAASSIIVVAILAAVIGTILG 690
                                    567777778899999**************.************************************************** PP

                           MMPL 170 allplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedreeaviravastgk 249
                                    +++p + ++ +l aal+++++la ++ +++++++ ++++  +++ G+DY   ++ ++r+ ++  + + ea+ +a   + +
  gi|118431903|ref|NP_148652.2| 691 VIIPFIGIGAGLTAALAILYFLASNDLVDVTSQSRAIVFTTGLGLGIDYSAYVTKKFRDNIRGSRGAWEAAGKAASNSVR 770
                                    ******************************************************************************** PP

                           MMPL 250 vvtaaGltvaiamlg.LvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.l 307
                                     v+a ++  a+ + + +++ ++p+++++G ++ +++l ++ ++lTl+PA+l+l+G a+ l
  gi|118431903|ref|NP_148652.2| 771 PVLAGAFAAAAGFSSlMLAFEFPFVKSIGATVPIAILSVAVASLTLTPAILALVGWAGiL 830
                                    ***********9999455669**********************************88752 PP

  == domain 2  score: 88.4 bits;  conditional E-value: 4.5e-29
                           MMPL   84 DgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdl.klievvtlvvilviL 160 
                                     Dg+ +++++ +  +p +tea + v+++r  v+e + + +    v+G+aa++ dlrd+  r     ++ +++v++++i 
  gi|118431903|ref|NP_148652.2|  944 DGRLIYVVLDT--NPLNTEAVKCVEELRGKVREVD-PGS---LVGGTAAVNLDLRDYLYRAFyNRVIPAAAVLVAAII 1015
                                     77776666555..5999******************.444...49************9988752788889999999*** PP

                           MMPL  161 livyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaagedree 238 
                                     ++ y+S+ aal  ++++++  + +l++v+il+   g+e  +f++ ll + l++vG DY  + v   re+  +ge+++ 
  gi|118431903|ref|NP_148652.2| 1016 AVFYGSIPAALAGVASILFAAAWSLSIVSILSGWTGIEAPWFAPVLLAAALLGVGMDYISFYVNHAREAYLRGEHSRY 1093
                                     ****************************************************************************98 PP

                           MMPL  239 aviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGraalakprrkrk 315 
                                      v  a ++tg v+   ++++ +a +gL+++r+++l+++Gv ++lGv+++ l++  ll P +++ll  +          
  gi|118431903|ref|NP_148652.2| 1094 YVEAASTGTGLVIGL-AMIMGGAYAGLTLSRVEALQAIGVSLSLGVILAGLLASLLLiPPVMALLKAR---------- 1160
                                     888888888888766.59*****************************998887777779999888777.......... PP

                           MMPL  316 krwWr 320 
                                      +wW+
  gi|118431903|ref|NP_148652.2| 1161 -FWWP 1164
                                     .4553 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 ?   -2.4   0.0      0.42   3.8e+03      21      53 ..     124     156 ..     107     159 .. 0.81
   2 ?   12.0   0.1   1.5e-05      0.13      21      78 ..     644     701 ..     627     710 .. 0.79
   3 ?   -7.1   4.5         2   1.8e+04      90     108 ..    1010    1028 ..    1006    1038 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.42
                                    HHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHH CS
                      MotA_ExbB  21 gaepeelrraleealsreeerlekglsilatig 53 
                                    ++ +e+l+ aleea++   +  e g si+++  
  gi|118431903|ref|NP_148652.2| 124 DKAMENLEPALEEAVRGGVQAFEGGYSIWNSYL 156
                                    567899999999999999999999999988765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      MotA_ExbB  21 gaepeelrraleealsreeerlekglsilatigslaPllGLlGTVlGlieafqalada 78 
                                     + + + ++al+++l+++  +  ++    ++i+ +a l  ++GT+lG+i  f  +++ 
  gi|118431903|ref|NP_148652.2| 644 ARVMLAGEEALRKELQEAVVEDLRRSDAASSIIVVAILAAVIGTILGVIIPFIGIGAG 701
                                    455556689999999999999999999*************************999974 PP

  == domain 3  score: -7.1 bits;  conditional E-value: 2
                                     HHHHHHHHHHHHHHHHHHH CS
                      MotA_ExbB   90 iaeALiaTalGlvvAipav 108 
                                     +  A ia ++G + A +a 
  gi|118431903|ref|NP_148652.2| 1010 LVAAIIAVFYGSIPAALAG 1028
                                     4456666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.87u 0.29s 00:00:01.15 Elapsed: 00:00:00.46
# Mc/sec: 7700.48
//
Query:       gi|118431904|ref|NP_148654.2|  [L=321]
Description: hypothetical protein APE_2502.1 [Aeropyrum pernix K1]
Scores for complete 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   97.6   0.1    1.4e-27   97.2   0.1    1.3  1  Amidohydro_2  Amidohydrolase
  ------ inclusion threshold ------
      0.055   13.4   0.0      0.093   12.7   0.0    1.3  1  DUF5411       Family of unknown function (DUF5411)


Domain annotation for each model (and alignments):
>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.1   1.6e-31   1.4e-27      74     289 ..     109     310 ..       9     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 1.6e-31
                                    HHHHHHHCTTCBECEEECTSSHCHHHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE....C CS
                   Amidohydro_2  74 laeaakrpdrfvggaavvpldpedaaaeleraveelgfkGvrlnphvggddllgdrldrpifealeelglpvdihtGpsp 153
                                    l  +    +rf+  +++  +  e+ +a++ r+     + Gv++ p ++  +++++rl+ p+++a ee g  v +htG   
  gi|118431904|ref|NP_148654.2| 109 LRACRSVEPRFFYTIVSYKPGMEEEVAQIVRSD--SSILGVKIFPTFHFTRPDSQRLY-PVYKAVEEAGGLVVVHTG--C 183
                                    556777788888888888888888888888875..7999*******************.****************99..* PP

                                    HHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTT.....TTCHHHHHHHHHHHHHCCEEECCGHHHSSEEECCHH CS
                   Amidohydro_2 154 ewlfggpqettraiqplllsgvarkfPnlkivlaHgGgp.....serlraalellarrpnvyvklsglytellyfdspla 228
                                    + +++  + ++r+  p +++++a +f+nl +v+aH+G         +++++l++l  ++nvy+++s+            a
  gi|118431904|ref|NP_148654.2| 184 DPGPWELTRFCREARPSYVARAAKRFENLVFVIAHLGAYsalkpGIYFEETLKAL-SLENVYADTSA------------A 250
                                    ***************************************9*99777777777775.5778**99999............8 PP

                                    CHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHHSSHHHHHHHHTHHHHHHC CS
                   Amidohydro_2 229 dppalarlieavgpdrilfGsDyPhptleaepealalldlvallsdeerekilggNAarly 289
                                    dp + a ++++ ++d+ilfGsDyP++++ +   a++++  +++ + +++e++l+ NA++l+
  gi|118431904|ref|NP_148654.2| 251 DPFFAAMAVKEGYADKILFGSDYPYVSGYNVAMAVKDILSLDI-DNNDKEAVLRYNAEKLL 310
                                    9***************************777777777776665.****************8 PP

>> DUF5411  Family of unknown function (DUF5411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     1e-05     0.093      38      77 ..      59     100 ..      38     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1e-05
                        DUF5411  38 ikeiteaslvdavdysyyret...Gelkiskekfvevfirrfa 77 
                                     +eitea++ d  dy ++++    G++ +  ekf++ f+  f 
  gi|118431904|ref|NP_148654.2|  59 PREITEAAMED-FDYLAFQQVgyiGRMIMEPEKFLDDFLGDFH 100
                                    59*******88.699999886222577999********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2228.18
//
Query:       gi|118431905|ref|NP_148655.2|  [L=250]
Description: 3-oxoacyl-ACP reductase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-60  205.0   0.1    1.5e-60  204.7   0.1    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    3.4e-55  186.5   0.1      4e-55  186.3   0.1    1.0  1  adh_short     short chain dehydrogenase
    2.5e-13   50.3   0.1    3.8e-13   49.7   0.1    1.3  1  KR            KR domain
    0.00084   18.9   0.0      0.002   17.7   0.0    1.9  1  Epimerase     NAD dependent epimerase/dehydratase family
     0.0086   15.5   0.0      0.016   14.6   0.0    1.6  1  DUF1776       Fungal family of unknown function (DUF1776)


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 !  204.7   0.1   4.1e-64   1.5e-60       3     232 ..      12     247 ..       9     249 .. 0.95

  Alignments for each domain:
  == domain 1  score: 204.7 bits;  conditional E-value: 4.1e-64
                                    TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                     +gIGra++ ++a+eG++vv+++ ++++ +++++e a++lg+  +  +++DV d+++v+++ ++v e + +l++lvn+ag
  gi|118431905|ref|NP_148655.2|  12 SRGIGRATVLRFAREGWSVVIAYKSRADlAEKTAEEARRLGSPeAytVRVDVGDPDSVTEMSSRVGELIPHLNVLVNAAG 91 
                                    59***************************9***********776447********************************* PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTT.HHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnyn.aygaaKaalealtryl 155
                                    + +   g ++ets +e++++l vnl++++l++k +lpl+++   +sivn++s+++e +      ay+a+Ka++++lt+ l
  gi|118431905|ref|NP_148655.2|  92 VLQL--GGIEETSISEWEETLRVNLTGVYLVTKLLLPLLRKAkwASIVNVASIAGETGNVVAGvAYSASKAGVIGLTKRL 169
                                    ****..*******************************8877668*************9777777**************** PP

                                    HHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSG.GGTT--SEEEEESTT CS
                   adh_short_C2 156 AvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasd.easyitGqtlvvDgG 232
                                    Av+l+ +giRvNav+p++++T++++++ +++e +e++++ +pl+ + +pe+vaea+lfLa + ++++itG++l +++G
  gi|118431905|ref|NP_148655.2| 170 AVQLAGYGIRVNAVAPSFVETDMTRSFLDTPEKRERIASLHPLKIILKPEDVAEAILFLADPrRSRGITGHVLSINAG 247
                                    ************************************************************9846889********999 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.3   0.1   1.1e-58     4e-55       3     190 ..       6     196 ..       4     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 186.3 bits;  conditional E-value: 1.1e-58
                                    EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldv 80 
                                    +lvtG+s+GIGra++ ++a+eG++vv+ ++++++ +e++a+e +++ + +a++++vDv d ++v ++ +++ + + +l+v
  gi|118431905|ref|NP_148655.2|   6 ALVTGGSRGIGRATVLRFAREGWSVVIaYKSRADLAEKTAEEARRLgSPEAYTVRVDVGDPDSVTEMSSRVGELIPHLNV 85 
                                    8**************************99999999***********999******************************* PP

                                    EEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-.TTBHHHHHHHHHHHHH CS
                      adh_short  81 LvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpv.agvaaYsAsKaavagl 159
                                    Lvn AG+ + g ++e+s +ewe+++ vNltgv+l+t+++lp + k+++++Ivnv+S+ag+ ++   ++aYsAsKa+v+gl
  gi|118431905|ref|NP_148655.2|  86 LVNAAGVLQLGGIEETSISEWEETLRVNLTGVYLVTKLLLPLLRKAKWASIVNVASIAGETGNvVAGVAYSASKAGVIGL 165
                                    ***********************************************************8775156899*********** PP

                                    HHHHHHHHGGGTEEEEEEEESSBSSHHHHHH CS
                      adh_short 160 trslakelaptgirvnavaPGlvdTdmakel 190
                                    t+ la +la +girvnavaP +v+Tdm+++ 
  gi|118431905|ref|NP_148655.2| 166 TKRLAVQLAGYGIRVNAVAPSFVETDMTRSF 196
                                    ***************************9976 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.1   1.1e-16   3.8e-13       4     151 ..       7     157 ..       4     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.1e-16
                                    EEETTTSHHHHHHHHHHHHHH.S-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHHHSS- CS
                             KR   4 litGGlGgLGlelarwlaekg.arhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeikaeepp 81 
                                    l+tGG  g+G++++   a++g    +++ sR     e+     +e ++lg  e  +v++Dv d+d+v+++ +++ +  p 
  gi|118431905|ref|NP_148655.2|   7 LVTGGSRGIGRATVLRFAREGwSVVIAYKSRA-DLAEKT---AEEARRLGSpEAYTVRVDVGDPDSVTEMSSRVGELIPH 82 
                                    9********************55556666777.444444...455555555478899******************999** PP

                                    --EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-H.HHHH CS
                             KR  82 ikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqa.nYaa 151
                                    ++  ++aAgvl+ + +ee++ +++e+ l+  ++G+  + +ll +     +   +v ++Siag +g+   + +Y+a
  gi|118431905|ref|NP_148655.2|  83 LNVLVNAAGVLQLGGIEETSISEWEETLRVNLTGVYLVTKLLLPllrkAKWASIVNVASIAGETGNVVAGvAYSA 157
                                    **********************************988877765555438888899*******9999765415555 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   5.5e-07     0.002       1      63 [.       6      76 ..       6     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.5e-07
                                   EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHH CS
                      Epimerase  1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl........elveldltdrsalerlfkee 63
                                   +lVtG++  iG+a+v +++++g+  vi+ +++ +  ++ ++e +          v++d+ d+++++++ +++
  gi|118431905|ref|NP_148655.2|  6 ALVTGGSRGIGRATVLRFAREGWSvVIAYKSRADLAEKTAEE-ArrlgspeaYTVRVDVGDPDSVTEMSSRV 76
                                   59********************99666666665544444433.3489*****9**********999887754 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 !   14.6   0.0   4.6e-06     0.016     104     167 ..      94     154 ..      12     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-06
                        DUF1776 104 ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapE 167
                                    + g ie+ ++s+w+++l  +l   +l+++ llpll++    k   iv  +si  +  ++ +++ 
  gi|118431905|ref|NP_148655.2|  94 QLGGIEETSISEWEETLRVNLTGVYLVTKLLLPLLRK---AKWASIVNVASIAGETGNVVAGVA 154
                                    7799********************************8...666667777777666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1903.66
//
Query:       gi|14602108|ref|NP_148656.1|  [L=153]
Description: ArsR family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-09   36.5   1.8    9.3e-09   35.1   0.2    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
    1.4e-06   28.1   0.1    1.4e-06   28.1   0.1    1.9  2  MarR_2           MarR family
    3.4e-06   26.8   0.4    1.4e-05   24.8   0.0    2.1  2  HTH_IclR         IclR helix-turn-helix domain
    3.9e-05   24.0   0.0    7.6e-05   23.0   0.0    1.5  1  Penicillinase_R  Penicillinase repressor
    3.9e-05   23.7   2.9      0.002   18.2   0.1    2.3  2  HTH_28           Helix-turn-helix domain
    4.9e-05   23.1   0.1    0.00029   20.6   0.0    2.3  2  HTH_5            Bacterial regulatory protein, arsR family
     0.0001   22.3   1.1    0.00047   20.2   0.0    2.4  2  HTH_20           Helix-turn-helix domain
    0.00019   20.9   2.8    0.00038   20.0   0.1    2.7  3  HTH_24           Winged helix-turn-helix DNA-binding
      0.002   18.1   1.2     0.0071   16.3   0.1    2.2  2  HTH_29           Winged helix-turn helix
     0.0047   16.8   0.2      0.022   14.7   0.1    2.1  2  PadR             Transcriptional regulator PadR-like family
     0.0048   17.1   1.7     0.0055   16.9   0.5    1.7  1  PaaX             PaaX-like protein
     0.0054   16.6   0.0      0.015   15.2   0.0    1.9  1  MarR             MarR family
     0.0059   17.1   0.6      0.015   15.8   0.2    1.9  2  HTH_27           Winged helix DNA-binding domain
     0.0078   16.4   1.3      0.014   15.6   1.3    1.4  1  ABC_tran_CTD     ABC transporter C-terminal domain
     0.0079   16.2   0.5      0.018   15.1   0.1    1.7  2  Sulfolobus_pRN   Sulfolobus plasmid regulatory protein
  ------ inclusion threshold ------
      0.016   15.4   0.1      0.027   14.7   0.1    1.4  1  VPS11_C          Vacuolar protein sorting protein 11 C termin
      0.023   14.9   1.3       0.03   14.5   1.3    1.2  1  ATG16            Autophagy protein 16 (ATG16)
      0.025   15.2   0.3      0.052   14.2   0.3    1.5  1  SlyX             SlyX
      0.027   14.6   0.4       0.11   12.6   0.1    2.1  2  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
       0.03   14.1   1.5        5.7    6.9   0.0    2.3  2  HTH_23           Homeodomain-like domain
      0.038   13.3   1.3       0.58    9.4   0.1    2.0  2  EAP30            EAP30/Vps36 family
      0.042   13.9   0.4      0.065   13.3   0.4    1.2  1  DivIVA           DivIVA protein
      0.046   13.4   0.1       0.27   10.9   0.0    1.9  2  DUF4423          Domain of unknown function (DUF4423)
      0.064   12.3   0.1      0.082   12.0   0.1    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.067   13.5   0.6       0.14   12.5   0.6    1.7  1  CCDC-167         Coiled-coil domain-containing protein 167
        0.1   12.5   0.1       0.21   11.5   0.1    1.5  1  TFIIE_alpha      TFIIE alpha subunit
       0.11   11.7   0.0       0.14   11.4   0.0    1.1  1  FmiP_Thoc5       Fms-interacting protein/Thoc5
       0.12   12.4   0.0        0.2   11.7   0.0    1.3  1  HTH_45           Winged helix-turn-helix
       0.13   12.1   0.1       0.31   10.9   0.1    1.7  1  SMC_Nse1         Nse1 non-SMC component of SMC5-6 complex
       0.18   11.8   0.0       0.49   10.4   0.0    1.8  2  HTH_36           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 ?    0.6   0.1      0.91   5.4e+02      16      36 ..      34      54 ..       4      74 .. 0.72
   2 !   35.1   0.2   1.6e-11   9.3e-09      18      63 ..      95     141 ..      92     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.91
                                  HHHHHCCCHHCHHCCCTTSSC CS
                          TrmB 16 aLlklgpatadeiaeelgvpr 36
                                  a l++ + +++ i+++lg++ 
  gi|14602108|ref|NP_148656.1| 34 AALARLEERISSISQALGRDA 54
                                  445555666777777777764 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.6e-11
                                   HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEE CS
                          TrmB  18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYr 63 
                                   l++g at +e+ +++g+++++vY vL++L+++G+Ve+++ gr+ +Y+
  gi|14602108|ref|NP_148656.1|  95 LEKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKRRdGRRVVYS 141
                                   789**********************************9945566876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2       4.6   2.7e+03      14      14 ..      36      36 ..      15      54 .. 0.60
   2 !   28.1   0.1   2.3e-09   1.4e-06      14      61 ..      95     136 ..      82     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.6
                                  H CS
                        MarR_2 14 L 14
                                  L
  gi|14602108|ref|NP_148656.1| 36 L 36
                                  1 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.3e-09
                                   HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                        MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61 
                                   L   + +d t++el r +glsk +v  +lkrLv++G ve+r++   +R
  gi|14602108|ref|NP_148656.1|  95 L---EKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKRRD---GR 136
                                   3...33468********************************85...55 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   0.2       3.6   2.1e+03      11      29 ..      35      51 ..      27      54 .. 0.73
   2 !   24.8   0.0   2.3e-08   1.4e-05      17      50 ..      98     131 ..      91     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.6
                                  T-CTTBSS-BHHHHHHHHT CS
                      HTH_IclR 11 alaeapqeltlselArrtg 29
                                  ala+  +  ++s +++++g
  gi|14602108|ref|NP_148656.1| 35 ALARLEE--RISSISQALG 51
                                  4566666..4888888887 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 2.3e-08
                                   SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                      HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                   ++ t sel r tgl+k  v++ L+ Lve+G+ve+
  gi|14602108|ref|NP_148656.1|  98 GDATPSELIRDTGLSKNRVYGVLKRLVERGIVEK 131
                                   34579***************************98 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.3e-07   7.6e-05      27      70 ..     105     148 ..      93     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-07
                                   --GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXX CS
               Penicillinase_R  27 leeekelaysTVktllrrLvkKgllsrekegrafiYsplvseee 70 
                                   l +++ l+++ V  +l+rLv++g+++++++gr+ +Ys +  e +
  gi|14602108|ref|NP_148656.1| 105 LIRDTGLSKNRVYGVLKRLVERGIVEKRRDGRRVVYSLRRVEAQ 148
                                   5566689999**************************97766655 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.028        17       1      29 [.      27      57 ..      27      71 .. 0.78
   2 !   18.2   0.1   3.3e-06     0.002       5      50 ..      91     134 ..      90     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.028
                        HTH_28  1 qRleiikllaa..GhsvreaArelgisrrtv 29
                                  +R+e++++++a   ++++ ++++lg + r+ 
  gi|14602108|ref|NP_148656.1| 27 RRIEALEAALArlEERISSISQALGRDARST 57
                                  69****999964445**********966654 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.3e-06
                        HTH_28   5 iikllaaGh.svreaArelgisrrtvyrWikryeegGiagLvprrrr 50 
                                   ii +l +G+ + +e+ r  g+s  +vy+ +kr+ e Gi   v +rr 
  gi|14602108|ref|NP_148656.1|  91 IISHLEKGDaTPSELIRDTGLSKNRVYGVLKRLVERGI---VEKRRD 134
                                   889999*******************************9...555553 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.1   1.3e+03      10      26 ..      35      51 ..      27      52 .. 0.82
   2 !   20.6   0.0   4.9e-07   0.00029       7      47 .]      91     131 ..      85     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.1
                                  HHTTSSEEHHHHHHHHT CS
                         HTH_5 10 lLaegelcvcelaeelg 26
                                  +La+ e  ++ ++ +lg
  gi|14602108|ref|NP_148656.1| 35 ALARLEERISSISQALG 51
                                  68888899999999986 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.9e-07
                                   HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                         HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                   I++ L++g ++ +el +++gls+  v   Lk+L e G+Vek
  gi|14602108|ref|NP_148656.1|  91 IISHLEKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEK 131
                                   8999***********************************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.3       1.2   7.2e+02      42      51 ..      26      35 ..       3      61 .. 0.71
   2 !   20.2   0.0   7.9e-07   0.00047      15      61 .]      91     136 ..      91     136 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.2
                                  HHHHHHHHHC CS
                        HTH_20 42 syHLrvLeea 51
                                  ++++++Le a
  gi|14602108|ref|NP_148656.1| 26 RRRIEALEAA 35
                                  5555555443 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 7.9e-07
                                   HHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                        HTH_20  15 ilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                   i ++L +++ +t+sel +  +lskn ++  L+ L+e g+ve +r gr
  gi|14602108|ref|NP_148656.1|  91 IISHL-EKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKRRDGR 136
                                   78999.9999**********************************997 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         7   4.2e+03      35      43 ..      26      34 ..      26      35 .. 0.81
   2 ?    0.4   0.1      0.83     5e+02      40      47 ..      84      91 ..      83      92 .. 0.87
   3 !   20.0   0.1   6.3e-07   0.00038      14      48 .]      96     130 ..      91     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7
                        HTH_24 35 nrrlkrLee 43
                                  +rr++ Le 
  gi|14602108|ref|NP_148656.1| 26 RRRIEALEA 34
                                  599999996 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.83
                        HTH_24 40 rLeeeGlI 47
                                   Le+eG+I
  gi|14602108|ref|NP_148656.1| 84 MLEDEGII 91
                                  59*****9 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 6.3e-07
                        HTH_24  14 knprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                   ++++ + +eL + +glS++ v   lkrL+e G+++
  gi|14602108|ref|NP_148656.1|  96 EKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVE 130
                                   4599*****************************96 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.7     1e+03      13      25 ..      40      53 ..      28      57 .. 0.62
   2 !   16.3   0.1   1.2e-05    0.0071       4      52 ..      91     136 ..      90     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.7
                        HTH_29 13 s.tvsqiAkllgls 25
                                    ++s i ++lg +
  gi|14602108|ref|NP_148656.1| 40 EeRISSISQALGRD 53
                                  23788898888886 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.2e-05
                        HTH_29   4 allllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgr 52 
                                   ++ +l++G  t+s++ + +gls+  vy +lkr +e G   + ++rr gr
  gi|14602108|ref|NP_148656.1|  91 IISHLEKGDATPSELIRDTGLSKNRVYGVLKRLVERG---IVEKRRDGR 136
                                   5677888888***************************...566676666 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         4   2.4e+03      41      53 ..      85      97 ..      84     107 .. 0.77
   2 !   14.7   0.1   3.6e-05     0.022      29      65 ..     111     142 ..     103     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4
                                  HHHTTSEEEEEE- CS
                          PadR 41 Lekeglvesewee 53
                                  Le+eg++ s+ e+
  gi|14602108|ref|NP_148656.1| 85 LEDEGIIISHLEK 97
                                  8999999887766 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.6e-05
                                   TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
                          PadR  29 lseGslYpaLkrLekeglveseweesgegpprkyYrl 65 
                                   ls+ ++Y +LkrL + g+ve++++     ++r +Y l
  gi|14602108|ref|NP_148656.1| 111 LSKNRVYGVLKRLVERGIVEKRRD-----GRRVVYSL 142
                                   67889****************966.....47888876 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   9.2e-06    0.0055      28      66 ..     104     142 ..     100     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.2e-06
                          PaaX  28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrL 66 
                                   +l+ + G+s + v   l Rl+++G + + ++grr++Y+L
  gi|14602108|ref|NP_148656.1| 104 ELIRDTGLSKNRVYGVLKRLVERGIVEKRRDGRRVVYSL 142
                                   5778899999999999**********************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.5e-05     0.015      14      52 ..      96     134 ..      85     139 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                                   HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                          MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                   e+g+++ seL +  g+sk  v  vl+rL+++G +e++++
  gi|14602108|ref|NP_148656.1|  96 EKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKRRD 134
                                   67999*******************************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.2   4.3e+03      19      32 ..      41      54 ..      22      59 .. 0.65
   2 !   15.8   0.2   2.5e-05     0.015      14      64 ..      94     142 ..      88     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.2
                        HTH_27 19 kkladlcgrlnved 32
                                   +++ ++++l +++
  gi|14602108|ref|NP_148656.1| 41 ERISSISQALGRDA 54
                                  44556666666655 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.5e-05
                        HTH_27  14 hrrrrkkl.adlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64 
                                   h + +++  ++l++ + +++  +  +lk+L+e+G v   ++++d+r++ ++l
  gi|14602108|ref|NP_148656.1|  94 HLEKGDATpSELIRDTGLSKNRVYGVLKRLVERGIV---EKRRDGRRVVYSL 142
                                   4455566669**************************...6668999999986 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 !   15.6   1.3   2.3e-05     0.014       7      44 ..      26      61 ..      20      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                  ABC_tran_CTD  7 qreleeleaeIeaLEeeiaeleaeladpelysdpekla 44
                                  +r++e+lea +++LEe+i+++ ++l   +     e l+
  gi|14602108|ref|NP_148656.1| 26 RRRIEALEAALARLEERISSISQALGRDA--RSTESLQ 61
                                  67799999999999999999999987665..4445555 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.6   3.3e+03      19      27 ..      34      42 ..       9      49 .. 0.65
   2 !   15.1   0.1     3e-05     0.018       8      51 ..      88     132 ..      82     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.6
                Sulfolobus_pRN 19 atleeleek 27
                                  a+l +lee+
  gi|14602108|ref|NP_148656.1| 34 AALARLEER 42
                                  344455555 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3e-05
                Sulfolobus_pRN   8 ekilli.lsrrcatleeleektGiekeellvyltrlykrGlisrk 51 
                                   e i+++ l ++ at  el   tG+ k+ +   l rl +rG++ ++
  gi|14602108|ref|NP_148656.1|  88 EGIIIShLEKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKR 132
                                   44555439999******************************9865 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 ?   14.7   0.1   4.5e-05     0.027       3      41 ..      14      52 ..      12      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.5e-05
                       VPS11_C  3 tirelrraQeesadrhdlFkaaLeeseDrFkvvadyFGR 41
                                   i+ l r++ee+  r + ++aaL + e r + ++  +GR
  gi|14602108|ref|NP_148656.1| 14 DIETLARSNEENRRRIEALEAALARLEERISSISQALGR 52
                                  6999*********************************99 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.3   5.1e-05      0.03      87     135 ..      12      60 ..       5      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                         ATG16  87 reelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraal 135
                                   r + ++l +s++e+  r+ +l+++l++lee++++ +++l +  ++ ++l
  gi|14602108|ref|NP_148656.1|  12 RRDIETLARSNEENRRRIEALEAALARLEERISSISQALGRDARSTESL 60 
                                   78999999**********************9999998886655555554 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   8.7e-05     0.052       3      36 ..      27      60 ..       7      64 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.7e-05
                                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SlyX  3 erleeLEiklafqedtieeLndvvaeqqqqidrl 36
                                   r+e+LE  la +e+ i + ++++ + ++  + l
  gi|14602108|ref|NP_148656.1| 27 RRIEALEAALARLEERISSISQALGRDARSTESL 60
                                  4666666666666666666666666666665555 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.6     4e+03      21      35 ..       6      21 ..       4      23 .. 0.59
   2 ?   12.6   0.1   0.00019      0.11      14      43 ..     100     134 ..      93     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.6
                       AbiEi_4 21 a.aGispsalrrLvrk 35
                                  a +G +++ +  L r+
  gi|14602108|ref|NP_148656.1|  6 AlLGFDRRDIETLARS 21
                                  5566666666655555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00019
                       AbiEi_4  14 fttrelea.aGispsa....lrrLvrkGwLvrlrr 43 
                                   +t +el++  G+s +     l rLv++G +++ r 
  gi|14602108|ref|NP_148656.1| 100 ATPSELIRdTGLSKNRvygvLKRLVERGIVEKRRD 134
                                   6899**********778*************99775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.5     0.018        11       5      32 ..      26      55 ..      22      58 .. 0.86
   2 ?    6.9   0.0    0.0095       5.7      11      46 ..      92     128 ..      89     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.018
                        HTH_23  5 reRlrillllae..GlsvreIAreLgvsrr 32
                                  r+R+++l +++     +++ I+++Lg+  r
  gi|14602108|ref|NP_148656.1| 26 RRRIEALEAALArlEERISSISQALGRDAR 55
                                  899999999998889***********8766 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0095
                        HTH_23  11 llllae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                   + +l +  ++++e  r  g s++ vy +lkr +e G+
  gi|14602108|ref|NP_148656.1|  92 ISHLEKgDATPSELIRDTGLSKNRVYGVLKRLVERGI 128
                                   555555778888999999*************999885 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5     0.034        21      12      58 ..      17      59 ..       7      66 .. 0.81
   2 ?    9.4   0.1   0.00097      0.58     197     232 ..      70     129 ..      43     130 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.034
                         EAP30 12 taaeyqdlgaellaealqdleallakfkesLvklaekhkakiksdpa 58
                                  t a+     +e ++++ ++lea la+++e++ ++++ + ++ +s+++
  gi|14602108|ref|NP_148656.1| 17 TLARS----NEENRRRIEALEAALARLEERISSISQALGRDARSTES 59
                                  44444....888999********************999999988765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00097
                         EAP30 197 g...........................ggvtaselaeeeenlgwsvarakeaLeelereGll 232
                                   +                           g  t sel    + +g+s++r+  +L++l+++G++
  gi|14602108|ref|NP_148656.1|  70 EteyeghngtveegmledegiiishlekGDATPSEL---IRDTGLSKNRVYGVLKRLVERGIV 129
                                   355556666666666666666676666689******...566******************986 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   0.00011     0.065      32      77 ..      13      58 ..      12      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                  HHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXX CS
                        DivIVA 32 kdyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetae 77
                                  +d+e+l + nee ++++++le +l++ +e+ ++++++l    +++e
  gi|14602108|ref|NP_148656.1| 13 RDIETLARSNEENRRRIEALEAALARLEERISSISQALGRDARSTE 58
                                  699*********************************9966666555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.84     5e+02     124     148 ..       8      32 ..       4      50 .. 0.75
   2 ?   10.9   0.0   0.00046      0.27      31      76 ..      94     137 ..      90     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.84
                       DUF4423 124 laiskedyekikkeirefrkkilai 148
                                   l+++++d+e +++  +e r++i a+
  gi|14602108|ref|NP_148656.1|   8 LGFDRRDIETLARSNEENRRRIEAL 32 
                                   6788888888888888888888754 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00046
                       DUF4423  31 plkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgky 76 
                                    l++++a+p+el + ++  +s+ +v   l++L++ g+++k +dg+ 
  gi|14602108|ref|NP_148656.1|  94 HLEKGDATPSELIRDTG--LSKNRVYGVLKRLVERGIVEKRRDGRR 137
                                   578899***********..************************875 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 ?   12.0   0.1   0.00014     0.082      87     131 ..      12      56 ..       8      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                         Atg14  87 kdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkk 131
                                   + ++++l +++ee ++++++l ++l++  ++++s+++ l    ++
  gi|14602108|ref|NP_148656.1|  12 RRDIETLARSNEENRRRIEALEAALARLEERISSISQALGRDARS 56 
                                   678999*************************99999998754433 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 ?   12.5   0.6   0.00024      0.14       5      44 ..      28      67 ..      26     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                      CCDC-167  5 eIdkleeklascrerLeaverrlrkeelseeeResleeEe 44
                                   I+ le +la+++er+ ++ + l ++  s+e  +++e+E 
  gi|14602108|ref|NP_148656.1| 28 RIEALEAALARLEERISSISQALGRDARSTESLQGVEKEG 67
                                  79******************************88888774 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00034      0.21      19      61 ..      91     133 ..      79     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                                   HHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEE CS
                   TFIIE_alpha  19 ldvLlekgevteedlakelkidlnelrklLnrLyearlvkykr 61 
                                   + + lekg  t  +l +++++ +n +  +L rL e ++v+ +r
  gi|14602108|ref|NP_148656.1|  91 IISHLEKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKRR 133
                                   3444569********************************9776 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.14     117     163 ..      14      60 ..       9      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                    FmiP_Thoc5 117 kkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkq 163
                                   + ++l   +ee ++++++L+ +L+ l++ ++ + +alg +  ++++ 
  gi|14602108|ref|NP_148656.1|  14 DIETLARSNEENRRRIEALEAALARLEERISSISQALGRDARSTESL 60 
                                   5688999*******************************988877765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00033       0.2      11      53 ..      91     133 ..      89     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                        HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikksk 53 
                                   I + +++g+a++++++ +  Ls +++   L+ Lve+g+++k+ 
  gi|14602108|ref|NP_148656.1|  91 IISHLEKGDATPSELIRDTGLSKNRVYGVLKRLVERGIVEKRR 133
                                   5566779********************************8854 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 ?   10.9   0.1   0.00052      0.31     143     183 ..      70     136 ..       5     144 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00052
                      SMC_Nse1 143 r............................stelsqeeaaadkgLtaseaeklLkrLveegWleksreGf 183
                                   +                            +++ s  e  +d+gL+++ +  +LkrLve g  ek r+G+
  gi|14602108|ref|NP_148656.1|  70 EteyeghngtveegmledegiiishlekgDATPS--ELIRDTGLSKNRVYGVLKRLVERGIVEKRRDGR 136
                                   0444444555555555556666655543211222..356799*************************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 ?   -2.5   0.0       8.4     5e+03      29      42 ..      16      29 ..       7      40 .. 0.66
   2 ?   10.4   0.0   0.00081      0.49      30      55 .]     104     129 ..      89     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.4
                        HTH_36 29 etlakrlglsknTv 42
                                  etla+  +++++ +
  gi|14602108|ref|NP_148656.1| 16 ETLARSNEENRRRI 29
                                  56666555555555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00081
                        HTH_36  30 tlakrlglsknTvsraikeLeqlGyi 55 
                                    l +++glskn v+  +k L++ G++
  gi|14602108|ref|NP_148656.1| 104 ELIRDTGLSKNRVYGVLKRLVERGIV 129
                                   566899*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      883  (0.0492498); expected 358.6 (0.02)
Passed Vit filter:                       178  (0.00992805); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 999.70
//
Query:       gi|118431906|ref|NP_148658.2|  [L=333]
Description: glyoxylate reductase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-58  195.5   0.0    6.1e-58  195.1   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    8.6e-27   93.4   0.0    9.8e-27   93.2   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    5.2e-05   23.5   0.0    8.8e-05   22.7   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.019   15.1   2.2        0.4   10.9   0.1    2.8  3  AbiEi_4        Transcriptional regulator, AbiEi antitoxin
      0.034   14.4   0.1       0.15   12.4   0.0    2.0  2  TrkA_N         TrkA-N domain
      0.037   13.6   0.0      0.079   12.5   0.0    1.6  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.042   14.7   0.0       0.16   12.8   0.0    2.0  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
       0.17   12.3   0.0          2    8.8   0.0    2.2  2  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 


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 !  195.1   0.0   2.7e-61   6.1e-58       1     178 []     115     298 ..     115     298 .. 0.94

  Alignments for each domain:
  == domain 1  score: 195.1 bits;  conditional E-value: 2.7e-61
                                    HHHHHHHHTTHHHHHHHHHTTCC..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregew..ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                    ++++lall+rl +a++e+ +g w  ++  ++   +l+gkt+GiiGlGrIG++vakrl++f+++ +++d+ + +++ e+el
  gi|118431906|ref|NP_148658.2| 115 IMAALALLKRLLYAHRETVAGGWpqWRLMEMGTFDLQGKTWGIIGLGRIGREVAKRLRPFEVRTVYFDKVRMEDA-EREL 193
                                    5789*******************98888889999************************************99776.9*** PP

                                    TCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSS CS
                   2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeep 158
                                    gve+ sl  ll+esD+vs+h+plt etr++i++ el++mk++a+liN +RG++vdeeaL++a+++++iagaa+Dv++ ep
  gi|118431906|ref|NP_148658.2| 194 GVEYRSLSRLLRESDVVSIHVPLTSETRGMIGEGELRMMKPTAVLINPSRGEIVDEEALARAVRERWIAGAAVDVYSREP 273
                                    ******************************************************************************** PP

                                    SGTCHHH.....HHSTTEEE-SS-T CS
                   2-Hacid_dh_C 159 lpedspl.....lelpnviltPHia 178
                                    +p+d+pl         n+iltPHia
  gi|118431906|ref|NP_148658.2| 274 PPPDHPLiraagEADVNLILTPHIA 298
                                    *******5444323558*******8 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 !   93.2   0.0   4.4e-30   9.8e-27      15     134 .]      19     330 ..       5     330 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 4.4e-30
                                    HHH...TTE.EEEEES..CSSHHHCHHHHTTESEEEE-TTS..-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-E CS
                                    xxx...xxx.xxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh  15 lke...egv.evevkd..ellteellekakdadalivrsnt..kvtaevlealpkLkviaragvGvDnvDldaakerGil 86 
                                    l +   ++v +++v +   l++e +le+++dad++i  ++   +++ae+ +a+++++++++ ++G+D++D++a++++G+ 
  gi|118431906|ref|NP_148658.2|  19 LFDpykKEVgDLRVVSvaGLPRERVLEELRDADVVIGDYTFqmRIDAEMCAAMERVRLVQQPSTGYDHIDVEACARHGVP 98 
                                    4444554566777777889*****************98877679************************************ PP

                                    EEE-TTTTHHHHHHHH................................................................ CS
                                    xxxxxxxxxxxxxxxx................................................................ RF
                     2-Hacid_dh  87 VtnvpgystesvAElt................................................................ 102
                                    V+n+ g+++ svAE+t                                                                
  gi|118431906|ref|NP_148658.2|  99 VANAGGANAVSVAEYTimaalallkrllyahretvaggwpqwrlmemgtfdlqgktwgiiglgrigrevakrlrpfevrt 178
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|118431906|ref|NP_148658.2| 179 vyfdkvrmedaerelgveyrslsrllresdvvsihvpltsetrgmigegelrmmkptavlinpsrgeivdeealaravre 258
                                    ******************************************************************************** PP

                                    ........................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                    ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 ........................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                            +a ++a+++i +  +en+v++lkg++p+ +vn
  gi|118431906|ref|NP_148658.2| 259 rwiagaavdvysreppppdhpliraageadvnliltphiaGANTDARSRIIQFSIENIVRVLKGGKPEAVVN 330
                                    **********************************************************************98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.9e-08   8.8e-05       3     107 ..     156     259 ..     154     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.9e-08
                                    EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC-- CS
                  NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llealk 81 
                                    g+iGlG +G++ a++l   + +++ ++    ++e++  e  + + s++ l+++ dvv + v+ +++++ +i +  l+ +k
  gi|118431906|ref|NP_148658.2| 156 GIIGLGRIGREVAKRLRPFEVRTVYFDKV--RMEDAERELGVEYRSLSRLLRESDVVSIHVPLTSETRGMIGEgELRMMK 233
                                    99**************9999988888855..899999998999****************************9989999** PP

                                    TT-EEEE-S---HHHHHHHHHHHHHT CS
                  NAD_binding_2  82 kgdilidgstsspedtrelakelkek 107
                                    + ++li+ s  ++ d + la++++e+
  gi|118431906|ref|NP_148658.2| 234 PTAVLINPSRGEIVDEEALARAVRER 259
                                    ******************99999887 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.2   7.2e+03      21      34 ..      34      49 ..      29      52 .. 0.73
   2 ?   10.9   0.1   0.00018       0.4      14      35 ..     184     206 ..     184     210 .. 0.94
   3 ?    2.8   0.1      0.06   1.4e+02      25      38 ..     248     261 ..     247     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
                        AbiEi_4 21 a.aGisp.salrrLvr 34
                                     aG+++ + l +L++
  gi|118431906|ref|NP_148658.2| 34 SvAGLPReRVLEELRD 49
                                   4489999555888876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00018
                        AbiEi_4  14 fttrelea.aGispsalrrLvrk 35 
                                    ++++++e+ +G+ +++l+rL+r+
  gi|118431906|ref|NP_148658.2| 184 VRMEDAEReLGVEYRSLSRLLRE 206
                                    79******************996 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.06
                        AbiEi_4  25 spsalrrLvrkGwL 38 
                                    ++ al+r+vr+ w+
  gi|118431906|ref|NP_148658.2| 248 DEEALARAVRERWI 261
                                    7889*********9 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.6     8e+03      32      50 ..      42      58 ..      39      61 .. 0.60
   2 ?   12.4   0.0   6.5e-05      0.15       3      39 ..     157     191 ..     156     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                                   HHHHHHHHTTSEEEES-TT CS
                         TrkA_N 32 erveelreeglevvvgdat 50
                                   +++eelr+  ++vv+gd+t
  gi|118431906|ref|NP_148658.2| 42 RVLEELRD--ADVVIGDYT 58
                                   44555553..457777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.5e-05
                                    EES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH CS
                         TrkA_N   3 iiGlGrvGrslaeeLseggkdvvvidkdeerveelre 39 
                                    iiGlGr+Gr++a++L+  +  v  +  d+ r+e +++
  gi|118431906|ref|NP_148658.2| 157 IIGLGRIGREVAKRLRPFE--VRTVYFDKVRMEDAER 191
                                    9**************9854..5555555566666654 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 ?   12.5   0.0   3.5e-05     0.079       2      70 ..     150     216 ..     149     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.5e-05
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHH.HHTT-EEEEHHHHHHT-SEEEE-S-H CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkA.keegfevltvaeavkkadvvmiliPD 70 
                                    l+gk+  +iG G  G+  a+ lr   +  v+   ++   ++ A +e g+e  +++ + +++dvv i +P 
  gi|118431906|ref|NP_148658.2| 150 LQGKTWGIIGLGRIGREVAKRLRPFEVRTVYF--DKV-RMEDAeRELGVEYRSLSRLLRESDVVSIHVPL 216
                                    899********************987765554..333.345551567*******************9995 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-05      0.16       3      72 ..     155     216 ..     153     234 .. 0.83
   2 ?   -2.4   0.0       3.6   8.1e+03      24      66 ..     285     328 ..     275     329 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                                    EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G CS
                   GFO_IDH_MocA   3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpn 72 
                                    ++iiG+G+ig++ ++ l    r  ev  ++  d+ r e++ +++gve y +l++ll+  e d+v++ +p 
  gi|118431906|ref|NP_148658.2| 155 WGIIGLGRIGREVAKRL----RPFEVRTVYF-DKVRMEDAERELGVE-YRSLSRLLR--ESDVVSIHVPL 216
                                    89***********9444....4447776664.5568999999****9.*********..88*****9996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                                    TTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEE CS
                   GFO_IDH_MocA  24 rleevvalldpdaeraeavaesfgve.aysdleelladpeidav 66 
                                     +++v  +l p+ + a + a+s  ++ + +++ ++l+  +++av
  gi|118431906|ref|NP_148658.2| 285 GEADVNLILTPHIAGANTDARSRIIQfSIENIVRVLKGGKPEAV 328
                                    45566666667766666666666665666677777777777776 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 ?    0.8   0.0      0.28   6.3e+02      24      74 ..      29      78 ..      16      91 .. 0.77
   2 ?    8.8   0.0   0.00089         2       4      20 ..     156     172 ..     154     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.28
                                   TCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE- CS
                        Gp_dh_N 24 elevvaindltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvla 74
                                   +l+vv +  l   + l+ l   D v g ++ +++++ e +    +++++++
  gi|118431906|ref|NP_148658.2| 29 DLRVVSVAGLPRERVLEELRDADVVIGDYTFQMRIDAE-MCAAMERVRLVQ 78
                                   789999999999999999999******99999998644.444445666555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00089
                                    EEESTSHHHHHHHHHHH CS
                        Gp_dh_N   4 ainGfGRIGrlvlrall 20 
                                    +i G+GRIGr v++ l 
  gi|118431906|ref|NP_148658.2| 156 GIIGLGRIGREVAKRLR 172
                                    799*********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2560.48
//
Query:       gi|14602111|ref|NP_148659.1|  [L=556]
Description: acetolactate synthase [Aeropyrum pernix K1]
Scores for complete 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  157.4   0.2    6.2e-46  156.1   0.2    1.7  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    2.1e-28   99.0   0.0    5.1e-28   97.8   0.0    1.7  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
      1e-21   77.1   0.0    2.1e-21   76.1   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   0.2     1e-49   6.2e-46       2     169 ..       3     170 ..       2     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 1e-49
                                   EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT..TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                  TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq.girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                   tvaea++r L a+gv +++g+ G++i++++dal + + +i++v++rhEq+a+ aAd+ +r+t+++++++v++gpG++n+l 
  gi|14602111|ref|NP_148659.1|   3 TVAEAIARGLVAAGVARIYGIIGTSIVDFVDALYDYRdRIDFVTTRHEQVAVSAADAEYRSTRRLAAAAVHAGPGFLNTLI 83 
                                   89***********************************9******************************************* PP

                                   HHHHHHHHT--EEEEEEE--CCCHH.S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEEEEEH CS
                  TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg.qgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvylelpk 161
                                   +l  A++dr+Pll++sg + ++lrg + +l  e+dq++++rp++ky   ++sp e+  +l +A+r als+++gP+++e+p+
  gi|14602111|ref|NP_148659.1|  84 SLGIAAKDRVPLLLVSGGVRRRLRGlDAWL--EVDQASIARPLVKYYGVLDSPGEVLDVLVEALRSALSPPMGPAVVEIPE 162
                                   *************************44444..59*********************************************** PP

                                   HHCC-EEE CS
                  TPP_enzyme_N 162 dvlleevd 169
                                   d+++++++
  gi|14602111|ref|NP_148659.1| 163 DLWRSQTT 170
                                   ****9987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       0.9   5.4e+03     134     153 .]     140     160 ..     112     160 .. 0.61
   2 !   97.8   0.0   8.6e-32   5.1e-28       3     153 .]     392     536 ..     390     536 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.9
                                   HHHHHHHHHH.CSSSEEEEEE CS
                  TPP_enzyme_C 134 eleealkeal.ekkgpaliev 153
                                    l eal+ al    gpa++e+
  gi|14602111|ref|NP_148659.1| 140 VLVEALRSALsPPMGPAVVEI 160
                                   345666666676668888886 PP

  == domain 2  score: 97.8 bits;  conditional E-value: 8.6e-32
                                   SHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-S CS
                  TPP_enzyme_C   3 GcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNe 83 
                                   G++ l++ +++++++p+s+l ++ lg+mGy+lpa iG + a p+    +++GDG ++m++q+++t+vr++l++++v++n+ 
  gi|14602111|ref|NP_148659.1| 392 GTHILYVYNHIQIYTPGSFLAATNLGAMGYALPAVIGSSKALPGGYHLCVAGDGELMMTVQDIETIVREGLDVKIVLVNDD 472
                                   899999999**********************************99************************************ PP

                                   BCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                  TPP_enzyme_C  84 gygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                   +y      q  + g+r +++    l ++df +laea+G++ a+v+++   + ee l eal++ gpal+ev
  gi|14602111|ref|NP_148659.1| 473 SYKVLYLRQVLQKGGRVYETL---LSNPDFSRLAEAFGVRYASVSRS--GDEEEGL-EALTSPGPALVEV 536
                                   ****************98877...9999************9999999..9999998.677899*****97 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.1   0.0   3.6e-25   2.1e-21       4     115 ..     196     308 ..     194     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 3.6e-25
                                   HHHHHHH-SSEEEEE-CHHCHT.T.GHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGS.CHHHHHHHHH-SEE CS
                  TPP_enzyme_M   4 aaellkaakrpvilvGggvars.g.aseelrelaeklgiPvvttlmgkgvipedhplylgmlglhg.skaanealeeaDlv 81 
                                   + ++l +a+rpvil+ g+  +s g  +e l +lae++g+ +v + +g+g+ pedhp++lg++g+ g s aa++ale++D v
  gi|14602111|ref|NP_148659.1| 196 LFSMLMQARRPVILATGELVYSpGfSQEMLLRLAEATGAYIVVSGNGRGACPEDHPRCLGRIGFGGgSLAADRALENSDMV 276
                                   6789****************9975477889**********************************9779************* PP

                                   EEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCC CS
                  TPP_enzyme_M  82 lalGarfddirttgsepefapeakiihididpae 115
                                   lalG +fddi+t+g++  + p++ ++ +  dp+ 
  gi|14602111|ref|NP_148659.1| 277 LALGHEFDDITTYGYN--MLPQGDVVMVSQDPSA 308
                                   **********999965..467889****999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 4342.65
//
Query:       gi|14602112|ref|NP_148660.1|  [L=268]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-16   58.1  14.2    1.1e-15   57.6  14.2    1.2  1  ABC2_membrane    ABC-2 type transporter
    3.4e-09   36.3  16.6    4.2e-09   36.0  16.6    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.3e-06   27.1  12.4    2.3e-06   27.1  12.4    1.4  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00011   22.1   4.3    0.00018   21.3   4.3    1.3  1  ABC2_membrane_6  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.017   13.4   1.1      0.027   12.8   1.1    1.2  1  OATP             Organic Anion Transporter Polypeptide (OATP)


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 !   57.6  14.2   3.2e-19   1.1e-15       6     209 ..       8     221 ..       5     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 3.2e-19
                 ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedglnr.............pgllffsvlflafsaltsv 71 
                                   +  +++l  + ++    l+rl  p++++   + v   +g  +      +             +g+   s+l+ +++ + + 
  gi|14602112|ref|NP_148660.1|   8 VYAKDLLALYSTWGFM-LVRLSVPMFMIATAWAVSRLAGgaSP-----FealgykdyvafvaIGFSLYSLLTATLFDVGER 82 
                                   5678899999999888.99999999999999999986555422.....12234466788899************9999999 PP

                 ABC2_membrane  72 apvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltalaasslgl 149
                                    +++e  +g+le  lv+p  s+++ +++++l++l vsll  +i+l+ + +++g       +   + ++l l ++ ++++gl
  gi|14602112|ref|NP_148660.1|  83 -LHRELVQGTLEAILVTPA-SRFSWLFGNALGSLGVSLLDLVIVLAYYTIIFGSGSLhlkAAPQAAAVLGLGFIGMVGMGL 161
                                   .******************.**************************8888874444434244888999999999******* PP

                 ABC2_membrane 150 lisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                   l++ + ++++    +  +++ +l+llsG+++p++ +p+ l   a+l Plt ++ea+rs l
  gi|14602112|ref|NP_148660.1| 162 LLGGIIVNLKEPHAFNVMLTPFLMLLSGMMFPVEVLPSPLDTAAELIPLTLTLEAVRSLL 221
                                   *************************************9*******************987 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 !   36.0  16.6   1.2e-12   4.2e-09     159     343 ..      58     248 ..      19     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.2e-12
               ABC2_membrane_3 159 vasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...lafgl.gip 234
                                   ++ f+++ + l+ l++ t++ +   + +E  ++++e +lv++ s+++ ++++ lg++ v+ll l+++l+   ++fg+ +++
  gi|14602112|ref|NP_148660.1|  58 YVAFVAIgFSLYSLLTATLFDVGERLHRELVQGTLEAILVTPASRFSWLFGNALGSLGVSLLDLVIVLAyytIIFGSgSLH 138
                                   222222236666666666666666779**********************************99999999555599988888 PP

               ABC2_membrane_3 235 fgnlglllllfllfglayialgyllsslfknsetaqil.ifivilllsgffgglfpledlpsalkwifsiiPffapglgll 314
                                    +    +  ++ l+++ ++ +g+ll+ ++ n ++  ++ ++++ + l++++g++fp+e lps+l +++ +iP++   ++  
  gi|14602112|ref|NP_148660.1| 139 LKAAPQAAAVLGLGFIGMVGMGLLLGGIIVNLKEPHAFnVMLTPF-LMLLSGMMFPVEVLPSPLDTAAELIPLTLTLEAVR 218
                                   8888999999999*****************999988885666666.99********************************* PP

               ABC2_membrane_3 315 rli.tgdplweillsliilalfavvyllla 343
                                   +l+ +g  ++++   li la++av+y+l++
  gi|14602112|ref|NP_148660.1| 219 SLLlKGGGISSVEGLLIKLAIEAVAYTLAG 248
                                   **7466677777799999********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 !   27.1  12.4   6.5e-10   2.3e-06      98     284 ..      84     253 ..      80     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.5e-10
               ABC2_membrane_2  98 agEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll.alaiilalgivlaledllllvvasvlllllvvf 177
                                    +E  +gTl++ L +P+sR + l+g+++g+l ++l+ +v++la + + +   +l l+ +++++++l l +  +        
  gi|14602112|ref|NP_148660.1|  84 HRELVQGTLEAILVTPASRFSWLFGNALGSLGVSLLDLVIVLAYYTIiFGSGSLHLKAAPQAAAVLGLGFIGM-------- 156
                                   589999*****************************96666666654403344444555555555555554444........ PP

               ABC2_membrane_2 178 lalglllS..svarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdln 256
                                   +++glll   +v  +   a  ++l  f++l +  +++  +v+  +++ a+        +l++ t   +++++ +l+g++  
  gi|14602112|ref|NP_148660.1| 157 VGMGLLLGgiIVNLKEPHAFNVMLTPFLML-LSGMMFPVEVLPSPLDTAA--------ELIPLTLTLEAVRSLLLKGGG-- 226
                                   555555552166666888999999999999.5556677777777777777........788888899999999999997.. PP

               ABC2_membrane_2 257 algstatnllilllllavllvl.gyvlFk 284
                                     +s ++ lli l++ av + l gy +Fk
  gi|14602112|ref|NP_148660.1| 227 --ISSVEGLLIKLAIEAVAYTLaGYMVFK 253
                                   ..899999999888777766551567776 PP

>> ABC2_membrane_6  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   4.3   5.2e-08   0.00018      28     217 ..      59     250 ..      51     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.2e-08
               ABC2_membrane_6  28 evllllglflilqglaavffapalsrigesvrdGsldflLlkPinlllqillkrlnlrrvgrllvgiilliyavkkld..i 106
                                    + + +g++ +   l a++f +  +r+ ++  +G+l+ +L+ P++   +++ + l++ +v  l + i+l  y+++  +  +
  gi|14602112|ref|NP_148660.1|  59 VAFVAIGFS-LYSLLTATLF-DVGERLHRELVQGTLEAILVTPASRFSWLFGNALGSLGVSLLDLVIVLAYYTIIFGSgsL 137
                                   444445554.7777777777.7778***********************************988666666666665433113 PP

               ABC2_membrane_6 107 kltaakillliislilglliltslffilgsl..sfwfvkseeii.eileglleaakyPltiyplilrklltfiiPvaflsy 184
                                   +l+aa   +   +l lg++ ++++ + lg +   ++  ++ +++   + +ll+ +++P+ ++p+ l     + iP++++  
  gi|14602112|ref|NP_148660.1| 138 HLKAAPQAA--AVLGLGFIGMVGMGLLLGGIivNLKEPHAFNVMlTPFLMLLSGMMFPVEVLPSPLDTAAEL-IPLTLTLE 215
                                   444333333..3334444444444444444400556666777776778888****************99999.9***9998 PP

               ABC2_membrane_6 185 vPaeivlgklsi..vfalvlqlilalvllvlskli 217
                                      + +l+   i  v+ l+ +l + +v ++l+ ++
  gi|14602112|ref|NP_148660.1| 216 AVRSLLLKGGGIssVEGLLIKLAIEAVAYTLAGYM 250
                                   88888886544444777777677777777776655 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 ?   12.8   1.1   7.5e-06     0.027     328     379 ..     141     192 ..     136     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-06
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          OATP 328 saseAnlltGvvvipgaalGillgGllvkklklsakklaklvlvvsllslll 379
                                   +a +A+ ++G+ +i ++++G+llgG++v+ ++++a +++   +++ l  +++
  gi|14602112|ref|NP_148660.1| 141 AAPQAAAVLGLGFIGMVGMGLLLGGIIVNLKEPHAFNVMLTPFLMLLSGMMF 192
                                   67899999***************************99999988888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2131.81
//
Query:       gi|14602113|ref|NP_148661.1|  [L=275]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-13   48.8  15.8    5.5e-13   48.8  15.8    1.6  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
       0.17   11.0  22.6        2.3    7.2  22.6    1.9  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 !   48.8  15.8   6.1e-17   5.5e-13       7     209 ..      14     228 ..       8     229 .. 0.82
   2 ?   -1.7   0.0      0.17   1.5e+03      23      43 ..     241     261 ..     236     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.1e-17
                 ABC2_membrane   7 lkreflqrwrdpslgllwrliqplllalvfgtvfgn.lgnsedglnr............pgllffsvlflafsaltsvapv 74 
                                     r+f+ r+     + + +liqp++++ ++ + +   lg++++ l+             +g  + + lf+a++  +++a+ 
  gi|14602113|ref|NP_148661.1|  14 ALRDFKIRITYIPWI-INSLIQPIIWTYILIYTYRAvLGETAQTLQKhgwpadyvgfliLG-QVLLSLFNALNWRAGMAIQ 92 
                                   556666444444445.889****************85446777776679999998666333.3445556666888999*** PP

                 ABC2_membrane  75 ferergvlerelvsplyslsayvlakv...lvelpvsllqalifllivyflvgldlsrfflflllllltalaasslgllis 152
                                   +er  g+le  + +p  s+ ++++++    l+++ +  + a+++++++  + g+++   + +ll + + ++ a+s+g+ ++
  gi|14602113|ref|NP_148661.1|  93 RERWFGTLEIVFLTPA-SRLVMLTGSSiygLLDAGWVSFSAALIVFLATGT-GFNIADPLAALLSVSMAVVGAVSMGIGLA 171
                                   ****************.7777777777255556667777777777777776.9999777********************** PP

                 ABC2_membrane 153 alapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                    l +  + a+ +a ++  pl ++sG  +p++ +p  lq+i y++Plty++ea r++l
  gi|14602113|ref|NP_148661.1| 172 GLYVLTRSAGPIAIAIQHPLRFFSGSSFPLSILPASLQYIGYALPLTYGIEAARISL 228
                                   **********************************9*******************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.17
                 ABC2_membrane  23 lwrliqplllalvfgtvfgnl 43 
                                   ++rl+ + l++++ g +f ++
  gi|14602113|ref|NP_148661.1| 241 ILRLALISLVGIIAGILFVRW 261
                                   567777777777777777765 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 ?    1.9   0.5     0.011        94     214     251 ..      28      80 ..      22      85 .. 0.80
   2 ?    7.2  22.6   0.00026       2.3     183     344 ..      91     256 ..      66     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.011
               ABC2_membrane_3 214 flvyllqlllilll.afgl..............gipfgnlglllllfllfgla 251
                                    +++l+q ++++++ ++ +              g+p + +g+l+l  +l +l 
  gi|14602113|ref|NP_148661.1|  28 IINSLIQPIIWTYIlIYTYravlgetaqtlqkhGWPADYVGFLILGQVLLSLF 80 
                                   578999*9**999645555788999***9999999999999999888887764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00026
               ABC2_membrane_3 183 iveEkesrikelqlvsgvsplqywlskilgdfl.vyllql..llilllafglgipfgnlglllllfllfglayialgylls 260
                                   i +E+  +++e+ ++++ s+l +++++ +  +l ++++++  +li++la g+g+++ + +++ll + +    ++++g  l 
  gi|14602113|ref|NP_148661.1|  91 IQRERWFGTLEIVFLTPASRLVMLTGSSIYGLLdAGWVSFsaALIVFLATGTGFNIADPLAALLSVSMAVVGAVSMGIGLA 171
                                   445555678899999999999999888543333244444411444456777689999************999999999999 PP

               ABC2_membrane_3 261 slfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrli..tgdplweillsliilalfavvy 339
                                    l   +++a  +++++  +l +f+g +fpl+ lp +l++i++ +P+++ +++  r++   g+p+ e+ + ++ lal+++v 
  gi|14602113|ref|NP_148661.1| 172 GLYVLTRSAGPIAIAIQHPLRFFSGSSFPLSILPASLQYIGYALPLTYGIEAA-RISllEGAPIDEVSPLILRLALISLVG 251
                                   99999999******************************************998.554458889999665555555555555 PP

               ABC2_membrane_3 340 lllal 344
                                   +++++
  gi|14602113|ref|NP_148661.1| 252 IIAGI 256
                                   55444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2011.47
//
Query:       gi|14602114|ref|NP_148662.1|  [L=323]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-26   91.9   0.0    8.3e-26   91.1   0.0    1.4  1  ABC_tran  ABC transporter
    2.1e-12   47.5   1.0    9.2e-07   29.0   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    7.2e-07   29.8   0.0    1.8e-06   28.6   0.0    1.7  1  DUF4162   Domain of unknown function (DUF4162)
    9.6e-05   22.3   0.0       0.31   10.7   0.0    2.1  2  AAA_15    AAA ATPase domain
    0.00013   21.6   0.1    0.00025   20.7   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
     0.0026   18.3   0.0     0.0041   17.6   0.0    1.2  1  AAA_23    AAA domain
     0.0029   17.5   0.4       0.55   10.1   0.0    2.3  2  NTPase_1  NTPase
     0.0054   17.1   0.1     0.0096   16.3   0.1    1.6  1  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
      0.052   13.4   0.0       0.11   12.3   0.0    1.5  1  WIYLD     Ubiquitin-binding WIYLD domain
      0.056   13.9   0.0       0.21   12.0   0.0    2.1  1  AAA       ATPase family associated with various cellular acti
      0.078   13.2   0.0        0.2   11.9   0.0    1.7  1  AAA_28    AAA domain
       0.11   12.4   0.1       0.25   11.2   0.0    1.5  2  Rad17     Rad17 P-loop domain
       0.12   12.3   0.1        1.4    8.8   0.1    2.2  2  NACHT     NACHT domain
       0.13   12.8   0.0       0.29   11.7   0.0    1.6  1  AAA_18    AAA domain
        0.2   11.2   0.0       0.36   10.4   0.0    1.3  1  SRP54     SRP54-type protein, GTPase domain
       0.21   11.6   0.1       0.44   10.5   0.1    1.5  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
       0.24   11.1   0.4        1.2    8.9   0.0    2.1  2  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 !   91.1   0.0   7.8e-29   8.3e-26       1     136 [.      29     173 ..      29     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 7.8e-29
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren. 79 
                                   l+ v+lk+ +g++  ++G+nGaGK+tL+k+l+ ll p++G  ++ g d+ + e + +r++igv+      l  +l+  +n 
  gi|14602114|ref|NP_148662.1|  29 LDGVDLKVGRGTLFSLLGPNGAGKTTLVKILSTLLLPDSGWARVAGFDVVR-EANNVRSRIGVVLGGeRALYWRLSGWDNl 108
                                   789***********************************************9.8999999999987765888999999999* PP

                                   ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e++++++++l+ +gl+e+++ +v    +++S+G+kqr+ +ar l+++p++lllDEpt
  gi|14602114|ref|NP_148662.1| 109 wffsqlygipprEAKRRVKELLEIVGLEEWAHVRV----ENYSKGMKQRLHIARGLINDPEVLLLDEPT 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 !   17.3   0.3     3e-06    0.0032       3      23 ..      43      63 ..      41      96 .. 0.78
   2 !   29.0   0.0   8.7e-10   9.2e-07     237     298 ..     146     204 ..      96     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                        AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                   l GpNg+GK++L ++l+ l 
  gi|14602114|ref|NP_148662.1| 43 SLLGPNGAGKTTLVKILSTLL 63
                                  589**************9885 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8.7e-10
                        AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    S G+k+ l ++  l+ ++    +ll+DEp  gL+Pk+ r++  ++++  r+g  v+ltTH 
  gi|14602114|ref|NP_148662.1| 146 YSKGMKQRLHIARGLINDP---EVLLLDEPTIGLDPKAAREVRSIIRRIVREGRTVLLTTHY 204
                                   4777777744444444444...9***********************999999*********6 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.7e-09   1.8e-06       1      80 [.     227     317 ..     227     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.7e-09
                                   E-HHHHHTTS.-SSEEEEE...--.-----...--.-EEE.E-TT.S-EEEEE--.-----------.----EEEEEEEE- CS
                       DUF4162   1 GtleeiKrsy.gknrieve...ad.aeellee.pg.veev.eeeg.gelelkled.eeaanellkal.tsgveirsFeeee 70 
                                   G++e++K+   g+  ie++   +d ++ lle   g v +v e++g + +++ +++ ++  ++ll++l + +++ir + ++ 
  gi|14602114|ref|NP_148662.1| 227 GPPEDLKSLVgGESVIELKvmgGDrVSMLLERlGGrVISVvERDGaRVFRVLVSEpDSFIEALLAELtRINASIRGLDVRS 307
                                   8999******55555669998855444444443667777746666777******99***********669999******** PP

                                   --HHHHHHHH CS
                       DUF4162  71 PsLndIFiek 80 
                                   PsL+d+Fi++
  gi|14602114|ref|NP_148662.1| 308 PSLEDVFIKL 317
                                   ********96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00067      0.71      25      47 ..      41      63 ..      27      83 .. 0.81
   2 !   10.7   0.0   0.00029      0.31     320     364 ..     160     203 ..     140     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00067
                        AAA_15 25 ltvliGkNnsGKSsilealdlFl 47
                                  l  l G+N++GK++++++l  +l
  gi|14602114|ref|NP_148662.1| 41 LFSLLGPNGAGKTTLVKILSTLL 63
                                  56789**************9876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00029
                        AAA_15 320 keeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                     +++ +ll++EP + L p+a +++   +++++++++  v++tTH
  gi|14602114|ref|NP_148662.1| 160 LINDPEVLLLDEPTIGLDPKAAREVRSIIRRIVREGR-TVLLTTH 203
                                   568899******************************9.9****** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   2.3e-07   0.00025      13      51 ..      30      69 ..      26      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.k 51
                                  dg ++++ +   + l Gp+G+GK+Tl+  +++lL+p++ +
  gi|14602114|ref|NP_148662.1| 30 DGVDLKVGRGTLFSLLGPNGAGKTTLVKILSTLLLPDSgW 69
                                  5666777744488899********************9854 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.9e-06    0.0041      14      43 ..      33      63 ..      24      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.9e-06
                        AAA_23 14 eidFsk.gltlItGpNGaGKTTildAiklaL 43
                                  ++  ++  l+ + GpNGaGKTT++  +   L
  gi|14602114|ref|NP_148662.1| 33 DLKVGRgTLFSLLGPNGAGKTTLVKILSTLL 63
                                  44444426999************98877655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00052      0.55       4      46 ..      44      89 ..      42      95 .. 0.73
   2 ?    5.3   0.1     0.016        17      86     144 ..     154     215 ..     127     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                                  EE--TTSSHHHHHHHHHHHH....GG.GEEEE.EEEEE-------E CS
                      NTPase_1  4 iTGppGvGKtTlvkkvlell.kssgv.kvgGf.yteevreggrrig 46
                                  + Gp G GKtTlvk ++ ll  +sg+ +v+Gf +++e  +  +rig
  gi|14602114|ref|NP_148662.1| 44 LLGPNGAGKTTLVKILSTLLlPDSGWaRVAGFdVVREANNVRSRIG 89
                                  569**********999987624556438999944455666666666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHH CS
                      NTPase_1  86 lealrkalseadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalveei 144
                                   l++ r  +++++v+++DE  iG     ++++++ +++++++++ vl + h     ++l +++
  gi|14602114|ref|NP_148662.1| 154 LHIARGLINDPEVLLLDEptIGLDPKAAREVRSIIRRIVREGRTVLLTTHYMVeAEELSDRV 215
                                   4444555589999999999999999999*********************9886555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   9.1e-06    0.0096       5      61 ..      22      76 ..      19     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.1e-06
                        AAA_16  5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcd 61
                                  R + +++L  +  +++ gr+ l  l G+ G GK++lv+ l + l  d g++  + +d
  gi|14602114|ref|NP_148662.1| 22 RARTIRALDGV--DLKVGRGTLFSLLGPNGAGKTTLVKILSTLLLPDSGWARVAGFD 76
                                  56666666554..344466689****************9999999986655444444 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.11      18      49 ..     115     147 ..     112     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                         WIYLD  18 lGfskeqvrpvlkkLLkvYgkn.WeliEednYr 49 
                                   +G++ ++ ++ +k+LL++ g + W+++  +nY+
  gi|14602114|ref|NP_148662.1| 115 YGIPPREAKRRVKELLEIVGLEeWAHVRVENYS 147
                                   8*******************999*********6 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    0.0002      0.21       3      22 ..      44      63 ..      42     173 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                  EESSTTSSHHHHHHHHHHHH CS
                           AAA  3 lyGppGtGKTllakavakel 22
                                  l Gp G GKT+l+k + + l
  gi|14602114|ref|NP_148662.1| 44 LLGPNGAGKTTLVKILSTLL 63
                                  89************998775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019       0.2       4      30 ..      44      81 ..      41      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                        AAA_28  4 itGgestGKTtlleaLa.........ar..gypvvpEa 30
                                  ++G+ ++GKTtl++ L+         ar  g+ vv+Ea
  gi|14602114|ref|NP_148662.1| 44 LLGPNGAGKTTLVKILStlllpdsgwARvaGFDVVREA 81
                                  89**************9666665555446666677665 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   0.00024      0.25      46      69 ..      40      63 ..      26      74 .. 0.81
   2 ?   -3.6   0.0       8.6     9e+03     150     166 ..     182     198 ..     166     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                         Rad17 46 riLLisGPsGCgkstvvkvLskel 69
                                   +  + GP G gk+t vk+Ls  l
  gi|14602114|ref|NP_148662.1| 40 TLFSLLGPNGAGKTTLVKILSTLL 63
                                  467789**************9876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.6
                         Rad17 150 dalrevirkylrsseal 166
                                   + +r +ir+ +r ++++
  gi|14602114|ref|NP_148662.1| 182 REVRSIIRRIVREGRTV 198
                                   67888999999888873 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0014       1.4       5      23 ..      44      62 ..      40      68 .. 0.85
   2 ?    0.9   0.0      0.36   3.7e+02      36      88 ..     108     170 ..      99     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                  EEC-TTTCHHHHHHHHHHH CS
                         NACHT  5 lqGeaGsGKTtLlqklala 23
                                  l G++G GKTtL++ l ++
  gi|14602114|ref|NP_148662.1| 44 LLGPNGAGKTTLVKILSTL 62
                                  89***********988765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.36
                                   EEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.....CHHHHCCSCCCEE.....EEEE CS
                         NACHT  36 lvFflslrelsrsgnarsladllfsqlpepaapvse.....vwavllelperlL.....lilD 88 
                                   l Ff +l  ++ +++ r++++ll  +++e++a+v+      +++ +l +++ l      l+lD
  gi|14602114|ref|NP_148662.1| 108 LWFFSQLYGIPPREAKRRVKELLEIVGLEEWAHVRVenyskGMKQRLHIARGLIndpevLLLD 170
                                   678888888888888899999999999999999987666664444444444444555545554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00028      0.29       3      33 ..      44      79 ..      43     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                        AAA_18  3 ltGtpGvGKttlakeLskrlgf......gvnlrdvak 33
                                  l G+ G+GKttl k Ls +l +       v   dv++
  gi|14602114|ref|NP_148662.1| 44 LLGPNGAGKTTLVKILSTLL-LpdsgwaRVAGFDVVR 79
                                  68**************9986.3445666444444444 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   0.0   0.00034      0.36       5      43 ..      43      81 ..      40      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                                  EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTT CS
                         SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaa 43
                                   l+G++GaGKTt +  L+ ll  +   + ++  D+ R a
  gi|14602114|ref|NP_148662.1| 43 SLLGPNGAGKTTLVKILSTLLLPDSGWARVAGFDVVREA 81
                                  589************999999988888888888888876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00042      0.44      19      41 ..      39      61 ..      23      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                                  TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                  g+++ L G+ GaGKTtlv+ l  
  gi|14602114|ref|NP_148662.1| 39 GTLFSLLGPNGAGKTTLVKILST 61
                                  667999************98765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011       1.2      20      42 ..      41      63 ..      33      97 .. 0.77
   2 ?   -0.6   0.1      0.86   9.1e+02      45     119 ..     194     274 ..     182     277 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                        AAA_30 20 vavltGpAGtGKttalkalreaw 42
                                  +  l Gp G+GKtt++k l  ++
  gi|14602114|ref|NP_148662.1| 41 LFSLLGPNGAGKTTLVKILSTLL 63
                                  66789************996654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.86
                        AAA_30  45 aggrviglAptgkaAkvLaeelgi..eastiakllkrlk.....grarlepgtllivDEagmvdtkqlaallkaaekagak 118
                                   +g++v++ ++    A++L++ + i  +++ +a+   + +     g +++ + +++  D ++m+  +   ++++ +e++ga+
  gi|14602114|ref|NP_148662.1| 194 EGRTVLLTTHYMVEAEELSDRVAIisKGRIVAEGPPE-DlkslvGGESVIELKVMGGDRVSMLLERLGGRVISVVERDGAR 273
                                   5666667677777777776666543322222211111.0112222223333344444555666666666666666666666 PP

                        AAA_30 119 v 119
                                   v
  gi|14602114|ref|NP_148662.1| 274 V 274
                                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                       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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2462.29
//
Query:       gi|118431907|ref|NP_148663.2|  [L=135]
Description: HxlR family transcriptional regulator [Aeropyrum pernix K1]
Scores for 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-24   83.4   0.1    9.2e-24   83.1   0.1    1.1  1  HxlR      HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.026   15.0   0.0      0.042   14.4   0.0    1.4  1  HTH_27    Winged helix DNA-binding domain
      0.085   12.7   0.1       0.14   12.0   0.1    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
        0.1   12.6   0.0       0.17   11.9   0.0    1.3  1  PadR      Transcriptional regulator PadR-like 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 !   83.1   0.1   2.1e-27   9.2e-24       1      89 [.      14     102 ..      14     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 2.1e-27
                                    HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                           HxlR   1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80 
                                    l++ kW+l+i+++ll+g k f el++ ++ is k+L+++L  L + g++er + p  P++v Y+lte+G++l+ v+ el+
  gi|118431907|ref|NP_148663.2|  14 LLSRKWSLVIVYHLLDGDKGFAELEKSIGAISSKTLSETLEDLRRLGIVERIIDPGPPVRVRYRLTEMGEDLRSVIMELA 93 
                                    5889**************************************************************************** PP

                                    HHHHHHHHC CS
                           HxlR  81 kwgeeylee 89 
                                     w  +++ +
  gi|118431907|ref|NP_148663.2|  94 RWSCKWVVR 102
                                    ***999865 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   0.0   9.3e-06     0.042      27      68 .]      41      82 ..      19      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.3e-06
                         HTH_27 27 rlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++ + s+ l+ L + G ver  d+ +  ++r+rlT+ G
  gi|118431907|ref|NP_148663.2| 41 IGAISSKTLSETLEDLRRLGIVERIIDPGPPVRVRYRLTEMG 82
                                   4567888999******************88888******977 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 ?   12.0   0.1   3.2e-05      0.14       7      46 ..      23      63 ..      21      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                                   HHHHHTTSSEEHHHHHHHHT.S-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  7 ILklLaegelcvcelaeelg.lsqstvShHLkkLreaGLVe 46
                                   I++ L +g + + el + +g +s  t+S+ L  Lr +G+Ve
  gi|118431907|ref|NP_148663.2| 23 IVYHLLDGDKGFAELEKSIGaISSKTLSETLEDLRRLGIVE 63
                                   8999999999999999999878******************7 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.17      20      71 ..      38      84 ..      32      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                   HCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                           PadR 20 eelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71
                                   e+++    ++s  +l  +L++L++ g+ve+  ++    p r  YrlT+ G++
  gi|118431907|ref|NP_148663.2| 38 EKSI---GAISSKTLSETLEDLRRLGIVERIIDP--GPPVRVRYRLTEMGED 84
                                   4443...36777888899*************997..6899999******986 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:                      290  (0.0161749); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1168.37
//
Query:       gi|118431908|ref|NP_148664.2|  [L=248]
Description: glyoxalase [Aeropyrum pernix K1]
Scores for 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-12   46.1   0.0    3.2e-05   24.1   0.0    2.6  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    7.3e-06   26.7   0.0    0.00055   20.7   0.0    2.8  2  Glyoxalase_6  Glyoxalase-like domain
     0.0027   18.0   0.0       0.86    9.9   0.0    3.0  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 !   24.1   0.0   5.3e-09   3.2e-05       4     128 .]       9     118 ..       6     118 .. 0.86
   2 !   19.2   0.0   1.8e-07    0.0011       2      56 ..     152     199 ..     151     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.3e-09
                                    EEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSCTSEEEEEEEEE CS
                     Glyoxalase   4 hvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkieetvhhvafiald 83 
                                     ++l+v+ l+++ +FYt +L+     + +        +  +  +gg  + l  n+ +  ++++      +  h+af++++
  gi|118431908|ref|NP_148664.2|   9 KAVLIVRRLDEAERFYTAILNRPPEPVQG--------GLLYRLEGGSELLLRQNPRARRPLPGA----AGLYHIAFTVDK 76 
                                    5789*************************........888888888877777777777777777....6899******** PP

                                    HCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                     Glyoxalase  84 vedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       + + +++l++ g +  +   +h+f+  +  y  Dp G+ +e+
  gi|118431908|ref|NP_148664.2|  77 PGALPAVVEKLRSLGSPLLGA-SDHCFTLAV--YTLDPEGNGVEV 118
                                    ***************777777.788888888..59******9995 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.8e-07
                                    EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEE CS
                     Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvl 56 
                                    i+h+ l v+ le++  FYtk+LG+ ++++         +++ ff  g+ h+ ++ 
  gi|118431908|ref|NP_148664.2| 152 IGHIHLKVAGLEEAEVFYTKILGMSVTERGY-------PGALFFAYGDYHHHVAA 199
                                    89*****************************.......99999999999998876 PP

>> Glyoxalase_6  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.2e-08   0.00055       6     106 ..      14     118 ..       9     119 .. 0.84
   2 ?    2.9   0.0     0.032   1.9e+02       5      29 ..     158     188 ..     154     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.2e-08
                   Glyoxalase_6   6 aadpaalaaFwaaalgwevereeaaledpegvgpaaedaatllfqrvpe.....pakn.rvHldlavedld...aevarl 76 
                                    ++  +++ +F+ a+l  + e+ +       g     e++  ll+++ p+     p+     H+ ++v+++    a v++l
  gi|118431908|ref|NP_148664.2|  14 VRRLDEAERFYTAILNRPPEPVQ------GGLLYRLEGGSELLLRQNPRarrplPGAAgLYHIAFTVDKPGalpAVVEKL 87 
                                    67889999*******99999999......77777889999*********999884444369******8884445****** PP

                   Glyoxalase_6  77 valGArvlreprdgthgr.vlaDPeGneFcv 106
                                     +lG   l+++++  +      DPeGn   v
  gi|118431908|ref|NP_148664.2|  88 RSLGSPLLGASDHCFTLAvYTLDPEGNGVEV 118
                                    *********9999886668889*****8765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.032
                   Glyoxalase_6   5 daadpaalaaFwaaalgweveree......a 29 
                                     +a  +++  F+ ++lg++v+++       +
  gi|118431908|ref|NP_148664.2| 158 KVAGLEEAEVFYTKILGMSVTERGypgalfF 188
                                    5666677778999999888888775544440 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 !    9.9   0.0   0.00014      0.86      48      96 ..      47      97 ..       8     103 .. 0.61
   2 ?    3.7   0.0     0.012        73       2      29 ..     154     181 ..     153     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                                   EEEEEEEESSTT-THHHTS-EEEEEEEEES...-HHHHHHHHCTTTEEEEEE CS
                   Glyoxalase_4 48 vqieLieplegpeflaehgeglhhlaywvd...dldaavarleeqGfevvqk 96
                                    ++ L ++ + + +l  + +gl+h+a+ vd    l a+v++l++ G +++ +
  gi|118431908|ref|NP_148664.2| 47 SELLLRQNPRARRPL-PGAAGLYHIAFTVDkpgALPAVVEKLRSLGSPLLGA 97
                                   455544444443332.3889*********95556999999999999888765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.012
                                    EEEEE-S-HHHHHHHHHH.TT-EESS-- CS
                   Glyoxalase_4   2 QigivVeDleaavarfsallGvgpwqry 29 
                                    +i + V  le+a  +++++lG+ +++r 
  gi|118431908|ref|NP_148664.2| 154 HIHLKVAGLEEAEVFYTKILGMSVTERG 181
                                    89999999**************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 2204.10
//
Query:       gi|118431909|ref|NP_148665.2|  [L=237]
Description: maleate cis-trans isomerase [Aeropyrum pernix K1]
Scores for complete 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-36  125.5   0.0    2.7e-36  125.2   0.0    1.0  1  Amdase        Arylmalonate decarboxylase
    3.7e-13   49.9   0.0      6e-13   49.2   0.0    1.4  1  Asp_Glu_race  Asp/Glu/Hydantoin racemase
     0.0037   16.7   0.0      0.096   12.1   0.0    2.4  2  AroM          AroM protein


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 !  125.2   0.0   4.5e-40   2.7e-36       4     215 ..      22     232 ..      19     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 4.5e-40
                         Amdase   4 eaaalYpe.vrFeAeGLglkelskegydevidrvveaArelaerGaqavslmGtsLsFyRGaafneeLvarleeatgLPa 82 
                                    e  ++ pe v+ +   + l+++s e   ++ +  +  A++la++G++ ++   t  s   G+ ++ ++  +l++a+g+ +
  gi|118431909|ref|NP_148665.2|  22 EMWMMAPEgVSIHTGRVPLEKVSVEELLKMEEYSAIEAEKLATAGVDLIVYGCTTGSLIGGPGYDLKIADKLSSASGVQV 101
                                    5556666667777777788888888888888888999******************************************* PP

                         Amdase  83 ttmssavvealralgarRvAvataYidevnerLvayLeesglevaalesLdiedveavakvtaeelvelgkkavaaapea 162
                                     t ++avveal+alga R+Avat Yi+evn+r  ++L+++g++++  +sL++    ++ +v+  ++  l++ +    + a
  gi|118431909|ref|NP_148665.2| 102 VTTATAVVEALKALGASRIAVATPYIEEVNKREEEFLRHHGFDIVDFKSLGLLGNLDIGRVPPWRVYRLARSLS--IEGA 179
                                    **********************************************************************9987..789* PP

                         Amdase 163 dallisCGGLrtldvvreledelglpvvssalAGlwdavrlagldaraagegr 215
                                    da++isC  Lrt++v+  le+++glpvvss +A +w a++++g  ++   +g+
  gi|118431909|ref|NP_148665.2| 180 DAIFISCTNLRTVEVIGLLERDTGLPVVSSNTASMWMALKTLGIREAGFKAGT 232
                                    ******************************************98877666665 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 !   49.2   0.0     1e-16     6e-13       1     221 [.       8     215 ..       8     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1e-16
                                    EEECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CCS-TCHHHHHCH.T..THHHHHHHHHHHHCTTESEEEE--CHH CS
                   Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdqehlplivlndsaipdrteaieeesgddpvlklleaakkLekagadaiviaCnTa 80 
                                    IG + p++++++  ++++++p+     h  ++ l++ ++++  +           ++ + +a+kL++ag+d+iv+ C+T 
  gi|118431909|ref|NP_148665.2|   8 IGLIVPSSNTTMEPEMWMMAPEGVS-IHTGRVPLEKVSVEELLKME---------EYSAIEAEKLATAGVDLIVYGCTTG 77 
                                    7888999999999999999999884.47777888888866444444.........388999******************9 PP

                                    HH.........HHHHHHHH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCH CS
                   Asp_Glu_race  81 ha.........vadelqkkikiPvlgiveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssv 151
                                    +           ad+l++++ + v+  + a++ealka g++++++ +++++  ++  +++l+  +g+++v     + +s+
  gi|118431909|ref|NP_148665.2|  78 SLiggpgydlkIADKLSSASGVQVVTTATAVVEALKALGASRIAVATPYIEEVNKREEEFLRH-HGFDIV-----DFKSL 151
                                    7522222222246777799********************************************.9**443.....22333 PP

                                    HCCHCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHH CS
                   Asp_Glu_race 152 nqaiyeelkaGevteearrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdilar 221
                                      +    l  G+v++   ++++  l+    +gada+++ CT+l+++ e +  le+++++pv++++++  +
  gi|118431909|ref|NP_148665.2| 152 G-LLG-NLDIGRVPPWRVYRLARSLS---IEGADAIFISCTNLRTV-EVIGLLERDTGLPVVSSNTASMW 215
                                    3.334.677*******9999999999...9**************99.99999**999*******998766 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   1.6e-05     0.096     126     217 ..       7     115 ..       3     116 .. 0.67
   2 ?    2.4   0.0     0.015        89     165     208 ..     167     211 ..     115     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                           AroM 126 qlgvivPleeqaeqaekkweelak.........evvvavaspy.gseeelaeaarelaeqgadlivldci........GY 187
                                    ++g ivP+ + + ++ + w  + +         +++ ++++   + ee  a  a++la++g+dliv  c         GY
  gi|118431909|ref|NP_148665.2|   7 RIGLIVPSSN-TTMEPEMWMMAPEgvsihtgrvPLEKVSVEELlKMEEYSAIEAEKLATAGVDLIVYGCTtgsliggpGY 85 
                                    6777777443.44466666666552222222222222222222233344445799**************6666667779* PP

                           AroM 188 teemkaavaealgkpVllarslvarllael 217
                                    + + ++++ +a+g++V++  + v+++l+ l
  gi|118431909|ref|NP_148665.2|  86 DLKIADKLSSASGVQVVTTATAVVEALKAL 115
                                    ************************999865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.015
                           AroM 165 laeaarelaeqgadlivldciGY.teemkaavaealgkpVllars 208
                                    +   ar+l+ +gad i + c    t e    +++ +g+pV+ +++
  gi|118431909|ref|NP_148665.2| 167 VYRLARSLSIEGADAIFISCTNLrTVEVIGLLERDTGLPVVSSNT 211
                                    566788888888888888888873456677888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 2061.09
//
Query:       gi|118431910|ref|NP_148666.2|  [L=427]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Aeropyrum pernix K1]
Scores for complete 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-55  187.9   0.2    4.5e-55  187.7   0.2    1.0  1  Peripla_BP_6  Periplasmic binding protein
      1e-20   74.2   0.0    1.7e-20   73.5   0.0    1.4  1  ANF_receptor  Receptor family ligand binding region
    1.7e-19   70.1   0.3    7.4e-18   64.7   0.3    2.8  1  Peripla_BP_5  Periplasmic binding protein domain
    0.00022   20.2   0.1    0.00035   19.5   0.1    1.3  1  LppC          LppC putative lipoprotein


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 !  187.7   0.2     1e-58   4.5e-55       1     310 [.      35     360 ..      35     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 187.7 bits;  conditional E-value: 1e-58
                                    EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET...TEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                   Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGin...GrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                    +ikiG++ plsG +a++g +l++g++ a++eiN +GG++   G k+++v  D a++p+++a+ a+rl++q+gv alvg+ 
  gi|118431910|ref|NP_148666.2|  35 EIKIGVILPLSGRLAETGADLRRGIEFAVDEINSQGGVKacgGAKLTVVYGDSAGKPETGAAEAERLISQEGVIALVGAY 114
                                    69***************************************9************************************** PP

                                    SHHHHHHHHHHHHHHT-EEEESS-HH...CCTTSTTEEESS--HH...HHHHHHHHHHHHHTT..SCEEEEEEESSHHHH CS
                   Peripla_BP_6  78 ssavaaavaevlakdgvpvigpaglt...gekcspyvfslgpsys...aqasalveylakelg..gkkvalvyadyafgr 149
                                     s+v++ ++ev+++ +vp+i+p +++   +e ++ ++f+++p++    aq + ++++l +++g   +++a++  d+ +g 
  gi|118431910|ref|NP_148666.2| 115 QSSVTKTASEVAERYQVPFINPDSTSpalTERGYKWFFRVTPHDEmfaAQQADFIDWLNQKYGlnLRTFAIIHEDTEWGS 194
                                    *********************8877734458***********7771114555788888899998888************* PP

                                    HHHHHHHHHHHCCTEEEEEEEEE-TTH.HHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEE.CCC- CS
                   Peripla_BP_6 150 egiaalkaaakaaGgevvgeepvplgt.tdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillv.swsg 227
                                     +++a k++++++G+++v+e+ + ++t t++++ v+++kaa++d++l+a++ +d++ l+++++++++ +k +l   +  +
  gi|118431910|ref|NP_148666.2| 195 KVAEAWKKYFTQHGYTLVEEVSYHAATvTSLDSEVQKLKAANPDILLAASYIQDAILLVQTMKAQNFAPKVVLAQdAGFI 274
                                    ************************9999*****************************************96655566669 PP

                                    CHHHHHHHHHHHHTTEEEEES.CSTC..CCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCC....THCC CS
                   Peripla_BP_6 228 seedlkalggeaaegvlavtp.yfpd..ldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaa....gslt 300
                                     ++ + ++g++    ++++   + pd     p+ ++  ++y+++yg +   +  +a+ y+++++l  al+ a     + +
  gi|118431910|ref|NP_148666.2| 275 NPSYVSQVGKD-GW-YIFSREvFSPDliDKIPRLKEVNDRYKKKYGVD--LNGNSARDYTGIWVLYYALEDAckkaSPSN 350
                                    9999*****96.33.455555377785334699**************8..999999999999998888877765314699 PP

                                    HHHHHHHHHH CS
                   Peripla_BP_6 301 reavraales 310
                                    +e++r al+ 
  gi|118431910|ref|NP_148666.2| 351 PEEFRRALRD 360
                                    *******985 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 !   73.5   0.0   3.7e-24   1.7e-20       5     295 ..      58     344 ..      55     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 3.7e-24
                                    HHHHHHHHHHT-TTS..STTEEEEEEEEE-TT-HHHHHHHHHHHCCCC.EEEEEE-SSHHHHHHHHHHHCCTT-EEEESS CS
                   ANF_receptor   5 AmklAveeinsdpnl..lpgiklgyeiidtccdfslaleaaldflkgk.vvaviGpssssvsdavaslanlfkiPvisyg 81 
                                     +++Av+eins++++   +g kl++   d++ +++++ + a  ++ ++ v a++G+++ssv+++++++a+ +++P+i + 
  gi|118431910|ref|NP_148666.2|  58 GIEFAVDEINSQGGVkaCGGAKLTVVYGDSAGKPETGAAEAERLISQEgVIALVGAYQSSVTKTASEVAERYQVPFINPD 137
                                    579**********98335799*************************966******************************* PP

                                    ---GGGG-TTTTTTEEESS--CHH....HHHHHHHHHHHTT-..-EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEE CS
                   ANF_receptor  82 stspelsdknryptflrtvpsdts....qaqAivdilkhfgW..kkvaliysdddygesglqaleeeleergicvalkek 155
                                    stsp+l++ + y+ f+r++p+d++    qa++i  + +++g   +++a+i++d ++g  +++a ++ ++++g++++ + +
  gi|118431910|ref|NP_148666.2| 138 STSPALTE-RGYKWFFRVTPHDEMfaaqQADFIDWLNQKYGLnlRTFAIIHEDTEWGSKVAEAWKKYFTQHGYTLVEEVS 216
                                    ******99.667**********863333777777777877652269******************************8888 PP

                                    ESTCHHHCHHHHHHHHHHTTT--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT-E CS
                   ANF_receptor 156 ipessnddevvrkllkeikskarvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaegvl 235
                                    +  + + +++ ++++k  + ++++ +  ++ +da  l+++++ ++++    v +a+da     +++++      + +   
  gi|118431910|ref|NP_148666.2| 217 YH-AATVTSLDSEVQKLKAANPDILLAASYIQDAILLVQTMKAQNFAP--KVVLAQDAGFINPSYVSQ------VGKDGW 287
                                    88.4444444444444445588999999999****************9..688877765555555544......355555 PP

                                    EEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHC CS
                   ANF_receptor 236 gfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllr 295
                                    ++  ++  sp++ + +    +l+++++ y++  +   + ++a  Y ++++l +Al+++ +
  gi|118431910|ref|NP_148666.2| 288 YIFSREVFSPDLIDKI---PRLKEVNDRYKKKYGVDLNGNSARDYTGIWVLYYALEDACK 344
                                    5555666666666666...55666666666666666666667778888888888887753 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 !   64.7   0.3   1.6e-21   7.4e-18       1     353 [.      36     413 ..      36     426 .. 0.71

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.6e-21
                   Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvl...grkieavvvdpasdwelfaekaeklieedkvevvfGcwt 77 
                                    ik+Gv+  lsG +a +   l +++ +a++ein++gGv+   g k+  v  d+a+ +e+ a++ae+li++++v +++G++ 
  gi|118431910|ref|NP_148666.2|  36 IKIGVILPLSGRLAETGADLRRGIEFAVDEINSQGGVKacgGAKLTVVYGDSAGKPETGAAEAERLISQEGVIALVGAYQ 115
                                    8************************************977789************************************* PP

                   Peripla_BP_5  78 SasRkavlpvveelnalLfYpvqYEG..eEssknviY....tGaapnqqaipavdyllselg..akrvflvGsdyvypre 149
                                    S+  k+  +v e+ +  ++ p       +E   + ++           q  +++d+l +++g   + ++++  d  +  +
  gi|118431910|ref|NP_148666.2| 116 SSVTKTASEVAERYQVPFINPDSTSPalTERGYKWFFrvtpHDEMFAAQQADFIDWLNQKYGlnLRTFAIIHEDTEWGSK 195
                                    ***************99999865543114555555551100455556688899*********977889999********* PP

                   Peripla_BP_5 150 tnrilkallkakggevvge.eYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikaekipvv.slsva 227
                                    +++  k++++++g + v+e +Y +   + +++ v+k+k+a+pd++l     + ++ + +++k++++ ++ +    +  + 
  gi|118431910|ref|NP_148666.2| 196 VAEAWKKYFTQHGYTLVEEvSYHAATVTSLDSEVQKLKAANPDILLAASYIQDAILLVQTMKAQNFAPKVVLAQdAGFIN 275
                                    ***************998747999999******************99999999999999999999999865433133344 PP

                   Peripla_BP_5 228 eeelaaidaealvGh.laawnYfqs..vdt.penkafvakfkarvgedrvtnd..pmeaayiqvklwaqAvekagstdve 301
                                     + +++++++   G  + +++ f+   +d+ p+ k++ +++k+++g d   n+       ++  + +  A +ka  +++e
  gi|118431910|ref|NP_148666.2| 276 PSYVSQVGKD---GWyIFSREVFSPdlIDKiPRLKEVNDRYKKKYGVDLNGNSarDYTGIWVLYYALEDACKKASPSNPE 352
                                    4445555443...3202334444322233225666666666666666543332002233344444444555555555555 PP

                   Peripla_BP_5 302 kvreallgqelk.........apeGevkidpenhhlsktvrigkikadGqfeivwetkkpv 353
                                    + r+al+++ ++          p   vk+d++ + +  +  i ++ +dG++++v+  + +v
  gi|118431910|ref|NP_148666.2| 353 EFRRALRDSLVNlqlspdqiiMPWKGVKFDEKGQNILGQGLIVQMFEDGKYHVVYPEDFAV 413
                                    5555554433221111111114445567777777777777777777777777776665555 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   7.8e-08   0.00035     221     418 ..      37     256 ..      31     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.8e-08
                                    -EEEEE--SSTTHHHHHHHHHHHHHHH............TT--S-EEEEETTTS...-HHHHHHHHHHTT--EEE---SH CS
                           LppC 221 kvalLLPlsGklakvaetirdGFlaak.........daetqsnaqvkvfDtaae...slediyaqakaagidlvVGPLlk 288
                                    k++++LPlsG la  ++ +r G ++a          +a +  + +v   D+a +   ++ ++ + + ++g+  +VG   +
  gi|118431910|ref|NP_148666.2|  37 KIGVILPLSGRLAETGADLRRGIEFAVdeinsqggvKACGGAKLTVVYGDSAGKpetGAAEAERLISQEGVIALVGAY-Q 115
                                    89************************9777655544444555566666687765566899999*************86.5 PP

                                    HHHHHHHHSGG.GTTSEEEES---TT---.BTTEEE----HHHHHHHH..HHHH..HHT....T-SSEEEEEESSHHHHH CS
                           LppC 289 qnvdkllaqeqlvqsidvLaLNssdnsra.iaqlcyfgLspEdeaesa..Askl..wad....gvRnplvlvpqndlGrR 359
                                      v k +++ +   +++ +   s++ + +       f  +p de  +a  A+ +  +++     +R+  ++    ++G +
  gi|118431910|ref|NP_148666.2| 116 SSVTKTASEVAERYQVPFINPDSTSPALTeRGYKWFFRVTPHDEMFAAqqADFIdwLNQkyglNLRTFAIIHEDTEWGSK 195
                                    7788888888887888998888888885526667889*******6655114322223332322679************** PP

                                    HHHHHHHHHHHHHSS--E.EEEES.SGGGHHHHHHHH-.TTTEEEEE---HHHHHHHHHHH CS
                           LppC 360 vveAFnerwqqlagtdaa.ielvd.qpadlaqqlkdasrqdidavyivanskelaeikptl 418
                                    v+eA+++ + q + t +  + +     + l  ++++ +  + d + ++   +++  +  t+
  gi|118431910|ref|NP_148666.2| 196 VAEAWKKYFTQHGYTLVEeVSYHAaTVTSLDSEVQKLKAANPDILLAASYIQDAILLVQTM 256
                                    *************999642544330345677777777766666666666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      867  (0.0483574); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 3036.46
//
Query:       gi|118431911|ref|NP_148667.2|  [L=289]
Description: branched-chain amino acid ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-39  134.7  47.0    3.7e-39  134.5  47.0    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        1.5    8.6   3.9       0.62    9.8   0.2    2.4  2  NCE101        Non-classical export 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 !  134.5  47.0   4.1e-43   3.7e-39       2     267 ..      10     276 ..       9     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 4.1e-43
                   BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlk 81 
                                    i+ +l  ++ +a++A+Gla+++g++ +in++hg fm+lGa +a ++ +l++  +l++ ++a+++ +a+g+ + + v+   
  gi|118431911|ref|NP_148667.2|  10 IVDGLLIGGAYALVAMGLAMIWGVMEIINFAHGDFMMLGALAAYYAFTLMGLDPLAGGVLAFVMVFALGVGVQRGVINRI 89 
                                    677889999*******************************************9*****************9999988777 PP

                   BPD_transp_2  82 vdeliitllllsvlvgltlllltgitsgvkgqs....svkellgfagallsflsavivllalllvlavllllrrtrfGra 157
                                    +d ++ t ++ +++v+l+  +  ++  g+++ +     ++  +g   + ++ ++  i+l+ l++++++++ll+rt +G a
  gi|118431911|ref|NP_148667.2|  90 LDAPLLTQIAATFAVLLIIRYGVQAVLGPYTRRlvtwYQDYYVGLGFTTVPLSKLLIFLVSLVILALLYILLNRTDMGIA 169
                                    7776666666555555555566666666666653554555566778888888888999********************** PP

                   BPD_transp_2 158 lravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgagsllgtviGali 237
                                    +ra+ +n+ +a+++Ginv rv  +tf i+ ++A++ Gal+al++ + p  +g  + + a++avvlGg g+++g+ +G+li
  gi|118431911|ref|NP_148667.2| 170 IRATSQNRMVAQLMGINVSRVYDVTFGIGVGVAAVGGALVALFYPIFP-EMGGFFALIAFIAVVLGGFGNVYGAYVGGLI 248
                                    ********************************************9999.******************************* PP

                   BPD_transp_2 238 igvvksllltllgiptelarvllgallilv 267
                                    igv +s  ++l+   ++l++v+ ++l+il+
  gi|118431911|ref|NP_148667.2| 249 IGVTES-VSALFI-EPALKDVVAFLLFILI 276
                                    ******.777774.59************97 PP

>> NCE101  Non-classical export protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.5         1   9.3e+03      17      22 ..      50      55 ..      46      56 .. 0.69
   2 ?    9.8   0.2   6.9e-05      0.62       3      19 ..     187     203 ..     187     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1
                         NCE101 17 vaaYyl 22
                                   +aaYy 
  gi|118431911|ref|NP_148667.2| 50 LAAYYA 55
                                   478886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.9e-05
                         NCE101   3 lsrflDPlLaifiGvaa 19 
                                    +sr+ D +++i +Gvaa
  gi|118431911|ref|NP_148667.2| 187 VSRVYDVTFGIGVGVAA 203
                                    79*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2146.12
//
Query:       gi|118431912|ref|NP_148668.2|  [L=309]
Description: branched-chain amino acid ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-34  117.2  34.1    8.2e-34  117.0  34.1    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 !  117.0  34.1   4.6e-38   8.2e-34       3     267 ..      19     291 ..      17     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 4.6e-38
                   BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkv 82 
                                    +n++ l++ ++i A++++l++g++G+++lgh+ f+++G+y++ +l+ ++   ++++l+va l++a+++++l  + lrl+ 
  gi|118431912|ref|NP_148668.2|  19 VNMIFLSLMYGISAMAWNLLMGYTGLFSLGHAVFFGVGGYTVIVLALRYNVTPWIGLPVAGLTAAMLAAALSPPLLRLRS 98 
                                    79999*************************************************************************** PP

                   BPD_transp_2  83 deliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvlavllllrrtrfGral 158
                                    + +  ++++l ++++l +   ++   g      + ++++ + +++ f++a +     + +l++ l++l+ + ++++G+ +
  gi|118431912|ref|NP_148668.2|  99 HWFTLATIALGEIFRLSF--AHWDYVGASAG-LQMPISERSIYYVQFAGATVYsyiaMAILAVELLFLWKIINSKTGFYM 175
                                    ******************..44444444433.44444555555555555555569977777778999************* PP

                   BPD_transp_2 159 ravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp...nigvglgfnaiaavvlGgagsllgtviGa 235
                                      ++e+e +a+ lGin++ +k+l+ vis+++ glaG l+a+++  ++p   +  ++++ ++ +a ++Gg+ + lg+ +G+
  gi|118431912|ref|NP_148668.2| 176 QTIREDELVAQTLGINTFNYKALSLVISAFFTGLAGGLYAMRFRYVDPfavFDLITISTYIAIAGIIGGIYTFLGPQVGS 255
                                    ************************************************87555566778888999*************** PP

                   BPD_transp_2 236 liigvvksllltllgi..p..telarvllgallilv 267
                                    +i++ +++  ++ + +  p    l++++lg++l+l+
  gi|118431912|ref|NP_148668.2| 256 FIFVPISEYVRANIVQafPrvYGLHVAVLGVILLLI 291
                                    *****9998887777755244888999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2271.02
//
Query:       gi|118431913|ref|NP_148669.2|  [L=239]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-27   95.3   0.0    5.4e-27   95.0   0.0    1.1  1  ABC_tran      ABC transporter
      5e-09   35.9   0.1    1.3e-08   34.6   0.1    1.8  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    1.6e-07   31.4   1.4    0.00021   21.2   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0013   18.4   0.0     0.0016   18.1   0.0    1.1  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
     0.0025   18.3   0.3     0.0054   17.3   0.1    1.6  2  AAA_23        AAA domain
     0.0028   17.3   0.0     0.0056   16.4   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.003   17.6   0.8      0.019   15.1   0.8    2.2  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0069   16.8   0.2       0.32   11.4   0.2    2.3  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.018   14.5   0.9        1.9    7.9   0.2    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.024   15.0   0.0      0.034   14.5   0.0    1.3  1  AAA_16        AAA ATPase domain
      0.036   13.5   0.2      0.046   13.2   0.2    1.2  1  KdpD          Osmosensitive K+ channel His kinase sensor doma
      0.037   13.8   0.3       0.65    9.7   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.055   13.7   1.7        8.9    6.6   0.2    2.2  2  AAA_22        AAA domain
       0.13   12.0   0.0       0.24   11.1   0.0    1.6  1  AAA_30        AAA domain
       0.16   11.9   0.2       0.37   10.7   0.1    1.6  2  RsgA_GTPase   RsgA GTPase
       0.33   10.9   2.1        3.8    7.4   0.1    2.5  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 !   95.0   0.0   4.8e-30   5.4e-27       1     135 [.      20     164 ..      20     166 .. 0.95

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 4.8e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren 79 
                                    lk vs+++++ge+v+++G+nGaGK+tL+++++g + p+ G++ ++g d++     +++r+ i+  +q  +   +ltv +n
  gi|118431913|ref|NP_148669.2|  20 LKGVSFSVRRGERVGLIGPNGAGKTTLFNIISGIYMPDRGRVIYKGVDITGwPAYRRSRAGIARTFQIVRPLANLTVLNN 99 
                                    799************************************************88899************************ PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                                 e++e++ +a++ +gl +++d  +    + L   +k+r++laral+++p+llllDE 
  gi|118431913|ref|NP_148669.2| 100 vivgallrtndirEARERAMEAIDMVGLAGKEDILA----KDLNLIEKKRLELARALATQPELLLLDEI 164
                                    **********999999999999*****999666666....99**************************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 !   34.6   0.1   1.1e-11   1.3e-08       1      23 []     214     236 ..     214     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.1e-11
                   BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                    ++IAeGtP Ev ++  VieAY+G
  gi|118431913|ref|NP_148669.2| 214 EKIAEGTPREVASNKLVIEAYMG 236
                                    69*******************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.9e-07   0.00021       3      22 ..      34      53 ..      33      80 .. 0.82
   2 !    9.2   0.3   0.00082      0.92     252     294 ..     153     192 ..     144     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +liGpNg+GK++L+ +++++
  gi|118431913|ref|NP_148669.2| 34 GLIGPNGAGKTTLFNIISGI 53
                                   69***************988 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00082
                         AAA_21 252 lralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQvil 294
                                    + ++    lll+DE+ +gL P+ +  l+ +ll++ +r g+ +i+
  gi|118431913|ref|NP_148669.2| 153 ATQP---ELLLLDEIAAGLRPREVDDLVyTLLEISKR-GITIIM 192
                                    3333...9********************566655555.999997 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 !   18.1   0.0   1.4e-06    0.0016       9      98 ..      25     218 ..      16     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
                                    S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEE....................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx....................................... RF
                    ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvg....................................... 48 
                                    f++ +G+r++++g +g Gkt++ + +s     d+  +iy g                                       
  gi|118431913|ref|NP_148669.2|  25 FSVRRGERVGLIGPNGAGKTTLFNIISGIYMPDRgRVIYKGvditgwpayrrsragiartfqivrplanltvlnnvivga 104
                                    8899***********************988888779******************************************** PP

                                    .............................................................ESEEHHHHHHHHHHCHH.. CS
                                    .............................................................xxxxxxxxxxxxxxxxx.. RF
                    ATP-synt_ab  49 .............................................................iGergnevaevleefpe.. 65 
                                                                                                  G r +ev +++ ++ e  
  gi|118431913|ref|NP_148669.2| 105 llrtndirearerameaidmvglagkedilakdlnliekkrlelaralatqpelllldeiaAGLRPREVDDLVYTLLEis 184
                                    *************************************************************************9999954 PP

                                    .SSGGGGEEEEEEETTS-HHHHHHHHHHHHHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  66 .gtimkrtvlvantsnepvaareasiytgitlAE 98 
                                     ++i   +v  +  + ++ a+r+++   g  +AE
  gi|118431913|ref|NP_148669.2| 185 kRGITIIMVEHVMRAVMNFAERVIVLHFGEKIAE 218
                                    3223322333344567788889999888888888 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.8e-06    0.0054      24      40 ..      35      51 ..      14      58 .. 0.89
   2 ?   -2.1   0.0         4   4.4e+03     174     174 ..     150     150 ..     106     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.8e-06
                         AAA_23 24 ItGpNGaGKTTildAik 40
                                   ++GpNGaGKTT+++ i 
  gi|118431913|ref|NP_148669.2| 35 LIGPNGAGKTTLFNIIS 51
                                   78***********9885 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                         AAA_23 174 k 174
                                    +
  gi|118431913|ref|NP_148669.2| 150 R 150
                                    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 !   16.4   0.0     5e-06    0.0056      14      50 ..      22      58 ..      18      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5e-06
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   g ++++++ + + l+Gp+G+GK+Tl+  i+ + +p++
  gi|118431913|ref|NP_148669.2| 22 GVSFSVRRGERVGLIGPNGAGKTTLFNIISGIYMPDR 58
                                   55677775558899************99988888876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.8   1.7e-05     0.019       1      57 [.      32     133 ..      32     196 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                    EEEEEESTTSSHHHHHHHHHT..............STEEESSSTTSSSSEEEEEEEETTEE................... CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg..............ekaivsdkpgtTrdinegrvklkgke................... 47 
                                    +v+++G   +GK+tL+n ++g              +          T  + ++r + +                      
  gi|118431913|ref|NP_148669.2|  32 RVGLIGPNGAGKTTLFNIISGiympdrgrviykgvD---------ITGWPAYRRSRAGI-Artfqivrplanltvlnnvi 101
                                    69*****************98666644433333330.........33333333333110.01122222222233333333 PP

                                    .................EEEEECGGC.....S CS
                       MMR_HSR1  48 .................ielvDtpGl.....i 57 
                                                     +e +D++Gl     i
  gi|118431913|ref|NP_148669.2| 102 vgallrtndireareraMEAIDMVGLagkedI 133
                                    33333333344444444888888886333331 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   0.2   0.00029      0.32       3      23 ..      35      57 ..      33     214 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                   EESSTTSSHHHHHHHHHHHH..T CS
                            AAA  3 lyGppGtGKTllakavakel..g 23
                                   l+Gp G GKT+l + +      +
  gi|118431913|ref|NP_148669.2| 35 LIGPNGAGKTTLFNIISGIYmpD 57
                                   89**********99998875331 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 ?    7.9   0.2    0.0017       1.9      28      44 ..      34      50 ..      21      54 .. 0.85
   2 ?    5.2   0.0     0.011        12     159     209 ..     156     208 ..     139     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                                   EEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnlldAi 44
                                    ++GpNG+GK+ l++ i
  gi|118431913|ref|NP_148669.2| 34 GLIGPNGAGKTTLFNII 50
                                   589********998766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                    -SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-S.SHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.xxxxxxxxxxxx RF
                          SMC_N 159 aplyllDeidaaLDeknvkkvaellkekskn.aQfivisl.reemlekadklv 209
                                      l llDei+a L  ++v  ++  l e sk+   +i++ +  + +++ a++++
  gi|118431913|ref|NP_148669.2| 156 PELLLLDEIAAGLRPREVDDLVYTLLEISKRgITIIMVEHvMRAVMNFAERVI 208
                                    45889*************99998888877663555544441344555556655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-05     0.034      19     144 ..      27     164 ..      13     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql.....esaipysalaqalareellrqllde..... 88 
                                    vr+g  e v l+G+ G GK++l + +   +  d+g +++   d       +  ++++ +a+++   +++r l++      
  gi|118431913|ref|NP_148669.2|  27 VRRG--ERVGLIGPNGAGKTTLFNIISGIYMPDRGRVIYKGVDITgwpayR--RSRAGIARTF---QIVRPLANLtvlnn 99 
                                    5555..67889****************999999888877777766333221..3335566666...67777776666666 PP

                         AAA_16  89 ......aesaeleawrekleeala....avpelagaea...srllellkrll..allsrderplvlvlDdl 144
                                          +++++ +++re+  ea+     a++e         ++l+   k+ l  a++    +p +l+lD++
  gi|118431913|ref|NP_148669.2| 100 vivgalLRTNDIREARERAMEAIDmvglAGKE-----DilaKDLNLIEKKRLelARALA-TQPELLLLDEI 164
                                    66654433444444444444444433333333.....2444333333333331133333.23477777776 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 ?   13.2   0.2   4.1e-05     0.046      45     118 ..     112     190 ..      76     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                           KdpD  45 rketealleglevi......prkeveykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagidV 118
                                    r+  e+ +e ++++      +  + + +  e ++l+l  +la +pe++l+De+a    p    +  y    e+ ++gi +
  gi|118431913|ref|NP_148669.2| 112 REARERAMEAIDMVglagkeDILAKDLNLIEKKRLELARALATQPELLLLDEIAAGLRPREVDDLVYT-LLEISKRGITI 190
                                    3344445555555544432222222344466789********************98777666555554.34455566655 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 ?    9.7   0.0   0.00058      0.65      35      64 ..      17      47 ..       7      67 .. 0.83
   2 ?    2.1   0.1      0.13   1.4e+02      98     135 ..     145     182 ..     130     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00058
                      IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKshla 64
                                   +++L + sf +++ e + l+Gp G+GK+ l 
  gi|118431913|ref|NP_148669.2| 17 IEALKGVSFsVRRGERVGLIGPNGAGKTTLF 47
                                   67889999978999**************885 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                      IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfevie 135
                                    +l+ a +  ++++ll+lD+++     ++   l++ ++e
  gi|118431913|ref|NP_148669.2| 145 RLELARALATQPELLLLDEIAAGLRPREVDDLVYTLLE 182
                                    444444445789*******9876666666666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0085       9.5      10      22 ..      35      47 ..      29      52 .. 0.89
   2 ?    6.6   0.2     0.008       8.9      85     128 ..     148     193 ..     106     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0085
                         AAA_22 10 vtGesGtGKTtll 22
                                   ++G+ G+GKTtl 
  gi|118431913|ref|NP_148669.2| 35 LIGPNGAGKTTLF 47
                                   79*********96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.008
                         AAA_22  85 alrarav.ielliiDEaqh.lrseealeeL.rsllnlsrkgvqliLv 128
                                     +ra a+ +ell++DE+   l +++ + +L  +ll++s+ g+++i+v
  gi|118431913|ref|NP_148669.2| 148 LARALATqPELLLLDEIAAgL-RPREVDDLvYTLLEISKRGITIIMV 193
                                    3333334678***********.6555555546667777788888875 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   0.00021      0.24      22      50 ..      34      62 ..      25     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                         AAA_30 22 vltGpAGtGKttalkalreaweaaggrvi 50
                                    l Gp G+GKtt+ + +  ++  + grvi
  gi|118431913|ref|NP_148669.2| 34 GLIGPNGAGKTTLFNIISGIYMPDRGRVI 62
                                   689**************999998854444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00033      0.37      99     121 ..      30      52 ..      14      66 .. 0.83
   2 ?   -2.6   0.0       4.1   4.6e+03     114     136 ..      95     117 ..      91     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                    TSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                    ++ + l+G+ G+GK+tL n + +
  gi|118431913|ref|NP_148669.2|  30 GERVGLIGPNGAGKTTLFNIISG 52 
                                    477789*************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                                    HHHHHHCTT-----S-------- CS
                    RsgA_GTPase 114 tLinallpelelktgevseklgr 136
                                    t++n+++  + l+t++++e+ +r
  gi|118431913|ref|NP_148669.2|  95 TVLNNVIVGALLRTNDIREARER 117
                                    56777777778999999998766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0034       3.8       2      21 ..      33      52 ..      32      89 .. 0.77
   2 ?    3.0   0.3     0.074        83      81     141 ..     141     200 ..      78     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0034
                                   EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvle 21
                                   v + Gp G GKtTl++ ++ 
  gi|118431913|ref|NP_148669.2| 33 VGLIGPNGAGKTTLFNIISG 52
                                   6788**********998865 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.074
                                    HHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHH CS
                       NTPase_1  81 feelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalv 141
                                    +e+  le  r   ++++++++DEi    l  +++ + v ++L+ +k  +++i +++  + v
  gi|118431913|ref|NP_148669.2| 141 IEKKRLELARALATQPELLLLDEIAA-GLRPREVDDLVYTLLEISKRGITIIMVEHVMRAV 200
                                    56666666666668899999999954.6777888888888888666666666666543444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1793.43
//
Query:       gi|14602122|ref|NP_148670.1|  [L=240]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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  107.0   0.0    1.4e-30  106.6   0.0    1.2  1  ABC_tran  ABC transporter
    3.2e-08   33.7   2.8     0.0024   17.7   0.1    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0018   18.6   0.3     0.0065   16.8   0.3    1.7  1  AAA_19    AAA domain
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.031   14.0   0.1    1.6  1  AAA_30    AAA domain
      0.038   13.7   0.1      0.065   13.0   0.1    1.3  1  AAA_29    P-loop containing region of AAA domain
      0.055   13.3   0.0      0.079   12.8   0.0    1.3  1  MukB      MukB N-terminal
      0.063   12.9   0.0      0.099   12.3   0.0    1.3  1  SRP54     SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   5.4e-34   1.4e-30       3     136 ..      24     167 ..      22     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 5.4e-34
                                   EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren... 79 
                                    vsl +++ge+va++G nGaGK+t l +++gllkp +G+i ++g+d++     +++++ i+ +p+   +fp+ltv+en   
  gi|14602122|ref|NP_148670.1|  24 GVSLRVYKGEIVALLGGNGAGKTTTLLTISGLLKPRNGSIIWQGRDITGlPAFKRVEEGISHVPEGRGIFPRLTVYENlrv 104
                                   69***********************************************9999**************************** PP

                                   .....HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   .....xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 .....esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                         ++e++++ l+++  +  + + + ++ + +LSgG++q++a+aral+++p ll++DEp+
  gi|14602122|ref|NP_148670.1| 105 aastrRAKEHFQDSLEQVYTIFpILKARRSQLAGTLSGGEQQMLAIARALIQRPILLMMDEPS 167
                                   976664444455555555444443333333557*****************************5 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 !   16.8   0.4   1.8e-06    0.0047       1      76 [.      34      96 ..      34     126 .. 0.77
   2 !   17.7   0.1   9.5e-07    0.0024     234     287 ..     137     187 ..     105     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                        AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76
                                  + +l G Ng+GK++ L ++++l             ++++g+i+++ + +++    +++e +i+ ++ +g  +  +l
  gi|14602122|ref|NP_148670.1| 34 IVALLGGNGAGKTTTLLTISGL------------LKPRNGSIIWQGRDITGLPAFKRVEEGIS-HVPEGRGIFPRL 96
                                  5789******************............67899999988888888887777776666.555555555555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 9.5e-07
                        AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                   a  lS G +++la++ al++++    ll  DEp +gL Pkl r ++ l ++l++
  gi|14602122|ref|NP_148670.1| 137 AGTLSGGEQQMLAIARALIQRP---ILLMMDEPSLGLAPKLARDVIYLASRLRE 187
                                   5678*******99999999988...9*****************99977755554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   2.6e-06    0.0065       9      75 ..      31     128 ..      27     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                        AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp...................................eeillvaftgrA 54 
                                   k +++++++G G GKT++l +i  ll+ ++g                                      e++ ++a t+rA
  gi|14602122|ref|NP_148670.1|  31 KGEIVALLGGNGAGKTTTLLTISGLLKPRNGSIIwqgrditglpafkrveegishvpegrgifprltvyENLRVAASTRRA 111
                                   678999*****************9999998775588899999999999999999999999999999998888889999999 PP

                        AAA_19  55 akelrerlaalgaeatTiHrl 75 
                                    +  +++l    ++ +Ti  +
  gi|14602122|ref|NP_148670.1| 112 KEHFQDSL----EQVYTIFPI 128
                                   99999888....556666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.2e-05     0.031      18      99 ..      32     168 ..      18     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                        AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g......................................grviglAptgkaA 59 
                                     +++l G+ G+GKtt+l ++  +++ + g                                      +++ ++A+t +a 
  gi|14602122|ref|NP_148670.1|  32 GEIVALLGGNGAGKTTTLLTISGLLKPRnGsiiwqgrditglpafkrveegishvpegrgifprltvyENLRVAASTRRAK 112
                                   458999*****************9999956888888888888888888888888888888888888877788888888888 PP

                        AAA_30  60 kvLaeelgieastiakllkrlk.................grarlepgtllivDEagm 99 
                                   +  +++l+ + +ti  +lk+ +                 +ra +++  ll+ DE ++
  gi|14602122|ref|NP_148670.1| 113 EHFQDSLE-QVYTIFPILKARRsqlagtlsggeqqmlaiARALIQRPILLMMDEPSL 168
                                   88888877.777777777666677777777777777777656666667777777665 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 ?   13.0   0.1   2.5e-05     0.065      19      50 ..      29      60 ..      15      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                        AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                  +  kg ++ l G +G+GK+T l  i+ lL p++
  gi|14602122|ref|NP_148670.1| 29 VY-KGeIVALLGGNGAGKTTTLLTISGLLKPRN 60
                                  44.445999***********9989999998876 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05     0.079      28      52 ..      34      58 ..      18     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                  HHHHHS--SHHHHHHHHHHHHHHS- CS
                          MukB 28 vttlsGgnGaGksttmaafvtaliP 52
                                  + +l GgnGaGk+tt+ ++   l P
  gi|14602122|ref|NP_148670.1| 34 IVALLGGNGAGKTTTLLTISGLLKP 58
                                  67899***********998877777 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.9e-05     0.099       3      40 ..      34      71 ..      32      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.9e-05
                                  EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                         SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                  +++l+G +GaGKTttl  ++ llk ++ +++    D+ 
  gi|14602122|ref|NP_148670.1| 34 IVALLGGNGAGKTTTLLTISGLLKPRNGSIIWQGRDIT 71
                                  7899************9999999988888777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1793.01
//
Query:       gi|118431914|ref|NP_148671.2|  [L=682]
Description: hydantoin utilization protein A [Aeropyrum pernix K1]
Scores for 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-104  347.0   0.2   6.6e-102  340.7   0.0    2.1  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    5.6e-49  166.3   0.0    1.6e-48  164.8   0.0    1.8  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
       0.01   15.4   0.0          1    8.8   0.0    2.5  2  BcrAD_BadFG     BadF/BadG/BcrA/BcrD ATPase family
      0.019   13.6   0.8        1.3    7.5   0.1    2.1  2  MutL            MutL protein
       0.12   12.2   0.0        0.7    9.7   0.0    2.2  3  DUF294          Putative nucleotidyltransferase DUF294
        0.2   12.1   0.2       0.88   10.0   0.0    2.1  2  FtsA            Cell division protein FtsA


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 !    4.4   0.0    0.0061        18      82     102 ..       4      24 ..       3      40 .. 0.87
   2 !  340.7   0.0  2.2e-105  6.6e-102       1     290 [.     200     497 ..     200     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0061
                 Hydantoinase_A  82 ItfDmGGTstDvslikdgeve 102
                                    +++D+GGT tD++++++g+ +
  gi|118431914|ref|NP_148671.2|   4 VGVDIGGTFTDLIVFDEGSGR 24 
                                    689************999765 PP

  == domain 2  score: 340.7 bits;  conditional E-value: 2.2e-105
                 Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklagekk 80 
                                    rt+tavvn+ l+pil++yl+++++ le rg+k  l++mqs+Gg+ ++d+a ++p+ +i+SGPaaG+++++++++++g+ +
  gi|118431914|ref|NP_148671.2| 200 RTSTAVVNGLLKPILSKYLKRLKSDLEGRGFKGILLLMQSSGGVSTVDYAVERPAAFIESGPAAGAIAVSYYATMQGVGR 279
                                    89****************************************************************************** PP

                 Hydantoinase_A  81 vItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrvgpesag 148
                                    +I+fDmGGT++++s i+dge+ v++e+e+            +g++vr+p +d+ +v+agGg+i++vd gg++rvgp sag
  gi|118431914|ref|NP_148671.2| 280 AIGFDMGGTTAKASSIIDGEPLVVREYEVgakvhmgrplrgSGYPVRYPYIDLVEVSAGGGTIAWVDPGGAVRVGPVSAG 359
                                    ******************************************************************************** PP

                 Hydantoinase_A 149 adpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegilsvavenmana 228
                                    adpgpacy+ Gg+++t+TDanlvLGrl+++ ++    g++kl ++la ra++ +a++ +l+v+e+A++++++a++ m +a
  gi|118431914|ref|NP_148671.2| 360 ADPGPACYGLGGDKPTLTDANLVLGRLPEA-LA---WGRIKLYRDLAVRALASIADKAGLEVDEAAWAVIRIANTVMGKA 435
                                    ***************************998.99...******************************************** PP

                 Hydantoinase_A 229 vrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290
                                    +r ++verg+dp+e+tl++fGGaG++haa++ eel v++v++ppy+gv+s lG+++Ad+r++
  gi|118431914|ref|NP_148671.2| 436 LRLVTVERGYDPREFTLYAFGGAGPLHAAEIGEELSVSRVVIPPYPGVFSSLGLLVADYRHD 497
                                    ************************************************************97 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.0   5.3e-52   1.6e-48       1     177 [.       3     179 ..       3     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 5.3e-52
                     Hydant_A_N   1 rigIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg...e 77 
                                    r+g+D+GGTfTD++++de+++++ +lK+l+tp++++ g+++alee++     + + +dvv+++TT+ tN++l ++g   +
  gi|118431914|ref|NP_148671.2|   3 RVGVDIGGTFTDLIVFDEGSGRLESLKVLTTPREPWVGVIRALEEASV----DIEGVDVVIHATTLGTNMFLGQEGlepP 78 
                                    79*******************************************954....499***********************99 PP

                     Hydant_A_N  78 rvaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagvesiav 155
                                     ++Lit++gfrd+leigrqnrp+l++l ++  kplv++++++ v++r++a+g+v++++d+ ev + +k++  + ++ ++v
  gi|118431914|ref|NP_148671.2|  79 SAVLITNRGFRDVLEIGRQNRPELYNLYFTrpKPLVPRDRRLVVKGRIDARGNVVEDIDRGEVARLAKEWCGR-ADVFIV 157
                                    **************************888899***************************************99.****** PP

                     Hydant_A_N 156 vllhSylnpehElrvaeiarei 177
                                    ++l+S++np hE +++ i+ ++
  gi|118431914|ref|NP_148671.2| 158 SMLNSHINPVHEDEIGSIITRE 179
                                    ******************9987 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 ?    8.8   0.0   0.00035         1       1      59 [.       4     225 ..       4     280 .. 0.66
   2 ?    4.1   0.0    0.0096        29       1      30 [.     281     418 ..     281     537 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00035
                                    EEEEE-SSEEEEEEEETTTEEEEEEEE--................................................... CS
                    BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitns................................................... 29 
                                    vG+D+G+T t  +++de +  l   +  +                                                   
  gi|118431914|ref|NP_148671.2|   4 VGVDIGGTFTDLIVFDEGSGRLESLKVLTtprepwvgviraleeasvdiegvdvvihattlgtnmflgqegleppsavli 83 
                                    8***************9876555544444556677777777777777777777777777777777777777777777777 PP

                                    ................................................................................ CS
                    BcrAD_BadFG  30 ................................................................................ 29 
                                                                                                                    
  gi|118431914|ref|NP_148671.2|  84 tnrgfrdvleigrqnrpelynlyftrpkplvprdrrlvvkgridargnvvedidrgevarlakewcgradvfivsmlnsh 163
                                    77777766666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                    ................................TTS-HHH.........HHHHHHHHHHT--G CS
                    BcrAD_BadFG  30 ................................anlesvrfeaaekvleealtealerageee 59 
                                                                    +++e++ ++ + + l+ +l++ l+r++ + 
  gi|118431914|ref|NP_148671.2| 164 inpvhedeigsiitrecpgaivvegaridpqeKEYERTSTAVVNGLLKPILSKYLKRLKSDL 225
                                    66666666666666666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0096
                                    EEEEE-SSEEEEEEEETTTEEEEEEEE--................................................... CS
                    BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitns................................................... 29 
                                    +G D+G+Tt ka  + + + ++ r + ++                                                   
  gi|118431914|ref|NP_148671.2| 281 IGFDMGGTTAKASSIIDGEPLVVREYEVGakvhmgrplrgsgypvrypyidlvevsagggtiawvdpggavrvgpvsaga 360
                                    699*********98877777666666666466666666666666666666666666666666666666666666666666 PP

                                    .........................................................T CS
                    BcrAD_BadFG  30 .........................................................a 30 
                                                                                             +
  gi|118431914|ref|NP_148671.2| 361 dpgpacyglggdkptltdanlvlgrlpealawgriklyrdlavralasiadkaglevD 418
                                    6666666666666666666666666665555555555555555555555555444441 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0038        12       4      51 ..       6      52 ..       3      64 .. 0.68
   2 ?    7.5   0.1   0.00043       1.3     227     269 ..     260     300 ..     242     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0038
                           MutL  4 iDiGSttTkvtlvdlekvderllgqaeapTtvee..edvleGleealeel 51
                                   +DiG t+T ++++d+ +  +r l + + +Tt  e    v ++leea  ++
  gi|118431914|ref|NP_148671.2|  6 VDIGGTFTDLIVFDEGS--GR-LESLKVLTTPREpwVGVIRALEEASVDI 52
                                   89999999999999965..44.4555666666544555666666665555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00043
                           MutL 227 TPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegsp 269
                                     PaA   av+  a+   +g+g ++++D+GG+T    s+++g+p
  gi|118431914|ref|NP_148671.2| 260 GPAAGAIAVSYYAT--MQGVGRAIGFDMGGTTAKASSIIDGEP 300
                                    56666666777776..6789******************99987 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   4.2e+03     105     131 ..     179     205 ..     177     208 .. 0.84
   2 ?    9.7   0.0   0.00023       0.7       4      59 ..     404     459 ..     402     460 .. 0.91
   3 ?   -1.9   0.0      0.86   2.6e+03      77     104 ..     509     536 ..     502     539 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                         DUF294 105 lCpggimasnpewrkslseWkeqfrkw 131
                                    +Cpg i+++  +   + +e++++ +++
  gi|118431914|ref|NP_148671.2| 179 ECPGAIVVEGARIDPQEKEYERTSTAV 205
                                    7******99999999999999887765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00023
                         DUF294   4 erlvrallaegvkaealarlvselndallrrlielaeeelgkppvpfallvmGSeG 59 
                                    ++l++ + ++g ++ ++a +v ++ ++++ ++++l+  e g +p++f+l+++G +G
  gi|118431914|ref|NP_148671.2| 404 RALASIADKAGLEVDEAAWAVIRIANTVMGKALRLVTVERGYDPREFTLYAFGGAG 459
                                    566667778999*****************************************887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.86
                         DUF294  77 deeeeaareyfaelaervneaLaalGyp 104
                                     e+++a++e f+ l e+ +++L   G+ 
  gi|118431914|ref|NP_148671.2| 509 PETQDAVEEAFKGLEEEAIKTLRSEGFS 536
                                    4789999***************999986 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00029      0.88       1      19 [.       4      22 ..       4      47 .. 0.81
   2 ?   -1.3   0.1      0.96   2.9e+03       3      29 ..     283     309 ..     281     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00029
                                   EEEEE-SSSEEEEEEETTE CS
                                   xxxxxxxxxxxxxxxxxxx RF
                           FtsA  1 alvDiGagktdvavaedga 19
                                   ++vDiG++ td++v+++g+
  gi|118431914|ref|NP_148671.2|  4 VGVDIGGTFTDLIVFDEGS 22
                                   69***************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.96
                                    EEE-SSSEEEEEEETTEEEEEEEES-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           FtsA   3 vDiGagktdvavaedgalvhlrvigvg 29 
                                     D+G+++ +++ + dg++  +r   vg
  gi|118431914|ref|NP_148671.2| 283 FDMGGTTAKASSIIDGEPLVVREYEVG 309
                                    6*********99999988877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); 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: 0.64u 0.23s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4903.80
//
Query:       gi|118431915|ref|NP_148673.2|  [L=552]
Description: hydantoin utilization protein B [Aeropyrum pernix K1]
Scores for 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-186  618.7   2.0   7.6e-186  618.5   2.0    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.5   2.0  4.3e-190  7.6e-186       1     516 []       4     522 ..       4     522 .. 0.97

  Alignments for each domain:
  == domain 1  score: 618.5 bits;  conditional E-value: 4.3e-190
                 Hydantoinase_B   1 DpitlevfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekfeg...e 77 
                                    D +t+ev+rn+   i eemg +l+ ta+Spnik+rlD sca++ +dg lvaqa+hipvhlgsms  v ++++++e+   +
  gi|118431915|ref|NP_148673.2|   4 DSVTIEVIRNSAIYISEEMGVVLRDTAFSPNIKDRLDHSCAVLAPDGSLVAQAEHIPVHLGSMSVGVVNLVKYIEDlgmD 83 
                                    89*********************************************************************988656567 PP

                 Hydantoinase_B  78 lkpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveegel 157
                                    l  GDv++tNdPy  gtHl+D++ i+Pv++ + ++++va++aHh+D+GG +pGs+   a+e+ eEG++i+pvk+ve+g  
  gi|118431915|ref|NP_148673.2|  84 LGVGDVVVTNDPYISGTHLNDLMAIKPVYAGDFHIAYVANKAHHVDVGGLVPGSIGGGAKELREEGIVIEPVKVVEAGSV 163
                                    899**************************7666*********************************************** PP

                 Hydantoinase_B 158 eedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraal...aelpdgtyea 234
                                    + d++++l+anvRtp++ +gDl Aqia+++vge+rl+el+ +yG +++ +a++ il ++er +r+ +   a+l++g+y+a
  gi|118431915|ref|NP_148673.2| 164 RWDIVRMLEANVRTPRYFRGDLMAQIASLNVGEARLRELAGRYGGSALVEAWESILGYTERYTREKIgevAALASGVYRA 243
                                    *******************************************************************66666777***** PP

                 Hydantoinase_B 235 edyldd.g...ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievklpeg 310
                                    +dy+++ +   ++i  t+tid+ ++tvD+tgts+qv+++iNa++ vt +a++++l++ +d+++p+N+G++r +e+k+peg
  gi|118431915|ref|NP_148673.2| 244 RDYMETsKgelLEIVATLTIDKGRLTVDYTGTSKQVDEPINAVYGVTVAATLFALKSTLDPEMPMNQGFFRIVEIKAPEG 323
                                    ****88436889******************************************************************** PP

                 Hydantoinase_B 311 sllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGArpgkdG 390
                                    +l+np +pa+v ggnvetsqr++dvv++ala+alperv+Aas+gtm+n+++g      g+ +++yet a+G+GArp  dG
  gi|118431915|ref|NP_148673.2| 324 TLVNPLKPAPVGGGNVETSQRIADVVFRALAEALPERVPAASCGTMSNVMVG------GRGWAFYETNACGSGARPCCDG 397
                                    ****************************************************......6678****************** PP

                 Hydantoinase_B 391 asavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfapwGlaGGep 470
                                    +++vh++mtnt nt++E++Er+yP+l+  +elrpdsgG+G yrGG+Gvvr +++le++vt++i++er  ++pwGl GG+p
  gi|118431915|ref|NP_148673.2| 398 VDGVHTNMTNTLNTPIEVIEREYPILFNAYELRPDSGGPGMYRGGLGVVRAFTALEDNVTITIFAERGLTRPWGLSGGRP 477
                                    ******************************************************************************** PP

                 Hydantoinase_B 471 Gargrvvlnllvr..geeenlggkatvelkagdvlvietpGGGGyGdp 516
                                    G++ ++v+   +r  ge+e+l +k+t++l++gd++ i+tpGGGGyGdp
  gi|118431915|ref|NP_148673.2| 478 GRSFEAVI---TRaaGEVERLMSKHTAKLNRGDTIAIYTPGGGGYGDP 522
                                    *****554...444599*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4020.61
//
Query:       gi|118431916|ref|NP_148674.2|  [L=688]
Description: hypothetical protein APE_2533.1 [Aeropyrum pernix K1]
Scores for complete 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-62  208.9   0.0    6.9e-62  208.2   0.0    1.3  1  Thioredox_DsbH  Protein of unknown function, DUF255
    3.8e-11   43.0   0.0    6.8e-11   42.2   0.0    1.5  1  Thioredoxin_7   Thioredoxin-like
  ------ inclusion threshold ------
      0.038   13.5   0.0        0.2   11.2   0.0    2.1  2  C5-epim_C       D-glucuronyl C5-epimerase C-terminus


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 !  208.2   0.0   1.2e-65   6.9e-62       2     157 ..      11     160 ..      10     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 1.2e-65
                 Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkvDre 81 
                                    nrlae+ s Yl+qh+ +pvdW+pwg+ea+eka++ dkp+++s+Gys+chWChvm++esf+d+ va++ln+ fv+vkvDre
  gi|118431916|ref|NP_148674.2|  11 NRLAEAGSRYLRQHSCDPVDWMPWGAEAFEKARRLDKPVFVSVGYSSCHWCHVMQRESFSDPMVAEVLNRAFVMVKVDRE 90 
                                    9******************************************************************************* PP

                 Thioredox_DsbH  82 erPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeeaee 157
                                    erPd+d+++m+++ + +gs+gWPlnv+ltpd+kpf+ +tY+pke      ++++++ +++++w+e+r e+ e ae+
  gi|118431916|ref|NP_148674.2|  91 ERPDVDTLLMRYCAIASGSCGWPLNVLLTPDGKPFYVATYLPKE------SLVALAVSLERVWRERRAEVLEVAER 160
                                    ******************************************95......799****************9998876 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   1.1e-14   6.8e-11       1      65 [.      30      94 ..      30     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.1e-14
                                   ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                  Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                   +w+ + +ea++ka++  kpv+v +g s c+ C++++r+  sd+ v+++l+  fv+++vd +er +
  gi|118431916|ref|NP_148674.2| 30 DWMPWGAEAFEKARRLDKPVFVSVGYSSCHWCHVMQRESFSDPMVAEVLNRAFVMVKVDREERPD 94
                                   7***********************************************************99865 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 ?   11.2   0.0   3.3e-05       0.2      30      61 ..     272     303 ..     256     329 .. 0.88
   2 ?   -1.7   0.0      0.29   1.8e+03      32      69 ..     425     462 ..     423     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.3e-05
                      C5-epim_C  30 aqgqaisvllrAYeltgdekYlkaakkalksf 61 
                                    +q+ +i+vl++AY ++gd  Yl+ a   l+++
  gi|118431916|ref|NP_148674.2| 272 DQAWIIQVLAEAYAASGDRLYLDFAVSTLEFA 303
                                    68999********************9999876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                      C5-epim_C  32 gqaisvllrAYeltgdekYlkaakkalksfkipvekGG 69 
                                    g ++ +l+  Y+++ d + l +ak + +++k  ++  G
  gi|118431916|ref|NP_148674.2| 425 GMMLHALAHLYWVSRDPEVLGVAKSLKALVKDRMNGDG 462
                                    7889999999***********99988877776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4829.06
//
Query:       gi|118431917|ref|NP_148675.2|  [L=190]
Description: hypothetical protein APE_2535.1 [Aeropyrum pernix K1]
Scores for 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-28   97.9  27.2    5.8e-28   97.8  27.2    1.0  1  DUF998         Protein of unknown function (DUF998)
  ------ inclusion threshold ------
       0.19   11.8   2.8       0.33   11.1   0.4    2.4  2  Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein


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 !   97.8  27.2   6.4e-32   5.8e-28       2     184 ..      11     183 ..      10     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 6.4e-32
                         DUF998   2 aaallalavilaaallrpgy.dplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavag 80 
                                    aaal+a++vi +++++++++  +++ha+S+Lg+ ++  +w++n+gl+l+gllv++++++  raa  r++++g++ll  ag
  gi|118431917|ref|NP_148675.2|  11 AAALVAWLVIGVSWAVNSDWfVFTEHAFSDLGGVKARMPWIYNYGLILVGLLVTLYSLCPYRAAVERLEAFGSGLLLTAG 90 
                                    79****************************************************************************** PP

                         DUF998  81 lglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaal.vwllaaald 159
                                    l+l+l+gv+p++++         +H+++s+++fl++ +a+++l+     + +a+++l+  +al+l +aa+ v++l  ++ 
  gi|118431917|ref|NP_148675.2|  91 LFLALIGVYPAGTR---------PHVFVSTWFFLQMDMALVALS---LGAYRACRNLANMAALALSLAAFpVYILIGITL 158
                                    **************.........9********************...88888888888888877766555155555599* PP

                         DUF998 160 gslllGlaerllvlaitawllalal 184
                                    g++++++ae  ++++i +++++l+l
  gi|118431917|ref|NP_148675.2| 159 GWPSAAVAEAYGIVVIDIVVIILTL 183
                                    *********************9976 PP

>> Herpes_UL49_5  Herpesvirus UL49.5 envelope/tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.15   1.3e+03      73      85 ..      57      69 ..      54      76 .. 0.86
   2 ?   11.1   0.4   3.6e-05      0.33      63      90 ..     110     137 ..     103     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.15
                  Herpes_UL49_5 73 vlvallavaynac 85
                                   +lv+ll+++y+ c
  gi|118431917|ref|NP_148675.2| 57 ILVGLLVTLYSLC 69
                                   5899999999999 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.6e-05
                  Herpes_UL49_5  63 svlFYisLlavlvallavaynacfrlft 90 
                                    s  F++ +  +lval ++ay+ac +l +
  gi|118431917|ref|NP_148675.2| 110 STWFFLQMDMALVALSLGAYRACRNLAN 137
                                    667********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1450.10
//
Query:       gi|118431918|ref|NP_148677.2|  [L=322]
Description: hypothetical protein APE_2537.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-21   77.3  40.4    2.6e-13   50.3  18.4    2.1  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.038   14.1   6.2        1.7    8.8   0.4    3.2  2  DUF2198   Uncharacterized protein conserved in bacteria (DUF2


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 !   33.2  14.0   5.6e-12     5e-08       4     136 ..      17     151 ..      14     152 .. 0.81
   2 !   50.3  18.4   2.9e-17   2.6e-13       2     136 ..     168     303 ..     167     304 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 5.6e-12
                           EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagilllii....allkegklaklslkdwllllllgllgtvlaf 79 
                                    +l++ la+   +++ +l +   + v+ ++++++r+++++il  +i    +++k++++++l+    lll+  + ++ +l f
  gi|118431918|ref|NP_148677.2|  17 YLVLALAVANVSTASILVRL--AGVHGFAAATWRLVLSTILTAAIlvaaYAVKKHRKPVLPGGVDLLLVAASGVALALHF 94 
                                    55555555566666666655..5999999999999988888855544435555555567777777777777889****** PP

                           EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                     l++ +l ++s++  + ++   P++ +i ++ l++ek t +qllg+v++++Gv+ i 
  gi|118431918|ref|NP_148677.2|  95 DLWMASLFHMSVAMSVTVVDSYPAVLAIVGFRLFKEKYTPLQLLGAVIAMVGVAGIA 151
                                    *****************************************************9886 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 2.9e-17
                           EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvlafl 80 
                                    +g lla++++l  a+yf + k l +k+s+l++t   + +a+i+ l+++ l  + +   ++ + +l+l+ll+ll+++ ++ 
  gi|118431918|ref|NP_148677.2| 168 KGFLLAFAGMLAVAAYFSIGKGLRSKYSTLEYTLPVYGFAAIVSLLLTTLVVRAPlTGYTAETYLYLILLALLPMLGGHT 247
                                    799**************************************9998887777777779*********************** PP

                           EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    l++ +l+++s   a++ ++ ePv ++ l+++llgek++ ++ l +v++l+G+ l+l
  gi|118431918|ref|NP_148677.2| 248 LINLLLRRLSLLAATVPILGEPVGAAALAWILLGEKVSTLEALLMVVVLAGIGLVL 303
                                    ****************************************************9997 PP

>> DUF2198  Uncharacterized protein conserved in bacteria (DUF2198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4   0.00019       1.7      15      47 ..      41      74 ..      29      85 .. 0.80
   2 ?    6.7   0.7   0.00084       7.5      24      66 ..     209     252 ..     203     257 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                        DUF2198 15 lftrvTynhyvGllltvaLivasv.ykgYtkely 47
                                    f+  T+  ++ ++lt+a++va++ +k + k++ 
  gi|118431918|ref|NP_148677.2| 41 GFAAATWRLVLSTILTAAILVAAYaVKKHRKPVL 74
                                   79999**999*******99999974688877766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00084
                        DUF2198  24 yvGllltvaLivasvykgYtkelyi..ividiiSllaGflyakkm 66 
                                    +v lllt  L+v + + gYt e y+  i+++++ +l G  +++ +
  gi|118431918|ref|NP_148677.2| 209 IVSLLLT-TLVVRAPLTGYTAETYLylILLALLPMLGGHTLINLL 252
                                    5666665.577788899***9977611556777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2424.89
//
Query:       gi|14602130|ref|NP_148678.1|  [L=559]
Description: Na(+)/H(+) antiporter [Aeropyrum pernix K1]
Scores for complete 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-96  321.9  25.1    3.9e-96  321.9  25.1    2.5  2  Na_H_antiporter  Na+/H+ antiporter family


Domain annotation for each model (and alignments):
>> Na_H_antiporter  Na+/H+ antiporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.5   9.0    0.0078   1.4e+02     113     252 ..      20     159 ..       7     162 .. 0.85
   2 !  321.9  25.1  2.2e-100   3.9e-96       1     303 []     161     510 ..     161     510 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.0078
               Na_H_antiporter 113 ivalafqntdvatalvvgalaglivatllela..slseidkllnrGiksmlgailil.llAwgiggvlealgvteslvssl 190
                                   ++ala+   +v+ al++g +ag ++ t+ + +   +++++ +++    s   +ili  ++  ++ g+l a g++ s  s +
  gi|14602130|ref|NP_148678.1|  20 AIALAIVTRQVLPALFLGVWAGGLMLTGYNPIsaTAQSLEWIVENATDSWNATILIFdFIIGAFVGLLFASGALHSAASAI 100
                                   56677777789999********999999999985666666666666999999999985667789***************** PP

               Na_H_antiporter 191 akgvvskgllplilflvallvafatGtswgtigIilpiavplaaklgisllalvraveaggt 252
                                   a +v s++ ++l+  +++ +v f     ++  ++++ +++p+a++l +s+  l+ +v + ++
  gi|14602130|ref|NP_148678.1| 101 AGRVRSALGATLASWIMGVIVFF---DDYANTIVVGSTMRPIADRLRVSREMLSYIVDSTAA 159
                                   *****999999999999998888...89**********************999999999887 PP

  == domain 2  score: 321.9 bits;  conditional E-value: 2.2e-100
               Na_H_antiporter   1 vavfgdkssplsdtvgliagilktdlieeia..........algmlvqsipanvysifallvvglvvlllrdigamlraea 71 
                                   va ++++s++++++vgli+++++t + e++a          a+++++qs+p+++ysifall+v+lvvl++r++g+ml+ae+
  gi|14602130|ref|NP_148678.1| 161 VAGMMLVSTWIGFEVGLIKEAIATLEEEALAglipaaptieAYAAWLQSVPYRFYSIFALLLVLLVVLTRRHFGPMLKAEH 241
                                   789****************************************************************************** PP

               Na_H_antiporter  72 ear..................eleekeltk.........lpiavliiltlskmpytgalalvaivkafivalafqntdvat 125
                                   +a+                  +l+ek ++k         ++iavli++tl +m++tg+++   +++++++++a++n+d+at
  gi|14602130|ref|NP_148678.1| 242 RAVatgkvlrdgaqplmptetVLGEKPAAKthapawlfaVSIAVLIGVTLLGMWVTGGGD---RWWETSFIDALMNADSAT 319
                                   *********************999999999999***************************...****************** PP

               Na_H_antiporter 126 alvvgalaglivatllela....slseidkllnrGiksmlgaililllAwgiggvlealgvteslvsslakgv.vskgllp 201
                                   al++g++a+++va++++la    s+s++++++++G+++m++a++illlAw+i+++++a+g t+++v +la+++ vs++l+p
  gi|14602130|ref|NP_148678.1| 320 ALLWGSFAAYLVALAGALAtrslSFSTAMEYTVKGMYLMVYANAILLLAWSIKSAADAVG-TAEYVVHLATAAgVSPLLVP 399
                                   ************************************************************.******************** PP

               Na_H_antiporter 202 lilflvallvafatGtswgtigIilpiavplaaklgisl..........lalvraveaggtlgdhlsPisdttilsstgln 272
                                    i+fl+a++++f+tGtswgt+gI++piavp+a+kl+i++          +a ++av+agg++gdh+sPisdtti+ss++++
  gi|14602130|ref|NP_148678.1| 400 PIIFLSAMFISFTTGTSWGTFGIMMPIAVPMAWKLAIQTgdvdlaytvmYASIAAVFAGGIYGDHSSPISDTTIMSSMFTG 480
                                   ********************************************************************************* PP

               Na_H_antiporter 273 adhidhvsytqlpyallvapitailllvfGi 303
                                   adhidhv+ tq+pyal++a++  +l+++f+i
  gi|14602130|ref|NP_148678.1| 481 ADHIDHVN-TQIPYALWAAITGGVLYVLFAI 510
                                   ********.*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); 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:                         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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 4202.52
//
Query:       gi|118431919|ref|NP_148681.2|  [L=151]
Description: ala-tRNApro hydrolase ProX [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-30  105.0   0.1    3.1e-30  104.8   0.1    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain
  ------ inclusion threshold ------
      0.043   14.0   1.5        0.1   12.8   0.0    2.3  3  HTH_17     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.1   3.4e-34   3.1e-30       2     122 ..      22     140 ..      21     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 3.4e-34
                      tRNA_edit   2 pgtktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgvgPl 81 
                                    ++t+t++e+aa lgv++s+i+Ktl++ d++g+ ++v++pgd++l+ +  ++l g k +rla + e+ el+g+++Ggv+P+
  gi|118431919|ref|NP_148681.2|  22 KPTRTVAEAAALLGVSESEIVKTLIVLDNAGGVYAVVIPGDKRLNINSMKELAG-KPVRLARANEVVELTGYPVGGVPPV 100
                                    689***************************************************.************************* PP

                      tRNA_edit  82 glkaagvpvllDeslkeyptvvvgagengatlelspedlrk 122
                                    +l + ++ +++D  l++++ v++g+g+++a+le sp +l++
  gi|118431919|ref|NP_148681.2| 101 AL-PPNIVLVVDRILLSRKKVYGGGGRENALLEFSPRELVE 140
                                    **.9********************************99985 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.22     2e+03      43      50 ..       4      11 ..       1      13 [. 0.71
   2 ?   12.8   0.0   1.1e-05       0.1       3      19 ..      26      42 ..      26      55 .. 0.89
   3 ?   -3.9   0.1       1.8   1.6e+04      13      19 ..     115     121 ..     115     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.22
                         HTH_17 43 leewlekr 50
                                   +eew+++r
  gi|118431919|ref|NP_148681.2|  4 VEEWIKAR 11
                                   78888765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.1e-05
                         HTH_17  3 tveEaAelLgvsrstvy 19
                                   tv+EaA+lLgvs+s + 
  gi|118431919|ref|NP_148681.2| 26 TVAEAAALLGVSESEIV 42
                                   9************9875 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.8
                         HTH_17  13 vsrstvy 19 
                                    +sr++vy
  gi|118431919|ref|NP_148681.2| 115 LSRKKVY 121
                                    6999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1196.62
//
Query:       gi|14602134|ref|NP_148682.1|  [L=110]
Description: hypothetical protein APE_2541 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 815.34
//
Query:       gi|118431920|ref|NP_148683.2|  [L=600]
Description: TRAP transporter membrane-spanning component [Aeropyrum pernix K1]
Scores for complete 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-93  314.3  49.7    1.1e-93  314.3  49.7    2.3  3  DctM      Tripartite ATP-independent periplasmic transporter,
  ------ inclusion threshold ------
       0.21   12.0   2.2       0.52   10.8   0.7    2.5  2  YfzA      YfzA-like protein
       0.52   10.4   5.8       0.48   10.5   0.7    3.1  3  GPHR_N    The Golgi pH Regulator (GPHR) Family N-terminal


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.2     0.011        65     216     291 ..      13      86 ..       2     106 .. 0.70
   2 !  314.3  49.7   1.9e-97   1.1e-93       1     415 [.     115     550 ..     115     551 .. 0.96
   3 ?   -6.0   2.5         3   1.8e+04     151     174 ..     563     585 ..     557     599 .. 0.40

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.011
                           DctM 216 aipalllpliiligillgiftpteagavavvyalviallv..yrrltleevaaallstakttaavlfilaaagifagl 291
                                     i++l++ + +l++ + g+  p+  ++v v y+ ++all+   r   +++    l  +a+   +vl ++aa  +  ++
  gi|118431920|ref|NP_148683.2|  13 IIASLFFTVALLYYYYTGLGGPILLATVMVPYTVFLALLAlyIRGGPISK----LPRAANAVLVVLSLIAALTVSGYI 86 
                                    46788888888999999999999988888888888888854444444444....444556666666666666555444 PP

  == domain 2  score: 314.3 bits;  conditional E-value: 1.9e-97
                           DctM   1 lvsllvllalgvpvaislalasllllallgel.llgv......pleqilaqrvve.......glssfallaipfFvlaGi 66 
                                    lv++++ll ++++    ++l++ll++++l+ + ++++      +le+i+++++ve        l + al++i++F+l+++
  gi|118431920|ref|NP_148683.2| 115 LVMFAALLKYRAI----FILNVLLFIYTLNGSwAPYPfdhpgiRLERIITAMSVEfetgvfeKLPQLALTLIGAFMLFIS 190
                                    6899999999999....9**************999999*****99999999999988887778***************** PP

                           DctM  67 vlersGlakrlidlaaalvGrvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaaviaasstlg 146
                                    +++++G+++++i+l++ ++G+ ++ l++++vvgs++++++SGs +An+a++Gsitip+mk++G+++ +aaa+++ass++g
  gi|118431920|ref|NP_148683.2| 191 IAQAFGAVDSVIRLVIGALGSRPRLLPQAAVVGSMVIAMVSGSGAANAASTGSITIPLMKKAGMPPVKAAAIETASSIGG 270
                                    ******************************************************************************** PP

                           DctM 147 qiiPPslglivfama.vlgvsigdlfaaaiipglllavglllavaiaakkenlrsktkaelkrlgqalkeaipalllpli 225
                                    q++PP++g+ +f+ma +lgvs++d++a++++p+l++++gl++av++a+k  ++ s t+a++  +g++ ++++++l++ ++
  gi|118431920|ref|NP_148683.2| 271 QLMPPIMGISAFVMAdYLGVSYFDVVARGWAPALIYYIGLAAAVYLASK--AFLSGTAALNIGYGRLEVYKATSLMASIL 348
                                    ************************************************9..***************************** PP

                           DctM 226 iligillgiftpteagavavvya..lviallv....yrrltleevaaa....llstaktt....aavlfilaaagifagl 291
                                    +li il+g+ +++  +a+a++++  l++all+    +r ++l+eva      l++t+k++    a+++++laa g+++gl
  gi|118431920|ref|NP_148683.2| 349 LLI-ILMGARREY--PAYAALQSsiLLLALLAaaeaSRGKSLHEVAGRilarLAETLKIFsgfvADITILLAALGVMTGL 425
                                    ***.*********..89999988767778877999999999999998888889999999999999*************** PP

                           DctM 292 ltltgvplklselllslsggkllfLilvnllvl..vlGmfldttaaiiilvpilaPaaaklgidpihfgvvivlnlsigl 369
                                    +t+tg+p++++ lll++++g+  +L++++++v+  ++G++l++++++i++v+++ P++ ++g++p++++++ +l++++++
  gi|118431920|ref|NP_148683.2| 426 MTITGIPTRVGFLLLEVGAGNK-ILLVMLAFVFgyLVGLGLPPVVTYILTVVVIGPYMLQAGFNPWAVHFYAFLLGVMSE 504
                                    *********************9.888888888888********************************************* PP

                           DctM 370 itPPvGlalfvassiakvsveeivkalvPflvvlvvalvlitlvpe 415
                                    ++PP+++++ v+s+ia + ++e+++++++f+++l+++++ ++l p 
  gi|118431920|ref|NP_148683.2| 505 LSPPTSVTAAVTSRIAGAGFVETMIESIKFAMPLFTVMAGVLLEPG 550
                                    *****************************************99986 PP

  == domain 3  score: -6.0 bits;  conditional E-value: 3
                           DctM 151 Pslglivfamavlgvsigdlfaaa 174
                                       +l++ +++v+g+s  ++++aa
  gi|118431920|ref|NP_148683.2| 563 AAKVLAATIAVVAGLSS-KIYIAA 585
                                    44444444444455443.233322 PP

>> YfzA  YfzA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   8.6e-05      0.52      10      75 ..     121     188 ..     115     203 .. 0.65
   2 ?   -2.9   0.0       1.6   9.6e+03      67      83 ..     341     357 ..     325     360 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.6e-05
                           YfzA  10 wlksigvfllvqlifiilevtawiP.nfkeGg.lydrvvns...efftewfapykephln..vltaffailll 75 
                                     lk+ ++f+l  l+fi     +w P  f++ g   +r++ +   ef t  f   k p+l   ++ af+   l+
  gi|118431920|ref|NP_148683.2| 121 LLKYRAIFILNVLLFIYTLNGSWAPyPFDHPGiRLERIITAmsvEFETGVF--EKLPQLAltLIGAFM---LF 188
                                    689999*******************98998773689998752113444444..455555400333333...22 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.6
                           YfzA  67 taffailllvnavigai 83 
                                    t ++a +ll+  ++ga 
  gi|118431920|ref|NP_148683.2| 341 TSLMASILLLIILMGAR 357
                                    77888888888888875 PP

>> GPHR_N  The Golgi pH Regulator (GPHR) Family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5     9e+03      26      37 ..      38      49 ..      37      63 .. 0.80
   2 ?   10.5   0.7   8.1e-05      0.48       7      33 ..     215     241 ..     210     267 .. 0.80
   3 ?    0.7   0.2     0.098   5.8e+02      20      35 ..     320     335 ..     318     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                         GPHR_N 26 Gavstpyetfsl 37
                                   ++v  py++f  
  gi|118431920|ref|NP_148683.2| 38 ATVMVPYTVFLA 49
                                   789999*99975 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 8.1e-05
                         GPHR_N   7 vlsrvsviGvtlmAiLSGfGavstpye 33 
                                    +l + +v+G +++A+ SG Ga +++ +
  gi|118431920|ref|NP_148683.2| 215 LLPQAAVVGSMVIAMVSGSGAANAAST 241
                                    677889****************98765 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.098
                         GPHR_N  20 AiLSGfGavstpyetf 35 
                                    A LSG +a +  y  +
  gi|118431920|ref|NP_148683.2| 320 AFLSGTAALNIGYGRL 335
                                    89******99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); 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:                         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: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4353.70
//
Query:       gi|118431921|ref|NP_148684.2|  [L=369]
Description: TRAP transporter solute-binding component [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-17   63.7   0.0    2.2e-17   63.4   0.0    1.1  1  NMT1_3    NMT1-like family
  ------ inclusion threshold ------
      0.051   13.8   0.3        0.1   12.8   0.3    1.4  1  TrbC      TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   2.4e-21   2.2e-17       2     289 .]      64     358 ..      63     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.4e-21
                         NMT1_3   2 gTastgGtyYpvGvaiatliseklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGegefegkkplkn 81 
                                    gT  +g++ Y     +a+++++++    ++++ ++   G++  ++   kg++d a+      +e y+ +g+feg     +
  gi|118431921|ref|NP_148684.2|  64 GTSRVGSSGYKALTTLAQVLNREI---PEIEIVVEPQSGAIASMKGFAKGDLDGAYGADIAFKEMYTSTGRFEG-FTA-D 138
                                    678888888998899999998888...578999***********************9999999**********9.344.4 PP

                         NMT1_3  82 lraitmlyaevfqlv....vskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalk 157
                                       + +l++ ++ +      +++ ++++ +d++gk++   p g+ t ++ r+ l+alg+++++    +el+ +  a+ l 
  gi|118431921|ref|NP_148684.2| 139 RLPVQTLWVFTIDIGlavpKDRADEFKCWSDFDGKTIFTLPLGWDTGTALRNALDALGINYNH----KELDLEAVATSLS 214
                                    4567888987777642212347779**********************************9755....4799********* PP

                         NMT1_3 158 dgqldga.alvaGvPv..savtqlaasedikliplddeqldkllkeypvftkyvipagtyp..qdedikTiavpnflvvr 232
                                    +g + ++ ++v+G  +    ++++ a+ d+ +++ + e++dkl ++  +  + v +++ ++  +  +   + +   + + 
  gi|118431921|ref|NP_148684.2| 215 RGDIVATgVYVTGERSvaPWIQNMLAQIDLVVVNPCPEEIDKLEQA-GIPVARVSANTFPEpvGVDEFVGVRIFYGFHTG 293
                                    ***99872567887663467***********************876.343444555555533567777778888889999 PP

                         NMT1_3 233 adldeelvYeitkaifenldelnsihkaakeisle......kalaglp..vplHpGAerYYkEqG 289
                                     +l+e+ vY+i+k+ ++n+del+s+ +a+++++ +      +a+++l   vp+HpG +++ kE+G
  gi|118431921|ref|NP_148684.2| 294 LNLSEDIVYKIIKTTYDNIDELASLDPAFSQLKEDfvgfqvQAIESLAdlVPVHPGLAKFLKEMG 358
                                    9******************************9998888888899877667*************99 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   1.1e-05       0.1      49      75 ..       8      33 ..       4      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                           TrbC 49 ltgplakviatiaiivaGimlafgrls 75
                                   l + ++ v+++++i+vaG+ml+ g+++
  gi|118431921|ref|NP_148684.2|  8 LIA-VGAVVVVLIILVAGYMLLGGGEE 33
                                   556.99******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2588.27
//
Query:       gi|14602137|ref|NP_148685.1|  [L=261]
Description: indole-3-glycerol phosphate synthase [Aeropyrum pernix K1]
Scores for 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-52  176.0   0.0    9.7e-52  175.6   0.0    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
    0.00017   20.9   0.0    0.00025   20.4   0.0    1.2  1  DHO_dh        Dihydroorotate dehydrogenase
    0.00022   20.8   0.0    0.00038   20.0   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein
    0.00027   20.2   0.0     0.0021   17.3   0.0    2.0  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.015   14.3   0.2      0.044   12.8   0.0    1.7  1  FMN_dh        FMN-dependent dehydrogenase
      0.016   15.2   0.2       0.65   10.1   0.0    2.3  2  PA            PA domain
      0.022   14.1   0.1      0.067   12.5   0.0    1.8  2  ThiG          Thiazole biosynthesis protein ThiG
      0.028   13.4   0.0      0.056   12.4   0.0    1.5  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.079   12.0   0.0       0.11   11.5   0.0    1.2  1  Dus           Dihydrouridine synthase (Dus)


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 !  175.6   0.0   4.9e-55   9.7e-52      10     251 ..       8     253 ..       5     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 175.6 bits;  conditional E-value: 4.9e-55
                                   HHHHHHHCCS-G.GCCCCG..-SS-SS-HHHHCHCH..TTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEE CS
                          IGPS  10 eevaeakkrqsl.adleaavklakpkrsfaeaLres..ekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSV 87 
                                   +++a+ak r+sl +++  + + ++   s+  ++re   +   a+iaE+K+ SPs g i +  dp+++ ++ ++a  +a SV
  gi|14602137|ref|NP_148685.1|   8 KAIASAKDRTSLlEEIAGNCSPKPGRPSLSSSIREWvyRVGGAVIAEYKRCSPSAGAISTL-DPVSYVQATRDA-SAAYSV 86 
                                   678888888887799999999999999********97788889***************875.9*********99.7789** PP

                                   E--CCCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSH CS
                          IGPS  88 LteekyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhde 168
                                   Lte+++F Gs+e ++  ++    pvl KdFi++e qi  a  +ga a LLi+++l+ +el+ela+aa ++g+evLvE+ d+
  gi|14602137|ref|NP_148685.1|  87 LTEPNWFCGSIELIPYFARY--KPVLAKDFIVSETQIRIAACMGASAALLIMEALTPRELQELAAAASRYGVEVLVETPDA 165
                                   ***************98875..79********************************************************* PP

                                   HHHHHHHHTT.-SEEEEESEETTTTEE-CHHH....HHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC- CS
                          IGPS 169 eeleralklg.akiiGvNnRnLktlevdlntt....eeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrq 244
                                   +    a +l   +iiGvN+R+Lktl+vd + +    ++ ++++p +v+lvaeSGi +++++ k  ++g++a+LvG+++m++
  gi|14602137|ref|NP_148685.1| 166 SHAVEASRLApGSIIGVNSRDLKTLRVDYEAMlrevSKAREQLPGEVILVAESGIDSPDKALKAFKAGAQAILVGTAFMKN 246
                                   *999999665169***************776511115667778899*********************************** PP

                                   TTHHHHH CS
                          IGPS 245 edvekai 251
                                   ++++++i
  gi|14602137|ref|NP_148685.1| 247 PQLREKI 253
                                   **99887 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.2e-07   0.00025     232     293 ..     199     259 ..     188     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHH CS
                        DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkelee 293
                                   + + + +++l +e+ +++  Gi s + al  ++aGA ++ v+ta+  ++p++ +ki  el +
  gi|14602137|ref|NP_148685.1| 199 REVSKAREQLPGEVILVAESGIDSPDKALKAFKAGAQAILVGTAF-MKNPQLREKILAELLQ 259
                                   5567778899999********************************.899********99975 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.9e-07   0.00038      50     118 ..     186     256 ..     182     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                                   EHHHHCTTHHHHHHHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHH CS
                  His_biosynth  50 Dldaakegreanldlveeiaeevf..ipvqvGGGIrsledveelleagadkviigtaavknpelikelaek 118
                                   Dl+  +   ea+l  v++ +e++   + +   +GI s +++ ++++aga+ + +gta +knp+l ++++ +
  gi|14602137|ref|NP_148685.1| 186 DLKTLRVDYEAMLREVSKAREQLPgeVILVAESGIDSPDKALKAFKAGAQAILVGTAFMKNPQLREKILAE 256
                                   66666677788888889999998744667789********************************9999865 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17   3.5e+02      34      58 ..     178     202 ..     145     208 .. 0.78
   2 !   17.3   0.0   1.1e-06    0.0021     144     182 ..     211     249 ..     204     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                   -EEEE-B---TTS---BS-SHHHHH CS
                          NanE  34 PiiGivkrdlpdsevritatlkdid 58 
                                    iiG+  rdl+   v   a+l+++ 
  gi|14602137|ref|NP_148685.1| 178 SIIGVNSRDLKTLRVDYEAMLREVS 202
                                   599*******999999999999986 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.1e-06
                                   T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHH CS
                          NanE 144 glkviaeGrintPekakkaieiGvdavvvGsaitrleei 182
                                   ++ ++ae  i++P+ka ka++ G++a+ vG+a  +  ++
  gi|14602137|ref|NP_148685.1| 211 EVILVAESGIDSPDKALKAFKAGAQAILVGTAFMKNPQL 249
                                   56789***************************9876655 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.2e-05     0.044     258     304 ..     198     244 ..     193     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                                   HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                        FMN_dh 258 idvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                   ++   + +e+++g++ +++ +Gi +   +lkA   GA+a+l+G +f+
  gi|14602137|ref|NP_148685.1| 198 LREVSKAREQLPGEVILVAESGIDSPDKALKAFKAGAQAILVGTAFM 244
                                   34445558888899999**************************9886 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.068   1.4e+02      35      54 ..     114     140 ..      89     167 .. 0.70
   2 ?   10.1   0.0   0.00033      0.65      22      53 ..     206     240 ..     186     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.068
                            PA  35 f...aeKarnAqaaGAagviiv....n 54 
                                   f    + +r A+  GA +++++    +
  gi|14602137|ref|NP_148685.1| 114 FivsETQIRIAACMGASAALLImealT 140
                                   3555789999***********955441 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                            PA  22 vdvkGkivLvqr...tfaeKarnAqaaGAagviiv 53 
                                   +++ G + Lv +   +  +Ka  A +aGA ++++ 
  gi|14602137|ref|NP_148685.1| 206 EQLPGEVILVAEsgiDSPDKALKAFKAGAQAILVG 240
                                   46789999996667788***************997 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.84   1.7e+03      52      80 ..     145     173 ..     113     178 .. 0.60
   2 ?   12.5   0.0   3.4e-05     0.067     175     208 ..     211     244 ..     194     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.84
                                   --CCCCCHCCTSEEEEE-TT-SSHHHHHH CS
                          ThiG  52 eellelleekevtllPntaGaktaeeAvr 80 
                                   +el+++ ++ +v++l  t  a+ a eA r
  gi|14602137|ref|NP_148685.1| 145 QELAAAASRYGVEVLVETPDASHAVEASR 173
                                   44555555556666666666665555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.4e-05
                                   SS-BEEES---SHHHHHHHHHTT-SEEEESHHHH CS
                          ThiG 175 kvPvivDAGigspsdaaqamelGadavllntava 208
                                   +v ++ + Gi sp +a +a++ Ga+a+l+ ta  
  gi|14602137|ref|NP_148685.1| 211 EVILVAESGIDSPDKALKAFKAGAQAILVGTAFM 244
                                   6778899************************975 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.8e-05     0.056     197     239 ..     199     243 ..     165     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHCTC..T-EEEEES---SHHHHHHHHHTT-SEEEESCCC CS
                                   xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         IMPDH 197 aevaeaakka..gvpviaDGGikysgdivkAlaaGadavmlGsll 239
                                    ev++a ++   +v ++a  Gi +  +  kA+ aGa+a+++G  +
  gi|14602137|ref|NP_148685.1| 199 REVSKAREQLpgEVILVAESGIDSPDKALKAFKAGAQAILVGTAF 243
                                   5666666665547999**************************987 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.6e-05      0.11     169     224 ..     195     251 ..     178     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                                   G--CHHHHHHHHH-S..S-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHH CS
                           Dus 169 tadweaIkevkqavs..ipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfa 224
                                   +a ++++++ +++++  + ++a  +I ++++a ++ +  Ga+++++g +  +nP l +
  gi|14602137|ref|NP_148685.1| 195 EAMLREVSKAREQLPgeVILVAESGIDSPDKALKAFKA-GAQAILVGTAFMKNPQLRE 251
                                   7788999*****************************99.***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); 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:                         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 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1879.66
//
Query:       gi|14602138|ref|NP_148686.1|  [L=215]
Description: N-(5'-phosphoribosyl) anthranilate isomerase [Aeropyrum pernix K1]
Scores for 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   39.4   0.0    2.6e-09   37.1   0.0    1.9  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   1.5e-13   2.6e-09       2     187 ..       5     202 ..       4     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.5e-13
                                   CE----SHHHHHHHHHHTSSEEEEE--T.TBTTB--HHHHHHHCCCS--E.EEEEESSS-HHHHHHHHHHCTECEEEE-CG CS
                          PRAI   2 kicgltrasdvkaavkagadelglifae.sskrevseeqaqellekvpak.lVGVfvNqpieevlriaqelgldvvQLHGd 80 
                                   kicg+++ + + +  +  +d++g++ +    +r+v  e a+++ +++++  +V V    + ++  + a+    dv+Q H  
  gi|14602138|ref|NP_148686.1|   5 KICGVKKLESALQL-DGLVDYIGFVHSLlGGPRSVPLEAARIMASQIEKSkTVLVVHGSSPSYAAAAADGF--DVLQYHEP 82 
                                   66666666666553.44456777776642457888888888888888855478777777777776666655..88888877 PP

                                   G..-HHHHHHHHH.....HS-TTSEE....EEEEE.-SSS--S-SSTT-.SEEEEESSS-SSSXXXXGGGGTTSXX..... CS
                          PRAI  81 e.deqeyeellkt.....elpvikal....kvaes.vdevkearradhv.dllllDsgaGGtGelldwsliskllks.... 145
                                     ++++++ ++        l v+ ++    +++++ + +++e+++     + +llD+ +G    ++ ++  +k   +    
  gi|14602138|ref|NP_148686.1|  83 LlPSSAASLQATLdplgvTLAVVVEYtgsaWKPQEpCGYINELNKEGVEpEYILLDTTKG-LRDRIPLNEAAK---Asrcs 159
                                   744433332222111100222222221111333321445555555444458889999888.334444444444...33447 PP

                                   TTEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEE..TEEXHHH CS
                          PRAI 146 lkviLAGGLtpeNvaeaiklegvlgvDvssGVEtn..GvkDlek 187
                                   ++v LAGGLtp    +a++ +gv ++Dvs GVEt   GvkD  +
  gi|14602138|ref|NP_148686.1| 160 HRVGLAGGLTPRDACKAVE-TGVSLIDVSRGVETGvpGVKDPLL 202
                                   *******************.***************9*****765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1590.00
//
Query:       gi|14602139|ref|NP_148687.1|  [L=427]
Description: tryptophan synthase subunit beta [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-47  161.9   1.5    2.7e-47  161.6   1.5    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 !  161.6   1.5   1.5e-51   2.7e-47       4     294 .]      69     406 ..      66     406 .. 0.85

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 1.5e-51
                                   CSSS--EEEECCTCCCCCCE....EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                          PALP   4 gigpTPlvrlprlskelgvp....lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                     +pTPl+r+++l+k lgv+    +++K E   ptgS+K+++a    +++k   +++ v+e+++G++g+a++ aaal+Glk
  gi|14602139|ref|NP_148687.1|  69 IGRPTPLIRAEGLEKVLGVKgrvrIYYKSEAVLPTGSHKINTAIAQAYYAKLDGAKEIVTETGAGQWGLAASTAAALMGLK 149
                                   579*****************************************99999666647888888888***************** PP

                                   EEEEEETTS-H...HHHHHHHHTT-EEEEE...................CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHH CS
                          PALP  81 vtivvpadasp...ekvallrllGaevvev...................ggdydeavaaaaelaaegegaylvsqfdnptv 139
                                   +t+++ a++ +   ++++l+++ Ga+v+ +                   +g+   a a a e++ e++++ +++ +  ++v
  gi|14602139|ref|NP_148687.1| 150 ATVFMTASSFKskiQRRLLMEAQGARVISSpskltdtgrealeeygsthPGSLGLAIAEAVEYTLESGDRRYLPGSVLEAV 230
                                   ********99645588899***********666666655555555544444455454444455555788888888879999 PP

                                   HHHHHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHH......HSTT-EEEEEEECTTCGGTTCCS..S.SS..B.. CS
                          PALP 140 iegygtiglEileqlggkpdavvvpvGgGgliaGiaaglke......rrpdvrvigvepegsdalarslragrrvtvpvs. 213
                                      ++ iglE l+ql+++pd+vv++vGgG++++G+  ++        ++ ++r+i++e++ +++l+r+    r++ +++s 
  gi|14602139|ref|NP_148687.1| 231 LMHQTVIGLEALDQLPEEPDVVVACVGGGSNFGGFTYPMIGarlrgeGFEKTRFIAAESTAAPKLTRGE--YRYDGLDSSl 309
                                   999*******************************98777776655566666******************..7777777778 PP

                                   .................SSS.CCSTCSCGTTCCHHHHSEEEE.EEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHH CS
                          PALP 214 .................dtiadglavgspselafelldrlvd.eivtvsdeealeamrllarregivvepssaaalaalkl 276
                                                    ++ a gl+ +   +  +++l+rl+  e+ ++++eeal+ + l+ar eg+v+ p s +a+a + +
  gi|14602139|ref|NP_148687.1| 310 ilplakmytlghrytppPSHAAGLRYH-GVSPSLSILRRLGLvEAEAIPQEEALASILLMARSEGVVPAPESSHAVALA-A 388
                                   89999999999999999*********9.44444555555554589**********************************.* PP

                                   HHHHCCTTCEEEEEEE-B CS
                          PALP 277 reagelkegdrvvviltg 294
                                   r a++l++g++v + l+g
  gi|14602139|ref|NP_148687.1| 389 RIARKLPDGSVVAFNLSG 406
                                   *********999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3007.78
//
Query:       gi|14602140|ref|NP_148688.1|  [L=252]
Description: tryptophan synthase subunit alpha [Aeropyrum pernix K1]
Scores for complete 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-23   82.4   0.0    3.4e-23   81.8   0.0    1.2  1  Trp_syntA       Tryptophan synthase alpha chain
     0.0011   18.1   0.0     0.0017   17.6   0.0    1.2  1  NanE            Putative N-acetylmannosamine-6-phosphate epim
      0.002   17.7   0.0     0.0028   17.1   0.0    1.2  1  PcrB            PcrB family
  ------ inclusion threshold ------
      0.034   13.5   0.0      0.074   12.4   0.0    1.5  1  TMP-TENI        Thiamine monophosphate synthase
      0.053   13.0   0.0      0.085   12.3   0.0    1.2  1  His_biosynth    Histidine biosynthesis protein
      0.065   12.5   0.1       0.13   11.5   0.1    1.4  2  ThiG            Thiazole biosynthesis protein ThiG
      0.086   11.8   0.0       0.13   11.2   0.0    1.4  1  FMN_dh          FMN-dependent dehydrogenase
       0.17   11.2   0.0       0.28   10.5   0.0    1.3  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
       0.18   11.0   0.0        0.4    9.8   0.0    1.5  2  DHO_dh          Dihydroorotate dehydrogenase


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 !   81.8   0.0   1.7e-26   3.4e-23       9     235 ..       5     230 ..       1     246 [. 0.85

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.7e-26
                                   B-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS- CS
                     Trp_syntA   9 raafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevP 89 
                                   r  f  y+t+  p+ +++lei ++l+   +d +ElG+p   Pl dGP+I+ ++l+a+++g +  k+l l ee+  +e  vP
  gi|14602140|ref|NP_148688.1|   5 RPGFSVYLTIAWPSPDTFLEIASTLKG-CVDYLELGIPTPKPLYDGPTIRLTHLKAVESGYSGPKTLSLAEEAS-QEAGVP 83 
                                   566888******************986.79*******************************************9.999*** PP

                                   EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCC...CHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-E CS
                     Trp_syntA  90 ivlltylnlvlsygeerflaelkeagvdglivpDlPle...eaeelveaakkkglelvflvapttsderlkevveqaegfv 167
                                    +++ y+     ++  + l+e+   g+ +++ pDlP e   + e +ve+ ++ g+e+   ++p  + + l++  +     +
  gi|14602140|ref|NP_148688.1|  84 YIVMAYATE-QPWSFSEVLREASRKGALSVLPPDLPFElpgHVEWYVEESRRLGMEPSLFASPKFPHRWLDRYRRLDPLLI 163
                                   ******976.67888999******************98333455567778889***********99999999888877777 PP

                                   EEESTTC-SSTTS..SB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC CS
                     Trp_syntA 168 YvvsraGvTgaen..avaaevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkkiee 235
                                   Y+   +  Tg++   a+ ++v+++ + +    +v ++ GF i+++e++ +v  ++ad+v+vGS + + + +
  gi|14602140|ref|NP_148688.1| 164 YL-GLQPATGVKLplAFLRNVKTARKIVG---QVYMLAGFSIKSPEDALRVLeAGADAVVVGSEVARLVSS 230
                                   75.78889999863345555555544444...6669***************99************999875 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 !   17.6   0.0   8.7e-07    0.0017     146     180 ..     194     228 ..     176     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.7e-07
                                   -EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                          NanE 146 kviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                    ++a   i++Pe a +++e G+davvvGs ++rl 
  gi|14602140|ref|NP_148688.1| 194 YMLAGFSIKSPEDALRVLEAGADAVVVGSEVARLV 228
                                   46677789************************985 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.4e-06    0.0028     170     211 ..     182     224 ..     162     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.4e-06
                                   HHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHH CS
                          PcrB 170 evialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvv 211
                                   +v+  +k + +  ++ G  i+s+E+A +v+ea AD++vvG  v
  gi|14602140|ref|NP_148688.1| 182 NVKTARKIVGQVYMLAGFSIKSPEDALRVLEAgADAVVVGSEV 224
                                   5677788888999999************************866 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.7e-05     0.074      85     124 ..     182     222 ..     169     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                      TMP-TENI  85 pvaearellgp.dliiGlSvhsleeaeeaealgadYigvGp 124
                                   +v++ar+++g+ +++ G S++s+e+a+++ ++gad ++vG+
  gi|14602140|ref|NP_148688.1| 182 NVKTARKIVGQvYMLAGFSIKSPEDALRVLEAGADAVVVGS 222
                                   6899999999835566***********************96 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05     0.085      64     106 ..     185     225 ..     179     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                                   HHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHH CS
                  His_biosynth  64 lveeiaeevfipvqvGGGIrsledveelleagadkviigtaav 106
                                     ++i+ +  + +  G  I+s ed+ ++leagad v++g++++
  gi|14602140|ref|NP_148688.1| 185 TARKIVGQ--VYMLAGFSIKSPEDALRVLEAGADAVVVGSEVA 225
                                   44555555..56667777**********************976 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   3.4e+03     116     135 ..      76      95 ..      63     114 .. 0.57
   2 ?   11.5   0.1   6.5e-05      0.13     182     219 ..     199     236 ..     171     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                   HHHHHHTT-EEEEEE-S-HH CS
                          ThiG 116 aeiLvkeGFevlpYvsdDlv 135
                                   a + +   ++v++Y ++ + 
  gi|14602140|ref|NP_148688.1|  76 ASQEAGVPYIVMAYATEQPW 95 
                                   44444444677777766654 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.5e-05
                                   S---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHH CS
                          ThiG 182 AGigspsdaaqamelGadavllntavaeakdpvamAra 219
                                     i sp+da  ++e Gadav++ + va+     ++ +a
  gi|14602140|ref|NP_148688.1| 199 FSIKSPEDALRVLEAGADAVVVGSEVARLVSSGRLGEA 236
                                   45899*********************986655555554 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.7e-05      0.13     207     244 ..     182     221 ..      58     232 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.7e-05
                                   HHHHHHHHHSSEEEEEE..E-SHHHHHHHHHTTESEEEE- CS
                        FMN_dh 207 dikwlreqtklplvvKG..vltaedakraveaGvdgivvS 244
                                   ++k+ r+ +    ++ G  + ++eda r++eaG+d++vv 
  gi|14602140|ref|NP_148688.1| 182 NVKTARKIVGQVYMLAGfsIKSPEDALRVLEAGADAVVVG 221
                                   5555555555555555533689****************96 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 ?   10.5   0.0   0.00014      0.28      93     197 ..     124     224 ..     118     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                   THHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEE.ESS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEE CS
                Ribul_P_3_epim  93 hlkrtiqeikeaGakaglvlnpatplealeyllekldlvll.msvePgfgGQkFipevlekikkvrklidekeldlkievD 172
                                   h++  ++e + +G+++ l   p+ p  +l++   +ld +l+ +  +P   G k   + l ++k++rk++ +    + + + 
  gi|14602140|ref|NP_148688.1| 124 HVEWYVEESRRLGMEPSLFASPKFPHRWLDRY-RRLDPLLIyLGLQPA-TGVKLPLAFLRNVKTARKIVGQ----VYMLAG 198
                                   66677889999**************9999886.677777762567775.68899999************99....444444 PP

                                   SS--.TTTCHHHHHHT--EEEESHHH CS
                Ribul_P_3_epim 173 GGvk.ldnieqiaeagadvlVagsav 197
                                     +k  + + ++ eagad++V+gs v
  gi|14602140|ref|NP_148688.1| 199 FSIKsPEDALRVLEAGADAVVVGSEV 224
                                   45552578999************987 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6   3.3e+03     112     135 ..      20      43 ..      18      46 .. 0.84
   2 ?    9.8   0.0    0.0002       0.4     235     276 ..     184     224 ..     171     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHGGGESEEEEES-SC CS
                        DHO_dh 112 ddyvevvrkigpfadilelNvSsP 135
                                   d + e++ +++  +d+lel +  P
  gi|14602140|ref|NP_148688.1|  20 DTFLEIASTLKGCVDYLELGIPTP 43 
                                   567889999999999999999888 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                                   HHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                        DHO_dh 235 relykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                    + +k +  ++ +++   i+s eDal  +eaGA +v v++++
  gi|14602140|ref|NP_148688.1| 184 KTARKIVG-QVYMLAGFSIKSPEDALRVLEAGADAVVVGSEV 224
                                   44444444.777777778*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1836.09
//
Query:       gi|14602141|ref|NP_148689.1|  [L=345]
Description: anthranilate phosphoribosyltransferase [Aeropyrum pernix K1]
Scores for 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-82  275.6   0.5    5.5e-82  275.2   0.5    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
      6e-11   42.0   0.0    1.7e-10   40.6   0.0    1.8  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.2   0.5   6.2e-86   5.5e-82       3     251 ..      81     330 ..      79     332 .. 0.99

  Alignments for each domain:
  == domain 1  score: 275.2 bits;  conditional E-value: 6.2e-86
                                   TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEEHHS CS
               Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflfape 83 
                                    l+D++gTGGdg +t+N Staaa+v+A++Gv+ akhgnrs ssksGsaDv+e lg+n++  ++++ ++l + g++fl ap+
  gi|14602141|ref|NP_148689.1|  81 VLLDTAGTGGDGLSTLNASTAAALVAASLGVPTAKHGNRSFSSKSGSADVMEMLGYNINHRADRAVRMLSTLGFTFLYAPN 161
                                   589****************************************************************************** PP

                                   SSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHHHHHHHHHH CS
               Glycos_transf_3  84 yhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldevsllakttv 163
                                   yh+amk v+pvrr+l +rT+fnl+GPL npa  + q++gv++ +l++ +a++++ lg  ++lvvhg  G+devs++++t +
  gi|14602141|ref|NP_148689.1| 162 YHPAMKAVVPVRRKLATRTIFNLVGPLANPAFNNVQVIGVARRSLMPVIASAASLLGYDAVLVVHGdPGMDEVSVTGETKI 242
                                   ******************************************************************99************* PP

                                   HHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHHHHHHHHH CS
               Glycos_transf_3 164 aelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslkegvakae 244
                                   +e+  g+i+ey+++ped+gl    l++l++ ++ e+ae ++++l+g+  +++   +++na+aal++ag  ++lk +++ a 
  gi|14602141|ref|NP_148689.1| 243 LEVRRGRIEEYSITPEDLGLPITGLKELRVANAVESAERVRRALSGRGRRSDEAFIAANAAAALYVAGFEKDLKGAAEAAV 323
                                   ********************************************************************************* PP

                                   HHHHTSH CS
               Glycos_transf_3 245 evidsGk 251
                                   ++i++G 
  gi|14602141|ref|NP_148689.1| 324 QAIREGR 330
                                   ****996 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 !   40.6   0.0   1.9e-14   1.7e-10       3      63 .]      12      72 ..      12      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.9e-14
                                  HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
               Glycos_trans_3N  3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63
                                  ++kkl++ge Lt+ e++++ +++l+ +   +  aA L+Alr++Ge + E++++a+A+r+++
  gi|14602141|ref|NP_148689.1| 12 LVKKLLEGEPLTPGEAAQLAQAMLDPSFDNSLKAAALAALRVRGEQPGEVVGFARALRDRA 72
                                  589*******************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2564.93
//
Query:       gi|118431922|ref|NP_148690.2|  [L=438]
Description: anthranilate synthase component I [Aeropyrum pernix K1]
Scores for complete 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-88  295.4   0.0      5e-88  295.0   0.0    1.2  1  Chorismate_bind  chorismate binding enzyme
    0.00037   20.7   0.0      0.069   13.4   0.0    3.1  3  Anth_synt_I_N    Anthranilate synthase component I, N termina


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.0   0.0   5.6e-92     5e-88       2     258 .]     170     424 ..     169     424 .. 0.97

  Alignments for each domain:
  == domain 1  score: 295.0 bits;  conditional E-value: 5.6e-92
                                    HCHHHHHHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTS CS
                Chorismate_bind   2 redYaeavekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggr 81 
                                    r+ ++++v+ + e+irag+ ++vvlsr  +++     + +++y++l  +np+py ++ +l+++ ++g+SPEll+k+e+g 
  gi|118431922|ref|NP_148690.2| 170 RKGFEAMVADALERIRAGEAFQVVLSRVERYR--VWGSLFSAYERLADANPSPYLYYARLGGRVIIGSSPELLVKLEAG- 246
                                    789*****************************..55667**************************************77. PP

                                    EEEEECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEE CS
                Chorismate_bind  82 rietepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstieg 161
                                    r+et+piaGTr+rg+tp ed +le ell+deKeraEh+m+vdl+rnd+++v+ pg+v+v++++ +ery++v+h+vs++eg
  gi|118431922|ref|NP_148690.2| 247 RVETHPIAGTRPRGSTPIEDIELEVELLNDEKERAEHVMLVDLARNDITRVSIPGTVQVTSFMDIERYETVMHIVSRVEG 326
                                    ******************************************************************************** PP

                                    EESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEE..ETTEEEEEEE CS
                Chorismate_bind 162 elkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavv..kdkelrlgaG 239
                                     ++++++++++lkal+P+g+v+GaPk rameii+elEe+ Rg+YaGa+g+++++  +e+a+v+R+a +  + ++l+++aG
  gi|118431922|ref|NP_148690.2| 327 VTRPSTTFVEALKALHPAGTVSGAPKPRAMEIIAELEEEARGPYAGAIGVAGSS-AGEAAIVLRSAWLldDGETLEARAG 405
                                    ****************************************************76.59***********854489****** PP

                                    EEEETT--HHHHHHHHHHH CS
                Chorismate_bind 240 aGIvadSdpeaEyeEtlaK 258
                                    aGIv dS+pe+Ey Et +K
  gi|118431922|ref|NP_148690.2| 406 AGIVYDSKPEREYMETVQK 424
                                    ****************998 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   7.7e-06     0.069      11      55 ..      33      75 ..      25      89 .. 0.78
   2 ?    2.3   0.0     0.019   1.7e+02      98     140 ..      98     140 ..      95     142 .. 0.79
   3 ?    0.6   0.0     0.068   6.1e+02      34      68 ..     231     265 ..     207     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-06
                  Anth_synt_I_N 11 klaeeehkflLeSaeneggegrySfigldpflelkskngeveveg 55
                                    +++ee+  lLeS+ + ++++rySf+++  + +  s++++++ ++
  gi|118431922|ref|NP_148690.2| 33 EVQGEEWIALLESGGGLQHRSRYSFLAWGRRKS--SETDAIRAYE 75
                                   5678889********99999********99665..6666665555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.019
                  Anth_synt_I_N  98 lgYDlvreie.klpksakddlnlpdarlilydtlivfDhkerrl 140
                                    ++Y++v   e  l+ +    +++p +  + ++ ++v+Dh  +r+
  gi|118431922|ref|NP_148690.2|  98 VSYEAVVGEEpWLS-RLVGRHEWPGMTAFSPEYVVVYDHAGGRV 140
                                    68999888886776.4555566*****************87776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.068
                  Anth_synt_I_N  34 Sfigldpflelkskngevevegpegeeleeeepld 68 
                                     +ig +p l +k + g+ve++   g++ + ++p +
  gi|118431922|ref|NP_148690.2| 231 VIIGSSPELLVKLEAGRVETHPIAGTRPRGSTPIE 265
                                    68999999999999999998885444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3404.54
//
Query:       gi|14602143|ref|NP_148691.1|  [L=196]
Description: anthranilate synthase component II [Aeropyrum pernix K1]
Scores for complete 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  175.0   0.0    1.7e-51  174.7   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
      5e-12   46.0   0.1    1.7e-11   44.3   0.1    1.7  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.066   13.0   0.0       0.28   11.0   0.0    1.8  2  DJ-1_PfpI      DJ-1/PfpI family
      0.074   12.6   0.0      0.092   12.3   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


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 !  174.7   0.0   3.8e-55   1.7e-51       1     187 [.       7     191 ..       7     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 3.8e-55
                                   EEEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-EEEE CS
                        GATase   1 lliDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPiLGI 77 
                                   l+iDnyds+++n+v+ l++lg++  v+++d+   +i   + +pd i++s+Gpg+p      + ++++++e++  ++P+LGI
  gi|14602143|ref|NP_148691.1|   7 LVIDNYDSFVYNIVDVLARLGAESIVLRNDEVSPKIA-RRLKPDRIVISPGPGNPLnprdSGRAPDIVREMAR-NTPVLGI 85 
                                   58****************************9888885.589**************999999*********999.******* PP

                                   THHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEE CS
                        GATase  78 CLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeii 158
                                   CLG+Q++++ +g+kv+++  k++hg+t+++++++++l++g +++++++++H+++v +    p++l+v  +s dd+ +m+i 
  gi|14602143|ref|NP_148691.1|  86 CLGHQIIGLLYGAKVERAP-KPMHGKTSPVEHYGHKLYRGVPRVFQAMRYHSLAVYD---PPEELQVDSVSLDDKVIMGIS 162
                                   *******************.9***********************************9...9******************** PP

                                   EETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                        GATase 159 ekknpfvgvQFHPEststpegpellfnfl 187
                                   + + p++gvQFHPEs+ tp+g+ +++nfl
  gi|14602143|ref|NP_148691.1| 163 HAELPVYGVQFHPESIGTPHGEVIVRNFL 191
                                   ***************************96 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   3.8e-15   1.7e-11      89     216 .]      63     176 ..      54     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.8e-15
                 Peptidase_C26  89 eRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqd.ieeqsgltdhreheqsaashavkvekgsllaellgseei 168
                                    Rd+   + i ++++r++P+lgiC+G+q++     G ly + +e++++ +         ++  v+    +l+  +   + +
  gi|14602143|ref|NP_148691.1|  63 PRDSGRAPDIVREMARNTPVLGICLGHQII-----GLLYGAkVERAPKPM-------HGKTSPVEHYGHKLYRGVP--RVF 129
                                   5888888889999*****************.....777654044322233.......3445566655555555554..589 PP

                 Peptidase_C26 169 evnslHhqaikelaeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                   +   +H+ a+ +  eel+v +v+  D vi  i++ e   +v+gvQ+HPE
  gi|14602143|ref|NP_148691.1| 130 QAMRYHSLAVYDPPEELQVDSVSLdDKVIMGISHAE--LPVYGVQFHPE 176
                                   9999*******************9788999999998..67********9 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.2e-05      0.28      60     106 ..      45      91 ..      27     102 .. 0.85
   2 ?   -0.6   0.0      0.23     1e+03      26      48 ..     144     166 ..     128     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                                   C.G-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                     DJ-1_PfpI  60 a.eyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpql 106
                                     + D +v+  G  +p + r++ ++ ++v+e+a ++++v  IC g q+
  gi|14602143|ref|NP_148691.1|  45 RlKPDRIVISPGPGNPLNPRDSGRAPDIVREMA-RNTPVLGICLGHQI 91 
                                   4478999**99999*****************87.689********987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.23
                                   TTEEEEEEESSTSEEEETTSEEE CS
                     DJ-1_PfpI  26 agikvdvvsvdkeevkgsrGlkv 48 
                                   ++++vd+vs+d++ + g +++++
  gi|14602143|ref|NP_148691.1| 144 EELQVDSVSLDDKVIMGISHAEL 166
                                   57899999999999888877766 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 ?   12.3   0.0   2.1e-05     0.092      60      92 ..      64      96 ..       8     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                      GATase_3 60 resgldeaikeaaeaggpvlgiCGGlqmLGeei 92
                                  r+sg + +i + +++++pvlgiC G q+ G  +
  gi|14602143|ref|NP_148691.1| 64 RDSGRAPDIVREMARNTPVLGICLGHQIIGLLY 96
                                  56788899999999**************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1501.17
//
Query:       gi|118431923|ref|NP_148692.2|  [L=1006]
Description: arsenite oxidase large subunit [Aeropyrum pernix K1]
Scores for 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-25   87.1   0.4    1.4e-24   86.3   0.4    1.4  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.2e-23   83.8   0.3    6.5e-10   38.5   0.0    3.4  4  Molybdopterin    Molybdopterin oxidoreductase
    2.5e-13   50.1   0.8    1.8e-10   40.9   0.8    2.9  1  Rieske_3         Rieske 3Fe-4S
     0.0078   16.2   0.2      0.019   14.9   0.2    1.7  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
     0.0082   16.3   0.0      0.025   14.7   0.0    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.4   3.8e-28   1.4e-24       2     110 ..     873     978 ..     872     979 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3.8e-28
                                    EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSH CS
                Molydop_binding   2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgw 80 
                                    ++++gr+   ++++++  +v +  +++p + v++npedAa+ G+++Gd+V++++++Gs+++ ++vt  v+pG++f+ +++
  gi|118431923|ref|NP_148692.2| 873 WVVNGRYNAIWQTGYADPNVVEIMARHPmNIVQVNPEDAAKEGLENGDIVVIYNDYGSTTAMVWVTRVVAPGTIFLIMAH 952
                                    7899**************************************************************************** PP

                                    CC.....S-GHCTS--SCSTTT--CSTT-E CS
                Molydop_binding  81 weagekggnaNaltddatdplsgtpefksv 110
                                    ++    ++ aNa+t +++dp +++p +k +
  gi|118431923|ref|NP_148692.2| 953 PK----AVGANAVTTPSVDPAAQNPDYKLT 978
                                    99....*********************976 PP

>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.2e-06     0.012       1      41 [.     151     187 ..     151     195 .. 0.92
   2 !   38.5   0.0   1.8e-13   6.5e-10     100     196 ..     255     377 ..     238     437 .. 0.79
   3 !   26.7   0.0   7.1e-10   2.5e-06     356     432 .]     614     693 ..     518     693 .. 0.82
   4 ?   -4.0   0.0       1.5   5.3e+03     343     380 ..     895     933 ..     876     934 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCS CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkyg 41 
                                    Rl++P+vR      G++++vsW+ A +l+a+ +k +i+k g
  gi|118431923|ref|NP_148692.2| 151 RLTKPLVR---F-GGRLEPVSWEYAIDLVARVVKGVIDKWG 187
                                    9*******...5.89********************999866 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 1.8e-13
                                    TS-SS-CCGGGG-SEEEEESS-HHHHSHHH............HHHHHHHHHTTC.....-EEEEECSSB-H........C CS
                  Molybdopterin 100 yessnpledlensdliilwGsNvreerpil............narirkaalkkk.....akvivigpryae........l 154
                                     +++++  dl  +d iilwG+N++ +++++            +  + +++++ +      ++i+++pr +e         
  gi|118431923|ref|NP_148692.2| 255 GAMNTSYHDLRLADTIILWGNNPYSTATVMfvkhvldnlrgaTKAEKQRWFNPGepvidSRIIIVDPRRTEtveaaeaaA 334
                                    56899999**********************999999977666555666666666************************98 PP

                                    GGGCSEEEEEHTTTHHHHHHHHHHHHHHC.CCCTCHHHHHHEE CS
                  Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqe.lkvdkeflrkyty 196
                                     k  +++l +kpgtd  la+a++ vi++  + v +ef++ y++
  gi|118431923|ref|NP_148692.2| 335 GKDRVLHLQVKPGTDIVLANAIARVIYERyGDVVEEFVNHYRS 377
                                    89***********************997613445666666654 PP

  == domain 3  score: 26.7 bits;  conditional E-value: 7.1e-10
                                    SCCCHCHHH.CSS.EEEEEESCSSHHHHTSSEEEEBE-.CCGSEEEEE-T.TSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                  Molybdopterin 356 enevekale.kld.lvvvldgrltstalyaDiiLPaat.wyEkedlytnd.egrfqhlkqavsppgeaksdwkIlkaLak 431
                                    e+ + +ale     +v+v d++ t  ++ a+++LPaa    E  d+ +   e+rf  +++  +ppgeak+dw+Il ++ak
  gi|118431923|ref|NP_148692.2| 614 EKVL-QALEeTGGlFVIVEDIYPTFMVEDAHVVLPAAFnNGEWPDVRMGVhERRFRIADAWLDPPGEAKPDWWILANVAK 692
                                    4444.555533341556667888*************96268*999998762666777*********************99 PP

                                    H CS
                  Molybdopterin 432 k 432
                                    +
  gi|118431923|ref|NP_148692.2| 693 R 693
                                    6 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 1.5
                                    EEESH..HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHH CS
                  Molybdopterin 343 yllgn.npevdhadenevekalekldlvvvldgrltsta 380
                                     ++++  ++v+   e   ++ le+ d vv++  + ++ta
  gi|118431923|ref|NP_148692.2| 895 IMARHpMNIVQVNPEDAAKEGLENGDIVVIYNDYGSTTA 933
                                    445544344444445555559999999999986666665 PP

>> Rieske_3  Rieske 3Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.8   5.1e-14   1.8e-10       1      92 [.      23     143 ..      23     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 5.1e-14
                                    -SSBTT--EEEEEEEETT----SSGG.........GSTT-S......-TTS---....TT-SS---GGGE.EEEE...ET CS
                       Rieske_3   1 CdyCivgCgYkvYkWpvnkeGGlkae.........enalgv......Dlskqqk....alseawvapsmy.nvvk...kd 57 
                                    C++C vgCgY vY Wp++ eG +++          + a+g       D++k+++    ++ e w++++m  + ++   + 
  gi|118431923|ref|NP_148692.2|  23 CQFCNVGCGYDVYVWPAGAEGSPEPGghgieykivDEAYGRnlvkqpDFTKEHTglsaEEGEPWISEAMVvKTIRrtwER 102
                                    *******************998776422222222234444411222366665431111455679**99962344423334 PP

                                    T......EEEEEEEEE-TT-TTTTT---TTGGGTTTTS-BT CS
                       Rieske_3  58 g......kdvnvvivpdkdcvvnkGdssirGgrlaeklyse 92 
                                    g      ++v v+ vp  +c +n G++s+rGg+ ae ++s+
  gi|118431923|ref|NP_148692.2| 103 GrgtggwREVYVAQVPSPECPINWGNHSVRGGTQAERIWSP 143
                                    42233445789999**********************99986 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   5.4e-06     0.019       4      21 ..      19      36 ..      16      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.4e-06
                                   EEEE-SSBTT--EEEEEE CS
                 Molybdop_Fe4S4  4 vktaCpyCgvgCglevhv 21
                                   + t C++C vgCg +v+v
  gi|118431923|ref|NP_148692.2| 19 YTTMCQFCNVGCGYDVYV 36
                                   78*************998 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 !   14.7   0.0     7e-06     0.025      14      51 ..     901     939 ..     894     948 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7e-06
                                    TTEEEE-HHHHHHHTS-TTSEEEEEC.CCCEEEEEEEBS CS
                        CDC48_N  14 rgivridpedmeelglepgdvveieg.krkTvaivwpae 51 
                                     +iv ++ped ++ gle+gd+v i +   +T a+vw  +
  gi|118431923|ref|NP_148692.2| 901 MNIVQVNPEDAAKEGLENGDIVVIYNdYGSTTAMVWVTR 939
                                    59************************6677******876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1006 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 6818.07
//
Query:       gi|14602146|ref|NP_148694.1|  [L=210]
Description: arsenite oxidase small subunit precursor [Aeropyrum pernix K1]
Scores for 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-13   48.5   0.0    1.4e-12   47.4   0.0    1.6  2  Rieske      Rieske [2Fe-2S] domain
     0.0061   16.4   4.5      0.012   15.4   4.5    1.5  1  TAT_signal  TAT (twin-arginine translocation) pathway signal 
  ------ inclusion threshold ------
      0.023   14.0   3.0      0.047   13.1   3.0    1.5  1  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


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 ?   -3.3   0.0       1.5   8.8e+03      13      27 ..      51      65 ..      43      77 .. 0.53
   2 !   47.4   0.0   2.3e-16   1.4e-12       3      84 ..      84     174 ..      82     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                                  TTCEEEEEETTEEEE CS
                        Rieske 13 egdpltvkvggeplv 27
                                  +g ++tv+   ++++
  gi|14602146|ref|NP_148694.1| 51 PGPTQTVTATATETA 65
                                  555555555544443 PP

  == domain 2  score: 47.4 bits;  conditional E-value: 2.3e-16
                                   EEEEEGGGC-TTCEEEEEETTEEEEEEE-T.........TS-EEEEESC-TTTT-BCGG.SEEETT.EEE-TTT--EEE.. CS
                        Rieske   3 vavakesdvpegdpltvkvggeplvvlrde.........dgevyAlsdvCtHrgaplse.gkidekgvleCpcHgwayd.. 71 
                                   v++a++s+++eg+p+  +++g+++vv++           d++++A+s  CtH+g +l   g++  k +l+Cp+H +++d  
  gi|14602146|ref|NP_148694.1|  84 VKIANVSELREGQPVFKEYIGHRIVVIKLGeeavngvgpDKDIVAFSMLCTHMGGFLIFdGNT--K-TLICPLHFSQFDps 161
                                   6899************************44457888999******************985666..4.9***********98 PP

                                   TTSBEEE-TTHHH CS
                        Rieske  72 adGkvikgPaprp 84 
                                   + G+ + g a++ 
  gi|14602146|ref|NP_148694.1| 162 RGGQPVVGHATEY 174
                                   8888877776665 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 !   15.4   4.5     2e-06     0.012       2      25 ..      15      38 ..      14      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                    TAT_signal  2 lSRRdFLKgsAAaaAAaalggcaa 25
                                  ++RR FL +++A+aAA  +g++++
  gi|14602146|ref|NP_148694.1| 15 ITRREFLAAAGAGAAAFIVGAVVG 38
                                  89**************99998876 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 ?   13.1   3.0   7.8e-06     0.047       8      31 ..      14      37 ..       8      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.8e-06
                    UCR_Fe-S_N  8 eptRRDFLyiATgavgaVGaaaaa 31
                                    tRR+FL +A ++++a  ++a++
  gi|14602146|ref|NP_148694.1| 14 RITRREFLAAAGAGAAAFIVGAVV 37
                                  579*******99999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1554.29
//
Query:       gi|118431924|ref|NP_148695.2|  [L=206]
Description: AsnC/Lrp family transcriptional regulator [Aeropyrum pernix K1]
Scores for complete 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   43.9   0.7    3.5e-11   42.5   1.0    1.6  2  HTH_24          Winged helix-turn-helix DNA-binding
    4.9e-11   42.3   0.3    9.5e-11   41.4   0.3    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
     0.0042   16.9   0.0     0.0089   15.9   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0055   16.6   0.0      0.017   15.0   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0083   16.0   0.0      0.023   14.6   0.1    1.7  2  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.012   15.3   0.0       0.02   14.7   0.0    1.3  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.017   15.0   0.0       0.59   10.1   0.0    2.3  2  MarR_2          MarR family
      0.031   14.1   0.0      0.055   13.3   0.0    1.4  1  RuvB_C          RuvB C-terminal winged helix domain
      0.046   14.0   0.0      0.084   13.1   0.0    1.4  1  Ribosomal_L24e  Ribosomal protein L24e
      0.091   12.6   0.1        0.2   11.5   0.0    1.5  2  TFIIE_alpha     TFIIE alpha subunit
       0.11   12.9   0.1       0.46   10.9   0.0    2.0  2  Rrf2            Transcriptional regulator
       0.11   12.2   0.0       0.22   11.2   0.0    1.5  1  GntR            Bacterial regulatory proteins, gntR family
       0.19   11.8   0.0       0.38   10.8   0.0    1.4  1  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   1.0   2.5e-14   3.5e-11       2      48 .]       9      55 ..       8      55 .. 0.98
   2 ?   -2.7   0.0       3.2   4.4e+03      31      45 ..     116     130 ..     114     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.5e-14
                         HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   d +d++IL++L  +  + ++ +++++g+S+++v++r++rL+  G+Ik
  gi|118431924|ref|NP_148695.2|  9 DAIDIEILRILANDCTTAINKISQAVGVSVPNVRKRIRRLKALGVIK 55
                                   89********************************************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                         HTH_24  31 pstvnrrlkrLeeeG 45 
                                    p+ v + ++r e++G
  gi|118431924|ref|NP_148695.2| 116 PGGVDEIVRRIEKAG 130
                                    677777788888887 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 !   41.4   0.3   6.9e-14   9.5e-11       1      42 []       8      49 ..       8      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.9e-14
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   +D+iD+ IL++L  d+ +   +++++vG+S + v++R+rrL+
  gi|118431924|ref|NP_148695.2|  8 IDAIDIEILRILANDCTTAINKISQAVGVSVPNVRKRIRRLK 49
                                   6***************************************96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.5e-06    0.0089       6      45 ..      14      54 ..      12      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.5e-06
                                   HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   +IL++La+   + +  ++ ++g+s ++v+   ++L+ +G++
  gi|118431924|ref|NP_148695.2| 14 EILRILANdCTTAINKISQAVGVSVPNVRKRIRRLKALGVI 54
                                   8*******55599**************************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 !   15.0   0.0   1.3e-05     0.017       3      53 ..       5      55 ..       3      71 .. 0.91
   2 ?   -2.3   0.0       3.2   4.4e+03      39      51 ..     119     131 ..     114     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                   HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                           TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                     G+   ++++   L + +   +++i++++gv+ ++v + +r+L+  G+++
  gi|118431924|ref|NP_148695.2|  5 SRGIDAIDIEILRILANDCTTAINKISQAVGVSVPNVRKRIRRLKALGVIK 55
                                   5699999*****************************************997 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                    HHHHHHHHHHCTS CS
                           TrmB  39 vYevLrsLedkGl 51 
                                    v e++r+ e++G+
  gi|118431924|ref|NP_148695.2| 119 VDEIVRRIEKAGF 131
                                    6688888888887 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   1.7e-05     0.023       5      44 ..      15      53 ..      13      59 .. 0.91
   2 ?   -2.8   0.0       4.7   6.5e+03      37      47 ..     124     134 ..     123     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                         HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   il++L +++ +  ++++++  +vS   vr++I++L++lgv
  gi|118431924|ref|NP_148695.2| 15 ILRIL-ANDCTTAINKISQAVGVSVPNVRKRIRRLKALGV 53
                                   88888.99999999************************95 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                         HTH_11  37 kaLeelgvpIe 47 
                                    +++e++g+++e
  gi|118431924|ref|NP_148695.2| 124 RRIEKAGFQVE 134
                                    67999999998 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.4e-05      0.02       4      53 ..      14      60 ..      12      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                       HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGavs 53
                                   +il  l+++ +  ++++++  gvS   +R+ ++ L++ g+   + G+ +s
  gi|118431924|ref|NP_148695.2| 14 EILRILANDCTTAINKISQAVGVSVPNVRKRIRRLKALGV---IKGCKAS 60
                                   799*************************************...5566555 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00042      0.59      23      54 ..      26      57 ..       7      62 .. 0.83
   2 ?    2.4   0.0       0.1   1.4e+02      33      50 ..     114     131 ..     110     131 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                                   EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +++ + ++ g+s ++v ++++rL a G +  +
  gi|118431924|ref|NP_148695.2| 26 AINKISQAVGVSVPNVRKRIRRLKALGVIKGC 57
                                   6788999********************99765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                                    SSHHHHHHHHHHHHHTTS CS
                         MarR_2  33 lsksavsrilkrLvaaGL 50 
                                    l+++ v  i++r ++aG+
  gi|118431924|ref|NP_148695.2| 114 LDPGGVDEIVRRIEKAGF 131
                                    7999999*********96 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05     0.055       2      43 ..       6      44 ..       5      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                                   T---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHT CS
                         RuvB_C  2 lGLdeldikyLkllkekfkggpvglktlaailgeeketiedv 43
                                    G+d +di++L++l+   ++ +++++ +++++g++  ++ + 
  gi|118431924|ref|NP_148695.2|  6 RGIDAIDIEILRILA---NDCTTAINKISQAVGVSVPNVRKR 44
                                   69************9...79*************998887665 PP

>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.1e-05     0.084       5      40 ..     160     194 ..     157     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                                    B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHH CS
                 Ribosomal_L24e   5 kCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklf 40 
                                    kCsF+ + i  G+  + v  Dg+++ F +++c++++
  gi|118431924|ref|NP_148695.2| 160 KCSFCQS-IIVGRPYTVVLDDGRILVFHNERCAEAY 194
                                    8****86.6679********************6544 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00015       0.2      16      61 ..      13      59 ..       6      76 .. 0.85
   2 ?   -3.0   0.0       4.9   6.7e+03      91      99 ..     121     129 ..     119     146 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                   HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE.EEE CS
                    TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk.ykr 61
                                   +++l +L+ +  ++ + +++ +++  +++rk + rL+  +++k +k 
  gi|118431924|ref|NP_148695.2| 13 IEILRILANDCTTAINKISQAVGVSVPNVRKRIRRLKALGVIKgCKA 59
                                   689*****99999****************************983444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.9
                                    HHHHHHHHH CS
                    TFIIE_alpha  91 evvkkLeek 99 
                                    e+v+++e++
  gi|118431924|ref|NP_148695.2| 121 EIVRRIEKA 129
                                    455555543 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00034      0.46      18      56 ..      20      55 ..       1      58 [. 0.80
   2 ?   -0.8   0.0       1.5     2e+03      57      82 ..     102     125 ..      99     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                                   HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                   a   ++ + ++++i++ +++s + ++k +++L+  g++k
  gi|118431924|ref|NP_148695.2| 20 A---NDCTTAINKISQAVGVSVPNVRKRIRRLKALGVIK 55
                                   3...334478***************************98 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                    EETTT-TCEEESSHCCCSBHHHHHHH CS
                           Rrf2  57 svrGkgGGyrLakppeeItlldvvra 82 
                                    s+rG   G++La+ ++   + ++vr 
  gi|118431924|ref|NP_148695.2| 102 SKRGF--GAVLARTLDPGGVDEIVRR 125
                                    67777..99****9999888888886 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   0.0   0.00016      0.22      27      54 ..      27      54 ..      15      56 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                   HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           GntR 27 ereLaaefgVsrttvReALrrLeaeglv 54
                                    ++++++ gVs + vR+ +rrL+a g++
  gi|118431924|ref|NP_148695.2| 27 INKISQAVGVSVPNVRKRIRRLKALGVI 54
                                   5899********************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 ?   10.8   0.0   0.00028      0.38      14      57 ..      14      57 ..      11      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   +ilr La +     + + +++++s  ++++++r L   g +++ 
  gi|118431924|ref|NP_148695.2| 14 EILRILANDCTTAINKISQAVGVSVPNVRKRIRRLKALGVIKGC 57
                                   6999996666666699*******************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1595.53
//
Query:       gi|14602148|ref|NP_148696.1|  [L=217]
Description: hypothetical protein APE_2567 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1660.07
//
Query:       gi|118431925|ref|NP_148697.2|  [L=190]
Description: hypothetical protein APE_2568.1 [Aeropyrum pernix K1]
Scores for complete 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-07   29.9   0.0    1.7e-06   27.9   0.0    1.9  1  AhpC-TSA         AhpC/TSA family
      8e-06   26.1   0.1      2e-05   24.8   0.1    1.6  1  Thioredoxin_8    Thioredoxin-like
    1.1e-05   25.3   0.0    9.3e-05   22.4   0.0    2.0  2  Thioredoxin      Thioredoxin
    9.3e-05   22.2   0.0    0.00039   20.2   0.0    1.9  1  Redoxin          Redoxin
    0.00046   20.6   0.0    0.00086   19.7   0.0    1.4  1  Thioredoxin_2    Thioredoxin-like domain
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.047   13.3   0.0    1.4  1  GSHPx            Glutathione peroxidase
      0.033   14.4   0.0      0.073   13.3   0.0    1.5  1  Glutaredoxin     Glutaredoxin
      0.059   13.2   0.0        0.1   12.4   0.0    1.3  1  TraF             F plasmid transfer operon protein
      0.063   11.7   0.0      0.081   11.4   0.0    1.1  1  Hanta_nucleocap  Hantavirus nucleocapsid protein
        0.1   12.3   0.0        0.2   11.4   0.0    1.4  1  Thioredoxin_9    Thioredoxin
       0.13   12.2   0.1       0.26   11.2   0.1    1.5  1  UL11             Membrane-associated tegument protein


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 !   27.9   0.0   1.1e-09   1.7e-06       7      75 ..      44     109 ..      39     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                                    --EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHH CS
                       AhpC-TSA   7 dfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkk 75 
                                    +f+l++ dge +sl+++ g++v+l f+++ wcp C   +  l +l e+++   + vi++   + e++k+
  gi|118431925|ref|NP_148697.2|  44 SFSLTTIDGEVISLNNVGGDVVILWFMAA-WCPSCVYMADLLDRLTEKYR--EISVIAIDFWTAEALKA 109
                                    79*****************9999999999.*****999999999999999..78888887777776555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   1.2e-08     2e-05       1      95 []      62     168 ..      61     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.2e-08
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-...................SS-HHHHHHHGGGS-TTS CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl...................dkkeeefekylkknkkpw 61 
                                    g+vv+L f a wcp+c  +   l++l ek++    + ++++ +                   d   e+f+k++++ + p 
  gi|118431925|ref|NP_148697.2|  62 GDVVILWFMAAWCPSCVYMADLLDRLTEKYR---EISVIAIDFwtaealkalglnkpgypppDT-PEMFRKFIANYGDPS 137
                                    59****************************8...9*******999999999***99***99655.6**********6654 PP

                                    EE.EE-TT-HHHHTT-S--TT-SEEEEE-TT-BE CS
                  Thioredoxin_8  62 lsvpfddkkrnklkkkynvkaiPtlvvldkngev 95 
                                      +  dd     l +k+nv +i  +v++dk+ +v
  gi|118431925|ref|NP_148697.2| 138 WIMVMDD---GSLVEKFNVRSIDYIVIMDKSSNV 168
                                    4445554...58*****************99887 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.7e-08   9.3e-05      19      62 ..      63     105 ..      55     114 .. 0.87
   2 ?    0.6   0.0      0.35   5.8e+02      63      87 ..     146     170 ..     138     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.7e-08
                                    SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSH CS
                    Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdene 62 
                                    + v++ F+A wC++C  +a  l++l e+++ ++ ++ +d  + e
  gi|118431925|ref|NP_148697.2|  63 DVVILWFMAAWCPSCVYMADLLDRLTEKYR-EISVIAIDFWTAE 105
                                    568899************************.9999999976655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.35
                                    HHHHHTT-SSSSEEEEEETTEEEEE CS
                    Thioredoxin  63 dlakkyevegiPtlklfkngkevkk 87 
                                    +l++k++v++i  ++++ ++ +v  
  gi|118431925|ref|NP_148697.2| 146 SLVEKFNVRSIDYIVIMDKSSNVLY 170
                                    78999******99999998886544 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.4e-07   0.00039       9     134 ..      45     175 ..      38     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.4e-07
                                    -ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEE.................EES CS
                        Redoxin   9 ftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvav.................vad 71 
                                    f+l  ++ dg+ +sl  + g + v+  + +a+cP C   +  l+ l+e++  + ++v+a+                 +  
  gi|118431925|ref|NP_148697.2|  45 FSL--TTIDGEVISLNNVGGDV-VILWFMAAWCPSCVYMADLLDRLTEKY--REISVIAIdfwtaealkalglnkpgYPP 119
                                    454..5589********86666.55555555*******998999999985..5678899888888888888888887555 PP

                                    SSHH..HHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESS CS
                        Redoxin  72 ndaf..vkefwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevep 134
                                     d++   ++f++++g +  +++  ++++++++++r          +   ++ d+  +v y ++ p
  gi|118431925|ref|NP_148697.2| 120 PDTPemFRKFIANYGDPSWIMVMDDGSLVEKFNVR---------SIDYIVIMDKSSNVLYAGTTP 175
                                    55555688888886655555444457888888855.........444444445555777776665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.2e-07   0.00086       5     101 ..      62     175 ..      59     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.2e-07
                  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkd................... 65 
                                    g  v+++f + +Cp C  + + l+ l   t++     + ++++ +a+++w+a+  k a+                     
  gi|118431925|ref|NP_148697.2|  62 GDVVILWFMAAWCPSCVYMADLLDRL---TEK-----Y-REISVIAIDFWTAEALK-ALGLnkpgypppdtpemfrkfia 131
                                    5679**************99977777...666.....5.55799*********995.55557799999999999999999 PP

                  Thioredoxin_2  66 .........ieenvelarkygvrgtPtivfldgk.eivarlpGyvp 101
                                             + +   l++k++vr+  +iv+ d++ ++   + G +p
  gi|118431925|ref|NP_148697.2| 132 nygdpswimVMDDGSLVEKFNVRSIDYIVIMDKSsNV--LYAGTTP 175
                                    ********9999999*****************99655..4556555 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.9e-05     0.047       4      59 ..      45     101 ..      43     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                    BEEEBTTSSEEEGGGGTTSEEEEEEEESSSTTHH.HHHHHHHHHHHHGGGTEEEEEE CS
                          GSHPx   4 lsakdidgekvkleklrgkvvlivnvaskCglte.qykeleelqkrykdkglvilgf 59 
                                    +s ++idge ++l++  g vv++  +a+ C         l+ l ++y++  ++ + f
  gi|118431925|ref|NP_148697.2|  45 FSLTTIDGEVISLNNVGGDVVILWFMAAWCPSCVyMADLLDRLTEKYREISVIAIDF 101
                                    78899*************************999944455789*****9988877776 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.5e-05     0.073       3      35 ..      68     100 ..      66     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.5e-05
                                    EEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH CS
                   Glutaredoxin   3 lftkptCpyCkkakrlLkelgvkfeeidvdkde 35 
                                     f+  +Cp C+ + +lL++l  k++ei v + +
  gi|118431925|ref|NP_148697.2|  68 WFMAAWCPSCVYMADLLDRLTEKYREISVIAID 100
                                    6999**********************9986655 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.2e-05       0.1     124     166 ..      57     100 ..      53     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.2e-05
                           TraF 124 lkklakeygLlfFyrgkcpyceaqapilqafadky.glevraVs 166
                                    l+++ +++ +l F+++ cp c  +a+ l+++++ky +++v+a++
  gi|118431925|ref|NP_148697.2|  57 LNNVGGDVVILWFMAAWCPSCVYMADLLDRLTEKYrEISVIAID 100
                                    5677788999*************************889999997 PP

>> Hanta_nucleocap  Hantavirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     5e-05     0.081     340     416 ..      24     101 ..       9     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5e-05
                                    HHHHHHHSXXXXXXXXXXXXXHHHHHHH.HHHTTSXXXXHHHHHHHHHHHHHHHHHTXXXSXXXXHHHHHHHHHHHHH CS
                Hanta_nucleocap 340 ntimasktvgtseeklrkkssfyqsylr.rtqsmgiqlgqriivlfmvawgkeavdnfhlgddmdpelrtlaqslidv 416
                                     ti   ++ g see l + +sf  + +     s+    g+ +i+ fm aw   +v    l d +  + r ++   id 
  gi|118431925|ref|NP_148697.2|  24 YTIAIPRAAGHSEEVLEREASFSLTTIDgEVISLNNVGGDVVILWFMAAWCPSCVYMADLLDRLTEKYREISVIAIDF 101
                                    58888999**************98887625678888889999999***********9999999999999988777775 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013       0.2      17      75 ..      36      96 ..      26     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHH---HH..HHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEE CS
                  Thioredoxin_9 17 ermlrvykkvelseetee..kiksiekklkilvltedwCgDaavnvPvlakiaelnpniev 75
                                   e++l+  ++++l++ + e   ++++  ++ il +++ wC+ ++ +   l+++ e   +i+v
  gi|118431925|ref|NP_148697.2| 36 EEVLEREASFSLTTIDGEviSLNNVGGDVVILWFMAAWCPSCVYMADLLDRLTEKYREISV 96
                                   6666777777777777775677899999999********************9999888876 PP

>> UL11  Membrane-associated tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00016      0.26      18      30 ..      47      59 ..      44      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                           UL11 18 LvTedGEvveLds 30
                                   L+T dGEv++L++
  gi|118431925|ref|NP_148697.2| 47 LTTIDGEVISLNN 59
                                   9**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1466.84
//
Query:       gi|118431926|ref|NP_148698.2|  [L=128]
Description: nickel responsive regulator [Aeropyrum pernix K1]
Scores for 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-07   28.9   0.0    1.3e-06   28.1   0.0    1.4  1  RHH_1            Ribbon-helix-helix protein, copG family
    2.6e-06   27.5   0.1    1.6e-05   25.0   0.0    1.9  2  NikR_C           NikR C terminal nickel binding domain
     0.0025   17.9   0.0     0.0044   17.1   0.0    1.3  1  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit
     0.0056   16.6   0.0     0.0099   15.8   0.0    1.4  1  VapB_antitoxin   Bacterial antitoxin of type II TA system, Va
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.013   15.6   0.1    1.4  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
      0.017   14.9   0.1       0.51   10.2   0.0    2.4  2  DAHP_snth_FXD    DAHP synthase ferredoxin-like domain
        0.1   13.0   0.0       0.21   12.0   0.0    1.5  1  ParD_antitoxin   Bacterial antitoxin of ParD toxin-antitoxin 
       0.11   12.8   0.0       0.12   12.6   0.0    1.2  1  VWA              von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   5.9e-10   1.3e-06       2      38 ..       5      42 ..       4      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.9e-10
                                   EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                   vs++l++ l++++d+ +++ g +SrS+lI+ Al  +le
  gi|118431926|ref|NP_148698.2|  5 VSVSLPDHLVRKVDRAVEEYGfKSRSDLIKTALQTFLE 42
                                   9*********************************9998 PP

>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.35   7.9e+02       9      41 ..      11      44 ..       3      46 .. 0.74
   2 !   25.0   0.0   7.1e-09   1.6e-05       4      73 ..      55     124 ..      54     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.35
                                   ETTSTTHHHHHHHHHHHH.SSEEEEEEEEEESSS CS
                         NikR_C  9 dhhqrelserltdiqhey.hdliisslhvhldhd 41
                                   dh +r++++ + +   ++ +dli+++l+  l+++
  gi|118431926|ref|NP_148698.2| 11 DHLVRKVDRAVEEYGFKSrSDLIKTALQTFLEDE 44
                                   7777777777777754443899999999988775 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 7.1e-09
                                    EEEEEET.TSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEE CS
                         NikR_C   4 itivydh.hqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvk 73 
                                    i+++ dh ++  +++++  + h+y+++ i+  h  l+  +c+ + v+ G  ++ +++++klr+l+gV +v+
  gi|118431926|ref|NP_148698.2|  55 IVVLSDHkSSPYVDKNIVGLIHSYSEELIALYHQILQGPYCITIAVV-GGKDDWRTIVKKLRSLSGVLSVQ 124
                                    7888999455679999**************************76666.556899*************9986 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     2e-06    0.0044      92     121 ..       5      35 ..       2      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                HicB_lk_antitox  92 iNitlpervlkriDaavkaag.esRSgflak 121
                                    + ++lp+++++++D+av++ g +sRS ++ +
  gi|118431926|ref|NP_148698.2|   5 VSVSLPDHLVRKVDRAVEEYGfKSRSDLIKT 35 
                                    789******************99****9976 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 !   15.8   0.0   4.4e-06    0.0099      12      42 ..      17      47 ..      11      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-06
                                   XXXXXXXXXXXXXXXXXXXXXXX-------H CS
                 VapB_antitoxin 12 laeAirltglktKrEaVnlALreLiqrrkre 42
                                   +++A++ +g k ++ +++ AL+++++ ++ +
  gi|118431926|ref|NP_148698.2| 17 VDRAVEEYGFKSRSDLIKTALQTFLEDEDNK 47
                                   7899**********************99865 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.1     6e-06     0.013      16      48 ..      15      47 ..       3     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6e-06
                          RHH_8 16 gqiDlLveeGfYsnRtDlirtairaqLakhdda 48
                                    ++D  vee  + +R+Dli+ta+++ L+++d++
  gi|118431926|ref|NP_148698.2| 15 RKVDRAVEEYGFKSRSDLIKTALQTFLEDEDNK 47
                                   57999999988899**************99986 PP

>> DAHP_snth_FXD  DAHP synthase ferredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.053   1.2e+02       1      28 [.       1      28 [.       1      39 [. 0.86
   2 ?   10.2   0.0   0.00023      0.51      28      63 ..      87     124 ..      54     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.053
                  DAHP_snth_FXD  1 MIivmkkgateeqieevierieelGlkv 28
                                   M+ v+  +  +  +++v + +ee+G+k 
  gi|118431926|ref|NP_148698.2|  1 MVTVVSVSLPDHLVRKVDRAVEEYGFKS 28
                                   77788888888999***********985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00023
                  DAHP_snth_FXD  28 vhvskGeertViGviGdts..kldkeqlealpgVekVv 63 
                                     ++ +G   + i+v+G ++  +++ ++l++l+gV +V+
  gi|118431926|ref|NP_148698.2|  87 HQILQGPYCITIAVVGGKDdwRTIVKKLRSLSGVLSVQ 124
                                    578999999*******766226889*********9996 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.3e-05      0.21       5      46 ..       5      47 ..       1      68 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.3e-05
                                   EEE---HHHHHHHHHHHCTTS-SSHHHHHHHHHH.HHHHHHHH CS
                 ParD_antitoxin  5 tsvvLgehfsafidsqvaaGrYgsaseviraaLr.LLeeretk 46
                                    sv L +h    +d  v++  ++s s+ i++aL+  Le+++ k
  gi|118431926|ref|NP_148698.2|  5 VSVSLPDHLVRKVDRAVEEYGFKSRSDLIKTALQtFLEDEDNK 47
                                   699******************************8468887766 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 ?   12.6   0.0   5.4e-05      0.12      62     124 ..      11      71 ..       2     123 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                    HHHHHHHHTGSGGGGSSC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHHH CS
                            VWA  62 eellsalnnlkysgggttntgkalkyaleklfkssagaRenakkviilltdGksndgdpkeaa 124
                                    ++l +++++  +++ g ++  + +k al+++++ + ++ ++  ++i++l+d ks+   +++++
  gi|118431926|ref|NP_148698.2|  11 DHLVRKVDR-AVEEYGFKSRSDLIKTALQTFLEDEDNKSSGSYRLIVVLSDHKSSP-YVDKNI 71 
                                    567788888.6888888888999999999999999997779**********88844.333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1019.68
//
Query:       gi|118431927|ref|NP_148699.2|  [L=585]
Description: cation-transporting P-type ATPase [Aeropyrum pernix K1]
Scores for complete 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-35  121.4   2.4    3.1e-35  121.4   2.4    2.0  2  E1-E2_ATPase     E1-E2 ATPase
    8.8e-29  101.3   0.1    1.5e-28  100.6   0.1    1.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
    9.7e-11   41.9   1.0    6.9e-05   22.7   0.0    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.025   15.0   0.0      0.076   13.4   0.0    1.9  2  HAD              haloacid dehalogenase-like hydrolase
      0.039   13.4   2.5       0.14   11.6   0.2    2.4  2  ProQ_C           ProQ C-terminal domain
       0.28   11.2   1.3         24    5.0   0.0    2.8  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
       0.44   11.1   5.0       0.39   11.2   0.4    2.6  2  DUF2190          Uncharacterized conserved protein (DUF2190)
        1.2    9.1   6.8       0.11   12.3   0.7    2.6  2  PsbJ             PsbJ


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 ?   -3.8   1.2       3.5   7.9e+03     123     154 ..      26      58 ..      18      71 .. 0.57
   2 !  121.4   2.4   1.4e-38   3.1e-35       2     180 ..     100     268 ..      99     269 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.5
                                    HHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHH CS
                   E1-E2_ATPase 123 vpvvlliallvflialllgksla.eallralal 154
                                     +v++li+ ++++  l+l++ l+ e l+ ++++
  gi|118431927|ref|NP_148699.2|  26 LWVITLILSIAAVRELVLERRLTvELLMAIVGF 58 
                                    445555555555555555555553444444444 PP

  == domain 2  score: 121.4 bits;  conditional E-value: 1.4e-38
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EE CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgea 81 
                                    l p++++v+rdg++ee+da++++pGD+vl+++g+ vp+Dg++++    +d  ++TGEs+pv++e g  + sG+++v +++
  gi|118431927|ref|NP_148699.2| 100 LIPKRVRVVRDGSIEEVDASQVKPGDVVLVRKGEAVPVDGVLLDTG-VFDLRLITGESEPVTVEGGRAIESGAINVGQPV 178
                                    78999**************************************977.9******************************** PP

                                    EEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-T CS
                   E1-E2_ATPase  82 kavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPc 161
                                    k+++++   ++++++i++++ e  ++k  +q+ +d+l+ +++++v+ +++++++++            ++++ll+a +P 
  gi|118431927|ref|NP_148699.2| 179 KVKAVKSPLESTIQRIVSSALELLREKGATQRLIDRLAPYMIVIVIGAFIAAYITL---------GPEKSVVLLLAGCPS 249
                                    **************************************************999997.........45689********** PP

                                    THHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 162 aLplavplalalgarrlak 180
                                    a+++a + a++++++ la 
  gi|118431927|ref|NP_148699.2| 250 AFIIASSAATSYSIATLAT 268
                                    ***************9996 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.1   6.6e-32   1.5e-28       1     210 []     285     491 ..     285     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 6.6e-32
                                    SSEEEEESBTTTBCHH..HHHHHHHHHH.....CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE...... CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                      Hydrolase   1 iktvvfDkdGTLttge..psvedvivsa.....alalaaaletgsehpigkalvaaakarsgaltgfatfigrg...... 67 
                                    ik+vv+Dk+GT+t g+  ps + v++ a      l l aa +  s hp+  a+ a      g+++++++++grg      
  gi|118431927|ref|NP_148699.2| 285 IKAVVLDKTGTITMGTlkPSRVVVLRGAasqdgLLNLVAAAASTSLHPLSIAI-ARRWRPMGNVEKVEEVPGRGlravvs 363
                                    89***********9996655555555555655555555555555*********.55555569**************9999 PP

                                    ..HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  68 ..ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnp 145
                                      +++ g++++l+++     +g + +    +   v+ +       ++i  + +v ++++ a+++ k++g+++vl++gd +
  gi|118431927|ref|NP_148699.2| 364 grTLLLGSERFLEEE-----VGYRPENPCVDEVPVFAH--VDGTTLAICMSEEVDEKTKAAINEMKRMGLNLVLASGDRR 436
                                    999999999999999.....888888888888888888..6666777776666*************************** PP

                                    HHHHHHHHHTTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 146 etaeraanqlGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    + +e++a++lG          ++e +a+ +pe+k++++ + ++k   v m+GDgvnD++alaa +
  gi|118431927|ref|NP_148699.2| 437 NKVEKIARELG----------IDEYHAELKPEDKLEIVSKVREKYDPVSMIGDGVNDLEALAASD 491
                                    ***********..........6666*******************999***************976 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   3.1e-08   6.9e-05       3      57 ..     395     451 ..     393     455 .. 0.92
   2 !   17.8   0.3   9.4e-07    0.0021     204     243 ..     472     510 ..     461     517 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.1e-08
                                    EEIIIIIS-..TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSE CS
                    Hydrolase_3   3 lDlDGTLln..sdkkisektkeaikklkekgikvviATGRslravlpvleelgldlp 57 
                                      +DGT l     ++++ektk+ai+++k  g ++v+A+G    +v+++++elg+d +
  gi|118431927|ref|NP_148699.2| 395 AHVDGTTLAicMSEEVDEKTKAAINEMKRMGLNLVLASGDRRNKVEKIARELGIDEY 451
                                    568***999878899***************************************976 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.4e-07
                                    GGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE CS
                    Hydrolase_3 204 eeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvt 243
                                    + v  +GDg ND+e L a++lgvA+gn  + v + Ad v 
  gi|118431927|ref|NP_148699.2| 472 DPVSMIGDGVNDLEALAASDLGVAVGN-IDAVRNLADAVL 510
                                    66889**********************.567778877765 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.6   5.8e+03      58     102 ..      75     125 ..      42     129 .. 0.49
   2 ?   13.4   0.0   3.4e-05     0.076      87     187 ..     411     487 ..     368     488 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                            HAD  58 leallaglseelaaelerfvaevirpk.....lldpgalellaahr.aaGd 102
                                    l+++ + l++++++ + r ++e++r       + + g  e ++a + + Gd
  gi|118431927|ref|NP_148699.2|  75 LYSFAETLEAQVEKLALRRLEEAKRLIpkrvrVVRDGSIEEVDASQvKPGD 125
                                    333333333333333333332222211112323445666666644445555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.4e-05
                            HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaeg 166
                                    d++ ++++++ ++ G  +v+ Sg  r  ve +++elg    +++       + +el++e+k+       +++re     +
  gi|118431927|ref|NP_148699.2| 411 DEKTKAAINEMKRMGLNLVLASGDRRNKVEKIARELG----IDE-------YHAELKPEDKLEIV----SKVRE-----K 470
                                    578899999999*************************....999.......88888888888888....99999.....4 PP

                            HAD 167 egidleevvayGDspsDlpll 187
                                    +++    v  +GD+++Dl++l
  gi|118431927|ref|NP_148699.2| 471 YDP----VSMIGDGVNDLEAL 487
                                    444....99*********997 PP

>> ProQ_C  ProQ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.13     3e+02       1      18 [.     117     134 ..     117     143 .. 0.79
   2 ?   11.6   0.2     6e-05      0.14       4      27 ..     171     194 ..     168     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.13
                                    -SSSS-TT--B---SSSS CS
                         ProQ_C   1 dlaeLkvGqqVkVklGks 18 
                                    d++++k G+ V V  G++
  gi|118431927|ref|NP_148699.2| 117 DASQVKPGDVVLVRKGEA 134
                                    689**********99985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6e-05
                                    SS-TT--B---SSSS---EEEEEE CS
                         ProQ_C   4 eLkvGqqVkVklGkspmpAtilei 27 
                                     + vGq VkVk+ ksp++ ti  i
  gi|118431927|ref|NP_148699.2| 171 AINVGQPVKVKAVKSPLESTIQRI 194
                                    689*****************9766 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 ?    4.0   0.1     0.022        49      29      57 ..     104     133 ..     103     141 .. 0.82
   2 ?   -2.9   0.0       3.1     7e+03      20      42 ..     286     297 ..     280     312 .. 0.53
   3 ?    5.0   0.0     0.011        24      39      74 ..     448     482 ..     434     484 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.022
                                    EEEEEEETHHHHHHHTTS-TTSEEEEE.EE CS
                tRNA_anti-codon  29 riqvvlfreeatklaenlkeGdvvrvt.Gr 57 
                                    r++vv + +  +  a+++k+Gdvv v+ G+
  gi|118431927|ref|NP_148699.2| 104 RVRVVRDGSIEEVDASQVKPGDVVLVRkGE 133
                                    6777777777777899**********9887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.1
                                    EEEEEETTEEEEEEEETHHHHHH CS
                tRNA_anti-codon  20 fidlrDgtgriqvvlfreeatkl 42 
                                     +++ D+tg+i           +
  gi|118431927|ref|NP_148699.2| 286 KAVVLDKTGTI-----------T 297
                                    34444555544...........4 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.011
                                    HHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                tRNA_anti-codon  39 atklaenlkeGdvvrvtGrvkrrpggelelkveeie 74 
                                     ++++ +lk++d +++  +v++ ++  ++++ + + 
  gi|118431927|ref|NP_148699.2| 448 IDEYHAELKPEDKLEIVSKVREKYDP-VSMIGDGVN 482
                                    6899********************99.998877665 PP

>> DUF2190  Uncharacterized conserved protein (DUF2190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00017      0.39      15      71 ..     119     184 ..     108     200 .. 0.71
   2 ?    0.7   0.5      0.32   7.1e+02      31      74 ..     251     297 ..     233     330 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                        DUF2190  15 aaitagqvvvlga...........lkvlGVAatdaaaGetvtvaveGvf.veaaaaiavGdkVywdasg 71 
                                    ++++ g+vv++ +               GV +    +Ge+ +v veG   +e+ +ai+vG++V ++a +
  gi|118431927|ref|NP_148699.2| 119 SQVKPGDVVLVRKgeavpvdgvllD--TGVFDLRLITGESEPVTVEGGRaIES-GAINVGQPVKVKAVK 184
                                    5666777777765333222223321..466666668***********996766.89*******999865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.32
                        DUF2190  31 lGVAatdaaaGetvtvaveGvf......veaaaaiavGdkVywdasgkvl 74 
                                    + +A+  a + + +t+a++G++       eaa+ i   ++V  d++g  +
  gi|118431927|ref|NP_148699.2| 251 FIIASSAATSYSIATLATRGIVarggrsLEAAGKI---KAVVLDKTGTIT 297
                                    56675566666778999999997885555555544...567777777763 PP

>> PsbJ  PsbJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.3       2.4   5.5e+03       9      19 ..      26      36 ..      25      39 .. 0.77
   2 ?   12.3   0.7   5.1e-05      0.11       5      25 ..     552     574 ..     548     577 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.4
                                   HHHHHHHHHHH CS
                           PsbJ  9 LWlVatvaGlg 19
                                   LW++ ++  ++
  gi|118431927|ref|NP_148699.2| 26 LWVITLILSIA 36
                                   8*999987655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.1e-05
                                    TSS-HHHHHHHH..HHHHHHHHH CS
                           PsbJ   5 GRIPLWlVatva..Glgvitvvg 25 
                                    G IPLWlVa+ +  G  +i+ v+
  gi|118431927|ref|NP_148699.2| 552 GSIPLWLVALLGddGSTIIGSVA 574
                                    88********9877999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.39
# Mc/sec: 4484.40
//
Query:       gi|14602152|ref|NP_148700.1|  [L=390]
Description: hypothetical protein APE_2574 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   11.7   0.0        2.4    8.0   0.0    2.2  2  DUF3088   Protein of unknown function (DUF3088)


Domain annotation for each model (and alignments):
>> DUF3088  Protein of unknown function (DUF3088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00013       2.4      42      76 ..      35      69 ..      24      77 .. 0.85
   2 ?    1.0   0.0     0.019   3.4e+02      11      40 ..     260     289 ..     257     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00013
                       DUF3088 42 kldvervdfarPRkavvallgeenqslPvLvLadg 76
                                  +++   v   rPR a   +l +    lP+LvL+++
  gi|14602152|ref|NP_148700.1| 35 AVEYYAVMAYRPRDAALYILAAHTLALPLLVLSKA 69
                                  5667778999**********************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.019
                       DUF3088  11 fedpkkpgerfyCpdcaaleGllasfPala 40 
                                   f + ++p++  +   c+++eG ++  P+ a
  gi|14602152|ref|NP_148700.1| 260 FAETHTPERLRIVDTCLTVEGRVSNIPSFA 289
                                   888999999999*********999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2907.68
//
Query:       gi|14602153|ref|NP_148701.1|  [L=397]
Description: aspartate aminotransferase [Aeropyrum pernix K1]
Scores for complete 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  128.1   0.0    5.8e-37  127.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0061   15.5   0.0      0.018   14.0   0.0    1.6  1  Alliinase_C      Allinase
  ------ inclusion threshold ------
      0.056   12.7   0.0      0.094   12.0   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  127.7   0.0   9.8e-41   5.8e-37      36     353 ..      67     377 ..      42     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 9.8e-41
                                   STTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSE CS
                 Aminotran_1_2  36 tlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsgge 116
                                    +  yg + g p l+e +a+ +    +  ++ e +v+ ++G+ +++ +    l + pgd++l + p+y +++  lr++g+ 
  gi|14602153|ref|NP_148701.1|  67 AVLGYGWTLGEPGLRESVASVYY---RGLVDSE-QVIITTGSAEANLLSVISL-VAPGDRVLFDMPNYMQIHGLLRMRGAR 142
                                   577899999**********9999...5566777.7777777777777776666.67************************* PP

                                   EEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSS CS
                 Aminotran_1_2 117 vvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgs 197
                                   + +   + e  ++ld   + e++k+      k++ +++++p+NPtG+va ++ l ++++ a + + +l++De Y g++  +
  gi|14602153|ref|NP_148701.1| 143 ILEAWRKREHRWKLDPGLYAELIKRE-----KPRAVFITNPNNPTGSVAGPKALGEIAAEAARTGSILVFDELYRGLEHST 218
                                   999999******************95.....789*********************************************97 PP

                                   SHTHHH.HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHH CS
                 Aminotran_1_2 198 ldavat.ranveeepnllivgslsKafGlaGeRvGyilg.naavvsqlrklsrpfls..ssllqaavaaalsdallkqsel 274
                                   + a ++  + +e++ + + v++lsK +Gl+G+R+G++++ + ++++ +  ++   ++  + +  +++ ++l++   k  +l
  gi|14602153|ref|NP_148701.1| 219 EPAPTVlEPALEQGAHAISVSGLSKVYGLPGLRIGWAAAtSRRLRDRMWMVKDYTTIspPKPSEHIAEQILEKGVWK--KL 297
                                   74444478999999999**********************7779****999999888889*************98876..99 PP

                                   HHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-H CS
                 Aminotran_1_2 275 eemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglte 353
                                    e+ +r+  +  e+ + L+      k + +++g + l++++  +  +++ kL + + ++v pg++f +pg +R+ + g+ +
  gi|14602153|ref|NP_148701.1| 298 AERGRRIVLSNLEILEDLTTRfrTAKLWRPDAGAYALVETTVGDTLSFAYKLYQTHSILVNPGECFKLPGTIRLGL-GHEN 377
                                   99999999999999999988899******************999******************************99.7765 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     3e-06     0.018     117     241 ..     148     290 ..     140     320 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3e-06
                                   -BTTEEEEEESTT-..--S..S-EEEEEESS-TTT--------........-TT-EEEEEE-TT-STTTS.........-- CS
                   Alliinase_C 117 dsklykweGdaaayv.kkknpeefielvtsPnnPdgllreavv........kgseakviyDlayYWPhyt.........pi 179
                                   ++++++w+ d   y+   k+ ++   ++t PnnP g +  +          +++ +++++D  y   +++         p 
  gi|14602153|ref|NP_148701.1| 148 RKREHRWKLDPGLYAeLIKREKPRAVFITNPNNPTGSVAGPKAlgeiaaeaARTGSILVFDELYRGLEHStepaptvlePA 228
                                   567788888887777312334566678999999999886532213333554455667899999875333212111111144 PP

                                   -S-B--SEEEEEHHHHHS-GGG-EEEEEES-HHHHHHHHHHHHHHHSS--HHHHHHHHHHHH CS
                   Alliinase_C 180 tskadedimLftlskltGhaGsrlGWalvkdkevakklveyieknsiGvskesqlrvlkilk 241
                                    ++  + i++  lsk+ G  G r+GWa    +++ +++      ++i   k s   + +il+
  gi|14602153|ref|NP_148701.1| 229 LEQGAHAISVSGLSKVYGLPGLRIGWAAATSRRLRDRMWMVKDYTTISPPKPSEHIAEQILE 290
                                   5667899**************************99999888888888777777777777665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05     0.094      42     167 ..      90     208 ..      77     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                   HHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT..TBE-HHHHHHHS-- CS
               Beta_elim_lyase  42 aelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea..Gkmdlekleaaike 120
                                   + l++ e+++ ++    An +++  l+ +g+ v+++ p+ +  +   ++  + g++  ++  k++   k+d+   +++ik+
  gi|14602153|ref|NP_148701.1|  90 RGLVDSEQVIITTGSAEANLLSVISLVAPGDRVLFDMPNYMQIH---GLLRMRGARILEAWRKREhrWKLDPGLYAELIKR 167
                                   56788888888888889*********************988876...4455666666666555444589999999999*99 PP

                                   S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
               Beta_elim_lyase 121 vgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                        ek++++ +t+ nn   G v  ++ l e+aa a + g  l++D
  gi|14602153|ref|NP_148701.1| 168 -----EKPRAVFITNPNNP-TGSVAGPKALGEIAAEAARTGSILVFD 208
                                   .....79***********5.9*******************9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 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:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2911.41
//
Query:       gi|118431928|ref|NP_148702.2|  [L=291]
Description: hypothetical protein APE_2577.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-12   47.8   0.0      7e-12   46.0   0.0    1.8  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   3.9e-16     7e-12       1     153 [.      45     211 ..      45     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 3.9e-16
                                    EEEESEESS--TTTSCCTT.............HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHH CS
                                    xxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpet.............vrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvel 66 
                                    +++  gC+++C+fC++                 ++++ g+   + +ile +ke   ++++++ev++++ +  + p ++++
  gi|118431928|ref|NP_148702.2|  45 INFAVGCTHACPFCYVDAInrryprrgledliTSTGWGGYLAVPTNILEAIKETPwWRWRGREVFMSSAHDPYLPALARW 124
                                    68999*******************************************************8888888887777799**** PP

                                    HHHHHHTC.CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSE CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  67 lerlakla.vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagik 143
                                    ++++ ++a  +g+ri + t  +l  ++ l+ + +++   r++ ++ + +    +++++ r + +  ++++l  + ++g+ 
  gi|118431928|ref|NP_148702.2| 125 AREILRRAlPAGLRIILHTRSILY-KRDLRMFEQYRdRIRIHASVATMSR--LHRIIEpRAPPPRVRVRVLAEASSRGLS 201
                                    *******9***************9.9*********966666667777766..8*****99999999*****999999998 PP

                                    TEEEEEEEBT CS
                                    xxxxxxxxxx RF
                    Radical_SAM 144 rvvdrivglp 153
                                       ++ ++lp
  gi|118431928|ref|NP_148702.2| 202 TGASISPILP 211
                                    8555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2162.33
//
Query:       gi|14602155|ref|NP_148703.1|  [L=283]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete 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-31  108.6  24.7    2.8e-31  108.6  24.7    2.3  1  ABC2_membrane    ABC-2 type transporter
    8.9e-19   67.8  21.5    8.9e-19   67.8  21.5    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
    3.6e-05   23.2  18.9    7.9e-05   22.1  18.9    1.5  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 !  108.6  24.7   4.7e-35   2.8e-31       4     208 ..       9     245 ..       6     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 4.7e-35
                 ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr................................ 52 
                                   ++l+kre+++++ ++s + l+++i+p++++ +fg  f   +                                        
  gi|14602155|ref|NP_148703.1|   9 LILTKREIIKWVNRRSVL-LVSIITPIFWIALFGKSFNLYN-------Lvqtsdpslnpavaealrtvmawrlesvfgtqd 81 
                                   789************999.99****************8422.......12223344456889999999999********** PP

                 ABC2_membrane  53 ......pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldl 127
                                          g+l+ + lf +  ++ +v++vf+r+ g l r+l+sp+ ++++++++kvl+ l ++++++li+l+i+y+l gl+l
  gi|14602155|ref|NP_148703.1|  82 yftyvaTGMLAVFSLFQS--MFGAVGVVFDRRIGYLTRLLASPI-PRFSIFASKVLGTLFRITVLSLILLAIAYPL-GLHL 158
                                   ***999888888888888..7888888*****************.******************************9.**** PP

                 ABC2_membrane 128 s......rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyav 202
                                   +        ++++l+l+l++l +ssl+  ++   +++e+   la+l+ lpl++ s +++pid mp+wl+ +a++nP+t+a 
  gi|14602155|ref|NP_148703.1| 159 KpgitiiDLVMAWLVLMLMSLGLSSLFTGMAFNITHQEVLFALANLINLPLMFSSSALFPIDLMPNWLKTVAQVNPITHAA 239
                                   987754444************************************************************************ PP

                 ABC2_membrane 203 ealrsn 208
                                   +++r+ 
  gi|14602155|ref|NP_148703.1| 240 DLVRYY 245
                                   ***986 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 ?   -0.3   0.5     0.076   4.5e+02       4      22 ..      26      44 ..      23      75 .. 0.57
   2 !   67.8  21.5   1.5e-22   8.9e-19     154     343 ..      78     272 ..      45     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.076
               ABC2_membrane_3  4 liitlllPiilvlllglif 22
                                  l+ +++ Pi+ ++l+g  f
  gi|14602155|ref|NP_148703.1| 26 LLVSIITPIFWIALFGKSF 44
                                  4444555555555544222 PP

  == domain 2  score: 67.8 bits;  conditional E-value: 1.5e-22
               ABC2_membrane_3 154 eelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl... 231
                                     ++ +++ + g+++++++f +++  av++v++++ + + ++l s++ +++++ sk+lg+++   + +l++l++a+ l   
  gi|14602155|ref|NP_148703.1|  78 GTQDYFTYVATGMLAVFSLFQSMF-GAVGVVFDRRIGYLTRLLASPIPRFSIFASKVLGTLFRITVLSLILLAIAYPLglh 157
                                   555556666666777777777777.7779********************************************98777778 PP

               ABC2_membrane_3 232 ...gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffap 309
                                      gi++ +l+ + l+++l++l +++l++ + + ++ +e  ++l+ +++l+l++ + +lfp++ +p++lk+++ ++P+++ 
  gi|14602155|ref|NP_148703.1| 158 lkpGITIIDLVMAWLVLMLMSLGLSSLFTGMAFNITHQEVLFALANLINLPLMFSSSALFPIDLMPNWLKTVAQVNPITHA 238
                                   8999999999999999999999999999999999*********************************************** PP

               ABC2_membrane_3 310 glgllrlitgdplweillsliilalfavvyllla 343
                                   +++    + g pl +  +s+++la++++++l+++
  gi|14602155|ref|NP_148703.1| 239 ADLVRYYLVGKPLEDPVMSIAYLAVLTLFLLAAG 272
                                   ***********999999*************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 !   22.1  18.9   1.3e-08   7.9e-05       2     271 ..      10     263 ..       9     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-08
               ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli.....dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvv 77 
                                   ++ k+E+++ v  r++ll++++ p++           ++  ++s++s ++a+ ea+ ++ + +  s +  ++ +++ +   
  gi|14602155|ref|NP_148703.1|  10 ILTKREIIKWVNRRSVLLVSIITPIFwialfGKSFNLYNLVQTSDPSLNPAVAEALRTVMAWRLESVFGTQDYFTYVA--- 87 
                                   7899**********************88887667788999999****************9999999999998888887... PP

               ABC2_membrane_2  78 stimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivla 157
                                    t m  ++ ++  +fga  ++ ++  g l +lL++P++R +i ++K++g l  + +  +++l +++ l+l +  +  i   
  gi|14602155|ref|NP_148703.1|  88 -TGMLAVFSLFQSMFGAVGVVFDRRIGYLTRLLASPIPRFSIFASKVLGTLFRITVlSLILLAIAYPLGLHLKPGITIIDL 167
                                   .99999999*******************************************95555555555555556666666555555 PP

               ABC2_membrane_2 158 ledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailv.pivlygvaellagpavpqeindflslls 237
                                   ++++l+l+++s+ l  l+      ++++  +    ++ + al+ ++ l +++ + +l+++  ++       ++  ++  ++
  gi|14602155|ref|NP_148703.1| 168 VMAWLVLMLMSLGLSSLF------TGMAFNIT--HQEVLFALANLINLPLMFsSSALFPIDLMP-------NWLKTVAQVN 233
                                   566666666666555533......33333222..333333333333333333033333322222.......2555567777 PP

               ABC2_membrane_2 238 ptsayntllneilagsdlnalgstatnllillll 271
                                   p+ +   l++  l g++l+    ++ + ++ l++
  gi|14602155|ref|NP_148703.1| 234 PITHAADLVRYYLVGKPLE----DPVMSIAYLAV 263
                                   7777777777777777633....33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2139.17
//
Query:       gi|118431929|ref|NP_148704.2|  [L=330]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-29  102.5   0.0    3.9e-29  101.9   0.0    1.3  1  ABC_tran         ABC transporter
    3.8e-14   53.2   0.1    6.1e-09   36.1   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      2e-08   34.8   0.0    3.6e-08   34.0   0.0    1.4  1  DUF4162          Domain of unknown function (DUF4162)
    0.00091   18.9   0.0     0.0017   18.0   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.004   17.7   0.1     0.0063   17.0   0.1    1.2  1  AAA_23           AAA domain
     0.0041   16.6   0.0     0.0097   15.4   0.0    1.6  1  KdpD             Osmosensitive K+ channel His kinase sensor d
     0.0055   17.1   0.1      0.069   13.6   0.1    2.5  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.017   15.1   0.0    1.2  1  Rad17            Rad17 P-loop domain
      0.017   15.4   0.1      0.075   13.3   0.1    2.2  1  AAA_28           AAA domain
      0.024   14.3   0.0      0.034   13.9   0.0    1.3  1  AAA_30           AAA domain
      0.036   13.7   0.0       0.06   13.0   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.038   13.6   0.0      0.059   13.0   0.0    1.3  1  AAA_27           AAA domain
      0.041   13.5   0.0        1.1    8.9   0.0    2.1  2  Thymidylate_kin  Thymidylate kinase
      0.042   13.3   0.0          8    5.8   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.043   13.8   0.1       0.11   12.5   0.1    1.7  1  HTH_11           HTH domain
      0.046   13.4   0.0       0.23   11.1   0.0    1.8  2  AAA_15           AAA ATPase domain
       0.05   13.9   0.0       0.19   12.0   0.0    2.1  2  AAA_22           AAA domain
      0.071   13.1   0.4        4.6    7.2   0.1    3.2  4  AAA_5            AAA domain (dynein-related subfamily)
      0.091   12.3   0.6       0.21   11.1   0.2    1.9  2  AAA_25           AAA domain
      0.098   12.0   0.0        0.4   10.0   0.0    1.9  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.13   12.6   0.1       0.29   11.5   0.1    1.7  1  AAA_16           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 !  101.9   0.0   4.6e-32   3.9e-29       2     136 ..      23     165 ..      22     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 4.6e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + vs+ + +ge+  ++G+nGaGK+t +k+l+ ll+pt+Ge ++ g ++ + e   +r+ ig +pq+ + ++e++  +n  
  gi|118431929|ref|NP_148704.2|  23 DGVSFRIARGELFSLLGPNGAGKTTTIKMLSTLLRPTSGEAWIAGYSIVR-EPGNVRRVIGLVPQDLTADDEMSGWDNvy 101
                                    78************************************************.888999*********************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e++e+  ++l+ l+l e ++++v    +++SgG+++++++a++l+  pk+l+lDEpt
  gi|118431929|ref|NP_148704.2| 102 iqarlyglpssEARERTREVLDYLDLMEAAHRRV----ATYSGGMRRKLEIAMSLVHSPKVLFLDEPT 165
                                    *********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 !   15.3   0.0   1.6e-05     0.014       3      52 ..      36      72 ..      34      80 .. 0.80
   2 !   36.1   0.0   7.1e-12   6.1e-09     236     298 ..     137     196 ..      92     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52
                                    l GpNg+GK++ ++ l+ l              ++++g+++i++++  +
  gi|118431929|ref|NP_148704.2| 36 SLLGPNGAGKTTTIKMLSTLL-------------RPTSGEAWIAGYSIVR 72
                                   589**************9995.............5777777777776655 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 7.1e-12
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                      S G++r l ++ +l   +   ++l++DEp +gL+ +  r+l++ +++l+r  + ++ltTH 
  gi|118431929|ref|NP_148704.2| 137 TYSGGMRRKLEIAMSLVHSP---KVLFLDEPTLGLDVHSRRSLWRYIEDLKRSAVTILLTTHY 196
                                    4599*************988...9**************************************5 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   4.2e-11   3.6e-08       1      81 []     219     306 ..     219     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.2e-11
                                    E-HHHHHTTS-SSEEEEE......--..-----..---EEE..E-TTS-EEEEE--.---------------EEEEEEEE CS
                        DUF4162   1 GtleeiKrsygknrieve......ad..aeelleepgveev..eeeggelelkled.eeaanellkaltsgveirsFeee 69 
                                    Gt+ee+K++ +++++++e      ++  + +l+e  g   +  +  +g++ ++++  ++  +el +al +g +++ ++ +
  gi|118431929|ref|NP_148704.2| 219 GTPEELKARVKGETVYIElkdpeyTEplVLALKEKLG---LepSVVEGKVAVRVDRaDTLLPELARAL-NGFPVKAISIT 294
                                    9*****************7543321122222223333...333444578******99***********.*********** PP

                                    ---HHHHHHHHH CS
                        DUF4162  70 ePsLndIFiekv 81 
                                    +++L+d+Fie++
  gi|118431929|ref|NP_148704.2| 295 RATLEDVFIELT 306
                                    *********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 !   18.0   0.0     2e-06    0.0017      12      50 ..      22      60 ..      15      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                         AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                    dg +++i + + + l Gp+G+GK+T +  +++lL p++
  gi|118431929|ref|NP_148704.2| 22 VDGVSFRIARGELFSLLGPNGAGKTTTIKMLSTLLRPTS 60
                                   56788999977799*********************9986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   7.4e-06    0.0063       6      40 ..      18      53 ..      13      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.4e-06
                         AAA_23  6 nfrsfrdqeidF.skgltlItGpNGaGKTTildAik 40
                                   +fr  +++++      l+ + GpNGaGKTT +  + 
  gi|118431929|ref|NP_148704.2| 18 GFRAVDGVSFRIaRGELFSLLGPNGAGKTTTIKMLS 53
                                   4444455555556668**************998776 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 !   15.4   0.0   1.1e-05    0.0097      41     139 ..     111     212 ..     105     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                           KdpD  41 ethgrketealleglevi...prkeveykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagid 117
                                    +++ r++t+++l+ l+++    r+  +y+g   ++l++   l ++p+v+++De      +  +++  ++ +e+l ++ + 
  gi|118431929|ref|NP_148704.2| 111 SSEARERTREVLDYLDLMeaaHRRVATYSGGMRRKLEIAMSLVHSPKVLFLDEPTLGL-DVHSRRSLWRYIEDLKRSAVT 189
                                    5678999999998887774436778899*************************87765.55566789************9 PP

                           KdpD 118 Vi.ttvnvqhleslndvvekitg 139
                                    ++ tt  +++ e l+d v+ i +
  gi|118431929|ref|NP_148704.2| 190 ILlTTHYMEEAEMLSDRVAIIDR 212
                                    85377788999999999987754 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1     8e-05     0.069       3     113 ..      37     198 ..      35     214 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8e-05
                                    EESSTTSSHHHHHHHHHHHHTHE..............................EEEEETTTCSSS............... CS
                            AAA   3 lyGppGtGKTllakavakelgve..............................fleisgsellsk............... 37 
                                    l Gp G GKT+++k + + l  +                                         +               
  gi|118431929|ref|NP_148704.2|  37 LLGPNGAGKTTTIKMLSTLLRPTsgeawiagysivrepgnvrrviglvpqdltA----------Ddemsgwdnvyiqarl 106
                                    88***************9985222223333333334444444444444344440..........1455555555555555 PP

                                    ...............................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
                            AAA  38 ...............................yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervv 86 
                                                                   y g + +k++  ++ +   + p++lf+DE                    
  gi|118431929|ref|NP_148704.2| 107 yglpssearertrevldyldlmeaahrrvatYSGGMRRKLEIAMSLVH--S-PKVLFLDEPTLGLDVH----------SR 173
                                    555555566667777777776666666666677777777777777653..3.7899999944333222..........23 PP

                                    HHHHHHHHHTTTSSSTEEEEEEESSGG CS
                            AAA  87 nqLlteldgvkkkeskvivigatnrpd 113
                                      L + ++++k++   v+++++t++++
  gi|118431929|ref|NP_148704.2| 174 RSLWRYIEDLKRS--AVTILLTTHYME 198
                                    4577777777663..466666666654 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     2e-05     0.017      46      86 ..      33      75 ..      20      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                          Rad17 46 riLLisGPsGCgkstvvkvLskelgikl.rewlnpvsl.kepd 86
                                   ++  + GP G gk+t++k+Ls  l +   + w+ + s+ +ep 
  gi|118431929|ref|NP_148704.2| 33 ELFSLLGPNGAGKTTTIKMLSTLLRPTSgEAWIAGYSIvREPG 75
                                   467789****************998765156888876425554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   8.8e-05     0.075       4      31 ..      37      75 ..      34     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.8e-05
                         AAA_28  4 itGgestGKTtlleaLa........ar...gypvvpEaa 31
                                   ++G+ ++GKTt+++ L+        +    gy++v+E++
  gi|118431929|ref|NP_148704.2| 37 LLGPNGAGKTTTIKMLStllrptsgEAwiaGYSIVREPG 75
                                   89***************6655544422677888887765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     4e-05     0.034      20      61 ..      34      92 ..      26     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaa.g................grviglAptgkaAkv 61
                                   +  l Gp G+GKtt++k l  +++   g                +rvigl p+   A++
  gi|118431929|ref|NP_148704.2| 34 LFSLLGPNGAGKTTTIKMLSTLLRPTsGeawiagysivrepgnvRRVIGLVPQDLTADD 92
                                   66789**************9999988678999999999999988889998888777765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     7e-05      0.06       5      34 ..      36      65 ..      33      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                                   EEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                          SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvll 34
                                    l+G++GaGKTtt+  L+ ll+    ++ +
  gi|118431929|ref|NP_148704.2| 36 SLLGPNGAGKTTTIKMLSTLLRPTSGEAWI 65
                                   589************999998877655555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.9e-05     0.059       9      50 ..      14      56 ..       6      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-05
                         AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                   + yG f     ++f+ ++ +l  ++GpN AGK+t+++ +s ll
  gi|118431929|ref|NP_148704.2| 14 KDYGGFRAVdGVSFRIARGELFSLLGPNGAGKTTTIKMLSTLL 56
                                   67899976536999999999999**************999987 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0013       1.1       3      23 ..      39      59 ..      38      90 .. 0.75
   2 ?    2.3   0.0      0.13   1.1e+02     118     173 ..     156     211 ..     135     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                                   ESTTSSHHHHHHHHHHHHHHT CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkee 23
                                   G +GaGKtt +++l   l+  
  gi|118431929|ref|NP_148704.2| 39 GPNGAGKTTTIKMLSTLLRPT 59
                                   889***********9999743 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                                    -SEEEEEESSHHHHHTSCCTTSS.TTTSHHHHHHHHHHHHHHHHHHHH.TTSTEEEEE CS
                Thymidylate_kin 118 PdltflldvdpevalkRlakrde.ldeeeeeqldflrkvrerylelak.ederiliid 173
                                    P ++++ld +p  +l   ++r+  ++ e+ ++  +   ++++y+e+a+   +r+ iid
  gi|118431929|ref|NP_148704.2| 156 P-KVLFLD-EPTLGLDVHSRRSLwRYIEDLKRSAVTILLTTHYMEEAEmLSDRVAIID 211
                                    4.467777.8999999999999999999********************9999999998 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 ?    5.8   0.0    0.0094         8      26      44 ..      34      52 ..      16      63 .. 0.75
   2 ?    5.5   0.0     0.012        10     123     208 ..     124     203 ..      87     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0094
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                   + +++GpNG+GK+  +  +
  gi|118431929|ref|NP_148704.2| 34 LFSLLGPNGAGKTTTIKML 52
                                   45789*******9887655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                                    HHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 123 vsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                    + +l+e a+    + SgG +  + +a+      v+   + +lDe    LD + ++ + ++++  + +a  + i l+++ +
  gi|118431929|ref|NP_148704.2| 124 YLDLMEAAHRRVATYSGGMRRKLEIAMS----LVHSPKVLFLDEPTLGLDVHSRRSLWRYIEDLKRSA--VTILLTTHYM 197
                                    5555555555556666666654444443....3333345569********************998654..4444455556 PP

                                    CC-SCE CS
                                    xxxxxx RF
                          SMC_N 203 ekadkl 208
                                    e+a+ l
  gi|118431929|ref|NP_148704.2| 198 EEAEML 203
                                    666544 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00012      0.11      25      47 ..     168     191 ..     167     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                         HTH_11  25 Lnv.SrrtvrrdIkaLeelgvpIe 47 
                                    L+v Srr  +r+I++L+ + v I 
  gi|118431929|ref|NP_148704.2| 168 LDVhSRRSLWRYIEDLKRSAVTIL 191
                                    7888*************9988886 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027      0.23      23      50 ..      33      59 ..      17     103 .. 0.80
   2 ?   -0.2   0.0      0.73   6.3e+02     324     364 ..     156     195 ..     141     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                         AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnk 50
                                   e l  l G+N++GK++ +++l  +l  +
  gi|118431929|ref|NP_148704.2| 33 E-LFSLLGPNGAGKTTTIKMLSTLLRPT 59
                                   3.78899**************9999865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.73
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    +++l+++EP + L     ++l++++ +l ++    +++tTH
  gi|118431929|ref|NP_148704.2| 156 PKVLFLDEPTLGLDVHSRRSLWRYIEDLKRSAV-TILLTTH 195
                                    6789***********************999996.8999999 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00022      0.19       9      38 ..      36      76 ..      30     203 .. 0.66
   2 ?   -2.3   0.0       5.7   4.9e+03      41      70 ..     231     260 ..     216     293 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                         AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee...........e 38
                                    + G+ G+GKTt++++l   l   +  ++           +
  gi|118431929|ref|NP_148704.2| 36 SLLGPNGAGKTTTIKMLSTLLRPTSGEAWiagysivrepgN 76
                                   678**************998844333333666666655553 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                         AAA_22  41 evvfvtlpsstsskdllrellralglelka 70 
                                    e+v+++l+ ++  + l  +l ++lgle + 
  gi|118431929|ref|NP_148704.2| 231 ETVYIELKDPEYTEPLVLALKEKLGLEPSV 260
                                    566666666666666666666666665544 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 ?    7.2   0.1    0.0054       4.6       4      23 ..      37      56 ..      35      66 .. 0.86
   2 ?   -1.5   0.0       2.7   2.3e+03      49      73 ..     139     163 ..     120     165 .. 0.74
   3 ?    1.6   0.0      0.29   2.5e+02      12      48 ..     173     209 ..     171     238 .. 0.73
   4 ?   -1.7   0.0       3.2   2.7e+03      15      39 ..     275     300 ..     273     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0054
                                   EE--SSSSHHHHHHHGGGGB CS
                          AAA_5  4 LvGppGtgKselaerlaaal 23
                                   L+Gp G gK++ ++ l+ +l
  gi|118431929|ref|NP_148704.2| 37 LLGPNGAGKTTTIKMLSTLL 56
                                   99**************9998 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                                    ........--------G-SEEEEES CS
                          AAA_5  49 ngttslvdsplvraaregeilvlDE 73 
                                    +g+ +++  +++  + ++++l+lDE
  gi|118431929|ref|NP_148704.2| 139 SGGMRRKLEIAMSLVHSPKVLFLDE 163
                                    5666666677777777999999998 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.29
                                    HHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--. CS
                          AAA_5  12 Kselaerlaaalnreveyvqltrdtteedlkgrreik 48 
                                    +++l++++  + ++ v++ + t +++e++++  r   
  gi|118431929|ref|NP_148704.2| 173 RRSLWRYIEDLKRSAVTILLTTHYMEEAEMLSDRVAI 209
                                    6789999999999999999999****99998776543 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 3.2
                                    HHHHGGGGB.S--EEEEE--TT--HH CS
                          AAA_5  15 laerlaaal.nreveyvqltrdttee 39 
                                    l  +la+al + +v  + +tr t e+
  gi|118431929|ref|NP_148704.2| 275 LLPELARALnGFPVKAISITRATLED 300
                                    6678999999999****999998776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00025      0.21      30      75 ..      29      78 ..      22     200 .. 0.67
   2 ?   -3.2   0.0       6.1   5.2e+03      79      91 ..     217     229 ..     214     276 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                         AAA_25 30 lpagelallaGapgtGKttla..ldlalavatGkpwlg..pvapeqgkVl 75
                                   +++gel  l G+ g+GKtt    l+  l  ++G+ w    +++ e+g+V 
  gi|118431929|ref|NP_148704.2| 29 IARGELFSLLGPNGAGKTTTIkmLSTLLRPTSGEAWIAgySIVREPGNVR 78
                                   789***************97522566666669999988897778888885 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.1
                         AAA_25  79 aEdsedelrrRlr 91 
                                    aE++ +el+ R++
  gi|118431929|ref|NP_148704.2| 217 AEGTPEELKARVK 229
                                    5555555555554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00047       0.4      25      53 ..      35      63 ..      17      75 .. 0.84
   2 ?   -1.2   0.0       1.3   1.1e+03      92     114 ..     140     163 ..     119     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00047
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseee 53
                                   + l+Gp G+GKt  +k l++ll p s e 
  gi|118431929|ref|NP_148704.2| 35 FSLLGPNGAGKTTTIKMLSTLLRPTSGEA 63
                                   5689******************9988765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                   Mg_chelatase  92 GggskpkpGeislahn.GvLfLDE 114
                                    Gg ++    ++sl h   vLfLDE
  gi|118431929|ref|NP_148704.2| 140 GGMRRKLEIAMSLVHSpKVLFLDE 163
                                    555566666778888635999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00034      0.29      23      51 ..      31      59 ..      21     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                   r+el  l G+ G GK++ +++l + l+ +
  gi|118431929|ref|NP_148704.2| 31 RGELFSLLGPNGAGKTTTIKMLSTLLRPT 59
                                   458899*************9999776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2415.83
//
Query:       gi|14602157|ref|NP_148705.1|  [L=263]
Description: flavoredoxin [Aeropyrum pernix K1]
Scores for 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-19   67.9   0.0    1.3e-18   67.5   0.0    1.2  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 !   67.5   0.0   7.3e-23   1.3e-18       9     149 ..      19     167 ..       9     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 7.3e-23
                                   EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCCCCCCCC CS
                 Flavin_Reduct   9 avvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtddksifa 89 
                                   +vvt+ +++++  g+ + + ++ s++Pp++a++++++++t++ ++e+g+f+ nll  +  + a  ++  s +    k+  a
  gi|14602157|ref|NP_148705.1|  19 VVVTA-EHQGRVGGMLAAWWMQASFTPPILAVAIAPERYTYKLVRESGVFAFNLLDFKLVDKAPFLGDVSERLLPGKIREA 98 
                                   45555.88999999******************************************************9997778888899 PP

                                   CCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTT.........BEECCCC CS
                 Flavin_Reduct  90 gltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadee.........pLlywrr 149
                                   gl+  ++   gap++++a a++e ++v+ ve+gdh++f+ge  av++ dd  +          pL+y  r
  gi|14602157|ref|NP_148705.1|  99 GLNIVRGeVLGAPLIAEASAAVELELVDVVEAGDHDVFLGEAKAVYTVDD-FRGgmwsletyrPLMYLGR 167
                                   9999999899**************************************99.4334677777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1981.07
//
Query:       gi|14602158|ref|NP_148706.1|  [L=405]
Description: hypothetical protein APE_2581 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3238.74
//
Query:       gi|118431930|ref|NP_148707.2|  [L=424]
Description: proton glutamate symport protein [Aeropyrum pernix K1]
Scores for 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-129  430.6  34.6   6.1e-129  430.4  34.6    1.0  1  SDF       Sodium:dicarboxylate symporter family


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.4  34.6  3.4e-133  6.1e-129       2     389 ..      14     410 ..      13     411 .. 0.97

  Alignments for each domain:
  == domain 1  score: 430.4 bits;  conditional E-value: 3.4e-133
                            SDF   2 llqiliglvlGlviGllelvkelaalisplgdlfinllkmlivPlvfasiisgiaslgdakklgklglktllyfllttli 81 
                                    l++i +g+vlG+++G+  +++ ++  ++plgdlfi+llkml++P+vf+s+++g as++ a+ lg++g+k+++y+l+tt++
  gi|118431930|ref|NP_148707.2|  14 LYKIAVGFVLGIIAGI--VIGGVMVDLKPLGDLFIRLLKMLVAPIVFFSLAVGAASIS-ASLLGRVGVKIFVYYLFTTAF 90 
                                    6899************..***************************************6.********************* PP

                            SDF  82 AaiiglilalllkpgselaleassakeaekketdslldlilslipsnifealaegnvlavivfailfGialaalgekg.. 159
                                    A++igli+a++++pg  + + a +ake + k  + +++++l+++p+n+f+alaegnvl++i+fai++G+a+a l+ ++  
  gi|118431930|ref|NP_148707.2|  91 AITIGLIVANIIQPG-RGLELAGEAKEIQVKPPPPISEVLLNIVPTNPFKALAEGNVLQIIFFAIVLGVAVALLRSSRdd 169
                                    ***************.788889999999999*******************************************998899 PP

                            SDF 160 ......epllkffeslnevvmkvvkivmklaPigvfaliaslvaskglgalsslakflltvylglaihllivlpllllvl 233
                                          e++ ++f+ l+e + k+v+ v+++aPigvfali ++va+ g g+l++la++++t+y+glaih+l+v++l+l+ l
  gi|118431930|ref|NP_148707.2| 170 rlrsggETVYRVFDGLAESMYKIVRGVLEYAPIGVFALIGYVVATAGPGVLGPLAVVVITLYIGLAIHVLGVYSLILR-L 248
                                    9****************************************************************************9.6 PP

                            SDF 234 tkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtalyeavaaifiaqlfgve 313
                                     +++plkf+k++l+a+ tAf+T+SS++tLPvt++ ae++l ++++i sf+lPlGatinmdGta+y+avaa+fia+++g++
  gi|118431930|ref|NP_148707.2| 249 FGFSPLKFFKGALEAMATAFVTRSSSGTLPVTMKVAEEELAIDRRIFSFTLPLGATINMDGTAMYQAVAALFIANTLGID 328
                                    778***************************************************************************** PP

                            SDF 314 lslgqllllvlvatlasiGaagvPgaglvalllvlsalglp......vegialilaidrllDmfrTavNvtGdavaaliv 387
                                    ls+gq+l ++l atlasiG+agvPgagl++l++vl+algl       + +++li++id++lDm+rT+vNvtGd+v+++iv
  gi|118431930|ref|NP_148707.2| 329 LSIGQQLSIILAATLASIGTAGVPGAGLIMLAIVLEALGLSltdptvALAYGLIAGIDVILDMGRTMVNVTGDLVGTTIV 408
                                    ****************************************9666554344****************************** PP

                            SDF 388 ak 389
                                    ak
  gi|118431930|ref|NP_148707.2| 409 AK 410
                                    98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2912.70
//
Query:       gi|14602160|ref|NP_148708.1|  [L=348]
Description: hypothetical protein APE_2585 [Aeropyrum pernix K1]
Scores for complete 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   93.9   3.4    1.8e-26   93.4   3.4    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0006   19.4   0.0     0.0011   18.5   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.14   12.2   1.8       0.49   10.5   0.0    2.7  3  HTH_20         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 !   93.4   3.4     3e-30   1.8e-26       3     197 .]      18     236 ..      16     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 3e-30
                                   CCSSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                   Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                   +++vn+y  +++ +++L+D+G+ + ++   l   l+++g++p+ v+++++TH+H+DH  g++ l+ea ++     + +++ 
  gi|14602160|ref|NP_148708.1|  18 LGSVNVYAFTDGASTVLVDSGMFSGKSVYTLlkGLRRVGVDPRSVERIVVTHYHVDHLTGAAILCEALGAELMLARGDLEL 98 
                                   689****************************************************************************** PP

                                   CHCHHHHHHHHHCCHH..........................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEE CS
                   Lactamase_B  82 lfmeeaddaasrkgll..........................lagvsadkpdvdeeeldgnaggrralyvtggpghghghg 136
                                   l++ +++ ++ r   l                          + +v + +p +  e++ ++ +g++++ v  +pgh++gh+
  gi|14602160|ref|NP_148708.1|  99 LLRVGVEEYFRRALELlalagtprevleeikryspavrvaeaYGAVAELGPKPLGEGDIIEMPGHGDYLVLETPGHTPGHI 179
                                   ************9999*************************766677777777777777777777788899********** PP

                                   EEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                   Lactamase_B 137 vveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                   v+ ++g++ ++ GD++l+  t++++l     + +d ++ ++y++sl ++a+  a +l + gH
  gi|14602160|ref|NP_148708.1| 180 VLVSHGKREVLLGDTVLPDITPHVSL-----HSIDSDPLGNYMSSLSRIATETAGYLGLpGH 236
                                   **************************.....********************99999888787 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 !   18.5   0.0   1.9e-07    0.0011      25      76 ..      56     114 ..      31     154 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-07
                                   S--..SEEEEE-SS--HHHHGGGGCCCC.......C--EEEEEEEEHHHHHHCCTTCGH CS
                 Lactamase_B_2  25 rdelppidaVllthaHyDHlaglltlre.......lrpkklplyapkgvlavleanfvy 76 
                                     ++++++ +++th H+DHl+g+  l e       l+  +l+l+   gv ++ ++ +  
  gi|14602160|ref|NP_148708.1|  56 GVDPRSVERIVVTHYHVDHLTGAAILCEalgaelmLARGDLELLLRVGVEEYFRRALEL 114
                                   45788999******************996655544333335555556666665555555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.2   6.9e+03      17      34 ..      73      89 ..      70      96 .. 0.72
   2 ?   -0.6   0.1      0.24   1.4e+03      41      50 ..     251     260 ..     239     264 .. 0.78
   3 ?   10.5   0.0   8.3e-05      0.49      15      56 ..     264     318 ..     261     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                  HHHSTCTTB-HHHHHHHH CS
                        HTH_20 17 raLaraegltaselaerl 34
                                  ++L ++++  +++l ++l
  gi|14602160|ref|NP_148708.1| 73 DHL-TGAAILCEALGAEL 89
                                  577.77888888887777 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                                   HHHHHHHHHH CS
                        HTH_20  41 lsyHLrvLee 50 
                                    ++H++ Lee
  gi|14602160|ref|NP_148708.1| 251 TRHHVERLEE 260
                                   799*****98 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 8.3e-05
                                   HHHHHSTCTTB-HHHHHHHHT................S-HHHHHHHHHHHHHCTTEEE CS
                        HTH_20  15 ilraLaraegltaselaerld................lskntlsyHLrvLeeagLvev 56 
                                   il+ L   +g+ta e+a+r++                l+  +   HLr Le  g ve+
  gi|14602160|ref|NP_148708.1| 264 ILSRL---AGATAFEVAQRVGwsvaggwrglpplgkyLALGETLSHLRRLEVLGVVER 318
                                   78888...************8778889999********************98999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2559.20
//
Query:       gi|118431931|ref|NP_148709.2|  [L=304]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-33  115.3  36.1    3.3e-33  115.0  36.1    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 !  115.0  36.1   1.8e-37   3.3e-33       6     261 ..      19     273 ..      14     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 1.8e-37
                   BPD_transp_2   6 ltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkvdel 85 
                                    ++   ++++a++G   +  +aG++n+g +g+m+ +a++a  +  l ++ +l++ l++ l+g+ +g+l g+ +++lk d++
  gi|118431931|ref|NP_148709.2|  19 ASAMVPITLASIGEIASE-RAGIVNIGLEGIMLASAWAAVAVYILTGWGPLAGYLLGALLGLSIGVLHGVVSVYLKGDQI 97 
                                    5667899***********.****************99999999999999******************************* PP

                   BPD_transp_2  86 iitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGralravgene 165
                                    +++++l+++ +g t+ + t   +g++++s ++e++  +     ++s   v l l++ ++v+l+l+rt  G++lr +ge++
  gi|118431931|ref|NP_148709.2|  98 VTGVGLNIFSAGATV-VGTYMLWGTFSNSPPVEPMPGFVIAGVRIS-PMVPLSLAAGVIVWLFLYRTIAGLRLRSCGEDP 175
                                    ***************.888999999999999999998877666665.455689999************************ PP

                   BPD_transp_2 166 eaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsllgtviGaliigvvksl 244
                                    + a+a+G+nv  +++++  ++g++AglaGa l+  ++++ + n+  g gf a+a v   g+ ++l++++G++++g++++l
  gi|118431931|ref|NP_148709.2| 176 RSAEAMGVNVALYQVAAAGFAGLMAGLAGAYLSIDYQGVFAkNMTAGRGFIALANVAFSGW-NPLAALLGGYVFGFSEAL 254
                                    *************************************************************.*****************7 PP

                   BPD_transp_2 245 lltllgi..ptelarvllg 261
                                    +++l  +  +t+ ++++  
  gi|118431931|ref|NP_148709.2| 255 AIYLNISleATAASNLVNT 273
                                    6666544665666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2253.55
//
Query:       gi|118431932|ref|NP_148710.2|  [L=359]
Description: ABC transporter permease [Aeropyrum pernix K1]
Scores for 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-39  133.4  27.2    8.1e-39  133.4  27.2    2.1  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 ?   -1.5   1.6      0.06   1.1e+03      14      70 ..      17      31 ..       6      50 .. 0.54
   2 !  133.4  27.2   4.5e-43   8.1e-39       5     267 ..      56     336 ..      52     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.06
                   BPD_transp_2 14 iaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavg 70
                                   +aA+Gl lv                                           ga+v 
  gi|118431932|ref|NP_148710.2| 17 LAAVGLGLVA------------------------------------------GAIVL 31
                                   2333333222..........................................22222 PP

  == domain 2  score: 133.4 bits;  conditional E-value: 4.5e-43
                   BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkvde 84 
                                    +l++++il+++Al++a+   ++G +n+g++g++  Ga +a++++  l+  +l al++a ++g+++gl+ gll ++l+++e
  gi|118431932|ref|NP_148710.2|  56 FLVRSSILVMTALAFAIPL-RMGFFNIGAEGQLYAGAAAALVAALTLPYTPLPALVAAAVAGGLMGLFAGLLRVKLNINE 134
                                    7999***************.******************999999999999****************************** PP

                   BPD_transp_2  85 liitllllsvlvgltlllltgitsgvkgqs.............svkellgfagallsflsaviv................ 135
                                    +++t++l++++++ + +++ ++  ++  +                               + +                 
  gi|118431932|ref|NP_148710.2| 135 VLSTIMLNWIAFWSLRYIVVEYLADPVYSHltlevplearipwI---------------PSELLppplqehlrsgfpmiv 199
                                    *********************99999977755555555544431...............222222444444455555556 PP

                   BPD_transp_2 136 llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp...nigvgl 212
                                    ++ l+ +la++ ++++t+ G++ r +g ne aa+  G+ v+rvkl++++ +g+lAgl Gall+l          +  +g+
  gi|118431932|ref|NP_148710.2| 200 FVSLATALAAWTVIYKTVPGLRYRFAGANEYAAASRGVAVGRVKLASMAAAGVLAGLGGALLILGHSYRIDstlSGLFGY 279
                                    **************************************************************99854433345677788* PP

                   BPD_transp_2 213 gfnaiaavvlGgagsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                    gf++i ++++G + ++lg+v+++l +g + s +++ +++    p ela+v+ ga+++ v
  gi|118431932|ref|NP_148710.2| 280 GFEGIGVALIGRN-NPLGIVAASLFVGDLAS-GSERIQVtariPAELADVVNGAIIFTV 336
                                    *************.*****************.999999989999***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2690.12
//
Query:       gi|14602163|ref|NP_148711.1|  [L=498]
Description: ABC transporter ATP-binding protein [Aeropyrum pernix K1]
Scores for complete 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-44  151.8   0.0    2.6e-30  105.7   0.0    2.2  2  ABC_tran     ABC transporter
      3e-06   27.3   0.0      0.015   15.1   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00048   19.8   0.0      0.044   13.5   0.0    2.4  2  AAA_29       P-loop containing region of AAA domain
      0.003   17.5   0.0      0.016   15.1   0.0    2.1  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.012   16.1   0.0      0.021   15.3   0.0    1.3  1  AAA_23       AAA domain
      0.035   14.4   0.1       0.92    9.8   0.1    2.8  1  AAA_22       AAA domain
      0.036   12.9   2.1       0.74    8.5   0.1    3.3  3  ABC_ATPase   Predicted ATPase of the ABC class
      0.087   13.2   0.1        0.5   10.7   0.0    2.3  3  AAA_16       AAA ATPase domain
       0.15   11.9   0.0       0.56   10.1   0.0    2.0  2  NACHT        NACHT domain
       0.18   11.8   0.1        0.4   10.7   0.1    1.5  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.19    9.2   0.1       0.26    8.8   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   1.6e-33   2.6e-30       1     137 []      29     175 ..      29     175 .. 0.97
   2 !   44.1   0.0   1.6e-14   2.7e-11       2     136 ..     279     428 ..     278     429 .. 0.84

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 1.6e-33
                                   EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                      ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                   l+nv+++l++ge++a++GenGaGK+tL+++l+g+ kpt+Gei + g++++   ++   r+ i+++ q+ +l + +tv+en 
  gi|14602163|ref|NP_148711.1|  29 LDNVDFTLRAGEVHALLGENGAGKTTLMRILYGEIKPTMGEIYVWGRKVSWrGPWDAIRNGIAMVYQQFRLVESMTVEENi 109
                                   79****************************************99999988779**************************** PP

                                   ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                   ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                               e++++  + +++lgl+ + +++v    + L  G +qrv++ +al   +k+l+lDEpt+
  gi|14602163|ref|NP_148711.1| 110 aiylsslglgrsEARRRTLETAERLGLEIDLAKTV----ADLPMGARQRVEIIKALSGGAKVLILDEPTS 175
                                   **********9999999999*******99999999....9****************************96 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 1.6e-14
                                   EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHHH. CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx. RF
                      ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvren. 79 
                                   ++vsl+++ege+v+i G  G G   L+ +++gl +p  G+i+++g+ ++  +l ++r+  g++  +  + l  +++v+en 
  gi|14602163|ref|NP_148711.1| 279 REVSLEVREGEIVGIAGVAGNGQEELVDAIIGLRRPVRGSIEVQGRRIEG-SLDFYRAGGGYIAGDrgKVLAMDYSVAENi 358
                                   689***********************************************.***************9999*********** PP

                                   ................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                   ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      ABC_tran  80 ................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     ++ + +++++++l+    +   +    LSgG +q+v +   +l+  kll++ +pt
  gi|14602163|ref|NP_148711.1| 359 aflyytasktlllrrsRLEDLFRRLVERFRLVA---RSPWTPVGRLSGGNQQKVIVGSEVLRGFKLLVAVNPT 428
                                   ***988777777443333333555555555555...2222334*****************9999999987776 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   0.0   9.4e-06     0.015       2      21 ..      42      61 ..      41      90 .. 0.89
   2 !    9.9   0.0   0.00037       0.6     252     297 ..     162     204 ..     143     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.4e-06
                        AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                   +l G Ng+GK++L+++l++
  gi|14602163|ref|NP_148711.1| 42 HALLGENGAGKTTLMRILYG 61
                                  689***************75 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00037
                        AAA_21 252 lralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + +++l++DEp ++L P   ++l+  l++l++ g+ v+  TH
  gi|14602163|ref|NP_148711.1| 162 S---GGAKVLILDEPTSNLTPLEAEKLFSTLRLLKDMGVSVVYITH 204
                                   3...3339********************999999999999999999 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.7e-05     0.044      13      39 ..      30      56 ..      27      62 .. 0.82
   2 ?    3.6   0.0     0.035        57      16      44 ..     282     310 ..     275     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                        AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                  d+ +++++  +++ l G++G+GK+Tl+
  gi|14602163|ref|NP_148711.1| 30 DNVDFTLRAGEVHALLGENGAGKTTLM 56
                                  566777775559*************98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.035
                        AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiqa 44 
                                   ++e+++ +++ ++G  G+G   l+DAi+ 
  gi|14602163|ref|NP_148711.1| 282 SLEVREGEIVGIAGVAGNGQEELVDAIIG 310
                                   45565444899***************975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.7e-06     0.016      88     130 ..      27      70 ..      13      75 .. 0.86
   2 ?   -1.8   0.0       1.6   2.6e+03      89     121 ..     277     310 ..     264     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.7e-06
                                   TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                   RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                   ++l+++   l+  ++ +l+G+ G+GK+tL+  l +e +  +ge+
  gi|14602163|ref|NP_148711.1|  27 KALDNVDFTLRAgEVHALLGENGAGKTTLMRILYGEIKPTMGEI 70 
                                   5678888889888**********************999888887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                   THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                   RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    ++e++ ++++ +++ ++G  G G   L++a+++
  gi|14602163|ref|NP_148711.1| 277 RVREVSLEVREgEIVGIAGVAGNGQEELVDAIIG 310
                                   5556665666659999999999999999999876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.3e-05     0.021       7      37 ..      26      57 ..      20      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                        AAA_23  7 frsfrdqeidF.skgltlItGpNGaGKTTild 37
                                  ++ ++++++ +    + ++ G+NGaGKTT+++
  gi|14602163|ref|NP_148711.1| 26 VKALDNVDFTLrAGEVHALLGENGAGKTTLMR 57
                                  566666667774346889************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00056      0.92       9      38 ..      43      88 ..      37     209 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00056
                        AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee....................e 38
                                  ++ Ge G+GKTtl+r l  + +    +++                    +
  gi|14602163|ref|NP_148711.1| 43 ALLGENGAGKTTLMRILYGEIK----PTMgeiyvwgrkvswrgpwdairN 88
                                  688***********98877752....112223344444444444444431 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 ?   -0.9   0.1      0.33   5.4e+02     243     264 ..      37      59 ..      34      63 .. 0.83
   2 ?    8.5   0.1   0.00046      0.74     364     425 ..     176     233 ..     150     243 .. 0.69
   3 ?    0.3   0.0      0.15   2.4e+02     374     423 ..     436     485 ..     432     493 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.33
                                   -SS.EEEEEE-TTSSHHHHHHHH CS
                    ABC_ATPase 243 pkG.vtlIvGggfhGKsTLLeAl 264
                                   + G v ++ G +  GK+TL++ l
  gi|14602163|ref|NP_148711.1|  37 RAGeVHALLGENGAGKTTLMRIL 59 
                                   667789999**********9865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00046
                                   HHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE-HHHHHH CS
                    ABC_ATPase 364 elvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdvtekake 425
                                   +l++ e+e    l + +r l k++gvs++ ++  +g+ ++vAd+v +++  ++++v e + +
  gi|14602163|ref|NP_148711.1| 176 NLTPLEAEK---LFSTLR-LLKDMGVSVVYITHKLGEVVRVADRVTVLRRGRVSAVIEDVGR 233
                                   344444433...333444.44888***********************999888888766555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                                   --HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEETTEEEE-HHHH CS
                    ABC_ATPase 374 tplvdrvrelykklgvstilvvggsgdyldvAdtvilmeeykpkdvteka 423
                                   t++v  + +  ++ g  ++lv+  +++ l+++d++ +m   +++ v e+ 
  gi|14602163|ref|NP_148711.1| 436 TSFVRNLLSELARQGAGILLVSTDLDEILELSDRIYVMSGGRVTGVLERS 485
                                   788888888889999***********************987777766665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00031       0.5      25      59 ..      40      75 ..      27     195 .. 0.67
   2 ?   -3.8   0.0         9   1.5e+04     137     153 ..     268     284 ..     262     287 .. 0.82
   3 ?   -1.1   0.0       1.3   2.2e+03      38      49 ..     436     447 ..     356     469 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                        AAA_16 25 elvllsGesGvGKsslvrellralekd.......ggiflrgk 59
                                  e+  l Ge G GK++l+r l+ +++ +       g      +
  gi|14602163|ref|NP_148711.1| 40 EVHALLGENGAGKTTLMRILYGEIKPTmgeiyvwG------R 75
                                  556799**************999999964333331......3 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9
                        AAA_16 137 lvlvlDdlqwadeaslq 153
                                   + +v+D +++++e sl+
  gi|14602163|ref|NP_148711.1| 268 VSVVVDGVERVREVSLE 284
                                   66899999999999987 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                        AAA_16  38 sslvrellrale 49 
                                   +s vr ll +l 
  gi|14602163|ref|NP_148711.1| 436 TSFVRNLLSELA 447
                                   223333333333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00034      0.56       3      21 ..      42      60 ..      40      66 .. 0.83
   2 ?   -3.2   0.0       4.2   6.8e+03     118     136 ..     416     434 ..     412     455 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00034
                                  EEEEC-TTTCHHHHHHHHH CS
                         NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   +l Ge+G GKTtL++ l 
  gi|14602163|ref|NP_148711.1| 42 HALLGENGAGKTTLMRILY 60
                                  5799***********9775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                                   TT--EEEEEEECCCHHHHC CS
                         NACHT 118 lpeasllltvrpralrdle 136
                                   l++ +ll++v p++  d++
  gi|14602163|ref|NP_148711.1| 416 LRGFKLLVAVNPTQGLDIA 434
                                   5666677777777665543 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00024       0.4      19      41 ..      39      61 ..      25      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                  TEEEEEEESTTSSHHHHHHHHHH CS
                          TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                  g+v +L G+ GaGKTtl+r l  
  gi|14602163|ref|NP_148711.1| 39 GEVHALLGENGAGKTTLMRILYG 61
                                  77899**************8865 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00016      0.26      22      37 ..      44      59 ..      35      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00016
                       DUF3584 22 ieGtNaaGKTtLlrLi 37
                                  + G N+aGKTtL+r++
  gi|14602163|ref|NP_148711.1| 44 LLGENGAGKTTLMRIL 59
                                  679***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 3628.43
//
Query:       gi|118431933|ref|NP_148712.2|  [L=447]
Description: membrane lipoprotein family protein [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-50  171.1   0.0    3.6e-50  170.7   0.0    1.3  1  Bmp              ABC transporter substrate-binding protein Pn
  ------ inclusion threshold ------
       0.12   12.2   0.1        8.2    6.3   0.0    3.0  3  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


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 !  170.7   0.0     4e-54   3.6e-50       1     280 [.      78     369 ..      78     420 .. 0.90

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 4e-54
                                    -EEEEEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC.GGGHHHHHHHHHHCTT.-SEEEEESCCHHHHHHHHH CS
                            Bmp   1 ivkvavlvegtidDksfnessyeGirrlkkeqnieliskesslltdedyiadlknlkeeg.sdlivatgfalqdalqevs 79 
                                    i++++++++g + D sfn ++  G  r+++e ++++++++ ++   + ++++l+++ + g +dliv++gf  q+ l++v+
  gi|118431933|ref|NP_148712.2|  78 ISVLVLFDVGGRGDLSFNDMAALGADRAAEELGVDVVFQTPQS--LAVMESVLDAASRSGeYDLIVLVGFLWQEPLEKVA 155
                                    57899***********************************999..6999999999877644******************* PP

                                    HH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHH........CTTTTEECSS-SCCCHHCHHHHHHHHH CS
                            Bmp  80 sdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsk........tnkigfvgGveipvvksfingFeaGik 151
                                     ++p++k++ iDa   ++y+nv+s+ Fr++e a L+G++aA +++        ++k g+v+G+ ip + +f +g+  G++
  gi|118431933|ref|NP_148712.2| 156 PRYPEQKYALIDAATRERYDNVASYLFREQEVASLVGIIAADIANniskatgeEAKAGAVAGMDIPPLWRFHIGYLYGVQ 235
                                    *****************************************88763333333368899999******************* PP

                                    HH-TT-EEEEE....E-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCT...EEEEEES--CGCST CS
                            Bmp 152 yvnpdievvvk....vagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsn...yvIgvdkdqsylap 224
                                    y n+++ ++v+    ++g f+D+++gk++A+++ ++gv v +++ag++  g ++a+ke        ++Ig d +q    p
  gi|118431933|ref|NP_148712.2| 236 YYNQAMGTDVEmvwtYTGRFDDPTLGKTTAEQMLQQGVRVFYGVAGLTHVGMFNAVKEAAARGviaFSIGQDASQEWYDP 315
                                    ***86655543222299****************************************987777777************** PP

                                    TCCEEEEEEEHHHHHHHHHHHHHCCT---TTEEEEE-CCCTSEEE-S--TCCHHHH CS
                            Bmp 225 envitsiiknvedlvvsiiekvakgevlaggevitlglkegvvgldeesdvledek 280
                                    +++i s  k v+ +v+ +i+ v++g+    g+++ lglkeg++gl++e+ + +++ 
  gi|118431933|ref|NP_148712.2| 316 QTIIISGLKRVDVAVYTAIKDVVEGR--FRGGIVSLGLKEGGLGLSDEEIIRYFAE 369
                                    **************************..5667889***********7766666655 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 ?    1.9   0.0     0.022     2e+02      10      23 ..     261     274 ..     260     279 .. 0.92
   2 ?   -1.8   0.0      0.33     3e+03       9      19 ..     304     314 ..     302     315 .. 0.87
   3 ?    6.3   0.0   0.00091       8.2      15      31 ..     395     412 ..     385     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.022
                DNA_pol_lambd_f  10 GpktAkkwyakGir 23 
                                    G +tA++  ++G+r
  gi|118431933|ref|NP_148712.2| 261 GKTTAEQMLQQGVR 274
                                    899*********99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                DNA_pol_lambd_f   9 VGpktAkkwya 19 
                                    +G+ + ++wy+
  gi|118431933|ref|NP_148712.2| 304 IGQDASQEWYD 314
                                    89999*****7 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.00091
                DNA_pol_lambd_f  15 kkwyak.Girtledlrak 31 
                                    +kw+++ G+r +e+l++k
  gi|118431933|ref|NP_148712.2| 395 EKWISNdGWRLVEELKQK 412
                                    79**888*********93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3199.01
//
Query:       gi|118431934|ref|YP_874950.1|  [L=65]
Description: hypothetical protein APE_2592a [Aeropyrum pernix K1]
Scores for 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   26.2   0.0      6e-06   26.0   0.0    1.1  1  TusA            Sulfurtransferase TusA
  ------ inclusion threshold ------
       0.11   11.2   0.0       0.11   11.2   0.0    1.0  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


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 !   26.0   0.0   6.7e-10     6e-06      22      69 ..      12      60 ..       6      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.7e-10
                                   CCC.GCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEE CS
                           TusA 22 ekl.eegevlevladdpaatediprfakklghelveveeedgeyrivir 69
                                   ++l ++gev ev++ dp++   ++r a+ +g+e++e   +dge ++++r
  gi|118431934|ref|YP_874950.1| 12 AQLaRPGEVYEVVMRDPDTWLAVQRIAEDMGFEVLEAGRRDGEKVYYVR 60
                                   56669**********************************9998888887 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.3e-05      0.11     276     315 ..      23      62 ..       4      65 .] 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.3e-05
                                    EEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHH CS
                 Oxidored_nitro 276 aiygdpdrvvalarllkelGmevvaagtetahrddeerlk 315
                                    +++ dpd+ +a++r+ +++G+ev  ag +++++ ++ r++
  gi|118431934|ref|YP_874950.1|  23 VVMRDPDTWLAVQRIAEDMGFEVLEAGRRDGEKVYYVRIR 62 
                                    6899***********************9999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 526.98
//
Query:       gi|118431935|ref|NP_148714.2|  [L=289]
Description: thiosulfate sulfurtransferase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-42  144.2   0.0    1.9e-22   79.8   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 !   62.5   0.0   2.5e-21   4.5e-17       2     105 ..      12     120 ..      11     122 .. 0.84
   2 !   79.8   0.0     1e-26   1.9e-22       6     105 ..     160     276 ..     157     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.5e-21
                      Rhodanese   2 akelkellekgkvallDvR..ppeeYekghIpgAvnv.skdtlsrakkseapllelpeellel.gidnkktvvvycdggg 77 
                                     ++l++++++ +v+++ v   p+ +Y  ghIpgA+ +  k+ l++  +++  + e +e+l+++ g+ n+++v++y+d ++
  gi|118431935|ref|NP_148714.2|  12 IEWLEANIKRSDVKVIEVDydPATAYFIGHIPGALLIdWKRDLNKYPERDIIDPEGFERLMSRlGVENGDHVILYGDYNN 91 
                                    68*********99977666448888************55555666666666666777777777***************** PP

                      Rhodanese  78 r.aaaaaallkklGyknvsvldGGfkawk 105
                                      aa+a++ +k +G+++vs+ldGG ++w 
  gi|118431935|ref|NP_148714.2|  92 WfAAFAYWVFKMYGHQRVSLLDGGRSKWI 120
                                    *99999********666***********7 PP

  == domain 2  score: 79.8 bits;  conditional E-value: 1e-26
                      Rhodanese   6 kellekgkvallDvRppeeY...............ek.ghIpgAvnvskdtlsrakkseapllelpeellelgidnkktv 69 
                                     + l++++++l+DvR+peeY               ++ ghIpgA+n++++ + r + s ++  el   ++++g++++k+v
  gi|118431935|ref|NP_148714.2| 160 LRKLNDPNTVLVDVRSPEEYrgditappeypeeqaQRgGHIPGALNIPWKQAVRDDGSFKSPEELRSLYEDRGVTPDKEV 239
                                    577899**99**********9999999999****9555*********7777666666666666666666666******** PP

                      Rhodanese  70 vvycdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                    +vyc+ g+ra+ ++  lk+ lGy+nv v+dG++++w 
  gi|118431935|ref|NP_148714.2| 240 IVYCRIGERASHTWFVLKElLGYPNVAVYDGSWSEWG 276
                                    *********88889999978****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 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:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2393.89
//
Query:       gi|14602168|ref|NP_148716.1|  [L=610]
Description: hypothetical protein APE_2598 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-17   63.0   0.0    4.1e-17   63.0   0.0    2.2  3  Radical_SAM      Radical SAM superfamily
      2e-07   31.1   0.4    5.3e-07   29.8   0.0    1.9  2  Fer4_14          4Fe-4S single cluster domain
    0.00054   20.3   0.0     0.0012   19.1   0.0    1.6  1  Fer4_12          4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.058   13.5   0.3       0.17   11.9   0.1    1.9  2  Leucyl-specific  Leucine-tRNA synthetase-specific 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 ?   -4.9   0.8         4   1.8e+04       7      18 ..     127     138 ..     123     140 .. 0.85
   2 !   63.0   0.0   9.2e-21   4.1e-17       1     166 [.     146     315 ..     146     316 .. 0.92
   3 ?   -2.0   0.0      0.91   4.1e+03      74      99 ..     536     582 ..     487     585 .. 0.49

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 4
                                   ESS--TTTSCCT CS
                                   xxxxxxxxxxxx RF
                   Radical_SAM   7 CnlrCsfCarpe 18 
                                   C+++C  C+ +e
  gi|14602168|ref|NP_148716.1| 127 CPYACGLCSLHE 138
                                   ********9886 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 9.2e-21
                                   EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT...SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg...vkevilgggepllypdfvellerlaklavpg 77 
                                   +vvt+ C l C +C ++   +r g+ ++ s+e+i+  v++++ +++g     ++ ++ggep+++ d+v+ ++++++     
  gi|14602168|ref|NP_148716.1| 146 IVVTNRCDLSCFYCFFYA--ERAGYIYEPSIEQIKFMVRQVArQRQGsdvHVNIQITGGEPTVREDLVDVVKAIREA--GA 222
                                   689**************9..5********************9999986433467889**********9999999999..8* PP

                                   EEEEEEECSSCHG..........HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEE CS
                                   xxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Radical_SAM  78 iritvetngtlpd..........eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdr 148
                                     i + tng+ +            ++++ l+e+gv +v+++ + ++++ v  ++   h    +  al+++ e g+++vv +
  gi|14602168|ref|NP_148716.1| 223 HYIQLNTNGINVArryldnppgaIDYVRSLREAGVSVVYMSFDGVTPK-VNWKN---HYEAPF--ALKAFQEGGLDNVVLV 297
                                   ************************************************.66666...555555..999999********** PP

                                   EEEBTTTSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                   Radical_SAM 149 ivglpGendeeleellel 166
                                    ++++  nd+e+ +++++
  gi|14602168|ref|NP_148716.1| 298 PTVIRTINDHEVGDIIRF 315
                                   **************9998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.91
                                   C....................CCTEEEEEEECSSCHG.HHHHHHHHH CS
                                   x....................xxxxxxxxxxxxxxxx.xxxxxxxxx RF
                   Radical_SAM  74 a....................vpgiritvetngtlpd.eeklerlle 99 
                                                         +++ri    +g + d +++++r+le
  gi|14602168|ref|NP_148716.1| 536 FcafnvlediyrdnvqkrfakAKNLRIKGFNPGEKYDrRRYIKRILE 582
                                   04444444444444444444444566666666666666666666655 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 ?   -3.0   0.3       1.7   7.6e+03       5      17 ..     124     136 ..     122     142 .. 0.77
   2 !   29.8   0.0   1.2e-10   5.3e-07       4      90 ..     148     232 ..     146     242 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.7
                       Fer4_14   5 lsgCnlsCkgCdn 17 
                                   ++ C+ +C  C  
  gi|14602168|ref|NP_148716.1| 124 TAPCPYACGLCSL 136
                                   678********74 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.2e-10
                       Fer4_14   4 rlsgCnlsCkgCd...nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                    +++C lsC  C+   +++ +  e   +q + ++ q+ ++ + s+++ + + +tGGeP      ++l+++vk ++e +  +
  gi|14602168|ref|NP_148716.1| 148 VTNRCDLSCFYCFfyaERAGYIYEPSIEQIKFMVRQVARQRQGSDVHVN-IQITGGEPTV---REDLVDVVKAIREAG-AH 223
                                   49***********543333333333334444455555558888888888.********94...599************.99 PP

                       Fer4_14  82 kiwletngt 90 
                                    i+l+tng 
  gi|14602168|ref|NP_148716.1| 224 YIQLNTNGI 232
                                   9******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 !   19.1   0.0   2.7e-07    0.0012       8      93 ..     145     231 ..     138     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-07
                       Fer4_12   8 lslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi.....egltllGGEPllpenaeallelvkevkeek 83 
                                    ++ +++C+lsC +Cf  + +     ++   e ++ ++++++ +++       + ++GGEP +   +e+l+++vk ++e++
  gi|14602168|ref|NP_148716.1| 145 NIVVTNRCDLSCFYCFFYAERAGYIYEPS-IEQIKFMVRQVARQRQgsdvhVNIQITGGEPTV---REDLVDVVKAIREAG 221
                                   5677899*********5555544444443.33333333444332223444599**********...9***********999 PP

                       Fer4_12  84 pekdiwlytg 93 
                                    +   + ++g
  gi|14602168|ref|NP_148716.1| 222 AHYIQLNTNG 231
                                   8666666666 PP

>> Leucyl-specific  Leucine-tRNA synthetase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.3     1e+04       7      28 ..     331     351 ..     327     357 .. 0.67
   2 ?   11.9   0.1   3.9e-05      0.17       7      36 ..     426     454 ..     423     458 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
               Leucyl-specific   7 VeVeGeivrLseeaRirLelee 28 
                                   V   G  +r  e  R+r+ +++
  gi|14602168|ref|NP_148716.1| 331 VSLTGM-MRKHERERMRITIPD 351
                                   555554.455677888888775 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.9e-05
               Leucyl-specific   7 VeVeGeivrLseeaRirLeleeseLsleev 36 
                                   ++VeG i +L+ee Ri+Le +++ Ls+  v
  gi|14602168|ref|NP_148716.1| 426 IDVEGFIEFLDEE-RIKLEHNSGRLSRLKV 454
                                   689*******976.9**********98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.36
# Mc/sec: 5020.16
//
Query:       gi|118431936|ref|YP_874951.1|  [L=80]
Description: hypothetical protein APE_2598a [Aeropyrum pernix K1]
Scores for complete sequence (score 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   11.9   0.2        8.8    5.9   0.1    2.1  2  MbtH      MbtH-like protein


Domain annotation for each model (and alignments):
>> MbtH  MbtH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1   0.00049       8.8      28      46 ..      28      46 ..      23      54 .. 0.80
   2 ?    4.6   0.0    0.0012        22       5      18 ..      54      67 ..      50      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00049
                                   TS---TTEEEEEEEEEHHH CS
                           MbtH 28 faavPaGWrvvggpgsree 46
                                   +++ P GW  v+ +g   e
  gi|118431936|ref|YP_874951.1| 28 ECDNPRGWYRVVAEGVDGE 46
                                   6899****99999885555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0012
                                   GG-SSSEEEEEEET CS
                           MbtH  5 fddedgtflVLvNd 18
                                   ++d + +fl++vN 
  gi|118431936|ref|YP_874951.1| 54 EEDAARRFLAVVNS 67
                                   68999********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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: 0.32u 0.19s 00:00:00.51 Elapsed: 00:00:00.32
# Mc/sec: 736.97
//
Query:       gi|118431937|ref|NP_148717.2|  [L=270]
Description: NG,NG-dimethylarginine dimethylaminohydrolase [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-21   75.3   0.0    8.6e-11   41.5   0.0    2.7  2  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   4.8e-15   8.6e-11     109     206 ..      65     156 ..      13     167 .. 0.89
   2 !   30.7   0.0   9.1e-12   1.6e-07     267     339 ..     197     267 ..     187     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.8e-15
                                    E---GGGG-TTTTEEE..EBSEEEE---SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-T.TS--TT----GGGEEEEETT CS
                  Amidinotransf 109 ipplpnlvFtrdwfst..igggvvlnpmaapnRrrErllaeliykkhpgvkvakvldis.gkeeesktlEGGdfvvlskg 185
                                    ++++p++vF  d+ +    ++ +vl ++ ap Rr E+ +   i+           ++++ +  ++++tlEGGd++v ++g
  gi|118431937|ref|NP_148717.2|  65 LEDYPDSVFIQDTAVIggGSRVAVLARFGAPSRRGEEGHVVSILSS---------MGLEiHPVKPPGTLEGGDVLVTGEG 135
                                    6899************86666789********************99.........4444446789*************** PP

                                    EEEEEESSSS-HHHHHHHHHH CS
                  Amidinotransf 186 vvaigvssRtdeegieelakk 206
                                    vv  g ssRt++eg+e l  +
  gi|118431937|ref|NP_148717.2| 136 VVFAGLSSRTNREGVETLKTA 156
                                    ****************98765 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 9.1e-12
                                    T-SS-EEEE-CS-SS-B---S-EEEETTEEEEETTGHHHHHHHHHTT-EEEEE-HTTTGGGS--TTTT-EEEE CS
                  Amidinotransf 267 kekgleiIeigeeeqwnfggNvLelkpgvvvaydrntvtnekleeagievievpiselerGgGgarCmsaplf 339
                                    k  g+++Iei+ ee   ++ N L l++g+v+  +  ++t  +le++g++++e +i++   ++Gg+ C s p++
  gi|118431937|ref|NP_148717.2| 197 KRHGFDLIEIPWEE--RDAANLLYLGEGRVLLPAGYNQTRDLLEQHGFRIVEAEIRQFMACMGGVTCLSLPIY 267
                                    6789*******999..9******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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 0.20s 00:00:00.62 Elapsed: 00:00:00.34
# Mc/sec: 2405.23
//
Query:       gi|14602170|ref|NP_148718.1|  [L=184]
Description: hypothetical protein APE_2602 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1457.13
//
Query:       gi|118431938|ref|NP_148719.2|  [L=513]
Description: acetyl-coenzyme A synthetase [Aeropyrum pernix K1]
Scores for complete 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-69  233.2   0.0    5.1e-69  232.9   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      2e-29  102.4   0.4    5.1e-29  101.1   0.4    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.11   12.5   0.0        1.1    9.3   0.0    2.5  3  TFX_C          DNA_binding protein, TFX, C-term


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 !  232.9   0.0   8.5e-73   5.1e-69      64     422 ..       1     386 [.       1     387 [. 0.84

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 8.5e-73
                                    HHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHH.SCC-EECEEEEESCCS-H CS
                    AMP-binding  64 llailkaGavvvplnptltaeelayiledseakvli.........atvdsel.leklleaa.akleavklvivldadell 132
                                    +la+ ++Ga+++++ +++++ +la  + d++a vli         + vd ++ ++++ + a ++  +v++viv+ +++ +
  gi|118431938|ref|NP_148719.2|   1 MLAVTRIGAIHSVVFSGFSSWALADRIVDAKADVLItadgfyrrgRIVDLKKnADEAVKLAaDNGVKVRKVIVVRRAG-N 79 
                                    79************************************9999876233444444444444404445566666666555.5 PP

                                    CCHCCCHCCCCSCTTS.......-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EE CS
                    AMP-binding 133 keeelkeeeeseekae.......kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvv 205
                                    + +++ e + ++++           +++e+ k+dd+++i+YTSGTTGkPKG+m+s + +++ v+++  +  ++ +++dv+
  gi|118431938|ref|NP_148719.2|  80 EVRWSSELNVWYHDLLkevpekvY-VKPEPRKSDDVLFILYTSGTTGKPKGIMHSVGGYMTYVYNVF-RWNWDPRPEDVF 157
                                    555666666666555256778852.466789*************************99999999985.32355568**** PP

                                    EESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT CS
                    AMP-binding 206 lsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlss 284
                                    ++ +++ +i+g+++ ++++l++G t +++++ ++ ++p++++e++e+++vtv+++ P++l+ l + g++   ++ +d+s+
  gi|118431938|ref|NP_148719.2| 158 WTAADIGWITGHTYIVYGPLMHGETQIMYEGAPDyPNPGRIWEMVERYGVTVFYTSPTLLRLLRKYGDEW--VEGRDFSR 235
                                    **********************************777**************************9976554..7889**** PP

                                    -SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE.....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTS CS
                    AMP-binding 285 lrlvllggeplspellrffralfge...evlegYGlTEttgvvtv.....lpleedkkklgsvGkplpgvevkivDeetg 356
                                    lrl+ ++gep++pe++++++++ g    ++++++++TEt+++++      +       k+gs+  plpg+ + ++  + g
  gi|118431938|ref|NP_148719.2| 236 LRLLGTVGEPINPEVWKWYYEKIGWkraPIVDTWWQTETGAAMISpapgiAL-VP--LKPGSATLPLPGIVADVLTSD-G 311
                                    **********************998999***************766766322.23..3699***************99.9 PP

                                    CBEETTSEEEEEEEET..TS-SEBTT-HHHHHHHEEE......TCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 357 epvpdgeeGellvrgp..gvmkgYlkkpeataeafds......egr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                    +  ++ge+G l+vr p  g+m g +++p++  ++++s      eg   +   D +++d+dGy++i+gR+++++++
  gi|118431938|ref|NP_148719.2| 312 RQAGPGEKGYLVVREPwpGMMLGIWGDPDRYVRTYWSrfskpeEGVwIYYPADYAVRDRDGYFWILGRADEVLNV 386
                                    9999***********9778****************988888743445799*********************9987 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 !  101.1   0.4   8.6e-33   5.1e-29       1      76 []     395     473 ..     395     473 .. 0.95

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 8.6e-33
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+E al++hpaV+eaaVvG pd+vkGe++vafVvl++g+e+   le+eL++ vr+ +gp+a p+k++fv++lpktrsGK
  gi|118431938|ref|NP_148719.2| 395 ELEDALLTHPAVSEAAVVGAPDPVKGEVPVAFVVLRAGYEPsdkLERELRETVRRLIGPIAEPSKIYFVEKLPKTRSGK 473
                                    89*********************************999533457**********************************9 PP

>> TFX_C  DNA_binding protein, TFX, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.25   1.5e+03      62      79 ..      23      40 ..      19      43 .. 0.87
   2 ?   -2.9   0.1       1.1   6.8e+03      34      44 ..      59      69 ..      49      71 .. 0.72
   3 ?    9.3   0.0   0.00019       1.1      29      65 ..     195     231 ..     186     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.25
                                   -----SSS-EEEEESSSS CS
                          TFX_C 62 ikgrvvkedlevyitedG 79
                                   + +r v+ + +v it dG
  gi|118431938|ref|NP_148719.2| 23 LADRIVDAKADVLITADG 40
                                   67999***********99 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                                   HHHHHHS-S-- CS
                          TFX_C 34 aeadkagikvk 44
                                   + a ++g+kv+
  gi|118431938|ref|NP_148719.2| 59 KLAADNGVKVR 69
                                   56788999997 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00019
                                    HHHHHHHHHHHS-S----HHHHHHHHHHH-SSS---- CS
                          TFX_C  29 pkiiyaeadkagikvkydtieLikllreeapeaikgr 65 
                                    p +i +  ++ g++v y++++L++llr+  +e ++gr
  gi|118431938|ref|NP_148719.2| 195 PGRIWEMVERYGVTVFYTSPTLLRLLRKYGDEWVEGR 231
                                    88999999*********************99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3750.86
//
Query:       gi|118431939|ref|YP_874952.1|  [L=140]
Description: acetyl-coenzyme A synthetase, partial [Aeropyrum pernix K1]
Scores for 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-20   70.6   0.2    1.4e-19   69.8   0.2    1.4  1  ACAS_N       Acetyl-coenzyme A synthetase N-terminus
    3.1e-11   42.5   0.0    4.1e-11   42.1   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> 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 !   69.8   0.2   1.5e-23   1.4e-19       4      55 .]      22      73 ..      19      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 1.5e-23
                                   HHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  4 lykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                    y++Sied e+FW+e a+el W kp+++vld  k+pf++WF+GG++Ni  N+
  gi|118431939|ref|YP_874952.1| 22 YYRKSIEDIERFWDERARELVWLKPWHQVLDRGKAPFYRWFVGGETNINLNA 73
                                   69**********************************************9886 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   4.6e-15   4.1e-11       9      62 ..      83     140 .]      75     140 .] 0.90

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.6e-15
                                    TTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHH CS
                    AMP-binding   9 pdkvalvd...sgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvv 62 
                                     +kva+++    g+ + l+Y++l+++vnrlA +L+  +Gvk+gdrVai+lp+ pe+ +
  gi|118431939|ref|YP_874952.1|  83 ENKVAYYWegePGDRRVLSYGDLYREVNRLAYALKeYIGVKPGDRVAIYLPMIPELPI 140
                                    5899998899988999*******************879*****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 1070.53
//
Query:       gi|118431940|ref|NP_148720.2|  [L=233]
Description: molybdopterin oxidoreductase, iron-sulfur binding subunit [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-27   94.3  10.1    3.8e-27   94.3  10.1    2.6  3  Fer4_11   4Fe-4S dicluster domain
    1.8e-14   54.0  33.0    1.9e-07   31.5   9.7    3.6  3  Fer4_7    4Fe-4S dicluster domain
    1.9e-13   50.4  44.4    4.8e-06   26.6   8.2    3.5  4  Fer4_9    4Fe-4S dicluster domain
    6.9e-13   48.1  39.7    4.3e-07   29.7   2.9    5.0  5  Fer4_6    4Fe-4S binding domain
    2.3e-12   46.8  50.1    1.6e-07   31.3   8.3    3.8  4  Fer4_10   4Fe-4S dicluster domain
    2.1e-11   43.1  50.6    3.4e-08   33.0   3.0    6.1  5  Fer4      4Fe-4S binding domain
    2.4e-09   36.7  43.5    1.3e-05   25.0   1.6    5.3  5  Fer4_2    4Fe-4S binding domain
    9.6e-09   35.6  48.9     0.0033   18.3   5.5    4.8  5  Fer4_3    4Fe-4S binding domain
    4.8e-05   23.4  18.8    0.00058   19.9   8.7    3.8  4  Fer4_21   4Fe-4S dicluster domain
    5.2e-05   23.7  23.2       0.68   10.5   2.1    4.5  3  Fer4_17   4Fe-4S dicluster domain
    0.00024   21.8  17.8     0.0065   17.2   2.7    4.2  4  Fer4_15   4Fe-4S single cluster domain
    0.00078   20.3  31.3       0.55   11.2   5.0    4.7  4  Fer4_16   4Fe-4S double cluster binding domain
     0.0039   17.6  33.3      0.086   13.3  10.2    4.4  3  Fer4_8    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   16.1  13.5      0.027   15.0   2.6    5.0  5  Fer4_4    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.69   8.8e+02      68      87 ..       6      25 ..       2      38 .. 0.68
   2 ?   -0.8   0.4       1.3   1.6e+03      68      78 ..      60      70 ..      54      82 .. 0.63
   3 !   94.3  10.1     3e-30   3.8e-27       4      99 ..      99     192 ..      97     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.69
                        Fer4_11 68 vekCdmcldrveaGllpacv 87
                                   +++C  c  r e  +++a  
  gi|118431940|ref|NP_148720.2|  6 STACSTCNTRREFLKKTAKA 25
                                   57899999998866665554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                        Fer4_11 68 vekCdmcldrv 78
                                   v kC +c++ v
  gi|118431940|ref|NP_148720.2| 60 VDKCYGCYACV 70
                                   45666666544 PP

  == domain 3  score: 94.3 bits;  conditional E-value: 3e-30
                        Fer4_11   4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGll 83 
                                    +++p+qC+hC +p+Cv+++p++a + +e +G+Vl+d++ +  ++ ++++ cPy + ++n  +g++ kC++c++r+ + +l
  gi|118431940|ref|NP_148720.2|  99 VYVPKQCNHCDNPSCVDVCPVKATYVNE-DGIVLVDDDLCI-GCGACIQNCPYGARFYNPIKGVADKCTFCVHRIYSDML 176
                                    69***********************998.***********7.************************************** PP

                        Fer4_11  84 pacvescptgalnfgd 99 
                                    pacve+cptga+ fg+
  gi|118431940|ref|NP_148720.2| 177 PACVEACPTGARVFGE 192
                                    **************97 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   7.8   0.00047       0.6      27      49 ..      52      74 ..       6      77 .. 0.69
   2 !   29.2  12.0   8.2e-10   1.1e-06       1      52 []      62     121 ..      62     121 .. 0.93
   3 !   31.5   9.7   1.5e-10   1.9e-07       2      52 .]     137     187 ..     136     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                         Fer4_7 27 gtekveidpekClgCgaCvavCP 49
                                   ++  + id +kC+gC+aCv +C 
  gi|118431940|ref|NP_148720.2| 52 RRFAMFIDVDKCYGCYACVVACA 74
                                   33567899**************6 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 8.2e-10
                         Fer4_7   1 rCigCgaCvaaC......pvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                    +C gC aCv+aC      p ++ +++ e + k+  +++++p +C +C++  Cv+vCP++a
  gi|118431940|ref|NP_148720.2|  62 KCYGCYACVVACahennvPIGVYRTWIERYVKEDGTPVYVPKQCNHCDNpsCVDVCPVKA 121
                                    7***********99999889999999888999999*************999******987 PP

  == domain 3  score: 31.5 bits;  conditional E-value: 1.5e-10
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgC.........gaCvavCPtga 52 
                                    CigCgaC ++Cp++a+ +++         ++++++kC++C          aCv++CPtga
  gi|118431940|ref|NP_148720.2| 137 CIGCGACIQNCPYGARFYNP---------IKGVADKCTFCvhriysdmlPACVEACPTGA 187
                                    ******************99.........5789*******77777776669*******98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.9   2.4e+03      35      39 ..       8      12 ..       3      16 .. 0.60
   2 !   26.6   8.2   3.8e-09   4.8e-06       1      50 [.      62     121 ..      62     122 .. 0.95
   3 !   24.4  12.3   1.9e-08   2.4e-05       1      50 [.     104     151 ..     104     152 .. 0.89
   4 !   25.3   7.9   9.5e-09   1.2e-05       2      50 ..     137     187 ..     136     188 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                         Fer4_9 35 aCigC 39
                                   aC +C
  gi|118431940|ref|NP_148720.2|  8 ACSTC 12
                                   34334 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.8e-09
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga..CveaCpkga 50 
                                    kC+gC aCv aC ++ +v+  + r++  r  +e        ++C +C    Cv++Cp +a
  gi|118431940|ref|NP_148720.2|  62 KCYGCYACVVACAHENNVPIGVYRTWIERYVKEdgtpvyvpKQCNHCDNpsCVDVCPVKA 121
                                    7**************************9999999**************999******875 PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.9e-08
                         Fer4_9   1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    +C+ C++  Cv++Cp +++   + +     +      CigCgaC++ Cp ga
  gi|118431940|ref|NP_148720.2| 104 QCNHCDNpsCVDVCPVKATYVNEDGIVLVDDD----LCIGCGACIQNCPYGA 151
                                    6****9778*********99999988888755....6************985 PP

  == domain 4  score: 25.3 bits;  conditional E-value: 9.5e-09
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaCpkga 50 
                                    C+gCgaC++ Cp+g+  +   ++ a        +C++C           CveaCp+ga
  gi|118431940|ref|NP_148720.2| 137 CIGCGACIQNCPYGARFYNPIKGVAD-------KCTFCVHriysdmlpaCVEACPTGA 187
                                    *******************9999999.......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 !   16.9   3.7   3.7e-06    0.0047       3      21 ..      57      75 ..      55      79 .. 0.89
   2 !   14.0   4.6   3.2e-05     0.041       2      23 ..      98     121 ..      97     122 .. 0.87
   3 !   29.7   2.9   3.3e-10   4.3e-07       1      23 [.     129     151 ..     129     151 .. 0.94
   4 ?   -1.6   0.2       2.6   3.4e+03      11      16 ..     163     168 ..     161     169 .. 0.68
   5 !    8.3   1.0     0.002       2.6      14      23 ..     178     187 ..     176     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                         Fer4_6  3 eidpdkCigCgdCvrvCPe 21
                                    id dkC gC++Cv++C +
  gi|118431940|ref|NP_148720.2| 57 FIDVDKCYGCYACVVACAH 75
                                   69***************86 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.2e-05
                         Fer4_6   2 veidpdkCigCgd..CvrvCPega 23 
                                    +++ p  C++C++  Cv+vCP +a
  gi|118431940|ref|NP_148720.2|  98 PVYVPKQCNHCDNpsCVDVCPVKA 121
                                    7788999****888*******987 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 3.3e-10
                         Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                    +v +d+d+CigCg+C+ +CP+ga
  gi|118431940|ref|NP_148720.2| 129 IVLVDDDLCIGCGACIQNCPYGA 151
                                    5889*****************98 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.6
                         Fer4_6  11 gCgdCv 16 
                                     C  Cv
  gi|118431940|ref|NP_148720.2| 163 KCTFCV 168
                                    577776 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.002
                         Fer4_6  14 dCvrvCPega 23 
                                    +Cv +CP+ga
  gi|118431940|ref|NP_148720.2| 178 ACVEACPTGA 187
                                    5*******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 ?   -1.6   0.2       2.5   3.2e+03       7      13 ..       7      13 ..       2      15 .. 0.54
   2 !   18.9  12.5   9.6e-07    0.0012       2      56 .]      56     118 ..      55     118 .. 0.91
   3 !   22.7  13.3   6.2e-08   7.9e-05       3      56 .]      99     148 ..      97     148 .. 0.86
   4 !   31.3   8.3   1.3e-10   1.6e-07       2      56 .]     130     184 ..     129     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.5
                        Fer4_10  7 dtCirCg 13
                                     C  C+
  gi|118431940|ref|NP_148720.2|  7 TACSTCN 13
                                   3344443 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 9.6e-07
                        Fer4_10   2 vvidddtCirCgkCvkaCPadl.......tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56 
                                    + id d+C +C +Cv aC a+         +   + + +e+++   ++++C +c   +Cv++CP
  gi|118431940|ref|NP_148720.2|  56 MFIDVDKCYGCYACVVAC-AHEnnvpigvYRTWIERYVKEDGTPVYVPKQCNHCDnpSCVDVCP 118
                                    689***************.6559***99988888899999999999********988******9 PP

  == domain 3  score: 22.7 bits;  conditional E-value: 6.2e-08
                        Fer4_10   3 vidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    v+ +++C +C    Cv++CP+      +  + +e++ v ++ + C+gcgaC++ CP
  gi|118431940|ref|NP_148720.2|  99 VYVPKQCNHCDnpSCVDVCPV------KATYVNEDGIVLVDDDLCIGCGACIQNCP 148
                                    67899******999*******......66666777777778999***********9 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 1.3e-10
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc.........gaCveaCP 56 
                                    v +ddd Ci+Cg+C + CP+          a   ++++++ +kCt+c          aCveaCP
  gi|118431940|ref|NP_148720.2| 130 VLVDDDLCIGCGACIQNCPY---------GARFYNPIKGVADKCTFCvhriysdmlPACVEACP 184
                                    6789****************.........5666677788888899986666655444******9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.9     1e-05     0.013       2      18 ..      57      73 ..      56      73 .. 0.95
   2 ?    5.3   5.9     0.015        19      13      22 ..     112     121 ..      98     123 .. 0.82
   3 !   33.0   3.0   2.7e-11   3.4e-08       2      22 ..     131     151 ..     130     153 .. 0.92
   4 ?    2.3   0.3      0.13   1.6e+02       5      11 ..     161     167 ..     158     167 .. 0.90
   5 !   13.2   1.3   4.7e-05      0.06      13      23 ..     178     188 ..     178     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                   EEETTTSSS-THHHHHS CS
                           Fer4  2 videekCigCGaCvevC 18
                                    id +kC gC aCv +C
  gi|118431940|ref|NP_148720.2| 57 FIDVDKCYGCYACVVAC 73
                                   69*************** PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                                    HHHHHSTTTE CS
                           Fer4  13 aCvevCPvgA 22 
                                     Cv+vCPv A
  gi|118431940|ref|NP_148720.2| 112 SCVDVCPVKA 121
                                    4*******98 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 2.7e-11
                                    EEETTTSSS-THHHHHSTTTE CS
                           Fer4   2 videekCigCGaCvevCPvgA 22 
                                     +d ++CigCGaC++ CP+gA
  gi|118431940|ref|NP_148720.2| 131 LVDDDLCIGCGACIQNCPYGA 151
                                    59******************9 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.13
                                    TTTSSS- CS
                           Fer4   5 eekCigC 11 
                                     +kC++C
  gi|118431940|ref|NP_148720.2| 161 ADKCTFC 167
                                    69***** PP

  == domain 5  score: 13.2 bits;  conditional E-value: 4.7e-05
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                    aCve+CP+gA 
  gi|118431940|ref|NP_148720.2| 178 ACVEACPTGAR 188
                                    7********95 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.7       1.7   2.2e+03      12      16 ..       8      12 ..       7      14 .. 0.66
   2 !   18.4   2.4   1.3e-06    0.0016       3      21 ..      56      74 ..      54      75 .. 0.91
   3 !   12.5   5.3   9.4e-05      0.12       3      21 ..      98     118 ..      96     119 .. 0.87
   4 !   25.0   1.6   9.8e-09   1.3e-05       3      22 .]     130     149 ..     128     149 .. 0.91
   5 ?    3.7   3.8     0.062        80      15      22 .]     178     185 ..     158     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                         Fer4_2 12 gCgaC 16
                                   +C++C
  gi|118431940|ref|NP_148720.2|  8 ACSTC 12
                                   67777 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.3e-06
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   +++d d+C gC aCv aC 
  gi|118431940|ref|NP_148720.2| 56 MFIDVDKCYGCYACVVACA 74
                                   799***************5 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 9.4e-05
                         Fer4_2   3 vvvdtdrCigCg..aCvsaCP 21 
                                    +v+++  C++C   +Cv++CP
  gi|118431940|ref|NP_148720.2|  98 PVYVPKQCNHCDnpSCVDVCP 118
                                    6788888****889******* PP

  == domain 4  score: 25.0 bits;  conditional E-value: 9.8e-09
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    v vd d CigCgaC+++CP+
  gi|118431940|ref|NP_148720.2| 130 VLVDDDLCIGCGACIQNCPY 149
                                    7899***************5 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.062
                         Fer4_2  15 aCvsaCPa 22 
                                    aCv aCP+
  gi|118431940|ref|NP_148720.2| 178 ACVEACPT 185
                                    8******7 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.4       6.2     8e+03       4       7 ..       9      12 ..       7      14 .. 0.66
   2 !    9.2   5.6     0.002       2.6       1      11 [.      63      73 ..      63      77 .. 0.94
   3 !   15.7   5.5   1.7e-05     0.022       1      15 []     105     121 ..     105     121 .. 0.91
   4 !   18.3   5.5   2.6e-06    0.0033       1      15 []     137     151 ..     137     151 .. 0.99
   5 !   16.3   2.5   1.1e-05     0.014       1      15 []     164     187 ..     164     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.2
                         Fer4_3  4 CgaC 7 
                                   C++C
  gi|118431940|ref|NP_148720.2|  9 CSTC 12
                                   6666 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                         Fer4_3  1 CtgCgaCvevC 11
                                   C gC+aCv++C
  gi|118431940|ref|NP_148720.2| 63 CYGCYACVVAC 73
                                   99********* PP

  == domain 3  score: 15.7 bits;  conditional E-value: 1.7e-05
                         Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                    C++C    Cv+vCPv+A
  gi|118431940|ref|NP_148720.2| 105 CNHCDnpSCVDVCPVKA 121
                                    ****7677*******98 PP

  == domain 4  score: 18.3 bits;  conditional E-value: 2.6e-06
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCgaC + CP+gA
  gi|118431940|ref|NP_148720.2| 137 CIGCGACIQNCPYGA 151
                                    **************9 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 1.1e-05
                         Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                    Ct C          aCve+CP+gA
  gi|118431940|ref|NP_148720.2| 164 CTFCVhriysdmlpACVEACPTGA 187
                                    999966788999999********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 ?   -2.3   0.0       3.9     5e+03      41      45 ..       9      13 ..       5      26 .. 0.70
   2 !   19.9   8.7   4.6e-07   0.00058       2      54 ..      57     120 ..      56     125 .. 0.81
   3 !   16.2   2.4   6.7e-06    0.0086       3      19 ..     132     148 ..     121     152 .. 0.64
   4 !    9.1  11.7    0.0011       1.4       3      44 ..     132     167 ..     130     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.9
                        Fer4_21 41 CvGCn 45
                                   C  Cn
  gi|118431940|ref|NP_148720.2|  9 CSTCN 13
                                   33333 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.6e-07
                        Fer4_21   2 ridedkCigCgkCliaCedtshqai........eidaktvlkv.vedeCvGCn..lCssvCPve 54 
                                    +id dkC gC  C++aC  +    i        ++ ++  ++v v ++C  C+   C++vCPv+
  gi|118431940|ref|NP_148720.2|  57 FIDVDKCYGCYACVVACAHENNVPIgvyrtwieRYVKEDGTPVyVPKQCNHCDnpSCVDVCPVK 120
                                    699***************9988888888777765555555566379******9446******95 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 6.7e-06
                        Fer4_21   3 idedkCigCgkCliaCe 19 
                                    +d+d CigCg C++ C+
  gi|118431940|ref|NP_148720.2| 132 VDDDLCIGCGACIQNCP 148
                                    45566666666666665 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0011
                        Fer4_21   3 idedkCigCgkCliaCedts..hqaieidaktvlkvvedeCvGC 44 
                                    +d+d CigCg C++ C+ ++  ++ i++ a++        C+ C
  gi|118431940|ref|NP_148720.2| 132 VDDDLCIGCGACIQNCPYGArfYNPIKGVADK--------CTFC 167
                                    89999***********9655334455544443........3333 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   2.1   0.00053      0.68       7      59 ..       8      76 ..       5      78 .. 0.63
   2 !    8.4   0.2    0.0025       3.2       1      19 [.     104     124 ..      83     131 .. 0.82
   3 !    9.7   8.4   0.00094       1.2       2      28 ..     137     163 ..     136     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                        Fer4_17  7 yClpeCpsyeaydnepkkllraakl...............glleeaeke.........ekaslCieCgeCerkCPqg 59
                                   +C   C + ++  ++ +k + a+++               +       +           +++C +C  C+ +C ++
  gi|118431940|ref|NP_148720.2|  8 ACST-CNTRREFLKKTAKAAVATSSlillgsvtiksqaasE-------RvrgrrfamfIDVDKCYGCYACVVACAHE 76
                                   4666.666666666666666665557777766554443222.......1334455544588*************875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                        Fer4_17   1 rCiqCgy..ClpeCpsyeayd 19 
                                    +C++C    C+++Cp  + y 
  gi|118431940|ref|NP_148720.2| 104 QCNHCDNpsCVDVCPVKATYV 124
                                    588888666888888776655 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00094
                        Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllra 28 
                                    Ci+Cg+C+++Cp++++  n  k ++ +
  gi|118431940|ref|NP_148720.2| 137 CIGCGACIQNCPYGARFYNPIKGVADK 163
                                    9***********999877766666555 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 !   12.3   0.3   0.00017      0.22       2      18 ..      57      73 ..      56      98 .. 0.87
   2 ?    0.5   0.3      0.83   1.1e+03      56      63 ..     114     121 ..     111     124 .. 0.82
   3 !   17.2   2.7   5.1e-06    0.0065       1      19 [.     130     148 ..     130     170 .. 0.88
   4 ?   -0.1   0.1       1.2   1.6e+03      14      62 ..     179     186 ..     174     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                        Fer4_15  2 vvDrdaCigcglCvaea 18
                                   ++D d+C gc +Cv ++
  gi|118431940|ref|NP_148720.2| 57 FIDVDKCYGCYACVVAC 73
                                   69*************99 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.83
                        Fer4_15  56 araCPvdA 63 
                                    +++CPv+A
  gi|118431940|ref|NP_148720.2| 114 VDVCPVKA 121
                                    589***99 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 5.1e-06
                        Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                    V vD d+Cigcg+C++++p
  gi|118431940|ref|NP_148720.2| 130 VLVDDDLCIGCGACIQNCP 148
                                    78****************8 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.2
                        Fer4_15  14 CvaeapevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvd 62 
                                    Cv++                                         CP++
  gi|118431940|ref|NP_148720.2| 179 CVEA-----------------------------------------CPTG 186
                                    5555.........................................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 ?    3.4   5.4      0.12   1.5e+02      52      65 ..      61      74 ..      10      76 .. 0.76
   2 !    9.6   1.8    0.0013       1.7       1      17 [.     104     122 ..     103     130 .. 0.82
   3 !   11.2   5.0   0.00043      0.55       2      16 ..     137     151 ..     136     169 .. 0.84
   4 !    9.0   0.0    0.0021       2.7       7      32 ..     178     201 ..     177     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                        Fer4_16 52 eaitgCdiCqdvCP 65
                                    +++gC +C+ +C 
  gi|118431940|ref|NP_148720.2| 61 DKCYGCYACVVACA 74
                                   55666666666664 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                        Fer4_16   1 rCgtCgk..CaevCPtnai 17 
                                    +C  C +  C++vCP++a 
  gi|118431940|ref|NP_148720.2| 104 QCNHCDNpsCVDVCPVKAT 122
                                    599999888******9996 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00043
                        Fer4_16   2 CgtCgkCaevCPtna 16 
                                    C++Cg+C++ CP +a
  gi|118431940|ref|NP_148720.2| 137 CIGCGACIQNCPYGA 151
                                    ************998 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0021
                        Fer4_16   7 kCaevCPtnaikekkekeiearecis 32 
                                    +C+e+CPt+a      + ++ + ++s
  gi|118431940|ref|NP_148720.2| 178 ACVEACPTGARVFG--ELADEESEVS 201
                                    6********96655..3333333333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.6     0.033        43      45      62 ..      57      74 ..       6      77 .. 0.53
   2 !   13.3  10.2   6.7e-05     0.086       2      64 ..      60     120 ..      59     121 .. 0.70
   3 !    7.8  10.5    0.0035       4.4       5      30 ..     137     162 ..     134     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.033
                         Fer4_8 45 eealwsCttcgaCtevCp 62
                                      +++C +c aC+++C 
  gi|118431940|ref|NP_148720.2| 57 FIDVDKCYGCYACVVACA 74
                                   556677777777777775 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.7e-05
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64 
                                    ++kC +C aC  aC   ++ +  +   r   +   ++e++ +  +  ++C++c +  C++vCpv+
  gi|118431940|ref|NP_148720.2|  60 VDKCYGCYACVVACA--HENNVPIGVYRTWIER-YVKEDG-TPVYVPKQCNHCDNpsCVDVCPVK 120
                                    78************4..4444455555555444.333333.346889******9888******97 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0035
                         Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldarg 30 
                                    Ci+CgaC ++Cp   r+ + ++   +
  gi|118431940|ref|NP_148720.2| 137 CIGCGACIQNCPYGARFYNPIKGVAD 162
                                    ************87776555444444 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.3     0.011        14       2      14 ..      61      73 ..      61      76 .. 0.95
   2 ?   13.7   3.3   5.2e-05     0.066       4      16 ..     105     119 ..     102     123 .. 0.89
   3 ?   15.0   2.6   2.1e-05     0.027       2      17 .]     135     150 ..     134     150 .. 0.92
   4 ?   -2.4   0.2       7.5   9.6e+03       2       5 ..     162     165 ..     161     169 .. 0.56
   5 ?    5.7   0.5      0.02        26       8      17 .]     177     186 ..     177     188 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                         Fer4_4  2 erCigCgsCvaaC 14
                                   ++C gC +Cv aC
  gi|118431940|ref|NP_148720.2| 61 DKCYGCYACVVAC 73
                                   79*********** PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.2e-05
                         Fer4_4   4 CigCg..sCvaaCPq 16 
                                    C++C+  sCv++CP+
  gi|118431940|ref|NP_148720.2| 105 CNHCDnpSCVDVCPV 119
                                    *****999******7 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.1e-05
                         Fer4_4   2 erCigCgsCvaaCPqg 17 
                                    + CigCg+C+  CP+g
  gi|118431940|ref|NP_148720.2| 135 DLCIGCGACIQNCPYG 150
                                    67************86 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 7.5
                         Fer4_4   2 erCi 5  
                                    ++C+
  gi|118431940|ref|NP_148720.2| 162 DKCT 165
                                    5554 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.02
                         Fer4_4   8 gsCvaaCPqg 17 
                                    ++Cv aCP+g
  gi|118431940|ref|NP_148720.2| 177 PACVEACPTG 186
                                    68******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 1791.81
//
Query:       gi|14602172|ref|NP_148721.1|  [L=404]
Description: molybdopterin oxidoreductase, membrane subunit [Aeropyrum pernix K1]
Scores for complete 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-72  243.5  20.7    6.3e-72  242.9  20.7    1.2  1  NrfD      Polysulphide reductase, NrfD
  ------ inclusion threshold ------
      0.086   12.1   0.0       0.16   11.3   0.0    1.5  1  7tm_1     7 transmembrane receptor (rhodopsin family)
       0.32   11.1   0.0       0.32   11.1   0.0    1.8  2  DUF5392   Family of unknown function (DUF5392)


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 !  242.9  20.7     1e-75   6.3e-72       4     309 ..      25     347 ..      23     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 242.9 bits;  conditional E-value: 1e-75
                          NrfD   4 ehsnsvvWglliavylFligisAg.alilaill....klfkkkegkslkliirtgall.aalavlagllilvldlgrpe.r 77 
                                   +++  ++Wg+l++vy++++gi Ag +l++a+++    k++++ +g s  lii++g+ll a+++++a       dl++p+ +
  gi|14602172|ref|NP_148721.1|  25 FKAGGAIWGVLLVVYPLMTGILAGsYLVSALAYgfgvKRLYRVAGLS--LIISVGLLLsAPIFPMA-------DLKQPQrA 96 
                                   577899******************99999999999999999999866..*****************.......******99 PP

                          NrfD  78 flklllyynfsSimswgv..llls..lyivvlv...lyllvifekdlaakglpalg.ilaklisla...........erva 139
                                   f+++l+++ ++S++++gv  ++++  lyi++lv   l+l++++++d+aak+ +a+g i+++++sl            +rv+
  gi|14602172|ref|NP_148721.1|  97 FEIFLRPHVIPSDAYPGVspMAFFgiLYIPLLVvalLNLIFVYRADMAAKA-EATGnIIYRIVSLGrgysredverdRRVV 176
                                   ********************9999889999998888***************.99999********8899999****9**** PP

                          NrfD 140 kilaiialilavllgsytgfllsavlsrplwnspllpvlFlasaiasGlavlllasllaarfek.esedagllkklellvi 219
                                   kil+ii +ila+l+++y+++ll++++sr+lw++p+lp+++lasa++sG+a++++a+++aarf++ es+dag++k+l+l+++
  gi|14602172|ref|NP_148721.1| 177 KILSIIGVILAILFHGYFDILLASIKSRILWVDPSLPIRLLASAVFSGAALVTVAYYIAARFSPgESIDAGTMKTLSLIML 257
                                   ****************************************************************9**************** PP

                          NrfD 220 lteagllv......ilfvglaleggekiealeaalsggfltvlFwlgvvllglaiplllslavprlrenvavvviasilal 294
                                   +++a++l+      il+vg++l +ge ie++e+ l+g    ++F +++++++la++ll+sl++pr+ren+++v   ++la+
  gi|14602172|ref|NP_148721.1| 258 FGLAAALIteitseILRVGYYLLPGEGIEYYES-LRG----SMF-IDNAYYILALILLVSLLIPRVRENIHSVAAIAALAI 332
                                   ********8888877******************.***....***.****************************88888888 PP

                          NrfD 295 vgvlllrfllliagq 309
                                   v  +l ++l++i  q
  gi|14602172|ref|NP_148721.1| 333 VAEILNKWLVVIVPQ 347
                                   888999999998766 PP

>> 7tm_1  7 transmembrane receptor (rhodopsin family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.7e-05      0.16     113     228 ..      77     200 ..      52     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.7e-05
                                   HHHHHHHHHHHCEECCCTTTT.CCEEECSSST........HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCHHHHS CS
                                   xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         7tm_1 113 slllsvpllvletvetnaedt.tkdCqittle........esvyiifsavlsfilPllvivilyarifrtvlktsrtktsk 184
                                    llls p++ + + + ++++  +        +        ++ +  + ++   ++Pllv+++l++  + ++   ++ +++ 
  gi|14602172|ref|NP_148721.1|  77 GLLLSAPIFPMADLK-QPQRAfEIFL-----RphvipsdaYPGVSPMAFFGILYIPLLVVALLNLIFVYRADMAAKAEAT- 150
                                   555566666555552.3444432222.....2223335566777788889999************999999999999998. PP

                                   HCCH.........HHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                   xxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         7tm_1 185 skng.........gsstpplkavrekkaartlgivvavfivcwlPftiiyllq 228
                                      g         g++  +  ++r+++++++l+i+ ++ ++ +  ++ i l +
  gi|14602172|ref|NP_148721.1| 151 ---GniiyrivslGRGYSREDVERDRRVVKILSIIGVILAILFHGYFDILLAS 200
                                   ...334899**99888888889999**********999999998888777665 PP

>> DUF5392  Family of unknown function (DUF5392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.4e-05      0.32      24      83 ..     114     172 ..     105     182 .. 0.70
   2 ?   -3.2   0.9       1.4   8.4e+03      39      68 ..     303     333 ..     295     336 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                       DUF5392  24 lkKsskysfislPLllvslinlillllkaeleedsliaiilyallgAlGlAlfkEsrlkk 83 
                                   +  +  + ++ +PLl+v+l+nli+++    + + ++   i+y ++  lG    +E   + 
  gi|14602172|ref|NP_148721.1| 114 VSPMAFFGILYIPLLVVALLNLIFVYRADMAAKAEATGNIIYRIV-SLGRGYSREDVERD 172
                                   5556779999*************9987666666666666666554.46666666655555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                       DUF5392  39 lvslinlillll.kaeleedsliaiilyall 68 
                                   +++li l++ll+  ++ + +s+ ai+  a++
  gi|14602172|ref|NP_148721.1| 303 ILALILLVSLLIpRVRENIHSVAAIAALAIV 333
                                   4556666655551344445666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3152.14
//
Query:       gi|14602175|ref|NP_148724.1|  [L=1165]
Description: molybdopterin oxidoreductase, molybdopterin binding subunit [Aeropyrum pernix K1]
Scores for complete 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   60.6   0.1    6.8e-13   48.4   0.0    2.3  2  Molybdopterin    Molybdopterin oxidoreductase
    3.4e-15   56.0   0.0    1.2e-14   54.3   0.0    1.9  1  Molydop_binding  Molydopterin dinucleotide binding domain
    7.7e-06   25.8   0.1     0.0012   18.8   0.1    2.4  2  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
     0.0037   17.1   0.1     0.0069   16.2   0.1    1.5  1  TAT_signal       TAT (twin-arginine translocation) pathway si
  ------ inclusion threshold ------
      0.035   14.3   0.0      0.092   12.9   0.0    1.7  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal


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 !    9.6   0.2   0.00011      0.41       1      27 [.     144     170 ..     144     175 .. 0.88
   2 !   48.4   0.0   1.9e-16   6.8e-13     111     395 ..     331     733 ..     291     744 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00011
                                   B--S-EEECTTTTTSEEEE--HHHHHH CS
                 Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAle 27 
                                   R+  P++R + rg Gk++++sW++   
  gi|14602175|ref|NP_148724.1| 144 RVLVPLKRAGPRGSGKWKPISWEQLIR 170
                                   8889*******************9665 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 1.9e-16
                                   G-SEEEEESS-HHHHSHHH..HHHHHHHHHTTC-EEEEECSSB-H.CGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTC CS
                 Molybdopterin 111 nsdliilwGsNvreerpil..narirkaalkkkakvivigpryae.llkfadewlaikpgtdaalalamghvilqelkvdk 188
                                    s++ii+ G+ + + +p    ++ ++ +a ++++k+ ++ p+     +  ++ w++ikpg daala+a+  +i+++  ++k
  gi|14602175|ref|NP_148724.1| 331 SSKVIIMAGASMGRLHPGTtgQGLLISRAGEGDLKIYYVNPTAPRtDAGGNIVWIPIKPGYDAALAFALIRWIIENERYNK 411
                                   689999999999999987766889999999999******987665536779****************************** PP

                                   HHHHHHEECHHHCCCCCCCEECCS......................................................... CS
                 Molybdopterin 189 eflrkytygkeetdmpllvtleee......................................................... 212
                                   efl+  +   +e           +                                                         
  gi|14602175|ref|NP_148724.1| 412 EFLEIPNEEAAE-----------Rkgypvhsnatwlvimeeghekwgeylkakdvgledsdkpvvftgeglatydsvdnae 481
                                   775543333322...........13555555556799999999************************************** PP

                                   .............................................HHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHT CS
                 Molybdopterin 213 .............................................tgkkkevvariarelarnaaktagksmiivGaglnh 248
                                                                                 + +    ++++ e+ar++a++a+ +   v  g+  
  gi|14602175|ref|NP_148724.1| 482 idwegevvlttgervkvktsfrilkdealsrsidqwlsvaspyepGSSEFREWKEKVLEMARDFAEAAPMAGTYVHRGVGM 562
                                   ********************************************988999999999999999999****999999****** PP

                                   STTHHHHHHHHHHHHHHCTHCSSTTC.....EEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT.................. CS
                 Molybdopterin 249 rqdgdaiyravinLallvgnvgqpgG.....gwahlnGqlilagaaekvgalpvllsvkslke.................. 306
                                   +++g+ +++a   L  lvgn+ ++gG     g  ++n+++++ ++       ++ +++++ k                   
  gi|14602175|ref|NP_148724.1| 563 HSNGEYAVWAYRALDTLVGNYHRKGGllaraGHTKYNSYVYHVDKKGFGEPVKWGPPIDRHKAkyedtleywlkvkkgenp 643
                                   *************************94444455578888899999999999999999999998999999999999999887 PP

                                   .HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHH...CSSEEEEEESCSSHHHHTS CS
                 Molybdopterin 307 .ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekale...kldlvvvldgrltstalya 383
                                     +++ ++ +  ++ + +++ +  + + + + g  +l++++  p+ ++   ++ ++ l+   kl l++++   +++t lya
  gi|14602175|ref|NP_148724.1| 644 yPAKRPWYPHTPEESY-TEIFAGIAEEYPYKMGALILFYAN--PVLSANYGVKFIEVLKdtkKLPLFIAITTTINETMLYA 721
                                   7556666655555555.333333345666665555555555..9999999998888887777******************* PP

                                   SEEEEBE-CCGS CS
                 Molybdopterin 384 DiiLPaatwyEk 395
                                   D+i P++t++E 
  gi|14602175|ref|NP_148724.1| 722 DYIVPDTTYLET 733
                                   ***********6 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   3.2e-18   1.2e-14      23      82 ..     980    1040 ..     964    1082 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 3.2e-18
                                    HHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC CS
               Molydop_binding   23 rlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe 82  
                                    + ++ +p +++ +np+dA++lG+++Gd Veve++ G+++++++v+++v+pGv+ +p+g ++
  gi|14602175|ref|NP_148724.1|  980 AIKQISPeNYLVVNPKDAEKLGLETGDVVEVETPTGRFKAPVVVEPTVPPGVIMVPYGMGR 1040
                                    556667778************************************************9987 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.3e-07    0.0012       3      39 ..      51      91 ..      49     105 .. 0.86
   2 !    4.5   0.0    0.0095        34      39      54 ..     125     140 ..     113     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.3e-07
                                  EEEEE-SSBTT--EEEEEE...ETTEEE.EEEE-TTSTTTT CS
                Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhv...kdgkiv.kvegdpdhpvne 39
                                  +v + C  C v+Cg+++ v    d +iv ++eg+p hp n+
  gi|14602175|ref|NP_148724.1| 51 YVYSSCLGCNVRCGIKARVvkvGDLEIVeRIEGNPYHPYNR 91
                                  6899*************998776666667*********998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0095
                                   TT---HHHHTCHHCCC CS
                Molybdop_Fe4S4  39 egrlCvKGrtllervy 54 
                                   +g+lC++G+ ++ ++y
  gi|14602175|ref|NP_148724.1| 125 HGTLCPRGQDGIYYLY 140
                                   6**********99998 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 !   16.2   0.1   1.9e-06    0.0069       1      23 [.       1      23 [.       1      26 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-06
                    TAT_signal  1 klSRRdFLKgsAAaaAAaalggc 23
                                  ++SRRdF Kgs A a ++++g+ 
  gi|14602175|ref|NP_148724.1|  1 MVSRRDFVKGSIAIASLLVAGAG 23
                                  69*********999999888865 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 ?   12.9   0.0   2.6e-05     0.092      13      42 ..     986    1016 ..     979    1034 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                    STTEEEE-HHHHHHHTS-TTSEEEEEC.CCC CS
                       CDC48_N   13 grgivridpedmeelglepgdvveieg.krk 42  
                                      ++ +++p+d e+lgle+gdvve+e  + +
  gi|14602175|ref|NP_148724.1|  986 PENYLVVNPKDAEKLGLETGDVVEVETpTGR 1016
                                    568889*******************986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.75u 0.26s 00:00:01.01 Elapsed: 00:00:00.41
# Mc/sec: 8472.87
//
Query:       gi|118431941|ref|NP_148725.2|  [L=194]
Description: hypothetical protein APE_2612.1 [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-06   27.9   0.2    5.3e-06   26.5   0.0    1.7  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 ?   -1.5   0.0      0.13   2.4e+03       7      28 ..      46      68 ..      41      81 .. 0.57
   2 !   26.5   0.0   2.9e-10   5.3e-06      67     128 ..      89     151 ..      75     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.13
                Nitrate_red_del  7 eveealaelaealaa.ededlle 28
                                   + e+ +ael+ea+++ ++ed+++
  gi|118431941|ref|NP_148725.2| 46 AAEKLVAELKEAVKSlSREDAAR 68
                                   55555556666662233333333 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.9e-10
                Nitrate_red_del  67 evrefyrqaglevaeefneppDHlaveLeflahLaereaeaeea...eeaealleaqkafleehl 128
                                     v++fy+ +g +    +  ppDHlav L+f +  ++++a a++    ee  ++l+    f + hl
  gi|118431941|ref|NP_148725.2|  89 TVEAFYENHGYSAGGPL--PPDHLAVQLAFASSILREAAMALARddrEEVVRYLKLFSRFASAHL 151
                                    599********999999..*******************999998888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1540.08
//
Query:       gi|118431942|ref|NP_148727.2|  [L=376]
Description: hypothetical protein APE_2615.1 [Aeropyrum pernix K1]
Scores for complete 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   59.9  47.2    1.9e-16   59.9  47.2    1.8  1  MFS_1         Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9  47.2   1.1e-20   1.9e-16      32     352 ..      36     340 ..       5     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.1e-20
                          MFS_1  32 seigllltl.yal...gaavaslplGrlsdrf...Grrr.vlllglllfalglllllfasslw.lllvlrvlqGlgagal 102
                                     e+gl++++ +++   +a va l++G ++ r+   G+ + +++lg+++ ++++ ll+f ++ w   ++l +l  +g g+ 
  gi|118431942|ref|NP_148727.2|  36 LEAGLVVAAaVSVgdlVAYVARLFGGLFAYRVgssGAYWgLVFLGYTVNLVAVPLLAF-AGRWeEAFLLVLLERAGKGVR 114
                                    5677755554555333568888999999999844469999999999999999666668.888989999************ PP

                          MFS_1 103 fpagaaliadwfpkeergraigllsagfslGailgpllgg.llasslgWravfyilaivsllafvlfllllpeepperkr 181
                                    +pa  a++a+++ +  rg ++++  a+ ++Gai gpll   +l+s +g+++vf +l++ +l++++l  l +   p+ ++ 
  gi|118431942|ref|NP_148727.2| 115 APARDAILAEVSGGLGRGVVYAVHEAMDQVGAIAGPLLVMaALSSGFGYSGVFALLGVPALVSLLLLTLAYILYPRLKSA 194
                                    ***********************************766551666*******************88433333333333333 PP

                          MFS_1 182 kspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgaila 261
                                    ++p               +  + +       l+a+++ +++ ++  ++  +   +v g + + l+++++a+++lv a +a
  gi|118431942|ref|NP_148727.2| 195 EKPPGG------------YPPFGRVA----PLAAAAGLSMAGFIHWIHASF-RYSVQGVD-ASLIAGAYAVAMLVDALAA 256
                                    333222............22222333....777888887777776666666.57899999.6777778************ PP

                          MFS_1 262 llagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglf 341
                                    l +g   d+    +r ++al+ +++aa +la+l  +   +l +l+ +l+G+++g +++ + ++++d++ p+ +g  +g++
  gi|118431942|ref|NP_148727.2| 257 LALGVAYDK---VTRGVVALVPIVAAASSLAVLLGA---PL-ALAAILWGVAMGGFQSVFRSVVADSLEPRLRGLGFGVV 329
                                    *********...777888888888888887777777...33.358899******************************** PP

                          MFS_1 342 ntagslggalg 352
                                     +a +lg+++g
  gi|118431942|ref|NP_148727.2| 330 YFAMGLGWSVG 340
                                    ********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2849.18
//
Query:       gi|14602179|ref|NP_148728.1|  [L=141]
Description: hypothetical protein APE_2616 [Aeropyrum pernix K1]
Scores for complete 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   57.7   0.6    1.8e-15   57.6   0.6    1.0  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.013   15.7   0.1      0.016   15.4   0.1    1.1  1  PIN_2     PIN domain
       0.09   12.7   0.7       0.13   12.1   0.1    1.5  2  DUF4411   Domain of unknown function (DUF4411)


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 !   57.6   0.6   2.9e-19   1.8e-15       2     118 ..       1     120 [.       1     124 [. 0.92

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.9e-19
                                   EE-HHHHHHHH....TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                           PIN   2 vlDTsvliall....rgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpid 74 
                                   ++DTsv+ +++     + e++e++r  l++l      ++ + l  +El++vl r   ++  +++l+ +   l+ ++++   
  gi|14602179|ref|NP_148728.1|   1 MIDTSVFADYYllypGDPERHERSRTVLDKLslrdVIVYEPFLFEIELRAVLVR---RIPPEQALRIVDTTLKHVNVVR-E 77 
                                   59*************999999999999999999766666677777*********...99999999999999********.* PP

                                   HHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                           PIN  75 aeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                   +e+ ++aaeial  g+++ Da+ +AtAk+ + +li t+D+ +++
  gi|14602179|ref|NP_148728.1|  78 EELHDKAAEIALITGCRAVDAYFIATAKHVDGILI-TNDKVMKD 120
                                   ***********************************.***98876 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   2.7e-06     0.016      31     115 ..      38     118 ..      19     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-06
                         PIN_2  31 apeeaveeiekhkealvkksklseeeleellelletkikiveeslyeskikeAkeriarvDpdDtpfvAlaLlleapiWTe 111
                                   + e  + eie +   lv  +++ +e++  ++++  +++++v e+++++k  e   ++      D+ f+A+a  ++  + T+
  gi|14602179|ref|NP_148728.1|  38 VYEPFLFEIELRAV-LV--RRIPPEQALRIVDTTLKHVNVVREEELHDKAAEIALITGC-RAVDAYFIATAKHVDGILITN 114
                                   44444557776654.77..99*************************9888776655554.799****************** PP

                         PIN_2 112 Dkdl 115
                                   Dk +
  gi|14602179|ref|NP_148728.1| 115 DKVM 118
                                   **88 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.59   3.5e+03       2      10 ..       1       9 [.       1      15 [. 0.72
   2 ?   12.1   0.1   2.2e-05      0.13      83     132 ..      69     123 ..      50     132 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.59
                       DUF4411  2 llDtnvfie 10
                                  ++Dt+vf  
  gi|14602179|ref|NP_148728.1|  1 MIDTSVFAD 9 
                                  799999953 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.2e-05
                       DUF4411  83 akwv.ivesekyskaakkefl.....svaDpfliAaAlaknatvVTkEvkkpnkkk 132
                                    k+v +v++e+  ++a +e +        D++ iA+A+  + +++T+++  +++ +
  gi|14602179|ref|NP_148728.1|  69 LKHVnVVREEELHDKA-AEIAlitgcRAVDAYFIATAKHVDGILITNDKVMKDNAQ 123
                                   3344334444444444.222224577889*******************99444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 1101.56
//
Query:       gi|118431943|ref|YP_874953.1|  [L=64]
Description: hypothetical protein APE_2616a [Aeropyrum pernix K1]
Scores for complete 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-17   62.5   4.2    4.3e-17   62.3   4.2    1.0  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   4.2   2.4e-21   4.3e-17       1      59 []       1      61 [.       1      61 [. 0.88

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.4e-21
                         DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIeeakeilkklkgilk....eadeeeleelle 59
                                   MskvI+++YE+GvLKP+++v L+EGee+++++ +  +  + +k   +    +ad+++++e++e
  gi|118431943|ref|YP_874953.1|  1 MSKVIRVRYEKGVLKPIGEVVLREGEELEVVVVR--KSFRGFKDEAGkymfKADRDTVKEFVE 61
                                   9*********************************..6666666666666678********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 468.66
//
Query:       gi|118431944|ref|NP_148729.2|  [L=147]
Description: hypothetical protein APE_2617.1 [Aeropyrum pernix K1]
Scores for 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   38.0   1.2    3.3e-09   37.3   1.2    1.4  1  PIN       PIN domain
    2.9e-09   37.7   0.2    3.5e-09   37.4   0.2    1.1  1  PIN_3     PIN domain
    4.4e-06   27.3   0.4    8.9e-05   23.0   0.1    2.1  2  PIN_12    PIN domain
    3.9e-05   23.9   0.6    4.7e-05   23.6   0.6    1.1  1  PIN_2     PIN domain
  ------ inclusion threshold ------
      0.059   13.1   0.1       0.18   11.6   0.1    1.8  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   1.2   9.1e-13   3.3e-09       2     119 ..       7     126 ..       6     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 9.1e-13
                                    EE-HHHHHHHH..TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHS..SCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                            PIN   2 vlDTsvliall..rgeekaeaarklleel.eelvtsalvlaEllyvlar..rkskrekaaelvelllllsalkilpidae 76 
                                    ++DT+ +ia++       ++ +++ll ++  elv  ++ l+E     +r   +    +++++++ +ll + + ++   +e
  gi|118431944|ref|NP_148729.2|   7 MVDTNLFIAAFksGYTAATKLLLRLLLDPdIELVADNILLEEYKKWFHRlsSRVPNIREQAETLYRLLEAKVTVVTPKKE 86 
                                    79*********86666666666666666699*********9999999996533444445555556666888889999*** PP

                                    HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                            PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrv 119
                                    + e+++ ++ +     +D ++aA +++++++li t+D+df+++
  gi|118431944|ref|NP_148729.2|  87 DIEIVKPYMPET--EFADIYHAAACLRSKAILI-TNDKDFDNI 126
                                    **********97..*******************.******987 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.2   9.8e-13   3.5e-09       1     115 [.       5     121 ..       5     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 9.8e-13
                          PIN_3   1 rvvlDtnvlldallfdsp.aarkildaletgaitlvvsprlldElervlarelaypqfklraadkaallakva..lerka 77 
                                    r ++Dtn +++a+ +  + a + +l++l + +i+lv++  ll+E+++ ++r + +    +++a+ + +l +    +   +
  gi|118431944|ref|NP_148729.2|   5 RLMVDTNLFIAAFKSGYTaATKLLLRLLLDPDIELVADNILLEEYKKWFHRLSSRVPNIREQAETLYRLLEAKvtVVTPK 84 
                                    789***********888877788899***********************8876665555555555444333332233377 PP

                          PIN_3  78 vapdaelrpllkcrDpdDqkvlelAlaaradvlVTkdr 115
                                     ++ + ++p +    ++D  +++++l   +++l+T d+
  gi|118431944|ref|NP_148729.2|  85 KEDIEIVKPYMPETEFADIYHAAACLRS-KAILITNDK 121
                                    88888999999999*************9.9******97 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   2.5e-08   8.9e-05       2      76 ..       7      81 ..       6     109 .. 0.75
   2 ?    2.7   0.1     0.044   1.6e+02     159     171 .]     110     123 ..     100     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.5e-08
                         PIN_12  2 fiDTnifldeffrlseeealkklleliesgkiklivpdivldEflknrekkieeskklekalks.lsklksakkkl 76
                                   ++DTn+f+   f++++ +a k ll+l+ + +i+l+  +i l+E++k + +  ++  +++++ ++ ++ l+++   +
  gi|118431944|ref|NP_148729.2|  7 MVDTNLFIA-AFKSGYTAATKLLLRLLLDPDIELVADNILLEEYKKWFHRLSSRVPNIREQAETlYRLLEAKVTVV 81
                                   79******7.*******9****************************999999988444444444444444444433 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
                         PIN_12 159 k.ekvifvsrDkDf 171
                                      +k i++++DkDf
  gi|118431944|ref|NP_148729.2| 110 LrSKAILITNDKDF 123
                                    33669********9 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.6   1.3e-08   4.7e-05       2     115 ..       8     123 ..       7     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.3e-08
                          PIN_2   2 vdaNivvsallk....srikkrlilvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslye 77 
                                    vd+N  ++a       + +  +++l ++ +el+a + ++ee +k +  l ++     e++e+l +lle k+++v+ +  +
  gi|118431944|ref|NP_148729.2|   8 VDTNLFIAAFKSgytaATKLLLRLLLDPDIELVADNILLEEYKKWFHRLSSRVPNIREQAETLYRLLEAKVTVVTPK--K 85 
                                    89998888744476655666778899************************9999999*****************986..5 PP

                          PIN_2  78 skikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdl 115
                                    + i+  k  ++++   D+   A+ L  +a + T+Dkd+
  gi|118431944|ref|NP_148729.2|  86 EDIEIVKPYMPETEFADIYHAAACLRSKAILITNDKDF 123
                                    677788999****************************9 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.9e-05      0.18      42      61 ..     107     126 ..      95     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                        DUF5615  42 eyAkeedriivTkDkDFgel 61 
                                    + + + ++i++T+DkDF ++
  gi|118431944|ref|NP_148729.2| 107 AACLRSKAILITNDKDFDNI 126
                                    5678899**********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1078.80
//
Query:       gi|118431945|ref|YP_874954.1|  [L=86]
Description: hypothetical protein APE_2617a [Aeropyrum pernix K1]
Scores for complete 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-07   29.6   1.8    4.8e-07   29.6   1.8    1.8  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
      1e-06   28.6   0.0    1.5e-06   28.1   0.0    1.2  1  MraZ            MraZ protein, putative antitoxin-like
  ------ inclusion threshold ------
      0.021   14.9   0.0      0.034   14.2   0.0    1.3  1  AbrB-like       AbrB-like transcriptional regulator
      0.035   14.5   0.1      0.041   14.3   0.1    1.2  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
       0.13   11.9   0.0       0.21   11.2   0.0    1.3  1  SH3_1           SH3 domain


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   1.8   1.3e-10   4.8e-07       3      38 ..       6      41 ..       4      48 .. 0.86
   2 ?   -1.1   0.2      0.55     2e+03      15      28 ..      58      73 ..      52      75 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.3e-10
                                   ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCC CS
                 MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiil 38
                                   v+  g+++iP  +r++lg+++Gd+ +++ +++++++
  gi|118431945|ref|YP_874954.1|  6 VDDRGRIVIPSRLRRKLGLKKGDTFIIINVKNDLLV 41
                                   7889**************************985443 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.55
                                   CHHHC.CEEC.TCEEE CS
                 MazE_antitoxin 15 vrfel.gire.Gdeve 28
                                   v++++ +++e G +ve
  gi|118431945|ref|YP_874954.1| 58 VARSGlDLEElGRKVE 73
                                   3444478888887776 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.1e-10   1.5e-06       9      59 ..       5      57 ..       2      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.1e-10
                                   EB-TTSEEE--CHHHHHTTSCSE..EEEEECCSEEEEEEHHHHHHHHHCHHTS CS
                           MraZ  9 elDakGRlllPaklreeakleke..vvviGvsncLeiwpraeWekyeeelaee 59
                                    +D+ GR+ +P++lr++++l+k    ++i v+n L++ +r + e++ +e+aee
  gi|118431945|ref|YP_874954.1|  5 VVDDRGRIVIPSRLRRKLGLKKGdtFIIINVKNDLLVLKRVDVERLAREIAEE 57
                                   68*******************7611556668899***9999999999998776 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.6e-06     0.034      33      61 ..       4      32 ..       3      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.6e-06
                      AbrB-like 33 vsVqknGnLliGsaYTkklgLkpGdefeI 61
                                   v V + G+++i s   +klgLk Gd+f I
  gi|118431945|ref|YP_874954.1|  4 VVVDDRGRIVIPSRLRRKLGLKKGDTFII 32
                                   679999*********************87 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   0.1   1.1e-05     0.041       4      53 ..       6      59 ..       4      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                 PrlF_antitoxin  4 ltergqttiPasvRkaLklkkgrdkiaytildd....gkvvisraeeeaeDpvl 53
                                   + +rg   iP  +R+ L+lkkg+  i  ++++d    ++v ++r + e  + v 
  gi|118431945|ref|YP_874954.1|  6 VDDRGRIVIPSRLRRKLGLKKGDTFIIINVKNDllvlKRVDVERLAREIAEEVA 59
                                   5689999**************999999999988444456777777777666665 PP

>> SH3_1  SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.9e-05      0.21      14      30 ..      22      38 ..      16      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                                   XEBSTTEEEEEEEECSS CS
                          SH3_1 14 LsfkkGDviivleksed 30
                                   L +kkGD++i+++ ++d
  gi|118431945|ref|YP_874954.1| 22 LGLKKGDTFIIINVKND 38
                                   89***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 681.37
//
Query:       gi|118431946|ref|YP_874955.1|  [L=80]
Description: hypothetical protein APE_2617b [Aeropyrum pernix K1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-12   47.6   0.0    2.2e-12   47.5   0.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   1.3e-16   2.2e-12      55     113 ..      19      77 ..       3      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.3e-16
                                    HHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESS CS
                            PIN  55 aaelvelllllsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfD 113
                                    ++ ++e+l +  +l +lpi+ ei++ea++ia kygll+nD liaAt+k++ i+ iat+ 
  gi|118431946|ref|YP_874955.1|  19 LQSFLEELYDEGRLVVLPITMEIVKEAGRIAVKYGLLSNDSLIAATCKHYSINTIATRE 77 
                                    677889999999********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.21s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 690.77
//
Query:       gi|118431947|ref|YP_874956.1|  [L=72]
Description: hypothetical protein APE_2617c [Aeropyrum pernix K1]
Scores for complete 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-19   69.9   4.7      2e-19   69.7   4.7    1.0  1  DUF104    Protein of unknown function DUF104


Domain annotation for each model (and alignments):
>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   4.7   1.1e-23     2e-19       1      58 [.       1      64 [.       1      65 [. 0.95

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.1e-23
                         DUF104  1 MskvIeavYEnGvLKPLekvdLkEGeevkikIee..akeilkklkgilk....eadeeeleell 58
                                   MskvI+a+YE+G+LKPLe++dL+EGee+ ++I+e   ++ +++++gi+k    e+ ee++ e++
  gi|118431947|ref|YP_874956.1|  1 MSKVIRAKYEKGMLKPLEPLDLEEGEELILEIKErsGSKGVRRFFGIVKvrkrETGEEDYYEYI 64
                                   9*********************************9999***********999988899888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 574.47
//
Query:       gi|14602181|ref|NP_148732.1|  [L=99]
Description: hypothetical protein APE_2617d [Aeropyrum pernix K1]
Scores for complete 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   44.3   0.0    1.8e-11   43.6   0.0    1.4  1  DUF5615   Domain of unknown function (DUF5615)
    0.00066   19.8   0.0    0.00073   19.7   0.0    1.1  1  Mut7-C    Mut7-C RNAse domain
     0.0019   17.7   0.0     0.0019   17.7   0.0    1.2  1  XPG_I_2   XPG domain containing
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.48   10.3   0.0    1.7  2  CHASE3    CHASE3 domain


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 !   43.6   0.0   4.1e-15   1.8e-11      21      75 ..       2      56 ..       1      58 [. 0.96

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 4.1e-15
                       DUF5615 21 ghdvlhvrelglegasDeeileyAkeedriivTkDkDFgellllggpppgvillr 75
                                  g+dv ++ ++g +g+sD+++ ++A++  rii+T+D+DF + +l+++  +g+i++ 
  gi|14602181|ref|NP_148732.1|  2 GLDVEWIPDTGYRGISDKQVARIANDSRRIILTRDSDFLKPYLRKDAKYGIIYIA 56
                                  789*************************************************986 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-07   0.00073      20      83 ..       2      74 ..       1      90 [. 0.69

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-07
                        Mut7-C 20 Gydalyasdv.....edeellalaakekrillTrdreLlkraklkkg....vlltsrdveeqlreviarlglk 83
                                  G d+ +  d+     +d++++++a++ +ri+lTrd+++lk    k++    +++ +   +++l ++ +++  +
  gi|14602181|ref|NP_148732.1|  2 GLDVEWIPDTgyrgiSDKQVARIANDSRRIILTRDSDFLKPYLRKDAkygiIYIAEPVRKDNLDKLARNIVKA 74
                                  5666655555555669**********************99655554444566666666666666665555443 PP

>> XPG_I_2  XPG domain containing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.3e-07    0.0019      31      53 ..      18      40 ..      15      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.3e-07
                       XPG_I_2 31 DkfcAvlArklgcaVLTsDSDLl 53
                                  Dk++A +A++++ ++LT DSD+l
  gi|14602181|ref|NP_148732.1| 18 DKQVARIANDSRRIILTRDSDFL 40
                                  9*********************9 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00011      0.48      22      50 ..      21      49 ..      18      52 .. 0.82
   2 ?   -0.6   0.0      0.25   1.1e+03      66      87 ..      58      79 ..      53      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                        CHASE3 22 lvdaEtgqRGYlltgdeefLepyeqarae 50
                                  + ++ +  R  +lt+d++fL+py +  a+
  gi|14602181|ref|NP_148732.1| 21 VARIANDSRRIILTRDSDFLKPYLRKDAK 49
                                  56677788899************987766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                        CHASE3 66 peqqerldrlealieqklaele 87
                                  p+ +++ld+l ++i + l++l 
  gi|14602181|ref|NP_148732.1| 58 PVRKDNLDKLARNIVKALELLK 79
                                  6777788888888877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 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:                        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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 810.96
//
Query:       gi|118431948|ref|NP_148733.2|  [L=80]
Description: hypothetical protein APE_2617e.1 [Aeropyrum pernix K1]
Scores for 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   67.8   0.1    6.5e-19   67.5   0.1    1.1  1  DUF433      Protein of unknown function (DUF433)
     0.0022   17.5   0.0     0.0029   17.1   0.0    1.2  1  Sigma70_r4  Sigma-70, region 4
     0.0027   17.5   0.0     0.0041   16.9   0.0    1.4  1  HTH_23      Homeodomain-like domain
  ------ inclusion threshold ------
      0.016   15.7   0.0        1.2    9.6   0.1    2.1  2  STAC2_u1    Unstructured on SH3 and cysteine-rich domain-cont
       0.12   12.5   0.1       0.33   11.1   0.1    1.6  2  Sigma70_r3  Sigma-70 region 3
       0.13   12.5   0.0       0.16   12.2   0.0    1.1  1  UPF0122     Putative helix-turn-helix protein, YlxM / p13 lik
       0.15   12.1   0.0       0.33   11.1   0.0    1.5  2  DUF5338     Family of unknown function (DUF5338)


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 !   67.5   0.1   2.5e-22   6.5e-19       3      56 .]      12      64 ..      10      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.5e-22
                                   E-TTSGGGS-EETTT--BTHHHHHHHHTT--HHHHHHHH.TS-HHHHHHHHT.. CS
                         DUF433  3 idpeilgGkPvIrgtRipVetilellaaGesieeiledyPdLtlediqaalaYA 56
                                   + p+ +gG+P+++gtRi+V++ile la+G+s+ee++++y  +  e++++al+YA
  gi|118431948|ref|NP_148733.2| 12 VVPGRRGGRPTVKGTRITVDDILEALANGWSVEEVADNY-RIPIEAVYEALRYA 64
                                   679************************************.*************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 !   17.1   0.0   1.1e-06    0.0029      19      50 .]      39      70 ..      33      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-06
                                   TT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                     Sigma70_r4 19 eglTleEIgerlgiSrerVrqiekrAlrkLRk 50
                                    g++ eE+++ + i+ e+V   +++Al+ LRk
  gi|118431948|ref|NP_148733.2| 39 NGWSVEEVADNYRIPIEAVYEALRYALETLRK 70
                                   589****************************7 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.6e-06    0.0041      10      39 ..      33      62 ..      27      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                         HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlk 39
                                   il +la+G+sv+e+A+ + ++   vy  l+
  gi|118431948|ref|NP_148733.2| 33 ILEALANGWSVEEVADNYRIPIEAVYEALR 62
                                   7899999****************9997765 PP

>> STAC2_u1  Unstructured on SH3 and cysteine-rich domain-containing protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.011        29      24      46 ..      20      42 ..      10      48 .. 0.85
   2 ?    9.6   0.1   0.00047       1.2      29      44 ..      49      64 ..      42      80 .] 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                       STAC2_u1 24 ppaqeaasvkvdpvyeaLrygtS 46
                                    p+ ++++++vd ++eaL  g S
  gi|118431948|ref|NP_148733.2| 20 RPTVKGTRITVDDILEALANGWS 42
                                   688899************98877 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00047
                       STAC2_u1 29 aasvkvdpvyeaLryg 44
                                     ++ +++vyeaLry 
  gi|118431948|ref|NP_148733.2| 49 NYRIPIEAVYEALRYA 64
                                   568899*********6 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.3   3.4e+03      31      41 ..      27      37 ..      25      40 .. 0.78
   2 ?   11.1   0.1   0.00013      0.33      22      46 ..      42      66 ..      42      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                   TXXHHHHHHHH CS
                     Sigma70_r3 31 glseekVrevl 41
                                    +++++++e+l
  gi|118431948|ref|NP_148733.2| 27 RITVDDILEAL 37
                                   58899999987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                                   XHHHHHHHHTXXHHHHHHHHHHHXX CS
                     Sigma70_r3 22 tpeEiAeeLglseekVrevleaare 46
                                   ++eE+A+   +++e V e+l+ a e
  gi|118431948|ref|NP_148733.2| 42 SVEEVADNYRIPIEAVYEALRYALE 66
                                   68******************98865 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 ?   12.2   0.0   6.2e-05      0.16      32      65 ..      39      72 ..      30      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.2e-05
                        UPF0122 32 dDlSlsEiAeefnvsrqavydnikrtekllekyE 65
                                   + +S++E+A+++ +  +avy+ ++ + + l k E
  gi|118431948|ref|NP_148733.2| 39 NGWSVEEVADNYRIPIEAVYEALRYALETLRKVE 72
                                   668********************99988888776 PP

>> DUF5338  Family of unknown function (DUF5338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.33      29      45 ..      30      46 ..      28      51 .. 0.89
   2 ?   -3.0   0.0       3.2   8.1e+03      42      50 ..      54      62 ..      53      64 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                        DUF5338 29 rkdikealkaGyalkti 45
                                    +di eal++G+++ ++
  gi|118431948|ref|NP_148733.2| 30 VDDILEALANGWSVEEV 46
                                   58************987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.2
                        DUF5338 42 lktiwehLh 50
                                   + +++e+L+
  gi|118431948|ref|NP_148733.2| 54 IEAVYEALR 62
                                   567888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 704.59
//
[ok]
